@article {pmid42705711, year = {2026}, author = {Du, J and Du, X and Wang, Y and Zhou, C and Zhang, Y and Teng, W and Wang, J and Zhuang, S and Cao, J}, title = {Microbial and flavor modulation of Jinhua ham at the fermentation stage by a synthetic mold and yeast community.}, journal = {Food research international (Ottawa, Ont.)}, volume = {243}, number = {Pt 2}, pages = {120202}, doi = {10.1016/j.foodres.2026.120202}, pmid = {42705711}, issn = {1873-7145}, mesh = {*Fermentation ; Odorants/analysis ; Animals ; Penicillium/metabolism ; *Food Microbiology/methods ; *Meat Products/microbiology/analysis ; *Taste ; Volatile Organic Compounds/analysis ; *Yeasts/metabolism ; Penicillium chrysogenum/metabolism ; Aldehydes/analysis ; Rhodotorula ; }, abstract = {This study investigated the effect of individual inoculation with Penicillium (Penicillium aethiopicum &amp; Penicillium chrysogenum, PP), yeast (Candida parapsilosis &amp; Rhodotorula mucilaginosa, CM) and their co-inoculation (MI) on the microbial ecology and flavor of Jinhua ham. Inoculation established target fungal populations (>6.0 log CFU/g) successfully increased lipase activity (peak in MI) and inhibited lipid oxidation, peroxide values and Aspergillus community to <10% compared to the control. PP accelerated the release of free fatty acid, especially unsaturated fatty acids, driving total volatile aldehyde concentrations by 5.0-, 1.5-, and 2.2-fold in PP, CM, and MI, respectively, compared to the control. Consequently, hams in the PP group exhibited stronger green and meaty odor scores, lower off-odor scores, and enhanced W1S, W2S and W3S sensor responses. In contrast, CM and MI increased monounsaturated fatty acids, alcohols, aldehydes, carboxylic acids, esters and pyrazines contents with stronger mellow, green &amp; meaty odor scores, as verified by robust W1W, W1S, W3S and W5S sensor responses than the control. These findings indicate that targeted Penicillium or yeast multi-species combination strategies promoted the formation of desirable aldehydes, ketones, esters and pyrazines contents and produced green, meaty and mellow flavor profile of Jinhua ham.}, }
@article {pmid42709016, year = {2026}, author = {Duysburgh, C and Govaert, M and Azmi, P and Finn, R and Simmons, N and Marzorati, M}, title = {Comparison of the Bioaccessibility of Two Formulations of Magnesium Bisglycinate Using an In Vitro Simulation of the Upper Gastrointestinal Tract.}, journal = {Journal of dietary supplements}, volume = {23}, number = {5}, pages = {690-704}, doi = {10.1080/19390211.2026.2727023}, pmid = {42709016}, issn = {1939-022X}, mesh = {Humans ; *Magnesium/pharmacokinetics ; Biological Availability ; *Upper Gastrointestinal Tract/metabolism ; *Dietary Supplements ; *Glycine/pharmacokinetics/analogs &amp; derivatives ; Intestinal Absorption ; Models, Biological ; Gastrointestinal Transit ; Capsules ; }, abstract = {Modern diets are often deficient in magnesium, making magnesium supplementation an important consideration for overall human health. However, the efficiency of magnesium release and absorption in the small intestine varies among different magnesium formulations. The objective of this study was therefore to assess whether using the same magnesium salt type in different formulations could affect efficiency of magnesium release and passive diffusion in the simulated human intestine. This study utilized an in vitro simulation of the upper gastrointestinal tract under fasted conditions to evaluate capsule dissolution and levels of bioaccessible and dialyzable magnesium during transit for two magnesium bisglycinate supplements containing a similar magnesium content (Chelamax[®] and Albion[®]). For this purpose, the validated Simulator of the Human Intestinal Microbial Ecosystem (SHIME[®]) technology platform was used and magnesium fractions were determined by inductively coupled plasma optical emission spectroscopy following sample extraction. Analytical validation proved that the model was fit for purpose (94-102% recovery, RSD ≤ 2.4%, R2 > 0.999, LOQ 0.04 mg/kg). Visual capsule scoring found that the Chelamax[®] product dissolved later in gastrointestinal transit than the Albion[®] product. Magnesium bioaccessibility was higher for the Chelamax[®] versus Albion[®] product in early phases of the gastrointestinal tract (i.e. duodenum), resulting in 17% higher overall Mg availability after the small intestinal incubation was complete. The level of dialyzable magnesium at the end of the small intestinal incubation was significantly higher with the Chelamax[®] versus Albion[®] product (53 mg vs. 39 mg; p = 0.0009). These results demonstrate that the Chelamax[®] product showed significantly higher in vitro efficiency of potentially absorbable magnesium, even upon using the same magnesium salt type, suggesting the crucial role of product formulation. Even though a proven valid in vitro methodology for the prediction of effectiveness of magnesium availability was used, future in vivo studies should confirm these findings.}, }
@article {pmid42709402, year = {2026}, author = {van Neerbos, FAC and Cusumano, A and Lievens, B and de Bobadilla, MF}, title = {Honeydew microbial ecology: A neglected frontier in multitrophic networks.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiag104}, pmid = {42709402}, issn = {1574-6941}, abstract = {Honeydew, the sugary excretion produced by sap-feeding Hemiptera, is one of the most common carbohydrate resources in many plant-based food webs. Honeydew supports a wide range of organisms, including ants, pollinators, (hyper-)parasitoids wasps, predatory insects, and microbes. As a sugar-rich resource, honeydew is frequently colonized by specific microbes (i.e., bacteria and fungi), which consume its sugars and other nutritional constituents. Recent research suggests that microbes within honeydew may modify its traits. Thereby driving microbial succession and acting as important "hidden players" in multitrophic ecological interactions. Yet its role as a dynamic microbial habitat remains largely unexplored. Here, we synthesize current evidence on the microbial ecology of honeydew and propose that honeydew is a dynamic rapidly changing microbial habitat. We further propose a four-stage successional model to frame its temporal dynamics. We discuss how the honeydew microbiome alters nutritional composition. Further, we discuss how the honeydew microbiome may mediate multitrophic interactions through the emission of volatile organic compounds that attract natural enemies of honeydew-producing insects. We propose that this process may pose a trade-off between the microbial secondary metabolism and its dispersal capacity of some microbes. We aim to stimulate research that will establish honeydew microbial ecology as a new frontier in plant-insect-microbe interactions.}, }
@article {pmid42705452, year = {2026}, author = {Tummala, R and Kondapalli, N and Katari, V and Manandhar, I and Dalal, K and Adapala, R and Paruchuri, S and Joe, B and Thodeti, C}, title = {TRPV4 deletion remodels the gut microbiota and increases colonic ammonia levels.}, journal = {Life sciences}, volume = {}, number = {}, pages = {124671}, doi = {10.1016/j.lfs.2026.124671}, pmid = {42705452}, issn = {1879-0631}, abstract = {AIMS: The transient receptor potential vanilloid 4 ion channel is widely expressed in the gastrointestinal tract and contributes to epithelial barrier regulation, mechanosensation and innate immune signaling. However, its role in shaping gut microbiota composition and intestinal metabolic homeostasis remains unclear. This study aimed to determine whether deletion of TRPV4 influences gut microbial composition and intestinal ammonia levels.<br><br>MATERIALS AND METHODS: Fecal microbiota from wild type and TRPV4 knockout mice were analyzed using taxonomic profiling and microbial diversity approaches. Alpha diversity and beta diversity metrics were used to evaluate microbial richness, evenness, phylogenetic diversity and community structure. Ammonia concentration and pH were measured in cecal and colonic contents.<br><br>KEY FINDINGS: Phylogenetic diversity differed significantly between wild type and TRPV4 knockout mice whereas microbial richness and evenness were not altered. Beta diversity analysis revealed marked differences in microbial community composition between genotypes. The ratio of Bacillota to Bacteroidetes was reduced by approximately 50 % in TRPV4 knockout mice due to decreased Bacillota and increased Bacteroidetes abundance. In addition, TRPV4 knockout mice exhibited significantly elevated ammonia levels in both the colon and cecum compared with wild type mice.<br><br>SIGNIFICANCE: Deletion of TRPV4 alters gut microbial community structure and intestinal nitrogen metabolism without affecting overall microbial richness or evenness. These findings identify TRPV4 as a novel regulator of gut microbiota composition and metabolic homeostasis and suggest that ion channel dependent signaling contributes to the regulation of gut microbial ecology and metabolite balance.}, }
@article {pmid42701922, year = {2026}, author = {Zhang, L and Tian, Q and Du, C}, title = {γ-Butyrolactones and γ-butenolides as autoregulatory systems: key mediators of intraspecific, interspecific, and interkingdom communication in Streptomyces.}, journal = {Archives of microbiology}, volume = {208}, number = {12}, pages = {}, pmid = {42701922}, issn = {1432-072X}, support = {Grant No.: 32572911//National Natural Science Foundation of China/ ; Grant No.: LH2024C096//Heilongjiang Provincial Natural Science Foundation/ ; }, mesh = {*4-Butyrolactone/analogs &amp; derivatives/metabolism/chemistry ; *Streptomyces/metabolism/genetics/physiology ; *Quorum Sensing ; Gene Expression Regulation, Bacterial ; Anti-Bacterial Agents/biosynthesis ; Signal Transduction ; }, abstract = {Streptomyces represent a phylogenetically coherent group of aerobic, Gram-positive, high-GC-content bacteria occupying diverse terrestrial and aquatic environments. They are renowned for their exceptional capacity to biosynthesize structurally diverse secondary metabolites, many of which serve as clinically essential antibiotics, antifungals, immunosuppressants, and anticancer agents, with broad applications in pharmaceuticals, agriculture, food, and industrial biotechnology. Quorum sensing (QS) represents a fundamental regulatory paradigm governing both intraspecies coordination and interspecies crosstalk in Streptomyces. Within this framework, gamma-butyrolactones (GBLs) and gamma-butenolides (GBNs) function as structurally analogous, receptor-specific signaling molecules that autoregulate antibiotic biosynthesis, morphological differentiation, and stress adaptation. However, despite growing insights into their intraspecies functions, the ecological range, molecular determinants, and functional outcomes of GBL- and GBN-mediated interspecies communication remain largely underexplored. This review summarizes recent advances in the chemical diversity and regulatory mechanisms of microbial GBLs and GBNs. Based on current empirical evidence, we categorize their interspecies communication functions into four distinct themes: experimentally validated ligand-receptor pairs, exogenous compound-mediated receptor responses, extract- or coculture-mediated complementation, and Streptomyces-fungi communication hypotheses. Furthermore, we propose a forward-looking research agenda integrating multi-omics, synthetic biology, and microbial ecology to decipher the mechanistic foundation of interspecies QS networks-ultimately facilitating the rational activation of silent biosynthetic gene clusters, the discovery of novel bioactive natural products, and the mitigation of antimicrobial resistance.}, }
@article {pmid42702405, year = {2026}, author = {Šulčius, S and Kuznecova, J and Kasperovičienė, J and Alzbutas, G and Šimoliūnas, E and Voss, M and Jürgens, K and Dziga, D}, title = {Cyanophage lysis reshapes nitrogen cycling and microbiome composition in diazotrophic cyanobacterium Aphanizomenon flos-aquae.}, journal = {Harmful algae}, volume = {159}, number = {}, pages = {103186}, doi = {10.1016/j.hal.2026.103186}, pmid = {42702405}, issn = {1878-1470}, mesh = {*Aphanizomenon/virology/metabolism/physiology/genetics ; *Bacteriophages/physiology ; *Microbiota ; Nitrogen Fixation ; *Nitrogen Cycle ; Nitrogen/metabolism ; }, abstract = {Although it is presumed that viruses play a significant role in nutrient cycling and bacterial community dynamics, this has only rarely been addressed in studies of diazotrophic cyanobacteria. In this study, we therefore examined how cyanophage infection affects the expression of nitrogen (N) cycling genes, N2 fixation rates, and population structure in the diazotrophic cyanobacterium Aphanizomenon flos-aquae, a prevalent bloom-forming species in temperate brackish and freshwater ecosystems. We also assessed the influence of A. flos-aquae lysis on co-occurring bacterial assemblages throughout an incubation experiment. We found that nitrogen fixation, its release, and the relative availability of different nitrogen forms (e.g. ammonium versus nitrate/nitrite) varied substantially during cyanophage infection, population lysis, and recovery phases. Interestingly, resistant A. flos-aquae subpopulation emerged during viral infection, showed increased expression of N fixation (e.g. nitrogenase (nifH) and heterocyst differentiation regulator (hetR)) and assimilation (e.g. glutamine (glnA) and glutamate (gltB) synthase) genes, as well as higher cell-specific N2 fixation rates. These changes were accompanied by a fast recovery of A. flos-aquae population structure (e.g. filament length and heterocyte-to-vegetative cell ratio) to pre-infection level, indicating A. flos-aquae ability to quickly compensate for short-term population decline. Lysis of the cyanobacterial host significantly altered the successional trajectory and increased diversification of the co-occurring bacterial community. The compositional changes corresponded well with the prevalent inorganic nitrogen form, implying a substantial, nitrogen-driven reorganization of the microbial network and its interactions within the A. flos-aquae microbiome. This study improves our understanding of nitrogen cycling and microbial dynamics within cyanobacteria-driven communities disturbed by viral infections and lysis.}, }
@article {pmid42702754, year = {2026}, author = {Sengupta, S and Ghorai, S and Bose, S and Hazra, S and Mukhopadhyay, A and Majumdar, A and Roychowdhury, T}, title = {Integrating Plant Physiology and Microbiome Engineering for Climate-Resilient Crops: Bridging Knowledge Gaps in Multi-Stress Tolerance.}, journal = {Physiologia plantarum}, volume = {178}, number = {5}, pages = {e71088}, pmid = {42702754}, issn = {1399-3054}, mesh = {*Crops, Agricultural/physiology/microbiology ; *Stress, Physiological/physiology ; *Microbiota/physiology ; Climate Change ; *Plant Physiological Phenomena ; }, abstract = {Climate change is intensifying the frequency and co-occurrence of abiotic and biotic stresses, posing significant challenges to global crop productivity and stability. Conventional approaches based on single-stress responses are increasingly insufficient for addressing complex field environments where plants experience multiple simultaneous stresses. This review synthesizes current knowledge on plant physiological responses, microbiome interactions, and emerging technological interventions to develop an integrative framework for climate-resilient agriculture. It highlights how stress perception, hormonal regulation, metabolic adjustments, and epigenetic mechanisms collectively shape plant adaptation under multi-stress conditions. The review further examines the role of plant-associated microbiomes in enhancing nutrient acquisition, regulating stress signaling, and improving resilience through mechanisms such as phytohormone modulation, antioxidant activity, and induced systemic resistance. Advances in microbiome engineering, including synthetic microbial communities and computational prediction frameworks, are discussed as promising strategies for improving stress tolerance. In addition, emerging tools such as nanotechnology-assisted delivery systems and biosensing platforms are considered for precision management of plant-microbe systems. By identifying critical knowledge gaps in multi-stress physiology, microbiome assembly, and field-level predictability, this review proposes an interdisciplinary approach that integrates plant physiology, microbial ecology, and technological innovations to support sustainable crop production under changing climatic conditions.}, }
@article {pmid42703030, year = {2026}, author = {de Lorenzo, V}, title = {Environmental Release of Genetically Intervened Microorganisms: Towards a New Narrative.}, journal = {Microbial biotechnology}, volume = {19}, number = {9}, pages = {e70441}, pmid = {42703030}, issn = {1751-7915}, support = {CL6-2021-UE 101060625//HORIZON EUROPE Excellent Science/ ; }, mesh = {*Microorganisms, Genetically-Modified/genetics ; Genetic Engineering/legislation &amp; jurisprudence ; *Containment of Biohazards ; Biotechnology/legislation &amp; jurisprudence ; }, abstract = {The deliberate release of genetically engineered microorganisms for environmental applications has remained largely blocked since the early days of recombinant DNA technology, when limited ecological knowledge, lack of success stories and public apprehension shaped a culture of caution and restrictive regulation. Despite profound advances in microbial ecology, synthetic biology and genetic design, current frameworks still rely on outdated assumptions and legacy regulations that equate engineered microbes with inherent danger and demand unrealistic forms of absolute containment. This review examines how laboratory-trained microorganisms exist on a continuum with naturally evolved life, and that their risks are neither categorically different nor greater. Rather than pursuing unachievable containment, governance should shift towards traceability, stewardship and long-term monitoring through genomic barcodes, digital twins and transparent oversight. The vision moves from domination and control to care and partnership recognizing engineered microbes as live amendments capable of restoring degraded ecosystems. Achieving this transformation requires new terminology, phased field-trial frameworks, improved scaling methods, and the integration of epistemological perspectives that emphasize reciprocity and coexistence with nature. Reframing biotechnology in this way could finally unlock the capacity of engineered microorganisms to contribute responsibly and effectively to planetary repair in an era of escalating environmental crises.}, }
@article {pmid42704537, year = {2026}, author = {de Freitas Germano, J and Leite, G and Pimentel, M}, title = {Do Multi-Omics Approaches Improve the Diagnosis of Microbial Overgrowth Syndromes?.}, journal = {Current gastroenterology reports}, volume = {28}, number = {1}, pages = {}, pmid = {42704537}, issn = {1534-312X}, mesh = {Humans ; Multiomics ; *Intestine, Small/microbiology ; Proteomics/methods ; *Blind Loop Syndrome/diagnosis/microbiology ; Breath Tests/methods ; Gastrointestinal Microbiome ; Metagenomics/methods ; Syndrome ; }, abstract = {PURPOSE OF REVIEW: This review investigates how advances in breath testing (BT), small bowel (SB) culture, metagenomics, metatranscriptomics, transcriptomics and proteomics are reshaping the definition and diagnosis of small intestinal bacterial overgrowth (SIBO). It also discusses whether SIBO should be redefined as part of a larger group of microbial overgrowth syndromes.<br><br>RECENT FINDINGS: Recent studies identify distinct hydrogen-, methane-, and hydrogen sulfide-associated overgrowth phenotypes, termed SIBO, intestinal methanogen overgrowth (IMO), and intestinal sulfide overproduction (ISO). SB sampling shows that these conditions involve different microbial patterns and functional activity, symptoms, and host responses. Quantitative shotgun metagenomics provides greater taxonomic and functional resolution than culture, while metatranscriptomics reveals active microbial pathways. On top of that, host transcriptomics and proteomics contribute to the better understanding of the predominant microbial effects in host cellular mechanisms in each of the distinct small bowel overgrowth types. SIBO has been increasingly identified as a disorder of microbial ecology and function rather than bacterial quantity alone. Integrating BT with SB sampling and multi-omics approaches may improve classification, clarify symptom mechanisms, and support a more individualized treatment, although standardized methods and further clinical validation remain necessary.}, }
@article {pmid42704659, year = {2026}, author = {Cahill, N and Kovarova, A and Alfahl, Z and O'Connor, L and Morris, D}, title = {Antimicrobial resistance in wastewater-impacted coastal waters: implications for environmental surveillance and public health.}, journal = {Microbiology (Reading, England)}, volume = {172}, number = {9}, pages = {}, pmid = {42704659}, issn = {1465-2080}, mesh = {*Wastewater/microbiology ; Ireland ; *Environmental Monitoring ; *Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics/drug effects/isolation &amp; purification ; *Seawater/microbiology ; *Bacteria/genetics/drug effects/isolation &amp; purification/classification ; Public Health ; Anti-Bacterial Agents/pharmacology ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; beta-Lactamases/genetics ; }, abstract = {Antimicrobial resistance (AMR) is a global public health concern, and wastewater-impacted aquatic environments are recognized as reservoirs and dissemination pathways for antimicrobial-resistant bacteria (ARB) and genes (ARGs). However, harmonized environmental AMR surveillance frameworks that integrate culture-based ARB enumeration with molecular ARG monitoring across wastewater and receiving surface waters remain limited. This pilot study, conducted in Ireland as part of a European harmonized monitoring initiative, assessed ARB and ARG abundances in wastewaters and surface waters. Wastewater treatment plant influent (n=3), effluent (n=3) and surface waters upstream and downstream of the discharge point (n=3 each) were sampled on three occasions in late 2024. Culture-based methods enumerated total and extended-spectrum β-lactamase (ESBL)-producing Escherichia coli, while quantitative real-time PCR quantified 16S rRNA and five AMR-associated genes (intI1, ermB, aadA1, bla CTX-M-1 and vanA). Total E. coli concentrations were highest in influent (~10[5]-10[6] c.f.u. dl[-1]), decreased in effluent (~10[3]-10[5] c.f.u. dl[-1]) and lowest in surface waters (~10[1]-10[2] c.f.u. dl[-1]). ESBL-producing E. coli were consistently detected in influent (~10[4] c.f.u. dl[-1]) and effluent (~10[1]-10[3] c.f.u. dl[-1]) but were not recovered from seawater. ARG abundances were highest in influent, reaching up to ~10[11] copies dl[-1] for intl1, remained elevated in effluent (up to ~10[10] copies dl[-1]) and were ~2-3 orders of magnitude lower in surface waters relative to effluent. Downstream seawater exhibited higher ARG levels than upstream freshwater despite low culturable E. coli. Peak ARG concentrations in effluent and surface waters were observed following a period of heavy rainfall; however, the limited number of sampling events precluded assessment of any statistical association. These findings highlight the impact of wastewater discharges on environmental AMR dissemination and suggest that faecal indicator-based monitoring may underestimate emerging risks, supporting integration of AMR indicators into EU water quality frameworks.}, }
@article {pmid42698632, year = {2026}, author = {Park, J and Cheon, S and Choi, YS and Kim, J and Ahn, SJ and Chung, JE}, title = {Anaerobic antibiotic exposure and risk of maculopathy: a nationwide dual design study.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1840229}, pmid = {42698632}, issn = {1663-9812}, abstract = {The pathogenesis of maculopathy remains incompletely understood, and emerging evidence implicates the gut-eye axis in retinal and macular diseases. Given that antibiotics with anti-anaerobic activity may disrupt gut microbial ecology, this study investigated their association with the risk of incident maculopathy. We conducted a nationwide population-based study using the National Health Insurance Service-National Sample Cohort of South Korea. A retrospective cohort study was used to assess cumulative systemic anaerobic antibiotic exposure during a 5-year baseline period and subsequent incident maculopathy from 2007 to 2019. After 1:1 propensity score matching, hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated using Cox proportional hazards regression. A nested case-control study was also conducted using risk-set sampling and 1:10 propensity score matching. Anaerobic antibiotic exposure during the 365 days before the index date was assessed, and odds ratios (ORs) and 95% CIs were estimated using conditional logistic regression. Duration-response relationships were evaluated using formal trend analyses. Sensitivity analyses included age restriction, Fine-Gray competing risk models, extended exposure assessment windows, lag-time analyses, and a negative control comparator analysis using first-generation cephalosporins. In the retrospective cohort study, 326,436 anaerobic antibiotic users were matched to 326,436 non-users. Anaerobic antibiotic use was associated with an increased risk of incident maculopathy in the fully adjusted model (HR, 1.07; 95% CI, 1.03-1.12), with a significant duration-response trend and the highest risk observed for ≥57 days of cumulative use (HR, 1.24; 95% CI, 1.09-1.42). In the nested case-control study, 55,776 cases were matched to 557,760 controls. Anaerobic antibiotic use within 365 days before the index date was associated with increased odds of maculopathy (OR, 1.04; 95% CI, 1.02-1.07), also showing a significant duration-response trend. Sensitivity analyses and first-generation cephalosporin comparator analyses, generally supported the robustness of the findings. Systemic exposure to antibiotics with anti-anaerobic activity was associated with an increased risk of incident maculopathy, with a duration-response pattern across cumulative exposure categories. These findings suggest further investigation into gut microbiome disruption and the gut-eye axis as potential pathways involved in maculopathy.}, }
@article {pmid42699672, year = {2026}, author = {Wu, D and Dong, T and Chen, X and Lin, Z and Pan, Q and Wei, J and Liang, J and Wei, J}, title = {Insights into microbiome and ARGs diversity in patients with upper and lower respiratory tract infections by targeted next-generation sequencing.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e21615}, pmid = {42699672}, issn = {2167-8359}, mesh = {Humans ; *Respiratory Tract Infections/microbiology ; *Microbiota/genetics ; Female ; High-Throughput Nucleotide Sequencing ; Retrospective Studies ; Male ; Middle Aged ; Adult ; *Bacteria/genetics/drug effects/isolation &amp; purification ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; *Drug Resistance, Bacterial/genetics ; Coinfection/microbiology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Respiratory tract infections (RTIs) cause substantial global morbidity and mortality, with antimicrobial resistance presenting an increasing challenge to the effective management. Characterizing the differences in microbiome composition and antimicrobial resistance genes (ARGs) between upper respiratory tract infections (URTIs) and lower respiratory tract infections (LRTIs) may inform site-specific diagnostic and therapeutic strategies. We retrospectively analyzed 1,340 URTIs samples (nasopharyngeal swab) and 699 LRTIs samples (bronchoalveolar lavage fluid) admitted to a single medical center to characterize the epidemiology of the respiratory microbes and ARGs using targeted next-generation sequencing (tNGS). Microbiome diversity, ARGs profiles, and coinfection patterns were compared between LRTIs and URTIs groups. Random forest machine learning was employed to identify discriminating species. LRTIs patients exhibited significantly higher microbiome abundance and ARGs diversity than URTIs patients (P < 0.001. Beta-lactam, multidrug, phenicol, and fluoroquinolone resistance genes were significantly more abundant in LRTIs (P < 0.01). Bacteria-virus coinfections predominated in both LRTIs (39.3%) and URTIs (54.6%). Thirty species were identified as potential discriminators between LRTIs and URTIs, with an Area Under Curve (AUC) of 0.852 in the training set. These findings reveal distinct microbial and ARGs profiles between URTIs and LRTIs patients, and provide a foundation for understanding site-specific microbial ecology in RTIs for clinical diagnosis and antimicrobial stewardship.}, }
@article {pmid42694744, year = {2026}, author = {Rajakaruna, S and Howard-Varona, C and Urvoy, M and AminiTabrizi, R and Ayala-Ortiz, C and Gittrich, M and Solonenko, N and Burris, M and Sanderson, C and Noel, C and Leopold, J and Quillin, L and Doshi, K and Walker, LR and Sullivan, MB and Tfaily, MM}, title = {Metabolome restructuring reveals distinct virocell infection strategies in bacteriophage-host interaction.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag223}, pmid = {42694744}, issn = {2730-6151}, abstract = {Viral infection transforms microbial cells into metabolically reprogrammed "virocells," yet the metabolic architecture underlying this transition remains poorly resolved. Here we investigate how bacteriophages reshape host metabolism in Cellulophaga baltica across time and phage types, uncovering coordinated metabolic reorganization during infection that includes pathway-level patterns consistent with membrane remodeling, amino-acid recycling, and redistribution of cellular resources. Temporal analyses further distinguished infection strategies: efficient phages produced structured, phased metabolic shifts indicative of controlled host reprogramming, whereas inefficient infection triggered abrupt metabolic collapse. These results suggest that the organization and timing of host metabolome restructuring represent defining features of the virocell state and may reflect underlying viral life-history strategies. These biological patterns were made accessible by an integrative annotation framework that combines previously validated computational tools, substantially expanding interpretable metabolite coverage beyond conventional approaches. This approach reveals coherent infection signatures that would otherwise remain hidden, demonstrating how expanded metabolite interpretability can uncover functional principles of virus-host interactions. The analytical strategy presented here is readily transferable to other virus-host systems and complex microbial communities, providing a path toward mechanistic interpretation of untargeted metabolomic data in microbial ecology.}, }
@article {pmid42695145, year = {2026}, author = {Van Etten, J and Han, S and Burns, JA and Lhee, D and Willoughby, AC and Stephens, TG and Chille, E and Sleith, RS and Bhattacharya, D and Yoon, HS}, title = {Crawling under the radar: Two novel Paulinella species expand knowledge about the ecology and evolution of a primary plastid-containing amoeba lineage.}, journal = {Journal of phycology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jpy.70230}, pmid = {42695145}, issn = {1529-8817}, support = {80NSSC19K1542/NASA/NASA/United States ; RS-2022-NR068987//National Research Foundation of Korea/ ; RS-2022-NR070837//National Research Foundation of Korea/ ; RS-2025-25434508//National Research Foundation of Korea/ ; NJ01180//USDA National Institute of Food and Agriculture Hatch Formula/ ; 2410274//National Science Foundation/ ; 2410358//National Science Foundation/ ; RS-2025-02304428//Korea Institute of Marine Science and Technology promotion/ ; }, abstract = {The genus Paulinella represents a rare, independent case of primary endosymbiosis, providing a unique system to study the early stages of organelle evolution. Here, we expand current understanding of primary plastid endosymbiosis through the discovery and characterization of two novel photosynthetic amoebae, Paulinella marae sp. nov. and Paulinella murrayi sp. nov., isolated from a brackish water habitat in North Carolina, United States. Complete chromatophore genomes and mitochondrial data revealed conserved gene content but notable structural variation, including genome rearrangements and inversion events. Phylogenetic analyses uncovered significant discordance between nuclear and organelle datasets, likely driven by substitution saturation, limited taxon sampling, and differing evolutionary signals across loci. Ecological observations over multiple years indicate that both species are in low abundance but consistently present, and when coupled with hobbyist data, support the hypothesis that photosynthetic Paulinella species are globally distributed yet under-sampled. These results increase known species diversity within the clade from four to six and highlight the importance of integrating field-based observations with genomic approaches. Overall, this work advances Paulinella as a model for studying ongoing primary endosymbiosis, lineage divergence, and the ecological strategies of low-abundance microbial eukaryotes.}, }
@article {pmid42696299, year = {2026}, author = {Román, R and Maestre, FT and Couradeau, E}, title = {Rainfall-induced microbial resuscitation reveals functional decoupling across biocrust succession.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag231}, pmid = {42696299}, issn = {1751-7370}, abstract = {Dryland ecosystems rely on infrequent rainfall pulses to activate soil microbial communities, yet the fraction and identity of microbes resuscitating after hydration remain unclear. We applied bioorthogonal non-canonical amino acid tagging coupled with fluorescence-activated cell sorting (BONCAT-FACS) and 16S rRNA gene sequencing to identify translationally active bacteria in early (L-BSC) and late (D-BSC) successional cyanobacteria-dominated biocrusts subjected to 3 mm simulated rainfall under light and dark conditions. Our results reveal that only a small subset of the microbial community resumes activity within six hours, with higher active cell abundances in mature crusts. Microbial activity patterns were largely independent of light exposure and showed partial decoupling from total community composition, indicating that presence does not predict short-term function. These findings suggest that biocrust maturity shapes microbial activation dynamics and that functional responses to precipitation pulses are governed by a conserved pool of fast responders, informing predictions of dryland soil microbiome resilience under changing precipitation regimes.}, }
@article {pmid42696594, year = {2026}, author = {Glasl, B and Kitzinger, K and Luter, HM and Legin, A and Schuster, S and Salas, E and Heldwein, N and Damjanovic, K and Rutsch, M and Vekeman, B and Geerlings, NMJ and Pjevac, P and Séneca, J and Watzka, M and Wanek, W and Speth, DR and Wagner, M}, title = {Branched-chain amino acid assimilation enables mixotrophy of ammonia-oxidizing archaeal sponge symbionts.}, journal = {Science advances}, volume = {12}, number = {36}, pages = {eaef9450}, doi = {10.1126/sciadv.aef9450}, pmid = {42696594}, issn = {2375-2548}, mesh = {Animals ; *Ammonia/metabolism ; *Symbiosis ; *Archaea/metabolism/physiology ; *Amino Acids, Branched-Chain/metabolism ; *Porifera/microbiology/metabolism ; Oxidation-Reduction ; }, abstract = {Marine sponges and ammonia-oxidizing archaea (AOA) represent one of the earliest animal-microbe symbioses. AOA are considered metabolically constrained chemolithoautotrophs that remove nitrogenous waste within the sponge holobiont. Here, we expand this view by demonstrating that symbiotic AOA assimilate branched-chain amino acids (BCAA) as additional carbon and nitrogen sources. By combining stable isotope probing with fluorescence and chemical imaging, we trace the assimilation of [13]C- and [15]N-labeled BCAA (leucine, isoleucine, and valine) in the sponge holobiont Ianthella basta at single-cell resolution. We show that the ability to take up, degrade, and biosynthesize BCAA is a common adaptation among symbiotic AOA lineages. This ability may enable symbiotic AOA to modulate BCAA concentrations in their auxotrophic sponge hosts. Modulation of BCAA availability by symbionts may regulate the leucine-sensitive mTOR (mechanistic target of rapamycin) signaling pathway in sponges.}, }
@article {pmid42697479, year = {2026}, author = {Luo, Y and Jiang, Y and Tingting, Z}, title = {Targeting Nrf2 in oxidative liver injury: expanding the role of gut microbiota and metabolites.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2026.09.006}, pmid = {42697479}, issn = {2090-1224}, abstract = {BACKGROUND: Liver diseases are a major cause of illness and death worldwide. Oxidative stress is a pivotal driver in the pathogenesis of a spectrum of liver diseases, including alcoholic liver disease (ALD), metabolic dysfunction-associated fatty liver disease (MAFLD), drug-induced liver injury (DILI), and hepatocellular carcinoma (HCC). The transcription factor Nrf2, a master regulator of cellular antioxidant responses, plays a central yet context-dependent role in modulating this injury. Additionally, the gut-liver axis is a critical regulator of hepatic homeostasis.<br><br>AIM OF REVIEW: This review presents recent advances to propose a refined gut-microbiota-Nrf2 axis as a key mechanistic link in the treatment of liver injury. We detail how specific gut-derived microbial metabolites, such as short-chain fatty acids (SCFAs), tryptophan derivatives, and urolithins, directly or indirectly activate the hepatic Keap1/Nrf2 signaling pathway. This activation orchestrates a cytoprotective program that enhances the redox balance, promotes detoxification, and induces selective autophagy, thereby protecting against oxidative liver injury. Conversely, we examine the dual role of Nrf2, highlighting how its dysregulated and constitutive activation in established HCC can paradoxically promote tumor progression and ferroptosis resistance. Finally, we evaluate the therapeutic potential of targeting this axis using microbiome-modulating strategies, including probiotic and prebiotic supplementation, fecal microbiota transplantation (FMT), dietary intervention, and synergy with Nrf2-targeting drugs.<br><br>This review provides an integrated framework that connects gut microbial ecology with host redox signaling, offering novel mechanistic insights and translational perspectives for the prevention and treatment of oxidative liver diseases.}, }
@article {pmid42697798, year = {2026}, author = {Ho, PM and Nazeer, RR and Askenasy, I and Quinn, RA and Welch, M}, title = {Microbial content versus microbial interaction: the impact of medications on CF airway microbial ecosystems.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jcf.2026.08.011}, pmid = {42697798}, issn = {1873-5010}, abstract = {BACKGROUND: The airways of people with cystic fibrosis (pwCF) are often colonized by a variety of different microbes. Although much effort has been put into cataloguing the impact of medication on the identities and abundances of these microbes, far less has been directed towards examining this from an ecological perspective, i.e., examining how medications affect the network and types of interactions between microbes.<br><br>METHODS: In the current work, we generated an ecological model of the CF airway microbiome and examined how medications affect interactions between co-habiting airway microbiota in six pwCF. Ecological interactions were inferred from a generalized Lotka-Volterra model, and the impact of medications was determined by principal component(s) regression analysis.<br><br>RESULTS: For the majority of the subjects studied, antimicrobial interventions had relatively little impact on the CF airway microbial ecology, and even appeared to stabilize ecological interactions between the microbiota. However, the microbial ecosystem in some individuals was more sensitive to external perturbations. More surprisingly, we found that some non-antimicrobial medications, and also certain carriers and excipients affect the ecosystem.<br><br>CONCLUSIONS: Medications affect the ecology of the CF airway microbiota. These impacts appear to be very patient-specific. We also note that some nominally non-bioactive ingredients in medications can also potentially impact the CF airway ecosystem. Our data highlight the importance of collecting patient-specific data and in employing suitable computational frameworks for disentangling medication-microbiota interactions in vivo.}, }
@article {pmid42693120, year = {2026}, author = {Burian, A and Wilson, R and Kratina, P and Ábrám, &#xd6; and Afonina, E and Alcocer, J and Alfonso, MB and Anderson, T and Anufriieva, E and Balci, N and Barbosa, LG and Baxter, BK and Bazarova, B and Bazhenov, Y and Beckmann, M and Boros, E and Borzenko, S and Bucher, EH and Camacho, A and Casamayor, EO and Chao, X and Coleman, P and Colla, MF and Datson, B and Echaniz, S and Farias, ME and Fetahi, T and García, CM and Golovatyuk, L and Hudson, P and Hueso-Kortekaas, K and Johnston, J and Karimov, BK and Kalioujnaia, I and Komova, A and Krienitz, L and Kulshreshtha, S and Larson, R and Lipka, O and Matyugina, E and Mauvisseau, Q and Melack, J and Mills, K and Morant, D and Moreno, E and Namsaraev, Z and Oren, A and Rogers, C and Ryves, DB and Sánchez, MI and Camacho-Santamans, A and Santamans, AC and Schagerl, M and Selivanova, E and Shadrin, N and Sima, S and Tashlykova, N and Teubner, K and Tsybekmitova, G and Timms, B and Ulanova, S and Vidal Quini, NE and Vignatti, A and Wurtsbaugh, WA and Zapitis, C and Zechmeister, T and Zhang, C and Zadereev, E}, title = {The overlooked conservation values of saline lakes.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42693120}, issn = {2041-1723}, mesh = {*Lakes/chemistry ; Biodiversity ; *Conservation of Natural Resources ; Animals ; Ecosystem ; Endangered Species ; Salinity ; }, abstract = {Saline lakes are hypersensitive to changes in their water balance and therefore show amplified responses to climatic and land-use changes in their catchment. Despite often dramatic ecological impacts, saline lakes rank low on policy agendas as they are assumed to support few ecosystem services and low levels of biodiversity. Here, we challenge this view and evaluate ecosystem services and threatened species in 85 saline lakes distributed across the globe. We show that saline lakes support, additionally to threatened aquatic biota, a diverse range of red-listed terrestrial species that contribute together with a large beta diversity to their conservation value. Further, our results highlight that saline lakes provide a number of culturally and economically important ecosystem services but several of them are 'hidden' and difficult to quantify. We conclude our analysis with best-practice recommendations for sustainable management of saline lakes. Their local adaptation and implementation will be key for safeguarding biodiversity and ecosystem services of these valuable and highly sensitive ecosystems.}, }
@article {pmid42694728, year = {2026}, author = {Bautista, J and Iñiguez-Ramírez, A and Villegas-Chávez, JA and Bunces-Larco, D and López-Cortés, A}, title = {Skin microbiome and cutaneous aging mechanisms and clinical implications.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1917816}, pmid = {42694728}, issn = {1664-302X}, abstract = {The skin microbiome is an integral component of the cutaneous ecosystem and contributes to barrier, immune, and metabolic homeostasis. Available evidence is examined across three distinct levels: microbial community structure, functional activity, and host biological response. This ecological-functional distinction is necessary because taxonomic abundance alone does not establish microbial activity, biological effects, or causality. Age-associated microbial variation is considered within the physiological context of cutaneous aging, including reduced sebaceous activity, altered hydration and surface pH, impaired barrier recovery, chronic low-grade inflammation, oxidative stress, and extracellular matrix deterioration. Microbial alterations reported in acne, atopic dermatitis, and rosacea further illustrate how changes in the cutaneous environment can modify host-microbiome interactions and contribute to clinically relevant phenotypes. Translational developments in dermatology and aesthetic medicine include microbiome-compatible skincare, prebiotic and postbiotic formulations, live biotherapeutic approaches, and strategies intended to preserve microbial and barrier recovery after dermatological procedures. Interpretation of the available literature remains limited by low microbial biomass, anatomical and interpersonal heterogeneity, contamination risk, differences in sampling and sequencing methods, and limited functional and longitudinal resolution. Observed microbial remodeling should be interpreted within a bidirectional host-microbiome relationship. Physiological changes that accompany aging can reshape microbial ecology, whereas microbial products may modify barrier and immune responses. Current evidence does not establish whether these microbial alterations are causes, consequences, or correlates of cutaneous aging. Integration of strain-resolved microbiome data with microbial gene expression, metabolite measurements, host molecular responses, and clinical phenotypes will be required to identify biologically relevant microbial functions and determine their value in dermatological practice.}, }
@article {pmid42691813, year = {2026}, author = {Hoebinger, C and Semmler, G and Petrenko, O and Rajcic, D and Hoffelner, DK and Duckova, T and Baranovskyi, T and Goederle, L and Khuu, MP and Paeslack, N and Reinhardt, C and Pjevac, P and Séneca, J and Mieczkowski, K and Burger, K and Bergheim, I and Gensluckner, S and Völkerer, A and Reiberger, T and Scheiner, B and Aigner, E and Wernly, B and Datz, C and Binder, CJ and Hendrikx, T}, title = {Corrigendum to: 'Alcohol intake reprograms hepatic immune-metabolic circuits to exacerbate murine atherosclerosis and human cardiovascular risk' [JHEP Reports (2026) 19;8(9):101932].}, journal = {JHEP reports : innovation in hepatology}, volume = {8}, number = {10}, pages = {102001}, doi = {10.1016/j.jhepr.2026.102001}, pmid = {42691813}, issn = {2589-5559}, }
@article {pmid42692668, year = {2026}, author = {Vanzetti, G and Traina, C and Rantsiou, K and Muñoz-Labrador, A and Gabaldón, M and Moreno, FJ and Peron, AC and Lemois, M and Landaud-Liautaud, S and Rossi, F and Ferrocino, I and Cocolin, L}, title = {Development of autochthonous yeast starter cultures for Taggiasca table olives: Microbial ecology and metabolomic profile under standard and reduced-salt fermentation conditions.}, journal = {Food research international (Ottawa, Ont.)}, volume = {243}, number = {Pt 1}, pages = {120246}, doi = {10.1016/j.foodres.2026.120246}, pmid = {42692668}, issn = {1873-7145}, mesh = {*Fermentation ; *Olea/microbiology ; *Food Microbiology/methods ; *Metabolomics ; *Yeasts/metabolism/classification ; *Sodium Chloride/metabolism ; Metabolome ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Italy ; Random Amplified Polymorphic DNA Technique ; Saccharomycetales ; }, abstract = {Taggiasca table olives are a native variety to Liguria (Italy) that undergo spontaneous fermentation in a traditional manner. The autochthonous microbiota of Taggiasca olives is typically dominated by yeasts, while lactic acid bacteria are often unable to compete probably due the high phenolic content of this variety. Consequently, the fermentation kinetics and metabolomic profile are determined primarily by indigenous yeasts. This study evaluated three autochthonous yeast starter cultures for Taggiasca fermentation under standard (10% w/v) and low (6% w/v) salt conditions. Three yeast strains (Pichia membranifaciens TUCC00000520, Candida diddensiae TUCC00000529, and Wickerhamomyces anomalus TUCC00000536), previously isolated from Taggiasca fermentations, were inoculated in different formulations. Dynamics of the microbial community were monitored with an integrated approach, using culture-dependent (plate counts, MALDI-TOF MS, and RAPD-PCR) and culture-independent methods (metataxonomics approach). The metabolome was characterized at the final stage of fermentation via organic acid determination, [1]H NMR and untargeted volatile organic compounds (VOCs) analysis. Results highlighted an influence of the selected yeasts on the microbial dynamics and metabolomic profile of the final product with P. membranifaciens TUCC00000520 isolated until late stages of fermentation. Overall, this study validates the feasibility of autochthonous yeast-driven, cultivar-specific starters and provides a strategic framework for optimizing Taggiasca olive fermentation.}, }
@article {pmid42680398, year = {2026}, author = {Mao, Y and Wang, C and Zhang, L and Zou, B and Han, M and Wang, Z}, title = {Depth-dependent multi-kingdom microbial interactions and biogeochemical cycling genes in eutrophic shallow lake sediments.}, journal = {Journal of environmental sciences (China)}, volume = {168}, number = {}, pages = {400-412}, doi = {10.1016/j.jes.2025.12.004}, pmid = {42680398}, issn = {1001-0742}, mesh = {*Lakes/microbiology/chemistry ; *Geologic Sediments/microbiology/chemistry ; China ; Bacteria ; Eutrophication ; *Microbial Interactions ; *Environmental Monitoring ; Nitrogen Cycle ; }, abstract = {Microorganisms are pivotal to lake ecosystem biogeochemical cycles, yet existing research often focuses on single microbial kingdoms or surface sediments, neglecting multi-kingdom interactions and depth-resolved dynamics. To address these gaps, we used metagenomic sequencing to characterize microbial communities and their functional associations across overlying water and 0-45 cm sediments in four shallow lakes of the middle Yangtze River basin, China. Despite increasing bacterial and fungal diversity with depth, the 0-9 cm surface sediments exhibited the strongest multi-kingdom network connectivity and the greatest microbial stability. Functional genes exhibited clear depth-dependent patterns: nitrogen cycling genes, including those involved in dissimilatory nitrate reduction to ammonium, were most enriched in the upper 0-9 cm of sediment; methane cycling genes were positively correlated with depth; phosphorus cycling genes and some sulfur cycling genes, such as assimilatory sulphate reduction, declined with depth. Sediment microbial assembly was dominated by deterministic processes, in which the vertical distribution of functional genes was primarily dictated by heavy metals and conventional environmental indicators. These findings highlight depth-specific multi-kingdom microbial interactions and their associations with biogeochemical cycling, advancing lacustrine microbial ecology understanding and providing references for lake conservation under environmental change.}, }
@article {pmid42680626, year = {2026}, author = {Liu, Y and Ji, M and Chen, Y and Liu, K and Liu, P and Liu, Y and Yao, T}, title = {Prokaryotic biogeography across atmospheric, aquatic, and terrestrial ecosystems in the Mount Everest region.}, journal = {Science bulletin}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.scib.2026.07.065}, pmid = {42680626}, issn = {2095-9281}, abstract = {The Mount Everest region encompasses one of the world's most fragile cryospheric landscapes, comprising diverse and interconnected habitats across atmospheric, aquatic, and terrestrial ecosystems. Despite growing interest in high-mountain microbial ecology, basin-scale assessments remain scarce. Here, we conducted a microbial survey in the Rongbuk River basin (3699-7000 m a.s.l.), analyzing 677 samples from aerosols, snow, stream water, stream sediments, and soils via 16S rRNA gene amplicon sequencing. We identified 58,141 operational taxonomic units (OTUs) across 67 prokaryotic phyla, dominated by Pseudomonadota, Actinomycetota, and Bacteroidota. Elevational diversity patterns were ecosystem-specific: richness declined with elevation in aerosols and stream water, showed a U-shaped pattern in snow, peaked at mid-elevations in soils, and remained stable in stream sediments. Evenness and Shannon diversity, however, displayed distinct elevational trends and environmental determinants compared to richness. Community assembly was largely stochastic in snow, aquatic, and soils but strongly deterministic in aerosols. Source-tracking analysis revealed strong landscape-scale connectivity, with snow serving as a microbial vector linking atmospheric inputs to downstream ecosystems (contributing 6.6%-12.0%). Soils served as a potential microbial reservoir, harboring 42% of the unique OTUs and contributing 3%-11.8% of communities to other habitats. While stream water and sediments showed reciprocal exchange, aerosols remained largely uncharacterized in terms of their sources. Collectively, these findings demonstrate that although prokaryotic responses to elevation are ecosystem-specific, these habitats are ecologically interconnected across the high-mountain landscape, providing a comprehensive overview of the prokaryotic biogeography of the region.}, }
@article {pmid42681282, year = {2026}, author = {Berruto, F and Bortolot, M and Lumini, E and Bianciotto, V}, title = {From Sampling to Identification of Arbuscular Mycorrhizal Fungi Through Next Generation Sequencing.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3045}, number = {}, pages = {185-208}, pmid = {42681282}, issn = {1940-6029}, mesh = {*Mycorrhizae/genetics/classification/isolation &amp; purification ; *High-Throughput Nucleotide Sequencing/methods ; Soil Microbiology ; DNA Barcoding, Taxonomic/methods ; DNA, Fungal/genetics ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; }, abstract = {In recent years, DNA sequencing technologies have advanced considerably with the rise of Next-Generation Sequencing (NGS) platforms, which have transformed microbial ecology research. These approaches enable the characterization of entire communities by using DNA traces to identify organisms taxonomically from a single sample. Arbuscular mycorrhizal fungi (AMF) are no exception and represent one of the most extensively studied groups of soil fungi. This chapter presents protocols for high-throughput, sequence-based analysis of AMF communities, covering the complete workflow from DNA extraction in plant or soil samples to the bioinformatic processing of sequencing data. It particularly focuses on rRNA gene metabarcoding, the most common strategy to provide estimates of AMF diversity and community composition through the amplification of DNA with taxon-specific primers followed by sequencing of barcode regions. Alternative strategies are described to accommodate different research objectives, including the selection of molecular markers.}, }
@article {pmid42681999, year = {2026}, author = {Harrison, F and Wheatley, RM}, title = {A special issue of Essays in Biochemistry on the social lives of bacteria.}, journal = {Essays in biochemistry}, volume = {70}, number = {3}, pages = {295-299}, pmid = {42681999}, issn = {1744-1358}, mesh = {*Bacteria/metabolism ; *Microbial Interactions ; *Bacterial Physiological Phenomena ; }, abstract = {The study of bacterial sociality, understanding when and how bacteria interact and the consequences of those interactions, has rapidly grown in popularity over the last 20 years. This has revealed that bacteria engage in a remarkable variety of social interactions, including complex cell-cell communication, the exchange of an arsenal of inhibitory molecules, and the sharing of metabolites. These interactions can have significant consequences for the host or environment they reside in, and numerous mechanisms of interaction have attracted significant interest for their therapeutic potential. The present special issue contains eight review articles addressing three major questions in bacterial sociality (Who is where? How are they interacting? And what are the implications of this?) alongside five methods-focused articles that introduce some particularly valuable approaches for the study of bacterial interactions.}, }
@article {pmid42682509, year = {2026}, author = {Ren, C and Xiu, Y and Zhang, Y and Wang, X and Zhao, H and Tang, J and Li, Q and Zhang, S and Zhao, F}, title = {Gut microbiome-immune-metabolic mechanisms in cerebrovascular disease: evidence-graded insights from cerebral small vessel disease, ischemic stroke, and intracerebral hemorrhage.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1927904}, pmid = {42682509}, issn = {1664-302X}, abstract = {Cerebrovascular disease is increasingly being examined in relation to the gut microbiome, but the field has not advanced evenly across disease phenotypes. A central challenge is to distinguish broad dysbiosis-based associations from microbial functions, host-facing metabolites, epithelial barrier injury, and immune pathways that may plausibly influence neurovascular vulnerability or recovery. This distinction is particularly important because cerebral small vessel disease, acute ischemic stroke, and intracerebral hemorrhage differ in time scale, vascular pathology, clinical exposure, and available microbiome evidence. This review evaluates gut microbiome-immune-metabolic mechanisms across these cerebrovascular contexts with a focus on microbial ecology, intestinal barrier dysfunction, microbial translocation, short-chain fatty acids (SCFAs), trimethylamine N-oxide (TMAO), bile acid derivatives, tryptophan-linked metabolites, lipopolysaccharide (LPS)-related inflammatory signaling, and emerging multi-kingdom signals, including the gut virome and mycobiome. Current evidence is most convincing in acute ischemic stroke, where human cohort studies and experimental perturbation models link microbiome disruption, microbial metabolites, immune programming, and functional outcome. Evidence for imaging-defined cerebral small vessel disease remains more limited and is largely cross-sectional, whereas intracerebral hemorrhage is an emerging but mechanistically distinct domain. Virome- and mycobiome-related mechanisms remain exploratory and require longitudinal, multi-omics, and perturbation-based validation. This review argues that cerebrovascular microbiome research should move beyond taxonomic association toward time-resolved microbial function, host-facing metabolites, disease-specific host-microbe interfaces, and experimentally testable mechanisms. Candidate microbiome-directed interventions-including dietary, prebiotic, probiotic, postbiotic, fecal microbiota transplantation, defined microbial consortia, metabolite-targeted, and phage-based approaches-remain investigational. Their translation will require disease- and time-window-specific evaluation of biological target engagement, safety, and clinically meaningful outcomes. Longitudinal multi-omics cohorts, disease-specific models, and careful control of diet, antibiotics, vascular medications, hospitalization, and frailty will be essential for determining which gut microbiome-related pathways are causal, context-specific, modifiable, and therapeutically actionable.}, }
@article {pmid42683650, year = {2026}, author = {Almalki, M and De Pierri, CR and Méric, T and Mkaouar, H and Slimani, D and Mariaule, V and Tebassi, S and Akermi, N and Maguin, E and Hernandez, J and Raittz, RT and Rhimi, M and Asnicar, F}, title = {Protease-serpin-microbiome interactions in inflammatory bowel disease: toward integrated biomarkers of gut health.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2726641}, pmid = {42683650}, issn = {1949-0984}, mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/metabolism/immunology ; *Serpins/metabolism ; Biomarkers/metabolism ; Intestinal Barrier Function ; *Gastrointestinal Microbiome ; Animals ; *Peptide Hydrolases/metabolism ; Intestinal Mucosa/microbiology/metabolism/immunology ; Bacteria/enzymology/classification/genetics/metabolism/isolation &amp; purification ; *Serine Proteases/metabolism ; Immunity, Mucosal ; }, abstract = {Proteolytic imbalance involving host and microbial serine proteases and their inhibitors (serpins) contributes to intestinal barrier disruption and chronic inflammation in inflammatory bowel disease (IBD). However, the interplay among these components remains insufficiently characterized. Here, we survey 13,304 publications over five decades, to map protease-serpin-microbiome literature in IBD. Our analysis reveals a fragmented literature structure, with uneven coverage and limited cross-domain integration among host proteases, microbial proteases, and inhibitory pathways. We synthesize evidence linking these components to intestinal barrier integrity, mucosal immunity, extracellular-matrix remodeling, and microbial ecology. Considering the protease-serpin-microbiome axis may provide an integrative direction for future studies of IBD pathogenesis, including the investigation of mechanisms underlying disease heterogeneity, prioritizing future biomarker and therapeutic studies.}, }
@article {pmid42683775, year = {2026}, author = {Bao, X and Wang, R and Qian, X and Wang, Y and Li, T and Wang, Q and Liu, S and Niu, S and Guo, J}, title = {Penicillium-mediated toxicity and microbial dysbiosis are associated with fruiting body abortion in artificially cultivated Chinese cordyceps.}, journal = {Virulence}, volume = {}, number = {}, pages = {2728527}, doi = {10.1080/21505594.2026.2728527}, pmid = {42683775}, issn = {2150-5608}, abstract = {Chinese cordyceps consists of fruiting body and sclerotia (larvae part) formed through the parasitism of the insect Hepialidae by the fungus Ophiocordyceps sinensis, but artificial cultivation is hindered by fruiting body abortion, severely impacting yield and quality. The interactions between the fungus, its host insects, and soil are critical for its development. Multi-omics analyses were conducted to compare normally and abnormally developing samples, examining microbial communities and metabolites in fungus-colonized host larvae and the mycosphere soil. Abnormal fruiting body development was associated with profound shifts in microbial ecology: fungal diversity increased significantly in both endophytic larvae and mycosphere soil, whereas bacterial diversity decreased within host larvae. The microbial composition in and around abnormal samples was markedly altered, characterized by a high enrichment of Penicillium fungi and a depletion of Bacillus bacteria. Cross-kingdom microbial network analysis showed fewer connections and lower stability in abnormally developing samples. Untargeted metabolomic profiling revealed significant accumulation of the antibiotics N1-hydroxy-roquefortine C and glandicoline A, both roquefortine C derivatives characteristic of Penicillium metabolism, along with enriched pathways involved in antibiotic biosynthesis. Exploratory Partial Least Squares Structural Equation Modeling (PLS-SEM) analysis supported an associative pathway in which Penicillium-mediated toxicity is correlated with microbial dysbiosis, which in turn is associated with fruiting body abortion. Conversely, Bacillus may play a critical role in suppressing Penicillium overgrowth and maintaining microbial homeostasis, representing a promising target for biocontrol strategies. This study is the first to reveal potential links between Penicillium‑mediated toxicity, microbial imbalance, and developmental disorders of Chinese cordyceps.}, }
@article {pmid42686967, year = {2026}, author = {Corinaldesi, C and Anantharaman, K and Aronson, JC and Baker, BJ and Candela, M and Cardinale, B and Dell'Anno, A and Gasol, JM and Grossart, HP and Laiolo, E and Levin, LA and Nomaki, H and Nunoura, T and Pusceddu, A and Ripple, WJ and Snelgrove, PVR and Suttle, CA and Zhang, R and Danovaro, R}, title = {Grounding microbial conservation in ecological principles.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {42686967}, issn = {2058-5276}, }
@article {pmid42678152, year = {2026}, author = {Grettenberger, CL and Williams, C and Hamilton, TL}, title = {The distribution of acidophilic iron oxidizers is consistent with environmental filtering, dispersal limitation, and competition.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0035126}, doi = {10.1128/msphere.00351-26}, pmid = {42678152}, issn = {2379-5042}, abstract = {UNLABELLED: Acid mine drainage (AMD) is a global pollution problem characterized by low pH and high concentrations of metals. Active remediation is often cost-prohibitive, but Fe(II)-oxidizing microbes may be used for passive bioremediation. To leverage these species, we must understand the factors that control their distribution. Here, we examined the environmental and ecological factors that control these species with the aim of determining if microbial seeding is a viable remediation strategy. Although stochastic processes appeared to control the distribution of the majority of taxa inhabiting AMD ecosystems, the distribution of Fe(II) oxidizers appeared to be driven by environmental filtering and competition. The abundance of all the major Fe(II)-oxidizing genera had significant relationships with pH, with pH explaining 10%-38% of the variation in their abundance. The genera appeared to have pH preferences, with Acidithiobacillus and Leptospirillum preferring environments with pH below 3, Gallionella, Sideroxydans, and Ferritrophicum preferring environments with pH above 3.5, and Ferrovum preferring intermediate-pH environments. Once the effect of pH is removed, genera that share pH preferences were negatively correlated, indicating that they were likely competing for the Fe(II)-oxidizing niche in their preferred environments. Communities were also shaped by dispersal limitation, which suggests that microbial seeding may be possible in these environments. Future seeding attempts should consider species interactions and ecology more generally to inform their efforts.<br><br>IMPORTANCE: Acid mine drainage (AMD) is a global pollution problem affecting streams worldwide. One method of remediating AMD is by using naturally occurring microbial communities to remove iron and other metals. However, we do not have a complete understanding of the factors that control the distribution of these species or if it is possible to seed species from one environment into another. Here, we examine the factors that control community assembly in AMD ecosystems. We find that individual species appear to be dispersal-limited; thus, microbial seeding may be a viable method for AMD remediation.}, }
@article {pmid42679733, year = {2026}, author = {Sun, Y and Zhao, Z and Lv, J and An, L and Yan, W and Wang, J and Li, Q and Qian, X and Tiedje, JM and Gu, J and Wang, X}, title = {Two typical residual surfactants facilitate the dissemination of antibiotic resistance genes: mechanisms of conjugation and community-level implications.}, journal = {Environment international}, volume = {215}, number = {}, pages = {110484}, doi = {10.1016/j.envint.2026.110484}, pmid = {42679733}, issn = {1873-6750}, abstract = {Since the outbreak of the COVID-19 pandemic, the reinforcement of personal hygiene practices has led to a significant increase in surfactant residues in municipal wastewater. As a reservoir of antibiotic resistance genes (ARGs), municipal wastewater has been reported to facilitate the conjugative transfer of ARGs by surfactants. However, the intrinsic mechanisms driving this process and the broader impact of surfactants on ARGs fate in real wastewater systems remain poorly understood. Here, we demonstrate that residual cetyltrimethylammonium bromide (CTAB) and sodium dodecylbenzenesulfonate (SDBS) promote ARGs transfer both between Escherichia coli (E. coli) strains and from E. coli to municipal wastewater indigenous microbiota. Exploration of the underlying mechanisms revealed that CTAB exerts its effects primarily by increasing cell membrane permeability, inducing oxidative stress, and activating the SOS response. Further investigation showed that CTAB increases membrane permeability through direct binding to membrane proteins. SDBS primarily acted by enhancing bacterial motility and reducing barriers to cell contact. Additionally, modulation of glutamate and aspartate metabolism supported the conjugative transfer process by providing supplementary energy. Furthermore, we found that harboring multidrug-resistant plasmids conferred a survival advantage to bacterial hosts in municipal wastewater environments, thereby promoting the enrichment of ARGs. These findings elucidate novel mechanisms underlying surfactant-facilitated dissemination of ARGs, revealing a significant but overlooked environmental risk associated with residual surfactants in wastewater.}, }
@article {pmid42680317, year = {2026}, author = {Leng, M and Zeng, Z and Zhu, X and Guo, Y and Xu, H and Chen, W and Xiang, X and Huang, W and Huang, R and Zhao, M and Song, C and Jin, S}, title = {Microbial diversity, functional activities, and safety risks in fermented tea: a comprehensive review.}, journal = {Food research international (Ottawa, Ont.)}, volume = {242}, number = {Pt 3}, pages = {120020}, doi = {10.1016/j.foodres.2026.120020}, pmid = {42680317}, issn = {1873-7145}, mesh = {*Tea/microbiology/chemistry ; *Fermentation ; *Food Microbiology ; Food Safety ; Mycotoxins ; *Fermented Foods/microbiology ; Fungi/metabolism ; }, abstract = {Microbial fermented teas are gaining global popularity due to their unique sensory profiles and health benefits. The quality and safety of these products are governed by complex microbial ecosystems that orchestrate the biotransformation of tea leaf components. This review addresses a critical paradox in the field: the same microbial activities that generate desirable bioactive metabolites, such as theabrownins and organic acids, also create ecological niches for mycotoxigenic fungi, posing significant health risks from contaminants like ochratoxin A, citrinin, and aflatoxins. While extensive research has cataloged the microbial diversity in these systems, a comprehensive framework linking processing environments to microbial community assembly, functional outcomes, and quantifiable safety risks remains elusive. This review systematically bridges this gap by synthesizing current knowledge on the microbial consortia-dominated by Aspergillus, Penicillium, Bacillus, and Lactiplantibacillus species-that drive tea fermentation. We critically analyze their functional roles in enhancing flavor, bioactivity, and potential probiotic activity while simultaneously evaluating the mechanisms of mycotoxin production and accumulation. By integrating microbial ecology, biochemistry, and food safety, we propose a forward-looking perspective focused on transitioning the industry from traditional, spontaneous fermentation to modern, controlled biotechnological processes. This approach, centered on the use of defined starter cultures, predictive modeling, and active biocontrol strategies, provides a roadmap for ensuring the consistent quality and safety of fermented tea products, ultimately unlocking their full potential as high-quality functional foods.}, }
@article {pmid42670971, year = {2026}, author = {Mahdy, A and Amin, I and Mohamed, HH and Hamdy, M and Abuelhaded, K and Alam-ElDein, KM and Elbakry, OM and Abdelkhalek, A and Elkhawanky, M and Elgebaly, AS and Faraag, AHI and Mohammed, OA and Doghish, AS}, title = {The Dysbiosis-Barrier-Immune Axis: Unraveling the Immune Consequences of Skin Microbial Imbalance.}, journal = {Immunology and cell biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/imcb.70161}, pmid = {42670971}, issn = {1440-1711}, abstract = {The skin microbiota has been reframed as a dynamic and active regulator of cutaneous barrier integrity and immune programming, moving beyond its traditional view as a passive microbial community. Dysbiosis represents a complex functional and ecological imbalance that disrupts barrier integrity and may promote sustained inflammatory immune remodeling. This mechanistic axis, in which disruption of the microbiota contributes to barrier failure and immune dysregulation, underpins chronic inflammatory skin conditions. Conventional antibiotic-centered therapies often fail to restore microbial homeostasis or immune balance, highlighting their limitations. Emerging precision microbiome therapeutics focus on targeted modulation of microbial function, signaling pathways, and ecological restoration to repair barrier defects and recalibrate immune responses. This review synthesizes current evidence linking skin microbiota dysbiosis with barrier dysfunction, inflammatory immune remodeling, and emerging microbiome-directed therapeutic strategies. We propose an integrative framework linking ecological disruption, epithelial barrier injury, and immune dysregulation while highlighting unresolved mechanistic, translational, and knowledge gaps, such as detailed molecular mechanisms of host-microbiota interactions and challenges in translating findings into clinically effective personalized interventions. Future research should prioritize multi-omics integration and biomarker-driven stratification to advance precision dermatology therapeutics grounded in mechanistic insights of skin microbial ecology.}, }
@article {pmid42671214, year = {2026}, author = {Qi, S and Zhang, S and Hu, Y and Sun, M and Xing, Z and Bao, S and Song, Y and Sun, L and Tong, X}, title = {Architectural confinement and seasonal forcing shape cross-domain pathogen-associated assemblages in complex built environments.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0191526}, doi = {10.1128/spectrum.01915-26}, pmid = {42671214}, issn = {2165-0497}, abstract = {Airborne microbial pathogens in built environments (BEs) may pose health threats, yet the ecological mechanisms governing their assembly and persistence across interconnected architectural spaces are less studied. Here, we conducted a year-long, multi-spatial investigation across a university building complex, sampling the exhaust outlets of three indoor environments and adjacent outdoor inlets. By integrating the 16S rRNA gene and ITS sequencing from 437 paired bacterial-fungal samples, we characterized the spatiotemporal dynamics of airborne opportunistic pathogen-containing genera. Our study showed that spatial filtering emerged as the dominant determinant of pathogen community structure, with confined elevator environments serving as reservoirs of potential pathogens, with limited but continuous microbial influx from surrounding spaces. Some potential pathogens exhibited distinct seasonal dynamics, as exemplified by pathogen-associated fungal genera such as Fusarium, which peaked in autumn and winter, possibly driven by enhanced aerosol persistence and dispersal under cooler, drier conditions. In contrast, the bacterial counterparts exhibited greater temporal resilience, with key taxa such as Listeria actively transcribed during winter, predisposing them to increased relative abundance in spring. Cross-domain ecological networks further revealed dynamic associations among potential pathogens, centered on the skeletal structure mediated by the keystone fungal genus Aspergillus, suggesting that coordinated microbial associations may reinforce their persistence across seasons. Together, our findings suggest that the dynamics of pathogen-containing genera within BEs arise from the coupled effects of spatial filtering, climatic modulation, and microbial associations. These results provide a foundation for transitioning from static environmental control toward predictive pathogen management in BEs.IMPORTANCEBuilt environments (BEs) are the primary settings of human microbial exposure, yet the ecological principles governing the persistence of airborne pathogens across interconnected indoor spaces remain poorly resolved. By integrating bacterial and fungal community dynamics across spatial environments over four seasons, this year-long study demonstrates that the ecology of airborne pathogen-associated taxa is not static but is instead mediated by a complex interplay of spatial, climatic, and biological forces. Our findings identify enclosed, high-transit elevator spaces as critical hotspots for the accumulation of potential pathogens and highlight the role of seasonal ecological reorganization in driving airborne health risks. More broadly, this work establishes a system-level ecological framework for understanding the dynamics of airborne pathogen-associated taxa in BEs and provides a conceptual basis for developing more adaptive strategies for indoor microbial risk management.}, }
@article {pmid42672061, year = {2026}, author = {Acheampong, R and Otu-Ayeboafo, JO}, title = {Dietary Sulfur Compounds and Halitosis: Bridging Food Science, Microbial Metabolism, and Oral Health: A Comprehensive Review.}, journal = {Molecular nutrition &amp; food research}, volume = {70}, number = {17}, pages = {e70526}, pmid = {42672061}, issn = {1613-4133}, mesh = {*Halitosis/microbiology/etiology ; Humans ; *Oral Health ; *Sulfur Compounds/metabolism/adverse effects ; Microbiota ; Biofilms ; *Diet ; Tongue/microbiology ; }, abstract = {Intraoral halitosis is predominantly caused by anaerobic microbes within the tongue biofilm that break down sulfur-containing amino acids, especially cysteine and methionine, to volatile sulfur compounds (VSCs). In addition to microbial activity, there is growing evidence to suggest that dietary factors are able to influence VSC formation by affecting substrate availability, redox equilibrium, and oral ecological stability and that some of these effects are due to extraoral metabolic activity. This review integrates food chemistry, microbial ecology, and oral health to explain how dietary exposures can interact with the oral microbiome to trigger and maintain halitosis. We synthesize current evidence on tongue biofilm ecology, key microbial taxa and metabolic pathways, and the modifying roles of salivary flow, periodontal inflammation, and common beverages and condiments. Diagnostic approaches are discussed with a mechanistic viewpoint, which has focused on combined organoleptic, gas specific analysis, tongue biofilm imaging, and selective provocation testing. Comprehensively, halitosis is presented as a diet modifiable, ecology-driven disease, the diagnostics of which should be guided by phenotype, and the intervention based on microbiomes and tailored care plans should be sustainable so that evidence-based functional foods and personalized care plans can be developed.}, }
@article {pmid42674646, year = {2026}, author = {Zuo, Z and Qiao, L and Cen, X and Liu, T and Zheng, M}, title = {Wastewater-Derived Comammox Nitrospira for Next-Generation Wastewater Management.}, journal = {Environmental science &amp; technology}, volume = {60}, number = {33}, pages = {23018-23034}, pmid = {42674646}, issn = {1520-5851}, support = {DE250100621//Australian Research Council/ ; DP230101340//Australian Research Council/ ; PolyU 25238324//Research Grants Council, University Grants Committee/ ; }, mesh = {*Wastewater ; Ammonia ; Oxidation-Reduction ; }, abstract = {The discovery of complete ammonia-oxidizing (comammox) Nitrospira in 2015 marked a major advance in our understanding of the nitrogen cycle and demonstrated that a single microorganism can catalyze the full oxidation of ammonia to nitrate, challenging the long-standing paradigm that separates ammonia- and nitrite-oxidizing microorganisms. Over the past decade, research on comammox has progressed rapidly from genomic discovery to detailed characterization of its physiology, kinetics, and ecological distribution across natural and engineered ecosystems. Wastewater-derived comammox Nitrospira have emerged as influential players in biological nitrogen transformations due to their exceptionally high substrate affinities, metabolic versatility, potentially low nitrous oxide emissions, and resilience under resource-limited conditions. These traits position comammox as promising catalysts for low-energy and sustainable nitrogen management in engineered systems. This review synthesizes the first decade of research on comammox Nitrospira, with a particular focus on wastewater-associated lineages. We examine the ecological niches that enable comammox Nitrospira to thrive in wastewater environments and analyze their competitive and cooperative interactions with canonical ammonia- and nitrite-oxidizing microorganisms. Building on these ecological insights, we discuss emerging comammox-centered biotechnological strategies for next-generation wastewater treatment and resource recovery. By linking microbial ecology with process engineering, this review highlights the potential for comammox-driven innovations to advance circular and energy-efficient nitrogen management in the coming decade.}, }
@article {pmid42677876, year = {2026}, author = {Van Leeuwen, P and Thinphovong, C and Sluydts, V and Nicolas, A and Kritiyakan, A and Kriengudom, A and Soisook, P and Chaisiri, K and Morand, S and Michaux, J}, title = {Microbiome Insights Into Zoonotic Risk at Wildlife-Human Interfaces in a Transitioning Landscape in Thailand.}, journal = {Integrative zoology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1749-4877.70167}, pmid = {42677876}, issn = {1749-4877}, support = {//Thai International Cooperation Agency/ ; ANR-24-CE35-5476//project rewild4Health/ ; 101059483//BCOMING project/ ; //European Union/ ; 40020126//FNRS/ ; }, abstract = {Land-use change is accelerating worldwide and is one of the strongest predictors of emerging zoonotic disease. These ecological transitions can disrupt host microbiomes, change pathogen carriage, and create novel opportunities for spillover at wildlife-livestock-human interfaces. Yet, little is known about how reforested landscapes influence microbiome diversity and the distribution of zoonotic bacteria in key reservoir hosts such as bats, rodents, treeshrews, and domestic dogs. We characterized the rectal microbiome of bats, rodents, and domestic dogs sampled across a land-use gradient in Nan Province, Thailand, spanning caves, forests, reforested zones, plantations, and village habitats. Full-length 16S rRNA sequencing was used to assess host- and habitat-specific patterns at the bacteria species level. Pathogen-associated taxa were identified, and their potential transmission pathways were explored using network analysis and qPCR validation targeting Salmonella spp. From 102 samples, 1816 taxa were identified, including 354 documented human pathogens. Hierarchical Modeling of Species Communities models confirmed that host species explained far more variation in pathogen occurrences than habitat type, with dogs, Menetes berdmorei, and Scotophilus heathii exhibiting particularly high pathogen diversity. Domestic dogs also displayed high network centrality and move freely across habitats, positioning them as a key bridging host. Salmonella screening detected both Salmonella enterica (serovars Newport/Typhimurium) and the reptile-associated Salmonella bongori, the latter unexpectedly in bats and rodents, with variable concordance between metabarcoding and qPCR results. Our findings demonstrate that host identity, more than habitat type, structures pathogen-associated microbiomes across a reforested landscape. Understanding these dynamics is essential to anticipate pathogen flow and strengthen One Health surveillance.}, }
@article {pmid42663042, year = {2026}, author = {Araujo, ASF and de Almeida Lopes, AC and Martins, LDV and Ferreira, GDNC and da Costa, RM and Rocha, SMB and Mendes, LW and de Medeiros, EV and Pereira, APA}, title = {Phytohormone-microbiome interactions and epigenetic regulation of plant stress responses and priming.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/erag417}, pmid = {42663042}, issn = {1460-2431}, abstract = {Plants continuously face fluctuating environmental conditions, requiring tightly coordinated regulatory systems to balance growth and stress responses. This review synthesizes current knowledge on phytohormones as central integrators of plant-microbiome interactions, highlighting their dual role as internal regulators and ecological gatekeepers that shape microbiome assembly and function. Phytohormones, such as auxins, cytokinins, gibberellins, abscisic acid, ethylene, salicylic acid, and jasmonates, dynamically regulate plant development, immunity, and rhizosphere chemistry, thereby influencing microbial recruitment and activity. In turn, plant-associated microbes actively modulate hormonal pathways through biosynthesis, degradation, and interference with signaling and transport processes, thereby reconfiguring plant physiological responses. Emerging evidence demonstrates that these interactions underpin microbial priming, enabling enhanced responsiveness to subsequent stresses without constitutive defense costs. Such primed states are frequently associated with epigenetic modifications, including DNA methylation and histone modifications, which contribute to stress memory and may persist across generations. We propose that microbiome-driven hormonal regulation represents a key mechanism for plant adaptation to environmental stress and that its integration can offer promising opportunities to enhance resilience, reduce agrochemical dependence, and improve agricultural sustainability under climate change.}, }
@article {pmid42663479, year = {2026}, author = {Liu, M and Su, X and Huang, X and Yang, X and Chen, Y and Xu, J and He, Y}, title = {Top-down/bottom-up consortia achieve robust γ-HCH degradation and reduced methanogenic contribution in wetlands.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0113326}, doi = {10.1128/aem.01133-26}, pmid = {42663479}, issn = {1098-5336}, abstract = {UNLABELLED: Generalist non-obligate organochlorine-degrading bacteria (ODB) play an important role in the bioremediation of γ-hexachlorocyclohexane (γ-HCH), yet their ecological roles and functional mechanisms remain underexplored. In this study, we used both "top-down" and "bottom-up" strategies to construct two functional consortia (M and Y13) based on non-obligate ODB. Both consortia demonstrated efficient degradation in sediment microcosms, reducing γ-HCH (C/C0) to 63.0% (M) and 56.1% (Y13). Simultaneously, functional microbial consortia inoculation significantly suppressed the CO2 reduction methanogenesis pathway compared with the non-inoculated group (P < 0.05), as evidenced by a marked decline in the CH4/CO2 ratio in inoculated groups. The well-known degradation gene pceA was enriched in the Y13 group, and the co-localization of pceA-encoding contigs with mobile genetic elements was identified. Notably, Enterococcus was found to have successfully colonized inoculated groups. It has strong environmental evolutionary adaptability and might acquire organochlorine-degrading genes through horizontal gene transfer under pollution stress. The broad applicability of non-obligate ODB (e.g., Enterococcus) makes them a promising candidate for future environmental remediation efforts, breeding new avenues of "One Health" win-win solutions in carbon reduction during pollution remediation for wetlands.<br><br>IMPORTANCE: &#x3b3;&#x2011;Hexachlorocyclohexane (&#x3b3;&#x2011;HCH) is a representative organochlorine pesticide and a well&#x2011;known persistent organic pollutant that poses significant risks to ecosystems and human health. Microbial anaerobic degradation is a key process in the natural attenuation and engineered cleanup of &#x3b3;&#x2011;HCH contamination. The effective application of obligate organohalide-respiring bacteria often requires precise management. In parallel, newly discovered non&#x2011;obligate organohalide-respiring bacteria capable of degrading &#x3b3;&#x2011;HCH have emerged as promising alternatives, yet their performance and ecological interactions in realistic sediment systems remain poorly understood. This study examines the degradation mechanisms and microbial ecology of non-obligate organohalide-respiring bacterial functional consortia in complex media. The findings provide critical insights for developing effective bioaugmentation strategies for lindane&#x2011;contaminated coastal wetlands and may offer a useful framework for managing other recalcitrant halogenated pollutants in similar environments.}, }
@article {pmid42664271, year = {2026}, author = {Lilja, E and Allen, RJ and Waclaw, B}, title = {Simple birth-death-mutation models predict some-but not all-aspects of the experimental evolution of antibiotic resistance.}, journal = {PLoS computational biology}, volume = {22}, number = {8}, pages = {e1014666}, doi = {10.1371/journal.pcbi.1014666}, pmid = {42664271}, issn = {1553-7358}, abstract = {Mathematical modelling of antibiotic resistance plays an important role in understanding the mechanisms of resistance emergence and spreading, testing the feasibility of new treatment protocols, and antimicrobial stewardship. However, many assumptions underlying some of the most commonly used mathematical models have not been rigorously tested experimentally. We verify whether one of these models - a birth-death-mutation process - is able to quantitatively predict the outcome of laboratory experiments. We grow bacteria in a bioreactor in conditions that closely resemble the assumptions of the model, and compare the model predictions with experimental observables such as the probability and time to resistance evolution, mutant number distribution, and the genetic composition of the evolved populations. We show that the model fails to reproduce some aspects of the experiments (failing differently for different antibiotics) but that simple modifications of the model significantly improve its predictive power. These modifications give insight into the population dynamics of resistant mutants for each antibiotic tested, and highlight the importance of quantitative modelling for accurate prediction of antibiotic resistance evolution.}, }
@article {pmid42667435, year = {2026}, author = {De, P and Chakraborti, S and Bhabai, B and Nath, S and Ghosh, PK and Khatun, N and Asif, SM}, title = {From traditional retting to precision bioprocessing: microbial ecology, enzymatic selectivity, and systems biology of jute retting.}, journal = {Antonie van Leeuwenhoek}, volume = {119}, number = {9}, pages = {}, pmid = {42667435}, issn = {1572-9699}, mesh = {*Systems Biology/methods ; *Lignin/metabolism/chemistry ; Microbial Consortia ; Bacteria/metabolism ; }, abstract = {Jute is one of the world's most important lignocellulosic fibre crops, yet its commercial value remains highly dependent on retting, a biologically mediated fibre extraction process still largely governed by empirical practices and variable environmental conditions. Recent advances in microbial ecology, enzymology, molecular biology, and bioprocess engineering have transformed retting from a traditional post-harvest operation into a controllable lignocellulosic bioconversion process. This review synthesizes current understanding of the structural organization of jute bast fibres, selective degradation of plant cell-wall polymers, microbial succession, extracellular enzyme networks, and physicochemical factors regulating fibre liberation. It highlights the coordinated interactions among cell-wall architecture, microbial communities, enzyme specificity, and environmental conditions that collectively determine retting efficiency and fibre quality. Emerging precision retting strategies, including defined microbial consortia, enzyme-assisted retting, ribbon retting, controlled processing systems, and water-efficient technologies, are critically evaluated for their potential to improve process reproducibility, fibre quality, and environmental sustainability. The review also examines metagenomics, metatranscriptomics, metaproteomics, metabolomics, systems biology, and artificial intelligence as enabling technologies for microbiome-guided process monitoring, predictive modelling, and digital decision support. Furthermore, this review discusses the integration of precision retting within circular bioeconomy frameworks through resource recovery, pollution mitigation, climate-resilient processing, and lignocellulosic biorefineries. Key knowledge gaps, including limited understanding of microbial interactions, lack of standardized microbial consortia, insufficient process-monitoring tools, fragmented multi-omics datasets, and challenges in industrial scale-up, are identified. Overall, this review presents a systems-level framework for advancing jute retting toward standardized, predictive, and environmentally sustainable precision bioprocessing.}, }
@article {pmid42667906, year = {2026}, author = {Barbosa, LMP and Silva, DEO and Ventura, SH and Costa, MKL and Rocha, SMB and Borges, JF and Costa, RM and de Medeiros, EV and Pereira, APA and Mendes, LW and Salles, JF and Araujo, ASF}, title = {Restoration contexts shape the bacterial and fungal soil communities in desertification hotspots in the Brazilian semiarid region.}, journal = {Journal of environmental management}, volume = {416}, number = {}, pages = {130831}, doi = {10.1016/j.jenvman.2026.130831}, pmid = {42667906}, issn = {1095-8630}, abstract = {Desertification in the Brazilian semiarid has compromised ecosystem functionality, impacting soil microbial biodiversity. Thus, restoration strategies have been implemented, aiming to mitigate the negative impacts. However, little is known about their effects on soil microbial communities. In this study, we hypothesized that the two restoration contexts would promote distinct trajectories of soil microbial community recovery. We evaluated 36 soil samples collected from two desertification hotspots in the Brazilian semiarid, representing active (Gilbués) and passive (Irauçuba) restoration contexts. Soil DNA was extracted and subjected to 16S and ITS amplicon sequencing to characterize bacterial and fungal communities, respectively. Community differences were assessed using alpha-diversity metrics, redundancy analysis (RDA), and PERMANOVA. The results showed that within Gilbués (active restoration), bacterial and fungal community composition differed among soils under desertification and restoration. In Irauçuba (passive restoration), only native soils differed from both soils under desertification and restoration. Proteobacteria, Actinobacteriota, and Firmicutes (bacteria), and Ascomycota and Basidiomycota (fungi), were the dominant phyla in both hotspots. Bacterial and fungal communities showed distinct taxonomic patterns among native, degraded, and restored soils within each restoration context. Niche occupancy patterns also differed between restoration contexts. In conclusion, the two hotspots followed contrasting microbial recovery trajectories, demonstrating that restoration responses are context-dependent and vary according to the microbial groups, rather than supporting the universal superiority of one restoration strategy over the other.}, }
@article {pmid42668748, year = {2026}, author = {Cao, C and Ma, B and Show, PL and Ngo, HH and Fu, X and Li, N and Zhou, J}, title = {Marine phycotoxins repurposed as bioresource: their antiviral potentials and molecular mechanisms in aquatic organism.}, journal = {Marine life science &amp; technology}, volume = {8}, number = {3}, pages = {727-741}, pmid = {42668748}, issn = {2662-1746}, abstract = {UNLABELLED: Marine phycotoxins produced by microalgae have traditionally been regarded as water pollutants or hazardous substances. Most studies have focused on their toxicity, with limited exploration of their therapeutic potential. In this study, we demonstrated that domoic acid (DA) exerts antiviral roles against largemouth bass ranavirus (LMBV). Mechanistic analyses revealed that DA disrupts the extracellular structure of LMBV and inhibits intracellular viral assembly. This may be attributed to the ATP depletion caused by the suppression of mitochondrial oxidative phosphorylation. In vivo, DA treatment reduced fish mortality by 12.5% and significantly alleviated pathological lesions in splenic and telencephalic tissues, thereby further confirming its protective effect. Additionally, transcriptomic analysis of liver tissue showed that DA enhanced digestive enzyme activity and activated the complement immune response in LMBV-infected fish. This study uncovers previously unappreciated antiviral activity of marine phycotoxin-DA and elucidates its underlying mechanisms preliminary, laying a foundation for developing marine phycotoxins as antiviral lead compounds.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1007/s42995-026-00412-2.}, }
@article {pmid42655784, year = {2026}, author = {Xi, H and Liu, J and Wang, J and Zhong, L and Xu, Y and Li, Y}, title = {Virus-Induced Intestinal Barrier Injury: Mechanisms and Therapeutic Perspectives.}, journal = {Veterinary sciences}, volume = {13}, number = {8}, pages = {}, pmid = {42655784}, issn = {2306-7381}, support = {LQ24C180001//Zhejiang Provincial Natural Science Foundation/ ; 32302845//National Natural Science Foundation of China/ ; 2025SZRJJ1032//Hangzhou Natural Science Foundation/ ; ZJSKXQT2025033//Zhejiang Association for Science and Technology/ ; }, abstract = {The intestinal barrier is a key interface maintaining host-microbial segregation and systemic homeostasis. A broad range of viruses, including enteric, respiratory, and systemic pathogens, can disrupt this barrier through effects on epithelial integrity, vesicular transport, immune responses, and microbial ecology. Whether these diverse insults converge on shared regulatory nodes or act through distinct virus-specific pathways that ultimately result in barrier failure remains unclear. Building on this premise, this review systematically delineates the molecular and cellular mechanisms underlying virus-induced disruption of the intestinal barrier. Viral infection disrupts epithelial integrity through multiple converging processes, including disassembly of tight junction architecture, activation of programmed cell death pathways, degradation of the mucus layer, impaired regeneration driven by intestinal stem cells, and dysregulation of transcellular transport. These processes are interconnected and collectively drive epithelial dysfunction and barrier breakdown. Beyond epithelial damage, we further highlight the pivotal contribution of host immune responses to barrier breakdown. Viral infection induces dysregulated cytokine production and aberrant immune activation, which amplify epithelial damage and further increase barrier permeability. In parallel, increasing evidence supports a bidirectional interaction between viral infection and gut microbiota dysbiosis, in which each process reinforces the other to accelerate barrier disruption and disease progression. We also discuss emerging therapeutic strategies aimed at restoring intestinal homeostasis, including antiviral therapies, host-targeted interventions, and microbiota modulation. Despite recent progress, key questions remain, particularly regarding mechanisms of failed barrier repair after viral clearance and the multilayered regulatory networks linking viruses, immunity, and the microbiota. Together, this review provides a framework for understanding virus-induced intestinal barrier dysfunction and identifies potential therapeutic nodes for intervention.}, }
@article {pmid42657533, year = {2026}, author = {Cristian, RE and Vrancianu, CO and Constantin, M and Paun, M and Milea, EC and Malaescu, D and Chifiriuc, MC}, title = {Microbiome-based therapeutics for Clostridioides difficile infection: additive, subtractive, and modulatory strategies in modern clinical practice.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2722482}, pmid = {42657533}, issn = {1949-0984}, mesh = {Humans ; *Clostridium Infections/therapy/microbiology ; *Clostridioides difficile/physiology/drug effects ; Fecal Microbiota Transplantation ; Animals ; Anti-Bacterial Agents/therapeutic use ; *Gastrointestinal Microbiome ; Biological Therapy/methods ; }, abstract = {Microbiome-based therapeutics have rapidly evolved into a transformative field at the intersection of infectious diseases, microbial ecology, and precision medicine. Clostridioides difficile infection (CDI) represents the most extensively studied model, providing a framework for understanding microbiome-driven disease and ecological restoration. This review synthesizes three major therapeutic strategies, additive, subtractive, and modulatory, and integrates recent advances from basic, translational, and clinical research. Additive approaches, including fecal microbiota transplantation (FMT), live biotherapeutic products (LBPs), and defined microbial consortia, aim to restore microbial diversity and colonization resistance. Subtractive strategies selectively target C. difficile or its ecological advantages through targeted antibiotics, bacteriocins, bacteriophages, and CRISPR-based antimicrobials. Modulatory therapies reshape host-microbe and microbe-microbe interactions, targeting toxin activity, bile acid metabolism, and spore germination. Together, these approaches reflect a paradigm shift from pathogen-centered treatment toward ecological therapeutics targeting the dysbiotic niche underlying CDI persistence and recurrence. Understanding the similarities and differences between these strategies can help guide the design of future microbiome-targeted interventions and explore their potential beyond CDI across microbiome-mediated diseases.}, }
@article {pmid42660056, year = {2026}, author = {Nair, PM and Alex, R and Mondal, G}, title = {Hydrogen flux and microbial interactions governing methane formation in the rumen: Implications for mitigation.}, journal = {The Science of the total environment}, volume = {1050}, number = {}, pages = {182213}, doi = {10.1016/j.scitotenv.2026.182213}, pmid = {42660056}, issn = {1879-1026}, abstract = {Enteric methane production in ruminants is the dominant metabolic consequence of microbial hydrogen (H2) disposal during anaerobic fermentation under typical rumen conditions, yet controlling it without disrupting rumen function remains a critical challenge in sustainable livestock production. Methanogenesis is not an isolated metabolic pathway but an emergent property of syntrophic microbial interactions that govern H2 flux within the rumen ecosystem. During ruminal fermentation, fibrolytic bacteria, anaerobic fungi, and ciliate protozoa generate H2 through coordinated carbohydrate degradation, which is continuously transferred to hydrogenotrophic microorganisms, primarily methanogenic archaea, through interspecies H2 transfer mechanisms that are essential for maintaining redox balance and fermentation efficiency. Molecular hydrogen (H2), serves as the primary vehicle for reductant transfer between microbial partners, and its dissolved concentration in rumen fluid governs the thermodynamic feasibility of all major fermentation pathways. This review uniquely frames enteric methane mitigation as a network-level H2 flux control problem, integrating microbial ecology, thermodynamics, hydrogenase biology, and multi-omics evidence within a unified mechanistic framework. Methanogenesis is more comprehensively understood as a system-level outcome of H2 partitioning within a complex microbial network rather than the activity of methanogens alone. H2 is distributed among competing metabolic sinks, including propionate formation, reductive acetogenesis, nitrate reduction, and sulfate reduction, with methanogenesis dominating due to thermodynamic and ecological advantages under standard rumen conditions. Mitigation strategies are evaluated through their effect on H2 flux: approaches that suppress H2 production, redirect H2 toward alternative sinks, or disrupt interspecies transfer are each constrained by microbial functional redundancy and adaptive compensation. Composite strategies simultaneously targeting multiple nodes within the H2 network achieve more consistent and sustained methane reductions. Reconceptualizing methane mitigation as coordinated control of microbial H2 flow provides a mechanistic, systems-level framework for designing interventions that reduce emissions without compromising rumen microbial stability or host productivity.}, }
@article {pmid42662711, year = {2026}, author = {Marian, M and Stringlis, I and Rolli, E and Barnes, CJ and Compant, S and Sessitsch, A}, title = {Microbiome modulation for sustainable crop production and climate resilience.}, journal = {Sustainable microbiology}, volume = {3}, number = {3}, pages = {qvag032}, pmid = {42662711}, issn = {2755-1970}, abstract = {The microbiome is fundamental to plant performance in agroecosystems, influencing primary productivity and climate resilience. Microbiome modulation refers to the targeted manipulation (or steering) and optimization of microbiota features, including taxonomic structure, diversity, composition, assembly dynamics, stability, functional capacity, interactions, and network architecture. Here, we review the current state-of-the-art knowledge and strategies used for microbiome modulation, encompassing biological interventions such as bacteria, fungi, protists, nematodes, and phages, as well metabolites, compounds, and nutrients derived from plants. We further discuss emerging tools and strategies for next-generation microbiome modulation, including function-oriented, multitrophic defined microbial communities assembled based on ecological traits and interactions across multiple trophic levels to enable their establishment and function within the phytobiome; temperate phages; microbiome transplantation and breeding; and functional synbiotics, defined as combinations of beneficial microorganisms and compounds that improve microbiome health and function. In addition, we highlight key knowledge gaps and research priorities for advancing precision microbiome modulation. Addressing current challenges will require integrated frameworks combining experimental validation in planta and reductionist approaches with in silico modeling and multiomics analyses to better predict, design, and sustain beneficial plant-microbiome outcomes. Overall, microbiome modulation represents a paradigm shift in advancing sustainable and climate-resilient agri-food systems.}, }
@article {pmid42655146, year = {2026}, author = {Zhang, Z and Yan, C and Li, J and Zhao, L and Li, L and Cai, R and Wei, W and Lu, S}, title = {Advances in Cider Flavor: Integrating Apple Raw Materials, Microbial Ecology, and Process Control.}, journal = {Microorganisms}, volume = {14}, number = {8}, pages = {}, pmid = {42655146}, issn = {2076-2607}, abstract = {Cider is a low-alcohol fruit wine produced by partial or complete fermentation of apple juice. In recent years, its consumption has grown significantly, especially in Asia. Its distinctive flavor profile reflects a complex interplay of aroma and non-volatile components. The composition of cider is mainly influenced by three factors: raw materials, starter cultures, and production process. This review begins by outlining the composition of cider, covering both its aromatic compounds and non-volatile components. The primary aroma profile is defined by higher alcohols, esters, fatty acids, and carbonyl compounds, while sugars, organic acids, and polyphenols are the key determinants of its taste. Subsequently, it provides a detailed analysis of how the raw material, the choice of starter cultures, and the applied production processes collectively shape the cider's flavor. Research shows that apple variety and maturity influence the levels of sugars, organic acids, and polyphenols, shaping the flavor foundation of cider. To enhance flavor diversity, inoculation strategies have shifted from single-strain fermentation with Saccharomyces cerevisiae to mixed fermentations using non-Saccharomyces yeasts and lactic acid bacteria, either simultaneously or sequentially. Currently, screening non-Saccharomyces strains has become a key strategy to increase cider flavor complexity. Precise micro-oxygenation and nutrient supply regulate microbial metabolism, thereby controlling the fermentation process and the production of specific flavor compounds. In the future, given the untapped diversity of non-Saccharomyces yeasts and lactic acid bacteria in winemaking traits, research in this direction may be key to improving cider quality. In addition, selecting apple cultivars tailored to specific cider styles and exploring pre-fermentation treatments such as cold maceration and enzymolysis may also contribute to enhancing the flavor diversity of cider.}, }
@article {pmid42655103, year = {2026}, author = {Yuan, H and Li, B and Shen, C and Xie, L and Hou, F}, title = {Microbiota-Immune Crosstalk in Pneumonia and Acute Lung Injury: Mechanisms, Evidence, and Therapeutic Opportunities.}, journal = {Microorganisms}, volume = {14}, number = {8}, pages = {}, pmid = {42655103}, issn = {2076-2607}, support = {YDZJ202501ZYTS283//Jilin Province Science and Technology Department/ ; }, abstract = {Mucosal microbiota contribute broadly to host defense and immune homeostasis, while the lung and gut microbiota form a particularly important bidirectional ecological and immunological network that shapes pulmonary host defense, inflammatory injury, and tissue repair. In pneumonia, loss of colonization resistance and altered microbial metabolite production may weaken innate and adaptive immunity; respiratory infection, antibiotics, and critical-care exposures can, in turn, remodel both microbial communities. In acute lung injury (ALI) and acute respiratory distress syndrome (ARDS), intestinal barrier failure, circulating microbial products, immune cell trafficking and, in selected settings, lymphatic or hematogenous dissemination of gut-derived organisms may aggravate alveolar-capillary injury. Alveolar macrophages integrate these signals through pattern-recognition, metabolic, and epigenetic pathways, linking microbial ecology to pathogen clearance and inflammatory resolution. The evidence, however, remains uneven. Mechanistic causality rests largely on animal studies, most human data are associative, and trials of microbiota-directed interventions are heterogeneous and strain-specific. This Review examines bacterial and viral pneumonia, sepsis-associated ALI and ventilator-associated injury; separates mechanistic, observational, and interventional evidence; and evaluates probiotics, live biotherapeutic products, microbial metabolites, and dietary approaches. Translation will depend on longitudinal sampling, source-resolved microbial tracking, metabolite-informed patient stratification, and adequately powered trials with clinically relevant endpoints.}, }
@article {pmid42655130, year = {2026}, author = {Rahman, MH and Jeon, H and Kim, H and Lee, S}, title = {Precision Nutrigenomics in Cultured Finfish: Dietary Regulation of Gene Expression, Microbial Ecology, Metabolism, and Immunity.}, journal = {Microorganisms}, volume = {14}, number = {8}, pages = {}, pmid = {42655130}, issn = {2076-2607}, support = {2025//Pukyong National University/ ; Global Partnership Exchange and Capacity Building for Overseas Fisheries" program//Ministry of Oceans and Fisheries/ ; }, abstract = {Precision nutrigenomics requires a diet-microbiome-host perspective because microorganisms can transform feed substrates, generate bioactive metabolites, compete with pathogens, and modify intestinal and systemic gene regulation. This structured narrative review synthesizes representative controlled feeding trials, transcriptomic and targeted gene-expression studies, microbiome analyses, and complementary multi-omic evidence concerning dietary regulations in cultured finfish. The available evidence is concentrated particularly on soybean-derived proteins, lipid-source replacements, selected amino acids and micronutrients, functional additives, probiotics, and fermented ingredients in a limited range of cultured finfish species; therefore, the synthesis is not intended to provide exhaustive coverage of every dietary intervention or finfish taxon. Recurrent host responses involve intestinal inflammation and barrier integrity, nutrient transport, lipid and bile-acid metabolism, long-chain polyunsaturated fatty-acid biosynthesis, targets of rapamycin/insulin-like growth factor (TOR/IGF) signaling, and nuclear factor erythroid 2-related factor 2/Kelch-like ECH-associated protein 1 (Nrf2/Keap1) antioxidant defense. The expanded microorganism-centered synthesis shows that dietary effects depend on microbial niche, substrate availability, community succession, metabolite production, and strain-specific probiotic or pathobiont activity. Lactic-acid bacteria, Bacillus-associated interventions, butyrate-generating strategies, fermented ingredients, and microbial biomass may support digestion, immune balance, and disease resistance, but taxonomic shifts alone do not demonstrate functional benefit. Current evidence is limited by extensive reliance on 16S ribosomal RNA (16S rRNA) relative-abundance data, inconsistent digesta-versus-mucosa sampling, inadequate feed and water controls, and weak causal validation. Future precision aquafeed studies should combine host transcriptomics with absolute microbial quantification, shotgun metagenomics, metatranscriptomics, metabolomics, culturomics, histology, and pathogen challenge. Integrating microbial function with host phenotype can improve sustainable feed design, intestinal health, and resilience.}, }
@article {pmid42654237, year = {2026}, author = {Diaz-Garrido, N and Regaldiz, A and Zagmutt, S and Cisternas, P and Bastías-Pérez, M and Cortés-Martín, A}, title = {Intermittent Fasting and the Gut Microbiota: Mechanisms Linking Microbial Remodeling to Metabolic and Immune Regulation.}, journal = {Nutrients}, volume = {18}, number = {16}, pages = {}, pmid = {42654237}, issn = {2072-6643}, mesh = {Humans ; *Intermittent Fasting ; *Gastrointestinal Microbiome/physiology ; Animals ; *Energy Metabolism ; Prebiotics ; Circadian Rhythm ; Fatty Acids, Volatile/metabolism ; *Fasting ; Probiotics/administration &amp; dosage ; Intestinal Barrier Function ; Immune System ; }, abstract = {Intermittent fasting (IF) has gained increasing attention as a dietary strategy to improve metabolic health and prevent cardiometabolic disorders. Accumulating evidence suggests that modulation of the gut microbiota may represent one of the mechanisms underlying the physiological benefits of IF. This review summarizes the current knowledge on the mechanisms by which IF modulates gut microbial ecology and how these changes influence host metabolic and immune functions. We examine the effects of IF on gut microbiota diversity and composition, highlighting shifts in key microbial taxa associated with metabolic regulation. In addition, we discuss how fasting-induced microbial remodeling affects microbiota-derived metabolites, including short-chain fatty acids and bile acids, which play central roles in energy homeostasis, intestinal barrier integrity, and inflammatory signaling. Increasing evidence indicates that IF interacts with circadian rhythms, influencing both microbial oscillations and host metabolic pathways that coordinate nutrient sensing and energy metabolism. Furthermore, we explore the bidirectional crosstalk between the gut microbiota and the intestinal immune system, emphasizing that fasting-driven microbial changes may modulate inflammatory responses, epithelial barrier function, and immune cell activity. Finally, we discuss nutritional strategies that may enhance the beneficial effects of IF, including the incorporation of prebiotics, dietary fiber, and probiotic supplementation, to promote microbial diversity and functional resilience. Collectively, these findings support a model in which IF acts as a key modulator of the gut microbiota-immune-metabolic axis. Future integrative studies combining gut microbiome, metabolomic, and immunological approaches are needed to better understand these interactions and optimize microbiota-targeted dietary interventions.}, }
@article {pmid42654492, year = {2026}, author = {Ingravalle, F and Ciotti, M and Gaetti, G and Morlino, G and Bulfone, G and Bardhi, D and Barbadoro, P and Pica, F and Di Carlo, S and Serafinelli, L and Vinci, A and Maurici, M}, title = {Microbial Epidemiology and Antimicrobial Resistance Trends in Urinary Isolates from a Tertiary Hospital in Rome, Italy: A Retrospective Study (2022-2025).}, journal = {Medicina (Kaunas, Lithuania)}, volume = {62}, number = {8}, pages = {}, pmid = {42654492}, issn = {1648-9144}, mesh = {Humans ; Retrospective Studies ; Rome/epidemiology ; Tertiary Care Centers/statistics &amp; numerical data/organization &amp; administration ; *Urinary Tract Infections/microbiology/epidemiology/drug therapy ; Anti-Bacterial Agents/therapeutic use/pharmacology ; Microbial Sensitivity Tests ; Female ; Male ; Aged ; Middle Aged ; Aged, 80 and over ; Italy ; Drug Resistance, Bacterial ; }, abstract = {Background and Objectives: Urinary tract infections are common in clinical practice, but in hospital settings, especially among older and catheterized patients, the microbial ecology and resistance burden may differ substantially from community-acquired infections. Local surveillance is therefore essential to support appropriate empirical treatment and antimicrobial stewardship. The objective is to describe the microbiological epidemiology of urinary isolates in a tertiary hospital and evaluate temporal trends in antimicrobial resistance among the most frequently isolated microorganisms. Materials and Methods: This retrospective observational study analyzed microbiology laboratory data from Tor Vergata University Hospital, Rome, Italy, collected from January 2022 to June 2025. After WHONET-based deduplication using a 30-day repeat-isolate rule, 5788 deduplicated urinary isolates and 85,888 microorganism-drug associations were included. Descriptive analyses, cumulative antibiograms/antimycograms, and quarterly resistance trends were assessed using univariable and multivariable regression analyses. Results: The population was predominantly elderly, inpatient, and catheter-exposed. Gram-negative organisms predominated, followed by Gram-positive bacteria and fungi. The most frequent isolates were E. coli, K. pneumoniae, E. faecalis, and C. albicans. Although microorganism distribution remained broadly stable over time, resistance increased in several clinically relevant organism-drug combinations, especially among major Enterobacterales. Conclusions: In this high-complexity hospital population, urinary isolates showed a relatively stable microorganism distribution but progressive changes in susceptibility among selected urinary isolates. These findings support setting-specific microbiological surveillance and stewardship-informed empirical treatment strategies.}, }
@article {pmid42654747, year = {2026}, author = {Koukouvini, KA and Fokas, R and Vantarakis, A}, title = {Beyond Infection-Indoor Airborne Pathogens as Contributors to Respiratory Inflammation and Immune Dysregulation: A Narrative Review.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {8}, pages = {}, pmid = {42654747}, issn = {2076-0817}, mesh = {Humans ; *Air Microbiology ; *Air Pollution, Indoor/adverse effects/analysis ; *Inflammation/etiology ; Fungi ; }, abstract = {Indoor-air research has largely examined infection, microbial ecology, immune effects and antimicrobial resistance separately, leaving the pathway from indoor biological sources to chronic respiratory outcomes insufficiently integrated. This narrative review synthesises evidence on indoor airborne pathogens and non-viable microbial components as health-relevant biological exposures beyond acute infection. Literature published between 2000 and February 2026 was reviewed from PubMed, Scopus and Web of Science, supplemented by guidance from WHO, ECDC, US EPA and ASHRAE. Viable microorganisms and non-viable components, including endotoxin, β-(1→3)-glucans, microbial DNA and extracellular vesicles, engage epithelial pattern-recognition pathways and promote inflammatory signalling. Findings included 6.5% higher TNF-α and 5% higher IL-8 per log-unit increase in fungal-spore exposure among sawmill workers; uncontrolled asthma in 45% of moisture- or mould-exposed versus 33% of non-exposed children; airborne resistance-gene and mobile-element loads of 0.55-479.44 copies/m[3] in hospital departments; and a 32.8% reduction in viral diversity, but no significant reduction in high viral exposure, following classroom HEPA filtration. These findings support biological plausibility but reveal a fragmented evidence base dominated by observational studies, heterogeneous sampling and limited longitudinal exposure-response data. Indoor bioaerosols should be considered continuous exposures within the exposome, requiring research and regulation across microbiology, environmental engineering, medicine and public health.}, }
@article {pmid42654952, year = {2026}, author = {Wang, J and Wang, K and Yuan, R and Xu, X and Ma, Q and Chen, K and Jiang, Y and He, X and Zhang, X and Liu, X}, title = {Effects of Combined Application of Mushroom Residue and Chemical Fertilizer on Greenhouse Soil Quality and Microbial Community Structure and Function.}, journal = {Microorganisms}, volume = {14}, number = {8}, pages = {}, pmid = {42654952}, issn = {2076-2607}, support = {2025QCY KXJ 128//Construction of the "Scientists+Engineers" Team, Shaanxi Qinchuangyuan/ ; }, abstract = {To explore the effects of different fertilization regimes on physicochemical properties and microbial ecology of greenhouse soil, we set five treatments with original soil (BS) as the control: chemical fertilizer alone (GF), high/low-rate mushroom residue combined with chemical fertilizer (MH, ML), and high/low-rate organic fertilizer combined with chemical fertilizer (OH, OL). Metagenomic sequencing and bioinformatic analyses were adopted to characterize soil nutrients, microbial communities, and C-N-P-S metabolic functions. All treatments increased soil nutrients. MH had the highest organic matter, total nitrogen, nitrate nitrogen, and available phosphorus, while GF contained the most available potassium and ammonium nitrogen. Bacteria dominated the soil microbiota, with Pseudomonadota and Pseudomonas as keystone taxa. Mushroom residue amendments improved microbial richness and diversity. By improving soil physicochemical properties, the combined application of organic fertilizer with chemical fertilizer and mushroom residue with chemical fertilizer both enriched some beneficial microorganisms. Chemical fertilizer alone enhanced anaerobic metabolism, which was reversed by high-rate mushroom residue. Available phosphorus, available potassium, and ammonium nitrogen were key environmental factors driving the differentiation of microbial communities and their functions. Overall, mushroom residue combined with chemical fertilizer is effective for greenhouse soil improvement, with proper dosage and tillage recommended.}, }
@article {pmid42654991, year = {2026}, author = {Kasimanickam, R and Bhowmik, P and Jiang, Z}, title = {Postpartum Uterine Diseases in Dairy Cattle: Integrating Microbiology, Immunology, and Reproductive Physiology.}, journal = {Microorganisms}, volume = {14}, number = {8}, pages = {}, pmid = {42654991}, issn = {2076-2607}, support = {GF002076//Population Theriogenology Development Fund/ ; //Department of Veterinary Clinical Sciences, Washington State University/ ; }, abstract = {Postpartum uterine diseases are among the most prevalent and economically important reproductive disorders affecting dairy cattle worldwide. These conditions, including metritis, clinical and subclinical endometritis, and pyometra, develop during the postpartum transition period when physiological, metabolic, endocrine, and immunological adaptations increase susceptibility to microbial invasion and persistent uterine inflammation. Although bacterial contamination of the postpartum uterus is nearly universal, healthy cows generally restore uterine homeostasis through coordinated immune responses, microbial regulation, and effective uterine involution. Failure of these defense mechanisms results in microbial dysbiosis, impaired endometrial repair, reduced fertility, and substantial economic loss. Major pathogens associated with postpartum uterine disease include Escherichia coli, Trueperella pyogenes, Fusobacterium necrophorum, Prevotella spp., and other anaerobic bacteria that interact synergistically to promote inflammation, tissue damage, and reproductive dysfunction. Advances in next-generation sequencing, metagenomics, and metatranscriptomics have transformed understanding of the postpartum uterine microbiota and host-microbe interactions involved in disease pathogenesis. This review synthesizes current evidence regarding uterine physiology, microbial ecology, immune regulation, virulence mechanisms, dysbiosis, diagnostic approaches, and emerging omics-based technologies relevant to postpartum uterine disease in dairy cattle. Particular emphasis is placed on the ecological and physiological interactions linking microbial succession, endocrine recovery, metabolic stress, and immune competence during the postpartum period. The review further discusses translational opportunities for precision diagnostics, microbiome-informed interventions, antimicrobial stewardship, and integrated herd management strategies to improve reproductive efficiency, animal welfare, and dairy herd sustainability.}, }
@article {pmid42639367, year = {2026}, author = {Mulaw, G and Kidanemariam, G and Bara, M and Tesfay, T}, title = {Probiotics in Human Health: Current Evidence, Mechanism of Action, and Future Perspectives.}, journal = {International journal of microbiology}, volume = {2026}, number = {}, pages = {1721210}, pmid = {42639367}, issn = {1687-918X}, abstract = {Probiotics are widely recognized for their potential to promote human health through diverse mechanisms that influence host physiology and microbial ecology. This review synthesizes current evidence on the biological functions, mechanisms of action, and therapeutic applications of probiotics. A comprehensive narrative literature review was conducted, with 143 records identified, screened, and assessed for eligibility before inclusion in the final analysis. The available evidence indicates that probiotics exert their beneficial effects through modulation of gut microbiota composition, enhancement of intestinal barrier integrity, competitive exclusion of pathogens, production of antimicrobial metabolites, and regulation of innate and adaptive immune responses. Clinical and experimental studies further suggest potential benefits in the prevention or management of antibiotic-associated diarrhea, lactose intolerance, allergic diseases, hypercholesterolemia, colorectal cancer, neurological disorders, and heavy metal toxicity. Despite promising findings, probiotic efficacy remains strain-specific and influenced by host characteristics, dosage, and treatment duration. Challenges related to strain selection, safety assessment, and standardization continue to limit broader clinical application. Overall, this narrative review provides an integrated overview of current knowledge on probiotic functionality, highlights emerging therapeutic opportunities, and identifies key research gaps that should be addressed to support evidence-based probiotic use.}, }
@article {pmid42642057, year = {2026}, author = {Mairet, F}, title = {Mitochondrial ribosome content as a proxy for respiration.}, journal = {Biology letters}, volume = {22}, number = {8}, pages = {}, doi = {10.1098/rsbl.2026.0144}, pmid = {42642057}, issn = {1744-957X}, mesh = {*Saccharomyces cerevisiae/metabolism/growth &amp; development ; *Mitochondrial Ribosomes/metabolism ; *Oxygen Consumption ; *Oxygen/metabolism ; Mitochondria/metabolism ; Cell Respiration ; *Ribosomes/metabolism ; }, abstract = {Quantifying cellular activities remains a major challenge across fields ranging from microbial ecology to biotechnology and biomedical sciences. Building on the well-established linear relationship between growth rate and ribosome content-the so-called microbial growth law-this study proposes using organelle ribosome content to infer metabolic activity. In exponentially growing yeast (Saccharomyces cerevisiae), including under overflow metabolism conditions, a strong linear correlation was observed between mitochondrial ribosome content and oxygen uptake rate, underscoring the potential of this approach. Additionally, under fully respiratory conditions, cytoplasmic and mitochondrial ribosome fractions were linearly correlated, whereas overflow conditions fell below this linear relationship, providing a means to identify such metabolic states. Although these findings require broader validation across additional species, organelle ribosome quantification may provide a promising proxy for deciphering cellular metabolism.}, }
@article {pmid42643400, year = {2026}, author = {Medaglia-Mata, A and Rojas-Rodríguez, P and Bystrý, V and Guillén-Watson, R and Gómez-Espinoza, O and Núñez-Montero, K}, title = {PUDU (pipeline for universal diversity unveiling): an accessible end-to-end workflow for taxonomic profiling and ecological visualization of environmental microbiomes across amplicon, shotgun, and long-read sequencing.}, journal = {Frontiers in bioinformatics}, volume = {6}, number = {}, pages = {1909327}, pmid = {42643400}, issn = {2673-7647}, abstract = {BACKGROUND: Environmental microbiome research has advanced through three complementary sequencing modalities, targeted 16S rRNA amplicon sequencing, whole-genome shotgun (WGS) metagenomics, and long-read full-length 16S rRNA profiling, each supported by distinct toolsets with heterogeneous outputs, variable configurations, and different levels of reproducibility documentation. Existing pipelines are typically modality-specific, require substantial configuration expertise, or produce outputs that need further custom scripting before standard ecological analyses can begin. This analytical fragmentation introduces avoidable technical variability and complicates cross-study reproducibility and comparability. PUDU addresses this by integrating all three modalities into a single reproducible workflow with simplified configuration, harmonized outputs across classifiers, and direct compatibility with downstream ecological analysis frameworks.<br><br>RESULTS: We present PUDU (Pipeline for Universal Diversity Unveiling), a modular Snakemake workflow that supports amplicon (short-read 16S), shotgun metagenomics (WGS), and long-read 16S analyses from raw reads to standardized outputs for downstream microbial ecology. PUDU performs technology-aware preprocessing and centralized quality control, and integrates established taxonomic approaches, including DADA2 for amplicons, Emu for full-length 16S long reads, and Kraken2/Bracken and Centrifuger for WGS. Across methods, PUDU produces harmonized count and relative-abundance tables at user-defined taxonomic ranks, Krona files, and a standardized Phyloseq-compatible R object to streamline diversity analyses and statistical workflows. PUDU also provides an integrated Shiny interface for metadata-aware alpha/beta diversity, ordination, community composition, and shared-taxa exploration with exportable figures and taxa tables. We demonstrate PUDU on two publicly available environmental datasets spanning rhizosphere WGS and long-read marine sediment 16S, yielding broadly consistent community-level patterns across classifiers (Spearman &#x3c1; = 0.936 at phylum level; PERMANOVA R[2] = 0.87-0.95) with peak memory below 45 GB on a standard Linux workstation.<br><br>CONCLUSION: PUDU is an end-to-end, reproducible, and extensible framework that enables standardized taxonomic profiling and ecology-oriented analysis across sequencing modalities. By combining harmonized outputs, Phyloseq interoperability, and an integrated visualization layer, PUDU facilitates reproducible, standardized, and comparable environmental microbiome analysis from raw reads to interpretable ecological insights.}, }
@article {pmid42644562, year = {2026}, author = {Rainey, PB and Timmis, KN and Williams, PA and Karahan, ZC and López-García, P and Chavarria, M and Greening, C and Steward, K and Silva Pereira, C and Giraldo, R and Verstraete, W and Jonjić, S and Ramos, JL and Nunes, O and Ventosa, A and Armstrong, R and Sessitsch, A and Ron, E and Wang, H and Hochberg, ME and Berryhill, B and Levin, BR}, title = {Stop paying predatory publishers of academic journals-A policy proposal to restore scientific integrity and transparency.}, journal = {FEBS letters}, volume = {}, number = {}, pages = {}, doi = {10.1002/1873-3468.70451}, pmid = {42644562}, issn = {1873-3468}, abstract = {Scientific publishing is undergoing a systemic breakdown. Thousands of journals now collect article processing charges (APCs)-increasingly paid from public research funds-while providing minimal editorial oversight. This erodes standards, distorts incentives and threatens public trust in science. APC payments to six major publishers exceeded 8 billion dollars between 2019 and 2023, with almost no transparency over how these fees are set or spent. This cannot continue. We propose that public and institutional funds support journals-whether through APCs, subscriptions or bundled agreements-only where they are accredited against a transparent, enforceable quality standard. Implemented in stages and led by funding bodies and learned societies, such accreditation would narrow the space in which predatory journals operate without resorting to blacklists.}, }
@article {pmid42645451, year = {2026}, author = {Lee, YC and Cheng, YC and Kung, CM and Huang, CJ}, title = {Modulating Oral Microbiota to Prevent Dental Caries: A Microbial Ecology Approach.}, journal = {Dentistry journal}, volume = {14}, number = {8}, pages = {}, pmid = {42645451}, issn = {2304-6767}, abstract = {Background: Dental caries is a highly prevalent, biofilm-mediated disease characterized by microbial dysbiosis, excessive acid production, and progressive enamel demineralization. Although traditionally managed through restorative treatment, increasing attention has shifted toward preventive strategies focused on modulation of the oral microbiota and maintenance of ecological balance within the oral cavity. Methods: This narrative review summarizes current evidence regarding the ecological and mechanistic basis of dental caries and microbiota-centered prevention strategies. Literature published between January 2000 and March 2026 was retrieved from PubMed/MEDLINE, Scopus, Web of Science, and Google Scholar using keywords related to dental caries, oral microbiota, cariogenic bacteria, biofilms, probiotics, prebiotics, salivary diagnostics, metabolomics, quorum sensing, and artificial intelligence. Results: Current evidence demonstrates that dental caries is driven by ecological shifts favoring acidogenic and aciduric microorganisms within cariogenic biofilms. Emerging preventive approaches include dietary modification, oral hygiene optimization, probiotics, prebiotics, synbiotics, and functional dietary agents aimed at restoring microbial homeostasis and inhibiting cariogenic biofilm maturation. In addition, advances in salivary microbiome profiling, metabolomics, artificial intelligence-assisted predictive modeling, and smart responsive materials have shown promising potential for improving early diagnosis, risk assessment, and personalized prevention strategies. Conclusions: Microbiota-based approaches represent a promising paradigm shift in dental caries prevention by emphasizing ecological modulation rather than pathogen eradication alone. Continued interdisciplinary research integrating microbial ecology, diagnostics, biomaterials, and digital technologies may facilitate the development of personalized and preventive oral healthcare strategies.}, }
@article {pmid42645525, year = {2026}, author = {Larsen, J and Efthymiou, A and Nicolaisen, MH and Jensen, B and Nybroe, O and Gómez-Muñoz, B}, title = {Penicillium aculeatum pre-activated with cellulose and different phosphorus sources promotes maize growth, nutrition and mycorrhiza formation, and decreases Microdochium bolleyi root infection.}, journal = {Current microbiology}, volume = {83}, number = {10}, pages = {}, pmid = {42645525}, issn = {1432-0991}, mesh = {*Zea mays/microbiology/growth &amp; development ; *Cellulose/metabolism ; *Mycorrhizae/growth &amp; development/physiology ; *Plant Roots/microbiology/growth &amp; development ; *Penicillium/metabolism/physiology ; *Phosphorus/metabolism ; Soil Microbiology ; Soil/chemistry ; *Glomeromycota/growth &amp; development/physiology ; }, abstract = {Microbial plant growth promoters often perform inconsistently under natural soil conditions most likely due to their poor establishment after inoculation. Here, we conducted a growth chamber pot experiment with maize using pre-activated inoculum of the P-solubilizing fungus Penicillium aculeatum to facilitate its establishment in a natural non-sterile agricultural soil. Hence, P. aculeatum was preincubated for one week in soil amended with cellulose as a C source and with different P sources, i.e. sewage sludge ash, Ca3(PO4)2, and no P fertilization as control. Control treatments of C and P sources without P. aculeatum were also included. The pre-activated inocula were mixed into natural agricultural soil (1:40 w/w), maize seeds were sown, and plants were grown for 42 days. Measured variables included shoot and root dry weight, nutrient content, and root colonization by arbuscular mycorrhizal fungi (AMF) and root infection with Microdochium bolleyi. Overall, P. aculeatum inoculation enhanced maize growth, nutrient content and AMF root colonization, while reduced root infection with M. bolleyi, independent of P source used. Both P sources increased maize growth and nutrient content, though sewage sludge ash showed stronger effect than Ca3(PO4)2. None of the P sources affected AMF root colonization, but sewage sludge ash decreased M. bolleyi root infection and increased the population density of P. aculeatum. In conclusion, inoculation with pre-activated P. aculeatum (with cellulose and P sources) enhances maize growth and nutrient uptake, and is associated with increased AMF root colonization and reduced root infection by M. bolleyi.}, }
@article {pmid42646070, year = {2026}, author = {Li, H and Jiao, X and Wang, Y and Sun, N}, title = {Co-Application of Organic and Ca, Mg, Zn Fertilizers Reshapes Depth-Stratified Arbuscular Mycorrhizal Fungal Communities in Orchard Soil.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {12}, number = {8}, pages = {}, pmid = {42646070}, issn = {2309-608X}, support = {KJCX20250926//Beijing Academy of Agricultural and Forestry Sciences/ ; Z191100004019001//Beijing Municipal Science and Technology Commission/ ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) are crucial symbiotic microorganisms in terrestrial ecosystems, playing a vital role in maintaining orchard soil health and productivity. However, how organic-and Ca, Mg, Zn fertilizers co-application affect vertical stratification and ecological functions of arbuscular mycorrhizal fungi (AMF) in perennial fruit orchards remains unclear. Based on a five-year in situ peach trial, we established three fertilization regimes: low- (LWF), medium- (MWF), and high-input (HWF) regimes. We systematically analyzed the AMF community structure, diversity, and their correlations with soil physicochemical properties, as well as peach tree physiology, fruit yield, and quality across two soil depths: 0-20 cm (topsoil) and 20-40 cm (subsoil). HWF significantly inhibited AMF root colonization rates and spore density (p < 0.05), while reducing community α-diversity AMF α-diversity (p < 0.05), characterized by the enrichment of genera such as Glomus and a decrease in the relative abundance of Rhizoglomus. Redundancy analysis (RDA) identified available Zn (AZn) and Mg (WMg) as key drivers of this restructuring. Integrating RDA results into depth-specific partial least squares structural equation models (PLS-SEM), we found that subsoil AZn/WMg indirectly boosted yield by reshaping AMF composition (β = 0.34, p = 0.006), mediated via improved canopy status (NDVI, PRI). Total effect analysis confirmed the dominant role of subsoil pathways. These findings challenge the prevailing topsoil-centric view of soil microbial ecology and underscore the importance of considering the full soil profile when evaluating the impacts of agricultural practices on beneficial symbionts. We conclude that sustainable management strategies should account for depth-dependent AMF responses to maintain both productivity and belowground biodiversity across the entire rooting zone.}, }
@article {pmid42646830, year = {2026}, author = {Liu, J and He, Y and Qiu, K and Zhao, S and Qiu, Z and Gao, S and Nagel, G and Zhu, M}, title = {TrcrtB regulates carotenoid biosynthesis, stress tolerance, conidiation and pathogenicity in the postharvest pink rot fungus, Trichothecium roseum.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-03-26-0608-RE}, pmid = {42646830}, issn = {0191-2917}, abstract = {Trichothecium roseum is a highly destructive postharvest pathogenic fungus that causes pink mold rot in various fruit and leads to significant agricultural and economic losses. Phytoene is crucial for phytopathogens, but the molecular mechanism by which the phytoene synthase gene crtB regulates fungal pathogenicity remains largely unclear. In this study, we evaluated the functions of TrcrtB a phytoene synthase, in T. roseum via in vivo and in vitro assays. Our results showed that knock-out of TrcrtB showed inhibition of production of phytoene and its relevant downstream metabolites, such as lycopene, carotenes and carotenal, resulting in colorless colony and branching at the mycelial edges in the knockout mutant ΔTrcrtB. Compared with the wild type (WT) strain, the colony expansion was significantly reduced 35% at 5 days post-inoculation (dpi), and conidiation was notably decreased to 45%, 36%, and 70% at 3, 5, and 7 dpi in ΔTrcrtB in vitro. Scanning electron microscope observation revealed similar results. Moreover, the ΔTrcrtB showed higher sensitivity to abiotic stresses than WT, as evidenced by inhibition rates of ΔTrcrtB colony expansion up to 71.76% (menadione), 47.73% (Congo red), 23.01% (SDS), and 17.13% (KCl). The pathogenicity of ΔTrcrtB was dramatically impaired by decreasing the rotten area up to 85.26% on apple fruit and 70.30% on pears fruit. These results suggest that TrcrtB and phytoene are critical for development, stress tolerance and pathogenicity of T. roseum. Collectively, our study highlights the roles of TrcrtB and phytoene in the pathogenic fungus T. roseum, providing new insights into the molecular mechanisms of pink rot pathogenesis.}, }
@article {pmid42647083, year = {2026}, author = {Lv, R and Jiang, Z and Zhong, Y}, title = {The role of gut-lung axis-targeted nursing strategies in immune regulation of COPD.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {}, number = {}, pages = {}, doi = {10.1556/030.2026.02947}, pmid = {42647083}, issn = {1588-2640}, abstract = {Chronic obstructive pulmonary disease (COPD) is featured by persistent airflow limitation and chronic inflammation. Considerable evidence highlights the role of the gut-lung axis, suggesting that disruption of gut microbial balance may contribute to aggravated systemic and pulmonary inflammation. This research intended to assess the impacts of a structured gut-lung axis-targeted nursing intervention on immune-inflammatory parameters, gut microbiota, and clinical outcomes in patients with stable COPD. The study involved the randomization of 115 patients to either the intervention or control group in a 1:1 ratio. The intervention group received a 12-week multimodal program, which included personalized high-fiber/probiotic nutrition, customized exercise plans, and stress management techniques. Patients in the control group did not receive the multimodal program and instead received routine care. The findings indicated that the intervention notably lowered serum IL-6, TNF-α, and CRP. Microbiome analysis further revealed that the intervention significantly enhanced α-diversity (Shannon and Chao1), enriched beneficial butyrate-producing genera (Faecalibacterium, Roseburia, and Bifidobacterium), and reduced the relative abundance of potential pathogens (Enterobacteriaceae), indicating a favorable shift in gut microbial ecology. Compared with the control group, the intervention group also experienced fewer moderate-to-severe exacerbations and showed greater sustained improvement in quality of life (SGRQ and CAT scores). In summary, a comprehensive nursing strategy centered on the gut-lung axis can regulate gut microbiota, alleviate systemic inflammation, lead to a reduction in exacerbation frequency and an improvement in the quality of life among patients with stable COPD, thus presenting a promising supplementary strategy to conventional care.}, }
@article {pmid42647465, year = {2026}, author = {Ali, S and Baig, A and Nagassar, RP and Burke, LP and Fitzpatrick, F and Fitzgerald-Hughes, D}, title = {The Caribbean under the radar? A scoping review of carbapenemase-producing Enterobacterales across the region.}, journal = {PLOS global public health}, volume = {6}, number = {8}, pages = {e0007176}, pmid = {42647465}, issn = {2767-3375}, abstract = {Carbapenemase-producing Enterobacterales (CPE) are a critical antimicrobial resistance (AMR) threat globally. The Caribbean region, despite its high global connectivity, varied healthcare infrastructure and rising antimicrobial use, remains underrepresented in CPE surveillance data. Our study aims to map and characterise the existing literature on CPE in the Caribbean, including bacterial species, carbapenemase types, detection methods, and epidemiological trends. A scoping review was conducted in accordance with PRISMA-ScR guidelines. MEDLINE, EMBASE, Cochrane CENTRAL and Web of Science were searched to 1st July 2025 in addition to grey literature (policy documents, guidelines, websites). Studies were included if they reported carbapenemase production among Enterobacterales from human, animal, or environmental sources in Caribbean nations (defined geophysically). Non-Caribbean studies and non-Enterobacterales organisms were excluded. Fourteen studies published between 2008 and 2024 met inclusion criteria. Reports originated from six countries: Cuba, Puerto Rico, Jamaica, Guadeloupe, the Dominican Republic, and Curaçao. Klebsiella pneumoniae was the most frequently reported species. The most common carbapenemase enzymes were KPC (including KPC-2 and KPC-8), NDM-1, NDM-5 and OXA-48. Co-production of NDM and KPC was documented. Detection was largely hospital-based, though community and environmental isolates were also identified. High levels of AMR were observed, with colistin often the only active agent. Surveillance gaps are evident across many populous Caribbean nations. CPE are established in multiple Caribbean countries, but surveillance remains irregular and limited. Addressing critical gaps in diagnostic capacity, reporting and molecular surveillance is essential to ensure the region's inclusion in the global AMR response.}, }
@article {pmid42649294, year = {2026}, author = {Sichert, A and Pollak, S and Priest, T and Goyal, A and Miravet-Verde, S and Sunagawa, S and Cordero, OX and Sauer, U}, title = {Synergistic degradation of fucoidans in the ocean.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {42649294}, issn = {1476-4687}, abstract = {Fucoidans, a class of complex polysaccharides produced by brown algae and diatoms, contribute to long-term carbon sequestration owing to their resistance to microbial degradation[1,2]. Although individual microorganisms can break down portions of these polysaccharides[3-5], it remains unclear whether complete breakdown is possible in nature and, if so, by what mechanisms. Here we show that fucoidans are degraded through synergistic interactions between specialized bacteria with complementary metabolic functions. Using metabolomic analysis of a reconstructed marine consortium, we uncovered metabolic guilds of bacteria that preferentially degrade either the sulfated fucose backbone or the side branches of rare monomers. This functional division of labour leads to an unexpectedly high number of synergistic interactions between different degraders that enhanced degradation efficiency up to 97.1%. Despite varying fucoidan structures across different types of algae[6], the metabolic functions of degraders remained conserved, enabling quantitative prediction of degradation outcomes based on community and substrate composition. The frequent co-occurrence of functionally complementary fucoidan degraders in ocean metagenomes suggests that synergistic degradation is a globally relevant strategy. Our findings suggest that the environmental turnover of complex biopolymers depends not only on individual metabolic capabilities of degraders but also on ecological interactions shaped by substrate architecture. This work provides a mechanistic framework for understanding carbon cycling in the ocean and for engineering synthetic microbial consortia to degrade recalcitrant polysaccharides.}, }
@article {pmid42650190, year = {2026}, author = {Godos, J and Caruso, G and Mainas, G and Micek, A and Di Mauro, A and Buccarello, L and Martínez López, NM and Frias-Toral, E and Giampieri, F and Lehoczki, A and Isola, G and Galvano, F and Ungvari, Z and Quiles, JL and Battino, M and Grosso, G}, title = {Oral Microbiota, the Oral-Brain Axis, and Neurodegeneration: Mechanisms and Dietary Modulation.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {15}, number = {8}, pages = {}, doi = {10.3390/antiox15080925}, pmid = {42650190}, issn = {2076-3921}, support = {NA//Italian Ministry of Health/ ; }, abstract = {The oral microbiota represents a complex and dynamic microbial ecosystem that plays a critical role in preserving both oral and systemic homeostasis. Emerging evidence suggests that alterations in oral microbial milieu (dysbiosis) may contribute to the pathogenesis of neurodegenerative disorders, especially Alzheimer's disease (AD), through the oral-brain axis. This review synthesizes current evidence on the pathways linking oral microbiota to cognitive decline, integrating microbial, immunological, and vascular perspectives. Oral pathogens may access the central nervous system via hematogenous dissemination or neural routes, including the trigeminal nerve, while simultaneously promoting systemic inflammation, immune activation, and blood-brain barrier disruption. These processes converge on key neurodegenerative mechanisms, including chronic neuroinflammation, amyloid-β accumulation, and tau pathology. In parallel, alterations in oral microbial composition have been linked to disease severity, supporting a potential role of dysbiosis in both initiation and progression of cognitive impairment. Diet emerges as a critical modifiable determinant of oral microbial ecology. Diets rich in refined sugars may promote dysbiosis and inflammatory signaling, whereas (poly)phenols, probiotics, and prebiotics may support microbial eubiosis and exert neuroprotective effects through modulation of host-microbe interactions. Although current evidence remains largely observational and mechanistic, the diet-oral microbiota-brain axis represents a promising target for preventive and therapeutic strategies aimed at mitigating cognitive decline and promoting healthy aging. Future longitudinal and interventional studies are required to establish causality and translate these insights into clinical practice.}, }
@article {pmid42650527, year = {2026}, author = {Li, S and Yu, X and Huang, H and Wang, C and Yi, C and Zhang, X and Wen, Y and Xiong, B and Jiang, Q and Yu, K and Ma, Y}, title = {Regulatory Effects of Tannin Supplementation on Microbial Succession and Flavor Formation During Xiaoqu Light-Flavor Baijiu Fermentation.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {16}, pages = {}, doi = {10.3390/foods15162833}, pmid = {42650527}, issn = {2304-8158}, support = {Y2025067//Sichuan University of Science and Engineering/ ; H72313005//Yibin Agricultural Science and Technology Innovation Project/ ; 2022ZDZX0016//Sichuan Province Major Science and Technology Special Project/ ; }, abstract = {Sorghum tannins have been suggested to influence microbial ecology and flavor formation in Xiaoqu light-flavor Baijiu (XLB), but their specific contribution is difficult to distinguish from confounding, cultivar-dependent variations in macromolecular components. To address this limitation, a controlled fermentation system was established using a uniform, low-tannin substrate. Based on preliminary gradient trials, a 1.0% tannin supplementation level was selected, and high-throughput sequencing combined with HS-SPME-GC-MS was employed to investigate tannin-related microbial and volatile changes. Compared with the group without tannin supplementation, 1.0% tannin supplementation altered bacterial and fungal community succession during the fermentation, reducing the relative abundances of Saccharomyces and Weissella, and enriching taxa including Cyberlindnera and Pantoea. The tannin-supplemented group exhibited a more complex and stable microbial co-occurrence network. Furthermore, PICRUSt2 predictions suggested enhanced metabolic potentials primarily related to carbohydrate and amino acid pathways. FUNGuild analysis further suggested that tannin supplementation shifted fungal trophic-mode composition, particularly saprotrophic and saprotroph-containing groups. At the end of fermentation, total volatile compounds increased from 4.208 μg/g to 4.983 μg/g, total esters and acids increased by 27.0% and 112.3%, respectively, whereas total alcohols decreased by 13.3%. Spearman correlation analysis revealed that the enriched non-Saccharomyces fungi and acid-producing bacteria in the tannin-supplemented group were positively associated with the accumulation of acids and esters, whereas the control microbiota was mainly linked to an alcohol-oriented profile. These findings may provide process-level evidence for tannin-related microbial and volatile changes during XLB fermentation.}, }
@article {pmid42650569, year = {2026}, author = {Hao, M and Liu, J and Kan, C and Zheng, X and Liu, C and Zhang, Y and Shen, L}, title = {Research Progress, Challenges, and Future Trends of Modified Atmosphere Packaging (MAP) Technology for Food and Agricultural Products: A Bibliometric Analysis (2016-2025).}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {16}, pages = {}, doi = {10.3390/foods15162875}, pmid = {42650569}, issn = {2304-8158}, abstract = {Modified atmosphere packaging (MAP) is a preservation and packaging technology used to extend the shelf life of foods and agricultural products, maintain quality stability, and ensure food safety. To systematically review and summarize the current research landscape, technical challenges, and development trends in the MAP field, this study selected 1568 publications related to MAP from the Web of Science Core Collection (WOSCC) database during 2016-2025 and conducted bibliometric and visualization analysis. The results indicate that research activity in the MAP field has remained robust over the past decade, mainly focusing on four research areas: atmosphere regulation and packaging system design; microbial ecology, safety, and spoilage control; physicochemical deterioration and quality regulation; functional packaging materials and integrated preservation technologies. Countries such as China, Italy, and Spain have demonstrated outstanding performance in terms of publication output and academic influence in the MAP field, forming a solid research foundation in the MAP of perishable foods such as fruit and vegetables, meat products, and aquatic products. Research in the MAP field has gradually shifted from the verification of application effects toward system design and mechanistic analysis. Active packaging, intelligent packaging, bio-based materials, natural functional ingredients, volatile organic compounds, microbial community succession, and quality deterioration mechanisms have gradually become research hotspots, indicating a trend toward precision, sustainability, and functionality. These findings may provide references for future research topic selection, innovative packaging system design, and the development of novel food preservation technologies in the MAP field for foods and agricultural products.}, }
@article {pmid42651919, year = {2026}, author = {Kahraman, O and Wilk, M and Bochynek, M and Bojanowski, K and Quijas, G and Inanc, ZS and Inal, F and Ahmed, I and Lewińska, A and Yilmaz, B}, title = {Effects of Complementary Feed with Postbiotics Derived from Bacillus subtilis on Nutrient Digestibility, Faecal Characteristics, Gut Microbiota, Metabolic and Immune Responses, and Coat Quality in Healthy Senior Dogs.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {16}, pages = {}, doi = {10.3390/ani16162515}, pmid = {42651919}, issn = {2076-2615}, abstract = {The aim of this study was to evaluate the effects of a Bacillus subtilis-derived postbiotic on apparent total tract nutrient digestibility, faecal fermentation characteristics, gut microbiota, immune response, blood biochemistry, hematological parameters, serum trace minerals, and coat quality in healthy senior dogs. Twenty-one healthy senior Golden Retriever dogs (9 ± 1.0 years old) were randomly allocated to three dietary treatments for 28 days: a control diet (CON) or the same diet supplemented with 0.3 (POS1) or 0.6 mL/day (POS2) of a Bacillus subtilis-derived postbiotic. Apparent nutrient digestibility, faecal characteristics, blood variables, and coat quality were evaluated, whereas faecal bacterial communities were characterized by 16S rRNA gene amplicon sequencing, followed by taxonomic classification and alpha- and beta-diversity analyses. Postbiotic supplementation significantly improved crude protein and crude fiber digestibility while reducing faecal pH and ammonia concentrations and increasing acetate, propionate, and total short-chain fatty acid concentrations (p < 0.05). Alpha diversity was minimally affected, with a significant difference observed only for amplicon sequence variant (ASV) richness, whereas beta diversity analyses demonstrated significant alterations in overall microbial community composition. Postbiotic supplementation increased the relative abundance of Faecalibacterium, Ligilactobacillus, Bifidobacterium, Prevotella, Turicibacter, and Fusobacterium, while reducing Bacteroides and Achromobacter. Serum IgG concentrations increased, whereas cholesterol and triglyceride concentrations decreased in supplemented dogs (p < 0.05). Coat morphology and gloss also improved, without adverse effects on hematological, biochemical, or serum trace mineral parameters. In conclusion, Bacillus subtilis-derived postbiotic supplementation improved nutrient utilization, beneficially modulated faecal microbial ecology and fermentation, enhanced selected metabolic and immune responses, and improved coat quality, supporting its potential as a functional dietary strategy for promoting gastrointestinal and systemic health in healthy senior dogs.}, }
@article {pmid42652455, year = {2026}, author = {Antonuccio, GI and López, PJ and Berretta, MF and Sauka, DH}, title = {Genomic Characterization of Aerobically Culturable Gut-Associated Bacteria and Yeasts Isolated from Pooled Larval Midguts of the Lesser Mealworm Alphitobius diaperinus (Coleoptera: Tenebrionidae).}, journal = {Insects}, volume = {17}, number = {8}, pages = {}, doi = {10.3390/insects17080800}, pmid = {42652455}, issn = {2075-4450}, support = {INTA 2023-PD-L06-I116//National Agricultural Technology Institute/ ; }, abstract = {Microbial communities associated with insect larvae play key roles in host nutrition, protection against pathogens, immune modulation, and represent a source of biotechnologically relevant traits. In Alphitobius diaperinus, a major poultry pest, the gut microbiota has been mainly studied at the community level, providing limited insight into the potential roles of individual microorganisms. Here, we characterized the aerobically culturable fraction of the larval gut microbiota derived from a single pooled homogenate of fifteen larvae under stable laboratory rearing conditions-an approach that uniquely enables strain-level genomic resolution, functional experimentation, and biotechnological exploitation. Ten bacterial strains and two yeasts were initially isolated; eight bacterial isolates were identical, revealing the most frequently recovered cultivable bacterial morphotype. We provide high-quality draft genomes for five members of the A. diaperinus cultivable gut microbiota-Enterobacter hormaechei subsp. xiangfangensis strain INTA AN1-1, Staphylococcus hominis subsp. novobiosepticus strain INTA AC1-4, Staphylococcus succinus subsp. succinus strain INTA AC1-8, Hyphopichia burtonii strain INTA AB1-1, and Debaryomyces fabryi strain INTA AB1-4-establishing a genome-resolved reference framework validated through a polyphasic approach. Genome-scale annotation enabled us to predict the metabolic potential and hypothesize the functional capabilities among cultivable members, providing a foundation for future studies on this economically relevant pest.}, }
@article {pmid42652525, year = {2026}, author = {Wu, PR and Shelomi, M}, title = {Effect of Protein Supplementation on the Gut Microbiome of Omnivorous and Herbivorous Goliath Beetles.}, journal = {Insects}, volume = {17}, number = {8}, pages = {}, doi = {10.3390/insects17080871}, pmid = {42652525}, issn = {2075-4450}, support = {NSTC-114-2311-B-002-017//National Science and Technology Council/ ; 113L7801//Ministry of Education/ ; }, abstract = {Scarab beetles depend on gut microbes for digestive enzymes. Some species' microbiomes show taxonomic conservation regardless of diet, while others have conserved functional profiles. We compared the hindgut microbiomes of two Cetoniinae beetle larvae: the obligately saproxylophagous Mecynorrhinella poggei and the omnivorous/predatory Goliathus goliatus, which requires protein supplementation when reared artificially. Two diets with and without supplementation were used. If diet drives the microbiome, then gut microbes in protein-supplemented hosts should produce fewer lignocellulolytic enzymes and more proteinases regardless of species. If microbiome composition is conserved within a species, then Mecynorrhinella is expected to have more lignocellulolytic microbes while Goliathus should have more proteinolytic microbes regardless of diet. In this study, low-protein diets reduced G. goliatus growth, but gut microbiome composition and predicted function remained largely stable, dominated by Bacteroidales including Dysgonomonas, Proteiniphilum, and Alistipes. Mecynorrhinella's gut microbiome showed some reduced Proteiniphilum and increased Dysgonomonas relative abundance, but otherwise the microbiome composition was statistically stable with no effect of diet on growth or predicted microbiome function. These results highlight that microbiomes of closely related insects can markedly differ even if diet does not and that microbiome functional conservation tied to host physiology may occur even if greater plasticity could theoretically reduce malnutrition.}, }
@article {pmid42652532, year = {2026}, author = {Gao, X and Li, Q and Yan, F and Su, C and Wang, X and Xu, P and Ren, G and Mao, M}, title = {Parental Broflanilide Exposure Impairs Offspring Fitness and Alters Detoxification Enzymes and Gut Microbiota in Helicoverpa armigera.}, journal = {Insects}, volume = {17}, number = {8}, pages = {}, doi = {10.3390/insects17080878}, pmid = {42652532}, issn = {2075-4450}, support = {110202401012(LS-02) and 110202401017(LS-07)//Major Special Projects for Green Pest Control/ ; Grant No. ASTIP-TRIC04//Agricultural Science and Technology Innovation Program/ ; }, abstract = {The cotton bollworm Helicoverpa armigera (Hübner, 1808) (Lepidoptera: Noctuidae) is a globally distributed polyphagous pest that damages various crops. Pesticides remain a primary and effective strategy for controlling cotton bollworm populations. This study evaluated the effects of broflanilide on H. armigera by integrating life-table analysis, detoxification enzyme activity assays, and gut microbiome characterization. Broflanilide showed high toxicity against third-instar larvae. Parental LC50 exposure prolonged larval development and reduced larval survival in the F1 generation. In addition, parental exposure to both LC30 and LC50 reduced adult emergence, fecundity and major population growth parameters, especially the intrinsic rate of increase (r) and net reproductive rate (R0), demonstrating a significant transgenerational inhibitory effect. Enzyme assays showed that carboxylesterase (CarE) activity was induced after broflanilide exposure, glutathione S-transferase (GST) activity showed a time-dependent response with the strongest induction generally observed under LC10 treatment, whereas cytochrome P450 monooxygenase (P450) activity was generally inhibited. Gut microbiota analysis showed that LC50 exposure significantly reduced the relative abundance of Enterococcus. Functional prediction further indicated enrichment trends in pathways related to xenobiotic degradation and metabolism. Overall, broflanilide not only exhibited strong lethal activity against H. armigera, but also produced sustained effects on population fitness, detoxification metabolism and gut microbial ecology. These findings provide a theoretical basis for the rational use of broflanilide and improve our understanding of its sublethal physiological and microbial effects on H. armigera.}, }
@article {pmid42652966, year = {2026}, author = {Martens, A and Schauer, M and Mair, S and Motevalli, M and König, B}, title = {Multidimensional Profiles of Microbial Contamination and Hygiene Risk Across Functional Areas in Family Hotels.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {8}, pages = {}, doi = {10.3390/life16081278}, pmid = {42652966}, issn = {2075-1729}, abstract = {Microbial contamination in hospitality settings remains understudied despite the high density of human contact and diverse operational activities that characterize hotel environments. This study aimed to characterize microbial contamination patterns and environmental hygiene risks across multiple functional areas of family-oriented hotels. A cross-sectional environmental microbiological investigation was conducted in family hotels in Bavaria, Germany. A total of 225 environmental surface samples were collected from guest rooms, child areas, food-related areas, service environments, and water-exposed locations. Bacterial isolates were identified using culture-based microbiology and MALDI-TOF mass spectrometry. Microbial prevalence, contamination severity, microbial richness, and pathogen prevalence were assessed using mixed-effects ordinal logistic regression, generalized additive model (GAM), and integrated hygiene profile, all performed in R (version 4.5.1). Microbial occurrence patterns differed markedly across functional areas. Contamination category distributions differed significantly among areas, with food-related environments showing the strongest enrichment in the highest contamination category (72.7%). Food-related areas showed significantly greater odds of severe contamination than guest rooms (OR = 8.37, 95% CI: 1.89-37.00), child areas (OR = 6.16, 95% CI: 1.20-31.46), and water-exposed environments (OR = 12.34, 95% CI: 2.45-62.10). Microbial richness differed across operational zones (p = 0.048) and was positively associated with contamination severity (β = 0.141, p < 0.001). GAM revealed a significant non-linear richness-contamination relationship (p < 0.001). Integrated hygiene profile consistently identified food-related and service areas as the highest risk environments. Environmental hygiene risks in hospitality settings display functional-area heterogeneity, highlighting the need for targeted, area-specific hygiene management strategies.}, }
@article {pmid42653681, year = {2026}, author = {Abbas, A and Weiskirchen, R and Bilal, M and Afzal, MK and Malik, A and Akhtar, S and Khan, M and Rashid, I and Khalid, F and Akram, S and Saleem, A and Okoduwa, SIR}, title = {Postbiotics as Next Generation Biotherapeutics Targeting the Gut-Immune-Metabolic Axis: An Integrative Review.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {19}, number = {8}, pages = {}, doi = {10.3390/ph19081184}, pmid = {42653681}, issn = {1424-8247}, abstract = {The gut-immune-metabolic axis has emerged as a central regulator of human health, with growing evidence indicating that microbiota-derived metabolites improve gut microbial ecology, enhance intestinal barrier integrity, reduce systemic inflammation, and maintain metabolic homeostasis. This review synthesizes current mechanistic and clinical evidence on the role of postbiotics in regulating intestinal barrier integrity, immune responses, oxidative stress, and metabolic-endocrine homeostasis. The literature was identified through the PubMed/MEDLINE, Scopus, and Web of Science, integrating evidence from experimental, mechanistic, animal and clinical studies on the therapeutic potential of postbiotics to modulate the gut-immune-metabolic axis. Preclinical studies suggest that postbiotics may enhance epithelial barrier function by improving tight junction integrity through multiple pathways such as PI3K/Akt signaling, stimulating mucin-2 (MUC2) production, and reducing intestinal permeability. They modulate immune responses through interactions with Toll-like receptors, nucleotide-binding oligomerization domain receptors, and G-protein-coupled receptors (GPR41/43), influencing key signaling pathways, including NF-κB and Nrf2, and altering cytokine profiles, such as IL-10, TNF-α, and IFN-γ. Similarly, preclinical investigations have demonstrated that short-chain fatty acids (SCFAs) and other microbial metabolites may improve insulin sensitivity, regulate hepatic gluconeogenesis, stimulate glucagon-like peptide 1 (GLP-1) secretion, and modulate lipid metabolism through the FXR and TGR5 signaling pathways. Emerging human studies suggest potential benefits of postbiotics in regulating gut, immune, and metabolic health; nevertheless, clinical evidence remains limited and is influenced by variability in postbiotic composition, dosage, formulation, and metabolite profiles. Therefore, standardized production approaches and well-designed large-scale randomized clinical trials are required to confirm therapeutic efficacy and establish evidence-based applications of postbiotics.}, }
@article {pmid42654201, year = {2026}, author = {Yin, J and Wang, Z and Ding, Y}, title = {Dynamic Succession of the Early-Life Gut Microbiota and the Regulatory Role of Human Milk Oligosaccharides.}, journal = {Nutrients}, volume = {18}, number = {16}, pages = {}, doi = {10.3390/nu18162621}, pmid = {42654201}, issn = {2072-6643}, support = {No. 82173503//National Natural Science Foundation of China/ ; No. 2024YFC2707606//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Oligosaccharides/metabolism ; *Milk, Human/chemistry ; *Gastrointestinal Microbiome/physiology ; Infant ; Infant, Newborn ; *Infant Nutritional Physiological Phenomena ; Intestinal Barrier Function ; }, abstract = {Early-life nutrition and the gut microbiota interact to shape host health programming. During early-life development, spanning the neonatal period of initial gut colonization through infancy to toddlerhood, the gut microbiota undergoes dynamic succession driven by feeding patterns, host genetic background, environmental exposures, and other intrinsic and extrinsic factors, among which early feeding practices play a particularly prominent role. Among these factors, human milk oligosaccharides (HMOs), key bioactive components of human milk, contribute to the shaping of infant gut microbial ecology by selectively supporting HMO-utilizing bacteria, influencing microbial metabolism and cross-feeding, and exhibiting structure- and context-dependent effects on pathogen-host interactions, intestinal barrier function, and immune responses. This narrative review summarizes the succession patterns of the gut microbiota in early life and the core regulatory mechanisms by which HMOs shape infant gut microbial ecology, aiming to provide a conceptual basis for understanding the potential long-term health implications of early nutritional interventions.}, }
@article {pmid42654221, year = {2026}, author = {Mu, K and He, M and Liao, R and Shao, C and Xie, P and Xie, J and Liu, Y and Ju, Z and Zhong, K and Yuan, Y and Pang, Y}, title = {Medicinal Plant Polysaccharides as Microbiota-Directed Modulators of Immunosenescence: Structural Determinants, Metabolite Reprogramming, and Host Immune Regulation.}, journal = {Nutrients}, volume = {18}, number = {16}, pages = {}, doi = {10.3390/nu18162641}, pmid = {42654221}, issn = {2072-6643}, support = {zyyzdxk-2023186//State Administration of Traditional Chinese Medicine of the People's Republic of China/ ; Qian Ke He Ji Chu ZD [2026] 141//Guizhou Provincial Science and Technology Department/ ; 2025YJSKYJJ296//Guizhou Provincial Education Department/ ; Guizhongyi TD He Zi [2022]001//Guiyang College of Traditional Chinese Medicine/ ; YCXKYB2025030//Guiyang College of Traditional Chinese Medicine/ ; Qian Ke Xie KJLYRC-2026[041]//Guizhou Provincial Science and Technology Department/ ; //Guizhou "Qian Liu Wei" Daodi Medicinal Materials Advantageous and Characteristic Industrial Cluster Construction Project/ ; }, mesh = {Humans ; *Polysaccharides/pharmacology/chemistry ; *Immunosenescence/drug effects ; *Plants, Medicinal/chemistry ; Animals ; *Gastrointestinal Microbiome/drug effects/immunology ; *Microbiota ; Aging/immunology ; }, abstract = {Immunosenescence is a major contributor to age-associated morbidity, yet microbiota-directed strategies capable of restoring immune homeostasis remain insufficiently validated. Medicinal plant polysaccharides (MPPs) are structurally diverse macromolecules that often resist host digestion and undergo microbial transformation in the colon, but their effects cannot be interpreted as those of a homogeneous intervention class. In this structured narrative review, we critically synthesize evidence across structural carbohydrate biology, microbial ecology, metabolite signaling, and immune aging and propose a structure-microbiota-metabolite-immunity framework for evaluating how MPPs may influence immunosenescence. Monosaccharide composition, glycosidic linkages, molecular-weight distribution, branching, uronic acid content, chemical substitutions, and higher-order conformation can shape microbial carbohydrate-active enzyme activity, polysaccharide utilization, and ecological cross-feeding. The resulting changes in short-chain fatty acids, secondary bile acids, tryptophan-derived indoles, and other metabolites may affect epithelial barrier integrity, regulatory T-cell/T helper 17-cell (Treg/Th17) balance, macrophage polarization, nuclear factor-κB (NF-κB) signaling, NLR family pyrin domain-containing 3 (NLRP3) inflammasome activation, and systemic inflammatory tone. However, evidence from in vitro systems and young disease models primarily supports mechanistic plausibility and should not be treated as direct evidence of immunosenescence modification. Translation will require structurally defined preparations, causal validation in aging-relevant models, comparison with established fermentable fibers, identification of responder phenotypes, and adequately powered trials in older adults.}, }
@article {pmid42631058, year = {2026}, author = {Medrano, M and Pacheco-Herrero, M and Borges, Z and Laureano, JR and Dominguez-Garcia, J and Gil-Ventura, R and Castro-Tejada, G}, title = {Characterization of the intestinal microbial profile in mild cognitive impairment and Alzheimer's disease.}, journal = {Dementia &amp; neuropsychologia}, volume = {20}, number = {}, pages = {e20250440}, pmid = {42631058}, issn = {1980-5764}, abstract = {UNLABELLED: Alzheimer's disease (AD) and mild cognitive impairment (MCI) are major contributors to dementia, with growing prevalence in Latin America. Evidence suggests that gut microbiota alterations may influence neurodegeneration, but data on Hispanic population are lacking.<br><br>OBJECTIVE: Characterize gut microbiota in individuals with AD, MCI, and controls in the Dominican Republic, exploring clinical, demographic, and dietary associations.<br><br>METHODS: Prospective-translational study including 88 participants aged &#x2265;60 years. Performed clinical, cognitive, and functional assessments. Stool samples analyzed using 16S rRNA gene sequencing. Bioinformatic processing using Quantitative Insights into Microbial Ecology Version 2 (QIIME2) and R. Alpha and beta diversity, taxonomy, and differential abundance were evaluated. Dietary influences were assessed using PERMANOVA.<br><br>RESULTS: No significant differences in alpha diversity (Shannon index 4-5, Simpson index 0.94-0.99, p>0.05) or beta diversity (p>0.05) were observed between groups. Firmicutes (51.9%) and Bacteroidota (34.1%) dominated the microbiota. Higher Desulfobacterota abundance in MCI and AD (0.54 and 0.61%, respectively, vs. 0.34% in controls; p<0.05). The Firmicutes/Bacteroidota ratio was lower in men with MCI (1.09) compared to controls and AD (1.70). MCI and AD were associated with increased levels of the genera Bilophila, Odoribacter, and Parabacteroides (p<0.05) and reduced levels of Mitsuokella and Eubacterium ruminantium. Dietary interactions, e.g., mango, lettuce, and carrot, influenced specific taxa (p<0.05).<br><br>CONCLUSION: This study pioneers gut microbiota characterization in AD and MCI in the Dominican Republic, identifying microbial alterations in cognitive impairment and highlighting regional dietary and ethnic factors. Longitudinal and multi-omics studies are warranted to clarify causality and therapeutic potential.}, }
@article {pmid42631186, year = {2026}, author = {Zdouc, MM and Augustijn, HE and Machushynets, NV and Bayona, LM and Soldatou, S and de Jonge, NF and Casu, S and Jaspars, M and van Wezel, GP and Medema, MH and van der Hooft, JJJ}, title = {FERMO: A Dashboard for Biochemometric Prioritization of Molecular Features from Mass Spectral Data.}, journal = {ACS measurement science au}, volume = {6}, number = {4}, pages = {1011-1022}, pmid = {42631186}, issn = {2694-250X}, abstract = {Many natural products can selectively modulate biological processes, making them prime candidates for drug discovery. However, the complexity of biological samples makes clear attribution of activity to molecules challenging, thereby hampering hypothesis-driven prioritization, with liquid chromatography-tandem mass spectrometry routinely detecting hundreds of molecules per sample. Existing biochemometric tools typically focus on facilitating data-driven exploration to support manual interpretation, rather than more objective, data-driven prioritization and hypothesis generation. Here, we introduce FERMO, a free online dashboard interface for biochemometrics-based prioritization of molecular features and samples. FERMO accepts qualitative and quantitative bioactivity assay data and further integrates group metadata and results from genome mining. FERMO performs automated data processing, organization, and annotation, supporting prioritization with the calculation of custom scores. FERMO supports both exploratory and targeted analysis through efficient interactive visualization, reproducible prioritization, and data filtering. We demonstrate FERMO's utility in benchmarking studies prioritizing bioactive natural products from complex biological matrices. FERMO is freely available at https://fermo.bioinformatics.nl/.}, }
@article {pmid42631634, year = {2026}, author = {Callejas, C and Bovio-Winkler, P and Etchebehere, C}, title = {Genome-resolved assessment of archaeal diversity in full-scale anaerobic digesters reveals variability in mcrA primer coverage.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxag212}, pmid = {42631634}, issn = {1365-2672}, abstract = {AIMS: Methanogenic archaea are key players in anaerobic digestion, driving methane production in biogas reactors. This study aimed to assess the diversity of methanogenic archaea in full-scale anaerobic digesters using genome-resolved metagenomics and to systematically evaluate the taxonomic coverage of commonly used mcrA-targeted qPCR primer sets against this genomic framework.<br><br>METHODS AND RESULTS: Methanogenic diversity was assessed using 113 dereplicated archaeal metagenome-assembled genomes (MAGs) recovered from 109 full-scale anaerobic digesters treating diverse substrates. Genome-resolved analyses revealed a diverse archaeal community spanning multiple phyla, dominated by Halobacteriota and Methanobacteriota, with additional representatives from Methanobacteriota_B, Thermoplasmatota, and Thermoproteota. The presence of the mcrA gene was identified in a subset 55 MAGs, which were subsequently used as the genomic framework to evaluate six commonly used mcrA qPCR primer sets in silico. This subset clustered into nine phylogenetic groups and formed the basis for the primer coverage analysis. The evaluation revealed marked differences in taxonomic coverage among primer sets. Most primers preferentially detected Methanobacteriales and Methanosarcinales, while underrepresenting or excluding other methanogenic lineages, including H&#x2082;-dependent methylotrophic Methanomassiliicoccaceae.<br><br>CONCLUSIONS: Commonly used mcrA primer sets differ substantially in their ability to capture methanogenic diversity, with some showing broad representation of reactor-associated methanogens and others exhibiting strong lineage-specific biases. Genome-resolved metagenomics provides an effective framework for benchmarking primer performance and supports the selection and improvement of molecular tools for more accurate monitoring of anaerobic digestion systems.}, }
@article {pmid42632980, year = {2026}, author = {Mondal, P and Ganguly, D and Das, B and Sarker, RK and Ghosh, A and Samanta, S and Chakraborty, P and Tribedi, P and Gupta, AD and Trivedi, S and Das, S and Sarkar, S}, title = {Isolation, characterization and identification of antibiotic-resistant biofilm forming bacteria from East Kolkata Wetland, a Ramsar site: an ecological concern.}, journal = {3 Biotech}, volume = {16}, number = {9}, pages = {382}, pmid = {42632980}, issn = {2190-572X}, abstract = {UNLABELLED: The current study holds major socio-economic importance of East Kolkata Wetland (EKW) in India, a Ramsar site, presently under constant threat of anthropogenic wastes that could accelerate antibiotic resistance (AR). The underlying mechanism behind the spread of AR in EKW requires proper investigation. Towards this direction, we focused on the isolation of antibiotic resistant bacteria (ARB) from EKW with adequate characterization by employing biochemical, molecular and antibiotic sensitivity tests. Thus, water samplings were carried out and a total of 32 ARB were isolated from three different study sites at EKW by selective agar plating. The isolates exhibited diverse biochemical properties with multi-antibiotic resistance (MAR) index exceeding 0.2 against 14 antimicrobial agents. MAR is strongly linked with biofilm formation. For comprehensive understanding of MAR among the isolates, their biofilm forming ability was checked. Henceforth, 14 potent biofilm formers were identified by measuring the total biofilm biomass through crystal violet (CV) assay and light microscopy. Furthermore, extracellular polymeric substance (EPS), metabolic activity, auto-aggregation property along with their motility pattern also confirmed their strong biofilm forming ability. Considering their pathogenicity, few exhibited hemolytic activities. Subsequently, these potent biofilm formers were identified by 16S rRNA gene and phylogenetic approach. These biofilm forming ARB in waterbodies of EKW requires vigilant monitoring before it is recycled for household, aquaculture and agricultural activities. Hence this study requires attention from the viewpoint of Sustainable Developmental Goals (SDGs) particularly related to good health (SDG 3) in the context of ensuring clean, sanitary water (SDG 6) and managing life below water (SDG 14).<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-05012-6.}, }
@article {pmid42633378, year = {2026}, author = {Aminullah, N and Danish, F and Zahir, A and Azizi, MN}, title = {Phytogenic as a natural resource for gut health management: a sustainable strategy for modern poultry production.}, journal = {Veterinary and animal science}, volume = {33}, number = {}, pages = {100804}, pmid = {42633378}, issn = {2451-943X}, abstract = {The increasing global demand for poultry products has intensified the need for intervention strategies that enhance productivity while maintaining animal health and food safety. Antimicrobials have historically been used in poultry production to support growth performance and maintain gut health; however, their routine and prolonged use have raised significant concerns regarding antimicrobial resistance, which poses a serious threat to public health. The growing concerns regarding antimicrobial resistance have motivated researchers to seek safer, more sustainable alternatives. This review critically evaluates the mechanisms by which phytogenic feed additives (PFAs) regulate gut health and their potential to support sustainable poultry production as alternatives to conventional antimicrobials. Phytogenic compounds have been shown to enhance intestinal barrier integrity by upregulating tight junction proteins, improve nutrient absorption by stimulating digestive enzyme activity, and promote villus development and mucosal health. Furthermore, these bioactive molecules have demonstrated potential to modulate microbial ecology by favoring beneficial taxa while suppressing pathogenic colonization, thereby improving gut homeostasis and immune competence. These combined effects contribute to improved overall production sustainability. Despite the beneficial effects of PFAs, variation in plant sources, bioactive component concentrations, extraction methods, and dosage leads to inconsistent poultry responses, a limitation that warrants further investigation and standardization. However, advances in formulation technologies and standardization strategies are progressively improving their consistency and practical application. Therefore, PFAs represent a viable nutritional strategy to support gut health and promote more sustainable poultry production with reduced reliance on conventional antimicrobials.}, }
@article {pmid42635434, year = {2026}, author = {Sakdinan, B and Sinha, A and Qadri, F and Khan, AI and Nelson, EJ and Shapiro, BJ}, title = {Species-specific prophage induction by ciprofloxacin in human gut metagenomes.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0030326}, doi = {10.1128/msystems.00303-26}, pmid = {42635434}, issn = {2379-5077}, abstract = {Antibiotics are known to trigger prophage induction in controlled laboratory settings, but it remains unclear whether this also occurs within microbiomes in nature. Current methods investigating the link between antibiotics and prophage induction within the human gut rely on in vitro culturing of human gut bacterial isolates. Using a metagenomic approach, we aimed to measure prophage induction, and whether it is associated with antibiotic exposure. In two independent human cohorts, we compared prophage to bacterial host read depth ratios (P:H) across known or measured antibiotic exposures. We found that induction is not broadly associated with antibiotic exposures at the level of the overall microbiome, but that ciprofloxacin increases P:H ratios in certain bacterial species. We documented heterogeneous trajectories of P:H ratios over the course of antibiotic exposure, sometimes increasing and remaining high, or returning to baseline. This study complements experimental models by providing in vivo evidence of induction in the human gut.IMPORTANCEBacteriophages are viruses that infect a bacterial host. The lytic and lysogenic cycles are the two classic outcomes of phage infection. In the lytic cycle, the phage immediately replicates and lyses its host cell to release new viral particles. In the lysogenic cycle, the phage, now called a prophage, integrates its genome into that of its host without killing it. Prophages can switch to the lytic cycle in a process called induction, in which the viral genome is replicated, the host cell is lysed, and viral particles are released. The most immediate consequence of induction is host cell death, which can impact bacterial populations and communities. Since prophages are mobile genetic elements that can move between bacteria, they are also an important vehicle for horizontal gene transfer. While induction has been well studied in vitro, whether and how induction occurs within the complex microbial ecosystem in humans is less well characterized. Understanding prophage induction in vivo is therefore critical in corroborating in vitro observations.}, }
@article {pmid42636907, year = {2026}, author = {Xiang, S and Tian, Y and Tong, C and Qi, X and Ren, T and Ji, B}, title = {Ionic synergy of Ca[2+], Mg[2+], and Fe[2+] Balances hydrophobicity and microbial ecology in microalgal-bacterial granular sludge.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135700}, doi = {10.1016/j.biortech.2026.135700}, pmid = {42636907}, issn = {1873-2976}, abstract = {Microalgal-bacterial granular sludge (MBGS) faces structural stability challenges that limit its engineering application. To investigate the regulatory mechanisms of divalent metal ions under light-dark cycles, five experimental groups were established: a blank control, Ca[2+] addition, Mg[2+] addition, Fe[2+] addition, and combined ion addition. Results showed that Fe[2+] was crucial for maintaining granule integrity and promoting photosynthetic taxa through regulating hydrophobic carbon group accumulation in extracellular polymeric substances (EPS), though its sole addition caused community specialization and compromised nitrogen/phosphorus removal stability, especially under dark conditions. Ca[2+] enhanced Proteobacteria proliferation and biomass accumulation, improving COD and TN removal, but this effect seemed to be insufficient to counteract granule disintegration caused by iron deficiency. Mg[2+] exhibited limited direct community effects but correlated positively with COD removal and Chl-a/Chl-b ratio. Notably, combined addition achieved balanced EPS hydrophilic-hydrophobic properties, maintained community diversity and functional redundancy, and demonstrated stable pollutant removal through ionic synergy. This study elucidates metal ion regulatory pathways in MBGS, providing theoretical foundations for targeted ion optimization.}, }
@article {pmid42630435, year = {2026}, author = {Peng, P and Cai, J and Zhang, L and Lu, Y and Kuang, P}, title = {The subgingival microbiome in periodontitis: from ecological dysbiosis and metabolic reprogramming to precision interventions.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1906205}, pmid = {42630435}, issn = {1664-302X}, abstract = {Periodontitis is a dysbiosis-driven chronic inflammatory disease characterized by complex interactions among the subgingival microbiome, microbial metabolism, and host immune responses. Accumulating evidence indicates that disease progression is not solely determined by the enrichment of specific periodontal pathogens but is critically associated with ecological disruption and functional reprogramming of the subgingival microbial community. During the transition from periodontal health to disease, microbial metabolism shifts from carbohydrate utilization toward proteolysis and amino acid fermentation, resulting in altered production of short-chain fatty acids, polyamines, volatile sulfur compounds, hydrogen sulfide, and nitric oxide. These metabolic alterations contribute to inflammasome activation, immune dysregulation, osteoclastogenesis, and progressive periodontal tissue destruction. Beyond local pathology, periodontal microorganisms and their metabolites can disseminate through the oral-systemic axis, thereby influencing the pathogenesis of multiple systemic disorders. Recent advances in multi-omics technologies have further revealed that metabolic reprogramming represents a critical mechanistic link connecting ecological dysbiosis with host inflammatory responses. Consequently, therapeutic strategies are evolving from conventional antimicrobial approaches toward precision microbiome-based interventions, including probiotics, postbiotics, bacteriophages, predatory bacteria, metabolic modulation, and oral microbiome transplantation. In this review, we integrate current evidence on microbial ecology, metabolism, and host interactions and propose the Ecological Dysbiosis-Metabolic Reprogramming-Host Crosstalk framework. This framework highlights metabolic reprogramming as the central bridge linking microbial dysbiosis to host inflammatory damage and provides a conceptual basis for the development of precision periodontal medicine.}, }
@article {pmid42630587, year = {2026}, author = {Boutin, S and Rondeau-Leclaire, J and Roy, A and Laforest-Lapointe, I}, title = {A field-based study of phyllosphere mycobiomes in apple orchards under varying agricultural management strategies.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag203}, pmid = {42630587}, issn = {2730-6151}, abstract = {Microbial communities in the phyllosphere are key players in plant health and disease resistance, yet their response to agricultural management strategies remains poorly understood under field conditions. Here, we compare fungal community composition and diversity across conventional and organic apple orchards using ITS amplicon sequencing. Leaf samples were collected from six sites at three distinct time points during the 2023 growing season (in May, July, and August) corresponding approximately to monthly intervals throughout the summer. Flower samples were collected from the same trees in May. Our analyses reveal that agricultural management strategies are significantly associated with fungal community structure, with effects intensifying from May to July. Both types of management strategies showed enrichment for different genera known to include common apple tree pathogens: Alternaria and Podosphaera were associated with conventional sites, while Didymella and Ramularia were associated with organic sites. Although fungal alpha diversity was higher in May at conventional orchards compared to organic orchards, it declined over time at conventional sites while it remained stable at organic sites. Together, these patterns indicate that distinct management interventions impose contrasting selective pressures on the apple tree phyllosphere mycobiome, thus shaping both broad fungal community composition and the dominance dynamics of key fungal taxa. Our findings underscore the ecological relevance and inherent challenges of field-based microbiome research, and provide insights to inform the development of sustainable orchard management strategies grounded in fungal community dynamics.}, }
@article {pmid42629862, year = {2026}, author = {Luo, HN and Wu, ZX and Guan, JY}, title = {Frequency locking to environmental forcing suppresses oscillatory extinction in phage-bacteria interactions.}, journal = {Physical review. E}, volume = {114}, number = {1-1}, pages = {014412}, doi = {10.1103/rch2-2hsr}, pmid = {42629862}, issn = {2470-0053}, mesh = {*Bacteriophages/physiology ; *Models, Biological ; *Bacteria/virology/growth &amp; development ; *Extinction, Biological ; *Environment ; }, abstract = {Bacteriophage-bacteria interactions are central to microbial ecology, influencing evolution, biogeochemical cycles, and pathogen behavior. Most theoretical models assume static environments and passive bacterial hosts, neglecting the joint effects of bacterial traits and environmental fluctuations on coexistence dynamics. This limitation hinders the prediction of microbial persistence in dynamic ecosystems such as soils and oceans. Using a minimal ordinary differential equation framework, we demonstrate that environmental fluctuations can suppress destructive oscillations through resonance, promoting coexistence where static models otherwise predict collapse. Counterintuitively, we find that lower bacterial growth rates are helpful in enhancing survival under high infection pressure, elucidating the observed postinfection growth reduction. Our studies highlight bacterial hosts as active builders of ecological dynamics and environmental variation as a potential stabilizing force. Our findings thus bridge a theory-experiment gap and provide a framework for predicting microbial responses to environmental stress, which might have potential implications for phage therapy, microbiome management, and climate-impacted community resilience as well.}, }
@article {pmid42629969, year = {2026}, author = {Iqbal, MM and Farooq, MA and Lal, R and Abdalla, M and Smith, P}, title = {The Fragile Sink: Reconceptualizing Soil Carbon Stabilization and Its Vulnerability Under Global Change.}, journal = {Global change biology}, volume = {32}, number = {8}, pages = {e71071}, pmid = {42629969}, issn = {1365-2486}, mesh = {*Carbon Sequestration ; *Climate Change ; *Soil/chemistry ; *Carbon/analysis ; *Soil Microbiology ; }, abstract = {Soil carbon sequestration (SCseq) is fundamental to global climate mitigation initiatives; however, growing evidence indicates an expanding disparity between carbon (C) accumulation and its long-term persistence. This article aims to integrate recent advances in microbial ecology, mineral biogeochemistry, and nutrient stoichiometry to examine why increases in soil C (SC) stocks do not necessarily translate into long-term persistence. The article introduces the fragile sink framework, wherein sink durability reflects the balance between internal C throughput and the strength of stabilizing barriers. Global change drivers, including warming, elevated CO2 (eCO2), nutrient enrichment, and anthropogenic disturbance, can accelerate internal C turnover, resulting in soils that are structurally younger, more reactive, and increasingly vulnerable to rapid C loss despite stable or rising stocks. The article shows that destabilization begins at predictable vulnerability frontiers where stoichiometric gating and mineral protection are overridden, while recovery is constrained by kinetic and architectural hysteresis. Thus, it recommends a shift away from stock- and input-centric C farming toward process-centric C defense, emphasizing the protection of slow-cycling, kinetically protected pools under increasing turnover.}, }
@article {pmid42629024, year = {2026}, author = {Wang, A and Jin, T and Tang, Y and Wang, S and Xia, X}, title = {Obligate anaerobic next-generation probiotics as natural antimicrobials in food systems: mechanisms, applications, and challenges.}, journal = {Food research international (Ottawa, Ont.)}, volume = {242}, number = {Pt 1}, pages = {119776}, doi = {10.1016/j.foodres.2026.119776}, pmid = {42629024}, issn = {1873-7145}, mesh = {*Probiotics ; Humans ; *Food Microbiology ; *Bacteria, Anaerobic/metabolism ; *Anti-Infective Agents ; Anaerobiosis ; *Foodborne Diseases/prevention &amp; control/microbiology ; Biofilms ; }, abstract = {Foodborne pathogens remain a persistent global challenge, threatening food safety and public health. Conventional probiotics have been explored as natural antimicrobials to antagonize foodborne pathogens but still exhibit varied efficacy in pathogen suppression within complex food systems. In recent years, multiple human commensals such as Akkermansia muciniphila, Faecalibacterium prausnitzii, and Anaerobutyricum hallii have emerged as promising next-generation probiotics (NGPs) due to their ecological relevance, metabolic versatility, and capacity to restore host-microbiota homeostasis. This review first summarizes the potential mechanisms by which these anaerobes and their metabolites contribute to pathogen suppression, including metabolite-mediated inhibition, quorum sensing interference, nutrient and adhesion competition, host immune modulation, and biofilm suppression. Special emphasis is placed on the interplay among key NGPs and their synergistic metabolic networks that reshape microbial ecology and enhance colonization resistance. Furthermore, recent advances in incorporating anaerobic probiotics and their postbiotic derivatives into food systems are discussed, noting that such applications remain emerging and currently limited by the challenges of maintaining obligate anaerobes in aerobic matrices. Finally, we highlight current challenges and future opportunities, emphasizing safety assessment and synthetic microbial consortia. Together, this review provides an integrated perspective on obligate anaerobes as potential solutions for improving food safety and human health through NGPs innovation.}, }
@article {pmid42629157, year = {2026}, author = {Wilborn, D and Constantinou, A and Franz, A and Schwarzer, R and Menzel, P and Engelhardt, G and Tomova-Simitchieva, T and Amin, R and Zhou, G and Hillmann, K and Kottner, J and Ralle, J and Konietschke, F and Blume-Peytavi, U}, title = {Maternal and Infant Skin Microbiome Synchrony and Divergence: A Longitudinal Study of Skin Microbial Ecology and Early-Life Assembly.}, journal = {Experimental dermatology}, volume = {35}, number = {8}, pages = {e70349}, pmid = {42629157}, issn = {1600-0625}, mesh = {Humans ; Female ; Longitudinal Studies ; Pregnancy ; *Skin Microbiome ; Infant ; *Skin/microbiology ; Infant, Newborn ; Adult ; *Microbiota ; Biodiversity ; }, abstract = {During pregnancy and after childbirth, women's skin undergoes significant changes which may affect the skin's functional and structural characteristics and microbial diversity. Like their mothers, the newborns also experience various skin challenges in the months following birth. Temporal changes in skin microbiome in special groups such as pregnant women and newborns, as well as the interrelation between their skin's microbial diversity, have not been investigated. We followed women from pregnancy through 6 months after delivery, and their infants from 4 weeks to 6 months of age to investigate their skin characteristics and the microbiome, and potential associations. We enrolled 109 pregnant females residing in Berlin, Germany, with 93 mothers-infant pairs completing the study. Microbiome investigations included DNA isolation as single-site sampling using volar forearm skin swabs. Bioinformatic analysis involved OTU clustering at 97% sequence identity, taxonomic assignment using NCBI reference databases, and calculation of biodiversity metrics, including relative abundance of the dominant bacterial phylotypes, bacterial diversity and Shannon diversity index. The maternal skin microbiome showed mild to moderate changes throughout pregnancy and the 6 months postpartum period. In infants, alpha diversity significantly increased (mean species richness from 82.6 at 4 weeks to 116.1 at 6 months), although it did not reach maternal diversity levels (145.4 at 6 months postpartum). Regarding the microbiome consistency of the included women and infants, the within-pair similarity was always significantly higher than between-pair similarity for both time points. Therefore, we conclude that there is likely a relationship between the microbiome of the mother and that of her child.}, }
@article {pmid42623063, year = {2026}, author = {Sgardioli, BF and Phillips, MC and Miklos, A and Fleiszig-Evans, K and Manson, AL and Scarpa de Mello, S and Shea, T and Urhan, A and Whipple, R and Salamzade, R and Sanders, J and Borges, PAV and Dapkevicius, MdLNE and Earl, AM and Gilmore, MS}, title = {Novelty, diversity, and genetic dark matter in enterococci of invertebrates.}, journal = {mBio}, volume = {}, number = {}, pages = {e0123426}, doi = {10.1128/mbio.01234-26}, pmid = {42623063}, issn = {2150-7511}, abstract = {Enterococci appear to have originated in the guts of early terrestrializing arthropods and invertebrates over 425 million years ago-hosts that are now highly diverse and widespread in nature today. Yet most knowledge of the genus comes from human infection-associated lineages with genomes swollen by the recent accretion of foreign DNA conveyed by mobile elements. Because invertebrates dominate terrestrial animal diversity and biomass, they would be predicted to constitute a major but little-explored reservoir of enterococcal diversity. We therefore systematically examined Enterococcus association and species diversification in invertebrate hosts of the comparatively natural, isolated, but well-characterized environment of the Azorean island of Terceira. Over 100 invertebrate specimens were examined for associated enterococci, which were taxonomically classified by whole-genome sequencing. Supporting the existence of a large pool of uncharacterized enterococci and Enterococcus-adapted genes, 40% (eight of 20) of the Enterococcus species identified were either undescribed, including four candidate new species described here, or very recently discovered. In contrast, control isolates from vertebrates were exclusively of known species typical of sampling elsewhere, discounting geographic isolation as a main driver of the novelty observed. Further, because of the abundance of E. casseliflavus and E. flavescens in this collection, we obtained the resolution necessary to quantify the divergence and decipher the drivers of speciation in the controversial division between these naturally vancomycin-resistant species. These findings provide robust support for the existence of a large pool of new species and unexplored adaptive traits in invertebrate-associated enterococci-diverse environmental survival traits optimized for expression in an enterococcal background, and well positioned for transmission into human-associated enterococcal strains.IMPORTANCEEnterococci are auxotrophic gut-associated bacteria that co-evolved with their terrestrial hosts over many eons. In the last 75 years-the "antibiotic era"-E. faecalis and E. faecium gained genes for antibiotic resistance and enhanced virulence, emerging as leading causes of multidrug-resistant infection. Little is known about the source of those genes or the pathway by which they entered human-associated strains. A recent global survey suggested a potentially large repository of uncharacterized genetic diversity in the enterococci of invertebrates. We directly tested this prospect by examining enterococci of invertebrate hosts in a largely natural and pastoral environment. Our findings provide clear evidence that invertebrates naturally harbor vast unexplored enterococcal diversity. Moreover, associations are likely driven by intrinsic host selection factors rather than geographic isolation. This expands our knowledge of Enterococcus biodiversity, including the identification of four novel species, identifying a vast reservoir of enterococcal genes available to species that colonize and infect humans.}, }
@article {pmid42623751, year = {2026}, author = {Ranjan, K and Gupta, N and Al-Mustapha, AI and Keenum, I and Shaheryar, M and Bose, D and Sharma, G and Tiwari, A}, title = {Environmental occurrence, ecotoxicity, and management perspectives of β-lactam antibiotics.}, journal = {Ecotoxicology and environmental safety}, volume = {323}, number = {}, pages = {120671}, doi = {10.1016/j.ecoenv.2026.120671}, pmid = {42623751}, issn = {1090-2414}, abstract = {β-Lactams are the most widely prescribed antibiotic class globally, comprising penicillins, cephalosporins, carbapenems, and monobactams. Their continual release to the environment raises concerns about both direct ecotoxicity and potential indirect effects on ecosystem function. This review highlights three key findings; 1) environmental concentrations can exceed predicted no-effect concentrations for resistance selection; for example ceftriaxone had been reported 6160 µg/L in wastewater influent and 4150 µg/L in effluent in India, indicating that many β-lactams have removal efficiency below 33%, 2) ecotoxicity data show that cyanobacteria (e.g. Microcystis aeruginosa, EC50 0.0037 mg/L for amoxicillin) are ≥ 1,000-fold more sensitive than macrofauna, and that chronic exposure at ng-µg/L levels may promote selection of antimicrobial resistance and facilitate horizontal gene transfer of these genes and 3). β-lactam resistance genes (blaCTX-M, blaNDM, blaOXA) are ubiquitous in wastewater and manure-amended soils and can persist even after the degradation of the parent compounds. Collectively, these finding indicates that β-lactam antibiotics pose significant risks to aquatic and soil ecosystems by contributing to the proliferation and maintenance of antimicrobial resistance in environmental reservoirs. The widespread environmental occurrence and persistence of β-lactams, along with associated resistance determinants, represent emerging One Health concerns. This narrative review synthesizes current literature on the ecotoxicological effects of β-lactam antibiotics, focusing on their major environmental sources, distribution across environmental matrices, impacts on non-target organisms, and emerging strategies to mitigate their environmental burdens. We further emphasize cross-disciplinary solutions spanning engineering, microbial ecology, policy, identify critical research gaps, and propose pragmatic pathways to reduce environmental selection pressure from β-lactams.}, }
@article {pmid42625292, year = {2026}, author = {Poppelsdorf, W and de Knijf, A and Melis, B and Rojas-Preciado, N and Yurduseven, R and Deleu, A and Bunkens, K and van Hee, S and Jacquemyn, H and Lievens, B}, title = {Biocontrol potential of Pseudomonas and Pantoea strains against the lettuce root aphid (Pemphigus bursarius L.) in witloof chicory (Cichorium intybus L. var. foliosum).}, journal = {Pest management science}, volume = {}, number = {}, pages = {}, doi = {10.1002/ps.71230}, pmid = {42625292}, issn = {1526-4998}, support = {//Agentschap Innoveren en Ondernemen/ ; }, abstract = {BACKGROUND: Although microbial biopesticides are widely applied to manage foliar insect pests, their application against belowground insect pests has received less attention. These pests are generally more challenging to manage due to their concealed soil-dwelling lifestyle and the limited availability of delivery methods. Here, we evaluated the potential of Pseudomonas and Pantoea strains as a biocontrol strategy against the lettuce root aphid (Pemphigus bursarius) in witloof chicory (Cichorium intybus L. var. foliosum) using a realistic delivery approach based on seed inoculation, preceded by a screening via root immersion to identify the most promising strains.<br><br>RESULTS: Root immersion of witloof chicory plants in bacterial suspensions significantly decreased aphid survival for 10 out of 19 tested strains, with median lethal times (LT50) ranging from 0.6 to 7.5&#x2009;days, compared to 10.7&#x2009;days for the untreated control. When the four best-performing strains, including two Pseudomonas and two Pantoea strains, and a reference strain (Pseudomonas fluorescens PpR24) were applied via seed inoculation, the strains successfully colonized chicory roots at densities exceeding 10[6] colony-forming unit (CFU)&#x2009;g[-1] of root tissue for at least 5&#x2009;weeks and retained aphicidal activity, albeit with reduced efficacy. In addition, the strains significantly suppressed aphid population development, reducing total aphid population size by up to 82% at 21&#x2009;days after aphid introduction.<br><br>CONCLUSION: In this study, we have identified novel Pseudomonas and Pantoea strains that effectively reduce survival and population development of Pemphigus bursarius on witloof chicory plants, highlighting their potential as a sustainable biocontrol strategy against root aphids. &#xa9; 2026 Society of Chemical Industry.}, }
@article {pmid42625563, year = {2026}, author = {Chen, WM and Sun, MY and Ye, JY and Tan, DC and Zhang, ZY and Liu, JJ}, title = {Towards a safer probiotic: clbD deletion attenuates EcN-induced DNA damage responses and epithelial inflammatory transcriptional responses.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1812973}, pmid = {42625563}, issn = {2235-2988}, mesh = {*DNA Damage ; *Epithelial Cells/microbiology/immunology ; *Probiotics ; *Escherichia coli/genetics ; *Gene Deletion ; Humans ; Polyketides/toxicity ; Cell Line ; Genomic Islands ; *Escherichia coli Proteins/genetics ; Transcription, Genetic ; Cytokines/metabolism ; Peptides ; }, abstract = {Escherichia coli Nissle 1917 (EcN) is widely used as a probiotic and engineering chassis, but its carriage of the pks genomic island raises safety concerns related to the genotoxin colibactin. Here, we constructed a clbD deletion mutant (EcNΔclbD) and a chromosomally complemented strain (EcNΔclbD::clbD) using a CRISPR/Cas9-based genome-editing strategy. Locus-specific PCR confirmed the expected clbD deletion and restoration patterns. DNA damage responses were evaluated by γH2AX immunofluorescence and alkaline comet assay after bacterial co-culture. Compared with EcN, EcNΔclbD markedly reduced γH2AX positivity and comet-positive cells, whereas clbD complementation restored both phenotypes to levels comparable to EcN. In NCM460 colonic epithelial cells, EcNΔclbD induced lower mRNA expression of pro-inflammatory cytokines and TLR4-MYD88-NFKB1-related transcripts than EcN. Additional CCK-8 and cell-associated bacterial load assays showed no significant differences between EcN- and EcNΔclbD-treated groups, suggesting that the reduced inflammatory transcription was not primarily attributable to altered host cell CCK-8 readout or bacterial exposure. qPCR analysis of neighboring pks genes showed detectable local transcriptional changes after clbD deletion that were restored toward the parental EcN pattern by complementation. Transmission electron microscopy revealed no detectable morphological or ultrastructural disruption after clbD deletion. Exploratory untargeted metabolomics suggested a metabolic shift associated with clbD deletion, while gastrointestinal stress assays revealed condition-dependent fitness effects without a generalized growth defect in LB medium. Together, these findings indicate that clbD deletion attenuates EcN-induced DNA damage responses and epithelial inflammatory transcription in vitro. EcNΔclbD may represent a candidate safety-optimized EcN chassis requiring further validation in additional epithelial models and in vivo systems.}, }
@article {pmid42627163, year = {2026}, author = {Harrison, DJ and Fullmer, MS and Takeuchi, N}, title = {Why are archaea not pathogenic? A hypothesis based on metabolism-habitat covariation.}, journal = {mBio}, volume = {}, number = {}, pages = {e0118526}, doi = {10.1128/mbio.01185-26}, pmid = {42627163}, issn = {2150-7511}, abstract = {Pathogenicity, the ability to cause infectious diseases in multicellular eukaryotes, is widespread among bacteria and eukaryotes but has not been reliably identified in archaea. To explore possible reasons for this disparity, we perform comparative analyses of thousands of bacterial and archaeal isolates. Our results show that isolated bacterial pathogens possess the ability to use organic compounds as sources of energy, electrons, and carbon (chemo-organo-heterotrophy or COH), suggesting that COH is a metabolic prerequisite for pathogenicity. Moreover, we find that isolated archaea capable of COH do not inhabit multicellular eukaryotes and instead predominantly inhabit extreme environments that preclude such eukaryotes. In contrast, all isolated archaea that inhabit multicellular eukaryotes are incapable of COH metabolism. This metabolism-habitat covariation in isolated archaea, together with COH as a potential prerequisite for pathogenicity in bacteria, suggests that the absence of archaeal pathogens may be due to a combination of the two factors: COH-capable archaea lack the environmental opportunity to inhabit multicellular eukaryotes, while non-COH archaea lack the metabolic prerequisite for pathogenicity.IMPORTANCEPathogenicity-the ability to cause infectious disease-is widespread among bacteria and eukaryotes but conspicuously absent from archaea, the third domain of life. To understand why archaea are non-pathogenic, we performed comparative analyses of thousands of bacterial and archaeal isolates. We found that the absence of pathogenic archaea can be explained by a combination of metabolic and environmental factors. Specifically, archaea living within eukaryotic, multicellular hosts lack a metabolic capability correlated with pathogenicity-chemo-organo-heterotrophy-whereas those possessing this metabolism typically live under extreme conditions, such as high temperature, and therefore lack the environmental opportunity to interact with eukaryotic hosts. These findings advance our understanding of microbes by revealing important links between their metabolism, habitats, and pathogenicity.}, }
@article {pmid42627175, year = {2026}, author = {Post, A and Webb, T and Indugu, N and Smith, BI and Pitta, DW}, title = {Dynamic changes in the hindgut bacterial community of pre-weaning crossbred beef calves in a pasture-based system.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0173026}, doi = {10.1128/spectrum.01730-26}, pmid = {42627175}, issn = {2165-0497}, abstract = {The early-life gut microbiome represents a window during which microbial alterations may impact long-term health and productivity. However, most research has focused on confined dairy systems with limited breed variation. To address this gap, we examined bacterial community dynamics in pasture-raised South Poll × Angus and Angus cow-calf pairs (n = 7). Fecal samples were collected from calves at birth and weekly through 8 weeks, with dam's samples collected post-calving. DNA was extracted from fecal samples, and bacterial communities were profiled using the V1-V2 region of the 16S rRNA gene. Alpha diversity increased significantly with age (richness ρ < 0.01, Shannon ρ < 0.01), while beta diversity exhibited strong temporal structuring (weighted R[2] = 0.33, ρ = 0.001; unweighted R[2] = 0.38, ρ = 0.001), as calf communities converged toward adult reference states by 8 weeks. Sex exerted modest but detectable effects on community structure. Taxonomic analyses identified a core microbiome of 25 taxa that accounted for most community structure and defined discrete temporal phases of development. Early fecal samples were dominated by Lactobacillus, Bacteroides, and facultative anaerobes. These taxa declined rapidly with age, coincident with increases in Ruminococcus, Blautia, Dorea, Lachnospiraceae, and Clostridiales (q < 0.05). Calf average daily gain was positively correlated with Streptococcus, Dorea, and Bacillus and negatively correlated with Ruminococcaceae (ρ > 0.3, q < 0.05). These findings demonstrate rapid gut microbiome development in pastured beef calves, similar in pace but distinct in composition from confined dairy systems, underscoring the importance of environment and breed diversity in shaping early-life microbial colonization.IMPORTANCEEarly-life microbial colonization plays a critical role in shaping gastrointestinal physiology and immune-cell maturation, with impacts on long-term productivity in cattle. However, most studies describing microbial succession focused on Holstein calves raised in confinement systems, leaving the microbial ecology of beef calves, particularly crossbreds and those on pasture, poorly characterized. In this study, we longitudinally characterized hindgut microbial development in Angus × South Poll and Angus calves during the first 8 weeks of life. We demonstrate a structured microbial succession driven by a core set of taxa that evolves with age, with continuous dominance of Lactobacillus. These findings establish foundational knowledge of microbiome assembly in a breed of beef calves growing in popularity and highlight microbial taxa and community structures that may relate to breed genetics influencing growth and health. Understanding microbial development in pasture-based beef systems provides an essential framework for designing microbiome-informed management or nutritional interventions aimed at improving productivity and sustainability, particularly in pasture-raised animals.}, }
@article {pmid42629006, year = {2026}, author = {Asadi, A and Sarand, I and Spuul, P and Fanning, S and Macori, G}, title = {Mapping spoilage microbiota in complex food systems: organisms, mechanisms, and omics-based characterization.}, journal = {Food research international (Ottawa, Ont.)}, volume = {242}, number = {Pt 1}, pages = {119633}, doi = {10.1016/j.foodres.2026.119633}, pmid = {42629006}, issn = {1873-7145}, mesh = {*Food Microbiology/methods ; *Microbiota ; Multiomics ; *Bacteria/classification/genetics ; Food Storage ; Food Loss and Waste ; }, abstract = {Food spoilage is a major cause of food loss, while it remains less understood in complex, multi-component foods than in single-ingredient products. This review reframes spoilage in such foods as a community-driven ecological process, not simply the result of single dominant organisms, and argues that spoilage is best understood through microbial activity rather than microbial presence or relative abundance alone. We develop this framework around three central ideas: (i) ingredient-derived microbiotas interact within a shared matrix, so spoilage depends on microbial succession and competition during storage; (ii) predictions based on individual specific spoilage organisms often perform poorly in heterogeneous mixed foods; and (iii) taxonomic dominance does not necessarily indicate spoilage activity. On this basis, we examine key spoilage-associated groups, including Leuconostoc gelidum, Lactococcus piscium, Latilactobacillus sakei, Latilactobacillus curvatus, Pseudomonas spp., Enterobacteriaceae, yeasts, and moulds, and link them to characteristic metabolites and spoilage patterns under refrigerated and modified-atmosphere storage. We then evaluate analytical approaches, from culture-based methods and MALDI-TOF MS to 16S rRNA and ITS sequencing, shotgun metagenomics, and activity-resolved multi-omics, according to what each can and cannot reveal about viable populations, microbial activity, community succession, and spoilage causation. We also discuss how bioinformatic choices influence interpretation and why gene detection does not necessarily indicate spoilage activity. Finally, we propose an integrated framework for study design and data integration to support more reliable quality control and shelf-life assessment in complex food systems.}, }
@article {pmid42614744, year = {2026}, author = {Hu, D and Wang, Z and Xue, Y and Li, X and Li, Y and Liu, S and Gao, L and Liu, H and Yan, H}, title = {Perioperative gut microbial ecology: a new frontier for improving the prognosis of hepatocellular carcinoma surgery.}, journal = {Precision clinical medicine}, volume = {9}, number = {3}, pages = {pbag021}, pmid = {42614744}, issn = {2516-1571}, abstract = {For patients diagnosed with hepatocellular carcinoma (HCC), surgical intervention remains the primary treatment modality. Nonetheless, challenges such as poor postoperative prognosis and the potential for recurrence contribute significantly to patient suffering. During the perioperative period, the stability of the gut microbiota in patients with HCC is significantly disrupted. This disruption can substantially affect the liver microenvironment and ultimately influence postoperative outcomes. Notably, the metabolic reprogramming of the liver induced by gut microbiota dysbiosis, persistent inflammation, and suppressed immune surveillance are key factors in HCC recurrence. Consequently, the gut microbiota has emerged as a critical risk factor in improving perioperative outcomes for patients with HCC. In this review, we summarize the factors contributing to changes in the gut microbiota during the perioperative period in patients with HCC, as well as the potential mechanisms by which gut microbiota dysbiosis affects prognosis. More importantly, we have proposed strategies based on the aforementioned mechanisms affecting prognosis, including restoring the gut microbiota, repairing the gut-liver barrier, providing perioperative relief, and enhancing liver regeneration. Further, this review also outlines potential challenges in clinical applications aimed at improving postoperative outcomes for HCC patients through gut microbiota-based interventions, particularly regarding sampling and patient susceptibility stratification. Collectively, these studies will further advance the development of personalized therapies targeting the microbiome, ultimately improving prognostic strategies for patients undergoing surgical intervention for HCC.}, }
@article {pmid42615635, year = {2026}, author = {Li, L and Zhang, J and Qu, S and Zhou, Z and Wang, B and Wu, H and Guo, Z and Shi, L and Yin, B and Zhu, X and Wang, Y and Teng, HH}, title = {The iron paradox and particle size sensing: transcriptomic response of Enterococcus faecalis to non-nutritive minerals.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0095426}, doi = {10.1128/aem.00954-26}, pmid = {42615635}, issn = {1098-5336}, abstract = {Minerals are known to influence microbial metabolism as nutrient sources or redox partners, yet whether chemically inert, non-nutritive minerals can regulate microbial physiology, and through what mechanisms, remains poorly understood. Here, we used transcriptomics to investigate the response of Enterococcus faecalis to Al2O3 and SiO2 particles spanning nanoscale to millimeter scale. Mineral exposure triggered extensive transcriptional reprogramming across hundreds of differentially expressed genes. Notably, a massive upregulation of iron acquisition genes (log2FC range from 3.8 to 4.2) concurrent with oxidative stress defenses (catalase, thiol peroxidase, and NADH oxidase) is suggestive of an "iron paradox," which is potentially attributable to mineral-mediated nutrient sequestration and steric hindrance of membrane transporters alongside interfacial reactive oxygen species generation. To adapt, E. faecalis orchestrated a coordinated metabolic shift, repressing serine catabolism (log2FC = -2.7) while investing nitrogen into glutathione biosynthesis (cystathionine synthase genes, log2FC = 3.7). Correlation analysis identified an ompR-sigV axis through which E. faecalis discriminates mineral particle size, with nanoscale particles eliciting stronger transcriptional responses than their larger counterparts. This stress response additionally upregulated virulence-associated genes and antibiotic resistance genes without direct antimicrobial selection pressure. These findings suggest that non-nutritive minerals shape microbial physiology through physical and surface-chemical cues independent of their nutritional value, highlighting the need for further exploration of the non-nutritional functions of minerals in microbial ecology.IMPORTANCEEven in the absence of utilizable nutrients, non-nutritive minerals such as Al2O3 and SiO2 can profoundly influence the transcriptional responses of Enterococcus faecalis. Using transcriptomic sequencing, we show that these inert minerals regulate microbial transcription, enhancing iron acquisition, oxidative stress repair, pathogenicity, and antibiotic resistance. Mineral-mediated transcriptional control is driven primarily by physical contact, surface chemistry, and particle size sensing, rather than conventional metabolic interactions. These findings identify inert minerals as signaling molecules that actively modulate microbial transcription, playing a proactive role in microbial evolution and environmental adaptation. This study redefines inert minerals as active carriers of transcriptional regulation, filling a critical gap in geomicrobiology and providing new insights into microbial environmental responses, biogeochemical cycling, and the mechanisms underlying microbial functional evolution and maintenance.}, }
@article {pmid42617679, year = {2026}, author = {Zhou, HZ and Sun, ZL and Xiao, YX and Xiao, W and Kang Ma,  and Zhou, CH and Ma, YH and He, T}, title = {Litter C/N ratio is associated with POC-to-MAOC transformation potential across forest types in subtropical restoration.}, journal = {Environmental research}, volume = {307}, number = {}, pages = {125520}, doi = {10.1016/j.envres.2026.125520}, pmid = {42617679}, issn = {1096-0953}, abstract = {Forest type is a critical determinant of soil organic carbon (SOC) dynamics during ecological restoration, yet how forest type shapes microbial community assembly and functional gene abundance to govern the partitioning of soil carbon into particulate (POC) and mineral-associated (MAOC) fractions remains poorly resolved. In May 2025, we collected soil samples from 12 plots representing three typical forest types (coniferous, mixed, and broad-leaved forests) in the Lingnan Nature Reserve and applied metagenomic sequencing to characterize soil microbial communities and functional processes. Following over three decades of restoration, SOC in mixed (25 ± 1.5 g/kg) and broad-leaved forest (26 ± 2.1 g/kg) soils increased by ∼18% and 23%, respectively, compared to coniferous forests (21 ± 1.6 g/kg). Litter C/N was lower in mixed and broad-leaved forests, corresponding with their higher SOC. Structural equation modeling further linked litter C/N ratio to POC and MAOC accumulation via microbial biomass carbon (MBC) as a key node, with POC, MAOC, and MBC increasing by 108-134%, 20-22%, and 26-31%, respectively, in mixed and broad-leaved versus coniferous soils. At the community level, variations in forest types selectively enriched Acidobacteriota or Actinomycetota, while co-occurrence network analysis revealed a shift from predominantly negative toward predominantly positive associations among bacterial taxa in broad-leaved and mixed forests, along with enhanced cross-module metabolic flow. Functionally, compared to coniferous forests, mixed and broad-leaved forests exhibited ∼15%/38% and 21%/47% increases in RPKM values of carbon fixation/degradation gene, respectively. GO enrichment analysis further indicated that litter inputs may be converted into stable humus via glycolysis and amino acid synthesis pathways. By integrating community-level microbial ecology, co-occurrence network analysis, and metagenomic functional profiling, this study provides novel mechanistic insight into how forest type shapes soil carbon fraction dynamics during restoration. These findings indicate the gene abundance variation in POC-to-MAOC transformation might be a plausible mechanistic link in the plant-microbe-soil carbon nexus and suggest that promoting broad-leaved or mixed forest restoration may represent a potentially effective strategy for enhancing soil carbon accumulation in subtropical regions.}, }
@article {pmid42618149, year = {2026}, author = {Mohr, MG and Tanabe, TS and Grosser, M and Dahl, C}, title = {Biochemistry and transcriptional regulation of bacterial sulfur oxidation.}, journal = {Advances in microbial physiology}, volume = {89}, number = {}, pages = {51-154}, doi = {10.1016/bs.ampbs.2026.06.003}, pmid = {42618149}, issn = {2162-5468}, mesh = {Oxidation-Reduction ; *Gene Expression Regulation, Bacterial ; *Sulfur/metabolism ; *Bacteria/metabolism/genetics/enzymology ; Bacterial Proteins/metabolism/genetics ; *Transcription, Genetic ; Oxidoreductases/metabolism/genetics ; Thiosulfates/metabolism ; }, abstract = {Sulfur is one of the most important and versatile elements in biology and forms the basis of energy metabolism in many prokaryotes. Its extensive large-scale redox transformations drive the global biogeochemical sulfur cycle and profoundly influence environmental chemistry. In dissimilatory sulfur oxidizers, the oxidation of reduced sulfur compounds is directly coupled to energy conservation via photosynthetic or respiratory electron transport chains. Sulfur-oxidizing bacteria and archaea are remarkably diverse, reflecting both the wide range of habitats they inhabit and the variety of metabolic pathways through which sulfur compounds are exploited as electron donors. Over the past decades, these pathways have been examined in depth using a spectrum of molecular genetic, biochemical, and omics-based approaches, primarily in model organisms amenable to genetic manipulation. Particular emphasis has been placed on thiosulfate oxidation mediated by the Sox multienzyme system and thiosulfate dehydrogenases, as well as on cytoplasmic sulfane sulfur oxidation involving dissimilatory sulfite reductase and the sulfur-oxidizing heterodisulfide reductase-like sHdr complex. Recent advances have highlighted the central role of specific lipoate-binding proteins that are essential for efficient sHdr-dependent sulfur oxidation. This review provides an overview of current knowledge on prokaryotic sulfur oxidation pathways. In addition, emerging insights into the complex regulatory networks operating in facultative sulfur oxidizers are provided, with particular attention to how these organisms coordinate sulfur metabolism with changing environmental and energetic conditions.}, }
@article {pmid42618789, year = {2026}, author = {Bartolec, T and Mitosch, K and Potel, C and Corona, F and Yang, ALJ and Karcher, N and Burtscher, ML and Koumoutsi, A and Becher, I and Müller, LS and Bobonis, J and Kumar, M and Galardini, M and Typas, A and Savitski, MM}, title = {Pervasive phosphorylation by phage T7 kinase disarms bacterial defences.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {42618789}, issn = {1476-4687}, abstract = {Bacteria and bacteriophages are in a constant arms race to develop defence and anti-defence systems, respectively. Currently known phage-encoded anti-defence systems are specific to the activity of the targeted bacterial defence system. Here we identify a mechanism by which the T7 bacteriophage broadly counteracts bacterial defences using protein phosphorylation. Its kinase (T7K), which has been reported to redirect the function of a few host proteins[1-5], is actually a hyperpromiscuous dual-specificity kinase that phosphorylates nearly all host and phage proteins during infection. The scale of phosphorylation vastly exceeds known phosphosites in Escherichia coli, has no sequence motif specificity and results in a higher proteome-wide phosphorylation density than mammalian cells with around 500 kinases. Stoichiometry analysis of phosphorylation sites revealed strong bias in T7K activity towards nucleic-acid-binding substrates mediated by its C-terminal DNA-binding domain. This highly stoichiometric phosphorylation enables the deactivation of DNA-targeting or DNA-containing bacterial defence systems. We provide mechanistic insights into how T7K weakens DNA-containing Retron-Eco9 through specific phosphorylation events, with single phosphomimetic mutations in key sites of the toxin abolishing defence. Moreover, by screening a large collection of E. coli strains, we provide evidence of broad anti-defence abilities of T7K in nature, as counteracted strains contain diverse bacterial defence systems. T7K homologues are found almost exclusively in phages, with hyperpromiscuous kinase activity probably being enabled by a divergent DFG-like motif in the catalytic centre.}, }
@article {pmid42621978, year = {2026}, author = {Sanabani, SS}, title = {Regenerative Microbiology: Harnessing Bacterial Antagonism and Spatiotemporal Signaling for Diabetic Wound Repair.}, journal = {Smart medicine}, volume = {5}, number = {4}, pages = {e70044}, pmid = {42621978}, issn = {2751-1871}, abstract = {Chronic diabetic foot ulcers represent a persistent clinical challenge characterized by a "locked" inflammatory phase, biofilm-mediated infection, and impaired tissue regeneration. Because conventional antibiotic and debridement therapies fail to resolve dysbiosis or stimulate healing, microbial antagonism has emerged as a potent biological principle for wound restoration. This narrative review integrates ecological evidence and mechanistic insights from animal models and early human studies to explore how beneficial microorganisms, including probiotics, bacteriophages, and competitive consortia, actively reshape diabetic wound environments. We examined the multifaceted mechanisms of these interactions, ranging from direct pathogen inhibition to host immunomodulation and metabolic signaling via conserved pathways such as the p40/epidermal growth factor receptor (EGFR)/PI3K axis. To address significant translational barriers, we introduce a "Regenerative Microbiology" framework that emphasizes spatiotemporal coordination and precision stratification. By tailoring the use of live biotherapeutics or metabolically independent postbiotics to a patient's vascular and microbial profiles, this approach offers a strategic roadmap for transforming the management of infection-driven tissue damage in chronic diseases.}, }
@article {pmid42622741, year = {2026}, author = {Okey-Ndeche, NF and Igwe, NH and Adewumi, CN and Ogundolie, FA}, title = {Seasonal shifts in microbial communities and physicochemical quality of a stream from a pristine waterfall in Abuja, Nigeria.}, journal = {Environmental monitoring and assessment}, volume = {198}, number = {9}, pages = {}, pmid = {42622741}, issn = {1573-2959}, mesh = {Nigeria ; Seasons ; *Environmental Monitoring ; *Rivers/microbiology/chemistry ; *Water Microbiology ; Bacteria/growth &amp; development ; *Microbiota ; Water Quality ; Fungi/growth &amp; development ; }, abstract = {The effects of seasonal changes on the physicochemical properties and microbial populations of a pristine waterfall stream located near Veritas University, Abuja, Nigeria, were evaluated. Water samples were collected monthly for 12 months during both dry and rainy seasons. Physicochemical parameters such as temperature, pH, conductivity, turbidity, and biochemical oxygen demand (BOD) were done by standard methods. The interaction effect of temperature and pH on the microbial organisms (heterotrophic bacteria, fungi, and yeast) and BOD was modeled using response surface methodology (RSM) based on central composite rotational design (CCRD). Findings indicate that physicochemical parameters such as conductivity (22.82 µS/cm), turbidity (0.96 NTU), and pH (8.23) as well as the number of microbial communities were higher in the rainy season than in the dry season. However, the physicochemical parameters (temperature, pH, conductivity, and turbidity) values are within the acceptable range of values for freshwater systems. The relationships between temperature, pH, and microbial counts were significantly explained through quadratic models (p < 0.05) that show high fitness values (R[2] = 0.7622-0.9728). The significant quadratic effect of temperature on the proliferation of bacteria and fungi and significant influence of pH on yeast and BOD was observed. BOD displayed a model response change from quadratic in the rainy season to linear in the dry season. The research demonstrates that even relatively pristine freshwater ecosystems are vulnerable to seasonal physicochemical variations that influence microbial ecology and probable public health risks. The discoveries in this work therefore, offer a predictive framework that can be adopted for monitoring freshwater ecosystems under increasing anthropogenic and climate-related pressures.}, }
@article {pmid42613647, year = {2026}, author = {Zarantonello, G and Puente-Sánchez, F and Schmidt, JG and Cuenca, A}, title = {From onset to healing: temporal dynamics of microbial communities pinpoint Midichloria-like organism's key role in the development of the fish skin disease red mark syndrome.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {42613647}, issn = {2524-4671}, support = {PhD funding//Danmarks Tekniske Universitet/ ; 101136346//European Union's Horizon Europe Project EUPAHW/ ; 2023-01573//Swedish Research Council for Sustainable Development (FORMAS)/ ; }, abstract = {BACKGROUND: Red mark syndrome (RMS) is an infectious disease affecting rainbow trout (Oncorhynchus mykiss), especially at market size, forcing farmers to downgrade the product with heavy economic repercussions. The causative agent of RMS has not been established according to Koch's postulates, since possible candidates have not been isolated and propagated in vitro. While the 16S rRNA gene of a Midichloria-like organism (MLO) is consistently detected in active skin lesions, the role of other bacteria in the disease has not been excluded. In this work, we provide a temporal perspective to elucidate the relationships between the bacteriome in rainbow trout skin and water, during the development and resolution of clinical disease in naive fish infected by cohabitation with RMS-affected fish in the same tank.<br><br>RESULTS: We quantified the MLO by qPCR in skin and, for the first time, in water using environmental DNA, showing that its quantity in both sample types corresponds with disease progression. Using 16S rRNA gene profiling, we provide further evidence that the MLO is likely the primary pathogen triggering RMS, as it was the only significantly enriched taxon in active lesions. Furthermore, the skin microbiome of affected fish reverted to a control-like state during healing. RMS also caused changes in the overall skin microbiome at peak pathology: the relative abundance of "Ca. Branchiomonas" and an unclassified gammaproteobacterium increased in apparently healthy skin areas of RMS-affected fish while remaining low in controls, suggesting they may be opportunistic bacteria implicated in skin dysbiosis.<br><br>CONCLUSIONS: Our findings on the temporal dynamics of the skin microbiome during disease progression and recovery strengthen the evidence that Midichloria-like organism is the primary pathogen of RMS. The observed shifts in other bacterial taxa suggest possible secondary roles in disease-associated skin dysbiosis. Finally, detection of MLO in environmental DNA from water provides new insights into RMS transmission and potential monitoring strategies.}, }
@article {pmid42613938, year = {2026}, author = {Adi, YK and Prakasita, VC and Wahyuni, AETH}, title = {Insights Into Boar Semen Under Tropical Conditions in Smallholder Production Systems: Semen Quality, Potential Microbiota Contamination and Antimicrobial Susceptibility.}, journal = {Reproduction in domestic animals = Zuchthygiene}, volume = {61}, number = {8}, pages = {e70311}, doi = {10.1111/rda.70311}, pmid = {42613938}, issn = {1439-0531}, support = {067/C3/DT.05.00/PL/2025//Directorate of Research and Community Service, Directorate General of Research and Development, Ministry of Higher Education, Science, and Technology, Republic of Indonesia/ ; }, mesh = {Animals ; Male ; *Semen/microbiology ; *Semen Analysis/veterinary ; Bacteria/drug effects/isolation &amp; purification ; *Microbiota ; Indonesia ; Tropical Climate ; Swine ; Microbial Sensitivity Tests/veterinary ; *Sus scrofa/microbiology ; Animal Husbandry ; }, abstract = {This study evaluated boar semen quality, seminal microbiome composition, and antimicrobial susceptibility of bacteria isolated from seminal plasma in a tropical smallholder pig production system in Indonesia. A total of 10 ejaculates were collected from eight sexually mature boars using the gloved-hand technique from two herds located in East Nusa Tenggara (Herd A) and East Java (Herd B). Semen quality was evaluated using conventional methods in Herd A (five ejaculates from three boars) and a mobile semen analysis unit in Herd B (five ejaculates from five boars). Seminal microbiome composition (three ejaculates from three boars in Herd A and five ejaculates from five boars in Herd B) was assessed using next-generation sequencing, and antimicrobial susceptibility of bacterial isolates recovered from seminal plasma (five ejaculates from three boars in Herd A and five ejaculates from five boars in Herd B) was determined using the disk diffusion method. Boar semen quality from Herd A was assessed only for gross motility using subjective observation, yielding a score of 2 out of 3. In Herd B, semen quality was generally high, with a mean ejaculate volume of 232.0 ± 28.6 mL and sperm concentration of 436.9 ± 109.3 × 10[6]/mL. Total and progressive motility were 89.5% ± 6.9% and 84.2% ± 9.5%, respectively, while the proportion of immotile spermatozoa was 10.5% ± 6.9%. Based on 16S rRNA gene sequencing, Chryseobacterium showed the highest relative abundance in semen samples from Herd A, whereas Streptococcus predominated in Herd B. Principal coordinates analysis based on Bray-Curtis dissimilarity demonstrated clear separation of seminal microbiota between herds, with Herd A samples forming a more compact cluster. LEfSe analysis further identified bacterial taxa differentially enriched between herds. Bacterial culture revealed that all semen samples were contaminated with either single or multiple bacterial species, including both Gram-negative and Gram-positive organisms. Escherichia coli and Klebsiella spp. were the most frequently detected isolates. Antimicrobial susceptibility test showed that Herd B exhibited a higher proportion of non-susceptible outcomes (58.3%) compared to Herd A (24.3%). In addition, the proportion of multidrug resistance in Herd A and Herd B were 42.9% and 83.3%, respectively. In conclusion, bacterial contamination in boar semen is unavoidable and may originate from the animal itself or the surrounding environment. Its impact on semen quality may vary depending on the bacterial load and the specific types of microorganisms present. In addition, variations in AMR and seminal microbiota between herds suggest that farm management practices may influence the microbial ecology and resistance patterns in boar semen.}, }
@article {pmid42614402, year = {2026}, author = {Zhang, Q and Cheng, Z and Tang, X and Yan, Y and Xia, Y}, title = {Wastewater treatment plant as a stable contributor affecting coastal ocean water viral communities.}, journal = {mLife}, volume = {}, number = {}, pages = {}, pmid = {42614402}, issn = {2770-100X}, abstract = {Coastal viruses play a vital role in sustaining ecosystem functioning, and yet, the degree to which they are influenced by human activities remains poorly understood. Our study demonstrates that wastewater discharge fundamentally reshapes the coastal ocean virome, overriding its natural seasonal variability and highlighting a profound anthropogenic influence on the distribution, host associations, and ecological roles of viral communities. These findings advance our understanding of viral dynamics in coastal marine systems and establish a critical scientific basis for evaluating how human activities alter marine microbial ecology.}, }
@article {pmid42614511, year = {2026}, author = {Bartkova, S and Valentino, F and Saraiva, M and Duman, M and Gerilovych, A and Radosavljevic, V and de Marco, A and Saticioglu, IB and Ay, H}, title = {Assessment of water prophylaxis and biosafety in finfish aquaculture - current and emerging technologies.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1841960}, pmid = {42614511}, issn = {1664-302X}, abstract = {Effective water quality management is a fundamental component of disease prevention, fish welfare, and sustainable production in finfish aquaculture. As aquaculture continues to expand to meet increasing global food demand, maintaining biosafe aquatic environments has become increasingly challenging due to production intensification, climate change, emerging pathogens, and the spread of antimicrobial resistance. While conventional approaches such as mechanical filtration, biofiltration, ultraviolet disinfection, ozonation, and water exchange remain central to water prophylaxis, increasing attention is being directed toward technologies that support earlier pathogen detection, improved risk assessment, and more targeted intervention strategies. This review examines water prophylaxis and biosafety through an integrated framework that links water quality, microbial ecology, pathogen surveillance, antimicrobial resistance, and preventive interventions. First, the biological and environmental mechanisms through which water quality influences disease susceptibility, microbiome stability, pathogen persistence, and antimicrobial resistance are evaluated. Conventional water-treatment technologies are then assessed alongside emerging approaches, including environmental DNA/environmental RNA monitoring, probiotics, phage therapy, biosensors, smart sensors, microfluidic platforms, and droplet-based molecular diagnostics. Emphasis is placed on their practical applicability, technological readiness, and suitability for different finfish production systems. The review highlights that effective biosafety management depends increasingly on integrating environmental monitoring with molecular diagnostics, risk assessment, and targeted interventions rather than relying solely on water-quality control or reactive disease treatment. Emerging technologies differ substantially in readiness, ranging from established and pilot-stage approaches to experimental technologies that require further validation before routine implementation. To support practical decision-making, the review synthesizes these technologies within an integrated water-prophylaxis and biosafety framework that links monitoring, diagnostics, risk assessment, intervention strategies, and reassessment pathways. Overall, sustainable finfish aquaculture will depend on combining conventional water-treatment infrastructure with advanced surveillance technologies and preventive biological interventions within coordinated biosafety programs. Such integration offers considerable potential to improve fish health, reduce environmental impacts, support responsible antimicrobial use, and enhance the long-term resilience of aquaculture production systems.}, }
@article {pmid42601898, year = {2026}, author = {Iorizzo, M and Pannella, G and Succi, M and Ganassi, S and Di Criscio, D and Tedino, C and Albanese, G and De Cristofaro, A}, title = {Seasonal dynamics of the gut microbiota in Apis mellifera ligustica: a two-year longitudinal study.}, journal = {Frontiers in insect science}, volume = {6}, number = {}, pages = {1920906}, pmid = {42601898}, issn = {2673-8600}, abstract = {The honey bee gut microbiota plays a crucial role in host nutrition, immunity, and colony health, yet the relative influence of seasonal and colony-specific factors on its long-term dynamics remains incompletely understood. This study investigated temporal variation in the gut bacterial community of three Apis mellifera ligustica colonies maintained in the same apiary and monitored over two consecutive years (2022-2023). Worker bees were sampled during eight seasonal periods, and gut microbiota composition was characterized using 16S rRNA gene amplicon sequencing. Across all sampling periods, the microbiome was consistently dominated by the characteristic honey bee-associated genera Gilliamella, Snodgrassella, Bartonella, Frischella, Commensalibacter, and Lactobacillus, indicating the persistence of a conserved core bacterial community. Seasonal variation was primarily associated with changes in the relative abundance of dominant taxa rather than with major changes in community composition. In particular, Gilliamella apicola and Snodgrassella alvi exhibited complementary seasonal patterns, with Gilliamella reaching its highest abundance during autumn, particularly in autumn 2023, whereas Snodgrassella predominated during spring and winter. Alpha-diversity metrics (Observed OTUs, Chao1, Shannon, and Simpson indices) showed limited seasonal variation, whereas beta-diversity analyses detected significant differences in community composition among seasons. Principal Coordinates Analysis and PERMANOVA identified season as the factor most strongly associated with microbiome variation, while colony identity did not significantly influence bacterial community composition under the standardized experimental conditions adopted in this study. Overall, these findings show that the gut microbiome of A. mellifera ligustica maintains a conserved core bacterial community while exhibiting reproducible seasonal variation in the relative abundance of its dominant members. This study provides a longitudinal baseline for future investigations aimed at understanding the ecological mechanisms underlying seasonal microbiome dynamics and their relationship with honey bee biology and environmental change.}, }
@article {pmid42602598, year = {2026}, author = {Apajalahti, J and Rinttilä, T}, title = {Strengths and weaknesses in techniques employed to measure the effects of dietary modulation on intestinal microbiota composition and function.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {26}, number = {}, pages = {682-698}, pmid = {42602598}, issn = {2405-6383}, abstract = {In this paper, intestinal microbial habitats in monogastric animals are discussed, with special reference to the intestinal segments of poultry. Physicochemical conditions in different segments vary and determine the selection of microbes that have nutritional and thermodynamic possibilities to thrive in the habitat. Understanding basic microbial ecology is a prerequisite for the knowledge-based development of microbiota modulating feed additives and ingredients. A prevalent research approach involves analysing intestinal parameters and calculating correlations between analytical data, animal health, and performance. However, this method cannot establish causal relationships or capture the dynamics of microbial metabolite production and their uptake by the intestinal brush border. An alternative or complementary approach is to use an ex vivo method, where the fresh, fully functional, authentic microbial community of the target intestinal segment is studied in the laboratory. For this approach to produce unbiased data, extremely careful handling of the oxygen-sensitive bacteria and precise replication of the physicochemical conditions of the target intestinal environment are critical. With such an ex vivo model, the effect of feed additives on the rate of metabolite production by the native microbiota can be accurately evaluated. All research approaches have their pitfalls, the details of which are discussed. Small methodological details can have a major impact on the reliability of the results. The most reliable approaches are unfortunately labour-intensive, and a successful outcome requires the use of multiple approaches in parallel. Although no research approach is perfect, combining multiple methods allows a comprehensive understanding to emerge gradually.}, }
@article {pmid42603915, year = {2026}, author = {Cherinet, MT and Bereded, NK and Van de Voorde, I}, title = {Traditional Ethiopian fermented condiments: a systematic review of microbial dynamics, nutritional transformations, and future perspectives.}, journal = {Journal of food science and technology}, volume = {63}, number = {9}, pages = {1637-1647}, pmid = {42603915}, issn = {0022-1155}, abstract = {UNLABELLED: Traditional Ethiopian fermented condiments, including Siljo, Datta, Awaze, Helbat, and Azo, are culturally significant and nutritionally valuable. Despite their importance, evidence on their microbial ecology, nutritional transformations, safety, and functional potential remains fragmented and insufficiently characterized. This systematic review, conducted in accordance with PRISMA 2020 guidelines, consolidates current knowledge on the microbial dynamics, nutritional changes, probiotic traits, and food safety of these traditional Ethiopian fermented condiments. A comprehensive literature search was carried out up to December 2025 across PubMed, Scopus, Cochrane Library, Epistemonikos, and Google Scholar. Studies consistently reported that lactic acid bacteria-particularly Lactiplantibacillus plantarum, Pediococcus pentosaceus, and Weissella spp.-dominate spontaneous fermentations, driving acidification to pH values typically between 3.6 and 4.5 and contributing to pathogen suppression. Fermentation also induced product-specific nutritional transformations, including changes in protein content and digestibility, mineral dynamics, and the formation of bioactive compounds. However, outcomes varied considerably depending on substrate composition, microbial consortia, and processing conditions. Data on antinutritional factor reduction (phytates, tannins, and trypsin inhibitors) were absent across all included studies, representing a critical knowledge gap. Despite these promising attributes, research on these condiments is largely limited by reliance on culture-dependent methods, heterogeneous fermentation practices, and inconsistent analytical approaches. The evidence base for some condiments, particularly Azo and Datta, is further constrained by reliance on grey literature and secondary data sources. To fully harness their microbial, nutritional, and commercial potential, future studies should employ integrated research methodologies based on standardized fermentation protocols, metagenomics, metabolomics, and comprehensive nutritional assessments.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13197-026-06764-y.}, }
@article {pmid42603993, year = {2026}, author = {Elias Masiques, N and De Vrieze, J and Gansemans, Y and Deforce, D and Van Nieuwerburgh, F and De Smet, S and Van Hecke, T}, title = {Pork and salmon diets differentially modulate lipid oxidation along the gastrointestinal tract in rats, with limited effects on gut microbiota.}, journal = {Current research in food science}, volume = {13}, number = {}, pages = {101517}, pmid = {42603993}, issn = {2665-9271}, abstract = {Red meat consumption has been associated with less favorable health outcomes, whereas fish intake is often considered beneficial. These differences may partly relate to variations in fatty acid composition and heme iron content, which can influence oxidative processes during digestion and thereby affect intestinal and systemic responses. This study investigated the effects of pork- and salmon-based diets, differing primarily in fatty acid profile and heme iron content but matched for macronutrient composition, on oxidative stress, gut microbiota, fermentation metabolites, and inflammation in rats. The pork-based diet supplied 2.3-fold more SFA and 14-fold more heme iron than the salmon-based diet, which in turn provided 14-fold more n-3 PUFA. Consumption of pork significantly increased propanal (+81%), hexanal (17-fold), and 4-hydroxy-2-nonenal (27-fold) in stomach contents, and elevated thiobarbituric acid reactive substances (TBARS, +45%) in plasma. In contrast, salmon consumption raised TBARS in duodenal mucosa (+19%) and C-reactive protein (+30%) in plasma. Only subtle diet-related changes were observed in gut microbiota composition and fermentation metabolites, with no difference in fecal calprotectin. A small number of discriminant taxa were identified, including Clostridioides and Muribaculum in salmon-fed rats and Eubacterium fissicatena, Sellimonas, and Dielma in pork-fed rats, while valerate levels were higher in pork-fed rats. Transcriptomic analysis revealed that no individual genes remained significant after correction for multiple testing. Overall, pork and salmon diets differentially modulated lipid oxidation along the gastrointestinal tract, whereas their effects on gut microbiota were limited.}, }
@article {pmid42608432, year = {2026}, author = {Feng, X and Xiang-Ling, T and ZhiJie, G}, title = {Functional response of bacterial communities in surface sediments of qingshitan reservoir to anthropogenic disturbance.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42608432}, issn = {2045-2322}, mesh = {*Geologic Sediments/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Anthropogenic Effects ; Biodiversity ; China ; Ecosystem ; *Microbiota ; }, abstract = {This study investigated the bacterial composition in surface sediments (0-5 cm) of Qingshitan Reservoir to elucidate their ecosystem functions in response to anthropogenic disturbances. Samples were collected in July 2023 from eight ecological points representing varying disturbance levels. High-throughput sequencing revealed significant variations in bacterial community structure. Sediments from the upstream cage aquaculture area (heavily disturbed) exhibited the highest bacterial richness, diversity, and evenness, while midstream and downstream areas (lightly disturbed) showed reduced diversity and uneven community structures. The dominant bacterial phyla included Firmicutes, Proteobacteria, Actinobacteriota, and Bacteroidota, with the most abundant genera being Lactobacillus, Escherichia-Shigella, Staphylococcus, Corynebacterium, and Brevibacterium.Functional predictions using PICRUSt2 indicated robust metabolic activity across all areas, particularly in amino acid metabolism within the cage aquaculture region. FAPROTAX analysis highlighted enhanced nitrate reduction in disturbed areas, suggesting a potential role in mitigating eutrophication through nitrogen cycling regulation. Additionally, BugBase identified elevated proportions of potentially pathogenic bacteria in upstream cage aquaculture and midstream residential areas, underscoring the need for targeted ecological risk management.These findings provide critical insights into the microbial ecology of Qingshitan Reservoir and its response to anthropogenic pressures, offering a scientific foundation for improving water resource utilization and ecological conservation efforts.}, }
@article {pmid42608796, year = {2026}, author = {Sahingur, SE and Grzech-Leśniak, K and Suslavich, SF and Deeb, JG}, title = {The Oral-Hepatic Axis: Epidemiological and Mechanistic Links Between Periodontal and Liver Diseases.}, journal = {Journal of periodontal research}, volume = {}, number = {}, pages = {}, doi = {10.1111/jre.70159}, pmid = {42608796}, issn = {1600-0765}, abstract = {Chronic liver diseases and periodontitis are prevalent inflammatory disorders that impose substantial global health and economic burdens. Increasing evidence supports an oral-hepatic axis through which periodontal dysbiosis and chronic oral inflammation may influence hepatic homeostasis and disease progression. Epidemiologic studies have linked periodontitis with metabolic dysfunction-associated steatotic liver disease (MASLD), nonalcoholic fatty liver disease (NAFLD), viral hepatitis, cirrhosis, and hepatocellular carcinoma. Although many associations persist after adjustment for shared risk factors, including obesity, diabetes, smoking, nutritional status, and socioeconomic factors, the independent contribution of periodontitis to liver disease remains unclear. Experimental and translational studies indicate that periodontal pathogens and their virulence factors promote systemic inflammation, endotoxemia, microbial translocation, immune dysregulation, and alterations in gut microbial ecology. Nutritional factors may further influence these interactions through their effects on host immunity, inflammation, and microbial communities. Together, these mechanisms converge along the oral-gut-liver axis to activate hepatic inflammatory, oxidative stress and profibrotic pathways that contribute to steatosis, immune activation, and fibrogenesis. Emerging evidence suggests that trained immunity, driven by metabolic and epigenetic reprogramming, may represent an additional mechanism linking periodontitis and liver disease warranting future studies. Preliminary studies indicate that periodontal therapy may reduce systemic inflammatory burden and improve hepatic biomarkers; however, evidence for an effect on liver disease progression or clinical outcomes remains limited. Similarly, hepatic dysfunction may exacerbate immune dysregulation and periodontal breakdown, reinforcing an inflammatory loop. However, overall causal relationships remain to be established. This review summarizes current epidemiological, clinical, and mechanistic evidence linking periodontitis and chronic liver diseases, highlighting the oral-gut-liver axis, shared immunometabolic and nutritional pathways. Understanding these interactions shows the significance of integrated dental-medical care and opens new avenues for prevention and adjunctive therapy to sustain oral and hepatic health.}, }
@article {pmid42609601, year = {2026}, author = {Park, MR and Bae, M}, title = {Metatranscriptomic characterization of active microbial communities in strawberry hydroponic drainage effluent.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1909518}, pmid = {42609601}, issn = {1664-302X}, abstract = {Hydroponic cultivation systems improve water and nutrient use efficiency; however, little is known about the active microbial communities inhabiting hydroponic drainage effluent. This study employed metatranscriptomic sequencing to characterize active microbial communities present in drainage effluent collected from strawberry cultivation beds within a commercial recirculating hydroponic system. Drainage effluent samples were collected during the spring and winter cultivation periods and subjected to RNA-based metatranscriptomic analysis. Following quality filtering, de novo assembly, and taxonomic classification, bacterial, fungal, and viral-associated transcripts were analyzed to characterize active microbial communities within the drainage environment. Metatranscriptomic sequencing generated 65.2 million and 53.2 million paired-end reads from the spring and winter samples, respectively. Taxonomic classification revealed distinct microbial profiles between the two analyzed drainage samples. Bacterial transcripts represented the dominant classified component in both samples. The spring sample exhibited a relatively diverse bacterial community composed of multiple taxa, whereas the winter sample was strongly dominated by Serratia marcescens and Serratia proteamaculans. Fungal community composition also differed between samples, with a greater representation of yeast-associated fungi in the winter sample. Viral-associated transcripts were detected in both samples and were primarily represented by bacteriophage-related sequences. A large proportion of transcripts remained unclassified, particularly in the spring sample, highlighting the limited representation of hydroponic drainage microorganisms in current reference databases. Although the study was limited to a single commercial production site, the findings should be interpreted as site-specific observations rather than representative characteristics of strawberry hydroponic systems in general. Nevertheless, the study provides an initial metatranscriptomic characterization of active microbial communities inhabiting strawberry hydroponic drainage effluent under commercial cultivation conditions and establishes a baseline dataset for further comparative investigations involving multiple hydroponic production systems. These findings provide baseline information on active microbial and viral assemblages associated with hydroponic drainage effluent and demonstrate the utility of metatranscriptomics for characterizing microbial communities in recirculating cultivation systems.}, }
@article {pmid42612319, year = {2026}, author = {Zhou, T and Zhang, R and Li, L and Yu, J and Li, H and Liu, H and Zhao, Y and Wang, Y}, title = {Oligomerized flavonoid nanointerfaces regulate gastrointestinal nutrient flux and metabolic inflammation.}, journal = {Biomaterials}, volume = {337}, number = {}, pages = {124554}, doi = {10.1016/j.biomaterials.2026.124554}, pmid = {42612319}, issn = {1878-5905}, abstract = {Oral strategies for obesity and its associated metabolic dysfunction rarely coordinate nutrient digestion, microbial ecology, barrier integrity and low-grade inflammation within the gastrointestinal lumen. Here we report an interface-engineering strategy that converts flavonoid monomers into oligomerized flavonoid-derived polyphenolic nanointerfaces for local gastrointestinal regulation. Five representative flavonoids were oligomerized through an acetaldehyde-mediated reaction and assembled into carrier-free nanoparticles with clustered surface phenolic motifs. Among them, oligomeric EGCG nanoparticles (O-EGCG NPs) showed the strongest interfacial activity, outperforming monomeric EGCG and non-assembled oligomers. Mechanistic analyses showed that O-EGCG NPs non-competitively modulated α-glucosidase, α-amylase, pancreatic lipase and pancreatic cholesterol esterase through enzyme binding and conformational remodeling. After oral administration, the nanoparticles maintained gastrointestinal colloidal stability, prolonged intestinal retention and reduced postprandial carbohydrate and lipid flux in substrate and mixed-meal tolerance tests. Repeated administration in high-fat diet-fed mice attenuated body-weight gain, hepatic lipid accumulation, dyslipidaemia and insulin resistance, accompanied by changes in intestinal barrier status, inflammatory cytokines and gut microbiota composition. These findings establish oligomerized flavonoid nanoparticles as locally acting luminal nanomaterials for regulating nutrient processing and microbiota-associated metabolic inflammation.}, }
@article {pmid42613563, year = {2026}, author = {G C, B and Wu, C}, title = {A Conditional Plasmid System for Markerless Gene Deletion in Genetically Recalcitrant Fusobacterium nucleatum subsp. animalis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3055}, number = {}, pages = {53-65}, pmid = {42613563}, issn = {1940-6029}, mesh = {*Plasmids/genetics ; *Fusobacterium nucleatum/genetics ; *Gene Deletion ; Bacterial Proteins/genetics ; Carbon-Sulfur Lyases/genetics ; Promoter Regions, Genetic ; Gene Expression Regulation, Bacterial ; Quorum Sensing/genetics ; }, abstract = {Fusobacterium nucleatum subsp. animalis (FNA) plays a prominent role in oral microbial ecology and is increasingly implicated in systemic diseases such as colorectal cancer. However, its genetic intractability has significantly hindered functional studies to understand its pathogenic mechanisms. To address this challenge, we developed a conditional plasmid system that enables efficient, markerless gene deletion in FNA strains. This system features inducible control of plasmid replication via a theophylline-responsive riboswitch regulating repA, and counterselection via the MazF toxin under the control of an anhydrotetracycline-inducible promoter. In this chapter, we provide a detailed, step-by-step protocol for implementing this system using FNA strain 7_1 as a model. We illustrate the procedure by deleting the luxS gene, which encodes S-ribosylhomocysteine lyase-an enzyme involved in AI-2 quorum sensing and biofilm regulation. Our protocol provides a powerful and adaptable tool for advancing genetic studies in this genetically recalcitrant subspecies.}, }
@article {pmid42597253, year = {2026}, author = {Stefanelli, N}, title = {Gut dysbiosis and vitamin-dependent immune regulation in degenerative musculoskeletal and bone diseases.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1920962}, pmid = {42597253}, issn = {1664-3224}, mesh = {Humans ; *Dysbiosis/immunology ; Animals ; *Gastrointestinal Microbiome/immunology ; *Bone Diseases/immunology/metabolism ; Vitamin D/metabolism ; *Immunomodulation ; *Vitamins/metabolism ; }, abstract = {Degenerative musculoskeletal and metabolic bone diseases are increasingly recognized as conditions sustained not only by endocrine and mechanical factors, but also by chronic low-grade immune activation and osteo-immune imbalance. This Perspective proposes a mechanistic framework in which gut dysbiosis may contribute to skeletal degeneration through alterations in vitamin-dependent immune regulation, with particular attention to the interaction between vitamin D signaling and microbiota-derived menaquinones. Dysbiosis may impair intestinal barrier integrity and increase exposure to microbial-associated molecular patterns, thereby sustaining innate and adaptive immune activation and promoting a pro-inflammatory cytokine milieu involving IL-6, TNF-α, IL-17, and IL-1β. These pathways may promote osteoclastogenesis and disrupt bone remodeling through the RANKL/RANK/OPG axis. While the immunomodulatory role of vitamin D is well established, microbiota-derived menaquinones may represent a less explored but biologically plausible interface between microbial metabolism, inflammatory signaling, and skeletal homeostasis . However, the extent to which microbiota-derived menaquinones significantly contribute to systemic vitamin K status in humans remains controversial and incompletely characterized. Within this framework, dietary patterns are conceptualized as modulators of microbial ecology and immune activation, while microbiota-modulating strategies may indirectly influence osteo-immune balance through immune-mediated mechanisms. This Perspective integrates microbial, immunological, and vitamin-dependent pathways into an immunology-centered model of skeletal degeneration and highlights the need for studies combining microbiome profiling, immune phenotyping, vitamin-dependent signaling, and bone remodeling outcomes.}, }
@article {pmid42598118, year = {2026}, author = {Weinbren, M and Surman-Lee, S}, title = {Sanitation, antibiotics, and the end of the antibiotic era.}, journal = {Public health in practice (Oxford, England)}, volume = {12}, number = {}, pages = {100839}, pmid = {42598118}, issn = {2666-5352}, abstract = {A decade after the publication of the highly influential O'Neill report, Tackling Drug-Resistant Infections Globally, antimicrobial resistance (AMR) continues to accelerate at an unprecedented rate. Despite being a cornerstone of global AMR strategies, antimicrobial stewardship has failed to reverse this trend. This failure reflects a fundamental misunderstanding of AMR as primarily a behavioural or prescribing problem, rather than an environmental one. A major driver of AMR is environmental pollution arising from the large-scale manufacture, release, and accumulation of antimicrobial substances that profoundly disrupt microbial ecosystems. While regulatory attention has focused on antibiotic contamination of local rivers during pharmaceutical manufacturing, this represents only a small fraction of the antibiotics produced and consumed globally. Following administration, and depending on the compound, up to 90% of biologically active antibiotic may be excreted unchanged and subsequently enter healthcare wastewater systems. Healthcare wastewater systems therefore function as a superhighway for the generation, amplification, and transmission of multidrug-resistant organisms-both within healthcare facilities and into surrounding municipal infrastructure. Traditional hospital defences, including Standard Infection Control Precautions, offer limited protection against pathogens originating from wastewater environments. Within these systems, high microbial biomass is continuously exposed to complex mixtures of antimicrobials, disinfectants, and other selective agents, distorting microbial ecology and creating conditions conducive to the selection of AMR. Recognising the healthcare wastewater system as a critical driver of AMR generation and dissemination reframes the problem and opens new opportunities for intervention. Addressing this overlooked reservoir may be essential to containing a global pandemic that, despite decades of effort, shows no sign of slowing.}, }
@article {pmid42600416, year = {2026}, author = {Lee, H and Haga, S and Roh, S}, title = {Physio-informatics linking rumen biology, systemic metabolism and meat quality in Japanese black cattle.}, journal = {Meat science}, volume = {242}, number = {}, pages = {110130}, doi = {10.1016/j.meatsci.2026.110130}, pmid = {42600416}, issn = {1873-4138}, abstract = {Japanese Black cattle (Wagyu) are raised under a distinctive long-term fattening system designed to enhance intramuscular fat (marbling) and carcass value. Because most metabolizable energy and many metabolic signals in ruminants derive from rumen fermentation products, variation in rumen microbial ecology and fermentation chemistry can extend to systemic metabolism and ultimately influence meat quality traits. Recent work in Japanese Black steers has provided a structured, multi-layered dataset spanning rumen fermentation characteristics, blood metabolites and hormones, liver transcriptome profiles, and rumen microbiome composition and predicted function across fattening stages and metabolic phenotypes. This review integrates these findings with established concepts in ruminant physiology to propose a physio-informatic framework linking rumen microbiota to hepatic metabolic regulation and adipose tissue development via the rumen-liver-adipose axis, with potential relevance to broader meat quality traits. We highlight (i) microbial succession across the three-stage feeding program, (ii) fermentation-derived short-chain fatty acids and their absorption and metabolic fates, and (iii) endocrine and transcriptional regulation of energy partitioning during fattening as an interpretable systems signal rather than a single downstream endpoint. Finally, we discuss potential analytic strategies, including longitudinal modeling, network inference, and machine learning approaches, that may support the future development of predictive biomarkers of carcass traits and intervention strategies potentially applicable to improving marbling consistency and metabolic efficiency.}, }
@article {pmid42600852, year = {2026}, author = {Pereira, A and Royen, GV and Ganigué, R and Sakarika, M}, title = {Can microbial biomass deliver the techno-functional properties required for more sustainable, animal-free foods? A quantitative synthesis linking microbial biomass type, processing, and techno-functionality.}, journal = {Bioresource technology}, volume = {462}, number = {}, pages = {135609}, doi = {10.1016/j.biortech.2026.135609}, pmid = {42600852}, issn = {1873-2976}, abstract = {The rising population levels and shift to protein-rich diets are increasing the harmful environmental impact of conventional food systems at unprecedented levels. To circumvent the inefficiency of traditional agricultural practices, natural microbial biomass (MB) of fungi, bacteria, yeasts and microalgae, emerges as an alternative source of nutritional protein that can be converted to microbial foods, as it relies on closed-system, climate-independent and efficient production. Although the environmental and nutritional benefits are widely studied, the techno-functional properties (foaming, emulsifying, gelling, oil and water retention properties) of MB and associated ingredients (whole-cell ingredients, cell-disrupted ingredients and protein-enriched extracts) are underexplored. This review compiled the current body of knowledge on MB production processes, including bioproduction, nucleic acid reduction treatments, downstream processing (DSP) to an appealing product, and their described impact on techno-functionality, as well as compared all reported techno-functional properties of MB-based ingredients and food products. MB-based ingredients show promising techno-functional potential, especially in water and oil retention properties, and versatility compared to their plant counterparts. We identified key issues hindering MB commercialization, including the lack of standardized terminology and methodology, limited synergies between upstream and DSP, insufficient diversity in selected microbial strains, ingredient types and final applications, and lack of interdisciplinary research. Strategies to address these challenges include focusing on properties beyond macromolecular composition, using computational approaches for faster screening, and critically evaluating DSP steps. These strategies ensure that the required techno-functional and sensory properties can be achieved without compromising the potential of MB for environmental sustainability and consumer acceptance.}, }
@article {pmid42593109, year = {2026}, author = {Ge, X and Song, J and Zhang, L and Zhang, C and Yang, Y and Kong, X and Guo, F and Pu, C}, title = {Occupational exposure to Baijiu fermentation environments alters nasal microbiota composition: a comparative analysis of Strong-flavor and Sesame-flavor production systems.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0220225}, doi = {10.1128/spectrum.02202-25}, pmid = {42593109}, issn = {2165-0497}, abstract = {UNLABELLED: Traditional Chinese Baijiu fermentation environments harbor complex microbial consortia critical for product quality, yet their effects on human nasal microbiota remain poorly characterized. This cross-sectional study compared nasal microbiota profiles of Strong-flavor (n = 25) and Sesame-flavor (n = 22) Baijiu workers against non-exposed individuals (n = 30) using 16S rRNA sequencing of environmental samples and nasal swabs. After adjusting for age and working age, no significant differences in Shannon diversity or species richness were observed among the three groups (ANCOVA, P > 0.05). However, community structure differed significantly (PERMANOVA, marginal R[2] = 0.075, P = 0.001), with Strong-flavor workers clustering closer to non-exposed individuals than Sesame-flavor workers. FEAST-based source tracking identified entry-pit fermented grains, Daqu, and air as primary contributors, accounting for 18.63% and 21.39% of nasal microbiota in Strong- and Sesame-flavor workers, respectively. ALDEx2 revealed six genera depleted in both exposed groups (FDR < 0.05): Caproiciproducens, Petrimonas, Proteiniphilum, Sporosarcina, Syntrophomonas, and an uncultured genus. No genera were significantly enriched in either exposed group. These findings indicate occupational exposure to Baijiu fermentation environments reduces the nasal carriage of several anaerobic taxa without altering overall alpha diversity.<br><br>IMPORTANCE: This study is the first to systematically compare how two major Baijiu fermentation environments-Strong-flavor and Sesame-flavor-affect the nasal microbiota of workers. By integrating environmental and nasal microbiome data, we show that entry pit grains, Daqu, and air are the main known sources of bacteria found in workers' noses. Occupational exposure in both production systems depletes several anaerobic genera, while overall microbial diversity remains unchanged. These findings connect microbial ecology with occupational health and support practical interventions: improving Daqu storage and ventilation, routine microbial surveillance, and preserving traditional fermentation practices without compromising safety. This work advances our understanding of human environment microbial exchange in traditional food systems with implications for global fermentation industries.}, }
@article {pmid42597171, year = {2026}, author = {Wang, T and Liang, H and Wu, Y and Zhang, X and Zhang, S and Wei, Z and Li, W and Song, W and Luo, Z and Al-Dalali, S}, title = {Multi-omics profiling of microbial ecology and non-volatile compounds across fermentation stages of spontaneous litchi (Litchi chinensis Sonn.) fermented vinegar-like beverage.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1908193}, pmid = {42597171}, issn = {2296-861X}, abstract = {INTRODUCTION: Litchi fruit vinegar-like beverages (LVBs) are notable processed products derived from litchi fruit, yet few studies have focused on the systematic characterization of microbial and metabolic dynamics during their natural fermentation process.<br><br>METHODS: This work employed a comprehensive methodology integrating metagenomics and untargeted metabolomics based on UHPLC-MS/MS (Orbitrap Q Exactive HF-X) to elucidate the dynamic profiles of the microbial community and non-volatile metabolites, as well as their interrelations, across the various spontaneous fermentation stages of LVBs.<br><br>RESULTS: Metagenomic analysis indicated reduced microbial diversity and substantial structural changes within the community. Bacteria dominated the fermentation, accounting for 69.16 - 99.04% of the microbial community based on the taxonomically classified reads at the kingdom level. During the preliminary stage, Leuconostoc, Enterobacter, and Klebsiella were the prevalent genera. During the mid-fermentation stage, Komagataeibacter and Lactiplantibacillus emerged as the predominant genera in acid production. In the final stage, the microbial community was dominated primarily by Zymomonas and the Acetobacteriaceae family, including Acetobacter and Komagataeibacter. The non-targeted metabolomics study identified 2,382 metabolites through comprehensive database matching (in-house library, HMDB, KEGG, and metDNA algorithm) and stringent quality filtering (identification score > 0.5 and QC CV < 0.5), which were categorized into 20 distinct groups. Thirty seven metabolites, including amino acids, organic acids, and benzene derivatives, were identified as probable distinct differential metabolites based on a p-value threshold of p <&#x202f;0.05, VIP > 1.0, and a fold change (FC &#x2265; 2 or &#x2264; 0.5) between consecutive fermentation stages in pairwise OPLS-DA of litchi vinegar-like beverage fermentation. Spearman correlation analysis revealed a highly organized ecological interaction network among dominant bacteria, physicochemical parameters, and non-volatile taste metabolites in the LVB fermentation system. Zymomonas mobilis, Acetobacter pasteurianus, Leuconostoc suionicum, and Lactiplantibacillus plantarum facilitated fermentation through metabolic synergy. Meanwhile, stage-specific enrichment of distinct Enterobacteriaceae species (Enterobacter hormaechei, and Enterobacter quasiroggenkampii) reflected species-level niche differentiation and resource competition, rather than a unified family-wide competitive behavior.<br><br>DISCUSSION: These findings provide a theoretical framework for engineering synthetic consortia and bioaugmentation approaches, informing the selection of starters and co-cultures to enhance LVB sensory and bioactive properties, alongside facilitating sfruit valorization.}, }
@article {pmid42589999, year = {2026}, author = {Alghoul, WI and Ashraf, R and Rafiuddin, S and Kharoufeh, AZH and Al-Shammari, WBJ and Abedi, M and Alabid, I and Patni, MM and Yousef, AJ and Hamdy, HA}, title = {The Urogenital Microbiome-Metabolic Interface in Postmenopausal Recurrent Urinary Tract Infection: Estrogen Deficiency, Diabetes, Obesity, and Microbial Reservoirs.}, journal = {Journal of clinical medicine}, volume = {15}, number = {15}, pages = {}, pmid = {42589999}, issn = {2077-0383}, abstract = {Background/Objectives: Recurrent urinary tract infection (rUTI) is common after menopause, but estrogen deficiency alone does not explain variation in recurrence, symptoms, and microbial profiles. This study aimed to synthesize evidence on the interactions among estrogen deficiency, urogenital microbial ecology, diabetes, obesity, microbial reservoirs, and anatomical, neurological, and functional modifiers of postmenopausal rUTI susceptibility. Methods: PubMed and Scopus were searched for original studies published from 1 January 2021 to 15 June 2026. A structured narrative synthesis included 62 original reports comprising clinical interventions, observational cohorts, microbiome and multi-omic studies, and cellular and animal experiments. Evidence was interpreted according to study design, population relevance, and biological directness. Results: Menopause was associated with reduced Lactobacillus dominance, higher vaginal pH, and altered vaginal or urinary communities, although findings were heterogeneous. Vaginal estrogen reduced recurrence and improved the local urogenital environment, but microbiome restoration is not established as its sole mechanism. Gut, rectal, vaginal, urinary, and bladder-wall reservoirs may contribute to persistence or repeated exposure. Diabetes was linked to dysbiosis and impaired urothelial defence, whereas obesity evidence remained less direct. Pelvic organ prolapse with incomplete emptying, elevated postvoid residual urine, age-related detrusor dysfunction, stroke, immobility, functional dependence, incontinence, and catheter exposure may further modify susceptibility. Conclusions: Postmenopausal rUTI is multifactorial. The urogenital microbiome-metabolic interface is a useful integrative framework, but not a validated causal or diagnostic model. Vaginal estrogen, urine culture, metabolic and bladder-function assessment, and antimicrobial stewardship remain the clinical foundation; microbiome-directed strategies require prospective validation.}, }
@article {pmid42593046, year = {2026}, author = {Barbi, F and Menzel, U and Simone, D and Niskanen, T and Lindahl, BD}, title = {Ectomycorrhizal Cortinariaceae species dominate class II peroxidase gene expression in a boreal forest soil.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.71506}, pmid = {42593046}, issn = {1469-8137}, support = {//Sveriges lantbruksuniversitet Uppsala (SLU)/ ; //Stiftelsen skogsvetenskaplig forskning/ ; }, abstract = {Boreal forest ecosystems constitute a large terrestrial reservoir of carbon. In these nitrogen-limited environments, release of nutrients through decomposition of soil organic matter is of fundamental importance. Fungi, particularly saprotrophic Agaricomycetes, are thought to drive this process using lignocellulolytic enzymes to degrade plant litter. However, some ectomycorrhizal fungal lineages have retained ancestral decomposition capabilities, yet evidence of their direct involvement in decomposition under field conditions is scarce. We used metatranscriptomics to examine the involvement of ectomycorrhizal fungi in the production of class II peroxidases in the soil of a Swedish boreal forest. We compared nutrient-poor plots with more fertile ones and related the peroxidase-expressing community to the total and cellulose-degrading fungal communities. We found that overall expression of class II peroxidase genes was upregulated in nutrient-poor soil, with ectomycorrhizal species in the Cortinariaceae family accounting for most of the transcripts. Among cellulose-degrading fungi, there was a shift from saprotrophic Agaricomycetes in nutrient-rich soil to dominance by Ascomycetes under nutrient-poor conditions. Symbiosis may enable ectomycorrhizal fungi to use tree photoassimilates to drive energetically costly oxidation belowground. Ectomycorrhiza-driven oxidation may, thereby, enable trees to indirectly regulate decomposition and nutrient cycling to maintain ecosystem productivity on unfertile soils.}, }
@article {pmid42585229, year = {2026}, author = {Fellows Yates, JA and Hübner, A and Borry, M and ,  and Warinner, C}, title = {De novo assembly and authentication of ancient DNA metagenomes with nf-core/mag.}, journal = {PLoS computational biology}, volume = {22}, number = {8}, pages = {e1014591}, pmid = {42585229}, issn = {1553-7358}, mesh = {*DNA, Ancient/analysis ; *Metagenomics/methods ; *Metagenome/genetics ; *Sequence Analysis, DNA/methods ; Computational Biology/methods ; Software ; Humans ; }, abstract = {Ancient DNA provides a direct window into the evolutionary processes that have shaped living microbial species today, as well as their now extinct relatives. Advances in both sequencing methods and de novo assembly techniques have not only resulted in a flood of modern metagenomic sequencing data, but they have also allowed palaeogenomicists to retrieve vast amounts of ancient DNA from past microorganisms, including species and strains without modern reference genomes. However, the degraded nature of ancient DNA means that the standard techniques of genome assembly developed for modern DNA are unlikely to perform effectively, unless heavily modified. This hinders the incorporation of ancient data into broader metagenomic studies that would otherwise benefit from having deep time information on the evolution of different microbial species. In this primer and protocol paper, we provide guidance on ways to adapt existing metagenomic de novo assembly processes, including data input, tools, and settings, in order to perform more robustly and effectively on ancient DNA. After assembly, we then further describe how ancient DNA contigs can be identified and validated. The key steps of ancient metagenomic assembly are now integrated in a dedicated ancient DNA mode in the established pipeline nf-core/mag. By introducing support for ancient DNA data in nf-core/mag, we aim to improve the ability of researchers to more regularly integrate de novo assembled ancient microbial data into broader metagenomics studies of microbial ecology and evolution.}, }
@article {pmid42586669, year = {2026}, author = {Luo, Z and Fang, Y and Qi, H and Peng, X and Zang, X and Yi, L and Zeng, J and He, L and Zeng, N}, title = {Natural polysaccharides modulate the microbiota-gut-brain axis through multiple targets: A new perspective on the pathogenesis and treatment of depression.}, journal = {Carbohydrate polymers}, volume = {389}, number = {}, pages = {125640}, doi = {10.1016/j.carbpol.2026.125640}, pmid = {42586669}, issn = {1879-1344}, mesh = {Humans ; Animals ; *Polysaccharides/pharmacology/chemistry/therapeutic use ; *Depression/drug therapy/metabolism/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Brain/drug effects/metabolism ; Blood-Brain Barrier/drug effects/metabolism ; }, abstract = {Depression is increasingly understood as a systemic disorder involving microbiota-gut-brain axis (MGBA) dysfunction rather than only central monoaminergic imbalance. Gut microbial dysbiosis, barrier disruption, immune inflammation, metabolic disturbance, oxidative stress, mitochondrial injury, and impaired neuroplasticity jointly drive depressive pathology. Natural polysaccharides offer a structurally diverse class of MGBA-oriented adjunctive candidates. Their effects are governed not simply by source or total sugar content, but by monosaccharide composition, glycosidic linkages, branching architecture, and molecular-weight distribution. These features determine microbial accessibility, fermentation kinetics, metabolite output, mucus and epithelial interactions, receptor recognition, and possible epithelial uptake, thereby defining distinct routes of MGBA regulation. Through these structure-dependent routes, natural polysaccharides may alleviate depression-related abnormalities by rebuilding gut microbial ecology, reprogramming short-chain fatty acids, tryptophan-derived indoles and bile acid metabolism, restoring intestinal and blood-brain barrier integrity, suppressing neuroimmune activation and oxidative injury, supporting mitochondrial homeostasis and promoting BDNF-TrkB-related neurogenesis and synaptic plasticity. This Review highlights structure-guided MGBA modulation and discusses translational challenges, including activity attribution, quality control, pharmacokinetics, and microbiome-dependent response variability for stratified, mechanism-guided adjunctive use.}, }
@article {pmid42587415, year = {2026}, author = {Peluso, E and van Uden, S and Visentin, S and Petrini, P and Pacheco, DP and Visai, L}, title = {Universal-Bac[3]Gel: A 3D Biofilm-Relevant Matrix That Supports In Vitro Growth and Biofilm Formation of ESKAPE Pathogens.}, journal = {MicrobiologyOpen}, volume = {15}, number = {4}, pages = {e70371}, pmid = {42587415}, issn = {2045-8827}, support = {190135075//HORIZON-EIC-2023-ACCELERATOROPEN-01/ ; //Italian Ministry of University and Research (MUR)/ ; }, mesh = {*Biofilms/growth &amp; development/drug effects ; Humans ; Anti-Bacterial Agents/pharmacology ; Microscopy, Confocal ; Staphylococcus aureus/growth &amp; development/drug effects ; }, abstract = {Human microbiota is increasingly considered to shape health and disease, drawing interest of pharma and biotech industries in advanced models of in vitro human microbiome to streamline drug development. In this context, Universal-Bac[3]Gel represents a new generation of 3D biomaterials designed to mimic the properties of human mucus and biofilm features, including micro-gradients that replicate the heterogeneous environments colonized by microorganisms in the human body. To evaluate the suitability of Universal-Bac[3]Gel for studying clinically relevant species in antimicrobial resistance, the so-called ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter cloacae) were cultured within this 3D environment. Bacterial growth was monitored at 24- and 48-h post-inoculation via spot plating, while viability, spatial distribution, and organization were assessed by confocal laser scanning microscopy. All ESKAPE strains successfully grew throughout the structure of Universal-Bac[3]Gel. Distinct 3D biofilm architectures were observed across species, ranging from diffuse colonization to compact microcolony formation, in agreement with species-specific biofilm patterns. Ciprofloxacin susceptibility assays revealed reduced susceptibility of bacteria cultured within Universal-Bac[3]Gel compared with their planktonic counterparts, supporting the development of biofilm-associated tolerance phenotypes. Consistent with these findings, crystal violet staining confirmed the accumulation of biofilm-associated biomass within the hydrogel. Notably, the platform's ready-to-use 96-well format allowed direct comparison of these high-priority pathogens under standardized conditions, highlighting species-specific biofilm traits that would be difficult to discern in conventional two-dimensional culture systems. This work highlights the versatility of Universal-Bac[3]Gel as a biofilm-relevant in vitro platform for studying pathogen colonization, biofilm development and antimicrobial susceptibility under controlled conditions.}, }
@article {pmid42588064, year = {2026}, author = {De Sales-Millan, A and Reyes-Ferreira, P and González-Cervantes, RM and Luna-Álvarez, M and Guillén-López, S and Cobo-Díaz, JF and Ramos, S and Aguirre-Garrido, JF and Velázquez-Aragón, JA}, title = {Clinical Improvement and Taxonomic-Functional Gut Microbiome Remodeling After Six Months of Multi-Strain Synbiotic Supplementation in Mexican Children with Autism Spectrum Disorder.}, journal = {Nutrients}, volume = {18}, number = {15}, pages = {}, pmid = {42588064}, issn = {2072-6643}, support = {E022 Program Recursos Fiscales para la Investigaci&#xf3;n//Instituto Nacional de Pediatria/ ; }, mesh = {Humans ; *Autism Spectrum Disorder/microbiology/therapy ; Male ; *Gastrointestinal Microbiome/genetics ; Female ; Mexico ; Longitudinal Studies ; *Synbiotics/administration &amp; dosage ; Child ; Feces/microbiology ; Child, Preschool ; Probiotics/administration &amp; dosage ; Dietary Supplements ; Treatment Outcome ; RNA, Ribosomal, 16S/genetics ; Dysbiosis/microbiology ; }, abstract = {Background/Objectives: Gut dysbiosis in children with autism spectrum disorder (ASD) has been associated with alterations in microbial ecology and metabolic function that may contribute to gastrointestinal dysfunction and the severity of clinical manifestations. Synbiotic and probiotic supplementation has emerged as a promising microbiome-targeted strategy for ASD; however, its effects on gut microbiome composition, functional potential, and clinical outcomes remain incompletely understood. We conducted a longitudinal study of Mexican children diagnosed with ASD to analyze changes in the composition, diversity, and functional potential of the gut microbiome during six months of multi-strain synbiotic supplementation. Methods: Stool samples were collected from 25 children with ASD at baseline and after 3 and 6 months of multi-strain synbiotic supplementation. Gut microbiome composition and diversity were analyzed by 16S rRNA gene sequencing, whereas whole metagenome sequencing (WMS) was performed in a subset of samples to evaluate the functional potential of the fecal microbiome. Gastrointestinal symptoms were assessed using the Rome IV criteria, and ASD severity was evaluated with the Childhood Autism Rating Scale (CARS). Results: Twenty-five children with ASD completed the 6 months of synbiotic supplementation. Overall, ASD severity decreased, reflected by a reduction in total CARS score, and improvements in several CARS domains. Gastrointestinal symptoms also decreased significantly. Longitudinal microbiome profiling revealed significant taxonomic and diversity changes over the supplementation period, while WMS identified changes in microbial metabolic potential, including enrichment of tryptophan biosynthesis pathways and reduced L-rhamnose degradation. Conclusions: This exploratory research provides proof-of-concept evidence supporting multi-strain synbiotic supplementation in children with ASD. Larger controlled studies are needed to confirm these findings and clarify their relevance to microbiota-gut-brain axis interactions. The observed concordance between clinical improvements and microbiome remodeling supports further investigation of microbiome-targeted interventions according to ASD severity and duration of supplementation.}, }
@article {pmid42588172, year = {2026}, author = {Wu, Y and Zhao, Y and Yao, W and Yang, Y and Bai, H and Bao, S and Li, X and Song, Y}, title = {Gut-Liver Axis Dysfunction in Alcohol-Associated Liver Disease and the Potential Role of Sheep Yogurt: A Scoping Review and Mechanistic Framework.}, journal = {Nutrients}, volume = {18}, number = {15}, pages = {}, pmid = {42588172}, issn = {2072-6643}, support = {2026KJTW0005//Inner Mongolia Autonomous Region's "Tech Breakout" Initiative: "Open Call for Technical Champions"/ ; No.10000-A22103030//2022 Inner Mongolia University "Steed Plan" high-level talent funding/ ; 2022YFD1302202//the National Key Research and Development Program of China/ ; }, mesh = {Animals ; *Yogurt/microbiology ; *Liver Diseases, Alcoholic/physiopathology/microbiology ; Sheep ; *Liver/physiopathology ; Humans ; Intestinal Barrier Function ; Gastrointestinal Microbiome ; }, abstract = {Background/Objectives: Alcohol-associated liver disease (ALD) is driven by gut-liver axis dysfunction, including intestinal barrier disruption, dysbiosis, microbial translocation, inflammation, metabolic dysfunction, and malnutrition. Fermented dairy foods may modulate several of these domains, yet whether sheep yogurt, as an intact fermented dairy matrix, is relevant in ALD is unknown. This scoping review mapped evidence relevant to sheep yogurt, ALD, and gut-liver axis biology. Methods: A PRISMA-ScR-guided scoping review searched PubMed/MEDLINE, Web of Science, Scopus, and Google Scholar from January 2006 to February 2026. Eligible sources were charted using a prespecified framework classifying evidence as direct, indirect, or mechanistic inference. Mapped domains included ALD pathophysiology; intestinal barrier integrity; bacterial and fungal microbial ecology; bile acid and tryptophan-aryl hydrocarbon receptor signaling; nutritional vulnerability; fermented dairy interventions; and ovine dairy-matrix characteristics. Results: Of 1388 records identified, 121 sources were included after duplication and screening. No eligible study directly tested sheep yogurt or a defined sheep yogurt preparation in ALD-relevant experimental or clinical settings. Indirect evidence supported the relevance of gut-liver axis dysfunction to ALD and indicated that selected fermented dairy products, probiotics, postbiotics, and microbial preparations may influence intestinal permeability, inflammatory signaling, microbial ecology, oxidative stress, and liver-injury outcomes. Compositional data supported sheep yogurt as a distinct food matrix. However, findings from isolated components, probiotic-only interventions, and non-ALD models could not be interpreted as evidence of sheep yogurt efficacy in ALD. Conclusions: The current literature supports a hypothesis-driven research framework rather than any therapeutic claim for sheep yogurt in ALD. Any potential benefit of sheep yogurt in ALD remains hypothetical and cannot support clinical or dietary recommendations until validated experimentally. Future direct, comparator-controlled studies of intact sheep yogurt should assess liver injury, barrier integrity, microbial translocation, relevant metabolites, and nutrition-related outcomes.}, }
@article {pmid42589861, year = {2026}, author = {Butera, A and Maiorani, C and Scribante, A and Rodriguez Y Baena, R and Cucinella, L and Parrotta, GE and Nappi, RE}, title = {Oral Health Across the Menopausal Transition: Biological Pathways, Clinical Implications, and Future Perspectives.}, journal = {Journal of clinical medicine}, volume = {15}, number = {15}, pages = {}, pmid = {42589861}, issn = {2077-0383}, abstract = {Background/Objectives: Menopause is a complex physiological transition characterized by progressive estrogen deficiency and systemic biological changes that can affect multiple organs and tissues, including the oral cavity. Growing evidence suggests that hormonal fluctuations during the menopausal transition may influence periodontal health, salivary function, oral sensory perception, and overall oral health-related quality of life. Objective: This narrative review aims to provide a comprehensive overview of the biological mechanisms and clinical manifestations associated with the relationship between menopause and oral health, with particular attention to periodontal outcomes, salivary changes, oral discomfort, dental status, and the potential role of hormone replacement therapy (HRT). Methods: This narrative review was based on a structured literature search conducted in PubMed/MEDLINE and Scopus to identify studies published between January 2005 and May 2026. Predefined eligibility criteria were applied to identify relevant human studies. The retrieved evidence was synthesized narratively according to major oral health domains and menopausal phenotypes. Results: Fifty studies met the inclusion criteria. Overall, menopause was associated with poorer periodontal parameters, including increased probing depth, clinical attachment loss, and periodontal inflammation. Reduced salivary flow, dry mouth, altered salivary composition, burning symptoms, and taste disturbances were frequently reported in peri- and postmenopausal women. A higher prevalence of caries and tooth loss was also reported, although the contribution of age and other confounding factors varied across studies. New evidence suggests that estrogen deficiency may influence oral health through interconnected pathways involving immune regulation, bone metabolism, salivary gland function, and host-microbiome interactions. Evidence regarding the effects of HRT has been mixed, although several studies have reported improvements in salivary function and periodontal outcomes among treated women. Conclusions: Menopause appears to act as an important systemic modifier of oral health through multifactorial biological mechanisms. Menopause-associated oral manifestations go beyond local tissue changes and reflect broader interactions between hormonal status, inflammation, bone metabolism, and microbial ecology. Increased awareness among dental and medical professionals and a multidisciplinary approach could improve the prevention, diagnosis, and management of oral diseases in postmenopausal women. Further, well-designed longitudinal studies are needed to clarify causal relationships and identify effective therapeutic strategies.}, }
@article {pmid42576889, year = {2026}, author = {O'Doherty, KC and Beijbom, M and Allen-Vercoe, E and Choudoir, MJ and Silva, DS and Bonilla, C and Debelius, J and Elton, S and Hauptmann, AL and Heyland, A and Morar, N and Skillings, D and Sun, Z and Wolf, PG and Beiko, RG and Ishaq, SL}, title = {Microbiome stewardship: definition and guiding principles for implementation.}, journal = {Sustainable microbiology}, volume = {3}, number = {3}, pages = {qvag028}, pmid = {42576889}, issn = {2755-1970}, abstract = {Microbiomes are essential for ecosystem, plant, animal, and human health. There is accumulating evidence that changes to microbiomes from anthropogenic activities are associated with adverse health outcomes. Despite this evidence and calls for action, almost no oversight mechanisms exist to protect microbiomes or their key functions, in part due to uncertainty about what to protect, and how. We have previously proposed microbiome stewardship as a foundational concept that can act across policy domains to facilitate the ongoing presence of key microbial communities and their functions. The purpose of this article is to provide a working definition of microbiome stewardship and develop guiding principles to support its implementation. The concept of microbiome stewardship is relevant to a wide range of policy domains, such as public health, clinical care, environmental protection, food production, and agriculture. Nonetheless, the implementation of microbiome stewardship will be highly specific, as it needs to be guided by considerations of microbial habitat, objectives of stewardship, and available opportunities for intervention. Accordingly, aligning stewardship responsibility with specific institutions and governance mechanisms will be context-dependent. We conclude with a discussion that situates microbiome stewardship relative to other initiatives.}, }
@article {pmid42576913, year = {2024}, author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA}, title = {Microbial solutions must be deployed against climate catastrophe.}, journal = {Sustainable microbiology}, volume = {1}, number = {1}, pages = {qvae029}, pmid = {42576913}, issn = {2755-1970}, }
@article {pmid42576914, year = {2024}, author = {Beattie, GA and Cotrufo, FM and Crowther, TW and Edlund, A and Salles, JF and Gilbert, JA and Jansson, JK and Jensen, PR and Lennon, JT and Makhalanyane, T and Martiny, JBH and Newman, DK and Stevenson, M}, title = {Soil microbial strategies for climate mitigation-report from a climate action workshop in Las Vegas, Nevada, February 2024.}, journal = {Sustainable microbiology}, volume = {1}, number = {1}, pages = {qvae033}, pmid = {42576914}, issn = {2755-1970}, abstract = {Life on Earth faces an existential crisis due to the enduring repercussions of unsustainable human activities since the beginning of the Industrial Revolution. Among the most pressing issues are greenhouse gas emissions, primarily from fossil fuel combustion, unsustainable agricultural practices, as well as the global erosion of the world's topsoil. While agrochemicals have temporarily increased land productivity, their frequent use has adversely impacted the environment and microbial biodiversity. With half of the global soils already degraded by erosion and a projected 90% at risk by 2050, humanity faces a critical crisis that threatens food production, soil carbon storage, and availability of clean water. In this precarious scenario, microbes and plants may provide promising allies for sustaining life on Earth. Thus, it is crucial for policymakers, scientists, NGOs, and the public to recognize the fundamental importance of the soil microbiome. In February 2024, the workshop "Soil Microbial Strategies for Climate Mitigation" gathered world-leading experts from the most relevant research fields, as well as industry innovators, communicators, artists, and policymakers, to propose soil microbiome-based interventions aimed at enhancing carbon dioxide (CO2) drawdown and mitigating soil erosion. The workshop focused on innovative soil microbial inoculant approaches, examining methodologies for measuring soil carbon, enhancing plant health and soil structure, proposing an action plan, and forming collaborative strategies.}, }
@article {pmid42576937, year = {2025}, author = {Prescott, SL and Logan, AC and Robinson, JM}, title = {Legalomics: why microbiology matters to the promotion of just societies.}, journal = {Sustainable microbiology}, volume = {2}, number = {4}, pages = {qvaf027}, pmid = {42576937}, issn = {2755-1970}, abstract = {Despite profound socioeconomic and ecological consequences, criminal justice remains an overlooked dimension of sustainability. Sustainable Development Goal (SDG) 16 calls for promoting inclusive societies and ensuring justice for all. Yet the SDG 16 framework largely ignores the biological and structural determinants of behavior related to justice involvement. This perspective article argues that microbial ecology plays a foundational role in cognition and behavior-factors central to justice outcomes. Advances in neuromicrobiology and omics technologies show how microbial disruptions linked to poverty and environmental factors may increase behavioral risks and reinforce inequality. We introduce the legalome concept-the systemic application of microbiome sciences and related omics technologies to forensic and legal psychology. From auto-brewery syndrome to microbial signatures tied to aggression, impulsivity, and neuropsychiatric conditions, evidence is mounting that microbiota-brain interactions have forensic relevance. Yet justice systems often remain rooted in prescientific notions of free will and blame. Carceral institutions often exacerbate dysbiosis through poor nutrition, social isolation, circadian disruptions, acoustic stress, and overall deprivation-further entrenching risk and undermining rehabilitation. We argue that SDG 16 should expand to reflect this evolving science. Integrating microbial ecology into justice reform offers a framework for prevention and healing-bridging sustainability, equity, and dignity.}, }
@article {pmid42577533, year = {2026}, author = {Dlakić, M and Inskeep, WP}, title = {Improved prediction of microbial optimal growth temperatures with neural networks and protein language models.}, journal = {Frontiers in genetics}, volume = {17}, number = {}, pages = {1874451}, pmid = {42577533}, issn = {1664-8021}, abstract = {INTRODUCTION: Temperature is one of the strongest selective forces that determines the composition of microorganisms in the environment. Structural properties of proteins shape the thermal adaptation of an organism at the macro level, and aggregate protein features can be used for many types of predictions. Because most microorganisms remain uncultured, the inference of physiological traits, such as optimal growth temperature, has become essential for microbial ecology and biotechnology.<br><br>METHODS: A large dataset of optimal growth temperatures for microorganisms was compiled from the literature and used to train several machine learning predictors. Our goal was also to test the usefulness of protein language models and to evaluate predictive performance on incomplete genomes.<br><br>RESULTS: We confirmed a strong correlation between protein sequence properties and optimal growth temperatures. The analysis showed that calculating better protein sequence features, specifically through protein language models, leads to more accurate predictions.<br><br>DISCUSSION: We used state-of-the-art tools and compared our models with several others developed for optimal growth temperature prediction over the past 2&#xa0;decades. Our models showed excellent ability to generalize across a range of temperatures. We concluded that larger datasets and increased representation of psychrophiles and thermophiles will be needed to continue improving the predictors.}, }
@article {pmid42580912, year = {2026}, author = {Buret, AG and Allain, T}, title = {The Giardia secretome disrupts gut microbiota biofilms.}, journal = {Trends in parasitology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pt.2026.07.011}, pmid = {42580912}, issn = {1471-5007}, abstract = {This review provides a state-of-the-art update on Giardia intestinalis pathogenesis and its immunomodulatory effects during enteric coinfections. We examine mechanisms underlying abnormalities in mucus structure and glycosylation, alongside parasite-induced alterations in host immunity. Recent evidence reveals a protective role for gut microbiota biofilms and demonstrates how the Giardia secretome disrupts these communities. In particular, trophozoite-derived cysteine proteases and extracellular vesicles, along with their small RNA cargo, remodel microbiota biofilms and drive the conversion of commensal bacteria into invasive pathobionts. Collectively, these findings establish Giardia as a central regulator of gut microbial ecology and intestinal barrier function, highlighting its value as a model for developing novel therapeutic strategies against enteric disease.}, }
@article {pmid42573249, year = {2026}, author = {Hansen, SC and Hamm, CW and Singer, JR and Weaver, CT and Gray, MJ}, title = {Ecology of protection: probiotic biogeography and sepsis prevention in the neonatal intestine.}, journal = {mBio}, volume = {}, number = {}, pages = {e0112726}, doi = {10.1128/mbio.01127-26}, pmid = {42573249}, issn = {2150-7511}, abstract = {Neonatal infection is a leading cause of morbidity and mortality worldwide, particularly among preterm and low birth weight infants. Probiotic bacteria are widely used in peri- and postnatal care and can reduce neonatal intestinal dysbiosis. However, formulations and efficacy remain highly variable, highlighting a critical gap in our understanding of the mechanisms that drive successful interventions in this population. Furthermore, current studies on probiotic efficacy rely on indirect or relative measures of intestinal bacterial burden. Here, we directly mapped the biogeography of intestinal colonization and quantified the probiotic effects of Escherichia coli Nissle 1917 (EcN) and Ligilactobacillus murinus strain V10 against Klebsiella pneumoniae dysbiosis across the neonatal murine intestine. Despite substantial differences in their spatial distribution along the intestine, both EcN and L. murinus V10 significantly reduced K. pneumoniae colonization and mortality from K. pneumoniae sepsis, with EcN providing greater protection. EcN's probiotic activity was partially dependent on high-affinity oxygen respiration, implicating luminal oxygen availability as a key ecological determinant of probiotic efficacy. Contrary to the common assumption that multi-strain probiotics are inherently superior, simultaneous administration of EcN and L. murinus V10 was less effective than EcN treatment alone at preventing sepsis-related death. These findings identify intestinal niche occupancy, oxygen utilization, and strain-strain interactions as critical variables which should inform the rational design of future probiotic interventions for high-risk neonates.IMPORTANCELate-onset sepsis (LOS) remains a devastating and difficult-to-treat complication of prematurity, and probiotics are increasingly used to reduce dysbiosis and infection risk in this vulnerable population. Probiotic regimens, however, are highly heterogeneous, and their mechanisms of action in the neonatal intestine are poorly defined, complicating efforts to design safe, effective, and regulatable interventions. In this work, we use a neonatal mouse model of LOS to rigorously test fundamental assumptions underlying the current paradigm for understanding the impact of probiotics on intestinal disease. We demonstrate that two distantly related probiotic bacteria, Escherichia coli Nissle 1917 and Ligilactobacillus murinus V10, each reduce intestinal colonization and mortality caused by the LOS pathobiont Klebsiella pneumoniae, but do so through distinct ecological and molecular mechanisms. These findings highlight ecological principles, including spatial niche occupancy, resource competition, and strain-strain interactions, as critical determinants of probiotic efficacy, and provide mechanistic insight that will be important for guiding rational probiotic strategies for high-risk neonates.}, }
@article {pmid42573621, year = {2026}, author = {Tang, J and Zhang, S and Xu, G and Cui, M and Ge, X and Gao, H and Zhang, F}, title = {Enterococcus in herbal fermentation: a genus-specific perspective on enzymatic capability, biotransformation outcomes and safety.}, journal = {Archives of microbiology}, volume = {208}, number = {11}, pages = {}, pmid = {42573621}, issn = {1432-072X}, support = {Grant No. 2025YFC3509000//National Key Research and Development Program of China/ ; }, mesh = {Biotransformation ; *Fermentation ; *Enterococcus/enzymology/metabolism/genetics/classification ; *Plants, Medicinal/microbiology/metabolism ; }, abstract = {Although Enterococcus species are consistently detected in traditional herbal fermentations, their functional contributions to medicinal plant biotransformation remain poorly characterised at the genus level. This review provides the first genus-specific synthesis of Enterococcus in medicinal and food-medicinal plant fermentation, integrating evidence across historical fermentation systems, microbial ecology, enzymatic capability, phytochemical transformation, and safety assessment. Enterococcus species frequently occupy an early-to-middle ecological niche in fermented herbal matrices, sustained by exceptional tolerance to acidic, saline, and polyphenol-rich conditions. This ecological fitness is coupled to a functionally diverse enzymatic repertoire-encompassing β-glucosidases, α-rhamnosidases, ferulic acid esterases, tannases, bile salt hydrolases, and phenolic acid decarboxylases-capable of targeting the major glycosidic, ester, amide, and carboxylate linkages present in plant secondary metabolite conjugates. Documented biotransformations include ginsenoside Rb1-to-F2 conversion, sequential flavonoid diglycoside hydrolysis, ellagic acid-to-urolithin A transformation, gallotannin degradation, and oxalate catabolism-reactions that collectively parallel key TCMs processing objectives of bioavailability enhancement, pharmacological activation, and toxicity reduction. Safety challenges, particularly the concentration of virulence factors and transferable antibiotic resistance in E. faecalis and E. faecium, are critically evaluated. Mitigation strategies-including whole-genome-based strain screening, heat-inactivated postbiotic preparations, and recombinant enzyme platforms-are discussed as viable pathways toward controlled, safety-validated medicinal applications. The evidence supports a fundamental reappraisal of Enterococcus as a mechanistically distinctive contributor to herbal fermentation. Future progress will require strain-resolved functional characterisation, multi-omics-guided analysis, and safety-validated bioprocess design. This review is intended for researchers in fermentation microbiology, natural-product biotransformation, and the modernisation of traditional medicine, as well as for those engaged in the safety evaluation of fermentation-associated bacteria.}, }
@article {pmid42573712, year = {2026}, author = {Guo, Y and Wang, B and Ren, C and Xin, S and Gao, H and Liu, X and Hua, R and Wang, H and Zhao, J and Wang, Y and Shi, W and Lu, X and Gao, L and Li, S and Xu, J}, title = {Bidirectional influences and clinical implications of psychological factors and oral health during orthodontic treatment.}, journal = {The Saudi dental journal}, volume = {38}, number = {8}, pages = {}, pmid = {42573712}, issn = {1013-9052}, abstract = {INTRODUCTION: Psychological factors such as anxiety and stress frequently affect orthodontic treatment outcomes, but the underlying mechanisms remain unclear. To review evidence on how psychological factors influence orthodontic outcomes and to describe the biological pathways involved.<br><br>METHODS: We conducted a narrative review of Web of Science and PubMed up to January 2025, including 102 peer-reviewed studies on orthodontics, psychology, oral microbiota, taste, and inflammatory markers.<br><br>RESULTS: Psychological factors affect orthodontic treatment through three pathways: First, nervous system activation (HPA axis and autonomic nervous system); Second, alterations in oral microbiota and salivary biomarkers (cortisol, &#x3b1;-amylase, s-IgA), and third, modulation of alveolar bone remodeling via pro-inflammatory cytokines (IL-1&#x3b2;, IL-6, IL-8). Taste changes under stress may indirectly alter dietary habits and oral microbial ecology. Most evidence is cross-sectional, limiting causal inference.<br><br>CONCLUSION: Psychological factors significantly influence orthodontic outcomes via measurable biological mechanisms. Routine psychological assessment and patient education should be integrated into orthodontic practice.}, }
@article {pmid42573928, year = {2026}, author = {Sheiber, J and Duque, A and Ranjan, A and Diokno, AC and Swana, H}, title = {Characterizing the role of the urobiome in the pathogenesis of recurrent urinary tract infections (rUTIs): a systematic review.}, journal = {International urology and nephrology}, volume = {}, number = {}, pages = {}, pmid = {42573928}, issn = {1573-2584}, abstract = {PURPOSE: Recurrent urinary tract infections (rUTIs) are associated with substantial morbidity, repeated antibiotic exposure, and increasing antimicrobial resistance. Emerging evidence suggests that alterations in the urinary microbiome (urobiome) may contribute to rUTI pathogenesis. This systematic review evaluated the role of the urobiome in the development and recurrence of rUTIs.<br><br>METHODS: This systematic review was conducted in accordance with the PRISMA 2020 guidelines. Literature searches were conducted and managed using Covidence systematic review software (Veritas Health Innovation, Melbourne, Australia). Searches included Web of Science, MEDLINE, PubMed, and CINAHL and covered studies published from 2014 through 2026. The final search was conducted on February 1, 2026. The search incorporated terms related to 'urobiome,' 'urinary microbiome,' 'urinary tract infection,' and 'recurrent urinary tract infection.' Searches were restricted to English-language studies and human participants. After deduplication, 213 unique records underwent title and abstract screening, and 62 articles were assessed in full text. 21 studies that directly evaluated recurrent or chronic UTI populations, or reported an rUTI-specific subgroup, were included in the qualitative synthesis. Data extraction included study design, patient population characteristics, definitions of rUTI, urine collection methods, microbiome assessment methodology (including 16S rRNA sequencing and enhanced quantitative urine culture), reported microbial diversity measures, taxonomic findings, and associations between microbiome characteristics and rUTI outcomes. Given heterogeneity in study design, sequencing platforms, urine collection techniques, and definitions of rUTI across studies, a quantitative meta-analysis was not performed. Findings were synthesized descriptively, with emphasis on recurring microbial patterns, diversity measures, and clinically relevant urobiome alterations associated with recurrent infection.<br><br>RESULTS: 21 studies met inclusion criteria. Recurrent urinary tract infection was associated with altered urinary microbial ecology although the direction of diversity changes varied across studies. Commonly reported differences included altered Lactobacillus abundance and enrichment of taxa, such as Gardnerella, Prevotella, and Enterobacterales. Mechanistic studies implicated intracellular bacterial persistence, biofilm formation, ecological shifts, and metabolite-microbiome interactions. Hormonal status and antibiotic exposure also influenced urobiome composition. Substantial methodological heterogeneity remained across studies.<br><br>CONCLUSION: Current evidence supports a potential role for the urobiome in rUTI pathogenesis. Altered microbial diversity, loss of protective organisms, and persistent bacterial reservoirs may contribute to recurrence. Further standardized longitudinal and mechanistic studies are needed to clarify causality and guide microbiome-targeted therapeutic strategies.}, }
@article {pmid42574048, year = {2026}, author = {Dey, R and Beach, R and Hambrick, KM and Sgouralis, I and Frémont, P and Demory, D and Carr, E and Beckett, SJ and Weitz, JS and Talmy, D}, title = {Microbial Primer: Bayesian learning of traits from microbial time series data.}, journal = {Microbiology (Reading, England)}, volume = {172}, number = {8}, pages = {}, pmid = {42574048}, issn = {1465-2080}, mesh = {Bayes Theorem ; Ecosystem ; Markov Chains ; *Models, Biological ; Population Dynamics ; *Haptophyta/physiology ; }, abstract = {Mathematical models are increasingly used to infer traits, interactions and functional dynamics of microbial systems. One common example is a rate-based ordinary differential equation model parameterized with microbial traits. However, fitting such models with associated parameters to data requires a principled approach to extract information from time series while accounting for prior knowledge and measurement noise. These principles often remain implicit and not necessarily well defined. Here, we make the implicit, explicit: introducing Bayesian inference of ecological models for microbial time series, including three detailed case studies of algal population dynamics that follow a birth-death process. Complementing this primer, we provide an online tutorial on Bayesian inverse modelling with cross-programming language support via Python (PyMC) and Julia (Turing). By connecting theory, code, data and a series of hands-on educational modules, this primer aims to bring the utility of Bayesian learning to the broader microbial ecology research community.}, }
@article {pmid42575094, year = {2026}, author = {Zhai, J and Li, Y and Liu, J and Su, X and Cui, R and Zheng, D and Sun, Y and Yu, J and Dai, C}, title = {Global gut microbiome atlas identifies epidemiologic-stage-specific signatures in inflammatory bowel disease.}, journal = {Cell reports. Medicine}, volume = {}, number = {}, pages = {102974}, doi = {10.1016/j.xcrm.2026.102974}, pmid = {42575094}, issn = {2666-3791}, abstract = {The global rise of inflammatory bowel disease (IBD) reflects environmental shifts, yet how these changes are embedded in the gut microbial ecology remains unclear. We construct a microbiome atlas comprising 245,627 profiles. By classifying countries into three epidemiologic stages, we establish a framework. As the IBD burden increases, the gut microbial alpha diversity declines, and community structures form distinct clusters. This transition is characterized by a gradient of core genera. Integrating six shotgun metagenomic cohorts, we identify the depletion of anabolic pathways in IBD patients. Strain-level analysis reveals that epidemiologic staging shapes genetic architecture within species, identifying an IBD-enriched subclade of Eisenbergiella associated with elevated fecal cholic acid. We develop a microbial inflammatory risk score (MIRS), based on 19 genera, that discriminates IBD from controls (area under the curve [AUC] = 0.92). MIRS correlates with IBD prevalence. Our study provides an atlas linking epidemiology to microbiome ecology and strain evolution, offering a foundation for population-level surveillance and interventions in IBD.}, }
@article {pmid42576567, year = {2026}, author = {Hernández, SR and Bueno-Camilo, FG and Olivares Ponce, PN and Palma-Vázquez, JR and Soimu, G and Maldonado-Álvarez, MA and Baasch, A and Brisson-Suárez, K and Roldán, LA and Vilas-Navós, B and Oyarzabal-Eula, S and Rendón, J and Martin, G and Campello, AF and Alves, FRF and Rôças, IN and Siqueira, JF}, title = {Prevalence of Apical Periodontitis in Eight Hispanic American Countries.}, journal = {International endodontic journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/iej.70254}, pmid = {42576567}, issn = {1365-2591}, abstract = {AIM: This multicenter cross-sectional study evaluated the prevalence and variables statistically associated with primary and post-treatment apical periodontitis (AP) in subjects from eight Hispanic American countries.<br><br>METHODOLOGY: Digital panoramic radiographs from subjects living in Argentina, Colombia, Ecuador, Guatemala, Mexico, Dominican Republic, Uruguay and Venezuela were analyzed. Teeth were evaluated for diverse factors, including the periapical status and presence of root canal treatment, caries, coronal restoration, intraradicular post, root resorption and periodontal involvement. Quality of root canal treatment and coronal restorations was also recorded. Associations between these diverse variables and AP were evaluated using chi-square tests and multivariable mixed-effects logistic regression with a random intercept for patient to account for within-patient clustering of teeth.<br><br>RESULTS: Overall, 11&#x2009;850 subjects (294&#x2009;662 teeth) were included; 51.5% of the subjects and 5.5% of the examined teeth had AP. Ecuador (62%) and Argentina (61%) had the highest AP prevalence per subject, whereas Mexico had the lowest (37%). Intermediate values were observed in Venezuela (57%), Guatemala (57%), Colombia (47%), Dominican Republic (46%) and Uruguay (45%). In general, 43% of the subjects had at least one root canal-treated tooth. Primary and post-treatment AP were observed in 3% and 42% of the teeth, respectively. Of the teeth with primary AP, 51% showed coronal restorations, and 32% had caries. Post-treatment AP was significantly associated with inadequate root canal fillings, inadequate coronal restorations and inadequate intraradicular posts (p&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: The prevalence of AP in the Hispanic American countries evaluated was high, affecting nearly half of the population. Post-treatment AP was highly prevalent and predominantly linked to inadequate root canal fillings, deficient or absent coronal restorations and intraradicular posts. These findings emphasize the importance of strengthening caries prevention strategies and improving the quality of endodontic and restorative care to reduce the burden of apical periodontitis in these regions.}, }
@article {pmid42576817, year = {2024}, author = {Kunselman, E and Manrique, D and Burge, CA and Allard, S and Daniel, Z and Mitta, G and Petton, B and Gilbert, JA}, title = {Temperature and microbe mediated impacts of the San Diego Bay ostreid herpesvirus (OsHV-1) microvariant on juvenile Pacific oysters.}, journal = {Sustainable microbiology}, volume = {1}, number = {1}, pages = {qvae014}, pmid = {42576817}, issn = {2755-1970}, abstract = {The ostreid herpesvirus (OsHV-1) was recently detected in San Diego Bay for the first time in farmed juvenile Pacific oysters (Crassostrea gigas). Due to the virus' ability to cause mass mortality (50%-100%), it is important to determine the factors that promote infection as well as the consequences of infection. Here, we assess the role of temperature in controlling OsHV-1 induced mortality. Pacific oysters were exposed to the San Diego Bay microvariant of OsHV-1 at four different temperatures (15°C, 18°C, 21°C, and 24°C). While OsHV-1 was able to replicate in oyster tissues at all temperatures, it did not induce mortality at 15°C, only at the higher temperatures. Additionally, we examined oyster tissue-associated bacterial response to OsHV-1 infection. As shown previously, bacterial richness increased following OsHV-1 exposure and then decreased as the oysters became sick and died. Four bacterial taxa linked to the San Diego Bay microvariant infection, including Arcobacter, Vibrio, Amphritea, and Pseudoalteromonas, were the same as those shown for other microvariant infections in other studies from globally distributed oysters, suggesting a similar spectrum of co-infection irrespective of geography and microvariant type. The significant shift in the bacterial community following exposure suggests a weakening of the host defenses as a result of OsHV-1 infection, which potentially leads to adverse opportunistic bacterial infection.}, }
@article {pmid42576819, year = {2025}, author = {Williams, A and Lynch, J}, title = {Bridging research gaps and advancing policy for healthy soils.}, journal = {Sustainable microbiology}, volume = {2}, number = {3}, pages = {qvaf017}, pmid = {42576819}, issn = {2755-1970}, abstract = {The policy framework previously presented by Neale and colleagues in Sustainable Microbiology highlights the central role of soil microorganisms in sustainable agriculture and global food security, offering actionable interventions grounded in emerging scientific advances. However, the translation of soil science and ecology into impactful policy and practice remains limited. This opinion article revisits the longstanding concept of soil biotechnology, and regulatory/societal barriers to progress. We emphasize that the soil microbiome holds untapped potential for improving plant health, reducing agrochemical reliance, and promoting sustainable food systems through continued research. Interkingdom microbial interactions, especially those involving root exudation as a mechanism for microbial recruitment, are proposed as pivotal but underexplored areas of study. Phenotype-driven, trait-based approaches are advocated over traditional phylogenetic methods to better identify functionally relevant microbial consortia and intervention strategies. Furthermore, we stress the need to integrate ecological, agronomic, and economic insights to develop soil-centric food systems. This includes monetizing ecosystem services provided by healthy soils and implementing incentivized conservation schemes. Unlocking the potential of soil microbial ecology requires coordinated, interdisciplinary efforts and a paradigm shift in policy, funding, and public perception.}, }
@article {pmid42576821, year = {2026}, author = {Faggionato, D and Muñoz-García, M and Kostic, T and Ferrari, ML and Vonaesch, P and Poyet, M and Portier, P and Ryan, MJ and Djeddour, D and Stumptner, C and Varese, GC and Zuzuarregui, A and Groussin, M and Schloter, M and Finn, RD and Haas, AS and Probert, I and Verkley, G and Overmann, J and Scholz, AH}, title = {Policy Briefing: from access to use-untangling the international legal frameworks that govern microbial resources.}, journal = {Sustainable microbiology}, volume = {3}, number = {1}, pages = {qvag005}, pmid = {42576821}, issn = {2755-1970}, abstract = {The wide geographic distribution of microorganisms, combined with their vast taxonomic and functional diversity, make them indispensable reservoirs of genetic variation that sustain ecosystem resilience and fuel biotechnological innovation. However, to use this diversity, microbiologists must navigate a complex legal and regulatory landscape governed by multiple United Nations treaties and their respective access and benefit-sharing frameworks as well as regulatory frameworks specific to particular ecosystems, biosecurity, pathogens, and intellectual property. This complex regulatory web is also actively growing and changing, which makes it immensely challenging for a "regular" microbiologist to navigate. For policymakers and negotiators, it is also difficult to appreciate the full complexity that practitioners experience. This policy briefing provides a concise regulatory guide for practitioners and policymakers alike, summarized in a graphical overview, to provide more clarity and understanding for those at the edge of decision-making and practice.}, }
@article {pmid42576822, year = {2026}, author = {Faggionato, D and Muñoz-García, M and Kostic, T and Ferrari, ML and Vonaesch, P and Poyet, M and Portier, P and Ryan, MJ and Djeddour, D and Stumptner, C and Varese, GC and Zuzuarregui, A and Groussin, M and Schloter, M and Finn, RD and Haas, AS and Probert, I and Verkley, G and Overmann, J and Scholz, AH}, title = {Policy in Practice: How to do the Nagoya Protocol: common misconceptions, challenges and best practices for access and benefit-sharing compliance.}, journal = {Sustainable microbiology}, volume = {3}, number = {2}, pages = {qvag007}, pmid = {42576822}, issn = {2755-1970}, abstract = {The Nagoya Protocol establishes an international framework for access and benefit-sharing including for microbial research. Yet many microbiologists have only a vague understanding of what the Nagoya Protocol requires and are unsure how to navigate its complexities, despite the fact that non-compliance can have significant legal consequences and far-reaching reputational and legal impacts. This paper discusses common misconceptions and practical challenges that microbiologists may encounter when complying with the Nagoya Protocol and a step-by-step guide on how to "do" the Nagoya Protocol. We present three case studies to showcase real-life experiences and provide best practice principles for access and benefit-sharing while fostering biodiversity conservation, equitable collaboration, and sustainable innovation.}, }
@article {pmid42576838, year = {2024}, author = {Kunselman, E and Wiggin, K and Diner, RE and Gilbert, JA and Allard, SM}, title = {Microbial threats and sustainable solutions for molluscan aquaculture.}, journal = {Sustainable microbiology}, volume = {1}, number = {1}, pages = {qvae002}, pmid = {42576838}, issn = {2755-1970}, abstract = {Aquaculture is responsible for producing almost half of the world's seafood. As the global climate changes and population continues to increase, we must prepare for increased disease in aquatic animals, a risk compounded by high-density aquafarms that are necessary to keep up with demand. This review will highlight major microbial threats to aquaculture and current and alternative solutions to these threats with consideration for the accessibility of the proposed solutions. Molluscs are ideal for sustainable aquaculture because they require less inputs than most other protein sources, and through filter feeding, they improve local ecosystem health. However, they are also plagued by microbial diseases, and rising water temperatures will only exacerbate this problem by enhancing pathogen survival, range, and growth. At the same time, microbial treatments hold great promise for reducing disease burden and increasing yield and food safety. In order to combat threats to sustainable aquaculture, it is critical to monitor and predict microbial behavior in coastal water and animal populations, explore sustainable microbial treatment options such as probiotics and phage therapy, reduce reliance on antimicrobials, and develop mitigation strategies through partnership with mollusc farmers, government regulators, industry, academic researchers, and indigenous peoples.}, }
@article {pmid42576842, year = {2025}, author = {Gilbert, JA and Scholz, AH and Bello, MGD and Korsten, L and Berg, G and Singh, BK and Boetius, A and Wang, F and Greening, C and Wrighton, K and Bordenstein, SR and Jansson, J and Lennon, JT and Souza, V and Allard, SM and Thomas, T and Cowan, D and Crowther, TW and Nguyen, N and Harper, L and Haraoui, LP and Ishaq, SL and McFall-Ngai, M and Redford, KH and Peixoto, R}, title = {Safeguarding microbial biodiversity: microbial conservation specialist group within the species survival commission of the International Union for Conservation of Nature.}, journal = {Sustainable microbiology}, volume = {2}, number = {4}, pages = {qvaf024}, pmid = {42576842}, issn = {2755-1970}, abstract = {As the first and dominant life forms on the planet, microorganisms underpin all ecological and organismal systems that drive planetary functioning, ecosystem health, and human wellbeing. Microbial communities are affected by anthropogenic pressures, and some microbial ecosystems may be at risk of permanent disruption, but microbiology remains conspicuously underrepresented in global conservation frameworks. This article provides a comprehensive overview of the Microbial Conservation Specialist Group (MCSG) of the International Union for Conservation of Nature, including its goals, operational framework, and broader relevance. The MCSG provides the first formal global structure dedicated to the assessment, monitoring, and protection of microbial life across ecosystems. We outline its core mission, strategic framework, and planned activities to integrate microbial conservation into international biodiversity agendas, One Health/planetary policies, and ecological restoration initiatives. We also make a call for all key stakeholders to get involved in this initiative; the microbial world is vast, and we need "all experts on deck" to drive effective solutions.}, }
@article {pmid42576854, year = {2024}, author = {Neale, D and Cullen, L and Ranout, AS}, title = {Improving soil health in the UK: why a microbial approach is indispensable in attaining sustainable soils.}, journal = {Sustainable microbiology}, volume = {1}, number = {1}, pages = {qvae026}, pmid = {42576854}, issn = {2755-1970}, abstract = {Current agricultural approaches in the UK-and across much of the world-are unsustainable, particularly due to their impacts on soil health. With evidence already showing diminishing returns in productivity, which are only predicted to get worse with the climate crisis, restoring the health of soils and soil-dwelling microbes is an essential prerequisite for a thriving planet. This report proposes taking a new approach to soil health based on the soil microbiome. The complex community of soil microbes and their interactions are known to underpin soil health and consequently food security, resilience to climate change, global health, biodiversity, and more. As such, an approach that holistically takes soil into account is needed, rather than the siloed approaches used to date. This report therefore highlights the opportunity to take a microbiome approach to soil and how such an approach could be implemented in the UK going forward, whilst also recommending microbial solutions that can be deployed to improve the UK's soils now.}, }
@article {pmid42576858, year = {2024}, author = {Alfahl, Z and Chueiri, A and Carolan, S and Darcy, G and Hussain, N and Cahill, N and O'Connor, L}, title = {Antimicrobial resistance detection methods in water environments: a scoping review.}, journal = {Sustainable microbiology}, volume = {1}, number = {1}, pages = {qvae034}, pmid = {42576858}, issn = {2755-1970}, abstract = {Antimicrobial resistance (AMR) in water environments poses a significant threat to public health, ecosystem stability, and the effectiveness of antimicrobial treatments. This review aims to provide a comprehensive overview of the methods used to detect AMR in various water environments. A literature search was conducted following the PRISMA guidelines. Original articles published in English relating to AMR in water environments were included. Reviews, protocols, and abstracts were excluded. A total of 115 publications were selected for full-text evaluation. Overall, river water samples were the most commonly assessed samples across all of the reviewed studies (49/115 studies, 42%). The top 3 countries investigating AMR genes in water samples were the USA (19 studies, 17%), China (11 studies, 10%), and Brazil (10 studies, 9%). The review revealed that polymerase chain reaction and metagenomic methods are increasingly preferred for their high sensitivity, specificity, and comprehensive detection capabilities, appearing in 65/115 (57%) and 31/115 (27%) studies, respectively. Despite higher costs and technical complexity, these methods provide valuable insights into the resistome of water environments. Culture-dependent methods, while most cost effective and straightforward, are limited by their time-consuming nature and inability to detect non-viable resistant organisms, reducing their effectiveness in comprehensive AMR surveillance. The review addresses the challenges and limitations of current detection methods and proposes directions for future research to develop more robust, cost-effective, and user-friendly detection methods. The review highlights the urgent need for integrated approaches to monitor and mitigate AMR in water environments, ensuring better public health and environmental protection.}, }
@article {pmid42576874, year = {2024}, author = {Cowan, DA and Babenko, D and Bird, R and Botha, A and Breecker, DO and Clarke, CE and Francis, ML and Gallagher, T and Lebre, PH and Nel, T and Potts, AJ and Trindade, M and Van Zyl, L}, title = {Oxalate and oxalotrophy: an environmental perspective.}, journal = {Sustainable microbiology}, volume = {1}, number = {1}, pages = {qvad004}, pmid = {42576874}, issn = {2755-1970}, abstract = {Oxalic acid is one of the most abundant organic acids produced by plants. Much of the global production of oxalic acid is deposited on soil surfaces in leaf litter to be oxidized by microorganisms, resulting in a pH increase and shifting the carbonate equilibria. In what is known as the oxalate-carbonate pathway, calcium oxalate metabolism results in CO2 being sequestered into soils as insoluble calcite (CaCO3). There is a growing appreciation that the global scale of this process is sufficiently large to be an important contribution to global carbon turnover budgets. The microbiomics, genetics, and enzymology of oxalotrophy are all soundly established, although a more detailed understanding of the landscape-scale kinetics of the process would be needed to incorporate oxalotrophy as an element of process models informing the relevant Sustainable Development Goals. Here, we review the current state of knowledge of oxalotrophs and oxalotrophy and the role they play in terrestrial ecosystem services and functions in terms of carbon sequestration and nutrient cycling. We emphasize the relevance of these to the Sustainability Development Goals (SDGs) and highlight the importance of recognizing oxalotrophy, when accounting for the natural capital value of an ecosystem.}, }
@article {pmid42576885, year = {2025}, author = {Lennon, JT and Bittleston, LS and Chen, Q and Cooper, VS and Fernández, J and Gilbert, JA and Häggblom, MM and Harper, LV and Jansson, JK and Jiao, N and Kuurstra, EM and Peixoto, RS and Rappuoli, R and Schembri, MA and Ventosa, A and Vullo, DL and Zhang, C and Nguyen, NK}, title = {Microbes without borders: uniting societies for climate action.}, journal = {Sustainable microbiology}, volume = {2}, number = {3}, pages = {qvaf021}, pmid = {42576885}, issn = {2755-1970}, abstract = {The climate crisis is one of the greatest challenges of our time, yet the role of microorganisms remains underrecognized in climate science and policy. Microbes are highly sensitive to environmental change and regulate essential biogeochemical processes, while also offering solutions for reducing emissions, restoring ecosystems, and enhancing resilience. Microbiology societies from five continents recently convened in Washington, DC, for the inaugural Global Strategy Meeting on Microbes and Climate Change. The gathering launched a global alliance to position microbial science as a pillar of climate action and identified four priorities: building a coalition, embedding microbes in climate frameworks, transforming communication, and advancing real-world demonstration projects. This initiative marks the beginning of coordinated global action to harness microbial life for climate solutions.}, }
@article {pmid42567435, year = {2026}, author = {Cicirelli, V and Peruzzo, A and Burgio, M and Bramante, G and Fabbri, G and Toscan, E and Losasso, C and Rizzo, A}, title = {Evaluation of neonatal oral and rectal microbiota in dogs delivered by c-section, from birth to weaning.}, journal = {Veterinary journal (London, England : 1997)}, volume = {319}, number = {}, pages = {106816}, doi = {10.1016/j.tvjl.2026.106816}, pmid = {42567435}, issn = {1532-2971}, abstract = {In recent years, the role of the microbiota in early-life health has gained increasing attention; however, data on the initial phases of microbial colonization in dogs remain limited. This study investigated the development of oral and rectal microbiota in puppies delivered by cesarean section from birth to weaning, and the contribution of maternal microbial sources. Four French Bulldog dams and their litters (18 puppies) were enrolled under uniform management conditions. Oral and rectal swabs were collected from puppies at birth and at 15, 30, 45, and 60 days of age, together with maternal oral, teat-skin, and rectal samples, and analyzed by 16S rRNA gene sequencing. Longitudinal analyses revealed a marked, time-dependent increase in microbial richness and diversity in both oral and rectal niches, reflecting a clear ecological succession from pioneer facultative anaerobes to taxa associated with a mature microbiota. Alpha diversity significantly increased from birth to weaning in both oral and rectal samples (p < 0.001), while beta diversity analyses showed progressive convergence toward maternal microbial profiles over time, particularly after the dietary transition from milk to solid food. Source tracking analysis identified maternal teat-skin microbiota as the primary contributor during early life, while maternal oral and rectal sources became increasingly dominant as puppies matured. These findings demonstrate that microbial colonization in dogs begins very early and undergoes dynamic, site-specific maturation throughout the neonatal period. From a One Health perspective, the observed mother-offspring microbial interactions highlight the translational value of canine models for studying early-life microbiota development.}, }
@article {pmid42568410, year = {2026}, author = {Amano, C and Willhelm, U and Koch, T and Reinthaler, T and Hansman, RL and Sintes, E and Herndl, GJ and González, JM and Baltar, F}, title = {Major contribution of anaplerosis to inorganic carbon fixation in the dark ocean.}, journal = {Nature geoscience}, volume = {19}, number = {8}, pages = {938-944}, pmid = {42568410}, issn = {1752-0894}, abstract = {While CO2 fixation by photo- and chemolithoautotrophs is a central process of the global carbon cycle, many organisms also incorporate inorganic carbon into organic compounds through anaplerotic carbon fixation, a process that replenishes intermediates of central metabolic pathways. However, the active drivers and quantitative importance of anaplerotic carbon fixation in the oceanic carbon cycling remain poorly understood. Here, through analysis of global ocean multi-omics datasets, we identified widespread expression of enzymes involved in this process, especially phosphoenolpyruvate carboxylase. The heterotrophic bacterial genus Alteromonas, a globally distributed marine taxon lacking genes for autotrophic carbon fixation pathways, exhibited particularly high transcriptional and proteomic activity for this enzyme. Laboratory incubations confirmed that Alteromonas assimilated dissolved inorganic carbon (DIC) into biomass, with rates regulated by temperature and organic matter availability. Single-cell tracer analyses of the deep ocean microbial communities quantified Alteromonas's contribution at about 17% of total dark DIC fixation (median; confidence interval, 10-28%), equivalent to a potential global flux of about 0.2 PgC yr[-1]. These results reveal substantial DIC fixation via anaplerosis, indicating that dark carbon fixation is partly supported by heterotrophic metabolism and modulated by environmental conditions, with responses that may differ from those of canonical autotrophic processes.}, }
@article {pmid42570393, year = {2026}, author = {McCarthy, FMG and Patterson, RT and Pendea, F}, title = {Meeting report: 11th international symposium on testate amoebae (ISTA-11 Niagara), Brock University, Canada, June 22-27, 2025.}, journal = {Protist}, volume = {182}, number = {}, pages = {126177}, doi = {10.1016/j.protis.2026.126177}, pmid = {42570393}, issn = {1618-0941}, abstract = {An international group of 49 scientists from 12 countries assembled at Brock University, St. Catharines, Ontario, Canada, from June 22-27, 2025, for the 11th International Symposium on Testate Amoebae (ISTA-11 Niagara). The meeting, jointly organized by the International Society of Testate Amoebae Research (ISTAR) and the Canadian Association of Palynologists (CAP), marked a significant milestone as the first ISTA meeting held in North America. Participation included 19 students, underscoring strong engagement from early-career researchers. The largest national delegation was from Canada (17 participants), followed by China, Switzerland, and the United States (six participants each). The scientific program comprised 41 oral and 12 poster presentations, reflecting the continued growth and diversification of research on testate amoebae.}, }
@article {pmid42570687, year = {2026}, author = {Xu, X and Fan, K and Ling, N and Li, J and Yang, T and Gao, GF and Ma, Y and Nie, L and Zhang, J and Chu, H}, title = {Soil pH regulates organic carbon pool by changing microbial life-history strategy.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2026.08.028}, pmid = {42570687}, issn = {2090-1224}, abstract = {INTRODUCTION: The stability of the vast soil carbon pool, crucial for climate regulation, depends on microbial processes that govern carbon loss as CO2 or its stabilization in soil. Microbial life-history strategies, representing tradeoffs between resource acquisition (A-strategy) and growth yield (Y-strategy), are central to soil organic carbon (SOC) dynamics. However, how abiotic factors modulate these strategies and, in turn SOC fate remains unclear.<br><br>OBJECTIVES: Using the black soil region of Northeast China, which harbors substantial yet vulnerable SOC reserves, this study aimed to identify the dominant abiotic driver shaping microbial life-history strategies and to elucidate how this driver influences SOC stabilization pathways.<br><br>METHODS: We conducted a field survey combining metagenomic profiling of microbial attributes (diversity, functional potential, and inferred life-history strategy) with measurements of soil properties including extracellular enzyme activities and SOC fractions. This integrative approach traced the pathway from abiotic drivers to microbial traits and ultimately to carbon allocation.<br><br>RESULTS: Soil pH emerged as the key environmental gradient, with a threshold at pH 6.43 marking a systemic shift in microbial ecology and carbon processing. Acidic soils (pH 4.60-6.43) favored A-strategists, characterized by large genomes, enriched carbohydrate-active enzymes, and high extracellular enzyme activity, enabling polymer degradation and humification but limiting mineral-associated organic carbon (MAOC) formation. In contrast, neutral soils (pH 6.43-8.87) supported Y-strategists with streamlined genomes and biosynthetic metabolism, promoting microbial necromass accumulation and MAOC stabilization. Distinct functional guilds underpinned the A- and Y-strategies and frequent horizontal gene transfer in acidic soils further reinforced the A-strategy dominance under low pH.<br><br>CONCLUSION: Our findings reveal a mechanistic link between microbial life-history strategies and SOC stabilization, demonstrating that pH may shape the balance between A- and Y-strategists and their contrasting carbon pathways. This insight enhances predictive models of SOC dynamics and highlights pH management as a key lever for agroecosystems carbon retention.}, }
@article {pmid42571267, year = {2026}, author = {Kose, A and Erdemci, L and Yasar, S and Memisoglu, F and Toplu, SA and Eren, C and Yazlak, G and Tanriverdi, ES and Usta, S and Ersoy, Y}, title = {Pandemic-associated shifts in microbial ecology and antimicrobial resistance in a high-volume liver transplant intensive care unit: a 10-year surveillance study.}, journal = {Infection prevention in practice}, volume = {8}, number = {3}, pages = {100564}, pmid = {42571267}, issn = {2590-0889}, abstract = {BACKGROUND: Healthcare-associated infections (HAIs) remain a major source of morbidity in solid organ transplant recipients, particularly in liver transplant (LT) intensive care units (ICUs), where profound immunosuppression and extensive antimicrobial exposure shape local microbial ecology. While reductions in overall infection incidence have been reported in structured surveillance programs, longitudinal changes in pathogen distribution and antimicrobial resistance (AMR) in transplant-specific ICUs remain insufficiently characterized. We aimed to evaluate pandemic-associated shifts in microbial ecology and AMR patterns across a 10-year surveillance period in a high-volume LT ICU.<br><br>METHODS: This retrospective analysis was based on prospectively collected surveillance data from adult LT recipients admitted between January 2015 and December 2024. The study period was categorized into prepandemic (2015-2019), pandemic (2020-2021), and postpandemic (2022-2024) phases. All analyses were performed at the HAI-episode level. Isolation density was calculated per 1000 patient-days. Incidence rate ratios were estimated using Poisson regression models with patient-days included as an offset. Period-related differences in AMR were evaluated using logistic regression. A two-sided P value <0.05 was considered statistically significant.<br><br>RESULTS: Among 7717 patients corresponding to 48,001 patient-days, 380 clinically significant isolates were analysed. Gram-negative organisms remained predominant throughout the study period, while Gram-positive isolates demonstrated a significant decreasing trend over time. Acinetobacter spp. (31.3%), Klebsiella spp. (25.8%), and Pseudomonas spp. (15.0%) were the leading pathogens. Isolation densities of Acinetobacter spp. and Escherichia coli were significantly higher in the prepandemic period than in the postpandemic period. In contrast, the pandemic and postpandemic phases were associated with significant increases in resistance probabilities among major Gram-negative pathogens. Acinetobacter spp. showed higher resistance to meropenem and amikacin, Klebsiella spp. demonstrated increased aminoglycoside and fluoroquinolone resistance, and Pseudomonas spp. exhibited increased ciprofloxacin resistance in 2020-2024 compared with 2015-2019.<br><br>CONCLUSIONS: In this transplant-specific ICU, microbial ecology and resistance trajectories evolved independently of overall infection incidence trends. Pandemic-associated healthcare disruptions were accompanied by organism-specific resistance shifts rather than uniform ecological changes. Continuous surveillance and locally tailored antimicrobial stewardship strategies are essential to preserve therapeutic efficacy and mitigate the growing threat of multi-drug-resistant (MDR) pathogens in transplant ICUs.}, }
@article {pmid42571401, year = {2026}, author = {Hu, M and Gao, Q and Ren, W and Li, A and Huang, M and Che, L and Chen, D and Wu, A}, title = {Effects of different acidifiers on the growth performance and diarrhea score of weaned piglets under commercial pig farm conditions.}, journal = {Translational animal science}, volume = {10}, number = {}, pages = {txag101}, pmid = {42571401}, issn = {2573-2102}, abstract = {Benzoic acid (BA)-based acidifiers are widely applied in nursery diets; however, formulation can shape their functional outcomes on intake, host robustness, and gut microbial ecology. This study assessed a new-type benzoic acid (NBA) strategy under commercial farm conditions. A total of 210 21-day-old DLY (Duroc × Landrace × Yorkshire) weaned piglets, with equal numbers of males and females and similar body weight (average 6.03 kg ± 0.01 kg), were randomly assigned to 5 groups with 6 replicates per group and 7 piglets per replicate. The control group was fed a basal diet, while the four experimental groups were fed the basal diet supplemented with 0.5% benzoic acid (BA), 0.3% new-type benzoic acid (NBA), 0.25% controlled-release-coated benzoic acid (CBA), or 0.5% compound acidifier (CA) powder, respectively. The trial lasted 42 days. The results showed that compared to the control group, the average daily feed intake (ADFI) from days 15 to 28 was significantly increased (P < 0.05) in the BA, NBA, and CA groups, indicating improved voluntary intake during the mid-nursery period. The diarrhea rate was significantly reduced (P < 0.05) during days 0-14 in the BA, NBA and CBA groups compared to the control group. Compared to the control group, serum total antioxidant capacity (T-AOC) was significantly elevated (P < 0.05) in the BA, CBA, and CA groups, and catalase (CAT) levels increased significantly in the NBA group. White blood cell (WBC), lymphocyte (Lym), and mean corpuscular hemoglobin concentration (MCHC) increased significantly in the BA group compared to the control group, while MCHC levels decreased significantly in the NBA, CBA, and CA groups. Notably, compared with the control group, 0.5% BA, 0.3% NBA, and 0.25% CBA increased the richness and diversity of the intestinal microbiota. Specifically, these treatments promoted the growth of beneficial bacteria such as Lactobacillus while inhibiting the proliferation of Escherichia coli. The results of this study indicate that adding 0.5% BA, 0.3% NBA, and 0.25% CBA all enhance piglets' antioxidant capacity, reduce diarrhea incidence, and enhance gut microbial diversity. Among these, 0.5% BA and 0.25% CBA demonstrated superior efficacy compared to 0.3% NBA, offering potential economic benefits by improving feed efficiency, thereby enhancing overall production performance.}, }
@article {pmid42572451, year = {2026}, author = {Butterbach-Bahl, K and Philippot, L and Serra, J and Silver, WL and Ogle, S and Abalos, D}, title = {Three Decades of Soil N2O Research-Insights and Gaps.}, journal = {Global change biology}, volume = {32}, number = {8}, pages = {e71038}, doi = {10.1111/gcb.71038}, pmid = {42572451}, issn = {1365-2486}, support = {NNF24SA0091172//the Novo Nordisk Foundation/ ; NNF25SA0112735//Agricultural nitrogen use efficiency platform/ ; }, mesh = {*Nitrous Oxide/analysis ; *Soil Microbiology ; *Greenhouse Gases/analysis ; *Soil/chemistry ; Agriculture ; Greenhouse Effect ; Environmental Monitoring ; }, abstract = {Nitrous oxide (N2O) is a potent greenhouse gas (GHG) whose atmospheric concentration continues to rise, largely driven by nitrogen (N) inputs to agricultural soils. Over the past three decades, research on soil N2O emissions has advanced substantially, yet key uncertainties still constrain mitigation efforts. Here, we synthesize developments in measurement techniques, process understanding, microbial ecology, and modelling from the 1990s to the present, and identify critical gaps for future research. Advances in high-frequency measurements, laser spectroscopy, and isotopic approaches have revealed the importance of temporal "hot moments" and spatial "hotspots," challenging earlier assumptions based on sparse sampling. Concurrently, molecular and multi-omic tools have transformed our understanding of the microbial drivers of N2O production and consumption, highlighting the role of community composition, truncated pathways, and previously overlooked N2O-producing and reducing organisms. Process-based models have evolved from research tools into policy-relevant frameworks underpinning GHG inventories, with emerging integration of data assimilation, ensemble modelling, and artificial intelligence. However, despite these advances, persistent challenges remain in linking scales, reducing uncertainties, and translating mechanistic insights into scalable mitigation strategies. Closing these gaps offers a unique opportunity to translate decades of scientific progress into next-generation mitigation strategies that align agricultural productivity with climate stabilization goals.}, }
@article {pmid42557861, year = {2026}, author = {Dai, M and Niu, Z and Lu, Y and Wei, A and Wang, X and Zheng, H and Lai, J and Zong, E and Sun, B and Zheng, J and Xu, Y}, title = {Unveiling the Acidic Backbone of Baijiu: A Comprehensive Review on Composition, Metabolic Pathways, and Quality Implications.}, journal = {Comprehensive reviews in food science and food safety}, volume = {25}, number = {5}, pages = {e70592}, pmid = {42557861}, issn = {1541-4337}, support = {32572513//National Natural Science Foundation of China/ ; 2023JJ002//Open Foundation of Key Laboratory of Wuliangye-Flavor Liquor Solid-State Fermentation, China National Light Industry/ ; }, mesh = {*Metabolic Networks and Pathways ; *Alcoholic Beverages/analysis/microbiology ; Fermentation ; *Acids/chemistry ; Taste ; Humans ; }, abstract = {Acids constitute fundamental molecular determinants that shape the sensory profile, typicity, and overall quality of Baijiu, a traditional Chinese distilled spirit. In this review, the latest advances in the studies of acidic compounds in Baijiu are systematically summarized within the framework of the "composition-function-microbe interaction" chain, with particular emphasis placed on the relationships among acid metabolism, flavor formation, microbial ecology, and product quality stability. We first catalog the diverse acid profiles in Baijiu, highlighting the four major acids (acetic, lactic, butyric, and caproic acids), and their dynamic evolution during product aging. In addition, the roles of acids in sensory perception, aroma regulation, and quality evaluation are comprehensively discussed, while their potential health-related implications are briefly and critically appraised. Crucially, we elucidate the microbial origins of these acids, detailing key metabolic pathways including glycolysis, amino acid catabolism, and reverse β-oxidation. Current studies have demonstrated that microbial community interactions play critical roles in shaping acid metabolism and acid-ester balance, although the underlying mechanisms remain insufficiently resolved. This review concludes by identifying critical knowledge gaps regarding in situ metabolic flux quantification and predictive modeling of microbial interaction networks governing acid-flavor compound dynamics. Future studies integrating multiomics approaches, ecological modeling, and targeted metabolic regulation are expected to facilitate the transition of Baijiu fermentation from descriptive characterization toward predictive and controllable bioprocesses.}, }
@article {pmid42562513, year = {2026}, author = {Liu, QJ and Mei, JL and Wen, X and Lu, YH and Zeng, Y and Liu, ZY and Xu, HY and Wang, ST and Jiang, F and Yang, CB and Chi, YL and Xu, ZH}, title = {Cellar age reshapes Huangshui micro-ecosystem and metabolism to drive flavor formation in strong-aroma baijiu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {241}, number = {}, pages = {119740}, doi = {10.1016/j.foodres.2026.119740}, pmid = {42562513}, issn = {1873-7145}, mesh = {Fermentation ; Metabolomics ; *Odorants/analysis ; *Taste ; Bacteria/metabolism/genetics ; *Wine/analysis/microbiology ; *Alcoholic Beverages/analysis/microbiology ; Metagenomics ; *Microbiota ; Flavoring Agents ; }, abstract = {Huangshui, a slurry-like liquid exuded during strong-aroma Baijiu fermentation, serves as the core medium for material exchange between pit mud and fermented grains. However, how its micro-ecosystem evolves with cellar age and drives flavor formation remains unclear. Using Huangshui as a dynamic window, this study integrated metagenomics, metabolomics, and flavoromics to compare its temporal dynamics in new and old cellars over a complete fermentation cycle, systematically characterizing how cellar age is associated with the restructuring of the microbial community and metabolic functions of Huangshui, and how these changes are consistent with the flavor profiles observed in the final base liquor. The results showed that Huangshui from old cellars harbored a more diverse and stable microbial community, forming a syntrophic consortium of caproic acid-producing bacteria (Caproicibacterium, Caproiciproducens), syntrophic bacteria (Syntrophomonas), and methanogenic archaea (Methanosarcina), whereas new cellars were dominated by lactic acid bacteria (Acetilactobacillus). Metabolically, the old-cellar community exhibited a clear phase-dependent division. During the acid-producing phase, the TCA cycle, arginine biosynthesis, and pyruvate metabolism were preferentially activated to generate core precursors; during esterification, butanoate metabolism and acyl-CoA supply pathways were enhanced. This orderly shift was associated with higher concentrations of ethyl caproate and ethyl octanoate in old-cellar base liquor. Functional gene analysis revealed coordinated upregulation of chain-elongation, methanogenic, and acetate-activating pathways in old cellars. Network analysis revealed a tightly coupled caproic acid-producing co-occurrence module in old cellars, which was not observed in new ones. Together, these findings suggest that Huangshui may serve as a rapid proxy for assessing both the fermentation status and the maturity level of the cellar. This work identifies potential bioaugmentation targets to accelerate flavor development in new cellars and provides a theoretical basis for the precise micro-ecological management of strong-aroma Baijiu quality.}, }
@article {pmid42551103, year = {2026}, author = {Esener, N and Kırbaş, M and Kal, Y and Aladağ, F}, title = {Microbial signatures of the vaginal microbiome associated with pregnancy outcome in central Anatolian Merino sheep.}, journal = {Theriogenology}, volume = {265}, number = {}, pages = {118119}, doi = {10.1016/j.theriogenology.2026.118119}, pmid = {42551103}, issn = {1879-3231}, abstract = {Reproductive efficiency is a key determinant of sustainability and profitability in sheep farming systems; however, the role of the vaginal microbiome in shaping pregnancy outcomes remains insufficiently understood. This study aimed to characterise the vaginal microbial communities of Central Anatolian Merino sheep using 16S rRNA gene amplicon sequencing and to explore their potential association with reproductive success. Vaginal samples were collected from 20 healthy ewes (10 non-pregnant (G1), that failed to conceive and returned to oestrus and 10 pregnant (G2), conceived at first service) with comparable physiological characteristics before breeding, followed by high-throughput amplicon sequencing to comprehensively profile the bacterial community structure. Comparative analyses were conducted between pregnant and non-pregnant animals to identify microbial patterns linked to pregnancy outcomes. The vaginal microbiome exhibited a diverse yet structured taxonomic composition across both groups, dominated by members of Bacillota (44.8% in G1 and 45.6% in G2), Actinomycetota (12.0% in G1 and 9.3% in G2), Pseudomonadota (6.6% in G1 and 6.2% in G2) and Bacteroidota (5.6% in G1 and 5.9% in G2). Alpha diversity did not differ significantly between groups (Wilcoxon rank-sum test, p > 0.05 across all indices), and beta diversity showed no significant separation (PERMANOVA, R[2] = 0.055, p = 0.38), indicating substantial community overlap. Differential abundance analysis (edgeR) identified 23 taxa that differed between groups (FDR < 0.05), suggesting that reproductive outcomes may be influenced by subtle ecological shifts rather than large-scale microbial restructuring. Collectively, these findings provide novel insights into the vaginal microbial ecology of Central Anatolian Merino sheep and identify candidate microbial signatures that may warrant further investigation as potential correlates of fertility. Given the observational design and limited sample size, these associations should be interpreted as preliminary and hypothesis-generating. By advancing our understanding of host-microbiome interactions within the reproductive tract, this study establishes a foundation for microbiome-informed strategies aimed at improving reproductive performance and supporting sustainable sheep production.}, }
@article {pmid42552662, year = {2026}, author = {Chen, M and Li, R and Xiang, Y and Ma, X and Yu, X and Zhao, J and Ren, D}, title = {Pasteurized Akkermansia muciniphila AKK PROBIO ameliorates inflammation and metabolic disorder in db/db mice with alterations in gut microbiota and hepatic TLR4/NF-κB and SREBP2/HMGCR signaling.}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.70969}, pmid = {42552662}, issn = {1097-0010}, support = {//This work was supported by the National Natural Science Foundation of China (Grant No. 32172189), the Natural Science Foundation of Jilin Province (Provincial-Local Joint Fund; Grant No. YDZJ202501ZYTS312), and Jilin Agricultural University (Horizontal Research Project-Safety Evaluation and Metabolic Regulation Function of Akkermansia; Grant No. H20250226)./ ; }, abstract = {BACKGROUND: Diabetes mellitus, especially type 2 diabetes mellitus (T2DM), represents a significant global health challenge. Growing evidence indicates that Akkermansia muciniphila, a promising next-generation beneficial microorganism, could help alleviate metabolic disorders. Nevertheless, its strain-specific effects and associated mechanisms require further investigation. Here, we investigated the potential effects of pasteurized A. muciniphila AKK PROBIO in T2DM using db/db mice.<br><br>RESULTS: Our findings show that pasteurized AKK PROBIO supplementation was associated with lower fasting glucose levels, reduced inflammatory markers, and improved cholesterol balance in db/db mice. Pasteurized AKK PROBIO administration was accompanied by changes in gut microbiota composition, including enrichment of bacterial taxa linked to short-chain fatty acid (SCFA) production, and by increased GLP-1 levels and altered serum metabolites, including 9,9'-di-cis-&#x3b6;-carotene and l-arginine. These changes were paralleled by reduced hepatic expression of proteins related to the TLR4/MyD88/IKK&#x3b1;/NF-&#x3ba;B and SREBP2/HMGCR signaling pathways.<br><br>CONCLUSIONS: Taken together, our findings indicate that pasteurized AKK PROBIO ameliorates metabolic disorder and inflammation in db/db mice, accompanied by changes in gut microbial ecology, serum metabolites, and hepatic inflammatory/lipid metabolic signaling. This study supports pasteurized A. muciniphila AKK PROBIO as a postbiotic for further investigation in metabolic disorders. &#xa9; 2026 Society of Chemical Industry.}, }
@article {pmid42554875, year = {2026}, author = {Zhang, H and Zhang, Y and Zhang, C and Yang, Y and Hu, B and He, T and Zhang, J and Song, X and Su, Y}, title = {Microbial architects of cigar fermentation: a critical review of beneficial roles in quality enhancement and detrimental potential for mould spoilage.}, journal = {Archives of microbiology}, volume = {208}, number = {11}, pages = {}, pmid = {42554875}, issn = {1432-072X}, support = {2023530000241002//the Science and Technology Plan Project of the China National Tobacco Corporation, Yunnan Provincial Company/ ; yxyc2023007//General Project of the Science and Technology Program of Yuxi Company, Yunnan Provincial Tobacco Company/ ; }, mesh = {*Fermentation ; *Fungi/metabolism/growth &amp; development ; *Nicotiana/microbiology/metabolism ; *Food Microbiology ; *Bacteria/metabolism/classification/isolation &amp; purification ; }, abstract = {Cigar tobacco fermentation is a microbially driven process that transforms raw tobacco leaves into a product with distinctive sensory attributes, yet the current understanding of the microbial roles in this process remains fragmented between descriptive community surveys and isolated mechanistic studies, with beneficial and detrimental microbial functions rarely integrated into a unified risk-benefit assessment. This review critically examines the microbiology of cigar fermentation through a dual-axis framework organized around beneficial metabolic functions and detrimental spoilage potential, each resolved into microbial identity, biochemical mechanism, and environmental modulation dimensions. We synthesize evidence from culture-dependent and culture-independent studies on microbial community assembly and succession, where Bacillus, Staphylococcus, and Aspergillus emerge as core fermentation genera, and evaluate the complementary three-pathway system - macromolecular enzymatic degradation, targeted biotransformation of tobacco alkaloids and polyphenols, and de novo biosynthesis of aroma-active volatiles - that drives flavor and quality enhancement. We further analyze the contrastive microbial balance governing tobacco-specific nitrosamine (TSNA) formation, where nitrate-reducing bacteria compete with nitrate-assimilating and nitrite-scavenging microorganisms to determine the net TSNA load. In parallel, we critically examine the mould spoilage microbiology of cigar fermentation, identifying the environmental thresholds - humidity above 80% RH, water activity above 0.85, and inadequate aeration - that select for mycotoxigenic Aspergillus and Penicillium species producing aflatoxins and ochratoxin A at levels that persist into the finished product. We survey emerging biotechnological strategies spanning bioaugmentation with defined starter cultures, biostimulation through environmental optimization, and biocontrol of spoilage fungi, and identify five critical research gaps - including the absence of gnotobiotic fermentation models and the predominance of correlative over causal studies - that must be addressed to translate microbial ecology into predictable fermentation biotechnology. By integrating microbial ecology, fermentation biochemistry, spoilage prevention, and applied biotechnology, this review is intended for researchers in tobacco microbiology and fermentation science, as well as cigar manufacturers, quality-control practitioners, and biotechnologists seeking microbiome-based strategies for quality improvement and risk mitigation.}, }
@article {pmid42550534, year = {2026}, author = {Celik, G and Yanik, E and Inan, N and Yalinay, AM}, title = {Absence of a Consistent Gut or Oral Microbial Signature in Fibromyalgia Under Strictly Controlled Clinical Conditions: A Multi-Compartment 16S rRNA Analysis.}, journal = {Pain physician}, volume = {29}, number = {5}, pages = {E407-E416}, pmid = {42550534}, issn = {2150-1149}, mesh = {Humans ; Female ; *Fibromyalgia/microbiology ; *RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Adult ; *Mouth/microbiology ; Middle Aged ; Prospective Studies ; *Microbiota ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; }, abstract = {BACKGROUND: Fibromyalgia (FM) has been increasingly studied in the context of gut-brain-immune interactions, and several reports have suggested an association between FM and alterations in gut or oral microbial communities. However, prior studies have often suffered from heterogeneous comorbidities, inconsistent sampling procedures, and limited control for environmental factors, making it unclear whether FM is associated with a reproducible, site-independent microbial signature.<br><br>OBJECTIVES: To determine whether women with FM exhibit consistent alterations in gut or oral microbiota when evaluated under strictly standardized physiological, clinical, and environmental conditions.<br><br>STUDY DESIGN: A prospective, observational, case-control study.<br><br>SETTING: The Department of Pain Medicine and Department of Medical Microbiology at Gazi University, T&#xfc;rkiye.<br><br>METHODS: The patient selection comprised 31 women (16 with FM; 15 healthy controls) who met rigorous inclusion and exclusion criteria, minimizing confounding from diet, metabolic disease, medications, hormonal status, and recent infections. No therapeutic intervention was performed; all patients provided paired oral mucosal and fecal samples during the follicular phase of the menstrual cycle. Sequencing of 16S rRNA V3-V4was performed on DNA extracted from all samples. Alpha and beta diversity metrics, taxonomic profiles, and differential abundance analyses (including LEfSe with FDR correction) were compared between groups. The clinical severity of FM was assessed using scores on the visual analog scale (VAS), Widespread Pain Index (WPI), and Symptom Severity Scale (SSS).<br><br>RESULTS: No statistically significant differences were observed between FM patients and controls in fecal or oral alpha diversity (Shannon, Simpson, Chao1, Observed OTU indices, all P > 0.05). Beta diversity analyses (Bray-Curtis PERMANOVA) revealed no between-group separation in either compartment (fecal R&#xb2; = 0.032, P = 0.529; oral R&#xb2; = 0.032, P = 0.464). Both groups displayed preserved core microbial communities in the gut, dominated by Firmicutes and Bacteroidota and, in the oral cavity, Streptococcus-enriched profiles. Minor genus-level variations were detected, but none remained significant after FDR correction. Cross-site analyses confirmed the expected ecological divergence between oral and fecal habitats but identified no FM-specific microbial pattern. Post hoc sensitivity analysis indicated that the study was powered to detect only moderate effect sizes (R&#xb2; &#x2265; 0.11), suggesting that subtle differences might have remained undetected.<br><br>LIMITATIONS: A modest sample size, a lack of quantitative dietary assessment, and reliance on 16S rRNA sequencing limited the detection of subtle or functional microbial alterations. Additionally, the cross-sectional design precludes causal inference.<br><br>CONCLUSIONS: Under highly controlled sampling and exclusion conditions, FM was not associated with detectable alterations in the diversity or composition of gut or oral microbes. These findings suggest that previously reported dysbiosis may reflect comorbidity-driven or phenotype-specific variation rather than a universal microbial hallmark. Larger, multi-omic and phenotype-stratified studies are needed to clarify functional host-microbiome interactions in FM.}, }
@article {pmid42548192, year = {2026}, author = {Feng, J and Wang, Z and Xu, Y and Peng, J and Xu, C and Xie, Q and Li, Y and Chen, W and Chen, J and Wang, X and Gao, WQ and Li, L and Meng, X}, title = {Intestinal epithelial SETD2 maintains gut microbial homeostasis to attenuate colitis.}, journal = {Clinical and translational medicine}, volume = {16}, number = {8}, pages = {e70754}, pmid = {42548192}, issn = {2001-1326}, support = {2022YFA1302704//National Key R&amp;D Program of China/ ; 2023YFC1404101//National Key R&amp;D Program of China/ ; YG2024ZD11//Interdisciplinary Program of Shanghai Jiao Tong University/ ; 32570684//National Natural Science Foundation of China/ ; 82372604//National Natural Science Foundation of China/ ; U23A20441//National Natural Science Foundation of China/ ; W2431055//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Mice ; *Colitis ; *Histone-Lysine N-Methyltransferase/metabolism/genetics ; *Homeostasis ; *Gastrointestinal Microbiome/physiology/drug effects/genetics ; Mice, Knockout ; *Intestinal Mucosa/metabolism ; Male ; }, abstract = {BACKGROUND: Disruption of host-microbiota homeostasis is a fundamental hallmark of inflammatory bowel disease (IBD) pathogenesis. Host epigenetic modifications and corresponding alterations in gene expression levels can impact the composition of gut microbes. SET domain containing 2 (SETD2) is a critical epigenetic regulator with established tumor-suppressive roles, but its function in intestinal microbial ecology and colitis progression remains unexplored. We aimed to investigate the specific role of SETD2 in maintaining gut microbial homeostasis and modulating colitis progression.<br><br>METHODS: RNA sequencing (RNA-seq), assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and cleavage under targets and tagmentation sequencing (CUT&amp;Tag-seq) were conducted on colonic epithelial cells from intestinal epithelial cell-specific SETD2 knockout (Setd2[vil-ko]) mice to identify key mediators contributing to colitis development. Faecal samples underwent 16S rRNA sequencing and non-targeted metabolomics analysis to characterise microbial dysbiosis and metabolic perturbations. Molecular experiments and faecal microbiome transplantation experiment were conducted to explore and validate the role of SETD2 in colitis development.<br><br>RESULTS: SETD2 deficiency induced overproduction of Reg3 lectins and disrupted gut microbiota composition. Beneficial commensal bacteria were depleted and dysregulated metabolites were accumulated in Setd2[vil-ko] mice. Supplementation with healthy-like gut microbiota significantly ameliorated the exacerbated colitis induced by SETD2 deficiency.<br><br>CONCLUSIONS: Our findings uncover a previously unrecognised role for SETD2 in maintaining microbial homeostasis, offering new mechanistic insights into how epigenetic regulation preserves intestinal homeostasis and suggesting novel therapeutic avenues for IBD.}, }
@article {pmid42549413, year = {2026}, author = {Feng, S and Si, X and Lu, C and Gao, Z and Wang, J and Yang, Q and Lu, S and Su, T and Yang, J and He, X and Wu, L}, title = {Washed microbiota transplantation improves clinical symptoms, gut microbiota, and metabolic profiles in autism spectrum disorder in a twin cohort.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1885281}, pmid = {42549413}, issn = {1664-302X}, abstract = {OBJECTIVE: Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental condition characterized by impaired social communication, repetitive behaviors, and restricted interests. Dysregulation of the microbiota-gut-brain axis is closely associated with the pathogenesis of ASD. Washed microbiota transplantation (WMT) has emerged as a promising intervention for ASD, but existing cohort studies lack genetically identical controls, making it difficult to distinguish intervention-related changes from genetic and environmental confounding factors. This twin-paired controlled study adopted a study design that minimizes the influence of genetics and shared environment, to explore the associations of WMT with clinical symptoms, gut microbiota, and metabolic profiles in children with ASD.<br><br>METHODS: Three pairs of age- and environment-matched twins (one ASD-affected, one typically developing sibling) were enrolled. WMT was administered to the ASD participant in each pair. Fecal samples were collected at baseline and post-intervention. Gut microbiota and metabolic profiles were analyzed using metagenomic sequencing and targeted metabolomics, respectively. Clinical outcomes were evaluated using the Childhood Autism Rating Scale (CARS), Autism Behavior Checklist (ABC), Sleep Disturbance Scale for Children (SDSC), and Bristol Stool Form Scale (BSFS). Relevant observations were carried out to explore potential changing trends.<br><br>RESULTS: After WMT, CARS, ABC, SDSC, and BSFS exhibited small numerical directional shifts toward healthier values, but none reached statistical significance. Gut microbial structure and function presented a shifting trend toward the profile of their typically developing twin siblings. Abnormal lipid and energy metabolism indicators showed partial ameliorative trends, and the number of differential metabolites between ASD patients and healthy siblings was markedly reduced. Tyrosine and phenylalanine metabolic pathways, together with Segatella, Negativibacillus, and Sangeribacter, may be associated with incomplete phenotypic changes in this cohort.<br><br>LIMITATIONS: Although the twin-pair design has high internal validity and can provide strong causal inference evidence for the effect of microbiota transplantation in treating ASD, this study has limitations such as a small sample size, a single-center non-randomized observational design. All findings in this pilot study are merely descriptive trends, and the relevant mechanism analysis only provides correlational clues. A single session of microbiota transplantation failed to fully adjust aromatic amino acid metabolism in ASD children. No definitive causal relationship can be concluded based on the findings of this small-sample pilot study.<br><br>CONCLUSION: Under tightly controlled genetic and environmental conditions, gut microbial dysbiosis presents correlational characteristics with ASD-related phenotypes. WMT was associated with consistent remodeling of gut microbial ecology and partial resolution of metabolic dysregulation in ASD children, with multi-omic signatures converging toward healthy twins. Clinical rating scales only displayed non-significant minor numerical shifts, which cannot be interpreted as evidence of clinical symptom improvement. These initial findings provide exploratory mechanistic clues and phenotypic data supporting WMT as a targeted microbiome intervention approach for ASD, and await further validation through large-scale randomized controlled trials.<br><br>CLINICAL TRIAL REGISTRATION: Identifier ChiCTR2400091105.}, }
@article {pmid42545919, year = {2026}, author = {Vielma-Puente, JE and Mosquera-Romero, S}, title = {Green Synthesis of Gold and Silver Nanoparticles Using Plant Extracts, Fungal Filtrates, and Bacterial Cultures.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {233}, pages = {}, doi = {10.3791/70729}, pmid = {42545919}, issn = {1940-087X}, mesh = {*Gold/chemistry/metabolism ; *Metal Nanoparticles/chemistry ; *Silver/chemistry/metabolism ; *Green Chemistry Technology/methods ; *Plant Extracts/chemistry ; Cupriavidus/metabolism/chemistry ; Shewanella/metabolism/chemistry ; Fungi/metabolism/chemistry ; }, abstract = {Green synthesis of metal nanoparticles (NPs) using biological systems provides a sustainable alternative to conventional chemical fabrication methods. This protocol presents reproducible experimental and analytical procedures for the synthesis of gold (Au) and silver (Ag) NPs using bacterial cultures, fungal filtrates, and plant leaf extracts as reducing and stabilizing agents. AgNPs were synthesized using extracts from Psidium guayaquilensis, Acanthophora spicifera, and Earliella sp., exhibiting characteristic ultraviolet-visible (UV-Vis) absorption bands between 405 and 425 nm that confirmed NP formation. A design-of-experiments approach was implemented to evaluate the influence of environmental factors, including oxygen conditions, pH, Au concentration, cell concentration, electron donor type, and temperature, on the synthesis of AuNPs by Shewanella oneidensis and Cupriavidus metallidurans. Under ideal conditions (0.2 mM Au and pH 5), S. oneidensis produced predominantly spherical AuNPs with an average size of 43.6 ± 11.0 nm and a characteristic absorption peak at 520 nm. NP formation and morphology were confirmed using UV-Vis spectroscopy and transmission electron microscopy. This workflow provides a reproducible platform for biogenic NP synthesis and supports applications in biosensing, bioremediation, and antimicrobial technologies.}, }
@article {pmid42547937, year = {2026}, author = {Li, S and Zhang, S and Liu, Y and Liu, Y}, title = {From Mood to Mouth: Unraveling the Impact of Emotional Dysregulation on Periodontitis.}, journal = {Oral diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/odi.70440}, pmid = {42547937}, issn = {1601-0825}, support = {L2510103//Natural Science Foundation of Beijing, China/ ; 82201053//National Natural Science Foundation of China/ ; BJPSTP-2025-29//Beijing Physician Scientist Training Project/ ; JLPYPT2025012//Basic-Clinical Joint Research and Cultivation Platform of Capital Medical University/ ; CXJJ25101//Innovation Foundation of Beijing Stomatological Hospital, Capital Medical University/ ; QML20231506//Beijing Municipal Administration of Hospitals' Youth Programme/ ; YSP202105//Beijing Stomatological Hospital, Capital Medical University Young Scientist Program/ ; CFH20242024-1-2141//Capital's Funds for Health Improvement and Research/ ; 202601AT070266//Yunnan Fundamental Research Projects/ ; }, abstract = {OBJECTIVES: Periodontitis is a chronic infectious disease which is recognized as a major cause of periodontal tissue destruction. Negative emotional states have been associated with periodontitis, although causal inference remains constrained by heterogeneous exposure and outcome measures. This narrative review critically examines the evidence linking emotional dysregulation with periodontitis and summarizes plausible psychoneuroimmunological pathways.<br><br>SUBJECTS: This review focuses on the association between psychological stress and periodontitis, including the psychoneuroimmunological pathways mediated by the hypothalamic-pituitary-adrenal axis and sympathetic nervous system. Current experimental models and clinical epidemiological evidence support this psychophysiological interconnection.<br><br>RESULTS: Psychological stress may influence periodontal inflammation through HPA axis and SNS/SAM-mediated changes in immune regulation and, potentially, alterations in oral microbial ecology. Converging experimental and clinical evidence supports the biological plausibility of this psychophysiological link, although heterogeneity in exposure assessment, periodontal outcome definitions, and study design limits causal inference.<br><br>CONCLUSIONS: Further understanding of stress-periodontitis interactions provides insights into an emerging oral-brain crosstalk mechanism, which may help identify prospective therapeutic targets for interceptive periodontal management.}, }
@article {pmid42544022, year = {2026}, author = {Doolittle, CJ and Crowther, TW and Delavaux, CS and LaManna, JA}, title = {Environmental stress strengthens plant-mycorrhizal associations: A novel extension of the stress gradient hypothesis.}, journal = {Ecology}, volume = {107}, number = {8}, pages = {e70465}, pmid = {42544022}, issn = {1939-9170}, support = {TMPFP3_209925//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; DEB-2024903//Division of Environmental Biology/ ; DEB-2025755//Division of Environmental Biology/ ; DEB-2310100//Division of Environmental Biology/ ; }, mesh = {*Mycorrhizae/physiology ; *Stress, Physiological ; Oregon ; *Plants/microbiology ; Trees/microbiology/physiology ; }, abstract = {Understanding how environmental stress alters the strength of local interactions is key to explaining diversity in current and future plant communities. Along gradients of increasing environmental stress, traditional theory posits that plants experience stronger facilitative interactions and weaker antagonistic interactions. However, it remains unclear whether this pattern extends to the relative host-specificity of plant-microbe interactions along stress gradients. Understanding these dynamics is particularly important for plant interactions with pathogenic and mycorrhizal fungi, which can drive opposing density-dependent processes that shape plant community compositions. We posit that increases in abiotic environmental stress are associated with stronger associations between plants and mutualists as plants increasingly rely on facilitative resource partnerships to cope with abiotic environmental stressors. We tested this prediction along an abiotic stress gradient in the central Cascade Range of Oregon, USA, using overlapping datasets of large high-resolution forest inventory plots, soil chemistry, and amplicon sequencing. Consistent with our predictions, in low-elevation forest stands with benign abiotic conditions and abundant nutrients, tree composition was more correlated with pathogenic fungal composition than ectomycorrhizal fungal composition. However, in forests at high elevations with limited nutrients and harsher climates, tree community composition was more correlated with ectomycorrhizal fungal composition than pathogenic fungal composition. Additionally, we find that spatial aggregation of ectomycorrhizal fungi increases as abiotic stress increases with elevation and opposing patterns of pathogen and ectomycorrhizal relative abundance in different substrate layers. Together, our findings suggest that facilitative interactions in stressful environments extend to mutualist-plant interactions and such interactions play a key role in shaping forest composition along environmental stress gradients.}, }
@article {pmid42544462, year = {2026}, author = {Rizaludin, MS and Dickschat, JS and Raaijmakers, JM and Garbeva, P}, title = {Volatile dialogues between plants and microorganisms.}, journal = {Natural product reports}, volume = {}, number = {}, pages = {}, doi = {10.1039/d6np00045b}, pmid = {42544462}, issn = {1460-4752}, abstract = {Covering: up to 2026Volatile organic compounds (VOCs) are key mediators of long-distance communication in biological systems. While their roles in plant-insect interactions are well established, emerging evidence highlights their importance in plant-microbe interactions. In this highlight, we discuss the biosynthesis and ecological functions of plant VOCs (pVOCs) and their impact on microbiome assembly and function. We examine how constitutive and stress-induced pVOCs shape microbial community composition and how microbial VOCs (mVOCs) influence plant growth and defense by modulating hormonal and metabolic pathways. We further address the bidirectional nature of volatile-mediated interactions and the challenges associated with studying complex VOC blends in natural environments. Understanding these dynamic volatile dialogues provides new opportunities for microbiome engineering and sustainable crop production.}, }
@article {pmid42545019, year = {2026}, author = {Kulosa, M and Belisário-Ferrari, MR and Semmler, F and Büttner, M and Duck, C and Namazi, Z and Jehmlich, N and von Bergen, M and Bonitz, T and Kaysser, L}, title = {Establishment of an in vitro aerobic bacterial community as a model of the human lung microbiome.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0049126}, doi = {10.1128/msystems.00491-26}, pmid = {42545019}, issn = {2379-5077}, abstract = {The human lung microbiome is increasingly recognized as a key player in drug metabolism, yet it remains largely understudied. To replicate this complex physiological environment in a controlled setting, we developed a simplified artificial lung microbiome model composed of four representative bacterial species: Pseudomonas koreensis, Rothia aeria, Neisseria cinerea, and Streptococcus downei. We successfully established a stable 10-day co-culture at 34°C using brain heart infusion medium, as validated by quantitative PCR, viability PCR, and conventional microbiological methodologies. Integrated bioinformatic analyses revealed a variety of potential microbe-microbe interactions, which were supported by metaproteomic analysis using mass spectrometry. Our model provides a foundation for in-depth studies, such as, for example, the effects of pulmonary drugs on the lung microbiome, and how, in turn, the microbiome may influence therapeutic outcomes.IMPORTANCEOnce thought to be sterile, the lung microbiome is now understood to host a dynamic microbiome capable of influencing respiratory health and disease. Understanding interactions among the microbes within this community is essential, as these relationships may drive disease progression or foster resilience in both acute and chronic inflammatory conditions. We developed a reproducible lung microbiome model comprising Pseudomonas koreensis, Rothia aeria, Streptococcus downei, and Neisseria cinerea. Simplified models enable controlled studies to dissect specific microbial interactions, laying the foundation for insights into lung microbial ecology. In the future, more complex models will enhance our understanding of microbial roles in disease outcomes, with our platform serving as a basis for testing therapeutic strategies.}, }
@article {pmid42545497, year = {2026}, author = {Hossen, S and Groß, C and Roy, F and Kellner, H and Noll, M and Borken, W}, title = {Chronic Nitrogen Deposition Alters Diazotrophic Community Composition, Reduces Biological Nitrogen Fixation, and Restructures Fungal-Diazotroph CO-Occurrence Networks in Deadwood.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, pmid = {42545497}, issn = {1432-184X}, mesh = {*Nitrogen Fixation ; *Nitrogen/metabolism/analysis ; *Fungi/metabolism/genetics/classification ; *Trees/microbiology/metabolism ; *Wood/microbiology/metabolism ; Soil Microbiology ; Oxidoreductases/genetics ; Bacteria/metabolism/genetics/classification/isolation &amp; purification ; }, abstract = {Biological nitrogen fixation (BNF) by diazotrophs contributes to increasing nitrogen (N) availability in nutrient-poor deadwood during the decomposition process. However, chronically elevated atmospheric N deposition may increase N availability, thereby reshaping diazotrophic community and suppressing BNF. We simulated high N deposition by repeatedly applying ammonium-nitrate solution to deadwood of 13 tree species over 9 years (N addition) and compared diazotrophic community composition and BNF rates with untreated controls. Deadwood N concentrations increased over time in both control and N addition, with N addition resulting in higher N concentrations at the final sampling, although significant treatment effects were detected only in Tilia and Pinus. Chronic high-N addition was associated with reduced BNF activity, with significant suppression primarily observed in coniferous deadwood, while responses among broadleaved species were weak, variable, or absent. The N addition altered diazotroph richness and community composition by increasing the abundance of Bradyrhizobium and by reducing Methylocapsa across all tree species. Under N addition, BNF correlated positively with nifH gene copy numbers in broadleaved deadwood but negatively in coniferous deadwood. Co-occurrence networks were more interconnected and modular under N addition, with diazotrophs (e.g., Azospirillum) central in broadleaved deadwood and fungi (e.g., Meliniomyces, Athelia) central in coniferous deadwood. Tree clade (coniferous vs. broadleaved) strongly shaped richness and community response, with broadleaved and coniferous species showing distinct patterns.Overall, the largely robust diversity and community composition of diazotrophs and BNF activity under high N addition suggest that moderately increasing N deposition has little influence on fungal deadwood decomposition and the function of deadwood as a carbon pool in forest ecosystems.}, }
@article {pmid42545607, year = {2026}, author = {Li, R and Yuan, B and Yi, X and Yin, E and Huang, B and Min, Q and Zhou, J and Lv, M and Zhang, B and Zhao, N}, title = {Dietary Bacillus sp. ‌Modulates Multi-tissue Metabolism Through Gut Microbiota Remodeling in High-fat Fed Larimichthys crocea.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {42545607}, issn = {1867-1314}, support = {ZJW-2023-01//the Fund of Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang)/ ; 2023A1515010576//the Guangdong Basic and Applied Basic Research Foundation/ ; 2025TQ09A155//Guangdong High-Level Talent Special Support Program-Young Top-Notch Talent in Science and Technology Innovation/ ; }, abstract = {High-fat diets (HFDs) are widely utilized in aquaculture and result in multiple health and welfare problems in aquatic animals, yet the systemic impacts on host metabolism and gut microbial ecology of HFDs remain insufficiently understood let alone the exact solutions. Here, we investigated the effects of Bacillus thuringiensis Sd_h10 (abbreviated as h10) supplementation on gut microbiota composition, metabolic homeostasis and growth performance in juvenile Larimichthys crocea fed with a high-fat diet. Our results showed that high-fat diet with h10 partially altered intestinal microbial community composition, enhanced the complexity of microbial co-occurrence and was associated with tissue-specific alterations in lipid distribution. Specifically, h10 promoted the deposition of polyunsaturated fatty acid (PUFA) and glucose utilization in intestinal and muscle tissues, while concurrently alleviating hepatic lipid accumulation. Moreover, the expression of genes associated with lipid metabolism, carbohydrate utilization and protein turnover was differentially regulated in the intestine, liver, and muscle, indicating coordinated metabolic adjustments across tissues. Fish in the HFD + h10 exhibited significantly higher relative weight gain and length gain than those in other treatments (P < 0.05). This enhanced growth performance was accompanied by upregulation of growth-promoting genes (gh1, igf1, and myod) and suppression of the growth-inhibitory gene (mstnb) in multiple tissues. Furthermore, partial least squares path modeling (PLS-PM) revealed significant structured associations linking gut microbiota composition, tissue-specific metabolic phenotypes, and growth performance. Collectively, our findings indicated that h10 supplementation may modulate gut microbiota and be associated with multi-tissue metabolic coordination under high-fat dietary conditions. This study provides new insights into the potential role of microbiota-associated metabolic regulation in supporting growth performance in marine aquaculture species.}, }
@article {pmid42535857, year = {2026}, author = {Szafrański, SP and Joshi, AA and Steglich, M and Yang, I and Qu, T and Behrens, W and Muthukumarasamy, U and Melidis, D and Schaefer-Dreyer, P and Grischke, J and Hegermann, J and Nejdl, W and Häussler, S and Stiesch, M}, title = {High-resolution taxonomic profiling and metatranscriptomics identify microbial, biochemical, host, and ecological factors in peri-implant disease.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0075425}, doi = {10.1128/msystems.00754-25}, pmid = {42535857}, issn = {2379-5077}, abstract = {UNLABELLED: Biofilm-associated diseases like peri-implant mucositis (PIM) and peri-implantitis (PI) are significant clinical challenges affecting millions of dental implant patients globally. Although studies have described the role of microbial, host, or environmental factors in disease development, their complex interplay, particularly during dysbiosis, remains poorly understood. This cross-sectional study characterized the microbiome composition and metatranscriptomes of 125 peri-implant biofilms from 48 individuals, uncovering molecular signatures linked to peri-implant health (PIH), PIM, and PI. Distinct variations were observed in biofilm amount, microbial composition and activity, phage populations, and host response. Biofilms were categorized into four community types (CTs) based on the bacterial transcriptional activity: one linked to PIH, one to PI, and two to PIM. PIH and PIM were primarily characterized by aerotolerant taxa with increased anabolic processes, while PI was dominated by obligate anaerobes with complex biofilm morphology. PIM samples, relative to PIH, were characterized by biofilm expansion with minimal functional changes, except for the Neisseria-rich PIM subtype showing higher pyruvate and lipoic acid metabolism. The phagome mirrored the bacterial compositional variations across disease states. Furthermore, human transcriptome responses varied, indicating increased keratinization in PIH, enhanced expression of ribosome components in PIM, and inflammatory signaling and hypoxia in PI. Additionally, we identified complex species-enzyme, phage-bacterium, and host-microbe associations within the peri-implant ecosystem. Our integrative multi-omics approach provides a comprehensive view of microbial, biochemical, host, and ecological factors associated with dysbiosis, offering novel insights into peri-implant disease dynamics.<br><br>IMPORTANCE: Peri-implant mucositis and peri-implantitis are highly prevalent inflammatory conditions that compromise the long-term survival and success of dental implants, yet their underlying biological mechanisms are largely unresolved. The full-length 16S rRNA gene amplicon sequencing (full-16S) allows for high-resolution taxonomic profiling of peri-implant biofilms, thereby advancing our understanding of microbial composition across health and peri-implant diseases. The integration of metatranscriptomics, furthermore, captures actively transcribed genes within the biofilm and offers direct insights into microbial community functions and the broader molecular context of peri-implant dysbiosis. DNA- and RNA-derived abundances were strongly correlated, with only a few microbial classes showing moderate diagnosis-related differences after DNA-based normalization of transcriptional activity. In this study, we integrated full-16S with metatranscriptomic profiling to simultaneously assess microbial taxonomy, functional activity, phage dynamics, and host gene expression in peri-implant biofilms. Importantly, we provide a systems-level view and report previously undescribed associations between different molecular signatures in the peri-implant ecosystem.}, }
@article {pmid42537292, year = {2026}, author = {Han, S and Mo, Q and Wen, X and Wang, X and Wang, X and Yu, Y and Yang, Y and Yang, C and Cai, Z and Zhou, J}, title = {AI-2 type quorum-sensing signal enhances mercury resistance and adsorption in thermotolerant Bacillus subtilis.}, journal = {Journal of hazardous materials}, volume = {515}, number = {}, pages = {143148}, doi = {10.1016/j.jhazmat.2026.143148}, pmid = {42537292}, issn = {1873-3336}, abstract = {Heavy metal contamination in coastal sediments threatens marine microbes and ecological health. Elucidating microbial community synergistic resistance mechanisms is essential for developing novel bioremediation strategies. Microorganisms are known to regulate population-level adaptation to environmental stress through quorum-sensing signals, yet the role of autoinducer-2 (AI-2) in mercury (Hg) resistance and immobilization remains poorly understood. Here, we isolated a thermotolerant Bacillus subtilis strain from coastal sediments and demonstrated that Hg stress selectively activated luxS-associated AI-2 production. AI-2 addition enhanced bacterial survival under combined Hg and heat stress by reducing intracellular reactive oxygen species, increasing antioxidant enzyme activities, promoting biofilm formation, and strengthening Hg adsorption. Sediment microcosm validation further showed that the B. subtilis + AI-2 treatment reduced soluble Hg by 29.6% after 24 h and increased the biomass-associated Hg fraction. These results reveal an AI-2-associated microbial strategy that links intracellular detoxification with extracellular Hg immobilization. While further genetic validation is needed to establish its causal role, this mechanism provides mechanistic insight for microbiome-assisted mercury remediation in thermally dynamic coastal sediments.}, }
@article {pmid42538384, year = {2026}, author = {Chang, M and Wang, Y and Ha, J and Neale, ZR and Ajami, NJ and Diggs, LP and Nalin, AP and Ma, Y and Dong, S and Hoballah, YM and Day, A and Jeong, SD and Wu, A and Schrank, BR and Edwards, JL and Wang, T and Wang, X and Chang, YT and Tang, C and Lim, AJ and Torres, MN and Deng, W and Peitsch, T and Dufilho, MJ and Goswami, S and Jiang, D and Koong, AC and Sharma, P and Wargo, JA and Jiang, W and Kim, BYS}, title = {A transferable gut microbiota-bile acid pathway programs nanomedicine pharmacokinetics and therapeutic response.}, journal = {Nature materials}, volume = {}, number = {}, pages = {}, pmid = {42538384}, issn = {1476-4660}, abstract = {The clinical efficacy of nanomedicines is often limited by hepatic sequestration, yet the endogenous programs determining this clearance state remain incompletely understood. Here we identify the gut microbiota as a regulator of nanomedicine biodistribution through bile-acid-associated programming of Kupffer cell phagocytic state. Using germ-free mice, microbial perturbation, faecal microbiota transplantation and multiomic profiling, we show that metronidazole remodels the gut microbial ecology and reprograms Kupffer cells into a reduced-uptake state, thereby suppressing hepatic clearance and enhancing the tumour accumulation of nanomedicines across multiple formulations and tumour models. Single-cell RNA sequencing reveals a shift in Kupffer cell populations from phagocytic to quiescent states, whereas metabolomic profiling identifies microbiota-dependent reductions in bile acid availability. Gut-bacteria-derived bile acids induce Kupffer cell phagocytosis, and faecal transfer transmits the low-clearance phenotype, defining a transferable gut microbiota-bile acid-Kupffer cell pathway affecting nanomedicine clearance.}, }
@article {pmid42539514, year = {2026}, author = {Li, Y and Zhu, J and Huang, M and Liu, X and Wang, L}, title = {Microbiota-innate immune crosstalk drives atherosclerosis: mechanisms, disease progression, and emerging therapeutic strategies.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1900899}, pmid = {42539514}, issn = {1664-3224}, mesh = {Humans ; *Atherosclerosis/immunology/metabolism/therapy/microbiology/etiology ; *Immunity, Innate ; Animals ; Disease Progression ; *Gastrointestinal Microbiome/immunology ; Signal Transduction ; }, abstract = {Atherosclerosis (AS) is a complex cardiovascular disease driven by the interplay of dysregulated lipid metabolism, chronic inflammation, and immune dysfunction. Increasing evidence has revealed that the gut microbiota not only regulates host metabolic homeostasis but also actively contributes to the initiation and progression of AS through intricate interactions with the innate immune system. Microbial-derived signaling molecules, including lipopolysaccharides, outer membrane vesicles, extracellular nucleic acids, and TMAO, can activate Toll-like receptors, the NLRP3 inflammasome, and nucleic acid-sensing pathways, thereby promoting inflammatory cytokine production, endothelial dysfunction, and foam cell formation. In contrast, beneficial microbial metabolites such as short-chain fatty acids, bile acids, and tryptophan-derived metabolites exert immunomodulatory and vasculoprotective effects through signaling pathways involving FFAR2/3, the AhR, the FXR, and TGR5. Conversely, the innate immune system shapes microbial composition and function through barrier defense, phagocytic clearance, and antimicrobial factor production, establishing a dynamic and reciprocal microbiota-immune interaction network. This review systematically summarizes alterations in microbial ecology and innate immune homeostasis associated with atherosclerosis, elucidates the key molecular mechanisms underlying microbiota-innate immune crosstalk, and examines its dynamic involvement across four critical stages of disease evolution: endothelial dysfunction, foam cell formation, plaque progression, and plaque destabilization and rupture. In addition, emerging therapeutic approaches, including microbiota remodeling, modulation of microbial metabolic pathways, and precision microbiome-based interventions, are comprehensively discussed. The microbiota-innate immune axis provides a novel conceptual framework for understanding atherosclerosis pathogenesis and represents a promising target for future disease prevention, risk stratification, and precision therapeutics.}, }
@article {pmid42541272, year = {2026}, author = {Duru, VC and Mustafa, BE and Beveridge, I and Gauci, C and Elati, K and Ghafar, A and Nijhof, AM and Jabbar, A}, title = {First in vitro feeding of the Australian marsupial tick, Ixodes hirsti Hassall, 1931, with preliminary microbiome profiling and observations on the nymphal morphology.}, journal = {Current research in parasitology &amp; vector-borne diseases}, volume = {10}, number = {}, pages = {100413}, pmid = {42541272}, issn = {2667-114X}, abstract = {Artificial tick feeding systems (ATFS) provide a valuable alternative to animal-based models for studying tick biology. Ixodes hirsti, an Australian tick species that parasitises marsupials, remains understudied due to challenges in laboratory maintenance. Here, we report the first successful in vitro feeding of I. hirsti larvae, provide preliminary microbiome profiles of unfed larvae and larvae recovered after artificial feeding and present the first molecularly confirmed morphological description of the nymphal stage. Field-collected engorged females of I. hirsti were allowed to oviposit under laboratory conditions. Hatched larvae were artificially fed on blood using silicone membranes supplemented with kangaroo hair and/or kangaroo hair extract. Microbiomes were characterised by 16S rRNA amplicon sequencing, while scanning electron microscopy (SEM) and sequencing of 16S rRNA and cox1 genes were used for morphological and molecular characterisation of nymphs. Membranes treated with hair extract alone yielded the highest attachment rate (71%), whereas kangaroo hair-treated membranes produced superior feeding performance, with shorter time to engorgement (9.26 ± 1.00 days) and a higher engorgement weight (0.91 ± 0.01 mg). Exploratory microbiome profiling showed that fed larval pools had numerically lower microbial richness and evenness than unfed larval pools, although these differences were not significant. A total of 80 microbial taxa were shared between groups, whereas seven and 17 taxa were unique to fed and unfed larvae, respectively. Stenotrophomonas was more abundant in fed larval pools, while Coxiella-like and Rickettsia-like endosymbionts were detected in both fed and unfed larvae. These findings demonstrate that ATFS can be adapted for wildlife-associated ticks with specialised host preferences and provide a practical framework for investigating the biology and microbial ecology of ticks.}, }
@article {pmid42542067, year = {2026}, author = {Mandal, A and Ghosh, A and Bhadury, P}, title = {Decoding the spatio-temporal dynamics within the benthic foraminiferal community structure from the northeast coastal Bay of Bengal.}, journal = {Marine environmental research}, volume = {221}, number = {}, pages = {108266}, doi = {10.1016/j.marenvres.2026.108266}, pmid = {42542067}, issn = {1879-0291}, abstract = {Benthic foraminiferal assemblages are widely used as bioproxy for coastal environment monitoring. The present study investigated seasonal variation in benthic foraminiferal assemblages and their co-occurrence patterns in response to freshwater influx and nutrient dynamics along the northeast coast of the Bay of Bengal. Over a one-year period (2021-2022), benthic foraminiferal communities, sediment total organic carbon and dissolved nutrient concentrations in surface and porewater were analyzed from intertidal zones spanning Junput and Tajpur. The benthic foraminiferal abundance varied seasonally, with Junput showing increased abundance during the post-monsoon, followed by a decline in the pre-monsoon. In Tajpur, the benthic foraminiferal abundance decreased from post-monsoon 2021 to pre-monsoon 2021, then increased in monsoon 2021 samples. The benthic foraminiferal assemblages were dominated by Asterorotalia pulchella, Ammonia sp.1, and Ammonia sp.2. Notably, Asterorotalia pulchella showed a significant positive correlation with monsoonal rainfall and sediment total organic carbon, suggesting its potential as bioproxy for monsoon-influenced environments. Network analysis revealed the negative association between Asterorotalia pulchella and members of Ammonia spp., while Asterorotalia pulchella positively co-occurred with Trochammina inflata and Quinqueloculina seminula during the monsoon. Pearson correlation and multivariate analyses revealed that surface and porewater concentrations of dissolved nitrate and ammonia, along with precipitation, were key environmental variables associated with the spatio-temporal dynamics and co-occurrence patterns within the foraminiferal communities. These findings highlight the responses of benthic foraminifera to episodic nutrient enrichment and freshwater input and underscore their utility in ecological monitoring and paleoenvironmental reconstructions across tropical estuarine systems.}, }
@article {pmid42543866, year = {2026}, author = {Turky, M and Cooper, PR and Dummer, PMH}, title = {Precision Endodontics-Advancing Towards Omics-Guided Personalisation: A Narrative Review.}, journal = {International endodontic journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/iej.70247}, pmid = {42543866}, issn = {1365-2591}, abstract = {AIM: To critically evaluate the emerging contribution of genomics, transcriptomics, proteomics, metabolomics and microbiomics to the development of precision endodontics, and to examine the opportunities and translational challenges associated with integrating omics technologies into clinical endodontic practice.<br><br>METHODOLOGY: This narrative review synthesises recent literature across the biomedical and dental sciences, encompassing endodontic research and the principles of translational precision medicine and dentistry to assess the potential applications of omics technologies in endodontics, focusing on how these innovative approaches can inform clinical practice.<br><br>RESULTS: Emerging evidence suggests that omics technologies may enhance understanding of the biological mechanisms underlying pulpal and periapical diseases and support the identification of candidate biomarkers relevant to diagnosis, prognosis, treatment selection and outcome monitoring. Genomic and transcriptomic studies have identified molecular signatures associated with host susceptibility, inflammatory responses and tissue repair processes. Proteomic and metabolomic investigations have revealed biomarkers and metabolic pathways that may improve disease characterisation and provide insight into pulpal vitality and periapical healing. Microbiomic analyses have expanded understanding of the complex microbial ecology of endodontic infections and may contribute to the development of more targeted disinfection strategies. Furthermore, integrating multi-omics platforms and data with artificial intelligence (AI) could yield sophisticated predictive models to support personalised decision-making, thereby advancing individualised patient care. However, despite these advances, the current evidence remains largely exploratory. Many reported biomarkers and molecular signatures have not undergone robust validation, and significant challenges persist regarding standardisation, reproducibility, data integration, cost-effectiveness and clinical implementation.<br><br>CONCLUSION: The concept of precision endodontics represents a potential evolution from conventional 'one-size-fits-all' approaches to more tailored interventions guided by extensive omics data. The synergistic integration of omics and AI may provide a roadmap for developing the next generation of biologically individualised endodontic therapies. However, translating omics-driven approaches into clinically applicable diagnostic and therapeutic tools remains at an early stage. Future progress will depend on rigorous validation studies, interdisciplinary collaboration and the development of practical translational frameworks. While the combined application of omics technologies and AI has considerable potential, substantial evidence gaps must be addressed before precision endodontics can be routinely implemented in clinical practice.}, }
@article {pmid42529392, year = {2026}, author = {Cambara, JCO and Cuber, P and Khattak, F and Lebre, PH and Galgano, S and Houdijk, J and Smallman, D and Estridge, P and Allen, MJ and Short, F and Sutcliffe, M and Mkrtchyan, HV}, title = {Long-reads metagenomics reveals the effects of dulse supplementation on the poultry caecal bacteriome and its associated genetic repertoire.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1868730}, pmid = {42529392}, issn = {1664-302X}, abstract = {INTRODUCTION: Dulse (Palmaria palmata) is a macroalgal feed ingredient rich in polysaccharides and bioactive compounds that offers a sustainable strategy to enhance animal health and productivity through modulation of gut microbiota. However, the impact of dulse supplementation on the taxonomic composition and genetic repertoire of the broiler chicken caecal microbiota remains poorly characterised.<br><br>METHODS: We applied long-read shotgun metagenomic sequencing on 18 caecal samples collected from 27-day-old male Ross 308 broilers following a 7-day feeding trial with three dietary treatments - a reference diet, a soyabean meal-supplemented diet, and a diet supplemented with 30% dulse - to investigate the effects of dulse inclusion on microbial community composition, genetic diversity, and antimicrobial resistance (AMR) and virulence determinants.<br><br>RESULTS: Across all dietary treatments, the Clostridia class predominated (71%), whereas primary fermenters (L. phocaeense), lactic acid bacteria (L. salivarius), and hydrogenotrophic cross-feeders (B. hydrogenotrophica) were enriched in the reference diet, dulse-supplemented and soyabean meal-supplemented groups, respectively (KW p&#x202f;<&#x202f;0.05), contributing to potential improvements in caecal function, immune resilience, and nutrient utilisation while reducing pathogen load. The overall resistome profiles were comparable across dietary treatments and were dominated by genes conferring resistance to tetracyclines, lincosamides, and aminoglycosides. In contrast, the virulome displayed diet-associated shifts: Enterobacteriaceae were enriched in the dulse and reference diets relative to the soyabean meal diet, with an expanded functional repertoire of virulence-associated genes, particularly those involved in adhesion, iron acquisition, and secretion systems. Multidrug resistance genes, virulence determinants, and Col/IncF-type plasmid replicons were associated with E. coli reads, highlighting its potential resistance and virulence arsenal within the caecal microbiota.<br><br>DISCUSSION: Our findings suggest that the benefits of dulse extend beyond its nutritional value, residing in its ability to foster ecosystem resilience; by promoting a diverse, niche-stabilised microbiota, dulse minimises the risk of opportunistic pathogen proliferation, supporting its use as a sustainable, functional feed ingredient.}, }
@article {pmid42530560, year = {2026}, author = {Boath, JM and Nardella, LL and Puschhof, J}, title = {Windows of Opportunity for Genotoxic E. coli in Colorectal Cancer Initiation.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxag192}, pmid = {42530560}, issn = {1365-2672}, abstract = {Polyketide synthase-positive Escherichia coli (pks+ E. coli) has attracted significant attention following the discovery that its genotoxic metabolite, colibactin, imprints distinct mutational signatures in intestinal epithelial cells that are detectable in ∼12% of colorectal cancer (CRC) cases. Although these signatures are present in established tumors, growing evidence suggests that colibactin acts early in tumorigenesis, positioning pks+ E. coli as a potential contributor to CRC initiation. Mechanistic studies show that colibactin genotoxicity is highly context dependent and requires direct epithelial contact-a condition that is typically restricted in the healthy adult intestine. Here, we propose that colibactin mutagenesis occurs during discrete temporal windows when host barriers and microbial ecology transiently permit pks+ E. coli-epithelial interactions. These windows may arise during inflammatory disease states or early-life gut development, two contexts that share disrupted epithelial defenses, expansion of facultative anaerobes, and dynamic oxygen gradients. Defining such permissive states will be essential for establishing causal links between pks+ E. coli exposure and CRC initiation and may reveal opportunities for prevention by targeting microbial colonization during critical periods of susceptibility.}, }
@article {pmid42534899, year = {2026}, author = {Guitart-Matas, J and Bravo, M and Tort-Miró, C and Giler-Baquerizo, N and Fraile, L and Caldas-Ramayo, Y and Ballester, M and Migura-Garcia, L}, title = {Dynamics of archaeal diversity and functionality in the piglet gut microbiome under common antimicrobial treatments.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1833734}, pmid = {42534899}, issn = {2235-2988}, mesh = {Animals ; *Archaea/classification/genetics/drug effects ; Swine ; Metagenomics ; *Gastrointestinal Microbiome/drug effects ; Feces/microbiology ; Metagenome ; Weaning ; *Biodiversity ; *Anti-Infective Agents/administration &amp; dosage/pharmacology ; Gene Expression Profiling ; Phylogeny ; Diarrhea/drug therapy/veterinary ; Anti-Bacterial Agents ; }, abstract = {INTRODUCTION: The gut microbiota comprises a diverse and dynamic community of microorganisms that collectively enhance host metabolism, physiology, and overall functionality. In this context, the swine archaeome remains largely underexplored despite growing evidence that archaea may greatly influence host health. Advances in high-throughput approaches provide new opportunities to reveal the dynamics and composition of archaea. Herein, we uncover the taxonomic and functional landscape of the piglet archaeome during the weaning transition under multiple experimental conditions, integrating shotgun metagenomic and metatranscriptomic analyses to elucidate its contribution to gut microbial ecology.<br><br>METHODS: The seven experimental conditions included four antibiotic treatments for post-weaning diarrhoea (trimethoprim/sulfamethoxazole, colistin, gentamicin, amoxicillin), an oral vaccine, acidifiers in drinking water, and a no-intervention group. A total of 280 faecal samples were collected longitudinally one day before weaning (ST1), three days (ST2), two weeks (ST3), and four weeks (ST4) after the start of the treatment. Treatment was initiated eleven days after arrival at the experimental farm following the onset of clinical signs. Shotgun metagenomics was used to assess archaeal taxonomic diversity and recover archaeal metagenome-assembled genomes (aMAGs), while metatranscriptomics was integrated to assess differentially expressed genes at ST1, ST2, and ST4.<br><br>RESULTS: The results revealed archaea as the second most abundant microorganism, exhibiting a longitudinal increase in diversity over the experimental time. The most predominant genus was Methanobrevibacter, including Methanobrevibacter smithii. Eleven high-quality aMAGs were recovered, belonging to the Methanobacteriota and Thermoplasmatota phyla. Genome-inferred functional analyses revealed that the predominant metabolic processes included the biosynthesis of nucleic acids, amino acids, organic anions, and vitamins. Additional functional traits suggested potential roles in the degradation of sugars, amino acids, and antibiotics were also observed. Moreover, significant differences were detected on the archaeal metatranscriptome between the experimental groups treated with antibiotics and the rest of the groups, underscoring their response to changes in microbial interactions, substrate availability and, in some cases, direct effect of the antimicrobials on metabolic pathways.<br><br>DISCUSSION: Altogether, this study highlights the biological significance of archaeal dynamics during initial life stages and demonstrates how combining metagenomics and metatranscriptomics uncovers their functional potential and the pathways actively expressed in the piglets' gut.}, }
@article {pmid42526436, year = {2026}, author = {Fang, Q and Schneider, KM}, title = {Bile acids in cancer: From metabolism to immunomodulation.}, journal = {Immunity}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.immuni.2026.07.003}, pmid = {42526436}, issn = {1097-4180}, abstract = {Bile acids have emerged as compartmentalized immunometabolic signals that link host metabolism, microbial ecology, and tumor immunity. Altered bile acid profiles are common across malignancies and are associated with tumor progression, immune tone, and responsiveness to immunotherapy. Bile acids shape the gut microbiota, and in turn, microbial enzymes diversify the bile acid pool, generating distinct bile acid species that can remodel the tumor immune landscape. Depending on species identity, concentration, and context, bile acids can support immune surveillance or enforce immune escape by reshaping antigen priming, lymphocyte fitness, myeloid suppression, and immune cell trafficking. Here, we synthesize emerging concepts defining a microbiome-bile acid-immune axis in cancer and highlight therapeutic opportunities to harness bile acid signaling as next-generation strategies in oncology.}, }
@article {pmid42528698, year = {2026}, author = {Selim, S and Adhikary, K and Sarkar, R and Ganguly, K and Misra, A and Kashmiry, AA and Alshareef, SA and Alkhatib, SN and Hagagy, N and Maiti, R}, title = {Ecological and functional roles of plant microbiomes in environmental detoxification.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1883316}, pmid = {42528698}, issn = {1664-302X}, abstract = {Plant-associated microbiomes play a crucial role in environmental detoxification by influencing the degradation, immobilization, and resistance to toxins in polluted settings. The ecological and functional activity of endogenous microbial communities, such as rhizobacteria and endophytic microorganisms, is not well studied when examining contaminants and their environments, despite the fact that plant-mediated bioremediation has garnered a lot of research attention. The majority of previously published research focuses on a single biodegradation route or solitary plant-microbe interactions. Our knowledge of how the microbiome's composition, functional diversity, and ecological stability of microbial communities work together to produce detoxifying results in practical applications is currently lacking. To advance understanding of how plant microbiomes cooperatively mediate environmental detoxification through metabolic interactions, adaptive responses, and host-microbiome communication, this review integrates insights from microbial ecology and functional microbiology. Its primary objective is to synthesize current knowledge on key microbial functions, including metal sequestration, xenobiotic degradation, redox regulation, and modulation of plant responses to biotic stress, while linking these functions to ecological processes such as host specificity, niche specialization, and community assembly. A distinctive aspect of this review is its ecosystem-level perspective, which shifts the focus from individual microbial taxa to the functional resilience of microbial communities in determining detoxification efficiency. The information provided in this review has a scope to provide framework to develop ecologically-sustaining, microbiome-based strategies for the detoxification of the environment and for conducting future bioremediation research.}, }
@article {pmid42528744, year = {2026}, author = {Wayah, SB and Arakawa, K and Philip, K}, title = {Bacteriocins from Limosilactobacillus and Ligilactobacillus: ecological logic, mechanistic diversity, and translational potential in the post-Lactobacillus taxonomy.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1875597}, pmid = {42528744}, issn = {1664-302X}, abstract = {Bacteriocins are ribosomally synthesized antimicrobial peptides that contribute to microbial competition, niche establishment, and community structure. The 2020 taxonomic reorganization of the former broad Lactobacillus genus provides a useful framework for reinterpreting bacteriocin diversity in lineage-specific ecological contexts. This review focuses on bacteriocins produced by species now assigned to Limosilactobacillus and Ligilactobacillus, two host- and food-associated genera that include several reported bacteriocin producers. These genera were selected because they contain bacteriocins with diverse structural features, including cyclic peptides, class IIa and IIb peptides, class IId peptides, defensin-like peptides, and larger proteinaceous bacteriocins, and because many producer strains originate from competitive ecological niches such as the gastrointestinal tract, oral cavity, vagina, milk, poultry, livestock, and fermented foods. We synthesize evidence on bacteriocin biosynthetic gene clusters, molecular diversity, antimicrobial mechanisms, ecological functions, physicochemical stability, and translational potential. This review also distinguishes bacteriocin-specific evidence from effects attributable to bacteriocin-producing strains, particularly for immunomodulation, co-aggregation, pathogen exclusion, and microbiota modulation. Finally, we address how comparative genomics, structured genome mining and artificial intelligence-aided prediction can speed bacteriocin discovery, emphasizing the necessity of experimental validation, standardized activity assays, safety evaluation and scalable production. This study gives a systematic framework to understand the bacteriocins of Limosilactobacillus and Ligilactobacillus in the post-Lactobacillus era by integrating taxonomy, ecology, mechanism and translational evidence.}, }
@article {pmid42528952, year = {2026}, author = {Liu, X and Cheng, W and Li, C and Dessie, W and Qi, C and Ayaz, M and Xu, X}, title = {Integrated metagenomic and metabolomic insights into microbial metabolic reprogramming in the rhizosphere of the invasive plant Praxelis clematidea under low-temperature stress.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1852122}, pmid = {42528952}, issn = {1664-302X}, abstract = {A primary factor preventing the spread of the invasive plant Praxelis clematidea to higher latitudes and altitudes is the low-temperature stress induced by global climate change. The present study investigated the impact of low-temperature stress on the rhizosphere soil micro-ecosystem of P. clematidea, with the aim of examining its adaptive micro-ecological mechanisms via a comprehensive multi-omics approach. The rhizosphere soils of plants were compared under low-temperature (LT, 5 °C) or normal-temperature (HT, 25 °C) treatments. Using soil physicochemical analysis, enzyme activity assay, metagenomics, and non-targeted metabolomics, we observed that LT stress did not significantly alter microbial alpha diversity but strongly shifted the community structure. This change enriched cold-tolerant bacterial taxa, including Nocardiopsis, Sphingobium and Azoarcus. The LT stress was associated with altered carbon and nitrogen cycling, as indicated by increased soil urease activity but decreased alkaline phosphatase and catalase activities. The nitrate-N and ammonium-N levels increased, but total nitrogen, total organic carbon, and organic matter were reduced. Additionally, metagenomic study revealed overexpression of major microbial carbon metabolism genes (e.g., TCA cycle and glycolysis) and downregulation of nitrogen assimilation genes (e.g., glnA and NasA). Furthermore, metabolomics indicated a rise in carbohydrates and vitamins, along with a notable accumulation of stress-resistant secondary metabolites such as phenolic acids, flavonoids, and terpenes in the rhizosphere soils under LT stress. Correlation analysis indicated strong positive associations between the enriched cold-tolerant genera and these stress-resistant metabolites (e.g., costunolide and choline sulfate). Functional enrichment analysis suggested a metabolic reprogramming signature coupled with low-temperature treatment. Finally, this integrated multi-omics study reveals that P. clematidea is associated with an altered rhizosphere microbiome, differential functional gene abundance, and reorganized metabolic networks under low-temperature conditions. These findings offer a vital micro-ecological elucidation for P. clematidea effective colonization and propagation in novel, colder habitats.}, }
@article {pmid42519700, year = {2026}, author = {Pellegrinetti, TA and Molligan, J and Mendes, LW and Pedrinho, A and Pérez-López, E}, title = {Rethinking metagenome-assembled genome completeness: are we truly recovering complete genomes?.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1884628}, pmid = {42519700}, issn = {1664-302X}, }
@article {pmid42520245, year = {2026}, author = {Lingappa, UF and Borrego, SD and Sindermann, ES and Edwards, JL and Chiang, LTE and Chastain, JL and Perrino, C and Craig, RJ and Nicora, CD and Purvine, SO and Merchant, SS}, title = {Field strains of the unicellular alga Chlamydomonas reinhardtii exhibit multicellular characteristics that shape their interactions.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag202}, pmid = {42520245}, issn = {1751-7370}, abstract = {Chlamydomonas reinhardtii is a unicellular green alga long studied as a biological model system but rarely considered from the perspective of its own ecology, thus epitomizing the disconnection between reductionist biology in the laboratory and life in nature. Here we present insights into its ecology understood from field strains. We examined bacterial communities that coenriched with C. reinhardtii from the field, revealing specific associations. We then compared the biology of C. reinhardtii field strains to laboratory strains, illuminating strain level heterogeneity and adaptations to life in the field vs. laboratory. Field strains exhibited more robust photosynthesis, higher abundances of pherophorin proteins, a propensity for pallmeloid formation, and high cell wall permeability. Finally, we phenotyped cocultures of C. reinhardtii with a coenriched bacterial partner, demonstrating how differences between field and laboratory strains manifest in biotic interactions. Although the organisms in question are classically understood as unicellular, our observations of field strains highlighted their participation in multicellular units, challenging the utility of unicellular frameworks in extending our knowledge of model organism biology in the laboratory towards understanding microbial ecology.}, }
@article {pmid42522045, year = {2026}, author = {Duan, L and Liang, L and Liu, W and Huang, Y and Xu, X and Liang, W and Pang, J and Wu, C}, title = {Polygonatum polysaccharides: structure-dependent gut microbiota modulation, SCFA-mediated mechanisms, and systematic health effects regulation.}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.70950}, pmid = {42522045}, issn = {1097-0010}, support = {KFB23129A//Science and Technology Innovation Special Fund Project of Fujian Agriculture and Forestry University/ ; }, abstract = {Dietary polysaccharide-gut microbiota interactions form a critical foundation of precision nutrition by shaping microbial ecology, metabolic outputs, and host systemic health. Polygonatum sibiricum is a traditional medicinal and edible plant rich in Polygonatum polysaccharides (PPs), which exhibit antioxidant, anti-inflammatory, and immunomodulatory activities. Despite increasing evidence for these bioactivities, the mechanistic relationships linking PPs structural characteristics with specific gut microbiota responses, defined metabolic outputs, and downstream host signaling pathways remain poorly integrated. Recent studies indicate that PPs can modulate gut microbiota composition and function by selectively enriching beneficial bacteria and enhancing short-chain fatty acid (SCFA) production. These microbial metabolites act as key signaling mediators regulating host immunity and metabolic homeostasis through G protein-coupled receptors and related pathways. However, the influence of PPs molecular weight, monosaccharide composition, branching architecture, and glycosidic linkages on microbial selectivity and metabolic specificity has not been systematically elucidated, limiting the rational design of PP-based interventions. To address these gaps, this review proposes a four-level regulatory framework, 'PPs structure-microbiota targets-SCFA pathways-host health,' which integrates PP structural features with microbiota modulation, SCFA-mediated signaling, and health outcomes, providing a theoretical basis for the precise development of PP-based functional foods and therapeutic agents. © 2026 Society of Chemical Industry.}, }
@article {pmid42524220, year = {2026}, author = {Crous, PW and Akram, W and Albuquerque, GMR and Alfenas, AC and Alfenas, RF and Altés, A and Alvarado, P and Amirmijani, AR and Arumugam, E and Asif, M and Bandini, D and Barreto, GG and Barreto, RW and Batista, VEC and Bezerra, JDP and Bilański, P and Bizio, E and Castañeda-Ruiz, RF and Chaves, J and Condé, TO and Costa, MM and Custódio, FA and Courty, PE and Czachura, P and Damm, U and Darmostuk, V and Dearnaley, J and De la Peña-Lastra, S and Delgado, G and de Silva, NI and Dovana, F and Drummond-Herdman, A and Eberhardt, U and Esteve-Raventós, F and Ferisin, G and Ferreira, RJ and Ferro, LO and Firmino, AL and Flakus, A and Fournier, J and Gardiennet, A and Gerbeau-Pissot, P and Ghobad-Nejhad, M and Gruhn, G and Guard, FE and Harms, K and Heilmann-Clausen, J and Hongsanan, S and Hülsewig, T and Inokuti, EM and Jankowiak, R and Kaliyaperumal, M and Kehlet, T and Lacerda, SR and Larsson, E and Leão, AF and Lebel, T and Lima, AA and López-Villalba, &#xc1; and Maciá-Vicente, JG and Mateos, A and Mejía, LC and Mendes, DR and Möller, L and Mombert, A and Monteiro, MBN and Moreno, G and Nagy, L and Niskanen, T and Nogueira, PTS and Oliveira, JA and Oliveira, PHF and Ortiz, DA and Pancorbo, F and Paz, A and Pazmiño, DA and Pereira, OL and Piątek, M and Plata, O and Pordel, A and Raaijmakers, JM and Ralaiveloarisoa, AB and Ramos, DO and Ravikumar, S and Rigueiro-Rodríguez, A and Rivas-Torres, GF and Rodrigues, JG and Rodriguez-Flakus, P and Romero, M and Saba, M and Sánchez, A and Sánchez-Dueñas, G and Santana, JS and Serrano, M and Silva, JAS and Stępniewska, H and Stryjak-Bogacka, M and Tennakoon, DS and van 't Hof, P and van Vuuren, NI and Varga, T and Vauras, J and Vieira, BS and Visagie, CM and Wipf, D and Woods, R and Groenewald, JZ}, title = {Fungal Planet description sheets: 1868-1920.}, journal = {Persoonia}, volume = {56}, number = {}, pages = {1-173}, pmid = {42524220}, issn = {0031-5850}, abstract = {Novel species of fungi described in this study include those from various countries as follows: Australia, Marasmius ballator on leaf litter in subtropical rainforest, Marasmius carbinensis on litter and twigs of Hyptis suaveolens, Marasmius clocca on leaf litter of regenerating subtropical rainforest. Bolivia, Aggregatorygma saraanense on trunk of Trichilia inaequilatera. Brazil, Arthropolymorpha endophytica (incl. Arthropolymorpha gen. nov.), from healthy roots of Coffea arabica, Didymella digitariae on Digitaria insularis, Geastrum baseiae on soil, Magnibotryascoma souzamottae as endophyte from cladodes of Tacinga inamoena, Neoleptosporella agapanthi from stalks of Agapanthus praecox, Penicillifer endoradicis as endophyte from roots of Musa acuminata, Sirastachys cavernicola from leaf litter, Toxicocladosporium atratum as root endophyte of Cattleya locatellii. China, Fasciatispora citri on dead twig of Citrus maxima. Denmark, Inocybe leucantheana on wet ground with Alnus, Betula and Picea. Ecuador (Galapagos Islands), Fusarium cristobalense on Scalesia gordilloi, Fusarium scalesiae on Scalesia pedunculata. Finland, Inocybe ranaria on mull soil, near Betula pendula and Abies sp. France, Bullatosporium pinophilum on the bark of Pinus nigra subsp. nigra, Dialonectria eutypellicola on Eutypella prunastri, on branches of Prunus spinosa, Mycobernardia involucriformis on dead Bambusa sp., Pseudocosmospora perforaticola on dead stromata of Hypoxylon perforatum on Fraxinus, Stylonectria colleeniae on Trimmatostroma scutellare, with Lophium mytillinum, on dead branch of Larix decidua. French Guiana, Neocosmospora duolechatii on dead bark of Bauhinia sp. Germany, Inocybe giovannii on soil under Abies alba, Fagus sylvatica and Picea abies, Triseptosporium fallopiae (incl. Triseptosporium gen. nov.) on Fallopia japonica. India, Phylloporia bharatavarsa on living tree of Phyllanthus emblica. Iran, Fusarium phoenicis on roots of Phoenix dactylifera. Italy, Inosperma confusum on soil under Quercus ilex and Pinus halepensis, Inosperma subinodorum on calcareous soil in Picea abies forest. Madagascar, Oudemansiella viscida on dead wood or branches. Netherlands, Colletotrichum urticicola from leaf spots on Urtica dioica. Pakistan, Agrocybe punjabensis on soil on fallen remains of Saccharum officinarum. Panama, Ijuhya panamaensis and Sarcopodium panamaense on twig litter of angiosperm. Poland, Cytospora tatrensis from dead stems of Pinus mugo, Myxotrichum flavum on resin of Picea abies, Symphoricola tarnoviensis (incl. Symphoricola gen. nov.) from sooty mould community on Symphoricarpos albus. Portugal, Hypoxylon azoricum on fallen branch of Laurus azorica, Tuber honstrassii in clayey and calcareous soil under Quercus rotundifolia and Arbutus unedo. South Africa, Paraphaeosphaeria andropogonicola on leaves of Andropogon eucomus, Talaromyces armstrongii from soil. Spain, Geoglossum martinae on soil under Quercus ilex and Cistus ladanifer, Inocybe percastanea on sandy, acidic soils under Cistus ladanifer and Pinus pinaster, Lamproderma stephensonii on twigs of Pinus sylvestris, Ramariopsis alboviolacea on soil under Prunus lusitanica subsp. lusitanica, Russula olivaceopinetorum on acidic sandy soil among Pinus sylvestris needles, Scolecobasidium endophyticum from root-associated soil collected in a grassland, Tuber danielis in acidic soil beneath Cistus ladanifer, Quercus ilex, and Genista scorpius. Sweden, Inocybe adusticans on soil, in snow bed area with Salix herbacea and Bistorta vivipara, Inosperma friesii on soil in mixed deciduous forest. Switzerland, Stylonectria stoeckliana on Cytospora sp. on twigs of Salix sp. Thailand, Neoleptosporella camporesiana on dead branch of unidentified plant. Uganda, Bjerkandera ugandensis on a rotting log. UK (Scotland), Narcissea scotica on decaying dung of Lagopus scotica. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Akram W, Albuquerque GMR, Alfenas AC, Alfenas RF, Altés A, Alvarado P, Amirmijani AR, Arumugam E, Asif M, Bandini D, Barreto GG, Barreto RW, Batista VEC, Bezerra JDP, Bilański P, Bizio E, Castañeda-Ruiz RF, Chaves J, Condé TO, Costa MM, Custódio FA, Courty P-E, Czachura P, Damm U, Darmostuk V, Dearnaley J, De la Peña-Lastra S, Delgado G, de Silva NI, Dovana F, Drummond-Herdman A, Eberhardt U, Esteve-Raventós F, Ferisin G, Ferreira RJ, Ferro LO, Firmino AL, Flakus A, Fournier J, Gardiennet A, Gerbeau-Pissot P, Ghobad-Nejhad M, Gruhn G, Guard FE, Harms K, Heilmann-Clausen J, Hongsanan S, Hülsewig T, Inokuti EM, Jankowiak R, Kaliyaperumal M, Kehlet T, Lacerda SR, Larsson E, Leão AF, Lebel T, Lima AA, López-Villalba Á, Maciá-Vicente JG, Mateos A, Mejía LC, Mendes DR, Möller L, Mombert A, Monteiro MBN, Moreno G, Nagy L, Niskanen T, Nogueira PTS, Oliveira JA, Oliveira PHF, Ortiz DA, Pancorbo F, Paz A, Pazmiño DA, Pereira OL, Piątek M, Plata O, Pordel A, Raaijmakers JM, Ralaiveloarisoa AB, Ramos DO, Ravikumar S, Rigueiro-Rodríguez A, Rivas-Torres GF, Rodrigues JG, Rodriguez-Flakus P, Romero M, Saba M, Sánchez A, Sánchez-Dueñas G, Santana JS, Serrano M, Silva JAS, Stępniewska H, Stryjak-Bogacka M, Tennakoon DS, van 't Hof P, van Vuuren NI, Varga T, Vauras J, Vieira BS, Visagie CM, Wipf D, Woods R, Groenewald JZ (2026). Fungal Planet description sheets: 1868-1920. Persoonia 56: 1-173. doi: 10.3114/persoonia.2026.56.01.}, }
@article {pmid42525349, year = {2026}, author = {Dos Reis, JBA}, title = {Functional diversity and ecological consequences of endophytic Bacillus-plant interactions.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {42525349}, issn = {1874-9356}, abstract = {The genus Bacillus, particularly endophytic species, has been widely studied as a source of plant growth-promoting bacteria in agricultural systems. These microorganisms contribute to plant performance through nutrient acquisition, phytohormone production, pathogen suppression, microbiome modulation, and enhanced tolerance to biotic and abiotic stresses. However, their ecological roles, functional plasticity, and genomic diversity remain poorly integrated into conceptual frameworks that extend beyond crop-based applications. Functional plasticity is reflected in their ability to colonize diverse plant hosts and tissues and to promote similar plant responses through distinct molecular mechanisms. Likewise, genomic diversity is evidenced by variation in accessory genomes, biosynthetic gene clusters, and regulatory networks that shape ecological functions and metabolite production. This review examines endophytic Bacillus as a model for understanding how metabolically versatile and genomically plastic bacteria establish functional, but context-dependent, associations with plants. Drawing on evidence from functional genomics, pangenomics, metabolomics, and microbial ecology, we discuss mechanisms associated with plant growth promotion and emphasize their dependence on host identity, environmental conditions, and microbial interactions. We address functional convergence arising from distinct genetic and metabolic routes, the contribution of accessory genomes and regulatory variation, and the ecological consequences of microbial inoculation in resident plant-associated microbiomes. We also highlight the limitations of in vitro screening approaches and the need for experimental validation across multiple biological scales to establish robust genotype-phenotype relationships. Finally, we extend the discussion beyond agricultural systems to consider the use of endophytic Bacillus in wild plant systems and ecological restoration, emphasizing the importance of evaluating both functional outcomes and ecological impacts.}, }
@article {pmid42518164, year = {2026}, author = {Sattar, Z and Asili, J}, title = {Probiotics and Plant Extracts in the Gut-Brain Axis: Mechanisms, Interactions, and Clinical Perspectives.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {42518164}, issn = {1867-1314}, abstract = {Growing evidence highlights the microbiota-Gut-Brain Axis (MGBA) as a critical pathway linking diet to neurological health. This review synthesizes current evidence on the complementary, additive, and potentially synergistic interactions between probiotics and plant-derived phytochemicals within the MGBA. While the individual benefits of these dietary components are well established, their combined synbiotic application offers expanded mechanistic breadth through coordinated modulation of microbial ecology, epithelial barrier integrity, immune inflammatory signaling, and neurochemical pathways. Probiotics and phytochemicals interact bidirectionally via microbial biotransformation, enhancing short-chain fatty acid production, reducing endotoxin translocation, and attenuating systemic and neuroinflammation. These effects are further linked to indirect modulation of neurotransmitter systems and neurotrophic signaling relevant to mood regulation, cognitive function, and neurodegenerative processes. Evidence from preclinical and emerging clinical studies supports the relevance of these mechanisms in conditions such as Alzheimer's disease, Parkinson's disease, mood disorders, and Autism Spectrum Disorder, although human data remain limited. Overall, this narrative review proposes a mechanistic framework describing how probiotics and plant-derived phytochemicals may interact through complementary microbial, immune, and neurochemical pathways within the Microbiota-Gut-Brain Axis. It also highlights current knowledge gaps and emphasizes the need for well-designed clinical studies to validate their combined therapeutic potential.}, }
@article {pmid42519323, year = {2026}, author = {Chen, W and Sun, Y and Meng, CF and Wu, ST and Jiang, XY and Meng, XM and Wang, QF}, title = {Aging-driven metabolic abnormalities remodel intercellular communication through the gut-liver-heart axis and may promote coronary artery disease: the key role of bile acid metabolism.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1870980}, pmid = {42519323}, issn = {1664-3224}, mesh = {Humans ; *Bile Acids and Salts/metabolism ; *Coronary Artery Disease/metabolism/etiology/immunology ; Animals ; *Aging/metabolism/immunology ; *Liver/metabolism/immunology ; *Cell Communication ; Gastrointestinal Microbiome ; Signal Transduction ; Receptor, Farnesoid X-Activated ; Cellular Senescence ; }, abstract = {Coronary artery disease (CAD) remains the leading cause of cardiovascular mortality worldwide and shows a strong age-dependence that classical risk-factor models do not fully explain. A growing body of work indicates that aging is closely associated with CAD and, in preclinical models, can promote it through immunometabolic remodeling of the gut-liver-heart axis, in which bile acid metabolism is proposed to act as a central molecular link. Here we integrate cellular, molecular, and clinical evidence to outline how aging perturbs this axis and sustains chronic vascular inflammation. At the cellular level, senescent cells in the intestinal, hepatic, and vascular compartments generate the senescence-associated secretory phenotype (SASP) - a process linked to cGAS-STING and NLRP3 inflammasome activation, mitochondrial dysfunction, and decline of the NAD[+]-SIRT3 axis - and help establish the systemic state of inflammaging. In the gut, age-related dysbiosis lowers bile salt hydrolase and 7α-dehydroxylase activities, contracts the secondary bile acid pool, weakens epithelial barrier integrity, and triggers metabolic endotoxemia that maintains LPS-TLR4-NF-κB signaling. In the liver, Kupffer cell M1 polarization, attenuated farnesoid X receptor (FXR) signaling, and altered exosomal cargo amplify systemic inflammatory output. Reduced FXR and Takeda G-protein-coupled receptor 5 (TGR5) signaling weakens the endogenous restraint of macrophage activation, vascular smooth muscle cell phenotypic switching, and cardiomyocyte metabolic protection. The downstream result is endothelial dysfunction, foam cell formation, plaque instability, and adverse cardiac remodeling. We then appraise emerging immune-metabolic interventions - microbiota remodeling, FXR/TGR5 agonists, senolytic therapies, metformin, and integrated biomarker frameworks for early risk stratification - while noting that most are currently supported only by preclinical or early-phase human data. By placing bile acid signaling at the interface of innate immunity, microbial ecology, and metabolic homeostasis, this review offers an immunological framework for aging-associated CAD and identifies candidate immune-metabolic targets for prevention and therapy in older adults.}, }
@article {pmid42519405, year = {2026}, author = {Van Holm, W and Marynissen, J and Van Campenhout, L and Minnebo, Y and Mermans, F and Lauwens, K and Teughels, K and Saghi, M and Zayed, N and Boon, N and Teughels, W}, title = {Oral colonization of probiotics: one size fits all?.}, journal = {Current research in microbial sciences}, volume = {11}, number = {}, pages = {100642}, pmid = {42519405}, issn = {2666-5174}, abstract = {The clinical application of probiotics for oral health is increasing, yet their colonization dynamics remain poorly understood. This study investigated whether administration timing, strain origin, and host-specific factors influence oral persistence. Two Limosilactobacillus reuteri strains (oral vs. non-oral isolate) were evaluated in two in vivo studies. In the first, participants consumed probiotics either during the day or before bedtime; in the second, daily administration continued for 28 days, followed by a 7-day washout. Probiotic abundance was qPCR quantified and oral microbiomes were sequenced. Additionally, a retrospective analysis of periodontitis patients receiving probiotics was performed. Bedtime administration significantly prolonged probiotic detectability compared to daytime intake. Both strains were largely transient, disappearing within days post-administration, though the oral isolate showed enhanced adhesion. Notably, a subset of participants retained the probiotic for up to a week, suggesting interindividual variability and potential biomarkers of colonization. Periodontitis patients who had higher concentrations of probiotics also displayed more improvement in pocket probing depth of deep pockets. These findings highlight the need to consider timing, strain selection, and host factors in probiotic-based oral health interventions.}, }
@article {pmid42276550, year = {2026}, author = {Gronniger, JL and Larin-Henriquez, D and Bernardin, JR and Shoemaker, LG and Bittleston, LS}, title = {Environmental complexity shapes maintenance of bacterial diversity through context-dependent interactions among niche axes.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {42276550}, issn = {1751-7370}, support = {DEB 2236782//National Science Foundation CAREER award/ ; 00001638//Simons Foundation Early Career Investigator Award in Aquatic Microbial Ecology and Evolution/ ; OIA 2019528//NSF/ ; DEB 2441720//NSF/ ; }, abstract = {Microbial communities are often more species-rich than predicted from classical ecological models. The high levels of coexistence observed in nature are typically attributed to forces that modulate niche availability and stabilize communities. Specific drivers of niche partitioning are often tested in isolation, and the interactive effects of niche variation across resources, space, and time have not been tested together experimentally to determine how they affect community responses. Here, we used 26 bacterial strains previously isolated from carnivorous pitcher plant (Sarracenia purpurea) aquatic pools to construct and expose species-rich synthetic communities to four factors that alter environmental complexity in a fully factorial design, creating combinations of resource complexity, spatial niche structure, and temporal fluctuations. Across treatments, increased niche complexity generally, but not always, promoted the long-term retention of more species, with a saturating effect at the highest levels of complexity. Resource complexity emerged as a primary driver of diversity, with its effects also depending on other niche axes. Interactions among factors frequently deviated from additive expectations, with both synergistic and antagonistic effects observed depending on the combination of conditions. Together, these results show that environmental complexity shapes bacterial diversity through context-dependent, nonlinear interactions among niche dimensions, highlighting that the relationship between niche dimensionality and diversity is contingent on how environmental factors combine.}, }
@article {pmid42505138, year = {2026}, author = {Chaput, G and Deen, EA and Pham, EQ and Crystal, S and Matayoshi, A and Andeer, P and Northen, TR and Eisen, JA and Stachowicz, JJ and Sogin, EM}, title = {Microbiota assembly in Zostera marina during early host development across controlled growth experiments.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0072226}, doi = {10.1128/msystems.00722-26}, pmid = {42505138}, issn = {2379-5077}, abstract = {Seagrass restoration practices are evolving to leverage microbiome applications, similar to agricultural systems that have demonstrated how targeted microbial communities enhance crop resilience in challenging environments. While adult seagrass microbiome research has expanded significantly, research on the seed microbiome remains critically understudied. This gap is important given that seeds represent a large portion of restoration efforts. Advancing seed microbiome research requires standardized experimental systems for controlled plant-microbe interaction studies, which are currently lacking in seagrass research. Here, we tested fabricated ecosystem devices (EcoFAB 2.0) as a standardized system for growing Zostera marina (eelgrass) seedlings, enabling a controlled study of aquatic plant-microbe interactions. Using these chambers, we addressed three key questions: (i) can we reliably grow eelgrass in a controlled laboratory setting, (ii) can we manipulate eelgrass microbiota assembly and its long-term trajectory, and (iii) can we detect shifts in the microbiota during plant development (host filtering)? Host morphology measurements and 16S rRNA gene amplicon sequencing were used to track microbiota assembly across three early developmental stages of the host. Because plants were grown in a sterile environment, surface sterilization of seeds (bleach and ethanol) removed epiphytes without disturbing the shared endophytic community, yet microbiota composition remained divergent at Stage 6 (143 differentially abundant ASVs), indicating that seed coat epiphytes make a lasting and distinct contribution to assembly trajectory. We also identified 26 stage-specific indicator ASVs across eelgrass development, suggesting stage-specific microbial associations during seedling establishment. This work demonstrates the potential for targeted manipulation of the microbiome in seagrass for restoration efforts.IMPORTANCEUsing the Fabricated Ecosystem 2.0 (EcoFAB 2.0), we were able to successfully control the microbial environment of eelgrass, Zostera marina, resulting in the reduction of epiphytes and maintaining low microbial diversity across plants without compromising the morphology and growth of seedlings. Our findings advance the marine plant model system, Z. marina, by identifying taxonomic indicators across life stages. This work lays the foundation for a targeted understanding and application of microbiomes for seagrass restoration, bridging the critical knowledge gap between agricultural seed microbiome success and marine restoration applications.}, }
@article {pmid42505610, year = {2026}, author = {Bariz, K and Saoudi, B and Lahcene, S and Moualek, I and Sebbane, H and Rekbi, F and Belkhalfa, H and Derguini, A and Ibrahim, NA and Alsalamah, SAA and Aleissa, MS and Basher, NS and Trabelsi, L and Houali, K}, title = {Antibiofilm Activity of Three Essential Oils Against ESBL-Producing Klebsiella pneumoniae: An In Vitro and In Silico Investigation of Putative Molecular Targets.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {7}, pages = {}, pmid = {42505610}, issn = {2079-6382}, support = {IMSIU-DDRSP2601//This work was supported and funded by the Deanship of Scientific Research at Imam Moham-mad Ibn Saud Islamic University (IMSIU)/ ; }, abstract = {Biofilm formation is a major contributor to antibiotic resistance in Klebsiella pneumoniae, posing a serious challenge to current therapeutic strategies. Thus, this study aims to evaluate the antibiofilm activity of three essential oils Thymus hirtus Willd. Ssp. algeriensis Boiss, Syzygiuma romaticum, and Eucalyptus globulus against four clinical isolates of ESBL-producing K. pneumoniae, along with the reference strain K. pneumoniae ATCC 700603. The antibiofilm activity of essential oils was assessed with crystal violet assay using MICs ranging from 3.38 ± 0.2 to 27.1 ± 0.56 mg/mL, 2 ± 0.19 to 32 ± 0.55 mg/mL, and 13.78 ± 0.62 to 110.25 ± 3.37 mg/mL, for TEO, SEO and EEO, respectively. In vitro tests showed that S. aromaticum EO and T. algeriensis EO exhibited the best anti-adhesive activity with a percentage of up to 75.39%, while no difference was observed between the EO in their eradication activity. Microscopic observations confirmed the disorganization of the biofilm after treatment with T. algeriensis. The molecular docking analysis of the three EOs main compounds with MrkH, SdiA and MrkD revealed that SdiA was the most favorable target, with p-cymene (-7.7 kcal/mol), α-pinene (-7.5 kcal/mol), and eucalyptol (-7.1 kcal/mol) showing the strongest binding affinities. Thymol and p-cymene showed also a favorable affinity with MrkD. Overall, p-cymene and α-pinene demonstrated the most favorable binding profiles, whereas linalool exhibited the weakest predicted interactions. These results highlight the promising potential of these EOs, as multi-target antibiofilm agents against MDR- K. pneumoniae biofilms.}, }
@article {pmid42505979, year = {2026}, author = {Liu, S and Wu, Y and Lv, Y and Shao, M and Lv, D and Li, Q and Shang, Q}, title = {Fermentation of Structurally Defined Alginate Oligosaccharides by the Human Gut Microbiota Enriched in Bifidobacterium, Bacteroides, Faecalibacterium, or Blautia.}, journal = {Marine drugs}, volume = {24}, number = {7}, pages = {}, pmid = {42505979}, issn = {1660-3397}, support = {32471335//National Natural Science Foundation of China/ ; 2024CXPT048//Key R&amp;D Program of Shandong Province/ ; }, mesh = {Humans ; *Alginates/chemistry/metabolism ; *Oligosaccharides/chemistry/metabolism ; Fermentation ; Prebiotics ; Bacteroides/metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome/physiology ; Fatty Acids, Volatile/metabolism ; Faecalibacterium/metabolism ; Bifidobacterium/metabolism ; }, abstract = {Alginate oligosaccharides (AOS) are attractive candidates for prebiotic development, yet how oligosaccharide structure and baseline microbial community composition interact to shape fermentation remains an open question. In this study, we stratified fecal microbiota from healthy donors into operational genus-predominance groups (Bifidobacterium, Bacteroides, Faecalibacterium, or Blautia) and selected representative samples for in vitro fermentation of six structurally distinct AOS preparations (SAOS-1, SAOS-2, OAOS, UAOS, SMOS, and SGOS). Substrate consumption, short-chain fatty acid (SCFA) production, and shifts in microbial community structure were profiled. The six preparations differed in structural type, number-average molecular weight, and average degree of polymerization. Among them, SAOS-1 exhibited the most consistent utilization across all four groups and yielded the highest total SCFA production. SAOS-1 fermentation also attenuated inter-group community divergence and enriched several beneficial or functionally relevant taxa, including Bacteroides and Faecalibacterium. Interestingly, the magnitude and direction of microbial responses remained enterotype-dependent, with the Bacteroides-predominant group assembling the most complex fermentative consortium. These findings demonstrate that AOS structure and baseline microbial ecology jointly dictate fermentation outcomes, positioning SAOS-1 as a strong candidate for precision prebiotic development. This structure-community interaction paradigm provides a rational basis for the targeted deployment of marine oligosaccharides in personalized gut health strategies.}, }
@article {pmid42507180, year = {2026}, author = {Hayat, M and Parveen, R and Nawaz, MS and Rao, MA and Waqar, A and Naqvi, RZ and Anwar, MA and Zahir, ZA and Qasim, M and Dogar, MA and Sandino, TS and Singh, BK and Imran, A}, title = {Plant growth-promoting rhizobacteria (PGPR) producing ACC deaminase and exopolysaccharides enhance salt tolerance in wheat.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {8}, pages = {}, pmid = {42507180}, issn = {1573-0972}, mesh = {*Triticum/microbiology/growth &amp; development/physiology ; *Carbon-Carbon Lyases/metabolism/biosynthesis ; *Salt Tolerance ; Rhizosphere ; Soil Microbiology ; *Polysaccharides, Bacterial/metabolism/biosynthesis ; Seedlings/growth &amp; development/microbiology ; Salinity ; Plant Roots/microbiology/growth &amp; development ; Bacillus/metabolism ; Plant Development ; Pseudomonas/metabolism/enzymology ; *Bacteria/metabolism/enzymology/genetics ; Sodium Chloride ; Biomass ; }, abstract = {Soil salinity severely impairs crop growth and yield by inducing ion toxicity, osmotic stress, and disrupting plant nutrient uptake. This pervasive stressor poses a major threat to global cereal production and food security, especially the wheat crop. Plant growth-promoting rhizobacteria (PGPR) capable of producing 1-aminocyclopropane-1-carboxylic acid deaminase (ACCD) and exopolysaccharides (EPS) offer a promising biological strategy to enhance plant tolerance under saline conditions. This study evaluated the combined application of halotolerant ACCD- and EPS-producing bacterial strains to mitigate salt stress (150 mM NaCl) in wheat. Eight strains were selected based on functional traits: ACCD producers (sz18 Brevibacterium frigoritolerans, sz30 Bacillus spizizienii, sz35 Pseudomonas glycinis, sz80 Pseudomonas grimontii) and EPS producers (EP5 Bacillus tequilensis, EP8 Bacillus spizizienii, EP29 Pseudomonas koreensis, EP35 Bacillus subtilis). All strains successfully colonized the wheat rhizosphere. Co-inoculation of ACCD and EPS-producing bacteria significantly enhanced seedling performance under salinity, increasing fresh biomass and root and shoot length by approximately 30% compared with uninoculated controls. Gene expression analysis further demonstrated that inoculated plants exhibited substantial upregulation of key salt-responsive genes: rbcS (~ 3-fold), rbcL (~ 6-fold), cAPX (~ 6-fold), and DREB2 (~ 2-fold). These transcriptional changes indicate improved photosynthetic capacity, antioxidant defense, and stress-responsive regulation in treated plants. Overall, the findings highlight the synergistic potential of ACCD- and EPS-producing PGPR in alleviating salinity stress in wheat. If validated under field conditions, this microbial consortium could serve as an effective, sustainable approach to improve wheat resilience and productivity in salt-affected soils.}, }
@article {pmid42508699, year = {2026}, author = {Chopra, C and Kukkar, D and Kaur, H and Samudrala, R}, title = {QIIME2-based pooled re-analysis of 16s rRNA sequences reveals gut microbiota dysbiosis in diabetic nephropathy mouse models.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {108732}, doi = {10.1016/j.micpath.2026.108732}, pmid = {42508699}, issn = {1096-1208}, abstract = {Diabetic nephropathy (DN) is a progressive microvascular and renal disease that develops due to chronic suffering from diabetes. Growing research evidences have suggested the role of gut microbiota dysbiosis advancement of DN. In this regard, our study analyses publicly available 16S rRNA sequencing datasets from murine models (38 DN, 37 healthy controls (HCs), and 33 diabetic mellitus (DM) samples) using the quantitative insights into microbial ecology 2 (QIIME2) pipeline to explore gut microbial alterations associated with disease progression. This study provides a focused re-analysis of publicly available 16S rRNA datasets from DN mouse models, complementing previous broader DM microbiome studies. Following quality filtration, trimmomatic, and DADA2 assisted denoising, taxonomic classification was performed using the SILVA database, and alpha diversity was assessed through shannon, faith's PD, pielou's evenness, and observed feature indices. Firmicutes and Bacteroidota were found to be the dominant group, with minor contributions from Proteobacteria and Actinobacteriota. Controls showed the higher abundance of Faecalibacterium, Roseburia, and Blautia, whereas Escherichia-Shigella and Alistipes were elevated in DN groups. Alpha diversity analysis revealed insignificant differences in richness or evenness between DN and control samples, suggesting that disease-associated microbial variations are primarily driven by specific taxonomic shifts rather than overall diversity. These findings highlight the potential involvement of gut dysbiosis in DN pathophysiology and support the therapeutic relevance of targeting the gut-kidney axis.}, }
@article {pmid42509522, year = {2026}, author = {Chen, PY and Hsu, TW and Chiang, TY and Huang, CL}, title = {Comparative analysis of root microbiomes in four Swertia species from Taiwan.}, journal = {Journal of plant research}, volume = {}, number = {}, pages = {}, pmid = {42509522}, issn = {1618-0860}, support = {NSTC 103-2621-B-006-002-//National Science and Technology Council/ ; }, abstract = {Swertia (Gentianaceae) comprises four species endemic to Taiwan that possess significant medicinal potential. While root microbiomes are known to promote plant adaptation, the microbial ecology of Taiwanese Swertia remains largely unexplored. We investigated the rhizosphere and root endosphere microbiomes of these species using 16S rRNA gene sequencing and predictive functional profiling, integrated with host phylogenetic data. Our results revealed that rhizosphere bacterial communities were significantly more diverse than those in the root endosphere. PERMANOVA indicated that host species and plant compartment significantly influenced bacterial communities, but the high residual variance suggests that much of the community variation remains unexplained by the variables measured in this study. Phylogenetic analysis indicated that the root endosphere is more strongly influenced by host phylogeny, with closely related species harboring more similar communities. Functional profiling further demonstrated that the rhizosphere is predicted to be enriched in pathways related to nitrogen fixation and organic matter degradation, whereas the endosphere harbors bacterial taxa potentially associated with pathogen suppression. These findings underscore the multifaceted roles of the root microbiome in supporting the development, stress adaptation, and ecosystem sustainability of Swertia species in Taiwan's unique altitudinal gradients.}, }
@article {pmid42510761, year = {2026}, author = {Tian, M and Liang, Y and Lu, J and Shi, W and Zhao, Y and Gan, W and Jia, S and Xiao, C and Zhao, T and Zhang, H}, title = {Global Genomic Analysis of Bovine-Associated Klebsiella pneumoniae Reveals Genetic Diversity and Resistance-Virulence Profiles.}, journal = {Biology}, volume = {15}, number = {14}, pages = {}, doi = {10.3390/biology15141215}, pmid = {42510761}, issn = {2079-7737}, support = {BT-2025-TCYC-0066//Xinjiang Uyghur Autonomous Region "Tianchi Talent" Youth Doctoral Talent Program/ ; RCZK202578//Shihezi University/ ; 2024AB034//Science and Technology Development Project of Xinjiang Production and Construction Program/ ; 2025YD013//Central Government-Guided Local Science and Technology Development Project/ ; 2025AB083, 2024AB034 and 2024AB035//Scientific and Technological Tackling Plan for Key Fields of Xinjiang Production and Construction/ ; }, abstract = {Bovine-associated Klebsiella pneumoniae is an important bacterial species linking animal health, microbial ecology, and One Health-oriented antimicrobial resistance research. In this study, we performed a global genomic analysis of 1291 publicly available bovine-associated K. pneumoniae genomes collected from 18 countries between 2005 and 2024 using data retrieved from NCBI. MLST, core-genome phylogenetic analysis, pangenome analysis, CARD, VFDB, and PlasmidFinder were used to characterize sequence types, genomic diversity, antimicrobial resistance-associated genes, virulence-associated genes, and plasmid replicons. A total of 256 sequence types were identified, among which ST107 was the most common. Core-genome phylogenetic analysis revealed multiple genomic lineages, while pangenome analysis identified 46,325 gene clusters, including 1967 core genes and 40,595 cloud genes, indicating an open pangenome structure and substantial accessory gene diversity. Virulence-associated genes were unevenly distributed, with yagZ/ecpA being the most frequently detected determinant. In total, 138 antimicrobial resistance-associated genes or potential resistance determinants were detected across 16 antimicrobial categories, including clinically important β-lactamase- and carbapenemase-associated genes. IncF-family plasmid replicons, particularly IncFIB(K)_1_Kpn3, were frequently detected, suggesting widespread plasmid replicon-associated genomic backgrounds; however, physical co-localization between resistance genes and specific plasmid backbones could not be confirmed. Overall, this study reveals the genetic diversity, resistance-associated gene reservoir potential, heterogeneity of virulence-associated genes, and plasmid replicon backgrounds of bovine-associated K. pneumoniae. Importantly, the genome-predicted AMR potential identified in this study should not be interpreted as confirmed phenotypic resistance without further experimental validation. These findings provide genomic insights for risk surveillance, candidate control-target screening, and microbiota-oriented intervention research.}, }
@article {pmid42511090, year = {2026}, author = {Liu, C and Chen, X and Fu, C and Ouyang, K and Qu, M and Qiu, Q}, title = {Dietary 4-Hydroxy-2,5-Dimethyl-3(2H)-Furanone Supplementation in Hu Sheep: Implications on Fecal and Rumen Microbiota.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {14}, pages = {}, doi = {10.3390/ani16142212}, pmid = {42511090}, issn = {2076-2615}, support = {32260861//National Natural Science Foundation of China/ ; 20243BCE51165//Major Discipline Academic and Technical Leaders Training Program of Jiangxi Province/ ; }, abstract = {This study aimed to investigate the effects of dietary 4-hydroxy-2,5-dimethyl-3(2H)-furanone (HDMF) supplementation on ruminal and fecal microbial diversity, community composition, and predicted functional pathways. A total of 24 four-month-old female Hu sheep with similar body weights (20.6 ± 0.5 kg) were randomly allocated to two groups, with six replicates per group and two sheep per replicate. One group was fed a basal diet (CON), and the other received the same basal diet supplemented with 100 mg/kg HDMF. The results showed that ruminal microbial alpha diversity did not differ between the CON and HDMF groups (p > 0.05), whereas fecal microbial richness and evenness were higher in the CON group than in the HDMF group (p < 0.05). Beta diversity of ruminal microbiota did not differ between groups (R = 0.0667, p = 0.217), whereas fecal microbiota exhibited significant differences (R = 0.7333, p = 0.002). Dietary HDMF supplementation increased the relative abundances of Lachnospiraceae and Oribacterium in the rumen, elevated Spirochaetota and Lachnospiraceae AC2044 group in feces, and concurrently decreased Desulfobacterota and Alistipes in feces. Correspondingly, PICRUSt2-based functional prediction indicated putative associations between HDMF-induced microbial shifts and altered functional pathways, including increased relative abundances of amino acids biosynthesis and ABC transporter pathways, concomitant with decreased relative abundances of glycolysis/gluconeogenesis and pyruvate metabolism pathways in feces. These results suggest that dietary HDMF supplementation was associated with more pronounced alterations in fecal microbiota than in ruminal microbiota. This study provides a preliminary microbial ecology perspective on gastrointestinal microbiota in response to dietary HDMF supplementation in ruminants.}, }
@article {pmid42511801, year = {2026}, author = {Cheng, A and Ee, KP}, title = {Deciphering Stress Resilience in Black Pepper (Piper nigrum L.): From Current Advances to Emerging Opportunities.}, journal = {International journal of molecular sciences}, volume = {27}, number = {14}, pages = {}, pmid = {42511801}, issn = {1422-0067}, support = {FRGS/1/2024/STG01/UM/02/1//Ministry of Higher Education/ ; }, abstract = {Black pepper (Piper nigrum Linn.), one of the world's most economically important spice crops, is increasingly challenged by climate-related stresses, emerging pests and diseases, and declining soil health, all of which threaten its productivity and sustainability. While previous reviews have predominantly focused on black pepper genomic resources, breeding strategies, and disease management, the integration of multi-omics technologies, microbiome science, and artificial intelligence (AI) to enhance its stress resilience has received comparatively limited attention. This review synthesizes recent advances in the molecular mechanisms underlying black pepper responses to biotic and abiotic stresses, with emphasis on omics approaches (such as genomics and transcriptomics), as well as the roles of beneficial microbial communities in enhancing stress tolerance, nutrient acquisition, and disease suppression. We further discuss emerging microbiome-assisted strategies, including the development of beneficial microbial consortia and targeted manipulation of microbial functions, for enhancing black pepper resilience under changing environmental conditions. In addition, we explore how AI-driven analytical approaches can integrate complex multi-omics and microbiome datasets to unravel the complex molecular networks governing black pepper-microbe interactions under stress conditions and accelerate precision breeding. By integrating genomics, microbial ecology, and AI, this review presents a systems-level framework for understanding and improving stress resilience in black pepper. This interdisciplinary perspective highlights new opportunities to accelerate the development of climate-resilient cultivars and advance sustainable black pepper production.}, }
@article {pmid42512165, year = {2026}, author = {Pereira, CV and Garcia, NG and Fonseca, DC and Machado, PG and Rezende, MF and Alcântara, SFM and Andrade, EF and Pereira, LJ}, title = {Smoking and Depth-Related Anaerobic Bacteria in Endodontic-Periodontal Lesions: A Pilot Study.}, journal = {International journal of environmental research and public health}, volume = {23}, number = {7}, pages = {}, pmid = {42512165}, issn = {1660-4601}, support = {309610/2023-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; APQ-01552-21//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; }, abstract = {Endodontic-periodontal lesions are complex conditions in which endodontic infection and periodontal breakdown coexist and may create anaerobic microbial niches along the root surface. Although smoking is a well-established modifier of periodontal disease progression and subgingival microbial ecology, its influence on the depth-related distribution of anaerobic periodontal bacteria in teeth affected by endodontic-periodontal lesions remains incompletely understood. This cross-sectional study investigated the distribution patterns and co-occurrence of selected anaerobic periodontal bacteria in smokers and non-smokers with endodontic-periodontal lesions, considering periodontal pocket depth and anatomical site. Subgingival samples were collected from periodontal pockets of different probing depths (3-4 mm, 5-6 mm, and ≥7 mm), as well as from healthy gingival sulci and oral mucosa, in 26 patients with endodontic-periodontal lesions. The presence of Porphyromonas gingivalis, Prevotella intermedia, Tannerella forsythia, Prevotella nigrescens, and Aggregatibacter actinomycetemcomitans was assessed. Detection was performed using polymerase chain reaction (PCR). Qualitative detection frequencies and microbial co-occurrence patterns were compared between smokers and non-smokers across sites and pocket depths. Non-smokers showed higher detection of Tannerella forsythia in pockets ≥ 7 mm (p < 0.05). Overall microbial co-occurrence was lower in smokers in deeper periodontal pockets, whereas detection patterns in healthy gingival sulci and oral mucosa were broadly comparable between groups. Our findings suggest that smoking may be associated with an attenuated depth-related detection pattern and reduced co-occurrence of selected anaerobic periodontal bacteria in endodontic-periodontal lesions.}, }
@article {pmid42513562, year = {2026}, author = {Hau, HM and Jahn, N and Karitnig, R and Hasenhütl, SM and Sucher, R and Stiegler, P and Laudi, S}, title = {Microbiome-Targeted Modulation in Renal Transplantation.}, journal = {Journal of clinical medicine}, volume = {15}, number = {14}, pages = {}, doi = {10.3390/jcm15145648}, pmid = {42513562}, issn = {2077-0383}, abstract = {The gut microbiome has emerged as a critical determinant of health and disease across virtually all organ systems. In the context of chronic kidney disease (CKD) and renal transplantation, mounting evidence reveals a complex bidirectional relationship between the intestinal microbiota and kidney function-commonly referred to as the gut-kidney axis. Patients with CKD harbor a profoundly altered gut microbial ecosystem characterized by reduced diversity, depletion of beneficial commensal organisms, and expansion of pathobiont taxa capable of generating uremic toxins and pro-inflammatory mediators. These perturbations are further compounded by the uremic milieu itself, dietary restrictions, frequent antibiotic exposure, and the use of immunosuppressive agents following transplantation. The gut-liver-kidney axis adds an additional layer of complexity, linking hepatic metabolism, bile acid signaling, endotoxemia, and systemic immune activation to the progression of renal disease. Gut-derived metabolites-including short-chain fatty acids (SCFAs), bile acids, trimethylamine N-oxide (TMAO), and tryptophan-derived uremic solutes such as indoxyl sulfate and p-cresyl sulfate-serve as molecular mediators of inter-organ crosstalk and have been identified as both biomarkers and therapeutic targets. A growing body of literature supports the diagnostic and prognostic utility of microbiome composition and its metabolic signatures in patients with CKD and those undergoing renal replacement therapy. Therapeutic strategies aimed at restoring microbial homeostasis-encompassing dietary interventions, prebiotics, probiotics, synbiotics, fecal microbiota transplantation (FMT), bile acid-based therapies, and novel pharmacological approaches-hold considerable promise for improving outcomes in CKD and transplant recipients. Importantly, the bidirectional relationship between immunosuppressive drugs and the gut microbiota has emerged as a clinically significant determinant of both microbial ecology and drug pharmacokinetics: each major immunosuppressive agent class-corticosteroids, calcineurin inhibitors, mycophenolate mofetil, and mTOR inhibitors-induces characteristic dysbiotic patterns, while in turn, the microbiota modulates drug bioavailability through enzymatic biotransformation (notably bacterial beta-glucuronidase activity affecting mycophenolic acid enterohepatic recirculation) and modulation of host drug-metabolizing enzymes. This narrative review provides a comprehensive overview of the current understanding of microbiome dysbiosis in the setting of renal disease and transplantation, examines the mechanistic underpinnings of the gut-liver-kidney axis, details the multifaceted impact of dysbiosis on transplant outcomes-including allograft function and rejection, infection, post-transplant diabetes, and cardiovascular complications-and critically appraises the translational potential of microbiome-targeted interventions. We conclude by highlighting ongoing challenges and future directions toward personalized, microbiome-informed clinical care.}, }
@article {pmid42513909, year = {2026}, author = {Luo, D and Ponsero, AJ and Wright, K and Baker, DJ and Telatin, A and Townsley, C and Giotis, ES}, title = {Microbiome Stability in Wild and Rehabilitated Insectivorous Bats Revealed by Shotgun Metagenomics.}, journal = {Microorganisms}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/microorganisms14071403}, pmid = {42513909}, issn = {2076-2607}, support = {MR/Z506242/1/MRC_/Medical Research Council/United Kingdom ; RGS\R2\242527//Royal Society/ ; BB/X011054/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CCG2260/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Wildlife rehabilitation can alter host-associated microbial communities, yet the effects of temporary managed care on the gut microbiome of insectivorous bats remain poorly understood. We used shotgun metagenomic sequencing to investigate gut microbiome composition in wild and rehabilitated bats from Yorkshire, United Kingdom. A total of 25 faecal metagenomes were analysed from four bat species (Myotis daubentonii, Pipistrellus pipistrellus, Nyctalus noctula, and Nyctalus leisleri), including wild baseline individuals and bats undergoing temporary managed care for 1-49 days. Microbial community structure clustered primarily according to host species and roost location, with no significant separation associated with rehabilitation status. Among bats in managed care, bacterial alpha diversity did not differ significantly with time in care (H = 2.30, p = 0.32). Archaeal communities displayed markedly lower interindividual variation than bacterial communities (coefficient of variation: 12.2% vs. 41.8%), indicating a highly conserved archaeal microbiome across hosts. Rehabilitated bats exhibited modest compositional shifts in bacterial communities, including increased relative abundances of Yersiniaceae and Lactobacillaceae and reduced abundances of environmentally associated taxa such as Pseudomonadaceae and Erwiniaceae. These changes may reflect controlled dietary provision and reduced environmental exposure during care. Overall, no marked rehabilitation-associated differences in gut microbiome diversity or community structure were detected under the current sampling design. These findings are consistent with microbiome stability during temporary managed care, although longitudinal studies are required to confirm microbiome dynamics within individual bats. Nonetheless, this study provides an initial baseline for future microbiome-informed wildlife rehabilitation studies.}, }
@article {pmid42514002, year = {2026}, author = {Semenzato, G and Barberini, S and Menicucci, F and Atzori, G and Brunetti, C and Marino, G and Palchetti, V and Fani, R and Centritto, M and Emiliani, G}, title = {Plant-Endophyte Cross-Talk in Origanum heracleoticum L. In Vitro Axenic Culture: Endosphere-Driven Bacterial Interactions and Plant Metabolic Responses.}, journal = {Microorganisms}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/microorganisms14071497}, pmid = {42514002}, issn = {2076-2607}, abstract = {Origanum L. (Lamiaceae) is a commercially important medicinal and aromatic plant genus worldwide. Endophytic bacterial communities are recognized for promoting plant growth and physiology, although their interactions with host metabolism remain insufficiently understood. In this work, an in vitro model of axenic Origanum heracleoticum plants was established to investigate the relationship between endophytic bacteria and their tissue of origin. Specifically, we evaluated the adaptation of two strains, Bacillus sp. OHL2 and Pseudomonas sp. OHS18, and the potential role of Bacillus sp. OHL2 in modulating plant physiology and secondary metabolism. Bacterial inoculation and re-isolation highlighted niche-specific adaptation and possible co-evolution within the host, suggesting an active role of the plant in regulating bacterial colonization within the endosphere. Inoculation with Bacillus sp. OHL2 significantly enhanced photosynthetic rate, leaf area, dry weight, and chlorophyll content. No substantial overall changes in secondary metabolism were detected. Rosmarinic acid was the predominant phenolic, while monoterpenes dominated, with carvacrol dominant. A significant tissue-by-inoculation interaction was observed for α-humulene, which decreased in leaves of inoculated plants. Overall, the in vitro system provides a valuable platform to study plant-endophyte interactions and bacterial mechanisms underlying the stimulation of plant growth and metabolic responses.}, }
@article {pmid42514056, year = {2026}, author = {Di Gregorio, F and Polizzi, A and Marmo, GM and Angjelova, A and Jovanova, E and Campagna, R and Mascitti, M and Isola, G}, title = {Revisiting the Oral-Gut Axis: Microbial Symbiosis, Dysbiosis, and Bidirectional Links Between Periodontitis and Inflammatory Bowel Disease.}, journal = {Microorganisms}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/microorganisms14071551}, pmid = {42514056}, issn = {2076-2607}, support = {PNRR-POC-2023-12&#x2009;377&#x2009;354//Ministero della Salute/ ; }, abstract = {BACKGROUND: Recent scientific evidence indicates that the oral-gut axis represents a critical interface in host-microbiota interactions, carrying profound implications for both periodontal and gastrointestinal diseases. This scoping review aims to evaluate the reciprocal influence between periodontitis and inflammatory bowel disease (IBD). Specifically, the underlying mechanisms of microbial translocation, immune interaction, and metabolite-mediated signaling linking the oral microbiota to gut microbial ecology are critically evaluated.<br><br>METHODS: Studies were selected from the PubMed, Web of Science, and Scopus databases up to May 2026. Eligible criteria included in vivo studies written in English and conducted within the last 10 years, whereas human studies involving participants under 18 years of age were excluded. The included studies analyze the effects of oral and gut dysbiosis on the opposing district. Through the database search, 2094 records were identified, and 34 articles were selected based on the eligibility criteria.<br><br>RESULTS: The included studies demonstrate the interconnection between the oral and gut microbiota. The included studies reveal that predominant oral taxa, specifically Porphyromonas gingivalis, Fusobacterium nucleatum, and Aggregatibacter actinomycetemcomitans, alter intestinal microbial composition. In particular, P. gingivalis colonizes the gut, exacerbating both oral and intestinal inflammation by stimulating pro-inflammatory cytokine expression via Th17 cell activation. Finally, salivary microbial composition appears to be associated with the presence and status of IBD.<br><br>CONCLUSIONS: Understanding these interconnected microbial ecosystems provides valuable insights that may support the future development of integrated diagnostic and therapeutic strategies for patients suffering from periodontitis and IBD. Further large-scale studies with longer follow-up periods are required to standardize potential salivary markers and multidisciplinary therapeutic protocols for the management of periodontitis and IBD.}, }
@article {pmid42514091, year = {2026}, author = {Valiakhmetov, EE and Frolov, M and Sukhanov, AY and Miftakhov, AK and Validov, SZ}, title = {Strain-Specific Loci in Bacterial Genomes: Whole-Genome Discovery, Genomic Context, and Application for Multi-Strain qPCR Monitoring.}, journal = {Microorganisms}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/microorganisms14071587}, pmid = {42514091}, issn = {2076-2607}, support = {FMEG-2027-0007//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {Monitoring individual strains in complex microbial communities remains a fundamental challenge in microbial ecology and biotechnology. Here, we present an integrated pipeline for identifying and validating strain-specific loci (SSL) in four biotechnologically relevant plant growth promoting strains from three genera (Stenotrophomonas, Bacillus, and Pseudomonas). The pipeline applies a two-round specificity-filtering strategy combining whole-genome comparison and high-sensitivity BLASTn validation of revealed strain-specific loci (SSL) against the NCBI nucleotide database. SSL count decreased with increasing Average nucleotide identity (ANIb) of the strains used for the analysis, ranging from one locus in B. halotolerans (ANIb = 98.91%) to 15 loci in S. rhizophila (ANIb = 86.49%). All 25 SSL were universally AT-rich, mainly accessory-genome-associated, with flanking regions enriched in genes of unknown function (34.6%) and mobile genetic elements (19.2%). TaqMan qPCR assays targeting SSL demonstrated high specificity-no target sequences were detected across ten geographically distinct soil samples, nor in a native rhizosphere metagenome-and sensitivity, with limits of detection of 0.01-0.1 pg of genomic DNA. Spike-in experiments in soil yielded method detection limits (MDL) of 850-15,000 CFU/g. All four strains were detected in the wheat rhizosphere seven days after consortium application in a field experiment, validating the pipeline for multi-strain field monitoring.}, }
@article {pmid42514156, year = {2026}, author = {Schulze-Makuch, D and Bartholomäus, A and Arens, FL and Mangelsdorf, K and Wagner, D}, title = {Small-Scale Mineral and Microbial Heterogeneities near a Fumarole at the Furnas Hydrothermal Zone on the Azores.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {7}, pages = {}, pmid = {42514156}, issn = {2075-1729}, abstract = {The Azores are characterized by intense volcanic activity, creating unique environments such as fumarole sites, where geothermal gases and high temperatures drive distinct chemical and biological processes. To investigate small-scale heterogeneity within such a site, six visually distinct samples were collected within a 30 cm radius at an active fumarole on São Miguel Island. The samples were analyzed for elemental and mineralogical composition, bacterial lipid biomarkers (PLFAs), and microbial community structure using a novel DNA separation technique to specifically target the living microbiome. Despite mineralogical similarities across all samples-predominantly composed of alunite, alkali-feldspar, and quartz-significant microbial heterogeneity was observed. Both PLFA and bacterial iDNA analyses revealed distinct microbial communities associated with specific conditions indicated by the specific colors: red and brown samples were dominated by Proteobacteria and Actinobacteriota, yellow and green by Thermoplasmatota and Actinobacteriota, and white and gray by Crenarchaeota. Interestingly, the gray samples exhibited a broader microbial composition, sharing some taxa with all other samples. These striking color variations are likely driven by differences in both specific mineral composition and microbial pigmentation, reflecting localized biogeochemical processes. Our findings demonstrate that extreme microbial heterogeneity can occur over remarkably small spatial scales within fumarolic systems, underscoring the complex interplay between chemical and biological factors in these dynamic volcanic habitats.}, }
@article {pmid42514643, year = {2026}, author = {Nassar, N and Tharwat, M and Tayel, A and Tariq, M and Khan, YM and Alshanbari, FA and Khan, IM}, title = {From Gut to Gain: The Microbiome's Contribution to Broiler Health and Productivity.}, journal = {Veterinary sciences}, volume = {13}, number = {7}, pages = {}, doi = {10.3390/vetsci13070633}, pmid = {42514643}, issn = {2306-7381}, support = {QU-APC-2026//Qassim University/ ; }, abstract = {The gut microbiome plays a central role in regulating nutrient utilization, immune function, and disease resistance, thereby directly influencing growth performance and feed efficiency. Existing microbiome modulation strategies, including probiotics, prebiotics, dietary interventions, and antibiotic alternatives, are critically evaluated. Despite their reported benefits, the effectiveness of these approaches often remains inconsistent across production systems. Evidence suggests that this variability is largely driven by complex interactions among microbial communities, host factors, and environmental and management conditions, which are frequently overlooked in conventional intervention-based approaches. To address this gap, this review proposes an integrated microbiome-host-environment framework that links microbial ecology with host physiology and production conditions. The framework provides a systems-level perspective for understanding the factors governing microbiome stability and production responses, offering a basis for more targeted and reliable microbiome management strategies. Finally, current challenges and future research priorities are discussed, including the integration of multi-omics technologies, precision nutrition, and data-driven approaches to support next-generation poultry production systems. By emphasizing the interconnected nature of microbiome regulation, this review contributes a conceptual foundation for improving broiler productivity and sustainability through more consistent and effective microbiome optimization.}, }
@article {pmid42514673, year = {2026}, author = {Zhou, G and Liu, Y and Pu, X and Ning, Q and Guo, X and Wang, L and Zhong, Y and Wang, G and Guo, X and Wang, M}, title = {Conjoint Analysis of Sheep Microbiome, Metabolome, and Transcriptome Revealed the Effect Mechanisms of Feeding with Broccoli Extract.}, journal = {Veterinary sciences}, volume = {13}, number = {7}, pages = {}, doi = {10.3390/vetsci13070663}, pmid = {42514673}, issn = {2306-7381}, support = {BSGJSYS202603//Key Laboratory of Livestock and Forage Resources Utilization around the Tarim Basin, Ministry of Agriculture and Rural Affairs-Provincial-Ministerial Co-construction Project/ ; }, abstract = {Alterations in microbiota, transcript and metabolites are critical to intestinal homeostasis and host health. This study used a combination of 16s rRNA, transcriptome sequencing and liquid chromatography-mass spectrometry to investigate intestinal microbiota, genes and metabolic profiles in the ileum of Hu sheep fed broccoli extract. Here, we randomly allocated 14 Hu sheep to two diets: a basal diet without any supplementation (NC) and a basal diet supplemented with 200 mg/kg broccoli tail (BT). After 60 days of treatment, blood and jejunal samples were collected for serum biochemical indicators and multi-omics analysis. In this study, the extract of broccoli tails had a significant effect on the serum biochemical indicators, including white blood cells, red blood cells, mean corpuscular volume, mean corpuscular hemoglobin concentration, mean platelet volume, triglycerides and total protein in Hu sheep (p < 0.05). Transcriptomic analysis showed that the 672 differentially expressed genes between the NC and BT groups were primarily enriched in linoleic acid metabolism, steroid hormone biosynthesis, and cholesterol metabolism. Metabolomics analysis using Kyoto Encyclopedia of Genes and Genomes enrichment showed that the 41 differentially abundant metabolites were mainly enriched in bile secretion, vitamin B6 metabolism, and the mTOR signaling pathway. 16S rRNA sequencing results indicated that the extract of broccoli tails increased the relative abundance of Peptostreptococcaceae and decreased the relative abundance of Lachnospiraceae, Lachnospirales, and Bacteroidaceae. Integrated transcriptome, metabolome, and microbiome analysis showed that the gut microbiota and host transcriptomic changes may participate in systemic metabolic regulation by modulating amino acid metabolism, lipid signal transduction, nucleotide metabolism, and vitamin B6-related metabolic pathways. These findings demonstrate that the extract of broccoli tails modulates intestinal gene expression, systemic metabolism, and gut microbial ecology in Hu sheep, providing new insights into the utilization of agricultural byproducts as a functional feed supplement for ruminants.}, }
@article {pmid42515062, year = {2026}, author = {Hussien, RHM and Kortsinoglou, AM and Wood, MJ and Kouvelis, VN and Mellikeche, W and Touray, M and Tembeni, B and Alzain, M and Alotaibi, F and Sobhy, IS and Saud, Z and Loveridge, EJ and Eastwood, DC and Butt, TM}, title = {Endophytic Entomopathogenic Fungi Shape Herbivore Behavior and Plant-Insect Interactions: Implications for Biological Control.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {7}, pages = {}, doi = {10.3390/pathogens15070735}, pmid = {42515062}, issn = {2076-0817}, support = {UKRI239//UK Research and Innovation/ ; EP/X525637/1//Engineering and Physical Sciences Research Council/ ; 2019-2022//Ministry of Higher Education and Scientific Research/ ; NA//Saudi Arabia Cultural Bureau in London/ ; }, abstract = {Entomopathogenic fungi (EPF) are well established as biological control agents, but their emerging role as endophytes reveals a broader and more powerful function in crop protection. By colonizing plant tissues, endophytic entomopathogenic fungi (EEPF) create a dynamic tripartite interaction between plants, fungi, and herbivores, enabling systemic, plant-mediated pest suppression. This review synthesizes current knowledge on the behavioral and ecological responses of herbivorous arthropods to EEPF-colonized plants, with an emphasis on the mechanisms and implications for integrated pest management (IPM). Growing evidence indicates that EEPF consistently modify herbivore behavior and performance across diverse crops and insect taxa. Colonization frequently alters feeding, host selection, and oviposition, often deterring pests, although mediated responses may vary among fungal species, host plants, insect taxa, and environmental conditions. These responses are driven by EEPF-induced changes in plant chemistry, including shifts in volatile organic compounds (VOCs) and defensive metabolites. In parallel, EEPF impair insect fitness by delaying development, reducing survival, and lowering fecundity, thereby suppressing pest populations. These plant-mediated and behavioral changes extend to multitrophic interactions, potentially affecting associations with natural enemies and the transmission efficiency of some insect vectors of plant viruses. Despite rapid progress, critical gaps remain in resolving the mechanistic basis of these interactions and their stability under field conditions. Advancing the application of EEPF will require integrated approaches combining microbial ecology, chemical ecology, and insect behavioral biology. Harnessing these interactions offers a compelling pathway to reduce reliance on synthetic pesticides while enhancing the resilience and sustainability of agricultural systems.}, }
@article {pmid42515698, year = {2026}, author = {Garcia, J and Olo-Fontinha, E and Silva, J and Dias-Costa, R and Alves, MJ and Gouvinhas, I}, title = {Mushroom-Derived Phenolic Compounds as Emerging Prebiotic-like Modulators of Gut Microbiota, Intestinal Health, and Metabolism.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {19}, number = {7}, pages = {}, doi = {10.3390/ph19071014}, pmid = {42515698}, issn = {1424-8247}, support = {2024.04884.RESTART//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; UID/04033/2025//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; UID/00772/2025//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; 2024.06281.BDANA//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; 01/C05-i02/2022//RE-C05-i02 - Miss&#xe3;o Interface/ ; }, abstract = {Background/Objectives: Mushroom-derived phenolic compounds are gaining attention as bioactive molecules with potential roles in gut microbiota modulation, intestinal health, and metabolic regulation. Although mushroom polysaccharides are well established as fermentable substrates, the contribution of fungal phenolics to microbiota-host interactions remains less defined. This review aimed to critically analyse the evidence supporting mushroom-derived phenolic compounds as emerging prebiotic-like modulators of gut microbiota, intestinal function, and host metabolism. Methods: A narrative critical review was conducted using scientific literature retrieved from PubMed, Scopus, Web of Science, and Google Scholar. Studies addressing phenolic profiling in edible and medicinal mushrooms, gastrointestinal digestion, colonic fermentation, microbial biotransformation, gut microbiota modulation, intestinal barrier function, inflammation, and metabolic outcomes were considered. Particular attention was given to chromatographic and mass spectrometry-based studies, in vitro digestion/fermentation models, mechanistic studies, animal experiments, clinical trials, systematic reviews, and meta-analyses. Results: Current evidence shows that mushrooms contain diverse phenolic compounds, mainly phenolic acids such as gallic, protocatechuic, caffeic, p-coumaric, ferulic, vanillic, syringic, and cinnamic acids. Due to limited small intestine absorption, a substantial fraction of these compounds may reach the colon, where they undergo microbial biotransformation into smaller phenolic metabolites. These metabolites may influence microbial ecology, support beneficial taxa, modulate short-chain fatty acid production indirectly, attenuate oxidative stress and inflammatory signaling, and contribute to intestinal barrier integrity. However, most evidence derives from in vitro and preclinical studies, while human data remain limited and are mainly based on whole-mushroom interventions. Conclusions: Mushroom-derived phenolic compounds are promising prebiotic-like modulators within the microbiota-metabolite-host axis. Nevertheless, their specific contribution cannot yet be quantitatively distinguished from that of other mushroom constituents, particularly β-glucans, chitin, and other fungal polysaccharides, because most available evidence derives from whole-mushroom matrices, crude extracts, or polysaccharide-rich preparations rather than isolated phenolic fractions. Future studies should compare whole mushroom preparations, polysaccharide-rich fractions, and standardized phenolic-rich extracts, integrating metabolomics, microbiome profiling, and well-designed clinical trials to clarify the relative mechanistic and therapeutic relevance of mushroom phenolics. Future studies should use standardized phenolic-rich extracts, metabolomics, microbiome analysis, and well-designed clinical trials to clarify their mechanistic relevance, clinical significance, and translational potential.}, }
@article {pmid42517205, year = {2026}, author = {Xiao, W and Zhou, X and Cheng, L and Bodelier, PLE and Wang, G and Yang, Z and Zhou, J}, title = {Microbial Functional Gene Abundance-Integrated Modeling of Global Methane Sinks in Upland Soils Under Future Climate Change.}, journal = {Global change biology}, volume = {32}, number = {7}, pages = {e71026}, pmid = {42517205}, issn = {1365-2486}, support = {32171635//National Natural Science Foundation of China/ ; }, abstract = {Methanotrophs are key microbial regulators of soil methane (CH4) sinks, but the global impact of their functional gene abundance on CH4 oxidation remains unquantified. This gap limits the integration of key functional genes abundance parameters (e.g., pmoA) into soil CH4 sink model. We integrated meta-analysis, machine learning, and process-based modeling to assess the relationship between pmoA gene abundance and soil CH4 uptake. Our developed Functional Gene Abundance-Based Methanotrophy Model (FGA-MeMo) incorporates pmoA as a proxy for CH4 oxidation capacity, significantly improving model simulations. FGA-MeMo estimates global upland soil CH4 uptake at 45.74 ± 0.26 Tg year[-1], which is 56%-58% higher than MeMo model. Under SSP5-8.5 scenario, this increases to 64.68 ± 0.35 Tg year[-1] by 2100, with mid- and high-latitude regions showing enhanced CH4 oxidation due to greater pmoA abundance. These findings highlight the importance of integrating microbial functional genes into Earth system models for improved CH4 cycle predictions.}, }
@article {pmid42517643, year = {2026}, author = {Ochsner, N and San Román, M and Jiménez-Fernández, A and Bonhoeffer, S and Pascual-Garcia, A}, title = {misosoup: a metabolic modeling tool for identifying minimal microbial communities, facilitates the exploration of microbial ecology and biotechnological applications.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0068826}, doi = {10.1128/msystems.00688-26}, pmid = {42517643}, issn = {2379-5077}, abstract = {UNLABELLED: Microbial survival and function often depend on metabolic interactions within communities. Therefore, a central question in disentangling microbial organization is determining which minimal groups of strains are able to thrive in a given medium-referred to as "minimal communities." Answering this question is essential for understanding microbial distribution, enhancing laboratory cultivation, and designing synthetic communities (SynComs). Here, we introduce misosoup, a Python package for identifying minimal communities (minimal supplying community search). Through genome-scale constraint-based metabolic modeling, misosoup enables the systematic identification of communities that support microbial growth in environments where individual strains fail to survive alone. We validate misosoup against experimentally verified minimal communities, demonstrating its ability to predict known cooperative interactions, cocultures, and consortia with biotechnological potential. We further illustrate the use of misosoup to investigate broad microbial ecology questions by applying it to a set of 60 marine microbes, finding pervasive cross-feeding-driven niche expansion, and showing how the detailed outputs provided by misosoup facilitate research on hot topics such as the identification of functional groups. In summary, misosoup provides a powerful tool for microbial ecology and community design, with potential applications in both research and biotechnological innovation.<br><br>IMPORTANCE: Microbes often rely on each other to survive, especially in environments where they cannot live alone. Understanding which small groups of microbes can thrive together-called minimal communities-is key to improving laboratory research, designing synthetic ecosystems, and exploring how microbes spread in nature. To support this, we developed misosoup, a Python tool that identifies these communities using advanced metabolic modeling. misosoup helps scientists discover how microbes cooperate by sharing nutrients, a process known as metabolic cross-feeding. When tested on sets of species from different origins, the tool showed that species could thrive in more environments when part of a group. This finding highlights the importance of cooperation in microbial life. misosoup not only predicts these interactions but also provides detailed insights that can guide ecological studies and biotechnological innovation. By revealing how microbes support each other, misosoup contributes to a deeper understanding of life's interconnectedness and offers tools for solving real-world challenges.}, }
@article {pmid42496113, year = {2026}, author = {Piperni, E and Blanco-Míguez, A and Mengoni, C and Piccinno, G and Punčochář, M and Ren, J and Segata, N and Asnicar, F and Poole, AC}, title = {Resistant starch types 2 and 4 induce distinct and reversible changes in the human gut microbiome.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0076326}, doi = {10.1128/spectrum.00763-26}, pmid = {42496113}, issn = {2165-0497}, abstract = {Resistant starch (RS) can confer benefits for the gut microbiome and host cardiometabolic health. However, different types of resistant starch can differentially affect gut microbiome composition and functional capacity, especially given interindividual variability in responses, thus limiting the application of resistant starch in dietary strategies. We used shotgun metagenomics to perform a secondary analysis of samples collected during a previously reported randomized clinical trial to determine the effects of dietary supplementation with two types of resistant starch (RS2 and RS4) and a digestible starch (control) on the gut microbiome. Both resistant starch types induced distinct but transient alterations in the gut microbial community. RS2 enriched the keystone degrader, Ruminococcus bromii, and Blautia glucerasea, whereas RS4 favored Parabacteroides distasonis and known but uncharacterized microbial species such as a Lachnospiraceae bacterium. Moreover, we detected strain-level differences in the response of Bifidobacterium adolescentis to resistant starch. Microbial functional profiling revealed an enhanced capacity for complex carbohydrate utilization following resistant starch intake, including increased abundance of specific α-amylases, glycoside hydrolases, starch utilization systems, and other currently uncharacterized genes. Identifying the bacterial strains and genes that respond to different RS types will help to more accurately predict who will benefit from a given RS type. Our findings demonstrate that RS2 and RS4 differentially shape microbial ecology and metabolic capacity and provide a foundation for microbiome-informed personalization of resistant starch-based dietary interventions.IMPORTANCEDietary intake influences human health by modulating metabolism, partly by shaping the microbiota inhabiting the gut. Resistant starch (RS), a dietary fiber, is associated with metabolic improvements. While previous research has explored how RS alters the gut microbiome, RS comprises five types with differing physical and chemical characteristics, and the distinct impacts of each type on the microbiome and host health have not been fully characterized, particularly using high-resolution approaches such as shotgun metagenomics. In this secondary analysis of samples from a longitudinal crossover intervention study, we link dietary supplementation with RS2 and RS4 with distinct and transient changes in the composition and functional potential of the human gut microbiome. Specifically, we identify species that increase in abundance with each RS type, accompanied by increases in genes and pathways involved in complex carbohydrate utilization. The findings support the development of precision nutrition strategies utilizing RS supplementation to improve metabolic health.This study is registered with ClinicalTrials.gov as NCT05743790.}, }
@article {pmid42498510, year = {2026}, author = {Li, Z and Yang, Q and Lv, L and Shang, Y and Sun, X and Dong, M and Xiao, Q and Huang, F and Cai, M and Zhang, J and Yu, Z and Zheng, L}, title = {Synergistic role of egg-associated bacteria in promoting egg hatching of black soldier fly (Hermetia illucens L.).}, journal = {Insect science}, volume = {}, number = {}, pages = {}, doi = {10.1111/1744-7917.70327}, pmid = {42498510}, issn = {1744-7917}, support = {2025BBB013//Key Research and Development Project of Hubei Provincial Department of Science and Technology/ ; 32172783//National Natural Science Foundation of China/ ; }, abstract = {The black soldier fly (Hermetia illucens L.) is a critical species for organic waste bioconversion, yet the microbial ecology regulating its embryonic development remains obscure. This study investigated the diversity, temporal dynamics, and functional role of the egg-associated microbiota in black soldier fly hatching. Surface sterilization experiments revealed that the presence of surface microbes significantly facilitates hatching, as sterilization reduced hatching rates from 77.06% to 33.72%. Notably, this reduction was substantially reversed by re-inoculation with native egg-derived bacteria. High-throughput 16S rRNA gene sequencing demonstrated dynamic temporal shifts within the bacterial community during the 72 h incubation period, which was consistently dominated by the phyla Proteobacteria and Firmicutes. Functional prediction via PICRUSt indicated that the abundance of genes encoding chorion-degrading enzymes, including chitinases and proteases, fluctuated synchronously with critical hatching stages. Furthermore, culture-dependent screening identified Bacillus and Staphylococcus as key hatching promoters. Co-inoculation of these two strains resulted in synergistic improvements in hatching success compared to single-strain treatments. These findings suggest that specific members of the egg-associated microbiota function cooperatively to assist hatching, likely through enzymatic modification of the chorion. This study provides new insights into early-stage insect-microbe interactions and offers a potential microbial management strategy for optimizing black soldier fly mass rearing.}, }
@article {pmid42499706, year = {2026}, author = {Chen, XP and Xu, JQ and Zhang, NN and Huang, Q and Zhu, TH and He, C}, title = {Gut microbiota-derived metabolites and EVs-mediated signaling in type 2 diabetes mellitus.}, journal = {Frontiers in cell and developmental biology}, volume = {14}, number = {}, pages = {1862369}, pmid = {42499706}, issn = {2296-634X}, abstract = {Type 2 diabetes mellitus is characterized by systemic insulin resistance, chronic low-grade inflammation, and progressive metabolic dysfunction. Increasing evidence identifies the gut microbiota as a central regulator of host immunometabolism through a diet-microbiota-host axis. Gut microbiota-derived metabolites, including short-chain fatty acids, bile acids, branched-chain amino acids, and trimethylamine N-oxide, integrate endocrine signaling, intracellular metabolic pathways, and inflammatory responses across intestinal and systemic compartments, thereby shaping glucose homeostasis and metabolic balance. Diet acts as an upstream determinant by modulating microbial composition and metabolic activity. Beyond soluble metabolites, extracellular vesicles have emerged as an additional mode of intercellular communication. Vesicles derived from diet or microbiota carry bioactive cargos such as proteins, lipids, and small RNAs, enabling the transfer of functional signals that may influence both microbial ecology and host immunometabolic processes. This review summarizes metabolite-dependent and vesicle-mediated signaling pathways and highlights how these interconnected mechanisms position the gut microbiota as a signaling hub linking dietary inputs to host cellular regulation. This framework provides a conceptual basis for microbiota-targeted strategies in the prevention and treatment of type 2 diabetes.}, }
@article {pmid42501131, year = {2026}, author = {Nithyapriya, S and Sundaram, L and Eswaran, SUD and Perveen, K and Alshaikh, NA and Sayyed, RZ and Mastinu, A}, title = {Retraction Note: Purification and Characterization of Desferrioxamine B of Pseudomonas fluorescens and Its Application to Improve Oil Content, Nutrient Uptake, and Plant Growth in Peanuts.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, doi = {10.1007/s00248-026-02838-8}, pmid = {42501131}, issn = {1432-184X}, }
@article {pmid42502862, year = {2026}, author = {Xu, Y and Ji, L and Liu, T and Qian, L and Zhou, H and Zhuang, C and Chen, H and Zhou, X and Zhao, L and Zhou, X}, title = {Volatile aroma profiles and associated microbiota of Yunnan Shiping sour-pulp-fermented stinky tofu.}, journal = {Food chemistry: X}, volume = {38}, number = {}, pages = {104217}, pmid = {42502862}, issn = {2590-1575}, abstract = {Yunnan Shiping stinky tofu is a traditional sour-pulp-fermented soybean product with distinctive volatile aroma characteristics. In this study, headspace solid-phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC-MS), relative odor activity value (ROAV) analysis, and 16S rRNA/ITS amplicon sequencing were used to characterize volatile organic compounds (VOCs) and associated microbial communities in samples collected from four local production facilities. A total of 418 VOCs were detected, and ROAV analysis indicated that sulfur-containing compounds, heterocyclic compounds, furanone derivatives, terpenoid-derived odorants, and unsaturated aldehydes contributed substantially to the volatile aroma profile. The bacterial communities were mainly composed of Proteobacteria, Bacteroidota, and Firmicutes, whereas the fungal communities were dominated by Ascomycota and Basidiomycota. Correlation analysis suggested potential associations between selected bacterial or fungal genera and aroma-active compounds; however, these associations should be interpreted as hypothesis-generating rather than causal evidence. These findings provide a descriptive basis for understanding the volatile aroma characteristics and microbial ecology of Yunnan Shiping sour-pulp-fermented stinky tofu and may guide future targeted isolation, safety assessment, and validation of aroma-associated microorganisms.}, }
@article {pmid42503325, year = {2026}, author = {Zhang, X and Li, J and An, Y and Zheng, J and Xu, G and Wang, J and Chen, L and Lu, Y}, title = {Vitamin B12-mediated microglial immunometabolic reprogramming: A novel mechanistic insight into diabetes-associated cognitive impairment.}, journal = {Progress in neuro-psychopharmacology &amp; biological psychiatry}, volume = {}, number = {}, pages = {111861}, doi = {10.1016/j.pnpbp.2026.111861}, pmid = {42503325}, issn = {1878-4216}, abstract = {Diabetes-associated cognitive impairment (DCI) is an increasingly recognized neurological complication of type 2 diabetes mellitus characterized by chronic neuroinflammation and microglial immunometabolic dysregulation. Vitamin B12 (VB12) deficiency, which is highly prevalent in patients with diabetes, has been strongly associated with cognitive decline, hippocampal atrophy, and white matter injury. Emerging evidence suggests that VB12 plays a critical role in maintaining one‑carbon metabolism, mitochondrial function, and redox homeostasis. Mechanistically, VB12 deficiency promotes homocysteine accumulation, disrupts the S-adenosylmethionine/S-adenosylhomocysteine balance, impairs mitochondrial oxidative phosphorylation, and enhances oxidative stress, thereby driving pro-inflammatory microglial activation and sustained neuroinflammation. In addition, gut microbiota dysbiosis, particularly reduced abundance of Akkermansia muciniphila and other VB12-producing bacteria, may further impair VB12 bioavailability and aggravate neuroinflammation through the gut-brain axis. This review summarizes current evidence linking VB12 deficiency to microglial immunometabolic remodeling in DCI and discusses the therapeutic potential of targeting VB12 metabolism and gut microbial ecology for preventing diabetes-related cognitive decline.}, }
@article {pmid42504676, year = {2026}, author = {Okechukwu, VO and Njobeh, PB and Okonkwo, JO}, title = {Photocatalytic and Biotechnological Strategies for Remediation of Persistent Organic Pollutants: Mechanisms, Toxicity, and Antimicrobial Perspectives.}, journal = {Environmental toxicology}, volume = {}, number = {}, pages = {}, doi = {10.1002/tox.70172}, pmid = {42504676}, issn = {1522-7278}, support = {PSTD250327306922//National Research Foundation (NRF) of South Africa/ ; }, abstract = {Persistent organic pollutants (POPs) pose significant ecological and human health risks due to their persistence, bioaccumulation, toxicity, and global distribution. Conventional remediation methods are often inadequate for achieving complete mineralization, demonstrating the need for advanced and substantial approaches. Recent studies have explored photocatalytic and biotechnological methods as promising alternatives; however, critical gaps remain regarding the toxicity of transformation products, implications for antimicrobial resistance (AMR), and the scalability of hybrid systems. This review assesses photocatalytic and biotechnological strategies for POP remediation, focusing on their mechanisms, performance, and environmental impacts. Photocatalysis enables the rapid degradation of recalcitrant compounds with reported removal efficiencies often exceeding 70%-95% under optimized conditions for pollutants. In contrast, biotechnological approaches facilitate selective and complete mineralization through microbial and enzymatic processes but are influenced by environmental conditions and pollutant bioavailability. Hybrid photocatalytic-biological systems demonstrate enhanced efficiency by coupling oxidative pretreatment with biodegradation, although their performance may vary depending on system integration and operational conditions. This review focuses on the formation and fate of intermediate by-products, their potential toxicity, and the influence of remediation processes on microbial communities and AMR dynamics. Unlike previous studies, this work integrates material science, environmental toxicology, and microbial ecology while emphasizing emerging tools such as omics technologies, synthetic biology, and digital optimization to advance risk-informed and sustainable remediation strategies.}, }
@article {pmid42504986, year = {2026}, author = {Han, JJ and Guzman, AR and Zhou, A and Zhang, H and Gupte, R and Jung, H and Delgado, K and Skariah, S and Sultan, A and Jayaraman, A and de Figueiredo, P and Han, A}, title = {Polychip-A High-Throughput Droplet Microfluidics Platform for Interrogating Microbial Interactions.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e23854}, doi = {10.1002/advs.202523854}, pmid = {42504986}, issn = {2198-3844}, support = {/NH/NIH HHS/United States ; 1R01AI168685-01A1//National Institute of Allergy and Infectious Diseases/ ; R01AI141607-01A1//National Institute of Allergy and Infectious Diseases/ ; R21AI139738-01A1//National Institute of Allergy and Infectious Diseases/ ; M2404535//Texas A&amp;M University Advancing Discovery to Market/ ; NPRP9-001-2-001//Qatar National Research Foundation/ ; W911NF1920013,HR00112320006//Defense Advanced Research Projects Agency (DARPA)/ ; }, abstract = {Microbial interactions are fundamental to ecology, health, and disease, yet high-throughput tools to study these complex relationships remain scarce. We introduce Polychip, a fully integrated, high-throughput droplet microfluidics platform that revolutionizes microbial interaction screening. By seamlessly combining six microfluidic operations onto a single chip, Polychip achieves 99.7% efficiency and accelerates screening by 11-14 times compared to traditional high-throughput liquid handling robotic methods, with minimal human input. Using the Polychip, we screened 2.24 × 10[6] soil-extracted microorganisms against the multidrug-resistant (MDR) pathogen Pseudomonas aeruginosa. This process recovered 1.96 × 10[4] hit droplets with an antimicrobial activity confirmation accuracy of 48%. Three environmental isolates (Stenotrophomonas sp.) exhibiting high potency and broad-spectrum antimicrobial activity were identified through this screen. Supernatants from these three environmental isolates suppressed growth of both gram-negative MDR pathogen Acinetobacter baumannii and gram-positive methicillin-resistant Staphylococcus aureus (MRSA). Through whole-genome sequencing, metabolic pathway analysis, and mass spectrometry, we identified the secreted compound as enterochelin. This demonstrates Polychip's unprecedented single-cell resolution and high throughput screening capability in rapidly discovering antimicrobial activities, opening new frontiers in combating resistant microbial pathogens, as well as more broadly advancing microbial ecology research.}, }
@article {pmid42493633, year = {2026}, author = {Rock, R and Zhang, S and Noecker, C and Turnbaugh, PJ}, title = {Eggerthella lenta: metabolism, pathogenesis and therapeutic implications.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, pmid = {42493633}, issn = {1740-1534}, abstract = {Despite a tremendous body of literature on environmental Actinomycetota, their role in the human gut remains poorly understood. In this Review, we highlight the representative species Eggerthella lenta, which has emerged as a major player in the gut microbiota and is increasingly amenable to mechanistic dissection. We discuss the unique metabolic niche of this asaccharolytic obligate anaerobe, including growth on amino acids and short-chain fatty acids, versatile anaerobic respiratory capacity, and the extensive biotransformation of endogenous, diet-derived and pharmaceutical small molecules. E. lenta is associated with a wide range of chronic diseases in humans and sufficient to exacerbate disease in preclinical models, prompting a renewed consideration of the pathogenic potential of this common member of the gut microbiota. Further mechanistic dissection coupled with the development of microbiome-editing tools is essential to understand E. lenta and its multifaceted contributions to gut microbial ecology and host pathophysiology.}, }
@article {pmid42494685, year = {2026}, author = {Li, D and Kyawt, Y and Wang, Q and Gao, J and Wang, R and Wang, M and Duan, C and Lv, D and Zhu, W and Wanapat, M and Cheng, Y}, title = {High-dose phytosterols supplementation improves lactation performance, modulates rumen microbiota, and reduces methane emission intensity in mid-lactation Holstein dairy cows.}, journal = {Veterinary world}, volume = {19}, number = {6}, pages = {2339-2357}, pmid = {42494685}, issn = {0972-8988}, abstract = {BACKGROUND AND AIM: Enteric methane emission from dairy cows contributes substantially to greenhouse gas production and represents an inefficient loss of dietary energy. Phytosterols are plant-derived bioactive compounds with lipid-modulating and rumen fermentation-regulating properties; however, their effects on methane emission intensity and rumen microbial ecology in lactating dairy cows remain insufficiently explored. This study evaluated the effects of dietary phytosterols supplementation on lactation performance, nutrient digestibility, serum biochemical parameters, rumen fermentation characteristics, methane emission intensity, and rumen microbial composition in mid-lactation Holstein dairy cows.<br><br>MATERIALS AND METHODS: Thirty-four multiparous Holstein dairy cows with similar days in milk and milk yield were randomly assigned to either a control (CON) group or a phytosterols (PHY) group receiving 15 g/d of a commercial phytosterols product containing 5% active phytosterols. The experimental period lasted 50 days, including 7 days of adaptation and 43 days of data collection. Feed intake and milk yield were recorded daily. Milk composition, apparent nutrient digestibility, serum biochemical indices, rumen fermentation parameters, methane emission intensity, quantitative polymerase chain reaction, and 16S rRNA gene sequencing were analyzed. Methane and carbon dioxide emissions were measured using an automated head-chamber system.<br><br>RESULTS: Dietary phytosterols supplementation significantly improved milk yield, milk fat percentage, milk protein percentage, energy-corrected milk, and 3.5% fat-corrected milk compared with the CON group (p < 0.05). Apparent digestibility of organic matter, crude protein, neutral detergent fiber, and ether extract was also significantly enhanced. Serum glucose and blood urea nitrogen concentrations increased, whereas total cholesterol and low-density lipoprotein cholesterol concentrations decreased in the PHY group. Phytosterols supplementation significantly reduced methane emission intensity per kilogram of energy-corrected milk. Ruminal acetate proportion and acetate-to-propionate ratio decreased, whereas microbial crude protein and branched-chain volatile fatty acids increased. In addition, phytosterols altered rumen microbial composition by increasing the abundance of beneficial bacterial genera, including Succinivibrionaceae UCG-001 and Prevotella, while reducing methanogenic archaea, particularly Methanobacteriota and Methanimicrococcus.<br><br>CONCLUSION: High-dose phytosterols supplementation improved lactation performance, enhanced nutrient utilization, modulated rumen microbial communities, and reduced methane emission intensity in mid-lactation dairy cows. These findings indicate that phytosterols may serve as a promising natural feed additive for improving dairy production efficiency while supporting methane mitigation strategies in sustainable dairy farming.}, }
@article {pmid42491472, year = {2026}, author = {Lusi, EA and Rifici, C}, title = {Nickel-resistant gut microbiota: a missing link between environmental exposure and metabolic disease.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1852314}, pmid = {42491472}, issn = {1664-302X}, abstract = {Environmental factors are emerging as important modulators of the gut microbiome, with significant implications for metabolic health. Among these, nickel-a ubiquitous dietary metal traditionally regarded as an allergen-is gaining recognition as a systemic immune-metabolic modulator. Chronic nickel exposure has been linked to overweight and metabolic alterations, particularly in nickel-allergic individuals, suggesting that environmental nickel may represent an underrecognized contributor to metabolic dysfunction in susceptible populations. Recent studies have identified nickel-resistant bacteria within the gut microbiota of affected individuals, providing a biologically plausible framework linking environmental metal exposure to microbial ecology. These microorganisms contribute to nickel detoxification and may influence host physiology through interactions with microbial metabolism, energy balance, and immune signaling. Under conditions of chronic exposure, ecological selection of nickel-resistant communities may contribute to dysbiosis and altered host-microbiome interactions. By integrating clinical observations with emerging microbiological evidence, this Perspective explores the hypothesis that nickel-resistant gut microbiota may represent candidate mediators at the intersection of environmental exposure, immunity, and metabolism. Understanding how dietary metals shape microbial ecosystems may provide new insights into metabolic disease and highlights metal-microbiota interactions as a promising area for future investigation.}, }
@article {pmid42492502, year = {2026}, author = {Majamäki, R and Wasiljeff, J and Purkamo, L and Hultman, J and Kohl, L and Asmala, E and Yli-Hemminki, P and Jørgensen, KS and Muurinen, J and Virtasalo, JJ}, title = {Different Ferromanganese Concretion Morphologies Host Distinct Microbial Communities and Metal Accumulation Patterns in the Baltic Sea.}, journal = {Environmental microbiology}, volume = {28}, number = {7}, pages = {e70390}, pmid = {42492502}, issn = {1462-2920}, support = {332249//Research Council of Finland/ ; 20240020//Foundation for Research of Natural Resources in Finland/ ; }, mesh = {*Bacteria/metabolism/classification/isolation &amp; purification/genetics ; *Seawater/microbiology/chemistry ; Finland ; *Manganese/metabolism ; *Iron/metabolism ; *Geologic Sediments/microbiology/chemistry ; *Microbiota ; *Metals/metabolism ; Gammaproteobacteria/metabolism ; *Ferric Compounds/metabolism ; }, abstract = {Ferromanganese (Fe-Mn) concretions are porous accumulations of iron and manganese (hydr)oxides. While recent studies suggest that microbes contribute to metal accumulation in Baltic Sea concretions, the detailed composition of microbial communities and their impact on metal enrichment across different concretion morphotypes remain unexplored. We investigated how microbes influence the accumulation and release of trace metals and rare-earth elements in Fe-Mn concretions from the Gulf of Finland through 15-week microcosm incubation experiments with biotic and abiotic treatments, focusing on three main concretion morphotypes: crust, discoidal, and spheroidal. Elemental analysis showed that microbes enhanced metal incorporation in discoidal and spheroidal morphotypes. Characterisation of microbial composition revealed that all three morphologies host distinct communities. Discoidal and spheroidal morphotypes had a higher relative abundance of Gammaproteobacteria and sulfate-reducing bacteria, and a lower abundance of Entotheonellaeota, compared to crusts. In all morphotypes, the bacterial phylum Pseudomonadota dominated, with several genera of Fe- and Mn-oxidisers and reducers. Fe-Mn concretions also host communities involved in methane oxidation and nitrogen cycling, consistent with decreased methane and increased nitrous oxide, nitrite, and nitrate concentrations in the microcosms. Our findings underscore that distinct microbial communities are associated with different concretion morphotypes, potentially influencing nutrient and metal cycling on the seafloor.}, }
@article {pmid42489313, year = {2026}, author = {Kim, SY and Kim, Y and Kim, DJ and Chang, HS}, title = {Long-read rRNA operon sequencing reveals bacterial community divergence between traditional and industrial soybean fermentations.}, journal = {Letters in applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/lambio/ovag064}, pmid = {42489313}, issn = {1472-765X}, abstract = {Traditional and industrial soybean fermentations harbor distinct microbial communities that influence product quality and safety. In this study, long-read rRNA operon sequencing was applied to investigate the bacterial communities of traditional and commercial doenjang and cheonggukjang. The 16S-23S rRNA operon (∼4.2 kb) was amplified and sequenced using the Oxford Nanopore MinION platform to obtain high-resolution taxonomic profiles. Traditional doenjang and cheonggukjang exhibited greater microbial diversity than commercial products, as revealed by alpha and beta diversity analyses. Bacillus species, particularly B. velezensis and B. subtilis, were dominant across all samples, while Loigolactobacillus coryniformis, Caldifermentibacillus hisashii, and Tetragenococcus halophilus were more abundant in traditionally fermented samples. These genera are associated with proteolysis, amino acid metabolism, and flavor compound formation during fermentation. Overall, these findings provide insights into the microbial ecology of fermented soybean foods and suggest that non-starter lactic acid bacteria and thermophilic species may contribute to the unique sensory characteristics of traditionally fermented doenjang.}, }
@article {pmid42490025, year = {2026}, author = {Pereira, D and Moreira, FC and da Silva, VCS and de Souza Avelar, D and Ramos, SAA and da Silva, JMC and da Silva Mourão, RM and da Silva, RF and Guimarães, KSP and Pinto, JBA and da Conceição, M and Barra, WF and Demachki, S and Casseb, SM and Burbano, RMR and de Assumpção, PP}, title = {Comprehensive analysis of the gastric metatranscriptome reveals specific viral signatures associated with gastric cancer.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {42490025}, issn = {1618-1905}, abstract = {Gastric cancer (GC) remains highly lethal, and although gastric microbiome dysbiosis has been linked to carcinogenesis, the viral component is still poorly explored. Here, we used metatranscriptomics to characterize the gastric virome and evaluate its association with GC and clinicopathological features. We analyzed 238 gastric tissues (214 GC and 24 non-tumors, NT) with clinicopathological data. Viral classification was performed using Kraken2 with the RVDB database. Virome diversity, composition, and clustering were assessed using phyloseq-based analyses, Jensen-Shannon divergence with PAM clustering, and ordination methods. Differential abundance and diversity were evaluated using LEfSe and statistical tests, and viral gene expression was investigated for clinical relevant viruses. We identified 106 viral genera, predominantly bacteriophages and dsDNA viruses, with distinct GC- and NT-associated viral signatures. Clustering revealed three viral community types (GT-1, GT-2, GT-3) that significantly separated GC and NT samples and showed reduced alpha diversity in GC-associated clusters. GT-1 was dominated by Lymphocryptovirus, GT-2 by Gorganvirus, and GT-3 (NT) exhibited the highest diversity. GC tissues were enriched in oncologically relevant viruses, including Lymphocryptovirus (EBV), Cytomegalovirus, and Alphapapillomavirus, whereas several bacteriophages predominated in NT. Virome composition was significantly associated with Lauren histological subtype, but not with clinical stage, tumor location, or neoadjuvant therapy. EBV-high tumors displayed a predominantly latent transcriptional program, with strong expression of ncRNAs (RPMS1, EBERs) and low lytic activity. These findings highlight major virome restructuring in GC and support a potential role of the gastric virome in tumor-associated microbial ecology, warranting further mechanistic and clinical investigation.}, }
@article {pmid42490939, year = {2026}, author = {Xie, Q and Yang, Y and Lin, J and Ye, Y and Lin, J and Wu, M and Guo, Z and Shen, A and Zeng, W and Peng, J}, title = {Gut microbiota-derived butyrate contributes to baicalin-induced attenuation of hypertensive vascular remodeling via adventitial immunity.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1835174}, pmid = {42490939}, issn = {1663-9812}, abstract = {BACKGROUND: Baicalin shows potent vasculoprotective effects against hypertension despite poor oral bioavailability. We investigated whether gut microbiota modulation contributes to the systemic vasculoprotective effects of orally administered baicalin.<br><br>METHODS: We utilized an Angiotensin II-induced hypertensive mouse model, employing broad-spectrum antibiotics, 16S rRNA sequencing, metabolomics, and in vitro co-culture assays to map the gut-immune-vascular axis.<br><br>RESULTS: Oral Baicalin significantly attenuated Ang II-induced blood pressure elevation and improved the intestinal barrier integrity. Antibiotic-induced microbiota depletion substantially weakened these protective effects, supporting a major microbiota contribution under the present experimental conditions. Baicalin reshaped the gut microbial community, enriched SCFA-supporting taxa, and restored a putative butyrate-associated microbial signature, enriching Akkermansia and Lactobacillus accompanied by increased cecal butyrate levels. Exogenous sodium butyrate recapitulated several major protective features of Baicalin treatment, including expansion of Foxp3+ regulatory T cells in mesenteric lymph nodes. These immune changes were accompanied by increased Foxp3+ regulatory immune-cell accumulation in the aortic adventitia. In vitro, butyrate-licensed Tregs suppressed Ang II-induced vascular smooth muscle cell (VSMC) proliferative responses, at least partly through IL-10-mediated inhibition of MAPK/ERK signalling.<br><br>CONCLUSION: Baicalin alleviates Ang II-associated vascular remodelling, at least in part, by reprogramming gut microbial ecology, increasing luminal butyrate availability, promoting regulatory immune responses, and suppressing VSMC proliferative signalling.}, }
@article {pmid42479765, year = {2026}, author = {Fant, L and Macocco, I and Grilli, J}, title = {Eco-evolutionary dynamics lead to functionally robust and redundant communities.}, journal = {PLoS computational biology}, volume = {22}, number = {7}, pages = {e1014437}, doi = {10.1371/journal.pcbi.1014437}, pmid = {42479765}, issn = {1553-7358}, abstract = {Microbial communities are taxonomically diverse and variable: species presence and abundances widely fluctuate over time, space, and even across biological replicates under controlled experimental conditions. However, environmental conditions exert strong selection on the traits of community members and their functions. Similar environmental conditions are expected to produce functionally similar communities. This environmental selection, combined with taxonomic variability, leads to the influential concept of functional redundancy - the idea that many species can perform the same function, allowing communities with different species compositions to maintain identical functional profiles. Despite the centrality of functional redundancy in microbial ecology, we lack a theoretical understanding of its origin. Here we study the eco-evolutionary dynamics of communities interacting through competition and cross-feeding. We show that eco-evolutionary trajectories rapidly converge to a "functional attractor" - a functional composition uniquely determined by environmental conditions. Taxonomic composition follows non-reproducible dynamics while being constrained by the conservation of functional composition. Our framework provides a theoretical foundation for understanding functional robustness and redundancy in microbial communities.}, }
@article {pmid42480918, year = {2026}, author = {Batistel, F and Perdomo, M}, title = {Characterization of potential sources of secretory immunoglobulin A reaching the rumen and its effects on microbial growth and fermentation.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2026-28569}, pmid = {42480918}, issn = {1525-3198}, abstract = {Secretory immunoglobulin A (SIgA) is a major mucosal antibody known to modulate intestinal microbial ecology in non-ruminant species; however, its role in the rumen remains largely unexplored. The objectives of this study were to identify potential sources of SIgA reaching the rumen and to evaluate whether colostrum-derived SIgA can influence rumen bacterial growth and fermentation. In Study 1, SIgA concentrations were quantified in colostrum and milk from 15 multiparous Holstein cows during the first 42 d of lactation and in saliva from their respective calves during the first 42 d of life. Milk SIgA concentrations peaked in colostrum (∼8,000 μg/mL) and declined postpartum, stabilizing at approximately 780 μg/mL by 14 d postpartum. In contrast, salivary SIgA concentrations in calves were low during the first days of life (∼4 μg/mL) but increased with age, reaching a plateau near 930 μg/mL at 21 d of age. In Study 2, expression of genes associated with SIgA synthesis and transcytosis was evaluated in salivary glands, reticulum, rumen, and small intestine of mature cows. Salivary glands exhibited SIgA-related gene expression comparable to the small intestine and greater than that of the reticulum and rumen, supporting saliva as a major source of SIgA reaching the forestomach. In Study 3, purified colostrum-derived SIgA positively affected the growth kinetics of the fibrolytic bacteria Fibrobacter succinogenus S85, Prevotella bryantii B14, Ruminococcus albus (strains 7 and 8) in pure culture, whereas heat-inactivated IgA had no effect, indicating a "bioactive"-dependent mechanism. In Study 4, inclusion of SIgA in an in vitro batch culture system increased NDF disappearance and short-chain fatty acid production. These findings indicate that colostrum and milk serve as primary sources of SIgA during early life in calves, whereas salivary gland-derived SIgA becomes the predominant source as animals mature, given the limited SIgA secretion within the rumen itself. Additionally, SIgA modulated rumen microbial growth kinetics and fermentation under in vitro conditions. Collectively, these findings identify SIgA as a previously underrecognized host-derived factor capable of modulating rumen microbial ecology and fermentation, warranting further investigation in vivo.}, }
@article {pmid42481765, year = {2026}, author = {Wood, E and Edvardsen, B and Skjånes, K and Šupraha, L}, title = {Effects of Culture History and Algal Taxonomy on Bacterial Communities in Long-maintained Filamentous Green Algae.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02840-0}, pmid = {42481765}, issn = {1432-184X}, abstract = {Algal cultures are widely used to study algae-bacteria interactions, yet the relative roles of algal taxonomy, culturing environment, and historical contingency in shaping bacterial communities of long-maintained monoalgal cultures remain unclear. In a two-stage experimental design, we used 16 S rRNA metabarcoding to first profile the bacterial communities of 14 filamentous freshwater algal strains from three orders (Chaetophorales, Oedogoniales, Zygnematales) maintained in two distinct culture collections, and then, in a second experiment to test community mixing using a co-culture and re-isolation design with two algal strains (Stigeoclonium sp. and Oedogonium sp.). The 14-strain profiling showed that bacterial communities were broadly similar at higher taxonomic ranks, with many shared orders within Pseudomonadota, whereas composition at the ASV level was largely algal-strain-specific. Ordination of phylogeny-aware UniFrac distances showed that culture collection of origin explained more variation in community composition than algal order, an effect reduced but not eliminated after standardizing the culture medium. The co-culture and re-isolation experiment showed that the two algal strains exchanged many bacterial community members, yet algal strain identity remained detectable after re-isolation. These results support a framework where culture history results in strain-specific ASV-level composition within recurrent higher-rank structure, and where algal-strain-specific effects on bacterial community composition become evident when cultures are exposed to a shared bacterial pool. Co-culture followed by algal re-isolation offers a practical approach to examine the persistence of algal-culture bacterial communities under mixing and may help identify candidate bacterial partners with potentially strong host-specific interactions without requiring axenic hosts.}, }
@article {pmid42482743, year = {2026}, author = {Roganović, J and Šutej, I and Barać, M and Radić Vuleta, M and Manojlović, D and Pavlović, D and Komlenić, V and Ilić, J and Radović, K}, title = {Oral health, antimicrobial resistance and the need for interprofessional education.}, journal = {Frontiers in oral health}, volume = {7}, number = {}, pages = {1894083}, pmid = {42482743}, issn = {2673-4842}, abstract = {This mini review examines how oral microbial ecology, dental antibiotic prescribing, fragmented clinical pathways at the medical-dental-pharmacy interface, and ethical pressures together contribute to antimicrobial resistance (AMR) in oral healthcare, and argues that interprofessional collaboration and interprofessional education are essential components of an effective response. Relevant literature was identified through targeted searches of PubMed/MEDLINE, Scopus, Web of Science, Google Scholar, and the Cochrane Library, relevant guidelines and policy documents resulting in selection of seventy-two references comprising four thematic domains: clinical coordination and decision-making across dental, medical, and pharmacy settings; antimicrobial stewardship and rational antibiotic use in dentistry; fragmented care pathways at the medical-dental-pharmacy interface; and ethical and educational dimensions of prescribing. The novelty of this review lies in bringing these domains together within a single conceptual framework that positions oral healthcare not as a peripheral issue, but as biologically, clinically, and ethically important site of AMR emergence and stewardship.}, }
@article {pmid42484923, year = {2026}, author = {Chen, J and Gan, L and Zhang, S and Liao, S and Lv, L}, title = {FUT2-mediated α1,2-fucosylation in inflammatory bowel disease: mechanisms and translational potential.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {}, pmid = {42484923}, issn = {1573-4978}, support = {2022CQBSHTB2064//Special support for postdoctoral of Chongqing/ ; CSTB2024NSCQ-MSX0403//Chongqing Natural Science Foundation/ ; 82173360//National Natural Science Foundation of China/ ; 2022M720606//China Postdoctoral Science Foundation/ ; 2024QNXM053//Chongqing Science and Health Joint Medical Research Project/ ; }, mesh = {*Fucosyltransferases/metabolism/genetics ; Humans ; *Inflammatory Bowel Diseases/metabolism/genetics ; Galactoside 2-alpha-L-fucosyltransferase ; Animals ; Glycosylation ; Fucose/metabolism ; Gastrointestinal Microbiome ; Intestinal Mucosa/metabolism ; Genetic Predisposition to Disease ; Trisaccharides/metabolism ; }, abstract = {Inflammatory bowel disease (IBD) arises from complex interactions among genetic susceptibility, immune dysregulation, the intestinal microbiota and environmental factors. Fucosyltransferase 2 (FUT2) regulates mucosal α1,2-fucosylation and the expression of histo-blood group antigens (HBGAs), thereby shaping host-microbe interactions at the intestinal surface. Loss-of-function FUT2 variants define the non-secretor phenotype and have been linked to IBD susceptibility and altered microbial communities. This review summarizes current evidence on FUT2 in IBD, including epithelial glycosylation-microbiota crosstalk, immune and barrier regulation, metabolite-related inflammatory pathways, intestinal stem-cell biology, and enteric nervous system/VIP-related signaling. We also evaluate translational strategies, including functional compensation with the FUT2-dependent human milk oligosaccharide 2'-fucosyllactose (2'-FL), secretor-status-stratified interventions, and preclinical approaches such as L-fucose and D-serine. Overall, FUT2 is an important node connecting host glycosylation, microbial ecology and intestinal immune homeostasis, but its value as a direct therapeutic or biomarker target in IBD remains exploratory. Most mechanistic and causal evidence currently derives from mouse models. Although human genetic and microbiome association data are relatively robust, interventional clinical evidence remains limited, which represents a major barrier to clinical translation.}, }
@article {pmid42485446, year = {2026}, author = {Curtis, TP and Allen, B and Brown, M and Bell, A and Swan, D and Davenport, R and Sloan, W}, title = {Probability, Parameters, and Duration of Immigration and Extinction in Microbial Communities.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag195}, pmid = {42485446}, issn = {1751-7370}, abstract = {We propose a suite of simple equations to estimate the probability and duration of two important processes in microbial ecology: immigration and extinction. Our work is based on the gambler's ruin equation, which determines the probability that a number of immigrants (i) can attain an abundance N given the ratio of the probabilities of death q and division (or birth) p. We estimate the probability of an organism attaining a value of N in the context of bioaugmentation, transplantation, infection, mutation, and extinction. For example, an inoculum of 108 bacteria with a q/p of 1.00000001 has a 10-43 chance of attaining an abundance of 1010. The ratio of deaths to births controls the immigration parameter used in neutral models (m), and infectious dose in pathogens. We use Vibrio cholerae infections to demonstrate that the gambler's ruin equation can be used to estimate the infectious dose in naturally occurring infections. We calculated the long-term average value of m and q/p in a wastewater treatment plant. All values of q/p were ≥1. We expect the long-term average value of q/p to be ~1 in all stable microbial communities. In the absence of migration, bacterial populations with q/p ≥1 will go extinct with probability 1. We use the ratio q/p and simple recurrence relationships to estimate the time for a given change in abundance to occur. When q/p=1, extinction in even a small microbial population will take thousands of years. Our simple mechanistic models could play a powerful role in theory and practice.}, }
@article {pmid42487487, year = {2026}, author = {Llaja, JC and Oyola, JE and Carrion, JV and Chuquizuta, F and Calderon, MS and Bustamante, DE}, title = {Hidden Microbiota Inhabiting in Pollen Reserves of Honey Bee (Apis mellifera) From Amazonas Region Revealed by DNA Metabarcoding.}, journal = {Environmental microbiology reports}, volume = {18}, number = {4}, pages = {e70392}, doi = {10.1111/1758-2229.70392}, pmid = {42487487}, issn = {1758-2229}, support = {PE501083491-2023-PROCIENCIA//Consejo Nacional de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n Tecnol&#xf3;gica/ ; PE501079652-2022-PROCIENCIA//Consejo Nacional de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n Tecnol&#xf3;gica/ ; CUI N&#xb0; 2315092//Universidad Nacional Toribio Rodr&#xed;guez de Mendoza de Amazonas/ ; VRIN//Vicerrectorado de Investigaci&#xf3;n de la Universidad Nacional Toribio Rodriguez de Mendoza/ ; }, mesh = {Bees/microbiology ; Animals ; *Pollen/microbiology ; DNA Barcoding, Taxonomic ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/isolation &amp; purification ; Ecosystem ; Peru ; Biodiversity ; Pollination ; }, abstract = {Pollen functions as a dynamic microbial habitat and the microbes living in pollen reserves play vital roles in pollinator health and nutrition. However, the microbiota composition of honeybee pollen reserves in biodiverse Neotropical regions remains largely unknown. This study provides the first comprehensive analysis of bacterial and fungal communities in honeybee pollen reserves across six ecosystems in the Amazonas region of Peru using high-throughput metabarcoding of the 16S rRNA gene and ITS2 markers. We found that ecosystem type is a primary driver of community structure, with bacteria and fungi responding differently to environmental changes. Despite high taxonomic heterogeneity and a limited number of shared core microbes, the main functions of these microbes were maintained, featuring enrichment of bacterial pathways involved in nutrient metabolism and saprotrophic fungal guilds. Lactobacillus and an unclassified Tremellomycetes fungus were dominant, yet their abundance varied with respect to floral resource diversity. The simplified Palm Swamp ecosystem showed significantly reduced microbial diversity, underscoring the vulnerability of these communities to habitat homogenization. Our results demonstrate that the pollen reserve microbiome is assembled through environmental filtering and pollinator-mediated selection, resulting in taxonomically flexible but functionally stable communities essential for hive processes. This work provides a foundation for understanding the microbial ecology of pollen in the Amazonas region.}, }
@article {pmid42477333, year = {2026}, author = {Ren, XY and Lin, XY and Tanabe, TS and Loy, A and Hu, L and Zhu, YG and Chen, SC}, title = {Evolutionary trajectory of microbial sulfur oxidation pathways recapitulates Earth's oxygenation history.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-75310-3}, pmid = {42477333}, issn = {2041-1723}, support = {42507165//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Dissimilatory sulfur oxidation mediated by the microbial sulfur-oxidizing (Sox) multienzyme complex has played a central role in Earth's oxidative sulfur cycle. However, the evolutionary trajectory leading to its current complexity remains poorly understood. Here, we integrated expanded genomic records with geochemical evidence to reconstruct the natural history of the Sox system along a geological timeline. Our analyses traced the origin of the truncated Sox system (SoxABXYZ) prior to the Great Oxidation Event (GOE). This early form was later assembled with reverse dissimilatory sulfite reductases (rDsr), facilitating a primitive pathway for sulfate formation during the anoxic Archean eon. Following the post-GOE atmospheric oxygen rise, the truncated system incorporated SoxCD components, evolving into a more fine-tuned, oxygen-adapted pathway compared to the rDsr-coupled alternative. The subsequent spread of these Sox pathway variants was constrained by the oxygen requirements and phylogenetic backgrounds of their prokaryotic hosts, shaping the modern ecological landscape of microbial sulfur oxidation. The viral recruitment of auxiliary Sox components marked the latest evolutionary events, enabling direct manipulation of sulfur cycling over centuries-to-millennia timescales. Collectively, the reconstructed molecular timeline offers deeper insights into the evolutionary dynamics of the global oxidative sulfur cycle and its billion-year interplay with Earth's changing environments.}, }
@article {pmid42478289, year = {2026}, author = {Guerrero, J and Fernández, J and Alves, FRF and Provenzano, JC and Brisson-Suárez, KM and Marceliano-Alves, MF and Rôças, IN and Siqueira, JF}, title = {Effect of Kinematics and Speed on Filling Material Removal, Canal Transportation, and Apical Extrusion During Retreatment of Curved Canals.}, journal = {Australian endodontic journal : the journal of the Australian Society of Endodontology Inc}, volume = {}, number = {}, pages = {}, doi = {10.1111/aej.70110}, pmid = {42478289}, issn = {1747-4477}, abstract = {This study evaluated the effects of kinematics (reciprocating vs. continuous rotation) and rotational speed (350 vs. 1200 rpm) on filling removal, canal transportation, and apical extrusion during retreatment of curved root canals. Vertucci type II mesial roots of mandibular molars were prepared, filled, and scanned by micro-computed tomography (micro-CT). After 30 days, specimens were assigned to four groups (n = 15): WOrec, WOctn, PF350, and PF1200. Retreatment time was recorded, and micro-CT was used to assess filling removal, canal transportation, and apical extrusion. Data were statistically evaluated and revealed that all systems significantly reduced the amount of filling material (p < 0.05). PF1200 and WOctn showed superior removal compared with PF350 and WOrec, respectively (p < 0.05). No differences were observed in extrusion (p > 0.05). Increased canal transportation occurred only in the mesiolingual canal with WOctn and PF1200 (p < 0.05). Higher speed and continuous rotation improved efficiency without increasing extrusion but resulted in greater transportation.}, }
@article {pmid42478812, year = {2026}, author = {Henige, M and Anklam, K and Yoon, I and Wheeler, J and Dawson, G and Döpfer, D}, title = {Effect of Saccharomyces cerevisiae fermentation postbiotic supplementation on metagenomics of digital dermatitis lesions in lactating Holstein cows.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0030426}, doi = {10.1128/spectrum.00304-26}, pmid = {42478812}, issn = {2165-0497}, abstract = {Digital dermatitis (DD) is the leading cause of lameness in cattle, posing major animal welfare and economic concerns. Effective prevention strategies are increasingly important given emerging antimicrobial resistance associated with common DD treatments. Supplementation with Saccharomyces cerevisiae fermentation postbiotics (SCFP) has been shown to enhance innate immunity and reduce DD lesion development. This study evaluated the effect of a commercial SCFP supplement on the microbial composition of DD lesions using shotgun metagenomic sequencing to characterize microbial communities and associated antimicrobial resistance genes. Beta diversity analysis revealed that stage M4 DD lesions from SCFP-supplemented cows had a trend for different microbial compositions compared with controls (P = 0.051). At the genus level, M2 lesions were found to have statistically significant lower abundance of the genera Desulfovibrio, Pseudomonas, Staphylococcus, Anaerotignum, Caproicibacterium, and Bacteroides in the SCFP treatment group compared with the control (P < 0.05). M2 lesions from the SCFP treatment group were also found to have statistically significant higher abundance of the genera Fusobacterium, Citricoccus, Listeria, and Fundicoccus as compared with the control (P < 0.05). M4 lesions were found to have statistically significant lower abundance of the genera Blautia and Petrimonas in the SCFP treatment group compared with the control (P < 0.05). At the species level, M2 lesions were found to have statistically significant lower abundance of the species Desulfovibrio sp. G11, Anaerotignum sp. MB30-C6, Caproicibacterium argilliputei, and Prevotella intermedia in the SCFP treatment group compared with the control (P < 0.05). M2 lesions from the SCFP treatment group were also found to have statistically significant higher abundance of the species Fundicoccus culcitae and Helcococcus ovis as compared with the control (P < 0.05). Metagenomic analysis identified antimicrobial resistance genes associated with multiple antibiotics commonly used for DD treatment, including tetracyclines, lincosamides, and pleuromutilins. These findings demonstrate the potential for SCFP supplementation to alter the microbial composition of DD lesions while highlighting the ongoing concerns regarding antimicrobial resistance in DD management.IMPORTANCEDigital dermatitis (DD) causes substantial economic loss and welfare concerns in cattle production systems worldwide. Our findings show that dietary supplementation with Saccharomyces cerevisiae fermentation postbiotics (SCFP) has the potential to alter the microbial ecology of DD lesions. Importantly, this work identifies antimicrobial resistance genes within DD lesions, underscoring the limitations of antibiotic-based control strategies. By linking nutritional supplementation to changes in microbial communities and resistance gene profiles, this study advances understanding of non-antibiotic approaches to disease mitigation and supports the development of sustainable, microbiome-informed management practices in food animal production.}, }
@article {pmid42478819, year = {2026}, author = {Lee, Y-H and Siewers, V and Larsbrink, J}, title = {Extracellular metabolite production by Bacteroides strains varies depending on carbohydrates used as carbon sources.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0054226}, doi = {10.1128/aem.00542-26}, pmid = {42478819}, issn = {1098-5336}, abstract = {UNLABELLED: The microorganisms comprising the gut microbiota perform various important functions, such as producing short-chain fatty acids (SCFAs) and other metabolites that can be taken up by the host and used as energy sources or as signaling molecules. A major nutrient for the microbiota is dietary fiber, mainly composed of complex polysaccharides that cannot be degraded by host enzymes. Species from the Bacteroidota phylum are regarded as proficient carbohydrate degraders, partly thanks to their multi-gene systems, known as polysaccharide utilization loci (PULs), encoding the necessary proteins for carbohydrate capture and cleavage. Linking which species can grow on which polysaccharides, depending on the presence of corresponding PULs encoded in their genomes, has been studied intensely in the last decades. However, little is known about which metabolites they produce from carbohydrate consumption, as previous investigations have mainly used glucose as the sole carbon source. In this study, we grew several Bacteroidota species on different carbohydrates, from monosaccharides to polysaccharides, and quantified the resulting extracellular metabolites produced. The results reveal different extracellular metabolite profiles, both intraspecies and interspecies, depending on the carbon sources. Surprisingly, in some cases, the production of extracellular metabolites differed between growth on a homopolysaccharide and its constituent monosaccharide. The results indicate that the metabolite output of gut species is not static but varies with the nutrients present, adding to the complexity of the interplay among dietary fiber, microbial ecology, and gut health.<br><br>IMPORTANCE: The human gut microbiota is closely linked to health, and metabolism of different types of dietary fibers is a core activity within this community. Many studies have investigated the composition of the microbiota and sought to relate the presence and abundance of species to health or disease, often attributing a genus or species to consumption or production of a certain metabolite to explain an overall phenotype. It is known that bacteria have different carbohydrate-degrading abilities, but they may not produce a static output of metabolites from the consumption of different carbohydrates, from monosaccharides to complex polysaccharides. This study demonstrates that common bacteria in the Bacteroides genus may drastically alter their production of extracellular metabolites. The findings add another layer of complexity to the dynamics of the gut environment and are important for better understanding the interplay among diet, the microbiota, and the host.}, }
@article {pmid42479179, year = {2026}, author = {Brealey, JC and Davey, ML and Pedersen, B}, title = {Bacterial and Green Algal Communities of Norwegian Birch Tree Bark.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02841-z}, pmid = {42479179}, issn = {1432-184X}, abstract = {Tree bark hosts a unique community of microorganisms, distinct from that of other plant tissues and from the microbial associates of macrophytic epiphytes. These corticolous communities are important components of tree-associated food webs. However, the factors influencing corticolous microbial diversity are understudied. We used amplicon sequencing to characterise and compare the bacterial and aerophytic algal communities colonising the bark of birch trees at three sites in southern Norway with differing histories of nitrogen deposition. Within each site, we investigated associations between the corticolous community and variation in placement on the trunk, including north-facing vs. south-facing aspect, height and trunk diameter. While the most abundant bacterial and algal taxa were similar across the three sites, there were clear differences among sites. Aspect had a strong effect at the most oceanic and open site, with increased abundance of cyanobacteria at northern compared to southern aspects. We observed a higher abundance of nitrogen-fixing cyanobacteria at the site where historical nitrogen deposition had been lowest and correspondingly higher abundance of non-diazotrophic green algae where historical nitrogen deposition had been highest. Generally, the bacterial and algal communities followed similar patterns and co-occurrence network analysis revealed that algal taxa were interspersed among bacterial clusters. Our study provides the first characterisation of both the bacterial and aerophytic algal bark-associated communities of birch, one of the most common and ecologically important trees in Norway. Our results add to the growing body of literature demonstrating that tree bark supports a complex microbial community that varies among sites.}, }
@article {pmid42470887, year = {2026}, author = {Belarbi, H and Algoet, V and Neri, J and Kebede, F and Dos Reis, AR and Sun, GX and Van de Wiele, T and Cakmak, I and Du Laing, G}, title = {Nutritional and toxicological trade-offs in selenium enrichment: a bioaccessibility-based comparison of biofortified and naturally enriched foods.}, journal = {Food chemistry}, volume = {525}, number = {Pt 2}, pages = {150400}, doi = {10.1016/j.foodchem.2026.150400}, pmid = {42470887}, issn = {1873-7072}, abstract = {Geological variation in soil selenium (Se) content shapes both the nutritional value and toxicological risk of food crops. This study compared Se-biofortified rice from Brazil with naturally Se-enriched rice, cereal-based noodles, teas, meat snacks, and supplements from seleniferous regions of China. Total Se and As concentrations, dietary intake, and bioaccessibility were further assessed using in vitro digestion. Brazilian biofortified rice contained 175-9037 μg/kg Se with negligible As (≤1 μg/kg), while geogenic rice showed 76-995 μg/kg Se and 48-321 μg/kg As. Cooking reduced As by up to 71%. Selenium intakes remained within safe limits across all products, though As exposure from geogenic rice exceeded EFSA thresholds (HQ > 3). Selenium bioaccessibility averaged 24% in cereals, 22% in supplements and up to 69% in teas, decreasing significantly with ultrafiltration. These results show the need to tailor Se enrichment strategies to local geochemical contexts to balance nutritional benefits with contaminant risks.}, }
@article {pmid42474175, year = {2026}, author = {Phillips, APR and Lee, AE and Mortensen, B and Martinez-Koury, P and Izadifar, S and Dutta, S and Baxter, BK and Schmid, AK}, title = {Microbial community dynamics during historic drought and flood in Great Salt Lake.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0023426}, doi = {10.1128/aem.00234-26}, pmid = {42474175}, issn = {1098-5336}, abstract = {UNLABELLED: Understanding human-driven environmental impacts on microbial community distribution, abundance, and function remains a central challenge in microbial ecology. In particular, the drivers of temporal succession in community membership following perturbation remain unclear. Great Salt Lake, Utah, bears clear hallmarks of human disturbance, including a rock-filled railroad causeway that sequestered its northern arm from freshwater river influx, leading to localized hypersalination and food web collapse. Following decades of riverine water diversion, the southern arm of this terminal lake reached a historic low elevation during a time of increased climatic change, placing strong environmental pressure on the robust saline ecosystem. Here, we use molecular methods to report microbial community composition during this severe drought year at sites across the lake, including where the north and south arm waters contact. At sites of hypersaline water intrusion, we observe surprising stability in the north arm community composition, in contrast with strong perturbation in the south arm community structure. We use hydrodynamic modeling to pinpoint physical water flow dynamics as a key driver of these community shifts. At hypersaline north arm sites far from hyposaline water intrusion, abundance shifts were detected in predatory and parasitic taxa, a discovery that reveals surprising ecological dynamics in saturated hypersaline systems. In sum, this study demonstrates drastic hypersaline microbial community shifts during salinity and extreme weather perturbations.<br><br>IMPORTANCE: The Great Salt Lake ecosystem is rapidly drying due to climate warming and human consumptive water use that diverts riverine input to the lake's south arm. In 2022, the lake dried to reach its lowest elevation in recorded history, dehydrating microbial mats and exposing the toxic dust of the lakebed. This endangers food webs, industry, and human health. In response, Utah agencies are regulating Great Salt Lake salinity with ongoing adaptive structural engineering interventions. We hypothesized that these interferences would lead to dynamic mixing of microbial communities across a salinity gradient. We find that physical mixing drives dynamic, ongoing diversity loss and food web disruption at these sites of intervention, providing insights into how salinity regulation could be improved.}, }
@article {pmid42474191, year = {2026}, author = {Flörl, L and Griggs, R and Bokulich, NA}, title = {Microbial terroir in winegrowing: revisiting the role of microbial biogeography in terroir expression.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0119026}, doi = {10.1128/aem.01190-26}, pmid = {42474191}, issn = {1098-5336}, abstract = {The concept of microbial terroir posits that microbial biogeography pre- and post-harvest contributes to regional variation in the sensory properties of wines and some other foods. Since the introduction of this concept, the field has rapidly advanced and accumulated strong evidence that regionally distinct microbial communities contribute to characteristic wine qualities. Biogeographic patterns of vineyard microbiomes by now have been documented across all major wine-producing regions, improving our understanding of microbial sources and dispersal, as well as the abiotic and biotic factors that shape community composition. Here, we summarize recent developments in microbial terroir research in winegrowing and address common misconceptions. Spatiotemporal environmental variation influences the composition of vineyard microbial communities, and we examine the specific reservoirs and contributing drivers of this diversity. We showcase how microbial biogeography, particularly the diversity of non-Saccharomyces species, influences fermentation dynamics and resulting wine characteristics and how this expression of terroir is further impacted by the winery environment and winemaking practices. Ultimately, we identify remaining knowledge gaps and discuss potential directions for future research to better understand the ecological and functional roles of microbial communities in viticulture and winemaking.}, }
@article {pmid42474195, year = {2026}, author = {Coe, A and Parker, SM and Vo, NN and Kearney, SM and Pollak, S and von Emster, K and Mullet, JI and Castro, KG and Chisholm, SW}, title = {Influence of heterotrophs on phage infection of marine picocyanobacteria.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0076926}, doi = {10.1128/msystems.00769-26}, pmid = {42474195}, issn = {2379-5077}, abstract = {UNLABELLED: Picocyanobacteria Prochlorococcus and Synechococcus coexist with lytic phages and heterotrophic bacteria in the oceans. These phages are a significant cause of mortality, while heterotrophic bacteria can increase Prochlorococcus fitness by reducing oxidative stress and cross-feeding during extended darkness. Studies of Prochlorococcus-phage interactions are often done with xenic cultures, as it has been historically difficult to obtain and maintain heterotroph-free cultures. Here, we examine how heterotrophic bacteria affect phage infection dynamics in Prochlorococcus and Synechococcus by comparing infections in cultures with and without heterotrophs. We found that Prochlorococcus populations resumed growth following infection only when heterotrophs were present, independent of phage-host or heterotroph-host ratios. In Synechococcus phage-host pairings, outcomes varied, suggesting that heterotrophic effects depend on the phage-host interaction. When hosts recovered from infection, heterotrophs appeared to facilitate this by mitigating oxidative stress and possibly supplying organic carbon sources that support post-infection growth. Recovered Prochlorococcus and Synechococcus populations were resistant to reinfection when transferred to fresh media. However, comparisons of host sequences before and after infection argue against genetic change as the mechanism of tolerance. Instead, we infer that hosts undergo non-genetic adaptations during recovery in the presence of heterotrophs, likely driven by heterotroph-derived organic compounds that reshape host metabolism and confer protection against future lysis. During this process, heterotrophic community composition shifted dynamically across sequential transfers, yet host recovery remained consistent, suggesting that either community function or host adaptations maintained support for growth.<br><br>IMPORTANCE: This study uncovers a previously unrecognized role of heterotrophic bacteria in shaping phage infection outcomes in marine cyanobacteria. Our findings demonstrate that the presence of heterotrophs can enable Prochlorococcus to recover from phage infection, irrespective of phage:host or heterotroph:host ratios. In contrast, Synechococcus exhibited variable outcomes, suggesting that the impact of heterotrophs is dependent on the heterotroph-host pairing. Recovery after phage infection appears to be driven by heterotroph-facilitated mitigation of oxidative stress and provision of organic carbon, which may alter host metabolism and contribute to protection against future phage infection. These results highlight the importance of the microbial community, particularly heterotrophs, in shaping cyanobacteria-phage dynamics and highlight the need to reframe host-phage interactions within a broader ecological framework.}, }
@article {pmid42474711, year = {2026}, author = {Márquez, FJ and Perez-Llano, Y and Sánchez-Carrión, SA and De Rojas, M and Caruz, A}, title = {Beyond Dominant Symbionts: Low-Abundance Taxa Govern Microbial Network Topology in Sympatric Ticks.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02842-y}, pmid = {42474711}, issn = {1432-184X}, abstract = {Ticks are obligate hematophagous arthropods and major vectors of diverse bacterial, parasitic, and viral pathogens. They host complex microbial communities that critically influence their biology, fitness, and interactions with pathogens. Using 16 S rRNA gene amplicon sequencing at the amplicon sequence variant (ASV) resolution combined with co-occurrence network analysis, we characterized the bacterial communities of questing adult ticks collected in the Cazorla, Segura y Las Villas Natural Park (Jaén, Spain). A total of 83 adult ticks (27 males and 56 females) representing six sympatric species, Dermacentor marginatus (n = 39), Haemaphysalis punctata (n = 9), H. sulcata (n = 15), Hyalomma lusitanicum (n = 7), Ixodes ricinus s. l. (n = 2), and Rhipicephalus bursa (n = 11), were analyzed. After stringent quality filtering, 3.77 million high-quality reads were recovered and resolved into 407 ASVs. Due to the inherent resolution limits of the V3-V4 region for species-level discrimination, taxonomic assignments were conservatively consolidated at the genus level (101 bacterial genera). Across all tick species, the bacteriome was heavily dominated by Pseudomonadota (98.6%), with species-specific differences primarily driven by variation in obligate symbionts. Coxiella-associated ASVs predominated in multiple tick species, whereas H. lusitanicum exhibited strong dominance by Francisella and secondary representation of Candidatus Midichloria. Alpha and beta diversity analyses revealed distinct compositional patterns shaped by host identity, with lower dispersion observed in D. marginatus and R. bursa, and greater variability among Hyalomma and Haemaphysalis individuals. Spearman-based co-occurrence network analysis indicated a highly cooperative and modular structure (> 98% positive correlations) across tick species. Notably, dominant endosymbionts (Coxiella, Rickettsia, and Francisella) occupied peripheral or weakly connected positions within the networks. In contrast, ecological connectivity was governed by a distinct set of low-abundance taxa, including Roseomonas, Friedmanniella, Methylobacterium, Sphingomonas, Aureimonas, Conexibacter, Marmoricola, Mycobacterium, and Nocardioides, which acted as central hubs bridging network modules, a topology robustly validated by an independent, composition-aware (SparCC) reanalysis within the D. marginatus cohort. These comparative findings demonstrate a functional decoupling between abundance and connectivity in tick microbiomes, highlighting how the "rare microbiome" can drive the topological organization and potential stability of microbial communities across sympatric host species.}, }
@article {pmid42466130, year = {2026}, author = {Kumar, V and Ahmad, F and Rai, A and Kushwaha, A and Parmar, K and Singh, R and Tomar, A and Kumar, C}, title = {Multi-omics and synthetic microbial ecology for engineering climate-resilient phytobiomes in cold-arid agroecosystems: current advances and future perspectives.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1876810}, pmid = {42466130}, issn = {1664-302X}, abstract = {Extreme environmental stressors, including freezing temperatures, strong ultraviolet radiation, and nutrient scarcity, pose a serious threat to global food security in high-altitude cold-arid agroecosystems. Ecological stability depends on the phytobiome, which is made up of plant hosts, their microbiomes, and the edaphic environment. Although plant-associated microbiomes are important in providing stress tolerance, existing management strategies predominantly employ descriptive single-strain inoculants, which often fail under open field conditions due to competitive exclusion and environmental drift. The review summarizes recent mechanistic insights into how psychrotolerant microorganisms modify host physiology to alleviate low-temperature stress. We examine the biophysical and biochemical processes involved, with a particular emphasis on the microbial impact on the host plant's internal ICE1-CBF-COR transcriptional cascade and redox homeostasis, the role of biofilm-mediated extracellular polymeric substances (EPS) in root-zone thermal buffering, and the kinetic inhibition of ice crystallization by antifreeze proteins. Furthermore, we evaluate how genome-scale metabolic modeling can be combined with sophisticated integrated multi-omics approaches, particularly metagenomics, metatranscriptomics, and metabolomics, to create structurally stable synthetic microbial communities (SynComs), going beyond traditional isolation methods. Lastly, we discuss how regional microbial biobanks and ecological network modeling can maximize consortia persistence, addressing the translational obstacles that prevent laboratory-scale efficacy from reproducing in the field. This synthesis presents a methodical approach for creating robust phytobiomes in vulnerable mountain agroecosystems by moving the emphasis from descriptive cataloging to predictable, function-driven synthetic ecology.}, }
@article {pmid42466715, year = {2026}, author = {Takahashi, N}, title = {Beyond Acidification: Microbial Lactate in the Oral Microbiome-Host Axis.}, journal = {Journal of dental research}, volume = {}, number = {}, pages = {220345261462879}, doi = {10.1177/00220345261462879}, pmid = {42466715}, issn = {1544-0591}, abstract = {Lactate, the major acidic end-product of carbohydrate metabolism in the oral microbiome, has long been recognized as a key driver of tooth demineralization by lowering the tooth surface pH below the critical threshold for enamel dissolution. Within the framework of the ecological plaque hypothesis, this frequent and prolonged acidification contributes to dysbiosis by favoring acidogenic and aciduric microorganisms. However, accumulating evidence indicates that microbiome-derived lactate plays broader roles in both microbial ecology and host physiology. This review synthesizes current knowledge on the multifaceted functions of lactate within the oral microbiome-host axis. Lactate produced by saccharolytic bacteria, mainly including Streptococcus, Actinomyces, and Lactobacillus, as well as Rothia and Gemella, is extensively used by commensal taxa, including Veillonella, Neisseria, Rothia, and Streptococcus oligofermentans, and is primarily converted into acetate, propionate, and carbon dioxide. These cross-feeding interactions form integral metabolic networks within oral biofilms that are tightly coupled to the production of bioactive molecules, including nitrite, hydrogen peroxide, and hydrogen sulfide, contributing to microbial ecological homeostasis. Nitrite may further enter the systemic circulation and exert physiological effects, such as peripheral vasodilation via nitric oxide production through the nitrate-nitrite-nitric oxide pathway. Furthermore, in addition to directly damaging host cells at high concentrations, lactate may function as a signaling molecule through hydroxycarboxylic acid receptor 1 on host cells, potentially modulating cellular responses by regulating metabolic and signal transduction pathways. Lactate is also transported into cells via monocarboxylate transporters, where it serves as a metabolic substrate for redox regulation and induces epigenetic modifications through histone and non-histone protein lactylation, thereby affecting host cell functions. These multifaceted functions highlight lactate as a metabolic and signaling hub in the oral microbiome-host axis. The modulation of the lactate flux, rather than simply inhibiting microbial lactate production, may offer a new strategy for maintaining and promoting oral and systemic health.}, }
@article {pmid42466884, year = {2026}, author = {D'Angelo, G and Kleiner, M and Mankowski, A and Cifuentes-Anticevic, J and Violette, MJ and De Anda, V and Mussmann, M and Kröber, E and Dubilier, N and Liebeke, M}, title = {Symbiosis reshapes metabolism of sulfate-reducing bacteria in gutless marine worms.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag190}, pmid = {42466884}, issn = {1751-7370}, abstract = {Sulfate-reducing bacteria (SRB) are widespread in marine and terrestrial environments, where they often form syntrophic associations with bacteria, archaea, and eukaryotes. Among the most intimate of these are multipartite symbioses in gutless marine oligochaete worms, which host SRB and sulfur-oxidizing endosymbionts that engage in a syntrophic exchange of sulfur compounds. Despite decades of research on free-living SRB, the metabolic traits that enable SRB to persist in symbiosis, and how these differ across hosts and environments, remain poorly understood. We show that a globally distributed clade of symbiotic SRB, which we named Candidatus Desulfoconcordia, has a conserved core metabolism that diverges from free-living relatives. Using comparative genomics and metaproteomics, we reveal that these endosymbionts retain key traits of SRB such as sulfate reduction, complete oxidation of acetate to CO2, amino acid degradation for nitrogen acquisition, and transport of essential nutrients. However, they exhibit a more oxygen-tolerant metabolism and lack typical nutrient-scavenging mechanisms of free-living SRB. One trait, the glyoxylate bypass, was consistently expressed in situ and may serve both in reactive oxygen species defence and in biomass generation. The expression of oxygen-tolerant pathways, coupled with the loss of nutrient-scavenging functions, indicate specialization to a host-associated, redox-fluctuating environment distinct from that of free-living SRB. The symbiont genomes are also larger than those of free-living relatives, contrasting with genome reduction in many endosymbionts and reinforcing the importance of metabolic versatility. Our findings provide a framework for understanding how metabolic flexibility enables SRB to persist in long-term multipartite symbioses across diverse marine ecosystems.}, }
@article {pmid42469434, year = {2026}, author = {Mayo-Muñoz, D and Koonin, EV and Pinilla-Redondo, R and Riber, L}, title = {Immune safeguarding as a conserved principle of antiviral defence.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, pmid = {42469434}, issn = {1740-1534}, }
@article {pmid42470720, year = {2026}, author = {Suazo, DD and Wang, E and Taga, ME}, title = {B vitamin-mediated interactions in synthetic microbial communities.}, journal = {Current opinion in microbiology}, volume = {93}, number = {}, pages = {102799}, doi = {10.1016/j.mib.2026.102799}, pmid = {42470720}, issn = {1879-0364}, abstract = {Microbial communities drive fundamental processes across the globe, from biogeochemical cycling to human health. Yet, their complexity often obscures mechanistic understanding. Synthetic communities (SynComs) have emerged as powerful tools to distill this complexity into tractable, rationally designed systems to study community function. Metabolic interactions - competition and sharing of resources between organisms - are a frequent focus of these controlled studies. The role of B vitamin cross-feeding remains a critical frontier because B vitamins are required in trace quantities for metabolism, but not all organisms can make their own, necessitating cross-feeding interactions. Here, we review recent advances in microbial ecology that use SynComs to investigate B vitamin-mediated interactions through mechanistic approaches across scales, domains of life, environments, and disciplines. We highlight key findings that demonstrate how auxotrophy, obligate cross-feeding networks, precursor sharing, exploitation and interference competition, and cell lysis together encompass B vitamin interactions. Collectively, these processes demonstrate how microbial B vitamin exchanges drive macroscale community functions like host-microbiome interdependencies. The mechanistic insights into microbial community interactions synthesized from these integrative approaches provide foundational insight into the structure and function of natural microbial communities, advancing the potential to engineer microbiomes for therapeutic and environmental applications.}, }
@article {pmid42465057, year = {2026}, author = {Hallberg, ZF and Alvarez-Aponte, ZI and Gaudinier, A and Taga, ME}, title = {Quenching corrinoid-based interactions in a model bacterial coculture.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag160}, pmid = {42465057}, issn = {2730-6151}, abstract = {Microbial community structure is driven, in part, by the metabolic interdependencies of resident microbes. Thus, manipulating specific metabolic interactions represents an attractive way to both understand how microbial communities perform complex functions and alter them for therapeutic or environmental effects. However, it is not yet possible to control the availability of those metabolites produced by some members of the community that are required by others. Here, we report the development of a metabolite "quenching" strategy that disrupts a specific metabolic interaction involving corrinoids, the vitamin B12 family of cofactors, by applying a high-affinity corrinoid-binding protein, BtuG, to bacteria engaged in corrinoid cross-feeding. Using a model coculture composed of Sinorhizobium meliloti, a bacterium that produces a corrinoid (cobalamin), and an Escherichia coli strain engineered to be corrinoid-dependent, we demonstrate corrinoid quenching by sequestration of extracellular corrinoid, leading to inhibition of corrinoid-dependent growth. This work establishes a strategy to selectively block microbial interactions that may be more broadly applied to dissecting community structure and function. We expect that applying high-affinity "molecular sponges" to quench nutrient sharing will allow for the identification of key nutrients that structure microbial communities and potentiate precision microbiome manipulation strategies.}, }
@article {pmid42465603, year = {2026}, author = {Yang, Y and Xia, Y and Li, Y and Li, W and Luo, J and Guo, C and Zhang, H and Jiang, B and Zhu, S and Li, J and Liu, Y and Wang, C}, title = {Relay maize after tobacco enhances rapeseed growth and nutrition by reshaping soil microbial communities in an annual triple cropping system.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1827060}, pmid = {42465603}, issn = {1664-462X}, abstract = {Multiple cropping systems are increasingly being adopted worldwide to improve land-use efficiency and promote sustainable agriculture. To optimize the traditional post-tobacco fallow period, we evaluated a novel tobacco-maize-rapeseed (T_M_R) triple-cropping system. Using field experiments and high-throughput amplicon sequencing, we investigated the effects of the preceding tobacco crop and the additional maize season on rapeseed performance and soil microbial ecology. The addition of a maize season enhanced early growth vigor of rapeseed and improved key yield components, resulting in a theoretical yield of 5388.48 kg/ha. Rapeseed nitrogen uptake significantly increased compared with the conventional rotation (P < 0.05), and was positively associated with soil alkali-hydrolyzable nitrogen and major yield components. Different cropping systems significantly reshaped the β-diversity of soil microbial communities in the root-zone soil of rapeseed. Under the maize addition treatment, bacterial co-occurrence networks exhibited greater connectivity and complexity. Chujaibacter, Sporosarcina, and Epicoccum were enriched and identified as discriminative taxa using random forest analysis. In conclusion, the tobacco-maize-rapeseed triple-cropping system enhances nitrogen nutrition and reshapes soil microbial communities, providing a sustainable strategy for improving crop performance and agroecosystem functioning.}, }
@article {pmid42459877, year = {2026}, author = {Romero-Arguelles, R and Ruiz-Ayma, G and Rodriguez-Castro, VA and Gonzalez-Rojas, JI and Gomez-Govea, MA}, title = {Next-generation soil monitoring: linking metagenomics, biosensors, and ecological modeling for sustainable agriculture.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1861333}, pmid = {42459877}, issn = {1664-302X}, abstract = {Soils represent one of the most complex and dynamic biological systems on Earth, where microbial communities play a central role in regulating ecosystem functions, including nutrient cycling, carbon sequestration, and plant productivity. However, increasing pressures from land-use intensification and climate change threaten soil health and biodiversity, highlighting the need for innovative monitoring and management approaches. In this review, we synthesize current advances in soil microbial ecology, sustainable soil management, environmental sensing technologies, and metagenomics to propose an integrative framework for soil monitoring and prediction. This review integrates environmental sensing, microbiome characterization, ecological modeling, and AI-based analytics into a unified framework for next-generation predictive soil monitoring systems. We discuss how high-resolution environmental sensors enable real-time characterization of soil physicochemical dynamics, while metagenomic approaches provide unprecedented insights into the taxonomic and functional diversity of soil microbiomes. Furthermore, we explore the role of microbial network analysis and ecological modeling in uncovering interaction patterns and predicting ecosystem responses to environmental change. The integration of these tools through machine learning and data-driven approaches is transforming soil science from a descriptive to a predictive discipline. We also address key challenges, including data standardization, scalability, and the interpretation of complex biological datasets. Finally, we highlight emerging directions such as microbiome-informed precision agriculture, microbiome engineering, and the development of soil digital twins. Together, these advances pave the way toward sustainable soil management strategies that enhance ecosystem resilience and agricultural productivity in the face of global change.}, }
@article {pmid42460974, year = {2026}, author = {Gouka, L and Groen, E and Makowicz, E and Christensen, JH and Raaijmakers, JM and Cordovez, V}, title = {Yeast-Fusarium interactions and mycotoxin modulation in the phyllosphere.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag187}, pmid = {42460974}, issn = {1751-7370}, abstract = {Yeasts are prevalent members of the phyllosphere microbiome, but fundamental knowledge of the chemical basis of their interactions with other members of the phyllosphere microbiota remains largely elusive. Our previous study revealed that wheat flag leaves harbor taxonomically diverse populations of yeasts with various traits important for successful colonization and survival in the harsh phyllosphere environment. In this study, we investigated interactions between two specific yeast genera, Aureobasidium and Metschnikowia, and the mycotoxigenic fungus Fusarium graminearum, causal agent of Fusarium head blight (FHB). Using multiple experimental approaches, we demonstrate that phyllosphere yeasts effectively colonize wheat leaves and heads, markedly reducing FHB incidence when established before pathogen arrival. Based on metabolomic data, we further show that Aureobasidium and Metschnikowia isolates can degrade the Fusarium mycotoxin deoxynivalenol (DON) and DON-inducing plant compounds produced during or in response to FHB. Our findings highlight the ecology of phyllosphere yeasts and the chemical basis of their multipartite interactions with a mycotoxigenic fungus and the host plant.}, }
@article {pmid42461036, year = {2026}, author = {Munford, KE and Grégoire, DS and Hug, LA}, title = {Tracking interlinked microbial and geochemical succession over decades in landfilled municipal solid waste.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0031126}, doi = {10.1128/aem.00311-26}, pmid = {42461036}, issn = {1098-5336}, abstract = {Landfills are heterogeneous built environments embedded in natural freshwater systems. They pose increasing risks of groundwater contamination from metal-bearing leachates over time. The interlinked succession of waste decomposition processes, microbial community membership, and metal cycling across a landfill's lifespan has not been explored, reducing our ability to predict the long-term environmental impacts of landfills. Working with 1,647 metagenome-assembled genomes from a single landfill, from samples spanning over 39 years of waste decomposition, we identified changes in landfill biogeochemistry and connected these changes to shifts in microbial community composition and predicted functions over time. Comparing Older (aged 31-39 years) and Newer (aged 3-20 years) waste cells identified significant shifts in the availability of labile carbon, redox-associated processes, and concentrations of mobile metals-all higher in Newer cells. Newer cells were dominated by chemoorganoheterotrophs, while Older cells contained higher proportions of chemolithoautotrophs and organisms with higher metabolic versatility. Metal resistance and metal cycling genes were significantly more abundant in Older cells. Using geochemical data from the time of filling to the present and microbial membership data across six landfill cells of different ages, we developed a conceptual model of landfill characteristics across time. This model connects redox conditions and metal fate, highlighting leachate recirculation as a key process impacting many geochemical parameters and defining site chemistry. Our work highlights the substantial changes occurring over the stabilization phase and provides a conceptual model for understanding this critical, final stage in a landfill's life cycle.IMPORTANCEAging landfills pose significant risks to environmental stability and are currently poorly modeled beyond ~20 years. Our examination of a single landfill across 39 years of waste degradation was a unique opportunity to examine the impact of time within a connected system. Our work connects geochemical data, microbial membership, and predicted function, as well as physical processes (e.g., leachate recirculation). Our conceptual model interlinks these facets across the lifespan of a landfill, providing an empirical data-based model of landfill aging. Previous models were extrapolated from younger waste and did not include the microbial dimension-a critical facet of the landfill ecosystem. Our model clarifies processes taking place in older wastes (30+ years), including oxygen infiltration, that have important implications for methane emission and metal mobility and fate over the longer term.}, }
@article {pmid42461822, year = {2026}, author = {Svendsen, CD and Nielsen, R and Larsen, TH and Kuiper, KKJ and Eagan, TM}, title = {The oral and lower airway microbiota and coronary heart disease in COPD patients and controls.}, journal = {PloS one}, volume = {21}, number = {7}, pages = {e0353738}, pmid = {42461822}, issn = {1932-6203}, mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/complications ; *Microbiota ; Male ; Female ; Middle Aged ; *Coronary Disease/microbiology/complications ; Aged ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; *Mouth/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; }, abstract = {BACKGROUND: Chronic obstructive pulmonary disease (COPD) and coronary heart disease (CHD) are major causes of morbidity and mortality, with shared risk factors and often co-occurring. This study investigated the association between both the oral and lower airway microbiome and CHD in healthy controls and COPD patients.<br><br>METHODS: 228 participants from the MicroCOPD study (101 controls and 127 COPD patients) underwent coronary CT angiography to assess calcium score (CaSc) and coronary stenosis. Oral wash (OW) and bronchoalveolar lavage (BAL) samples were collected. Microbial DNA was analyzed using 16S rRNA gene sequencing with the Illumina MiSeq platform. Microbiome composition and diversity were analysed using established pipelines in Quantitative Insights into Microbial Ecology 2 (QIIME 2) and R.<br><br>RESULTS: Alpha diversity (Shannon index) differed significantly between COPD patients and controls in OW (p&#x2009;<&#x2009;0.01), but not BAL. No statistically significant alpha (Shannon or Faith's PD) diversity differences were found between CHD and non-CHD groups. Beta diversity analysis (Bray-Curtis dissimilarity) revealed no significant differences in microbial composition between CHD and non-CHD groups, both for COPD patients and controls (p&#x2009;>&#x2009;0.05). Firmicutes dominated across all subgroups, followed by Bacteroidetes and Actinobacteria. Several taxa were found to be differentially abundant between CHD and non-CHD groups but comprised less than 1% of all taxa.<br><br>CONCLUSION: The microbiome differed between COPD patients and controls, but we could not find evidence that either the oral or lower airway microbiome differed between those with and without coronary heart disease.}, }
@article {pmid42462426, year = {2026}, author = {Zhang, F and Zhang, X and Wang, Y and He, Y and Qiu, Z and Zhao, S and Gao, S and Zhu, M}, title = {A fungal CRY-DASH photoreceptor mediates light-dependent and-independent regulation of growth and conidiation in Trichothecium roseum.}, journal = {International journal of food microbiology}, volume = {460}, number = {}, pages = {111972}, doi = {10.1016/j.ijfoodmicro.2026.111972}, pmid = {42462426}, issn = {1879-3460}, abstract = {Light is a key environmental cue shaping fungal growth and development. Among the several photoreceptor families, cryptochrome-DASH (CRY-DASH) proteins are conserved blue-light receptors best known for photolyase/photoreactivation activity, but emerging evidence suggests broader regulatory roles in fungi. Here, we demonstrate that the CRY-DASH photoreceptor acts as a key regulator governing fungal development in the postharvest pathogen Trichothecium roseum under white light and dark conditions. We generated TrCRY-DASH knockout (ΔTrCRY-DASH) and complementation (ΔTrCRY-DASH-C) strains and integrated phenotyping with transcriptomic, metabolomic, and molecular analyses. Loss of TrCRY-DASH caused contrasting light-dependent phenotypes: under white light condition, ΔTrCRY-DASH displayed growth arrest and reduced conidiation, whereas in darkness it exhibited excessive hyphal expansion with minimal conidiation, indicating a critical role in light-dependent growth regulation. Stress assays further showed strong light-dependent sensitivity to osmotic, cell-wall, and oxidative stress that was mitigated in darkness. Multi-omics revealed a far larger transcriptional reprogramming in darkness than in light, with enrichment of pathways linked to cell-wall metabolism, signaling, Reactive Oxygen Species (ROS) homeostasis, and secondary metabolism. TrCKI was predicted as a putative candidate for TrCRY-DASH interaction based solely on bioinformatic analysis, providing a hypothesis for future experimental exploration. Together, our data indicate that TrCRY-DASH is an important regulator that modulates dark-associated growth to maintain growth-conidiation balance and thereby influencing the virulence of T. roseum toward fruits.}, }
@article {pmid42462719, year = {2026}, author = {Michoud, G and Geers, A and Peter, H and Thorpe, AC and Zhong, ZP and Rich, V and Battin, TJ}, title = {Evolutionary radiation of Polaromonas from mountain glaciers downstream.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2026.06.070}, pmid = {42462719}, issn = {1879-0445}, abstract = {Habitat transitions are central to microbial ecology and evolution and have been extensively studied across vastly different environments, such as between saline and non-saline environments. However, microbial habitat transitions along other large-scale environmental gradients remain poorly studied. This is particularly true for transitions involving the cryosphere, despite building evidence suggesting the Cryogenian as important for evolutionary radiation. Here, we investigated ecosystem transitions and the related genomic adaptations of the cosmopolitan cryospheric Polaromonas bacterium. We constructed a pangenome from 282 high-quality genomes, sourced from glaciers, glacier-fed streams (GFSs), lakes, wetlands, groundwater, rivers, and soils. Phylogenetic reconciliation suggested that the ancestral Polaromonas genome radiated from glacier ecosystems into various downstream environments through multiple independent transitions. These transitions were likely marked by extensive horizontal gene transfer and gene loss, with mobile genetic elements such as plasmids and prophages playing key roles in genomic diversification. Predicted ancestral genomes encoded versatile metabolic and stress-response capacities, which support adaptation to fluctuating and extreme conditions in the various cryospheric habitats. Compared to the ancestral Polaromonas genome, distinct genomic signatures were associated with specific habitats: GFS lineages possess expanded stress-tolerance repertoires, glacier lineages gained chemolithotrophic and anaerobic pathways, lake and wetland genomes acquired phototrophic functions, and soil lineages expanded substrate transport and stress tolerance. Together, our findings highlight the role of genomic plasticity in the ecological success of Polaromonas and also underscore the cryosphere as a potential evolutionary cradle from which lineages dispersed and adapted to downstream aquatic and terrestrial environments.}, }
@article {pmid42464117, year = {2026}, author = {Kazemifard, N and Shahrokh, S and Dimitrov, G and Totonchi, M and Dimitrov, S}, title = {From signals to systems: the epigenetic-microbiome-mitochondrial axis in IBD pathogenesis.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2692755}, doi = {10.1080/19490976.2026.2692755}, pmid = {42464117}, issn = {1949-0984}, mesh = {Humans ; *Epigenesis, Genetic ; *Inflammatory Bowel Diseases/microbiology/genetics/metabolism ; *Mitochondria/metabolism/genetics ; Animals ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology ; Intestinal Mucosa/microbiology ; }, abstract = {Inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, is increasingly recognized not merely as an immune-mediated disorder, but as a systems-level condition arising from dynamic interactions among host genetics, environmental exposures, the gut microbiome, and epigenetic regulation. While genetic susceptibility confers risk, accumulating evidence indicates that epigenetic mechanisms act as molecular integrators that translate environmental and microbial signals into sustained transcriptional programs governing immune tolerance, epithelial integrity and tissue repair. Concurrently, intestinal dysbiosis, characterized by loss of short-chain fatty acid-producing commensals and expansion of pro-inflammatory taxa, reshapes host metabolism and chromatin states through microbial-derived metabolites including short-chain fatty acids, secondary bile acids, and tryptophan catabolites. These metabolites affect epigenetic enzymes and modulate the epigenetic chromatin landscape as well as mitochondrial bioenergetics, linking microbial ecology to inflammatory gene regulation. In turn, epigenetic alterations in epithelial and immune compartments influence antimicrobial defense, barrier function, and cytokine networks, thereby sculpting microbial community organization. This bidirectional microbiome-epigenome dialogue creates self-reinforcing circuits that can either sustain mucosal homeostasis or drive chronic inflammation and colitis-associated tumorigenesis. In this review, we synthesize emerging insights into the microbiome-epigenome-mitochondrial axis in IBD and propose a conceptual framework in which metabolic, microbial, and genome-mediated signals converge to determine disease trajectory. We discuss how this integrative perspective may assist biomarker discovery and therapeutic innovation, including epigenetic modulators and microbiota-targeted interventions. Understanding IBD as a dynamically regulated host-microbe ecosystem may accelerate the development of precision strategies aimed at restoring resilient mucosal equilibrium.}, }
@article {pmid42464327, year = {2026}, author = {Dhiman, C and Kumar, A and Sonak, SS and Erukulla, P and Nimbarte, VD and Narayan, KP}, title = {Microbiota-derived metabolite landscapes modulate Fusobacterium fitness and colorectal cancer cell behaviour.}, journal = {Gut pathogens}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13099-026-00859-9}, pmid = {42464327}, issn = {1757-4749}, abstract = {BACKGROUND: Gut microbiota dysbiosis is increasingly viewed as a disruption of microbial metabolic functions rather than only a shift in microbial composition. Microbiota-derived metabolites not only shape microbial ecology but also directly influence surrounding host tissues by modulating epithelial cell signaling, inflammation, and tumor-associated processes. Among dysbiosis-associated microbes, Fusobacterium is consistently enriched in colorectal cancer (CRC) and contributes to tumor progression, yet the ecological factors regulating its expansion and interaction with host tissues remain unclear. Here, we investigated how microbiome-derived metabolite environments associated with healthy and dysbiotic microbial communities influence Fusobacterium fitness and colorectal epithelial cell behavior.<br><br>METHODS: CRC-associated dysbiosis was generated using an orthotopic murine CRC model combined with antibiotic-induced microbiota perturbation. Gut microbial communities were profiled using 16&#xa0;S rRNA gene sequencing. Metabolite-enriched supernatants derived from healthy gut microbiota, oral microbiota, dysbiotic microbiota and probiotic cultures were evaluated for their effects on CRC-associated bacteria and Fusobacterium sp. growth, adhesion and invasion. These metabolite supernatants were applied to colorectal cancer cells and their effects on viability (MTT assay), migration (scratch assay), apoptosis (Annexin V-FITC flow cytometry), and inflammatory signaling (Western blot analysis of inflammatory markers) were evaluated.<br><br>RESULTS: CRC-associated dysbiosis showed reduced microbial diversity with enrichment of opportunistic taxa including Fusobacterium and depletion of beneficial commensals such as Lactobacillus and Bifidobacterium. Metabolite-enriched supernatants from healthy gut and oral microbiota suppressed Fusobacterium growth by 55-65% and reduced bacterial adhesion and invasion in epithelial cells. In epithelial models, these metabolite environments reduced CRC viability to 60% of untreated control, with comparatively smaller effects observed in non-cancerous epithelial cells. They also inhibited cell migration, accompanied by suppression of inflammatory signaling pathways including IL-6, IL-1&#x3b2;, NF-&#x3ba;B, and HIF-1&#x3b1;. In contrast, conditioned media from dysbiotic cancer-microbiota interactions increased tumor cell viability to 120-140% of controls. These findings suggest an association between microbiota-derived metabolite landscapes, pathobiont fitness and epithelial responses under CRC-associated dysbiosis.}, }
@article {pmid42451600, year = {2026}, author = {Garcia, J and Silva, J and Alves, MJ and Gouvinhas, I}, title = {Microbiome-Driven Bioactives for Chronic Wound Repair: Microbial Metabolites, Host-Microbe Mechanisms and Paths to Clinical Translation.}, journal = {Molecules (Basel, Switzerland)}, volume = {31}, number = {13}, pages = {}, doi = {10.3390/molecules31132229}, pmid = {42451600}, issn = {1420-3049}, mesh = {Humans ; *Wound Healing/drug effects ; *Microbiota ; Chronic Disease ; *Host Microbial Interactions ; Animals ; Probiotics/therapeutic use ; Skin Microbiome ; Biofilms ; Translational Research, Biomedical ; }, abstract = {Chronic wounds represent a substantial and growing clinical burden, yet durable healing remains difficult to achieve in a large proportion of patients. The skin microbiome plays a central role in this challenge: in healthy tissue, resident microorganisms support barrier integrity and calibrate immune responses, whereas in chronic wounds, community disruption-often combined with persistent biofilm formation-drives non-resolving inflammation, impairs re-epithelialisation, and increases antimicrobial tolerance. As antibiotic resistance escalates, these features strengthen the rationale for microbiome-directed strategies that target wound ecology while reducing reliance on conventional antimicrobials. Current evidence is still dominated by mechanistic and preclinical studies, with only early clinical signals for selected approaches; therefore, next-generation probiotics, including Lactiplantibacillus/Lactobacillus spp., as well as defined prebiotic and postbiotic formulations, should be interpreted as promising adjuncts rather than clinically established therapies. Causal mechanisms, optimal formulations, reproducibility, and patient-level determinants of response remain insufficiently defined, representing a critical knowledge gap that limits translation. Here, we synthesise current evidence linking microbial ecology to key wound-healing pathways and propose a precision framework that integrates metagenomics, transcriptomics, metabolomics, and spatial profiling to map host-microbe interactions, identify predictive biomarkers, and guide stratified therapy. We further highlight combinatorial approaches pairing ecological engineering with biofilm-disruptive materials and immune-modulatory molecules. Realising the potential of these interventions will require mechanism-resolved clinical trials, standardised outcome frameworks, and patient stratification tools-advances that could improve chronic wound management while reducing selective pressure for antimicrobial resistance.}, }
@article {pmid42452138, year = {2026}, author = {Bodur, S and Asiloglu, R and Yazici, K}, title = {Soil Acidification Reshapes Microbial Trophic Interactions, with Implications for Plant Responses and Ecosystem Functioning in Tea Plantation Systems.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {13}, pages = {}, doi = {10.3390/plants15131929}, pmid = {42452138}, issn = {2223-7747}, abstract = {Soil acidification is a widespread consequence of intensive agriculture and represents a major abiotic stress affecting plant performance, nutrient availability, and ecosystem functioning. Long-term tea (Camellia sinensis) plantations provide model systems of chronic acidification, where sustained low pH imposes strong environmental filtering on soil microbial communities. Although microbial responses to acidification have been extensively studied, research has focused predominantly on bacteria and fungi, leaving other key functional groups, particularly protists, largely overlooked. Here, we synthesize current knowledge on microbial communities in acidified soils and highlight trophic interactions, especially protist-mediated regulation, as a potentially critical but underexplored dimension linking abiotic stress to plant-soil processes. We propose that soil acidification may not only filter microbial community composition but also reshape trophic interactions. Based on evidence from other soil systems, protist-mediated trophic interactions could influence nutrient cycling, pathogen suppression, and ultimately plant responses under stress conditions. Integrating environmental filtering with trophic perspectives provides a conceptual framework for understanding microbiome dynamics in acidified soils. However, direct evidence linking protist-mediated trophic regulation to ecosystem functioning and plant performance in tea plantation soils remains limited and requires experimental validation. We further suggest that these systems provide unique opportunities to investigate how abiotic constraints and biotic interactions jointly shape plant performance. Addressing this gap is essential for advancing predictive understanding of plant-microbiome interactions under ongoing environmental change.}, }
@article {pmid42453107, year = {2026}, author = {Rigerte, L and Sommer, A and Vlot, AC and Prada-Salcedo, LD and Reitz, T and Heintz-Buschart, A and Tarkka, MT}, title = {Synthetic rhizosphere bacterial communities induce systemic resistance to barley powdery mildew without major shifts in the native bacterial community.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1818676}, pmid = {42453107}, issn = {1664-302X}, abstract = {INTRODUCTION: Synthetic microbial communities (SynComs) could help plants withstand biotic stress and reduce the need for pesticides. However, it remains unclear whether SynComs composed of host- or non-host-associated rhizosphere bacteria can trigger induced systemic resistance (ISR) in barley without causing major shifts in the native rhizosphere bacterial community.<br><br>METHODS: Here, we constructed two SynComs with known strain composition, composed of bacterial strains isolated from the host-associated barley rhizosphere and non-host-associated wheat rhizosphere. Their ability to trigger induced systemic resistance (ISR) against the barley powdery mildew pathogen Blumeria graminis f. sp. hordei (Bgh) was tested. To investigate plant-microbe interactions from both plant and microbial perspectives, we quantified Bgh propagation in leaves by DAF staining, analysed leaf transcriptomes, and profiled the rhizosphere microbiome using 16S rRNA gene amplicon sequencing and metatranscriptomics.<br><br>RESULTS: Both SynComs reduced fungal growth in barley leaves to a similar extent as the positive control strain, Pseudomonas simiae WCS417r, suggesting that ISR-like protection can also be achieved by defined multi-strain communities. Although both SynComs provided similar overall protection, the barley SynCom exhibited the strongest numerical reduction in fungal growth. These findings build on previous single-strain ISR studies and suggest that community-mediated protection is not restricted to host-derived bacterial consortia. Inoculations with both SynComs and WCS417r were not associated with statistically significant changes in the rhizosphere bacterial community structure. All treatments induced only subtle pre-infection transcriptional responses in barley leaves that were consistent with ISR-mediated priming. However, treatment with WCS417r yielded a higher number of differentially expressed genes than either SynCom. Rhizosphere metatranscriptomics revealed treatment-specific functional shifts. The two features K05516 and PF02868 were affected by all three treatments, implying the existence of shared changes related to stress adaptation and microbial activity. OTUs matching the inoculated SynCom members were still present in the rhizosphere at harvest, suggesting the persistence of at least some of the introduced communities.<br><br>CONCLUSION: Together, these findings suggest that SynCom-based ISR is potentially a more ecologically relevant approach to microbiome-mediated disease protection in barley.}, }
@article {pmid42454909, year = {2026}, author = {Götz, F}, title = {mSphere Legacy: Fritz about Fritz.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0036126}, doi = {10.1128/msphere.00361-26}, pmid = {42454909}, issn = {2379-5042}, abstract = {Looking back over the past 50 years, staphylococcal research has evolved from a relatively narrow niche into a broad, interdisciplinary field encompassing genetics, genomics, bioinformatics, host-bacterium interactions, immunity, microbial ecology, the microbiota, and commensalism. My career progressed in parallel with these research developments. Much of what contributed to my success was the ability to recognize emerging questions early on, to combine classical microbiology with new technologies as they emerged, and to collaborate with talented students and colleagues across disciplines. Despite the diversity of the topics I have explored, my work has consistently been driven by a central question: what do staphylococci do, and how do they manage to persist so tenaciously? A brief overview of my research interests may illustrate this trajectory.}, }
@article {pmid42455235, year = {2026}, author = {Radaelli, E and Palladino, G and Leuzzi, D and Scicchitano, D and Rampelli, S and Turroni, S and Randhawa, HS and Candela, M}, title = {Unraveling the Influence of Behavioural Ecotypes on Fish Gut Microbiome: Focus on the Atlantic cod (Gadus morhua) in Icelandic Waters.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02832-0}, pmid = {42455235}, issn = {1432-184X}, abstract = {This study investigated the gut microbiome of Atlantic cod in northern Icelandic waters to assess how resident (coastal) and migratory (frontal) behavioural ecotypes influence gut microbial community composition, with a focus on the effects of ecological adaptation and the potential drivers of microbial shifts within this species. A total of 81 intestinal samples from coastal and frontal Atlantic cod collected in northern Iceland in December 2021 and January 2024 were analysed using 16S rRNA gene metabarcoding. Environmental datasets from the Copernicus Marine Service were used to assess the relationship between annual shifts in microbiome composition and changes in environmental conditions. Our results highlight that the Icelandic cod gut microbiome is a highly dynamic system primarily shaped by environmental shifts, such as warming trends and anthropogenic stressors. Because different behavioural ecotypes are inherently exposed to distinct environmental configurations, these distinct macro-scale exposures may indirectly translate into ecotype-specific microbial signatures that shape the differentiation between coastal and offshore habitats; the effects were particularly evident in the coastal populations, underscoring the greater vulnerability of nearshore habitats to environmental shifts and anthropogenic stressors. These findings suggest the role of the microbiome in ecological plasticity of Atlantic cod; concurrently, they reveal distinct ecotype-specific sensitivities to environmental shifts, particularly those of anthropogenic origin, providing a valuable framework that may support future marine conservation strategies.}, }
@article {pmid42455310, year = {2026}, author = {Gopakumar, A and Billah, MM and Vezzi, A and De Pascale, F and De Battisti, D and Bonato, M and Dafforn, KA and Airoldi, L}, title = {Microbial Diversity, Structure and Predicted Carbon-cycling Pathways Show Partial Convergence in Restored and Natural Salt Marshes in Venice Lagoon.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02836-w}, pmid = {42455310}, issn = {1432-184X}, abstract = {Salt marshes are increasingly restored following widespread degradation, yet the responses of sediment microbial communities to restoration remain poorly understood, despite their central role in ecosystem functioning. We compared microbial diversity, composition, structure and predicted function between natural (N) and two types of restored salt marshes in Venice lagoon, Italy: marshes restored with tidal creeks (RC), favouring a more natural tidal exchange and creek formation at the low marsh, and marshes restored with barriers (RB), which constrain tidal flow. We analysed sediment microbial communities in the three dominant habitat types of each marsh (unvegetated low marsh, vegetated low marsh, vegetated mid marsh) by amplicon sequencing of the V4 and V5 hypervariable regions of the 16 S rRNA gene. Microbial diversity was similar across natural and restored salt marshes, but community composition and structure were different. Natural marshes were characterised by higher abundances of taxa associated with sulphate reduction and organic matter degradation (e.g. Syntrophobacterales, Bacteroidales and Desulfatiglandales), whereas restored marshes showed greater representation of Desulfobacterales, Desulfobulbales and Chromatiales. In vegetated habitats, microbial communities also differed between low- and mid-marsh elevations, with low marshes enriched in Syntrophobacterales and Desulfobulbales and mid marshes characterised by Ignavibacteriales and Defluviicoccales. Despite these taxonomic differences, predicted carbon-cycling pathways were remarkably similar across restoration types and elevations. This suggests that key microbial functions can recover even when community composition remains distinct, indicating rapid re-establishment of microbial functional potential following restoration.}, }
@article {pmid42458642, year = {2026}, author = {Scheelings, TF and Beale, DJ and Van, TTH and Moore, RJ and Arnould, JPY}, title = {The faecal microbiota and its influence on fur seal (Arctocephalus sp.) physiology.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00603-3}, pmid = {42458642}, issn = {2524-4671}, abstract = {BACKGROUND: The gastrointestinal microbiota is a key determinant of vertebrate physiology, metabolism, and adaptation, forming a dynamic holobiont system that supports host health and resilience. However, while the gut microbiota of several fur seal species has been described, most studies have focused primarily on taxonomic composition, leaving a major gap in understanding how microbial communities influence host physiology in marine mammals. This study provides the first comprehensive comparison of the faecal microbiota and blood metabolomic profiles of Australian (Arctocephalus pusillus doriferus) and New Zealand fur seals (A. forsteri) across age classes (adult vs. pup), integrating 16S rRNA gene sequencing, and untargeted metabolomics and untargeted lipidomics to examine host-microbe interactions.<br><br>RESULTS: Adult fur seals exhibited a conserved microbial structure dominated by the phyla Bacillota, Fusobacteriota, and Bacteroidota, while pups displayed lower microbial diversity and higher relative abundances of Actinobacteriota and Campylobacterota, alongside enrichment of metabolites involved in DNA synthesis (2-deoxy-D-ribose, 2-deoxycytidine, and 2-deoxyuridine) and lipid metabolism. Correlations between bacterial taxa and metabolites implicated in growth, fat deposition, and hair development suggest that it is possible that early-life microbial communities may play an important role in supporting rapid development and thermoregulation.<br><br>CONCLUSIONS: Despite logistical constraints inherent to field-based sampling of wild marine mammals, our findings demonstrate consistent microbial patterns within the Arctocephalus genus and clear age-related differences in blood metabolic profiles. Together, these results enhance understanding of the complex interplay between host development, diet, and microbial ecology in fur seals, and establish a foundation for future research into the functional significance of microbiota in marine mammal health and adaptation.<br><br>CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid42459125, year = {2026}, author = {Chen, S and Nie, C and Wang, Y and Guo, Z and Zhao, K and Yu, Q and Xie, J and Chen, Y}, title = {The Ganoderma atrum Polysaccharide PSG-1 Attenuates Acrylamide-Induced Hepatotoxicity by Modulating the FXR-FGF15-Mediated Gut-Liver Axis.}, journal = {Molecular nutrition &amp; food research}, volume = {70}, number = {14}, pages = {e70543}, pmid = {42459125}, issn = {1613-4133}, support = {2024YFF1106100//National Key R&amp;D Program of China/ ; 20242BAB20329//Natural Science Foundation of Jiangxi Province/ ; 20232BCD44004//Science and Technology Innovation Base Construction Project of Jiangxi Province/ ; }, mesh = {Animals ; Receptor, Farnesoid X-Activated ; *Receptors, Cytoplasmic and Nuclear/metabolism ; *Fibroblast Growth Factors/metabolism ; *Liver/drug effects/metabolism/pathology ; *Ganoderma/chemistry ; *Acrylamide/toxicity ; *Chemical and Drug Induced Liver Injury/prevention &amp; control/drug therapy/metabolism ; Male ; Bile Acids and Salts/metabolism ; *Polysaccharides/pharmacology ; Gastrointestinal Microbiome/drug effects ; Oxidative Stress/drug effects ; Antioxidants ; }, abstract = {Acrylamide (AA), a widespread food-processing contaminant, induces intestinal injury and hepatotoxicity by disrupting barrier function, redox balance, bile acid metabolism, and gut microbial ecology. This study examined the protective benefits of Ganoderma atrum polysaccharide (PSG-1), focusing on the gut-liver axis. PSG-1 reduced serum aspartate aminotransferase (AST), alanine aminotransferase (ALT), alkaline phosphatase (ALP), and total bile acid (TBA) levels and improved liver histology. It also restored antioxidant defense by enhancing superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GSH-Px) activities while lowering malondialdehyde (MDA). At the intestinal level, PSG-1 alleviated barrier disruption and reversed gut dysbiosis, restoring Lactobacillus abundance. This microbial modulation coincided with reactivation of the farnesoid X receptor (FXR)/fibroblast growth factor 15 (FGF15) pathway, which normalized hepatic cholesterol 7α-hydroxylase (CYP7A1) expression and improved bile acid homeostasis. PSG-1 also corrected retinol metabolism disorders by reducing lecithin-retinol acyltransferase (LRAT) and restoring retinol-binding protein 4 (RBP4). These results demonstrate that PSG-1 protects against AA-induced intestinal and hepatic injury through coordinated regulation of oxidative stress, gut microbiota composition, and FXR-mediated bile acid signaling along the gut-liver axis.}, }
@article {pmid42459365, year = {2026}, author = {Xu, H and Chen, W and Xiao, Q and Ren, J and Yang, D and Li, S and Cai, Y and Tuerheng, J and Tang, R and He, K and Wu, D}, title = {Microbiota-gut-brain axis imbalance: a promising therapeutic target for preserving brain health in high-altitude environment.}, journal = {Frontiers in neuroscience}, volume = {20}, number = {}, pages = {1820153}, pmid = {42459365}, issn = {1662-4548}, abstract = {High-altitude hypobaric hypoxia poses a significant threat to brain function, yet effective neuroprotective strategies remain limited. Emerging evidence highlights the microbiota-gut-brain axis (MGBA) as a key mediator in high-altitude-induced cognitive impairment, positioning it as a potential therapeutic target. This review synthesizes current knowledge on how high-altitude exposure dynamically reshapes gut microbial ecology, characterized by reduced diversity, phylum-level instability, and functional metabolic shifts. Furthermore, we delineate how such altitude-induced dysbiosis has been associated with neural dysfunction through interconnected pathogenic mechanisms that are proposed to link gut ecology to brain outcomes: intestinal barrier disruption with metabolic dysregulation, LPS/TLR4-mediated neuroinflammation, vagal and enteric nervous system alterations, oxidative stress imbalance, and neuroendocrine dysregulation. Most current evidence is correlational, and further research is needed to establish causality. A critical unresolved question is whether short-term, transient gut dysbiosis at high altitude can instigate long-lasting neurological deficits independent of ongoing microbial perturbation. We further evaluate microbiota-targeted neuroprotective strategies, including probiotics, prebiotics, and fecal microbiota transplantation, highlighting their distinct mechanisms and summarizing the current evidence supporting MGBA-targeted interventions for high-altitude brain health. Preclinical studies suggest these approaches hold promise by restoring barrier integrity, attenuating inflammatory signaling, and rebalancing microbial metabolite profiles, while human intervention evidence remains scarce. Finally, we discuss critical challenges and future directions for translating these mechanistic insights into personalized interventions, emphasizing deeper mechanistic exploration and the synergistic interactions among microbial taxa. These insights may inform more effective therapeutic strategies for the growing populations residing in or traveling to high-altitude regions.}, }
@article {pmid42446838, year = {2026}, author = {Dias-Souza, MV and Alves, AL and de Cássia Mourão Silva, U and Júlio, ADL and Veiga, A and Pagnin, S and Dos Santos, VL}, title = {Diversity, biofilm formation and antimicrobial susceptibility of aerobic heterotrophic bacteria isolated from cooling towers.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {8}, pages = {}, pmid = {42446838}, issn = {1573-0972}, mesh = {*Biofilms/growth &amp; development ; RNA, Ribosomal, 16S/genetics ; Microbial Sensitivity Tests ; *Anti-Bacterial Agents/pharmacology ; Brazil ; *Bacteria, Aerobic/isolation &amp; purification/classification/drug effects/genetics/physiology ; Phylogeny ; *Water Microbiology ; Drug Resistance, Bacterial ; Refrigeration ; Biodiversity ; *Bacteria/classification/isolation &amp; purification/drug effects/genetics ; DNA, Bacterial/genetics ; }, abstract = {Cooling towers (CTw) are essential for industrial refrigeration but provide favourable conditions for microbial growth and biofilm formation, potentially facilitating the spread of antimicrobial-resistant bacteria (ARB). This study examines bacterial diversity, biofilm potential and antimicrobial susceptibility in two industrial CTw in Brazil using culture-based and metataxonomic (16 S rRNA gene amplicon sequencing) approaches. Fourteen bacterial genera and 22 species were identified, including Bacillus spp. (60% of isolates), Acinetobacter spp. (14%) and others like Pseudomonas, Serratia, and Ochrobactrum, many linked to biofilm formation and ARB. Metataxonomic analysis revealed a broader and more diverse microbial community, comprising families such as Burkholderiaceae, Comamonadaceae, and Sphingomonadaceae, which are known for their biofilm resilience. Pathogens including Legionella were also detected. Bacterial richness was higher in CTw 2, likely due to untreated industrial and domestic effluent inputs, whereas CTw 1, supplied with treated secondary industrial effluent, exhibited lower diversity. Functional predictions indicated genes associated with biofilm formation, quorum-sensing, motility and xenobiotic degradation. Antimicrobial susceptibility testing showed high resistance to β-lactams and nitrofurantoin, with meropenem being the most effective. Higher resistance rates in CTw 2 suggest selective pressure from industrial contaminants. These findings underscore the complex microbial ecology of CTw and the coexistence of cultivable and non-cultivable bacteria with biofilm-forming capacity and antimicrobial resistance traits in these systems.}, }
@article {pmid42446994, year = {2026}, author = {Cortés-Tapia, C and Cid-Rojas, F and Moya-Beltrán, A and García-Yunge, J and Castro, M and Rojas-Villalobos, C and Gil, F and Quatrini, R and Pizarro-Guajardo, M and Paredes-Sabja, D}, title = {Distinctive spore architecture and developmental biology of Turicibacter sanguinis reveal unexpected diversity among gut spore formers.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {e0002926}, doi = {10.1128/jb.00029-26}, pmid = {42446994}, issn = {1098-5530}, abstract = {Sporulation is a widespread but incompletely characterized trait among gut commensals, where it underpins microbial persistence, transmission, and ecological resilience. Most insights into spore biology derive from Bacilli and Clostridia; however, little is known about sporulation in phylogenetically distant gut-associated lineages. Turicibacter sanguinis, a strict anaerobe linked to host serotonin metabolism, lipid homeostasis, and neurodegenerative disease, represents one such understudied taxon. Here, we integrate ultrastructural, physiological, and comparative genomic analyses to define the sporulation and germination program of T. sanguinis. We show that T. sanguinis forms heat-resistant spores with a canonical core-cortex-coat architecture but displays previously undescribed features, including a dual-layered outer envelope and bimodal electron-dense coat morphotypes. Developmental stages of sporulation follow canonical stages of Bacillus- and Clostridium-like sporulation, while genomic analyses reveal a hybrid regulatory architecture combining Clostridial-type Spo0A initiation with Bacillus-like late-stage sigma factor control. Germination assays and genomic signatures further indicate a nutrient-responsive, Bacillus-like pathway involving Ger-family receptors, SpoVA-mediated Ca-DPA release, and CwlJ- and SleM-type cortex hydrolases. Together, these findings identify T. sanguinis as a distinct spore-forming lineage within the human gut microbiota and expand the known diversity of sporulation strategies across the Firmicutes.IMPORTANCEThe gut bacterium Turicibacter sanguinis is linked to critical host functions, including serotonin production and lipid homeostasis. In this work, we show that T. sanguinis forms spores as a potential mechanism to survive and transmit. Unlike well-studied bacteria, T. sanguinis encodes a unique, hybrid sporulation program that mixes regulatory and structural elements from distant bacterial species. These observations fill a significant gap in our understanding of gut microbial ecology. It suggests that T. sanguinis persists in the gut through a distinct, specialized survival program. The outlined mechanisms provide a roadmap to study how this bacterium persists in the gut and impacts host health.}, }
@article {pmid42447623, year = {2026}, author = {Su, K and Tian, S and Xia, Y and Zhao, X and Huang, J and Hu, S and Ye, J}, title = {Species composition and functional characteristics of the human multi-organ microbiome: A metagenomic study.}, journal = {Journal of forensic and legal medicine}, volume = {122}, number = {}, pages = {103213}, doi = {10.1016/j.jflm.2026.103213}, pmid = {42447623}, issn = {1878-7487}, abstract = {Postmortem microbial communities may provide useful information for forensic microbiology, but species-level and functional profiles across multiple cadaveric anatomical sites remain poorly characterized. Here, shotgun metagenomic sequencing was performed on 144 samples from six anatomical sites, including the oral cavity, nasal cavity, trachea, lung, colon, and anus, collected from 24 human cadavers. A total of 15,301,799,968 raw reads were obtained, and 6565 species were identified, and KEGG pathways were annotated at the L1, L2, and L3 levels. Species-level microbial composition differed significantly among anatomical sites. PERMANOVA with permutations blocked by individual identity showed that anatomical site was the dominant factor explaining microbial community variation (R[2] = 0.3778, p = 0.001, q = 0.001), whereas postmortem interval did not show a significant independent effect within the 1-38-day interval. KEGG functional profiles also differed significantly among anatomical sites at the L2 and L3 levels, and 182 of 214 L3 pathways showed significant site-associated differences after false-discovery-rate correction. Pathway-level mixed-effect models further indicated that anatomical site remained significantly associated with most L3 pathways after accounting for postmortem interval, age, sex, cause of death, and repeated sampling from the same individual. Species-pathway correlation analysis identified significant taxon-function associations, but these were interpreted as correlative rather than direct evidence of species-specific functional contribution. Low-biomass sensitivity analyses indicated that respiratory-site results, especially lung and tracheal findings, should be interpreted cautiously because of high host DNA proportions and low non-host read counts. Inter-site shared occurrence and intra-site co-occurrence analyses further described distributional associations across anatomical sites. This study establishes a multi-site postmortem metagenomic reference framework for characterizing anatomical-site-specific microbial and functional patterns, offering insights into forensic microbiology and postmortem microbial ecology.}, }
@article {pmid42447669, year = {2026}, author = {Kim, IT and Jeong, Y and Lee, YE and Ahn, KH and Jung, JH}, title = {Biogas-driven sidestream nitrogen removal: A perspective on replacing partial nitritation with aerobic methane oxidation-denitrification toward carbon-neutral wastewater treatment.}, journal = {Water research}, volume = {305}, number = {}, pages = {126456}, doi = {10.1016/j.watres.2026.126456}, pmid = {42447669}, issn = {1879-2448}, abstract = {Sidestream reject water from anaerobic digesters imposes a disproportionately high nitrogen load (typically ∼15-25% of the total plant nitrogen load despite comprising <5% of total influent volume) on wastewater treatment plants. However, existing biological removal technologies, including partial nitritation/anammox and anaerobic methane oxidation-based processes, are structurally disconnected from onsite biogas valorization. In this review, we evaluated the feasibility of replacing the conventional partial nitritation stage with aerobic methane oxidation coupled with denitrification (AME-D) in an integrated two-stage system toward carbon-neutral sidestream nitrogen removal. We synthesized the current knowledge on methane-oxidizing microbial ecology, interguild carbon transfer networks, and the enabling roles of reject water composition and biogas-derived CO2 in sustaining integrated process performance. The key findings indicate that AME-D can serve as a multifunctional upstream stage, concurrently supplying nitrite, reducing ammonium load, and providing carbon intermediates to the downstream nitrate/nitrite-dependent anaerobic methane oxidation (n-DAMO) consortium. This enables biogas-driven complete nitrogen removal without external carbon input. The principal challenges involved in this process include greenhouse gas emission management, membrane fouling under high-strength sidestream conditions, and constraints on micronutrient bioavailability, which may compromise long-term microbial stability. This review proposes an integrated conceptual framework for AME-D/n-DAMO process design, identifies research priorities in pilot-scale validation and multi-guild community engineering, and articulates a pathway toward circular bioeconomy implementation in urban water resource recovery.}, }
@article {pmid42447682, year = {2026}, author = {Löffler, T and Feckler, A and Roodt, AP and Schulz, R and Bundschuh, M}, title = {Holding poison: Retention and biodegradation of pesticides by freshwater biofilms.}, journal = {Ecotoxicology and environmental safety}, volume = {322}, number = {}, pages = {120496}, doi = {10.1016/j.ecoenv.2026.120496}, pmid = {42447682}, issn = {1090-2414}, abstract = {Biofilms play a central role in the self-cleaning capacity of freshwater ecosystems and bioremediation of chemical contaminants. In this study, we evaluated the contribution of biofilms developing on organic and inorganic substrates to the retention and degradation of pesticides in freshwater streams under controlled laboratory conditions. Experiments were conducted at two temperatures (16 and 20°C) and using a mixture of ten pesticides at three concentrations (0, 2.5 and 35 µg/L). Our results confirmed a significant contribution of biofilms to pesticide retention, as evidenced by reduced concentrations in the water column being partially more than a factor of two higher than in absence of biofilms. This is supported by pesticide-specific sorption-factors to biofilms between 0.3 and 28734. Biofilm origin had a significant effect on microbial taxonomic composition and enzyme profiles (PERMANOVA, p < 0.001), which in turn influenced interaction mechanisms and the efficiency of pesticide removal. Biofilms associated with inorganic substrates primarily functioned as sinks, retaining pesticides, whereas those associated with organic substrates predominantly acted as bioremediators, promoting pesticide degradation. In contrast, temperature and pesticide concentration had no significant effects, indicating comparatively minor influence on the retention and degradation efficiency of pesticides by biofilms under the tested conditions. Therefore, this study highlights the important role of biofilms in reducing xenobiotic concentrations in aquatic environments, with this function being resilient to temperature and pesticide concentration. Moreover, we are - to the best of our knowledge - the first to document functional differences in pesticide retention and reduction between biofilms associated to organic and inorganic substrate, respectively.}, }
@article {pmid42449053, year = {2026}, author = {Maurice, K and Baldovini, N and Zaremski, A and Damay, J and Lehnebach, R and Estevez, Y and Ducousso, M}, title = {The Microbial and Chemical Terroir of Agarwood in French Guiana.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02824-0}, pmid = {42449053}, issn = {1432-184X}, support = {Acquilascent//Agence Nationale de la Recherche/ ; }, abstract = {Agarwood is a highly valued aromatic resinous wood formed in Aquilaria species following stress or infection, yet the putative microbial drivers of its quality remain poorly understood, particularly outside its native range. In this study, we investigated the bacterial and fungal communities associated with agarwood produced from Aquilaria crassna Pierre ex Lecomte planted in French Guiana and examined their relationships with volatile chemical compounds relevant to agarwood fragrance. Using high‑throughput sequencing and comprehensive chemical profiling, we characterized microbial community composition and agarwood volatile profiles across multiple cultivation plots. Despite spatial variability in microbial assemblages, agarwood samples exhibited a conserved chemical signature dominated by chromone derivatives and sesquiterpenoids, indicating the presence of a stable chemical terroir under Guianese environmental conditions. Network analysis revealed numerous bacterial and fungal taxa significantly associated with key chemical classes, suggesting potential microbial contributions to agarwood chemical complexity through plant-microbe interactions or microbial metabolic activity, although causality remains to be established. Comparative analyses with commercial agarwood samples from South-East Asia and the Middle East revealed a distinct chemical profile for Guianese agarwood, highlighting the influence of geographic origin on agarwood quality and supporting an extension of the terroir concept to woody aromatic products. Overall, this study demonstrates that Aquilaria trees cultivated in French Guiana can produce high‑quality agarwood and provides new insights into the interplay between microbial communities and agarwood chemistry. These findings lay the groundwork for the development of locally adapted, microbiome‑informed strategies for sustainable agarwood production.}, }
@article {pmid42449225, year = {2026}, author = {Maqbool, F and Naqvi, RZ and Rehman, R and Amin, I and Imran, I and Imran, A}, title = {PGPR-induced regulation of Zn and Fe transporters in wheat (Triticum aestivum L.) uncovered through integrated genome-wide analysis and functional validation.}, journal = {BMC plant biology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12870-026-09415-8}, pmid = {42449225}, issn = {1471-2229}, abstract = {Zinc (Zn) and iron (Fe) deficiencies affect more than two billion people globally, particularly in cereal-dependent regions where wheat, despite its high consumption, provides inadequate micronutrient levels. Conventional interventions such as genetic modification and mineral supplementation remain costly, unevenly accessible, and insufficient for large-scale nutritional improvement. Agronomic biofortification using plant growth-promoting rhizobacteria (PGPR) offers a promising yet underexplored alternative, especially for regulating metal homeostasis genes in wheat. This research integrates multi-season field trials of Zn-biofortified Akbar-19 and the local cultivar Khaista-17, conducted under reduced fertilizer conditions with PGPR consortia. Afterwards, genome-wide analyses including phylogenetic relationships, promoter elements, gene interaction networks, expression profiles, and conserved domains/motifs of the TaNAS (19 genes), TaNAAT (6), TaDMAS (3), and TaVIT (31) gene families was performed. This was followed by transcriptional expression (qPCR) of six candidate genes in wheat grown under hydroponic Zn/Fe stress in the presence of PGPR. Field evaluation showed that PGPR inoculation boosted yield by 15-18% and increased grain Zn/Fe by 15-20% in Akbar-19 and 25-28% in Khaista-17, consistently outperforming fertilizer-only controls across both seasons. The genome-wide analyses exhibited the phylogenetic relationship of wheat TaDMAS, TaNAAT, and TaNAS genes with barley, while TaVIT and TaVTL genes with rice and maize. Promoter analyses of these genes showed an enrichment of stress-responsive cis-elements, such as IDE1/2, ZDRE1/2, IRO2-binding sites, and metal-responsive elements suggesting coordinated regulation of micronutrient chelation, uptake, and homeostasis. qPCR results confirmed PGPR-induced upregulation of NAS1, NAS6, NAS9, NAAT2, DMAS1, and VIT2 under Zn/Fe stress, with stronger induction in Khaista-17. Overall, the results show that PGPR modulate metal‑transporter gene networks and improve micronutrient biofortification in wheat, providing a genotype‑responsive and sustainable approach to address micronutrient deficiency.}, }
@article {pmid42449422, year = {2026}, author = {Webster, SJ and Cock, IE and Matheson, C and Sweeney, EL}, title = {Vaginal microbiomes and their pertinent social context: a microbial ecological review proffering AMR-STI acquisition and emergence.}, journal = {Biology of sex differences}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13293-026-00953-2}, pmid = {42449422}, issn = {2042-6410}, support = {Research Training Program (RTP) Domestic Scholarship//Australian Government/ ; }, abstract = {BACKGROUND: In the landscape of sexual health, sex, gender, and sexuality are inextricably linked and highly relevant to sexually transmitted infections (STIs). Globally, key sexual and reproductive health concerns of women have been associated with the socioeconomic status of their country, indicating that social context bears influence over sexual health outcomes. Further, the increasing prevalence of antimicrobial resistant STIs (AMR-STIs) in the sexual networks of gay and bisexual men-who-have-sex-with-men (GBMSM) suggests an implicit connection between microbiological and social phenomena, although research to date is relatively limited and often fails to reflect the complexity and nuance of sexual networks. Vulval and vaginal microbiome composition may influence STI acquisition and transmission, yet the relationships between composition, microenvironment, and STIs remain largely overlooked, especially in the context of women and gender-diverse people. In this article, we explore the possibility that a combination of social, sexual, and behavioural factors, combined with biological features, shape the microbiological context of STIs within the vaginal microenvironment. MAIN: The human vaginal microbiome (VMB) forms an ecological niche home to a complex ecosystem of microorganisms. The microbial composition of the VMB is diverse between individuals, with variations observed across racial and ethnic groups, and intrapersonal fluctuations linked to a plethora of factors both within and outside of personal control. Importantly, VMB health is a crucial component of wellbeing for people assigned female at birth (AFAB), transgendered women with neovaginas, and their sexual partners. Clinical context also remains important; in Australia, doxycycline prophylaxis (Doxy-PEP) has recently become available to GBMSM networks aimed to protect against the acquisition of STIs. However, Doxy-PEP guidelines exclude AFAB people and fail to specify regarding use among gender diverse individuals. Given the high prevalence of AMR-STIs within GBMSM networks, the impact of this intervention on excluded partners should be thoroughly investigated. Factors in the VMB such as biofilm formation and necessary microbial balance with opportunistic pathogens renders this ecological microbial niche a hypothetically perfect platform for AMR development and emergence within the social context.<br><br>CONCLUSION: This review explores the social context of vaginal microbiomes, their potential influence on AMR-STI development, and highlight several important knowledge gaps to benefit from further research.}, }
@article {pmid42449926, year = {2026}, author = {Mitova, N and Lazarova, Z}, title = {Microbial Composition of Carious Dentin and the Impact of Minimally Invasive Excavation Techniques: A Narrative Review.}, journal = {International journal of molecular sciences}, volume = {27}, number = {13}, pages = {}, doi = {10.3390/ijms27135648}, pmid = {42449926}, issn = {1422-0067}, mesh = {Humans ; *Dental Caries/microbiology/therapy ; *Dentin/microbiology ; *Microbiota ; Biofilms/growth &amp; development ; }, abstract = {Dental caries is a biofilm-mediated dysbiotic disease characterized by ecological shifts within the oral microbiome and progressive demineralization of dental hard tissues. The microbiological composition of carious dentin and the impact of minimally invasive excavation techniques on residual microbial communities remain subjects of ongoing investigation due to methodological heterogeneity and inconsistencies among published studies. This narrative review aimed to summarize current evidence regarding the microbial ecology of carious dentin, compare culture-based and molecular methods for microbiological assessment, and evaluate the microbiological outcomes associated with contemporary approaches to managing minimally invasive caries. The relevant literature on dentinal caries microbiology, microbial detection methods, and excavation techniques was analyzed. The available evidence indicates that carious dentin contains a highly diverse polymicrobial community composed of acidogenic, aciduric, anaerobic, and proteolytic microorganisms. Culture-based methods primarily detect viable and cultivable taxa, whereas molecular approaches reveal substantially greater microbial diversity, including uncultivable and low-abundance species. Comparative studies demonstrate that minimally invasive excavation techniques significantly reduce microbial load but rarely achieve complete microbial elimination. The available evidence suggests that successful caries management is associated with a reduction in and ecological modulation of the residual microbiota within a sealed environment. The integration of culture-based and molecular findings provides a more comprehensive understanding of the microbiology of carious dentin and supports biologically oriented, minimally invasive strategies for caries management.}, }
@article {pmid42450045, year = {2026}, author = {Urbanowicz, T and Mattina, A and Cielecka-Piontek, J and Raffa, GM and Pisano, C and Grywalska, E and Hymos, A and Rahnama, M and Kowalewski, M and Suwalski, P and Jemielity, M and Krasiński, Z}, title = {Advanced Functional Wound Dressings in Precision Surgery: Immunometabolic Reprogramming, Bioadaptive Biomaterials, and Intelligent Regenerative Interfaces.}, journal = {International journal of molecular sciences}, volume = {27}, number = {13}, pages = {}, doi = {10.3390/ijms27135772}, pmid = {42450045}, issn = {1422-0067}, support = {PNRR-POC-2023-12378186 CUP I73C24000330006//European Union/ ; }, mesh = {Humans ; *Biocompatible Materials ; *Wound Healing ; Animals ; *Bandages ; Metabolic Reprogramming ; Regenerative Medicine/methods ; *Precision Medicine/methods ; }, abstract = {Postoperative wound complications remain a major cause of morbidity, prolonged hospitalization, increased healthcare costs, and reduced quality of life. While traditional wound dressings functioned primarily as passive barriers against contamination and exudate, advances in wound biology have transformed surgical wound management. Tissue repair is now recognized as a dynamic immunometabolic process involving coordinated interactions among immune cells, stromal populations, extracellular matrix remodeling, mechanotransduction, mitochondrial function, redox balance, microbial ecology, and bioelectrical signaling. Consequently, modern wound dressings are increasingly designed as bioactive systems capable of actively modulating the wound microenvironment. Recent developments in biomaterials science, immunoengineering, nanotechnology, extracellular vesicle biology, bioelectronics, and artificial intelligence have enabled the creation of advanced wound platforms, including stimuli-responsive hydrogels, immunomodulatory biomaterials, nanozyme-based dressings, conductive scaffolds, oxygen-generating matrices, extracellular vesicle-loaded systems, and biosensor-integrated interfaces. Therapeutic strategies are progressively shifting from antimicrobial-focused approaches toward immune-regenerative modulation targeting chronic inflammation, mitochondrial dysfunction, ferroptosis, cellular senescence, and impaired mechanobiological signaling. This review examines emerging surgical wound dressings from mechanistic, translational, and biomaterial perspectives, highlighting current innovations, translational challenges, and future directions. Collectively, these technologies may enable intelligent therapeutic systems capable of sensing and directing tissue regeneration in real time.}, }
@article {pmid42450455, year = {2026}, author = {Zhao, D and Zhang, J}, title = {From Molecular Flavor Signatures to Mechanism-Oriented Food Quality: Advances in Flavoromics, Fermentation Ecology, Functionality, and Safety.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {13}, pages = {}, doi = {10.3390/foods15132337}, pmid = {42450455}, issn = {2304-8158}, abstract = {Food quality is now understood less as a single attribute than as an integrated system of flavor perception, nutritional value, microbial ecology, processing history, and safety assurance [...].}, }
@article {pmid42450684, year = {2026}, author = {Cheng, S and Wang, HH and Chi, ML and Jiang, WP and Liu, SL and Zou, WW and Chen, ZL and Li, F}, title = {Time-Dependent Polystyrene Nanoplastic Toxicity in Cherax quadricarinatus: Oxidative Stress, Gut Dysbiosis, and Hepatopancreatic Bioaccumulation.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {13}, pages = {}, doi = {10.3390/ani16131977}, pmid = {42450684}, issn = {2076-2615}, support = {2025SNJF010//Zhejiang Province Agriculture, Rural Areas, and Nine Directions Project/ ; 2026YSZX01-5//Zhejiang Provincial Research Institute Special Project/ ; 2023NKY05//The Seed Capital for Innovation and Entrepreneurship of Wencheng County/ ; Zdwc2401//Research and Demonstration of Localized Artficial Seeding Cultivation of Australian Blue Shrimp/ ; 2025RAC//Research and Application of Characteristic Breeding Technology for Rice Fields in Wencheng Mountain Creek and Model Breeding Equipmengt in Hilly and Mountainous Areas/ ; }, abstract = {Polystyrene nanoplastic (PS-NP) contamination poses an emerging threat to aquaculture species, yet time-resolved assessments integrating host physiology, gut microbial ecology, and tissue bioaccumulation remain limited. Here, we evaluated the temporal effects of 100 mg/L PS-NPs (100 nm) on Cherax quadricarinatus (Von Martens, 1868) over a 3-week exposure period. Crayfish were assigned to a control group (Group A) and three treatment groups exposed for 1 (Group B), 2 (Group C), or 3 (Group D) weeks. No mortality occurred. Hepatopancreatic antioxidant enzyme activities (superoxide dismutase and glutathione peroxidase) displayed a hormetic response (upregulation at weeks 1-2 followed by depletion at week 3), indicating oxidative stress overload. Alkaline phosphatase activity declined progressively, reflecting cumulative immunosuppression. Histological examination revealed time-dependent structural damage in the hepatopancreas: hepatic tubule enlargement, increased vacuolation, B cell hypertrophy, and cellular disorganization/lysis after three weeks. 16S rRNA sequencing revealed that PS-NPs induced time-dependent gut dysbiosis, characterized by depletion of beneficial taxa and enrichment of opportunistic pathogens. Alpha-diversity metrics (ACE, Chao1, Shannon) were significantly reduced in Group D compared to controls, confirming loss of microbial evenness and richness. Pyrolysis gas chromatography-mass spectrometry quantification demonstrated marked PS-NP bioaccumulation in the hepatopancreas, with concentrations rising from 6.94 μg/g in controls to 65.38 μg/g in Group D, a 9.4-fold increase. Collectively, prolonged PS-NP exposure is associated with oxidative stress, immune dysfunction, progressive gut dysbiosis, and substantial hepatopancreatic nanoplastic burden in C. quadricarinatus. These findings carry implications for ecological risk assessment and highlight the need for further investigation into food safety risks associated with human consumption of crayfish from PS-NP-contaminated environments.}, }
@article {pmid42451154, year = {2026}, author = {Biagioli, V and Matera, M and Imola, I and Mela, F and Lemmi, D and Verrotti, A and Striano, P}, title = {Beyond Ketosis: Dietary Therapies and the Microbiota-Gut-Brain Axis in Epilepsy.}, journal = {Nutrients}, volume = {18}, number = {13}, pages = {}, doi = {10.3390/nu18132151}, pmid = {42451154}, issn = {2072-6643}, mesh = {Humans ; *Epilepsy/diet therapy/microbiology ; Diet, Ketogenic ; Probiotics/administration &amp; dosage ; *Gastrointestinal Microbiome/physiology ; Prebiotics/administration &amp; dosage ; *Ketosis ; *Brain ; *Brain-Gut Axis/physiology ; Animals ; Diet, Carbohydrate-Restricted ; Diet, Mediterranean ; Diet, High-Protein Low-Carbohydrate ; }, abstract = {Background: Epilepsy is a complex neurological disorder in which growing evidence supports a significant role for the microbiota-gut-brain axis (MGBA) in modulating neuroinflammation, neuronal excitability, and treatment responsiveness. Beyond their traditional role in inducing ketosis, dietary therapies may influence epilepsy by modulating gut microbial ecology, intestinal barrier integrity, immune signaling, and microbiota-derived metabolites. Methods: This narrative review critically examines current clinical and experimental evidence regarding the relationship between epilepsy, gut microbiota, and dietary interventions. Particular attention was given to ketogenic dietary therapies, the Modified Atkins Diet (MAD), low-glycemic-index treatment (LGIT), Mediterranean dietary patterns, restrictive diets, and microbiota-targeted supplementation, including probiotics, prebiotics, and postbiotics. Results: Available evidence suggests that patients with epilepsy exhibit alterations in gut microbial composition associated with impaired short-chain fatty acid production, intestinal inflammation, and altered neuroimmune regulation. Ketogenic and microbiota-supportive dietary approaches may modulate these pathways beyond ketosis alone, potentially contributing to seizure reduction through integrated metabolic, inflammatory, and microbial mechanisms. Emerging evidence also supports a role for probiotics, prebiotics, and postbiotics in modulating gut-brain communication and neuroinflammatory signaling, although current clinical data remain limited. Conclusions: Dietary therapies in epilepsy should no longer be viewed exclusively as metabolic interventions aimed at inducing ketosis, but rather as potential modulators of the microbiota-gut-brain axis and neuroimmune homeostasis. While further mechanistic and clinical studies are needed, microbiota-targeted nutritional approaches may represent valuable complementary strategies to be integrated alongside conventional antiseizure therapies within more personalized models of epilepsy management.}, }
@article {pmid42440521, year = {2026}, author = {Lv, M and Xu, W and Wang, T and Mou, K and Ni, Z and Tu, Q and Zhang, J and Wu, X and Song, S and Cheng, G}, title = {Host-microbiome-immune disequilibrium in oral disease: mechanisms, dysbiosis, and precision therapeutics.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1854213}, pmid = {42440521}, issn = {1664-3224}, mesh = {Humans ; *Dysbiosis/immunology ; *Microbiota/immunology ; Animals ; Immunity, Mucosal ; *Mouth Diseases/immunology/microbiology/therapy ; Precision Medicine ; *Host Microbial Interactions/immunology ; Mouth/microbiology/immunology ; }, abstract = {BACKGROUND: The oral cavity harbors a dynamic microbial ecosystem that interacts with epithelial barriers, host immunity, and local tissue environments. Disruption of this balance is increasingly recognized as a key driver of major oral diseases, including periodontitis, dental caries, and oral squamous cell carcinoma (OSCC). However, the biological links between microbial ecology, immune regulation, and disease progression are insufficiently integrated, limiting mechanistic understanding and translational progress.<br><br>METHODS: This structured narrative review searched PubMed/MEDLINE, Web of Science, Embase, and Scopus for relevant studies on oral microbiome ecology, mucosal immunity, dysbiosis, oral diseases, and emerging therapies. Evidence was narratively synthesized across microbiome ecology, mucosal immunology, disease pathogenesis, and translational research, with consideration of study type, mechanistic relevance, and translational significance.<br><br>RESULTS: Current evidence supports that oral homeostasis relies on coordinated interactions among commensal microbial communities (CMC), epithelial and salivary barriers, and immune surveillance. Dysbiosis disrupts this equilibrium by promoting the expansion of pathobionts, amplifying inflammatory responses, and contributing to tissue injury. This systems-level perspective helps explain the persistence and heterogeneity of oral diseases beyond pathogen-centered models. Emerging technologies are reshaping this field. These include microbiome-modulating therapies, host-directed interventions, multi-omics approaches, and artificial intelligence (AI). These approaches are advancing disease stratification, biomarker discovery, and precision therapeutic development.<br><br>CONCLUSION: Oral diseases should be understood as disorders of host-microbiome-immune disequilibrium rather than as isolated infections. This perspective highlights the need for integrated strategies that consider microbial ecology, immune regulation, epithelial barrier function, and clinical context to improve prevention, diagnosis, and treatment in precision oral medicine.}, }
@article {pmid42440971, year = {2026}, author = {Gahlot, KD}, title = {Dietary modulation of the gut resistome: ecological and metabolic pathways driving antimicrobial resistance.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1868638}, pmid = {42440971}, issn = {2296-861X}, abstract = {Antimicrobial resistance (AMR) is traditionally viewed as a consequence of antibiotic exposure and genetic adaptation; however, resistance also emerges from the ecological and metabolic context of microbial communities. The human gut microbiome represents a major reservoir of antibiotic resistance genes (ARGs), and diet is increasingly recognised as a dominant regulator of its structure and function. Here, I synthesise current evidence and propose a conceptual framework in which diet shapes resistome dynamics through three interrelated pathways: ecological selection, metabolic regulation, and physicochemical modulation of horizontal gene transfer. Dietary components influence microbial composition, metabolic activity, and the spatial organisation of fermentation along the colon. Diverse fibre types differentially regulate short-chain fatty acid production and microbial competition, whereas high-fat, low-diversity diets destabilise communities and favour opportunistic taxa. Beyond macronutrients, food additives and the physical structure of food alter gut barrier function, microbial stress responses, and spatial ecology, thereby influencing resistome stability. Diet-induced metabolic states further determine antibiotic susceptibility, including transitions between tolerance and resistance. Taken together, this integrated ecological perspective positions diet as a modifiable driver of AMR and highlights nutritional strategies as complementary approaches to mitigating resistome expansion.}, }
@article {pmid42441583, year = {2026}, author = {Luo, H and Zhang, H and Xu, L and Hong, L and Tang, H and Wang, C}, title = {Application of Acupuncture in the Management of Skin Diseases: A Review from the Perspective of the Microbiome.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {232}, pages = {}, doi = {10.3791/71199}, pmid = {42441583}, issn = {1940-087X}, mesh = {Humans ; *Acupuncture Therapy/methods ; *Microbiota ; *Skin Diseases/therapy/microbiology/immunology ; Skin Microbiome ; }, abstract = {Inflammatory skin diseases (e.g., atopic dermatitis, psoriasis, acne vulgaris, and chronic urticaria) are increasingly recognized as systems-level disorders arising from the interplay among immune dysregulation, barrier impairment, neuroendocrine imbalance, and microbial dysbiosis. High-resolution microbiome studies have moved the field beyond species-level associations to strain-level and functional insights, highlighting pathogenic Staphylococcus aureus lineages in atopic dermatitis (AD), disease-relevant Cutibacterium acnes phylotypes in acne, and gut microbial signatures that may prime type 17 helper T cell/regulatory T cell (Th17/Treg) imbalance and systemic inflammation across multiple dermatoses. Acupuncture is widely applied in dermatology to alleviate pruritus and reduce disease burden, with emerging sham-controlled trials and high-quality randomized evidence in chronic spontaneous urticaria (CSU) suggesting clinically meaningful symptomatic improvement. Mechanistically, acupuncture can engage neuro-immune circuits (including vagal anti-inflammatory pathways), modulate cytokine networks, and improve epithelial barrier integrity-host processes that strongly shape microbial ecology and metabolite production. Meanwhile, accumulating microbiome-focused studies in non-dermatologic conditions indicate that acupuncture can alter gut microbiota composition and diversity, as well as microbial metabolites (e.g., short-chain fatty acids), providing a plausible biological bridge to the gut-skin axis. In this narrative review, we synthesize evidence linking (i) skin/gut microbiome dysbiosis with inflammatory skin pathogenesis, (ii) acupuncture-mediated neuro-endocrine-immune modulation, and (iii) microbiome remodeling as a potential mediator of systemic and cutaneous immune modulation. We propose an integrative mechanistic framework and discuss methodological pitfalls (heterogeneous acupuncture protocols, challenges with sham designs, limited dermatology-specific microbiome endpoints, and gaps in causal inference), providing actionable directions for multi-omics longitudinal trials and mechanistic validation.}, }
@article {pmid42441839, year = {2026}, author = {Deng, S and Yang, Y and Guo, X and Yuan, MM and Zhang, Y and Wu, L and Shi, W and Zhou, X and Cornell, CR and Bates, CT and Liu, XA and Zhang, Q and Tian, R and Jian, S and Liu, S and Liang, Z and Lei, J and Gao, Q and Shi, Z and Wu, L and Liu, X and Luo, Y and Ning, D and Tiedje, JM and Zhou, J}, title = {Experimental drought drives divergent succession of soil microbiota.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {29}, pages = {e2537753123}, doi = {10.1073/pnas.2537753123}, pmid = {42441839}, issn = {1091-6490}, support = {32161123002//MOST | National Natural Science Foundation of China (NSFC)/ ; DE-SC0004601//U.S. Department of Energy (DOE)/ ; DE-SC0010715//U.S. Department of Energy (DOE)/ ; EF-2025558//National Science Foundation (NSF)/ ; DEB-2129235//National Science Foundation (NSF)/ ; }, mesh = {*Soil Microbiology ; *Droughts ; *Microbiota/physiology ; Bacteria/genetics/classification ; Biodiversity ; Ecosystem ; Fungi/genetics/classification ; Soil/chemistry ; Biomass ; }, abstract = {As droughts become increasingly severe and prolonged worldwide, understanding how belowground biodiversity changes over time under water limitation is critical for assessing ecosystem resilience. However, long-term and continuous observations of soil microbial responses to drought remain rare. Here, using a 6-y experimental drought in a tallgrass prairie ecosystem, we showed that experimental drought reshaped the community compositions of soil bacteria, fungi, and protists, accompanied by progressive declines in microbial diversity and biomass. Analyses of time-decay relationships and paired community differences between drought and ambient conditions revealed increasingly divergent successional trajectories of soil microbiota under drought. Although stochastic processes dominated community assembly overall, their relative importance declined over time, particularly for bacteria in drought-treated soils, suggesting increasingly strong deterministic environmental filtering imposed by drought. In addition, drought reduced microbial network size but increased the complexity and stability of bacterial networks by favoring drought-tolerant taxa. Furthermore, drought-driven shifts in microbial community compositions significantly altered functional genes and associated ecosystem functioning. These findings suggest that microbial communities may become less variable but more vulnerable, and the detrimental effects of biodiversity loss on ecosystems could be more severe in an increasingly drought-prone world.}, }
@article {pmid42441851, year = {2026}, author = {Landry, ZC and Foffi, R and Anelli, V and Arosio, P and Gil-Garcia, M and Henshaw, RJ and Müller, O and Paccagnan, G and Schneider, TN and Schubert, CJ and Słomka, J and Lee, KS and Zambelli, T and T Zweifel, S and Stocker, R}, title = {Raman imaging of the phycosphere reveals sharp gradients of organic matter exuded by single phytoplankton cells.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {29}, pages = {e2535317123}, doi = {10.1073/pnas.2535317123}, pmid = {42441851}, issn = {1091-6490}, support = {955910//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; GBMF9197//Gordon and Betty Moore Foundation (GBMF)/ ; 542395FY22//Simons Foundation (SF)/ ; 205321_207488//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (SNF)/ ; PZ00P2_202188//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (SNF)/ ; ETH-07 24-2//Eidgen&#xf6;ssische Technische Hochschule Z&#xfc;rich (ETH)/ ; LT000192/2018//Human Frontier Science Program (HFSP)/ ; BPN/PPO/2024/1/00008//Narodowa Agencja Wymiany Akademickiej (NAWA)/ ; RS2025-00554860//Korea Basic Science Institute (KBSI)/ ; 1.260002.01//Ulsan National Institute of Science and Technology (UNIST)/ ; }, mesh = {*Phytoplankton/metabolism/chemistry ; *Spectrum Analysis, Raman/methods ; *Xanthophylls/metabolism ; Diffusion ; }, abstract = {Phytoplankton cells exude a wide array of chemicals in the water column, generating a localized microenvironment known as the phycosphere. Although it is now well accepted that the phycosphere mediates interactions between phytoplankton and bacteria, the chemical gradients around individual phytoplankton cells have never been explicitly measured, and their shape has been classically assumed to be set by ideal diffusion. Here we used Raman microspectroscopy to obtain micrometer-scale measurements of the concentration profile of a phytoplankton metabolite (fucoxanthin) around individual phytoplankton cells of different species, having radii between [Formula: see text] and 60 [Formula: see text]m. We found that fucoxanthin concentration decreases more rapidly with distance from the cell than predicted by ideal diffusion, showing that the phycosphere includes compounds whose diffusion is characterized by nonideal effects. We explain this observation using a space-dependent diffusivity model where nonideality arises from viscosity and solubility gradients in the extracellular environment. Our results suggest an onion-structured model of the phycosphere, in which small hydrophilic solutes that obey ideal diffusion generate broad but weak gradients, whereas insoluble compounds are retained within [Formula: see text] to [Formula: see text] from the phytoplankton cell surface and yield steep gradients of organic matter. These observations, supported by evidence that fucoxanthin can act as an effective chemoattractant for marine bacteria, show the existence of strong and highly localized chemical cues with potentially far-reaching impacts on microbial interactions in aquatic environments. These findings highlight the importance of directly measuring the microscale chemical landscape experienced by marine microbes.}, }
@article {pmid42443490, year = {2026}, author = {Zhang, Y and Ma, K and Hu, T and Ma, Y and Zhao, H and Peng, X and Yin, G and Zhang, H and Lin, F and Pan, Y and Zhang, T and Ban, H and Zhu, Y and Gao, T and Qiu, L}, title = {Vegetation structure shapes behavioral, neuroimmune and gut microbial recovery after chronic stress in mice.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-10628-8}, pmid = {42443490}, issn = {2399-3642}, support = {32572139//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32572141//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Chronic stress impairs behavior, neuroimmune regulation and gut microbial ecology, but whether natural-environment structure shapes recovery remains unclear. Here, we tested whether landscape design, beyond greenness alone, promotes recovery in chronically stressed male mice. During a 28-day recovery phase, mice were exposed to five parameterized vegetated landscapes differing in openness, canopy density and visual complexity, a matched urban-gray setting, or standard housing. Vegetated exposure improved anxiety-like behavior, behavioral despair and anhedonia, whereas the gray setting showed little benefit. Recovery was design-dependent: multistrata, color-rich landscapes produced the fastest and most sustained behavioral improvement, while open lawn-dominant layouts showed weaker, partly transient effects. These gains were accompanied by lower interleukin-1β and interleukin-6, normalized hippocampal Iba-1, preserved brain-derived neurotrophic factor, and restored gut microbial diversity. Predicted microbial functions linked butyrate-related pathways with neuroimmune-behavioral indices. These findings support vegetation structure as a tunable environmental variable for coordinated recovery after chronic stress.}, }
@article {pmid42444003, year = {2026}, author = {Taylor, T and Benti, G and F A Leite, M and Arias-Giraldo, LM and Etalo, DW and Abera, S and Lombard, L and Maciá-Vicente, JG and Sanow, S and Rybka, D and Mostert, T and Martinez de la Parte, E and Legesse, D and Tulu, UT and Daksa, J and van Doorn, R and Rosa Leite, R and Tessema, T and Crous, PW and Kawa, D and Kuramae, EE and Raaijmakers, JM and Brady, SM}, title = {Disentangling the importance of microbiological and physico-chemical properties of Ethiopian field soils for the Striga seed bank and sorghum infestation.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00926-3}, pmid = {42444003}, issn = {2524-6372}, abstract = {BACKGROUND: Striga hermonthica (Striga) is a parasitic weed that severely affects sorghum yield in sub-Saharan Africa. Recent studies highlighted the soil microbiome's potential to suppress Striga through interference with specific stages in its life cycle.<br><br>RESULTS: Statistical analyses of data collected from 48 Ethiopian sorghum field soils sampled across a&#x2009;>&#x2009;1000-km-transect revealed that microbial communities and their interactions with soil physico-chemical properties correlated with Striga occurrence in the field. Striga infestation of sorghum and seedbank levels were negatively correlated with potassium and sulfur soil content and positively correlated with calcium and magnesium nutrient profile proportions. Microbiome analyses indicated that fungal communities were more responsive than bacteria to changes in Striga infestation and seedbank levels, with distinct microbial composition even in soils where Striga was not detected. Specific fungal and bacterial genera showed both positive and negative correlations with Striga measures, but patterns rarely held across taxonomic levels. To begin to validate these correlations, we tested an isolate from the fungal genus Neocosmospora, which negatively correlated with the Striga seedbank, and showed that this isolate promotes Striga seed germination in vitro. The data and analysis methods are integrated and shared in a public Shiny App for broader analysis and continued research on soil-Striga interactions.<br><br>CONCLUSIONS: This study highlights the complexity of soil-microbiome-Striga interactions and the potential for observational studies to reveal candidates for biological control of Striga.}, }
@article {pmid42444523, year = {2026}, author = {Santucci, NR and Dike, CR and Hellmann, J and Ollberding, NJ and Duan, Q and Minar, P and Denson, LA and Haslam, DB and Castillo, D and Abu-El-Haija, M}, title = {Gut microbiome in pediatric acute pancreatitis and Crohn's disease versus irritable bowel syndrome and healthy controls.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1002/jpn3.70504}, pmid = {42444523}, issn = {1536-4801}, support = {K23DK135797//National Institutes of Health - National Institute of Diabetes and Digestive and Kidney Disease/ ; 23DK118190//National Institutes of Health - National Institute of Diabetes and Digestive and Kidney Disease/ ; R03 DK131156/DK/NIDDK NIH HHS/United States ; P30 DK078392/GF/NIH HHS/United States ; //Digestive Diseases Research Core Center in Cincinnati/ ; NCT04131504//Leona M. and Harry B. Helmsley Charitable Trust for the ENvISION study/ ; }, abstract = {OBJECTIVES: Pediatric acute pancreatitis (AP), Crohn's disease (CD), and irritable bowel syndrome (IBS) are associated with gut dysbiosis, but differences and similarities between conditions are unknown. We hypothesized that gut microbial ecology would differ across these disorders.<br><br>METHODS: Stool was collected from 120 subjects (AP [n&#x2009;=&#x2009;30], CD [n&#x2009;=&#x2009;29], IBS Rome IV [n&#x2009;=&#x2009;27], and healthy controls [HC, n&#x2009;=&#x2009;34]). Shotgun metagenomic sequencing was performed on extracted DNA and taxonomic and functional profiles obtained using sylph and HUMAnN3 with default parameters.<br><br>RESULTS: Age interquartile range for all participants was 8.1-17.7 years. Shannon diversity was decreased in AP compared to IBS or HC (p&#x2009;<&#x2009;0.0001) and similar to CD (p&#x2009;=&#x2009;0.97). CD differed from IBS (p&#x2009;=&#x2009;0.001) and HC (p&#x2009;<&#x2009;0.0001) while IBS and HC were similar (p&#x2009;=&#x2009;0.61). Ordination of the first two principal coordinate analyses axes showed sample clustering by condition (R[2]&#x2009;=&#x2009;0.12, p&#x2009;<&#x2009;0.001), and differences between all conditions in pairwise comparisons (p&#x2009;<&#x2009;0.001). Escherichia coli, Ruminococcus gnavus, Staphylococcus aureus, and Thomasciavelia ramosa remained enriched when all conditions (AP, CD, and IBS) were compared as a single group to HC. Using a random forest machine learning algorithm for species relative abundance, the ability to classify a sample to each condition versus all others was highest for CD (area under the receiver operative characteristic curve, AUC&#x2009;=&#x2009;0.97), followed by AP (AUC&#x2009;=&#x2009;0.92), HC (AUC&#x2009;=&#x2009;0.88), and IBS (AUC&#x2009;=&#x2009;0.83).<br><br>CONCLUSION: Organic disorders (AP and CD) are associated with significant gut dysbiosis than IBS which appears more like HC. Interventions targeting shifts in commensals in AP and CD may be helpful in improving outcomes in both disorders.}, }
@article {pmid42445284, year = {2026}, author = {Xi, M and Li, S and Tang, Y and Zhu, J and Deng, S}, title = {Interactions between taste and oral microbiome: mechanisms and implications for oral and systemic diseases.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2699527}, pmid = {42445284}, issn = {2000-2297}, abstract = {BACKGROUND: The oral microbiome is a complex microbial ecosystem that contributes to oral and systemic health. Emerging evidence suggests a bidirectional interaction between oral microbiota and taste, although its underlying mechanisms and disease implications remain incompletely understood.<br><br>OBJECTIVE: This review aims to summarize current knowledge regarding the interactions between the oral microbiome and taste, elucidate the potential mechanisms involved, and discuss their relevance to human diseases.<br><br>DESIGN: Recent advances in clinical and experimental studies were reviewed, focusing on microbial metabolism, immunoinflammatory regulation, taste receptor modulation, and microbial-host interactions.<br><br>RESULTS: Oral microorganisms may influence taste perception through metabolite production, inflammatory pathways, alteration of taste receptor expression, and other mechanisms such as physical barriers. Conversely, taste perception and taste receptors can regulate microbial colonization by shaping dietary behaviors and local immune responses. These interactions may contribute to the development and progression of oral diseases, extraoral inflammatory diseases, cardiometabolic disorders, cancer, and neurodegenerative conditions.<br><br>CONCLUSIONS: The taste-oral microbiome axis represents an emerging regulatory network linking microbial ecology, sensory function, and disease pathogenesis. Further longitudinal and mechanistic studies are required to clarify causal relationships and explore microbiome-targeted therapeutic strategies.}, }
@article {pmid42445494, year = {2026}, author = {Zhang, H and Xu, J and Zhou, X and Han, R and Li, H and Li, J and Zuo, J and Bai, Y and Wang, W and Li, B and Hu, R and Zhang, J}, title = {Effects of lubabegron fumarate on ruminal fermentation and microbial community in a rumen simulation system.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1863733}, pmid = {42445494}, issn = {1664-302X}, abstract = {INTRODUCTION: The expansion of the global beef industry intensifies concerns regarding ammonia emissions, posing a significant challenge to environmental sustainability and production efficiency. Lubabegron fumarate (LBF), a novel β-adrenergic receptor modulator approved to mitigate these emissions, lacks a defined ruminal mode of action. This study aimed to characterise the effects of LBF on in vitro rumen fermentation, microbial ecology, and nitrogen metabolism.<br><br>METHODS: Using a rumen simulation system, we evaluated the effects of LBF on fermentation parameters, nutrient digestibility, and urease activity. To elucidate the underlying mechanisms, an integrated multi-omics approach was employed to characterise shifts in microbial community structure, functional potential, and metabolic output, with a specific focus on nitrogen-cycling microbiota.<br><br>RESULTS: LBF did not directly inhibit urease. Instead, it optimised the rumen microenvironment by increasing total volatile fatty acids and pH, while reducing ammonia nitrogen (NH&#x2083;-N) and enhancing starch digestibility. Crucially, LBF orchestrated a selective enrichment of key taxa (e.g., Ruminococcus_E, specific Prevotella spp.) and promoted pivotal pathways (e.g., starch metabolism and amino acid biosynthesis) without eroding microbial diversity. Metabolomics revealed a redirected carbon flux towards propionic acid production, facilitating efficient microbial nitrogen assimilation and redirecting nitrogen from ammonia into microbial protein (MCP).<br><br>DISCUSSION: LBF reshaped the rumen microecosystem to synchronise carbohydrate fermentation and nitrogen assimilation, thereby optimising nutrient capture and reducing nitrogen waste. These findings provide a mechanistic basis for the strategic application of LBF as a pharmaceutical intervention to improve nitrogen efficiency and mitigate ammonia emissions in cattle production.}, }
@article {pmid42434299, year = {2026}, author = {Shen, Q and Bian, C and Zhou, M and Shen, X and Jin, X and Li, B}, title = {Microbiota-mediated mechanisms of natural products in atherosclerosis: focus on metabolic and inflammatory pathways.}, journal = {Frontiers in endocrinology}, volume = {17}, number = {}, pages = {1818349}, pmid = {42434299}, issn = {1664-2392}, mesh = {Humans ; *Atherosclerosis/metabolism/microbiology/drug therapy ; *Biological Products/pharmacology ; Animals ; *Gastrointestinal Microbiome/physiology ; *Inflammation/metabolism/microbiology ; Signal Transduction ; }, abstract = {BACKGROUND: Atherosclerosis (AS) is a chronic inflammatory vascular disease characterized by lipid accumulation, endothelial dysfunction, immune dysregulation, and plaque formation. Beyond conventional lipid-related mechanisms, gut microbiota dysbiosis and microbiota-derived metabolites have emerged as important regulators of atherogenesis. Natural products, including polyphenols, flavonoids, alkaloids, fatty acids, polysaccharides, saponins, and terpenoids, may modulate AS by reshaping gut microbial ecology and metabolic outputs.<br><br>METHODS: This narrative review qualitatively synthesized English-language studies published from 2016 to 2026, with emphasis on recent preclinical and emerging clinical evidence. Literature was retrieved from PubMed and Google Scholar using terms related to natural products, gut microbiota, and atherosclerosis. Evidence was integrated across natural product categories, microbial metabolites, host signaling pathways, preclinical models, clinical observations, and translational limitations.<br><br>RESULTS: Natural products consistently acted on convergent microbiota-dependent pathways rather than isolated mechanisms. They reduced trimethylamine/trimethylamine N-oxide production, promoted short-chain fatty acid generation, remodeled bile acid metabolism, and modulated microbial tryptophan-derived metabolites. These metabolic changes were associated with improved intestinal barrier integrity, suppression of TLR4/NF-&#x3ba;B and NLRP3-mediated inflammation, immune rebalancing, reduced oxidative stress, enhanced cholesterol efflux, and attenuation of plaque-related phenotypes. Polyphenols and berberine showed relatively stronger mechanistic support, whereas polysaccharides, saponins, terpenoids, and complex formulas remain mainly exploratory. Most evidence derives from animal and in vitro studies, while clinical studies remain limited by small samples, short follow-up, heterogeneous interventions, surrogate endpoints, and insufficient causal validation.<br><br>CONCLUSIONS: Natural products provide an integrated framework for targeting the gut microbiota-metabolite-vascular pathology axis in AS. Although current evidence supports their biological plausibility and adjunctive therapeutic potential, standardized preparations, causal microbiome validation, multi-omics-based biomarkers, and well-designed clinical trials with vascular or cardiovascular endpoints are required before clinical translation.}, }
@article {pmid42434559, year = {2026}, author = {Saraiva, M and Gerilovych, A and Ay, H}, title = {Editorial: Harnessing aquatic microbial symbioses for sustainable aquaculture: unveiling biodiversity and ecosystem dynamics.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1897215}, doi = {10.3389/fmicb.2026.1897215}, pmid = {42434559}, issn = {1664-302X}, }
@article {pmid42434790, year = {2026}, author = {Afeeza, K and Priya Dharshini, B and Vasugi, S and Dilipan, E}, title = {Comparative microbial ecology of seagrass and coral reef sediments in the Lakshadweep archipelago using high-throughput 16S rRNA sequencing.}, journal = {3 Biotech}, volume = {16}, number = {8}, pages = {319}, pmid = {42434790}, issn = {2190-572X}, abstract = {Seagrass and coral reef sediments from Minicoy Island were investigated to compare bacterial community composition and predicted functional potential using 16S rRNA gene (V3-V4) amplicon sequencing. Sequence data were processed in QIIME2 with Deblur-generated amplicon sequence variants and taxonomic classification against the SILVA database. Alpha and beta diversity analyses revealed high similarity in microbial community composition between seagrass and coral reef sediments, indicating strong ecological connectivity within the atoll environment. Proteobacteria, Bacteroidota, and Desulfobacterota were dominant across both habitats, while sulfate-reducing families such as Desulfobulbaceae and Desulfobacteraceae were relatively enriched in seagrass sediments. Correlation analysis showed that microbial diversity was positively associated with nutrient concentrations and turbidity, and negatively associated with temperature and particulate organic carbon. Functional prediction using PICRUSt2 and KEGG pathway annotation identified habitat-associated trends in transport- and signalling-related pathways, although these functional differences were interpreted cautiously due to the limitations of predictive approaches. Henceforth, the study provides a baseline assessment of benthic microbial communities in Lakshadweep ecosystems and highlights the need for geographically independent sampling and multi-omics approaches to validate functional and ecological inferences.}, }
@article {pmid42435155, year = {2026}, author = {Kim, H and Park, D and Kwon, YJ and Imm, JY}, title = {Dietary milk polar lipids ameliorate hepatic lipid accumulation through coordinated regulation of Wnt-PPARγ signaling and remodeling of the gut microbiota.}, journal = {Food science of animal resources}, volume = {46}, number = {1}, pages = {}, pmid = {42435155}, issn = {2636-0780}, support = {RS-2020-NR048142//Ministry of Science, ICT and Future Planning/ ; }, abstract = {This study investigated the protective effects of milk polar lipids (MPL) against non-alcoholic fatty liver disease (NAFLD) and explored the underlying mechanisms using a high-fat high-sucrose (HFHS) diet-induced mouse model. MPL diet significantly reduced body weight gain, adiposity, and hepatic lipid accumulation, in addition to decreasing serum levels of liver injury markers. Mechanistically, MPL diet activated hepatic Wnt/β-catenin signaling, as evidenced by increased expression of low-density lipoprotein receptor-related protein 6 (LRP6), Wnt family member 3 A (Wnt3a), and β-catenin. Concurrently, MPL treatment suppressed peroxisome proliferator-activated receptor gamma (PPARγ) and downstream lipogenic proteins involved in triglyceride synthesis and de novo lipogenesis. In addition, MPL diet markedly reshaped the gut microbiota composition disrupted by HFHS feeding. Notably, MPL group showed a significant increased the abundance of Akkermansia muciniphila and short-chain fatty acid-producing bacteria, including members of Romboutsia and Christensenellaceae. These findings demonstrate that dietary MPL effectively attenuates HFHS diet-induced NAFLD through coordinated regulation of hepatic Wnt-PPARγ signaling and gut microbial ecology.}, }
@article {pmid42435199, year = {2026}, author = {Roncero-Ramos, B and Romano-Rodríguez, E and Mateos-Naranjo, E and Valle-Romero, P and Redondo-Gómez, S}, title = {Correction to: Hydro- and Xerohalophyte Species Drive Compositional and Functional Divergence in Bacterial Leaf Endosphere.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, doi = {10.1007/s00248-026-02821-3}, pmid = {42435199}, issn = {1432-184X}, }
@article {pmid42436636, year = {2026}, author = {Deng, S and Shi, W and Tian, R and Guo, X and Ning, D and Zhou, X and Yuan, M and Feng, J and Zhou, A and Fu, Y and Xu, G and Mu, D and Shi, P and Fan, X and Teng, Y and Zhao, X and Li, Z and Liu, J and Liu, X and Wu, L and He, Z and Liu, X and Luo, Y and Tiedje, JM and Yang, Y and Zhou, J}, title = {Increased precipitation decelerates temporal succession of grassland soil microbial communities.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag176}, pmid = {42436636}, issn = {1751-7370}, abstract = {Global precipitation regimes have been shifted in recent decades, imposing significant consequences in water-limited grassland ecosystems. However, the effects of increased precipitation on the succession of soil microbial communities remain unclear, mainly due to the scarcity of long-term experiments with time-series data. Here, we examined temporal succession of grassland soil microbial communities in a long-term increased precipitation experiment. Both soil microbial taxonomic and functional structures were significantly altered by increased precipitation. Increased precipitation significantly decelerated the succession rates of soil microbial functional structure (ie, time-decay relationships). Consistent with the increased microbial decomposition and heterotrophic respiration, the abundances of soil microbial carbon decomposition genes were markedly enhanced by increased precipitation. Furthermore, increased precipitation stimulated genes involved in nutrient cycling processes, potentially promoting plant growth. Collectively, the contributions of stochastic processes in shaping microbial communities were increased under increased precipitation, suggesting that microbial successional trajectories may shift toward multiple alternative states characterized by greater stochasticity under future altered precipitation regimes.}, }
@article {pmid42439608, year = {2026}, author = {Huo, W and Qiao, Y and Wang, C and Li, R and Li, E}, title = {Mycotoxins as silent modulators of enteric viral susceptibility and vaccine responsiveness.}, journal = {Critical reviews in food science and nutrition}, volume = {}, number = {}, pages = {1-12}, doi = {10.1080/10408398.2026.2700434}, pmid = {42439608}, issn = {1549-7852}, abstract = {Enteric viral infections remain a major cause of morbidity and mortality worldwide, particularly in children and intensively raised livestock. Although live oral vaccines have reduced disease burden, vaccine efficacy varies greatly across regions. Factors such as host genetics, microbiota, maternal antibodies, and nutrition have been widely studied, whereas chronic exposure to dietary toxicants has received less attention. Mycotoxins, fungal metabolites contaminating staple crops including maize, wheat, and peanuts, are commonly consumed at low but persistent levels in regions heavily affected by enteric viral diseases. Increasing evidence shows that mycotoxins disrupt intestinal barrier integrity, alter innate and adaptive immune responses, and reshape gut microbial ecology even without overt toxicity. These effects target pathways essential for antiviral defense and oral vaccine efficacy. This review proposes a mechanistic framework in which chronic mycotoxin exposure alters epithelial-immune-microbiota interactions, thereby increasing susceptibility to enteric viral infection and reducing vaccine-induced protection. We summarize evidence linking mycotoxins to barrier dysfunction, interferon dysregulation, antigen-presenting cell impairment, IgA suppression, intestinal stem cell injury, and microbiota-mediated changes in viral infectivity. Recognizing mycotoxins as covert regulators of mucosal antiviral immunity may provide new strategies to improve oral vaccine performance and reduce global enteric viral disease burden.}, }
@article {pmid42433682, year = {2026}, author = {Wan, R and Nong, S and Zhang, C and Wang, Z and Wang, K and Zou, Z}, title = {Effects of fermented mulberry leaves on growth performance, nutrient digestibility, diarrhea, and intestinal microecology in weaned piglets: a preliminary study.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1874983}, pmid = {42433682}, issn = {2297-1769}, abstract = {This study investigated the effects of dietary fermented mulberry leaves (FML) on growth metrics, nutrient digestibility, diarrhea incidence, and gut microbial ecology in weaned piglets. A total of 200 piglets (28 days old) were randomly allocated into five groups: a basal diet control group and four treatment groups receiving the basal diet supplemented with 5%, 10%, 15%, or 20% FML (co-fermented with Lactobacillus and cellulase) over a 28-day period. Growth performance, apparent nutrient digestibility, diarrhea rate, intestinal pH, short-chain fatty acid (SCFA) concentrations, and cecal microbiota (via 16S rRNA sequencing) were evaluated. No notable differences in growth performance were detected across groups (P > 0.05); however, the feed-to-gain ratio was significantly lower in the 5% and 20% FML groups (P < 0.05). Diarrhea incidence declined across all FML-supplemented groups, with the greatest reduction (52.46%) in the 15% group during days 28-42. Duodenal pH decreased significantly in all treatment groups (P < 0.05). Cecal acetate and propionate levels rose markedly in the 10%, 15%, and 20% groups (P < 0.05), with the 15% group showing a 47.05% increase in acetate. FML supplementation also altered cecal microbial diversity and community composition. At the genus level, the 15% group had the highest relative abundance of Prevotella (22.46%), while Lactobacillus and Bifidobacterium tended to increase in FML groups. Overall, dietary inclusion of 5-20% FML did not significantly enhance growth performance but effectively reduced diarrhea, optimized intestinal pH, increased cecal acetate and propionate production, and modulated cecal microbiota composition, with 15% FML identified as the optimal level.}, }
@article {pmid42429666, year = {2026}, author = {Zhao, Y and Chen, L and Li, C and Xu, Y and Huang, J and Chen, S and Yu, Z and Liu, X}, title = {Sialidase inhibitor modulates gut microbiota and enhances mucosal protection in the treatment of ulcerative colitis.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0019426}, doi = {10.1128/msystems.00194-26}, pmid = {42429666}, issn = {2379-5077}, abstract = {Ulcerative colitis (UC) is characterized by mucosal barrier erosion, a process exacerbated by bacterial sialidases. We investigated the therapeutic efficacy of the sialidase inhibitor (SI) in UC. In a pilot randomized clinical trial, SI intervention significantly improved clinical symptoms and endoscopic outcomes in mild-to-moderate UC patients. This improvement correlated with an enrichment of butyrate-producing taxa and beneficial metabolic pathways. In a dextran sulfate sodium-induced colitis mouse model, SI attenuated inflammation and restored mucus layer integrity, accompanied by increased expression of Muc2 and Tff3. Crucially, unlike broad-spectrum antibiotics, SI preserved microbial community resilience while specifically enriching beneficial mucolytic commensals, Akkermansia muciniphila and Bacteroides acidifaciens. These findings identify SI as a promising therapeutic strategy that targets sialidase activity to reinforce the mucosal barrier and restore gut homeostasis.IMPORTANCEThe gut microbiota plays a pivotal role in maintaining mucosal integrity and intestinal homeostasis; however, dysbiosis-driven mucus layer degradation remains a hallmark of ulcerative colitis (UC). Current interventions like antibiotics often disrupt microbial diversity, exacerbating dysbiosis and failing to address mucosal thinning, which is a critical factor in UC progression. Developing strategies to reinforce the mucus barrier without compromising microbial balance is urgently needed, but such approaches remain underexplored. Our study demonstrates that sialidase inhibitors (SIs) uniquely preserve mucosal thickness by curbing microbial mucin degradation while selectively enriching beneficial taxa and butyrate-producing bacteria. Unlike antibiotics, SIs enhance mucosal protection without destabilizing microbial communities, offering a dual-action therapeutic strategy. This work bridges a critical knowledge gap, providing evidence for microbiota-targeted therapies that synergistically restore mucosal health and microbial ecology in UC.CLINICAL TRIALSThis study was registered with the Chinese Clinial Trial Registry as ChiCTR2000028767.}, }
@article {pmid42429763, year = {2026}, author = {Tribbia, DZ and Lebre, PH and Vázquez-Campos, X and Ray, AE and Laird, T and Machado de Lima, N and Maggs-Kölling, G and Cowan, DA and Ferrari, BC}, title = {Trace gas oxidation supports sub-surface microbial communities across Namib Desert fog and aridity gradients.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0026526}, doi = {10.1128/aem.00265-26}, pmid = {42429763}, issn = {1098-5336}, abstract = {UNLABELLED: Widely accepted climate predictions indicate that drylands will expand to cover more than half of the Earth's terrestrial surface by the end of the 21st century. In these environments, harsh conditions, including nutrient and water limitations, restrict plant and animal life, thereby increasing the importance of soil microbial communities in nutrient cycling and ecosystem functioning. The Namib Desert is a distinctive dryland ecosystem characterized by a steep natural aridity gradient, transitioning from a coastal hyperarid zone influenced by frequent fog deposition to an inland arid region receiving seasonal rainfall. This study investigates the impact of water availability and moisture regime on microbial trace gas oxidation and community composition across this aridity gradient. Quantitative analyses revealed that total microbial abundance and activity indicators, including ATP concentrations and respiration rates, were significantly (P < 0.005) reduced in hyperarid soils compared to their arid counterparts. In contrast, hyperarid fog-dominated soils exhibited significantly (P < 0.0005) elevated rates of atmospheric hydrogen oxidation, even in the absence of water inputs. We propose that sustained high-affinity hydrogen oxidation, coupled with rapid microbial resuscitation following wetting events, supports shallow sub-surface microbial communities in the Namib Desert, particularly in the coastal hyperarid zone. Together, these findings challenge current understanding of the lower limits of microbial activity and reveal alternative metabolic pathways that enable microbial persistence in hyperarid hot desert soils.<br><br>IMPORTANCE: Drylands are expanding globally, yet the mechanisms that allow microbial life to persist under extreme and sustained water limitation remain poorly understood. This study demonstrates that atmospheric trace gas oxidation, particularly high-affinity hydrogen oxidation, supports active and resilient microbial communities in hyperarid soils of the Namib Desert, even in the absence of liquid water inputs. By revealing how microbes may couple trace gas metabolism to energy and water generation, our findings provide new insight into the lower limits of microbial activity in dry, hot desert soils and highlight the need to investigate how microbes persist and sustain soil ecosystem functioning.}, }
@article {pmid42429816, year = {2026}, author = {Basu, DN and Khangar, P and Joshi, K and Krishna, S and Khan, I}, title = {Tracking Microbiome Composition and Stability Across Indian Social Honeybees Foraging in a Homogeneous Mustard Crop Landscape.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02828-w}, pmid = {42429816}, issn = {1432-184X}, abstract = {Microbial communities are essential for host health and ecosystem stability. However, whether host identity or shared foraging resources shapes microbiome structure among co-occurring species remains poorly understood. We studied bacterial and fungal communities of four Indian honeybee species in a mustard monoculture resource condition, integrating behavioural observation-based pollinator data with microbial co-occurrence networks derived from metabarcoding. Microbiome composition was more strongly associated with host identity rather than with foraging behaviour, bee abundance, or landscape use. This has strong implications for how microbial sharing among co-occurring social honeybee species can be limited, thereby preventing them from influencing each other's microbiomes through shared foraging and driving variable pollinator health within a shared ecosystem. While core bacterial taxa were shared, relationships among bacterial cobionts, unlike those among fungal genera, remained species-specific. Microbial diversity, along with community structure and function, influenced network stability, with a highly modular microbial network of Apis cerana exhibiting more predicted network robustness to simulated perturbations. In summary, host-specific filtering shaped the microbiome more than resource homogenisation, with closely related species facing unique risks of disruption of microbial co-occurrence, with broader implications for vulnerability to microbiome imbalance, environmental stress, and emerging infections.}, }
@article {pmid42429927, year = {2026}, author = {Lirio, CPT and Albino, EED and Nisnisan, KKS and Castro, AE}, title = {Gut bacterial community profile of the endemic catfish Arius manillensis from Pasig River, Philippines.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0037026}, doi = {10.1128/mra.00370-26}, pmid = {42429927}, issn = {2576-098X}, abstract = {The Pasig River is a highly urbanized waterway, yet the microbial ecology of its native fauna remains poorly understood. This study provides the first report of the gut bacterial community of the catfish Arius manillensis, revealing bacterial taxa and underscoring the need to study host-associated microbiomes in urban aquatic ecosystems.}, }
@article {pmid42429961, year = {2026}, author = {Jordan, S and Pothier, JF and de Maayer, P and Kvitko, BH and Coutinho, TA and Smits, THM}, title = {Genome sequences of 71 ecologically and geographically diverse Enterobacter strains.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0033426}, doi = {10.1128/mra.00334-26}, pmid = {42429961}, issn = {2576-098X}, abstract = {We sequenced the genomes of 77 bacterial strains, tentatively identified as Enterobacter. Of these, 71 were identified as Enterobacter based on genomic analysis. These strains span 11 species of diverse ecological and geographical origin.}, }
@article {pmid42430702, year = {2026}, author = {Bermúdez-Monsalve, JR and Berger, SA and Yalçın, G and Nejstgaard, JC}, title = {Correspondence on "Long-Term Changes in the Abundance, Size, and Morphotype of Marine Plastics in the North Pacific".}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c02999}, pmid = {42430702}, issn = {1520-5851}, }
@article {pmid42430909, year = {2026}, author = {Maranho, LT and Geraldo, MR and Nogueira, KDS and Gomes, MP}, title = {Associations between rhizosphere microbial community structure and antibiotic attenuation in a pilot-scale hybrid constructed wetland.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142886}, doi = {10.1016/j.jhazmat.2026.142886}, pmid = {42430909}, issn = {1873-3336}, abstract = {Constructed wetlands are widely used as nature-based solutions for wastewater treatment; however, the role of rhizosphere-associated microbial communities in the attenuation of emerging contaminants remains unclear. In this study, we evaluated the antibiotic removal and microbial community structure in a pilot-scale hybrid constructed wetland treating municipal wastewater by integrating vertical upflow (Sagittaria montevidensis), floating (Salvinia molesta + Lemna gibba), and horizontal subsurface flow (Canna indica) units. Antibiotics from different therapeutic classes were quantified using LC-MS/MS across the treatment compartments. The system achieved high attenuation efficiencies, with removal efficiencies exceeding 98% for the target compounds. The floating macrophyte unit showed the greatest reduction in concentrations relative to the upstream compartments. Microbial community analyses based on 16S rRNA gene sequencing revealed marked shifts in the community structure along the treatment gradient. Alpha diversity indices varied (Shannon index: 1.066-4.954), with higher diversity observed in rhizospheric communities associated with Sagittaria and Canna than in influent wastewater and pre-exposure samples. Beta diversity analysis (Bray-Curtis dissimilarity) showed a clear separation between the wastewater and rhizospheric communities (PERMANOVA, p = 0.001; R[2] = 0.66). Redundancy analysis and correlation-based approaches indicated that variations in dominant groups were statistically associated with antibiotic attenuation patterns across treatment compartments. These relationships represent ecological covariation patterns and should not be interpreted as direct evidence of microbial biodegradation activity. Overall, the results indicate that hybrid CW promote structured rhizosphere microbial communities that co-vary with antibiotic attenuation, supporting the future integration of microbial ecology into nature-based wastewater treatment optimization.}, }
@article {pmid42432346, year = {2026}, author = {Muñoz-Laiton, P and Hernandez-Valencia, JC and Isaza, JP and Araújo, MDS and Salles, JF and Correa, MM}, title = {Bacterial and Fungal Microbiota in Anopheles darlingi Exhibit Differences in Diversity Across Three Main Colombian Malaria-endemic Regions.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02829-9}, pmid = {42432346}, issn = {1432-184X}, abstract = {Anopheles darlingi is the main malaria vector in the Neotropics. Despite their importance, little is known about the microbiota composition in areas where these vectors are found. Since the microbiota may influence host biology and vector competence, it is essential to understand these microbial communities in endemic regions. This study explores the bacterial and fungal communities in An. darlingi from three malaria-endemic areas in Colombia and examined how geography influences microbial composition. Mosquitoes were collected from the Bajo Cauca, Pacific and Amazonas regions, and their microbiota was characterized by amplifying and sequencing the 16 S rRNA V3-V4 region for bacteria and the ITS2 region for fungi. Analysis indicated greater alpha diversity in An. darlingi mosquitoes from the Amazonas region. Beta diversity findings demonstrated differences in bacterial and fungal community compositions across regions, especially between Amazonas and the other two regions. Additionally, the similarity of microbial communities declined slightly with increasing geographic distance. This study significantly advances our understanding of the microbiota associated with An. darlingi in endemic regions of Colombia, by revealing notable differences in bacterial and fungal community composition and abundance across diverse geographical populations. Importantly, these new insights extend beyond species and geographic boundaries by providing evidence of specific fungal communities linked to the vector, paving the way for innovative microbiota-based vector control strategies in malaria vector research.}, }
@article {pmid42432352, year = {2026}, author = {Wang, X and Chen, J and Tang, Y and Liu, H}, title = {Insights into the Mechanism Underlying the Symbiosis between Seagrass and a Lulworthiaceae Fungus.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02808-0}, pmid = {42432352}, issn = {1432-184X}, support = {AoE/P-601/23N//Hong Kong Research Grants Council/ ; MCEF23SC02//Hong Kong Offshore Liquefied Natural Gas Terminal/ ; }, abstract = {Various fungi have been identified in seagrass compartments; however, the exact nature of their interactions with these marine flowering plants remains largely uncharacterized. The partnership between seagrasses and Lulworthiaceae fungi represents a typical and compelling example of such an underwater association. Here, we combine UHPLC-MS/MS, transcriptomics, and plant growth assays to validate the putative symbiosis between the seagrass Halophila ovalis and the Lulworthiaceae fungus Halophilomyces hongkongensis, and elucidate the underlying mechanism of this relationship. We confirmed that H. hongkongensis produces the phytohormone indole-3-acetic acid (IAA). Through transcriptomic analysis, we proposed its IAA biosynthesis pathways. All identified IAA biosynthesis genes were upregulated in seagrass roots/rhizomes compared to rhizosphere sediments, with the tryptophan aminotransferase gene (indole-3-pyruvic acid pathway) exhibiting a significant increase. Furthermore, H. hongkongensis was confirmed as a plant growth-promoting fungus; its culture filtrates promoted Arabidopsis thaliana shoot and lateral root/root hair growth, an effect strongly correlated with IAA production and highly likely in seagrass. Beyond IAA-specific analyses, its upregulated genes were significantly enriched in pathways such as tryptophan metabolism, starch/sucrose metabolism, and DNA replication. Collectively, these results indicate that H. hongkongensis establishes a growth-promoting symbiosis with H. ovalis by upregulating its IAA biosynthesis genes and secreting IAA; in return, the host provides carbohydrates that sustain fungal metabolism and support active DNA replication. This study provides the first mechanistic verification of a seagrass-Lulworthiaceae symbiosis, significantly advancing our understanding of marine plant-fungal interactions. It also demonstrates the first IAA-linked plant growth-promoting capacity of a member from the cryptic marine fungal family Lulworthiaceae.}, }
@article {pmid42432384, year = {2026}, author = {Alías-Segura, S and Patiño, B and Gil-Serna, J}, title = {Metabarcoding Characterization of Fungal Communities in Spanish Cereals with a Special Focus on Fusarium Species.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02833-z}, pmid = {42432384}, issn = {1432-184X}, support = {PID2022-136803OB-I00//MICIU/AEI/10.13039/501100011033 and FEDER, UE/ ; PID2022-136803OB-I00//MICIU/AEI/10.13039/501100011033 and FEDER, UE/ ; PID2022-136803OB-I00//MICIU/AEI/10.13039/501100011033 and FEDER, UE/ ; CT25/24//Complutense University of Madrid and Banco Santander/ ; }, abstract = {Cereal safety is a critical public health concern, as crops are frequently compromised by mycotoxin-producing fungi, particularly those from the genus Fusarium. Although metabarcoding is a powerful tool for characterizing these fungal communities, the universal internal transcribed spacer 2 (ITS2) marker lacks the resolution required to distinguish closely related species with distinct toxigenic profiles. The objective of this work was to accurately characterize the mycobiota and specific Fusarium community structure in Spanish cereal field samples. We propose a high-resolution metabarcoding workflow within the QIIME 2 environment to optimize Fusarium identification using the translation elongation factor 1-α (TEF1) gene. We developed a TEF1 Naive Bayes classifier trained on a curated database derived from FUSARIUM-ID v.3.0, expanded with eukaryotic sequences to prevent false-positive assignments. This approach was validated through direct comparison with ITS2 in the same samples. As expected, ITS2 significantly underestimates Fusarium diversity, whereas TEF1 enables precise species-level resolution within this genus. General mycobiota analysis performed using ITS2 revealed that fungal communities are shaped primarily by geographical location rather than host cereal species. Crucially, our approach confirmed the persistence of key toxigenic species, such as F. langsethiae and F. graminearum, and revealed broader diversity through the consistent detection of species often overlooked by traditional methods, including F. equiseti, F. acuminatum, and F. culmorum. We conclude that our metabarcoding framework reveals a high Fusarium diversity in Spanish cereal grains, and this knowledge is essential for designing targeted strategies to predict and mitigate mycotoxin contamination in these crops.}, }
@article {pmid42433202, year = {2026}, author = {Buessecker, S and Klos, AS and Quan, ME and Finch, AH and Sobol, MS and Evans, GN and Anbar, AD and Kaçar, B and Dekas, AE}, title = {Microbial N2O Reduction in Sulfidic Waters: Implications for Proterozoic Oceans.}, journal = {Geobiology}, volume = {24}, number = {4}, pages = {e70056}, doi = {10.1111/gbi.70056}, pmid = {42433202}, issn = {1472-4669}, support = {80NSSC17K0296/NASA/NASA/United States ; }, mesh = {*Nitrous Oxide/metabolism ; Oxidation-Reduction ; *Seawater/microbiology/chemistry ; *Sulfides/metabolism ; *Rhodopseudomonas/metabolism ; Oceans and Seas ; Oxidoreductases/metabolism/genetics ; Copper/metabolism ; }, abstract = {Throughout Earth's history, shifts in ocean redox influenced the bioavailability of trace metals, shaping the activity of microorganisms. In Proterozoic oceans, the precipitation of copper (Cu) with sulfide was hypothesized to limit the bioavailability of Cu. This limitation may have suppressed microbial reduction of nitrous oxide (N2O), due to the Cu dependency of nitrous oxide reductase (Nos). It is thought that without this critical microbial sink, Proterozoic oceans were a significant net source of N2O. Here, we revisit this paradigm in light of recently derived ~20-fold lower estimates for sulfide in Proterozoic seawater and an empirical evaluation of the potential for microbial N2O reduction under sulfidic conditions. Leveraging publicly available environmental metatranscriptomes, we infer active N2O reduction from the detection of nosZ transcripts in multiple marine and lacustrine systems in which sulfide and Cu concentrations are analogous to those of the Proterozoic. In controlled culture experiments, we demonstrate that the purple non-sulfur bacterium Rhodopseudomonas palustris can reduce N2O at sulfide concentrations up to 50 μM, well above levels predicted for Proterozoic oceans. Based on trace metal speciation modeling, we suggest that Cu remains bioavailable under Proterozoic-like conditions as a dissolved CuHS[0] complex. Collectively, these observations suggest microbial N2O reduction occurs under euxinic conditions, implying that Proterozoic marine N2O emissions were lower than previously proposed. Our conclusions inform our understanding of the microbial ecology in sulfidic waters, the early climate, and the search for extraterrestrial life.}, }
@article {pmid42420641, year = {2026}, author = {Kittredge, HA and Dougherty, KM and Glanville, K and Evans, SE}, title = {Extracellular DNA Alters Detection of Subtle Bacterial Responses to Soil Rewetting.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02827-x}, pmid = {42420641}, issn = {1432-184X}, support = {DE-SC0018409//Great Lakes Bioenergy Research Station/ ; DE-SC0018409//Great Lakes Bioenergy Research Station/ ; DE-SC0018409//Great Lakes Bioenergy Research Station/ ; DE-SC0018409//Great Lakes Bioenergy Research Station/ ; DEB 2224712//Directorate for Biological Sciences/ ; DEB 2224712//Directorate for Biological Sciences/ ; DEB 2224712//Directorate for Biological Sciences/ ; DEB 2224712//Directorate for Biological Sciences/ ; }, abstract = {Microbial communities are often characterized using DNA-based sequencing, but these approaches also capture extracellular DNA (exDNA) released from dead cells, potentially altering inference about microbial responses to environmental change. This may be especially important during pulse disturbances, such as soil drying-rewetting, which can increase microbial mortality and transient necromass pools. We assessed whether exDNA altered inference about bacterial responses to drying-rewetting (an 80 mm simulated rainfall event following a 28-day drought) in conventionally tilled corn and perennial switchgrass soils. We quantified bacterial abundance (16 S rRNA gene copies), alpha diversity, and community composition in paired soil samples with exDNA included (+ exDNA) and in samples treated with propidium monoazide (PMAxx) to reduce amplification of exDNA (- exDNA). At our level of replication (n = 4), PMAxx treatment did not significantly alter overall temporal response patterns (i.e., no significant main effect of DNA treatment or DNA × time interaction). However, PMAxx treatment increased sensitivity to detect some pairwise temporal changes in bacterial abundance and community composition in corn soils following rewetting. exDNA pools were proportionally highest immediately after rewetting in corn soils, suggesting transient extracellular DNA may contribute to masking during disturbance recovery. In contrast, PMAxx treatment had comparatively small effects in switchgrass soils, which exhibited weaker temporal responses overall. Inclusion of exDNA also changed which taxa appeared most responsive to rewetting. Together, our results suggest that exDNA does not uniformly bias soil microbial inference, but may reduce detectability of subtle disturbance-driven shifts in certain soils. Future studies should advance knowledge of microbial turnover and necromass dynamics, particularly using multiple complementary methods, to help predict when exDNA is most likely to influence ecological inference.}, }
@article {pmid42421214, year = {2026}, author = {Raya Tonetti, F and Han, H and Fondevila, MF and Wei, W and Özdirik, B and Bajaj, JS and Schubert, ML and Sikaroodi, M and Gillevet, PM and Lang, S and Demir, M and Rahman, IR and van der Donk, WA and Bosques-Padilla, F and Verna, EC and Abraldes, JG and Brown, RS and Vargas, V and Altamirano, J and Caballería, J and Shawcross, DL and Louvet, A and Lucey, MR and Mathurin, P and Garcia-Tsao, G and Stärkel, P and Bataller, R and Hsu, CL and Llorente, C}, title = {Non-absorbable antibiotics worsen alcohol-associated liver disease in gastric acid-suppressed mice.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2694797}, doi = {10.1080/19490976.2026.2694797}, pmid = {42421214}, issn = {1949-0984}, mesh = {Animals ; *Anti-Bacterial Agents/adverse effects/administration &amp; dosage/therapeutic use ; *Proton Pump Inhibitors/adverse effects/administration &amp; dosage ; Mice ; *Gastric Acid/metabolism ; Male ; *Gastrointestinal Microbiome/drug effects ; *Liver Diseases, Alcoholic/microbiology/pathology ; Dysbiosis/chemically induced ; Humans ; Mice, Inbred C57BL ; Disease Models, Animal ; Liver/pathology/drug effects ; }, abstract = {Gastric acid-suppressive medications, particularly proton pump inhibitors (PPIs), are commonly used in patients with alcohol-associated liver disease (ALD) to prevent and manage upper gastrointestinal bleeding, gastroesophageal reflux disease, and non-steroidal anti-inflammatory/aspirin-induced gastroesophageal damage. By inhibiting the gastric H[+]/K[+]-ATPase, PPIs suppress acid secretion and impair bacterial killing, thereby promoting gut dysbiosis that disrupts barrier integrity and enhances bacterial translocation, ultimately exacerbating liver injury. PPIs are frequently co-administered with antibiotics for indications such as gastrointestinal bleeding, Spontaneous Bacterial Peritonitis (SBP), other infections, or hepatic encephalopathy prophylaxis, but the consequences of this combined therapy on gut microbial ecology and disease outcomes remain unclear. Our study addresses this gap by showing how PPI use, alone or with antibiotics, reshapes the gut microbiome and aggravates liver disease progression. In previous studies, we showed that PPIs promote dysbiosis and ALD progression in mice and humans by facilitating intestinal expansion and hepatic translocation of Gram-positive Enterococcus. Fecal cytolysin, an Enterococcus faecalis exotoxin that induces hepatocyte death, predicts mortality in patients with alcohol-associated hepatitis (AH). In this study, we have examined the mechanism by which PPIs alone and in combination with non-absorbable antibiotics targeting Gram-positive bacteria influence ALD, as well as the disease mechanisms associated with cytolytic Enterococcus faecalis and the development of therapeutic strategies. In mice, alcohol administration during gastric acid suppression promoted expansion of Gram-positive taxa, including cytolysin-producing Enterococcus. Similarly, PPI use in patients with AH was associated with increased fecal Enterococcus and higher 30-d mortality, underscoring the translational relevance of our findings. Unexpectedly, treatment of acid-suppressed mice with non-absorbable antibiotics designed to suppress Gram-positive bacteria worsened ethanol-induced steatohepatitis: while Enterococcus abundance decreased, Streptococcus and other potentially pathogenic taxa expanded, leading to increased bacterial translocation and aggravated liver injury. In patients with cirrhosis or metabolic dysfunction-associated steatotic liver disease (MASLD), PPIs did not promote Enterococcus expansion, indicating etiology-dependent microbiome responses. Finally, we identified dipalmitoylphosphatidylcholine and Caspase-1 inhibitor as in vitro and in vivo modulators of cytolysin activity, highlighting potential therapeutic avenues. Collectively, our study demonstrates how PPIs and non-absorbable antibiotics targeting Gram-positive bacteria interact with the gut microbiome to drive ALD, underscoring the need for careful therapeutic management.}, }
@article {pmid42421228, year = {2026}, author = {Serrano-García, L and Martínez-Salvador, E and Belda-Marco, A and Herrero-Oliva, C and Cortés, J and Llombart-Cussac, A and Fernández-Murga, L}, title = {Modulation of the response to immunotherapy in triple-negative breast cancer: the role of the microbiota and microbial metabolites in the tumor microenvironment.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2697600}, doi = {10.1080/19490976.2026.2697600}, pmid = {42421228}, issn = {1949-0984}, mesh = {Humans ; *Tumor Microenvironment/immunology ; *Triple Negative Breast Neoplasms/therapy/immunology/microbiology ; Female ; *Immunotherapy ; *Gastrointestinal Microbiome/immunology ; Animals ; }, abstract = {Triple-negative breast cancer is an aggressive and heterogeneous breast cancer subtype for which immune checkpoint inhibitors combined with chemotherapy have improved outcomes in selected patients. However, primary and acquired resistance remain common, underscoring the need to identify extrinsic, modifiable determinants of antitumor immunity. Increasing evidence indicates that the gut and tumor-associated microbiota shape systemic and intratumoral immune tone and influence the efficacy of cancer therapies. Beyond microbial composition, microbiota-derived metabolites-including short-chain fatty acids, indole-tryptophan derivatives, bile acids, polyamines, and other small molecules-can act as functional mediators linking microbial ecology to immune-cell programming and tumor biology. These metabolites modulate dendritic cell function, T-cell priming and fitness, myeloid polarization, inflammatory set points, and metabolic pathways within the tumor microenvironment, thereby potentially enhancing or constraining responses to chemoimmunotherapy. Importantly, while some studies propose intratumoral microbial effects, most clinically actionable evidence currently supports systemic gut-derived metabolites and immune tone modulation that secondarily shapes the TNBC tumor microenvironment. In this review, we synthesize current knowledge on (i) the immunobiology of triple-negative breast cancer (TNBC) relevant to microbiota-driven modulation, (ii) mammary and gut microbiome features reported in TNBC, and (iii) mechanistic pathways through which microbial metabolites may regulate antitumor immunity and immune checkpoint inhibitors (ICI) sensitivity. We also discuss methodological considerations for integrating microbiome profiling with metabolomics and immune phenotyping and evaluate emerging opportunities to leverage microbiota-derived metabolites as biomarkers and therapeutic targets. Finally, we highlight translational strategies-including diet, pre/probiotics, antibiotic stewardship, fecal microbiota transplantation, and metabolite-centric ("postbiotic") approaches-and outline priorities for TNBC-focused, prospective multi-omics studies to move from associative signatures toward actionable interventions.}, }
@article {pmid42423764, year = {2026}, author = {Righetti, D and Soliman Tamayo, BK and Lampis, S and Lens, PNL}, title = {Effects of Per- and Polyfluoroalkyl Compounds (PFASs) on Anaerobic Granular Sludge: Methane Production and Microbial Community Composition.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02793-4}, pmid = {42423764}, issn = {1432-184X}, abstract = {PFASs are a group of pollutants ubiquitous in the environment, for which their effects on the microbial community composition and activity of anaerobic granular sludge are still poorly understood. With our study, we aimed to provide insight into the impact of four PFASs on the methane yield of anaerobic granular sludge (AGS) using acetate as the substrate. Anaerobic granular sludge was exposed to different concentrations of 1H,1H,2H,2H-Tridecafluorooctan-1-ol (6:2FTOH), 1H,1H,2H,2H-Perfluoro-1-decanol (8:2FTOH), Tridecafluorohexane-1-sulfonic acid (PFHxS) and Perfluorooctanoic acid (PFOA). While the two fluorotelomers caused marginal changes in methane production, PFHxS and PFOA greatly inhibited acetoclastic methanogenesis. Depending on the concentration, the AGS could recover its activity after a certain number of hours when incubated with PFASs. The 50% Inhibitory Concentration (IC50) of the methane production was estimated to be 278.98 (± 3.2) mg/L for PFOA and 1,091.9 (± 26.78) mg/L for PFHxS. PFASs exposure also influenced the archaeal and eubacterial communities. The most significant change was observed with the eubacterial community, which showed an increase in the relative abundance of the genus Sulfurospirillum in the samples treated with 2,000 mg/L of 8:2FTOH and 600 mg/L of PFOA, whose presence grew to represent 16.65% and 45.4% of all reads in those samples. These findings provide insight into the differential impact of PFASs on methanogenic processes and highlight their potential to disrupt key microbial functions in anaerobic systems.}, }
@article {pmid42424815, year = {2026}, author = {Tang, Q and Zhang, Y and Garza, DR and Ruan, C and Liu, B and Rocha, U and Shen, P and Wei, Y and Deng, Y and Zhang, J and Richnow, HH}, title = {Virus-mediated fate of antimicrobial resistance genes in livestock manure anaerobic digestion.}, journal = {Water research}, volume = {305}, number = {}, pages = {126401}, doi = {10.1016/j.watres.2026.126401}, pmid = {42424815}, issn = {1879-2448}, abstract = {Antimicrobial resistance (AMR) poses a critical global health challenge, with livestock manure acting as a significant environmental reservoir for antimicrobial resistance genes (ARGs). Anaerobic digestion (AD) is a pivotal process for mitigating ARG dissemination at the livestock-environment-human interface. This study aims to elucidate the global dynamics of ARGs in AD systems, focusing on virus-host interactions and arms race, to identify actionable strategies for AMR control. We analyzed 205 metagenomic (4.5 Tb) and 36 meta-transcriptomic (640 Gb) datasets, including 15 newly generated datasets, revealing that pig manure AD harbors the highest ARG abundance (0.668 ARGs/16S rRNA), while AD systems generally exhibit limited transcriptional activation of ARGs. We constructed a viral dataset for livestock manure AD (GVD_LMAD), comprising 59,316 DNA and 727 RNA viral operational taxonomic units (vOTUs). Virus-host interactions established by CRISPR-Cas spacer, tRNA and homology matches revealed 889 lytic infections of antimicrobial-resistant bacteria (ARB) compared to only 18 ARG transduction events. Further analysis showed that the relative abundance of vOTUs assigned to the reduction role (4.11% ± 3.19%) was substantially higher than that of reproduction (0.72% ± 0.64%) and transduction (0.19% ± 0.30%), demonstrating that, among viral processes, lysis outweighs transduction in contributing to ARG abundance reduction in AD. Furthermore, an antiviral defense system (ADS) catalogue (GADSC_LMAD), derived from 2760 high-quality metagenome-assembled genomes (MAGs) containing 39,307 ADS, with ADS prevalence in ARB (7.8 ± 6.0 per MAG), indicating an intensified virus-host arms race in AD that may shield ARB from phage lysis. The resulting CRISPR-Cas immune network with expressed spacers targets foreign ARG-carrying sequences (primarily plasmids and ICEs), suggesting a mechanism that restricts horizontal gene transfer (HGT) via conjugation and transformation, despite shielding ARB from phage lysis. Collectively, these findings highlight that viral communities significantly contribute to ARG reduction through phage lysis relative to transduction, while the ADS-mediated arms race, despite protecting ARB, constructs a biological firewall that potentially limits HGT of ARGs. This study provides novel insights into virus-host dynamics as a key mechanism for controlling ARG dissemination in AD systems.}, }
@article {pmid42425005, year = {2026}, author = {Murugan, SG and Lee, CW and Wong, WACY and Wong, YY and Liu, B and Narayanan, K and Sim, EUH and Bong, CW and Wang, A}, title = {Growth Dynamics of selected Vibrio spp. in mono-, co-culture and multi-bacterial microcosms: Investigating the prevalence of Vibrio parahaemolyticus in seawater.}, journal = {Marine environmental research}, volume = {221}, number = {}, pages = {108257}, doi = {10.1016/j.marenvres.2026.108257}, pmid = {42425005}, issn = {1879-0291}, abstract = {We examined the growth dynamics and interspecific competition of six environmental Vibrio isolates (V. parahaemolyticus, V. vulnificus, V. cholerae, V. mimicus, V. cincinnatiensis, and V. zhanjiangensis) recovered from Malaysian seawater. Monoculture assays were conducted across temperature (25-37°C), salinity (0.3-40 ppt), and nutrient (0.001X-0.05X Marine Broth or MB equivalent strength) gradients, followed by co-culture and multi-bacterial microcosm experiments (at 31°C, 26 ppt, 0.01X MB). Regression analyses showed no significant positive response to increasing temperature, whereas tested species responded positively to increasing salinity. Responses to nutrient enrichment suggested that V. parahaemolyticus, V. mimicus and V. vulnificus exhibited r-strategy framework, whereas V. zhanjiangensis represented K-strategy. In contrast, V. cholerae and V. cincinnatiensis could not be clearly classified. In co-culture and multi-bacterial microcosms, V. parahaemolyticus consistently outcompeted both Vibrio and non-Vibrio competitors, even when introduced at lower initial abundance. Therefore, the ecological success of V. parahaemolyticus in these systems was not solely determined by intrinsic growth capacity or environmental suitability, but also by interspecific dynamics. The frequent involvement of V. parahaemolyticus in aquaculture disease outbreaks may be driven by previously underappreciated interspecific competitive advantages that enable it to outcompete other microbes.}, }
@article {pmid42427432, year = {2026}, author = {Davar, D and Zarour, HM and Trinchieri, G}, title = {Toward a Dual-Axis Model of Microbiome Modulation in Cancer Immunotherapy: Pathobiont Elimination and Functional Ecosystem Restoration.}, journal = {Cellular and molecular bioengineering}, volume = {}, number = {}, pages = {}, pmid = {42427432}, issn = {1865-5025}, abstract = {PURPOSE: The gut microbiome is increasingly recognized as a modulator of cancer immunotherapy efficacy, including responses to immune checkpoint inhibitors (ICIs) and chimeric antigen receptor T-cell (CAR-T) therapy. Recent clinical trials of microbiome-targeted interventions such as fecal microbiome transplantation (FMT) and live biotherapeutic products (LBPs) suggest the potential to enhance antitumor immunity and improve clinical outcomes. Yet responses remain heterogeneous and are not fully explained by engraftment of donor taxa alone.<br><br>METHODS: We integrate evidence from interventional trials, observational cohort studies, and principles from gut microbial ecology to develop a model hypothesis on how microbiome-targeted therapies may shape response to immunotherapy, with potential to inform future trial design, analyses, and interpretation.<br><br>RESULTS: Drawing on the available evidence, we propose that therapeutic perturbation of the gut microbiome may augment immunotherapy efficacy through two parallel axes: (1) elimination of immunosuppressive pathobionts that restrain CD8+ T-cell activation and promote myeloid-mediated immunosuppression, and (2) functional restoration of the gut ecosystem through engraftment of taxa that provide metabolites, structural cues, and immunoregulatory signals required for effective antitumor immunity. The success of both axes appears to depend on ecological processes governed by predator-prey dynamics, including colonization resistance, resilience of the resident microbiota, and the ability of administered organisms to displace entrenched dysbiotic communities. This ecological lens may help to explain discrepancies across trial designs, donor types, and intervention modalities, and suggests that complete donor engraftment is neither necessary nor sufficient for clinical benefit.<br><br>CONCLUSIONS: A dual-mechanism model of pathobiont elimination and functional microbial restoration may help explain microbiome-mediated enhancement of cancer immunotherapy, highlighting a balanced immune permissive gut ecosystem as a key determinant of therapeutic success.}, }
@article {pmid42429144, year = {2026}, author = {Wei, L and Kong, X and Li, Y and Wu, H and Gan, Y and Sun, F}, title = {Gut dysbiosis‑derived butyrate loss predicts feeding intolerance: Multiomics evidence guiding nurse‑driven microbiota‑supportive interventions (Review).}, journal = {Molecular medicine reports}, volume = {34}, number = {3}, pages = {}, doi = {10.3892/mmr.2026.13958}, pmid = {42429144}, issn = {1791-3004}, mesh = {Humans ; *Dysbiosis/microbiology/metabolism ; Multiomics ; *Gastrointestinal Microbiome ; *Butyrates/metabolism ; Critical Illness ; }, abstract = {Feeding intolerance (FI) is a common and debilitating challenge among critically ill patients that is linked to a pathway involving the collapse of the gut microbial ecology. The present review synthesizes multiomics evidence supporting a framework whereby critical illness‑associated gut dysbiosis results in a functional deficit of a microbially derived short‑chain fatty acid butyrate, a pivotal metabolite involved in maintaining intestinal barrier integrity, immuneoregulation and gastrointestinal motility. The loss of butyrate‑producing bacteria and their genetic pathways is strongly correlated with FI and may represent a contributory pathogenic mechanism. Key butyrate‑producing organisms diminished during this process include Faecalibacterium prausnitzii and Roseburia spp. Building upon this mechanistic framework, a pragmatic, nurse‑driven intervention model aimed at preserving and restoring microbial health in critically ill patients was proposed. This model is founded on four principal strategies: Minimizing iatrogenic harm (such as antibiotic/proton pump inhibitor stewardship), targeted microbiota nourishment (pre/synbiotics), cautious microbial restoration (probiotics/fecal microbiota transplantation) and innovative monitoring approaches. By integrating principles of microbial ecology with clinical nursing science, the present review provides a framework for developing nurse‑driven protocols designed to address the underlying pathophysiology of FI and improve patient outcomes.}, }
@article {pmid42429610, year = {2026}, author = {Yu, C and Ao, J and Long, M and Xu, Z and You, S and Jiao, Y and Zhu, S and Liu, S-L and Wang, S and Bao, H}, title = {Deciphering the in vitro mucin-driven interaction dynamics of a synthetic gut bacterial community.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0028926}, doi = {10.1128/msphere.00289-26}, pmid = {42429610}, issn = {2379-5042}, abstract = {The gut microbiota is a complex microbial community that plays a crucial role in host health. Environmental and biological factors within the ecosystem influence the dynamic interactions among its members. Although dietary and host-derived nutrient availability play a key role in shaping microbial ecology and interaction patterns, the dynamics of these interactions within the mucus layer remain poorly understood. In this study, we analyzed a synthetic community comprised of six species with variable abilities to utilize mucin. We performed in vitro growth analyses and monitored the interactions among community members in monoculture, co-culture, and community batch culture under different nutrient conditions. Our results showed that positive interactions were prevalent among bacteria when mucin served as the sole carbon source. In contrast, the addition of glucose or high nutrient availability significantly increased inter-bacterial competition. These findings suggest that mucin mitigates competitive antagonism and potentially promotes community diversity. Further in vivo studies supported the role of mucin in increasing community diversity and modulating bacterial metabolic patterns. Deciphering these intricate relationships is essential for understanding how gut microbiota stability is maintained, and what factors might disrupt this delicate balance.IMPORTANCEThe gut microbiota is essential for host health, yet microbial interactions within the intestinal mucus layer remain poorly understood. Current understanding of gut microbial ecology is largely based on nutrient-rich media that do not accurately reflect the mucosal environment. Here, we demonstrate that when bacteria rely solely on mucin as a carbon source, cooperative interactions predominate. In contrast, the introduction of simple sugars shifts the balance toward intensified interbacterial competition. Mucin mitigates competitive antagonism, promotes resource utilization, and enhances community diversity. By demonstrating that mucus actively shapes microbial interaction patterns, this study provides a mechanistic framework for understanding gut ecosystem resilience. Furthermore, these findings support the development of more physiologically relevant in vitro models for predicting gut microbial dynamics and may guide microbiome-based therapies.}, }
@article {pmid42418012, year = {2026}, author = {Hanström, N and Jan, KMG and Winder, M}, title = {Environmental Gradients Shape the Distribution of Free-Living and Host-Associated Syndiniales Life Stages.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, pmid = {42418012}, issn = {1432-184X}, mesh = {*Dinoflagellida/genetics/physiology/classification ; Animals ; *Seawater/parasitology/chemistry ; *Life Cycle Stages ; RNA, Ribosomal, 18S/genetics ; *Host-Parasite Interactions ; Salinity ; *Alveolata/genetics/physiology/classification ; Environment ; }, abstract = {Marine alveolate parasites, particularly early-branching dinoflagellates of the order Syndiniales, play critical yet often overlooked roles in shaping marine microbial communities. These parasitoids infect diverse hosts, including dinoflagellates, copepods, and fish eggs, and rely on short-lived, free-living dinospores for transmission. Despite their ecological significance, the distributions of Syndiniales dinospores and host-associated life stages across environmental gradients remain poorly understood. We used 18S rRNA gene region DNA metabarcoding combined with size-fractionated water filtration across vertical and horizontal gradients of salinity, oxygen, and nutrients in the Baltic Sea-Skagerrak system to characterize Syndiniales life-stage distributions and identify clades producing dinospores. This approach enables the differentiation of free-living dinospores and host-associated life stages. Most reads were assigned to Syndiniales groups I and II, indicating the presence of both host associations and dinospore presence. Dinospore communities were more diverse than host-associated life stages and showed variation in spatial distribution and community composition. The spatial variation was related to salinity, oxygen, and nitrogen concentrations, emphasizing the role of environmental conditions in shaping niches suitable for host-parasite associations and infection transmission. Our findings highlight the prevalence of Syndiniales communities across an environmental gradient and the influence of environmental conditions on their distribution patterns.}, }
@article {pmid42418271, year = {2026}, author = {Touati, A}, title = {Beyond bacterial communication: host factors that modulate quorum sensing and virulence in human pathogens.}, journal = {Future microbiology}, volume = {}, number = {}, pages = {1-16}, doi = {10.1080/17460913.2026.2700916}, pmid = {42418271}, issn = {1746-0921}, abstract = {Quorum sensing (QS) coordinates collective bacterial behavior, but during infection, its activity is also shaped by host biology. This review examines how host-derived factors modulate QS-linked virulence in enteric pathogens, Pseudomonas aeruginosa and Staphylococcus aureus. Across these systems, host control operates through three recurring modes: activation or signal mimicry, enzymatic signal degradation, and extracellular sequestration or receptor-level interference. Catecholamines and related metabolites can feed into bacterial sensory pathways and promote virulence signaling; PONs (paraoxonases) and other host enzymes can degrade autoinducers; and lipoproteins, immune mediators, and epithelial surveillance systems can intercept or reinterpret quorum signals. Together, these data support the view that the host is an active signal-processing environment that reshapes colonization, persistence, and tissue damage, and they point to host-inspired anti-virulence strategies that target signaling rather than viability.}, }
@article {pmid42419260, year = {2026}, author = {Heredia, MY and Caballero-Flores, G}, title = {An acidic welcome: How microbial metabolites keep fungi in line.}, journal = {Cell host &amp; microbe}, volume = {34}, number = {7}, pages = {1151-1153}, doi = {10.1016/j.chom.2026.06.011}, pmid = {42419260}, issn = {1934-6069}, mesh = {*Candida/growth &amp; development/metabolism ; *Fungi ; Antifungal Agents/metabolism/pharmacology ; *Fatty Acids, Volatile/metabolism/pharmacology ; *Microbiota ; Humans ; }, abstract = {Microbiota-derived metabolites shape gut microbial ecology, but how they limit expansion of potentially pathogenic fungi remains elusive. In this Cell Host &amp; Microbe issue, Mishra et al. and Yasuma-Mitobe et al. identify short-chain fatty acids as antifungal metabolites promoting colonization resistance against Candida species via intracellular acidification and metabolic stress.}, }
@article {pmid42419828, year = {2026}, author = {Ekanayaka, R and Chaurasia, A}, title = {Factors influencing the head and neck microbiome.}, journal = {Advances in immunology}, volume = {169}, number = {}, pages = {111-126}, doi = {10.1016/bs.ai.2026.03.009}, pmid = {42419828}, issn = {1557-8445}, mesh = {Humans ; *Microbiota/immunology ; *Neck/microbiology ; *Head/microbiology ; *Dysbiosis/microbiology/immunology ; *Mouth/microbiology ; Animals ; Bacteria ; Host Microbial Interactions ; }, abstract = {The head and neck microbiome comprises a diverse and complex community of microorganisms, including bacteria, archaea, fungi, and viruses. It contributes to oral homeostasis by maintaining a harmonious balance within the oral environment. Disruptions in the balance of the oral microbiota, known as dysbiosis, can lead to the development of various oral health conditions and may extend their effect beyond the oral cavity and influence the initiation or worsening of systemic diseases. Changes in the head and neck microbiome are attributed to interactions between the host, the environment, and the resident microbial ecology. Host-related factors, including genetic background, immune competence, age and physiological status interact closely to mould the microbial colonization across different anatomical sites within the head and neck region. Anatomical and local environmental factors create discrete ecological niches that further support site-specific microbial populations. Microbial communities interact with one another through cooperative and competitive mechanisms. In healthy conditions, the oral microbiome maintains a favorable commensal relationship with its environment. However, in certain circumstances, opportunistic microorganisms within the oral microbiome may undergo a shift and become pathogenic, thereby influencing the stability, resilience, and pathogenic potential of microbiome. Microbial changes within the head and neck region are highly dynamic and respond to both short term, transient influences such as dietary intake and oral hygiene practices, as well as long term, chronic exposures, systemic disease, and sustained immune dysregulation Host related, environmental, and microbial influencing factors therefore exhibit a complex interplay in both health and disease, such that alterations in one component are capable of inducing shifts across the entire microbial ecosystem.}, }
@article {pmid42419832, year = {2026}, author = {Chaurasia, A and Ponangi, K}, title = {The microbiome of the head and neck region.}, journal = {Advances in immunology}, volume = {169}, number = {}, pages = {25-51}, doi = {10.1016/bs.ai.2026.03.002}, pmid = {42419832}, issn = {1557-8445}, mesh = {Humans ; *Microbiota/immunology ; *Dysbiosis/immunology/microbiology ; *Head and Neck Neoplasms/microbiology/immunology ; Animals ; *Head/microbiology ; *Squamous Cell Carcinoma of Head and Neck/microbiology/immunology ; }, abstract = {The head and neck region is a host to a diverse and complex microbiome, comprising of very specific microbial communities across different anatomical niches such as the oral cavity, nasal sinuses, pharynx, larynx, salivary glands, and middle ear. The existence of these communities is determined by various factors such as physicochemical conditions, local environment and host genetics playing a critical role in maintaining mucosal integrity, immune modulation, colonization resistance, and thereby achieving metabolic homeostasis. As the human ages, the microbiome constantly evolves, influenced by diet, hormonal changes, and lifestyle even causing disruptions such as dysbiosis linked to diseases like head and neck squamous cell carcinoma (HNSCC). This chapter attempts to explore the anatomical and ecological diversity, site-specific microbial compositions, functional roles, developmental trajectories, and the challenges in understanding these microbial communities. Even though there were significant advances in sequencing technologies helping in identifying the microbial protective and pathogenic potential, hurdles like sampling difficulties and low biomass contamination tend to complicate the research process. Therefore it is of utmost importance to understand the baseline microbiome thereby helping in laying a foundation for studying its role in HNSCC, creating a pathway for microbial diagnostics and curative therapies.}, }
@article {pmid42410982, year = {2026}, author = {Alanazi, A}, title = {Organ-Specific Human Microbiomes and Dysbiosis: Mechanistic Links to Disease and Emerging Therapeutic Strategies.}, journal = {Journal of clinical laboratory analysis}, volume = {}, number = {}, pages = {e70307}, doi = {10.1002/jcla.70307}, pmid = {42410982}, issn = {1098-2825}, abstract = {BACKGROUND: The human microbiome is a dynamic and diverse community of microorganisms that affects susceptibility to illness and promotes wellness. Dysbiosis, or disruption of this delicately regulated microbial ecology, has been identified as a major factor in the emergence and development of systemic and organ-specific disorders.<br><br>OBJECTIVE: With an emphasis on dysbiosis-driven illness processes and therapeutic intervention implications, this study attempts to critically analyze host-microbiome interactions across key human organ systems.<br><br>METHODS: Using predetermined microbiome-related keywords, a systematic literature search (2001-2025) was carried out in PubMed, Scopus, Web of Science, and Google Scholar. To assess microbiome formation, organ-specific distribution, disease correlations, and therapeutic implications, English-language peer-reviewed original papers, meta-analyses, and clinical or validated animal studies were chosen and methodically compiled.<br><br>RESULTS: Microbiome dysbiosis is linked to cardiovascular, metabolic, inflammatory, neurological, hepatic, renal, and cancer-related illnesses by interfering with immune modulation, metabolic balance, and epithelial barrier integrity, according to evidence from human and verified animal research. Modified production of short-chain fatty acids, immunological signaling imbalance, chronic inflammation, and communication between the gut-organ axis are examples of mechanistic linkages. Immune and metabolic indicators improved condition-specifically with interventions such as probiotics, fecal microbiota transplantation, and diet-based regulation.<br><br>CONCLUSION: Collectively, current evidence supports the microbiome as a modifiable determinant of disease risk and therapeutic response, underscoring its translational potential for precision medicine.}, }
@article {pmid42413662, year = {2026}, author = {Petrosino, S and Escobar, JVF and Di Marzo, V and Iannotti, FA}, title = {Diet, microbiota, and lipidomics: How fatty acids shape the endocannabinoidome and host metabolism.}, journal = {Progress in lipid research}, volume = {}, number = {}, pages = {101396}, doi = {10.1016/j.plipres.2026.101396}, pmid = {42413662}, issn = {1873-2194}, abstract = {The endocannabinoidome (eCBome) is a complex lipid signaling network that integrates metabolic, immune, and neurobehavioral processes in response to environmental cues. Dietary lipids and gut microbiota have emerged as major modulators of its activity and signaling tone. Intake of specific fatty acids, including the monounsaturated oleic acid, the omega-6 polyunsaturated linoleic acid, and omega-3 polyunsaturated fatty acids, influences the eCBome not only by serving as structural precursors of bioactive lipid mediators, but also by altering the relative abundance of these mediators through changes in substrate availability, enzymatic competition, and receptor-mediated feedback loops. Concurrently, the gut microbiota shapes host eCBome signaling by regulating lipid metabolism, inflammatory tone, and intestinal barrier integrity, while eCBome mediators reciprocally modulate microbial composition and function. Dysregulation of this complex diet-microbiota-eCBome interplay has been implicated in the pathogenesis of metabolic disorders, chronic inflammation, and neuropsychiatric conditions. In this review, we critically examine the molecular mechanisms underlying the interactions between dietary lipid composition, gut microbial ecology, and eCBome signaling. We discuss the implications for human health and highlight emerging diet-based therapeutic strategies targeting this axis.}, }
@article {pmid42414614, year = {2026}, author = {Suárez, JP and Cevallos, S and Herrera, P}, title = {Multiscale Structuring of Mycorrhizal Fungal Communities of Tropical Epiphytic Orchids.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02830-2}, pmid = {42414614}, issn = {1432-184X}, support = {PIC-13-ETAPA-003//Secretar&#xed;a de Educaci&#xf3;n Superior, Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n/ ; }, abstract = {Symbiotic interactions with root-associated fungi are essential for orchid germination, nutrient acquisition and survival, yet the factors structuring these symbioses in tropical epiphytic orchids remain poorly understood. Tropical montane forests provide an ideal system for examining these interactions because steep environmental gradients occur over short geographic distances. We investigated how elevation, variation among populations within elevational belts and host identity shape root-associated fungal communities in the southern Ecuadorian Andes, a region of exceptional epiphytic orchid diversity. Root samples from 699 individuals representing 11 orchid species were analyzed using ITS2 amplicon sequencing. A total of 4,697 operational taxonomic units (OTUs) were recovered, including 271 putative orchid mycorrhizal fungi. Fungal richness peaked at mid elevation and declined at higher elevations. Community composition varied significantly among elevational belts, sites and host species, with differences among elevations driven primarily by species turnover rather than nestedness. Despite this turnover, mycorrhizal assemblages maintained a persistent core across elevations, while site-level heterogeneity contributed to fine-scale differentiation. These results indicate that fungal community assembly in epiphytic orchids is structured across multiple spatial scales by elevational gradients, local environmental conditions and host identity. The mid-elevation diversity peak and stronger filtering at higher elevations indicate that orchid-fungus symbioses are highly sensitive to environmental gradients, with potential consequences for their stability under ongoing environmental change in tropical montane forests.}, }
@article {pmid42414880, year = {2026}, author = {Shen, N and Shan, X and Zheng, L and Qiao, J and Jiang, Y and Wu, R and Ning, T and Liu, S and Dong, C and Yan, J and Lu, T and Zhu, S}, title = {Oral microbiota characteristics in children younger than 3 years with febrile seizures: a prospective observational study.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05375-z}, pmid = {42414880}, issn = {1471-2180}, support = {Z2025119//Suqian Sci &amp; Tech Program/ ; XZSYSKF2024040//Jiangsu Key Laboratory of Immunity and Metabolism Project/ ; }, abstract = {This study investigated the oral microbiota of children younger than 3 years with febrile seizures (FS). Oral swab samples were collected from 48 children with FS and 47 healthy controls, and the V4 region of the bacterial 16 S rRNA gene was sequenced. The Shannon index did not differ significantly between groups, whereas the ACE index was significantly lower in the FS group. Although beta-diversity analysis based on weighted and unweighted UniFrac distances showed no significant between-group differences, partial least squares discriminant analysis provided an exploratory supervised visualization showing apparent separation between the FS and control groups. Among the key genera, Streptococcus, Prevotella, and Granulicatella were significantly enriched in the FS group, whereas Neisseria, Haemophilus, Porphyromonas, and Capnocytophaga were significantly depleted. Predicted functional analysis showed increased relative abundances of pathways related to translation, replication and repair, nucleotide metabolism, cell growth and death, and bacterial infectious diseases, whereas pathways related to energy metabolism, cell motility, signaling molecules and interaction, and transport and catabolism were reduced. These findings suggest that FS is associated with selective ecological reconfiguration of the early-life oral microbiota, mainly reflected by altered proportions of key resident genera.}, }
@article {pmid42415201, year = {2026}, author = {Srithanasuwan, A and Zou, Y and Zadoks, RN and Suriyasathaporn, W and Schukken, YH}, title = {Recombination, mobile genetic elements, and genetic transfer contribute to the adaptation of Streptococcus uberis causing mastitis.}, journal = {Veterinary research}, volume = {57}, number = {1}, pages = {}, pmid = {42415201}, issn = {1297-9716}, mesh = {Animals ; *Streptococcus/genetics/physiology ; *Mastitis, Bovine/microbiology ; *Interspersed Repetitive Sequences ; *Streptococcal Infections/veterinary/microbiology ; *Recombination, Genetic ; Cattle ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Female ; Thailand ; Adaptation, Physiological/genetics ; }, abstract = {Streptococcus uberis is a major cause of bovine mastitis. However, the genomic mechanisms that facilitate adaptation of the pathogen within different host-associated environment or selection pressures remain poorly understood. This study analyzed whole-genome sequence data from three Thai dairy herds to investigate the contributions of recombination and mobile genetic elements (MGEs) to S. uberis evolution and adaptation. Among the 138 S. uberis genomes, 42 core genome sequence types (cgSTs) were identified, along with frequent detection of MGEs such as plasmid-associated genes (81.1% of isolates), prophages (67.4% of isolates), and insertion sequences (26.1% of isolates). The isolates from farm A exhibited the longest recombined fragment size, but with extremely low recombination frequency and recombination-to-mutation ratio. By contrast, the isolates from farm B, which had the highest prevalence of antimicrobial resistance (AMR) gene, showed a high recombination-to-mutation ratio (R/θ = 4.42) and more frequently contained MGEs associated with AMR genes. Finally, isolates from farm C shared a single core genome and AMR profile but harbored diverse prophages. Several prophages shared high sequence similarity (>99%) with phages infecting other bacterial genera, suggesting that ecological overlap between bacterial species may facilitate cross-genus genetic exchange, highlighting the influence of microbial ecology on the evolution of S. uberis. Collectively, our results illustrate the variety of mechanisms and genetic elements that contribute to the adaptive evolution of S. uberis in dairy farming environments.}, }
@article {pmid42415234, year = {2026}, author = {Shahin, K and Wang, L and He, Z and Lv, B and Van Alin, A and Lo-Man, R and Wu, H and Sansonetti, P and Collard, JM}, title = {A metabolite-dependent mechanism by which Bifidobacterium animalis subsp. lactis promotes Bacteroides colonization.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2696647}, doi = {10.1080/19490976.2026.2696647}, pmid = {42415234}, issn = {1949-0984}, mesh = {Animals ; *Bacteroides/growth &amp; development/metabolism ; Humans ; Mice ; Feces/microbiology ; *Bifidobacterium animalis/metabolism/growth &amp; development ; *Gastrointestinal Microbiome ; Symbiosis ; Bifidobacterium/metabolism ; Metabolome ; Coculture Techniques ; Bacteroides fragilis/growth &amp; development/metabolism ; }, abstract = {Prokaryote-prokaryote symbiotic relationships influence interactions within microbial communities, affecting colonization, survival, and organization. Unlike competition, consortium species facilitate growth via metabolite cross-feeding. This study explored interactions between two early human gut colonizers: partially aerotolerant Bifidobacterium spp. and strict anaerobic Bacteroides spp., using omics techniques. Promotion of Bacteroides spp. growth by Bifidobacterium animalis subsp. lactis was demonstrated through co-culture experiments in anaerobic conditions. Metabolomic analysis revealed over 150 unique metabolites present in B. animalis subsp. lactis supernatants are absent in other Bifidobacterium species, including 3-hydroxycapric acid, D-alanyl-D-alanine, 2-isopropylmalic acid, and D-glucose 2-phosphate. These compounds served as nutritional substrates, including carbon and nitrogen sources, significantly enhancing Bacteroides spp. growth. In murine models, early colonization by B. animalis subsp. lactis consolidated Bacteroides fragilis colonization (1.7 × 10[4] to 9.7 × 10[6] copy number/g fecal sample) by providing these metabolites as a niche. These findings highlight B. animalis subsp. lactis plays a critical role in gut colonization of Bacteroides spp. via its exclusive metabolic profile, offering insights into partitioned metabolic activity within gut communities and emphasizing the importance of specific metabolites in early microbial establishment.}, }
@article {pmid42405327, year = {2026}, author = {Kusuma, SAF}, title = {Selective Modulation of Cutibacterium acnes Biofilms in Acne: Limitations of Conventional Therapies and Emerging Anti-Virulence Strategies.}, journal = {Clinical, cosmetic and investigational dermatology}, volume = {19}, number = {}, pages = {621646}, pmid = {42405327}, issn = {1178-7015}, abstract = {Acne vulgaris is a multifactorial inflammatory skin disorder in which Cutibacterium acnes biofilm formation contributes to disease persistence, antimicrobial tolerance, and treatment failure. Conventional therapies primarily target bacterial viability but often fail to address biofilm-associated resilience and strain-specific virulence. Emerging strategies have therefore shifted toward the selective modulation of bacterial behavior rather than broad-spectrum eradication, with the aim of attenuating pathogenicity while minimizing disruption of the skin microbiome. This review critically evaluates selective modulation approaches targeting biofilm integrity, virulence pathways, and microbial ecology, including anti-virulence therapy, quorum-sensing inhibition, biofilm disruption, nanocarrier-based delivery systems, and microbiome-informed interventions. Preclinical studies suggest that these strategies may disrupt biofilm architecture, attenuate virulence factor expression, and potentially reduce selective pressure associated with conventional antimicrobial therapies. Approaches such as antimicrobial peptides, quorum-sensing inhibitors, and advanced delivery systems have demonstrated promising in vitro, ex vivo, and early preclinical outcomes; however, clinical evidence remains limited. Significant challenges remain, including insufficient in vivo validation, formulation instability, biofilm-associated delivery barriers, regulatory considerations, and limited long-term safety data. Overall, selective modulation represents a promising emerging framework for acne management, although its successful clinical translation will require robust clinical validation, improved disease-relevant models, and the integration of personalized strategies based on microbiome profiling and advanced delivery technologies.}, }
@article {pmid42405599, year = {2026}, author = {O'Keefe, KP and Boice, MN and Samuel, AM and Andrade, CC}, title = {Detection of Ehrlichia, Francisella, and Rickettsia in Dermacentor Ticks in Eastern Washington.}, journal = {Journal of vector ecology : journal of the Society for Vector Ecology}, volume = {51}, number = {1}, pages = {27-38}, doi = {10.52707/1081-1710-51.1-27}, pmid = {42405599}, issn = {1948-7134}, mesh = {Animals ; *Dermacentor/microbiology ; *Francisella/isolation &amp; purification/genetics ; *Rickettsia/isolation &amp; purification/genetics ; *Ehrlichia/isolation &amp; purification/genetics ; Washington ; Polymerase Chain Reaction ; }, abstract = {Dermacentor ticks are widespread in eastern Washington and are known vectors of bacterial pathogens and harborers of endosymbionts belonging to the genera Francisella and Rickettsia. Some Dermacentor species can become infected with Ehrlichia chaffeensis Anderson et al. (Rickettsiales: Ehrlichiaceae); it remains unclear if any are competent vectors for this bacterial pathogen. This study reports the abundance of Dermacentor species and prevalence of select tick-borne bacterial pathogens collected from two conservation areas popular among hikers in Spokane County, Washington. In total, DNA from 599 adult ticks was analyzed using PCR; 87.8% (526/599) were identified as Dermacentor andersoni Stiles and 12.2% (73/599) as D. similis Lado, Glon and Klompen (Ixodida: Ixodidae). Ticks were also screened for the presence of bacterial DNA using genus- or species-specific primers targeting Rickettsia spp., Francisella spp., and E. chaffeensis. Rickettsia endosymbionts, R. peacockii Niebylski et al. or R. rhipicephali (Burgdorfer et al.) Weiss and Moulder (Rickettsiales: Rickettsiaceae), were found in 4.0% (21/526) of D. andersoni. Francisella-like endosymbionts were detected in 65.9% (395/599) of all ticks. No species known to be pathogenic belonging to either Rickettsia or Francisella were detected. However, E. chaffeensis was detected in 15.3% (12/73) of D. similis, which to our knowledge is the first report of ticks harboring this species of bacteria in Washington state. These findings contribute to understanding the microbial ecology of ticks in the Inland Northwest.}, }
@article {pmid42405791, year = {2026}, author = {Alexander, AM and Loo, HQ and Askew, L and Raghuram, V and Satola, SW and Read, TD and Goldberg, JB}, title = {Intraspecific diversity of Staphylococcus aureus populations isolated from cystic fibrosis respiratory infections.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0036726}, doi = {10.1128/spectrum.00367-26}, pmid = {42405791}, issn = {2165-0497}, abstract = {UNLABELLED: Long-term associations within an individual host allow bacterial populations to diversify over time, sometimes resulting in the coexistence of multiple species or variants of the same species. Traditional methods for identifying infective agents generally involve isolating a single pathogen and potentially even a single colony from a given sample. While screening samples for virulent or difficult-to-treat pathogens is an important part of informing clinical treatment and correlative research, these reductive methods alone do not provide researchers or healthcare providers with the potentially important perspective on the true pathogen population. In this study, we begin to address this limitation by comparing the phenotypic and genotypic diversity of single colonies and pooled isolates of Staphylococcus aureus taken from fresh sputum samples from three patients with cystic fibrosis. Additionally, we compare the results collected in our research laboratory to those processed by the Emory Clinical Microbiology Laboratory with the identical sputum samples. We identified unrelated coexisting lineages in two out of three sputum samples, as well as clinically relevant population structures that were not apparent from studying single-colony isolates alone. Altogether, our observations presented here demonstrate that the true nature and phenotype of a clinically isolated pathogen can be missed with standard sampling methods when assessing chronic infections. More broadly, this work outlines the potential impact that comprehensive population-level sampling may have for both research efforts and more effective treatment practices.<br><br>IMPORTANCE: When obtaining bacterial isolates from infections, it is important to consider the ecological biases introduced by methods used for collection and processing. In this study, we demonstrate how reductive sampling and processing methods traditionally used by clinical microbiology labs often do not adequately capture complex and clinically relevant traits present in diverse pathogen populations. When treating or studying bacteria like Staphylococcus aureus that can maintain multiple variants within a population over a long period of time, it may be more effective and informative to employ sampling methods that account for the potential diversity within a population, as outlined in our approach presented here.}, }
@article {pmid42406122, year = {2026}, author = {Joseph, S and Abraham, LS and Premachandran, K and Samrot, AV and Thirugnanasambandam, R and Ragavendhar, K and Alodaini, HA and Moubayed, NM and Hatamleh, AA and Mani, RR and Chang, SW and Ravindran, B}, title = {Unravelling Extremophilic Microbiome Diversity and Functional Dynamics in Hypersaline Environment.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02817-z}, pmid = {42406122}, issn = {1432-184X}, support = {REIG-FPS-2025/038//UCSI University/ ; }, abstract = {Solar salt pans are extreme hypersaline environments that represent functionally specialised microbial communities mediating essential biogeochemical transformation. Vedaranyam, a coastal region of the Bay of Bengal containing artificially constructed solar salterns for salt production. There is limited information available on the metagenome diversity and functional profiling of this saltpan, which prompted us to investigate it. Here, we report the first whole metagenome sequencing to explore the dynamics of the functional structure of microbial communities in saltpan during the preharvest and postharvest phases of salt production. Methanobacteriota and Pseudomonadota dominated both phases at the phylum level, while Halobacteria comprised the most abundant class (53.2% preharvest; 48% postharvest). A notable bloom of Dactylococcopsis salina was observed during postharvest (4.28% to 12.67%) and flock doubling of Cyanobacterota relative abundance (5.5% to 10.6%), reflecting photosynthetic primary production following salt removal. Conversely, during postharvest phase sulfur oxidising Guyparkeria halophila reduced 23 fold, while the DMSP accumulating osmolyte producer Salinibaculum marinum dominated preharvest (6.98%). However, functional classification of the metagenome revealed active participation of the microbial community across five major biogeochemical cycles. Encompassing carbon fixation by cyanobacteria and diverse haloarchaea, nitrogen cycling through diazotrophy and denitrification, a cryptic preharvest sulfur cycle coupling sulfate reduction and sulphide oxidation, phase shifted DMSP catabolism, and light driven bacteriorhodopsin through archaeal energy conservation. Metagenomic assembly yielded ten metagenomic assembled genomes (MAGs), revealing the taxonomic diversity and metabolic potential of the dominant halophilic community across biogeochemical cycles. These results provide critical insights into the ecological succession from an anaerobic, chemolithotrophy-rich preharvest microbial community to an aerobic, photosynthetically driven postharvest assemblage, advancing our understanding of microbial biogeochemistry in managed hypersaline ecosystems.}, }
@article {pmid42406144, year = {2026}, author = {Garrigós, M and Veiga, J and Garrido, M and García-López, MJ and Morales-Yuste, M and Marín, C and Recuero, J and Rosales, MJ and Moreno-Indias, I and Martínez-de la Puente, J}, title = {Drivers of Mosquito Microbiome Composition: Effects of Species, Locality, Season, and Plasmodium Infection.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02801-7}, pmid = {42406144}, issn = {1432-184X}, abstract = {Mosquito microbiota influences mosquito physiology and pathogen development, finally affecting their vectorial capacity. Identifying the factors that affect the composition of mosquito microbial communities in nature is essential for designing effective strategies to control vector-borne pathogens. Here, we used a 16 S rRNA metabarcoding approach to analyse the microbiome of 196 mosquito pools (four females per pool) of three common species: Culex pipiens, Aedes albopictus, and Culiseta longiareolata. Mosquitoes were collected from spring to autumn 2022 in five sampling localities of southern Spain. Mosquito bacterial alpha diversity was higher in Cs. longiareolata compared to Cx. pipiens and Ae. albopictus. In addition, beta diversity and the relative abundance of different bacterial taxa differed among mosquito species. Wolbachia dominated the bacterial community of Cx. pipiens and Ae. albopictus, but were virtually absent in Cs. longiareolata. Furthermore, using Cx. pipiens -the most extensively sampled species here- we further investigated differences in the microbiome composition according to sampling localities, seasons, and avian Plasmodium infection status. Locality and season affected the bacterial alpha and beta diversity, with mosquitoes collected in autumn from the Fuengirola locality showing a higher observed richness. Differences in beta diversity among localities and seasons could be, at least in part, influenced by differences in beta dispersion. The relative abundance of different taxa in Cx. pipiens varied by locality, season, and avian Plasmodium infection status. In sum, both intrinsic and environmental factors influence mosquito microbiome, yet the potential consequences for pathogen transmission should be further addressed. This study provides a comprehensive framework to understand the ecological drivers of wild mosquito microbiome, a key step for predicting vector-pathogen interactions and improving strategies for vector-borne disease control.}, }
@article {pmid42410155, year = {2026}, author = {Ali, H and Khaleque, A and Sadia, T and Azmuda, N and Parvez, MAK and Adnan, N and Akter, S and Ahmed, MF}, title = {Cross-domain microbial differences across freshwater and marine habitats in a tropical delta.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-61157-7}, pmid = {42410155}, issn = {2045-2322}, abstract = {Microbial communities are central to aquatic ecosystem functioning, yet integrated cross-domain comparisons of prokaryotic and microeukaryotic microbiomes remain underexplored in tropical regions, particularly in Bangladesh. Here, we investigated habitat-associated differences in microbial community structure across freshwater and marine ecosystems of the Bangladesh tropical delta using 16S and 18S rRNA gene amplicon sequencing and assessed inferred functional potential for prokaryotic communities. Six freshwater and ten seawater samples were analyzed, comprising eight newly generated datasets (six freshwater and two seawater) and eight previously published seawater datasets. Prokaryotic communities exhibited significantly higher alpha diversity in freshwater, whereas microeukaryotic diversity showed no significant habitat-associated differences after correction, despite a weak freshwater enrichment trend. Beta diversity revealed clear compositional separation between habitats for both domains, with prokaryotes exhibiting centroid shifts and microeukaryotes showing greater within-group dispersion. Taxonomic profiles showed seawater dominance by Gammaproteobacteria and Alphaproteobacteria, whereas freshwater communities were more evenly distributed across Bacteroidota, Actinomycetota, and Verrucomicrobiota. Microeukaryotic assemblages also displayed pronounced habitat-associated restructuring. Functional inference of prokaryotic communities indicated conservation of core pathways across habitats despite taxonomic turnover. Exploratory cross-domain correlation analysis identified mixed positive and negative associations, although none remained significant after multiple-testing correction. Collectively, these findings reveal consistent habitat-associated microbial differentiation across tropical freshwater and marine ecosystems and provide a comparative baseline for understanding cross-domain microbial biogeography in climate-sensitive aquatic environments.}, }
@article {pmid42410848, year = {2026}, author = {Huang, X and Gao, Y and Sun, J and Shi, L}, title = {Association between oral microbiome diversity and cardiovascular-kidney-metabolic syndrome in US adults: Analysis of NHANES 2009 to 2012.}, journal = {Medicine}, volume = {105}, number = {27}, pages = {e49530}, doi = {10.1097/MD.0000000000049530}, pmid = {42410848}, issn = {1536-5964}, mesh = {Humans ; *Microbiota/genetics ; *Metabolic Syndrome/epidemiology/microbiology ; United States/epidemiology ; Nutrition Surveys ; Female ; Cross-Sectional Studies ; Male ; Adult ; *Cardiovascular Diseases/epidemiology/microbiology ; *Mouth/microbiology ; Middle Aged ; *Kidney Diseases/epidemiology/microbiology ; }, abstract = {The present study aimed to examine the association between oral microbiome alpha diversity and the severity of cardiovascular-kidney-metabolic (CKM) syndrome among US adults. Emerging evidence suggests that the oral microbiome may influence systemic cardiometabolic health; however, its relationship with integrated CKM syndrome remains unclear. We conducted a cross-sectional analysis of adults aged ≥20 years from the 2009 to 2012 National Health and Nutrition Examination Survey, a nationally representative survey of the US population, including participants with available oral microbiome data (n = 4834). Alpha diversity was assessed using observed amplicon sequence variants richness, Faith's phylogenetic diversity Shannon index, and Simpson index. CKM syndrome was classified into 5 stages (0-4), with advanced CKM defined as stages 3-4, representing subclinical or clinical cardiovascular disease and/or significant kidney involvement. Weighted multivariable logistic regression models were used to estimate odds ratios and 95% confidence intervals. Higher oral microbiome diversity was consistently associated with lower odds of advanced CKM. In fully adjusted models, each unit increase in observed amplicon sequence variants was associated with a 2% lower odds of advanced CKM (odds ratio = 0.98, 95% confidence interval = 0.97-1.00). Participants in the highest tertile of diversity had 10% to 12% lower odds of advanced CKM compared with the lowest tertile across diversity indices, with significant trends. Associations were consistent across demographic and clinical subgroups. Greater oral microbial diversity was inversely associated with advanced CKM syndrome in US adults. These findings support a potential association between oral microbial ecology and integrated cardiometabolic-renal health, although longitudinal and mechanistic studies are required to clarify temporality and causality.}, }
@article {pmid42399628, year = {2026}, author = {Yuan, J and Zhang, XY and Yang, S and Luo, CL and Wang, ZH and Wang, QQ and Hao, YY and He, Y and Wang, S and Kong, FL and Zhao, M and Cao, ZJ and Li, SL and Wang, W}, title = {Peripartum hypophosphatemia is associated with a hindgut-centered microbiota-metabolite-host axis in transition dairy cows.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01078-5}, pmid = {42399628}, issn = {2055-5008}, support = {32202713//National Natural Science Foundation of China/ ; }, abstract = {The transition period in dairy cows is accompanied by profound shifts in mineral homeostasis and gut microbial ecology. While endocrine regulation of hypocalcemia has been extensively characterized, adaptive responses to hypophosphatemia-and the potential involvement of the gut microbiota-have received far less attention. Twenty-four Holstein dairy cows were randomly assigned to control or low-phosphorus groups. Hypophosphatemia was induced by dietary supplementation with 300 g/d synthetic zeolite from 21 days prepartum to 3 days postpartum. Blood and feces samples were collected at -21, -7, 0, 1, and 3 d relative to calving for longitudinal analysis of physiology, hindgut microbiome and plasma metabolomics to investigate host-microbiome adaptation to peripartum hypophosphatemia in dairy cows. Cows with hypophosphatemia exhibited pronounced compositional remodeling of their hindgut microbiota and extensive, persistent alterations in their plasma metabolome, with glycerophospholipid metabolism being a consistently affected pathway. Integrated correlation and mediation analyses revealed close associations between hindgut microbial variation, host metabolic reprogramming, and circulating phosphorus dynamics. In addition, a plasma feature putatively annotated as α-methyl-m-tyrosine (AMT) was identified as a candidate statistical mediator associated with the observed relationships between Lachnospiraceae_NK3A20_group abundance with systematic phosphorus concentrations. Collectively, these findings indicate that peripartum hypophosphatemia in dairy cows is accompanied by coordinated host metabolic and hindgut microbial remodeling, supporting a hindgut-centered host-metabolite-microbiome framework for understanding phosphorus adaptation during early lactation.}, }
@article {pmid42399737, year = {2026}, author = {Steele, S and Mazengenya, P and Chambuso, R}, title = {Pathology-derived clinical micro-architectural diagnostics of tumour-microbiome interactions in colorectal cancer.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {}, pmid = {42399737}, issn = {1479-5876}, abstract = {BACKGROUND: Classical tumour pathology reports contain a largely untapped layer of information that may indicate tumour-microbial interactions. However, routine colorectal cancer pathology staging does not take into account microbiome-associated tumour micro-architecture signatures, thus limiting insights into intratumoral microbial ecology, prognostic stratification and treatment-relevant microbial information. In this study, we analysed scanned USA pathology reports to quantify likely intratumoral microbiome-associated micro-architectural signatures.<br><br>METHODS: We studied 1,978 TCGA colorectal cancer pathology reports from 1,249 colon adenocarcinomas, 559 rectal adenocarcinomas and 170 reports without a definitive anatomic site using rule-based natural language processing to extract microbiome-linked micro-architectural features. Barrier-disruption and invasion-access signatures were identified from the reports as microbiome-associated pathology micro-architecture signatures that occur with microbial-related necrosis, hypoxia, toxins, colonisation, persistence, metabolic activity and/or tumour interaction. We developed a z-scored composite index called Report-based Microbial Ecology Likelihood Score (RMELS) and used Kaplan-Meier log-rank analyses, multivariable Cox regression, Kruskal-Wallis tests and receiver operation characteristic curves with bootstrap confidence intervals. Proportional hazards assumptions were tested for statistical significance at two-sided p&#x2009;<&#x2009;0.05.<br><br>RESULTS: Microbiome-associated pathology micro-architectural signatures were highly prevalent in the pathology reports. Barrier-disruption features, including ulceration (41.1%) and mucin alteration (16.7%), were common and increased with tumour stage (Kruskal-Wallis p&#x2009;<&#x2009;0.0001). Prominent invasion-access features included infiltrative growth (59.4%, 95% CI 57.2-61.5), lymphovascular invasion (18.6%, 95% CI 17.0-20.4) and perineural invasion (22.9%, 95% CI 21.1-24.8). All showed heterogeneous, non-monotonic distributions across pathologic stages, indicating activation of microbial injury and invasion programmes. Integration of these features into our signature score, ordered tumours along a continuous microbiome-permissiveness gradient independent of pathological stage. With limited information, our signature score discriminated early (T1) from advanced (T4) disease more effectively than barrier or invasion features alone (AUC&#x2009;=&#x2009;0.66, 95% CI 0.58-0.74, p&#x2009;<&#x2009;0.0001). Right-sided colonic tumours exhibited significantly higher scores than left-sided colonic and rectal tumours (FDR q&#x2009;<&#x2009;0.001), aligning with known microbial biogeography. In multivariable Cox models adjusted for pathological stage, our signature score RMELS showed modest but directionally consistent association with overall and progression-free survival, capturing microbiology-relevant risk not resolved by pathological staging.<br><br>CONCLUSIONS: Routine classical colorectal cancer pathology reports contain intratumoral microbiome-associated pathology micro-architectural signatures. Quantifying these exploratory tumour-microbial signatures using digital pathology will enable scalable, microbiology-informed risk stratification and prognostic modelling to complement the current pathological staging.}, }
@article {pmid42401776, year = {2026}, author = {Zapata-Peñasco, I and Herrera-Díaz, J}, title = {Proteomic Sample Preparation for the Petroleum Industry: A Biocorrosion Case Study.}, journal = {Advances in experimental medicine and biology}, volume = {1510}, number = {}, pages = {121-145}, pmid = {42401776}, issn = {0065-2598}, mesh = {*Proteomics/methods ; *Petroleum/microbiology ; Corrosion ; *Oil and Gas Industry ; Biodegradation, Environmental ; Biofilms/growth &amp; development ; *Bacterial Proteins/metabolism ; Sewage/microbiology ; *Bacteria/metabolism/genetics ; }, abstract = {Petroleum-associated environments are among the most chemically complex and biologically extreme systems encountered in the field of industrial biotechnology. Here, microbial activity plays a pivotal role in hydrocarbon biodegradation, reservoir souring, and microbiologically influenced corrosion (MIC). In these systems, proteins constitute the functional interface between microbial metabolism and physicochemical processes affecting infrastructure integrity and environmental impact. This chapter presents an integrated proteomics-based workflow for the characterization of microbial communities inhabiting oil pipeline sludges, with particular emphasis on sample preparation strategies tailored to hydrocarbon-rich, metal-laden, and saline matrices. Optimized phenol-based extraction, electrochemical in vitro corrosion assays, two-dimensional gel electrophoresis, and high-resolution mass spectrometry are combined with metagenomic information to enable robust identification and functional interpretation of proteins involved in redox metabolism, biofilm formation, extracellular electron transfer, sulfur and nitrogen cycling, and stress adaptation. The approach is illustrated through a biocorrosion case study of marine pipeline sludge, revealing key enzymatic systems, including oxidoreductases, hydrolases, cytochromes, ABC transporters, and biofilm-associated structural proteins that mediate metal dissolution and microbial energy conservation. By integrating proteomics with electrochemical measurements and systems-level analysis, this chapter highlights how tailored sample preparation and functional protein profiling can overcome the limitations of culture-dependent methods, providing mechanistic insight into complex petroleum microbiomes. These advances establish proteomics as a critical tool for monitoring, predicting, and ultimately mitigating biocorrosion, as well as for guiding the development of biotechnology-based strategies in the oil and gas industry.}, }
@article {pmid42402041, year = {2026}, author = {Gao, Z and Pang, M and Li, M and Ming, Y and Liu, H and Yin, K}, title = {Assessing the effects of ocean alkalinity enhancement on marine protozoa: physiological dynamics and transcriptomic responses.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0029826}, doi = {10.1128/aem.00298-26}, pmid = {42402041}, issn = {1098-5336}, abstract = {Ocean alkalinity enhancement (OAE) is proposed as a potential tool to remove atmospheric CO2 and mitigate climate change. However, the effects of OAE on marine protozoa remain poorly understood. In this study, we conducted acute and acclimated experiments on two heterotrophic nanoflagellates, i.e., Cafeteria burkhardae and Paraphysomonas longispina, to investigate their responses to two substances (NaHCO3 and NaOH) at low (set ~2,600 µmol L[-1]) and high (set ~4,000 µmol L[-1]) levels, respectively. Our results showed that the two species had similar negative reactions under acute exposure. However, the two species showed different tolerances after acclimation. The growth rates of C. burkhardae decreased under all OAE treatments, while its reactive oxygen species accumulated only at the high OAE level. The low-level OAE treatments had no significant effects, but high-level OAE was more adverse for P. longispina, which grew more slowly and grazed more, indicating lower growth efficiency. Underlying transcriptomic mechanisms were only analyzed for low-level OAE, which were consistent with the physiological responses. Replication and repair and metabolism-related pathways were significantly inhibited, with translation-related pathways stimulated in C. burkhardae. For P. longispina, in addition to translation-related pathways, replication and repair, and metabolism pathways were significantly upregulated. Overall, our findings suggest the potential negative effects of OAE on marine protozoa, and the effects can vary depending on the species, level, and substances. Given the critical role of protists in marine ecosystems, these adverse effects raise important concerns about the broader implications of OAE for marine biodiversity and ecosystem stability.IMPORTANCEOcean alkalinity enhancement (OAE) represents a novel approach to mitigate climate change by increasing the ocean's CO2 sequestration capacity. However, the potential ecological and environmental impacts of OAE on marine microorganisms, particularly protozoa, remain poorly understood. This study investigates the responses of two heterotrophic nanoflagellates, Cafeteria burkhardae and Paraphysomonas longispina, to varying levels of OAE treatments using NaHCO3 and NaOH. Our findings reveal significant species-specific differences in tolerance and physiological responses, with implications for microbial community dynamics in marine ecosystems. By employing transcriptomic analysis, we uncover the underlying molecular mechanisms. Ultimately, our study informs the development of sustainable ocean-based climate solutions, emphasizing the importance of considering microbial ecology in environmental management and policy.}, }
@article {pmid42402236, year = {2026}, author = {Na, M and Xiang, M and Wu, Y and Wu, D and Xu, S and Wang, L and Zhou, J and Rousk, J}, title = {Cadmium pollution alters the priming effect of biochar application on soil organic carbon mineralization.}, journal = {Journal of environmental management}, volume = {413}, number = {}, pages = {130426}, doi = {10.1016/j.jenvman.2026.130426}, pmid = {42402236}, issn = {1095-8630}, abstract = {Biochar has high potential to reduce cadmium (Cd) bioavailability in polluted soils. While effective in Cd remediation, biochar amendment can stimulate native soil organic carbon (SOC) mineralization via the priming effect, resulting in soil C release. However, it remains unclear whether Cd pollution alters the impact of biochar application on SOC mineralization, and how microbes modulate biochar-induced priming effect in Cd-polluted soils. To address these questions, a 120-day laboratory experiment was conducted by applying two types of biochar derived from C4 crop residues to C3 paddy soils under Cd pollution (0, 4 and 8 mg kg[-1]). In unpolluted soils, sorghum biochar, with higher C availability and C:nitrogen (N) ratios, triggered stronger positive priming of SOC mineralization than sugarcane biochar. This process was mediated by bacterial groups, where higher N-degrading gene abundances and associated enzyme activities promoted N-mining from soil organic matter (SOM). Low Cd pollution reduced priming responses, resulting in an overall negative priming. This result coincided with increased DOC and mineral N, which mitigated microbial resource demand from SOM. Under high Cd, sorghum biochar induced a positive cumulative priming at the late stage, whereas sugarcane biochar triggered an overall negative priming. This could be because higher labile C in sorghum biochar sufficiently activated microbes to produce enzymes which co-metabolized SOM, a process driven by fungal groups and persistent C-degrading genes. These findings highlight a double-edged sword effect that biochar remediation of highly Cd-polluted soils has the potential to trigger soil C emissions.}, }
@article {pmid42402256, year = {2026}, author = {Ferreira, J and Rediers, H}, title = {Phytophthora cactorum: From Pathogen Biology to Disease Management.}, journal = {Phytopathology}, volume = {}, number = {}, pages = {}, doi = {10.1094/PHYTO-04-26-0120-RVW}, pmid = {42402256}, issn = {0031-949X}, abstract = {Phytophthora cactorum is a versatile plant pathogen with a wide host spectrum causing substantial yield losses in various forest and agricultural systems, the most affected being apple, ginseng, and strawberry. This review synthesizes the current knowledge on the biology and epidemiology of P. cactorum and presents an extensive overview of the available management strategies, including preventive measures, cultural practices, detection tools, chemical and biological control. Beyond compiling existing data, this review also highlights emerging conceptual shifts in our understanding of P. cactorum, particularly the transition from viewing it as a single broadly infective generalist to recognizing the presence of partially specialized lineages with host- and organ-specific adaptations. We further link advances in molecular biology, including effector repertoire characterization, with practical implications for disease management in agricultural and nursery systems. By integrating insights across disciplines, we aim to establish a strong foundation for deciphering the mechanisms underlying pathogenicity and to support the development of more effective and sustainable management strategies.}, }
@article {pmid42403403, year = {2026}, author = {Zhou, J and Zhang, K and Shah, F and Lam, SS and Xie, Z}, title = {Biochar and milk vetch synergistically enhance rice yield and soil fertility via regulating N-cycling in reddish paddy fields.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1839609}, pmid = {42403403}, issn = {1664-462X}, abstract = {INTRODUCTION: Biochar and milk vetch (MV) are known to improve soil fertility and crop yield. However, the effects of the combined application of rice straw biochar (RSB) and MV over multiple years on nitrogen (N) dynamics, microbial ecology, and rice yield remain unclear. This study is to evaluate the synergistic effects of RSB and MV over multiple growing seasons.<br><br>METHODS: A three-year field experiment was conducted with four treatments, N fertilizer alone (CK), N+RSB (B), N+MV (M), and N+RSB+MV (BM), and measured various indicators of soil health and rice yield.<br><br>RESULTS: Soil organic C, total N, inorganic N (NH4 [+] and NO3 [-]), microbial biomass C/N, and enzyme activities (urease, nitrate, and nitrite reductase) were 14%-30%, 12%-25%, 18%-40%, 20%-45%, and 15%-50% higher in the B and M treatments than in the CK; the greatest increases in these parameters (by 14%-89%) were observed in the BM treatment. Microbial diversity (&#x3b1;-diversity of soil microbes) was increased and the expression of N-cycling functional genes (nifH, amoA, narG, nirS/nirK, nosZ) was 9.1%-400% higher in the BM treatment than in the CK. High gene abundances (AOA amoA, AOB amoA, narG, nirS, nirK, and nosZ) were associated with increased N uptake and grain yield. Microbial biomass C and N were key drivers of shifts in microbial communities influencing N-cycling genes. Increased soil C and N availability in the BM treatment stemmed from changes in the expression of microbial genes and enzyme activities enhancing N assimilation and rice yield.<br><br>DISCUSSION: Hence, combining RSB with MV can promote soil fertility, rice productivity and ecological benefits.}, }
@article {pmid42396672, year = {2026}, author = {Flint, HJ}, title = {Combining sequence-based approaches with anaerobic microbiology and modelling to understand gut microbial communities.}, journal = {The Proceedings of the Nutrition Society}, volume = {}, number = {}, pages = {1-29}, doi = {10.1017/S0029665126105072}, pmid = {42396672}, issn = {1475-2719}, abstract = {Gut micro-organisms possess biochemical capabilities that far exceed those of their mammalian hosts, particularly in the ability to gain energy from the breakdown of diet-derived plant material (fibre). This article reviews investigations into gut microbial communities conducted by Harry Flint and his research group. First, extracellular cellulosome and amylosome enzyme complexes were found to mediate the breakdown of plant cell walls and resistant starch by specialised Firmicutes bacteria, both in the human colon and in the rumen. In contrast, Bacteroidetes (Bacteroides, Prevotella spp.) rely on their ability to capture soluble carbohydrates. Human dietary studies examining the impact of fibre sources upon microbiota composition and metabolism identified 'diet-responsive' species. In addition, dominant species of butyrate-producing bacteria, including a subset able to convert lactate to butyrate, were isolated from healthy human volunteers. Most produce butyrate from carbohydrates via butyryl-CoA:acetate CoA-transferase, with uptake of external acetate, while lactate conversion is associated with a highly inducible gene cluster (lct). In pH-controlled chemostat studies, mildly acid pH depressed growth of propionate-producing Bacteroidetes, but favoured butyrate production by Firmicutes. This may explain why % butyrate among SCFA increases with total faecal SCFA concentration in human studies. Although lactate is normally consumed by lactate-utilising bacteria, destabilisation of the microbial community associated with lactate accumulation can result in radically altered microbiota and metabolite profiles. A theoretical model based on microbial functional groups (MFG) was developed to better understand community dynamics. Consequences for nutritional research of our expanding knowledge of the microbial ecology of the human gut are considered.}, }
@article {pmid42397708, year = {2026}, author = {Marinos, G and Moors, KA and Schlicht, K and Rühlemann, M and Waschina, S and Lieb, W and Franke, A and Laudes, M and Groussin, M and Poyet, M and Kaleta, C and Kadibalban, AS}, title = {Genome-scale metabolic models predict diet- and lifestyle-driven shifts of ecological interactions in the gut microbiome.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2694811}, doi = {10.1080/19490976.2026.2694811}, pmid = {42397708}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Diet ; *Life Style ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Microbial Interactions ; Models, Biological ; }, abstract = {Microbiomes and their host environments form complex, interconnected ecosystems. The microbial species within a microbiome, on the one hand, compete for resources, while on the other hand, they exchange vital metabolites to support their survival. These interactions are influenced by the microbial genetic repertoire, environmental conditions, and availability of nutrients. We developed EcoGS (http://www.github.com/KaletaLab/EcoGS), a metabolic modeling tool designed to predict the ecological interactions between pairs of microbes. Applying EcoGS to the microbiomes of two distinct human cohorts revealed a shift from collaborative to exploitative ecological interactions associated with increased dietary intake of simple sugars (glucose and fructose) in diabetic individuals and those living industrialized lifestyles. On the other hand, the consumption of cobalamin (vitamin B12), phylloquinone (vitamin K1), and biotin (vitamin B7), among other compounds, was associated with increased collaboration in the gut microbiome. We conclude that the abundance of simple sugars as an energy source reduces the necessity for microbes to cooperate, thereby increasing competition and hostility among microbiome members. Moreover, our study proposes multiple compounds, such as urate, deoxyadenosine, deoxyguanosine, and hypoxanthine, for in vitro validation tests as dietary interventions that have the potential to restore the ecological balance within the community. EcoGS serves as a valuable tool for exploring microbiome dynamics and their connections to environmental changes and disease.}, }
@article {pmid42397960, year = {2026}, author = {J Bruggeman, F and Paez-Watson, T and Teusink, B and Kleerebezem, R}, title = {Stoichiometric analysis of microbial communities links function, structure, and biomass carrying capacity.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag133}, pmid = {42397960}, issn = {1751-7370}, abstract = {Microbial communities carry out important ecological functions. Their activities emerge from interactions between species, often potentiated by metabolic traits. We lack a quantitative understanding of how these traits shape community properties. Here, we present theory for microbial communities, leveraging concepts from quantitative microbial physiology. We focus on how steady-state metabolic exchanges between species determine their fractional abundances, given their biomass and byproduct yields on nutrients. We start by deriving formal conditions for the steady states of communities of microbes that grow, die and cross-feed metabolites. We describe the metabolic stoichiometry of nutrient uptake and the formation of biomass and byproducts for each species in terms of charge- and chemical-element balanced reactions (macrochemical reactions). Byproducts function as nutrients for other species. Next, we express the relative abundances of species (living and dead), the net metabolic conversion of a community, and the biomass carrying capacity in terms of the metabolic stoichiometry, growth rates and death rates of the species. We show how niche creation can emerge from stoichiometric imbalances in cross-feeding communities. Finally, we discuss how relative species abundances depend on the ATP stoichiometries of intracellular metabolism.}, }
@article {pmid42396632, year = {2026}, author = {Gandhi, RR and Khandeparker, RDS and Nikhita, PR and Chudasama, K}, title = {Mangrove health shapes lignocellulolytic bacterial communities.}, journal = {Letters in applied microbiology}, volume = {79}, number = {7}, pages = {}, doi = {10.1093/lambio/ovag049}, pmid = {42396632}, issn = {1472-765X}, support = {//Council for Scientific and Industrial Research (CSIR)/ ; }, mesh = {*Lignin/metabolism ; *Bacteria/enzymology/classification/isolation &amp; purification/genetics/metabolism ; India ; *Wetlands ; Temperature ; *Geologic Sediments/microbiology ; Hydrogen-Ion Concentration ; }, abstract = {The process of lignocellulosic biofuel production needs enzymes that are resistant to high temperatures and low pH. The mangrove sediments, which are typified by variable conditions, can contain bacteria that synthesize intrinsically steady enzymes. We selected 193 bacterial isolates of 12 mangrove sites in Goa, India and tested them to produce lignocellulolytic enzymes (cellulase, laccase, xylanase, xylose isomerase) under the conditions of neutral (37°C, pH 7), acidic (37°C, pH 5), thermophilic (50°C, pH 7), and combined stress (50°C, pH 5). Bacillus and Vibrio dominated, with 22 genera identified. There were no significant differences in alpha diversity following Benjamini-Hochberg FDR correction (all P_adj = 1.00, Cohen d < 0.5) but significant compositional differentiation in beta diversity (PERMANOVA: R[2] = 0.243, P = 0.017). Salinity (R[2] = 0.903, P_adj = 0.003) and temperature (R[2] = 0.722, P_adj = 0.006) were major structuring factors. Site-type differentiation was the most significant factor in xylanase-producing communities (R[2] = 0.272, P = 0.013). Although there was limited replication of dead sites (n = 3), the results confirmed that candidates undergo biochemical characterization and that ecosystem degradation does not decrease diversity but alters community composition.}, }
@article {pmid42389176, year = {2026}, author = {Ubani, O and Ngole-Jeme, VM}, title = {Long-read whole-genome sequencing dataset of microbial communities from industrially and municipally impacted freshwater wetlands in South Africa.}, journal = {Data in brief}, volume = {67}, number = {}, pages = {112987}, pmid = {42389176}, issn = {2352-3409}, abstract = {This article describes a long-read whole-genome shotgun sequencing dataset generated from microbial communities inhabiting industrially and municipally impacted freshwater wetlands in South Africa. Surface water samples were collected from five strategically selected sites exposed to distinct anthropogenic pressures, including industrial effluent discharge, sewage overflow, greywater inputs, informal settlement runoff, and landfill leachate to generate a unique microbial genomic data. Environmental DNA was extracted and sequenced using the PacBio Sequel IIe platform, producing high-fidelity long reads suitable for improved assembly contiguity and functional reconstruction. Post-quality control processing yielded 4.9 × 10[4] to 1.6 × 10[5] HiFi reads per sample, corresponding to 0.34-1.02 Gb of high-accuracy sequence data per site. Long-read assemblies generated between 16,080 and 54,670 predicted protein-coding genes per sample. Taxonomic classification using Kaiju assigned 94.1-99.8% of assembled sequences to reference taxa. Domain-level profiles were exclusively bacterial dominated, with few rare or undetected (0.000-0.001%) archaeal, eukaryotic, or viral representation. Phylum-level composition was strongly dominated by Pseudomonadota (83-95%), followed by Bacillota (3-10%) and Bacteroidota (1-14%), with Actinomycetota consistently below 1%. Functional annotation using the DRAM pipeline identified 9390-31,251 KEGG orthologs, 969-3039 MEROPS peptidases, 13,454-45,103 Pfam domains, and 202-776 carbohydrate-active enzyme (CAZy) genes across assemblies. Distilled metabolic modules indicated the presence of near‑complete electron transport chain complexes (I-V), denitrification-associated pathways, sulfur oxidation and dissimilatory reduction genes, and diverse carbohydrate degradation functions; methanogenesis‑associated modules were not detected among the annotated metabolic pathways recovered in this dataset. The dataset provides genomic coverage of urban wetland microbiomes shaped by mixed industrial and municipal stressors and represents one of the few long-read metagenomic resources available for southern African freshwater wetlands. The availability of assembled contigs, gene annotations, metabolic reconstructions, enables reuse for comparative environmental genomics, biogeochemical modelling, bioremediation gene discovery, resistome screening, and microbial ecology investigations. This high-fidelity long-read sequencing resource expands opportunities for structural and functional analyses of anthropogenically influenced wetland ecosystems and supports future research in environmental biotechnology, bioinformatics-driven ecosystem monitoring, and microbial adaptation to urban pollution gradients.}, }
@article {pmid42389292, year = {2026}, author = {Wang, Y and Liu, X and Zhang, Z and Jing, R and Zhao, X and Han, W and Huang, C and Yang, Q}, title = {In-sewer microplastics drive microbial metabolic shifts toward enhanced methanogenesis.}, journal = {Environmental science and ecotechnology}, volume = {32}, number = {}, pages = {100726}, pmid = {42389292}, issn = {2666-4984}, abstract = {Microplastics (MPs) in sewer systems can be transported extensively before entering wastewater treatment plants. Sewer systems harbor complex microbial communities under low-oxygen, sulfide-rich conditions that drive key biogeochemical cycles. These conditions drive microplastic aging, whereas these particles concurrently perturb sewer microbial ecology and metabolic functions. However, the underlying mechanisms of in-sewer microplastic aging and their subsequent impacts on sewer microbiomes remain unclear. Here we show that hydroxyl radicals preferentially attack ester bonds (C-O) in polyethylene terephthalate (PET) and polybutylene adipate terephthalate (PBAT) MPs, increasing surface roughness, reducing particle size, promoting surface oxidation, and ultimately inducing polymer chain scission. Exposure to PET and PBAT MPs at 30-500 particles L[-1] intensified oxidative stress, disrupted membrane integrity and permeability, impaired microbial activity, and suppressed sulfide production in a dose-dependent manner. These disruptions coincided with weakened microbial co-occurrence networks and a shift from stochastic toward deterministic community assembly. High doses of PET and PBAT MPs reduced hydrolytic/fermentative bacteria and sulfate-reducing bacteria by up to 63.4% and 49.7%, respectively, while enriching hydrogen-producing acetogenic bacteria and methanogenic archaea by 48.4-67.0%, consistent with reduced sulfidogenic potential and enhanced methanogenic potential. Changes in genes related to antioxidant defense, SOS response, quorum sensing (e.g., sodA, katG, lexA, and luxS), and redox signaling suggested potential mechanisms of microbial metabolic perturbations aggravated by PET and PBAT MPs. Our results indicate that sewer systems are not passive conduits but active reactors that promote MP aging, and that MPs reshape microbial functions. Microplastic control may therefore help reduce downstream particle pollution and limit perturbations to urban sewage biogeochemistry.}, }
@article {pmid42390568, year = {2026}, author = {Pepori, AL and Berto, H and Gionni, A and Luchi, N and Pecori, F and Santini, A}, title = {Exploring Metabolic Interaction between Ophiostoma novo-ulmi and Geosmithia spp.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02822-2}, pmid = {42390568}, issn = {1432-184X}, abstract = {Dutch elm disease (DED), caused by the invasive vascular pathogen Ophiostoma novo-ulmi, is one of the most devastating pandemics affecting elms. Within beetle galleries and on elm bark beetle vectors, O. novo-ulmi co-occurs with fungi of the genus Geosmithia, yet the functional significance of this association remains poorly understood. This study investigates metabolic interactions between O. novo-ulmi and Geosmithia spp. using in vitro dual-culture experiments and phenotype microarray analysis to elucidate ecological mechanisms potentially influencing disease development and vector ecology. Dual-culture assays on dH2O agar revealed that O. novo-ulmi subsp. novo-ulmi exhibited significantly enhanced radial growth rates when cultured in proximity to Geosmithia isolates. Phenotypic analysis revealed distinct metabolic strategies: O. novo-ulmi subsp. novo-ulmi utilised substrates within 12-24 h and preferred polyols and simple carbohydrates, while G. pumila adopted a progressive colonization strategy, ultimately utilising 92 substrates in 90 h and demonstrating greater utilisation of nitrogen-enriched substrates, nucleosides and complex organic acids. Co-culture revealed utilization of adenosine and nitrogen-rich compounds, but antagonistic interactions for polyols and amino sugars. Niche overlap analysis showed asymmetric resource partitioning: O. novo-ulmi subsp. novo-ulmi utilized 98% of G. pumila's substrates versus 81% reciprocal overlap, while fungal competitiveness analysis indicated G. pumila superiority. The distinct metabolic strategies and complementary patterns of substrate utilisation suggest niche construction and the functional partitioning of resources. These findings provide evidence supporting the hypothesis of a functional association within the DED pathosystem. The results highlight the ecological importance of microbial community complexity in pathogenic interactions and suggest that understanding these multitrophic relationships is essential for the development of effective disease management strategies.}, }
@article {pmid42390575, year = {2026}, author = {Cukier, S and Gawor, J and Grzesiak, J}, title = {Gut Microbiota and Feeding Patterns of the Antarctic Fairy Shrimp (Branchinecta gaini Daday, 1910): A Metabarcoding Perspective.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02820-4}, pmid = {42390575}, issn = {1432-184X}, abstract = {Understanding how feeding ecology and environmental conditions shape gut microbiota is essential for interpreting host-microbe interactions in extreme environments. Here, we investigated the diet and gut-associated bacterial communities of the Antarctic fairy shrimp Branchinecta gaini across multiple postglacial freshwater ponds on King George Island. We combined microscopic gut content analysis with 18 S and 16 S rRNA gene metabarcoding and distinguished between gut content and gut tract-associated bacterial fractions in pooled, pond-level samples to assess the relative roles of diet, host filtering, and environmental context in structuring gut-associated communities. Our results reveal pronounced dietary flexibility of B. gaini, with strong site-specific differences in consumed eukaryotic taxa reflecting local resource availability. This trophic variability was mirrored by highly variable gut-associated bacterial communities, characterized by low taxonomic overlap among ponds and the absence of a stable core microbiota at the pooled sample level. Although bacterial assemblages differed between gut contents and gut tract, consistent at the composite-sample scale, this pattern suggests limited evidence for strong host filtering. Gut-associated communities retained pond-specific signatures, indicating a dominant role of environmental sourcing. Environmental drivers influenced different aspects of gut microbiome organization: hydrological connectivity and associated conductivity gradients were linked to shifts in bacterial community composition, whereas water temperature showed a non-linear association with bacterial alpha diversity but not with overall community structure. Water pH showed no detectable effect on either metric. Together, these findings indicate that gut-associated bacterial communities of B. gaini, as captured by pooled samples, largely reflect environmentally acquired assemblages shaped by opportunistic feeding and local environmental filtering. This ecological flexibility may represent a key strategy enabling persistence of B. gaini across highly heterogeneous Antarctic freshwater ecosystems.}, }
@article {pmid42391470, year = {2026}, author = {Plominsky, AM and Peoples, LM and Norenberg, M and Ramirez-Flandes, S and Podell, S and Mullane, KK and Casagrande, D and Roman, C and Pockalny, R and Smith, DC and Belser, C and Poulain, J and Allen, EE and Glud, RN and Ulloa, O and Barber, N and D'Hondt, S and Bartlett, DH}, title = {Minimising decompression and warming during deep seawater collection increases abundance and activity of autochthonous bacteria and archaea.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag064}, pmid = {42391470}, issn = {1751-7370}, abstract = {The deep ocean hosts autochthonous pressure-adapted microorganisms that are unique to this environment, as well as allochthonous pressure-sensitive members transported from shallow depths by vertical advection and particle-sinking. However, conventional sampling instruments decompress and warm deep-sea samples during retrieval, potentially altering microbial properties when studied ex situ. Here, we assess this potential sampling bias by comparing seawater microbial communities collected with or without measures aimed at minimising pressure and temperature effects. When compared to samples collected under pressurised conditions, conventional sampling (using Niskin bottles) was found to affect prokaryotic cells retrieved by reducing their total numbers, diminishing protein synthesis activity (>10%), and also causing overall shifts in the community composition. The most significant compositional change was a > 20% decrease in metagenomic archaeal representation (TACK-group/Thaumarchaeota/Nitrososphaerota). Deep-sea bacterial groups had mixed responses to preserving pressure during retrieval, with some groups exhibiting higher representation when samples were maintained pressurised (e.g., members of the family Pelagibacteraceae, unclassified Thiotricales, Thioglobaceae, and Chitinophagaceae), whereas others increased their representation when decompressed (e.g., Burkholderiaceae, Comamonadaceae, and Oxalobacteraceae). This study reveals the existence of bias introduced by the complete decompression of samples retrieved with traditional instrumentation, as well as a decrease in overall bacterial activity when samples are completely decompressed during retrieval. Additionally, incubations lasting for >24 h were shown to transform the original prokaryotic community composition. Precautions addressing these effects are necessary to enhance the reliability of ex situ measurements and improve our understanding of deep-sea microbial ecology and biogeochemistry.}, }
@article {pmid42393338, year = {2026}, author = {Cornell, CR and Olatinwo, RO and Kozhar, O and Wharton, K and Stewart, JE}, title = {Emerging Threats in Southern U.S. Pine Plantations: Temporal Dynamics of Fungal Communities and the Impact of Lecanosticta acicola.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02825-z}, pmid = {42393338}, issn = {1432-184X}, abstract = {Globally, pine forest ecosystems are under increased threat of foliar fungal pathogens. This includes brown spot needle blight (BSNB), caused by Lecanosticta acicola. High disease severity of BSNB has been observed in loblolly pine plantations across the Southeastern U.S., causing substantial declines in productivity. Because foliar disease outcomes depend on phyllosphere community interactions, shifts in community composition under climate variation may influence outbreak potential of L. acicola. To investigate these interactions, fungal communities in first- and second-year symptomatic and asymptomatic needle tissue were examined over two years across six loblolly pine plantations in central Louisiana. L. acicola was consistently enriched in symptomatic needles and emerged as a strong indicator of disease, including increasing crown dieback, particularly in first-year needles. Disease progression was associated with reduced fungal diversity and pronounced shifts in community composition, consistent with microbiome dysbiosis. Additional fungi, including Lophodermium and Soleella, were enriched in symptomatic needles, likely representing opportunistic associates with a potential role in disease. There were distinct differences in the relationship with climate variables for symptomatic and asymptomatic communities. Symptomatic communities were associated with higher humidity, higher minimum temperatures, and reduced solar radiation, whereas asymptomatic communities were correlated with warmer, drier conditions. Our findings demonstrate that BSNB severity reflects both L. acicola infection and broader needle fungal community disruption, with first-year needles being especially vulnerable. These results underscore the need to integrate microbial community dynamics and climate into disease monitoring and management, as increasing humidity, warmer nights, and more variable precipitation likely elevate fungal pathogen risk.}, }
@article {pmid42395019, year = {2026}, author = {Li, X and Zhao, Y and Liu, N and Zhang, Y and Liu, R and Shan, W and Zhang, J and Chen, T}, title = {Panax ginseng as a microbial ecosystem modulator: implications for systemic health via the gut-organ axes.}, journal = {Journal of ginseng research}, volume = {50}, number = {4}, pages = {101059}, pmid = {42395019}, issn = {1226-8453}, abstract = {Panax ginseng C.A. Meyer, a renowned medicinal herb, exerts many of its systemic effects through intricate interactions with the gut microbiota, a relationship that also addresses the challenge of its own limited oral bioavailability. This review comprehensively examines the role of ginseng and its bioactive constituents in modulating gut microbiota and their subsequent influence on host health through key gut-organ axes. Based on an in-depth analysis of literature, we summarize how ginseng intervention is associated with a modulated gut microbial ecology-characterized by enriched beneficial taxa and suppressed pathogens-and is further linked to enhanced barrier integrity, regulated microbial metabolites, and reduced inflammation and oxidative stress. These mechanisms underlie its protective effects across multiple organ systems, including the gut-brain, gut-liver, gut-lung, gut-heart, and gut-kidney axes, ameliorating conditions such as cognitive decline, hepatic inflammation, pulmonary fibrosis, atherosclerosis, and renal injury. Clinical evidence further associates ginseng with improved metabolic and cognitive parameters correlated to microbial changes. We conclude that the therapeutic activity of ginseng appears to involve, and is likely modulated by, its prebiotic-like influence on the gut microbiota. However, the degree to which its efficacy is microbiota-dependent varies across different organ systems, as established by current evidence. Further mechanistic and clinical studies, particularly those employing causal models, are essential to definitively validate its potential in treating chronic diseases via microbiota-based strategies.}, }
@article {pmid42396625, year = {2026}, author = {San Román, AX and Chen, G and Ronda, K and Muratore, T and Knorr, MA and Frey, SD and Wang, J and Simpson, AJ and Simpson, MJ}, title = {High-Resolution Molecular Analyses Reveal Non-additive Impacts of Chronic Warming and Nitrogen Addition on Soil-Derived Dissolved Organic Matter.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c04800}, pmid = {42396625}, issn = {1520-5851}, abstract = {Dissolved organic matter (DOM) plays a central role in soil carbon (C) cycling as the most mobile and reactive C fraction in forests, regulating the microbial metabolism, nutrient availability, and C export. However, molecular-level DOM responses to environmental stressors such as warming and nitrogen (N) deposition remain poorly constrained, particularly under their combined influences. Thus, we investigated how 14 years of soil warming, N-addition, and combined heat + N influence soil-derived DOM quantity and chemistry. Using solution-state NMR spectroscopy and Fourier transform ion cyclotron resonance mass spectrometry, we resolved DOM composition across molecular size, biochemical class, mobility, and oxidation state. While the DOM quantity remained unchanged, warming enhanced microbial processing and oxidative transformation, yielding DOM enriched in oxidized, structurally complex compounds, whereas N-addition suppressed decomposition, limiting the release of plant-derived biopolymers and shifting DOM toward more microbial-derived constituents. Heat + N produced the most compositionally diverse DOM, with molecular shifts more closely resembling warming-induced responses, indicating that temperature-driven decomposition dominates under interacting stressors. These results demonstrate that chronic warming and N addition influence C cycling through distinct, yet nonadditive molecular pathways not captured by single-factor studies. This underscores the necessity of multifactor experiments to accurately capture the current and future ecosystem responses to interacting environmental stressors.}, }
@article {pmid42379814, year = {2026}, author = {Eilers, T and Van Rillaer, T and Wittouck, S and Tuyaerts, I and Michiels, K and Victor, M and Gehrmann, T and Bron, PA and Van Beeck, W and Lebeer, S}, title = {From diversity to dominance: how salt and CO2 shape LAB-dominated ecosystems in vegetable fermentations.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0357825}, doi = {10.1128/spectrum.03578-25}, pmid = {42379814}, issn = {2165-0497}, abstract = {UNLABELLED: Research on microbial ecosystems is often challenging due to the high diversity of microbial taxa present and the complexity of controlling environmental variables. Fermented foods offer simpler and more reproducible model ecosystems in which both community composition and environmental factors can be more precisely controlled and manipulated. In this study, we focused on fermented vegetables, which are typically dominated by lactic acid bacteria (LAB). However, it remains unclear why LAB consistently drive the spontaneous fermentation of vegetables and how factors such as vegetable substrates, salt addition, and carbon dioxide levels shape microbial community dynamics. We characterized the temporal microbial succession in standardized spontaneous fermentations of 11 different vegetables (including beetroot, bell pepper, cabbage, carrot, cucumber, fennel, green asparagus, leek, parsnip, sunroot, and tomato), revealing a robust and recurrent dominance of Leuconostoc and other LAB across substrates. Additionally, we investigated the impact of varying salt concentrations and found that lower salt levels delayed the establishment of the typically LAB-dominated community, while promoting a higher abundance of Weissella and multiple Enterobacterales taxa. Notably, these salt reduction-induced effects were mitigated by CO2 injection, which reduced Enterobacterales levels and increased the overall abundance of Lactobacillales. Together, these findings demonstrate how targeted manipulation of environmental parameters, such as salinity and gas composition, can be used to uncover ecological principles governing microbial succession and community assembly in reproducible fermentation-based model ecosystems.<br><br>IMPORTANCE: Understanding the ecological principles that shape microbial community assembly is essential for advancing our knowledge of microbial ecosystems. Fermented vegetables, which are increasingly popular among the general population, provide a tractable and reproducible model system to study microbial succession. By systematically manipulating variables such as vegetable substrate, salinity, and gas composition, we identified the effects of these factors on microbial dynamics throughout the fermentation. These insights not only enhance our understanding of the microbial ecology of these man-made food systems but also suggest directions for novel strategies to optimize fermentation processes for the production of faster, safer, and more flavorful foods.}, }
@article {pmid42383736, year = {2026}, author = {Zhang, C and Hammer, BK}, title = {Microbial Primer: The T6SS, a deadly bacterial harpoon.}, journal = {Microbiology (Reading, England)}, volume = {172}, number = {7}, pages = {}, doi = {10.1099/mic.0.001721}, pmid = {42383736}, issn = {1465-2080}, }
@article {pmid42384095, year = {2026}, author = {Hernández-Zulueta, J and Raygoza-Alcantar, LN and Avila-Castro, E and Rodríguez-Zaragoza, FA and Cáceres, I and Delgado-Hernández, JI and Bonilla-Urzúa, MG}, title = {Biotechnological potential of marine invertebrate-associated bacteria with antibacterial activity against aquaculture and human pathogens.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {57}, number = {1}, pages = {}, pmid = {42384095}, issn = {1678-4405}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology/metabolism ; *Bacteria/isolation &amp; purification/classification/metabolism/genetics ; Aquaculture ; Humans ; *Aquatic Organisms/microbiology ; Biotechnology ; Microbial Sensitivity Tests ; Phylogeny ; *Anthozoa/microbiology ; Sea Urchins/microbiology ; }, abstract = {Marine invertebrates harbor diverse bacterial communities that contribute to host defense by producing antibacterial compounds. In this study, 258 cultivable bacterial isolates from corals (Porites panamensis, P. lobata), the sea urchin Echinometra vanbrunti, and the ctenophore Mnemiopsis leidyi were screened against aquaculture and human pathogens. 14% (37 isolates) exhibited antibacterial activity, predominantly from E. vanbrunti and M. leidyi. Multiple assays revealed strong, broad-spectrum inhibition, particularly against aquaculture pathogens such as Listonella anguillarum, Photobacterium damselae, and Vibrio parahaemolyticus, whereas human pathogens showed limited sensitivity. Notably, isolates MT26 and MT43 displayed the widest inhibitory spectra, and EV78 and MM7 demonstrated high inhibition rates in growth assays. Taxonomic analysis showed that Bacillus was the dominant genus (65%), followed by Vibrio and Pseudoalteromonas. These findings highlight marine invertebrate-associated bacteria as promising sources of bioactive compounds with potential applications in aquaculture and biotechnology.}, }
@article {pmid42384698, year = {2026}, author = {Wang, J and Ai, C and Tiedje, JM and Ge, Y}, title = {A molecular timescale for evolution of cobamide biosynthesis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {27}, pages = {e2610446123}, doi = {10.1073/pnas.2610446123}, pmid = {42384698}, issn = {1091-6490}, support = {32322076//MOST | National Natural Science Foundation of China (NSFC)/ ; Y2026QC22//Central Public-interest Scientific Institution Basal Research Fund/ ; 2023YFD1700803//MOST | National Key Research and Development Program of China (NKPs)/ ; DBI-1759892//Us NSF grant DBI-1759892 computational/ ; 42307162//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Cobamides/biosynthesis/genetics ; *Evolution, Molecular ; Phylogeny ; Bayes Theorem ; }, abstract = {Cobamides are essential nutrients for most organisms but are only biosynthesized by a limited number of taxa through aerobic and anaerobic pathways. Although the origin of these widespread shared cofactors changed ecosystems and the metabolisms of living organisms, little evolutionary information is available about the biosynthetic genes and the producers. Here, we established a timeframe for the emergence of cobamide biosynthesis genes and producers, using a series of Bayesian molecular clock analyses combined with phylogenetic reconciliation. We revealed the partial producers of tetrapyrrole precursor and corrin ring were earlier than the oldest cobamide producer, suggesting the possibility that cobamide-like compounds may have existed before the emergence of their de novo producers. We also found that the anaerobic de novo producers and corrin ring producers emerged first (Pelobacter, around 2458 Mya), and that the Great Oxidation Event postdated emergence of aerobic producers (Kribbella, around 1784 Mya). These findings reveal the chronology of cobamide biosynthesis, which greatly changed global ecological frameworks and resulted in the current biosphere, and can guide the exploration of cross-feeding and the origin of diverse organisms on the planet.}, }
@article {pmid42385456, year = {2026}, author = {Hodžić, A and Cizek, V and Kunert, M and Berry, D and Collingro, A}, title = {Qualitative profiling of the gut-specific chlamydial population in Ixodes ricinus ticks.}, journal = {Ticks and tick-borne diseases}, volume = {17}, number = {4}, pages = {102679}, doi = {10.1016/j.ttbdis.2026.102679}, pmid = {42385456}, issn = {1877-9603}, abstract = {Members of the phylum Chlamydiota are obligate intracellular bacteria increasingly recognized across a wide range of arthropod hosts, including ticks. In this study, we investigated the diversity and distribution of chlamydiae in Ixodes ricinus ticks and their potential association with Lyme borreliosis spirochetes. A total of 250 questing nymphal and female I. ricinus ticks were collected from three recreational sites in Vienna, Austria. Individual tick guts were screened for chlamydiae using pan-Chlamydiota PCR assays targeting the 16S rRNA gene, followed by sequencing for taxonomic identification. The presence and abundance of Borrelia burgdorferi sensu lato were quantified by specific qPCR to evaluate potential co-occurrence patterns. Chlamydiota DNA was detected in ticks from all investigated areas, with prevalence varying according to geography and developmental stage. Phylogenetic analyzes revealed high chlamydial diversity within the gut microbiome, predominantly comprising members of the metagenomic family MCF-D, followed by Parachlamydiaceae, Endochlamydiaceae, and Parasimkaniaceae. A positive, albeit not statistically significant, association between Chlamydiota and Borrelia was also observed. These findings indicate that the I. ricinus gut microbiome harbours a diverse assemblage of chlamydiae, suggesting potential ecological and functional relevance. Overall, our study highlights the importance of tissue-specific, single-tick analyzes for elucidating microbiome complexity and advances current understanding of Chlamydiota diversity in the tick vector. Further experimental and multi-omics studies are warranted to elucidate the biological roles of these bacteria in tick physiology and pathogen infection dynamics.}, }
@article {pmid42386020, year = {2026}, author = {Fousekis, F and Lianos, GD and Stavropoulou, E and Patrikiou, E and Vradelis, S and Cassimos, D and Tsigalou, C}, title = {Decoding gut microbiome alterations in celiac disease: Implications for pathogenesis and treatment.}, journal = {Autoimmunity reviews}, volume = {25}, number = {9}, pages = {104127}, doi = {10.1016/j.autrev.2026.104127}, pmid = {42386020}, issn = {1873-0183}, abstract = {Celiac disease (CD) is a chronic immune-mediated disorder triggered by dietary gluten in genetically predisposed individuals and characterized by intestinal inflammation, epithelial damage, and loss of immune tolerance. While a strict lifelong gluten-free diet (GFD) remains the cornerstone of treatment, accumulating evidence indicates that it does not consistently restore gut microbiome composition or function, and many patients experience persistent symptoms despite good dietary adherence. The gut microbiome has emerged as a key modulator of immune homeostasis, intestinal barrier integrity, and gluten metabolism, implicating microbial dysbiosis in both the initiation and progression of CD. Alterations in microbial composition and metabolic activity have been documented in genetically at-risk individuals prior to disease onset, in patients with active disease, and in treated patients on a GFD, suggesting a potential role of the microbiome in early pathogenesis, disease heterogeneity, and symptom persistence. In this review, we summarize current evidence on the bidirectional interactions between the gut microbiome and CD, including microbial-mediated gluten degradation, microbiome signatures associated with genetic susceptibility and disease activity, and the effects of a GFD on microbial ecology. We further discuss emerging strategies aimed at modulating the gut microbiome, including probiotics, prebiotics, postbiotics and precision probiotics, as potential adjunctive therapeutic approaches. A better understanding of microbiome-host interactions in CD may support the development of personalized therapeutic strategies that go beyond gluten avoidance and aim to restore microbial balance and immune regulation, thereby improving long-term outcomes.}, }
@article {pmid42387523, year = {2026}, author = {de Amorim, JE and Ferronatto, JA and Polydoro, LS and Batista, CF and Toledo-Silva, B and Costa, LBSBC and Heinemann, MB and Blagitz, MG and Della Libera, AMMP}, title = {Ovine milk-derived non- aureus Staphylococcus and Mammaliicoccus spp. (NASM) isolates and their cell-free supernatants inhibit major mastitis pathogens in vitro.}, journal = {BMC veterinary research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12917-026-05683-6}, pmid = {42387523}, issn = {1746-6148}, abstract = {BACKGROUND: Innovative strategies to control ovine mastitis pathogens and reduce dependence on conventional antimicrobials are globally essential for One Health and sustainable livestock production. Non-aureus Staphylococci and Mammaliicoccus spp. (NASM) are commonly isolated in cases of ovine mastitis and may influence the microbial ecology of the mammary gland. This study evaluated the inhibitory potential of these microorganisms against key ovine mastitis pathogens, Staphylococcus aureus and Escherichia coli, through two experimental approaches. In experiment 1, 30 isolates of NASM were screened for their inhibitory activity using the cross-streaking method, assessing total, partial, or absent inhibition of S. aureus and E. coli. In experiment 2, the antimicrobial effect of cell-free supernatants from non-aureus Staphylococcus cultures (NAS CFS) cultures was tested at varying concentrations (12.5%, 25%, and 50%) under different treatments (heat treatment, pH adjustment, combined heat treatment + pH adjustment, and control). Pathogen growth was quantified by colony forming unit (CFU)/mL counts after incubation, and data were analyzed via ANOVA followed by Tukey's test.<br><br>RESULTS: Results from experiment 1 revealed that 36.7% of the isolates partially or totally inhibited S. aureus, while 20% partially inhibited E. coli. In experiment 2, the combined heat treatment and pH adjustment at a concentration of 12.5% significantly reduced S. aureus and E. coli CFU/mL when tested, for example, in the presence of S. xylosus (p < 0.01 for both cases).Results from experiment 1 revealed that 36.7% of the isolates partially or totally inhibited S. aureus, while 20% partially inhibited E. coli. In experiment 2, the combined heat treatment and pH adjustment at a concentration of 12.5% significantly reduced S. aureus and E. coli CFU/mL when tested, for example, in the presence of S. xylosus (p < 0.01 for both cases).<br><br>CONCLUSIONS: These findings highlight the preliminary potential of antimicrobial compounds derived from NASM for ovine mastitis control, while underscoring the need for further studies to confirm their applicability as sustainable strategies alongside conventional approaches.}, }
@article {pmid42388110, year = {2026}, author = {Gross, M and Koll, U and Sonntag, B and Stoeck, T}, title = {From Gene Copies to Cell Numbers: Advancing Quantitative Approaches in Protistan Ecology Using Digital PCR.}, journal = {Molecular ecology resources}, volume = {26}, number = {5}, pages = {e70177}, doi = {10.1111/1755-0998.70177}, pmid = {42388110}, issn = {1755-0998}, support = {STO 414/13-3//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Polymerase Chain Reaction/methods ; *Gene Dosage ; *Ciliophora/genetics/classification ; *Ecology/methods ; Fresh Water/parasitology ; *Oligohymenophorea/genetics ; }, abstract = {Quantifying abundances of unicellular eukaryotes (protists) remains a central challenge in microbial ecology, as methodological differences can strongly influence abundance estimates and ecological interpretation. Although molecular tools have thus far greatly improved our understanding of protists, high rRNA gene copy numbers limit quantitative inferences. Digital PCR (dPCR) has emerged as a promising tool for absolute quantification, yet its application for unicellular eukaryotes and its comparability to established cell-based methods remain insufficiently explored. Here, we develop species-specific dPCR assays for two important freshwater ciliates (Urotricha castalia and Urotricha pseudofurcata) and establish gene copy number correction factors to enable highly accurate quantitative abundance estimates. We assess assay performance using controlled laboratory experiments and apply the approach to environmental samples, directly benchmarking dPCR against catalyzed reporter deposition-FISH (CARD-FISH). Under controlled conditions, dPCR and CARD-FISH yielded comparable accuracy, with dPCR showing superior precision. In field applications, method-dependent differences emerged, reflecting both methodological constraints and biological variability. Notably, dPCR provided an overall higher sensitivity, enabling robust detection of low-abundance taxa. Our results highlight dPCR as a scalable and sensitive approach that, when combined with appropriate correction strategies, represents a significant step towards more reliable molecular quantification of protists. At the same time, differences between methods underscore the value of integrating molecular and microscopy-based approaches. We propose that combining dPCR with tools such as CARD-FISH can offer complementary insights into protist population dynamics. Such integrative frameworks provide a powerful path forward for improving abundance estimates and advancing quantitative microbial ecology.}, }
@article {pmid42361920, year = {2026}, author = {Petrognani, C and Mariën, Q and Vos, L and Oijen, MV and Boon, N and Ganigué, R}, title = {CO2 availability as process tool to enhance isobutyric acid production in methanol fermentation by Clostridium luticellarii.}, journal = {Bioresource technology}, volume = {459}, number = {}, pages = {135255}, doi = {10.1016/j.biortech.2026.135255}, pmid = {42361920}, issn = {1873-2976}, abstract = {The bioconversion of CO2‑derived methanol into higher‑value chemicals offers an attractive route for hybrid catalytic-biotechnological carbon capture and utilization (CCU). Clostridium luticellarii is one of the few acetogens able to produce isobutyric acid. However, operational and metabolic factors driving its production are poorly understood. This work investigates how CO2 availability shapes the product spectrum of C. luticellarii during methylotrophic growth and assesses whether CO2 supply can be used as a process lever to promote isobutyric acid formation. Batch experiments with varying initial bicarbonate concentrations revealed that conditions leading to CO2 limitation (i.e., DIC depletion at ≤ 30 mM NaHCO3) redirected carbon and electron fluxes away from acetic acid toward butyric and isobutyric acids, with the latter accounting for up to 41% of total products. This metabolic switch was not observed when CO2 was in excess (>45 mM). High acetic acid supplementation (100 mM) triggered isobutyric acid production even while CO2 was still available, indicating a combined regulation of dissolved inorganic carbon (DIC) and acetic acid availability. Net acetic acid consumption took place in all isobutyric acid-producing experiments. These observations were reproduced in 3-L bioreactors and further exploited through a fed‑batch strategy in which an initial acetic‑acid‑accumulating phase was followed by CO2‑limited feeding. This approach achieved complete conversion of methanol and CO2 and yielded an isobutyric acid titer of 2.70 ± 0.04 g·L[-1]. Controlling CO2 availability is a viable operational tool to steer C. luticellarii metabolism toward isobutyric acid production, in interaction with electron acceptor availability.}, }
@article {pmid42378725, year = {2026}, author = {Marques, HM}, title = {The chemistry of the cobalt corrinoids - Recent advances and emerging themes. Part 3. Cobalamins and health.}, journal = {Journal of inorganic biochemistry}, volume = {283}, number = {}, pages = {113395}, doi = {10.1016/j.jinorgbio.2026.113395}, pmid = {42378725}, issn = {1873-3344}, abstract = {Vitamin B12 (cobalamin) is an essential micronutrient whose biological importance extends beyond its traditional classification as a haematinic vitamin. This third and final part of a review covering work published between 2020 and 2025 synthesises selected illustrative studies that have advanced understanding of B12 physiology, nutrition, deficiency, delivery, and systems-level biology. At the molecular level, B12 functions as a cofactor in one‑carbon metabolism and mitochondrial pathways, influencing DNA synthesis, methylation capacity, and energy metabolism. These biochemical roles translate into organism-level consequences, particularly in the nervous system, where deficiency may cause irreversible neurological injury even in the absence of overt haematological abnormalities.Population-level analyses show that B12 status reflects the interaction of didetary intake, absorption efficiency, life stage, and food-system dynamics. Although animal-source foods remain the most reliable sources, shifts towards plant-based diets and inconsistent fortification practices are altering risk profiles. Clinical evidence further indicates that B12 deficiency is heterogeneous, frequently under-recognised, and complicated by the limitations of conventional biomarkers. Advances in delivery science point towards more controlled and targeted interventions, including encapsulation technologies, alternative administration routes, and receptor-mediated transport strategies. Emerging evidence also suggests biological activities for cobalamin derivatives beyond classical cofactor function, while microbiome research increasingly implicates corrinoid metabolism in host-microbe interactions relevant to immune and metabolic regulation. These developments support an integrated systems-level view of B12 biology spanning dietary supply, physiology, microbial ecology, and therapeutic innovation. SYNOPSIS: The final part of this review examines recent advances in vitamin B12 biology, spanning physiology, nutrition, deficiency, biomarker limitations, therapeutic delivery, and microbiome-linked corrinoid metabolism. These developments support an integrated systems-level view linking molecular function, dietary ecology, population health, and emerging therapeutic opportunities.}, }
@article {pmid42378946, year = {2026}, author = {Vila, JC and Estrela, S}, title = {From coarse-grained metabolic rules to fine-grained control of microbial communities.}, journal = {Current opinion in microbiology}, volume = {92}, number = {}, pages = {102788}, doi = {10.1016/j.mib.2026.102788}, pmid = {42378946}, issn = {1879-0364}, abstract = {Over the past decade, microbial ecology has revealed remarkable coarse-grained regularities in community assembly and metabolic function. Across diverse systems, distinct taxonomic compositions can converge on similar functional outputs, and simple physiological principles can predict steady-state outcomes. These findings suggest that complex microbiomes may, in some regimes, be governed by emergent simplicity and therefore be predictable. Yet many of the traits we want to understand or engineer seem to depend on fine-grained dynamics that may be transient, strain-specific, and history dependent. Here, we argue that bridging the gap between coarse-grained metabolic rules and fine-grained metabolic complexity is essential for a predictive and engineering-oriented microbiome ecology. While progress is limited by the lack of (or insufficient) temporal, spatial, and chemical resolution, we highlight both conceptual advances and emerging technologies that may help fill that gap by providing temporal, spatial, single-cell resolved, dynamic, quantitative measurements.}, }
@article {pmid42379319, year = {2026}, author = {Zhu, Y and Vrieze, J and Li, Y and Wang, S and Li, D and Zhang, Z and Dong, R and Li, X}, title = {Comparative assessment of endogenous, integrated, and exogenous biomethanation strategies: performance, microbial community and metabolic pathways.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135179}, doi = {10.1016/j.biortech.2026.135179}, pmid = {42379319}, issn = {1873-2976}, abstract = {Biological methanation is a promising approach for enhancing methane production rates and upgrading biogas during anaerobic digestion. However, few studies have examined the key biological rate-limiting factors or systematically compared different CO2 biomethanation strategies. In this study, anaerobic digestion of rice straw was subjected to H2/CO2 supplementation to evaluate three CO2 biomethanation strategies, i.e., endogenous, exogenous, and integrated. All CO2 biomethanation strategies increased methane production rate and achieved methane content over 83.9 %. Exogenous CO2 biomethanation achieved the highest methane production rate of 983 ± 68 mL·L[-1]·d[-1], which was 121 % and 41 % higher than endogenous and integrated CO2 biomethanation, respectively. In the integrated strategy, CO2 addition supplied buffer capacity to limit the pH increase. Rice straw hydrolysis and specific acetoclastic methanogenic activity was partially inhibited. In the CO2 biomethanation system, Methanobacterium formicicum was enriched, which is the dominant archaeal genus (50 %-69 % relative abundance). The relative abundance of 5,10-methylenetetrahydromethanopterin reductase (EC:1.5.98.2) suggested a potential functional limitation within the hydrogenotrophic methanogenesis pathway. Overall, this comparative assessment of these biomethanation strategies offers valuable references to optimizing full-scale biogas upgrading systems.}, }
@article {pmid42379595, year = {2026}, author = {Fullmer, MS and van Dijk, B and Takeuchi, N}, title = {Interaction range of common goods shapes Black Queen dynamics beyond the cheater-cooperator narrative.}, journal = {Proceedings. Biological sciences}, volume = {293}, number = {2074}, pages = {}, doi = {10.1098/rspb.2026.0911}, pmid = {42379595}, issn = {1471-2954}, support = {//Royal Society of New Zealand | Marsden Fund (Royal Society of New Zealand Marsden Fund)/ ; }, mesh = {*Biological Evolution ; Models, Biological ; Ecosystem ; *Symbiosis ; Ecotype ; *Microbial Interactions ; }, abstract = {Dependencies among microorganisms often appear mutualistic, as microbes grow faster together than alone. However, the Black Queen hypothesis (BQH) posits that these dependencies are underpinned by benefits from 'cheating' when others supply necessary common goods (CGs). The BQH often describes the evolution of a pair of ecotypes, a cooperator producing a CG and a cheater free-riding upon it. With multiple goods, their production can be centralized, with one ecotype producing everything and others cheating. We previously proposed an alternative BQH endpoint describing a community of 'mutual cheating', with production distributed over multiple interdependent ecotypes. Here, we present an individual-based eco-evolutionary model that predicts BQH dynamics resulting in various endpoints, including both distributed and centralizedproduction, and novel intermediate ecosystems involving apparent functional redundancy. These endpoints critically depend on the interaction range, the number of beneficiaries a producer can locally support. The intermediate ecosystems involve stable coexistence among ecotypes partially distributing production, with this coexistence punctuated by rare evolutionary transitions resulting in further distribution. These punctuated dynamics arise from cheaters stalling the division of labour by occupying the limited space within the producers' interaction ranges. Overall, our findings unveil complex evolutionary dynamics beyond the simple cheater-cooperator narrative, broadening the predictions of BQH.}, }
@article {pmid42367191, year = {2026}, author = {Bischofberger, AM and Cairns, J and Aapalampi, IK and Pausio, S and Lindqvist, M and Mustonen, V and Hiltunen, T}, title = {Community state shifts driven by total carbon availability over resource complexity in a synthetic microbial community.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag149}, pmid = {42367191}, issn = {2730-6151}, abstract = {Even though complex microbial communities are ubiquitous and provide essential services for natural and human-associated ecosystems, our knowledge about their assembly and dynamics is incomplete. There is an ongoing debate about whether the behavior of complex communities can be predicted from the outcome of pairwise competition of species, and whether communities reach alternative stable states depending on the level and complexity of resources provided for growth. To estimate the effect of two resource gradients, total carbon availability and resource complexity, on the compositional dynamics of a microbial community, we conducted a 16-day serial passage experiment, transferring a 16-species synthetic community in 96 different resource environments. We observed that although both resource dimensions influenced community composition, total carbon exerted a considerably larger effect. Additionally, we saw strong, discrete community state shifts along the total carbon gradient, a feature not observed for the resource complexity gradient. Using monoculture assays, we identified lag phase duration as the dominant predictor of competitive success at carbon extremes, with maximum growth rate increasing in importance as lag times converged. Total carbon availability thus structured community state transitions and regulated which growth trait governed competitive sorting. These results suggest the importance of total carbon level over resource complexity and identifying dominant species for the quest to successfully manage, maintain, and manipulate complex microbial communities.}, }
@article {pmid42368719, year = {2026}, author = {Kumar, C and Ghosh, A and Sanyal, P and Bhadury, P}, title = {Genome description of a potentially novel species of Billgrantia sp. strain SL18_1 isolated from Sambhar Lake, India.}, journal = {Access microbiology}, volume = {8}, number = {6}, pages = {}, pmid = {42368719}, issn = {2516-8290}, abstract = {A potentially novel species belonging to the genus Billgrantia bearing strain number SL18_1 has been isolated from Sambhar Lake, the largest inland salt water wetland located in the north of India. Based on 16S rRNA sequence search in International Nucleotide Sequence Database Collaboration, the isolate showed 99.3% identity with Billgrantia chromatireducens. Based on long-read sequencing using Oxford Nanopore Technologies chemistry, followed by annotation, the genome size of this organism has been found to be ~4.14 Mb. The genome has a G+C content of 66.27 mol% and is closest to Billgrantia campisalis based on genome relatedness. The functional annotation of draft genome has revealed the presence of key genes involved in nitrate reduction and denitrification pathways, including nirB, nirD and nasD (nitrate reductase), nirS (nitrite reductase) and norB and norC (nitric-oxide reductase). The nosZ coding for nitrous-oxide reductase has been also identified from the draft genome. This strain also possesses genes linked to the breakdown of benzoate compounds as well as osmoregulatory genes, which can possibly allow the bacterium to adapt to high osmotic stress. Besides, the presence of ibaG gene within the genome may allow this organism to adapt to acidic stress. Genes linked to multidrug resistance, including mdtA, mdtB and mdtK, have been identified within the genome of Billgrantia sp. strain SL18_1.}, }
@article {pmid42368866, year = {2026}, author = {O'Dwyer, J and Hynds, PD and Hooban, B and Ryan, M and Burke, LP}, title = {Editorial: Antimicrobial resistance in aquatic environments - Bridging surveillance, ecology, and one health action.}, journal = {One health (Amsterdam, Netherlands)}, volume = {22}, number = {}, pages = {101421}, pmid = {42368866}, issn = {2352-7714}, }
@article {pmid42370343, year = {2026}, author = {Emmanuel-Fashagba, MA and Obafemi, YD and Oranusi, SU}, title = {Fermented garlic as a functional food strategy for malnutrition: microbial ecology, bioactive compounds, and clinical perspectives.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1839155}, pmid = {42370343}, issn = {2296-861X}, abstract = {Fermented garlic (Allium sativum) represents a promising functional food with potential applications as a complementary nutritional intervention for malnourished populations. Through microbial fermentation and thermal processing two mechanistically distinct pathways, garlic undergoes significant biochemical transformations that enhance the availability of bioactive compounds, including S-allyl-L-cysteine (SAC), polyphenols, and γ-aminobutyric acid (GABA), which collectively contribute to improved antioxidant capacity and gut health. This comprehensive review examines the microbial ecology underlying garlic fermentation, the biochemical pathways that generate bioactive metabolites, and the mechanistic basis by which fermented garlic employed in the broader food fortification strategy or incorporated into fortified therapeutic food formulations targeting clinical malnutrition, may support nutritional recovery in the context of Environmental Enteric Dysfunction (EED), the dominant gut pathology underlying stunting and wasting in low- and middle-income countries (LMICs). Fermented garlic is a bioactive-dense nutritional adjuvant rather than a macronutrient source, its clinical relevance lies in potential enhancement of gut barrier integrity, reduction of mucosal inflammation, and support of micronutrient bioavailability, rather than direct caloric contribution. Preclinical evidence from animal models demonstrates improvements in intestinal morphology, metabolic parameters, and immune function, suggesting potential utility in nutritionally stressed populations. However, well-designed human clinical trials specifically examining fermented garlic in malnourished populations are currently underrepresented in the literature, and all translational implications discussed herein remain preliminary. Substantial research gaps persist regarding optimal dosage, long-term clinical safety, and standardization of fermentation protocols. This review identifies critical research priorities necessary to establish fermented garlic as a scalable, culturally acceptable food-based complementary intervention for vulnerable populations worldwide.}, }
@article {pmid42370364, year = {2026}, author = {Campos, ACMO and Siqueira, AEB and Figueiredo, MIDS and Soares, MA and Puerari, C and Morzelle, MC and Briceno, JCC and Bento, JAC}, title = {Valorization of wine industry by-products as a flavoring agent in water kefir: microbiological viability and functional properties.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1856957}, pmid = {42370364}, issn = {2296-861X}, abstract = {INTRODUCTION: This study developed a functional water kefir beverage flavored with grape pomace (Vitis labrusca.) and evaluated its physicochemical, microbiological, and sensory properties, alongside its functional effects in a Caenorhabditis elegans model.<br><br>METHODS: Four treatments were tested: 0% (KC), 25% (K25), 37.5% (K37.5), and 50% (K50) pomace addition.<br><br>RESULTS: Anthocyanin and phenolic contents were dose-dependent, peaking in K50 (33.56&#x202f;mg&#x202f;L[-1] and 4.31&#x202f;mg&#x202f;g[-1], respectively). During 21&#x202f;days of refrigerated storage, a decrease in reducing sugars, pH (4.3 to 3.5), and a concomitant increase in acidity (up to 6.60%) were observed, reflecting continuous microbial metabolic activity. Due to excessive acidity and residual taste, K37.5 and K50 were deemed unfeasible. Consequently, K25 was selected for biological and sensory validation. In K25, yeast and acetic acid bacteria (AAB) maintained high viability (10[7]&#x202f;CFU&#x202f;mL[-1]), whereas lactic acid bacteria (LAB) remained below 10[5]&#x202f;CFU&#x202f;mL[-1] due to the selective pressure of the grape pomace. K25 achieved a sensory acceptance index of 76.11% and a 65% purchase intention.<br><br>DISCUSSION: These results indicate that water kefir flavored with 25% grape pomace is a viable probiotic carrier rich in bioactive compounds with promising sensory appeal.}, }
@article {pmid42370813, year = {2026}, author = {Fernandez Diaz, A and Keck, F and Melby, MK and Nguyen, VK and Haraoui, LP}, title = {Rethinking One Health: Microbial Foundations for Ecological Governance.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {48}, number = {6}, pages = {e70155}, pmid = {42370813}, issn = {1521-1878}, support = {CF-0399 - CP24-033//CIFAR/ ; //Faculty of Medicine and Health Sciences of Universit&#xe9; de Sherbrooke/ ; //Centre de recherche Charles-Le Moyne/ ; 349522//Fonds de recherche du Qu&#xe9;bec-secteur Sant&#xe9;/ ; }, mesh = {Humans ; Animals ; *One Health ; Ecosystem ; Climate Change ; Ecology ; Zoonoses/microbiology/prevention &amp; control ; Biodiversity ; }, abstract = {The One Health (OH) framework has gained prominence in recent years, promoting an approach integrating the health of humans, animals, and the environment. However, its implementation as it pertains to the microbial world has largely prioritized zoonotic diseases, antimicrobial resistance, as well as pandemic preparedness and management, narrowing its ecological scope and confining microorganisms to the realm of pathogens. We explore the historical development of OH to identify key gaps and limitations and argue for the integration of microorganisms as ecologically constitutive, critical to sustain life processes and ecosystem functioning. We provide actionable recommendations, beginning with a shift in how microorganisms are conceptualized, extending to the development of microbial metrics and culminating in proposals for microbial governance to address current shortcomings and inform future policymaking. Collectively, these measures aim to strengthen the OH framework in confronting global challenges, including biodiversity loss and climate change, while aligning with its broader commitments to health and sustainable development.}, }
@article {pmid42377392, year = {2026}, author = {Karthikeyan, A and Javaid, A and Tabassum, N and Kim, TH and Kim, YM and Jung, WK and Khan, F}, title = {Bacterial extracellular membrane vesicles as multifunctional defense systems: Roles in immune evasion, phage interactions, and antimicrobial resistance.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {}, pmid = {42377392}, issn = {1573-4978}, support = {RS-2021-NR060118//Basic Science Research Program through the National Research Foundation of Korea (NRF), funded by the Ministry of Education/ ; RS-2023-00241461//Basic Science Research Program through the National Research Foundation of Korea (NRF), funded by the Ministry of Education/ ; }, mesh = {*Extracellular Vesicles/immunology/metabolism ; *Bacteria/immunology/metabolism/virology ; *Immune Evasion ; *Bacteriophages/physiology/immunology ; Biofilms/growth &amp; development ; *Drug Resistance, Bacterial ; Humans ; Antimicrobial Peptides ; Host-Pathogen Interactions/immunology ; Animals ; }, abstract = {Bacterial extracellular membrane vesicles (EMVs) are multifunctional nanoparticles released by Gram-negative and Gram-positive bacteria, which are involved in microbial ecology and pathogenesis. Their functions include facilitating intercellular communication, biofilm development, and nutrient acquisition within microbial communities, host-microbe interactions, and modulating host immune responses. EMVs help bacteria adapt and survive in different environments by serving as detergents, mediators in biochemical cycles, and defense systems. EMVs contain immunomodulatory components that interfere with host immune signaling pathways, allowing bacteria to evade the immune system. EMVs sequester antimicrobial peptides, thereby attenuating their antimicrobial efficacy. Additionally, EMVs are responsible for the transmission of antibiotic resistance, storage of resistance determinants and efflux pumps, and regulation of the action of antimicrobial drugs. The interactions between EMVs and bacteriophages add a degree of complexity, as EMVs can serve as protective barriers against viral entities and influence phage-bacteria interactions by binding and encapsulating bacteriophages. EMVs in biofilms may facilitate communication and cooperation among bacterial cells, which increases their survival capabilities against antimicrobials. This review comprehensively discusses EMVs' defenses against host immune responses, bacteriophage, and antimicrobials, which is vital for developing potential treatment techniques and combating antibiotic resistance.}, }
@article {pmid42377547, year = {2026}, author = {Crucitti-Thoo, RM and Aykut, TO and Rudak, A and Jasser, I}, title = {Comparing Aquatic Environmental DNA, Microscopy and Sedimentary DNA to Investigate Cyanobacterial Community Dynamics Across a Trophic Gradient.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02806-2}, pmid = {42377547}, issn = {1432-184X}, support = {560583//Polish National Science Centre/ ; }, abstract = {As a result of increasing temperatures and anthropogenic stressors, freshwater biomonitoring indicates that toxigenic and non-native cyanobacterial species are increasing globally. Because of the high-effort nature of traditional microscopy, aquatic Environmental DNA (eDNA) metabarcoding as a form of biomonitoring is becoming commonplace. While eDNA has been found to complement microscopic phytoplankton analysis, it has also been demonstrated that recent eDNA from surficial sediments (sedDNA) can also be a powerful tool to monitor a variety of organisms including benthic and planktonic microorganisms. However, comparisons between all three methods are rare. Therefore, we compared cyanobacterial metabarcoding data derived from aquatic eDNA and sedDNA to cell density and biomass determined by traditional planktonic microscopic analysis on samples taken from more than 20 lakes in the Masurian and Suwałki Lakelands of north-east Poland; an area composed of thousands of lakes with diverse morphologies, land-use histories, and varying trophic states. We found that there was a high degree of within method (eDNA/sedDNA, cell density/biomass) correspondence between the approaches, with trophic changes plausibly driving general patterns in taxa leading to these underlying agreements. Between methods, cell density proved to be more closely associated with eDNA, but was not found to be statistically significant. We postulate that cell numbers are a more similar metric to sequence read numbers than biomass, but that unique qualities of each measure mean that the approaches examined are complementary, rather than redundant. We detected several invasive taxa, which appear to have increased in abundance along the trophic gradients, and postulate that the accumulating nature of sediments may prove useful in detecting invasive taxa, particularly in the low-abundance early introductory stages.}, }
@article {pmid42364128, year = {2026}, author = {Preshaw, PM and Chew, RJJ and Goh, CE and Abdulkareem, AA and Graves, DT}, title = {Periodontitis and Diabetes: Mechanistic Evidence of a Circular Relationship.}, journal = {Journal of periodontal research}, volume = {}, number = {}, pages = {}, doi = {10.1111/jre.70131}, pmid = {42364128}, issn = {1600-0765}, support = {R01DE017732/DE/NIDCR NIH HHS/United States ; }, abstract = {The circular relationship between periodontitis and diabetes mellitus is one of the most established oral-systemic links. Uncontrolled diabetes contributes to an increased susceptibility and severity of periodontitis, while periodontitis contributes to poorer glycaemic control and greater insulin resistance. This reciprocal interaction is mediated by a network of interconnected mechanisms that extends beyond the traditional paradigm of bacteraemia and the hepatic acute phase response triggered by the systemic cytokine spillover from affected periodontal tissues. Experimental and clinical evidence indicate that dissemination of periodontal pathogens and virulence factors can directly affect the pancreas and liver, which are key organs in the pathogenesis of diabetes. Periodontal microbes and their virulence factors have been detected in the pancreas, eliciting β-cell dysfunction and apoptosis, compensatory alpha cell expansion and disruption of insulin-glucagon homeostasis. In addition to haematogenous spread, swallowed oral biofilm can promote oral-gut translocation, altering gut microbial ecology and contributing to entero-hepatic metabolic perturbations that exacerbate insulin resistance. The detection of periodontal pathogens by Toll-like receptors in peripheral tissues, including adipose tissue and the kidney, links periodontitis to adipose inflammation, dysregulated lipid metabolism and diabetic nephropathy. Similarly, other than eliciting the acute phase response, the systemic inflammatory spillover from periodontitis also dysregulates hepatic metabolism, increasing gluconeogenesis and impairing glycogenesis, thus contributing to hyperglycaemia. Beyond metabolic tissues, periodontal inflammation, mediated by pro-inflammatory mediators such as interleukin-6, can promote maladaptive myelopoiesis and the generation of hyperresponsive neutrophils and monocytes. In uncontrolled diabetes, chronic hyperglycaemia induces a similar trained, pro-inflammatory myeloid phenotype and the convergence of these processes may synergistically increase systemic inflammatory burden. The resulting pool of primed circulating innate immune cells can exacerbate periodontal tissue destruction and contribute to inflammatory injury in distant organs, thereby worsening diabetic complications. Overall, this review considers the complex mechanistic framework in which microbial dissemination, immune amplification and metabolic reprogramming collectively connect periodontitis and diabetes. While focused on the periodontitis-diabetes axis, this review also underscores the broader systemic relevance of periodontal inflammation in chronic metabolic disease and supports the inclusion of periodontal care as part of chronic disease management.}, }
@article {pmid42364172, year = {2026}, author = {Zhang, H and Liu, P and Chen, Y and Lv, J and Zhang, X and Zhang, J and Sun, Y and Wang, C and Wei, S and Wang, X and Gao, S and Qian, X and Jia, H and Tiedje, JM}, title = {Density-mediated freshwater plastisphere microbiomes preferentially degrade conventional rather than biodegradable microplastics.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag167}, pmid = {42364172}, issn = {1751-7370}, abstract = {The escalating demand for plastics leads to ubiquitous microplastic pollution worldwide. Existing evidence suggests that biodegradable microplastics degrade faster than conventional microplastics in aquatic environments. Here, we demonstrate the greater biodegradability of conventional polypropylene (PP) over biodegradable polylactic acid (PLA) in freshwater based on field survey, mesocosm experiment, co-culture assay, and multi-omics analysis. The biodegradation rate is 3.3-fold higher for PP compared to PLA, and this difference is more pronounced between photoaged microplastics (5.7-fold). The unexpected superior biodegradability of PP is supported by a greater diversity of microplastic-degrading bacteria in PP biofilm (predominantly aerobes) than in PLA biofilm (mainly facultative and obligate anaerobes). The inferior biodegradability of PLA is attributed to microbial growth constraints in the plastisphere driven by oxic-to-hypoxic/anoxic transition, oxygen-containing functional group detachment from the polymer, and lactide accumulation during long-term biodegradation. Our findings reveal previously overlooked but important environmental fates and impacts of biodegradable plastics against increasing substitution of conventional plastics with biodegradable alternatives.}, }
@article {pmid42365131, year = {2026}, author = {Zhu, S and Yang, Z and Zhao, H and Ma, Y and Chen, K and Qi, D}, title = {Rainfall Drives Differentiation of Plant Rhizosphere Microbial Communities in Two Different Types of Alpine Wetlands: A Perspective Based on a Carbon-Water Coupling Framework.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02823-1}, pmid = {42365131}, issn = {1432-184X}, support = {Qing[2025]TG04//Demonstration of Techniques for Wetland Protection, Restoration, and Carbon Sink Capacity Enhancement in the Qinghai Lake Basin - Qinghai Provincial Finance Budget/ ; }, abstract = {The alpine wetlands of the Qinghai-Tibet Plateau are confronting significant ecological challenges due to drastic shifts in precipitation patterns. Elucidating the response mechanisms of rhizosphere microbial communities in wetland plants to precipitation events is critical to understanding ecosystem resilience. In this study, sandy wetlands at Niaodao and riverine wetlands at Haergai in the Qinghai Lake basin were selected as study sites. Using Poa alpigena rhizosphere and non-rhizosphere soils as the research subjects, metagenomic DNA sequencing combined with environmental factor analysis was employed to compare the microbial community responses before and after a single pulse precipitation event. The results showed that Proteobacteria and Actinobacteria were the dominant phyla in both wetland types (combined relative abundance > 70%). Rainfall induced a differentiated restructuring of soil microbial community composition across different habitats. In rhizosphere soils, rainfall significantly reduced microbial alpha diversity. Co-occurrence network analysis revealed that the rhizosphere community shifted from a competition-coexistence pattern before rainfall to a cooperative adaptation pattern after rainfall, with significant increases in modular cohesion and the proportion of positive correlations. Metagenomic analysis indicated that the number of differentially abundant metabolic pathways in soil microorganisms increased markedly after rainfall, rising to 46 and 40 pathways in the rhizosphere and non-rhizosphere, respectively (compared to 3 and 31 before rainfall), indicating a shift from carbon reserve metabolism to energy-producing metabolism. Total carbon and water content were identified as the core environmental factors jointly regulating community assembly. This study reveals the mechanism by which regional background, precipitation disturbance, and the rhizosphere effect synergistically drive the succession of microbial communities in alpine wetlands, providing a new paradigm for understanding ecosystem adaptation to climate change.}, }
@article {pmid42365269, year = {2026}, author = {Fassarella, M and Smidt, H}, title = {Translational human gut microbiome research: What are the missing pieces of the puzzle?.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-08490-7}, pmid = {42365269}, issn = {1479-5876}, abstract = {BACKGROUND: Human gut microbiome research has expanded remarkably over the past two decades, revealing the fundamental role of gut microbes in human health and disease. Despite these advances, translation into evidence-based clinical practice and public health implementation remains exceptionally limited. This integrative translational perspective review evaluates human gut microbiome research across four critical aspects: translational successes, barriers to effective translation, applicability of frameworks from other medical disciplines, and strategies to enhance translational progress.<br><br>MAIN TEXT: Human gut microbiome research was evaluated through the lens of translational medical research principles, as summarised below. (1) Translational successes in human gut microbiome research are explored by analysing the developmental pathways of major microbiome-based or microbiome-targeted approaches, including faecal microbiota transplantation, probiotics, postbiotics, prebiotics, and dietary interventions, despite overall limited clinical and public health translation. (2) Established translational medical research frameworks served as a foundation to identify missing elements in current human gut microbiome research, including progression through T0-T4 phases, bidirectional knowledge flow, prioritization of unmet patient and societal health needs, patient-centric approaches, stakeholder engagement, and interdisciplinary collaboration. Integration of these principles is discussed in light of the specific characteristics, challenges, and limitations of human gut microbiome research. (3) Translational barriers in human gut microbiome research were analysed beyond limited integration of translational medical principles. These arise from the inherent complexity and high-dimensional nature of the gut microbiome, temporal and inter-individual variability, confounding factors, inconsistent methodological standardization and validation, and fragmentation across research efforts. Collectively, these barriers hinder causal inference, resulting in a low-quality evidence base and limiting effective translation. (4) A framework to advance translational human gut microbiome research is proposed based on the previous findings, including strategic priorities such as education and training in translational research principles for gut microbiome researchers.<br><br>CONCLUSIONS: Human gut microbiome research remains largely confined to early translational phases, with progression toward effective translation limited by intrinsic and methodological barriers that hinder causal inference and high-level evidence generation. Integration of core translational medical research principles offers a pathway to bridge these gaps, with education and training of gut microbiome researchers emerging as a key priority for advancing translational progress.}, }
@article {pmid42365883, year = {2026}, author = {Wu, W and Wang, W and Liu, H and Ganigué, R and Zhang, J and Liu, B and Liu, G and Wang, A}, title = {Multi-omics analysis reveals propanol is superior electron donor for odd-chain elongation.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135265}, doi = {10.1016/j.biortech.2026.135265}, pmid = {42365883}, issn = {1873-2976}, abstract = {Chain elongation from organic wastes has primarily targeted even-chain carboxylates, leaving the production of equally valuable odd-chain compounds underexplored. Propanol, abundant in industrial wastewater, offers a promising electron donor to address this gap, yet the underlying metabolic pathways and microbial consortia driving efficient odd-chain elongation remain unclear. The present study systematically investigated the characteristics of odd-chain elongation. The results demonstrated that the propanol-acetate (PA) group, using propanol as the electron donor and acetate as the electron acceptor, achieved an excellent selectivity of 84% for n-valerate and n-heptanoate, compared with 55% in the conventional ethanol-propionate (EP) group. Multi-omics analysis guided the specialized metabolic route construction, showing that electrons from propanol oxidation are channeled to drive acetyl-CoA synthesis from acetate and activate the reverse β-oxidation pathway. The propionate generated from propanol oxidation serves as the initial three-carbon backbone for odd-chain carboxylates generation. The keystone microorganisms for propanol-based odd-chain elongation are suggested to be Clostridium kluyveri and Oscillibacter valericigenes. Techno-economic analysis confirmed the metabolic selectivity inherent to the PA group confers superior economic resilience, yielding higher profitability than the EP group. This work positions propanol-based chain elongation as an efficient and economically viable strategy for the targeted production of valuable odd-chain carboxylates from propanol-containing wastewater.}, }
@article {pmid42366230, year = {2026}, author = {Ibrahim, D and Ali, AH and Refaat, A and Abdallah, RZ and AbouZid, S and Elsayed, T and El Mokadem, M and Berg, G and Nour, E}, title = {Shifts in the Rhizosphere Bacterial Community and Improved Essential Oil Yield and Quality in Chamomilla recutita L. Plant Through Cyanobacterial Inoculation.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, pmid = {42366230}, issn = {1432-184X}, mesh = {*Oils, Volatile/metabolism/analysis ; *Rhizosphere ; Soil Microbiology ; *Matricaria/microbiology/growth &amp; development/chemistry/metabolism ; *Bacteria/classification/genetics/isolation &amp; purification ; Plant Roots/microbiology/growth &amp; development ; *Cyanobacteria/physiology ; Egypt ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Nostoc/physiology ; }, abstract = {Rhizosphere bacterial communities play a crucial role in improving nutrient availability, disease and stress resistance, and overall development in plants. Biofertilizers can enhance plant growth, but little is known about their mode of interaction. Here, we studied the impact of seedling coating with two nitrogen-fixing cyanobacterial strains, Nostoc sp. NoHu, or Anabaenopsis circularis AnHu, on chamomile (Chamomilla recutita L.) growth, essential oil yield and quality, apigenin-7-O-glucoside, and the composition of rhizosphere bacterial communities, under field conditions in Egypt. The rhizosphere bacterial community, analyzed by 16 S rRNA amplicon libraries, composed of 31 phyla and 164 different genera. Compared to untreated plants, the application of both strains showed contrasting effects. Nostoc sp. application significantly enhanced almost all tested plant growth parameters, including fresh and dry weights of shoots, roots, and flowers, as well as the yield and content of vital essential oil constituents and the apigenin-7-O-glucoside. Furthermore, Nostoc sp. application increased both the abundance and diversity of the rhizosphere bacterial community compared to untreated plants, suggesting an indirect effect mediated through altering the rhizosphere bacterial community structure. In contrast, A. circularis application negatively affected essential oil yield and quality, exhibited the lowest bacterial abundance and diversity. These findings highlight potential of Nostoc sp. NoHu to boost chamomile productivity and essential oil quality. The contradictory responses between the two cyanobacterial strains emphasize strain-specific effects with Nostoc sp. NoHu as a promising biofertilizer candidate for chamomile.}, }
@article {pmid42366467, year = {2026}, author = {Muratore, TJ and Chari, NR and Robinson, A and Gooijer, I and Welsh, SG and Taylor, BN and Frey, SD and Tumber-Dávila, SJ}, title = {Coordination between root exudation rates and root conservation traits under simultaneous warming and nitrogen addition.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.71398}, pmid = {42366467}, issn = {1469-8137}, support = {1950364//Division of Biological Infrastructure/ ; DEB-1456610//Division of Environmental Biology/ ; DEB-1832110//Division of Environmental Biology/ ; }, abstract = {Fine-root traits and exudation shape plant-microbe interactions and nutrient cycling, yet it remains unclear whether exudation correlates with root traits or responds independently to soil conditions. In a 16-yr factorial warming × nitrogen addition experiment, we quantified fine-root morphology, chemistry, and exudation in two dominant temperate trees: Quercus rubra and Acer rubrum. Root exudation responded more strongly to experimental treatments than most root morphological traits. Nitrogen addition increased exudation in both A. rubrum and Q. rubra, whereas warming reduced exudation in Q. rubra. These shifts were not explained by root foraging traits, which were largely species-specific and stable. Instead, exudation was most closely associated with traits related to root construction and nutrient conservation, including root tissue density, root nitrogen concentration, and branching intensity. The contrasting effects of warming and nitrogen addition on exudation, despite stable root morphology, suggest that rhizosphere carbon inputs can shift without changes in root morphology. As such, future rhizosphere carbon fluxes may depend more on root tissue construction and belowground carbon allocation than on changes in root morphology. This suggests that physiological shifts in root carbon release may be a key pathway by which warming and nitrogen availability alter belowground carbon cycling.}, }
@article {pmid42367189, year = {2026}, author = {Erdem, ED and Li, B and Berendonk, TU and Klümper, U}, title = {Selective shifts in mobile antibiotic resistance genes under carbamazepine exposure in wastewater microbiomes.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag140}, pmid = {42367189}, issn = {2730-6151}, abstract = {Carbamazepine (CBZ) is a widely used nonantibiotic pharmaceutical that frequently persists through wastewater treatment and enters aquatic environments. CBZ has been, in simplified experimental systems, reported to stimulate horizontal gene transfer (HGT), a major process of antimicrobial resistance gene (ARG) dissemination in microbial communities. Moreover, it may facilitate selection for ARGs, directly or via co-selection. However, whether CBZ significantly modulates these processes in complex microbiomes remains insufficiently characterized. To address this gap, we exposed wastewater microbial communities to a gradient of CBZ concentrations for 3 days to evaluate early responses in community composition, ARG, and mobile genetic element (MGE) dynamics. Community structure remained largely unchanged across environmentally relevant CBZ concentrations. Most ARGs showed no consistent concentration-dependent response. However, a subset of clinically relevant ARGs increased in relative abundance in a dose-dependent manner. For the beta-lactam ARGs (bla CMY, bla OXA-48, bla CTX-M), and the trimethoprim ARG dfrA1, this increase was significantly correlated with IncP and IncW plasmid markers and the transposable element IS26, consistent with enhanced HGT-mediated dissemination. By contrast, the macrolide resistance gene ermF increased independently of the tested MGE markers, suggesting direct or host-specific selection or association with a nontested MGE. The strongest shifts occurred at sub-inhibitory CBZ concentrations within the upper range of concentrations reported in wastewater-impacted environments. These findings show that CBZ exposure can indeed influence the dissemination of selected ARGs in complex microbial communities without major effects on overall community composition, highlighting the potential for nonantibiotic pharmaceuticals to shape early resistome responses to pollutants in the environment.}, }
@article {pmid42361993, year = {2026}, author = {Kazmi, SAD and Jabeen, B and Huda, NU and Urooj, S and Khan, FZ and Abbas, T and Mirani, ZA}, title = {Influence of Prosthetic Surface Roughness on Biofilm Density and Prosthesis Longevity.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {108662}, doi = {10.1016/j.micpath.2026.108662}, pmid = {42361993}, issn = {1096-1208}, abstract = {Dental prosthesis failure is often associated with biofilm-mediated infections, yet the combined roles of surface roughness and material chemistry remain underexplored. This observational, retrospective study investigated associations between these factors and biofilm density, pathogen selection, and prosthesis longevity. Surface roughness (Ra) and microbial colonization were analyzed for 85 explanted prostheses (fixed, removable, implant-supported, and orthodontic) and compared to control samples (polished enamel, sealants). Biofilm formation was quantified via optical density (OD) and colony-forming units (CFU/cm[2]), while pathogen profiles were identified using selective culture and biochemical assays. A strong positive correlation (R[2] = 0.84, interpreted as a very strong correlation according to Evans' (1996) classification) was observed between surface roughness and biofilm accumulation. Smooth surfaces like zirconia (Ra ∼320 nm) exhibited low biofilm (OD 0.45), whereas rougher surfaces, particularly removable PMMA dentures (Ra ∼1100 nm), showed dense biofilms (OD up to 1.85) dominated by Candida spp. and Pseudomonas aeruginosa. Material chemistry was associated with distinct pathogen profiles: PMMA favored fungal and Gram-negative adhesion, while titanium promoted staphylococcal colonization. In this cohort, biofilm-associated infections were associated with reduced functional longevity; for example, implant crowns designed for 15+ years were removed after a mean of 5.4 years due to peri-implantitis. The study concludes that prosthetic failure is associated with the synergistic effect of surface topography, which correlates with biofilm quantity, and material composition, which is associated with distinct microbial ecology. These findings underscore the need for prostheses engineered with optimized surface smoothness and antimicrobial material chemistry. However, the observational, retrospective design limits causal inference; the culture-based methodology likely underestimates the full microbial diversity, particularly of anaerobic species; and the heterogeneity of device types limits direct comparability between groups.}, }
@article {pmid42363830, year = {2026}, author = {de Vos, MGJ and Jansen, V and El Bouhlali, O and Vlasblom, AA and Zandbergen, LE and van der Windt, I and Sey, CI and Kool, J and Nijland, R and de Jong, A and Kuipers, OP and Dunn, S and McNally, A and de Visser, JAG}, title = {Pyocyanin produced by Pseudomonas aeruginosa creates legacy effects that promote antibiotic resistance evolution in enterococci.}, journal = {Antimicrobial agents and chemotherapy}, volume = {}, number = {}, pages = {e0007826}, doi = {10.1128/aac.00078-26}, pmid = {42363830}, issn = {1098-6596}, abstract = {Polymicrobial infections are small communities of multiple interacting bacterial species. Interactions among constituent species may modify the growth of community members in the presence of antibiotics, for example, via degradation of the antibiotic, the induction of specific resistance mechanisms, or increased mutation supply rates. However, for most polymicrobial infections, the nature of such interactions is opaque, while they may affect both treatment efficacy and the evolution of antibiotic resistance. Here, we describe that past interaction of enterococci with Pseudomonas aeruginosa creates legacy effects that substantially enhance their antibiotic tolerance and promote resistance evolution. Specifically, we find that the temporary exposure to pyocyanin, a secondary metabolite produced by P. aeruginosa, increases antibiotic efflux in enterococci. We show that these tolerance legacy effects enhance the tolerance to rifampicin and nalidixic acid, and thereby promote the evolution of antibiotic resistance of enterococci. This work shows that transient interactions in polymicrobial communities can alter the evolutionary fate of community members.}, }
@article {pmid42358270, year = {2026}, author = {Hernanz-Torrijos, M and Ortega, MJ and Escobar-Niño, A and Fernández-Acero, FJ and Bartual, A}, title = {Polyunsaturated aldehydes induce distinct proteomic responses in two diatom-associated bacterial communities.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1838042}, pmid = {42358270}, issn = {1664-302X}, abstract = {Diatom-derived polyunsaturated aldehydes (PUAs) significantly influence marine bacterial dynamics, yet the underlying proteomic mechanisms remain elusive. We employed high-resolution comparative proteomics to decipher the functional reprogramming of two bacterial communities-one naturally associated with a PUA-producing diatom (N-community) and another with a non-PUA producing (I-community)-under ecologically relevant PUA exposure. While growth rates and cell densities remained unaffected, indicating an absence of acute toxicity, proteomics revealed pronounced community-specific reorganization. N-community displayed stable, regulation-oriented adjustments consistent with physiological accommodation, whereas I-community exhibited dose-dependent stress responses at the endpoint of the growth curve, shifting toward protein repair and antioxidant defense. Our findings demonstrate that PUAs trigger profound proteomic reprogramming conditioned by the communities' prior ecological history. This functional divergence provides a molecular basis for understanding bacterial fitness and succession during diatom blooms, where PUA-mediated interactions could act as a selective filter shaping the phycosphere's microbial landscape.}, }
@article {pmid42360048, year = {2026}, author = {Mauri, M and Unger, K and Gershenzon, J and Allen, RJ and Agler, MT}, title = {Bacterial degradation of a plant toxin and nutrient competition with commensals trade off to constrain pathogen growth.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0006426}, doi = {10.1128/msystems.00064-26}, pmid = {42360048}, issn = {2379-5077}, abstract = {Healthy plant leaves potentially host both commensal bacteria and opportunistic pathogens, which, under some circumstances, may cause disease. The interactions between commensals and opportunistic pathogens are generally poorly understood, but such understanding is crucial for developing effective biocontrol strategies. In Arabidopsis thaliana, isothiocyanates (ITCs) are defense metabolites that suppress most bacteria; commensals are especially affected as they do not express ITC resistance genes. The ITC hydrolase SaxA detoxifies ITCs, making it an important virulence factor for bacterial and fungal pathogens. To investigate pathogen-commensal interactions based on SaxA-mediated ITC degradation, we used five ITC-sensitive bacterial commensals and the opportunistic pathogen Pseudomonas viridiflava 3D9 (PS). All strains were isolated from healthy A. thaliana leaves. PS degrades 4-methylsulfinylbutyl-ITC (4MSOB-ITC) with SaxA. We examined commensal growth in the presence of 4MSOB-ITC, both in monoculture and in coculture with PS or a saxA-deficient mutant (PSKO). We used the growth data to develop a generalizable consumer-resource mathematical model incorporating ITC toxicity, ITC degradation, and nutrient use. We predicted and confirmed experimentally that the extent to which SaxA benefits the pathogen depends on its effects on commensals. In some contexts, commensal rescue and the resultant nutrient competition limit pathogen growth. In addition, we tested in silico how commensal ITC susceptibility, pathogen ITC degradation rates, and growth parameters affect the trade-off between SaxA-mediated virulence (strong pathogen growth) and commensal rescue (commensal growth). Our findings suggest that the effects of microbial traits-traditionally viewed as either virulence or plant-beneficial factors-are constrained in the microbiome context. This underscores the need to reconsider how such traits are classified in the context of plant-microbiome interactions.IMPORTANCEHealthy plant leaves host a variety of bacteria; these can be beneficial, but some (opportunistic pathogens) can also be harmful under certain conditions. To design effective biocontrol strategies to sustainably protect plants, it is important to understand how opportunistic pathogens thrive as part of a healthy leaf microbiome. Plant defense metabolites, such as isothiocyanates (ITCs), which kill commensal leaf bacteria, and bacterial ITC resistance mechanisms, such as the ITC hydrolase SaxA, which are often expressed in pathogens and degrade ITCs, may play key roles in the plant microbiome composition. In this study, we explore how SaxA-mediated ITC degradation by a pathogen also benefits diverse ITC-sensitive commensals and how this, in turn, could shape microbiome stability and plant health. Using mathematical modeling based on growth data from Pseudomonas viridiflava with diverse commensals, we find that interaction dynamics can be explained by ITC detoxification and nutrient competition. We predict and experimentally confirm that conditions exist under which SaxA favors commensal growth so strongly that the pathogen is outcompeted for resources, thus not benefiting from its own virulence factor. Our findings suggest that the effects of microbial traits, including virulence factors, are context-dependent, especially when functioning as a public good in a community context like SaxA. Moreover, we propose that this concept, which has been known from antibiotic-degrading microbes, may be worth considering as well when studying plant-pathogen interactions under natural conditions where the commensal microbiome might play an important role in plant disease outcomes.}, }
@article {pmid42360481, year = {2026}, author = {Bhandari, R and Wills, Z and Harris, J and Salie, M and Ankrah, NYD and Wong, AC and Eastman, K and Ringbauer, J and Striegler, RK and Kang, DS}, title = {Rare Taxa and Stochastic Drift Drive the Microbiome Assembly of the Invasive Pest Drosophila suzukii, While Host Filtering Structures the Grape Sour Rot Community.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02819-x}, pmid = {42360481}, issn = {1432-184X}, abstract = {Understanding the processes that shape microbial community structure is a central challenge in ecology. The relative importance of deterministic and stochastic processes in driving the microbiome assembly and composition remains poorly understood across diverse animal and plant hosts. Here, we characterized the bacterial (16 S rRNA) and fungal (ITS rRNA) communities in invasive pest spotted wing Drosophila (SWD, Drosophila suzukii) and sour-rot-affected grapes from seven California vineyards using high-throughput sequencing. We found that while the bacterial microbiome of male and female SWD was compositionally similar, these communities were entirely distinct from those on sour rot-affected grapes, indicating strong host-specific filtering. SWD also harbored substantially higher microbial density and greater diversity compared to grapes. Ecological modeling revealed a fundamental divergence in assembly mechanisms: SWD communities were predominantly shaped by stochastic processes, with a neutral model explaining 40% of the variation. In contrast, sour-rot-affected grape communities were structured by a combination of stochastic and deterministic factors. Importantly, taxa that deviated from neutral predictions, thereby indicating selection, were primarily classified as rare or intermediate in abundance. This suggests that low-abundance taxa may act as keystone drivers of dysbiosis during rot development. These results highlight the differing assembly rules governing a vector-host system: the mobile vector acts as a stochastic reservoir, promoting pathogen dispersal, while the sessile host imposes strict environmental filtering. This underscores the critical role of rare taxa in shaping community structure and ecosystem stability in SWD and its host grapes.}, }
@article {pmid42361873, year = {2026}, author = {Shi, W and Mo, Y and Zhang, H and Jeppesen, E and Yan, X and Chen, H and Zhang, H and Yang, J}, title = {Microeukaryotes are more vulnerable than picoeukaryotes to reservoir salinization: Evidence from multi-year high-frequency monitoring.}, journal = {Environmental research}, volume = {}, number = {}, pages = {125098}, doi = {10.1016/j.envres.2026.125098}, pmid = {42361873}, issn = {1096-0953}, abstract = {In freshwater ecosystems, rising salinity driven by factors such as climate change and urbanization can severely threaten ecosystem services. Eukaryotic plankton, a vital component of freshwater ecosystems, spans a size range from picoeukaryotic plankton (0.2-3 μm) to microeukaryotic plankton (3-200 μm), each exhibiting unique ecological functions and environmental response traits. Changes in the composition of eukaryotic plankton communities may have a substantial effect on material transfer and energy flow within freshwater reservoir ecosystems. However, the differential effects of salinization on timescales on the diversity, assembly, and stability of pico- and micro-eukaryotic plankton remain to be elucidated. We utilized a four-year high-frequency monitoring dataset comprising 892 samples to disentangle the responses of pico- and micro-eukaryotic plankton to salinity fluctuations. Results showed that as salinity increased, the α-diversity of microeukaryotic plankton declined more sharply than that of picoeukaryotes. The β-diversity of microeukaryotes remained consistently lower than that of picoeukaryotes. During the initial phase of salinity increase, deterministic processes became significantly more important in microeukaryotic community assembly. In contrast, picoeukaryotic community assembly was jointly influenced by stochastic and deterministic processes throughout the salinity gradient. Most notably, the stability of the microeukaryotic community decreased with rising salinity, whereas that of the picoeukaryotic community increased. These findings highlight the differential stability responses of different size fractions of eukaryotic plankton to salinity stress and offer a scientific basis for predictive modeling of ecological responses to freshwater salinization.}, }
@article {pmid42361923, year = {2026}, author = {Huang, Y and Zhang, Q and Li, M and Zhang, B and Ding, Y and Chen, J and Wu, D and Liu, X and Huang, Z}, title = {Investigating mechanisms of gradient applied voltages on electro-enhanced algal-bacterial symbiosis system for mariculture wastewater: system performance, symbiotic community characteristics, and microbial ecology.}, journal = {Bioresource technology}, volume = {459}, number = {}, pages = {135246}, doi = {10.1016/j.biortech.2026.135246}, pmid = {42361923}, issn = {1873-2976}, abstract = {This study investigated the effect of applied voltage gradients on pollutant degradation and nitrogen removal in an electro-enhanced algal-bacterial symbiotic system treating marine aquaculture wastewater. Three groups with different voltage gradient conditions were set up in the experiment: E1 (1.8 V), E2 (2.2 V), and E3 (2.6 V). While all reactors achieved stable chemical oxygen demand (COD) removal (>70%), their total nitrogen (TN) removal efficiencies varied markedly. The system operating at 2.2 V achieved the best TN removal efficiency (77%), surpassing those at 1.8 V (68%) and 2.6 V (44%). The lower voltage limited anoxic denitrification, whereas the higher voltage suppressed ammonium assimilation and nitrification. Excessive voltage led to severe loss of microalgal biomass and a sharp decline in extracellular polysaccharide production, whereas insufficient voltage reduced extracellular polymeric substance secretion and biomass accumulation. Voltage gradients also shifted microbial community composition and enhanced deterministic processes during community assembly, with stochastic sub‑processes transitioning from "homogenizing dispersal" toward "drift". At voltages 2.2 V, broader ecological niches for both bacteria and microalgae supported a stable, highly functional denitrifying consortium dominated by unclassified_f__Rhodobacteraceae (24.90%) and Denitromonas (13.90%). Therefore, 2.2 V is identified as the optimal voltage for achieving high nitrogen removal and stable algal-bacterial symbiosis. These findings provide a mechanistic basis for optimizing mariculture wastewater treatment through voltage‑controlled engineering of algal‑bacterial symbiosis.}, }
@article {pmid42344072, year = {2026}, author = {Sharma, V and Kumar, S and Kasana, D and Roy, RP}, title = {Establishment of two Hypotheses for Gut Bacterial Alteration Process for Minimizing the Intestinal Communicable Diseases.}, journal = {Indian journal of community medicine : official publication of Indian Association of Preventive &amp; Social Medicine}, volume = {51}, number = {3}, pages = {447-451}, pmid = {42344072}, issn = {0970-0218}, abstract = {Intestinal communicable diseases like diarrhea, dysentery, nausea, vomiting, cholera, typhoid fever, paratyphoid fever, botulism, gastroenteritis, etc., are caused by different microbes. Intestinal microbial ecology is the most mysterious and complex environment for microbes. Bacteriophages are the dominant viruses in the intestinal microbiota. It is well established that gut microbial composition directly affects human health. Microbes use the gastrointestinal tract as niches there some factors or theories exist such as dietary, quorum sensing, and biosignaling, including biomass and biofilm production. Whereas if some microbial disbalance happens due to the effect of antibiotics or different toxin production or uninterrupted and unexpected factors dysbiosis occurs. The outcome of dysbiosis is different communicable diseases in the intestine. Alteration in microbiota can make crucial improvements in the microbiota environment and to the body's health. After reviewing evidence authors are of the opinion that two natural microbial phenomena that may be utilized as a hypothetical approach to prevent communicable diseases in the intestine, i.e., microbes-microbes competition strategy and introduction of bacteriophage to kill the target bacteria in the gut.}, }
@article {pmid42345567, year = {2026}, author = {Rojas-Preciado, N and Poppelsdorf, W and Berings, L and Van Hee, S and Jacquemyn, H and Lievens, B}, title = {Draft genome sequences of six bacterial isolates from aphid-infested sugar beet and witloof chicory.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0034326}, doi = {10.1128/mra.00343-26}, pmid = {42345567}, issn = {2576-098X}, abstract = {Aphid-infested plants can recruit beneficial bacteria that support plant protection and offer potential for sustainable aphid management. We present the draft genome sequences of six bacteria isolated from aphid-infested sugar beet and witloof chicory. These resources will support the identification of traits relevant to plant-microbe-insect interactions and aphid biocontrol.}, }
@article {pmid42346347, year = {2026}, author = {He, J and Qin, L and Sun, X}, title = {Bile Acids and the Gut-X Axis: TCM-Mediated Systemic Protection and Therapeutic Opportunities for Multi-Organ Diseases.}, journal = {Metabolites}, volume = {16}, number = {6}, pages = {}, doi = {10.3390/metabo16060366}, pmid = {42346347}, issn = {2218-1989}, support = {82405310//National Natural Science Foundation of China/ ; 1020241792//Natural Science Foundation of the Jiangsu Higher Education Institutions of China/ ; }, abstract = {The gut microbiota regulates host physiology and drives extraintestinal diseases through the gut-X axis. Bile acids (BAs) function as key mediators of this interorgan crosstalk by activating nuclear and membrane receptors (FXR, TGR5, PXR, VDR). Traditional Chinese Medicine (TCM) demonstrates efficacy across multiple organ systems through multi-component formulations. This narrative review synthesizes evidence from preclinical and clinical studies supporting that TCM exerts systemic protection via strategic modulation of the microbiota-BA-host receptor axis, which functions as a core regulatory circuit within a larger network of microbial metabolites. Mechanistically, representative TCM formulas remodel gut microbial ecology and reinforce intestinal barrier integrity, leading to optimized BA profiles. These favorable BA signatures engage tissue-specific receptor signaling to resolve inflammation, mitigate fibrosis, and restore metabolic homeostasis across the gut-heart, gut-kidney, gut-liver, gut-bone, and gut-endocrine axes. Support for this causal relationship is provided by microbiota depletion, fecal transplantation, and multi-omics studies, collectively suggesting that TCM's benefits are microbiota-dependent and at least partially BA-mediated. Moreover, context-dependent modulation of BA receptors, such as differential regulation of FXR, enables TCM to achieve pathology-specific outcomes. Current evidence is derived predominantly from preclinical models, and clinical data remain lacking. Nonetheless, the microbiota-BA-organ axis thus provides a potential framework for understanding TCM's systemic actions and establishes a molecular basis for developing microbiome-informed precision therapeutics. Future directions include patient stratification and precision intervention design inspired by TCM's ecological modulation strategies.}, }
@article {pmid42349322, year = {2026}, author = {Steuer, P and Tejeda, C and Hernández-Agudelo, JM and Ulloa, F and Addis, MF and Salgado, M}, title = {Subtle shifts in fecal microbiota diversity during early stages of Mycobacterium avium subsp. paratuberculosis pathogenesis in dairy cattle.}, journal = {Veterinary microbiology}, volume = {320}, number = {}, pages = {111119}, doi = {10.1016/j.vetmic.2026.111119}, pmid = {42349322}, issn = {1873-2542}, abstract = {Mycobacterium avium subsp. paratuberculosis (MAP) in cattle causes an intestinal infection that can induce persistent inflammation or tissue remodeling. Several studies have reported differences in microbial diversity between MAP-infected and non-infected ruminants. Still, most of these studies have focused on animals in advanced stages of the disease, whether subclinical or clinical. The present study aimed to describe fecal microbiota composition in dairy cattle during early stages of MAP-associated pathological processes, which remain poorly characterized. A cross-sectional study was conducted in a pasture-based dairy herd in southern Chile. Fecal samples from 25 clinically healthy multiparous cows, including MAP culture-positive and negative animals, were analyzed using 16S rRNA gene sequencing. MAP culture-positive animals showed significantly reduced alpha diversity and subtle but significant differences in community structure compared with MAP-negative animals, despite no major taxonomic differences at the phylum or genus level. These findings suggest that low-level MAP infection is associated with early alterations in fecal microbial ecology, supporting a potential role of microbiota disruption in the initial stages of MAP pathogenesis and highlight the need for longitudinal studies to clarify their role in disease progression.}, }
@article {pmid42350967, year = {2026}, author = {Yang, X and Wang, Q and Wang, P and Li, J and Wang, L and Bian, X}, title = {Leaf development is associated with coupled metabolome-fungi trajectories in the phyllosphere of Panax ginseng.}, journal = {BMC plant biology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12870-026-09388-8}, pmid = {42350967}, issn = {1471-2229}, support = {82304677//the National Natural Science Foundation of China/ ; YDZJ202301ZYTS333//Jilin Province Science and Technology Development Project/ ; JJKH20261521KJ//Jilin Provincial Education Department Project/ ; }, abstract = {BACKGROUND: Leaf development underpins physiological performance and secondary metabolite accumulation, yet its influence on phyllosphere fungal communities in perennial medicinal plants such as ginseng (Panax ginseng C.A. Meyer) remains poorly understood. Understanding how developmental stage affects leaf chemistry and microbial assembly is important for linking plant metabolism with aboveground microbial ecology.<br><br>RESULTS: We analyzed ginseng leaves across four developmental stages (S1-S4) using physiological measurements, ginsenoside profiling, untargeted metabolomics, ITS amplicon sequencing, fungal association networks, and metabolite-fungus correlations. Leaf physiological traits and ginsenoside content peaked at stage S2, representing a developmental optimum. Metabolomics revealed early enrichment of sugar phosphates, nucleotide metabolites, and membrane lipids, followed by late accumulation of raffinose-family oligosaccharides, phenylpropanoids, flavonoids, oxylipin-related lipids, and brassinosteroid-linked metabolites. Fungal richness and evenness increased from S1 to S4, with communities shifting from Ascomycota-dominated at early stages to Basidiomycota-enriched on senescing leaves. Fungal association networks showed stage-related increases in network size and changes in topological organization. Integrative analyses indicated that stage-specific metabolic changes were closely associated with fungal community succession, with amino acid, carbohydrate, lipid, flavonoid, and terpenoid pathways potentially linked to stage-specific fungal association patterns.<br><br>CONCLUSIONS: Ginseng leaf development was accompanied by coordinated physiological and metabolic reprogramming that was associated with shifts in phyllosphere fungal composition and inferred association networks. These findings highlight leaf developmental stage as an important context for aboveground microbial dynamics and provide a framework for linking plant metabolism with microbial ecology in perennial crops, while emphasizing that causal relationships between specific metabolites and fungal taxa require further experimental validation.}, }
@article {pmid42351207, year = {2026}, author = {Ross, C and Laitinen, V and Khalighi, M and Salojärvi, J and de Vos, WM and Sommeria-Klein, G and Lahti, L}, title = {Reconstructing community dynamics from limited observations.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02449-y}, pmid = {42351207}, issn = {2049-2618}, support = {340314//Research Council of Finland/ ; 330887//Research Council of Finland/ ; 20210172//Sakari Alhopuro foundation/ ; 352604//Strategic Research Council in Finland/ ; 952914//European Union's Horizon 2020 research and innovation programme/ ; }, abstract = {BACKGROUND: Ecosystems tend to fluctuate around stable equilibria in response to internal dynamics and environmental factors. Occasionally, they enter an unstable tipping region and collapse into an alternative stable state. Being able to quantify and predict these dynamics is key to our understanding of how microbial communities vary over time and respond to perturbations.<br><br>RESULTS: Mechanistic models of microbial community dynamics often fail to characterise observed fluctuations in naturally occurring microbiomes and inform us about key dynamical properties such as stability and resilience. An alternative approach is to characterise the dynamical landscape using non-parametric models. However, the scarcity of long, dense time series data poses a severe bottleneck for characterising community dynamics using existing methods. We overcome this limitation by combining information across multiple short time series using Bayesian inference. By decomposing dynamics into deterministic and stochastic components using Gaussian process priors, we are able to predict stable and tipping regions along a unidimensional stability landscape while simultaneously addressing the associated uncertainty. In particular, we estimate a recently proposed probabilistic metric for resilience in multistable systems: the expected "exit time" out of the current stable state under stochastic fluctuations. We validate our approach on simulated data and highlight in particular that our model is able to distinguish bistability from bimodality, which are often conflated in classical potential analyses. We further demonstrate our approach by re-analysing ecological time series data of lake cyanobacteria abundance, for which we recover similar results as a previous study using three orders of magnitude fewer data points. Finally, we use our model to re-evaluate the stability of previously proposed "tipping elements" in the human gut microbiota.<br><br>CONCLUSIONS: We introduce a probabilistic non-parametric approach to characterise stationary community dynamics from short time series, which is potentially applicable to a broad range of systems in microbial ecology and beyond. We use this model to clarify the distinction between bistable and bimodal dynamics and to contribute to contemporary debates on the stability and resilience of ecological communities, in particular the human gut microbiota. Video Abstract.}, }
@article {pmid42352875, year = {2026}, author = {Hashim, NT and Chaitanya, NCSK and Babiker, R and Ahmed, A and Rahman, MM and Mohammed, R and Padmanabhan, V and Islam, MS and Elsheikh, M and Abduljalil, SMA and Gismalla, BG and El Bahra, S}, title = {Antibiotic Exposure and Periodontal Susceptibility: A Risk-Modifying Hypothesis.}, journal = {International journal of molecular sciences}, volume = {27}, number = {12}, pages = {}, doi = {10.3390/ijms27125150}, pmid = {42352875}, issn = {1422-0067}, mesh = {Humans ; *Anti-Bacterial Agents/adverse effects/therapeutic use/pharmacology ; Disease Susceptibility ; Animals ; *Periodontitis/microbiology/etiology/drug therapy ; Dysbiosis ; Microbiota/drug effects ; }, abstract = {Systemic antibiotics are among the most widely prescribed therapeutic agents worldwide, and their effects on host-microbe equilibrium extend well beyond the infection for which they are intended. Periodontitis is conventionally framed as a biofilm-initiated, host-mediated inflammatory disease, although recent work has shifted this framework toward microbial homeostasis as a regulator of periodontal stability. We hypothesize that antibiotics are not direct etiologic agents of periodontitis but instead act as risk-modifying factors that lower the threshold at which plaque-mediated inflammation progresses to destructive disease. We propose that this effect may operate through several mechanisms: broad-spectrum or repeated exposure could deplete protective commensals and narrow microbial diversity, creating ecological space for opportunistic and pathogenic taxa; antibiotics may also alter host neutrophil function, cytokine profiles, and antimicrobial peptide regulation and may interfere with the osteoblastic and osteoclastic dynamics governing alveolar bone remodelling; and antibiotic-induced gut dysbiosis may propagate systemic inflammatory signals that further modulate periodontal susceptibility. To evaluate this hypothesis, we synthesize the available clinical, epidemiological, and experimental data across four converging axes-oral microbial ecology, immune regulation, alveolar bone remodelling, and the gut-oral axis-and identify the predictions the hypothesis generates and the evidence gaps it exposes. We emphasize that no clinical study has yet demonstrated a causal link between antibiotic exposure and periodontitis; the framework advanced here is therefore intended to inform antimicrobial stewardship in dentistry and to define a research agenda for determining whether antibiotic exposure constitutes a clinically meaningful modifier of periodontal disease susceptibility.}, }
@article {pmid42354839, year = {2026}, author = {Matera, M and Biagioli, V and Cavecchia, I and Illiceto, MT and Pennazzi, L and Morandin, M and Lenzi, MB and Baldassarre, ME and Mennini, M}, title = {Maternal Microbiome in Fetal Programming: A One Health Perspective on Translational Implications for Early-Life Health.}, journal = {Microorganisms}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/microorganisms14061214}, pmid = {42354839}, issn = {2076-2607}, abstract = {Pregnancy represents a critical eco-biological window during which maternal physiology integrates environmental exposures, lifestyle factors, and interconnected microbial ecosystems to shape fetal development and long-term health. From a One Health perspective, defined here as the interconnection between maternal health, environmental determinants, and microbial ecosystems across generations, the maternal microbiome functions as a dynamic interface linking the external environment to the intrauterine milieu, translating ecological signals into immunological, metabolic, and neuroendocrine pathways that influence placental function and developmental programming. Across gut, vaginal, oral, and mammary niches, maternal microbial communities operate as an integrated network regulating systemic inflammation, metabolic homeostasis, and the production of bioactive metabolites, including short-chain fatty acids, bile acids, and tryptophan derivatives. This review proposes an integrated systems framework in which pregnancy is viewed as a transient ecological system shaped by ten interconnected maternal determinants, encompassing microbial niches, nutrition, lifestyle factors, medical interventions, mode of delivery, and postnatal microbial transmission, that converge on shared microbiome-mediated signaling pathways affecting fetal and neonatal immune, metabolic, and neurodevelopmental trajectories. Broader macro-environmental drivers, including biodiversity loss, urbanization, pollution, and industrialized lifestyles, are considered as upstream modulators of maternal microbial ecology within a One Health context. A systems model is presented to illustrate how environmental inputs are biologically transduced through maternal microbial networks to influence placental function, fetal development, and early-life health trajectories. Framing pregnancy as an integrated eco-biological continuum highlights the maternal microbiome as a central hub of intergenerational health and may support microbiome-informed preventive strategies and public health approaches aimed at reducing the burden of non-communicable diseases (NCDs) of early-life origin.}, }
@article {pmid42354933, year = {2026}, author = {Saadeh, M and Hong, G and Rabeeah, S and Dutta, P and Oldfield, EC and Johnson, DA}, title = {Dietary Intake of Micro- and Nanoplastics: Potential Adverse GI Effects on Microbiome, Inflammation, and Neoplasia.}, journal = {Microorganisms}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/microorganisms14061309}, pmid = {42354933}, issn = {2076-2607}, abstract = {Micro- and nanoplastics (MNPs) are pervasive in food-contact environments and the human diet, positioning the gastrointestinal (GI) tract as the primary portal of entry and a plausible site of early biological effects. Human exposure is supported by detection of microplastics in stool and colon tissue, and emerging clinical studies report associations between fecal microplastic burden and GI disease states, including inflammatory bowel disease (IBD) and colorectal cancer (CRC). Preclinical studies provide mechanistic plausibility, reporting that ingested MNPs can modulate microbial ecology, alter mucus membrane integrity, increase intestinal permeability through changes in cellular tight junction biology, and induce inflammatory gene expression. These effects can vary by MNP polymer type, particle size/shape, aging state, and exposure dose. Human-relevant experimental platforms increasingly demonstrate size- and concentration-dependent uptake and host responses while revealing substantial inter-individual variability. We synthesize current evidence on dietary sources and key physiochemical properties as they relate to mechanistic pathways connecting MNP exposure to dysbiosis-immune activation-neoplasia axes, in addition to methodological limitations that constrain current clinical utility. Further research including standardized biomonitoring and exposure protocols, environmentally realistic chronic low-dose mixtures, longitudinal human cohorts, and interventional designs that test whether exposure reduction modifies GI inflammation biomarkers and cancer-relevant pathways are critical to clarifying causality.}, }
@article {pmid42354949, year = {2026}, author = {Zhang, Y and Zhu, J and Xu, H and La, ATZ and Liu, B and Zhang, Z and Liu, L and Bian, Y and Liang, S and Li, M and Zhao, G and Qiao, Y and Zhang, Z and Xu, M and Wu, D}, title = {Comparative Analysis of Gut Microbiome Diversity, Stability, and Predicted Function in Captive Guanacos (Lama guanicoe) and Alpacas (Vicugna pacos).}, journal = {Microorganisms}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/microorganisms14061325}, pmid = {42354949}, issn = {2076-2607}, support = {Q/EDWY DG020-2025//Ordos Longsheng Wildlife Park Co., Ltd./ ; NDYB2024-11//Inner Mongolia Agricultural University/ ; }, abstract = {The gut microbiota plays a vital role in host health. In response to the scarcity of comparative studies examining wild and domesticated South American camelids under identical captive conditions, this study was conducted to compare the gut microbiota of 16 captive guanacos (Lama guanicoe) and 8 alpacas (Vicugna pacos) housed in the same zoo and fed identical diets, using 16S rRNA gene sequencing and multiple ecological metrics for analysis. Alpha diversity indices (Shannon, observed richness, and Shannoneven) did not differ between the two species, but beta diversity (principal component analysis) indicated significant separation (p < 0.05), and the guanacos exhibited significantly lower within-group Bray-Curtis dissimilarity, indicating more consistent microbial communities. Guanacos exhibited a lower average variation degree (AVD), indicating greater community stability, a broader niche, and a co-occurrence network with 81.1% positive edges and high modularity (0.691). In contrast, the alpacas showed a higher AVD (lower stability), a narrower niche, and a network with only 62.2% positive edges and lower modularity (0.534). Linear discriminant analysis effect size analysis revealed that Monoglobus and Bacteroides are enriched in guanacos, while Rikenellaceae_RC9_gut_group is enriched in alpacas. Functional predictions revealed that alpacas had higher predicted abundances of potentially pathogenic taxa and Kyoto Encyclopedia of Genes and Genomes pathways related to Staphylococcus aureus infection (p < 0.05). These findings demonstrate that, despite sharing environments, guanacos have a more stable, generalist-dominated gut microbiota with a higher proportion of positive co-occurrences, whereas alpacas exhibit a less stable, specialist-oriented community with a higher proportion of negative co-occurrences and greater predicted pathogenic potential. These results suggest that domestication may have contributed to the observed divergence in gut microbial ecology between the two species.}, }
@article {pmid42355447, year = {2026}, author = {Bogdan-Andreescu, CF and Cadar, E and Bubulac, L and Eremia, IA and Tudor, V and Albu, CC and Gheorghe, IR and Spînu, AD and Bănăţeanu, AM and Slăvescu, DA}, title = {Heavy Metal-Driven Oral Dysbiosis: Salivary Toxicometallomics at the Host-Microbiome Interface Across Pathologies.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {6}, pages = {}, doi = {10.3390/life16060920}, pmid = {42355447}, issn = {2075-1729}, abstract = {Microbiome dysbiosis has become recognized as an important interface connecting environmental exposures to chronic inflammatory and degenerative diseases. Although prior research has largely considered heavy metals as biomarkers of exposure and toxicity, their function as ecological modulators of host-associated microbial communities remains underexplored. The oral cavity is a distinct exposome-microbiome interface where environmental, behavioral, and intraoral metal sources converge and interact with structured biofilms and mucosal immunity. This review adopts an ecological systems perspective, interpreting chronic low-dose exposure to metals such as cadmium, lead, mercury, nickel, chromium, arsenic, and aluminum as a sustained selective force on oral microbial networks. A resilience-threshold model is proposed in which cumulative metal pressure progressively diminishes microbial community stability, alters network topology, and drives transitions toward persistent dysbiosis. These modifications are further reinforced by oxidative-inflammatory feedback loops at the host-microbiome interface, facilitating a self-sustaining ecological imbalance. Sketching on insights from microbial ecology, environmental toxicology, and host response biology, this review presents a framework that links metallomic patterns to microbial restructuring, redox imbalance, immune activation, and regulatory adaptation. The analysis emphasizes ecological perturbations from stable dysbiotic states and identifies key methodological limitations that currently restrict causal inference. By conceptualizing heavy metals as active ecological drivers rather than passive exposure indicators, this work establishes a foundation for understanding microbiome-mediated disease susceptibility within an exposome-informed systems biology framework.}, }
@article {pmid42356226, year = {2026}, author = {Zhao, L and Chen, Z and Sun, Y and Jia, K and Liu, Y and Li, P}, title = {Dietary Polysaccharides in Skin Health: Structure-Function Relationships and Implications for Nutritional Dermatology.}, journal = {Nutrients}, volume = {18}, number = {12}, pages = {}, doi = {10.3390/nu18121838}, pmid = {42356226}, issn = {2072-6643}, support = {2026-JYB-XJSJJ006//Beijing University of Chinese Medicine/ ; }, mesh = {Humans ; *Polysaccharides/chemistry/administration &amp; dosage/pharmacology ; Structure-Activity Relationship ; *Skin/drug effects/metabolism/microbiology ; *Dietary Carbohydrates/administration &amp; dosage ; Animals ; Psoriasis ; Dermatitis, Atopic ; *Skin Physiological Phenomena ; Skin Aging ; Skin Diseases ; Diet ; Skin Microbiome ; }, abstract = {Skin health depends on the coordinated maintenance of barrier integrity, immune homeostasis, redox balance, microbial ecology, and systemic metabolic status. Among dietary constituents, polysaccharides have attracted increasing attention because they represent a structurally heterogeneous class of complex carbohydrates whose biological behavior is shaped by molecular weight, monosaccharide composition, glycosidic linkage patterns, branching, higher-order conformation, and physicochemical properties. However, many current skin-related studies remain primarily phenomenon-driven, with insufficient attention to how specific structural features influence biological function and dermatologic relevance. From a structure-function perspective, key structural features of dietary polysaccharides may influence several skin-relevant biological processes, including microbiota-associated signaling, immune regulation, barrier homeostasis, oxidative balance, and extracellular matrix protection. The relevance of these structure-linked functions differs across dermatologic contexts: it appears most direct in photoaging, more conditional in atopic dermatitis, and relatively indirect in psoriasis, whereas wound-repair-related settings are less closely aligned with strict dietary relevance. Current evidence therefore supports structure-function associations more strongly than direct associations between specific structural features and dermatologic outcomes. Dietary polysaccharides are not functionally interchangeable in skin-related contexts, and their skin-related effects depend on structural background, disease setting, and mode of application. Where non-dietary evidence is discussed, it serves primarily as mechanistic or translational contextualization rather than as a basis for nutritional recommendation. Clarifying these relationships may support future mechanistic research and facilitate more rational nutritional applications of dietary polysaccharides in skin health.}, }
@article {pmid42356333, year = {2026}, author = {Bragazzi, NL and Ceylan, H&#x130; and Rosi, A and Scazzina, F and de Giorgio, A and Dergaa, I and Scoditti, E and Garbarino, S}, title = {The Co-Evolution of Sleep and Diet: Toward an Emerging Framework of Evolutionary Chrononutrition in Circadian-Metabolic Health.}, journal = {Nutrients}, volume = {18}, number = {12}, pages = {}, doi = {10.3390/nu18121947}, pmid = {42356333}, issn = {2072-6643}, mesh = {Humans ; *Sleep/physiology ; *Biological Evolution ; *Circadian Rhythm/physiology ; *Diet ; *Feeding Behavior/physiology ; Animals ; Energy Metabolism ; }, abstract = {Sleep and dietary behavior are deeply conserved biological processes that co-evolved under ecological pressures shaping human anatomy, metabolism, immunity, cognition, and life history strategies. Major transitions in human dietary ecology, including plant-dominant hominin foraging, increased meat consumption, control of fire and cooking, agricultural domestication, industrialization, and postindustrial globalization, restructured nutrient intake, pathogen exposure, microbial ecology, metabolic demands, and temporal organization of behavior. Emerging evidence from evolutionary genomics, chronobiology, neuroendocrinology, and microbiome science indicates that sleep-feeding interactions represent a conserved adaptive regulatory module optimized for fluctuating energy availability and strong photoperiodic entrainment. Modern environments characterized by widespread availability of highly palatable, energy-dense foods rich in refined carbohydrates, added sugars, and multiple industrial additives, together with artificial light at night, continuous caloric access, sedentary behavior, and psychosocial stress produce a profound evolutionary mismatch destabilizing circadian-metabolic homeostasis. This mismatch is characterized by circadian disruption, temporal misalignment of feeding and sleep behaviors, and, in many populations, insufficient sleep duration. Within this conceptual landscape, the emerging framework of "evolutionary chrononutrition" proposes that metabolic health and sleep integrity depend not only on what humans eat, but critically on when food is consumed in relation to endogenous circadian architecture shaped across deep evolutionary time. This review synthesizes anthropological, physiological, and molecular evidence to develop an integrative evolutionary framework linking sleep and diet to contemporary cardiometabolic, neurodegenerative, inflammatory, and psychiatric disorders, with particular emphasis on how each major dietary transition plausibly altered sleep duration, architecture, circadian timing, neuroendocrine regulation, and the temporal alignment between feeding behavior and biological rhythms.}, }
@article {pmid42357828, year = {2026}, author = {Prabhakara, KH and Zhao, Y and Ullrich, K and Farr, AD and Rainey, PB}, title = {Diverse Microbial Communities Assemble on Both Recalcitrant and Labile Carbon Sources.}, journal = {Environmental microbiology}, volume = {28}, number = {7}, pages = {e70351}, doi = {10.1111/1462-2920.70351}, pmid = {42357828}, issn = {1462-2920}, support = {//Max-Planck-Gesellschaft/ ; }, mesh = {*Cellulose/metabolism ; *Carbon/metabolism ; Glucose/metabolism ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Soil Microbiology ; Biodiversity ; }, abstract = {Microbial community assembly is shaped by the nature of available resources, with labile carbon sources like glucose often expected to support low diversity due to rapid growth and competitive exclusion. In contrast, recalcitrant substrates like cellulose are thought to support higher diversity through slower growth and increased niche partitioning. In previous work, we showed that compost-derived microbial communities propagated on cellulose maintained high diversity over nearly a year. To determine whether such diversity is specific to recalcitrant substrates or reflects more general features of assembly, we tracked community dynamics in three environments-cellulose paper, cellulose broth and glucose-using daily 16S rRNA profiling. Communities maintained through four bi-weekly serial transfers, with five replicates per treatment, yielded a high-resolution dataset of over 800 samples. Despite originating from the same inoculum, communities diverged sharply in both taxonomic and functional composition. Cellulose environments yielded stable communities enriched in specialists, while glucose environments exhibited rapid succession and dominance by generalists. Surprisingly, all environments sustained comparably high levels of taxonomic diversity. Functional inference suggested extensive cross-feeding and resource salvaging in both cases. Our results reveal distinct assembly trajectories under simple carbon regimes and provide a foundation for future mechanistic study.}, }
@article {pmid42358268, year = {2026}, author = {Peng, B and Shu, J and Chen, B and Li, C and Han, Y}, title = {Microbial architecture and metabolic profiles in Xiaoqu: insights into traditional glutinous rice wine fermentation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1869908}, pmid = {42358268}, issn = {1664-302X}, abstract = {Xiaoqu is a traditionally propagated multi-species starter used in Chinese sweet glutinous rice wine fermentation and represents a low-temperature solid-state fermentation system distinct from Japanese pure-culture Aspergillus oryzae koji and Western malt-based saccharification platforms. Unlike defined inoculation systems, Xiaoqu functions as a process-shaped microbial architecture assembled through repeated ecological selection under artisanal production conditions. This review synthesizes current knowledge regarding the microbial ecology, guild organization, fermentation trajectories, and metabolite modulation associated with Xiaoqu-mediated glutinous rice wine production. Xiaoqu communities are typically structured around amylolytic molds, fermentative yeasts, non-Saccharomyces yeasts, and lactic acid bacteria (LAB), which collectively regulate saccharification, acidification, ethanol restraint, and flavor formation through coupled ecological and metabolic interactions. We propose a process-phytochemical selection framework, presented as a literature-derived conceptual hypothesis, to explain how botanical inputs, matrix properties, and processing conditions jointly shape microbial succession, interaction topology, and metabolic trajectories. The review further develops an architecture-to-trajectory perspective in which sugar-acid-ethanol coupling emerges as a systems-level phenotype governed by guild interactions, cross-feeding, feedback regulation, and environmental constraints rather than by individual taxa alone. Functional redundancy, hybrid starter systems, temporal trajectory analysis, and safety constraints associated with toxigenic risks are also discussed as key factors influencing fermentation robustness, reproducibility, and sensory stability. Finally, we highlight the need for architecture-preserving control strategies integrating strain-level multi-omics, synthetic-community reconstruction, and trajectory-oriented process analysis to support mechanistic understanding and controllable design of Xiaoqu-mediated fermentations.}, }
@article {pmid41922943, year = {2026}, author = {Kaiyue, P and Yanlong, F and Jiahua, D and Jiahai, W and Bing, Z}, title = {Fermentation quality and microbial communities of mixed silage from Pennisetum glaucum × purpureum and Rosa roxburghii residue.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-04973-1}, pmid = {41922943}, issn = {1471-2180}, support = {Qiankehe Zhongyindi [2026] No. 011//Guizhou Provincial Department of Science and Technology Funded Project/ ; }, abstract = {This study investigates the mechanism by which varying mixing ratios of Pennisetum glaucum × purpureum and Rosa roxburghii residue influence the overall quality of silage feed. A completely randomized design with three replicates per treatment was used. By establishing mixed fermentation ratios of Pennisetum glaucum × purpureum and Rosa roxburghii residue at 0:100 (R), 20:80 (P20), 40:60 (P40), 60:40 (R40), 80:20 (R20), and 100:0 (P), the study systematically measured the nutritional components, fermentation quality, Cornell Net Carbohydrate and Protein System (CNCPS) protein fractions, and microbial community structure of the mixed fermented products. Analysis was conducted using Kyoto Encyclopedia of Genes and Genomes (KEGG) functional prediction and correlation networks. The results indicate that at mixing ratios of 60:40 (R40) or 80:20 (R20), silage quality was optimal: the content of starch in the feed significantly increased, fiber content decreased, lactic acid levels markedly rose to 1.35–1.67 g/kg DM, and pH dropped to 3.60–3.63, while both ammonium nitrogen (AN) and butyric acid levels remained low. The analysis of CNCPS protein fractions revealed a high retention of true protein, accompanied by a notable decrease in the proportion of nonprotein nitrogen (NPN). Microbial community analysis showed that these optimal mixing ratios were associated with higher relative abundances of beneficial lactic acid bacteria (Levilactobacillus and Lactiplantibacillus) and lower abundances of potentially harmful bacteria (Enterobacter). Functional predictions further indicated that these microbial shifts correlated with enhanced metabolic pathways, including carbohydrate metabolism. In summary, mixing Pennisetum glaucum × purpureum and Rosa roxburghii residues at 60:40 or 80:20 ratios are associated with improved substrate composition and microbial ecology. This approach not only enhances the nutritional value and fermentation stability but also improves the preservation efficiency of silage protein, thereby providing a viable technical solution and theoretical foundation for the utilization of agricultural byproducts and the production of high-quality silage.}, }
@article {pmid42008215, year = {2026}, author = {Zhang, J and Yang, X and Xie, L and Liu, Q and Zhang, X}, title = {Sympathetic denervation alters pulmonary microbiota diversity and composition in mice.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {42008215}, issn = {1618-1905}, support = {SBGJ202103001//Health Commission of Henan Province/ ; }, abstract = {BACKGROUND: The pulmonary sympathetic nervous system (SNS) regulates airway tone, vascular resistance, and immune responses, yet its role in shaping the lung microbiome remains poorly understood. OBJECTIVES: This study investigated the effects of chemical pulmonary sympathetic denervation (SD) on lung microbial diversity and community structure in mice. METHODS: Male C57BL/6 mice were randomly assigned to a control group or an SD group that received intrapulmonary 6-hydroxydopamine (6-OHDA) to ablate sympathetic nerve terminals. Lung tissues were analyzed for histopathology, tyrosine hydroxylase (TH), and norepinephrine (NE) levels, and bronchoalveolar lavage fluid (BALF) was analyzed for TNF-α concentrations. Lung tissue microbiota was profiled by 16 S rRNA gene sequencing (V3–V4 regions), processed with QIIME 2/DADA2, and taxonomically assigned using the SILVA 138 database. Alpha- and beta-diversity metrics, amplicon sequence variants (ASVs), and differential taxa were compared between groups. RESULTS: SD significantly reduced TH expression and NE content in lung tissue (P < 0.01), confirming effective denervation, without inducing histological injury or increasing BALF TNF-α. Compared with Ctrl, SD mice exhibited significantly higher species richness and phylogenetic diversity (ACE, Chao1, Observed species, PD whole tree; P < 0.01) but no significant change in Shannon or Simpson indices. Beta-diversity analysis showed clear separation between groups (PERMANOVA, P = 0.007–0.04). Flower plot and taxonomic annotation revealed more unique ASVs and broader phylogenetic representation in SD mice. Differential abundance analysis identified enrichment of Staphylococcus, Pelomonas, and Burkholderiales in the SD group. CONCLUSIONS: Pulmonary sympathetic denervation significantly increases lung microbial richness and alters key taxa without triggering overt inflammation, suggesting that SNS activity is an important regulator of pulmonary microbial ecology under resting conditions.}, }
@article {pmid42338306, year = {2026}, author = {Goldberg, A and Shtossel, O and Louzoun, Y and Shnerb, NM}, title = {Niche Overlap Is Not Enough: Same Overlap, Contrasting Fluctuations.}, journal = {Ecology letters}, volume = {29}, number = {6}, pages = {e70425}, pmid = {42338306}, issn = {1461-0248}, support = {7578//Israel Ministry of Science (Italy-Israel cooperation)/ ; 2435/24//Israel Science Foundation/ ; }, mesh = {*Ecosystem ; *Models, Biological ; }, abstract = {Niche overlap (NO) is a cornerstone of coexistence theory, summarising the strength of competitive coupling among species. Yet NO collapses distinct mechanisms into a single value and may miss key dynamical features. We quantify this limitation by examining temporal correlations in species abundances, a key out-of-equilibrium observable in microbial ecology. Using a MacArthur-type consumer-resource model, we show that communities with identical NO can display opposite dynamical patterns. Within the resource-mediated fluctuation regime studied here, a yield-depletion mismatch (YDM)-the difference between depletion and yield dissimilarities-consistently predicts the sign and magnitude of abundance correlations across analytical approximations, stochastic simulations, and a reanalysis of microbial time series. In contrast, growth-rate correlations are governed by NO. More broadly, our results show that dynamical observables can depend on mechanistic details beyond those summarised by niche overlap.}, }
@article {pmid42338743, year = {2026}, author = {Zhao, H and Ao, L and Hao, L and Wei, Y and Yin, HZ and Lee, XQ and Guo, C and Wang, Z and Yang, J and Yang, R and Zhou, GL}, title = {Integrative mechanisms and intervention targets of the microbiota-gut-brain axis in depressive disorders: advances across immune, endocrine, and central nervous system pathways.}, journal = {Frontiers in psychiatry}, volume = {17}, number = {}, pages = {1848918}, pmid = {42338743}, issn = {1664-0640}, abstract = {Depressive disorders are highly heterogeneous syndromes characterized not only by depressed mood but also by cognitive impairment, sleep-circadian rhythm disturbances, altered appetite, somatic discomfort, and metabolic or gastrointestinal comorbidities. In recent years, the microbiota-gut-brain axis (MGBA) has been increasingly recognized as an integrative biological framework linking abnormalities in mood regulation, immune responses, endocrine function, metabolism, and neuroplasticity. This review provides a systematic synthesis of gut microbial ecology and host phenotypic features associated with depressive disorders, with particular emphasis on the depletion of short-chain fatty acid-producing commensals, the enrichment of potentially pro-inflammatory taxa, and the functional remodeling of key metabolic pathways, including the tryptophan-kynurenine pathway, short-chain fatty acids, bile acids, and trimethylamine N-oxide. We further discuss how bidirectional gut-to-brain and brain-to-gut communication may contribute to the onset and progression of depressive disorders through intestinal barrier disruption, low-grade systemic inflammation, hypothalamic-pituitary-adrenal axis activation, vagal signaling, and dysregulation of neurotransmitter and neurotrophic pathways. Current interventional evidence suggests that dietary and lifestyle modification, psychobiotics, and fecal microbiota transplantation may exert antidepressant potential in selected populations; however, the overall effect sizes remain limited and between-study heterogeneity is substantial. Patients with prominent gastrointestinal symptoms, metabolic abnormalities, or low-grade inflammatory states may represent priority candidates for MGBA-targeted interventions; nevertheless, a putative microbiota-responsive phenotype should not be simply equated with high stress exposure alone, and its definition requires prospective validation integrating stress burden, host responses, and microbial/metabolic readouts. Overall, MGBA research is gradually moving beyond descriptive profiling of microbial composition toward functional integration and clinical translation; however, causal inference, multi-omics standardization, and the identification of stratification biomarkers remain major challenges. Future studies should incorporate phenotype-based stratification, strengthened functional readouts, and precision intervention designs to determine which patients are most likely to benefit from microbiota-targeted therapies.}, }
@article {pmid42340359, year = {2026}, author = {Bandopadhyay, S and Danczak, RE and Patel, KF and Beilsmith, KR and Weisenhorn, PB and Spanbauer, TL and Reichart, NJ and Weintraub, MN and Bailey, VL}, title = {Soil microbial ecology and microbiome-metabolite linkages improve understanding of ecosystem states along terrestrial-aquatic interfaces.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiag066}, pmid = {42340359}, issn = {1574-6941}, abstract = {Coastal soils are dynamic systems where unique microbial niches are shaped by the intensity and duration of flooding between the terrestrial and aquatic boundaries of the terrestrial-aquatic interface (TAI). We aimed to understand the soil microbial community (16S rRNA gene) along the TAIs of a freshwater versus estuarine region and how it relates to organic matter (OM, FTICR-MS). We studied the TAI gradients along a transect from upland (forested), transition (stressed forest), to wetland at three sites in each of the Lake Erie (freshwater) and Chesapeake Bay (estuarine) regions. Microbial communities differed significantly by region, transect position, and site. Contrary to expectations, given their dynamic hydrologies, transitions represented midpoints in microbial richness and diversity. We identified a core microbiome conserved across all transect positions within a region, highlighting potential microbial functions most resilient to environmental change. Indicator taxa unique to each transect position defined specific niches shaped by soil biogeochemistry. Co-expression networks of feature-level β-nearest-taxon indices revealed positive relationships in bacterial and OM feature contributions to community assembly. Our study provides critical insights into microbial communities at the forefront of hydrological changes in coastal areas that connect the land to lakes and oceans and remain vulnerable to changing weather patterns.}, }
@article {pmid42340399, year = {2026}, author = {Mattar, MM and Eraqi, WA and Zaki, MB and Elkashlan, AM and Abouzid, KAM and Aziz, RK and Yassin, AS and Elbehery, AHA}, title = {Metagenomic Analysis of Rural Groundwater Viromes Reveals Bacteriophage Contributions to Groundwater Microbial Ecology.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, pmid = {42340399}, issn = {1432-184X}, mesh = {*Groundwater/virology/microbiology ; *Bacteriophages/genetics/classification/isolation &amp; purification/physiology ; Metagenomics ; *Virome ; Genome, Viral ; *Bacteria/virology/genetics/classification ; Microbiota ; Phylogeny ; Ecosystem ; }, abstract = {Groundwater ecosystems host diverse microbial communities, yet the diversity and ecological roles of their associated viral genomes remain poorly characterized. Here, we investigated viral community composition, diversity, host associations, lifestyles, and auxiliary metabolic potential in groundwater from three hand pumps located in Toukh, Qalyubia, Egypt, representing distinct local surroundings and potential contamination pressures. Using complementary viral detection approaches and a quality assessment workflow, we recovered 9,534 non-redundant viral contigs spanning a wide range of viral genome quality. Taxonomic profiling revealed dominance of tailed dsDNA bacteriophages (Uroviricota/Caudoviricetes) across all pumps, with ~ 99% of contigs not assigned below the class level. Whereas the viral composition of pump 3 was distinct and its diversity was consistently higher, pumps 1 and 2 clustered together, a pattern mirrored across taxonomic scales and diversity metrics. The majority of predicted viral hosts belonged to phylum Pseudomonadota, followed by Actinomycetota, Bacillota and Bacteroidota, with levels that varied between pumps. Correlation and network analyses showed strong concordance between the relative abundance of bacteria and the abundance of viruses that potentially infect them. Lifestyle prediction indicated a descending relative abundance of viruses with lysogenic lifestyle from pumps 1 through 3. Auxiliary metabolic genes (AMGs) related mainly to nucleotide, amino acid, and cofactor metabolism were detected in all pumps, with distinct pump-specific repertoires suggesting localized viral metabolic strategies. Together, these results demonstrate that groundwater viromes are ecologically structured and highly novel, with the potential ability to modulate host metabolism, highlighting their potential role in shaping subsurface microbial communities.}, }
@article {pmid42342198, year = {2026}, author = {Gonzalez, JAC and Brant, CF and Pigossi, SC and Wiegand, A and Sabino-Silva, R and Massignan, C and Zanatta, RF}, title = {Is Erosive Tooth Wear a Truly Non-Bacterial Condition? A Scoping Review.}, journal = {Journal of dentistry}, volume = {}, number = {}, pages = {106859}, doi = {10.1016/j.jdent.2026.106859}, pmid = {42342198}, issn = {1879-176X}, abstract = {OBJECTIVE: This scoping review examined the current knowledge on oral biofilm ecology and erosion-associated dysbiosis, proposing pathways by which the oral microbiome may contribute to erosive tooth wear (ETW).<br><br>DATA: The PRISMA-ScR guidelines were followed (OSF platform, doi: 10.17605/OSF.IO/KM4JQ). Primary research articles (in vitro, in situ, or clinical trials) that investigated ETW associated with oral biofilm ecology, erosion-associated dysbiosis, or microbiome pathways were included.<br><br>SOURCES: A systematic search of PubMed/MEDLINE, Scopus, Web of Science, Embase, and the Cochrane Library was conducted up to April 2026 using predefined terms.<br><br>STUDY SELECTION: A total of 2355 records were identified. After screening, 16 full texts were eligible, and 7 studies were included for data extraction. The included studies were highly heterogeneous in design [including observational (3), randomized (1), and in situ/ex vivo (3) models], outcomes, and biological targets. Two studies evaluated the biofilm&#xb4;s protective effect against erosive challenge, showing reduced enamel erosion but limited protection of dentin. Two studies assessed bioactive compounds' influence on microbiome, demonstrating reduced bacterial adhesion, altered pellicle structure, and improved erosion protection. Three studies investigated microbial ecology directly with inconsistent findings: one found no significant differences in microbial counts, another reported similar alpha- and beta-diversity but taxon-level differences, and a third showed lower microbial diversity, proteolytic protein degradation, altered gene expression, and metabolic profiles compatible with acid-adapted and proteolytic communities.<br><br>CONCLUSIONS: The findings suggest that the oral microbiome may act as an ecological modifier of ETW by influencing biofilm organization, and local metabolic behavior, but current evidence is insufficient to determine whether ETW is truly a non-bacterial condition.<br><br>CLINICAL SIGNIFICANCE: The oral microbiome can influence erosive tooth wear, which impacts risk assessment and prevention strategies.}, }
@article {pmid42342731, year = {2026}, author = {Schäfer, C and Bonatelli, ML and Burgos, IMT and Kleinsteuber, S and Machado, D and Øyås, O and Harms, H and Sträuber, H}, title = {Functional roles of degraders and non-degraders in anaerobic trophic networks converting lignocellulose into monocarboxylates.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {42342731}, issn = {2055-5008}, support = {100572058//S&#xe4;chsische Aufbaubank/ ; 100572058//S&#xe4;chsische Aufbaubank/ ; 100572058//S&#xe4;chsische Aufbaubank/ ; 323134//Norges Forskningsr&#xe5;d/ ; 323134//Norges Forskningsr&#xe5;d/ ; }, mesh = {*Lignin/metabolism ; Metagenomics ; Xylans/metabolism ; *Carboxylic Acids/metabolism ; Anaerobiosis ; Fermentation ; Ethanol/metabolism ; Metabolic Networks and Pathways ; *Bacteria/metabolism/classification/genetics ; Cellulose/metabolism ; Microbial Consortia ; Lactic Acid/metabolism ; Acetic Acid/metabolism ; Carbon Dioxide/metabolism ; }, abstract = {Lignocellulose is a promising renewable resource for anaerobic biochemical production, but its microbial conversion remains challenging. To elucidate metabolic networks in lignocellulose-degrading consortia, inocula of various origins were enriched on cellulose or xylan. Community composition and metabolic functions were revealed by amplicon sequencing, metagenomics, genome-scale metabolic modelling, and metabolic simulations. In cellulose-enriched communities, Fibrobacter and Lacrimispora consistently dominated as primary cellulose degraders, whereas Bacteroides likely functioned as secondary degraders. Acetic acid (up to 1.3 g l[-1]) and CO2 were the main fermentation products. Xylan enrichments produced C2-C6 fatty acids (up to 3.9 g l[-1]), lactic acid (up to 1.2 g l[-1]), ethanol (up to 1.2 g l[-1]), CO2, and H2. Clostridium dominated one xylan community and produced mainly butyric acid, while Bifidobacterium dominated another and produced mainly lactic acid. Caproic acid production was experimentally observed in one xylan enrichment. Metagenomic annotations and metabolic simulations suggest that Lacrimispora amygdalina degraded xylan and Robinsoniella peoriensis consumed xylobiose as a secondary consumer, both likely producing ethanol and lactic acid that supported caproic and butyric acid production by Caproicibacter fermentans. Integrated analysis identified functional guilds and clarified the roles of degraders and non-degraders, providing a blueprint for engineering synthetic consortia for sustainable biochemical production.}, }
@article {pmid42344006, year = {2026}, author = {Tepson, JA and Agyirifo, DS}, title = {Microbial Ecology at the Nexus of Food Safety and Biotechnology With Ecological Mechanisms, Risks, and Emerging Innovations.}, journal = {International journal of food science}, volume = {2026}, number = {}, pages = {6618960}, pmid = {42344006}, issn = {2314-5765}, abstract = {Food systems are complex microbial ecosystems in which microorganisms play dual and often contrasting roles as agents of foodborne contamination and as essential drivers of food production and biotechnological innovation. Microbial ecology provides an integrative framework for understanding how microbial interactions, environmental conditions, and human interventions shape food safety outcomes and technological processes. This narrative integrative review is aimed at synthesizing current literature on microbial ecology at the nexus of food safety and food biotechnology and at identifying key research gaps and future directions. In this study, peer-reviewed journal articles addressing microbial interactions, contamination pathways, and ecological mechanisms relevant to food safety and biotechnology published between 2015 and 2025 were retrieved from major scientific databases and were synthesized using a narrative integrative approach. The review highlights ecological factors including microbial competition, stress adaptation, and biofilm formation across pre- and postharvest environments. At the same time, these same ecological principles are harnessed in food biotechnology to drive controlled fermentations, enhance shelf life through biopreservation, develop functional probiotics and enzymes, and engineer microbial systems via synthetic biology. Advances in high-throughput sequencing technologies, including whole genome sequencing, metagenomics, and multiomics integration, are identified as transformative tools for linking food-associated microbial community structure to functional outcomes. Despite significant progress, challenges remain in translating ecological insights into reliable industrial and regulatory practices due to microbial complexity, data integration limitations, and safety considerations. The review positions microbial ecology as a strategic framework for advancing food safety, biotechnological innovation, and sustainable food systems.}, }
@article {pmid42332311, year = {2026}, author = {Cai, P and Xiong, Y and Wang, W and Du, X and Lu, C and Li, Y and Li, Q and Hong, Y}, title = {Foliar Application of Bacillus thuringiensis Regulates Soil Physicochemical Properties and Microbial Ecological Functions in Tea Plantations.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02813-3}, pmid = {42332311}, issn = {1432-184X}, support = {JZ240071, JAT241155//Fujian Province Young and Middle-Aged Research and Education Projects/ ; 2025N0013, 2025FJSYCXM03//Project of Fujian Provincial Department of Science and Technology/ ; YJ202307, YJ202432, YJ202433//Wuyi University Talent Introduction Project/ ; N2023Z005, N2023Z007, N2024Z009, N2025K019//Nanping Academy of Resource Industrialization Chemistry Project/ ; }, abstract = {Bacillus thuringiensis (Bt) is widely employed as a biological control agent against pests in tea plantations, yet its impacts on soil health and microbial ecology remain insufficiently understood. This study investigated the effects of two Bt application regimes, namely moderate-frequency conventional Bt application (Bt1, 3 sprays over 21 days) and high-frequency intensive Bt application (Bt2, 6 sprays over 42 days), on soil physicochemical properties, enzyme activities, and microbial community structure and function in tea soils. The moderate-frequency conventional Bt1 significantly improved soil nutrient status by increasing organic matter, available nitrogen, and potassium, and boosted acid protease, sucrase, and cellulase activities, while Bt2 achieved the maximum urease and polyphenol oxidase activities but failed to promote soil available nutrients and organic matter as effectively as Bt1. Although neither Bt treatment induced notable shifts in overall microbial alpha-diversity indices, community composition differed distinctly between the two treatments. Bt1 enriched beneficial taxa related to nitrogen fixation and organic matter degradation including Pseudomonas, Bradyrhizobium, and Sphingomonas, and sharply suppressed pathogenic fungi such as Aspergillus and Curvularia, whereas Bt2 caused an 18.29% reduction in Sphingomonas abundance with limited enrichment of beneficial bacteria. Functional predictions indicated that Bt1 amplified microbial carbon degradation and nitrogen cycling, enriched saprotrophic and symbiotic fungi and reduced plant pathogens by 85.78%, while both Bt treatments elevated saprotrophic fungi yet Bt2 only reduced pathogens by 11.84%. Co-occurrence network analyses revealed enhanced microbial interactions and community stability under Bt1, while excessive high-frequency Bt2 reduced network connectivity and stability compared with CK and Bt1. These results suggest that moderate-frequency conventional Bt application can positively modulate soil microbial communities and ecosystem functions, providing valuable insights for sustainable pest management and soil health maintenance in tea agroecosystems.}, }
@article {pmid42333012, year = {2026}, author = {He, Y and Qiu, K and Zhang, W and Duan, X and Zhao, S and Qiu, Z and Zhu, M}, title = {A Plant Growth-Promoting Fungus Cladosporium sphaerospermum Attenuates Cadmium Stress in Wheat via Gene Expression and Metabolite Production.}, journal = {Physiologia plantarum}, volume = {178}, number = {3}, pages = {e70974}, doi = {10.1111/ppl.70974}, pmid = {42333012}, issn = {1399-3054}, support = {32302431//National Natural Science Foundation of China/ ; 242301420142//the Natural Science Foundation of Henan/ ; 242300420163//the Natural Science Foundation of Henan/ ; 242102110213//the Scientific and Technological Project of Henan Province/ ; GZS2025009//Henan Center for Outstanding Overseas Scientists/ ; 25A180018//Henan provincial key research projects for institutions of higher learning/ ; }, mesh = {*Triticum/microbiology/drug effects/genetics/metabolism/physiology ; *Cadmium/toxicity ; *Cladosporium/physiology ; Gene Expression Regulation, Plant/drug effects ; Stress, Physiological/drug effects ; Seedlings/drug effects/microbiology ; Glutathione/metabolism ; }, abstract = {Cadmium (Cd) contamination has threatened plant health and resulted in a notable reduction of crop yields. Cladosporium sphaerospermum is known as a plant growth-promoting fungus that modulates plant development under abiotic conditions. However, the molecular mechanisms underlying C. sphaerospermum-mediated alleviation of Cd toxicity in wheat is unknown. By integrating physio-biochemical, transcriptomic and metabolomic analysis, the beneficial roles of C. sphaerospermum in moderating Cd-induced (100 μM CdCl2) toxicity in wheat seedlings (Triticum aestivum L.) were studied here. C. sphaerospermum enhanced plant growth under Cd conditions by reducing MDA content and increasing antioxidant enzyme activities to re-establish redox homeostasis. Expression of wheat genes in MAPK pathways, plant hormone signal transduction, glutathione metabolism and cysteine metabolism pathways were notably differentially regulated by C. sphaerospermum under Cd conditions. The metabolites involved in oxidative phosphorylation, amino acid metabolism and tRNA biosynthesis were significantly modulated by C. sphaerospermum under Cd conditions. Integrated transcriptome and metabolome analysis indicated that the genes and metabolites in glutathione metabolism and cysteine metabolism pathways were crucial for C. sphaerospermum-mediated mitigation of Cd toxicity in wheat. The findings provide new insights into the molecular mechanisms of fungus-regulated wheat tolerance to Cd toxicity. C. sphaerospermum, as a promising and eco-friendly plant growth-promoting fungus, is suggested to be applied in Cd contaminated soil for food safety production.}, }
@article {pmid42334364, year = {2026}, author = {Cockell, CS}, title = {Fifty Years after Viking: The Promise of Solar System Microbiology and Microbial Ecology.}, journal = {Astrobiology}, volume = {}, number = {}, pages = {15311074261464013}, doi = {10.1177/15311074261464013}, pmid = {42334364}, issn = {1557-8070}, abstract = {The ambiguity of the Viking lander life-detection experiments left microbiology and microbial ecology out of space missions for 50 years. However, this was largely because the scientific process inherent in the search for life was misunderstood by a space exploration community that wanted clear-cut answers. Since Viking, enormous advances have been made in our knowledge of microorganisms, their biochemistry, and physical and chemical limits. Coupled with improvements in methods for culturing microorganisms and measuring their active metabolism, this has made possible more sophisticated experiments to search for life in extreme environments on Earth and on other planetary bodies. By overcoming misunderstandings surrounding the Viking lander experiments, microbiology and microbial ecology can take center stage in renewed efforts to seek life elsewhere. Furthermore, new knowledge in these fields should be used to overhaul assumptions in planetary protection, and it can be used to achieve permanent human space settlement.}, }
@article {pmid42334609, year = {2026}, author = {Zheng, Y and Chen, C and Guan, D and Huang, Y and Xiong, L and Liu, R}, title = {Viral community dynamics and functional succession in advanced drinking water treatment processes.}, journal = {Archives of microbiology}, volume = {208}, number = {9}, pages = {}, pmid = {42334609}, issn = {1432-072X}, mesh = {*Drinking Water/virology/microbiology ; *Water Purification/methods ; Bacteria/genetics/classification/isolation &amp; purification ; *Viruses/genetics/classification/isolation &amp; purification ; China ; Metagenomics ; Water Microbiology ; }, abstract = {Viruses play a significant role in microbial ecology, yet their impact on drinking water systems remains poorly understood. We collected water from different treatment process streams of an ozone-bioactivated carbon (O3-BAC) advanced drinking water treatment plant in eastern China. DNA viral metagenomic sequencing was then performed to analyze viral abundance, community structure, diversity, host prediction, virulence factors, potential viral pathogens, and functional genes, including carbohydrate-active enzymes (CAZymes), auxiliary metabolic genes (AMGs), and antibiotic resistance genes (ARGs). The results revealed that treatment reduced viral abundance and diversity, although certain taxa not detected in raw water or sedimentation water (e.g., Preplasmiviricota) were detected in sand-filtered water and finished water. Caudoviricetes were the most abundant viruses in the water treatment process. The virus host types were predominantly bacteria, mainly Lactobacillus, Mycoplasma, Staphylococcus, Bacillus, and Streptococcus. Functional analysis revealed viral involvement in carbohydrate degradation via CAZymes and modulation of host metabolism through AMGs and ARGs to support viral replication. Potential human pathogens were identified within Poxviridae and Herpesviridae. This study provides novel insights into DNA viral ecological dynamics in engineered water systems and supports enhanced pathogen control strategies.}, }
@article {pmid42334633, year = {2026}, author = {Deng, Q and Li, J and Luo, X and Peng, Z and Xian, W and Xiong, H and Ye, L and Liu, H and Ren, J and Wu, J and Li, W and Wang, P}, title = {Third-generation RNA Amplicon Sequencing Reveals the Dynamics of Microbial Communities in the Tidal Reach of a Subtropical Estuary.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02804-4}, pmid = {42334633}, issn = {1432-184X}, support = {32200090//National Natural Science Foundation of China/ ; }, abstract = {Estuarine ecosystems are characterized by periodic tidal cycles that induce dynamic salinity fluctuations, yet how these dynamic salinity changes affect microbial diversity, community composition, and network structure remains poorly understood. Answering this question would enhance our understanding of the effects of periodic tides on microbial communities in estuaries. To address this knowledge gap, we collected hourly water samples over a 24-h time series from the tidal reach of the Pearl River Estuary (PRE) and explored the dynamics of both prokaryotic and eukaryotic microbial diversity and their co-occurrence networks during a complete tidal cycle by utilizing RNA-derived cDNA combined with third-generation (PacBio) amplicon sequencing. This approach targets the active microbial community (by using RNA) while providing high taxonomic resolution (by full-length sequencing of 16S rRNA gene / ITS regions). Our results revealed that salinity was the dominant driver of the changes of microbial diversity and community compositions in the tidal reach, with a significant decrease in microbial alpha diversity as salinity increased. Furthermore, we observed a non-linear relationship between salinity and microbial network complexity and stability. Notably, network stability in both single- and cross-domain networks was positively correlated with connectance and P/N (the positive-to-negative edge ratio). Additionally, cross-domain networks exhibited higher complexity (node numbers, total links, and average node degree), but lower network stability (robustness and vulnerability) compared to single-domain co-occurrence networks. Overall, our findings provide comprehensive insights into how periodic salinity fluctuations regulate microbial community structure and cross-domain interactions in dynamic estuarine environments.}, }
@article {pmid42331254, year = {2026}, author = {Wu, W and Zhou, Y and Liu, F and Zhu, Y and Dong, Z}, title = {Evaluation of lipid pretreatment methods for microbial identification using linear negative-ion MALDI-TOF MS.}, journal = {Journal of microbiological methods}, volume = {}, number = {}, pages = {107604}, doi = {10.1016/j.mimet.2026.107604}, pmid = {42331254}, issn = {1872-8359}, abstract = {Accurate microbial identification based on lipid profiling offers promising applications in diagnostics and microbial ecology. In this study, five lipid pretreatment methods-Maldixin, chloroform-methanol, tert-butyl methyl ether, isobutyric acid-ammonium hydroxide, and sodium acetate (SA) buffer (pH 4.0)-were systematically evaluated using MALDI-TOF mass spectrometry operated in linear negative-ion mode. Among the tested methods, the SA buffer method provided a favorable balance between operational feasibility, extraction efficiency, and spectral quality. Compared with positive-ion mode, negative-ion mode yielded high-intensity lipid peaks and superior spectral clarity, particularly for Acinetobacter baumannii. Lipid profiles were generated from 203 bacterial strains representing six species, revealing distinct species-specific lipid fingerprints. A lipid fingerprint database was subsequently constructed and validated using an independent set of 144 strains, achieving identification accuracies of 81.9% at the species-level and 97.2% at the genus-level. While overall species-level accuracy remains lower than that of conventional protein-based systems, these results indicate that linear negative-ion mode MALDI-TOF MS provides complementary lipid information that may enhance microbial characterization. Further optimization of sample preparation and database algorithms is warranted to support broader clinical application.}, }
@article {pmid42331541, year = {2026}, author = {Yuan, JH and Wei, AH and Tao, R}, title = {[Application of salicylic acid in inflammatory skin diseases and the effect on skin microbiome].}, journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]}, volume = {60}, number = {6}, pages = {988-995}, doi = {10.3760/cma.j.cn112150-20250708-00634}, pmid = {42331541}, issn = {0253-9624}, support = {7254317//Beijing Municipal Natural Science Foundation/ ; PYZ24107//Research Cultivation Program of Capital Medical University/ ; 82173447//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Salicylic Acid/therapeutic use ; *Skin Diseases/drug therapy/microbiology ; *Microbiota/drug effects ; Skin Microbiome ; *Skin/microbiology ; }, abstract = {Emerging evidence underscores the pivotal role of the skin microbiome in the pathogenesis of inflammatory skin diseases. Dysbiosis (an imbalance in microbial composition), significantly drives the onset and exacerbation of these conditions. This article synthesizes current applications of salicylic acid in the management of common inflammatory skin diseases, with a specific focus on its capacity to modulate the skin microbiome. By elucidating the interplay between inflammatory states and microbial ecology, this article aim to offer new perspectives on utilizing salicylic acid novel insights for both therapeutic and preventive strategies.}, }
@article {pmid42331816, year = {2026}, author = {Corrêa, TLR and Li, Z and Moroz, O and Pickles, IB and Lebedev, AA and Akkad, S and Willems, LI and Codée, JDC and Overkleeft, HS and Davies, GJ}, title = {A chemoproteomic biotechnological toolkit for resolving xylanase specificity in decorated xylan.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-74484-0}, pmid = {42331816}, issn = {2041-1723}, support = {ERC-2020-SyG-951231//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; BB/R001162/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; Ken Murray Research Professorship//Royal Society/ ; }, abstract = {Xylanases are central to lignocellulosic biomass degradation, yet current methods lack the specificity to resolve how enzymes distinguish complex xylan structures decorated with arabinofuranose (Araf) and 4-O-methyl-glucuronic acid (MeGlcA). Here, we report a suite of chemically-defined activity-based probes (ABPs) that enable the selective detection of arabinoxylan- and glucuronoxylan-specific xylanases (AXXs and GXXs). These cyclophellitol-derived ABPs covalently label retaining xylanases at their active sites, allowing precise mapping of substrate specificity across diverse glycoside hydrolase families. Crystallographic and mass spectrometric analyses reveal the molecular basis of probe selectivity, while in-gel and pull-down assays demonstrate their effectiveness in profiling xylanase activities in complex bacterial and fungal proteomes, including cellulosomes. By integrating activity-based protein profiling (ABPP) with sequence similarity networks (SSNs), we further show that xylanase specificity can be predicted from sequence alone, enabling rapid functional annotation of uncharacterized xylanases. This chemoproteomic strategy provides a powerful platform for discovering and engineering substrate-specific enzymes for biomass valorisation, microbial ecology, and biotechnological applications.}, }
@article {pmid42332011, year = {2026}, author = {Ghimire, S and Sohrabi, MS and Zhou, X and Malinen, M and Keinänen, M and Goffart, S and Keski-Saari, S and Strandberg, U}, title = {Vitamin B12 Availability and Interaction with Bacterium Mesorhizobium loti Affect Growth and Biochemical Composition of Mixotrophic Alga Euglena Gracilis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02816-0}, pmid = {42332011}, issn = {1432-184X}, abstract = {Over 90% of the mixotrophic algae surveyed require vitamin B12 (B12), a micronutrient synthesized exclusively by certain prokaryotes. Bacteria-mediated B12 supply presents an important but poorly understood control on physiology and nutritional quality of freshwater algae. Here, we examined the effects of B12 availability and the B12-synthesizing bacterium, Mesorhizobium loti, on the growth and biochemical composition of the freshwater bloom-forming mixotrophic alga, Euglena gracilis. We also investigated bacteria-alga interactions under highly labile dissolved organic carbon (DOC) supplementation with and without physical contact. Our results indicate that B12 deficiency reduced algal growth and the accumulation of the essential fatty acids, eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). Co-culture with M. loti resulted in higher EPA and DHA accumulation than supplementation with exogenous B12 alone. Despite this, E. gracilis accumulated less intracellular B12 in co-culture than under direct B12 addition, suggesting altered B12 acquisition or utilization during bacterial interactions. Increasing B12 concentration enhanced total protein content in E. gracilis under sufficient nitrogen conditions but had no effect under nitrogen limitation. The addition of labile DOC directly promoted algal growth, indicating its direct utilization. No significant difference was observed in algal growth in co-cultures with and without physical contact, indicating that possible B12 sharing from bacteria mainly occurs through diffusible metabolites. These findings demonstrate that B12-synthesizing bacteria influence the growth and nutritional quality (in terms of EPA, DHA and protein content) of E. gracilis, with potential consequences for freshwater ecosystem productivity and trophic transfer.}, }
@article {pmid42320402, year = {2026}, author = {Ortiz, C and Hatam, F and Quon, H and Hamilton, KA and Faucher, SP and Prévost, M}, title = {Meta-analysis of growth and inactivation kinetics of Legionella.}, journal = {Water research}, volume = {304}, number = {}, pages = {126280}, doi = {10.1016/j.watres.2026.126280}, pmid = {42320402}, issn = {1879-2448}, abstract = {Quantitative risk assessments intended to inform evidence-based water management plans and public health targets for Legionella in engineered water systems are constrained by fragmented and heterogeneous growth and inactivation kinetics. We conducted a meta-analysis of 25 growth and 39 thermal- and chemical-inactivation studies, fitting microbial persistence models to harmonize parameters. Nonlinear models outperformed first-order formulations, indicating that lag phases and resistant or protected subpopulations are central to Legionella persistence. Random forest analysis identified environmental and methodological drivers of variability based on 226 growth rates and reduction times for thermal (209) and chemical (135) inactivation. Growth was primarily governed by temperature, nutrient availability, and compatible Legionella-host pairings; thermal inactivation by quantification method, temperature, and turbidity; and chemical inactivation by inoculum size, disinfectant type, concentration, and host-associations. Accordingly, temperature-dependent growth parameters and exposure metrics for heat, free-chlorine, and monochloramine, expressed as TT (Temperature×time) and CT (Concentration×time), were derived as condition-specific inputs for predictive models. Growth optima around 37-40 °C, together with lag-time estimates, indicate that hot-water temperature setbacks and energy-saving practices may favor Legionella proliferation under repeated or prolonged lukewarm exposure. Culture- and viability-based TT differences highlight the need to consider viable‑but-non-culturable persistence in monitoring programs. CT comparisons suggest monochloramine may be advantageous because of its lower apparent sensitivity to host-associated protection. Although limited by restricted experimental conditions, the findings show that predictive models should account for microbial ecology, water matrix effects, and quantification endpoints. Future kinetic studies should prioritize realistic multi-host systems, strain pre-adaptation, complementary viability measurements, and standardized protocols and reporting to ensure reproducibility and enable robust system-level predictive modeling.}, }
@article {pmid42320622, year = {2026}, author = {Hoebinger, C and Semmler, G and Petrenko, O and Rajcic, D and Hoffelner, DK and Duckova, T and Baranovskyi, T and Goederle, L and Khuu, MP and Reinhardt, C and Pjevac, P and Séneca, J and Mieczkowski, K and Burger, K and Bergheim, I and Gensluckner, S and Völkerer, A and Reiberger, T and Scheiner, B and Aigner, E and Wernly, B and Datz, C and Binder, CJ and Hendrikx, T}, title = {Alcohol intake reprograms hepatic immune-metabolic circuits to exacerbate murine atherosclerosis and human cardiovascular risk.}, journal = {JHEP reports : innovation in hepatology}, volume = {}, number = {}, pages = {101932}, doi = {10.1016/j.jhepr.2026.101932}, pmid = {42320622}, issn = {2589-5559}, abstract = {BACKGROUND AND AIMS: Recent reclassification of steatotic liver disease (SLD) distinguishes metabolic dysfunction-associated steatotic liver disease (MASLD) from MetALD, a newly defined entity combining MASLD with alcohol consumption. Since the mechanisms linking alcohol consumption in the context of SLD to cardiovascular disease (CVD), the leading cause of SLD mortality, remain elusive, we investigated how metabolic dysregulation and alcohol intake synergistically promote atherosclerosis.<br><br>METHODS: Low-density lipoprotein receptor-deficient (Ldlr[-/-]) mice were fed a high-fat, high-cholesterol (HFC) diet with regular or ethanol-containing drinking water (10-20% v/v). Germ-free and antibiotic-treated Ldlr[-/-] mice were used to assess the contribution of ethanol-induced dysbiosis. Associations between alcohol consumption and cardiometabolic risk were assessed in two human cohorts (N = 5115, N = 2515).<br><br>RESULTS: Ethanol intake in HFC diet-fed Ldlr[-/-] mice exacerbated hepatic steatosis and systemic dyslipidemia, despite only modest elevations in systemic ethanol levels (ps&#x2264;0.05). Liver transcriptomic profiling revealed ethanol-induced alterations in lipid metabolism and enhanced proinflammatory signatures, accompanied by increased recruitment of Ly6C[high] monocytes to the liver (p=0.0121) and elevated levels in circulation (p=0.0043). Correspondingly, ethanol-consuming HFC diet-fed Ldlr[-/-] mice developed enlarged aortic root lesions (p=0.0105). Neither germ-free conditions nor antibiotic treatment mitigated CVD progression. Metabolomic profiling revealed hyperuricemia in ethanol-exposed HFC diet-fed Ldlr[-/-] mice, which was associated with an upregulation of inflammasome-related genes in the liver, along with an increase in hepatic NLRP3 protein expression (ps&#x2264;0.05). Notably, human data mirrored these findings, demonstrating a dose-dependent association between alcohol intake, dyslipidemia, monocytosis, hyperuricemia, and increased cardiovascular risk (ps&#x2264;0.05).<br><br>CONCLUSION: Our findings identify alcohol as an important immune-modulatory lifestyle factor that contributes to elevated cardiovascular risk.<br><br>IMPACT AND IMPLICATIONS: Alcohol consumption, even at moderate levels, contributes to cardiovascular risk, particularly in individuals with SLD. Combining murine models with human cohort data, we show that alcohol intake in SLD is associated with coordinated immune-metabolic alterations, including dyslipidemia, monocytosis, hyperuricemia, and enhanced NLRP3 inflammasome signaling, collectively indicating an elevated cardiovascular risk profile. These findings are relevant to hepatology and cardiovascular medicine, linking alcohol consumption to measurable systemic pathways beyond liver injury. Clinically, systematic assessment of alcohol intake and incorporation into cardiovascular risk evaluation may improve risk stratification and support closer surveillance and preventive strategies in patients with SLD.}, }
@article {pmid42321844, year = {2026}, author = {Li, Y and Chen, Q and Bin, X and Xu, S and Ma, H}, title = {Bronchoalveolar lavage microbiota signatures and stage-associated alterations in early-stage and advanced-stage non-small cell lung cancer: a pilot study.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-08501-7}, pmid = {42321844}, issn = {1479-5876}, support = {2023YXZX17//Tianjin Municipal Education Commission/ ; TJYXZDXK-3-032C//National Key Clinical Specialty Discipline Construction Program of China/ ; }, abstract = {OBJECTIVES: The aims of this study were to characterize the microbial flora in the bronchoalveolar lavage fluid (BALF) of patients with early-stage (stage I, II, IIIA) and advanced-stage (stage IIIB, IIIC, IV) non-small cell lung cancer (NSCLC), and to explore the associations between microbial flora and lung cancer stage.<br><br>METHODS: We collected BALF from NSCLC patients (early-stage group 26 cases; advanced-stage group 31 cases). Absolute quantitative metagenomic sequencing was performed to identify differential taxa, genes, and enriched pathways. Flow cytometry was used to profile T cell subsets. We correlated the microbial species with immune cell and gene expression. Receiver operating characteristic (ROC) curve analysis was performed to assess the ability of differential taxa to distinguish advanced-stage from early-stage NSCLC.<br><br>RESULTS: Dokdonia (q&#x2009;=&#x2009;0.040, LDA&#x2009;=&#x2009;5.704) and Cocleimonas (q&#x2009;=&#x2009;0.026, LDA&#x2009;=&#x2009;5.329) were enriched in the early-stage group, whereas Barnesiella (q&#x2009;=&#x2009;0.046, LDA&#x2009;=&#x2009;4.784), Pedobacter (q&#x2009;=&#x2009;0.040, LDA&#x2009;=&#x2009;4.913) and unclassified Bacteroides (q&#x2009;=&#x2009;0.046, LDA&#x2009;=&#x2009;4.932) were significantly enriched in the advanced-stage group. The microbial genes gmhD (q&#x2009;<&#x2009;0.001, LDA&#x2009;=&#x2009;3.926), rfaD (q&#x2009;<&#x2009;0.001, LDA&#x2009;=&#x2009;3.918), nudF (q&#x2009;=&#x2009;0.004, LDA&#x2009;=&#x2009;4.283) and sfsA (q&#x2009;=&#x2009;0.004, LDA&#x2009;=&#x2009;3.915) were expressed remarkably in the advanced-stage group. The advanced-stage group exhibited altered T cell subset distributions, including a higher proportion of CD8&#x207a; T lymphocytes (q&#x2009;<&#x2009;0.001), whereas it showed a lower proportion of CD4&#x207a; T cells and a decreased CD4/CD8 ratio (q&#x2009;<&#x2009;0.001; q&#x2009;<&#x2009;0.001). Bifidobacterium was negatively associated with the CD4/CD8 ratio (q&#x2009;=&#x2009;0.015) and positively significant correlated with the genes which enriched in the advanced-stage group.<br><br>CONCLUSIONS: This study delineated the microbial structure and function of early-stage and advanced-stage of NSCLC. We identified discriminating taxa, genes, and pathways linked to cancer progression, characterized the T cell subset distributions in the advanced-stage of NSCLC. Bifidobacterium abundance was associated with altered T cell subset distributions and stage-related microbial genes, providing hypotheses for future mechanistic studies on microbiota-driven NSCLC progression.}, }
@article {pmid42322538, year = {2026}, author = {Deore, P and Upadhyay, A and Thekkumpurath, AS and Devarumath, R and Saha, S}, title = {Amplicon sequencing reveals impact of imidacloprid residues on diversity profile of grape fructosphere microbiota.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {7}, pages = {}, pmid = {42322538}, issn = {1573-0972}, mesh = {*Neonicotinoids/pharmacology/analysis ; *Bacteria/classification/genetics/drug effects/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; *Vitis/microbiology ; *Nitro Compounds/pharmacology/analysis ; *Insecticides/pharmacology/analysis ; *Fungi/drug effects/classification/genetics/isolation &amp; purification ; *Microbiota/drug effects/genetics ; *Pesticide Residues/analysis/pharmacology ; Fruit/microbiology ; Biodiversity ; Tandem Mass Spectrometry ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; }, abstract = {In grape, fructosphere microbiota play an important role in nutrient cycling, pathogen suppression, berry quality, and fermentation processes. Insecticide imidacloprid (IM) is used to manage several insect pests of grape. However, the non-targeted effect of insecticide residues on grape-associated microbial communities is poorly understood. In the present study, the effect of IM applied at the recommended dose (RD) and ten times the recommended dose (10RD) on microbiota of grape berry surface was investigated under sub-tropical field conditions. Imidacloprid residues were quantified using LC-MS/MS, while bacterial and fungal community dynamics were analysed through 16S rRNA and ITS amplicon sequencing at three time points. Residue analysis revealed gradual dissipation of IM over time, although detectable residues persisted until harvest. Amplicon sequencing identified 1,556 bacterial and 1,348 fungal operational taxonomic units (OTUs). IM treatment significantly affected bacterial OTU abundance, whereas fungal OTUs were not significantly influenced. Beta diversity analysis demonstrated significant differences in bacterial community composition between control and IM-treated samples, while within-group dispersion remained non-significant. In contrast, fungal community composition did not differ significantly among treatments. Pseudomonadota (55-73%) was the dominant bacterial phylum across treatments, whereas Ascomycota (80-94%) predominated among fungal communities. IM exposure reduced the relative abundance of several ecologically important bacterial genera, including Pseudomonas, Sphingomonas, and Methylobacterium, at later sampling stages. Among fungal taxa, Lachnellula remained dominant across all treatments at day 30, whereas several low-abundance fungal genera showed reduced representation. Overall, the study indicated that persistent IM residues can restructure grape fructospheric microbial populations without causing much loss of microbial diversity. The findings suggested that pesticide residues may favour stress-tolerant microbial taxa, with potential implications for vineyard microbial ecology, vine health and berry quality.}, }
@article {pmid42323440, year = {2026}, author = {Carboni, S and Macfarland, C and Cheves Hernandez, S and Buret, AG and Kutz, S and Melin, AD}, title = {Ecological and methodological insights from genetic and coprological profiling of gastrointestinal communities in wild howler monkeys.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-57628-6}, pmid = {42323440}, issn = {2045-2322}, support = {RGPIN-2017-03782//Natural Sciences and Engineering Research Council of Canada/ ; 950-231257//Canada Foundation for Innovation and Canada Research Chairs/ ; }, abstract = {The gastrointestinal tract hosts a complex community of microorganisms and helminth parasites that collectively contribute to host health and fitness. Analysis of these communities provides insight into diverse aspects of host dietary ecology, immunity, nutrition, and host-parasite interactions. However, research methodologies, such as sample preservation and sequencing approach, can influence how we understand and characterize these features. Here, we profiled the gastrointestinal microbial and helminth communities in different groups of wild Costa Rican mantled howler monkeys (Alouatta palliata palliata). We compared samples stored in ethanol versus directly flash frozen, and contrasted conclusions drawn from 16S versus shotgun sequencing approaches. Bacterial, archaeal, and eukaryotic taxa associated with the digestion of plant material dominated the GI communities. Storage and sequencing methods influenced microbial profiles: ethanol-stored samples exhibited higher diversity than frozen samples, and 16S sequencing detected lower diversity than shotgun. Helminths were detected via coprological microscopy in 71% of individuals, whereas metagenomic detection was inconsistent. This study provides new data on the microorganisms and their putative digestive functions in the gut of a folivorous primate, and highlights the pros and cons of different methodological choices when profiling host-microbiome and host-parasite interactions.}, }
@article {pmid42324861, year = {2026}, author = {Lí, JT and Hicks, LC and Brangarí, AC and Rousk, J}, title = {Cross-stressor resilience of soil microbial growth and carbon metabolism under climate change.}, journal = {Ecology}, volume = {107}, number = {6}, pages = {e70439}, doi = {10.1002/ecy.70439}, pmid = {42324861}, issn = {1939-9170}, support = {2023-02438//Swedish research council Formas/ ; KAW 2022.0175//Knut and Alice Wallenberg Foundation/ ; KAW 2023.0384//Knut and Alice Wallenberg Foundation/ ; }, mesh = {*Soil Microbiology ; *Climate Change ; *Carbon/metabolism ; *Bacteria/metabolism/growth &amp; development ; *Stress, Physiological ; Droughts ; }, abstract = {The microbial ability to recover metabolism after perturbation events ensures ecosystem functional stability in a changing climate, where multiple climatic stressors increasingly occur in sequential and seasonally cyclic patterns. While prior exposure to a specific stress can enhance microbial resilience to that stress, whether this resilience extends to different stressors remains largely unexplored. Here, we investigated cross-stressor resilience of microbial communities by testing how prior exposure to one type of perturbation (frost or drought) affects microbial resilience to subsequent perturbations of either type in soil systems. We found that prior exposure to drought or frost enhanced the resilience of microbial growth to subsequent perturbations of either type and enabled the maintenance of higher microbial carbon use efficiency. It is likely that this cross-stressor resilience arose because frost and drought both can exert stress on microbes via effects on water potential. This suggests that induced microbial perturbation resilience can extend beyond the stressor they originally were exposed to, indicating that ecological memory transcends the original stressor. Repeated perturbation cycles did not confer additional resilience beyond a single event, indicating that a single perturbation could shape the microbial community's perturbation resilience. We also identified the lag phase as a critical period defining microbial perturbation resilience. Our findings demonstrate a broader adaptive capability within microbial communities under climate change so far overlooked, where winter frost could impact summer drought resilience and vice versa, creating a need to consider selective environmental drivers across seasons.}, }
@article {pmid42326782, year = {2026}, author = {Fu, B and DeSchepper, LB and Sun, J and McKeithen-Mead, SA and Kapili, B and Ochoa-Andersen, P and Spencer, SP and Fardeen, T and Ricardo, M and El Kamari, V and Sinha, S and Relman, DA and Grembi, JA and Shalon, D and Estrela, S and Huang, KC}, title = {Multi-region sampling of the human small intestine using an ingestible device.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.06.09.26353912}, pmid = {42326782}, abstract = {The human small intestine (SI) plays a central role in nutrient processing, host-microbe interactions, and immune regulation, yet remains poorly characterized due to the lack of minimally disruptive sampling methods. Here, we present a protocol for deploying, recovering, and analyzing samples collected using an ingestible device that enables multi-region, lumen-targeted SI sampling during normal digestion. The device incorporates a ∼30-cm collapsible tube wound into pH- or time-responsive layers that sequentially unfurl in situ , typically capturing three spatially ordered samples with high yield and reliable retrieval. This protocol outlines study design, participant handling, device recovery, contamination control, and standardized workflows for analyses, including cell quantification, culturomics, sequencing, and metabolomics. We further describe benchmarking approaches for evaluating spatial resolution and strategies for assay prioritization when sample volume is limiting. By reducing participant burden and facilitating integration with stool, saliva, and clinical metadata, this approach enables longitudinal and large-cohort studies linking SI microbial ecology and host physiology to human health.}, }
@article {pmid42328308, year = {2026}, author = {Sharma, N and Felsberger, M and Kurt, Z and Möst, M and Bayer, B}, title = {Seasonal differences and potential biological drivers of the methane paradox in two peri-Alpine lakes.}, journal = {Limnology and oceanography letters}, volume = {11}, number = {3}, pages = {}, pmid = {42328308}, issn = {2378-2242}, abstract = {Seasonal variations and the biological drivers underlying the methane paradox in freshwater lakes are poorly understood. Here, we investigated the relationship between subsurface methane inventories and phytoplankton in two peri-Alpine lakes across different seasons. Surface waters of both lakes were consistently saturated in methane, with maxima reaching 570 and 205 nmol L[-1] during summer in the metalimnion of lakes Mondsee and Attersee, respectively. Methane concentrations were positively correlated with phytoplankton abundance in meso-oligotrophic lake Mondsee but not in ultra-oligotrophic lake Attersee. However, although phytoplankton peaked in abundance at the methane maxima in Mondsee, incubation experiments with [13]C-labeled bicarbonate revealed negligible methane production from primary productivity. Instead, our results suggest that phytoplankton might only be indirectly involved in methane production through alternative pathways, or by providing precursor compounds to other members of the microbial community in these oligotrophic lakes.}, }
@article {pmid42319826, year = {2026}, author = {Lin, SZ and Chen, Y and Wu, C and Sun, WH and Li, Z and Chen, HC and Wang, JY and Ji, CM and Li, SB and Wang, ZW and Tsai, WC and Ma, XQ and Lan, SR and Zhang, FP and Xie, YC and Yao, L and Zhang, Y and Lü, MM and Zhang, JJ and Zhang, DY and Ye, YQ and Yu, X and Xu, SS and Ma, ZH and Ding, GC and Cao, GQ and He, ZM and Wu, PF and Lin, KM and Liu, AQ and Lin, YQ and Ruan, SN and Liu, B and Cao, SJ and Zhou, LL and Li, M and Shuai, P and Hou, XL and Wu, YH and Li, N and Xiong, S and Hao, Y and Zhou, Z and Liu, XD and Zuo, DD and Li, J and Wang, P and Zhang, J and Liu, DK and Chen, GZ and Huang, J and Huang, MZ and Li, YY and Zheng, QY and Zhao, XW and Zhao, X and Zhong, WY and Zhang, XW and Xia, ZB and Yu, Y and Liu, ZW and Zheng, HK and Ming, R and Van de Peer, Y and Liu, ZJ}, title = {Cunninghamia lanceolata genome illuminates the evolutionary dynamics of gymnosperms.}, journal = {Cell reports}, volume = {45}, number = {7}, pages = {117566}, doi = {10.1016/j.celrep.2026.117566}, pmid = {42319826}, issn = {2211-1247}, abstract = {Cupressaceae , a gymnosperm family, draws attention due to its controversial phylogenetic position. Here, we present a comprehensive genome analysis of Chinese fir (Cunninghamia lanceolata), a Cupressaceae species, to enhance our understanding of gymnosperm evolution. The 11.24 Gb assembled genome, shaped by inefficient long terminal repeat removal, offers insights into its phylogenetic position. Phylogenetic analysis refines gymnosperm relationships between Cycads-Ginkgo and their relation to Gnetales-Pinaceae. Whole-genome duplication (WGD) analysis reveals no evidence for an ancient polyploidization event in the lineage of C. lanceolata, and confirms a seed-plant-shared WGD event. We also explore genomic evidence to explain the population history and adaptability of C. lanceolata, including potential glacial refugia, dispersal centers, and unique sterility. Furthermore, the refined (A)B(C) model for reproductive organ development in C. lanceolata has broader applications across gymnosperms. This study provides a valuable genome sequence and contributes to the understanding of gymnosperm evolution.}, }
@article {pmid42320159, year = {2026}, author = {Jo, YH and Kim, WS and Kim, YR and Ju, MS and Ghassemi Nejad, J and Kim, KH and Lee, HG}, title = {Seasonal heat stress alters rumen fermentation, microbial community, and microbial amino acid composition in cattle.}, journal = {Journal of thermal biology}, volume = {139}, number = {}, pages = {104509}, doi = {10.1016/j.jtherbio.2026.104509}, pmid = {42320159}, issn = {0306-4565}, abstract = {In this study, we investigated the effects of seasonal changes on ruminal temperature, pH, fermentation characteristics, microbial composition, and microbial amino acids (AAs) in cattle. The experiment was conducted using six fistulated Holstein steers in two separate 9-d trials conducted in spring and summer (3 d adaptation and 6 d sampling). The average ambient temperature and relative humidity were 10.7 °C and 58% in spring and 24.5 °C and 83.5% in summer, respectively. Ruminal temperature was approximately 0.9 °C higher in summer than in spring, whereas ruminal pH was 0.15 units lower in summer. Among rumen fermentation parameters, butyrate concentration increased during summer, while the concentrations of acetate, propionate, branched-chain fatty acids, total volatile fatty acids, and NH3-N decreased (p < 0.05). Despite identical feed intake, ruminal degradation rates increased after 24 h in summer, with significant increases in the degradation of dry matter, crude protein, and neutral detergent fiber (p < 0.05). Microbial community analysis revealed that at the phylum level, Spirochaetota decreased, whereas Planctomycetota and Chloroflexi increased during summer (p < 0.05). At the genus level, Succiniclasticum and Treponema decreased, while Eubacterium coprostanoligenes and Oscillospiraceae increased compared with spring (p < 0.05). Changes in microbial composition were accompanied by alterations in microbial AA profiles, characterized by increases in alanine, glutamate, histidine, and non-essential AAs, and decreases in glycine, serine, methionine, threonine, and essential AAs during summer (p < 0.05). Notably, methionine content decreased by 13% in summer relative to spring. Overall, these findings demonstrate that seasonal thermal conditions directly alter rumen fermentation, microbial ecology, and microbial AA composition, even under identical feeding conditions. This study provides foundational evidence for developing nutritional and management strategies to optimize rumen function under heat stress conditions.}, }
@article {pmid42313156, year = {2026}, author = {Quintanilla, E and Salazar, J and van de Water, J and Madurell, T}, title = {Bacterial Microbiota Signatures Suggest Acclimation of the Gorgonian Leptogorgia sarmentosa to Highly Impacted Environments in the Mediterranean Sea.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02809-z}, pmid = {42313156}, issn = {1432-184X}, abstract = {Anthropogenic disturbances increasingly compromise marine environments, with severe consequences for vulnerable coral ecosystems. While global stressor impacts on stony corals are well-documented, the mechanisms by which local perturbations influence gorgonians remain poorly characterized. This limits our ability to predict the tolerance of temperate octocorals in human-dominated coastal landscapes. The Mediterranean gorgonian Leptogorgia sarmentosa is remarkably resilient, thriving in both marine protected areas (MPAs) and highly impacted urban habitats. To investigate the microbiota's role in this adaptability, we characterized the bacterial communities of L. sarmentosa from a protected site (Western Mediterranean) and an impacted seaport (Barcelona). For broader regional context, results were compared in parallel with a re-analysis of datasets from similarly contrasting Mediterranean sites (Cassis and La Spezia). Our results reveal distinct site-specific microbial signatures, but no differences in alpha diversity or dispersion between seaport and the MPA. However, significant compositional shifts occurred in the impacted Barcelona seaport, characterized by a reconfiguration of the dominant symbiont genus Endozoicomonas and an enrichment of Spongiibacteraceae_clade BD1-7. Similarly, Endozoicomonas strain abundances differed between Cassis and the high-runoff environment of La Spezia, which exhibited increased Mycoplasma abundance. Collectively, these findings suggest a high degree of microbiome flexibility. This microbiota plasticity, alongside predicted functional pathways, suggests a contribution to preserving and acquiring key holobiont functions, highlighting the capacity of L. sarmentosa to persist in disturbed habitats through strategic microbial reconfiguration. This study provides crucial insights into the mechanisms underlying coral acclimation; essential for developing conservation strategies and predicting the long-term viability of Mediterranean marine biodiversity.}, }
@article {pmid42314820, year = {2026}, author = {Du, Z and Yang, J and Li, W and Huang, C}, title = {Selection-Driven Shifts in Airborne Bacterial Communities and Potentially Pathogenic Genera Across Environmental and PM2.5 Gradients in Urban Beijing.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128603}, doi = {10.1016/j.envpol.2026.128603}, pmid = {42314820}, issn = {1873-6424}, abstract = {Air pollution poses the greatest public health threat among environmental risks, and fine particulate matter with diameter ≤ 2.5 μm (PM2.5) is one of the most harmful air pollutants. PM2.5 is often associated with airborne microorganisms, making their investigation important for both microbial ecology and potential exposure assessment. In this study, airborne bacterial communities in PM2.5 samples collected during autumn and winter in urban Beijing were analyzed using 16S rRNA gene sequencing, null-model community assembly analysis, and co-occurrence network analysis. Distinct differences in microbial communities were observed between autumn and winter sampling periods based on PCoA and PERMANOVA analyses (p < 0.05), whereas no consistent differences between daytime and nighttime samples were detected. Community assembly shifted from stronger stochasticity in autumn to greater homogeneous selection in winter, with homogeneous selection contributing 47.22% and 53.33% in winter daytime and nighttime samples, respectively . We further characterized microbial composition and identified potentially pathogenic genera under different environmental conditions. Most pathogens were less abundant in winter. However, Streptomyces, Saccharopolyspora, and Nocardiopsis were enriched under low temperature and absolute humidity conditions, and their abundance further increased with high PM2.5 levels, as supported by microbial community composition analyses. Co-occurrence network analysis further revealed more interconnected positive microbial associations in autumn, whereas winter communities exhibited greater modularity and increased negative correlations under colder and drier conditions. These findings provide insights into airborne microbial diversity, community assembly, community composition, and co-occurrence patterns across contrasting environmental conditions and their associations with air quality, with potential relevance for understanding airborne microbial exposure and respiratory health concerns in urban environments.}, }
@article {pmid42315001, year = {2026}, author = {Weltz, TK and Peng, S and Larsen, A and Bak, EEF and Tran, JVQ and Gudjonsdottir, LR and Hemmingsen, MN and Ørholt, M and Mielke, LV and Trillingsgaard, J and Elberg, JJ and Hölmich, LR and Jensen, LT and Vester-Glowinski, P and Bjarnsholt, T and Trivedi, U and Clemens, MW and Li, X and Sørensen, SJ and Herly, M}, title = {Breast implant surface texture is associated with distinct implant microbiome profiles in humans.}, journal = {Acta biomaterialia}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.actbio.2026.06.038}, pmid = {42315001}, issn = {1878-7568}, abstract = {Surface topography of silicone breast implants modulates foreign body responses, but its connection to implant-associated microbial communities remains unclear. We analyzed the microbiome of 391 explanted breast implants from 221 patients with different surface textures using 16S rRNA gene sequencing. We found that the surface texture is associated with distinct microbial communities depending on a surface roughness gradient. Rougher surfaces had lower microbial diversity, driven by lower evenness and a higher relative abundance of Staphylococcus than smoother surfaces. Compositional differences across surface groups followed this gradient. In a subset of samples, absolute bacterial quantification using digital PCR showed increasing total bacterial burden with increasing surface roughness. Smooth and minimally textured implants displayed similar microbiome profiles despite large differences in implantation time. Together, these findings suggest that surface roughness is associated with the local microbial microenvironment, linking material design with microbial burden and the foreign body response. STATEMENT OF SIGNIFICANCE: Breast implant surface topography may influence implant-associated microbial communities, but human evidence across commonly used textures is limited. Using 16S rRNA gene sequencing of 391 explanted implants from multiple manufacturers, we found that microbial diversity and composition varied systematically with a surface roughness gradient. Rougher textures showed lower diversity driven by reduced evenness and a higher relative abundance of Staphylococcus, while compositional differences across surface groups followed the same gradient. Quantitative digital PCR further suggested a higher total bacterial burden on rougher surfaces. In contrast, smooth and minimally textured implants displayed similar microbiome profiles despite large differences in implantation time. These findings link implant surface design to microbial ecology and may help explain texture-associated differences in foreign body responses.}, }
@article {pmid42315252, year = {2026}, author = {Lin, Y and Liu, YK and Mi, P and Zhao, XL and Lin, JH and Cheng, XS and Liang, LY and Huang, YD and Huo, YN and Xie, GJ and Ye, ZY and Guleng, B}, title = {Integrin CD11b/CD18 reprograms macrophage polarization by suppressing ERK/STAT3 signaling to enhance antitumor immunity in colitis-associated colorectal cancer.}, journal = {Journal for immunotherapy of cancer}, volume = {14}, number = {6}, pages = {}, doi = {10.1136/jitc-2025-014026}, pmid = {42315252}, issn = {2051-1426}, mesh = {Animals ; *STAT3 Transcription Factor/metabolism ; *CD11b Antigen/metabolism/genetics ; *CD18 Antigens/metabolism/genetics ; Mice ; *Macrophages/immunology/metabolism ; Humans ; *Colitis-Associated Neoplasms/immunology/pathology/metabolism ; *Colitis/complications ; *Colorectal Neoplasms/pathology/immunology ; Tumor Microenvironment/immunology ; Signal Transduction ; Mice, Knockout ; Male ; Mice, Inbred C57BL ; }, abstract = {BACKGROUND: Chronic inflammation is a well-established driver of colorectal cancer (CRC), with the resulting inflammatory microenvironment facilitating tumor initiation and progression. The integrin CD11b/CD18, a leukocyte-specific heterodimeric adhesion receptor, mediates critical immunoregulatory functions during inflammatory responses. However, the roles and mechanisms of CD11b/CD18 in colitis-associated colorectal cancer (CAC) remain unclear.<br><br>METHODS: To investigate the impact of CD11b/CD18 deficiency on colorectal carcinogenesis, an azoxymethane/dextran sodium sulfate-induced CAC model was established with CD11b and CD18 single-knockout and double-knockout mice. The tumor immune microenvironment was characterized using multicolor flow cytometry. Transcriptomic changes in tumor-associated neutrophils (TANs) and macrophages (TAMs) on CD11b/CD18 ablation were profiled by RNA sequencing. Functional crosstalk between TANs and TAMs was assessed via co-culture experiments. The direct role of CD11b/CD18 in TAM polarization and antitumor activity was evaluated using in vitro agonist assays, and the involvement of the extracellular signal-regulated kinase (ERK)/signal transducer and activator of transcription 3 (STAT3) axis was validated with pathway-specific inhibitors.<br><br>RESULTS: Bioinformatics analysis revealed significant downregulation of ITGAM (CD11b) and ITGB2 (CD18) expression in CRC tissues. In the CAC model, CD11b and CD18 exhibited non-redundant and cooperative functions, and double deficiency significantly exacerbated tumor progression, with increased STAT3 phosphorylation and reduced yes-associated protein phosphorylation. Flow cytometric analysis identified neutrophils as the predominant CD11b[+]CD18[+] population within the tumor microenvironment (TME). Mechanistically, CD11b/CD18 deficiency promoted TME remodeling, including protumor skewing of TANs and TAMs, with TAM polarization mediated partly by TAN-TAM crosstalk. Beyond this indirect mechanism, direct activation of CD11b/CD18 in TAMs attenuated the immunosuppressive properties and enhanced their tumoricidal activity. At the molecular level, CD11b/CD18 deficiency activated janus kinase (JAK)-STAT and mitogen-activated protein kinase pathways in TAMs, whereas CD11b/CD18 activation effectively suppressed ERK1/2 and STAT3 signaling. Combined inhibition of ERK1/2 and STAT3 reversed M2 polarization and restored TAM-mediated tumor killing.<br><br>CONCLUSIONS: Our findings establish that integrin CD11b/CD18 orchestrates antitumor immunity by modulating the TME, particularly through direct TAM reprogramming and indirect TAN-TAM crosstalk, highlighting its potential as an immunotherapeutic target for CAC.}, }
@article {pmid42315481, year = {2026}, author = {Thomas, C and Laakkonen, AK and Rast, DR and Sauter, G and Kremer, K and Max, S and Vogel, H}, title = {Long vs. short read sequencing for microbial ecology of sedimentary environments: a case study from Lake Arnon, Switzerland.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnag072}, pmid = {42315481}, issn = {1574-6968}, abstract = {Microbial communities in the subsurface biosphere remain poorly characterized because many taxa lack cultured representatives and genomic references, limiting the accuracy of taxonomy inferred from short-read 16S ribosomal RNA gene sequencing. We tested the hypothesis that long-read 16S sequencing improves taxonomic resolution and detection of rare lineages compared with short-read approaches in low-biomass, diversity-rich sediments. Microbial communities from a sediment core of Lake Arnon (Switzerland) were analyzed using both long-and short-read sequencing, and community composition, diversity metrics, and taxonomic resolution were compared. Sequencing technology influenced observed community structure, but sediment depth also exerted a strong effect. Taxonomic profiles were broadly consistent across methods for most bacterial groups, whereas archaeal diversity was underrepresented in long-read datasets due to primer mismatches. When detected, long reads provided higher taxonomic resolution, frequently to species level, improving ecological interpretation and inference of metabolic potential. Finer-scale analyses, including species contributions to beta diversity and co-occurrence networks, showed greater specificity with long reads. These results demonstrate that long-read sequencing can substantially enhance subsurface microbial characterization, provided that primer design is optimized, and highlight its potential to improve assessments of microbial identity, structure, and function in low-biomass environments.}, }
@article {pmid42315857, year = {2026}, author = {Buthelezi, ZM and Pierneef, RE and Bezuidt, OKI and Gregori, MNJ and Pesant, S and Iudicone, D and Hanwell, L and Todd, JD and Makhalanyane, TP}, title = {Dimethylsulfoniopropionate metabolism shapes microbial ecology and physiological adaptation during the austral winter in Southern Ocean sea ice and seawater.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42315857}, issn = {2041-1723}, support = {SANAP23042496849//National Research Foundation (NRF)/ ; 110717//National Research Foundation (NRF)/ ; }, mesh = {*Sulfonium Compounds/metabolism/analysis ; *Seawater/microbiology/chemistry ; *Ice Cover/microbiology/chemistry ; *Adaptation, Physiological ; Seasons ; Oceans and Seas ; Bacteria/metabolism/genetics ; }, abstract = {Dimethylsulfoniopropionate (DMSP) is a highly abundant marine organosulfur compound, with important roles in stress protection and climate-cooling gases production. Polar regions, particularly seawater and sea ice interfaces, are critical yet understudied DMSP cycling hotspots. Here, we reveal up to 38-fold higher DMSP concentrations in Southern Ocean sea ice versus seawaters, identifying sea ice as a concentrated reservoir of DMSP with implications for microbial stress tolerance and sulfur recycling. Eukaryotic algae harboring DSYB and DSYE genes were predicted to dominate DMSP production, but diverse and previously unidentified bacterial producers were also detected. This elevated abundance of algal biosynthetic genes likely underpins the higher DMSP concentrations in sea ice. Notably, DMSP catabolism, particularly the dmdA demethylase and dddD and dddK lyase genes, were more abundant than biosynthesis genes. Taken together, these findings reveal the widespread metabolism for DMSP cycling and underscore a dynamic reservoir and transformation hub influencing polar climate-cooling sulfur fluxes.}, }
@article {pmid42317759, year = {2026}, author = {Jiya, N and Sha, SP and Khudai, W and Yadav, S and Sasane, R and Sah, SP and Ghatani, K and Sharma, A}, title = {Distinct bacterial and fungal communities linked to functional potential in fermented fish and vegetables.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1850075}, pmid = {42317759}, issn = {1664-302X}, abstract = {INTRODUCTION: Traditional fermented foods constitute a vital component of ethnic community diets; consequently, characterizing their specific food microbiome is essential for elucidating their nutritional, functional and health related attributes.<br><br>METHODS: In this study, targeted metagenomics was employed to investigate the bacterial and fungal compositions of fermented fish and vegetables from North Bengal, India. The functional predictions of the fermented food microbiomes was performed using PICRUSt2.<br><br>RESULTS AND DISCUSSION: High throughput sequencing of 16S rRNA and ITS genes revealed substantial differences in the diversity indices amongst the fermented fishes and vegetables. Fish samples were dominated by Pseudomonadota (23.05%), whereas vegetables were enriched in Bacillota (32.17%), with Psychrobacter and Aliivibrio prevalent in fishes and lactic acid bacteria including Levilactobacillus, Paucilactobacillus and Pediococcus dominant in vegetables. The fungal genera Bisifusarium belonging to Ascomycota and Cystobasidium affiliated to Basidiomycota, were abundant in the fermented fishes and vegetables, respectively. Functional predictions of bacterial and fungal communities revealed enhanced carbohydrate metabolism, biosynthesis pathways related to vitamins, short-chain fatty acids, organic acids, proteolytic enzymes and compounds contributing to organoleptic attributes in these fermented foods. The assessment of microbial communities associated with the traditionally fermented foods of North Bengal revealed the key microbial taxa involved in the fermentation process and their nutritional properties.}, }
@article {pmid42317952, year = {2026}, author = {Andafa, TW and Imoh, EC and Adekanmbi, SA}, title = {Artificial Intelligence Applied to the Brain-Gut Axis in Irritable Bowel Syndrome: Advancing Toward Clinical Translation.}, journal = {Cureus}, volume = {18}, number = {5}, pages = {e109142}, pmid = {42317952}, issn = {2168-8184}, abstract = {Irritable bowel syndrome (IBS) is one of the most common functional gut disorders affecting the global population, characterized by chronic abdominal pain and altered bowel habits in the absence of structural disease. The brain-gut-microbiota axis, a bidirectional network integrating central nervous system processing, enteric and autonomic function, immune signaling, and gut microbial ecology, provides a mechanistic framework that helps explain the substantial symptom heterogeneity and variable treatment response observed across patients. Artificial intelligence (AI) and machine learning (ML) approaches offer the ability to model complex, nonlinear relationships across high-dimensional biological datasets generated from this axis, including microbiome composition profiles, resting-state functional MRI connectivity matrices, multiomics data layers, and psychological and clinical feature sets. This narrative review evaluated primary human studies applying AI and ML to brain-gut axis data in IBS, identified through structured searches of PubMed/MEDLINE and Scopus supplemented by citation chaining, with literature included up to April 2026. Across microbiome profiling, neuroimaging, multiomics integration, and psychological feature modeling, ML approaches have demonstrated proof-of-concept performance for IBS classification and, in a smaller number of studies, for prediction of clinically meaningful outcomes, including cognitive behavioral therapy (CBT) response. A notable early signal is the integration of baseline microbiome and brain features to predict CBT response, with high reported discrimination, although these results are derived from small, single-center cohorts with only internal validation and should be regarded as hypothesis-generating. The current evidence base is limited by small single-center cohorts, reliance on internal validation, healthy-control comparators, limited external replication, and substantial overfitting and data-leakage risk in high-dimensional small-sample settings. AI and ML applications in IBS are promising but remain exploratory and are not yet suitable for routine clinical use. Clinical translation will require larger multicenter datasets, harmonized preprocessing pipelines, external validation, calibration reporting, and evaluation against clinically realistic comparators and decision points.}, }
@article {pmid42318064, year = {2026}, author = {Li, XT and Zhang, X and Liang, ZL and Jiang, Z and Huang, Y and Han, YQ and Tan, ZB and Ying-Liu,  and Liu, ZH and Yin, HQ and Liu, SJ and Jiang, CY}, title = {A culturomics biobank decodes extremophile evolution and metabolism in acid mine drainage.}, journal = {Environmental science and ecotechnology}, volume = {32}, number = {}, pages = {100722}, pmid = {42318064}, issn = {2666-4984}, abstract = {Extreme environments such as acid mine drainage (AMD) host highly specialized microbial communities that drive profound biogeochemical cycles. Within these ecosystems, iron- and sulfur-metabolizing taxa catalyze mineral weathering, generating intense acidity and mobilizing heavy metals. However, more than 97% of these microorganisms remain uncultured "microbial dark matter," heavily restricting our understanding of extremophile metabolism and adaptation. Here we present the Microbial Biobank of AMD (mbAMD), a culturomics-derived collection of 652 isolates spanning 42 species-including 21 novel taxa-that achieves 86.7% coverage of the global AMD core microbiome. Functional validation demonstrates that 36 of these taxa possess active iron or sulfur metabolic capacities, including the discovery of the first pure cultures of acid-tolerant sulfate reducers. Comparative genomic analyses across these isolates reveal that extreme environmental adaptation is predominantly driven by pervasive horizontal gene transfer. Specifically, extremophiles preferentially acquire adaptive genes governing acid tolerance and metal resistance from phylogenetically proximal relatives rather than distant donors. These findings elucidate the modular evolutionary strategies of extremophiles and provide critical functional resources for advancing biohydrometallurgy and environmental bioremediation. This mbAMD resource will accelerate biohydrometallurgical process optimization and environmental bioremediation strategies while advancing evolutionary microbial ecology research.}, }
@article {pmid42319473, year = {2026}, author = {Książkiewicz, Z and Górzyńska, K and Kosicka, E and Wejnerowski, &#x141; and Rybak, M}, title = {Microbial Resource Regimes Shape Early Survival, Growth, and Reproductive Morphology in a Phally Polymorphic Terrestrial Gastropod.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02814-2}, pmid = {42319473}, issn = {1432-184X}, abstract = {Microorganisms are fundamental components of terrestrial ecosystems, acting not only as symbionts or pathogens but also as key nutritional resources for invertebrates. Despite their ubiquity, their role in shaping early-life survival and phenotypic variation in terrestrial animals remains poorly understood. Here, we investigated how microbial resource regimes act as early-life ecological filters influencing survival, growth, and reproductive morphology in the phally polymorphic wetland microsnail Vertigo antivertigo. Using eggs and early juveniles, life stages characterized by high natural mortality, we conducted a series of laboratory experiments manipulating access to the species' fecal- and litter-associated bacteria, soil and litter fungi, and the cyanobacterium Limnothrix sp. Survival emerged as the most consistent response variable across treatments. Fungal supplementation combined with plant litter supported growth and survival to sexual maturity, whereas bacterial resources alone did not compensate for the absence of intact litter-associated microorganisms. Exposure to Limnothrix sp. resulted in severe growth suppression and complete juvenile mortality, irrespective of bacterial supplementation. Disrupted microbial conditions were also associated with shifts in reproductive morphology, including reduced or absent male copulatory organs. Our findings demonstrate that microbial resource regimes can function as strong early-life ecological filters, shaping survival, growth and reproductive morphology.}, }
@article {pmid42319514, year = {2026}, author = {Ståhle, M and Johnson, A and Turner, S and Mårtensson, P and Kalinowski, B and Dopson, M}, title = {Multi-Year Biofilm Formation on Granitic Surfaces Reveals Dynamic Microbial Communities in Fennoscandian Shield Deep Groundwaters.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02812-4}, pmid = {42319514}, issn = {1432-184X}, abstract = {The deep terrestrial biosphere is the vast biome beneath the soil layer that contains the majority of the Earth's prokaryotic biomass, yet it is one of the least investigated communities. Although, estimates of deep biosphere biomass suggest biofilm cells outnumber the planktonic biomass by several orders of magnitude, most investigations target planktonic communities captured from groundwaters. This multi-year study used 16S rRNA gene sequencing to compare planktonic and biofilm communities attached to natural granitic rock, demonstrating that biofilm formation selected for taxa with distinct relative abundances and exhibited temporal development. The biofilm communities also showed a decreasing influence of introduced populations on the natural rock surfaces (macadam) present at the onset of the incubations. After two- and four-years of biofilm incubation, a community developed that was dominated by sulfur/sulfate reducing Desulfocapsaceae, Desulfobacteraceae, and BM004 along with the families UBA5619, Rhodocyclaceae, Profunditerraquicolaceae, and UBA2206. This long-term community included populations predicted to be host-associated ultra-small cells. This contrasted with previous studies of early biofilm development in deep Fennoscandian Shield groundwaters that suggested biofilm initiation was mediated by lithotrophic carbon and nitrogen fixing populations. However, metabolic predictions based upon the 16S rRNA gene-based communities also showed an autotrophic and diazotrophic community including sulfur cycling in line with the previous studies. In conclusion, this study showed long-term biofilm composition to be dissimilar to the planktonic communities with a consistent strategy for energy conservation similar to previous studies of early biofilm formation from these groundwaters.}, }
@article {pmid42319657, year = {2026}, author = {Shon, WJ and Kim, KA and Kim, JS and Kim, BG and Im, JP and Lee, HJ and Kim, SH and Kim, JW and Kang, HW and Kim, KW and Choi, JW and Cheon, DH and Kim, D and Choi, J and Kim, ES and Koh, SJ}, title = {Habitual Ultra-processed Food Intake Is Associated with Gut Dysbiosis and Pro-inflammatory Metabolite Profiles in Korean Patients with IBD.}, journal = {Digestive diseases and sciences}, volume = {}, number = {}, pages = {}, pmid = {42319657}, issn = {1573-2568}, abstract = {BACKGROUND AND AIMS: Ultra-processed food (UPF) is increasingly consumed worldwide and may influence gut microbial ecology relevant to inflammatory bowel disease (IBD). However, patient-level multi-omics data remains scarce. We investigated whether habitual UPF intake is associated with specific microbiota and metabolite profiles in Korean patients with IBD.<br><br>METHODS: Dietary intake was assessed using a validated food frequency questionnaire, and food was categorized by the NOVA system. UPF intake was expressed as percent of energy, and 313 patients were stratified into UPF low (Q1-Q2) and UPF high (Q3-Q4). Fecal samples of 174 patients underwent 16S rRNA sequencing and untargeted metabolomics. Microbiome differences were tested using PERMANOVA for beta-diversity and Mann-Whitney U tests for taxa. Differential metabolites were defined by p&#x2009;<&#x2009;0.05 and |fold change|&#x2265;&#x2009;1.5, followed by Reactome enrichment with FDR correction. Correlations among microbiota, metabolites, and UPF subgroups were examined using Spearman tests with Benjamini-Hochberg adjustment. Associations between UPF intake and clinical characteristics were analyzed using Spearman tests, &#x3b7;[2] from ANOVA and point-biserial correlation.<br><br>RESULTS: Microbial beta-diversity differed significantly between UPF low and UPF high participants. UPF high participants showed expansion of pro-inflammatory pathobionts (Escherichia-Shigella, Proteus, Parasutterella, Enterococcus, Fusobacterium, and Clostridium innocuum group) and depletion of anti-inflammatory commensals (Faecalibacterium, Butyricicoccus, Lachnospiraceae ND3007 group, and Bifidobacterium). Metabolomic profiling revealed enrichment of inflammatory pathways (phospholipid metabolism, eNOS/NO signaling, mitochondrial &#x3b2;-oxidation, FMO3-mediated TMA to TMAO, tryptophan catabolism) and reduction of anti-inflammatory metabolites (AHR ligands, BAAT-conjugated bile acids). Integrated analyses demonstrated significant correlations between dysbiotic taxa and inflammatory metabolites. Among NOVA-defined UPF subgroups, sugar-sweetened beverages, ready-to-eat dishes, and packaged snacks and confectioneries showed the strongest associations with these adverse signatures. Analysis of clinical characteristics showed trends between total UPF intake and inflammatory markers (WBC, CRP, fecal calprotectin), and association with upper gastrointestinal tract involvement in patients with CD. Subgroup analysis showed that sugar-sweetened beverage intake was significantly associated with CRP elevation and upper gastrointestinal involvement in patients with CD.<br><br>CONCLUSIONS: In IBD, higher UPF intake, particularly from specific NOVA-defined subgroups, is associated with gut dysbiosis and a pro-inflammatory metabolome, which in turn correlates with unfavorable clinical characteristics. These findings provide patient-based multi-omics evidence and underscore clinically relevant dietary targets for IBD management.}, }
@article {pmid42303895, year = {2026}, author = {Cornelio-Martínez, S and Frade-Pérez, MD and González-Dávalos, ML and Varela-Echavarría, A and Mora-Izaguirre, O}, title = {Diet-Dependent Variations in the Gut Microbiota and Metabolic Pathways of the land slug Deroceras laeve.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02811-5}, pmid = {42303895}, issn = {1432-184X}, support = {IN204526//PAPIIT-UNAM/ ; IN203924//PAPIIT-UNAM/ ; CBF2023-2024-834//SECIHTI/ ; CF-2023-I-1881//SECIHTI/ ; }, abstract = {The slug Deroceras laeve has emerged as a valuable model for biological research, but limited knowledge exists of the microbiota that inhabit the digestive tract of this species. This study assessed the bacterial microbiota of the stomach and intestine of D. laeve fed either a diet formulated for rodents (RD) or a diet of fresh vegetables (VD). Pseudomonadota was the most abundant phylum in both digestive compartments, although it decreased in abundance with the VD diet. The genus Rahnella was the most abundant in both regions with a decrease caused by the VD diet and a concomitant increase in richness. Predicted metabolic pathways indicated that fatty acid biosynthesis predominated in the stomach of slugs fed the RD, whereas pyruvate fermentation and amino acid biosynthesis were enriched in VD animals. In the intestine, aerobic respiration, pyruvate fermentation, fatty acid and amino acid biosynthesis were identified as conserved pathways. Predictive functional profiling revealed that signaling and cellular processes, genetic information processing, and metabolism were predominant functions across all groups. These results reveal a more diverse microbiome in slugs fed VD, paralleling the findings in other animals and providing a good grounding for the study of ecological adaptations of this species to its environment.}, }
@article {pmid42304377, year = {2026}, author = {Ghodraty, M and Fekri, M and Kiani, M and Esmaeel Zadegan, S and Abdoli Rezaei, S and Mousavi Gilani, SS and Manafi Varkiani, M and Ghafouri, A and Mehrnia, N and Amudi, M and Khodayar, Z and Jouya Talaei, A and Baadkoubehazaveh, M}, title = {Gut microbiota, brown adipose tissue whitening, and obesity: nutritional modulators and metabolic crosstalk.}, journal = {Nutrition &amp; metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12986-026-01152-x}, pmid = {42304377}, issn = {1743-7075}, abstract = {Obesity reflects a chronic imbalance between energy intake and expenditure, accompanied by metabolic inflammation and ectopic lipid deposition. Accumulating evidence indicates that gut microbiota dysbiosis reshapes host nutrient handling and endocrine-immune signaling, with downstream consequences for thermogenic adipose tissues. Brown adipose tissue (BAT) supports energy dissipation via UCP1-dependent adaptive thermogenesis; however, in obesity, BAT often undergoes "whitening," a maladaptive transition characterized by lipid accumulation, mitochondrial dysfunction, and reduced thermogenic capacity. This review synthesizes mechanistic and translational evidence linking obesity-associated microbiota alterations to BAT dysfunction through integrated gut-adipose and gut-liver communication. We discuss how microbially derived metabolites (including short-chain fatty acids and secondary bile acids), endotoxin-driven inflammation, and bile acid receptor signaling (FXR/TGR5) may converge on sympathetic tone, mitochondrial biogenesis, and lipid flux to favor BAT whitening. We further evaluate nutrition- and lifestyle-based strategies (dietary fiber and polyphenols, exercise, pre/pro/postbiotics, and bile acid-targeted approaches) that modulate microbial ecology and metabolic outputs, with potential to preserve BAT thermogenic identity and improve metabolic health. Clarifying the causal pathways and clinically actionable microbial signatures within this gut-adipose-liver network may inform future nutrition-oriented interventions for obesity and related metabolic disorders.}, }
@article {pmid42308545, year = {2026}, author = {Yuan, Y and Yin, X and Liu, J and Jing, J and Shi, Y and Tao, S and Guo, L and Wang, D and Jiang, W and Liong, MT and Chen, D and Zhang, J}, title = {Bifidobacterium lactis XLTG11 Reduces Eczema and Infections in Infants: A Randomized Trial.}, journal = {QJM : monthly journal of the Association of Physicians}, volume = {}, number = {}, pages = {}, doi = {10.1093/qjmed/hcag148}, pmid = {42308545}, issn = {1460-2393}, abstract = {BACKGROUND: Early-life gut microbiota profoundly influences immune system maturation and disease susceptibility. Perturbations in microbial development have been linked to rising rates of allergic and infectious diseases in children. Probiotic interventions offer a promising strategy to restore microbial-immune homeostasis; however, evidence from rigorously designed, strain-specific randomized trials integrating clinical and microbiome outcomes remains limited.<br><br>OBJECTIVE: To evaluate the efficacy of Bifidobacterium animalis subsp. lactis XLTG11 in reducing the incidence of eczema and respiratory infections during early childhood, and to explore its associations with gut microbial ecology and immune function.<br><br>METHODS: In this randomized, double-blind, placebo-controlled trial, 352 healthy infants and young children (aged <3&#x2009;years) were randomly allocated to receive XLTG11 (1&#x2009;&#xd7;&#x2009;1010 CFU/day) or placebo for 180&#x2009;days. Primary outcome was eczema incidence; secondary outcomes included respiratory and gastrointestinal symptoms, growth parameters, gut microbiota composition (16S rRNA gene sequencing), and gut immune biomarkers.<br><br>RESULTS: Children receiving XLTG11 showed significantly lower incidence of eczema (p&#x2009;=&#x2009;0.017) and erythema (p&#x2009;=&#x2009;0.028), and a lower incidence of physician-confirmed pneumonia (RR&#x2009;=&#x2009;0.40, 95% CI 0.17-0.94; p&#x2009;=&#x2009;0.030) compared with placebo. Probiotic supplementation improved stool consistency (p&#x2009;=&#x2009;0.018) without affecting growth. 16S rRNA gene sequencing revealed enrichment of Faecalibacterium, Akkermansia, and other short-chain fatty acid-producing taxa, alongside suppression of Helicobacter and Citrobacter. Predictive functional profiling suggested enrichment of pathways related to energy metabolism, vitamin biosynthesis, and antimicrobial peptide (DEFB2, LL-37) production, alongside preservation of secretory IgA.<br><br>CONCLUSIONS: Daily B. lactis XLTG11 supplementation safely reduces eczema and respiratory infection risk in early childhood by remodeling the gut microbiome and reinforcing mucosal immunity. These findings support its use as a preventive strategy for allergy and infection via gut-immune modulation.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov (NCT07490587).<br><br>ETHICS APPROVAL: Shanghai Sixth People's Hospital Human Ethics Committee (No. 2023-142).}, }
@article {pmid42308849, year = {2026}, author = {Noman, MA and Adyel, TM and Callahan, DL and He, D and Macreadie, PI and Trevathan-Tackett, SM}, title = {Microplastics and co-occurring nitrogen synergistically accelerate blue carbon loss.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142641}, doi = {10.1016/j.jhazmat.2026.142641}, pmid = {42308849}, issn = {1873-3336}, abstract = {Blue carbon ecosystems (BCEs)-including seagrass meadows, mangroves, and salt marshes-store vast amounts of organic carbon, yet their carbon sink function is increasingly threatened by hazardous microplastics and co-occurring nitrogen pollution. Here, we used a controlled microcosm experiment and multi-omics analysis (16S rRNA amplicon sequencing, Fourier Transform Ion Cyclotron Resonance Mass Spectrometry, and Ultra-Performance Liquid Chromatography-Mass Spectrometry) to investigate how two common microplastics-polyethylene terephthalate (PET) and polylactic acid (PLA)-interact with nitrogen fertiliser (N-dominated fertiliser with co-delivered nutrients) to influence seagrass soil biogeochemistry. We showed that PLA combined with N-fertiliser increased CO2 emissions from seagrass soil by 106% relative to nitrogen alone and by 195% compared to controls (p < 0.01), while PET addition had negligible effects. PLA degradation released carboxylic acid and derivatives, supporting putative sulphate-reducing and fermentative bacteria, and increasing the formation of organic-oxygen compounds (e.g., disaccharides, o-glycosyl compounds). N-fertiliser addition further enriched putative organic matter-degrading microbial taxa, particularly Clostridia and Bacteroidia, and elevated microbial metabolic potential across pathways. Combined PLA and nitrogen treatments resulted in the lowest (-37% vs control) residual dissolved organic carbon concentrations, indicating accelerated carbon loss. These findings suggest that microplastics, especially PLA biopolymer, and nitrogen act as hazardous co-contaminants that enhance microbial mineralisation of soil organic matter, potentially weakening blue carbon storage. Plastic waste and fertiliser inputs should therefore be considered together in future risk assessments of coastal carbon stocks and in the development of strategies to safeguard BCEs.}, }
@article {pmid42309236, year = {2026}, author = {Ali, S and Burke, LP and Fitzpatrick, F and Fitzgerald-Hughes, D}, title = {Following the mobile genome: plasmids as a missing layer in surveillance of carbapenemase-producing Enterobacterales.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmi.2026.06.010}, pmid = {42309236}, issn = {1469-0691}, }
@article {pmid42311765, year = {2026}, author = {Xu, H and Hu, J}, title = {Traditional Chinese medicine-based modulation of gut microbiota in coronary heart disease: probiotic synergy and translational perspectives.}, journal = {Frontiers in cardiovascular medicine}, volume = {13}, number = {}, pages = {1857702}, pmid = {42311765}, issn = {2297-055X}, abstract = {Gut microbiota has emerged as an important contributor to the pathogenesis and progression of coronary heart disease (CHD). Increasing evidence indicates that gut dysbiosis promotes atherosclerosis and cardiovascular dysfunction through microbiota-derived metabolites, including trimethylamine N-oxide (TMAO), short-chain fatty acids (SCFAs), and bile acid-related pathways, as well as through effects on inflammation, cholesterol metabolism, endothelial injury, and intestinal barrier integrity. In recent years, phytomedicine, particularly Traditional Chinese Medicine (TCM), has attracted growing attention as a microbiota-modulating strategy because of its multi-component, multi-target, and system-level regulatory properties. In parallel, probiotics may provide targeted supplementation of beneficial strains and functional pathways. This review summarizes the major microbiota-mediated mechanisms involved in CHD and examines how phytomedicine regulates gut microbial composition, microbial metabolism, host inflammatory responses, and barrier function. We further discuss the complementary potential of phytomedicine and probiotics, highlighting their possible synergistic roles in restoring microbial ecology and improving cardiometabolic homeostasis. In addition, we critically evaluate current limitations in the field, including insufficient standardization of phytomedicine-probiotic combinations, heterogeneity of host-microbiota responses, limited clinical evidence, and unresolved long-term safety issues. Overall, this review provides an ethnopharmacology-oriented and mechanistically integrated perspective on microbiota-targeted interventions in CHD, and suggests that phytomedicine-based modulation, alone or in combination with probiotics, may represent a promising direction for future precision prevention and management of CHD.}, }
@article {pmid42297811, year = {2026}, author = {Senoo, DKJ and Acton, L and Hall, LJ}, title = {From diet to function: using synthetic microbial communities to map gut microbial interactions.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01012-9}, pmid = {42297811}, issn = {2055-5008}, support = {220876/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; BB/Y011619/1; BB/X011054/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Diet shapes gut microbial ecology and function, but causal mechanisms are hard to resolve in native communities. Synthetic microbial communities provide defined systems to test how dietary substrates alter community structure, metabolism, and host responses. This review summarises SynCom design, experimental platforms, and dietary applications, highlights multi-omics and modelling approaches, proposes reporting standards, and considers challenges and future directions, including multi-kingdom and AI-enabled function-first SynComs.}, }
@article {pmid42300034, year = {2026}, author = {Dhakal, D and Liang, Z and Zhang, P and Barr, JJ and Subedi, D and Dhital, S}, title = {Microbiota dynamics and their impact on the metabolite in lupin oat yoghurt analogues.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d5fo05594f}, pmid = {42300034}, issn = {2042-650X}, abstract = {The growing demand for nutritious, flavour-rich plant-based yoghurt analogues calls for innovative fermentation strategies. This study examined the impact of three probiotic combinations-Y1 (Lactobacillus delbrueckii subsp. bulgaricus, Streptococcus thermophilus and Lactobacillus rhamnosus), Y2 (Lactobacillus delbrueckii subsp. bulgaricus, Streptococcus thermophilus and Lactobacillus paracasei) and Y3 (Lactobacillus plantarum and Bifidobacterium sps.)- on microbial dynamics and metabolite formation in lupin-oat yoghurt analogues, using unfermented milk analogues as a control. Samples were assessed during fermentation and throughout 28 days of refrigerated storage (4 °C) using microbial enumeration, 16S rRNA sequencing, acidification profiling, and mass spectroscopy-based metabolomics. Fermentation increased volatile compounds, from 23 in the control to 28 (Y1), 41 (Y2) and 54 (Y3). Probiotic combination Y3 exhibited the most complex and stable aroma profile, enriched in pleasant volatiles such as butanoic acid, phenylacetaldehyde, and butyl esters which effectively masked off-flavours like hexanal and heptanal. Microbiota analysis revealed stable formulation-specific communities, with- Streptococcus dominating in yoghurt analogues Y1 and Y2, and Bifidobacterium prevailing in yoghurt analogues Y3. KEGG-based functional prediction linked these transformations to microbial enzymatic activities within metabolic pathways. Notably, Bifidobacterium dominance in Y3 facilitated enhanced ester biosynthesis and conversion of aldehydes to acids, highlighting the "bifid shunt" as a key contributor to flavour enhancement. This integrated multi-omics approach highlights the critical role of targeted probiotic selection in modulating fermentation biochemistry, microbial ecology, and sensory attributes in plant-based lupin-oat yoghurt analogues. Notably, Bifidobacterium-driven fermentation in Y3 offers a promising strategy for improving the flavour profile and consumer acceptance of lupin-oat yoghurt analogues.}, }
@article {pmid42301310, year = {2026}, author = {Cosoveanu, A and González-Carracedo, MA and Sopena Lasala, J and Pérez Pérez, JA and Cabrera, R}, title = {Shaping Fungal Communities in Cenchrus setaceus: Host Condition and Habitat Filtering.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02805-3}, pmid = {42301310}, issn = {1432-184X}, abstract = {We investigated the leaf-associated fungal communities of Cenchrus setaceus across a host condition gradient (high- vs. low-condition plants) and environmental zones (coast vs. hill; trade-wind exposure) on Tenerife (TF) and La Palma (LP). We hypothesized that community assembly reflects both host-driven deterministic filtering and abiotic promotion of richness in favourable environments via two mechanisms: (i) high-condition plants promote stable, guild-structured communities; (ii) humid, topographically buffered zones enhance fungal richness, especially for endophytes and saprotrophs. Nanopore sequencing and functional guild annotation revealed island- and zone-specific fungal assemblages. In TF, low-condition plants were associated with genera linked to stressed or exposed conditions whereas high-condition plants, especially in humid northern hills, supported more recurrent yeast-like and niche-associated taxa. In LP, high-condition plants in eastern hill zones were associated with distinct taxa, while drier western coastal low-condition plants were enriched in stress-related fungi. Fungal genera richness (Hill0) was consistently higher in low-condition plants (TF: 146 vs. 95; LP: 94 vs. 76; p < 0.05), while Shannon diversity diverged: greater in high-condition plants on LP (3.29 vs. 2.98), but lower on TF (3.10 vs. 3.28; p < 0.05). Community structure was shaped primarily by host condition in TF (PERMANOVA R[2] = 8.6%, p < 0.05), and by zone in LP (R[2] = 15.0%, p < 0.05). On TF, low-condition plants hosted significantly higher richness of saprotrophic, endophytic and plant-pathogenic genera (all p ≤ 0.001), whereas in LP zone × condition effects shaped guild richness patterns, with saprotroph richness increasing 2.66-fold in high condition plants from eastern hills relative to the eastern coast. Overall, high-condition plants supported less diverse but compositionally more stable fungal communities, while favourable environments enhanced guild richness independently of host condition.}, }
@article {pmid42302619, year = {2026}, author = {Kim, M and Al Hakeem, WG and Rothrock, MJ}, title = {Random forest modeling to identify key farm-to-fork factors influencing Campylobacter ecology in pastured poultry systems.}, journal = {Poultry science}, volume = {105}, number = {9}, pages = {107274}, doi = {10.1016/j.psj.2026.107274}, pmid = {42302619}, issn = {1525-3171}, abstract = {Campylobacter in poultry flocks poses significant food safety challenges, yet the drivers of its prevalence and load across the farm-to-fork continuum are not well understood. This study applied two-part random forest models to identify key factors influencing Campylobacter prevalence and load in pastured poultry systems. Data were collected from 11 farms in the southeastern United States between 2014 and 2017. The study included 1,942 broiler samples across five types: pasture soil, feces, ceca, whole carcass rinse after processing (WCR-P), and after storage (WCR-F). Two predictor sets were evaluated by 5-fold stratified cross-validation: farming practices with soil physicochemical properties and meteorological variables. Partial dependence plots were used to assess directional trends for key predictors. Models showed strong overall classification and regression performance across most sample types. Subsequent analyses focused on feces, ceca, and WCR-F to focus on the broiler specific farm-to-fork continuum. Classification models consistently identified farm as the dominant predictor of Campylobacter prevalence. This suggests the cumulative effect of site-specific management and processing practices unique to each farm. Flock age was the second most important predictor for fecal samples. Prevalence increased as birds matured. Day of year was another leading predictor for cecal and WCR-F samples, predicting the highest prevalence during summer. Regression models identified flock age as the top predictor of Campylobacter load in feces and the second most important predictor in ceca. Campylobacter load declined with bird age in feces whereas cecal loads continued to accumulate as an internal reservoir. Meteorological models showed that sustained high wind speed reduced fecal Campylobacter prevalence. Lower rolling-average humidity and higher rainfall on the sampling day were each associated with lower fecal loads. These findings indicate that Campylobacter prevalence and load are affected by distinct drivers at each production stage. Targeted interventions such as optimizing flock management schedules and implementing farm-specific biosecurity measures could improve Campylobacter control throughout the pastured poultry production continuum.}, }
@article {pmid42294705, year = {2026}, author = {Wang, J and Jiang, P and Yan, J and Shen, H and Wu, L and Wei, F and Lin, X and Xu, L}, title = {Spatial ecology meets quality control: a GIS-integrated strategy for visualizing and managing microbial contamination in sterile pharmaceutical cleanrooms.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0026826}, doi = {10.1128/spectrum.00268-26}, pmid = {42294705}, issn = {2165-0497}, abstract = {To enhance contamination source identification in sterile drug manufacturing, this study innovatively developed an integrated strategy combining geographic information system (GIS) spatial visualization with microbial contamination control. Between 2022 and 2025, researchers collected 1,117 environmental microbial isolates from sterile preparation workshops, analyzing their population structure, distribution patterns, and potential risks through 16S rRNA/ITS sequencing. GIS technology was employed to associate strain data with workshop spatial information, thereby providing a visual representation of microbial quantity, species composition, and distribution patterns. Results showed that Staphylococcus and Micrococcus dominated in clean areas, with microbial diversity highest in Controlled Not Classified (CNC) environments and lowest in A-grade areas. The microbial community structure in A-grade areas significantly differed from that in CNC/C/B-grade areas, while CNC/C/B-grade areas exhibited relative similarity. In the case study, the environmental microbial distribution maps clearly demonstrated regional variations and aggregation patterns. By identifying critical control areas and transmission pathways through contamination risk analysis, targeted interventions were designed and implemented, reducing the microbial contamination rate in target C-grade areas from 4.3% to 2.2%, thereby validating the strategy's effectiveness. This study targets the deficiency of "spatial visualization analysis" in clean area environmental monitoring. The proposed comprehensive strategy effectively fills the methodology gap in spatial analysis and contamination control for current clean area microbial monitoring. It provides a feasible framework for transforming environmental monitoring in the pharmaceutical industry from a passive surveillance system to an active early-warning system, assisting in enhancing the sterility assurance level of pharmaceutical production.IMPORTANCEAnalyzing the spatial distribution characteristics of microorganisms is crucial for developing effective pollution control strategies. However, existing environmental monitoring methods have limitations in revealing these spatial distribution patterns. This paper proposes an innovative strategy that integrates geographic information system (GIS) spatial analysis with microbial ecology research to enhance the accuracy and scientific rigor of pollution source identification and risk control. This approach enables the visualization of environmental microbial quantities, types, and spatial distribution, providing a quantitative tool for analyzing microbial contamination patterns and tracing transmission pathways. The developed "GIS-integrated strategy" methodology promotes a paradigm shift from merely confirming "microbial presence" to systematically analyzing the multidimensional relationships among "microorganism-environment-control." This study not only provides a scientific basis for formulating pollution control protocols in the pharmaceutical industry, contributing to improved sterility assurance, but also serves as a practical example of interdisciplinary integration between microbial ecology and spatial information science, demonstrating significant theoretical value and industry application prospects.}, }
@article {pmid42294914, year = {2026}, author = {Miller, MGA and Bergmann, GE and Alcalá Briseño, RI and Lan, Y-H and Søndreli, KL and Busby, PE and LeBoldus, JM}, title = {The interaction between Septoria stem canker and the mycobiome of Populus trichocarpa stems.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0005526}, doi = {10.1128/msystems.00055-26}, pmid = {42294914}, issn = {2379-5077}, abstract = {UNLABELLED: Sphaerulina musiva, a fungal pathogen causing leaf spot and canker disease of poplar trees (Populus spp.), was recently introduced to the Pacific Northwest, where it threatens commercially valuable plantations and native riparian ecosystems. Vascular tissue was collected from the stems of 410 symptomatic and asymptomatic trees in an S. musiva-infested Populus trichocarpa plantation. Resident fungal endophyte communities were characterized with ITS amplicon sequencing. Canker expression and S. musiva presence corresponded with reduced fungal diversity across multiple indices. Fungal endophyte communities of symptomatic tissues were frequently dominated by S. musiva and thus compositionally distinct from those of asymptomatic tissues. Asymptomatic-tissue communities from healthy and diseased stems did not differ in composition or diversity, indicating disease-associated low-diversity mycobiome states are local to the cankered site. The relative abundance of S. musiva was positively correlated with stem cankering. S. musiva was negatively correlated with key non-pathogenic fungal endophytes, which were themselves strongly inter-correlated. Our results illustrate S. musiva's ability to exploit the vascular microhabitat of susceptible Populus trichocarpa stems and dominate resident fungal assemblies at the site of infection.<br><br>IMPORTANCE: Plant-associated microbial communities can both mediate and be modified by pathogen infection. Thus, understanding disease outcomes of complex plant pathosystems requires characterization of pathogen-phytobiome interactions. Efforts to characterize these interactions have yielded microecological insights with applied relevance for disease management in herbaceous leaf- and root-associated pathosystems. However, pathogen-phytobiome interactions in the vascular tissues of hardwood stems remain largely unexplored. Our findings illuminate the ecological organization of the Populus trichocarpa stem mycobiome under S. musiva disease pressure and advance understanding of microfungal community dynamics in the Septoria stem canker pathosystem. Additionally, we identify potentially interactive fungal taxa that may disproportionately shape mycobiome structure and disease dynamics in Populus trichocarpa stems.}, }
@article {pmid42294941, year = {2026}, author = {Friebel, L and Knepper, J-P and Becker, NS and Abbaszade, G and Stückrath, K and Soltwisch, J and Müller, S and Dreisewerd, K and Mascher, T}, title = {Cannibalism shapes biofilm structure and composition in Bacillus subtilis.}, journal = {mBio}, volume = {}, number = {}, pages = {e0052526}, doi = {10.1128/mbio.00525-26}, pmid = {42294941}, issn = {2150-7511}, abstract = {UNLABELLED: In Bacillus subtilis colony biofilms, phenotypic diversification confers tissue-like properties and enhanced competitive fitness within a structural framework that allows both colony expansion and long-term survival via endospore formation. Cannibalism is a sporulation delay strategy, in which one subpopulation produces the sporulation delay protein SDP, the sporulation killing factor SKF, and the epipeptide EPE. These toxins are thought to lyse susceptible nonproducers, thereby releasing nutrients to prevent premature sporulation. However, the molecular mechanisms orchestrating this bacterial type of programmed cell death during biofilm development are poorly understood. Here, we comprehensively characterized mutants defective in either toxin production or the corresponding autoimmunity by a multiscale approach, combining luminescence reporters, colony biopsy, multi-parameter flow cytometry, and MALDI-mass spectrometry imaging to resolve cannibalism function and distribution. The toxins are produced in distinct, only partially overlapping areas of the colony, and are interdependent in their spatial distribution. Both EPE and SDP, but not SKF, are crucial for delaying sporulation. Loss of EPE or SDP autoimmunity resulted in severe morphological changes and stress-induced occurrence of suppressor mutants. The absence of all three toxins led to small, hyper-sporulating colonies with excessive wrinkle formation, indicating that cannibalism is essential for maintaining biofilm structure and lateral expansion. Our results provide the first evidence for the complex interactions between the three cannibalism toxins that shape biofilm architecture through bacterial programmed cell death. Localized toxin production and its spatial distribution affect the spatiotemporal organization, morphology, and subpopulation dynamics within B. subtilis biofilms.<br><br>IMPORTANCE: Programmed cell death (PCD) is a ubiquitous and crucial mechanism to structure eukaryotic multicellular tissues. PCD-like processes have also been described in bacteria, but their contribution to multicellular development is poorly understood. Cannibalism in Bacillus subtilis has been described as a sporulation delay strategy, in which one subpopulation produces antimicrobial peptides that kill susceptible nonproducing siblings. Their lysis is thought to release nutrients that delay the sporulation in the producing subpopulation. This study comprehensively analyses the role of the three cannibalism toxins in shaping colony biofilms. By combining MALDI-mass spectrometry imaging, colony biopsy, flow cytometry, and luminescence reporters, we demonstrate that cannibalism toxins are crucial for biofilm structure. They show a discrete and interdependent localization within the colonies. While cannibalism inhibits sporulation and causes severe envelope stress within biofilms, our data challenge the established role of cannibalism-dependent killing as the mechanism behind this sporulation delay.}, }
@article {pmid42295802, year = {2026}, author = {Zhang, S and Jiang, Q and Ma, J and Zou, J and Wang, F and Lv, F and Huang, Y and Wang, Y and Xu, Z}, title = {A Single-Cell Transcriptomic Atlas of the Ovine Rumen Microbiome Characterizes Lineage-Specific Metabolic Shifts Associated with Host Heat Tolerance.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e76152}, doi = {10.1002/advs.76152}, pmid = {42295802}, issn = {2198-3844}, support = {8257030475//National Natural Science Foundation of China/ ; 2025M770277//China Postdoctoral Science Foundation/ ; 2025YFF0512800//National Key R&amp;D Program of China/ ; 2024C03005//Pioneer R&amp;D Programs of Zhejiang/ ; 2024SSYS0022//Key R&amp;D Program of Zhejiang/ ; nycytxgxcxtd-2021-09//Guangxi Innovation Team Construction Project of National Modern Agricultural Industry Technology System/ ; AB2506910008//Science and Technology Major Project of Guangxi/ ; }, abstract = {The adaptation of complex, host-associated microbiomes to environmental perturbations is a critical determinant of ecosystem stability and resilience to climate change, as exemplified in ruminants. While single-microbe RNA sequencing advances community interrogation, complex microbial cell walls severely constrain unbiased single-cell transcriptomic profiling in the rumen. In this study, we developed an optimized 25 min time-resolved enzymatic lysis strategy using smRandom-seq to map the sheep rumen microbiome at single-cell resolution. By profiling 60 748 cells across 21 samples, we captured previously intractable lineages, resolving the transcriptional states of 213 genera and 662 species, achieving a physiologically relevant 0.303% recovery of methanogenic archaea. Unsupervised clustering partitioned the ecosystem into seven cross-species functional clusters, uncovering a spatial coupling between microbial lifestyle and metabolic specialization. Applying this framework to a model of host thermal adaptation demonstrated that host resilience was associated with rapid transcriptional activation of key energy-metabolism clusters. Notably, a lineage-specific metabolic shift toward a glycolytic phenotype in Anaerovibrio lipolyticus contributes to a compensatory "nutritional sparing" effect associated with host resilience. This dataset provides a foundational resource for rumen microbial ecology and establishes a technical framework for dissecting phenotypic plasticity within complex microbiomes.}, }
@article {pmid41831128, year = {2026}, author = {Zhao, Y and Bi, J and Zhao, Y and Wang, C and Li, Y}, title = {Characterization of capillary water absorption in microbially modified strongly weathered phyllite under the effect of thermal fatigue.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {3}, pages = {}, pmid = {41831128}, issn = {1573-0972}, support = {52164001, 52364004, 52464005//National Natural Science Foundation of China/ ; No. QianKeHeJiChu-ZK[2024]YiBan011//Guizhou Provincial Basic Research Program (Natural Science)/ ; [2023]40//the Basic Research Project of Guizhou University/ ; No. GCC[2022]005-1//the Guizhou Provincial Science and Technology Foundation/ ; No. 202412//the Special Research Fund of Guizhou University/ ; No. QianJiaoJi[2024]18//The Youth Talent Growth Project of Guizhou Provincial Department of Education/ ; }, abstract = {Phyllite, when used as a cement subgrade, is susceptible to thermal fatigue degradation due to temperature fluctuations resulting from prolonged exposure to natural environments. However, limited research exists on the anti-seepage properties of microbial-modified phyllite. This study investigates the capillary water migration characteristics of two types of strongly weathered modified phyllite subjected to thermal fatigue cycles, focusing on their anti-seepage performance and structural integrity for use as roadbed fillers or in infrastructure applications. Through spontaneous imbibition and thermal fatigue experiments, the effects of microbial modification on phyllite’s permeability were explored. The results indicated that microbial modification reduced phyllite’s porosity, improved its internal pore structure, and enhanced its anti-seepage performance. Compared to unmodified phyllite, the modified materials exhibited greater resistance to capillary water absorption. This study highlights the potential of microbial treatment as a sustainable method to enhance the properties of weathered phyllite. By combining knowledge of phyllite and microbial ecology, we aim to foster a deeper understanding of the relationship between these fields and better assess how microorganisms affect phyllite’s permeability.}, }
@article {pmid41843084, year = {2026}, author = {Madhusoodhanan, R and Raman, K and Akbar, R and Pambayan Ulagan, M and Mariadoss Arokia, VA and P, T}, title = {Modulating gut microbiota in type 2 diabetes mellitus: advances and challenges in precision medicine.}, journal = {Acta diabetologica}, volume = {}, number = {}, pages = {}, pmid = {41843084}, issn = {1432-5233}, abstract = {Type 2 Diabetes Mellitus (T2DM) is increasingly recognized as increasingly recognized as not only a metabolic disorder, but also a disease of microbiome–host dysregulation. While the role of the gut microbiota in T2DM has been extensively studied, the emerging convergence of precision medicine and microbiome modulation has not been systematically integrated into prior reviews. This work provides a critical synthesis that unites the classical concepts of dysbiosis with cutting-edge insights into microbial metabolites, strain-specific effects, and host–microbe–drug interactions, including the influence of metformin on microbial ecology and the therapeutic potential of Akkermansia muciniphila. We further discuss the underexplored domains, such as the gut virome, microbial gene editing, and short-chain fatty acid subtype-targeted interventions, which may transform T2DM management. We propose a novel conceptual framework for microbiome-guided, individualized T2DM care by framing gut microbiota as a dynamic, patient-specific therapeutic target. The review concludes with a roadmap for translating microbiota signatures into predictive biomarkers and tailored interventions, emphasizing standardized methodologies, multi-omics integration, and cross-disciplinary clinical trials. This perspective shifts the field from descriptive correlations to actionable precision-guided microbiome therapeutics in T2DM. Notably, this review extends beyond existing summaries by integrating emerging concepts, including gut virome contributions, microbial metabolite engineering, and host–microbe–drug interaction frameworks, to position the gut microbiota as a precision-modifiable therapeutic axis. This synthesis not only reviews established associations but also identifies underexplored therapeutic frontiers, including the gut virome, mycobiome, and microbial genome editing, which could reshape precision T2DM management.}, }
@article {pmid42020676, year = {2026}, author = {Purohit, HV and Chakraborty, J and Kothari, RK and Bhatt, AR}, title = {Gene Exchange Mechanisms in Natural and Engineered Probiotics Within the Human Gut Implications for Antibiotic Resistance and Metabolic Modulation.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {42020676}, issn = {1867-1314}, abstract = {The human gut microbiome is a dynamic and densely populated ecosystem where microbial gene exchange plays a central role in shaping both ecological interactions and host physiology. This review critically examines the mechanisms and implications of horizontal gene transfer (HGT) among natural and engineered probiotics within the human gut, with a specific focus on antibiotic resistance dissemination and metabolic modulation. We provide an in-depth analysis of the molecular pathways of conjugation, transformation, and transduction under anaerobic gut conditions, highlighting their roles in the spread of mobile genetic elements, including antibiotic resistance genes (ARGs) and functional metabolic traits. Special emphasis is placed on the dual nature of gene exchange: while beneficial traits such as vitamin biosynthesis and polysaccharide degradation can be horizontally acquired to enhance probiotic efficacy and host-microbe symbiosis, the uncontrolled dissemination of ARGs or synthetic constructs poses significant clinical and ecological risks. Through a synthesis of recent findings from metagenomics, microbial ecology, and synthetic biology, we explore how natural probiotics may act as reservoirs of ARGs, and how engineered strains—if not properly contained—may contribute to genetic instability in the gut. We also evaluate current containment strategies such as chromosomal integration, kill switches, auxotrophy, and orthogonal circuit design to limit horizontal spread, alongside emerging tools for in situ gene transfer monitoring. Finally, we discuss regulatory challenges and propose a context-dependent risk assessment framework in which the consequences of probiotic gene exchange are determined by cargo properties, host ecological niche, gut inflammatory status, and biocontainment design.}, }
@article {pmid42050727, year = {2026}, author = {Ivanova, M and Svensmark, B and Bruun Jensen, EE and Aarestrup, FM and Vigre, H and Otani, S}, title = {Metagenomics provides broad detection of pathogens, antimicrobial resistance, and virulence genes in pig diarrhoea and complement conventional methods.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00577-2}, pmid = {42050727}, issn = {2524-4671}, abstract = {BACKGROUND: Post-weaning diarrhoea (PWD) remains a major cause of morbidity in pig production and is commonly associated with enterotoxigenic Escherichia coli (ETEC). Conventional diagnostics rely on culturing and targeted qPCR, which provide limited resolution of pathogen diversity, virulence and antimicrobial resistance. Here, we evaluated Oxford Nanopore Technologies (ONT) metagenomic sequencing as a diagnostic tool for direct detection of pathogens, virulence factors and antimicrobial resistance genes (ARGs) from diarrhoeal pig faeces. RESULTS: Twenty-six diarrhoeal and six healthy pig faecal samples were analysed using culture, qPCR and ONT metagenomics with both high-output and rapid workflows. Culturing recovered 26 haemolytic E. coli and nine Clostridium perfringens isolates. PromethION metagenomics detected a significantly higher diversity of bacterial species, virulence factors and ARGs compared with GridION. Direct read mapping achieved 71–96% genome coverage for six E. coli isolates. Fourteen high- and medium-quality E. coli metagenome-assembled genomes (MAGs) were reconstructed, of which seven clustered closely with corresponding cultured isolates. All virulence factors detected in isolates were captured by metagenomics, while metagenomics identified additional fimbrial and enterotoxin genes not recovered by culture. Metagenomic ARG profiling identified resistance to 16 antibiotic classes, compared to eight classes in cultured isolates. No ESBL, carbapenemase or mcr genes were detected. CONCLUSIONS: Long-read ONT metagenomics enables culture-independent, strain-resolved characterisation of the pig gut microbiome during PWD, capturing pathogen diversity together with virulence and antimicrobial resistance profiles. This approach reveals within-sample strain heterogeneity and functional potential that are not resolved by conventional culturing, supporting its value for studying microbial ecology and dysbiosis in diseased animal microbiomes.}, }
@article {pmid42182427, year = {2026}, author = {Lu, C and Tashev, SA and Pessoa, P and Kruithoff, R and Shepherd, DP and Presse, S}, title = {Stochastic colonization and host-to-host transmission shape gut bacterial variability.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {42182427}, issn = {2692-8205}, abstract = {Understanding the kinetic processes that govern bacterial population dynamics within hosts is critical in developing effective strategies to control microbiota. However, inferring population dynamics is challenging due to large host-to-host bacterial population variability stemming from stochastic colonization events, as well as the inability to continuously monitor the bacterial population without disturbing the host. Using C. elegans fed E. coli under different diets, we show that early colonization acts as a stochastic bottleneck that drives substantial divergence in host-level bacterial loads, and that the spreading of bacteria from colonized worms to sterile ones regulates this variability by altering effective colonization pressure. These conclusions are reinforced using a simulation-based inference framework that quantifies stochastic within-host population dynamics from discrete snapshot data, enabling inference of effective colonization and growth rates across heterogeneous hosts with variable carrying capacities. Applying this framework, we further demonstrate that the bacterial predator B. bacteriovorus reduces average gut bacterial loads by two orders of magnitude, primarily by suppressing environmental recolonization and subsequent host-to-host transmission rather than eliminating established intra-host populations. Together, these results reveal that host-associated microbial population dynamics are strongly impacted by environmental colonization processes that modulate stochastic entry events.}, }
@article {pmid42278620, year = {2026}, author = {Lu, Z and Chen, G and Chang, M and Wang, N and Xia, T and Zhang, Y and Xu, G and Zhao, Q and Shen, P and Zhou, W and Ni, Z and Gao, Y}, title = {Effects of High-Altitude Environments on Gut Microbiota and Their Mechanisms in Immune Regulation and High-Altitude Adaptation.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, pmid = {42278620}, issn = {1422-0067}, support = {2025YFC3507500//National Natural Science Foundation of China/ ; 2025YFC3507502//National Natural Science Foundation of China/ ; zyyzdxk-2023311//State Administration of Traditional Chinese Medicine of the People's Republic of China/ ; }, mesh = {Humans ; *Altitude ; Animals ; *Gastrointestinal Microbiome/immunology ; *Acclimatization ; *Adaptation, Physiological ; Intestinal Barrier Function ; Dysbiosis ; Homeostasis ; }, abstract = {High-altitude environments, characterized by hypoxia, low temperature, and intense ultraviolet radiation, profoundly disrupt host intestinal homeostasis and reshape the gut microbiota, thereby influencing immune regulation and acclimatization. This review systematically summarizes the dynamic compositional and functional changes in the gut microbiota in high-altitude natives, immigrant populations, short-term visitors, and relevant animal models. Current evidence indicates that long-term high-altitude adaptation is associated with directional microbial remodeling, including the enrichment of anaerobic and short-chain fatty acid (SCFA)-associated taxa, which may support energy metabolism and immune homeostasis. In contrast, acute high-altitude exposure more readily induces dysbiosis, impairs intestinal barrier integrity, and promotes the translocation of endotoxins and bioactive metabolites. Mechanistically, the gut microbiota and its metabolites participate in high-altitude adaptation and high-altitude-related disease pathogenesis by modulating barrier function, inflammatory responses, oxidative stress, and immune signaling, and by mediating interorgan communication-characterized by metabolite-driven systemic inflammation or tolerance-through the gut-lung, gut-heart, gut-brain, gut-kidney, and gut-testis axes. SCFAs, bile acids, amino acid-derived metabolites, and succinic acid may control immune homeostasis and inflammatory responses through pathways including TLR4/NF-κB and NLRP3. Although the causal relationships, core microbial effectors, and population-specific heterogeneity remain incompletely defined, microbiota-targeted interventions, including probiotics, prebiotics, and fecal microbiota transplantation, have shown promise for promoting acclimatization and preventing high-altitude-related disorders. Overall, this review provides an integrated framework linking environmental stress, gut microbial ecology, and host immune-metabolic adaptation at high altitude, and highlights future directions for mechanistic and translational research in high-altitude medicine.}, }
@article {pmid42282557, year = {2026}, author = {Adelfio, M and Bonzanni, M and Callen, GE and Diaz, AR and Paster, BJ and He, X and Hasturk, H and Ghezzi, CE}, title = {Profiling Gingival Inflammation in a 3D Oral Tissue Model Reveals Early Features of Disease Progression.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.06.05.730462}, pmid = {42282557}, issn = {2692-8205}, abstract = {Gingival health depends on a balanced interplay among the gingival epithelium, immune system, and oral microbiome. Disruption of this equilibrium through sustained biofilm accumulation and host inflammatory responses leads to gingivitis, a highly prevalent yet reversible condition which if left untreated could progress into more severe and irreversible condition called periodontitis. The early onset of gingivitis remains poorly defined due to subtle clinical presentation and pronounced interindividual variability. Current diagnostic approaches rely largely on clinical assessment and endpoint biomarkers, limiting insight into the early host-microbiome interactions that drive disease initiation. Here, we employ a previously validated, physiologically relevant oral tissue model (OTM) to longitudinally investigate epithelial-microbiome interactions following inoculation with patient-derived dysbiotic microbiomes from early-stage gingivitis. The OTM maintained host tissue integrity and microbial viability over a seven-day period, preserving epithelial barrier function, dynamic inflammatory responses, and disease-associated microbial signatures. Notably, we establish, for the first time in an in vitro platform, clinical calibration against gingival crevicular fluid (GCF), demonstrating that OTM responses recapitulate inoculum-dependent inflammatory signatures, increased microbial dissimilarity under dysbiotic conditions, and coordinated host-microbiome metabolic interactions. While pro-inflammatory responses were most pronounced at early time points, subsequent modulation toward anti-inflammatory states highlights the temporal complexity of host responses and suggests that longer culture durations may further resolve disease trajectories. Collectively, these findings validate the OTM as a robust, physiologically relevant platform that captures key features of periodontal health and inflammation. By integrating host viability, microbial ecology, and clinical benchmarking, this system enables mechanistic interrogation of early disease-driving processes and provides a translational framework for advancing predictive diagnostics and preventive therapeutic strategies in periodontal disease.}, }
@article {pmid42283811, year = {2026}, author = {Costanzo, M and Di Gregorio, L and Tabacchioni, S and Bevivino, A and Visca, A}, title = {Mobile Genetic Elements as Key Drivers of Bacterial Evolution and Adaptation in Agroecosystems.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02803-5}, pmid = {42283811}, issn = {1432-184X}, abstract = {Mobile genetic elements (MGEs), including plasmids, transposons, integrative and conjugative elements, and phage-derived sequences, are central drivers of bacterial evolution in agroecosystems. By enabling horizontal gene transfer, MGEs allow soil- and plant-associated bacteria to rapidly acquire complex functional traits, facilitating adaptation to fluctuating environmental conditions and different agricultural management practices. In agricultural soils, MGEs underpin key microbial functions such as nutrient acquisition and cycling, stress tolerance, rhizosphere competence, and interactions with plant hosts, thereby influencing soil fertility and crop performance. Selective pressures in agroecosystems extend beyond antimicrobial exposure and include fertilizers, pesticides, plant defense compounds, recurrent biotic and abiotic stress, as well as high-yielding crop varieties. These pressures generate co-selection dynamics that shape mobilome composition and activity, linking traits such as resistance, pathogenicity, and biocontrol to broader ecological functions relevant to plant health. Rather than acting as exceptional genetic entities, MGEs form a dynamic and environmentally responsive genetic network that enables rapid ecological tuning while preserving core genome stability. Comparative genomics has revealed that major lifestyle transitions in agroecosystem-associated bacteria, from free-living to commensal, mutualistic, or pathogenic states, are frequently mediated by the gain and loss of genomic islands and other MGEs. This review synthesizes the latest research on the ecological functions and evolutionary dynamics of MGEs in agroecosystems and explores how mobilome-informed approaches can support microbial-based strategies for sustainable agriculture.}, }
@article {pmid42283827, year = {2026}, author = {Wiśniewski, P and Maździarz, M and Kwietniewska, K and Krawczyk, K}, title = {Shifts in Rhizosphere Bacterial Community Composition and Predicted Functional Potential Associated with Impatiens parviflora Invasion in Temperate Forest.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02807-1}, pmid = {42283827}, issn = {1432-184X}, support = {No. 12.610.002-110//Uniwersytet Warmi&#x144;sko-Mazurski w Olsztynie/ ; No. 12.610.002-110//Uniwersytet Warmi&#x144;sko-Mazurski w Olsztynie/ ; No. 12.610.002-110//Uniwersytet Warmi&#x144;sko-Mazurski w Olsztynie/ ; }, abstract = {Impatiens parviflora is a widespread invasive plant in temperate European forests, yet its influence on rhizosphere microbial communities remains poorly understood. This study provides initial metagenomic insights into taxonomic shifts and predicted functional potential of bacterial communities associated with this invader. Rhizosphere soils were collected from eight I. parviflora-invaded and eight non-invaded control plots in a mixed coniferous forest in northern Poland and analysed using Oxford Nanopore shotgun sequencing, with functional inference performed using the taxonomy-dependent FAPROTAX database. Bacterial richness was significantly higher in invaded soils, whereas Shannon and Simpson diversity indices did not differ between treatments, indicating an expansion of rare taxa without changes in overall diversity structure. The invaded rhizosphere was characterised by a uniform depletion of dominant bacterial orders, with no significantly enriched taxa detected, contrasting with the selective enrichment of microbial groups often reported for other invasive plant species. FAPROTAX-based predictions indicated consistently lower inferred abundances of 37 metabolic processes in invaded plots, including those related to nitrogen cycling and degradation of complex plant polymers. Because these functional predictions are derived from taxonomic composition, they represent inferred ecological potential rather than measured activity. Overall, these results generate testable hypotheses regarding plant-soil feedbacks and highlight the utility of long-read metagenomics for exploring microbial dynamics potentially contributing to the ecological success of I. parviflora in temperate forests.}, }
@article {pmid42287050, year = {2026}, author = {Gao, J and Li, W and Li, X and Tan, Y and Li, Y and Duan, L and Wu, T and Chen, D and Hu, Y and Wang, M}, title = {[Association between wearable-derived physical activity patterns and gut microbiota in older adults].}, journal = {Beijing da xue xue bao. Yi xue ban = Journal of Peking University. Health sciences}, volume = {58}, number = {3}, pages = {551-559}, pmid = {42287050}, issn = {1671-167X}, mesh = {Humans ; Aged ; *Wearable Electronic Devices ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Exercise/physiology ; Male ; Female ; Feces/microbiology ; China ; }, abstract = {OBJECTIVE: To identify real-world physical activity patterns in older adults using objective measurements from wearable devices, and to analyze the associations between these patterns and gut microbiota composition.<br><br>METHODS: Based on data collected from a real-world health management project, a total of 743 participants from Eastern, Central, and Northern China were enrolled between January 2018 and June 2025. A 180-day objective physical activity dataset prior to fecal sampling was collected via smart wearable devices to extract features including mean daily steps, coefficient of variation of steps, and the proportion of active days. Fecal samples underwent 16S ribosomal RNA (rRNA) gene (V3-V4 region) amplicon sequencing to obtain genus-level relative abundance matrices. Covariates, including demographics, lifestyle, and chronic disease history, were collected via questionnaires and physical examinations. The discriminative dimensionality reduction via learning a tree (DDRTree) algorithm combined with K-means clustering was applied to identify physical activity phenotypes. Alpha diversity was evaluated using the Shannon index (Kruskal-Wallis test), and beta diversity was assessed using covariate-adjusted permutational multivariate analysis of variance (PERMANOVA) based on Bray-Curtis distance. Multivariable linear regression with false discovery rate (FDR) correction was used to screen differential taxa. A microbial risk score (MRS) was constructed based on taxa with a raw P < 0.05, defined as the difference between the standardized abundance of beneficial and harmful taxa. Co-occurrence networks were constructed to evaluate micro-ecological topological structures.<br><br>RESULTS: The cohort comprised 381 (51.3%) individuals aged 60-74 years and 362 (48. 7%) aged &#x2265;75 years. Compared with the 60-74 group, the &#x2265;75 group had higher prevalences of hypertension (45.9% vs. 36.7%, P=0.045) and heart disease (34.0% vs. 25.2%, P=0.032), higher systolic blood pressure (median 130 mmHg vs. 120 mmHg, P < 0.001), and fewer mean daily steps (median 6 200 steps vs. 7 000 steps, P < 0.001). Clustering identified three activity patterns: active group (n=143, 19.2%; high steps, low variation, high adherence), moderate group (n=429, 57.7%), and irregular group (n=171, 23.0%; low steps, high variation, low adherence). The active group exhibited the lowest prevalences of hypertension (35.0%) and heart disease (21.7%), and the lowest systolic blood pressure (mean 124.4 mmHg), whereas the irregular group showed the highest values (51.5%, 40.4%, and 127.6 mmHg, respectively). Alpha diversity showed no significant differences among the groups. After adjusting for covariates, physical activity patterns showed no statistically significant effect on beta diversity (R[2]=0.003 7, P=0.115). Compared with the irregular group, two genera in the active group showed significant differences (P < 0.05). Specifically, the relative abundance of Roseburia in the active group was significantly lower than that in the irregular group (P < 0.05), and the relative abundance of Butyricimonas was also significantly lower than that in the moderate group (P < 0.01). However, these differences did not remain statistically significant after FDR correction. The MRS exhibited a significant gradient distribution across the groups, with the active group scoring the highest (P < 0.001). Co-occurrence network analysis revealed that the active group had the highest network density and proportion of positive correlations (84.5%), whereas the irregular group had the lowest (60.3%).<br><br>CONCLUSION: Physical activity patterns identified from wearable device data are associated with gut microbiota composition and ecological network characteristics in older adults. Active and regular physical activity patterns indicate a higher MRS and more stable microbial co-occurrence networks, suggesting potential associations between activity regularity and gut microbial ecology, though causal inference requires longitudinal confirmation.}, }
@article {pmid42287443, year = {2026}, author = {Pires, D and Castañeda, F and Galvez, L and Balendres, MA}, title = {Soil as a Battlefield and a Reservoir: Linking Soil Components to the Epidemiology of Soilborne Plant Diseases.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02810-6}, pmid = {42287443}, issn = {1432-184X}, abstract = {This paper focuses on how microbial diversity, soil organic matter, and soil structure influence the activities of soilborne pathogens and plant disease epidemiology. Microbial diversity, soil organic matter, and soil structure are soil components that can reshape plant-pathogen-soil interactions by altering nutrient dynamics and the composition of the soil microbiome. When beneficial microorganisms are enriched in soil ecosystems, suppression of soilborne pathogens may be enhanced, thereby decreasing disease incidence and severity. However, microbial diversity, soil organic matter, and soil structure may also promote pathogen growth or facilitate cooperative microbial interactions that improve pathogen persistence, thereby elevating disease risk. Future progress requires a shift from descriptive surveys toward functional and predictive approaches, as these soil components influence epidemiological processes that can either suppress or intensify the development of plant diseases caused by soilborne plant pathogens. Rather than acting as deterministic drivers of disease outcomes, microbial diversity, soil organic matter, and soil structure modify the ecological context in which host-pathogen interactions occur, altering the likelihood of pathogen establishment, persistence, and transmission. This paper highlights the importance of soil management in regulating microbial community dynamics and supporting plant disease control within this probabilistic ecological framework.}, }
@article {pmid42287449, year = {2026}, author = {Mertin, AA and Blackall, LL and Brumley, DR and Liew, ECY and van der Merwe, M}, title = {Host Species Mediate Distinct Seed Microbiome Responses to Restoration.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02802-6}, pmid = {42287449}, issn = {1432-184X}, abstract = {Microbial diversity is a key driver of ecosystem function, yet it remains poorly integrated into ecological restoration frameworks. While seeds are the primary dispersal unit of plants and the foundation of most restoration programs, the microbial communities they carry are rarely considered. Here, we assess whether sites that have undergone restoration have altered seed-associated microbial communities. We do this by comparing bacterial and fungal seed microbiomes across natural and restored landscapes. Using a landscape-scale sampling design, seeds were collected from multiple plant host species and populations across 41 sites spanning a broad latitudinal gradient. High-throughput sequencing of the 16S rRNA gene and ITS2 region was used to characterise bacterial and fungal communities, respectively, and differences in diversity, composition, and network structure were assessed using multivariate and network-based approaches. Seed microbiomes differed between natural and restored sites, but the magnitude and nature of these changes varied among host species. Restored sites were associated with shifts in microbial diversity, community composition, and network structure, including changes in the retention of putative keystone taxa. In some species, restoration was linked to pronounced restructuring of seed-associated microbial communities, whereas in others, microbiomes remained comparatively stable. Together, these results demonstrate that restoration can alter seed microbial communities in ways that are not consistently predicted by soil-focused restoration outcomes and that host identity mediates these responses. Incorporating seed microbiome data into restoration monitoring may therefore provide a complementary and previously overlooked indicator of restoration success, with implications for improving plant germination and health.}, }
@article {pmid42287489, year = {2026}, author = {da Silveira Bastos, IMA and Cardoso, MS and Laux, M and Ribeiro, RR and García, GJY and Bahia, PA and de Sousa, PMV and Alves, BGT and de Rezende, DHC and Rosado, AS and Bezerra, JDP and Landell, MF and Melo, VMM and Tavares, TCL and Góes-Neto, A}, title = {Worldwide diversity and ecology of mangrove fungi: a systematic review of ITS metabarcoding studies and a quantitative, integrative analysis of raw sequence data.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {7}, pages = {}, pmid = {42287489}, issn = {1573-0972}, mesh = {*Fungi/classification/genetics/isolation &amp; purification ; *DNA Barcoding, Taxonomic ; *Biodiversity ; *Wetlands ; *Mycobiome ; Basidiomycota/genetics/classification ; Geologic Sediments/microbiology ; *Rhizophoraceae/microbiology ; Ecosystem ; Ascomycota/genetics/classification/isolation &amp; purification ; Phylogeny ; }, abstract = {Fungi are integral components of the mangrove microbiome, playing critical roles in decomposition, nutrient cycling, and symbiosis. Our study synthesizes the findings from a global systematic review of fungal ITS metabarcoding studies conducted in mangrove ecosystems. This review consolidates data from 23 original research articles (1,154 samples) and provides a comprehensive overview of the diversity, community structure, and ecological functions of fungi in these critical coastal habitats. The analyses revealed a consistent core fungal mycobiome in mangroves worldwide. This community is dominated by Ascomycota, with Basidiomycota as the second most abundant phylum. A consistent set of ten highly abundant genera underpins this core community, and fungal diversity and composition are strongly influenced by the specific substrate. Non-rhizospheric sediment harbors the highest diversity, while live plant organs host a more specialized and less diverse community, slightly dominated by potential plant pathogens. Rhizospheric sediment supports a unique assemblage rich in wood-decomposing fungi. The primary ecological role of fungi in mangroves is decomposition, which is essential for breaking down lignocellulosic litter, cycling nutrients, and storing carbon in sediments. A surprisingly high relative abundance of fungi classified as plant pathogens was identified on mangrove plant tissues, suggesting an underappreciated role of fungal diseases in these ecosystems. Metabarcoding provides a far broader view of fungal diversity than traditional collection and culturing methods. It has uncovered a vast number of uncultured taxa and has been particularly effective in revealing the significant, and likely underestimated, presence of macrofungi in mangrove soils. Our study also highlights that current short-read metabarcoding can severely underestimate certain fungal groups, particularly the endomycorrhizal Glomeromycota, due to technical limitations. Altogether, our synthesis provides a global baseline against which future mangrove mycobiome studies can be benchmarked.}, }
@article {pmid42289496, year = {2026}, author = {Liu, J and Zhao, Y and Wang, Y and Shi, Y and Zhi, Q and Chen, L and Ke, Y and Ren, J}, title = {ARHI as a key regulator of EMT and metastasis in pancreatic cancer via the Notch-1 pathway.}, journal = {Human genetics}, volume = {145}, number = {1}, pages = {}, pmid = {42289496}, issn = {1432-1203}, support = {81772630//the National Natural Science Foundation of China/ ; 2017J01377//the Natural Science Foundation of Fujian Province/ ; 2024GZL-GG36//Xiamen Young and Middle-Aged Key Talents Program for High-Quality Development/ ; 2022050901//the Science and Technology Programs of the Tan Kah Kee Innovation Laboratory/ ; }, mesh = {*Pancreatic Neoplasms/pathology/genetics/metabolism ; *Epithelial-Mesenchymal Transition/genetics ; *Receptor, Notch1/metabolism/genetics ; Humans ; Animals ; Mice ; Signal Transduction ; Cell Line, Tumor ; Neoplasm Metastasis ; Gene Expression Regulation, Neoplastic ; *rho GTP-Binding Proteins/genetics/metabolism ; Liver Neoplasms/secondary/genetics ; Neoplasm Invasiveness ; Cell Proliferation ; }, abstract = {Pancreatic cancer cell metastasis is a major factor influencing prognosis. A Ras homologue member I (ARHI) was reported to regulate proliferation and apoptosis in pancreatic cancer; however, its role in invasion remains unclear. This study aimed to explore the role and related mechanisms of ARHI in pancreatic cancer metastasis. We revealed that in pancreatic cancer ARHI expression levels were consistent with aggressive cellular phenotypes, and that changes in endogenous ARHI protein expression led to corresponding alterations in epithelial-mesenchymal transition (EMT) markers. Furthermore, ARHI accelerated tumor invasion in pancreatic cancer cells and in a mouse hepatic metastasis model. Notably, this unusual promoting effect of ARHI on EMT and invasion in pancreatic cancer was primarily exerted through the Notch-1 signaling pathway. Collectively, our findings provide insight into the function and molecular mechanisms of ARHI in pancreatic cancer metastasis.}, }
@article {pmid42292476, year = {2026}, author = {Zhou, Y and Li, Z and Chu, Y and Zhou, Z and Zhang, T and Yi, N and Sun, W and Yan, J and Yan, Z and Zhu, A}, title = {Reframing precision nutrition in irritable bowel syndrome: a mechanism-informed conceptual framework for responder prediction and clinical translation.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1809221}, pmid = {42292476}, issn = {1664-3224}, mesh = {Humans ; *Irritable Bowel Syndrome/diet therapy/microbiology/metabolism ; *Gastrointestinal Microbiome ; FODMAP Diet ; *Precision Medicine/methods ; Multiomics ; Translational Research, Biomedical ; }, abstract = {BACKGROUND: The low-Fermentable Oligosaccharides, Disaccharides, Monosaccharides and Polyols (FODMAP) diet is widely used for irritable bowel syndrome (IBS), but response varies markedly across patients. This heterogeneity has shifted the field from testing average efficacy toward forecasting individual benefit and translating microbiome science into practical precision-nutrition tools.<br><br>METHODS: We present a conceptual analysis grounded in evidence mapping from human IBS studies that paired dietary interventions (primarily low-FODMAP pathways) with baseline microbiome and/or multi-omics measurements. Findings are organized within a "microbiome-to-model" roadmap that specifies responder endpoints, candidate data layers (taxa, functions, metabolites and volatile signatures), modeling choices, and the validation and implementation requirements needed for clinical decision support.<br><br>RESULTS: Three recurring signals emerge across cohorts. Baseline microbial ecology can stratify response, but taxonomic features alone often fail to transport across studies. Functional readouts, including metabolites and volatile signatures, are closer to symptom mechanisms and can improve interpretability; however, clinical deployment is still limited by endpoint heterogeneity, imperfect exposure and adherence measurement, batch effects, and insufficient external validation and calibration.<br><br>CONCLUSION: IBS is well suited for microbiome-informed responder prediction, provided that models are developed with deployment in mind. Progress will depend on validation-first study designs, harmonized responder endpoints and adherence capture, robust multi-omics pipelines, and biologically interpretable decision rules that can be prospectively tested and monitored for temporal instability in real-world care.}, }
@article {pmid42293159, year = {2026}, author = {Ike, I and Teymouri, F and Crook, C and Guzman, S and Hazeltine, M and Castillo, D and Li, D and Brar, G}, title = {The interplay between bile acid metabolism and gut microbiome in biliary tract cancers.}, journal = {Frontiers in microbiomes}, volume = {5}, number = {}, pages = {1774429}, pmid = {42293159}, issn = {2813-4338}, abstract = {The gut microbiota and bile acids (BAs) exist in a tightly regulated, bidirectional relationship that influences host metabolism, immune function, and disease. Primary BAs synthesized in the liver are chemically transformed by intestinal microbes into a diverse pool of secondary BAs, which exert antimicrobial effects and activate host signaling pathways including Farnesoid X Receptor (FXR), Takeda G protein-coupled receptor 5 (TGR5), and sphingosine-1-phosphate receptor 2 (S1PR2). These pathways regulate BA homeostasis, epithelial barrier integrity, inflammation, and carcinogenesis. Disruption of this BA-microbiome axis has been implicated in biliary tract cancers (BTCs), a group of aggressive malignancies with rising global incidence and limited therapeutic options. Secondary BAs and BA receptor signaling contribute to tumor initiation and progression through NF-κB activation, oxidative stress, and altered cell survival, whereas reduced FXR signaling and obstructed enterohepatic circulation further promote inflammatory dysregulation. Emerging evidence demonstrates that microbial dysbiosis and altered BA metabolism are associated with distinct BTC microbial profiles, enriched in taxa such as Fusobacterium, Salmonella, Prevotella, and Actinomyces, alongside depletion of commensals including Lactobacillus. These taxa influence inflammatory signaling, BA transformation, and epithelial injury, contributing to carcinogenesis. Microbiome-BA interactions also shape anti-tumor immunity and responses to immune checkpoint inhibitors (ICIs). Specific microbial signatures-particularly enrichment of Lachnospiraceae, Erysipelotrichaceae, Bacteroidetes, and Alistipes-correlate with enhanced immune activation and improved clinical outcomes in hepatobiliary cancers. Modulation of gut microbiota through antibiotics, probiotics, or fecal microbiota transplantation can influence BA composition, immune surveillance, and therapeutic efficacy. Collectively, these data highlight the central role of the BA-microbiome axis in BTC pathogenesis and treatment response. Microbial and BA metabolite profiling represent promising avenues for biomarker development, while targeted manipulation of BA signaling and microbial ecology offers potential therapeutic strategies to improve BTC outcomes.}, }
@article {pmid42293552, year = {2026}, author = {Aldriwesh, MG and Bin Shuraym, H and Asiri, NY and Asiri, WY and Abukhalid, NF and Alasiri, A and Alghoribi, MF}, title = {Microbiome and One Health in GCC countries: current status, research gaps, and future directions.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1821688}, pmid = {42293552}, issn = {1664-302X}, abstract = {BACKGROUND: Microbiome science has emerged as a central component of the One Health framework, linking human, animal, and environmental health. Although global microbiome research has expanded rapidly, a comprehensive evaluation of microbiome research development and integration across the Gulf Cooperation Council (GCC) countries remains lacking. This systematic review aimed to characterize microbiome research in the GCC countries, identify major research gaps, and evaluate alignment with One Health principles while proposing a strategic framework to support coordinated regional development.<br><br>METHODS: This systematic review followed PRISMA 2020 guidelines. A structured search of PubMed, ScienceDirect, Google Scholar, and EBSCO databases identified microbiome-related studies published up to January 31, 2025. Eligible studies included original research conducted in the GCC countries (Saudi Arabia, Qatar, Kuwait, United Arab Emirates, Oman, and Bahrain) investigating human, animal, or environmental microbiomes. Findings were synthesized descriptively to assess study distribution, research design, analytical methodologies, and thematic focus.<br><br>RESULTS: A total of 110 studies met the inclusion criteria. Human microbiome studies accounted for 49% of publications, followed by environmental microbiome studies (40%) and animal microbiome studies (11%). Research output increased substantially after 2020 but remained uneven among the GCC countries, with Saudi Arabia contributing 44% of publications, whereas Bahrain and Oman together accounted for fewer than 7%. Most studies were observational and primarily used 16S rRNA gene sequencing on Illumina platforms. Human studies focused mainly on gut and oral microbiomes and frequently investigated metabolic disorders such as obesity and diabetes. Animal microbiome research was limited and largely centered on camels, with minimal investigation of livestock relevant to food security. Environmental studies predominantly examined soil and desert environments. No included study simultaneously investigated human, animal, and environmental microbiomes within an integrated One Health study design.<br><br>CONCLUSION: Microbiome research in the GCC countries is growing but remains uneven and largely disconnected across human, animal, and environmental studies, with limited adoption of One Health approaches. A coordinated regional strategy integrating governance, infrastructure, funding, and workforce development is needed to advance translational microbiome research and strengthen the GCC's contribution to global health, food security, and environmental sustainability.}, }
@article {pmid42294667, year = {2026}, author = {Aponte Rolón, B and Kristy, B and Shade, A and Stopnisek, N and Lebeis, SL and Howe, A and Benucci, GMN}, title = {BRCore: an R package implementing flexible selection of core taxa using contribution to Bray-Curtis dissimilarity and neutral model fitting.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0025126}, doi = {10.1128/mra.00251-26}, pmid = {42294667}, issn = {2576-098X}, abstract = {Identifying core taxa in microbial ecology highlights groups likely to participate in a broad range of potential ecological interactions. Here, we present BRCore, an R package to identify core taxa using abundance-occupancy distributions and beta-diversity contributions across ecological niches, and predict stochastic and deterministic taxa.}, }
@article {pmid42294679, year = {2026}, author = {Henkel, JV and Røy, H and Jørgensen, BB and Rotaru, A-E and Jovicic, D and Marshall, IPG and Jiang, C and Nielsen, PH and Singleton, CM and Arz, HW and Plewe, S and Kjeldsen, KU}, title = {Desulfatiglans-related bacteria associated with conductive mineral particles in marine subsurface sediments.}, journal = {mBio}, volume = {}, number = {}, pages = {e0083826}, doi = {10.1128/mbio.00838-26}, pmid = {42294679}, issn = {2150-7511}, abstract = {UNLABELLED: Acetate is a key intermediate in anaerobic mineralization of organic matter in marine sediments. Recent observations suggest that acetate is oxidized syntrophically in the methanic zone of marine sediments, and that electrically conductive mineral particles could provide niches for electroactive microbial communities that perform this process. We combined radiotracer measurements, a novel procedure for ferromagnetic mineral particle extraction, and metagenomic analyses to examine this process in Baltic Sea sediments. Our results confirm that acetate is oxidized syntrophically across and below the sulfate-methane transition zones of the sediments, where the transfer of reducing equivalents from acetate oxidation to CO2 fuels methanogenesis. Ferromagnetic particles consistently occurred throughout the geochemical zones and mainly consisted of the electrically conductive minerals magnetite and pyrite-greigite. The microbial communities associated with ferromagnetic particles were dominated by members phylogenetically affiliated with the bacterial genus Desulfatiglans. Known Desulfatiglans species are dissimilatory sulfate reducers; however, metagenome-assembled genomes indicate that Desulfatiglandales populations associated with ferromagnetic particles lack genetic potential to respire sulfate. Instead, they may grow by acetate oxidation coupled with extracellular electron transfer, consistent with a conductive mineral-associated lifestyle. We hypothesize that Desulfatiglans relatives are acetate-oxidizing partners in a syntrophic process facilitated by interspecies electron transfer via conductive particles. We identified cytochrome-rich ANME-1 archaea as the predominant methane-cycling microorganisms associated with ferromagnetic particles; however, their potential role as methanogenic syntrophic partners remains uncertain. Overall, our study reveals that distinct microbial communities are associated with ferromagnetic particles and shows conductive minerals as a niche for electroactive microorganisms in marine sediments.<br><br>IMPORTANCE: Acetate is a central intermediate in the anaerobic breakdown of organic matter. In Baltic Sea sediments at and below the sulfate-methane transition zone, we observed acetate oxidation to carbon dioxide at rates similar to methane formation from carbon dioxide reduction, a pattern indicative of syntrophic acetate oxidation. Previous enrichment studies suggest that electrically conductive mineral surfaces can facilitate this process. Motivated by this observation, we extracted ferromagnetic conductive particles from sediments and compared particle-attached microbial communities with bulk sediment. Particle-attached communities were distinct and enriched in the bacterial genus Desulfatiglans. Their genomes lacked genes for sulfate respiration, yet encoded traits consistent with acetate oxidation and extracellular electron transfer. Our findings suggest conductive minerals as distinct microbial niches and highlight Desulfatiglans-related bacteria as a potential key organism in particle-associated acetate oxidation.}, }
@article {pmid42294682, year = {2026}, author = {Ai, C and Tang, X and Han, H and He, Y and Zhang, H and Liu, C and Liao, H and Zhou, S}, title = {Active prophages as key drivers of microbial adaptation in global soil ecosystems.}, journal = {mBio}, volume = {}, number = {}, pages = {e0069326}, doi = {10.1128/mbio.00693-26}, pmid = {42294682}, issn = {2150-7511}, abstract = {Soils harbor the most complex microbial diversity on Earth, in which bacteria are ubiquitously infected by temperate phages. While integrated prophages often enhance host fitness, active (inducible) prophages are traditionally perceived as "molecular time bombs" due to their intrinsic lysis threat. This dual nature has raised fundamental questions about the true contribution of temperate phages to microbial adaptation and ecosystem stability. To address this gap, we conducted a global-scale integrative analysis by synthesizing 123,207 high-quality bacterial genomes, 183 soil-specific viromic data sets, and 3,749 metagenomes. We established the Global Soil Active Prophage Database (GSAPD), comprising 21,397 high-confidence active prophages, which we found to represent 34.3% of the total soil viral population within our analytical framework. Our comparative genomic analysis reveals that active prophages possess significantly larger genomes and greater genetic complexity compared with their dormant counterparts. Crucially, by mapping phage-encoded auxiliary metabolic genes (AMGs) across diverse biomes, we found that active prophages are disproportionately enriched in key pathways for carbon, nitrogen, and sulfur cycling, as well as specialized resistance mechanisms against heavy metal toxicity. These findings suggest that active prophages act as dynamic reservoirs of functional diversity. We demonstrate that their lytic potential is not merely a survival risk, but a sophisticated mechanism underpinning host environmental adaptation and niche expansion. Ultimately, this study provides a comprehensive global catalog of soil viral pathways and redefines the role of temperate phages as pivotal drivers of microbial evolution and biogeochemical cycling in terrestrial ecosystems.IMPORTANCESoils contain immense microbial diversity, yet the ecological role of temperate phages-especially their active (inducible) forms-remains poorly understood. This study provides the first global-scale assessment of active prophages in soils, revealing that they are widespread and functionally distinct from dormant forms. By building a comprehensive database and integrating multi-omics data, we show that active prophages are enriched in genes linked to key biogeochemical processes and stress resistance. These findings challenge the traditional view of active prophages as purely harmful agents and instead highlight their role as dynamic contributors to microbial function and adaptation. Our work offers new insights into how viruses shape ecosystem processes and provides a valuable resource for future studies on soil microbial ecology and nutrient cycling.}, }
@article {pmid42294696, year = {2026}, author = {Han, J and Li, Y and Xu, Y and Li, S and Zeng, J}, title = {Reliable delineation of Clostridioides difficile and related members of the family Peptostreptococcaceae using phylogenomics and spore coat protein-specific molecular markers.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0418525}, doi = {10.1128/spectrum.04185-25}, pmid = {42294696}, issn = {2165-0497}, abstract = {Traditional bacterial classification relies on phenotypic traits (e.g., morphology and metabolic profiles), but these methods lack resolution for closely related taxa and are biased by culture conditions. While 16S rRNA gene sequencing is a widely used molecular complement, it fails to resolve closely related Peptostreptococcaceae species, including Clostridioides difficile. These limitations have caused family-level taxonomic confusion and ambiguous Clostridioides genus boundaries, hindering clinical identification of pathogenic strains and posing public health risks. To address these limitations, we developed an integrated approach combining multi-scale phylogenomic and protein-based molecular evidence, adopting a hierarchical workflow: first, constructing a 16S rRNA phylogeny of 151 Firmicutes strains to demonstrate traditional marker inadequacies; second, generating a whole-genome protein phylogeny of 51 representative Peptostreptococcaceae genomes and defining taxonomic boundaries via average amino acid identity (AAI); third, analyzing spore-associated protein patterns across C. difficile isolates and related genomes. Results revealed high conservation of C. difficile spore coat/exosporium proteins and clear genus-level phylogenetic distinctiveness of these proteins. Combined with AAI-validated whole-genome data, our findings support key Peptostreptococcaceae taxonomic revisions: redefining polyphyletic Romboutsia, reassigning Eubacterium tenue to Paraclostridium, and elevating Alkalithermobacter to genus status. This study establishes spore coat proteins as core taxonomic markers for spore-forming bacteria, with our integrated strategy overcoming traditional limitations to improve classification accuracy and C. difficile surveillance.IMPORTANCEConventional classification struggles to resolve closely related Peptostreptococcaceae species (e.g., Clostridioides difficile). We developed an integrated framework combining 16S rRNA sequencing, whole-genome protein analysis, and spore trait assessment, with a key innovation: identifying spore coat/exosporium proteins as robust, conserved taxonomic markers. This approach enabled three pivotal Peptostreptococcaceae revisions-redefining Romboutsia, reassigning Eubacterium tenue to Paraclostridium, and elevating Alkalithermobacter to genus rank. The findings resolve a longstanding microbial systematics bottleneck for spore-forming bacteria, provide critical taxonomic context for C. difficile's precise monitoring and prevention, and expand taxonomic markers beyond nucleic acid-based methods. This advances classification precision, critical for microbial ecology, pathogenesis, and industrial microbiology research.}, }
@article {pmid42277415, year = {2026}, author = {Prada, J and Pereira-Dias, L and Santos, JA and Santos, C}, title = {Influence of Environment and Rootstock On the Rhizosphere Bacterial Communities in Four Vineyards of the Douro Demarcated Region.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02798-z}, pmid = {42277415}, issn = {1432-184X}, abstract = {The Douro Demarcated Region (DDR) is a worldwide acknowledged winemaking region. Climate change is threatening the sector, as climatic shifts are expected. This work analyzed environmental and genetic traits modulating the rhizobiome of four vineyards in the DDR, focusing on understanding the hierarchy of ecological conductors for these communities. These vineyards' terroir was environmentally, genetically, and culturally characterized. Rhizosphere bacterial community composition was analyzed using 16S metabarcoding from soil samples collected between July 2022 and January 2024. Results support the hypothesis of an ecological profiling hierarchy. The soil physicochemical properties likely acted as a primary environmental modulator, determining the composition of the bacterial microbiome and contributing to the diversity and richness of the bacterial communities. The major drivers among the soil's physiochemistry were organic/inorganic profile, mainly influenced by organic matter content and pH. Rootstock genotype appears to exert a secondary selection on the microbiome, focusing on the microorganisms' functional traits. The 1103-P rootstock positively influenced the abundance of copiotrophic bacteria, compared to the R110, demonstrating that the first recruits a more versatile, exploratory, and expansionist microbiome, whilst the second focuses on attracting a highly specialized community, more focused on maximizing energy gathering and optimizing resource use. This work demonstrates that the microbial terroir is a result of multiple factors, promoting abiotic modulation and host-mediated selection, which establishes a very specific community for each scenario. The assessment of these holistic dynamics is fundamental to establishing a baseline for future precision viticulture strategies, namely bio-inoculants, to support and promote a better grapevine adaptation to climate change.}, }
@article {pmid42000857, year = {2026}, author = {Krishnakumar, A and Juárez-Castelán, CJ and Vélez-Ixta, JM and Benitez-Guerrero, T and Murugesan, S and Piña-Escobedo, A and Rico-Arzate, E and Castro-Arellano, JJ and Romero-Maldonado, S and Cruz-Narváez, Y and Pizano-Zárate, ML and García-Mena, J}, title = {Maternal obesity modifies the vertical transmission of gut microbiota and metabolites: Insights from mother-infant dyads in a mexican cohort.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42000857}, issn = {2045-2322}, support = {CONACyT 302670 INFR-2019//Secretar&#xed;a de Ciencia, Humanidades, Tecnolog&#xed;a e Innovaci&#xf3;n (SECIHTI)/ ; CONACyT FORDECYT-PRONACES/6669/2020_Programa Presupuestario F003-Ciencia de Frontera 2019//Secretar&#xed;a de Ciencia, Humanidades, Tecnolog&#xed;a e Innovaci&#xf3;n (SECIHTI)/ ; CONACyT 163235 INFR-2011-01//Secretar&#xed;a de Ciencia, Humanidades, Tecnolog&#xed;a e Innovaci&#xf3;n (SECIHTI)/ ; }, abstract = {UNLABELLED: Maternal obesity is increasingly recognized as an important modulator of early-life microbial and metabolic environments. This study investigates the association between maternal body mass index (BMI) and the microbiota and metabolite profiles of colostrum and neonatal feces in a Mexican mother–infant cohort. Milk and fecal samples were collected from dyads of obese and normal-weight mothers. Bacterial microbiota composition was characterized by sequencing the 16 S rRNA gene (V3 region) using Ion Torrent technology, and metabolomic profiling was performed using Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry. The results provide evidence consistent with vertical microbial and metabolic transmission, with Firmicutes and Patescibacteria predominating in Colostrum. Neonates born to obese mothers exhibited reduced relative abundances of Lactobacillus in neonatal fecal samples, alongside increased levels of Lactobacillus and Staphylococcus in both colostrum and mother´s feces. Overall microbial diversity across maternal stool, colostrum, and neonatal stool samples was not significantly associated with maternal BMI; however, distinct metabolite signatures linked to maternal obesity, like oligopeptides, glycoside-related compounds, Phosphatidic Acid (PA) Derivatives, bioactive molecules such as enkephalinamide derivatives, were observed. These findings highlight the role of breastfeeding as a key interface in shaping the neonatal gut microbiota and metabolome and suggest potential pathways linking maternal metabolic status with early-life microbial and metabolic programming. This study advances understanding of maternal–infant microbial ecology and supports further investigation into the long-term health implications of maternal obesity.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-49183-x.}, }
@article {pmid42270219, year = {2026}, author = {Zhang, Z and Zhang, K and Hou, Q and Yang, C and Guo, Z and Li, Y and Wang, C and Wang, Y}, title = {Microbial ecology and flavor formation mechanisms of high-temperature Daqu in the Huang-Huai River basin and adjacent regions: A comparative study from eastern Henan, Jiaodong peninsula, and southern Anhui.}, journal = {Food research international (Ottawa, Ont.)}, volume = {239}, number = {}, pages = {119489}, doi = {10.1016/j.foodres.2026.119489}, pmid = {42270219}, issn = {1873-7145}, mesh = {China ; Fermentation ; *Hot Temperature ; *Microbiota ; *Taste ; *Food Microbiology ; Bacteria/metabolism/classification/genetics ; Rivers ; Flavoring Agents ; *Fermented Foods/microbiology ; }, abstract = {High-temperature Daqu (HTD) serves as a critical fermentation starter for sauce-aroma type Baijiu. Although strong-aroma Baijiu dominates production in the Huang-Huai River Basin and surrounding regions, knowledge regarding the microbial ecology and flavor-forming potential of HTD in this area remains limited. In this study, we collected HTD samples from Eastern Henan, Jiaodong Peninsula (Qingdao), and Southern Anhui, and performed physicochemical analyses, enzyme activity assays, electronic sensory evaluation, and metagenomic sequencing. Significant differences in microbial community structure were observed among the three regions. Nevertheless, Kroppenstedtia eburnea, Aspergillus chevalieri, and Aspergillus oryzae were consistently dominant across all sites. Compared with the other two regions, HTD from Qingdao showed markedly higher abundances of Bacillus velezensis, Bacillus licheniformis, and Bacillus amyloliquefaciens. However, the overall relative abundance of Bacillus spp. in the Huang-Huai region was lower than that typically reported in HTD from Hubei and Guizhou provinces. Physicochemical factors, particularly density and acidity, were the primary drivers of microbial community heterogeneity and flavor profile variation across regions. Metagenomic analysis revealed a relatively complete dimethylpyrazine synthesis pathway in Qingdao Daqu, whereas the other two regions appeared to depend more on multi-species cooperation. Limosilactobacillus fermentum, enriched in Qingdao samples, harbored key acetoin synthesis genes and showed strong potential for tetramethylpyrazine (TTMP) precursor accumulation. Additionally, gene-potential profiling identified Pichia kudriavzevii as the main candidate for higher alcohol production. Subsequent validation confirmed that isolated P. kudriavzevii strains produced 2-phenylethanol, a key bitter volatile compound in sauce-flavor Baijiu. These results elucidate the regional microbial mechanisms underlying flavor formation in HTD for sauce-aroma Baijiu production in the Huang-Huai River Basin and adjacent areas, providing a theoretical basis for targeted starter culture improvement.}, }
@article {pmid42274251, year = {2026}, author = {Zhu, C and Wei, T and Lin, Y and Yan, G and Qian, P-Y}, title = {The patterns of microbial community distribution and co-occurrence in water columns and sediments of Haima cold seep.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0025626}, doi = {10.1128/spectrum.00256-26}, pmid = {42274251}, issn = {2165-0497}, abstract = {Deep-sea cold seeps are essential components of global biodiversity and biogeochemical cycles, whereas the community distribution and co-occurrence patterns of cold seep microorganisms remain poorly understood. Here, we investigated the microeukaryotic and prokaryotic communities across different water layers and benthic habitats in the Haima cold seep of the South China Sea and revealed distinct vertical and horizontal patterns in microbial distribution and co-occurrence between the water columns and sediments. Prokaryotic intra-domain interactions predominated over inter-species correlations in networks, and bacteria-microeukaryote interactions were more abundant in the network of water columns than in sediments, indicating that environmental preferences of microorganisms differed between these environments. The environmental factors and deterministic processes appeared to exert a more pronounced influence on the distribution patterns of microeukaryotes than on prokaryotes in the water columns, whereas the opposite was observed in the sediments. Additionally, microbial co-occurrence patterns were segregated and primarily shaped by deterministic processes. The species interactions were more complex in the euphotic zone and clam (one of the most dominant megabenthos) habitats than those in other water layers and benthic habitats, and the microbial co-occurrence patterns in the euphotic zone and mussel beds were likely influenced by strong selection factors such as light, organic carbon, mussel activities, and high methane concentrations. Our study provides new perspectives on how microorganisms adapt to the different environmental conditions in deep-sea cold seeps, deepening our understanding of microbial ecology in deep-sea extreme environments.IMPORTANCEOur study revealed the vertical and horizontal patterns of microbial community distribution and co-occurrence, highlighting how different ecological processes shape microbial communities in the water column and sediments, as well as between microeukaryotes and prokaryotes. This indicated that the balance of deterministic and stochastic processes was influenced by the environment and taxonomic classification in deep-sea cold seeps. The species interactions in the euphotic zone and clam habitat were more complex than those in other water layers and benthic habitats, and the euphotic zone and mussel beds served as hotspots of intense environmental selection. Our findings revealed that microorganisms responded to these challenging environments in deep-sea cold seeps through various strategies, including different environmental preferences. By elucidating the mechanisms driving the microbial community diversity and species coexistence, this work provides new perspectives on how microorganisms adapt to the environments in deep-sea cold seeps.}, }
@article {pmid42274959, year = {2026}, author = {Gianaris, A and Ramalho, MO and de Oliveira, AA and de Castro Morini, MS and Martins, C and Bueno, OC}, title = {Bacterial Diversity in Leaf-Cutter Ant Species: Host-Microbe Interactions and Environmental Effects.}, journal = {Neotropical entomology}, volume = {55}, number = {1}, pages = {}, pmid = {42274959}, issn = {1678-8052}, support = {NSF DEB 1900357//Natural Science Foundation/ ; }, mesh = {Animals ; *Ants/microbiology ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; *Bacteria/classification/genetics ; *Host Microbial Interactions ; *Biodiversity ; Fungi ; }, abstract = {Historically, studies have sought to identify host-specific factors in host-microbe interactions as a means of understanding evolutionary success. The genus Atta, comprising leaf-cutter ants, is native to the southern Neotropics and obligately mutualistic with cultivated fungi. It hosts a remarkably diverse range of bacterial communities, yet this variability remains poorly understood. Using high-throughput amplicon sequencing of the 16S rRNA genes of the whole worker, we showed significant difference between the bacterial communities among 4 dominant Atta species: Atta sexdens (Linnaeus), Atta laevigata (Smith), Atta capiguara (Gonçalves), and Atta bisphaerica (Forel). We also discovered significant differences in bacterial communities from laboratory conditions, pesticide treatment, and the fungal garden symbiont of Atta sexdens. Surprisingly, bacterial communities of Atta sexdens kept in the laboratory were not significantly different from pesticide-treated Atta sexdens, laying the groundwork for potential refinement of standard research methods.}, }
@article {pmid42277207, year = {2026}, author = {Su, H and Liu, DH and Shang, HY and Huang, D and Liang, C and Wang, ZH and Zhai, JN and Zhang, XT and Jiang, HL and Shum, FY and Chen, HY and Qin, N and Xu, ZH and Liu, XD and Tan, LK and Zhang, L and Ho, KM and Chan, MTV and Wu, WKK and Chen, HR}, title = {METTL3 loss exacerbates colitis via m[6]A-dependent Slc39a8 regulation and epithelial lineage depletion.}, journal = {Acta pharmacologica Sinica}, volume = {}, number = {}, pages = {}, pmid = {42277207}, issn = {1745-7254}, abstract = {The intestinal epithelium maintains host-microbiota homeostasis, while inflammatory conditions, such as inflammatory bowel disease (IBD), induce pathological shifts in intestinal epithelial cell (IEC) subtypes. We unveil METTL3, an RNA m[6]A methyltransferase, as a pivotal regulator of this balance. METTL3 is enriched in intestinal stem cells and transit-amplifying cells (TACs), and upregulated in patients with IBD and a mouse model of IBD. DSS-challenged, intestine-specific Mettl3 knockout mice exhibited exacerbated colitis as exemplified by more weight loss, elevated disease activity index (DAI), and higher extent of colon shortening. Single-cell transcriptomics of colonic tissues from DSS-challenged intestine-specific Mettl3 knockout mice revealed that Mettl3 ablation depleted epithelial lineages (TACs, goblet cells, enterocytes) but amplified immune infiltration (macrophages, neutrophils, T cells) within the intestinal mucosa. Crucially, METTL3 loss impaired TAC multipotency and increased epithelial-neutrophil crosstalk mediated by the TNF pathway. Mechanistically, METTL3-mediated m[6]A modification increases Slc39a8 expression, whose knockdown in colon organoids phenocopied METTL3 deficiency in impairing self-renewal. Our work establishes METTL3 as a dual guardian of intestinal homeostasis-preserving epithelial regeneration and restraining inflammation by calibrating epithelial-immune dialogue. The former is mediated at least in part by regulating Slc39a8 expression through m[6]A modification.}, }
@article {pmid42266678, year = {2026}, author = {Rao, X and Zou, L and Cai, X and Yao, Y and Zhong, L}, title = {Microbiome-orchestrated cross-organ immunity in autoimmunity: from metabolites to therapeutic targets.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1761834}, pmid = {42266678}, issn = {1664-3224}, abstract = {Autoimmune diseases are systemic disorders in which barrier-site immune activation, especially in the gut, can reshape inflammatory programs in distant organs. This review advances a metabolite-centered, cross-organ framework for understanding how gut microbial ecology influences autoimmunity beyond individual gut-organ axes. We synthesize evidence that short-chain fatty acids, bile acid derivatives, tryptophan catabolites, polyamines and related microbial products act as mobile biochemical checkpoints linking intestinal barrier integrity, pattern-recognition signaling, immune-cell metabolism and tissue-specific inflammation in joints, kidneys, skin, lungs and the central nervous system. Across these axes, shared mechanisms include barrier failure, altered microbial metabolite pools, dysregulated MAMP sensing, trafficking or systemic conditioning of lymphoid and myeloid cells, and local stromal imprinting in target organs. We also discuss sex-dependent microbiome-immune interactions, including the microgenderome concept, as a framework for explaining why microbiome composition, hormone metabolism and immune responses may shape autoimmune risk and treatment response differently in females and males. Finally, we evaluate multi-omics, single-cell and spatial profiling, organ-on-chip platforms and causal computational tools, and we outline translational strategies ranging from diet, probiotics, fecal microbiota transplantation and engineered consortia to pharmacologic targeting of metabolite receptors. By treating microbial metabolites as actionable cross-organ immune checkpoints, this review highlights opportunities and limitations for biomarker-guided, metabolite-focused precision therapy in autoimmunity.}, }
@article {pmid42266934, year = {2026}, author = {Bautista, J and Lara-Hernández, ME and Hidalgo-De La Cruz, M and Andino-Araque, V and León-Rivera, M and López-Cortés, A}, title = {Host-microbiome interactions in breast cancer progression and treatment response.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1827694}, pmid = {42266934}, issn = {2296-858X}, abstract = {Breast cancer (BC) is a biologically heterogeneous disease in which tumor progression and therapeutic response vary substantially across patients and molecular subtypes. Alongside genetic, endocrine, and immunological determinants, microbial ecosystems have been proposed as components of the host environment that interact with tumor biology. Microorganisms detected in breast tissue, the gastrointestinal tract, and the oral cavity coexist with epithelial and immune compartments and participate in metabolic and inflammatory processes relevant to mammary physiology. Differences in microbial composition have been reported between non-malignant and malignant breast tissue, while intestinal microbial metabolism generates bioactive compounds capable of interacting with immune regulation and systemic endocrine signaling. Microbial enzymatic activity involved in estrogen deconjugation further connects intestinal ecology with hormone-responsive disease. Microbiome-related variation has also been examined in relation to systemic therapies, where differences in microbial composition have been observed alongside variability in therapeutic outcomes. This review examines current knowledge on host-microbiome interactions across breast, gut, and oral environments and discusses how microbial ecology intersects with inflammatory signaling, metabolic regulation, and endocrine pathways relevant to breast cancer progression and treatment response. Methodological challenges and future research directions for microbiome-informed oncology are also considered.}, }
@article {pmid42267103, year = {2026}, author = {Min, L and Ablitip, A and Wang, Q and Li, T and Di, Q and Ma, X and Fang, W}, title = {Combined heat and exercise stress disrupt gut microbiota and promote microbial translocation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1779295}, pmid = {42267103}, issn = {1664-302X}, abstract = {PURPOSE: The incidence of exertional heat stroke (EHS) has increased markedly in recent decades. Although intestinal barrier dysfunction and gut microbiota alterations are increasingly implicated in EHS pathophysiology, the respective contributions of heat exposure and physical exercise to these processes remain incompletely defined.<br><br>METHODS: Male C57BL/6 mice were assigned to Control (C), Exercise (E), Heat shock (H), or Exercise + Heat shock (HE) groups. Exercise and/or heat exposure were applied to induce exertional heat stress. Intestinal injury and permeability were assessed by histopathology and circulating D-lactate levels. Gut and blood microbial profiles were characterized using 16S rRNA gene sequencing, and associations between microbial signatures and intestinal injury markers were analyzed.<br><br>RESULTS: Both heat exposure and exercise induced intestinal injury and increased circulating D-lactate levels, with the most severe effects observed in the combined HE group. Heat exposure was associated with pronounced alterations in gut microbial diversity and community structure, whereas exercise was associated with increased microbial diversity and gut-associated microbial signatures detected in blood samples. Differential abundance analyses revealed distinct taxonomic profiles associated with heat, exercise, and their combination. Correlation analyses demonstrated significant associations between intestinal injury markers and circulating microbial profiles.<br><br>CONCLUSION: These findings indicate that heat exposure and exercise exert distinct yet interacting associations with intestinal barrier integrity and microbial community distribution. Heat stress primarily disrupts gut microbial ecology and barrier function, whereas exercise is more closely associated with increased systemic detection of gut-derived microbial signatures. Together, these results highlight the gut microbiota-barrier axis as a key interface linking environmental and physiological stressors to systemic responses during exertional heat stress.}, }
@article {pmid42267567, year = {2026}, author = {Liu, BZ and Zhao, XY and Sun, ZW and Wang, J and Zeng, JT and Huang, Y and Cai, KQ and Zhao, JG and Yang, SH and Yuan, JL}, title = {Gut microbiota remodeling in HBB-mutant cynomolgus monkeys reveals blood-gut axis disruption associated with β-thalassemia-related gastrointestinal dysfunction.}, journal = {Zoological research}, volume = {47}, number = {3}, pages = {827-842}, doi = {10.24272/j.issn.2095-8137.2025.141}, pmid = {42267567}, issn = {2095-8137}, abstract = {Gastrointestinal symptoms frequently accompany anemia caused by HBB mutations, such as β-thalassemia; however, the mechanisms linking disordered hemoglobin biology to intestinal dysfunction remain incompletely understood. In this study, HBB-mutant cynomolgus monkeys were generated and analyzed together with wild-type (WT) controls through integrated metabolomic and metagenomic profiling. HBB mutation was associated with a marked shift in gut microbial ecology, characterized by reduced microbial diversity and altered abundances of Lactobacillus and Bacteroides. Metabolic profiling revealed broad perturbation of amino acid, lipid, energy, and immune-related metabolic pathways, with 3-oxooctadecanoic acid (HMDB0254633) emerging as a discriminative metabolite between WT and HBB-mutant animals. Multiomics integration indicated that HBB mutation reshaped microbiota-metabolite interactions and may thereby affect host metabolism and immune responses. To examine the functional relevance of this metabolite, 3-oxooctadecanoic acid was administered to C57BL/6 mice with castor oil-induced diarrhea. High-dose treatment alleviated diarrhea severity, improved stool parameters, limited body weight loss, and partially restored gut microbial composition. These findings provide non-human primate evidence that β-thalassemia-associated HBB mutation disrupts intestinal microbiota homeostasis and metabolic output, identifying 3-oxooctadecanoic acid as a candidate biomarker and potential regulator of gastrointestinal dysfunction. This study provides a valuable framework for understanding how host genetic variation contributes to gut microbiome remodeling and gastrointestinal manifestations in β-thalassemia.}, }
@article {pmid42267811, year = {2026}, author = {Gołębiowska, J and Woodhouse, JN and Tobias-Hünefeldt, SP and Grossart, H-P}, title = {Salinity-driven niche partitioning of aquatic viruses in one of Europe's largest estuaries.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0080726}, doi = {10.1128/aem.00807-26}, pmid = {42267811}, issn = {1098-5336}, abstract = {UNLABELLED: Viruses are a vital part of the aquatic food web and hold a profound role in carbon and energy cycling at different trophic levels. Despite the rising interest in aquatic viruses, very few studies were conducted in estuaries, where freshwater and marine communities meet along the salinity gradient. We present a paired analysis of metagenomic and metatranscriptomic data focusing on the viral fraction derived from seasonal sampling between May 2021 and November 2022 in one of Europe's largest estuaries, the temperate mesotidal Elbe River downstream of Hamburg. Our results reveal a sharp delineation of viral communities along specific salinity niches and provide evidence for their adaptation. This implicates viruses as a structural component of microbial and phytoplankton ecology across the estuary. We provide a detailed overview of the spatiotemporal distribution of viruses, including taxonomy and hosts, which emphasizes the role of giant viruses (Megaviricetes) in waters of lower salinity and RNA viruses in marine environments. We identify, besides salinity, total dissolved phosphate and temperature as the main drivers of estuarine viral communities. We find a broad spectrum of metabolic pathways, potentially altered by viruses via auxiliary metabolic genes. Potential metabolisms impacted included the underlying carbon processes like photosynthesis or methane metabolism, but may also extend to some xenobiotics and antibiotics metabolisms in this anthropogenically altered estuary. This is the first detailed molecular study of viruses in the Elbe Estuary, shedding light on viral communities and their ecological roles in controlling microbial populations at the base of the estuarine food web.<br><br>IMPORTANCE: Estuaries are the interfaces between marine and limnic waters, with their own specific hydrological and biochemical processes due to, e.g., salinity gradients, tides, and terrestrial inflows. In particular, they are sites of intensive carbon cycling. Their often high economic importance causes substantial anthropogenic pressure on the ecosystem. All of these result in extremely complex factors interacting and influencing microbial populations. Our study provides a first comprehensive overview of the viral communities in Europe's largest estuary. We made an attempt to disentangle the numerous environmental parameters, and we highlight salinity as the most important factor, providing evidence of its multidimensional influence on the estuarine virome. Our findings deepen our understanding of viral communities and their interactions with microbes and bring us a step closer to their role in aquatic food webs, particularly in carbon turnover in estuaries.}, }
@article {pmid42269463, year = {2026}, author = {Liu, B and Leekitratanapisan, W and Pardon, M and Theus, A and Daenen, R and Jia, M and Kundu, K and Springael, D and Cabooter, D and De Schamphelaere, KAC and Boon, N}, title = {Hydrogen supplementation enhances microbial removal of selected organic micropollutants, reduces associated ecotoxicity, and improves nutrient removal in domestic wastewater effluent.}, journal = {Water research}, volume = {303}, number = {}, pages = {126211}, doi = {10.1016/j.watres.2026.126211}, pmid = {42269463}, issn = {1879-2448}, abstract = {Organic micropollutants (OMPs) compose a group of emerging contaminants that occur in environmental waters at trace concentrations (μg/L to ng/L) with suspected adverse effects on ecosystems and human health. Conventional wastewater treatment plants (WWTPs) are not designed to eliminate the more recalcitrant OMPs. As such, WWTP-effluents are a major source of OMPs in the aquatic environment, and sustainable advanced treatment options are required. One option concerns the biodegradation of OMPs, but several studies show that it might be constrained by the residual low energy content in effluent waters. Since molecular hydrogen (H2) has been identified as a universally available energy source utilised by various bacteria in oligotrophic environments, supporting mixotrophic growth, we examined the hypothesis that H2 can enhance OMP-removal and concomitant ecotoxicity from domestic wastewater effluent. To this end, a lab-scale biological trickling filter supplemented with H2 (1.5% in the aeration with ambient air) was operated in continuous mode for treating a field-collected domestic WWTP-effluent. In total, 51 OMPs were detected in the WWTP-effluent, of which azithromycin and clarithromycin contributed to 76.5% of the total ecotoxic effects, as demonstrated in a cyanobacterial growth inhibition assay. The H2-supplemented trickling filter enhanced the removal of azithromycin and clarithromycin by (69.5 ± 1.5)% and (46.0% ±2.9)%, respectively, and increased the reduction of total OMP-associated ecotoxic effects by 56.5%, compared to the non-H2-supplemented control. Moreover, H2 supplementation improved PO4[3-] and NO3[-] removal by a factor of 2.3 and 1.5, respectively. These findings demonstrate that H2 supplementation may support microbial processes involved in OMP-removal from domestic wastewater in a microbial treatment system, thereby reducing concomitant ecotoxicity.}, }
@article {pmid42270181, year = {2026}, author = {Wejnerowski, &#x141; and Pełechata, A and Rybak, M and Piasecka, A and Antonowicz, JP and Belniak, G and Kamiński, O and Dziuba, MK and Koreivienė, J and Meriluoto, J and Dawidowicz, P}, title = {From lakes to the sea: testing the survival of freshwater bloom-forming cyanobacteria and cyanotoxin-related risk in Baltic coastal waters under a changing climate.}, journal = {Harmful algae}, volume = {157}, number = {}, pages = {103144}, doi = {10.1016/j.hal.2026.103144}, pmid = {42270181}, issn = {1878-1470}, abstract = {Brackish coastal waters are increasingly susceptible to harmful cyanobacterial blooms and toxin contamination, and climate change may enhance the persistence of bloom-forming species across salinity gradients. The Baltic Sea, one of the world's largest brackish basins is characterised by distinct salinity gradients, high productivity, and pronounced sensitivity to cyanobacterial blooms. Cyanobacteria are highly adaptable and tolerat of diverse environmental conditions. However, the response of freshwater strains to brackish water from various Baltic coastal sites, and the extent to which such conditions limit their persistence, remains uncertain. This study addressed three main objectives: (1) evaluating the ability of common freshwater bloom-forming filamentous cyanobacteria to grow in water from different Baltic coastal sites; (2) examining the combined effects of warming and CO2 enrichment on their performance under simulated brackish conditions; and (3) testing whether selected freshwater strain can persist in pairwise co-culture with the resident Baltic cyanobacterium Nodularia spumigena. Results showed that several freshwater strains grew in water from both the fresher northern and more saline southern Baltic coastal sites. However, their responses varied by strain and were influenced by site-specific water properties, climate conditions, and biotic interactions. Notably, a cylindrospermopsin-producing strain of Aphanizomenon gracile from an eutrophic inland lake showed the highest performance and also grew in co-culture with Nodularia. Simulations indicate that certain freshwater cyanobacteria can tolerate brackish water from different Baltic coastal sites under controlled short-term conditions. Moreover, findings suggest that freshwater strains capable of persisting under brackish conditions may contribute to cyanotoxin presence risk. This risk may affect water from both the fresher northern and saltier southern Baltic coasts, highlighting an emerging ecological and public health concern. The simplified, nature-safe experimental approach provides a foundation for more complex, field-based studies assessing the ecological relevance of freshwater cyanobacteria in transitional brackish coastal systems.}, }
@article {pmid42095674, year = {2026}, author = {Robes, JMD and Liebergesell, TCE and Medvedeva, VP and Puri, AW}, title = {Inverse stable isotope labeling (InverSIL) links predicted catecholate siderophore gene clusters to their products in diverse bacteria.}, journal = {mBio}, volume = {17}, number = {6}, pages = {e0339125}, doi = {10.1128/mbio.03391-25}, pmid = {42095674}, issn = {2150-7511}, support = {R35 GM147018/GM/NIGMS NIH HHS/United States ; R35 GM147018/GM/NIGMS NIH HHS/United States ; 00006628//Simons Foundation Early Career Investigator in Aquatic Microbial Ecology and Evolution/ ; T32 AI055434/AI/NIAID NIH HHS/United States ; }, abstract = {UNLABELLED: Bacteria produce high-affinity, iron-chelating secondary metabolites called siderophores to access insoluble Fe(III) in their environments. Genome mining has revealed many predicted siderophore biosynthetic gene clusters (BGCs) in bacterial genomes; however, the structures of their siderophore products remain mostly undetermined. This limits our molecular-level understanding of how bacteria acquire iron. Here, we apply inverse stable isotope labeling (InverSIL) to rapidly connect predicted siderophore BGCs to their products. With InverSIL, bacteria are grown on [13]C-substituted carbon sources and then fed predicted biosynthetic precursors at their natural isotopic abundance to identify BGC products by mass spectrometry, removing issues with the availability of isotopically substituted precursors. We use InverSIL to determine the structures of the siderophore products of predicted BGCs from the methylotrophic genera Methylophilus and Methylorubrum, as well as the siderophores produced by the opportunistic pathogen Chromobacterium violaceum, which were previously shown to be essential for virulence yet remained structurally uncharacterized. We next use this approach to reveal the unexpected production of enterobactin by the genera Kushneria and Paracoccus, which was difficult to predict from genome sequences due to the distributed nature of the biosynthetic genes within the genomes. Finally, we use InverSIL to discover new siderophores, the cellulochelins, from the cellulose-degrading plant symbiont Cellulomonas sp. strain Leaf334. These findings demonstrate the utility of InverSIL for functional BGC characterization and expand our molecular understanding of bacterial iron acquisition strategies.<br><br>IMPORTANCE: Iron acquisition is important for microbial survival, and bacteria produce secondary metabolites called siderophores to scavenge iron from the environment. While bacterial genome sequences show many predicted genes for making siderophores, most remain unlinked to their metabolic products. Understanding which siderophores bacteria produce is critical for elucidating microbial iron acquisition strategies, ecological interactions, and potential roles in host-microbe interactions. Here, we demonstrate how inverse stable isotope labeling (InverSIL) can rapidly link predicted siderophore gene clusters to their corresponding metabolites. By applying InverSIL to diverse bacterial strains, we validate known siderophore products and uncover unexpected products, highlighting the limitations of current in silico predictions. This study highlights the value of combining experimental approaches with genome mining to advance our understanding of how bacteria acquire iron from their environment.}, }
@article {pmid42260218, year = {2026}, author = {Chauhan, PK and Tomar, S and Kumari, S and Srivastava, AK}, title = {Climate Warming and Plant Disease: Mechanistic Insights Into Pathogenic Stress Resilience.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.70648}, pmid = {42260218}, issn = {1365-3040}, abstract = {Climate warming is rapidly reshaping plant-pathogen interactions, leading to increased disease incidence and substantial crop losses worldwide. This review examines how rising temperature, humidity and shifting precipitation patterns intensify plant disease, while highlighting advances in sustainable microbe-based and molecular strategies to enhance plant immunity and crop resilience. A systematic literature-based synthesis highlights the role of root-adhering microbes (RAM), plant-microbe-environment crosstalk under combined stresses and engineered microbial consortia. It also explores advanced molecular tools, including CRISPR/Cas9 and RNA Interference (RNAi), for precise targeting of pathogen virulence and regulation of host defence pathways. Evidence shows that RAM and tailored microbial consortia enhance induced systemic resistance (ISR) and systemic acquired resistance (SAR), improving tolerance to multiple stresses. Meanwhile, molecular approaches are accelerating the development of climate-resilient, disease-resistant crop genotypes. Integrating beneficial microbes with precision molecular innovations offers a transformative path toward climate-smart agriculture. Strengthening links between plant immunity, microbial ecology and genetic technologies will be essential for building resilient food systems in a warming world.}, }
@article {pmid42260689, year = {2026}, author = {Wang, K and Peng, Q and Geng, L and Zhang, F and Liu, R and Liu, X and Zhang, J and Shu, C}, title = {Protaetia brevitarsis larvae frass affects substrate microecological systems via two suggestive pathways to enhance cherry tomato growth.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00915-6}, pmid = {42260689}, issn = {2524-6372}, support = {2023YFD1701502//National Key Research and Development Program of China/ ; 32570599//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: The identification and development of high-quality humus sources to enhance the productivity and performance of substrate-based vegetable cultivation systems remains a significant challenge in sustainable agriculture. Protaetia brevitarsis larvae (PBL) exhibit exceptional efficiency in decomposing decaying crop straw and produce nutrient-rich frass with high humic acid content and a complex microbial community. However, its impacts on substrate microecological systems and the underlying functional mechanisms remain unclear, limiting its rational application in substrate cultivation. This study aimed to investigate the effects of PBL frass on substrate microecology and elucidate the associated mechanisms using cherry tomato (Lycopersicon esculentum Mill. var. cerasiforme Alef) pot experiments.<br><br>RESULTS: Incorporation of 2% or 4% (w/w) PBL frass into cherry tomato cultivation substrates significantly promoted plant growth, characterized by reduced plant height (indicating more robust, dwarf-type growth) and increased aboveground (stem) and belowground (root) biomass. Furthermore, PBL frass application enhanced substrate microbial diversity through two distinct, complementary pathways: (&#x2170;) Frass-derived microbes, which possess specific colonization capabilities, directly augmented microbial communities in both the rhizoplane and bulk substrate; and (&#x2171;) Organic compounds in PBL frass may have activated a broad range of microbes, enriching the rhizosphere microbiome. This enhanced microbial diversity was associated with an increased abundance of plant-beneficial taxa, which likely contributed to growth promotion and substrate health maintenance.<br><br>CONCLUSIONS: This study uncovers the multifaceted contributions of PBL frass to substrate microbial ecology and reveals its two suggestive regulatory pathways. These results provide a theoretical basis for the sustainable utilization of PBL frass and advance the development of eco-friendly amendments for modern vegetable production.}, }
@article {pmid42261086, year = {2026}, author = {Wang, B and Yang, F and Zhou, L and Li, ZZ and Zhang, S and Zhang, N and Liang, J and Mu, BZ}, title = {Pilot-Scale Biodesulfurization of Natural Gas: Microbial Ecology and Community Dynamics of an In Situ Enriched System.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxag136}, pmid = {42261086}, issn = {1365-2672}, abstract = {AIMS: This study investigated the microbial ecology of a biodesulfurization system inoculated with indigenous (rather than commercial) sulfur-oxidizing bacteria (SOB), aiming to assess their rapid enrichment feasibility and identify optimization strategies.<br><br>METHODS AND RESULTS: Pilot-scale Shell-Paques reactors were established to remove hydrogen sulfide from natural gas, using an inoculum of indigenous SOB. Microbial community dynamics were tracked via high-throughput sequencing, while ecological interactions were analyzed by combining co-occurrence network analysis and niche overlap indices. Indigenous SOB were successfully enriched to an abundance of ~30% within 13 days. Thioalkalimicrobium emerged as the dominant SOB genus, differing from strains typically employed in commercial technologies. A key finding was the production of bipyramidal elemental sulfur with a rhombic structure as the primary product. Both network and niche overlap analyses revealed complex ecological interactions, indicating potential competition and mutualism between Thioalkalimicrobium and other dominant genera.<br><br>CONCLUSIONS: Indigenous SOB can be rapidly enriched within two weeks to achieve effective desulfurization and sulfur recovery. The ecological insights lay the groundwork for optimizing enrichment through targeted microbiota management.}, }
@article {pmid42261608, year = {2026}, author = {Shelat, VG}, title = {Microbial ecology and hepatocellular carcinoma: should a subset be viewed as a microbiome-conditioned malignancy?.}, journal = {Expert review of gastroenterology &amp; hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1080/17474124.2026.2687711}, pmid = {42261608}, issn = {1747-4132}, }
@article {pmid42262077, year = {2026}, author = {Ran, S and Fu, S and Dai, T and Wei, H and Peng, J and Zhou, Y}, title = {Multi-omics profiling of gut-serum axis dynamics in gestational sows with different reproductive performance.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0113225}, doi = {10.1128/spectrum.01132-25}, pmid = {42262077}, issn = {2165-0497}, abstract = {UNLABELLED: Sustainable swine production hinges on optimizing sow reproductive efficiency, yet mechanisms driving healthy litter size and weak piglet rates remain unclear. This study categorized sows into high (group H) and low (group L) healthy litter size groups based on median performance. Multi-omics analyses (16S rRNA sequencing, metagenomics, and serum metabolomics) revealed distinct fecal microbiota and metabolic profiles between groups. The results showed significant differences in microbiota composition between groups L and H. Group H exhibited a marked increase in Bacteroidetes abundance (particularly Prevotella sp. CAG1092), concurrent with reduced Firmicutes populations. Metabolomic analysis identified 197 differentially abundant metabolites, with 85 metabolites significantly enriched in group H. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that the differentially abundant metabolites were mainly involved in amino acid synthesis and metabolism, and multiple amino acid metabolic pathways were associated with polyamine synthesis. The correlation results showed a significant correlation (P < 0.05) between these metabolites and litter size as well as litter weight. For instance, Prevotellaceae NK3B31 abundance positively correlated with L-alanine, urea, and securinine, while Prevotella sp. CAG1092 exhibited direct associations with reproductive performance. These findings suggest that gut microbiota dysbiosis may disrupt amino acid homeostasis and polyamine regulation, potentially serving as mechanistic links to reproductive efficiency. Reproductive performance dynamically shapes gut microbiota and systemic metabolism in gestating sows, with litter size influencing fecal metabolite diversity and microbial structure. This integrative analysis establishes a framework for improving both sow productivity and economic viability in pig farming.<br><br>IMPORTANCE: Optimizing sow reproductive efficiency is vital for sustainable swine production. This study identifies gut microbiota dysbiosis and metabolic imbalances as key drivers of litter size variability. Sows with lower productivity displayed marked reductions in Bacteroidetes (notably Prevotella spp.) and disrupted amino acid/polyamine metabolism, directly linking microbial shifts to poorer litter outcomes. Integrated multi-omics approaches revealed strong correlations between specific taxa (Prevotella sp. CAG1092), metabolites (L-alanine and urea), and reproductive metrics, underscoring the gut-reproductive axis. These findings elucidate mechanistic connections between microbial ecosystems and host physiology, providing a foundation for targeted strategies like microbiota modulation or dietary interventions to enhance metabolic homeostasis and farrowing success. By bridging microbial ecology with livestock productivity, this work advances practical solutions to improve both animal health and agricultural profitability within precision farming frameworks.}, }
@article {pmid42264080, year = {2026}, author = {Abdullah, M and Jayadevan, K and Therayil, A and Kumaraguruparan, N and Kavyasree, PKV and Dilna, P and Faiza, A}, title = {Pharmaco-microdynamics (PMD): Redefining Dose, Exposure, and Control for Living Drug Carriers.}, journal = {Annales pharmaceutiques francaises}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pharma.2026.06.002}, pmid = {42264080}, issn = {2772-803X}, abstract = {Living drug delivery systems including probiotics, engineered microbial therapeutics, and live biotherapeutic products represent a rapidly emerging therapeutic modality whose behavior fundamentally diverges from the assumptions underlying classical pharmacokinetics and pharmacodynamics (PK/PD). Unlike chemically defined, non-replicating drugs, living therapeutics persist, replicate, adapt, and generate bioactive molecules in situ, such that therapeutic exposure is not externally imposed but biologically generated over time. As a result, administered dose functions only as an initiating condition, while realized exposure emerges from population dynamics, ecological establishment, spatial localization, and regulated functional output. These properties render concentration-based PK/PD frameworks insufficient for predicting efficacy, safety, and controllability of living drug carriers. We introduce pharmaco-microdynamics (PMD) as a quantitative delivery-science framework designed to define, measure, and control exposure for living therapeutics. PMD is operationalized through a set of formal metrics including the functional exposure integral (F-AUC), colonization efficiency (CE), residence-time-weighted activity (RTWA), effective functional concentration (EFC50), and the genetic stability index (GSI)that serve as living-system analogues of AUC, bioavailability, mean residence time, EC50, and product-identity specifications. PMD reconceptualizes exposure as a time-integrated biological process governed by four interdependent axes: population kinetics, functional output kinetics, spatial pharmacology, and evolutionary dynamics. By integrating principles from pharmacology, microbial ecology, synthetic biology, biomaterials science, and systems modeling, PMD provides an operational vocabulary for translating adaptive biological agents into predictable and engineerable delivery systems. We further delineate PMD from adjacent frameworks such as quantitative systems pharmacology (QSP) and ecological microbiome modeling, and critically discuss boundary conditions under which classical PK/PD remains applicable to non-replicating or transient microbial interventions. This review critically examines the limitations of classical PK/PD in modeling living drug carriers, formalizes the core principles of PMD, and illustrates them through three quantitative case studies: SYNB1618 for phenylketonuria, synchronized-lysis bacterial tumor therapies, and fecal microbiota transplantation for recurrent Clostridioides difficile infection. Regulatory and clinical implications are addressed, emphasizing the need to shift from dose- and concentration-centric evaluation toward functional biomarkers, persistence metrics, and model-informed assessment of biological activity. Collectively, pharmaco-microdynamics establishes a unifying conceptual and quantitative foundation for the rational development of living medicines.}, }
@article {pmid42265261, year = {2026}, author = {Pazos, T and Moya, P and Chiva, S and Škaloud, P and Kantnerová, V and Barreno, E and Garrido-Benavent, I}, title = {The Impact of Visible Symptoms of Thallus Damage on the Phycobiota of Mediterranean Epiphytic Lichens.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02794-3}, pmid = {42265261}, issn = {1432-184X}, abstract = {Lichens are excellent bioindicators of overall ecosystem health. The symbiotic nature of their thalli enables tracking changes in humidity, temperature, habitat disturbance and air pollution, often before larger plants do. Sensitive species usually show visible thallus damage, such as bleaching or changes in colour (including total or partial necrosis, and death of the photosynthetic component of the symbiosis), slow growth, and/or biases in reproductive strategies. Particularly, the extent to which these damages are associated with changes in the microscopic photosynthetic community inhabiting lichen thalli (phycobiota) remains poorly understood. Here, we combined Sanger and Illumina sequencing techniques to characterize the diversity and community structure of the eukaryotic phycobiome in selected epiphytic macrolichens showing different levels of thallus damage. Phylogenetic analyses revealed a high microalgal diversity, largely dominated by a few Trebouxia species, which are the most prevalent lichenized microalgae, accompanied by several low-abundance co-occurring genera. Notably, microalgal diversity peaked at intermediate levels of thallus damage. This pattern is consistent with disturbance-mediated modulation of microalgal community evenness rather than a categorical shift in symbiotic composition. These findings reveal previously unrecognized variability within the lichen phycobiota, providing new insights into the ecological dynamics and stress responses of these communities. In conclusion, our work offers a new perspective on the potential of lichens as sensitive bioindicators of air quality and ecosystem health.}, }
@article {pmid42265539, year = {2026}, author = {Schoeman, C and Roodt, D and Mc Menamin, A and Bezuidt, O and Dithugoe, C and Pinard, D and Mizrachi, E}, title = {Conserved symbiosis-associated genes in the cycad Encephalartos natalensis suggest co-option for cyanobacterial symbiosis.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.71311}, pmid = {42265539}, issn = {1469-8137}, support = {116239//National Research Foundation/ ; 118981//National Research Foundation/ ; }, abstract = {Plant-cyanobacterial symbioses have evolved independently at least four times across land plants, yet their underlying molecular mechanisms remain largely elusive. Here, we elucidate the pathways involved in this specialised symbiosis and nutrient exchange within coralloid roots (CRs) of Encephalartos natalensis. Using anatomical analysis and RNA sequencing, we characterise the structural and transcriptional features of CRs harbouring active, heterocyst-rich, nitrogen-fixing Nostoc cyanobacteria. Notably, no fungal hyphae or arbuscular structures were observed under the sampled conditions. CR-associated upregulation of core common symbiosis signalling pathway (CSSP) genes was evident, genes shared across multiple nodulating symbioses. Transcriptome-wide analysis further revealed elevated expression of citrulline and ornithine biosynthesis genes, indicating host assimilation of Nostoc-fixed ammonia. Together, these findings demonstrate that cycads retain and transcriptionally upregulate conserved symbiosis signalling genes during cyanobacterial associations. Building on the evolutionary link between CSSP genes and the ancient arbuscular mycorrhizal (AM) signalling toolkit, our results support differential retention of these genes across plant lineages. Specifically, in E. natalensis, CSSP gene expression in CRs suggests transcriptional co-option for cyanobacterial symbiosis in CRs. This study provides a framework for understanding the role of ancient molecular pathways in driving plant-microbe symbiosis evolution and diversification.}, }
@article {pmid42266025, year = {2026}, author = {Campillo-Cora, C and Rodríguez-Seijo, A and Arias-Estévez, M and Santás-Miguel, V and Fernández-Calviño, D}, title = {Relevance of pollution-induced community tolerance (PICT) methodology in the soil assessment of heavy metal pollution. A review.}, journal = {Integrated environmental assessment and management}, volume = {}, number = {}, pages = {}, doi = {10.1093/inteam/vjag097}, pmid = {42266025}, issn = {1551-3793}, abstract = {Heavy metal (HM) accumulation in soils may negatively affect soil microbial communities and ecosystem functioning. Several microbial-based methodologies have been applied to assess HM pollution in soils. However, it is often difficult to distinguish whether microbial responses are driven by HM accumulation or soil properties influence, particularly in field studies. In this context, methodologies specifically linked to HM toxicity, such as the pollution-induced community tolerance (PICT) approach, represent useful tools for environmental assessment. The PICT methodology is based on determining microbial community tolerance to a pollutant by comparing previously exposed communities with unexposed reference communities, enabling the identification of pollutant-induced effects on microbial communities. This review provides and updated overview of the conceptual basis, strengths, and limitations of the PICT approach for assessing HM-contaminated soils. In particular, it has been addressed the influence of soil properties on both PICT phases (selection and detection), methodological artifacts that may led to over- or underestimation of microbial community tolerance, as well as the occurrence of co-tolerance mechanisms among pollutants. Finally, current limitations and future perspectives for the application of PICT in soil ecotoxicology are discussed.}, }
@article {pmid42266442, year = {2026}, author = {Sun, G and Shen, H and Xiao, Z and Yang, C}, title = {Gut Microbiota and Hypertension: Mechanisms, Drug Interactions, and Translational Directions for Individualized Therapy.}, journal = {International journal of general medicine}, volume = {19}, number = {}, pages = {613324}, pmid = {42266442}, issn = {1178-7074}, abstract = {Hypertension remains a major global health challenge, with suboptimal treatment and blood pressure (BP) control rates and apparent or confirmed resistant hypertension (RHT) affecting approximately 10-20% of treated patients. Increasing evidence suggests that the gut microbiota may contribute to BP regulation through interconnected metabolic, immune-inflammatory, intestinal barrier, gut-brain, and gut-kidney pathways. Short-chain fatty acids (SCFAs) may support vasodilation, renal sodium handling, epithelial barrier integrity, and anti-inflammatory signaling through receptor- and tissue-specific mechanisms, whereas trimethylamine N-oxide (TMAO) has been associated with adverse vascular and cardio-renal phenotypes but may function either as a pathogenic mediator or as a biomarker of altered microbial-host metabolism or impaired renal clearance. Beyond the SCFA-TMAO axis, bile acid metabolism, tryptophan/indole derivatives, phenylacetylglutamine, uremic toxins, and the nitrate-nitrite-nitric oxide pathway provide additional mechanistic links between microbial ecology and BP phenotypes. This review synthesizes mechanistic, pharmacological, clinical, and translational evidence on microbiota-hypertension interactions, with particular emphasis on drug-microbiota bidirectionality. We propose a three-layer framework in which bacterial enzymatic transformation, host metabolic regulation, and epithelial transport/barrier functions jointly shape antihypertensive drug exposure and response. Human interventional evidence remains preliminary: colon-targeted acetylated and butyrylated high-amylose maize starch increased circulating SCFAs and reduced 24-hour systolic BP by approximately 5-6 mmHg in a small, short-duration trial of untreated essential hypertension, whereas probiotics and prebiotics generally show modest BP reductions of approximately 1-3 mmHg systolic and 1-2 mmHg diastolic in meta-analyses. These findings support microbiota-informed hypertension research and risk stratification, but clinical implementation, particularly in well-defined RHT populations, remains investigational.}, }
@article {pmid42266459, year = {2026}, author = {Van Landuyt, J and Oosterlinck, J and De Vrieze, J}, title = {The anaerobic digestion microbiome is robust toward variation in the waste activated sludge feed.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycaf072}, pmid = {42266459}, issn = {2730-6151}, abstract = {Anaerobic digestion stands out as the foremost technology for maximizing the valorization of waste activated sludge (WAS) to recover energy and recover resources. The physical/chemical and microbial makeup of WAS is susceptible to seasonal fluctuations, due to the open-air nature of wastewater treatment facilities, potentially impacting subsequent digester performance and the quality of the resulting digestate. This study delved into a comprehensive analysis of both the initial WAS and the digestate produced by 12 full-scale digesters during both a summer and winter sampling campaign. A significant influence of seasonal variations was observed on the physical/chemical and microbial composition of WAS. Interestingly, the digestate microbiome exhibited a high resilience with minimal seasonal fluctuations, but instead showed variations between different digesters. In summary, this research demonstrates that while WAS composition manifests in specific physical/chemical attributes, it does not exert a discernible influence on the microbial composition of the resulting digestate.}, }
@article {pmid42257736, year = {2026}, author = {Di Nezio, F and Di Cesare, A and García-Cobo, M and Brankovits, D and Sabatino, R and Borgomaneiro, G and Fresno-López, Z and Neunschwander Kurtz, M and Boulamail, S and Cozzoli, F and Fumarola, L and Gonzalez, BC and Roldán, A and Camacho, C and García-Herrero, A and Moro, L and Valdivia, C and Mateo-Mederos, E and García-Gómez, G and Fontaneto, D and Corno, G and Eckert, EM and Martínez, A}, title = {Multilayered Human Activities Shape the Microbial Communities of Groundwater-Dependent Ecosystems on an Arid Oceanic Island.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02797-0}, pmid = {42257736}, issn = {1432-184X}, abstract = {Island coastal aquifers, though spatially limited, sustain key ecosystem functions linked to locally critical provisioning, maintenance and cultural ecosystem services. These functions are largely dependent on the presence of highly adapted biological communities, whose microbial components remain poorly understood. Here, we describe bacterial communities across groundwater-dependent ecosystems on Lanzarote (Canary Islands, Spain), spanning habitats with contrasting environmental conditions and degrees of human influence, using 16 S rRNA gene amplicon sequencing. We then infer the processes shaping community variation by integrating diversity partitioning, indicator species analysis, and machine-learning classification. Bacterial taxonomic diversity varied significantly among habitats, with community composition primarily structured by turnover, consistent with environmental filtering. In contrast, predicted human-associated and potentially pathogenic taxa showed patterns dominated by nestedness, indicating localized enrichment linked to anthropogenic inputs. Caves, enclosed marine bays, and hypersaline systems hosted the most compositionally distinct microbial communities, whereas wells and anchialine pools showed greater overlap in community composition. Together, our results suggest that groundwater microbial communities are influenced by the interplay between environmental filtering and anthropogenic inputs, and that coastal aquifers can act simultaneously as reservoirs of natural biodiversity and sinks of human-associated bacteria. These findings highlight the need for integrative monitoring and conservation strategies that incorporate both hydrological and biological components to safeguard groundwater-dependent ecosystems on oceanic islands.}, }
@article {pmid42259270, year = {2026}, author = {Bonte, D and Van de Peer, Y}, title = {A three-step model for the establishment of polyploid plants.}, journal = {Current biology : CB}, volume = {36}, number = {11}, pages = {R553-R564}, doi = {10.1016/j.cub.2026.03.078}, pmid = {42259270}, issn = {1879-0445}, abstract = {Polyploidy, the result of whole genome duplication, is widespread in plants. Over long timescales, polyploids seem to go extinct more often than diploids. Clear genomic signs of long-term polyploid success exist across plants, but they are comparatively rare within individual lineages. To address the 'polyploid paradox' - early success followed by long-term decline - we propose a three-step framework. The first step is 'Supply', the rate at which new polyploids arise, which can spike in stressful conditions because of elevated formation of gametes with unreduced genomes and relatively weak ecological filtering of the generated polyploids. The second step is 'Bridging', which can occur in one or other of two ways: a short-term route, in which genome duplication increases phenotypic and genetic variation and rarely produces phenotypes that fit the new environment; or a longer-term route, when processes that normally exclude rare cytotypes are weakened and polyploids can persist despite the early costs. The third and last step, 'Consolidation' determines evolutionary outcomes, where some polyploids achieve niche divergence and persist alone or jointly with diploids, while many are removed by long-term costs. As a result, even though polyploids often succeed in the short term, relatively few persist over macroevolutionary timescales. We refer to this sequence as Supply-Bridging-Consolidation (SBC). In this view, polyploid success reflects demographic assembly and ecological opportunity; adaptation usually follows establishment, rather than causing it. The framework yields testable predictions and offers a unified understanding of when polyploids flourish and when they falter, and why only a small fraction is ultimately retained.}, }
@article {pmid42259455, year = {2026}, author = {Wang, Y and Huang, Y and Yin, D and Gong, B and Fan, G}, title = {A segmented electron donor dosing strategy for enhancing thiosulfate-driven partial denitrifying efficiency: Insights into sulfur oxidation pathway, electron transfer and metagenomic microbial ecology.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135106}, doi = {10.1016/j.biortech.2026.135106}, pmid = {42259455}, issn = {1873-2976}, abstract = {Thiosulfate-driven partial denitrification (TPD) is a highly efficient denitrification process that exhibits good stability when coupled with Anammox. This study aimed to enhance the performance of the TPD system by employing different electron donor dosing strategies. The data show that the NO3[-]-N removal efficiency (NRE) and NO2[-]-N accumulation efficiency (NAE) in the segmented dosing group reached 98 % and 90 %, respectively. The study indicates that segmented electron donor dosing significantly enhances the activity of the electron transport chain. Specifically, Complex I and Complex III are associated with electron utilization by nitrate reductase (Nar) and nitrite reductase (Nir). The increased activity of Complex I and the inhibited activity of Complex III in the segmented dosing group contribute to improved NRE and NAE. Metagenomic analysis revealed that Thiobacillus predominated and served as the key functional species for Nar, Nir, and sulfur oxidation. Combined with qPCR analysis, segmented dosing significantly increased the expression levels of functional genes and elevated the NarG/(NirK + NirS) ratio, which further facilitated the accumulation of NO2[-]-N. Furthermore, the segmented dosing group possessed a complete sulfur oxidation pathway capable of fully oxidizing S2O3[2-] to SO4[2-], suggesting a reduced metabolic potential for S[0] production within the system. Overall, this study offers a potential strategy for ensuring a stable supply of nitrite in future anaerobic ammonium oxidation processes.}, }
@article {pmid42259791, year = {2026}, author = {Koch, H and Clavel, T and Mayr, C and Coltman, BL and Schloter, M and Vorholt, JA and Sanz, Y and Cernava, T and Beattie, GA and Lange, L and Chaillou, S and Kovács, &#xc1;T and Smidt, H and Pieterse, CMJ and Kostic, T and Finkel, OM and Lawson, CE and Cocolin, L and Mercado-Blanco, J and Finn, RD and Papadopoulou, KK and Ryan, M and Candela, M and Cotter, PD and Berg, G and O'Sullivan, O and Delgado-Baquerizo, M and Trivedi, P and Charles, TC and Singh, BK and Brader, G and Marian, M and Sessitsch, A}, title = {From "synthetic" to defined microbial communities for clearer terminology.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-74251-1}, pmid = {42259791}, issn = {2041-1723}, support = {doi.org/10.55776/COE7//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; 10.55776/P36288//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; doi.org/10.55776/COE7//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; doi.org/10.55776/COE7//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; 101131818//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101083671//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101131818//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101084485//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101060218//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101166968//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101060693//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101131818//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101094353//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101084163//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101131818//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 395357507 - SFB1371//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 403224013 - SFB1382//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 460129525 - NFDI4Microbiota//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; CL 481/17-1 - SPP2474//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SPI.2022.003//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; 024.004.014//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; }, }
@article {pmid42244647, year = {2026}, author = {Zeng, X and Meng, X and Weakley, AM and Higginbottom, S and Lopez, EM and Cabrera, AV and Gray, IJ and DeFelice, BC and Terasaki, M and Zhao, A and Hall, KR and Levia, M and Arreola, J and Fischbach, MA}, title = {A single-strain dropout screen reveals mechanistic links between microbial ecology and metabolism.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.23.727446}, pmid = {42244647}, issn = {2692-8205}, abstract = {The complexity of the gut microbiome has made it challenging to define the role of individual species in community-level function. Here, we constructed 56 single-strain dropout variants of a defined 118-member community and used each one to colonize a group of germ-free mice. In many cases, removing a single strain triggered a large reordering of a small group of species, which in turn altered the community's metabolic output. En bloc removal of the eight-strain acetogen compartment markedly reduced acetate production and caused intestinal H 2 accumulation and bloating; a specific subset of four acetogens was sufficient to relieve bloating and restore acetate production. Together, these data show that small disturbances in community composition can trigger a confined ecological reorganization with a large chemical phenotype, and they reveal novel strategies for engineering communities with altered metabolic output.}, }
@article {pmid42246391, year = {2026}, author = {Ramadier, G and Chakraborty, S and Fonquernie, I and Dessauvages, TT and Boudoux, C and Brun, YV and Berne, C and Weiss, LE}, title = {Single-Cell Probing of Nanoscale Bacterial Adhesion in Real-Time Using Optical Tweezers.}, journal = {ACS nano}, volume = {}, number = {}, pages = {}, doi = {10.1021/acsnano.6c03697}, pmid = {42246391}, issn = {1936-086X}, abstract = {Bacterial biofilms are organized microbial communities that profoundly impact medicine, industry, and microbial ecology. Biofilm formation begins with nanoscale adhesion events between single bacteria and a surface, and the earliest stages of surface colonization involve reversible interactions that transition to irreversible attachment through the secretion of specialized nanoscale bioadhesins. Understanding and controlling the initial interactions between adhesin and surface is key to control and prevent biofilm formation. Here, we investigate the nanoscale adhesion dynamics of single Caulobacter crescentus cells, a dominant early colonizer in environmental biofouling, focusing on its holdfast, a strong nanoscale adhesive organelle that mediates irreversible attachment within seconds of contact. To characterize the time-dependent mechanical properties of holdfast, we developed the Trapezoid, a custom optical tweezers platform that combines nanometer spatial precision with millisecond temporal control of cell position, contact timing, and applied force on defined surfaces. We implemented a trapezoidal temporal profile of these programmed contact cycles, in which a single cell is brought into contact with the surface, maintained for a defined duration, retracted, and subjected to controlled pulling forces. This approach enables real-time quantification of nanoscale adhesion onset, holdfast deployment kinetics, and influence of surface chemistry at the level of individual live adhesion events. Our results dissect the physical and biochemical determinants of bacterial adhesion, providing a quantitative framework for the rational design of antiadhesive coatings, nanoscale biofouling control strategies, and bioinspired adhesives functional in wet environments.}, }
@article {pmid42247161, year = {2026}, author = {Fablet, L and Belcour, A and Stephant, S and Michel, C and Ropers, D and Cerna, K and Bombach, P and Riha, J and Tremosa, J and An-Stepec, BA and Fadrhonc, K and Dopffel, N and Rad, S}, title = {Microbial-geochemical Interactions in Underground Reservoirs: Implications for Hydrogen Storage.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02800-8}, pmid = {42247161}, issn = {1432-184X}, support = {No101069750//European Commission/ ; No101069750//European Commission/ ; No101069750//European Commission/ ; No101069750//European Commission/ ; No101069750//European Commission/ ; No101069750//European Commission/ ; No101069750//European Commission/ ; No101069750//European Commission/ ; No101069750//European Commission/ ; No101069750//European Commission/ ; No101069750//European Commission/ ; No101069750//European Commission/ ; No101069750//European Commission/ ; ANR-23-CETP0002//Agence Nationale de la Recherche/ ; }, abstract = {Understanding microbial life in deep geological environments is essential for assessing natural biogeochemical processes and their implications for subsurface activities such as underground hydrogen storage. This study investigates the water chemistry, microbial community composition, and metabolic potential of two contrasting geological settings: porous reservoirs and salt caverns. This study is among the first to provide a large-scale comparison of microbial and geochemical processes across reservoirs. Our results show that porous reservoirs, particularly those with carbonate facies, are characterized by carbonate-rich fluids and host anaerobic microbial communities dominated by methanogenic archaea, fermentative bacteria, and acetogens. In contrast, the studied salt caverns contain salt-saturated brines and are dominated by halophilic and chemoorganotrophic microorganisms adapted to oligotrophic, high-salinity conditions. Some reservoirs showed atypical microbial profiles influenced by anthropogenic activities or hydrogeological connections, which alter local geochemistry and microbial structures. This study highlights the influence of salinity, carbon availability, temperature, and human impact on microbial community structure and metabolic functional potential. The presence of hydrogenotrophic microorganisms raises concerns about their potential to consume injected hydrogen and alter gas quality. These findings underscore the need to move beyond detection toward activity-based assessments of microbial hydrogen consumption, in order to anticipate biogeochemical dynamics and develop effective mitigation strategies. A better understanding of the interplay between reservoir chemistry, geology, and microbiology is crucial for ensuring safe and efficient underground hydrogen storage.}, }
@article {pmid42250808, year = {2026}, author = {Sabina, R and Kharmawphlang, IM and Charan, K and Hussain, N}, title = {Per- and polyfluoroalkyl substances stress in soil ecosystems: decoding microbial dysbiosis mechanisms and advanced remediation strategies.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135036}, doi = {10.1016/j.biortech.2026.135036}, pmid = {42250808}, issn = {1873-2976}, abstract = {Per- and polyfluoroalkyl substances (PFAS), the so-called "forever chemicals," are emerging contaminants that severely disrupt soil ecosystems by rewiring microbial networks that sustain biogeochemical processes. This review deciphers the mechanisms underlying PFAS-induced microbial dysbiosis, revealing how these contaminants reconfigure community architecture, metabolic functions, and enzyme-mediated processes critical for biogeochemical cycling. It further integrates multi-omics approaches, spanning genomics to metabolomics, to elucidate molecular signatures and adaptive responses that govern microbial resilience and vulnerability across trophic hierarchies. Furthermore, the review examines PFAS biotransformation pathways, emphasising oxidoreductase-mediated mechanisms, kinetic bottlenecks, and catalytic constraints within complex soil matrices. By bridging microbial ecology with advanced material science, the review introduces a transformative paradigm of hybrid catalytic systems, including nanozyme-enabled transformations, engineered enzymes, and photocatalytic assemblies for targeted PFAS degradation. Thus, by linking microbial dysfunction with engineered catalytic innovation, the review offers a systems-level blueprint for sustainable and efficient strategies to restore PFAS-contaminated soils. Notably, this review highlights the urgent need for integrated multidisciplinary approaches to mitigate PFAS-induced ecological risks and advance sustainable soil restoration technologies.}, }
@article {pmid42252423, year = {2026}, author = {Becerra-Lucio, PA and Pérez-Rueda, E and Dias, GM and Labrín-Sotomayor, NY and Mendoza-Mendoza, A and Partida-Martínez, LP and Zarza, E and Peña-Ramírez, YJ}, title = {Environmental contributors to bacterially dominated fermenting consortia of artisanal Mezcal.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05199-x}, pmid = {42252423}, issn = {1471-2180}, support = {786763//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; IN220523//PAPIIT-DGAPA UNAM/ ; 5103711808 2021-2024//El Colegio de la Frontera Sur/ ; Omics Unravel Mezcal, a Drink with a Complex Spirit//Qu&#xed;mica Valaner-MGI Mexico/ ; }, abstract = {The production of spontaneously fermented beverages worldwide relies on native microorganisms acquired incidentally through cross-contamination from environmental reservoirs. We examined the microbiota involved in Mezcal fermentation, exploring their origins, dynamics, and ecology. Using shotgun metagenomics, we analyzed four batches of Mezcal, spanning the entire production process from crop to distillation. Bacterial genera such as Leuconostoc and Lentilactobacillus dominated the fermentation samples, whereas Bacillus was the most abundant in the environmental samples. Fermenting yeasts, such as Saccharomyces, accounted for only ~ 10% of the microbial abundance. No significant differences in microbial community structure were observed between the sampled batches, fermentation times, or depths of the fermentation tanks. Weevil samples clustered with fermentation and plant samples, suggesting they may serve as natural reservoirs for Leuconostoc and Lentilactobacillus. Functional differences were observed in COGs related to secondary metabolism during fermentation and correlated with sensory notes identified by a panel of expert tasters, suggesting that variations in the sensory profiles of the final spirit are directly linked to the metabolic products of genes associated with secondary metabolism. Our work analyzed the spontaneous fermentation microbiota, providing fundamental insights into its natural reservoirs and its contribution to Mezcal terroir.}, }
@article {pmid42252693, year = {2026}, author = {Jourdain, L and Leininger, A and Pacheco, AR and Gu, W}, title = {Environmental selection constrains metabolic network architecture despite taxonomic turnover in anaerobic digestion communities.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag145}, pmid = {42252693}, issn = {1751-7370}, abstract = {Microbial ecosystems often sustain stable metabolic functions despite pronounced taxonomic turnover, yet the mechanisms underlying such reproducible functional states remain poorly understood. Here, we investigated how physicochemical constraints shape functional convergence in anaerobic digestion communities using replicated serial enrichments seeded from four distinct inocula. Across three pH levels and six substrate regimes, replicate communities from different inocula consistently converged toward reproducible metabolite profiles, with pH emerging as the dominant organizing factor. Community composition became progressively environment-driven over time, and after 30 generations, pH explained the largest fraction of compositional variance (PERMANOVA R2 = 0.21, P = 0.001), followed by substrate. Genome-resolved metagenomics revealed that convergence was accompanied by strong pH-dependent structuring of redox-balancing and terminal electron-sink pathways, whereas upstream carbohydrate-entry pathways were conserved. Taxonomic convergence was incomplete and scale-dependent: the ability to correctly assign communities to their inoculum declined from 75% at the genus level to 53% at the phylum level, indicating increasing similarity across inocula at coarser taxonomic resolution despite persistent fine-scale variability. Despite this taxonomic flexibility, communities assembled under identical conditions consistently recruited similar sets of metabolic pathways organized into comparable network architectures. Functional redundancy analyses showed high redundancy and flexible taxonomic implementation for upstream fermentative processes, contrasted with lower redundancy and stronger convergence for terminal methanogenic functions. Together, these results demonstrate that reproducible metabolic function in AD emerges from environmentally constrained assembly of shared metabolic network architectures, rather than deterministic fixation of species composition, highlighting environmental control of metabolic organization as a central principle governing microbiome function.}, }
@article {pmid42253950, year = {2026}, author = {Han, X and Guo, XL and Qiu, J}, title = {From gut-reproductive microbiota to ferroptosis: a comprehensive insight into the molecular-pathogenicity of endometriosis.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1762013}, pmid = {42253950}, issn = {1664-3224}, abstract = {Endometriosis (EMS) is a highly heterogeneous chronic gynecological disease characterized by pain, infertility, and relapse, with its etiology and pathogenesis not yet fully elucidated. Traditional theories, including "retrograde menstruation," "implantation theory," and "abnormalities in immune tolerance," struggle to adequately explain the complex lesion behavior, diverse phenotypic characteristics, and accompanying immune-metabolic disorders. In recent years, the key roles of imbalances in the gut and reproductive microbiomes, abnormal iron metabolism, and the newly proposed ferroptosis in the occurrence and development of EMS have gradually gained attention, suggesting that this disease may be a systemic condition involving the interplay of microbial ecology, iron metabolism, and cell death. Existing studies indicate that the gut-reproductive microbiome profoundly influences the body's iron homeostasis and iron load by regulating mucosal immunity, systemic inflammatory responses, and metabolic environments. This, in turn, activates the ferroptosis pathway through iron-dependent lipid peroxidation and cell membrane damage, participating in the formation, maintenance, and inflammatory microenvironment shaping of ectopic lesions. Based on these findings, this article systematically reviews the interactions between gut-reproductive microbiome imbalance and iron metabolism disorders, integrating multi-omics evidence such as microbiome analysis, metabolomics, and iron metabolism/ferroptosis-related molecular markers. It proposes a new pathological mechanism framework of "dysbiosis-iron overload-ferroptosis" incorporating microecological imbalance and ferroptosis into a unified picture of the pathogenesis of EMS. Furthermore, this article discusses potential therapeutic strategies and application prospects surrounding microbiome remodeling (such as probiotics, fecal microbiota transplantation, dietary and lifestyle interventions) and pharmacological targeting of key ferroptosis-related molecules. Through a comprehensive and critical analysis of existing evidence, this review aims to provide a more systematic theoretical framework for the mechanistic research of EMS and offer ideas and directions for future clinical translation of precise classification, individualized intervention, and novel treatment plans.}, }
@article {pmid42254836, year = {2026}, author = {Xu, L and Sun, X and Zakem, EJ}, title = {Dependency-competition tradeoffs structure microbial niches and nitrogen cycling.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag134}, pmid = {42254836}, issn = {2730-6151}, abstract = {The marine nitrogen cycle is regulated by ecological interactions among diverse microbial populations. In anoxic zones, populations carrying out anaerobic metabolisms, mainly multi-step denitrification and anammox, drive the loss of bioavailable nitrogen, some of which is emitted as the potent greenhouse gas nitrous oxide ([Formula: see text]). While competition for limiting resources is well studied, the combined effects of competition and dependencies, where a "feeder" population supplies a required resource to a "recipient," remain poorly understood. Here, we develop a trait-based consumer-resource framework to test how recipient populations reshape the ecological niches of their feeders and competitors. Our analysis demonstrates how recipients may expand either their feeder's or their feeder's competitor's niche, depending on relative competitive abilities on limiting resources. We analyze and identify equilibrium co-existence regions, threshold regimes, and the dominant pathways of nitrogen loss as a function of varying both organic matter (OM) and nitrate supply, rather than just their ratio. Examining this 2D supply space identifies a distinct zone where OM and nitrate co-limitation results in [Formula: see text] production but not consumption, and thus an ecological niche for [Formula: see text] accumulation. Additionally, the model suggests that anammox bacteria occupy a wider range of OM and nitrate supply regimes than denitrifying populations, consistent with their more frequent detection across diverse marine environments. The results link microbial interaction networks to biogeochemical fluxes relevant at global scales and extend ecological theory to multi-resource systems with nested competitive and dependent interactions.}, }
@article {pmid42254896, year = {2026}, author = {Vaggi, C and Vötterl, JC and Lerch, F and Yosi, F and Koger, S and Ricci, S and Verhovsek, D and Metzler-Zebeli, BU}, title = {Characterization of fecal bacterial microbiomes according to fecal color, consistency, and sample type in piglets before and after weaning.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1815748}, pmid = {42254896}, issn = {2297-1769}, abstract = {Fecal samples are widely used as a proxy for the large intestinal microbiota; however, phenotypic characteristics (e.g., color and consistency) may be associated with divergent microbial profiles, especially around weaning, when diet and physiological adaptation rapidly alter gut function. The relationship between fecal phenotype, sample type, and piglet gut microbiota under physiological conditions remains poorly understood. This study investigated the bacterial communities in different fecal phenotypes of piglets shortly before and immediately after weaning. The fecal consistency of 192 piglets across two replicate batches was scored daily from day of life (DoL) 28 to 36, and fecal or rectal swab samples were collected at DoL28 and DoL33. The samples were classified by type (feces/swab), color (brown/yellow), and consistency (balls/liquid). DNA was extracted for quantification of total bacterial gene copies and 16S rRNA gene sequencing, and microbial composition was analyzed using Quantitative Insights Into Microbial Ecology 2 (QIIME2), Statistical Analysis System (SAS), and R. Fecal consistency changed markedly over time, shifting from predominantly ball-shaped on DoL28-32 to softer feces thereafter (p < 0.001). Age strongly influenced microbiota structure, with marked increases in relative abundance of Prevotella and Alloprevotella from DoL28 to DoL33, whereas the abundance of Escherichia, Methanobrevibacter, and Fusobacterium declined. Microbial communities differed between sample types, with swabs potentially reflecting mucosa-associated taxa more closely than fecal samples. Shannon and Simpson indices indicated reduced diversity in yellow and liquid feces on DoL28 (p < 0.001). Swabs and yellow liquid feces on DoL28 showed higher relative abundances of Escherichia, Bacteroides, and Fusobacterium, whereas brown ball-shaped feces were enriched in Lachnospiraceae, Prevotella, and Lactobacillus on both sampling days (p < 0.05). Overall, each fecal phenotype exhibited a distinct bacterial signature, and the sample type influenced the composition of the captured community. Monitoring fecal phenotypes alongside selecting appropriate sample types may enhance the interpretation of microbiome data and offer a practical, non-invasive approach to assess gut health during the critical weaning period.}, }
@article {pmid42256221, year = {2026}, author = {Giju, JK and John, S and Sivadas, A and Prabhakar, M and K, K and Sunilkumar, D and Nair, BG and Pal, S and Prakash, V}, title = {From dysbiosis to precision medicine: targeting the microbial-metabolic axis in IBD management.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1826972}, pmid = {42256221}, issn = {2235-2988}, abstract = {Inflammatory bowel disease (IBD) is a chronic relapsing inflammatory condition that has a rapidly changing global epidemiology. IBD has been traditionally viewed as a primary immune system dysfunction, but emerging evidence more accurately describes IBD as a perturbance of the intricate balance between host immunity, the intestinal microbiome, and intestinal metabolism. Although genetic and environmental components have long been recognized as contributors, accumulating evidence increasingly highlights the pivotal role of microbial dysbiosis in the pathogenesis of IBD. In patients with IBD, intestinal dysbiosis, which is often characterized by reduced Firmicutes and increased pro-inflammatory bacteria, triggers a cascade of pathogenic events. These pathogenic events include impaired epithelial barrier function, dysregulated immune activation against luminal antigens, and immune reprogramming. Central to these processes are functional changes in microbial metabolism, particularly in pathways involving short-chain fatty acids (SCFAs), bile acids, and redox homeostasis, which critically contribute to the development of chronic mucosal inflammation. The current therapeutic backbone of IBD-including aminosalicylates, biologics, and immunomodulators-largely targets the inflammatory response. However, the challenges such as primary non-response, secondary loss of response, and systemic side effects are often problematic. Consequently, there is an urgent need to develop novel therapeutic and preventive strategies that target the underlying microbial and metabolic causes of the disease rather than modulating immune responses. This review integrates the pathomechanistic implications of the microbiome-metabolic axis in the maintenance of gut homeostasis and its disruption in IBD, with particular emphasis on the global epidemiology of the disease. We further evaluate emerging therapeutic and preventive strategies aimed at restoring the microbiome-metabolic axis, including fecal microbiota transplantation (FMT), probiotic therapy, bacteriophage therapy, and helminth-based therapies. In addition, we explore the potential of advanced approaches such as microbiome engineering and precision genome editing to enable highly personalized therapeutic paradigms. By bridging microbial ecology with clinical pathology, this review highlights the transformative potential of targeting the host-microbiota interface to achieve improved long-term outcomes in IBD.}, }
@article {pmid42256599, year = {2026}, author = {Keum, HL and Sul, WJ and Kim, HS}, title = {Comparison of skin microbiota profiles in chronic scratch lesions using tape strip and swab sampling.}, journal = {JAAD international}, volume = {27}, number = {}, pages = {19-20}, pmid = {42256599}, issn = {2666-3287}, }
@article {pmid42243144, year = {2026}, author = {Qin, Z and Wang, Q and Yang, Q and Wang, Q and Li, Y and Ma, H and Gao, J and Li, X}, title = {Agricultural fungicides shape soil and sediment reservoirs of multidrug-resistant fungi.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73958-5}, pmid = {42243144}, issn = {2041-1723}, support = {42277409//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Fungicide resistance in environmental fungi represents a growing One Health challenge, yet its ecological extent and clinical relevance remain poorly studied. Here, we integrate residue monitoring, community profiling, large-scale culture isolation, and mechanistic assays to investigate the resistance of fungi in agricultural soils and adjacent river sediments. The results indicate that fungicides are widely detected in environmental samples and pose substantial ecological risks, particularly carbendazim and tebuconazole. Resistant fungi are also widespread and account for a large proportion of the genera detected in fungal communities. Among >3,900 resistant isolates, we recover 358 multidrug-resistant (MDR) strains showing cross-resistance to multiple agricultural fungicides. Transcriptomic, qPCR, and molecular docking analyses suggest that environmental MDR phenotypes arise from synergistic effects of target-gene alterations, efflux pump overexpression, and adaptive stress responses. Notably, triazole exposure coordinately upregulates virulence genes and mycotoxin biosynthetic clusters, indicating transcriptional activation of genes associated with virulence and secondary metabolism. Together, these findings highlight agricultural landscapes as reservoirs of fungicide-resistant fungi and underscore the need to re-evaluate fungicide practices to protect crop health, ecosystem stability, and the effectiveness of clinical antifungals.}, }
@article {pmid42026592, year = {2026}, author = {Li, Y and Zhu, Y and Zhang, F and Huang, C and Wang, Z}, title = {The interaction between microbes and cytokines in cancer: unraveling the underlying effects.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {}, pmid = {42026592}, issn = {1479-5876}, support = {Nos. 32370628,92159302, 32170592//National Natural Science Foundation of China/ ; Nos. 2022ZDZX0018, 2023NSFSC004,2024NSFSC0402//Jiangsu Provincial Agricultural Science and Technology Independent Innovation Fund/ ; No. 2023-YF09-00039-SN//National Science and Technology Planning Project/ ; No. ZYGD22009//1.3.5 project for Disciplines of Excellence, West China Hospital, Sichuan University/ ; }, abstract = {An increasing number of studies have found that microbes are involved in the development and treatment of tumors, and the impact of microbes on the tumor microenvironment has emerged as a prominent field in cancer studies. Although microbiome–immunity interactions in cancer have extensively reviewed in previous studies, the molecular integration of microbes with cytokines within the tumor microenvironment remains insufficiently resolved. This review examines how microbes influence the immunological and inflammatory regulatory systems in cancer. The activation of important signaling axes, such as IL-6/STAT3, TNF-α/NF-κB, and interferon pathways, by microbial components and metabolites (LPS, SCFA, and EPS) changes immune surveillance, encourages immune evasion, and affects the spread of metastases. Recent studies indicate that Microbiota-induced alterations in cytokine signaling increasingly influence cancer immunotherapy, suggesting that microorganisms and their metabolites may emerge as potential targets for novel anti-tumor immunotherapy. Evidences from multiple cancer types, combined with studies on specific non-malignant diseases, reveals synergistic alterations in microbial communities and cytokine networks. These interactions form a microbe-cytokine axis linking inflammation, tumor progression, and treatment response. Understanding the mechanisms underlying the interplay between microbial ecology and host cytokines may provide strategic guidance for enhancing precision cancer immunotherapy.}, }
@article {pmid42241895, year = {2026}, author = {Hodžić, A and Cizek, V and Kunert, M}, title = {Gut immune and redox transcriptional responses to Borrelia infection in questing Ixodes ricinus.}, journal = {Ticks and tick-borne diseases}, volume = {17}, number = {4}, pages = {102668}, doi = {10.1016/j.ttbdis.2026.102668}, pmid = {42241895}, issn = {1877-9603}, abstract = {Ticks of the genus Ixodes are major vectors of pathogens of medical and veterinary importance, including the causative agents of Lyme borreliosis. While much is known about tick immune responses during feeding, the molecular mechanisms that enable pathogen persistence during the off-host period remain poorly understood. Here, we investigated the gut immune landscape of questing Ixodes ricinus females naturally infected with members of the Borrelia burgdorferi sensu lato species complex. Transcriptional profiling of gut tissues revealed sustained upregulation of the NF-κB transcription factor dorsal and redox-associated genes in Borrelia-infected individuals, whereas other selected immune signalling pathway genes and antimicrobial peptides remained unchanged. Correlation analyses further indicated that Borrelia load was positively associated with gene expression levels, while redox genes were strongly co-regulated, indicating a coordinated control of oxidative homeostasis. These findings point to a targeted immune response that supports gut homeostasis rather than triggering broad antimicrobial activity. However, the limited number of Borrelia-positive questing ticks analyzed in this study highlights the need for further investigations with larger sample sizes, multiple developmental stages, and additional infection experiments to validate and expand these findings.}, }
@article {pmid42239137, year = {2026}, author = {Fu, B and Porter, RL and Shi, H and Ea, AC and Espeleta, AM and Ambat, A and Relman, DA and Huang, KC and Xue, KS}, title = {CUPID-seq enables highly multiplexed amplicon sequencing via combinatorial in-line dual indexing.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.20.726713}, pmid = {42239137}, issn = {2692-8205}, abstract = {Targeted amplicon sequencing is widely used to profile genetic variation in defined genomic regions. In microbial ecology, for example, amplicon sequencing of the 16S and 18S ribosomal RNA genes has been transformative for characterizing microbial communities. However, on high-capacity sequencing platforms with patterned flow cells, throughput is constrained by the requirement for unique dual indexes (UDIs), which increases primer costs and limits the number of samples that can be pooled per sequencing run. Here, we introduce CUPID-seq (C ombinatorial, U nique, P hased, In-line D ual-indexed seq uencing), a highly multiplexed amplicon-sequencing strategy that increases scalability through combinatorial indexing across two rounds of PCR. CUPID-seq introduces phased, in-line UDIs during Round 1 gene-specific amplification, enabling multiple samples to share the same Illumina UDI during Round 2 PCR while remaining uniquely identifiable. This design reduces upfront costs by up to 85% and reduces library preparation time and reagent use by up to 40%. We develop and validate CUPID-seq primers targeting the 16S V4 region and provide a computational workflow for demultiplexing in-line indexes. Although optimized here for 16S-based profiling, CUPID-seq can be readily adapted to other user-defined amplicons. By reducing cost and increasing multiplexing capacity, CUPID-seq enables users to leverage high-throughput sequencing platforms more effectively across diverse biological contexts.}, }
@article {pmid42240949, year = {2026}, author = {Mosca, K and Turbant, F and Achouak, W and Wien, F and Arluison, V}, title = {RNAs Associated With Bacterial Outer Membrane Vesicles: Structural Insights Into Surface Composition.}, journal = {Journal of extracellular vesicles}, volume = {15}, number = {6}, pages = {e70306}, doi = {10.1002/jev2.70306}, pmid = {42240949}, issn = {2001-3078}, support = {//CEA high-risk research program Audace!/ ; }, abstract = {Gram-negative bacteria release outer membrane vesicles (OMVs) that deliver various molecules, including virulence factors, allowing them to interact with their host. Recent evidence suggests that OMVs may serve as carriers for RNAs, in particular small regulatory noncoding RNAs (sRNAs). However, for these sRNAs to function effectively, they often require a protein cofactor, typically the Hfq RNA chaperone. In our previous studies, we demonstrated that Hfq, after interacting with the bacterial inner membrane, can be translocated to the periplasm and subsequently exported within OMVs, potentially in association with RNAs. In the present study, we build upon this previous work and provide evidence that RNA molecules are not only a key component of the OMV lumen, but can also be inserted into the vesicle membrane in an Hfq-dependent manner. This new finding suggests that surface-presented RNAs may be directly delivered to the host. Overall, our results reveal a previously unrecognized aspect of OMV-associated RNA and emphasizes the need to explore the role of RNAs in cell-to-cell communication, as OMV-host interplay may not be governed solely by protein-protein or protein-membrane contacts.}, }
@article {pmid42241453, year = {2026}, author = {Taillefer, B and Schattenberg, F and Doan, T and Müller, S and Cascales, E}, title = {Phenotypic heterogeneity optimizes trade-offs during adaptive deployment of the type VI secretion system.}, journal = {PLoS biology}, volume = {24}, number = {6}, pages = {e3003838}, doi = {10.1371/journal.pbio.3003838}, pmid = {42241453}, issn = {1545-7885}, abstract = {The type VI secretion system (T6SS) is a widespread nanoweapon deployed by bacteria to eliminate competitors in polymicrobial environments, allowing niche colonization or host invasion. Fluorescent microscopy recordings have shown that T6SS expression and/or activation is heterogeneous in clonal populations of many bacterial species. However, it is still unknown whether T6SS heterogeneity is genetically controlled or arises from stochastic processes and what its physiological relevance is. Here, we report that enteroaggregative Escherichia coli (EAEC) exhibits stable phenotypic heterogeneity in T6SS expression. Under iron-limiting conditions, the Sci1 T6SS is expressed in only a subset of the population, creating distinct ON and OFF subpopulations in a reversible, heritable, and epigenetically controlled equilibrium. This heterogeneity is governed by the interplay between the iron-responsive regulator Fur- and Dam-dependent DNA methylation at the sci1 promoter. Mutations in Fur binding sites or GATC methylation motifs shift the population to homogeneous ON or OFF states, respectively. Functional analyses reveal that while ON cells mediate antibacterial activity, OFF cells buffer the population against lethal retaliatory responses from defensive T6SS[+] competitors. Our results suggest that T6SS heterogeneity in EAEC represents a finely tuned attenuation strategy optimizing the trade-off between competitive killing and survival in hostile microbial communities. This work uncovers a novel layer of regulation in T6SS deployment and highlights phenotypic heterogeneity as an adaptive trait in interbacterial warfare.}, }
@article {pmid42233996, year = {2026}, author = {Hama Soor, TA and Mustafa, AM and Abdulkarim, MM}, title = {Epigenetic Phase Variation in Bacterial Adaptation to Environmental Stress: A Narrative Review.}, journal = {Current microbiology}, volume = {83}, number = {7}, pages = {}, pmid = {42233996}, issn = {1432-0991}, abstract = {Epigenetic phase variation (ePV) represents a sophisticated regulatory mechanism by which bacteria rapidly adapt to environmental stressors without permanent genetic alterations. This review examines the molecular mechanisms underlying bacterial ePV mediated by DNA methylation, with particular emphasis on restriction-modification systems, orphan methyltransferases, and their roles in stress adaptation. ePV systems enable bacteria to generate phenotypically diverse populations through reversible ON/OFF switching of gene expression, facilitated by phase-variable DNA methyltransferases. These systems, termed phasevarions when controlling multiple genes, provide adaptive advantages in fluctuating environments by coordinating responses to antimicrobial stress, oxidative damage, heat shock, and nutrient limitation. The integration of genome-wide methylation patterns with transcriptional networks creates complex regulatory hierarchies that govern bacterial survival strategies. Recent advances in single-molecule real-time sequencing and methylome analysis have revealed the widespread distribution of ePV systems across diverse bacterial species, highlighting their fundamental importance in microbial ecology and pathogenesis. Understanding these epigenetic mechanisms provides important insight into bacterial adaptation and evolutionary dynamics. However, their translation into antimicrobial resistance management and therapeutic development remains largely exploratory.}, }
@article {pmid42234026, year = {2026}, author = {Palacios Ganoza, B and Kuuri-Riutta, O and Laine, AM and Väliranta, MM and Mitchell, EAD and Tuittila, ES}, title = {Contrasting Trait-Mediated Mechanisms Shape Peatland Testate Amoeba Communities Under Long-Term Drying Across Fen-Bog Gradient.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02796-1}, pmid = {42234026}, issn = {1432-184X}, abstract = {Boreal peatlands store vast amounts of carbon and regulate regional hydrology, making their stability critical under accelerating climate change. This stability depends on community-level resilience and resistance shaped by the functional traits of organisms. Although climate-induced drying is already reshaping peatland communities, the trait-based mechanisms supporting stability in soil biota remain poorly resolved. We assessed stability in testate amoebae (TA) - a key group of the soil food web - by comparing functional trait patterns in ambient control plots with plots subjected to two decades of experimental water level drawdown (WLD) across three peatland types (rich fen, poor fen, and bog). In ambient conditions, null models revealed strengthened environmental filtering along the fertility gradient; nutrient-rich fen showed highest diversity and functional redundancy. Long-term WLD, however, intensified environmental filtering by reshaping the communities across all peatland types. Functional beta diversity revealed contrasting stability mechanisms: rich fen maintained functional stability through resilience, with major species turnover but minimal functional change, whereas bog communities retained function through resistance, relying on drought-adapted traits and showing minimal species turnover. Contrastingly, the poor fen lost functional stability, as low redundancy combined with dominance of wet-adapted traits led to both species and functional turnover. Under moderate drying, bogs are most likely to maintain functional stability, whereas fens, particularly poor fens, are more vulnerable. These trait-mediated differences indicate peatland type-specific functional thresholds with implications for predicting stability and carbon dynamics under future climates. Overall, continued warming increasingly compromises peatland soil biota and the ecosystem functions they mediate.}, }
@article {pmid42235221, year = {2026}, author = {Huang, Y and Zhong, S and Lin, W and Zhang, S and Jiang, H and Wang, X and Mu, J}, title = {Microplastic pollution and ecological risks in the wet season: Potential effects on bacterial communities and nitrogen cycling in a coastal watershed of Southeast China.}, journal = {Marine pollution bulletin}, volume = {231}, number = {}, pages = {119923}, doi = {10.1016/j.marpolbul.2026.119923}, pmid = {42235221}, issn = {1879-3363}, abstract = {Microplastics (MPs) are emerging contaminants in freshwater ecosystems, posing ecological risks via physical presence and biological interactions. MP pollution, ecological risks, and potential impacts on bacterial communities were assessed during wet season in the Minjiang River Watershed, a coastal watershed in Southeast China. Average MP concentrations (0.3-5.0 mm) were 0.22 ± 0.12, 0.17 ± 0.05, and 0.48 ± 0.27 n/L in tributaries, midstream, and downstream, respectively. MPs were predominantly composed of fibers, transparent and black particles, and PET, with the 0.3-1.0 mm size fraction being the most abundant. Urban section exhibited higher MP concentrations, whereas tributaries showed greater variability, likely reflecting heterogeneous sources. Socioeconomic factors were positively correlated with MP concentration and diversity, while NH4[+]-N, NO3[-]-N, pH, and conductivity were identified as key water chemistry parameters associated with MP distribution. Dams appeared to reduce upstream MP transport, whereas high-flow operations may release previously retained MPs. Ecological risk indices (PLI, PERI, and MPERI) indicated minor to high risks. MPs were significantly associated with dominant bacterial taxa, including Proteobacteria, Verrucomicrobia, Nitrospirota, Burkholderiaceae, and Pseudomonadaceae, as well as some predicted nitrogen-cycling genes (e.g., hao, pmoA-amoA, pmoB-amoB, pmoC-amoC, and hcp), suggesting potential shifts in community structure and function. This study highlights the importance of microbial ecology in MP risk assessments and informs river management and mitigation strategies.}, }
@article {pmid42235395, year = {2026}, author = {Li, Y and Zhu, T and Tao, C and Li, S and Cheng, H and Chen, W}, title = {Threshold-dependent control of ARG removal in global wastewater treatment plants: Molecular mechanisms of low-abundance functional genes deciphered via metagenomics and explainable AI.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142574}, doi = {10.1016/j.jhazmat.2026.142574}, pmid = {42235395}, issn = {1873-3336}, abstract = {Wastewater treatment plants (WWTPs) serve as critical barriers against the dissemination of antibiotic resistance genes (ARGs) from urban water environments to nature, yet the molecular mechanisms governing their biological removal remain poorly understood. By combining experimental metagenomic data from 19 Chinese WWTPs with additional data from 31 global WWTPs (50 WWTPs in total), an explainable machine learning (ML) framework was developed. The RFE-SHAP (Recursive Feature Elimination-SHapley Additive exPlanations) based on feature importance was applied to identify key biological features driving ARG removal. The study revealed that low-abundance microbial functional genes particularly those involved in DNA repair, energy metabolism, and quorum sensing exhibit threshold-dependent control over ARG attenuation. ML models (BFGs-GBDT) incorporating the RFE-SHAP-selected functional genes achieved exceptional predictive accuracy (R[2]test = 0.967), outperforming taxonomy-based models (average R[2]test = 0.805). Strikingly, these functionally critical genes, despite their low abundances (0.04 - 0.15%), exerted disproportionate influence on ARG removal efficiency, challenging the prevailing high-abundance-centric paradigm in WWTPs design. The findings not only elucidated the molecular mechanisms of ARG mitigation but also provided a predictive framework for precision engineering of microbial communities to enhance ARG elimination. This study advances wastewater treatment strategies from empirical ARG removal to mechanism-driven environmental risk control.}, }
@article {pmid42235702, year = {2026}, author = {Li, S and Li, Z and Yang, H}, title = {Two-stage microbial assembly and compact co-occurrence networks in encapsulated biofiller AAOA systems with low sludge yield.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135064}, doi = {10.1016/j.biortech.2026.135064}, pmid = {42235702}, issn = {1873-2976}, abstract = {Previous long-term studies have reported low sludge yield and high nitrogen removal in encapsulated biofiller-based anaerobic/anoxic/oxic/anoxic systems (EB-AAOA), but the microbial ecology within individual reactor zones remains unclear. Biofiller-associated microbial communities (EB communities) from two long-term EB-AAOA systems were compared with curated public municipal anaerobic/anoxic/oxic (AAO) 16S rRNA amplicon datasets processed using the same bioinformatics workflow. The AAO datasets were used as heterogeneous municipal suspended-growth references, and the analysis focused on the shared anaerobic, anoxic, and oxic zones. Null-model inference based on the beta-nearest taxon index (βNTI) and the Bray-Curtis-based Raup-Crick metric (RCbray) revealed a two-stage assembly pattern in EB communities, with stronger deterministic filtering in the upstream anaerobic unit followed by dispersal limitation in downstream units. Compared with AAO references, EB communities showed lower diversity, distinct taxonomic enrichment patterns, and a compact, connected genus-level co-occurrence network. PICRUSt2 predictions suggested zone-level differences in carbon-use and nitrogen-cycling potential. The results suggest a working Selection-Stabilization model in which encapsulated biofillers may favor zone-specific selection and help maintain microbial organization under low-sludge nitrogen-removal conditions. Future studies using direct functional measurements and controlled comparisons matched for influent carbon-to-nitrogen ratio should test the inferred links among assembly, metabolism, and sludge minimization.}, }
@article {pmid42238881, year = {2026}, author = {Kumar, A and Das, N and Gawdiya, S and Kumar, R and Pal, P and Sachan, S and Ghosh, P and Jatav, HS and Babatunde, CA}, title = {Microbial-driven nature-based solutions for environmental antimicrobial resistance and emerging contaminants: mechanisms, platform trade-offs, and decision framework.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1804764}, pmid = {42238881}, issn = {1664-302X}, abstract = {INTRODUCTION: Antimicrobial resistance (AMR) and emerging contaminants (ECs), including pharmaceuticals, personal care products, microplastics, and endocrine-disrupting chemicals, pose interconnected threats to environmental and human health. Nature-based solutions (NbS) have emerged as sustainable and cost-effective approaches for mitigating these challenges through ecosystem-driven processes.<br><br>METHODS: This review follows a PRISMA-guided narrative-systematic synthesis of literature published between 2000 and 2024, using data sources including Scopus, Web of Science, and PubMed. The analysis integrates evidence on microbial mechanisms, NbS platform performance, and environmental AMR-EC interactions.<br><br>RESULTS: The synthesis highlights that microbial-driven NbS exploit metabolic diversity, functional plasticity, and plant-microbe interactions to degrade, transform, immobilize, or eliminate contaminants in soil, water, and wastewater systems. Advances in microbial ecology, synthetic biology, and omics approaches have enabled the design of functional microbial consortia capable of targeting antibiotic residues, resistance genes, and recalcitrant pollutants. NbS platforms such as constructed wetlands, rhizosphere-based systems, biofilters, and microbial electrochemical technologies demonstrate variable performance influenced by microbial diversity, redox processes, and system design. However, trade-offs exist, including the potential for microbial biofilms to act as reservoirs of antibiotic resistance genes.<br><br>DISCUSSION: Despite their potential, microbial-driven NbS face challenges related to scalability, long-term performance, ecological risks, and regulatory acceptance. This review proposes a microbial NbS decision framework linking environmental sources, microbial mechanisms, platform design, and monitoring indicators to support sustainable and risk-aware implementation. Overall, the effectiveness of NbS depends on optimizing microbial functional diversity, system design, and resistance suppression strategies to ensure long-term environmental and public health benefits.}, }
@article {pmid42238977, year = {2023}, author = {Head, D and Marsh, PD and Devine, D and Tenuta, LMA}, title = {In silico study of hyposalivation and sugar exposure on biofilm dysbiosis.}, journal = {JADA foundational science}, volume = {2}, number = {}, pages = {100019}, pmid = {42238977}, issn = {2772-414X}, abstract = {BACKGROUND: Dental caries develops under actively sugar-fermenting dental biofilms, but the most successful control methods available only target mineral loss. Reduced salivary flow rates (hyposalivation) significantly exacerbate caries progression by lessening sugar and acid clearance near tooth surfaces. Maintaining dental biofilm symbiosis (health) under hyposalivation requires knowledge of the impact of acid inhibition under given dietary regimens.<br><br>METHODS: An individual-based mathematical model was used to predict biofilm dysbiosis under normal or hyposalivatory conditions by regulating the frequency of sugar intake and inhibiting microbial glycolysis, reducing the acid challenge to the tooth mineral. The impact of pH-dependent (stronger inhibition at lower pH [eg, fluoride]) and pH-independent (general percentage reduction in acid production) strategies on pH near the tooth surface during sugar intake, and the corresponding compositional changes in the biofilm, were quantified.<br><br>RESULTS: Under normal saliva flow, reducing the frequency of sugar intake and increasing the inhibition of acid production by pH-dependent or pH-independent strategies could prevent bacterial dysbiosis and prevent the biofilm from having a caries-associated (dysbiotic) to a health-associated (symbiotic) composition. However, under hyposalivatory conditions, dysbiosis occurred beyond 2 sugar intakes per day, and the degree of inhibition of glycolysis required to prevent dysbiosis was not feasible with available therapeutics.<br><br>CONCLUSIONS: Model data predict that to counteract the drastic effect of hyposalivation on biofilm dysbiosis, it will be essential to significantly reduce the frequency of fermentable sugar intake and any direct inhibition of bacterial metabolism.}, }
@article {pmid42226576, year = {2026}, author = {Skalny, M and Czeremuga, J and Roman, M and Wróbel, TP and Dziewit, L and Bajda, T}, title = {Bacterial Biomolecules Drive Extracellular DNA Adsorption onto Ferrihydrite: Interfacial Interactions and Spectroscopic Insights.}, journal = {Langmuir : the ACS journal of surfaces and colloids}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.langmuir.6c00302}, pmid = {42226576}, issn = {1520-5827}, abstract = {The reactivity of extracellular DNA (exDNA) at the mineral interface, modulated by interactions with other biomolecules, may play an important role in governing the fate of genetic information in the environment. However, there is a limited understanding of exDNA-mineral interactions with biomolecule-enriched matrices. Herein, we investigate the mechanisms of exDNA adsorption onto ferrihydrite in the presence of bacterial lysate biomass. The interactions within the system were explored by combining exDNA adsorption studies, zeta potential measurments, spectroscopic studies, and advanced spectrochemical imaging by scattering-type Scanning Near-Field Optical Microscopy (s-SNOM). Bacterial lysate biomass is found to enhance the immobilization efficiency of exDNA by the ferrihydrite. A key role in this process is played by proteins bearing positively charged groups, which facilitate interactions and co-adsorb with exDNA. When the bacterial biomass concentration reaches 14.03 μg/mL, the exDNA removal efficiency nearly doubles relative to the system with sole ferrihydrite. The effect of biomolecules in promoting exDNA adsorption onto ferrihydrite is further demonstrated by s-SNOM. The spectral bands of biomolecules tend to overlap and co-occur in specific regions of conjugates as biomass concentration increases. Our results provide important mechanistic insight into the process potentially influencing the fate of exDNA in environments such as biofilms, soils, and sediments.}, }
@article {pmid42228062, year = {2026}, author = {Kang, D and Kim, MJ and Lee, S}, title = {Bacterial and microeukaryotic assemblage transitions during a harmful algal bloom in the Nakdong River.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiag057}, pmid = {42228062}, issn = {1574-6941}, abstract = {Harmful algal blooms (HABs) represent major ecological disturbances that can alter microbial community composition and reduce ecosystem resilience. Here, we investigated bacterial and microeukaryotic assemblage transitions during a bloom-affected period in the Nakdong River, a regulated river system in South Korea. By integrating microcystin (MC) measurements, cyanobacterial dominance, water-quality parameters, and amplicon-based community profiling (16S rRNA gene and ITS2), we characterized how microbial communities reorganized along gradients of bloom intensity. MC concentrations increased markedly across the sampling period, and early-phase qPCR data showed concurrent increases in mcyE gene abundance through 6 August 2021. Bacterial communities shifted from Actinobacteriota- and Proteobacteria-dominated assemblages toward Microcystaceae-enriched communities. Microeukaryotic communities similarly transitioned from diverse Chlorophyta, fungi, and ciliates to Chlamydomonadaceae- and ciliate-dominated assemblages under high-MC conditions. Both domains exhibited significant reductions in alpha diversity with increasing bloom intensity, although microeukaryotic responses were comparatively moderate. Correlation analyses revealed strong associations of MC concentration and Microcystis abundance with declining pH, elevated BOD, and the enrichment of bloom-associated taxa. These results indicate that bloom-associated conditions in this regulated river system were accompanied by parallel restructuring of bacterial and microeukaryotic assemblages. The integration of environmental and microbial indicators presented here provides a framework for understanding HAB-associated microbial reorganization and for informing monitoring strategies in hydrologically altered freshwater ecosystems.}, }
@article {pmid42228096, year = {2026}, author = {Wang, C and Yang, W and Bian, W and Song, G and Wang, Y and Xu, Z and Wang, X and Fu, L and Wang, J and Zhang, Z and Wang, Y and Guo, Z and Zhao, L}, title = {Physicochemical Parameters Govern Winter Pelagic Microbial Food Web Dynamics in China's Marginal Seas.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02786-3}, pmid = {42228096}, issn = {1432-184X}, support = {42449302//the open research cruise NORC2025-302 supported by NSFC Ship time Sharing Project/ ; }, abstract = {Pelagic microbial food webs (MFWs) functionally govern marine biogeochemical fluxes, oceanic productivity and climate feedbacks via complex trophic-level interactions, yet their compositional dynamics, trophic-level interactions and tightly coupled physicochemical driving factors remain insufficient in China's marginal seas (CMS: South China Sea, East China Sea, Yellow Sea, Bohai Sea). Here, we elucidate the MFW trophic structure (picoplankton [Pico], nanoplankton [Nano], microzooplankton [Micro]) and its physicochemical drivers across four CMS subzones during January 2025, utilizing flow cytometry, microscopy, and satellite remote sensing-derived hydrographic datasets. Results revealed a latitudinal northward shift in the MFW from Pico- to Micro-dominated assemblages. A size-structured framework was proposed, with consistent negative slopes for normalized abundance spectrum (-3.0 ± 0.2) and biomass spectrum (-1.8 ± 0.2)-validating metabolic ecological theory, with the biomass of 20-200 μm plankton accounting for 9.9% of that of 0.2-2.0 μm plankton. Specifically, trophic-level abundance ratios conformed to a ecological pyramid structure, with Pico: Micro and Nano: Micro ratios spanning 5 and 2 orders of magnitude, respectively. Concerning biotic-abiotic interplays, nutrient-driven bottom-up control emerged as the primary regulatory mechanism for both Pico and Nano spanning all seas except the Kuroshio-influenced zones. Multivariate analyses further identified synergistic environmental forcing-where nitrate-phosphate co-limitation interacts with strong current mixing-as the key modulator of MFW stability thresholds. Our findings provide a trait-based framework for predicting eutrophic marginal sea resilience and modeling carbon export under climate change.}, }
@article {pmid42228529, year = {2026}, author = {Backman, T and Cui, J and Caullireau, E and Bleak, E and Bezrukov, I and Girardi, P and Hawks, A and Lasky, JR and Latorre, SM and Erberich, JM and Lopez, L and Neumann, M and Perkins, AM and Symeonidi, E and Azadi, P and Horvath, MP and Muszyński, A and Lang, PLM and Karasov, TL and Burbano, HA}, title = {Persistent trade-offs balance competition and colonization across centuries.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {23}, pages = {e2534310123}, doi = {10.1073/pnas.2534310123}, pmid = {42228529}, issn = {1091-6490}, abstract = {Microbial competition drives rapid adaptation, often forcing organisms to specialize in new ecological niches. Adaptations that improve competitive ability can reduce performance in other environments creating trade-offs. Whether such trade-offs persist in nature-or are eroded as lineages adapt through compensatory changes-remains largely unknown. Here we show that a trade-off between competitive ability and host colonization has been stably maintained in natural Pseudomonas populations for centuries. Wild plant-pathogenic Pseudomonas compete using tailocins-phage-derived molecular weapons that bind to specific cell-surface receptors. Genomic surveys and functional assays reveal that the most broadly lethal tailocins remain rare-while the tailocin's production increases competitive killing, it also compromises plant colonization. We determine that the polymorphisms behind this trade-off are not transient-historical genomes spanning two centuries show that the trade-off has been maintained for at least 10[5] to 10[6] generations. Our results demonstrate that, in natural populations, a trade-off between competition and pathogenicity is fundamental and not easily overcome.}, }
@article {pmid42229597, year = {2026}, author = {Fard, MB and Kwon, S and Vrieze, J and Wu, D}, title = {Long-term inhibition under continuous perfluorooctanoic acid exposure during anaerobic digestion of waste microalgal-bacterial aerobic granular sludge: Metagenomic-metatranscriptomic insights.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135056}, doi = {10.1016/j.biortech.2026.135056}, pmid = {42229597}, issn = {1873-2976}, abstract = {Microalgal-bacterial aerobic granular sludge (MB-AGS) is a promising wastewater treatment technology, but the effect of residual perfluorooctanoic acid (PFOA) on the anaerobic digestion of waste MB-AGS (WMB-AGS) remains poorly understood. This study evaluated PFOA effects (100, 500, and 1000 µg/L) on anaerobic digestion of WMB-AGS by comparing short-term single-exposure batch assays with long-term semi-continuous digestion. Under control conditions, methane production reached 76 ± 2 mL CH4/g volatile solids. Relative to the control, methane yield changed marginally in the presence of PFOA, indicating no measurable inhibition in a single-exposure biochemical methane potential (BMP) assay. In contrast, during continuous exposure in the semi-continuous digester, biogas output decreased after introducing 1000 µg/L PFOA (31 ± 1 to 19 ± 1 mL/day) and coincided with increased residual soluble chemical oxygen demand. During 3-day hydrolysis-acidogenesis tests, total volatile fatty acids increased from 82 ± 9 mg/L (control) to 122 ± 12 mg/L (1000 µg/L), suggesting greater accumulation of fermentation intermediates in the early digestion phase. The PFOA distribution showed substantial partitioning into extracellular polymeric substance fractions and sludge solids, with 28.3% remaining in supernatant, 23.2% in loosely bound extracellular polymeric substances, 16.0% in tightly bound extracellular polymeric substances, and 32.6% in sludge solids with no transformation products. Multi-omics analysis supported that dominant microbial communities remained broadly stable, whereas reduced transcription of glycolysis and pyruvate-to-acetyl-coenzyme A conversion genes was consistent with soluble organic accumulation and reduced biogas production. Overall, single-exposure BMP assays underestimated the long-term operational impact of continuous PFOA exposure during anaerobic digestion of WMB-AGS.}, }
@article {pmid42147183, year = {2026}, author = {Topacio, TM and Maltz, MR and Lo, DD and Zaza, M and Porter, WC and Freund, L and Lyew, A and Cocker, D and Biddle, T and Yisrael, K and Castillo, DD and Dingilian, H and Drover, RW and Botthoff, J and Aronson, E}, title = {Chronic exposure to Salton Sea aerosols elicits pulmonary inflammation and shifts in murine lung and fecal microbiome diversity.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {42147183}, issn = {2693-5015}, abstract = {Lung disease is rampant around the Salton Sea, California's largest inland lake and a major source of airborne particulates. To examine root causes of pulmonary disease, we investigated the exposure impacts of spatiotemporal variation in aerosols collected near the Salton Sea on lung and fecal microbiomes. We collected dust during the summer and fall at three different sites around the Salton Sea from 2020 to 2022. Dust was filtered to remove microbial cells and aerosolized for 7-day chronic murine exposures within controlled environmental chambers, after which mouse lung and fecal samples were used for 16S rRNA V3-V4 amplicon sequencing. We verified that chronic exposure to aerosols elicits neutrophilic pulmonary inflammation, particularly in mice exposed to collections from the Wister site near the Salton Sea. We found that spatiotemporal variation drove variation in lung microbiome composition in mice exposed to aerosols from 2022. The lung microbiomes of Salton Sea aerosol-exposed mice were found to increase in alpha-diversity and richness, while simultaneously decreasing in evenness. In contrast, the fecal microbiomes of aerosol-exposed mice decreased in diversity and richness. Our findings suggest that chronic exposure to aerosols from Wister, a site immediately Southeast of the Salton Sea, triggers a systemic stress response in mice characterized by high pulmonary neutrophil recruitment, increased lung microbiome diversity, and decreased fecal microbiome diversity. Back trajectory analyses for aerosol surface type frequencies revealed higher contributions from the Salton Sea in 2020 and 2022 collections from Wister. These findings suggest that chronic exposure to Salton Sea aerosols have impacts on host pulmonary and systemic health, as emphasized by significant but opposing effects on lung and fecal microbiome diversity. Furthermore, these findings demonstrate the variable capacity of environmental aerosol exposure to elicit health consequences relative to seasonal weather events.}, }
@article {pmid42217234, year = {2026}, author = {Touati, A and Boufahja, F and Touaitia, R and Khezami, L and Idres, T and Grenni, P}, title = {Inhibiting horizontal gene transfer to contain antimicrobial resistance: conjugation and plasmid maintenance as druggable targets.}, journal = {Expert review of anti-infective therapy}, volume = {}, number = {}, pages = {1-23}, doi = {10.1080/14787210.2026.2683605}, pmid = {42217234}, issn = {1744-8336}, abstract = {INTRODUCTION: Antimicrobial resistance (AMR) is propelled by horizontal gene transfer (HGT), with conjugative plasmids enabling rapid, cross-species spread and stable carriage of resistance. Interventions that reduce plasmid transmission or persistence can complement bactericidal therapies and infection-control programs.<br><br>AREAS COVERED: We review druggable vulnerabilities in conjugation (mating-pair formation, type IV secretion/ATPase motors, coupling proteins, and relaxosome functions) and in plasmid maintenance (replication, partition, and toxin-antitoxin enforcement). The review is grounded in a narrative search of recent mechanistic, ecological, and in vivo literature. We cover biological antagonists (exclusion, fertility inhibition, and host defenses), chemical and metabolic inhibitors, and genetic strategies that repress transfer functions or selectively eliminate resistance elements.<br><br>EXPERT OPINION: HGT inhibition is moving from proof-of-concept to actionable containment, but progress depends on mechanism-confirmed leads, standardized transfer metrics, plasmid confirmation, and safety evaluation in complex microbiomes and environments. Near-term impact is most likely an adjunct to stewardship and infection prevention, aiming to reduce new acquisition and shorten carriage of high-risk resistance plasmids.}, }
@article {pmid42222261, year = {2026}, author = {Wassermann, B and Kögl, I and Gokul, JK and Wicaksono, WA and Schweitzer, M and Korsten, L and Berg, G}, title = {Diversity and selected functional traits of microbiota associated with traditional dried plant foods from South African informal markets.}, journal = {FEMS microbes}, volume = {7}, number = {}, pages = {xtag026}, pmid = {42222261}, issn = {2633-6685}, abstract = {Traditional plant-based products provide nutritional benefits and support cultural heritage; however, their sale in urban informal markets raises potential food safety considerations. We characterized the microbiota of five traditional dried plant products (baobab, masau, nyii, dinawa, and lude) obtained from three informal markets in South Africa (n = 51 samples) using 16S rRNA gene sequencing and quantitative real-time PCR; bacterial isolates (n = 87) were further evaluated using selected phenotypic assays. Bacterial abundance and composition varied across products and vendors. Baobab exhibited the highest microbial richness (1460 ASVs) but relatively low bacterial loads (10[6] 16S rRNA gene copies g[-1]), whereas dried leafy greens showed the lowest richness (470 ASVs) but the highest bacterial abundance (10[9] copies g[-1]). Across products, higher bacterial diversity correlated with genera such as Bifidobacterium and Prevotella, while higher bacterial abundance correlated with genera such as Salmonella, Vibrio, and Acinetobacter. Notably, health implications of detected taxa cannot be inferred from genus-level identification based on 16S rRNA gene sequencing. Phenotypic traits observed among selected isolates included growth in the presence of several antibiotics (particularly sulfadiazine and ampicillin), protease activity, and inhibition of indicator strains under laboratory conditions. Overall, traditional dried plant foods harbor diverse microbial communities shaped by plant characteristics and vendor-related practices, highlighting the importance of improved handling and drying practices.}, }
@article {pmid42222739, year = {2026}, author = {Batista, JBO and de Souza Oliveira, EH and Penteado, LAM and Nascimento, VX and Matsumura, S and Silva, JMM and Nóbrega, DF and Retamal-Valdes, B and Feres, M and Ferreira, SMS}, title = {Periodontal status and microbial profiles across the clinical spectrum of liver cirrhosis.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2678639}, pmid = {42222739}, issn = {2000-2297}, abstract = {OBJECTIVES: Periodontitis is common in patients with cirrhosis, but this association remains underexplored. This cross-sectional study aimed to assess periodontal conditions and characterize periodontal biofilm composition in individuals with liver cirrhosis.<br><br>METHODS: Adults with liver cirrhosis were enrolled. Periodontal parameters were recorded, and supragingival and subgingival biofilm samples were collected. Forty bacterial species were quantified using checkerboard DNA-DNA hybridization. Findings were stratified by Child-Pugh class and MELD score.<br><br>RESULTS: Forty-five patients were included; 88.9% exhibited periodontal disease (57.8% gingivitis on a reduced periodontium, 31.1% periodontitis), and 11.1% were periodontally healthy. Periodontal diagnosis was not associated with liver-disease severity (p&#x2009;>&#x2009;0.05). Gingivitis showed the highest supragingival bacterial load, with enrichment of orange- and red-complex pathogens, particularly Tannerella forsythia. Patients with compensated liver disease (Child-Pugh A; MELD&#x2009;<&#x2009;15) showed higher counts of Aggregatibacter actinomycetemcomitans and Fusobacterium nucleatum ssp. nucleatum (p&#x2009;<&#x2009;0.05). Among patients with periodontitis, higher subgingival proportions of red-complex pathogens were observed in those with MELD&#x2009;<&#x2009;15.<br><br>CONCLUSIONS: Periodontal disease was highly prevalent in patients with cirrhosis. Although periodontal diagnosis was not associated with liver-disease severity, distinct microbiological patterns were observed. These findings highlight the potential relevance of periodontal monitoring in patients with cirrhosis and warrant further investigation in larger, longitudinal studies.}, }
@article {pmid42223272, year = {2026}, author = {Borton, MA and Oliverio, AM and Narrowe, AB and Villa, JA and Rinke, C and Hoyt, DW and Liu, P and McGivern, BB and Bechtold, EK and Ellenbogen, JB and Daly, RA and Smith, GJ and Angle, JC and Flynn, RM and Freiburger, AP and Louie, KB and Stemple, B and Northen, TR and Henry, C and Miller, CS and Morin, TH and Bohrer, G and Wrighton, KC}, title = {Mapping the soil microbiome functions shaping wetland methane emissions.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0068025}, doi = {10.1128/msystems.00680-25}, pmid = {42223272}, issn = {2379-5077}, abstract = {Accounting for only 8% of Earth's land cover, freshwater wetlands remain the foremost contributors to global methane emissions. Yet the microorganisms and processes underlying methane emissions from wetland soils remain poorly understood. Over a five-year period, we surveyed the microbial membership and in situ methane measurements from over 700 samples in one of the most prolific methane-emitting wetlands in the United States. We constructed a catalog of 2,502 metagenome-assembled genomes (MAGs), with more than half of the 70 bacterial and archaeal phyla sampled containing novel lineages. Integration of these data with 133 soil metatranscriptomes provided a genome-resolved view of the biogeochemical specialization and versatility expressed over wetland soil spatial and temporal gradients. Centimeter-scale depth differences best explained patterns of microbial community structure and transcribed functionalities, even more than land cover or temporal information. Moreover, while extended flooding restructured soil redox, this perturbation failed to reconfigure the transcriptional profiles of methane-cycling microorganisms, contrasting with theoretically expected responses to hydrological perturbations. Co-expression analyses, coupled with depth-resolved methane measurements, revealed the metabolisms and trophic structures most predictive of methane hotspots. Mapping the spatiotemporal transcriptional patterns on this compendium of biogeochemically classified soil-derived genomes begins to untangle the microbial carbon, energy, and nutrient processing contributing to wetland methane production.IMPORTANCESoil microbial ecology is increasingly recognized as essential to climate mitigation, but realizing its full potential requires shifting from static genome inventories to dynamic assessments of microbial activity. This study shows that methane-cycling microbes exhibit stable, depth-stratified expression patterns, even in response to major redox and flooding shifts, undermining assumptions that water-table manipulations common in wetland management can alone reduce methanogenesis. Instead, methane cycling is shaped by spatially organized, transcriptionally active networks involving not only methanogens but also methanotrophs, fermenters, and iron reducers. These findings expose the limitations of genome-only models and highlight the need for soil diagnostics that capture in situ activity. Together, we provide a foundation for developing activity-based microbiome tools, embedding microbial functions into Earth system models, and designing interventions that move beyond "single-lever" strategies and instead work with the structure and dynamics of microbial communities as complex, layered systems.}, }
@article {pmid42225162, year = {2026}, author = {Wu, G and Wang, Z and Tsigkou, K and Vrieze, J and Angelidaki, I}, title = {A stress-response-recovery framework integrating microbial life-history strategies for stressed anaerobic digestion.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135055}, doi = {10.1016/j.biortech.2026.135055}, pmid = {42225162}, issn = {1873-2976}, abstract = {Anaerobic digestion (AD) is a mature biotechnology; however, its operational stability remains constrained by the limited predictability of microbial responses to environmental stress. In this review, stressed AD systems are defined as microbial ecosystems in which one or more environmental stressors disrupt microbial functioning, reduce microbial growth and survival, and drive deterministic and/or stochastic shifts in the AD microbiome, thus impacting process performance. For stressed AD, this review proposes a unifying stress-response-recovery framework integrating microbial life-history strategies. Specifically, stress acts as an ecological filter that suppresses stress-sensitive microorganisms while selecting stress-tolerant ones. During the response phase, system resilience can be achieved through multiple forms of microbial plasticity, including spatial reorganization (e.g., granulation), metabolic rerouting (e.g., shifts from acetoclastic methanogenesis to syntrophic acetate oxidation), and alternative electron-transfer pathways such as direct interspecies electron transfer. Importantly, recovery does not necessarily ensure a return to the original community structure; instead, it is governed by functional redundancy, microbial memory, and ecological hysteresis, often resulting in alternative stable states with reconfigured metabolic networks while preserving methane production. Collectively, these insights provide complementary ecologically informed management strategies, highlighting the potential of strategy-based monitoring, microbiome engineering, and targeted interventions to enhance system resilience. By integrating ecological theory with engineering practice, this review advances the understanding of AD stress and provides a framework for designing more robust and adaptable anaerobic systems.}, }
@article {pmid42225894, year = {2026}, author = {Skordos, I and Gilis, E and Callewaert, C and Aidarova, A and Haegman, M and Driege, Y and Kreike, M and Afonina, IS and Staal, J and Demeyer, A and Elewaut, D and Beyaert, R}, title = {Preventing MALT1-mediated CYLD cleavage induces intestinal dysbiosis and reduces EAE severity.}, journal = {EMBO reports}, volume = {}, number = {}, pages = {}, pmid = {42225894}, issn = {1469-3178}, support = {3G046612//Fonds Wetenschappelijk Onderzoek (FWO)/ ; 3G0I1422//Fonds Wetenschappelijk Onderzoek (FWO)/ ; bof/baf/4y/2024/01/511//UGent | Bijzonder Onderzoeksfonds UGent (BOF)/ ; bof/baf/2y/2024/01/024//UGent | Bijzonder Onderzoeksfonds UGent (BOF)/ ; }, abstract = {The paracaspase MALT1 is essential for lymphocyte activation and also plays roles in non-immune cells and cancer. Its protease activity regulates immune signaling by cleaving specific substrates, making it a promising therapeutic target. However, broad inhibition of MALT1 protease activity causes multiorgan inflammation in mice, highlighting the need to understand the effects of individual substrate cleavage. We generated CYLD(R321A) knock-in mice expressing a MALT1-resistant form of the deubiquitinase CYLD. These mice are healthy, with normal lymphocyte development and preserved immune signaling. Unlike MALT1 protease-dead mice, they do not develop spontaneous inflammation. Notably, they exhibit altered gut microbiota and reduced disease severity in a model of multiple sclerosis. Together, our work shows that blocking cleavage of a single MALT1 substrate is sufficient to modulate microbiota and neuroinflammation without causing overt defects in lymphocyte cell development or activation, providing in vivo evidence for substrate-specific targeting of MALT1 as a refined therapeutic strategy.}, }
@article {pmid42215197, year = {2026}, author = {Cazzaniga, M and Shen, P and Flegar, D and Bra, KK and Villoria Recio, M and Bahey-El-Din, M and Hueston, C and Claesson, MJ and Melgar, S and Gahan, CGM}, title = {Functional impact of dietary chitin upon Listeria monocytogenes pathogenesis.}, journal = {Food microbiology}, volume = {139}, number = {}, pages = {105117}, doi = {10.1016/j.fm.2026.105117}, pmid = {42215197}, issn = {1095-9998}, mesh = {*Chitin/administration &amp; dosage/metabolism ; Animals ; *Listeria monocytogenes/pathogenicity/genetics/drug effects ; Mice ; *Listeriosis/microbiology/immunology ; Virulence ; Macrophages/immunology/microbiology ; Humans ; Interleukin-6/immunology/genetics ; Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; Female ; Dietary Supplements/analysis ; Diet ; }, abstract = {Chitin, the second most abundant polymer in nature, is recognized for biocompatibility and diverse effects on microbes and the host. However, the role of dietary chitin against foodborne pathogens such as Listeria monocytogenes remains underexplored. Here, we show that chitin functions as an environmental signal that attenuates L. monocytogenes virulence and mitigates infection outcomes. Consistent with previous studies, exposure of L. monocytogenes to chitin resulted in downregulation of key virulence genes and we demonstrate that this is accompanied by reduced pathogenesis in intestinal epithelial cells. While chitin can act as a pathogen-associated molecular pattern, stimulation of murine macrophages revealed no excessive induction of IL-6 or TNF-α after 24 h, indicating that it does not provoke detrimental inflammatory responses. In vivo, dietary supplementation with chitin significantly reduced bacterial burden in faeces and secondary organs within 24 h post-infection. These protective effects were further enhanced when mice were challenged with chitin-pretreated bacteria, highlighting the combined importance of host nutritional context and pathogen pre-exposure. Chitin also modulated host responses, promoting early IL-6 production and selectively shaping gut microbiota, with enrichment of potentially beneficial genera such as Alistipes, Eubacterium, and Duncaniella and suppression of pro-inflammatory Prevotella. Transcriptomic analyses revealed that L. monocytogenes responds to chitin by upregulating virR and dltD, indicative of an envelope stress response, though no direct link between VirR and virulence gene downregulation was observed. These findings establish chitin as a dietary molecule that simultaneously modulates pathogen virulence, host immunity, and microbial ecology, representing a potential strategy to mitigate gastrointestinal infection.}, }
@article {pmid42215729, year = {2026}, author = {Abergel, C and Abrahão, JS and Coulibaly, F and Fischer, M and Jeudy, S and Knorr, RL and Krupovic, M and Legendre, M and Pérez-Núñez, D and Nwokolo, C and Queiroz, V and Schmitt, A and Van Etten, JL and Willemsen, A and Bisio, H}, title = {Infection cycles of viruses of the phylum Nucleocytoviricota.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, pmid = {42215729}, issn = {1740-1534}, abstract = {The phylum Nucleocytoviricota, formerly known as nucleocytoplasmic large DNA viruses (NCLDVs), comprises evolutionarily related viruses with remarkably diverse genome sizes, coding capacities and virion morphologies. These viruses infect hosts across the eukaryotic tree of life, from protists to humans, and are believed to have emerged during the early stages of eukaryotic evolution. How the basic aspects of virus-host interaction have evolved in different lineages and whether they share a conserved infection cycle remain unclear. In this Review, we synthesize the information on the infection cycles of model representatives from the major orders within the phylum, revealing both shared traits and lineage-specific innovations. We compare the information available for the extensively studied poxviruses, asfiviruses, iridoviruses and chloroviruses with insights from the rapidly expanding literature on the mimiviruses, pandoraviruses, marseilleviruses and pithoviruses. We provide an overview of the molecular details underlying the key stages of Nucleocytoviricota infection cycles: entry via membrane fusion, formation of viral factories organized via phase separation, genome replication, virion morphogenesis through a crescent intermediate, and egress. We highlight outstanding questions in the field, unify concepts across traditionally separated research areas, and provide a conceptual framework to guide future cell biology studies on large double-stranded DNA viruses.}, }
@article {pmid42216257, year = {2026}, author = {Timmis, K and Karahan, ZC and Byrne, JA and Robinson, JM and Bernal, P and Rainey, PB and López-García, P and McGenity, TJ and Chavarria, M and Sato, K and Verstraete, W and Blank, LM and Lal, R and Colom, MF and Ramos, JL}, title = {Scientists' Warning to Humanity: Unnecessary Bureaucracy Is a Global Impediment to Productivity, Advancement of Human and Planetary Wellbeing, Science and Sustainability.}, journal = {Microbial biotechnology}, volume = {19}, number = {6}, pages = {e70371}, doi = {10.1111/1751-7915.70371}, pmid = {42216257}, issn = {1751-7915}, mesh = {Humans ; COVID-19/prevention &amp; control ; *Efficiency ; Global Health ; }, abstract = {Bureaucracies are essential to the proper functioning of almost all human activities. However, they are diverse in their quality and success-promoting potential. While many bureaucratic measures make sense and are necessary for the wellbeing and success of their organisations, some are unnecessary or ill-conceived/implemented, and yet others may harm system functioning and achievement. Unnecessary bureaucratic measures limit productivity, waste vital resources and drain workforces of engagement, enthusiasm, motivation, commitment and cohesion. (The term "unnecessary bureaucratic measures" used in this discourse is used in the sense of poor value and lacking a compelling basis-cost: benefit; see also GOV.UK 2020-but also includes poorly-conceived or -implemented measures, measures delegated to frontline and other workers that could/should be handled by the administrations, online tools promoted as reducing workloads but that in fact increase work and frustration because they are poorly designed and/or not subjected to adequate quality control.) They create frustration, anger and increased stress among those affected. Stress is considered by the World Health Organisation to be one of the foremost health crises of the 21st century. While the impact of unnecessary bureaucratic measures within an enterprise may go unnoticed by those not directly affected, the aggregate negative global impact on productivity, economic success and the wellbeing of workforces is concerning. Humankind is currently faced with a range of challenges, some existential, that urgently require solutions. Scientific research and discovery are generally considered to be major drivers of progress of humankind and a source of solutions to major problems and crises faced by society. Science innovation depends upon the creativity, originality and productivity of scientists. In the fields of biomedical sciences, the plant-agriculture-nutrition sciences, and the environmental sciences, progress in the past can be approximately quantified in terms of reduction in preventable human suffering, disease and premature death (as illustrated by the recent development of mRNA vaccines against the SARS-CoV-2 virus, which saved millions of lives), as well as the resulting socio-economic benefits. Unnecessary bureaucratic measures needlessly slow down research progress by diverting the time and effort of scientists from their essential tasks-creative thinking and research-to mundane tasks, and are responsible for delays in humanitarian improvements that translate into avoidable suffering and premature loss of life. Unnecessary bureaucracy is a global crisis of diversion from primary essential tasks, lowered human achievement and ensuing frustration, that is intertwined with and reinforces other problems, such as societal fragmentation. It requires a global response. A new, fit-for-purpose framework is needed that supports the functioning of bureaucracies and the necessary measures they impose, while constraining the imposition of unnecessary measures. Here, we consider some of the causes of unnecessary bureaucracy and measures needed to directly address these causes. These considerations lead us to propose an actionable solution strategy involving a Bureaucracy Charter and an implementation mechanism that will ensure best practice and adherence to the Charter. The rationale of this strategy incorporates key issues of benchmarking-best practice, transparency-accountability, oversight, stakeholder engagement-involvement, duty of care, Health in All Policies, and awareness and avoidance of cost externalisations.}, }
@article {pmid42217062, year = {2026}, author = {Mafe, AN and Makut, MD and Owuna, JE and Nkene, IH and Edo, GI and Salisu, SM and Said, MA}, title = {Development, functional profiling, and probiotic evaluation of indigenous LAB from Nigerian fermented foods: Antimicrobial mechanisms, in vivo validation, and applications in food preservation and mycotoxin risk reduction.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {6}, pages = {}, pmid = {42217062}, issn = {1573-0972}, mesh = {*Probiotics/pharmacology ; Animals ; RNA, Ribosomal, 16S/genetics ; *Fermented Foods/microbiology ; Nigeria ; *Food Preservation/methods ; *Mycotoxins ; *Lactobacillales/isolation &amp; purification/genetics/classification/physiology ; Drosophila melanogaster/microbiology ; Phylogeny ; Food Microbiology ; Microbial Sensitivity Tests ; Anti-Infective Agents/pharmacology ; Fungi/drug effects ; Weissella ; }, abstract = {Indigenous fermented foods are rich sources of functionally diverse lactic acid bacteria (LAB) and associated microorganisms with relevance to food safety, health promotion and sustainable bioprocessing. This study aimed to evaluate the probiotic potential of bacterial isolates recovered from selected Nigerian fermented foods. Bacterial isolates were molecularly identified by 16S rRNA gene sequencing and evaluated for probiotic attributes, including stress tolerance, safety, antimicrobial activity and functional bioactivity. Selected strains were further validated in vivo using Drosophila melanogaster. The isolates included classical LAB (Lactobacillus fermentum PZ070868, Lactococcus lactis PZ070869 and Weissella confusa PZ070870) as well as non-LAB species such as (Lysinibacillus fusiformis PZ070871 and Priestia flexa PZ070873) which were serendipitously identified, likely reflecting the diverse microbial ecology of foods, while Enterococcus gallinarum (PZ070872), phylogenetically related to LAB, was assessed separately due to safety considerations. The isolates exhibited strain-dependent antibacterial and antifungal activities against foodborne and pathogenic microorganisms, presented as mean ± SD (n = 5, mm), with statistically significant differences among strains (p < 0.05). Notably, cell-free supernatants of P. flexa (32.00 ± 1.58) and L. fermentum (30.40 ± 0.89) showed the highest inhibition against Aspergillus fumigatus, demonstrating antifungal activity with potential implications for reducing mycotoxin risk. Moderate antifungal efficacy against Candida albicans, Fusarium solani, Aspergillus flavus and F. solani was observed with E. gallinarum (23.20 ± 1.30), L. fusiformis (21.60 ± 1.14), P. flexa (17.80 ± 1.30) and W. confusa (20.40 ± 1.14), while W. confusa and L. lactis exhibited more selective inhibition. Antibacterial activity for L. fermentum (17.4 ± 2.3) showed the highest inhibition against Klebsiella pneumoniae, L. lactis (16.0 ± 1.0) against Staphylococcus aureus and E. gallinarum (15.8 ± 1.9) against Proteus mirabilis, with moderate inhibition observed against Pseudomonas aeruginosa, Escherichia coli, Salmonella typhi and Listeria monocytogenes. In vivo validation further supported the biological relevance of these findings, with L. fermentum and W. confusa providing notable host protection. Beyond health functionality, L. fermentum (PZ070868) extended the shelf life of zobo beverage by 17-21 days, demonstrating potential as natural biopreservatives. Collectively, this study integrates probiotic screening, antimicrobial and antifungal activity, in vivo validation and food preservation, the study investigates microbial isolates from fermented foods, including both LAB and non-LAB species, while probiotic assessment primarily focuses on LAB strains, to present a scalable probiotic-postbiotic platform for enhancing food safety, functional food development and potential for mitigating mycotoxin risks.}, }
@article {pmid42218700, year = {2026}, author = {Zhang, Y and Wang, Y and Yang, Y and Mei, H and Liu, X and He, Y and Qin, S and Feng, B}, title = {Gut-Liver Axis Failure in Critical Alcohol-Associated Liver Disease: From ICU Secondary Hits to Microbiome-Targeted Therapy.}, journal = {Mediators of inflammation}, volume = {2026}, number = {1}, pages = {e3968719}, doi = {10.1155/mi/3968719}, pmid = {42218700}, issn = {1466-1861}, support = {82460373//National Natural Science Foundation of China/ ; 82560382//National Natural Science Foundation of China/ ; HZ (2025) 312//Zunyi Science and Technology Bureau, China/ ; HZ (2023) 366//Zunyi Science and Technology Bureau, China/ ; HZ (2025) 172//Zunyi Science and Technology Bureau, China/ ; QZYY-2024-137//Guizhou Administration of Traditional Chinese Medicine/ ; gzwkj2024-310//Guizhou Provincial Health Commission/ ; MTyk2024-55//Kweichow Moutai Hospital Research Project/ ; HZ202411//Traditional Chinese Medicine Hospital of Zunyi Medical and Pharmaceutical College/ ; }, mesh = {Humans ; Intensive Care Units ; *Liver Diseases, Alcoholic/therapy/microbiology/metabolism ; *Liver/metabolism ; *Gastrointestinal Microbiome/physiology ; Animals ; Intestinal Barrier Function ; Fecal Microbiota Transplantation ; Dysbiosis ; }, abstract = {Alcohol-associated liver disease (ALD) can progress to critical illness phenotypes requiring intensive care, including severe alcohol-associated hepatitis, acute decompensation, and alcohol-associated acute-on-chronic liver failure (ACLF). In these patients, short-term outcomes are driven less by the burden of fibrosis alone than by systemic inflammation, immune dysfunction, infection, and multiorgan failure. At the core of this process is gut-liver axis failure, which links alcohol-induced dysbiosis and intestinal barrier disruption to microbial translocation, hepatic innate immune activation, and systemic inflammatory amplification. In the intensive care unit (ICU), secondary hits such as broad-spectrum antibiotics, acid suppression, parenteral nutrition, shock, sedatives or opioids, and mechanical ventilation may further exacerbate these mechanisms and disturb microbial ecology and barrier integrity. Microbiome-targeted therapies (probiotics, postbiotics, and fecal microbiota transplantation) are biologically plausible. However, current evidence is mainly derived from non-ICU or relatively stable ALD populations. Therefore, their use in critically ill patients requires strict safety boundaries, including severe barrier disruption, invasive devices, uncontrolled infections, and profound immune dysfunction. This narrative review synthesizes the pathophysiological continuum from gut barrier failure to systemic inflammation and multiorgan dysfunction in critical ALD, with particular emphasis on ICU-specific secondary hits, safety-aware microbiome modulation, and future phenotype-informed precision strategies.}, }
@article {pmid42220316, year = {2026}, author = {Lv, Y and Fan, Y and Gao, Q and Chen, Q and Hu, Y and Wang, L and Shi, H and Chen, E and Xu, Q and Cai, Y and Fan, Q and Li, L and Du, D and Ren, J and Cheng, SC and Xu, H}, title = {Beta-Glucan modulates monocyte plasticity and differentiation capacity to mitigate DSS-induced colitis.}, journal = {eLife}, volume = {14}, number = {}, pages = {}, doi = {10.7554/eLife.107339}, pmid = {42220316}, issn = {2050-084X}, support = {2022YFA1304000//National Key R&amp;D Program of China/ ; 82300630//National Natural Science Foundation of China/ ; 2023GGB09//Healthcare System Youth Backbone Talent Training Project of Fujian Province/ ; 3502Z20227271//Municipal Natural Science Foundation of Xiamen/ ; 2023XAKJ0101012//Foundation of State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory/ ; 3502Z20204007//Medical and Health Key Project of Xiamen/ ; 32161133020//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *beta-Glucans/pharmacology ; *Colitis/chemically induced/immunology ; *Monocytes/drug effects/immunology ; Dextran Sulfate/toxicity ; *Cell Differentiation/drug effects ; Mice ; Trained Immunity ; Mice, Inbred C57BL ; Adoptive Transfer ; Macrophages/immunology/drug effects ; Immunity, Innate/drug effects ; Disease Models, Animal ; *Cell Plasticity/drug effects ; }, abstract = {Trained immunity involves the reprogramming of innate immune cells after an initial exposure, resulting in heightened inflammatory responses to subsequent stimuli and enhanced bactericidal capacity during infection. However, this pro-inflammatory state could also exacerbate chronic conditions like inflammatory bowel disease (IBD), which is characterized by persistent inflammation and microbial imbalance. It remains unclear how trained immunity influences IBD pathogenesis and whether it can be harnessed therapeutically. In our study, pretreatment with β-glucan reprogrammed bone marrow hematopoietic progenitors and peripheral monocytes, inducing a profound shift in monocyte plasticity and significantly reducing the severity of dextran sulfate sodium (DSS)-induced colitis. Adoptive transfer of bone marrow or peripheral monocytes from β-glucan-trained mice into naive mice conferred robust protection against colitis, demonstrating that this protective effect is transferable. Trained mice also displayed improved clearance of intestinal bacterial infections. Single-cell RNA sequencing revealed an expansion of reparative Cx3cr1[+] macrophages derived from Ly6C[hi] monocytes, correlating with accelerated colonic epithelial regeneration. Collectively, these findings reveal how β-glucan-induced trained immunity modulates monocyte differentiation to ameliorate experimental colitis, highlighting the potential of harnessing trained immunity as a therapeutic strategy to recalibrate innate immune responses and restore gut homeostasis in IBD, shedding light for future clinical applications.}, }
@article {pmid42215097, year = {2026}, author = {Wang, Z and Ding, Y and Cheng, S and Xun, Z and Li, Z and Zhu, M and Zhao, X and Hu, W and Meng, X and Zhang, S and Qiu, L}, title = {Integrating multi-omics to link core and region-specific microbiota to flavor metabolism in medium-temperature Daqu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {238}, number = {}, pages = {119428}, doi = {10.1016/j.foodres.2026.119428}, pmid = {42215097}, issn = {1873-7145}, mesh = {Multiomics ; *Microbiota/physiology ; Fermentation ; *Alcoholic Beverages/microbiology/analysis ; Gas Chromatography-Mass Spectrometry ; Volatile Organic Compounds/analysis/metabolism ; China ; Metabolomics/methods ; *Food Microbiology ; *Taste ; *Flavoring Agents/metabolism ; Metagenomics ; Bacteria/metabolism/classification ; Temperature ; Fungi/metabolism/classification/genetics ; }, abstract = {Medium-temperature Daqu (MTD) is a critical fermentation starter for strong-aroma Baijiu, where its complex microbiota governs flavor development. We combined metagenomics with GC-MS metabolomics to analyze 15 MTD samples from six major producing regions in China, moving from descriptive profiling to mechanistic insight. Although microbial communities exhibited substantial regional variation, a conserved core microbiota emerged, consisting of eight fungal genera, including Aspergillus and Rhizopus, and five bacterial genera such as Bacillus. Beta diversity analysis indicated that producer-specific practices were more influential than geography in structuring these communities. Functional metagenomic profiling showed enriched pathways for carbohydrate, amino acid, and ester metabolism. Volatile metabolite analysis identified 94 compounds, primarily esters, with 12 common to all samples. We constructed multi-omics correlation networks to predict functional linkages, which notably connected genera like Talaromyces and Aspergillus to key flavor esters. Based on these predictions, we isolated Wickerhamomyces anomalus and Bacillus velezensis from Daqu. In vitro validation demonstrated their functional roles: W. anomalus produced ethyl acetate, while co-culturing B. velezensis with Saccharomyces cerevisiae significantly enhanced the yield of ethyl decanoate and ethyl laurate. This work delineates both the core and region-specific metabolic features of MTD and translates multi-omics correlations into confirmed microbial activities. It thereby establishes a targeted framework for identifying flavor-active microorganisms, offering a scientific foundation for quality control and directed bioaugmentation in Daqu production.}, }
@article {pmid42215106, year = {2026}, author = {Liao, S and Hu, Y and Li, X and Guo, Z and Wang, Y and Kong, C and Wang, B and de Vos, P}, title = {White kidney bean episperm polysaccharides improve cognitive impairment in D-galactose-induced aging mice via modulation of oxidative stress, neuroinflammation, and the gut-brain axis.}, journal = {Food research international (Ottawa, Ont.)}, volume = {238}, number = {}, pages = {119439}, doi = {10.1016/j.foodres.2026.119439}, pmid = {42215106}, issn = {1873-7145}, mesh = {Animals ; *Oxidative Stress/drug effects ; Galactose ; *Polysaccharides/pharmacology ; Gastrointestinal Microbiome/drug effects ; *Aging/drug effects ; *Phaseolus/chemistry ; Mice ; *Cognitive Dysfunction/chemically induced/drug therapy ; Male ; *Neuroinflammatory Diseases ; Hippocampus/drug effects ; *Brain/drug effects/metabolism ; Mice, Inbred C57BL ; Disease Models, Animal ; Antioxidants/pharmacology ; Dietary Fiber ; }, abstract = {White kidney bean (Phaseolus vulgaris L.) episperm is an abundant by-product of legume processing that contains a distinct class of non-digestible polysaccharides with high resistance to small intestinal hydrolysis. These features confer unique fermentability and the potential to modulate gut microbial ecology. Given emerging links between age-related cognitive decline, oxidative stress, inflammation, and gut microbiota dysbiosis, whether dietary white kidney bean episperm polysaccharides (WKBEP) could alleviate cognitive impairment in a D-galactose-induced aging mouse model was investigated. WKBEP supplementation significantly improved spatial learning and memory. It also preserved hippocampal neuronal morphology. These effects were associated with enhanced antioxidant capacity, attenuation of neuroinflammatory signaling, and suppression of apoptosis-related markers. In parallel, WKBEP reshaped gut microbial composition and increased the production of short-chain fatty acids. Collectively, these findings highlight WKBEP as a promising functional dietary fiber and provide a mechanistic basis for its potential application in mitigating aging-associated cognitive decline.}, }
@article {pmid42214871, year = {2026}, author = {Sun, Y and Liu, Y and Su, Q and Li, C and Zhao, S and Zhou, J}, title = {From carbonate chemistry to community responses: Thematic evolution in ocean acidification and microbial research- a bibliometric analysis.}, journal = {Marine environmental research}, volume = {220}, number = {}, pages = {108154}, doi = {10.1016/j.marenvres.2026.108154}, pmid = {42214871}, issn = {1879-0291}, abstract = {Ocean acidification (OA) is reshaping marine biogeochemistry and threatens microbial communities that regulate carbon and nutrient cycling. Although existing bibliometric reviews have examined OA in relation to coral reefs, calcifying organisms, and broader marine ecosystems, no study has systematically mapped the specific sub-domain of OA impacts on microbial ecology, a gap that hinders identification of methodological blind spots, collaboration imbalances, and under-explored research frontiers unique to microbial systems. Meanwhile, research progress on OA-driven microbial change remains fragmented and lacks a systematic analysis of the field's evolutionary trajectory and emerging frontiers. This study presents a comprehensive bibliometric analysis of 495 publications retrieved from the Web of Science Core Collection (2005-2025), utilizing CiteSpace to map the knowledge domain of OA impacts on microbial ecology. Temporal analysis reveals three distinct developmental phases: emergence (2005-2010), exponential growth (2011-2021), and recent stabilization (2022-2025). The global collaboration network spans 53 countries, characterized by a triadic leadership structure involving China, the United States, and Germany, with the GEOMAR Helmholtz Centre serving as a central institutional hub. Keyword co-occurrence and burst detection analyses uncover a significant paradigm shift: the research focus has transitioned from foundational carbonate chemistry parameters to complex ecosystem-relevant microbial processes, including community structure, functional genes, and biogeochemical cycling. Notably, "responses" emerges as the most active contemporary research frontier with the strongest recent citation burst, reflecting a consolidated focus on how microbial communities adapt to acidification stress at physiological, community-structural, and functional levels. However, network analysis also reveals structural blind spots: archaea and viral ecology remain conspicuously absent from high-frequency keyword clusters despite their recognized ecological importance, and research contributions from Africa, Southeast Asia, and Small Island Developing States are markedly limited. Based on these findings, we propose four evidence-linked strategic directions centered on multi-omics integration, spatiotemporal expansion through global observatory networks, factorial multi-stressor experimental designs, and bridging molecular processes to ecosystem-scale biogeochemical cycles. This study provides a data-driven roadmap for next-generation research on OA-microbe interactions, essential for predicting ecosystem resilience in a changing ocean.}, }
@article {pmid42095475, year = {2026}, author = {Aguilar, D and Riedel, T and Maaß, S and Trautwein-Schult, A and Neumann-Schaal, M and Kirstein, S and Schober, I and Bunk, B and Acuña-Amador, L and López-Ureña, D and Quesada-Gómez, C and Becher, D and Overmann, J and Rodríguez, C}, title = {Beyond difficile: three novel toxin B-producing Clostridioides species from human patients with diarrhea.}, journal = {Emerging microbes &amp; infections}, volume = {15}, number = {1}, pages = {2671473}, doi = {10.1080/22221751.2026.2671473}, pmid = {42095475}, issn = {2222-1751}, mesh = {Humans ; *Bacterial Toxins/genetics/metabolism ; Animals ; *Diarrhea/microbiology ; *Bacterial Proteins/genetics/metabolism ; Mice ; *Clostridium Infections/microbiology ; *Clostridioides difficile/genetics/isolation &amp; purification/metabolism/classification ; Female ; Phylogeny ; Virulence ; Male ; *Clostridioides/genetics/isolation &amp; purification/classification/metabolism ; }, abstract = {Clostridioides difficile infection (CDI), primarily mediated by toxin B (TcdB), is a leading cause of healthcare-associated and community-acquired diarrhea worldwide. Although this genus exhibits substantial genomic diversity, functional studies have focused mainly on a limited set of isolates, leaving other genomospecies understudied in this regard. Here, we characterized five isolates derived from five distinct patients with suspected CDI cases that tested negative for the tcdC PaLoc marker. Integrated genomic, proteomic, and phenotypic analyses confirm that these strains constitute three novel toxin-producing species and their distinct carbon utilization profiles, exoproteomes, and spore protein repertoires suggest niche specialization within the human gut ecosystem. These species harbour monotoxin PaLoc architectures encoding TcdB7 or TcdB11, located on either chromosomal or extrachromosomal elements, which frequently co-occur with binary toxin loci. Functional assays confirmed secretion of active TcdB, cytotoxicity in mammalian cells, and moderate enterotoxicity in a murine ileal loop model, although virulence was attenuated relative to C. difficile R20291 from Clade 2. Collectively, these findings expand the taxonomy of toxigenic Clostridioides, highlight the dynamic evolution of TcdB-mediated pathogenicity, and emphasize the importance of refining diagnostic workflows and surveillance strategies to address emerging diarrheal diseases. The three novel species were designated as Clostridioides cryptodifficilis sp. nov., Clostridioides divergens sp. nov., and Clostridioides subdifficilis sp. nov.}, }
@article {pmid42201886, year = {2026}, author = {Wonnemann, M and Lipowicz, B and Duysburgh, C and Rotsaert, C and Verstrepen, L and Marzorati, M and Langhorst, J}, title = {Repeated dosing of myrrh, chamomile extract, and coffee charcoal reveals potential health-beneficial effects in patients with irritable bowel syndrome in the M-SHIME simulator.}, journal = {PloS one}, volume = {21}, number = {5}, pages = {e0348791}, pmid = {42201886}, issn = {1932-6203}, mesh = {Humans ; *Charcoal/administration &amp; dosage/pharmacology/therapeutic use ; *Plant Extracts/administration &amp; dosage/pharmacology/therapeutic use ; *Irritable Bowel Syndrome/drug therapy/microbiology ; Caco-2 Cells ; *Chamomile/chemistry ; *Coffee/chemistry ; Colon/microbiology/drug effects ; Female ; Male ; Intestinal Barrier Function ; Cytokines/metabolism ; Gastrointestinal Microbiome/drug effects ; }, abstract = {OBJECTIVE: To define the potential functional roles of a herbal preparation of myrrh, chamomile extract, and coffee charcoal in patients suffering from diarrhea dominant irritable bowel syndrome (IBS-D).<br><br>METHODS: The study utilized the Mucosal Simulator of the Human Intestinal Microbial Environment (M-SHIME&#xae;) with proximal (PC) and distal colon (DC) compartments and fecal samples from four IBS-D donors. Eight-day (d) repeated dosing with the herbal product (6 tablets/day) was initiated compared to a negative control. Changes in microbial metabolism and community composition were assessed, and colonic ferments were evaluated for their effects on intestinal barrier permeability and cytokine production in a Caco-2/THP-1 co-culture model.<br><br>RESULTS: Product treatment significantly increased gas pressure versus negative control, indicating microbial fermentative activity. Product supplementation significantly increased proximal acetate (d3, d5), propionate (d3), and butyrate (d5, d8) levels (p&#x2009;<&#x2009;0.05 for all), while no significant changes were observed distally. Ammonium levels were significantly elevated following product supplementation in PC (d3, d5, d8; p&#x2009;<&#x2009;0.05) and DC (d8; p&#x2009;<&#x2009;0.01), though remained within physiological range. Repeated dosing enriched members of Bifidobacteriaceae, Bacteroidota, Lachnospiraceae, and Butyricicoccus versus negative control. Treated colonic ferments had a protective effect on intestinal membrane integrity (DC; p&#x2009;<&#x2009;0.001) and positive immunomodulatory effects (increased IL-10, PC and DC [both p&#x2009;<&#x2009;0.0001], and IL-6, PC [p&#x2009;<&#x2009;0.001] and DC [p&#x2009;<&#x2009;0.01]) in Caco-2/THP-1 co-cultures.<br><br>CONCLUSIONS: Treatment with a herbal preparation of myrrh, chamomile extract, and coffee charcoal showed a potential beneficial effect on the microbiota of patients with IBS-D in vitro, suggesting further exploration of its efficacy in IBS-D and other chronic gastrointestinal disorders.}, }
@article {pmid42203413, year = {2026}, author = {Baker, JM and Dickson, RP}, title = {The Role of the Respiratory Microbiome in Pneumonia.}, journal = {Clinics in chest medicine}, volume = {47}, number = {2}, pages = {199-213}, doi = {10.1016/j.ccm.2025.12.004}, pmid = {42203413}, issn = {1557-8216}, mesh = {Humans ; *Microbiota ; COVID-19 ; *Lung/microbiology ; SARS-CoV-2 ; *Pneumonia, Viral/microbiology ; Pandemics ; *Pneumonia/microbiology ; Betacoronavirus ; }, abstract = {The lung microbiome field has matured into a promising area of translational research. Emerging evidence from the past decade, including studies of COVID pneumonia, indicates a role for respiratory microbiota in pneumonia pathogenesis. Here, the authors discuss areas of investigation that will be essential to refine an ecology-based conceptual framework of pneumonia pathogenesis, which will ultimately guide the development of microbiome-targeted diagnostics and therapeutics for pneumonia management.}, }
@article {pmid42203690, year = {2026}, author = {Fullam, A and Prasoodanan Pk, V and Kuhn, M and Bork, P and Schmidt, TSB}, title = {microntology: a lightweight, data-driven controlled vocabulary to describe Earth's microbial habitats.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btag343}, pmid = {42203690}, issn = {1367-4811}, abstract = {MOTIVATION: Data-enabled studies of microbial ecology and evolution depend on high-quality descriptions of microbial habitats, based on curated and consolidated vocabularies.<br><br>RESULTS: We introduce microntology v1.0, a pragmatic controlled vocabulary of 148 terms to describe microbial habitats and lifestyles, and provide manually curated microntology annotations for >300k metagenomic samples from public repositories.<br><br>AVAILABILITY: microntology controlled vocabulary terms and term hierarchies (doi: 10.5281/zenodo.19730167), and curated annotations for 305,626 metagenomic samples (doi: 10.5281/zenodo.18164252) are available via Zenodo and spire.embl.de/downloads. Underlying code is available via github.com/grp-schmidt/microntology and Zenodo (doi: 10.5281/zenodo.20323497). User feedback, suggestions and bug reports are welcome at github.com/grp-schmidt/microntology/issues.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid42207174, year = {2026}, author = {Liao, Y and Zhang, Q and Zheng, J and Zhang, J and Dai, T and Zhu, F and Carrión, VJ and Delgado-Baquerizo, M and Sonne, C and Cao, F and Li, X}, title = {CHD-18g-modulated Pseudomonas taxa support poplar salt tolerance.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag138}, pmid = {42207174}, issn = {1751-7370}, abstract = {Against the background of global climate change, soil salinization has emerged as a major abiotic stressor constraining agroforestry productivity worldwide. Root-recruited microbes enhance plant stress resilience, and host-microbe interactions depend on plant root metabolism. Stress-tolerant plant genotypes exhibit a marked capacity to enrich beneficial root-associated microbes through specialized metabolic responses, thereby facilitating phenotypic plasticity. However, the molecular mechanisms underlying these plant-microbe interactions remain unclear. In this study, we compared salt tolerance among three poplar varieties under aseptic and non-aseptic conditions, and analyzed their rhizosphere bacterial community responses to salt stress. We found that microbial inoculation modulated poplar salt tolerance, and poplar shaped rhizosphere bacterial communities in a genotype-dependent manner. Transcriptome sequencing and targeted metabolomic analysis indicated that salt-tolerant poplar plants preferentially activate the phenylpropanoid biosynthesis pathway, accompanied by the enhanced root secretion of benzoic acid (BA) and salicylic acid (SA) and up-regulation of CHD-18g encoding cinnamoyl-CoA hydratase/dehydrogenase. Overexpression of CHD-18g increased rhizosphere Pseudomonas abundance by enhancing BA and SA biosynthesis. Binary interaction assays further showed that the BA-induced Pseudomonas taxa mitigated salt stress and promoted poplar growth under salt stress. Our findings propose a framework linking host gene expression, root metabolism, and key microbial taxa in conferring salt tolerance. This work uncovers a metabolic signaling mechanism by which trees shape their root microbiome to enhance stress adaptation, offering actionable genetic and ecological strategies for improving tree resilience in sustainable agroforestry systems.}, }
@article {pmid42207421, year = {2026}, author = {Wang, X and Shaukat, A and Al-Rasheed, M and Ujjan, NA and Buzdar, JA and Yuan, T}, title = {Paraprobiotics in Modern Broiler Production: Stability, Safety, and Multifunctional Benefits - a Comprehensive Review.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {42207421}, issn = {1867-1314}, abstract = {The growing restrictions on in-feed antibiotics and the global rise of antimicrobial resistance have intensified the demand for safe and sustainable alternatives to support animal health and productivity. Paraprobiotics, defined as non-viable or inactivated bacterial cells, have recently emerged as a promising class of functional bioactives capable of conferring health benefits without the risks associated with live probiotics. Unlike conventional probiotics, paraprobiotics mediate their effects through intact cell structures and microbial metabolites that engage host pattern-recognition receptors, thereby modulating both innate and adaptive immune responses. This review critically examines the antimicrobial efficacy of paraprobiotics in poultry, emphasizing their mechanistic role in maintaining gut barrier integrity, regulating microbial ecology, and mitigating inflammation-induced oxidative stress. Evidence indicates that paraprobiotics suppress pathogenic colonization enhance epithelial function, stimulating antimicrobial peptide production, and improve nutrient utilization and growth performance. Moreover, their stability during feed processing, prolonged shelf-life, and minimal risk of horizontal gene transfer further enhance their suitability for large-scale, intensive production systems. Additionally, emerging inactivation technologies, optimized dosing strategies, and synergistic applications with prebiotics and phytobiotics offer avenues to maximize their functional potential. Collectively, paraprobiotics exemplify a paradigm shift in antimicrobial nutrition providing "dead cells with living functions" that combine safety, efficacy, and sustainability. Their integration into antibiotic-free poultry system hold significant promise for enhancing disease resilience, productive performance and overall sustainability of modern poultry production.}, }
@article {pmid42208386, year = {2026}, author = {Varghese, P and Kumar, K and Yun, K}, title = {Triclosan as a selective pressure on nitrifying microbial guilds: functional, genetic, and biogeochemical perspectives.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {297}, number = {}, pages = {107877}, doi = {10.1016/j.aquatox.2026.107877}, pmid = {42208386}, issn = {1879-1514}, abstract = {Triclosan (TCS), a widely used antimicrobial biocide, has raised significant concerns due to its environmental persistence and toxicity to aquatic organisms. TCS enters aquatic environments primarily through wastewater effluents, where it can disrupt critical steps of biogeochemical processes, such as nitrification, which is essential for maintaining nutrient balance in ecosystems. TCS inhibits ammonia monooxygenase (AMO) and nitrite oxidoreductase (NXR) activity and downregulates key nitrification gene expression including amoA and nxrB, thereby impairing nitrogen transformation pathways in aquatic ecosystems, and its effects are modulated by co-pollutants such as heavy metals and microplastics. This review outlines current evidence on the impact of TCS on nitrifying bacteria and associated shifts in microbial community structure integrating omics-based insights that reveal nitrification gene abundance and co-enrichment of TCS degraders and antibiotic resistance determinants. It emphasises the need for integrated research on the long-term effects of TCS on biogeochemical cycling and nitrification, and highlights implications for regulation and advanced green chemistry based wastewater management.}, }
@article {pmid42210085, year = {2026}, author = {Mermans, F and Poelman, B and Saghi, M and Teughels, W and Boon, N}, title = {Interindividual differences in acidogenic potential of the salivary microbiome after mouthwash exposure.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05207-0}, pmid = {42210085}, issn = {1471-2180}, support = {G0B2719N//Fonds Wetenschappelijk Onderzoek/ ; G0B2719N//Fonds Wetenschappelijk Onderzoek/ ; G0B2719N//Fonds Wetenschappelijk Onderzoek/ ; }, abstract = {BACKGROUND: Fluoride mouthwashes are commonly used for prevention of dental caries. The most common forms of fluoride are stannous fluoride (SnF2), amine fluoride (AmF) and sodium fluoride (NaF), each with differing activities against oral bacteria. Since the microbiome has been linked to interindividual differences in responses to treatment, the phenotype of the microbiome may provide information on potential treatment responses. Flow cytometry successfully tracks microbial phenotypic heterogeneity and may prove useful for capturing interindividual treatment responses.<br><br>METHODS: We compared the effect of fluoride-containing mouthwashes, Elmex Anti Caries (AmF/NaF), Listerine Anti Caries (NaF) and Meridol (AmF/SnF2) on the salivary microbiome in vitro. We determined the effect on the microbial community structure using 16&#xa0;S rRNA gene amplicon sequencing, assessed the acidogenic potential by measuring organic acids after incubation, and constructed flow cytometric fingerprints of the microbial community to evaluate if it could be used to capture the response to treatment and to assess if it has potential for precision medicine.<br><br>RESULTS: We observed mouthwash- and donor-dependent changes in the salivary microbiome composition and acidogenic potential. Meridol affected more bacterial taxa and showed the strongest reduction in organic acids, followed by Elmex. The response to treatment could be captured in the flow cytometric fingerprint of the initial intact salivary microbiota and a random forest classifier predicting the optimal mouthwash for each donor was successfully trained (MCC&#x2009;=&#x2009;0.95).<br><br>CONCLUSIONS: Treatment with fluoride mouthwashes induces a shift in the salivary microbiome in vitro and alter its potential to produce organic acids, contributing to the prevention of dental caries. Moreover, flow cytometry shows promise for tailoring treatments to patients.}, }
@article {pmid42210522, year = {2026}, author = {Kralova, S and Spacek, P and Gafriller, J and Bezdicek, M and Medvedcova, V and Séneca, J and Osvatic, J and Grienke, U and Rattei, T and Sekurova, ON and Zotchev, SB and Zehl, M and Loy, A}, title = {Kineochelins-A New Group of Siderophores From an Antarctic Bacterium.}, journal = {Microbial biotechnology}, volume = {19}, number = {6}, pages = {e70386}, doi = {10.1111/1751-7915.70386}, pmid = {42210522}, issn = {1751-7915}, support = {No.101020356//Horizon 2020 Framework Programme/ ; MetaBac//Universit&#xe4;t Wien/ ; VAN2025//Ministry of Education, Youth and Sports of the CR/ ; MUNI/SC/1946/2024//Masarykova Univerzita/ ; 10.55776/COE7//Austrian Science Fund/ ; FNBr,65269705//Ministerstvo Zdravotnictv&#xed; Cesk&#xe9; Republiky/ ; VEGA 1/0498/23//Vedeck&#xe1; grantov&#xe1; agent&#xfa;ra Ministerstva &#x161;kolstva, v&#xfd;skumu, v&#xfd;voja a ml&#xe1;de&#x17e;e Slovenskej republiky a Slovenskej akad&#xe9;mie vied/ ; }, mesh = {*Siderophores/chemistry/pharmacology/isolation &amp; purification/metabolism/biosynthesis/genetics ; Antarctic Regions ; Multigene Family ; *Actinobacteria/genetics/metabolism/isolation &amp; purification/chemistry/classification ; Peptide Synthases/genetics ; Iron/metabolism ; Phylogeny ; Genome, Bacterial ; Biosynthetic Pathways/genetics ; }, abstract = {The global rise of antimicrobial resistance has intensified the search for new microbial metabolites from underexplored environments and taxonomic groups. Extreme and geographically isolated habitats such as Antarctic terrestrial ecosystems represent promising reservoirs of biosynthetic diversity, particularly among rare and difficult-to-cultivate actinomycetes that may produce chemically diverse metabolites with potential biotechnological applications. Here, we report the characterization of kineochelins, a previously undescribed group of siderophores produced by the Antarctic isolate Actinokineospora sp. UV203, representing a difficult-to-cultivate actinomycete lineage. Structural elucidation revealed a set of closely related congeners with a mixed-ligand architecture consistent with metal-chelating activity. Genome mining combined with transcriptomic analysis identified a dedicated nonribosomal peptide synthetase-encoding biosynthetic gene cluster responsible for kineochelin production. Comparative genomic analyses indicated that, although kineochelin biosynthetic genes share limited similarity with known mixed-ligand siderophores, their gene content and organization differ substantially, suggesting a distinct biosynthetic lineage. Functional characterization of the culture supernatant and an enriched pre-purified kineochelin fraction demonstrated strong and selective iron chelation, with high affinity for ferric and ferrous iron. Crude culture extracts inhibited the growth of bacterial strains isolated from the same Antarctic environment, indicating that kineochelins may contribute to iron-mediated microbial competition. In addition, kineochelin-enriched pre-purified fractions showed moderate selective inhibitory activity against the opportunistic yeast pathogen Nakaseomyces glabratus and a clinical isolate of Saccharomyces cerevisiae associated with invasive infection. These findings expand the chemical and biosynthetic diversity known within the genus Actinokineospora and demonstrate that Antarctic rare actinomycetes represent valuable sources of previously unexplored natural products. The discovery of kineochelins highlights the potential of genome-guided exploration of polar microorganisms for identifying bioactive metabolites with relevance for antimicrobial discovery and biotechnology.}, }
@article {pmid42211837, year = {2026}, author = {Singh, AP and Bulzu, PA and Lanta, V and Chaloupský, P and Salcher, MM and Shabarova, T}, title = {From soils to lake: interplay between hydrology and local environmental settings drives species selection across a karst landscape.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1813326}, pmid = {42211837}, issn = {1664-302X}, abstract = {Terrestrial and aquatic ecosystems are interconnected through runoff and hydrological networks that facilitate the transfer of microbial communities across landscapes. While microbial transport along surface waters is well documented, the role of subsurface hydrological paths in shaping microbial community composition remains poorly understood, particularly in complex karst systems. Here, we studied bacterial communities under stable hydrological conditions across a peri-alpine karst landscape, where mixed limestone-sandstone catchments drain via both surface and subsurface hydrological networks into Lake Thun (Switzerland). We profiled 16S rRNA gene sequences from soils, sediments, surface and subsurface waters, and distinct lake strata. All environments except the lake exhibited high microbial diversity. We observed a clear transitional gradient in bacterial communities along the terrestrial-aquatic interface, with environment type explaining 19% of total variation. Core microbiome analyses revealed both environment-specific and shared taxa, with the strongest overlap between surface and subsurface hydrological networks (63.8%-84.6% shared core taxa). Co-occurrence network analysis identified six major modules. Three of them represented distinct metabolic assemblages tightly associated with specific environment types: peat soils, lake strata, and the subsurface network, respectively. One recurrent module spanned multiple environments and was linked to redox-driven processes, including the oxidation of nitrogen compounds, metals, and methane. Two additional modules comprised aquatic copiotrophs associated with streams and soil heterotrophs prone to export and short-term persistence within the hydrological network. Overall, our results demonstrate that specific environmental settings and hydrological connectivity jointly contribute to selection of microbial species within the karst landscape.}, }
@article {pmid42211842, year = {2026}, author = {Guo, C and Long, X and Li, X and Wang, L}, title = {Identification and isolation of spoilage microbes in conventional dark leafy green vegetable juice during cold storage.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1831321}, pmid = {42211842}, issn = {1664-302X}, abstract = {Chard, collard greens, and kale juices as representative dark leafy green vegetable juices (DLGVJs) have gained increasing attention due to their rich nutritional profiles and health-promoting properties. Conventional dark leafy green vegetables (DLGVs) represent the majority of the DLGV market; however, the microbial changes in conventional DLGVJs during refrigerated storage remain poorly understood. This study aimed to characterize the microbial profiles of fresh and spoiled conventional DLGVJs using both culture-dependent and culture-independent methods, alongside monitoring physicochemical changes (pH and color) over 21 days of refrigerated storage. Results showed a general decrease in pH and a shift toward more saturated color in all DLGVJs. Initial aerobic plate counts (APC) in chard, collard greens, and kale juices were 7.71 ± 0.03, 7.57 ± 0.14, and 7.61 ± 0.09 Log CFU/mL, respectively, while fungal populations were 5.85 ± 0.03, 6.01 ± 0.15, and 6.15 ± 0.03 Log CFU/mL. APC showed an overall decrease while fungal populations exhibited an initial increase followed by a decline during refrigerated storage. High-throughput sequencing revealed Pseudomonas, Leuconostoc, and Periweissella as core spoilage-associated bacterial genera, while Sporobolomyces, Alternaria, and Symmetrospora were predominant fungal genera in spoiled conventional DLGVJs. Although microbial compositions showed similarities between conventional and organic DLGVJs, distinct microbial communities were observed, with some taxa uniquely associated with a specific cropping system. The dominant lactic acid bacteria isolated from DLGVJs were identified as Enterococcus faecium and Leuconostoc mesenteroides. These findings advance our understanding of microbial ecology in DLGVJs and provide a scientific basis for developing targeted interventions to ensure microbial quality and safety, supporting the growth of the DLGVJ market.}, }
@article {pmid42212641, year = {2026}, author = {Mueller, EP and Duong, R and Eiler, J and Hess, M and Sessions, A}, title = {Shifts in ruminant fermentation during inhibition of methanogenesis are reflected in the isotope compositions of volatile fatty acids.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0048926}, doi = {10.1128/aem.00489-26}, pmid = {42212641}, issn = {1098-5336}, abstract = {Ruminant animals are a major source of the potent greenhouse gas methane, but they are also a tractable target for climate solutions. Several strategies have been developed to lower methane emissions from ruminants, including feed additives that inhibit methanogenic archaea. Sustainable solutions must eliminate methane emissions without hampering the microbial fermentation of plant material, which the animal host relies on for nutrients. However, current tools cannot directly quantify or characterize the metabolic pathways of in vivo ruminant fermentation. To fill this gap, we developed an electrospray (ESI) Orbitrap mass spectrometry technique to measure the stable isotope ratios ([Formula: see text]C/[Formula: see text]C and [Formula: see text]H/[Formula: see text]H) of volatile fatty acids (VFAs) at their natural isotopic abundances directly from rumen fluid. We tested this technique on in vitro incubations of rumen fluid fed three different substrates with and without the methanogen-inhibiting additive Asparagopsis taxiformis. We found that the isotope composition of VFAs changed and reflected a remodeling of microbial fermentation pathways. Specifically, acetate's [Formula: see text] value increased when methanogens were inhibited, suggesting a lower relative rate of acetate synthesis and a lack of acetogenic activity. Furthermore, the [Formula: see text] value of propionate decreased, which may indicate a change in the balance between the two pathways of propionate synthesis toward the less energetic acrylate pathway. Both signals were consistent across feed types. Taken together, our results provide evidence that under the conditions of our study, fermentative metabolism is remodeled during methanogenesis inhibition. More broadly, this study demonstrates the utility of ESI-Orbitrap-based isotopic analysis for studying fermentation pathways in the rumen.IMPORTANCESlowing methane production from ruminant animals (e.g., cows) is a major target for the mitigation of anthropogenic climate change. While strategies that inhibit microorganisms producing methane have been successful, they have cascading impacts on the microbial ecology of the rumen, possibly affecting animal health and productivity. Of particular importance is microbial fermentation, which generates easily digested volatile fatty acids (VFAs) from hard-to-breakdown plant matter. To better understand how fermentation responds to methane mitigation strategies, we measured the isotope composition of VFAs in cow rumen. Our results indicate that fermentation changes pathways when methane production is inhibited under our conditions. As methane mitigation strategies are developed in the coming decade, isotopic analysis of VFAs may be a useful and accessible contribution to our understanding of rumen microbiology.}, }
@article {pmid42212794, year = {2026}, author = {Fukui-Silva, L and de Moraes, J}, title = {Climate change and the emerging ecology of helminthiases: a One Health perspective integrating microbial and environmental drivers.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0026526}, doi = {10.1128/msphere.00265-26}, pmid = {42212794}, issn = {2379-5042}, abstract = {Helminthiases affect more than one billion people worldwide and remain tightly linked to environmental conditions, yet they are often underrepresented in discussions of climate-sensitive infectious diseases. As global temperatures rise and ecosystems shift, the life cycles, geographic distributions, and transmission dynamics of parasitic helminths are being reshaped in complex and sometimes contrasting ways. Here, we argue that helminthiases should be understood as ecological outcomes emerging from interactions among climatic drivers, environmental conditions, microbial communities, and host populations, rather than as the result of isolated environmental shifts. Drawing on examples from schistosomiasis, soil-transmitted helminthiases, and angiostrongyliasis, as well as climate-sensitive helminths affecting animal populations, we examine how climate change can alter parasite development, host ecology, and environmental persistence. We further highlight the role of microbial communities as mediators of transmission. Finally, we discuss how integrating environmental monitoring, microbiological data, and predictive modeling within a One Health framework can support more adaptive and anticipatory surveillance and control strategies.}, }
@article {pmid42213731, year = {2026}, author = {Mullet, JI and Zhang, L and Pruden, A and Brown, CL}, title = {Phage-plasmid-like elements are found throughout diverse environments and encode niche-specific functional traits.}, journal = {PloS one}, volume = {21}, number = {5}, pages = {e0350027}, doi = {10.1371/journal.pone.0350027}, pmid = {42213731}, issn = {1932-6203}, mesh = {*Plasmids/genetics ; *Bacteriophages/genetics ; Humans ; Animals ; Genome, Viral ; Environment ; }, abstract = {Phage-plasmids are unique mobile genetic elements that function as plasmids and temperate phages. While it has been observed that such elements often encode antibiotic resistance genes and defense system genes, little else is known about other functional traits they encode. Further, no study to date has documented their environmental distribution and prevalence. Here, we performed genome sequence mining of public databases of phages and plasmids utilizing a random forest classifier to identify phage-plasmids. We recovered 5,712 unique phage-plasmid-like genomes from a remarkable array of disparate environments, including human, animal, plant, fungi, soil, sediment, freshwater, wastewater, and saltwater environments. The resulting genomes were used in a comparative sequence analysis, revealing functional traits/accessory genes associated with specific environments. Host-associated elements contained the most defense systems (including CRISPR and anti-CRISPR systems) as well as antibiotic resistance genes, while other environments, such as freshwater and saltwater systems, tended to encode components of various biosynthetic pathways. Interestingly, we identified genes encoding for certain functional traits, including anti-CRISPR systems and specific antibiotic resistance genes, that were enriched in phage-plasmid-like elements relative to both plasmids and phages. Our results highlight that phage-plasmid-like elements are found across a wide-array of environments and likely play a role in shaping microbial ecology in a multitude of niches.}, }
@article {pmid42213775, year = {2026}, author = {Yuan, K and Lian, Y and Huang, P and Cao, F and Yang, X and Lu, Y and Ding, X and Wang, L and Yang, H and Ye, Z and Chen, Q and Fu, J and Yuan, S and Fan, Y and Cai, S and Du, D and Ren, J and Zhang, X and Xu, H}, title = {Integrative analysis reveals intra-tumoral microbial enterotypes shape host transcriptomes in colorectal cancer.}, journal = {Cell reports}, volume = {45}, number = {6}, pages = {117413}, doi = {10.1016/j.celrep.2026.117413}, pmid = {42213775}, issn = {2211-1247}, abstract = {The intratumor microbiome and host gene regulation are key contributors to colorectal cancer (CRC), yet their interactions remain unclear. To investigate the interplay between intra-tumoral microbe and host gene, we analyzed paired tumor and normal tissues from 31 patients. Integrated multi-omics analysis identified 4,197 significant bacteria-gene correlation pairs involving 30 bacterial taxa. Patient stratification based on these associations reveals two distinct molecular subgroups characterized by unique microbial signatures and immune profiles. In a mouse model, Bacteroides fragilis alters the tumor immune microenvironment, promoting myeloid-derived suppressor cell (MDSC)-mediated CXCL signaling that impaired CD8[+] T cell activation and promotes exhaustion. B. fragilis directly promotes CXCL2 expression and ROS production in MDSCs, which subsequently drives CD8[+] T cell exhaustion and immune evasion. These findings reveal that intra-tumoral microbiota influence host transcriptomes and immune modulation in CRC, supporting microbiome-based molecular stratification and offering insights into potential microbiota-targeted therapies.}, }
@article {pmid42213881, year = {2026}, author = {Liu, Y and Huang, Q and Xu, Y and Qin, X and Sun, Y and Liang, X and Wang, L}, title = {Effects and mechanisms of different organic manure on minimizing cadmium concentrations in rice grains.}, journal = {International journal of phytoremediation}, volume = {}, number = {}, pages = {1-10}, doi = {10.1080/15226514.2026.2677688}, pmid = {42213881}, issn = {1549-7879}, abstract = {Cadmium (Cd) contamination in agricultural soils represents a global issue for soil health and food safety. This study aimed to investigate the effects of organic fertilizers from different sources on Cd uptake and accumulation in rice plants, as well as the biochemical properties of Cd-contaminated soil. We performed high-throughput sequencing of 16S ribosomal RNA (16S rRNA) gene amplicons to characterize soil bacterial communities. The zeta potential of the soil colloids became more negative following the application of GM and EM. In terms of Cd fractionation, chicken manure (CM) amendment reduced the residual fraction of soil Cd, while GM and EM exerted an opposing effect. FT-IR spectroscopy demonstrated that organic fertilizers derived from different sources possessed distinct chemical structural features. At the phylum level, the relative abundance of soil bacteria was largely comparable among treatments receiving different manure application rates. Taxonomic analysis further revealed that Proteobacteria, Actinobacteria, Gemmatimonadetes, Bacteroidetes, and Acidobacteria were the five dominant bacterial phyla in the Cd-contaminated soil. Furthermore, GM and EM applications mitigated Cd uptake by rice plants at all growth stages and across all examined Cd concentration gradients. By contrast, excessive CM amendment amplified the risk of heavy metal bioaccumulation in rice tissues.}, }
@article {pmid42201393, year = {2026}, author = {Jeong, SY and Lee, JW and Lee, CW and Kim, TG}, title = {Unraveling the Independent Effects of Species Richness and Composition on Microbial Biofilm Growth.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02789-0}, pmid = {42201393}, issn = {1432-184X}, support = {RS-2025-25400857//Ministry of Education/ ; }, abstract = {Species richness is often positively linked to ecosystem functioning. However, conventional approaches that manipulate richness frequently confound the richness effect with those of species composition. In this study, we quantitatively disentangled the independent effects of species richness and composition on biofilm productivity as a measure of ecosystem functioning. We constructed 300 independent richness gradients, each comprising 3-20 species, from a pool of 24 bacterial isolates spanning six taxonomic classes (Actinomycetia, Alphaproteobacteria, Bacilli, Betaproteobacteria, Gammaproteobacteria, and Sphingobacteriia). Our results revealed diverse richness-biofilm relationship forms, predominantly positive (68%), but also hump-shaped (16%), U-shaped (6%), null (6%), and negative (4%). When assessed individually, richness accounted for an average of 53.9% of the variation in biofilm growth, surpassing two measures of compositional variation-species-inherent ability (SIA) and species-dependent ability (SDA)-based on species' biofilm-forming potential, which explained 9.6% and 14.4%, respectively. Collectively, richness, SIA, and SDA explained 73.4% of the variation. Notably, biofilm growth exceeded expectations in the mid-richness range (10-15 species). When richness and composition were assessed collectively across entire assemblages, richness explained 24.2% of the variation in biofilm growth, while SIA and SDA explained 12.7% and 28.7%, respectively. In contrast, species combination, assuming equal potential for all species, had only a marginal effect on biofilm growth. Our results demonstrate that species richness is a key, independent driver of biofilm growth, and that its effects are substantially underestimated when not properly separated from composition.}, }
@article {pmid42201411, year = {2026}, author = {Marzanni, A and Landolfi, M and Tiziani, R and Bombardelli, S and Celi, D and Pittertschatscher, M and Buttarelli, A and Bruni, S and Pecchioni, E and Perito, B and Cnudde, V and Cappitelli, F and Mimmo, T and Villa, F and Borruso, L}, title = {Rosy Discolouration in an Alpine Chapel: Beyond Salt Dependence.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02795-2}, pmid = {42201411}, issn = {1432-184X}, abstract = {Stone heritage is central to cultural identity, yet alpine monuments remain understudied and vulnerable to deterioration. In mountain environments, moisture and temperature fluctuations promote salt crystallisation in porous geomaterials, frequently associated with rosy discolouration attributed to pink biofilms, a phenomenon still poorly explored at higher elevations. Here, we investigated rosy discolouration at about 1000 m altitude on the walls of St. Cyprian Chapel (South Tyrol) using metabarcoding and chemical analyses. We compared two cases of rosy discolouration: one on the north wall, where salt efflorescence is present, and one on the south wall, where it is absent. The aim was to characterise how salt efflorescence modulates rosy discolouration by comparing the two walls and linking substrate chemistry and mineralogy to biofilm pigments, structure, and microbial community composition. Despite similar mineralogy, the north wall exhibited distinct surface chemistry consistent with salt efflorescence. Biofilm biomass was comparable between walls, and no photosynthetic organisms were detected in either biofilm, yet microbial communities differed markedly. The south wall hosted carotenoid-producing biomarkers, including Rubrobacter and Pontibacter, although Raman did not detect carotenoid signals, indicating low pigment expression. In contrast, the north wall showed stronger discolouration and clear detection of bacterioruberin. Notably, the north-wall biomarker Chryseobacterium may also contribute to the rosy discolouration through flexirubin-type pigments. Overall, salt efflorescence is not required for pink biofilm establishment, but salt-rich microhabitats appear to enhance pigment production. This study provides new insights into the drivers of rosy discolouration and contributes to the still-limited research on alpine cultural heritage.}, }
@article {pmid41826827, year = {2026}, author = {Duduk, B and Galic, I and Stanojević, N and Stankovic, N and Rekanović, E}, title = {Microbial diversity of plant pathogens and insect endosymbionts in Reptalus artemisiae.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41826827}, issn = {1471-2180}, support = {451-03-136/2025-03/200214//Ministarstvo Prosvete, Nauke i Tehnolo&#x161;kog Razvoja/ ; 451-03-136/2025-03/200042//Ministarstvo Prosvete, Nauke i Tehnolo&#x161;kog Razvoja/ ; }, abstract = {BACKGROUND: Phloem-sap-feeding planthopper Reptalus artemisiae is an emerging vector of rubbery taproot disease (RTD) and syndrome basses richesses (SBR) in sugar beet, diseases associated with 'Candidatus Phytoplasma solani' and 'Candidatus Arsenophonus phytopathogenicus', respectively. Despite studies on related cixiids, the microbiome of R. artemisiae remains uncharacterized. Using a PCR-free metagenomic long-read shotgun sequencing approach, this study investigates the bacterial diversity associated with R. artemisiae, and provides genomic insight into two plant pathogens 'Ca. P. solani' and 'Ca. A. phytopathogenicus'.<br><br>RESULTS: Taxonomic assignment revealed six prokaryotic taxa in R. artemisiae: two plant pathogens ('Ca. P. solani' and 'Ca. A. phytopathogenicus') and four insect endosymbionts &#x2013; three primary endosymbionts ('Candidatus Vidania', 'Candidatus Purcelliella', and 'Candidatus Karelsulcia') and a secondary endosymbiont (Wolbachia). Community profiles showed a consistent presence of all four endosymbionts across five evaluated R. artemisiae individuals. Phylogenetic analyses of 16S rRNA gene sequences of primary endosymbionts confirmed strong congruence with the cytochrome oxidase subunit I phylogeny of the insect host, indicative of long coevolution and vertical transmission. In contrast, plant pathogen presence in R. artemisiae varied, with 'Ca. P. solani' and 'Ca. A. phytopathogenicus' each detected in three individuals. Genome assembly yielded a complete 774&#xa0;kb circular chromosome for 'Ca. P. solani' with streamlined metabolism featuring limited biosynthetic pathways, but a full arsenal of genes related to host&#x2013;pathogen interactions and pathogenicity typical for this biotrophs. The draft genome of 'Ca. A. phytopathogenicus' comprising 18 scaffolds totalling 3.11&#xa0;Mb and two plasmids shows a self-sufficient metabolism with several missing metabolic modules and presence of genomic islands, virulence factors, and a dynamic mobilome indicating a bacterium in transition that is reorganizing its genetic material, possibly in response to host interactions.<br><br>CONCLUSION: These findings represent the first in-depth characterization of R. artemisiae microbiome, highlighting a stable endosymbiont consortium and variable pathogen presence that emphasize ecological complexity in vector-pathogen-endosymbiont interactions. The assembled genomes enhance the understanding of microbial ecology, pathogen adaptation and transmission, offering resources for comparative genomics and potential applications in disease management strategies.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04915-x.}, }
@article {pmid42188046, year = {2026}, author = {Tang, G and Guo, L and Liu, Z and Quan, Y}, title = {Hypothesis of the Causal Mechanisms Between Gut Microbiota and Neurodegenerative Diseases: An Elucidation from Evolutionary Perspective and Metabolic Consideration.}, journal = {Metabolites}, volume = {16}, number = {5}, pages = {}, pmid = {42188046}, issn = {2218-1989}, support = {Grant 32570777 and Grant 32300545//National Natural Science Foundation of China/ ; Grant 2662025XXPY004//Fundamental Research Funds for the Central Universities/ ; }, abstract = {Growing evidence links gut microbiota dysbiosis to neurodegenerative diseases (NDs) such as Alzheimer's disease and Parkinson's disease, yet the field remains dominated by correlational observations rather than experimentally validated causal mechanisms. In this hypothesis-generating Perspective, we propose that causal inference in microbiota-associated neurodegeneration may be strengthened by combining two complementary lenses: evolutionary biomedicine and microbial metabolism. Because evolutionary information carries intrinsic temporal and causal structure, it can provide biological prior knowledge for inferring causal mechanisms of diseases. Human Accelerated Regions (HARs), genomic loci conserved across mammals but rapidly divergent in the human lineage, offer an anchor for identifying human-specific host-microbe co-evolutionary units relevant to NDs. We further hypothesize that microbial metabolites represent one class of mechanistically testable intermediates linking host genetic background, gut microbial ecology, and neurodegenerative phenotypes. This integrated evolutionary-metabolic perspective offers a tractable path from correlation toward mechanism in gut microbiota-ND research.}, }
@article {pmid42188320, year = {2026}, author = {Mustika, A and Gorica, E and Harbuwono, DS and Kurniawati, EM and Hadinata, E and Hidayat, AA and Siahaan, SCPT and Hendarto, H and Santini, A and Nurkolis, F}, title = {Algae-Derived Bioactives Reprogram the Gut-SIRT1-Kisspeptin Axis in Polycystic Ovary Syndrome.}, journal = {Marine drugs}, volume = {24}, number = {5}, pages = {}, pmid = {42188320}, issn = {1660-3397}, mesh = {*Polycystic Ovary Syndrome/drug therapy/metabolism/physiopathology/microbiology ; Humans ; Female ; *Sirtuin 1/metabolism ; Animals ; Gastrointestinal Microbiome/drug effects ; Signal Transduction/drug effects ; }, abstract = {Polycystic ovary syndrome (PCOS) is increasingly recognized as a complex, multi-system disorder involving interactions among metabolic dysfunction, chronic low-grade inflammation, and neuroendocrine dysregulation, rather than a condition confined to the ovary. While current management strategies primarily target symptomatic manifestations, such as menstrual irregularity, hyperandrogenism, and insulin resistance, they do not directly address the underlying integrative pathways linking the gut microbiome, cellular energy sensing, and hypothalamic reproductive control. This review proposes a mechanistic framework in which algae-derived bioactives modulate a gut-SIRT1-kisspeptin axis, thereby offering a systems-level perspective on PCOS pathophysiology and intervention. Gut dysbiosis in PCOS contributes to altered bile acid signaling, disrupted microbial metabolite profiles, and increased inflammatory tone, all of which may impair both metabolic and reproductive functions. Concurrently, reduced activity of the NAD[+]-dependent deacetylase SIRT1 has been documented across ovarian, endometrial, and metabolic tissues, linking energy imbalance to oxidative stress, inflammation, and impaired steroidogenesis. At the neuroendocrine level, dysregulated kisspeptin signaling contributes to abnormal gonadotropin-releasing hormone pulsatility and luteinizing hormone hypersecretion, key features of PCOS. Algae-derived compounds, including polysaccharides, phlorotannins, fucoidan, fucoxanthin, and microalgae bioactives, exhibit prebiotic, anti-inflammatory, and metabolic regulatory properties that intersect with these pathways, particularly through modulation of gut microbiota and activation of AMPK/SIRT1 signaling. The central proposition of this review is that algae-derived bioactives may act across interconnected biological layers: reshaping gut microbial ecology, restoring SIRT1-mediated metabolic balance, and retuning kisspeptin-driven neuroendocrine activity. While individual components of this axis are supported by substantial evidence, direct experimental validation of the complete pathway remains limited. Therefore, this framework is positioned as a translationally grounded but hypothesis-driven model that integrates currently fragmented findings into a coherent and testable paradigm. Future research should prioritize multi-level experimental and clinical studies that simultaneously assess microbiota composition, metabolic signaling, and reproductive neuroendocrine outcomes to establish the therapeutic potential of algae-based interventions in PCOS.}, }
@article {pmid42189994, year = {2026}, author = {Kauai, F and Van de Peer, Y and Bonte, D}, title = {Ecological opportunity and the onset of polyploid niche expansion waves.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {22}, pages = {e2522071123}, doi = {10.1073/pnas.2522071123}, pmid = {42189994}, issn = {1091-6490}, support = {No. 833522//EU Horizon ERC/ ; BOF.MET.2021.0005.01//UGent Special Research Fund, Methusalem/ ; }, mesh = {*Polyploidy ; *Ecosystem ; Animals ; Biological Evolution ; Models, Genetic ; Models, Biological ; Diploidy ; }, abstract = {Polyploidy, the presence of more than two sets of chromosomes, has evolved many times across the tree of life, yet we still do not know why some polyploid lineages persist while most go extinct. The establishment of polyploid populations is often reported to be associated with harsh environmental conditions, and stress tolerance in particular, which has led to the widespread view that polyploidy-specific niche requirements are key to their persistence at ecological and evolutionary timescales. Here, we reevaluate this perspective using a classical mathematical model of polyploid establishment, presenting analytical and numerical results, along with an empirical case study. We show that simple eco-evolutionary processes at the margins of diploid range-expansion waves, more specifically ecological drift and dispersal limitation, can be sufficient to allow polyploid populations to carve out their own space, without any a priori adaptive advantage over their diploid ancestors. Our modeling effort reveals three key insights. First, polyploids most readily gain a foothold at the low-density front of a diploid range expansion wave, where ecological drift is strongest. Second, limited dispersal accelerates spatial clustering of polyploid organisms through assortative mating. Third, once spatially segregated along gradients, diploid and polyploid populations are expected to experience distinct environments, allowing natural selection to drive niche divergence. We illustrate these interconnected principles by simulating the phylogeographic history of a well-documented autopolyploid complex of Neobatrachus, Australian burrowing frogs. Altogether, our results provide a neutral baseline against which the ecological consequences of polyploidization can be more easily inferred within natural populations.}, }
@article {pmid42189996, year = {2026}, author = {Peeters, MKR and Van de Peer, Y}, title = {Polyploidy: A macromutational force pushing bioeconomic developments.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {22}, pages = {e2522065123}, doi = {10.1073/pnas.2522065123}, pmid = {42189996}, issn = {1091-6490}, support = {833522//EC | Horizon Europe | Excellent Science | HORIZON EUROPE European Research Council (ERC)/ ; Methusalem funding BOF.MET.2021.0005.01//UGent | Bijzonder Onderzoeksfonds UGent (BOF)/ ; }, mesh = {*Polyploidy ; *Biotechnology/economics ; Biofuels ; Agriculture/economics ; Biomass ; }, abstract = {Polyploidization, the consequence of genome doubling, is a macromutation that reshapes genomes, phenotypes, and ecological interactions. Polyploidization often results in novel phenotypes, including alterations in size, physiology, biochemistry, and enhanced stress tolerance. Here, we discuss how strategically leveraging polyploidy can provide significant advancements within the modern bioeconomy committed to reducing our ecological footprint through the sustainable production and use of biological resources. The bioeconomy spans diverse sectors, including agriculture, health sciences, and biotechnology. By elucidating and leveraging the immediate, or short-term, effects of polyploidization, such as harnessing genetic diversity, extensive biomass production, diversification of metabolites, and improved stress resilience, we highlight how this process unlocks vast, underexplored bioeconomic opportunities. This includes accelerating the exploration of new breeding techniques, speeding up the domestication of new local varieties or medicinal plants, and offering possibilities for improved biofuel production, bioremediation strategies, therapies, and production and discovery of bioactive compounds. The multilayered effects of polyploidization shared across sectors can foster interdisciplinary exchange and are essential for advancing toward a more sustainable bioeconomy.}, }
@article {pmid42190448, year = {2026}, author = {Alves, AF and Andrade Reis, RJ and Bittencourt, PP and da Rocha, LO and Seabra, SH and de Paula Soares, C and Canellas, LP and Olivares, FL}, title = {Mutualistic interaction between Herbaspirillum seropedicae and Trichoderma longibrachiatum enhances maize plant growth.}, journal = {Microbiological research}, volume = {310}, number = {}, pages = {128562}, doi = {10.1016/j.micres.2026.128562}, pmid = {42190448}, issn = {1618-0623}, abstract = {The soil biota community is predominantly composed of bacteria and fungi that modulate key processes in the biosphere. Mutualistic microbial interactions represent a promising strategy for developing biotechnological products. We investigated the mutualistic association between the diazotrophic bacterium Herbaspirillum seropedicae and the saprophytic fungus Trichoderma longibrachiatum, assessing structural compatibility, diazotrophic activity, and plant growth promotion. Microscopical evaluation revealed compatible cell-to-cell interaction, characterized by bacterial attachment to and dispersal along fungal hyphae, followed by biofilm formation. In co-culture studies using a nitrogen-free semi-solid medium, the bacterial population increased, accompanied by a 500% increase in acetylene reduction, a 120% increase in nifH gene expression, and a 50% increase in protein content compared to monoculture. Immunogold-labeling coupled with transmission electron microscopy using polyclonal antibodies against nitrogenase (nifH-subunit) and bacterial cell surface domains revealed, respectively, that nitrogenase per bacterial cell was not affected by hyphae presence, but cell-wall surface epitopes were enhanced. Inoculation of maize with this consortium increased shoot biomass by up to 226%, root biomass by up to 250%, and doubled the photosynthetic rate relative to controls. Confocal imaging of maize-inoculated plants confirmed the presence of bacterial aggregates and biofilms on root surfaces and in intercellular spaces, often associated with fungal hyphae and mineral particles, which supports the "fungal highway" model for bacterial dispersion. These findings demonstrate that T. longibrachiatum not only supports H. seropedicae survival and spatial distribution but also increases diazotrophic activity, benefiting plant growth. This work highlights the potential of the targeted bacterial-fungal consortium as a biotechnological tool to improve nutrient acquisition, reduce chemical fertilizer use, and enhance crop productivity in agroecosystems.}, }
@article {pmid42193098, year = {2026}, author = {Zhong, L and Wang, T and Tang, L and Han, J and Zhao, Q and Lin, N}, title = {Microbial Dysbiosis in Photodermatoses: Formation, Pathogenesis and Intervention Strategies.}, journal = {Current issues in molecular biology}, volume = {48}, number = {5}, pages = {}, doi = {10.3390/cimb48050493}, pmid = {42193098}, issn = {1467-3045}, abstract = {Recent studies have reported skin microbiome dysbiosis in patients with photodermatoses, featuring enriched Staphylococcus aureus colonization and decreased microbiome diversity. We propose that ultraviolet radiation (UVR), along with atypical antimicrobial peptides, may exert selective pressure on the skin microbiome, while cytokine dysregulation and a reduction in commensal bacteria amplify microbial dysbiosis. Dysbiotic microorganisms further release pathogen-associated patterns and virulence factors, and activate tissue-resident memory T cells, which collectively contribute to local inflammation. These mechanisms establish the skin microbiome as a potential target for early intervention. Potential therapeutic strategies may include antibiotics, phototherapy, bleach baths, phage therapy, and microbiota-based therapies. This review integrates current findings from microbial ecology, molecular biology, and host immunology to outline a conceptual framework linking UVR exposure, microbiome alterations, and cutaneous immune responses, while emphasizing the current limitations and evidence gaps in this field.}, }
@article {pmid42195307, year = {2026}, author = {Mogoşanu, GD and Biţă, A and Scorei, IR and Pop, MI and Dinu, IR and Gheonea, DI}, title = {Boron as a Molecular Architect of Host-Microbiome Symbiosis: Implications for Dysbiosis and Aging-Related Pathologies.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {5}, pages = {}, doi = {10.3390/life16050750}, pmid = {42195307}, issn = {2075-1729}, abstract = {Boron (B) is increasingly recognized as more than a trace dietary element, emerging as a context-dependent organizer of molecular interactions at the host-microbiome interface. B exhibits reversible covalent chemistry driven by Lewis' acidity and selective affinity for cis-diol-rich biomolecules, enabling dynamic complexation with polyols, glycans, and phenolic ligands that dominate the intestinal mucus environment and shape microbial ecology. We synthesize evidence supporting an architecture-based framework in which B modulates biological function by conditioning the physicochemical context of microbial communication rather than acting as a single-pathway effector. Central to this model is spatial bioavailability, distinguishing plasma-accessible boron from microbiota-accessible boron (MAB), species that persist in the lumen and mucus layer long enough to influence interface-level processes. We propose that insufficient or altered MAB availability may contribute to dysbiosis (DYS) by destabilizing quorum-associated coordination, signal persistence, and mucosal microstructure, thereby promoting barrier dysfunction and inflammaging. Particular attention is given to B-mediated symbiotaxis, a hypothesis-driven concept describing how B-containing molecular assemblies may bias microbial communities toward cooperative, barrier-supportive configurations and reduce ecological volatility. We identify key knowledge gaps and experimental priorities (speciation-aware measurements, signal-centric readouts) necessary to determine when, where, and how B-mediated molecular architecture may counteract DYS and support healthspan.}, }
@article {pmid42196222, year = {2026}, author = {Zhang, X and Cai, L and Bai, Y and Peng, F}, title = {Comparative Metagenomic Studies Reveal Different Evolutionary Directions of Synthetic Indoor Microbial Communities Under Different Nutritional Conditions.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, doi = {10.3390/ijms27104238}, pmid = {42196222}, issn = {1422-0067}, support = {2022YFC2807501//Ministry of Science and Technology of the People's Republic of China/ ; NYWSWZX2025-2027-11//Major Special Project on Agricultural Microbial Industry Development in Hubei Province/ ; NIMR-2025-8//the R&amp;D Infrastructure and Facility Development Program of the Ministry of Science and Technology of the People's Republic of China/ ; }, mesh = {*Metagenomics/methods ; Humans ; *Microbiota/genetics ; *Bacteria/genetics/classification ; *Metagenome ; Nutrients ; }, abstract = {The relationship between microorganisms and human health is inseparable. In today's increasingly urbanized world, the relationship between indoor microbial communities and human health is particularly close. Studies have shown that the composition of indoor microbial communities is influenced by various factors, including temperature, humidity, and nutrient conditions. However, research on how to alter indoor microbial community structures by adjusting nutrient components to improve human health is still limited. In this work, we constructed artificial microbial communities composed of common indoor microorganisms, and analyzed the species composition, metabolic capabilities, antibiotic resistance, and virulence of the microbial communities before and after cultivation using metagenomic sequencing technologies and metatranscriptomic sequencing technologies. We then assessed their community characteristics and evolutionary direction under different nutrient conditions. Overall, when the nutrient conditions were altered and reduced, the evolutionary direction of indoor microbial communities changed significantly. Specifically, this evolutionary direction was manifested in a taxonomic succession of community composition, with marked shifts in the relative abundances of constituent species, as well as in a significant alteration of the community-level metabolic functions. In-depth research in this field can help improve the composition of indoor microbial communities, thereby benefiting human health and public health construction in urbanized environments.}, }
@article {pmid42196944, year = {2026}, author = {Mosca, L and Pagano, C and Tafuri, MG and Di Maio, G and Rejano-Gordillo, CM and Della Marca, R and D'Angelo, S and Monda, M and Messina, G and Polito, R and Perrone, P}, title = {The Gut Microbiota-Polyphenol-NLRP3 Inflammasome Axis: A Key Regulatory Network Linking Diet to Chronic Inflammation.}, journal = {Nutrients}, volume = {18}, number = {10}, pages = {}, doi = {10.3390/nu18101483}, pmid = {42196944}, issn = {2072-6643}, mesh = {*NLR Family, Pyrin Domain-Containing 3 Protein/metabolism ; Humans ; *Polyphenols/metabolism/pharmacology ; *Inflammasomes/metabolism ; *Gastrointestinal Microbiome/physiology ; Animals ; *Inflammation/metabolism/microbiology ; Chronic Disease ; *Diet ; Signal Transduction ; }, abstract = {Background/Objectives: Chronic low-grade inflammation, underpinned by persistent activation of the NLRP3 inflammasome, is a central pathological mechanism in non-communicable diseases including cardiovascular disease, type 2 diabetes, inflammatory bowel disease, and neurodegeneration. Dietary polyphenols have been consistently associated with reduced inflammatory burden; however, the mechanisms underlying these effects remain incompletely understood. This review aims to characterize the gut microbiota-polyphenol-NLRP3 inflammasome axis as a central regulatory network through which diet modulates innate immune signaling and chronic inflammatory tone. Methods: A comprehensive narrative review of the available literature was conducted, integrating evidence from mechanistic studies in cell culture and animal models, microbiome research, metabolomics, and human epidemiological and interventional data. Results: The gut microbiota emerges as a critical biochemical intermediary that transforms dietary polyphenols into bioactive metabolites, including urolithins, phenyl-γ-valerolactones, protocatechuic acid, and short-chain fatty acids, with enhanced bioavailability and potent inflammasome-modulating properties. These compounds suppress NLRP3 activation through multiple converging mechanisms, including inhibition of NF-κB-dependent priming, mitochondrial quality control via mitophagy, Nrf2-mediated antioxidant responses, and HDAC inhibition. Evidence across cardiovascular, metabolic, neurological, and respiratory disease models supports the translational relevance of this axis. Conclusions: The microbiota-polyphenol-NLRP3 axis functions as an integrated, self-regulated network in which each component simultaneously shapes and is shaped by the others: dysbiosis primes NLRP3 and depletes protective metabolites, while inflammasome hyperactivation further destabilises microbial ecology; polyphenol biotransformation by specific taxa interrupts this feed-forward loop at multiple nodes, restoring homeostasis.}, }
@article {pmid42197026, year = {2026}, author = {Alsinani, Y and Rostamkhani, F and Shirvani, H}, title = {Exercise and the Gut Microbiome: From Mechanisms to Clinical Applications.}, journal = {Nutrients}, volume = {18}, number = {10}, pages = {}, doi = {10.3390/nu18101565}, pmid = {42197026}, issn = {2072-6643}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; *Exercise/physiology ; Fatty Acids, Volatile/metabolism ; }, abstract = {Background/Objectives: The gut microbiome is a critical regulator of host metabolism, immunity, and the gut-brain axis. Exercise is a promising non-pharmacological modulator of microbial ecology, yet human evidence remains heterogeneous and the translational gap persists. This narrative review synthesizes mechanisms, human and animal evidence, and future directions for the exercise-gut microbiome axis. Methods: PubMed, Scopus, Web of Science, and SID were searched for articles published between January 2000 and February 2025. Keywords included exercise, physical activity, gut microbiome, gut microbiota, short-chain fatty acids, and gut-muscle axis. From 218 initial records, 89 original studies (47 human, 42 animal) met inclusion criteria and were critically appraised. Results: Exercise modulates the gut microbiome via splanchnic hypoperfusion, hyperthermia, altered transit time, and immune-mediated barrier regulation. Moderate-intensity continuous training consistently increases alpha diversity and enriches butyrate-producing taxa (Faecalibacterium prausnitzii, Roseburia hominis) and mucin-degrading Akkermansia muciniphila. High-intensity interval training transiently increases intestinal permeability in untrained individuals but, following adaptation, stimulates butyrate production via lactate cross-feeding metabolism-a recent breakthrough. Effects are transient and reversible upon detraining. Animal models establish causality through fecal microbiota transplantation; human randomized controlled trials demonstrate modest, intensity-dependent, and highly individualistic responses. Emerging evidence supports the gut-muscle axis in sarcopenia and personalized exercise prescription guided by microbiome profiling. Conclusion: Exercise shows promise as a low-cost modulator of the gut microbiome for enriching health-associated taxa and improving metabolic outcomes. Definitive evidence linking exercise-induced microbial shifts to enhanced athletic performance in humans remains lacking. Future research requires diet-controlled randomized controlled trials with ≥12-week interventions, shotgun metagenomics, and mechanistic validation of the gut-muscle axis in humans.}, }
@article {pmid42197451, year = {2026}, author = {Zou, P and Yang, Q and Defoirdt, T}, title = {The Quorum Sensing Inhibitor Qstatin Has Broad-Spectrum Antivirulence Activity Towards Shrimp-Pathogenic Vibrios.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14051065}, pmid = {42197451}, issn = {2076-2607}, support = {G057725N//Research Foundation - Flanders/ ; }, abstract = {The emergence of antibiotic resistance in aquaculture not only makes antibiotic treatments ineffective in aquaculture but also poses a threat to public health. In order to overcome this, novel strategies to control bacterial diseases are needed. Antivirulence therapy, which disrupts virulence without affecting bacterial viability, represents a promising alternative approach. This study evaluated the antivirulence activity of Qstatin against pathogenic vibrios belonging to the Harveyi clade. Qstatin specifically inhibited the three-channel quorum sensing system in Vibrio campbellii, significantly downregulated the expression of quorum sensing-regulated virulence genes (flaA, flaK, vpsR, vpsT, and vhp) and attenuated the corresponding phenotypes: swimming motility was reduced by up to 57% and biofilm formation by up to 76%. Protease activity, in contrast, was slightly increased rather than decreased. Finally, treatment with 100 μM Qstatin significantly increased the survival of gnotobiotic brine shrimp larvae upon challenge with each of 13 tested pathogenic Harveyi clade strains (belonging to the species V. campbellii, V. harveyi, or V. parahaemolyticus), without an impact on Vibrio densities in the rearing water. These findings indicate that Qstatin has a broad-spectrum antivirulence activity against Harveyi clade vibrios by inhibiting quorum sensing, thus supporting its potential as a sustainable disease control agent.}, }
@article {pmid42198293, year = {2026}, author = {Galinytė, D and Juodžiukynienė, N and Balnytė, I and Zigmantaitė, V and Karosienė, J and Bernatoniene, J and Savickienė, N}, title = {Topical C-Phycocyanin-Loaded Transfersomes Attenuate Early Proinflammatory Epidermal Remodelling in a DMBA/TPA-Induced Mouse Model of Skin Dysplasia.}, journal = {Pharmaceutics}, volume = {18}, number = {5}, pages = {}, doi = {10.3390/pharmaceutics18050600}, pmid = {42198293}, issn = {1999-4923}, abstract = {Background/Objectives: Cutaneous squamous cell carcinoma (cSCC) develops through inflammation-driven preneoplastic alterations characterized by epidermal hyperplasia, dysplasia, and increased proliferative activity. C-phycocyanin (C-PC) possesses antioxidant and anti-inflammatory properties; however, its topical potential to attenuate a tumour-promoting cutaneous microenvironment is limited by poor skin penetration. This study evaluated the effects of C-PC-loaded transfersomes in a 7,12-dimethylbenz[a]anthracene (DMBA)/12-O-tetradecanoylphorbol-13-acetate (TPA)-induced mouse model of skin carcinogenesis. Methods: Male BALB/c mice were assigned to six groups (n = 10 per group). Carcinogenesis was initiated with a single topical application of DMBA, followed by twice-weekly TPA application for 16 weeks. C-PC-loaded transfersomes (1 mg/mL or 10 mg/mL) were applied topically. Histopathological assessment included epidermal thickness, rete ridge depth, mitotic activity, mast cell density, and semi-quantitative scoring of hyperplasia, dysplasia, and inflammation. Ki-67 immunohistochemistry was used to evaluate basal and suprabasal proliferation. Results: Carcinogen exposure induced marked epidermal thickening, severe dysplasia, increased mitotic activity, elevated Ki-67 expression, and pronounced dermal inflammation. Treatment with C-PC-loaded transfersomes significantly reduced epidermal thickness, rete ridge depth, mast cell density, mitotic counts, and suprabasal Ki-67 index. The 1 mg/mL concentration demonstrated the most consistent attenuation of dysplasia severity and inflammatory changes. No adverse histopathological alterations were observed in internal organs. Conclusions: These findings indicate that transfersome-mediated topical delivery of C-PC attenuates early inflammation-driven epidermal remodelling and tumour-promoting alterations in experimental skin carcinogenesis, supporting its potential as a topical preventive strategy.}, }
@article {pmid42198379, year = {2026}, author = {Zanoni, A and Facchin, S and Mari, V and Bertin, L and Savarino, EV}, title = {Rethinking Long-Term PPI Therapy in GERD: A Narrative Review from a Microbial Ecology Perspective Beyond Acid Suppression.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {19}, number = {5}, pages = {}, doi = {10.3390/ph19050705}, pmid = {42198379}, issn = {1424-8247}, abstract = {Gastroesophageal reflux disease (GERD) is a common chronic disorder of the upper gastrointestinal tract, traditionally explained by an acid-centric model in which gastric acid causes mucosal injury and symptoms. Proton pump inhibitors (PPIs) are the mainstay of therapy and effectively control symptoms in many patients. However, up to 50% of individuals remain symptomatic despite adequate acid suppression, suggesting that GERD is a multifactorial condition involving anti-reflux barrier dysfunction, impaired mucosal defense, immune activation, and alterations in the esophageal microbiota. This study is a narrative review aimed at evaluating current evidence on the interactions between acid suppression, esophageal microbial ecology, and host-microbe interactions in GERD, and at exploring the potential role of microbiota-targeted therapeutic strategies. The literature search was conducted using electronic databases (e.g., PubMed and Scopus), without formal time restrictions, prioritizing recent and clinically relevant studies. Evidence was qualitatively synthesized to provide an integrated overview. Recent studies suggest that the esophagus hosts a microbial ecosystem that may contribute to mucosal homeostasis. In GERD and Barrett's esophagus, several studies report a shift toward Gram-negative anaerobic bacteria with potential pro-inflammatory activity. Long-term PPI therapy has been associated with increased gastric pH and changes in gastrointestinal microbiota composition, including a relative increase in taxa such as Streptococcus and Veillonella, and a reduction in short-chain fatty acid-producing bacteria. These alterations may be linked to dysbiosis and a possible increase in susceptibility to certain infections, although causality remains to be fully established. The main limitations of this review include its narrative design, the absence of systematic study selection, and the heterogeneity of the available evidence. Understanding the impact of acid suppression on microbial ecology may support the development of more integrated and personalized therapeutic strategies.}, }
@article {pmid42198875, year = {2026}, author = {Wong, SH and Kwong, TNY and Zhang, R and Lam, TYT and Ho, AMY and Leung, WW and Kang, X and Lau, HCH and Chu, ESH and Wong, MTL and Lau, LHS and Lui, RNS and Tang, RSY and Lau, JYW and Ng, SSM and Yu, J and Sung, JJY}, title = {Comprehensive microbiome profiling reveals mucosal microbiome heterogeneity in patients with left- and right-sided colorectal neoplasia.}, journal = {Cancer biology &amp; medicine}, volume = {}, number = {}, pages = {}, doi = {10.20892/j.issn.2095-3941.2025.0846}, pmid = {42198875}, issn = {2095-3941}, support = {CIRG23jan-0004//Singapore National Medical Research Council Clinician Scientist Individual Research Grant/ ; OFLCG22may-0009//Large Collaborative Grant/ ; OFLCG23may-0031//Large Collaborative Grant/ ; OFLCG24may-0025//Large Collaborative Grant/ ; }, abstract = {OBJECTIVE: Left- and right-sided colorectal cancer (CRC) exhibit distinct molecular and clinicopathologic features. However, little is known about the spatial heterogeneity of microbial signatures. In this study the profiles and ecologic patterns of disease-associated intestinal microbiome were investigated in patients with an adenoma(s) or CRC at different anatomic locations.<br><br>METHODS: A total of 690 stool, colonic aspirate, and mucosal biopsy samples were prospectively collected from 32 healthy, 30 adenoma, and 31 CRC patients.<br><br>RESULTS: CRC was associated with alterations in fecal and mucosal microbiomes. Furthermore, the overall composition of the mucosal microbiome, stratified by metacommunities, differed between the patients with left- and right-sided neoplastic lesions. Patients with right-sided CRC had an elevated inter-phylum ecologic network, while patients with left-sided CRC had an enriched abundance of Fusobacterium. Interestingly, rectal neoplasia harbored a tumor microbiome that was distinctly different from the tumor microbiome at other anatomic sites.<br><br>CONCLUSIONS: The mucosal microbiome of right-sided CRC was distinctly different from the mucosal microbiome of left-sided CRC patients, suggesting distinct microbial ecology and heterogeneous host-microbial ecologic relationships that may contribute to differences in the tumor microenvironment between left- and right-sided CRC.}, }
@article {pmid42198884, year = {2026}, author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW}, title = {Rhizosphere microbes are partners in plant stress adaptation.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/erag254}, pmid = {42198884}, issn = {1460-2431}, }
@article {pmid42199501, year = {2026}, author = {Yu, Y and Yuan, R and Zhang, J and Wang, L and Guo, T and Shen, H and Xie, H}, title = {Systems perspectives on pediatric otitis media: environmental exposures, genetic susceptibility, and biomarker-guided interventions.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1758098}, pmid = {42199501}, issn = {2296-2360}, abstract = {BACKGROUND: Pediatric otitis media remains one of the most common childhood diseases worldwide and is a major cause of hearing impairment, recurrent healthcare utilization, and antibiotic exposure. Its pathogenesis is highly heterogeneous and can no longer be adequately explained by a traditional single-pathogen model.<br><br>OBJECTIVE: This review aims to synthesize current evidence on the roles of environmental exposures, host genetic susceptibility, biomarkers, and microbial factors in pediatric otitis media, with particular emphasis on their interactions and translational relevance.<br><br>CONTENT: Current evidence suggests that early-life environmental exposures may contribute to pediatric otitis media through convergent pathways involving epithelial dysfunction, impaired mucociliary clearance, inflammation, oxidative stress, and altered immune regulation, while host genetic variation may further modify susceptibility and disease heterogeneity. Emerging biomarker and microbial studies also support a systems-level understanding of pediatric otitis media and its therapeutic complexity.<br><br>CONCLUSION: Pediatric otitis media should be understood as a multifactorial disorder arising from dynamic interactions among environmental exposures, host susceptibility, and microbial ecology. This integrated framework extends beyond pathogen-centered models and provides a conceptual basis for future biomarker validation, mechanistic stratification, and the development of more precise preventive and therapeutic strategies.}, }
@article {pmid42200509, year = {2026}, author = {Nouioui, I and Kirstein, S and Pötter, G and Jando, M and Gomez Escribano, JP and Neumann-Schaal, M and Müsken, M and Spröer, C and Bunk, B and Mast, Y}, title = {Taxonomic description of a novel genus, Parajatrophihabitans gen. nov., in the family Jatrophihabitantaceae.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {76}, number = {5}, pages = {}, doi = {10.1099/ijsem.0.007176}, pmid = {42200509}, issn = {1466-5034}, mesh = {*Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Sequence Analysis, DNA ; Base Composition ; DNA, Bacterial/genetics ; Nucleic Acid Hybridization ; Bacterial Typing Techniques ; Fatty Acids/chemistry/analysis ; Genome, Bacterial ; }, abstract = {Strain DSM 45814[T], isolated from forest soil in Canada, was subjected to a polyphasic taxonomic study and genome mining for plant growth-promoting genes. The strain had a 16S rRNA gene sequence similarity of 97.1% with that of Jatrophihabitans telluris N237[T] and 94.8-96.8% similarity with other validly named Jatrophihabitans species. Average nucleotide identity and digital DNA-DNA hybridization values between DSM 45814[T] and its closely related Jatrophihabitans strains were below the established prokaryotic species demarcation. In the genome-based phylogeny, strain 45814[T] was divergent from the Jatrophihabitans cluster and was loosely associated with the family Geodermatophilaceae. The average amino acid identity (AAI) values between DSM 45814[T] and type (63.5-71.6%) and non-type (63.0-71.6%) strains of Jatrophihabitantaceae, as well as members of Geodermatophilaceae (58.6-59.2%), fell within the defined AAI range of 65-72% and below the recently established cut-off point of 74-76% for genus demarcation. The percentage of conserved proteins (POCP) between strain DSM 45814[T] and the type strains of Jatrophihabitantaceae and Geodermatophilaceae was below the defined threshold of 50% for genus demarcation, excluding J. telluris, which had a POCP of 55%. Strain DSM 45814[T] displayed cocci-to-cuboid cells with a flagellum and a G+C content (63.4 mol%) that distinguished it from Jatrophihabitans and Geodermatophilaceae strains, but it had chemotaxonomic features closer to those of Jatrophihabitantaceae than Geodermatophilaceae. The strain appeared to have ecological potential based on a genome mining approach. Based on these results, strain DSM 45814[T] (=899[T]=LMG 34134[T]) represents a novel genus within the family Jatrophihabitantaceae, for which the name Parajatrophihabitans canadensis gen. nov. sp. nov. is proposed.}, }
@article {pmid42200521, year = {2026}, author = {Wright, RJ and Fisher, BR and Comeau, AM and Langille, MGI}, title = {From classification to confirmation: verifying taxonomic classifications by mapping metagenomic reads to reference genomes.}, journal = {Microbial genomics}, volume = {12}, number = {5}, pages = {}, doi = {10.1099/mgen.0.001739}, pmid = {42200521}, issn = {2057-5858}, mesh = {*Metagenomics/methods ; Humans ; *Metagenome ; *Bacteria/classification/genetics ; Genome, Bacterial ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Microbiota/genetics ; }, abstract = {Obtaining high precision while maintaining high recall is an ongoing problem for metagenomic taxonomic classification in microbial ecology research. Parameter adjustments can achieve this in simulated samples, but in real samples - especially from environments like marine and soil - the proportion of classified reads drops sharply with precision increases. We, therefore, suggest verification of metagenomic taxonomic classifications obtained from a tool like Kraken by mapping their assigned reads to reference genomes to assess genomic coverage. In simulations, filtering the identified species to only those with ≥0.5% reference genome coverage removed 99.7% of false-positive taxa. Applying this method to samples from real datasets requires a more nuanced approach that considers sequencing depth, whether the samples are high- or low-microbial biomass, and database completeness with respect to the sampled environment. Nevertheless, we show that clinically relevant Kraken-identified taxa, such as Helicobacter pylori identified in human stool samples, lack any reads mapping to their reference genome and are likely false positives driven by contaminating phage sequences within reference genomes. Similarly, in human blood and lung tumour datasets, only 18 and 11 species, respectively, have ≥1% reference genome coverage and likely represent sample collection or sequencing contaminants. Marine and soil samples pose additional challenges due to lower representation in reference databases, leading to low nucleotide identity between sequenced reads and reference genomes and similarity only at higher taxonomic ranks. We recommend genome coverage checking to researchers in all fields of microbial ecology and provide an open-source pipeline on GitHub (GeCoCheck): https://github.com/R-Wright-1/GeCoCheck.}, }
@article {pmid42201006, year = {2026}, author = {Garibay-Padilla, IE and Hernandez-Del Río, JE and Orozco-Sepulveda, DE and Gonzalez-Padilla, C and Miranda-Aquino, T and Salas-Bonales, V and De Arcos-Jiménez, JC and Briseño-Ramírez, J}, title = {In-Hospital Mortality Predictors and a Bayesian Weighted-Incidence Antibiogram in Infective Endocarditis: A Seven-Year Cohort Study from a Mexican Tertiary University Hospital.}, journal = {Medical sciences (Basel, Switzerland)}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/medsci14020214}, pmid = {42201006}, issn = {2076-3271}, mesh = {Humans ; *Hospital Mortality ; Bayes Theorem ; Tertiary Care Centers ; Retrospective Studies ; *Endocarditis/mortality/drug therapy/microbiology ; Mexico/epidemiology ; Female ; Male ; Microbial Sensitivity Tests ; *Anti-Bacterial Agents/therapeutic use ; Middle Aged ; Aged ; Hospitals, University ; Incidence ; }, abstract = {Background/Objectives: Infective endocarditis (IE) carries substantial mortality, particularly in middle-income settings where patient profiles and microbial ecology differ from those of cohorts used to derive international prognostic scores. Syndrome-specific, locally grounded decision aids for empirical therapy are also scarce. We aimed to identify predictors of in-hospital mortality, externally evaluate the RiskE and ICE scores, and construct a Bayesian weighted-incidence syndromic combination antibiogram (WISCA) for IE. Methods: We conducted a retrospective cohort study of consecutive adults with definite or possible IE admitted between January 2019 and January 2026. Candidate predictors were screened in two phases, and a clinically specified model was estimated with maximum-likelihood and Firth penalization, with 1000-replicate bootstrap optimism correction. Calibration was assessed with bootstrap calibration plots and the Hosmer-Lemeshow test. Discrimination was compared against RiskE and ICE using DeLong's test and reclassification metrics. For empirical coverage, we built a WISCA using identified pathogens, reporting both non-Bayesian bootstrap estimates and Bayesian hierarchical partial-pooling estimates with species- and antibiotic-level random intercepts; analyses were also stratified by IE type. Results: In-hospital mortality was 22.9% in a young cohort (median 37 years) characterized by high hemodialysis prevalence (47.4%), substantial right-sided IE (46.4%), and Staphylococcus aureus predominance (32%) with no methicillin-resistant isolates. Vasopressor-requiring shock (Firth OR 9.23, 95% CI 2.40-40.61) and acute heart failure (OR 10.01, 95% CI 2.78-41.07) were the strongest predictors; the final model achieved an AUC of 0.922 (optimism-corrected 0.908), significantly outperforming RiskE (0.598) and ICE (0.632). The Bayesian WISCA identified multiple carbapenem-sparing and anti-MRSA-sparing regimens with adequate coverage (≥80%), particularly for community-acquired IE, supporting stewardship-oriented empirical selection. Coverage was consistently lower in healthcare-associated IE. Conclusions: A parsimonious three-variable model provided strong, locally valid mortality prediction in this hemodialysis-predominant, MRSA-free cohort, substantially outperforming European-derived scores. External validation in independent cohorts is required before clinical adoption. The Bayesian WISCA demonstrated that adequate empirical coverage is achievable without routine broad-spectrum agents, offering institution-specific guidance for stewardship-compatible regimen selection; multicenter validation is warranted.}, }
@article {pmid42201256, year = {2026}, author = {Saberian, E and Petrášová, A and Jenča, A and Jenčová, J and Shirali, K and Jenča, A and Więckiewicz, MA and Zare-Zardini, H and Ebrahimi Far, M}, title = {Oral microbiota diversity and composition in patients with oral lichen planus: An observational molecular analysis study.}, journal = {Dental and medical problems}, volume = {}, number = {}, pages = {}, doi = {10.17219/dmp/210087}, pmid = {42201256}, issn = {2300-9020}, abstract = {BACKGROUND: Oral lichen planus (OLP) is a chronic inflammatory condition affecting the oral mucosa. The oral microbiome has been identified as a potential contributing factor to OLP.<br><br>OBJECTIVES: The aim of the study was to evaluate the prevalence and diversity of the oral microbiota in patients with OLP.<br><br>MATERIAL AND METHODS: This observational study included 78 patients with clinically and histopathologically confirmed OLP, recruited in accordance with the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) guidelines. Buccal mucosa samples were collected using standardized protocols. DNA was extracted from 12 high-quality samples and subjected to 16S rRNA gene amplification and sequencing. Alpha and beta diversity indices were calculated using the Quantitative Insights Into Microbial Ecology (QIIME) platform. Statistical analyses were performed using the IBM SPSS Statistics for Windows software, v. 26.0 (IBM Corp., Armonk, USA) (p < 0.05).<br><br>RESULTS: Intratissue bacterial communities exhibited decreased alpha diversity and increased beta diversity compared with those present on the mucosal surface. Streptococcus, a genus within the Firmicutes phylum, was found to be the most abundant, with 5 Streptococcus strains identified in the OLP samples. Following Streptococci, Bacilli and Clostridia displayed considerable diversity. Other frequently detected species included Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa, Eikenella corrodens, Actinobacillus, as well as members of the Proteobacteria phylum, which are commonly found in high quantities in the oral cavity. Prevotella and Capnocytophaga, belonging to the Bacteroidetes phylum, were also frequently observed. Alpha diversity analysis revealed significant differences in the colony numbers of the investigated species across studied samples.<br><br>CONCLUSIONS: The findings indicate an association between the composition of the oral microbiota and OLP. The microbial populations obtained from affected individuals exhibited distinct bacterial compositions. Modulation of the oral microbiome may represent a potential strategy for improving the management of OLP.}, }
@article {pmid42182019, year = {2026}, author = {Wu, L and Li, S and Han, F and Guo, J and Zhang, X and Xu, L}, title = {Restoring circadian disrupted gut microbial metabolite rhythms with phytochemicals: a new avenue against metabolic disease.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1801367}, pmid = {42182019}, issn = {1664-302X}, abstract = {The global epidemic of metabolic diseases-encompassing obesity, type 2 diabetes mellitus (T2DM), non-alcoholic fatty liver disease (NAFLD), and cardiovascular disease-represents a defining public health challenge of our era. The traditional model of simple caloric excess vs. expenditure has proven insufficient, giving way to a paradigm that acknowledges complex interactions between genetics, environment, and lifestyle, mediated by intricate physiological systems. Among these, the host circadian timing system and the gut microbiome have ascended as pivotal, deeply intertwined regulators of metabolic homeostasis. The gut microbiome, far from a static collection of microbes, constitutes a dynamic and metabolically active community whose composition and, critically, its functional output exhibit profound and predictable diurnal oscillations. The host's circadian clocks regulate microbial rhythms primarily by controlling the daily cycle of feeding and fasting. Modern life induces circadian disruption (CD) through ubiquitous exposure to artificial light at night, shift work, social jet lag, and erratic eating patterns. It perturbs the rhythmic dynamics of the gut ecosystem, leading to a fundamental dysregulation in the temporal production of key microbial metabolites. These metabolites, including short-chain fatty acids, secondary bile acids (BAs), indoles and other tryptophan derivatives, function as indispensable chemical messengers that coordinate peripheral metabolism, immune responses, and energy homeostasis in a precise, time-of-day-dependent manner. Their desynchronization-manifesting as mistimed, deficient, or incessant signaling-directly instigates the core pathologies of metabolic disease: insulin resistance, adipocyte dysfunction, hepatic lipid accumulation, and chronic low-grade inflammation. This review synthesizes current evidence to delineate the multilevel mechanisms through which CD drives the dysregulation of gut microbiome metabolite rhythms and establishes the causal pathways linking this dysrhythmia to metabolic pathogenesis. Furthermore, we undertake a critical evaluation of the promising therapeutic potential of dietary phytochemicals-a diverse class encompassing polyphenols, glucosinolates, and prebiotic fibers-to act as chrono-therapeutic agents. Through their multifaceted capacity to remodel microbial ecology, calibrate microbial enzymatic output, and reinforce host circadian-metabolic coupling, phytochemicals present a novel, physiologically aligned, and sustainable dietary strategy for the prevention and management of metabolic disorders. We conclude by outlining key translational challenges and propose future research directions essential for harnessing the potential of the "clock-microbiome-metabolite" axis within the framework of precision nutrition and medicine.}, }
@article {pmid42182034, year = {2026}, author = {McLeish, M and Zamfir, A and Babalola, B and Mora, M&#xc1; and Fraile, A and García-Arenal, F}, title = {Spatial scale break in ecological strategies for host use by plant viruses.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1797573}, pmid = {42182034}, issn = {1664-302X}, abstract = {Processes that involve performance traits such as host range underlie pathogen diversity and infection risk. Host range performance (HRP) is expected to be distributed across spatially explicit conditions, but rarely considered in microbial ecology. Merging of spatially discrete processes in epidemiological model selection exacerbates error propagation. We combine high throughput sequencing and reverse transcriptase polymerase chain reaction approaches to test whether HRP of 18 plant virus species influences species diversity across spatial scales. The results indicated a scaling break in the effect of HRP between the individual host and community scales. Regression analyses showed weaker (i.e., random) associations between viruses in individual hosts than at broader spatial scales of cooccurrence among hosts. Contrasting variances in effect sizes between the spatial scales indicated HRP informs on disease risk at the plant community level, but is a poor predictor of infection in individual plants. The evidence of contrasting HRP between the domains of scale set in this study, suggests heterogeneity among multiple processes across scales drive virus species diversity. Epidemiological model selection should consider variation in species trait performance across scales.}, }
@article {pmid42184066, year = {2026}, author = {Al Awawdeh, S and Shafie, NH and Ishak, AH and Mohd Esa, N and Loh, SP and Nurdin, A}, title = {Green tea polyphenol-iron oxide chitosan nanoparticles modulate gut microbiota and regulate metabolic pathways.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {6}, pages = {}, pmid = {42184066}, issn = {1573-0972}, support = {GP-IPS/2023/9772000//Universiti Putra Malaysia/ ; FRGS/1/2018/SKK10/UPM/02/5//Ministry of Higher Education, Malaysia/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Polyphenols/pharmacology/chemistry/administration &amp; dosage ; Rats, Sprague-Dawley ; Male ; Rats ; *Chitosan/chemistry ; *Tea/chemistry ; *Metabolic Networks and Pathways/drug effects ; Liver/metabolism/drug effects ; *Nanoparticles/chemistry ; *Ferric Compounds/chemistry ; Proteome ; Proteomics ; Bacteria/classification/genetics/drug effects ; }, abstract = {Green tea polyphenols (GTPP) exhibit antioxidants, anti-inflammatory, and anticancer properties; however, their poor bioavailability limits clinical translation. Nanoparticle-based formulations may enhance absorption and therapeutic potential. This study investigates the therapeutic effects of GTPP encapsulated in iron oxide chitosan nanoparticles (GTPP-IOCHNP) on gut microbiota and hepatic proteome, with particular attention to pathways relevant to inflammation, drug metabolism, and tumorigenesis. Male Sprague Dawley rats were administered a single oral dose of GTPP or GTPP-IOCHNP (200 mg/kg). Cecal microbiota composition was analyzed by metagenomic sequencing, while liver proteome alterations were assessed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Metagenomic analysis revealed that GTPP-IOCHNP promoted Actinobacteriota and Collinsella, both linked to reduced inflammation and improved gut health, while inhibiting Bacteroides and Ruminococcus genera associated with intestinal barrier dysfunction, inflammation, and nephropathy. Blautia was significantly enriched (p < 0.05), supporting short chain fatty acid production, modulation of lipid and carbohydrate metabolism, and transformation of polyphenols into bioactive antioxidant metabolites. Proteomics profiling identified 20 differentially expressed hepatic proteins (p < 0.05). GTPP-IOCHNP significantly downregulated cytochrome P4502D26 (CYP2D6), indicating modulation of CYP2D6 mediated drug metabolism, and suppressed glutamate dehydrogenase 1, implicating inhibition of glutamine-driven energy metabolism linked to cancer and hyperinsulinism. Conversely, significant upregulation of elongation factor 1-alpha-1 (eEF1A1), albumin, and adenosine kinase (ADK) highlighted improved GTPP absorption, systemic transport, and regulation of hepatic energy metabolism. The integrative metagenomic and proteomic analyses reveal that GTPP-IOCHNP improves polyphenol bioavailability by modulating gut microbial ecology and hepatic metabolic pathways, offering a mechanistically driven platform for therapeutic advancement.}, }
@article {pmid42184815, year = {2026}, author = {Bełkot, Z and Adamski, MG and Strzałkowska, ZJ and Domańska, ED and Kłosińska, D and Kunstman, G and Skoczek, D and Pławińska-Czarnak, J}, title = {Full-Length 16S and 18S rRNA Long-Read Sequencing Reveals Gut Microbiome Diversity in the European Brown Hare (Lepus europaeus).}, journal = {Environmental microbiology reports}, volume = {18}, number = {3}, pages = {e70358}, doi = {10.1111/1758-2229.70358}, pmid = {42184815}, issn = {1758-2229}, mesh = {Animals ; *Hares/microbiology ; *Gastrointestinal Microbiome/genetics ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *RNA, Ribosomal, 18S/genetics ; Phylogeny ; Sequence Analysis, DNA ; Biodiversity ; }, abstract = {The European brown hare (Lepus europaeus) is a declining wildlife species of ecological and epidemiological importance, yet its intestinal microbiome remains poorly characterized. Here, Oxford Nanopore long-read sequencing was used to analyse full-length 16S and 18S rRNA genes from pooled large-intestine contents of 30 healthy hares divided into three groups. Comparative taxonomic assignment at 95% and 80% sequence identity thresholds revealed striking differences in diversity estimates, with the lower threshold uncovering up to ten-fold more taxa. Across all samples, 40 phyla, 360 families, 1027 genera, and 3373 species were identified, including 30 taxa not previously reported in lagomorphs. These included Monoglobus pectinilyticus, Ruminococcus champanellensis, Odoribacter splanchnicus, Butyricimonas virosa, and Akkermansia muciniphila, associated with pectin degradation, cellulose hydrolysis, butyrate production, mucin degradation, bile acid transformation, and nitrogen recycling. Several taxa relevant to both animal and human health were also detected, supporting hares as sentinels of environmental microbiota within a One Health framework. These findings show that analytical parameter selection strongly shapes microbiome interpretation and provide the most comprehensive gut microbiome profile of the European brown hare to date. The study expands lagomorph microbial ecology and highlights long-read sequencing as a valuable tool for wildlife microbiome surveillance in undercharacterized host species globally.}, }
@article {pmid42185792, year = {2026}, author = {Mirzaei, S and Tefagh, M}, title = {MOFA: microbial optimization without forced altruism.}, journal = {BMC bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12859-026-06485-1}, pmid = {42185792}, issn = {1471-2105}, abstract = {BACKGROUND: Microorganisms typically exist in communities, where interactions among them define the complexity of these ecosystems. Developing in silico frameworks to investigate the behavior and functionality of these communities is therefore essential for advancing our understanding of microbial ecology. In recent years, several computational modeling frameworks based on genome-scale models have been developed for the community-level analysis of microbial systems.<br><br>RESULTS: Here, we introduce microbial optimization without forced altruism (MOFA), a bilevel optimization framework that considers both species-level and community-level fitness criteria. By imposing constraints on species biomass in the outer problem, it prevents the forced altruism observed in previous algorithms. We applied MOFA to a toy model and to community models of Desulfovibrio vulgaris and Methanococcus maripaludis, which exhibit a cross-feeding relationship that causes the community objective to override individual fitness goals by prioritizing the export of metabolites for other community members. For this microbial community, a comparison with the results of NECom, OptCom, and Joint-FBA shows that MOFA yields predictions that better match the experimental results. Additionally, for pairs with a cross-feeding relationship in which exported metabolite production associated with this mutual interaction competes with species biomass, such as D. vulgaris and M. maripaludis, NECom fails to predict the community growth rate, whereas our method succeeds.<br><br>CONCLUSIONS: MOFA effectively analyzes community growth rates without relying on forced altruism. In cases where NECom fails to predict community growth, MOFA successfully predicts these growth rates. Furthermore, MOFA enhances computational efficiency by eliminating the need for the binary variables required in the NECom algorithm.}, }
@article {pmid42187718, year = {2026}, author = {Wen, F and Chen, X and Chen, Q and Li, L and Zhao, Y and You, Y and Niu, S and Xia, Z}, title = {Nutrient Supply Gradients Modulate Cultivation-Driven Restructuring of Microbial Communities in Desert Soils.}, journal = {Biology}, volume = {15}, number = {10}, pages = {}, doi = {10.3390/biology15100755}, pmid = {42187718}, issn = {2079-7737}, abstract = {Understanding how cultivation conditions influence the recovery of microbial diversity is critical for interpreting cultivation-derived communities in relation to in situ microbial ecology, particularly in nutrient-limited environments such as desert soils. In this study, we investigated how an oligotrophic nutrient gradient shapes cultivation outcomes and enrichment-derived bacterial community structure in soils from the Taklimakan Desert. Three enrichment treatments representing decreasing nutrient availability-standard low-nutrient medium (R2A), diluted medium (DR2A), and sterile water-were used to compare enrichment-derived communities with the original soil microbiome. Amplicon sequencing revealed that cultivation substantially altered community composition and reduced both taxonomic richness and diversity relative to the original soil. Across enrichment treatments, bacterial communities were dominated by a limited number of taxa, whereas the original soil contained a broader range of low-abundance lineages. Within the enrichment system, variation in nutrient supply influenced the relative abundance of specific taxa, with differential responses observed at the genus level. In contrast, beta diversity analysis showed only limited separation among enrichment treatments, and co-occurrence network analysis indicated generally simple and weakly connected community structures across all conditions. Overall, our results demonstrate that cultivation represents the primary selective force shaping enrichment-derived bacterial communities, while nutrient supply intensity acts as a secondary modulator of taxon-specific enrichment. These findings highlight the importance of incorporating nutrient gradients into cultivation strategies to improve ecological interpretation and facilitate the recovery of oligotrophy-associated microorganisms from desert soils.}, }
@article {pmid42187796, year = {2026}, author = {Aramburu, A and Beltran-Sanz, N and Raggio, J and Divakar, PK and Pintado, A and de Los Ríos, A and Sancho, LG}, title = {Islands of Biodiversity: Characterization of Lichen Flora in Antarctic Nunataks.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {12}, number = {5}, pages = {}, doi = {10.3390/jof12050314}, pmid = {42187796}, issn = {2309-608X}, support = {PID2019-105469RB-C21//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; CT82/20-CT83/20//Universidad Complutense de Madrid - Banco Santander/ ; PID2023-147388NB-I00//MCIN/AEI/10.13039/501100011033/FEDER, UE/ ; }, abstract = {Antarctic terrestrial photosynthetic biota is dominated by cryptogamic communities, which are largely restricted to scarce ice-free areas. Among these, nunataks constitute habitats of remarkable biogeographical interest, as they may harbor distinctive biotic assemblages worthy of investigation. This work presents a comprehensive assessment of lichen diversity on Antarctic nunataks. The lichen flora of four nunataks on the Hurd Peninsula (Livingston Island, maritime Antarctica) was investigated. Specimens were identified using an integrative approach combining morphological assessment and DNA barcoding. This survey revealed a high and potentially underestimated species richness, with 39 confidently identified and several additional taxa requiring further taxonomic resolution. A review of published records of lichen occurrence in nunatak and non-nunatak environments throughout Antarctica was used to evaluate patterns in taxonomic, biogeographical, and morphotype composition. This synthesis showed that nunataks support lower species richness than other ice-free environments. Most of their taxa occur in non-nunatak areas, consistent with patterns observed locally on the Hurd Peninsula. Floristic overlap seems greater in continental Antarctica, suggesting a stronger influence of nunatak-associated environmental constraints in the maritime region. These results underscore the ecological significance of nunataks as environmentally filtered habitats and highlight their relevance for understanding biodiversity patterns and community assembly in Antarctica's terrestrial ecosystems.}, }
@article {pmid42174303, year = {2026}, author = {Kim, CH and Ciloglu, A and Yan, J and Mackay, A and Noel, KR and Cooper, M and Oluoch, A and Canam, T and Stone, CM}, title = {Habitat Type and Locality Structure the Midgut Microbiota of Aedes albopictus.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02792-5}, pmid = {42174303}, issn = {1432-184X}, abstract = {The mosquito midgut microbiome plays a crucial role in nutrition, reproduction, and immunity, yet how locality and urban development shape these communities and their potential relevance to mosquito-pathogen interactions remains poorly understood. Here, we investigated bacterial community composition and diversity in the midguts of adult female Aedes albopictus collected from residential and woodland habitats of Champaign-Urbana and Charleston in Illinois, USA. We sequenced the V4 region of the 16 S rRNA gene from 160 samples and analyzed the data using QIIME 2. After quality and feature filtering, 112 samples were retained, yielding 2,531 unique amplicon sequence variants assigned to 34 bacterial phyla, 246 families, and 404 genera. Because formal contaminant assessment was not possible, findings should be interpreted with appropriate caution. Woodland habitats showed significantly higher Shannon diversity, observed ASV richness, and phylogenetic diversity than residential habitats, with Charleston woodland samples exhibiting the highest richness and phylogenetic diversity. Factorial analyses showed significant associations of both city and habitat type with Shannon diversity, observed richness, and Faith's phylogenetic diversity, with significant interaction terms also detected. Beta diversity analyses revealed distinct clustering of Charleston woodland samples, and factorial PERMANOVA indicated significant associations of both city and habitat type across all four beta diversity metrics, with the strongest interaction effect observed for unweighted UniFrac. In conclusion, these results show that habitat type and locality are strongly associated with the composition and diversity of the Ae. albopictus midgut microbiota, underscoring the importance of habitat-specific microbial patterns in mosquito biology.}, }
@article {pmid42175702, year = {2026}, author = {Meadows, NML and Delahay, RJ and McDonald, RA and Powell, S and Hopkins, K and Arnold, L and Harrison, XA}, title = {Fecal Microbiome Varies With Social Group, Age and Bovine Tuberculosis Infection in the European Badger (Meles meles).}, journal = {Molecular ecology}, volume = {35}, number = {10}, pages = {e70369}, doi = {10.1111/mec.70369}, pmid = {42175702}, issn = {1365-294X}, support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Mustelidae/microbiology ; *Feces/microbiology ; *Tuberculosis, Bovine/microbiology ; Cattle ; *Gastrointestinal Microbiome/genetics ; Age Factors ; Mycobacterium bovis/pathogenicity ; RNA, Ribosomal, 16S/genetics ; Social Behavior ; Social Group ; }, abstract = {Host-associated microbes are key components of animal health and physiology, with particular importance for determining responses to pathogen infection. The gut microbiota is highly variable at the individual level, being shaped by a multitude of factors including diet, social behaviour, and age. Yet the relative influence of these traits on microbiota composition, and the consequences of this variation for host responses to pathogens remain unresolved. Here we investigate factors that shape the faecal microbiome in European badgers (Meles meles). Badgers act as a wildlife reservoir of Mycobacterium bovis, a zoonotic pathogen and the causative agent of bovine TB (bTB) in cattle, but the potential role of the microbiome in shaping patterns of infection and severity of disease is not known. Analysing 165 samples from 72 badgers over 3 years, we found that social group and age were key determinants of faecal microbiota composition and identified several bacterial genera associated with bTB infection. Investigation of microbiome dynamics at the individual level using longitudinally sampled badgers revealed marked heterogeneity in age-dependent microbiome trajectories that were not detectable from population level trends in chronological age. These data provide novel insights into the factors associated with microbial community dynamics in complex wild systems and highlight the need for individual-level and longitudinal approaches to studying host-microbiome associations.}, }
@article {pmid42176010, year = {2026}, author = {Davolos, D and Chimenti, C and Fassio, G and Russini, V and Lepri, A and Nocella, E}, title = {Understanding Hepatopancreas-Associated Microbiota in the Supralittoral Tylos ponticus (Crustacea, Isopoda, Oniscidea): Insights from Next-Generation Sequencing Approaches.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02785-4}, pmid = {42176010}, issn = {1432-184X}, abstract = {Tylos isopods, which are found exclusively in supralittoral beaches, play an important ecological role in the harsh sea-land interface contributing significantly to lignocellulose degradation. Herein, we investigated the hepatopancreatic microbiota in the oniscidean isopod Tylos ponticus Grebnitzky, 1874 from an Italian supralittoral zone characterized by the accumulation of beached leaves from the seagrass Posidonia oceanica. To characterize this Tylos-microbe system, we combined three Next Generation Sequencing techniques: 16S rRNA gene metabarcoding, whole-genome sequencing of cultured hepatopancreatic bacteria and shotgun metagenomic sequencing of uncultured bacterial communities. Comparative analyses revealed that some bacterial taxa were associated with the hepatopancreas of T. ponticus but were also detected in the supralittoral sandy beach where the detritivores Tylos live. However, distinct components of the microbial community may be adapted within the hepatopancreas. Moreover, the assembled and annotated genomes of hepatopancreatic bacteria allowed us to identify genes encoding lignocellulose-degrading CAZymes for a better understanding of the role of symbionts in aiding lignocellulose degradation. Finally, our shotgun sequencing data confirmed the presence of an uncultured Candidatus Hepatoplasma (Mollicutes) in the hepatopancreas of T. ponticus, with the provisional taxonomic assignment as Candidatus Hepatoplasma cf. vulgare Tp. We compared this data with recently reported metagenome-assembled genomes of uncultured Hepatoplasmataceae members from isopods, including Candidatus Tyloplasma litorale identified from the semiterrestrial isopod Tylos granuliferus, Candidatus Hepatoplasma vulgare from the terrestrial isopod Armadillidium vulgare, and Candidatus Hepatoplasma scabrum from the terrestrial isopod Porcellio scaber. In such a scenario, a deeper understanding of halophilic bacteria in the supralittoral zone also has broad relevance to applied research, particularly to the biotechnological sector related to marine biomass conversion and plastic degradation.}, }
@article {pmid42176025, year = {2026}, author = {Muhammad, N and Ansar, W and Bashir, T and Khan, HR}, title = {Bacillus-derived antimicrobial peptides as alternatives to antibiotics in poultry: mechanisms, applications, and future prospects- a review.}, journal = {Archives of microbiology}, volume = {208}, number = {8}, pages = {}, pmid = {42176025}, issn = {1432-072X}, mesh = {Animals ; *Antimicrobial Peptides/pharmacology/chemistry ; *Poultry/microbiology ; *Bacillus/chemistry/metabolism ; *Anti-Bacterial Agents/pharmacology ; Biofilms/drug effects ; *Poultry Diseases/microbiology/drug therapy ; }, abstract = {Bacterial enteric pathogens, antimicrobial resistance, and mycotoxin-associated intestinal injury remain important challenges in poultry-associated systems. In this context, Bacillus-derived antimicrobial peptides (AMPs) have attracted attention as potential alternatives to conventional antibiotics due to their structural diversity and multifunctional properties. These peptides include ribosomally synthesized bacteriocins and non-ribosomally synthesized lipopeptides, such as surfactin, iturin, and fengycin. Their amphipathic structures enable interaction with microbial membranes, leading to permeabilization and disruption of cellular homeostasis. In addition to direct antimicrobial activity, these AMPs may interfere with biofilm-associated processes, modulate host immune responses, and help protect against toxin-induced epithelial injury. This review summarizes current knowledge on the diversity, structural characteristics, biosynthesis, mechanisms of action, and microbiological relevance of Bacillus AMPs in poultry-associated environments. Emphasis is placed on membrane targeting, biofilm regulation, immunomodulation, and mycotoxin-related gut protection, as well as limitations associated with antimicrobial resistance. Available evidence indicates that these peptides have diverse mechanisms of action; however, their activity is influenced by peptide class, formulation, microbial ecology, and host physiological factors. In addition, the potential for adaptive or genetically encoded resistance should be considered. Key translational challenges include peptide instability, variability in in vivo efficacy, strain-specific differences, safety considerations, and the lack of standardized comparative models. Future progress will depend on improved delivery systems, microbiome-resolved in vivo studies, and the integration of genomic mining, synthetic biology, and computational peptide design. These approaches may support the development of AMPs with improved stability, specificity, and functional performance in poultry-associated microbial systems.}, }
@article {pmid42176189, year = {2026}, author = {Plum-Jensen, LE and Mohr, MG and Tanabe, TS and Wang, B and Echers, SG and Madsen, NS and Thorup, C and Linhartova, M and Nielsen, LP and Dueholm, MKD and Boesen, T and Marshall, IPG and Dahl, C and Schramm, A}, title = {Distribution of a novel DsrEFH sulfur transferase suggests widespread sulfur oxidation capacity in sulfate reducers.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag130}, pmid = {42176189}, issn = {1751-7370}, abstract = {Microbial sulfur cycling is typically divided into an oxidative and a reductive branch, with microbes driving either sulfide oxidation or sulfate reduction distinguished by their genomic setup. Paradoxically, filamentous cable bacteria perform electrogenic sulfide oxidation but contain genes indicative of sulfate reduction, including the reductive type of dissimilatory sulfite reductase (DsrAB), whereas they apparently lack the canonical sulfur transferase DsrEFH essential for sulfur oxidation. AlphaFold2 structure prediction of conserved cable bacteria proteins with unknown functions identified a protein complex resembling canonical DsrEFH (hereafter termed DsrEFH type II). In vitro characterization of heterologously expressed DsrEFH type II confirmed its sulfur transferase function and, together with site-directed mutagenesis, verified that the conserved cysteine, Cys67, is the active sulfur transfer residue. Genes encoding the novel DsrEFH type II were found in 985 prokaryotic genomes. They typically co-occurred with genes for reductive DsrAB in microbes characterized as sulfate reducers or sulfur disproportionators. This study not only fills an important gap in the sulfide oxidation pathway of cable bacteria, but also suggests that a wide range of sulfate reducing bacteria may be more metabolically versatile than currently understood, representing a major shift in the perception of this globally significant physiological group of microorganisms.}, }
@article {pmid42178691, year = {2026}, author = {Kang, Z and Huang, H and Lin, J and Niu, Y and Chen, J and Tang, J and Hu, Z and Liu, P and Qu, J}, title = {Unraveling Oral Dysbiosis: Microbial Complexity in Common Oral Diseases.}, journal = {MicrobiologyOpen}, volume = {15}, number = {3}, pages = {e70305}, doi = {10.1002/mbo3.70305}, pmid = {42178691}, issn = {2045-8827}, support = {S202510555045//Hunan Provincial College Students' Innovation and Entrepreneurship Training Program/ ; S202410555239//Hunan Provincial College Students' Innovation and Entrepreneurship Training Program/ ; S202310555226//Hunan Provincial College Students' Innovation and Entrepreneurship Training Program/ ; }, mesh = {*Dysbiosis/microbiology ; Humans ; *Microbiota ; *Mouth/microbiology ; *Mouth Diseases/microbiology ; Periodontal Diseases/microbiology ; Dental Caries/microbiology ; Biofilms/growth &amp; development ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {The oral microbiome is highly intricate, hosting billions of bacteria and other microorganisms that form biofilms on various oral surfaces. An imbalanced ecological relationship between the microbial community and the host can lead to various oral diseases. This narrative review explores the current understanding of the correlation between the microbiome and oral diseases. The main body of this manuscript is divided into seven parts, including a review of current research on oral microbial colonization and early life development, an introduction to five common oral diseases related to microorganisms, and a discussion on the relationship between dental caries and periodontal disease at the microbial level. Our aim in presenting this review is to offer a valuable resource for further research on the role of oral microorganisms in diagnosing and treating oral diseases. The oral microbiome's significant impact and diversity characteristics on health and disease have been recognized; however, there remains a severe lack of systematic understanding of its functions, host interactions, and environmental factors. Comprehensive research is urgently needed to elucidate the mechanisms that maintain its ecological balance, providing a scientific foundation for the precise prevention and control of oral diseases. This review comprehensively synthesizes current knowledge regarding oral microbial dysbiosis in the context of the major oral diseases mentioned and proposes a conceptual framework grounded in microbial ecology to elucidate disease progression and guide therapeutic strategies.}, }
@article {pmid42178776, year = {2026}, author = {Lukan, T and Pogačar, K and Kraigher, B and Stare, K and Kovačič, TG and Zagorščak, M and Petek, M and Stefanic, P and Vozelj, A and Levak, V and Povalej, TM and García, JM and Pozo, MJ and Álvarez, E and Franco-Zorrilla, JM and Križnik, M and Baebler, &#x160; and Mandić-Mulec, I and Gruden, K}, title = {ERF transcription factor StPti5 is a regulator of endophyte community maintenance in potato.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.71240}, pmid = {42178776}, issn = {1469-8137}, support = {J4-3089//Slovenian Research and Innovation Agency/ ; J4-4550//Slovenian Research and Innovation Agency/ ; J4-9302//Slovenian Research and Innovation Agency/ ; P4-0116//Slovenian Research and Innovation Agency/ ; P4-0165//Slovenian Research and Innovation Agency/ ; P4-0463//Slovenian Research and Innovation Agency/ ; Z1-60169//Slovenian Research and Innovation Agency/ ; MCIN/AEI/PID2021-124813OBC31//"ERDF A way of making Europe" financed by the European Union/ ; }, abstract = {We have recently identified an ethylene response factor, StPti5, as a susceptibility factor that negatively regulates immune responses to diverse pathogens. Here, we investigated the role of StPti5 in the processes involved in the colonization of potato with beneficial organisms. RNA-seq showed that at the time of Bacillus subtilis biofilm establishment, immune responses in interacting roots were attenuated, and a complex transcriptional network was triggered, with ethylene signaling being a central module and StPti5 strongly induced. Interestingly, the response is intensified if plants are inoculated by two antagonistic B. subtilis strains. While StPti5 is not involved in the establishment of biofilm on roots, we show that bacterial abundance increases in shoots of StPti5-silenced plants. Remarkably, root colonization by the arbuscular mycorrhizal fungus Rhizophagus irregularis was also higher in the StPti5-silenced plants. To decipher the mechanistic basis of StPti5 function, we performed a DAP-seq experiment and showed that StRIN13, a regulator of plant immune signaling, is a direct target of StPti5. StPti5 is involved both in suppressing defense against harmful and limiting colonization by beneficial microbes. Such a mechanistic understanding of plant-microbe interaction paves the way for sustainable crop management.}, }
@article {pmid42181278, year = {2026}, author = {De Yebra, P and Zoccarato, L and Galindo, JA and Numberger, D and Abdulkadir, N and Grossart, HP and Greenwood, AD}, title = {Diversity of antibiotic resistance genes increases in urbanized lakes: A multi-tool screening.}, journal = {iScience}, volume = {29}, number = {6}, pages = {115892}, pmid = {42181278}, issn = {2589-0042}, abstract = {Antimicrobial resistance (AMR) threatens to cause up to 10 million deaths annually by 2050 if no action is taken. Using shotgun sequencing, we examined the eco-evolutionary dynamics of AMR across urban-rural environment gradients in lake water and sediments, a farm pond and a wastewater treatment plant (WWTP). ARGs were identified using multiple databases and five bioinformatic tools, detecting up to 18 ARG classes-more than any single tool alone. ARG diversity was higher in urban lake sediments, urban waters, and wastewater compared to rural lake sediments and water. Among all environments, urban lake water showed the highest overall ARG abundance, second only to wastewater, and this pattern held across all ARG classes, except for aminoglycoside resistance, which was most prevalent in rural lake sediments. These findings highlight multi-tool ARG screening efficiency, WWTPs and urban sediments as major ARG reservoirs, and emphasize the need for enhanced urban-rural AMR surveillance.}, }
@article {pmid42181306, year = {2026}, author = {Bhadury, P and Danda, AA and Ghosh, A and Yash,  and Saini, N and Chowdhury, DR and Saha, S and Dubey, SK}, title = {Dataset of prokaryotic and eukaryotic community structures from sediment and surface water eDNA of a sustainable mangrove fisheries (SMF) aquaculture pond.}, journal = {Data in brief}, volume = {66}, number = {}, pages = {112800}, pmid = {42181306}, issn = {2352-3409}, abstract = {Sustainable mangrove fisheries (SMF) is an integrated mangrove fisheries approach used in coastal aquaculture ponds that brings sustainability to coastal aquaculture practices. To track the positive value of mangrove on the aquaculture practices, sediment and overlying surface water based environmental DNA (eDNA) biomonitoring has been initiated in SMF pond of Haroa Block (West Bengal, India), in close proximity to Sundarbans mangrove. In the post-monsoon of 2025 (January), sediment and overlying surface water samples were collected from the same SMF pond, followed by application of eDNA extraction and Oxford Nanopore Technologies (ONT) sequencing to deduce biological communities. During sampling, in-situ environmental parameters were recorded and dissolved nutrients were also measured. The dissolved nitrate and reactive silicate concentrations (320.32 and 46.85 µM respectively) were high in SMF pond reflecting effective mimicry of natural mangroves within the studied SMF pond. Using MinION platform integrating ONT, prokaryotic communities based on 16S rRNA metabarcoding revealed high abundance of Proteobacteria, followed by Firmicutes which were higher in sediment compared to surface water. There was high abundance of Bacteroidetes and Actinobacteria in sediment compared to the surface water reflecting the potential pool of complex forms of organic carbon. Microphytobenthos in the sediment was represented by members of Cyanobacteria. At the 18S rRNA level, members of Bacillariophyta dominated both sediment and water reflecting their importance in photosynthetic primary production and potential food for shrimps growing in the SMF pond. Besides, sequences representing other groups of alveolates were also encountered in sediment and surface water. The presence of Ascomycota and Basidiomycota within the eukaryotic pool reflecting their specific role in breakdown and utilization of mangrove litter, in addition to Firmicutes. This study generates key baseline information for long-term monitoring and represents the first eDNA-based dataset for sediment and surface water of prokaryotic and eukaryotic biological communities within the SMF.}, }
@article {pmid42181765, year = {2026}, author = {Gervasi, A and Schutz, L and Cardol, P and Meyer, PE}, title = {Motilitometer: A compact modular microscope for motility and photoresponse analysis of microorganisms.}, journal = {HardwareX}, volume = {26}, number = {}, pages = {e00788}, pmid = {42181765}, issn = {2468-0672}, abstract = {In biology, cell motility is a valuable indicator, revealing how cells sense their environment, adapt to stimuli, and reflect their physiological state. In this paper, we present a modular microscopy system designed to study the motility of microorganisms. The setup is compact, assembled from low-cost 3D-printed and widely available components. It integrates programmable multispectral illumination to enable controlled photo stimulation and investigation of light-induced behavioral responses, including phototaxis. Initially developed for the investigation of photosynthetic microalgae, the system is easily adaptable to a wide range of motile microorganisms. It supports two complementary observation modes: a droplet-based chamber that minimizes sedimentation for cell speed analysis, and a deeper chamber that allows sedimentation, enabling quantitative assessment of motility fraction and orientation relative to directional light. The optical system provides a magnification of up to approximately 9×, sufficient for the precise centroid detection and tracking of single cells. This open-source, DIY (Do It Yourself) microscopy platform offers an accessible tool for photobiology, microbial ecology, and biophysics, helping democratize quantitative motility studies.}, }
@article {pmid42168408, year = {2026}, author = {Maskow, T and Duong, HL and Fernández Merayo, N and Schlosser, D}, title = {Biocalorimetry for the biotechnological use of natural and synthetic macromolecules.}, journal = {Applied microbiology and biotechnology}, volume = {110}, number = {1}, pages = {}, pmid = {42168408}, issn = {1432-0614}, mesh = {*Biotechnology/methods ; *Calorimetry/methods ; Biomass ; *Macromolecular Substances/metabolism ; Fermentation ; Plastics/metabolism ; }, abstract = {Biocalorimetry offers a powerful approach for real-time process monitoring and optimization in the biotechnological utilization of both natural and synthetic macromolecules, particularly in complex solid-state systems aiming at the valorization of plant biomass or plastics' waste. This review critically examines general strengths and limitations of biothermodynamics and calorimetry for monitoring microbial activity, which can be tracked across diverse scales and substrates via metabolic heat measurements. Metabolic heat-derived activity parameters enable the robust quantitative evaluation of the performance of microorganisms for substrate conversion, hence potentially representing valuable tools for bioprocess development and operation. While biocalorimetry is established in liquid-phase cultivation systems to some extent, its adaptation to solid-state fermentation, composting, and the biochemical breakdown of solid plastics still remains in early stages while holding promise for real-time control and upscaling. Challenges and limits of the applicability of this technology currently persist especially for mixed cultures and non-sterile processes. Nevertheless, expanding metabolic heat-based datasets to microbial functional traits could advance ecological and industrial applications. Overall, biocalorimetry is positioned as a valuable tool for advancing circular bioeconomy strategies, though further validation and methodological development are needed for broader adoption in both research and industrial contexts. KEY POINTS: • Biocalorimetry reliably quantifies microbial activity on complex solid substrates. • Biocalorimetry can support plant biomass and plastic waste valorization in a circular bioeconomy. • Biocalorimetric monitoring is applicable from the laboratory to the technical scale.}, }
@article {pmid42168837, year = {2026}, author = {Tong, L and Liu, Y and Han, F and Jiang, Y and Ying, S and Zhang, B and Cheng, Y and Liu, Z and Shi, Y and Xu, M and Tang, C and Sui, S and Chen, T}, title = {Exploring microbial ecology in public swimming pools: a metagenomic investigation of community structure and environmental correlates.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05157-7}, pmid = {42168837}, issn = {1471-2180}, support = {GWVI-4//The Key Projects in the Three-year Plan of Shanghai Municipal Public Health System (2023-2025)/ ; }, abstract = {Epidemiological studies have identified correlations between swimming and outbreaks of various infectious diseases. However, a comprehensive understanding of the pathogens present in public swimming pool water has yet to be systematically established. Swimming pool water samples were collected from 20 indoor public swimming pools in Shanghai, China during the summer of 2023. After quality inspection of the extracted nucleic acid, the qualified samples were subjected to metagenomic sequencing to profile the microbial communities of swimming pool water. A total of 24,035 microbial species were identified with the abundance of bacteria (99.46%), followed by archaea (0.29%), viruses (0.20%), and fungi (0.05%), including 441 pathogenic species, 23 of which were classified as biosafety level 3 (BSL-3) microorganisms. Environmental sources constituted the dominant origin (86.00%) of the pool water microbiome. Additionally, suburban pools demonstrated greater microbial diversity than urban pools (P < 0.05). The abundance of viruses exhibited a positive correlation with the concentration of urea in pool water (r = 0.31, P < 0.05). This study demonstrated that swimming pool water serves as a potent reservoir and mixing vessel for various highly pathogenic microorganisms. Effective water quality management strategies are essential to mitigating the potential public health threats of public swimming pools.}, }
@article {pmid42171373, year = {2026}, author = {Schroer, HW and Beghini, F and Raygoza Garay, JA and Christakis, NA and Bosch, DE}, title = {Metagenomic polymorphic toxin effector and immunity profiling predicts microbiome development and disease-related dysbiosis.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0030526}, doi = {10.1128/msystems.00305-26}, pmid = {42171373}, issn = {2379-5077}, abstract = {Bacteria use antagonistic interbacterial weapons, such as polymorphic toxin secretion systems (TSS), to compete for niches in the human gut microbiome. We hypothesized that TSS influence gut microbiome development and disease-related dysbiosis. We developed a bioinformatic marker gene approach (PolyProf) to quantify TSS including ~200 effector and immunity genes and applied it to ~15,000 publicly available human metagenomes. PolyProf alpha and beta diversity readily distinguished 12 different human disease states and enabled the construction of highly accurate linear regression classifier machine learning models. Elastic net machine learning models integrating bacterial taxonomy with PolyProf had strong predictive value for 12 disease states, outperforming models utilizing taxonomy alone. During microbiome development in the first year of life, PolyProf alpha diversity increases, and beta diversity becomes increasingly like the maternal microbiome, influenced by vertical transfer, delivery mode, and breastfeeding. PolyProf is related to strain sharing among adults through social interactions. In summary, TSS genes strongly correlate with microbiome development and interpersonal strain sharing, suggesting roles for interbacterial antagonism. Since PolyProf distinguishes diverse adult disease statuses, these dynamics may contribute to non-genetic inheritance.IMPORTANCEPrevious research has demonstrated that bacteria compete within the gut microbiome using toxin secretion systems (TSS). How TSS contribute to human microbiome development and the microbiome alterations observed in human diseases is not known. This study develops a new bioinformatic tool for profiling TSS-related genes in metagenomic data. Application of this approach to large-scale human fecal metagenomic data demonstrates the dynamic association of TSS during microbiome development, including the exchange of strains among social contacts. TSS gene abundance patterns are highly predictive of 12 disease states. This study advances the field by enabling TSS profiling in metagenomes and by identifying disease and microbiome development biomarkers that provide hypotheses for future mechanistic studies and may be useful for disease diagnosis.}, }
@article {pmid42167281, year = {2026}, author = {Bambakidis, T and Liu, S and Wettengel, AM and Holmes, RM and Dinga, BJ and Koning, AA and McIntyre, PB and Borton, MA and Mann, PJ and Crump, BC}, title = {Congo River Bacterioplankton Genomic Diversity Reflects Water Travel Time, Wetland Habitats, and Greenhouse Gases.}, journal = {Environmental microbiology}, volume = {28}, number = {5}, pages = {e70327}, doi = {10.1111/1462-2920.70327}, pmid = {42167281}, issn = {1462-2920}, support = {DEB-1840243//National Science Foundation/ ; OCE-0851101//National Science Foundation/ ; OCE-0851015//National Science Foundation/ ; DGE-0718123//National Science Foundation/ ; DEB-1501836//National Science Foundation/ ; 52379057//China Natural Science Foundation/ ; //David and Lucile Packard Foundation/ ; //U.S. Geological Survey/ ; 10.46936/10.25585/60001289//Joint Genome Institute/ ; }, mesh = {*Wetlands ; *Rivers/microbiology/chemistry ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Greenhouse Gases/analysis/metabolism ; Congo ; RNA, Ribosomal, 16S/genetics ; *Plankton/genetics/classification ; Ecosystem ; Methane/metabolism ; Phylogeny ; Carbon Cycle ; Biodiversity ; Metagenome ; }, abstract = {Tropical rivers are major contributors to global carbon cycling, yet the microbial communities driving these transformations remain largely uncharacterized. We investigated bacterioplankton communities along the northwest Congo watershed using 16S rRNA and metagenomic sequencing, paired with hydrological, biogeochemical, and greenhouse gas data. In large rivers, community composition correlated with temperature and water travel time, while smaller streams were shaped by nutrient chemistry and landscape. Most sites were dominated by Burkholderiales, but composition varied, especially in DOC-rich Cuvette Centrale wetland streams that hosted distinct communities associated with high methane and CO2, and low oxygen. Indicator species analysis identified specific taxa and metagenome-assembled genomes (MAGs) strongly associated with long travel times, wetlands, and methane, including methanotrophs (Methylcoccaceae, Methylophilaceae, Methylomonas) and MAGs encoding diverse carbon-processing metabolisms. For global context, Congo and northern Thailand river bacterioplankton were more similar to each other than to temperate Connecticut River communities, possibly reflecting shared tropical features such as high precipitation, temperature, and travel time. As in temperate systems, bacterioplankton in large tropical rivers are shaped by temperature and hydrology, while smaller tropical streams reflect localized environmental drivers. The striking similarity of tropical river bacterioplankton from Africa and Asia suggests the primacy of environmental controls on river bacterioplankton.}, }
@article {pmid42167521, year = {2026}, author = {Wolacewicz, M and Decewicz, P and Valdes, ME and Iaconi, OS and Todiras, M and Ferdohleb, A and Rodriguez-Mozaz, S and Borrego, CM and Dziewit, L}, title = {The occurrence and removal of antibiotic residues and antibiotic resistance genes in the largest European constructed wetland at Orhei (Moldova).}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128381}, doi = {10.1016/j.envpol.2026.128381}, pmid = {42167521}, issn = {1873-6424}, abstract = {Constructed wetlands (CWs) are increasingly promoted as low-cost, nature-based solutions for wastewater treatment, particularly in low- and middle-income countries (LMICs), yet their performance in removing pharmaceutical compounds, antibiotic resistance genes (ARGs), and bacterial pathogens remains insufficiently characterized under real-field-scale conditions. Here, we investigated the fate of pharmaceutical compounds (including antibiotic residues), wastewater bacterial communities, and the associated ARGs in the largest European passive treatment system, the vertical-flow CW of Orhei (Moldova), serving nearly 26,000 inhabitants. Metagenomic profiling revealed 783 bacterial families, with a reduction from 33 families in raw sewage to 25 in the final effluent and clear enrichment of autochthonous wetland taxa. A total of 150 ARG types conferring resistance to 16 antibiotic classes were detected. The cumulative ARG load decreased by approximately 78% from influent to effluent. ARGs conferring resistance to fosfomycin, nitroimidazoles, rifamycins, streptothricin, oxazolidinones, and pleuromutilins were not detected in the final effluent, suggesting effective removal to below the detection limit of the applied metagenomic method, while sulfonamide resistance genes (sul1, sul2) persisted across all stages. Out of 29 antibiotic residues analyzed, 13 (including two sulfamethoxazole metabolites) were detected, together with 14 non-antibiotic pharmaceuticals (out of 30 residues analyzed). The removal of individual antibiotics ranged between 85 and 100%, and for other pharmaceuticals between 34 and 100%, although some compounds (e.g., carbamazepine, 10,11-epoxycarbamazepine, alprazolam) showed negative removals. Environmental risk assessment (risk quotients, RQ) indicated no significant risk to freshwater biota (RQ < 0.1) for all detected compounds in the treated effluent. Results demonstrated that a large-scale CW in the LMIC context can substantially reduce antibiotic residues and ARGs, supporting its role as an effective, nature-based component of One Health-oriented wastewater management.}, }
@article {pmid42094371, year = {2026}, author = {Zhang, C and Sabonis, D and Cai, Y and Zang, Z and Tamulaitiene, G and Gerdt, JP}, title = {Chemical suppression of a bacterial immune system revives repressed phages.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {42094371}, issn = {2692-8205}, abstract = {Many antiviral immune systems have recently been discovered in bacteria. The mechanisms of several are obscure, as are their individual significance for antiphage defense. To shed light on the mechanism and significance of the two-component type I Thoeris antiphage immune system, we leveraged high-throughput phenotypic screening to identify three small molecule inhibitors. The inhibitors target the ThsA NADase component, inhibiting its 3'-cADPR-activated filamentation. The temporal control afforded by the small-molecule inhibitors allowed us to answer an outstanding question in antiviral immunity-is persistent immunity required to repress phage titers, or do immune systems become unnecessary after eradicating infectious phages? We found that Thoeris immunity must be maintained, as chemical inhibition enabled repressed phages to revive and overtake the bacterial population. Furthermore, due to the cooperative nature of antiviral immunity, we found that Thoeris must be inhibited in only 10% of the bacteria to cause phage-induced lysis of the entire population.}, }
@article {pmid42166181, year = {2026}, author = {Hijri, M and Aliyat, FZ and Legeay, J and Lee, SJ and Idbella, M and Anwar, AF and Errafii, K and Marasco, R and Biswas, MK and Venturi, V and Zézé, A and Gemeda, M and Eziuzor, SC and Makhalanyane, T and Ahmed, B}, title = {Advancing microbial ecology, microbiomes, and One Health in Africa: From regional initiatives to pan-African flagship programs.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag132}, pmid = {42166181}, issn = {1751-7370}, abstract = {Microbial ecology and microbiome science are increasingly central to global "One Health" efforts, a framework that recognizes the interconnected health of humans, animals, and the environment. In Africa, these fields are particularly important for addressing interconnected challenges in public health, agriculture, and ecosystem resilience. Discussions at the ISME-Africa Morocco 2025 regional meeting highlighted both progress and persistent gaps in African microbiome research. Initiatives such as the African BioGenome Project and Human Heredity and Health in Africa demonstrate the feasibility of population-representative studies, regional training, networking, and open-science frameworks; however, the research landscape remains fragmented, with limited intra-African collaboration and continued reliance on external funding and leadership. The development of Africa-specific reference genomes, population-based microbiome datasets, is essential to address these gaps and ensure global representation. This perspective synthesizes current evidence and outlines strategic priorities to transition from toward coordinated pan-African research networks and flagship programs. Key recommendations include developing Africa-specific genome reference datasets, establishing pan-continental consortia, fostering equitable African-non-African partnerships, integrating microbiome science into policy frameworks, and adopting FAIR open-science practices. Strengthening bioinformatics and computational capacity will be essential to transform fragmented data into high-impact, coordinated insights. Advancing these priorities will accelerate translation into One Health outcomes, including antimicrobial resistance surveillance, food security, climate-resilient agriculture, and precision medicine. Africa's rich microbial diversity offers significant potential for antibiotic discovery, improved crop productivity, and sustainable agricultural systems. Collectively, strengthening Africa-led, collaborative microbiome research will enable the continent's microbial diversity to drive impactful solutions with regional and global relevance.}, }
@article {pmid42166940, year = {2026}, author = {Ali, S and Chaudhary, AA and Sheikh, WM and Ali, MAM and Chopra, C and Dar, MA and Wani, AK and Bashir, SM}, title = {Genome-resolved metagenomics of the tumour microbiome: From strain diversity to functional cancer ecology.}, journal = {Pathology, research and practice}, volume = {285}, number = {}, pages = {156543}, doi = {10.1016/j.prp.2026.156543}, pmid = {42166940}, issn = {1618-0631}, abstract = {Advances in genome-resolved metagenomics, spatial transcriptomics, and single-cell sequencing have revealed that tumour-associated microbes are not random contaminants but structured, functionally heterogeneous components of the tumour microenvironment. Strain-level genomic reconstruction uncovers substantial intra-species diversity, encompassing accessory genes, mobile elements, and metabolic modules that collectively influence genotoxicity, immune modulation, drug metabolism, redox regulation, and biofilm formation. These microbial traits often assemble into convergent functional guilds that drive DNA damage, immune polarization, therapeutic resistance, and metastatic potential across tumour types. Integrative multi-omics analyses demonstrate that only a subset of detected microbial taxa is transcriptionally and metabolically active within tumours, underscoring the importance of combining metatranscriptomics, proteomics, metabolomics, and spatial profiling to delineate biologically meaningful host-microbe interactions. Spatial and single-cell mapping further reveal that intratumoural microbes occupy defined intracellular and extracellular microniches often aligned with hypoxic regions, myeloid-rich aggregates, T-cell exclusion zones, and metabolically reprogrammed epithelial states, reinforcing their role as active participants in tumour physiology rather than passive passengers. Mechanistic evidence now indicates that tumour-resident microbial ecosystems modulate responses to chemotherapy, immune checkpoint blockade, and radiotherapy, while contributing to premetastatic niche conditioning. Low-abundance but high-impact keystone microbial genomes can exert a disproportionate influence on tumour progression and therapeutic outcomes, providing new opportunities for biomarker discovery and microbiome-targeted interventions. This review integrates genome-resolved, spatial, and functional perspectives to propose an onco-metagenome framework that links tumour microbial ecology to cancer evolution, immune regulation, and translational intervention.}, }
@article {pmid42153623, year = {2026}, author = {Diaz-Colunga, J and Catalan, P and San Roman, M and Arrabal, A and Sanchez, A}, title = {Full factorial construction of synthetic microbial communities.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {42153623}, issn = {2050-084X}, support = {PID2021-125478NAI00//Spanish National Plan for Scientific and Technical Research and Innovation/ ; PID2022-142185NB-C21//Spanish National Plan for Scientific and Technical Research and Innovation/ ; PID2022-142185NB-C22//Spanish National Plan for Scientific and Technical Research and Innovation/ ; 101088469/ERC_/European Research Council/International ; }, mesh = {*Pseudomonas aeruginosa/genetics/growth &amp; development ; *Microbial Consortia ; *Synthetic Biology/methods ; *Microbial Interactions ; Biomass ; }, abstract = {Constructing combinatorially complete species assemblages is often necessary to dissect the complexity of microbial interactions and to find optimal microbial consortia. At the moment, this is accomplished through either painstaking, labor-intensive liquid handling procedures, or through the use of state-of-the-art microfluidic devices. Here, we present a simple, rapid, low-cost, and highly accessible liquid handling methodology for assembling all possible combinations of a library of microbial strains, which can be implemented with basic laboratory equipment. To demonstrate the usefulness of this methodology, we construct a combinatorially complete set of consortia from a library of eight Pseudomonas aeruginosa strains, and empirically measure the community-function landscape of biomass productivity, identify the highest-yield community, and dissect the interactions that lead to its optimal function. This easy-to-implement, inexpensive methodology will make the assembly of combinatorially complete microbial consortia easily accessible for all laboratories.}, }
@article {pmid42153658, year = {2026}, author = {Chen, X and Chen, GG and Gong, Z and Zhu, H and Liang, Z and Chan, JYK and Tong, MCF and Chen, Z and Chang, WT}, title = {The middle ear-nasopharyngeal microbiome axis associated with obstructive Eustachian tube dysfunction in chronic otitis media.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0000726}, doi = {10.1128/msystems.00007-26}, pmid = {42153658}, issn = {2379-5077}, abstract = {Obstructive Eustachian tube dysfunction (ETD) commonly complicates chronic otitis media (COM), yet microbial factors at the Eustachian tube (ET) openings remain poorly understood. In this prospective cohort study, we characterized the microbiota at both the middle ear (ME) and nasopharyngeal (NP) ET openings in COM patients undergoing ear surgery and examined associations with obstructive ETD over one year of follow-up. Using 16S rRNA gene sequencing and functional inference, we profiled microbial communities from the ME-side ET opening and the torus tubarius on both surgical-side and contralateral nasopharynx. Among 37 patients (18 with ETD, 19 without), ME and NP microbiota differed significantly in composition. Ears with ETD showed increased ME microbial diversity and enrichment of Neobacillus, Agrobacterium, and Sphingomonas. Paired NP-ME analyses indicated an altered NP-ME microbial relationship in ETD, with Neobacillus showing a nasopharyngeal source signal. Functional prediction revealed increased porphyrin metabolism and decreased pyruvate metabolism in ME microbiota with ETD, suggesting a shift toward biofilm formation and altered redox states. Anaerococcus was increased in the nasopharynx of patients with bilateral COM. These findings identify distinct microbial and metabolic features of COM with obstructive ETD, supporting a role for nasopharyngeal-microbial influence on ME pathology.IMPORTANCEChronic otitis media (COM) is a common and often persistent ear disease, especially when complicated by Eustachian tube dysfunction (ETD). By profiling microbiota at both Eustachian tube openings, this study links upper-airway microbial ecology with middle-ear microbial states in COM and helps clarify where clinically relevant signals may arise along the Eustachian tube pathway. The paired nasopharyngeal-middle ear design revealed that nasopharyngeal microbes may be linked to middle-ear community shifts in COM with obstructive ETD, consistent with a potential upper airway contribution to the middle-ear microbiota, generating testable hypotheses about microbial exchange and persistence. These findings highlight the upper airway microbiome as a potential target for developing new preventive and therapeutic strategies in COM.}, }
@article {pmid42156649, year = {2026}, author = {Rangamaran, VR and Sushmitha, TJ and Tamilmani, KK and Murugesan, H and Gopal, D}, title = {Exploring the Ocean's Microbial World: Techniques and Protocols for Microbiome Research.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {33-46}, pmid = {42156649}, issn = {1940-6029}, mesh = {*Microbiota/genetics ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; RNA, Ribosomal, 16S/genetics ; Oceans and Seas ; *Seawater/microbiology ; Computational Biology/methods ; }, abstract = {Marine microbiomes play a crucial role in oceanic ecosystems, influencing biogeochemical cycles, climate regulation, and marine biodiversity. Accurate characterization of these microbial communities requires standardized protocols for sample collection, processing, sequencing and data analysis. This chapter provides a comprehensive guide to essential methodologies for marine microbiome research including field sampling strategies, DNA and RNA extraction techniques, high-throughput sequencing approaches (such as 16S rRNA amplicon sequencing and metagenomics) and bioinformatics pipelines for data interpretation. Additionally, we discuss quality control measures, best practices for reproducibility, and challenges associated with marine microbiome profiling. By adopting standardized methodologies, researchers can generate reliable, comparable datasets that enhance our understanding of marine microbial ecology and its broader environmental implications.}, }
@article {pmid42156652, year = {2026}, author = {Kosmopoulos, JC and Anantharaman, K}, title = {Computational Microbial and Viral Ecology Analysis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {83-141}, pmid = {42156652}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; *Computational Biology/methods ; Metagenome ; *Microbiota/genetics ; *Viruses/genetics/classification ; Virome ; Bacteriophages/genetics ; Bacteria/genetics ; Archaea/genetics ; }, abstract = {The explosion in known microbial diversity in the last two decades has made it abundantly clear that microbes in the environment do not exist in isolation; they are members of communities. Accordingly, omics approaches such as metagenomics have revealed that interactions between diverse groups of community members such as archaea, bacteria, and viruses (bacteriophages) are common and have significant impacts on entire microbiomes. Thus, to have a well-developed understanding of microbes as they naturally exist in the environment, biological entities of all kinds must be studied together. While numerous protocols for metagenome analysis exist, comprehensive published protocols for the simultaneous analysis of viruses and prokaryotes together are scarce. Further, as bioinformatic methods for microbiology rapidly advance, existing metagenomic tools and pipelines require frequent re-evaluation. This ensures the adherence to best practices for microbiome and metagenomic data analysis. Here, we offer an expansive approach for the joint analysis of bulk sequence data from a mixed microbial community (metagenomes) and viral-sized fraction communities (viromes). This chapter serves as a beginner's-level guide for researchers with limited bioinformatics expertise who wish to engage in multiscale metagenome and virome analyses. We cover steps from initial study design to sequence read processing, metagenome assembly, quality control, virus identification, microbial and viral genome binning, taxonomic characterization, species-level clustering, and host-virus predictions. We also provide the bioinformatic scripts used in our workflow for reuse in one's own computational methods. Lastly, we discuss additional approaches a researcher can take after processing data with this workflow.}, }
@article {pmid42158881, year = {2026}, author = {Marzi, M and Sener, G and Sener, TE}, title = {The gut-kidney axis in calcium oxalate nephrolithiasis: Nutritional and microbial insights.}, journal = {Northern clinics of Istanbul}, volume = {13}, number = {2}, pages = {252-262}, pmid = {42158881}, issn = {2536-4553}, abstract = {Calcium oxalate (CaOx) nephrolithiasis is the most common type of kidney stone disease worldwide. Recent studies show that its development cannot be explained solely by renal solute handling; instead, it reflects a broader interaction between dietary habits, the intestinal microbiota, and host metabolic responses. Intestinal absorption of calcium and oxalate-two central drivers of lithogenesis-is shaped by both microbial composition and dietary patterns. Although Oxalobacter formigenes was initially regarded as the main oxalate-degrading organism, newer studies indicate that a wider disturbance of the gut microbiota, especially the loss of short-chain fatty acid (SCFA)-producing species, may increase susceptibility to stone formation. In this review, nutritional, microbial, and mechanistic evidence is brought together to examine how diet-particularly salt, animal protein, calcium, oxalate, fruits, vegetables, and water intake-modulates the gut-kidney axis. Diets high in salt or animal protein tend to shift the microbiota toward more pro-inflammatory and acidogenic profiles, while fiber-rich, plant-based diets and adequate hydration appear to support microbial diversity, SCFA production, and epithelial barrier integrity. Probiotic and synbiotic interventions have also gained attention as potential strategies to reduce stone recurrence by targeting gut microbial function. Taken together, current findings suggest that the gut-kidney axis is a dynamic metabolic link between diet, microbial ecology, and renal physiology. Future studies combining multi-omics methods with personalized nutritional approaches may help develop more effective microbiota-based prevention and treatment strategies for CaOx nephrolithiasis.}, }
@article {pmid42160933, year = {2026}, author = {Geng, C and Deng, T and Ren, K and Chen, X and Xue, S and Chen, L and Huang, C and Xu, M}, title = {Divergent structure but convergent metabolic organization of tetrabromobisphenol A degrading microbial consortia from aerobic and anaerobic conditions.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142454}, doi = {10.1016/j.jhazmat.2026.142454}, pmid = {42160933}, issn = {1873-3336}, abstract = {Microbial consortia drive the degradation of persistent pollutants through complex metabolic interactions. However, how these interactions are reconfigured under contrasting redox conditions to maintain functional efficiency remains a fundamental question in microbial ecology. Here, we used a top-down enrichment approach to investigate the collaborative degradation of tetrabromobisphenol A (TBBPA) under both aerobic and anaerobic conditions, integrating sequential transfer cultivation, metagenomics, network analysis, pure culture experiments, and predictive modeling. Sequential transfers significantly (p < 0.05) enhanced TBBPA degradation efficiencies under both regimes, driving distinct structural successions in the microbial communities. Specialist taxa such as Sphingopyxis (aerobic) and Novosphingobium (anaerobic) were phase-specifically enriched, whereas generalists like Pseudomonas and Comamonas emerged as highly interconnected keystone taxa under both conditions. Pure culture experiments and genomic reconstruction indicated functional partitioning among different taxa, where specialists might mediate debromination and β-scission by haloalkane dehalogenase and cytochrome P450, respectively. Furthermore, generalists harbored genetic modules for downstream ring-cleavage pathways, collectively forming a metabolic network that partitions degradation steps across the community. Partial least squares (PLS) regression and random forest analysis supported this functional partitioning and indicated that the overall TBBPA degradation is an emergent community property driven by community‑level interactions. This study suggests a principle of structure-divergent but convergent metabolic organization in collaborative TBBPA-degrading consortia, providing a mechanistic basis for designing synthetic communities to optimize bioremediation of brominated pollutants across diverse environmental settings.}, }
@article {pmid42161759, year = {2026}, author = {Chen, Y and Wilschut, RA and Garbeva, P}, title = {The legacy of soil chemistry: a hidden manipulator driving plant-soil feedbacks.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2026.04.009}, pmid = {42161759}, issn = {1878-4380}, abstract = {Plants actively reshape the soil environment through their roots and associated microbes, creating lasting changes known as soil legacies that influence future plant generations via plant-soil feedbacks. While biotic factors such as pathogens and mutualists have received much attention, the chemical legacies, including water-soluble and volatile organic compounds, remain underexplored. These metabolites, produced by plants and soil microbes, modulate microbial communities, nutrient dynamics, and plant defenses, driving positive or negative feedbacks. This opinion article synthesizes recent evidence on soil chemical diversity, their role in legacy formation and persistence, while highlighting analytical challenges and promising applications in agriculture and ecology.}, }
@article {pmid42162823, year = {2026}, author = {Naying, L and Bo, Z and Wei-Min, W and Xin, L and Ruixi, L and Xintong, M and Xiaofeng, W and Li, Z and Shaoliang, Y and Honghui, L and Yixin, H}, title = {Simulated freeze-thaw cycles restructure plastisphere microbiomes and functional gene co-occurrence networks in alpine lake sediment microcosms.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128322}, doi = {10.1016/j.envpol.2026.128322}, pmid = {42162823}, issn = {1873-6424}, abstract = {Microplastics (MPs) are increasingly recognized as dynamic ecological interfaces rather than inert contaminants, yet their role in shaping microbial functional interactions under climate-driven disturbances remains poorly understood. In particular, how climate driven freeze-thaw cycles (FTCs) influence the dynamics of mobile genetic elements (MGEs) within the plastisphere remains unclear. Here, we used controlled microcosms containing sediments from Tibetan Plateau lakes and polyethylene/polyethylene terephthalate particles to examine how simulated extreme FTCs were associated with changes in plastisphere microbial communities and functional gene co-occurrence patterns. FTCs reshaped plastisphere microbial communities, but their assembly trajectories differed between habitats. In the plastisphere, deterministic selection was pronounced at early FTC stages, whereas it did not further intensify with increasing FTC frequency. In contrast, sediment communities exhibited a progressive shift toward deterministic assembly with increasing FTCs. Concomitantly, MGEs were relatively enriched in the plastisphere and co-occurrence with genes involved in carbon metabolism, antibiotic resistance genes (ARGs), and virulence factors (VFs), forming interconnected functional networks. Notably, FTCs were associated with the enrichment of specific carbon metabolizing taxa (e.g., Comamonas and Brevundimonas) within the plastisphere that also carried relatively high abundances of MGEs, ARGs, and VFs. These patterns suggest that MPs may provide ecological niches linking carbon utilization and gene exchange potential. Collectively, this work highlights the interactive influence of climate-related disturbance and emerging pollutants on plastisphere microbial ecology, and provides a mechanistic basis for future assessment of ecological implications in fragile alpine ecosystems.}, }
@article {pmid42163999, year = {2026}, author = {Kumar, C and Saini, N and Ghosh, A and Bhadury, P}, title = {Genome description of a potentially novel species of Rossellomorea sp. strain H39_3 isolated from the Hindon River, India.}, journal = {Access microbiology}, volume = {8}, number = {5}, pages = {}, pmid = {42163999}, issn = {2516-8290}, abstract = {In October 2024, a putative novel species, belonging to the genus Rossellomorea, designated as strain H39_3, was isolated using Luria-Bertani medium from surface water representing station H39, located on the Hindon River, in close proximity to Gautam Buddha Nagar in Uttar Pradesh, India. The 16S rRNA sequence of this isolate showed 100% identity to Rossellomorea marisflavi from the International Nucleotide Sequence Database Collaboration (INSDC) DNA databases (GenBank/DDBJ/ENA). Whole-genome sequencing was undertaken using long-read sequencing with Oxford Nanopore Technologies (ONT) chemistry on the MinION platform, followed by genome annotation against the NCBI Reference Sequence Database (RefSeq) and Genome Taxonomy Database (GTDB) databases. The genome is ~4.46 Mb in size, with a G+C content of 48.64 mol%. The low average nucleotide identity (92.23%) and digital DNA-DNA hybridization (46.1%) values showed affiliation with the reference strain R. marisflavi, indicating the isolate as a potential novel species. Functional analysis of the draft genome of this isolate revealed an array of genes, including the presence of arsC (arsenate reductase), the assimilatory nitrate reduction pathway and the ability to degrade polysaccharides. The presence of nitrogen metabolizing genes such as nirB (nitrite reductase subunit B), along with the ability to break down complex forms of carbon, offers the potential of this strain for application in bioremediation of contaminated river ecosystems.}, }
@article {pmid42164315, year = {2026}, author = {O'Connor, BRW and Allen, D and Quinn, M and Kozey, M and Léveillé, RJ and Whyte, LG}, title = {Bipolar investigation of near-surface glacial ice reveals an active microbial ecosystem driven by photosynthesis and chemolithoautotrophy.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag105}, pmid = {42164315}, issn = {2730-6151}, abstract = {Despite extreme conditions including freezing temperatures, low water activity, and few nutrients, active microorganisms are thought to inhabit glacial ice, yet little is known about their identities and methods of survival. We used flow cytometry, cultivation, metagenomics, and metatranscriptomics to characterize viable and active microbial communities from near-surface englacial ice from White Glacier in the Canadian High Arctic and Johnsons Glacier on Livingston Island, Antarctica. The ice, though low in microbial biomass (10[4] cells/ml), harbors communities capable of growth at subzero temperatures (-5°C), high salinity (12% NaCl), and low pH (pH 3). The communities of both poles were different, with metagenome-assembled genomes (MAGs) from White Glacier belonging to Cyanobacteriota and novel phyla and MAGs from Johnsons Glacier belonging to Pseudomonadota and Actinomycetota. Despite this, both glacial communities shared key metabolic functions, including aerobic respiration, aerobic carbon monoxide oxidation, sulfide oxidation, and denitrification. Metatranscriptomics from White Glacier revealed dominant Cyanobacteriota, performing oxygenic photosynthesis and carbon fixation and accompanied by active lithoautotrophs performing metabolisms such as carbon fixation via the 3-hydroxyproprionate cycle, anoxygenic photosynthesis, sulfide oxidation, and nitrate reduction/denitrification. These metabolisms appear to support an active heterotrophic community performing aerobic respiration and aerobic carbon monoxide oxidation. This study highlights the distinct but functionally similar microbial communities in Arctic and Antarctic glaciers, hinting that there may be a core set of metabolisms required for surviving in englacial ice and suggesting that similar communities could persist in glacial ice on Mars or the icy outer moons, Europa and Enceladus.}, }
@article {pmid42165578, year = {2026}, author = {Hernández-Villamor, D and Bautista Angeli, J-R and Jeaidi, A and Joaquín-García, A and Rabaey, K and Prévoteau, A}, title = {Propionate oxidation by Geobacter sulfurreducens is electron acceptor dependent.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0006426}, doi = {10.1128/aem.00064-26}, pmid = {42165578}, issn = {1098-5336}, abstract = {UNLABELLED: The accumulation of propionate is a challenge in numerous fermentative industrial processes because its degradation is energetically unfavorable and limited to few microbial species. Here, we report for the first time the oxidation of propionate by the extracellular electron transfer (EET)-capable bacterium Geobacter sulfurreducens in axenic cultures. G. sulfurreducens was capable of utilizing propionate both as an electron donor (ED) and a source of carbon, with fumarate as an electron acceptor (EA). In contrast, propionate was metabolized only in the presence of acetate with soluble Fe(III) citrate and was not oxidized when insoluble iron oxides or glassy carbon electrodes poised at +0.1 V vs SHE served as the EA. Biomass yield (per mole of electrons available) was lower with propionate alone than with propionate and acetate together, and acetate was preferentially consumed when both were present. Transcriptomic analysis of cultures grown with either propionate or acetate (with fumarate as EA) showed significant gene expression shifts, strongly suggesting the methylmalonyl-CoA pathway as the main route for propionate degradation. Furthermore, propionate-consuming cultures exhibited an upregulation of branched-chain amino acid (BCAA) biosynthesis, as well as sulfur, nitrogen, and 2-oxocarboxylic acid metabolism.<br><br>IMPORTANCE: The accumulation of propionate is a challenge in anaerobic and fermentative processes because it inhibits methanogenesis, and few microbial species within such systems can degrade it. G. sulfurreducens is a model electroactive bacterium widely used in bioelectrochemical systems and is increasingly studied in wastewater treatment and anaerobic digestion because of its ability to enhance syntrophic metabolism via direct interspecies electron transfer. We show for the first time that G. sulfurreducens can oxidize propionate, expanding its known metabolic repertoire, and that this capability is controlled by the nature of the terminal electron acceptor. Transcriptomic analyses strongly suggest that the methylmalonyl-CoA pathway is the main pathway for propionate degradation and reveal additional associated transcriptional changes. These findings, together with insights into propionate degradation kinetics, could inform future strategies aimed at using this bacterium to mitigate propionate buildup and improve the stability of anaerobic treatment systems.}, }
@article {pmid42166056, year = {2026}, author = {Jayaneththi, U and Sneddon, NW and Burkitt, LL and Jeyakumar, P and Anderson, CWN and Fermin, LM and Donaghy, DJ}, title = {Host Filtering Shapes the Soil-gut Microbiome Linkages in Pastoral Systems.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02791-6}, pmid = {42166056}, issn = {1432-184X}, abstract = {Soil and ruminant gut microbiomes are linked within grazing pastoral systems, yet the strength and direction of these connections under different pasture management systems remain poorly understood. This study characterised bacterial communities in soil and faeces from cattle and sheep grazing standard and diverse pastures managed under contemporary and regenerative practices using 16 S rRNA gene sequencing. Shared bacterial taxa between soil and gut were identified, and their dominance patterns and soil-gut diversity relationships were evaluated using Spearman correlations and Procrustes analyses. Several taxa, including Prevotella copri, Faecalibacterium prausnitzii, Akkermansia muciniphila, Bacteroides uniformis, Clostridium perfringens and Fibrobacter succinogenes were commonly shared between soil and gut but were usually more prevalent in the gut, indicating predominant host‑associated dominance. Soil exhibited significantly greater bacterial alpha diversity than the gut across all treatments, and neither pasture diversity nor management significantly affected soil-gut alpha diversity differences or the contributions of shared taxa. Correlations between soil and gut alpha diversity were weak and non-significant, and correlations for beta diversity between soil and gut varied through time and among treatments without reaching significance. These findings indicate that, although soil-gut microbial connectivity exists, gut communities are primarily shaped by host-related ecological processes and internal filtering, with soil acting mainly as a diverse reservoir and sink for gut-derived taxa. This highlights that host-driven gut microbiomes primarily shape the soil-gut microbiome link, limiting the strong direct influence of pasture diversity or management.}, }
@article {pmid42152548, year = {2026}, author = {Costa Júnior, PSP and Melo, DS and Buttrós, VH and Magalhães-Guedes, KT and Dias, DR and Schwan, RF}, title = {Coffea arabica Infusion as a Potential Substrate for Kombucha Fermentation Modulates Microbial Populations, Symbiotic Culture of Bacteria and Yeast Ultrastructure, and Functional Attributes: Insights From Machine Learning.}, journal = {Journal of food science}, volume = {91}, number = {5}, pages = {e71117}, doi = {10.1111/1750-3841.71117}, pmid = {42152548}, issn = {1750-3841}, support = {//CNPq/ ; //FAPEMIG/ ; //CAPES/ ; //FINEP/ ; }, mesh = {Fermentation ; *Coffea/chemistry ; *Kombucha Tea/analysis/microbiology ; Machine Learning ; *Yeasts/metabolism ; *Bacteria/metabolism ; Volatile Organic Compounds/analysis ; Lactic Acid/metabolism ; Symbiosis ; Humans ; }, abstract = {Kombucha is traditionally produced from sweetened Camellia sinensis tea fermented by a symbiotic culture of bacteria and yeasts (SCOBY). However, limited information is available on the effects of replacing tea with Coffea arabica infusion on fermentation parameters, microbial ecology, and overall quality of the beverage. This study evaluated the effects of substituting green tea with C. arabica infusion (25%-100%, v/v) during kombucha fermentation on fermentation kinetics, microbial populations, SCOBY structure, and physicochemical, functional, and sensory attributes. Coffee substitution reduced sugar consumption rates without significantly affecting final pH (2.8-3.2) or titratable acidity (∼0.4). Increasing coffee proportions markedly reshaped microbial populations, reducing acetic acid bacteria and increasing lactic acid bacteria, thereby shifting metabolism toward lactic acid production. Structural analyses revealed preserved SCOBY integrity, with a more porous cellulose network in coffee-based formulations. Total phenolic content decreased after fermentation in most treatments, whereas the 100% coffee kombucha remained stable and maintained antioxidant capacity. GC-MS analysis identified 111 volatile compounds, and multivariate and machine learning approaches revealed coffee-associated biomarkers associated with lactic acid and aroma-active compounds. Overall, C. arabica infusion proved to be a suitable alternative substrate for kombucha fermentation, enabling substrate-driven modulation of microbial dynamics and metabolic profiles while maintaining product safety and functional potential. PRACTICAL APPLICATIONS: Replacing green tea with C. arabica infusion in kombucha production enables the development of beverages with differentiated microbial, chemical, and sensory profiles while maintaining fermentation performance and safety. Coffee-based kombucha promotes a shift toward lactic acid-oriented fermentation, distinct aroma signatures, and functionality without requiring significant changes to conventional SCOBY-based processes. From a practical perspective, coffee infusion is a feasible strategy for product diversification, allowing manufacturers to modulate fermentation outcomes through raw material selection and to support the development of innovative, scalable, and consumer-oriented kombucha beverages.}, }
@article {pmid42096509, year = {2026}, author = {Kholwadwala, A and Katkov, E and Lypaczewski, P and Gonzalez, A and Barrett, RDH and Shapiro, BJ}, title = {Nutrient enrichment and connectivity jointly shape bacterioplankton taxonomic and functional diversity.}, journal = {FEMS microbiology letters}, volume = {373}, number = {}, pages = {}, doi = {10.1093/femsle/fnag056}, pmid = {42096509}, issn = {1574-6968}, support = {RGPIN-2019-04549//NSERC/ ; RGPIN-2019-05455//NSERC/ ; //Canada Foundation for Innovation/ ; }, mesh = {*Bacteria/classification/genetics/metabolism ; *Plankton/classification ; *Nutrients/metabolism ; *Biodiversity ; Fresh Water/microbiology ; Ecosystem ; Lakes/microbiology ; }, abstract = {It is increasingly important to understand the response of freshwater communities and ecosystems to fertilizers given their widespread usage and the propensity for these fertilizers to runoff into rivers and lakes. Dispersal, an important ecological factor mediated by landscape connectivity, could potentially counteract the impacts of anthropogenic stressors through the reintroduction of communities unperturbed by local stressors. However, this potential has not yet been studied in the context of nutrient stressed natural communities. Here, we investigate the impacts of nutrient enrichment and connectivity on freshwater bacterioplankton communities. We subjected mesocosms stocked with native bacterioplankton communities to different combinations of nutrient enrichment and connectivity (volumes of water transferred between mesocosms). We show that nutrient enrichment strongly structures the bacterioplankton community, favoring nutrient tolerant taxa and depressing taxonomic diversity. Connectivity, however, interacts with nutrient enrichment to restore functional diversity in communities subjected to the highest levels of nutrient stress. Despite the ameliorating effects of dispersal, nutrient enrichment leaves a consistent signature in communities, driving a shift from more heterotrophic to more phototrophic communities. Taken together, our results demonstrate that while nutrient enrichment significantly impacts freshwater bacterioplankton communities, connectivity can help restore functional diversity to a certain extent.}, }
@article {pmid42147301, year = {2026}, author = {Barbosa, MC and Pellegrinetti, TA and da Cunha, ICM and da Silva, AVR and Marcandalli Boleta, EH and Losovoi, LA and Mendes, R and Tsai, SM and Mendes, LW}, title = {Genotype-dependent stability and specialization of arbuscular mycorrhizal fungal communities under drought in common bean.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1786322}, pmid = {42147301}, issn = {1664-462X}, abstract = {Arbuscular mycorrhizal fungi (AMF) represent a key biological strategy for enhancing agricultural resilience under extreme climatic events such as drought. However, how AMF interact with drought-tolerant plant genotypes to sustain performance under water limitation remains poorly understood. Here, we used high-throughput DNA sequencing to investigate AMF communities associated with drought-tolerant (BAT477 and SEA5) and drought-susceptible (IAC-Milênio and IAC-80SH) common bean genotypes, integrating taxonomic, structural, and functional perspectives under contrasting water regimes. We hypothesized that drought tolerance is not simply linked to AMF presence, but rather to the ability of host genotypes to structure and stabilize their mycorrhizal communities under stress. Our results reveal genotype-specific responses to drought, with distinct community restructuring dynamics observed across individual genotypes. Drought-tolerant genotypes maintained or increased AMF relative abundance, diversity, and functional integrity under drought, whereas susceptible genotypes displayed opposing changes in the community's structure. Although most genotypes displayed high dissimilarity in AMF community structure between control and drought conditions, tolerant genotypes reorganized their communities through increase in the relative abundance of key ASVs, whereas susceptible genotypes experienced substantial reductions in abundance, diversity, and specialist ASVs. Niche occupancy and functional guild analyses further showed that AMF communities in tolerant genotypes were dominated by specialist and symbiotrophic ASVs, whereas susceptible genotypes shifted toward rare and functionally reduced assemblages. At the plant level, AMF community stability was positively associated with root biomass and negatively associated with foliar nutrient, indicating a tight coupling between mycorrhizal community structure, host nutritional status, and growth. Collectively, our findings indicate that drought tolerance in common bean emerges, at least in part, from a cooperative host-microbiome strategy in which the host actively regulates the structure and functional stability of AMF communities under water stress. These results advance our understanding of plant-mycorrhizal interactions in drought adaptation and highlight the potential of integrating mycorrhizal functionality into plant breeding strategies aimed at developing climate-resilient crops.}, }
@article {pmid42148754, year = {2026}, author = {Heredia, MY and Kuehnert, PA and March, K and Knoll, LJ and O'Leary, CE}, title = {Competition between commensal protists shapes gut mucosal immunity in mice.}, journal = {mBio}, volume = {}, number = {}, pages = {e0080226}, doi = {10.1128/mbio.00802-26}, pmid = {42148754}, issn = {2150-7511}, abstract = {UNLABELLED: Intestinal protists are emerging as key modulators of host immunity and microbial ecology, yet their impact on mammalian hosts remains poorly defined. Here, we investigated the role of two distinct protists, the amoeba Entamoeba muris, and the parabasalid, Tritrichomonas, to determine how they shape gut immunity in vivo individually and together. Unlike the well-characterized inducer of type 2 immunity, Tritrichomonas, which activates the tuft cell-IL-25-ILC2 circuit in the small intestine, E. muris failed to elicit robust immune responses in the intestine or colon. However, the introduction of E. muris into mice naturally colonized by Tritrichomonas spp., or co-infection with E. muris and Tritrichomonas spp. reduced Tritrichomonas-induced type-2 response in the small intestine and Tritrichomonas-dependent immune activation in the colon. Our data suggest that E. muris may limit the abundance of Tritrichomonas spp., with reduced protist loads in the cecum specifically correlating with diminished tuft cell activation. We also identified sex-specific differences in the intestinal response to Tritrichomonas spp., which have not previously been reported. Taken together, these findings reveal that the presence of E. muris reduces Tritrichomonas-dependent activation of type 2 immunity in the small intestine, even when both protists can be detected in the cecum, without triggering overt inflammation. This work provides a framework for understanding how protists interact within the gut ecosystem and shape mucosal immunity in the absence of pathogenicity.<br><br>IMPORTANCE: Single-cell parasites called protists are common in mammalian intestinal tracts, yet their modulation of the host immune response and interactions with each other remain poorly defined. Here, we investigated the role of two protists, Entamoeba and Tritrichomonas, to determine how they shape gut immunity individually and together. Unlike the well-characterized inducer of type 2 immunity, Tritrichomonas, which activates the tuft cell circuit, Entamoeba failed to elicit a robust immune response. The introduction of Entamoeba into mice naturally colonized by Tritrichomonas, or co-infection with Entamoeba and Tritrichomonas, reduced the Tritrichomonas-induced immune response. Our data suggest that Entamoeba limits the abundance of Tritrichomonas, correlating with diminished tuft cell activation. We also identified sex-specific differences in the intestinal response to Tritrichomonas. These findings show that Entamoeba reduces Tritrichomonas-dependent activation of type 2 immunity without triggering much inflammation. It helps our understanding of how protists interact within the gut and shape immunity without disease.}, }
@article {pmid42150376, year = {2026}, author = {Grzesiak, J and Brzykcy, J and Young, P and Krakowska, E and Stasiuk, R and Krakowski, K and Decewicz, P and Kiedryńska, A and Matlakowska, R and Bartosik, D}, title = {Gelidimonas denitrificans gen. nov., sp. nov., and Gelidimonas diazotrophica sp. nov. psychrophilic bacteria involved in the nitrogen cycle in tundra soils of South Spitsbergen.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {4}, pages = {126730}, doi = {10.1016/j.syapm.2026.126730}, pmid = {42150376}, issn = {1618-0984}, abstract = {Two Gram-negative, psychrophilic, denitrifying bacterial strains, D2 and D11, were isolated from ornithogenic soil collected at a breeding colony of the marine bird Alle alle on Spitsbergen Island, Svalbard (Norway; High Arctic). Complete genome sequencing revealed that each strain possesses a single circular chromosome (3.83 Mbp and 3.63 Mbp, respectively) with similar GC content (55.3% and 55.5%), as well as plasmids - one shared by both strains (26.3 kb) and one unique to strain D11 (16.3 kb). Despite their striking genetic similarity, the two strains exhibit distinct physiological characteristics. Strain D2 is a facultative chemolithoautotroph capable of using hydrogen as an energy source and assimilating carbon dioxide and dinitrogen, whereas strain D11 displays a strictly heterotrophic lifestyle. Although the 16S rRNA genes of D2 and D11 share a high level of sequence identity (99.6%), whole-genome comparative analyses, including digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI), indicated that they represent two distinct species within the family Oxalobacteraceae (class Betaproteobacteria). Core proteome-based phylogenetic analysis of Oxalobacteraceae unambiguously placed both strains within the family; however, neither clustered with any currently described genus. We therefore propose that these strains represent a novel genus, Gelidimonas gen. nov., with type species Gelidimonas denitrificans sp. nov. (type strain D11[T]) and a second species Gelidimonas diazotrophica sp. nov. (type strain D2[T]).}, }
@article {pmid42150526, year = {2026}, author = {Thompson, LR}, title = {Microbial ecology: Rise of the planet of the microbes.}, journal = {Current biology : CB}, volume = {36}, number = {10}, pages = {R432-R434}, doi = {10.1016/j.cub.2026.03.072}, pmid = {42150526}, issn = {1879-0445}, mesh = {*Microbiota/genetics ; Metagenomics ; Ecosystem ; *Bacteria/genetics ; *Metagenome ; }, abstract = {A long-standing tenet of microbiology is that Earth's microbiomes are structured by environment, not geography. In a new study, Kim et al. report the largest metagenomic analysis yet performed, revealing that microbial generalists transcend these boundaries, ferrying genes - including antibiotic resistance determinants - across ecologically distant habitats.}, }
@article {pmid42151475, year = {2026}, author = {Kobiałka, M and Świerczewski, D and Walczak, M and Pisarek-Pacek, A and Wóycicki, RK}, title = {Complementary Microscopic and Metabarcoding Studies Allow for a Better Understanding of the Symbiotic Microbiome of Leafhopper Species Iassus lanio (Hemiptera, Cicadellidae).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02790-7}, pmid = {42151475}, issn = {1432-184X}, support = {Sonata 17, project no. 2021/43/D/NZ8/02183//National Science Centre, Poland/ ; }, abstract = {Leafhoppers' microbiome patterns were shaped by deep co-evolutionary adaptation driven by dietary specialization. Their microbiome is dominated by obligate symbionts that supplement their nutrient-poor phloem-sap diet, as well as facultative symbionts, including both bacterial and fungal microorganisms. In this study, NGS metabarcoding techniques were performed, supplemented by confocal and electron microscopy, to thoroughly investigate the symbiotic system of the Auchenorrhyncha species Iassus lanio, a representative of the poorly studied leafhopper subfamily Iassinae. The obtained results include descriptions of the composition, distribution, and ultrastructure of microorganisms, as well as the phylogeny of ancient symbionts. Two obligate symbionts were found: the ancient Auchenorrhyncha symbiont Karelsulcia bacterium and the yeast-like symbiont Ophiocordyceps. Karelsulcia bacteria occur exclusively in specialized organs called bacteriomes, while fungal microorganisms inhabit mycetocytes within the fat body. Both symbionts are transmitted transovarially from mother to offspring. The presence of Wolbachia, Sodalis and Cardinium was detected. Sodalis and Cardinium were observed in the fat body. The ultrastructure of Cardinium showed a characteristic microtubule crest inside. The obtained phylogeny of Karelsulcia bacteria indicates Iassinae affinity with the Coelidiinae and Deltocephalinae subfamily symbionts. Taxonomic profiling revealed that both sequencing methods detected the same range of bacterial taxa, while ONT exhibited improved resolution for dominant species. Differential abundance analysis emphasized platform-specific biases. These studies highlight the complementary roles of different microscopy and metabarcoding techniques, demonstrating the complexity of symbiotic systems in leafhoppers and thereby improving our understanding of the host-symbiont relationship and expanding our knowledge of the structure and localization of insect microorganisms.}, }
@article {pmid42152232, year = {2026}, author = {Mortier, F and Bafort, Q and Bonte, D and Van de Peer, Y}, title = {Repeatability of phenotypic consequences due to whole-genome duplication in Spirodela polyrhiza.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.71256}, pmid = {42152232}, issn = {1469-8137}, support = {BOF.MET.2021.0005.01//Bijzonder Onderzoeksfonds UGent/ ; 1238124N//Fonds Wetenschappelijk Onderzoek/ ; 833522//H2020 Excellent Science/ ; }, abstract = {Whole-genome duplication (WGD) is widespread in plants, yet the extent to which it yields predictable phenotypic outcomes remains unclear. Here, we show that the phenotypic consequences of genome doubling in a duckweed model system, Spirodela polyrhiza, are highly repeatable and largely deterministic. We previously generated three independent colchicine-induced autotetraploids from each of nine globally distributed diploid genotypes and now quantified growth and morphology across a salt gradient. In benign conditions, diploids grew faster, whereas tetraploids had larger, thicker fronds. As salinity increased, the diploid growth advantage diminished, and tetraploids frequently matched or exceeded diploid growth rates. By partitioning the components of variance in growth in our experimental design, we found that ploidy per se explained a comparable amount of phenotypic variation in growth and substantially more variation in salt tolerance than the genotypic background, with evidence of rare within-genotype stochastic differences between tetraploids. These results indicate that the shifts in morphology and stress tolerance from genome doubling are predictable and can match the phenotypic effect from genetic sequence diversity.}, }
@article {pmid42140125, year = {2026}, author = {Lv, Y and Wang, W and Liu, Z and Ji, Y and Liu, X}, title = {Divergent fates: Polystyrene microplastics alter trifloxystrobin degradation and microbial ecology differently in agricultural soil vs. river sediment.}, journal = {Ecotoxicology and environmental safety}, volume = {318}, number = {}, pages = {120268}, doi = {10.1016/j.ecoenv.2026.120268}, pmid = {42140125}, issn = {1090-2414}, abstract = {This study investigates the effects of polystyrene microplastics (PS-MPs) on trifloxystrobin (TRI) degradation behavior and microbial community structure in agricultural soil and river sediment. Degradation kinetics and machine learning modeling (R[2] > 0.95) revealed that PS-MPs significantly inhibited TRI dissipation, with biological degradation identified as the primary driver. Specifically, the half-life of TRI was prolonged from 2.7 to 9.7 days to 4.0-18.1 days in soil, and from 3.1 to 8.3 days to 4.8-9.7 days in sediment. Trifloxystrobin acid remained the major transformation product overall, though a unique cyanide-containing compound appeared exclusively in sediment, suggesting distinctive metabolic routes. 16S rRNA sequencing showed that TRI and PS-MPs significantly altered the bacterial community structure. The PS-MPs treatment significantly reduced the relative abundance of potential TRI degrading bacteria, such as Sphingomonas and Pseudomonas, which is related to the observed delayed degradation. Microbial network analysis further revealed that TRI simplified the soil microbial network, reducing the number of nodes and connections by about 7%, while PS-MPs increased the complexity of the sediment network, increasing the number of nodes and connections by about 36%. These findings provide quantitative insights into the comprehensive ecological risks of microplastics and fungicides in different environmental matrices.}, }
@article {pmid42140850, year = {2026}, author = {Fagundes, D and Costa, LMS and Cagliari, A and de Vargas, DP and Rieger, A}, title = {Microbial Community Shifts and Plant Performance Improvements Driven by Bacillus firmus in Pampa Agroecosystems.}, journal = {Environmental microbiology reports}, volume = {18}, number = {3}, pages = {e70315}, pmid = {42140850}, issn = {1758-2229}, mesh = {*Bacillus/physiology ; *Soil Microbiology ; *Microbiota ; Rhizosphere ; *Glycine max/growth &amp; development/microbiology/parasitology ; Plant Roots/growth &amp; development/microbiology ; Animals ; Fungi/classification/genetics/isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; Nematoda ; Ecosystem ; Soil ; }, abstract = {The impact of Bacillus firmus-based bionematicides on rhizosphere microbiota and plant performance remains poorly understood in complex agroecosystems. This study evaluated the effects of B. firmus application on soil microbial communities, nematode dynamics, and soybean productivity in the Pampa biome. Our results demonstrate that B. firmus significantly modulates the composition and diversity of soil microbiota, with effects varying across locations and over time. Treated areas exhibited shifts in bacterial communities, including increased abundance of beneficial taxa, while fungal diversity tended to decrease, likely due to the combined effect of the fungicide used in seed treatment. Despite persistent populations of target nematodes such as Pratylenchus brachyurus and Heterodera glycines, treated areas showed reduced root infestation in specific stages and locations. Importantly, the application of B. firmus consistently enhanced soybean shoot and root growth, resulting in productivity gains of 6%-7% across all sites. These findings reveal that B. firmus not only contributes to plant growth promotion but also induces significant, yet context-dependent, shifts in rhizosphere microbial communities. The study highlights the ecological complexity of microbial responses to biocontrol agents and underscores the importance of integrating microbiome dynamics into sustainable nematode management strategies in agroecosystems.}, }
@article {pmid42141775, year = {2026}, author = {Zhou, F and Wang, L and Zhao, Y and Hu, C and Meng, Y and Fan, J and Fraser, WD and Baillargeon, JP and Ouyang, F and Lye, SJ and Dennis, CL and Shen, J and Wu, Y and Huang, H}, title = {Antenatal depressive symptoms impair offspring neurodevelopment by inducing maternal gut microbiota dysbiosis during pregnancy.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2672188}, doi = {10.1080/19490976.2026.2672188}, pmid = {42141775}, issn = {1949-0984}, mesh = {Female ; Pregnancy ; Humans ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/microbiology ; *Depression/microbiology/complications ; Fecal Microbiota Transplantation ; Adult ; Case-Control Studies ; *Pregnancy Complications/microbiology/psychology ; Prospective Studies ; Butyrates/metabolism ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Prenatal Exposure Delayed Effects ; Feces/microbiology ; Infant ; Brain/growth &amp; development/metabolism ; *Neurodevelopmental Disorders/etiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The effects of maternal antenatal depression (AND) across different stages of pregnancy on offspring neurodevelopment remain poorly understood, and the underlying microbiota-related mechanisms are largely unknown. In a multicenter prospective cohort of 2053 pregnant women, we found that elevated depressive symptoms at any trimester were significantly associated with delayed infant neurodevelopment. Using a nested case‒control design with 16S rRNA sequencing of 504 maternal fecal samples, we identified a consistent reduction of butyrate-producing bacteria and disruption of amino acid metabolism in women with AND symptoms - features that correlated with poorer infant cognitive outcomes. To establish causality, fecal microbiota transplantation (FMT) from women with AND symptoms was administered to germ-free dams, resulting in impaired intestinal barrier integrity, heightened neuroinflammatory signaling, and altered polyunsaturated fatty acid and amino acid metabolism in fetal brains at E18.5, leading to postnatal cognitive deficits in the offspring. Remarkably, maternal butyrate supplementation partially rescued these molecular and neurodevelopmental abnormalities. Together, these findings reveal a mechanistic link between maternal mood, gut microbial ecology, and fetal brain development, and identify the maternal gut microbiota and its metabolites as potential therapeutic targets to prevent the intergenerational effects of antenatal depression.}, }
@article {pmid42143132, year = {2026}, author = {Rescan, M and Dachs Rojo, M and Borrego, CM}, title = {Gene expression plasticity under multiple stresses drives higher tolerance to a macrolide in saline and warmer environments.}, journal = {npj antimicrobials and resistance}, volume = {}, number = {}, pages = {}, doi = {10.1038/s44259-026-00214-7}, pmid = {42143132}, issn = {2731-8745}, support = {101062450//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; }, abstract = {The widespread presence of antibiotics in the environment at sub-inhibitory concentrations imposes a selective pressure that promotes the spread of resistance. In the field, antibiotics interact with diverse physicochemical parameters that can attenuate or intensify their fitness effects. Gene expression is a central plastic trait that governs phenotypes at a higher level of integration and modulates the strength of selection, yet how synergistic or antagonistic fitness effects arise from interactions among transcriptional responses remains poorly understood. Here, we characterized gene-expression interactions underlying fitness-level interactions previously identified between a macrolide, temperature and salinity, and proposed a general methodological framework for assessing the impact of multiple stressors on gene expression. We analyzed the transcriptional response of Escherichia coli to azithromycin (AZI) across two salinity and temperature conditions. De novo and antagonistic interactions were prevalent, with evidence of cross-regulations between salt and AZI. High salinity increased tolerance by two orders of magnitude and, similarly to AZI, induced a downregulation of carbon metabolism. Reduced temperature, which canceled the salinity protective effect, enhanced carbon metabolism and counteracted this shift. Salinity additionally restored stress-response pathways, largely repressed by AZI. Third-order interactions attenuated the contribution of salinity relative to AZI, but the number of affected genes declined exponentially with interaction order, suggesting that higher-order interactions at the gene-expression level should play a minor role in the responses to multiple stressors. By modulating transcriptional responses to AZI, simple environmental parameters could reshape the adaptive landscape of antibiotic resistance, potentially altering the spectrum of resistance mutations likely to spread.}, }
@article {pmid42143576, year = {2026}, author = {Xu, X and Tan, Y and Xiecun, S and Wang, J and Zhao, W and Wang, L and Dai, R and Tang, L and Li, X and Jin, D and Fan, Y}, title = {Galactosaminogalactan orchestrates Verticillium dahliae virulence and rhizosphere microbial ecology through multi-partite interactions.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag123}, pmid = {42143576}, issn = {1751-7370}, abstract = {The infection of plants by soil-borne fungal pathogens is a complex process and depends on their adhere ability to host surfaces and interactions with the rhizosphere bacteria. In this study, we identify galactosaminogalactan (GAG) as a pivotal virulence determinant in the pathogenesis of Verticillium dahliae. By characterizing the VdGAG biosynthetic gene cluster, we show that the glycosyltransferase VdGtb is essential for GAG synthesis. The knockout of GAG increased fungal sensitivity to the cell wall-perturbing agent calcofluor white (CFW) and reduced mycelial ball formation in liquid culture. The absence of GAG polysaccharides reduced root-binding capacity by 50% and increased cotton immune responses 1 day post fungal infection. The ΔVdGtb mutant exhibited a significant 30.5% decrease in the pathogenicity toward cotton seedlings compared with the wild type V991. Microbiome and bacterial enrichment analysis indicate that the GAG polysaccharides promote the enrichment of soil bacteria and alter the bacterial community structure in the plant rhizosphere. Several bacteria enriched by GAG-contained fungal cells, including Achromobacter animicus, Pseudomonas aeruginosa, and Acinetobacter pittii exhibited strong growth-inhibitory effects against V. dahliae and showed distinct effects on fungal virulence in a GAG-dependent manner. Together, these results reveal that GAG is not merely a cell wall component but a multi-functional molecule that orchestrates fungal protection, host infection, and inter-kingdom microbial communication.}, }
@article {pmid42144578, year = {2026}, author = {Pinheiro, &#xc2; and Martins, TM and Varela, A and Domingos, P and Escórcio, R and Bento, A and Martins, I and Afonso, CAM and Silva Pereira, C}, title = {Extremotolerant fungi in resinous soils: a unique diversity of generalists and specialized hydrocarbon degraders.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05128-y}, pmid = {42144578}, issn = {1471-2180}, support = {CENTRO-01-0247-FEDER-072630//European Regional Development Fund/ ; }, abstract = {Filamentous fungi are ubiquitous and constitute more than 75% of the soil biomass. Fungal diversity increasingly emerges as a key factor in soil ecosystem resilience against climate change and pollution, yet much of this diversity remains hidden and potentially in decline. While investigations have primarily focused on fungal tolerance to extreme physical conditions, such as temperature and salinity, chemically stressed environments remain underexplored reservoirs of novel fungal diversity. These habitats may harbor strains with significant biotechnological potential. This study tested the hypothesis that long-term contamination of soil with Pinus resin alters fungal diversity and promotes the growth of specialized fungal lineages enriched in hydrocarbon-degrading capabilities. We analyzed a resinous soil sample collected from an inactive resin processing site undisturbed for nearly 50 years. Initial physicochemical and microscopy analyses confirmed the presence of viable fungi despite extreme environmental constraints. High-throughput sequencing of fungal ITS2 regions revealed a fungal community composition highly distinct from adjacent forest soil, characterized by unusual taxonomic profiles and a high proportion of poorly classified or novel lineages. Functional inference and taxonomic analyses identified hydrocarbon-associated taxa including Sorocybe resinae (one of the most abundant OTUs) and Amorphotheca resinae (detected at low abundance). These fungi are known resinicolous and extremophilic species, illustrating the unique ecological adaptation of fungi within resin-rich, chemically stressful soils.}, }
@article {pmid42146037, year = {2026}, author = {Sun, L and Wang, X and Long, Y and Wang, X and Niu, X and Li, H and Taethaisong, N and Meethip, W and Paengkoum, S and Paengkoum, P}, title = {A review on the use of coconut oil to mitigate methane emissions in ruminants: mechanisms of action and research progress.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1774322}, pmid = {42146037}, issn = {2297-1769}, abstract = {Methane (CH4) generated during ruminal fermentation in ruminants is a major contributor to greenhouse gas emissions and represents a substantial loss of dietary energy. Therefore, mitigating enteric CH4 emissions through safe and efficient nutritional strategies is of considerable ecological and economic significance. Coconut oil (CO) has received increasing attention due to its distinctive fatty acid profile. Accumulating evidence indicates that the medium-chain fatty acids (MCFA) abundant in CO exert direct inhibitory effects on rumen protozoa and methanogenic archaea, thereby conferring strong antimethanogenic potential. However, the CH4 mitigation efficacy of CO is often accompanied by trade-offs related to rumen microbial ecology, animal productive performance, and the nutritional quality of animal-derived products, particularly at higher doses where fiber digestibility and dry matter intake (DMI) may decline. Consequently, a clearer definition of safe and effective inclusion levels across different ruminant species and production stages is needed. This review systematically summarizes the physicochemical properties and safety of CO, with particular emphasis on its mechanisms of action within the rumen. Furthermore, current application studies and future research prospects of CO in ruminant production are discussed, providing a scientific reference for its use in nutritional strategy to lower methane in ruminant systems.}, }
@article {pmid42146303, year = {2026}, author = {Maity, A and Bhowmik, R and Das, A and Trivedi, S and Mondal, SK and Gupta, AD and Paul, P and Das, S and Chakraborty, P and Tribedi, P}, title = {Cuminaldehyde potentiates antimicrobial efficacy of gentamicin and ciprofloxacin against Escherichia coli: a response surface methodology (RSM) based study.}, journal = {3 Biotech}, volume = {16}, number = {6}, pages = {193}, pmid = {42146303}, issn = {2190-572X}, abstract = {UNLABELLED: The increasing prevalence of antibiotic resistance poses a serious threat to public health, significantly reducing the effectiveness of conventional antibiotics against bacterial infections, particularly those caused by multidrug-resistant Escherichia coli (E. coli). As monotherapy becomes increasingly unreliable due to the rapid evolution of resistance, combination therapy has emerged as a promising strategy to address this challenge. In this context, the present study aimed to evaluate the effect of cuminaldehyde (CA) in combination with two conventional antibiotics, gentamicin (GN) and ciprofloxacin (CF), against five drug-resistant clinical strains of E. coli. In silico analyses using PASS Online, SwissADME, ProTox 3.0, and Osiris predicted the potential antimicrobial properties of the test compounds. In vitro investigations further demonstrated significant antimicrobial activity, with minimum inhibitory concentration (MIC) values ranging from 400 to 450 µg/mL for CA, 6-8 µg/mL for GN, and 2-3 µg/mL for CF against different E. coli strains. Furthermore, fractional inhibitory concentration index (FICI) analysis revealed that diverse interaction patterns, including synergistic effects, exist between CA and the conventional antibiotics. To optimize these combinations, response surface methodology (RSM) was employed to determine the optimal doses of the test compounds. The experimental validation of the RSM model showed high predictive accuracy (98-99%), confirming its robustness and reliability. Overall, the present findings successfully identified potent synergistic triple-drug combinations exhibiting significant inhibitory effects against drug-resistant E. coli, thereby proposing a promising approach for developing effective therapeutic strategies to combat antibiotic resistance.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04832-w.}, }
@article {pmid42137812, year = {2026}, author = {Pane, M and De Prisco, A and Amoruso, A and Deusebio, G and Marzorati, M and Corazzari, M and Monzani, R and Saverio, V and Bron, PA}, title = {Probiotic detoxification of heavy metals: functional assessment in simulated intestinal and ex vivo models.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1821114}, pmid = {42137812}, issn = {1664-302X}, abstract = {INTRODUCTION: Bioremediation is an emerging, sustainable strategy that relies on microbial processes to detoxify environmental pollutants. Among these pollutants, heavy metals (HMs) are pervasive, non-degradable toxic elements that pose serious risks to human health. In this study, we individually evaluated three probiotic lactobacilli strains-Lactiplantibacillus plantarum LP14, Lactobacillus crispatus LCR04, and Lactobacillus acidophilus LA12-for their capacity to detoxify cadmium, chromium, mercury, and lead in the gastrointestinal (GI) tract, as well as their capacity to mitigate heavy metal-induced intestinal damage, with a single-strain product strategy in mind.<br><br>METHODS: After initial selection of the strains for their in vitro detoxifying potential, we employed a dynamic Simulator of the Human Intestinal Microbial Ecosystem (SHIME&#xae;) model and each strain's survival, growth, and heavy metal detoxification capacity was assessed under sequential gastric, small-intestinal, and colonic conditions.<br><br>RESULTS: Strain- and metal-specific differences in HMs sequestration emerged: L. plantarum LP14 and L. crispatus LCR04 showed robust persistence and significantly reduced HMs bioavailability, whereas L. acidophilus LA12 displayed minimal detoxification under GI simulation. Mechanistically, only the strains that proliferated in the colonic phase achieved substantial HM removal, underscoring the importance of metabolic activity in situ. In a gut ex vivo system (GEVS), heavy metal exposure alone compromised epithelial barrier integrity and triggered pro-inflammatory responses. Pre-incubation of the HMs with each of the probiotic strains markedly alleviated these effects, restoring intestinal permeability and cytokine profiles.<br><br>DISCUSSION: Overall, the results demonstrate a novel probiotic-based intestinal bioremediation strategy and highlight the translational potential of targeted single-strain probiotic interventions, reducing heavy metal exposure to protect gut health.}, }
@article {pmid42139623, year = {2026}, author = {Khudhair, HM and Alhamdani, ASH and Al Tameemi, AMH}, title = {Microbiology of dental decay and periodontal disease: A review.}, journal = {Wiadomosci lekarskie (Warsaw, Poland : 1960)}, volume = {79}, number = {4}, pages = {829-846}, doi = {10.36740/WLek/216932}, pmid = {42139623}, issn = {0043-5147}, mesh = {Humans ; *Periodontal Diseases/microbiology/therapy ; *Dental Caries/microbiology/therapy ; Biofilms ; Porphyromonas gingivalis/pathogenicity ; Mouth/microbiology ; }, abstract = {OBJECTIVE: Aim: This review attempts to examine the microbiology, pathogenesis and current therapeutic approaches of dental caries and periodontal diseases with a special focus on the role of polymicrobial biofilms, the host-microbe interaction and the major pathogenic species involved in disease progression.<br><br>PATIENTS AND METHODS: Materials and Methods: A thorough literature review was performed using major scientific databases such as PubMed, Scopus, Web of Science and Google Scholar. Studies that were published between 2000 and 2025 were included. Relevant experimental, clinical and review articles that focused on the etiology, microbial composition, virulence mechanisms, host immune responses and therapeutic approaches of dental caries and periodontal disease were analyzed.<br><br>CONCLUSION: Conclusions: The oral cavity harbors over 700-800 bacterial species, of which the primary cariogenic pathogen is Streptococcus mutans and Porphyromonas gingivalis has been implicated as a major cause of periodontal disease. Dental caries progression is mostly attributed to acid production and demineralization of enamel, whereas periodontal disease is a result of dysbiotic shift in the subgingival microbiome with destructive host inflammatory responses. The "red complex" (P. gingivalis, Treponema denticola and Tannerella forsythia) has a high degree of synergistic virulence in advanced periodontitis. Biofilm formation, production of extracellular polysaccharide (EPS) matrix, quorum sensing and immune components (neutrophils, macrophages and matrix metalloproteinases or MMPs) are all factors that contribute to disease formation. Prevention strategies include oral hygiene measures, fluoride exposure, dietary modification, and antimicrobial agents, whereas treatment measures include mechanical debridement, systemic antibiotics, antimicrobial peptides, probiotics, and photodynamic therapy. Dental caries and periodontal diseases are the result of complex interactions between polymicrobial biofilms and immune responses by the host. A better understanding of the microbial ecology, virulence pathways and host-pathogen interactions is crucial in the process of improving prevention and treatment. Advances in targeted antimicrobial therapies and innovative therapeutic approaches hold promise for enhancing global oral health outcomes.}, }
@article {pmid42136267, year = {2026}, author = {Saraswati, BD and Wicaksono, AW and Valles, SL and Poeggeler, B and Singh, SK}, title = {Exploring the Gut Microbiome as a Promising Frontier in Alzheimer's Disease Therapy.}, journal = {Current neuropharmacology}, volume = {}, number = {}, pages = {}, doi = {10.2174/011570159X444975260408044214}, pmid = {42136267}, issn = {1875-6190}, abstract = {Alzheimer's Disease (AD) is a major global health challenge, particularly in ageing populations, and current therapies offer limited modification of disease progression. Emerging evidence indicates that the gut microbiome contributes to AD pathogenesis through metabolic, immune, and neuroendocrine mechanisms. Microbial metabolites, including Short-Chain Fatty Acids (SCFAs), bile acids, and trimethylamine-N-oxide (TMAO), regulate neuronal signalling and blood-brain barrier integrity, and dysbiosis has been linked to amyloid-β (Aβ) accumulation, tau hyperphosphorylation, chronic neuroinflammation, oxidative stress, and synaptic dysfunction. Host genetic factors, particularly APOE ε4 and immune-regulatory variants such as TREM2 and CD33, further influence microbial composition and susceptibility to metabolite-driven pathology. This review provides a deeper synthesis of current evidence by integrating findings across multi-omics studies and identifying key unresolved issues in the microbiome-AD field. The discussion evaluates whether microbiome alterations act as early initiators or downstream consequences of neurodegeneration, examines sources of heterogeneity in microbiome-targeted interventions, and considers how inter-individual variability in host genetics and microbial ecology may inform precision therapeutics. Conceptual frameworks presented here, including a two-phase dysbiosis trajectory and a metabolite "tipping-point" network, aim to reconcile conflicting results and support the development of testable mechanistic hypotheses. Microbiome-directed strategies, such as probiotics, prebiotics, dietary modulation, faecal microbiota transplantation, and antiviral therapies, demonstrate promise but require rigorous mechanistic validation and methodological standardisation. Continued advancement in longitudinal, genotype-stratified, and multi-omics research will be essential for translating microbiome science into clinically actionable approaches. Overall, current evidence positions the gut microbiome as a compelling frontier for the development of personalised, diseasemodifying strategies in AD.}, }
@article {pmid42128003, year = {2026}, author = {Gutsfeld, S and Wray, C and Schweiger, N and Röhrig, A and Paschke, H and Fu, Q and Kasmanas, JC and Abdulkadir, N and Kader, S and Rocha, U and Ebert, A and Tal, T}, title = {N-Ethyl Perfluorooctane Sulfonamide (N-EtFOSA) Exposure Alters Microbiome Composition and Causes Microbiome-Dependent Behavior Effects in Larval Zebrafish.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c16330}, pmid = {42128003}, issn = {1520-5851}, abstract = {We hypothesized that host-associated microorganisms can alter host behavior by modifying perfluorooctane sulfonamides to produce perfluorooctanesulfonic acid (PFOS) or other potentially neuroactive metabolites. Zebrafish larvae (Danio rerio) were exposed to PFOS (0.28-5 μM), N-ethyl perfluorooctane sulfonamide (N-EtFOSA, 0.07-1.25 μM), or perfluorooctane sulfonamido ammonium iodide (PFOSAmS, 0.83-15 μM) from 5 to 6 days post fertilization (dpf). This resulted in altered dark-phase swimming behavior at 8 dpf. Exposure to PFOS, or N-EtFOSA, but not PFOSAmS caused a similar shift in community structure. We exposed microbiome-depleted (axenic, AX), conventionally colonized (CC), or axenic conventionalized on day 1 (AC1) zebrafish larvae to N-EtFOSA (0.22-0.7 μM) from 5 to 6 dpf. In comparison to CC and AC1 larvae, AX-larvae did not exhibit concentration-dependent hypoactivity at 8 dpf. Chemical analysis at 7 dpf revealed a significant increase in N-EtFOSA levels in AX-larvae and AX-water samples, relative to colonized cohorts. The main metabolite detected was perfluorooctane sulfonamide (FOSA), which was not microbiome-dependent. Perfluorooctane sulfonamidoacetic acid (FOSAA) was detected at lower levels in AX-larvae, relative to colonized groups. This study revealed that the presence of the microbiome enhanced N-EtFOSA-dependent behavior effects at the level of the host. This supports the concept that chemical-microbiome interactions can influence host phenotypic outcomes.}, }
@article {pmid42129350, year = {2026}, author = {Parkin, K and Christophersen, CT and Verhasselt, V and Palmer, DJ and Cooper, MN and Prescott, SL and Silva, D and Martino, D}, title = {Chlorinated drinking water exposure enriches antimicrobial resistance pathways in the infant gut microbiome: a randomized trial.}, journal = {Communications medicine}, volume = {}, number = {}, pages = {}, doi = {10.1038/s43856-026-01626-2}, pmid = {42129350}, issn = {2730-664X}, abstract = {BACKGROUND: Water chlorination is essential for controlling harmful microbes in drinking water; however, the antimicrobial effects of chlorine-based disinfectants present in tap water may influence early-life gut microbial ecology.<br><br>OBJECTIVE: To investigate the functional and compositional impact of chlorinated drinking water on the gut microbiome of infants.<br><br>DESIGN: The waTer qUality and Microbiome Study (TUMS) was an Australian-based double-blinded, randomised controlled trial. Six-month-old infants (n&#x2009;=&#x2009;197) received either de-chlorinated drinking water via benchtop filtration (treatment, n&#x2009;=&#x2009;99), or regular chlorinated water (control, n&#x2009;=&#x2009;98) for twelve months. Tap water and stool samples were collected at baseline and at end of intervention. Metagenomic sequencing was used for faecal microbiome analysis. Primary outcomes were differences in gut microbiota between groups, secondary outcomes included incidence of allergic sensitization and respiratory conditions.<br><br>RESULTS: At baseline, 170 stool samples (83 control, 87 intervention) were collected, with 130 samples obtained at the end of the intervention (65 control, 65 intervention). Overall community structure was similar between groups after the intervention, including beta diversity (0.56% variance explained; p&#x2009;=&#x2009;0.84), richness (-4.25, 95% CI; -14.85 to 6.35, p&#x2009;=&#x2009;0.43) or Shannon Index (-0.14, 95% CI; -0.32 to 0.04, p&#x2009;=&#x2009;0.12). The chlorinated water group showed enrichment of antibiotic resistance MetaCyc groups and pathways (adjusted p&#x2009;<&#x2009;0.05). Stratified analysis suggested this effect was potentiated by clinical antibiotic use.<br><br>CONCLUSION: Chlorinated drinking water may enhance resistance functions in the infant gut microbiome. While remaining vital for public health, future studies should explore whether adjusting the timing or method of drinking water disinfectants into the infant diet can reduce selective pressures.<br><br>TRIAL REGISTRATION: ACTRN12619000458134; https://www.anzctr.org.au.}, }
@article {pmid42129646, year = {2026}, author = {Mannan, SJ and Roqunuzzaman, M and Mannan, ABA and Begum, K and Yasmin, M and Yihune, E and Al-Mutairi, AA and Zaki, MEA and Ahsan, CR}, title = {Exploring genetic variations and plasmid diversity in Escherichia coli strains isolated from Hospital Wastewater.}, journal = {BMC genomics}, volume = {27}, number = {1}, pages = {}, pmid = {42129646}, issn = {1471-2164}, mesh = {*Wastewater/microbiology ; *Escherichia coli/genetics/isolation &amp; purification/pathogenicity/classification ; *Plasmids/genetics ; *Genetic Variation ; Hospitals ; Polymorphism, Single Nucleotide ; Phylogeny ; Drug Resistance, Multiple, Bacterial/genetics ; beta-Lactamases/genetics ; Whole Genome Sequencing ; }, abstract = {The multidrug-resistant (MDR) Escherichia coli, particularly β-lactamase producing strains, has become a global health challenge, where wastewater systems, specially from hospitals, serve as critical reservoirs for the dissemination of resistance genes. The objectives of the study were to investigate the whole genome sequence diversity and genetic variations focusing on their evolutionary relationships, genetic similarity, and single nucleotide polymorphisms (SNPs) of pathogenic β-lactamase producing E. coli strains. A total of four β-lactamase producing E. coli strains, from differently located tertiary care hospitals, were included in this study. A heatmap of genetic similarity revealed near-identical genetic makeup among the strains. A number of genes including AcrAB-TolC, β-lactamases, and resistance determinants such as glpT, gyrA, msbA, and tet(M) were identified in these strains. However, the presence of virulence genes of the aerobactin synthesis gene (iucA, iutA) and type III secretion systems (espX1, espX4, espX5) in the strain has the potential for pathogenicity. These resistance genes were identified at the genomic level; however, their transcriptional expression was not evaluated and the detection of virulence-associated genes suggests that the isolates have the potential to cause disease and pathogenicity. These findings provide insights into the whole genome sequence diversity of E. coli in urban based tertiary care hospital wastewater, emphasizing the genetic variation and plasmid diversity in these E. coli strains, which may have implications in public health and microbial ecology of the environment.}, }
@article {pmid42133112, year = {2026}, author = {S, S and V, SP and B, R and C, S and N, S and P, C}, title = {Impact of lifestyle on salivary microbiota composition and antibiotic resistance in adult periodontitis patients.}, journal = {Antonie van Leeuwenhoek}, volume = {119}, number = {6}, pages = {}, pmid = {42133112}, issn = {1572-9699}, support = {RGP/2019-20/BDU/HECP-0042//Tamil Nadu State Council for Higher Education/ ; }, mesh = {Humans ; *Saliva/microbiology ; Adult ; *Life Style ; *Periodontitis/microbiology/drug therapy ; Anti-Bacterial Agents/pharmacology ; Male ; Female ; *Microbiota/drug effects ; Middle Aged ; *Bacteria/drug effects/classification/isolation &amp; purification/genetics ; Microbial Sensitivity Tests ; *Drug Resistance, Microbial ; *Drug Resistance, Bacterial ; Dysbiosis/microbiology ; }, abstract = {Adult periodontitis is a chronic inflammatory disease characterized by microbial dysbiosis and host-microbe imbalance in the oral cavity. In this study, the composition and antibiotic susceptibility of the salivary microbiota in adults with mild periodontitis were analyzed to emphasize the influence of lifestyle factors on microbial ecology and resistance trends. Saliva samples collected from clinically diagnosed individuals were analyzed using selective culture-based methods and the Kirby-Bauer disc diffusion assay. Statistical analyses were performed to evaluate interspecies growth variability and antimicrobial responses. It revealed distinct salivary microbial profiles in patients with periodontitis compared to those of healthy individuals. Fusobacterium nucleatum exhibited the highest optical density, indicating increased proliferation and potential involvement in disease progression. Lifestyle variables, particularly smoking and dietary habits, significantly influenced microbial composition (r = 0.73 for smoking; r = 0.59 for tobacco use). Antibiotic susceptibility testing has revealed substantial interspecies variation, with ciprofloxacin and tetracycline showing the highest inhibitory efficacy, whereas azithromycin and clindamycin were largely ineffective. Moderate positive correlations between Prevotella, Clostridium, and F. nucleatum (r = 0.61-0.65) suggest possible shared resistance mechanisms or ecological adaptation. Overall, combined effects of behavioral and microbial factors can shape early periodontal dysbiosis and antibiotic resistance.}, }
@article {pmid42135341, year = {2026}, author = {Huang, Y and Hong, L and Li, S and Zhang, L and Guo, X and Han, J and Yu, W and Chen, H and Luo, N and Chen, J and Peng, W and Zhou, Y and Hong, S and Yan, W and Jiang, S and Cao, Y}, title = {Neonatal intensive care unit exposures reprogram microbiome-metabolome trajectories and modulate host calprotectin in preterm infants: a longitudinal multi-omics study.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01008-5}, pmid = {42135341}, issn = {2055-5008}, support = {82402017//National Key Research and Development Program of China/ ; 82402017//National Key Research and Development Program of China/ ; }, abstract = {Early-life gut microbiota development is critical for orchestrating mucosal barrier function and immune priming, as disruptions in this process can increase susceptibility to life-threatening diseases such as necrotizing enterocolitis (NEC) and sepsis. This longitudinal multi-omics study of 186 preterm infants (<32 weeks of gestation or <1500 g birth weight) explores the impact of early-life exposures in the neonatal intensive care units (NICUs) on gut microbiota, metabolism, and immune responses. We analyzed 1153 stool samples using quantitative microbial profiling, untargeted metabolomics, and fecal S100A8/A9 (calprotectin) levels. Antibiotic exposure suppressed anaerobic colonization and microbial diversity in a cumulative exposure-dependent manner, with breastmilk feeding partially mitigating these effects. The stool metabolome correlated with microbial colonization, showing antibiotic-driven disruptions in polyamine metabolism linked to anaerobe abundance. Host calprotectin levels followed a biphasic pattern, correlating with microbial diversity and polyamine metabolites. Mediation analysis identified anaerobe suppression and polyamine depletion as key drivers of antibiotic-associated reductions in calprotectin. This study reveals that NICU interventions, particularly antibiotics, reprogram the preterm gut ecosystem and immune response, with anaerobes and polyamines being key mediators linking microbial ecology to immune maturation during early life.}, }
@article {pmid42123938, year = {2026}, author = {Chiang, CK and Lai, CL and Chiu, MH and Huang, CJ}, title = {The Gut-Lung Axis in Allergic Asthma: A Narrative Review of Microbial Dysbiosis, Immune Regulation, and Nutritional Modulation.}, journal = {Nutrients}, volume = {18}, number = {9}, pages = {}, pmid = {42123938}, issn = {2072-6643}, support = {CGH-MR-B-11316//Cathay General Hospital/ ; }, mesh = {Humans ; *Dysbiosis/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; *Asthma/immunology/microbiology ; *Lung/immunology/microbiology ; Animals ; Diet ; }, abstract = {Allergic asthma is a prevalent chronic inflammatory disease of the airways whose pathogenesis has traditionally been attributed to localized immune dysfunction within the lung. However, accumulating evidence from microbiome research supports a broader system-level perspective in which cross-organ interactions contribute to disease susceptibility and progression. In particular, the gut-lung axis has emerged as a key regulatory pathway linking intestinal microbial ecology, immune development, and respiratory health. This review synthesizes current epidemiological, mechanistic, and experimental evidence supporting the role of gut microbiota dysbiosis in allergic asthma. We examine how early-life environmental and nutritional exposures and gut microbiota establishment during critical developmental windows shape long-term immune tolerance and asthma susceptibility. We then summarize characteristic features of asthma-associated gut dysbiosis and discuss how microbial-derived metabolites, including short-chain fatty acids, tryptophan metabolites, pro-allergic lipid mediators such as 12,13-dihydroxy-9Z-octadecenoic acid, and bacterial-derived histamine, modulate distal airway immune responses through epigenetic, receptor-mediated, and immune trafficking mechanisms. Particular emphasis is placed on the role of diet as a key upstream regulator of gut microbiota composition and metabolic function. Finally, we evaluate experimental and translational studies targeting the gut-lung axis, including dietary modulation, microbiome-targeted interventions such as fecal microbiota transplantation, and emerging postbiotic approaches. Collectively, current evidence indicates that gut microbial composition and metabolic function are critical determinants of respiratory immune homeostasis. Targeting the gut-lung axis through nutrition- and microbiome-based strategies offers a promising avenue for the prevention and precision treatment of allergic asthma.}, }
@article {pmid42124636, year = {2025}, author = {Perez, L and Cremer, J}, title = {A mismatch between slow protein synthesis and fast environmental fluctuations determines tradeoffs in bacterial proteome allocation strategies.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.07.22.666192}, pmid = {42124636}, issn = {2692-8205}, abstract = {Microbes live in environments that fluctuate faster than they can adjust their cellular machinery. To survive these fluctuations, they must dynamically regulate protein synthesis-a resource-intensive process that is often slower than environmental changes. Here, we develop a mechanistic model coupling antibiotic kinetics with dynamic proteome allocation to understand how limitations in translational capacity shape acclimation strategies. Using translation-inhibiting antibiotics and resistance proteins, we show that the temporal mismatch between environmental perturbations (seconds) and protein synthesis responses (hours) creates a growth advantage for anticipatory strategies where cells pre-synthesize resistance proteins before antibiotic exposure. Further, we find that the largest benefits of anticipation and the largest protein fractions reserved for anticipation are realized in environments with multiple antibiotics, suggesting that anticipation is most important in complex environments. This work establishes a framework for quantifying the costs and benefits of various acclimation strategies in dynamical environments based on the fundamental constraints of protein synthesis, with implications for microbial ecology, antibiotic resistance, and biotechnology applications.}, }
@article {pmid42126160, year = {2026}, author = {Monteiro, T and Romeiro, K and Brisson-Suárez, K and Aazzouzi-Raiss, K and Marceliano-Alves, M and Campello, A and Alves, F}, title = {Accuracy of Digital Radiography and Cone Beam Computed Tomography in Assessing Filling Material Extrusion Using Micro-Computed Tomography as Gold Standard: A Study in Human Cadavers.}, journal = {European endodontic journal}, volume = {11}, number = {2}, pages = {45-49}, doi = {10.65717/eej.2026.25090}, pmid = {42126160}, issn = {2548-0839}, mesh = {Humans ; *Cone-Beam Computed Tomography ; Cadaver ; *X-Ray Microtomography ; *Radiography, Dental, Digital ; *Root Canal Filling Materials/adverse effects ; Sensitivity and Specificity ; }, abstract = {OBJECTIVE: This study compared the accuracy of digital periapical radiography (DPR) and cone beam computed tomography (CBCT) in detecting extruded filling material, using a human cadaver model. Micro-computed tomography (Micro-CT) served as the gold standard.<br><br>METHODS: A total of 27 single-rooted teeth embedded in cadaveric mandibular segments, obtained from a prior retreatment study, were included: 25 with confirmed apical extrusion of filling material on micro-CT and 2 without extrusion serving as negative controls. The segments were imaged using both DPR and CBCT. Two calibrated endodontists independently assessed the images for visible extrusion; discrepancies were resolved by a third evaluator.<br><br>RESULTS: Although DPR demonstrated lower overall sensitivity than CBCT, both modalities showed identical specificity (100%). Diagnostic accuracy was 70% for DPR and 74% for CBCT, without statistically significant difference between them (P > .05). Moreover, the volume of extruded filling material was not a significant predictor of detection accuracy for either DPR (P > .05) or CBCT (P > .05).<br><br>CONCLUSION: In conclusion, both DPR and CBCT demonstrated low accuracy in detecting filling material extrusion, with no significant difference between them. The occurrence of false-negative results may compromise the reliable assessment of extruded filling materials. In cases of true extrusion, approximately one-third would go undetected by both methods.}, }
@article {pmid41917812, year = {2026}, author = {Shi, K and Zhang, H and Ji, L and Li, W and Zhang, Q and Liu, N and Liu, J and Guo, S and Huang, S and Chen, Y and Zhang, X and Wang, W and Lei, W and Yang, S and Shen, Q and Wang, X and Wu, P and Liu, Y and Ma, X and Yang, H and Zhang, W}, title = {Systemic remodeling of the multi-organ virome following Echinococcus infection in mice.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41917812}, issn = {1471-2180}, support = {No. 2023YFD1801300//the National Key Research and Development Programs of China/ ; No. 82341106//the National Natural Science Foundation of China/ ; No. 202208170046//Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents-Leading Talents/ ; }, abstract = {UNLABELLED: The interaction between parasitic infection and the host virome represents a frontier issue in microbial ecology, yet how Echinococcus infection affects the multi-organ virome and whether these alterations hold diagnostic or interventional potential remains poorly understood. In this study, we performed viral metagenomic sequencing on gut, liver, and lung samples from both infected and uninfected mice, integrating community structure clustering, diversity indices, and differential analyses, including STAMP and LEfSe. Our results reveal that Echinococcus infection induced significant tissue-specific virome remodeling. Compared to healthy controls, gut virome diversity increased, characterized by marked expansion of the class Caudoviricetes, particularly the family Siphoviridae (LDA > 4), alongside Picornaviridae enrichment (LDA > 4). In contrast, virome diversity decreased in both the liver and lung, with significant enrichment of Reoviridae (LDA > 4) in the liver and Retroviridae (LDA > 4) in the lung, respectively. Conversely, Picobirnaviridae (LDA > 4) was significantly reduced in the infected liver and lung. Based on phylogenetic analysis, Echinococcus infection significantly altered the murine gut viral community, with eukaryotic viruses (e.g., norovirus, picobirnavirus, and picornavirus) detected exclusively in infected animals, while bacteriophage populations remained stable across groups. Phage host prediction further revealed that phages enriched in infected samples targeted opportunistic pathogens (Clostridium septicum, Trueperella pyogenes), whereas control phages predominantly targeted commensals (Bacteroides thetaiotaomicron). Together, these findings demonstrate that Echinococcus infection drives both eukaryotic virus enrichment and a shift in phage predation toward pathogens, suggesting that infection-induced immune modulation creates a permissive environment for viral replication and associated bacterial dysbiosis.<br><br>GRAPHICAL ABSTRACT: [Image: see text]<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04923-x.}, }
@article {pmid42116847, year = {2026}, author = {Williams, NLR and Bei, Q and Raut, Y and Fuhrman, JA}, title = {Converting relative amplicon abundances to absolute abundances via flow cytometry: metagenomic validation and application to long ocean transects.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag081}, pmid = {42116847}, issn = {2730-6151}, abstract = {With microbes critical for ocean ecological and biogeochemical processes, we need to understand their abundance and diversity distributions. While traditional amplicon sequencing provides only relative abundance data, and the strongly preferred absolute abundances can be determined from samples spiked with internal standards, few oceanographic studies with absolute abundances exist. However, many have flow cytometry (FCM) data that should allow us to retrospectively "anchor" the relative abundances into absolute abundances. We tested this hypothesis with data from the 29th Atlantic Meridional Transect (AMT29) cruise where we had FCM of Synechococcus and Prochlorococcus, amplicons corrected with internal standards, and absolute cell count estimates from single copy recA and radA metagenomics. Anchoring the AMT29 amplicon data with Synechococcus FCM (used because phycoerythrin in Synechococcus is reliably detected by FCM in surface waters) yielded results strongly correlated with amplicon data corrected with internal standards (Pearson's r = 0.94, slope = 0.73), FCM (r = 0.80, slope = 0.43), and recA-based genome counts (Pearson's r = 0.94, slope = 0.62). Seeing this method worked reasonably well, we then generated estimates of absolute rRNA gene abundances from the Global rRNA Universal Metabarcoding of Plankton (GRUMP) transects that had FCM data (Pacific ~65 N to ~40S). These FCM-anchored gene copy estimates also showed strong correlations to FCM data (i.e. anchor with Synechococcus and predict Prochlorococcus), with r values ranging from 0.48-0.86. While the results are clearly only reasonable estimates, we believe the approach has the potential to significantly enhance the value of amplicon data which have accompanying FCM data.}, }
@article {pmid42117636, year = {2026}, author = {Chuang, Y-C and Behringer, MG and Patton, GE and Bird, JT and Mazny, JL and Gliessman, JR and Love, CE and Dalia, AB and McKinlay, JB}, title = {Reciprocal cross-feeding between bacteria can limit the emergence of metabolic dependencies.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0036326}, doi = {10.1128/aem.00363-26}, pmid = {42117636}, issn = {1098-5336}, abstract = {Cross-feeding is prevalent in microbial communities. Through time, cross-feeding is thought to enrich for loss-of-function mutations, thereby creating or reinforcing dependencies between community members. However, few studies have compared how cross-feeding affects the evolutionary trajectory of partners compared to monoculture conditions. Here, we compared mutations that were differentially enriched in bacterial monocultures versus cocultures pairing phototrophic Rhodopseudomonas palustris with fermentative Escherichia coli in an obligate cross-feeding relationship based on the exchange of nitrogen and carbon for 650-800 generations. Opposite trends for the number of differentially enriched mutations were observed for each species; R. palustris accumulated more unique mutations in monoculture, whereas E. coli accumulated more unique mutations in co-culture. Contrary to expectations, the emergence of additional dependencies was observed in monoculture, but not in coculture, even though additional layers of cross-feeding involving iron and adenine were present in coculture. We reasoned that iron and adenine cross-feeding occurred at levels sufficient to repress gene expression in the recipient, thereby promoting gene retention by lowering gene cost. We also observed that E. coli acquired mutations in coculture that were suggestive of enhanced adenine uptake, whereas R. palustris gained the ability to oxidize H2, but only in monoculture. Thus, the influence of cross-feeding on evolutionary trajectories can vary with organisms and conditions, and there are situations where cross-feeding can limit, rather than promote, emergent dependencies.IMPORTANCEBacteria commonly engage in cross-feeding, where nutrients are transferred between neighbors. Cross-feeding is thought to alleviate energy expenditures for genes whose role can be met by cross-fed nutrients, leading to eventual gene loss. However, few examples have been documented, especially in comparison to monocultures that lack a cross-feeding partner. We grew cocultures pairing phototrophic Rhodopseudomonas palustris with fermentative Escherichia coli alongside corresponding monocultures for 650-800 generations. While coculture conditions required obligate exchange of nitrogen and carbon, additional cross-feeding of adenine and iron likely occurred. Contrary to expectations, dependencies for iron and unknown compounds emerged in monocultures, but expected iron and adenine dependencies were not observed in cocultures. Low expression of iron scavenging and adenine synthesis genes in cocultures suggested that cross-feeding repressed expression, thereby lowering gene cost. Thus, although cross-feeding can sometimes make costly genes dispensable, there are also cases where cross-feeding lowers gene cost, thereby promoting gene retention.}, }
@article {pmid42118196, year = {2026}, author = {Stewart, J and Ockert, LE and Hawke, T and Power, M and Bino, G}, title = {First insights into the Drivers of the Cloacal Microbiome of the Wild Platypus (Ornithorhynchus anatinus).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02788-1}, pmid = {42118196}, issn = {1432-184X}, abstract = {The host microbiome plays a critical role in wildlife health, reproduction, and environmental responses. The platypus (Ornithorhynchus anatinus), a semi-aquatic monotreme endemic to eastern Australia, has remained microbiologically understudied despite conservation concern. Here, we present the first characterisation of the wild platypus cloacal microbiome using 16 S rRNA amplicon sequencing of samples collected across its eastern range, including sites recently affected by drought and bushfire. We found that region, and environmental disturbances such as bushfire and drought were significant drivers of bacterial community structure and composition, with influence from sex and breeding season also. Bushfire and drought both disrupted microbial community structure. The microbiome partially recovered following low-severity fires, but not after severe fire or prolonged drought, suggesting that microbiome resilience is linked to disturbance intensity. These findings suggest that the platypus microbiome is sensitive to environmental pressures and may offer a minimally invasive indicator of individual and ecosystem health. In addition to these ecologically important findings, across all sampled regions the platypus cloacal microbiome was consistently dominated by Campylobacterota and Fusobacteriota, with Pseudomonadota and Bacillota also prominent in the core microbiomes. Our results provide a critical baseline for integrating microbial health into conservation planning for this unique mammal.}, }
@article {pmid42119198, year = {2026}, author = {Lemos, ACF and da Cruz, ILS and Mello, IS and Cruz, IF and Soares, MA}, title = {Free-living amoeba diversity in river waters of western Brazil and their in vitro and in vivo pathogenic potential.}, journal = {Protist}, volume = {181}, number = {}, pages = {126164}, doi = {10.1016/j.protis.2026.126164}, pmid = {42119198}, issn = {1618-0941}, abstract = {Free-living amoebae (FLA) are key components of aquatic and terrestrial ecosystems, but their diversity and distribution in central-western Brazil remain poorly characterized. Some FLA are pathogenic and may harbor bacteria of public health relevance. We aimed to identify and to characterize the FLA biodiversity in the Cuiabá River basin and to infer their pathogenic potential. Water samples were collected at eight sites across two hydrological periods, and physicochemical and microbiological parameters were quantified. FLA were isolated on non-nutrient agar seeded with heat-inactivated Escherichia coli and identified by using morphology and molecular markers. We obtained 39 isolates (six genera and 14 species); Acanthamoeba (51.3%), Vannella (23.1%), and Vermamoeba (12.8%) were predominated. Only V. vermiformis was detected during both the high-water (when four exclusive species were detected) and low-water (when nine exclusive species were detected) periods. Seventeen FLA strains (n = 35) killed zebrafish larvae (Danio rerio); 11 of these strains (64.7%) were Acanthamoeba species, and the remaining strains belonged to the genera Flamella, Naegleria, Ptolemeba, Vannella, and Vermamoeba. Thermo- and osmotolerance did not correlate with zebrafish larval mortality. These findings expand current knowledge of FLA biodiversity in Brazil and reinforce that integrated FLA monitoring in the Cuiabá River basin is needed.}, }
@article {pmid42119482, year = {2026}, author = {Paula, MPO and Varani, AM and da Silva, VLC and Roesch, LFW and Tótola, MR and Ramos, AC and Pylro, VS}, title = {Genome-resolved characterization of microbial consortia driving glyphosate degradation in soil.}, journal = {Chemosphere}, volume = {405}, number = {}, pages = {144948}, doi = {10.1016/j.chemosphere.2026.144948}, pmid = {42119482}, issn = {1879-1298}, abstract = {Glyphosate is a widely used non-selective herbicide associated with ecological and human health concerns due to its environmental persistence, highlighting the need for effective remediation strategies. Among available approaches, microbial enzyme-mediated degradation represents a promising biological solution. This study aimed to enrich and characterize glyphosate-degrading microbial consortia from coffee plantation soils, validate glyphosate and aminomethylphosphonic acid (AMPA) degradation by chromatographic analyses, and integrate genome-based functional annotation with comparative structural analyses to investigate enzymatic systems involved in C-P and C-N bond cleavage. The enrichment process, followed by metataxonomic and metagenomic analyses, revealed dynamic shifts in microbial community composition. Achromobacter and Serratia were identified as key genera, harboring genetic potential for glyphosate and AMPA degradation. High-performance liquid chromatography with diode array detection confirmed efficient transformation of both compounds, with consortia Con_CC and Con_CC-G achieving the highest removal efficiencies under carbon- and phosphorus-limited conditions. Genome-based functional annotation showed that both genera encode gene clusters associated with the C-P lyase pathway, while only Achromobacter harbors the gene encoding glyphosate oxidoreductase (GOX), linked to oxidative C-N bond cleavage. Structural modeling indicated conservation of key catalytic residues in PhnJ, whereas GOX-related sequences in Serratia corresponded to partial homologs lacking a complete catalytic site. By integrating chromatographic, genomic, and structural analyses, this study provides a multi-level framework linking microbial community dynamics, functional potential, and molecular mechanisms underlying glyphosate degradation.}, }
@article {pmid42121034, year = {2026}, author = {Xu, P and Zhu, Z and Liu, Y and Wang, H and Li, H and Kong, Q and Tan, Z and Li, K and Liu, S and Jamal, MA and Shang, Z}, title = {Revealing growth performance in weaned Tibetan pigs along with gut microbial diversity and oxidative status under the impact of ambient temperature.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05004-9}, pmid = {42121034}, issn = {1471-2180}, support = {32260859//National Natural Science Foundation of China for Regional Foundation/ ; 32260859//National Natural Science Foundation of China for Regional Foundation/ ; }, abstract = {The physiological parameters of Tibetan piglets have been found to be significantly influenced by environmental factors particularly during the weaning period and in the context of large fluctuations in ambient temperature in plateau regions. This study was designed to examine the effects of different ambient temperatures on gut microbiota diversity, serum antioxidant status, and growth performance of weaned Tibetan piglets. The study comprised of n = 40 weaned Tibetan piglets that were randomly allocated to five temperature-controlled groups with increase in temperature as BC4 (18 °C), BD4 (22-24 °C), BE4 (25-27 °C), BF4 (28-30 °C), and BG4 (31-33 °C). The growth performance was calculated by average daily weight gain (ADG) while serum antioxidant capacity was assessed through malondialdehyde (MDA), superoxide dismutase (SOD), total antioxidant capacity (T-AOC), and glutathione peroxidase (GSH-Px) levels. Fecal samples were taken and through 16 S rRNA gene sequencing the gut microbiota profiling was checked. Microbial α- and β-diversity indices, community composition, and taxa-specific shifts were evaluated by temperature-dependent changes. Results indicated that moderate increase in ambient temperature (25 ~ 27 °C) significantly improved the growth performance with higher ADG in the BE4 group. The serum antioxidant markers SOD, T-AOC, and GSH-Px level were higher than MDA concentrations, indicating enhanced oxidative resistance. The beneficial bacterial taxa such as Paraprevotella, Limosilactobacillus, and Paralachnospira flourished and change the gut microbiota diversity and structure, whereas potentially harmful taxa (Bifidobacterium_388775 and Ligilactobacillus) were decreased at the moderate temperatures. The LEfSe and multiple t-tests determine the gut microbial ecology when temperature-dependent shifts in microbial composition indicate a regulatory effect of ambient temperature. It is concluded that the optimal growth performance and enhanced serum antioxidant capacity in weaned Tibetan piglets maintained by moderate raise of ambient temperature (25 ~ 27 °C) to support a balanced gut microbiota. These findings indicated that during the weaning period temperature played an important role in regulating oxidative status and gut microbial diversity.}, }
@article {pmid42121736, year = {2026}, author = {Özdemir, &#xd6;S and Ahsan, U and Raza, I and Cengiz, &#xd6;}, title = {Effects of Calf Starter Neutral Detergent Fiber Levels and Weaning on Growth and Rumen Microbial Diversity of Holstein Calves.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {9}, pages = {}, doi = {10.3390/ani16091316}, pmid = {42121736}, issn = {2076-2615}, support = {VTF- 22012//Directorate of Scientific Research Projects/ ; }, abstract = {A study was conducted to evaluate the effect of neutral detergent fiber (NDF) levels of calf starter and weaning time on growth, rumen fermentation characteristics, serum metabolites, and rumen microbial diversity of Holstein calves. A total of 24 newly born male Holstein calves were randomly distributed to four groups in a completely randomized design with a 2 × 2 factorial arrangement of NDF levels (14% and 24%) and weaning time (d 44 and d 54). There was no interaction between starter NDF levels and weaning time for any trait except rumen acetic acid in the immediate post-weaning phase (p = 0.013). Starter NDF levels had no effect on growth, feed intake, and hay intake. Late-weaned calves had greater (p = 0.050) weight gain in the pre-weaning phase whereas, early-weaned calves showed greater weight gain (p = 0.004) and starter intake (p = 0.004) in the post-weaning phase although overall weight gain, and starter and hay intakes were not affected by weaning time. Rumen pH, ammonia nitrogen, and most volatile fatty acids remained unaffected by starter NDF levels and weaning except isobutyric acid which was greater in calves fed 24% NDF starter (p = 0.001) in the immediate post-weaning and isovaleric acid which was greater in early-weaned calves (p = 0.044) at the end of experiment. Serum metabolites were largely affected (p < 0.05) by starter NDF levels and weaning time in the pre-weaning phase only. Alpha diversity of rumen microbes was greater and chaotic in 14% NDF starter group (early- and late-weaned) in the pre-weaning phase which converged in the immediate post-weaning phase and diverged on starter NDF basis at the end of experiment. Microbial ecology at phylum and genus levels composition were greatly driven by starter NDF levels in the pre-weaning phase, by weaning time in the immediate post-weaning phase, and two distinct bifurcated microbial ecologies based on starter NDF levels appeared at the end of experiment. In conclusion, the comparable growth with distinct microbial diversity but largely in favor of 24% NDF starter suggests that calves can be subjected to early weaning with 24% starter NDF levels for smooth transition from liquid to solid feed in Holstein calves.}, }
@article {pmid41918091, year = {2026}, author = {Luo, S and Chen, X and Guo, S and Hu, S and Dong, Z and Geng, J}, title = {Temperature-driven metabolic adaptation in thermophilic microbial communities of Western Sichuan hot springs.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41918091}, issn = {1471-2180}, support = {2022YFC26023002//National Key Research and Development Program of China/ ; }, abstract = {BACKGROUND: Understanding microbial adaptation to extreme environments remains a key challenge in microbial ecology. Geothermal hot springs, characterized by temperature gradients and varying geochemical conditions, represent valuable natural laboratories for studying microbial diversity, adaptive strategies, and evolutionary mechanisms. However, despite many studies of hot spring communities, how temperature gradients shape key microbial adaptation strategies remains insufficiently understood, limiting our ability to explain survival and function in extreme environments.<br><br>RESULTS: Our study investigated microbial community composition and functional profiles across a natural thermal gradient (50&#x2013;93&#xa0;&#xb0;C) in six hot springs on the Western Sichuan Plateau using optimized contig- and MAG-based metagenomic strategies. Enhanced annotation approaches significantly improved taxonomic resolution in these extreme environments. Metagenomic analyses revealed distinct shifts in microbial communities along the thermal gradient: moderate-temperature springs (50&#x2013;70&#xa0;&#xb0;C) were dominated by Pseudomonadota and Bacteroidota, exhibiting heterotrophic flexibility and utilizing the Calvin&#x2013;Benson&#x2013;Bassham cycle and diverse nitrogen reduction pathways; high-temperature springs (70&#x2013;90&#xa0;&#xb0;C) were enriched in Chloroflexota, which primarily employed the Wood&#x2013;Ljungdahl pathway coupled with enhanced sulfur metabolism; and extreme-temperature springs (&#x2265;&#x2009;90&#xa0;&#xb0;C) were characterized by Aquificota and Thermoproteota, relying on specialized autotrophic pathways (rTCA, DH/HH cycles), streamlined nitrogen assimilation, and sulfur oxidation pathways. These thermophilic lineages showed genome streamlining, reduced regulatory complexity, and specialized metabolic strategies, reflecting narrower ecological niches and deeper phylogenetic branches.<br><br>CONCLUSIONS: This metagenomic investigation across a temperature gradient in western Sichuan hot springs highlights temperature as an essential driver of microbial community structure, genome evolution, and adaptive specialization. Thermophilic lineages in extreme-temperature environments exhibited streamlined genomes, specialized metabolic functions, and narrower ecological niches, consistent with adaptation to persistent thermal stress. The findings enhance understanding of microbial evolutionary strategies and underscore the ecological significance of temperature-driven adaptation in extreme environments.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04921-z.}, }
@article {pmid42112348, year = {2026}, author = {Hua, M and Luo, J and Li, P and Zhang, Y and Zhang, X and Wu, Y and Dong, H}, title = {The microbiota-systemic lupus erythematosus axis: mechanisms, diagnostics, and therapeutic frontiers.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1782828}, pmid = {42112348}, issn = {1664-3224}, mesh = {Humans ; *Lupus Erythematosus, Systemic/therapy/diagnosis/immunology/microbiology ; Dysbiosis/immunology ; Animals ; *Microbiota/immunology ; *Gastrointestinal Microbiome/immunology ; Autoimmunity ; }, abstract = {Systemic lupus erythematosus (SLE) is a prototypical autoimmune disease in which host-microbiota crosstalk plays a pivotal role in immune dysregulation. Recent metagenomic studies have revealed that disease-specific dysbiosis--characterized by the expansion of pathobionts and depletion of immunoregulatory commensals--occurs across the gut, oral cavity, skin, and genital tract. Integrative multi-omics analyses have identified three mechanistic pathways linking microbial imbalance to autoimmunity: (1) microbial peptides trigger molecular mimicry and epitope spreading, activating autoreactive lymphocytes: (2) microbial metabolites disrupt redox homeostasis, impair epithelial barriers, and skew the AhR-mediated Th17/Treg balance; and (3) dysbiosis alters epigenetic regulation by inhibiting DNA methyltransferases, leading to hypomethylation of SLE-risk genes. Translational studies have shown that microbiome-targeted interventions, including probiotics, prebiotics, fecal microbiota transplantation, and even B cell-depleting chimeric antigen receptor T-cell (CAR-T) therapy, can restore microbial balance, reduce autoantibody levels, and modulate the gut-immune axis. Furthermore, microbial signatures are emerging as potential biomarkers for disease activity and treatment response. Despite this promise, challenges remain, such as the impact of immunosuppressants on the microbiota, spatial heterogeneity in host-microbe interactions, and limitations in causal inference. Looking forward, integrating single-cell metagenomics, microbiota-directed diets, and engineered microbial consortia may pave the way for personalized microbiome-based therapies. Reframing SLE as a "meta-organismal imbalance" positions microbial ecology at the forefront of precision medicine.}, }
@article {pmid42112445, year = {2026}, author = {Furuya, R and Nishikawa, Y and Ota, Y and Prah, I and Mahazu, S and Kifushi, M and Yoshida, M and Suzuki, M and Hoshino, Y and Suzuki, T and Takeyama, H and Ablordey, A and Saito, R}, title = {Single-cell genomic profiling of antimicrobial resistance in Escherichia coli from the Densu River, Ghana.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1797725}, pmid = {42112445}, issn = {1664-302X}, abstract = {INTRODUCTION: River water serves as a natural reservoir for antimicrobial resistance (AMR) factors. Although environmental AMR poses a global threat to public health as it spreads to local communities through the microbiome in aquatic environments, the actual situation remains unclear, especially in developing countries. In this study, we sought microbiome data, including AMR information, for multiple bacterial strains from river water samples using a single-cell genomics platform.<br><br>METHODS AND RESULTS: After antimicrobial selection of samples from the Densu River in Ghana, 16S rRNA amplicon sequencing revealed a high proportion of the genus Escherichia-Shigella with ampicillin and sulbactam selection. Single-cell genomic analysis revealed differences in AMR and virulence factor profiles among the same species of Escherichia coli, including the CTX-M-15 extended-spectrum &#x3b2;-lactamase-producing ones. Pan-genome analysis predicted 4,814 gene clusters, of which 2,264 were accessory, including 605 singletons. Phylogenetic tree analysis using the maximum likelihood method showed the heterogeneity of single-cell amplified genomes (SAGs), and cluster of orthologous gene analysis for each SAG confirmed the difference in the ratio of each functional group.<br><br>CONCLUSION: This study demonstrates the potential of single-cell genomics using the single-cell amplified genome in gel method to enhance environmental AMR surveillance with high resolution and accuracy. It also represents the first application of this approach to aquatic environments in Ghana, thereby contributing to the development of microbial ecology and genomic resources.}, }
@article {pmid42112933, year = {2026}, author = {Gee, M and Sharp, C}, title = {Bacterial weaponry and the ecological factors of competitive success.}, journal = {Essays in biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1042/EBC20250028}, pmid = {42112933}, issn = {1744-1358}, support = {N/A//University of Reading (UoR)/ ; }, abstract = {Bacteria have evolved complex protein systems known as bacterial weapons to inhibit or kill their competitors. These bacterial weapons are a remarkably diverse arsenal that influence the composition and function of important microbial communities such as the human microbiome. In turn, the spatial constraints, nutrient availability, environmental stressors, and the presence of competitors determine not only whether weapons are expressed, but which weapons provide the greatest advantage. While bacterial weaponry is widespread, the types, mechanisms, and abundance of these systems vary between, and even within, species. Recent research has highlighted the importance of bacterial weaponry in community invasion and pathogenicity. Their potency and narrow killing spectrum have also generated interest in exploiting bacterial weapons to engineer microbial communities or develop therapeutics that avoid the disruption of broad-spectrum antibiotics. Understanding how ecological context affects weapon efficacy could reveal new virulence mechanisms used by pathogens and inform the design of novel treatments and microbiome-based therapies. This review outlines three of the best-studied bacterial weapon systems (protein bacteriocins, the type VI secretion system, and contact-dependent inhibition), highlighting their roles in microbial ecology, pathogenicity and their potential as therapeutics.}, }
@article {pmid42114326, year = {2026}, author = {Esen, S}, title = {An update on heat stress impacts on rumen microbiome composition, fermentation parameters, and mitigation approaches in ruminants.}, journal = {Journal of thermal biology}, volume = {139}, number = {}, pages = {104480}, doi = {10.1016/j.jtherbio.2026.104480}, pmid = {42114326}, issn = {0306-4565}, abstract = {Over the past decade, there has been an increasing amount of literature on heat stress (HS) effects on ruminant production systems, yet much uncertainty still exists about the relationship between HS and rumen microbial ecology across species. This narrative review synthesizes peer-reviewed evidence from 2020 to 2025, with the aim of providing a critical appraisal of HS effects on rumen microbiome composition and fermentation parameters in cattle, buffalo, sheep, and goats. A convergent pattern emerges from the available data: HS consistently reduces cellulolytic bacteria (Fibrobacter, Ruminococcus) while increasing lactate-producing and starch-fermenting taxa. Acetate proportions declined by 29-33% in buffalo and beef cattle, whereas total VFA in sheep increased during mild HS, reflecting species-dependent fermentation responses. A strong relationship between breed-level heat tolerance and rumen microbiome diversity has been reported in several recent studies, providing converging evidence that heat tolerance may be characterized as a holobiont phenotype. It has been demonstrated that HS extends beyond classical VFA changes to disrupt B-vitamin synthesis, amino acid metabolism, biogenic amine homeostasis, and bile acid biotransformation. Nutritional interventions, including probiotics, chromium, herbal supplements, and rumen-protected amino acids, have been shown to partially restore microbial balance, although responses vary with HS severity and host genotype. Notwithstanding these findings, the generalisability of much published research on this topic is limited by methodological heterogeneity across studies. Taken together, these findings highlight the need for standardized experimental protocols, multi-omics integration, and microbiome-targeted intervention strategies.}, }
@article {pmid42115446, year = {2026}, author = {Huang, M and Zhou, H and Du, X and Xia, P}, title = {Nitrogen Application Under Integrated Water-Fertilizer Management Regulates Rhizosphere Nitrogen Dynamics, Microbial Communities, and Maize Productivity.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02784-5}, pmid = {42115446}, issn = {1432-184X}, support = {2025JC-YBMS-645//Shaanxi Provincial Department of Science and Technology/ ; }, abstract = {Nitrogen management strongly regulates rhizosphere nutrient availability, microbial ecological processes, and maize productivity in fertigation-based systems. Yet, the mechanisms by which nitrogen application gradients shape rhizosphere nitrogen transformations and microbial community stability remain insufficiently understood. In this study, a field experiment with four nitrogen levels (N0 0 kg·hm[-2], N1 100 kg·hm[-2], N2 140 kg·hm[-2], and N3 180 kg·hm[-2]) was conducted to clarify how nitrogen inputs influence rhizosphere nitrogen forms, microbial community assembly, and yield performance in maize under an integrated water-fertilizer regime. Moderate nitrogen application (N2) significantly enhanced rhizosphere nitrogen availability throughout the jointing, silking, and grain-filling stages. Nitrate-N and dissolved organic nitrogen (DON) reached 297.15 mg·kg[-1] and 152.14 mg·kg[-1] at jointing-substantially higher than N0-and remained elevated during subsequent stages, indicating sustained nitrogen supply. This improved nutrient status promoted plant growth and resulted in the highest grain yield (5281.85 kg·hm[-2]), representing a 25.7% increase compared with N0. In contrast, excessive nitrogen input (N3) failed to further elevate nitrogen fractions and may have reduced nitrogen-use efficiency. Nitrogen application influenced rhizosphere microbial communities. Moderate nitrogen (N2) increased bacterial richness and altered community composition, with several dominant bacterial and fungal taxa showing changes in relative abundance. Core microbial taxa remained largely stable, whereas transient taxa exhibited modest variations. Co-occurrence network analysis indicated increased cohesiveness in bacterial networks and reduced connectivity in fungal networks under nitrogen input. Functional predictions revealed that nitrogen application reduced bacterial chemoheterotrophy, aerobic-chemoheterotrophy, and nitrogen-cycling-related functions, while enhancing aromatic-compound-degradation potential. Predicted abundance of potential plant pathogenic fungi decreased following nitrogen application. Overall, moderate nitrogen input optimized rhizosphere nitrogen fractions, influenced microbial community composition and functional potential, and improved maize productivity, providing insight into microbiological responses to nitrogen management in semi-arid fertigation systems.}, }
@article {pmid42107798, year = {2026}, author = {Song, Z and Rawat, A and Herrmann, C and Kabelitz, T and Yi, Q and Amon, B and Janke, D and Mehmood, T and Vieira, S and Overmann, J and Amon, T}, title = {Inoculation effects on microbial and methane dynamics in daily filled dairy manure storage.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134831}, doi = {10.1016/j.biortech.2026.134831}, pmid = {42107798}, issn = {1873-2976}, abstract = {Liquid manure storage is one of the major global sources of agricultural methane (CH4) emissions, and storage tanks on livestock farms are rarely emptied completely. Although the effects of residual slurry acting as an inoculum on subsequent microbial activity and CH4 generation have been examined previously, most studies have used batch or static storage systems that do not reflect the continuously filled conditions typical of dairy farms. To address this, this study for the first time simulated farm-like daily continuous filling by incubating dairy cattle manure for 92 days in laboratory-scale storage tanks with inoculum (WI) and without inoculum (WOI). Microbial community dynamics were assessed using 16S rRNA gene sequencing, while physicochemical properties and methane emissions were monitored simultaneously. Within this continuously fed system, inoculation reshaped microbial succession, leading to the early enrichment (day 8) of hydrolytic bacteria and methanogens in WI tanks. These shifts corresponded to distinct physicochemical trajectories: WI tanks maintained stable pH (7.0-7.6), accumulated fewer volatile fatty acids, reached peak daily CH4 emissions much earlier (day 31) than WOI tanks (day 79), and exhibited 17.9% higher cumulative CH4 emissions. Modified Gompertz modelling showed that inoculation shortened the apparent methanogenic lag phase by 20.64 days, confirming its accelerating effect on system-level CH4 emission dynamics under continuous filling. This study provides the first investigation of inoculation effects in daily filled manure storage, linking microbial community dynamics with CH4 emission patterns and offering a framework for identifying CH4 emission trajectories and key control windows.}, }
@article {pmid42108251, year = {2026}, author = {Yin, M and Chen, X and Lu, R and Dong, Y and Luo, W and Tang, Z and Zeng, M and Xu, Y and Qing, Y and Xi, C and Feng, X and Guo, H and Mo, S and Luo, J}, title = {Diversity of fecal viromes and zoonotic risk assessment in captive wild felids using viral metagenomics.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-52077-7}, pmid = {42108251}, issn = {2045-2322}, support = {(Grant No. HX2023115P).//This research was supported by the grant for "Metagenomic Analysis of Viruses Carried by Amur Tigers and Leopards" (Grant No. HX2023115P)./ ; }, abstract = {Emerging viral diseases-particularly zoonotic pathogens-affect the health and conservation of endangered felids, including Panthera tigris altaica (Amur tiger) and Panthera pardus (leopard). To address this challenge, we employed a viromics approach to investigate the diversity of the fecal virome in wild felids and assess its zoonotic potential. Using in-depth metagenomic sequencing and analysis of fecal samples from captive wild felids housed in a wildlife institution, this study characterized the enteric virome and evaluated associated risks. A total of 18 viral families and 48 viral genera were identified. The DNA virus community exhibited stability in abundance and composition, dominated by the phyla Heunggongvirae and Bamfordvirae. Within Heunggongvirae, the class Caudoviricetes was the core component, with its abundance aligning with the intestinal bacterial community, suggesting a potential role of these bacteriophages in regulating microbial ecology. Additionally, sequences of the family Poxviridae, homologous to Variola virus (VARV), were detected. In contrast, the RNA virus community displayed higher diversity and variability, with the order Ortervirales as the predominant group. Sequences highly homologous to feline leukemia virus (FeLV) were repeatedly identified, suggesting potential latent infections. The detection of sequences related to rare environmental viruses, such as Casadabanvirus, highlights the potential risk of cross-species virus transmission under captive conditions. Stability analysis revealed that dominant DNA virus groups exhibited low abundance variability across samples. In contrast, unclassified RNA viral taxa showed higher abundance variability. KEGG functional annotation mapped DNA viral contigs primarily to microbial metabolic modules. Conversely, RNA assemblies extensively mapped to eukaryotic pathways (e.g., arachidonic acid and energy metabolism); due to the total nucleic acid extraction methodology, these mappings primarily reflect co-extracted host transcriptomic background rather than viral-encoded functions, providing an indirect snapshot of the concurrent enteric microenvironment. These baseline data delineate the virome structure in captive environments and provide practical targets for zoological biosecurity and proactive veterinary surveillance.}, }
@article {pmid42108292, year = {2026}, author = {Guo, JX and Gao, YZ}, title = {Absolute Quantification of Bacteria in the Microbiome and Its Application.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3033}, number = {}, pages = {91-103}, pmid = {42108292}, issn = {1940-6029}, mesh = {*Microbiota/genetics ; *Bacteria/genetics/isolation &amp; purification/classification ; High-Throughput Nucleotide Sequencing/methods ; Humans ; DNA, Bacterial/genetics ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; }, abstract = {The advent of genomics and deep sequencing technologies has facilitated the development of absolute quantification techniques, which offer researchers more objective and precise sequencing outcomes. Unlike traditional relative quantification methods, which provide comparative data, absolute quantification delivers definitive measurements of genes or taxa. This analytical approach mitigates the potential for extraneous influences when comparing disparate samples, thereby reducing analytical errors. The implementation of absolute quantification techniques enhances our comprehension of microbial community structures, ecological dynamics, and their associations with host health or disease conditions. This chapter emphasizes a straightforward and broadly applicable method for genomic quantification, which necessitates the incorporation of a specified amount of internal standard DNA into the samples, eliminating the need for subsequent adjustments during library construction and sequencing. By assessing the proportion of internal standard DNA across various samples, sequencing data can be transformed into absolute quantification metrics. The internal standard method for absolute quantification is versatile and can be effectively utilized across multiple domains, including disease diagnosis, microbial ecology research, the fermentation industry, and environmental monitoring. Overall, absolute quantification methods furnish a more accurate and holistic perspective for microbiome research.}, }
@article {pmid42108299, year = {2026}, author = {Wang, F and Zhang, H}, title = {Microbial Omics Analysis for Multispecies Symbioses in Staple and Traditional Fermented Foods.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3033}, number = {}, pages = {217-240}, pmid = {42108299}, issn = {1940-6029}, mesh = {*Fermented Foods/microbiology ; *Food Microbiology/methods ; Fermentation ; *Symbiosis ; *Microbiota ; *Metabolomics/methods ; Humans ; Genomics/methods ; }, abstract = {Fermented foods represent a cornerstone of global culinary traditions, underpinned by intricate microbial communities that drive flavor development and preservation. This chapter examines the microbial ecology and functional interactions across representative staple and traditional fermented foods, including fermented vegetables (sauerkraut, kimchi), fermented condiments (soy sauce, vinegar, miso, doubanjiang), and fermented alcoholic beverages (Chinese baijiu, wine, sake, Huangjiu). Recent meta-omics advances have revealed dynamic community succession, cross-feeding networks, quorum-sensing mechanisms, and key microorganisms contributing to flavor metabolites and health-promoting compounds. Furthermore, synthetic microbial communities and starter engineering are discussed as strategies to standardize fermentation, enhance quality, and develop novel functional products.}, }
@article {pmid42108422, year = {2026}, author = {Shetty, P and Vuong, T and Li, C and Wagner, V and Myrzakhmetova, D and Peng, CC and Li, W and Ching, J and Zander, A and Weiser, S and Rosenbaum, MA and Allen, RJ and Lakemeyer, M and Mittag, M}, title = {Multi-omics studies reveal how ambient temperature changes govern cellular responses of Chlamydomonas.}, journal = {The Plant cell}, volume = {}, number = {}, pages = {}, doi = {10.1093/plcell/koag136}, pmid = {42108422}, issn = {1532-298X}, abstract = {Photosynthetic protists, known as microalgae, face increasing temperatures due to climate change. The green biflagellate alga Chlamydomonas reinhardtii (Chlamydomonas) serves as a model for thermoregulation. While responses to thermal stress are well characterized, much less is known about the impact of ambient temperature shifts. Understanding microalgal responses to environmental temperature changes is critical, as these primary producers drive ecosystem productivity and food web dynamics. Here, Chlamydomonas grew mixotrophically at ambient temperatures from 18 °C to 33 °C. Transcriptomic profiling revealed extensive reorganization, with over 5,000 transcripts significantly affected, including those involved in algal-bacterial interactions, photoreception, lipid metabolism, photosynthesis, cilia formation, and the secretome. CO2 transfer rates and acetate levels measured at 18 °C and 28 °C suggest decreased photoautotrophic algal growth at 28 °C at first. Antagonistic bacterial activity was sustained longer at lower temperatures. Proteomic analyses of isolated cilia and secreted proteins corroborate major abundance changes within these sub-proteomes, particularly in ciliary intraflagellar transport complexes and mating-related proteins in the secretome. Together, these molecular alterations resulted in pronounced changes in growth, the lengths of cells and cilia swimming behavior, mating ability and bacterial antagonism. These data reveal major cellular responses caused by ambient, even short-term temperature shifts.}, }
@article {pmid42110957, year = {2026}, author = {Skidmore, AM and Goodfellow, SM and Nofchissey, RA and Jiang, L and Dunnum, J and Cook, JA and Guo, Y and Mali, I and Bradfute, SB}, title = {Characterization of the gut microbiome of wild Peromyscus sonoriensis in New Mexico, USA.}, journal = {Frontiers in microbiomes}, volume = {5}, number = {}, pages = {1672092}, pmid = {42110957}, issn = {2813-4338}, abstract = {The microbiome is highly important to the physiologies of all multicellular organisms, particularly metazoans. However, the microbiomes of many wild animals remain understudied and poorly understood. Peromyscus mice are commonly used as models of adaptation, mental health, and human disease in biomedical research, and are also common in the environment across North America, frequently coming into close contact with humans. Additionally, Peromyscus sonoriensis are implicated as the primary reservoir for Sin Nombre hantavirus, a rare but severe disease of high morbidity and mortality in humans. Here we characterize the fecal microbiomes of 311 Peromyscus sonoriensis, the western deer mouse, collected from across New Mexico, USA, which will further their usefulness as models of disease and behavior as well as increase our understanding of their ecology. The animals used in this study are geographically diverse, collected from multiple ecoregions, and encompass mice of all ages and sexes. We sequenced the entire 16S rRNA gene in a PCR independent approach and characterized the microbiomes with Shannon entropy, Faith phylodiversity, and weighted UNIFRAC. We found that these mice have diverse microbiomes, with individuals varying in the presence and proportions of various identified bacteria. We analyzed the total population of mice according to age, sex, and trapping location, and found that trapping location was the only condition to significantly impact the microbiome. When the mice were subdivided by the location of collection, there were mild effects of age and sex. When comparing mice from archival museum storage, storage of samples in 95% ethanol resulted in significant alterations to the microbiome when compared to cryopreservation. Differential bacterial family presence was determined using ANCOMBC at the 0.05 significance threshold, and there were many differentially abundant families across all groups of mice. This data set can now be used as a reference for further research into the microbiomes of related Peromyscus species, enhance the use of P. sonoriensis as model laboratory animals, and as a source of novel research questions regarding the physiology of these rodents.}, }
@article {pmid42111288, year = {2026}, author = {Sanches, P and Mescher, MC and De Moraes, CM}, title = {Endosymbionts affect plant virus transmission by winged and wingless aphids.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag096}, pmid = {42111288}, issn = {2730-6151}, abstract = {Vector-borne pathogens frequently modify host-vector interactions, and their influence can be modulated by other microbial symbionts. We recently documented endosymbiont effects on aphid traits involved in plant virus transmission, showing that facultative endobacteria-particularly Hamiltonella defensa-enhanced transmission of pea enation mosaic virus. Here, we examine transmission steps and associated molecular signatures in winged and wingless aphid morphs. Consistent with our previous findings, we observed enhanced pea enation mosaic virus transmission, as well as elevated viral titer in wingless aphids harboring H. defensa. However, winged aphids with this endosymbiont displayed similar effects on virus titer but not transmission. Furthermore, whereas wingless aphids exhibited higher transmission than winged aphids when H. defensa was present, this pattern was reversed for aphids harboring only the obligate endosymbiont Buchnera aphidicola; in parallel, we observed no differences between morphs of lines harboring other facultative endosymbionts. Subsequent experiments comparing lines harboring H. defensa versus the obligate symbiont alone revealed divergent effects on winged and wingless morphs on (i) virus inoculation efficiency (i.e., delivery of acquired virus; H. defensa), (ii) key salivary proteins (carbonic anhydrases, CAs; both lines), and (iii) plant defense-related marker transcripts (PR-1, salicylic acid pathway; LOX, jasmonic acid pathway; both lines). The correspondence of these patterns to the observed transmission effects suggests that endosymbiont-mediated effects on transmission may reflect changes in salivary secretions and related feeding traits. Our findings highlight the role of vector endosymbionts in disease transmission and provide insights into candidate processes by which they may influence virus-vector-host interactions.}, }
@article {pmid42111323, year = {2026}, author = {Belarbi, H and Kebede, F and Lambrecht, F and Lampaert, H and Grootaert, C and De Leyn, I and Van Bockstaele, F and Van de Wiele, T and Cakmak, I and Du Laing, G}, title = {Food-gut continuum of biofortified micronutrients: Influence of breadmaking processes on iodine, selenium, and zinc bioaccessibility and epithelial responses in an in vitro intestinal model.}, journal = {Food chemistry: X}, volume = {36}, number = {}, pages = {103882}, pmid = {42111323}, issn = {2590-1575}, abstract = {Micronutrient malnutrition affects over 3 billion people worldwide. This study evaluated biofortified wheat breads with iodine, selenium, and zinc, applied individually or in combination, and examined mineral retention, bioaccessibility, and intestinal epithelial responses. Mineral concentrations in wheat and their changes after baking unfermented flatbread and fermented sourdough were quantified, while intestinal bioaccessibility and epithelial effects were assessed using in-vitro digestion and cell culture models. Biofortification significantly increased mineral concentrations in wheat; however, retention during baking varied by mineral and product. Flour composition and baking method influenced iodine and zinc levels, whereas selenium retention was primarily affected by wheat cultivar and fermentation. In biofortified Bezostaja-1, Se bioaccessibility reached 68% in flatbread, while iodine and zinc reached 49% and 12% in sourdough. Selenium enhanced mitochondrial activity in intestinal cells in both bread types, and zinc-enriched sourdough increased epithelial integrity by 15% and reduced cellular permeability by 30%.}, }
@article {pmid42101887, year = {2026}, author = {van den Bergh, SG and Chardon, I and Meima-Franke, M and Rocha, GS and Cheng, X and Raaijmakers, C and de Boer, W and Bodelier, PLE}, title = {Unraveling underlying mechanisms and responsible microbes of organic residue-stimulated atmospheric methane uptake in agricultural soils.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiag048}, pmid = {42101887}, issn = {1574-6941}, abstract = {It has been reported that compost amendment improves atmospheric CH4 uptake of agricultural soils. However, microbes involved as well as the underlying mechanisms responsible for the observed effect remain unclear. Here we identified active MOB at (circum-) atmospheric CH4 concentrations in agricultural soils amended with green compost, and investigated three complementary hypotheses: (i) atmospheric CH4 consumption is driven by highly activated, flush-feeding MOB; (ii) stimulation of internal CH4 production which fuels flush-feeding methanotrophic activity; and (iii) increased availability of H2 that can serve as additional energy source for mixotrophic methanotrophy. First, we showed that MOB previously activated by exposure to high CH4 concentrations can subsequently oxidize atmospheric CH4 via the flush-feeding lifestyle. Second, no internal CH4 production in soil was observed following compost amendment, likely due to lack of suitable substrates for methanogenesis. Third, provision of elevated H2 concentrations did not affect the concurrent atmospheric CH4 oxidation. Phospholipid fatty acid-stable isotope probing (PLFA-SIP) revealed that four distinct MOB groups were active at (circum-) atmospheric CH4 concentrations in agricultural soils and green compost: Methylocaldum sp., Methylosinus sporium, Methylocystis sp./Methylosinus trichosporium, and USCα. These findings enhance our understanding of methanotroph ecology and can be used to craft more effective strategies of creating "climate-smart" soils.}, }
@article {pmid42102504, year = {2026}, author = {IJdema, F and Broeckx, L and Deruytter, D and Frooninckx, L and van Miert, S and De Smet, J}, title = {Short communication: The persistent influence of host lineage on the gut microbiomes of black soldier fly and yellow mealworm.}, journal = {Animal : an international journal of animal bioscience}, volume = {20}, number = {5}, pages = {101828}, doi = {10.1016/j.animal.2026.101828}, pmid = {42102504}, issn = {1751-732X}, abstract = {Production insects such as the black soldier fly (BSF) and yellow mealworm (YM) are increasingly recognised as sustainable protein sources, and selective breeding of genetically distinct lines offers opportunities to improve production efficiency. However, insect performance is also influenced by the gut microbiome, which provides essential metabolic and protective functions. Despite this, current breeding programmes typically focus on host genetics and phenotypes, assuming that microbiome composition remains stable under consistent rearing conditions. However, this hypothesis remains largely untested. We examined gut bacterial communities in ten distinct BSF and YM populations reared for multiple generations under identical conditions. Each species shared a distinct set of ten zero-radius operational taxonomic units (zOTUs) across all populations, but their relative abundances varied, indicating host-specific effects on microbiome composition. Strain-specific zOTUs also persisted despite uniform environments. These findings suggest that host genetic background exerts a more persistent influence on gut microbiome composition than previously assumed.}, }
@article {pmid42104021, year = {2026}, author = {De Lara-Del Rey, IA and Pérez-Fernández, M and Magadlela, A}, title = {The Interplay of Light and Microbial Symbiosis in Shaping Plant Economic Spectrum Strategies.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02777-4}, pmid = {42104021}, issn = {1432-184X}, abstract = {Legume-rhizobia symbiosis are fundamental drivers of nitrogen cycling and plant performance, yet their role in facilitating species strategies along the Plant Economic Spectrum (PES) remains insufficiently understood. We conducted a field experiment with four legume species subjected to light and shade treatments, with and without rhizobial inoculation, to assess plant survival, biomass accumulation, nodulation, nitrogen acquisition, and isotopic signatures, alongside microbial community diversity and shifts in vegetation composition. Results demonstrate that inoculation significantly enhanced survival, growth rates, nitrogen accumulation, and nodulation across species, particularly under light conditions, indicating that microbial symbiosis promotes acquisitive strategies within the PES framework. Contrary, shaded environments consistently favoured higher survival and root allocation but reduced growth, nodulation, and nitrogen fixation, reflecting more conservative resource-use strategies. Species-specific responses revealed differential PES positioning: Trifolium repens L. exhibited high acquisitive capacity under light, while Coronilla juncea L. showed poor survival and growth under both conditions, highlighting the interaction between phylogenetic identity and resource availability. Additionally, δ[15]N and %Ndfa values confirmed that inoculation increased nitrogen fixation efficiency, whereas microbial diversity analyses indicated strong shifts in soil bacterial communities associated with inoculated plants, suggesting feedback between symbiosis and soil microbiota. These findings support two main hypotheses: (i) rhizobial inoculation acts as a biotic driver promoting acquisitive strategies by enhancing resource acquisition and growth efficiency, and (ii) light availability serves as an abiotic axis that modulates species positions along the PES continuum. Together, our study provides novel evidence that both microbial interactions and resource availability jointly determine legume strategies within the PES.}, }
@article {pmid42104085, year = {2026}, author = {Tan, S and Wang, J and Luciano, A and Li, J and Huo, Y and Ma, Y and Yang, J and Guo, J and Zhang, B and He, X and Zhao, M and Meng, F}, title = {Medium- and Large-sized Mammals on the Plateau: An Evolutionary Crucible for Zoonotic Pathogens - Ecological Drivers, Adaptive Evolution, and One Health Control.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02772-9}, pmid = {42104085}, issn = {1432-184X}, support = {32370554 and 32460248//the National Natural Science Foundation of China/ ; }, abstract = {Plateau regions have emerged as pivotal epicenters of diverse zoonoses because of their distinctive ecological conditions and rich biodiversity. Against the backdrop of intensifying climate change, escalating interactions between wildlife, livestock, and humans, and expanding human activities, these regions now face formidable challenges. To assess public health threats within plateau ecosystems and establish targeted prevention frameworks, this review systematically synthesizes the prevalence and potential cross-species transmission risks of zoonotic pathogens-spanning parasites, viruses, and bacteria-carried by large- and medium-sized wild mammals across China's four major plateaus (Tibetan Plateau, Yunnan-Guizhou Plateau, Loess Plateau, and Inner Mongolia Plateau). Critical issues, including ecological fragility, complexity of pathogen transmission networks, and delayed responsiveness of control measures, are comprehensively analyzed. Future strategies must embrace the One Health concept to construct a multidimensional, coordinated prevention system. By integrating pathogen surveillance, ecological regulation, and technological innovation, a refined zoonosis control framework anchored in safeguarding plateau biosafety and public health can be systematically advanced.}, }
@article {pmid42104451, year = {2026}, author = {Zhao, R and Huang, P and Pu, C and Zhu, F and Wang, C and Cai, C and Xiang, N and Ren, M and Ma, Q and Li, J}, title = {Azolla reshapes rhizosphere microbiomes and nutrient cycling in paddy fields.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00903-w}, pmid = {42104451}, issn = {2524-6372}, support = {1+9KJGG008//Sichuan Academy of Agricultural Sciences/ ; NKYRCZX2024024//Sichuan Academy of Agricultural Sciences/ ; 5+1QYGG006//Science and Technology Program of Sichuan Academy of Agricultural Sciences/ ; 2024NSFSC1229//National Natural Science Foundation of Sichuan Province of China/ ; }, abstract = {BACKGROUND: Soil quality is a critical determinant of agricultural productivity and sustainability. The symbiotic nitrogen fixation by Azolla plays a key role in enhancing soil quality. However, despite its potential as a green manure for enhancing soil quality, the role of Azolla in paddy systems remains inadequately characterized. This study aims to elucidate the effects of Azolla on soil quality by examining nutrient cycling dynamics and microbial community composition, along with their interactions.<br><br>RESULTS: We integrated soil physicochemical analyses, enzyme activity assays, bacterial community profiling, co-occurrence network analysis, and correlation assessments to evaluate the effects of Azolla on soil microbial ecology. Rice monoculture (R) and rice-Azolla co-cultivation (RA) systems were established. RA significantly increased activities of carbon- and nitrogen-cycle-related enzymes by 3-44% (P&#x2009;<&#x2009;0.05), while phosphorus-cycle-related enzyme activities decreased by 12-42%. Under high nitrogen fertilization, Azolla altered bacterial community structure and reduced alpha diversity. Notably, Azolla recruited specific functional taxa-including Haliangium, SC-I-84, Candidatus_Solibacter, Anaerolinea, and Sphingomonas-whose relative abundances were 1.03-1.33 times higher in RA than in R.<br><br>CONCLUSIONS: This study elucidates the interactions between soil properties and microbial communities under Azolla application and uncovers the mechanisms by which Azolla enhances soil quality through nutrient cycling. Our findings demonstrate that Azolla, as a green manure, not only elevates soil nutrient content but also improves soil quality by driving microbe-mediated nutrient recycling. These results underscore the potential of Azolla as a sustainable alternative to conventional fertilization practices, offering novel insights into biofertilizer strategies for agricultural soil enhancement.}, }
@article {pmid42105173, year = {2026}, author = {Prasad, H and Song, S and Jang, MJ and Kim, H and Razzak, MA and Haque, MA and Ahn, J and Ku, S}, title = {A Multidisciplinary Review of the Microbial, Functional, and Consumer Advancement of Indian Lassi.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {42105173}, issn = {1867-1314}, support = {8000-0//Hatch program of USDA/ ; }, abstract = {Indian Lassi, a traditional yogurt-based fermented beverage, holds cultural, nutritional, and technological relevance, yet remains comparatively underrepresented in indexed scientific literature. This review synthesizes current evidence on Lassi's composition and fermentation characteristics, emphasizing its probiotic potential and nutrient profile while clearly distinguishing findings derived from Lassi-specific studies from those extrapolated from related matrices such as yogurt and buttermilk. Potential health-related effects, including support for gut and immune function and contributions to cardiometabolic risk modulation, are discussed as hypothesized benefits inferred largely from broader fermented dairy research rather than confirmed Lassi clinical trials. The diverse variations of Lassi, from sweet and salty formulations to spiced desi buttermilk style beverages, are examined alongside regional and global adaptations and their implications for microbial ecology, sensory properties, and consumer acceptance. A bibliometric and text-mining analysis of indexed Lassi-related publications maps prevailing research themes, highlighting a concentration on product formulation, quality, and safety, with comparatively sparse human and mechanistic health studies. Emerging technological developments, including precision fermentation, starter culture optimization, and innovative preservation and packaging strategies, are evaluated in relation to microbial stability, regulatory expectations, and cultural authenticity. Collectively, the review identifies critical gaps, particularly the limited experimental validation of Lassi-specific functional and health outcomes, and outlines priorities for future work.}, }
@article {pmid42105759, year = {2026}, author = {Chen, H and Almeida-Silva, F and Logghe, G and Maere, S and Bonte, D and Van de Peer, Y}, title = {The rise of polyploids during environmental upheaval.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2026.04.008}, pmid = {42105759}, issn = {1097-4172}, abstract = {Polyploidy, or whole-genome duplication (WGD), serves as both a significant evolutionary force and a potential evolutionary dead end, particularly among angiosperms. Despite the prevalence of polyploid organisms, instances of ancient polyploidy are surprisingly rare, presenting a paradox that remains poorly understood. In this study, we constructed a comprehensive genomic dataset of 470 angiosperm species and dated 132 ancient WGD events that are non-randomly distributed, revealing a clustering around pivotal periods of environmental upheaval and extinction. Notably, our findings highlight a strong correlation between waves of paleopolyploidization and significant events such as the Middle Miocene Disruption, the Eocene-Oligocene Transition (EOT), the Paleocene-Eocene Thermal Maximum (PETM), the Cretaceous-Paleogene (K-Pg) extinction, and different oceanic anoxic events (OAEs). We propose that polyploid organisms have an increased chance of survival during times of great environmental turmoil, a conclusion with important implications in the context of contemporary climate change and rapid global warming.}, }
@article {pmid42092154, year = {2026}, author = {Yu, XA and Strachan, CR and Herbold, CW and Lang, M and Gasche, C and Makristathis, A and Segata, N and Pollak, S and Tett, A and Polz, MF}, title = {Genome-wide sweeps create ecological units in the human gut microbiome.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {42092154}, issn = {1476-4687}, abstract = {The human gut microbiome is shaped by diverse selective forces that originate from host and environmental factors and it substantially influences health and disease. Whereas the association of microbial lineages with various health conditions has been shown at different taxonomic levels[1-5], the extent to which unifying adaptive mechanisms sort microbial lineages into ecologically differentiated populations remains poorly understood. Here we show that genome-wide selective sweeps are a pervasive mechanism that differentiates bacteria in the microbiome. This mechanism leads to population structures akin to global epidemics across geographically and ethnically diverse human populations. Such sweeps arise when an adaptation allows a clone to outcompete others in its niche followed by rediversification, and they manifest as clusters of closely related genomes on long branches in phylogenetic trees. This structure is revealed by excluding recombination events that mask the clonal descent of the genomes. Indeed, we show that genome-wide sweeps originate under a wide range of recombination rates in at least 66 taxa from 25 bacterial families. Estimated ages of divergence suggest that sweep clusters can spread globally within decades and that this process has occurred throughout human history. Sweep clusters are associated with different host conditions-such as age, colorectal cancer, inflammatory bowel diseases and type 2 diabetes-as an indication of their ecological differentiation. Our results reveal an evolutionary mechanism for the observation of stably inherited strains with differential associations and provide a theoretical foundation for analysing adaptation among microbial populations.}, }
@article {pmid42092264, year = {2026}, author = {Vargas-Robles, D and Santos Agrait, JL and Suárez-Pérez, J and Vázquez, F and Dominicci-Maura, A and Sariol, CA and Zorrilla, C and Romaguera, J and Godoy-Vitorino, F}, title = {Oral Microbiome Resilience During SARS-CoV-2 Infection and Diversity Shifts After COVID-19 Vaccination in a Hispanic Population.}, journal = {MicrobiologyOpen}, volume = {15}, number = {3}, pages = {e70310}, pmid = {42092264}, issn = {2045-8827}, support = {U54 MD007600/MD/NIMHD NIH HHS/United States ; U54GM133807/GM/NIGMS NIH HHS/United States ; 1P20GM156713-01/GM/NIGMS NIH HHS/United States ; 2U54MD007600/MD/NIMHD NIH HHS/United States ; U54 GM133807/GM/NIGMS NIH HHS/United States ; U01CA260541/CA/NCI NIH HHS/United States ; COVID-19 RAPID GRANT #2020-00269//Puerto Rico Science, Technology and Research Trust/ ; P20 GM103475/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *COVID-19/prevention &amp; control/microbiology/immunology/virology ; *Microbiota ; Hispanic or Latino ; Female ; Male ; SARS-CoV-2 ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Adult ; *Mouth/microbiology ; *COVID-19 Vaccines/administration &amp; dosage/immunology ; Longitudinal Studies ; Vaccination ; Bacteria/classification/genetics/isolation &amp; purification ; Aged ; White ; }, abstract = {The relationship between SARS-CoV-2 infection and the oral microbiome remains poorly understood, particularly in the Hispanic population. Oral samples from 62 individuals (38 SARS-CoV-2 positive, 24 negative) were analyzed using 16S rRNA sequencing, comparing diversity and taxa by infection and symptoms. Longitudinal data from 11 participants assessed microbiome changes as the infection resolved over time. To assess the impact of vaccination, we further examined 68 consistently SARS-CoV-2-negative individuals with paired samples collected before and after vaccination. SARS-CoV-2 infection was not significantly associated with alpha diversity, while beta diversity showed a non-significant but marginal trend (p = 0.051). Prevotella nanceiensis was consistently depleted in infected individuals, even after excluding recent antibiotic users, suggesting a reproducible association with infection status rather than a diagnostic marker. Among infected participants, mucosa-related symptoms were associated with lower Veillonella parvula abundance. Longitudinal data revealed stable microbiome profiles with slightly reduced variance in alpha diversity following viral clearance. In contrast, COVID-19 vaccination in consistently negative individuals was associated with significant increases in Shannon (p = 0.050) and Simpson diversity (p = 0.017), indicating greater evenness without expansion of richness. Beta diversity analyses showed vaccination-related shifts in community composition (PERMANOVA p = 0.026), with increases in Treponema, Campylobacter, Oribacterium, and Selenomonas, and a decrease in Haemophilus. The oral microbiome of Hispanics with mild SARS-CoV-2 infection appeared resilient, with only subtle taxonomic alterations. In contrast, COVID-19 vaccination was associated with short-term increases in diversity and compositional shifts, highlighting its influence on oral microbial ecology.}, }
@article {pmid42095322, year = {2026}, author = {Liu, Q and Xu, P and Zhang, C}, title = {LL-37: Biological Mechanisms and Emerging Therapeutic Applications in Intestinal Disease.}, journal = {Immunity, inflammation and disease}, volume = {14}, number = {5}, pages = {e70451}, pmid = {42095322}, issn = {2050-4527}, support = {2024JH2/102600293//Liaoning Provincial Joint Program of Science and Technology/ ; }, mesh = {Humans ; *Cathelicidins ; *Antimicrobial Cationic Peptides/therapeutic use/metabolism ; Animals ; Gastrointestinal Microbiome/immunology ; *Inflammatory Bowel Diseases/immunology/drug therapy ; Immunity, Innate ; *Colorectal Neoplasms/immunology/drug therapy ; *Intestinal Diseases/immunology/drug therapy ; Immunity, Mucosal ; }, abstract = {Human cathelicidin peptide LL-37 is encoded by the CAMP gene and plays a key role in innate immunity. It maintains intestinal homeostasis through antibacterial, immunomodulation, and tissue repair functions. This paper reviews the multiple functions of LL-37 in the intestinal-immune axis and its contribution to intestinal immune homeostasis. A large amount of evidence shows that the biological effect of LL-37 is highly dependent on the environmental background, and its effects vary with peptide concentration, receptor binding status, disease stage, and local microenvironment. This article reviews the latest findings of the dual role of LL-37 in inflammatory bowel disease (IBD) and colorectal cancer (CRC), and focuses on the conditional mechanism of the transformation of its activity from protective to pathogenic. We also discuss the interaction between LL-37 and intestinal microbiota, focusing on how microbial signals and host peptides can coordinate to regulate mucosal immunity. At the same time, this article examines the key obstacles to the therapeutic application of LL-37 and its clinical promotion: cytotoxicity, rapid degradation by proteases, and drug resistance. We have further explored new strategies to overcome these challenges in the near future, including peptide engineering, nanocarrier delivery systems, and combined therapy. These findings together position LL-37 at the intersection of intestinal immunity and microbial ecology, providing a theoretical basis for its therapeutic application in IBD, CRC and infectious colitis.}, }
@article {pmid42095931, year = {2026}, author = {da Cruz, MO and Montoya, QV and de Sousa, RL and Pennachioni, GGP and Rodrigues, A}, title = {Unraveling Culturable Microfungal Communities Associated with Colonies of the Fungus-Farming Ant Mycetomoellerius urichii (Forel, 1893).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02776-5}, pmid = {42095931}, issn = {1432-184X}, support = {2022/16087-7//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2021/04706-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2019/03746-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 126804/2024-9//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, abstract = {Microfungal communities inhabit the fungus gardens of fungus-growing ants (Formicidae: Myrmicinae: Attini: Attina, the "attines") and may play cryptic yet important ecological roles within this symbiosis. While the diversity and composition of these microorganisms are relatively well characterized in leaf-cutting ant colonies, they remain poorly understood in non-leaf-cutting attine species, including Mycetomoellerius urichii. To address this gap, we investigated the microfungal communities in colonies of M. urichii using culture-dependent methods. Based on analyses of four independent molecular loci, we identified 94 microfungal species, with Trichoderma spirale, Syncephalastrum sp., and Cladosporium sp. as the most abundant taxa. Several of the microfungi found in this study have also been reported from leaf-cutting ant colonies. The microfungal communities were dominated by fungi exhibiting a multitrophic lifestyle (pathotroph-saprotroph-symbiotroph). Community composition showed considerable variation among colonies, with no consistent species co-occurrence patterns detected. Together, these findings provide the first community-level characterization of culturable microfungi inhabiting the fungus gardens of M. urichii and offer new insights into the microbial communities associated with the fungus-farming ant symbiosis.}, }
@article {pmid42096486, year = {2026}, author = {Colorado Gómez, MA and Melo-Bolívar, JF and Ruíz Pardo, RY and Junca, H and Alzate, JF and Villamil Díaz, LM}, title = {Anaerobic bacteria Cetobacterium sp. nov C33 plays a crucial role in the intestinal microbial balance and regulation of gene expression to immune and metabolic responses in Nile tilapia.}, journal = {PloS one}, volume = {21}, number = {5}, pages = {e0344851}, pmid = {42096486}, issn = {1932-6203}, mesh = {Animals ; *Cichlids/microbiology/immunology/metabolism/genetics ; *Gastrointestinal Microbiome ; Probiotics ; RNA, Ribosomal, 16S/genetics ; *Bacteria, Anaerobic/physiology/genetics ; Aquaculture ; Gene Expression Regulation ; }, abstract = {Aquaculture ranks among the largest global food production industries, with Nile tilapia (Oreochromis niloticus) being one of the most widely farmed species. However, increasing consumer demand and higher stocking densities place considerable stress on aquaculture systems, often leading to a rise in fish diseases. Probiotics have emerged as valuable tools in this sector, promoting fish health by modulating physiological functions such as metabolism, digestion, immune responses, stress tolerance, and disease resistance. Here, the probiotic potential of Cetobacterium sp. nov C33, an anaerobic bacterium isolated from the intestine of Nile tilapia, was evaluated on short-term dietary supplementation in fingerlings in laboratory conditions. Using 16S rRNA amplicon sequencing, we assessed the impact of Cetobacterium sp. nov C33 on gut microbiota, while transcriptomic analysis of the head kidney provided insights into immune system modulation. Results indicate that dietary inclusion of this anaerobic bacterium significantly alters the gut microbiota structure in tilapia fingerlings and regulates genes associated with key metabolic pathways, including the immune system, underscoring its potential as a probiotic for enhancing tilapia health. Our results offer promising evidence of its potential as a probiotic to improve tilapia health.}, }
@article {pmid42100688, year = {2026}, author = {Yadav, J and Gehlot, P and Soni, P and Jain, T}, title = {Plant microbiome engineering: from inoculation to genome editing.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1781381}, pmid = {42100688}, issn = {1664-302X}, abstract = {Plant-associated microbiomes are central to crop productivity, nutrient efficiency, and stress resilience, yet conventional microbiome manipulation strategies, largely based on microbial inoculation and agronomic management, often suffer from inconsistent field performance and limited persistence. Although several recent reviews have discussed CRISPR-mediated plant-microbe engineering and synthetic microbial community (SynCom) design separately, few reviews integrate genome editing, ecological stability of microbiomes, and climate-resilient agricultural applications within a unified conceptual framework. Recent advances in molecular biotechnology are transforming this landscape by enabling precision engineering of plant-microbe interactions at genetic, metabolic, and community levels. In particular, synthetic biology tools including CRISPR/Cas genome editing, RNA interference, and synthetic microbial communities (SynComs), now allow targeted modification of plant traits governing microbial recruitment, microbial pathways underpinning nutrient cycling and stress tolerance, and community-level functional complementarity. This review integrates molecular genetics, microbial ecology, and systems-level microbiome design to frame the plant and its microbiome as an engineerable holobiont. We integrate insights from genome editing in plants and microbes, omics-guided SynCom design, climate-resilience mechanisms, and emerging AI-assisted decision frameworks, including machine learning and ecological modeling approaches used to analyze multi-omics datasets, and predict plant-microbiome interactions across experimental and field-based studies. Importantly, we critically assess limitations related to ecological stability, trait trade-offs, biosafety, and regulatory challenges that constrain large-scale deployment. By bridging genome-enabled microbiome manipulation with ecological design principles, this review proposes an integrative framework for climate-smart microbiome engineering and identifies key research priorities required to transition from empirical inoculation toward predictive, sustainable, and socially responsible agricultural biotechnology.}, }
@article {pmid42101618, year = {2026}, author = {Nguyen, PN and Rehan, SM}, title = {Microbial Communities Across Social Roles in Small Carpenter Bee Nests.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02787-2}, pmid = {42101618}, issn = {1432-184X}, abstract = {Bee microbiota form important symbiotic relationships with their hosts, but microbial communities vary across bee species, sociality, and environment. Comparing the microbiome of bees with different social roles and foraging behaviours may uncover the ways in which microbiota are environmentally acquired and subsequently introduced and spread into the nest environment. Here, we performed metabarcoding of the 16S rRNA, ITS, and ribulose biphosphate carboxylase large (rbcL) regions on mothers, dwarf eldest daughters, and regular daughters in nests of the facultatively social, small carpenter bee, Ceratina calcarata, contrasting bacteria, fungi, and plant associates. We also performed two different sampling types by characterizing the microbiome using whole-guts and whole-bodies. Social role in nest impacted the microbial community composition and mothers were found to demonstrate increased plant diversity compared to their daughters, more specifically in whole-bodies, highlighting the ability to determine plants that bees are visiting during foraging through DNA metabarcoding. We also found that metabarcoding of the whole-body recovered increased fungal and plant diversity compared to whole-guts, suggesting that including microbiota from beyond the gut offers an opportunity to characterize uncommon associates that bees encounter, particularly through plant-pollinator relationships. As the transmission of beneficial symbionts and pathogens between individuals are studied for its impact on bee health, microbial analyses of bees across different environments and levels of sociality provides unique biomonitoring that can indicate the health of the larger bee community.}, }
@article {pmid42089016, year = {2026}, author = {Chen, X and Wang, M and Luo, L and An, L and Liu, X and Nie, Y and Wu, XL}, title = {Substrate toxicity drives successive range expansions opposing spatial intermixing in cross-feeding consortia.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag085}, pmid = {42089016}, issn = {2730-6151}, abstract = {Spatial organization plays a critical role in shaping microbial community structure and function, influencing ecological stability, resource utilization, and evolutionary dynamics. Microbial interactions such as competition and cooperation are key drivers of spatial patterning, yet the environmental factors modulating these interactions remain incompletely understood. Here, we investigated how toxic substrates influence the spatial organization of synthetic microbial communities engaged in metabolic cross-feeding. Using a synthetic Pseudomonas stutzeri consortium consisting of the detoxifier and consumer that cooperatively degrade the toxic compound salicylate, we found that increasing the substrate concentration leads to a distinct shift in spatial organization: the detoxifier increasingly dominates the outer periphery of the expanding colony, forming a "detoxifier-first" succession pattern. Mathematical modeling further revealed that this spatial arrangement emerges from substrate toxicity, which selectively favors the detoxifier. Substrate toxicity inhibits consumer proliferation. However, the detoxifier, capable of degrading the substrate, locally reduces toxicity and creates a protective microenvironment that enables nearby consumer cells to survive and grow. In return, the consumer provides essential final products that support the growth and expansion of the detoxifier. This reciprocal interaction establishes a directional dynamic in which the detoxifier, favored by its detoxification capability, colonizes first, paving the way for subsequent consumer proliferation. Our findings demonstrate that substrate toxicity is a crucial environmental factor shaping spatial organization and diversity in microbial communities. This study highlights the importance of considering both metabolic interactions and substrate properties in understanding microbial ecology.}, }
@article {pmid42089638, year = {2026}, author = {Nagakubo, T and Nishiyama, T and Asamizu, S and Onaka, H and Nomura, N and Toyofuku, M}, title = {A phage-derived reconfigurable effector associated with an actinobacterial contractile nanomachine tailors bacterial responses to competition.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {e0053225}, doi = {10.1128/jb.00532-25}, pmid = {42089638}, issn = {1098-5530}, abstract = {Contractile injection systems (CISs) are derivatives of phage tails and are widely distributed in prokaryotes. CISs load cognate effectors and eject them through contractile actions resembling those of phage tails. Ejected effectors play central roles in CIS functionality by acting on target cells and mediating various biological processes. Here, we report a novel group of CIS effectors related to phage tape measure protein, the transmembrane component of the phage infection machinery. This group is broadly distributed within the class Actinobacteria, one of the bacterial classes in which CIS gene clusters are highly conserved, and is represented by Sle1, a cognate effector of the intracellularly localized Streptomyces lividans phage tail-like nanoparticle (SLP). This effector is associated with Sle2, which contains a CIS effector core domain and interacts with the SLP core component. Sle1 is packaged inside SLP and is translocated to lipid membranes along with SLPs. The functional domain of Sle1 enriches the membrane-associated subproteome in S. lividans and E. coli. This effect modifies the physiological properties of S. lividans, ultimately enhancing its adaptation to microbial competition. In addition, we revealed that Sle1-type effectors conserved among actinobacterial species are structurally and functionally diverse in their functional domains. One of them from Micromonospora eburnea constitutes a novel toxin-antitoxin system, and introducing its functional domain into Sle1 reprograms the phenotypic responsiveness of S. lividans to neighboring bacteria. Our findings illustrate that phage elements can be incorporated into CISs as reconfigurable platforms for bacterial adaptation to various environmental conditions.IMPORTANCEBacterial CISs have attracted interest for their importance in microbial ecology and potential in biotechnological applications. However, understanding of their functional diversity is currently limited because many CIS effectors remain unannotated due to a lack of inferable structural and genetic signatures. Our findings on Sle1 and its relatives illuminate a previously unidentified class of CIS effectors with phage tape measure protein-related modular architecture, association with the CIS effector core domain, and wide distribution within the major class of Actinobacteria, substantially expanding the known repertoire of effector classes. The impact of Sle1 on S. lividans suggests a link between CIS effectors and bacterial adaptation to environmental conditions, highlighting unexplored functional diversity of CIS effectors as tuners of bacterial phenotypes in communities.}, }
@article {pmid42090000, year = {2026}, author = {Šnábl, J and Kaňa, A and Pelešková, G and Steinbauerová, J and Rudolf, P and Borovička, J and Leonhardt, T and Sácký, J}, title = {Arsenic Speciation and Distribution in Three Hebeloma Species: Insights into Arsenic Handling and Transformation in Mycorrhizal Fungi.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02780-9}, pmid = {42090000}, issn = {1432-184X}, abstract = {Arsenic accumulation and biotransformation in fungi remain poorly understood, particularly in mushrooms. This study investigated arsenic distribution, speciation, and detoxification mechanisms in three mushroom species of the genus Hebeloma: H. bulbiferum, H. sinapizans, and H. mesophaeum. Wild collected fruit bodies and laboratory mycelial cultures were analysed using size-exclusion chromatography (SEC) and ion-pair reversed-phase ICP-MS to determine total arsenic concentrations and speciation patterns. H. bulbiferum exhibited the highest arsenic accumulation in fruit bodies (up to 563 mg kg[-1] dry mass), predominantly as dimethylarsenate, whereas H. sinapizans accumulated less total As (up to 41.2 mg kg[-1] dry mass), comprising mainly arsenobetaine and dimethylarsenate, and H. mesophaeum (up to 4.2 mg kg[-1] dry mass) was dominated by inorganic arsenic and arsenocholine. SEC revealed that arsenic was present as low-molecular-weight fractions, although a minor protein-associated peak was observed in H. sinapizans, suggesting a possible presence of an arsenic-binding protein. Mycelial cultures demonstrated species-specific tolerance to arsenate and the ability to transform inorganic arsenic into organic arsenicals, with varying degrees of arsenate reduction, arsenite efflux, and methylation. In particular, H. sinapizans and H. mesophaeum exhibited a higher degree of As(III) efflux than H. bulbiferum, indicating a more efficient As reduction and export. Notably, some organoarsenicals, dimethylarsenate and trimethylarsine oxide, were actively excreted into the growth medium, indicating a role for mushroom mycelia in environmental arsenic cycling. These findings highlight distinct arsenic detoxification strategies in Hebeloma species, reveal fungal de novo arsenobetaine synthesis, and provide insights into arsenic transformation and sequestration in ectomycorrhizal mushrooms.}, }
@article {pmid42079559, year = {2026}, author = {Müller, O and Gardner, J and Olsen, LM and Salganik, E and Assmy, P and Gradinger, R and Bratbak, G and Hoppe, CJM and Lange, BA and Muilwijk, M and Divine, DV and Aberle, N and Krause, JW and Reigstad, M and Leu, E and Tsagaraki, TM and Larsen, A and Høyland, KV and Balmonte, JP and Boulton, W and Dahle, H and Eggers, L and Fong, AA and Guillou, G and Lebreton, B and Metfies, K and Mock, T and Petelenz, E and Tatarek, A and Torres-Valdés, S and Torstensson, A and Wiktor, J and Granskog, MA}, title = {Arctic sea-ice ridges are biomass hotspots harboring diverse microbial communities.}, journal = {Communications earth &amp; environment}, volume = {7}, number = {1}, pages = {385}, pmid = {42079559}, issn = {2662-4435}, abstract = {Although sea-ice ridges are prominent features of the Arctic Ocean, very little is known about their role as habitats and in biogeochemical cycles. Here, we show that ridges provide complex sea-ice habitats which host unique and diverse biological communities. Seasonally, ridges appear to transition from a biological repository in winter to biological hotspots in summer, surpassing algal biomass in level ice and surface waters by up to eight-fold. In summer, ridges can contain up to 80% of the total area integrated sea-ice algal biomass, emphasizing their importance in the Arctic sea-ice ecosystem. However, environmental shifts, such as meltwater infiltration and freezing inside the ridge in late summer, alter microbial communities from being predominantly autotrophic to heterotrophic. Our work provides evidence of contrasting roles of sea-ice ridges for Arctic carbon cycling in summer and shows that the habitats in the ridge interior harbor unique microbial communities, adding complexity to Arctic biodiversity.}, }
@article {pmid42083308, year = {2026}, author = {Thakur, BK and Choudhury, SR and Turpin, W and Martin, A}, title = {Gut microbiota and diet in colorectal cancer: Converging determinants of carcinogenesis.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2664684}, doi = {10.1080/19490976.2026.2664684}, pmid = {42083308}, issn = {1949-0984}, mesh = {Humans ; *Colorectal Neoplasms/microbiology/etiology/pathology/prevention &amp; control ; *Diet/adverse effects ; *Carcinogenesis ; *Gastrointestinal Microbiome ; Animals ; *Gastrointestinal Tract/microbiology ; *Bacteria/metabolism/genetics/classification ; }, abstract = {Diet and the gut microbiome are major, interdependent determinants of colorectal cancer (CRC) risk. This review discusses current evidence on how dietary patterns reshape microbial ecology, modulate microbial virulence, and alter host metabolic, inflammatory, and oncogenic pathways to influence colorectal carcinogenesis. We highlight key CRC-associated microbes, including pks[+] Escherichia coli, Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis, and Streptococcus gallolyticus, and discuss how diet governs their abundance, toxin production, and oncogenic potential. Mechanistic investigations into diet-microbe interactions reveal how pro-inflammatory, low-fiber Western-style diets foster mucosal inflammation, generation of reactive oxygen and nitrogen species, and genotoxic microbial niches, whereas fiber- and polyphenol-rich diets support protective commensals and production of anti-inflammatory metabolites. We also outline major challenges, including interindividual microbiome variability and limited translational models, and propose future directions for integrating dietary, microbial, and host-targeted strategies for CRC prevention and therapy.}, }
@article {pmid42085791, year = {2026}, author = {Besharati Fard, M and Ahmadi, N and Chen, Y and How, SW and De Vrieze, J and Wu, D}, title = {Tetracycline and ciprofloxacin reduce nitrification and denitrification activity and alter microbial community composition and activity in microalgal-bacterial aerobic granular sludge.}, journal = {Journal of hazardous materials}, volume = {511}, number = {}, pages = {142255}, doi = {10.1016/j.jhazmat.2026.142255}, pmid = {42085791}, issn = {1873-3336}, abstract = {Microalgal-bacterial aerobic granular sludge (MB-AGS) systems offer promising potential for wastewater treatment under chemical stress. However, their performance in the presence of antibiotics remains poorly understood. This study evaluated the response of MB-AGS to 1000 µg/L of tetracycline and ciprofloxacin in two separate bioreactors operated under alternating dark (60 min) and light (170 min) cycles at 20 °C. Chemical oxygen demand (COD) removal remained stable at 90 ± 4% (tetracycline) and 91 ± 6% (ciprofloxacin) over 80 days, suggesting that COD conversion was not impacted by antibiotic exposure. However, phosphate removal declined from ∼63% (antibiotic-free bioreactors) to 45 ± 6% (under tetracycline exposure) and 38 ± 8% (under ciprofloxacin exposure) after addition of antibiotics. Ciprofloxacin inhibited nitrification (declined to ∼50% NH4[+] removal), associated with reduced abundance of Nitrosomonas, while tetracycline impacted denitrification, evidenced by a lower Thauera abundance. Despite these impacts, the system removed 88.3 ± 5.6% of tetracycline and 69.5 ± 12.4% of ciprofloxacin, primarily through biosorption (for both antibiotics were more than 80%). Extracellular polymeric substances content increased by ∼19% under antibiotics exposure. Metagenomic analysis indicated changes in microbial community composition and function, while the overall antibiotic resistance gene profile remained relatively stable despite dynamic changes in individual resistance genes under antibiotic exposure. These findings demonstrate the strong potential of MB-AGS systems for effective organic carbon removal, while also highlighting opportunities to further enhance nutrient removal and mitigate antibiotic resistance genes under antibiotic stress.}, }
@article {pmid42086586, year = {2026}, author = {Mikryukov, V and Dulya, O and Abarenkov, K and Anslan, S and Hagh-Doust, N and Prins, V and Panksep, K and Põlme, S and Ibrahim, KS and Bahram, M and Adamson, K and Agan, A and Ahmed, T and Alatalo, JM and Albornoz, FE and Al-Hatmi, AM and Alkahtani, S and Alvarez-Manjarrez, J and Ankuda, J and Antonelli, A and Ariyan, M and Armolaitis, K and Aslani, F and Barrio, IC and Bauters, M and Biersma, EM and Bitenieks, K and Bonito, G and Brearley, FQ and Bråthen, KA and Buegger, F and Butterbach-Bahl, K and Bálint, M and Cameron, EK and Canini, F and Casique-Valdés, R and Corrales, A and Davydov, EA and De Crop, E and De Kesel, A and Djeugap, JF and Drenkhan, R and Duarte Ritter, C and Dudov, SV and Espenberg, M and Fanuel, O and Fedosov, VE and Florence, L and Furneaux, BR and Furtado, ANM and Färkkilä, S and Gamova, NS and Garibay-Orijel, R and Geml, J and Ghosh, S and Godoy, R and Gohar, D and Gryzenhout, M and Hasan, AH and Hashem, AH and Heilmann-Clausen, J and Henkel, TW and Hiiesalu, I and Hiiesalu, I and Hosseyni Moghaddam, MS and Hyde, KD and Inostroza, K and Kariman, K and Karimullina, E and Kepfer-Rojas, S and Khalid, AN and Klavina, D and Kohout, P and Korotkov, YN and Kupagme, JY and Kurina, O and Lamit, LJ and Lateef, AA and Ledoux, NA and Lim, YW and Maciá-Vicente, JG and Makovskis, K and Martínez, S and Marín, C and Meidl, P and Mortimer, PE and Mundra, S and Naluyange, V and Netherway, T and Newsham, KK and Nouhra, E and Nyamukondiwa, C and Nteziryayo, V and Ochieno, DMW and Oja, J and Onipchenko, VG and Otsing, E and Owaid, MN and Piepenbring, M and Pochekutova, P and Pombo, MM and Pritsch, K and Puusepp, R and Pärn, J and Põldmaa, K and Rahimlou, S and Rinaldi, AC and Rojas, O and Roslin, T and Runnel, K and Rähn, E and Saba, M and Saitta, A and Salih, TS and Sarapuu, J and Serrano, E and Serrano, O and Sharmah, D and Sharp, C and Skalska-Tuomi, MW and Tchan, KI and Truong, C and van der Merwe, H and Vanié-Léabo, LLP and Vasco-Palacios, AM and Verbeken, A and Vlk, L and Wijayawardene, NN and Wood, JL and Yasanthika, WAE and Yorou, NS and Zahn, G and Zettur, I and Zucconi, L and Kõljalg, U and Tedersoo, L}, title = {Global dataset of soil eukaryotic communities created with a uniform protocol and long read sequencing.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07315-y}, pmid = {42086586}, issn = {2052-4463}, support = {2024-04303//The Swedish Research Council/ ; BioPath//The Swedish Foundation for Strategic Environmental Research MISTRA/ ; PRG1789//The Estonian Research Council/ ; PRG632//The Estonian Research Council/ ; Center of Excellence AgroCropFuture "Agroecology and new crops in future climates", TK200//The Estonian Ministry of Education and Research/ ; 101200758 (PhylFun ERC-2024-ADG)//The European Research Council (ERC)/ ; }, abstract = {Soil eukaryotes, including fungi, protists, plants, and animals, are central to biosphere functioning and resilience. The Global Standardised Soil Eukaryome Dataset (GloSED) is the first dataset encompassing the entire spectrum of soil eukaryotes, covering 4,063 sampling sites in 121 countries on all continents, revealing nearly one million operational taxonomic units. All samples were collected and analysed using a standardised protocol minimizing technical biases. Long-read sequencing of full-length ITS and 18S-V9 regions provide broad taxonomic coverage and high-resolution identification supported by specialist curation of "dark taxa". A rigorous bioinformatic processing ensures against homopolymer errors, PCR-mediated chimeras, and index switching providing high data quality. The dataset is supported by raw sequences and an open-source containerised workflow for reproducible analyses. The samples are accompanied by land-cover description and directly measured soil pH, δ[13]C, δ[15]N, as well as P, K, Ca, Mg, and total C and N contents. GloSED is the first database that enables ecological and biogeographic studies of entire soil eukaryotic communities from local to global scales.}, }
@article {pmid42086631, year = {2026}, author = {Moon, K and Kang, I and Cho, JC}, title = {Virome datasets and viral metagenome-assembled genomes from aquaculture-impacted freshwater environments.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07383-0}, pmid = {42086631}, issn = {2052-4463}, support = {NRF-2022R1A2C3008502//National Research Foundation of Korea (NRF)/ ; NA//Hankuk University of Foreign Studies (HUFS)/ ; }, abstract = {Bacteriophages in natural environments play a critical role in microbial ecology by regulating bacterial populations, mediating nutrient cycling, and facilitating horizontal gene transfer. Aquaculture operations, particularly inland fish farms, are major sources of anthropogenic influence on freshwater ecosystems. Here, we present three viral metagenomic datasets derived from freshwater samples collected at an inland aquaculture effluent site and adjacent upstream and downstream locations along the Sung-am River in Jincheon County, South Korea. The datasets were generated using the Illumina HiSeq X sequencing platform, yielding approximately 10.0-11.2 Gbp per sample. Quality assessments confirmed minimal bacterial contamination, with negligible proportions of rRNA and bacterial marker genes. Assembly using metaSPAdes and MEGAHIT, application of Phables to resolve high-quality phage genomes (viral metagenome-assembled genomes; vMAGs), viral identification with VirSorter2, and clustering using Vclust, resulted in 2,837-3,156 virus operational taxonomic units (vOTUs; ≥10 kb) per sample. Each vOTU sequence is analyzed for taxonomic assignment and putative host prediction. These datasets provide a valuable resource for further studies on viral diversity and microbial ecology in freshwater ecosystems affected by aquaculture.}, }
@article {pmid42087678, year = {2026}, author = {Shen, Y and Wang, H and Gao, W and Luo, W and Fan, T and Shi, Y and Xie, X and Li, L and Xiang, S and Chai, A and Li, B}, title = {On-site, highly-sensitive and multi-signal detection of cucumber bacteria via CRISPR/Cas12a coupled with duplex RPA.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-11-25-2416-RE}, pmid = {42087678}, issn = {0191-2917}, abstract = {Pseudomonas amygdali pv. lachrymans (Pal) and Pectobacterium brasiliense (Pb) are highly destructive bacterial pathogens that cause severe oozy diseases in cucumber crops, often resulting in significant yield losses. Rapid and accurate detection is essential for effective disease management, yet current molecular detection methods are limited by their reliance on sophisticated instrumentation, time-consuming procedures, and laboratory-dependent operations, significantly limiting their practicality in field settings. To address these limitations, we developed a portable detection platform that integrates dual recombinase polymerase amplification with CRISPR/Cas12a technology. This system demonstrated exceptional sensitivity with a detection limit of 10[-5] ng/μL for both Pal and Pb, while exhibiting high specificity and enabling multi-signal output capabilities. For rapid on-site detection, we further developed a portable device integrating a heating unit and a blue-light-excited fluorescence detection system, coupled with a smartphone-based readout for high-throughput field testing. The entire process was completed within one hour. This platform not only provides a powerful tool for rapid field detection of plant pathogens, but also pioneers a novel universal nucleic acid detection strategy with broad application prospects in point-of-care molecular diagnostics across healthcare, agriculture and other fields. By bridging the gap between laboratory precision and field practicality, this technology opens new avenues for decentralized diagnostics in crop protection, microbial ecology, and public health.}, }
@article {pmid42075295, year = {2026}, author = {Liu, Y and Sun, X and Lai, J and Wei, S and Sheng, Y and Zhang, Y and Zhang, Q and Ye, P and Huang, L and Zeng, H}, title = {Research Progress on Rhizosphere Microbiota for Controlling Soil-Borne Diseases: Mechanisms, Applications, and Challenges.}, journal = {Microorganisms}, volume = {14}, number = {4}, pages = {}, doi = {10.3390/microorganisms14040900}, pmid = {42075295}, issn = {2076-2607}, support = {2025ZNSFSC0203//Natural Science Foundation of Sichuan Province of China/ ; SCCXTD-2024-19//Sichuan Innovation Team of the Chinese National Modern Agriculture Industry Technology System/ ; }, abstract = {Soil-borne diseases pose a severe threat to global agricultural production and food security. Traditional chemical control methods face significant challenges, including environmental pressure, pathogen resistance, and food safety concerns. The rhizosphere microbial community, often termed the plant's 'second genome', plays a pivotal role in maintaining plant health and defending against pathogen invasion. Recent advances in multi-omics technologies, synthetic microbial communities (SynComs) construction, and rhizosphere metabolomics have significantly advanced our understanding of the mechanisms by which rhizosphere microbiomes suppress soil-borne diseases. This review systematically summarizes the following: 1. key drivers of rhizosphere microbial community assembly, particularly plant "cry for help" signaling; 2. core beneficial microbial taxa and their disease-suppressive mechanisms; 3. the critical role of microbial interaction networks; 4. microbiome-based management strategies and their application progress; and 5. current challenges and future research directions. Compared with previous reviews that separately discussed rhizosphere microbiota, disease-suppressive soils, synthetic microbial communities (SynComs), or prebiotics, this review uniquely integrates multiple levels of regulation, from plant genetic determinants ('M genes') and root exudate-mediated 'crying for help' to microbiome engineering (SynComs and prebiotics) and cross-kingdom interactions (bacteria-fungi-protists-phages). A central conceptual axis of 'M genes → microbiome engineering → breeding' is proposed, bridging plant genetics, microbial ecology, and crop improvement for durable disease suppression. Ultimately, this work aims to provide a theoretical foundation for developing efficient and sustainable green control technologies against soil-borne diseases.}, }
@article {pmid42076832, year = {2026}, author = {Carracedo Lorenzo, Z and Rizaludin, MS and Wang, J and Berdaguer, R and Brito-López, C and Sánchez-Arcos, C and Garbeva, P and Pieterse, CMJ and Dicke, M and Testerink, C and Kloth, KJ and Karlova, R}, title = {Pseudomonas volatiles shape the root transcriptome and microbiome to promote plant growth under drought.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.71203}, pmid = {42076832}, issn = {1469-8137}, support = {024.004.014//NWO Dutch Research Council (NWO/OCW)/ ; }, abstract = {Volatile organic compounds (VOCs) emitted by soil bacteria influence interactions with other soil microbes and plants. While their potential as plant growth promoters is well recognized, their role in promoting plant resilience to abiotic stress and the underlying molecular mechanisms remain poorly understood. Here, we investigate the role of Pseudomonas VOCs in enhancing plant resilience to drought stress Arabidopsis seedlings were exposed to VOCs emitted by Pseudomonas strains under control and osmotic stress conditions. Plant biomass and root architecture were evaluated. Root transcriptomics analysis was performed and validated using Arabidopsis mutants and metabolomics. Volatile organic compounds effects were also tested on soil-grown Brassica oleracea and on its rhizosphere microbiome. Pseudomonas VOCs promoted plant growth under both axenic and soil conditions in A. thaliana and in B. oleracea, and under control and drought conditions. Transcriptomics, metabolomics, and functional analysis revealed interactions between Pseudomonas VOCs, glucosinolates, and ABA signalling, as well as a positive association between VOC exposure and coumarin biosynthesis. VOC treatment also reshaped the rhizosphere microbiome under drought, leading to a community composition more similar to that of well-watered plants. Overall, Pseudomonas VOCs promote plant growth under drought conditions, linked to root transcriptional reprogramming and direct or indirect microbiome modulation.}, }
@article {pmid42078518, year = {2026}, author = {Batistel, F}, title = {Using gnotobiotic ruminants to dissect host-microbe interactions for sustainable agriculture.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1771182}, pmid = {42078518}, issn = {1664-302X}, abstract = {Ruminant animals host one of the most complex gut microbial ecosystems, enabling the conversion of fibrous plant biomass into nutrient-dense foods such as meat and milk, which are essential for global food security. Over time, successive waves of research-from the initial recognition of microbes in the rumen, through anaerobic cultivation, to more recent multi-omics approaches-have progressively expanded our understanding of rumen microbial composition and its links to animal production and greenhouse gas emissions. Despite these advances, most insights into rumen microbial composition and traits of interest are based on associative or correlative evidence, and the host-derived mechanisms that actively shape rumen microbial composition and function remain poorly defined. Early gnotobiotic studies in ruminants demonstrated the value of maintaining animals under defined microbial conditions to dissect host-microbe interactions; however, this experimental capability has largely been lost from contemporary rumen research. This Perspective argues that revisiting gnotobiotic ruminant models is both timely and necessary for establishing causal mechanisms that govern host-microbe interactions in the rumen. Integrating gnotobiotic ruminant models is essential for establishing causal relationships between host biology and rumen microbial composition, thereby providing a foundation for biologically informed strategies that can enhance the sustainability of ruminant production systems.}, }
@article {pmid42078675, year = {2026}, author = {Yang, X and Dong, LL and Jin, XX and Liu, XJ and Gao, M and Fang, J}, title = {Composition and Diversity Characteristics of Gut Microbiota during the Development of Telchinia issoria (Lepidoptera: Nymphalidae).}, journal = {Ecology and evolution}, volume = {16}, number = {}, pages = {e73596}, pmid = {42078675}, issn = {2045-7758}, abstract = {Ramie (Boehmeria nivea) was a traditional economic crop of high commercial value, whose cultivation was threatened by the leaf-feeding pest Telchinia issoria. This study investigated how the gut microbiota of T. issoria shifted across its larval, pupal, and adult stages using 16S rRNA amplicon sequencing. We found that Pseudomonadota and Bacillota dominated across all stages, with stage-specific enrichments of key genera: Burkholderia-Caballeronia-Paraburkholderia in early larvae, Acinetobacter and Culicoidibacter in mid-instars, Serratia in late larvae, Enterococcus in pupae, and Pseudomonas in adults. Alpha diversity exhibited a U-shaped pattern during larval development, decreasing initially before rising again, with the lowest overall diversity observed in the pupal stage. Beta diversity confirmed distinct community structures in pupae and adults. Functionally, as predicted by PICRUSt2 based on 16S rRNA gene sequencing data, carbohydrate metabolism was enriched in pupae, whereas pathways associated with amino acid, cofactor, and vitamin metabolism were significantly decreased relative to other developmental stages. Correlation analysis suggested that elevated temperature may contribute to the decreased diversity observed in this study, which warranted further verification under controlled temperature gradients. This work establishes a foundational understanding of stage-specific microbial symbiosis in T. issoria and offers insights for future research into lepidopteran gut microbial ecology and potential biocontrol applications.}, }
@article {pmid42066856, year = {2026}, author = {Zhang, F and Wang, C and Zuo, Y and Xu, H and Che, Y and Cui, Y and Yao, Q and Sun, Y and Che, K and Chen, H}, title = {Astragalin alleviates ulcerative colitis via FPR1 inhibition and restores Microbiota-Metabolite Homeostasis: A mechanism revealed by deep learning.}, journal = {Biochemical pharmacology}, volume = {}, number = {}, pages = {118022}, doi = {10.1016/j.bcp.2026.118022}, pmid = {42066856}, issn = {1873-2968}, abstract = {The pursuit of multi-targeted therapies that simultaneously address mucosal immune dysregulation, barrier dysfunction and gut microbiota imbalance in ulcerative colitis (UC) remains a major challenge. Astragalin, a natural flavonoid, represents a promising therapeutic candidate, yet its mechanisms of action have remained poorly defined. Here, we used an integrated deep-learning platform that combines multiple neural architectures to predict a high-confidence target of Astragalin, and then validated these predictions in a DSS-induced murine colitis model using pharmacological assays, 16S rRNA sequencing, untargeted metabolomics and complementary cellular studies. Our framework identified formyl peptide receptor 1 (FPR1) as a high-confidence target, and we show that Astragalin directly binds to FPR1, promotes its degradation through a proteasome-dependent pathway and consequently inhibits NF-κB activation. Consistent with this mechanism, Astragalin ameliorated colitis symptoms, suppressed pro-inflammatory cytokines and enhanced intestinal barrier integrity. Beyond host signalling, Astragalin restored gut microbial ecology, notably enriching Akkermansia muciniphila, and reversed colitis-associated metabolic disturbances, with prominent effects on glutathione and L-ascorbate metabolism. Correlation analyses further revealed a strong positive association between A. muciniphila abundance and key protective metabolites. Together, these findings uncover Astragalin as a natural FPR1 inhibitor that alleviates colitis through a self-reinforcing circuit involving targeted protein degradation, suppression of inflammation, restoration of a beneficial microbiota and reinforcement of the mucosal barrier, positioning Astragalin as a multi-faceted therapeutic strategy for UC..}, }
@article {pmid42068599, year = {2026}, author = {He, J and Hu, H and Huang, Y and Xu, B and Yang, J and Lv, W and Wang, M and Ren, Q and Li, X and Zhu, Y and Wang, K and Wang, Q}, title = {Bacterial extracellular vesicles in the oral-gut axis: Roles in periodontitis and inflammatory bowel disease.}, journal = {Microbiological research}, volume = {309}, number = {}, pages = {128534}, doi = {10.1016/j.micres.2026.128534}, pmid = {42068599}, issn = {1618-0623}, abstract = {The oral-gut axis links the oral and gut microbiomes, both anatomically and functionally, and its dysregulation is implicated in periodontitis and inflammatory bowel disease (IBD). Bacterial extracellular vesicles (BEVs), nano-sized particles (20-250 nm) released by diverse microbes, serve as key mediators of inter-organismal communication along this axis. Carrying virulence factors, nucleic acids, and immunomodulators, BEVs influence microbial ecology and host immunity. In the oral cavity, pathogen-derived BEVs (e.g., from Porphyromonas gingivalis) promote biofilm formation, immune evasion, and tissue destruction. In the gut, BEVs from commensals (e.g., Akkermansia muciniphila) reinforce barrier function and suppress inflammation, whereas those from pathogens exacerbate dysbiosis. Critically, BEVs mediate bidirectional crosstalk: oral pathogen BEVs can translocate to the gut and worsen IBD, while beneficial gut-derived BEVs may attenuate periodontal inflammation. This review summarizes the roles of BEVs in oral-gut communication, their involvement in inflammatory disease pathogenesis, and their potential as biomarkers and therapeutics.}, }
@article {pmid42068885, year = {2026}, author = {Ke, H and Zhang, X and Xamxidin, M and Zhang, C and Fei, M and Li, J and Zhan, L and Lan, J and Chen, Y}, title = {Microbial community divergence and environmental responses across multi-phase landfill environments.}, journal = {Waste management (New York, N.Y.)}, volume = {219}, number = {}, pages = {115578}, doi = {10.1016/j.wasman.2026.115578}, pmid = {42068885}, issn = {1879-2456}, abstract = {Municipal solid waste landfills are highly heterogeneous ecosystems comprising solid waste, leachate, and subsoils wherein complex microbial consortia regulate organic matter degradation and contaminant transformation. However, comprehensive insights into their microbiome structure across multi-phase and depth profiles and responses to environmental gradients remain scarce. This study presents a rare, multidimensional characterization of landfill microbiomes that integrates deep drilling (to 50 m), 16S rRNA gene sequencing, and biogeochemical pathway analysis. To quantify the extent of waste stabilization, a solid-phase stabilization index (β) is proposed to link degradation stages with microbial succession. This index indicates a clear transition from a Firmicutes-dominated rapid degradation phase (β < 0.58) to a Proteobacteria-dominated stabilization phase (β > 0.83). Spatially, the microbiomes exhibit distinct solid-liquid niche partitioning, as evidenced by the prevalence of biofilm formers (Advenella and Brevundimonas) on solid waste surfaces and specific enrichment of the thermophilic planktonic Defluviitoga in the surrounding leachate. At the critical waste-soil interface, leachate infiltration exerts strong environmental filtering that drives a pronounced enrichment of the dual-tolerant Ralstonia, which constitutes up to 46.49% of the community. Cu, Be, and Cd emerge as the key heavy metals driving the evolution of subsoil microorganisms. These findings collectively provide an integrated framework that advances the mechanistic understanding of waste stabilization and leachate-soil interactions, offering new insights for assessing landfill maturity and understanding pollution fronts.}, }
@article {pmid42069693, year = {2026}, author = {Sha, H and Chen, J and He, J and He, B and Huang, J and Zhou, J and Dong, X and Xiong, J}, title = {Precisely designed keystone metabolites boost shrimp disease resistance by recruiting symbionts via the lipoxin A4-AP-1 pathway.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02418-5}, pmid = {42069693}, issn = {2049-2618}, abstract = {BACKGROUND: Gut metabolites and symbionts are indispensable for host health, yet the precise identification of keystone metabolites and construction of synthetic microbial communities (SynComs) to enhance disease resistance remains limited.<br><br>RESULTS: Using Litopenaeus vannamei as a model, we identified pyruvic acid and DL-glutamine (1:2) as keystone metabolites by borrowing the microbial ecology principles of bio-indicators and driver taxa. Dietary supplementation with these metabolites sufficiently protected shrimp from white feces syndrome (WFS). Multi-omics analyses demonstrated that keystone metabolites exerted positive effects by enriching beneficial Ruegeria lacuscaerulensis, Bacillus subtilis and Nioella nitratireducens, strengthening the gut network stability, and&#xa0;enhancing shrimp immunity, which collectively potentiated WFS resistance. The recruited three strains were consumers and producers of the two keystone metabolites, and discriminative strains between healthy and diseased shrimp across global datasets. A SynCom constructed from the three strains (4:3:2) replicated the efficacy of keystone metabolites. Both keystone metabolites and SynCom elevated shrimp gut and hepatopancreas lipoxin A4 (LXA4) levels, which suppressed the pro-inflammatory transcription factor AP-1, as validated by in vivo inhibition assay.<br><br>CONCLUSIONS: Our findings demonstrate that precisely designed keystone metabolites enhance shrimp disease resistance through the recruitment of key symbionts-LXA4-AP-1 axis. The rationally designed keystone metabolites and SynCom are compelling biocontrol solutions in improving host disease resistance. Video Abstract.}, }
@article {pmid42070584, year = {2026}, author = {Nasseh, N and Tahergorabi, M}, title = {Pesticides and the microbial world: a review of disturbance, resilience, and the road to recovery.}, journal = {Journal of environmental science and health. Part. B, Pesticides, food contaminants, and agricultural wastes}, volume = {}, number = {}, pages = {1-18}, doi = {10.1080/03601234.2026.2648405}, pmid = {42070584}, issn = {1532-4109}, abstract = {Pesticides are widely used tools in modern crop production, yet their impacts on soil ecosystems are often context-dependent and not fully quantified. Over several decades, research has shown that pesticides and their metabolites can alter the diversity, structure, and functional capacity of soil microbial communities, with effects that may be either inhibitory or stimulatory depending on the context. However, their long-term influence on microbial resilience and recovery remains insufficiently understood. This review synthesizes current knowledge by integrating microbial ecology, soil chemistry, and environmental toxicology, with a focus on how pesticides alter microbial community composition and enzyme-mediated nutrient cycling. Particular attention is given to key soil enzymes, such as dehydrogenases, ureases, and phosphatases, which serve as sensitive, though sometimes limited, indicators of soil disturbance, and recovery. Furthermore, the review emphasizes how soil physicochemical properties, contamination history, and management practices collectively modulate microbial responses to pesticide exposure. By bringing these perspectives together, this synthesis offers a conceptual framework for interpreting pesticide-microbe interactions and provides a foundation for monitoring soil health and guiding sustainable pest management strategies that maintain agricultural productivity while preserving soil vitality.}, }
@article {pmid42071994, year = {2026}, author = {Han, B and Shi, X and Zheng, C and Zeng, H and Wang, Y and Liu, T}, title = {Effects of Active Dry Yeast on Production Performance, Meat Quality, and Rumen Microecology in Lambs.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {8}, pages = {}, doi = {10.3390/ani16081228}, pmid = {42071994}, issn = {2076-2615}, abstract = {In this study, we examined whether dietary ADY improves growth, digestibility of feed nutrients, meat quality, and rumen microbial ecology in lambs. This experiment enrolled 90 healthy, similarly weighted (29.0 ± 0.5 kg) four-month-old Duhan lambs, which were randomly and evenly distributed into two treatment groups: a control group fed the basal diet and an ADY group fed the basal diet supplemented with 0.3 g/d per lamb of active dry yeast. The supplementation amount was adjusted weekly according to feed intake to maintain a constant daily dose. The results showed that, compared with the control group, ADY significantly increased the lambs' average daily gain (ADG) and enhanced the apparent digestibility of neutral detergent fiber (NDF), crude protein (CP) (p < 0.05), and significantly reduced the feed conversion ratio (F/G) (p < 0.05). These improvements were accompanied by a shift in rumen fermentation toward propionate production, evidenced by higher NH3-N, Total volatile fatty acids (TVFAs) and propionate proportion and a lower acetate proportion and acetate-to-propionate ratio (p < 0.05). ADY also altered the rumen microbiota, increasing Proteobacteria and Succinivibrionaceae_UCG-001 while decreasing norank_o_Clostridia_UCG-014 (p < 0.05). In muscle, ADY significantly increased the proportions of C14:0 and C18:3n-3 (p < 0.05). In addition, the proportion of C13:0, C18:0 and C18:2n-6t were significantly reduced (p < 0.05). In conclusion, dietary supplementation with ADY enhanced rumen fermentation, improved rumen microbial composition, and promoted nutrient utilization in lambs, thereby improving growth performance and meat quality. In addition, certain rumen microbial taxa may be associated with the formation of specific muscle fatty acids.}, }
@article {pmid42072091, year = {2026}, author = {Tao, T and Ye, J and Li, R and Ke, Y and Zheng, X and Zhang, Q and Zheng, L and Wang, S and Zhang, Z and Wang, L and Li, C}, title = {Chiglitazar Activates PPAR-α/γ to Suppress Oxidative Stress and Angiogenesis in Corneal Neovascularization.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {15}, number = {4}, pages = {}, doi = {10.3390/antiox15040449}, pmid = {42072091}, issn = {2076-3921}, support = {82471048, 82271045//National Natural Science Foundation of China/ ; JCYJ20240813145510014//Shenzhen Science and Technology Program/ ; 3502Z20224ZD1018//Xiamen Municipal Health and Medical Guidance Projects/ ; 2022J05302//Fujian Provincial Natural Science Foundation Projects/ ; }, abstract = {PURPOSE: Chiglitazar (Chi) is a pan-peroxisome proliferator-activated receptor (PPAR) agonist with reported anti-oxidative effects in metabolic disorders. In this study, we investigate its therapeutic effects and potential mechanisms in corneal neovascularization (CNV).<br><br>METHODS: Scratch-wound and tube formation assays in human umbilical vein endothelial cells (HUVECs) were performed to evaluate the effects of Chi under recombinant human vascular endothelial growth factor (VEGF) stimulation. An oxidative stress model was established in human corneal epithelial cells (HCEs), and intracellular reactive oxygen species (ROS) levels were quantified by flow cytometry. A corneal alkali burn mouse model of CNV was established. Chi was then administered and compared with vehicle, pioglitazone, or fenofibrate. Corneal epithelial healing and neovascularization were assessed. Public drug-disease-target resources were integrated with RNA-seq data and single-cell transcriptomes to prioritize Chi-associated targets and pathways, which were examined by immunofluorescence, RT-PCR, and Western blotting. Ocular safety was evaluated by comprehensive ophthalmic evaluation.<br><br>RESULTS: Chi significantly inhibited migration and tube formation in VEGF-induced HUVECs, and flow cytometry confirmed effective ROS reduction. In vivo, Chi markedly improved corneal conditions compared with the vehicle and showed efficacy comparable to or superior to selective PPAR-&#x3b1;/&#x3b3; agonists, depending on the outcome measures. Bioinformatic analyses predicted PPAR-&#x3b3; as the dominant isoform, with PPAR-&#x3b1; secondary and PPAR-&#x3b4; appearing less prominent, collectively implicating oxidative stress and VEGF pathways. Immunofluorescence verified PPAR-&#x3b3; activation, predominantly localized to the corneal epithelium. RT-PCR and Western blotting supported activation of antioxidant pathways and suppression of angiogenic signals, with Western blotting confirming PPAR-&#x3b3; and PPAR-&#x3b1; activation, whereas PPAR-&#x3b4; activation appeared less evident under the present conditions. Ocular examinations demonstrated a favorable safety profile.<br><br>CONCLUSIONS: Chi primarily activates PPAR-&#x3b3; and PPAR-&#x3b1;, producing antioxidant and anti-angiogenic benefits, supporting its potential as a multi-target PPAR therapy for CNV.}, }
@article {pmid42074155, year = {2026}, author = {Kurhaluk, N and Mazur, Z and Kołodziejska, R and Tkaczenko, H}, title = {Gut Microbiota, Diet and Lipid Metabolism in Adolescents with NAFLD and Their Role in Preventive Strategies.}, journal = {International journal of molecular sciences}, volume = {27}, number = {8}, pages = {}, doi = {10.3390/ijms27083511}, pmid = {42074155}, issn = {1422-0067}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Non-alcoholic Fatty Liver Disease/metabolism/prevention &amp; control/microbiology/etiology ; *Lipid Metabolism ; Adolescent ; Dysbiosis ; *Diet ; Animals ; Liver/metabolism ; }, abstract = {Adolescence is a metabolically vulnerable period, during which rapid physiological maturation coincides with the dynamic remodelling of the gut microbiome. This narrative review summarises evidence from 2015 to 2025 to clarify how disturbances to the gut-liver axis driven by dysbiosis contribute to the development and progression of non-alcoholic fatty liver disease (NAFLD) in young people. Based on a systematic search of the databases PubMed, Scopus and Web of Science, we outline the basis of bidirectional communication between the gut and liver and emphasise how microbial imbalance alters the handling of lipids in the liver by enhancing de novo lipogenesis, impairing fatty acid oxidation and disrupting AMPK signalling and mitochondrial function. Consistent findings from clinical and experimental studies show that adolescents with NAFLD exhibit reduced microbial diversity, the enrichment of ethanol- and LPS-producing taxa, and altered short-chain fatty acid profiles. Each of these is associated with hepatic inflammation and metabolic reprogramming. Microbial molecules, including LPS, secondary bile acids and branched-chain amino acid metabolites, activate TLR4-NF-κB pathways, promote Kupffer cell activation and intensify oxidative stress. These mechanisms intersect with factors specific to adolescence, such as increased adiposity, hormonal shifts and diet-induced metabolic strain. Dietary patterns emerge as key modulators of these processes. Westernised diets promote dysbiosis and endotoxemia, whereas Mediterranean, fibre-rich and plant-based diets enhance SCFA production, strengthen epithelial integrity and modulate adiponectin-dependent hepatic metabolism. Micronutrient-sensitive epigenetic regulation, particularly that involving folate, choline and polyphenols, also plays a role in shaping lipid homeostasis and inflammatory tone. We also highlight emerging evidence that the activation of cytoprotective pathways, especially Nrf2, is dependent on lifestyle factors and links antioxidant-rich functional foods and physical activity to improved mitochondrial resilience and microbiome stability. We evaluate therapies targeting the microbiome, including probiotics, prebiotics, synbiotics and postbiotics, which reduce endotoxemia, restore microbial balance and complement dietary strategies. Thus, these findings emphasise the importance of age-specific, mechanistically informed interventions that integrate diet quality, microbial ecology, and the molecular pathways that govern metabolic health in adolescents with NAFLD.}, }
@article {pmid42075160, year = {2026}, author = {Matera, M and Biagioli, V and Leo, S and Drago, L}, title = {Probiotics and Antibiotics: From Empirical Practice to a Biological Rationale for Targeted Choice During Antibiotic Therapy.}, journal = {Microorganisms}, volume = {14}, number = {4}, pages = {}, doi = {10.3390/microorganisms14040763}, pmid = {42075160}, issn = {2076-2607}, abstract = {Antibiotic therapy represents one of the strongest ecological perturbations of the human gut microbiota, inducing rapid and often prolonged alterations in community structure, metabolic activity, and functional resilience. While the use of probiotics to mitigate antibiotic-associated dysbiosis is widely adopted in clinical practice, probiotic selection is still largely empirical and insufficiently grounded in biological compatibility with specific antibiotic pressures. In this conceptual review, antibiotics are reframed not merely as antimicrobial agents, but as ecological forces that shape microbial survival, quiescence, and recolonization dynamics. We propose a biologically informed framework that distinguishes genetic antibiotic resistance from functional or ecological insensitivity, highlighting how microbial traits, such as the absence or inaccessibility of the antibiotic target, metabolic state, sporulation, and cellular architecture, influence the persistence of probiotics during antibiotic exposure. By integrating the mechanisms of action of antibiotics with key physiological and structural features of probiotic microorganisms, we develop a conceptual framework aimed at rationalizing the compatibility of probiotics and antibiotics. This framework does not imply clinical efficacy but provides an interpretative tool to guide hypothesis generation, experimental validation, and the design of future targeted probiotic strategies. A more ecologically grounded approach to probiotic selection may ultimately improve microbiota support during antibiotic therapy and advance personalized microbiome modulation.}, }
@article {pmid42063761, year = {2026}, author = {Chen, YJ and Yang, BW and Gu, ZC and Han, J}, title = {Interplay between circadian rhythms, gut microbiota, and MASLD: from mechanistic foundations to therapeutic opportunities.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1767462}, pmid = {42063761}, issn = {2296-858X}, abstract = {Metabolic dysfunction-associated fatty liver disease (MASLD), previously known as non-alcoholic fatty liver disease (NAFLD), has become the most common chronic liver disease worldwide. Although excessive lipid accumulation, insulin resistance, and chronic low-grade inflammation are recognized as the main pathophysiological drivers, an increasing body of research indicates that the relationship between circadian rhythms, gut microbiota, and liver metabolism is far more complex than previously imagined, forming a systemic regulatory network. Disruption of circadian rhythms can affect the temporal coordination of metabolic pathways in the liver and other surrounding tissues. At the same time, the gut microbiota itself also exhibits circadian rhythm variations. The dysregulation of these rhythms, leading to microbial imbalance, intestinal permeability defects, and imbalances in microbial metabolites, can exacerbate lipid deposition and inflammatory responses in the liver. Research shows that important microorganisms can produce short-chain fatty acids, regulate bile acid balance, and enhance intestinal barrier function, creating a synergistic effect with the host's circadian rhythms. Conversely, during circadian disruption, the proliferation of harmful symbionts can exacerbate the entry of lipopolysaccharides into the bloodstream, oxidative stress, and the development of steatohepatitis. This relationship among the three establishes the ' circadian rhythm-gut microbiota-liver axis' as a new model for understanding the mechanisms underlying MASLD and for developing temporal therapies and microbiome interventions. This review systematically explores how circadian rhythms regulate the relationship between the gut microbial ecology and liver metabolism, focusing on the microbial species closely related to the interaction between circadian rhythms and MASLD. It also introduces emerging therapeutic strategies, including time-restricted feeding, circadian probiotics, postbiotics supplementation, and circadian rhythm drugs. These findings collectively suggest that targeting the temporal dimension of the interactions between the host and microbiota holds clinical potential for the prevention and treatment of MASLD.}, }
@article {pmid42064799, year = {2026}, author = {Ali, S and Alioui, Y and Khan, I and Ullah, H and Rahman, MU and Atta, A and Abusidu, M and Ilyas, M and Noor, U and Ma, R and Ali, M and Farooqui, NA and Deng, T and Wang, G and Xin, Y and Sha, S and Ma, Y}, title = {Laetiporus sulphureus polysaccharides mitigate colitis by reshaping the gut microbiota and regulating immune responses.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1705032}, pmid = {42064799}, issn = {1663-9812}, abstract = {BACKGROUND: Inflammatory bowel disease (IBD) involves epithelial barrier disruption, immune dysregulation, and microbial imbalance. The present study investigated the protective mechanisms of Laetiporus sulphureus polysaccharides (LSP) in dextran sulfate sodium (DSS)-induced colitis, focusing on intestinal barrier restoration, immunomodulation, and gut microbiota remodeling.<br><br>METHODS: LSP was structurally characterized using HPLC, FTIR, and SEM analyses, revealing a heteropolysaccharide primarily composed of glucose (55.16%), galactose (16.55%), and mannose (13.52%). Experimental colitis was induced in BALB/c mice with 3% DSS, followed by oral LSP administration (200 or 400&#xa0;mg/kg). Disease severity, histopathology, barrier markers, cytokine profiles, macrophage polarization, and gut microbiota composition were evaluated using biochemical assays, immunofluorescence, IHC, and 16S rRNA sequencing.<br><br>RESULTS: LSP significantly mitigated DSS-induced colitis by reducing the disease activity index by approximately 60% (&#x223c;2.5-fold, p < 0.001) and restoring colon length (&#x223c;1.5-fold, p < 0.01). Barrier integrity improved via enhanced mucin-2 expression (&#x223c;3.5-fold) and tight junction proteins Occludin, Claudin-1, and ZO-1 (&#x223c;5-9-fold). LSP suppressed pro-inflammatory cytokines TNF-&#x3b1;, IL-6, and IL-1&#x3b2; (&#x223c;2-3-fold) while upregulating anti-inflammatory mediators IL-10 and TGF-&#x3b2; (&#x223c;2.5-3-fold), reflecting a rebalanced mucosal immune milieu. 16S rRNA sequencing demonstrated reversal of DSS-induced dysbiosis, characterized by a reduction in pathogenic Escherichia-Shigella (&#x223c;3.8-fold) and Enterobacteriaceae (&#x223c;3.5-fold), and enrichment of beneficial taxa including Lactobacillus, Bifidobacterium, and Ruminococcus (&#x223c;2-4-fold).<br><br>CONCLUSION: LSP exerts multi-targeted protection against colitis by reinforcing epithelial barrier function, attenuating inflammation, and reshaping gut microbial ecology. These findings highlight LSP as a promising natural therapeutic candidate for IBD. Further metabolomic and meta transcriptomic analyses are warranted to elucidate the microbial metabolites and molecular pathways mediating these protective effects.}, }
@article {pmid42065823, year = {2026}, author = {Esteban, DJ and Feeley, M and Goud, M and Abban-Demitrus, AM and Mishalani, L and Touchon, J and Czesak, ME}, title = {Alteration of the Microbiome is Associated with Changes in Mating and Locomotion in Callosobruchus Maculatus.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02783-6}, pmid = {42065823}, issn = {1432-184X}, abstract = {The seed beetle Callosobruchus maculatus is a model organism used to study environmental and genetic factors in the evolution of mating behaviors and life history traits. We sought to address the hypothesis that the microbiome of C. maculatus is associated with host life history traits and mating. To manipulate the microbiome, we developed a chemical treatment protocol to surface sterilize C. maculatus eggs and the food source on which they develop and examined the effect on microbial community structure, beetle life history traits, and mating behaviors including mate choice, and locomotion. Treatment eliminated culturable bacteria from the surface and altered the emerged adult beetle microbiome such that diversity was reduced and the community structure was altered. Treatment reduced survival of small male and female beetles; among the adults that did survive and emerge, females had higher fecundity compared to controls. We found that the treatment also affected mating behavior. Treated beetle pairs had a higher percentage of successful matings and a shorter mating latency period than control beetles. In mate choice tests in which a female was presented with either a treated or control male, females were more likely to mate with treated males. Finally, treated beetles exhibited increased locomotion. Treatment caused selective mortality of smaller individuals and reduced the diversity and altered the structure of the whole-body microbiome of the surviving adults. The treatment was also associated with enhanced mating behavior, increased fecundity and increased locomotion. These experiments revealed that treatment-induced perturbations in larvae result in altered adult behavior and life history traits that are associated with shifts in the beetle microbiome.}, }
@article {pmid42066640, year = {2026}, author = {Sim, M and Hwang, GS and Shin, DM and Jeong, Y}, title = {Associations of solute carrier family 23 member 1 (SLC23A1) rs6596473 genetic variant with serum vitamin C status and gut microbial profiles in healthy adults: A cross-sectional study.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {61}, number = {}, pages = {106669}, doi = {10.1016/j.clnu.2026.106669}, pmid = {42066640}, issn = {1532-1983}, abstract = {BACKGROUND &amp; AIMS: Solute carrier family 23 member 1 (SLC23A1) encodes sodium-dependent vitamin C transporter 1, which mediates intestinal vitamin C absorption. Although SLC23A1 variants are associated with vitamin C bioavailability, their relationship with gut microbiome remains unexplored. We aimed to investigate the associations of SLC23A1 polymorphism with serum vitamin C status and gut microbial profiles in healthy Korean adults.<br><br>METHODS: We genotyped the SLC23A1 rs6596473 polymorphism in 257 healthy individuals (20-39 years) and measured their serum vitamin C concentrations, which were categorized as optimal (&#x2265;50 &#x3bc;M) or suboptimal (<50 &#x3bc;M). Logistic regression analysis was used to evaluate the association between genotypes and suboptimal serum vitamin C status after adjusting for covariates. A subset of 43 participants with suboptimal serum vitamin C status underwent gut microbiota analysis and serum short-chain fatty acid (SCFA) measurements. Microbial profiles and SCFA concentrations were compared across the genotypes.<br><br>RESULTS: The genotype distributions were 92 CC, 131 CG, and 34 GG, with G as the minor allele. After covariate adjustment, GG carriers had higher odds of suboptimal serum vitamin C status than CC carriers (odds ratio = 2.65; p = 0.03). Among individuals with suboptimal serum vitamin C status, GG carriers (n = 7) exhibited distinct microbial community structures compared with CC (n = 13) and CG (n = 23) carriers, with elevated richness and evenness. GG carriers had higher abundances of Bifidobacterium (vs. CC, p < 0.01; vs. CG, p = 0.054) and Ruminococcaceae incertae sedis (all p < 0.05) compared with CC and CG carriers. In line with these microbial findings, GG carriers had higher propionate and butyrate concentrations than CC and CG carriers (all p < 0.05).<br><br>CONCLUSIONS: The SLC23A1 rs6596473 variant was associated with reduced vitamin C absorption into systemic circulation in the overall population; however, among individuals with suboptimal serum vitamin C status, it was associated with beneficial gut microbial profiles. Our findings suggest that this genetic variant in the vitamin C transporter has complex health effects that extend beyond circulating vitamin C levels to gut microbial ecology, supporting the use of genotype-informed nutritional approaches.<br><br>CLINICAL TRIAL REGISTRY: Clinical Research Information Services KCT0005074 (https://cris.nih.go.kr/cris/search/detailSearch.do?seq=16832&amp;status=5&amp;seq_group=16832&amp;search_page=M) and KCT0004276 (https://cris.nih.go.kr/cris/search/detailSearch.do?seq=14590&amp;status=5&amp;seq_group=14590&amp;search_page=M).}, }
@article {pmid42059394, year = {2026}, author = {Murphy, MM and Pinnell, LJ and Doster, E and Wolfe, CA and Baker, LA and Machado, VS and Morley, PS}, title = {Early-life development of the microbiome and resistome in antibiotic-naïve dairy calves.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0251025}, doi = {10.1128/spectrum.02510-25}, pmid = {42059394}, issn = {2165-0497}, abstract = {This study aimed to characterize early-life changes in the fecal microbiome and resistome of calves. Fecal samples were collected from 49 Holstein heifers born and raised at a large organic dairy in Texas without antimicrobial drug exposures. Samples were collected from five age groups: early pre-weaning at 2-3 days old (Pre 1), late pre-weaning at 5 weeks old (Pre 2), prior to weaning at 12-13 weeks old (Pre 3), post-weaning in group hutches at 12-13 weeks old (Post 1), and later post-weaning at 13-14 weeks old (Post 2). Fecal samples were analyzed using 16S rRNA gene sequencing to characterize microbial communities and target-enriched shotgun sequencing to characterize antimicrobial resistance genes in the resistome. Richness of microbial communities increased as calves aged through the Pre 1, 2, and 3 samplings, before plateauing in the Post 1 and 2 groups. Diversity also increased in the Pre 1 and 2 groups, remaining similar thereafter. In contrast, resistome richness and diversity decreased during early life and then stabilized at around 5 weeks of age (Pre 2). Changes in microbial community structures were dramatic during the first 12 weeks, largely due to a significant decrease in the relative abundance (RA) of Pseudomonadota (Proteobacteria) and an increase in the RA of Bacillota (Firmicutes) and Bacteroidota. The resistome changed with an increased RA of tetracycline resistance genes, while drug and biocide resistance genes decreased. The apparent stabilization of microbial community features after 12 weeks of age may reflect a period when gut microbiome structure begins to establish greater stability.IMPORTANCEEarly-life development of the gut microbiome can have lasting effects on animal health, immune maturation, and productivity. Using 16S rRNA gene sequencing together with target-enriched metagenomic sequencing, we provide an in-depth characterization of the fecal microbiome and resistome of antibiotic-naïve dairy calves during early life. We demonstrate that microbiome diversity increased with age while resistome diversity decreased, revealing distinct temporal trajectories and suggesting ecological succession as a potential driver of resistance gene dynamics independent of antimicrobial drug exposure. Major resistome features appeared to stabilize earlier than overall microbiome structure, highlighting critical windows in early development when resistance gene composition may be most dynamic. These findings establish an important baseline for interpreting microbiome-resistome interactions and for evaluating how management practices and antimicrobial exposures may influence calf health and antimicrobial resistance ecology in dairy production systems.}, }
@article {pmid42059556, year = {2026}, author = {Dunham, SJB and Willkeen, GA and Darby, B and Corley, JM and Hahn, A and Klapper, I and Bean, HD and Caverly, LJ and Thornton, CS and Martin, C and Quinn, RA and Widder, S and Bailey, BA and Wagner, BD and Garg, N and Planet, PJ and Hunter, RC and LiPuma, JJ and Rohwer, F and Whiteson, KL}, title = {The Guild Model of CF Airway Microbial Ecology.}, journal = {mBio}, volume = {}, number = {}, pages = {e0366825}, doi = {10.1128/mbio.03668-25}, pmid = {42059556}, issn = {2150-7511}, abstract = {Ecological guilds are groups of organisms that utilize the same class of resources and occupy similar niches, regardless of their taxonomic identities. Here we propose the Guild Model for Cystic Fibrosis Airway Microbial Ecology, which considers the ecological function and wider role of each microbe in the ecosystem. This model consists of four functional guilds: (i) "Brewers" metabolize host-derived substrates (e.g., mucins) and produce fermentation products; (ii) "Drunkards" exploit the metabolic niche built by Brewers, consuming fermentation products and secreting exopolysaccharides to build biofilms; (iii) "Putrifiers" produce toxic compounds causing inflammation and tissue necrosis; and (iv) "Nihilists" are specialist pathogens characterized by intracellular or lytic life cycles and cytotoxin production. By focusing on microbial function and the broader community context, this model offers a refined framework for interpreting cystic fibrosis airway ecology. Although developed for CF, the Guild Model is adaptable to other diseases influenced by microbial ecology.}, }
@article {pmid42059599, year = {2026}, author = {Cowan, DA}, title = {Surviving through a dry spell: microbial responses to drying and rewetting.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0017526}, doi = {10.1128/msystems.00175-26}, pmid = {42059599}, issn = {2379-5077}, abstract = {The issues of how microorganisms survive very long periods of desiccation and how they react during both drying and rehydration phases have long been topics of interest in a range of relevant fields, including desert ecosystem microbiomics, food storage, ancient microbe studies, and even astrobiology. The recently published study by Carini et al., who used a combination of transcriptomics and metabolomics to investigate steady-state gene expression and cellular metabolite profiles at different states of bacterial cellular desiccation, during both drying and rewetting phases, adds some valuable insights into how members of bacterial communities can survive in the driest habitats on earth (P. Carini, A. Gomez-Buckley, C. R. Guerrero, M. R. Kridler, et al., mSystems 11:e00493-25, 2026, https://doi.org/10.1128/msystems.00493-25).}, }
@article {pmid42059625, year = {2026}, author = {Giacomini, JJ and Torres-Morales, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL}, title = {Spatial ecology of the Capnocytophaga genus in the human oral cavity.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0362625}, doi = {10.1128/spectrum.03626-25}, pmid = {42059625}, issn = {2165-0497}, abstract = {UNLABELLED: The human oral microbiome, a complex ecosystem of niche-specific communities influenced by local ecological factors, plays a critical role in health and disease. Capnocytophaga species are prevalent in the human mouth, often abundant in dental plaque and linked to both commensalism and pathogenicity, motivating a detailed study of their ecological and functional diversity. This study employs metapangenomics to reveal Capnocytophaga strain-level distributions and functional adaptations across distinct sites in the human oral cavity. Pangenomic, phylogenetic, and average nucleotide identity analyses enabled classification of unnamed genomes and identified 13 groups, of which 8 include validly named species, and the remainder are named using Human Microbial Taxon (HMT) designations in the Human Oral Microbiome Database (HOMD; https://www.homd.org/). Mapping metagenomic reads to the pangenome revealed a strong preference of most Capnocytophaga genomes for dental plaque (both supra- and subgingival), yet identified strain-level variants of C. sputigena, C. gingivalis, C. granulosa, and C. leadbetteri detected more often on the tongue. Among dental plaque-abundant taxa, functional analyses uncovered two clades: one with cbb3-type cytochrome oxidase that is tied to enhanced denitrification and could help the organism adapt to hypoxic zones, and another with bd-type ubiquinol oxidase, more suited to aerobic metabolism. Carbohydrate and amino acid metabolism pathways also differed between these clades. These findings identify metabolic adaptations that may underlie sub-specialization within the plaque habitat and highlight the strain-level diversity of Capnocytophaga, including low-prevalence strains that are preferentially detected in sites outside the primary plaque habitat of this taxon.<br><br>IMPORTANCE: Understanding the ecological roles of Capnocytophaga in the oral microbiome is critical for deciphering its contributions to health and disease, including periodontal and systemic infections. This metapangenomics study reveals a pronounced specialization by Capnocytophaga to dental plaque (including supragingival, subgingival, and periodontal pockets) and identifies metabolic adaptations, such as distinct respiratory, carbohydrate, and amino acid pathways, that may drive niche-specific survival. These findings support the site-specialist hypothesis and enhance our understanding of oral microbial community structure, laying a foundation for future research into microbial interactions and targeted therapies for oral health.}, }
@article {pmid42061253, year = {2026}, author = {Peruzzo, A and Tiengo, A and Furlan, M and Salerno, B and Ortali, G and Barco, L and Losasso, C}, title = {Competitive exclusion modulates broiler microbiota structure and microbial interaction networks.}, journal = {Poultry science}, volume = {105}, number = {7}, pages = {106974}, doi = {10.1016/j.psj.2026.106974}, pmid = {42061253}, issn = {1525-3171}, abstract = {Competitive exclusion (CE) strategies represent a promising complementary approach to control foodborne pathogens in poultry production by modulating gut microbiota assembly. This field study evaluated the impact of a CE intervention applied at chick placement on cloacal microbiota temporal development, structure, and pathogen integration in commercial broiler chickens. Fifteen broiler farms with a history of Salmonella Infantis persistence were enrolled, including CE-treated farms and untreated controls. Cloacal samples were collected at 7, 18, 31, and 42 days of age and analyzed by 16S rRNA gene amplicon sequencing. Microbiota dynamics were evaluated through diversity metrics, differential abundance analysis, and microbial association network inference. CE treatment significantly altered microbiota composition and structure throughout the production cycle. Treated flocks showed a progressive increase in microbial richness and Shannon diversity from day 18 onward, while evenness remained largely unaffected. Beta-diversity analyses revealed persistent separation between treated and Un-Treated communities at all time points, indicating long-lasting treatment effects. Differential abundance analysis highlighted enrichment of beneficial genera, including Lactobacillus, Faecalicoccus, Roseburia, and Butyricimonas, in treated birds, whereas untreated flocks showed higher relative abundances of Campylobacter and other taxa associated with unstable community dynamics. Microbial network analysis revealed marked treatment-dependent differences in community organization. CE-treated networks exhibited higher modularity and edge density, suggesting increased structural complexity and potential resilience. Notably, Campylobacter showed strong early network integration and hub-like behaviour in untreated birds, while being completely disconnected in treated flocks at early life stages, indicating reduced ecological embedding. Overall, these findings demonstrate that competitive exclusion modulates broiler microbiota not only at the compositional level but also through restructuring microbial interaction networks. Early-life microbiota modulation appears to constrain pathogen ecological integration, providing a mechanistic framework for microbiota-driven control strategies under commercial poultry production conditions.}, }
@article {pmid42063506, year = {2026}, author = {ALSaleh, E}, title = {Comparative genomics links ecological dominance and genome plasticity in sediment-derived Vibrio diabolicus.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1813524}, pmid = {42063506}, issn = {1664-302X}, abstract = {Marine sediments harbor diverse Vibrio populations that play critical roles in benthic microbial ecology; however, the genomic determinants underlying the dominance of sediment-associated Vibrio taxa remain insufficiently characterized at the genome level. In this study, culture-based enumeration revealed Vibrio diabolicus as the dominant Vibrio species in marine sediment samples, providing ecological rationale for genome-resolved investigation. Because sediment-associated vibrio species, often responds rapidly to environmental fluctuations and organic enrichment in coastal ecosystems, their distribution and genomic characteristics may also reflect changes in sediment microbial community structure and local environmental conditions. Four sediment-derived V. diabolicus isolates (Vdiab_L2, Vdiab_L3, Vdiab_VA, and Vdiab_B48) were subjected to whole-genome sequencing and comparative genomic analysis alongside closely related reference genomes. Average nucleotide identity (ANI) analyses confirmed species-level assignment, with all isolates exhibiting ANI values exceeding 95% relative to V. diabolicus references, while remaining clearly distinct from V. alginolyticus and V. parahaemolyticus references. Core-genome phylogenetic reconstruction resolved the sediment isolates into a coherent V. diabolicus lineage, consistent with ANI-based relationships and demonstrating strong concordance between whole-genome similarity metrics and evolutionary history inferred from conserved genes. Pangenome analysis revealed a relatively small, conserved core genome accompanied by a dominant accessory gene pool composed primarily of shell and cloud genes, indicative of an open pangenome structure. Accessory gene clustering and presence-absence profiling further highlighted strain-specific genomic heterogeneity within the species. Importantly, this study focuses specifically on comparative genomic structure rather than comparative functional genomics, aiming to establish a genome-level evolutionary framework for sediment-associated V. diabolicus populations. Together, these findings demonstrate that V. diabolicus combines ecological dominance in marine sediments with extensive genomic plasticity, a combination likely facilitating persistence and adaptation within heterogeneous benthic environments. This study provides a comprehensive comparative genomic baseline for understanding sediment-associated V. diabolicus populations and establishes a framework for future ecological and functional genomic investigations.}, }
@article {pmid42063559, year = {2026}, author = {Hodžić, A and Kunert, M and Juračić, M and Veinović, G and Sukara, R and Tomanović, S and Seki, D and Berry, D}, title = {Immune-mediated microbial interference governs Borrelia colonization of the tick gut.}, journal = {iScience}, volume = {29}, number = {5}, pages = {115628}, pmid = {42063559}, issn = {2589-0042}, abstract = {The tick gut represents a dynamic environment where various ecological and molecular factors, including interactions between the tick innate immune system and its resident microbiota, govern the success of pathogen colonization. Yet, the mechanisms by which these microbial communities shape pathogen infection dynamics remain unclear. Here, we demonstrate that oral inoculation with the gut bacterium Pseudomonas putida modulates immune responses in Ixodes ricinus and restricts infection by Borrelia afzelii. Transcriptional profiling of immune-related genes revealed that Pseudomonas specifically induces the expression of the gene encoding the antimicrobial peptide defensin, reinforcing epithelial defenses without extensive activation of canonical signaling pathways. Functional assays demonstrated that Pseudomonas impedes Borrelia colonization through a host-mediated mechanism rather than direct microbial antagonism. These findings reveal a microbiota-driven immune pathway that constrains pathogen persistence in the tick gut and provide insights into the tripartite interplay between the tick host, its microbiota, and borrelial pathogens.}, }
@article {pmid42053608, year = {2026}, author = {Çağatay, NS and Dageri, A and Saruhan, I and Tuncer, C and Guz, N}, title = {Diversity and Composition of the Microbiome Associated with Adult of the Green Shield Bug Palomena prasina (Hemiptera: Pentatomidae).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02779-2}, pmid = {42053608}, issn = {1432-184X}, support = {Project number: 116O328//T&#xfc;rkiye Bilimsel ve Teknolojik Ara&#x15f;t&#x131;rma Kurumu/ ; }, }
@article {pmid42055170, year = {2026}, author = {Shehabeldine, AM and Basher, NS and Hashem, AH and Ibrahim, NA and Dora, MS and Abdelaziz, AM}, title = {Targeting Quorum Sensing to Combat Bacterial Biofilms: Natural Biomass as Emerging Anti-Virulence Strategies.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {108519}, doi = {10.1016/j.micpath.2026.108519}, pmid = {42055170}, issn = {1096-1208}, abstract = {Bacterial biofilms are no longer viewed as passive surface-associated aggregates but as highly coordinated, multicellular microbial systems governed by intricate regulatory and metabolic networks. Encased within a dynamically structured extracellular polymeric substance (EPS) matrix, these communities exhibit emergent properties-enhanced tolerance, phenotypic heterogeneity, and adaptive resilience-that challenge conventional antimicrobial paradigms. At the core of this collective behavior lies quorum sensing (QS), a sophisticated communication circuitry that synchronizes gene expression, virulence deployment, metabolic cooperation, and biofilm maturation. The accelerating crisis of antimicrobial resistance necessitates a decisive conceptual shift from bactericidal strategies toward precision interference with microbial social behavior. In this emerging framework, biomass-derived bioactives and nano-enabled natural compounds from plants, endophytes, algae, and their metabolomes are being repositioned as ecological modulators rather than traditional antibiotics. These agents function as quorum quenchers, signal disruptors, and matrix destabilizers, capable of rewiring QS regulatory networks, enzymatically degrading autoinducers, modulating EPS biosynthetic pathways, and attenuating adhesion and virulence expression. By targeting communication hierarchies and cooperative resilience mechanisms, biomass-based interventions dismantle biofilm integrity while minimizing selective evolutionary pressure. This review advances a systems-level perspective on biofilm control, framing natural biomass as a multifunctional, sustainable, and evolution-informed platform for anti-virulence therapy. By integrating insights from microbial ecology, nanobiotechnology, and chemical signaling interference, we highlight a transformative shift toward next-generation strategies that disrupt bacterial collective intelligence rather than merely suppress growth.}, }
@article {pmid42055940, year = {2026}, author = {Bailac, L and Arnaldi, L and Mallam, L and Leblanc, L}, title = {Evaluation of the Effect of Single-Temperature Incubation on the Recovery and Behavior of Microbiota in the Context of Environmental Monitoring.}, journal = {PDA journal of pharmaceutical science and technology}, volume = {}, number = {}, pages = {}, doi = {10.5731/pdajpst.2025-000051.1}, pmid = {42055940}, issn = {1948-2124}, abstract = {Environmental monitoring is essential for the prevention and control of microbial contamination. Accurate and reproducible monitoring is critical, and standardized precise conditions of incubation in regulatory documents for environmental sampling are still lacking. This study investigated microbial recovery and growth dynamics under a controlled single-temperature incubation setting (25°C, 27.5°C and 30°C) across 83 microbial agents (49 bacteria, 24 molds and 10 yeast strains). We showed that at the temperature of 25°C, all microbial strains investigated were recovered. Elevated incubation temperatures did not alter the recovery of bacteria and yeast strains but affected the recovery and recovery rate of specific mold strains. In addition, time-to-result (TTR), defined as the time necessary for 90% colony recovery, varied with incubation temperatures and microbiota. It decreased with increasing temperature for all bacterial strains tested, while showing more complex patterns for molds. Altogether, our results contribute valuable insights into microbial ecology and highlight the complex interaction between temperature and microbial behavior. This study emphasizes the necessity for precise temperature regulation in microbial culture methodologies for accurate and reproducible environmental monitoring.}, }
@article {pmid42056339, year = {2026}, author = {Thenappan, DP and Joshi, V}, title = {Host genotype Impacts the Assembly and Functional Potential of Bacterial Communities in the Spinach Phyllosphere Within Commercial Organic Farming Systems.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02762-x}, pmid = {42056339}, issn = {1432-184X}, support = {2022-51300-37886//USDA-NIFA-OREI/ ; 9647-1//USDA- NIFA- HATCH/ ; }, }
@article {pmid42056695, year = {2026}, author = {Kim, KM and Hwang, K}, title = {Phylogenomic Tree Reconstruction from Bacterial Genomes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2981}, number = {}, pages = {221-233}, pmid = {42056695}, issn = {1940-6029}, mesh = {*Phylogeny ; *Genome, Bacterial ; *Genomics/methods ; *Bacteria/genetics/classification ; *Computational Biology/methods ; Software ; Databases, Genetic ; Gene Transfer, Horizontal ; }, abstract = {The recent, rapid expansion of available prokaryotic genomes has fueled significant advancements in phylogenomics within microbial ecology and evolution. However, comprehensive protocols for reconstructing phylogenomic trees from bacterial genomes remain scarce. To address this gap, we present a series of essential bioinformatics steps. This protocol begins with setting up a Docker environment to ensure consistent implementation across different operating systems. We demonstrate phylogenomic tree reconstruction using the Genome Taxonomy Database and its toolkits with five test genomes, which were retrieved from the NCBI database, quality-checked with CheckM, aligned using GTDB-Tk, and analyzed for tree reconstruction with RAxML. Genome-level phylogenetic analyses are often complicated by gene duplication, horizontal gene transfer, and computational demands that increase with the number of taxa. We discuss practical strategies for addressing these issues and highlight the value of orthologous gene concatenation in generating accurate phylogenomic trees.}, }
@article {pmid42057793, year = {2026}, author = {Bautista, J and López-Cortés, A}, title = {The hallmarks of host-microbiome decoupling.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1801100}, pmid = {42057793}, issn = {1664-302X}, abstract = {The human host and its resident microbiome maintain continuous interactions that influence immune regulation, metabolism, neuroendocrine signaling, epithelial barrier function, and circadian organization. Although multi-omics approaches have improved mechanistic understanding of host-microbiome interactions, dominant translational models remain largely based on compositional descriptions and often do not capture persistence, systemic propagation, or temporal instability in microbiome-associated disease. Host-microbiome decoupling is defined here as a progressive reduction in functional coordination between host regulatory systems and microbial ecological behavior. The concept refers to conditions in which microbial signals, activities, or rhythmic patterns no longer remain aligned with host physiological regulation. A hallmarks-based framework is proposed to examine biological domains in which coordination between host regulation and microbial ecology deteriorates. Core hallmarks include breakdown of signaling fidelity, microbiome-driven immune miscalibration, barrier compartment failure, endocrine-microbiome uncoupling, ecological destabilization, and temporal desynchronization between host circadian programs and microbial oscillations. Additional dimensions include pathological microbial metabolite dominance with epigenetic embedding, endocrine and neuro-microbiome regulatory uncoupling, ecological destabilization of microbiome functional capacity, and temporal desynchronization between host circadian programs and microbial oscillations. Across inflammatory, metabolic, neurodegenerative, and neoplastic conditions, microbial activity may operate outside normal ecological constraints, influencing immune regulation, metabolic signaling, neuroimmune communication, and tumor-associated processes. Within this framework, resilience, signaling proportionality, host responses appropriately scaled to microbial input, and temporal coordination represent central properties of host-microbiome compatibility.}, }
@article {pmid42058649, year = {2026}, author = {Kwarteng, A and Amedorme, D and Addy, HPK and Amewu, EKA and Osei-Poku, P and Larbi, A}, title = {Brukina in Focus: A Narrative Review on Metagenomic Approaches to Fermentation and Food Safety.}, journal = {International journal of microbiology}, volume = {2026}, number = {}, pages = {6677609}, pmid = {42058649}, issn = {1687-918X}, abstract = {Brukina, a traditional fermented beverage smoothie made from milk and millet, is popular in Ghana and other West African countries due to its tasty flavor, high nutritional content, and affordability. Despite its widespread consumption, the nature of its production through artisanal fermentation processes presents concerns regarding microbial consistency, nutritional optimization, and food safety. This literature review explores the potential of metagenomic approaches to uncover microbial diversity, functional capacity, and safety profiles of Brukina. By integrating insights from amplicon-targeted and shotgun whole-genome sequencing studies on fermented foods, we highlight how next-generation sequencing technologies can characterize lactic acid bacteria, yeast, and other microorganisms that drive fermentation. Additionally, we discuss how metagenomics can identify functional genes influencing carbohydrate metabolism, flavor and aroma generation, and production of antimicrobial resistance compounds. Thus, metagenomics provides a powerful framework for assessing public health risks and nutritional benefits. Bioinformatic tools have also been highlighted, and their relevant application in analyzing sequenced data to achieve taxonomic classification, identification of biochemical pathways, and functional profiling of microbial ecology of fermented foods. This review outlines key research gaps and recommends future directions, including starter culture development, standardization of Brukina production, multi-omics integration in metagenomics, and microbiome-informed food safety standards. Metagenomic profiling of Brukina holds promise for improving product quality, consumer safety, and scientific understanding of traditional fermented foods. By tackling the challenges raised, metagenomic techniques can be extremely helpful in maximizing Brukina fermentation, guaranteeing food safety, and maintaining the customs that give this product its distinctive character.}, }
@article {pmid42046678, year = {2026}, author = {Dayrit, G and Mabrok, M and Chaiyapechara, S and Rodkhum, C}, title = {Habitat-structured fungal mycobiomes at the water-gill interface of farmed red tilapia in Central Thailand: An internal transcribed spacer rRNA amplicon sequencing study.}, journal = {Veterinary world}, volume = {19}, number = {3}, pages = {1196-1214}, pmid = {42046678}, issn = {0972-8988}, abstract = {BACKGROUND AND AIM: Tilapia aquaculture is rapidly expanding across Southeast Asia and plays a critical role in regional food security. While bacterial microbiomes of farmed fish have been widely investigated, the fungal component of aquatic microbial communities remains poorly characterized, particularly at the biologically important interface between rearing water and fish gills. Fungi may influence fish health, environmental microbial ecology, and occupational exposure risks within aquaculture systems. This study aimed to characterize fungal mycobiomes associated with rearing water and gills of clinically healthy red tilapia (Oreochromis spp. hybrids) cultured in Central Thailand using internal transcribed spacer (ITS) rRNA amplicon sequencing and to determine how habitat type, farming system, and environmental variables shape fungal community structure.<br><br>MATERIALS AND METHODS: Samples were collected from ten tilapia farms located in five provinces of Central Thailand, representing two aquaculture systems: open river cages and closed earthen ponds. A total of 27 rearing water samples and 30 composite gill samples were analyzed. Fungal DNA was extracted and the ITS1 region was amplified and sequenced using the Illumina MiSeq platform. Sequence processing and amplicon sequence variant inference were performed in QIIME2 using the DADA2 pipeline. Alpha diversity indices and beta diversity analyses were used to evaluate community structure, while multivariate statistical approaches assessed the influence of habitat type, geographic location, farming style, and physicochemical water parameters.<br><br>RESULTS: Fungal communities displayed considerable taxonomic diversity and differed significantly between habitats. Rearing water samples exhibited significantly higher alpha diversity than gill-associated communities. Dominant genera included Cladosporium, Candida, Aspergillus, Fusarium, and Rhodotorula. Gill communities were relatively enriched in Candida and Fusarium, whereas rearing water contained higher abundances of Cladosporium and Rhodotorula. Beta diversity analyses demonstrated significant effects of sampling source, province, and farming system on fungal community composition. Environmental parameters such as pH, nitrate concentration, and ionic strength were associated with variations in fungal diversity, particularly in rearing water. Several detected genera included taxa with known opportunistic pathogenic potential for fish and humans.<br><br>CONCLUSION: This study provides the first ITS-based baseline characterization of fungal mycobiomes associated with red tilapia aquaculture systems in Central Thailand. Distinct fungal assemblages occur at the water-gill interface, with environmental conditions and aquaculture practices influencing community composition. The presence of opportunistic fungal genera highlights the importance of incorporating fungal community monitoring into aquaculture biosecurity and One Health surveillance frameworks to support sustainable fish production, environmental health, and occupational safety.}, }
@article {pmid42049134, year = {2026}, author = {Gajendiran, TY and Ganamurali, N and Sabarathinam, S}, title = {The host-steroid-microbiome axis: Microbial remodeling of steroid scaffolds and its implications for metabolic and endocrine disorders.}, journal = {Drug discovery today}, volume = {}, number = {}, pages = {104683}, doi = {10.1016/j.drudis.2026.104683}, pmid = {42049134}, issn = {1878-5832}, abstract = {Steroids, chemically conserved yet functionally diverse, integrate metabolic, endocrine and microbial networks. Beyond host hormones acting via specific receptors, the gut microbiome edits steroid scaffolds, yielding metabolites that reshape systemic signaling. We introduce the host-steroid-microbiome axis, framing steroids as holobiont currencies coordinating metabolism, immunity and endocrine balance. This continuum links endogenous steroidogenesis, microbial transformations (via hydroxysteroid dehydrogenases, sulfatases and β-glucuronidases) and host receptor modulation (farnesoid X, TGR5, estrogen, androgen and glucocorticoid receptors), impacting bile acid signaling, glucose/lipid metabolism and hormone-related diseases. Steroidomics, multiomics, cryo-EM, artificial intelligence (AI) modeling and digital twins illuminate these interactions, enabling precision endocrinology informed by the microbiome, diet and genetics. A roadmap unites microbial ecology, steroid chemistry and AI for therapeutic targeting.}, }
@article {pmid42049610, year = {2026}, author = {Barrientos, G and Fahlbusch, FB and Conrad, ML}, title = {Microbes, molecules, and the maternal-fetal interface: rethinking the gut-placenta axis.}, journal = {Trends in immunology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.it.2026.03.010}, pmid = {42049610}, issn = {1471-4981}, abstract = {Placental biology is increasingly framed through a signaling paradigm in which maternal microbiome-derived mediators-rather than microbial colonization-affect the function of the interface. This review synthesizes evidence that circulating microbial signals, including short-chain fatty acids, tryptophan-derived indoles, bile-acid-linked ligands, microbe-associated molecular patterns, and bacterial extracellular vesicles, are associated with placental vascular development, immune regulation, nutrient transport, and endocrine programs-processes central to pregnancy outcomes. We integrate mechanistic insights from gnotobiotic and supplementation models with limitations of human evidence and identify key translational gaps. The current evidence supports a model in which maternal microbial ecology shapes a network of circulating mediators that converge on interlinked placental pathways essential for placental function and fetal development.}, }
@article {pmid42049755, year = {2026}, author = {Zhou, K and Kosmopoulos, JC and Colón, ED and Badciong, PJ and Anantharaman, K}, title = {V- and VL-scores unveil viral signatures and origins of protein families.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-72028-0}, pmid = {42049755}, issn = {2041-1723}, support = {DBI2047598//National Science Foundation (NSF)/ ; 42576129//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Viruses are key drivers of microbial ecology and evolution, yet their study is hindered due to challenges in culturing. Traditional gene-centric methods, which focus on a few hallmark genes like for capsids, miss much of the viral genome, leaving key viral proteins and functions undiscovered. Here, we introduce two powerful annotation-free metrics, V-score and VL-score, designed to quantify the "virus-likeness" of protein families and genomes and create an open-access searchable database, 'V-Score-Search'. By applying V- and VL-scores to public protein databases, we link 19 - 59% of protein families with viruses representing a 5 - 8x increase over current estimates. These metrics outperform existing approaches, enabling high efficiency in detection of viral genomes, prophages, and host-derived auxiliary viral genes (AVGs) from fragmented sequences. Remarkably, we identify up to 17 times more AVGs dominated by non-metabolic proteins of unknown function. This innovation unlocks new insights into virus signatures and host interactions, with wide-ranging implications from genomics to biotechnology.}, }
@article {pmid42050290, year = {2026}, author = {Araujo, MS and da Silva Souza, IJ and Martins, RP and Dos Santos, CC and Mafia, RG and Rachid, CTCDC}, title = {Enhancing Eucalyptus seedling quality through multi-strain bacterial inoculation.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {5}, pages = {}, pmid = {42050290}, issn = {1573-0972}, }
@article {pmid42053316, year = {2026}, author = {Vo, HH and Le, TT and Nguyen, TV and Scott, J and Gutierrez, T and Kaiser, MJ and Ngo, HTT}, title = {Developing an optimized method for biofilm extraction from microplastic surfaces for high-efficiency analysis of adherent bacterial communities.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0041626}, doi = {10.1128/aem.00416-26}, pmid = {42053316}, issn = {1098-5336}, abstract = {Microplastics (MiPs, ×5 mm in size) harbor complex biofilms that facilitate pathogen dissemination, yet standardized extraction protocols are lacking. Here, we developed and optimized a method for biofilm extraction from environmentally weathered MiPs. To reflect real-world conditions, the protocol was applied directly to bulk, heterogeneous, field-collected MiP mixtures (size range: 80 µm-5 mm) without prior sorting by polymer type or morphology. By optimizing extraction buffers, mechanical disruption, and MiP quantities (100-150 particles), we established an optimal protocol combining phosphate-buffered saline with 0.1% Tween 80, ultrasonication (40 kHz, 10 min), vortexing with glass beads, and a two-cycle extraction-disaggregation workflow. This approach involves an initial extraction followed by a repeated, exhaustive extraction step designed to maximize the recovery of recalcitrant biofilm residues. This protocol markedly enhanced recovery of viable, culturable cells, delivering a 2,950-fold enhancement in the recovery of viable, culturable cells (evaluated via CFU counts; 28,020 ± 11,034 CFU MiP[-1]) vs. conventional PBS extraction (9.5 ± 3 CFU MiP[-1]) and 102-fold vs. passive extraction (274 ± 59 CFU MiP[-1]). The 10-min sonication empirically maximized viable cell recovery within the tested duration range. The two-step protocol with Tween 80-mediated disaggregation proved critical, increasing recovery 208-fold by disaggregating biofilm fragments. While DNA yields (26.5 ± 3.93 ng µL[-1]) were sufficient for targeted PCR-based pathogen detection (Aeromonas spp., Salmonella enterica), the co-extraction of complex environmental matrices (A260/A280 ratio: 0.17-0.19) strictly requires an additional purification step prior to next-generation sequencing. Validation across contrasting aquatic environments confirmed the method's robustness. Comparative analysis demonstrates that conventional single-step approaches fail to recover the majority of viable cells trapped within weathered MiP biofilms. This optimized and validated protocol provides a critical methodological foundation for investigating plastisphere microbial ecology and pathogen transport dynamics, supporting evidence-based risk assessment of MiP contamination, especially public health risks associated with microplastic pollution.IMPORTANCEMicroplastic-associated biofilms (the "plastisphere") serve as vectors for waterborne pathogens and antibiotic resistance genes; however, the persistent use of inadequate extraction methods has systematically underestimated microbial abundance, presenting a critical barrier to global environmental risk assessment. By overcoming the limitations of conventional extractions-which fail to penetrate recalcitrant extracellular polymeric matrices on environmentally weathered microplastics-our standardized methodology liberates previously undetectable bacterial populations. The ability to accurately quantify these hidden communities, including key pathogens like Aeromonas spp. and Salmonella enterica, fundamentally transforms our understanding of microplastics as hidden biological reservoirs. Ultimately, this methodological advancement bridges a critical gap in microbial ecology, delivering the reliable, quantitative data strictly required by policymakers, environmental agencies, and public health officials to establish evidence-based guidelines mitigating the impacts of microplastic pollution on global water systems.}, }
@article {pmid42053432, year = {2026}, author = {Spaeth, MK and Barberán, A and Funk, JL and Eastburn, DJ and Roche, LM and Gornish, ES}, title = {Impacts of targeted grazing, controlled burning, and strip seeding on soil microbial communities.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {36}, number = {3}, pages = {e70245}, doi = {10.1002/eap.70245}, pmid = {42053432}, issn = {1051-0761}, support = {//The Russell L. Rustici Rangeland and Cattle Research Endowment/ ; DGE-2022055//National Science Foundation/ ; }, mesh = {*Soil Microbiology ; Animals ; *Fires ; *Herbivory ; Bacteria/classification ; California ; *Agriculture/methods ; Sheep ; *Microbiota ; *Conservation of Natural Resources/methods ; Grassland ; }, abstract = {Increased vegetation management efforts are crucial due to the magnitude of global land degradation. Most modern land management projects focus on either controlling undesirable plant species or attempting to reconstruct the historical plant community. While most strategies are generally expected to enhance native vegetation establishment and diversity, there may be unintended impacts on vital soil microbial communities. Soil microbial communities play a crucial role in biogeochemical processes like nutrient cycling, organic matter decomposition, and the development of soil structure, all of which influence plant productivity, nutrient acquisition, and the regulation of plant diversity and composition. We sought to investigate the consequences of different combinations of vegetation management strategies used to restore a former cropland to a perennial grassland in Davis, California, USA. Specifically, we assessed soil microbial community diversity, composition, and putative functional group abundances across different combinations of (1) targeted sheep grazing, (2) low and high frequency controlled burning, and (3) native plant strip seeding. We found that microbial taxonomic diversity was largely unchanged across vegetation management practices, but grazing, burning, and seeding led to shifts in soil microbial community composition. Microbial community shifts were primarily associated with changes in plant community composition; however, indirect modifications to carbon: nitrogen and pH were also differentially associated with compositional shifts in bacteria and fungi, respectively. Overall, our findings highlight that soil bacterial communities are resistant to increasing management intensities. Future studies should investigate how changes in soil microbial communities within managed ecosystems impact ecosystem processes and whether these processes align with land management objectives.}, }
@article {pmid42053606, year = {2026}, author = {Koch, H and Lessard, B and Escobar-Correas, S and Thurman, JH and Paten, AM and Morgan, MJ}, title = {A Comparative Survey of Soldier Fly (Stratiomyidae) Larval Gut Microbiomes Across Five Subfamilies Reveals Novel Bacterial Diversity and a "Wild Core" in Hermetia illucens.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02760-z}, pmid = {42053606}, issn = {1432-184X}, }
@article {pmid42041913, year = {2026}, author = {Wang, T and Wang, Z and Yang, X and Zhang, L}, title = {From Microbial Ecology to Functional Components in Microbe-Host Interactions.}, journal = {Biology}, volume = {15}, number = {8}, pages = {}, pmid = {42041913}, issn = {2079-7737}, support = {82370785//National Natural Science Foundation of China/ ; tscy20190612//TaiShan Industrial Experts Program/ ; tshw20120206//TaiShan Scholars Program of Shandong Province/ ; }, abstract = {Microbiome research is shifting from a focus on "whole microorganisms" to an emphasis on microbial functional components. This review systematically describes how the effects of microbial communities on the host are mediated by bioactive functional components released by microbes. These components primarily exert their effects through interactions with host Pattern Recognition Receptors (PRRs) and metabolic sensing receptors, thereby regulating host immune, metabolic, and barrier function networks. The biological effects of these functional components are highly context-dependent. Under homeostasis, metabolites such as SCFAs and bile acids promote mucosal immune tolerance and maintain epithelial barrier integrity. However, the same signals can become deleterious under dysbiosis, driving inflammation and contributing to colorectal tumorigenesis. Mechanistic dissection of individual components, such as lipopolysaccharide (LPS), is now propelling a transition in clinical translation from whole-microbe-based interventions toward component-oriented diagnostics and therapeutics. Component-oriented diagnostics and therapeutics use defined microbial molecules rather than whole microorganisms. Microbial nucleic acids (e.g., HPV DNA), metabolites (e.g., SCFAs), and proteins can serve as biomarkers for disease risk, diagnosis, and prognosis. Therapeutic strategies include targeted modulation of beneficial components, neutralization of harmful molecules, and engineered microbial delivery.}, }
@article {pmid42042999, year = {2026}, author = {Zhang, Q and Yan, B and Sun, X and Lin, Z and Liu, L and Guo, H and Ma, F}, title = {Advances and Challenges in Aerobic Granular Sludge Membrane Bioreactors for Treating Sulfamethoxazole in Wastewater.}, journal = {Membranes}, volume = {16}, number = {4}, pages = {}, pmid = {42042999}, issn = {2077-0375}, support = {No. 2025ZD1200800//the Jing-Jin-Ji Regional Integrated Environmental Improvement-National Science and Technology Major Project of Ministry of Ecology and Environment of China/ ; }, abstract = {Sulfamethoxazole (SMX) is one of the most frequently detected antibiotics in aquatic environments and is difficult to remove by conventional biological treatment because of its persistence, potential toxicity to microbial communities, and associated risk of antibiotic resistance selection. Aerobic granular sludge membrane bioreactors (AGMBRs), which combine the compact and stratified structure of aerobic granular sludge with membrane-based solid-liquid separation, have emerged as a promising platform for SMX-contaminated wastewater treatment because they provide high biomass retention, decoupled sludge retention time (SRT) and hydraulic retention time (HRT), and stable effluent quality. This review systematically summarizes recent advances in AGMBRs for SMX removal, with emphasis on how operating parameters (e.g., dissolved oxygen, hydraulic retention time, organic loading rate, C/N ratio, and sludge retention time) and membrane-related factors (e.g., membrane flux, aeration-induced shear, membrane type, and pore size) affect treatment performance and process stability. The main SMX attenuation pathways in AGMBRs are discussed from three perspectives: sorption and partitioning within granules and extracellular polymeric substances (EPSs), microbial biodegradation and co-metabolism, and membrane retention that prolongs effective contact time and shapes microbial ecology. Particular attention is given to the dual role of EPS and soluble microbial products (SMPs), which contribute to granule stability and SMX tolerance but also accelerate membrane fouling through cake-layer formation, pore blocking, and transmembrane pressure increase. Current challenges include incomplete understanding of transformation products, ARG- and MGE-related risks, long-term fouling-biodegradation interactions, and the lack of pilot-scale validation. Future research should therefore focus on mechanism clarification, integrated control of removal and fouling, energy-efficient operation, and scale-up of AGMBRs for practical antibiotic wastewater treatment.}, }
@article {pmid42045390, year = {2026}, author = {Jonnagiri, NPKR and Kieliszek, M}, title = {Anhydrobiosis as a Model of Aging and Longevity: The Role of Autophagy and Metabolism in Yeast Cells.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02782-7}, pmid = {42045390}, issn = {1432-184X}, }
@article {pmid42045635, year = {2026}, author = {Sarkar, AK and Roy, S and Chakraborty, N and Das, A and Maity, R and Maity, T and Samanta, BC and Minkina, T and Rajput, VD and Adak, MK}, title = {A Rice Rhizosphere-Associated Bacillus sp. With Dual Biosorption and Enzymatic Pathways for Chromium (VI) Detoxification.}, journal = {Journal of basic microbiology}, volume = {66}, number = {4}, pages = {e70170}, doi = {10.1002/jobm.70170}, pmid = {42045635}, issn = {1521-4028}, support = {NTARef.No.//University Grants Commission/ ; 231620043667//University Grants Commission/ ; 231610099992//University Grants Commission/ ; 211610058334//University Grants Commission/ ; FENW-2026-0019//University Grants Commission/ ; Priority-2030//University Grants Commission/ ; }, mesh = {*Chromium/metabolism/toxicity ; *Oryza/microbiology/growth &amp; development ; *Bacillus/metabolism/enzymology/isolation &amp; purification/genetics ; *Rhizosphere ; Biodegradation, Environmental ; *Soil Pollutants/metabolism ; Soil Microbiology ; Oxidoreductases/metabolism ; Kinetics ; Adsorption ; }, abstract = {Hexavalent Cr(VI) is well known hazardous pollutant which not only impairs the soil health but also drastically reduces the plant developmental processes. Here, we observed a plant growth promoting rhizobacterium (Bacillus sp. AKS_bp1) isolated from rice rhizosphere modulating dual roles in Cr(VI) detoxification and plant responses. Initially, Bacillus sp. (AKS_bp1) showing PGPR characteristic along with a high tolerance to varying Cr(VI) concentrations in laboratory condition. Moreover, the strain also reduce the Cr(VI) concentration (~80%) with a bio-sorption capacity reaching 95.21% under 72 h incubation followed by pseudo first order kinetics. Further, biosorption studies through infrared spectroscopy and scanning micrograph showing the presence of hydroxyl, polysaccharides, and amino-nitrogen based functional groups for Cr binding. Likewise, internal Cr(VI) bio-removal the activity of Cr reductase was recorded with changes through 20, 40, 60, and 80 ppm of Cr(VI) in solution. Enzyme activity was validated with varying pH (5-8), temperature (21°C-45°C) and metal (Ag[2+]), salt (sodium dodecyl sulphate) etc. In detoxification pathways, the strain recorded further upregulation of antioxidative enzymes highlighting a well-established defence against Cr induced toxicity. Remarkably, application the strain was able to remove 36.86% of Cr(VI) when incubated in tannery effluents through 72 h. Conclusively, the present work provides importance of Bacillus sp. (AKS_bp1) mediated bio-removal of contaminated industrial effluents, which predominantly rich in Cr(VI). This bacterial strain also significantly reduced lipid peroxidation and polyphenol oxidation. Moreover, it offers potential for additional chemical modifications and sustainable bioremediation of Cr and other toxic metals, thereby improving crop growth and productivity.}, }
@article {pmid42045880, year = {2026}, author = {Till, J and López-Gálvez, J and Schattenberg, F and Schmidt, M and Müller, S and Toepel, J and Bühler, B}, title = {Synechocystis sp. PCC 6803 shows high cell cycle dynamics reflected by an extraordinary genome copy number variation.}, journal = {Microbial cell factories}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12934-026-02982-3}, pmid = {42045880}, issn = {1475-2859}, }
@article {pmid42034120, year = {2026}, author = {Tripathi, DK and Sharma, P and Elbaum, R and Nguyen, H and Deshmukh, R}, title = {Mineral Nutrient Acquisition Under Stress: Sensing, Signaling, and Transportation.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {}, number = {}, pages = {113166}, doi = {10.1016/j.plantsci.2026.113166}, pmid = {42034120}, issn = {1873-2259}, }
@article {pmid42034665, year = {2026}, author = {Sato, Y}, title = {RuSpacer: a CRISPR spacer database derived from ruminant-associated prokaryotes for virome analysis.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-49729-z}, pmid = {42034665}, issn = {2045-2322}, support = {25K18347//Japan Society for the Promotion of Science/ ; }, abstract = {Microorganisms in the ruminant gastrointestinal tract play key roles in lignocellulose degradation and energy conversion. Prokaryote-infecting viruses play a pivotal role in shaping host abundance and metabolism. Despite their importance, host-virus prediction in this environment remains limited, partly due to the lack of specialized clustered regularly interspaced short palindromic repeat spacer datasets. Here, RuSpacer, a database of 181,023 clustered regularly interspaced short palindromic repeat spacers extracted primarily from publicly available rumen-associated prokaryotic genomes, was established. Each spacer is annotated with the taxonomic identity of the genome from which it was derived. RuSpacer enables host-virus prediction via spacer-protospacer matching, particularly in the rumen ecosystem. It can also be integrated with existing publicly available spacer datasets and used for host-virus prediction in environments other than the rumen. Overall, this resource supports research on host-virus interactions, microbial ecology, and virus-based biocontrol strategies in livestock and other complex microbiomes.}, }
@article {pmid42034962, year = {2026}, author = {Petrucelli, JV and Borrás, P and Jiménez, Y and Samaniego, G and Ruybal, P and Hodžić, A}, title = {The first clinical case of Hepatozoon felis infection in a cat from Panama.}, journal = {Veterinary parasitology, regional studies and reports}, volume = {70}, number = {}, pages = {101480}, doi = {10.1016/j.vprsr.2026.101480}, pmid = {42034962}, issn = {2405-9390}, mesh = {Animals ; Cats ; Male ; Panama/epidemiology ; *Cat Diseases/parasitology/drug therapy/diagnosis/epidemiology ; *Coccidiosis/veterinary/drug therapy/parasitology/diagnosis/epidemiology ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; *Eucoccidiida/genetics/isolation &amp; purification ; Doxycycline/therapeutic use ; Antiprotozoal Agents/therapeutic use ; }, abstract = {Hepatozoon felis is the most prevalent Hepatozoon species infecting domestic cats worldwide; however, clinical disease is considered uncommon. This study describes the first clinically confirmed case of H. felis infection in a domestic cat from Panama. A 3-year-old male cat presented with painful periostitis of long bones, poor body condition and leukocytosis with marked neutrophilia. Hepatozoon gamonts were detected in neutrophils, and infection was confirmed by PCR and sequencing of the 18S rRNA gene. Phylogenetic analysis revealed a highly divergent H. felis lineage clustering separately from predominant European haplotypes. The cat was successfully treated with imidocarb, doxycycline and toltrazuril, achieving complete clinical recovery and PCR negativity. This report extends the known geographic range of H. felis to Central America and highlights its potential pathogenicity in immunocompetent cats.}, }
@article {pmid42034975, year = {2026}, author = {Wang, H and Chen, Z and Qi, L and Wang, Z and Xu, D and Mao, Y and Shen, Z and Chen, K}, title = {Metagenomic profiling of Poa alpigena rhizosphere and bulk soil microbiomes across differing land-use contexts in the Qinghai lake alpine wetland.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-04999-5}, pmid = {42034975}, issn = {1471-2180}, support = {This work was supported by the Natural Science Foundation Project of Anhui Provincial Universities (No. 2022AH052150 and 2024AH051553). Research on Ecosystem Changes in the Qinghai Lake Littoral Zone Under Water Level Rise and Their Impacts on Carbon Cycle (2023-ZJ-905T).//This work was supported by the Natural Science Foundation Project of Anhui Provincial Universities (No. 2022AH052150 and 2024AH051553). Research on Ecosystem Changes in the Qinghai Lake Littoral Zone Under Water Level Rise and Their Impacts on Carbon Cycle (2023-ZJ-905T)./ ; }, }
@article {pmid42035169, year = {2026}, author = {Wu, Y and Li, J and Yu, J and Yang, C and Mao, S}, title = {Temporal dynamics shifts in multi-kingdom rumen microbiota and fermentation profiles of water buffalo under heat stress.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00570-9}, pmid = {42035169}, issn = {2524-4671}, support = {32361143788//National Natural Science Foundation of China/ ; }, }
@article {pmid42036976, year = {2026}, author = {Vignolle, A and Zehl, M and Garzón, JFG and Schneider, O and Gafriller, J and Grienke, U and Kirkegaard, RH and Zotchev, SB}, title = {Identification and Characterisation of the Gene Cluster Governing Biosynthesis of the Anti-Mycobacterial Antibiotic Acidomycin.}, journal = {Microbial biotechnology}, volume = {19}, number = {4}, pages = {e70357}, doi = {10.1111/1751-7915.70357}, pmid = {42036976}, issn = {1751-7915}, support = {//Universit&#xe4;t Wien/ ; }, mesh = {*Multigene Family ; *Streptomyces/genetics/metabolism/isolation &amp; purification ; *Biosynthetic Pathways/genetics ; Gene Knockout Techniques ; *Antitubercular Agents/metabolism ; Biotin/biosynthesis ; }, abstract = {Acidomycin is an anti-mycobacterial antibiotic with a unique mode of action, targeting the biotin biosynthesis pathway. Despite being highly active against mycobacteria in vitro, its development as an anti-tubercular agent has been hindered due to suboptimal pharmacokinetics. Engineering of the acidomycin biosynthesis may yield new analogues with improved pharmacological properties. Here, we describe the identification of the acidomycin biosynthetic gene cluster (BGC) in a Streptomyces bacterium isolated from the rhizosphere of Edelweiss. Notably, the acidomycin BGC is located in proximity to the genes for the biosynthesis of stravidins, secondary metabolites targeting a different enzyme in the biotin biosynthesis pathway, and two genes for streptavidins, proteins that strongly bind and sequester biotin. The identity of the acidomycin BGC was confirmed via both gene knock-out and heterologous expression, which suggested that the fatty acid required for the formation of acidomycin's acyl chain is most likely scavenged from the biotin biosynthesis pathway. CRISPR/Cas9-assisted knock-out of the cytochrome P450-encoding gene in the acidomycin BGC resulted in a significant decrease in its yield but did not abrogate the biosynthesis completely.}, }
@article {pmid42037543, year = {2026}, author = {Potenza, L and Krzak, J and Andrzejewski, MS and Pyzik, A and Kaminski, TS}, title = {Ultra-high throughput droplet microfluidics for cultivation and functional screening of environmental microbial strains and consortia.}, journal = {Lab on a chip}, volume = {}, number = {}, pages = {}, doi = {10.1039/d5lc01115a}, pmid = {42037543}, issn = {1473-0189}, abstract = {Screening of microbial diversity is critical for discovering novel strains with enhanced biocatalytic capabilities. Traditional cultivation techniques often miss rare or slow-growing microorganisms, limiting our understanding of environmental microbiomes and their practical applications. Droplet-based microfluidics has emerged as a powerful platform for ultra-high-throughput screening of single cells or microbial consortia, encapsulated within microscale droplets that act as precisely controlled bioreactors. This tutorial review focuses on the application of droplet microfluidics for microbial cultivation and isolation, emphasizing advantages such as high throughput and the ability to perform functional assays on cultures originated from individual cells. Unlike previous reviews that broadly address microfluidic technologies or target specific applications like antibiotic resistance or enzyme discovery, we concentrate on protocols specifically designed for the clonal and parallel cultivation of microorganisms from environmental samples. Droplet microfluidics has already shown significant potential in environmental biotechnology, bioremediation, and microbial ecology. Reducing assay volumes and costs while increasing screening efficiency, positions droplet microfluidics as a key technology for the future of environmental microbiology research.}, }
@article {pmid42037782, year = {2026}, author = {Ma, X and Yu, Q and Kuang, Z}, title = {Timekeepers of the gut: host circadian rhythms and microbial modulators.}, journal = {Life metabolism}, volume = {5}, number = {2}, pages = {loag003}, pmid = {42037782}, issn = {2755-0230}, abstract = {The intestine is more than a digestive organ. It is a system under circadian control, where cellular renewal, barrier integrity, absorption, immunity, and microbial ecology are orchestrated in time. Emerging evidence reveals that circadian rhythms not only regulate the daily turnover of intestinal epithelium but also fine-tune digestive enzyme expression, mucosal defense, and gut hormone secretion. These processes are driven by core clock proteins and synchronized by feeding cues, neural signals, and microbial metabolites. The gut microbiota consists of essential symbionts that themselves exhibit diurnal oscillations in composition and function, in turn feeding back to modulate host circadian pathways. Disruption of this host-microbiota temporal alignment, as occurs with jet lag, shift work, or high-fat diets, impairs intestinal homeostasis and elevates risk for inflammation, infection, and metabolic disorders. This review integrates evidence from mouse, zebrafish, fly, and human studies to highlight the rhythmic regulation of gut physiology, emphasizing how coordination between the host clock and microbiota sustains health. Viewing the gut as a circadian conductor underscores new opportunities for chronotherapy and microbiota-targeted interventions.}, }
@article {pmid42039089, year = {2026}, author = {Nakhal, MM and Nafees, F and Mydeen, AB and Al Ali, A and Baloch, S and Alkhalaf, R and Albalas, HM and Albalas, GM and Alharbi, G and Statsenko, Y and Marzouka, NA and Hamad, MIK}, title = {Maternal gut dysbiosis is associated with altered enteric and cortical inhibitory circuit development.}, journal = {Frontiers in neuroanatomy}, volume = {20}, number = {}, pages = {1801873}, pmid = {42039089}, issn = {1662-5129}, abstract = {INTRODUCTION: Maternal environmental factors critically influence neural circuit maturation during early development. The maternal gut microbiota has emerged as an important upstream regulator of offspring neurodevelopment, yet its role in shaping the structural organization of enteric and cortical inhibitory circuits remains poorly defined. Here, we examined whether gestational disruption of the maternal gut microbiota is associated with alterations in parallel enteric and cortical inhibitory circuit development.<br><br>METHODS: Maternal gut dysbiosis was induced in pregnant GAD67-GFP mice by oral vancomycin administration during gestation. Maternal and offspring microbiota were analyzed using full-length 16S rRNA gene sequencing to assess microbial diversity and vertical transmission. Offspring were examined at postnatal day 14 for intestinal morphology, altered barrier integrity, and enteric nervous system (ENS) organization. Cortical inhibitory circuits were analyzed by quantifying GAD67-positive interneuron density and performing three-dimensional morphological reconstruction in layers II/III of the somatosensory cortex, motor cortex, medial entorhinal cortex, and CA1 region of the hippocampus.<br><br>RESULTS: Maternal dysbiosis significantly reduced microbial diversity and disrupted maternal-offspring microbial transmission. These changes were associated with impaired intestinal development, including reduced crypt height, thinning of the muscularis propria, fragmented Claudin-1 expression, and reduced Auerbach's plexus area without changes in neuronal density, indicating altered enteric network organization. In the brain, maternal dysbiosis induced region-specific cortical vulnerability, with reduced dendritic length and branching of GAD67-positive interneurons in the somatosensory and motor cortices, while interneuron morphology in the medial entorhinal cortex and hippocampus was preserved. Interneuron density was selectively reduced in the motor cortex.<br><br>DISCUSSION: These findings indicate that gestational maternal dysbiosis is associated with co-occurring structural alterations in intestinal and cortical inhibitory systems, selectively affecting inhibitory circuit architecture in sensorimotor regions. While the present model does not isolate microbiota-specific mechanisms from potential antibiotic-induced maternal physiological changes, the data support an association between disrupted maternal microbial ecology and offspring enteric and cortical neuroanatomical development during early postnatal life. These findings should be interpreted as descriptive associations and do not establish mechanistic gut-brain interactions.}, }
@article {pmid42039186, year = {2026}, author = {Baruah, K and Debnath, D and Patabandi, PPSK and Bossier, P and Yang, Q and Defoirdt, T and Norouzitallab, P}, title = {Carvacrol as a one health-relevant antimicrobial agent: mechanistic insights on its impact on gnotobiotic Artemia and Vibrio campbellii interactions.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1797445}, pmid = {42039186}, issn = {1664-3224}, mesh = {Animals ; *Artemia/microbiology/drug effects/immunology ; *Cymenes/pharmacology ; *Vibrio/drug effects/pathogenicity/physiology ; Germ-Free Life ; *Anti-Infective Agents/pharmacology ; *Vibrio Infections/immunology/microbiology/drug therapy ; *Anti-Bacterial Agents/pharmacology ; Host-Pathogen Interactions/drug effects ; }, abstract = {INTRODUCTION: Bacteria belonging to the Harveyi clade of vibrios, including Vibrio campbellii infect many wild and cultured aquatic organisms and cause major losses in global aquaculture. Although not a primary human pathogen, V. campbellii can act opportunistically, particularly following exposure to marine environments or seafood, and in immunocompromised individuals, highlighting the links between aquatic ecosystems, food production systems, and human health. Carvacrol, a phenolic monoterpenoid found in oregano and thyme essential oils, is approved for use in human and animal food. Beyond its safety profile, this compound has also been reported to possess diverse pharmacological effects, including anticarcinogenic, anti-inflammatory and antimicrobial.<br><br>METHODS: Using gnotobiotic brine shrimp Artemia as an in vivo model, we examined whether carvacrol can provide dual protection against V. campbellii by inhibiting the production of bacterial virulence and modulating host immune responses.<br><br>RESULTS AND DISCUSSION: Carvacrol significantly improved the survival of Artemia during V. campbellii challenge while showing low toxicity at effective concentrations. The protection was associated with reduced bacterial virulence, including decreased biofilm formation and lower hemolytic and caseinase activities. Additionally, carvacrol modulated the expression of defence-related genes (hsp70, prophenoloxidase, transglutaminase, and ferritin) in time-dependent and stochastic patterns, rather than sustained upregulation. Overall, these findings suggest that carvacrol enhances disease resistance through both pathogen- and host-directed mechanisms. Given its food-grade safety status, carvacrol holds strong translational potential as a functional antimicrobial strategy to support disease control and health management in aquaculture, warranting further evaluation under realistic farming conditions.}, }
@article {pmid42039802, year = {2026}, author = {Adhikary, K and Selim, S and Sarkar, R and Ganguly, K and Das, J and Almuhayawi, MS and Alruhaili, MH and Gattan, HS and Karak, P}, title = {Synthetic microbiomes in bioengineered rhizospheres: new frontiers for climate-resilient agriculture.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1780132}, pmid = {42039802}, issn = {1664-302X}, abstract = {Climate change poses significant threats to global agricultural productivity, necessitating innovative strategies to ensure food security and ecological sustainability. One promising avenue lies in the deliberate design and deployment of synthetic microbiomes and engineered rhizospheres to enhance plant resilience under environmental stress. This review places particular emphasis on multi-kingdom microbial interactions including bacteria, fungi, protists, and archaea and their potential for tailored, stress-specific applications within engineered rhizosphere systems. By integrating knowledge from microbial ecology, genomics, and systems biology, researchers have begun to unravel the complex interactions between plants and their associated microbial communities. Engineered microbial assemblies tailored to specific host plants and environmental conditions have shown potential in stabilizing crop performance during drought, salinity, and nutrient limitations. Moreover, the manipulation of root exudation patterns and soil physicochemical properties can be harnessed to recruit beneficial microbes and suppress harmful ones. The review also examines the role of synthetic biology tools, such as CRISPR-based genome editing and metabolic pathway engineering, in optimizing microbial traits for enhanced plant support. However, knowledge gaps remain in understanding multi-kingdom dynamics, optimizing SynComs for specific environmental contexts, and translating laboratory successes to reliable, field-scale applications. Additionally, advances in high-throughput screening, machine learning, and metagenomic profiling are accelerating the identification of key microbial taxa and functions relevant to plant health. Despite these promising developments, challenges remain in scaling these approaches for field applications and ensuring their ecological safety and consistency. This review explores the need for interdisciplinary efforts to translate laboratory insights into field-ready technologies, ultimately contributing to the development of climate-resilient and sustainable agricultural systems.}, }
@article {pmid42039826, year = {2026}, author = {Gini, C and Tiezzi, F and Jiang, J and Byrd, MH and Wen, H and Johnson, JS and Brito, LF and van Vliet, S and Maltecca, C}, title = {Data-driven enterosignatures link gut microbiome reorganization to heat stress responses in lactating sows.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1797687}, pmid = {42039826}, issn = {1664-302X}, abstract = {BACKGROUND: Heat stress (HS) can disrupt the gut microbiome, yet most livestock studies rely on taxonomic summaries that overlook the ecological structure of microbial communities. Enterosignatures (ES) as latent, co-occurring microbial assemblages learned from metagenomic data, offer a framework to capture these dynamics but have scarcely been applied in livestock HS research.<br><br>METHODS: Shotgun metagenomes were obtained from 25 lactating sows, belonging to two genetic lines (TOL, n = 13; SEN, n = 12), which were divergently selected based on genomic breeding values (GEBVs) for heat tolerance, and exposed to HS conditions. Results were decomposed using non-negative matrix factorization (NMF), yielding 8 taxonomic (T-ES) and 5 functional (F-ES) subcommunities. Functional profiles (based on KEGG Orthology, KOs) were mapped to metagenome-assembled genomes (MAGs) to integrate metabolic attributes within each ES.<br><br>RESULTS: Temporal shifts dominated T-ES variation, with limited genetic-line effects. T-ES 1 (p = 5.42 &#xd7; 10[-4], Cohen's d = 0.723) and T-ES 7 (p = 0.007, Cohen's d = 0.303) showed increases from day 4 to day 14. Despite modest overall genetic line effects, TOL animals progressively transitioned toward phylogenetically diverse and balanced communities, whereas SEN animals shifted toward imbalanced states characterized by enrichment of taxa with pathobiont potential or single-taxon dominance. Other T-ES displayed small to moderate effects, and T-ES 8 showed a potentially noteworthy genetic line-specific effect size at late lactation (Cohen's d = 0.960; 95% CI: -1.80 to -0.10), though omnibus tests were non-significant (p = 0.757), and the wide confidence interval underscores substantial uncertainty at this sample size. No F-ES reached statistical significance (p > 0.05); moderate effect sizes (up to d = 0.638) suggest possible functional restructuring warranting investigation in larger cohorts.<br><br>CONCLUSION: This work presents the first use of ES to track microbiome responses to HS in lactating sows. ES revealed latent taxonomic and functional subcommunities with clear temporal reorganization, offering insights not detectable with standard clustering or diversity metrics. Although genetic-line effects were modest, several ES showed biologically relevant shifts, supporting ES as a hypothesis-generating exploratory framework for linking microbial ecology to physiological adaptation under HS conditions, while warranting validation in larger, controlled trials.}, }
@article {pmid42040271, year = {2026}, author = {Asinari, F and Bellotti, G and Fedele, G and Puglisi, E and Caffi, T}, title = {Soil management modulates vineyard airborne fungal communities and impacts fungal disease pressure.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1770877}, pmid = {42040271}, issn = {1664-462X}, abstract = {Viticulture increasingly faces challenges posed by global warming and its effects on yield and berry composition, highlighting the need for sustainable yet effective management strategies. In a two-year field trial conducted in one vineyard, we compared conventional tillage (T) and no-till (NT) regimes with three inter-row treatments: compost mulch (C), pruning-wood mulch (PW), and living cover crops (CC), while using a high-efficiency captaspore vacuum sampler to track shifts in the airborne fungal diversity followed by visual assessment of fungal disease symptoms during each growing season. Under relatively dry seasonal conditions, compost mulching was associated with lower downy and powdery mildew pressure, whereas these differences were not detectable under wetter conditions. The use of cover crops appeared to modulate grape sugar content, resulting in lower bunch weight and higher °Brix. Tillage regime was associated with shifts in airborne fungal richness and composition, including changes in the relative abundance of taxa related to Erysiphe necator. However, seasonal climatic conditions explained a substantial proportion of the observed variability. Overall, soil tillage emerged as the dominant driver shaping the airborne fungal community composition, while compost mulching exerted disease-suppressive effects only under moderate climatic pressure. These findings suggest that soil management may modulate the soil-air microbial interface and disease pressure in a climate-dependent manner, rather than acting as a dominant standalone driver.}, }
@article {pmid42040505, year = {2026}, author = {Collado, C and Romero-Tena, P and Wegener, G and Elvert, M and Menapace, W and Laso-Pérez, R}, title = {Anaerobic oxidation of methane supports a minimal microbial community in a subsurface biofilm at Ginsburg mud volcano.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag072}, pmid = {42040505}, issn = {2730-6151}, abstract = {Deep marine sediments generate large amounts of methane, but most of this gas is consumed by the anaerobic oxidation of methane (AOM) mediated by microscopic consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). In this study, we investigated the AOM within a sulfate-methane transition zone (SMTZ) at a depth of ~9.6 m at the rim of the Ginsburg mud volcano in the Gulf of Cádiz. The SMTZ is supplied with sulfate from both overlying seawater and an underlying evaporitic deposit, and it coincides with a fracture zone that hosts a visible biofilm. Here, carbon dioxide shows the strongest [13]C-depletion, indicating intense methane consumption. Metagenomic and lipid biomarker analysis of the biofilm revealed an exceptionally simple microbial community dominated by ANME-1b archaea (63%), which predominantly produce strongly [13]C-depleted glycerol dialkyl glycerol tetraethers and, to a lesser extent, the less common macrocyclic archaeols. The putative partner bacterium Seep-SRB1c (Desulfobacterota) is less abundant (9%). Additionally, the biofilm contained five low-abundance heterotrophs that likely rely on biomass or metabolites released from the ANME-SRB consortium. Our study highlights the presence of active methanotrophic biofilms in subsurface sediments and suggests that these communities may play an overlooked role in mitigating seafloor methane emissions.}, }
@article {pmid42041346, year = {2026}, author = {Dadashizadeh, G and Elloso, M and Jeschke, MG}, title = {Burn Infections and Sepsis: Challenges and Future Prospects of Antibacterial Therapy.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {4}, pages = {}, doi = {10.3390/antibiotics15040383}, pmid = {42041346}, issn = {2079-6382}, support = {R01AG080040-01A1//The Juravinski Research Institute and grants from the National Institutes of Health/ ; }, abstract = {Infectious complications remain a principal determinant of late morbidity and mortality following major thermal injury, reflecting a convergence of barrier disruption, microbial adaptation, and host immune dysfunction. The post-burn environment creates a uniquely permissive niche for pathogen persistence, characterized by altered tissue perfusion, biofilm formation, and dynamic shifts in microbial ecology toward multidrug-resistant organisms. Concurrently, profound and evolving changes in host immunity and metabolism reshape both susceptibility to infection and response to therapy. This review integrates current evidence across pathophysiology, microbiology, diagnostics, and treatment, with a focus on challenges that limit effective infection control in burn patients. Particular attention is given to diagnostic uncertainty arising from overlap between sterile inflammation and true infection, the clinical implications of biofilm-associated tolerance, and the impact of burn-specific pharmacokinetic variability on antimicrobial efficacy. We further examine emerging diagnostic and therapeutic innovations, including host-response profiling, rapid molecular detection platforms, and next-generation anti-infective strategies targeting microbial virulence, biofilm structure, and host immune pathways. Despite substantial scientific advances, translation into clinical practice remains constrained by limited burn-specific trials, heterogeneous definitions, and systemic barriers to antimicrobial development. Collectively, these challenges underscore the need for integrated, precision-based approaches that combine early source control, individualized antimicrobial optimization, and advanced diagnostic frameworks. Future progress will depend on coordinated efforts to standardize definitions, generate high-quality multicenter data, and align innovation with clinical applicability across diverse healthcare settings.}, }
@article {pmid42029983, year = {2026}, author = {Schmitz, AM and Kern, NL and Ward, H and Sauerbrey, M and Mrosk, F and Wagendorf, O and Nahles, S and Rendenbach, C and Neckel, N and Heiland, M and Koerdt, S}, title = {Cultured microbial community complexity is associated with antimicrobial resistance and Enterobacterales enrichment in adult odontogenic infections.}, journal = {Oral and maxillofacial surgery}, volume = {30}, number = {1}, pages = {}, pmid = {42029983}, issn = {1865-1569}, abstract = {BACKGROUND: Odontogenic infections are polymicrobial entities with increasing antimicrobial resistance. Although immunosuppression is commonly considered a major risk factor for resistant and complex infections, concepts from microbial ecology suggest that community complexity itself may be associated with distinct microbial phenotype and susceptibility patterns.<br><br>METHODS: We performed a retrospective cohort study of consecutive patients undergoing surgical treatment for odontogenic infections at a tertiary maxillofacial center between 2017 and 2022. Intraoperative specimens were processed using standardized aerobic and anaerobic culture protocols. Primary outcomes were polymicrobial infection, Enterobacterales detection, and antimicrobial resistance; MRSA and Candida spp. were secondary outcomes. Immunosuppression was defined by systemic immunosuppressive therapy, chemotherapy, solid organ transplantation, or HIV infection. Cultured microbial community complexity was operationalized as the number of distinct pathogens detected by routine culture in each patient.<br><br>RESULTS: Among 695 included patients, polymicrobial infection was detected in 62.0% and antimicrobial resistance in 40.6%, without differences by immune status. Enterobacterales were more frequently detected in immunosuppressed patients (13.9% vs. 3.9%). Unsupervised clustering of pathogen profiles did not segregate by immune status. High microbial complexity was associated with a distinct microbiological profile associated with near-universal polymicrobial infection (97.2% vs. 55.3%), increased antimicrobial resistance (72.9% vs. 34.8%), and marked Enterobacterales enrichment (19.6% vs. 2.9%) (all p&#x2009;<&#x2009;0.001). In fully adjusted models, higher cultural microbial complexity showed the strongest adjusted association with all adverse microbiological outcomes, whereas no independent association was observed for the broad immunosuppression variable used in this study. Dose&#x2013;response analyses demonstrated a graded increase in Enterobacterales detection and antimicrobial resistance with rising pathogen burden.<br><br>CONCLUSIONS: In this retrospective cohort of surgically treated odontogenic infections, higher cultured microbial complexity was strongly associated with polymicrobial infection, Enterobacterales detection, and antimicrobial resistance. These findings support support further investigation of community-level microbiological features for future risk stratification approaches.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10006-026-01563-3.}, }
@article {pmid42031215, year = {2026}, author = {Deng, Y and Yang, X and Shi, D and Liu, X and Xia, J and Xu, J}, title = {Multimetallic biochar as an ecosystem engineer: Orchestrating synergistic IHT-DIET pathways via spatial niche partitioning for enhanced anaerobic digestion.}, journal = {Journal of biotechnology}, volume = {416}, number = {}, pages = {1-13}, doi = {10.1016/j.jbiotec.2026.04.011}, pmid = {42031215}, issn = {1873-4863}, abstract = {The efficacy of anaerobic digestion (AD) is limited by inefficient interspecies electron flow and metabolic pathways. While conductive materials promote direct interspecies electron transfer (DIET), their potential to engineer microbial ecosystems remains underexplored. This study engineered multimetallic biochar (Fe, Ni, Co, and Mn loaded) via mechanochemistry, integrating electron shuttle and microbial niche regulator functions. Physicochemical characterization confirmed redox-active metal-carbon interfaces and mesoporous structures, enhancing electron exchange and microbial colonization. In cow manure-corn straw co-digestion, optimized BC-Fe-Ni addition group achieved the highest cumulative methane yield (224.7 NmL/g.VS) and shortened the lag phase from 22.3 to 3.7 days. Microbial co-occurrence network analysis revealed phase-specific functional differentiation: the BC phase formed a DIET module centered on Methanosarcina as the core hub, while the slud phase established a syntrophic hydrogenotrophic (IHT) module with hydrolytic-acidogenic bacteria (Clostridium sensu stricto 1, Ruminofilibacter), syntrophic bacteria (Pelotomaculum, Synergistaceae), and hydrogenotrophic methanogens (Methanobacterium, Methanocorpusculum). Fisher's exact test confirmed significant phase-specific enrichment of these taxa (FDR-adjusted q < 0.05), validating non-random niche partitioning between electroactive archaea and hydrogenotrophic consortia. KEGG profiling showed biochar enriched DIET-related redox enzymes (EC 1.12.98.1) and downstream methanogenic enzymes (EC 2.8.4.1), while slud phase had more hydrolysis-acidification enzymes (EC 6.2.1.1) and IHT-related hydrogenases (EC 1.2.7.12). This niche partitioning establishes a division-of-labor strategy where DIET and IHT operate in parallel and synergistically, optimizing overall system efficiency. This work transcends biochar as a mere additive, presenting a new paradigm of tailored multimetallic biochar reprogramming microbial ecology to boost AD performance.}, }
@article {pmid42031220, year = {2026}, author = {Coccurello, R}, title = {The skin microbiome and affective symptoms: neuroimmune, neuroendocrine, and sensory pathways linking inflammatory dermatoses to mood and anxiety burden.}, journal = {Frontiers in neuroendocrinology}, volume = {}, number = {}, pages = {101251}, doi = {10.1016/j.yfrne.2026.101251}, pmid = {42031220}, issn = {1095-6808}, abstract = {The skin functions as a neuro-immuno-endocrine organ with an extensive microbial interface capable of bidirectional signaling with the central nervous system. While the gut-brain axis is well established, the skin-microbiota-brain (SMB) axis remains underexplored, particularly with respect to affective symptom dimensions (depression, anxiety, stress) that commonly co-occur with chronic inflammatory dermatoses. This review synthesizes evidence across clinical, translational, and experimental studies and organizes it by strength (associational findings, mechanistic plausibility, and limited interventional signals). We outline a systems-level model in which cutaneous microbial dysbiosis is associated with brain-relevant pathways via immune, neuropeptide, and metabolic routes. Candidate mediators include cytokines (IL-6, IL-17, TNF-α), neuropeptides (e.g., substance P, CGRP), and microbial-derived metabolites (e.g., SCFA-like compounds and tryptophan catabolites). These signals are hypothesized to influence neuroimmune tone and neurovascular signaling based largely on broader systemic inflammation and stress biology; direct causal evidence specifically attributing affective outcomes to skin microbiome perturbations in humans remains limited. In parallel, top-down neuroendocrine signaling via hypothalamic-pituitary-adrenal (HPA) axis activation, cortisol-related signaling, and sympathetic outflow can alter skin barrier function, antimicrobial peptide expression, and microbial ecology, potentially contributing to symptom-maintaining loops (e.g., itch-sleep disruption-stress). Importantly, we consider counterarguments (psychosocial burden, reverse causality, treatment effects, and the localized nature of lesions) and identify research priorities required to test causality (longitudinal sampling, mechanistic biomarker panels, and preregistered interventional studies with affective endpoints and mediation analyses). By integrating dermatological, microbiological, and neuroimmunological evidence within a symptom-centered framework, the SMB axis is positioned as a biologically plausible but still evolving model that may help explain affective symptom burden in subsets of patients with inflammatory skin disease and guide mechanism-informed translational research.}, }
@article {pmid42031826, year = {2026}, author = {Sekerci Keles, P and Esen, Y}, title = {Genome editing and food safety: bridging the validation gap.}, journal = {NPJ science of food}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41538-026-00843-2}, pmid = {42031826}, issn = {2396-8370}, abstract = {Genome editing is increasingly positioned as a tool for improving food safety and nutritional quality, yet its real-world impact depends on outcomes that extend far beyond molecular precision. This review synthesizes evidence on how genome edits translate through phenotypes, food matrices, processing, microbial ecology, and dietary exposure, revealing a persistent validation gap between early-stage technical metrics and food-safety-relevant endpoints. We argue for an exposure-anchored, multi-layered validation framework incorporating omics, post-harvest behavior, and post-market monitoring. Closing this gap is essential for aligning genome editing innovations with measurable improvements in food system safety and consumer protection.}, }
@article {pmid42032085, year = {2026}, author = {Haseeba, KP and Ramasamy, KP and Mustafa, G and Veerasingam, S and Aboobacker, VM and Abdulla, CP and Al-Khayat, JA and Vethamony, P}, title = {Taxonomic Profiling of Bacterial Communities Associated with Metals in the Tar Mats and Cyanobacterial Mats of the Qatar Coast, Arabian Gulf.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02761-y}, pmid = {42032085}, issn = {1432-184X}, }
@article {pmid42032393, year = {2026}, author = {Babele, P and Singh, P and Pant, A and Chawla, M and Das, B}, title = {Proteomic Insights into Antimicrobial Resistance Mechanisms in Human-Associated Bacterial Pathogens.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02770-x}, pmid = {42032393}, issn = {1432-184X}, support = {No. BT/PR30159/MED/15/188/2018//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, }
@article {pmid42020819, year = {2026}, author = {Eberly, JO and Berríos-Ortiz, L and Hurd, A and Shergill, L and Dyer, AT and Menalled, FD}, title = {Wheat Rhizosphere Bacterial Community Response to Bromus tectorum (L.) and Fusarium pseudograminearum Crown Rot.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02778-3}, pmid = {42020819}, issn = {1432-184X}, support = {2020-70006-32978//National Institute of Food and Agriculture/ ; }, abstract = {Annual crop yield losses due to plant diseases and weeds can be substantial. In the northern Great Plains, Bromus tectorum (L.) (also known as cheatgrass or downy brome) and Fusarium pseudograminearum (causing crown rot) form a multi-trophic pest complex threatening wheat production sustainability. This study assessed the impact of these pests on the wheat rhizosphere bacterial community. Field trials were conducted over four site-years in plots inoculated with F. pseudograminearum using a randomized split-plot design with two seeding and nitrogen fertilizer rates and B. tectorum presence/absence. A seed fungicide treatment was also used to evaluate its effect on F. pseudograminearum abundance. Rhizosphere bacterial communities were analyzed using full-length 16 S rRNA sequencing on the Oxford Nanopore platform, followed by diversity analysis, structural equation modeling (SEM), and co-occurrence network analysis. Alpha and beta diversity were significantly different between location-years. The SEM results showed a negative relationship (β = -0.180, p = 0.002) between F. pseudograminearum presence and rhizosphere bacterial community alpha and beta diversity. Effects of B. tectorum presence, seeding rate, nitrogen fertilizer, and fungicide treatment were not significant. Correlation analysis identified specific bacterial taxa responsive to F. pseudograminearum presence, including putatively beneficial species belonging to the genera Massilia, Bacillus, and Neobacillus, which were positively correlated with pathogen presence, suggesting a stress response mechanism. Network analysis revealed that F. pseudograminearum presence reduced network cohesion, and connectivity measures compared to treatments with lower pathogen load. These findings demonstrate that fungal pathogen presence can impact rhizosphere bacterial networks even when overall diversity metrics show minimal changes, highlighting the importance of network-based approaches in understanding plant-microbe-pathogen interactions in agricultural systems.}, }
@article {pmid42023843, year = {2026}, author = {Olagoke, O and Zheng, X and Chung, S and Mengistie, HD and Asfaha, K and Read, TD and Dean, D}, title = {Phylogenetic diversity, functional pathways, and network interactions of ocular chlamydia-like organisms (CLOs) in trachoma-endemic Ethiopia.}, journal = {mBio}, volume = {}, number = {}, pages = {e0053426}, doi = {10.1128/mbio.00534-26}, pmid = {42023843}, issn = {2150-7511}, abstract = {Trachoma is the leading infectious cause of blindness worldwide and classically attributed to Chlamydia trachomatis (Ct). However, other members of the phylum Chlamydiae, particularly environmental chlamydia-like organisms (CLOs), may modulate ocular ecology and influence disease outcomes. Here, we investigated CLO distribution, phylogeny, and microbiome associations among 1,059 individuals from trachoma-endemic communities in Ethiopia using targeted 16S rRNA sequencing and metagenomic shotgun sequencing. CLOs were detected in 249 (23.3%) participants of all ages and sexes and were significantly less likely to be associated with Ct or trachomatous scarring (TS) and trichiasis (TT). Phylogenetic analyses revealed extensive CLO diversity with six novel phylotypes, the most abundant of which was ancestral to Sorochlamydiaceae-a family linking pathogenic Chlamydiaceae, which includes the genus Chlamydia, and symbionts of protists. CLO-positive microbiomes exhibited significantly greater species richness and evenness with distinct differences in community composition relative to CLO-negative microbiomes. These effects were most pronounced among males and older adults. Functional profiling revealed widespread depletion of biosynthetic and metabolic pathways in CLO-positive microbiomes, particularly in participants with TS/TT, suggesting reduced community biosynthetic capacity and niche modification. Species interaction network analyses demonstrated substantial reorganization of microbial associations in the presence of CLOs with increased connectivity and centrality compared to CLO-negative networks. These findings identify CLOs as prevalent, phylogenetically diverse, and ecologically influential members of the microbiome. Their inverse association with Ct and TS/TT underscores the importance of considering intracellular symbionts beyond Ct in understanding conjunctival microbial ecology, resilience, and trachoma pathogenesis and for designing novel control strategies.IMPORTANCETrachoma caused by Chlamydia trachomatis (Ct) remains the leading infectious cause of blindness globally. While control efforts focus exclusively on Ct, other members of the phylum Chlamydiae, such as chlamydia-like organisms (CLOs), inhabit mucosal surfaces but remain understudied in the eye. Using targeted 16S rRNA and metagenomic shotgun sequencing of conjunctival samples from villagers in trachoma-endemic Ethiopia, CLOs were prevalent (23.3%; 249/1,059), phylogenetically diverse, including novel Chlamydiae phylotypes, and inversely associated with both Ct infection and severe scarring disease. CLO microbiomes had increased microbial diversity, altered community composition, depleted metabolic pathway abundance, and reorganized species interaction networks compared to CLO-negative microbiomes. These findings challenge the singular focus on Ct in trachoma control and research and suggest that CLOs represent ecologically significant members of the conjunctival microbiome. Further research on their interactions with ocular microbial communities could reveal new insights into trachoma pathogenesis and inform more holistic approaches to disease control.}, }
@article {pmid42023847, year = {2026}, author = {Imaura, Y and Yamamoto, K and Kamikawa, R and Yoshida, T}, title = {Diversity and geographical distribution of potential carbon monoxide oxidizers using molybdenum-containing enzymes in the ocean.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0006226}, doi = {10.1128/msphere.00062-26}, pmid = {42023847}, issn = {2379-5042}, abstract = {Carbon monoxide (CO) evolves from photochemical or thermal reactions in the ocean. It is estimated that 90% of oceanic CO is consumed by CO-oxidizing prokaryotes, which convert CO to carbon dioxide using molybdenum-containing CO dehydrogenase (Mo-CODH). Investigation of form I cox, which encodes Mo-CODH, has revealed that oceanic prokaryotes with form I cox (potential cox-containing CO oxidizers: pcox-CO oxidizers) belong to eight phyla and occupy 10%-20% of prokaryotes. However, previous studies may have overestimated their diversity due to the use of less stringent criteria, and their ecology remains poorly understood. In this study, we characterized pcox-CO oxidizers by identifying form I cox from prokaryotic genomes reconstructed from the ocean. We used criteria that considered the phylogeny of Cox, their active site motifs, and the operon structure of cox. As a result, 233 species from nine phyla, which included 207 species unknown to be pcox-CO oxidizers, were found. We investigated the biogeography of each species and found 34 species that dominate in particular oceanic regions. Among the 34 species, 11 co-occurred with either of 20 prokaryotic species, and the co-occurring partners varied among species. No functional genes except those related to CO oxidation were shared between the 11 species, which implied the absence of common molecular basis that underlies ecological interaction between pcox-CO oxidizers and other prokaryotes. Finally, we performed absolute quantification of four species of pcox-CO oxidizers that were predicted to be dominant in Osaka Bay, Japan. It showed that pcox-CO oxidizers occupied over 8.49% of the bacterial community.IMPORTANCEThe ocean is a source of carbon monoxide (CO), an indirect greenhouse gas that supports the accumulation of methane and the production of a precursor of tropospheric ozone. The primary sink of CO in the ocean is prokaryotic CO oxidizers which possess molybdenum-containing CO dehydrogenase (Mo-CODH). Understanding CO flux therefore requires ecological characterization of prokaryotes carrying cox, which encode Mo-CODH. We provide a comprehensive, well-curated catalog of such prokaryotes (potential cox-containing CO oxidizers: pcox-CO oxidizers) in the ocean that not only revealed their diversity but also enabled species-specific ecological assessments. Co-occurrence analyses and genomic analysis of pcox-CO oxidizers uncovered substantial variation in their co-occurring prokaryotic partners and functional gene repertoires. The lack of shared co-occurrence and conserved genes suggests that CO oxidation via Mo-CODH does not mediate ecological interactions. These findings provide a foundation for future studies of pcox-CO oxidizers and offer new insight into ecological roles of CO oxidizers.}, }
@article {pmid42025567, year = {2026}, author = {Araujo, ASF and de Medeiros, EV and da Costa, DP and Mendes, LW and Cherubin, MR and Beirigo, RM and Lambais, GR and Melo, VMM and Santana, RM and Kavamura, VN and Pereira, APA}, title = {Soil biodiversity first: reframing desertification and restoration governance in Brazil's semiarid region.}, journal = {Trends in ecology &amp; evolution}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tree.2026.04.004}, pmid = {42025567}, issn = {1872-8383}, abstract = {Desertification in Brazil's Caatinga is driven by largely overlooked belowground degradation. Integrating whole-soil microbial indicators into policy enables earlier diagnosis, function-based restoration, and climate-resilient dryland management. We discuss how soil biodiversity can be positioned as an early indicator, a restoration target, and a governance tool within the Caatinga Microbiome Initiative.}, }
@article {pmid42026383, year = {2026}, author = {Owen, EAM and Griffiths, RI and Golyshin, PN and Chernikova, TN and Kurr, M}, title = {Patterns in Marine Fungal Diversity and Community Structure on Native Versus Invasive Macroalgae at a Local Geographic Scale.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02781-8}, pmid = {42026383}, issn = {1432-184X}, support = {81280//European Regional Development Fund (ERDF)/ ; 81280//European Regional Development Fund (ERDF)/ ; }, }
@article {pmid42027463, year = {2026}, author = {Drago, L and De La Motte, LR}, title = {The eye's coral reef: toward a planetary-health agenda for ocular-microbiome stewardship.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1816460}, pmid = {42027463}, issn = {1664-302X}, abstract = {Coral reefs and the human ocular surface represent ecologically distinct yet structurally comparable microbial ecosystems in which resilience depends on finely regulated host-microbe interactions. In coral reef science, microbial shifts precede visible bleaching and ecosystem collapse, enabling the development of predictive stress indices such as Degree Heating Weeks (DHW). Comparable principles are emerging in host-associated, low-biomass microbiomes, where subtle perturbations may trigger disproportionate functional consequences. Here, we propose a systems-level conceptual framework linking coral reef holobionts and the ocular surface as sentinel ecosystems governed by cumulative stress, threshold dynamics, and microbial instability. We introduce two heuristic constructs-the Cumulative Desiccating Load (CDL) and the Ocular Dysbiosis Sentinel Index (ODSI)-to frame dysbiosis as a trajectory of resilience loss driven by cumulative perturbations. Aging-related conditions such as age-related macular degeneration are discussed as examples of microbial and metabolic senescence within the human holobiont, conceptually paralleling coral reef decline under chronic sublethal stress. By integrating environmental and host-associated microbiome research within a planetary-health perspective, this article advances a resilience-oriented systems framework applicable across biological scales.}, }
@article {pmid42029022, year = {2026}, author = {Bornbusch, SL and Muletz-Wolz, CR}, title = {Applying microbial ecology frameworks to microbial therapies for wildlife.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0059825}, doi = {10.1128/msystems.00598-25}, pmid = {42029022}, issn = {2379-5077}, abstract = {Microbial ecology is increasingly incorporated into human and animal medicine via the study and purposeful manipulation of host-associated microbiomes. Microbial therapies-treatments with the aim of beneficially modulating microbiomes-are a burgeoning area of research and industry. These microbial therapies include prebiotic dietary items, live probiotics, and whole microbiota transplants (e.g., fecal microbiota transplants). Although microbial therapies for humans and domestic animals are now widely produced for commercial use and application, evidence supporting the efficacy of commercial microbial therapies is mixed. We suggest that microbial therapies are most effective when paired with concepts from ecology and rigorous empirical research. This is particularly relevant for the development and use of microbial therapies in wildlife animal species, in which we see large-scale variation in microbial communities across hosts of varying ecologies. Identifying and developing microbial therapies that can simultaneously be accessible and effective in a variety of hosts poses a novel challenge for microbial ecologists, animal scientists, and human and animal medical professionals. In addition to pre- and probiotics, we suggest that whole microbiota transplants provide a method of microbial supplementation that may better align with species-specific microbial ecology. Moving forward, emerging methods used in human medicine such as machine learning, network analysis, and microbiome engineering using high-throughput culturomics will likely be key to identifying and applying functionally relevant (e.g., disease suppressive) microbial taxa for wildlife therapies.}, }
@article {pmid42029730, year = {2026}, author = {Restrepo-Benavides, M and Jiménez, P and Figueras, MJ and Restrepo, S and Zambrano, MM and Pujol, I and Guevara-Suarez, M and Fernández-Bravo, A}, title = {Genomic and Functional Diversity of Pseudoalteromonas Associated with the Tropical Bivalve Anadara Tuberculosa.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02753-y}, pmid = {42029730}, issn = {1432-184X}, }
@article {pmid42019472, year = {2026}, author = {Ayres, ICB and Lima, AV and Rodrigues, AB and Souza, PEL and Nascimento, CHD and Assunção, MAV and Vieira, DVG and Brito, AB and Ribeiro, AG and Guerra, RR and Correia, TBD and Pinto, JAF and Costa, FGP and Carvalho, LRRA and Lima, MR}, title = {Xylanase and phytase as modulators of gut microbiota and phytate degradation in wheat-based diets for meat quail.}, journal = {Poultry science}, volume = {105}, number = {7}, pages = {106935}, doi = {10.1016/j.psj.2026.106935}, pmid = {42019472}, issn = {1525-3171}, abstract = {This study evaluated the interactive effects of xylanase and phytase in corn- or wheat-based diets on growth performance, phytate degradation, digesta pH, and gut microbiota of meat-type quail. A total of 224 European quail were assigned to a 2 × 2 × 2 factorial arrangement with two basal diets (corn-soybean meal or wheat-soybean meal), two xylanase levels (0 or 16,000 BXU/kg), and two phytase levels (0 or 2,000 FTU/kg). Growth performance was evaluated from 7 to 42 d of age, and carcass traits, intestinal pH, inositol phosphate (InsP) concentrations, and gut microbiota were assessed at 42 d. Birds fed wheat-based diets exhibited greater body weight gain and improved feed conversion compared with those fed corn-based diets (P < 0.05). Phytase and xylanase supplementation enhanced phytate degradation, reduced concentrations of higher-order inositol phosphates (InsP6-InsP4), and modified digesta pH (P < 0.05), with more pronounced effects in wheat-based diets. Alpha diversity analysis indicated no effect of treatments on bacterial richness (Chao1), whereas Shannon diversity differed markedly among treatments (P < 0.001), indicating changes in microbial evenness. Beta diversity analyses revealed a clear separation of microbial communities according to basal diet and enzyme supplementation (PERMANOVA, P = 0.001). Correlation network analysis demonstrated matrix-dependent reorganization of microbial interactions in response to phytase and xylanase. In conclusion, phytase and xylanase supplementation modulated gut microbial community structure and phytate degradation in a basal diet-dependent manner. Productive performance responses were influenced by interactions between enzyme supplementation and diet composition. These findings highlight the importance of enzyme-matrix interactions in shaping nutrient availability and intestinal microbial ecology in meat-type quail.}, }
@article {pmid42020426, year = {2026}, author = {Seki, D and Pollak, S and Kujawska, M and Kiu, R and Acuna-Gonzalez, A and Crouch, LI and Bakshani, CR and Chivers, PT and Mommers, M and van Best, N and Penders, J and Hall, LJ}, title = {Human milk oligosaccharide mediates mutualism between Escherichia coli and Bifidobacterium bifidum.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42020426}, issn = {2041-1723}, support = {220876/Z/20/Z//Wellcome Trust (Wellcome)/ ; }, mesh = {*Milk, Human/chemistry/metabolism ; Humans ; *Oligosaccharides/metabolism ; *Escherichia coli/physiology/growth &amp; development/genetics/metabolism ; *Symbiosis/physiology ; Female ; *Bifidobacterium bifidum/physiology/genetics/metabolism/growth &amp; development ; Gastrointestinal Microbiome ; Feces/microbiology ; Infant, Newborn ; Infant ; Breast Feeding ; Trisaccharides/metabolism ; Male ; Metagenomics ; Adult ; }, abstract = {Infant gut microbiota development involves frequent colonization by Enterobacteriaceae, particularly Escherichia coli, yet their ecological role in healthy infants is unclear. Here, we analyse longitudinal stool samples from healthy, term-born, breastfed infants (n = 41) and related mothers (n = 30) using shotgun metagenomics and novel computational approaches. Strain-resolved profiling indicates that Bifidobacterium species are frequently shared within families, whereas E. coli derive from external sources, but often persist within individuals. Despite differing ecological strategies, these genera co-exist and share evolutionary adaptations related to lactose acquisition in the infant gut. In vitro, we demonstrate that interactions between E. coli and Bifidobacterium bifidum are mutualistic in co-culture, where E. coli supplies cysteine to its auxotrophic partner, facilitating cooperative degradation of 2'-fucosyllactose, the predominant human milk oligosaccharide. In turn, the liberated monosaccharides sustain E. coli growth, highlighting a cooperative cross-feeding interaction that may contribute to regulating E. coli abundance within the infant host.}, }
@article {pmid42020537, year = {2026}, author = {Zarrabian, M and Sherif, SM}, title = {Taxonomic Restructuring of Rhizosphere Guilds is Driven By Agricultural Management and Scion Genotype in Apple.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02774-7}, pmid = {42020537}, issn = {1432-184X}, support = {33522-38314//Biotechnology Risk Assessment Research Grants Program (BRAG)/ ; }, }
@article {pmid42020762, year = {2026}, author = {Signorile, L and Yaghoubi Khanghahi, M and Calabrese, FM and Crecchio, C and Addesso, R and Chiarini, M and Sofo, A}, title = {Land use and Season Drive Compositional Shifts in Cyanobacteria-dominated Soil Bacterial Communities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02759-6}, pmid = {42020762}, issn = {1432-184X}, }
@article {pmid41807604, year = {2026}, author = {Santacroce, M and Baranek, J and Adamski, Z and Trzebny, A and Dabert, M and Bufo, SA and Scrano, L}, title = {Prevalence of Bacillus species in the lytic cultural heritage of Santa Lucia alle Malve Rupestrian Church.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41807604}, issn = {2045-2322}, abstract = {UNLABELLED: Santa Lucia alle Malve (SLM) is a unique rupestrian heritage site, entirely carved into limestone. This monument, which was a church in the ancient settlement of Benedictine nuns over a millennium ago in southern Italy, holds exceptional value not only from an architectural and cultural perspective but also in terms of its microbial ecology. Until now, the specific microbiota of this site had remained unexplored. In this study, the bacterial community inhabiting the interior walls of Santa Lucia alle Malve was investigated using a metagenomic approach, alongside the isolation and comprehensive characterization of cultivable strains from various sampling sites. Both methodologies consistently revealed a dominance of spore-forming bacteria from the phylum Bacillota, particularly the genus Bacillus. Notably, most of the cultivable strains belonged to the Bacillus cereus sensu lato group and the Bacillus. licheniformis clade. Despite the high genetic similarity among these microorganisms, each strain exhibited a unique set of phenotypic traits, highlighting the potential complexity of the SLM metabolome. Additionally, two isolates were identified as Bacillus thuringiensis, entomopathogenic bacteria with possible applications in biological pest management. Finally, Staphylococcus warneri, a human skin commensal found in the church, suggests human influence on the microbial landscape.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-41655-4.}, }
@article {pmid42010313, year = {2026}, author = {Qi, YL and Zou, DY and Hou, JJ and Zhang, ZF and Du, H and Feng, XY and Pan, YP and Zhang, CJ and Liu, Y and Li, M}, title = {A seven-year metagenomic genome catalogue of mangrove and mudflat sediments from the Futian Reserve, China.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07291-3}, pmid = {42010313}, issn = {2052-4463}, support = {42430707//National Natural Science Foundation of China/ ; 32370055//National Natural Science Foundation of China/ ; 32225003, 32393970, 92251306//National Natural Science Foundation of China/ ; JCYJ20230808105711023//General Program supported by Shenzhen Natural Science Foundation in Basic Research Fund/ ; 2023B0303000017//Guangdong Major Project of Basic and Applied Basic Research/ ; 2022B002//Shenzhen University 2035 Program for Excellent Research/ ; 2024T001//Shenzhen University Special Funding Initiative/ ; }, abstract = {Mangrove wetlands are ecologically and biogeochemically important "blue-carbon" ecosystems, yet long-term genomic resources for their microbial communities remain scarce. Here we present a seven-year (2017-2023) metagenomic dataset from the Futian Mangrove National Nature Reserve, China, comprising 65 sediment samples collected from paired habitats (mangrove forest and adjacent mudflat) across multiple depths. Sequencing produced ~5.3 Tbp of data, from which 6,922 metagenome-assembled genomes (MAGs) were reconstructed and dereplicated into 3,404 representative genomes (336 Archaea and 3,068 Bacteria). Quality control ensured that all genomes achieved medium- or high-quality standards, with assembly statistics and read recruitment rates supporting robustness and representativeness. Taxonomic annotation revealed broad phylogenetic diversity spanning 13 archaeal and 69 bacterial phyla, with many lineages lacking formal nomenclature and representing potential novel taxa. All raw sequences, genome assemblies, and detailed metadata have been deposited in public repositories, providing a standardized, time-resolved resource for comparative genomics, microbial ecology, and ecosystem restoration studies in coastal wetlands.}, }
@article {pmid42012223, year = {2026}, author = {Martin, G and Slanzon, GS and Dhungana, I and Prasadh, RR and Pires de Paula, CC and Nguyen, NH}, title = {Navigating complexity: key considerations for studying fungal-bacterial interactions.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0172825}, doi = {10.1128/msystems.01728-25}, pmid = {42012223}, issn = {2379-5077}, abstract = {Fungal-bacterial interactions are widespread phenomena that are currently gaining attention across diverse research fields. But what are interactions, how do we identify them, and why should we adopt ecological theory when studying them? While microbial interactions are often conceptualized and characterized as static properties, these relationships are dynamic and complex. They are shaped by the interplay of numerous variables, which themselves fluctuate over space and time, that scale from molecules to ecosystems. In this perspective, we discuss the theoretical and practical challenges of studying the interactions between these two ubiquitous and diverse groups of microorganisms and propose a framework grounded on mechanistic and systems approaches rather than relying on correlations or fragmented practices. We hope to inspire efforts to build and integrate a more comprehensive understanding of this fascinating and quickly growing subdiscipline of microbial ecology.}, }
@article {pmid42014453, year = {2026}, author = {Treichel, NS and Pauvert, C and Séneca, J and Pjevac, P and Berry, D and Penders, J and Hitch, TCA and Clavel, T}, title = {Benchmarking of shotgun sequencing depth reveals the potential and limitations of shallow metagenomics and strain-level analysis.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {42014453}, issn = {2058-5276}, support = {460129525//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 445552570//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 10.55776/DOC69//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; 10.55776/COE7//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; }, abstract = {Shotgun metagenomics can provide both taxonomic and functional insights, but benchmarking is necessary to determine the sequencing depth appropriate for specific analyses. Here we used complex mixtures of DNA from cultured bacteria and analysed taxonomic composition, strain-level resolution and functional profiles at up to 11 sequencing depths (0.1-50.0 Gb). Reference-based analysis provided accurate strain-level taxonomy at 0.5-1.0 Gb. By contrast, de novo metagenome-assembled genome (MAG) reconstruction required deep sequencing (>10 Gb), and even MAGs deemed high quality by standard metrics were chimeric, with 54.5-81.8% accurately representing original strains, depending on the bioinformatic approach. Functionally, 2 Gb provided reliable insights at the pathway level for each of the mock communities tested, but sufficient proteome coverage was achieved only at or above 10 Gb. Library preparation and host DNA contamination were identified as confounders in shallow metagenomic analysis. This analysis highlights the potential and limitations of shallow metagenomics and provides guidance to accurately capture strain-level diversity using MAGs.}, }
@article {pmid42014730, year = {2026}, author = {Wang, Y and Yu, P and Huang, ES and Lu, DC and Zhang, W}, title = {Decoding a Microbial Community for Healthy Kelp: 403 MAGs from the World's Largest Kelp Farming Region.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07250-y}, pmid = {42014730}, issn = {2052-4463}, support = {2023-004//2023 Weihai Key Postdoctoral Research Funding Program/ ; }, abstract = {Kelp is economically and ecologically significant, with its organic nutrient-rich aquaculture water harboring diverse microbial communities that critically influence kelp health and productivity. To characterize these communities, we collected ten water samples from major kelp farming areas and reconstructed 403 medium- to high-quality Metagenome-Assembled Genomes (MAGs). Of these, 110 (27.3%) met high-quality criteria (completeness >90%, contamination <5%). Phylogenomic analysis classified these MAGs into 21 archaeal and 382 bacterial species across 19 phyla, with Pseudomonadota (n = 217), Bacteroidota (n = 74), and Patescibacteria (n = 24) as the dominant groups. UpSet plot analysis revealed the presence of a core set of 30 MAGs across all sampling sites. Notably, diseased samples exhibited a marked increase in Pseudomonadota MAGs, suggesting their potential as biomarkers for disease monitoring. Together, these findings provide foundational insights into the microbial ecology of kelp aquaculture systems, supporting improved disease management and sustainable practices.}, }
@article {pmid42014792, year = {2026}, author = {Głowska-Patyniak, E and Ostrowska, K and Olechnowicz, J and Hubert, J and Konecka, E and Sharma, AK and Som, A and Dabert, M and Trzebny, A}, title = {A Wolbachia lineage likely representing a new supergroup (Y) dominates the microbiome of the quill mite Syringophilus bipectinatus Heller, 1880 (Acariformes: Syringophilidae).}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-48644-7}, pmid = {42014792}, issn = {2045-2322}, support = {UMO-2021/03/Y/NZ8/00060//The National Science Centre of Poland/ ; }, abstract = {The microbiome plays a key role in animal biology, including host reproduction. Quill mites (Acariformes: Syringophilidae) are understudied ectoparasites of birds, with many species exhibiting strongly female-biased sex ratios. Previous studies have identified unique strains of Wolbachia and Spiroplasma in quill mites, both known to manipulate host reproduction in other arthropods. To further investigate this association, we analyzed the microbiome of Syringophilus bipectinatus Heller, 1880, a relatively early-diverging quill mite species parasitizing the Red Junglefowl (domestic type) (Galliformes: Phasianidae), using 16S rRNA gene profiling. We categorized mite specimens by sex and developmental stage to test for potential associations between microbiome composition and sex ratios. We report the first detection of Wolbachia in S. bipectinatus with a single amplicon sequence variant (ASV) consistently detected across all analyzed samples, accounting for 56-99% of total bacterial sequence reads. Phylogenetic analysis based on 16S rRNA gene and four protein-coding genes (fbpA, ftsZ, gatB, hcpA) recovered this strain as a deeply divergent Wolbachia lineage that does not cluster with any previously described supergroup. This lineage is therefore interpreted as likely representing a novel Wolbachia supergroup (Y), although its formal status requires further validation using genome-scale data. Its consistent presence across both sexes and all developmental stages suggests a stable and potentially obligate association, although its functional role remains to be determined. In addition, we identified bacterial taxa also reported from avian hosts, including potentially pathogenic genera such as Arcobacter, highlighting the complex microbial ecology of quill mites.}, }
@article {pmid42015346, year = {2026}, author = {Li, Z and Samui, S and Liu, J and Yang, Y and Liu, X and Chen, Q and Li, J and Gopinath, D and Luo, P and Shan, D}, title = {Gut microbiome and metabolic health: mechanisms and precision interventions.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2644677}, doi = {10.1080/19490976.2026.2644677}, pmid = {42015346}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; Fecal Microbiota Transplantation ; Probiotics ; Precision Medicine ; *Metabolic Diseases/microbiology/metabolism/therapy ; Prebiotics/administration &amp; dosage ; Obesity/microbiology/metabolism ; Diabetes Mellitus, Type 2/microbiology/metabolism ; Metabolic Syndrome/microbiology/metabolism ; }, abstract = {The gut microbiome is increasingly recognized as a fundamental regulator of metabolic health, shaping energy balance, insulin sensitivity, inflammatory tone, and inter-organ communication through a broad spectrum of microbial metabolites that engage host signaling pathways. In this review, we synthesize current mechanistic insights into how gut microbial communities shape metabolic function, with particular emphasis on short-chain fatty acids, secondary bile acid signaling, gut barrier integrity, immune modulation, and the microbiota-gut-brain-pancreas axis. We further summarize disease-associated alterations in microbial composition and function across obesity, type 2 diabetes, metabolic dysfunction-associated steatotic liver disease, and metabolic syndrome, highlighting key microbial and metabolic features that contribute to metabolic dysfunction. Evidence from germ-free models, fecal microbiota transplantation studies, and strain-level interventions suggests that shifts in microbial ecology may causally shape metabolic outcomes. We also critically evaluate emerging microbiome-centered therapeutic strategies, including targeted probiotics, prebiotics, dietary modulation, and fecal microbiota transplantation, while addressing factors that underlie inter-individual variability in treatment responses. In addition, we discuss the growing influence of multi-omics technologies, microbial metabolic modeling, and machine learning approaches in advancing precision microbiome medicine. To integrate these advances within a coherent framework, we outline a precision microbiome intervention pipeline linking multidimensional profiling to functional stratification and targeted therapeutic design. We also introduce a conceptual Precision Microbiome Intervention Triangle to mechanistically explain heterogeneity in responses to microbiome-targeted therapies. Collectively, these insights establish and position the gut microbiome as both a mechanistic driver and a modifiable therapeutic target in metabolic disease, and highlight key challenges and future directions for the development of personalized microbiome-based metabolic interventions.}, }
@article {pmid42017823, year = {2026}, author = {Wilkie, I and Von Possel, N and Sauma-Sánchez, T and Reintjes, G and Orellana, LH}, title = {Conserved glycan-utilization strategies shape Akkermansiaceae success across aquatic and gut ecosystems.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag096}, pmid = {42017823}, issn = {1751-7370}, abstract = {Elucidating interaction mechanisms and substrate specialization is central to understanding bacterial adaptation across ecological niches. Specialized mucin-degrading bacteria of the genus Akkermansia are widely recognized for their beneficial roles in the human gut, yet it remains unclear whether this specialization is unique to the gut or reflects a conserved ecological strategy across different hosts and environments. Here, we show that members of the family Akkermansiaceae share a deeply conserved genetic and mechanistic framework enabling colonization across gut and aquatic ecosystems. Comparative genomics of Akkermansiaceae representatives revealed niche-specific gene repertoires tightly adapted to substrate source and availability. Marine representatives encode distinct combinations of CAZymes and comparatively expanded sulfatase repertoires that enable the degradation of sulfated polysaccharides such as fucoidan, a recalcitrant substrate linked to carbon sequestration. Structural predictions and comparisons identified a conserved molecular system centered on a type IV-like pilus that mediates attachment to complex, fucose-rich glycans. The genes underlying this system are syntenic with the recently described mucin utilization locus in Akkermansia muciniphila, revealing an evolutionary continuity between aquatic and gut lineages. Seawater incubations with fluorescently labeled substrates confirmed fucoidan uptake and degradation by marine Akkermansiaceae. Together, these results reveal a unified glycan-utilization strategy spanning the environmental breadth of Akkermansiaceae and provide a mechanistic framework linking ecological success in marine environments to traits associated with probiotic functions in the human gut.}, }
@article {pmid42018003, year = {2026}, author = {Cui, Y and Zhang, Y and Shao, C and Long, H and Cao, W and Wang, Y and Zhu, J and Hu, X and Geng, X and Sun, H}, title = {Identification and Growth-Promoting Traits of Bacillus Species within the Bacterial Community Structure Isolated From Saline-Alkali Soil Based on High-Throughput Analysis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02775-6}, pmid = {42018003}, issn = {1432-184X}, support = {20240305009YY//Jilin Provincial Key Research and Development Plan Project/ ; }, }
@article {pmid42018159, year = {2026}, author = {Agan, A and Orumaa, A and Drenkhan, R and Köster, K and Stanturf, JA and Tedersoo, L and Tullus, T and Metslaid, M}, title = {Post-fire Succession and Soil Chemical Properties Shape Soil Fungal Community Structure and Diversity in Hemiboreal Scots Pine Forests in Estonia.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02769-4}, pmid = {42018159}, issn = {1432-184X}, support = {PRG1615//Eesti Teadusagentuur/ ; PRG1586//Eesti Teadusagentuur/ ; }, }
@article {pmid42019285, year = {2026}, author = {Yang, C and Lin, X and Xu, JL and Ferreira, ROG and Van de Wiele, T and Marinelli, L and Canga, EM and Gowen, AA}, title = {Deep Learning-Assisted identification and quantification of cell-associated microplastics using darkfield hyperspectral imaging.}, journal = {Talanta}, volume = {308}, number = {}, pages = {129864}, doi = {10.1016/j.talanta.2026.129864}, pmid = {42019285}, issn = {1873-3573}, abstract = {Microplastics (MPs) interaction with human cells poses potential health risks yet quantifying this process and its extensiveness remains challenging. In this study, we developed an automated strategy combining darkfield hyperspectral imaging (HSI) with a deep learning pipeline to detect and quantify cell-associated polystyrene (PS) microplastics at the single-cell level. This pipeline includes 3 main steps: the Mask R-CNN segmented individual cells, the least-squares support vector machine (LS-SVM) distinguished microplastic particles from cellular material, and the circular Hough transform (CHT) was used to count the particles detected within segmented cellular regions. This image analysis pipeline demonstrated high performance: Mask R-CNN detected cells with 95% precision, LS-SVM classified particle spectra with 99.7% accuracy, and the CHT detected particles with a precision of 99.6%. Together, these components enabled reliable quantification of particles within cells. Results showed a dose-dependent effect on the number of PS MPs in Caco-2 cells. At lowest concentrations (1 × 10[3] particles/mL), 21% of cells were detected with PS, while no impact on cell viability was observed. In contrast, at higher concentrations (1 × 10[8] and 1 × 10[9] particles/mL), 100% of cells were detected with PS and showed significant reductions in cell viability. Our findings demonstrated that integrating darkfield HSI with deep learning provides a robust quantitative assessment of MPs and cells interaction at single-cell resolution. This approach may be adaptable to other particle types and cell lines, subject to retraining and validation, offering a valuable tool for microplastic toxicology studies and complementing traditional high-throughput assays in evaluating the level of cell association and dose-response relationships.}, }
@article {pmid42003613, year = {2026}, author = {Pang, T and Li, B and Sun, Q and Deng, Z and Cao, C and Kang, Z and Andika, IB and Sun, L}, title = {A beneficial endornavirus enhances the fitness of the phytopathogenic fungus Rhizotonia solani.}, journal = {mBio}, volume = {}, number = {}, pages = {e0016626}, doi = {10.1128/mbio.00166-26}, pmid = {42003613}, issn = {2150-7511}, abstract = {Although viruses are primarily characterized as pathogenic agents, certain viruses confer advantages to their hosts. The extent to which a virus can improve host biological performance, however, remains a fascinating topic in virology. An endornavirus, Rhizoctonia solani endornavirus IM (RsEV-IM), was identified as prevalent in . Rhizoctonia solani isolates obtained from potato plants. Comparative analysis with a virus-free isogenic strain demonstrated that RsEV-IM infection enhances mycelial growth, sclerotium formation, stress tolerance, and fungal virulence across multiple plant species. Inoculation tests involving numerous R. solani strains confirmed that only RsEV-IM-infected strains exhibited high pathogenicity, independent of other mycovirus infections. Additionally, the secreted protein fraction of RsEV-IM-infected fungus contained elevated levels of various proteins, including those involved in cell wall degradation. This fraction not only facilitated R. solani infection but also suppressed the growth of other fungi and bacteria. These findings position RsEV-IM as a beneficial virus that widely enhances its host's biological fitness. From both pathological and ecological perspectives, these observations are significant, as they reveal that a mycovirus can serve as a key virulence determinant in fungal populations and potentially shape microbial community dynamics in natural environments.IMPORTANCEFungal pathogenicity and ecological traits have long been thought to be primarily governed by endogenous genetic factors. However, this study reveals a mutualistic relationship between an endornavirus (RsEV-IM) and Rhizoctonia solani, demonstrating that viral infection enhances fungal virulence and ecological fitness. RsEV-IM stimulates fungal growth and the secretion of cell wall-degrading enzymes, resulting in a severe disease phenotype. Ecologically, RsEV-IM-infected fungi potentially gain a competitive advantage over soil microbiota. These findings present a key example of a virus acting as an essential extrachromosomal determinant of fungal pathogenicity and ecosystem interactions. Our results advance the understanding of fungal virulence mechanisms and underscore the broader significance of beneficial virus-fungus associations in agriculture and microbial ecology.}, }
@article {pmid42003634, year = {2026}, author = {Armstrong, C and Eagle, M and Wakelin, SA}, title = {Genome sequences of bacteria isolated from Pinus radiata-associated soils.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0149825}, doi = {10.1128/mra.01498-25}, pmid = {42003634}, issn = {2576-098X}, abstract = {Complete bacterial genomes and functional annotations of 20 isolates from planted Pinus radiata forest soils in New Zealand are reported. These genomes expand the taxonomic and functional representation of forest soil microbes in genome databases, supporting future microbial ecology studies.}, }
@article {pmid42003643, year = {2026}, author = {Galib, FA and Kafi, AA and Biswas, S and Hasnat, S and Gupta, DR and Hoque, MN and Rahman, MM and Rahman, MM and Islam, T}, title = {Genome sequence of Escherichia coli H1G2: a B1 lineage isolated from the gut of Hilsa shad (Tenualosa ilisha) of Bangladesh.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0013826}, doi = {10.1128/mra.00138-26}, pmid = {42003643}, issn = {2576-098X}, abstract = {We characterized the 4.8 Mbp genome of Escherichia coli H1G2, a B1 lineage isolated from the gut of Bangladesh's national fish, Hilsa (Tenualosa ilisha). The complete assembly reveals specialized genes for sugar metabolism and adhesion, facilitating niche-specific colonization, thereby providing insights into the microbial ecology of this commercially significant species' gastrointestinal tract.}, }
@article {pmid42004255, year = {2026}, author = {Yuan, C and Wu, X and Yang, Y and Han, Y and Su, C and Paengkoum, P and Wang, X and Zhao, J and Lu, S and Chen, H and Wang, D and Xiao, W and Long, Y}, title = {Effects of dietary allicin supplementation on nutrient digestion and gastrointestinal health of Guizhou black goats.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {25}, number = {}, pages = {397-413}, pmid = {42004255}, issn = {2405-6383}, abstract = {This study aimed to reveal the effects of allicin on nutrient digestion, gastrointestinal enzyme activity, rumen fermentation parameters, gastrointestinal morphology, intestinal barrier function, and gastrointestinal microbial ecology of Guizhou black goats. Thirty-two male Guizhou black goats, each aged five months, with an initial body weight of 18.28 ± 0.41 kg, were divided into one of four groups in a completely randomized design: control (CON, without allicin), low allicin (L; 0.5 g/d per head), medium allicin (M; 0.75 g/d per head), and high allicin (H; 1 g/d per head), respectively. Each group consisted of eight replicates with one growing goat per replicate. The experiment lasted for 75 d, including a 15-d acclimation period and a 60-d experimental period. The results showed that the apparent digestibility of crude protein (CP), dry matter (DM), and neutral detergent fiber (NDF) was highest in the M group, being significantly higher than those in the CON group (P < 0.05). Moreover, ruminal cellulase and cellobiase activities, jejunal trypsin activity, cecal cellulase activity, ruminal total volatile fatty acids (TVFA), acetate, propionate, and butyrate concentrations were all highest in the M group (P < 0.05). In contrast, ruminal ammoniacal nitrogen (NH3-N) concentration was the opposite (P = 0.015). As allicin inclusion increased, the jejunal trypsin activity and ruminal butyrate concentration exhibited linear responses (P < 0.05), while the apparent digestibility of DM and NDF, rumen TVFA, acetate, and propionate concentrations, as well as cellulase and cellobiase activities were affected quadratically (P < 0.05). In the jejunal mucosa, the protein expression levels and the relative mRNA expression levels of claudin 1, claudin 4, and ZO-1 were higher in the M group than in the CON group (P < 0.05). As allicin supplementation increased, claudin 1, claudin 4, and ZO-1 protein expressions exhibited both linear and quadratic responses (P < 0.001), whereas the relative mRNA expression levels were modulated solely by the quadratic term (P < 0.05). Moreover, the L and M groups had significantly greater papillae height and muscle layer thickness than the CON group (P < 0.05), and papillae width increased in a quadratic manner (P = 0.029). However, the M group showed increased villus density compared with the CON group (P = 0.026), with significant quadratic effects on papillae density and villus height (P < 0.05). Importantly, allicin also improved the gastrointestinal microecological balance by reconstructing the gastrointestinal microbial composition. In conclusion, allicin improves gastrointestinal health by regulating gastrointestinal microbial composition, promoting nutrient absorption and tissue development, enhancing rumen fermentation and gastrointestinal enzyme activities, and strengthening the intestinal barrier. The optimal supplementation level of allicin is 0.75 g/d per head.}, }
@article {pmid42004407, year = {2026}, author = {Chu, D and Liu, N and Liu, Q and Li, X and Yang, H and Zhu, N and Liu, Z and Wang, R and Yuan, S and Fu, H}, title = {Diet-Driven Divergence in Gut Microbiota Variation Between Two Sympatric Gerbil Species.}, journal = {Ecology and evolution}, volume = {16}, number = {}, pages = {e73367}, pmid = {42004407}, issn = {2045-7758}, abstract = {Gut microbiota provide various benefits to their mammalian hosts; however, knowledge regarding interspecific differences in gut microecology remains limited. This study employed 16S rRNA sequencing combined with metagenomic functional prediction (potential functions or functional potential) to conduct a comparative analysis of the gut microbial composition and functional adaptability of two sympatrically distributed gerbil species with distinct diets: the herbivorous Rhombomys opimus (RO) and the omnivorous Meriones meridianus (MM). The results revealed that the omnivorous MM exhibited a level of gut microbial alpha diversity comparable to that of the herbivorous RO, whereas RO showed significant enrichment of norank_f__Muribaculaceae, a taxon associated with fiber degradation, and demonstrated higher abundance of genes related to complex fiber degradation. Notably, bacterial genera significantly enriched in the gut of MM, such as Lachnospiraceae_NK4A136_group and Desulfovibrio, may play important roles in maintaining gut health and enhancing chitin degradation efficiency. Furthermore, the abundance of genes related to monosaccharide and chitin degradation was significantly higher in MM than in RO. Functional network analysis indicated that the cellulose degradation gene networks in both gerbil species were predominantly synergistic, but the synergistic effect was stronger in RO than in MM (ratios of positive to negative correlation edges: 2.44: 1.59). Further analysis revealed that the monosaccharide and chitin degradation gene networks in MM both exhibited synergistic interaction patterns (ratios of positive to negative correlation edges: 1.69 and 2.95, respectively), whereas these two networks in RO were primarily antagonistic (ratios of positive to negative correlation edges: 0.831 and 0.73, respectively). This suggests that the gut microbiota of RO are more conducive to digesting complex plant fibers, while those of MM are better adapted for digesting starch and chitin. This differentiation in gut microbiota optimizes the utilization of different food resources by the two species, thereby promoting their sympatric coexistence. This study enhances our understanding of the adaptive mechanisms of gut microecology in rodents with different diets and provides an important foundation for further research on the microbial ecology of wild rodents and the mechanisms underlying sympatric species coexistence.}, }
@article {pmid42008316, year = {2026}, author = {Li, C and Zhou, Y and Jiao, Y and Qian, X and Wang, X and Chen, H and Zhao, L and Zhang, H and Lu, Q}, title = {Therapeutic Promise of the Panax Genus in Ulcerative Colitis: Unraveling the Multitarget Mechanisms of Saponins and Polysaccharides.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c10069}, pmid = {42008316}, issn = {1520-5118}, abstract = {Ulcerative colitis (UC) is a chronic inflammatory bowel disease with a rising global incidence. Panax genus plants, recognized for their anti-inflammatory and immunomodulatory properties, present as a promising therapeutic candidate. This review summarizes the last few decades of research on Panax species, including Panax ginseng, Panax notoginseng, Panax quinquefolius, Panax japonicus, and Panax vietnamensis, for UC management. Therapeutic efficacy is primarily attributed to saponins (e.g., ginsenosides) and polysaccharides, which operate through distinct yet complementary pathways. Advancing beyond traditional single-species investigations, this work adopts a novel genus-wide perspective to elucidate functional synergy between bioactive families. Saponins exert precise immunomodulatory actions by inhibiting intracellular signaling cascades, including NF-κB, MAPK, and NLRP3 pathways, and modulating T-cell differentiation. Conversely, polysaccharides primarily orchestrate intestinal homeostasis at the epithelial interface by reinforcing barrier integrity and regulating microbial ecology. This comparative analysis identifies species-specific therapeutic advantages, establishing a strategic framework for sustainable resource utilization and precision drug development in UC therapy.}, }
@article {pmid42008684, year = {2026}, author = {Wei, Z and Li, C and Song, F and Zhang, X and Li, S and Xu, N and Zhang, J and Luo, Y and Zuo, Y and Jiao, J and He, H and Wang, R and Liu, X and Sun, Z and Yang, Y and Wang, Y and Chang, W and Lou, H and Feng, J and Zhao, K and Zhu, L and Shen, X}, title = {A farnesol-sensing triad in Pseudomonas aeruginosa drives interkingdom predation on Candida albicans via signal transduction.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {17}, pages = {e2529531123}, doi = {10.1073/pnas.2529531123}, pmid = {42008684}, issn = {1091-6490}, support = {32330004//MOST | National Natural Science Foundation of China (NSFC)/ ; 32100034//MOST | National Natural Science Foundation of China (NSFC)/ ; 32470197//MOST | National Natural Science Foundation of China (NSFC)/ ; 32470039//MOST | National Natural Science Foundation of China (NSFC)/ ; 22JHZ008//Shaanxi Fundamental Science Research Project for Chemistry &amp; Biology/ ; CSBAAKF2021005//National Key Laboratory of Crop Stress Resistance and Efficient Production/ ; }, mesh = {*Pseudomonas aeruginosa/metabolism/genetics/physiology/pathogenicity ; *Candida albicans/metabolism/physiology/pathogenicity ; *Farnesol/metabolism ; *Signal Transduction ; Quorum Sensing ; Bacterial Proteins/metabolism/genetics ; Type III Secretion Systems/metabolism/genetics ; Virulence ; Hyphae/metabolism ; Microbial Interactions ; }, abstract = {Microbial interactions, particularly bacteria-fungus interactions, are research hotspots within microbial ecology and pathogenic biology. However, their underlying molecular mechanisms remain poorly understood, especially how bacterial pathogens recognize and exploit fungal signaling molecules for fungal predation. Here, we demonstrate that Pseudomonas aeruginosa employs an integrated tripartite farnesol-sensing system to detect and eliminate Candida albicans hyphae: The chemoreceptor PctA mediates directional migration toward hyphae; the type IV pilus sensor PilJ activates antifungal type III secretion system (T3SS) expression; and the quorum regulator PqsR monitors farnesol levels to coordinate virulence-metabolic switching. This mechanism enables bacteria to convert farnesol into their own signaling language (Pseudomonas quinolone signal) according to fungi status, thereby adaptively modulating their virulence expression and metabolism to cope with complex competitive microbial environments. Furthermore, bioinformatics analysis and functional validation confirm that the PctA-PilJ-PqsR triad is conserved across P. aeruginosa, suggesting that this interkingdom communication is widespread. In conclusion, this study reveals that P. aeruginosa orchestrates a targeted predation strategy against filamentous fungi by coordinating three interkingdom receptors, providing a theoretical foundation and potential molecular targets for understanding of interkingdom communication strategies among microorganisms and the development of signal molecule-based microbial prevention and control technologies.}, }
@article {pmid42009250, year = {2026}, author = {Ramond, P and de Groot, T and Niemann, H and Engelmann, JC}, title = {Community Turnover and Connectivity at Two Study Sites in the North and Wadden Seas: Dynamics From Hours to Seasons.}, journal = {Environmental microbiology}, volume = {28}, number = {4}, pages = {e70310}, doi = {10.1111/1462-2920.70310}, pmid = {42009250}, issn = {1462-2920}, support = {ERC-CoG-772923/ERC_/European Research Council/International ; //Wise NWO/ ; }, mesh = {Seasons ; *Microbiota ; *Seawater/microbiology ; *Geologic Sediments/microbiology ; North Sea ; Ecosystem ; *Bacteria/classification/genetics/isolation &amp; purification ; Temperature ; Salinity ; Oceans and Seas ; }, abstract = {Microbial communities underpin ecosystem processes and biogeochemical cycles in marine ecosystems, yet their spatial and temporal dynamics at hourly scales remain poorly understood. We surveyed two stations from the North Sea (NS) and Wadden Sea (WS), generating six high-frequency time-series datasets across depths and seasons, complemented by sediment cores. Across seasons, the sites in the NS and the WS harbored distinct microbial communities shaped by contrasts in salinity, temperature, and potentially the quantity and lability of organic matter. Connectivity between communities was limited but favoured by known seasonal hydrographic exchanges. Despite taxonomic contrasts between sites, functional turnover remained low, with communities harbouring similar metabolic potential but being adapted to local conditions, suggesting potential functional redundancy. At hourly scales, community turnover was weaker and largely driven by vertical and horizontal mixing between water masses, occasional resuspension from sediments, or a summer bloom from a copiotroph. These shifts were transient and did not disrupt the coupling between taxonomic and functional composition. However, their immediate effects on ecosystem processes, such as organic matter remineralisation and nutrient recycling remain unclear. Continued high-resolution microbiome monitoring, paired with biogeochemical flux measurements, is needed to better predict climate-driven changes in coastal ecosystem functioning.}, }
@article {pmid41997958, year = {2026}, author = {Duan, S and Dong, J and Chen, Y and Yu, L and Liu, S and Yu, R and Du, Z and Shen, Y and Lu, X and Fu, J and Yang, R and Fang, C}, title = {Kombucha inoculated fermentation reshapes microbial ecology and flavour metabolism in Yunnan Arabica coffee.}, journal = {NPJ science of food}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41538-026-00852-1}, pmid = {41997958}, issn = {2396-8370}, support = {Yunnan International Joint Laboratory of Green Health Food (China &amp; Thailand) (grant no.202203AP140011)//Chongye Fang/ ; }, abstract = {This study evaluates the flavor-enhancing effects of kombucha-inoculated fermentation on Coffea arabica L. and uncovers regulatory mechanisms across microbial succession, physicochemical shifts, amino acid remodeling, and volatile formation. Controlled fermentations using kombucha symbiotic consortium for 144 h was comparedwith spontaneous fermentation. At endpoint, bacterial richness in the KT group was 34% higher compared to the CK group. The KT group exhibited a significantly lower pH (4.21) than the CK group (4.95). Komagataeibacter and Zygosaccharomyces were enriched 2-6 fold, while Enterobacter and Aspergillus were suppressed. Kombucha coffee showed lower pH, titratable acidity increased by 64%, and reducing sugars decreased by 43%. Sweet-taste FAAs increased and bitter FAAs decreased, correlating with floral-fruity esters (r ≥ 0.74). Volatiles such as phenylethyl alcohol (42%), phenethyl acetate (200%), and ethyl isovalerate (89%), while off-flavor acids and smoky phenols decreased. Sensory scores improved in floral, fruity, and sweet attributes. Multi-omics linked dominant taxa to upregulated pathways (ester biosynthesis, aromatic amino acid degradation, Maillard products) and key functional genes. These results establish kombucha Inoculated Fermentation as a reproducible, mechanism-based strategy for targeted flavor optimization in speciality coffee and other high-value agricultural products.}, }
@article {pmid41998361, year = {2026}, author = {Thiyagarasaiyar, K and Paul, D and Kerttula, J and Keski-Karhu, M and Soosaar, K and Mander, &#xdc; and Hallin, S and Machacova, K and Pumpanen, J and Siljanen, HMP}, title = {Genetic Potential for N2O Metabolism in Tree Tissues: Insights From Nitrogen Cycling Gene Prevalence and nosZ Diversity Across Tree Species.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02773-8}, pmid = {41998361}, issn = {1432-184X}, }
@article {pmid41998806, year = {2026}, author = {Tang, R and Wang, J and Zhang, Z and Li, Y and Lan, Y and Fan, Z}, title = {Temporal Shifts in Gut Microbiota and Host Immunity During Chronic Diarrhea in an Infant Rhesus Macaque: A Longitudinal Case Study Based on Multi-Omics.}, journal = {Journal of medical primatology}, volume = {55}, number = {3}, pages = {e70074}, doi = {10.1111/jmp.70074}, pmid = {41998806}, issn = {1600-0684}, support = {2023NSFSC1935//Sichuan Province Science and Technology Support Program/ ; 32370450//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Macaca mulatta/immunology ; *Gastrointestinal Microbiome ; *Diarrhea/veterinary/microbiology/immunology ; *Monkey Diseases/immunology/microbiology ; Longitudinal Studies ; Transcriptome ; Male ; Anti-Bacterial Agents/therapeutic use ; Female ; Chronic Disease ; Multiomics ; }, abstract = {Diarrhea remains a major health challenge in captive rhesus macaques (RMs; Macaca mulatta), particularly among infants, yet the dynamic interplay between gut microbiota and host immune responses during disease progression remains poorly understood. Here, we conducted a longitudinal multi-omics study on a captive infant RM, analyzing 25 fecal metagenomes and 18 blood transcriptomes across diarrheal, antibiotic treatment, and recovery phases. Our results demonstrated that disease state was the primary driver of gut microbiota variation. The diarrheal phase was characterized by a significant reduction in microbial α-diversity and marked expansion of multidrug-resistant Enterobacteriaceae, including Escherichia, Shigella, and Salmonella, accompanied by severe depletion of probiotic genera such as Lactobacillus and Bifidobacterium. Correspondingly, antibiotic resistance genes targeting fluoroquinolones and cephalosporins accumulated substantially during diarrhea, explaining the limited efficacy of empirical antibiotic therapy. Blood transcriptome analysis revealed heightened innate immune activation, evidenced by upregulation of interferon-related genes, alongside suppression of adaptive immune pathways including interleukin-5 signaling. Integrated correlation analysis uncovered synchronized host-microbiome interactions, with inflammatory gene expression positively associated with opportunistic pathogens and negatively correlated with beneficial commensals. Clinical recovery coincided with re-establishment of probiotic populations, reduction in resistance gene burden, and normalization of immune function. These findings demonstrate that infant macaque diarrhea profoundly disrupts both gut microbial ecology and systemic immunity, supporting management strategies that prioritize targeted antimicrobial intervention and microbiome restoration over prolonged empirical antibiotic use in captive primates.}, }
@article {pmid41999240, year = {2026}, author = {Wyss, J and Baehler, S and Ferracini, J and Kroell, D and Rossier, AM and Krupka, N and Misselwitz, B and Yilmaz, B and Wiest, R}, title = {The duodenal microbiota is compartmentalized and clinically stable yet rapidly responsive to nutrient exposure.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2657053}, doi = {10.1080/19490976.2026.2657053}, pmid = {41999240}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; *Duodenum/microbiology ; Female ; Adult ; *Bacteria/classification/genetics/isolation &amp; purification ; Middle Aged ; *Nutrients/metabolism ; RNA, Ribosomal, 16S/genetics ; Obesity/microbiology ; Intestinal Mucosa/microbiology ; Phylogeny ; Bariatric Surgery ; }, abstract = {The duodenum is one of the most nutrient-exposed and immunologically active regions of the human gastrointestinal tract, yet its microbial ecology and short-term responses to dietary stimuli remain poorly defined. Most studies rely on fasting luminal aspirates, which fail to capture mucosa-associated communities and miss rapid ecological shifts during nutrient exposure, limiting insight into the spatial organization and dynamic behavior of the upper small intestinal microbiota (SIM). To address these limitations, we performed a compartment-resolved analysis of the duodenal microbiota in 94 individuals, including healthy controls, patients with obesity before and after bariatric surgery, individuals with IBS, and subjects with other SIBO-associated risk states. Paired luminal aspirates and mucosal biopsies were obtained during upper endoscopy; bacterial load was quantified by culture, and the community structure was assessed using 16S rRNA gene sequencing and PICRUSt-based pathway inference. In addition, healthy volunteers underwent a controlled intraluminal fat challenge with dense serial duodenal sampling over 180 min to resolve short-term nutrient-driven dynamics. Across all participants, the anatomical niche emerged as the dominant ecological determinant. Mucosal communities displayed higher species richness, broader phylogenetic representation, and distinct beta-diversity signatures compared with luminal aspirates, which were narrowly dominated by Streptococcaceae. Under fasting conditions, SIM remained remarkably stable across obesity, IBS, and culture-defined SIBO, with only minor taxonomic differences in SIBO-positive individuals. In contrast, acute nutrient exposure triggered rapid microbial blooming, increased culture positivity, and a transient rise in species richness within 30-60 min, revealing a highly responsive ecosystem not captured by fasting samples. Together, these findings show that the defining feature of the human duodenal microbiota is not disease-associated dysbiosis under fasting conditions, but rather a conserved spatial architecture coupled with rapid, nutrient-driven ecological plasticity, highlighting the dynamic and compartmentalized nature of the upper small intestinal microbiome.}, }
@article {pmid41999489, year = {2026}, author = {Nelson, K and Peterson, N and Olson, R and Castillo, H and Antwi, C and Cromwell, S and Benbow, ME and Ayayee, P}, title = {Gut Microbial Nitrate Reduction to Ammonia: A Possible Pathway of Biological Nitrogen Provisioning in Freshwater Insects.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02771-w}, pmid = {41999489}, issn = {1432-184X}, }
@article {pmid42002450, year = {2026}, author = {Coleine, C and Obermeier, W and Lehnert, L and Leung, PM and Donati, C}, title = {Linking microbial function and remote sensing for understanding drylands.}, journal = {Trends in ecology &amp; evolution}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tree.2026.04.002}, pmid = {42002450}, issn = {1872-8383}, abstract = {Drylands, covering over 40% of Earth's land surface, are expanding due to accelerating aridification and vegetation loss. Their microbial communities sustain essential processes such as carbon fixation, nitrogen cycling, and trace gas regulation; yet they remain largely invisible to global models. While microbiome studies reveal mechanistic details at local scales, environmental monitoring requires spatial continuity. We argue that advances in remote sensing, with its increasing resolutions, now allow microbial processes to be observed, scaled, and modeled across regions. Linking omics and spectral data can reveal microbial 'sentinels' of ecosystem change, transforming microbial ecology into a spatially predictive science. This integration provides a foundation for early-warning systems of biodiversity loss and land degradation, positioning microbes as measurable actors in Earth system dynamics.}, }
@article {pmid42002654, year = {2026}, author = {Martínez-Reyes, CM and González-Macedo, M and Rojas-Oropeza, M and Rodríguez-Zaragoza, S and Cabirol, N}, title = {Influence of seasonal humidity and nitrogen on soil ciliate and bacterial diversity beneath the canopy of Neltuma laevigata.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {42002654}, issn = {1618-1905}, support = {PhD Grant//Secretar&#xed;a de Ciencia, Humanidades, Tecnolog&#xed;a e Innovaci&#xf3;n/ ; PAPIIT IN224716//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; }, }
@article {pmid41993414, year = {2026}, author = {Liu, S and Mehta, P}, title = {Ecology of metagenomes: incorporating genotype-to-phenotype maps into ecological models.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.07.717079}, pmid = {41993414}, issn = {2692-8205}, abstract = {UNLABELLED: A major theoretical problem in community ecology is to understand how genes, organisms, and environments combine to shape the structure and diversity of ecological communities. However, most classic ecological models work entirely with phenotypic parameters, neglecting the central role played by genes. This limitation is particularly acute in microbial ecology, where the widespread use of sequencing technologies allows researchers to directly measure the genomic and metagenomic properties of communities. Here, we bridge this gap by incorporating genotype-to-phenotype maps into classical ecological models, including the generalized Lotka-Volterra model (GLV) and consumer resource models (CRMs). We focus on the case where genotype-to-phenotype maps are linear, which provides a tractable yet powerful framework for analyzing complex traits. Even in this simple setting, the resulting ecological dynamics give rise to novel gene-level ecological dynamics that can be recast entirely in terms of genes, allowing us to develop an ecology of metagenomes. We find that ecological interactions between genes lead to pervasive "metagenomic hitchhiking" - low-fitness genes can survive in the ecosystem because they are integrated into genomes of high-fitness species. We also show that phylogenetic relationships between species mold the ability of closely related strains to stably coexist in complex communities. This highlights how lineage structure and competitive interactions jointly shape community composition. Our framework provides a principled foundation for interpreting metagenomic data through the lens of ecological theory.<br><br>AUTHOR SUMMARY: Recent advances in sequencing technologies have transformed our ability to characterize microbial communities at the genomic level. However, most classic ecological models work entirely with phenotypic parameters, neglecting the central role played by genes. Here, we address this gap by extending classical ecological models to explicitly include genotype-to-phenotype maps. We focus on complex traits where the genotype-to-phenotype map is approximately linear. We show that the resulting ecological dynamics that can be recast entirely in terms of genes, allowing us to develop an ecology of metagenomes. Our framework provides a novel perspective for interpreting metagenomic data through the lens of ecological theory.}, }
@article {pmid41995611, year = {2026}, author = {Elkatmis, B and Türksoy, GM and Rodríguez, E and Rahmoune, B and Koprivova, A and Kopriva, S}, title = {Sulfur as a Central Integrator of Plant-Microbe Interactions: From Nutrient Cycling to Immune Signalling and Microbiome Assembly.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/erag186}, pmid = {41995611}, issn = {1460-2431}, abstract = {Sulfur (S) is an essential macronutrient that underpins plant growth, stress resilience, and immunity. Beyond its role in primary metabolism, sulfur is incorporated into a diverse array of secondary metabolites that mediate plant-microbe interactions. In this review, we summarize current knowledge on how microbial sulfur metabolism contributes to plant sulfur nutrition and how plant-derived sulfur-containing compounds shape microbial community assembly and disease outcomes. Microorganisms mobilize organic sulfur in soils through sulfatase activity, volatile sulfur production, and sulfoquinovose degradation, thereby enhancing plant sulfur availability, particularly under limiting conditions. Conversely, plants deploy sulfur-rich metabolites, including volatile organic compounds, glucosinolates, and the phytoalexin camalexin, to restrict pathogens, modulate beneficial associations, and structure rhizosphere communities. These compounds act not only as antimicrobial agents but also as ecological filters that balance defense with microbiome homeostasis. Emerging evidence indicates that sulfur availability and metabolic flux influence the composition and function of plant-associated microbiota, linking primary nutrient assimilation to immune regulation. By integrating insights from sulfur biochemistry, microbial ecology, and plant immunity, we highlight sulfur metabolism as a central node in plant-microbe interactions. Understanding the dynamic exchange of sulfur between plants and their microbiota will be essential for improving crop resilience and sustainable nutrient management in sulfur-limited agricultural systems.}, }
@article {pmid41808017, year = {2026}, author = {Yu, S and Hong, P and Chou, S and Liang, TF and Lin, KS and Lai, CH and Wang, CM}, title = {Probiotic potential of novel Lactobacillus and Limosilactobacillus isolated from Formosan pangolin feces.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41808017}, issn = {1471-2180}, support = {MOST 111-2313-B-415-008//Ministry of Science and Technology in Taiwan/ ; NSTC 114-2313-B-415-010//National Science and Technology Council/ ; }, abstract = {BACKGROUND: The critically endangered Formosan pangolin (Manis pentadactyla pentadactyla) faces severe conservation challenges, with gastrointestinal (GI) disorders being a primary driver of mortality in captivity. These ailments are often exacerbated by dietary transitions and anthropogenic stress. While the gut microbiota is crucial for host health, the probiotic potential of the pangolin’s native microbes remains unexplored. This study aimd to isolate lactic acid bacteria (LAB) from wild pangolin feces and preliminarily characterize their probiotic properties.<br><br>RESULTS: Ten LAB strains with <&#x2009;97.3% 16S rRNA gene similarity to known species likely represent undescribed lineages within Lactobacillus and Limosilactobacillus. Phylogenetic analysis revealed two clusters: three Lactobacillus strains related to L. jensenii and L. psittaci, and seven Limosilactobacillus strains close to L. fermentum. All isolates showed strong acid and bile tolerance and high cell surface hydrophobicity (>&#x2009;90%). The Lactobacillus cluster exhibited superior auto-aggregation (>&#x2009;80%), pathogen co-aggregation, and organic acid-mediated antibacterial activity, along with cellular component-driven inhibition of &#x3b1;-glucosidase (66.5&#x2013;69.4%) and &#x3b1;-amylase (75.8&#x2013;77.2%). In contrast, Limosilactobacillus strains demonstrated metabolite-mediated enzyme inhibition (up to 84.1%) and antioxidant activity (25.6&#x2013;48.2% TAC; 36.3&#x2013;46.3% DPPH). All isolates were susceptible to cell wall and protein synthesis inhibitors, confirming a safe antibiotic profile.<br><br>CONCLUSION: These findings identify a reservoir of novel, pangolin-derived LAB with multifaceted probiotic traits. These isolates represent promising candidates for targeted nutritional strategies to mitigate GI distress and improve the survival of this endangered mammal. This work bridges the gap between microbial ecology and practical wildlife conservation, offering a scientific basis for enhancing the health of captive pangolin populations.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04935-7.}, }
@article {pmid41992364, year = {2026}, author = {Cummins, C and Sutton, W and McLeod, T and Dallas, JW and Ghotbi, M and Vargas-Gastélum, L and Alexander, NR and Rurik, AJ and McGinnity, D and Reinsch, SD and Sandonato, P and Arbour, J and Freake, M and Ashley, A and Ternes, W and Culp, E and Spatafora, J and McPhail, K and Stajich, JE and Hardman, R and Walker, DM}, title = {Effects of environmental setting and diet on the gut microbial ecology of eastern hellbenders (Cryptobranchus alleganiensis alleganiensis).}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {41992364}, issn = {2524-4671}, support = {EF-2125067//National Science Foundation/ ; EF-2125066//National Science Foundation/ ; EF-2125065//National Science Foundation/ ; }, abstract = {BACKGROUND: Eastern hellbenders (Cryptobranchus alleganiensis alleganiensis) have undergone substantial population declines throughout their range, leading them to become the focus of increased conservation efforts, including care in zoo and university settings. However, effective implementation of such conservation strategies often relies on a comprehensive understanding of host health, which can be directly influenced by the gut microbiome, yet characterization of gut microbiota often remains overlooked in ex situ conservation facilities. Additionally, effects on the gut microbiome associated with releasing zoo-reared animals into the wild are poorly understood. Therefore, these circumstances make hellbenders an ideal species to examine the relationship between zoo management strategies and gut microbial dynamics.<br><br>METHODS: 16S rRNA sequencing was used to investigate dissimilarities between the gut microbiome of hellbenders in zoo and wild settings and to evaluate the impact of implementing a wild diet in zoo-reared hellbenders. Additionally, the bacterial composition of zoo-released individuals and wild resident hellbenders was compared to examine the response of the gut microbiome upon release into natural habitat. Selected samples were also chosen for ITS1 rDNA sequencing as a preliminary investigation of the hellbender gut mycobiome.<br><br>RESULTS: Human rearing strongly affected the gut microbiome, leading to reduced bacterial richness as well as differing community structure than wild hellbenders. However, implementation of a wild diet in a zoo setting modulated the microbiome and appeared to be mainly driven by bacterial turnover. Additionally, both bacterial and fungal gut assemblages demonstrated the capacity for restructuring upon release into native habitat to become more reflective of a wild-type microbiome.<br><br>CONCLUSIONS: We completed the first study elucidating the gut microbial composition patterns of hellbenders, across both zoo and wild settings. These results provide an understanding of the potential impacts of conservation populations in zoos on gut microbial communities and also inform headstart programs of the transition of the gut microbiome post-reintroduction to the wild.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00537-w.}, }
@article {pmid41988476, year = {2026}, author = {Kokisi, P and Nchu, F and Kambizi, L and Bvenura, C}, title = {Finger millet and soybean as functional ingredients in next-generation fermented foods: a review of nutritional, technological, and health-promoting perspectives.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1718090}, pmid = {41988476}, issn = {2296-861X}, abstract = {INTRODUCTION: The ever-increasing global malnutrition, environmental degradation, and food insecurity challenges have intensified interest in sustainable food systems and underutilized crops. Fermentation improves the nutritional quality, digestibility, shelf life, and sensory attributes of plant-based foods. Finger millet (Eleusine coracana) and soybean (Glycine max) are promising for functional food development due to their complementary nutrient profiles. Finger millet is rich in minerals, fibre, and polyphenols, while soybean provides high-quality protein and bioactive compounds. Their synergistic amino acid profiles and the benefits of fermentation-such as improved micronutrient bioavailability and reduced antinutritional factors-make them suitable for developing innovative fermented foods. Therefore, this review evaluates the nutritional value, fermentation potential, and health-promoting properties of finger millet and soybean for sustainable nutrition and food security.<br><br>METHODS: A narrative review following PRISMA principles was conducted using Google Scholar, PubMed, ScienceDirect, and Scopus. Literature from 2000-2025 on finger millet, soybean, fermentation, and functional foods was searched, yielding 116 records. After screening, 59 peer-reviewed studies were included. Two reviewers independently extracted and analysed data through thematic synthesis on nutritional composition, fermentation methods, microbial ecology, functional properties, and health benefits.<br><br>RESULTS: The literature shows that fermentation significantly enhances the nutritional and functional value of both crops. Fermentation reduces antinutritional factors such as phytates and tannins, improves protein digestibility, and increases mineral bioavailability. Lactic and acetic acid fermentation also enhance flavour, texture, and shelf stability. However, the review identified a major research gap: few documented fermented foods combine finger millet and soybean despite their complementary nutritional profiles.<br><br>DISCUSSION: Finger millet and soybean present strong potential for developing next generation fermented functional foods that address malnutrition, lactose intolerance, and dietary protein deficiencies. Nevertheless, several challenges remain, including fermentation standardization, sensory acceptance, limited infrastructure, and insufficient characterization of microbial communities and bioactive metabolites. Advancing multi-omics research, improving fermentation technologies, and promoting supportive policies and value chains will be critical for translating these crops into scalable, sustainable food innovations.}, }
@article {pmid41988769, year = {2026}, author = {Yuan, YG and Smagghe, G and Chen, XS and Tian, L and Long, JK and Luo, M and Chang, ZM}, title = {Dietary titanium dioxide nanoparticles impair pollinator health: integrative analysis of colony performance, gut microbiota, and transcriptomic responses in Bombus terrestris.}, journal = {Journal of economic entomology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jee/toag103}, pmid = {41988769}, issn = {1938-291X}, abstract = {Titanium dioxide nanoparticles (TiO2 NPs) are widely used in industrial, agricultural, and consumer products and are increasingly detected in terrestrial and floral environments that are critical for pollinators. However, the mechanistic and ecological consequences of TiO2 NPs exposure on pollinator health remain poorly understood. Here, we present a multi-level ecotoxicological assessment of dietary TiO2 NPs exposure in the bumblebee Bombus terrestris L. (Hymenoptera: Apidae), integrating colony performance, gut microbiota composition, and host transcriptomic responses. Using both environmentally relevant and worst-case concentrations, we conducted short-term (3-d) and chronic (15-d) exposures to evaluate physiological disruption, microbial dynamics, and potential compensatory or recovery processes. TiO2 NPs ingestion reduced worker survival and syrup consumption, delayed oviposition, and shortened egg development, indicating impaired colony performance. Gut microbiota exhibited pronounced dysbiosis after 3 d, followed by partial converged toward control-like profiles after 15 d, suggesting microbial potential resilience and compensatory restructuring. Transcriptomic analyses revealed dose-dependent activation of immune, oxidative stress, calcium signaling, and programmed cell death pathways. Correlative analyses identified associations between specific microbial taxa, including Apibacter and Klebsiella, and host gene expression linked to immunity, detoxification, and metabolism, highlighting coordinated microbe-host responses under TiO2 NPs stress. This study provides novel mechanistic insight into how engineered nanoparticles affect pollinators across biological scales, from colony physiology and microbial ecology to molecular pathways, and emphasizes the practical importance of safeguarding pollinator health for both wild plant reproduction and crop pollination. The findings advance understanding of nanoparticle ecotoxicology and support evidence-based strategies for sustainable nanomaterial use and pollinator protection.}, }
@article {pmid41990227, year = {2026}, author = {Parween, S and Nagarajan, AP and Alghamdi, AK and Eida, AA and Lafi, FF and Albanna, L and Salem, N and Abu-Irmaileh, B and Pirzada, ZA and Siddique, S and Garrido-Oter, R and Schulze-Lefert, P and Saad, MM and Hirt, H}, title = {Desert Plant Endophyte Genome Database: a curated repository of endophytic bacterial genomes across arid ecosystems.}, journal = {Database : the journal of biological databases and curation}, volume = {2026}, number = {}, pages = {}, doi = {10.1093/database/baag020}, pmid = {41990227}, issn = {1758-0463}, support = {BAS/1/1062-01-01//KAUST/ ; }, mesh = {*Endophytes/genetics ; *Desert Climate ; *Genome, Bacterial ; *Databases, Genetic ; *Plants/microbiology ; *Ecosystem ; *Bacteria/genetics ; }, abstract = {Microbial communities associated with desert plants play a pivotal role in enhancing host survival under extreme environmental stressors, including drought, salinity, and nutrient limitation. The Desert Plant Endophyte Microbial Collection is one of the largest curated repositories of 2500 cultivable endophytic bacteria isolated from 23 native desert plant species across Saudi Arabia, Jordan, and Pakistan. Representing a broad spectrum of arid microhabitats from inland deserts and mountain wadis to coastal mangroves and date palm oases, the collection supports integrative studies on microbial ecology and plant-microbe interactions in water-limited ecosystems. A central component of this initiative is the Desert Plant Endophyte Genome Database, which currently hosts whole-genome sequences of 534 endophytic bacterial isolates annotated with extensive ecological metadata, assembly statistics, functional traits, and host associations. The database interface provides tools for genome exploration, metadata filtering, and functional gene mining, enabling users to identify taxa and traits of agronomic interest, particularly for applications in sustainable agriculture and sustainable desert revegetation. By combining genomic, ecological, and functional data, the Desert Plant Endophyte Genome Database serves as a foundational platform for the development of targeted microbial inoculants and fosters data-driven research into desert microbiomes and plant resilience mechanisms.}, }
@article {pmid41990601, year = {2026}, author = {Kholif, AE and Olafadehan, OA and Anele, UY}, title = {Tannins in ruminant feeding: effects of tannin type and dosage on rumen fermentation, production performance, health, and sustainability.}, journal = {Research in veterinary science}, volume = {206}, number = {}, pages = {106181}, doi = {10.1016/j.rvsc.2026.106181}, pmid = {41990601}, issn = {1532-2661}, abstract = {Tannins are plant-derived polyphenolic compounds of variable molecular weights that have attracted considerable attention as natural feed additives in ruminant nutrition. Their ability to modulate rumen microbial ecology, improve nutrient utilization, mitigate enteric methane (CH4) emissions, and promote animal health has positioned them as potential tools for improved, sustainable ruminant production systems. This review critically evaluates and synthesizes published evidence on the effects of tannins on rumen fermentation dynamics, nutrient digestibility, hematological and biochemical parameters, production performance, and overall health status of ruminants. A systematic literature search was conducted using Scopus, Web of Science, ScienceDirect, Google Scholar, and PubMed, targeting peer-reviewed English-language studies published between January 2000 and September 2025. Search terms were organized using Boolean operators across tannin chemistry and type, ruminant species, and production-, environmental-, or health-related outcomes. Studies were included if they reported in vitro or in vivo responses of ruminants to tannins, while non-ruminant studies, conference abstracts, and non-English publications were excluded to ensure comprehensive comparability. Collectively, available evidence indicates that hydrolyzable tannins generally exert more consistent positive effects on feed intake, nutrient digestibility, and CH4 mitigation than condensed tannins, although responses remain highly dependent on tannin source, chemical structure, diet composition, dietary inclusion level, and the extent of animal adaptation. Low to moderate inclusion levels (generally <3% of dietary dry matter [DM]) were associated with neutral to beneficial effects on feed intake, rumen fermentation characteristics, nitrogen utilization, and animal performance. In contrast, higher rates (>5% of dietary DM) frequently impair digestibility, depress feed intake, compromise nitrogen efficiency, and reduce productive performance, indicating dose-dependent responses. Besides nutritional modulation, other ancillary benefits of tannins include reduced internal parasite burden and decreased incidence of ruminal bloat. Positive changes in hematological and biochemical indices further suggest potential improvements in physiological response and health status at moderate levels, although high rates may induce adverse metabolic alterations. In summary, tannins represent a promising nutritional strategy for improving the sustainability of ruminant production systems; however, their successful application depends on careful selection of tannin type, strategic dosage optimization, and feeding strategy. Future research should prioritize defining optimal inclusion thresholds, elucidating rumen microbiome adaptation mechanisms at the molecular level, and assessing long-term production and health outcomes under practical production conditions.}, }
@article {pmid41991810, year = {2026}, author = {González-Sánchez, A and Cordero-Martínez, E and Rodríguez-Torres, MD and Islas-Robles, &#xc1; and Decena-Segarra, LP and García-Miranda, N and Navarro-Miranda, M and Zapién-Campos, R and García-Oliva, F and Eguiarte, LE and Souza, V and Olmedo-Álvarez, G}, title = {Dormancy as a Signature of Microbial Community Disassembly during Hydrological Collapse in a Desert Oasis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02744-z}, pmid = {41991810}, issn = {1432-184X}, support = {Carlos Slim Grant//World Wild Life/ ; Fronteras 778 (2015) and Fronteras 39589 (2020)//secihti/ ; }, }
@article {pmid41979732, year = {2026}, author = {Pedregal-Montes, A and Mercado-Bettín, D and Futter, M and Ledesma, JLJ and Farré, MJ and Marcé, R and Jennings, E}, title = {Seasonal forecasting of dissolved organic carbon in a Mediterranean catchment: Enhancing upstream control of disinfection by-product precursors.}, journal = {Environmental monitoring and assessment}, volume = {198}, number = {5}, pages = {}, pmid = {41979732}, issn = {1573-2959}, support = {RYC2022-035220-I//Spanish Ministry of Science, Innovation, and Universities/ ; 956623//Horizon 2020 Framework Programme/ ; }, mesh = {*Environmental Monitoring/methods ; Seasons ; *Carbon/analysis ; *Water Pollutants, Chemical/analysis ; Rivers/chemistry ; Forecasting ; *Disinfectants/analysis ; Disinfection ; Mediterranean Region ; }, abstract = {Increasing climatic aridity and growing anthropogenic pressures are expected to alter dissolved organic matter (DOM) dynamics in Mediterranean river basins, with implications for environmental monitoring and drinking water source management. Dissolved organic carbon (DOC), a bulk indicator of DOM and an operational surrogate for disinfection by-products (DBP) precursors, is routinely monitored at drinking water sources but remains difficult to anticipate on seasonal timescales. Here, we present a reproducible open-source workflow that extends conventional monitoring by integrating seasonal climate forecasts (SEAS5) with coupled hydrological and catchment carbon models to generate probabilistic monthly predictions of streamflow and DOC at the inflow of a Mediterranean drinking water reservoir. Seasonal hindcast evaluation using the Continuous Ranked Probability Skill Score (CRPSS) showed limited skill for meteorological variables beyond 1 month, while streamflow exhibited positive skill at short lead times across most seasons. Notably, DOC forecasts achieved the highest and most persistent skill, with CRPSS values exceeding 0.3 for winter initializations and lead times up to 4 months, consistent with catchment system memory. Forecast experiments successfully distinguished contrasting wet and dry hydroclimatic conditions, reproducing higher and more persistent DOC concentrations during the dry period. To support operational use, the forecasts were translated into a co-developed monthly report to provide early warning of periods with elevated organic matter levels in source waters. While DOC alone does not capture the full complexity of DBP formation, the workflow provides a transferable approach for seasonal assessment of source water organic matter dynamics in hydroclimatically variable, human-impacted catchments.}, }
@article {pmid41981331, year = {2026}, author = {Salamon, S and Havrysh, P and Banachewicz, P and Mikołajczak, K and Błaszczyk, L}, title = {Differential Modulation of Wheat Transcriptional Programs Driven by Native Endophytic Fungi.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02731-4}, pmid = {41981331}, issn = {1432-184X}, support = {2017/27/B/NZ9/01591//National Science Center in Poland/ ; 2017/27/B/NZ9/01591//National Science Center in Poland/ ; 2017/27/B/NZ9/01591//National Science Center in Poland/ ; }, }
@article {pmid41981704, year = {2026}, author = {Li, M and Wu, S and Zi, X}, title = {Identification of silage bacterial clusters and analysis of their microecological characteristics.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00891-x}, pmid = {41981704}, issn = {2524-6372}, abstract = {BACKGROUND: Enterotypes refer to the different bacterial clusters in the gut microecosystem, which are closely related to host physiology, digestion, disease, and other phenotypes. However, whether there are clear clusters in the silage microecosystem, and the fermentation quality and characteristics of unique cluster silage remain unknown. To determine whether distinct bacterial clusters exist in the silage microecosystem and to characterize their fermentation properties, we analyzed the bacterial community composition and fermentation quality of 156 silage samples, and further explored their underlying microbial ecological features.<br><br>RESULTS: We confirmed three distinct clusters in the silage microbiome, which were named according to their dominant bacterial taxa: the E-cluster (characterized by a higher abundance of unclassified Enterobacteriaceae (UG)), the P-cluster (enriched with Pseudomonas and Janthinobacterium), and the L-cluster (dominated by Lactobacillus). These microbial clusters were closely associated with fermentation quality: the L-cluster exhibited superior silage quality compared to the E- and P-clusters. Meanwhile, the microbial functional profiles differed significantly among the three clusters of silage. Numerous pathways were significantly enriched in the P-cluster, such as the Biosynthesis of other secondary metabolites, etc. Moreover, bacterial co-occurrence networks of three clusters silage displayed cooperative interactions mainly, P-cluster silage network was more complex and tighter, E-cluster silage has more functional microbial units and more stable. Furthermore, the assembly of microbial communities in the three silage clusters was dominated by stochastic processes. Specifically, the E-cluster and L-cluster were governed by ecological drift, while dispersal limitation was more influential in the P-cluster.<br><br>CONCLUSIONS: Overall, we found in our study that the silage microbiome can be divided into three clusters, and different clusters have significant differences in fermentation quality, microbial diversity and compositions, functional profiles, microbial network characteristics and community assembly mechanisms. These results could broaden our comprehension of the silage microbial ecology processes and also provide a scientific basis on which to develop a method to precisely regulate silage quality.}, }
@article {pmid41984230, year = {2026}, author = {Lee, HB and Heiss, AA and Jeong, DH and Cho, J and Lee, C and Cho, BC and Park, JS}, title = {Characterization of Dominant Heterotrophic Flagellates in Anaerobic Digesters Using Combined Culture-based and Metabarcoding Approaches.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02768-5}, pmid = {41984230}, issn = {1432-184X}, support = {NRF-2022R1I1A206411//National Research Foundation of Korea/ ; RE202201941//Korea Environmental Industry and Technology Institute/ ; }, }
@article {pmid41986376, year = {2026}, author = {Khan, A and Breselge, S and O'Mahony, AK and O'Sullivan, O and Cotter, PD and McCarthy, SN and Mahony, J and Kenny, JG}, title = {Water kefir as a paradigm for multi-omics and genome-scale metabolic modelling in fermented food.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00985-x}, pmid = {41986376}, issn = {2055-5008}, support = {101060218//European Union's Horizon Europe research and innovation program/ ; 101060218//European Union's Horizon Europe research and innovation program/ ; 101060218//European Union's Horizon Europe research and innovation program/ ; 101060218//European Union's Horizon Europe research and innovation program/ ; 101060218//European Union's Horizon Europe research and innovation program/ ; 101060218//European Union's Horizon Europe research and innovation program/ ; }, abstract = {Water Kefir is a plant-based fermented beverage, traditionally produced on a small scale by fermenting a sucrose solution with fresh or dried fruits, using water kefir grains as inoculum. The grains are relatively simple communities that consist of both eukaryotes and prokaryotes, rendering them a paradigm for studying microbial ecology and interspecies interactions. Recently, water kefir has attracted growing research and industrial interest due to its potential and perceived health benefits. Owing to its increasing popularity, there is a growing demand for controlled and standardised production on an industrial scale. However, industrial-scale production remains a challenge due to the limited knowledge of the biological interactions of the microbial consortia and the lack of defined starter cultures. This review examines the current understanding of microbial and metabolic complexity of water kefir obtained from various omics studies. It further investigates the potential of an integrated multi-omics approach to elucidate mechanisms of microbial interactions and provides a roadmap for conducting multi-omics studies on fermented foods using water kefir as an example. This review also explores the potential application of genome-scale metabolic modelling in the development of functional and defined microbial communities for food fermentation. It identifies key challenges associated with such modelling and provides perspectives to address them. Finally, this review briefly discusses the regulatory challenges associated with the use of defined communities in food systems.}, }
@article {pmid41987215, year = {2026}, author = {Yan, M and Firkins, J and Guo, J and Relling, A and Yu, Z}, title = {Genome-resolved multi-omics provide new insights into microbial nitrogen utilization by the rumen microbiota.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02422-9}, pmid = {41987215}, issn = {2049-2618}, abstract = {BACKGROUND: Optimizing nitrogen (N) utilization in ruminant production systems holds both economic and environmental significance. However, traditional paradigms of N metabolism, derived primarily from well-studied model rumen bacteria, do not fully reflect the diverse and complex N metabolism in the rumen ecosystem.<br><br>RESULTS: To address this gap, we utilized comparative genomics and genome-resolved multi-omics analyses using a curated set of microbial genomes to investigate N assimilation and regulation in rumen microbes. We discovered that well-established mechanisms of ammonia assimilation and regulation, such as the glutamine synthetase (GS)/glutamate synthase (GOGAT) pathways and their regulatory proteins, are absent in many of the predominant rumen microbes, which likely utilize alternative pathways for ammonia assimilation. These findings challenge the applicability of E. coli-based N regulation models to rumen bacteria in response to ammonia availability. We further linked polysaccharide utilization and ammonia assimilation across hundreds of rumen microbial species. Furthermore, we identified specific microbial species involved in ureolysis and denitrification, as well as phages carrying auxiliary metabolic genes involved in N assimilation. Using an animal trial involving 11 pairs of lamb twins in a crossover design, we demonstrated that dietary crude protein (CP) at 10% and 13% had minimal impact on rumen microbiome composition and expression of N assimilation genes. Instead, changes in concentrate levels altered N assimilation, notably increasing expression of amino acid biosynthesis pathways.<br><br>CONCLUSION: These findings indicate a nuanced, species-specific microbial response to dietary interventions, highlighting the limitations of traditional N metabolism models applied to rumen microbes and the need for more granular studies of rumen microbial ecosystems.}, }
@article {pmid41987615, year = {2026}, author = {Eliwa, AI and Eldahshan, MM}, title = {CRISPR-Cas at a crossroads: from microbial immunity to precision biotechnology.}, journal = {Journal of immunoassay &amp; immunochemistry}, volume = {}, number = {}, pages = {1-24}, doi = {10.1080/15321819.2026.2658465}, pmid = {41987615}, issn = {1532-4230}, abstract = {Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) form RNA-guided adaptive immune systems in bacteria and archaea that mediate sequence-specific defense against invading genetic elements. Beyond their ecological role in restricting bacteriophage infection and horizontal gene transfer (HGT), CRISPR-Cas systems have been repurposed as programmable nucleases, enabling rapid, scalable, and precise genome engineering. Over the past decade, CRISPR platforms, most prominently Cas9, have transformed functional genomics, accelerated target discovery and drug development, and progressed from experimental tools to clinically evaluated gene and cell therapies. In parallel, growing attention has focused on both native and engineered roles of CRISPR-Cas in shaping HGT, plasmid ecology, and antimicrobial resistance (AMR), as AMR continues to expand globally. In this Review, we integrate advances spanning eukaryotic genome editing and prokaryotic antimicrobial applications. We summarize CRISPR-Cas classification and molecular mechanisms, highlighting spacer acquisition, guide RNA biogenesis, target recognition, and nucleic acid cleavage. We then examine how cellular DNA repair pathways influence editing outcomes and discuss strategies to enhance precision. We further review delivery strategies, such as conjugative plasmids, bacteriophages and phagemids, extracellular vesicles, and nanoparticles, together with evolutionary countermeasures encoded by mobile genetic elements, including anti-CRISPR proteins. Finally, we outline current limitations.}, }
@article {pmid41987827, year = {2026}, author = {Bornbusch, SL and Thacher, PR and Francisque, M and DeCandia, AL and Bortner, R and Garelle, D and Kendrick, EL and Maslanka, MT and Muletz-Wolz, CR}, title = {How "pro" are probiotics for wildlife species? Novel data, lack of evidence, and future directions.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag036}, pmid = {41987827}, issn = {2730-6151}, abstract = {Treatments that aim to purposefully manipulate host-associated microbiomes are now prevalent in human and animal medicine. Probiotics that contain live bacteria are purported to improve microbiome function and host health. Although research is advancing, commercial probiotic development has outpaced empirical study of probiotic efficacy. Probiotics are widely used in ex-situ wildlife care despite a lack of empirical study or support. We interrogate the relevance of commercial probiotics in ex-situ wildlife by (a) sequencing the composition of commercial probiotics used to treat wildlife, (b) comparing the probiotic sequences to data on the microbiomes of >900 animal species, and (c) characterizing the effects of a commercial probiotic on probiotic colonization, prevalence of a potential enteric pathogen (Clostridium perfringens), and metagenomic function in endangered black-footed ferrets (Mustela nigripes). We found mislabeling and potential contaminants in probiotics marketed for a range of species. The probiotic bacteria were rare or absent in published animal microbiomes. In black-footed ferrets, probiotic treatment induced minimal probiotic colonization, negligible functional change, and limited influence on the potential enteric pathogen. Given our findings, which reiterate concerns about the efficacy of commercial probiotics across human and animal sectors, greater effort must be put towards identifying species-specific probiotic candidates and studying alternative microbial therapies for wildlife under human care.}, }
@article {pmid41988037, year = {2026}, author = {Berings, L and Rojas-Preciado, N and Poppelsdorf, W and Van Hee, S and Jacquemyn, H and Lievens, B}, title = {Aphid-killing bacteria: diversity, origin, mechanisms and biocontrol potential.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1805793}, pmid = {41988037}, issn = {1664-302X}, abstract = {Aphids are among the most destructive agricultural pests worldwide and cause substantial yield losses through direct feeding, virus transmission, and indirect plant damage. While chemical insecticides have been the primary control strategy of aphids, increasing resistance, environmental concerns, and regulatory restrictions have prompted the search for alternative approaches. In recent years, aphid-killing bacteria have emerged as a promising yet underexplored group of biological control agents. Growing evidence shows that aphids are susceptible to a diverse range of bacteria spanning multiple taxonomic groups. Many of these bacteria originate from plant-associated environments or from the aphids themselves and employ different mechanisms to reduce aphid survival and fitness, including toxin production, immune suppression, and disruption of aphid symbioses. This mini-review summarizes current knowledge on the diversity, ecological origins, and modes of action of aphid-killing bacteria. We further discuss their potential advantages, limitations, and challenges for practical implementation in biological control and integrated pest management strategies of aphids. Improved understanding of these bacteria may facilitate their application as effective, sustainable alternatives to chemical insecticides for aphid management.}, }
@article {pmid41979287, year = {2026}, author = {Yue, C and Zhang, C and Zhang, R and Yuan, J}, title = {Enhanced bacterial chemotaxis in confined microchannels occurs at lane widths matching circular swimming radius.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {41979287}, issn = {2050-084X}, support = {12090053//National Natural Science Foundation of China/ ; 12474204//National Natural Science Foundation of China/ ; 12104436//National Natural Science Foundation of China/ ; JYB2025XDXM502//Ministry of Education of the People's Republic of China/ ; YD2030002501//University of Science and Technology of China/ ; 2019YFA0709303//Ministry of Science and Technology of the People's Republic of China/ ; XKBF (2025)010//Guizhou Provincial Major Scientific and Technological Program/ ; }, mesh = {*Chemotaxis ; *Escherichia coli/physiology ; Microfluidics ; }, abstract = {Understanding bacterial behavior in confined environments is helpful for elucidating microbial ecology and developing strategies to manage bacterial infections. While extensive research has focused on bacterial motility on surfaces and in porous media, chemotaxis in confined spaces remains poorly understood. Here, we investigate the chemotaxis of Escherichia coli within microfluidic lanes under a linear concentration gradient of L-aspartate. We demonstrate that E. coli exhibits significantly enhanced chemotaxis in lanes with sidewalls compared to open surfaces. We attribute this phenomenon primarily to the intrinsic chiral clockwise circular motion of surface-swimming bacteria and the subsequent alignment effect upon collision with the sidewalls. By varying lane widths, we identify that an 8 μm width-approximating the radius of bacterial circular swimming on surfaces-maximizes chemotactic drift velocity. These results are supported by both experimental observations and stochastic simulations, establishing a clear proportional relationship between optimal lane width and the radius of bacterial circular swimming. Further geometric analysis provides an intuitive understanding of this phenomenon. Our results may offer insights into bacterial navigation in complex biological environments such as host tissues and biofilms, providing a preliminary step toward exploring microbial ecology in confined habitats and potential strategies for controlling bacterial infections.}, }
@article {pmid41979517, year = {2026}, author = {Pioppi, A and Gomes, SIF and Nicolaisen, M and Xu, X and Kovács, &#xc1;T}, title = {Successive cultivation under drought selects for specific microbiome members in the wheat rhizosphere.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiag037}, pmid = {41979517}, issn = {1574-6941}, abstract = {Growing knowledge on plant microbiomes demonstrates the contribution of the host plant during microbiome assembly, especially under stress conditions commonly threatening crops. To dissect the influence of a plant on its microbiome, repeated cycling of microbiomes can be utilized to enhance functional properties in the enriched microbial communities. We used such a successive cultivation approach for wheat (Triticum aestivum) microbiome under drought conditions and selected lineages for drought resilience and susceptibility, with and without enriching the starting community with a library of bacterial isolates obtained from wheat. Significant differences in the rhizosphere microbiome between selection regimes were confirmed through 16S rRNA gene amplicon sequencing. Notably, replicate lineages of each selection regime showed convergence to similar microbiomes. Specific genera were abundant depending on the selection regimes; Stenotrophomonas under drought resilience, while Rahnella under drought conditions when the strain library was added initially. Applying Stenotrophomonas or Rahnella as single inoculum did not improve drought resilience in wheat. We hypothesize that complex microbiome dynamics take place during successive cultivation, which underscores the importance of considering complex plant-microbiome systems for studying plant stress resilience. Successive cultivation remains a valuable approach for observing rhizosphere microbiome changes under different conditions.}, }
@article {pmid41971533, year = {2026}, author = {Huang, H and Ghosh, D and Worrich, A}, title = {A One Health perspective on bacterial extracellular vesicles as mediators of antimicrobial resistance spread.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag052}, pmid = {41971533}, issn = {2730-6151}, abstract = {Antimicrobial resistance (AMR) is a global health threat requiring a One Health approach across human, animal, and environmental sectors. Bacterial extracellular vesicles (BEVs), membrane-bound particles secreted by bacteria, have emerged as potential vectors of antibiotic resistance and mediators of horizontal gene transfer. Found across clinical, agricultural, and natural environments, BEVs carry resistance genes, mobile genetic elements, and virulence factors. They protect genetic cargo, function without direct cell contact, and can cross ecological boundaries more easily than whole bacteria. This review synthesises current knowledge on BEVs in AMR transmission, highlights their cross-sector potential, and identifies key research gaps. Recognising their role is essential for improving AMR surveillance and informing future mitigation strategies.}, }
@article {pmid41971983, year = {2025}, author = {Yoshida, H and Shigeyoshi, S and Goto, S and Sassa, M and Tsuji, K and Yoshimi, A and Tanaka, C and Sumita, T and Irie, T and Suzuki, K and Izumitsu, K}, title = {Dual regulation of appressorium development in the maize pathogen Bipolaris maydis: BmOPY2-mediated hydrophobic surface recognition and pectin recognition.}, journal = {Mycoscience}, volume = {66}, number = {4}, pages = {240-248}, pmid = {41971983}, issn = {1618-2545}, abstract = {The CHK1 MAPK pathway is crucial in appressorium formation and is highly conserved among plant pathogenic fungi. Here, we investigated a putative upstream regulator of this pathway, BmOPY2, in the maize pathogen Bipolaris maydis. Yeast two-hybrid analysis confirmed the interaction between BmOPY2 and BmSTE50, suggesting that BmOPY2 functions as an upstream regulator of the CHK1 MAPK pathway. To investigate the role of BmOPY2 in appressorium formation, we generated BmOPY2-disrupted (∆BmOPY2) mutants. These mutants formed appressoria normally on maize leaves, but did not form them on plastic Petri dishes. This suggests that BmOPY2 regulates appressorium formation via hydrophobic surface recognition but not via recognition of host-derived chemicals. Plant waxes or cutin monomers are recognized by other fungal pathogens, but these substances failed to restore appressorium formation in ∆BmOPY2 mutants. In comparison with the wild type, the ∆BmOPY2 mutants showed increased appressorium formation on intercellular spaces of maize leaves, suggesting that pectin-a component of these spaces-may promote this process. The addition of pectin restored appressorium formation by ∆BmOPY2 mutants on plastic surfaces. These findings reveal a novel dual regulation of appressorium formation in B. maydis, involving both BmOPY2-mediated hydrophobic surface recognition and a distinct pectin-dependent pathway.}, }
@article {pmid41973048, year = {2026}, author = {Rao, X and Zou, L and Yao, Y and Liu, C}, title = {Innate Immunity and Microbial Recognition in Reproduction: From Barrier Defense to Maternal-Fetal Tolerance.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {40}, number = {8}, pages = {e71799}, pmid = {41973048}, issn = {1530-6860}, mesh = {*Immunity, Innate/immunology ; Female ; Humans ; Pregnancy ; *Reproduction/immunology ; Animals ; *Microbiota/immunology ; Male ; *Maternal-Fetal Exchange/immunology ; *Immune Tolerance ; }, abstract = {Reproduction requires the innate immune system to perform two opposing tasks simultaneously: prevent microbial invasion while preserving tolerance to sperm, the semi-allogeneic embryo, and the developing fetus. This review proposes a unified barrier defense-tolerance framework to explain how reproductive success depends on the coordinated integration of epithelial and mucus barriers, antimicrobial peptides, complement, tissue-resident innate immune cells, pattern-recognition receptor signaling, microbial ecology, and endocrine-metabolic regulation across the female and male reproductive tracts and the maternal-fetal interface. We summarize how Toll-like receptors, NOD-like receptors, RIG-I-like receptors, and cGAS-STING pathways shape early reproductive events, including gamete quality control, sperm transit, implantation, placentation, and antiviral defense, and how tightly constrained physiological inflammation supports tissue remodeling, whereas excessive or unresolved activation contributes to infertility, recurrent pregnancy loss, preeclampsia, fetal growth restriction, and preterm birth. We further examine microbiota-host interactions in reproduction, emphasizing that evidence is strongest for cervicovaginal communities, while endometrial, placental, and male genital microbiota findings require more cautious interpretation because of low-biomass sampling, contamination risk, and limited reproducibility. Beyond local microbial niches, gut-derived metabolites emerge as important regulators of immune tone and barrier function in reproductive tissues. We also discuss downstream effector mechanisms, including inflammasomes, regulated cell death, extracellular vesicles, and soluble innate mediators, and evaluate their translational relevance for biomarker development and targeted intervention. Overall, reproductive disorders are best viewed as systems-level outcomes of disturbed interactions among host barriers, innate sensing thresholds, microbial signals, and metabolic context, providing a conceptual basis for future multi-omics and mechanism-driven reproductive immunology.}, }
@article {pmid41973238, year = {2026}, author = {Gao, S and Zhong, L and Zhang, Y and Zhu, R and Shao, Y and Li, R and Zhu, Y and Cai, W}, title = {Optimal Preservation Method for Long-term Preservation in ddH2O and Starvation Adaptive Mechanisms of Flavobacterium columnare Revealed by Multi-omic Analysis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02756-9}, pmid = {41973238}, issn = {1432-184X}, support = {9610574, 7006064//APRC-CityU New Research Initiatives/Infrastructure Support from Central/ ; 9048294//Early career scheme/ ; }, }
@article {pmid41973243, year = {2026}, author = {Charaabi, K and Hamden, H and Fadhel, S and Tanfouri, N and Bouzenbila, S and Djobbi, W and Cherif, A and Msaad Guerfali, M}, title = {Probiotic Modulation of Gut Microbiota Enhances Immunity and Nutrition in SIT Ceratitis Capitata Sterile Males.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02754-x}, pmid = {41973243}, issn = {1432-184X}, }
@article {pmid41975513, year = {2026}, author = {Castro-Severyn, J and Pardo-Esté, C and Saraiva, J and Fortt, J and Mörchen, R and Albarracin, VH and Saavedra, CP and Bol, R and Castro-Nallar, E and da Rocha, UN and Remonsellez, F}, title = {Distinct taxonomic signatures in the rhizobiome of two native plants from the polyextreme Salar de Huasco ecosystem.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00894-8}, pmid = {41975513}, issn = {2524-6372}, support = {2021 Postdoctoral FONDECYT 3210156//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; 2021 Postdoctoral FONDECYT 3230189//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; Regular FONDECYT 1250419//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; FONDECYT 1240871//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; Regular FONDECYT 1220902//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; }, abstract = {BACKGROUND: Global food security faces mounting pressure from population growth, climate change, and deteriorating soil conditions. Rhizospheric microbial communities (rhizobiomes) play a key role in plant physiology, enhancing growth and tolerance to abiotic stress. To explore their potential contribution to plant resilience in extreme environments, we characterized the rhizobiomes of Deyeuxia curvula and Werneria incisa across the Salar de Huasco (SH) in the Chilean Altiplano (~ 3800 masl), a polyextreme ecosystem characterized by high UV radiation, salinity gradients, water scarcity, and high metal concentrations. Our objectives were to identify microbial taxa associated with plant adaptation and to infer functional traits linked to survival under these conditions.<br><br>RESULTS: We generated 16S rRNA amplicon sequencing data from 200 rhizosphere samples. Both host plant identity and geographic location significantly shaped microbial community composition, with site explaining a larger proportion of variance than plant identity alone. Actinomycetota dominated both rhizobiomes, with genera such as Modestobacter and Blastococcus (known for UV resistance, desiccation tolerance, and genomic plasticity) contributing to species-specific profiles. At the genus level, Ilumatobacter, Nesterenkonia, Tropicimonas, and Nitriliruptor were enriched in D. curvula, whereas Pseudarthrobacter, Kocuria, Crossiella, and Blastococcus were more abundant in W. incisa. Network analysis revealed greater complexity and functional redundancy in D. curvula, while W. incisa harbored a more generalist network. Functional predictions indicated that chemoheterotrophy dominates both rhizobiomes, while denitrification, methylotrophy, and ureolysis were enriched in W. incisa, and osmotic stress-tolerance functions such as glycine betaine cycling were enriched in D. curvula.<br><br>CONCLUSION: The two plants follow contrasting ecological strategies: D. curvula relies on a specialization and resilience strategy supported by a diverse, stress-adapted rhizobiome, while W. incisa employs a nutritional versatility strategy through a generalist, metabolically flexible community. These findings highlight the value of high-altitude Andean rhizobiomes as reservoirs of great biodiversity with relevant functions for future biotechnological applications particularly for agriculture under arid and saline conditions. This underscores the importance of extending conservation policies to native microbial communities in protected areas such as the Salar de Huasco.}, }
@article {pmid41976101, year = {2026}, author = {Wang, E and Han, X and Sun, W and Zheng, C and Du, W}, title = {Replacing up to 50% of Corn Silage with Triticale Silage Alters the Fecal Microbiome but Not Milk Yield or Composition in Mid-Lactation Holstein Cows.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {7}, pages = {}, pmid = {41976101}, issn = {2076-2615}, abstract = {Diversifying forage sources may improve the sustainability and flexibility of dairy production. In a 60 d feeding trial, 72 mid-lactation Holstein cows were assigned to three treatments (24 cows/group) and fed a total mixed ration in which corn silage represented 41.16% of dietary dry matter in the control diet; 25% or 50% of this corn silage fraction was replaced with triticale silage (TS) on a dry matter basis. The study evaluated whether partial TS substitution could maintain lactational performance while affecting fecal fermentation and microbiota. Replacing corn silage with TS did not affect milk yield, 4% fat-corrected milk, major milk components, or metabolic indicators. However, 50% replacement increased fecal bacterial richness and diversity, as reflected by ACE, Chao1, and Shannon indices, and altered the overall microbial community structure. This treatment also changed fecal volatile fatty acid profiles, including increasing the proportions of branched-chain volatile fatty acids. Overall, TS can replace up to 50% of the corn silage fraction in the ration of mid-lactation cows without compromising milk production or composition, while modifying hindgut microbial ecology and fermentation patterns, thereby offering greater ration flexibility when corn silage availability is limited or costly.}, }
@article {pmid41976210, year = {2026}, author = {Chandran, A and Wyka, J and Klein, GR and Stefanska, B and Kolniak-Ostek, J}, title = {Shaping the Bioactive Properties of Kombucha Drinks by Using Raw Materials Alternative to Tea.}, journal = {Molecules (Basel, Switzerland)}, volume = {31}, number = {7}, pages = {}, pmid = {41976210}, issn = {1420-3049}, mesh = {Antioxidants/chemistry/pharmacology ; Fermentation ; *Kombucha Tea/analysis ; Humans ; *Tea/chemistry ; Anti-Inflammatory Agents/pharmacology/chemistry ; Phenols/chemistry ; }, abstract = {Alternative substrates to traditional Camellia sinensis tea are increasingly investigated to diversify kombucha and enhance its functional properties. This review synthesizes evidence (2020-2025) on how non-tea substrates influence microbial ecology, metabolite composition, and bioactivity of kombucha. A semi-systematic search of PubMed, Scopus, Web of Science, and publisher platforms identified studies on fruit, vegetable, herbal, algal, cereal, dairy, and food-industry by-product substrates reporting compositional or functional outcomes. Extracted data included substrate characteristics, fermentation conditions, SCOBY features, analytical methods, and reported antioxidant, anti-inflammatory, metabolic, probiotic, and dermatological effects. Fermentation often leads to an increase in total phenolic content and antioxidant capacity. These effects are highly dependent on fermentation conditions, particularly duration and substrate composition. In some cases, prolonged fermentation may result in phenolic degradation or transformation, leading to reduced levels of certain compounds. Fruit- and hibiscus-based systems enhanced anthocyanin-driven antioxidant and anti-inflammatory activity. Vegetable and cereal substrates supplied phenolic acids and β-glucans associated with metabolic regulation and gut health, whereas by-products and algal fermentations supported waste valorization and enrichment in chlorogenic acids, pigments, fibers, and peptides. Despite promising functionality, substantial inter-study variability and limited in vivo validation and the lack of standardized fermentation protocols constrain translational application. In addition, the inherent variability in SCOBY microbial composition represents a major source of inconsistency, as differences in microbial communities can significantly influence fermentation dynamics, metabolite profiles, and functional outcomes.}, }
@article {pmid41976435, year = {2026}, author = {Cele, NP and Kewuyemi, YO and Adiamo, O and Bobasa, EM and Zhang, J and Seididamyeh, M and Sultanbawa, YF and Sivakumar, D}, title = {Probiotic Lactic Acid Bacteria-Fermented Beverages from Bambara Groundnut and Cowpea Sprouts Modulate Gut Microbiota and Short-Chain Fatty Acids.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {7}, pages = {}, pmid = {41976435}, issn = {2304-8158}, support = {98352,//National Research Foundation/ ; }, abstract = {Underutilised, nutrient-dense legumes in their sprouted form provide promising substrates for developing functional fermented foods capable of influencing gut microbial activity and metabolite production. This study evaluated the effects of probiotic lactic acid bacteria-fermented beverages derived from sprouted Bambara groundnut (Vigna subterranea) and cowpea (Vigna unguiculata) on gut microbiota composition and short-chain fatty acid (SCFA) production using an in vitro colonic fermentation model. The beverages were fermented with either Bifidobacterium animalis BB-12 (BCBF24) or Lactiplantibacillus plantarum 75 (BCL7524). During colonic fermentation, at 0, 12, 24, and 38 h, faecal slurries were collected for SCFA analysis using gas chromatography-mass spectrometry (GC-MS) and deoxyribonucleic acid (DNA) sequencing (Oxford Nanopore Technologies). Microbial diversity decreased, indicating selective enrichment of taxa. BCL7524 induced a major shift, significantly (p < 0.05) enriching Bacillota and driving Megasphaera to ~42% dominance within 24 h. This reflected cross-feeding from L. plantarum to lactate-utilising Megasphaera spp. Spearman correlation linked Megasphaera to a broad SCFA profile, including isobutyric, isovaleric, valeric, and hexanoic acids, with a significant (p < 0.05) positive correlation observed for hexanoic acid. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated proteolysis and mapped hexanoic acid to fatty acid biosynthesis pathways, suggesting chain-elongation activity contributing to hexanoate formation. In line with this, BCL7524 produced significantly (p < 0.05) higher levels of hexanoate (3-14 mM) and valerate (10-15 mM), supporting chain-elongation activity within the community. In contrast, BCBF24 enriched Actinomycetota and Bifidobacterium, correlating with acetate production (18-23 mM). This study demonstrates that specific synbiotic beverages can modulate gut microbial ecology and metabolic output under in vitro conditions.}, }
@article {pmid41976452, year = {2026}, author = {Li, X and Li, Y and Li, Q and Jin, Y and Chen, Y}, title = {Rumen Metagenomic and Muscle Metabolomic Characterization of Meat Quality in Duolang Sheep at Different Ages.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {7}, pages = {}, pmid = {41976452}, issn = {2304-8158}, support = {2022TSYCLJ0014//Program for Science and Technology Innovation Talents/ ; 2023B02015//Key Research and Development Program Project of Xinjiang Uygur Autonomous Region/ ; }, abstract = {This study aimed to investigate the changes in the meat quality characteristics of Duolang sheep using rumen metagenomic and muscle metabolomic analyses across different age groups. A total of 24 three-month-old male Duolang sheep were selected and reared, and samples of longissimus thoracis muscle and rumen contents were collected at 4, 6, and 8 months of age to evaluate meat quality, metabolites, rumen metagenome, and volatile fatty acids (VFAs). The results indicated that the lightness (L*45min) and yellowness (b*45min) of the longissimus thoracis muscle at 45 min post-slaughter were significantly higher at 4 and 6 months than at 8 months of age (p < 0.05). In terms of ruminal VFAs, butyrate concentration was significantly higher at 6 months than at 4 months (p < 0.05), and valerate concentration exhibited a quadratic relationship with age (p = 0.02). With increasing age, the relative abundances of Prevotella and Fibrobacter increased, whereas those of Methanobrevibacter and Bacteroides decreased (p < 0.05), leading to shifts in functional pathways related to amino acid, lipid, and carbohydrate and energy metabolism. Untargeted metabolomics revealed that muscle betaine and inosine peaked at 4 months of age, whereas L-arginine, L-proline, and inosinic acid were most abundant at 6 months of age (p < 0.05). Correlation analysis revealed that the b*45min was positively associated with ruminal concentrations of propionate, butyrate, and valerate, as well as with the relative abundances of key Selenomonadales taxa (p < 0.05). Inosinic acid exhibited a positive correlation with the abundance of the genus Sodaliphilus and ruminal butyrate concentration (p < 0.05), while Sodaliphilus abundance was negatively correlated with inosine (p < 0.05). In summary, this study demonstrates that age-related variations in the meat quality of Duolang sheep are closely associated with rumen microbial ecology and muscle metabolites, offering novel insights into the molecular mechanisms underlying meat quality formation and identifying potential biomarkers.}, }
@article {pmid41976454, year = {2026}, author = {Olupot, CK and Sheehan, O and Kampff, Z and McDonnell, B and Woods, DF and Lugli, GA and Ventura, M and Reen, FJ and Sinderen, DV and Mahony, J}, title = {Raw Milk Cheese Microbiomes: A Paradigm for Interactions of Lactic Acid Bacteria in Food Ecosystems.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {7}, pages = {}, pmid = {41976454}, issn = {2304-8158}, abstract = {While industrial-scale dairy fermentations often employ pasteurized milk as the substrate, many farmhouse and traditional production practices apply raw milk derived from a variety of mammals. Certain artisanal production systems rely on the autochthonous microbiota of the milk, fermentation vessels, equipment and/or environment to initiate milk coagulation. While the technological properties of lactic acid bacteria associated with dairy fermentations are well described, their interactions with other organisms during fermentation and cheese ripening are poorly investigated. This study presents an overview of the microbial ecology of raw and pasteurized milk used in the production of Irish farmhouse cheeses using metagenomic and culture-based approaches. Metagenomic analysis of four raw milk-derived cheeses established the dominant presence of either lactococci or Streptococcus spp. and with a secondary population of various lactobacilli. Interestingly, the Brie sample was also demonstrated to possess significant proportion of Hafnia spp. This was corroborated in culture-based analysis where Hafnia isolates were also identified. Furthermore, we report on the motility phenotype, lactose utilization ability and metabolic products of isolates of Hafnia paralvei and Hafnia alvei, and determine that these strains could grow in a non-antagonistic manner on plates with strains of Lactococcus lactis and Streptococcus thermophilus. As artisanal and farmhouse production systems are often associated with protected or regionally significant products, it is essential to develop a clear understanding of the microbial communities within and the complex relationships between the community members.}, }
@article {pmid41976549, year = {2026}, author = {Wang, Y and Wei, Q and Zhang, Z and Xuan, L and Yang, J and Lei, M and Liang, T and Shi, X}, title = {Effects of Different Packaging Materials on Egg Translucency, Quality, and Shell Surface Microbiota.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {7}, pages = {}, pmid = {41976549}, issn = {2304-8158}, support = {ZX01080033424004//Guangxi University/ ; }, abstract = {Egg quality during storage is a critical factor influencing consumer acceptance and food safety. However, the effects of storage methods on eggshell translucency and surface microbiota remain insufficiently understood. In this study, three common packaging methods, paper pulp trays (PPT), expanded polyethylene foam trays (EPE), and transparent plastic boxes (TPB), were evaluated to assess their impact on egg translucency, internal quality, and microbial communities. Egg quality traits were measured, and microstructural and elemental characteristics were examined using scanning electron microscopy and compositional analysis. In addition, 16S rRNA sequencing was performed to characterize the eggshell surface microbiota. The packaging method significantly influenced translucency development, with EPE mitigating mottling better than PPT and TPB. Storage duration was the predominant driver of internal quality deterioration, particularly affecting the albumen height and Haugh units. Translucency was not associated with shell thickness or mineral content but was likely associated with moisture dynamics. Distinct microbial communities are shaped by different packaging materials. These findings provide new insights into the mechanisms underlying translucency and microbial ecology during egg storage. This highlights the practical implications of optimizing packaging strategies to maintain egg quality, extend the shelf life, and ensure microbial safety.}, }
@article {pmid41977084, year = {2026}, author = {Crișan, IM and Crețu, A and Bucur, SM}, title = {Observational Study of the Association Between Oral Helicobacter pylori, Fixed Orthodontic Appliances, and Gastric Cancer Risk.}, journal = {Journal of clinical medicine}, volume = {15}, number = {7}, pages = {}, pmid = {41977084}, issn = {2077-0383}, abstract = {Background:Helicobacter pylori is a well-established risk factor for gastric carcinogenesis. Increasing evidence suggests that the oral cavity may serve as an extragastric reservoir for the bacterium, potentially contributing to persistent infection and reinfection. Orthodontic appliances can modify oral biofilm ecology and may facilitate bacterial colonization. This study aimed to investigate the association between oral H. pylori colonization and gastric cancer, while exploring the potential modifying role of fixed orthodontic appliances. Materials and Methods: In this cross-sectional observational study, 212 participants were recruited from gastroenterology and dental clinics between January 2023 and March 2025. Oral samples were collected and analyzed for H. pylori DNA using polymerase chain reaction (PCR). Gastric diagnoses were established through endoscopic examination and histopathological evaluation, classifying participants into gastric cancer, precancerous gastric lesions, non-atrophic gastritis, and control groups. Demographic, clinical, and oral health variables were recorded. Multivariable logistic regression models were used to evaluate the association between oral H. pylori detection and gastric cancer while adjusting for potential confounders, including age, sex, smoking status, oral hygiene indicators, and socioeconomic factors. Results: Oral Helicobacter pylori DNA was detected in 35/54 (64.8%) patients with gastric cancer, 30/56 (53.6%) with precancerous lesions, 21/52 (40.4%) with non-atrophic gastritis, and 15/50 (30.0%) controls. Gastric H. pylori infection was identified in 41/54 (75.9%) gastric cancer cases compared with 18/50 (36.0%) controls. Oral H. pylori positivity was more frequent among patients undergoing active orthodontic treatment (22/36, 61.1%) than among those without orthodontic appliances (79/188, 42.0%). In multivariable analysis, oral H. pylori positivity remained independently associated with gastric cancer (adjusted OR 3.02, 95% CI 1.51-6.03, p = 0.002). Conclusions: Our findings support an association between oral-gastric microbial interactions and H. pylori-associated disease, and suggest that the oral cavity may serve as a potential reservoir for gastric infection dynamics. The presence of orthodontic appliances may be associated with altered oral microbial ecology and could be linked to sustained H. pylori colonization.}, }
@article {pmid41964722, year = {2026}, author = {Liedtke, J and Rodenburg, F and Du, C and Zhang, L and Raaijmakers, JM and van Wezel, GP and Briegel, A}, title = {Morphological plasticity of endophytic Chitinophaga pinensis.}, journal = {Antonie van Leeuwenhoek}, volume = {119}, number = {5}, pages = {}, pmid = {41964722}, issn = {1572-9699}, mesh = {*Endophytes/genetics/cytology/physiology ; Microbiota ; }, abstract = {Environmental changes, whether due to climate change or human influences, compromise the resilience of plants to biotic and abiotic stresses, such as pathogens, drought and heat. Plant microbiota are known to promote plant resilience. To be able to harness the power of the plant microbiome we need to identify microbiota with health-promoting properties. Recent studies have demonstrated that the bacterium Chitinophaga pinensis enhances plant health and increases resistance to fungal infections. Here, we show that C. pinensis exhibits an unusually high morphological plasticity, switching between a filamentous and a spherical cell state, each of which is characterized by a distinct transcriptional profile. Despite these transcriptional differences, spherical cells remained metabolically active and replicating, while lacking structural characteristics typically associated with dormant states. Furthermore, the spherical cell morphology of C. pinensis facilitates hitchhiking behaviour and motility via surfactin cheating, potentially influencing its dispersal and interactions within the plant microbiome. To investigate the structural dynamics and transcriptional adaptation of this plant endophyte, we applied a combination of microscopy and culture-based techniques. Taken together, our study provides new insights into the morphological flexibility and transcriptional regulation of the plant-beneficial C. pinensis.}, }
@article {pmid41964929, year = {2026}, author = {Arboleda-Baena, C and Correa, FB and Saraiva, JP and Castillo-Rivadeneira, S and Kasmanas, JC and Chatzinotas, A and Jurburg, SD}, title = {HVRLocator: A Computationally Efficient Tool for Identifying Hypervariable Regions in Large 16S rRNA Datasets.}, journal = {GigaScience}, volume = {}, number = {}, pages = {}, doi = {10.1093/gigascience/giag040}, pmid = {41964929}, issn = {2047-217X}, abstract = {BACKGROUND: Metabarcoding of the 16S rRNA gene is widely used to assess microbial diversity due to its cost-effectiveness and efficiency. However, publicly available 16S rRNA metabarcoding datasets often lack standardized metadata, particularly information on the sequenced hypervariable regions or primers used, which are critical to their accurate reuse. To address this, we present HVRLocator, a computational tool that (1) identifies the start and end positions of 16S rRNA amplicons, (2) determines their corresponding hypervariable regions, and (3) detects the presence of primer sequences. This tool was validated on four datasets comprising 41,513 samples generated with different primers and sequencing platforms.<br><br>RESULTS: HVRLocator can process archived 16S rRNA sequences from NCBI SRA at an average rate of 6.5 samples per minute. Validation showed it reliably detects amplicon start and end positions across datasets sequenced with different primers and platforms, achieving 100% accuracy within single-platform studies and correctly revealing length heterogeneity across platforms. It also flagged misannotated metadata and problematic sequences, underscoring its value as a sequence data curation tool. Finally, HVRLocator can select comparable sequences to build large 16S rRNA amplicon databases spanning the same hypervariable region, facilitating cross-study comparisons.<br><br>CONCLUSION: HVRLocator overcomes unreliable metadata by accurately identifying 16S rRNA amplicon start and end positions, determining hypervariable regions, and detecting primer sequences, enabling accurate curation and large-scale processing of 16S rRNA data for reliable and reproducible microbial studies, syntheses, and meta-analyses.}, }
@article {pmid41965068, year = {2026}, author = {Wu, H and Hu, L and Pu, J and Yang, L and Han, F and Wang, Y and Tu, A and Gao, R and Lin, K and Liang, Y and Wu, Z and Pan, S and Song, J and Tang, J and Wang, X}, title = {Oral Microbiome Dysbiosis in Primary Sjögren's Syndrome: A Systematic Review and Meta-Analysis.}, journal = {Rheumatology (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/rheumatology/keag178}, pmid = {41965068}, issn = {1462-0332}, abstract = {OBJECTIVES: Dry mouth symptoms in patients with primary Sjögren's syndrome (pSS) may be associated with oral microbiome dysbiosis, which plays a critical role in the pathogenesis of pSS and potentially contributes to disease progression. This study systematically reviews and meta-analyzes the latest research on the relationship between the oral microbiome and pSS to identify potential diagnostic biomarkers.<br><br>METHODS: A systematic search was conducted across nine international databases (PubMed, Cochrane Library, Embase, Web of Science, Scopus, VIP, CNKI, Wanfang, and SinoMed) up to October 1, 2024, using a combination of Medical Subject Headings (MeSH) and free-text terms: "oral microbiome" OR "oral flora" AND "Sj&#xf6;gren's Syndrome" OR "pSS." Only studies analyzing the oral microbiota of pSS patients were included. A random-effects meta-analysis was performed for quantitative synthesis. And use a funnel chart to assess the publication bias of the included articles. The conclusions are tempered by the moderate risk of bias in some included studies, substantial heterogeneity (partly attributed to methodological), and the limited number of studies for certain subgroup analyses, which may affect the precision of the pooled estimates.<br><br>RESULTS: A total of 833 studies were identified, 21 of which were included, with 16S rRNA sequencing being the most commonly used technique. QIIME (Quantitative Insights Into Microbial Ecology) is a mainstream bioinformatics analysis tool. Of the 21 studies (1094 participants) included, 19 provided data on &#x3b1; diversity. Overall, declines in the &#x3b1; diversity index were common in pSS (Chao1: SMD = -0.79, [95% CI = -1.381, -0.21], p&#xff1c;0.001; Shannon index: SMD = -0.16, [95%CI = -0.53, -0.21], p=0.400; Simpson index: SMD = -0.14, [95% CI = -0.79, -1.06]), p=0.770. Ten of these studies provided data on &#x3b2; diversity, suggesting a clear difference between the pSS group and the healthy control group. Firmicutes (mainly including Streptococcus spp., Velon spp., etc.) showed a significant enrichment trend in pSS patients, and the relative relative abundance of Proteobacteria (Haemophilus), Actinomycetes and Spiromycetes decreased in pSS patients.<br><br>CONCLUSION: pSS patients demonstrate reduced oral microbiome diversity compared to HCs&#xff08;Healthy controls&#xff09;. Enrichment of Veillonella, Streptococcus, and Prevotella may correlate with pSS pathogenesis, whereas Haemophilus parainfluenzae might serve as a protective taxon. Oral dysbiosis appears to be a distinctive feature of pSS compared to systemic lupus erythematosus (SLE). Further mechanistic studies are needed to explore causal relationships and therapeutic targets.}, }
@article {pmid41966474, year = {2026}, author = {Guimarães Silva, CM and Ferreira, RBR and Lobo, LA}, title = {Microbial Adaptation and Host Signaling: Bacteroides-Bile Acid Interactions in Gut Health.}, journal = {Anaerobe}, volume = {}, number = {}, pages = {103041}, doi = {10.1016/j.anaerobe.2026.103041}, pmid = {41966474}, issn = {1095-8274}, abstract = {Bile acids are amphipathic molecules synthesized from cholesterol that act not only as digestive agents but also as key signaling molecules regulating host metabolic and immune pathways via FXR (farnesoid X receptor) and TGR5 (G protein-coupled bile acid receptor). In the colon, microbial metabolism profoundly transforms bile acids, reshaping their composition, physicochemical properties, and signaling capacity. Among gut microbes, Bacteroides spp. are abundant, metabolically versatile, and immunologically active, displaying high resilience to bile acids through efflux pumps, membrane adaptations, and bile salt hydrolase activity (BSH). These bacteria degrade complex polysaccharides via polysaccharide utilization loci, producing short-chain fatty acids and vitamins such as K2 that reinforce epithelial barrier integrity, modulate immune responses, and influence systemic metabolic and anticancer pathways. While microbial BSHs in other bacteria have been shown to generate bile acid amides (BBAAs) with immunomodulatory and signaling functions, such production has not yet been observed in Bacteroides, though it is plausible given their BSH activity. Strain-specific diversity of Bacteroides and their bile acid interactions underpins both microbial ecology and host physiology. Understanding these mechanisms is essential for microbiota-targeted interventions and therapies, highlighting the metabolic and immunological modulation by Bacteroides-bile acid interplay, bacterial bile resistance strategies, and potential biotechnological and clinical applications.}, }
@article {pmid41967501, year = {2026}, author = {Deschamps, C and Tronel, A and Bailly, E and Tanfede, MRS and Gilibert, S and Denis, S and Soranzo, T and Van De Wiele, T and Marinelli, L and Blanquet-Diot, S}, title = {Small intestinal microbiome, the underrated maestro of SIMO disease.}, journal = {FEMS microbiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuag016}, pmid = {41967501}, issn = {1574-6976}, abstract = {Small intestinal microbial overgrowth (SIMO) results from a breakdown in the delicate equilibrium between luminal environment, gut motility, and microbial ecology. Despite extensive research, these factors have largely been investigated as separate entities, with limited integrative insights into their interplay. This review is the first comprehensive synthesis of physicochemical, mechanical, and microbial parameters shaping SIMO pathogenesis. By reviewing both clinical and experimental data, we reveal how alterations in pH, transit time, digestive secretion dynamics, bile acid composition and impaired intestinal absorption collectively reshape microbial load, diversity, and metabolic output, establishing a self-perpetuating loop of dysfunction. We further discuss the limitations of current diagnostic tools and the transformative potential of emerging approaches, from sampling capsules enabling molecular analyses, to in vitro models simulating human small intestinal ecosystem. This integrative perspective shifts the paradigm from a microbe-centered to an ecosystem-based understanding of SIMO, outlining key challenges and opportunities for personalized diagnostics, mechanistic research, and microbiota-targeted next-generation therapeutics including pre-, pro-, postbiotics and faecal transplantation.}, }
@article {pmid41971323, year = {2026}, author = {David, EM and Parthasarathi, T}, title = {Soil microbial processes shaping seed performance: linking soil microbiomes to sustainable agriculture.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1797362}, pmid = {41971323}, issn = {1664-302X}, abstract = {Soil microorganisms are fundamental to soil sustainability, governing organic matter turnover, nutrient cycling, soil structure formation, and plant health regulation. In the context of accelerating soil degradation, climate change, and expanding agricultural salinization, understanding how soil microbial communities contribute to ecosystem resilience is crucial for sustainable soil management. Although rhizosphere and plant nutrition roles are well recognized, their influence across plant life cycles and generations remains insufficiently integrated. This Review synthesizes recent advances to propose the soil seed microbiome continuum as a unifying concept linking soil microbial processes to seed quality, early plant establishment, and crop stress tolerance under salinity stress. Unlike existing microbiome salinity reviews that predominantly focus on rhizosphere interactions or microbial inoculants under salt stress, this review advances an integrative soil seed continuum framework that connects soil ecological processes, microbial transmission, and seed associated microbiomes with a transgenerational context. We discuss how this ecosystem acts as a dynamic reservoir of beneficial and stress-adapted microorganisms that are selectively recruited by plants, transmitted through plant associated pathways, and ultimately incorporated into developing seeds. Under saline conditions, ecological filtering favors halotolerant microbial taxa that stabilize soil functions, and enhancing plant stress tolerance, with potential transgenerational benefits mediated through seed-associated microbiomes. The evidence from soil microbial ecology, plant microbe interactions, and emerging microbiome-enabled technologies, this review highlights the role of soil microorganisms as biological connectors between soil sustainability and crop performance. We further discuss implications for reduced chemical inputs, yield stability, nature-based restoration, and contributions to the United Nations Sustainable Development Goals. Positioning soil microorganisms within a soil seed continuum offers new perspectives for managing soil biodiversity and functionality, reinforcing their central role in sustainable agriculture and resilient soil ecosystems. This integrative perspective provides a strategic foundation for developing microbiome informed soil management approaches aimed at enhancing long term crop performance under increasing salinization and climate change.}, }
@article {pmid41971525, year = {2026}, author = {Adekoya, AE and Boggs, TE and Ibberson, CB}, title = {Revealing community dynamics in polymicrobial infections through a quantitative framework.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag061}, pmid = {41971525}, issn = {2730-6151}, abstract = {Laboratory models provide tractable, reproducible systems that have long served as foundational tools in microbiology. However, the extent to which these models accurately mimic the biological environments they represent remains poorly understood. A quantitative framework was recently introduced to assess how well laboratory models capture microbial physiology in situ. However, applications of this framework have been limited to characterizing the physiology of a single species in human infections, leaving a gap in our understanding of overall microbial community physiology in polymicrobial contexts. Here, we extended this framework to evaluate the accuracy of laboratory model systems in capturing community-level functions in polymicrobial infection. As a proof of concept, we applied the extended framework to a polymicrobial model of human chronic wound (CW) infection. CWs harbor metabolically diverse bacterial species that engage in a range of microbe-microbe interactions, ultimately impacting community dynamics and disease progression. However, studies on the mechanistic drivers of chronic wound infection have relied on single species or pairwise approaches. Here, we demonstrate that our adapted framework can be used to develop accurate polymicrobial models. Further, we demonstrate that this extended framework can evaluate the occurrence of known microbe-microbe interactions. Building on our prior work in large-scale metagenomic and metatranscriptomic analysis, we propose a highly accurate 6-member synthetic bacterial community model i.e. representative of the taxonomic and functional complexity of human CW infections. This approach will support the development of ecologically relevant polymicrobial models and better treatment strategies.}, }
@article {pmid41971529, year = {2026}, author = {Garefelt, K and Karlson, B and Brosnahan, ML and Kraft, K and Torstensson, A and Seppälä, J and Cembella, A and Andersson, AF}, title = {High throughput in situ imaging reveals widely occurring diel vertical migration among phytoplankton.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag049}, pmid = {41971529}, issn = {2730-6151}, abstract = {Phytoplankton undertake daily vertical migration through the water column to optimize light and nutrient access while avoiding predators. However, diel vertical migration (DVM) patterns remain poorly characterized for many taxa due to limitations of labor-intensive traditional microscopy. Here, we employed high-throughput in situ imaging flow cytometry to investigate DVM. An Imaging FlowCytobot (IFCB) was deployed to continuously profile the vertical water column for ~10 weeks (August-October 2016) at a location in the Skagerrak, eastern North Sea. This revealed significant DVM for several morpho-taxonomic groups, including taxa belonging to ciliates, dinoflagellates, and diatoms, shifting median depth by 2-6 m between night and day. The analysis also revealed that DVM can be inferred from diel pulses in surface water biomass, which we leveraged to study DVM in an extensive IFCB time-series dataset from the central Baltic Sea (June-October in 2020 and 2021). Migratory taxa accounted for 77% and 79% of total phytoplankton biomass (size range <10-150 μm) in the Skagerrak and Baltic Sea, respectively, underscoring the ecological significance of DVM. Most populations peaked near the surface at midday, although other patterns were also observed. While many taxa displayed consistent migration behaviors across both regions, others differed-likely due to population-specific traits or local environmental conditions. Seasonal changes in migration patterns suggest a role for community turnover and shifting environmental conditions. This study highlights the prevalence of DVM in phytoplankton and showcases the power of automated, high-throughput imaging technologies to advance our understanding of plankton ecology.}, }
@article {pmid41971531, year = {2026}, author = {Zhang, W and Han, N and Zhang, T and Qiang, Y and Peng, X and Li, X and Kan, B}, title = {Dynamic change patterns of the human gut microbiota-fluctuation, loss-acquisition, and turnover-and their underlying causes.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag046}, pmid = {41971531}, issn = {2730-6151}, abstract = {The temporal dynamics of the gut microbiome are critical to human health, yet their patterns and underlying drivers remain poorly characterized at a monthly resolution and strain level. This knowledge gap limits the development of targeted microbiome interventions. Here, we integrate longitudinal analyses across three human cohorts-a cross-sectional cohort (n = 190), an intensive 52-month time series (n = 7), and a paired 6-month cohort (n = 43)-together with a humanized mouse model under antibiotic perturbation. Using shotgun metagenomics (516 samples), we resolve microbial dynamics at species and strain resolution. We identify three distinct modes of temporal variation: relative abundance fluctuations, species loss-acquisition events, and strain turnover. Strain turnover contributes substantially to the dynamic reservoir of functional genes, including those associated with virulence and antibiotic resistance. These dynamics are influenced by antibiotic exposure and microbial interspecies interactions. Our work provides a month-scale atlas of gut microbiome variation, revealing widespread transient colonization and strain-level plasticity, thereby offering a refined framework for understanding microbiome stability and personalized microbial ecology.}, }
@article {pmid41960424, year = {2026}, author = {Avila-Nuñez, G and Hernández-Jiménez, S and Ruiz-Ruiz, P and Revah, S}, title = {Efficient methane removal by thermophilic methanotrophs in a compost biofilter.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1777601}, pmid = {41960424}, issn = {1664-302X}, abstract = {Methane (CH4) is a potent greenhouse gas, and biofiltration has proved to be a valuable strategy for treating diffuse emissions from composting and landfill systems. This study characterized the activity of a thermophilic methanotrophic consortium enriched from compost. It also evaluated the consortium's performance, under controlled conditions, in a liquid stirred-tank bioreactor and a compost biofilter for 90 and 65 days, respectively. The consortium, specifically the thermophilic methanotroph Methylocaldum, showed robust CH4 oxidation at 50 °C, attained a maximum elimination capacity (EC) of 342 mg CH4/kg compost·h with 75% removal efficiency (RE), and maintained an EC of ~250 mg CH4/kg compost·h from day 28 with 100% RE. Heat treatment of compost followed by inoculation with the methanotrophic consortium enhanced start-up, reduced microbial competition, and improved stability. Oxygen availability and moisture were identified as critical parameters, while nutrient supplementation had minimal effect. Analysis of respiratory coefficients indicated that heterotrophic microorganisms competed for oxygen, influencing CH4 removal efficiency. Compared with mesophilic systems, the thermophilic biofilter achieved a higher EC, demonstrating the microbes' ability to adapt to higher temperatures. These findings confirm the potential of thermophilic biofiltration for effective CH4 migration and provide guidance for optimizing design and operational strategies in large-scale applications.}, }
@article {pmid41960429, year = {2026}, author = {Freund, L and Topacio, TM and Miao, Y and Porter, WC and Swenson, M and Maltz, M and Botthoff, J and Aronson, EL}, title = {Weather conditions structure the taxonomic and functional diversity of the aeolian dust microbiome.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1691133}, pmid = {41960429}, issn = {1664-302X}, abstract = {INTRODUCTION: The aeolian dust microbiome is composed of uniquely adapted microorganisms that can withstand the harsh conditions of the atmosphere. Specific microbial taxa and survival strategies have been observed in dust microbiomes from around the world, yet the environmental processes that select for microbial composition and function are poorly understood.<br><br>METHODS: Here we explore the taxonomic and functional diversity of the aeolian dust microbiome from sites around the Salton Sea, a hypersaline lake in Southern California, and how dust sources and weather influenced the microbiome. Dust samples were collected from four locations around the Salton Sea in the summer and fall of 2020 and 2021, and 16S (V3-V4) rRNA amplicon sequencing and shotgun metagenomic sequencing was used to characterize the aeolian dust microbiome.<br><br>RESULTS: We observed significant differences in microbial composition between sites, and we were able to identify 13 microbial genera that were members of the core dust microbiome across samples. We also found that genes involved in sporulation, UV-radiation resistance, thermal resistance, osmotic stress resistance, quorum sensing, and antibiotic resistance were shared across the aeolian dust metagenomes. Lastly, local wind conditions and estimated dust source surface categories were significant predictors of the microbial adaptations we found in the aeolian dust metagenomes.<br><br>DISCUSSION: Our results demonstrate the ability of airborne dust microorganisms to readily adapt to their harsh environment and highlight the survival mechanisms that allow them to disperse across broad distances, thus posing a potential health risk to exposed communities.}, }
@article {pmid41960607, year = {2026}, author = {Gonçalves Lima, CM and Amorim-Neto, DP and de Castro, BG and Perini Leme Giordano, AL and Dal Pian, BM and Silva Láscaris, MP and da Silva Ramos, LC and Schreiber, AZ and Colombo, LF and Sant'Ana, AS}, title = {Microbiological Characterization of Baru Nuts From the Cerrado Biome, Brazil.}, journal = {Journal of food science}, volume = {91}, number = {4}, pages = {e71043}, pmid = {41960607}, issn = {1750-3841}, support = {22/10849-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2021/15224-8//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; //Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; //Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Brazil ; *Nuts/microbiology ; Enterobacteriaceae/isolation &amp; purification/classification ; *Food Microbiology ; Fungi/isolation &amp; purification/classification ; *Bacteria/isolation &amp; purification/classification ; Yeasts/isolation &amp; purification/classification ; Colony Count, Microbial ; Salmonella/isolation &amp; purification ; }, abstract = {This study aimed to microbiologically characterize baru nuts, a seed widely consumed in Brazil with growing relevance in the export market. Analyses were conducted for mesophilic and thermophilic aerobic spore-forming bacteria, total mesophilic aerobes, Enterobacteriaceae, Salmonella, Staphylococcus aureus, lactic acid bacteria, molds, and yeasts. Subsequently, Enterobacteriaceae isolates were identified by MALDI-TOF. It was found that in all baru nut samples, counts of S. aureus, lactic acid bacteria, and thermophilic aerobic spore-forming bacteria were below the quantification limits (< 2log10 CFU/g, < 1log10 CFU/g, and 1log10 spore/g, respectively). All samples had counts above the quantification limits for mesophilic aerobic spore-forming bacteria (> 1log10 CFU/g) and total mesophilic aerobes (> 2log10 CFU/g). Enterobacteriaceae counts were below 2.22log10 CFU/g, while molds and yeasts reached up to 2.70log10 CFU/g. Identification of 17 species from the Enterobacteriaceae family revealed potentially pathogenic microorganisms that serve as important biological markers, including emerging and multidrug-resistant species. Franconibacter pulveris was the most abundant, representing 41.9% of all isolates, followed by Pseudescherichia vulneris and Pantoea septica, each accounting for 10.5%. In addition, Cronobacter sp. (3.8%) and Salmonella sp. (1.0%) were identified-both pathogens commonly associated with nuts and low-water-activity products. The presence of these sanitation-relevant and understudied species highlights the need for ongoing microbiological monitoring and a better understanding of the microbial ecology in food products. PRACTICAL APPLICATIONS: This study provides information on the microorganisms found in baru nuts. These results can help producers improve handling and processing practices, contributing to safer products for consumers and supporting the development of quality standards for this native Brazilian nut.}, }
@article {pmid41961080, year = {2026}, author = {Rocabert, A and Pareras, L and Egea, R and Alaraby, M and Rubio, L and Marcos, R and García-Rodríguez, A and Hernández, A}, title = {Life-Stage-Dependent Variation in Gastrointestinal Microbial Communities of Drosophila melanogaster.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02757-8}, pmid = {41961080}, issn = {1432-184X}, abstract = {Drosophila melanogaster has been a useful biological model since its first use, more than 100 years ago. Mainly due to its genetic similarity with humans, as it allowed it to be an accurate representation of how different biological systems work, such as immune function, illness related pathways, gene inheritance, egg development and, in this case, the microbial ecosystem. Age-related changes in the gut microbiota of D. melanogaster offer valuable insights into the dynamic relationship between a host and its microorganisms across lifespan and can be extrapolated to other organisms. This study focusses on the potential changes that microbiota undergoes across the several stages of the fly life cycle, generating robust and high-resolution data using MinION nanopore sequencing as a cutting-edge approach to microbiota analysis Our findings highlight the highly dynamic nature of the gut microbiota across the D. melanogaster lifespan and underscore the necessity of explicitly accounting for developmental stage and chronological age in microbiota-focused studies. Moreover, a clearer understanding of these temporal microbial shifts provides valuable insight into how host-microbiota interactions are shaped during development, maintained during adulthood, and ultimately altered during aging. Currently, the gut microbiota stabilized following post-eclosion establishment, while age-associated dysbiosis and immune decline have not yet emerged. Consequently, using flies around 1-week-old maximizes experimental consistency and sensitivity, making them an optimal model for investigating microbiota-targeted interventions.}, }
@article {pmid41963046, year = {2026}, author = {García Guerrero, JT and Peinado Guevara, LI and Campista León, S}, title = {Microbial ecology of artisanal fresh cheese from Sinaloa: Influence of geographic terroir on diversity, functionality, and safety.}, journal = {Food microbiology}, volume = {138}, number = {}, pages = {105073}, doi = {10.1016/j.fm.2026.105073}, pmid = {41963046}, issn = {1095-9998}, mesh = {*Cheese/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; *Microbiota ; Mexico ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; Animals ; Food Microbiology ; Phylogeny ; }, abstract = {Artisanal fresh cheese is fundamental to Mexico's heritage and economy, although its production with raw milk poses significant safety challenges. Given that the microbiota of Sinaloa cheeses and their ecological determinants remained unexplored, this study characterized their bacterial diversity and functional potential through massive sequencing of the 16S rRNA gene. Thirty samples from 10 locations along a latitudinal gradient were analyzed, V3 amplicon-based sequencing under Illumina Miniseq platform was performed, processing the data with DADA2 to infer Amplicon Sequence Variants (ASVs). The community was dominated by Proteobacteria (73.5%) and Firmicutes (25.9%). Canonical Correspondence Analysis (CCA) showed that altitude and geographic region were major drivers of microbiota structure, each explaining approximately 40% of the constrained variance, allowing the identification of a distinctive "terroir" (e.g., Marinomonas in the north, Streptococcus in the center). Genera of biotechnological interest such as Lactococcus, Lactobacillus, and Leuconostoc were found, a high prevalence of taxa associated with enteric contamination and opportunistic pathogens (Salmonella, Aeromonas, Acinetobacter) was detected. Predicted activities of microbial communities were primarily associated with core metabolic processes, including carbohydrate and energy metabolism. Predicted resistance-related functions were mainly linked to stress response mechanisms and antimicrobial peptide resistance, while virulence-associated traits were related to adhesion, biofilm formation, and iron acquisition, reflecting microbial strategies for environmental persistence and community interactions. In conclusion, this first amplicon-based characterization reveals a complex ecosystem driven by the environment, highlighting the duality of Sinaloa cheese as a reservoir of native lactic biodiversity and a source of health risks that requires immediate control strategies.}, }
@article {pmid41964659, year = {2026}, author = {Vulart, L and Izcara, N and Estévez, &#xc1; and Peiro, E and Gòdia, F and Ganigué, R}, title = {Carbohydrate concentration and type drive product selectivity to a mixture of volatile fatty acids or lactic acid in thermophilic mixed-culture fermentation.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-026-13806-0}, pmid = {41964659}, issn = {1432-0614}, support = {101153341//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; BOF.BAF.2024.0502.01//Bijzonder Onderzoeksfonds UGent/ ; }, abstract = {Carboxylic acids are key platform chemicals that can be biologically produced in mixed-culture fermentations. In these systems, product formation is determined by the microbial community composition, which is shaped by operational conditions. A general trend has been observed linking substrate availability to the production of either lactic acid or volatile fatty acids, but it remains unclear at which substrate concentration this shift occurs. This study investigates the effect of carbohydrate concentrations (from 0 to 670 mg COD·L[-1]) and type (hexoses and pentoses) on product selectivity and microbial community composition in thermophilic mixed-culture fermentations. Fermentation experiments were conducted in thermophilic reactors (55 °C, pH 5.3, HRT 4 days), fed either with glucose or xylose. Higher substrate concentrations (650-670 mg COD·L[-1]) favored lactic acid production, accounting for 60-76% of the soluble products. Lower carbohydrate concentrations reduced lactic acid production and increased volatile fatty acid concentrations. Volatile fatty acids became the main product under low substrate concentrations (continuous operation; 0 mg COD·L[-1]), with a selectivity of 83-97%. Despite this general trend, the substrate concentration at which the shift from lactic acid to volatile fatty acids occurred depended on the carbohydrate type. Microbial community analyses revealed Thermoanaerobacterium as the dominant genus in all reactors, with genera within the Bacillaceae family (putatively involved in lactic acid production) increasing in relative abundance under high carbohydrate concentrations. This suggests that the product shift resulted from both a metabolic shift within the dominant species and a change in the microbial community composition. KEY POINTS: Low carbohydrate concentrations favor VFA production.High carbohydrate concentrations promote lactic acid formation.Carbohydrate type influences the shift from lactic acid to VFAs.}, }
@article {pmid41955946, year = {2026}, author = {Jiang, S and Li, T and Lu, J and Cai, F and Pang, G and Liu, J and Liu, D and Shen, Q}, title = {From degradation to alleviation: Trichoderma facilitates plants resisting the PBAT stress through secreting a cutinase-like enzyme.}, journal = {Environment international}, volume = {210}, number = {}, pages = {110228}, doi = {10.1016/j.envint.2026.110228}, pmid = {41955946}, issn = {1873-6750}, abstract = {The ecological impacts of biodegradable plastics like poly (butylene adipate-co-terephthalate) (PBAT) demand urgent investigation due to their unresolved risks to soil-plant systems, including physical interference with root development, disruption of indigenous microbial ecology. While PBAT depolymerization is a prerequisite for its removal, the slow and inefficient breakdown of these polymers in soil often results in the persistent accumulation of phytotoxic monomers, creating a bottleneck for biological remediation. In this study, through transcriptomic and phylogenetic analyses, we identified a key secreted hydrolase CUT2, belonging to a distinct clade of cutinase-like polyester hydrolases. Overexpression of cut2 (OEThcut2) significantly enhanced PBAT depolymerization, resulting in 27.0% and 22.4% increases in the release of terephthalic acid (TPA) and butanediolic acid (BTA) compared to the wild-type strain, respectively. The direct catalytic activity of purified CUT2 was confirmed through vitro film weight-loss assays with a degradation rate of 4.3% observed. In pot experiments, integrated multi-omics analysis revealed that the OEThcut2 strain reconfigured the rhizosphere microbial community and activated the aromatic degradation pathways, coinciding with the attenuated accumulation of degradation monomers. Furthermore, the enrichment of carbohydrate-active enzymes (CAZys) and the reduction of monomer burdens which revitalized the tricarboxylic acid cycle (TCA) and normalized redox homeostasis thereby clearing the metabolic bottleneck for intermediate turnover. Complementary monomer-exposure assays established that the reduction of PBAT monomers is critical for alleviating plant oxidative stress and growth inhibition. These findings provide a depolymerization to detoxification framework that links fungal enzymatic activity to rhizosphere metabolic recovery, offering a robust strategy for mitigating biodegradable plastic toxicity in agroecosystem.}, }
@article {pmid41955982, year = {2026}, author = {Besharati Fard, M and Guo, H and De Vrieze, J and Wu, D}, title = {Chronic ciprofloxacin exposure reduces anaerobic digestibility of waste microalgal-bacterial aerobic granular sludge: Metagenomics and metatranscriptomics overview.}, journal = {Water research}, volume = {299}, number = {}, pages = {125876}, doi = {10.1016/j.watres.2026.125876}, pmid = {41955982}, issn = {1879-2448}, abstract = {Microalgal-bacterial aerobic granular sludge (MB-AGS) is a promising wastewater treatment technology, but its long-term sustainability depends on whether its waste biomass (WMB-AGS) can be effectively stabilized through anaerobic digestion, particularly under antibiotic stress. Here, we compared the digestibility and ciprofloxacin response of WMB-AGS and conventional waste activated sludge (WAS) using 21-day biochemical methane potential (BMP) tests, 3-day hydrolysis-acidogenesis assays, and 90-day semi-continuous digesters, supported by enzyme activity, extracellular polymeric substances (EPS) characterization, and multi-omics profiling. The WAS produced substantially higher methane yields (302 ± 7 mL CH4/g VS) than WMB-AGS (62 ± 4 mL CH4/g VS), confirming the superior digestibility of WAS. Ciprofloxacin effects were exposure-regime dependent, a single initial dose up to 1000 µg/L did not affect methane production in BMP assays. However, continuous ciprofloxacin exposure in semi-continuous digesters significantly reduced daily biogas production, from 114 ± 9 to 96 ± 6 mL/day in WAS and from 23 ± 1 to 15 ± 2 mL/day in WMB-AGS. During the hydrolysis-acidogenesis, ciprofloxacin promoted volatile fatty acid accumulation and inhibited key hydrolytic, acidogenic, and methanogenic enzymes. Biotransformation was the dominant ciprofloxacin removal mechanism. The EPS acted as an initial protective interface but also contributed to hydrolysis limitation. Multi-omics analyses showed that chronic ciprofloxacin exposure did not suppress core methanogenesis genes, but reconfigured upstream electron-transfer and methyl-transfer functions, with enrichment of Corynebacterium and Methanobacterium. Overall, WMB-AGS is inherently less digestible than WAS. These findings highlight the need to consider substrate-specific matrix effects and long-term antibiotic pressure when evaluating the downstream anaerobic valorization.}, }
@article {pmid41956788, year = {2026}, author = {Gao, WK and Yan, SQ and Che, JK and Yang, Y and Chu, HK and Yang, L}, title = {[Gut microbiota-associated metabolites with drug-induced liver injury].}, journal = {Zhonghua gan zang bing za zhi = Zhonghua ganzangbing zazhi = Chinese journal of hepatology}, volume = {34}, number = {3}, pages = {256-262}, doi = {10.3760/cma.j.cn501113-20250417-00146}, pmid = {41956788}, issn = {1007-3418}, support = {2023YFC2413804, 2022YFA1305600//National Key R&amp;D Program of China/ ; 82270614, 82470584//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Chemical and Drug Induced Liver Injury/microbiology/metabolism ; Fatty Acids, Volatile/metabolism ; Bile Acids and Salts/metabolism ; Liver/metabolism ; Lipopolysaccharides/metabolism ; Amino Acids/metabolism ; }, abstract = {Drug-induced liver injury (DILI) is a condition that is induced by the hepatocellular toxicity of drugs or their metabolites or by hypersensitivity reactions of the liver to drugs and their metabolites. Clinical heterogeneity is high, with diverse liver injury patterns associated with drug toxicity, the body's functioning status, and individual susceptibility. The incidence rate shows an increasing trend year by year, and there is a lack of efficient and specific treatment methods. In recent years, the role of gut microbiota and its metabolites has received considerable attention in DILI. Patients with DILI exhibit imbalances in gut microbial ecology, with changes in the relative abundance of specific microbial populations and their associated metabolites (such as lipopolysaccharides, bile acids, short-chain fatty acids, amino acids, etc.), which can further participate in the DILI process through the "gut-liver axis." Therefore, gut microbiota-targeted regulation and metabolite intervention are expected to become novel targets for DILI diagnosis and treatment. This review focuses on the impact of microbiota-associated metabolites on DILI and explores their potential value in clinical prevention and treatment, aiming to provide a theoretical basis for a deeper understanding of DILI pathogenesis and the development of novel intervention strategies.}, }
@article {pmid41957208, year = {2026}, author = {Metz, BN and Gallagher, P and Profet, P and Raymann, K and Tarpy, DR}, title = {Impact of Two Common Beekeeper-Applied Chemicals on Honey Bee Queen Fecundity and Gut Microbial Communities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02755-w}, pmid = {41957208}, issn = {1432-184X}, support = {2022-67013-42296//National Institute of Food and Agriculture/ ; 2022-67013-42296//National Institute of Food and Agriculture/ ; }, }
@article {pmid41957610, year = {2026}, author = {Sun, J and Luo, Q and Yang, T and Xu, X and Luo, T and Jian, H and Chen, X and Cui, G and Chen, Z}, title = {Association of Helicobacter pylori with Candida albicans enhances fungal virulence and stress tolerance.}, journal = {Gut pathogens}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13099-026-00831-7}, pmid = {41957610}, issn = {1757-4749}, support = {82260402//the Natural Science Foundation of China/ ; ZDSYS[2023]004//Guizhou Key Laboratory of Microbio and Infectious Disease Prevention &amp; Control, China/ ; GYFYMF001, GYFYMF002//the Marshall Joint Laboratory Fund of Affiliated Hospital of Guizhou Medical University/ ; Qiankehe [2025] 024//the Central-Guided Local Science and Technology Projects of Guizhou Province, China/ ; GZWKJ 2022-521//the Science and Technology Fund Project of the Guizhou Health Commission/ ; D20009//the 111 Project/ ; }, abstract = {BACKGROUND: Bacterial associations with fungal hosts are increasingly recognized as common rather than exceptional. Among these interactions, Candida spp. and Helicobacter pylori are of particular interest, as evidence suggests that Candida may serve as a potential host for H. pylori, facilitating its persistence and dissemination. Although interactions between Candida spp. and members of the bacterial microbiota-particularly H. pylori-are increasingly recognized for their role in modulating microbial ecology and influencing pathological outcomes in the host, the impact of H. pylori on Candida albicans remains poorly characterized. Whether this interaction alters the biological behavior or pathogenic potential of Candida spp. remains poorly understood. In this study, C. albicans strains CacoHp, which were detected to be positive for H. pylori-specific genes, were generated through co-culture, and the effects of this bacterial-fungal interaction on tolerance and virulence were investigated.<br><br>RESULTS: Co-culture with H. pylori S7 and C. albicans SC5314 yielded Hp-positive C. albicans CacoHp. Compared with the parental strain SC5314, CacoHp exhibited increased tolerance to antifungal agents, sodium dodecyl sulfate, and H2O2; enhanced inhibition of GES-1 cell proliferation; elevated aspartic protease secretion; and increased hyphal formation. Proteomic and quantitative polymerase chain reaction analyses indicated upregulation of ergosterol transport (SNQ2) and vacuolar ATPase (VMA8) pathways, and enhanced stress tolerance. In mice, CacoHp induced a stronger inflammatory response and more severe gastric tissue damage than the SC5314 strain.<br><br>CONCLUSIONS: Co-culture with H. pylori generates C. albicans strains CacoHp, which were detected to be positive for H. pylori-specific genes, that exhibit enhanced chemical stress tolerance and increased virulence. This study first revealed the influence of H. pylori on Candida phenotypes, further supporting the clinical relevance of their interaction.}, }
@article {pmid41957921, year = {2026}, author = {Husaini, AF and Christita, M and Rukmana, RM and Susilowati, A and Vidilaseris, K}, title = {Reduction of Hexavalent Chromium by Stenotrophomonas and Bacillus.}, journal = {MicrobiologyOpen}, volume = {15}, number = {2}, pages = {e70286}, doi = {10.1002/mbo3.70286}, pmid = {41957921}, issn = {2045-8827}, support = {7092.1/UNS.1.R/PPM/2023//PKUU-PT QS WUR Universitas Sumatera Utara/ ; 2024//BRIN-LPDP (Indonesia Endowment Fund for Education)/ ; }, mesh = {*Chromium/metabolism ; *Stenotrophomonas/metabolism ; Biodegradation, Environmental ; *Bacillus/metabolism ; Oxidation-Reduction ; *Environmental Pollutants/metabolism ; }, abstract = {Hexavalent chromium [Cr(VI)] is a widespread environmental pollutant, posing a significant health risk to ecosystems and humans. Bioremediation using microorganisms offers a cost-effective strategy for its detoxification. This review highlights recent advances in Cr(VI) reduction by Stenotrophomonas and Bacillus species, two bacterial genera with strong potential for chromium detoxification. Stenotrophomonas species primarily rely on intracellular enzymatic reduction mechanisms, often mediated by chromate reductases such as ChrR and heme proteins that link chromium detoxification with iron homeostasis. In contrast, Bacillus species employ a broader range of strategies, combining intracellular and extracellular enzymatic reduction, biosorption, and bioaccumulation, supported by stress-response and efflux systems that confer exceptional tolerance to Cr(VI). Comparative analysis reveals complementary metabolic strengths: Stenotrophomonas excels in rapid enzymatic detoxification, while Bacillus offers long-term stability through spore formation and surface-associated sequestration. Together, these traits underscore the promise of mixed consortia featuring both genera for scalable and resilient chromium bioremediation systems. Future research integrating omics-guided pathway mapping, microbial engineering, and biosafety control is expected to accelerate the deployment of efficient and safe Cr(VI) bioremediation technologies.}, }
@article {pmid41958159, year = {2026}, author = {Kaba, E and Addo, SO and Captain-Esoah, M and Salley, SN and DeWitt, ME and Baako, BOA and Angyiereyiri, ED and Frempong, KK and Obuam, PK and Duker, EO and Obuobi, D and Boakye, JD and Agbotse, GD and Yanney, JN and Tawiah-Mensah, CNL and Malm, RO and Amoah, S and Donkor, MN and Azameti, MK and Fuseini, I and Adugbire, LA and Aryee, HA and Asoala, V and Dadzie, SK}, title = {Molecular identification of Rickettsia conorii subsp. israelensis and other tick-borne pathogens in dog ticks from the Upper East region of Ghana.}, journal = {Medical and veterinary entomology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mve.70067}, pmid = {41958159}, issn = {1365-2915}, abstract = {Ticks continue to facilitate the spread of pathogens that affect both humans and domestic animals. Domestic dogs interact with humans and other domestic animals, playing a crucial role in the spread of ticks and tick-borne pathogens. This study examined the diversity of tick species infesting domestic dogs and the occurrence of tick-borne pathogens in the Upper East region. Domestic dogs were randomly selected and examined for tick infestation. The sampled ticks were morphologically identified, pooled and screened for tick-borne pathogens using polymerase chain reaction (PCR) and Sanger sequencing. From the 93 dogs examined, all 749 ticks collected were adult Rhipicephalus sanguineus. Out of the 177 tick pools screened, pathogen DNA was detected in 43 pools (24.29%). The identified pathogens were uncultured Anaplasma sp. (14.12%), Ehrlichia canis (7.34%), Rickettsia conorii subsp. israelensis (3.95%) and Coxiella burnetii (2.82%). Factors such as dog age or sex, or tick sex, did not influence the occurrence of a tick-borne pathogen (p > 0.05). This study reports the first molecular detection of R. conorii subsp. israelensis in Ghana. The occurrence of zoonotic pathogens suggests an increased risk to dog owners and a need to adopt protective measures to prevent infection spread. These findings highlight the importance of integrated tick control, improved diagnostic capabilities and epidemiological surveillance in Ghana to reduce the burden of tick-borne diseases on animal and human health.}, }
@article {pmid41959551, year = {2026}, author = {Lv, W and Hu, H and Huang, Y and Yang, J and Li, Y and He, J and Wang, K and Liu, Y and Wang, Q}, title = {Microbial mechanisms and therapeutic interventions in the periodontitis-inflammatory bowel disease axis: a comprehensive review.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2656084}, pmid = {41959551}, issn = {2000-2297}, abstract = {BACKGROUND: Periodontitis and inflammatory bowel disease (IBD) are chronic inflammatory conditions of the oral and gastrointestinal tracts that exhibit bidirectional microbial and immunological crosstalk.<br><br>OBJECTIVE: Aimed at elucidating the bidirectional crosstalk between periodontitis and IBD at both microbiological and immunological levels and evaluate related therapeutic interventions, this review comprehensively summarizes recent evidence on their interaction via the oral-gut-bone axis, focusing on microbial ecology, host responses, and innovative therapies.<br><br>DESIGN: Distinct yet overlapping dysbiotic signatures are observed in both diseases, with periodontal pathogens such as Porphyromonas gingivalis and Fusobacterium nucleatum capable of translocating to the gut and perturbing intestinal homeostasis, while gut inflammation reciprocally reshapes the oral microbiome. Mechanistic links include a spectrum of convergent pathways: (i) microbial metabolites-short-chain fatty acids, choline metabolites, indole derivatives, polyamines, and bile acids-that modulate barrier integrity and immune responses; (ii) shared immune cells and inflammatory mediators driving mucosal damage at both sites; (iii) bacterial extracellular vesicles (BEVs) and lysine lactylation (Kla)-mediated signaling; and (iv) oxidative stress, iron metabolism dysregulation, and ferroptosis contributing to tissue destruction.<br><br>RESULTS: Therapeutic strategies targeting this axis encompass bidirectional interventions: periodontal and IBD treatments that mutually influence oral and gut health, natural anti-inflammatory and antimicrobial compounds, probiotics and prebiotics, oral and fecal microbiota transplantation, and emerging bacteriophage therapy. Critically, the clinical translation of collaborative dentistry-gastroenterology management is highlighted as a promising avenue for integrated care.<br><br>CONCLUSIONS: By integrating findings across microbial ecology, host response, and therapeutic innovation, this review provides a comprehensive framework for understanding and targeting the periodontitis-IBD axis.}, }
@article {pmid41945106, year = {2026}, author = {Chiang, TH and J, SJP and Lin, YC and Chiang, KP}, title = {Dissolved Organic Carbon Regulates Bacterial Ingestion by Tetraselmis sp.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02752-z}, pmid = {41945106}, issn = {1432-184X}, support = {NSTC 114-2811-M-019-001//National Science and Technology Council, Taiwan/ ; NSTC 114-2611-M-019-003//National Science and Technology Council, Taiwan/ ; 113-2119-M-001-011//National Science and Technology Council/ ; }, }
@article {pmid41950827, year = {2026}, author = {San Román, AX and Frey, SD and Knorr, MA and Tong, H and Melillo, JM and Simpson, MJ}, title = {Three decades of continuous warming in temperate forests destabilizes persistent forms of soil organic matter.}, journal = {The Science of the total environment}, volume = {1029}, number = {}, pages = {181777}, doi = {10.1016/j.scitotenv.2026.181777}, pmid = {41950827}, issn = {1879-1026}, abstract = {Rising temperatures have altered the balance of soil carbon stored versus respired in forest ecosystems worldwide. Yet, the molecular-level mechanisms driving changes to soil biogeochemical processes and the long-term changes to soil organic matter (SOM) dynamics remain unclear. Thus, we leveraged the world's longest soil warming experiment, spanning over three decades in a temperate forest, to investigate changes in SOM chemistry and microbial responses. Using advanced molecular-level techniques, we identified significant perturbations to SOM composition and novel shifts in microbial degradation pathways. Chronic warming enhanced the breakdown of plant-derived lipids typically thought resistant to microbial decomposition. Concomitant shifts in microbial communities indicate altered carbon use strategies, with microbes acclimating to warming and increasingly targeting persistent compounds. We provide new molecular-level evidence that chronic warming disrupts chemically resistant carbon compounds through altered microbial breakdown, revealing mechanisms by which persistent SOM pools may be lost. This further demonstrates that long-term stability is not solely governed by intrinsic chemical properties. Our findings underscore the need to fully elucidate long-term microbial functional shifts and their impacts on the stability of persistent SOM pools in a changing world.}, }
@article {pmid41950840, year = {2026}, author = {Li, X and Cheng, X and Wu, M and Han, S and Wen, X and Tang, S and Cai, Z and Zhou, J}, title = {Auxin is a signal for algal-bacterial inter-kingdom interactions in marine diatom algal blooms.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {141950}, doi = {10.1016/j.jhazmat.2026.141950}, pmid = {41950840}, issn = {1873-3336}, abstract = {Elucidating the signal molecules involved in algal-bacterial interactions is crucial for unraveling the mechanisms driving marine harmful algal blooms (HABs). As a cross-kingdom signaling molecule, indole-3-acetic acid (IAA), however, its chemical-ecological role in algal-bacterial interactions during HABs remains underexplored. Here, we induced a diatom bloom at mesocosm scale, and the role of IAA was explored using cellular, molecular and multi-omics approaches. The results demonstrated IAA-related functional gene abundance was strongly correlated with HAB stages, and two complete IAA synthesis pathways were detected. Non-targeted metabolite analysis showed that IAA's precursor-tryptophan was significantly enriched during the peak stage. PLS-PM analysis further showed that IAA-driven algal-bacterial interaction was significantly correlated with algal bloom trajectory. After co-culturing IAA-produced bacteria (Pseudoalteromonas phenolica) with model diatom Thalassiosira weissflogii, we found the wild type promotes algal photosynthetic efficiency and growth, while the mutant does not. Transcriptomic analysis and [13]C labeling revealed that IAA activates the auxin pathway to form amino acid conjugates (IAA-aa) through the GH3 gene, which are key molecular mechanisms for algal growth promotion. Our results indicated that IAA functions as a cross-talking signal driving algal-bacterial communication, providing new insights into algal bloom's formation mechanism and potential HABs control methods from a signal manipulation perspective.}, }
@article {pmid41950970, year = {2026}, author = {Yang, R and Liu, Z and Liu, Y and Zhang, Y and Lei, J and Yang, Z and He, H and Wang, J and Chen, R}, title = {Multilayer microbial framework of aerobic granule microecosystems: Integrating community ecology, genetic networks, and enhancement strategies.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134569}, doi = {10.1016/j.biortech.2026.134569}, pmid = {41950970}, issn = {1873-2976}, abstract = {Aerobic granular sludge (AGS), a next-generation wastewater treatment technology, has advanced worldwide. Microbiological mechanisms underlying its formation and stability lack a unified explanation. Based on the concept that AGS construction involves progressive participation and stabilization of microbial organization under environmental selection, this review integrates evidence from community ecology and gene-regulatory networks and proposes a unified conceptual framework. The findings show that AGS formation follows a functional trait-driven self-organization process rather than simple cellular aggregation. Selection pressures shape community structure, promoting enrichment of microorganisms. On this basis, quorum-sensing (QS) system is activated with cell density. Rather than acting independently, QS is associated with the reinforcement of existing aggregates, the strengthening of metabolic synergy, and the stabilization of functional zonation. As a density-dependent coordination mechanism, it is involved in regulating the luxI/luxR pathway and key functional genes involved in extracellular polymeric substance synthesis, nitrogen removal, and phosphorus removal. This regulation primarily targets existing aggregates to enhance metabolic synergy and reinforce C/N/P-coupled functional zonation. Operational stability and system performance are improved, bridging community ecological processes with cross-scale gene-regulatory mechanisms. Within this framework, the rationale and limitations of enhancement strategies are evaluated, including QS regulation, microbial reinforcement, and synthetic biology. In the future, quantitative cross-scale coupling models and AI-driven process control may enable engineering universality and designability of AGS. Overall, the proposed paradigm of multilayer microbial programming provides a unified perspective on AGS formation and stability, supporting predictable and designable applications in next-generation biological wastewater treatment systems.}, }
@article {pmid41951653, year = {2026}, author = {He, L and Yuan, D and Li, Q and Zhang, X and Niu, K and Li, X and Ou, Y and Du, H and Yuan, J and Duan, Y and Niu, H}, title = {Fecal virome transplantation attenuates arthritis in mice by remodeling gut ecology, systemic tryptophan metabolism, and innate immune responses.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00980-2}, pmid = {41951653}, issn = {2055-5008}, support = {2024VPPC-S02//the Open Project of the Key Laboratory of Viral Pathogenesis and Infection Prevention and Control (Jinan University), Ministry of Education/ ; 2025A1515012786//the Natural Science Foundation of Guangdong Province/ ; 2022YFF0710702 and 2022YFF0710701//the National Key &amp;D Programs of China/ ; 202201020381//the Guangzhou Joint Fund for Key Laboratory/ ; YXJC2022004//the Medical Joint Fund of Jinan University/ ; }, abstract = {Rheumatoid arthritis (RA) is an autoimmune disorder characterized by chronic joint inflammation and systemic immune dysregulation. Emerging evidence suggests that the gut microbiome plays an important role in immune modulation in RA, yet the role of the gut virome remains poorly understood. Here, using the K/BxN serum-transfer arthritis model, we systematically evaluated the potential role of fecal virome transplantation (FVT) in modulating gut ecology and innate inflammatory responses. Arthritic mice exhibited marked alterations in gut virome composition compared with healthy controls. Administration of purified virus-like particles (VLPs) from healthy donors correlated with reductions in paw swelling, histopathological inflammation, bone erosion, circulating proinflammatory cytokines, and myeloid cell infiltration in inflamed tissues. In parallel, 16S rRNA sequencing showed that FVT remodeled the gut bacterial community toward a composition more similar to that of healthy controls. Targeted serum metabolomics revealed increased levels of microbiota-derived tryptophan metabolites, including indole-3-lactic acid and related indole derivatives, suggesting a link between gut microbial remodeling and systemic immunometabolic regulation. Collectively, these findings indicate that FVT may attenuate inflammatory arthritis by remodeling gut microbial ecology, potentially involving virome-bacteriome interactions and immunometabolic pathways.}, }
@article {pmid41952630, year = {2026}, author = {Wim, T and Mehraveh, S and Katalina, L and Cheah, CW and Pisha, P and Ana, C and Andy, T and Naiera, Z and Wannes, VH}, title = {Not a miracle, not a myth: The role of probiotics in periodontal health.}, journal = {Periodontology 2000}, volume = {}, number = {}, pages = {}, doi = {10.1111/prd.70039}, pmid = {41952630}, issn = {1600-0757}, support = {C3/24/081//KU Leuven/ ; }, abstract = {BACKGROUND: As the understanding of periodontal disease has evolved, therapeutic strategies have increasingly shifted from pathogen eradication toward ecological modulation of the oral microbiome. Within this paradigm, probiotics have emerged as potential adjuncts for maintaining periodontal health by promoting microbial balance and modulating host responses.<br><br>OBJECTIVE: To summarize the historical development, definitions, and mechanisms of probiotics and to critically evaluate the current clinical evidence supporting their use in periodontal therapy.<br><br>METHODS: This narrative review examines the conceptual framework of probiotics in oral health, distinguishing them from related approaches including prebiotics, postbiotics, and synbiotics. Literature from randomized controlled trials and meta-analyses was reviewed to assess the clinical effectiveness of probiotic interventions in periodontal therapy and to explore their proposed mechanisms of action.<br><br>RESULTS: Probiotic effects are highly strain-specific and involve multiple mechanisms, including production of antimicrobial compounds, competition for ecological niches, inhibition of biofilm formation and quorum sensing, strengthening of epithelial barrier integrity, and modulation of host immune and inflammatory responses. Evidence from randomized controlled trials and meta-analyses, particularly those evaluating Limosilactobacillus reuteri strains, suggests that probiotics used as adjuncts to nonsurgical periodontal therapy can significantly improve clinical parameters such as probing pocket depth, clinical attachment level, and bleeding on probing. However, substantial heterogeneity in study design, probiotic strains, delivery systems, and follow-up periods limits the comparability and generalizability of findings.<br><br>CONCLUSIONS: Probiotics represent a biologically plausible and ecologically oriented adjunct in periodontal therapy. While current evidence indicates beneficial clinical effects, further standardized and long-term clinical trials incorporating advanced microbiome analyses (e.g., next-generation sequencing) are needed to clarify mechanisms, optimize formulations, and support personalized probiotic strategies in periodontal care.}, }
@article {pmid41953022, year = {2026}, author = {Han, W and Li, Q and Yuan, G}, title = {The gut microbiome as an actionable drug-sensitivity modulator for immune checkpoint blockade: clinical evidence for FMT, live biotherapeutics, and defined consortia.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1802676}, pmid = {41953022}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology/drug effects ; *Immune Checkpoint Inhibitors/therapeutic use/adverse effects/pharmacology ; *Fecal Microbiota Transplantation/methods ; Animals ; }, abstract = {Immune checkpoint inhibitors (ICIs) deliver durable benefit to only a subset of patients and can be limited by immune-related adverse events (irAEs). The gut microbiome has emerged as an actionable, host-level modulator of ICI drug sensitivity and toxicity. This mini-review links microbial ecology to antigen presentation, T-cell priming and fitness, metabolite signaling, and barrier inflammation, and summarizes interventional evidence across three modalities. Responder-derived fecal microbiota transplantation (FMT) provides the strongest proof-of-concept for re-sensitization in anti-PD-1-refractory melanoma. Microbiome repair can also improve refractory ICI-associated colitis. Early trials of live biotherapeutics and defined consortia support scalability but highlight context dependence and design pitfalls, including antibiotic preconditioning. We discuss practical determinants of reproducibility, including co-medications, diet, engraftment and functional readouts, and conclude with safety, regulatory, and reporting priorities for clinically deployable microbiome engineering.}, }
@article {pmid41953448, year = {2026}, author = {Bautista, J and López-Cortés, A}, title = {Biohacking the human gut microbiome for precision health and therapeutic innovation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1776983}, pmid = {41953448}, issn = {1664-302X}, abstract = {Biohacking, the self-directed application of biotechnology, digital tools, and lifestyle interventions, has rapidly converged with gut microbiome science to create adaptive, individualized, and minimally invasive precision-health paradigms. This narrative review integrates current evidence on diet-based modulation, microbial therapeutics (probiotics, prebiotics, postbiotics, and fecal microbiota transplantation), and synthetic-biology approaches (engineered strains and phage or synthetic consortia) within a multi-omics and continuous-phenotyping framework. Mechanistically, short-chain fatty acids (SCFAs), bile-acid derivatives, and tryptophan catabolites operate as endocrine-like mediators linking gut microbial ecology with host immunity, metabolism, and neuroendocrine signaling. Pathways mediated by microbial metabolites underpin translational applications that span metabolic optimization, through improved insulin sensitivity, reduced adiposity, and attenuation of inflammation, and neurocognitive enhancement via the microbiome-gut-brain axis. Evidence from oncology further indicates that microbial metabolites and engineered taxa remodel stromal and immune niches, shaping therapeutic response and disease progression. Concurrently, emerging digital infrastructures, wearables, biosensors, metabolic avatars, and AI-driven "health twins," enable real-time, closed-loop modulation of host-microbe dynamics. Persistent challenges include methodological heterogeneity, safety concerns regarding live biotherapeutics and unsupervised fecal microbiota transplantation (FMT), fragmented regulation, and vulnerabilities in cyberbiosecurity and data equity. We propose a translational roadmap emphasizing standardized metadata (STORMS), validated reference frameworks, longitudinal multi-omics for causal inference, strain-level safety genomics, and governance integrating ethical and cybersecurity oversight. Under these conditions, microbiome-focused biohacking may evolve from anecdotal experimentation into a more reproducible and scientifically grounded component of preventive and personalized medicine. This manuscript is presented as a narrative and conceptual review, integrating validated microbiome research with emerging biohacking frameworks while explicitly distinguishing evidence-based findings from exploratory or speculative concepts.}, }
@article {pmid41954752, year = {2026}, author = {Saha, S and Shah, AS and Wang, P and Burgess, TI and Bayliss, KL}, title = {Seed Potato Bacteria Transfer Across Generations Within the Tuber Flesh.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02758-7}, pmid = {41954752}, issn = {1432-184X}, abstract = {Potato crops are susceptible to pathogens and environmental extremes. Microbiomes support plant health and stress tolerance, and microbes can transfer across generations in vegetatively propagated potatoes. However, the extent and functional relevance of this transfer are poorly understood. This study investigated bacterial transfer across three tuber generations, from seed to granddaughter in two potato cultivars, Nadine and Royal Blue. Bacterial communities in the peel and flesh compartments were sequenced. The granddaughter generation was cultivated in two separate fields to determine the consistency of vertical transfer, and the tare soil bacterial community was a proxy for environmental acquisition. The overall community composition was influenced by generation, compartment, cultivar and field. Horizontal acquisition significantly increased across generations and was the primary source, accounting for more than 98% of the granddaughter tuber bacteria. Peel had a significantly higher number of horizontally acquired ASVs than flesh. Only a small set of seed tuber bacteria ASVs were vertically transferred to the granddaughter tubers. The overall vertical transfer probability was 1.8% across compartments, cultivars, and fields, and it was higher in flesh than in peel. Cultivar-specific probabilities were 1.8% for Nadine and 1.5% for Royal Blue. Field variance was minimal, indicating consistent vertical transfer regardless of where the tubers were grown. Taxa with stable vertical transfer included Streptomycetaceae, Xanthobacteraceae, Devosiaceae, Sphingomonadaceae, and Micrococcaceae. Vertically transferred ASVs were predicted to have functions associated with core metabolic and stress response pathways. This study confirmed consistent vertical transfer of bacteria across potato tuber generations, mainly in the flesh.}, }
@article {pmid41955218, year = {2026}, author = {Yaakop, S and Senen, MA and Adila Rosli, NA and Mohammed, MA}, title = {Molecular identification and microbiome profiling of household casebearer, Phereoeca sp. (Lepidoptera: Tineidae) from Malaysia: Potential implications for human skin irritation.}, journal = {PloS one}, volume = {21}, number = {4}, pages = {e0346590}, doi = {10.1371/journal.pone.0346590}, pmid = {41955218}, issn = {1932-6203}, mesh = {Animals ; Malaysia ; *Microbiota/genetics ; Humans ; RNA, Ribosomal, 16S/genetics ; Larva/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; Phylogeny ; Skin/microbiology ; *Lepidoptera/microbiology/genetics ; DNA Barcoding, Taxonomic ; DNA, Bacterial/genetics ; *Moths/microbiology/genetics ; High-Throughput Nucleotide Sequencing ; Electron Transport Complex IV/genetics ; }, abstract = {In Malaysia, anecdotal accounts have linked the household casebearer (Lepidoptera: Tineidae) to skin lesions and localized inflammation; however, scientific evidence is lacking, and the species' taxonomic identity remains unclear. This study aimed to confirm the species identity and examine the bacteria associated with larvae that may be linked to skin irritation. Larvae were collected from three locations in Peninsular Malaysia and preserved. DNA was extracted from the larvae, and species identification was conducted by analyzing the cytochrome c oxidase subunit I (COI) gene through DNA barcoding. To study the bacteria present, the bacterial 16S rRNA gene was amplified and sequenced using Next-generation sequencing technology. The DNA sequences were analyzed to determine the species and profile the bacterial communities. The results identified the specimens as Phereoeca sp., suggesting they may represent an undescribed lineage. Microbiome analysis revealed that Proteobacteria (40.18%) and Actinobacteriota (32.13%) were the dominant bacterial phyla, with Cutibacterium acnes, Enterobacter, and Pseudomonas among the taxa previously associated with skin irritation or opportunistic infections. Several unclassified but potentially relevant taxa were also identified. These findings provide new insights into the microbial ecology and taxonomy of Phereoeca and underscore its potential role in medically significant interactions within human environments.}, }
@article {pmid41955350, year = {2026}, author = {Moran, J and Graham, LC and Tikhonov, M}, title = {Emergent predictability in microbial ecosystems.}, journal = {Science (New York, N.Y.)}, volume = {392}, number = {6794}, pages = {eadr1440}, doi = {10.1126/science.adr1440}, pmid = {41955350}, issn = {1095-9203}, mesh = {*Microbiota ; *Ecosystem ; Biodiversity ; *Bacteria/classification ; }, abstract = {A long-standing hypothesis of microbial ecology is that simple patterns might persist despite community complexity or even emerge because of it. However, the concept of "emergent simplicity" remains partly intuitive. Here, we defined emergent predictability of microbial ecosystems based on the predictive power of coarsened descriptions that group individual microbial strains into broader classes. We used two published datasets to show that coarse descriptions became more predictive for more species-rich communities. This behavior was not explained by simple averaging effects in large communities. To the contrary, our analysis indicates that emergent predictability arises when physiological or environmental feedback counteracts these averaging effects along certain axes of community variation, allowing these axes to become more informative as diversity increases.}, }
@article {pmid41955630, year = {2026}, author = {Wu, Z and Chen, H and Yao, Y and Wu, J and Li, H and Wang, W and Jiang, Q and Li, P and Zhou, H}, title = {Clinical evaluation of probe capture based targeted next generation sequencing for pulmonary infection in immunocompromised patients: a cross-sectional diagnostic accuracy study.}, journal = {Infectious diseases (London, England)}, volume = {}, number = {}, pages = {1-12}, doi = {10.1080/23744235.2026.2654559}, pmid = {41955630}, issn = {2374-4243}, abstract = {BACKGROUND: Timely aetiological diagnosis of pulmonary infection in immunocompromised patients (ICPs) remains challenging because clinical presentations may be atypical and conventional microbiological tests (CMTs) have limited sensitivity. Probe capture based targeted next generation sequencing (ptNGS) has emerged as a potential alternative to metagenomic next generation sequencing (mNGS), but its clinical performance in this population remains incompletely defined.<br><br>METHODS: In this cross-sectional diagnostic accuracy study, immunocompromised adults undergoing bronchoalveolar lavage for suspected pulmonary infection were enrolled. Bronchoalveolar lavage fluid (BALF) samples were analysed using CMTs, mNGS, and ptNGS. Composite clinical adjudication served as the reference standard. Diagnostic performance was compared at the case level, and pulmonary microbiota characteristics were explored.<br><br>RESULTS: Among 78 enrolled patients, 60 were classified as having pulmonary infection. Causative pathogens were identified in 52 cases, and fungal pathogens, particularly Pneumocystis jirovecii, were the most frequently detected. At the case level, ptNGS and mNGS demonstrated higher sensitivity than CMTs (80.0% vs 80.0% vs 26.7%) and showed high concordance in microorganisms identified (91.7%). Specificity was 72.2% for CMTs, compared with 44.4% for mNGS and 38.9% for ptNGS. Positive sequencing results were also observed in patients without pulmonary infection (n&#x2009;=&#x2009;18), predominantly involving viral or opportunistic microorganisms. Microbiota analysis of 65 samples revealed reduced microbial alpha diversity and altered community composition in patients with pulmonary infection.<br><br>CONCLUSIONS: In ICPs with suspected pulmonary infection, ptNGS substantially increases pathogen detection compared with CMTs and demonstrates diagnostic performance comparable to mNGS. Sequencing results require careful clinical interpretation, given the difficulty in distinguishing infection from colonisation in respiratory specimens. Exploratory microbiota analyses suggest infection associated alterations in lung microbial ecology that warrant further validation.}, }
@article {pmid41937469, year = {2026}, author = {Wee, GN and Hwang, J and Kwon, B and Kim, J and Kim, S and Seo, SC and Jang, S}, title = {Human Contact Frequency as a Dominant Ecological Driver of Fungal Community Assembly and Homogenization in Public Built Environments.}, journal = {Journal of microbiology and biotechnology}, volume = {36}, number = {}, pages = {e2602016}, doi = {10.4014/jmb.2602.02016}, pmid = {41937469}, issn = {1738-8872}, mesh = {Humans ; *Fungi/classification/genetics/isolation &amp; purification ; *Mycobiome/genetics ; *Air Microbiology ; Republic of Korea ; Cladosporium/isolation &amp; purification/genetics ; Air Pollution, Indoor/analysis ; *Built Environment ; Public Facilities ; DNA, Fungal/genetics ; Malassezia/isolation &amp; purification/genetics/classification ; Aspergillus/isolation &amp; purification/genetics ; }, abstract = {As modern populations spend the majority of their time indoors, understanding indoor microbial ecology is crucial for public health. While research has addressed abiotic pollutants, the ecological dynamics of surface-associated mycobiomes remain insufficiently understood. This study assessed fungal communities across 25 types of public facilities in South Korea to evaluate the relative influence of environmental parameters and human-driven factors. A total of 327 surface samples from six surface types (handles, tables, chairs, walls, pillars, floors) were analyzed using internal transcribed spacer (ITS) sequencing, yielding 27 million reads and 31,721 amplicon sequence variants (ASVs). Although temperature and humidity significantly correlated with airborne fungal concentration, they exerted minimal influence on community diversity and structure. Instead, the intensity of human contact with indoor surfaces emerged as a primary driver of fungal community composition. We found that the relative abundance of the human-associated genus Malassezia is strongly associated with two distinct ecological states of indoor surface mycobiomes; high-Malassezia samples exhibited significantly distinct communities (ANOSIM R = 0.217, p < 0.001) and dense co-occurrence networks among genera of potential clinical relevance, with strong correlations between Malassezia and both Aspergillus and Cladosporium (|corr| = 0.81). These Malassezia-associated patterns persisting across diverse facilities demonstrate that human-driven microbes are the primary ecological drivers of surface mycobiomes in public spaces, providing foundational evidence for human contact-based microbial assessments in public health monitoring and hygiene-conscious environment design.}, }
@article {pmid41938569, year = {2026}, author = {Yausheva, E and Kholodilina, T and Sizova, E and Shoshin, D and Ryazantseva, K and Nechitailo, K and Klimova, T and Mustafina, A}, title = {Dietary calcium citrate enhances nutrient digestibility and modulates cecal microbiota function in pre-laying hens.}, journal = {Veterinary world}, volume = {19}, number = {2}, pages = {821-839}, pmid = {41938569}, issn = {0972-8988}, abstract = {BACKGROUND AND AIM: Calcium source and bioavailability are critical determinants of nutrient utilization, gut microbial ecology, and future productivity in laying hens, particularly during the pre-laying period. Organic calcium salts may exert additional functional effects through microbiota modulation beyond mineral supply alone. This study evaluated the effects of replacing calcium carbonate with calcium citrate on nutrient digestibility, cecal microbiota composition, short-chain fatty acid (SCFA) production, and predicted microbial metabolic pathways in pre-laying hens.<br><br>MATERIALS AND METHODS: Sixty Hisex Brown pre-laying hens (13-20 weeks of age) were allocated to two dietary treatments: a control diet containing calcium carbonate and an experimental diet in which calcium carbonate was fully replaced with calcium citrate. Diets were formulated to be isocaloric, isonitrogenous, and equal in total calcium content. Nutrient digestibility coefficients were determined using a physiological balance trial. Cecal SCFA concentrations were quantified by gas chromatography. Cecal microbiota composition was analyzed by 16S rRNA gene sequencing, and functional pathway prediction was performed using Kyoto Encyclopedia of Genes and Genomes-based bioinformatic analysis. Statistical significance was set at p < 0.05.<br><br>RESULTS: Replacement of calcium carbonate with calcium citrate significantly increased the digestibility of crude fat (+28.7%, p &#x2264; 0.001), crude protein (+7.29%, p &#x2264; 0.001), calcium (+7.56%, p &#x2264; 0.05), and phosphorus (+2.92%, p &#x2264; 0.05). Cecal concentrations of propionic, butyric, and valeric acids were significantly higher in the calcium citrate group (p &#x2264; 0.001). Microbiota analysis revealed a higher relative abundance of Bacillota, particularly Lactobacillaceae and Oscillospiraceae, and a reduced proportion of Bacteroidota, including Alistipes. Alpha diversity indices were higher in the experimental group. Functional prediction indicated enrichment of microbial genes associated with carbohydrate, amino acid (phenylalanine, tyrosine, tryptophan), and fatty acid metabolism, alongside reduced methane metabolism.<br><br>CONCLUSION: Dietary calcium citrate markedly improves nutrient digestibility and beneficially reshapes cecal microbiota composition and function in pre-laying hens. These findings highlight calcium citrate as a promising nutritional strategy to enhance gut health, mineral utilization, and feed efficiency, with potential implications for subsequent egg production and sustainable poultry systems.}, }
@article {pmid41941070, year = {2026}, author = {de Leite, DPSBM and de Pinto, GOA and da Silva, MEUCM and da Silva, VV and Goncalves, LMT and de Albuquerque, MCF and Santos, RS and da Silva, LTR and Valença, YM and Beraldo, KRF and Juliano, MA and de Oliveira, PRF and da Silva, JG and Mota, RA}, title = {Antimicrobial Resistance and Biofilm in Bacteria from Rehabilitated Sapajus libidinosus.}, journal = {EcoHealth}, volume = {}, number = {}, pages = {}, pmid = {41941070}, issn = {1612-9210}, abstract = {Antimicrobial resistance (AMR) in natural environments and wildlife is an escalating threat to global health and biodiversity conservation. Neotropical primates of the genus Sapajus may act as reservoirs and ecological sentinels of resistant bacteria. The absence of systematic microbiological screening in wildlife rehabilitation centers, coupled with empirical antimicrobial use, can facilitate resistance spread in vulnerable ecosystems. This study characterized phenotypic and genotypic resistance profiles and biofilm-forming ability of Staphylococcus spp. and Mammaliicoccus sciuri isolated from Sapajus libidinosus undergoing rehabilitation in Northeastern Brazil. Rectal swabs were collected, and bacterial isolates identified by MALDI-TOF MS, followed by antimicrobial susceptibility testing, molecular detection of resistance genes, and biofilm assays. Nineteen isolates were recovered: 63.2% Staphylococcus spp. and 36.8% Mammaliicoccus spp. The predominant species were M. sciuri (36.8%) and S. simiae (31.6%). Rates of resistance to penicillin (63.2%) and tetracycline (57.9%) were the most frequent. The main resistance genes detected included tetM (36.8%), tet(38) (31.6%), blaZ (26.3%), msrA (26.3%), and mecA (5.3%). Perfect agreement existed between mecA presence and cefoxitin resistance (κ = 1.00; p < 0.01), with moderate agreement between msrA and non-susceptibility to erythromycin and clindamycin (j= 0.56; p = 0.0265). Biofilm production was mostly weak (94.7%), with moderate production in one isolate. Multidrug resistance occurred in 21.1% of isolates. This pioneering Brazilian study highlights wildlife rehabilitation centers as critical hotspots for AMR surveillance and contributes to understanding the ecological health and conservation of Neotropical primates.}, }
@article {pmid41943256, year = {2026}, author = {Maciá-Vicente, JG and Gomes, SIF and Ampt, EA and Hennecke, J and Bakker, LM and van Ruijven, J and Mommer, L}, title = {The phylogenetic structure of plant communities drives the belowground transmission of fungal pathogens.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.71156}, pmid = {41943256}, issn = {1469-8137}, support = {BG23/00164//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; 864.14.006//Exacte en Natuurwetenschappen/ ; }, abstract = {Biodiversity is known to influence disease risk, yet the pathways of pathogen transmission within plant communities remain poorly understood, especially belowground. In particular, how soil-borne pathogens move from resident vegetation and soil to colonize new hosts is unresolved. We traced belowground pathogen transmission using phytometer seedlings of two plant species planted in a long-term grassland biodiversity experiment. After 3 months, we characterized the fungal communities of phytometer roots, resident plant roots, and soil using high-throughput sequencing and the FungalTraits database to identify associations between pathogen taxonomy and plant families. Next, we related pathogen abundance to phytometer growth. The phylogenetic similarity of phytometers with resident plant species strongly predicted the relative abundance of pathogens that were considered family-specific, but not of pathogens without a clear host preference. However, neither pathogen abundance in phytometers nor resident plant biomass affected phytometer growth, which was best explained by the resident communities' species richness. Combining sequencing of fungal communities with in situ field manipulations enabled us to track the associations between multiple soil-borne pathogens and plant hosts within the full complexity of plant-soil systems. While pathogen dynamics were readily detectable, their consequences for plant performance may only become apparent over longer ecological timescales.}, }
@article {pmid41936687, year = {2026}, author = {Viswan, A and Augustine, N}, title = {Insect Gut Microbiota as a Reservoir of Industrially Relevant Enzymes: A Comprehensive Review.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02726-1}, pmid = {41936687}, issn = {1432-184X}, }
@article {pmid41936761, year = {2026}, author = {Yang, T and Xu, A and Huang, Z and Wang, C and An, Y and Gong, X and Gao, D}, title = {Discharge strategy modulates microbial cooperation and nitrogen cycling in composite carbon-based tidal flow wetlands.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129591}, doi = {10.1016/j.jenvman.2026.129591}, pmid = {41936761}, issn = {1095-8630}, abstract = {Tidal flow constructed wetland (TFCW) cannot effectively remove excess nitrogen from municipal effluent under carbon-limited conditions. By adding a novel slow-release carbon source to TFCW, carbon utilization can be significantly accelerated, stimulating enhanced nitrogen transformation within the system. However, how HRT and discharge strategies shape the microenvironment-and in turn affect microbial processes, nitrogen cycling, and greenhouse gas emissions-remains poorly understood. Building upon previous research, this study investigated the impacts of different HRT and discharge modes on water quality characteristics and microbial community dynamics in TFCW equipped with a slow-release carbon source (BCP). Over 150 tidal cycles, TFCW performance and its influence on microbial ecology were evaluated. Results showed that the system operating at a 24-h HRT combined with full discharge achieved the highest TN removal efficiency (92.70%). This was primarily attributed to enhanced reoxygenation capacity, improved carbon utilization, and plant uptake, which synergistically promoted nitrification-denitrification processes. Microbial activity was more uniform, with key denitrifying enzymes (Nar, Nir) and electron transport system activity synergistically enhanced. High-throughput sequencing revealed Denitratisoma (1.55%) and Nitrospira (0.94%) involved in the cooperative removal of nitrate and ammonium. Correlation and redundancy analyses identified COD and DO as key drivers of microbial community assembly and function (rd ≥ 0.4). Overall, optimizing HRT and discharge strategies can effectively regulate microbial interactions and enhance nitrogen removal for TFCW with BCP. These findings provide new theoretical insights and practical guidance for the engineering design and operational management of advanced treatment systems for urban tailwater.}, }
@article {pmid41935026, year = {2026}, author = {Pawaiya, A and Pradhan, RK and Johri, AK and Dua, M}, title = {Advanced breeding techniques in Brassica juncea L. for sustainable production under changing climate.}, journal = {Plant signaling &amp; behavior}, volume = {21}, number = {1}, pages = {2648963}, doi = {10.1080/15592324.2026.2648963}, pmid = {41935026}, issn = {1559-2324}, mesh = {*Mustard Plant/genetics ; *Climate Change ; *Plant Breeding/methods ; Crops, Agricultural/genetics ; Stress, Physiological ; }, abstract = {Brassica juncea (L.) Czern. &amp; Coss. is an agronomically important crop cultivated worldwide as a valuable source of oil. It is a major source of edible oil in South Asia because of its high oil content, nutraceutical value, and balanced fatty acid contents. In addition to being considered a relatively hardy crop with high economic value, its productivity potential is restricted by susceptibility to various biotic and abiotic stresses, including diseases, pests, drought, heat, frost, and salinity. These constraints adversely affect yield, often leading farmers to move towards alternative crops. In this context, the use of advanced genomics, transcriptomics, and proteomics approaches can provide molecular insight into the evolutionary history, genetic diversity and adaptive response of B. juncea under stress and at different developmental stages. A comprehensive understanding of its molecular architecture and advanced crop improvement strategies will culminate in the development of high-yielding, stress-resistant cultivars, facilitating sustainable mustard production under a changing climate.}, }
@article {pmid41936227, year = {2026}, author = {Alonso-Fernandes, E and Durante-Rodríguez, G and Cano, I and García-García, P and García-Salgado, S and Quijano, M&#xc1; and Díaz, E and Carmona, M}, title = {Unraveling the arsenite response mechanisms in the,facultative anaerobe Aromatoleum sp. CIB.}, journal = {Microbiological research}, volume = {308}, number = {}, pages = {128509}, doi = {10.1016/j.micres.2026.128509}, pmid = {41936227}, issn = {1618-0623}, abstract = {Arsenite is a highly toxic metalloid for living organisms; however, numerous microorganisms have evolved effective mechanisms to adapt to arsenic stress. The facultative anaerobic betaproteobacterium Aromatoleum sp. CIB exhibits a good level of arsenite tolerance, mediated by the coordinated action of multiple molecular systems involved in detoxification and cellular homeostasis. Here, we identified the arsSM genes, encoding enzymes responsible for the production of methylated arsenic species and putative precursors of arsenosugar biosynthesis. The organization of these genes within the arsSM operon suggests a role in arsenic homeostasis, potentially supported by their constitutive expression. This finding extends the known taxonomic distribution of arsSM-mediated arsenic transformation mechanisms beyond cyanobacteria and supports horizontal gene transfer as a likely route for arsSM operon acquisition. Moreover, we present the first comparative analysis of arsenite responses under aerobic and anaerobic conditions within a single bacterial species, revealing distinct physiological constraints and adaptive strategies. Transcriptomic profiling of Aromatoleum sp. CIB exposed to arsenite revealed a stronger global transcriptional response under aerobic conditions. Although canonical arsenic resistance genes (the ars cluster) were induced under both conditions, oxygen availability markedly intensified the global stress response, particularly oxidative stress-related pathways. In contrast, genes encoding protein-folding chaperones were preferentially upregulated under anaerobic conditions. These results indicate a context-dependent reorganization of cellular functions in response to arsenite stress, favoring survival over growth. Overall, this study highlights the complexity and flexibility of bacterial arsenic resistance and provides insights relevant to microbial ecology and arsenic biogeochemical cycling.}, }
@article {pmid41936639, year = {2026}, author = {Aykut, TO and Crucitti-Thoo, RM and Rudak, A and Jasser, I}, title = {Caught Between Invasions: Community Structure and Environmental Drivers of Cyanobacteria in a Vulnerable Post-glacial Lake Region.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02749-8}, pmid = {41936639}, issn = {1432-184X}, support = {BOB-IDUB-622-666/2023//Ministerstwo Edukacji i Nauki/ ; }, }
@article {pmid41929694, year = {2026}, author = {Srivastava, A and Kim, M and Lee, SA and Yun, JH}, title = {Editorial: Microalgae-microbe interactions: advances and applications.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1815619}, doi = {10.3389/fmicb.2026.1815619}, pmid = {41929694}, issn = {1664-302X}, }
@article {pmid41930262, year = {2025}, author = {Bertoldi, S and Klaes, S and Claus, S and Marsans, A and Heipieper, HJ and Eberlein, C}, title = {Cross-feeding drives degradation of phthalate ester plasticizers in a bacterial consortium.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1757196}, pmid = {41930262}, issn = {1664-302X}, abstract = {Reports of plastic pollution across diverse ecosystems continue to emphasize the environmental risks associated with the increasing consumption of synthetic polymers. Plastics frequently contain additives such as phthalic acid esters, which are extensively employed as plasticizers to enhance flexibility in plastic materials and as constituents of numerous consumer products. These compounds are not chemically bound to polymers, allowing them to leach into the environment and have been implicated as potential endocrine disruptors in animals. In the present study, the bacterial degradation of selected phthalate esters was examined, with diethyl phthalate (DEP) utilized as a model compound. A bacterial consortium capable of degrading DEP was enriched from a biofilm of a polyurethane tubing. The consortium was capable to mineralize DEP as the sole carbon and energy source at concentrations of up to 4 mM, whereas concentrations above 6 mM inhibited its activity due to DEP toxicity. This degradation was only possible by the whole consortium and not by single isolates. The degradation of DEP as well as the timely occurrence of monoethyl phthalate as degradation intermediate was confirmed by UPLC analysis. Metagenomic sequencing identified the consortium as comprising a Microbacterium sp. strain and two Pseudomonas spp. Metaproteomic analyses of the consortium, performed under varying time points and carbon sources and integrated with complementary growth experiments, facilitated the reconstruction of the degradation pathway and the identification of putative enzymes involved in DEP metabolism. Microbacterium sp. DEP1M initiated the degradation by hydrolysis of DEP into ethanol and monoethyl phthalate, which is then taken up by the cells and further metabolized to ethanol and phthalate. The latter is subsequently oxidized by a dioxygenase and further transformed to the central intermediate 3,4-dihydroxybenzoic acid (protocatechuate). Protocatechuate is then exclusively degraded via the ortho cleavage pathway. Notably, the distribution of enzymatic functions among different community members strongly supports the occurrence of microbial cross-feeding, indicating that DEP mineralization is a cooperative process within the consortium.}, }
@article {pmid41931990, year = {2026}, author = {Gao, J and Yi, Y and Ran, W and Cheng, Y and Deng, W and Duan, S and Shi, F and Wei, Y and Zhang, Y and Gong, Q}, title = {Targeting astrocytic Nrf2 by Trilobatin alleviates lipopolysaccharide-induced depressive-like behaviors and cognitive impairment in mice: Mechanistic insights into gut microbiota and metabolites modulation.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {155}, number = {}, pages = {158118}, doi = {10.1016/j.phymed.2026.158118}, pmid = {41931990}, issn = {1618-095X}, abstract = {BACKGROUND: Clinical and preclinical evidence links major depressive disorder (MDD) and Alzheimer's disease (AD), suggesting MDD treatment could prevent some AD. Dysfunction within the microbiota-gut-brain axis contributes to MDD and AD pathogenesis via dysregulated microbial metabolites. Trilobatin (TLB) functions as a neuroprotective agent modulating gut microbiota. However, its capacity to alleviate depressive-like behavior and cognitive deficits through restoration of gut microbial ecology and metabolite profiles requires clarification.<br><br>OBJECTIVE: The present research was designed to examine the impact of TLB on depressive-like behavior and cognitive impairments, and the role of the gut microbiota and metabolites.<br><br>METHODS: Neuroprotective effects of TLB on MDD and AD were evaluated using an LPS mouse model exhibiting depressive-like behavior and memory impairment. The principal molecular target of TLB was identified through a combination of single-cell sequencing, surface plasmon resonance, and gene knockout approaches. Mechanistic insights into gut microbiota and metabolites were gained through 16S rRNA sequencing and fecal microbiota transplantation (FMT).<br><br>RESULTS: TLB attenuated LPS-induced depressive-like behaviors manifested as lowered sucrose preference, extended immobility, and improved cognitive deficits as reflected by Y-maze and novel object recognition. Mechanistically, TLB directly bound Nrf2, enhanced Nrf2-ARE activity, and suppressed neuroinflammation and oxidative stress. TLB restored gut microbiota homeostasis, elevated Akkermansia muciniphila (AKK) abundance and short-chain fatty acids, and strengthened intestinal tight junction proteins. FMT from TLB-treated mice replicated these benefits in wild-type but not Nrf2-knockout mice. AKK supplementation similarly ameliorated behavioral and cognitive deficits via Nrf2 activation.<br><br>CONCLUSION: Our findings reveal that TLB mitigates neuropsychiatric deficits by activating Nrf2, remodeling restructuring gut microbiota and fortifying intestinal barrier function. The Nrf2-mediated microbiota-gut-brain axis is suggested as a potential therapeutic target for MDD and AD, positioning TLB as a promising natural Nrf2 activator.}, }
@article {pmid41933473, year = {2026}, author = {Spieck, E and Koch, H and Kop, LFM and Keuter, S and Malinowski, M and Sass, K and Sand, W and Donati, E and Garcia, PP and Lücker, S and Giaveno, A}, title = {Cultivation-Based Detection of a Novel High-GC Nitrospira Derived From the Argentinian Copahue Volcano Area.}, journal = {Environmental microbiology}, volume = {28}, number = {4}, pages = {e70290}, pmid = {41933473}, issn = {1462-2920}, support = {SP 667/7-1//Deutsche Forschungsgemeinschaft/ ; SP 667/7-2//Deutsche Forschungsgemeinschaft/ ; SP 667/11-1//Deutsche Forschungsgemeinschaft/ ; SP 667/11-2//Deutsche Forschungsgemeinschaft/ ; doi.org/10.55776/COE7//Austrian Science Fund/ ; VI.Veni.192.086//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 024.002.002//SIAM/ ; }, mesh = {Argentina ; *Hot Springs/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Genome, Bacterial ; Nitrification ; Nitrites/metabolism ; }, abstract = {Nitrification is an essential process within the global nitrogen cycle and also occurs under extreme conditions, such as in geothermal environments. The nitrite-oxidizing group Nitrospira represents key nitrifiers in these systems, as several species inhabit hot springs worldwide. Using different initial incubation temperatures, two novel moderately thermophilic Nitrospira enrichments, Nitrospira sp. Vd2 and Ca. N. neuquenensis E2OT, were obtained from sulfur-rich mud pools in the geothermal field Las Máquinas (Neuquén Province, Argentina). Nitrospira sp. Vd2 belongs to the N. bockiana lineage V, whereas the second enrichment (E2OT) represents the novel taxonomic lineage VIII, together with cultures from Kamchatka (Kam-Ns4a) and Garga hot springs (Ga3a). The vibrioid morphology of Ca. N. neuquenensis E2OT is strikingly different from all described, twisted rod-shaped Nitrospira. Our study expands the knowledge of the taxonomic and genomic diversity of moderately thermophilic Nitrospira, by comparing the high-quality draft genomes with those of previously described species. The recent discovery of quorum-sensing genes outside the Nitrospira lineage II was confirmed for both Argentinian cultures. Notably, the genome GC contents of the enrichments Vd2 and E2OT are 60.6% and 69.4%, respectively. The latter is the highest observed for Nitrospira to date and might support thermotolerance up to 50°C.}, }
@article {pmid41934143, year = {2026}, author = {Cruz-Paredes, C and Brangarí, AC and Tájmel, D and Hicks, L and Leizeaga, A and Wondie, M and Sandén, H and Rousk, J}, title = {Soil Microbial Communities Adjust Thermal Traits and Carbon Allocation in Response to Climate Manipulations in Subtropical Forest and Cropland.}, journal = {Global change biology}, volume = {32}, number = {4}, pages = {e70836}, pmid = {41934143}, issn = {1365-2486}, support = {2016-06327//Vetenskapsr&#xe5;det/ ; 9036-00004B//Danmarks Frie Forskningsfond/ ; KAW 2022.0175//Knut och Alice Wallenbergs Stiftelse/ ; KAW 2023.0384//Knut och Alice Wallenbergs Stiftelse/ ; }, mesh = {*Soil Microbiology ; *Forests ; *Climate Change ; *Microbiota ; *Carbon/metabolism ; Temperature ; Tropical Climate ; Carbon Cycle ; Soil/chemistry ; Bacteria/metabolism ; Fungi ; Droughts ; }, abstract = {Soil microorganisms regulate carbon (C) cycling, and their growth and respiration are strongly dependent on temperature. Yet it remains unclear how warming alters microbial thermal traits, community structure, and the balance between microbial respiration and growth, particularly in subtropical ecosystems where high temperatures coincide with low soil moisture, potentially constraining microbial activity. In this study, we investigated soil microbial thermal traits for growth and respiration, and the microbial community composition in two subtropical land-uses with contrasting microclimates: a cooler, moist pristine forest and a warmer, drier cropland. Using open top chambers (OTCs) or rain exclusion shelters over 1.5 years, we quantified how experimental warming and drought altered microbial functioning and upscaled these effects using field soil temperature and moisture records. Field warming increased the abundance of warm-adapted bacterial and fungal taxa and led to shifts in microbial thermal trait distributions toward higher minimum temperature values for microbial growth, indicating community-level thermal adaptation. These thermal trait adaptations resulted in a modeled 36% reduction in annual soil CO2 efflux in warmed plots. Overall, our results show that thermal trait adaptation, driven partly by community restructuring, buffers soil C losses under warming and may enhance soil C sequestration in subtropical ecosystems. These findings showcase the importance of integrating microbial thermal traits into soil C models to improve predictions of climate-carbon feedbacks.}, }
@article {pmid41926446, year = {2026}, author = {Lelis, ALJ and da Silva, LAF and Casali, DM and Leiva, T and Rodrigues, MC and Barroso, JPR and Lasmar, PVF and Tomaz, CL and Barbosa, AJ and Sartini, CCF and de Souza, JM and Millen, DD}, title = {The effects of increasing dosages of narasin on ruminal fermentation patterns, bacterial community composition, and nutrient digestibility in beef cattle receiving feedlot diets.}, journal = {PloS one}, volume = {21}, number = {4}, pages = {e0346130}, pmid = {41926446}, issn = {1932-6203}, mesh = {Animals ; Cattle ; *Rumen/microbiology/drug effects/metabolism ; *Fermentation/drug effects ; *Digestion/drug effects ; Animal Feed ; Male ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome/drug effects ; Diet/veterinary ; Bacteria/drug effects ; Dietary Supplements ; Hydrogen-Ion Concentration ; Nutrients/metabolism ; }, abstract = {This study evaluated the effects of increasing narasin doses on ruminal fermentation, nutrient digestibility, ruminal pH stability, papillae histology, and microbial composition in Angus cattle fed feedlot diets. Three rumen-cannulated Angus steers (average body weight: 680 kg) were assigned to a 3 × 3 Latin square design and received diets containing 13, 20, or 27-ppm of narasin. Each experimental period consisted of 14 days of adaptation followed by seven days of sampling. Ruminal degradability was assessed on days 15-17, apparent digestibility on days 15-19, continuous ruminal pH on days 19-20, and samples for short-chain fatty acids (SCFA), microbiota, and ruminal histology were collected on days 20 and 21. Ruminal degradability was not affected by narasin dose. Digestibility of acid detergent fiber (ADF) was significantly influenced, with the greatest values observed at 27-ppm (P = 0.01). Increasing narasin doses improved ruminal pH stability, as indicated by a linear increase in minimum pH (P = 0.01) and a reduction in the duration of pH below 5.6 (P = 0.10). At 13 ppm, SCFA production, particularly acetate and propionate, increased (P < 0.05), indicating enhanced fermentation efficiency. In contrast, supplementation with 27-ppm reduced ammonia (P < 0.01), acetate (P = 0.02), and butyrate (P < 0.01) concentrations and increased the acetate-to-propionate ratio (P < 0.01). Lactate concentration decreased linearly with increasing narasin doses (P = 0.03). Narasin supplementation altered ruminal microbial composition, increasing the relative abundance of Lachnospiraceae and Isotricha while reducing lactic acid-producing bacteria. In terms of ruminal morphology, supplementation with 20-ppm of narasin increased the keratin layer thickness of ruminal papillae (P = 0.02), suggesting enhanced epithelial development. Overall, narasin supplementation modulated ruminal function and microbial ecology, with doses between 13 and 20-ppm providing the most favorable balance between fermentative efficiency and ruminal health in feedlot cattle.}, }
@article {pmid41926667, year = {2026}, author = {Chen, Y and Duan, R and Zhang, C and Li, G and Ji, X and Zhang, Q and Pei, F and Wang, K and Duan, L}, title = {Maternal Preconception Antibiotic Exposure Disrupts Microbial Succession: A Transgenerational Risk for Offspring Gut Mucosal Immaturity and Colitis Susceptibility.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e16931}, doi = {10.1002/advs.202516931}, pmid = {41926667}, issn = {2198-3844}, support = {2021YFA1301300//National Key R&amp;D Program of China/ ; 82470578//National Natural Science Foundation of China/ ; 7254451//Beijing Natural Science Foundation/ ; }, abstract = {The early-life microbiome plays a pivotal role in host development and lifelong health. Maternal factors are increasingly recognized as crucial in shaping offspring microbiome. However, how maternal preconception perturbations affects offspring health remain unclear. Thus, we combined animal and clinical data to elucidate whether preconception microbial perturbations disrupt microbial succession and increase offspring susceptibility to colitis. In animals, preconception antibiotic exposure induced long-lasting disruptions in offspring microbial ecology, through enhanced maternal-offspring microbial transmission, altered microbial developmental trajectories, and increased selective pressures during microbial community assembly. Ultimately, these alterations resulted in persistent gut mucosal immaturity and heightened susceptibility to colitis in adulthood. Complementary clinical studies revealed concordant alterations in gut microbiome and metabolome of children with inflammatory bowel disease (IBD) and their seemingly healthy mothers, characterized by pro-inflammatory taxa and metabolites. Notably, mothers of IBD children reported significantly higher antibiotic exposure than controls, which was also associated with enhanced maternal-offspring microbial transmission and increased selective pressures during microbial community assembly. Our findings reveal a potential intergenerational mechanism in which preconception perturbations are associated with disrupted microbial succession, transgenerational propagation of gut mucosal immaturity, and susceptibility to colitis. These results underscore the importance of judicious antibiotic use during the often-overlooked preconception period.}, }
@article {pmid41923642, year = {2026}, author = {Gallego-Del-Sol, F and Sin, D and Chmielowska, C and Mancheño-Bonillo, J and Li, Y and Zamora-Caballero, S and Quiles-Puchalt, N and Penadés, JR and Marina, A}, title = {Phages communicate across species to shape microbial ecosystems.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2026.03.004}, pmid = {41923642}, issn = {1097-4172}, abstract = {Arbitrium is a communication system that helps bacteriophages to decide between lysis and lysogeny through secreted peptides. In this system, the arbitrium communication peptide (AimP) binds its cognate arbitrium receptor (AimR) to repress aimX (a negative regulator of lysogeny) expression, promoting lysogeny. It has been assumed that each AimR responds exclusively to its own AimP. Here, we challenge this view by demonstrating cross-communication between arbitrium systems. Using prototypical arbitrium phages, we show that AimP peptides can bind and repress non-cognate AimR receptors, promoting lysogeny and reducing prophage induction. Structural and biochemical analyses reveal conserved receptor features that permit cross-recognition of non-cognate peptides while preserving recognition of cognate partners. In mixed lysogenic cultures, these interactions alter induction outcomes, underscoring their ecological significance. Extending to infection contexts, we demonstrate that crosstalk favors lysogeny of incoming phages in cells harboring compatible systems. These findings establish that phages engage in cross-species communication via peptide signaling, reshaping microbial communities in unexpected ways.}, }
@article {pmid41924123, year = {2026}, author = {Grinshpan, I and Lavy, O and Zorea, A and Amit, I and Levin, L and Furman, O and Somekh, D and Guevara, N and Moraïs, S and Cordero, OX and Mizrahi, I}, title = {Endemic within endemics: the microbiota of the Galapagos marine iguanas.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag040}, pmid = {41924123}, issn = {2730-6151}, abstract = {The ecological processes shaping host-associated microbial communities in geographically isolated ecosystems remain poorly understood-particularly the interplay between dispersal, selection, and microbial speciation. Here, we characterize the fecal microbiota of the Galápagos marine iguana (Amblyrhynchus cristatus), an iconic endemic vertebrate that depends on its microbiota to digest an algae-based diet. We analyzed fecal samples from 111 individuals across three remote colonies and found that fecal microbial composition is dominated by Clostridia, closely following a neutral dispersal model. Yet, ecological and phylogenetic analyses revealed novel, host-restricted Clostridia clades-spanning species to family level-that appear to have diversified within marine iguanas. These lineages are consistently retained across host populations through strong purifying selection, resulting in striking microbiota homogenization. Our findings demonstrate that endemic hosts can support microbially distinct lineages shaped by stochastic dispersal and parallel selection, advancing our understanding of microbial community assembly in obligate host-microbiota systems.}, }
@article {pmid41925447, year = {2026}, author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW}, title = {The rhizosphere microbiome as a decentralized immune system.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2026.03.006}, pmid = {41925447}, issn = {1878-4380}, abstract = {Plant immunity should be reconsidered beyond the boundaries of the plant genome. We propose that the rhizosphere microbiome may function analogously to a decentralized immune system, contributing adaptive defenselike properties and memory effects. In this forum article, we discuss how this perspective reframes immunity as an emergent property of plant-microbiome interactions, shifting the focus from a solitary host toward an integrated holobiont.}, }
@article {pmid41742154, year = {2026}, author = {Ullah, H and Selvarajan, R and Lau Vetter, MCY}, title = {Genome-mining revealed biosurfactant production capacity and gene co-occurrence patterns in diverse ecosystems.}, journal = {Microbial cell factories}, volume = {25}, number = {1}, pages = {}, pmid = {41742154}, issn = {1475-2859}, support = {Scholarship//Alliance of International Science Organizations/ ; IDSSE-SJBS-202501//Institute of Deep-sea Science and Engineering/ ; Y970011001//Knowledge Innovation Program of Chinese Academy of Sciences/ ; E2500001//Hainan Provincial Talent Development Bureau/ ; }, abstract = {UNLABELLED: Biosurfactants produced by microorganisms play essential roles in ecosystem function and hold significance promise for biotechnological applications. However, their diversity and distribution remain poorly depicted due to the limitations of culture-based approaches. In this study, we conducted a large-scale genomic data mining of 142,135 microbial genomes of putative biosurfactant-producing taxa, spanning 21 distinct ecosystems, to systematically profile gene association with 10 major biosurfactant classes. Using a list of 18 key functional genes, we mapped their taxonomic and ecological distribution and analyzed patterns of gene co-occurrence. We found that rhamnolipid biosynthesis genes are nearly ubiquitous across microbial lineages, reflecting their fundamental role in microbial adaptation. In contrast, emulsan and serrawettin pathways are more restricted to plant-associated and fungal ecosystems. The highest diversity of biosurfactant-related genes was found in genomes recovered from nutrient-rich habitats, including plant-associated, algal, and wastewater ecosystems. Co-occurrence network analysis revealed two distinct organizational strategies: a rare, conserved core cluster of genes associated with fengycin, surfactin, iturin lichenysin and plipastatin production, and a widespread, modular periphery linked to rhamnolipid, emulsan, and serrawettin W1 pathways, that are likely driven by the need to adapt to environmental complexity. Notably, we identified previously unreported genomes with biosurfactant production potential, significantly expanding the known biodiversity and ecological range of potential producers. Our findings establish biosurfactant production as a key microbial trait shaped by habitat, with broad implications for microbial ecology, ecosystem monitoring and sustainable biotechnology. This work provides comprehensive genomic resource for biosurfactant research, laying the foundation for targeted bioprospecting and integrative functional studies.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12934-026-02932-z.}, }
@article {pmid41916728, year = {2026}, author = {Henry, GBL and Tremblay, J and Stenuit, BA and Gerin, PA}, title = {Microbial Ecology of Mixotrophic Chain Elongation: Megasphaera spp. as Drivers of Medium-Chain Carboxylate Production From H2, CO2, and Carboxylates.}, journal = {Environmental microbiology}, volume = {28}, number = {4}, pages = {e70287}, doi = {10.1111/1462-2920.70287}, pmid = {41916728}, issn = {1462-2920}, support = {SPW-DGO3-D65-1454//Service Public de Wallonie/ ; SPW-DGO3-D31-1397//Service Public de Wallonie/ ; 2019-BRIDGE-4D//R&#xe9;gion de Bruxelles-Capitale/ ; //European Regional Development Fund/ ; }, mesh = {*Carbon Dioxide/metabolism ; *Hydrogen/metabolism ; *Carboxylic Acids/metabolism ; Fermentation ; Bioreactors/microbiology ; Clostridium/metabolism ; }, abstract = {The production of medium-chain carboxylates (MCC) by mixed culture fermentation of complex organic feedstocks is often constrained by the availability of reducing equivalents. Therefore, mixotrophic fermentation processes, which integrate diverse carbon and reducing equivalents sources, are gaining more attention. However, the microbial communities evolving in such complex environments, where organic and inorganic substrates interact, remain insufficiently understood. To identify the key microorganisms involved in mixotrophic MCC production, two bioreactors were initially fed with brewer's spent grain as organic feedstock and supplemented daily with H2 and CO2 as inorganic substrates. Time-course analyses of net metabolite production rates and microbial community composition identified Megasphaera spp. (likely M. elsdenii and M. hexanoica) as the main chain elongators in the system. The results suggest that these Megasphaera species metabolize short-chain carboxylates, H2 and CO2, with potential cross-feeding interactions with acetogens (likely Clostridium ljungdahlii and Clostridium luticellarii). The homoacetogenic acetate produced is subsequently elongated, likely by Megasphaera species, using H2 and CO2 as electron and carbon sources for production of elongated carboxylates. This study paves the way for the development of MCC production strategies that integrate organic waste valorization with direct CO2 utilization, using H2 as an electron donor, a process that aligns with low-carbon-footprint technologies.}, }
@article {pmid41919917, year = {2026}, author = {Mall, A and Rode, KJ and Marx, CJ}, title = {Evolution uncovers a general tradeoff between recovery after heat shock and growth at elevated temperatures.}, journal = {mBio}, volume = {}, number = {}, pages = {e0330525}, doi = {10.1128/mbio.03305-25}, pmid = {41919917}, issn = {2150-7511}, abstract = {Fitness tradeoffs between different environments enable the maintenance of microbial diversity. While the importance of tradeoffs is clear, it has been surprisingly difficult to predict which traits they will occur between and at how granular a level. For example, it is unclear whether performance between a constant versus pulsed exposure of the same stress tends to be positively correlated, independent of each other, or negatively correlated. Empirically, it has been shown that a critical feature structuring microbial communities is temperature. However, the compatibility between strategies to deal with different forms of heat stress is unclear. For instance, are strains that grow well at higher temperatures also stronger at withstanding heat shock? To understand how environmental microbes can adapt to better deal with heat stress, we performed an evolution experiment using a dominant phyllosphere microbe Methylobacterium extorquens in a regime of intermittent heat shock. We identified the genetic basis of adaptation, discovering a large number of loci capable of mediating adaptation to heat shock, many of which had not been previously linked to heat stress. Despite the genetic divergence among evolved isolates, we discovered a general tradeoff between heat shock resistance and growth at consistently elevated temperatures. We found this tradeoff was not limited to evolved isolates, but also represented across a sample of environmentally isolated Methylobacterium strains. These findings indicate a generic conflict between strategies to deal with heat shock recovery and growth at elevated temperatures, suggesting even variation in intensities of a stressor can drive diversity in microbial strategies.IMPORTANCEOne of the key forces shaping the microbial diversity in nature is temperature. However, temperature in ecological settings is variable, and it is unknown if strategies to deal with different intensities of high temperature are compatible or not. Using evolution experiments, we identify the genetic basis of adaptation to heat shock in Methylobacterium extorquens, a dominant member of the phyllosphere microbiome. We discover a number of genetic targets where beneficial mutations improve heat shock resistance, most of which have not been implicated with heat stress before. For both the evolved isolates and a set of environmentally isolated Methylobacterium strains, we discover a general tradeoff between recovery after heat shock and growth at elevated temperatures. While the strategies to deal with increasing temperatures have garnered significant interest, our results suggest that even different intensities of heat stress can select for distinct and incompatible strategies and can drive microbial diversification in ecological settings.}, }
@article {pmid41920852, year = {2026}, author = {Kim, H and Kim, S and Kimbrel, JA and Morris, MM and Mayali, X and Buie, CR}, title = {Multidimensional scaling informed by F-statistic: Visualizing grouped microbiome data with inference.}, journal = {PLoS computational biology}, volume = {22}, number = {4}, pages = {e1014102}, doi = {10.1371/journal.pcbi.1014102}, pmid = {41920852}, issn = {1553-7358}, abstract = {Multidimensional scaling (MDS) is a widely used dimensionality reduction technique in microbial ecology data analysis that captures the multivariate structure of the data while preserving pairwise distances between samples. While improvements in MDS have enhanced the ability to reveal group-specific data patterns, these MDS-based methods require prior assumptions for inference, limiting their application in general microbiome analysis. In this study, we introduce a new MDS-based ordination method, "F-informed MDS," which configures the data distribution based on the F-statistic, the ratio of dispersion between groups sharing common and different characteristics. Using semisynthetic datasets, we demonstrate that the proposed method is robust to hyperparameter selection while maintaining statistical significance throughout the ordination process. Various quality metrics for evaluating dimensionality reduction confirm that F-informed MDS is comparable to state-of-the-art methods in preserving both local and global data structures. Its application to a diatom-associated bacterial community suggests the role of this new method in interpreting the community's response to the host. Our approach offers a well-founded refinement of MDS that aligns with statistical test results, which can be beneficial for broader multidimensional data analyses in microbiology and ecology. This new visualization tool can be incorporated into standard microbiome data analyses.}, }
@article {pmid41922370, year = {2026}, author = {López-Gálvez, J and Schönfelder, E and Mayer, H and Schiessl, K and Silva, MOD and Harms, H and Müller, S}, title = {A double-staining automated flow cytometry method for real-time monitoring of bacteria in continuous bioreactors.}, journal = {NPJ systems biology and applications}, volume = {12}, number = {1}, pages = {}, pmid = {41922370}, issn = {2056-7189}, support = {No 101000733//Horizon 2020/ ; }, mesh = {*Flow Cytometry/methods ; *Bioreactors/microbiology ; *Staining and Labeling/methods ; Escherichia coli/growth &amp; development ; *Bacteria/growth &amp; development ; }, abstract = {In biotechnological processes, cell density and physiology are critical parameters for controlling the feed rate, harvest time, and process performance. We developed an automated flow cytometry approach that enables continuous, real-time (fully automated, hourly) monitoring of bacterial populations in continuous bioreactors. The method employed a double-staining protocol that combined DAPI to assess total DNA content and Alexa Fluor 488-EdU via Click-iT technology to identify the proportions of cells undergoing active DNA replication through EdU incorporation. The integrated workflow included fixation, permeabilization, staining, and measurement steps and was applied to three Gram-negative strains: Bradyrhizobium sp., Escherichia coli, and Stenotrophomonas rhizophila. Automated analysis captured growth dynamics and cell cycle progression, providing insights into population behavior under different dilution rates. In this study, automated on-line sampling enabled hourly flow cytometry measurements of cell concentration and physiological indicators during continuous cultivation, supporting real-time monitoring and control in industrial biotechnology.}, }
@article {pmid41922553, year = {2026}, author = {Cloud, RE and Irwin, P and Muturi, EJ and Cáceres, CE}, title = {Characterizing the Microbiome and Prevalence of Wolbachia in Culex pipiens Complex and Culex restuans Mosquitoes in the Midwest United States.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02750-1}, pmid = {41922553}, issn = {1432-184X}, support = {DEB - 1754115//National Science Foundation/ ; DEB - 1754115//National Science Foundation/ ; DBI - 2022049//Genomics and Eco-evolution of Multi-scale Symbioses Institute/ ; }, }
@article {pmid41914961, year = {2026}, author = {Maigoro, AY and Lee, JH and Heo, D-R and Yun, B-R and Lee, HI and Kwon, H-W}, title = {Spatiotemporal variation in the microbiome of Aedes vexans from Korea reveals regional markers linked to environmental risk factors.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0258725}, doi = {10.1128/spectrum.02587-25}, pmid = {41914961}, issn = {2165-0497}, abstract = {Aedes vexans is a widespread mosquito species known to carry West Nile virus (WNV); however, our understanding of how its microbiome changes across different regions and seasons, particularly in temperate areas such as South Korea, remains limited. In this study, we examined the microbiome of Aedes vexans collected from 16 locations over 3 consecutive summer months. Using 16S rRNA sequencing, we found that the microbiome was largely made up of Proteobacteria, but the specific genera present, like Dickeya, Spiroplasma, and members of Enterobacterales, varied depending on the location and time of collection. Dickeya, in particular, was more common in inland areas and stayed relatively stable over time, which suggests it could serve as a useful microbial marker. We also observed a significant absence of Wolbachia, a common endosymbiont in mosquitoes, which hypothesizes potential increased risk of WNV transmission. Diversity analyses showed clear differences in microbial communities by region, and we found seasonal patterns in genera like Asaia and Pseudomonas, which were correlated to mosquito abundance and local environmental conditions. These patterns held up when we looked at co-occurrence networks between microbes. Altogether, this is the first study to track Aedes vexans microbiome across both space and time in Korea, and our findings offer new insights into mosquito ecology and the potential use of bacteria in disease control strategies.IMPORTANCEUnderstanding the dynamics of the mosquito microbiome is essential for predicting disease risk and developing targeted vector control strategies. Aedes vexans, a globally distributed species and potential vector for West Nile virus (WNV), has seen a notable population increase in South Korea, yet its microbial ecology remains poorly characterized. This study provides the first comprehensive spatiotemporal analysis of Aedes vexans microbiota across Korea, identifying key microbial taxa that vary by region and season. The absence of Wolbachia, a known antiviral symbiont, and the dominance of Dickeya, a plant-associated genus with potential ecological implications, underscore the need for microbiome-informed surveillance tools. By highlighting native microbial signatures and their environmental drivers, this work lays the groundwork for microbiota-based monitoring of vector populations and opens new avenues for symbiont-based interventions in arbovirus control.}, }
@article {pmid41915129, year = {2026}, author = {Kang, L and Dumack, K}, title = {Protistan Predators Outshine Fungi in Forest Soil Activity.}, journal = {The Journal of eukaryotic microbiology}, volume = {73}, number = {3}, pages = {e70072}, pmid = {41915129}, issn = {1550-7408}, support = {2023-57678375//China Scholarship Council - Deutscher Akademischer Austauschdienst (CSC - DAAD)/ ; 24JK0749//Shaanxi Provincial Department of Education/ ; 2023GK84//Yulin University/ ; 2024XZGY05//Yulin University/ ; 20250710//Yulin University/ ; }, mesh = {Forests ; *Soil Microbiology ; *Fungi/genetics/classification/physiology/isolation &amp; purification ; *Soil/chemistry/parasitology ; Biodiversity ; *Eukaryota/classification/genetics ; Spain ; Ecosystem ; Canada ; France ; Sweden ; }, abstract = {Despite extensive research on fungal communities in forest soils, our understanding of the whole eukaryotic diversity and distribution remains limited. Moreover, traditional amplicon sequencing methods often introduce severe PCR and primer biases, further hindering accurate assessment of the microbial community composition in forest soils. To address these challenges, this study used a public metatranscriptomic data set to analyze 51 forest soil samples comprising four countries (Canada, France, Spain, and Sweden). Our results reveal that Arcellinida, a eukaryotic order of shell-bearing amoebae, represent the most abundant eukaryotic taxon in forest soils, with an average relative abundance of 12.6%. This finding challenges the conventional view that fungi dominate eukaryotic diversity in these ecosystems. Furthermore, our study demonstrates that Arcellinida (R[2] = 0.066, p = 0.006) and soil pH (R[2] = 0.126, p < 0.001) are key biological and environmental drivers, respectively, shaping the composition of eukaryotic communities in forest soils, suggesting distinct impact on the microbial community through predation. These findings offer novel insights into the ecological significance of microbial eukaryotes in forest ecosystems and provide a new framework for investigating the predatory dynamics centered on Arcellinida in forest soil microbial networks.}, }
@article {pmid41915160, year = {2026}, author = {Kou, C and Li, D and Liu, Z and Gao, W and Zhang, W and Xiong, L and He, L and Li, M and Shu, A and Ma, J and Gao, Z}, title = {Correction to: Rare Microbial Taxa Dominate the Microecological Landscape of Cadmium Exposure in Rice Rhizosphere.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, doi = {10.1007/s00248-026-02737-y}, pmid = {41915160}, issn = {1432-184X}, }
@article {pmid41915167, year = {2026}, author = {Venetsianou, NK and Paragkamian, S and Kalaentzis, K and Loukas, A and Damianou, C and Lagani, V and Jensen, LJ and Pafilis, E}, title = {LLM-Assessed Relatedness of Microbiome Study Descriptions Aligns more Strongly with Functional than with Taxonomic Profile Similarity.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02730-5}, pmid = {41915167}, issn = {1432-184X}, }
@article {pmid41910204, year = {2026}, author = {Green, L and Marchesani, A and Joyner, JL}, title = {The Atlanta Urban Watershed Harbors Antibiotic Resistant Halotolerant Bacteria.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxag084}, pmid = {41910204}, issn = {1365-2672}, abstract = {AIMS: Rapid urbanization of the Chattahoochee River has decreased the water quality with higher levels of anthropogenic bacteria from nonpoint source pollution. Introduced bacteria are variable across urban watersheds but only monitored by the abundance of fecal indicator bacteria. Staphylococcus aureus is a halotolerant, opportunistic pathogen associated with aquatic pollution, but impact on the microbial ecology is not well understood in freshwater systems. Describing the halotolerant subset of the aquatic microbiome, can expand upon the health risk of bacterial pollution.<br><br>METHODS &amp; RESULTS: Surface water samples along the Chattahoochee River were collected and halotolerant bacteria were cultured using selective agar, typical for growing Staphylococcus species. Bacteria colonies were isolated then characterized by morphology, biochemical tests, and antibiotic resistance screening. Antibiotic resistance profiles showed isolates with a high percentage of resistance to penicillin (86.2%) and novobiocin (17.2%). Biofilm formation was common with 41.4% of isolates formed moderate to strong biofilms. 16S rRNA gene sequencing identified isolates to not be Staphylococcus spp. but within two predominant groups, Bacillus spp. and Priestia spp.<br><br>CONCLUSIONS: The Priestia genus is poorly known in freshwater systems; though the combination of antibiotic resistance, biofilm formation, and spore-forming traits indicate that it has key survival characteristics. Halotolerant bacteria harbor opportunistic human pathogens and a public health risk because the bacteria have a high prevalence of antibiotic resistance and biofilm capability, which contribute to environmental persistence and reservoirs for antibiotic resistance genes. This environmental resistome is a notable and developing characteristic of the urban aquatic microbiome.}, }
@article {pmid41910273, year = {2026}, author = {Tobias-Hünefeldt, SP and Woodhouse, JN and Ruscheweyh, H-J and Sunagawa, S and Russnak, V and Streit, WR and Grossart, H-P}, title = {Osmotolerance is a driver of microbial carbon processes in the Elbe estuary.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0179025}, doi = {10.1128/msystems.01790-25}, pmid = {41910273}, issn = {2379-5077}, abstract = {UNLABELLED: Estuaries are blue carbon loci, storing and exchanging carbon between aquatic, atmospheric, and terrestrial environments. Estuarine particles facilitate the transformation and transport of organic matter. The fate of particulate organic matter in estuaries is driven by structural changes in polymers that modify buoyancy, determining the proportions of sinking and suspended particles. In the open ocean and coastal ecosystems, the microbial composition and function of sinking and suspended particles differ, impacting carbon remineralization and sedimentation rates. We leverage 190 metagenomes and 73 metatranscriptomes to assess free-living, sinking, and suspended particle-associated microbial composition and function across the Elbe estuary. The salinity gradient in the Elbe estuary is the primary driver of microbiome composition and function. Transparent exopolymer particles (TEP) production was localized to freshwater, with seemingly no TEP-associated organisms detected above 20 practical salinity units (PSU). We observed differences in the function of free-living and particle-associated microbial communities, with diazotrophs enriched on particles. We observed that sinking particles may better support methanogenesis, and suspended particles showed signs of continued primary and secondary production. From this, we conclude that activities such as dredging, which resuspend sediment, will exacerbate carbon turnover and greenhouse gas emissions, and reduced dredging may lower greenhouse gas (GHG) emissions in the Elbe estuary. Many of these GHG linking processes are inhibited by salinity due to the osmosensitivity of methanogens and methanotrophs along the estuary. Changes in sea level and precipitation rates will likely directly interact with activities such as dredging, with as yet uncertain impacts on microbial carbon processing and storage.<br><br>IMPORTANCE: Estuaries, lower river areas that merge into oceans, play a large role in Earth's carbon cycle. Estuaries store carbon and manage greenhouse gases, exchanging carbon between land, water, and the air. As carbon travels down estuaries, it is processed by free-living and particle-associated microbes. We explore the relationship between environmental conditions and present and expressed genes. Based on gene profiles, methane concentrations in the water column may be related to the abundance of sinking particles, while suspended particles are linked to growth and energy acquisition. Therefore, the balance of suspended vs. sinking particles is important in highly turbid estuaries, like the Elbe estuary, where urban activities affect greenhouse gas emissions and salinity intrusions. Dredging often tips the balance toward sinking particles and therefore increased greenhouse gas emissions. Our study thereby informs future policy decisions and the impact these decisions will have on our future climate.}, }
@article {pmid41910276, year = {2026}, author = {Woodruff, GC and Moser, KA and Wang, J}, title = {The bacteria of a fig community.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0301324}, doi = {10.1128/spectrum.03013-24}, pmid = {41910276}, issn = {2165-0497}, abstract = {Understanding the biotic drivers of diversity is a major goal of microbial ecology. One approach toward tackling this issue is to interrogate relatively simple communities that are easy to observe and perturb. Figs (syconia) of the genus Ficus represent such a system. Here, we describe the microbial communities of Ficus septica figs, which are associated with the nematode Caenorhabditis inopinata (the sister species of the C. elegans genetic model system). In 2019, 38 Ficus septica figs (across 12 plants in Taiwan) were dissected, and metadata, such as foundress wasp number and nematode occupancy, were collected for each fig. Suspensions derived from interior fig material and fig surface washes were prepared for 16S microbial metabarcoding. Over 2,000 ASVs were detected, and microbial communities were dominated by members of Proteobacteria, Bacteroidota, and Actinobacteriota. Although microbial communities of fig exteriors and interiors can be distinguished, levels of microbial alpha diversity were comparable across these areas of the fig. A joint analysis of fig and previously published C. elegans substrate microbiomes revealed similarities and differences among the biotic environments of these nematode sister species. Fig microbial community composition was driven in large part by variation among individual plants. Conversely, nematodes had no detectable impact on microbial community composition or alpha diversity. A handful of ASVs (associated with the genera Ochrobactrum and Stenotrophomonas) revealed potential differential abundance among figs varying in nematode occupancy. Additionally, foundress wasp number was negatively correlated with microbial alpha diversity. These findings set the stage for future studies that directly test the role of nematode and wasp occupancy on microbial communities, as well as investigations that probe nematode-microbe interactions through laboratory experiments. Taken together, these results constitute a fundamental step in characterizing the natural microbial communities of figs and Caenorhabditis nematodes.IMPORTANCEUnraveling why different species live in different places is a longstanding open question in ecology. It is clear that interspecific interactions among species are a major contributor to species distributions. Ficus figs are a useful system for ecological studies because they are relatively simple microcosms where characterizing animal community composition of multiple samples is straightforward. Additionally, Caenorhabditis inopinata, a close relative of the C. elegans genetic model system, thrives in Ficus septica figs. Here, we tie 16S microbial metabarcoding to nematode and wasp occupancy data to understand the causes of bacterial community composition in F. septica figs. We found that microbial composition, but not total diversity, varies among fig surface and interiors. Additionally, microbial diversity is driven in large part by individual plant of origin. Likewise, we found that nematode occupancy does not appear to impact microbial composition. Moreover, we show that as the number of foundress wasps increases, the microbial α-diversity decreases. Finally, we identified ASVs that are potentially associated with nematode occupancy. Taken together, these results represent a key step in describing a community wherein ecological genetic hypotheses can be tested, as well as one that can potentially reveal the roles of uncharacterized genes in established model systems.}, }
@article {pmid41910755, year = {2026}, author = {Liu, L and Zhao, X and Wang, X and Zhao, Y and Luo, P and Sun, C and Li, W and Zhu, J and Fan, G and Ying, Y and Zhang, J and Xu, Q and Mu, X}, title = {Dynamics of Micro-Diatoms in the Austral Autumn/Winter Reveal Ecological Strategies in the Northern End of the Antarctic Peninsula.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02748-9}, pmid = {41910755}, issn = {1432-184X}, support = {42306259//the National Natural Science Foundation of China/ ; 2022YFC2807504//National Key Research and Development Program of China/ ; 2025TD02//the Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences, China/ ; }, }
@article {pmid41912631, year = {2026}, author = {Liu, L and Liu, Y and Tang, S and Zhang, B and Zhong, Y and Liu, D and Zhou, J and Cai, Z}, title = {The coexistence of r and K strategy in a unicellular microalga Haematococcus lacustris.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-09922-2}, pmid = {41912631}, issn = {2399-3642}, abstract = {Understanding how organisms balance growth and defence is a general goal in biology. r (high reproductivity but stress-sensitive offspring) and K (low reproductivity but high stress-resistant offspring) selection are two classical life history strategy theories. Contrary to the common belief that an organism can only be classified as either r or K strategist, by integrating physiological, microscopic and transcriptomic data, we present experimental evidence for the coexistence of both strategies in the unicellular microalga Haematococcus lacustris. Under standard conditions, swimming vegetative cells (SVCs) normally grow and reproduce via binary fission (r strategy) and gradually transform into non-swimming cells (NSCs) over time. Intriguingly, unlike the prevailing notion that NSCs cannot propagate, they are found to reproduce via multiple fission at a barely detectable growth rate, resulting in stress-resistant, non_mobile daughter cells, demonstrating a complete life history (thus are defined as K strategy). Collectively, our findings suggest that H. lacustris adopts both r and K strategies, enhancing the understanding of the adaptation and survival of microbial populations in challenging environments.}, }
@article {pmid41914631, year = {2026}, author = {Arogundade, AA and Dumaguit, CDC and Melton, A and Buerki, S and Bittleston, LS}, title = {Exploring sagebrush leaf microbial metagenomes from deep, host-derived sequencing.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0219825}, doi = {10.1128/spectrum.02198-25}, pmid = {41914631}, issn = {2165-0497}, abstract = {Advanced sequencing technologies and improvements in bioinformatics have provided a new way to study plant-associated microbial communities, including the use of host genomic sequencing. Our study focuses on the leaf microbiome of basin big sagebrush (Artemisia tridentata subsp. tridentata), a foundational shrub of western North America. We analyzed Illumina shotgun sequences from sagebrush leaves to investigate the metagenomes of leaf-associated microbes that were sequenced alongside their plant hosts. We aimed to profile the leaf microbiome across different sample sources (magenta box, greenhouse, and field/wild), reconstruct metagenome-assembled genomes (MAGs) where possible, and investigate functional gene annotations of the resulting MAGs, specifically with regard to the potential metabolism of sagebrush chemicals. To achieve this, Illumina shotgun sequence reads (containing both host and associated microbial reads) were mapped to the reference genomes of Artemisia tridentata, Artemisia annua, and the human reference genome to remove plant host and human-associated sequences. Host-cleaned reads were then analyzed using microbial metagenomics techniques. Taxonomic profiling revealed that Phyllobacterium and Sphingomonas were the most abundant microbial genera in greenhouse-grown plants, with very little variation among the samples. Wild, field-collected samples were much more variable and were dominated by Klebsiella and Aureobasidium species. From the co-assembly of greenhouse samples, we reconstructed two high-quality MAGs (a Phyllobacterium species and a Sphingomonas species) with >98% completion and <1% contamination. Functional annotation of these MAGs uncovered genes associated with the degradation and metabolism of camphor and other essential oils such as pinene, geraniol, and limonene, which are part of sagebrush leaf chemistry.IMPORTANCEBig sagebrush (Artemisia tridentata), the foundation species of the sagebrush steppe, has broad ecological importance because its evergreen leaves offer nutrients and shade that facilitate the establishment of diverse understory plants in arid environments. Sagebrush leaves contain various secondary metabolites, including terpenoids, flavonoids, and phenolic compounds. These chemicals contribute to the plant's defense mechanisms against herbivores and pathogens. Despite this, sagebrush hosts diverse bacterial and fungal communities. We found that the microbial metagenome-assembled genomes (MAGs) we recovered contained genes that have the potential to degrade some of the chemical compounds in sagebrush leaves that could inhibit the growth of other microbes. This is the first study to mine plant genome data using host-derived sequences to generate microbial MAGs. Our results showed that MAGs can be recovered from plant host-derived sequence data, providing a new way to explore the identity and functional capabilities of difficult-to-culture microbes.}, }
@article {pmid41914732, year = {2026}, author = {Pasman, R and Krom, BP and Zhang, J and Brul, S and Zaat, SAJ}, title = {Secreted factors of Staphylococcus aureus promote co-invasion with Candida albicans by inducing hypha formation and invasion.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0196125}, doi = {10.1128/aem.01961-25}, pmid = {41914732}, issn = {1098-5336}, abstract = {Interkingdom interactions between Candida albicans and Staphylococcus aureus promote lethal dissemination of the bacterium. During this process, C. albicans hypha invasion aids S. aureus dissemination through Als1p/Als3p-facilitated co-invasion. The effects of S. aureus on C. albicans hypha formation and invasion are, however, unknown. In this study, we used both liquid mDMEM-DMP as well as a previously constructed semi-solid adaptation of the medium (mDMEM-DMPA) to study the effects of C. albicans/S. aureus co-culturing on hypha formation and invasion. Semi-solid-based co-culturing significantly increased colony size and generally increased hypha invasion. Liquid growth-based time-lapse microscopy showed that S. aureus significantly promoted both C. albicans hypha length and elongation rate. Further semi-solid-based growth results revealed that >3 kDa-secreted S. aureus factors were accountable for the increase in C. albicans hypha growth. A newly constructed in vitro assay confirmed the co-invasion of S. aureus during co-culturing and showed that deletion of C. albicans Als1p/Als3p abolished the co-invasion of S. aureus during co-culturing. In conclusion, our study shows that S. aureus affects C. albicans virulence by actively stimulating C. albicans hypha extension through the production of, presently unknown, secreted factors and sequentially using hypha proteins Als1p and Als3p to co-invade. Therefore, S. aureus can stimulate C. albicans epithelial invasion even prior to attaching to its hyphae, providing the foundation for subsequent co-invasion.IMPORTANCEEpithelial barriers normally protect against invasion and systemic infection by S. aureus, but frequently, such infections occur without a port of entry. One route of S. aureus epithelial traversal is through co-invasion with the highly invasive Candida albicans. Understanding this interaction in detail is of high importance in view of the prevention of these infections. Our study shows how the S. aureus and C. albicans interaction results in mutual benefit. S. aureus appeared to affect C. albicans virulence by actively stimulating C. albicans hypha extension through the production of, presently unknown, secreted factors and sequentially using hypha proteins Als1p and Als3p to bind to the hyphae and co-invade. These insights are important from a microbial ecological perspective and offer important potential targets for interfering with the interaction and reducing the virulence of these opportunistic pathogens.}, }
@article {pmid41914849, year = {2026}, author = {Deng, T and Wang, H and Zhang, S-F and Wu, X-Y and Yang, Z-S and Wang, D-Z and Zheng, Y}, title = {Functional determinism amid taxonomic stochasticity: insights into rules governing the assembly of algal-microbial symbioses.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0035926}, doi = {10.1128/aem.00359-26}, pmid = {41914849}, issn = {1098-5336}, abstract = {Marine algal-microbial symbioses constitute essential functional units that drive ocean biogeochemical cycles and trigger harmful algal blooms. Yet, a long-standing controversy persists regarding the mechanisms of algal-microbial symbiose assembly, specifically whether phycosphere microbiota are predominantly shaped by deterministic algal-driven selection or by stochastic environmental processes, with no definitive resolution to date. Here, we examined phycosphere communities associated with a series of Skeletonema strains, tracking their taxonomic and functional dynamics across successive growth stages. Despite pronounced taxonomic diversity, reflected in distinct community compositions, successional trajectories, and microbial networks, shotgun metagenomic analyses revealed highly conserved functional repertoires across samples, with consistently abundant core pathways, including amino acid biosynthesis, secondary metabolite and antibiotic production, and ABC transport systems. Statistical analyses further revealed a marked decoupling of taxonomy and function, with functional redundancy enabling taxonomically distinct lineages to perform equivalent metabolic roles. Based on these findings, we propose a dual assembly model in which deterministic algal host-driven selection constrains functional composition, while stochastic processes govern species-level membership. This "function-first, taxonomy-stochastic" paradigm reconciles opposing assembly theories, underscores functional resilience in the face of taxonomic turnover, and provides a conceptual foundation for the rational design of synthetic algal-microbial consortia in marine biotechnological applications.IMPORTANCEMarine algae live in close association with diverse microorganisms that influence nutrient cycling and ecosystem stability. Yet, how these algal-microbial partnerships assemble and maintain functional integrity remains unresolved. Using Skeletonema as a model, this study demonstrates that while the microbial species surrounding different algal strains vary greatly, their metabolic functions remain remarkably consistent. This finding reveals that algal hosts deterministically shape the functional needs of their microbiome, whereas the specific bacterial members fulfilling those roles are interchangeable. Such a "function-first" organization explains how algal-microbial symbioses persist despite environmental fluctuations. Understanding these assembly rules not only advances our knowledge of marine microbial ecology but also provides a conceptual foundation for engineering stable and resilient algal-microbial consortia for sustainable ocean biotechnologies.}, }
@article {pmid41847008, year = {2026}, author = {Yancey, CE and Brumfield, KD and Ettwiller, L and Colwell, RR}, title = {Microbial Community multi-omic analysis of marsh sediment post crustacean shell compost enrichment: pathogen emergence and community response.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41847008}, issn = {2692-8205}, abstract = {Changes in nutrient availability can rapidly alter microbial processes in natural environments, with implications in biogeochemical cycling and pathogen emergence. Short-term, functional responses of microbial communities to nutrient amendment in coastal communities remain poorly understood, particularly in temperate environments. A 48-hour microcosm pulse experiment was completed in which paired metagenomic and metatranscriptomic sequencing were employed to examine how the decomposition of chitin rich substrates, namely crab and lobster shell compost, alters salt marsh microbiome structure and function. Within 48 hours of amendment, pronounced shifts in community metabolism were observed, including increased chitin degradation and utilization, stress-response, and sporulation. These responses coincided with marked decreases in genes associated with key biogeochemical processes, including carbon fixation, sulfur oxidation and reduction, and other metabolic pathways. Shell compost addition also enriched putative pathogens and virulence-associated genes, accompanied by modest transcriptional activation, notably aerolysin A (aerA), which encodes the pore-forming exotoxin aerolysin. These results demonstrate temperate salt marsh sediment microbiomes can undergo shifts in community composition and function that is associated with chitin-rich nutrient perturbation. The sensitivity of temperate coastal systems to organic matter input and the potential for ecological and public-health relevant outcomes are underscored, notably given that chitin is among the most abundant and readily available bionutrients in aquatic ecosystems globally.}, }
@article {pmid41902972, year = {2026}, author = {Rodriguez-Cruz, UE and Ochoa-Sánchez, M and Sierra, JL and Pagaza-Straffon, EC and Hurtado-Ramírez, JM and Quispe-Ricalde, MA and Castelán-Sánchez, HG and Dávila-Ramos, S}, title = {Unveiling a Microbial Treasure Trove: Phylogenetic Diversity and Bioremediation Potential in a High-Altitude Andean Saline System.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02712-7}, pmid = {41902972}, issn = {1432-184X}, support = {227-2015-FONDECYT//Fondo Nacional de Desarrollo Cient&#xed;fico, Tecnol&#xf3;gico y de Innovaci&#xf3;n Tecnol&#xf3;gica/ ; Contract No. 23 2018 UNSAAC//UNSAAC/ ; grant No. 103.5/15/10446//Programa de Mejoramiento del Profesorado, Universidad Aut&#xf3;noma del Estado de Morelos, Secretar&#xed;a de Educaci&#xf3;n P&#xfa;blica/ ; }, }
@article {pmid41903008, year = {2026}, author = {Heyse, J and Props, R and Defoirdt, T and Boon, N}, title = {Life strategies of bacterial taxa in rearing water microbiomes of whiteleg shrimp (Litopenaeus vannamei) larviculture.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41903008}, issn = {1573-0972}, support = {1S80618N//Fonds Wetenschappelijk Onderzoek/ ; 1221020N//Fonds Wetenschappelijk Onderzoek/ ; }, }
@article {pmid41903868, year = {2026}, author = {Manfredonia, I and Chioso, L and Mateescu, I and Konu, M and Brons, JK and Deelman-Driessen, C and Viljakainen, L and Wertheim, B and Lequime, S}, title = {Prevalence and distribution of two polycipiviruses in wild black garden ants (Lasius niger L.) in the Netherlands.}, journal = {Journal of invertebrate pathology}, volume = {217}, number = {}, pages = {108611}, doi = {10.1016/j.jip.2026.108611}, pmid = {41903868}, issn = {1096-0805}, abstract = {Metagenomic studies have revealed diverse viruses in insects. Yet, our understanding of the ecology of insect viruses, especially in ants, remains limited, despite the insects' ecological importance. Viruses of the family Polycipiviridae are increasingly recognized as widespread yet poorly characterized components of ant viromes. In this study, we investigated the prevalence and genetic diversity of Lasius niger virus 1 (LniV-1) and Myrmica scabrinodis virus 1 (MsaV-1) in wild colonies of the black garden ant (Lasius niger L.) across the Netherlands. We surveyed 40 wild L. niger colonies, sampled at geographically distinct locations, using RT-PCR to assess viral prevalence and genetic diversity. Viral prevalence was estimated at both colony and individual levels. Amplicons were sequenced to explore potential correlations between geographic distribution and genetic diversity for both viruses. In addition, complete or almost complete viral genome sequences were obtained and assembled for one MsaV-1 genome from Groningen, The Netherlands, and one MsaV-1 and one LniV-1 from Vienna, Austria. In the Netherlands, LniV-1 was detected in 17.5% of colonies, whereas MsaV-1 was detected in 27.5%, including evidence of co-infection at the colony level. Neither the geographical distribution of infected colonies nor the inferred phylogenies for both viruses showed strong geographic structuring. The prevalence in workers within colonies was variable, ranging from 10 to 60%. These findings suggest that polycipiviruses are common in natural L. niger populations and may transmit via both horizontal and vertical routes. This study provides baseline data on ant-virus interactions in natural environments, advancing understanding of viral ecology in social insects and informing future research on virus transmission dynamics in natural ecosystems.}, }
@article {pmid41904277, year = {2026}, author = {M Davidson, I and Nikbakht, E and M O'Neill, H and Haupt, LM and Dunn, PJ}, title = {Shaping the Female Microbiome: A Review of Lifestyle Factors Influencing the Vaginal, Gut, Oral, and Skin Microenvironments.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02747-w}, pmid = {41904277}, issn = {1432-184X}, abstract = {The female microbiome, spanning the vaginal, gut, oral, and skin sites, harbours distinct microbial communities. Although the diversity and function of microbial communities across these sites are becoming increasingly understood, the extent to which modifiable lifestyle and environmental factors such as smoking, diet, alcohol intake, obesity, physical activity, stress, hygiene, and sexual behaviours shape these microbiomes remains underexplored. This review is restricted to modifiable lifestyle and environmental factors and does not comprehensively assess pharmaceutical exposures (e.g., antibiotics or hormonal therapies) or hormonal influence. To date, no review has comprehensively assessed and compiled evidence across the four microbial sites in females, despite their unique hormonal, physiological, and reproductive characteristics that distinctly influence microbial composition and function. This review provides a comprehensive examination of how such factors influence the dynamics of microbial composition and function along with site-specificity while also assessing cross-site microbial interactions. We focus exclusively on females to address a critical knowledge gap to provide a foundation from which future research and interventions can be tailored to women's health. This review discusses the underlying mechanisms driving microbial shifts and their impact on host health, highlighting critical gaps in our current knowledge. The integration of findings from multi-site microbiome research, highlights the potential to inform targeted, preventative, and therapeutic strategies that utilise the inherent dynamic nature of the microbiome to improve health outcomes across the female lifespan.}, }
@article {pmid41904356, year = {2026}, author = {Vojtkuf, I and Čačković, A and Soares, AR and Probst, AJ and Orlić, S}, title = {Seasonal Dynamics of Freshwater Bacterial Communities in Continental and Mediterranean Lakes.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02743-0}, pmid = {41904356}, issn = {1432-184X}, support = {426547801//Deutsche Forschungsgemeinschaft/ ; IP-2020-02-9021//Hrvatska Zaklada za Znanost/ ; }, }
@article {pmid41908552, year = {2026}, author = {Yu, N and Pang, S and Li, Y and Diao, H}, title = {Integrated microbiome-metabolome analysis reveals multiorgan toxicity of 1-nitropyrene and the limited efficacy of ferroptosis inhibitor Fer-1 in rats.}, journal = {Frontiers in toxicology}, volume = {8}, number = {}, pages = {1771766}, pmid = {41908552}, issn = {2673-3080}, abstract = {INTRODUCTION: 1-Nitropyrene (1-NP), a prevalent nitro-polycyclic aromatic hydrocarbon, is increasingly recognized as a potential metabolic disruptor, yet its systemic biological effects remain insufficiently characterized.<br><br>METHODS: This study investigated the metabolic, immunological, hepatic, and microbiome alterations induced by chronic 1-NP exposure in rats and assessed whether ferroptosis inhibition via Fer-1 could mitigate these effects.<br><br>RESULTS: Although body weight was not significantly altered overall, high-dose exposure impaired growth from week 4. Exposed groups exhibited progressively elevated fasting blood glucose and impaired glucose tolerance, indicating significant disruption of glucose homeostasis. Serum biochemistry revealed dose-dependent reductions in HDL and total cholesterol, while histopathology confirmed hepatocyte ballooning, inflammation, and steatosis consistent with NAFLD-like progression. Hematological changes, including shifts in neutrophil and lymphocyte populations, suggested chronic inflammatory activation. Untargeted metabolomics identified extensive alterations in pathways related to glycolysis, tryptophan metabolism, glycerophospholipid metabolism, and ABC transporters. Gut microbiota analysis demonstrated reduced richness and significant compositional shifts, with functional predictions linking dysbiosis to xenobiotic degradation, lipid metabolism, and phosphotransferase systems. Integrated microbiome-metabolome analysis revealed coordinated disruptions in host-microbial metabolic networks. Fer-1 intervention modified specific metabolic and microbial signatures but did not substantially alleviate major toxic outcomes.<br><br>CONCLUSION: Overall, chronic 1-NP exposure causes widespread metabolic injury driven by combined effects on host metabolism, immune regulation, hepatic function, and gut microbial ecology. These findings highlight 1-NP as a potent environmental metabolic disruptor and underscore the need for further mechanistic studies to inform mitigation strategies.}, }
@article {pmid41909255, year = {2026}, author = {Sai, LO and Zhu, X and Lipson, DA and Xu, X}, title = {Spatial biogeography of microbes in soils vs. aquatic ecosystems in U.S.'s major natural biomes.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1752205}, pmid = {41909255}, issn = {1664-302X}, abstract = {INTRODUCTION: Microbial macroecology has gained recognition as a critical component of microbial ecology. Using data from the National Ecological Observatory Network (NEON), this study examined the spatial patterns of microbial abundance and their environmental controls in soil and aquatic ecosystems across major natural biomes in the United States.<br><br>METHODS: Microbial cell density in aquatic ecosystems and soil microbial biomass carbon in terrestrial ecosystems were analyzed, and their relationships with environmental variables were evaluated using correlation analyses.<br><br>RESULTS: In aquatic ecosystems, microbial cell density ranged from 1.8 &#xd7; 10 5 to 4.1 &#xd7; 10 6 cells mL[-1] and was positively associated with specific conductance (r = 0.32, p < 0.01) and water temperature (r = 0.19, p = 0.03), but negatively associated with dissolved oxygen (r = -0.21, p = 0.01). Across all locations, the cell density averaged approximately 1.4 &#xd7; 10 6 cells mL[-1]. In terrestrial ecosystems, soil microbial biomass carbon ranged from 27 to 2.5 &#xd7; 10 4 &#x3bc;g C g[-1] dry soil and was positively correlated with soil moisture (r = 0.57, p < 0.01), soil carbon content (r = 0.67, p < 0.01), and soil nitrogen content (r = 0.66, p < 0.01). It was negatively associated with soil temperature (r = -0.42, p < 0.01) and soil pH (r = -0.42, p < 0.01). Across all locations, the microbial biomass carbon averaged approximately 2.9 &#xd7; 10 3 &#x3bc;g C g[-1]. Bacteria were dominant across both aquatic and terrestrial environments, ranging from 28% to 88%, while Eukarya ranged from 0% to 48%. Archaea made a minor contribution to the microbial community across all sites. Unclassified microbes varied across the United States, ranging from less than 1% at the Lower Tombigbee River in southwest Alabama to 57% at Sycamore Creek in Arizona.<br><br>DISCUSSION: In aquatic systems, cell density increased with specific conductance and water temperature but decreased where dissolved oxygen was high. In terrestrial ecosystems, biomass was higher in soils with greater soil nitrogen content, soil carbon content, and moisture, indicating that nutrient-rich and humid environments favored microbial growth. In contrast, abundances declined in warmer and more alkaline soils. These biogeographic patterns show divergent environmental factors driving microbial abundance in various ecosystems, reflecting high microbial adaptation to surrounding physical and chemical conditions.}, }
@article {pmid41909260, year = {2026}, author = {Wang, XL and Zhang, C and Lu, DS and Dong, ZY and Jin, BM and Wan, SY and Zhang, ZW and Zhang, CJ and Li, L}, title = {Paeoniflorin protects against NAFLD through antioxidant, anti-inflammatory effects and restoration of gut microbiota homeostasis.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1766068}, pmid = {41909260}, issn = {1664-302X}, abstract = {Non-alcoholic fatty liver disease (NAFLD) is a widespread chronic metabolic disorder characterized by hepatic lipid accumulation, oxidative stress, inflammation and gut dysbiosis. Paeoniflorin (PAF) exhibits potential against NAFLD, yet its antioxidant mechanism via the gut-liver axis remains unclear. In a high-fat/sucrose (HFS) diet-induced NAFLD mouse model, C57BL/6 mice received PAF (50 or 100 mg/kg/day) for 10 weeks. Oxidative stress markers, histopathology, gut microbiota, and serum metabolomics were conducted, with fecal microbiota transplantation (FMT) applied for causal validation. PAF ameliorated metabolic disorders by suppressing hepatic lipogenesis and promoting cholesterol excretion. PAF significantly ameliorated oxidative stress by enhancing hepatic and colonic anti-oxidant capacity, evidenced by increased SOD activity and decreased MDA levels. It concurrently reduced systemic inflammation and enhanced intestinal barrier integrity via upregulation of tight junction proteins. Furthermore, PAF reshaped the gut microbiota, elevating beneficial Akkermansia and microbial-derived SCFAs, while suppressing pro-oxidant and pro-inflammatory pathogens like Desulfovibrio and Helicobacter. FMT confirmed that these antioxidant and metabolic benefits were mediated by the gut microbiota. In conclusion, PAF alleviates NAFLD primarily through potent antioxidant actions and anti-inflammatory, achieved via remodeling gut microbial ecology and reinforcing intestinal barrier.}, }
@article {pmid41900402, year = {2026}, author = {Mokrani, S and Benouguef, Z and Houali, K and Bensidhoum, L and Derguini, A and Ibrahim, NA and Basher, NS and Nabti, EH}, title = {Resistance Mechanisms of Rhizospheric Bacillus and Pseudomonas Strains Against Heavy Metal Contamination (Cu, Cr and Cd) and Their Antifungal Properties.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900402}, issn = {2076-2607}, support = {IMSIU-DDRSP2601//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)/ ; }, abstract = {Environmental pollution caused by persistent chemical compounds, particularly heavy metals, poses a significant global challenge. Current strategies focus on eco-friendly and sustainable approaches, such as the application of microorganisms, to mitigate this issue. In this study, four strains of Bacillus and Pseudomonas were phylogenetically identified and assessed for their resistance to three heavy metals: copper (Cu), chromium (Cr), and cadmium (Cd) up to 500 µg/mL. Various tolerance mechanisms related to heavy metal resistance were elucidated, including salinity tolerance, antibiotic resistance, production of exopolysaccharides (EPS), and biosurfactant synthesis. The antifungal activities of these strains were evaluated against the fungal isolates Fusarium oxysporum fs. phaseoli (Fop) and Stemphylium botryosum (St-bt) using dual culture assays. Phylogenetic analysis revealed that three strains belong to the genus Bacillus, while one strain is classified under Pseudomonas. Additionally, these strains exhibited diverse mechanisms for heavy metal tolerance, including salinity tolerance (up to 600 mM), multi-antibiotic resistance (to imipenem, ampicillin, and sodium fusidate), and the production of viscous, slimy colonies indicative of EPS synthesis. Biosurfactant production led to a significant reduction in surface tension, ranging from 10.51 ± 3.87% to 82.89 ± 5.01%. The antifungal assays demonstrated that the strains effectively inhibited the mycelial growth of the fungal isolates, with inhibition percentages varying from 0% to 83.34 ± 2.22%. The strains characterized in this study exhibit considerable potential for application in the bioremediation of metal-contaminated soils and as biocontrol agents.}, }
@article {pmid41900653, year = {2026}, author = {Constantin, CE and Holban, AM and Iordache, F and Curutiu, C}, title = {Antimicrobial Nanomaterials in the Food Industry: Applications in Meat Packaging.}, journal = {Materials (Basel, Switzerland)}, volume = {19}, number = {6}, pages = {}, pmid = {41900653}, issn = {1996-1944}, abstract = {A thorough understanding of the microbial ecology of meat products, dominated by critical pathogens such as Salmonella spp., Campylobacter jejuni, Escherichia coli, and Listeria monocytogenes, and marked by risks of resistant biofilm formation and vulnerabilities specific to informal commercial sectors, underscores the need to transition from conventional inert barriers to active nanostructured packaging systems. This review critically analyses the current state of antimicrobial nanomaterials, dissecting their molecular mechanisms of action and dynamic interactions designed to preserve sensory and nutritional food quality. Beyond technical effectiveness, the paper highlights the inherent tension between technological innovation and toxicological uncertainties, addressing major challenges related to migration kinetics in complex lipid matrices and the uneven global regulatory landscape. Main limitations of frequently investigated materials, along with regulatory discrepancies among international authorities and safety variables, are discussed to contextualise the current barriers to industrial implementation. We conclude that although nanotechnology represents a transformative force for extending shelf life, safety validation through rigorous assessment of migration remains imperative to harmonise scientific progress with public health protection. This integrative perspective highlights the imperative of calibrating nanostructural architecture to the bioactive profile, providing strategic design directions essential for the sustainable translation of experimental innovation to industrial scale.}, }
@article {pmid41900772, year = {2026}, author = {Karimian Azari, E and Govaert, M and Duysburgh, C and Glab, S and Marzorati, M and Saiyed, Z}, title = {Evaluation of Targeted-Release Capsule Formulations for Protection of the Acid-Sensitive Enzyme Pancreatin Under Fasted and Fed Intestinal Conditions In Vitro.}, journal = {Pharmaceutics}, volume = {18}, number = {3}, pages = {}, pmid = {41900772}, issn = {1999-4923}, support = {N/A//Lonza Capsules &amp; Health Ingredients/ ; }, abstract = {Objective: This study assessed the ability of capsule formulations to improve the oral delivery and retain activity of an acid-sensitive enzyme during gastrointestinal transit. Methods: The dissolution characteristics of five capsule formulations-single DRcaps[®] [DR], single Vcaps[®] Plus [VCP], and three DUOCAP[®] capsule-in-capsule combinations, DRcaps[®] inside DRcaps[®] (DR-in-DR), DRcaps[®] inside Vcaps[®] Plus (DR-in-VCP), and Vcaps[®] Plus inside DRcaps[®] (VCP-in-DR)-were evaluated in an in vitro simulation of a healthy human upper gastrointestinal tract under fasting and fed conditions using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME)[®] platform. Capsules contained caffeine as a marker of capsule dissolution, and pancreatin as an active ingredient for which activity was determined by the conversion of tributyrin. Readouts included visual capsule scoring, the analysis of caffeine release, and the quantification of tributyrin-to-butyrate conversion at the end of each gastrointestinal tract segment. Results: The single VCP capsules had a high level of caffeine release at the end of the stomach incubation with low butyrate recovery (16-21%), suggesting the rapid release and gastric degradation of the unprotected enzyme. The single DR, DR-in-VCP, and VCP-in-DR formulations showed caffeine release at the end of the duodenum and/or jejunum and had high butyrate recovery, ranging from 53% to 87%. The DR-in-DR formulation had the most delayed release, with incomplete caffeine release and low-to-moderate butyrate recovery (10-36%). Conclusions: Fast capsule dissolution led to the reduced enzymatic activity of the active ingredient, while delayed dissolution resulted in inadequate time for the enzymatic conversion of tributyrin to butyrate. These results highlight that capsule selection should align with the intended use and targeted nutrient delivery, with DUOCAP[®] formulations being best suited for small intestinal (VCP-in-DR and DR-in-VCP) and colonic (DR-in-DR) delivery.}, }
@article {pmid41901002, year = {2026}, author = {Chang, J and Yang, W and Jin, Y and Zhou, Z and Song, Z and Zhao, W and Liang, S and Ma, Y}, title = {Microbial Biosurfactants: A Bridge from Aquatic Environments to Subsurface Oil Recovery: Mechanisms, Challenges, Prospects.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {3}, pages = {}, pmid = {41901002}, issn = {2075-1729}, support = {Study on the Structure of Hydration layers on Clay Mineral Surfaces and the Regulatory Mechanisms of Aggregation-Dispersion Behavior of Fine Mineral Particles//2024 Annual Xi'an University of Science and Technology Excellent Youth Science Foundation Project/ ; }, abstract = {Microbial biosurfactants, derived from diverse aquatic and extreme ecosystems, offer a sustainable and environmentally compatible strategy for enhanced oil recovery by fundamentally altering subsurface rock wettability. These biologically produced amphiphiles can efficiently transform oil-wet rock surfaces into water-wet states, thereby mobilizing otherwise trapped crude oil. The primary aim of this review is to provide an integrative understanding of how these biomolecules function at the interface between aquatic microbial ecology and subsurface petroleum engineering, with a particular focus on wettability alteration as a key mechanism for enhancing oil recovery. This review surveys major biosurfactant classes-glycolipids, lipopeptides, and polymeric bioemulsifiers-and their core mechanisms, emphasizing their relevance to challenging reservoir conditions such as high temperature and salinity. A detailed assessment is devoted to persistent hurdles such as stability, adsorption onto rock formations, and economic scalability. Future prospects center on three key approaches: advancing synergistic "bio-hybrid" systems that integrate biosurfactants with complementary agents such as biopolymers and nanomaterials; achieving cost-effective production through the valorization of waste feedstocks; and expanding targeted bioprospecting of microbial diversity from extreme aquatic environments. Together, these strategies are reviewed to drive the advancement of robust, green microbial-enhanced oil recovery (MEOR) technologies, charting a course from fundamental insights to field-scale implementation.}, }
@article {pmid41901079, year = {2026}, author = {Cirio, S and Mantegazza, G and Salerno, C and Guglielmetti, S and Allam, A and Campus, G and Cagetti, MG}, title = {Assessing the Impact of Heyndrickxia coagulans Administered Through Sugar-Free Chewing Gum on Dental Biofilm: A Double-Blind Randomized Controlled Trial.}, journal = {Nutrients}, volume = {18}, number = {6}, pages = {}, pmid = {41901079}, issn = {2072-6643}, mesh = {Humans ; *Chewing Gum ; Double-Blind Method ; *Biofilms/drug effects ; Male ; Female ; Adult ; *Dental Plaque/microbiology ; *Probiotics/administration &amp; dosage ; Middle Aged ; Young Adult ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Background:Heyndrickxia coagulans has emerged as a candidate for oral health applications, and chewing gum offers a promising delivery method. This study evaluates whether H. coagulans delivered via sugar-free chewing gum can induce detectable changes in plaque microbial ecology. Methods: A randomized, double-blind, placebo-controlled clinical trial was conducted on 52 healthy adults. Participants consumed probiotic or control gum for 4 weeks. Dental plaque was collected at baseline (T0), mid-intervention (T1), end of intervention (T2), and one week post-intervention (T3). qPCR quantified H. coagulans, while 16S rRNA gene profiling assessed microbial diversity and taxonomic composition. Statistical analyses included rank-based difference-in-differences models, Wilcoxon and Mann-Whitney tests, and differential abundance inference based on negative binomial modeling. Results: Forty-four subjects completed the study. In the Intervention group, the strain was detected in 71.4% of participants at T1 and 61.9% at T2, and it persisted in 9.5% at T3. Differential abundance analysis revealed a broad depletion of taxa linked to oral dysbiosis at T2 with partial persistence at T3, along with selective enrichment of beneficial strains. Conclusions:H. coagulans delivered via chewing gum can reach the dental biofilm and induce modest, transient shifts in microbial composition. However, these biofilm ecology findings should be interpreted in the context of clinical outcomes.}, }
@article {pmid41889812, year = {2026}, author = {Leisch, N and Baars, S and Beavis, T and Bertucci, P and Bhickta, C and Bonadonna, M and Brannon, CM and Burgués-Palau, L and Cherek, P and Chevalier, F and Decelle, J and Demulder, M and Dey, G and Dudin, O and Duke, E and Engel, BD and Flaum, E and Flori, S and Gallet, B and Guichard, P and Halavatyi, A and Hamel, V and Jacobovitz, M and Juery, C and Laporte, M and Mattei, S and Mikus, F and Mocaer, K and Moog, K and Olivetta, M and Pavie, M and Pepperkok, R and Perez-Boerema, A and Planat, L and Prakash, M and Pyle, EW and Rhodes, CR and Romero-Brey, I and Ronchi, P and Rosa, H and Ramos, AR and Saint-Donat, C and Schwab, Y and Shah, H and Steyer, AM and Svetlove, A and Toullec, G and Vincent, F and Wiegand, T and Wietrzynski, W and Yee, D and Zwahlen, S}, title = {An Advanced Mobile Laboratory to enable field-based microbial ecology and cell biology across scales.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.02.23.707475}, pmid = {41889812}, issn = {2692-8205}, abstract = {Microbial biodiversity is central to ecosystem function, yet mechanistic insights into the cell biology of environmental organisms remain limited. The underlying challenges are twofold: most microbes remain uncultivable, and a persistent gap exists between field sampling and laboratory analyses. Here, we introduce the Advanced Mobile Laboratory (AML), a field-deployable platform that integrates confocal microscopy, image-enabled cell sorting, and cryo-preparation for expansion and electron microscopy. This setup enables immediate, standardized processing and analysis of environmental communities directly at the sampling site. We demonstrate its capability using marine eukaryotic plankton, showing how the AML enables multiscale investigations, from live imaging of natural communities to enabling ultrastructural and single-cell omics analyses, while minimizing sample degradation and enabling on-site experimentation. By bringing high-end sample preparation and analytical capacity into the field, the AML enables studying life in its natural context to mechanistically understand life's diversity in the environment.}, }
@article {pmid41891698, year = {2026}, author = {Li, Y and Ji, M and Tu, Q}, title = {Patterns and drivers of macro- and micro-diversity of mudflat intertidal archaeomes along the Chinese coasts.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0143425}, doi = {10.1128/msystems.01434-25}, pmid = {41891698}, issn = {2379-5077}, abstract = {Archaea are widespread in Earth's ecosystems, contributing to ecosystem multifunctioning and stability. Compared to bacteria, our understanding of the biodiversity and underlying drivers of archaeal communities in representative ecosystems remains much less tapped. In this study, the macro- and micro-diversity of mudflat intertidal archaeomes were comprehensively analyzed at a large geographic scale, aiming to resolve the ecological drivers determining the variations in archaeal biodiversity. The compositions of mudflat intertidal archaeal taxa highly varied, especially the dominant Thaumarcheota and Euryarchaeota, but maintained relatively stable functional potential across space, demonstrating that functional traits were selected by the ecosystem in priority. While archaeal communities carried important functional traits mediating various biogeochemical cycling processes, horizontal gene transfer played critical roles in endowing functional genes for many archaeal lineages, such as the citric acid cycle in Methanosarcinia and various amino acid metabolism genes in Thermoplasmata. Spatial scaling, including latitudinal diversity gradient and distance-decay patterns (DDR), was clearly observed for archaeal taxonomic groups, but only DDR was weakly observed for functional traits. Intra-population genetic variations were significantly and positively associated with community macro-diversity, demonstrating covariations between nucleotide-level micro- and community-level macro-diversity. The compositions of intertidal archaeomes were mainly structured by homogeneous selection, with different phylogenetic bins being shaped by distinct ecological processes and remarkable variations across different sites. The study contributes to a comprehensive insight into the mechanisms shaping archaeal diversity and ecological characteristics within a fluctuating ecosystem.IMPORTANCEThe dynamic intertidal mudflat ecosystems host intense biogeochemical activities mediated by microbial communities, among which archaea contribute as an essential component but remain much less understood compared to bacteria. To gain better insights into the diversity, functional potential, and ecological drivers of archaeal communities in intertidal mudflats, archaeal phylogenetic signatures and genomic sequences were recovered via amplicon sequencing of 16S rRNA genes and shotgun metagenomes, targeting both macro- and micro-diversity. The results showed that archaeal taxonomic composition highly varied across space, whereas the functional potential remained relatively stable. Horizontal gene transfer served as an important source of archaeal metabolic diversity, obtaining additional genes linked to key biochemical pathways. The dominance of environmental selection further demonstrated the ecological forces governing archaeal communities in highly variable coastal habitats. This study established a large-scale framework for understanding the microbial ecology of intertidal archaeomes in dynamic coastal ecosystems.}, }
@article {pmid41892593, year = {2026}, author = {Krasenbrink, J and Chen, SC and Tanabe, TS and Sarikeçe, H and Meurs, P and Borusak, S and Samrat, R and Guan, G and Priemer, C and Osvatic, J and Séneca, J and Hausmann, B and Speth, DR and Selberherr, E and Wanek, W and Schleheck, D and Mussmann, M and Loy, A}, title = {Sulfoquinovose degradation by cow rumen microbiota.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag069}, pmid = {41892593}, issn = {1751-7370}, abstract = {Sulfoquinovose, a sulfonated sugar derived from the thylakoid membrane lipid sulfoquinovosyl diacylglycerol, is abundant in photosynthetic organisms and plays a key role in global sulfur cycling. Its degradation in nature is mediated by specialized bacteria, many of which rely on the enzyme sulfoquinovosidase (YihQ) to release sulfoquinovose from sulfoquinovosyl (diacyl)glycerol. Despite its ecological importance, the diversity and functional roles of sulfoquinovose-degrading microorganisms remain poorly characterized in natural environments. Here, we developed a yihQ-targeted amplicon sequencing approach to investigate the richness and distribution of SQ-degrading bacteria across selected environments. We revealed high richness of yihQ-containing microorganisms in the analyzed cow rumen samples, far exceeding that observed in human and mouse gut microbiomes, suggesting an important role of sulfoquinovose metabolism in ruminant digestion. Anoxic microcosm experiments with sulfoquinovose-amended rumen fluid revealed cooperative microbial degradation of sulfoquinovose to sulfide via isethionate cross-feeding. Amplicon sequencing and genome-resolved metagenomics and metatranscriptomics identified yet undescribed and uncultured sulfoquinovose-degrading taxa. Members of Caproiciproducens (Acutalibacteraceae), Candidatus Limivicinus (Oscillospiraceae), and Sphaerochaetaceae transcribed the isethionate-producing sulfo-transketolase pathway, whereas isethionate was likely respired by a Candidatus Mailhella bacterium (Desulfovibrionaceae). This study presents a functional gene-based assay for tracking environmental yihQ richness, highlights sulfoquinovose degradation as a central metabolic process in the cow rumen, describes previously unknown sulfoquinovose-metabolizing bacteria, and advances understanding of sulfur physiology in complex microbial communities.}, }
@article {pmid41895437, year = {2026}, author = {Rinanda, T and Riani, C and Artarini, A and Sasongko, L}, title = {Exploring the role of gut methanogenic archaea in childhood stunting in Aceh Province, Indonesia.}, journal = {Anaerobe}, volume = {}, number = {}, pages = {103040}, doi = {10.1016/j.anaerobe.2026.103040}, pmid = {41895437}, issn = {1095-8274}, abstract = {BACKGROUND: Emerging evidence highlights the critical role of gut microbiota in childhood growth; however, the contribution of methanogenic archaea remains underexplored. In this study, we investigated the involvement of gut methanogens in linear growth impairment by analyzing their abundance, diversity, methanogenesis, and interactions with bacterial short-chain fatty acids (SCFAs) and glucagon-like peptide-1 (GLP-1) levels in stunted versus normal children.<br><br>METHODS: This case-control study included 42 children aged 24-59 months from Pidie, Aceh, Indonesia. Gut archaea were profiled through 16S rDNA amplicon sequencing, and mcrA gene expression was measured using quantitative Polymerase Chain Reaction. SCFAs were analyzed using gas chromatography-mass spectrometry, and GLP-1 levels were quantified using immunoassay. The microbial co-occurrence networks were also assessed.<br><br>RESULTS: Archaeal 16S rDNA amplicon sequencing revealed a lower abundance of Methanobacteriaceae, particularly Methanobrevibacter, in stunted children, although their presence contributed to greater microbial diversity. Reduced mcrA gene expression in stunted children indicates a decrease in methanogenesis. Although not statistically significant, mcrA gene expression positively correlated with height, SCFA concentrations, and GLP-1 levels. Microbial network analysis revealed a lower density of microbial networks, indicating reduced stability and resilience in stunted children, with Methanobrevibacter playing a substantial role. Notably, Methanobrevibacter exhibited a positive association with Elusimicrobium, a rare human-associated microbe, and a negative correlation with Lachnospiraceae in normal children, indicating unique microbial interactions that may influence metabolic health.<br><br>CONCLUSION: Methanogens, particularly Methanobrevibacter, may play a crucial role in shaping gut microbial ecology and supporting metabolic pathways relevant to linear growth during early childhood.}, }
@article {pmid41895935, year = {2026}, author = {Li, H and Hu, H and Lu, W and Liu, J and Peng, Q and Wang, S and Dan, T}, title = {Metagenomic analysis of lactic acid bacteria communities in inner Mongolian fermented dairy products: influence of milk source and geography.}, journal = {Food research international (Ottawa, Ont.)}, volume = {232}, number = {}, pages = {118849}, doi = {10.1016/j.foodres.2026.118849}, pmid = {41895935}, issn = {1873-7145}, mesh = {Animals ; *Cultured Milk Products/microbiology ; China ; *Metagenomics/methods ; *Lactobacillales/genetics/classification/isolation &amp; purification ; Cattle ; *Milk/microbiology ; *Food Microbiology ; Fermentation ; Geography ; Horses ; }, abstract = {Inner Mongolia, a key grassland region in China, has a long-standing tradition of fermented dairy products. This study aimed to elucidate the influence of milk source and geographical origin on the community structure and functional characteristics of lactic acid bacteria (LAB) in fermented milk. Twenty-four fermented milk samples from four regions were subjected to metagenomic sequencing analysis including α/β-diversity assessment, taxonomic classification, and functional annotation. The milk source and geographical region jointly shaped the diversity of LAB. The LAB community structure in fermented mare milk displayed more pronounced geographical differentiation than that in fermented cow milk. The core dominant LAB species included Lactobacillus kefiranofaciens, Lactobacillus helveticus, and Lactococcus lactis, with L. helveticus being more abundant in fermented mare milk. The functional profiles of LAB varied depending on the milk source used. The data indicated that milk source was a primary factor associated with the core LAB composition, while geographical origin was associated with the modulation of community diversity and functional attributes. These findings provide region-specific insights into the microbial ecology of traditional Inner Mongolian fermented dairy products.}, }
@article {pmid41896360, year = {2026}, author = {Yang, X and Tang, J and Lai, Z and Dong, Z and Liao, J and Guo, Y and Wang, Z}, title = {Comparative Analysis of Nasal and Cloacal Bacterial Communities in Three Sea Turtle Species under Rescue Center Conditions.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02751-0}, pmid = {41896360}, issn = {1432-184X}, support = {No. 2021B1212110005//Science and Technology Infrastructure Project of Department of Science and Technology of Guangdong Province/ ; }, }
@article {pmid41896556, year = {2026}, author = {Walsh, LH and Soni, V and Ancla, J and Somerville, V and Segata, N and Joyce, S and Sinderen, DV and Mahony, J and Shkoporov, AN and Kenny, JG and Cotter, PD and O'Sullivan, O}, title = {Mining of food metagenomes reveals an unexplored diversity of dsDNA bacteriophages.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00941-9}, pmid = {41896556}, issn = {2055-5008}, support = {DOMINO-101060218//European Union's Horizon Europe programme/ ; }, abstract = {Bacteriophages are key drivers of microbial ecology, co-existing and co-evolving with bacteria across diverse environments. Limitations in culturing, alongside advances in sequencing and bioinformatics, have driven the use of metagenomics to explore viral diversity. Viral-specific analysis of >3000 food metagenomes from cFMD produced the FVGC, comprising ~3400 metagenome-assembled viruses, most of which belong to novel Caudoviricetes lineages (n = 91), with only ~15% represented in IMG/VR v4. Together, these findings reveal extensive uncharacterized viral diversity in food systems. Beyond serving as a reference, the FVGC facilitates detailed investigation of virus-host interactions. Viral sequences were pervasive across microbial genomes, with several bacterial families exhibiting near-universal associations with viral elements. Bacterial antiviral defence systems were abundant and taxonomically diverse, dominated by restriction-modification systems, while CRISPR-Cas systems showed pronounced lineage-specific distributions; in contrast, viral anti-defence genes were detected at low frequency (<10% of MAVs). Host prediction linked MAVs to clinically relevant taxa, including expanded ESKAPE pathogens such as Klebsiella pneumoniae, Acinetobacter baumannii, Staphylococcus aureus, and Enterobacter spp., highlighting the ecological connectivity between food-associated viruses and clinically important bacteria. Antimicrobial resistance signals were scarce, suggesting minimal phage-mediated AMR dissemination in food environments. This new publicly available viral database represents a valuable resource for further exploration of viral diversity.}, }
@article {pmid41896600, year = {2026}, author = {Lajoinie, DM and Rocco Welsh, R and Rey, C and Nilsson, JF and Toscani, AM and Djurhuus, AM and Sauka, D and Hansen, LH and Jofré, E and Pistorio, M}, title = {Comparative genomics and biocontrol potential of five Bacillus strains isolated from grapevine rhizosphere.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-44555-9}, pmid = {41896600}, issn = {2045-2322}, support = {PICT2021-0277//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica (ANPCyT, Argentina)/ ; PIP2022-0367//Consejo Nacional de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas (CONICET, Argentina)/ ; }, }
@article {pmid41897466, year = {2026}, author = {Lyu, X and Zhang, L and Si, J and Dai, S and Su, H and Lyu, S and Chen, L and Sun, J and Jin, X and Li, H}, title = {Activation of the Nrf2 Signaling Pathway by a Ginseng-Salvia Root-Notoginseng Composite Alleviates Ulcerative DSS-Induced Colitis via Restoring Gut Microbiota and the Intestinal Barrier.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, doi = {10.3390/antiox15030320}, pmid = {41897466}, issn = {2076-3921}, support = {JJKH20250214CY//the Jilin Provincial Department of Education Scientific Research Project/ ; }, abstract = {Current treatments for ulcerative colitis (UC) often fail to adequately address its multifactorial pathogenesis, which involves oxidative stress, barrier dysfunction, and gut microbiota dysbiosis. This study evaluated the therapeutic potential and multi-targeting mechanism of a ginseng, salvia root, and notoginseng oral solution (GSNS) in a mouse model of colitis induced by dextran sulfate sodium (DSS). Based on high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) technology, 25 major bioactive components were identified. Following the induction of colitis with 3.5% DSS in C57BL/6J mice, the animals were treated with the GSNS (40, 80, or 160 mg/kg/day) or 5-Amino Salicylic Acid (5-ASA). The therapeutic efficacy was assessed via disease activity, histopathological staining, cytokines and oxidative stress analysis, and a barrier integrity test. Combined data from Western blot, qPCR, immunohistochemistry, electron microscopy, and 16S rRNA sequencing indicate that the therapeutic effect of the GSNS against colitis is attributable to its dual role in dampening pro-inflammatory cytokines and potentiating antioxidant defenses via the Nrf2/HO-1 signaling pathway. It also upregulated Occludin expression, repaired tight junctions, and was associated with beneficial alterations in the gut microbiota, as evidenced by increased Prevotellaceae and suppressing Escherichia-Shigella. These findings demonstrated that the GSNS exerts a multi-target effect against colitis by synergistically enhancing antioxidant defense, repairing the intestinal barrier, and modulating microbial ecology, supporting its potential as a promising natural compound-based candidate for DSS-induced colitis treatment.}, }
@article {pmid41897732, year = {2026}, author = {Lee, H and Na, W and Sohn, C}, title = {Comparative Microbiome Profiles of Korean Fermented Foods Based on Production Type and Additive Use.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/foods15061010}, pmid = {41897732}, issn = {2304-8158}, support = {NRF-RS-2024-00463020//National Research Foundation of Korea/ ; }, abstract = {Fermented foods are produced through controlled microbial activity and are valued for their extended shelf life, sensory attributes, and potential health benefits. This study examined the effects of production methods on microbial ecology by comparing microbial community structure, Shannon diversity, and pH changes in traditional and commercially produced Korean fermented foods. Cabbage and radish kimchi were fermented for four weeks to assess microbial succession and physicochemical changes, and additional fermented foods, including soy sauce, soybean paste, pepper paste, fruit vinegar, yogurt, and aged kimchi, were compared according to production method. Microbial communities were analyzed using amplicon sequencing targeting the V3-V4 regions of the bacterial 16S rRNA gene and the fungal internal transcribed spacer (ITS) region. Traditionally produced cabbage kimchi exhibited high microbial diversity at the early fermentation stage, initially dominated by Weissella and Leuconostoc, followed by a gradual shift toward lactic acid bacteria dominance at later stages. In contrast, commercially produced cabbage kimchi maintained a simplified microbial community dominated by a limited number of lactic acid bacteria throughout fermentation. Radish kimchi showed production-method-dependent patterns, with the rapid dominance of lactic acid bacteria during traditional fermentation and partial recovery of microbial diversity during commercial fermentation. Shannon diversity was consistently higher in traditionally produced kimchi during fermentation. In contrast, commercially produced kimchi exhibited more rapid acidification. Across other fermented foods, traditionally produced soy-based products exhibited complex microbial communities dominated by Bacillus spp., whereas commercially produced products were characterized by yeast-dominant profiles. Fruit vinegar and yogurt showed low microbial diversity regardless of the production method. These findings demonstrate the importance of production strategies in shaping microbial ecology, fermentation dynamics, and resulting product characteristics across various Korean fermented foods.}, }
@article {pmid41897857, year = {2026}, author = {Yang, Y and Wang, J and Wang, Z and Li, C and Hu, X and Liao, S and Wang, L}, title = {Airborne Microbiome of Tropical Ostrich Farms: Diversity, Antibiotic Resistance, and Biogeochemical Cycling Potential.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {6}, pages = {}, doi = {10.3390/ani16060880}, pmid = {41897857}, issn = {2076-2615}, support = {42367014//The National Natural Science Foundation of China/ ; }, abstract = {The expansion of tropical specialty livestock farming raises urgent concerns about airborne pathogen and antibiotic resistance dissemination. Ostrich farming, characterized by high-density stocking and feed exposure, yet their microbial ecology remain poorly characterized. This study analyzed 48 bioaerosols samples from an ostrich farm in Hainan, China, across dry and rainy seasons using 16S rRNA sequencing and metagenomics. The bacterial community were dominated by Firmicutes, Proteobacteria, and Actinobacteria, followed by Staphylococcus, Bacillus, and Acinetobacter as predominant genera, with particle size significantly shaping their structure. Large particles (>7.0 μm) carried higher species richness, while medium particles (2.1-3.3 μm) exhibited the highest diversity and evenness. Notably, small particles (0.65-1.1 μm), which can penetrate deep into the lungs, were enriched with Brevibacillus and Corynebacterium. Metagenomic analysis identified 638 antibiotic resistance genes (ARGs), dominated by efflux pump-associated determinants. The detection of clinically relevant ARGs (e.g., mcr-1 and blaTEM) reflects the genetic potential of the airborne resistome, rather than confirmed resistance phenotypes or active horizontal gene transfer. Functional analysis revealed a strong potential for organic matter degradation, driven by abundant carbohydrate-active enzymes (CAZymes) and their corresponding CAZyme genes, as well as a nitrogen cycle dominated by assimilation and reduction pathways, while genes for nitrogen fixation and nitrification were absent. Our findings demonstrate that ostrich farming enhanced airborne microbial diversity and functional potential, facilitating the ARG dissemination and nitrogen transformation. This study provides critical insights into the ecological and health risks of bioaerosols in tropical livestock farms, informing environmental monitoring and risk management strategies.}, }
@article {pmid41898277, year = {2026}, author = {Qiu, D and Suo, L and Wei, T and Lu, Z and Weng, Q and Xiao, J and Wang, X and Xu, Q and Wu, J}, title = {Mediation Role of Gut Microbiota in the Causal Relationship Between m6A Regulatory Genes and Metabolic Dysfunction-Associated Steatotic Liver Disease: A Mendelian Randomization Study.}, journal = {Biomedicines}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/biomedicines14030630}, pmid = {41898277}, issn = {2227-9059}, support = {3502Z20227102//Qinyu Xu/ ; }, abstract = {Background: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a globally prevalent condition with a complex pathogenesis. While both m6A RNA methylation regulators and gut microbiota have been independently implicated in MASLD, their potential causal interplay remains unexplored. This study aimed to investigate the causal relationships among m6A regulatory genes, gut microbiota, and MASLD, and to assess the mediating role of gut microbiota. Methods: We performed a two-sample Mendelian randomization (MR) analysis using publicly available genome-wide association study (GWAS) data. Genetic instruments for m6A regulators were derived from blood expression quantitative trait loci (eQTL) data. Gut microbiota and MASLD data were obtained from large-scale metagenomic and disease GWAS, respectively. The inverse-variance weighted method was the primary analysis, supplemented by sensitivity and mediation analyses to evaluate potential mediating pathways. Results: Genetically predicted levels of four m6A regulators showed significant causal associations with MASLD risk: ALKBH3 increased risk (OR = 1.17), whereas ALKBH5 (OR = 0.89), CBLL1 (OR = 0.76), and RBM15B (OR = 0.83) were protective. Nineteen gut microbial taxa were causally linked to MASLD. Among these, seven taxa were influenced by the four identified m6A genes. Although no mediation effects reached strict statistical significance, the pathway from ALKBH5 to MASLD via Parabacteroides abundance showed a suggestive indirect effect accounting for 21.9% of the total effect (p = 0.068). Given the limited statistical power of mediation analyses in MR settings, this observation should be interpreted with caution and requires validation in larger, well-powered studies. Conclusions: This MR study provides genetic evidence supporting causal roles of specific m6A regulators in MASLD and suggests that gut microbiota may partially mediate these relationships. The findings highlight a potential "m6A-gut microbiota-liver" axis in MASLD pathogenesis.}, }
@article {pmid41898837, year = {2026}, author = {Li, S and Chiodi, C and Maucieri, C and Della Lucia, MC and Zardinoni, G and Ravi, S and Squartini, A and Concheri, G and Geng, G and Wang, Y and Stevanato, P}, title = {Profiling Soil-Plant-Microbial Communities: DNA and Multi-Omics Techniques.}, journal = {Genes}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/genes17030303}, pmid = {41898837}, issn = {2073-4425}, mesh = {*Soil Microbiology ; Rhizosphere ; Metagenomics/methods ; *Microbiota/genetics ; *Plants/microbiology/genetics ; Genomics/methods ; Metabolomics/methods ; Plant Roots/microbiology/genetics ; Crops, Agricultural/microbiology/genetics ; Multiomics ; }, abstract = {Interactions among plant roots, soil, and microorganisms in the rhizosphere regulate nutrient cycling, plant health, and ecosystem resilience. Recent advances in DNA sequencing and multi-omics are contributing to a shift from primarily descriptive surveys toward more mechanistic and predictive frameworks. This review synthesizes methodological developments and conceptual insights spanning microbial ecology, functional genomics, and agricultural applications. We first summarize DNA-based approaches-marker-gene sequencing, shotgun metagenomics, and quantitative nucleic acid assays-and then complementary omics layers, including metatranscriptomics, metaproteomics, metabolomics, epigenomics, ionomics, and phenomics. We next outline computational advances in data integration, network modeling, and visualization that help represent complex multi-layered datasets as biologically interpretable systems. Applications relevant to climate resilience and sustainable agriculture are discussed, including the design of synthetic microbial communities, the identification of biomarkers for soil health and stress tolerance, and case studies in which rhizosphere multi-omics informs crop breeding and soil management strategies. Overall, these developments underscore the potential of treating microbes as functional and, to some extent, manageable components of the plant holobiont. Looking ahead, we identify key research gaps involving standardized workflows, cross-scale causal inference, and real-time monitoring pipelines that integrate molecular diagnostics with remote sensing and edge-cloud analytics. By linking ecological mechanisms with translational practice, multi-omics frameworks may support the development of more sustainable, data-driven agriculture that better aligns productivity with environmental stewardship.}, }
@article {pmid41898972, year = {2026}, author = {Derguini, A and Basher, NS}, title = {Cockroaches as Vectors of Pathogens and Antimicrobial Resistance: Evidence from Healthcare, Community, and Agricultural Settings.}, journal = {Insects}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/insects17030310}, pmid = {41898972}, issn = {2075-4450}, support = {IMSIU-DDRSP2502//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)./ ; }, abstract = {Synanthropic cockroaches, especially Blattella germanica and Periplaneta americana, are persistent pests of human dwellings, healthcare facilities, food establishments, farms, and transport infrastructure. Accumulating field and laboratory studies indicate that synanthropic cockroaches carry clinically important bacteria, fungi, and parasites, including multidrug-resistant strains harbouring extended-spectrum β-lactamase, carbapenemase, and other antimicrobial-resistant determinants. Cockroaches acquire these organisms from sewage, waste, food residues, animal excreta, and contaminated clinical environments, and retain them on the cuticle and within a complex gut microbiota. Dissemination is predominantly mechanical, via contact transfer and deposition of regurgitate and faeces on food, equipment, and surfaces, but may be amplified by gut colonisation, microbial interactions, and horizontal gene transfer within the cockroach microbiome. In hospitals, cockroaches can connect high-burden reservoirs (drains, waste areas, kitchens) with vulnerable units, including intensive care units (ICUs), neonatal intensive care units (NICUs), burn units, and haemato-oncology wards. In food and livestock systems, they may contaminate housing, ingredients, and finished products, enabling spillover along supply chains and at ports. This review synthesises current evidence and highlights the following priorities: integrate cockroaches into infection prevention, food safety, and biosecurity; incorporate cockroach sampling into antimicrobial resistance (AMR) and genomic surveillance; and advance mechanistic research on cockroach-microbiota-pathogen interactions to improve pest management and safely explore cockroach-derived antimicrobial compounds. In this review, we distinguish external mechanical carriage (cuticular contamination) from internal gut carriage; we use "gut colonisation" only when persistence/replication or prolonged shedding is demonstrated.}, }
@article {pmid41900294, year = {2026}, author = {Ramírez-Saad, HC and Hernández-Rodríguez, CH}, title = {Editorial for Special Issue "Genomics Approaches in Microbial Ecology".}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/microorganisms14030534}, pmid = {41900294}, issn = {2076-2607}, abstract = {Microbial ecology has entered a phase of methodological consolidation where genomic and molecular tools are being used to address ecological questions rather than being subordinate to culture-based approaches [...].}, }
@article {pmid41900372, year = {2026}, author = {Faragó, V and Borsodi, AK and Nagy, B}, title = {The Taxonomic Diversity of Prokaryotic Communities from Permafrost Active Layers of the Chilean Andes.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/microorganisms14030613}, pmid = {41900372}, issn = {2076-2607}, support = {NKFIH OTKA K147424//National Research, Development and Innovation Office, Hungary/ ; EK&#xd6;P-25-3-I-ELTE-244//Ministry for Culture and Innovation, Hungary/ ; }, abstract = {The study of microorganisms inhabiting extreme environments offers a valuable opportunity to explore their potential ecological roles. This study aimed to reveal and compare the microbial taxonomic diversity of largely unexplored permafrost regions located in different climatic zones (dry and wet) in the Chilean Andes, separated by thousands of kilometers. Permafrost active layer samples were collected from the Ojos del Salado (Atacama Desert) and the Torres del Paine (Patagonia) from different sampling depths. Illumina 16S rRNA gene-based amplicon sequencing revealed that the Andean permafrost active layer provides diverse habitats for distinct microbial communities, with higher taxonomic diversity of Bacteria than Archaea. The wet Patagonian Andes samples showed higher diversity, with a greater abundance of Chloroflexota and Bacteroidota, while the dry Ojos del Salado samples were dominated by Actinomycetota, indicating desiccation stress. Archaea were classified as ammonia-oxidizing members of the Thermoproteota phylum. Beta-diversity analyses suggested that differences in environmental conditions (mainly available moisture) contributed more to community structure differentiation than geographical distances. Nevertheless, the effect of sampling depth on microbial diversity was insignificant.}, }
@article {pmid41883800, year = {2026}, author = {Diao, N and Cai, A and Zhou, Y and Long, B and Mo, Z and Shang, S and Liu, Y and Xu, J and Hu, W and Feng, K and Sarengaowa, }, title = {Recent advances on fermentation of mustard plant (Brassica juncea L.): microbial community, fermentation processing and sensorial quality: a review.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1784857}, pmid = {41883800}, issn = {1664-302X}, abstract = {Mustard (Brassica juncea L.), rich in vitamins, minerals, and glucosinolates, yields fermented products valued for their distinct flavor and health benefits, particularly across East and Southeast Asia. The fermentation process is primarily driven by a complex microbial community dominated by lactic acid bacteria (LAB) such as Lactobacillus fermentum, Lactobacillus pentosus, and Lactobacillus plantarum. These microbes metabolize substrates to generate organic acids, volatile compounds, and free amino acids, which collectively shape the product's flavor and sensory quality. This review systematically summarizes recent progress in mustard fermentation, focusing on: the composition, succession, and function of microbial communities across different regions and fermentation stages and their influence on fermentation characteristics; the regulatory effects of key processing parameters-including fermentation vessel, temperature, and salt concentration-on microbial ecology, metabolic pathways, and final product quality; the chemical basis of taste attributes such as sourness, umami, bitterness, and pungency alongside the formation and evolution of aroma compounds during fermentation, and their links to microbial metabolism and biochemical pathways like glycolysis and the tricarboxylic acid cycle; and the formation patterns of potential risk factors such as biogenic amines and nitrite during fermentation, along with strategies to control their levels through process optimization and starter culture selection. Finally, future research directions are outlined, emphasizing the integration of omics and synthetic biology technologies to elucidate flavor formation mechanisms, develop stable starter cultures, and establish standardized processes. These advances aim to achieve consistent flavor, improved quality, and safe production of fermented mustard products, supporting the sustainable development of the industry.}, }
@article {pmid41884457, year = {2026}, author = {Saeed, NK and Elbeltagi, YM and Al-Beltagi, M}, title = {Unveiling the viral dimension: The paediatric gut virome as a key modulator of gastrointestinal metabolic, and neurodevelopmental health.}, journal = {World journal of virology}, volume = {15}, number = {1}, pages = {118362}, pmid = {41884457}, issn = {2220-3249}, abstract = {Paediatric gut microbiome research has long been bacteriocentric, overlooking the extensive viral component known as the gut virome. Composed of bacteriophages, eukaryotic viruses, and endogenous viral elements, the paediatric gut virome is the most abundant and genetically diverse biological entity in the intestine. Emerging evidence indicates that the virome is a key regulator of microbial ecology, immune maturation, and systemic physiological programming during early life. This narrative review synthesizes current knowledge on the establishment, development, and functional roles of the paediatric gut virome, with emphasis on its interactions with the bacterial microbiome and host immune system. We highlight how early-life viral exposures influence mucosal immune imprinting, epithelial barrier integrity, and immune tolerance, particularly during the first 1000 days of life. Virome dysbiosis is increasingly associated with paediatric gastrointestinal disorders, including inflammatory bowel disease, necrotizing enterocolitis, celiac disease, and functional gastrointestinal disorders. Beyond the gut, the virome also contributes to metabolic regulation, type 1 diabetes risk, and gut-brain axis signaling, influencing neurodevelopment. Mechanistic pathways involving phage-mediated bacterial modulation, innate immune sensing, cytokine signaling, and metabolic intermediates are discussed, positioning the paediatric gut virome as a central regulator of gastrointestinal and systemic homeostasis.}, }
@article {pmid41884809, year = {2026}, author = {Ren, L and Li, M and Wu, L and Lin, Z and Chen, A}, title = {Microbial transformation of secondary bile acids: roles in gut ecology and autoimmune diseases.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1769792}, pmid = {41884809}, issn = {1664-3224}, mesh = {*Bile Acids and Salts/metabolism/immunology ; *Gastrointestinal Microbiome/immunology ; Humans ; *Autoimmune Diseases/immunology/microbiology/metabolism/etiology ; Animals ; }, abstract = {Secondary bile acids (SBAs) attracted interest due to their regulatory functions in gut microbial ecology and immune responses. These intricate microbial transformations decisively shape the biochemical properties of SBAs. Recent advancements in artificial intelligence and mass spectrometry technologies have substantially expanded our understanding of the diversity within the SBAs pool. To date, hundreds of SBAs, a minor portion of the natural SBA repertoire, have been identified, alongside the prediction of tens of thousands of associated enzymes. Integrative multi-omics studies have further substantiated the role of SBAs in the pathogenesis of autoimmune diseases. This review synthesizes current knowledge on the microbial modification of bile acids, their effects on gut microbial ecology and immune function, with a particular emphasis on autoimmune disorders. Collectively, these findings highlight SBAs as critical regulators of gut microbiota and immune system homeostasis, with their functions intricately linked to their molecular structures.}, }
@article {pmid41886209, year = {2026}, author = {Singh, AP and Dongre, S and Sharma, S and Joshi, K and Bagdare, H and Bobade, R and Prakash, O and Sharma, R}, title = {Decolourizing distillery spent wash using fungal biotechnologies: from pollution to potential.}, journal = {Bioresources and bioprocessing}, volume = {13}, number = {1}, pages = {}, pmid = {41886209}, issn = {2197-4365}, }
@article {pmid41887850, year = {2026}, author = {Fang, K and He, Y and Rao, S and Wang, J and Xu, J and Shi, J}, title = {Neglected but significant: High mercury alkylation but low carbon sequestration in paddy field as revealed by soil profiles survey.}, journal = {Journal of environmental sciences (China)}, volume = {163}, number = {}, pages = {301-310}, doi = {10.1016/j.jes.2025.08.016}, pmid = {41887850}, issn = {1001-0742}, mesh = {*Mercury/analysis/chemistry ; *Soil Pollutants/analysis ; *Soil/chemistry ; *Environmental Monitoring ; Alkylation ; *Carbon Sequestration ; Oryza ; Carbon ; Soil Microbiology ; Methylation ; }, abstract = {The global environmental crisis caused by simultaneous increasing mercury (Hg) alkylation and organic carbon deficit has restricted the implementation of the "One Health" framework. Here, we report a neglected but significant phenomenon of high Hg alkylation but low carbon sequestration in paddy field through soil profiles survey deep to the parent material horizon (defined as deepsoil). We found that ratios of Hg methylation and ethylation were increased by 69.0 % and 64.2 % in deepsoil compared to that in topsoil (P < 0.05). This inhibition of Hg alkylation in topsoil is likely regulated by Nitrosomonadaceae (enriched by 64.9 % vs. deepsoil), which harbors the merA gene (Hg demethylation marker). Furthermore, through deciphering molecular level of dissolved organic matter, we found the content of labile carbon increased by 12.7 %, compared to those in topsoil. Conversely, in deepsoil, labile carbon (e.g., carbohydrates) enriches Spirochaetaceae (abundance +69.2 %, carrying the hgcA gene for Hg methylation), thereby facilitating Hg alkylation. This microbial shift enhanced Hg alkylation in deepsoil relative to topsoil. In summary, this study bridges human health, microbial ecology, and climate resilience (carbon storage) within the "One Health" paradigm, revealing depth-dependent mechanisms that reconcile soil Hg remediation with carbon management for sustainable agroecosystems.}, }
@article {pmid41888223, year = {2026}, author = {Afshar Jahanshahi, D and Ariaeenejad, A and Hasannejad, A and Zabihi, MR and Ghaffari, MR and Ariaeenejad, S and Kavousi, K}, title = {MiGPC: a comprehensive catalog of enzybiotics from environmental metagenomes.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-44250-9}, pmid = {41888223}, issn = {2045-2322}, support = {4020052//Center for International Scientific Studies &amp; Collaborations (CISSC)/ ; }, abstract = {Antimicrobial agents play a vital role in human and environmental health, with applications spanning medicine, food preservation, agriculture, and biotechnology. Among them, enzybiotics enzyme-based antimicrobials have emerged as powerful alternatives to conventional antibiotics due to their targeted mechanisms and lower propensity for resistance. Beyond their medical relevance, enzybiotics have emerging applications in food preservation, animal health, and agriculture, thereby broadening their industrial and environmental value. To support the discovery and characterization of these versatile biomolecules, we present the first genome-resolved metagenomic gene and protein targeted enzybiotic catalog focused on enzybiotics, derived from diverse environmental microbiomes. The Microbial Enzybiotic Gene and Protein Catalog (MiGPC), integrates 15 whole-metagenome datasets from oceans, soils, fecal samples, vegetation, and plastic-contaminated environments, capturing a wide ecological spectrum. Enzybiotic sequences were compiled through a hybrid strategy combining public database mining and manual literature curation, yielding over 136,000 enzybiotic sequences, 7654 metagenome-assembled genomes (MAGs), and ~ 100 million unique genes and proteins. MiGPC integrates taxonomic and enzybiotic gene profiles, offering a robust platform for the discovery, annotation, and ecological mapping of antimicrobial enzymes. Functional analyses using KEGG and eggNOG revealed that approximately 62% of the genes remained uncharacterized, highlighting a rich source of potentially novel functions. Glycoside hydrolases and glycosyl transferases were the most prevalent CAZyme families, while the dominant enzybiotic-producing taxa belonged primarily to the Pseudomonadota and Bacillota phyla. Statistical modeling uncovered two major ecological clusters that distinguished polluted from relatively pristine environments. MiGPC enables high-throughput screening of previously unexplored metagenomes, facilitating the identification of novel antimicrobial agents from under characterized ecosystems. Overall, MiGPC represents a landmark resource that will support multi-omics research, microbial ecology, and the development of next-generation biotechnological solutions based on enzybiotics.}, }
@article {pmid41888251, year = {2026}, author = {Perliński, P and Mudryk, ZJ and Zdanowicz, M and Kubera, &#x141;}, title = {Culturable Airborne Microorganisms in Urban and Coastal Recreation Areas (Southern Baltic Sea).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02729-y}, pmid = {41888251}, issn = {1432-184X}, }
@article {pmid41878569, year = {2026}, author = {Uma Mageswary, M and Hanglian, L and Li, P and Richmond, RV and Azianey, Y and Tan, JS and Liong, MT and Ali, A and Vejayantheran, M and Hua, J and Jian, H and Abd Hamid, IJ and Taib, F and Zhang, Y}, title = {Probiotic improves respiratory and gastrointestinal health, immune homeostasis, and gut microbiota composition in infants: a randomized controlled trial.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1746679}, pmid = {41878569}, issn = {2296-861X}, abstract = {INTRODUCTION: The early postnatal period is a critical window for shaping the gut microbiota, which plays a pivotal role in immune maturation, infection resistance, and metabolic programming. Disruptions to this process may predispose infants to infections and allergic or metabolic disorders. Probiotics such as Bifidobacterium infantis have shown promise in modulating gut microbial ecology and immune function, but strain-specific and mechanistic evidence in infants remains limited. This study aimed to evaluate the effects of B. infantis YLGB-1496 supplementation on clinical outcomes, immune markers, and gut microbiota composition in healthy infants below one year of age.<br><br>METHODS: In a 12-week, randomized, double-blind, placebo-controlled trial, 119 healthy infants were enrolled (B. infantis YLGB-1496 n=59, placebo n=60). Participants received one daily sachet of B. infantis YLGB-1496 (1 &#xd7; 10&#xb9;&#x2070; CFU) or placebo. Clinical outcomes for respiratory health and gastrointestinal (GI) health were assessed via validated questionnaires. Oral and fecal samples were collected for analysis of sIgA, cortisol, and cytokines (TNF-&#x3b1;, IFN-&#x3b3;, IL-1&#x3b2;, IL-10, calprotectin). Gut microbiota was profiled by 16S rRNA sequencing, and diversity indices and taxonomic shifts were analyzed.<br><br>RESULTS: Compared with placebo, B. infantis YLGB-1496 supplementation was associated with consistent numerical reductions in respiratory symptom days, although these did not remain statistically significant after false discovery rate (FDR) adjustment. In contrast, gastrointestinal outcomes showed robust improvements after FDR correction, including reduced stomach ache (q = 0.010), lower diarrhea incidence (q < 0.001), and fewer diarrhea-related clinical visits (q < 0.001). Fecal sIgA remained elevated in the B. infantis YLGB-1496 group (P = 0.138 vs P = 0.000 in placebo), accompanied by increased IL-10 (P < 0.001) and reduced IL-1&#x3b2; (P = 0.002). Oral sIgA was enhanced (P = 0.001), while cortisol declined similarly in both groups. Microbiota analysis revealed enrichment of beneficial taxa in the B. infantis YLGB-1496 group with concurrent reductions in pathobionts. In contrast, the placebo group exhibited increases in Campylobacter, Staphylococcus, and Desulfovibrio desulfuricans, and decreases in Faecalibacterium prausnitzii and Anaerostipes caccae, indicative of dysbiosis. These compositional changes support improved gut barrier function and immune development.<br><br>CLINICAL TRIAL REGISTRATION: https://clinicaltrials.gov/study/NCT05794815?term=NCT05794815&amp;rank=1, Identifier: NCT05794815.}, }
@article {pmid41879866, year = {2026}, author = {Finch, JTD and Riegler, M and Cook, JM and Brettell, LE}, title = {Filth Flies, Flowers and Food: Pollination by Flies (Calliphoridae) Does Not Affect the Strawberry Microbiome.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02741-2}, pmid = {41879866}, issn = {1432-184X}, support = {PH16002//Horticultural Innovation Australia Limited/ ; }, }
@article {pmid41879886, year = {2026}, author = {Chen, W and Li, X and Zhao, X and Zuo, Z and Wang, D and Zhao, F}, title = {GMW: a hybrid graph-based approach for post-assembly metagenome analysis and decontamination.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {41879886}, issn = {1869-1889}, abstract = {Accurate genome assembly from metagenomic sequencing data remains challenging, particularly in mixed infections involving multiple pathogens, due to data complexity and contaminant sequences. Here, we present GMW (Genomic Microbe-Wise), a novel computational tool that improves pathogen genome assembly accuracy and enhances contaminant removal capabilities by simplifying the post-assembly graph. GMW leverages community detection algorithms, sequence similarity analysis, and coverage patterns to resolve strain mixtures and improve assembly accuracy. Using datasets of influenza A virus subtypes, we demonstrate GMW's ability to disentangle mixed infections and reconstruct complete viral genomes with high precision. Additionally, GMW outperforms traditional sequence similarity methods in classifying target contigs from contaminants. This tool also provides interactive visualization modules to streamline the inspection of assembly outputs, including simplified representations of complex assembly graphs. By enhancing assembly quality and contamination filtering, GMW emerges as a versatile solution for applications in clinical diagnostics, microbial ecology, and pathogen surveillance.}, }
@article {pmid41879986, year = {2026}, author = {Couradeau, E and Vanegas, J and Betancurt-Anzola, D and Glass, S and Eckert, K and Bechtold, EK and Ellenbogen, JB and Zaragoza, LR and Wrighton, K and Vanegas, JS}, title = {Soil Microbial Diversity in Páramos Wetland of the Colombian Andes Reveals Novel and Unique Features Within a Global Wetland Database.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02738-x}, pmid = {41879986}, issn = {1432-184X}, support = {2325922//NSF/ ; 7006508//USDA Hatch/ ; DE-SC0023084 and DE-SC0023456//DOE/ ; DE-SC0023084 and DE-SC0023456//DOE/ ; DE-SC0023084 and DE-SC0023456//DOE/ ; }, abstract = {Tropical wetlands are the largest natural source of methane on Earth, yet they remain the least studied, particularly high-altitude wetlands like those in the Páramo of Chingaza, Colombia. These ecosystems are crucial for water provisioning, carbon sequestration, and biodiversity conservation but are threatened by rapid climate change. While the páramo biome supports thousands of endemic plant species and plays a vital role in balancing carbon inputs and greenhouse gas outputs (CO2 and CH4), its soil microbial diversity and functional roles in soil processes are largely unexplored. To fill this knowledge gap, we conducted amplicon sequencing of the ITS, 16S rRNA, and 18S rRNA genes to examine microbial diversity across three distinct ecosites at Laguna Seca, Chingaza, characterized by different macrotopographies, water-table levels, and vegetation assemblages. Our findings revealed significant variations in microbial community structure, with the peatland ecosite showing the highest diversity across all amplicons. Comparative analysis with global wetland datasets indicated that microbial communities at Laguna Seca share similarities with subarctic Stordalen Mire fen and other peat-forming wetlands. Notably, our targeted assessment identified a diversity of potential methanogens and methanotrophs exclusively within the peatland ecosite, at low but comparable abundance to other wetlands. This suggests that methane cycling in the other ecosites of this wetland may either be less prominent than expected or involve organisms not previously associated with known methane processes. These findings establish a baseline for understanding microbial diversity in tropical high-montane wetlands and underscore the unique ecological significance of páramo peatlands amid climate change.}, }
@article {pmid41880444, year = {2026}, author = {Moore, PJ and Kent, LA and Hunter, RC}, title = {Anaerobic microbiota promote pathogen association with the airway epithelium.}, journal = {Journal of medical microbiology}, volume = {75}, number = {3}, pages = {}, doi = {10.1099/jmm.0.002149}, pmid = {41880444}, issn = {1473-5644}, mesh = {Humans ; *Pseudomonas aeruginosa/physiology ; *Bacteria, Anaerobic/physiology ; *Microbiota ; Epithelial Cells/microbiology ; *Sinusitis/microbiology ; Mucins/metabolism ; *Rhinitis/microbiology ; *Respiratory Mucosa/microbiology ; Cell Line ; *Pseudomonas Infections/microbiology ; Chronic Disease ; }, abstract = {Introduction. Chronic rhinosinusitis (CRS) is a prevalent condition characterized by mucus stasis, persistent inflammation and infection of the paranasal sinuses. CRS often involves infection by the bacterium Pseudomonas aeruginosa, especially in individuals with cystic fibrosis or a history of antibiotic use. While P. aeruginosa is a well-established opportunistic pathogen that deploys a diverse array of virulence factors to drive airway infections, its persistence in the airway mucosa is also likely influenced by its local microbial ecology. For instance, anaerobic bacterial genera, such as Streptococcus, Veillonella and Prevotella, are also commonly found in CRS and may contribute to pathogen establishment.Hypothesis. Although anaerobes are common members of the CRS microbiota, their role in promoting P. aeruginosa association with the airway epithelium remains poorly defined. We hypothesized that anaerobes facilitate P. aeruginosa attachment by degrading mucin glycoproteins that decorate the epithelial surface.Aim. To determine whether CRS-associated anaerobic microbiota enhance P. aeruginosa colonization of the airways through mucin modification.Methodology. Using a novel dual oxic-anoxic culture platform, Calu-3 epithelial cells were co-cultured with a CRS-derived anaerobic microbial community. Inflammatory gene expression, mucin integrity and subsequent P. aeruginosa epithelial association were assessed. Additionally, mucins isolated from anaerobe-treated cells were evaluated for their ability to promote P. aeruginosa attachment in vitro.Results. Anaerobe exposure increased epithelial inflammatory marker gene expression and led to degradation of mucin glycoproteins. Anaerobe pre-treatment significantly enhanced P. aeruginosa association with the epithelial surface. Moreover, mucins isolated from anaerobe-treated cells promoted greater pathogen attachment in vitro compared to intact mucins.Conclusion. CRS-associated anaerobic microbiota can remodel the sinonasal microenvironment in ways that enhance P. aeruginosa epithelial association. These findings highlight the importance of polymicrobial interactions in CRS pathogenesis and suggest that targeting anaerobe-mediated mucin degradation may represent a novel therapeutic strategy for chronic airway disease.}, }
@article {pmid41882188, year = {2026}, author = {Anokyewaa, MA and Wang, Z and Amenyogbe, E and Lu, Y and Zhen, G}, title = {Impacts of Probiotics on Microbial Populations in Aquaculture Systems.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02710-9}, pmid = {41882188}, issn = {1432-184X}, support = {(2022A1515110243)//Guangdong Basic and Applied Basic Research Foundation/ ; }, }
@article {pmid41882189, year = {2026}, author = {Chewe, M and Shembo, TK and Dumfeh, EP and Zhou, S and Odinga, ES and Yang, G and Ohore, OE}, title = {Assessing the Ecological Roles of Resistomes within Microbial Communities in Antibiotic-contaminated Ecosystems.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02740-3}, pmid = {41882189}, issn = {1432-184X}, support = {Hnky2025ZC-3//Hainan Province Higher Education Scientific Research Project/ ; RZ2300006042//Hainan Medical University Talent Research Launch Fund/ ; }, }
@article {pmid41883376, year = {2026}, author = {Mao, C and Wang, Y and Li, X and Kong, Q and Al-Farraj, SA and Xu, EG and Grossart, HP and Huang, J and Song, W}, title = {Resistance Gene Dynamics, Biogeochemical Coupling, and Ecological Risks in Sediments of Anthropogenically Impacted Lake Wetlands in China.}, journal = {Environment &amp; health (Washington, D.C.)}, volume = {4}, number = {3}, pages = {420-433}, pmid = {41883376}, issn = {2833-8278}, abstract = {Antibiotic resistance is a growing global threat to both public health and ecosystem stability. While the "One Health" framework emphasizes the need to monitor antibiotic resistance genes (ARGs) across diverse environments worldwide, the risks posed by ARGs in lakes affected by human activities, particularly in lake sediments that serve as natural reservoirs of ARGs, remain poorly understood. Metagenomics enables culture-independent analysis of microbial communities and resistance genes, providing essential insights into ARG dynamics. This study investigates microbial communities, ARGs, metal resistance genes (MRGs), and mobile genetic elements (MGEs) in sediments from Lake Donghu and Lake Weishan in China, two contrasting lake ecosystems subject to urbanization and agricultural activities for over four decades, using high-throughput metagenomic sequencing and assembly. ARGs and MRGs were more strongly influenced by deterministic environmental factors, particularly heavy metals (Cd, Pb, Cu), whereas microbial community structures were predominantly shaped by stochastic processes. Metagenomic binning yielded 293 metagenome-assembled genomes (MAGs), 125 of which were identified as potential ARG hosts, with Proteobacteria and Desulfobacterota being the most common. These hosts frequently cocarried MGEs, virulence factor genes (VFGs), and MRGs and exhibited metabolic pathways linked to carbon, nitrogen, and greenhouse gas (CO2 and N2O) cycling. Dissolved organic carbon (DOC) was determined as a key factor influencing microbial metabolism and promoting resistance gene dissemination. Our findings highlight a tight coupling between ARG dissemination, microbial ecological functions, and biogeochemical processes, underscoring ecosystem-level risks associated with resistance proliferation in human-impacted wetlands of China and elsewhere.}, }
@article {pmid41883787, year = {2026}, author = {Lin, H and Shao, C and Yu, J and Chen, H and Ren, Y and Ren, J and Zeng, Y and Wu, Y and Zhang, Q and Xiao, X}, title = {Maternal probiotic and prebiotic supplementation on glucose metabolism in pregnant women and their offspring: effects and related mechanisms.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1782361}, pmid = {41883787}, issn = {1664-302X}, abstract = {INTRODUCTION: The global diabetes epidemic has brought gestational diabetes mellitus (GDM) and its long-term impacts on maternal-child health into sharp focus. Emerging evidence indicates that early-life metabolic programing, mediated significantly by gut microbiota, profoundly influences offspring glucose homeostasis. Notably, microbial-targeted nutritional interventions, including probiotic and prebiotic supplementation, have considerable potential as innovative therapeutic approaches. These strategies may effectively prevent intergenerational transmission of metabolic diseases by improving glucose metabolism in both mother and offspring.<br><br>METHODS: This narrative review synthesizes evidence from clinical trials and animal studies investigating the effects of maternal probiotic and prebiotic supplementation on glucose metabolism. We searched and analyzed literature focusing on glycemic outcomes in pregnant women with or without GDM and their offspring, as well as studies exploring underlying mechanisms including gut microbiota modulation, metabolite production, inflammatory pathways, and epigenetic regulation.<br><br>RESULTS: Clinical and animal studies have shown that probiotics and prebiotics can significantly alleviate metabolic parameters such as elevated fasting glucose and insulin resistance in patients with GDM, but their preventive effect on the incidence of GDM is unclear. In addition, maternal supplementation with probiotics or prebiotics may positively affect glucose metabolism in offspring through multiple interconnected mechanisms, which include the modulation of intestinal microbial ecology, the increased generation of microbial- derived metabolites such as short-chain fatty acids (SCFAs), the mitigation of inflammatory responses, and epigenetic regulation (e.g., DNA methylation, lncRNA and miRNA modification).<br><br>DISCUSSION: Despite some heterogeneity in the results of existing studies, there is overall support for the therapeutic potential of probiotic and prebiotic interventions in optimizing metabolic outcomes for both maternal and pediatric populations. Future studies need to further define the optimal type, dose and timing of intervention for probiotics and prebiotics and explore precise intervention strategies on the basis of individual gut microbiota characteristics. In conclusion, probiotic and prebiotic supplementation during pregnancy and lactation may become an adjunctive tool to improve glucose metabolism in mothers and infants, resulting in innovative approaches for the primary prevention of metabolic diseases.}, }
@article {pmid41883797, year = {2026}, author = {Sui, C and Qiao, H}, title = {The Type VI secretion system in enteric pathogen colonization: molecular mechanisms, ecological dynamics, and therapeutic potential.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1809019}, pmid = {41883797}, issn = {1664-302X}, abstract = {The Type VI Secretion System (T6SS) is a sophisticated, phage-tail-like contractile nanomachine that mediates contact-dependent protein translocation in a wide range of Gram-negative enteric pathogens. As a primary weapon for interference competition, T6SS enables pathogens like Salmonella and Vibrio cholerae to directly eliminate commensal rivals. This targeted elimination allows pathogens to dismantle microbiota-mediated colonization resistance and seize essential nutritional niches. Beyond interbacterial warfare, the system facilitates "exploitative competition" by secreting effectors for the acquisition of limited micronutrients such as iron and zinc. Furthermore, T6SS acts as a crucial virulence determinant by manipulating host cell signaling, disrupting cytoskeletal integrity, and even enhancing intestinal contractions to physically expel competitors. The expression and activity of T6SS are dynamically regulated by gastrointestinal cues, including bile salts, pH fluctuations, and quorum sensing signals, ensuring its activation is precisely timed during infection. Elucidating these multifaceted roles not only deepens our understanding of microbial ecology in the gut but also highlights T6SS as a promising target for microbiome engineering and the development of customizable, precision antimicrobial therapies.}, }
@article {pmid41689060, year = {2026}, author = {Li, M and Lin, J and Ma, C and Wei, G and Hu, Q and Li, X}, title = {Effects of L-selenomethionine supplementation on nutrient digestibility and metabolism, antioxidant capacity, hormone levels, and fecal microbiota diversity in pregnant Yili mares during mid- to late gestation.}, journal = {BMC veterinary research}, volume = {22}, number = {1}, pages = {}, pmid = {41689060}, issn = {1746-6148}, abstract = {BACKGROUND: L-selenomethionine (L-SeMet), a highly bioavailable organic form of selenium, plays a critical role in maintaining antioxidant homeostasis, regulating reproductive hormone secretion, and improving intestinal microbial ecology. Previous studies have demonstrated that appropriate supplementation with L-SeMet can significantly enhance the production performance and health status of ruminants. However, the nutritional regulatory mechanisms and physiological effects of L-SeMet in monogastric herbivores, particularly horses during mid- to late gestation, remain inadequately understood. Therefore, this study investigated the effects of different levels of L-SeMet supplementation on nutrient digestibility and metabolism, antioxidant capacity, reproductive hormone profiles, and fecal microbiota diversity in pregnant Yili mares.<br><br>RESULTS: The results showed that selenium (L-SeMet) supplementation at 0.4, 0.6, or 0.8&#xa0;mg Se mare&#x207b;&#xb9; day&#x207b;&#xb9; significantly increased apparent crude protein digestibility and serum glutathione peroxidase (GSH-Px) activity in pregnant mares compared with controls. Compared with the control group, the 0.6 and 0.8&#xa0;mg Se mare&#x207b;&#xb9; day&#x207b;&#xb9; groups exhibited significantly higher neutral detergent fiber (NDF) digestibility, nitrogen metabolism rate, total antioxidant capacity (T-AOC), catalase (CAT) activity, progesterone, and estradiol levels, while malondialdehyde (MDA) and urinary estrone levels were reduced. Fecal microbiota analysis further revealed an increased relative abundance of methanogens and Actinobacteriota, particularly in the 0.6&#xa0;mg Se mare&#x207b;&#xb9; day&#x207b;&#xb9; group. Functional predictions indicated enrichment of microbial metabolic pathways related to carbohydrates and energy metabolism.<br><br>CONCLUSIONS: Collectively, these findings indicate that selenium supplementation (provided as L-SeMet) enhances nutrient utilization, antioxidant defenses, and the endocrine milieu during pregnancy, with 0.6&#x2013;0.8&#xa0;mg Se mare&#x207b;&#xb9; day&#x207b;&#xb9; appearing to confer the broadest benefits; dose optimization and long term outcomes warrant further investigation.}, }
@article {pmid41699524, year = {2026}, author = {Tshimbila Kabangu, JMV and Tsiwedi-Tsilabia, E and Faida-Kitoga,  and Cizungu-Namugusha, J and Muhindo-Kabuyaya, P and Arung Kalau, W and Lundimu Tugirimana, P and Mushagalusa Kasali, F and Kadima Ntokamunda, J and Mukadi-Bamuleka, D}, title = {Prevalence of wound infections and related antimicrobial resistance in Goma, Democratic Republic of the Congo: a multicenter cross-sectional study.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {}, pmid = {41699524}, issn = {1471-2334}, abstract = {BACKGROUND: The morbidity and mortality related to wound infections and microbial resistance are real public health concern in low-income settings where data are lacking, empirical antibiotic use is common and microbiological diagnostics are limited. This study aimed to describe the prevalence and antimicrobial resistance (AMR) patterns resulting from wound infections.<br><br>METHODS: We conducted a one-year multicenter cross-sectional study across hospitals in Goma, Democratic Republic of the Congo. Consecutive patients with clinically infected wounds were enrolled. Wound swabs were processed using standard culture and susceptibility testing. Firth&#x2019;s bias-reduced logistic regression was used to assess factors associated with surgical site infection (SSI) and AMR, with analyses stratified by Gram staining.<br><br>RESULTS: Most patients were below 40 years old, with a median age of 27 years (IQR: 22&#x2013;39), predominantly males (64.5%). Gunshot injuries (33.2%), road traffic accidents (24.5%) and cesarean section&#xa0; (14.8%) were the leading cause of wounds. SSIs accounted for 21.25% of all clinically diagnosed infected wounds; they were significantly associated with female sex (OR&#x2009;=&#x2009;3.65, 95% CI: 1.18&#x2013;11.92, p&#x2009;=&#x2009;0.03) and abdominal surgery (OR&#x2009;=&#x2009;272.92, 95% CI: 85.66&#x2013;1208.58, p&#x2009;<&#x2009;0.001). In female patients, a high rate of SSIs was observed following cesarean section&#xa0; (86.8%). Overall microbial swab cultures were negative in 21.0%. Among 18 isolated species, Gram-negative bacteria were predominant with Proteus mirabilis (24.1%), Pseudomonas aeruginosa (13.6%), and Escherichia coli (12.7%), as the leading pathogens. In Gram-stratified Firth models, empirical antibiotic therapy was not independently associated with increased in vitro AMR. Amikacin showed a protective association among Gram-negative isolates, while estimates for Gram-positive cocci were imprecise due to small sample size. Pseudomonas aeruginosa exhibited reduced susceptibility to multiple drug classes.<br><br>CONCLUSION: Wound infections in Goma are largely linked to trauma and cesarean deliveries, with Gram-negative microorganisms dominating. The microbial ecology comprises ESKAPE pathogens and species known for their emerging resistance patterns such as Proteus mirabilis, Pseudomonas aeruginosa and Escherichia coli. Empirical antibiotic therapy was not independently associated with AMR after adjustment. These findings underscore the urgent need for enhanced diagnostic strategies, strengthened infection prevention measures, and effective antimicrobial stewardship in this resource-limited and conflict-affected setting.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12879-026-12867-w.}, }
@article {pmid41873801, year = {2026}, author = {Martins, GL and Zandt, DI' and Merloti, LF and Bieluczyk, W and Rocha, GS and Timmers, R and Rodrigues, RR and Tsai, SM and van der Putten, WH}, title = {Connectivity and Age of Restored Atlantic Forest Fragments Drives Composition and Functionality of the Fungal Community in the Leaf Litter Layer.}, journal = {Molecular ecology}, volume = {35}, number = {6}, pages = {e70325}, pmid = {41873801}, issn = {1365-294X}, support = {2018/19000-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2018/19000-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2022/05561-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; Process 2021/00976-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2023/18333-8//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 101110604//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; //Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, mesh = {*Forests ; *Plant Leaves/microbiology ; Brazil ; Biodiversity ; *Fungi/classification/genetics ; Trees/microbiology ; Soil Microbiology ; Conservation of Natural Resources ; Ecosystem ; }, abstract = {The restoration of biodiversity and functional tropical forests is critical to mitigating global biodiversity losses. Aboveground, increasing the connectivity of regenerating forest fragments facilitates the recolonization of tropical forest biodiversity. However, restoring functional ecosystems also requires the recovery of decomposition processes as these are essential in shaping aboveground biodiversity. Therefore, we investigate the role of forest connectivity in restoring the composition and functioning of fungal communities in the leaf litter layer during a chronosequence of forest restoration. In the Brazilian Atlantic Forest, we studied secondary forests regrown between 18 and 55 years after deforestation and different levels of forest connectivity and compared their litter to recently abandoned pastures and undisturbed primary forests. We quantified how forest age and connectivity between fragments influenced the litter fungi composition in relation to tree diversity, litter chemistry and litter isotopes. We show that fungal composition was highly heterogeneous in forest litter, whereas pasture litter exhibited a more homogeneous community. Moreover, forest connectivity had stronger effects on litter fungal composition compared to forest age. Connectivity promoted wood saprotrophs and endophytes, while suppressing soil saprotrophs, with its effects being more evident during later stages of restoration. Fungal guilds such as endophytes and saprophytes were primarily influenced by tree diversity and leaf litter chemistry. We conclude that forest connectivity promotes the re-establishment of saprophytic fungi capable of decomposing recalcitrant litter substrates, driven mainly by enhancing tree diversity and litter quality. Practical implications of increasing connectivity may relate to forest resilience in front of future climate change scenarios.}, }
@article {pmid41873837, year = {2026}, author = {Kazmi, SSUH and Batool, SM and Pastorino, P and Barcelò, D and Grossart, HP and Yaseen, ZM and Khan, ZH and Azeem, M and Li, G}, title = {The plastisphere as a nexus for antimicrobial resistance: micro(nano)plastics in pathogen colonization, gene transfer, and global health risks.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {}, number = {}, pages = {}, doi = {10.1002/brv.70163}, pmid = {41873837}, issn = {1469-185X}, support = {42595620//National Natural Science Foundation of China/ ; 32361143523//National Natural Science Foundation of China/ ; 2023J05078//Natural Science Foundation of Fujian Province, China/ ; //Fujian Province Excellent Postdoctoral Project/ ; 2021-DST-004//Ningbo S&amp;T Project/ ; }, abstract = {Microplastics (MPs) and nanoplastics (NPs) have emerged as pervasive vectors of antimicrobial resistance (AMR), with the plastisphere being a microbial niche on plastic surfaces acting as a nexus for pathogen colonization, gene transfer, and global health risks. These particles adsorb antibiotics, transport pathogens, and serve as reservoirs for antibiotic resistance genes (ARGs), fostering pathogen-ARG coevolution and horizontal gene transfer (HGT) through biofilm-mediated mechanisms. Despite their recognized role in AMR dissemination, critical gaps persist in understanding how environmental stressors (e.g. salinity, pH) modulate plastisphere dynamics and socioeconomic disparities in exposure. This review synthesizes evidence positioning MPs/NPs as triple threats: microbial habitats, ARG reservoirs, and HGT conduits. We also discuss synergistic interactions of plastisphere biofilms with antibiotics to amplify selective pressures, enabling resistance dissemination across ecosystems and food chains, thereby escalating global health risks. Current research lacks mechanistic insights into real-world plastisphere interactions and longitudinal data linking MPs/NPs to clinical AMR outcomes. We propose actionable One Health strategies including artificial intelligence (AI)-enhanced surveillance, circular economy frameworks, and pathogen-resistant biodegradable polymers to disrupt the plastisphere-driven AMR nexus. Our synthesis underscores the urgency of integrating environmental science, epidemiology, and policy to mitigate risks to ecological and human resilience.}, }
@article {pmid41874170, year = {2026}, author = {Chen, H and Liang, Y and Zhou, X and Cai, W and Qiu, H and Dandekar, AA and Dai, W}, title = {Novel dual regulatory roles of RpoA in quorum sensing regulation and social behavior switching in Pseudomonas aeruginosa.}, journal = {mBio}, volume = {}, number = {}, pages = {e0003226}, doi = {10.1128/mbio.00032-26}, pmid = {41874170}, issn = {2150-7511}, abstract = {Understanding the social structure and evolutionary dynamics of microbial communities requires the identification and characterization of relevant mutant subpopulations. While Pseudomonas aeruginosa employs quorum sensing (QS) to coordinate population-wide behaviors, the social traits of many QS mutants remain poorly defined. In this study, we developed an iterative "targeted gene duplication followed by mutant screening" (TGD-MS) approach to systematically identify noncanonical QS cheater mutants. We discovered that a single-nucleotide mutation in rpoA, which encodes the α subunit of RNA polymerase (RNAP), produces a QS-deficient phenotype resembling QS-null mutants. This RpoA variant mutant exhibits characteristic features of social cheating, including a competitive growth advantage in mixed populations, impaired QS-dependent virulence factor production, and attenuated pathogenicity. Structural and biochemical analyses revealed that the RpoA variant impairs RNAP binding to the promoters of core QS genes (lasI and lasR), leading to diminished QS activity. Further examination of natural RpoA variants uncovered a spectrum of QS-related phenotypes, suggesting that RpoA has a dual regulatory role in QS control. Within the C-terminal domain (α-CTD) of RpoA, we identified two distinct functional determinants that, through adaptive mutations, can acquire opposing regulatory effects on QS. This enables an environmentally dependent phenotypic switch between cooperation and cheating. Our discovery of noncanonical RpoA-mediated QS cheaters expands the framework of bacterial social evolution, demonstrating that mutations outside the canonical QS circuitry can disrupt cooperative behaviors. These findings underscore how core transcriptional machinery can be evolutionarily co-opted to modulate complex social interactions in dynamic environments.IMPORTANCETo understand how bacterial populations function and evolve, it is essential to identify socially significant subpopulations, including previously unrecognized types of cheaters. In this study, we uncover an unexpected role of RNA polymerase (RNAP) in regulating quorum sensing (QS) and QS-associated social behaviors in P. aeruginosa. Specifically, we demonstrate that the α subunit of RNAP (RpoA) is a key regulatory component in this process. A single-nucleotide mutation within the C-terminal domain of RpoA was found to alter QS activity, driving an environment-dependent transition between cooperative and cheating phenotypes. This discovery of this novel, noncanonical QS cheater mutant offers new insights into intra-population interactions, population stability, and evolutionary dynamics. These findings carry significant implications for microbial ecology and deepen our understanding of social evolution in bacterial communities.}, }
@article {pmid41874404, year = {2026}, author = {Kück, AC and Leibrecht, L and Morel-Letelier, I and Gros, O and Wilkins, LGE and Yuen-Simović, B and Petersen, JM}, title = {Host species-specific gene expression by a widespread and flexible chemosynthetic symbiont.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag065}, pmid = {41874404}, issn = {1751-7370}, abstract = {Associations with microbial symbionts shape the ecology and evolution of almost all eukaryotes. One of their defining features is their specificity, but despite this, many symbioses show a degree of flexibility, with some symbiont species capable of colonizing multiple (often closely related) host species. Although widespread, the functional and evolutionary consequences of flexibility in host-symbiont pairings is poorly understood. Bivalves from the diverse, globally distributed, and ecologically important family Lucinidae are ideal for investigating this, as multiple host species can associate with the same symbiont species, often at the same location. We used metatranscriptomics to investigate the molecular responses of one symbiont species, Candidatus Thiodiazotropha endolucinida, in association with three different host species that co-occur in seagrass meadows in the Caribbean Sea. In replicated experiments, we identified host species-specific patterns of symbiont gene expression including those for key functions such as carbon fixation, cell division, and sulfide oxidation. Our work shows that the symbiont consistently responds in different ways to association with different host species. Because all samples were collected at the same site on the same day, and were thus exposed to the same environmental conditions, these differences are likely driven by host rather than environmental factors. In addition, host species had significantly different carbon isotope signatures, which were consistent with distinct modes of host-microbe interaction indicated by transcriptomics. Our results show that not only symbiont genotype, but also symbiont phenotype may enable coexistence of closely related host species, demonstrating the power of symbiosis in promoting and maintaining biodiversity.}, }
@article {pmid41874663, year = {2026}, author = {Hu, C and Lin, M and Hu, T and Zeng, Y and Zeng, R and Wang, C}, title = {Linking Bacterial r/k Ecological Shifts to Spatiotemporal Nitrogen Removal Dynamics in Recirculating Aquaculture Systems.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02742-1}, pmid = {41874663}, issn = {1432-184X}, support = {NO.2024SJRC4//the Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; NO.LTO2326//State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences/ ; NO.2023A04J0897//Guangzhou Science and Technology Program Project/ ; NO.SL2023E04J00185//Demonstration and Promotion of Key Technologies for Land-based Factory Farming of Hybrid Eleotris oxycephala/ ; }, }
@article {pmid41877017, year = {2026}, author = {Ibanga, IA and Ekong, US and Akan, OD and Akpabio, U and Christopher, M}, title = {Antibiotic resistance in chicken gut bacteria: a study on bacterial diversity and drug sensitivity in some Nigerian poultry farms.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-04972-2}, pmid = {41877017}, issn = {1471-2180}, }
@article {pmid41869816, year = {2026}, author = {Tumeo, A and Miliotis, G and O'Connor, A and Vijayakumar, V and Sengupta, P and McDonagh, F and Kovarova, A and Clarke, C and Hooban, B and Kumar Singh, N and Rosado, AS and Raman, K and Venkateswaran, K}, title = {Plasmidome, resistome, and virulence-associated gene characterization of Acinetobacter johnsonii in NASA cleanrooms and a clinical setting.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0250325}, doi = {10.1128/spectrum.02503-25}, pmid = {41869816}, issn = {2165-0497}, abstract = {Evidence suggests the persistence of non-spore-forming Acinetobacter johnsonii in high-stakes controlled and nutrient-limited environments. Here, we investigated the mechanisms underlying this adaptability through a comprehensive genomic analysis of 22 isolates of A. johnsonii from NASA's Payload Hazardous Servicing Facility (PHSF) and one carbapenem-resistant strain (E154408A) from patient colonization in Ireland. Core-genome phylogeny revealed clustering of PHSF-originating isolates in a monophyletic clade divergent from the main species lineage. Species-wide virulence-associated genes and metabolic reconstruction indicated the exclusive presence in PHSF-originating isolates of two complete efflux pumps and a conserved allantoin racemase, suggesting adaptability for multiple environmental stresses. The ubiquity of blaOXA in genomes analyzed (n = 112) and the phenotypically validated multidrug-resistant profile of the E154408A strain highlight A. johnsonii's potential as an antimicrobial resistance (AMR) reservoir. Plasmidome analysis suggested gain/loss events across the monophyletic population and potential AMR acquisition pathways. Genome-to-metagenome mapping identified genomic signatures of A. johnsonii in PHSF >10 years post-initial isolation.IMPORTANCEAcinetobacter johnsonii is increasingly recognized as an emerging human pathogen, with growing evidence of its ability to persist in controlled, high-stakes environments, posing risks as both a persistent environmental contaminant and an antimicrobial resistance (AMR) reservoir. Yet, gaps remain in our understanding of its AMR profile and the mechanisms that enable its enhanced environmental adaptability. This knowledge is necessary in contexts where biological cleanliness is a priority, such as clinical settings and spacecraft assembly facilities' cleanrooms, where contamination of hardware with terrestrial microorganisms is concerning. In this study, we aim to address some of the key knowledge gaps by providing genomic insights into a rare multidrug-resistant clinical isolate and 22 NASA cleanroom isolates that persisted for over a decade in extremely clean conditions. Our findings will help assess the contamination risk of A. johnsonii in high-stakes environments and ultimately strengthen our ability to manage this microbial contaminant across terrestrial and extraterrestrial settings.Cleanroom-derived A. johnsonii genomes show traits consistent with increased adaptability.Genomic signatures of A. johnsonii persisted in the cleanrooms for over 10 years.blaOXA is ubiquitously found in all 112 A. johnsonii genomes analyzed.Isolate E154408A is the first reported patient colonization case by carbapenem-resistant A. johnsonii in Europe.}, }
@article {pmid41870091, year = {2026}, author = {Garabello, E and Yoon, H and Reid, MC and Giometto, A}, title = {Tunable low-rate genomic recombination with Cre-lox in Escherichia coli: a versatile tool for anoxic environmental biosensing and synthetic biology.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0176825}, doi = {10.1128/aem.01768-25}, pmid = {41870091}, issn = {1098-5336}, abstract = {The ability to induce heritable genomic changes in response to environmental cues is valuable for environmental biosensing, for experimentally probing microbial ecology and evolution, and for synthetic biology applications. Site-specific recombinases provide a route to genetic memory via targeted DNA modifications, but their high specificity and efficiency are offset by leaky expression and limited tunability in prokaryotes. We developed a tightly regulated, titratable Cre recombinase system for Escherichia coli that achieves low recombination rates and minimal basal activity. Implemented on both plasmids and the chromosome, the latter showed superior retention of genetic memory across generations. These features make the system broadly useful for environmental biosensing and other applications. To demonstrate applicability to environmental biosensing, we developed a whole-cell recombination-based biosensor for arsenite, a toxic and ubiquitous pollutant that is primarily mobilized in anoxic environments, such as flooded soils, sediments, and aquifers. However, existing arsenite whole-cell biosensors face limitations in sensitivity and workflow in anaerobic settings. Our biosensor reliably recorded anoxic arsenite exposure as a stable genetic memory for delayed fluorescence readout in aerobic conditions, with detection sensitivity comparable to conventional wet chemical methods. By decoupling exposure from measurement, this approach offers a foundation for arsenite biosensing under field-relevant conditions, including redox variability and other physicochemical gradients, without the constraints of anoxic measurement. More broadly, the ability to induce low-rate, heritable genetic changes expands the genetic toolkit for environmentally responsive systems, with applications in environmental monitoring, bioproduction, and bioengineering, as well as experimental studies of microbial ecology, evolution, and host-microbe interactions.IMPORTANCEArsenic is a toxic and globally prevalent pollutant, mobilized primarily under anoxic conditions where detection is challenging. Whole-cell biosensors offer a promising route for monitoring bioavailable arsenic in situ, but their development has largely focused on aerobic conditions, with anoxic assays limited by sensitivity and workflow constraints. Genetic tools that enable heritable, low-frequency genomic changes in bacteria can expand biosensor capabilities by recording transient exposures and supporting applications in environmental monitoring, synthetic biology, and quantitative microbial population dynamics research. Here, we developed a tightly regulated, chemically inducible Cre-lox system in Escherichia coli that enables recombination at low, tunable rates. We demonstrate its utility by constructing an arsenite biosensor that reliably detects low concentrations and records exposures under both aerobic and anoxic conditions. This approach is broadly applicable for biosensors designed for field deployment and for experiments investigating microbial ecology and evolution, where controllable genetic diversification may be desirable.}, }
@article {pmid41870584, year = {2026}, author = {Muhammad, W and Zhou, X and Yu, X and Yang, K and Bai, R and Feng, L and Luo, Q and Zhou, Z and Wang, C and Li, J and Ji, K and Lu, HZ}, title = {Forest Succession Shapes Soil microbial Communities through Region-specific Edaphic Filters in Tropical and Subtropical Forests.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02734-1}, pmid = {41870584}, issn = {1432-184X}, support = {32471599, 31872685//National Natural Science Foundation of China/ ; }, }
@article {pmid41871362, year = {2026}, author = {Soto, C and Almendras, K and Orlando, J}, title = {Functional hierarchy and redundancy organize phosphorus cycling potential in Peltigera lichen microbiomes.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnag029}, pmid = {41871362}, issn = {1574-6968}, abstract = {Lichen symbioses host complex microbial communities whose functional organization remains poorly understood. In Peltigera lichens, bacterial partners mediate key nutrient transformations, but it is unclear whether the spatial distribution of phosphorus-cycling functions follows the hierarchical control previously observed for community composition. We hypothesized that Peltigera microbiomes follow a thallus-to-soil gradient of control, in which host-driven specialization within thalli transitions toward environmentally driven reconfiguration in the substrate and soil. To test this, we quantified five bacterial genes involved in phosphorus turnover (gcd, phoD, phoN, phnX, and appA) across thalli, underlying substrates, and adjacent soils of several Peltigera species collected along contrasting Patagonian bioclimates. Absolute and relative gene abundances, together with diversity and variance partitioning analyses, were used to evaluate the influence of host identity, edaphic properties, and climate. Gene profiles revealed a shift from host-associated specialization to environmentally filtered assemblages, indicating that symbiotic and abiotic factors jointly structure phosphorus-cycling potential. The coexistence of functional specialization and redundancy provides a plausible mechanism for sustaining phosphorus turnover under changing environmental conditions.}, }
@article {pmid41871945, year = {2026}, author = {Vázquez-Castellanos, JF and Yoon, SJ and Won, SM and Raes, J and Kwon, HC and Si, J and Suk, KT}, title = {Stage-dependent gut microbiome and functional signatures across the liver disease spectrum: an integrative multicohort study.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-337436}, pmid = {41871945}, issn = {1468-3288}, abstract = {BACKGROUND: The gut-liver axis plays a critical role in liver disease progression; however, how gut microbial ecology and function vary across disease stages remains unclear.<br><br>OBJECTIVE: To define stage-specific microbial and functional signatures and evaluate their diagnostic potential.<br><br>DESIGN: We analysed faecal samples from 1168 individuals spanning healthy controls, fatty liver, hepatitis, cirrhosis and hepatocellular carcinoma by 16S rRNA sequencing, with a subset (n=141) profiled by shotgun metagenomics. To increase statistical power and enable external validation, 2376 publicly available metagenomic datasets, including 734 liver-related, were integrated. Machine learning-based multicohort analysis was used to identify microbial biomarkers, assess risk factors and classify disease stages.<br><br>RESULTS: Microbial diversity declined and a low-richness enterotype expanded with disease severity. Machine learning revealed a discordance in hepatitis, which lacked taxonomic markers but was defined by a conserved functional signature of biosynthetic upregulation. In contrast, advanced stages featured consistent markers like Ligilactobacillus and Veillonella, with strain-level evidence confirming oral-gut transmission. Functional profiling delineated a metabolic continuum from anabolic precursor synthesis in hepatitis to virulence factor production in cirrhosis and putrefactive metabolism in carcinoma. Comparative analysis confirmed that these signatures were distinct from those in non-liver metabolic and oncologic disorders. Importantly, the expansion of oral-derived Veillonella spp and the low-richness enterotype were significantly associated with increased mortality.<br><br>CONCLUSION: This large-scale study delineates stage-dependent ecological and functional remodelling of the gut microbiome across liver diseases. These findings highlight the potential of microbiome-based markers for non-invasive diagnosis and prognostic risk stratification in liver diseases.}, }
@article {pmid41861947, year = {2026}, author = {Guo, J and Liang, X and Lei, W and Zhang, Z and Shen, Y and Han, S and Wang, H and Qian, Y and Nie, B and Wang, L and He, S}, title = {Contrasting microbial sources of soil N2O emissions revealed by metagenomics in natural and agricultural soils along the Yellow River.}, journal = {Environmental research}, volume = {299}, number = {}, pages = {124311}, doi = {10.1016/j.envres.2026.124311}, pmid = {41861947}, issn = {1096-0953}, abstract = {Soil nitrous oxide (N2O) emission is a potent greenhouse gas source, yet the dominant production pathway (nitrification vs. denitrification) and its microbial mechanisms in regions like the Yellow River Basin remain unclear, particularly under different land uses. In this study, we integrated qPCR quantification, metagenomic sequencing and binning, as well as microbial network analysis to investigate the dominant microbial processes and regulatory mechanisms underlying potential soil N2O production. Results showed that denitrification dominated regional potential N2O production (N2ODen, 56.71 ± 102.94 nmol/(kg·h)), significantly exceeding nitrification (N2ONif, 4.34 ± 4.27 nmol/(kg·h)). On average, both N2ODen (115.34 ± 143.60 nmol/(kg·h)) and N2ONif (5.29 ± 4.42 nmol/(kg·h)) in natural soils were higher than in cultivated soils (28.56 ± 62.52 and 3.88 ± 4.22 nmol/(kg·h), respectively). Mechanistically, natural soils were enriched with ammonia-oxidizing archaea (AOA) and incomplete denitrifiers (e.g., Acidobacteriota), which, along with a higher norB/nosZ and more stable co-occurrence network, favored N2O accumulation. In cultivated soils, microbial community stability was reduced; however, they were enriched with strong N2O reducers (e.g., Pseudomonadota, Gemmatimonadota), resulting in lower potential N2O production. Altitude, total nitrogen, and pH collectively influenced the potential N2O emission patterns by regulating functional genes and microbial metabolism. This study provides a scientific basis for regional greenhouse gas mitigation from a microbial ecology perspective.}, }
@article {pmid41862473, year = {2026}, author = {Daniels, M and Wijayagunasekera, D and Berry, D}, title = {Widespread effects of catecholamines on growth of human gut bacteria.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00948-2}, pmid = {41862473}, issn = {2055-5008}, support = {Grant-DOI 10.55776/ESP558//Austrian Science Fund/ ; }, abstract = {The interactions between hosts and their microbiomes are driven in part by chemical communication, which influences immune responses, metabolism, and microbial community structure. Neuroendocrine signals are central to this bidirectional communication, forming the basis of microbial endocrinology. Although host-derived hormones, including catecholamines, are known to affect microbial physiology, much of the existing literature focuses on a limited number of model organisms or complex in vivo systems, where disentangling direct microbial responses from host-mediated effects is challenging. As a result, systematic comparative analyses of direct bacterial responses under controlled conditions remain scarce. Here, we performed a systematic in vitro screen under anaerobic conditions to assess catecholamine effects on the growth dynamics of phylogenetically diverse human gut bacteria. Catecholamines altered multiple growth parameters in a species-specific manner, with effects detectable at nanogram concentrations. Multivariate analyses, including principal component analysis and non-metric multidimensional scaling, revealed lineage-associated response patterns across taxa. Although derived from monoculture experiments, these intrinsic responses provide a comparative framework for understanding how direct hormone-microbe interactions may contribute to microbiome dynamics under host stress. Overall, this study provides a quantitative cross-species dataset to inform future systems-level investigations in microbial endocrinology.}, }
@article {pmid41865107, year = {2026}, author = {Estruch, J and Almeida, T and Serrano, E and Pereira, L and Rouco, C and Lavín, S and Abrantes, J and Velarde, R and Lopes, AM}, title = {Temporal Dynamics and Turnover of Rabbit Hemorrhagic Disease Virus 2 (RHDV2/GI.2) in Wild Lagomorphs from Northeastern Spain.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02746-x}, pmid = {41865107}, issn = {1432-184X}, }
@article {pmid41865111, year = {2026}, author = {Oliveira, AGG and Dias, MF and Haq, IU and Ferreira, JFG and Silva, CP and Moreira, M and da Silva Lanna, MC and Santos Rodrigues, LD and de Mâcedo Farias, L and Magalhães, PP}, title = {Seasonal and Source-Associated Microbiome Dynamics in Brazilian Drinking Water.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02735-0}, pmid = {41865111}, issn = {1432-184X}, }
@article {pmid41865966, year = {2026}, author = {Zhou, L and Zhu, S and Wu, J and Wang, W and Zhao, Z and Hao, X and Wang, J and Yu, W and Li, Y and Liang, J}, title = {Co-inoculation of arbuscular mycorrhizal fungi and rhizobia reshapes microbial ecology and nutrient metabolism to rehabilitate iron ore tailings.}, journal = {Environmental research}, volume = {}, number = {}, pages = {124325}, doi = {10.1016/j.envres.2026.124325}, pmid = {41865966}, issn = {1096-0953}, abstract = {Arbuscular mycorrhizal fungi (AMF) and rhizobia play crucial roles in soil-plant systems for ecological restoration. However, their specific remediation characteristics and synergistic effects on tailings remain poorly understood. In this study, we investigated the remediation characteristics of tailings inoculated with AMF and rhizobia, focusing specifically on synergy mechanism for iron tailings improvement under the co-inoculation. The results demonstrated that microbial inoculation significantly enhanced overall remediation performance. The co-inoculation led to a 6.25-fold increase in alfalfa biomass, substantial improvements in nutrient availability (N/C/P), and enhanced soil structure through aggregate formation. Concurrently, the cadmium bioavailability was effectively reduced by 35.56%. Functional metabolic analysis revealed that the upregulation of phosphate-related genes (phoB, phoR) enhanced microbial phosphate solubilization and plant phosphate uptake efficiency. Furthermore, the primary pathways for nitrogen uptake shifted from reliance on biological nitrogen fixation to prioritizing internal nitrogen cycling, while activation of the GABA shunt reduced dependence on the TCA cycle. Notably, the restructured microbial community preferentially stimulated organic carbon-nitrogen (C/N) metabolism, and these metabolic shifts were key to enhanced plant nutrients acquisition efficiency. These findings indicate that AMF and rhizobia could stimulate microbial community restructuring and drive the remodeling of nutrient metabolism in tailings, representing a pivotal process in promoting soil formation from tailings.}, }
@article {pmid41866381, year = {2026}, author = {Wang, M and Xu, Z}, title = {PGPR-mediated enhancement of soil nutrients, rhizosphere microbial ecology, and plant growth: a review.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00966-0}, pmid = {41866381}, issn = {2055-5008}, support = {2025NC-YBXM-241//Key Research and Development Project of Shaanxi Provincial Department of Science and Technology (Agriculture and Rural Areas Field)/ ; 24JC028//2024 Shaanxi Provincial Education Department Service Local Special Scientific Research Project (Industrialization Cultivation project)/ ; 2025-CXY-071//Yulin City Science and Technology Program/ ; }, abstract = {Plant Growth-Promoting Rhizobacteria (PGPR) are key bio-agents for sustainable agriculture. This review conceptualizes PGPR as rhizosphere engineers that enhance soil nutrients, restructure microbial networks, and boost plant stress tolerance. While their mechanisms are well-understood in the lab, a significant translational gap limits field efficacy due to inconsistent colonization and environmental context-dependency. We critically analyze this gap and propose integrated strategies-from advanced formulations to synthetic consortia-to unlock the reliable application of PGPR for global food security.}, }
@article {pmid41866413, year = {2026}, author = {Berkelmann, D and Zuñiga-Umaña, JM and Chaverri, P and Solano, W and Gatica-Arias, A}, title = {Fungal diversity associated with coffee leaf rust (Hemileia vastatrix) pustules based on ITS1 amplicon sequencing.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41866413}, issn = {1573-0972}, support = {111-C1-472//Vicerrector&#xed;a de Investigaci&#xf3;n, Universidad de Costa Rica/ ; }, mesh = {*Plant Diseases/microbiology ; *Coffea/microbiology ; Plant Leaves/microbiology ; *Basidiomycota/genetics/classification/isolation &amp; purification ; DNA, Fungal/genetics ; Costa Rica ; Phylogeny ; Sequence Analysis, DNA ; Biodiversity ; *Fungi/genetics/classification/isolation &amp; purification ; Coffee/microbiology ; DNA, Ribosomal Spacer/genetics ; }, abstract = {Coffee leaf rust (CLR), caused by Hemileia vastatrix, is one of the biggest economic challenges for coffee cultivation and leads to high economic losses each year. Co-occurring fungal microbial communities and their diversity in the presence of CLR are widely understudied but may harbor potential agents or indicators to reduce CLR infections. In this study, the fungal communities associated with CLR pustules in Coffea arabica L. plants across different regions of Costa Rica were analyzed. To this end, individual pustules were excised from infected leaf tissue and used as source material for DNA extraction and subsequent amplification and sequencing of the fungal taxonomic marker region ITS1. Effects of altitude and location on fungal community structure were also observed. High taxonomic variance within regions and a large proportion of unclassified taxa were detected as well as similar community structures across regions, possibly reflecting small effects of the analyzed regions on the identified taxa. However, altitude was a significant factor on the detected community structure, indicating either less favorable growth conditions for the pathogen in higher regions or favorable conditions for co-occurring taxa. This emphasizes that taxonomic identification of co-occurring fungi and their ecological relevance (e.g., potential mycoparasites) during CLR infection requires further research. This study provides a foundational framework for global coffee research by emphasizing the untapped potential of fungal community analyses to develop innovative, microbiome-informed strategies for managing coffee leaf rust and improving crop resilience.}, }
@article {pmid41866874, year = {2026}, author = {Iriarte-Mesa, C and Juère, E and Bileck, A and Kremsmayr, T and Goodson, ML and Ehrlich, A and Hodžić, A and Kunert, M and Gerner, C and Kählig, H and Marko, D and Muttenthaler, M and Berry, D and Del Favero, G and Kleitz, F}, title = {Mesoporous Silica Nanoparticles-Based Formulations for Enhanced Oral Delivery of Peptide Drugs: A Case Study on Insulin.}, journal = {Small (Weinheim an der Bergstrasse, Germany)}, volume = {}, number = {}, pages = {e13347}, doi = {10.1002/smll.202513347}, pmid = {41866874}, issn = {1613-6829}, support = {714366/ERC_/European Research Council/International ; FT210100266//Australian Research Council/ ; 2037680//National Health and Medical Research Council/ ; 10.55776/P36130//Austrian Science Fund/ ; //University of Vienna/ ; }, abstract = {Peptide drugs have revolutionized modern medicine owing to their high potency, selectivity, and excellent tolerability. However, oral delivery remains limited, and most peptide drugs are administered parenterally due to their inherent instability to proteolytic digestion and poor ability to cross gastrointestinal barriers, which hinders efficient absorption into the bloodstream. This study presents a multifunctional oral delivery system based on mesoporous silica nanoparticles (MSN) customized for insulin administration. Insulin-loaded MSN were co-formulated with succinylated β-lactoglobulin to produce pH-responsive tablets that limited premature gastric release (≤13% after 2 h at pH 1.2) and protected insulin from enzymatic degradation, while enabling controlled intestinal release (up to 88%-98% at pH 7.4). Surface functionalization with polyethylene glycol and phosphonate moieties improved colloidal stability and increased insulin solubility by ∼2.5-fold. The interaction of phosphonated MSN with intestinal epithelial cells further induced transient reorganization of tight junction proteins, enhancing paracellular insulin transport (26% after 24 h, compared with 13% for non-confined insulin). Delivered insulin retained bioactivity, as demonstrated by activation of insulin-responsive signaling pathways in vitro and reduced blood glucose levels in hyperglycemic mice. These results highlight MSN as a promising platform for oral peptide delivery with improved efficacy and patient compliance.}, }
@article {pmid41868377, year = {2026}, author = {Cui, Y and Sun, W and Wei, L and Fan, S and Li, Q and Duan, L}, title = {Complex interactions of gut-derived short-chain fatty acids in hyperuricemia and gout pathophysiology.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1772631}, pmid = {41868377}, issn = {1664-302X}, abstract = {Hyperuricemia is a common metabolic disorder associated with gout, kidney injury, cardiovascular disease, and chronic low-grade inflammation. Increasing evidence indicates that abnormalities in intestinal uric acid handling and gut microbial metabolism contribute substantially to systemic urate imbalance, particularly when renal excretion is impaired. Among microbiota-derived metabolites, short-chain fatty acids (SCFAs) have emerged as key regulators linking gut microbial ecology with uric acid metabolism through coordinated effects on epithelial barrier integrity, inflammatory signaling, and urate transport. Growing interest in prebiotics and probiotics has further highlighted the therapeutic potential of targeting SCFAs production as a complementary strategy to traditional urate-lowering drugs. Given that hyperuricemia is the primary pathogenic precursor to gout, this review also examines the role of SCFAs in modulating gout-associated inflammation. This review integrates current findings on the microbiota-SCFA-urate axis and outlines how SCFA-centered gut modulation may provide a viable framework for managing hyperuricemia and gout.}, }
@article {pmid41869502, year = {2026}, author = {Wang, D and Xu, X and Liu, L and Wang, C and Deng, Y and Polz, MF and Zhang, T}, title = {Hi-C sequencing deciphers phage and plasmid host networks in wastewater biofilms.}, journal = {Environmental science and ecotechnology}, volume = {30}, number = {}, pages = {100683}, pmid = {41869502}, issn = {2666-4984}, abstract = {Mobile genetic elements (MGEs) such as bacteriophages and plasmids profoundly shape microbial community structure and drive horizontal gene transfer across ecosystems. Wastewater treatment systems, with their high cell densities, steep physicochemical gradients and close cell-to-cell contact, act as hotspots for MGE proliferation and exchange, yet the in situ assembly dynamics and host interaction networks of these elements have remained largely unresolved because conventional methods fail to establish direct MGE-host linkages in complex matrices. Here we show that an integrated framework combining metagenomics, metatranscriptomics, metaviromics, and Hi-C proximity ligation sequencing enables the efficient elucidation of DNA phage and plasmid assembly dynamics alongside their host interaction networks in biofilms. We reconstructed 17,672 viral operational taxonomic units and 11,454 high-confidence non-redundant plasmids, and established 529 phage-host and 5739 plasmid-host associations that link up to 52 % of phages to 56 % of prokaryotes and 70 % of plasmids to 91 % of prokaryotes, respectively. Hi-C substantially expanded and refined these networks, revealing taxon-specific and multi-host patterns. Host community composition and biofilm architecture emerge as primary drivers of MGE occurrence and abundance along the reactor flow path. Expression of auxiliary metabolic genes, antibiotic resistance genes and virulence factors carried by these MGEs demonstrates their active roles in modulating biogeochemical cycles and maintaining ecosystem stability. These findings establish a scalable, cultivation-independent framework for deciphering MGE-host networks in complex microbial ecosystems, and underscore the power of Hi-C sequencing to transform our mechanistic understanding of gene flow, resistome dissemination, and ecological resilience in engineered and natural microbiomes.}, }
@article {pmid41860729, year = {2026}, author = {Martin-Pozas, T and Fernandez-Cortes, A and Calaforra, JM and Ledesma-Hernandez, G and Cuezva, S and Sanchez-Moral, S and Saiz-Jimenez, C and Jurado, V}, title = {Habitat Specialization and Airborne Dispersal Shape the Microbiome of a Gypsum Karst Cave.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02745-y}, pmid = {41860729}, issn = {1432-184X}, }
@article {pmid41860788, year = {2026}, author = {Duarte, GCK and Crispim, D and Wittée, SC and Lemos, JRN and Lemos, NE and de Oliveira, MS and Alves, MD and Massignam, ET and Assmann, TS and Pellenz, FM}, title = {An ultra-processed food-based cafeteria diet induces obesity, metabolic dysfunction, and tissue-specific gene dysregulation in C57BL/6 mice.}, journal = {Animal models and experimental medicine}, volume = {}, number = {}, pages = {}, doi = {10.1002/ame2.70160}, pmid = {41860788}, issn = {2576-2095}, support = {//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Rio Grande do Sul (FAPERGS)/ ; //Financiamento e Incentivo &#xe0; Pesquisa e Eventos (FIPE) - Hospital de Cl&#xed;nicas de Porto Alegre/ ; //Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior (CAPES)/ ; //Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; //Postgraduation Program in Medical Sciences: Endocrinology at Universidade Federal do Rio Grande do Sul, Brazil/ ; }, abstract = {BACKGROUND: The cafeteria diet (CAFD) model has been used to mimic the Western-style "junk food" eating pattern, inducing obesity in rodents. As the dietary composition varies across studies, we developed a CAFD model based on commonly consumed Brazilian ultra-processed foods to evaluate its effect on weight gain, metabolic parameters, and gene expression in C57BL/6 mice.<br><br>METHODS: Forty male C57BL/6 mice were assigned to either a standard diet (SD) group or a CAFD group for 16&#x2009;weeks. Biometric data, glycemic control, insulin resistance (IR), hepatic steatosis, and serum leptin and adiponectin levels were assessed. Expressions of 27 genes involved in adipocytokine signaling, inflammation, apoptosis, lipid, and glucose metabolism were analyzed using quantitative real-time polymerase chain reaction in visceral (VAT) and subcutaneous (SAT) adipose tissues, liver, and skeletal muscle.<br><br>RESULTS: CAFD-fed mice exhibited significantly greater weight gain, hyperglycemia, elevated IR, and hepatic steatosis compared to SD controls. Circulating leptin and adiponectin levels increased in the CAFD group. Gene expression analysis revealed significant dysregulation in VAT (19 genes), SAT (6 genes), liver (11 genes), and muscle (4 genes) of the CAFD group, affecting pathways related to adipocytokine signaling, oxidative stress, inflammation, apoptosis, and lipid and glucose metabolism. Additionally, an increased Itgax-to-Llgl1 ratio in VAT of the CAFD mice indicated a phenotypic shift in macrophages from M2 to pro-inflammatory M1.<br><br>CONCLUSION: This CAFD model efficiently induces obesity, metabolic dysfunction, and tissue-specific alterations in gene expression in C57BL/6 mice, supporting its use as a relevant model for studying the molecular and inflammatory mechanisms underlying diet-induced obesity.}, }
@article {pmid41861859, year = {2026}, author = {Ye, Q and Fang, H and Tang, R and Li, M and Li, X}, title = {Synergistic parameter optimization Unlocks High-Efficiency H2/CO2 Bio-methanation: Decoupling mass transfer enhancement from microbial Trade-offs.}, journal = {Bioresource technology}, volume = {450}, number = {}, pages = {134459}, doi = {10.1016/j.biortech.2026.134459}, pmid = {41861859}, issn = {1873-2976}, abstract = {The advancement of CO2 biomethanation represents a crucial pathway for renewable energy storage and carbon neutrality. However, its widespread application is often constrained by inefficient gas-liquid mass transfer of H2 and suboptimal operational parameters. This study investigates the synergistic effects and underlying mechanisms of three key engineering parameters-agitation intensity, gas recirculation rate, and H2/CO2 feed ratio-on the performance of an in-situ H2/CO2 biomethanation process at mesophilic temperature (37 ± 1℃). Enhanced agitation (up to 160 rpm) and increased gas recirculation (up to 1200 mL·min[-1]) significantly improved (p＜0.05) the volumetric mass transfer coefficient (kla) for H2, thereby boosting the maximum volumetric methane production (VMP) to 0.97 L·L[-1]·d[-1]. Optimizing the H2/CO2 feed ratio to 5:1 strengthened the thermodynamic driving force for hydrogenotrophic methanogenesis, increasing methane content by ∼15% compared to the stoichiometric 4:1 ratio. High-throughput sequencing revealed that intensified mass transfer selectively enriched dominant hydrogenotrophic methanogenic archaea phylum (e.g., Methanobacteriota reached 75.2% at an H2/CO2 feed ratio of 5:1), while suppressing hydrolytic and acidogenic bacterial phylum (e.g., Bacteroidetes decreased from 23.7% to 6.8%, under intensified agitation), indicating a functional trade-off between enhanced methanogenic efficiency and complex organic degradation. This work emphasized the long-term, integrated evaluation of hydrodynamics and microbial ecology of the biomethanation systems, leading to superior methane yield and system stability. The findings provide critical insights and practical guidance for scaling up efficient and stable biomethanation systems, addressing a key bottleneck in industrial Power-to-Gas applications.}, }
@article {pmid41860227, year = {2026}, author = {Chaput, G and Hanley, TC and Eisen, JA and Sogin, EM and Hughes, AR and Hays, C}, title = {Microbiota characterization of Zostera marina seeds at early stage development.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0116325}, doi = {10.1128/mra.01163-25}, pmid = {41860227}, issn = {2576-098X}, abstract = {Understanding seagrass seed microbiomes is crucial for developing microbial-mediated methods to improve germination in restoration efforts. Here, we used 16S rRNA gene and ITS2 amplicon sequencing to characterize the bacterial and fungal communities of seeds from the model seagrass, Zostera marina.}, }
@article {pmid41610050, year = {2026}, author = {Moreno-Mirón, JM and Ruiz-Argüelles, GJ and Gallardo-Pérez, MM and Moreno-Mirón, A and Rivera-Aguilar, AP and Gale, RP}, title = {The Gastro-Intestinal Microbiota in Haematology.}, journal = {Acta haematologica}, volume = {}, number = {}, pages = {1-11}, doi = {10.1159/000550689}, pmid = {41610050}, issn = {1421-9662}, abstract = {BACKGROUND: The gastro-intestinal microbiota is a key regulator of systemic immunity and inflammatory tone and it contributes to normal haematopoiesis through microbial metabolites, barrier integrity, and host-microbe immune signalling. Disruption of this has been increasingly linked to the development, clinical course, and treatment-related complications of haematological disorders, including clonal haematopoiesis of indeterminate potential (CHIP), leukaemias, and plasma cell neoplasms (PCNs).<br><br>SUMMARY: This review synthesises current evidence on how gut microbiota composition and function intersect with haematopoietic regulation and haematological disease biology. We summarise proposed mechanisms - including microbe-derived metabolites (e.g., short-chain fatty acids), pattern-recognition receptor signalling, intestinal permeability, and cytokine-mediated inflammation - that may influence haematopoietic stem and progenitor cell behaviour and immune cell differentiation. We then discuss disease-specific associations of dysbiosis with CHIP, leukaemias, and PCN, as well as the impact of common haematology interventions (antibiotics, chemotherapy, immunomodulatory therapies, and transplantation) on microbial ecology and downstream clinical outcomes. Finally, we highlight methodological challenges and outline priorities for longitudinal, mechanistic, and multi-omics studies to enable microbiota-informed risk stratification and therapeutic modulation.<br><br>KEY MESSAGES: (1) The gut microbiota influences haematopoiesis via immune signalling, microbial metabolites, and maintenance of mucosal barrier function. (2) Dysbiosis is associated with CHIP, leukaemias, and PCN, and may contribute through chronic inflammation and altered immune homeostasis. (3) Haematological therapies frequently reshape the microbiota; these changes may affect infection risk, treatment tolerance, and outcomes. (4) Current evidence is largely associative; rigorously designed longitudinal and interventional studies are needed to establish causality and guide clinical translation.}, }
@article {pmid41853994, year = {2026}, author = {Yang, Q and Aghdam, R and Tran, PQ and Anantharaman, K and Solís-Lemus, C}, title = {Activity-Informed Network Analysis Reveals Keystone Microbes Shaping Freshwater Ecosystem Function.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70245}, doi = {10.1111/1758-2229.70245}, pmid = {41853994}, issn = {1758-2229}, support = {506328//A Community Science Program New Investigator award/ ; //Natural Science and Engineering Research Council of Canada (NSERC)/ ; DBI-2047598//National Science Foundation/ ; DEB-2144367//National Science Foundation/ ; Hatch 1025641//USDA National Institute of Food and Agriculture/ ; //University of Wisconsin-Madison/ ; //Joint Genome Institute/ ; //Office of Science/ ; }, mesh = {*Ecosystem ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Microbiota/genetics ; Metagenome ; *Lakes/microbiology ; *Fresh Water/microbiology ; Metagenomics ; Transcriptome ; }, abstract = {Freshwater lakes are dynamic ecosystems, with varying oxygen dynamics that influence microbiome structure, composition, and transcriptomic activity. In many freshwater studies, ecological function and abundance metrics are used to discover keystone species; however, it is well established that abundance does not equal activity. Despite the existence of long-term time series spanning multiple years, no previous study has looked at how microbial community and activity (metatranscriptomics) are influenced by shifting oxygen conditions across depths at the microbial network level. In this study, we leverage metagenome-assembled genomes and transcriptomic activity to identify keystone taxa in the ecosystem. Using the SPIEC-EASI and CARlasso methods, we mapped key microbial associations and used permutation-based analyses to assess the robustness of keystone identification. Our results reveal that a taxon's ecological centrality is context-dependent and that many species identified as keystone by abundance alone do not exhibit corresponding transcriptional activity. Notably, members of Bacteroidota and other lineages emerged as keystone taxa only when both abundance and activity were considered. Our study underscores the importance of combining metagenomic and metatranscriptomic approaches for accurate identification of functionally relevant keystone species in freshwater ecosystems, providing a framework for future microbial ecology studies.}, }
@article {pmid41854259, year = {2026}, author = {Almela, P and Hamilton, TL}, title = {Enhancing DNA recovery in low-biomass snow algae samples: a comparative study of extraction methods and their effect on community composition.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0003126}, doi = {10.1128/aem.00031-26}, pmid = {41854259}, issn = {1098-5336}, abstract = {High-throughput sequencing is a powerful tool for environmental microbiology and can be particularly important for examining community structure and function for organisms that are difficult to culture or environments that are difficult to mimic, like snow. Nucleic acid extraction significantly impacts these analyses, often introducing more variation between samples than PCR or sequencing. Snow algae are widespread on mountain and polar snowfields, where they contribute to biogeochemical cycling and accelerate melt. Despite increasing research on snow algae, DNA extraction remains challenging, as the thick, resilient walls of snow algal cysts can limit cell lysis, and differences among extraction methods may therefore affect the estimates of community composition and richness. Here, we compared three common extraction methods (Qiagen DNeasy PowerSoil Pro, Qiagen DNeasy PowerWater, and phenol-chloroform) alongside ultrasonication in samples with varying snow algae abundance. The extraction method strongly influenced the resulting microbial profiles assessed by amplicon sequencing of rRNA genes. Ultrasonication improved DNA yield in low-biomass samples and enhanced the recovery of DNA from resilient cells, including mature-phase snow algae, likely due to improved cell lysis. Our findings provide insights to improve standardization and facilitate comparison among studies in snow and ice environments.IMPORTANCEHigh-throughput sequencing has transformed environmental microbiology, allowing for detailed, culture-independent analyses of microbial communities. However, multiple methodological factors, including DNA extraction, can introduce variability in results, making cross-study comparisons challenging. This research contributes to improving our understanding of snow algae, which play a role in alpine and polar ecosystems by influencing biogeochemical cycles and snow reflectivity. By evaluating common DNA extraction techniques for snow algae, this study helps improve the reliability and reproducibility of sequencing data, supporting broader efforts toward methodological standardization in microbial ecology.}, }
@article {pmid41855561, year = {2026}, author = {Berne, C and Debidour, M and Paniconi, M and Danis, N and Sprowls, ED and Kavanagh, K and Gilbert, L and Brun, Y}, title = {Exploring the diversity of bacterial holdfast polar adhesins from Québec aquatic environments.}, journal = {Canadian journal of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1139/cjm-2025-0310}, pmid = {41855561}, issn = {1480-3275}, abstract = {Biofilms are complex microbial communities that adhere to surfaces, often in response to their environment. Irreversible attachment in these biofilms is mediated by bacterial adhesins, and, in many Alphaproteobacteria, those adhesins are located at the cell pole. To examine the prevalence and natural variation of polar adhesins, 76 water samples were collected across Québec through a citizen science initiative. Environmental isolates were screened for their ability to form biofilms, and strains exhibiting polar attachment were selected. A subset of 21 representative strains was used for phenotypic assays and whole-genome sequencing. Phylogenetic analysis showed that most belonged to the order Caulobacterales, and microscopic characterization indicated variability in the polysaccharide composition of polar adhesins in these environmental strains. By integrating comparative genomics with phenotypic assays, this work establishes a unique framework for linking microbial ecology to molecular mechanisms of adhesion. Our results highlight intra-order natural variations in polar adhesin structure and composition. Such variations may be signatures of adaptive adhesive performances across diverse environments. These findings not only advance the understanding of biofilm biology but also open avenues for bio-inspired applications, including the development of next-generation adhesives and anti-biofouling materials.}, }
@article {pmid41855876, year = {2026}, author = {Lou, J and Zhu, Z and Zheng, Y and Chen, J and Su, Q and Zhu, J}, title = {Response mechanism of the DAMO-associated denitrification system to oxytetracycline stress.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129409}, doi = {10.1016/j.jenvman.2026.129409}, pmid = {41855876}, issn = {1095-8630}, abstract = {Antibiotics and denitrifying anaerobic methane oxidation (DAMO) processes frequently coexist in natural ecosystems and wastewater treatment systems. This study investigated the performance and microbial ecology of a denitrification system coupled with Nitrite-dependent anaerobic methane oxidation (N-DAMO) under oxytetracycline (OTC) stress. Specifically, 1 mg/L OTC enhanced nitrogen removal efficiency by 15% relative to the control, whereas 10 mg/L OTC exerted a significant inhibition of 58%. The Michaelis-Menten kinetic model predicted that the system could tolerate the maximum OTC concentration of 26.76 mg/L. Mechanistically, the secretion of protein-rich extracellular polymeric substances (EPS) served as a protective barrier against toxicity. The abundance of the DAMO bacterium Candidatus Methylomirabilis correlated negatively with OTC concentration. At 1 mg/L OTC, denitrification was enhanced through the enrichment of Thauera. However, 10 mg/L OTC damaged EPS structure and suppressed microbial activity, and led to a decrease in the abundance of related functional bacteria and an increase in the abundance of antibiotic resistant bacteria such as Hyphomicrobium and Thermomonas. Metagenomic analysis revealed that denitrification genes (e.g., norB, norC) were upregulated with 1 mg/L OTC, whereas high-concentration OTC induced pronounced enrichment of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), with frequently co-localization within the same hosts. This suggests an increased potential for horizontal gene transfer (HGT) occurred within the DAMO community, which may contribute to the dissemination of ARGs. These findings provide new insights into the adaptive mechanisms of N-DAMO systems under antibiotic stress and highlight their potential for nitrogen removal in contaminated environments.}, }
@article {pmid41856914, year = {2026}, author = {Sorouri, B and Bernardin, J and Favier, AI and Garces, KR and McMullen, JG and McGuire, RM}, title = {Microbial ecology for all: A vision of accessibility, unity, and responsibility.}, journal = {Ecology}, volume = {107}, number = {3}, pages = {e70342}, doi = {10.1002/ecy.70342}, pmid = {41856914}, issn = {1939-9170}, support = {2305844//National Science Foundation/ ; 2305876//National Science Foundation/ ; 2305992//National Science Foundation/ ; }, mesh = {*Ecology ; Ecosystem ; Biodiversity ; Microbiota ; }, abstract = {Microorganisms are ubiquitous in nature, representing a significant portion of global biodiversity and playing vital roles in ecosystem functions, biogeochemical cycles, and organismal health. The growing recognition of microbial importance and their potential to address ecological and global challenges has inspired a renewed interest and innovation in microbial ecology. This field has benefited immensely from sequencing technologies that allow scientists to explore diversity at scales previously unimaginable. While the rapid growth of the field has offered significant positive advancements and foreshadows promising potential, there are aspects that need careful consideration. New technology has led to exponential growth in available microbial data, yet not everyone has easy access to sequencing technology, data mining and analysis tools, or the time to acquire new skills. Thus, we are at a crossroads in ensuring that these resources are accessible for all, and that traditional methods of microbiology are still appreciated as tools to progress the field in meaningful ways. As early-career researchers, we want to raise these points as principles for shaping the future of microbial ecology. Here, we outline a vision for a more accessible, united, and responsible microbial ecology field, one with applications equipped to address the needs of both society and the environment. To democratize the field, we advocate to destigmatize microbes and increase awareness of their beneficial roles by integrating microbes into early education. We believe unity and collaboration among microbial ecologists, as well as with professionals and community members in other STEM fields, are essential for advancing the field. Data should be accessible and standardized for collaboration, and greater integration across disciplines is essential to address future ecological challenges effectively and innovatively. It is our responsibility to ensure that we are asking relevant research questions with the potential to engage with socio-environmental issues and prioritize sustainable practices. As a collective field, our research should strive to not only expand scientific knowledge but also support community resilience and policy-making for a sustainable future. Together, this vision will promote a more equitable, diverse, and collaborative future for microbial ecology; and has applications for the broader ecology field.}, }
@article {pmid41857392, year = {2026}, author = {Zhai, X and Jin, J and Yu, M and Liu, R and Li, J and Liu, Y and Zhang, XH and Liu, J}, title = {Spatial Heterogeneity of Microbial Communities and Biogeochemical Function in Water Column of Site F Cold Seep, South China Sea.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02722-5}, pmid = {41857392}, issn = {1432-184X}, support = {202172002//the Fundamental Research Funds for the Central Universities/ ; LSKJ202203206//the Science &amp; Technology Innovation Project of Laoshan Laboratory/ ; ZR2022YQ038, ZR2024JQ006//Shandong Province Natural Science Foundation/ ; }, }
@article {pmid41859237, year = {2026}, author = {Xiao, Y and Zhao, R and Zhao, W and Wang, P and Xiao, X and Peng, X and Jing, H}, title = {Genomics-based insights into the expanded diversity and adaptation strategies of hadal trench anammox bacteria.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag011}, pmid = {41859237}, issn = {2730-6151}, abstract = {Anaerobic ammonium oxidation (anammox) bacteria are an important functional guild in the nitrogen cycle and contribute up to 50% of nitrogen loss in the global ocean. Hadal trenches have been recognized as a hotspot of marine biogeochemical cycles; however, the metabolic traits, ecological adaptations, and potential origins of anammox bacteria in this critical habitat remain largely unexplored. Here, we reconstructed eight anammox metagenome-assembled genomes from sediments of four hadal trenches (Diamantina, Kermadec, Mariana, and Yap), which represent four out of the five distinct anammox bacterial families (i.e. Candidatus Scalinduaceae, Ca. Anammoxibacteraceae, Ca. Subterrananammoxibiaceae, and Ca. Bathyanammoxibiaceae). The dominant trench anammox bacteria, affiliated with Ca. Scalindua, were similar to those found in shallow coastal sediments and oxygen-deficient seawaters. Beyond the core anammox metabolism, the hadal Ca. Scalindua genomes contain genes encoding cyanase and urease, indicating that they can utilize cyanate and urea besides ammonium to thrive in the hadal trenches. Compared to trench-derived Ca. Subterrananammoxibiaceae and Ca. Bathyanammoxibiaceae, ABC-type Fe[3+] transporter and sulfate transporter CysZ could help trench-derived Ca. Anammoxibacteraceae genomes to uptake Fe[3+] and synthesize sulfur-containing amino acids. Molecular clock analysis suggests that the ancestors of the hadal anammox bacterial lineages appeared on Earth 1.46-0.07 billion years ago, significantly earlier than the geological formation of the trenches. The first hadal anammox bacteria were likely derived from shallower sediments and were transported into the trenches via sediment wasting. Overall, our study reveals a remarkable diversity of hadal anammox bacteria and their origin as well as survival strategies in hadal sediments.}, }
@article {pmid41859451, year = {2026}, author = {Cristofolini, M and Ronsivalle, M and Pramazzoni, M and Zaccarini, G and Pizzamiglio, V and Solieri, L}, title = {Role of microbial interactions in the impaired cultivability of thermophilic lactic acid bacteria in natural whey starter for Parmigiano Reggiano PDO cheese production.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1755652}, pmid = {41859451}, issn = {1664-302X}, abstract = {Natural whey starter (NWS) cultures play a pivotal role in the production of Parmigiano Reggiano (PR) Protected Designation of Origin (PDO) cheese; however, their microbial ecology and functional dynamics remain only partially understood. In particular, Lactobacillus delbrueckii subsp. lactis, a dominant species in type-D NWS communities, exhibits impaired cultivability that limits its isolation and characterization. Consequently, most studies have focused on strain variability within Lactobacillus helveticus, which is predominant in type-H NWS communities. In this study, we evaluated the effects of 14 different medium supplementations on the recovery and maintenance of L. delbrueckii subsp. lactis isolates from two PR NWS samples representatives of type-D and type-H communities. Although most supplementations increased lactobacilli plate counts compared with the control MRS medium, they failed to sustain cell viability during the purification for culture collection establishment. Moreover, these media altered species ratios in favor of L. helveticus, even when L. delbrueckii dominated the community according to metagenomic profiling (type-D NWS). Supplementation of MRS medium with cysteine and formic acid enabled the recovery of viable L. delbrueckii subsp. lactis isolates, accounting for 35% of the strains obtained from type-D NWS. Cross-feeding experiments further revealed that co-culturing L. delbrueckii with the formate-producing Streptococcus thermophilus significantly enhanced milk acidification compared with monocultures, indicating a beneficial metabolic interaction. In contrast, no such improvement was observed in the presence of L. helveticus, likely due to negative interactions with L. delbrueckii subsp. lactis. Accordingly, the impaired cultivability of L. delbrueckii subsp. lactis could thus be partially alleviated either in co-culture with S. thermophilus or under axenic conditions mimicking natural metabolite exchange between these species.}, }
@article {pmid41860215, year = {2026}, author = {Chaudhary, A and Lin, H and Guo, L and Poretsky, R}, title = {Metatranscriptomics-based investigation of bacterial community dynamics across a dissolved organic matter gradient in southern Lake Michigan.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0026326}, doi = {10.1128/aem.00263-26}, pmid = {41860215}, issn = {1098-5336}, abstract = {Bacterial communities in freshwater ecosystems play a critical role in biogeochemical and food web dynamics. However, our understanding of environmental controls on bacterial community function, particularly in large lakes, is limited. We characterized Lake Michigan water chemistry, bacterial community function, and substrate preferences to better understand bacteria-water chemistry relationships. Using metatranscriptomics, we investigated bacterioplankton gene expression in surface waters across a nearshore-to-offshore transect during 2017-2018. Additionally, we measured nutrients, dissolved organic carbon (DOC), chromophoric dissolved organic matter (DOM), as well as changes in major fluorescent DOM components across this transect. The results highlighted similarities in inorganic N and P measurements and a minor reduction in DOC levels from nearshore to offshore. However, significant changes in the composition of DOM were observed across the transect, including a higher presence of terrestrially derived and high-molecular-weight DOM in the nearshore. These differences in DOM quality were associated with the differential expression of several gene families between nearshore and offshore bacterioplankton. Notably, genes involved in the acquisition of various DOM, N, and P substrates, including peptidases, proteases, and transporter genes for amino acids, nucleobases, sugars, urea, and inorganic phosphate, were over-represented in the offshore bacterioplankton. A focused analysis of all the transporter gene expression for C, N, and P substrates revealed similar trends-higher expression of DOM transporter genes in the offshore versus nearshore. When viewed in the context of changing DOM quality across the transect, these results imply that offshore bacterial communities are more substrate-limited (particularly C) than in nearshore and are investing more energy in acquiring DOM substrates.IMPORTANCEVarious environmental, geological, and climatic factors influence bacterial community dynamics in freshwater ecosystems in complex and interactive ways. It thus becomes challenging in microbial ecology studies to disentangle the specific effects of these factors on microbial community function. Spatial environmental gradients in large lake ecosystems can provide a unique opportunity to test important questions about bacterial function and water chemistry relationships in a relatively consistent geological and climatic framework. Lake Michigan, one of the five largest lakes in the world, is one such example. The lake has witnessed significant ecological changes in the last few decades, and the impact of these changes on the physico-chemical environment and bacterioplankton function is not fully understood. In a relatively novel approach for freshwater systems, this study assesses Lake Michigan bacterial metabolism using robust transcriptomics techniques in the context of rich environmental data, including characterization of the lake chromophoric DOM and fluorescent DOM pool.}, }
@article {pmid41846126, year = {2026}, author = {Wang, X and Zhao, L and Teng, Y and Hu, W and Xu, Y and Ma, J and Song, J and Ren, W and Zhang, J and Zhu, H and Wang, X and Wang, Y and Luo, Y and Kuramae, EE}, title = {Decoding the adaptive strategies of versatile diazotrophs to multi-metal(loid) stress in mercury-mining impacted farmland soils.}, journal = {Journal of hazardous materials}, volume = {507}, number = {}, pages = {141760}, doi = {10.1016/j.jhazmat.2026.141760}, pmid = {41846126}, issn = {1873-3336}, abstract = {Diazotrophs are crucial for Earth's nitrogen cycle via biological nitrogen fixation, while also modulating other elemental cycles and exhibiting bioremediation potential. However, their responses to co-occurring heavy metal(loid) (HM) contaminants in polluted soils remain poorly understood. Using combined nifH (encoding nitrogenase) amplicon and metagenomic sequencing, we characterized the taxonomic structure and metabolic potential of diazotrophic community across multi-HM contamination gradients in mercury-mining impacted farmlands (paddy vs. upland). Results identified selenium (upland soils: 0-3.08 mg kg[-1]) and arsenic (paddy soils: 5.38-17.1 mg kg[-1]) as the primary HMs shaping diazotrophic diversity, whereas mercury (0.067-99.6 mg kg[-1]) showed a significant but weak correlation. Selenium and mercury correlated positively with diversity in upland soils (arsenic negatively), whereas all three HMs correlated negatively in paddy soils. Diazotrophic indicator taxa varied by HM type, yet certain taxa tolerated all three HMs simultaneously-notably Chromatiaceae/Pseudomonadaceae in upland soils and Xanthobacteraceae in paddy soils. Moreover, diazotrophs in upland soils exhibited synergistic associations with functional guilds involved in HM resistance and element cycling (e.g., carbon fixation and hydrogen metabolism), contrasting with the negative correlations in paddy soils. Metagenomic binning indicated that dominant diazotrophs were primarily aerobic heterotrophs with versatile metabolic potentials, including multi-HM resistance (e.g., arsenic/mercury reduction, efflux, and antioxidation) and energy acquisition via trace gas (CO, H2), manganese, and sulfide oxidation. These findings provide novel insights into diazotrophic adaptive strategies under multi-HM stress, advancing our understanding of their ecological and environmental functions.}, }
@article {pmid41846605, year = {2026}, author = {Allner, R and Decewicz, P and Allner, T and Bluszcz, A and Dziewit, L}, title = {Development of molecular biomarkers for monitoring of arable crops colonization with Methylobacterium symbioticum SB0023/3, a methylotrophic bacterium commonly used as a biostimulant in agriculture.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1718185}, pmid = {41846605}, issn = {1664-462X}, abstract = {INTRODUCTION: The intensive use of synthetic fertilizers has led to increased nitrous oxide emissions, declining soil fertility, and reduced biodiversity. Biological alternatives, such as the use of endophytic bacteria to improve plant growth, are promising alternatives but require reliable monitoring tools to assess colonization success and biological effectiveness under field conditions. One of the most commonly used microbial biostimulants is Methylobacterium symbioticum SB0023/3; thus, monitoring the efficacy of inoculation and maintenance of this strain is required for adequate evaluation of fertilization practices.<br><br>METHODOLOGY: The resequencing of the genome of M. symbioticum SB0023/3, followed by comparative genomics and functional annotation were performed. Specific real-time PCR primers were developed and validated for strain-specific detection. The colonization of various crops (wheat, corn, rapeseed, peas, and&#xa0;tomatoes) was tested under controlled conditions using developed molecular markers.<br><br>RESULTS: The resequencing of the SB0023/3 genome revealed novel genetic content and updated previous records. The resequenced genome showed 121 novel regions with 165 protein-coding genes and five tRNA. Based on the newly obtained genome, two highly specific biomarker genes (copG and ubik) were identified and, together with the (Methylobacterium spp./methylotrophs-specific) xoxF gene, validated for their strain/genus-specificity. The developed real-time PCR assays using copG and ubik biomarkers demonstrated high specificity for M. symbioticum SB0023/3, distinguishing it from related species. In contrast, the xoxF gene showed relaxed specificity and cannot be used for SB0023/3 detection. Successful endophytic colonization was confirmed in all tested crops, with high detection rates exceeding 80% in tomatoes. Classical culturing on a novel nitrogen-free medium additionally confirmed colonization, with the same validating the real-time PCR assays.<br><br>DISCUSSION: This study provides a robust, genome-informed molecular detection system for monitoring M. symbioticum SB0023/3 in crops. The presented approach enables direct detection from plant tissues, facilitating studies on colonization dynamics and biosafety. This methodology can be extended to other microbial biostimulants, supporting sustainable agricultural practices.}, }
@article {pmid41848198, year = {2026}, author = {Skoupý, S and Stanojković, A and Johansen, JR and Casamatta, DA and McGovern, C and Jungblut, AD and Fastner, J and Dvořák, P}, title = {Population and herbarium genomics provide a comprehensive framework for a revision of Microcoleus (Cyanobacteria).}, journal = {Journal of phycology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jpy.70145}, pmid = {41848198}, issn = {1529-8817}, support = {//European Community Research Infrastructure Action under the FP7 "Capacities" Program/ ; 23-06507S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; }, abstract = {Microcoleus is a cosmopolitan, filamentous cyanobacterium and a key component of biological soil crusts-complex microbial communities essential for primary production in diverse terrestrial environments. Here, we performed a taxonomic revision of several species of Microcoleus based on a large population genomic dataset. The dataset was based on a Microcoleus speciation continuum characterized by variable levels of gene flow between the species. The putative species ranged from cryptic to distinctly morphologically defined lineages. We identify the type herbarium specimen and obtained a genome for the type species M. vaginatus and herein describe 10 novel species of Microcoleus. We provide epitypifications for the previously described species M. vaginatus and M. attenuatus. This research contributes to a more comprehensive understanding of terrestrial cyanobacterial biodiversity and cryptic species in cyanobacteria. It highlights the need for an extensive genomic and phenotypic dataset in the taxonomy of Cyanobacteria.}, }
@article {pmid41850628, year = {2026}, author = {Tumeo, A and Kovářová, A and McDonagh, F and Ryan, K and Clarke, C and Miliotis, G}, title = {Patient colonization with Phytobacter spp. co-harboring blaIMP-4, blaSHV-12, and mcr-9.1 highlights its role as an under-recognized reservoir of antimicrobial resistance.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108562}, doi = {10.1016/j.ijid.2026.108562}, pmid = {41850628}, issn = {1878-3511}, abstract = {We report two uncommon identifications of patient colonization with multidrug-resistant, carbapenemase-encoding Phytobacter in Ireland. Phytobacter is a recently delineated genus within the Enterobacterales that is frequently misidentified in clinical laboratories. Two isolates were recovered from rectal swabs in 2024 and were initially identified as Phytobacter ursingii by MALDI-TOF. Whole-genome sequencing with in silico species typing (average nucleotide identity and digital DNA-DNA hybridization) resolved them as Phytobacter diazotrophicus E787336 and P. ursingii E980862. We reconstructed a genus-wide maximum-likelihood core-genome phylogeny and profiled all publicly available Phytobacter genomes to contextualize antimicrobial resistance (AMR) and plasmid content. Across the dataset, we detected 22 plasmid replicon types and a resistome comprising 71 genes, over half predicted to be plasmid-borne. These included carbapenemases in 26.5% (9/34) of the genomes, and disinfectant-associated resistance determinants in 29.5%. E787336 and E980862 represent the first Phytobacter isolates identified to co-harbor plasmid-borne blaIMP-4, blaSHV-12, and mcr-9.1 in association with IncHI2A plasmid reconstructions. Phenotypic testing confirmed resistance to aztreonam, aminoglycosides, cephalosporins, fluoroquinolones, and piperacillin-tazobactam, yet susceptibility to carbapenems and colistin. These findings expand the clinical and genomic evidence that Phytobacter can act as an under-recognized colonizer and reservoir for plasmid-borne AMR, including carbapenemases, and underscore the need for improved clinical identification, genomic surveillance, and preparedness for limited therapeutic options.}, }
@article {pmid41850929, year = {2026}, author = {Garcés-Ruiz, M and Díaz-Otero, BG and Antonielli, L and Saraiva, JP and Karpouzas, D and Declerck, S}, title = {Machine learning for designing low-risk microbial consortia pesticides.}, journal = {Trends in biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tibtech.2025.12.027}, pmid = {41850929}, issn = {1879-3096}, abstract = {Microbial consortia, considered low-risk pesticides (LRPs), appear to be valuable tools for reducing our dependence on chemical pesticides. However, their use is limited by inconsistent product efficacy and registration difficulties. Artificial intelligence (AI) and machine learning (ML) offer solutions for designing and evaluating synthetic microbial communities (SynComs), predicting their compatibility, ecological stability, and biocontrol efficacy. The transition from laboratory discovery of SynCom-based LRPs to field application and commercialization could be significantly accelerated. Here, we review the methods and steps necessary to establish reliable SynComs and describe how AI and ML approaches could improve the construction and validation of SynCom-based LRPs to obtain more specific results that can contribute to their risk assessment.}, }
@article {pmid41851145, year = {2026}, author = {Shen, J and Han, M and Sun, J and Yu, H and Yang, Y and Shen, K and Su, Y and Chen, X and He, H and Shao, H and Sun, J and McMinn, A and Wang, M and Liang, Y}, title = {Diversity and ecological potential of sediment viruses from Chinese continental shelf seas.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00940-w}, pmid = {41851145}, issn = {2055-5008}, abstract = {Continental shelves are important areas for global biogeochemical cycling, yet the roles of sediment viruses in these areas remain poorly understood. Here, 48 surface sediment samples from the Chinese continental shelf were analyzed, and 12,540 viral operational taxonomic units (vOTUs) were identified. Taxonomic classification found that 93.6% of the vOTUs could not be assigned at the family level, and protein-sharing networks showed that 60.4% were singletons. Viral community structure was shaped primarily by temperature and water depth. A total of 557 auxiliary metabolic genes (AMGs) were identified, including those involved in sulfur reduction and phosphorus acquisition (Pho-family proteins). Additionally, diverse antibiotic resistance genes (ARGs) were detected, suggesting anthropogenic influence. This study reveals the diversity, ecological function, and environmental drivers of viral communities in continental shelf sediments, providing new insights into viral contributions to microbial ecology and biogeochemical processes.}, }
@article {pmid41852400, year = {2025}, author = {Fischer, A and Singh, JP and Van Hamme, J and Bottos, E and Fraser, LH}, title = {Investigating impacts from topsoil stockpile height on soil microbial communities.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1607677}, pmid = {41852400}, issn = {2813-4338}, abstract = {Mining activities are often severely disruptive to the landscape, and a significant barrier to reclamation following mining operations is the lack of quality topsoil. This project addresses knowledge gaps in the industry by exploring the compositional nature of topsoil stockpiles and their ability to facilitate post-mining revegetation after long-term storage. To do this, we conducted a microbial profiling of two topsoil stockpiles in the interior of British Columbia, Canada. Both stockpiles show depleted soil quality and significant changes compared to reference soils. Notably, there were declines in microbial diversity and significant shifts in community structure with increasing stockpile depths in one of the stockpiles. These results highlight the influence of topsoil-stockpile height on microbial communities in the soil, which ultimately influences the success of restoration. This research can help the industry to optimize restoration and expedite recovery in their mine-closure practices and provides insights into the general structure of the microbiome existing across a gradient in severely disturbed mining soils.}, }
@article {pmid41852403, year = {2025}, author = {Helal, M and Bari, VK}, title = {Insights into human respiratory microbiome under dysbiosis and its analysis tool.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1549166}, pmid = {41852403}, issn = {2813-4338}, abstract = {The human respiratory tract microbiome is a multi-kingdom microbial ecology that inhabits several habitats along the respiratory tract. The respiratory tract microbiome promotes host health by strengthening the immune system and avoiding pathogen infection. The lung microbiome mostly originates in the upper respiratory tract. The balance between microbial immigration and removal determines the nature of the lung microbiome. Identification and characterization of microbial communities from airways have been made much easier by recent developments in amplicon and shotgun metagenomic sequencing and data analysis techniques. In pulmonary medicine, there is a growing interest in the respiratory microbiome, which has been linked to human health and illness. However, the primary causes of bacterial co-occurrence seem to be interactions with fungi and bacteria as well as host and environmental factors. This study focused on identifying techniques and the current understanding of the relationship between the microbiota and various lung diseases.}, }
@article {pmid41852418, year = {2025}, author = {Berdy, BM and Williams, CE and Sizova, M and Jung, D and Tandogan, N and Goluch, ED and Epstein, S}, title = {Diverse cultivation strategies are necessary to capture microbial diversity in High Arctic lake sediment.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1619859}, pmid = {41852418}, issn = {2813-4338}, abstract = {While metagenomics has revolutionized our understanding of microbial diversity and function, the cultivation of microorganisms remains indispensable for elucidating their physiological characteristics and potential biotechnological applications. Cultivation provides context to the vast metagenomic datasets and helps verify metagenome-based hypotheses on microbial interactions. The majority of microorganisms remain uncultivated, and this is particularly prominent from extreme environments such as the Arctic. Here we aimed to contribute to the growing body of work investigating microbial ecology in extreme environments by assessing the efficacy of a variety of cultivation approaches in lake sediment in the High Arctic. To try and capture the full breadth of organisms present, we used standard, in situ, and anoxic cultivation methods. We cultured a total of 1,109 microorganisms which clustered into 155 OTUs (97% rRNA gene sequence similarity), representing organisms from Proteobacteria, Actinobacteria, Bacteroidota, and Firmicutes. Importantly, no single method of cultivation proved to be sufficient to represent the cultivable organisms within the environment. Rather, each method resulted in many unique OTUs. Therefore, multiple approaches should be used in conjunction to access the bulk of microbial taxa in a given environment.}, }
@article {pmid41853343, year = {2023}, author = {Ionescu, D and Zoccarato, L and Cabello-Yeves, PJ and Tikochinski, Y}, title = {Extreme fluctuations in ambient salinity select for bacteria with a hybrid "salt-in"/"salt-out" osmoregulation strategy.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1329925}, pmid = {41853343}, issn = {2813-4338}, abstract = {Abundant microbial biofilms inhabit underwater freshwater springs of the Dead Sea. Unlike the harsh (i.e., over 35% total dissolved salts) yet stable environment of the basin, the flow rate of the springs changes with random amplitude and duration, resulting in drastic shifts in salinity, pH, and oxygen concentrations. This requires the organisms to continuously adapt to new environmental conditions. Osmotic regulation is energetically expensive; therefore, the response of the biofilm organisms to rapid and drastic changes in salinity is interesting. For this purpose, we studied the metagenome of an enrichment culture obtained from a green biofilm-covered rock positioned in a spring. We obtained metagenome-assembled genomes (MAGs) of Prosthecochloris sp. (Chlorobiales), Flexistipes sp. (Deferribacterales), Izemoplasma (Izemoplasmatales), Halomonas sp. (Oceanospirillales), and Halanaerobium (Halanaerobiales). The MAGs contain genes for both the energetically cheaper "salt-in" and more expensive "salt-out" strategies. We suggest that the dynamic response of these bacteria utilizes both osmoregulation strategies, similar to halophilic archaea. We hypothesize that the frequent, abrupt, and variable-in-intensity shifts in salinity, typical of the Dead Sea spring system, select for microorganisms with scalable adaptation strategies.}, }
@article {pmid41853537, year = {2024}, author = {Klimasmith, IM and Wang, B and Yu, S and Yoshikuni, Y and Kent, AD}, title = {Translating macroecological models to predict microbial establishment probability in an agricultural inoculant introduction.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1452476}, pmid = {41853537}, issn = {2813-4338}, abstract = {The use of potentially beneficial microorganisms in agriculture (microbial inoculants) has rapidly accelerated in recent years. For microbial inoculants to be effective as agricultural tools, these organisms must be able to survive and persist in novel environments while not destabilizing the resident community or spilling over into adjacent natural ecosystems. Despite the importance of propagule pressure to species introductions, few tools exist in microbial ecology to predict the outcomes of agricultural microbial introductions. Here, we adapt a macroecological propagule pressure model to a microbial scale and present an experimental approach for testing the role of propagule pressure in microbial inoculant introductions. We experimentally determined the risk-release relationship for an IAA-expressing Pseudomonas simiae inoculant in a model monocot system. We then used this relationship to simulate establishment outcomes under a range of application frequencies (propagule number) and inoculant concentrations (propagule size). Our simulations show that repeated inoculant applications may increase establishment, even when increased inoculant concentration does not alter establishment probabilities. Applying ecological modeling approaches like those presented here to microbial inoculants may aid their sustainable use and provide a monitoring tool for microbial inoculants.}, }
@article {pmid41841597, year = {2026}, author = {Ye, Z and Kuang, J and Bates, CT and Escalas, A and Ning, D and Wu, L and Liu, S and Deng, S and Lei, J and Chen, X and Pett-Ridge, J and Saha, M and Hale, L and Wang, G and Tian, R and Fu, Y and Tang, Y and Firestone, M and Zhou, J and Yang, Y}, title = {Bioenergy Cropping Reduces the Spatiotemporal Scaling of Soil Bacterial Biodiversity.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e18964}, doi = {10.1002/advs.202518964}, pmid = {41841597}, issn = {2198-3844}, support = {KY-23ZK01//Hainan Institute of National Park/ ; 32161123002//National Natural Science Foundation of China/ ; //Office of Science/ ; DE-SC0014079//Office of Biological and Environmental Research Genomic Science program/ ; //UC Berkeley/ ; //Nobel Research Institute/ ; //University of Oklahoma/ ; //Lawrence Livermore National Laboratory (LLNL)/ ; AC52-07NA27344//Lawrence Berkeley National Laboratory/ ; SCW1555//Lawrence Berkeley National Laboratory/ ; EF-2025558//Lawrence Berkeley National Laboratory/ ; }, abstract = {Widespread bioenergy cropping can transform landscapes, strongly affecting biodiversity. However, the impact of bioenergy cropping on the spatiotemporal scaling of soil biodiversity remains virtually unknown, despite its profound implications for the functioning of the ecological community. Here, we investigated how bioenergy cropping influenced the spatiotemporal scaling of soil bacterial biodiversity in marginal soils (sandy loam and clay loam soils) in Oklahoma, USA. We detected strong, significant species-time-area relationships (STARs) and phylogenetic-time-area relationships (PTARs) in bacterial communities and their lineages, suggesting that STARs and PTARs exist in microbial ecology within the studied system. Also, spatiotemporal scaling rates (the slopes of STAR and PTAR models) varied substantially among bacterial lineages and were positively correlated with their 16S rRNA gene copy numbers, a genomic trait indicative of microbial growth potentials. Strikingly, bioenergy cropping significantly reduced spatiotemporal scaling rates by 6.8%-14.1%, with a more pronounced reduction observed in sandy loam soils, where those rates were significantly lower than in clay loam soils. The heterogeneity of soil phosphorus and carbon resulted in variations in bacterial spatiotemporal scaling rates. Collectively, our findings suggest that bioenergy cropping may alleviate rapid shifts in soil biodiversity across space and time, thereby stabilizing soil biodiversity and supporting its role as part of sustainable land management and climate mitigation strategies.}, }
@article {pmid41841793, year = {2026}, author = {Dey, R and Coenen, AR and Solonenko, NE and Burris, MN and Mackey, AI and Galasso, J and Sun, CL and Demory, D and Muratore, D and Beckett, SJ and Sullivan, MB and Weitz, JS}, title = {Density-dependent feedback and higher-order interactions enable coexistence in phage-bacteria community dynamics.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag041}, pmid = {41841793}, issn = {1751-7370}, abstract = {Diverse phage-bacteria communities coexist at high densities in environmental, agricultural, and human-associated microbiomes. Phage-bacteria coexistence is often attributed to coevolutionary processes mediated by complex, pairwise infection networks. Here, using in vitro experiments and mathematical models, we explore how higher-order interactions function as a complementary, ecological feedback mechanism to stabilize phage-bacteria communities. To do so, we examine an environmentally-derived, synthetic phage-bacteria community comprised of five marine heterotrophic bacteria (Cellulophaga baltica and Pseudoalteromonas strains) and five associated phage. We used Bayesian inference to reconstruct free phage production in one-step growth experiments and then forecasted pairwise phage-bacteria community dynamics over multiple infection cycles. In contrast to model predictions of rapid bacterial population collapse, each bacterial strain persisted in the community. We hypothesized and then experimentally validated the relevance of infection attenuation at relatively high viral densities. We extended models into a community context, corroborating complex coexistence of all phage and bacteria. Life history traits inferred in community fits often differed from those inferred in a pairwise context, implicating higher-order interactions as an additional, ecological stabilization mechanism. Follow-up experiments confirm that phage traits (including burst size) can shift when infecting single vs. multiple strains. More broadly, these findings suggest that complex community coexistence of phage and bacteria may be more common than anticipated when including feedback mechanisms outside of the growth-dominated regimes of fitted pairwise models that do not reflect the full scope of ecologically relevant contexts.}, }
@article {pmid41841797, year = {2026}, author = {Coskun, &#xd6;K and Orsi, WD and Marshall, IPG and Muschler, KA and Mitschke, N and Ferdelman, TG and Gomez-Saez, GV}, title = {Hypoxia increases microbial carbon assimilation of taurine in a seasonally anoxic fjord.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag057}, pmid = {41841797}, issn = {1751-7370}, abstract = {Hypoxic zones are expanding globally altering marine biogeochemical cycles. Within these low-oxygen regions, microbial communities play a key role in the production, degradation, and transformation of dissolved organic sulfur (DOS) compounds. Taurine is a bioavailable DOS compound widely utilized by marine microbes with a central role in nutrients exchange, energy production and biomass generation. However, in stratified water columns with varying oxygen conditions, the specific microbial taxa assimilating taurine as a carbon source remain poorly characterized. Here, we applied quantitative stable isotope probing (qSIP) experiments using 13C-labeled organosulfur compounds (taurine and methionine) and 13C-glucose to identify active microbial utilizers in oxic and hypoxic waters in the seasonally anoxic Mariager Fjord (Denmark, Kattegat Sea). Our qSIP results were supported by physicochemical measurements and geochemical data. Taurine-derived 13C-carbon was assimilated into microbial biomass exclusively under hypoxic conditions, primarily by Flavobacteriaceae (Bacteroidota), indicating that taurine serves as a carbon source only when oxygen is limited. 13C-taurine and 13C-methionine assimilation were strongly associated, suggesting a flexible metabolic strategy for utilizing organosulfur compounds in hypoxic waters. In oxic waters, 13C-methionine and 13C-glucose were assimilated by distinct taxonomic groups, dominated by Bacteroidota and Verrucomicrobiota, respectively. Overall, our study identifies active microbial communities assimilating organosulfur compounds under varying oxygen levels in the seasonally anoxic Mariager Fjord, providing new insights into key microbial processes in low-oxygen coastal systems.}, }
@article {pmid41842987, year = {2026}, author = {Reardon, CL and Manter, DK}, title = {Amplification Efficiency of Quantitative PCR Reactions is Improved by Addition of Non-Target DNA.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02719-0}, pmid = {41842987}, issn = {1432-184X}, }
@article {pmid41843121, year = {2026}, author = {Dou, WH and Li, TC}, title = {Rapid Genomic Adaptation of Drosophila Melanogaster to Wolbachia Elimination.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02732-3}, pmid = {41843121}, issn = {1432-184X}, support = {ZR2024QC383//Natural Science Foundation of Shandong Province/ ; ZR2024QC222//Natural Science Foundation of Shandong Province/ ; }, }
@article {pmid41844028, year = {2026}, author = {Sun, L and Huang, L and Jia, S and Wei, Y and Cao, Z and Zhang, P and Zhang, G}, title = {Enhancing wastewater denitrification in constructed wetlands: microbial mechanisms driven by lotus leaf-based carbon.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129368}, doi = {10.1016/j.jenvman.2026.129368}, pmid = {41844028}, issn = {1095-8630}, abstract = {The performance of constructed wetlands (CWs) in treating low C/N domestic wastewater is often constrained by limited carbon availability for denitrification. This study proposes an innovative approach using alkali-pretreated lotus leaves as a biodegradable, slow-release carbon source to enhance denitrification efficiency and uncover the underlying metabolic and microbial mechanisms. Results demonstrated that wet lotus leaves-especially those wet-4% NaOH-released carbon more efficiently than dried leaves, with a peak rate of 25.93 mg g[-1]·h[-1] (calculated as ΔCOD/Δt normalized to wet mass and measured within the first 20 h of the static experiment). This pretreatment also mitigated nitrogen and phosphorus leaching risks. Supplementation with 400 g of 4% NaOH-treated wet lotus leaves (CW2) significantly improved the TN removal efficiency, reaching a peak of 91.89 ± 3.56% during days 1-16, with an overall average of 85.63% ± 7.72%. Mechanistically, tryptophan-like DOM signals (EEM) suggest that small-molecule soluble organics released from plant-derived carbon sources can be rapidly taken up and utilized by denitrification-associated microorganisms, thereby supporting the denitrification process. Microbial characteristics analysis revealed that CW2 enriched microbial richness (Shannon = 6.96; Chao 1 = 2015.9) and shifted community composition toward denitrification-favorable taxa. Notably, Proteobacteria abundance increased from 21.5% to 38.5%, accompanied by the proliferation of key genera including Pseudomonas and Janthinobacterium. The taxa associated with nitrifiers, denitrifiers, and anammox bacteria collectively contributed to a more robust nitrogen removal pathway. These findings suggest that the supplementary carbon source-by regulating dissolved oxygen distribution, supplying bioavailable carbon, and establishing spatially structured redox gradients-strategically modulates microbial ecology and functional metabolism, offering a low-cost and sustainable solution for enhancing nitrogen removal in constructed wetlands.}, }
@article {pmid41844516, year = {2026}, author = {Muratore, TJ and Chari, NR and Phillips, RP and Taylor, BN and Knorr, MA and Frey, SD}, title = {Increased root-derived carbon buffers soil carbon loss under simultaneous warming and nitrogen addition.}, journal = {Ecology}, volume = {107}, number = {3}, pages = {e70351}, doi = {10.1002/ecy.70351}, pmid = {41844516}, issn = {1939-9170}, support = {DEB-1832110//U.S. National Science Foundation (NSF) Long Term Ecological Research Program/ ; DEB-1456610//U.S. National Science Foundation (NSF) Long-Term Research in Environmental Biology/ ; 2106096//Macrosystems Biology and NEON-Enabled Science" (MSB-NES)/ ; 1950364//U.S. National Science Foundation (NSF) Directorate for Biological Sciences Division of Biological Infrastructure/ ; 3018//New Hampshire Agricultural Experiment Station/ ; Hatch NH-00701//New Hampshire Agricultural Experiment Station/ ; }, mesh = {*Soil/chemistry ; *Nitrogen/chemistry ; *Carbon/chemistry/metabolism ; *Plant Roots/metabolism/physiology ; *Global Warming ; Soil Microbiology ; *Carbon Cycle ; }, abstract = {Plant roots are primary drivers of soil organic matter dynamics, mediating belowground carbon (C) inputs, stabilization, and losses. Yet, how global changes such as rising temperatures and altered nitrogen (N) availability interact to affect these dynamics has rarely been tested empirically in the field. Here, we quantify how inputs to soil organic matter from fine-root production, root exudates, and root-associated fungi respond to long-term (16 years) soil warming (+5°C), nitrogen (N) enrichment (+5 g N m[-2] year[-1]), and their combination in a temperate hardwood forest. Warming alone reduced root-derived C inputs by 21% and increased microbial respiration by 46%, resulting in a net soil C loss of 135 g C m[-2] year[-1]. In contrast, N enrichment increased root-derived soil organic carbon (SOC) accumulation by 47% and reduced root respiration by 40%, contributing to a near-neutral soil C balance. When combined, warming × N addition increased root-derived SOC fourfold (from 70 to 281 g C m[-2] year[-1]), fully offsetting warming-induced C losses and maintaining soil C stocks at control levels. Root-derived SOC accumulation was positively related to fine-root production (r[2] = 0.42) and to maple:oak exudate ratios (r[2] = 0.31), highlighting species-specific control over C stabilization. These findings demonstrate that interacting global change factors can have balancing effects on root C allocation and microbial losses, highlighting soil N availability as a critical control determining whether warming accelerates SOC depletion or stabilizes new root-derived C.}, }
@article {pmid41844664, year = {2026}, author = {Ruiz-Muñoz, B and Bretscher, KM and Carrión, VJ and Cazorla, FM and Gutiérrez-Barranquero, JA}, title = {Long-term organic farming shapes the avocado rhizosphere microbiota through the enrichment of drought-tolerant Bacillus spp.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00957-1}, pmid = {41844664}, issn = {2055-5008}, support = {PID2021-123713OB-I00//Ministerio de Ciencia, Innovacion y Universidades (Spain)/ ; }, abstract = {Long-term farming practices leave an imprint on soil microbiomes, but how these changes influence crop drought resilience remains poorly understood. Here, we examined avocado orchards managed organically or conventionally for two decades and recurrently exposed to drought, to assess how management history shapes the rhizosphere microbiota and its contribution to plant stress tolerance. Organic and conventional systems resulted in distinct soil physicochemical profiles that were associated with shifts in rhizosphere microbial community composition. Organic management was characterized by higher soil pH, phosphorus availability, water content, and C:N ratio, together with a consistent enrichment of spore-forming bacteria, especially members of the Bacillaceae family. We established a culture collection from the organic rhizosphere, dominated by Bacillaceae, and identified three top-performing strains: Bacillus halotolerans B19 and B21, and Bacillus subtilis B26. In greenhouse assays, B. halotolerans strains mitigated drought stress by preserving biomass and reducing leaf proline accumulation, while B. subtilis provided partial protection. Gene expression analysis revealed strain-specific responses that nonetheless converged on bdh (2,3-butanediol dehydrogenase) induction, highlighting a common mechanism for drought mitigation. Together, these findings establish a mechanistic link between long-term organic farming and microbial functions underpinning drought resilience in perennial agroecosystems, paving the way for climate-smart farming strategies.}, }
@article {pmid41845564, year = {2026}, author = {Zhang, Y and Wang, DD}, title = {Gut microbiome in type 2 diabetes: insights from metagenomics, multi-omics, and diet-microbe interactions.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2644682}, doi = {10.1080/19490976.2026.2644682}, pmid = {41845564}, issn = {1949-0984}, mesh = {*Diabetes Mellitus, Type 2/microbiology/metabolism ; Humans ; *Gastrointestinal Microbiome ; Metagenomics ; Animals ; *Diet ; Metabolomics ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Proteomics ; Multiomics ; }, abstract = {Type 2 diabetes (T2D) is a heterogeneous metabolic disorder in which environmental exposures interact with host biology to drive insulin resistance and progressive β-cell dysfunction. This review synthesizes recent advances showing how the gut microbiome mediates these processes across multiple levels of resolution. First, large-scale shotgun metagenomic studies consistently identify a reproducible T2D-associated signature characterized by depletion of short-chain fatty acid-producing taxa and enrichment of opportunistic, pro-inflammatory microorganisms, while highlighting the importance of controlling for major confounders such as adiposity and glucose-lowering medications. Second, functional profiling and metabolomics link microbial community shifts to coordinated pathway changes-including reduced short-chain fatty acid and secondary bile acid production and increased endotoxin- and branched-chain amino acid-related metabolism-that influence gut barrier integrity, inflammatory tone, insulin sensitivity, and pancreatic β-cell function. Third, we discuss how integrative multi-omics (metagenomics, metatranscriptomics, proteomics, and metabolomics) can connect microbial genetic potential to in vivo activity and circulating metabolites, while introducing key challenges such as temporal variability, anatomical heterogeneity, and "dark matter" in gene and metabolite annotation. Fourth, strain-resolved analyses reveal that many disease-associated functions are carried by specific lineages within species, refining microbial targets and helping explain inconsistent species-level associations. Fifth, we summarize how diet shapes microbial ecology and function-supporting microbiome-informed precision nutrition-and highlight emerging evidence beyond bacteria, including viral and fungal community components. Finally, we outline translational opportunities and evidence gaps, emphasizing the need for diverse longitudinal cohorts, mechanistic validation, and well-controlled interventional trials to evaluate microbiome-directed strategies for T2D prevention and treatment.}, }
@article {pmid41834869, year = {2026}, author = {Ruff, SE and Murali, R and Rubin-Blum, M and Teske, AP}, title = {Editorial: Rising stars in geomicrobiology: microbial life in subsurface, seep and hydrothermal ecosystems.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1808625}, doi = {10.3389/fmicb.2026.1808625}, pmid = {41834869}, issn = {1664-302X}, }
@article {pmid41835129, year = {2026}, author = {Milke, F and Garcia, SL and Simon, M and Pacheco-Valenciana, A and Lennartz, ST}, title = {Microbial cohorts: bringing ecological meaning to the modularity concept of co-occurrence networks.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag037}, pmid = {41835129}, issn = {2730-6151}, abstract = {Microbial communities are structured through complex interactions that are difficult to observe directly. Co-occurrence networks offer a way to infer community structure, revealing (not exclusively) potential biotic interactions. Such networks have been inferred for diverse biomes and repeatedly found to be modular, yet the ecological significance of this modularity remains underexplored. We tested whether clusters within co-occurrence networks ("cohorts"), are universal and ecologically meaningful units by assessing their ubiquity, stability, and environmental specificity across diverse ecosystems. Our meta-analysis spans 25 previously published 16S rRNA gene amplicon sequencing datasets (14 160 samples) and covers high environmental variability ranging from aquatic, terrestrial to anthropogenic environments. Microbial co-occurrence networks consistently exhibited high modularity across biomes. Inferred cohorts were ubiquitous and represented up to 90% of the community composition. Our findings demonstrate that modularity is a fundamental and generalizable feature of microbial community organization, indicating the existence of stable subcommunities. Highly similar cohorts were inferred even across different, unconnected environments and datasets, and showed consistent responses to environmental gradients, indicating that their composition is to a large degree deterministic and predictable. The overall cohort structure and environmental preferences were independent of the sample size and the inference algorithm, underlining the robustness and applicability of the results. Recognizing these microbial cohorts as a meaningful level of microbial organization will refine microbial community ecology, cultivation strategies, and predictive modelling of microbial dynamics.}, }
@article {pmid41836789, year = {2026}, author = {Manzoor, M and Pussinen, PJ and Saarela, RK and Pitkälä, K and Hiltunen, K and Mäntylä, P}, title = {Denture-associated oral microbiome in dentate and edentulous older adults living in long-term care facilities.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2641915}, pmid = {41836789}, issn = {2000-2297}, abstract = {BACKGROUND: The denture-associated oral microbiome (DAOM) may act as reservoirs of pathogenic microorganisms with potential health effects.<br><br>OBJECTIVES: To characterize the compositional and functional activity of the DAOM in dentate and edentulous older adults residing in long-term care facilities (LTCFs).<br><br>METHODS: Participants (51 dentate and 56 edentulous) aged &#x2265;64 years were recruited from the Finnish Oral Health Studies in Older Adults. Clinical oral examinations were performed, and biofilm samples for shotgun metagenomics were collected from the acrylic surface of removable dentures. Diversity indices, taxonomic composition, and functional pathways were assessed to characterize DAOM.<br><br>RESULTS: Alpha diversity was similar, whereas beta diversity showed modest differences between groups. Dentate participants had a higher abundance of Streptococcus mutans, Veillonella parvula, and Parascardovia denticolens, whereas edentulous participants were enriched with Haemophilus parainfluenzae and Propionibacterium acidifaciens. Edentulous participants had reduced microbial network stability and interconnectedness but highly active microbial metabolic functions, particularly those associated with Streptococcus pneumoniae.<br><br>CONCLUSION: Although tooth loss does not markedly alter the overall microbial diversity of DAOM, it is associated with distinct taxonomic and functional shifts. Edentulous individuals have less stable and less interconnected microbial networks alongside heightened metabolic activity, reflecting notable changes in the DAOM of older adults living in LTCFs.}, }
@article {pmid41837593, year = {2026}, author = {Mailem, RC and Tsai, PW and Tayo, L and Hsueh, CC and Hsieh, CY and Chen, BY}, title = {Uncovering the Redox and Immunoregulatory Basis of the Chinese Herbal Formula Ping An Fang Yu Yin using Network Pharmacology and In Silico Target Profiling.}, journal = {Current pharmaceutical design}, volume = {}, number = {}, pages = {}, doi = {10.2174/0113816128418247251211153057}, pmid = {41837593}, issn = {1873-4286}, abstract = {INTRODUCTION: Ping An Fang Yu Yin (PAFYY) is a traditional Chinese herbal tea formula commonly used to treat respiratory infections, including COVID-19. Previous research indicates potential antiinflammatory activities; however, the underlying mechanisms remain unclear. This study aimed to investigate the mechanisms underlying the therapeutic effects of PAFYY, specifically its electron-transport and bioenergetic properties, through network pharmacology, electrochemical analysis, and Microbial Fuel Cell (MFC) assessments.<br><br>METHODS: Active compounds and their respective targets were identified via database searches. Proteinprotein interaction networks were constructed using the STRING database and further analyzed using Cytoscape and MCODE software. Molecular docking was employed to assess the binding affinity between identified key compounds and their targets. Cyclic voltammetry (CV) and MFC assays evaluated the electrontransport characteristics of PAFYY water and ethanol extracts.<br><br>RESULTS: The analysis identified 298 active compounds associated with 1,940 biological targets, highlighting key targets including EP300, CREBBP, ESR1, AKT1, MAPK3, MAPK1, and STAT3. GO and KEGG pathway enrichment analyses revealed that PAFYY significantly influences immune system processes and neuronal signaling pathways. Molecular docking confirmed the anti-inflammatory and antiviral potential of the identified active compounds. Additionally, electrochemical studies demonstrated that PAFYY contains electroactive substances mediating electron-driven redox reactions.<br><br>DISCUSSION: Recent studies have demonstrated that traditional Chinese herbal teas contain electron shuttles capable of mediating electron transfer in electrogenic bacteria. Emerging evidence further indicates that electroactive plant polyphenols can modulate microbial ecology through redox-mediated mechanisms. Our findings suggest that PAFYY may act on the microbiota-immune axis, with its electron-shuttling constituents contributing not only to direct cellular effects and antioxidant activity but also to modulation of the gut microbiome in ways that support antiviral immunity and attenuate inflammation. These results may inform future research into the mechanistic basis of medicinal herbs, while highlighting the potential of MFCs as a functional screening platform for identifying bioactive redox compounds.<br><br>CONCLUSION: The anti-COVID-19 properties of PAFYY may be largely attributed to its electron-transport capabilities, mediated through electroactive compounds. These findings provide novel insights into the mechanistic basis of traditional Chinese medicine prescriptions, potentially enhancing their therapeutic application.}, }
@article {pmid41839398, year = {2026}, author = {Kawuribi, V and Awere-Duodu, A and Adjei, FA and Osman, AH and Bomansaan, H and Madadi, MM and Tampuri, JU and Adu-Amankwaah, J}, title = {The Gut-Tumor Metabolic Axis: A Comprehensive Exploration of Bidirectional Crosstalk in Cancer Immunotherapy.}, journal = {Critical reviews in oncology/hematology}, volume = {}, number = {}, pages = {105280}, doi = {10.1016/j.critrevonc.2026.105280}, pmid = {41839398}, issn = {1879-0461}, abstract = {The gut-tumor metabolic axis represents a bidirectional immunometabolic network in which tumor-derived metabolites reshape microbial ecology, while gut microbiome-derived metabolites recalibrate systemic and intratumoral immunity, ultimately influencing cancer progression and immunotherapy outcomes. Tumor aerobic glycolysis generates excess lactate and acidity that suppress cytotoxic immune function, remodel the tumor immune microenvironment, and indirectly perturb intestinal microbial composition. In turn, microbial metabolites including short-chain fatty acids, bile acid derivatives, tryptophan catabolites, inosine, and trimethylamine N-oxide signal through defined host pathways such as GPR109A, AHR, and adenosine A2A receptors to regulate antigen presentation, T-cell differentiation, macrophage polarization, and immune checkpoint sensitivity. Preclinical and emerging clinical evidence demonstrates that dietary modulation, rational probiotics, and fecal microbiota transplantation can enhance immune checkpoint inhibitor efficacy in selected contexts. However, metabolite effects are highly context dependent, with dose, timing, tumor type, and immune state critically shaping therapeutic benefit or resistance. This review integrates mechanistic insights and clinical evidence, highlights translational challenges including safety, donor heterogeneity, and biomarker validation, and proposes a framework for biomarker-guided microbiome-based strategies to advance precision cancer immunotherapy.}, }
@article {pmid41840154, year = {2026}, author = {Garza-González, DA and Quezada-Euán, JJG and Medina-Medina, LA and Solís-Sánchez, T and O'Connor-Sánchez, A}, title = {Comparative analysis of the gut microbiota of the sympatric stingless bee species Melipona beecheii and Melipona yucatanica.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {57}, number = {1}, pages = {}, pmid = {41840154}, issn = {1678-4405}, support = {INFR2016 01-269833//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; CAR-21861//Universidad Aut&#xf3;noma de Yucat&#xe1;n/ ; }, }
@article {pmid41826531, year = {2026}, author = {Eckertová, T and Palyzová, A and Műllerová, M and Řezanka, T}, title = {Radioactive Springs and Archaeal Life in Deep Groundwater Systems.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02720-7}, pmid = {41826531}, issn = {1432-184X}, support = {(VEGA project No. 1/0019/22//Scientific Grant Agency/ ; CZ.02.01.01/00/22_008/0004597//Grant Talking Microbes/ ; APVV-21-0356//Slovak Research and Development Agency/ ; RVO 61388971//Institutional Research Concept/ ; }, }
@article {pmid41826538, year = {2026}, author = {Teban-Man, A and Erdem, ED and Berendonk, TU and Klümper, U and Coman, C and Szekeres, E}, title = {Hydrodynamics Shape Antibiotic Resistance in Wastewater-Impacted River Biofilms.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02725-2}, pmid = {41826538}, issn = {1432-184X}, }
@article {pmid41828603, year = {2026}, author = {Reytor-González, C and Román-Galeano, NM and Aules-Curicama, LS and Cevallos-Villacis, CD and González, E and Jima Gavilanes, D and Horowitz, R and Simancas-Racines, D}, title = {The Oral-Gut-Immune-Nutrition Axis in Rheumatoid Arthritis: Molecular Mechanisms and Therapeutic Implications.}, journal = {International journal of molecular sciences}, volume = {27}, number = {5}, pages = {}, pmid = {41828603}, issn = {1422-0067}, mesh = {Humans ; *Arthritis, Rheumatoid/immunology/microbiology/therapy ; *Gastrointestinal Microbiome/immunology ; Diet ; Animals ; *Mouth/microbiology/immunology ; }, abstract = {Rheumatoid arthritis is a chronic systemic autoimmune disease that arises from complex interactions among genetic susceptibility, environmental factors, and immune dysregulation. Growing evidence indicates that microorganisms residing in the oral cavity and gastrointestinal tract, together with dietary factors, play a central role in shaping inflammatory and autoimmune responses in rheumatoid arthritis, forming an interconnected microbiome-immune-nutrition axis. Alterations in the composition and function of oral and intestinal microbial communities are associated with disruption of mucosal barrier integrity, activation of innate and adaptive immune pathways, increased differentiation of proinflammatory T lymphocyte subsets, and loss of immune tolerance that promotes autoantibody production. In addition, microbially derived metabolites, particularly short-chain fatty acids, provide a mechanistic link between microbial ecology, immune regulation, and bone metabolism. Diet represents a key upstream modulator of this axis. Dietary patterns rich in anti-inflammatory nutrients support microbial diversity and immunoregulatory metabolite production, whereas diets high in processed foods and saturated fats favor proinflammatory microbial profiles. Accumulating clinical evidence suggests that nutritional strategies and microbiome-targeted dietary interventions may reduce systemic inflammation and disease-related comorbidities when used alongside standard pharmacological treatments. Taken together, the microbiome-immune-nutrition axis represents a modifiable and clinically meaningful target in rheumatoid arthritis, emphasizing the need for interdisciplinary research and well-designed clinical trials to translate these insights into personalized approaches for disease management. The aim of this review is to integrate current mechanistic and clinical evidence on the interactions between the microbiome, immune system, and nutrition in rheumatoid arthritis, with a focus on their pathogenic relevance, therapeutic potential, and implications for personalized, diet-based interventions.}, }
@article {pmid41832088, year = {2026}, author = {Schwalbe, M and Bosch, T and El Aidy, S}, title = {Gut motility as a driver of microbial community architecture and host-microbe evolution.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2025.12.016}, pmid = {41832088}, issn = {1878-4380}, abstract = {Digestive systems are dynamic, contractile ecosystems that continually shape the physical and chemical niches inhabited by gut microbes. Patterns of mixing and propulsion generate flow, shear, and nutrient gradients that select for microbial traits such as adhesion, biofilm formation, and metabolic timing. Microbial metabolites, in turn, influence smooth muscle excitability and enteric neural circuits, creating bidirectional feedback that structures microbial communities and affects host physiology. We argue that gastrointestinal motility, an ancient and nearly universal feature of metazoan digestive systems, functions as an evolutionary scaffold, linking microbial spatial organization with host neuromuscular diversification. Comparative evidence from cnidarians to mammals highlights how these interactions have shaped both microbial ecology and host adaptation, with relevance for understanding modern dysmotility-microbiome disorders.}, }
@article {pmid41832279, year = {2026}, author = {Choran, N and Örmeci, B}, title = {Microfibres versus fragments: differential impacts of polyethylene terephthalate (PET) and polyamide (PA6) microplastics on anaerobic digestion efficiency and microbial ecology.}, journal = {Biodegradation}, volume = {37}, number = {2}, pages = {}, pmid = {41832279}, issn = {1572-9729}, mesh = {*Polyethylene Terephthalates/chemistry/metabolism ; Methane/metabolism ; Biodegradation, Environmental ; Anaerobiosis ; *Microplastics/metabolism/chemistry ; *Caprolactam/analogs &amp; derivatives/chemistry ; Polymers ; Bacteria/metabolism/drug effects ; }, abstract = {Rising microplastic (MP) pollution can significantly affect engineered treatment systems such as anaerobic digestion (AD). While prior studies have investigated the influence of individual polymers, varying concentrations and sizes on AD, the role of MP morphology and polymer interactions remains underexplored. This study investigated these factors using polyethylene terephthalate (PET) and polyamide 6 (PA6) MPs, both in isolation and in combination (1:1 ratio), introduced as microfibres (MFs) and fragments at three concentrations, 1, 5, and 15 mg/gTS. Results revealed morphology-dependent effects on methane production. MF exposure inhibited methane yield by 10-17% (p < 0.01), with PET and mixed polymers exhibiting a correlation to MP concentration. In contrast, fragments enhanced methane yield, particularly PA6 and mixed (PET and PA6) polymers increased methane output by 9 and 17% at the highest dose, respectively. Kinetic modelling further revealed that MFs consistently reduced methane production potential, apparent degradation and hydrolysis rate, whereas fragment trends were polymer-driven. Scanning electron microscopy (SEM) micrographs showed greater surface roughness in PA6, which enhanced microbial colonization compared to PET. Elevated reactive oxygen species (ROS) levels with MF addition, especially at the highest concentration, suggested higher oxidative stress and microbial inhibition. Microbial community analysis showed that exposure to MP fragments resulted in similar bacterial shifts across different polymer types, compared to the more diverse effects observed with MFs. Archaeal diversity was more affected by particle shape than polymer composition. All MP treatments favoured a shift toward hydrogenotrophic over aceticlastic methanogenesis. PET and mixed MF addition resulted in a substantial decline in the relative abundance of Actinobacteria (18-20%) from 42% in the control and other methanogenic taxa compared to their fragment counterparts. MF addition disrupted community structure, suppressed additive-degrading taxa, and increased acetogenic groups such as Synergistetes. Overall, the findings suggest that a comprehensive understanding of all influencing factors, including MP morphology, polymer type and concentrations, is important for effective AD system management.}, }
@article {pmid41834349, year = {2026}, author = {Zhao, S and Fan, Z and Wu, Y and Liu, J and Tang, X and Qiu, Z and Zhu, M}, title = {Biocontrol potential of Talaromyces purpureogenus against the wheat powdery mildew fungus Blumeria graminis f. sp. tritici.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-11-25-2383-SC}, pmid = {41834349}, issn = {0191-2917}, abstract = {Talaromyces purpureogenus is known as a mycoparasite that is capable of suppressing plant pathogenic fungi. However, to date, there is little information about the impact of T. purpureogenus on powdery mildews. Based on morphological and molecular biological analyses, T. purpureogenus was identified and confirmed as a mycoparasite on the wheat powdery mildew fungus (Blumeria graminis f. sp. tritici, Bgt, recently clarified as B. graminis s. str.). T. purpureogenus effectively inhibited the colony formation and conidial distribution of Bgt. By inoculation with T. purpureogenus on Bgt, the abundance of Bgt notably decreased by 2.15-, 1.89-, 3.86-, and 25.90-fold at 2, 4, 6, and 8 days post inoculation (dpi), respectively, while the abundance of T. purpureogenus significantly increased by 4.16-, 12.11-, 11.07-, and 6.02-fold at the corresponding time points. In vitro, T. purpureogenus exudates significantly impaired the formation of Bgt appressoria. Therefore, T. purpureogenus acts as a potential biocontrol agent by suppressing the formation, distribution, and development of Bgt conidia, making it a viable alternative for controlling wheat powdery mildew. These results indicate that T. purpureogenus is an antagonistic parasite of wheat powdery mildew, providing new insights for the management of plant pathogenic fungi.}, }
@article {pmid41824189, year = {2026}, author = {Azizian, A and Roomiani, L and Mehrgan, MS and Shekarabi, SPH}, title = {Advancing Fish Health: Systematic and Bibliometric Insights into Functional Feed Additives for Common Carp and Rainbow Trout.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41824189}, issn = {1867-1314}, }
@article {pmid41825203, year = {2026}, author = {Fu, Q and Dai, H and Wang, J and Zheng, S and Zhou, Y and Liu, H and Xu, F and Cheng, C and Jiang, H and Qian, Y and Zhang, S and Liu, L and Zheng, H and Li, Y and Zhang, L and Chen, Y and Cheng, X and Yang, T}, title = {Multi-omics analysis of dynamic profiles in response to various nutrient loads provides novel insights into obesity.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {59}, number = {}, pages = {106607}, doi = {10.1016/j.clnu.2026.106607}, pmid = {41825203}, issn = {1532-1983}, abstract = {BACKGROUND&amp; AIMS: Obesity is a global health issue driven by improper nutrient intake and metabolic dysregulation. The complexity of dietary components and the dynamic nature of postprandial metabolism limit our understanding of how different nutrient loads associated with obesity. This study aims to characterize the dynamic metabolic responses to nutrient intake using multi-omics approaches, assess the influence of dietary habits and gut microbiota, and evaluate the acute obesity-risk signature (AORS) associated with different macronutrients.<br><br>METHODS: We conducted a mixed meal tolerance test (MMTT) in 147 non-diabetic individuals (54 controls, 38 overweight, 55 obese). Blood samples were collected at multiple time points for untargeted metabolomics, lipidomics, proteomics, and hormone assays. Gut microbiota was profiled via metagenomic sequencing. A separate single macronutrient tolerance test (SMNTT) involving glucose, whey protein, butter, and olive oil was performed in 24 healthy volunteers to compare acute metabolic responses and derive an AORS based on postprandial multi-omics data.<br><br>RESULTS: Postprandial multi-omic analytes showed stronger associations with obesity indicators than fasting measures. Distinct temporal changes in metabolites, lipids, and proteins were observed across different BMI groups, with enrichment in pathways such as bile acid biosynthesis, triglyceride metabolism, and complement activation. Dietary habits and gut microbiota significantly influenced postprandial metabolic profiles, with specific metabolites and proteins mediating their effects on obesity. In SMNTT, glucose load exhibited the lowest AORS among isocaloric macronutrients (0.1082 &#xb1; 0.1917 %). Gut microbiota composition further modulated metabolic responses, with olive oil showing divergent AORS between Bacteroides- and Prevotella-dominated enterotypes (p = 0.043).<br><br>CONCLUSION: Postprandial multi-omics provides superior insights into obesity pathophysiology compared to fasting measurements. Our findings reveal that dietary habits and gut microbiota significantly influence postprandial metabolism and obesity risk, and demonstrate that different macronutrients confer distinct AORS values, which are further modified by an individual's gut microbiota composition. This underscores the potential for personalized nutritional strategies based on dynamic metabolic responses and microbial ecology.}, }
@article {pmid41824030, year = {2026}, author = {Jankowska, K and Łukomska-Kowalczyk, M and Milanowski, R and Zakryś, B}, title = {Multiscale environmental analysis on autotrophic euglenid communities: insights from DNA metabarcoding.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02721-6}, pmid = {41824030}, issn = {1432-184X}, support = {OPUS 2016/23/B/NZ8/00919//Narodowe Centrum Nauki/ ; }, }
@article {pmid41823408, year = {2026}, author = {Thorn, AV and Brinch, C and Aarestrup, FM and Munk, P}, title = {Urban sewage resistomes partially reflect clinical resistomes.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0003126}, doi = {10.1128/msystems.00031-26}, pmid = {41823408}, issn = {2379-5077}, abstract = {Antimicrobial resistance (AMR) poses a major global public health threat, and ongoing surveillance of antimicrobial resistance genes (ARGs) is critical to mitigate current and future risks. Sewage-based ARG surveillance is gaining traction, but insight into how it compares to surveillance by clinical bacterial isolates is limited, especially when it comes to ARG mutational variants. We compared ARGs identified in clinical bacterial isolates (n = 2,989) with those detected in sewage metagenomes (n = 468) across 33 countries. ARG variant detection data from clinical isolates and sewage metagenomes shared some regional patterns in detection, but many ARG variants were detected exclusively in either sewage metagenomes or clinical isolates. We found that across all samples, only 69% of ARG clusters detected in clinical isolates were also detected via read mapping in sewage. Some ARGs highly prevalent in clinical isolates were not detected in sewage. Among clinically widespread ARGs, prevalence varied across bacterial species and clinical isolate types depending on whether the ARGs were also detected in sewage. This could indicate that sewage surveillance is better suited for detection of clinically relevant ARGs prevalent in certain bacterial species and infection sites than others. Spearman correlation between ARG abundance in sewage and the proportion of clinical isolates from the same country with detection was 0.28 overall, with stronger correlations for certain ARGs. The results demonstrate that sewage ARG profiles correlate, to some extent, to the clinical AMR landscape, but do not capture the full spectrum of clinically relevant ARGs at currently realistic sequencing depths.IMPORTANCEAntimicrobial resistance (AMR) is a major public health threat. Surveillance of AMR is important and can be conducted via the detection of antimicrobial resistance genes (ARGs). Sewage can be used as a medium for surveillance as an alternative to analyzing individual bacterial isolates from health clinics. We compared detection in large global data collections of sewage metagenomes and clinical isolates. We found that while there were significant positive correlations between findings in sewage and clinical isolates, some widespread clinical ARGs were not detectable in sewage. This should be considered if establishing sewage surveillance systems.}, }
@article {pmid41823069, year = {2026}, author = {Savini, F and Indio, V and Prandini, L and Tomasello, F and De Cesare, A and Oliveri, C and Seguino, A and Zanato, E and Serraino, A}, title = {Outside in: assessment of microbial composition of the crust of dry-aged beef and its relevance in relation to food business operator practices.}, journal = {Italian journal of food safety}, volume = {}, number = {}, pages = {}, doi = {10.4081/ijfs.2026.14620}, pmid = {41823069}, issn = {2239-7132}, abstract = {Dry aging of beef has recently been defined in Delegated Regulation 1141/2023, amending Regulation 853/2005. The delegated regulation lists specific measures to be applied when processing such a product. Specifically, a point is dedicated to the crust trimming that should be carried out in a hygienic manner, since the interventions performed at the end of the process might determine contamination of the edible parts. Nevertheless, despite the punctual application of good hygiene practices (GHP) and good manufacturing practices (GMP), a certain degree of contamination with pathogenic and spoilage microorganisms of the cut portions cannot be avoided, as demonstrated by some authors reporting contamination of the inner parts of dry-aged meat. In order to investigate the level of contamination occurring in field conditions during trimming and portioning, we performed two different trials: the sterility trial with the aim of evaluating the sterility of the inner parts of beef during aging and the contamination trial to assess the transfer of microbial populations from the outer to the inner part of the dry-aged beef. All tests were performed by means of cultural and non-cultural methods. Results of the sterility trial show that a very limited percentage of non-host DNA is present in the inner parts of the meat starting from the beginning of the test and that the detectable DNA increases slightly during the time of aging. Besides, the contamination trial results showed that the contamination of the trimmed meat is qualitatively and quantitatively related to the contamination of the crust. As a consequence, adherence to GHP and GMP during trimming and handling of dry-aged meat according to scientific literature is crucial to avoid/minimize cross-contamination since our data clearly demonstrate that processing practices are fully reflected in the final product quality.}, }
@article {pmid41821696, year = {2025}, author = {Gao, X and Ju, Z and Wang, X and Wei, X and Gao, Y and Yang, C and Shi, Y and Huang, N and Liu, W and Jiang, Q and Wang, J and Zhang, Y and Xiao, Y and Huang, J}, title = {Dietary Supplement with Milk that Contains Different β-Caseins Influences Gut Microbiota and Serum Metabolites in Mice.}, journal = {Food science of animal resources}, volume = {45}, number = {5}, pages = {1491-1513}, pmid = {41821696}, issn = {2636-0780}, abstract = {The composition and metabolites of gut microbiota are shaped by dietary protein, consequently affecting host physiology, health, and diseases. This study aimed to elucidate the role of β-caseins in remodeling the composition of colon microbiota and the relationship between microbiota and serum metabolites. A total of 32 mice were randomly assigned to 4 groups and gavaged with A2, A1/A2, A1 milk, or saline for 5 wk. The supplementation of A1/A2 and A2 milk led to increased weight gain, while the A2 group exhibited an increase in goblet cell number and occludin expression in the colon. 16S ribosomal RNA gene analysis revealed differences in operational taxonomic units across groups, with Bacteroidetes and Firmicutes being predominant. Notably, A2 milk was associated with increased levels of Romboutsia and Anaerostipes compared to A1 milk. Untargeted metabolomics detected 537 and 371 metabolites in positive and negative ion modes, respectively. In the A2 group, 15 metabolites (e.g., vindoline, glycerol-3-phosphate, diphenylamine) were increased, while 13 metabolites (e.g., deoxyinosine, O-arachidonoyl ethanolamine) were decreased. Muribaculum, Ruminococcus, and Bifidobacterium genera showed significant associations with these metabolites. These findings suggest that β-casein supplementation in milk alters gut microbial ecology and metabolites, potentially impacting weight gain and colonic health positively.}, }
@article {pmid41821177, year = {2026}, author = {Jordan, S and de Maayer, P and Smits, THM and Coutinho, TA}, title = {Enterobacter Species: Opportunistic Human and Plant Pathogens With Plant-Beneficial Traits.}, journal = {Molecular plant pathology}, volume = {27}, number = {3}, pages = {e70231}, doi = {10.1111/mpp.70231}, pmid = {41821177}, issn = {1364-3703}, support = {SNSF210305588900//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, mesh = {*Enterobacter/pathogenicity/physiology/genetics ; Humans ; *Plant Diseases/microbiology ; *Plants/microbiology ; }, abstract = {UNLABELLED: Enterobacter species occur across diverse habitats and are best known for causing opportunistic and nosocomial infections in humans. The taxonomy of this genus is complex, with many species reassigned to and from this genus. Their interaction with plants is multifaceted. Strains of certain species cause opportunistic plant diseases.<br><br>HOST RANGE: Enterobacter species affect a wide range of plant hosts.<br><br>DISEASE SYMPTOMS: They cause a range of symptoms including leaf spots and blight, wilt and root diseases, decay and soft rot and cankers.<br><br>PLANT-BENEFICIAL TRAITS: Some Enterobacter species include strains that are plant growth promoters and occur either in the rhizosphere or as endophytes. Additionally, some strains can protect their hosts from pathogen attack and are regarded as promising biological control agents. Some strains also have potential for the bioremediation of various compounds.<br><br>GENOMIC FEATURES: Information on the pathogenicity and virulence mechanisms of plant-pathogenic Enterobacter species is limited. Comparison of diverse genomic features revealed no overall differences between plant-pathogenic and plant-beneficial strains.<br><br>CONCLUSION: While often reported as a plant pathogen, there is currently no evidence that Enterobacter is the primary cause of any of the reported diseases. In many cases, they would rather act opportunistically. This remains a significant concern, as a wide range of hosts are affected, and problems may intensify due to global warming. It is crucial to investigate these strains for plant pathogenicity and evaluate the risks to human health.}, }
@article {pmid41821176, year = {2026}, author = {Bıçakcı, G and Eren, &#xd6;}, title = {Main effects of ascorbic acid levels and organic acid type on physicochemical properties, microbial populations, texture, and biogenic amine formation in sucuk.}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.70568}, pmid = {41821176}, issn = {1097-0010}, support = {BAP - 2013.09.01.676//Bolu Abant &#x130;zzet Baysal University/ ; }, abstract = {BACKGROUND: Sucuk is a traditional Turkish dry fermented sausage, the quality and safety of which depend on physicochemical, microbiological, and biochemical changes during fermentation and ripening. Organic acids, their salts, and antioxidants such as ascorbic acid (AA) are widely used in fermented meat products; however, information about their main effects on quality attributes and microbial ecology in sucuk is limited. This study evaluated the main effects of AA levels (0, 500, and 1000 mg kg[-1]) and selected organic acids or salts (acetic, lactic, citric, and sorbic acids, and potassium sorbate; 1000 mg kg[-1]) on sucuk quality and safety.<br><br>RESULTS: The pH, moisture, protein, fat content, lipolysis, proteolysis, thiobarbituric acid (TBA) values, and color parameters were not affected significantly by treatments (P&#x2009;>&#x2009;0.05), whereas water activity was influenced significantly (P&#x2009;<&#x2009;0.05). Increasing AA levels were associated with higher nitrate concentrations, whereas other anions, cations, and biogenic amine content did not differ among treatments. Higher AA levels, as well as sorbic acid and potassium sorbate treatments, increased shear force, shear work, hardness, and chewiness (P&#x2009;<&#x2009;0.05). Lactic acid bacteria counts were affected significantly, whereas Micrococcus and Staphylococcus populations were not. Enterobacteriaceae and yeast and mold counts remained below the detection limit.<br><br>CONCLUSION: These results show that AA levels and organic acid or salt type influenced water activity, texture, and lactic acid bacteria populations selectively in sucuk without markedly affecting basic composition or biogenic amine content, providing practical guidance for improving microbial stability and technological quality in fermented sausages. &#xa9; 2026 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley &amp; Sons Ltd on behalf of Society of Chemical Industry.}, }
@article {pmid41820526, year = {2026}, author = {Chen, HL and Huang, JT and Guo, JJ and Wang, LS}, title = {Enteric nervous system in exercise physiology: a microbiota-neural interface.}, journal = {npj metabolic health and disease}, volume = {4}, number = {1}, pages = {}, pmid = {41820526}, issn = {2948-2828}, support = {2024MHBJ02//Bajian project of Minhang hospital/ ; }, abstract = {Exercise responses vary widely among individuals, yet the biological basis of this variability remains poorly understood. Microbiota-derived metabolites operate on timescales of hours to days, making them insufficient to explain rapid gastrointestinal and performance changes that emerge within minutes of exercise. We propose that the enteric nervous system (ENS) fills this regulatory gap by integrating mechanical, immune, and microbial signals in real time. We review evidence that the ENS modulates gut motility, barrier function, and microbial ecology during exercise, engages in bidirectional crosstalk with the microbiota, and relays gut-derived signals to muscle and brain via neural and humoral routes. We further introduce the concept of neuro-enteric phenotypes to account for inter-individual differences in exercise tolerance and adaptation.}, }
@article {pmid41819903, year = {2026}, author = {Miftari, H and Nikolovska Nedelkoska, D and Rampanti, G and Harasym, J and Ferrocino, I and Ferati, I and Cardinali, F and Orkusz, A and Milanović, V and Franciosa, I and Garofalo, C and Aquilanti, L and Osimani, A}, title = {A taste of North Macedonia: Seasonal variation in the microbiota, physico-chemical traits, and morpho-textural profile of a traditional brined raw goat's milk cheese.}, journal = {Food research international (Ottawa, Ont.)}, volume = {231}, number = {Pt 2}, pages = {118806}, doi = {10.1016/j.foodres.2026.118806}, pmid = {41819903}, issn = {1873-7145}, mesh = {*Cheese/microbiology/analysis ; Animals ; *Seasons ; Goats ; *Taste ; *Milk/microbiology/chemistry ; *Microbiota ; *Food Microbiology ; RNA, Ribosomal, 16S/genetics ; Salts/chemistry ; Food Handling/methods ; Bacteria/classification/genetics ; Hydrogen-Ion Concentration ; }, abstract = {This study provides a comprehensive characterization of a traditional Macedonian brined raw goat's milk cheese, focusing on how seasonal production (spring vs. autumn) shapes its physicochemical traits, morpho-textural properties, and microbial ecology. Cheese samples produced in autumn exhibited stronger acidification, higher titratable acidity, lower water activity, and higher NaCl content than spring cheeses, reflecting variability associated with artisanal, non-standardized processing. Texture profile analysis showed that cohesiveness and springiness were significantly affected by season, whereas hardness and adhesiveness remained comparable across batches. A combined culture-dependent and 16S rRNA gene-based metataxonomic approach revealed seasonally distinct microbiota. Viable microbial populations composed of mesophilic aerobes (up to 6.51 log cfu g[-1] at 60 days of ripening), presumptive mesophilic lactobacilli and lactococci (up to 6.51 and 7.18 log cfu g[-1] at 60 days of ripening, respectively), presumptive coagulase-negative and coagulase-positive staphylococci (up to 6.97 and 1.76 log cfu g[-1] at 60 days of ripening, respectively), and Enterobacteriaceae (up to 1.25 log cfu g[-1] at 60 days of ripening) were detected. Spring cheeses were characterized by higher relative abundances of Carnobacteriaceae, Enterococcus, Serratia, and Tetragenococcus halophilus, whereas autumn cheeses were dominated by Companilactobacillus and Lactococcus, alongside various Enterobacteriaceae. Beta-diversity analysis confirmed significant clustering of cheese microbiota by season. In total, 134 lactic acid bacteria isolates were obtained from the dairy environment, milk, brine, and cheese. These included Lactococcus lactis, Levilactobacillus brevis, multiple Enterococcus species, Pediococcus pentosaceus, Lacticaseibacillus paracasei, Marinilactibacillus psychrotolerans, and Companilactobacillus alimentarius. Many isolates showed strong proteolytic activity, several produced exopolysaccharides, and a subset exhibited lipolytic capacity, underscoring their technological potential. Screening for the histidine decarboxylase gene hdcA revealed that only the C. alimentarius isolate was positive, excluding this strain from consideration as an adjunct culture, whereas all other isolates were hdcA-negative and therefore suitable candidates from a histamine-safety perspective. Overall, this integrated analysis highlights the rich microbial diversity and seasonal variability of this artisanal cheese and supports the selection of safe autochthonous lactic acid bacteria for future product valorization.}, }
@article {pmid41818334, year = {2026}, author = {Tong, C and Yu, R and Hu, A and Dong, R and Yang, W}, title = {Manure source distance and soil depth: a natural screening system for nutrient-solubilizing bacteria.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxag072}, pmid = {41818334}, issn = {1365-2672}, abstract = {AIMS: To develop and validate an ecology-driven strategy that leverages natural manure-soil depth gradients as a screening system for the targeted isolation of nutrient-solubilizing bacteria (NSB) with high biofertilizer potential.<br><br>METHODS: A full-factorial sampling design was implemented across gradients of distance-from-manure (5 points, 8-m intervals) and soil depth (0-20, 20-40, 40-60 cm) in a coconut plantation. Culturable bacteria were isolated using a culture-dependent approach on a nutrient-rich medium, identified via 16S rRNA gene sequencing, and functionally screened in vitro for nitrogen fixation, phosphate solubilization (PS), and potassium solubilization (KS) capabilities.<br><br>RESULTS: Manure input and soil depth interacted to form a heterogeneous soil nutrient landscape, with available phosphorus (AP) identified as the most influential environmental factor shaping the bacterial community. Phosphate-solubilizing bacteria (PSB) were significantly enriched in low-P habitats, verifying the niche-based selection of functional bacteria. This gradient-based screening strategy enabled the targeted recovery of multifunctional NSB strains (e.g., Klebsiella and Enterobacter) with concurrent nitrogen fixation, phosphate and potassium solubilization capacities, which were isolated from specific microhabitats including deep, nutrient-depleted soil layers.<br><br>CONCLUSIONS AND IMPLICATIONS: This study demonstrates that intersecting manure and soil depth gradients form a powerful, predictable natural screening system for the targeted isolation of beneficial bacteria. This ecology-driven strategy effectively links microbial ecology to bioprospecting. It provides a curated library of isolates with defined ecological origins and a predictive framework for developing customized biofertilizers, thereby enhancing microbial resource mining efficiency and contributing to sustainable agriculture.}, }
@article {pmid41816689, year = {2026}, author = {Jian, Z and Qian, Y and He, S and Zhao, R and Li, K and Cha, J and Ning, Z and Ye, Y and Bao, Z and Wang, K and Ge, C and Jia, J and Dou, T and Hu, Y and He, X and Zi, X}, title = {The gut resistome in poultry production: microbial ecology, antibiotic use, and sustainable control approaches.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1768747}, pmid = {41816689}, issn = {1664-302X}, abstract = {Antibiotics remain central to modern poultry production, but their long-term and sometimes poorly managed use has markedly altered gut microbial ecology, effectively transforming the intestine into a substantial reservoir of antibiotic resistance genes (ARGs). In poultry, the composition of ARGs reflects not only resistant bacterial taxa but also the activity of mobile genetic elements, shifts in gut metabolic conditions, and features of the surrounding production system. This review synthesizes current understanding of both the structural and functional features of the poultry resistome, with particular attention to key bacterial hosts and the mobile genetic elements they carry. We further evaluate how different antibiotic-use patterns and additional co-selective pressures alter microbial communities and contribute to the persistence of ARGs. We also delineate the major transmission pathways that link breeder flocks, hatcheries, production facilities, and manure management, and interpret these connections within a One Health perspective. Particular emphasis is placed on microbial and nutritional interventions that influence gut microbial interactions, epithelial barrier integrity, and metabolic signaling. Drawing on these findings, we propose a resistome-microbiome-metabolome axis that links microbial taxa, resistance elements, and key metabolic signals, offering a conceptual framework for developing more targeted antimicrobial resistance mitigation strategies in poultry systems.}, }
@article {pmid41815892, year = {2025}, author = {Avouris, DM and Maciel, F and Sharp, SL and Craig, SE and Dekker, AG and Di Vittorio, CA and Gardner, JR and Goldsmith, E and Gossn, JI and Greb, SR and Grunert, BK and Gurlin, D and Jampani, M and Khan, RM and Lowin, B and McKinna, L and Mouw, CB and Ogashawara, I and Calle, SR and Salls, W and Sánchez-Cabeza, JA and Schaeffer, B and Seegers, BN and Silander, J and Smail, EA and Wang, M and Werdell, J}, title = {Advancements in Satellite Observations of Inland and Coastal Waters: Building Towards a Global Validation Network.}, journal = {Remote sensing}, volume = {17}, number = {24}, pages = {4008}, pmid = {41815892}, issn = {2072-4292}, support = {EPA999999/ImEPA/Intramural EPA/United States ; }, abstract = {The use of satellite-based remote sensing imagery for water quality monitoring of inland and coastal waters has become widespread over the last few decades, with the expansion of, and investment in, operational Earth-observing missions. Satellite-based sensors are uniquely suited to provide synoptic, system-wide water quality parameter estimates that supplement traditional field-based sampling methods. The remote sensing of water quality parameter estimates is particularly valuable in systems with high temporal and spatial variability, as well as in areas that are difficult to access, or where agencies lack funding for routine monitoring. However, optically complex inland and coastal waters pose additional challenges for developing robust remote sensing retrieval models for optical properties and water quality parameters. One of the biggest challenges is collecting high quality field measurements that are used to calibrate and validate the retrieval algorithms. Here, we present the current status of satellite missions, field methods that include instruments used and commonly measured parameters, and repositories of historical field data that are relevant to inland and coastal water studies. We then present data requirements for model validation and highlight gaps in validation coverage. Finally, we provide considerations for future field campaigns to improve coordination with remote sensing data collection and ensure that field data is well suited for use in model or algorithm development.}, }
@article {pmid41814632, year = {2026}, author = {Ferreti, JD and Ribeiro, B and Bonetti, JA and Camargo, LEA and Creste, S and Kuramae, EE and Monteiro-Vitorello, CB}, title = {Soil and Genotype Shape the Sugarcane Phytobiome for Enhanced Environmental Adaptation.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70314}, doi = {10.1111/1758-2229.70314}, pmid = {41814632}, issn = {1758-2229}, support = {2022/03962-7//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 405314/2021-3//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 305961/2017-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {*Saccharum/microbiology/genetics/growth &amp; development ; *Soil Microbiology ; Genotype ; *Soil/chemistry ; *Bacteria/genetics/classification/isolation &amp; purification ; *Microbiota ; *Adaptation, Physiological ; Transcriptome ; }, abstract = {Soil properties critically shape sugarcane growth and its microbiome, yet their influence on gene expression remains unclear. We investigated the combined effects of soil type (clayey and sandy loam) and sugarcane genotype (IACSP-5503 and IACSP-6007) on microbiome composition and plant transcriptional profiles. Bacterial communities from soils and stalk tissues, as well as transcriptomes of 48-h sprouted buds grown for 10 months, were analysed. Results showed that IACSP-5503 (adapted to low-fertility soils) and IACSP-6007 (less adapted) recruited endophytic microbiota in a soil-genotype-dependent manner. In sandy loam, IACSP-5503 promoted diverse plant growth-promoting bacteria (PGPB) (including Burkholderia, Leifsonia and Mycobacterium), associated with nitrogen fixation, hormone production and stress tolerance, while IACSP-6007 displayed reduced PGPB diversity and transcriptomic signatures of nutrient deficiencies. Conversely, in clayey soil, IACSP-6007 recruited more PGPBs (such as Pseudomonas, Bacillus and Klebsiella) linked to nutrient acquisition and defence responses. Both genotypes exhibited enhanced expression of defence- and antioxidant-related genes in clayey soil, suggesting priming effects. Overall, our findings reveal soil-dependent, genotype-specific microbial recruitment strategies, particularly in IACSP-5503, reflecting adaptive responses to nutrient-poor conditions. The combined 16S metataxonomic and transcriptome data offered insights into how soil and genotype shape microbial recruitment and transcriptional plasticity in sugarcane.}, }
@article {pmid41821950, year = {2025}, author = {De León, ME and Fox, EGP and Dunaj, S and Jenner, RA and Keiser, CN and Macrander, J and Nixon, SA and Nobile, CJ and Petras, D and Rodriguez-Roman, E and Saviola, AJ and Trim, SA and Varona, NS and Yeager, J and Ul-Hasan, S and Herzig, V and Colston, TJ}, title = {A review of the venom microbiome and its utility in ecology and evolution including future directions for emerging research.}, journal = {Symbiosis (Philadelphia, Pa.)}, volume = {95}, number = {1}, pages = {3-27}, pmid = {41821950}, issn = {0334-5114}, abstract = {Microbes play vital roles in ecological systems, yet their presence and functions within venom environments of venomous organisms remain understudied. Despite the prevalent belief in the sterility of venoms, recent findings reveal diverse microbial communities within venom systems. This review aims to explore the relationships between venoms and microbes, highlighting their potential roles in evolutionary processes, ecological interactions, and therapeutic advancements. Venoms, composed of toxins utilized in hunting or defense, represent a rich source of natural products with applications in drug discovery and therapy, exemplified by FDA-approved venom toxin-derived drugs. Understanding microbial resistance mechanisms against antimicrobial peptides can illuminate coevolutionary processes and guide therapeutic development. Integrating hologenomic evolution and microbial ecology frameworks will facilitate comprehensive research on venom-microbiome interactions, and reveal the evolutionary drivers of venom diversification. Investigating and investing in these relationships promises advancements in understanding evolution, ecology, and biotechnology, with implications for human health and ecological conservation. This review synthesizes existing knowledge, identifies many gaps in literature, and investigates critical unanswered questions in the field of venom microbiology, encouraging ongoing and future collaborative research.}, }
@article {pmid41813906, year = {2026}, author = {Vass, M and Abramova, A and Bengtsson-Palme, J}, title = {Antimicrobial resistance dissemination via horizontal gene transfer is constrained in stratified waters.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-09857-8}, pmid = {41813906}, issn = {2399-3642}, support = {KAW 2020.0239//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; KAW 2020.0239//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; 2024-05922//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; }, abstract = {Aquatic ecosystems are major reservoirs of antibiotic resistance genes (ARGs) and hubs for microbial interactions that can facilitate their spread through horizontal gene transfer (HGT). While mobile genetic elements (MGEs), including plasmids and viruses, are recognized as important drivers of ARG mobility, the extent to which water column stratification constrains their vertical dissemination remains unresolved. Here, we analysed depth-resolved metagenomic data from stratified freshwater and marine systems to assess the role of HGT in ARG spread. We found that ARG diversity is consistently lower in marine than freshwater environments and that only a small fraction of ARGs is mobilized by plasmids and viruses. Importantly, we detected no evidence for recent HGT-mediated dissemination of ARGs across depth layers, despite genetic compatibility among co-occurring bacteria. Instead, ARGs appear largely confined to lineage-specific inheritance and within-layer persistence. These findings suggest that stratification acts as a barrier, limiting vertical ARG transfer while promoting within-layer accumulation. Given projections of intensified and prolonged stratification under climate change, our results imply reduced vertical connectivity of ARGs in aquatic environments, with potential consequences of further mitigation in its dynamics by water stratification.}, }
@article {pmid41812564, year = {2026}, author = {Defoirdt, T}, title = {Interfering with the response of bacterial pathogens to host substances: An unexplored strategy to control bacterial diseases in aquaculture.}, journal = {Microbiological research}, volume = {308}, number = {}, pages = {128492}, doi = {10.1016/j.micres.2026.128492}, pmid = {41812564}, issn = {1618-0623}, abstract = {Bacterial infections represent a significant challenge in aquaculture, and the widespread use of antibiotics has accelerated the development of resistance, diminishing their efficacy and posing serious global public health concerns. Antivirulence therapy, disarming pathogens rather than killing them or inhibiting their growth, offers a promising alternative approach as it exerts reduced selective pressure on pathogens, thereby limiting the spread of resistance. Targeting the response of pathogens to host substances, molecules typically produced by host organisms, is an unexplored strategy for the development of novel disease control agents for aquaculture. Bacterial aquaculture pathogens have been shown to respond to host substances such as catecholamines, mucin, and bile acids and salts, leading to increased production of virulence factors (molecules or cell structures that enable pathogens to cause disease), and increased virulence to aquatic animals. This paper provides an overview of the impact of these host substances on the virulence of bacterial aquaculture pathogens and of currently known methods to interfere with this in order to control disease.}, }
@article {pmid41811973, year = {2026}, author = {Martin, AN and Stuligross, C and Williams, NM and Noroian, HM and Vannette, RL}, title = {Floral microbes provisioned by Osmia lignaria establish in larval food stores, but do not affect bee development or survival.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiag025}, pmid = {41811973}, issn = {1574-6941}, abstract = {Microbial dispersal and subsequent establishment among linked habitats can be used to examine drivers of community assembly and function. Flowers host microbial communities that can be acquired and vectored by bees to new flowers, establish within the adult bee gut, and enter food stores (e.g. pollen provisions) of developing larvae. Yet, whether microbes vectored by insects or applied for biocontrol can establish across these habitats and if they affect bee fitness remain unknown. Here, we applied microbes to flowers visited by blue orchard bees (Osmia lignaria) and compared microbial communities in flowers, adult bee guts, and pollen provisions before and after inoculation to determine microbial establishment, environmental filtering, and overlap across habitat types. We also inoculated provisions with microbes to test their effects on larval survival, development, and weight. Experimentally inoculated microbes were detected in all habitats, demonstrating that flowers are a source of microbial acquisition for adult and larval bees; however, the tested larval health metrics were largely unaffected by microbe supplementation.}, }
@article {pmid41811506, year = {2026}, author = {Cervera, L and Álvarez-Torres, D and Barreto-Bailet, M and Béjar, J and Cuesta, A and Martín, MV and Jerez, S and Chaves-Pozo, E}, title = {Diagnosis of Betanodavirus Infection in the Gonad of Greater Amberjack Broodstocks Shows a Sex-Biased Infection and Immune Responses.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02733-2}, pmid = {41811506}, issn = {1432-184X}, }
@article {pmid41810611, year = {2026}, author = {Rigali, S}, title = {When, where, and why specialised metabolites are produced: inferring function from expression control.}, journal = {Essays in biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1042/EBC20250024}, pmid = {41810611}, issn = {1744-1358}, support = {NA//Fonds De La Recherche Scientifique - FNRS (FNRS)/ ; }, abstract = {Although some microbial compounds have been repurposed for human use, microorganisms did not evolve their specialised metabolites with us in mind. Many natural products likely possess hidden activities, while others may be exploited in ways that ignore their most biologically relevant roles. Uncovering the true function of these compounds is essential not only for understanding microbial interactions in native environments but also for unlocking their most appropriate use. To facilitate prioritisation in discovering new natural products, computational tools have been developed to predict the function of compounds hidden in cryptic biosynthetic gene clusters. Yet beyond in silico predictions, understanding when, where, and why metabolites are produced is critical for both fundamental biology and targeted discovery. After all, what nature chooses to activate at a specific time or condition tells us what it is really for. Based on the principle 'function follows regulation', it is no coincidence that expression of metal chelators, phytotoxins, pigments, and antibiotics is controlled by metal availability, plant byproducts, radiations, and competitor sensing, respectively. Likewise, metabolite localisation and production timing also provide clues to function such as intracellular antiproliferative agents coordinating programmed cell death or pigments protecting against oxidative stress. These controlled expression patterns suggest a strategic approach for natural product discovery: focusing on culture conditions that mimic the environmental or developmental contexts under which metabolites are needed for the producer. Integrating expression control information offers a predictive framework to guide experimental design, increases the likelihood of identifying compounds with meaningful ecological roles, and anticipates their applications.}, }
@article {pmid41806463, year = {2026}, author = {Atasever, &#xdc;}, title = {Bile acid-microbiota interactions in multiple sclerosis: From experimental models to early clinical evidence.}, journal = {Journal of neuroimmunology}, volume = {415}, number = {}, pages = {578898}, doi = {10.1016/j.jneuroim.2026.578898}, pmid = {41806463}, issn = {1872-8421}, abstract = {This article examines the bidirectional relationship between bile acid metabolism and the intestinal microbiota and explores how disruptions in this interaction may contribute to the pathophysiology of multiple sclerosis. Bile acids are presented not merely as digestive end-products but as bioactive signaling molecules capable of regulating immune responses, maintaining epithelial and neural homeostasis, and influencing neuroinflammatory processes. Experimental work demonstrates that alterations in microbial composition affect bile acid diversity and circulation, while bile acids themselves shape gut microbial ecology through antimicrobial and signaling mechanisms. In preclinical models, specific bile acid species modulate the balance between pro-inflammatory and regulatory immune cells, suppress harmful activation states in astrocytes and microglia, and reduce neuroinflammation. Human studies show consistent disturbances in circulating bile acid profiles in individuals with multiple sclerosis, with some patterns associated with increased disability progression and markers of neurodegeneration. Early clinical interventions also indicate that therapeutic modulation of bile acid pathways is feasible and biologically active, although clinical efficacy remains to be established. Overall, the article highlights bile acid-microbiota interactions as a unifying conceptual framework linking environmental influences, metabolic status, immune dysregulation, and central nervous system injury. By integrating evidence from experimental models and emerging clinical observations, the authors propose that this metabolic and microbial axis may serve both as a source of novel biomarkers and as a target for future disease-modifying therapies.}, }
@article {pmid41757095, year = {2026}, author = {Wang, F and Holmes, AJ and Browne, GV and He, X and Bockmann, MR and Davis, KM and Hughes, TE and Adler, CJ}, title = {Ecological and evolutionary dynamics of the oral microbiome across childhood.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41757095}, issn = {2692-8205}, abstract = {Childhood represents a critical period for oral microbiome development, yet evolutionary trajectories and the relative roles of host and environment remain unclear. Using a large longitudinal metagenomic dataset of 920 samples from a twin cohort spanning the first decade of life, we characterised microbial shifts and population dynamics of key bacterial groups. Microbiome diversity was initially reduced and highly heterogeneous and became increasingly complex and convergent with age. Microbial community state was associated with developmental age, environment and in late childhood was surprisingly strongly associated with host genotype. Strain-level analyses revealed species-specific temporal patterns of genetic variation particularly within Streptococcus, reflecting adaptive responses to host and environmental pressures. Fusobacterium exhibited consistently high replication rates, indicating sustained growth dynamics. Phylogenetic reconstruction further revealed host and niche specific genomic diversification of Saccharibacteria lineages. These findings establish childhood as a decisive period of oral microbial evolution and highlight the role of host-microbiome and epithelial interactions in shaping community structure, providing guidance for oral management strategies that promote lifelong oral health.}, }
@article {pmid41665259, year = {2025}, author = {Gaisin, VA and Hadjicharalambous, C and Mujakić, I and Villena-Alemany, C and Li, J and Koblížek, M and Pilhofer, M}, title = {Thermophilic bacteria employ a contractile injection system in hot spring microbial mats.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, doi = {10.1093/ismejo/wrag021}, pmid = {41665259}, issn = {1751-7370}, support = {CZ.02.01.01/00/22_008/0004624//OP JAK project Photomachines/ ; CoG 101000232/ERC_/European Research Council/International ; }, mesh = {*Hot Springs/microbiology ; RNA, Ribosomal, 16S/genetics ; *Chloroflexi/genetics/physiology/classification/metabolism ; Cryoelectron Microscopy ; Phylogeny ; Metagenomics ; *Bacteria/genetics ; Computational Biology ; Proteomics ; }, abstract = {Bacterial contractile injection systems (CISs) are multiprotein complexes that facilitate the bacterial response to environmental factors or interactions with other organisms. Multiple novel CISs have been characterised in laboratory bacterial cultures recently; however, studying CISs in the context of the native microbial community remains challenging. Here, we present an approach to characterise a bioinformatically predicted CIS by directly analysing bacterial cells from their natural environment. Using cryo-focused ion beam milling and cryo-electron tomography (cryoET) imaging, guided by 16S rRNA gene amplicon sequencing, we discovered that thermophilic Chloroflexota bacteria produce intracellular CIS particles in a natural hot spring microbial mat. We then found a niche-specific production of CIS in the structured microbial community using an approach combining metagenomics, proteomics, and immunogold staining. Bioinformatic analysis and imaging revealed CISs in other extremophilic Chloroflexota and Deinococcota. This Chloroflexota/Deinococcota CIS lineage shows phylogenetic and structural similarity to previously described cytoplasmic CIS from Streptomyces and probably shares the same cytoplasmic mode of action. Our integrated environmental cryoET approach is suitable for discovering and characterising novel macromolecular complexes in environmental samples.}, }
@article {pmid41806051, year = {2026}, author = {Tomachewski, D and Souza, RF and Lammel, DR and Schiebelbein, LM and Galvão, CW and Ribeiro, MF and Karas, LP and Galvão, F and Baura, VA and Rillig, MC and Etto, RM}, title = {Tree diversity shapes soil bacterial community structure under low abiotic heterogeneity in the Atlantic forest.}, journal = {Archives of microbiology}, volume = {208}, number = {5}, pages = {}, pmid = {41806051}, issn = {1432-072X}, }
@article {pmid41806036, year = {2026}, author = {You, JH and Jeong, HJ and Park, SA and Kwon, H and Eom, SH and Kwon, M and Kang, NS}, title = {Feeding and growth of the new mixotrophic dinoflagellate Gymnodinium sp. GSTY2405 and the prey spectrum extension of its sister species Gymnodinium smaydae.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02739-w}, pmid = {41806036}, issn = {1432-184X}, support = {RS-2024-00452214//National Research Foundation of Korea/ ; RS-2021-NR058847//National Research Foundation of Korea/ ; 2026M00200//National Marine Biodiversity Institute of Korea/ ; }, }
@article {pmid41806019, year = {2026}, author = {Su, ZZ and Hou, Y and Lin, JJ and Duan, YF and Obeten, AU and Dong, S and Huang, Q and Huang, H and Pan, Z}, title = {Extracellular vesicles from biofilm and planktonic Pseudomonas aeruginosa: proteomic profiles, iron chelation and functional Implications.}, journal = {Archives of microbiology}, volume = {208}, number = {5}, pages = {}, pmid = {41806019}, issn = {1432-072X}, }
@article {pmid41805951, year = {2026}, author = {López-Puentes, D and Ojeda-Pérez, ZZ and Arias-Moreno, DM}, title = {Metagenomic Insights into the Microbial Composition and Functional Potential of Cocoa (Theobroma Cacao L.) During Fermentation and Drying in Colombia.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02704-7}, pmid = {41805951}, issn = {1432-184X}, }
@article {pmid41805181, year = {2026}, author = {Wallnisch, JL and Wünschmann, T and Baborski, A and Rau, M and Refisch, A and Opel, N and Allen, RJ and Busch, A}, title = {Draft genome of an Escherichia coli gut isolate from a sertraline-treated patient suggests potential antibiotic resistance induction.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0108725}, doi = {10.1128/mra.01087-25}, pmid = {41805181}, issn = {2576-098X}, abstract = {The draft genome of Escherichia coli ADAR08_002, from feces of a patient with major depressive disorder (MDD) treated long-term with sertraline, is 5,247,898 bp (GC 50.65%) in 273 contigs (N50 153,410 bp). It harbors mobile elements and antibiotic resistance, persistence, and metabolic adaptation genes, serving as a resource to study antidepressant impacts.}, }
@article {pmid41805117, year = {2026}, author = {Chen, S and Li, C and Wang, Z and Teng, Y and Ren, W and Wang, H and Ma, J and Ma, W and Luo, Y and Kuramae, EE}, title = {Specific Metabolites Modulate Core Microbes and Microbial Interactions to Drive Fomesafen Dissipation in the Soybean Rhizosphere.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c15254}, pmid = {41805117}, issn = {1520-5118}, abstract = {Rhizosphere metabolites regulate organic pollutant dissipation through microbiome modulation, yet dynamic interrelationships among metabolite shifts, microbial assembly, and pollutant removal remain unclear. Using multiomics (16S rRNA sequencing, metabolomics, and metagenomics), this study deciphered the temporal dynamics of rhizosphere metabolites and microbiome during the dissipation of fomesafen in soybean pots. Fomesafen dissipation exhibited biphasic kinetics during soybean growth, with an initial rapid phase followed by prolonged stabilization, which was synchronized with time-dependent microbiome perturbations of initial enrichment and subsequent attenuation. Metabolomics revealed fomesafen-induced shifts in rhizosphere metabolites, with 2-naphthalenesulfonic acid (↓20.84%) and 2-hydroxyoctadecanoic acid (↑13.30%) exhibiting opposing effects on microbial assembly, which ultimately affect fomesafen dissipation, as outlined in our conceptual model. Microcosm experiments further demonstrated 2-naphthalenesulfonic acid enhanced while 2-hydroxyoctadecanoic acid inhibited fomesafen dissipation. Our findings highlight the significance of rhizosphere metabolite-mediated interactions between core microbes and potential fomesafen-degraders in governing fomesafen dissipation.}, }
@article {pmid41803472, year = {2026}, author = {da Silva Figueiredo, MI and Mello, IS and de Guimarães Bueno, L and Mendes, RRW and Dos Santos Almeida, JM and Eriksson, A and da Silva, GF and Soares, MA}, title = {Lactic acid bacteria isolated from mammalian feces exhibit distinct diversity and probiotic traits.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {3}, pages = {}, pmid = {41803472}, issn = {1573-0972}, }
@article {pmid41803467, year = {2026}, author = {Struk, M and Sakarika, M and Estévez, &#xc1; and Ganigué, R and Rabaey, K}, title = {Growth and protein content of Cupriavidus necator on organic acids derived from fermented grey starch.}, journal = {Applied microbiology and biotechnology}, volume = {110}, number = {1}, pages = {}, pmid = {41803467}, issn = {1432-0614}, support = {No. 101081776//European Union's Horizon Europe research and innovation programme/ ; BOF.PDO.2025.0007.01//Ghent University/ ; BOF.BAF.2024.0502.01//Special Research Fund of Ghent University/ ; }, abstract = {Grey starch (GS) is a byproduct of potato processing and is conventionally valorised as low-grade animal feed or for biogas generation. In this manuscript, we systematically investigate the mixed culture fermentation of GS to organic acids and their subsequent aerobic upgrading to microbial protein via Cupriavidus necator. We focused on protein content, growth kinetics, biomass yield on individual, and mixed organic acids (C1-C6), using both synthetic media and real fermented effluents. High-throughput cultivation in microtiter plates was employed to evaluate performance across both straight-chain forms and isoforms of the acids. C. necator demonstrated growth on all tested individual substrates, although with distinct individual behaviour. Lactate, butyrate, and hexanoate supported the highest biomass yields, reaching up to 0.24 gCDW/gCOD (grammes of cell dry weight per grammes of COD fed). Lactate enabled the highest specific growth rate (0.6 h[-1]) with 29 ± 4% of protein. The maximum protein content (70 ± 11%) was observed on acetate at an initial concentration of 2 g/L. Depending on the acid, higher initial concentrations (2 and 4 g/L) led to increased cell dry weight but reduced growth rates or inhibition in some cases. Real fermented GS, primarily composed of lactate and butyrate, proved to be a viable substrate for microbial protein production. Undiluted fermented GS yielded the highest protein content (70 ± 9%), while a 1/4 dilution (2.6 gCOD/L) enabled the fastest growth (0.84 h[-1]) compared to all tested fermented GS and acid concentrations. These findings highlight the potential of GS-derived organic acids as feedstock for microbial protein production for feed and food. KEY POINTS: C. necator grows on all tested individual organic acids (C1-C6). Protein production varies by acid type and initial concentration. Grey starch was converted to organic acids for microbial protein production.}, }
@article {pmid41802809, year = {2026}, author = {Jin, N and Sul, WJ and Do, HR and Kim, HS}, title = {ITS1-based profiling of the skin mycobiome in truncal acne reveals altered baseline ecology and heterogeneous doxycycline-associated patterns.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {64}, number = {2}, pages = {e2512013}, doi = {10.71150/jm.2512013}, pmid = {41802809}, issn = {1976-3794}, support = {2023R1A2C1007759//National Research Foundation of Korea/ ; //Korea Health Industry Development Institute/ ; RS-2023-KH-136575//Ministry of Health and Welfare/ ; RS-2025-02217860//Ministry of Health and Welfare/ ; //Incheon St. Mary's Hospital/ ; //Catholic University of Korea/ ; }, mesh = {Humans ; *Doxycycline/therapeutic use/pharmacology ; *Acne Vulgaris/microbiology/drug therapy ; *Skin/microbiology ; *Mycobiome/drug effects/genetics ; Female ; Male ; Malassezia/genetics/isolation &amp; purification/classification/drug effects ; Adult ; DNA, Ribosomal Spacer/genetics ; Young Adult ; *Fungi/genetics/classification/isolation &amp; purification/drug effects ; Anti-Bacterial Agents/therapeutic use ; DNA, Fungal/genetics ; }, abstract = {Truncal acne represents a biologically distinct manifestation of acne vulgaris, yet its fungal ecology remains incompletely characterized. Previous work using internal transcribed spacer 2 (ITS2) sequencing suggested that truncal acne is associated with altered fungal richness and Malassezia species composition; however, fungal marker choice may influence ecological inference, particularly in sebaceous skin dominated by Malassezia. In this study, we characterized the truncal skin mycobiome of patients with truncal acne and healthy controls using internal transcribed spacer 1 (ITS1) amplicon sequencing. Skin swabs were collected from the upper back, and fungal communities were analyzed using QIIME 2 with taxonomic assignment against the UNITE v10.0 database. Baseline acne-control differences and doxycycline-associated patterns were evaluated using alpha- and beta-diversity metrics and differential abundance analyses. Doxycycline-associated patterns were assessed using paired, within-patient pre- and post-exposure comparisons. ITS1 profiling demonstrated that truncal acne was associated with altered baseline fungal ecology compared with controls, characterized by reduced alpha diversity and ASV-level differences within Malassezia-dominated communities. Beta-diversity analyses showed substantial overlap between acne and control samples, indicating limited global separation. Following doxycycline exposure, fungal communities remained Malassezia-dominant and did not demonstrate uniform convergence toward control profiles; instead, species- and ASV-level differences were heterogeneous across individuals and exposure durations. Together with prior ITS2-based findings, these results underscore the importance of marker-dependent perspectives when interpreting fungal ecology in sebaceous skin.}, }
@article {pmid41802390, year = {2026}, author = {Mondal, A and Parvez, SS and Bera, D and Alam, M and Banik, A}, title = {Trichoderma in multitrophic plant-microbe interactions: a pan-genome guided roadmap for resilient physiology and sustainable bio-economy.}, journal = {Plant physiology and biochemistry : PPB}, volume = {232}, number = {}, pages = {111193}, doi = {10.1016/j.plaphy.2026.111193}, pmid = {41802390}, issn = {1873-2690}, abstract = {By 2050, the global population is projected to reach 9 billion, necessitating innovative approaches beyond traditional agricultural methods to ensure adequate food security. Several biological control agents have been used throughout the world to control plant diseases by re-programming natural prey-predator interactions. Trichoderma's biocontrol capabilities and plant growth-promoting effects have been extensively studied and documented, paving the way for its widespread adoption in agricultural practices. Here we performed a comprehensive pan-genome analysis of 25 industrially and agriculturally important Trichoderma strains, revealing an open pan-genome indicative of continuous genetic innovation. A combined total of 4960 core genes were shared between both industrial and biocontrol strains, which encode for fundamental functions with accessory and unique genes being enriched in adaptive functions. Industrial strains like T. reesei QM6a with 322 unique genes had enrichment of features for secretion of cellulase and lignocellulose degradation, validating their commercial dominance in industries producing enzymes and biofuels, while biocontrol-associated strains like T. harzianum CBS226.95 and T. virens Gv29-8 showed expanded accessory gene repertoires enriched in defense-related functions and secondary metabolism. Comparative biosynthetic gene cluster analysis across 25 genomes further demonstrated pronounced strain-level variation. Core-genome phylogeny revealed conserved ancestral relationships, whereas pan-genome phylogeny highlighted accessory gene-driven divergence among closely related strains. Remarkably, many strains had dual promise, being both industrial producers of enzymes and agriculturally desirable, highlighting their interdisciplinary applications. These results demonstrate the genomic malleability of Trichoderma and the adaptability of its evolution, facilitating agriculture and biotechnology, and provide a template for strain selection with precision and rational bioformulation design for promoting sustainable agriculture, environmental robustness, and green industry.}, }
@article {pmid41800395, year = {2026}, author = {Li, J and Xiao, D and Gigena, ML and Wang, M and Li, P and Fu, R and Toure, MAM and Li, F}, title = {Dataset of microbial community evolution in synthetic black-clay-based soils during ecological reconstruction.}, journal = {Data in brief}, volume = {65}, number = {}, pages = {112593}, pmid = {41800395}, issn = {2352-3409}, abstract = {Ecological reconstruction of mine dump sites in cold-region environments is frequently constrained by limited availability of natural topsoil and harsh climatic conditions that hinder soil development and biological succession. In such settings, artificial soils derived from mineral substrates are increasingly used as alternatives to surface soil; however, their biological maturation relies strongly on microbial community establishment and evolution. This data article presents a microbial diversity dataset derived from black-clay-based artificial soils applied in a mine dump restoration system located in a cold and arid desert grassland. Soil samples were collected from restoration zones subjected to different microbial inoculation regimes, including full-process application of an ecological restoration bacteria consortium, single application, and untreated controls. To capture spatial and vertical heterogeneity, samples were obtained independently from upper aerobic layers and lower anaerobic layers across multiple sampling batches corresponding to different restoration stages. Microbial community composition was characterized using high-throughput sequencing of the bacterial 16S rRNA gene, generating raw sequence reads and a suite of processed datasets. These include taxonomic abundance tables, alpha- and beta-diversity metrics, distance matrices, hierarchical clustering outputs, shared operational taxonomic unit profiles, ecological niche breadth indices, beta-deviation measurements, and core community identification based on prevalence criteria. Network topology metrics derived from Zi-Pi analysis are also provided to support structural assessments of microbial associations. In addition, functional profiles were inferred from 16S rRNA gene data using PICRUSt2, producing pathway- and category-level functional prediction tables. All data files are organized with standardized metadata and fully documented analytical parameters to facilitate independent reuse. This dataset supports reanalysis of microbial community assembly, stratification, and temporal variation in artificial soil systems and can be applied in comparative studies, methodological benchmarking, and synthesis efforts related to mine-site restoration, artificial soil development, and microbial ecology in cold-region environments.}, }
@article {pmid41799378, year = {2026}, author = {Kaur, M and Babu, R and Baweja, S and Gupta, R and Singh, SP and Pamecha, V and Bihari, C}, title = {Human Leukocyte Antigen Alleles and Oral Microbiome Association With Antibody-mediated Rejection in Living-donor Liver Transplant Patients.}, journal = {Journal of clinical and experimental hepatology}, volume = {16}, number = {3}, pages = {103494}, pmid = {41799378}, issn = {0973-6883}, abstract = {BACKGROUND/AIMS: Antibody-mediated rejection (ABMR) is an important cause of graft dysfunction after liver transplantation, yet the combined influence of human leukocyte antigen (HLA) immunogenetics and the oral microbiome on ABMR risk is not well defined.<br><br>METHODS: In this prospective cohort of 180 living donor-recipient pairs, pre-transplant 16S ribosomal ribonucleic acid sequences and high-resolution HLA genotyping were done. The human leukocyte antigen epitope mismatch algorithm quantified amino acid and solvent-accessible mismatches. Oral microbiome profiles were generated using the Divisive Amplicon Denoising Algorithm (DADA2) and quantitative insights into microbial ecology version 2 (QIIME2). Associations between HLA alleles and microbial taxa were assessed using generalized linear models and linear discriminant analysis effect size (LEfSe). ABMR was diagnosed as per Banff criteria over one year.<br><br>RESULTS: ABMR was diagnosed in 15 patients. These patients had significantly higher mismatch burdens at HLA-DPB1, DQB1, and DRB1 than non-ABMR recipients. Across the cohort, 68 HLA alleles demonstrated distinct microbial associations at phylum, family, and genus levels. Alleles such as HLA-DRB108, HLA-DPB1575, and HLA-C05 were linked to differential abundance of Actinobacteriota, Campylobacterota, and Fusobacteriota, respectively. Genus-level analyses revealed strong allele-specific associations with Veillonella, Enterobacter, Streptococcus, and other immunomodulatory taxa. LEfSe identified HLA-DQB106 and HLA-DQB1&#x2217;104 as associated with enrichment of Enterobacter, Citrobacter europaeus, Bacteroides plebeius, Rothia dentocariosa, Megasphaera, and Burkholderiaceae-microbial signatures also prominent in ABMR cases.<br><br>CONCLUSION: Class II HLA mismatch burden and allele-specific oral microbial signatures are closely linked to ABMR. Combined HLA-microbiome profiling may enhance early risk stratification and inform targeted peri-transplant microbial interventions.}, }
@article {pmid41799257, year = {2026}, author = {Zhao, Y and Ren, Z and Xu, Q and Zhu, T and Hu, H and Fu, Y and Jiang, J and Zhai, Q}, title = {Factors influencing gut microbial colonization: A host-microbe-environment interaction perspective.}, journal = {Current research in food science}, volume = {12}, number = {}, pages = {101361}, pmid = {41799257}, issn = {2665-9271}, abstract = {Gut microbial colonization is a dynamic balance shaped by host genetics and immunity, microbial ecology, and environmental exposures. This review synthesizes evidence on host barriers and immunity-mucus architecture, antimicrobial peptides, pattern recognition receptors, and secretory IgA-and on genetic loci such as LCT and ABO/FUT2 that modulate nutrient landscapes and strain selection. Microbial adaptability is summarized, including polysaccharide utilization loci and human milk oligosaccharide metabolism, bile salt hydrolase-mediated tolerance, extracellular polysaccharide-driven immune modulation, oxygen-gradient-linked metabolic partitioning, and adhesion mechanisms that secure niche occupancy. Environmental perturbations are evaluated, spanning dietary patterns, protein sources, polyphenols, food additives, pharmaceuticals, and lifestyle factors such as physical activity, circadian alignment, and smoking, which reshape resource competition, barrier integrity, and community resilience. Interaction frameworks that govern stability and dysbiosis are delineated, including competitive inhibition, cross-feeding, quorum sensing, cross-kingdom crosstalk among bacteria, fungi, and phages, and horizontal gene transfer that accelerates adaptation and resistance. Niche elasticity is proposed as a systems metric to quantify stability and recovery after perturbation. Translational strategies combine engineered probiotics, anti-adhesion approaches, and rationally designed phages and lysins with in situ multi-omics to enable mechanism-guided, personalized interventions for food science and microbial engineering.}, }
@article {pmid41798180, year = {2026}, author = {Cakin, I and Millington, R and Pawar, S and Buckling, A and Smirnoff, N and Padfield, D and Duffy, J and Yvon-Durocher, G}, title = {A novel method to simultaneously estimate bacterial respiration and growth from oxygen dynamics.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag024}, pmid = {41798180}, issn = {2730-6151}, abstract = {Bacterial growth and respiration are fundamental metabolic processes that drive energy transformation and allocation within organisms and impact carbon sequestration at the ecosystem scale. However, these traits are usually measured independently; bacterial growth is quantified with endpoint biomass measurements, while respiration is determined by monitoring oxygen or carbon dioxide. Because the two physiological traits are collected at different temporal and volumetric scales (hours-to-days for growth versus minutes-to-hours for respiration), reconciling them is challenging and often introduces scale-mismatch bias, obscuring causal links between metabolism and environmental drivers. In this study, we develop a novel method for quantifying the rates of bacterial growth and respiration from a single dissolved-oxygen time series. Our approach introduces a model that couples exponential biomass growth with biomass-specific respiration, enabling simultaneous inference of growth rate and respiration rate from each oxygen trajectory. We applied our high-throughput method to 15 bacterial taxa isolated from natural environments. Our approach yielded growth estimates in close agreement with measurements based on popular methods using optical density or flow cytometry ([Formula: see text] > 0.9) with no evidence of taxon-specific bias. We also tested our approach in quantifying the effects of temperature on respiration, growth, and carbon use-efficiency in Pseudomonas sp. Our method yielded typical unimodal thermal response curves for growth and respiration where rates were highest at moderate temperatures, while carbon use efficiency increased with temperature, peaked around the growth thermal optimum (∼30°C-35°C), and declined at the highest temperature. By quantifying respiration and growth within a single assay and in high throughput, our approach effectively enables measurement of microbial metabolic strategies and adaptations to stress. It offers a noninvasive and scalable tool for high-throughput phenotyping and studies of environmental perturbations, enabling a new class of trait-based microbial ecology that links cellular physiology to broader ecosystem function.}, }
@article {pmid41797016, year = {2026}, author = {Ghannem, S and Labiadh, H and Ishak, S and Louiz, S and Derguini, A and Idres, T and Grassi, E and Semprucci, F and Badraoui, R and Ben Hamadi, N and Chaudhary, AA and Alsalamah, SA and Bendif, H and Rebai, A and Boufahja, F}, title = {Investigation of the impacts of second-generation antihistamines on free-living marine nematodes and their interaction with ZnS nanoparticles: Mechanistic insights from community and population approaches and molecular interactions modeling.}, journal = {Marine environmental research}, volume = {217}, number = {}, pages = {107969}, doi = {10.1016/j.marenvres.2026.107969}, pmid = {41797016}, issn = {1879-0291}, abstract = {The current research investigates the impact of loratadine and its active metabolite desloratadine, applied at environmentally relevant concentrations (40 and 80 ng/L), using community-level, population-based, and molecular modeling approaches, on meiofauna from the Dammam coast, Saudi Arabia. The results indicate a significant reduction in the abundance of meiobenthic organisms, accompanied by a marked decline in nematode diversity across treatments, especially under combined exposures at higher concentrations. Additionally, trophic groups 1B and 2B, characterized by clavate tail morphologies, were the main contributors to the observed dissimilarity patterns across treatments. The mixture of 40 ng/L of antihistamines with ZnS nanoparticles (4.1 nm) enhanced catalase and GST activities in Metoncholaimus pristiurus. An increase in growth rate was also observed, along with larger pharyngeal lumens, suggesting higher food pumping under stress. Locomotion issues and decreased fertility are also suggested, with signs of masculinization. This highlights the intensified toxic effects of antihistamines following the addition of ZnS NPs. Overall, the findings suggest synergistic or additive interaction between loratadine, desloratadine, and ZnS nanoparticles. Their toxicokinetic properties, along with strong binding affinities and stable molecular interactions with GLD-3 and SDP receptors, provide a mechanistic basis and support ecotoxicological impacts of these antihistamines and ZnS NPs on nematodes.}, }
@article {pmid41795790, year = {2026}, author = {Özkan Vardar, D and Ekmen, B and Çalı, A}, title = {Interactions between polystyrene-derived micro- and nanoplastics and the microbiota: a systematic review of multi-omics mouse studies.}, journal = {Journal of environmental science and health. Part C, Toxicology and carcinogenesis}, volume = {}, number = {}, pages = {1-19}, doi = {10.1080/26896583.2026.2636868}, pmid = {41795790}, issn = {2689-6591}, abstract = {Micro- and nanoplastics (MNPs), especially polystyrene-derived particles (PS-MPs/PS-NPs), have become a growing concern due to their increasing presence in the environment and their proven biological toxicity. Although PS particles have been identified in various human tissues, including feces, placenta, and blood, their impact on the gut microbiota and microbiota-driven metabolic pathways remains insufficiently synthesized. This systematic review aims to compile current in vivo evidence from mouse studies to assess how PS-MP/NP exposure influences gut microbial diversity, taxonomic composition, microbial metabolites, and subsequent physiological outcomes. A PRISMA-guided literature search identified 15 controlled mouse studies published between 2010 and 2024. Across these studies, PS exposure consistently induced gut dysbiosis, characterized by reductions or shifts in alpha-diversity, distinct beta-diversity clustering, loss of beneficial commensals such as Lactobacillus, Bifidobacterium, and members of Ruminococcaceae, and enrichment of opportunistic or pro-inflammatory taxa including Proteobacteria, Helicobacter, and Staphylococcus. Notably, MNPs particles induced more pronounced microbial disruption than micro-sized forms. Overall, current experimental evidence indicates that PS-MPs/PS-NPs induce multidimensional toxicity by simultaneously disrupting gut microbial ecology and host metabolic pathways. These findings emphasize the need for standardized methodologies in microplastic research and highlight the importance of clarifying the long-term health effects of human exposure to micro- and nanoplastics.}, }
@article {pmid41794478, year = {2026}, author = {Chiarini, E and Buzzanca, D and Devizia, A and Giordano, M and Dipietro, F and Zeppa, G and Alessandria, V}, title = {Kombucha meets circular economy: A microbiome and metabolite perspective on second fermentation with plant by-products.}, journal = {Food research international (Ottawa, Ont.)}, volume = {230}, number = {}, pages = {118597}, doi = {10.1016/j.foodres.2026.118597}, pmid = {41794478}, issn = {1873-7145}, mesh = {*Fermentation ; *Microbiota ; *Kombucha Tea/microbiology/analysis/economics ; Food Microbiology ; Bacteria/metabolism/classification ; Yeasts/metabolism ; Volatile Organic Compounds/analysis ; Gas Chromatography-Mass Spectrometry ; }, abstract = {Kombucha is a traditional fermented beverage produced through the fermentation of sugared tea by a symbiotic culture of bacteria and yeasts (SCOBY). In recent years, the valorisation of plant-based by-products as fermentation substrates has gained attention as a sustainable approach to improving both the nutritional and economic efficiency of fermented beverages. The present study investigated the production of kombuchas supplemented with pineapple, fennel, and carrot by-products during the secondary fermentation phase, aiming to evaluate their influence on fermentation dynamics, microbial ecology, and the chemical and aromatic profiles of the final products. The experimental design integrated culture-dependent and culture-independent approaches, including amplicon sequencing, to characterize microbial community composition and evolution throughout fermentation. Chemical profiling was carried out using gas chromatography coupled with quadrupole mass spectrometry (GC-qMS) and high-performance liquid chromatography equipped with diode-array and refractive index detectors (HPLC-DAD/RI). The fermentation process was monitored during both the primary and secondary stages, and a shelf-life assessment was conducted over 14 days of refrigerated storage (4 °C) to evaluate product stability. Microbiological results indicated a predominance of Schizosaccharomyces spp., while Komagataeibacter spp. was the only bacterial genus identified. A significant reduction in α-diversity was observed over time, suggesting selective adaptation of the microbial community to the fermentation environment. β-diversity analysis revealed clear differences among samples collected after 8 and 22 days, reflecting the combined influence of time and substrate composition on microbial succession. Chemical analyses demonstrated an increase in acetic acid concentration and a progressive decline in pH throughout fermentation, consistent with the metabolic activity of acetic acid bacteria. Among volatile organic compounds (VOCs), alcohols and organic acids were the most abundant chemical classes detected. Several VOCs were associated with minor yeast genera, including Hannaella, Galactomyces, Aureobasidium, and Millerozyma, whereas Schizosaccharomyces spp. showed a strong correlation with specific aroma-active compounds, highlighting its key role in defining the sensory characteristics of the beverage. Overall, this study provides new evidence on how different vegetable by-products and microbial consortia influence the development of chemical and aromatic compounds in kombucha. The findings highlight the potential of using by-products as a sustainable, value-added strategy for producing fermented beverages, while also supporting the principles of the circular economy and resource-efficient food systems.}, }
@article {pmid41794468, year = {2026}, author = {Wang, A and Qiu, C and Tang, J}, title = {Multidimensional synergy between yeast and lactic acid bacteria: mechanisms, quality formation, and precision fermentation strategies.}, journal = {Food research international (Ottawa, Ont.)}, volume = {230}, number = {}, pages = {118586}, doi = {10.1016/j.foodres.2026.118586}, pmid = {41794468}, issn = {1873-7145}, mesh = {*Fermentation ; *Lactobacillales/metabolism/physiology ; Biofilms/growth &amp; development ; *Microbial Interactions ; *Food Microbiology ; Quorum Sensing ; *Fermented Foods/microbiology ; *Yeasts/metabolism ; }, abstract = {The complex functional characteristics of fermented foods stem from dynamic microbial interactions rather than the activities of individual microorganisms. Traditional research has primarily focused on single-strain cultures and metabolic functions, whereas contemporary studies increasingly emphasize the pivotal role of interactions between different species in shaping fermentative ecosystems. This review explores the multifaceted interactions between yeast-lactic acid bacteria (LAB), focusing on three key aspects: (1) nutritional interactions and cross-feeding mechanisms; (2) molecular communication via metabolite exchange and quorum sensing; (3) collective adaptation strategies encompassing biofilm formation and environmental remodeling. Synergistic interactions promote metabolic complementarity, thereby enhancing substrate utilization efficiency and biosynthetic capacity beyond the limitations of single-strain cultures. Competitive interactions maintain ecological equilibrium within microbial communities while suppressing undesirable microorganisms. Quorum sensing mechanisms synchronize gene expression across entire populations, coordinating metabolic pathways and optimizing collective behavior. Biofilm formation creates structured microenvironments that enhance microbial resilience and metabolic specialization. Advanced methodologies, particularly multi-omics technologies and synthetic microbial ecology approaches, have become indispensable tools for unravelling these intricate interaction networks. Integrating genome-scale metabolic modelling with experimental validation offers unprecedented insights into the molecular mechanisms underpinning microbial interactions. This systems-level understanding enables the purposeful design of synthetic microbial communities and precise fermentation processes, highlighting the imperative shift from single-species optimization towards ecological management strategies. Future research should translate laboratory discoveries into industrial applications through standardized evaluation systems and dynamic regulatory strategies.}, }
@article {pmid41794110, year = {2026}, author = {Wei, C and Hu, J and Wang, X and Chen, Y and Zhang, S and Peng, Y}, title = {Optimization of sulfate-reducing ammonium oxidation based on N/S: nitrogen and sulfur removal performance, microbial community, and response surface methodology.}, journal = {Environmental research}, volume = {}, number = {}, pages = {124143}, doi = {10.1016/j.envres.2026.124143}, pmid = {41794110}, issn = {1096-0953}, abstract = {Sulfate-reducing ammonium oxidation (Sulfammox) offers a novel strategy for simultaneous nitrogen and sulfur removal. However, the microbial-driven metabolic pathways under different N/S and the optimal operational conditions remain unclear. This study operated three anaerobic sequencing batch reactors at N/S of 2.5, 2.0, and 1.5 to investigate the removal performance and microbial ecology. The reactor with an N/S of 1.5 (R3) achieved the highest removal efficiencies of 91.82% for NH4[+]-N and 47.95% for SO4[2-]-S, while the reactor with an N/S of 2.5 (R1) showed efficiencies below 15% for both, indicating that a lower N/S is critical for efficient removal. X-ray photoelectron spectroscopy confirmed the formation of elemental sulfur, indicating active sulfur transformation that alleviated sulfide inhibition and enhanced system stability. Batch tests identified optimal operating conditions: pH 8.0, hydraulic retention time 48 h, and COD 50 mg/L. When COD is greater than 300 mg/L, sulfate reduction dominated and inhibited the sulfammox process. Response surface methodology models (R[2]>0.98) predicted the optimal parameters in N/S 1.57, pH 7.66, HRT 46.53 h, and COD of 48.61 mg/L, achieving NH4[+]-N and SO4[2-]-S removal efficiencies of 93.13% and 47.35%. This represents 9.5% enhancement in NH4[+]-N removal over the pre-optimization phase. Microbial analysis revealed that N/S of 1.5 abundance of Desulfobacterota increased by 1.67%, driving sulfate reduction, while Chloroflexi constituted 26.07% in R3, the anammox bacterium Candidatus-Brocadia was inhibited, exhibiting a relative abundance of less than 0.1%. By elucidating sulfammox interactions, this study offers a practical, low-carbon and synergistic framework for the effective co-treatment of high NH4[+]-N and SO4[2-]-S wastewater.}, }
@article {pmid41792903, year = {2026}, author = {Liang, MQ and Yuan, L and Liu, QH and Wu, J and Liu, DF and Sheng, GP}, title = {Membrane perturbation by the last-resort antibiotic polymyxin B drives biphasic regulation of horizontal gene transfer.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag046}, pmid = {41792903}, issn = {1751-7370}, abstract = {Although it is increasingly recognized that anthropogenic chemicals modulate horizontal gene transfer (HGT), the nature of these interactions is often more complex than a simple promotion or inhibition. The potential for a single chemical to exert opposing, concentration-dependent effects represent a critical and less-explored frontier in microbial ecology. Here, we investigate the last-resort antibiotic polymyxin B, a membrane-targeting peptide, and reveal a concentration-dependent, biphasic regulation of plasmid conjugation. Sub-inhibitory concentrations (0.125-0.5 mg/L) consistently inhibited the transfer of antibiotic resistance genes (ARGs) by up to 65.4%, whereas bactericidal concentrations (≥ 1 mg/L) strongly promoted it by up to 15.9-fold. This regulatory switch is driven by distinct physiological states: low-level exposure triggers defensive responses including reduced membrane permeability, whereas high-level exposure causes catastrophic membrane damage, inducing a synergistic stress response involving oxidative damage (>2-fold ROS increase) and a surge in cellular energy (up to 83.0% ATP increase) that facilitates HGT. High-concentration polymyxin B also promotes plasmid transfer in complex microbial communities derived from activated-sludge biofilms. Our findings reveal a new paradigm for the interaction between chemical stressors and microbial evolution, demonstrating that the ecological impact of contaminants on HGT cannot be predicted by monotonic models and highlighting the role of environmental hotspots in shaping the dissemination of antibiotic resistome.}, }
@article {pmid41791723, year = {2026}, author = {Raj, A and Pant, A and Kumar, A and Kumar, A and Kalamdhad, AS and Khwairakpam, M}, title = {Systems-Level Insights Into Microbial Naphthalene Biodegradation: An Integrated In Silico and Omics Perspective.}, journal = {Environmental microbiology}, volume = {28}, number = {3}, pages = {e70264}, doi = {10.1111/1462-2920.70264}, pmid = {41791723}, issn = {1462-2920}, support = {IITG/R&amp;D/IPDF/2024-25/20240815P852//Indian Institute of Technology Guwahati/ ; }, mesh = {*Naphthalenes/metabolism ; Biodegradation, Environmental ; *Bacteria/metabolism/genetics ; Systems Biology ; Computer Simulation ; *Environmental Pollutants/metabolism ; Microbial Consortia ; }, abstract = {Naphthalene, a widely detected polycyclic aromatic hydrocarbon (PAH), is among the 16 priority PAHs identified as major environmental hazards due to its persistence, ubiquity, and toxicity to ecosystems and human health. Its occurrence in crude oil, combustion residues, vehicle emissions, and household products highlights the urgent need for sustainable remediation strategies. Microbial-based bioremediation stands out as an eco-friendly and cost-effective approach that harnesses the metabolic versatility of diverse microorganisms, their genes, and enzymes responsible for naphthalene degradation. Recent advances in omics technologies and high-throughput sequencing have expanded our understanding of novel microbial taxa, metabolic pathways, and stress responses under naphthalene exposure. Complementarily, computational modelling, in silico tools, machine learning, and systems biology have enabled the prediction of degradation dynamics and the design of synthetic microbial consortia optimised for field use. Despite these advances, challenges such as environmental fluctuations, co-contaminant effects, and the gap between laboratory and field outcomes remain. Overcoming these requires an integrative framework that connects microbial ecology, omics insights, and computational modelling. This review consolidates current knowledge on microbial degradation of naphthalene, emphasising key taxa, genes, and pathways, and highlights how omics, in silico tools and systems biology can drive sustainable remediation in the Anthropocene.}, }
@article {pmid41790321, year = {2026}, author = {Sahoo, A and Maity, A and Das, B and Paul, RC and Paul, P and Chakraborty, P and Chaudhuri, BN and Ghosh, MM and Das, S and Tribedi, P}, title = {Combined application of Vancomycin and Levofloxacin potentiates the antimicrobial activity against MRSA: a response surface methodology-based study.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {41790321}, issn = {1874-9356}, support = {TNU/R&amp;D/MG/24/02//The Neotia University, India/ ; TNU/R&amp;D/MP/2021/010//The Neotia University, India/ ; }, }
@article {pmid41789424, year = {2026}, author = {Katrak, C and Reed, S and Carter, M and Khatib, M and Peterson, A and Martin, K and Kajfasz, JK and Abranches, J}, title = {Oral hygiene agents at work: effects on Streptococcus mutans and caries risk.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1768512}, pmid = {41789424}, issn = {2235-2988}, mesh = {Humans ; *Dental Caries/prevention &amp; control/microbiology ; *Streptococcus mutans/drug effects/physiology/growth &amp; development ; Biofilms/drug effects/growth &amp; development ; *Oral Hygiene/methods ; Probiotics/pharmacology ; Dental Plaque/microbiology/prevention &amp; control ; Chlorhexidine/pharmacology/therapeutic use ; Hydrogen Peroxide/pharmacology ; Fluorides/pharmacology/therapeutic use ; Prebiotics ; Zinc/pharmacology ; }, abstract = {Dental caries remains one of the most prevalent chronic polymicrobial diseases worldwide, driven by acidogenic and aciduric bacteria, most notably Streptococcus mutans, that thrive within oral biofilms. Conventional strategies for caries prevention rely on mechanical plaque removal combined with agents that inhibit bacterial growth, disrupt biofilm formation, or enhance enamel remineralization. Here, we synthesize current evidence regarding a range of key agents that are incorporated into modern oral hygiene products. In addition to describing the mechanisms and efficacy of these agents, we describe their distinct biochemical and ecological effects on S. mutans metabolism, acid tolerance, and biofilm development. The agents that are relevant in the present day include fluoride, hydrogen peroxide, chlorhexidine, zinc, prebiotics (such as arginine and xylitol), and probiotics. Fluoride remains the cornerstone of caries prevention through its dual effects on enamel fluorapatite formation and inhibition of bacterial glycolysis, while chlorhexidine and hydrogen peroxide provide broad-spectrum antimicrobial activity. Zinc exhibits multifaceted roles in metabolic inhibition and plaque reduction, whereas pre- and probiotics aim to restore ecological balance by favoring health-associated commensal species. Finally, the review highlights evidence supporting combinatorial and synergistic use of these agents, particularly fluoride pairings, which may yield additive or enhanced protective effects. Understanding the molecular mechanisms that drive the efficacy of these compounds and gaining insight into cumulative influence on oral microbial ecology will drive the development of future treatment strategies.}, }
@article {pmid41788582, year = {2026}, author = {Wang, E and Chen, C and Li, Q}, title = {Current obstacles for continuous cropping of Panax species and mitigation strategies.}, journal = {Journal of ginseng research}, volume = {50}, number = {2}, pages = {100925}, pmid = {41788582}, issn = {1226-8453}, abstract = {Panax species-represented here by Panax ginseng Meyer, Panax quinquefolius L., and Panax notoginseng (Burk.) F. H. Chen-are valued for their saponins and polysaccharides and thus have significant clinical and commercial value. Rising global demand has driven intensive, large-scale cultivation, but repeated monoculture has produced persistent continuous cropping obstacles that now threaten the sustainability of the industry. These obstacles are not attributable to a single factor. Rather, they arise from interacting processes including degradation of soil physical and chemical properties, accumulation of plant-derived toxins that inhibit growth (allelopathic autotoxicity), and shifts in the soil microbial community that impair soil health and plant resilience. Together, these changes lead to stunted growth, reduced yields, and increased disease incidence. This review synthesizes recent advances in understanding continuous cropping obstacles in Panax species. It evaluates evidence for the primary causal factors, assesses current mitigation strategies, and highlights areas where findings are robust or still uncertain. By integrating soil science, plant physiology, and microbial ecology, the review identifies practical approaches already in use and emerging technologies with potential to improve outcomes. Finally, we identify critical knowledge gaps and outline priority directions for future research aimed at clarifying mechanisms and translating that knowledge into an effective management framework. The ultimate goal is to provide a theoretical basis to guide the development of scalable, evidence-based practices that alleviate continuous cropping obstacles in the cultivation of Panax species.}, }
@article {pmid41788258, year = {2026}, author = {Keles, E and Celik, O}, title = {Metagenomic and microbiological analyses of historical manuscripts for bacterial community profiling and bacteria-related biodeterioration assessment.}, journal = {Microbial cell (Graz, Austria)}, volume = {13}, number = {}, pages = {117-130}, pmid = {41788258}, issn = {2311-2638}, abstract = {Bacteria are important agents in the biodeterioration of cultural heritage objects, including historical manuscripts. Characterizing bacterial communities and generating robust microbiological data has therefore become crucial for conservation and restoration strategies. In this study, we investigated the bacterial communities associated with biodeterioration in six historical manuscripts using both culture-dependent and culture-independent (Illumina MiSeq) approaches. Culture-dependent methods yielded only 16 viable and culturable isolates, highlighting the limitations of traditional techniques. In contrast, metagenomic analysis revealed a far richer and more diverse bacterial community, capturing both living and non-living microbial traces accumulated over centuries. Bacterial genera with known cellulolytic and/or proteolytic activities, such as Bacillus, Stenotrophomonas, Pseudomonas and Acinetobacter, were identified as part of a core microbiome commonly associated with paper deterioration. High abundances of gut-associated bacteria (Prevotella, Faecalibacterium, Bacteroides, Porphyromonas) and human-related taxa (Staphylococcus, Streptococcus, Cutibacterium) indicated extensive historical human handling. A notable finding was the detection of Pseudonocardia broussonetiae, an endophytic bacterium associated with paper mulberry (Broussonetia papyrifera), suggesting the possible use of this plant as a papermaking material in one manuscript. This represents an important contribution to understanding Islamic paper production. Overall, our results demonstrate that effective conservation strategies require a detailed understanding of each manuscript's microbial ecology, together with evidence of past environmental conditions, handling history, and production materials.}, }
@article {pmid41787281, year = {2026}, author = {Van Rossum, U and Heyndrickx, M and Rasschaert, G and Demaître, N and Sadiq, FA and Boon, N and Cools, A and De Reu, K}, title = {Hidden threats: exploring biofilm communities in broiler houses and pig nursery units drinking water lines.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-04790-6}, pmid = {41787281}, issn = {1471-2180}, support = {HBC.2021.1060//VLAIO-LA/ ; }, }
@article {pmid41787131, year = {2026}, author = {Stanovcic, S and Milisavljevic, M and Azanjac, N and Kojic, S and Kojic, M}, title = {Biomolecules Generated During Programmed Cell Death (PCD) Enhance the Capacity of Proliferating Ustilago maydis Cells to Overcome the Negative Impacts of Non-PCD Necromass.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02736-z}, pmid = {41787131}, issn = {1432-184X}, support = {7730230//Science Fund of the Republic of Serbia/ ; }, }
@article {pmid41786226, year = {2026}, author = {Li, Y and Wang, WJ and Zhang, S and Luo, Q and Qian, NF and Chen, DZ and Jin, RC and Feng, LJ and Yang, GF}, title = {Chaotic effects in completely autotrophic nitrogen removal over nitrite process: how minor dissolved oxygen variations reshape microbial community and functional genes to drive divergent nitrogen removal.}, journal = {Bioresource technology}, volume = {448}, number = {}, pages = {134333}, doi = {10.1016/j.biortech.2026.134333}, pmid = {41786226}, issn = {1873-2976}, abstract = {To elucidate how dissolved oxygen (DO) regulates nitrogen removal in the completely autotrophic nitrogen removal over nitrite (CANON) process, three continuous-flow reactors were operated under micro-aerobic conditions. Results revealed that minor DO variations (0.36-0.51 mg/L) triggered dramatic bifurcation in performance and microbial ecology, demonstrating chaotic effects characterized by nonlinear dynamics and sensitive dependence on initial conditions. A superior total nitrogen removal rate of 0.38 kg/m[3]/d and a NH4[+]-N removal efficiency of 86.7% were achieved at 0.36 mg/L DO. However, a slight increase to 0.51 mg/L DO significantly enhanced nitrite-oxidizing bacteria (NOB) activity and nitrate accumulation. Lower DO favored anammox bacteria and their essential genes (hzs/hdh), while elevated DO promoted NOB competition and oxidative stress responses, evidenced by Fe-Mn SOD gene upregulation and altered extracellular polymers composition. Our findings establish a direct link between minor DO fluctuations and macro-scale functional outcomes, providing a mechanistic framework for predicting and controlling CANON process.}, }
@article {pmid41778806, year = {2026}, author = {Wasson, PA and McRose, DL}, title = {Nitrous oxide produced by denitrifying pseudomonads inhibits the growth of rhizosphere bacteria by inactivating the cobalamin-dependent methionine synthase.}, journal = {mBio}, volume = {}, number = {}, pages = {e0269925}, doi = {10.1128/mbio.02699-25}, pmid = {41778806}, issn = {2150-7511}, abstract = {Microbial communities are shaped by complex metabolic interactions, whereby the byproducts of one organism influence the physiology of others. This is exemplified in the microbial nitrogen cycle, where diffusion of free intermediates can drastically reshape the chemical landscape of the environment. One such intermediate, nitrous oxide (N2O), is often overlooked as biologically inert. However, emerging evidence suggests this gas may inhibit the activity of some cobalamin-dependent enzymes through a reaction with the cofactor. This raises the possibility that, through such an interaction, N2O-producing organisms may shape the microbial communities in which they reside, selecting against organisms that rely on these sensitive cobalamin enzymes. At the plant root, a hotspot of microbial activity, the impact of such interactions may be especially important. To investigate this, we focused on microbial N2O production and its effect on methionine biosynthesis, a ubiquitous bacterial process carried out by cobalamin-dependent (MetH) or independent (MetE) methyltransferases. In this study, we show that deleting metE and forcing reliance on MetH sensitizes the denitrifier Pseudomonas aeruginosa to exogenous and self-produced N2O. We extend these findings to plant-associated bacteria, where we find that a significant portion of an Arabidopsis thaliana rhizosphere culture collection relies exclusively on cobalamin-dependent methionine synthases and experimentally demonstrate their sensitivity to N2O. Finally, we show that the growth of one MetH-reliant rhizosphere isolate is suppressed in co-culture with N2O-producing P. aeruginosa. Together, these findings suggest that N2O producers can shape microbial ecology at the plant root.IMPORTANCEMicrobes that live on plant roots can make important contributions to plant health and often exist in tight-knit communities held together by chemical exchanges. This study investigates an interaction between two such metabolites: the climate-active gas nitrous oxide (N2O) and cobalamin. N2O can become toxic through a reaction with methionine synthase enzymes that use cobalamin as a cofactor. We asked whether the production of N2O by some bacteria curtails the growth of others that rely on these enzymes. Using genetic mutants of a model bacterium and natural isolates from the roots of the plant Arabidopsis thaliana, we showed that N2O-producing microbes suppress growth of their sensitive neighbors and that N2O sensitivity is common in rhizosphere bacteria. As natural and agricultural soils periodically experience bursts of N2O, our results suggest that exposure to this gas may shape the assembly of plant-beneficial microbial communities.}, }
@article {pmid41786065, year = {2026}, author = {Wang, X and Liu, R and Liu, J and Lin, Y and Zhou, M}, title = {Gut microbiota-derived indole metabolites in depression: mechanisms and therapeutic potential.}, journal = {European journal of pharmacology}, volume = {}, number = {}, pages = {178720}, doi = {10.1016/j.ejphar.2026.178720}, pmid = {41786065}, issn = {1879-0712}, abstract = {Depression, a prevalent neuropsychiatric disorder with complex pathophysiology and often insufficient treatment efficacy, is increasingly associated with disruptions in the gut-brain axis. This review focuses on the underappreciated role of the microbial indole pathway, a key route in tryptophan metabolism orchestrated by the gut microbiota. We synthesize recent evidence demonstrating that gut microbiota-derived indole metabolites, such as indole-3-propionic acid (IPA) and indole-3-aldehyde (IAld), are significantly reduced in depression. These metabolites exert multifaceted antidepressant effects by enhancing intestinal and blood-brain barrier integrity, suppressing neuroinflammation, and promoting neuroplasticity. Furthermore, we explore the therapeutic potential of targeting this axis through interventions like specific probiotics, prebiotics, dietary modifications, and fecal microbiota transplantation to restore microbial ecology and indole metabolite levels. By highlighting the microbiota-indole-brain pathway as a critical mechanistic and therapeutic frontier, this review provides a novel perspective on the pathogenesis and treatment of depression, moving beyond conventional monoaminergic theories.}, }
@article {pmid41785727, year = {2026}, author = {Wang, C and Luo, M and Chen, Q and Zheng, L and Jiang, T and Dai, M}, title = {Hedyotis diffusa Willd. extract alleviates CCl4-induced liver fibrosis via modulation of the gut microbiota and FXR/SHP/CYP7A1-mediated bile acid metabolism.}, journal = {Journal of ethnopharmacology}, volume = {363}, number = {}, pages = {121450}, doi = {10.1016/j.jep.2026.121450}, pmid = {41785727}, issn = {1872-7573}, abstract = {Liver fibrosis is a critical stage in the progression of chronic liver diseases, yet effective therapeutic agents are limited. Hedyotis diffusa Willd., a traditional Chinese medicine herb with heat-clearing and detoxifying properties, has long been used to treat inflammatory disorders, hepatic dysfunction and malignancies. Although accumulating studies suggest that Hedyotis diffusa Willd. Extract (HDW) possesses hepatoprotective and antifibrotic potential, the underlying mechanisms, particularly those involving gut microbiota and bile acid (BA) metabolism along the gut-liver axis, remain largely undefined.<br><br>AIM OF THE STUDY: To investigate the protective effects of HDW against carbon tetrachloride (CCl4)-induced liver fibrosis in mice, and to determine whether its antifibrotic efficacy is mediated by modulation of the gut microbiota-bile acid-FXR/SHP/CYP7A1 axis.<br><br>MATERIALS AND METHODS: Liver fibrosis was induced by intraperitoneal injection of 10% CCl4 in olive oil for five weeks. Histopathological changes were evaluated using H&amp;E, Sirius red and Masson staining. Liver function was assessed using serum levels of ALT, AST, ALP and &#x3b3;-GT. Collagen deposition was evaluated by measuring hepatic hydroxyproline (HYP) and fibrosis-related markers (HAase, IV-C, LN and PC-III). Activation of hepatic stellate cells was determined by &#x3b1;-SMA and Col1a1 expression. The composition of the gut microbial was profiled using 16&#xa0;S rRNA sequencing, and the necessity of gut microbiota for HDW efficacy was evaluated through an antibiotic (ABX) cocktail intervention. Targeted BA metabolomics quantified BA profiles, while RT-qPCR and Western blotting evaluated FXR/SHP/CYP7A1 pathway activity. Intestinal barrier integrity was assessed by villus morphology, tight junction protein levels (Claudin-1, ZO-1, Occludin), and serum lipopolysaccharide (LPS).<br><br>RESULTS: HDW treatment markedly alleviated CCl4-induced liver fibrosis, demonstrated by improved hepatic architecture, reduced serum transaminases and ALP/&#x3b3;-GT, decreased hydroxyproline levels, and downregulation of &#x3b1;-SMA and Col1a1. HDW reshaped the gut microbial composition by enriching beneficial taxa, whereas ABX treatment markedly attenuated its antifibrotic effects, indicating that the therapeutic action of HDW is largely microbiota-dependent. HDW restored BA homeostasis and significantly increased fecal odeoxycholic acid. Consequently, hepatic FXR/SHP/CYP7A1 signaling was upregulated at both the mRNA and protein levels. Furthermore, HDW strengthened the intestinal epithelial barrier by enhancing tight junction integrity and reducing serum LPS.<br><br>CONCLUSION: HDW exerts significant antifibrotic effects in CCl4-induced liver fibrosis via a gut microbiota-dependent mechanism involving the restoration of BA metabolism and the activation of the hepatic FXR/SHP/CYP7A1 axis. Given its ability to modulate gut microbial ecology, BA homeostasis and intestinal barrier integrity simultaneously, HDW is a promising therapeutic candidate for targeting the gut microbiota in the treatment of liver fibrosis.}, }
@article {pmid41785576, year = {2026}, author = {Poirier, S and Rondeau-Leclaire, J and Faticov, M and Roy, A and Lajeunesse, G and Lucier, JF and Tardif, S and Kembel, SW and Ziter, C and Laprise, C and Paquette, A and Girard, C and Laforest-Lapointe, I}, title = {Season and city shape urban bioaerosol composition beyond vegetation and socioeconomic gradients.}, journal = {The Science of the total environment}, volume = {1023}, number = {}, pages = {181623}, doi = {10.1016/j.scitotenv.2026.181623}, pmid = {41785576}, issn = {1879-1026}, abstract = {Urban vegetation varies with socio-economic gradients, as lower-income neighborhoods often host sparser and less diverse green spaces. This disparity may affect respiratory health by influencing exposure to bioaerosols. Understanding the characteristics of this aerobiome could help anticipate risks related to allergies and other respiratory conditions. Here, we hypothesized that urban vegetation cover and socio-economic status shape urban bioaerosol dynamics. We sampled bioaerosols at 65 sites across three Canadian cities of varying population size and density using an active air sampler over four months, and characterized their bacterial, fungal, and plant particles composition using amplicon sequencing. Seasonal alpha diversity varied significantly for fungi and plant particles. Based on beta diversity, sampling period alone explained up to 40% of plant particle, 29% of fungal, and 11% of bacterial bioaerosol composition variation. In contrast, vegetation cover explained only a minor portion of the variance in bioaerosol composition, and median household income, almost none. These findings provide a critical baseline for understanding the urban aerobiome and highlight the need to study how vegetation identity and diversity, rather than cover alone, may shape bioaerosol dynamics in cities. As cities grow and urban greening initiatives expand, demystifying the aerobiome dynamics becomes an urgent public health priority.}, }
@article {pmid41782409, year = {2026}, author = {Yang, J and Xiao, Y and Cui, J and Song, R and Ma, W and Liu, J and Miao, C and Sun, X and Kong, X and Zhang, ZS and Zhou, L and Yao, Z and Wang, Q}, title = {A 4-guanidinobutanoic acid-SLC36A1 axis drives a microbiota‒host feedback loop to regulate intestinal homeostasis.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2639216}, doi = {10.1080/19490976.2026.2639216}, pmid = {41782409}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/physiology ; Humans ; Mice ; Homeostasis ; *Intestinal Mucosa/metabolism/microbiology/drug effects ; *Guanidines/metabolism/pharmacology ; Colitis, Ulcerative/microbiology/metabolism ; Mice, Inbred C57BL ; Bacteroides/metabolism ; *Butyrates/metabolism ; Disease Models, Animal ; Stem Cells/metabolism ; Feedback, Physiological ; *Amino Acid Transport System y+/metabolism/genetics ; Akkermansia ; }, abstract = {The role of gut microbiota‒derived metabolites in regulating the intestinal mucosal barrier remains poorly defined. Here, we identified 4-guanidinobutanoic acid (4-GBA), produced by Bacteroides stercorirosoris, as a critical regulator of intestinal homeostasis. Using untargeted metabolomics, organoid co-cultures, mouse models, and single-cell RNA sequencing, we demonstrated that 4-GBA enhances intestinal stem cells (ISCs) function and goblet cell differentiation. This promotes Akkermansia muciniphila enrichment through mucus-dependent niche expansion, establishing a microbiota‒host feedback loop. Mechanistically, 4-GBA upregulates the proton-coupled amino acid transporter SLC36A1 and activates the Hedgehog signaling pathway to drive epithelial reprogramming. Clinically, SLC36A1 expression inversely correlates with ulcerative colitis (UC) severity in human samples. Furthermore, the SLC36A1 agonist sarcosine enhances barrier homeostasis and attenuates colitis in mice, highlighting the diagnostic and therapeutic potential of this axis in UC. Our findings reveal a novel microbiome-host axis through which a microbial metabolite modulates epithelial function and microbial ecology, offering a potential therapeutic strategy targeting microbiota-epithelial crosstalk for UC management.}, }
@article {pmid41781688, year = {2026}, author = {Cinek, O and Hubáčková, K and Litošová, K and Hlináková, L}, title = {Heterogeneity Primer Spacers Improve the Performance of Massively Parallel Amplicon Sequencing of the V3-V4 Region of the 16 S rDNA as well as the 18 S Region for Blastocystis Subtyping.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02708-3}, pmid = {41781688}, issn = {1432-184X}, }
@article {pmid41779172, year = {2026}, author = {Roldán, DM and Carrizo, D and Sánchez-García, L and Menes, RJ}, title = {Temperature Response of Aerobic Methane-Oxidizing Bacteria in Lake Sediments from King George Island, Maritime Antarctica.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02717-2}, pmid = {41779172}, issn = {1432-184X}, }
@article {pmid41779071, year = {2026}, author = {Lygis, V and Marčiulynas, A and Plepytė, T and Šulčius, S and Menkis, A}, title = {Metabarcoding Reveals Rich and Diverse Aeromycobiota in Protected Oak Forests.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02714-5}, pmid = {41779071}, issn = {1432-184X}, abstract = {Old-growth oak (Quercus robur) forests in Europe are biodiversity hotspots, yet their airborne fungal diversity remains poorly studied. We investigated aeromycobiota in three Lithuanian oak stands (Punia, Dūkštos and Šilinė) using passive spore traps combined with DNA metabarcoding. Weekly sampling between August and September 2022 yielded 75 spore samples, producing 262,755 high-quality fungal sequences clustered into 1,881 operational taxonomic units (OTUs) representing six phyla and 36 classes. Ascomycota (53.1% of OTUs) and Basidiomycota (44.3%) dominated in richness, while Basidiomycota prevailed in relative sequence abundance (62.8%). Major taxa included Exobasidiaceae sp., Cladosporium sp., Melampsora sp., and Thelephora terrestris. Airborne fungal communities exhibited a substantial core assemblage shared among stands, accompanied by stand-associated differences in species richness and relative sequence abundance. The Punia stand showed the highest richness and the greatest proportion of stand-specific OTUs. Temporal variation was detectable but moderate relative to spatial differences among stands. Functional guild analysis revealed dominance of saprotrophs (46.5% of assigned OTUs), followed by pathotrophs (14.5%) and symbiotrophs (13.2%). Overall, our results demonstrate that passive spore traps-based airborne metabarcoding captures high fungal diversity and resolves both widespread and stand-associated community patterns in old-growth oak forests. This study provides the first characterization of aeromycobiota in old-growth Q. robur forests of Northern Europe and highlights the value of airborne metabarcoding for fungal biodiversity assessment and long-term forest monitoring.}, }
@article {pmid41777393, year = {2026}, author = {Zhang, B and Liu, Y and Zhou, D and Lv, Y and Cao, M and Li, H and Yang, Z and Liu, Z and Yin, H and Wang, X and Huang, Z and Meng, D}, title = {The role of quorum sensing in rhizosphere community regulation during bacterial wilt pathogen invasion.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1685007}, pmid = {41777393}, issn = {1664-462X}, abstract = {Bacterial wilt, caused by the soil-borne pathogen Ralstonia solanacearum is a major threat to solanaceous crops worldwide. The onset of this disease is frequently associated with disruptions in the rhizosphere microbial community. Quorum sensing (QS), a key mechanism for microbial communication, plays a critical role in regulating microbial interactions and maintaining community structure. However, whether and how QS is involved in reshaping the rhizosphere microbiome during R. Solanacearum infection remains poorly understood. In this study we compared QS-related genes, signaling pathways, and network structures in metagenomes of healthy and wilt-infected rhizospheres. The results show QS-related genes of the plant beneficial bacterial were significantly down-regulate, whereas QS-related genes of pathogenic R. Solanacearum were up-regulated in wilt-infected rhizosphere. The up-regulated QS genes of pathogens belong to eight QS signaling pathways (AI-1, GABA, PapR, NprX, Phr, cCF10, and DSF). Network analysis showed a simplified structure in the wilt-infected rhizosphere. It is also found the number of connectors in the QS gene co-occurrence network was reduced in wilt-infected rhizosphere network. This is due to the upregulation of QS system allows the pathogen to mediate the rhizosphere microbial ecology network, and leads to destabilization of rhizosphere community. These findings demonstrate that QS system contributes to bacterial wilt infection by suppressing the QS-based interactions among plant beneficial microbes, thereby triggering community function disruption.}, }
@article {pmid41776739, year = {2026}, author = {Tang, X and Liu, H and Qin, P and Wang, T and Du, W and Zhang, M and Zhu, M and Feng, J}, title = {Identification and Fungicide Efficacy of Leaf Spot on Euonymus fortunei Caused by Alternaria alternata in China.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-01-26-0167-RE}, pmid = {41776739}, issn = {0191-2917}, abstract = {Leaf spot disease has recently emerged on Euonymus fortunei in Shanxi Province, China, causing noticeable foliar lesions and reducing ornamental value. The causal agent was identified as Alternaria alternata based on morphological characteristics and multilocus phylogenetic analysis using five loci (Alt a1, gapdh, RPB2, ITS, and OPA10-2). Biological characterization showed that mycelial growth was optimal at 27 ℃ on oatmeal agar, whereas conidial germination was favored under alkaline conditions (pH 9.0). The pathogen was sensitive to NaCl stress but showed no significant response to different light regimes. In vitro fungicide sensitivity assays revealed marked differences in inhibitory efficacy between mycelial growth and conidial germination, indicating strong developmental stage-dependent responses. Certain fungicide mixtures exhibited enhanced inhibitory effects compared with single compounds, suggesting potential synergistic interactions. Microscopic observations further revealed fungicide-induced morphological abnormalities, including hyphae swelling, roughened surfaces, reduced sporulation, and deformation of conidial germ tubes. This study represents the first report of A. alternata causing leaf spot disease on E. fortunei in China and provides a basis for understanding pathogen biology and developing effective chemical management strategies for this emerging ornamental disease.}, }
@article {pmid41774190, year = {2026}, author = {Noirungsee, N and Pitaktham, T and Nakkaew, A and Chantanaorrapint, S and Klinnawee, L}, title = {Microbial Communities of the Mycoheterotrophic Plant Thismia Gardneriana in a Lowland Tropical Rainforest of Southern Thailand.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02727-0}, pmid = {41774190}, issn = {1432-184X}, support = {N25A650472//National Research Council of Thailand/ ; }, }
@article {pmid41773092, year = {2026}, author = {Lamanna, OK and Hu, R and Khemmani, M and Wolfe, AJ and Groah, SL and Forster, CS}, title = {Differential Effects of Uropathogenic and Non-Uropathogenic E. coli on the Mouse Urobiome and Urine NGAL Levels.}, journal = {Research and reports in urology}, volume = {18}, number = {}, pages = {580953}, pmid = {41773092}, issn = {2253-2447}, abstract = {OBJECTIVE: To determine whether urine neutrophil gelatinase-associated lipocalin (uNGAL) or urobiome alterations can differentiate urinary tract infections (UTI) from asymptomatic bacteriuria (ASB).<br><br>METHODS: Female 8-week-old C57BL/6 mice were instilled with either Escherichia coli CFT073 (UTI model, n=12), E. coli 83972 (ASB model, n=12), or saline (control, n=3). uNGAL was measured daily for 3 days post-instillation. Urobiome composition was assessed pre- and post-instillation using 16S rRNA sequencing. At day 3, kidneys were harvested for culture. Comparisons were made across groups for uNGAL levels and urobiome diversity.<br><br>RESULTS: Baseline &#x3b2; diversity did not differ between groups. Post-instillation, &#x3b2; diversity significantly differed across groups (p=0.01), driven by increased relative abundance of E. coli in UTI mice compared to ASB mice. Median uNGAL levels increased significantly in both UTI and ASB groups relative to controls, but no significant difference was observed between UTI and ASB groups.<br><br>CONCLUSION: Introduction of a uropathogenic E. coli strain reduced urobiome diversity, while a non-uropathogenic strain did not, suggesting strain-specific effects on microbial ecology. Bladder instillation itself also altered the urobiome. Elevated uNGAL levels were observed in both UTI and ASB models, indicating that while uNGAL reflects bacterial exposure, it does not distinguish between uropathogenic and non-uropathogenic E. coli. These findings highlight urobiome analysis as a potential tool for differentiating UTI from ASB, whereas uNGAL alone is insufficient.}, }
@article {pmid41772134, year = {2026}, author = {Sadiq, FA and Yang, N and Goeteyn, J and De Reu, K and Heyndrickx, M and Burmølle, M}, title = {Microbial Interactions Shape Spatial Organisation and Transcriptional Responses in a Model Mixed-Species Biofilm.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02701-w}, pmid = {41772134}, issn = {1432-184X}, abstract = {Dynamic social interactions within bacterial biofilms drive distinct spatial organisation and transcriptional responses. Here, we combine fluorescence in situ hybridisation (FISH), confocal laser scanning microscopy (CLSM), and RNA sequencing (RNA-Seq) to investigate a model three-species biofilm community derived from a dairy pasteuriser, comprising Stenotrophomonas rhizophila, Microbacterium lacticum, and Bacillus licheniformis. CLSM revealed species-specific biovolume dynamics and stratified 3D structures over 24 h, with S. rhizophila as the dominant species and M. lacticum exhibiting the lowest abundance yet playing an essential role as the initial coloniser. Spatial patterns reflected known pairwise interactions - commensalism, exploitation, and neutral interaction. Transcriptomic profiling of S. rhizophila revealed extensive gene expression changes in dual-species biofilms with M. lacticum, including upregulation of genes related to flagellar motility, nutrient acquisition, energy metabolism, and TonB-dependent transport. In contrast, co-culture with B. licheniformis induced minimal transcriptional changes in S. rhizophila, consistent with a neutral interaction among the two. Our findings demonstrate how interspecies interactions govern both spatial topology and functional specialisation in mixed-species biofilms which is of relevance to microbial ecology, industrial biofilm control, and the targeting of keystone biofilm species.}, }
@article {pmid41771260, year = {2026}, author = {Vaughn, SN and Pavlovsky, JC and Jackson, CR}, title = {Bacterial Communities in Sand and Seawater of Northern Gulf Coast Beaches: Temporal, Spatial, and Environmental Influences.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70309}, pmid = {41771260}, issn = {1758-2229}, support = {//U.S. Department of the Treasury/ ; //Mississippi Department of Environmental Quality/ ; //Mississippi Based RESTORE Act Center of Excellence/ ; }, abstract = {Coastal microbial communities play critical roles in marine food webs and biogeochemical cycling, yet their diversity and function remain poorly characterised in many regions. This is especially evident along the northern Gulf coast, a dynamic system with substantial freshwater influences. We used high throughput 16S rRNA sequencing to characterise bacterial communities in sand and seawater collected every 3 months (March 2024 through March 2025) from 10 beaches along a 53 km stretch of the Mississippi coast. The diversity and composition of these communities were related to environmental variation and to biogeochemical function as determined from the activity of enzymes related to carbon, nitrogen, and phosphorus mineralisation. Our findings revealed distinct bacterial communities in sand and seawater, with the microbiome of each habitat showing greater temporal variation over the course of the study than spatial variation between beaches. Patterns in bacterial community structure and proportions of abundant taxa were strongly linked to physicochemical variables, while enzyme activities suggested how microbial communities may contribute to biogeochemical processes in these habitats. Collectively, these findings provide critical information for understanding microbial ecology in this system and highlight the central role of bacteria in mediating ecosystem function along a dynamic and understudied coastline.}, }
@article {pmid41770930, year = {2026}, author = {Bai, X and Li, Z and Chen, B and Qian, X and Guo, Y and Wang, Q and Chen, C and Chen, W and Shen, X and Liu, J and Jin, J and Zhang, W and Liu, Q and Chen, S and Yang, S and Xu, L and van der Heijden, MGA and Tiedje, JM and Jiao, S and Wei, G}, title = {High bacterial diversity drives the suppression of a soilborne plant disease.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {10}, pages = {e2509303123}, doi = {10.1073/pnas.2509303123}, pmid = {41770930}, issn = {1091-6490}, abstract = {The rhizosphere microbiome plays a crucial role in the resistance to soilborne plant diseases. However, the principles needed to explain and predict which microbiota will be effective against soilborne pathogens are still lacking due to the complexity of the soil microbial community. We hypothesized that, independent of particular microbial strains, a high diversity is associated with, or increases the probability of, effective suppression. We tested this hypothesis by demonstrating that random combinations of rhizosphere microbial isolates, with the same bacterial diversity, had an equal impact on suppressing root diseases. The incidence of root rot was significantly reduced when soil bacterial diversity was high. We further investigated how high-diversity bacterial communities suppress root rot by constructing synthetic bacterial communities (SynComs). The results suggest that high bacterial diversity suppresses pathogens through mechanisms potentially including nutrient competition and the formation of physical barriers on the root surface. Our study highlights that high bacterial diversity is beneficial for suppressing soilborne plant diseases, offering a nonchemical and sustainable approach for crop disease management.}, }
@article {pmid41770403, year = {2026}, author = {D'Souza, R and Pujare, K and Balu, SK and Kanojiya, D and Garg, Y and Ghag, SB}, title = {Differential Response of Banana Root Exudates and its Components on the Growth and Development of Banana Wilt Pathogen.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02693-z}, pmid = {41770403}, issn = {1432-184X}, }
@article {pmid41770335, year = {2026}, author = {Suarez-Silva, R and Saucedo-Bazalar, M and Ramirez Saenz, M and La Torre Ramirez, RD and Caycho Ortiz, E and Orjeda, G}, title = {Exploring the Algarrobo Decline in the Pómac Forest: Unraveling the Relationship between the Endomicrobiome of Neltuma Pallida and Enallodiplosis Discordis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02711-8}, pmid = {41770335}, issn = {1432-184X}, support = {No. 042-2022-RFNP//Servicio Nacional de &#xc1;reas Naturales Protegidas Servicio Nacional de &#xc1;reas Naturales Protegidas/ ; R. R. No 009412-2021-UNMSM and Project number B2110006i - PINTERDIS - 2021//Universidad Nacional Mayor de San Marcos/ ; }, }
@article {pmid41770002, year = {2026}, author = {Feliu-Paradeda, L and Amorós-Espuña, Q and Perona-Vico, E and Casals, E and Esteve-Codina, A and Puig, S and Bañeras, L}, title = {Synergies revealed: RNA-seq study of C. acetobutylicum and C. carboxidivorans co-cultured in the presence of conductive materials.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0326225}, doi = {10.1128/spectrum.03262-25}, pmid = {41770002}, issn = {2165-0497}, abstract = {Co-cultures can improve substrate utilization and product yields, yet the dynamics between species remain highly variable and poorly understood. In this study, we investigated the metabolic and transcriptional interplay between Clostridium acetobutylicum and Clostridium carboxidivorans when co-cultured in the presence of activated carbon or magnetite, with the aim of evaluating these materials as metabolism enhancers. Fermentation profiling showed that magnetite accelerated glucose consumption and favored acid over alcohol production, with butyrate and acetate reaching yields of 0.65 and 0.62 mol/mol glucose, respectively. Alcohols (ethanol and butanol) accumulated in late fermentation and occurred concomitantly to a metabolic shift from acidogenesis to solventogenesis, potentially driven by interspecies dynamics as RNA-seq data suggested. RNA-seq analysis detected 7,369 genes and revealed C. carboxidivorans dominated in early fermentation, and C. acetobutylicum was activated later (in view of the number of reads detected for each species). Magnetite-treated samples displayed the most transcriptional variation, and species-specific patterns emerged. Changes in electron-active genes (e.g., hydA and rnf genes) suggest enhanced redox communication, highlighting the capacity of conductive materials to influence metabolic flow and regulatory pathways in microbial consortia, opening possibilities for improved bioproduction and carbon utilization.IMPORTANCEMicrobial co-cultures offer a promising strategy to expand metabolic capabilities beyond those of individual strains, yet their internal coordination remains poorly understood. This study demonstrates that conductive materials not only accelerate substrate utilization but also modulate cooperation in a co-culture of Clostridium carboxidivorans and Clostridium acetobutylicum. According to gene expression levels, we demonstrate a clear temporal division of labor between the two partners, with C. carboxidivorans initiating acidogenesis and C. acetobutylicum later driving solventogenesis. Magnetite and activated carbon addition had little effect, but changes in the expression pattern of electron-active genes (hydA and rnf) could be detected for the two species. Understanding and controlling these dynamics are key to optimizing co-cultures for industrial fermentation and biofuel production.}, }
@article {pmid41769348, year = {2026}, author = {Sun, M and Zang, D and Zhou, H and Che, YL and Chen, J}, title = {Epistemic compression in large language model explanations of the gut-liver axis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1773593}, pmid = {41769348}, issn = {2235-2988}, abstract = {BACKGROUND: The gut-liver axis integrates intestinal barrier function, microbial ecology, metabolism, immune regulation, and hepatic feedback, yet remains causally non-closed and strongly context dependent. As large language models (LLMs) increasingly mediate biomedical explanation, their ability to preserve evidentiary structure within such epistemically open frameworks requires systematic evaluation.<br><br>METHODS: We conducted a cross-platform, mixed-methods infodemiology analysis of five widely accessible LLMs. Twenty clinically grounded questions spanning five hierarchical domains from basic mechanisms to intervention and evaluation generated 100 single-turn responses. Linguistic accessibility was assessed using seven established readability indices, while epistemic integrity was evaluated using the Journal of the American Medical Association Benchmark Criteria, Global Quality Score, and a modified DISCERN framework.<br><br>RESULTS: Linguistic complexity increased as prompts progressed toward intervention and evaluation, without corresponding gains in transparency, reliability, or educational quality. Informational integrity clustered primarily by platform rather than domain. Readability indices showed strong internal concordance, whereas integrity metrics aligned only moderately and correlated weakly with readability. Item-level analysis revealed consistently high narrative clarity but systematic under-signaling of source attribution and uncertainty, resulting in over-coherent explanations that compressed conditional associations into mechanism-like claims.<br><br>CONCLUSIONS: LLM explanations of the gut-liver axis are susceptible to epistemic compression driven by narrative fluency rather than factual error. Readability does not reliably indicate epistemic robustness in decision-adjacent contexts. These findings support shifting evaluation and governance from platform comparison toward concept-conditioned requirement engineering that enforces provenance, calibrated uncertainty, and explicit separation of correlation, mechanism, and actionability as generative outputs approach clinical relevance.}, }
@article {pmid41769190, year = {2026}, author = {Al-Jamal, FF and Abuassaf, RA and Abusara, OH and Zihlif, M and Deeb, AA and Al-Rshaidat, MMD}, title = {Ethanolic extracts from deep marine sponges: A new frontier in antibacterial discovery from the Jordanian Gulf of Aqaba.}, journal = {Biomedical reports}, volume = {24}, number = {4}, pages = {44}, pmid = {41769190}, issn = {2049-9442}, abstract = {The urgent need for new antibiotics to counter bacterial resistance has led to renewed interest in marine natural products. The present study evaluated the antibacterial potential of ethanolic extracts from three deep-sea sponges: Stelletta sp., Dactylospongia cf. elegans (D. cf. elegans) and Axinella sp., which were collected from the Gulf of Aqaba off the coast of Jordan. Antibacterial activity was assessed against Gram-negative and Gram-positive bacteria using the well diffusion method, followed by determination of the Minimum Inhibitory Concentration (MIC) and Minimum Bactericidal Concentration (MBC). Only D. cf. elegans exhibited potent activity, which was limited to Gram-positive bacteria and showed inhibition zones of 7 to 21 mm and MIC and MBC values of 1 and 2 mg/ml, respectively. Stelletta sp. showed no detectable activity, and Axinella sp. displayed minimal effects. DNA barcoding (28S rRNA) confirmed that all three species belong to the class Demospongiae. LC-MS/MS analysis of the extract from D. cf. elegans identified bioactive constituents, including bolinaquinone, dactyloquinone, gallic acid and caffeic acid, which are compounds known for antibacterial properties and likely contributed to the observed activity. Thus, D. cf. elegans could be a promising source of antibacterial agents against Gram-positive pathogens and warrants further evaluation of the mechanisms involved, its toxicity, and its effects in vivo.}, }
@article {pmid41767570, year = {2026}, author = {Souza, JM and Silva, LAF and Casali, DM and Souza, JCSM and Wolfe, LA and Skarlupka, JH and Zuniga-Chaves, I and Steinberger, AJ and Deblois, CL and Scheftgen, AJ and Lelis, ALJ and Leiva, T and Rodrigues, MC and Barroso, JPR and Lasmar, PVF and Suen, G and Millen, DD}, title = {Rumen and cecum microbial dynamics following narasin inclusion in Nellore cattle diets.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1645979}, pmid = {41767570}, issn = {1664-302X}, abstract = {This study investigated the effects of narasin supplementation on the ruminal and cecal bacterial communities of feedlot Nellore cattle. We hypothesized that narasin would selectively modulate microbial populations in distinct gastrointestinal compartments without causing broad-scale disruption of overall community diversity. Sixty-four Nellore bulls (393 ± 24 kg) were assigned to a completely randomized block design and fed finishing diets containing either 0 or 20 ppm of narasin for 112 days. Rumen and cecal contents were collected at slaughter and analyzed using 16S rRNA gene sequencing to characterize bacterial community structure and composition. Overall, the rumen exhibited greater bacterial diversity and richness than the cecum, regardless of dietary treatment. Narasin supplementation did not affect Shannon diversity in either the rumen (p = 0.182) or the cecum (p = 0.298); however, Chao richness was reduced in the rumen of narasin-fed cattle (p = 0.028). Beta-diversity analyses based on Bray-Curtis and Jaccard dissimilarities revealed no significant differences in overall community structure between treatments in either compartment (p > 0.198). At the phylum level, narasin supplementation was associated with a reduction in Firmicutes and a concomitant increase in Bacteroidetes in the rumen. In contrast, Firmicutes predominated in the cecum, and narasin significantly increased the relative abundance of this phylum, particularly members of the order Clostridiales (p = 0.05). In conclusion, narasin exerts selective effects on specific bacterial populations rather than inducing widespread shifts in microbial diversity. These results provide novel insights into how narasin modulates microbial ecology in both the rumen and the understudied cecum, highlighting compartment-specific responses that may contribute to improved feed efficiency in beef cattle.}, }
@article {pmid41764142, year = {2026}, author = {Brayley, ODM and McCready, K and Liu, S and Convey, P and Chen, Y and Ullah, S and Teets, N and Hayward, SAL}, title = {The Microbiome of an Invasive Antarctic insect, Eretmoptera Murphyi (Diptera: Chironomidae), and its Potential Role in Nutrient Cycling.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02706-5}, pmid = {41764142}, issn = {1432-184X}, support = {NE/S007350/1//NERC CENTA2/ ; NE/S007350/1//NERC CENTA2/ ; NE/T009446/1//NSFGEO-NERC/ ; NE/T009446/1//NSFGEO-NERC/ ; NE/T009446/1//NSFGEO-NERC/ ; OPP-1850988//National Science Foundation/ ; 700545//USDA National Institute of Food and Agriculture Hatch Project/ ; RF-2024-396/2//Leverhulme Research Fellowship/ ; }, }
@article {pmid41763651, year = {2026}, author = {Angebault, C and Bardoul, M and Fillâtre, P and Bouju, P and Rieul, G and Fedun, Y and Launey, Y and Reizine, F}, title = {Clinical landscape and mortality risk in Intensive Care Unit peritonitis in a low-MultiDrug Resistant setting: A multicentre cohort study.}, journal = {Anaesthesia, critical care &amp; pain medicine}, volume = {}, number = {}, pages = {101783}, doi = {10.1016/j.accpm.2026.101783}, pmid = {41763651}, issn = {2352-5568}, abstract = {INTRODUCTION: Peritonitis is a frequent cause of sepsis in the intensive care unit (ICU) and is characterized by substantial microbiological variability, including multidrug-resistant organisms (MDROs).<br><br>METHOD: We conducted a retrospective, multicenter cohort study including ICU patients diagnosed with intra-abdominal infection across 4 hospitals 2020-2022). The primary objective was to describe clinico-biological features, and microbiological characteristics according to the setting of the peritonitis (Community peritonitis (CP), early nosocomial peritonitis (ENP), or late nosocomial peritonitis (LNP)). Additionally, we analyzed 90-day survival using Kaplan-Meier curves and multivariable Cox regression.<br><br>RESULTS: Among the 392 patients included in the study period, 195 experienced a CP, 88 an ENP, and 109 an LNP. Extended-spectrum beta-lactamase-producing bacteria were identified in 24 patients (6.1%), and carbapenem-resistant bacteria in 5 patients (1.3%). MDRO rates differed significantly: carbapenem-resistant bacteria were more frequent in LNP patients (3.7% vs. 0.0% in CP and 0.5% in ENP; p&#x2009;=&#x2009;0.03), and cephalosporinase-producing bacteria were more common in nosocomial settings (40.4% in LNP vs. 19.0% in CP; p&#x2009;<&#x2009;0.001). Ninety-day mortality was 34.7% overall and did not differ across settings (p&#x2009;=&#x2009;0.345). Age and SAPS II were independently associated with mortality. Finally, appropriate empirical antimicrobial therapy was not associated with improved 90-day survival (p&#x2009;=&#x2009;0.128).<br><br>CONCLUSION: Through this large cohort study of ICU patients with peritonitis, we observed a low prevalence of MDRO. Our findings challenge the relevance of broad-spectrum empirical therapy in low-MDRO regions and underscore the need for tailored antimicrobial stewardship strategies.}, }
@article {pmid41762238, year = {2026}, author = {Phauk, S and Sin, S and Terenius, O}, title = {Symbiotic Diversity of Sap-Feeding Auchenorrhyncha (Hemiptera) in the Upland Landscapes of Central Cardamom Mountains, Cambodia.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02724-3}, pmid = {41762238}, issn = {1432-184X}, }
@article {pmid41757148, year = {2025}, author = {Bektaş, A and Ulusoy, M}, title = {Gluten Tolerance through Microbial and Cultural Adaptation: A Holistic Model for Celiac Disease and Non-celiac Gluten Sensitivity.}, journal = {Euroasian journal of hepato-gastroenterology}, volume = {15}, number = {2}, pages = {185-189}, pmid = {41757148}, issn = {2231-5047}, abstract = {AIM AND BACKGROUND: Celiac disease (CD) and nonceliac gluten sensitivity (NCGS) are increasing in public and scientific focus. Interestingly, regions with traditionally high gluten consumption such as Turkey, Iran, and the Mediterranean show lower CD prevalence than the Western countries. This paradox indicates that genetic predisposition alone, such as HLA DQ2 or DQ8 carriage, does not fully explain gluten intolerance. Understanding environmental, microbial, and cultural contributors may clarify the development of gluten tolerance.<br><br>METHODS: This narrative review synthesizes current evidence from epidemiology, microbiology, immunology, and nutritional science to propose an integrative hypothesis. Relevant literature was examined to explore interactions among diet, gut microbiota, and immune tolerance mechanisms that influence responses to gluten exposure.<br><br>RESULTS: Findings suggest that early life gluten exposure, microbial diversity, and long-term dietary adaptation enhance mucosal tolerance to gluten. Specific microorganisms such as Lactobacillus, Bifidobacterium, and Prevotella can enzymatically degrade immunogenic gluten peptides including the 33-mer &#x3b1;2-gliadin fragments. Reduced microbial diversity and the consumption of ultra-processed foods may contribute to heightened gluten sensitivity and immune dysregulation.<br><br>CONCLUSION: Gluten is not inherently toxic; its immunogenicity depends on host microbiota composition, environmental exposures, and dietary context. A systems biology approach that integrates microbial ecology, evolutionary adaptation, and immunonutrition may better explain gluten tolerance variability across populations.<br><br>CLINICAL SIGNIFICANCE: Recognizing gluten tolerance as a modifiable, microbiota influenced process may guide more individualized dietary recommendations, reduce unnecessary gluten avoidance, and promote evidence-based clinical management of gluten-related disorders.<br><br>HOW TO CITE THIS ARTICLE: Bekta&#x15f; A, Ulusoy M. Gluten Tolerance through Microbial and Cultural Adaptation: A Holistic Model for Celiac Disease and Non-celiac Gluten Sensitivity. Euroasian J Hepato-Gastroenterol 2025;15(2):185-189.}, }
@article {pmid41757127, year = {2026}, author = {Saha, A and Jones, JM and Plummer, A and Larkin, JW}, title = {Formation of a swelling gel underlies a morphological transition in Bacillus subtilis biofilms.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.02.20.707077}, pmid = {41757127}, issn = {2692-8205}, abstract = {Microbes across species and environments form biofilms, living materials composed of cells and extracellular polymers. Biofilm-dwelling cells benefit from emergent soft matter physics that sculpts three-dimensional morphologies and osmotically absorbs nutrients. Although biofilms are modeled as viscoelastic gels, the physical origins of the phase transition underlying their conversion from groups of cells to living gels have not been systematically investigated. Here, we show that Bacillus subtilis biofilms use polymer composition to tune their physical properties and drive gel formation. Using imaging and water immersion experiments with matrix knockout strains, we demonstrate the complementary roles of two polymers in this developmental transition: hydrophilic poly- γ -glutamate swells colonies by absorbing water and exopolysaccharides serve as effective cross-linkers, causing a sol-gel-like phase transition that imparts structural integrity. With matrix knockout co-culture biofilms, we independently modulate the production of each polymer and reveal a phase space of biofilm morphologies. Colonies that produce both polymers develop macroscopic wrinkles. A thin-film model predicts biofilm wrinkling from swelling-generated internal strain coupled to elasticity. The model reproduces the shape of our observed morphological phase diagram. Our results demonstrate that bacteria leverage gelation to vary their material properties and morphologies, with implications for microbial ecology and engineering living matter.}, }
@article {pmid41754095, year = {2026}, author = {Mafe, AN and Büsselberg, D}, title = {The Diet-Microbiota-Polyamine Axis in Intestinal Aging: Microbial Pathways, Functional Foods, and Physiological Implications.}, journal = {Nutrients}, volume = {18}, number = {4}, pages = {}, pmid = {41754095}, issn = {2072-6643}, support = {NPRP 14S0311-210033//Qatar National Research Fund/ ; }, abstract = {Intestinal aging is characterized by a gradual decline in epithelial renewal capacity, barrier function, immune balance, and metabolic regulation, often accompanied by shifts in gut microbial composition. Polyamines, including putrescine, spermidine, and spermine, are vital microbial-host metabolites that support intestinal cell growth, autophagy, immune modulation, and mucosal repair. With advancing age, both host-derived and microbiota-mediated polyamine production declines, contributing to intestinal dysfunction and heightened vulnerability to inflammation and age-related disorders. This review explores the diet-microbiota-polyamine axis as a key biological framework influencing intestinal aging. It aims to integrate evidence on how dietary components and functional foods shape gut microbial ecology and, in turn, regulate microbial polyamine biosynthetic pathways that impact intestinal health. The review highlights major microbial contributors to polyamine metabolism, particularly lactic acid bacteria, and outlines mechanistic pathways linking polyamines to epithelial regeneration, inflammatory control, and gut barrier maintenance. It further discusses how age-associated dysbiosis disrupts these interactions and evaluates nutritional and microbial-based strategies such as fermented foods, prebiotics, and probiotics that may enhance polyamine availability and restore gut homeostasis. From the standpoint of food microbiology and human physiology, this synthesis underscores the translational potential of targeting microbial polyamine production through diet-based interventions. This article presents a narrative review synthesizing experimental, animal, and emerging human evidence on microbial and dietary polyamines in intestinal aging. In conclusion, modulating the diet-microbiota-polyamine axis represents a promising strategy to promote healthy intestinal aging, meriting deeper mechanistic exploration and validation through clinical studies.}, }
@article {pmid41753780, year = {2026}, author = {Palanisamy, V and Bosilevac, JM and Barkhouse, DA and Velez, SE and Dass, SC}, title = {Unraveling the Coevolutionary Dynamics of Phage and Bacterial Protein Warfare Occurring in the Drains of Beef-Processing Plants.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, pmid = {41753780}, issn = {2076-2607}, support = {2020-67017-30776//USDA-NIFA/ ; }, abstract = {Phages, the most abundant entities on Earth, exhibit a complex interplay with bacteria, especially within environmental biofilms, resulting in an ecological arms race. This study investigates the interaction between phages and bacteria in the drains of beef-processing plants using high-throughput sequencing and metagenomic analysis. Metagenomic data collected from 75 drain samples from beef-processing plants were analyzed to investigate phage-bacterial interactions. First, assembled contigs were screened to identify viral sequences, which were then taxonomically annotated to determine the viral composition, including phages. Functional annotation of these viral sequences provided information about the viral genes and their roles in bacterial interactions specifically associated with attack and counterattack of bacteria. In parallel, bacterial contigs were examined to identify genes associated with antiphage defense systems, providing insights into the strategies adapted by bacteria to resist phage infection. Taxonomic annotation of viral sequences from the bulk metagenomic data revealed the presence of phages targeting Pseudomonas, Klebsiella, and Enterococcus. The higher abundance of Pseudomonas phages aligns with our previous study, where Pseudomonas was identified as the dominant bacterial genus, suggesting potential copersistence of phages and their hosts. Functional annotation of phage contigs revealed infective and lysis-related genes, highlighting their potential role in bacterial attack. Conversely, bacterial contigs encoded antiphage defense systems, including CRISPR-Cas, restriction-modification, and other defense-related genes. The study also uncovered the presence of anti-CRISPR proteins in phages, suggesting a counterattack on the bacterial defense. These findings provide evidence for phage attack, bacterial defense, and phage counterattack and may showcase the ongoing coevolutionary arms race between phages and bacteria. While this evidence looks promising, these results remain preliminary and further studies are needed to validate these findings. Still, this study provides a foundational understanding of bacteria-phage coexistence in beef-processing plant drains and paves the way for further explorations of these intricate interactions and their possible applications in controlling pathogenic microorganisms within biofilms.}, }
@article {pmid41753774, year = {2026}, author = {Dobrzyński, J and Naziębło, A and Kulkova, I and Szpytma, M and Antosik, A and Sitarek-Andrzejczyk, M and Wróbel, B}, title = {Paenibacillus-Pseudomonas Consortium Improves Barley Performance with Minimal Impact on Native Rhizobacterial Community.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, pmid = {41753774}, issn = {2076-2607}, abstract = {The intensive use of mineral nitrogen fertilizers in cereal production contributes to environmental degradation, highlighting the need for more sustainable crop management strategies. Plant growth-promoting bacteria (PGPB) offer a promising alternative; however, their effects on native rhizosphere communities remain underexplored, particularly in barley. This study evaluates the impact of a bacterial consortium composed of Paenibacillus sp. Z15 and Pseudomonas sp. KR227 on barley growth, yield, and rhizosphere bacteria under field conditions in temperate climate (2025). Plant biometric traits, photosynthetic pigment content, and soil properties were measured, and rhizobacterial communities were analyzed using 16S rRNA gene (V3-V4) sequencing. The PGPB consortium significantly increased early root biomass (120%), shoot height (7.8%), and grain yield (15.5%), while no significant effects were observed on soil chemistry or photosynthetic pigments. Sequencing revealed no major changes in alpha or beta diversity; however, transient shifts in the relative abundance of specific taxa were detected relatively shortly after inoculation and mostly disappeared by harvest. These findings indicate that the Paenibacillus-Pseudomonas consortium can enhance barley performance without disrupting native rhizobacterial communities. Overall, the results support the potential of PGPB as a sustainable agronomic tool and provide new insights into PGPB-microbiome interactions in barley under field conditions.}, }
@article {pmid41753768, year = {2026}, author = {Frantz, CM and Crump, BC and Carpenter, S and Firth, E and Orellana, MV and Light, B and Junge, K}, title = {Microbial Ecology of Rotten Sea Ice: Implications for Arctic Carbon Cycling with Global Warming.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020482}, pmid = {41753768}, issn = {2076-2607}, support = {1656026//USA National Science Foundation/ ; PLR-1304228//USA National Science Foundation/ ; }, abstract = {"Rotten" sea ice, ice in an advanced stage of melt, represents an important but understudied habitat in the rapidly changing Arctic. As Arctic warming accelerates, this late-season ice type will become more prevalent, yet little is known about its microbial inhabitants or their roles in Arctic marine biogeochemical cycles. We examined microbial communities (prokaryote and algal abundance, 16S and 18S rRNA gene and transcript sequencing) and biogeochemical properties of rotten sea ice and earlier-season ice near Utqiaġvik, Alaska, USA. Rotten ice was comparatively warm, isothermal, and largely drained of brine, with extensive, interconnected pore networks linked to melt ponds above and seawater below. Unlike earlier-season ice, fluids saturating rotten ice were vertically homogeneous in pH, dissolved inorganic carbon, prokaryote and phytoplankton abundance, and microbial community composition. However, particulate carbon and nitrogen exhibited strong vertical gradients, with the highest concentrations near the surface. Microbial communities in rotten ice were significantly different from those in earlier-season ice and varied between individual floes. These findings indicate that rotten ice constitutes a distinct microbial habitat and may serve as an important source of nutrient-rich particulate matter in the future Arctic Ocean during the summer melt season.}, }
@article {pmid41753753, year = {2026}, author = {Lerner, A and Lieber, AD and Nelson-Dooley, C and Leu, A and Perro, M and Koch, G and Benzvi, C and Smith, J}, title = {Genetically Modified Microorganisms: Risks and Regulatory Considerations for Human and Environmental Health.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020467}, pmid = {41753753}, issn = {2076-2607}, abstract = {Advances in affordable genetic engineering have accelerated the creation and large-scale environmental release of genetically modified microorganisms (GMMs). While beneficial applications exist, GMMs may present unique, long-term risks to human and environmental health. Unlike static chemicals, GMMs are biologically active, self-replicating entities capable of rapid mutation and global dispersal. Current regulatory frameworks place responsibility on each country to regulate GMMs, without a clear, coordinated international policy. This review details critical risk scenarios, including horizontal gene transfer to native species and the possible disruption of vital human microbiomes (gut, oral, and infant), which could increase resistance to degradation, promote traits that expand a microbe's range of hosts or ecological niches, and enhance the production of novel metabolites with unexpected biological activity. In soil, GMMs may support the emergence of "super bugs" or destabilize carbon sequestration cycles, potentially impacting climate resilience. Engineered microbial enzymes in the food supply may also act as environmental drivers of autoimmunity. Given the limited understanding of microbial ecology, we propose a decision-based biosafety workflow emphasizing pre-release risk assessment and continuous post-release monitoring. We urge national and international regulators to adopt the precautionary principle to better protect human health and the environment from the potential negative outcomes of GMMs.}, }
@article {pmid41753641, year = {2026}, author = {Pérez-García, LA and Sáenz-Mata, J and Fortis-Hernandez, M and Preciado-Rangel, P}, title = {Plant Growth-Promoting Rhizobacteria as a Strategy to Enhance Enzymatic and Metabolic Tolerance of Cucumis sativus L. Under Salinity Stress.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020351}, pmid = {41753641}, issn = {2076-2607}, abstract = {Cucumis sativus L., a salt-sensitive horticultural crop, is severely affected by soil salinity, which disrupts photosynthetic efficiency and metabolic homeostasis. This study quantified the effects of Plant Growth-Promoting Rhizobacteria (PGPR)-Pseudomonas paralactis, Bacillus cereus, Sinorhizobium meliloti, and Acinetobacter radioresistens-on key enzymatic indicators of cucumber seedlings exposed to 0, 50, 100, and 150 mM NaCl. PGPR inoculation significantly enhanced bacterial stress-mitigation and hormonal pathways, with ACC-deaminase activity increasing by up to 78.8% (A. radioresistens, 150 mM NaCl) and nitrilase activity by 50.5% (S. meliloti, 50 mM NaCl). Auxin-related pathways were strongly induced, as reflected by increases of up to 51.1% in the IAM pathway (P. paralactis) and 42.9% in the IPA pathway (A. radioresistens). In plant tissues, key metabolic enzymes exhibited high stability under salinity, with ProDH and NDPK activities increasing by up to 4.5% and 2.35%, respectively, while RuBisCO activity remained unaffected across treatments. These results demonstrate that PGPR function as effective bioestimulants by coordinating hormonal regulation and metabolic resilience, providing a sustainable biotechnological strategy to enhance cucumber tolerance to salinity stress.}, }
@article {pmid41751059, year = {2026}, author = {Tapingkae, W and Srinual, O and Srinual, P and Khamtavee, P and Pintalerd, N and Chaiyaso, T and Yachai, M and Tapingkae, T and Kanmanee, C}, title = {Dietary Coffee Silverskin Supplementation: Effect on Growth Performance, Carcass Traits, and Gastrointestinal Health of Broilers.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {4}, pages = {}, doi = {10.3390/ani16040598}, pmid = {41751059}, issn = {2076-2615}, support = {FF66/045//Fundamental Fund 2023, Chiang Mai University/ ; }, abstract = {Coffee silverskin (CSS) remains a neglected poultry additive; investigating its bioactive potential is essential for optimizing agricultural productivity and enhancing food security via advanced nutrition. This study analyzed how dietary CSS supplementation influences broiler growth, slaughter characteristics, meat quality, cecal microbial ecology, and intestinal histomorphology. A total of 400 one-day-old male Ross 308 broilers were randomly assigned to four dietary treatments with 10 replicates of 10 birds each. Experimental treatments consisted of a negative control (NC, basal diet) and CSS-supplemented groups (0.5, 1.0, and 2.0 g/kg, designated CSS0.5, CSS1.0, and CSS2.0, respectively). All data were subjected to one-way ANOVA using the procedure of SPSS 23.0. Coffee silverskin supplementation, specifically at 1.0-2.0 g/kg, optimized broiler growth performance, significantly elevating body weight and average daily gain (p < 0.05). While carcass yield improved in a dose-dependent manner, fundamental meat quality-pH and shear force-remained stable. Crucially, CSS inclusion reconfigured cecal ecology, selectively suppressing Escherichia coli and Salmonella sp. while enhancing Lactobacillus populations (p < 0.001). This microbial shift mirrored histological gains, notably enhanced villus height and villus height-to-crypt ratios (p < 0.05). These findings demonstrate that CSS, particularly at 1.0-2.0 g/kg, enhances broiler performance, carcass quality and gut health.}, }
@article {pmid41750824, year = {2026}, author = {Oh, SC and Lee, SJ and Ding, K and Shen, J and Huang, C and Kang, SN and Reaney, MJT and Kim, YJ and Shim, YY}, title = {Kimchi Fermentation-Driven Detoxification of Flaxseed: Impact on Physicochemical Quality and Antioxidant Potential.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {4}, pages = {}, doi = {10.3390/foods15040632}, pmid = {41750824}, issn = {2304-8158}, support = {RS-2023-00263064//Ministry of Science and ICT/ ; }, abstract = {Flaxseed (Linum usitatissimum L.) is a rich source of α-linolenic acid (ALA) and lignans but contains toxic cyanogenic glycosides (CGs) that limit its application in foods. This study investigated the efficacy of a specialized Lactobacillaceae consortium in detoxifying flaxseed and the subsequent effects of adding this cyanogenic glycoside-depleted flaxseed (CGDF) to a kimchi matrix. Ground flaxseed and CGDF were added to the kimchi seasoning mixture at concentrations of 0.5%, 1.0%, and 2.0% (w/w) and fermented at 4 °C for 8 weeks. Analytical results confirmed that the fermentation process reduced linustatin and neolinustatin to undetectable levels (<500 mg/kg) and reduced total hydrogen cyanide (HCN) to below the Japanese regulatory limit of 10 mg/kg established under the Food Sanitation Act. During fermentation, CGDF-supplemented groups exhibited a delayed decrease in pH and higher retention of free sugars and vitamin C compared to the control and raw flaxseed groups. Notably, the 2.0% CGDF group maintained high oxidative stability of ALA, which we attribute to a putative antioxidant protection mechanism driven by the bioconversion of lignan glycosides into bioactive aglycones. These findings suggest that incorporating biologically detoxified flaxseed into kimchi creates a functional food system that ensures safety while enhancing nutritional stability. Overall, this work provides foundational evidence for developing safe, nutritionally enhanced functional foods within the One Health framework, integrating food safety, microbial ecology, and improved bioactive compound availability.}, }
@article {pmid41750446, year = {2026}, author = {Magnano San Lio, R and Maugeri, A and Barchitta, M and Favara, G and La Rosa, MC and La Mastra, C and Ferrante, M and Agodi, A}, title = {The Wastewater Resistome: A Shotgun Metagenomics Analysis of Urban Treatment Plants in Sicily.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/antibiotics15020148}, pmid = {41750446}, issn = {2079-6382}, support = {MUR-PNRR project SAMOTHRACE (ECS00000022)//European Union (NextGeneration EU)/ ; }, abstract = {Background/Objectives: Antimicrobial resistance (AMR) in wastewater represents a valuable reservoir of information for wastewater-based epidemiology (WBE) and a major environmental and public health concern, as wastewater treatment plants (WWTPs) are recognized hotspots for the accumulation and dissemination of antimicrobial resistance genes (ARGs). Within the One Health framework, and to better understand the contribution to AMR spread and the potential of metagenomic surveillance, this study aimed to characterize the taxonomic, functional, and resistome profiles of three WWTPs in Sicily, specifically those located in Catania, Giarre, and Syracuse. Methods: Sixty-nine composite influent samples were collected between February 2022 and December 2023. Shotgun metagenomic sequencing was performed on the Illumina NovaSeq platform. Bioinformatic analyses were conducted to assess microbial community composition, functional pathways, and ARG prevalence across sites. Results: Dominant genera included Aliarcobacter, Bacteroides, and Acinetobacter. Site-specific taxonomic variations reflected differences in local microbial ecology. Functional profiling revealed enrichment in membrane-associated, ribosomal, and energy metabolism pathways, consistent with the expected functional redundancy of wastewater microbiomes. Resistome analysis detected a diverse and ubiquitous array of ARGs, dominated by β-lactam and macrolide resistance genes, followed by aminoglycoside, sulphonamide, and tetracycline classes. Conclusions: These findings highlight urban wastewater as a relevant reservoir and dissemination route for AMR and support the integration of metagenomic approaches into wastewater surveillance programs. By providing region-specific, integrated taxonomic, functional, and resistome data from Sicilian WWTPs, this study contributes to the growing body of evidence supporting WBE as a valuable tool for AMR monitoring and One Health-oriented risk assessment.}, }
@article {pmid41749772, year = {2026}, author = {Shang, J and Dong, C and Zhou, Q and Chai, J and Wei, Y}, title = {The Bacteriophage VMY 22 Has Enhanced the Stability of Its Functional Proteins via Adaptive Evolution in a Temperature-Varying Environment.}, journal = {Bioengineering (Basel, Switzerland)}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/bioengineering13020233}, pmid = {41749772}, issn = {2306-5354}, abstract = {Temperature fluctuations strongly affect microbial viability, often inducing adaptive responses. In this study, we employed the psychrophilic bacterium Bacillus mycoides 41-22 and its associated phage VMY22, originally isolated from the Mingyong Glacier, to investigate phage adaptability under varied temperature conditions. Through selective enrichment at 4 °C, 15 °C, 28 °C, and 32 °C, we observed clear differences in phage infectivity, as assessed by plaque assays, along with genomic mutations and protein structural changes. Notably, mutations predominantly occurred in functional genes (ATPase, endolysin), while the examined structural loci remained conserved. Homology modeling revealed distinct adaptations in protein tertiary structures corresponding to environmental temperatures, suggesting that phage evolution mainly affects post-adsorption processes. Our findings elucidate a novel mechanism of temperature-driven functional protein evolution among cold-adapted bacteriophages (phage) and providing insights into their potential applications in microbial ecology and biotechnology.}, }
@article {pmid41748761, year = {2026}, author = {de Lima, LVA and da Silva, MF and de Oliveira, LM and de Assis, MCT and Carvalho, ICO and Fuzinatto, IM and Semprebon, SC and de Oliveira Nocetti, RV and Lazarin-Bidoia, D and Nakamura, CV and Felicidade, I and Lepri, SR and Favaron, PO and Dealis, ML and Cabeça, LF and Filho, GA and Mantovani, MS}, title = {PEGylated liposomal fluopsin C triggers cuproptosis and ferroptosis pathways and suppresses 3D tumor spheroid growth in NCI-H460 cells.}, journal = {Archives of toxicology}, volume = {}, number = {}, pages = {}, pmid = {41748761}, issn = {1432-0738}, }
@article {pmid41747730, year = {2026}, author = {Matias Rodrigues, JF and Tackmann, J and Malfertheiner, L and Patsch, D and Perez-Molphe-Montoya, E and Näpflin, N and Gaio, D and Rot, G and Danaila, M and Peluso, ME and Dmitrijeva, M and Schmidt, TSB and von Mering, C}, title = {The MicrobeAtlas database: Global trends and insights into Earth's microbial ecosystems.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2026.01.021}, pmid = {41747730}, issn = {1097-4172}, abstract = {Environmental DNA sequencing has revolutionized our understanding of microbial diversity and ecology. Microbiomes have now been sequenced across the entire planet-from the deep subsurface to the mountaintops-covering a myriad of hosts, biomes, and conditions. Yet, the diversity of sequencing and processing strategies hampers universal insights. MicrobeAtlas unifies more than two million microbiome samples in a single resource, harmonized to facilitate discoveries across technologies. Communities are hierarchically quantified at adjustable small subunit rRNA marker gene resolution and feature detailed metadata, including rich geographic information. Connections to the genome, phenotype, and ecological resources enable multimodal insights. Microbial lineages can be reliably tracked across environments, including a "long tail" of rare, uncharacterized species. Recurring community structures and geographic preferences become apparent, and global, taxonomy-specific generalism trends emerge. With MicrobeAtlas (www.microbeatlas.org), known and newly described species and communities can readily be placed into their ecological context, taking full advantage of earlier work.}, }
@article {pmid41746386, year = {2026}, author = {Wang, Z and Wang, Q and Liu, Y and Du, W and Hong, L and Zhou, D and Asiegbu, FO and Wu, P and Ma, X and Wang, K}, title = {Soil Nutrient Availability By Beneficial Bacteria of Forest Trees: From Mechanisms To Applications.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02728-z}, pmid = {41746386}, issn = {1432-184X}, abstract = {As global environmental challenges intensify, enhancing forest health and soil quality has emerged as a crucial area of research. Understanding and application of beneficial bacteria in forestry industry is urgently needed as an environmentally friendly and sustainable approach. Although thousands of patents have been registered for microbial application in agriculture and forestry, the mechanisms and application of beneficial bacteria on the soil nutrient availability have not been well summarized. This review investigated the role of beneficial bacteria in tree growth, particularly their contributions to soil nutrient availability in forest trees. We summarized that beneficial bacteria significantly enhance the availability of essential elements such as nitrogen, phosphorus, potassium, and iron by promoting nutrient cycling and transformation within the soil. This process supports tree growth and improves soil quality. Additionally, beneficial bacteria facilitate plant growth by synthesizing plant hormones and inducing resistance to biotic and abiotic stresses. This review concludes by discussing practical implications of beneficial bacterial colonization and application for enhancing soil nutrient levels, along with potential future research directions. We have enriched the theoretical framework of forest-associated bacteria and provided a scientific basis that can inform forest management and ecological restoration.}, }
@article {pmid41745260, year = {2026}, author = {Christinaki, AC and Floudas, D and Myridakis, AI and Gonou-Zagou, Z and Kouvelis, VN}, title = {Cladobotryum rhodochroum sp. nov. (Hypocreales, Ascomycota): A New Fungicolous Species Revealed by Morphology, Phylogeny, and Comparative Genomics.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, pmid = {41745260}, issn = {2309-608X}, support = {19620//Hellenic Foundation for Research and Innovation/ ; }, abstract = {Species of the ascomycetous genus Cladobotryum (Hypocreales, Hypocreaceae) are ecologically and economically important mycoparasites that cause cobweb disease in cultivated and wild mushrooms. Despite their significance as fungal pathogens and producers of bioactive metabolites, the taxonomy of Cladobotryum remains unresolved due to extensive morphological plasticity, complex teleomorph-anamorph connections, and the presence of cryptic species. This study employs an integrative approach combining micro- and macromorphological characterization, multi-locus phylogeny (ITS, rpb2, and tef-1a), and comparative genomics to clarify the taxonomic position of the Greek isolate Cladobotryum sp. ATHUM 6904, previously designated as an unclassified red-pigmented (URP) strain. Phylogenetic analyses demonstrated that URP strains form a distinct, well-supported clade closely related to C. tenue and C. rubrobrunnescens, yet genetically and morphologically distinct from both. Comparative genomic analyses of isolate ATHUM 6904 and the ex-type strains of C. tenue and C. rubrobrunnescens revealed pronounced divergence in transposable element content, mitochondrial genome architecture, gene order, orthologous gene composition, secondary metabolite biosynthetic potential, and overall genomic distance. Micro- and macromorphological comparisons further supported the differentiation of isolate ATHUM 6904 from both reference species. Based on the combined molecular, morphological, and genomic evidence, the Greek isolate ATHUM 6904 is described as a novel species, Cladobotryum rhodochroum sp. nov.}, }
@article {pmid41744634, year = {2026}, author = {Pérez, E and Sanjuán, E and Jůzl, M and Raposo, A and Saraiva, A and Jaber, JR and Carrascosa, C}, title = {Active Antimicrobial Packaging Systems: Mechanisms of Microbial Control and Applications in Food Preservation.}, journal = {Biology}, volume = {15}, number = {4}, pages = {}, pmid = {41744634}, issn = {2079-7737}, abstract = {Microbial spoilage and foodborne pathogens remain central challenges in food safety, driven by the metabolic resilience and ecological adaptability of bacteria, yeasts, and molds across diverse food matrices. Active antimicrobial packaging has emerged as a biologically informed strategy that directly targets microbial physiology through controlled release or contact-mediated mechanisms. These systems employ natural antimicrobials, bacteriocins, essential oils, and metal nanoparticles to disrupt cell membranes, inhibit enzymatic pathways, generate reactive oxygen species, or interfere with quorum sensing, resulting in substantial reductions in microorganisms such as Listeria monocytogenes, Salmonella spp., E. coli O157:H7, Pseudomonas spp., Brochothrix thermosphacta, and spoilage fungi. In real food environments, these interventions achieve multi-log reductions and attenuate microbial metabolism, though efficacy varies with pH, water activity, fat content, and storage temperature. Oxygen scavengers further reshape microbial ecology by suppressing aerobic spoilage organisms while inadvertently favoring anaerobic competitors. Despite promising outcomes, concerns regarding nanoparticle migration, microbial resistance potential, and matrix-dependent performance highlight the need for deeper microbiological validation. Future progress will require integrative research linking microbial ecology, packaging material science, and mechanistic toxicology. By aligning with microbial behavior at the cellular and ecosystem levels, active antimicrobial packaging represents a powerful, biologically grounded approach to mitigating foodborne risks.}, }
@article {pmid41744504, year = {2026}, author = {Firrman, J and Liu, L and Mahalak, K and Lemons, JMS and Narrowe, A and Friedman, ES and Wu, GD and Van de Weile, T}, title = {An in vitro model of the small intestinal microbiota provides key insights into interindividual variability in structure and function.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0137325}, doi = {10.1128/msystems.01373-25}, pmid = {41744504}, issn = {2379-5077}, abstract = {UNLABELLED: Although there is clear evidence demonstrating the importance of the small intestinal microbiota (SIM) for nutrient utilization within the upper gastrointestinal tract, research is limited by difficulties accessing this community in vivo. Additionally, the high level of interindividual variability in taxonomic structure, which is well documented for the SIM, raises the question of how such divergent communities fill the same physiological roles. Here, we designed and evaluated an in vitro model of the terminal ileum representative of four unique donors and utilized it to interrogate interindividual variability. Shotgun sequencing confirmed that the in vitro communities were representative of their specific inocula and composed of facultative and obligate anaerobic taxa typical of the SIM, such as Klebsiella, Escherichia, Streptococcus, and Enterococcus. Untargeted metabolomics revealed a high degree of similarity between communities in terms of which metabolites were produced. Combining metagenomics and metabolomics, a core set of genes, features, and metabolites was found shared across all communities despite the high degree of structural variability observed. These results indicated that while the taxonomic structure of the SIM was variable between individuals, there were similarities in functional outcome due to underlying gene representation in the microbiome. Moving forward, this model system may serve as a starting point to further elucidate the role of the SIM in nutrition and health.<br><br>IMPORTANCE: The small intestinal microbiota (SIM) plays a pivotal role in nutrient digestion and absorption and immune function, with researchers continuing to find connections between this community and human health. Expanding on the currently available methods within the field to study this community, here, an in vitro model of the SIM was developed and designed to mimic the terminal ileum. Metagenomic and metabolomic analysis confirmed that this model recapitulated the unique communities of four different donors while maintaining the interindividual variability canonical of the SIM. Despite variation in taxonomic structure, in-depth analysis found that there was a core set of genes shared among the four in vitro communities that correlated with a relatively consistent metabolomic signature. These significant findings provided unique insight into the relationship between structural and functional variability for the SIM and furthered the field's understanding of how such structurally variable communities have such similar physiological outcomes.}, }
@article {pmid41743866, year = {2025}, author = {Tarigan, MB and Saragih, RM and Tarigan, KA and Ginting, F}, title = {Antimicrobial resistance and empirical antibiotic use in diabetic foot infections: A retrospective study from Indonesia.}, journal = {Narra J}, volume = {5}, number = {3}, pages = {e2895}, pmid = {41743866}, issn = {2807-2618}, abstract = {Diabetic foot infection (DFI) represents a major complication of diabetes mellitus with significant morbidity, frequently leading to amputation if not optimally managed. The aim of this study was to analyze clinical, microbiological, and antibiotic susceptibility data from patients with type 2 diabetes who presented with foot infections in Indonesia. The retrospective study, conducted at St. Elisabeth Hospital in North Sumatra, Indonesia, predominantly comprised male farmers with a mean diabetes duration of 8.6 years, most of whom exhibited advanced ulcer severity (64.5% at Wagner grade III). Surgical debridement was performed in 79.0% cases, and amputation in 21.0% of cases. Laboratory investigations revealed poor glycemic control (mean HbA1c 10.12%) and biochemical markers indicative of systemic inflammation and renal impairment. Microbial cultures identified a predominance of Gram-negative bacteria (58.1%), primarily Klebsiella pneumoniae, Proteus mirabilis, and Escherichia coli, whereas Gram-positive isolates (41.9%) were dominated by Staphylococcus aureus, including methicillin-resistant strains. Empirical outpatient and inpatient antibiotic regimens commonly included amoxicillin, ciprofloxacin, metronidazole, and ceftriaxone; however, in vitro susceptibility testing demonstrated limited efficacy of β-lactams such as ampicillin and amoxicillin (<10% sensitivity). In contrast, linezolid, amikacin, vancomycin, carbapenems, and fosfomycin exhibited superior activity against the isolated pathogens. These findings emphasize the critical need for empirical antibiotic guidelines tailored to local microbial ecology and resistance profiles, integrated with early surgical management, stringent glycemic control, and multidisciplinary care. This comprehensive approach is essential to reduce the risk of amputation and improve clinical outcomes in tropical, resource-limited settings.}, }
@article {pmid41743643, year = {2026}, author = {Markfeld, M and Talpaz, I and Biton, B and Maheriniaina Randriamoria, T and Soarimalala, V and Goodman, SM and Nunn, CL and Titcomb, G and Pilosof, S}, title = {Host traits and environmental factors shape infection heterogeneity in wild rat-protozoa networks.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag026}, pmid = {41743643}, issn = {2730-6151}, abstract = {The occurrence of microbes in animal hosts is highly heterogeneous, shaped by interactions among host traits, environmental context, and microbial diversity. Understanding this heterogeneity is particularly critical for endoparasite infections, where some hosts harbor diverse, high-burden assemblages that elevate disease spread and spillover risk. Yet the mechanisms underlying such heterogeneity remain poorly understood in wild systems, especially at the individual-host level. We addressed this challenge by studying protozoan infections in introduced black rats (Rattus rattus) across environmental gradients in Madagascar. Using network-based stochastic block modeling, we identified three infection profiles capturing meaningful variation in protozoan richness and composition, providing a structured framework for understanding heterogeneity. To uncover the predictors of these profiles, we trained machine-learning models incorporating host traits with environmental variables. Our models consistently outperformed no-skill baselines, with host traits contributing [Formula: see text]40% more to predictions than environmental factors. Body mass and gut microbiome composition emerged as the strongest host predictors, while rat and other non-native species densities were the most influential environmental predictors. These results show that infection heterogeneity arises from the interplay of intrinsic host traits and extrinsic environmental conditions. Our approach illustrates how combining network analysis with predictive modeling can (i) uncover latent heterogeneity in host-microbe associations, (ii) identify the relative contribution of the factors driving this heterogeneity, and (iii) predict host infection profiles. Our framework advances microbial ecology by linking host traits, microbial communities, and environmental context, while also informing disease ecology at human-animal interfaces where zoonotic pathogens circulate.}, }
@article {pmid41743513, year = {2025}, author = {Hylling, O and Forero-Junco, LM and Ellegaard-Jensen, L and Dedon, PC and Cui, L and Nielsen, TK and Hansen, M and Neve, H and Johansen, A and Kot, W}, title = {Novel Modification Sites of dPreQ0 in Aminobacter niigataensis Phage Erebus Provide New Insights into the Role of 7-Deazaguanine Modifications in Bacteriophages.}, journal = {PHAGE (New Rochelle, N.Y.)}, volume = {6}, number = {4}, pages = {250-258}, pmid = {41743513}, issn = {2641-6549}, abstract = {BACKGROUND: Bacteriophages protect themselves against host-encoded defense systems through DNA modifications. This study introduces Erebus, a newly identified phage infecting Aminobacter niigataensis, a bacterium capable of mineralizing 2,6-dichlorobenzamide- a common pesticide metabolite. The use of such bacterial degraders has been proposed for the bioremediation of contaminated groundwater. However, the presence of bacteriophages targeting these degraders poses a potential challenge to the success of such strategies.<br><br>MATERIALS AND METHODS: The Erebus phage was isolated and subjected to whole-genome sequencing. Phylogenetic analysis was performed to determine its taxonomic placement and genomic synteny. DNA modifications were identified using a combination of liquid chromatography-mass spectrometry (LC-MS) and Oxford Nanopore Technologies sequencing. Transmission electron microscopy was used to determine the phage morphology.<br><br>RESULTS: Phylogenetic analysis revealed that Erebus belongs to an unclassified genus, showing high synteny with Rhizobium phages of the Kleczkowskaviridae family. The phage possesses a double-stranded DNA genome of 52,229 base pairs, which includes a functional 7-deazaguanine DNA-modification system. Nanopore sequencing and LC-MS analysis confirmed the presence of PreQ0 modifications at novel GG and AG motifs, conferring resistance against multiple restriction endonucleases.<br><br>CONCLUSIONS: This is the first report of a phage infecting the genus Aminobacter, highlighting the potential impact of bacteriophages on microbial biodegradation strategies. The findings underscore the importance of considering phage-host interactions when deploying bacterial degraders for environmental remediation.}, }
@article {pmid41743133, year = {2026}, author = {Zhang, W and Jiang, H and Zhu, Q and Shi, Z and Chen, W and Xu, X and Peng, F and Chi, Y}, title = {Microbial diversity and water quality changes in mangrove sediments in Quanzhou Bay.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1743704}, pmid = {41743133}, issn = {1664-302X}, abstract = {This study investigated the diversity, composition, and environmental drivers of bacterial communities in the mangrove sediments of Quanzhou Bay, a subtropical estuary under anthropogenic pressure. Using high-throughput sequencing of the 16S rRNA gene, we analyzed samples from four sites (Fengze-FZ, Jinjiang-JJ, Luojiang-LJ, and Shishi-SS) representing a gradient of terrestrial influence and environmental conditions. The bacterial communities were predominantly composed of Pseudomonadota and Chloroflexi, a pattern consistent with global mangrove ecosystems but with distinct local structuring. Beta-diversity analyses (NMDS/PCA) revealed a significant spatial divergence, with the FZ site forming a distinct cluster separate from JJ, LJ, and SS, correlating with its unique environmental profile. Redundancy analysis (RDA) identified dissolved oxygen (LDO) and salinity as the key environmental factors shaping community structure. Functional prediction indicated a conserved potential for core metabolic processes (e.g., amino acid biosynthesis, bacterial chemotaxis) across sites, suggesting functional redundancy, while differences in the relative abundance of these pathways pointed to adaptive metabolic adjustments along the environmental gradient. Our findings demonstrate that the sedimentary microbial community structure in Quanzhou Bay is primarily shaped by localized environmental heterogeneity, providing critical insights into the microbial ecology of mangroves in urbanized coasts and a baseline for assessing ecosystem health and biogeochemical functioning under anthropogenic influence.}, }
@article {pmid41740962, year = {2026}, author = {Scheuerl, T and Rivett, DW}, title = {A Concept Using α-Niche Evolution Within Bacterial Communities to Direct β-Niche Evolution of Focal Species.}, journal = {Environmental microbiology}, volume = {28}, number = {3}, pages = {e70255}, doi = {10.1111/1462-2920.70255}, pmid = {41740962}, issn = {1462-2920}, support = {316807//UIBK/ ; 325779//Tyrolian Science Foundation/ ; 101067338//MSCA Postdoctoral Fellowship/ ; EP/X024830/1//EPSRC Postdoc Fellowship/ ; ISS-2021-109666//Vertex Pharmaceuticals Research/ ; }, abstract = {The process of bacterial adaptation has a profound impact on human wellbeing and health, but our toolkit to modify evolution is limited. Here, we present a concept of how steering adaptation can be achieved by integration of bacterial evolution and microbial ecology. The fundamental question is how specific species bloom after community perturbation and subsequently evolve. We consider two kinds of traits-α-niche traits involved in partitioning resources (e.g., broadened resource consumption) and β-niche traits driven by changes in the abiotic environment (e.g., pH adaptation or resistance after antibiotic treatment). We suggest that the evolution of the second trait can be directed indirectly via the evolution of the first trait, exploiting specific interspecies interactions. Thus, understanding how these traits interact in co-evolving communities may offer unprecedented opportunities to deflect trait evolution. Summarising current knowledge, emphasising open questions and highlighting conceptual ideas, we hope to stimulate new studies that are needed to move this field forward.}, }
@article {pmid41739277, year = {2026}, author = {Silva, MLOM and Martins, AKS and Sandes, SHC and Alvim, LB and Nunes, &#xc1;C and Camargo, ILBC and Tinoco, HP and Nicoli, JR and Martins, FS}, title = {Isolation and evaluation of antagonistic activity against pathogenic bacteria by Lactobacillus and Enterococcus spp. from the saliva of Speothos venaticus and Chrysocyon brachyurus.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {57}, number = {1}, pages = {}, pmid = {41739277}, issn = {1678-4405}, abstract = {UNLABELLED: Saliva plays a crucial role in oral defense across mammals by combining host-derived antimicrobial factors with antagonistic indigenous microbiota. Understanding the composition of the oral lactic microbiota in wild canids may provide valuable insights into microbial ecology and animal health. In this study, Lactobacillus and Enterococcus spp. isolated from the saliva of South American bush dogs (Speothos venaticus) and maned wolves (Chrysocyon brachyurus) were enumerated, identified, and evaluated for their antagonistic activity against pathogenic bacteria. For bacterial isolation, MRS agar and BHI agar supplemented with sodium azide (BHI-SA) were used for Lactobacillus and Enterococcus, respectively. Identification of the bacterial isolates was performed using PCR-ARDRA and multiplex PCR. Antagonistic activity was assessed using a double-layer agar diffusion assay, which detects diffusible inhibitory effects without identifying the compounds involved. A total of 23 bacterial isolates were obtained from BHI-SA and 24 from MRS for bush dogs, while 15 were recovered from BHI-SA and 23 from MRS for maned wolves. Salivary bacterial counts ranged from 4.0 to 5.0 log10 CFU/mL. In bush dogs, Enterococcus faecalis and Enterococcus faecium were identified, while E. faecalis and Enterococcus hirae were found in maned wolves. Limosilactobacillus reuteri, Lactiplantibacillus paraplantarum, Lactiplantibacillus plantarum and Lactobacillus johnsonii were isolated from bush dogs, while Ligilactobacillus salivarius and Latilactobacillus curvatus were identified in maned wolves. Antagonistic activity against indicator pathogens was more frequent among Lactobacillus isolates. These results suggest that the antibacterial properties observed in the saliva of these wild canids may be partly attributed to indigenous Lactobacillus and Enterococcus species.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42770-026-01877-0.}, }
@article {pmid41739174, year = {2026}, author = {Sánchez-Astráin, B and Borrego-Ramos, M and Viso, R and de la Hoz, CF and Blanco, S and Juanes, JA}, title = {Unravelling Diatom-Microbiome Dynamics in the Red Alga Gelidium Corneum (Florideophyceae, Rhodophyta).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02723-4}, pmid = {41739174}, issn = {1432-184X}, }
@article {pmid41738851, year = {2025}, author = {Kim, M and Hakeem, WGA and Rothrock, MJ}, title = {Key Farm-to-Fork Factors Influencing E. coli Levels in Pastured Poultry Production.}, journal = {Avian diseases}, volume = {69}, number = {4}, pages = {395-406}, doi = {10.1637/aviandiseases-D-25-00033}, pmid = {41738851}, issn = {1938-4351}, mesh = {Animals ; *Escherichia coli/isolation &amp; purification/physiology ; *Animal Husbandry/methods ; *Chickens ; Feces/microbiology ; *Escherichia coli Infections/veterinary/microbiology/epidemiology ; Soil Microbiology ; *Poultry Diseases/microbiology/epidemiology ; Farms ; Southeastern United States ; }, abstract = {Pastured poultry farms offer a unique model for investigating microbial ecology in less controlled environments, presenting challenges and opportunities for food safety management. This study aims to identify the key factors that influence Escherichia coli levels with two complementary modeling approaches: a linear mixed-effect model (LMM) and a random forest (RF) model. Data were collected from 11 pastured poultry farms in the southeastern United States from 2014 to 2017. Five sample types were analyzed: soil (n = 812), feces (n = 817), ceca (n = 206), postprocessing whole carcass rinse (WCR-P; n = 235), and final product whole carcass rinse (WCR-F; n = 230). Two different sets of predictor variables were used separately: 1) 32 farming practices and 26 physicochemical properties and 2) 80 meteorological factors. The model performance was compared with the randomized mean squared error (RMSE) with a test dataset. LMM was not used for meteorological factors because of the multicollinearity. Significant differences (α = 0.05) in E. coli levels were observed between all sample types, with feces samples showing the highest level. Compared to LMMs, RF models generally showed higher predictive accuracy (lower RMSE) on the test dataset. For soil samples, higher pH and sodium levels were linked to higher E. coli levels. The same trend with pH was observed in fecal samples. WCR-P samples showed that the organic acid treatment in the rinse water led to lower E. coli levels than other treatments. In WCR-F samples, longer storage time led to lower E. coli levels. Meteorological factors showed a weaker relationship with E. coli levels compared to farming practices and physicochemical properties, but in soil samples, mild and stable temperature played an important role in E. coli survival. This study can help stakeholders develop data-driven management strategies targeting key factors to aid in the reduction of food safety and animal health risk.}, }
@article {pmid41736367, year = {2026}, author = {Keum, HL and Sul, WJ and Kim, S and Chung, IY and Koh, A and Kim, HS}, title = {Preliminary characterization of the skin microbiota in basal cell carcinoma: An exploratory pilot study in Korean patients.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {}, number = {}, pages = {}, doi = {10.71150/jm.2511012}, pmid = {41736367}, issn = {1976-3794}, abstract = {Basal cell carcinoma (BCC) is the most common form of skin cancer, with ultraviolet radiation recognized as the primary environmental driver; however, the potential contribution of alterations in the skin microbiota remains incompletely understood, particularly in Asian populations. This exploratory pilot study describes bacterial community patterns in BCC lesions compared with contralateral clinically normal skin in 20 Korean patients. Lesional and contralateral samples were obtained using paired skin swabs and punch biopsies and analyzed by full-length 16S rRNA gene sequencing, with targeted quantitative PCR (qPCR) of the roxP antioxidant gene of Cutibacterium acnes. Given the low-biomass nature of skin samples and the exploratory design, analyses focused on descriptive trends rather than confirmatory inference. Across available samples, C. acnes was the dominant taxon, with a trend toward lower relative abundance in BCC lesions, particularly in biopsy-derived datasets. Microbial evenness appeared higher in lesions than controls. Predictive functional profiling suggested reduced representation of vitamin B6 metabolism pathways in lesions, while qPCR analysis of swab samples showed a trend toward lower roxP/16S rRNA ratios in BCC-associated microbiota. These findings should be interpreted cautiously in light of methodological constraints, including sample heterogeneity, lidocaine exposure prior to biopsy, absence of sequencing-based negative controls, and reliance on predictive functional inference. Overall, this pilot study highlights potential differences in skin bacterial community structure between BCC lesions and contralateral skin in a Korean cohort. Larger, methodologically optimized studies incorporating metagenomic and functional validation will be required to determine whether these microbiota shifts contribute to, or result from, BCC-associated changes in the cutaneous environment.}, }
@article {pmid41735517, year = {2026}, author = {Piaszczyk, W and Lasota, J and Foremnik, K and Błońska, E}, title = {Tree species determine soil microbial diversity: variation in fungal and bacterial communities in temperate forests.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-41297-6}, pmid = {41735517}, issn = {2045-2322}, support = {2022/06/X/NZ9/00006//Narodowe Centrum Nauki/ ; }, abstract = {This study investigates the influence of three deciduous tree species: small-leaved linden (Tilia cordata), common beech (Fagus sylvatica), and sessile oak (Quercus petraea) on soil microbial diversity in temperate forest ecosystems. Conducted on loess soils in southern Poland, the research clarifies species-specific effects on soil microbiota and chemical properties, providing insights into tree-microbe-soil interactions in forest environments. Soil samples were collected from monospecific stands and analysed using next-generation sequencing (NGS). Fungal and bacterial DNA was extracted, and libraries targeting the ITS1 (fungi) and 16 S rRNA V3-V4 (bacteria) regions were sequenced using the Illumina MiSeq platform. Microbial communities were evaluated in relation to soil pH, nutrient content, and exchangeable cations. Linden soils had the highest pH (5.1-7.0) and calcium content (18.9 cmol(+)·kg[-1]), while beech soils were the most acidic (pH 3.8-5.7) with the lowest calcium (8.0 cmol(+)·kg[-1]). Fungal communities were dominated by Basidiomycota, Ascomycota, and Mortierellomycota, with varying proportions across species. Bacterial diversity was highest in linden and oak stands. Dominant bacterial phyla included Actinobacteriota, Proteobacteria, and Acidobacteriota. Each tree species hosted a distinct microbial community, reflecting its impact on soil properties and microbial structure. Tree species significantly shape soil microbial diversity and chemistry. Incorporating microbial data into forest management may enhance soil function, biodiversity conservation, and ecosystem resilience. Broader spatial sampling is recommended to generalize findings.}, }
@article {pmid41734518, year = {2026}, author = {Dhillon, A and Yadav, P and Gupta, S and Singh, SV and Sohal, JS and Rawat, KD}, title = {Microbiome alterations and host-pathogen interactions in paratuberculosis: A one health perspective.}, journal = {Veterinary microbiology}, volume = {315}, number = {}, pages = {110940}, doi = {10.1016/j.vetmic.2026.110940}, pmid = {41734518}, issn = {1873-2542}, abstract = {Paratuberculosis is a chronic ruminal-enteric infection caused by Mycobacterium avium subsp. paratuberculosis (MAP). It has significant economic, trade, and public health implications. In addition to evading host immunity, MAP modulates the gut microbiome, resulting in dysbiosis that exacerbates disease progression. A conceptual framework is proposed in which Johne's disease (JD) can serve as the paradigm of chronic infection, based on dysbiosis in microbial imbalance, immune escape, and pathogen survival in a self-sustaining loop, as in human tuberculosis and Crohn's disease. This review evaluates the evidence on MAP-induced microbiome alterations and their impact on host-pathogen relations, immune responses, and metabolic processes in cattle, sheep, goats, and other ruminants. JD-associated dysbiosis is characterized by reduced microbial diversity, depletion of butyrate-producing taxa (e.g., Ruminococcaceae and Lachnospiraceae), enrichment of pro-inflammatory Enterobacteriaceae, and disruption of short-chain fatty acid (SCFA) metabolic pathways. Recent studies suggest that such alterations in microbes can be the initial signs of diagnosis and pre-treatment components, such as probiotics, prebiotics, dietary modifications, and microbiome-based vaccinations. This summary bridges the research on the veterinary and human microbiome, revealing that MAP-Microbiome interactions reflect immunological evasion and microbial persistence schemes observed with other intracellular pathogens. Evidence across species and disciplines highlights the interdependence between host microbiome stability, pathogen persistence, and disease progression. However, variances between studies show the need to adopt standardized methodologies, longitudinal studies, and multi-omics designs to establish whether dysbiosis precedes or follows MAP infection. The review is the first to combine molecular, immunological, and microbiome-level data into the One Health concept of MAP persistence. Moreover, this review takes a One Health approach where the investigation of MAP-induced dysbiosis offers an understanding of chronic inflammation, microbial ecology, and persistence strategies applicable to veterinary as well as human health. This way, we can emphasize the diagnostic, therapeutic, and translational opportunities of microbiome-based interventions in JD using a One Health model that connects ruminant disease to human inflammatory bowel diseases, including Crohn's disease.}, }
@article {pmid41733768, year = {2026}, author = {Zhou, S and Yao, Y and Yuan, R and Chu, W}, title = {Comparative Microbiome Analysis of Rhodiola fastigiata Rhizosphere Versus Bulk Soil in Xizang with Targeted Isolation of Rhizosphere-Derived Functional Strains.}, journal = {Molecular biotechnology}, volume = {}, number = {}, pages = {}, pmid = {41733768}, issn = {1559-0305}, support = {PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; }, abstract = {Rhodiola fastigiata, a critically endangered medicinal plant of the Qinghai-Xizang Plateau, faces severe threats from habitat degradation. This study aimed to support its microbial-assisted conservation by characterizing the rhizosphere microbiome and isolating functional plant growth-promoting (PGP) bacteria. Using high-throughput sequencing of the 16S rRNA gene and ITS region, we found the rhizosphere community to be distinct and enriched in key taxa (e.g., Sphingomonas, Mortierella). Metabolic predictions suggested upregulated stress-adaptive pathways. Crucially, from 126 isolates, we obtained four Bacillus strains that concurrently produce protease, amylase, and cellulase and solubilize phosphate-quantifying a multifunctional PGP profile critical for nutrient-poor soils. These culturable, spore-forming strains provide direct resources for developing synthetic inoculants. Our work bridges microbial ecology with applied biotechnology, delivering both a foundational microbial map and candidate strains to enable the cultivation and conservation of this endangered species in extreme environments.}, }
@article {pmid41733363, year = {2026}, author = {Ziegert, ZA and Troester, A and Frebault, J and Goffredo, P and Gaertner, WB and Jahansouz, C and Staley, C}, title = {SparCC co-occurrence networking reveals intracommunity dynamics of the microbiome following colorectal surgery.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0397325}, doi = {10.1128/spectrum.03973-25}, pmid = {41733363}, issn = {2165-0497}, abstract = {The intestinal microbiota plays a critical role in post-surgical wound healing following bowel resection; however, perioperative, prophylactic antibiotic administration may deleteriously affect it. We previously used 16S rRNA amplicon sequencing of stool samples to assess perioperative and longitudinal changes in the microbiome through 6 months in patients undergoing (i) colonoscopy after mechanical bowel prep (MBP) alone, (ii) non-resectional colorectal surgery after MBP with oral antibiotics and prophylactic intravenous antibiotics no longer than 24 h post-operative (surgical bowel prep [SBP]), and (iii) resectional colorectal surgery with SBP. Our objective in this study was to investigate the translational utility of SparCC co-occurrence networking to uncover biologically relevant patterns. Network topological parameters and hub species were calculated using NetCoMi, and permutational statistical tests were used to compare parameters. Network similarity among cohorts and time points generally matched changes in beta diversity, except in the resectional cohort, where all networks could not be differentiated statistically. Similarity in centrality measures among hub species was frequently significantly less similar than expected by chance and corresponded to an increased edge density and modularity, suggesting the latter parameters may reflect re-stabilization of the microbiome following surgery. We further noted the infrequently reported genera Enterocloster and Ruthenibacter were hub species during time points associated with surgical recovery, suggesting potentially novel roles for these genera in wound healing. Streptococcus, frequently implicated in surgical site infections at our center, was also frequently positively associated with Blautia throughout all networks, suggesting an increasing abundance of commensal bacteria serves as a prophylactic strategy.IMPORTANCEThis study employs the emerging approach of co-occurrence networking to assess ecological dynamics in the microbiome following colonoscopy and colorectal surgery. We expand upon applications of this approach to determine hub species and investigate clinically translational interpretations of network topological parameters in the context of recovery across three different trajectories of perturbation. Our results provide a context in which to interpret these network parameters biologically and represent a foundational step in beginning to quantitatively leverage network-based approaches to study microbial ecology. Furthermore, we identify network hub taxa that may play previously unexplored roles in wound healing.}, }
@article {pmid41733159, year = {2026}, author = {Diab, E and Du, C and Tigani, W and Elsayed, SS and van Wezel, GP}, title = {Plant Coumarins Modulate Natural Product Biosynthesis in a Streptomyces Root Endophyte.}, journal = {Journal of natural products}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jnatprod.5c01626}, pmid = {41733159}, issn = {1520-6025}, abstract = {The plant microbiome plays a central role in regulating plant health and resilience, providing eco-friendly alternatives to agrochemicals. Plant-associated Streptomyces species are prolific producers of structurally diverse natural products with a demonstrated role in promoting plant growth. Coumarins are prevalent plant metabolites that shape the root microbiome, but their impact on microbial natural product biosynthesis is poorly understood. Here, we demonstrate that the coumarins scopoletin and its glucoside scopolin remodel specialized metabolism in the Arabidopsis root endophyte Streptomyces sp. ATMOS53. Multiomics analyses revealed that the coumarins activate the biosynthesis of the pyrrolizidine alkaloids bohemamines and alter the balance in anthracycline biosynthesis, with reduced production of late-stage anthracycline congeners and accumulation of shunt metabolites earlier in the pathway. These metabolic shifts resulted in a marked reduction of the antimicrobial activity of ATMOS53 against plant-associated Bacillus and Paenibacillus species. Notably, coumarin-mediated repression of anthracycline production was also observed in the established producers Streptomyces peucetius and Streptomyces galilaeus, indicating that the regulatory effect on anthracycline biosynthesis is conserved in streptomycetes. Our findings highlight coumarins as modulators of specialized metabolism of Streptomyces and show the significance of plant-derived chemicals for the control of the biosynthetic capacity of plant-associated microbes.}, }
@article {pmid41732360, year = {2026}, author = {Yash,  and Ghosh, A and Dey, A and Sinha, M and Bera, N and Chakraborty, S and Bhadury, P}, title = {Dataset on ecological health and microbial communities of coastal aquaculture ponds from surrounding region of Sundarban mangroves.}, journal = {Data in brief}, volume = {65}, number = {}, pages = {112542}, pmid = {41732360}, issn = {2352-3409}, abstract = {Integrated Mangrove Aquaculture (IMA) and Sustainable Aquaculture in Mangrove Ecosystem Fisheries (SAIME) are key activities undertaken across coastal regions globally to meet growing demand for brackish-water aquaculture products through sustainable practices. An in-depth biomonitoring study was conducted to map the ecological health of IMA and non-IMA aquaculture ponds in the surrounding region of the Indian Sundarbans mangroves located along the northeast coast of Bay of Bengal. Surface water samples were collected from six aquaculture ponds, four IMA (IMA_C1, IMA_C3, IMA_DB1, and IMA_DB4) and two non-IMA (C6_NM and DB5_NM) in the month of October 2022, for characterizing niche-specific biological communities using the environmental DNA (eDNA) approach. During sampling, in-situ environmental parameters were recorded. Mangrove litter-derived phenolics (tannic and gallic acids) and dissolved nutrients were estimated using a UV-Vis spectrophotometer, while dissolved organic carbon (DOC) was measured with the elemental analyzer. Metal and metalloid concentrations were determined by inductively coupled plasma mass spectrometry approach (ICP-MS). IMA ponds showed ideal conditions for shrimp aquaculture, with pH ranging from 7.913 to 8.633 and dissolved oxygen (DO) between 5.32 and 6.03 mg/L, indicating no hypoxic conditions despite higher concentrations of phenolics. High-throughput sequencing (HTS) based on Oxford Nanopore Technologies (ONT) sequencing chemistry was undertaken on the MinION platform, revealing the predominance of Proteobacteria among prokaryotes and Bacillariophyta as well as Chlorophyta among eukaryotes from extracted eDNA in each studied pond. Additionally, members of the family Cyprinidae were also detected, reflecting the biodiversity of fish population in these ponds. Functional gene profiling indicated signatures associated with nitrogen, phosphorus, sulphur, potassium and iron acquisition and metabolism, along with pathways related to aromatic compound degradation. Overall, dissolved nutrients, dissolved organic carbon (DOC), metal and metalloid ion concentrations as well as structure and functional profiles of biological communities provide a comprehensive basis for evaluating the ecological health of aquaculture ponds. This study generates important baseline information for long-term monitoring and represents the first eDNA-based high-throughput sequencing assessment of IMA and non-IMA aquaculture ponds from surface water in close proximity to the Sundarbans mangrove.}, }
@article {pmid41729252, year = {2026}, author = {Li, Y and Chen, D and Liu, X and Li, Y and Chen, F}, title = {Zooplankton-associated Bacterial Communities are Dominated by Host-Specific Rather than Environmentally Random Taxa.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02702-9}, pmid = {41729252}, issn = {1432-184X}, }
@article {pmid41725809, year = {2026}, author = {Zenati, K and Braun, SD and Belhadi, D and Moawad, AA and Müller, E and Diezel, C and Brandt, C and Mostefaoui, R and Monecke, S and Zaidi, FZ and Belmahdi, M and Touati, A and Ehricht, R}, title = {The oral cavity as a reservoir for resistance- and hypervirulence-associated genes of Klebsiella pneumoniae in hospitalized patients.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1751947}, pmid = {41725809}, issn = {1664-302X}, abstract = {INTRODUCTION: This study investigated the epidemiology and distribution of carbapenem resistance and virulence genes in Klebsiella pneumoniae strains isolated from the oral cavity of hospitalized patients, highlighting their role as reservoirs in non-epidemic contexts.<br><br>METHODS: Carbapenem-resistant Klebsiella spp. were isolated from the oral cavity of 180 hospitalized patients in medical wards at two hospitals in Bejaia, Algeria. Screening for carbapenem resistance was performed on oral mucosa and saliva using Carba-MTL broth. Antibiotic susceptibility was assessed with the Vitek2 system and interpreted according to EUCAST guidelines. Whole genome sequencing (WGS) was carried out using Oxford Nanopore Technologies, with ABRicate used for resistance/virulence gene detection and Kleborate for hypervirulence assessment. Whole-genome sequences were further examined to identify single-nucleotide polymorphisms (SNPs) and to reconstruct a SNP-based phylogenetic tree in order to assess the genetic relatedness among the isolates.<br><br>RESULTS: Twenty Klebsiella strains were identified as K. pneumoniae. Among these, 85% were carbapenem-resistant, carrying OXA-48 (80%) or NDM-5 (5%), and all harbored blaCTX-M-15. WGS of the 20 K. pneumoniae strains revealed a broad resistome, including &#x3b2;-lactamases (CTX-M-15, CMY-4, OXA-1, TEM-1), sulfonamide (sul1, sul2), aminoglycoside (aac(3)-IIa, aadA2, aph(3')-VI, armA, strA, strB), trimethoprim (dfrA12, dfrA5, dfrA14), and tetracycline (tetA). Quinolone resistance was linked to QRDR mutations (gyrA S83I, parC S80I) and plasmid-mediated genes (qnrS1, qnrB10, qnrS10, aac(6')-Ib-cr). Five distinct sequence types (STs) were identified, including high-risk clones ST13 and ST48. Virulence profiling revealed yersiniabactin (85%), frequently linked to ICEKp elements (ICEKp4, ICEKp10), and colibactin (40%) among OXA-48 isolates. Notably, a single K. pneumoniae isolate harboring NDM-5 (K21) carried both hypervirulence markers (ybt9/ICEKp3, iuc1, rmp1/kpvp-1) and carbapenem resistance, documenting, for the first time in Algeria, the convergence of these traits in oral isolates. ICEKp was identified as the key vehicle for dissemination of yersiniabactin and colibactin, and a novel association between ICEKp and kpvp-1 was observed. Capsular typing showed predominance of K57-O1/O2v2 among OXA-48 producers and K27/O4 among NDM-5 strains.<br><br>CONCLUSION: This study provides the first evidence in Algeria of OXA-48- and NDM-5-producing K. pneumoniae in the oral cavity of hospitalized patients. The coexistence of carbapenem resistance and hypervirulence underscores the oral cavity as a critical reservoir, potentially fueling nosocomial infections and the dissemination of high-risk clones within hospitals and the wider community.}, }
@article {pmid41720792, year = {2026}, author = {Mohammadzadeh, R and Mahnert, A and Zurabishvili, T and Wink, L and Kumpitsch, C and Habisch, H and Sprengel, J and Filek, K and Mertelj, P and Pernitsch, D and Hingerl, K and Durdevic, M and Gorkiewicz, G and Diener, C and Loy, A and Kolb, D and Trautwein, C and Madl, T and Moissl-Eichinger, C}, title = {Cross-domain metabolic interactions link Methanobrevibacter smithii to colorectal cancer microbial ecosystems.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-69711-7}, pmid = {41720792}, issn = {2041-1723}, support = {10.55776/P32697//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; 10.55776/CoE7//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; 10.55776/CoE7//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; }, abstract = {The human gut is colonized by trillions of microbes that influence the health of their human host. Whereas many bacterial species have now been linked to a variety of different diseases, the involvement of Archaea, an evolutionarily distinct group of microbes, in human disease remains elusive. By analyzing 19 independent clinical studies, we demonstrate that associations between Archaea and human diseases are widespread yet highly heterogeneous, with a pronounced and consistent enrichment of Methanobrevibacter smithii in colorectal cancer (CRC) patients. Metabolic modelling and in vitro co-culture identified distinct mutualistic interactions of M. smithii with CRC-causing bacteria such as Fusobacterium nucleatum, including metabolic enhancement. Metabolomics further reveal archaeal-derived compounds with tumor-modulating properties. Together, our results provide mechanistic insights into how the human gut archaeome may participate in CRC-associated microbial networks through metabolic cooperation with bacteria.}, }
@article {pmid41720095, year = {2026}, author = {Wang, T and George, AB and Maslov, S}, title = {Higher-order interactions in auxotroph communities enhance their resilience to resource fluctuations.}, journal = {Cell systems}, volume = {}, number = {}, pages = {101491}, doi = {10.1016/j.cels.2025.101491}, pmid = {41720095}, issn = {2405-4720}, abstract = {Auxotrophs are prevalent in microbial communities, enhancing their diversity and stability-a counterintuitive effect considering their dependence on essential resources from other species. To address the ecological roles of auxotrophs, our study introduced a consumer-resource model (CRM) to capture the complex higher-order interactions within these communities. We also developed an intuitive graphical and algebraic framework, which assesses the feasibility of auxotroph communities and their stability under resource fluctuations and biological invasions. Validated against experimental data from synthetic E. coli auxotroph communities, the model accurately predicted outcomes of community assembly. Our findings highlight the critical role of higher-order interactions and resource dependencies in maintaining the diversity and stability of microbial ecosystems dominated by auxotrophs. A record of this paper's transparent peer review process is included in the supplemental information.}, }
@article {pmid41716220, year = {2026}, author = {Gomes-Neto, JC and Crook, A and Hestrin, R and Li, G and Liew, CS and Rosa, G and Singh, KD and Tuggle, CK and Summers, KL and Valdes, C and Fahlgren, N and Clarke, J}, title = {Challenges and opportunities: computational biology and the future of agriculture.}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbag003}, pmid = {41716220}, issn = {2635-0041}, abstract = {MOTIVATION: The world of agriculture is rapidly changing with advances in artificial intelligence and demands for greater feed and food security considering environmental and sustainability challenges. The 30th Conference on Intelligent Systems in Molecular Biology (ISMB) held in July 2022 featured an invited session on the role of computational biology in Digital and Precision Agriculture. This session featured presentations by experts from various subdisciplines on novel research discoveries and a panel discussion on Digital Agriculture at Scale. Topics discussed during the session included genetics, epigenetics, and genomics of agriculturally relevant species; foodborne pathogen genomics and epidemiology; plant and animal phenomics; AI/machine learning; image analysis; remote sensing; educational innovations; discoveries resulting from public-private partnerships; data sharing and findable, accessible, interoperable, and reproducible (FAIR) data standards; biotechnology; and soil microbial ecology and biogeochemistry.<br><br>RESULTS: We present several of the current and future challenges and opportunities for computational biology in agriculture including why these challenges are important to address, what barriers exist, and what skills and competencies are required to be successful as a computational biologist in agriculture. We intend this summary to engage the computational biology community and attract them to the opportunities available for interesting and impactful work toward ensuring sustainable food security.}, }
@article {pmid41715924, year = {2026}, author = {Marín, MDC and Konno, M and Rozenberg, A and Béjà, O and Inoue, K}, title = {Novel light-driven schizorhodopsins from Antarctic patescibacteria and cyanobacteria.}, journal = {Biophysical journal}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.bpj.2026.02.022}, pmid = {41715924}, issn = {1542-0086}, abstract = {Microbial rhodopsins represent a diverse superfamily of light-sensitive proteins composed of seven transmembrane helices with expanding phylogenetic diversity driven by advances in metagenomics. Among these, schizorhodopsins constitute a divergent family originally identified as inward proton pumps from Promethearchaeota (Asgard archaea). Here, we report that in addition to archaeal schizorhodopsins, many members of the family originate from bacteria and detail a comprehensive biophysical characterization of two schizorhodopsins from uncultured Antarctic bacteria: paSzR from Minisyncoccota (Patescibacteria) and psSzR from a Pseudanabaenacea cyanobacterium. Both proteins function as light-driven inward proton pumps, as confirmed through pH measurements in Escherichia coli cells. Laser-flash photolysis experiments identified multiple photointermediates (K, L, and M) characteristic of microbial rhodopsin photocycles, though with slower turnover rates compared to archaeal schizorhodopsins. Site-directed mutagenesis of conserved residues in the third and sixth transmembrane helices demonstrates differential structural requirements between paSzR and psSzR. Our phylogenetic reconstruction reveals that most bacterial schizorhodopsins cluster in a single lineage distinct from archaeal variants. These findings expand our understanding of microbial rhodopsin diversity and provide crucial insights into alternative molecular mechanisms for light-driven proton translocation, with implications for microbial ecology in extreme environments.}, }
@article {pmid41715245, year = {2026}, author = {Luna, N and Hernández, C and Ramírez, AL and Urbano, P and Barragán, K and Ariza, C and Muñoz, M and Patiño, LH and Ramírez, JD}, title = {Ecological insights into the cross-domain microbiome interactions in the hematophagous bat Desmodus rotundus.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {22}, pmid = {41715245}, issn = {2524-4671}, abstract = {BACKGROUND: Bats are recognised as reservoirs for a wide range of microorganisms, including viruses, bacteria, fungi, and parasites, some of which are of zoonotic concern. The common vampire bat (Desmodus rotundus) is particularly important due to its hematophagous feeding behaviour and ecological adaptability, both of which enhance its potential for cross-species pathogen transmission. Despite its well-established relevance to public health, the microbial communities associated with D. rotundus remain poorly characterised. This study aimed at investigating the composition, diversity, and interactions of prokaryotic, eukaryotic, and viral communities, alongside feeding sources, using high-throughput sequencing in 27 D. rotundus individuals from a rural area in Casanare, eastern Colombia.<br><br>RESULTS: We analysed a total of 81 samples (blood, faeces, and oral swabs) using long-read amplicon sequencing of the 16S- and 18S-rRNA genes and viral metagenomics via Oxford Nanopore Technologies. The microbial profiles revealed highly diverse assemblages, encompassing a wide range of bacterial, fungal, eukaryotic parasites, and viral taxa, with significant variation in community structure and diversity metrics across the three sample types collected from each bat. Taxa of public health concern were detected, including Enterococcus faecalis, Mycoplasma spp. Acanthamoeba spp. and viruses from the families Coronaviridae, Retroviridae, and Circoviridae. Correlation analyses suggested potential intra- and inter-domain interactions and co-occurrence dynamics among these microbes. Additionally, feeding source profiling, based on vertebrate assignments from faeces and swab samples, indicated evidence of livestock consumption, suggesting possible transmission pathways between bats and domestic animals.<br><br>CONCLUSIONS: The detection of multiple co-occurring pathogens across distinct sample types, coupled with their association with feeding sources, highlights the role of D. rotundus as a functionally specialised reservoir capable of harbouring and potentially disseminating zoonotic microbes. This study provides new insights into the cross-domain microbial ecology of hematophagous bats and underscores the need to integrate microbial community profiling with host behavioural data to enhance surveillance and mitigation strategies for zoonotic disease transmission.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-025-00504-x.}, }
@article {pmid41714654, year = {2026}, author = {Rabaey, JS and Lewis, ASL and Attermeyer, K and Aurich, P and Bansal, S and Bartosiewicz, M and Bertolet, BL and Bussmann, I and Cadieux, SB and Calamita, E and Capelli, C and Carey, CC and Cillero, C and Clayer, F and D'Ambrosio, SL and Davidson, TA and Deemer, BR and Denfeld, BA and Eckert, W and Esposito, C and Ford, P and Gorsky, A and Griffiths, NA and Grossart, HF and Hamilton, DP and Holgerson, MA and Huser, BJ and Iwata, T and Jansen, J and Jones, SE and Juutinen, S and Kortelainen, P and Koschorreck, M and Kragh, T and Laas, A and Larmola, T and Läubli, S and Laurion, I and Lehmann, MF and Liu, L and Martikainen, PJ and Matoušů, A and McCord, SA and Montes-Pérez, JJ and Nizzoli, D and Ordóñez, C and Peacock, M and Pilla, RM and Prėskienis, V and Pu, J and Riis, T and Saarela, T and Santoso, AB and Schubert, CJ and Sepulveda-Jauregui, A and Sherman, BS and Sø, JS and Stenehjem, KJ and Strock, KED and Tsuchiya, K and Wendt-Potthoff, K and Weyhenmeyer, GA and Znachor, P and Zopfi, J}, title = {Depth-resolved carbon dioxide and methane concentrations in 522 lakes, ponds, and reservoirs worldwide.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-06751-0}, pmid = {41714654}, issn = {2052-4463}, abstract = {Lakes, ponds, and reservoirs (hereafter: "lakes") are important sources of the greenhouse gases carbon dioxide (CO2) and methane (CH4). Emissions of CO2 and CH4 from lakes are regulated in part by in-lake processes, including the production and storage of gases in the lower parts of the water column (bottom waters). However, while substantial efforts have been made to improve estimates of greenhouse gas emissions from lakes, limited data on gas concentrations along depth profiles have prevented the incorporation of bottom-water processes in global emission estimates. Here, we present GHG-depths: the largest existing dataset of depth-profile CO2 and CH4 measurements worldwide, including 522 lakes across 38 countries and all seven continents. These data include contributions from 45 research teams and 56 published studies, totaling 2558 discrete sampling events. As global change continues to alter biogeochemical cycling in lakes, these data can help improve mechanistic models to better predict greenhouse gas production and emission from lakes worldwide.}, }
@article {pmid41714186, year = {2026}, author = {Wang, B and Gao, P and Zhang, P and Zheng, Y and Liu, X and Ling, N and Shan, J and Yao, R and Zhao, S and Zhang, Z and Zhu, G and Jung, MY and Zou, J and Yan, X and Lee, S and Hazard, C and Nicol, GW and Zhou, J and Yang, Y and Zhu, Y and Stahl, DA and Wagner, M and Gao, Y and Jiang, J and Qin, W}, title = {Elevated Temperature Simulating Heatwaves Restructures Active Nitrifying Communities and Associated Viruses in Tidal Flats and Agricultural Soils.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag037}, pmid = {41714186}, issn = {1751-7370}, abstract = {Global heatwave intensification under climate change will impact the nitrogen cycle, yet its effect on active nitrifier groups or their interactions with viruses remains unclear. Using 13CO2-DNA-based stable-isotope probing coupled with metagenomics, we show that elevated temperatures under heatwave conditions fundamentally restructure active nitrifying communities and their associated viruses in Yangtze River estuary upper tidal flats and adjacent agricultural soils. In tidal flats, sustained high temperature constrained nitrification by reducing the abundance of active ammonia-oxidizing archaea and bacteria (AOA, AOB) and canonical nitrite-oxidizing bacteria (NOB). This was accompanied by a shift in the active community from marine to more thermotolerant but less salt-tolerant terrestrial ecotypes. Conversely, heatwave conditions in agricultural soils suppressed AOB but enhanced nitrification activity in thermotolerant terrestrial AOA ecotypes. Across both ecosystems, inferred virus-nitrifier interactions were temperature dependent. 13C-labeled nitrifier-infecting viruses exhibited coordinated shifts in virus-to-host abundance ratios and predicted lifestyles with their hosts, with sustained high temperatures reducing virus-to-host abundance ratios and favoring temperate infections, relative to higher abundance ratios and a greater proportion of predicted lytic cycles at lower temperatures. We identified AOA-infecting viruses that carry plastocyanin (pcy), encoding a key copper-dependent electron carrier in the AOA respiratory chain, with conserved active sites and a predicted protein fold that supports its capacity for electron transfer, potentially augmenting host energy metabolism. Together, our findings demonstrate that prolonged heatwaves drive coupled shifts in nitrifier community composition and virus-host interaction strategies in a land-use-dependent manner, with implications for nitrogen transformations and ecosystem feedbacks under climate extremes.}, }
@article {pmid41713418, year = {2026}, author = {Shao, Y and Wang, S and Gichuki, BM and Stares, MD and Rozday, TJ and Kumar, N and Browne, HP and Dawson, NJR and Njunge, JM and Tigoi, C and Ngao, N and Chisti, MJ and Singa, BO and Kariuki, S and Diallo, AH and Saleem, AF and Ali, SA and Mupere, E and Mbale, E and Tickell, KD and Voskuijl, WP and Lancioni, CL and Bandsma, RHJ and Ahmed, T and Walson, JL and Berkley, JA and Lawley, TD}, title = {Genomic atlas of Bifidobacterium infantis and B. longum informs infant probiotic design.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2026.01.007}, pmid = {41713418}, issn = {1097-4172}, abstract = {Bifidobacterium longum and B. infantis are pioneer colonizers of the neonatal gut and are widely used as probiotics to support infant growth, development, and disease resistance. However, commercial strains derived largely from high-income countries (HICs) may be suboptimal for infants in low- and middle-income countries (LMICs). We assembled a global genomic atlas of more than 4,000 genomes from 48 countries, increasing representation from LMICs by 12- to 17-fold. High-resolution phylogenomic and functional analyses support delineating B. longum and B. infantis as distinct species with divergent functions and epidemiological patterns. B. infantis dominates early-life microbiota in LMICs but is rarely detected in HICs. Natural B. infantis strains show extreme biogeographic stratification and predicted adaptations to local plant-glycan-rich diets and breast-milk-derived substrates, including urea and B vitamins. This genomic resource enables genome-guided selection of geographically matched strains to inform more effective probiotics and precision microbiome therapeutics for diverse infant populations.}, }
@article {pmid41713400, year = {2026}, author = {Wang, XW and Wang, T and Liu, YY}, title = {Artificial intelligence for microbiology and microbiome research.}, journal = {Cell systems}, volume = {17}, number = {2}, pages = {101531}, doi = {10.1016/j.cels.2026.101531}, pmid = {41713400}, issn = {2405-4720}, mesh = {*Artificial Intelligence/trends ; *Microbiota/physiology ; Humans ; Machine Learning ; *Microbiology/trends ; }, abstract = {Advancements in artificial intelligence (AI) have transformed many scientific fields, with microbiology and microbiome research now experiencing significant breakthroughs through machine-learning applications. This review provides a comprehensive overview of AI-driven approaches tailored for microbiology and microbiome studies, emphasizing both technical advancements and biological insights. We first introduce foundational AI techniques and offer guidance on choosing between traditional machine-learning and sophisticated deep-learning methods based on specific research goals. The primary section on application scenarios spans diverse research areas from taxonomic profiling, functional annotation and prediction, microbe-X interactions, microbial ecology, metabolic modeling, precision nutrition, and clinical microbiology to prevention and therapeutics. Finally, we discuss challenges in this field and highlight some recent breakthroughs. Together, this review underscores AI's transformative role in microbiology and microbiome research, paving the way for innovative methodologies and applications that enhance our understanding of microbial life and its impact on our planet and our health.}, }
@article {pmid41708342, year = {2026}, author = {Alfahl, Z and Lynch, R and O'Dwyer, C and Kelly, JP}, title = {Medical versus science students: Knowledge, perceptions and learning of core pharmacology concepts.}, journal = {British journal of clinical pharmacology}, volume = {}, number = {}, pages = {}, doi = {10.1002/bcp.70498}, pmid = {41708342}, issn = {1365-2125}, abstract = {AIMS: Pharmacology is a core discipline underpinning both medical and biomedical science education, essential for understanding drug action, safety and therapeutic efficacy. This study compared pharmacology knowledge, perceptions and learning experiences between second-year medical and science students to evaluate how effectively each curriculum supports acquisition of internationally defined core pharmacology concepts.<br><br>METHODS: A mixed-methods design was employed, involving pre- and post-module surveys and curriculum mapping against the global pharmacology core concept framework. Quantitative data were analysed using chi-squared tests, while qualitative responses were evaluated thematically. Participants included students enrolled in MD214 Introduction to Pharmacology (medical) and PM208 Fundamental Concepts in Pharmacology (science) at the University of Galway.<br><br>RESULTS: Medical students demonstrated stronger baseline and post-module understanding of pharmacokinetic and pharmacodynamic principles, particularly in applied pharmacokinetics such as drug-drug interactions and variability in drug response. Science students showed significant improvement over time, reflecting effective conceptual learning. Both cohorts reported positive perceptions of module relevance and teaching effectiveness (mean scores 7.7-8.9/10) and moderate to high confidence in mastering core concepts. YouTube and textbooks were the most common supplementary resources. Curriculum mapping showed alignment with 23 of 24 core concepts in the medical module and 20 in the science module.<br><br>CONCLUSIONS: Medical students exhibited greater initial competence and perceived relevance, whereas science students benefited substantially from targeted instruction. Findings highlight the value of concept-based, contextually integrated pharmacology teaching and support continued curriculum development guided by international core concept frameworks.}, }
@article {pmid41705859, year = {2026}, author = {Medeiros, WB and Centurion, VB and Silva, JB and Duarte, AW and Hidalgo-Martinez, KJ and Dos Santos, JA and Penna, DDPS and Bagci, C and Ziemert, N and Oliveira, VM}, title = {Antarctic soil prokaryotic diversity: a dataset of 319 metagenome-assembled genomes from Deception and Livingston Islands.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0134625}, doi = {10.1128/mra.01346-25}, pmid = {41705859}, issn = {2576-098X}, abstract = {A total of 319 bacterial metagenome-assembled genomes (MAGs) were recovered from soil samples collected on the Antarctic Peninsula (Deception and Livingston Islands). These MAGs reveal microbial life's phylogenetic diversity and functional potential in extreme polar environments, providing resources for advancing microbial ecology, evolution, and Antarctic biotechnology.}, }
@article {pmid41705204, year = {2026}, author = {Verbunt, J and Mennens, L and Jocken, J and Blaak, EE and Savelkoul, P and Stassen, FRM}, title = {From food to vesicle: nutritional influences on gut microbial inflammatory signaling.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1756462}, pmid = {41705204}, issn = {2296-861X}, abstract = {Diet is a pivotal determinant of gut microbial ecology, giving not only rise to specific bacterial compositionality but also its functional output. Studying functional readouts-such as microbial metabolite production-could provide a more accurate and mechanistically informative measure of intervention outcome than traditional compositional profiling alone. Bacterial membrane vesicles (bMVs) are gaining attention as mediators of microbial metabolism and output. These nanoparticles are selectively released as carriers of bioactive proteins, lipids, nucleic acids, and metabolites reflective of the activity of the parent bacteria. Importantly, bMVs are rigid, can efficiently be isolated from feces, and are able to stably transport their cargo to interact with the host. In interacting with immune cells or pathogen recognition receptors, they can potentiate inflammatory responses. Given their extensive, multifaceted involvement in inter-Kingdom communication, bMVs represent an important biomarker for evaluating dietary modulation of gut microbial function. We propose that characterization of gut-derived bMVs offers a highly sensitive, mechanistically grounded approach to titrating impact of dietary interventions. By capturing shifts in microbial metabolic activity and inflammatory potential, bMV-based assessments could complement or surpass traditional measures of microbiome compositional change. Integrating bMV profiling into dietary intervention studies may therefore provide new insight into the functional consequences of diet-microbiome interactions and help refine strategies aimed at reducing inflammation and promoting host health.}, }
@article {pmid41704769, year = {2026}, author = {Yinhang, W and Xueli, J and Zheng, W and Xiaojian, Y and Shu, X and Qingjie, Z and Ying, L and Shuwen, H}, title = {Gut fungal landscape in colorectal cancer and its cross-kingdom interplay with gut microbial ecology.}, journal = {iScience}, volume = {29}, number = {2}, pages = {114664}, pmid = {41704769}, issn = {2589-0042}, abstract = {The gut microbiota is a key hallmark of colorectal cancer (CRC), yet gut fungi remain understudied. We characterized the gut fungal landscape and its associations with bacteria, metabolites, and trace elements in CRC using fecal samples from healthy controls (n = 401), colorectal polyp patients (n = 162), and CRC patients (n = 253). Fungal annotation was performed using genomic data from NCBI (PRJNA833221) as reference. Fungal diversity increased in CRC patients, with seven genera showing differential abundance. Rhizopus was specifically enriched in CRC, while Sporisorium, etc. enriched in polyps. Ablation study identified an optimal 31-microbial-marker panel (28 bacteria and three fungi) that effectively distinguished intestinal disease groups (AUC = 0.89). Structural equation modeling revealed three fungal markers-Penicillium citrinum, Penicillium sp. PG10607D, and Rhizopus stolonifera-that influence bacterial-metabolite-trace element networks. This study delineates the gut fungal atlas in CRC and reveals complex cross-kingdom interactions, offering new insights into CRC pathogenesis.}, }
@article {pmid41703880, year = {2026}, author = {Mipun, P and Sarma, P and Dey, G and Terangpi, L and Hajong, B and Chakraborty, D and Kshetriya, D and Mandal, SM and Dinata, R and Baindara, P}, title = {Ethnic fermentation secrets of Northeast India and emerging functional food insights.}, journal = {Food research international (Ottawa, Ont.)}, volume = {228}, number = {}, pages = {118431}, doi = {10.1016/j.foodres.2026.118431}, pmid = {41703880}, issn = {1873-7145}, mesh = {India ; *Fermentation ; *Fermented Foods/microbiology ; Humans ; *Functional Food/microbiology ; *Food Microbiology ; *Ethnicity ; Probiotics ; }, abstract = {Northeast India is home to an incredible variety of ethnic fermented foods, shaped over centuries by cultural wisdom and adaptation to the local environment. From bamboo shoots, soybeans, and rice to fish, dairy, vegetables, and traditional beverages, these foods are deeply woven into daily life and are rich in beneficial microorganisms with probiotic potential. Understanding the microbial ecology, biochemical transformations, and functional metabolites of Northeast India's traditional fermented foods provides a scientific basis for improving safety, identifying bioactive ingredients, and guiding the development of next-generation fermented products. This review brings together insights from ethnomicrobiological surveys and culture-based studies to explore the microbes, fermentation pathways, and biochemical changes that give these foods their distinctive qualities, as well as their nutritional benefits and safety considerations. We highlight lesser-known products, examine toxin-producing pathogens, and profile antimicrobial peptides (AMPs), uncovering varying levels of pathogen risk across products. Additionally, fermentation space analysis reveals exciting opportunities to create new foods by creatively combining local ingredients. Finally, we look at how modern tools, including artificial intelligence (AI) and machine learning (ML), can help scale up production, standardize quality, and ensure safety. Overall, by blending traditional knowledge with modern biotechnology and AI, these unique fermentation foods could find their place globally while preserving their cultural roots.}, }
@article {pmid41568973, year = {2026}, author = {Downing, BE and Gupta, D and Shalvarjian, KE and Nayak, DD}, title = {Genus-specific remodeling of carbon and energy metabolism facilitates acetoclastic methanogenesis in Methanosarcina spp. and Methanothrix spp.}, journal = {Journal of bacteriology}, volume = {208}, number = {2}, pages = {e0044825}, doi = {10.1128/jb.00448-25}, pmid = {41568973}, issn = {1098-5530}, support = {F32GM150233/NH/NIH HHS/United States ; Packard Fellowship in Science and Engineering//David and Lucile Packard Foundation/ ; S589706//U.S. Department of Energy/ ; Sloan Research Fellowship//Alfred P. Sloan Foundation/ ; Early Career Investigator in Marine Microbial Ecology and Evolution//Simons Foundation/ ; Beckman Young investigator Award//Arnold and Mabel Beckman Foundation/ ; Searle Scholars Award//Kinship Foundation/ ; 202299857//National Science Foundation Graduate Research Fellowship Program/ ; }, mesh = {*Methane/metabolism/biosynthesis ; *Methanosarcina/metabolism/genetics ; *Energy Metabolism ; Acetates/metabolism ; *Carbon/metabolism ; Archaeal Proteins/metabolism/genetics ; Gene Expression Regulation, Archaeal ; Acetyl Coenzyme A/metabolism ; }, abstract = {UNLABELLED: Methanogenic archaea (methanogens) are microorganisms that obligately produce methane as a byproduct of their energy metabolism. While most methanogens grow on CO2+H2, isolates of the genera Methanosarcina and Methanothrix can use acetate as the sole substrate for methanogenesis. Methanogenic growth on acetate, i.e., acetoclastic methanogenesis, is hypothesized to require two distinct genetic modules: one for the activation of acetate to acetyl-CoA and another for producing a chemiosmotic gradient using electrons derived from ferredoxin. In Methanosarcina spp., the activation of acetate to acetyl-CoA is mediated by acetate kinase (Ack) and phosphotransacetylase (Pta), whereas Methanothrix spp. encode AMP-forming acetyl-CoA synthetases (Acs). The Rhodobacter nitrogen fixation complex (Rnf) or energy-converting hydrogenase (Ech) is critical for energy conservation in Methanosarcina spp. during growth on acetate, and a F420:methanophenazine oxidoreductase-like complex (Fpo') likely plays an analogous role in Methanothrix spp. Here, we tested the proposed modularity of these pathways to facilitate acetoclastic methanogenesis. First, we surveyed over 100 genomes within the class Methanosarcinia to show that the genomic potential for acetoclastic methanogenesis is widespread. We then used the genetically tractable strain, Methanosarcina acetivorans, to build all modular combinations that might support acetoclastic methanogenesis. Our results indicate that Acs, while functional, cannot replace Ack+Pta to rescue acetate growth in M. acetivorans. Similarly, the Fpo' bioenergetic complex cannot replace Rnf. As such, our work suggests that, in addition to horizontal gene transfer of core catabolic modules, acetoclastic metabolism in methanogens requires changes to core energy metabolism too.<br><br>IMPORTANCE: A large fraction of biogenic methane is derived from acetate, yet acetoclastic methanogens, i.e., methanogens that grow on acetate, remain poorly characterized due to their slow growth. Two groups of methanogens, Methanosarcina spp. and Methanothrix spp., perform acetoclastic methanogenesis using distinct sets of genes for acetate activation and energy conservation. It is widely hypothesized that these genetic modules from Methanosarcina spp. and Methanothrix spp. are functionally analogous and would thus be interchangeable. To test this hypothesis, we engineered different combinations of modules for acetoclastic growth in Methanosarcina acetivorans. Our results challenge this hypothesized paradigm of modularity, and we posit that other changes to the carbon and electron transfer pathways are crucial for the emergence of acetoclastic methanogenesis.}, }
@article {pmid41703847, year = {2026}, author = {Gil, MI and Tudela, JA and Illán, G and Hernández, N and Andújar, S and Sabater, D and Allende, A and Truchado, P}, title = {Industrial-scale application of bacteriophages on baby spinach: One-year study of Listeria control, quality and microbial community shifts.}, journal = {Food research international (Ottawa, Ont.)}, volume = {228}, number = {}, pages = {118384}, doi = {10.1016/j.foodres.2026.118384}, pmid = {41703847}, issn = {1873-7145}, mesh = {*Spinacia oleracea/microbiology ; *Bacteriophages ; *Food Microbiology/methods ; *Listeria/virology ; Listeria monocytogenes/virology ; Microbiota ; *Food Preservation/methods ; Food Handling/methods ; Food Contamination/prevention &amp; control ; }, abstract = {Bacteriophages have emerged as promising biocontrol agents against pathogenic bacteria due to their strong antimicrobial activity and host specificity. In this study, we evaluated a previously validated industrial bacteriophage cocktail (PhageGuard Listex™) for its performance on baby spinach, focusing on product quality and microbial community dynamics. Twenty industrial trials conducted over one year compared non-treated and phage-treated baby spinach samples after processing (day 0) and after 10 days of storage under commercial (3 d at 4 °C followed by 7 d at 7 °C) and abusive (continuous 10 °C) temperature conditions. Phage stability was confirmed in the application solution and persistence on the product surface after storage. Although Listeria monocytogenes was not detected in any sample (0/600), the proportion of samples positive for Listeria spp. was significantly lower in the phage-treated group (6%) than in the non-treated group (12%). The preventive phage application did not affect headspace gas composition, sensory attributes, or objective color parameters. Quality deterioration was observed only at 10 °C, regardless of phage treatment. Despite the reduction in Listeria spp. prevalence, microbial diversity and community structure were unaffected by phage application, consistent with the low relative abundance of Listeria spp. in the microbiota and the narrow host range of the phage cocktail; storage conditions, particularly temperature, were the most influential factor affecting bacterial taxonomic composition. The relative abundance of Pseudomonas and Flavobacterium increased during storage, while Bacillus and Exiguobacterium decreased. These findings support the feasibility of using this bacteriophage-based treatment as a preventive intervention that does not affect product quality and preserves the natural microbial ecology of baby spinach during storage.}, }
@article {pmid41703844, year = {2026}, author = {Fang, X and Pu, Q and Qu, A and Wang, C and Shen, T and Wu, S and Li, M and Sui, M and Ji, Z and Huang, Y}, title = {Mechanisms of phenolic conversion in anaerobic fermentation of tea leaves revealed by integrating microbiome and metabolome analysis.}, journal = {Food research international (Ottawa, Ont.)}, volume = {228}, number = {}, pages = {118381}, doi = {10.1016/j.foodres.2026.118381}, pmid = {41703844}, issn = {1873-7145}, mesh = {*Fermentation ; *Phenols/metabolism/analysis ; *Plant Leaves/microbiology/metabolism/chemistry ; *Microbiota ; *Tea/microbiology/chemistry/metabolism ; *Metabolome ; Anaerobiosis ; Metabolomics/methods ; Bacteria/metabolism ; *Camellia sinensis/microbiology ; Flavonoids/metabolism ; }, abstract = {To systematically investigate the phenolic transformation mechanisms during tea anaerobic fermentation, the changes in phenolics and microbial communities of pickled teas under varying extrusion degrees were analyzed by combining metabolomics and microbiomics. The changes in 118 differential phenolics (p < 0.05, variable importance in projection >1.0, and fold change >1.2 or < 1/1.2) revealed that anaerobic fermentation drives the bioconversion of bound phenolics into free phenolics and their derivatives in tea leaves. Additionally, the potential metabolic pathways of tea phenolics in anaerobic fermentation were comprehensively proposed, mainly including hydrolysis of polymerized/galloylated catechins, hydrolysis of flavonoid glycosides, and hydrolysis of galloylated phenolics to release gallic acid and its further derivatization. The degree of extrusion significantly influenced microbial community succession: high-extrusion enriched Enterobacter, Cladosporium, Setophoma, and Vishniacozyma, enhancing the hydrolysis of flavonoid glycosides and depsides, while light-extrusion promoted Candida, Cyberlindnera, Lactobacillus, and Pantoea, favoring the accumulation of free phenolics and their derivatives. These findings establish a mechanistic link between microbial ecology and phenolic biotransformation, providing a foundation for precision fermentation in tea processing.}, }
@article {pmid41700860, year = {2026}, author = {Machushynets, NV and Elsayed, SS and Du, C and Lysenko, V and de la Cruz, M and Sanchez, P and Genilloud, O and Martin, NI and Liles, MR and van Wezel, GP}, title = {Paenitracins, a novel family of bacitracin-type nonribosomal peptide antibiotics produced by plant-associated Paenibacillus species.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0149625}, doi = {10.1128/msystems.01496-25}, pmid = {41700860}, issn = {2379-5077}, abstract = {The growing threat of antimicrobial resistance necessitates the discovery of novel antibiotics with activity against drug-resistant pathogens. Members of the genus Paenibacillus are a rich source of nonribosomal peptides (NRPs), including well-known antibiotics such as polymyxins, paenibacterin, and tridecaptins. Here, we use a targeted mass spectrometry query language (MassQL)-based approach to identify the NRPs produced by a collection of 227 taxonomically diverse plant-associated Paenibacillus strains, providing detailed insights into their NRP-producing potential. Using MassQL to zoom in specifically on NRPs containing basic amino acids, we discovered a novel family of bacitracins, which we designated paenitracins. The paenitracins are the first bacitracin-type peptides reported in Paenibacillus and are distinguished from canonical bacitracins by three previously unseen amino acid substitutions. The paenitracins exhibit potent activity against gram-positive pathogens, including vancomycin-resistant Enterococcus faecium E155. Our work provides a novel metabolomics-guided and genomics-guided workflow for the discovery of bioactive NRPs as a strategy to prioritize natural product chemical space and accelerate antibiotic discovery.IMPORTANCEMembers of the genus Paenibacillus play an important role in soil ecology, producing a range of important nonribosomal peptides (NRPs). A collection of plant-associated Paenibacillus spp. were analyzed for their phylogenetic and metabolic diversity. We developed a novel discovery pipeline that combines feature-based molecular networking with mass spectrometry query language queries to systematically prioritize bioactive NRPs containing basic amino acids. Thus, we provide a comprehensive genus-wide inventory of NRPs produced by Paenibacillus spp. We thereby identified the paenitracins, a new sub-family of bacitracins active against multidrug-resistant gram-positive pathogens. Our pipeline enables the discovery of novel peptidic natural products to accelerate the prioritization of chemical space for antibiotics.}, }
@article {pmid41700805, year = {2026}, author = {Zhou, S and Bai, X and Xue, B and Chu, W}, title = {A Vaginal Microbiota-Ovary Axis in Chemotherapy-Accelerated Ovarian Aging: Single-Cell Insights into Cellular Dysregulation.}, journal = {Biology of reproduction}, volume = {}, number = {}, pages = {}, doi = {10.1093/biolre/ioag042}, pmid = {41700805}, issn = {1529-7268}, abstract = {BACKGROUND: Chemotherapy-induced premature ovarian failure (POF) represents a major challenge to female reproductive health, yet the potential regulatory role of vaginal microbiota in this process remains largely unexplored.<br><br>RESULTS: Using a well-established model of chemotherapy-induced ovarian aging, we observed significant disruptions in vaginal microbial ecology characterized by depletion of Lactobacillus species and concomitant enrichment of pathogenic bacteria. Microbiota transplantation effectively reversed these dysbiosis patterns and restored ovarian function. Single-cell transcriptomic analysis revealed that microbial intervention promoted the recovery of granulosa and luteal cell populations while simultaneously suppressing inflammatory activation in ovarian stromal cells, demonstrating the vaginal microbiota's capacity to maintain follicular integrity. Further mechanistic insights showed that microbiota transplantation upregulated key antioxidant defense systems and ribosomal protein networks within ovarian cells, suggesting coordinated actions to mitigate oxidative stress and enhance cellular repair capacity, although the specific microbial metabolites mediating these effects require further elucidation.<br><br>CONCLUSIONS: Our findings establish for the first time the existence of a functional vaginal microbiota-ovary axis and delineate its critical role in protecting against chemotherapy-induced ovarian damage. This work not only advances our fundamental understanding of microbial-endocrine crosstalk but also identifies concrete microbial targets for developing innovative strategies to preserve fertility in cancer patients.}, }
@article {pmid41697449, year = {2026}, author = {Zavřel, T and Pohland, AC and Pfennig, T and Matuszyńska, AB and Tóth, SZ and Bernát, G and Červený, J}, title = {Correction to: Estimating the redox state of the plastoquinone pool in algae and cyanobacteria via OJIP fluorescence: perspectives and limitations.}, journal = {Photosynthesis research}, volume = {164}, number = {2}, pages = {14}, doi = {10.1007/s11120-026-01203-7}, pmid = {41697449}, issn = {1573-5079}, }
@article {pmid41697388, year = {2026}, author = {Ding, Z and Guo, Y and Guo, L and Ren, B and Yang, J and Li, J and Bai, L}, title = {Reintroduction of Grassland Plant Species Shapes Soil Bacterial Ecological Groups and Contributes Differently To Bacterial Diversity.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02718-1}, pmid = {41697388}, issn = {1432-184X}, support = {LJKMZ20221053//Foundation of Liaoning Province Education Administration/ ; X2021012//Shenyang Agricultural University/ ; }, }
@article {pmid41696024, year = {2026}, author = {Pendleton, A and Schmidt, ML}, title = {Interpreting UniFrac with absolute abundance: a conceptual and practical guide.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycaf250}, pmid = {41696024}, issn = {2730-6151}, abstract = {[Formula: see text]-diversity is central to microbial ecology, yet commonly used metrics overlook changes in microbial load (or "absolute abundance"), limiting their ability to detect ecologically meaningful shifts. Popular for incorporating phylogenetic relationships, UniFrac distances currently default to relative abundance and therefore omit important variation in microbial abundances. As quantifying absolute abundance becomes more accessible, integrating this information into [Formula: see text]-diversity analyses is essential. Here, we introduce "Absolute UniFrac" ([Formula: see text]), a variant of Weighted UniFrac that incorporates absolute abundances. Using simulations and a reanalysis of four 16S rRNA metabarcoding datasets (from a nuclear reactor cooling tank, the mouse gut, a freshwater lake, and the peanut rhizospere), we demonstrate that Absolute UniFrac captures microbial load, composition, and phylogenetic relationships. While this can improve statistical power to detect ecological shifts, we also find Absolute Unifrac can be strongly correlated to differences in cell abundances alone. To balance these effects, we also incorporate absolute abundance into the generalized extension ([Formula: see text]) that has a tunable, continuous ecological parameter ([Formula: see text]) that modulates the relative contribution of rare versus abundant lineages to [Formula: see text]-diversity calculations. Finally, we benchmark GU[A] and show that although computationally slower than conventional alternatives, GU[A] is comparably sensitive to noise in load estimates compared to conventional alternatives like Bray-Curtis dissimilarities, particularly at lower [Formula: see text]. By coupling phylogeny, composition, and microbial load, Absolute Unifrac integrates three dimensions of ecological change, better equipping microbial ecologists to quantitatively compare microbial communities.}, }
@article {pmid41695957, year = {2026}, author = {Dobrzyński, J and Gradowski, M and Radkowski, A and Bujak, H}, title = {Chloroflexota in agricultural soils: current knowledge and future research directions.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1705889}, pmid = {41695957}, issn = {1664-302X}, abstract = {The review organizes current knowledge on the biofunctions, life-history strategies, and environmental responses of Chloroflexota in agricultural soils. Members of this phylum play key roles in carbon, nitrogen, and phosphorus cycling through a high degree of metabolic versatility, including photosynthesis, redox reactions, and the degradation of complex organic compounds such as cellulose and lignin. Chloroflexota contribute to major soil processes, including nitrification, denitrification, and nitrogen fixation. In agricultural soils, the predominant classes are Anaerolineae and Ktedonobacteria, each exhibiting distinct ecological strategies. Anaerolineae members, such as Leptolinea, Bellilinea, and Anaerolinea, are often associated with nutrient-enriched conditions, suggesting copiotrophic or competitor- and ruderal-like traits. In contrast, Ktedonobacteria show negative responses to increased soil carbon and nitrogen, suggesting that its members are oligotrophic. Despite these trends, responses to soil organic carbon, nitrogen, phosphorus, and pH vary substantially across studies, likely due to functional heterogeneity within the phylum and insufficient taxonomic resolution in metataxonomic datasets. Emerging evidence from metagenome-assembled genomes (MAGs) reveals that Chloroflexota harbor genes involved in carbon fixation, nitrogen transformations, and phosphorus solubilization, highlighting their previously underestimated ecological significance. However, most Chloroflexota remain uncultured, and available genomic data are still limited. Future research integrating high-resolution taxonomic profiling, metagenomics, and cultivation-based approaches is needed to clarify the ecological roles and life-history strategies of Chloroflexota members. Such advances may ultimately establish this phylum as an important microbial indicator of soil fertility and environmental change in agricultural soils.}, }
@article {pmid41695945, year = {2026}, author = {Kothe, CI and Mak, T and Julienne, A and Okazaki, K and Jahn, LJ and Evans, JD}, title = {Miso without kōji: nesashi miso ecology driven by spontaneous fermentation with Mucor plumbeus.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1759987}, pmid = {41695945}, issn = {1664-302X}, abstract = {Nesashi miso is a rare, traditionally fermented soybean paste from Japan, and unlike most misos is produced through spontaneous fermentation without the use of a kōji starter. Here we analyzed a nesashi miso alongside two other misos from the same producer (rice and black soybean) as well as a hatchō miso from another producer which, like the nesashi, is based only on soybeans. Shotgun metagenomics confirmed that while Aspergillus oryzae dominated the three kōji-based misos, nesashi miso lacked this starter culture, and revealed that it was instead dominated by other filamentous fungi, mainly Mucor spp. and Penicillium spp., and contained typical yeast and bacterial genera found in traditional misos such as Zygosaccharomyces and Tetragenococcus. Principal component analysis (PCA) of 65 publicly available metagenomes showed that the nesashi miso sample clustered with other spontaneous solid-state fermentations like Chinese qu rather than with traditional kōji-based misos. To further characterize this unique fermentation, we isolated the Mucor sp. from nesashi miso, and sequenced it using long-read genomic sequencing. Pangenomic analysis confirmed its identity as M. plumbeus, and revealed close relationships between food- and environment-derived strains, suggesting that some Mucor species may already be naturally equipped to grow, establish and function in food fermentation niches. The nesashi strain specifically shared a large core genome with M. racemosus C, a strain patented for use in food, suggesting the former's potential for use in and potentially even adaptation to food environments. Functional annotation highlighted unique genes in the food strain group associated with amino acid metabolism, which may contribute to flavor formation. Together, these findings bridge traditional fermentation practices with meta/genomic insights, highlighting the built fermentation environment as a reservoir of potential starter cultures and the genus Mucor as a worthy candidate for future food fermentation research and innovation.}, }
@article {pmid41695141, year = {2025}, author = {Uh, YR and Park, SN and Song, MJ}, title = {Characterization of the gut micro biota in Koreans and investigation of its association with probiotic consumption: implications for microbial ecology and host health.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1745533}, pmid = {41695141}, issn = {1664-302X}, abstract = {INTRODUCTION: The gut micro biota is reportedly closely related to human health, and its composition and diversity are determined by a variety of factors, including age, diet, and probiotic intake. Although many studies on the gut micro biota have been conducted, most have focused on Western populations or have been limited by small sample sizes, making it difficult to understand micro biota differences across populations and lifestyles. In this study, we analyzed a large Korean cohort of 3,450 individuals, focusing on gut micro biome differences according to age and host-related markers, as well as the impact of probiotic supplementation.<br><br>METHODS: Fecal samples from 3,450 Koreans were analyzed using 16S rRNA gene sequencing (V3-V4 region). Bioinformatics and taxonomic analyses were performed to compare microbial composition and diversity according to age and probiotic intake.<br><br>RESULTS: The data revealed a significant increase in microbial diversity with age and distinct shifts in taxonomic composition between younger and older participants. In addition, probiotic intake did not alter overall community diversity but increased the detection of probiotics, suggesting that they serve as moderators rather than direct drivers of diversity.<br><br>CONCLUSION: These findings emphasize the importance of population-specific micro biome research and suggest that diverse host-related and lifestyle factors jointly contribute to shaping gut microbial ecology in Koreans. Probiotic supplementation primarily increased the detection of specific lactic acid bacteria and bifidobacterial species without substantially altering overall alpha diversity, consistent with a modulatory role on targeted taxa rather than broad community restructuring. Together, these results provide a useful framework for future studies linking probiotic-responsive microbial features to human health outcomes and for developing precision nutrition and probiotic strategies in Korean and similar populations.}, }
@article {pmid41695122, year = {2026}, author = {Yash,  and Ghosh, A and Dey, A and Sinha, M and Bera, N and Chakraborty, S and Bhadury, P}, title = {Genomic insights into Brevibacterium sediminis strain IMA_C3 isolated from an integrated mangrove aquaculture pond.}, journal = {Access microbiology}, volume = {8}, number = {2}, pages = {}, pmid = {41695122}, issn = {2516-8290}, abstract = {Brevibacterium sediminis strain IMA_C3, a Gram-positive bacterium, was isolated from an integrated mangrove aquaculture pond near the Sundarbans mangrove. The bacterium was isolated from mangrove leaf litter and grown on Luria-Bertani medium at a salinity of 20. Phylogenetic analysis based on 16S rRNA sequencing showed a 99.67% identity with Brevibacterium linens AE038-8 from the International Nucleotide Sequence Database Collaboration DNA databases (GenBank/DDBJ/ENA). Whole-genome sequencing was carried out using long-read sequencing on the Oxford Nanopore MinION platform, with genome annotation performed against the NCBI Reference Sequence Database and The Genome Taxonomy Database databases. The genome is ~4.1 Mb in size, with a G+C content of 64.59 mol%. Functional analysis of the genome revealed genes related to complex carbon utilization, nitrogen and phosphate metabolism and metal transport. Additionally, the genome encodes secondary metabolites, including ε-poly-l-lysine, ectoine, terpene and phenazine, which could have potential applications in controlling viral infections in indigenous shrimp populations within integrated mangrove aquaculture systems.}, }
@article {pmid41695029, year = {2026}, author = {Qin, H and Zhang, L and Rao, Z and Wei, X and Táncsics, A and Sheng, R and Liu, Y and Chen, A and Fang, C and Huang, F and Long, P and Zhu, B}, title = {Decoding endophytic microbiome dynamics: engineering antagonistic synthetic consortia for targeted fusarium suppression in monoculture regimes.}, journal = {Horticulture research}, volume = {13}, number = {2}, pages = {uhaf286}, pmid = {41695029}, issn = {2662-6810}, abstract = {Biological control leveraging endophytic microbes represents a promising eco-friendly strategy to mitigate soil-borne diseases, yet the efficacy and mechanistic underpinnings of synthetic microbial communities (SynComs) derived from plant endophytes remain poorly understood. This study employed a holistic approach-integrating field sampling, microbial profiling, and functional validation-to investigate the dynamics of edible lily (Lilium) microbiomes under continuous cropping and develop targeted SynComs against Fusarium oxysporum. Metacommunity analysis revealed that prolonged monoculture co-enriched both potentially beneficial taxa (e.g. Pseudomonas, Bacillus) and pathogenic Fusarium, reflecting a dynamic equilibrium where naturally recruited antagonists were insufficient to prevent pathogen dominance, while increasing the complexity of endophytic co-occurrence networks. Keystone bacterial lineages, including Burkholderiaceae and Pseudomonas, emerged as critical stabilizers of the endosphere microbiome. Notably, 50% of endogenous bacterial taxa exhibited rhizospheric origins, contrasting with fungal communities where <10% derived from soil-a finding underscoring host-specific filtering mechanisms. Through systematic isolation and combinatorial testing, we engineered SynComs combining core antagonistic strains (Rhizobium, Methylobacterium, Talaromyces) with auxiliary microbes. Fungal-integrated SynComs outperformed bacteria-only consortia in plant growth promotion and pathogen suppression. By bridging fundamental microbial ecology with translational agriculture, our findings establish SynComs as scalable tools for sustainable soil health management, reducing reliance on synthetic fungicides while addressing the yield-limiting challenges in continuous cropping systems.}, }
@article {pmid41694331, year = {2026}, author = {Mourot, R and Lebert, S and Martinez-Rabert, E and Barani, A and Grégori, G and Nunige, S and Dufour, A and Guasco, S and Larose, C and Bradley, JA}, title = {SIESTA Project: Svalbard summer 2025 expedition report.}, journal = {Open research Europe}, volume = {6}, number = {}, pages = {23}, pmid = {41694331}, issn = {2732-5121}, abstract = {Microbial dormancy plays an important role in the persistence, dispersal, and functioning of microbial communities in moderate to extreme environments. The activity or inactivity of microbial communities also has implications for rates of biogeochemical transformations and thus elemental stocks and redox conditions. Microbial communities inhabiting glacier surface environments encounter harsh and variable environmental conditions including nutrient limitation, low temperatures, and light availability across various micro-habitats including cryoconite and the bare ice surface. The metabolic states of cells within these microhabitats and in relation to their environment is fundamental to the functioning of the ecosystem and has implications for ecosystem resilience, responses to environmental change, and biogeochemical cycling. This report describes an expedition to Brøggerhalvøya, north-west Svalbard, carried out in July 2025, within the framework of the ERC SIESTA project. A major objective of the project is to resolve microbial activity and dormancy on an individual cell basis, to characterise the adaptive and functional traits of active and dormant fractions of the native glacier microbial population, and to link microbial metabolic states to broader ecological and biogeochemical dynamics. Here we report the site characteristics, the samples collected, the analyses undertaken, and the future analyses planned. Two small valley glaciers near to Ny-Ålesund were selected for investigation during this summer campaign: Midtre Lovénbreen and Austre Brøggerbreen. The data collected in the field, combined with subsequent laboratory analyses, will provide insights into the spectrum of dormancy and activity in situ among glacier microbial communities, and the taxa and functions associated with active and inactive fractions of the communities. These findings will contribute to a deeper understanding of the impacts and role of both short- and long-term microbial dormancy in glacial environments.}, }
@article {pmid41692701, year = {2026}, author = {Keneally, C and Gaget, V and Chilton, D and Dornan, TN and Hensel, J and Keneally, AE and Kidd, SP and Brookes, JD}, title = {Extreme Salinity Change Governs Microbial Community Assembly and Interactions.}, journal = {Environmental microbiology reports}, volume = {18}, number = {1}, pages = {e70301}, doi = {10.1111/1758-2229.70301}, pmid = {41692701}, issn = {1758-2229}, support = {2024316//Medical Research Future Fund/ ; }, mesh = {*Salinity ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Microbiota ; *Geologic Sediments/microbiology/chemistry ; *Archaea/genetics/classification/metabolism/isolation &amp; purification ; South Australia ; Ecosystem ; Seawater/microbiology/chemistry ; Wetlands ; Sulfur/metabolism ; }, abstract = {Coastal wetlands are highly vulnerable to climate-driven salinisation, which reshapes critical microbial processes underpinning nutrient cycling and energy flow. We examined how sediment microbial communities vary with salinity across the Coorong Lagoon (South Australia), spanning estuarine (0-40 g L[-1]), intermediate (40-100 g L[-1]) and hypersaline (100-150 g L[-1]) waters. Salinity was found to be the dominant driver of sediment microbial community composition, diversity and assembly. High salinity favoured specialists and homogenous community structures, with generalist bacteria persisting across intermediate salinities and supporting ecosystem resilience. Sulfur and carbon cycling is likely dependent on salinity, as bacterial sulfur-oxidisers were abundant estuarine specialists, whereas methane producers (Archaeal methanogens) and sulfate-reducers were enriched at high salinity. Deterministic microbial community assembly (homogeneous selection) was dominant, increasing at extreme salinity, which acted as a strong environmental filter. Community complexity increased at both high and low salinity ranges, with intermediate salinity exhibiting less complexity, suggesting community reorganisation under osmotic stress. The varied roles of specialists and generalists at different salinities support ecosystem function, where increased heterogeneity and specialisation in hypersaline conditions suggest vulnerability of the community to disturbance. These findings provide insight into how microbially underpinned ecosystems may respond to future climate-driven salinisation, important for making predictions and informing mitigation strategies.}, }
@article {pmid41691943, year = {2026}, author = {Huang, J and Tan, Z and Sun, R and Dai, Z and He, L and Li, C}, title = {Vertical and spatial variations of microbial communities in sediment cores from the mangrove of Gaoqiao National Nature Reserve.}, journal = {Marine pollution bulletin}, volume = {226}, number = {}, pages = {119416}, doi = {10.1016/j.marpolbul.2026.119416}, pmid = {41691943}, issn = {1879-3363}, abstract = {Sediment microbial communities act as key regulators of mangrove ecosystem functions. However, systematic studies on the spatial distribution characteristics, potential functions, and environmental driving mechanisms of microbial communities within sediment cores in mangrove ecosystems remain scarce. In this study, fifteen sediment cores were obtained from the mangrove within the Gaoqiao National Nature Reserve. The microbial community composition within the sediment cores was investigated using 16S rRNA high-throughput sequencing. Significant differences in microbial community structure were observed among the three designated zones (Nearshore, Mangrove, and Offshore) and across different sediment depths ranging from 0 to 80 cm. The dominant bacterial phyla identified comprised Pseudomonadota, Actinomycetota, and Chloroflexota, along with the archaeal phylum Thermoplasmatota. Their distributions demonstrated clear biogeographic and vertical stratification patterns. Functional prediction revealed that microbial communities extensively involved in carbon, nitrogen, and sulfur cycles exhibited higher richness, as these communities demonstrated stronger expression of metabolic functional genes. Furthermore, the abundance of metabolic functional genes was found to be higher in the mid-depth sediments at depths of 30 to 45 cm. Redundancy analysis (RDA) and variation partitioning analysis (VPA)demonstrated that sediment pH, electrical conductivity (EC), and total organic carbon (TOC) content were identified as the primary environmental factors governing the succession of both microbial community structure and function. This study advances our understanding of mangrove sediment microbial ecology and provides a scientific basis for targeted conservation and restoration of the Gaoqiao mangrove ecosystem.}, }
@article {pmid41691853, year = {2026}, author = {Wei, Y and Chen, Y and Lv, S and Ou, D and Tao, Y and Zhou, Y and Yang, J and Song, X}, title = {Persistence of the coccidiostat robenidine in soil and its impacts on the soil microbiome and enzyme functions.}, journal = {Ecotoxicology and environmental safety}, volume = {311}, number = {}, pages = {119858}, doi = {10.1016/j.ecoenv.2026.119858}, pmid = {41691853}, issn = {1090-2414}, abstract = {Robenidine is a synthetic coccidiostat that is excreted from animals in its prototype form, leading to soil contamination. Despite its widespread use, comprehensive environmental risk assessments remain limited. Consequently, we initially constructed a manure-soil microcosm and investigated the degradation pattern of robenidine using a highly efficient HPLC-dSPE method. The degradation half-lives of robenidine in soil were 14.74 days at 0.8 mg/kg and 21.26 days at 8 mg/kg. Exposure to 8 mg/kg of robenidine significantly altered the soil microbial community, leading to a 140.0 % increase in the abundance of Proteobacteria. However, the Shannon index indicated that soil microbial diversity decreased by 32.4 % from 1 d to 60 d. Compared to the control check group, 8 mg/kg of robenidine significantly increased the abundance of harmful bacteria (e.g., unclassified_Intrasporangiaceae increased by 33.5 %) in the soil at 60 d, while simultaneously reducing the populations of beneficial bacteria such as Bacillaceae (decreased by 23.8 %), Pseudograilibacillus (decreased by 39.6 %), and Massilia (decreased by 31.7 %). Network correlation and FAPROTAX analyses indicated that long-term exposure to robenidine inhibited chitinolysis and aromatic compound degradation pathways. Furthermore, low-dose robenidine increased the activities of dehydrogenase, acid phosphatase, and β-glucosidase by 34.0 %, 24.7 %, and 21.6 % at 1 d, respectively, while these enzymes returned to control levels over time. These findings provide critical insights into the biological and metabolic impacts of robenidine exposure on soil microbial communities, which is crucial for clarifying the ecological concerns associated with robenidine.}, }
@article {pmid41691349, year = {2026}, author = {Fan, S and Liu, H and Yan, Y and Xu, M and Wan, X and Hao, Y and Gong, C and Wang, C and Zhang, Y and Liu, D and Zheng, J and Chen, J}, title = {Metatranscriptomic analyses of gut bacterial and viral communities in the critically endangered Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) under distinct environments.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00528-x}, pmid = {41691349}, issn = {2524-4671}, }
@article {pmid41690572, year = {2026}, author = {Koffel, T and Grimaud, G and Litchman, E and Klausmeier, CA}, title = {Metabolically structured population models: a unifying framework for microbial ecology and evolution.}, journal = {Journal of theoretical biology}, volume = {}, number = {}, pages = {112410}, doi = {10.1016/j.jtbi.2026.112410}, pmid = {41690572}, issn = {1095-8541}, abstract = {Cells grow by acquiring external resources and transforming them internally, forming new cells as they divide. Metabolic networks focus on the flow of such resources within the cell as they undergo series of biochemical reactions. How population growth emerges from these complex dynamical networks remains unclear. Modeling the emergence of population growth, a central ecological concept, is thus essential to understand the forces shaping microbial communities. Here we present a novel theoretical framework that builds on structured population theory to model the growth of cell populations whose intracellular dynamics are driven by arbitrarily complex metabolic networks. Population growth is driven by limitation regimes, which capture how reaction-level limitations combine in the network to determine growth rate. Resource availability changes trigger switches between limitation regimes, capturing resource interaction and colimitation. We also discovered alternative metabolic states, where different regimes are reached depending on initial metabolite concentrations. We first use a minimal metabolic network of limitation by two essential resources to illustrate our framework, then apply it to E. coli's glycolysis pathway to showcase its capabilities on a more realistic, albeit still simplistic, network. By integrating metabolic networks into ecological theories, our work provides a mechanistic foundation for understanding the structure and evolution of microbial communities.}, }
@article {pmid41646430, year = {2026}, author = {Thompson, AW and Lamberson, K and Sutherland, KR}, title = {Coexisting salps exhibit distinct feeding selectivity on microorganisms in the North Pacific Subtropical Gyre.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {41646430}, issn = {2693-5015}, abstract = {Mortality mechanisms play an important role in how oceanic microorganisms contribute to global biogeochemical cycles. Salps are widespread pelagic tunicates known to remove phytoplankton from coastal and high-latitude waters, but their interaction with microorganisms in the vast tropical and subtropical gyres is not well quantified. Using quantitative measurements of six major marine microorganisms in the guts of six distinct but co-occurring salp species from the North Pacific Subtropical Gyre, we examined the impact and dynamics of salp feeding on marine microorganisms in a vast open ocean region. All salps preferentially removed prey greater than 1 μm in diameter, including marine Synechococcus, diatoms, Crocosphaera, and Chrysochromulina, while the smaller Prochlorococcus and SAR11 were not a major source of prey biomass. We also found that salp feeding varied between salp taxa with some salp guts dominated by both Crocosphaera and Chrysochromulina while others were dominated by Crocosphaera alone. Together, these results suggest that salp impacts are not uniform across taxa and their patterns of selective feeding among marine microbes requires consideration of species-specific feeding strategies and environmental context. Further, this work suggests that the mortality pressure of salp feeding on marine microorganisms may shape microbial community structure and that this pressure varies with the diversity and dynamics of macrozooplankton predators.}, }
@article {pmid41690245, year = {2026}, author = {Hu, J and Zhou, Y and Ishii, S and Ahmed, W and Sadowsky, MJ and Xia, X and Du, Z and Cytryn, E and Mwakalapa, EB and Rivera, WL and Zhou, Y and Rensing, C and Zhang, Q}, title = {Sources, contamination pathways, and monitoring of pathogens in urban estuaries.}, journal = {Marine pollution bulletin}, volume = {226}, number = {}, pages = {119415}, doi = {10.1016/j.marpolbul.2026.119415}, pmid = {41690245}, issn = {1879-3363}, abstract = {Urban estuaries are critical ecological and socio-economic interfaces but are increasingly impacted by microbial pathogen contamination driven by anthropogenic activities such as wastewater discharge, stormwater runoff, agriculture, and wildlife inputs. Despite extensive documentation of estuarine pathogens, effective risk assessment and management remain constrained by key knowledge gaps related to source apportionment, environmental fate, and monitoring relevance. This review synthesizes current understanding of pathogen sources and transmission pathways in urban estuaries and critically examines the physicochemical, hydrodynamic, and sediment-mediated processes that regulate pathogen persistence, redistribution, and exposure risk. We identify three interconnected challenges: (i) limited resolution in differentiating human and non-human contamination sources due to overlapping microbial signatures; (ii) inadequate incorporation of estuarine hydrodynamics and sediment reservoirs into fate-and-transport frameworks; and (iii) misalignment between conventional monitoring indicators and actual pathogen and antimicrobial resistance risks. Emerging approaches, including microbial source tracking, sequencing-based surveillance, biosensors, and hybrid predictive modelling, are evaluated for their capacity to support risk-relevant decision-making. Framed within a One Health perspective, this review integrates microbial ecology, environmental processes, and surveillance technologies to support evidence-based management and sustainable mitigation of pathogen risks in urban estuaries.}, }
@article {pmid41689629, year = {2026}, author = {Mohammadzadeh, MH and Asadollahpour, M and Sharbatdar, HR and Darbouy, MS and Fekrirad, Z}, title = {Voices of Eukaryotic Microbes: Chemical Communication Via Quorum Sensing.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02716-3}, pmid = {41689629}, issn = {1432-184X}, abstract = {Quorum sensing (QS) is a cell-cell communication mechanism mediated by secreted hormone-like signaling molecules that operates in both Gram-positive and Gram-negative bacteria, driving coordinated alterations in gene expression once a critical cell density is reached. In these prokaryotic systems, bacteria produce, release, detect, and respond to small autoinducers, such as acyl-homoserine lactones in Gram-negative bacteria, oligopeptides in Gram-positive bacteria, and the universal autoinducer-2, to regulate community behaviors including biofilm formation, virulence factor production, and stress adaptation. The concept of QS in eukaryotic microbes emerged decades ago, and later investigations confirmed that unicellular fungi and protozoa similarly measure population density to regulate collective activities. In Saccharomyces cerevisiae, aromatic alcohols (2-phenylethanol, tryptophol, tyrosol) serve as QS signals to control filamentous growth, biofilm assembly, and environmental stress responses. Candida albicans employs farnesol to suppress hyphal development while utilizing tyrosol to accelerate germ tube emergence and biofilm maturation. African trypanosomes, including Trypanosoma brucei and related species, generate oligopeptides via secreted peptidases that accumulate as stumpy induction factors (SIFs), triggering a density-dependent shift from proliferative slender forms to transmission-competent stumpy forms essential for tsetse fly infection. QS-based mechanisms influence virulence factors in fungal and protozoan pathogens, affecting their ability to colonize hosts. Exploring QS in eukaryotic organisms opens new possibilities for antifungal treatments and parasite management. By interfering with QS signaling, researchers can disrupt fungal biofilm formation and regulate protozoan development, paving the way for innovative disease control methods.}, }
@article {pmid41687498, year = {2026}, author = {Liao, B and Wang, Q and Zhang, T and Lu, X and Fang, N}, title = {Optimizing carbon source strategy for denitrification using food waste fermentation liquid: Synergistic mechanisms of butyrate and sucrose.}, journal = {Journal of environmental management}, volume = {401}, number = {}, pages = {128950}, doi = {10.1016/j.jenvman.2026.128950}, pmid = {41687498}, issn = {1095-8630}, abstract = {Food waste fermentation liquid, rich in volatile fatty acids (VFAs) and carbohydrates, serves as a sustainable electron donor for biological nitrogen removal. However, the compositional fluctuation of fermentation liquid often leads to unstable denitrification, and the mechanistic influence of mixed VFA-saccharide interactions on microbial ecology remains poorly understood. In this study, four carbon-source systems-three simulating typical mixed fermentation products (acetate + sucrose, propionate + sucrose, butyrate + sucrose) and one single-carbon control (acetate alone)-were systematically evaluated in sequencing batch reactors (SBRs). Results indicated that the butyrate-sucrose system (A3) exhibited superior performance, achieving a nitrate removal efficiency of 98.5%, which was 13.5% and 8.2% higher than that of the acetate-sucrose (A1) and propionate-sucrose (A2) systems, respectively. Furthermore, A3 maintained the lowest nitrite accumulation (<0.5 mg/L). Mechanistically, A3 facilitated the selective enrichment of functional genera Ferruginibacter and Terrimonas. PICRUSt2 functional predictions revealed that this specific combination significantly enhanced KEGG pathways related to membrane transport (ABC transporters) and energy metabolism, suggesting a synergistic effect that accelerates electron transfer and metabolic turnover. This study demonstrates that regulating acidogenic fermentation towards a butyrate-dominant composition is a promising strategy to maximize the utility of food waste as a carbon source, ensuring robust nitrogen removal in wastewater treatment.}, }
@article {pmid41687164, year = {2026}, author = {Kim, D and Yun, N and Du, H and Li, C and Preheim, S and Rossi, R}, title = {Enabling microbial electrolysis cell scale-up via electrochemistry-, hydrodynamic-, and microbial ecology-informed framework.}, journal = {Water research}, volume = {294}, number = {}, pages = {125503}, doi = {10.1016/j.watres.2026.125503}, pmid = {41687164}, issn = {1879-2448}, abstract = {Microbial electrolysis cells (MECs) can produce green hydrogen while removing organic contaminants from liquid waste streams by leveraging the metabolic activity of electroactive microorganisms. Despite their potential in a sustainable, circular economy, large-scale MECs that can treat relevant volumes of wastewater have failed to deliver performance proportional to their lab-scale counterparts. The reason behind this lower performance at scale remains unclear. In this study, we developed a combined electrochemistry-, hydrodynamic-, and microbial ecology-informed framework to analyze and optimize MEC performance during scale-up, enabling accurate quantification of major limitations and the identification of strategies to overcome them, ultimately facilitating equivalent performance at scale. Applying this framework to the scale-up of a zero-gap MEC from 9 cm[2] electrode area to 100 cm[2] electrode area, resulted in similar maximum current densities in a 100 cm[2] MEC (21.7 ± 1.1 A/m[2]) compared to a 9 cm[2] system (25.1 ± 2.7 A/m[2]), as well as equivalent hydrogen production rates of 69.3 L/L-d (100 cm[2]) and 67.7 ± 2.4 L/L-d (9 cm[2]). COMSOL flow dynamics simulations were used to scale up the reactor configuration without negatively affecting electrolyte velocity and distribution in the cell, minimizing the increase in internal resistances during scale-up (11.7 ± 0.5 mΩm[2] at 9 cm[2]; 19.7 ± 1.3 mΩm[2] at 100 cm[2]). Microbial community structures were assessed at both scales using high-throughput sequencing, highlighting the differences of populations across electrode dimensions and operational parameters. The framework presented here accelerates the development of effective strategies toward the scale-up of MECs by furthering the understanding of how electrochemical, hydrodynamic, and microbial ecology parameters change as the reactor dimension is increased. Ultimately, this approach contributes to advancing electrochemical biotechnology toward practical deployment in energy-efficient wastewater treatment systems.}, }
@article {pmid41686264, year = {2026}, author = {Wu, CY and Cheng, HY and Lin, YC and Wang, YC and Meng, YZ and Hsieh, YE and Liu, AC and Yang, SH}, title = {Role of Core Microbiome Shifts in Octocoral Litophyton Under Diurnal Temperature Fluctuations.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02715-4}, pmid = {41686264}, issn = {1432-184X}, support = {NSTC 112-2611-M-002 -020//National Science and Technology Council/ ; NTUCCP- 115L891306//National Taiwan University/ ; }, abstract = {Climate change is projected to raise sea surface temperatures and intensify diurnal temperature fluctuations (DTF), threatening the survival of both scleractinian corals and octocorals. Litophyton, a common octocoral in Taiwan's shallow reefs, is frequently exposed to large DTF and summer heat stress, making it a suitable model to study thermal resilience. Coral-associated bacterial communities are known to shift under thermal stress, and key bacterial taxa may play crucial roles in host acclimation. This study aimed to address two questions: (1) Can higher DTF mitigate cumulative heat stress in octocorals? (2) If so, what physiological and microbial community changes accompany this effect? To answer these questions, we conducted tank experiments under constant warming and two short-term DTF regimes (± 5 °C and ± 7 °C; baseline 25-27.8 °C), along with a no-fluctuation control. We measured physiological stress indicators, including superoxide dismutase (SOD) and catalase (CAT) activities, and monitored bacterial community dynamics. Our results show that DTF helped maintain stable photosynthetic efficiency (Fv/Fm) compared to constant warming. Notably, significant differences in ROS activity were only observed in the ± 5 °C group, rather than in the larger ± 7 °C group, indicating a measurable alleviation of thermal stress and greater plasticity in Litophyton coping with temperature changes. Moreover, 29.4% more significantly abundant in the ± 7 °C group compared to the control in the core microbiome Endozoicomonas preceded detectable physiological changes in the host, suggesting a potential role in early stress mitigation. These findings deepen our understanding of octocoral holobiont resilience under fluctuating thermal regimes and highlight Endozoicomonas diversity as a potential indicator of Litophyton health.}, }
@article {pmid41685888, year = {2026}, author = {Gilson, M and Bayon-Vicente, G and Krings, S and Toubeau, L and Wattiez, R and Leroy, B}, title = {Fundamental aspects of sucrose metabolism reveal a trophic link between Rhodospirillum rubrum and Rhodobacter capsulatus.}, journal = {mBio}, volume = {}, number = {}, pages = {e0371725}, doi = {10.1128/mbio.03717-25}, pmid = {41685888}, issn = {2150-7511}, abstract = {Purple non-sulfur bacteria (PNSB) are well known to have an exceptional metabolic versatility. However, while the growth of PNSB on sugar-rich streams has been extensively explored, their ability to metabolize sugars is poorly understood. Here, we explore the metabolic mechanisms of sucrose, glucose, and fructose utilization in two phototrophic PNSB, Rhodospirillum rubrum and Rhodobacter capsulatus. Our findings demonstrate distinct carbohydrate assimilation capacities, as well as the use of different metabolic strategies for each species. Moreover, a trophic link was identified between the two species during co-cultivation, resulting from the production of fermentation by-products by Rh. capsulatus, which are then reassimilated by Rs. rubrum. Finally, we demonstrate that the synergy observed between Rs. rubrum and Rh. capsulatus can be successfully scaled up in a photobioreactor system. Our study highlights how fundamental knowledge of metabolism and the establishment of a trophic link between two PNSB species might be useful for the development of biobased economy and resource recovery strategies.IMPORTANCEThe diverse metabolic capacities found in microbial communities expand the possibilities of microbial biotechnological exploitation. In this study, we demonstrate that Rhodospirillum rubrum and Rhodobacter capsulatus, two purple non-sulfur bacteria, adopt different metabolic strategies for sugar assimilation. These differences allow them to benefit from each other, resulting in enhanced carbon yield and productivity compared to pure cultures. We also showed that the trophic link between both species can be scaled up in a photobioreactor system. Understanding these interactions expands the potential for designing microbial consortia optimized for the valorization of carbohydrate-rich waste streams using purple non-sulfur bacteria.}, }
@article {pmid41683185, year = {2026}, author = {Song, D and Song, L and Zhong, X and Wu, Y and Zhang, Y and Yang, L}, title = {Integrated Molecular Informatics and Sensory-Omics Study of Core Trace Components and Microbial Communities in Sauce-Aroma High-Temperature Daqu from Chishui River Basin.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {41683185}, issn = {2304-8158}, support = {MTXYTD202501//Science and Technology Innovation Team of Moutai Institute/ ; QianKeHeJiChu-ZD[2025]018//Guizhou Provincial Basic Research Program (Natural Science)/ ; ZunShiKeHe HZ Zi[2023]112//The Fund of Zunyi Technology and Big data Bureau, Moutai Institute Joint Science and Technology Research and Development Project/ ; mygccrc[2022]011, mygccrc[2022]013//Research Foundation for Scientific Scholars of Moutai Institute/ ; XYNJ20240104//Moutai Institute &amp; Guangdong Li'er'an Chemical Industry Group Co., Ltd/ ; }, abstract = {Flavor-relevant trace volatiles and microbial communities were examined in six sauce-aroma high-temperature Daqu samples. Headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME-GC-MS) quantified 210 trace volatile compounds across 14 chemical classes. Orthogonal partial least squares discriminant analysis (OPLS-DA) with variable importance in projection (VIP) screening was integrated with sensory scoring, correlation analysis, and molecular docking to an olfactory receptor model. Volatile profiles showed clear stratification in total abundance. Pyrazines dominated the high-total group. Tetramethylpyrazine served as a major driver. Sensory evaluation indicated that aroma explained overall quality best. (E)-2-pentenal and dimethyl trisulfide showed significant positive associations with aroma and overall scores. In the olfactory receptor, the polar residue module that provides directional constraints for Daqu odor activation was formed by Ser75, Ser92, Ser152, Ser258, Thr74, Thr76, Thr98, Thr200, Gln99, and Glu94. The hydrogen-bond or charge network was further reinforced by Arg150, Arg262, Asn194, His180, His261, Asp182, and Gln181. The core discriminant set comprised acetic acid, hexanoic acid, (E)-2-pentenal, nonanal, decanal, dimethyl trisulfide, trans-3-methyl-2-n-propylthiophane, 2-hexanone oxime, ethyl linoleate, propylene glycol, 2-ethenyl-6-methylpyrazine, 4-methylquinazoline, 5-methyl-2-phenyl-2-hexenal, and 1,2,3,4-tetramethoxybenzene. Sequencing revealed higher bacterial diversity than fungal. Bacillus and Kroppenstedtia were dominant bacterial genera. Aspergillus, Paecilomyces, Monascus, and Penicillium were major fungal genera. Correlation patterns suggested that Bacillus and Monascus were positively linked to acetic acid and 1,2,3,4-tetramethoxybenzene. Together, these results connected chemical fingerprints, sensory performance, receptor-level plausibility, and microbial ecology. Concrete targets are provided for quality control of high-temperature Daqu.}, }
@article {pmid41683077, year = {2026}, author = {Jiang, X and Li, X and Song, P and Dou, Y and Xue, J and Wu, Z and Ma, S and Wei, W and Zheng, W and Dou, S and Dong, L}, title = {Analysis of Microbial Interactions During the Production of Chinese Ethnic Fermented Foods.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {41683077}, issn = {2304-8158}, support = {No.2025-MSLH-016//Liaoning Provincial Science and Technology Plan Joint Plan (Natural Science Foundation-General Program)/ ; 2014020134//Natural Science Foundation of Liaoning Province/ ; JYTMS20230376//Liaoning Provincial Department of Education University Basic Scientific Research Surface Project/ ; }, abstract = {Food fermentation is an ancient bioprocess characterized by complex biochemical transformations driven primarily by microbial communities. Across the diverse regions of China, various ethnic groups have developed a rich array of traditional fermented foods through long-term practical experience. These foods are integral to local culinary heritage and provide valuable systems for studying microbial ecology and function. From the perspective of microbial interactions, this review summarizes key concepts and major interaction types-including mutualism, commensalism, and competition-and describes how bacteria, yeasts, and molds interact via metabolic division of labor to drive substrate conversion, flavor formation, preservation, and biosynthesis of functional compounds. Focusing on four representative ethnic fermented foods-Dong fermented fish, Mongoslian milk curd, Miao sour soup, and Manchurian kombucha-we analyze how microbial interactions contribute to product quality, safety, and sensory attributes. Given current challenges in industrializing traditional fermented foods, such as poor standardization and variable quality, we propose future research directions centered on modern microbiome tools, designed microbial consortia, and process optimization. This work aims to provide a scientific foundation and practical strategies for modernization and quality improvement of traditional fermented foods.}, }
@article {pmid41681446, year = {2026}, author = {Onbaşılar, EE and Yalçın, S and Batur, B and Yalçın, S and Kılıçlı, &#x130;B and Bakıcı, C and Bakır, B and Kartal, YK and Sel, T}, title = {Effects of Xylanase and Protease Supplementation on Growth Performance, Meat Quality, Gut Health, Cecal Fermentation, and Bone Traits in Broiler Chickens.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {3}, pages = {}, doi = {10.3390/ani16030465}, pmid = {41681446}, issn = {2076-2615}, abstract = {This study investigated the effects of dietary xylanase and protease supplementation, applied individually or in combination, on growth performance, intestinal characteristics, gut fermentation, meat quality, and skeletal traits in broiler chickens. A total of 540-day-old male broiler chicks were allocated to six experimental groups and fed a control corn-soybean meal-based diet or diets supplemented with xylanase, protease, or a xylanase-protease combination. Enzyme supplementation significantly improved body weight gain and feed efficiency, particularly between days 22 and 42, and reduced intestinal digesta viscosity. Improvements in gut morphology were reflected by increased villus height and villus-to-crypt ratios, accompanied by higher cecal total volatile fatty acid concentrations, increased Lactobacillus populations, and reduced coliform counts. In contrast, breast meat physicochemical composition and antioxidant status were not affected by dietary treatments. Skeletal development was positively influenced, with improvements observed in selected morphometric and structural bone traits. Overall, dietary xylanase and protease supplementation enhanced broiler performance and skeletal development primarily through improved digestive efficiency and favorable modulation of gut morphology, microbial ecology, and intestinal fermentation, without adverse effects on meat quality.}, }
@article {pmid41681371, year = {2026}, author = {Tang, D and Chen, S and Tang, C and Li, X and Li, M and Li, X and Zhang, K and Ma, J}, title = {The Analysis of Transcriptomes and Microorganisms Reveals Differences Between the Intestinal Segments of New Zealand Rabbits.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {3}, pages = {}, doi = {10.3390/ani16030390}, pmid = {41681371}, issn = {2076-2615}, support = {2021YFYZ0009//Main livestock and poultry molecular breeding platform (Breeding research project)/ ; CARS-43-A-3//Supported by the earmarked fund for China Agriculture Research System/ ; }, abstract = {This study systematically characterized functional compartmentalization along the intestinal tract of New Zealand rabbits by analyzing mucosal tissue and luminal contents from distinct segments, including the duodenum, jejunum, ileum, cecum, and colon, using RNA-seq and 16S rRNA sequencing. Transcriptomic analysis revealed that differentially expressed genes identified between the small and large intestines were mainly enriched in digestion, absorption, and immune functions. Genes associated with the transport of amino acids, sugars, vitamins, and bile salts showed significantly higher expression in the small intestine, whereas genes related to water absorption, short-chain fatty acids (SCFAs), nucleotides, and metal ion transport were preferentially expressed in the large intestine. From an immunological perspective, genes involved in fungal responses were enriched in the small intestine, while bacterial response pathways and pattern recognition receptor (PRR) signaling genes were upregulated in the large intestine. Microbiota analysis demonstrated significantly greater diversity and abundance in the large intestine compared with the small intestine. Specifically, Proteobacteria and Actinobacteria were enriched in the small intestine, whereas Firmicutes, Verrucomicrobia, and Bacteroidetes dominated the large intestine. Correlation analysis further identified significant associations between gut microbiota composition and host genes involved in nutrient digestion and absorption. Together, these findings provide transcriptome-based evidence for regional specialization of nutrient transport, immune responses, and microbial ecology along the rabbit intestine.}, }
@article {pmid41680172, year = {2026}, author = {Lu, Q and Wang, K and Gu, S and Ma, J and Cui, D and Chi, Z and Li, B and Zai, X and Wang, N and Wang, T and Dou, Z and Zhang, F and Geisen, S and Raaijmakers, JM and Song, C and Zuo, Y}, title = {Siderophore-producing Bacillus and free-living nematodes are associated with soil suppressiveness to banana root-knot nematodes.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-69647-y}, pmid = {41680172}, issn = {2041-1723}, support = {No. 32372810//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 32302668//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 42577142//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {The control of soil-borne diseases is crucial for ensuring global food security. Here, we investigate the impact of the root-knot nematode (Meloidogyne) on banana continuous cropping over a period of 11 years. The results show significant root infestation initially, but disease incidence declined markedly from the 7th cropping year onwards. Soil community profiling revealed that this intriguing onset of nematode suppressiveness was associated with changes in free-living nematode populations and rhizosphere microbiome composition. Rhizosphere microbiome analyses and strain isolation pinpointed Bacillus velezensis as a keystone taxon in soil suppressiveness to Meloidogyne. Genomics, metabolomics and bioassays validated the suppressive effects of B. velezensis against Meloidogyne and identified the siderophore bacillibactin as key metabolite with repellent and nematicidal activities. By integrating long-term field studies with multi-omics approaches, this study uncovered co-occurring increases in specific rhizobacterial genera and free-living nematodes associated with reduced root-parasitic nematode populations, offering valuable insights for sustainable agriculture.}, }
@article {pmid41679819, year = {2026}, author = {Ding, Y and Li, X and Hao, Y and Ding, P and Chen, N and Luo, L and Wan, C and Wu, M}, title = {Structural elucidation and effects on gut microbiota of soluble galactans from edible Boletus.}, journal = {Carbohydrate polymers}, volume = {378}, number = {}, pages = {124886}, doi = {10.1016/j.carbpol.2026.124886}, pmid = {41679819}, issn = {1879-1344}, mesh = {*Gastrointestinal Microbiome/drug effects ; *Galactans/chemistry/pharmacology/isolation &amp; purification ; Fermentation ; *Agaricales/chemistry ; Molecular Docking Simulation ; Fatty Acids, Volatile/metabolism ; Prebiotics ; }, abstract = {Edible Boletus mushrooms hold considerable development potential due to their exceptional nutritional and biological profiles. This study characterized two novel galactans, NBP and BRP, extracted from Neoboletus brunneissimus and Butyriboletus roseoflavus, respectively. Structural analysis revealed that both NBP and BRP possess a backbone composed of α-1,6-linked galactopyranosyl residues substituted at O-2, with structural diversity arising from variations in the side-chain substituents. Although both polysaccharides exhibit low viscosities, BRP forms a shear-stable elastic gel network, contrasting with the predominantly linear structure of NBP. In vitro fermentation demonstrated that both galactans markedly promoted the proliferation of beneficial probiotics, optimized gut microbiota composition, and enriched butyrate-producing bacteria including Faecalibacterium prausnitzii. Furthermore, they stimulated the production of lactic acid and short-chain fatty acids (SCFAs), leading to a reduction in fermentation pH and thereby modulating microbial ecology and host energy metabolism. Metagenomic annotation revealed that galactan degradation was driven by glycoside hydrolases (GHs) from Bacteroidaceae, and molecular docking analyses indicated that these GHs exhibit distinct binding preferences for specific structural regions of the polysaccharides. These results explain the basis for the microbiota-dependent improvement of gut health by Boletus galactans, providing a theoretical foundation for their development as precision prebiotics.}, }
@article {pmid41679575, year = {2026}, author = {Kovarova, A and Ryan, K and Tumeo, A and McDonagh, F and Clarke, C and Cormican, M and Miliotis, G}, title = {Emergence of dual β-lactam and Colistin resistance via blaFRI-8 and mcr-10.2 co-carriage on an IncFII family plasmid in Enterobacter vonholyi.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {}, number = {}, pages = {105899}, doi = {10.1016/j.meegid.2026.105899}, pmid = {41679575}, issn = {1567-7257}, abstract = {OBJECTIVES: Enterobacter vonholyi isolate E323169 represents a rare case of co-carriage of the antimicrobial resistance genes (ARGs) blaFRI-8, mcr-10.2, isolated from a clinical rectal swab. E323169 represents one of only 11 known E. vonholyi genomes. To date, within the NCBI Pathogen Detection resource, blaFRI-8 was identified in three assemblies and mcr-10.2 in two. In that dataset, blaFRI-8 co-occurred with an mcr-10 hit only once (Enterobacter asburiae). This study analyzes the genomic, phenotypic and epidemiological importance of this rare co-occurrence.<br><br>METHODS: Species identification for E323169 was initially assigned by MALDI-TOF and subsequently confirmed using a multifactorial genomic workflow. Antimicrobial susceptibilities were determined by MIC assay. The genome of E323169 was sequenced on an Illumina-NextSeq-1000, assembled, and annotated for ARGs, virulence factors, and plasmid replicons detection. Comparative phylogenomics used all canonical E. vonholyi RefSeq assemblies, and NCBI metadata were analysed for plasmid distributions of blaFRI-8 and mcr-10.2.<br><br>RESULTS: E323169 carried six ARGs: four chromosomally encoded (blaACT-91, fosA, oqxA10, oqxB9) and two plasmid-borne (blaFRI-8 and mcr-10.2) co-located on IncFII(p14)_1_p14 replicon. Additional plasmid replicons: Col(MG828)_1 and ColRNAI_1 were also identified. By mining the NCBI Pathogen Detection pipeline, we identified blaFRI-8 on IncFII replicon in E. asburiae JBIWA002, and mcr-10.2 on a multi-replicon (IncFIB/IncFII) plasmid in E. kobei 11,778-yvys.<br><br>CONCLUSION: This report, to our knowledge, represents the first E. vonholyi isolate co-harboring blaFRI-8 and mcr-10.2 on a single IncFII family plasmid in a non Enterobacter cloacae complex species, showing the widening host range of plasmid-mediated resistance to carbapenems/colistin. These findings suggest IncFII-family plasmids as recurrent scaffolds for the accumulation of high-impact resistance determinants in Enterobacter and suggest that monitoring IncFII backbones may provide an early warning signal for future convergence events.<br><br>IMPACT STATEMENT: The detection of Enterobacter vonholyi across human, animal, plant, and environmental sources underscore its relevance within a One Health framework, highlighting the potential for cross-sectoral circulation of antimicrobial resistance. The convergence of blaFRI-8 and mcr-10.2 on an IncFII plasmid in E. vonholyi exposes an unrecognized reservoir of last-line resistance in a species prone to misidentification. Together, these findings emphasize the importance of integrating genomic surveillance into routine diagnostics to identify hidden reservoirs of carbapenem and colistin resistance and to strengthen infection prevention strategies before wider dissemination occurs.}, }
@article {pmid41677726, year = {2026}, author = {Zeng, T and Zuo, L and Yu, Q and Wu, Q and Bao, Z and Xiong, H and Luo, M and Li, B}, title = {Role and Mechanisms of Gut Microbiota in Infectious Diseases: Recent Evidence from Animal Models.}, journal = {Biology}, volume = {15}, number = {3}, pages = {}, pmid = {41677726}, issn = {2079-7737}, support = {XGKJ2024010037//Xiaogan Municipal Bureau of Science and Technology (Hubei Province&#xff0c; China)/ ; 2025K009//Hubei Small Town Development Research Center, Hubei University of Engineering/ ; }, abstract = {Infectious diseases present persistent and complex challenges to global public health, with conventional antibiotic therapies increasingly limited by antimicrobial resistance, microbiota disruption, and adverse effects. There is a critical need to explore complementary strategies that augment host defense mechanisms without exacerbating these limitations. Accumulating evidence underscores the integral role of the gut microbiota-a diverse microbial ecosystem within the gastrointestinal tract-in regulating systemic immunity and pathogen susceptibility. This review synthesizes recent advances from animal models to delineate the multi-faceted mechanisms by which commensal microbes and their metabolites confer protection against enteric and respiratory infections. Key processes include competitive exclusion for nutrients and ecological niches, production of antimicrobial compounds, reinforcement of intestinal barrier integrity, and orchestration of local and systemic immunity via gut-lung axes. We further discuss the potential of microbiota-targeted interventions to enhance treatment efficacy and patient outcomes. By integrating mechanistic insights with translational applications, this review aims to inform the rational design of next-generation anti-infective strategies grounded in microbial ecology and host immunobiology.}, }
@article {pmid41674154, year = {2026}, author = {Măgălie, A and Marantos, A and O'Brien, JM and Schwartz, DA and Marchi, J and Lennon, JT and Weitz, JS}, title = {Phage infection fronts trigger early sporulation and viral entrapment in bacterial populations.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag023}, pmid = {41674154}, issn = {1751-7370}, abstract = {Bacteriophage (phage) infect, lyse, and propagate within bacterial populations. However, physiological changes in bacterial cell state can protect against infection even within genetically susceptible populations. One such example is the generation of endospores by Bacillus and its relatives, characterized by a reversible state of reduced metabolic activity that protects cells against stressors including desiccation, energy limitation, antibiotics, and infection by phage. Here we tested how sporulation at the cellular scale impacts phage dynamics at population scales when propagating amongst B. subtilis in spatially structured environments. Plaques resulting from infection and lysis were approximately 3-fold smaller on lawns of spore-forming bacteria vs. non-spore-forming bacteria. Analysis of plaque growth revealed that final plaque size was reduced due to an early termination of expanding phage plaques rather than the reduction of plaque growth speed. Microscopic imaging of the plaques revealed "sporulation rings", i.e., spores enriched around plaque edges relative to phage-free regions. We developed a series of mathematical models of phage, bacteria, spore, and small molecules that recapitulate plaque dynamics. We show evidence that phage infections trigger the formation of sporulation rings that reduce the productivity of phage infections and halt plaque spread even when resources are available for infection and lysis further away from plaque centers. Moreover, sporulation rings are also enriched in viable virospores, suggesting that although dormancy limits phage infections at population scales in the near-term, viruses may co-opt phage-avoidance strategies to re-emerge over the long-term, opening new avenues to explore the entangled fates of phages and their bacterial hosts.}, }
@article {pmid41673345, year = {2026}, author = {Lafont, A and Violle, C and Ranchou-Peyruse, M and Guignard, M and Mura, J and Fargetton, T and Cézac, P and Ranchou-Peyruse, A}, title = {Successional Trajectories of Deep Subsurface Microbiomes in Response To Experimental Dihydrogen Injection.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02697-3}, pmid = {41673345}, issn = {1432-184X}, support = {ANR-20-CHIN-0001//Agence Nationale de la Recherche/ ; ANR-20-CHIN-0001//Agence Nationale de la Recherche/ ; ANR-20-CHIN-0001//Agence Nationale de la Recherche/ ; }, abstract = {Converting pre-existing gas storage facilities to dihydrogen storage raises critical questions about storage quality and dihydrogen consumption by prokaryotes. To investigate biologically driven changes during such transitions, we analyzed data from five dihydrogen pulse experiments conducted in pressurized bioreactors that replicate deep aquifer pressure and temperature conditions. Our goal was to determine whether consistent community-level responses to dihydrogen injection could be identified. We found that dihydrogen exposure consistently led to a decline in fermentative ASVs, likely driven by environmental filtering. Hydrogenotrophic sulfate reducers initially dominated in some experiments, with total sulfate depletion observed in certain cases, followed by the emergence of methanogenic archaea. In some instances, a succession pattern involving Thermodesulfovibrio and Methanothermobacter appeared across taxonomically distinct communities, suggesting deterministic ecological processes. Additionally, we observed potential dispersal limitation and selection pressures, possibly linked to pH shifts caused by autotrophy. These findings underscore the importance of considering microbial dynamics in dihydrogen storage strategies in deep aquifers and suggest that, despite initial variability, predictable ecological succession may occur under specific geochemical conditions.}, }
@article {pmid41675503, year = {2025}, author = {Gu, S and Shao, J and He, R and Xiong, G and Qu, Z and Shao, Y and Yu, L and Zhang, D and Wang, F and Xu, R and Guo, P and Xi, N and Li, Y and Wu, Y and Wei, Z and Li, Z}, title = {Forging the iron-net: Towards a quantitative understanding of microbial communities via siderophore-mediated interactions.}, journal = {Quantitative biology (Beijing, China)}, volume = {13}, number = {2}, pages = {e84}, pmid = {41675503}, issn = {2095-4697}, abstract = {Iron is a critical yet limited nutrient for microbial growth. To scavenge iron, most microbes produce siderophores-diverse small molecules with high iron affinities. Different siderophores are specifically recognized and uptaken by corresponding recognizers, enabling targeted interventions and intriguing cheater-producer dynamics. We propose constructing a comprehensive iron interaction network, or "iron-net", across the microbial world. Such a network offers the potential for precise manipulation of the microbiota, with conceivable applications in medicine, agriculture, and industry as well as advancing microbial ecology and evolution theories. Previously, our successful construction of an iron-net in the Pseudomonas genus demonstrated the feasibility of coevolution-inspired digital siderophore-typing. Enhanced by machine learning techniques and expanding sequencing data, forging such an iron-net calls for multidisciplinary collaborations and holds significant promise in addressing critical challenges in microbial communities.}, }
@article {pmid41675709, year = {2025}, author = {Lin, W and Niu, M and Mu, C and Wang, C and Ye, Y}, title = {Key species drive community and functional stability of segment-specific gut microbiomes after the swimming crab molting.}, journal = {iMetaOmics}, volume = {2}, number = {1}, pages = {e51}, pmid = {41675709}, issn = {2996-9514}, abstract = {Molting is a crucial process for crab growth and development. However, the impacts of molting on the structure and function of the gut bacterial community in swimming crab Portunus trituberculatus are poorly understood. Then, dynamic changes in the microbiotas of gut segments (foregut, midgut, and hindgut) after molting were investigated using 16S rRNA gene amplicon and shotgun metagenomic sequencing. We highlight the segment-specific responses in bacterial community compositions, alpha-diversity, and co-occurrence patterns, emphasizing the significant impact of hindgut bacteria on the analysis of the whole gut. The identification of enriched and emerged species and their source, coupled with insights into functional stability and multifunctionality, adds granularity to our understanding of postmolt microbial ecology. We offer potential keys to driving microbial community succession. These findings provide essential insights into the stability and dynamics of gut microbiota, which are crucial for both ecological understanding and sustainable management of crab probiotic regulation.}, }
@article {pmid41673333, year = {2026}, author = {Lu, L and Wang, X and Qin, Y and Xiao, Y and Zhang, Y and Ma, H and Wang, D and Li, Z}, title = {Hydrological Fragmentation Driving Microbial Carbon Necromass Reduction in Columnar Sediments: Evidence from CAZyme Genomic Signatures in Cascade Reservoirs.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02705-6}, pmid = {41673333}, issn = {1432-184X}, support = {52470202//National Natural Science Foundation of China/ ; U2340222//National Natural Science Foundation of China/ ; NBWL202200489 and 202403005//China Three Gorges Corporation/ ; 309GJHZ2024110GC//Chinese Academy of Sciences/ ; }, abstract = {Microbial necromass carbon (MNC), a key component of soil organic carbon, plays a vital role in aquatic carbon sequestration. Its accumulation and transformation are highly sensitive to environmental changes, particularly in reservoir sediments-critical zones for organic matter storage and biogeochemical cycling. This study investigated the vertical distribution and regulatory mechanisms of MNC in cascade reservoir systems through sediment analysis and metagenomic sequencing. Our findings reveal that MNC constitutes 15 ~ 35% of total sediment organic carbon (SeOC) , with fungal-derived necromass consistently dominating over bacterial contributions. Metagenomic data highlight distinct functional potentials in carbon cycling, showing that bacterial necromass exhibits higher lability than fungal necromass, as evidenced by shifts in carbohydrate-active enzyme (CAZyme) gene abundances-particularly those involved in glucan and peptidoglycan degradation. Notably, cascade damming introduced spatial heterogeneity in MNC distribution , with downstream reservoirs experiencing reduced MNC accumulation due to altered hydrological connectivity and nutrient regimes. These results underscore the pivotal role of MNC in aquatic carbon storage while highlighting the complex interplay between environmental factors, microbial metabolic traits, and anthropogenic disturbances in regulated river systems. Therefore, our findings demonstrate that fungal necromass is a dominant and relatively stable component of sediment carbon, and its dynamics must be integrated to accurately assess and predict carbon sequestration in dammed rivers.}, }
@article {pmid41671169, year = {2026}, author = {Saati-Santamaría, Z and Pérez-Mendoza, D and Khashi U Rahman, M and de Sousa, BFS and Montero-Calasanz, MDC and Rey, L and Roy, S and Sanjuán, J and García-Fraile, P}, title = {Evolutionary mechanisms underlying bacterial adaptation to the plant environment.}, journal = {FEMS microbiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuag005}, pmid = {41671169}, issn = {1574-6976}, abstract = {Plants and bacteria have coevolved over hundreds of millions of years, forming complex associations ranging from mutualism to pathogenicity that are essential for plant survival and ecosystem function. Bacterial adaptation to plant environments involves dynamic evolutionary mechanisms including horizontal gene transfer, gene regulation, and metabolic specialization, enabling bacteria to persist and specialize within diverse plant-associated niches. Here we review how evolutionary forces such as selection, drift, and gene flow shape bacterial genomes, regulatory networks, and ecological strategies in response to plant-imposed pressures, underpinning both beneficial and pathogenic lifestyles. Understanding these processes provides a unified evolutionary framework for bacterial adaptation to plants and highlights their implications for sustainable agriculture and microbiome-based innovations.}, }
@article {pmid41668299, year = {2026}, author = {Frings, DM and Mellinger, JM and Drace, KM}, title = {Microbial Diversity Across Chemolithotrophic and Phototrophic Biofilms in Cold Sulfur Springs.}, journal = {MicrobiologyOpen}, volume = {15}, number = {1}, pages = {e70223}, pmid = {41668299}, issn = {2045-8827}, mesh = {*Biofilms/growth &amp; development ; *Sulfur/metabolism ; RNA, Ribosomal, 16S/genetics ; Alabama ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Phototrophic Processes ; *Microbiota ; Phylogeny ; *Biodiversity ; DNA, Bacterial/genetics/chemistry ; DNA, Ribosomal/genetics/chemistry ; Chemoautotrophic Growth ; Cold Temperature ; *Natural Springs/microbiology ; Sequence Analysis, DNA ; Oxidation-Reduction ; }, abstract = {Sulfur-rich environments host specialized microbial communities that drive key biogeochemical processes, particularly sulfur cycling. While sulfur-oxidizing microbiota from hydrothermal vents and volcanic systems are well studied, microbial communities in cold terrestrial sulfur springs remain less understood. In this study, we used 16S rRNA gene sequencing to examine how sulfur availability and environmental conditions shape microbial assemblages across different biofilm types in a cold sulfur spring system at Blount Springs, Alabama (33.9301° N, 86.7928° W). Sulfur-oxidizing chemolithotrophs, including Sulfurovum and Halothiobacillus, represented the majority of the recovered reads in sulfur-rich white biofilms, while purple phototrophic biofilms were enriched with anoxygenic sulfur-oxidizing bacteria, such as Chromatium and Chlorobium. Nonsulfur biofilms from adjacent environments displayed greater microbial diversity, including a high abundance of photosynthetic diatoms, like, Melosira. Notably, Sulfurovum was abundant across both sulfur-rich and phototrophic niches, suggesting ecological flexibility and a central role in sulfur metabolism. These findings highlight the influence of sulfur chemistry and light availability in structuring microbial communities and contribute to a broader understanding of microbial adaptation and sulfur cycling in cold sulfur spring ecosystems.}, }
@article {pmid41668183, year = {2026}, author = {Zhang, Y and Jing, G and Chen, R and Gong, Y and Li, Y and Wang, Y and Wang, X and Zhang, J and Mao, Y and He, Y and Zheng, X and Wang, M and Yuan, H and Xu, J and Sun, L}, title = {RamEx: an R package for high-throughput microbial ramanome analyses with accurate quality assessment.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02339-3}, pmid = {41668183}, issn = {2049-2618}, abstract = {BACKGROUND: Microbial single-cell Raman spectroscopy (SCRS) has emerged as a powerful tool for label-free phenotyping, enabling rapid characterization of microbial diversity, metabolic states, and functional interactions within complex communities. However, high-throughput SCRS datasets often contain spectral anomalies from noise and fluorescence interference, which obscure microbial signatures and hinder accurate classification. Robust algorithms for outlier detection and microbial ramanome analysis remain underdeveloped.<br><br>RESULTS: Here, we introduce RamEx, an R package specifically designed for high-throughput microbial ramanome analyses with robust quality control and phenotypic classification. At the core of RamEx is the Iterative Convolutional Outlier Detection (ICOD) algorithm, which dynamically detects spectral anomalies without requiring predefined thresholds. Benchmarking on both simulated and real microbial datasets-including pathogenic bacteria, probiotic strains, and yeast fermentation populations-demonstrated that ICOD achieves an F1 score of 0.97 on simulated datasets and 0.74 on real datasets, outperforming existing approaches by at least 19.8%. Beyond anomaly detection, RamEx provides a modular and scalable workflow for microbial phenotype differentiation, taxonomic marker identification, metabolic-associated fingerprinting, and intra-population heterogeneity analysis. It integrates Raman-based species-specific biomarkers, enabling precise classification of microbial communities and facilitating functional trait mapping at the single-cell level. To support large-scale studies, RamEx incorporates C++&#x2009;acceleration, GPU parallelization, and optimized memory management, enabling the rapid processing of over one million microbial spectra within an hour.<br><br>CONCLUSIONS: By bridging the gap between high-throughput Raman-based microbial phenotyping and computational analysis, RamEx provides a comprehensive toolkit for exploring microbial ecology, metabolic interactions, and antibiotic susceptibility at the single-cell resolution. RamEx is freely available under the MIT license at https://github.com/qibebt-bioinfo/RamEx. Video Abstract.}, }
@article {pmid41667848, year = {2026}, author = {González-Azcona, C and Solano-González, F and Jiménez-Ruiz, S and Santos, N and Marañón-Clemente, I and Álvarez-Gómez, T and Eguizábal, P and Alonso, CA and Benito, D and Zarazaga, M and Torres, C and Lozano, C}, title = {High Nasal Carriage of MRSA-mecC in Wild Rabbits in the Iberian Peninsula: a Wildlife Reservoir?.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02713-6}, pmid = {41667848}, issn = {1432-184X}, }
@article {pmid41666926, year = {2026}, author = {Kim, CY and Podlesny, D and Schiller, J and Khedkar, S and Fullam, A and Orakov, A and Schudoma, C and Robbani, SM and Grekova, A and Kuhn, M and Bork, P}, title = {Planetary microbiome structure and generalist-driven gene flow across disparate habitats.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2025.12.051}, pmid = {41666926}, issn = {1097-4172}, abstract = {Microbes are ubiquitous on Earth, forming microbiomes that sustain macroscopic life and biogeochemical cycles. Microbial dispersal, driven by natural processes and human activities, interconnects microbiomes across habitats, yet most comparative studies focus on specific ecosystems. To study planetary microbiome structure, function, and inter-habitat interactions, we systematically integrated 85,604 public metagenomes spanning diverse habitats worldwide. Using species-based unsupervised clustering and parameter modeling, we delineated 40 habitat clusters and quantified their ecological similarity. Our framework identified key drivers shaping microbiome structure, such as ocean temperature and host lifestyle. Regardless of biogeography, microbiomes were structured primarily by host-associated or environmental conditions, also reflected in genomic and functional traits inferred from 2,065,975 genomes. Generalists emerged as vehicles thriving and facilitating gene flow across ecologically disparate habitat types, illustrated by generalist-mediated horizontal transfer of an antibiotic resistance island across human gut and wastewater, further dispersing to environmental habitats, exemplifying human impact on the planetary microbiome.}, }
@article {pmid41666603, year = {2026}, author = {Cristino, S and Caligaris, L and Salaris, S and Derelitto, C and Bonincontro, C and Marino, F and Grottola, A and Girolamini, L}, title = {Legionella petroniana sp. nov., a novel species isolated in Bologna, Italy: taxonomic, genomic and ecological insights in the era of environmental change.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {2}, pages = {126694}, doi = {10.1016/j.syapm.2026.126694}, pmid = {41666603}, issn = {1618-0984}, abstract = {This study presents the characterization of a novel Legionella species isolated in Italy over three different years from one company and two hospitals. Starting from standard techniques such as culture of water samples, agglutination test, MALDI-TOF MS and gene sequencing analysis used to identify the isolates, genomic and metabarcoding approaches were subsequently employees to further characterize the species. Legionella contamination ranged from 400 to 700 CFU/L. The tiny colonies displayed atypical morphology compared to typical Legionella features, although they grew on BCYE medium supplemented with L-cysteine. Microscopic and phenotypic analyses revealed Gram-stain negative, Ziehl-Neelsen-negative, rod-shaped, motile cells capable of growing at 32-37 °C, including on selective media such as GVPC and MWY. The isolates tested positive for oxidase and gelatinase activity. Fatty acid profiling identified the dominant components as Summed Features 3 (C16:1 ω7c/C16:1 ω6c, 28.9%), C16:0 iso (18.4%), and C15:0 anteiso (15.4%). Ubiquinone Q13 was the major quinone. Sequence analysis of the mip and rpoB genes showed 98.2% and 95.1% similarity, respectively, to L. feeleii (WO-44C ATCC 35072[T]). Whole genome sequencing (WGS) revealed a GC content of 41.5%, a dDDH value of ≤54.9%, and an ANI of 94.06% with L. feeleii (WO-44C ATCC 35072[T]), supporting the classification of a novel species within the genus Legionella. Furthermore, taxonomic resolution of water samples revealed the presence of 168 bacterial genera, including several respiratory, opportunistic, and zoonotic pathogens, as well as seven Legionella species. The name Legionella petroniana sp. nov. is proposed, with strain 31fI33[T] (=DSM 114357[T]=CCUG 76442[T]) designated as type strain.}, }
@article {pmid41663799, year = {2026}, author = {Gao, S and Zhao, W and Guan, X and Zhao, Z and Wang, B and Xiao, Y and Zhang, G and Pan, Y and Sun, H and Jiang, P and Mi, R and Jiang, J and Zhou, Z}, title = {Stronger Adaptability of Eukaryotic Communities than Prokaryotes in Seawater across an Extensive Salinity Gradient.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {28}, number = {1}, pages = {32}, pmid = {41663799}, issn = {1436-2236}, support = {U24A200104//National Natural Science Foundation of China/ ; XLYC2203191//Liaoning Revitalization Talents Program/ ; 2023JH1/10200007//Science and Technology Project of Liaoning Province/ ; 2023RJ007//Dalian Science and Technology Talent Innovation Support Program/ ; 2025HQ1304//Fundamental Research Funds of Liaoning Academy of Agricultural Sciences/ ; }, mesh = {*Salinity ; *Seawater/microbiology/chemistry ; *Eukaryota/physiology/genetics/classification ; *Prokaryotic Cells/physiology ; *Adaptation, Physiological ; *Microbiota ; Biodiversity ; }, abstract = {Researching microbial ecology in extreme environments is crucial for advancing the basic ecological theory and exploring their potential applications in biotechnology. The salt drying system provides an accessible but harsh environment that covers a maximum salinity gradient. In this study, we conducted a comparative analysis of the salinity adaptation and assembly mechanisms of prokaryotic and eukaryotic communities in several salt drying tanks using high-throughput amplicon sequencing and multiple ecological analyses. The beta diversity analysis, based on the unweighted and weighted Unifrac distances, revealed significant variations in microbial community compositions along the salinity gradient, with stronger influences on prokaryotes. Species turnover was the primary mechanism driving the beta diversity patterns, which was regulated by the local species pool. Further comparisons of multiple niche and adaptation indices indicated that seawater eukaryotic communities exhibited stronger salinity adaptability than prokaryotes. In addition, the beta deviation index suggested that heterogeneous processes shaped the microbial communities. Moreover, the neutral community model showed higher dispersal ability of eukaryotes than prokaryotes. Also, they were stochastic and deterministic dominant communities along the salinity gradient, respectively. Overall, our findings contributed significantly to understanding the microbial ecology in relation to salinity gradients.}, }
@article {pmid41661138, year = {2026}, author = {Bäcker, M and Doekes, HM and Garza, DR and Meijer, J and van Vliet, S and Allen, RJ and Hogeweg, P and Dutilh, BE and van Dijk, B}, title = {Spatial structure: Shaping the ecology and evolution of microbial communities.}, journal = {FEMS microbiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuaf067}, pmid = {41661138}, issn = {1574-6976}, abstract = {Most microbes grow in spatially structured communities, and this profoundly shapes their ecology and evolution. At the microscale, short interaction ranges and steep nutrient gradients underlie cross-feeding, quorum sensing, and niche construction, generating spatial patterns that influence microbial behavior, community assembly, and stability. Here, we review theoretical and experimental evidence for how spatial organization drives eco-evolutionary processes, including founder effects during colonization, allele surfing during range expansion, emergent patterns that facilitate multilevel selection, and the exploration of rare epistatic genotypes. While the ecological and evolutionary consequences of spatial structure at the microscale are becoming clearer, linking these processes across scales to predict community- and ecosystem-level outcomes remains a major challenge. Addressing spatial interactions explicitly in microbiome research will be key. Recent advances in computational modeling, cultivation approaches, and omics now offer unprecedented opportunities to meet this challenge, providing fresh insights into how spatial structure governs the organization and dynamics of the microbial world across scales.}, }
@article {pmid41660022, year = {2026}, author = {Shaji, A and Ramachandran, AK and Chandrasekaran, N and Savarimalai, KC and Adhira, R}, title = {A cross-sectional metagenomic analysis of the microbial ecology in symptomatic apical periodontitis - An in vivo study.}, journal = {Journal of conservative dentistry and endodontics}, volume = {29}, number = {1}, pages = {60-64}, pmid = {41660022}, issn = {2950-4708}, abstract = {BACKGROUND: Symptomatic apical periodontitis (SAP) is a painful inflammatory disease driven by root canal infection. A detailed understanding of its microbial ecology, compared to a noninfectious baseline, is needed.<br><br>AIMS: This study aimed to characterize the microbial ecology of SAP using 16S ribosomal (RNA) 16S rRNA metagenomic sequencing and compare it to control teeth undergoing root canal treatment after trauma.<br><br>MATERIALS AND METHODS: This cross-sectional study included 10 patients with SAP and 10 control patients. Pulpal samples were collected aseptically. Microbial DNA was extracted, and the full-length 16S rRNA gene was sequenced through Oxford Nanopore Technology. Analysis was performed using QIIME2.<br><br>STATISTICAL ANALYSIS USED: Microbial abundances and diversity indices were compared using an independent samples t-test or Mann-Whitney U-test (P < 0.05 significant).<br><br>RESULTS: The SAP microbiome was dysbiotic and enriched in anaerobes. Veillonella parvula was highly abundant in SAP (mean 13.1%) but absent in controls. Species like Dialister pneumosintes and Prevotella melaninogenica were found almost exclusively in SAP. Commensals including Faecalibacterium prausnitzii were significantly reduced.<br><br>CONCLUSION: SAP is associated with a distinct microbial signature defined by the enrichment of anaerobic pathobionts and a loss of commensals, revealing a polymicrobial, dysbiotic community.}, }
@article {pmid41659429, year = {2026}, author = {Vallecillo-Zuniga, ML and Akeefe, A and Brown, DG and Wahlig, TA and Marchetti, M and Heiner, T and Davis, KL and Nieznanski, C and Flynn, A and Leung, DT}, title = {Longitudinal Changes in Nasal and Oral Microbiome and Antimicrobial Resistance Gene Profiles in Response to Human Fecal Microbiota Transplantation.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.01.27.701854}, pmid = {41659429}, issn = {2692-8205}, abstract = {The gut-lung axis describes interactions between intestinal and respiratory mucosal systems through microbial, metabolic, and immune pathways, but the systemic impact of gut-targeted therapies on upper respiratory tract (URT) communities remains underexplored. We conducted a longitudinal study in adult patients undergoing fecal microbiota transplantation (FMT) for recurrent Clostridioides difficile infection (CDI) alongside healthy controls. Fecal, nasal, and oral samples were collected at baseline (Day 0) and on Days 14 and 56 following FMT. Shotgun metagenomic sequencing was performed to quantify microbial diversity, taxonomic composition, and the abundance of antimicrobial resistance genes (ARGs). FMT was associated with increased gut diversity and decreased levels of key intestinal taxa commonly considered pathobionts, including Klebsiella spp., Escherichia spp., Shigella spp., and Klebsiella pneumoniae . At the phylum level, fecal Bacteroidota increased, while Mucoromycota decreased following treatment. Post-FMT nasal microbiome changes included reduced richness and diversity, expansion of Moraxella , and decreases in taxa linked with respiratory colonization, including Staphylococcus aureus and Streptococcus pneumoniae . By Day 56, nasal communities partially recovered toward healthy profiles. Baseline nasal ARG abundance decreased following FMT, particularly among β-lactam, aminoglycoside, and fluoroquinolone resistance genes, and remained comparable to healthy controls by Day 56. In contrast, the oral microbiome and oral resistome remained largely stable, with only minor fluctuations, and no consistent increases in respiratory pathobiont-associated taxa. In summary, FMT was associated with broader effects beyond the gut, including changes in the URT microbial ecology and antimicrobial resistance profiles. Together, these findings are consistent evidence of gut-lung microbial interactions, linking intestinal dynamics with respiratory microbial composition and antimicrobial resistance patterns.}, }
@article {pmid41655393, year = {2026}, author = {Tao, S and Gao, J and He, B and Zhang, T and Chen, B and Yin, Y and Shi, J and Mao, Y and Hu, L and Jiang, G}, title = {Understanding microbial mercury methylation via metabolic pathways: Processes associated with one-carbon metabolism.}, journal = {Journal of hazardous materials}, volume = {504}, number = {}, pages = {141373}, doi = {10.1016/j.jhazmat.2026.141373}, pmid = {41655393}, issn = {1873-3336}, abstract = {Microbial mercury methylation is the key step responsible for the high toxicity and bioaccumulation potential of mercury. Since metabolic pathways serve as a bridge between mercury methylation and microbial activity, studying mercury methylation from the perspective of metabolic pathways will offer valuable insights into its underlying mechanism and integration into microbial metabolism. This review aims to summarize current understanding of the metabolic pathways that supply methyl groups for mercury methylation and to elucidate the relationships between them. The acetyl-coenzyme A pathway is extensively studied and well recognized for its role in methyl group transfer. The Wolfe cycle, representing the methanogenesis pathway in methanogenic archaea, has recently been identified as a distinct source of methyl groups contributing to mercury methylation. In addition, at the chemical level, S-adenosyl-L-methionine from the methionine biosynthesis pathway has been shown to donate a methyl group to mercury via the HgcAB complex, although this process has not yet been validated in vivo. Finally, the dimethylsulfoniopropionate degradation pathway is proposed as a speculative and potential route for mercury methylation. By integrating these pathways, we provide a comprehensive overview of their interconnections, demonstrating that microbial mercury methylation is embedded within the broader framework of one-carbon metabolism. The close association between methylation and one-carbon flux suggests that mercury methylation may function as an interspecies competition strategy that enhances microbial survival in mercury-rich environments. This pathway-centered perspective advances our understanding of the biochemical basis of microbial mercury methylation and may inform future research into its environmental controls and microbial ecology.}, }
@article {pmid41654744, year = {2026}, author = {Wünschmann, T and Ghaderiardakani, F and Homeier-Bachmann, T and Quartino, ML and Wichard, T and Busch, A}, title = {Genomic and functional characterization of Pseudosulfitobacter pseudonitzschiae BPC-C4-2: a growth-promoting symbiont in Antarctic Ulva communities.}, journal = {BMC genomics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12864-026-12626-w}, pmid = {41654744}, issn = {1471-2164}, }
@article {pmid41653958, year = {2026}, author = {Gamez, I and Fouladi, F and Gonzalez, A and Ward, J and Wang, Z and Beane Freeman, LE and Motsinger-Reif, A and Peddada, SD and Knight, R and Lee, M and London, SJ}, title = {Household Environmental Characteristics Influence House Dust Metagenome.}, journal = {Environmental research}, volume = {}, number = {}, pages = {123889}, doi = {10.1016/j.envres.2026.123889}, pmid = {41653958}, issn = {1096-0953}, abstract = {Environmental exposures can shape microbial community compositions inside homes. Metagenomic sequencing methods can further elucidate the role of household exposures like indoor moisture and the surrounding landscape. To identify household environmental exposures associated with the house dust metagenome. Microbial communities in vacuumed dust from 771 homes in the Agricultural Lung Health Study were characterized using whole metagenome shotgun sequencing (5,821 taxa across 45 phyla). Household characteristics (i.e. presence of leaks, de-humidifier, humidifier use) were assessed by questionnaires or field technicians. We evaluated associations between exposures and both overall microbial diversity and differentially abundant taxa (ANCOM-BC2). Additionally, we explored microbial networks based on Spearman correlations (SECOM). Microbial diversity was higher in homes with mold/mildew (p-value<0.05), leaks, humidifier use, or occupants removing shoes before entering (p-value<0.1). Examining individual species, <10 taxa were significantly differentially abundant (p-value<0.05 after Holm-Bonferroni correction) in relation to both mold/mildew and leaks. Greater than 10 species were significantly differentially abundant in relation to removing shoes and humidifier use. Additionally, the genera Clostridium, Prevotella, and Cryptobacteroides were positively associated with removing shoes. In this farming population, the house dust microbiome differed by moisture-related exposures, and removing shoes before entering the home. Many novel associations were identified between individual taxa and these exposures. Our findings further knowledge of the impact of environmental conditions inside the home on the indoor microbiome.}, }
@article {pmid41653300, year = {2026}, author = {Zenelt, W and Hoffmann, A and Sadowska, K and Krawczyk, K}, title = {Insects as a New Source of Plant Growth Promoting Bacteria - Review.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02692-0}, pmid = {41653300}, issn = {1432-184X}, }
@article {pmid41653280, year = {2026}, author = {Kalatehjari, P and Wolf, R and Jedlitschky, G and Tolksdorf, C and Rauch, BH and Müller, C}, title = {The great diversity: monomeric and oligomeric hirudins, hirudin-like factors and decorsins in the Asian medicinal leeches Hirudo nipponia and Hirudo tianjinensis.}, journal = {Parasitology research}, volume = {125}, number = {1}, pages = {18}, pmid = {41653280}, issn = {1432-1955}, mesh = {Animals ; *Hirudins/genetics/chemistry/metabolism ; *Leeches/genetics/classification/metabolism ; Phylogeny ; Platelet Aggregation/drug effects ; Amino Acid Sequence ; }, abstract = {Medicinal leeches express a broad variety of anticoagulants and other bioactive factors that are involved in the blood feeding process. For most of the anticoagulants, several genes exist that may encode isoforms of the respective proteins, including hirudins and decorsins. Decorsins negatively affect platelet aggregation, whereas hirudins are potent thrombin inhibitors. Both factors belong to the hirudin superfamily that also includes the group of hirudin-like factors, and all hematophagous leeches analyzed so far contain several gene copies that encode representatives of at least two of the three groups of these factors. Members of the hirudin superfamily may contain only one central globular domain, but others may contain two or more copies. Here we describe the molecular identification and partial functional characterization of a broad variety of putative mono-, bi and multimeric hirudins, decorsins and hirudin-like factors in two Asian medicinal leech species, namely Hirudo nipponia and H. tianjinensis. Some of the monomeric hirudins and decorsins have already been described before, but they represent only a small part of the overall diversity. For the first time, putative monomeric and one oligomeric decorsins of H. tianjinensis were expressed as recombinant proteins, functionally characterized and successfully verified as platelet aggregation inhibitors. In addition we have conducted phylogenetic analyses based on genomic and mitochondrial markers and found convincing evidence that H. nipponia and H. tianjinensis together with members of the genus Whitmania form a monophyletic clade that is clearly distinct from clades that are formed either by European members of the genus Hirudo or by members of the genus Hirudinaria.}, }
@article {pmid41652742, year = {2026}, author = {Van Meulebroek, L and Ghyselinck, J and Van Elst, D and Duysburgh, C and Gessner, A and Thas, O and Marzorati, M}, title = {The impact of Symprove™ multi-strain probiotic on enterotoxigenic Escherichia coli- or antibiotic-induced gut microbiome dysbiosis using high-throughput in vitro screening.}, journal = {Food research international (Ottawa, Ont.)}, volume = {227}, number = {}, pages = {118172}, doi = {10.1016/j.foodres.2025.118172}, pmid = {41652742}, issn = {1873-7145}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Probiotics/pharmacology ; *Dysbiosis/microbiology/chemically induced ; *Anti-Bacterial Agents/adverse effects ; Feces/microbiology ; *Enterotoxigenic Escherichia coli/drug effects ; Fatty Acids, Volatile/metabolism ; Adult ; Male ; High-Throughput Screening Assays ; Female ; Escherichia coli Infections/microbiology ; Fermentation ; Young Adult ; }, abstract = {The gut microbiome plays a significant role in host physiology, both in health and disease. Assessment of changes in microbial metabolites beyond short-chain fatty acids (SCFAs) following probiotic supplementation may identify additional metabolic pathways that are activated or suppressed in response to probiotics. This study assessed changes in microbial metabolites in healthy and dysbiosed microbiomes following supplementation with Symprove™, a multistrain probiotic, using the Colon-on-a-plate® miniaturized short-term batch fermentation system with a fractional factorial design. The fecal microbiome from 10 healthy human donors was evaluated under healthy and dysbiosed (enterotoxigenic Escherichia coli infection and/or low-, medium-, or high-dose antibiotics) conditions. Samples were supplemented with Symprove™ or water (control) and evaluated for microbial metabolites at 24 h and 48 h using untargeted metabolic fingerprinting, capillary gas chromatography, and targeted metabolic profiling. Favorable impacts were observed with Symprove™ supplementation across the different antibiotic doses. SCFA levels (acetate, propionate, butyrate) were significantly increased and levels of branched SCFAs were significantly decreased with Symprove™ supplementation versus control in both the healthy and dysbiosed populations. Significant increases and decreases in several other microbial metabolites were also observed with Symprove™, many of which could be considered to have beneficial effects on intestinal inflammation, intestinal barrier health, and the gut-brain axis. Symprove™ supplementation significantly affected microbial metabolism, with many of the observed changes being considered positive for human health. Importantly, these benefits were shown not only in healthy fecal microbiomes, but also in fecal microbiomes with in vitro antibiotic-induced dysbiosis, showing therapeutic potential.}, }
@article {pmid41652077, year = {2026}, author = {Jeong, YS and Jeon, BS and Park, MG}, title = {Dinopallor Comventus n. gen., n. sp., a Novel Parasitoid of Marine Dinoflagellates Representing a Sister Lineage to Seagrass Parasites and Expanding the Host Range of Phytomyxea (Rhizaria, Endomyxa).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02707-4}, pmid = {41652077}, issn = {1432-184X}, support = {RS-2025-00552993//National Research Foundation of Korea/ ; RS-2022-NR068504//National Research Foundation of Korea/ ; RS-2023-00256330//Korea Institute of Marine Science and Technology promotion/ ; }, abstract = {Phytomyxea (SAR: Rhizaria: Endomyxa) is a group of obligate biotrophic parasitic protists comprised of two orders: Plasmodiophorida, found in terrestrial or freshwater environments, and Phagomyxida, found in marine environments. While Plasmodiophorida has been extensively studied due to its economic importance as plant pathogens, Phagomyxida remains poorly investigated despite its ecological significance in marine ecosystems. During intensive sampling along the Korean coast from April to December 2023, novel parasitoids infecting dinoflagellates were discovered in seawater collected at 10 coastal stations. A total of 23 isolates were successfully established in culture, and the morphology of infected host cells resembled that of known Phagomyxa infections. The newly identified parasitoid exhibits a life cycle that includes zoospore penetration, multinucleate plasmodium development, and formation of a sporangiosorus composed of numerous zoosporangia. Each zoosporangium produces three biflagellate zoospores, and no resting spores were observed. A key morphological feature distinguishing this parasitoid from Phagomyxa species is the presence of a sporangiosorus wall enclosing the zoosporangia. Phylogenetic analysis based on small subunit (SSU) ribosomal DNA (rDNA) revealed that this parasitoid forms a distinct clade with Marinomyxa and the environmental sequence TAGIRI-5, suggesting a disparity between its morphological similarity to Phagomyxa and its molecular phylogenetic position. The SSU rRNA gene sequence of the new parasitoid showed 99.87% identity to the TAGIRI-5 sequence obtained from an anoxic sediment in Kagoshima Bay, Japan. Cross-infection experiments demonstrated that infections occurred only in five dinoflagellate genera among the taxa tested. Based on morphological and molecular data obtained in this study, we propose a new genus and species, Dinopallor comventus n. gen., n. sp., for this newly discovered parasitoid.}, }
@article {pmid41648583, year = {2026}, author = {Bald, S and Zhang, J and Nelson, R and Scott, DC and Dukovski, I and de Raad, M and Northen, TR and Segrè, D}, title = {Metabolic blueprints of monocultures enable prediction and design of synthetic microbial consortia.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.01.11.698878}, pmid = {41648583}, issn = {2692-8205}, abstract = {Synthetic microbial ecology aims at designing communities with desired properties based on mathematical models of individual organisms. It is unclear whether simplified models harbor enough detail to predict the composition of synthetic communities in metabolically complex environments. Here, we use longitudinal exometabolite data of monocultures for 15 rhizosphere bacteria to parametrize a consumer-resource model, which we use to predict pairwise co-cultures and higher order communities. The capacity to artificially "switch off" cross-feeding interactions in the model demonstrates their importance in ecosystem structure. Leave-one-out and leave-two-out experiments demonstrate that pairwise co-cultures do not necessarily capture inter-species interactions within larger communities and broadly highlight the nonlinearity of interactions. Finally, we demonstrate that our model can be used to identify new sub-communities of three strains with high likelihood of coexistence. Our results establish hybrid mechanistic and data-driven metabolic models as a promising and extendable framework for predicting and engineering microbial communities.}, }
@article {pmid41646503, year = {2025}, author = {Abjani, F and Er, YX and Lee, SC and Madhavan, P and Rhodes, A and Lim, YAL and Chong, PP and Chinna, K}, title = {Gut Microbiota of Sarawak's "Orang Ulu" Indigenous Community in East Malaysia Reveals Vanish Microbes: A Comparison With Urban Communities.}, journal = {British journal of biomedical science}, volume = {82}, number = {}, pages = {15378}, pmid = {41646503}, issn = {2474-0896}, mesh = {Humans ; Malaysia ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Adult ; Feces/microbiology ; Urban Population ; RNA, Ribosomal, 16S/genetics ; Cross-Sectional Studies ; Middle Aged ; Bacteria/genetics/classification ; Indigenous Peoples ; }, abstract = {INTRODUCTION: Urbanization often correlates with reduced diversity in human gut microbiota, with notable variations observed between the gut microbiota among the Indigenous communities in rural villages and urban citizens residing in modern settings. Although research has been conducted on the gut microbiota of healthy adults in Malaysia, there has been no study characterising the gut microbiota of Sarawak's Indigenous communities to date. This study aims to fill this gap by examining the gut microbiota profile of the Sarawak Indigenous groups (specifically Orang Ulu subethnic groups Kayan and Kenyah), comparing them with semi-urbanized Selangor Indigenous communities from Peninsular Malaysia (represented by Proto Malay subtribe Temuan) and Urban communities from Kuala Lumpur.<br><br>METHODS: We conducted a cross-sectional study and collected stool samples from 86 Indigenous participants from Sarawak and compared them with published data from 45 Malaysian Indigenous participants from Selangor and 18 Urban citizens living in Kuala Lumpur City. DNA was extracted from the stool samples, and subsequently, the V4 hypervariable region of the 16S rRNA gene was sequenced. The raw sequence data were analyzed using the Quantitative Insights into Microbial Ecology 2 (QIIME2) bioinformatics platform.<br><br>RESULTS AND DISCUSSION: Analysis revealed that the Sarawak Indigenous community exhibited the highest gut microbial diversity, followed by the Peninsular Indigenous and Urban groups. The Prevotella/Bacteroides (P/B) ratio revealed that the Sarawak Indigenous community showed the highest presence of Prevotella at 88.3%, while Kuala Lumpur Urban residents had a predominantly Bacteroides composition at 61%. The Selangor Indigenous community also exhibited a Prevotella-dominant profile at 75.5%. VANISH microbes (Prevotella, Faecalibacterium, and Succinivibrio) were identified as dominant genera in the Sarawak Indigenous gut microbiota, contrasting with the BIoSSUM microbe (Bacteroidaceae) found in the Kuala Lumpur cohort.<br><br>CONCLUSION: This study sheds light on the distinct gut microbiota composition of Sarawak's Indigenous community, which has not been previously explored. It highlights the impact of urbanization on gut microbiota composition during lifestyle transitions.}, }
@article {pmid41642996, year = {2026}, author = {Ma, W and Liu, Y and Wei, X and Zhang, X and Li, X and Liu, Z and Yuan, L and Li, G and Zhang, S and Yang, Q and Chang, X and Han, Z and Liang, H and Luan, Z and Wang, Q and Gu, Y and Wang, X and Zhao, X and Liu, Q and Sun, X and Liu, M and Feng, D and Lu, Y and Luo, S and Yang, L and Li, M and Allaby, R and Wang, K and Zhang, T and Shen, S and Van de Peer, Y and Hong, Y and Yuan, Y and Zhao, J}, title = {Gapless pangenome analyses reveal fast Brassica rapa subspeciation.}, journal = {Science (New York, N.Y.)}, volume = {391}, number = {6785}, pages = {eady7590}, doi = {10.1126/science.ady7590}, pmid = {41642996}, issn = {1095-9203}, mesh = {*Brassica rapa/genetics/classification/anatomy &amp; histology ; *Genome, Plant ; Genes, Plant ; Centromere/genetics ; Plant Leaves/anatomy &amp; histology/genetics/growth &amp; development ; Genome-Wide Association Study ; Plant Proteins/genetics ; Telomere/genetics ; Plant Breeding ; Genetic Variation ; }, abstract = {Brassica rapa (Br) encompasses many morphotypes and subspecies, so it is a good model with which to investigate plant diversification and subspeciation. Here, we resequenced the genomes of 1720 Br accessions and de novo assembled 11 representative telomere-to-telomere gapless genomes for seven elite subspecies that underwent intensive morphotypification and developed distinct agronomic traits valued to agriculture. We identified 6992 unknown genes, 110 complete (peri)centromeres, and five new satellites associated with Br morphotypes and subspecies and Brassica species evolution. The pangenome, built on 11 gapless and 20 published genomes, reveals structural variations and gene diversities among Br subspecies. Pangenome-wide association studies uncovered that the gene BrLH1 controls leaf-head formation. We show that structural changes have occurred in satellites, (peri)centromeres, and genes, contributing to fast subspeciation and morphotypification during the short history of Br cultivation, providing invaluable resources for Brassica breeding.}, }
@article {pmid41642984, year = {2026}, author = {Spohn, M and Arnillas, CA and Bakker, JD and Borer, ET and Bråthen, KA and Cadotte, MW and Carbutt, C and Catford, JA and DuPre, ME and Dwyer, C and Eisenhauer, N and Estrada, C and Hagenah, N and Haider, S and Harms, KE and Hautier, Y and Hersch-Green, EI and Knops, JMH and Laanisto, L and Laungani, R and Macek, P and Martinson, H and Millett, J and Pärtel, M and Pennings, SC and Peri, PL and Power, SA and Risch, AC and Roscher, C and Seabloom, EW and Smith, NG and Stevens, C and Virtanen, R and Wardle, GM and Zhang, P}, title = {Intense solar radiation constrains plant species richness in global grasslands.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {6}, pages = {e2527128123}, doi = {10.1073/pnas.2527128123}, pmid = {41642984}, issn = {1091-6490}, mesh = {*Biodiversity ; *Grassland ; *Plants/radiation effects/classification ; Biomass ; *Sunlight ; Poaceae/radiation effects ; Photosynthesis/radiation effects ; }, abstract = {The search for predictors of plant diversity has challenged scientists for decades. Here we identify intense photosynthetically active radiation (PAR) as a major factor constraining plant species richness in global grasslands. We show that the strength of the negative relationship between species richness and PAR increases with increasing elevation and that species richness is more strongly correlated with intense PAR than with UV-B radiation, climate variables, and atmospheric nitrogen deposition. In addition to species richness, plant biomass was also negatively correlated with PAR at higher elevations, indicating that intense PAR also constrains plant biomass in montane grasslands. Furthermore, we show that the decrease in plant species richness with increasing PAR is mainly caused by a decrease in species richness of forbs, sedges, and rushes. In contrast, species richness of grasses was only negatively correlated with PAR at high elevations, and species richness of legumes was not significantly correlated with PAR. Our results suggest that PAR constrains plant species richness in global grasslands and limits the extent to which plant species of specific functional groups can migrate uphill in response to climate warming.}, }
@article {pmid41640738, year = {2025}, author = {Zöhrer, PA and Unterberger, S and Aschauer, R and Draxler, A and Somloi, S and Kapeller, M and Bauer, T and Heinz, C and Reichstam, S and Franzke, B and Strasser, EM and Hausmann, B and Pjevac, P and Berry, D and Wessner, B and Wagner, KH}, title = {The impact of a high-protein diet with strength training on the gastrointestinal microbiota in community-dwelling older adults: subanalysis of a randomized controlled trial.}, journal = {Frontiers in nutrition}, volume = {12}, number = {}, pages = {1712451}, pmid = {41640738}, issn = {2296-861X}, abstract = {BACKGROUND: A balanced gastrointestinal (GI) microbiota is essential for healthy aging. Although high-protein diets and strength training are recommended for older adults to maintain muscle mass, their effects on GI microbiota remain unclear.<br><br>METHODS: This randomized controlled trial examined the effect of a habitual diet with recommended protein intake or high protein intake combined with strength training on the GI microbiota of 112 community-dwelling adults aged 65-85&#x202f;years. The participants were divided into three groups: no intervention control (CON), recommended protein intake plus strength training (RP&#x202f;+&#x202f;T), and high protein intake plus strength training (HP&#x202f;+&#x202f;T). Over 17&#x202f;weeks, protein intake increased significantly from 0.80 (IQR: 0.30-0.50) g/kg body weight at baseline, reaching 1.07&#x202f;&#xb1;&#x202f;0.25&#x202f;g/kg in RP&#x202f;+&#x202f;T, and 1.62&#x202f;&#xb1;&#x202f;0.37&#x202f;g/kg in HP&#x202f;+&#x202f;T groups. Stool samples collected at baseline, after dietary intervention, and after combined dietary and training intervention were analyzed using 16S rRNA gene amplicon sequencing.<br><br>RESULTS: Despite increased protein intake, microbiota richness, diversity, and composition showed no significant changes within or between groups. Residual energy and inflammatory markers indicated that higher protein intake was well tolerated.<br><br>CONCLUSION: The findings suggest that increasing protein intake via food sources up to 1.6&#x202f;g/kg body weight for more than 4&#x202f;months, with or without strength training, does not adversely affect the GI microbiota composition in older adults.}, }
@article {pmid41640304, year = {2026}, author = {Hart, DW and Ng, AS and Gazińska, P and Goldin, R and Gopal, P and O'Dell, N and Zargar, A and Pytowski, L and Montazid, S and Bardella, C and East, JE and Tomlinson, IP and Koch, N and Bennett, NC and Irshad, S}, title = {Characterisation of bacteria-induced colitis and its modulation by probiotics in naked mole rats: a new mammalian model for acute inflammatory disease.}, journal = {The Journal of pathology}, volume = {}, number = {}, pages = {}, doi = {10.1002/path.70034}, pmid = {41640304}, issn = {1096-9896}, support = {DST-NRF (GUN 64756)//Department of Science and Technology-National Research Foundation/ ; //The National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre (BRC)/ ; }, abstract = {Enteropathogenic bacteria are a major cause of morbidity and mortality globally. While mouse models have been indispensable in advancing our understanding of infectious enteric diseases, key differences in intestinal microbiota and immunobiology between mice and humans underscore the need for alternative mammalian models that better recapitulate human disease states. The naked mole rat (NMR), the longest-lived rodent and a model of healthy ageing, presents a unique opportunity. It possesses an exceptionally robust intestinal barrier, an abundance of goblet cells, a thicker mucin layer, and reduced gut permeability compared to mice. Additionally, the NMR gut microbiome exhibits compositional and functional features shared with human centenarians and traditional-lifestyle populations (e.g. Hadza hunter-gatherers), including an enrichment of health-associated taxa and metabolic pathways. Here, we leverage this model to show that systemic Citrobacter braakii infection is associated with colonic inflammation and epithelial injury that closely mimics human haemorrhagic colitis. Infected NMRs develop mucosal erosions, ulcerations, depletion of goblet cells, expansion of proliferative compartments, and active inflammation in the lamina propria. Without intervention, systemic inflammation associated with sepsis ensues and results in high mortality. Furthermore, we demonstrate the utility of this model for therapeutic testing by showing a strong effect of a probiotic cocktail comprising lactobacilli, bifidobacteria, streptococci, and enterococci. Treatment with this cocktail promoted mucosal healing, restored intestinal homeostasis, and exerted an anti-inflammatory effect. Taken together, we establish the NMR as a translatable model for investigating disease mechanisms in infectious colitis, including disruptions in mucosal barrier permeability, gut microbial ecology, and local and systemic immune regulation, as well as for testing functional probiotic strains as potential therapeutics. © 2026 The Author(s). The Journal of Pathology published by John Wiley &amp; Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.}, }
@article {pmid41637059, year = {2026}, author = {Xiong, S and Liu, Z and Xiao, N and Hua, Y and Wan, X and Zhao, J}, title = {Vallisneria Invasion into Myriophyllum Community: Differential Responses of Comammox Community in Changing Rhizosphere Environment.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxag038}, pmid = {41637059}, issn = {1365-2672}, abstract = {AIMS: Species invasion is one of the key issues in global ecosystems. This study investigated the changes in the rhizosphere community structure of complete ammonia-oxidizing bacteria (Comammox) after the invasion of the long-rooted submerged macrophyte Vallisneria spiralis L. into the community of the short-rooted submerged macrophyte Myriophyllum spicatum L.<br><br>METHODS AND RESULTS: Different planting ratios simulated varying invasion intensities. Increasing invasion intensity significantly altered rhizosphere factors, increasing invasion intensity significantly reduced dissolved organic carbon (DOC) and lowered pH, thereby causing distinct alterations in the rhizosphere environment. Comammox Clade A remained dominant with stable abundance, indicating strong adaptability. In contrast, Clade B abundance increased under low-moderate invasion but declined sharply under high intensity, suggesting a preference for mixed roots or low-intensity invasion. Higher pH and dissolved organic carbon provided a stable niche for Clade A. High invasion intensities elevated NH&#x2084;&#x207a;-N and NO&#x2083;&#x207b;-N concentrations, which coupled with stronger oxidative conditions promoted ammonia-oxidizing bacteria (AOB) and certain Clade A subgroups, thereby suppressing the low-nitrogen-adapted Clade B.<br><br>CONCLUSIONS: This study demonstrates that submerged macrophyte invasion reshapes the rhizosphere environment and drives Comammox community differentiation, offering new insights into plant invasion's ecological effects and nitrogen cycling regulation.}, }
@article {pmid41635904, year = {2025}, author = {Fan, X and Wang, X and Chao, Y and Xu, E}, title = {Probiotic and prebiotic mechanisms in IBD-associated colorectal carcinogenesis: recent advances.}, journal = {Frontiers in nutrition}, volume = {12}, number = {}, pages = {1693875}, pmid = {41635904}, issn = {2296-861X}, abstract = {Inflammatory bowel disease (IBD), a chronic relapsing inflammatory disorder of the gastrointestinal tract, significantly increases the risk of progression to colorectal cancer (CRC). Emerging studies highlight the critical roles of gut microbial dysbiosis and sustained intestinal inflammation in driving this pathological transformation. Probiotics and prebiotics, as modulators of gut microbial ecology, have attracted considerable attention as potential interventions to restore microbial balance, regulate immune responses, and mitigate carcinogenic processes. In this review, we integrate the interplay mechanisms among inflammation, microbiota, and immunity in IBD-associated colorectal carcinogenesis (IBD-CRC), with a focus on the roles of probiotics and prebiotics in microbial remodeling, enhancement of epithelial barrier integrity, inhibition of inflammatory signaling, and activation of antitumor immunity. Furthermore, we discuss preclinical and clinical evidence supporting their efficacy in delaying or preventing IBD-CRC. The review also provides perspectives on future customized synbiotic strategies in microbiota-targeted therapy and cancer prevention.}, }
@article {pmid41635399, year = {2026}, author = {Morton, SG and Vucelic-Frick, G and Dickey, JR and Rajput, BS and Spiegel, CJ and Loomis, DA and Jackrel, SL and Burkart, MD and Shurin, JB}, title = {Microplastic pollution induces algae blooms in experimental ponds but bioplastics are less harmful.}, journal = {Communications sustainability}, volume = {1}, number = {1}, pages = {16}, pmid = {41635399}, issn = {3059-4308}, abstract = {An ever-growing sea of plastic waste permeates even the most remote ecosystems; however, its ecological impact is unclear. Less persistent bioplastic alternatives are available but also have unknown environmental effects. We conducted a three-month experiment exposing plankton in experimental ponds to 10 concentrations of three different thermoplastic polyurethane microplastics, including two biodegradable bioplastics. Algal blooms with dense chlorophyll occurred consistently at high concentrations of the petroleum-derived thermoplastic polyurethane, but only occasionally with the two bioplastics. Herbivorous zooplankton density was strongly reduced by typical thermoplastic polyurethane and only weakly by bioplastics, therefore the effect on algae is at least partly due to reductions in top-down grazing pressure. Microbial communities exhibited compositional shifts in response to all three plastic types, with petroleum-derived plastic associated with the most pronounced differences across both prokaryotic and eukaryotic domains. Our results show that plastic pollution may contribute to the growing global problems of eutrophication, coastal hypoxia and harmful algae blooms, and that biodegradable plastics may have smaller environmental footprints.}, }
@article {pmid41632325, year = {2026}, author = {Lyons, R and Chan, CM and Hodal, CME and Parry, AR and Lant, P and Pratt, S and Laycock, B and Dennis, PG}, title = {The Diversity of Plastisphere Bacterial and Fungal Communities Differs between Biodegradable Polymer Types in Soil.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02677-z}, pmid = {41632325}, issn = {1432-184X}, }
@article {pmid41632308, year = {2026}, author = {Gayithri, M and Singh, S and Pradhan, B and Boorla, V and Chand, S}, title = {Multifunctional Roles of Bacillus spp. in Sustainable Agriculture: Advances in Biocontrol, Omics, and Ecological Applications.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02709-2}, pmid = {41632308}, issn = {1432-184X}, }
@article {pmid41630783, year = {2026}, author = {Sachdeva, C and Prasad, SS and Shenoy, KR and Kudva, A and Badareesh, L and Veerabhadrappa, BS and Krishna, SM and Murali, TS}, title = {A longitudinal profiling of microbiome of diabetic foot ulcers shows functional role of microbial communities in wound worsening and chronicity.}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100544}, pmid = {41630783}, issn = {2666-5174}, abstract = {Microbial communities in infected diabetic foot ulcers (DFUs) play a critical role in wound morbidity and healing outcomes. While cross-sectional studies that profile the microbial communities using culture-independent approaches are available, we conducted a longitudinal microbiome analysis of 30 diabetic individuals to elucidate the relationship between microbial composition, host factors, and wound healing trajectories. Using a 16S rRNA-based metagenomic approach, we characterized the core microbial communities associated with DFU. Alpha diversity analysis revealed significant differences between DFU microbiome from same individuals across visits, and between DFU and non-DFU cohorts, while no significant differences in beta diversity was observed. Core microbiome analysis identified Pseudomonas to be consistently present across all cohorts, higher abundance of Escherichia and Prevotella in DFU samples across visits while Acinetobacter and Morganella were predominant in non-DFU wounds. Healed DFUs were enriched in Alcaligenes and Corynebacterium while worsened DFUs showed increased abundance of Enterococcus and Serratia. In amputated individuals, Escherichia was found in high abundance, while Staphylococcus was reduced. DFU subjects with high HbA1c levels (7.3-14.9%) had higher abundance of Pseudomonas and Acinetobacter, while Prevotella and Escherichia were abundant in individuals with lower HbA1c (<7.2%). Functional predictive profiling of microbiome communities using MicrobiomeAnalyst showed significant differences between healed and worsened DFUs, especially related to genes with roles in wound healing, drug resistance, biofilm formation, tissue invasion and pathogenicity. Our findings provide insights into the microbial ecology of DFUs, while the longitudinal screening of microbes associated with DFU revealed microbial dynamics and their probable role on wound outcome.}, }
@article {pmid41628729, year = {2026}, author = {Romeiro, K and Siqueira, JF and Rôças, IN and Gominho, LF and Villela, LB and Brisson-Suárez, K and Carmo, FL}, title = {Root Canal Microbiome in Patients Undergoing Antineoplastic Therapy: a Next-Generation Sequencing Study.}, journal = {Journal of endodontics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.joen.2026.01.020}, pmid = {41628729}, issn = {1878-3554}, abstract = {INTRODUCTION: This study compared the intracanal microbiome of teeth with apical periodontitis in oncological and healthy patients using 16S rRNA gene-based next generation sequencing.<br><br>METHODS: Root canal samples were taken from 46 teeth with pulp necrosis and primary apical periodontitis (23 from oncological patients and 23 from healthy controls). DNA was extracted and sequenced using the Illumina MiSeq platform targeting the V3-V4 region of the 16S rRNA gene. Bioinformatics processing was conducted using QIIME2 and DADA2. Alpha and beta diversity analyses, genus-level abundance comparisons, and indicator species analyses were performed.<br><br>RESULTS: After quality filtering, 3,307,822 sequence reads were retained, averaging 68,912.96 reads/sample, and resulting in 3,241 unique amplicon sequence variants. Oncological patients exhibited significantly higher bacterial richness (p = 0.01), while Shannon diversity showed no significant difference between groups. Beta diversity analysis (Bray-Curtis, MDS stress = 0.14) did not reveal significant differences between groups. Indicator species analysis identified some specific taxa more associated with oncological patients, including the candidate endodontic pathogens Prevotella, Selenomonas, Alloprevotella, Rothia, and Fretibacterium.<br><br>CONCLUSIONS: The root canal microbiome of oncologic patients with apical periodontitis was broadly similar to that of healthy controls. The oncologic group showed higher species richness, but no significant differences in the overall bacterial diversity or community structure.}, }
@article {pmid41628277, year = {2026}, author = {Marrec, L and Lehtinen, S}, title = {Cluster dispersal shapes microbial diversity during community assembly.}, journal = {PLoS computational biology}, volume = {22}, number = {2}, pages = {e1013918}, doi = {10.1371/journal.pcbi.1013918}, pmid = {41628277}, issn = {1553-7358}, abstract = {Identifying the drivers of diversity remains a central challenge in microbial ecology. In microbiota, within-community diversity is often linked to host health, which makes it all the more important to understand. Since many communities assemble de novo, microbial dispersal plays a critical role in shaping community structure during the early stages of assembly. While theoretical models typically assume microbes disperse individually, this overlooks cases where microbes disperse in clusters, such as, for example, during host feeding. Here, we investigate how cluster dispersal impacts species richness, between-community dissimilarity, and species abundance in the initial steps of microbial community assembly. We developed a model in which microbes disperse from a pool into communities as clusters and then replicate locally. Using both analytical and numerical approaches, we show that cluster dispersal promotes community homogenization by increasing within-community richness and reducing dissimilarity across communities, even at low dispersal rates. Moreover, it modulates the influence of local selection on microbial community assembly and, consequently, on species abundance. Our results demonstrate that cluster dispersal has distinct effects from simply increasing the dispersal rate. This work reveals new evidence for the role of cluster dispersal in the early dynamics of microbial community assembly.}, }
@article {pmid41627727, year = {2026}, author = {Ginger, ML and Karnkowska, A and McCall, LI and Silber, AM and Michels, PAM}, title = {Why Euglenozoans.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3013}, number = {}, pages = {3-22}, pmid = {41627727}, issn = {1940-6029}, mesh = {*Euglenozoa/physiology/genetics/classification ; Animals ; }, abstract = {To accompany a new collection of methods and protocols, we discuss the relevance of the microbial eukaryotes belonging to the protist phylum Euglenozoa. For those interested by Euglena, applied biology is often relevant: as a starting point for useful natural products including biofuels, nutritional supplements, and metabolites with biomedical potential, or as an environmental agent for bioremediation. Arguably the most widely studied euglenozoans are the parasitic trypanosomatids. Collectively, trypanosomatids cause several serious neglected tropical diseases and economically important diseases of animals and plants; since the early 1900s, drug discovery and disease intervention have been prominent research areas. Yet for those interested in evolution, trypanosomatids and Euglena are host to all sorts of extreme biology either not seen or so pronounced in other eukaryotes. Euglenozoans are also relevant in an ecology context: free-living relatives of the trypanosomatids are abundant in freshwater environments. Moreover, the other major euglenozoan group, the diplonemids, are recently recognized as the most abundant heterotrophic protists in the world's oceans, their diversity and abundance at least comparable to major algal groups. Finally, the long history of euglenozoan study illustrates nicely the evolving nature of scientific discovery and reporting since Van Leeuwenhoek first saw Euglena in the pioneering days of microscopy.}, }
@article {pmid41627051, year = {2026}, author = {Shoemaker, WR and Grilli, J}, title = {The macroecological dynamics of sojourn trajectories in the human gut microbiome.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0122125}, doi = {10.1128/msystems.01221-25}, pmid = {41627051}, issn = {2379-5077}, abstract = {The human gut microbiome is a dynamic ecosystem. Host behaviors (e.g., diet) provide a regular source of environmental variation that induces fluctuations in the abundances of resident microbiota. Despite these displacements, microbial community members remain highly resilient. Population abundances tend to fluctuate around a characteristic steady-state over long timescales in healthy human hosts. These temporary excursions from steady-state abundances, known as sojourn trajectories, have the potential to inform our understanding of the fundamental dynamics of the microbiome. However, to our knowledge, the macroecology of sojourn trajectories has yet to be systematically characterized. In this study, we leverage theoretical tools from the study of random walks to characterize the duration of sojourn trajectories, their shape, and the degree that diverse community members exhibit similar qualitative and quantitative dynamics. We apply the stochastic logistic model as a theoretical lens for interpreting our empirical observations. We find that the typical timescale of a sojourn trajectory does not depend on the mean abundance of a community member (i.e., carrying capacity), although it is strongly related to its coefficient of variation (i.e., environmental noise). This work provides fundamental insight into the dynamics, timescales, and fluctuations exhibited by diverse microbial communities.IMPORTANCEMicroorganisms in the human gut often fluctuate around a characteristic abundance in healthy hosts over extended periods of time. These typical abundances can be viewed as steady states, meaning that fluctuating abundances do not continue towards extinction or dominance but rather return to a specific value over a typical timescale. Here, we empirically characterize the (i) length (i.e., number of days), (ii) relationship between length and height, and (iii) typical deviation of a sojourn trajectory. These three patterns can be explained and unified through an established minimal model of ecological dynamics, the stochastic logistic model of growth.}, }
@article {pmid41627043, year = {2026}, author = {Tan, Y and Liang, J and Yi, Q}, title = {Study on geographic differentiation and environment-host synergistic assembly mechanism of root-associated fungal communities in Paphiopedilum purpuratum.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0257325}, doi = {10.1128/spectrum.02573-25}, pmid = {41627043}, issn = {2165-0497}, abstract = {The orchid-fungus symbiosis is fundamental to orchid survival and reproduction; however, the diversity patterns and assembly mechanisms of the root-associated mycobiota in Paphiopedilum purpuratum remain inadequately characterized. We utilized high-throughput sequencing of the internal transcribed spacer 2 region to investigate the composition, diversity, sources, and assembly processes of the endophytic fungal communities across eight geographically distinct populations, with complementary profiling of rhizosphere soil fungi. Our results indicated that Ascomycota constituted the dominant phylum within the root mycobiota, while core taxonomic groups exhibited pronounced geographic differentiation at both family and genus levels. Significant inter-population disparities in α-diversity metrics reflected underlying community compositional divergence. Environmental variables, particularly longitude, exerted a stronger influence on community structure than biotic factors. Approximately 44.05% of root fungal operational taxonomic units were soil-derived, and the host plant selectively enriched fungal taxa, most of which possessed unknown trophic modes. Community assembly processes were compartment-specific: the root endophytic mycobiota was primarily governed by stochastic ecological drift, whereas the rhizosphere communities were predominantly shaped by deterministic dispersal limitation. This compartment-specific assembly was evidenced by the prevalence of stochastic processes (|βNTI| < 2) in the root endosphere, contrasting with the dominance of deterministic processes (|βNTI| > 2) in the rhizosphere. Co-occurrence network analysis revealed higher connectivity and robustness in the endophytic mycobiota. The interaction network between orchid mycorrhizal fungi and other root-associated soil fungi formed an efficient and stable functional system whose complexity showed population-specific differentiation. Collectively, our findings demonstrate clear geographic divergence in the root fungal communities of P. purpuratum and underscore a synergistic environment-host assembly mechanism, thereby providing critical ecological insights for informing conservation strategies for this endangered orchid.IMPORTANCEThis study investigates the root-associated fungal communities of the endangered orchid Paphiopedilum purpuratum across its geographical distribution. We identified clear geographical differentiation in community composition and diversity, predominantly driven by abiotic factors-particularly longitude-rather than biotic factors. A key finding reveals that 44% of root fungal taxa originate from the soil, indicating active host-mediated selection. A fundamental dichotomy in assembly mechanisms was observed: stochastic ecological drift dominated within roots, whereas deterministic dispersal limitation prevailed in the rhizosphere. Co-occurrence networks demonstrated that the root fungal community is highly connected and robust, suggesting a stable functional system. Our findings elucidate the synergistic roles of environment and host in shaping fungal assembly, providing novel insights into orchid-fungus symbiosis with theoretical implications for mycorrhizal ecology and practical relevance for conservation strategies.}, }
@article {pmid41626752, year = {2026}, author = {Demeter, K and Savio, D and Kirschner, AKT and Reischer, GH and Kolarevic, S and Parajka, J and Derx, J and Jakwerth, S and Wurzbacher, C and Blaschke, AP and Mach, RL and Blöschl, G and Farnleitner, AH and Eiler, A}, title = {Hydrological regime of a continental river system predicts bacterial macroecological patterns.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag013}, pmid = {41626752}, issn = {1751-7370}, abstract = {Modelling bacterial dynamics in large river systems is crucial for predicting continental-scale ecosystem functioning under anthropogenic pressures. Although the River Continuum and Metacommunity concepts have provided theoretical frameworks, quantitative parameters necessary for microbial macroecological models remain scarce. Here, we present results from two whole-river surveys, conducted six years apart along 2600 km of the Danube River. Using bacterial secondary production, cell counts, and 16S rRNA gene amplicon sequencing, we quantified carbon, cell, phylotype, and diversity turnover along the river. Carbon incorporation per cell declined with water travel time by 6,000 - 21,000 atoms per hour. Bacterial cells multiplied every eight days, resulting in four to six doublings during downstream transport. Growth responses at the level of individual phylotypes differed up to a hundredfold from these bulk community estimates. Bacterial diversity dynamics were dominated by phylotype turnover rather than phylotype loss. Turnover ranged 0.92 to 0.96 across the river, indicating an almost complete replacement of phylotypes with 2-11% of headwater-associated ASVs persisting under base-flow conditions. Richness declined gradually downstream at a rate of approximately 0.13 ASVs per hour. Variations in bacterial secondary production, cell abundance, and observed ASVs were best explained by models combining hydrological and water quality parameters, whereas beta diversity followed a gradual development primarily structured by water travel time. Together, these results identify water travel time as the key integrative parameter governing microbial macroecological dynamics along large rivers, with environmental conditions fine-tuning local responses. These models can help predict changes in microbial diversity and functioning under anthropogenic alterations.}, }
@article {pmid41626630, year = {2026}, author = {Lin, L and Neves, ALA and Ominski, KH and Guan, LL}, title = {Metatranscriptomics uncovers diet-driven structural, ecological, and functional adaptations in the rumen microbiome linked to feed efficiency.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycaf251}, pmid = {41626630}, issn = {2730-6151}, abstract = {The rumen microbiome plays a pivotal role in modulating feed efficiency in ruminants, yet the ecological mechanisms mediating the active interactions among microbial adaptations, dietary inputs, and host feed efficiency within the rumen remain poorly understood. To address this gap, we analyzed 120 metatranscriptomic datasets obtained from 30 purebred Angus bulls (each sampled four times) classified as high-feed-efficiency or low-feed-efficiency based on feed conversion ratio, and fed either forage-based (n = 15) or grain-based (n = 15) diets. We constructed a comprehensive active gene catalog comprising 1 744 067 non-redundant genes and compiled a reference set of 25 115 ruminant microbial genomes. Using integrated Neutral Community Model analysis and carbohydrate-active enzyme profiling, we examined how ecological processes and functional capacities differed across host phenotypes and diets. Neutral Community Model fits revealed that stochastic processes broadly governed rumen microbial community structures (R[2] = 0.779 for high-feed-efficiency; R[2] = 0.781 for low-feed-efficiency). Within the predominantly stochastic processes, however, high-feed-efficiency bulls exhibited strong positive selection for diet-responsive microbial lineages: Fibrobacter spp. (positively selected species-level genome bins: 61.3%-76.0%; negatively selected: 0%-1.3%), Butyrivibrio spp. (positively selected: 13.3%-46.0%; negatively selected: 1.0%-11.2%) under forage feeding, and UBA1067 spp. (positively selected: 33.3%-48.5%; negatively selected: 0%-8.3%) under grain feeding. These lineages encoded catalytic domains appended with carbohydrate-binding modules, such as tandem carbohydrate-binding modules linked to glycoside hydrolases, thereby enhancing substrate adhesion and degradation. In contrast, low-feed-efficiency bulls showed more random community structures and reduced functional specialization. Therefore, these suggest that cattle hosts with higher feed efficiency promote microbial populations functionally aligned with dietary inputs, a process we define as efficient host-mediated microbial amplification. These findings offer new insight into how ecological assembly and functional adaptation of the microbiome contribute to feed efficiency and lay the foundation for microbiome-informed strategies to enhance ruminant production sustainability.}, }
@article {pmid41624311, year = {2026}, author = {Marchal, C and Ballan, D and Azib, S and Innocent, M and Urien, B and Tamaro, A and Gall-Ely, ML and Coton, E and Picot, A and Mounier, J and Coroller, L and Gabriel, P}, title = {Participatory and multi-disciplinary science dataset and surveys for the assessment of the microbiological and behavioural factors influencing fresh fruits and vegetables' waste at home.}, journal = {Data in brief}, volume = {65}, number = {}, pages = {112434}, pmid = {41624311}, issn = {2352-3409}, abstract = {Fresh fruits and vegetables (FFV) represent the largest part of food waste at the consumer level. This waste directly results from FFV physiological and microbiological spoilage, itself intricately linked to behavioural factors such as consumer practices, including purchase, storage and hygiene practices, but also consumers' perceptions towards spoilage. Based on a dual approach combining microbiological and behavioural sciences, we examined the link between FFV waste produced by 49 volunteering French households, measured using connected bins, the microbial ecology of their storage compartments, using culture-dependent and -independent approaches, and their consumer behaviour, cleaning and storage practices, through in-depth interviews and a dedicated survey. An exploratory qualitative survey carried out on 17 individuals followed by two quantitative data collections on 1048 and 815 representative French consumers enabled us to identify anti-FFV waste practices and to cluster consumers according to their anti-FFV waste behaviours. Spoilage dynamics of commonly consumed FFV, according to storage temperature, microbial contamination level and the presence or absence of surface wounds, were also performed in controlled conditions. This citizen-science-based dataset covers a wide array of microbiological and behavioural factors related to domestic FFV waste, as well as real measurements of waste volumes thanks to the innovative use of connected bins. Altogether, this data could provide interesting insights into more effective and accessible guidelines for FFV waste reduction at the consumer level, and thus to a potential reduction of global food waste and its related costs.}, }
@article {pmid41624200, year = {2025}, author = {Xu, H and Liu, X and Sun, W and Dong, X and Liu, X and Xie, Y and He, J and Ali, A and Chen, M and Wu, L and Ma, J and Shao, K}, title = {Multi-omics elucidation of Lactiplantibacillus plantarum NKK20 in preventing PCOS via the gut-ovary axis: SCFAs-mediated microbiota-metabolite-immune crosstalk.}, journal = {Frontiers in nutrition}, volume = {12}, number = {}, pages = {1709581}, pmid = {41624200}, issn = {2296-861X}, abstract = {PURPOSE: Polycystic ovary syndrome (PCOS) is a clinically prevalent endocrine and metabolic disorder characterized by gut microbial disturbances and chronic low-grade inflammatory responses.<br><br>METHODS: This study explores the therapeutic potential and mechanistic insights of Lactiplantibacillus plantarum NKK20 (LP) in a PCOS murine model established through high-fat diet (HFD) and letrozole co-induction. By integrating multi-omics profiling (16S rRNA sequencing and untargeted metabolomics) with histopathological evaluation, we systematically assessed LP-mediated modulations of gut microbiota composition, metabolic signatures, ovarian function, and intestinal barrier integrity.<br><br>RESULTS: The results demonstrated that LP administration effectively counteracted metabolic dysregulation in PCOS mice, mitigating body weight gain, ameliorating lipid abnormalities (reduced total cholesterol, triglycerides, and LDL-C alongside elevated HDL-C), and lowering fasting glucose levels. Hormonally, LP suppressed hyperandrogenism, as evidenced by decreased testosterone, while rebalancing inflammatory mediators through IL-10 upregulation and concomitant reduction of TNF-&#x3b1;, IL-6, IL-1&#x3b2;, and MCP-1. Ovarian histomorphology revealed attenuated follicular cysts and enhanced luteinization. Critically, LP restored intestinal homeostasis by (i) augmenting short-chain fatty acid (SCFA) production-particularly butyrate-(ii) fortifying the gut barrier via increased ZO-1 and occludin expression, and (iii) diminishing circulating endotoxin. Microbial sequencing identified enrichment of Bacteroidetes and Muribaculum following LP treatment. Serum metabolomics further uncovered LP-induced normalization of steroid hormone biosynthesis and glycerophospholipid metabolism, coinciding with elevated anti-inflammatory mediators such as 6a-prostaglandin I1.<br><br>CONCLUSION: Collectively, these findings delineate a novel preventive axis through which LP inhibits PCOS progression&#x202f;-&#x202f;namely, via coordinated "gut microbiota-metabolite-ovarian" crosstalk involving SCFA-mediated barrier restoration, microbial ecology stabilization, and suppression of ovarian inflammatory onset. This work advances the translational rationale for probiotic-based strategies in PCOS prevention.}, }
@article {pmid41624197, year = {2025}, author = {Govaert, M and Duysburgh, C and Kesler, B and Marzorati, M}, title = {Effects of NatureKnit™ organic, a blend of organic fruit and vegetable fibers rich in naturally occurring bound polyphenols, on the metabolic activity and community composition of the human gut microbiome using the M-SHIME[®] gastrointestinal model.}, journal = {Frontiers in nutrition}, volume = {12}, number = {}, pages = {1740906}, pmid = {41624197}, issn = {2296-861X}, abstract = {OBJECTIVES: The effects of a proprietary blend of organic fruit and vegetable fibers rich in naturally occurring bound polyphenols (commercially known as NatureKnit™ Organic) on the human gut microbiome were assessed.<br><br>METHODS: Short-term (48&#x202f;h) in vitro colonic simulations using the validated Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME[&#xae;]) platform, with fecal inoculum from nine individual healthy human donors, were performed. Purified organic fibers (inulin and psyllium) were evaluated as comparators and a negative control was included. Primary measures included pH, gas pressure, short-chain fatty acid (SCFA) production, and microbial community composition.<br><br>RESULTS: All test products were well fermented with NatureKnit&#x2122; Organic showing slower fermentation kinetics than the purified fibers. SCFAs were significantly increased with all test products versus the negative control (p&#x202f;<&#x202f;0.0001 for all) and NatureKnit&#x2122; Organic reached significance versus both purified fibers (p&#x202f;<&#x202f;0.0001 for both). While relative abundances in the mucosal compartment were similar among all test conditions, luminal bacterial abundance increased with NatureKnit&#x2122; Organic and psyllium versus the negative control. The latter was mainly associated with statistically increased abundance (p&#x202f;<&#x202f;0.05) of the genera Eisenbergiella and Monoglobus, with an additional strong enrichment of Bacteroidaceae. Furthermore, bacterial species richness was significantly increased with NatureKnit&#x2122; Organic versus the negative control (p&#x202f;=&#x202f;0.0495), which was not observed for the purified organic fibers (p&#x202f;=&#x202f;0.0567 and p&#x202f;=&#x202f;0.4285 for inulin and psyllium, respectively).<br><br>CONCLUSION: Overall, the obtained results indicate that NatureKnit&#x2122; Organic may have a greater and gentler prebiotic effect compared with established purified prebiotic fibers.}, }
@article {pmid41621727, year = {2026}, author = {De Luca, D}, title = {FastqOrienter: A Python utility for the automated orientation and quality diagnostics of paired-end Illumina metabarcoding reads.}, journal = {Journal of microbiological methods}, volume = {}, number = {}, pages = {107413}, doi = {10.1016/j.mimet.2026.107413}, pmid = {41621727}, issn = {1872-8359}, abstract = {FastqOrienter is a Python tool that corrects inconsistent read orientations in Illumina paired-end metabarcoding reads using a primer-aware logic and IUPAC-compliant matching. In addition, it provides detailed diagnostics and actionable insights for discarded reads. It ensures data integrity for downstream pipelines like DADA2 and QIIME 2.}, }
@article {pmid41620541, year = {2026}, author = {Wang, Y and Han, S and Zhang, W and Shen, W and Dong, B and Wang, N}, title = {Microbial Mediators of Pine Defense Resistance: Stage-Specific Gut Symbionts Enable Acantholyda posticalis to Overcome Terpenoid Barriers.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02641-x}, pmid = {41620541}, issn = {1432-184X}, support = {SDAIT-24//Modern Agricultural Technology Industry System of Shandong province/ ; ZR2022MC198//Natural Science Foundation of Shandong Province/ ; 2023TSGC0345//Science and Technology of Small and Medium Enterprises Innovation Ability Enhancement in Shandong Province/ ; }, abstract = {Acantholyda posticalis (Matsumura) is a globally significant forest pest that inflicts substantial economic losses through its feeding activity on Pinus species. As an oligophagous insect, A. posticalis relies critically on its gut microbiota to overcome the defensive secondary metabolites of pine needles, particularly α- and β-pinene terpenoids. This study investigated the dynamic compositional changes of gut bacterial communities across different developmental stages of A. posticalis and characterized their functional roles in host adaptation. Through traditional culturing methods, two pinene-degrading bacterial strains-Klebsiella variicola and Enterobacter hormaechei-were isolated from the larval gut. In vitro assays demonstrated their significant capacity to degrade the two pinenes. High-throughput 16S rRNA sequencing revealed stage-specific bacterial enrichment patterns. Functional prediction suggested these microbial communities participate in critical metabolic processes, including phosphotransferase systems, GST activity, and detoxification pathways. This work advances understanding of insect-microbe symbiosis in oligophagous systems and proposes novel strategies for ecologically sustainable A. posticalis control through manipulation of its gut microbiota.}, }
@article {pmid41618023, year = {2026}, author = {Han, D and Hong, HW and Kim, H and Richter-Heitmann, T and Ryu, JS and Yoo, KC}, title = {Unraveling the Complex Planktonic Microbial Community in the Amundsen Sea, Southern Ocean.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02696-4}, pmid = {41618023}, issn = {1432-184X}, support = {NRF- 2022R1F1A1065719//National Research Foundation of Korea/ ; 2025-RISE-10-004//the Ministry of Education (MOE) and the Gangwon State (G.S.)/ ; KOPRI PE24090//Ministry of Oceans and Fisheries/ ; }, abstract = {Spatial differences in microbial community structure and function were examined across polynyas, sea ice zones (SIZ), and ice-free waters of the Amundsen Sea, Southern Ocean, using 16 S and 18 S rRNA gene-based eDNA metabarcoding and quantitative PCR targeting nitrogen cycling and dimethylsulfoniopropionate (DMSP) degradation genes. The SIZ exhibited enrichment of psychrophilic bacteria (Colwellia spp.) and dominant eukaryotic taxa such as Diatomea and Prymnesiophyceae, likely linked to sea-ice-driven shifts in nutrient stoichiometry (elevated N: P and positive N*). Network analysis revealed interactions among primary producers, bacteria, and zooplankton, highlighting complementary roles in trophic energy transfer and nutrient recycling. Metabolic pathway predictions implied active bacterial processes related to sulfur and nitrogen cycling in the SIZ, particularly dissimilatory nitrate reduction and DMSP demethylation, suggesting coupling between carbon, nitrogen, and sulfur pathways. Quantitative PCR showed higher copy numbers of nitrogen cycling genes and DMSP degradation genes in the SIZ than in other regions, consistent with enhanced microbial denitrification, nitrogen fixation, and sulfur cycling under cold conditions shaped by sea-ice-driven nutrient dynamics. These findings demonstrate that environmental variation in Antarctic waters influences microbial diversity, reshapes ecological interactions, and modulates biogeochemical functions, with implications for nutrient cycling, food web dynamics, and ecosystem resilience in this climate-sensitive region.}, }
@article {pmid41617658, year = {2026}, author = {Yan, Z and Liu, R and Zhang, ZA and Dai, T and Zhu, D and Zhang, Y}, title = {Intestinal Microplastic Retention Reshapes Gut Microbial Ecology through Surface-Associated Colonization and Additive Leaching.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c16988}, pmid = {41617658}, issn = {1520-5851}, abstract = {Microplastics (MPs) have attracted increasing attention due to their potential impacts on the human gut microbiota, yet the mechanisms governing MP-microbiota interactions remain insufficiently resolved. Here, we employed the Simulator of the Human Intestinal Microbial Ecosystem, a dynamic host-free in vitro model, to investigate how intestinally retained poly(ethylene terephthalate) MPs influence gut microbial communities. We show that MP retention is associated with two separable processes: surface-mediated spatial redistribution of microbes and additive-associated perturbations. Compared with additive-eluted MPs and inert SiO2 particles, MPs exhibited greater surface roughness and hydrophobicity, promoting selective colonization by hydrophobic, potentially pathogenic, and organic-degrading taxa. This surface-associated colonization coincided with the displacement of luminal keystone taxa and pronounced restructuring of microbial co-occurrence networks, reflected by reduced negative cohesion and altered community stability. In parallel, leachable MP-associated additives independently shifted microbial composition and predicted functional potential, including enrichment of pathways related to xenobiotic degradation. This work provides mechanistic insight into how retained MPs may condition gut microbial ecosystems and underscores the importance of considering MP-associated microbial perturbations in gut-relevant exposure assessments.}, }
@article {pmid41615200, year = {2026}, author = {Yang, J and Qin, X and Zhang, D and Dong, C}, title = {Microbial landscape: composition and health associations of environmental microbiome in key functional spaces of premium elderly care facilities.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0183725}, doi = {10.1128/spectrum.01837-25}, pmid = {41615200}, issn = {2165-0497}, abstract = {The environmental microbiome in elderly care facilities plays a crucial role in the health of aging populations with immunosenescence; however, its composition and health associations remain underexplored. This study characterizes the microbial ecology of premium elderly care facilities, focusing on key functional spaces, environmental drivers, and implications for resident health. We conducted 16S rRNA gene sequencing (V3-V4 regions) on 320 surface and air samples from six functional spaces (dining areas, medical facilities, bedrooms, bathrooms, recreational rooms, and corridors) across four premium elderly care facilities. Environmental parameters (temperature, humidity, CO2, and occupancy) were measured concurrently. Bioinformatics analysis (QIIME 2, DADA2, and Silva database) and statistical modeling (permutational multivariate analysis of variance, distance-based redundancy analysis, and PICRUSt2) were employed to assess microbial diversity, taxonomic composition, functional potential, and environmental correlations. Using 16S rRNA gene sequencing across four facilities in different geographic regions, we identified significant spatial heterogeneity in microbial diversity and composition, with dining areas and recreational rooms exhibiting higher richness (Shannon index: 6.07 ± 0.37) and human-associated taxa (e.g., Firmicutes), while medical facilities and bathrooms harbored lower diversity but elevated opportunistic pathogens (Pseudomonas and Klebsiella). Environmental parameters-particularly relative humidity (explaining 13.8% of community variation) and occupancy-strongly influenced the microbial structure. A core microbiome dominated by Proteobacteria, Firmicutes, and Actinobacteria was conserved across facilities, while functional predictions revealed space-specific traits, including predicted enrichment of antibiotic resistance genes in medical facilities (ARG Shannon diversity: 4.87 ± 0.42) and carbohydrate metabolism pathways in dining areas. Negative correlations between beneficial (Lactobacillus) and pathogenic taxa (Staphylococcus aureus) were consistent with potential ecological strategies for microbial balance, although validation with absolute quantification is needed. This study highlights the need for space-specific microbial management in elderly care environments, emphasizing humidity control, ventilation, and targeted hygiene to mitigate pathogen risks while preserving beneficial communities. Our findings suggest the potential value of ecologically informed stewardship over pathogen-centric approaches. Future research should integrate multi-omics and longitudinal health data to optimize microbiome-resident health interactions.IMPORTANCEAs people age, their immune systems weaken, making the elderly especially vulnerable to germs in their surroundings. This study reveals that the types and amounts of bacteria living on surfaces and in the air within premium elderly care facilities differ significantly depending on the room's purpose-such as dining areas, medical rooms, or bathrooms. We found that humidity and how many people use a space strongly influence these bacterial communities. Crucially, areas like medical rooms had more bacteria linked to infections and antibiotic resistance, while social spaces hosted more diverse and potentially beneficial bacteria. This shows that a "one-size-fits-all" cleaning approach is not ideal. Instead, tailoring hygiene practices and environmental controls (like managing humidity) to specific spaces could better protect residents' health by reducing harmful germs while supporting helpful ones, offering a smarter way to manage these critical living environments for our aging population.}, }
@article {pmid41615027, year = {2026}, author = {Jiménez, DJ and Marasco, R and Schultz, J and Rodríguez, CAD and Nogales, J and Rodriguez-R, LM and Overmann, J and Rosado, AS}, title = {Discovery and cultivation of prokaryotic taxa in the age of metagenomics and artificial intelligence.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag012}, pmid = {41615027}, issn = {1751-7370}, abstract = {Despite advances in sequencing, microbial genomics, and cultivation techniques, the vast majority of prokaryotic species remain uncultured, which is a persistent bottleneck in microbiology and microbial ecology. This perspective outlines a conceptual framework to improve the transition from genome-resolved metagenomics to the targeted isolation of yet-uncultured prokaryotic taxa. The proposed framework integrates the induced reshaping of microbiomes, genome-based inferences of physiological and phenotypic traits, culture media design, and targeted culturomics, enabling hypothesis-driven cultivation. In addition, this manuscript addresses the critical limitations in the field, including the sequence-to-function gap, and emphasizes the synergistic potential of experimental microbiology, microbial ecology, metagenomics, and artificial intelligence (AI)-based predictions to enhance rational and actionable roadmaps for discovering and cultivating novel prokaryotic lineages.}, }
@article {pmid41614284, year = {2026}, author = {Karmakar, R and Paul, P and Malik, M and Maity, A and Mishra, MC and Tribedi, P and Ghosh, MM}, title = {In Silico and In Vitro Investigations of Novel Strategies to Combat Drug-Resistant Comamonas aquatica.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {134}, number = {2}, pages = {e70152}, doi = {10.1111/apm.70152}, pmid = {41614284}, issn = {1600-0463}, support = {BT/INF/22/SP41296/2020//Department of Biotechnology, Ministry of Science and Technology, India/ ; IMSXC2022-23/010//St. Xavier's College (Autonomous) Kolkata/ ; }, mesh = {*Biofilms/drug effects ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; *Tetracycline/pharmacology ; Computer Simulation ; *Benzaldehydes/pharmacology ; Humans ; *Drug Resistance, Bacterial ; Reactive Oxygen Species/metabolism ; }, abstract = {Comamonas aquatica, an emerging nosocomial pathogen, poses significant clinical challenges through biofilm-mediated antimicrobial resistance. This study investigated the efficacy of cuminaldehyde combined with tetracycline against C. aquatica biofilms using an integrated approach. In silico predictions (PASS online, SwissADME, PROTOX 3.0, OSIRIS) indicated that cuminaldehyde exhibited favorable oral bioavailability with acceptable toxicity profiles, while tetracycline showed limited oral absorption due to molecular size and polarity constraints. Experimentally, individual minimum inhibitory concentrations (MICs) were determined as 300 μg/mL for cuminaldehyde and 0.2 μg/mL for tetracycline. The fractional inhibitory concentration index (FICI) of 0.66 demonstrated additive interactions between the compounds (cuminaldehyde and tetracycline). The result indicated that the combinatorial application of compounds exhibited enhanced antimicrobial potential against the test organism. Furthermore, co-application of cuminaldehyde and tetracycline was found to show increased antibiofilm potential against the same organism. The result showed that the biofilm inhibition under the influence of the combinatorial application could be attributed to the enhancement of bacterial cell membrane permeability and accumulation of intracellular reactive oxygen species. In a nutshell, the findings of this study highlight a promising strategy of using combinatorial therapy involving cuminaldehyde-tetracycline for dealing with biofilm-associated infections caused by C. aquatica.}, }
@article {pmid41614084, year = {2026}, author = {Kwarteng, SA and Mensah, JO and Obuam, PK and Odenteh, EA and Foriwaah, PD and Mbelede, AI and Dziwornu, E and Duker, EO and Boakye, JD and Agbotse, GD and Yanney, JN and Aba Aude Koffi, MC and DeWitt, ME and Addo, SO}, title = {Occurrence of Tick-Borne Pathogens in Rhipicephalus sanguineus Sensu Lato From Domestic Dogs in Kumasi, Ghana.}, journal = {Veterinary medicine international}, volume = {2026}, number = {}, pages = {8881048}, pmid = {41614084}, issn = {2090-8113}, abstract = {Tick-borne pathogens, transmitted by ticks, infect humans and animals worldwide. The brown dog tick, Rhipicephalus sanguineus sensu lato, is a significant vector of a number of pathogens, including Ehrlichia canis, Rickettsia and Anaplasma species. In Ghana, there is limited information on the pathogens carried by Rh. sanguineus s.l. As such, Rh. sanguineus ticks taken from domestic dogs in Kumasi were screened for tick-borne pathogens, including Coxiella burnetii, Rickettsia, Babesia, Theileria, Anaplasma, Ehrlichia and Hepatozoon species. A total of 204 ticks collected from 56 infested dogs were morphologically identified as Rh. sanguineus s.l. From the 88 pools screened, 36 (40.9%) were positive for pathogen DNA. The pathogens identified were Rickettsia africae (5 pools), Ehrlichia canis (10 pools) and uncultured Anaplasma sp. (21 pools) with maximum likelihood estimates as 2.48% (95% CI: 0.93, 5.38%), 5.22% (95% CI: 2.69, 9.15%) and 11.20% (95% CI: 7.32, 16.29%), respectively. There was no association between the detection of a pathogen and the tick sex or dog breed, age or sex. This study provides important baseline data on the circulation of tick-borne pathogens in Rh. sanguineus s.l. ticks in Kumasi, with implications for both veterinary and human health. The presence of uncultured Anaplasma sp. suggests a wider diversity of tick-borne bacteria with unknown pathogenicity. There is a need for integrated tick control, improved diagnosis and additional epidemiological studies to mitigate the impact of tick-borne diseases in Ghana.}, }
@article {pmid41613253, year = {2026}, author = {Samimi, A and Verdon, N and Allen, RJ and Rosenbaum, MA}, title = {Probing Antibiotic Inhibition in Small Bacterial Populations With Combinatorial Droplet Microfluidics.}, journal = {Small science}, volume = {6}, number = {1}, pages = {e202500421}, pmid = {41613253}, issn = {2688-4046}, abstract = {Bacterial infections often involve small, local populations of bacteria, yet antibiotic treatment decisions are generally based on bulk population susceptibility assays. Stochastic variability among local small populations can influence susceptibility, limiting the predictive capability of bulk assays. Therefore there is a need to better understand antibiotic response in small populations. Droplet-based microfluidics enables the high-throughput production of tens of thousands of picolitre droplets, in which small populations of bacteria (e.g., 8 cells) can be encapsulated and their responses to different environmental conditions tracked. Here, we use a combinatorial droplet-generation platform, combined with microscopy and image analysis, to interrogate the responses of small populations of Escherichia coli to different bulk-determined sub-inhibitory concentrations of the antibiotics tetracycline, streptomycin, and ampicillin within a single experiment. We observe qualitatively distinct small-population responses for these antibiotics. For the bacteriostatic ribosome-targeting antibiotic tetracycline, growth varies nonmonotonically at low antibiotic concentrations. For the bactericidal ribosome-targeting antibiotic streptomycin, we observe apparent bistability, some replicate populations growing while others die. For the bactericidal cell-wall targeting antibiotic ampicillin, we observe stochastic bacterial filamentation. Our study shows how distinct phenomena impacting antibiotic susceptibility may emerge in small bacterial populations, laying a foundation for deeper studies into potential treatment implications.}, }
@article {pmid41612472, year = {2026}, author = {Wang, Y and Shen, Y and Shen, J and Bi, J and Xu, J and Wei, T and Wang, R and Wu, X and Li, F and Bai, J and Jie, Z and Hou, D and Song, Y}, title = {Airway microbiome dysbiosis in severe pneumonia: metagenomic evidence of pathogen expansion and commensal depletion.}, journal = {European journal of medical research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40001-026-03892-1}, pmid = {41612472}, issn = {2047-783X}, support = {ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; GWVI-11.1-18//Shanghai Three-year Action Plan to Strengthen the Construction of Public Health System/ ; 82130001//National Natural Science Foundation of China/ ; 2024YFC3044400//National Key Research and Development Program of China/ ; GZNL2024A02003//R&amp;D Program of Guangzhou National Laboratory/ ; W2020-013//The Construction of Multi-Disciplinary Treatment System for Severe Pneumonia/ ; 22Y11900800//Science and Technology Commission of Shanghai Municipality/ ; shslczdzk02201//Shanghai Municipal Key Clinical Specialty/ ; }, abstract = {BACKGROUND: The pulmonary microbiome is increasingly recognized as a key determinant of pneumonia severity, yet its clinical implications remain incompletely understood. Disruption of microbial ecology, or dysbiosis, may impair host immune responses and exacerbate disease progression. This study aimed to characterize microbiome alterations associated with severe pneumonia and their correlation with host inflammatory and coagulative parameters.<br><br>METHODS: In this multicenter, prospective observational cohort study conducted across nine hospitals in Shanghai (2021-2025), bronchoalveolar lavage fluid (BALF) samples from 306 patients with clinically diagnosed pulmonary infections were analyzed using metagenomic next-generation sequencing (mNGS). Patients were stratified into severe (n&#x2009;=&#x2009;196) and non-severe (n&#x2009;=&#x2009;110) groups using WHO-derived severe pneumonia criteria at the time of bronchoalveolar lavage (BAL). Microbial taxonomic profiles, diversity indices, co-occurrence networks, and correlations with clinical markers were comprehensively assessed using standard bioinformatic and statistical approaches.<br><br>RESULTS: Severe pneumonia was associated with marked microbial dysbiosis, including reorganization of co-occurrence network topology with centrality shifting away from commensals toward opportunistic taxa in severe disease, characterized by reduced &#x3b1;-diversity, altered &#x3b2;-diversity, and enrichment of opportunistic Gram-negative pathogens including Acinetobacter and Klebsiella. In contrast, commensals such as Rothia and Prevotella were depleted. Co-occurrence network analysis revealed fragmentation of microbial interactions in severe cases, with centrality shifting from commensals to opportunists like Corynebacterium striatum. Shannon diversity negatively correlated with SOFA scores, and specific taxa positively associated with systemic inflammation (CRP, PCT) and coagulation abnormalities. Nearly all samples demonstrated polymicrobial infection, with distinct microbial patterns observed across monomicrobial and polymicrobial subgroups.<br><br>CONCLUSION: Our multicenter observational analysis suggests that severe pneumonia is associated with marked ecological disruption of the lower-airway microbiome, characterized by commensal loss, opportunist expansion, and fragmented interspecies networks, and with concurrent inflammatory and coagulative abnormalities. These hypothesis-generating findings warrant external validation in independent, multi-region cohorts and longitudinal sampling to test directionality and causality before informing clinical decision-making.}, }
@article {pmid41612032, year = {2026}, author = {Li, Q and Shen, J and Feng, J and Liu, Y and Huang, Z and Wang, X}, title = {Patterns of ARGs and VFs Driven by Short-Term Seasonal Hydro-Environmental Stress Interactions in a Eutrophic Plateau Lake.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02703-8}, pmid = {41612032}, issn = {1432-184X}, support = {No. 202303AC100016//the Key Research and Development Program of Yunnan/ ; Project No. 202301AT070001//the Yunnan Fundamental Research Projects/ ; No. 2024YFD1700100//the National Key Research and Development Program of China/ ; }, abstract = {With the intensification of human activities, large amounts of antibiotics, heavy metals, and disinfectants enter lakes, exerting continuous selective pressure and driving the enrichment and dissemination of ARGs and VFs in aquatic microbial communities. Previous studies have primarily focused on the occurrence and abundance of ARGs in extreme plateau environments. However, the diversity and abundance of ARGs and VFs in eutrophic plateau lakes under different seasons and environmental pressures remain underexplored. In this study, we analyzed the presence of ARGs and VFs in the eutrophic plateau lake Qilu Lake across different seasons. From the perspective of hydrology and water quality, there is no inflow into the lake during the dry season, while the wet season sees an inflow of 28.1724 million cubic meters. Organic matter and metal ions are significantly higher in the dry season, whereas total nitrogen and pH levels rise notably in the wet season. We found 29 types of ARGs and 601 types of VFs in the dry season, compared to 45 types of ARGs and 637 types of VFs in the wet season. In both seasons, glycopeptide antibiotic resistance genes were the most abundant ARGs. LPS was the most abundant VFs in the dry season, while Type IV pili dominated in the wet season. The primary microbial-driven resistance mechanism strategy in both seasons was Antibiotic target alteration. The microorganism with the highest abundance of ARGs and VFs in both seasons was Pseudomonadota. Correlation analysis showed a positive relationship between the abundance of ARGs and VFs in both seasons, with this relationship being more pronounced in the dry season. Our findings indicate that the increased diversity and abundance of ARGs during the wet season may be directly linked to the heightened input of exogenous antibiotic-resistant bacteria and the promotion of plasmid conjugation transfer by hydraulic disturbances. Although VFs diversity was higher in the wet season, the low-water concentration effect and metal ion stress during the dry season significantly elevated the relative abundance of core VFs (e.g., type IV pili), resulting in the abundance of VFs per unit volume surpassing that of the wet season.}, }
@article {pmid41611907, year = {2026}, author = {Capri, FC and Prazzi, E and Casamento, G and Alduina, R}, title = {Influence of Nest Microbiota on Hatching Success of Caretta Caretta on Lampedusa Island.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02699-1}, pmid = {41611907}, issn = {1432-184X}, abstract = {Egg hatching success in sea turtle nests can be influenced by multiple abiotic and biotic factors. Although interest in nest microbiota as a determinant of embryo development and viability is increasing, its role has not yet been fully elucidated. In this study, we profiled the bacterial communities of four Caretta caretta nests on Lampedusa Island: Cala Pisana (P1 and P2) and Spiaggia dei Conigli (C1 and C2), which showed different hatching success rates (P1 = 85.2%, P2 = 1.1%, C1 = 1.1%, C2 = 0.0%). Using 16S rRNA gene (V3-V4) sequencing, we analyzed different sample types, including sand from inside and outside the nest chamber, eggshells, and inner membranes. Alpha diversity was highest in sand and lower in eggshells and inner membranes. β-diversity clearly separated the only successful nest (P1) from the others (P2, C1, and C2) (PERMANOVA p < 0.001). Across all nests, the dominant phyla were Proteobacteria, Firmicutes, Actinobacteriota, and Bacteroidota; notably, the Firmicutes/Bacteroidota (F/B) ratio was lowest in P1 compared with P2, C1, and C2. Nests with low hatching success were Firmicutes-dominated, enriched in Bacillus and Pseudomonas, and harbored hydrocarbon-degrading genera (Pseudoxanthomonas and Devosia), suggesting environmental influences. Opportunistic pathogens (Ochrobactrum and Simkaniaceae), likely associated with vertical transmission, were detected exclusively in C1 and C2 nests. Overall, our findings highlight the potentially critical role of nest microbiota in reproductive success. Both vertical (maternal) and horizontal (environmental and anthropogenic) transmission appear to shape microbial composition, potentially affecting hatchling viability and offering useful insights for conservation monitoring.}, }
@article {pmid41611865, year = {2026}, author = {Ulloa, MA and Serrano, AV and Camelo, LC and Guyot, R and Vela, D and Muñoz, AR}, title = {Bacterial genome reconstruction and community profiling in Neotropical Drosophila.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-36282-y}, pmid = {41611865}, issn = {2045-2322}, abstract = {Drosophila species serve as key models for microbiota research due to their relatively simple microbial communities. However, microbial diversity and dynamics in Neotropical Andean Drosophila remain underexplored. Here we applied shotgun metagenomics to characterize the microbiota of 24 Neotropical Drosophila species from Ecuador, reconstructing 64 high-quality bacterial genomes predominantly from Acetobacteraceae and Enterobacterales. Microbial communities were consistently dominated by yeasts, lactic acid bacteria, acetic acid bacteria, and Wolbachia. Comparative analyses revealed no strong correlation between host phylogeny and microbial community composition, suggesting environmental factors and microbial interactions shape these communities. Notably, shifts in relative abundances indicate dynamic ecological succession and metabolic cooperation among microbes. These findings expand genomic resources for Drosophila-associated bacteria and highlight the complex ecological processes influencing host-microbiota relationships in natural populations.}, }
@article {pmid41611114, year = {2026}, author = {Young, RB and Correia, GDS and MacIntyre, DA}, title = {Host, microbial and environmental drivers of vaginal microbiota composition.}, journal = {Fertility and sterility}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.fertnstert.2026.01.020}, pmid = {41611114}, issn = {1556-5653}, abstract = {The human vagina harbours a microbial community that differs markedly in compositional structure from all mammals, including closely related primates. Lactobacilli are the most abundant vaginal species, and their dominance in this niche are associated with protection against adverse health outcomes including preterm birth, sexually transmitted infections and bacterial vaginosis. However, the vaginal environment can also support compositions of diverse anaerobic bacteria, which have been linked to poor reproductive health outcomes. Here, we review current knowledge on host and microbial determinants that influence microbial community structure within the vaginal niche, emphasising the interplay between host physiology, immune and metabolic interactions as well as lifestyle factors. This integrated understanding provides a foundation for linking vaginal microbiome compositions to clinically relevant phenotypes and highlights mechanisms that could be exploited to promote improved reproductive health.}, }
@article {pmid41610262, year = {2026}, author = {Wrightson, I and Man, M and Castañeda-Gómez, L and Srikanthan, N and Tong, H and Knorr, MA and Frey, SD and Nadelhoffer, KJ and Lajtha, K and Simpson, MJ}, title = {Three Decades of Litter Manipulation Distinctly Shifts Soil Organic Matter Composition and Constrains Soil Carbon Sequestration in Temperate Forest Soils.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c11996}, pmid = {41610262}, issn = {1520-5851}, abstract = {The capacity of forest soils to sequester carbon (C) is susceptible to shifts in the litter quantity and chemistry. Using measurements from the third decade of a long-term Detrital Input and Removal Treatment (DIRT) experiment at Harvard Forest (MA, USA), extending previously published work from 20 years, we examined how litter inputs shape soil organic matter (SOM) chemistry. Elemental analysis, targeted compound analysis, solid-state [13]C nuclear magnetic resonance (NMR) spectroscopy, and microbial biomass and community composition measurements were used. Despite doubled litter inputs over 30 years, no net soil C accumulation occurred, and the SOM decomposition stage was similar to the control, suggesting continuous microbial processing of added inputs. The exclusion of litter, roots, or both led to lower soil C and more advanced SOM decomposition in mineral soils. Shifts in microbial community composition, particularly an increase in Gram (+) to Gram (-) bacteria under exclusion treatments, point to microbial reorganization in response to altered substrate availability. This long-term study underscores the limited potential for long-term soil C sequestration due to sustained microbial decomposition and the role of continuous plant inputs in shaping SOM chemisty under changing detrital regimes in a temperate forest.}, }
@article {pmid41610138, year = {2026}, author = {Dubey, S and Shukla, S and Gupta, N and Dixit, R and Bhadury, P and Kumar, A}, title = {Effect of perchlorate on biocementation capable bacteria and Martian bricks.}, journal = {PloS one}, volume = {21}, number = {1}, pages = {e0340252}, pmid = {41610138}, issn = {1932-6203}, mesh = {*Perchlorates/pharmacology ; *Mars ; *Bacteria/drug effects/metabolism/genetics ; Calcium Carbonate/chemistry ; *Construction Materials/microbiology ; Urease/metabolism ; }, abstract = {With the recent discovery of perchlorate (0.5-1%) in Martian regolith, more experiments related to the impact of perchlorate on microbial life are crucial to understanding the possibility of earth life forms that could sustain on the Martian terrain. While we are familiar with the idea of bioconsolidated Martian bricks made via Microbially Induced Calcite Precipitation (MICP), studies on the effect of perchlorate on Martian bricks &amp; biocementation capable microbes have been obscure. In this work, we investigated the effect of perchlorate (MgClO4- salt) on a lab-isolated biocementation capable bacteria &amp; Martian bricks bioconsolidated by the same, with 1% perchlorate in Mars Global Simulant-1 (MGS-1). The screening of biocementation-capable bacteria involved phenol red assay for urease activity followed by Scanning Electron Microscopy (SEM) and X-ray diffraction (XRD) study of the precipitate formed through MICP via ureolytic pathway. The biocementation capable bacterium SI_IISc_isolate was found to be phylogenetically closest to Sporosarcina pasteurii strain S2135 with a draft genome size of 3.69 Mb. To understand the effect of perchlorate on SI_IISc_isolate, we majorly relied on Gram-staining &amp; SEM. The negative effect of perchlorate stress on the isolate was evident by its decreased growth in the presence of varying concentrations of perchlorate through plate assays, growth curve studies in broth &amp; live-dead staining. Gram-staining study and SEM both revealed that perchlorate induces the release of extracellular matrix (ECM) and promotes clustering of cells by the bacteria, which we termed as 'multicellularity-like behavior.' Further, we constructed Martian bricks with Martian Global Simulant (MGS-1) along with 1% perchlorate, utilizing the microbially induced calcite precipitation ability of the Sporosarcina sp. strain SI_IISc_isolate via ureolysis, following an established protocol at our lab. The bioconsolidation experiments showed that in the presence of a natural adhesive - guar gum, perchlorate tends to significantly improve the compressive strength of Martian bricks. However, the end result eventually relies on the overall effect of various additives in the regolith.}, }
@article {pmid41609879, year = {2026}, author = {Sánchez Espinosa, KC and Fernández-González, M and Dias-Lorenzo, DA and Rodríguez-Rajo, FJ}, title = {First Report of Alternaria in the Olive Agroecosystem of NW Spain: Aerobiological Characterization and Relationship with Meteorological Factors.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02700-x}, pmid = {41609879}, issn = {1432-184X}, abstract = {Alternaria spp. is one of the fungal genera affecting olive cultivation, and its temporal dynamics are influenced by climatic variations occurring throughout the crop's vegetative cycle. The aim of this study was to determine the presence of Alternaria spp. in an olive-growing area in northwestern Spain and to examine the relationship between its airborne concentrations and meteorological variables, in order to preliminarily predict its presence in the atmosphere during the olive tree's phenological cycle. To achieve this, a phenological, aeromycological, and meteorological study was conducted from 2021 to 2024. Alternaria spp. conidia were detected in the air throughout all major phenological stages, with peak concentrations occurring mainly during fruit development. The highest percentages of spores were recorded between 11:00 and 22:00, primarily influenced by temperature and sunlight. During the maturity of fruit stages in 2023 and 2024, isolates from the Alternaria section Alternaria were identified as the cause of olive rot. A predictive model was obtained that estimates the atmospheric concentrations of this type of fungus in the study area, based on average temperature values and hours of sunshine. This study constitutes the first report of Alternaria spp. in an olive-growing area of northwestern Spain and provides models that preliminarily predict its presence. These models can inform growers of the pathogen's presence in the air before visible symptoms appear, thereby reducing the likelihood of infection in susceptible plants when environmental conditions favor its development.}, }
@article {pmid41608689, year = {2025}, author = {Yan, W and Du, N and Zhang, K and Yang, P and Guo, J and Xu, L}, title = {Bilirubin-microbiota interaction: molecular mechanisms and therapeutic strategies in neonatal jaundice.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1749152}, pmid = {41608689}, issn = {1664-302X}, abstract = {Recent studies have revealed a complex interplay between bilirubin metabolism and the gut microbiota. Bilirubin functions as a potent antioxidant and signaling molecule in humans, and its concentration-dependent effects on distinct microbial taxa indicate that the compound exerts selective pressure on the gut ecosystem. The gut microbiota modulates bilirubin metabolism by altering intestinal pH, producing and activating Bilirubin metabolic enzyme, and bile acids. Because perturbations in bilirubin handling are especially common-and potentially neurotoxic-in neonates, a concise synthesis of recent progress is warranted. Here we review how microbial communities reshape bilirubin flux, how bilirubin and its conjugates, in turn, sculpt microbial ecology, and how the dynamic equilibrium between conjugated and unconjugated bilirubin in hyperbilirubinaemia is influenced by the microbiome. Regulating gut microbiota to accelerate bilirubin clearance or attenuate its toxicity may therefore offer a tractable therapeutic avenue.}, }
@article {pmid41607130, year = {2026}, author = {Stewart, JD and Ramirez, DX and Leon-Reyes, A and Barriga, N and Llerena, S and Manley, BF and Carpintero-Salvador, N and Ruiz-Uriguen, M and Raaijmakers, JM and Kiers, ET and Weedon, JT}, title = {Land Use Change Reshapes Climate-Driven Diversity Patterns of Tropical Arbuscular Mycorrhizal Fungi.}, journal = {Molecular ecology}, volume = {35}, number = {2}, pages = {e70253}, doi = {10.1111/mec.70253}, pmid = {41607130}, issn = {1365-294X}, support = {MICROP 024.004.014//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; //Jeremy and Hannelore Grantham Environmental Trust/ ; //Paul G. Allen Family Foundation/ ; //Schmidt Family Foundation/ ; }, mesh = {*Mycorrhizae/genetics/classification ; *Biodiversity ; *Soil Microbiology ; Agriculture ; Tropical Climate ; Temperature ; Ecosystem ; Soil ; Climate ; *Climate Change ; }, abstract = {Land use change and agricultural expansion threaten biodiversity yet the effects on soil life remain poorly understood, especially for microbes. Arbuscular mycorrhizal (AM) fungi are microbes that form associations with most plant species and are essential for plant nutrient uptake. The diversity of these fungi is also sensitive to both land use change and regional climatic conditions. We therefore asked whether variation in AM fungal diversity is driven by land use change, and whether these effects are further influenced by interactions with temperature and precipitation gradients. To test this, we quantified AM fungal biodiversity in cultivated and adjacent uncultivated soils across a 1700 m elevational gradient (temperature: 7.7°C-16.5°C and precipitation: 1000-3500 mm). We found that conversion of uncultivated soils to agriculture reduced AM fungal richness by 80%, on average. Richness in uncultivated soils increased with the temperature gradient, while richness in farms declined. A similar but inverted trend was found for precipitation, where richness in uncultivated sites declined as precipitation increased. Uncultivated soils contained approximately three-fold more unique AM fungal species compared to cultivated soils. Our findings demonstrate that interactions between climate and land use strongly influence AM fungal biodiversity patterns in tropical mountain ecosystems. Incorporating both factors into conservation and sustainable agriculture strategies will be critical to preserving belowground biodiversity under global change.}, }
@article {pmid41606790, year = {2026}, author = {Clutter, CH and Leung, DT}, title = {Tracing MR1 expression across tissues to find the perfect MAIT.}, journal = {Journal of leukocyte biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jleuko/qiag014}, pmid = {41606790}, issn = {1938-3673}, abstract = {Mucosal associated invariant T (MAIT) cells are part of a T cell subset that is activated upon presentation of B2 vitamin (riboflavin) metabolites by the major histocompatibility complex, class I related (MR1) protein. Though there is a clear relationship between microbial production of riboflavin and MAIT cell development and persistence, little is known about the cells that primarily communicate with MAIT cells and other MR1-restricted T cells. Elegant work by Deng et al demonstrates that it is macrophages from the lung and peritoneum that express the highest amount of MR1 and are the most efficient at presenting vitamin B antigens to MAIT cells. This landmark study not only definitively identifies and maps the key antigen presenting cell populations involved in MAIT cell activation, it also reveals a bidirectional relationship between MR1 expression and the host microbiome. While further work on how these findings translate to human MAIT cell biology is needed, this study has provided us with unprecedented insights into the mechanistic interplay and microbial ecology of MR1 presentation of riboflavin metabolites.}, }
@article {pmid41606115, year = {2026}, author = {Hao, YQ and Li, BH and Chen, JY and Shu, WS and Zhao, XF}, title = {Bacterial necromass recycling promotes diversity maintenance in bacterial communities via resource partitioning.}, journal = {Nature ecology &amp; evolution}, volume = {}, number = {}, pages = {}, pmid = {41606115}, issn = {2397-334X}, support = {32371597//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32271600//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Understanding how high species diversity is maintained in natural bacterial communities is a central question in microbial ecology. Due to the versatile heterotrophic capacities of bacteria and the rich nutrients released by deceased bacterial cells, necromass recycling plays an important role in sustaining bacterial growth. Such nutrient cycling within communities can provide additional resource niches for bacteria, but its potential effects on bacterial diversity maintenance have been neglected. Here we conducted two independent experiments and studied the assembly of 276 soil-derived bacterial communities sustained by a wide range of bacterial necromass combinations, from single-species necromass to combinations of up to nearly 1,000 species. Our results highlight the existence of a species-rich bacterial necrobiome in soil. We found that the composition of necromass-decomposing communities was determined by the various organic compounds in the different necromass combinations, and the increases in necromass-producing species constantly promoted species diversity of necromass-decomposing communities. Moreover, the average niche breadth and overlap of coexisting necromass-decomposing species in utilizing distinct single-species necromass decreased with increases in necromass diversity, supporting the hypothesis of resource partitioning in utilizing different single-species necromass. Our study provides insights into diversity maintenance in bacterial communities from a perspective of internal nutrient cycling.}, }
@article {pmid41605992, year = {2026}, author = {Dickerson, AL and Jechow, A and Nößler, M and Walles, TJW and Berger, SA and Hölker, F and Nejstgaard, JC}, title = {High-resolution in situ imaging reveals size-specific moonlight responses in zooplankton diel vertical migration.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {4086}, pmid = {41605992}, issn = {2045-2322}, mesh = {Animals ; *Zooplankton/physiology ; *Moon ; Copepoda/physiology ; Light ; *Animal Migration/physiology ; Body Size ; Germany ; Cladocera/physiology ; Lakes ; }, abstract = {Light is the primary cue driving zooplankton diel vertical migration (DVM), a strategy that balances predation risk with resource access. However, DVM is often oversimplified, with limited consideration of how light-driven risks and resource needs vary across taxa and life stages. This simplification is partly due to constraints on collecting high-resolution, size-resolved data -especially at night, when subtle shifts in illumination reshape nocturnal risk landscapes. To overcome these limitations, we deployed a high-resolution in situ modular Deep-focus Plankton Imager and an image-recognition approach to quantify fine scale DVM and body sizes of Cladocerans and Copepods in Lake Stechlin, Germany. Data was collected from day into night and across moonrise and was compared with environmental data from vertical profiling sondes. Typical DVM patterns emerged, with deeper daytime distributions, however, moonlight introduced additional behavioural complexity: larger individuals avoided illuminated layers, likely managing predation risk, while smaller individuals moved into these layers, possibly exploiting foraging opportunities and reduced risk. These light-mediated shifts were further shaped by ecological conditions; copepods tracked food-rich layers regardless of light levels at night, while cladocerans showed light-dependent responses to both temperature and food, such that light caused them to avoid otherwise favourable (warm, food-rich) layers. Our approach provides new insight into how zooplankton navigate nocturnal lightscapes, revealing size- and taxon-specific strategies. By establishing size-dependent responses to natural moonlight, this work provides a crucial baseline for predicting how artificial light at night may restructure zooplankton communities and destabilize freshwater food webs.}, }
@article {pmid41605068, year = {2026}, author = {Truswell, A and Jordan, D and Pang, S and Cherrington, T and Hampson, DJ and Blinco, J and Adsett, S and Abraham, R and Stegger, M and Abraham, S}, title = {Genomic analysis of a porcine exudative epidermitis outbreak caused by Staphylococcus hyicus.}, journal = {Veterinary microbiology}, volume = {314}, number = {}, pages = {110883}, doi = {10.1016/j.vetmic.2026.110883}, pmid = {41605068}, issn = {1873-2542}, abstract = {Exudative epidermitis (EE) causes substantial morbidity and mortality in piglets. This study investigated the microbial ecology, antimicrobial resistance (AMR), and genomic diversity of Staphylococcus hyicus associated with an EE outbreak in an Australian piggery. Lesion swabs from 20 affected piglets yielded 160 bacterial isolates (including S. hyicus and cohabiting species). Isolates underwent species identification, antimicrobial susceptibility testing, and whole-genome sequencing (WGS) of S. hyicus for AMR/virulence gene profiling and core-genome SNP analysis to assess genomic relatedness. S. hyicus predominated among lesion isolates. Phenotypic testing showed varied AMR, with frequent resistance to erythromycin and tetracycline. WGS of 27 S. hyicus isolates identified five distinct genotypic AMR profiles, including combinations spanning multiple drug classes. All S. hyicus carried the exfoliative toxin gene shetA, and 24 also carried exhD. Core-genome analysis indicated a highly clonal outbreak: 24/27 genomes differed by 0 core SNPs, with the remaining three closely related. Despite this clonality, resistance gene carriage varied across isolates. Consequently, reliance on a single colony to represent an outbreak could understate resistance and overstate treatability. These findings support routine multi-isolate sampling to capture within-clone AMR variability, bolster antimicrobial selection during EE management, and inform consideration of autogenous vaccines targeting dominant outbreak clones.}, }
@article {pmid41604921, year = {2026}, author = {De, J and Banerjee, G and De Leon, EV and Martinez, AG and Wong, C and Banerjee, P}, title = {Polystyrene nanoplastics and pathogen plasticity: Toxic threat or tolerated stressor in Salmonella enterica?.}, journal = {Journal of hazardous materials}, volume = {503}, number = {}, pages = {141264}, doi = {10.1016/j.jhazmat.2026.141264}, pmid = {41604921}, issn = {1873-3336}, abstract = {Polystyrene nanoplastics (PS-NPs), a group of increasingly common environmental pollutants, pose emerging risks to microbial ecology and food safety. This study examines the concentration- and time-dependent effects of PS-NPs (low exposure: 2.5-5 mg/L; moderate exposure: 10-20 mg/L; high exposure: 50-100 mg/L) on Salmonella enterica, a major foodborne pathogen. Under realistic environmental conditions, PS-NPs influenced bacterial viability, membrane integrity, and oxidative stress levels, with higher concentrations causing lipid peroxidation and membrane disruption. Gene expression analyses showed early upregulation of stress-related, biofilm-associated, virulence, and adhesion genes, indicating an adaptive response to PS-NP-induced stress. Biofilm formation increased with moderate to high PS-NP exposure, confirmed by exopolysaccharide measurement and confocal microscopy. However, prolonged or high-dose exposure resulted in downregulation of efflux systems (acrB, tolC), quorum-sensing regulators (lsrA, invF), and antimicrobial resistance genes (marR, tetC), suggesting stress-related trade-offs. Notably, transient activation of marA and acrA indicates potential NP-induced cross-resistance mechanisms. These results imply that PS-NPs act as environmental stressors capable of altering bacterial virulence and survival strategies, with significant implications for microbial behavior in plastic-contaminated ecosystems and food processing environments. Collectively, our results emphasize the urgent need to reevaluate NP exposure in the context of public health and antimicrobial resistance.}, }
@article {pmid41604057, year = {2026}, author = {Silveira, KA and Ramiro-Garcia, J and Lawless, C and Espinosa-Vazquez, JM and Fermoso, FG and Collins, G and O'Flaherty, V}, title = {Mutual dosing of tungsten, molybdenum and selenium impact anaerobic digestion microbiome.}, journal = {Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine}, volume = {}, number = {}, pages = {}, pmid = {41604057}, issn = {1572-8773}, support = {861088//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; }, abstract = {Metals are critical in anaerobic digestion, but their co-occurrence effects on microbiome structure and function are underexplored. This study hypothesized that exposure of methanogenic granules to a trace element (TE) mixture alongside molybdenum (Mo), tungsten (W) or selenium (Se)-would alter (i) extracellular polymeric substances (EPS) protein and carbohydrate content, (ii) microbial composition and function (iii) methanogenic pathways.To test this, anaerobic batch reactors (n = 35) were set up in a fed batch mode, with sacrificial reactors (n = 14) used to collect biomass for analyses, including DNA: RNA co-extraction, amplicon sequencing, and determination of the concentrations of total and soluble metals, Scanning Electron Microscopy- Energy Dispersive X-ray (SEM-EDX) and EPS extraction over a 24-day period.The results reveal that, Mo and W increased the concentration of soluble Fe in abiotic controls, enhancing Fe and S retention. The presence of W, Mo, W + Se, and Se had a positive effect on methane production, with W + Se and W enhancing acetoclastic methanogenesis. Additionally, Se increased EPS protein and carbohydrate contents in the biomass. Shifts in the microbiome composition were mainly driven by Mo and Se, with typically dominant Anaerolineacaeae, Capriciproducens, Macelibacteroides and Clostridium sensu stricto 5 taxa. Functional potential suggested an enrichment of nucleotide metabolism and, importantly, Vitamin (B12, B6 and B9) metabolic potential.These finding inform Anaerobic digestion (AD) stakeholders about the impacts of Fe, W, Mo, and Se co-dosing on process performance and microbiome structure and function, offering insights to optimize biogas production through tailored metal supplementation combinations, given demonstrations at lab and pilot scales.}, }
@article {pmid41603638, year = {2026}, author = {Kosztik, J and Baka, E and Táncsics, A and Ábrahám, R and Szabó, G and Nagy, I and Orsini, M and Bata-Vidács, I and Szalontai, H and Kukolya, J and Nagy, I}, title = {Genomic and proteomic analyses of the maize root isolate Rhodococcus erythropolis NI86/21 reveal extensive genome plasticity and parallel evolution of herbicide degradation.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0240725}, doi = {10.1128/aem.02407-25}, pmid = {41603638}, issn = {1098-5336}, abstract = {Rhodococcus erythropolis NI86/21, isolated from maize rhizosphere in Hungary, possesses one of the largest genomes (8.046 Mb) within the species. The genome comprises a 6.83 Mb chromosome and 1.22 Mb of extrachromosomal elements, including three circular and two fragmented linear plasmids. Comparative analysis identified five horizontally acquired genomic islands (HGTi), totaling 0.64 Mb with mosaic-like architecture derived from plasmids, phages, and chromosomal segments of other Nocardiaceae. Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomic analysis revealed a lower expression of genes located in HGT elements (53%) compared to core chromosomal genes (73%), indicating regulatory silencing of foreign DNA. Nevertheless, an inducible cytochrome P450 monooxygenase (CYP116) responsible for thiocarbamate and atrazine degradation is encoded on HGTi_V and actively expressed upon herbicide exposure. Strikingly, an identical CYP450 locus is present on a conjugative plasmid in Rhodococcus sp. TE1 isolated from thiocarbamate-treated soil in Canada, demonstrating independent acquisition of the same catabolic module from a high GC% content Rhodococcus, under similar selective pressure. Frequent recombination between chromosomal and mobile elements generates the observed mosaic-like HGT structures, which we found common for R. erythropolis strains. These results highlight extraordinary genomic plasticity and rapid adaptive evolution in Rhodococci, enabling efficient colonization of herbicide-contaminated agro-ecosystems.IMPORTANCERhodococcus erythropolis NI86/21 exemplifies how bacterial genomes evolve through horizontal gene transfer and mobile elements. Its unusually large, plastic genome contains extensive HGT islands and a high load of active transposons, which shape mosaic genomic architectures and hinder complete genome assembly. These horizontally acquired regions, although partially silenced, encode key adaptive functions such as an inducible CYP116 monooxygenase enabling thiocarbamate and atrazine degradation. Remarkably, an identical CYP116 module is present in Rhodococcus sp. TE1 from thiocarbamate-treated Canadian soil, demonstrating that similar environmental pressures can drive independent acquisition of the same biodegradation trait. Together, the dynamic transposon activity, mosaic HGT structure, and geographically convergent gene recruitment highlight the extraordinary genomic plasticity of R. erythropolis and underscore its rapid adaptive potential in agro-ecosystems, with implications for microbial evolution and bioremediation strategies.}, }
@article {pmid41601066, year = {2026}, author = {Chen, Y and Cai, S and Zhang, P and Sun, C and Huang, D and Zhang, M and Tian, S}, title = {Effects of soil covering on bacterial communities and C/N functional genes during phytoremediation of copper tailings.}, journal = {Ecotoxicology and environmental safety}, volume = {309}, number = {}, pages = {119639}, doi = {10.1016/j.ecoenv.2025.119639}, pmid = {41601066}, issn = {1090-2414}, mesh = {*Copper/metabolism ; Biodegradation, Environmental ; *Soil Pollutants/metabolism/analysis ; *Soil Microbiology ; *Soil/chemistry ; Mining ; Nitrogen/metabolism ; Carbon/metabolism ; *Bacteria/genetics/metabolism ; China ; Metals, Heavy/analysis ; Genes, Bacterial ; }, abstract = {Copper tailings, a mining waste, pose environmental threats, and phytoremediation commonly employs soil covering to improve substrate properties and promote vegetation recovery. This study was conducted at the Yangshanchong Tailings Reservoir in Tongling City, Anhui Province, to comprehensively evaluate changes in soil physicochemical properties, bacterial community structure, and carbon/nitrogen functional genes during copper tailings remediation. We compared areas with and without soil covering, which were vegetated by two dominant species, Imperata cylindrica and Miscanthus floridulus, across profile depths of 0-20 cm, 20-40 cm, and 40-60 cm. Results indicated that: (i) soil covering significantly modified substrate pH, elevated levels of organic matter, organic carbon, and ammonium nitrogen, decreased surface total nitrogen, total phosphorus, and selected heavy metals, and altered the depth-dependent distribution of copper, manganese, and cadmium, (ii) soil covering reduced bacterial richness and diversity in I. cylindrica areas, increased the relative abundance of phyla such as Deinococcota, and significantly enriched genera including Brevundimonas, Acidisoma, and Acinetobacter, while enhancing the influence of heavy metals on dominant genera, (iii) soil covering reduced the abundance of genes related to nitrogen cycling (nifH, amoA, nosZ) and methane metabolism (pmoA1), and altered their correlations with specific bacterial genera. Overall, soil covering shapes bacterial community structure and the dynamics of carbon/nitrogen functional genes by altering the physicochemical properties and heavy metal distribution in tailings substrates, thereby playing a key regulatory role in microbial ecology during copper tailings revegetation. This study provides valuable insights for the restoration management of mining areas.}, }
@article {pmid41601011, year = {2026}, author = {Staley, BT and DeWitt, ME and Wenner, JJ and Sanders, JW and Wierzba, TF and Poehling, K}, title = {Trusted Sources of COVID-19 Vaccine Information by County Characteristics in North Carolina.}, journal = {Vaccines}, volume = {14}, number = {1}, pages = {}, pmid = {41601011}, issn = {2076-393X}, support = {49927//NC Department of Health and Human Services/ ; }, abstract = {BACKGROUND/OBJECTIVES: The COVID-19 pandemic disproportionately impacted rural areas across the United States, including rural North Carolina (NC). Consistent with national patterns, COVID-19 vaccination coverage as of December 2022 was higher for non-rural (72%) than rural (58%) NC counties. The role of trusted sources of vaccine information used by rural and non-rural residents is unknown.<br><br>METHODS: Using data from two surveys distributed by the COVID-19 Community Research Partnership from 8 June 2021 through 21 December 2021, we compared self-reported sources of trusted COVID-19 vaccine information by non-rural and rural counties and by county-level predominant political vote in the 2020 Presidential election.<br><br>RESULTS: While NC respondents were highly vaccinated (94%), fewer residents from rural counties self-reported COVID-19 vaccination than those from non-rural counties (91% versus 95%). The most common reported source of trusted vaccine information was federal health agencies. The proportion citing a federal health agency was higher for respondents from non-rural (80%) than rural (72%) counties and was higher for vaccinated (75%) than unvaccinated (42%) rural respondents. The next two most trusted sources of vaccine information were state/local health officials (48%) and health care providers (42%). Among trusted resources reported by 10-15% of respondents, those from rural counties were less likely to use hospital websites, employers, or news sources than those from non-rural counties. More respondents from counties with >60% vote for the 2020 Democratic Presidential candidate cited federal health agencies, state and local officials, and new sources than respondents from counties with >60% vote for the 2020 Republican Presidential candidate.<br><br>CONCLUSIONS: By identifying the trusted sources of vaccine information for residents in non-rural and rural NC counties, future vaccine implementation efforts can tailor communication efforts to increase vaccine uptake and potentially reduce the rates of hospitalizations and death from vaccine-preventable diseases such as COVID-19 or other future pandemics.}, }
@article {pmid41503489, year = {2026}, author = {Goddard, TR and Carlson-Jones, JA and Judith, M and Ooi, CY and Andrew, T and Warner, MS and John, W and Evans, IE and Hopkins, E and Iredell, JR and Jersmann, HP and Whiteson, KL and Bouras, G and Doane, MP and Falk, NW and Green, R and Grigson, SR and Mallawaarachchi, V and Martin, B and Roach, MJ and Ryan, FJ and Tarasenko, A and Papudeshi, B and Drigo, B and Giles, SK and Harker, CM and Hesse, RD and Hodgson, RJ and Hussnain, A and Hutton, A and Inglis, LK and Keneally, C and Kerr, EN and Liddicoat, C and Peddle, SD and Watson, CD and Yang, Q and Decewicz, P and Speck, PG and Mitchell, JG and Dinsdale, EA and Edwards, RA}, title = {Microbial Ecological Signatures Predict Pathogen Emergence and Multidrug Resistance in Cystic Fibrosis Airways up to a Year in Advance.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {41503489}, abstract = {Chronic infections in cystic fibrosis (CF) emerge from gradual ecological transitions in the airway microbiome, yet early predictive markers remain poorly defined. We developed a new autoencoder-based framework that outperforms read-based or metagenome-assembled genome-based analyses at capturing the continuum from health-associated commensals to pathogen-dominated, antibiotic-tolerant communities. This improvement is achieved by integrating taxonomic and functional data from 127 sputum and bronchoalveolar lavage metagenomes from 64 people with CF into latent "Clusters of Phylogeny and Functions" (COPFs). Coupled with gradient-boosted random forests, COPFs predicted Pseudomonas aeruginosa colonisation, multidrug resistance, and impending infection up to a year before clinical detection. The multidrug-resistant P. aeruginosa signature showed the same resistance-mechanism evolution as found in laboratory experiments. The inclusion of eukaryotic markers revealed persistent Aspergillus fumigatus signatures even during culture-negative intervals. Applying our South Australian-trained model to over 1,000 global metagenomes from 22 independent CF datasets, we achieved 94% accuracy in predicting P. aeruginosa status across platforms and geographies, validating the model's universal utility. Our results demonstrate that combining datasets with deep learning reveals conserved ecological and metabolic mechanisms in disease progression, transforming metagenomics into a predictive framework for managing chronic infections.}, }
@article {pmid41600663, year = {2025}, author = {Polyorach, S and Suphalucksana, W and Klompanya, A and Yuangklang, C and Wanapat, M and Cheas, S and Cherdthong, A and Kang, S and Gunun, P and Gunun, N and Foiklang, S and Kongmun, P and Montri, N and Srikijkasemwat, K}, title = {Ensiling Time and Mixed Microbe Fermented Liquid Modulate In Vitro Digestibility and Rumen Fermentation of Fermented Total Mixed Rations.}, journal = {Veterinary sciences}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/vetsci13010006}, pmid = {41600663}, issn = {2306-7381}, support = {Grant No. 2561-01-04-006//Faculty of Agricultural Technology, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand/ ; }, abstract = {This study investigated how varying the ensiling period and the level of mixed microbes fermented liquid (MMFL) influences the chemical composition, in vitro degradability, rumen fermentation profile, and microbial ecology of fermented total mixed rations (FTMR). A completely randomized 4 × 4 factorial design was used, incorporating four fermentation durations (0, 7, 14, and 21 days) and four MMFL inclusion rates (0, 0.5, 1.0, and 1.5% of DM). Both factors exerted significant effects on FTMR quality (p < 0.05). The combination of a 14-day fermentation period with 0.5% MMFL consistently produced the most desirable outcomes. Under these conditions, crude protein concentration rose from 12.0% to 14.3% of DM, while neutral-detergent fiber declined from 54.2% to 49.1%. Improvements were also observed in in vitro digestibility, with DM and OM increasing by 9-12% relative to the untreated control (p < 0.05). Fermentation end-products were enhanced, as total volatile fatty acids increased by 15% (92.4 vs. 80.1 mmol/L), and the molar proportion of propionate increased from 24.5 to 29.2 mol/100 mol, thereby lowering the acetate-to-propionate ratio (2.4 vs. 3.0; p < 0.05). Estimated methane production declined by 18% (p < 0.01). Microbial counts reflected a shift toward a more efficient fermentative community, with bacterial and fungal populations increasing by 21% and 18%, and protozoa decreasing by 25% (p < 0.05). Overall, moderate MMFL supplementation during a 14-day ensiling phase enhanced nutrient conservation and fermentation efficiency, suggesting practical value for improving FTMR utilization in ruminant systems. Further in vivo and economic evaluations remain necessary.}, }
@article {pmid41600038, year = {2026}, author = {Shen, H and Liu, Z and Wang, C and Chu, Y and Zhang, C and Yu, Y and Yang, S}, title = {EDDS-Enhanced Phytoremediation of Cd-Zn Co-Contaminated Soil by Sedum lineare: Mechanisms of Metal Uptake, Soil Improvement, and Microbial Community Modulation.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/plants15020231}, pmid = {41600038}, issn = {2223-7747}, support = {32271705//National Natural Science Foundation of China/ ; }, abstract = {Soil co-contamination with cadmium (Cd) and zinc (Zn) poses serious threats to environmental safety and public health. This study investigates the enhancement effect and underlying mechanism of the biodegradable chelator Ethylenediamine-N,N'-disuccinic acid (EDDS) on phytoremediation of Cd-Zn contaminated soil using Sedum lineare. The results demonstrate that EDDS application (3.65 g·L[-1]) effectively alleviated metal-induced phytotoxicity by enhancing chlorophyll synthesis, activating antioxidant enzymes (catalase and dismutase), regulating S-nitrosoglutathione reductase activity, and promoting leaf protein synthesis, thereby improving photosynthetic performance and cellular integrity. The combined treatment significantly increased the bioavailability of Cd and Zn in soil, promoted their transformation into exchangeable fraction, and resulted in removal rates of 30.8% and 28.9%, respectively. EDDS also modified the interaction patterns between heavy metals and essential nutrients, particularly the competitive relationships through selective chelation between Cd/Zn and Fe/Mn during plant uptake. Soil health was substantially improved, as evidenced by reduced electrical conductivity, enhanced cation exchange capacity, and enriched beneficial microbial communities including Sphingomonadaceae. Based on the observed ion antagonism during metal uptake and translocation, this study proposes a novel "Nutrient Regulation Assisted Remediation" strategy to optimize heavy metal accumulation and improve remediation efficiency through rhizosphere nutrient management. These findings confirm the EDDS-S. lineare system as an efficient and sustainable solution for remediation of Cd-Zn co-contaminated soils.}, }
@article {pmid41599027, year = {2025}, author = {Maçin, S and Özden, &#xd6; and Samadzade, R and Saylam, E and Çiftçi, N and Arslan, U and Yormaz, S}, title = {Oral Microbiota Alterations and Potential Salivary Biomarkers in Colorectal Cancer: A Next-Generation Sequencing Study.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {1}, pages = {}, doi = {10.3390/pathogens15010043}, pmid = {41599027}, issn = {2076-0817}, support = {23401136//Sel&#xe7;uk University/ ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology/diagnosis ; Male ; Female ; *Saliva/microbiology ; Middle Aged ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing ; Aged ; RNA, Ribosomal, 16S/genetics ; Pilot Projects ; *Biomarkers, Tumor ; Phylogeny ; Bacteria/classification/genetics/isolation &amp; purification ; *Mouth/microbiology ; Biomarkers ; Case-Control Studies ; Gastrointestinal Microbiome ; }, abstract = {Colorectal cancer (CRC) has a high mortality rate worldwide. Oral and intestinal microbiota members may have an effect on gastrointestinal tumors' pathogenesis, particularly in CRC. Designed as a pilot study, this study's aim was to investigate the relationship between CRC and oral microbiota and to identify potential biomarkers for CRC diagnosis. Saliva samples were collected from recently diagnosed CRC patients (n = 14) and healthy controls (n = 14) between March 2023 and December 2023. Microbiota (16S rRNA) analyses were conducted on these saliva samples using a next-generation sequencing method. Phylogenetic analyses, including alpha diversity, principal component analysis (PCA), principal coordinate analysis (PCoA), beta diversity, biomarker, and phenotype analyses, were conducted using the Qiime2 (Quantitative Insights Into Microbial Ecology) platform. Alpha diversity indices (Shannon: p = 0.78, Cho1: p = 0.28, Simpson: p = 0.81) showed no significant difference between CRC and control groups. Beta diversity analysis using Bray-Curtis PCoA indicated significant differences in the microbial community between the two groups (p = 0.003). Examination of OTU distributions revealed that the Mycoplasmatota phylum was undetectable in the oral microbiota of healthy controls but was significantly elevated in CRC patients (CRC: 0.13 ± 0.30, Control: 0.00 ± 0.00, p < 0.05). Additionally, Metamycoplasma salivarium, Bacteroides intestinalis, and Pseudoprevotella muciniphila were undetectable in healthy controls but significantly more prevalent in CRC patients (p < 0.05 for all three species). LEfSe analysis identified eight species with an LDA score > 2, Granulicatella adiacens, Streptococcus thermophilus, Streptococcus gwangjuense, Capnocytophaga sp. FDAARGOS_737, Capnocytophaga gingivalis, Granulicatella elegans, Bacteroides intestinalis, and Pseudoprevotella muciniphila, as potential biomarkers. The results of this study contribute critical evidence of the role of oral microbiota in the pathogenesis of colorectal cancer. Alterations in the microbiota suggest potential biomarkers in understanding the biological mechanisms underlying CRC and developing diagnostic and therapeutic strategies.}, }
@article {pmid41597698, year = {2026}, author = {Mohammed, A and Negm, E and Amarin, N and Sayed, S and Soliman, A and Askar, H and Yusuf, S and Rayan, AA}, title = {Impact of Dietary Supplementation of Probiotics on Cecal Microbial Ecology, Immune Response, and Meat Quality of Muscovy Ducks.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, doi = {10.3390/microorganisms14010182}, pmid = {41597698}, issn = {2076-2607}, support = {United Animal Health//United Animal Health (United States)/ ; }, abstract = {Probiotics represent a beneficial approach to boost the welfare, health, and meat quality of poultry. One hundred and twenty one-day-old male Muscovy ducklings were divided among 24 floor pens (five ducklings per pen). The pens were randomly distributed among one of four dietary treatments with six replicates (G-C) without any supplementation of probiotics; (G-A) was supplemented with 0.4 g/kg of Amnil[®]; (G-M) was supplemented with 0.5 g/kg of M-Mobilize[®]; and (G-A-M) was supplemented with 0.4 g/kg of Amnil[®] (1-30 day) and 0.5 g/kg of M-Mobilize[®] (31-60 day), respectively. The results indicated that BW at day 60 was improved in (G-A) birds compared with (G-C) ones, IL-6 was decreased in (G-A) and (G-A-M) in liver and spleen in comparison with (G-C) (p < 0.05), but no differences were observed between (G-C) and (G-M) (p > 0.05); IL-10 was decreased in all the probiotic-fed ducklings compared with (G-C) birds in the spleen (p < 0.05), and IL-10 was decreased in the (G-A) birds compared with the other treatments in the liver (p < 0.05). Probiotic-fed birds showed a higher enumeration of Lactobacillus spp. compared to (G-C) group (p < 0.05). In addition, the (G-M) group showed improved breast meat flavor, general acceptability, and water-holding capacity (WHC%) compared to (G-C) group (p < 0.05). These results suggest that the probiotic supplement (G-A), could be a good management tool for improving Muscovy ducks' health and production and further research is needed to improve meat quality traits.}, }
@article {pmid41597665, year = {2026}, author = {Khachatryan, A and Vardanyan, A and Zhang, R and Zhang, Y and Shi, X and Willscher, S and Nguyen, NHA and Vardanyan, N}, title = {Metagenome Insights into Armenian Acid Mine Drainage: A Novel Thermoacidophilic Iron-Oxidizing Bacterium with Perspectives for Copper Bioleaching.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, doi = {10.3390/microorganisms14010146}, pmid = {41597665}, issn = {2076-2607}, support = {22rl-031//Higher Education Science Committee of Armenia/ ; 23-YSIP-012//Higher Education Science Committee of Armenia/ ; }, abstract = {The microbial ecology of acid mine drainage (AMD) systems in Armenia, with a long mining history, remains unexplored. This study aimed to characterize the microbial diversity and functional potential of AMD in the Syunik region and to isolate novel microorganisms with biotechnological value. A comprehensive analysis of the microbial communities' structure of Kavart abandoned, Kapan exploring mines effluent, and Artsvanik tailing was conducted. Metagenomics revealed bacterial-dominated communities, comprising Pseudomonadota (previously "Proteobacteria") (68-72%), with site-specific variations in genus abundance. A high abundance and diversity of metal resistance genes (MRGs), particularly for copper and arsenic, were identified. Carbohydrate-active enzyme (CAZy) analysis showed a dominance of GT2 and GT4 genes, suggesting a high potential for extracellular polymeric substances (EPS) production and biofilm formation. A novel strain of iron-oxidizing bacteria Arm-12 was isolated that shares only ~90% similarity with known Leptospirillum type species, indicating it may represent a new genus without culturable representatives. The strain exhibits enhanced copper extraction from concentrate. This study provides the first metagenomic insights into Armenian AMD systems and tailing, revealing a unique community rich in metal resistance and biofilm-forming genes. The isolation of a novel highly effective iron-oxidizer Arm-12 highlights the potential of AMD environments as a source of novel taxa with significant applications in biomining and bioremediation processes.}, }
@article {pmid41597639, year = {2026}, author = {Yin, Y and Xu, W and Xu, M and Wang, Y and Liu, H and Cao, H and Wang, F}, title = {Prokaryotic Microbial Diversity and Community Assembly in Reclaimed Coastal Agricultural Soils.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, doi = {10.3390/microorganisms14010120}, pmid = {41597639}, issn = {2076-2607}, support = {32471725//National Natural Science Foundation of China/ ; 2021S018//Ningbo Municipal Bureau of Science and Technology/ ; 2022Z169//Ningbo Municipal Bureau of Science and Technology/ ; }, abstract = {Coastal reclamation profoundly alters soil physicochemical conditions and strongly influences soil microbial ecology; however, the millennial-scale successional patterns and assembly mechanisms of prokaryotic communities under such long-term disturbance remain insufficiently understood. In this study, we investigated archaeal and bacterial communities in the plow layer along a 0-1000-year coastal reclamation chronosequence on the southern shore of Hangzhou Bay. We analyzed community abundance, diversity, composition and assembly processes, and quantified the relative contributions of geographic distance, environmental factors and reclamation years to microbial biogeographic patterns. The results showed that reclamation markedly drove continuous soil desalination, acidification, nutrient accumulation, and particle-size refinement. Bacterial abundance exhibited a sharp decline during the early stages of reclamation, whereas archaeal abundance remained relatively stable. The α-diversity of both archaea and bacteria peaked at approximately 210-230 years of reclamation. Community assembly processes differed substantially between the two microbial domains: the archaeal communities were dominated by stochastic processes (77.78%) identified as undominated processes and dispersal limitation, whereas bacterial communities were primarily shaped by deterministic processes (70.75%) driven as variable selection. Distance-decay analysis indicated that bacterial communities were more sensitive to environmental gradients. Multiple regression and variance partitioning further demonstrated that soil pH and electrical conductivity were the key drivers of community structure. Overall, this study reveals the millennial-scale community dynamics and assembly mechanisms of archaea and bacteria in response to coastal reclamation, providing mechanistic insights into long-term microbial ecological succession and offering valuable guidance for sustainable agricultural management and ecological restoration in reclaimed coastal regions.}, }
@article {pmid41597573, year = {2025}, author = {Si, W and Zhang, J and Zhang, Y and Ji, Y and Khan, MZ and Chen, Y and Cheng, Z and Zhuang, J and Zhao, X and Liu, W}, title = {Characterization of Bacterial Communities in Air and Bedding Materials of Intensive Donkey Farms During Summer.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, doi = {10.3390/microorganisms14010053}, pmid = {41597573}, issn = {2076-2607}, support = {SDAIT-27-11//Shandong Donkey Industry Technology System Fund/ ; }, abstract = {This study investigated the bacterial community composition and diversity in air and exercise yard bedding samples from large-scale donkey farms in Liaocheng, China, during summer using 16S rRNA high-throughput sequencing. Air samples were collected from five functional areas of donkey barns, while bedding samples were obtained from eight farms housing Dezhou donkeys. Sequencing analysis revealed 894 operational taxonomic units (OTUs) in air samples and 3127 OTUs in bedding samples. Alpha diversity indices indicated that the mare barn exhibited the highest microbial diversity in air, while the foal barn showed the lowest. Actinobacteriota, Proteobacteria, and Firmicutes were the dominant phyla across different functional areas. Rhodococcus was identified as the predominant airborne genus, representing a potential pneumonia risk in foals. In bedding materials, Firmicutes, Actinobacteriota, and Proteobacteria predominated, with Corynebacterium, Salinicoccus, and Solibacillus as dominant genera. Several potentially pathogenic bacteria were detected, including Rhodococcus, Corynebacterium, Clostridium, Streptococcus, and Escherichia-Shigella. These findings provide critical insights into the microbial ecology of intensive donkey farming environments and offer scientific evidence for developing targeted biosecurity strategies to safeguard animal health and promote sustainable livestock production.}, }
@article {pmid41597522, year = {2025}, author = {Tamahara, T and Kouketsu, A and Fukase, S and Sripodok, P and Saito, T and Ito, A and Li, B and Kumada, K and Shimada, M and Iikubo, M and Shimizu, R and Yamauchi, K and Sugiura, T}, title = {Ecological and Functional Landscape of the Oral Microbiome: A Multi-Site Analysis of Saliva, Dental Plaque and Tongue Coating.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, doi = {10.3390/microorganisms14010002}, pmid = {41597522}, issn = {2076-2607}, support = {JP24K1310 and JP22K17150//JSPS KAKENHI/ ; }, abstract = {The oral cavity contains several microbial niches, including saliva, dental plaque and tongue coating, each shaped by distinct local environments and host factors. This study compared the ecological and functional characteristics of the microbiomes of these three oral sites within the same individuals and examined host conditions associated with their variation. Saliva, supragingival plaque and tongue coating samples were collected simultaneously from 31 adults without clinical oral lesions. The bacterial 16S rRNA gene (V3-V4 region) was sequenced using the Illumina MiSeq platform, and analyses included α and β diversity, Mantel correlations, differential abundance tests, network analysis and functional prediction. The three sites displayed a clear ecological gradient. Saliva and tongue coating were taxonomically similar but were influenced by different host factors, whereas plaque maintained a distinct, biofilm-like structure with limited systemic influence. Functional divergence was most pronounced on the tongue coating despite its taxonomic similarity to saliva, whereas functional differences between saliva and plaque were modest despite larger taxonomic separation. These findings indicate that microbial composition and function vary independently across oral niches and support the need for multi-site sampling to more accurately characterize oral microbial ecology.}, }
@article {pmid41596857, year = {2026}, author = {Tsouggou, N and Korozi, E and Pemaj, V and Drosinos, EH and Kapolos, J and Papadelli, M and Skandamis, PN and Papadimitriou, K}, title = {Advances in Shotgun Metagenomics for Cheese Microbiology: From Microbial Dynamics to Functional Insights.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/foods15020259}, pmid = {41596857}, issn = {2304-8158}, abstract = {The cheese microbiome is a complex ecosystem strongly influenced by both technological practices and the processing environment. Moving beyond traditional cultured-based methods, the integration of shotgun metagenomics into cheese microbiology has enabled in-depth resolution of microbial communities at the species and strain levels. The aim of the present study was to review recent applications of shotgun metagenomics in cheese research, underscoring its role in tracking microbial dynamics during production and in discovering genes of technological importance. In addition, the review highlights how shotgun metagenomics enables the identification of key metabolic pathways, including amino acid catabolism, lipid metabolism, and citrate degradation, among others, which are central to flavor formation and ripening. Results of the discussed literature demonstrate how microbial composition, functional traits, and overall quality of cheese are determined by factors such as raw materials, the cheesemaking environment, and artisanal practices. Moreover, it highlights the analytical potentials of shotgun metagenomics, including metagenome-assembled genomes (MAGs) reconstruction, characterization of various genes contributing to flavor-related biosynthetic pathways, bacteriocin production, antimicrobial resistance, and virulence, as well as the identification of phages and CRISPR-Cas systems. These insights obtained are crucial for ensuring product's authenticity, enabling traceability, and improving the assessment of safety and quality. Despite shotgun metagenomics' advantages, there are still analytical restrictions concerning data handling and interpretation, which need to be addressed by importing standardization steps and moving towards integrating multi-omics approaches. Such strategies will lead to more accurate and reproducible results across studies and improved resolution of active ecosystems. Ultimately, shotgun metagenomics has shifted the field from descriptive surveys to a more detailed understanding of the underlying mechanisms shaping the overall quality and safety of cheese, thus bringing innovation in modern dairy microbiology.}, }
@article {pmid41595487, year = {2026}, author = {Ucero-Carretón, A and Puente, H and Ithurbide, M and Estellé, J and Carvajal, A and Argüello, H}, title = {Factors Involved in Host Resilience to Enteric Infections in Pigs: Current Knowledge in Genetic, Immune, and Microbiota Determinants of Infection Resistance.}, journal = {Genes}, volume = {17}, number = {1}, pages = {}, doi = {10.3390/genes17010067}, pmid = {41595487}, issn = {2073-4425}, support = {PID2024-160714OB-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; MICIU/AEI/10.13039/501100011033//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; LE088P23//Junta de Castilla y Le&#xf3;n/ ; JDC2023-051122-I//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; ULE-Predoc/2024//Universidad de Le&#xf3;n/ ; }, mesh = {Animals ; Swine/genetics ; *Gastrointestinal Microbiome/genetics/immunology ; *Disease Resistance/genetics ; *Swine Diseases/microbiology/genetics/immunology/virology ; *Host-Pathogen Interactions/genetics/immunology ; Quantitative Trait Loci ; }, abstract = {Enteric infections remain a major health and economic challenge in swine production, with outcomes determined not only by pathogen virulence but also by the complex interplay between host genetics, immune competence, and the intestinal microbiota. This review synthesises current knowledge on host-pathogen genomic interactions in pigs, with a focus on resilience mechanisms against enteric diseases in swine. For this purpose, 103 articles were used as information sources, retrieved through structured keyword searches in PubMed. The review first addresses host genetic factors, highlighting genomic variants and quantitative trait loci associated with resistance or resilience to viral and bacterial pathogens such as porcine epidemic diarrhoea virus (PEDV) or Escherichia coli. Next, the key factors of the immune system to confer protection are also reviewed, emphasising the role of innate and adaptive responses in controlling each pathogen and disclosing the contribution of regulatory networks that balance pathogen clearance. Finally, the last section of the review is devoted to exploring current knowledge in the involvement of the microbiota in resilience against enteric pathogens, mostly, but not exclusively, enteric bacteria. In this sense, competitive exclusion is a concept which has gained attention in recent years. The review pinpoints and discusses the state of the art about how the microbial community provides colonisation resistance, shapes immune development, and influences pathogen fitness within the intestinal niche. As final perspectives, the review explores future drivers in the genetic immune and microbiota resistance. By bridging host genomic data with functional insights into immunity and microbial ecology, this review underscores the potential of multi-omics approaches to enhance resilience against enteric infections in pigs and advance sustainable swine health management.}, }
@article {pmid41593721, year = {2026}, author = {Xi, J and Tao, H and Zhang, Z and Lian, B and Sun, W and Zhang, Y and Bu, S and Yang, X and Qian, X}, title = {Captive breeding of specialty animals represents an overlooked yet critical reservoir for spreading antibiotic resistance genes.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag009}, pmid = {41593721}, issn = {1751-7370}, abstract = {Driven by wildlife conservation and economic demands, captive breeding has expanded globally, intensifying wildlife-human interactions. In specialty animal breeding, particularly for species with short domestication histories and underdeveloped breeding protocols, clinically important antibiotics are commonly misused, posing potential ecological and health risks that remain largely unexplored. We collected fecal samples from three groups of musk deer (Moschus berezovskii): those exposed to clinically important antibiotics, those not exposed for six months, and wild musk deer, and analyzed their microbiomes and resistomes using metagenomic and culture-based methods. We found that captivity significantly expanded and reshaped the fecal resistome of musk deer. The antibiotic-exposed musk deer harbored a significantly higher diversity and abundance of antibiotic resistance genes (ARGs) compared to those non-exposed to antibiotics and wild deer. We observed a higher abundance of clinically important ARGs within Enterobacteriaceae in fecal samples of captive musk deer. This observation was further supported by the antibiotic susceptibility profiles of 124 Escherichia coli strains isolated from antibiotic-exposed musk deer. Seven identical mobile genetic element-associated ARGs were detected in distinct bacterial hosts across fecal samples from musk deer and farm workers, indicating potential conjugative transfer between the two groups. Our results suggest that captive breeding of specialty animals is an overlooked but significant reservoir for disseminating clinically important ARGs, and underscore the transmission risk at the animal-human interface.}, }
@article {pmid41592901, year = {2026}, author = {Pedreira, A and Vázquez, JA and García, MR}, title = {The mini revolution: application of mini-bioreactors in adaptive laboratory evolution.}, journal = {Critical reviews in biotechnology}, volume = {}, number = {}, pages = {1-19}, doi = {10.1080/07388551.2025.2608012}, pmid = {41592901}, issn = {1549-7801}, abstract = {Adaptive laboratory evolution (ALE) is a powerful tool for understanding and controlling the evolutionary trajectories of microorganisms. The scope of applications extends widely, including areas such as: biotechnology, synthetic biology, microbial ecology, and fundamental evolutionary research. In this work, we systematically explore the implementation and advantages of mini-bioreactors, defined as reactors with working volumes below 0.5 L, in ALE experiments. Mini-bioreactors offer substantial improvements over traditional large-scale reactors, including: reduced costs, enhanced parallelization capabilities, customizable configurations, and ease of automation. Through the utilization of illustrative case studies, which facilitate a comparative and critical evaluation of: batch, chemostat, turbidostat, and morbidostat operational modes, this review underscores the distinct capabilities of mini-bioreactors in enabling precise, dynamic control of evolutionary pressures. The novelty of this review lies in its comprehensive synthesis of recent advancements in mini-bioreactor technologies and operational strategies, particularly emphasizing innovations, such as: integrated automation, advanced sensors, and novel control algorithms adapted or specially designed for ALE. The ultimate objective is to provide both novices and experienced researchers with an updated, in-depth resource that addresses current technological limitations and future directions of mini-bioreactors in ALE.}, }
@article {pmid41592403, year = {2026}, author = {Zhang, B and Wang, M and Zheng, J and Yu, C and Wei, C and Ren, J and Sun, S and Wang, G and Wang, J and Lu, Y and Lin, L and Zhang, C}, title = {Strain-specific impacts of Pichia kudriavzevii on metabolite profiles and microbial community dynamics in Chinese Baijiu fermentation: Integrated metabolomics and metagenomics analysis.}, journal = {International journal of food microbiology}, volume = {450}, number = {}, pages = {111660}, doi = {10.1016/j.ijfoodmicro.2026.111660}, pmid = {41592403}, issn = {1879-3460}, abstract = {Pichia kudriavzevii is a dominant yeast species in Chinese baijiu fermentation, yet its intraspecific diversity remains underexplored. This study used metabolomics and metagenomics analysis to investigate the impact of four distinct P. kudriavzevii strains (PK12, PK25, PK97, and PK360) on the metabolite profiles and microbial community structure in a controlled baijiu solid-state fermentation. Metabolomics analysis identified 49 key volatile compounds and 2792 non-volatile metabolites. Strain PK97 exhibited exceptional capacity for butanoic acid metabolism, inducing a 55.27-fold increase in butanoic acid and a 30.54-fold enhancement in ethyl butanoate production. Strain PK25 specialized in acetoin biosynthesis, while PK360 maximized 2-phenylethanol production. Metagenomic analysis uncovered that strains PK12, PK25, and PK360 promoted Lactobacillus acetotolerans population, increasing its relative abundance to 67.39%, 58.57%, and 71.79%, respectively. In contrast, strain PK97 orchestrated a dramatic ecological shift, elevating Enterobacter mori abundance from 0.56% to 17.60%, transforming the community from Lactobacillus-dominated to Enterobacteriaceae-enriched. Integration of metabolomic and metagenomic data revealed that strain PK97's promotion of Enterobacter mori correlated with significant upregulation of key enzymes including α-amylase (EC 3.2.1.1), enoyl-CoA hydratase (EC 4.2.1.17), and succinyl-CoA synthetase (EC 6.2.1.5), creating a metabolic environment favoring enhanced starch hydrolysis, altered TCA cycle flux, and butanoic acid accumulation. Strain PK25 specifically upregulated acetyl-CoA hydrolase (EC 3.1.2.1), facilitating acetic acid and acetoin formation. Strain PK360 enhanced glucose pyrophosphorylase (EC 2.7.7.9) and asparagine synthetase (EC 6.3.1.1) activities, accelerating galactose metabolism and amino acid transformations. These findings illustrate the impact of P. kudriavzevii intraspecific diversity on reshaping microbial ecology and flavor chemistry in Chinese baijiu, offering novel insights for targeted fermentation control and quality enhancement strategies in baijiu production.}, }
@article {pmid41592132, year = {2026}, author = {Rathod, DR and Silverman, JD}, title = {PCR bias impacts microbiome ecological analyses.}, journal = {PLoS computational biology}, volume = {22}, number = {1}, pages = {e1013908}, doi = {10.1371/journal.pcbi.1013908}, pmid = {41592132}, issn = {1553-7358}, abstract = {Polymerase Chain Reaction (PCR) is a critical step in amplicon-based microbial community profiling, allowing the selective amplification of marker genes such as 16S rRNA from environmental or host-associated samples. Despite its widespread use, PCR is known to introduce amplification bias, where some DNA sequences are preferentially amplified over others due to factors such as primer-template mismatches, sequence GC content, and secondary structures. Although these biases are known to affect transcript abundance, their implications for ecological metrics remain poorly understood. In this study, we conduct a comprehensive evaluation of how PCR-bias influences both within-samples (α-diversity) and between-sample (β-diversity) analyses. We show that perturbation-invariant diversity measures remain unaffected by PCR bias, but widely used metrics such as Shannon diversity and Weighted-Unifrac are sensitive. To address this, we provide theoretical and empirical insight into how PCR-induced bias varies across ecological analyses and community structures, and we offer practical guidance on when bias-correction methods should be applied. Our findings highlight the importance of selecting appropriate diversity metrics for PCR-based microbial ecology workflows and offer guidance for improving the reliability of diversity analyses.}, }
@article {pmid41591842, year = {2026}, author = {Islam, H and Sharma, A and Blair, J and Lopatkin, AJ}, title = {PlasAnn: a curated plasmid-specific database and annotation pipeline for standardized gene and function analysis.}, journal = {Nucleic acids research}, volume = {54}, number = {3}, pages = {}, doi = {10.1093/nar/gkaf1507}, pmid = {41591842}, issn = {1362-4962}, support = {1R35GM150871-01/NH/NIH HHS/United States ; //Pew Charitable Trusts Foundation/ ; 2440082//National Science Foundation/ ; //Edward Mallinckrodt Jr. Foundation/ ; }, mesh = {*Plasmids/genetics ; *Molecular Sequence Annotation/methods ; *Databases, Genetic ; Genome, Bacterial ; Software ; DNA Transposable Elements ; Genes, Bacterial ; Bacteria/genetics ; }, abstract = {Conjugative plasmids are key drivers of bacterial adaptation, enabling the horizontal transfer of accessory genes within and across diverse microbial populations, yet annotating them remains challenging due to their highly mosaic genetic architectures and inconsistent gene naming conventions that complicate functional predictions and comparative analyses. To address this, we developed PlasAnn, a database designed specifically for genes encoded on natural plasmids, paired with a dedicated annotation pipeline (available via Bioconda or through the URL https://plasann.rochester.edu/). The curated database provides highly accurate, plasmid-type-specific gene names with standardized functional annotations, enabling direct comparison across plasmids without manual curation or specialized expertise, while the integrated annotation tool incorporates other common plasmid features for a fast, one-stop solution that outperforms broad prokaryotic genome annotation pipelines in both accuracy and efficiency. We demonstrate PlasAnn's utility by showing that plasmid accessory genes from different groups often share conserved repertoires, suggesting dynamic, modular networks of interconnected genes, and by revealing that plasmid-encoded transposable elements frequently carry genes related to bacterial adaptation beyond antibiotic resistance, including metabolism, virulence, and stress responses, emphasizing their broader contributions to fitness and adaptability. These insights, not captured by current field-standard tools, highlight how PlasAnn improves plasmid annotation and advances our understanding of plasmid biology, microbial ecology, and evolution.}, }
@article {pmid41590453, year = {2026}, author = {Zhang, K and Cai, Y and Shi, X and Yan, Z and Huang, Q and Perez-Moreno, J and Liu, D and Yang, Z and Yang, C and Yu, F and Liu, W}, title = {Symbiosis Among Naematelia aurantialba, Stereum hirsutum, and Their Associated Microbiome in the Composition of a Cultivated Mushroom Complex JinEr.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {12}, number = {1}, pages = {}, doi = {10.3390/jof12010041}, pmid = {41590453}, issn = {2309-608X}, support = {202205AD160036//Fuqiang Yu/ ; Yunnan Revitalization Talent Support Program//Jes&#xfa;s P&#xe9;rez-Moreno, Xinhua He/ ; }, abstract = {The JinEr mushroom ("Golden Ear"), a globally rare edible and medicinal macrofungus, comprises a symbiotic complex formed by the symbiotic association of Naematelia aurantialba (Tremellomycetes) and Stereum hirsutum (Agaricomycetes). However, the interactions between these fungi and their associated microbiome remain poorly understood. This study employed high-throughput amplicon sequencing, in situ microbial isolation and culture, and microbial confrontation assays to analyze microbial diversity, community structure, and potential functional roles of the endomycotic bacterial community within JinEr basidiomata and its cultivation substrate. Molecular analysis confirmed the heterogenous composition of the basidiomata, revealing N. aurantialba constitutes less than 20% of the fungal biomass, while S. hirsutum predominates, accounting for approximately 80%. Endomycotic fungi accounted for 0.33% (relative abundance) of the fungal community. Prokaryotic analysis identified Delftia and Sphingomonas as the dominant endomycotic bacterial genera within basidiomata, comprising 85.42% of prokaryotic sequences. Endomycotic bacterial diversity differed significantly (p < 0.05) between basidiomata and substrate, indicating host-specific selection. Cultivation-based approaches yielded 140 culturable bacterial isolates (spanning four families and seven genera) from basidiomata core tissues. In vitro co-culture experiments demonstrated that eight representative bacterial strains exhibited compatible growth with both hosts, while one Enterobacteriaceae strain displayed antagonism towards them. These findings confirm that the heterogeneous JinEr basidiomata harbor a specific prokaryotic assemblage potentially engaged in putative symbiotic or commensal associations with the host fungi. This research advances the understanding of microbial ecology in this unique fungal complex and establishes a culture repository of associated bacteria. This collection facilitates subsequent screening for beneficial bacterial strains to enhance the JinEr cultivation system through the provision of symbiotic microorganisms.}, }
@article {pmid41589897, year = {2026}, author = {Huang, J and Cai, M and Han, M and Fang, B and Dong, L and Zhang, G and Han, J-R and Li, S and Rustamova, N and Liu, Y and Li, W-J and Jiang, H}, title = {Habitat heterogeneity drives microbial community assembly and functional specialization in extremely arid ecosystems.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0258825}, doi = {10.1128/aem.02588-25}, pmid = {41589897}, issn = {1098-5336}, abstract = {UNLABELLED: Extreme arid ecosystems present significant environmental challenges, yet the mechanisms by which habitat heterogeneity (e.g., salinity gradients, soil-sediment contrasts) shapes microbial community assembly and functional specialization remain poorly understood. This study integrated culture-dependent and culture-independent approaches to investigate microbial diversity, assembly processes, and metabolic potential across wasteland soils, desert soils, and saline lake sediments in the Turpan-Hami Basin. High-throughput sequencing revealed habitat-specific patterns, with lake sediments exhibiting significantly greater OTU richness and Shannon diversity than wasteland and desert soils (P < 0.05). These shifts were driven by salinity-dependent taxonomic succession, notably the dominance of Gammaproteobacteria, Halobacteria, and Desulfobacteria in hypersaline lakes. Ecological assembly processes diverged across habitats, with deterministic processes (heterogeneous/homogeneous selection) dominated in deserts and moderate saline lakes, whereas stochastic processes (dispersal limitation, drift) prevailed in wastelands and hypersaline systems. Metabolic profiling highlighted habitat-specific functional specialization: terrestrial systems were characterized by nitrogen-cycling, while saline lakes displayed partitioned sulfur metabolism (e.g., sulfate respiration in high-salinity sediments). Co-occurrence network analyses revealed greater topological complexity in freshwater lakes than in extreme environments, reflecting contrasting resilience strategies. Cultivation strategies informed by sequencing results recovered 4.02% to 21.76% of the sequence-detected genera, significantly improving access to the uncultured majority. These findings demonstrate that habitat heterogeneity drives microbial community assembly and functional evolution in extremely arid ecosystems, underscoring the value of integrating omics with cultivation to uncover microbial dark matter.<br><br>IMPORTANCE: Understanding microbial adaptation in hyperarid environments is crucial for predicting ecosystem responses to extreme stressors. This study provides an integrative framework linking environmental heterogeneity to microbial community assembly and metabolic specialization across diverse habitats in one of Earth's driest basins. Our findings demonstrate that deterministic environmental filtering dominates community assembly in deserts and moderately saline lakes, whereas stochastic processes prevail in wastelands and hypersaline systems. Habitat&#x2011;specific metabolic specialization is evident, with nitrogen cycling being key in terrestrial soils and sulfur metabolism central to saline lakes. By significantly improving the recovery of uncultured diversity through targeted strategies, this study bridges a major gap between molecular surveys and cultivable microorganisms. These findings advance ecological theory on community assembly and offer a model for studying microbial resilience and functional evolution under extreme aridity.}, }
@article {pmid41589889, year = {2026}, author = {Wang, S and Su, Y}, title = {Challenging the paradigm of metabolic exclusivity: coexistence of methanogenesis and sulfate reduction in oil reservoirs.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0217225}, doi = {10.1128/aem.02172-25}, pmid = {41589889}, issn = {1098-5336}, abstract = {The prevailing dogma in microbial ecology holds that sulfate-reducing microorganisms (SRMs) outcompete methanogenic archaea for common substrates (e.g., H2/formate and acetate), leading to the mutual exclusion of sulfate reduction and methanogenesis in sulfate-rich anaerobic environments. This principle underpins models of organic carbon flow to sulfate-respiration-derived CO2 in ecosystems like oil reservoirs, where seawater injection introduces high concentrations of sulfate. In an Applied and Environmental Microbiology article by S. Beilig, L. Voskuhl, I. Geydirici, L. K. Tintrop, T. C. Schmidt, and R. U. Meckenstock (91:e00141-25, 2025, https://doi.org/10.1128/aem.00141-25), the authors challenge this view by demonstrating coexistence of methanogenesis and sulfate reduction in a sulfate-adapted enrichment culture from an oil reservoir. The authors employ incubation experiments and microbial activity assessment via the reverse stable isotope labeling (RSIL) method to argue for metabolic coexistence, even under conditions thought to favor complete competitive exclusion. This commentary discusses the mechanistic reasons underlying the coexistence and explores the broader implications for predicting microbial activities and interactions. The study compellingly argues that thermodynamic and kinetic arguments alone are insufficient to predict microbial community function, necessitating a more nuanced understanding of microbial interactions in complex environments.}, }
@article {pmid41588828, year = {2026}, author = {Shaw, D and Gentekaki, E and Tsaousis, AD}, title = {The Microbiome Within a Microbe: Rethinking Blastocystis Biology.}, journal = {The Journal of eukaryotic microbiology}, volume = {73}, number = {1}, pages = {e70056}, doi = {10.1111/jeu.70056}, pmid = {41588828}, issn = {1550-7408}, support = {CA21105//COST/ ; //University of Kent/ ; }, mesh = {*Blastocystis/physiology/microbiology/virology ; Humans ; *Microbiota ; Blastocystis Infections/parasitology ; *Gastrointestinal Microbiome ; }, abstract = {Blastocystis spp., one of the most prevalent microeukaryotes in the human gut, has long puzzled researchers with its ambiguous role in health and disease. Decades-old microscopy studies reported bacterial- and viral-like particles within Blastocystis spp. cells, but these findings have been mainly overlooked. Comparable associations in other protozoa, such as those between Trichomonas vaginalis and Mycoplasma, as well as protozoan-virus interactions, are known to influence metabolism, immune evasion, and ecological fitness. Here, we revisit these neglected observations in Blastocystis spp., framing them within the holobiont concept and proposing that this protist may host its own microbial consortium. We also propose potential mechanisms, ecological implications, and modern experimental strategies-from organ-on-a-chip to single-cell multi-omics-to rigorously test this hypothesis. Recognizing Blastocystis spp. as a possible "microbiome within a microbe" could transform our understanding of its biology and its place in gut microbial ecology.}, }
@article {pmid41588461, year = {2026}, author = {Zheng, H and Payne, L and He, W and Mestre, MR and Yang, L and Dechesne, A and Pinilla-Redondo, R and Nesme, J and Sørensen, SJ}, title = {Plasmids as persistent genetic reservoirs of bacterial defense systems in wastewater treatment.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-025-02297-2}, pmid = {41588461}, issn = {2049-2618}, abstract = {BACKGROUND: Bacterial antiphage defense systems play essential roles in microbial ecology, yet their dynamics within urban wastewater systems (UWS) remain poorly characterized.<br><br>RESULTS: In this study, we performed comprehensive metagenomic and plasmidome analyses on 78 wastewater samples collected during two seasons and four sampling points across UWS from three European countries. We observed a significant reduction in the abundance, diversity, and mobility potential of defense systems during biological treatment. However, these reductions were not directly correlated with changes in microbial abundance. Defense systems were significantly enriched on plasmids, particularly conjugative plasmids, where their gene density was approximately twice as high as on chromosomes and remained relatively stable across compartments. In contrast to chromosomal defense systems, plasmid-borne systems exhibited more frequent co-localization with a wide range of mobile genetic elements (MGEs)-associated genes, thereby facilitating multilayered dissemination networks. Furthermore, we detected a strong correlation between phage abundance and host defense system profiles, indicating ongoing phage-host co-evolutionary dynamics in these environments.<br><br>CONCLUSIONS: In summary, our results demonstrate that UWS reduce the abundance and diversity of bacterial defense system genes. However, plasmid-associated defense systems can persist through shared mobile genetic reservoirs. These findings underscore the critical role of plasmids in bacterial immunity and provide new insights into defense system dynamics within urban wastewater environments.}, }
@article {pmid41588066, year = {2026}, author = {Pániková, L and Ondreičková, K and Pánik, P and Janiga, M and Oxikbayev, B}, title = {Linkages Between Trace Elements and Bacterial Communities in Glacial Freshwater Systems of Zhongar Alatau National Park, Kazakhstan.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02674-2}, pmid = {41588066}, issn = {1432-184X}, abstract = {Glacial ecosystems of Central Asia represent extreme environments where microbial communities are shaped by both physicochemical conditions and hydrological dynamics. In this study, we analysed 21 surface and meltwater samples collected in September 2023 from a lake, river, glacier, glacial river, and sedimentary lake in the Zhongar Alatau National Park (Kazakhstan, 1 040-3 360 m a.s.l.). Bacterial community structure was assessed using ARISA profiling, while spectrometric methods determined concentrations of chemical elements. Alpha diversity indices revealed the highest richness and diversity in lake and sedimentary lake samples, moderate diversity in river samples, and the lowest values in glacier samples. The glacial river samples showed the strongest variability among the samples. Unique operational taxonomic units (OTUs) were most abundant in the lake, but the glacier exhibited the highest relative proportion of habitat-specific OTUs. Principal component analysis revealed that DNA yield, along with heavy metals and other elements (Rb, Fe, Mn, K, Ba), covaried along the major axes, primarily reflecting differences driven by habitat. Overall, our results demonstrate that glacial valley habitats host distinct bacterial assemblages and that the chemical environment is consistent with the observed spatial structuring of microbial communities. These findings highlight the vulnerability and sensitivity of mountain freshwater ecosystems to glacier retreat and associated changes in water chemistry.}, }
@article {pmid41587649, year = {2026}, author = {Shi, J and Li, LK and Lin, LH and Li, DK and Lu, J and Saleh, SM and Zhang, TY and He, H and Dong, ZY and Xiao, Q and Xu, B and Zeng, C}, title = {Magnetic properties driving nitrogen removal improvement in magnetite-enhanced activated sludge: Mechanistic insights and process validation.}, journal = {Environmental research}, volume = {294}, number = {}, pages = {123870}, doi = {10.1016/j.envres.2026.123870}, pmid = {41587649}, issn = {1096-0953}, abstract = {The magnetite-enhanced activated sludge (MEAS) process offers a promising in situ strategy for upgrading wastewater treatment plants (WWTPs) to meet increasing treatment demands and stricter discharge regulations. Unlike conventional materials, magnetite possesses intrinsic magnetic properties, yet their influence on biological treatment efficiency and microbial ecology remains underexplored. This study systematically evaluated three types of magnetite particles with varying properties, focusing on their roles in denitrification, sludge settling, and microbial responses. Batch experiments under low carbon-to-nitrogen conditions (C/N = 4.4) demonstrated that magnetite with high saturation magnetization (65.9 emu/g) achieved 79.3 ± 10.2 % nitrate removal, 3.3 times higher than the control. It reduced the sludge volume index (SVI) from 84.7 to 28.4 mL/g by promoting compact floc formation through extracellular polymeric substance (EPS) protein conformational changes and enhanced microbe-particle interactions. It also increased bio-capacitance of the sludge and achieved a 77.0 % increase in electron transport system activity (ETSA). Surface analysis confirmed that magnetite served as a passive electron mediator rather than actively participating in redox cycling. Metagenomic sequencing further demonstrated the selective enrichment of denitrifying and magnetotactic bacteria and enrichment of key nitrogen metabolism genes (narG, nirK, narK, narH). Validation in an anaerobic-anoxic-aerobic (AAO) reactor treating real municipal wastewater achieved NH4[+]-N and total nitrogen removal efficiencies of 98.7 % and 73.6 %, respectively, meeting stringent discharge limits. These results identify saturation magnetization as a critical parameter for selecting or engineering magnetite materials and provide mechanistic insights and engineering guidance for deploying MEAS as an efficient, retrofit-friendly technology for WWTP upgrading.}, }
@article {pmid41586525, year = {2026}, author = {Díaz-González, F and Rojas-Villalobos, C and Issotta, F and Reyes-Impellizzeri, S and Hedrich, S and Johnson, DB and Temporetti, P and Quatrini, R}, title = {Trait-based meta-analysis of microbial guilds in the iron redox cycle.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0148825}, doi = {10.1128/msystems.01488-25}, pmid = {41586525}, issn = {2379-5077}, abstract = {UNLABELLED: Microbial iron (Fe) redox cycling underpins key biogeochemical processes, yet the functional diversity, ecological roles, and trait architectures of iron-transforming microbes remain poorly synthesized across global environments. Here, we present a systematic review and trait-based meta-analysis of 387 microbial taxa spanning 314 studies and 76 years of research, integrating phenotypic, genomic, and environmental data to define ecologically coherent microbial iron redox cycle guilds. Rather than relying on taxonomy, our framework delineates first-order functional guilds-Fe(III) reducers, Fe(II) oxidizers, and dual-capacity Fe oxidizers/reducers-and resolves second-order guilds based on trait syndromes, such as acidophily, redox flexibility, or metabolic breadth. Trait profiling revealed that iron-cycling capacities frequently transcend phylogenetic boundaries, with multiple guilds converging in chemically stratified hotspots like hot springs, hydrothermal vents, and acid mine drainages. Dual-capacity Fe oxidizers/reducers (e.g., Acidithiobacillus ferrooxidans and Metallosphaera sedula) emerged as overlooked mediators of "cryptic" iron cycling, possessing genomic repertoires capable of toggling between oxidative and reductive modes in response to redox oscillations. Hierarchical clustering and kernel density analyses of ecophysiological traits highlighted niche partitioning along key environmental filters, including pH, iron availability, salinity, and temperature. Collectively, this work introduces the Guild Exploitation Pattern as a conceptual lens for understanding iron microbiome assembly, providing a data-driven foundation for predicting microbial contributions to iron cycling under changing environmental conditions.<br><br>IMPORTANCE: Iron redox reactions shape nutrient turnover, contaminant mobility, and primary productivity, yet the microbes driving these processes are often studied in isolation. By integrating decades of data into a trait-based guild framework, we reveal the ecophysiological diversity and niche differentiation of microbial iron redox cycling taxa across environments. Our synthesis exposes major gaps, such as limited trait data for >80% of dual-capacity Fe oxidizing/reducing species and highlights the need for functional trait surveys to complement metagenomics and cultivation efforts. The guild framework presented here advances predictive microbial ecology by linking metabolic traits with environmental gradients, offering a robust foundation for incorporating iron cycling into ecosystem models and biogeochemical forecasts.}, }
@article {pmid41586521, year = {2026}, author = {Wang, N and Liu, Q and Huo, F and Zhang, S and Lv, S and Mi, T and Liu, H}, title = {Intestinal epithelial Tet2 deficiency reprograms the gut microbiota through bile acid metabolic alterations.}, journal = {mBio}, volume = {}, number = {}, pages = {e0356225}, doi = {10.1128/mbio.03562-25}, pmid = {41586521}, issn = {2150-7511}, abstract = {Epigenetic mechanisms are increasingly recognized as critical regulators of host-microbiota interactions, yet their specific roles in gut homeostasis remain elusive. Here, we demonstrate that intestinal epithelial-specific deletion of the DNA demethylase Tet2 leads to structural abnormalities, impaired barrier function, and remarkable reprogramming of the gut microbiota. Mechanistically, Tet2 deficiency downregulated the apical sodium-dependent bile acid transporter ASBT/Slc10a2, resulting in altered bile acid homeostasis with luminal accumulation of hyocholic acid (HCA). This metabolic shift created a favorable niche for the selective expansion of bile salt hydrolase (BSH)-expressing Lactobacillus species. Furthermore, we identified an age-dependent regulatory role of HCA, which promoted Lactobacillus in young mice but enriched Akkermansia in aged animals. Our findings establish an epigenetic-metabolic-microbial axis centered on Tet2-mediated bile acid regulation, providing new insights into how host epigenetic factors shape the gut microbial ecosystem in an age-sensitive manner.IMPORTANCEWhile the gut microbiota is known to influence host physiology, the molecular mechanisms by which the host epigenetically regulates microbial composition remain largely unexplored. Our work reveals that the epigenetic enzyme Tet2 in intestinal epithelial cells acts as a master regulator of gut microbial ecology by modulating bile acid metabolism. The discovery that Tet2 deletion drives hyocholic acid (HCA) accumulation-which exerts age-dependent effects on Lactobacillus and Akkermansia-provides a novel principle for understanding host-microbe interactions across the lifespan. By linking epithelial DNA demethylation to bile acid transport and microbial phenotype, we establish a previously unrecognized Tet2-ASBT-HCA pathway that expands the conceptual framework for microbiota research. These insights open new avenues for therapeutic interventions aimed at reversing microbial dysbiosis through epigenetic or metabolic modulation.}, }
@article {pmid41586352, year = {2025}, author = {Pandey, A and Dhakar, K}, title = {Extreme thermal environments: reservoirs of industrially important thermozymes.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1739143}, pmid = {41586352}, issn = {1664-302X}, abstract = {Extreme thermal environments, both natural (e.g., hot springs, fumaroles, geysers, mud pots, deep-sea hydrothermal vents) and man-made (e.g., compost heaps, sawdust, coal refuse piles), are rich sources of thermophilic microorganisms, including Bacteria and Archaea. These organisms possess unique adaptations that allow survival and metabolic activity at elevated temperatures, making them valuable sources of thermostable and thermoactive enzymes. This review synthesizes current knowledge on thermophiles, including their phylogeny, adaptation mechanisms, and cultivation strategies. We discuss the industrial applications of thermozymes, such as DNA polymerases and other thermostable enzymes, and highlight the role of genomics, systems biology, and bioinformatics in accelerating enzyme discovery. The review also addresses the astrobiological relevance of thermophiles as models for life in extreme extraterrestrial environments and emphasizes the importance of conservation and sustainable use of natural thermal habitats. Collectively, this overview provides a comprehensive perspective on the ecological, biotechnological, and fundamental research significance of thermophiles and their enzymes.}, }
@article {pmid41584899, year = {2026}, author = {Zhou, H and Li, L and Gong, Y and Liu, H and Wu, H and Bravo, A and Soberón, M and Zheng, J and Peng, D and Sun, B and Sun, M}, title = {Geographic and seasonal variation of culturable bacteria associated with the diseased silkworm (Bombyx mori).}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100529}, pmid = {41584899}, issn = {2666-5174}, abstract = {The domesticated silkworm, Bombyx mori, is critically impacted by bacterial pathogens, yet the environmental and ecological drivers of their spatiotemporal dynamics remain poorly defined. In this study, 514 bacterial strains were isolated from diseased and healthy silkworm larvae across major sericultural regions in China. Through 16S rRNA gene sequencing and multi-tier pathogenicity assays, 51 isolates were identified as potential novel insect pathogens. Fulfilling Koch's postulates via oral infection tests, the pathogenicity of nine strains belonging to the genera Raoultella, Stenotrophomonas, and Citrobacter were confirmed, while the remaining isolates are considered putative pathogens. All isolates were classified into 33 genera within the phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes, with Enterobacter, Bacillus, and Serratia being the most prevalent. Multivariate analysis indicated that geographic and climatic factors-specifically distance from the coastline and key thermal and radiative variables-collectively explained a significant though modest portion of the variance in bacterial community composition. Bacterial diversity correlated positively with cocoon yield. Guangxi presented the highest potential pathogen diversity and co-infection frequency, aligning with its intensive sericulture practices. Seasonal analyses indicated higher bacterial abundance and virulence in spring-summer compared to summer-autumn. Many isolates are taxonomically affiliated with genera containing insect gut microbiota, plant-associated bacteria, and human (opportunistic) pathogens, suggesting diverse environmental and anthropogenic origin. The detection of bacteria related to mulberry phyllosphere microbes underscore the role of host plant ecology in shaping the silkworm microbiome. These findings illuminate the ecological drivers of silkworm-associated bacterial communities and highlight the complex microbial connections within sericulture ecosystems, suggesting potential pathways relevant to a One Health perspective. Furthermore, the repository of 514 identified bacterial isolates from the model lepidopteran B. mori here provides a valuable resources for exploring novel biocontrol agents against other lepidopteran pests.}, }
@article {pmid41584691, year = {2026}, author = {Forte, L and Parabita, N and Santoro, M and Longobardi, F and Natrella, G and Quiñones, J and Ponnampalam, EN and Tomasevic, I and De Palo, P and Maggiolino, A}, title = {From rumen to milk: Dietary polyphenols in dairy cows-A critical review.}, journal = {Veterinary and animal science}, volume = {31}, number = {}, pages = {100569}, pmid = {41584691}, issn = {2451-943X}, abstract = {Polyphenols represent a large and structurally diverse family of plant secondary metabolites with bioactive properties. In ruminants, these compounds can influence rumen fermentation, microbial ecology, and nutrient metabolism, offering potential benefits for animal health, productivity, and environmental sustainability. This review synthesizes evidence on the fate of dietary polyphenols in dairy cows from ingestion to their possible secretion into milk. It outlines the main dietary sources and classes of polyphenols, their microbial biotransformations in the rumen, and subsequent host metabolism involving absorption, conjugation, and systemic circulation. Particular attention is given to the mechanisms of mammary uptake and secretion, where most compounds appear as conjugated metabolites such as glucuronides, sulfates, and urolithins rather than parent forms. Although the transfer efficiency from feed to milk is typically low, consistent detection of isoflavone derivatives, phenyl-γ-valerolactones, urolithins, and hippuric acid demonstrates the feasibility of diet-to-milk modulation. Factors affecting bioavailability and transfer include polyphenol structure, dietary matrix, dose, rumen microbiota composition, animal physiology, and feed processing. Advances in high-resolution analytical techniques have improved the characterization of these low-abundance metabolites, yet large variability among studies persists. In vivo studies indicate that polyphenol-derived metabolites in bovine milk occur at low ng/mL to low µg/mL levels, with compounds such as equol, enterolactone, urolithins, phenyl-γ-valerolactones and phenolic acids typically detected in the sub-micromolar range. Overall, dietary polyphenols offer promising opportunities to improve ruminant health and produce milk with enhanced functional quality, but quantitative and mechanistic research is still required to optimize feeding strategies and understand their contribution to milk bioactivity.}, }
@article {pmid41584621, year = {2026}, author = {Garcia-Rodriguez, AF and Moreno-Racero, FJ and Álvarez, R and Colmenero-Flores, JM and Knicker, H and Rosales, MA}, title = {Biochar enhances nitrogen use efficiency in lettuce by promoting its metabolic assimilation.}, journal = {Plant and soil}, volume = {518}, number = {1}, pages = {299-317}, pmid = {41584621}, issn = {0032-079X}, abstract = {BACKGROUND AND AIMS: Peat replacement with biochar (BC) offers a sustainable strategy in horticultural substrates but its effects on plant nitrogen (N) metabolism and N use efficiency (NUE) remain unclear. This study tested whether vineyard-pruning-derived BC can boost NUE and metabolic activity in lettuce, providing a pathway toward more productive and sustainable horticulture.<br><br>METHODS: Plant substrates (BC, peat and vermiculite) were prepared in the following proportions (v:v:v): B0 (0:70:30), B15 (15:55:30) and B30 (30:40:30) for growing lettuce (Lactuca sativa L. var. Batavia) under greenhouse conditions for 31&#xa0;days. We assessed plant growth and physiological traits, quantified N species and calculated NUE parameters and the activities of key N assimilation enzymes.<br><br>RESULTS: B30 plants produced 44.2% more biomass and 23.2% larger leaf area than B0, resulting in lower specific leaf area and greater succulence. BC addition decreased available NO&#x2083;&#x207b; and NH&#x2084;&#x207a; in substrate and roots without causing any plant stress symptoms, as chlorophyll content and PSII efficiency remained stable. B30 increased N uptake flux, N utilization efficiency, partial N balance, and N productivity by 31.8%, 34.8%, 27.8%, and 13.8%, respectively, relative to B0, coinciding with enhanced N-assimilation enzymatic activity. Despite lower total N in roots and shoots, protein accumulation increased, indicating more efficient N conversion into organic compounds.<br><br>CONCLUSION: These findings demonstrate the potential of BC-based substrates (especially 30% BC) to enhance lettuce productivity by improving NUE through the stimulation of N assimilation pathway, offering a promising strategy to optimize N-fertilizer needs to support more sustainable agriculture and soil management practices.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11104-025-07997-0.}, }
@article {pmid41582111, year = {2026}, author = {Afonso, AC and Botting, J and Simões, M and Simões, L and Liu, J and Saavedra, MJ}, title = {Ultrastructure Analysis by Cryo-Electron Tomography Revealed Mesosomes in the Gram-negative Delftia Acidovorans.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02698-2}, pmid = {41582111}, issn = {1432-184X}, abstract = {Delftia acidovorans, a Gram-negative bacterium commonly found in diverse environments, can occasionally cause infections in immunocompromised individuals. Despite its environmental prevalence and clinical relevance, there is a notable lack of studies on the cellular ultrastructure of D. acidovorans. Characterizing this aspect is essential for understanding the bacterium aggregation behavior, which significantly influences biofilm formation, environmental adaptability, and potential pathogenicity in clinical contexts. This study employs cryo-electron tomography to investigate the cellular ultrastructure of Delftia acidovorans. Our observations of D. acidovorans revealed a supercoiling pattern in flagellar filaments and diverse outer membrane projections. Our major finding was the observation of cytoplasmic membrane invaginations resembling mesosomes seen in Gram-positive bacteria, offering new insights into the cellular architecture and potential functions of these structures in Gram-negative bacteria. Together, these ultrastructural insights reveal adaptations potentially linked to environmental persistence and interspecies aggregation.}, }
@article {pmid41579275, year = {2026}, author = {Sasaki, K and Emoto, S and Yokoyama, Y and Ishihara, S}, title = {Circulating tumor DNA methylation and gut microbiota in colorectal cancer: diagnostic, prognostic, and therapeutic implications.}, journal = {International journal of clinical oncology}, volume = {}, number = {}, pages = {}, pmid = {41579275}, issn = {1437-7772}, abstract = {Colorectal cancer remains one of the leading causes of cancer-related mortality worldwide, and early detection is essential for improving outcomes. Advances in liquid biopsy technologies and microbiota research have shed new light on diagnostic and therapeutic strategies for colorectal cancer. Notably, circulating tumor DNA methylation has emerged as a sensitive and specific biomarker for early detection, recurrence surveillance, and treatment monitoring. Recent progress in methylation-based assays, including stool- and plasma-derived approaches, highlights their potential clinical utility; however, challenges remain in detecting minimal residual disease at the earliest stages. Parallel to these developments, the gut microbiota has been recognized as a critical modulator of colorectal carcinogenesis and treatment response. Specific bacterial species, such as Fusobacterium nucleatum, polyketide synthase-positive Escherichia coli, and enterotoxigenic Bacteroides fragilis, have been implicated in tumor initiation and progression through epigenetic reprogramming, including aberrant DNA methylation. Microbial metabolites, particularly short-chain fatty acids such as butyrate, influence DNA methyltransferase activity and histone modifications, linking microbial ecology to the host epigenome. Microbiota composition also affects responses to chemotherapy, radiotherapy, and immunotherapy, underscoring its potential as a predictive biomarker and therapeutic target. Integrating circulating tumor DNA methylation profiling with microbiota analysis provides a promising strategy for personalized colorectal cancer management, combining early detection with treatment outcome prediction. This review summarizes the current evidence and future directions at the interface of DNA methylation and the gut microbiota, emphasizing their synergistic role as composite biomarkers in precision oncology.}, }
@article {pmid41576057, year = {2026}, author = {Lagneaux, P and Widjaja, N and Lagneaux, B and Nguyen, TKC and Licandro, H and Winckler, P and Waché, Y}, title = {Optical photothermal infrared (OPTIR) spectroscopy assisted by machine learning for lactic acid bacteria identification at strain level.}, journal = {The Analyst}, volume = {}, number = {}, pages = {}, doi = {10.1039/d5an01093d}, pmid = {41576057}, issn = {1364-5528}, abstract = {Lactic acid bacteria (LAB) are widely used in food, health, and biotechnology sectors, where accurate strain level identification is critical. Conventional methods, such as 16S rRNA sequencing, PCR-based fingerprinting (RAPD, AFLP), and MALDI-TOF mass spectrometry are powerful tools to identify bacteria at species level but often fail to resolve closely related strains due to limited taxonomic resolution, protocol sensitivity, or database dependence. In this study, we evaluated the capacity of Optical photothermal infrared (OPTIR) spectroscopy, a single-cell vibrational imaging technique, combined with supervised neural networks, to classify LAB at both species and strain levels. A total of 13 strains were analysed, including five Lactiplantibacillus plantarum, one Lactiplantibacillus pentosus, one Limosilactobacillus fermentum, three Lacticaseibacillus casei/paracasei, and three Streptococcus thermophilus, covering both intra- and inter-species diversity. Spectral data from LAB were acquired using a mIRage LS OPTIR system, preprocessed, and used to train a fully connected neural network for each level. The models achieved macro F1-scores of 97% for species level and 91% for strain level classification. These results demonstrate the potential of OPTIR, when integrated with machine learning, as a robust tool for high-resolution bacterial classification, with promising applications in microbiological quality control, probiotic selection, and microbial ecology.}, }
@article {pmid41575584, year = {2026}, author = {Ma, Y and Xu, Q and Sun, F and Wang, X and Zhou, W and Yue, M and Gao, L and Li, W}, title = {Potassium-Solubilizing Bacteria Mediate Light-Potassium Synergy to Enable Native Pueraria lobata to Outcompete Invasive Mikania micrantha.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02695-5}, pmid = {41575584}, issn = {1432-184X}, support = {2022A1515011169//National Natural Science Foundation of China-Guangdong Joint Fund/ ; 2023S017084//Guangdong Province Science and Technology Innovation Strategic Special Project/ ; 2022s037//the Maoming City Science and Technology Plan Project/ ; 32172430//National Natural Science Foundation of China/ ; }, abstract = {The invasive vine Mikania micrantha H. B. K. poses severe threats to biodiversity and ecosystem stability in tropical and subtropical regions, calling for sustainable ecological approaches. This study explores how the native legume Pueraria lobata var. thomsonii Benth displaces M. micrantha in the field, with a focus on the synergistic roles of light capture advantage and rhizosphere potassium (K) dynamics driven by specialized bacteria. In competitive ecotones, P. lobata demonstrated superior growth and photosynthetic performance relative to M. micrantha. Its main stem length was 1.31 times greater, while net photosynthetic rate, stomatal conductance, and chlorophyll content were 80%, 110.7%, and 21.4% higher, respectively. Soils associated with P. lobata contained significantly higher available K, correlated with enhanced enzyme activities, indicating a "microbe-enzyme-K" activation cascade. P. lobata specifically enriched efficient potassium‑solubilizing bacteria (KSB), such as Pseudomonas and Acinetobacter. Isolated KSB strains exhibited K‑solubilizing and plant‑growth‑promoting capacities and increased the competitive balance index of P. lobata in inoculation assays. Partial least‑squares discriminant analysis confirmed that KSB‑mediated K mobilization boosted stem elongation primarily by improving photosynthetic potassium use efficiency (PKUE), forming a reinforcing "light-K-microbe" loop that drives competitive displacement. This work establishes a "microbe‑mediated invasion suppression" framework, demonstrating how a native plant can couple superior light‑use efficiency with a specialized rhizosphere microbiome to outcompete an invasive species. We propose that managing potassium‑solubilizing microbiomes offers a sustainable strategy for ecological restoration in K‑limited ecosystems.}, }
@article {pmid41574941, year = {2026}, author = {Lhoste, E and David, J and Ponsin, V and Maikel, R and Lazar, CS}, title = {Seasons and vertical dynamics influence community composition in a flooded and abandoned mica mine.}, journal = {FEMS microbiology ecology}, volume = {102}, number = {2}, pages = {}, pmid = {41574941}, issn = {1574-6941}, abstract = {Artificial lakes formed from past mining activities represent unique but underexplored ecosystems that support diverse microbial communities. This study examined how seasonal variation and depth influence bacterial, archaeal, and micro-eukaryotic assemblages in the stratified water column of the Blackburn Mine (Outaouais, Quebec, Canada). Water and biofilm samples were collected by technical divers from the surface to 52 m during spring, summer, and autumn of 2021-2022, and analyzed by 16S/18S rRNA gene sequencing. Seasonal changes had little effect on physicochemical parameters but strongly shaped microbial community composition, together with depth. Archaeal taxa displayed greater stability across depths compared to bacteria and eukaryotes. Oxygen profiles defined three ecological zones: an oxic layer dominated by Actinobacteria and the methanogen Methanosarcina; a transition zone enriched in Chlorobium and methanogens such as Methanospirillum and Methanosaeta; and an anoxic layer containing sulfur-reducing (Desulfomonile, Desulfobacca), sulfur-oxidizing (Sulfuricurvum), and methane-cycling archaea. Eukaryotic communities included algae, particularly Chrysophyceae, and diverse protists. These findings suggest that microbial communities in the mine are integral to sulfur and carbon cycling, emphasizing the ecological significance of such stratified, mining-associated aquatic systems. The Blackburn mine provides valuable insight into how anthropogenic legacies shape microbial diversity and ecosystem functioning in artificial aquatic environments.}, }
@article {pmid41571998, year = {2026}, author = {Cheng, C and Bennett, BD and Savalia, P and Asrari, H and Biel, C and Evans, KA and Tang, R and Thrash, JC}, title = {Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {41571998}, issn = {2058-5276}, support = {Investigator in Aquatic Microbial Ecology Award//Simons Foundation/ ; Early Career Investigator in Marine Microbial Ecology and Evolution Award//Simons Foundation/ ; }, abstract = {Genome streamlining is hypothesized to occur in bacteria as an adaptation to resource-limited environments but can result in gene losses affecting fundamental aspects of cellular physiology. The most abundant marine microorganisms, SAR11 (order Pelagibacterales), exhibit canonical genome streamlining, but the consequences of this genotype on core cellular processes such as cell division remain unexplored. Here, analysis of 470 SAR11 genomes revealed widespread absence of key cell cycle control genes. Growth experiments demonstrated that although SAR11 bacteria maintain a normal cell cycle under oligotrophic conditions, they exhibit growth inhibition and aneuploidy when exposed to nutrient enrichment, carbon source shifts or temperature stress. Detailed growth measurements and antibiotic inhibition experiments showed that these phenotypes resulted from cell division disruption with continuing DNA replication, leading to heterogeneous subpopulations of normal and polyploid cells. This vulnerability raises questions about microbial genome evolution and the evolutionary trade-offs between adaptation to stable nutrient-limited conditions and physiological resilience.}, }
@article {pmid41571114, year = {2026}, author = {Han, H and Wang, S and Zhou, L and Li, S and Huang, J and Peng, X}, title = {Insights into impact of tire additives on activated sludge systems: Treatment performance, extracellular polymeric substances, and microbial community.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134049}, doi = {10.1016/j.biortech.2026.134049}, pmid = {41571114}, issn = {1873-2976}, abstract = {This study systematically investigated the impacts of seven common tire additives (TAs) and their derivatives on the performance and microbial ecology of an activated sludge system exposed to environmental concentrations (0.2-20.0 μg/L) over 160 days. While most individual TAs showed minimal effects, the mixture of TAs (MIX) and 2-((4-Methylpentan-2-yl)amino)-5-(phenylamino)cyclohexa-2,5-diene-1,4-dione (6PPD-Q) significantly inhibited nitrogen removal efficiency. At 20.0 μg/L, the abundances of key nitrification and denitrification genes (amoA, nirK, nirS, nosZ) were markedly suppressed, leading to reductions in NH4[+]-N (12-14%) and total nitrogen (18-23%) removal efficiencies. The impairment was associated with elevated oxidative stress level, as indicated by a sharp increase in reactive oxygen species (0.9-1.1 fold) and lactate dehydrogenase (1.5-2.1 fold) release, alongside suppressed adenosine triphosphate (ATP) synthesis. Concurrently, sludge settleability deteriorated and mixed liquor volatile suspended solids (MLVSS) decreased, which correlated with reduced sludge hydrophobicity and enhanced hydrogen bond intensity (3435 cm[-1]). Microbial community restructuring was observed, with tolerant genera (e.g., Comamonadaceae, Rhodobacteraceae) increasing, while key nitrogen-removing genera (e.g., Nitrosomonas, Thauera) decreased. Three-dimensional fluorescence spectroscopy analysis revealed a decline in tryptophan and tyrosine like proteins in tightly bound extracellular polymeric substances. Molecular docking demonstrated that 6PPD-Q exhibited the strongest binding affinity to tryptophan and tyrosine synthases, suggesting a high potential for enzymatic interference even at low concentrations. This study demonstrated that MIX and 6PPD-Q, at environmental concentrations, significantly affect activated sludge systems and investigated the mechanisms involved, thereby providing important evidence for the ecological risk assessment of such pollutants during wastewater treatment.}, }
@article {pmid41570927, year = {2026}, author = {Magalhães, AP and Jorge, P and Neiva, J and Sousa, AM and Cerca, N and Pereira, MO}, title = {Contribution of viable but non culturable cells and small colony variants in antibiotic insusceptibility and therapeutic failure against S. aureus and P. aeruginosa biofilm co-infections.}, journal = {Microbial pathogenesis}, volume = {212}, number = {}, pages = {108312}, doi = {10.1016/j.micpath.2026.108312}, pmid = {41570927}, issn = {1096-1208}, abstract = {P. aeruginosa and S. aureus are often co-isolated from biofilm-associated infections, such as those afflicting cystic fibrosis (CF) patients. Biofilms, along with the interspecies interactions, play a significant role in fostering antibiotic insusceptibility, contributing to infection chronicity. Previously, we showed that S. aureus adopts a viable but non-culturable (VBNC) state in biofilms with P. aeruginosa. Here, we aimed to gain insight into the impact of VBNC and phenomena such as phenotypic switching on antimicrobial treatment and vice-versa. Single- and dual-species biofilms of two isolates from each species were characterised in terms of viability, culturability, clonal diversification, and pathogenic potential, upon treatment with ciprofloxacin and vancomycin. Data show that S. aureus became less susceptible to antibiotics in its VBNC state induced by P. aeruginosa and by the treatments. P. aeruginosa's susceptibility to ciprofloxacin diminished in dual-species biofilms, suggesting mutual benefits. Following treatment, S. aureus persisted as VBNC in the dual-species biofilm and its tolerance to ciprofloxacin endured after planktonic regrowth. P. aeruginosa triggered S. aureus's small colony variants (SCV), but P. aeruginosa's rugose SCV probably explains S. aureus's protection due to enhanced biofilm formation. This work sheds light on P. aeruginosa and S. aureus' co-increased tolerance to antibiotics, with cooperative interactions, phenotypic diversification, and VBNC underpinning this and the persistence of S. aureus within P. aeruginosa biofilms. This work is the first relating S. aureus's decreased susceptibility in dual-species biofilms to its VBNC state. Findings highlight the importance of microbial ecology, viability and colony morphotyping studies when designing treatments for multispecies infections.}, }
@article {pmid41568955, year = {2026}, author = {Baborski, A and Rohland, O and Wuenschmann, T and Bauer, M and Allen, RJ and Busch, A}, title = {Biofilm-derived bile duct microbiota in liver transplantation: high-quality genomes of Klebsiella pneumoniae, Enterococcus faecalis, and Enterococcus faecium.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0088625}, doi = {10.1128/mra.00886-25}, pmid = {41568955}, issn = {2576-098X}, abstract = {We present draft genomes of Klebsiella pneumoniae (K. pneumoniae), Enterococcus faecalis (E. faecalis), and Enterococcus faecium (E. faecium) isolated from a bilioenteric catheter after liver transplantation. Genome sizes were 5.58 Mb, 2.95 Mb, and 2.78 Mb, with G+C contents of 57.25%, 37.6%, and 37.99%, respectively, highlighting biofilm-associated bile duct colonizers.}, }
@article {pmid41568039, year = {2025}, author = {Dong, W and Chen, S and Hu, Y}, title = {Editorial: Diversity, function, and application of microbes in the fermentation or production of traditional food.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1751159}, doi = {10.3389/fmicb.2025.1751159}, pmid = {41568039}, issn = {1664-302X}, }
@article {pmid41567175, year = {2026}, author = {Hussain, N and Ramadan, A and Al Haddad, AHI and Alfahl, Z}, title = {A Review of Emerging Biomarkers Connecting Diabetes and Ischemic Stroke: Implications for Early Detection and Risk Stratification.}, journal = {Journal of diabetes research}, volume = {2026}, number = {}, pages = {2719491}, pmid = {41567175}, issn = {2314-6753}, mesh = {Humans ; *Biomarkers/blood ; *Ischemic Stroke/diagnosis/blood/genetics ; Early Diagnosis ; Risk Assessment ; Risk Factors ; *Diabetes Mellitus/blood/diagnosis/genetics ; }, abstract = {Diabetes substantially increases the risk of ischemic stroke through complex metabolic, inflammatory, and vascular mechanisms, yet early identification of high-risk individuals remains challenging. This narrative review synthesizes emerging circulating and genomic biomarkers that illuminate the pathways linking diabetes and ischemic stroke and evaluates their potential for early detection and precise risk stratification. Systematic searches of PubMed, Scopus, and Web of Science identified 141 relevant studies examining biomarkers, genetic and epigenetic factors, or risk prediction models in adults with diabetes. Evidence highlights several biomarker domains. Inflammatory markers such as high-sensitivity C-reactive protein, interleukin-6, and tumor necrosis factor-α indicate immune activation driving atherogenesis and plaque instability. Endothelial markers, including endothelin-1, soluble vascular cell adhesion molecule-1, and asymmetric dimethylarginine, reflect endothelial dysfunction and a prothrombotic state. Metabolic indicators, notably glycated hemoglobin, adipokines, and lipoprotein(a), capture cumulative glycemic burden, adipose signaling, and inherited atherothrombotic risk. Genetic and epigenetic measures, including polygenic risk scores, microRNAs, long noncoding RNAs, and DNA methylation, quantify inherited susceptibility and molecular imprints of the diabetic environment. Renal markers such as albuminuria and reduced eGFR reflect microvascular injury and consistently associate with stroke risk. Multimarker panels and multi-omics integration using machine learning approaches show promise for improving predictive accuracy, though standardization, external validation, and demonstration of clinical utility are needed. Integrating these biomarkers with established clinical risk factors could transform stroke prevention in diabetes from reactive to proactive, enabling personalized, mechanism-informed strategies for early detection and risk stratification.}, }
@article {pmid41566387, year = {2026}, author = {Xu, M and Chen, S and Pei, H and Hu, L and Zhang, Y}, title = {Engineering bacteriophages for gut health: precision antimicrobials and beyond.}, journal = {Journal of nanobiotechnology}, volume = {24}, number = {1}, pages = {62}, pmid = {41566387}, issn = {1477-3155}, support = {12275192//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Bacteriophages/genetics ; Phage Therapy/methods ; *Gastrointestinal Microbiome/drug effects ; Animals ; Precision Medicine ; *Anti-Infective Agents/pharmacology ; Inflammatory Bowel Diseases/therapy/microbiology ; Colorectal Neoplasms/therapy/microbiology ; }, abstract = {Engineered bacteriophages are emerging as a promising class of precision antimicrobials at a time when gastrointestinal diseases are increasingly linked to microbial dysbiosis, antibiotic resistance, and disruptions in host-microbe interactions. Conventional antibiotics often provide limited benefit in these settings because they lack selectivity and fail to restore microbial ecology. Advances in synthetic biology and nanotechnology have made it possible to redesign phages with enhanced specificity, expanded functionality, and improved stability, positioning them as versatile tools for microbiota-centered therapies. This review summarizes the major engineering approaches, and examines their applications in inflammatory bowel disease (IBD), colorectal cancer (CRC), and infectious enteritis. Key mechanistic insights into pathogen targeting, immune modulation, and barrier protection are highlighted. Remaining challenges, such as ensuring long-term stability, avoiding resistance development, and enabling scalable manufacturing, are discussed together with emerging interdisciplinary strategies that may advance the clinical translation of personalized phage therapies.}, }
@article {pmid41565754, year = {2026}, author = {Solís-Marín, FA and Vergara-Ovando, C and Rojas-Oropeza, M and Calderón-Gutiérrez, F and Medina-Tanco, G and Cabirol, N}, title = {Asterinides sp. an endemic stygobitic seastar from an anchialine cave and its interactions among prokaryotic communities.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-36065-5}, pmid = {41565754}, issn = {2045-2322}, support = {PAPIIT-IN207021//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; PAPIIT-IN207021//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; Posgraduate grant//Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; }, abstract = {Anchialine caves house a vast variety of organisms that support complex ecological relationships among themselves and their environment. The following study was made in the anchialine karst cave El Aerolito, found on Cozumel Island, Quintana Roo, Mexico. It explores the relationship between wall microbial mats and the diet of Asterinides sp., an endemic stygobitic seastar. Wall microbial mats inside the cave were sampled and the stomach microbiome of Asterinides sp. was obtained through regurgitation. Asterinides sp. sampling was made through the Catcher Collection Chamber (CCC), an innovative technology for the exploration of these ecosystems. The obtained results suggest that microbial mats are part of the diet of Asterinides sp. The following results highlight the potential relevance of the microbial communities inside the trophic chain present in El Aerolito. Additionally, the methodology presented here provides a useful framework for future ecological research in El Aerolito cave.}, }
@article {pmid41563471, year = {2026}, author = {Luo, W and Liu, P and Qiu, Y and Li, M and Huang, Y}, title = {Diversity and Functional Analysis of Epiphytic and Endophytic Bacteria in Three Different Parts of Brasenia Schreberi.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02688-w}, pmid = {41563471}, issn = {1432-184X}, support = {24XJQN04//Nanchang Normal University 2024 Youth Science and Technology Talent Training Project/ ; NSBSJJ2023003//Nanchang Normal University Doctoral Research Start-up Fund/ ; 24FZZX13//Nanchang Normal University Funds for Improvement and Research/ ; }, }
@article {pmid41563055, year = {2026}, author = {Sadiq, S and Xue, P and Tang, Y and Du, M and Van Brussel, K and McBratney, AB and Holmes, EC and Minasny, B}, title = {Limited effect of short- to mid-term storage conditions on an Australian farmland soil RNA virome.}, journal = {Journal of virology}, volume = {}, number = {}, pages = {e0145925}, doi = {10.1128/jvi.01459-25}, pmid = {41563055}, issn = {1098-5514}, abstract = {Soils represent one of the largest and most diverse reservoirs of microbial life on Earth, yet their associated RNA viruses remain underexplored compared to animal and aquatic systems. Viral discovery in soils has been further limited by technical hurdles, particularly difficulties in obtaining sufficient yields of high-quality RNA for sequencing. To address this, we evaluated a range of storage and preservation strategies, including the use of commercial preservative solutions and ultra-cold snap-freezing, followed by standardized RNA extraction, sequencing, and virus discovery pipelines. This work aimed to establish minimum sample storage requirements that maintain RNA integrity, generate sufficient RNA sequencing data, and subsequently enable reliable soil virome characterization. While no preservative solution proved effective, "neat" soil samples were stable at 2°C-8°C and -30°C for at least 2 weeks, and at -80°C for at least 3 months, with no measurable reduction in RNA quality, sequencing data, or viral abundance and diversity. From 32 resulting libraries, we identified 1,475 putative novel RNA viruses, with the majority belonging to the microbe-associated phylum Lenarviricota. Several novel viruses formed divergent clusters with other environmentally derived sequences distantly related to traditionally animal-associated families, such as the Astroviridae and Picornaviridae. Furthermore, unique clusters within the Picobirnaviridae, Alsuvirucetes, Ghabrivirales, and Amabiliviricetes comprised exclusively Australian viruses, suggesting instances of region-specific evolution. Together, these findings highlight soils as rich reservoirs of RNA viral diversity and provide practical minimum standards for storage, expanding opportunities to investigate the ecological and evolutionary roles of RNA viruses in terrestrial systems.IMPORTANCERNA viruses are the most abundant and diverse biological entities on Earth and are likely present in all other organisms and ecosystems, including soil-dwelling invertebrates, microbes, and plants. Despite this, their diversity and role in soil systems remain largely unknown. Methodological challenges in preserving and extracting sufficient quantities of RNA from soils have hindered the study of these communities. Here, we identified 1,475 previously undescribed RNA viruses in Australian soils while systematically testing different preservation strategies. The significance of our research lies in the demonstration that snap-freezing soil is a viable and robust storage strategy for at least 3 months, while also highlighting the extraordinary scale of viral diversity present in terrestrial environments. This work establishes a foundation for reliable exploration of terrestrial RNA viruses, improving the accessibility of more remote environmental viromes and enabling future efforts to integrate them into broader models of microbial ecology and ecosystem function.}, }
@article {pmid41561919, year = {2026}, author = {Phyu, KK and Zhi, S and Liang, J and Yang, Z and Zhao, R and Liu, J and Cao, Y and Wang, H and Zhang, K}, title = {Dataset on microbial community structure in response to microalgal cultivation in dairy wastewater.}, journal = {Data in brief}, volume = {64}, number = {}, pages = {112407}, pmid = {41561919}, issn = {2352-3409}, abstract = {This data article describes a comprehensive dataset investigating the dynamics between microalgae, bacteria, and pollutant removal in dairy wastewater treatment. Data was collected from a 12-day laboratory-scale experiment employing three distinct cultivation systems: monoculture, co-culture, and sequential culture of four algal/cyanobacterial strains (Chlorella sorokiniana, Euglena gracilis, Synechocystis sp., and Desertifilum tharense). The generated dataset includes high-frequency measurements of water quality parameters (COD, NH4 [+]-N, TN, TP), algal physiological data (biomass production, total chlorophyll, biochemical compositions like proteins, lipids, and polysaccharides), and 16S rRNA gene sequencing data of the associated bacterial communities, which were fractionated into free-living and tightly bound phycosphere populations. The reuse potential of this data is significant. It provides a detailed profile of microbial community assembly driven by different cultivation strategies and environmental factors, offering a benchmark for future ecological studies in engineered systems. Researchers in the fields of wastewater biotechnology, microbial ecology, and synthetic ecology can reuse this data to validate microbial interaction models, optimize consortia design for bioremediation, and inform life-cycle assessments of algal-based treatment processes. The dataset generated in this study is publicly available in the NCBI BioProject repository under the accession number [PRJNA1265442].}, }
@article {pmid41558125, year = {2026}, author = {Armstrong, R}, title = {Biocatalytic surfaces in architecture.}, journal = {Current opinion in biotechnology}, volume = {97}, number = {}, pages = {103435}, doi = {10.1016/j.copbio.2025.103435}, pmid = {41558125}, issn = {1879-0429}, abstract = {This review explores the reconceptualisation of microbial colonisation on buildings: from a detrimental process (biofouling) to a source of beneficial, programmable biocatalysis. Strategies for embedding microbial and fungal communities into architectural materials to perform functions such as bioremediation, biomineralisation, and energy generation are explored. The analysis includes the multiscalar design of bioreceptive substrates, engineered living paints, mycelium composites, and probiotic surfaces, which transform passive structures into metabolically active interfaces. These approaches are regarded as Engineered Eco-Ornamentation, where surface design intentionally supports microbial ecology and urban metabolism. The integration of these living systems with computational modelling and digital fabrication to create adaptive building systems is considered. Key challenges include scaling biological processes for architectural application, ensuring long-term material durability, and aligning metabolic activity with practical construction constraints. Addressing these challenges positions functionally designed biocatalytic surfaces as a foundational research field for more regenerative and ecologically integrated architecture.}, }
@article {pmid41557960, year = {2026}, author = {Machushynets, NV and Terlouw, BR and Zhang, L and Du, C and Al Ayed, K and Schill, J and Trebosc, V and Elsayed, SS and Pieren, M and Liles, MR and Medema, MH and Martin, NI and van Wezel, GP}, title = {Diversification of Tridecaptin Chemical Space via a Chimeric Biosynthetic Pathway in Paenibacillus.}, journal = {Journal of natural products}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jnatprod.5c01298}, pmid = {41557960}, issn = {1520-6025}, abstract = {Paenibacillus species produce a wide array of bioactive nonribosomal peptides (NRPs). The structural diversity of NRPs is shaped by various diversification strategies that support bacterial ecological adaptation and create opportunities for new antibiotic discovery. Here, we show that chimeric biosynthesis occurs within the family of tridecaptin antibiotics. Genome mining revealed that 15 Paenibacillus strains harbored both a full tridecaptin BGC and a stand-alone tridecaptin-like NRPS predicted to encode a truncated decamer. The encoded NRPS domain architectures suggested the capability of these strains to produce multiple tridecaptin variants through collaborative action between this tridecaptin-like NRPS and a second NRPS homologous with TriE encoded within the complete tridecaptin BGC. Indeed, Paenibacillus sp. JJ-1683 produced both tridecaptin A5 and tridecaptin B1, while deletion of triE in the canonical BGC prevented the biosynthesis of all tridecaptins. This provides strong evidence for the existence of chimeric biosynthesis of lipopeptide antibiotics. Bioactivity testing revealed that the synthetic analogue of tridecaptin A5, Oct-TriA5, has unusual broad-spectrum activity against Gram-positive and Gram-negative ESKAPE pathogens, while Oct-TriB1 displays moderate activity against Gram-negative strains and is not active against Gram-positive bacteria. We hypothesize that chimeric biosynthesis is a strategy that enables bacteria to produce compounds with distinct chemistry and bioactivity profiles.}, }
@article {pmid41557197, year = {2026}, author = {Dos Santos, JFM and Mello, IS and da Cruz, ILS and Soares, MA}, title = {Non-Saccharomyces yeasts contribute to longevity, mitigated protein toxicity, and protection against abiotic stress in Caenorhabditis elegans.}, journal = {Archives of microbiology}, volume = {208}, number = {3}, pages = {128}, pmid = {41557197}, issn = {1432-072X}, support = {445388/2024-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Animals ; *Caenorhabditis elegans/microbiology/physiology/genetics ; *Longevity ; Caenorhabditis elegans Proteins/genetics/metabolism ; Oxidative Stress ; Probiotics ; *Stress, Physiological ; *Cryptococcus/physiology/isolation &amp; purification ; Amyloid beta-Peptides/toxicity ; *Yeasts/physiology/isolation &amp; purification ; Saccharomyces/physiology/isolation &amp; purification ; DNA-Binding Proteins ; Receptor, Insulin ; Transcription Factors ; }, abstract = {The search for probiotic microorganisms that can be applied beyond gut health has advanced into areas that seek to promote longevity and to prevent neurodegenerative diseases. In this study, we have investigated non-Saccharomyces strains isolated from the Amazon, Cerrado, and Pantanal biomes and evaluated how they affect Caenorhabditis elegans. During our initial screening, based on increased body size and population, we selected eight yeast strains and characterized their cells. Then, we selected three of these strains for in vivo testing. Cryptococcus sp._T038 and Cryptococcus sp._T248 prolonged longevity and reduced the effects of thermal and oxidative stress in C. elegans. Hanseniaspora opuntiae_W164 and Saccharomyces boulardii_SB delayed beta-amyloid-induced paralysis in C. elegans CL4176. The antioxidant genes of the DAF-2/SKN-1 pathway were activated by Cryptococcus_T038 and _T248 and H. opuntiae_W164 in C. elegans strain LD1171 (GCS-1p::GFP) and by Cryptococcus_T038, H. opuntiae_W164, and S. boulardii_SB in C. elegans strain CF1553 (SOD-3p::GFP). These data reinforce that wild yeasts are potential functional probiotics.}, }
@article {pmid41554215, year = {2026}, author = {Mekureyaw, MF and Pandey, C and Sorty, AM and Hennessy, RC and Nicolaisen, MH and Liu, F and Nybroe, O and Roitsch, T}, title = {Biofilm formation by Pseudomonas putida KT2440 contributes to improve tomato drought stress resilience and priming for enhanced gene regulation.}, journal = {Journal of plant physiology}, volume = {317}, number = {}, pages = {154704}, doi = {10.1016/j.jplph.2026.154704}, pmid = {41554215}, issn = {1618-1328}, abstract = {Pseudomonas putida KT2440 is a plant growth-promoting rhizobacterium (PGPR), known to enhance tolerance to pathogen infection, but its role in drought stress mitigation remains largely unexplored. This study aimed to assess whether inoculation with KT2440 improves tomato tolerance to drought. Inoculation with the KT2440 wild type (WT) significantly improved ecophysiological drought stress responses by increasing leaf water potential and photosynthetic rate. It also resulted in an impact on the holobiont cell physiology through modulation of the activity signature of key enzymes of carbohydrate (e.g., PGM and vacInv) and antioxidant (e.g., GR, MDHAR, and cwPOX) metabolism under drought conditions. To functionally assess the role of biofilm formation in drought response, biofilm-deficient mutants KT2440 Alg, with only one gene cluster for the exopolysaccharide alginate deleted, and KT2440 Q, with four exopolysaccharide gene clusters (alg, bcs, pea and peb) deleted, were used. Inoculation with these two mutants led to reduced drought resilience, with partial or complete loss of protective effects in the Alg and Q mutants, respectively. This was reflected in lowered leaf water potential, photosynthetic rate, and reduced antioxidant and carbohydrate metabolism enzyme activities compared to inoculation with the corresponding wild type. Global RNA sequencing revealed that under drought conditions 360 % more genes were differentially regulated in the presence of KT2440 WT compared to the mock inoculated control, whereas this value decreased again to only 140 % more differentially regulated genes after recovery from the drought stress. Thus, KT2440 specifically primes the plant for a much more pronounced transcriptional response only during the impact of drought, thus providing resilience protection on demand. This priming for enhanced abiotic stress responsiveness was partially dependent on the ability to form biofilm. Both under well-watered and drought stress the number of differentially regulated genes was strongly reduced in plants inoculated with KT2440 Q compared to WT. Gene ontology and expression analyses showed significant upregulation of pathways involved in photosynthesis, phytohormone signaling, antioxidant metabolism, and drought resilience in KT2440-inoculated plants. Although KT2440 WT showed higher biofilm formation compared to the Alg and Q mutants, the strains did not differ in their ability for root colonization. These findings provide novel insights into the contribution of biofilm formation to PGPR-mediated drought tolerance and protection on demand via priming for enhanced transcriptional regulation under stress, supporting the potential of KT2440 for environmentally friendly mitigating of drought stress responses in crops.}, }
@article {pmid41553662, year = {2026}, author = {Sarkar, B and Bag, S and Mandal, A and Saha, D and Saha, S and Bhaduri, R and Chatterjee, S}, title = {Cresol Derivatives from Bacillus subtilis as Natural Oviposition Modulator of Culex quinquefasciatus: A Molecular Docking Approach.}, journal = {Applied biochemistry and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {41553662}, issn = {1559-0291}, abstract = {Mosquitoes rely heavily on olfactory cues for locating suitable oviposition sites, with microbial communities in aquatic habitats playing a crucial role in producing volatile organic compounds (VOCs) that influence mosquito behaviour. In this study, we isolated Bacillus subtilis DHB13 from the breeding habitat of Culex quinquefasciatus, a major vector of several human diseases. The partial 16S rRNA gene sequence of the isolate has been submitted to NCBI GenBank with the accession number PV698100. The identity and resistance profile of the strain was confirmed through biochemical and antibiotic susceptibility tests. The bacterial suspension demonstrated a notable oviposition activity index (OAI) of 0.77 ± SE, with moderate variation among treatments (F(3, 8) = 3.631, p = 0.0642). Multiple comparison analysis (Tukey's test) showed that OAI values for DHB13-treated media did not differ significantly from natural habitat water but were significantly higher than the sterile control, indicating a biologically relevant attraction of gravid female mosquitoes. LC-MS analysis of the bacterial culture supernatant revealed the presence of three cresol derivatives: diisopropyl-m-cresol, 3-ethyl-p-cresol, and 6-ethyl-o-cresol. These compounds were evaluated through molecular docking against Cx. quinquefasciatus Odorant Binding Protein 1 (CxOBP1), a protein known to mediate olfactory-driven oviposition behaviour. However, mosquito olfaction involves several OBPs, receptors, and enzymes, so interaction with CxOBP1 represents only part of this complex sensory system. Molecular docking revealed strong binding of CxOBP1 with diisopropyl-m-cresol (-6.7 kcal/mol), 3-ethyl-p-cresol (-6.2 kcal/mol), and 6-ethyl-o-cresol (-5.9 kcal/mol), indicating potential oviposition attractant activity. All three ligands were found to bind within a conserved binding pocket of CxOBP1, behavioural assays confirmed the oviposition-stimulant properties of the bacterial suspension, indicating that the detected compounds mimic natural semio-chemicals such as p-cresol, previously recognized as an oviposition cue. These findings reinforce the role of microbiota in shaping mosquito reproductive behaviour through the production of volatile attractants. Moreover, they highlight the potential of using microbial VOCs as environmentally sustainable tools for mosquito surveillance and vector control. This integrative approach linking microbial ecology, chemical analysis, and mosquito behaviour provides novel insights for the development of attractant-based control strategies.}, }
@article {pmid41553583, year = {2026}, author = {Zavřel, T and Pohland, AC and Pfennig, T and Matuszyńska, AB and Tóth, SZ and Bernát, G and Červený, J}, title = {Estimating the redox state of the plastoquinone pool in algae and cyanobacteria via OJIP fluorescence: perspectives and limitations.}, journal = {Photosynthesis research}, volume = {164}, number = {1}, pages = {6}, pmid = {41553583}, issn = {1573-5079}, }
@article {pmid41551586, year = {2026}, author = {Rahlff, J and Amato, P}, title = {A look into the virosphere of clouds: A world yet to be explored.}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100545}, pmid = {41551586}, issn = {2666-5174}, abstract = {Clouds are aqueous atmospheric systems hosting diverse and active microorganisms. Viruses may also persist despite harsh conditions, support active viral infections, and contribute to microbial dynamics during aerial transport. However, assessing viruses, and even more, virus-bacteria interactions in the atmospheric environment is highly challenging, and knowledge remains very limited. Here, based on current knowledge in cloud microbiology, we estimate the cloud virome at ∼10[21] virus particles globally. One out of a million of cloud droplets is susceptible to host virus-bacteria interactions, which represents considerable volume at global scale, and we discuss potential implications for microbial ecology. We finally propose future research directions to explore further the cloud virosphere and its ecological roles.}, }
@article {pmid41222968, year = {2026}, author = {Le, OTH and Chu, LK and Pham, QV and Tran, HT and Nguyen, HN and Nguyen, HT and Dinh, HT}, title = {Enhancing compost maturity and nitrogen content through cocomposting of chicken feather waste with rice husk and vegetable residues.}, journal = {Journal of the Air &amp; Waste Management Association (1995)}, volume = {}, number = {}, pages = {1-13}, doi = {10.1080/10962247.2025.2587011}, pmid = {41222968}, issn = {2162-2906}, abstract = {Chicken feather waste is a potential low-cost nitrogen source for fertilizer production. However, due to its recalcitrant biodegradability, low C/N ratio, and high water content, composting chicken feather waste requires amendments. Optimizing the initial substrate composition plays a key role in improving composting performance. This study investigated the effects of varying chicken feather waste proportions, which altered the initial C/N ratio of the composting substrate, on the physicochemical evolution and final product quality of compost mixtures containing rice husk as a bulking agent and readily degradable vegetable residues. The substrates were composted in static compost bins of 20 L for 126 days under ambient conditions (~28°C). Significant differences were observed in physicochemical evolution and compost quality. A higher proportion of chicken feather waste or a lower initial C/N ratio led to increased total nitrogen (TN), extractable NH4[+], and SO4[2‒] concentrations during composting and in the final products. The addition of rice husk and vegetable residue improved the germination index of compost products from chicken feather waste. It was found that more-nutrient-rich compost could be produced by co-composting chicken feather waste with a low C/N ratio.Implications: This study highlights the interrelation of cosubstrates (rice husk, vegetable residue) in the decomposition of chicken feather waste. Nutrient-rich composts were obtained when chicken feather waste was cocomposted with low C/N ratios. Higher proportion of chicken feather waste or lower initial C/N ratio of composting substrate increased total N, extractable NH4[+], and SO4[2-] concentrations in compost product. Cocomposting of chicken feather waste with rice husk and vegetable residue enhanced compost maturity and germination index. The findings contribute a scientific basis for promoting the utilization of chicken feather waste to produce N-rich fertilizer.}, }
@article {pmid41549150, year = {2026}, author = {Negi, R and Sharma, B and Jyothi, RS and Gupta, A and Parastesh, F and Kaur, T and Jhamta, S and Thakur, N and Singh, S and Yadav, N and Yadav, AN}, title = {Phyllosphere microbiome: Exploring the unexplored frontiers for precision agricultural and environmental sustainability.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {2}, pages = {50}, pmid = {41549150}, issn = {1573-0972}, mesh = {*Microbiota ; *Agriculture/methods ; Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Fungi/metabolism/classification ; *Plant Leaves/microbiology ; *Plants/microbiology ; }, abstract = {The phyllosphere, encompassing the aerial surfaces of plants, represents one of the largest microbial habitats on Earth and plays a pivotal yet underutilized role in sustainable agriculture and environmental health. Colonized by diverse bacterial, fungal, and yeast communities, the phyllosphere microbiome significantly influences plant growth, disease resistance, nutrient dynamics, and abiotic stress tolerance. These microorganisms engage in complex interactions with host plants, often functioning as biofertilizers, biopesticides, and stress protectants by producing phytohormones, antimicrobial metabolites, and stress-responsive compounds. Importantly, phyllospheric microbes also contribute to atmospheric and ecological balance by participating in carbon and nitrogen cycling, degrading volatile organic compounds (VOCs), and mitigating air pollution. However, despite their immense potential, the practical application of phyllospheric microbes remains limited by challenges such as environmental instability, poor field persistence, and incomplete functional characterization. The highly variable microclimate of the leaf surface poses survival barriers to both native and introduced microbial inoculants. Moreover, the specificity of plant-microbe associations and the complexity of microbial interactions necessitate precision-based approaches for successful deployment. Recent advances in omics technologies, microbial consortia engineering, and nano-enabled delivery systems provide new opportunities to overcome these limitations. A deeper understanding of phyllosphere microbial ecology, combined with innovations in synthetic biology and ecological modeling, can facilitate the development of robust microbial tools tailored to specific crops and climates. Harnessing the potential of phyllospheric microorganisms is not merely an academic pursuit, it is a strategic imperative for transitioning toward climate-resilient, low-input, and ecologically sound agricultural systems.}, }
@article {pmid41548260, year = {2026}, author = {Ravikumar, BN and Carvajal-Arroyo, JM and Jia, M and Ganigué, R}, title = {Ecophysiological characterization of thermophilic anammox process: Impact of environmental conditions and wastewater constituents on the activity of a novel granular thermophilic anammox culture.}, journal = {Water research}, volume = {292}, number = {}, pages = {125402}, doi = {10.1016/j.watres.2026.125402}, pmid = {41548260}, issn = {1879-2448}, abstract = {Understanding the ecophysiology of thermophilic anammox bacteria is crucial for expanding anaerobic ammonium oxidation (anammox)-based nitrogen removal to warm (>45[0]C), nitrogen-rich and carbon-deficient wastewaters (bCOD/N < 3 g/g) such as, centrate from thermophilic anaerobic digesters. Despite recent enrichments of thermophilic anammox cultures, their ecophysiological responses to process variables remain largely unknown. This study provides the first systematic characterization of the short-term response of a granular thermophilic anammox culture, enriched in Candidatus Brocadia sp., to key environmental conditions (pH, temperature, salinity) and wastewater constituents (ammonium, nitrite, phosphate, sulfide, volatile fatty acids (VFAs)). The culture displayed an optimal pH range of 7.3-7.8 and a temperature optimum of 50-53 °C, the highest short-term activity temperature recorded for any anammox species, yet. Ammonium caused only slight inhibition (IC50>57 mM), and free ammonia was not the primary inhibitory species, in contrast to mesophilic observations. Thermophilic Ca. Brocadia culture showed higher salinity (IC50=159 mM NaCl) and phosphate tolerance (IC50=44.9 mM) tolerance than most mesophilic counterparts, whereas nitrite (IC50=25.9 mM) and sulfide (IC50=0.03 mM H2S) elicited strong inhibition. Among VFAs, propionate was the most inhibitory (IC50=22 mM), while low concentrations (2.5 mM) of acetate and formate slightly enhanced anammox activity. These results identify the inhibitory thresholds and operational boundaries of thermophilic anammox systems, demonstrating that the culture is sufficiently robust for application in warm nitrogenous wastewaters, paving the way for developing sustainable and cost-efficient wastewater treatment technologies for high temperatures.}, }
@article {pmid41547661, year = {2026}, author = {Dasgupta, M and Maity, A and Sarker, RK and Paul, P and Chakraborty, P and Sarkar, S and Roy, R and Malik, M and Das, S and Tribedi, P}, title = {Antibiotic-phytochemical combinations against Enterococcus faecalis: a therapeutic strategy optimized using response surface methodology.}, journal = {Antonie van Leeuwenhoek}, volume = {119}, number = {2}, pages = {41}, pmid = {41547661}, issn = {1572-9699}, support = {TNU/R&amp;D/MG/24/02//The Neotia University/ ; TNU/R&amp;D/MP/2021/010//The Neotia University/ ; }, mesh = {*Enterococcus faecalis/drug effects ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; *Phytochemicals/pharmacology ; Vancomycin/pharmacology ; Ciprofloxacin/pharmacology ; Drug Synergism ; Benzoquinones/pharmacology ; }, abstract = {Enterococcus faecalis, a Gram-positive bacterium that causes nosocomial infections, has been reported to be resistant to several antibiotics, posing a significant threat to public healthcare. In the present study, we explored a combinatorial therapeutic approach involving conventional antibiotics alongside phytochemicals against E. faecalis. Vancomycin and ciprofloxacin were chosen for the current study due to their different modes of action. The minimum inhibitory concentration (MIC) of cuminaldehyde and thymoquinone was found to be 500 µg/mL and 30 µg/mL, respectively. Co-administering vancomycin with thymoquinone or cuminaldehyde reduced the MIC of vancomycin from 5 to 2 µg/mL, resulting in a 60% drop in MIC dose. Ciprofloxacin's MIC reduced from 1.5 to 1 µg/mL in the presence of the same phytochemicals, resulting in 33% reduction in its MIC dose. Furthermore, fractional inhibitory concentration indices (FICI) suggested additive interactions (FICI range: 0.66-1) between the antibiotics and phytochemicals against E. faecalis. Since precision dosing is important for any combinatorial application, we explored response surface methodology (RSM) to optimize dosing regimens of the selected compounds. It was observed that the predicted optimal concentrations of the test compounds (in different combinations) could closely match the actual observations when tested under the in-vitro laboratory conditions (R[2] range: 0.97-0.99). These findings suggested that combining conventional antibiotics with phytochemicals may offer a promising strategy to enhance the antimicrobial efficacy for effective control of infections caused by E. faecalis.}, }
@article {pmid41547536, year = {2026}, author = {Banik, M and Bashyal, S and Ahmed, KA and Banik, K and Dua, K and Choi, JP and Paudel, KR and Majumder, R}, title = {The Gut Microbiome of Australian Cats and Dogs: Dietary Influences, Health Impacts, and Emerging Research.}, journal = {Veterinary journal (London, England : 1997)}, volume = {}, number = {}, pages = {106566}, doi = {10.1016/j.tvjl.2026.106566}, pmid = {41547536}, issn = {1532-2971}, abstract = {The gut microbiome plays a pivotal role in the health, metabolism, and behaviour of companion animals, yet comprehensive syntheses of its composition and functional relevance in cats and dogs in Australia are overlooked and remain limited globally. This review synthesises current knowledge on the gut microbial communities inhabiting the gastrointestinal tracts of dog and cats, with a particular focus on taxonomic diversity, dietary modulation, and associations with disease states within Australian context. Core phyla including Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria dominate the canine and feline gut, but marked interspecies and individual variability is shaped by factors such as feeding practices, living environment, obesity, and chronic disease. Recent studies have elucidated functional signatures linked to conditions ranging from the influence of microplastics to pet gut health, as well as gut-microbiome transmission between pets and their owners, highlighting this area as a promising field of investigation. In parallel, this review contextualizes the broader landscape of pet ownership in Australia, where nearly 70% of households own pets, and significant resources are devoted to nutrition, veterinary care, and preventive health. Emerging evidence also suggests bidirectional influences between pets and their human companions' microbiota, highlighting opportunities for integrated approaches. We identify critical knowledge gaps, including the need for region-specific microbial baselines, standardized methodologies, and controlled intervention trials targeting microbiome modulation and transmission. By consolidating advances across microbial ecology, veterinary medicine, and translational research, this review provides a foundation for future studies that aim to harness the diagnostic and therapeutic potential of the pet microbiome, thereby improving health outcomes for animals and humans alike.}, }
@article {pmid41546932, year = {2026}, author = {Verduzco Garibay, M and Hernández-Guardado, I and Yebra-Montes, C and Díaz-Torres, O and Fernández Del Castillo, A and Díaz-Vázquez, D and Kreft, JU and Cortés-Aguilar, J and Senés-Guerrero, C and Gradilla-Hernández, MS}, title = {Exploring the resilience of playa lake ecosystems to climate change: A microbial perspective.}, journal = {Journal of environmental management}, volume = {399}, number = {}, pages = {128474}, doi = {10.1016/j.jenvman.2025.128474}, pmid = {41546932}, issn = {1095-8630}, abstract = {Playa lakes, ephemeral water bodies found in arid and semi-arid regions, are increasingly impacted by climate change. The Mexican playa Lake Atotonilco has experienced a significant decline in water volume, leading to increased salinity and making it a valuable model for assessing climate impacts. Using 16S rRNA sequencing, this study investigated the responses of microbial communities and their contributions to key biogeochemical cycles, including those related to greenhouse gas dynamics. Spatial differences in physicochemical parameters were observed: channels and wastewater treatment plant (WWTP) effluent showed elevated BOD5, COD, coliforms, and pH above regulatory limits, whereas the lake displayed higher DO but increased TP and TKN. Bacterial communities exhibited marked seasonal and depth-related shifts, reflecting strategies that support ecosystem resilience. To robustly identify differentially abundant taxa, two methods (ANCOM-BC2 and DESeq2) were implemented, which consistently detected significant differences across seasons. Despite strong environmental fluctuations, a core microbial community persisted, suggesting functional continuity in biogeochemical cycling. This study provides a comprehensive assessment of microbial dynamics in a playa lake, integrating community structure with physicochemical variability to reveal bacterial responses to climate-driven environmental change. Because playa and other shallow lakes worldwide are experiencing increasing desiccation, salinization, and nutrient imbalances, defining these microbial processes is essential for anticipating ecological change. This study provides a needed baseline for future research and offers key insights for managing climate-vulnerable aquatic ecosystems in arid regions.}, }
@article {pmid41545601, year = {2026}, author = {Shin, S and Bang, D and Lee, M and Kang, Y}, title = {Heavy Rain, Less Bloom Under Heat: Succession of Size-Structured Phytoplankton Community Without Biomass Increases in a Monsoonal Korean Coastal Ecosystem.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02680-4}, pmid = {41545601}, issn = {1432-184X}, support = {R2025011//National Institute of Fisheries Science/ ; NRF2022R1C1C1008380//National Research Foundation of Korea/ ; }, }
@article {pmid41545035, year = {2026}, author = {Eggestein, A and Rauer, D and Herrmann, SM and Kolek, F and Leier-Wirtz, V and Urban, S and Foesel, B and Schloter, M and Bhattacharyya, M and Pyrri, I and Reiger, M and Schwierzeck, V and Hülpüsch, C and Traidl-Hoffmann, C and Damialis, A and Gilles, S}, title = {A Walk in the Park: Influence of Natural Co-Exposure to Grass Pollen and Fungal Spores on Nasal Mycobiome and Cytokine Responses.}, journal = {Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology}, volume = {}, number = {}, pages = {}, doi = {10.1111/cea.70216}, pmid = {41545035}, issn = {1365-2222}, support = {//Christine K&#xfc;hne-Center for Allergy Research and Education (CK-Care)/ ; }, abstract = {BACKGROUND: During the grass flowering season, fungal spores are abundant in outdoor air. We tested for co-sensitisations to grass pollen and fungal spores, assessed the degree of co-exposure, and studied its impact on the nasal mycobiome and immune responses.<br><br>METHODS: Fungi-specific IgE-levels were studied in 277 individuals with and without grass pollen sensitisation. In a small cohort (n&#x2009;=&#x2009;7), exposure to grass pollen and fungal spores was monitored during 5 consecutive indoor and outdoor stays in a flowering meadow and correlated with changes in the nasal mycobiome. Cytokines of nasal epithelial cells were studied under stimulation with recombinant grass pollen allergens, with and without fungal spores derived from outdoor isolates.<br><br>RESULTS: IgE-sensitisation against the studied fungi was significantly more frequent among individuals with grass pollen sensitisation than among those without grass pollen sensitisation. Outdoor exposure resulted in changes in the nasal mycobiome, with a transitory enrichment of environmental fungi, for example, Cladosporium species. Most of the fungi cultivated from outdoor air samples belonged to the genera Fusarium, Cladosporium and Penicillium. Apical co-stimulation of nasal epithelial cells with grass pollen allergens and Fusarium, Cladosporium or Penicillium spores led to an increased loss of transepithelial electrical resistance and induction of pro-inflammatory cytokine release compared to mono-stimulation.<br><br>CONCLUSION: Frequent co-exposure to fungal spores and grass pollen may increase the chance of acquiring a co-sensitisation to both allergens. Environmental fungi interact with and transitorily change the local mycobiome. Under co-exposure, fungal spores induce nasal inflammation and foster immune responses to otherwise poorly immunogenic pollen allergens.}, }
@article {pmid41544570, year = {2026}, author = {Aminullah, N and Langar, H and Mahaq, O and Azizi, MN and Zahir, A}, title = {Microbial ecology, functional implications, and associated factors influencing poultry intestinal health.}, journal = {Veterinary immunology and immunopathology}, volume = {293}, number = {}, pages = {111065}, doi = {10.1016/j.vetimm.2026.111065}, pmid = {41544570}, issn = {1873-2534}, abstract = {Gut health is a dynamic phenomenon regulated by the balanced interaction among gastrointestinal tract morphological structure, resident microbiota, and available nutrients, producing an integrated barrier that ensures efficient physiological functions, enhanced immune competence and optimal productivity. Gut health is recognised as a crucial factor for optimum management, farming economy, and sustainable commercial poultry production. Poultry gut health has become a central focus, particularly following restrictions applied on the use of antimicrobial growth promoters in poultry production due to rising global concerns about microbial resistance. Intestinal integrity and health are being regulated by microbiota metabolites such as short-chain fatty acids (SCFAs), which modulate intestinal morphogenesis vis-à-vis villus size, crypt depth and physiological functions, including feed digestion, nutrients synthesis and absorption, and immune response. Any disturbances arising from nutritional imbalances, microbial infections, environmental stress, or poor management practices compromise epithelial health, barrier integrity, and physiological functions, leading to impaired growth performance and productivity. This review provides an overview of poultry gut health, highlighting the interdependence of gut microbiota, gut morphogenesis, physiology, environmental factors affecting gut health, and management approaches for sustainable poultry production.}, }
@article {pmid41540283, year = {2026}, author = {Bueno, RS and Catania, V and Auteri, M and Grilli, E and di Iorio, T and di Sarra, A and Castaldi, S and Quatrini, P}, title = {Patterns and Drivers of Plant Arbuscular Mycorrhizal Traits Across a Pedo-Climatic Gradient in Mediterranean Agroecosystems Under Desertification Risk.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02689-9}, pmid = {41540283}, issn = {1432-184X}, abstract = {Desertification is a global concern, reducing vegetation cover and soil fertility. Arbuscular mycorrhizal symbiosis (AM), the most common plant-fungi association, can enhance plant fitness and stress tolerance. Despite its significance, comprehensive data on community-wide patterns and drivers of plant AM traits are limited in the Mediterranean, one of the regions most vulnerable to desertification. We examined four traits: colonization frequency, intensity, arbuscule abundance, and spore density in the rhizosphere of 20 plant species across ten agroecosystems in desertification-prone areas of Italy, Spain, and Portugal. We analysed whether these traits varied across Raunkiær's plant life forms and were affected by vegetation cover, soil properties, precipitation, and temperature, both overall and regionally, to explore potential context-dependency. All plants showed a high frequency of AMF colonization, with an average intensity of 54%, indicating obligate AMF interactions, and arbuscule abundance was significantly correlated with spore density. These traits were significantly higher in microhabitats dominated by trees and shrubs compared to those dominated by herbaceous plants. Phanerophytes (perennials) presented lower trait values than therophytes (annuals), while the highest values were found in hemicryptophytes. Lampedusa, a region with hotter and drier climate conditions in Southern Europe, had significantly lower AMF trait levels, though Spanish site values resembled those in Sicily more than Portugal. Soil organic carbon, nitrogen, and the overall positive interaction between precipitation and temperature significantly influenced all AMF traits. However, the magnitude and direction of soil and climate related effects differed among regions, indicating strong context dependency. Our study contributes to better define indicators for monitoring desertification and evaluating restoration efforts while highlighting the need of site-specific evaluations and careful interpretation of broad generalisations.}, }
@article {pmid41537975, year = {2026}, author = {Sless, T and Chau, K and Nguyen, P and Rehan, S}, title = {Microbial communities of wild bees and comparative phylogenetics of key bacterial taxa across the bee tree of life.}, journal = {Proceedings. Biological sciences}, volume = {293}, number = {2062}, pages = {}, doi = {10.1098/rspb.2025.1823}, pmid = {41537975}, issn = {1471-2954}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Animals ; Bees/microbiology ; Phylogeny ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics/analysis ; *Microbiota ; *Fungi/classification/genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic ; }, abstract = {Recent years have seen a rapidly growing interest in the study of microbiomes to understand the health and well-being of host animals. Within bees, much of this work has focused on managed species of agricultural importance, such as honeybees and bumblebees. However, unmanaged wild bees are also vital to both agricultural and natural systems, and studying their microbial associates is essential to understanding the impacts of microbiomes on bee health. We used metabarcoding based on 16S rRNA and internal transcribed spacer region (ITS1) loci to identify bacterial and fungal associates of adult bees from 16 species, 10 genera and 5 families, representing a diverse sampling of wild bees common to eastern North America. Overall, Apilactobacillus was the largest component of bacterial communities, while fungal communities were dominated by Cladosporium. Alpha diversity of both bacteria and fungi differed significantly across genera and species, while beta diversity varied at all taxonomic levels. Additionally, we conducted a broad phylogenetic comparison of bacterial communities across bees using previously published 16S rRNA datasets and contrasted these findings with functional traits across the bee tree of life. Several bacterial taxa showed evidence of strong phylogenetic signal in prevalence, while the presence of corbiculae was more strongly associated with bacterial community composition than sociality or nesting habit. This study provides expanded insights into the microbial associates of wild bees, as well as the broadest investigation to date into patterns of phylogenetic conservation in bacterial communities across a total of 42 species representing the five most diverse bee families.}, }
@article {pmid41536172, year = {2026}, author = {Carboni, S and Asangba, AE and Melin, AD}, title = {Microbial Contributions to Primate Reproduction.}, journal = {Evolutionary anthropology}, volume = {35}, number = {1}, pages = {e70023}, pmid = {41536172}, issn = {1520-6505}, mesh = {Animals ; *Primates/microbiology/physiology ; Female ; *Reproduction/physiology ; *Microbiota/physiology ; Male ; Humans ; Pregnancy ; Anthropology, Physical ; Sexual Behavior, Animal ; Biological Evolution ; Copulation/physiology ; }, abstract = {Reproduction is a complex process, and microbes play a far greater role than previously imagined. This review explores the ways that microbiomes influence the rich tapestry of reproductive processes and outcomes within the primate lineage, including pre-copulatory and post-copulatory mechanisms. We discuss microbiomes in a sexual selection framework, specifically how they might influence mate choice and sexual competition across multiple sensory modalities. We then consider how copulatory behavior and mating systems may in turn shape reproductive microbiomes. Moving to post-copulatory processes, we discuss the potential impact of microbes on cryptic choice and sperm competition and call for additional research in this area. Finally, we explore the influence of microbes on pregnancy outcomes, emphasizing evolutionary perspectives often overlooked in clinical research. Importantly, we compare human studies to those on nonhuman primates, bridging the two areas of inquiry and outlining future research directions. Our aim is to highlight the vast potential for microbes to contribute to all stages of reproduction, and to inspire creative, synthetic future research that moves forward this fascinating area of inquiry.}, }
@article {pmid41534871, year = {2026}, author = {Xie, Y and Artacho, A and Yu, X and Bi, M and Li, H and Li, Y and Roccuzzo, A and Mira, A and Rosier, BT and Tonetti, MS}, title = {Oral-Rinse-Sourced Microbiota in Oral Health and Diseases in a Representative US Adult Population: Implications for Diagnostics.}, journal = {Journal of clinical periodontology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jcpe.70101}, pmid = {41534871}, issn = {1600-051X}, support = {JYLJ202404//Clinical+ programme of the Ninth People's Hospital/ ; }, abstract = {AIMS: To investigate the associations between oral-rinse microbiota and distinct oral conditions, and further evaluate its potential ability to distinguish periodontitis severity.<br><br>METHODS: Oral-rinse-sourced microbiota with 16S ribosomal RNA sequencing from 3770 adults in US National Health and Nutrition Examination Survey 2009-2012 were analysed across oral health, caries, periodontitis, co-existing caries and periodontitis and edentulism. Diagnostic potential of the oral-rinse microbiota for periodontitis severity was evaluated using multi-class random forest (RF) model with internal validation and external validation in an independent cohort (n&#x2009;=&#x2009;392).<br><br>RESULTS: Oral condition accounted for substantial variance in oral-rinse microbiota, revealing disease or tooth loss-associated shifts. Increasing acidogenic/aciduric taxa (Veillonella, Lactobacillus, Atopobium) or periodontitis-associated taxa (Filifactor, Treponema, Tannerella) were identified in caries-only or periodontitis-only groups, respectively, while the co-existing disease group showed overlapping shifts. Taxa shifted dose-dependently with increasing periodontitis severity. The RF model achieved moderate performance in identifying severe periodontitis, with the area under the receiver operating characteristic curve (AUROC) of 0.81 (0.75-0.87) internally and 0.83 (0.77-0.88) externally. Key contributing taxa aligned with established periodontitis-associated genera, supporting model interpretability.<br><br>CONCLUSION: Based on our results, oral-rinse microbiota captures disease-specific signatures across oral conditions, supporting its potential as a non-invasive tool to monitor oral microbial ecology and assess periodontitis severity at the population level.}, }
@article {pmid41534410, year = {2026}, author = {Cardinali, F and Rampanti, G and Lucci, P and Ferrocino, I and Pacetti, D and Fanesi, B and Ismaiel, L and Milanović, V and Garofalo, C and Petruzzelli, A and Savelli, D and Gabucci, C and Aquilanti, L and Osimani, A}, title = {Novel insights into hákarl: A deep dive into the microbiological and physico-chemical features of Iceland's traditional fermented shark.}, journal = {International journal of food microbiology}, volume = {450}, number = {}, pages = {111629}, doi = {10.1016/j.ijfoodmicro.2026.111629}, pmid = {41534410}, issn = {1879-3460}, abstract = {Hákarl, the traditional Icelandic product obtained from the fermentation of Greenland shark (Somniosus microcephalus), represents a unique food item from both cultural and microbiological perspectives. This study investigated commercial samples of hákarl using an integrated approach, combining physico-chemical analyses, lipid and volatile profiling, metataxonomic sequencing, and microbial isolation. Results confirmed the alkaline nature of the product (pH ∼8) and a water activity (aw) of 0.96, sufficient to sustain an active and diverse microbial community. Lipid profiling revealed the predominance of monounsaturated fatty acids, with differences in PUFA and DHA levels between the analyzed producers, consistent with nutritionally favorable characteristics. Microbiological analysis highlighted bacterial communities dominated by Firmicutes, particularly Bacilli and Clostridia, with significant abundances of Tissierella creatinini and Atopostipes suicloacalis. Culture-dependent methods led to the isolation of Carnobacterium antarcticum cultures, which were subsequently characterized for their enzymatic activities. These findings suggest potential biotechnological applications of the isolates, especially in fermentation and aroma development. Volatile compound analysis identified thirteen VOCs including alcohols, aldehydes, ketones, phenols, sulfur- and nitrogen-containing compounds. Trimethylamine was the predominant metabolite responsible for the strong ammonia-like odor, followed by phenol and sulfur-containing compounds, which also contributed to the sensory profile. Overall, the results provide novel insights into the microbial ecology, physico-chemical traits, and volatile characteristics of hákarl, confirming its variability linked to artisanal production methods. The study emphasizes hákarl's role as a reservoir of pro-technological microorganisms and advances current understanding of the factors influencing its safety, quality, and identity as traditional fermented food.}, }
@article {pmid41533097, year = {2026}, author = {Huertas-Díaz, L and Hosek, J and Gram-Hansen, D and Frei, R and Roduit, C and Sasaki, M and Lauener, RP and Schwab, C and , }, title = {pH-Dependent Effects of Short-chain Carboxylic Acids and Buffer Systems On Clostridioides difficile in Vitro and in Vivo.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02694-6}, pmid = {41533097}, issn = {1432-184X}, abstract = {The spore-forming anaerobe Clostridioides difficile colonizes the highly dynamic gut environment early after birth, frequently without causing disease. In this study, we aimed to determine how environmental conditions indicative of the infant gut impacted prevalence and physiology of C. difficile. We examined the effect of pH, fermentation derived short-chain carboxylic acids (SCCA) and buffering systems combining in vitro and in vivo analysis, and experimental and modelling approaches. In vivo, the prevalence of Clostridioides significantly increased between 3 months (30.2%) and 12 months (56.2%) after birth. At 12 months, the occurrence of Clostridioides was the highest in feces with near neutral pH (6.7 (IQR 6.5‒7.3). In vitro, C. difficile showed pH-dependent growth and metabolic activity with an optimum around pH 5.8-6.3. Most SCCA conferred antimicrobial activity at pH 5.2 and 6.1 while at pH 6.5, high concentrations of SCCA promoted growth. The presence of phosphate buffer enhanced antimicrobial activity of SCCA, particularly at lower pH values (5.2-5.8). Two multilinear regression models indicated that ionic strength was inversely related to optical density in vitro, while in vivo, the abundance of Clostridioides was inversely linked to the presence of undissociated SCCA. Together, this study highlights that the that occurrence and performance of the opportunistic pathogen C. difficile was affected by chemical systems such as pH, the presence of buffer systems and concentration and chemical state of SCCA. Our results suggest novel targets that could be modulated to impact C. difficile colonization.}, }
@article {pmid41531331, year = {2026}, author = {Wu, H and Xu, S and Chen, Y and Yuan, Z and Yao, Y and Hao, J and Han, L}, title = {Phenazine-1-Carboxamide from Streptomyces Suppresses Phytophthora nicotianae via CDC48-Targeted Mitochondrial Disruption.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.70383}, pmid = {41531331}, issn = {1365-3040}, support = {32272594//National Natural Science Foundation of China/ ; 2024QCY-KXJ-097//Technology Innovation Leading Program of Shaanxi/ ; }, abstract = {Phytophthora nicotianae is a plant-pathogenic oomycete, posing a serious threat to global agriculture due to its highly destructive infections and challenges in management. To explore a biologically based disease management strategy, we investigated Streptomyces ardesiacus HL-06, which produces phenazine-1-carboxamide (PCN), a potent anti-oomycete metabolite that effectively suppresses the growth of P. nicotianae in vitro and reduces tobacco black shank severity by over 80% under field conditions, surpassing the efficacy of commercial fungicides. Mechanistically, we identified CDC48, a AAA+ ATPase essential for mitochondrial homeostasis, as the direct molecular target of PCN. Drug affinity responsive target stability (DARTS), molecular docking, and isothermal titration calorimetry revealed that PCN binds to CDC48's ATPase domain, thereby disrupting mitochondrial protein quality control. This interaction leads to mitochondrial cristae loss, ATP synthase inhibition, and reactive oxygen species (ROS) accumulation, ultimately triggering oomycete apoptosis. This is the first report of a phenazine compound targeting a eukaryotic AAA+ ATPase, revealing a novel mode of action against oomycete pathogens. Our findings integrate microbial ecology with chemical biology, positioning PCN as a promising eco-friendly candidate for sustainable plant disease management.}, }
@article {pmid41531312, year = {2026}, author = {Boldt, J and Porten, C and Haeckl, FPJ and Hug, JJ and Panter, F and Steglich, M and Wink, J and Overmann, J and Göker, M and Krug, D and Müller, R and Nübel, U}, title = {Phylogeny-Aware Metabologenomics Accurately Assigns Natural Products to Biosynthetic Gene Clusters.}, journal = {Microbial biotechnology}, volume = {19}, number = {1}, pages = {e70298}, doi = {10.1111/1751-7915.70298}, pmid = {41531312}, issn = {1751-7915}, support = {09.720//Deutsches Zentrum f&#xfc;r Infektionsforschung/ ; }, mesh = {*Multigene Family ; *Biological Products/metabolism ; *Phylogeny ; *Biosynthetic Pathways/genetics ; *Metabolomics/methods ; Genomics/methods ; Mass Spectrometry ; }, abstract = {Tens of thousands of biosynthetic gene clusters (BGCs) have been identified in microbial genomes, but the vast majority of associated natural products (NPs) and their underlying biosyntheses remain unknown. Metabologenomics approaches integrate genomic and metabolomic datasets to statistically associate BGCs to their cognate NPs, yet often suggest many false links. Here, we show that incorporating information on the producer strains' phylogeny greatly improves accuracy. We sequenced 72 Sorangium spp. genomes (myxobacteria), predicting 2030 BGCs in 265 gene cluster families (GCFs). Mass spectrometry (MS[1]) revealed 99 metabolite families (MFs) from the same strains. Using a phylogeny-aware statistical analysis, we identified 43 high-confidence associations between GCFs and MFs, correctly including 89% of previously characterised links and reducing spurious associations by 33-fold, compared to simple correlational analysis. Our approach identified previously unknown BGCs for rowithocin and an undescribed poly-glycosylated NP. It also identified a distinct BGC associated with the production of chlorotonil C variants and refined the BGC for maracen. This study demonstrates the effectiveness of phylogeny-aware metabologenomics as a scalable strategy for NP discovery and biosynthetic pathway elucidation, and provides a roadmap to improved analyses of paired-omics data towards NP discovery.}, }
@article {pmid41528150, year = {2026}, author = {Guo, M and Xia, Z and He, X and Wan, S and Wang, Y and Fan, S and Pérez-Moreno, J and Yang, Z and Yang, C and Liu, D and Yu, F}, title = {High-throughput sequencing reveals endophytic bacterial differentiation of common truffles (Tuber spp.) in China: diversity, biogeographical patterns, and fungal health implications.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0186625}, doi = {10.1128/spectrum.01866-25}, pmid = {41528150}, issn = {2165-0497}, abstract = {UNLABELLED: As valuable hypogeous fungi, truffles depend on fruiting-body-associated microorganisms for lifecycle functions like growth and nutrient cycling. This study sampled fruiting bodies of 10 Tuber species from 16 sites across six major truffle-producing provinces in China, characterizing endophytic bacterial communities via high-throughput sequencing and multivariate analysis. Proteobacteria dominated the endophytic bacteria, with Bradyrhizobium as the prevalent genus. Significant genus-level compositional differences occurred across provenances and species: Bradyrhizobium reached 99.80% relative abundance in Tuber sinense from Mengzi, Yunnan, versus 7.90% in Tuber shii from Dali (12.6-fold difference). Shannon diversity indices (n = 48) revealed striking species- and altitude-related variations (P < 0.001): Tuber lijiangense (5.111) and T. shii (5.091) had the highest diversity, while T. sinense (1.336) had the lowest (3.8-fold gap). Subtropical Dali samples exhibited a sevenfold higher diversity compared to those from the Mengzi region, which is geographically closer to the tropics. Non-metric scaling and principal coordinates analysis identified environmental factors (soil, climate) and host species as primary drivers, with species effects potentially overriding environment. Five core taxa (all Rhizobiales) suggested nitrogen-fixing roles, while Variovorax (via linear discriminant analysis effect size) emerged as an external-disturbance-sensitive opportunist. This study clarifies endophytic bacterial variation patterns and drivers, identifies key taxa, and informs truffle ecological interactions, providing a scientific basis for sustainable resource management and conservation.<br><br>IMPORTANCE: This study underscores the critical importance of truffle endophytic bacteria in mediating fungal health and ecological resilience, addressing a major knowledge gap in hypogeous fungal microbiome research. By integrating high-throughput sequencing across 10 Tuber species in China, we reveal how bacterial communities (dominated by Bradyrhizobium) shape biogeographical patterns and functional roles like nitrogen fixation. These findings advance understanding of microbe-fungal symbioses, with direct applications for sustainable truffle cultivation (e.g., microbial inoculants) and climate-resilient management-aligning perfectly with AEM's focus on applied microbial ecology and biotechnological relevance.}, }
@article {pmid41524991, year = {2026}, author = {Ding, Q and Li, J and Xue, F and Cui, W and Hu, S and Yu, L and Huang, W and Li, L and Cheng, P}, title = {Distinct soil microbial community composition and structure: evidence from soil inside and outside the cattle farm.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {57}, number = {1}, pages = {31}, pmid = {41524991}, issn = {1678-4405}, support = {No. 32402941//National Natural Science Foundation of China/ ; No. 2308085QC108//Natural Science Foundation of Anhui Province/ ; No.rc392109//Talent research fund project of Anhui Agricultural University/ ; }, mesh = {*Soil Microbiology ; Cattle ; Animals ; Soil/chemistry ; *Bacteria/classification/genetics/isolation &amp; purification ; Manure/microbiology ; Farms ; *Fungi/classification/genetics/isolation &amp; purification ; *Microbiota ; Biodiversity ; }, abstract = {The contrast between the soils inside and outside the cattle farm may reflect the prolonged manure exposure within the farm, potentially creating distinct properties and microbial structure. However, comparative studies are scarce on the microbial composition and co-occurrence patterns between soils inside and outside the cattle farm. To address this gap, this study combined Illumina MiSeq sequencing with co-occurrence network analysis and soil physicochemical characterization to compare the microbial community structures between the two sites. The soil inside the cattle farm exhibited higher microbial alpha diversity than that outside the farm. Volcano plots revealed significant differences in the relative abundances of microbial taxa between sites. Notably, the relative abundances of Devosia was significantly higher inside the cattle farm, whereas Paenibacillus and Nitrospira were markedly higher outside the cattle farm (|log2FC| ≥ 1.2). The fungal network inside the cattle farm demonstrated higher complexity and stability than outside, with larger nodes and edges (Nodes: 194 vs. 153; Edges: 13231 vs. 8007) and superior topological characteristics. To elucidate the specific manure-induced environmental factors driving these differences, Mantel tests confirmed that soil organic carbon and alkali-hydrolyzable nitrogen significantly influenced the microbial communities. This study identifies the specific manure-derived drivers of microbial community structure and network stability, providing critical insights for utilizing cattle manure to improve soil microbial ecology and thereby contributing to sustainable agricultural management.}, }
@article {pmid41520335, year = {2026}, author = {Sang, J and Li, S and Xu, C and Pan, X and Zhu, Y and Li, Y and Ma, C and Zhang, Y and Chen, S and Qiu, Q and Si, H and Huang, Z and Wang, J and Jiao, J and Li, Z}, title = {Rumen microbiome biogeography and ventral epithelial architecture in three ruminant species.}, journal = {Cell reports}, volume = {45}, number = {1}, pages = {116779}, doi = {10.1016/j.celrep.2025.116779}, pmid = {41520335}, issn = {2211-1247}, abstract = {Ruminants thrive in diverse ecosystems by leveraging their rumen microbiome to ferment fibrous plants. However, the spatial biogeography of rumen microbiome and the genetic diversity of the ventral rumen epithelium remain unknown. Here, we present a multi-omics study in roe deer, sika deer, and sheep, integrating region-resolved microbiome and metabolome across 11 ruminal sacs, as well as single-cell RNA sequencing (scRNA-seq), assay for transposase-accessible chromatin using sequencing (ATAC-seq), and bulk RNA sequencing (RNA-seq) of ventral epithelium. We reveal species-specific microbial compositions and metabolic capacities contributing to differences in short-chain fatty acid and vitamin B production. We uncover functional divergence, genomic specialization, and metabolic changes across the microbiome of distinct ruminal sacs. Single-cell profiling reveals changes of immune responses and structural remodeling of the ruminal ventral epithelium. We demonstrate that vitamin B12 promotes epithelial growth and we identify genes enhancing stem cell differentiation. Our results highlight variation in microbial ecology and epithelial architecture among three ruminant species, offering insights to improve livestock productivity.}, }
@article {pmid41520281, year = {2026}, author = {Tang, TWH and Ullah, K and Lee, JJ and Chen, HC and Hsieh, PCH}, title = {Comparative insights into the gut-heart axis: cross-species and cross-population perspectives.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2611617}, pmid = {41520281}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; *Cardiovascular Diseases/microbiology ; *Heart/physiology ; Swine ; Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Host Microbial Interactions ; Species Specificity ; *Gastrointestinal Tract/microbiology ; Disease Models, Animal ; }, abstract = {Gut microbiota research has rapidly expanded our understanding of host-microbe interactions in cardiovascular diseases, yet translation of these insights remains challenged by species-specific differences and substantial population heterogeneity. In this review, we synthesize current evidence across rodents, swine, non-human primates, and multi-ethnic human cohorts to delineate conserved versus context-dependent features of the gut-heart axis. Rodent models remain indispensable for mechanistic discovery, enabling causal testing through germ-free, antibiotic-treated, and humanized microbiota platforms, whereas large-animal models better replicate human cardiac anatomy, physiology, and microbial ecology. Human studies provide essential clinical relevance, demonstrating that patients with myocardial infarction, coronary artery disease, atrial fibrillation, and heart failure harbor distinct microbial and metabolite signatures. However, these findings vary across populations due to differences in diet, lifestyle, host genetics, medication exposure, and environmental transitions. Despite taxonomic variability, several functional pathways, most notably short-chain fatty acid production, bile acid biotransformation, and aromatic amino acid metabolism generating molecules such as trimethylamine-N-oxide and phenylacetylglutamine, consistently associate with cardiovascular risk. At the same time, population-specific features, including glycan-microbe interactions shaped by ABO and FUT2 genotypes, diet-responsive metabolite profiles, and variable drug-microbiome interactions, highlight the importance of genetic and environmental context. By integrating cross-species and cross-population evidence, this review outlines a framework for identifying robust microbial pathways, clarifying their translational boundaries, and guiding the development of microbiota-informed diagnostics and interventions that account for biological, cultural, and environmental diversity.}, }
@article {pmid41519975, year = {2026}, author = {Christoffersen, SN and Østergaard, SK and de Jonge, N and Pertoldi, C and Sørensen, JG and Noer, NK and Kristensen, TN and Nielsen, JL and Bahrndorff, S}, title = {Arctic Insects Show a Highly Dynamic Microbiome Shaped by Abiotic and Biotic Variables.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02685-z}, pmid = {41519975}, issn = {1432-184X}, abstract = {Arctic regions are inhabited by terrestrial ectotherms that have adapted to an extreme environment where food resources are limited. The host associated microbiome may partly explain their ability to live under these conditions, but very little is known about the microbiome of Arctic ectotherms. We investigate how the bacterial community of the Greenlandic seed bug (Nysius groenlandicus) and damsel bug (Nabis flavomarginatus) is affected by different abiotic and biotic factors (time, acclimation temperature, humidity, and diet) under both field and laboratory conditions. We found large differences in the bacterial composition and diversity between the two species including species-specific presence of potentially symbiotic bacteria. The bacterial community of both species changed across the season, which may be explained by the changing climatic conditions, such as temperature and humidity. This was further supported by results from the laboratory experiments. We also found that diet changed the bacterial composition in both species and that bacteria could be transferred from prey to predator. Together, these results show that the bacterial community of some Arctic insects are highly dynamic and modulated by different abiotic and biotic factors, suggesting that the microbiome plays an important role for these organisms to persist in an extreme and resource-limited Arctic environment.}, }
@article {pmid41509481, year = {2026}, author = {Hallberg, ZF and Alvarez-Aponte, ZI and Gaudinier, AC and Taga, ME}, title = {Quenching corrinoid-based interactions in a model bacterial coculture.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41509481}, issn = {2692-8205}, abstract = {Microbial community structure is driven, in part, by the metabolic interdependencies of resident microbes. Thus, manipulating specific metabolic interactions represents one attractive way to both understand how microbial communities perform complex functions and alter them for therapeutic or environmental effects. However, it is not yet possible to control the availability of those metabolites produced by some members of the community that are required by others. Here, we report the development of a metabolite 'quenching' strategy that disrupts a specific metabolic interaction involving corrinoids, the vitamin B12 family of cofactors, by applying a high-affinity corrinoid-binding protein, BtuG, to bacteria engaged corrinoid cross-feeding. Using a model coculture composed of Sinorhizobium meliloti, a bacterium that produces a corrinoid (cobalamin), and an Escherichia coli strain engineered to be corrinoid-dependent, we demonstrate corrinoid quenching by sequestration of extracellular corrinoid and show that BtuG specifically blocks corrinoid-dependent growth. We use this tool to calculate the amount of cobalamin released by S. meliloti cells and find that the cobalamin release rate is dependent on the growth phase of the producer, increasing to a maximum of approximately 40 cobalamin molecules per minute per cell in late exponential phase. This work establishes a strategy to selectively block microbial interactions that may be more broadly applied to dissecting community structure and function. We expect that applying high-affinity 'molecular sponges' to quench nutrient sharing will allow for the identification of key nutrients that structure microbial communities and empower precision microbiome manipulation strategies.}, }
@article {pmid41292826, year = {2025}, author = {Backman, T and Cui, J and Caullireau, E and Bleak, E and Bezrukov, I and Girardi, P and Hawks, A and Lasky, JR and Latorre, SM and Erberich, JM and Lopez, L and Neumann, M and Perkins, AM and Symeonidi, E and Azadi, P and Horvath, MP and Muszyński, A and Lang, PLM and Karasov, TL and Burbano, HA}, title = {Persistent trade-offs balance competition and colonization across centuries.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41292826}, issn = {2692-8205}, support = {T32 GM007276/GM/NIGMS NIH HHS/United States ; T32 AI055434/AI/NIAID NIH HHS/United States ; R24 GM137782/GM/NIGMS NIH HHS/United States ; R35 GM138300/GM/NIGMS NIH HHS/United States ; R35 GM150722/GM/NIGMS NIH HHS/United States ; }, abstract = {Microbial competition drives rapid adaptation, often forcing organisms to specialize in new ecological niches. Adaptations that improve competitive ability can reduce performance in other environments creating trade-offs. Whether such trade-offs persist in nature-or are eroded as lineages adapt through compensatory changes-remains largely unknown. Here we show that a trade-off between competitive ability and host colonization has been stably maintained in natural Pseudomonas populations for centuries. Wild plant-pathogenic Pseudomonas compete using tailocins-phage-derived molecular weapons that bind to specific cell-surface receptors. Genomic surveys and functional assays reveal that the most broadly lethal tailocins remain rare-while the tailocin's production increases competitive killing, it also compromises plant colonization. We determine that the polymorphisms behind this trade-off are not transient - historical genomes spanning two centuries show that the trade-off has been maintained for at least 10[5]-10[6] generations. Our results demonstrate that, in natural populations, a trade-off between competition and pathogenicity is fundamental and not easily overcome.}, }
@article {pmid41518539, year = {2026}, author = {Kou, C and Li, D and Liu, Z and Gao, W and Zhang, W and Xiong, L and He, L and Li, M and Shu, A and Ma, J and Gao, Z}, title = {Rare Microbial Taxa Dominate the Microecological Landscape of Cadmium Exposure in Rice Rhizosphere.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02690-2}, pmid = {41518539}, issn = {1432-184X}, support = {2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&amp;D Program of China/ ; 2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&amp;D Program of China/ ; 2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&amp;D Program of China/ ; 2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&amp;D Program of China/ ; 2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&amp;D Program of China/ ; 2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&amp;D Program of China/ ; 2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&amp;D Program of China/ ; 2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&amp;D Program of China/ ; 2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&amp;D Program of China/ ; 2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&amp;D Program of China/ ; 2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&amp;D Program of China/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; }, abstract = {Cadmium (Cd) contamination in soil is a growing problem, posing a significant threat to soil microorganisms and plant growth. Understanding how Cd exposure disrupts the evolution of soil microbial communities and the mechanisms underlying community remodeling requires further investigation. In this study, the rice rhizosphere treated with 0 (CK), 2.5 (LC), 5 (MC), and 15 (HC) mg kg[-1] Cd was used as a model and combined with 16S rRNA gene sequencing to systematically evaluate the response patterns of rice rhizosphere microbial communities under Cd gradient treatments. The study found that rice rhizosphere microbial communities responded to Cd exposure with a unimodal pattern of "low-promotion and high-suppression". LC treatment significantly increased the alpha diversity of rare fungal taxa and significantly enriched rare genera such as Candidatus Solibacter and Penicillium. Network analysis further confirmed that LC treatment significantly enhanced symbiotic relationships within and across rare taxa. The assembly of abundant bacterial and fungal taxa was consistently dominated by stochastic diffusional constraints, while rare taxa were primarily driven by deterministic homogeneous selection. In summary, rice rhizosphere microbial communities showed specific response patterns under Cd gradient treatment. Rare fungal taxa, as core members, actively responded to Cd exposure, made prominent contributions to shaping the community composition, and played a crucial role in maintaining the complexity and stability of the microbial network.}, }
@article {pmid41518434, year = {2026}, author = {Klammsteiner, T and Heussler, CD and Stonig, KT and Insam, H and Schlick-Steiner, BC and Steiner, FM}, title = {Stage-Specific Microbiota Transitions Throughout Black Soldier Fly Ontogeny.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02691-1}, pmid = {41518434}, issn = {1432-184X}, abstract = {The growing global population increases the demand for protein, while organic waste management has become more challenging. Alternative protein sources are essential to mitigate the environmental impact of food production. The black soldier fly (BSF; Hermetia illucens) has emerged as an alternative to traditional protein sources (e.g., soybean meal, fishmeal) due to its ability to convert diverse organic waste, addressing both issues simultaneously. This makes the BSF a promising candidate for industrial rearing, with its successful development closely tied to microbial influences on growth and behaviour, particularly bacterial influences on oviposition. In this study, we focus on the microbiota throughout insect development with a special focus on egg surface microbiota and their origin. We analysed the microbiota in the haemolymph and gut of larvae raised on sterilized and non-sterilized feed, pupal cell pulp, the wash of the ovipositor, eggs directly collected after oviposition, ovarian eggs, the empty female abdomen, eggs exposed to adult BSF, and surface-sterilized eggs. Our analysis revealed distinct bacterial community profiles across life stages, indicating a transition from larval dominance of Enterobacteriaceae to Burkholderiaceae on all analysed eggs. At the genus level, larval stages were characterized by Morganella, Escherichia, and Proteus, transitioning to less diverse communities in egg samples predominated by Burkholderia-Caballeronia-Paraburkholderia. Our study reveals that while predominant microbiota persist throughout all life stages, microbial community composition transforms progressively during maturation, particularly before oviposition. Understanding egg surface microbiota and the cues guiding oviposition has the potential to boost egg production and simplify mass harvesting of BSF larvae.}, }
@article {pmid41515900, year = {2025}, author = {Wu, J and Zhou, L and Qiu, D and Wei, T and Xie, C and Chen, E and Lin, M and Fan, Y}, title = {Integrating Bioinformatics and Experimental Validation Identifies SCD as a Ferroptosis-Related Immune Regulator and Therapeutic Target in Crohn's Disease.}, journal = {International journal of molecular sciences}, volume = {27}, number = {1}, pages = {}, doi = {10.3390/ijms27010019}, pmid = {41515900}, issn = {1422-0067}, support = {2025J011410//the Natural Science Foundation of Fujian Province/ ; 2025J08298//the Natural Science Foundation of Fujian Province/ ; }, mesh = {*Ferroptosis/genetics/immunology ; *Crohn Disease/genetics/immunology/metabolism/pathology/drug therapy ; *Computational Biology/methods ; Humans ; Animals ; Mice ; Disease Models, Animal ; Gene Expression Profiling ; Colitis/genetics/chemically induced/immunology ; }, abstract = {This study investigates the role of ferroptosis-related genes (FRGs) in the intestinal inflammation of Crohn's disease (CD). Through integrated bioinformatics and experimental validation, we identified differentially expressed genes from RNA-seq data and intersected them with known FRGs to obtain ferroptosis-related differentially expressed genes (FEDGs). Functional enrichment and immune infiltration analyses were performed, and seven hub FEDGs were selected using machine learning. A diagnostic model based on these genes showed strong predictive ability. Immune analysis revealed significant associations with macrophages, neutrophils, dendritic cells, and CD4+ T cells. Protein expression of key hub genes was validated in clinical CD samples and a DSS-induced colitis model. Importantly, localized inhibition of SCD alleviated disease severity in experimental colitis. These findings highlight the involvement of ferroptosis in CD immune dysregulation and propose SCD as a potential therapeutic target.}, }
@article {pmid41514812, year = {2026}, author = {Huang, Q and Chang, M and Sun, P}, title = {Early-Life Galacto-Oligosaccharide Supplementation Induces Persistent Immunoglobulin and Metabolic Alterations in Holstein Dairy Calves by Shaping Gut Microbiota.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {1}, pages = {}, doi = {10.3390/ani16010126}, pmid = {41514812}, issn = {2076-2615}, support = {2022YFD1301101//National Key Research and Development Program of China/ ; 2022YFD1300505//National Key Research and Development Program of China/ ; CARS-37//The earmarked fund for China Agriculture Research System/ ; Y2025YC52//Central Public-interest Scientific Institution Basal Research Fund/ ; ASTIP-IAS07//Agricultural Science and Technology Innovation Program/ ; }, abstract = {Early-life development of immune functions is crucial for calf health, growth, and future productivity. Galacto-oligosaccharides (GOSs) have been reported to facilitate ruminal microbial establishment and improve growth in Holstein dairy calves, but their prolonged influence on immunoglobulin levels, hindgut microbiota, and metabolic regulation remains insufficiently understood. This study evaluated the effects of early-life GOS supplementation on immune-related indicators, intestinal microbial ecology, and metabolic profiles in Holstein calves. Twenty-four newborn Holstein female dairy calves were randomly assigned to a control group (CON, n = 12) or a GOS group (GOS, n = 12; 10 g/day from birth to day 28). After supplementation ceased on day 28, calves previously receiving GOS were referred to as the GOSS group (n = 6). Immunoglobulin levels, gut microbiota, and fecal and serum metabolomes were evaluated during supplementation and six weeks after withdrawal. GOS supplementation significantly increased serum IgA and IgG levels during the treatment, with IgG levels remaining elevated for six weeks after discontinued supplementation. Although overall microbial diversity was not markedly altered, GOS selectively enriched bacterial taxa and function pathways linked to amino acid synthesis, unsaturated fatty acid production, and coenzyme-related metabolism. On day 70, GOSS group displayed distinct fecal and serum metabolomic profiles, with altered metabolites primarily associated with vitamin B6, folate, cobalamin metabolism, branched-chain amino acid biosynthesis, and purine and arginine pathways. These results demonstrate that early-life GOS supplementation promotes sustained immune and metabolic alterations following supplementation cessation, potentially mediated by modulation of gut microbial functions. These findings suggest that early dietary GOS supplementation may support physiological maturation in calves and could be useful as a nutritional strategy in calf-rearing systems.}, }
@article {pmid41514032, year = {2026}, author = {Roncero-Ramos, B and Romano-Rodríguez, E and Mateos-Naranjo, E and Valle-Romero, P and Redondo-Gómez, S}, title = {Hydro- and Xerohalophyte Species Drive Compositional and Functional Divergence in Bacterial Leaf Endosphere.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02679-x}, pmid = {41514032}, issn = {1432-184X}, support = {PAIDI-DOCTOR 21_00571//Junta de Andaluc&#xed;a/ ; FPU21/04133//Ministerio de Universidades/ ; FPU22/02078//Ministerio de Universidades/ ; PID2021-124750NB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, abstract = {Hydro- and xerohalophytes withstand stress thanks to the resistance traits they have, complemented with the functions of their associated microbiota. Besides, given a higher exposition of the phyllosphere to environmental conditions compared to roots, their endospheric bacteria should be more resistant to stress. In this study, we analysed the composition and functional traits of the bacterial leaf endosphere of six xero- and hydrohalophytes species in two seasons. We sequenced their endospheric metagenomes by shotgun and annotated genes related with Plant-Growth-Promoting (PGP) properties. We showed that the composition, structure and functions of the bacterial endosphere are mainly influenced by host plant species, followed by functional type. Moreover, plant species and functional type promoted a different relative abundance of, respectively, 62 and 6 PGP properties. This study shows that not only the composition but also the functionality of the bacterial leaf endosphere of halophytes is more influenced by host species than functional type. Moreover, the leaf endosphere of the different plant species and functional type could be an important source of bacteria with diverse PGP properties.}, }
@article {pmid41513996, year = {2026}, author = {Zhang, R and Mayer, L and Hikida, H and Shichino, Y and Mito, M and Willemsen, A and Iwasaki, S and Ogata, H}, title = {A giant virus forms a specialized subcellular environment within its amoeba host for efficient translation.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {41513996}, issn = {2058-5276}, support = {JP18H02279//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP22H00384//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP23KJ1258//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP24H02307//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JPMJFS2123//MEXT | Japan Science and Technology Agency (JST)/ ; }, abstract = {Many eukaryotic viruses, including amoeba-infecting mimiviruses, have codon usage that deviates from their hosts. However, codon usage patterns that align with the cellular tRNA pool enable efficient translation. How these viruses cope with the mismatch between tRNA supply and demand is unclear. Here we show that Acanthamoeba polyphaga mimivirus (APMV) generates a subcellular area to translate viral mRNAs. tRNA sequencing showed that the tRNA pool was not substantially altered during the infection, even though the virus encodes tRNA genes. Using in situ labelling, we found that viral mRNAs and newly synthesized proteins were localized in the periphery of the viral factory, suggesting that APMV creates a discrete subcellular environment to facilitate translation. Frequently used codons in viral mRNAs had higher tRNA accessibility than the same type of codons in amoeba mRNAs. Our data show how local translation assists the virus in overcoming the mismatch between tRNA supply and demand.}, }
@article {pmid41513647, year = {2026}, author = {Lu, Y and Eisenhauer, N and Patoine, G and Chen, Y and Heintz-Buschart, A and Küsel, K and Wegner, CE and Buscot, F and Liu, X and Araujo, ASF and Frey, B and Maestre, FT and Vadeboncoeur, M and van den Brink, L and Ponette, Q and Didion, M and Wohlfahrt, G and Gaxiola, A and Branquinho, C and Meesenburg, H and Fukuzawa, K and Adair, EC and Andrić, A and Barna, M and Bei, Q and Bruelheide, H and Caliman, A and Canessa, R and Carbognani, M and Cazzolla Gatti, R and Chen, C and Christiansen, CT and Danger, M and Davydov, EA and de Graaff, MA and Delire, C and Cecco, VD and Martino, LD and Djukic, I and Drollinger, S and Enoki, T and Fekete, I and Fransson, P and Freitag, M and Frenzel, M and Gavilán, RG and Glatzel, S and Glushkova, M and González, G and Gripp, ADR and Haase, P and Hamer, U and Hishi, T and Hiura, T and Hornung, E and Hoshizaki, K and Jäger, H and Jiménez, JJ and Kelly-Slatten, MJ and Kepfer-Rojas, S and Kotroczó, Z and Kriiska, K and Kurokawa, H and Lajtha, K and Loehr, J and Löfgren, S and Maire, V and Martins, RL and Maunoury-Danger, F and Melece, I and Ochoa, V and Ostonen, I and Paquette, A and Parker, WC and Peri, PL and Mast, R and Petraglia, A and Petřík, P and Pușcaș, M and Rebmann, C and Reich, PB and Rillig, MC and Schädler, M and Schaub, M and Schmidt, A and Seeber, J and Serrano, HC and Sousa, AI and Scheu, S and Stefanski, A and Tomaselli, M and Tóth, Z and Trevathan-Tackett, SM and Trogisch, S and Turtureanu, PD and Ursu, TM and Venn, SE and Verstraeten, A and Vijayanathan, J and Vujanović, D and Wagner, M and Weih, M and Zehetner, F and Guerra, CA}, title = {Landscape effects on global soil pathogenic fungal diversity across spatial scales.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-025-67929-5}, pmid = {41513647}, issn = {2041-1723}, support = {EI 862/29-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, abstract = {Growing evidence has shown that, apart from local environmental factors, changes in landscape-level factors by accelerated land-use change can also shape soil pathogenic fungal diversity. However, the global representativeness of such patterns remains unclear. Here, we assess how pathogenic fungal diversity in 511 soil samples worldwide responds to landscape factors, including landscape complexity index based on eight landscape metrics and quantity of different land cover types across six spatial scales (i.e., surrounding landscape, 250 m to 10,000 m radii from the sampling coordinate). We find that while soil variables explain over half of the variance, pathogenic fungal alpha diversity increases with landscape complexity and crop cover proportion, but decreases with grass and tree cover proportion, together explaining 23.4% of the total variance. Landscape factors have weaker impacts on beta diversity, explaining 13.0% of the variance. Across spatial scales, grassland ecosystems exhibit increasingly stronger responses to landscape variables compared to forest ecosystems. Landscape factors have a higher relative contribution to root-associated fungi than leaf/fruit/seed-associated fungi. Our results emphasize the importance of local factors and the complementary role of landscape patterns in shaping global soil pathogenic fungal distributions, highlighting scale-dependent effects across ecosystems and fungal functional groups.}, }
@article {pmid41511110, year = {2026}, author = {Gallardo Molina, P and Choi, BI and Vanek, M and Khan, MH and Tomasek, K and Kwant, AN and Dijkstra, P and de Vos, MGJ and Wolfe, AJ}, title = {SimUrine: a novel, fully defined artificial urinary medium for enhanced microbiological research of urinary bacteria.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0155925}, doi = {10.1128/aem.01559-25}, pmid = {41511110}, issn = {1098-5336}, abstract = {UNLABELLED: Urinary tract infections represent one of the most prevalent bacterial diseases, yet current diagnostic and research methodologies are hampered by inadequate culture media that fail to replicate the bladder biochemical environment. Conventional artificial urine formulations contain undefined components, lack essential nutrients, or inadequately support urinary microbiome (urobiome) growth. To address these limitations, we developed SimUrine, a fully defined synthetic urine medium that aims to replicate human bladder chemistry while supporting diverse microbial growth requirements. SimUrine was systematically developed through iterative optimization of multi-purpose artificial urine, incorporating defined concentrations of carbon sources, vitamins, trace elements, and amino acids within physiologically relevant ranges. The modular design enables component substitution without complete reformulation, facilitating customization for culturomics, antimicrobial susceptibility testing, and microbial ecology studies, while reducing batch-to-batch variability associated with authentic urine. Performance evaluation demonstrated SimUrine's capability to support the growth of fastidious urobiome members, including Lactobacillus species, Aerococcus urinae, and Corynebacterium riegelii, which fail to proliferate in conventional minimal media. Physicochemical characterization confirmed that SimUrine formulation exhibits properties within normal human urine ranges for density, conductivity, osmolarity, and viscosity, ensuring physiological relevance. Clinical applications revealed reduced antibiotic susceptibility compared to standard media, suggesting a more accurate representation of in vivo conditions. Co-culture experiments using Escherichia coli and Enterococcus faecalis demonstrated previously unobserved microbial interactions, highlighting SimUrine's utility for investigating urobiome dynamics. SimUrine represents a significant advancement in urobiome research methodology, providing a standardized, reproducible platform for investigating the urobiome under physiologically relevant conditions, potentially improving fundamental understanding and clinical diagnostic approaches.<br><br>IMPORTANCE: Urinary tract infections (UTIs) affect millions globally, yet current research and diagnostic methods rely on inadequate culture media that fail to replicate the bladder's unique biochemical environment. This fundamental limitation has hindered accurate UTI research and potentially compromised clinical treatment decisions. SimUrine addresses this critical gap as the first fully defined synthetic urine medium that mimics human bladder chemistry while supporting the growth of diverse urinary microbes. The breakthrough enables the cultivation of urobiome organisms in a minimal medium that resembles natural conditions, revealing novel microbial interactions that influence urinary health. Crucially, SimUrine demonstrates different antimicrobial susceptibility patterns compared to standard clinical media, suggesting current testing protocols may inaccurately predict treatment outcomes. This standardized, reproducible platform eliminates the variability of authentic urine samples while maintaining physiological relevance, potentially transforming urobiome research methodology and providing a new tool for the study of UTIs worldwide.}, }
@article {pmid41508507, year = {2026}, author = {Lee, G and Heo, S and Jeong, DW}, title = {Origin and prevalence of food-derived coagulase-negative staphylococci in fermentation: impact of protein, lipid, salt, and pH conditions.}, journal = {Food research international (Ottawa, Ont.)}, volume = {225}, number = {}, pages = {118096}, doi = {10.1016/j.foodres.2025.118096}, pmid = {41508507}, issn = {1873-7145}, mesh = {*Staphylococcus/isolation &amp; purification/classification/enzymology/metabolism ; Hydrogen-Ion Concentration ; *Fermentation ; *Food Microbiology ; *Fermented Foods/microbiology ; Coagulase/metabolism ; Sodium Chloride/analysis ; }, abstract = {Coagulase-negative staphylococci (CNS) are primarily detected in protein-rich and high-salt fermented foods, such as fermented meat and soybean products. This review investigates the relationship between CNS species and the nutritional and physicochemical properties of fermented foods, focusing on protein, fat, carbohydrate composition, salt concentration, and pH. Published studies over the past 20 years were systematically analyzed to identify CNS species and their distribution across food types and regions. Among the species, Staphylococcus saprophyticus, S. xylosus, S. equorum, and S. gallinarum were most frequently reported. S. saprophyticus was detected across a broad range of conditions, whereas S. xylosus was more common in acidic environments (pH 4-6). S. equorum dominated in higher pH (5-8) and high-salt (>20%) conditions, whereas S. gallinarum persisted even in salt concentrations exceeding 15%. These findings indicate that nutrient composition, pH, and salt concentration shape the dominant CNS species in fermented foods. Such correlations not only improve our understanding of microbial ecology in fermentation but also provide a basis for the selection and application of tailored starter cultures in the food industry.}, }
@article {pmid41506929, year = {2026}, author = {Rodríguez-Gijón, A and Laso-Pérez, R}, title = {Deep-learning dive into the antimicrobial potential of Archaea.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2025.12.004}, pmid = {41506929}, issn = {1878-4380}, abstract = {The global burden of antimicrobial resistance demands the urgent development of new antibiotics. To face this threat, Torres et al. leveraged deep-learning models to identify archaeal encrypted peptides (termed 'archaeasins') with potential antimicrobial activity. This work highlights Archaea as an underexplored but potentially rich source of antibiotics.}, }
@article {pmid41506577, year = {2026}, author = {Sagar, K and Priti, K and Chandra, H}, title = {Artificial intelligence in metagenome-assembled genome reconstruction: Tools, pipelines, and future directions.}, journal = {Journal of microbiological methods}, volume = {}, number = {}, pages = {107390}, doi = {10.1016/j.mimet.2026.107390}, pmid = {41506577}, issn = {1872-8359}, abstract = {Metagenomic sequencing has revolutionised the field of microbial ecology, as it has led to cultivation-independent exploration of complicated microbial communities. The assembly of metagenome-assembled genomes has provided genome-scale information about uncultivated microorganisms, but issues such as sequencing errors, fragmented assemblies, residual redundancy, uneven coverage, recovery of low-abundance taxa, and highly diversified taxa continue to impair the quality of these genomes. The latest achievements in artificial intelligence, particularly in machine learning and deep learning, have played a significant role in overcoming these limitations by enhancing quality control, error correction, assembly, binning, refinement, and annotation procedures. It is demonstrated that representation learning and graph-based binning methods have high strain-level resolution and can reduce contamination in complex microbial communities, whereas artificial intelligence-based assemblers and polishing tools improve base-level precision and assembly contiguity. This review synthesises traditional and artificial intelligence-based workflows involved in the reconstruction of metagenome-assembled genomes, encompassing quality control, assembly, binning, refinement, and annotation, as well as quantitative benchmarking of significant artificial intelligence-based pipelines. As future directions, the focus on emerging trends, such as explainable artificial intelligence, federated learning, cloud-native scalable pipelines, multimodal and multi-omics integration, and large language model-based annotation, is covered. In general, the incorporation of artificial intelligence represents a paradigm shift in the reconstruction of metagenome-assembled genomes, allowing for a more relevant, scalable, and biologically informative search of the microbial dark matter in various ecosystems.}, }
@article {pmid41504899, year = {2026}, author = {Cottorello-Fonsêca, M and Rezende, EGF and Freitas, FRS and Carneiro, RB and Sakamoto, IK and Ribeiro, R and Zaiat, M}, title = {Understanding the kinetics of antibiotic mixture biotransformation and microbial interactions in an anaerobic fixed-bed reactor for wastewater treatment.}, journal = {Bioprocess and biosystems engineering}, volume = {}, number = {}, pages = {}, pmid = {41504899}, issn = {1615-7605}, support = {2020/15087-8//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 22/04367-5//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2019/22532-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2020/15087-8//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; Financial Code 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; PCI2022-121990//EU and the State Research Agency (AEI)/ ; PCI2022-121990//EU and the State Research Agency (AEI)/ ; 869178//ERA-NET AquaticPollutants Joint Transnational Call/ ; 869178//ERA-NET AquaticPollutants Joint Transnational Call/ ; }, abstract = {The increase of antibiotics in aquatic environments, along with the emergence of antibiotic-resistant bacteria, highlights the improvement of wastewater treatment technologies. This study investigates a plug-flow structured anaerobic fixed-bed reactor (PF-AnFBR) for removal nine antibiotics representing different classes-an approach rarely explored in anaerobic systems. By integrating spatially resolved sampling along the reactor bed with advanced kinetic modeling, the study provides the first mechanistic evaluation of antibiotic mixture removal in a PF-AnFBR. COD removal remained high (COD > 97%) despite the presence of antibiotics, and significant removal was observed for trimethoprim (100%), sulfamethoxazole (83.3%), and enrofloxacin (81.3%). The first-order model accurately described COD removal, while the reversible biotransformation model (RevBio) successfully captured antibiotic fate (NRMSE < 3.5%), revealing class-specific mechanisms: fluoroquinolones dominated by adsorption (high KD and ksor), sulfonamides exhibiting reversible biotransformation, and trimethoprim characterized by highly irreversible biotransformation. Microbial community and KEGG-based functional analyses identified key taxa (e.g., Pseudomonas, Lactivibrio, Syntrophorhabdus, Methanothrix) and metabolic pathways (ABC transporters, cytochrome P450 enzymes) responsible for antibiotic transformation. By coupling reactor hydrodynamics, kinetic modeling, and microbial ecology, this study provides novel mechanistic insight into the removal of complex antibiotic mixtures in anaerobic fixed-bed reactors and supports PF-AnFBR as a robust technology for decentralized wastewater treatment.}, }
@article {pmid41504158, year = {2025}, author = {Chen, T and Guo, Y and Liang, D and Li, D and Xing, S and Li, D and Zhang, C and Wang, F}, title = {Discriminative Gut Microbial Signatures in Hyperuricemia and Overweight Populations Revealed by Metagenomic Sequencing.}, journal = {International journal for vitamin and nutrition research. Internationale Zeitschrift fur Vitamin- und Ernahrungsforschung. Journal international de vitaminologie et de nutrition}, volume = {95}, number = {6}, pages = {42590}, doi = {10.31083/IJVNR42590}, pmid = {41504158}, issn = {0300-9831}, support = {S2023KFKT-12//Ministry of Agriculture and Rural Affairs/ ; 2024YFF1107000//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Hyperuricemia/microbiology ; Male ; Female ; *Overweight/microbiology ; Middle Aged ; Cross-Sectional Studies ; Feces/microbiology ; Adult ; Metagenomics ; Metagenome ; }, abstract = {BACKGROUND: This cross-sectional study aimed to investigate the relationships between gut microbiota compositional alterations and chronic metabolic disorders by analyzing taxonomic diversity, community structure, and species-level differences in individuals with hyperuricemia (HUA) and a history of being overweight. Our findings offer novel insights into microbiota-targeted therapeutic strategies for managing metabolic diseases. A total of 144 participants were recruited and divided into three diagnostic categories: healthy controls (HL, n = 29), hyperuricemia group (HU, n = 24), and overweight (OW, n = 91).<br><br>METHODS: Comprehensive phenotypic profiles and metagenomes were analyzed for fecal samples from the three groups.<br><br>RESULTS: Significant differences were observed in psychological states and microbial ecology between the metabolic disorder groups (HU and OW) and the control group (HL) (p < 0.05). Both the overweight individuals and those with HUA presented significant changes in gut microbial composition, with reduced &#x3b1;-diversity indices (Shannon index: HU vs HL Mann-Whitney U = 306; p = 0.462; OW vs HL Mann-Whitney U = 1008; p = 0.040; richness index: HU vs HL Mann-Whitney U = 307; p = 0.469; OW vs HL Mann-Whitney U = 1072; p = 0.092) compared to healthy individuals. Moreover, analysis of the linear discriminant analysis effect size (LEfSe) identified four discriminatory species in the HU group (Alistipes putredinis, Mediterraneibacter faecis, Streptococcus oralis, and Gemella sanguinis), and five in the OW group (Pantoea endophytica, Pantoea vagans, Phocaeicola coprophilus, Ruminococcus SGB4421, and Klebsiella oxytoca), representing potential biomarkers for the progression of chronic metabolic diseases.<br><br>CONCLUSION: This study elucidates the characteristics of overweight individuals and those with HUA in terms of phenotypic features and gut microbiota, providing a theoretical reference for gut microbiota-targeted therapies and lifestyle interventions in chronic metabolic diseases.}, }
@article {pmid41502987, year = {2026}, author = {Mohan, R and Johnson, SD and Dean, PN and Acharya, A and Byrareddy, SN}, title = {Methods to characterize the vaginal microbiome in a rhesus macaque model of simian human immunodeficiency virus (SHIV) transmission uncover epithelium-associated enrichment of Prevotella.}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100526}, pmid = {41502987}, issn = {2666-5174}, abstract = {The vaginal microbiome plays a crucial role in maintaining mucosal integrity and mitigating pathogen transmission, yet its comprehensive characterization remains challenging due to limited sampling and analysis methods. In this study, we aimed to characterize bacterial and fungal taxa diversities in the vaginal microbiomes of Simian Human Immunodeficiency (SHIV)-infected rhesus macaques, as well as their metabolic activities, using three sampling methods. The cervicovaginal lavage (CVL), vaginal swab, and vaginal mucosal tissue methods offer novel insights into microbial diversity and their potential impacts on HIV transmission. Using 16S rRNA and Internal Transcribed Spacer (ITS) sequencing, we assessed bacterial and fungal community composition and abundances, respectively, across all sampling methods. PICRUSt2 was used for functional predictions, and a modified glycosidase assay to further characterize glycan-degrading enzymatic activity in CVL samples. Our findings reveal that tissue samples were uniquely enriched for microbial taxa such as Prevotella spp. and Helicobacter spp., showing notable abundance differences compared to CVL and swab samples. Tissue samples exhibited higher alpha diversity and distinct metabolic prediction profiles, particularly elevated sialidase activity. While fewer differences were found in fungal microbiome composition and diversity, marked correlations were observed between bacterial and fungal taxa, emphasizing complex interkingdom interactions. These results highlight the significance of sampling methods in microbial ecology studies, which should be carefully considered due to their potential influence on pathogen transmission risk.}, }
@article {pmid41502854, year = {2025}, author = {Su, JW and Qin, SY and Liu, J and Lei, CC and Zhang, XT and Shi, WH and Xie, LH and Liu, Y and Ni, HB and Yu, MY and Liang, HR and Qin, Y and Jiang, J and Sun, HT and Ma, H and Li, ZY and Zhang, XX}, title = {Blastocystis presence alters gut archaeal communities and metabolic functions in Tibetan antelopes (Pantholops hodgsonii).}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1744013}, pmid = {41502854}, issn = {2297-1769}, abstract = {BACKGROUND: Archaea are vital members of the gut microbiota, yet their diversity and functions in high-altitude wildlife remain poorly understood. Understanding their ecological roles can provide insights into host health and microbial community dynamics.<br><br>METHODS: We applied metagenome-assembled genome (MAG)-based approaches to investigate gut archaea in Tibetan antelopes (Pantholops hodgsonii) and assess their shifts in the presence of Blastocystis. A total of 463 non-redundant archaeal MAGs were reconstructed and analyzed for taxonomic diversity and functional potential.<br><br>RESULTS: The MAGs encompassed 16,189 protein clusters, with over 70% representing potentially novel species, highlighting substantial unexplored archaeal diversity. Alpha diversity showed no significant differences between healthy and Blastocystis-present groups, but beta diversity analysis revealed marked community restructuring, including decreased Methanobacteriota and increased Halobacteriota and Thermoplasmatota in the Blastocystis-present group. Functional annotation indicated changes in energy and nucleotide metabolism and alterations in carbohydrate-active enzyme composition. Additionally, putative viral sequences were detected within archaeal MAGs, suggesting potential virus-microbe interactions.<br><br>CONCLUSION: Our findings provide novel insights into the diversity and ecological functions of gut archaea in Tibetan antelopes, offering a foundation for future research on their contributions to host health and microbial ecology.}, }
@article {pmid41501262, year = {2026}, author = {Carofano, I and Martinez-Sañudo, I and Riegler, M and Hancock, DL and Morrow, JL and Mazzon, L}, title = {Detection of a Conserved Bacterial Symbiosis in non-frugivorous Australian Fruit Flies (Diptera, Tephritidae, Tephritinae) Supports its Widespread Association.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02686-y}, pmid = {41501262}, issn = {1432-184X}, support = {DOR2271053/22//Universit&#xe0; degli Studi di Padova/ ; }, abstract = {Several insect lineages, including some fruit flies, have evolved mutualistic associations with primary symbiotic bacteria. Some species of Tephritinae, the most specialized subfamily of fruit flies (Diptera, Tephritidae) harbour co-evolved, vertically transmitted and non-culturable bacterial symbionts in their midgut, known as Candidatus Stammerula spp. (Enterobacteriaceae). While such associations have previously been reported in the Palearctic and Hawaiian Archipelago, their occurrence in Australasia had not been investigated. In this study we assessed the genetic diversity of eight Australian fruit fly's species from six genera belonging to the Tephritini tribe using mitochondrial markers (16 S rRNA and COI-tRNALeu-COII genes) and compared their bacterial diversity using the 16 S rRNA gene. We detected the presence of specific symbiotic bacteria in all sampled species. Analysis of bacterial 16 S rRNA showed that, with one exception, all Australian symbionts clustered in a well-supported monophyletic clade with Ca. Stammerula detected in Palearctic and Hawaiian Tephritini. Distinct Stammerula lineages were identified in several taxa, while two species, Trupanea prolata and Spathulina acroleuca shared identical symbiont sequences and the same host plant. Notably, Australian and Palearctic Sphenella spp. harboured closely related symbionts. The cophylogenetic analysis revealed a substantial congruence between host and symbiont tree, supporting a history of cospeciation and suggesting biogeographic links between Australasian and Palearctic taxa. Overall, the results expand the geographic knowledge of Tephritini-Ca. Stammerula association and highlight a global pattern of co-diversification.}, }
@article {pmid41499160, year = {2026}, author = {Hai, Q and Li, D and Huang, T and Dang, X and Xu, J and Ma, Z and Zhou, Z}, title = {The Honeybee Gut Microbiome: A Novel Multidimensional Model of Antimicrobial Resistance Transmission and Immune Homeostasis from Environmental Interactions to Health Regulation.}, journal = {FEMS microbiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuag001}, pmid = {41499160}, issn = {1574-6976}, abstract = {The honeybee gut microbiome has emerged as a model system in microbial ecology, valued for its structural stability and host specificity, and has garnered significant attention for elucidating universal principles of host-microbe interactions. This review advocates for the honeybee as a multidisciplinary model organism, highlighting the unique role of its gut microbiota in maintaining colony immune homeostasis, driving host co-evolution, unraveling the transmission mechanisms of antibiotic resistance genes (ARGs), and enhancing host adaptability to environmental stressors. By integrating multidimensional factors, including environmental gradients and apicultural practices, we construct an "Environment-Microbiota-Host Health" interaction framework to transcend the limitations of single-factor analyses. This framework provides a novel paradigm for the ecological containment of antimicrobial resistance, the conservation of pollinator resources, and microbiome-based engineering interventions. The review underscores the unique value of the honeybee model in unraveling social insect-microbe coevolution and resistance transmission dynamics, while also prospecting its application potential in developing novel antimicrobial peptides, designing probiotic formulations, and monitoring environmental resistance.}, }
@article {pmid41499039, year = {2026}, author = {Madjirebaye, P and Penga, Z and Mueeda, A and Huang, T and Peng, F and Muyan, X and Liua, Z and Mahamat, B and Allasra, Y and Xu, Y and Xiong, T and Xie, M}, title = {Unraveling Streptococcus Thermophilus NCU074001-Based Anti-Diarrheal Actions Via Integrated Immune-Gut Microbiota and Tryptophan Metabolic Pathway Identification.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41499039}, issn = {1867-1314}, support = {Project No. 20243BCC31004; Project No. S20251709//Key Research and Development Projects of Jiangxi Province/ ; Project No. 20232BCD44005//National Key Laboratory Project/ ; Project No. 2022-PYXM-04//), Jiangxi Medicine Academy of Nutrition and Health Management 2022 Cultivation project/ ; Project No. JXNK202303-05//Agricultural key core technology research project of Jiangxi Province/ ; Project No. JXARS-06//Vegetable Industry Technology System Post Expert Project of Jiangxi Province/ ; Project No. ZDYF2024XDNY277//the Hainan Provincial Key Research and Development Project/ ; }, abstract = {Diarrhea, a common gastrointestinal disorder, is often exacerbated by conventional antibiotic treatments that disrupt gut microbiota, necessitating the exploration of Lactic acid bacteria (LAB) alternatives. This study investigates the therapeutic potential and mechanisms of Streptococcus thermophilus NCU074001 (ST) in a rat model of PEG3350-induced osmotic diarrhea. ST treatment mitigated diarrheal symptoms and improved key markers of intestinal health by acting as a key modulator of the gut ecosystem. Its efficacy was driven by balancing immune responses via elevated IL-10 and suppressed pro-inflammatory cytokines (IL-6, IL-1β, TNF-α, IFN-γ). Furthermore, ST reinforced the intestinal barrier by upregulating MUC2 expression and reshaping gut microbial ecology by suppressing certain genera (Bacteroides and Anaerofilum) while enriching others (Lactobacillus, Akkermansia, Phascolarctobacterium, and Parabacteroides). This taxonomic restoration was accompanied by a functional metabolic shift, characterized by increased production of short-chain fatty acids (acetate and butyrate) and a targeted modulation of tryptophan metabolism that enhanced the production of anti-inflammatory indole derivatives. Correlation analyses suggested potential links between ST-mediated microbiota remodeling and barrier strengthening and immunomodulation. Collectively, these results indicate that ST functions as a promising probiotic integrating immunomodulation, microbiota restoration, and metabolic reprogramming to alleviate diarrhea, and thus presents a promising therapeutic alternative to conventional antibiotics.}, }
@article {pmid41495312, year = {2026}, author = {Kiran, R and Sharma, M and Subramanian, S and Patil, SA}, title = {Halophilic Anaerobic Cultures Enriched with CO2:H2 from Different Saline Environments Reveal Unknown Autotrophic Bacterial Diversity and Modular Carbon Fixation Pathways.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02654-6}, pmid = {41495312}, issn = {1432-184X}, abstract = {The subsurface sediments of saline-aquatic systems host diverse microbes, with unclear ecological roles and challenging lab cultivability. Chemolithotrophic anaerobes involved in CO2-fixation are one of the poorly studied groups. This study focused on understanding these bacteria from subsurface sediments of four representative saline environments, two marine (i.e., Coastal Arabian and Bay of Bengal seas) and two lake (Sambhar and Lonar) systems through enrichment and metagenomics. Enrichment cultures with bicarbonate/CO2 and hydrogen as the carbon and energy sources, respectively, showed CO2 fixation, producing acetic and formic acids as the major organic products. Enriched culture with Sambhar Lake sediment produced more formic acid (391 ± 8 mg/L) than acetic acid (92 ± 20 mg/L); however, other enriched cultures produced considerably higher acetic acid (up to 966 ± 24 mg/L) than formic acid (up to 367 ± 30 mg/L). The organics production was accompanied by unique thread-like (up to 500 μm long) aggregates, harbouring chains of rod and oval-shaped microbes in all cultures. Metagenome sequencing revealed dominance of Vibrio spp. (relative sequence abundance of 91% to 97%) across all cultures, while canonical CO2-fixing taxa were nearly absent (< 0.01%). KEGG analysis revealed partial genes for various CO2 fixation pathways, including Wood-Ljungdahl, reverse-TCA, dicarboxylate-hydroxybutyrate, hydroxypropionate bicycle, hydroxypropionate-hydroxybutyrate, and the reductive-glycine pathway. The presence of a near-complete serine variant of the reductive glycine pathway, which has been demonstrated in engineered systems, suggests that this pathway may play an operational role in natural systems. The consistent production of organic acids and incomplete pathway representation suggests modular CO2 fixation within the Vibrio-dominated enriched mixed cultures.}, }
@article {pmid41493483, year = {2026}, author = {Sharma, N and Pal, J and Mahajan, R and Chandel, S and Sud, D and Sanspal, A}, title = {Pathogens without borders: a review on cross-kingdom transmission strategies and pathogenicity of plant and human pathogens.}, journal = {Archives of microbiology}, volume = {208}, number = {2}, pages = {98}, pmid = {41493483}, issn = {1432-072X}, }
@article {pmid41493101, year = {2026}, author = {Hoffert, M and Gorman, E and Lladser, ME and Fierer, N}, title = {Constructing a "periodic table" of bacteria to map diversity in trait space.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf289}, pmid = {41493101}, issn = {1751-7370}, abstract = {Despite an ever-expanding number of bacterial taxa being discovered, many of these taxa remain uncharacterized with unknown traits and environmental preferences. This diversity makes it challenging to interpret ecological patterns in microbiomes and understand why individual taxa, or assemblages, may vary across space and time. Although we can use information from the rapidly growing databases of bacterial genomes to infer traits, we still need an approach to organize what we know, or think we know, about bacterial taxa to match taxonomic and phylogenetic information to trait inferences. Inspired by the periodic table of the elements, we have constructed a "periodic table" of bacterial taxa to organize and visualize monophyletic groups of bacteria based on the distributions of key traits predicted from genomic data. By analyzing 50 745 genomes across 31 bacterial phyla, we used the Haar-like wavelet transformation, a model-free transformation of trait data, to identify clades of bacteria which are nearly uniform with respect to six selected traits - oxygen tolerance, autotrophy, chlorophototrophy, maximum potential growth rate, GC content, and genome size. The identified functionally uniform clades of bacteria are presented in a concise periodic table-like format to facilitate identification and exploration of bacterial lineages in trait space. While our approach could be improved and expanded in the future, we demonstrate its utility for integrating phylogenetic information with genome-derived trait values to improve our understanding of the bacterial diversity found in environmental and host-associated microbiomes.}, }
@article {pmid41492298, year = {2025}, author = {Jones, MK and Morris, D and Zhu, H and Marty, AM}, title = {One Health turns 10: A decade at the intersection of human, animal, and environmental health.}, journal = {One health (Amsterdam, Netherlands)}, volume = {21}, number = {}, pages = {101218}, pmid = {41492298}, issn = {2352-7714}, }
@article {pmid41492005, year = {2026}, author = {Miyamoto, K and Sujino, T}, title = {Microbiota-derived D-amino acids in intestinal homeostasis and inflammatory bowel disease.}, journal = {Inflammation and regeneration}, volume = {}, number = {}, pages = {}, doi = {10.1186/s41232-025-00403-3}, pmid = {41492005}, issn = {1880-9693}, abstract = {Inflammatory bowel disease (IBD) encompasses chronic, relapsing inflammatory disorders of the gastrointestinal tract, which are driven by intricate interactions between the host immune system and intestinal microbiota. Recent studies have revealed that microbiota-derived D-amino acids (D-AAs), once considered biologically inert, play critical roles in maintaining mucosal homeostasis and modulating immune responses. These metabolites, which are increasingly classified as postbiotics, directly influence epithelial barrier integrity, immune cell activity, and microbial ecology. In this review, we summarize the current insights into the biosynthesis, bacterial functions, and immunological implications of D-AAs in the gut, with a particular focus on their involvement in IBD pathogenesis. Specific D-AAs, such as D-alanine, contribute to bacterial cell wall integrity and quorum sensing and interact with host immune cells, alter microbial communities, and regulate mucosal barrier function. Evidence from both human studies and murine models highlights how disrupted D-AAs' metabolism through dysbiosis or impaired host sensing via enzymes such as D-amino acid oxidase (DAO) exacerbates inflammation. Finally, we discuss the translational potential of D-AAs as non-invasive biomarkers and therapeutic targets in IBD, emphasizing the need for integrative multi-omics approaches that connect microbial metabolism with host immune regulation and disease outcomes.}, }
@article {pmid41490489, year = {2026}, author = {Pontrelli, S and Guessous, G and Trouillon, J and Krishna, A and Hwa, T and Sauer, U}, title = {Hypersensitivity of chitin degradation to initial species densities due to monomer diffusion.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {2}, pages = {e2512676123}, doi = {10.1073/pnas.2512676123}, pmid = {41490489}, issn = {1091-6490}, support = {542395//Simons Foundation (SF)/ ; }, mesh = {*Chitin/metabolism ; Acetylglucosamine/metabolism ; Diffusion ; *Bacteria/metabolism ; Chitinases/metabolism ; }, abstract = {Resource competition strongly shapes microbial community dynamics and functionality. In polysaccharide-degrading communities, primary degraders release hydrolytic enzymes, whereas exploiters consume released products without producing enzyme themselves. We investigate the competitive strategies employed by marine chitin degraders and N-acetylglucosamine (GlcNAc) exploiters, revealing various mechanisms that impact community viability and growth dynamics. In addition to direct competition strategies such as antibiotic secretion or cell aggregation on chitin particles (which helps monopolize enzyme access), exploiters also inhibit degraders by diverting limiting GlcNAc flux during the early stages of particle degradation. This critical phase requires degraders to overcome the diffusive loss of GlcNAc to sustain their chitinase production. Through quantitative measurements and modeling, we demonstrate that nutrient competition among species and nutrient loss through diffusion during the initial stages of community dynamics strongly influence the long-term success of the community. The initial community composition dictates the former mechanisms, while the latter is closely related to particle size, both of which have profound implications for environmental carbon cycling. The resulting hypersensitivity of the community is analogous to the Allee effect observed in population biology, where the outcomes-in our case polymer degradation-are heavily dependent on starting conditions. This study sheds light on how metabolic competition in the early phases of particle degradation governs species interactions, resource partitioning, and overall community viability, even under identical environmental and genetic conditions.}, }
@article {pmid41485602, year = {2026}, author = {Adejumo, S and Lewis, G and Das, P and Lim, CKY and Malas, J and Oli, AN and Allen, JM and Hampton-Marcell, J}, title = {Dietary Protein Source Shapes Gut Microbial Structure and Predicted Functional Potential: A Systematic Integrative Re-analysis Using Machine Learning.}, journal = {Advances in nutrition (Bethesda, Md.)}, volume = {}, number = {}, pages = {100582}, doi = {10.1016/j.advnut.2025.100582}, pmid = {41485602}, issn = {2156-5376}, abstract = {BACKGROUND: Dietary proteins shape gut microbial ecology, yet the taxonomic and functional consequences of plant- versus animal-based proteins remain poorly defined. Although digestibility and fermentation profiles differ by protein type, a systematic evaluation of how these differences influence microbial diversity, community structure, and metabolic capacity is lacking. This study represents a systematic integrative re-analysis of raw 16S rRNA sequencing datasets derived from independent controlled animal feeding studies.<br><br>METHODS: Following PRISMA guidelines, we analyzed 16S rRNA sequencing data from 10 murine studies (n = 187) comparing plant- and animal-protein diets. Alpha diversity was assessed using Shannon, Inverse Simpson, and Chao1 indices, and beta diversity with Aitchison distances. Differentially abundant taxa were identified using LEfSe and class-weighted Random Forest models. Functional potential was inferred with PICRUSt2, and taxon-pathway relationships were explored using correlation and network analyses.<br><br>RESULTS: Plant-protein diets increased gut microbial diversity across all alpha diversity metrics and were associated with higher representation of saccharolytic and nitrogen-recycling genera such as Bacteroides, Muribaculaceae, and Allobaculum. Animal-protein diets favored proteolytic taxa, including Clostridium sensu stricto 1 and Colidextribacter. Microbial community structure differed significantly between diets (ANOSIM R = 0.663, p < 0.001). Random Forest models achieved >88% accuracy (AUC = 0.995) in predicting dietary groups, and LEfSe identified consistent discriminating taxa. Functional profiling showed that plant-based diets enriched pathways linked to short-chain fatty acid and aromatic amino acid metabolism, whereas animal-based diets favored sulfur- and branched-chain amino acid-associated pathways. Network analysis identified Muribaculaceae as a plant-associated hub and Lactobacillus as an animal-associated hub.<br><br>CONCLUSION: Dietary protein source significantly influences gut microbiota composition and functional potential in mice. Plant- and animal-based proteins generate distinct metabolic signatures with implications for nitrogen cycling, sulfur metabolism, and microbial ecology. Future controlled dietary studies that harmonize protein source with other macronutrient variables are needed to isolate protein-specific effects.<br><br>STATEMENT OF SIGNIFICANCE: This study presents the first standardized systematic integrative re-analysis of murine protein-intervention microbiome datasets, integrating taxonomic, machine learning, and predicted functional profiling to identify robust microbial and metabolic signatures that differentiate plant- from animal-based protein diets. By harmonizing raw sequencing data across diverse experimental contexts, this work clarifies foundational ecological responses to protein source and provides mechanistic hypotheses to guide future controlled nutrition and microbiome research.}, }
@article {pmid41485298, year = {2026}, author = {Chopra, C and Kukkar, D and Kaur, H}, title = {A 16S rRNA-based meta-analysis of gut microbiota in diabetic nephropathy using QIIME2 and publicly available NGS datasets.}, journal = {Computational biology and chemistry}, volume = {121}, number = {}, pages = {108876}, doi = {10.1016/j.compbiolchem.2026.108876}, pmid = {41485298}, issn = {1476-928X}, abstract = {Gut microbial profiles can differ significantly between diabetic nephropathy (DN), diabetic patients, and healthy controls (HCs). The exact microbial taxa involved in DN progression is yet to be fully characterized. Therefore, this study aims to compare the gut microbiota od DN patients with diabetic and healthy individuals. Accordingly, this study executes a pioneering metanalytical view using the publicly available datasets (National centre for biotechnology information) to evaluate DN associated variation in gut-microbiota diversity. We hypothesize that the DN patients should have a smaller number of beneficial microbes along with a greater fraction of pathogenic microbial composition relative to the other two groups. Specifically, this report utilizes quantitative insights into microbial ecology 2 (QIIME2) platform to identify an association between gut microbiota composition and DN advancement. This novelty provides distinctive nature to our work in comparison to the broader diabetes microbiome studies. Our study enables comprehensive taxonomic profiling, differential abundance testing, and alpha and beta diversity analyses across multiple studies. A total of six studies were included, comprising 684 samples from both DN patients and HCs. Post quality control check, these samples were processed using QIIME2 platform for taxonomic profiling and diversity analysis to characterize microbial dysbiosis in DN patients in relation to other two groups. Alpha diversity indicates insignificant trend towards reduction of microbial diversity as observed using the Kruskal-Wallis test, Shannon index, Observed features (richness), and Faith's PD analysis (p > 0.05). Additionally, beta diversity analyses revealed a trend toward microbial richness in DN compared to diabetic individuals and HCs, though differences were statically insignificant (P > 0.05). Taxonomic profiling showed a depletion of beneficial genera (e.g., Faecalibacterium, Roseburia, and Bifidobacterium) with false discovery rate (FDR)-adjusted p < 0.05. Contrarily, pathogenic and pro-inflammatory taxa including Escherichia-Shigella, Enterococcus, and Klebsiella showed higher abundance in the DN group (FDR-adjusted p < 0.05). These compositional shifts highlight pronounced gut dysbiosis during the transition from diabetes to DN, suggesting a potential association between gut-kidney axis.}, }
@article {pmid41485297, year = {2025}, author = {Chen, Y and Li, Y and Niu, L and Grossart, HP and Wang, Y and Ma, X and Lin, L}, title = {Hydrodynamics regulates microbial degradation of microplastics by modulating bottom-up and top-down effects in a river-lake confluence zone.}, journal = {Water research}, volume = {292}, number = {}, pages = {125311}, doi = {10.1016/j.watres.2025.125311}, pmid = {41485297}, issn = {1879-2448}, abstract = {River-lake confluence zones, characterized by unique hydrodynamic conditions, are critical areas for pollutant transformation. Nevertheless, degradation of microplastics (MP) mediated by multi-trophic microbial communities remains poorly understood under such complex hydrodynamic disturbances. This study investigated the characteristics of multi-trophic microbiota of the microplastome and explored their roles in MP degradation across four distinct hydrodynamic zones, i.e., maximum velocity zone (Z1), flow buffer zone (Z2), flow deflection zone (Z3), and flow reestablishment zone (Z4), in a river-lake confluence. A pronounced spatial heterogeneity in MP abundance and available nutrients was revealed among the four flow zones, with Z3 exhibiting the most intense MP degradation. Additional microcosm experiments demonstrated that microbial MP degradation was primarily driven by the enriched degrading bacteria and fungi, facilitated by multi-trophic microbial interactions. Furthermore, in situ analysis revealed that both bottom-up and top-down effects occurred across all flow zones, with their intensity being positively correlated with the degree of MP degradation. Thereby, nutrient availability driven by hydrodynamics stimulated the growth of MP degrading bacteria and fungi through a bottom-up effect. The increase in the relative abundance of MP degrading bacteria, concurrent with enhanced protozoan predation on bacteria, suggested that this top-down control operated through the selective predation of protozoa on non-MP degrading bacteria. Across the entire river-lake confluence zone, directional flow fluctuations were identified as the paramount environmental factor through the causal effect model, explaining >50% of the variance in bottom-up and top-down effects. Our study demonstrates how hydrodynamics governs MP degradation via multi-trophic microbial interactions, advancing our fundamental understanding of MP fate in aquatic ecosystems.}, }
@article {pmid41446066, year = {2025}, author = {Link, AC and Moser, KA and Wang, J and Woodruff, GC}, title = {A novel, fig-associated microbe promotes reproductive success via variable life history mechanisms in C. elegans and C. inopinata.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41446066}, issn = {2692-8205}, support = {P40 OD010440/OD/NIH HHS/United States ; }, abstract = {Variation in life history strategies is among the most striking features of animal diversity. Simultaneously, the microbes an animal interacts with are a critical and dynamic aspect of the host environment that can have profound impacts on their life history traits. As microbial environments diverge across animal lineages, life histories and their responses to such microbial contexts are expected to evolve as a consequence. Caenorhabditis nematodes are bacterivores that exhibit a diversity of life history strategies and fill diverse ecological niches. C. elegans thrives on rotting plants and grows rapidly with high fecundity; C. inopinata thrives in fresh figs and grows more slowly with lower fecundity. To understand how hosts with divergent life histories and ecologies respond to the microbes they interact with, we isolated over forty bacterial species from the natural fig environment of C. inopinata. This microbial survey revealed an isolate, Klebsiella sp. WOUb2, that doubles the population growth rate of C. inopinata. While this isolate also increases the population growth rate of C. elegans, Klebsiella sp. WOUb2 increases individual fecundity and developmental rate in C. elegans, whereas it only increases developmental rate of C. inopinata. Thus, fitness is modulated by variable life history mechanisms in the two species. Comparisons with nucleotide databases reveal Klebsiella sp. WOUb2 is closely related to other Klebsiella isolates known to influence Caenorhabditis nematode fitness. Additionally, the similarity of Klebsiella sp. WOUb2 to microbes associated with fig wasps and figs suggests C. inopinata frequently encounters this microbe in its natural context. Taken together, this shows that different physiological responses can underlie conserved, beneficial interspecific interactions.}, }
@article {pmid41484934, year = {2026}, author = {Gouka, L and Serra I Melendez, C and Vardazaryan, N and Nor Nielsen, K and Riber, L and Hestbjerg Hansen, L and Raaijmakers, JM and Seidl, MF and Melkonian, C and Cordovez, V}, title = {Genomic insights into adaptative traits of phyllosphere yeasts.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-025-00839-7}, pmid = {41484934}, issn = {2524-6372}, support = {Grant NNF19SA0059348//Novo Nordisk Fonden/ ; Grant OCENW.XS23.3.113//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; Grant NWO/OCW 024.004.014//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 24AA-IF0651//higher education and science committee MESCS RA PhD Support Program/ ; }, abstract = {BACKGROUND: Yeasts are ubiquitous microorganisms thriving in diverse environments. They are prevalent members of the phyllosphere microbiome, but genomic studies of plant-associated yeasts remain limited.<br><br>RESULTS: We established a taxonomically diverse yeast culture collection from flag leaves of field-grown wheat. This collection captured between 48-56% of the genus-level diversity detected by ITS amplicon sequencing conducted over two consecutive years, including the core members Aureobasidium, Dioszegia, Filobasidium, Papiliotrema, Sporobolomyces, and Vishniacozyma. De novo sequencing of 96 high-quality genomes from this collection, representing 14 yeast genera, and comparative genomics revealed specific signatures associated with life in the phyllosphere, the aboveground part of the plant. These adaptive traits encompass enriched carbohydrate metabolism, secondary metabolite biosynthetic pathways, and pectin degradation. The substantially smaller genomes of the phyllosphere yeast genera Candida and Metschnikowia suggest niche specialization via prioritizing metabolic pathways that are essential for survival in the nutrient-limited phyllosphere.<br><br>CONCLUSIONS: This study represents a significant advancement in our understanding of the diverse and largely unknown genomic traits of environmental yeasts and their adaptation to life in the phyllosphere environment. Our findings highlight their untapped functional potential for biotechnological applications in sustainable crop production.}, }
@article {pmid41483762, year = {2026}, author = {Ortiz-Rivero, J and Gultemirian, ML and Oliva, F and Sànchez-Melsió, A and Freixa, A and Sabater, S}, title = {Pesticide exposure sequence and duration modify the effects of heatwaves and water level reduction on river biofilms.}, journal = {Journal of environmental management}, volume = {398}, number = {}, pages = {128482}, doi = {10.1016/j.jenvman.2025.128482}, pmid = {41483762}, issn = {1095-8630}, abstract = {Fluvial ecosystems are increasingly affected by stressors from anthropogenic activities and climate change-related pressures. Here we examined the potential relevance of stressor interaction, sequence and timing of exposure through a controlled laboratory experiment. We selected both chemical (mixture of pesticides) and physical (temperature heatwave and decreased water level) stressors and we performed two 96 h microcosm experiments designed to assess the effects on the structure and function of epilithic biofilms. Biofilms respond rapidly to these stressors, making them valuable indicators of global change. Our results showed that pesticides negatively impacted photosynthetic activity, while heatwaves increased both structural (chlorophyll concentration) and functional (glucosidase activity) biofilm descriptors. In contrast, water level reduction had comparatively mild effects. The impacts of pesticides were more pronounced when exposure was continuous or occurred during the final 48 h of the experiment, whereas early exposure combined (first 48 h) with a water level reduction resulted in weaker effects, accompanied by an increase and partial recovery of microbial abundance. Furthermore, adverse pesticide effects were more pronounced at 8 °C than at 15 °C. Overall, our results highlight that the sequence, timing and duration of stressor exposure play a critical role in the biofilm structure and function, with likely effects on the whole river ecosystem.}, }
@article {pmid41483182, year = {2026}, author = {Caviedes-Triana, K and Vivero-Gómez, R and Duque-Granda, D and Junca, H and Cadavid-Restrepo, G and Moreno-Herrera, CX}, title = {Structure and Diversity of the Microbiome in Amazonian Sand Flies: Insights into Vector-Microbe Interactions.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02663-5}, pmid = {41483182}, issn = {1432-184X}, support = {Scholarship Program of Ministerio de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n, Call 15, for Human Capital Development in the context of the Bicentennial and the 2021-2022 Biennial Plan.//Ministerio de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n/ ; Hermes 57545//Universidad Nacional de Colombia/ ; }, abstract = {This study uses high-throughput sequencing of the 16 S rRNA gene and specific PCR to analyze the microbiome and identify secondary endosymbionts in sand flies from the Amazon region, important vectors of parasitic and viral diseases. Specimens of Psychodopygus, Trichophoromyia, Nyssomyia, Trichopygomyia and Brumptomyia were collected and analyzed. The results revealed that the richness, diversity, and composition of the microbiome are influenced by several factors, such as insect species specific composition, and insect sex. The core microbiome community was represented by 18 genera, with Novosphingobium, Cutibacterium, Methylobacterium and Staphylococcus being the most prevalent. The highest diversity at the genus level was observed in sand flies of epidemiological relevance as Psychodopygus and Nyssomyia, dominated by Novosphingobium (66.5%), Cutibacterium (29.4%) and Methylobacterium (20.4%), while in non-vectors such as Trichophoromyia, Delftia predominated (59.9%). Endosymbiont analysis showed a high prevalence of Cardinium (20%) and Wolbachia (33%), as well as the presence of Spiroplasma, Arsenophonus and Rickettsia. In addition, some bacterial genera related to the inhibition of parasite development, which have entomopathogenic activity and are involved in the degradation of insecticides were identified. Our results are relevant and contribute to the knowledge of the characterization of the microbiome and the endosymbionts in leishmaniasis vectors in the Amazon region and show promise for improving vector management, highlighting the importance of investigating their interaction with pathogens and their impact on vector biology.}, }
@article {pmid41482669, year = {2026}, author = {Islam, W and Zhihao, Z and Khan, KA and Zeng, F}, title = {Resilience and Adaptation in Desert Ecosystems: Unveiling Microbial Legacies and Plant Functional Trait Coordination Under Climate Change.}, journal = {Global change biology}, volume = {32}, number = {1}, pages = {e70678}, doi = {10.1111/gcb.70678}, pmid = {41482669}, issn = {1365-2486}, support = {2023TSYCLJ0046//Tianshen Talent Training Program/ ; 42271071//National Natural Science Foundation of China/ ; 42571075//National Natural Science Foundation of China/ ; }, mesh = {*Climate Change ; *Desert Climate ; *Ecosystem ; *Soil Microbiology ; *Microbiota ; *Plant Physiological Phenomena ; *Adaptation, Physiological ; *Plants ; }, abstract = {Desert ecosystems, which cover more than one-third of Earth's land surface, are experiencing intensifying pressures from land-use disturbances and climate change that threaten their stability and biodiversity. Yet despite their global extent and ecological importance, deserts remain among the least studied biomes, particularly with respect to the belowground processes that sustain productivity, biogeochemical cycling, and long-term ecosystem resilience. Most prior work has focused on vegetation, leaving the roles of soil microbiomes and plant functional trait coordination comparatively underexplored. This knowledge gap is significant because growing evidence shows that microbial dynamics and plant trait syndromes jointly regulate nutrient cycling, carbon stabilization, and drought recovery, potentially determining whether desert ecosystems cross critical thresholds under future climate scenarios. This review synthesizes recent advances in understanding the influence of microbial legacies (persistent effects of past environmental conditions) on ecosystem processes, and how desert plants adapt via coordinated traits that optimize water and nutrient use under extreme conditions. We propose a novel framework that integrates belowground microbial responses and aboveground plant trait strategies, highlighting their interactions and feedback loops in shaping desert ecosystem resilience. By explicitly linking these two domains, the review addresses a major knowledge gap in predicting dryland responses to intensifying climate extremes, offering a mechanistic foundation for improving ecological models and management strategies. This integrated perspective provides new insights into the mechanisms that underlie adaptation to climate stress and offers actionable pathways for conservation, restoration, and climate adaptation in desert landscapes. By bridging microbial ecology and trait-based plant science, this review contributes to a more comprehensive understanding of how desert ecosystems can persist and function in a rapidly changing world.}, }
@article {pmid41482468, year = {2026}, author = {Xiao, Y and Zhao, S and Wang, W and Asante, KA and Habib, A and Bong, CW and Syed, JH and Bartilol, S and Weber, R and Jones, KC and Li, J and Njeru, M and Zhang, G}, title = {Highly Volatile POPs in Urban Air across Asia and Africa: Dominance of Volatile Methylsiloxanes.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c16890}, pmid = {41482468}, issn = {1520-5851}, abstract = {Highly volatile persistent organic pollutants (HV-POPs) are characterized by high volatility, environmental persistence, bioaccumulative potential, toxicity, and ability for long-range transport, posing environmental and health concerns. However, research on HV-POPs remains limited, particularly in rapidly urbanizing regions, constraining understanding of their sources, environmental fate, and risks. This study investigated 52 HV-POPs, including Stockholm Convention-listed POPs like hexachlorobutadiene (HCBD) and hexa-/pentachlorobenzene (HCB/PeCB), and nonlisted HV-POPs such as volatile methylsiloxanes (VMS) and chlorinated nitrobenzenes (CNBs), using active air samplers in six major cities across Asia and Africa. The median total concentrations of HV-POPs were highest in Guangzhou (351 ng/m[3]), followed by Kuala Lumpur (167 ng/m[3]), Accra (82.4 ng/m[3]), Dhaka (73.3 ng/m[3]), Nairobi (44.9 ng/m[3]), and Islamabad (33.5 ng/m[3]). VMS dominated at all sites, accounting for 84 ± 18% of total HV-POPs, up to 2-5 orders of magnitude higher than other compounds. Source analysis showed VMS emissions in Guangzhou were mainly from industrial activities, while in the other cities, they were from usage of personal care products. Inhalation risk assessments indicated negligible noncarcinogenic and carcinogenic risks at all sites. This study provides the first multiregional HV-POPs data set in urban air, supporting chemical risk assessment efforts and broader international regulatory initiatives.}, }
@article {pmid41482032, year = {2025}, author = {Wu, D and Zhang, L and Zhang, Z and Xu, M}, title = {Early-life high-dose sodium butyrate supplementation in milk inhibits growth via sterol metabolism in 15-month-old dairy cattle: Insights from gastrointestinal microbiota and host metabolism.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2025-27618}, pmid = {41482032}, issn = {1525-3198}, abstract = {Sodium butyrate (SB) is a common feed additive used in calf nutrition to support early growth and gastrointestinal health; however, its long-term programming effects remain poorly characterized. This study examined the dose-dependent effects of preweaning SB supplementation in milk on long-term growth, metabolic profiles, and gastrointestinal microbiota in dairy cattle. Eighty Holstein calves were assigned to one of 4 treatments beginning at 2 to 4 d of age: milk supplemented with 0 (CON), 4.4 (LSB), 8.8 (MSB), or 17.6 (HSB) g/d of SB. The same animals were evaluated later as heifers at 15 mo of age for performance, metabolic parameters, and microbial communities. Ruminal fluid, fecal, and plasma samples were collected from 8 animals per group and analyzed via 16S rRNA sequencing (V3-V4 regions) and liquid chromatography-tandem MS-based metabolomics. The HSB group showed a significant reduction in withers height compared with CON, although no significant differences were detected in BW, heart girth, or reproductive measures. Metabolomic and biochemical profiling indicated disrupted sterol metabolism and signs of hepatic stress in HSB heifers, reflected by increased alanine aminotransferase and total bilirubin, alongside decreased total cholesterol and creatine. Ruminal microbiota in the HSB group exhibited reduced diversity, richness, and evenness, accompanied by a decline in beneficial bacteria such as Rikenellaceae_RC9_gut_group. Predicted microbial function indicated inhibited steroid biosynthesis in the rumen. In contrast, the intestinal microbiota composition remained largely unchanged, though steroid degradation function was suppressed. Correlation and network analyses linked these changes, suggesting that early high-dose SB disrupts ruminal microbial ecology, resulting in lasting impairments in host metabolic health and growth. Key biomarkers included Rikenellaceae_RC9_gut_group, steroid biosynthesis, and plasma creatine. Collectively, these results indicate that milk-supplemented high-dose SB in early life leads to long-term inhibitory effects on growth and metabolic homeostasis in dairy heifers, largely mediated through rumen microbiota-driven alterations in sterol metabolism.}, }
@article {pmid41481725, year = {2026}, author = {Shi, T and Van de Peer, Y}, title = {Revisiting ancient whole-genome duplications in the seed and flowering plants through the lens of dosage-sensitive genes.}, journal = {Science advances}, volume = {12}, number = {1}, pages = {eaea9797}, pmid = {41481725}, issn = {2375-2548}, mesh = {*Gene Duplication ; *Magnoliopsida/genetics ; *Genome, Plant ; *Gene Dosage ; *Seeds/genetics ; Phylogeny ; Evolution, Molecular ; *Genes, Plant ; }, abstract = {Whole-genome duplication (WGD) has been proposed as a catalyst for evolutionary innovation in seed plants and angiosperms, yet their occurrence remains contentious. By integrating gene dosage balance principles with phylogenomic reconciliation and probabilistic modeling, we revisit the debated ancestral seed and angiosperm WGDs. Leveraging dosage-sensitive orthologous gene groups (OGs) as evolutionary markers across representative plants for gene tree/species tree reconciliation, we demonstrate that gene retention patterns in Amborella and Aristolochia-early-diverging plants lacking post-angiosperm origin WGDs-reveal a single gene duplication peak predating the seed plant diversification, with no signal of ancestral angiosperm WGD. Correlation analyses of observed and expected OG copy numbers, given proposed WGD(s), further refute an angiosperm WGD. Probabilistic retention modeling analysis corroborates these findings and shows that retention rates of dosage-sensitive genes from the putative angiosperm WGD are extremely low. Besides, our study establishes that genes inferred to have higher dosage sensitivity based on their sequential retention following WGD events may have increased utility in resolving ancestral polyploidy.}, }
@article {pmid41480114, year = {2025}, author = {Robayo-Cuevas, C and Junca, H and Uribe, S and Gómez-Palacio, A}, title = {Detection of endosymbiotic, environmental, and potential bacterial pathogens in diverse mosquito taxa from Colombian tropical forests using RNAseq.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1727830}, pmid = {41480114}, issn = {1664-302X}, abstract = {INTRODUCTION: Mosquitoes of the subfamily Culicinae transmit pathogens of major medical and veterinary importance, particularly in tropical regions where urbanization and ecological change promote arbovirus circulation. In Colombia, rural Culicinae species are diverse and harbor microbiomes that may influence vector competence, yet their bacterial communities remain poorly characterized.<br><br>METHODS: We characterized the bacterial microbiota of multiple Culicinae species and morphotypes collected from two rural localities in Antioquia, Colombia, using an integrated metagenomic approach. Ribosomal 16S rRNA sequences were extracted from total RNA-seq datasets to infer bacterial community composition and assess &#x3b1;- and &#x3b2;-diversity. Diversity metrics (Chao1 and Shannon indices), Discriminant Analysis of Principal Components (DAPC), and Bray-Curtis ordination were used to evaluate community structure. In parallel, de novo assembled contigs were taxonomically annotated against the NCBI NR bacterial database to obtain complementary taxonomic and functional insights.<br><br>RESULTS: Culex morphotypes exhibited the highest richness and evenness, whereas Aedes and Trichoprosopon showed lower diversity. Ordination and DAPC analyses revealed partial clustering by species and tribe. Both the 16S and assembly-based analyses showed complex bacterial assemblages dominated by Wolbachia (up to 60% of reads in several Aedes and Culex morphotypes), followed by environmental genera such as Pseudomonas and Acinetobacter (10-20%). Lower-abundance taxa of medical and veterinary importance-including Salmonella, Borrelia, and Clostridium (<5%)-were also detected. Bacterial community structure differed among mosquito species; Aedes albopictus was enriched in lactic acid bacteria, while Culex morphotypes exhibited broader environmental and endosymbiotic profiles.<br><br>DISCUSSION: This study provides the first comprehensive metagenomic description of bacterial communities associated with rural Culicinae mosquitoes in Colombia. The predominance of symbionts such as Wolbachia and Spiroplasma, coupled with distinct bacterial signatures among host species, highlights the ecological complexity of these microbiomes and their potential relevance for microbiome-based strategies in sustainable arboviral disease management.}, }
@article {pmid41479530, year = {2025}, author = {Guo, T and Wang, M and Chen, Y and Yue, K and Ma, L and Huang, S and Xu, X and Song, X and Su, S and Zhang, Z and Zhang, Q and Zhang, K}, title = {Nitrogen addition accelerated straw in-situ decomposition by promoting specific microbial taxa growth and straw decomposing enzyme activities.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1703916}, pmid = {41479530}, issn = {1664-462X}, abstract = {INTRODUCTION: Crop residue represents the largest input of organic carbon in agricultural ecosystems and its decomposition is fundamentally mediated by soil microbial communities. However, the mechanism of N fertilization regulating decomposition of the plant residue especially the associated key microbial taxa remain unclear.<br><br>METHODS: To address this gap, we conducted a 100-day field decomposition experiment using the litterbag method to track temporal shifts in straw physicochemical properties and associated microbial communities under three N regimes: no nitrogen (N0), 200 kg N ha[-1] (N200), and 300 kg N ha[-1] (N300).<br><br>RESULTS AND DISCUSSIONS: Results showed that nitrogen addition significantly accelerated the decomposition of wheat straw, increasing mass loss and the degradation rates of cellulose, hemicellulose, and lignin relative to N0 treatment. Enzyme activities linked to carbon acquisition, including &#x3b1;-glucosidase (AG), &#x3b2;-glucosidase (BG), cellobiohyrolase (CBH), and &#x3b2;-xylosidase (XYL), were consistently elevated under N-amended treatments during mid- to late-stage decomposition. Similarly, activities of N-acquiring enzymes (&#x3b2;-N-acetyl-glucosaminidase, NAG; leucine aminopeptidase, LAP) and oxidative enzymes (polyphenol oxidase, PPO; laccase) were significantly enhanced, particularly after Day 14. Microbial community succession was tightly coupled with decomposition progression. Random forest modeling identified key bacterial biomarkers (e.g., Terribacillus, Bacillus, Solibacillus, Oceanobacillus, and Cellulosimicrobium) and fungal biomarkers (e.g., Neocosmospora, Actinomucor, Fusarium, Chaetomium, and Aspergillus), all of which are known for their capacity to degrade lignocellulosic and recalcitrant substances. Variation partitioning revealed that straw properties, especially the C/N ratio, TN content, and CBH activity, collectively explained the majority of microbial community variation. These findings support a mechanistic pathway in which nitrogen fertilization reduces residue C/N, thereby reshaping microbial community composition and stimulating enzyme production, which in turn accelerates decomposition. Our study provides novel insights into how nitrogen management influences the coupling of microbial ecology and biogeochemical cycling during straw decomposition, with direct implications for&#xa0;optimizing N fertilization management and sustaining soil fertility in agroecosystems.}, }
@article {pmid41478687, year = {2026}, author = {Wang, G and Liu, Y and Ma, F and Qiu, W}, title = {Insights into meat-microbiome interactions: from community assembly to meat spoilage.}, journal = {Food microbiology}, volume = {136}, number = {}, pages = {105010}, doi = {10.1016/j.fm.2025.105010}, pmid = {41478687}, issn = {1095-9998}, mesh = {*Meat/microbiology ; *Microbiota ; Animals ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Food Microbiology ; Microbial Interactions ; Ecosystem ; }, abstract = {Meat spoilage represents a critical challenge in food security and sustainability. Although extensive research has characterized meat microbiota composition and identified specific spoilage organisms, comprehensive understanding of the complex ecological dynamics within meat microbiomes remains limited. This review critically examines current knowledge of meat-associated microbiomes by applying an ecological perspective to address four key questions: the functional roles assigned to microorganisms during community assembly, microbial colonization and adaptation mechanisms in meat ecosystems, nutrient utilization patterns driving metabolic activities and ecological interactions, and microbial interaction effects on community ecology and functional outcomes. Through systematic exploration of these questions, we reveal that meat spoilage is determined by community dynamics and functional activities of entire microbial ecosystems rather than individual species alone. Our analysis identifies critical research gaps including inadequate understanding of core and keystone taxa contributions, limited exploration of microbial interactions, and insufficient integration of multi-omics approaches with ecological modeling. Based on these findings, future practical applications should focus on ecology-guided preservatives that target key spoilage pathways and predictive models integrating metabolic fluxes with environmental parameters. This comprehensive paradigm shift from composition-focused to function-oriented research will enhance theoretical understanding and provide practical insights for more effective spoilage control in the food industry.}, }
@article {pmid41478108, year = {2025}, author = {Idbella, M and Abelouah, MR and Djebaili, R and Idbella, A and Raho, O and Nouj, N and Iacomino, G and Bonanomi, G and Hazzoumi, Z}, title = {Microplastic pollution drives soil bacterial community shifts and alters phosphorus cycling across land use gradients.}, journal = {Journal of hazardous materials}, volume = {501}, number = {}, pages = {140968}, doi = {10.1016/j.jhazmat.2025.140968}, pmid = {41478108}, issn = {1873-3336}, abstract = {Microplastics (MPs) pollution is increasingly recognized as a pervasive threat to terrestrial ecosystems, yet its functional impacts on soil processes remain poorly understood under field conditions. Here, we conducted a landscape-scale study across four land-use types, urban, mining, agricultural, and rural, to quantify environmentally accumulated MP and assess their effects on phosphorus (P) cycling and microbial communities. High-resolution spectroscopy revealed that urban and mining soils contained the highest MP loads (600-1000 particles/kg), with distinct polymer types linked to anthropogenic activities. MP abundance was negatively correlated with P solubilization (R = -0.59, p < 0.01) and soil enzymatic activity, and positively with P immobilization (R = 0.53, p < 0.05), indicating impaired nutrient availability. Amplicon sequencing showed that MP-rich soils were enriched in certain taxa within Firmicutes and Actinobacteria often associated with stress tolerance, while low-MP soils supported functionally important groups, including specific Acidobacteria and nitrifying archaea (e.g., Candidatus Nitrososphaera). Co-occurrence network analysis revealed simplified and cooperative microbial structures in MP-polluted soils. Multivariate analyses confirmed that MP are independent drivers of microbial beta-diversity beyond land use. Overall, our findings provide in situ evidence that MP, even at moderate levels, alter microbial ecology and disrupt soil nutrient cycling, posing a potential risk to biogeochemical resilience in human-impacted landscapes.}, }
@article {pmid41475142, year = {2025}, author = {Gallego-Cartagena, E and Morillas, H and Maguregui, M}, title = {Biodeterioration of built heritage in the context of climate change and atmospheric pollution: Toward transdisciplinary conservation strategies.}, journal = {The Science of the total environment}, volume = {1013}, number = {}, pages = {181313}, doi = {10.1016/j.scitotenv.2025.181313}, pmid = {41475142}, issn = {1879-1026}, abstract = {The built heritage -encompassing monuments, historic buildings and sculptural ensembles- is increasingly threatened by the synergistic impacts of climate change, atmospheric pollution and biological activity. This review critically analyses current understanding of the mechanisms driving the biodeterioration of built heritage, focusing on calcareous materials (e.g., limestone, marble and lime-based mortars), which are both widespread in built heritage and highly susceptible to degradation. We examine how environmental drivers -such as elevated humidity, temperature fluctuations, and pollutant deposition (SOₓ, NOₓ, particulate matter)-trigger complex physicochemical and biochemical reactions that compromise structural stability and aesthetic integrity. The review explores the metabolic strategies of biodeteriative organisms (fungi, algae, cyanobacteria), the interactions of pollutants and mineral substrates, and the consequent formation of salts, black crusts and corrosion products. We highlight the role of biomonitoring as a methodological and interpretive bridge linking atmospheric pollution to biodeterioration processes. In addition, we discuss emerging interdisciplinary methodologies - including functional metagenomics, microbial network analysis, and metabolomic profiling -and introduce the Function-Based Biodegradation Risk Assessment model, extended into a Multi-Level Risk Assessment Framework that connects microbial functionality, material diagnostics, and climate modeling. We contend that safeguarding built heritage in a changing climate requires transitioning from static, material-centred diagnostics to integrated, predictive frameworks that link microbial ecology, materials science, and climate dynamics, providing the basis for adaptive and anticipatory conservation strategies.}, }
@article {pmid41472882, year = {2025}, author = {Gómez-Pérez, D and Keller, A}, title = {Integrating natural language processing and genome analysis enables accurate bacterial phenotype prediction.}, journal = {NAR genomics and bioinformatics}, volume = {7}, number = {4}, pages = {lqaf174}, pmid = {41472882}, issn = {2631-9268}, mesh = {*Natural Language Processing ; Phenotype ; *Genome, Bacterial ; *Bacteria/genetics ; *Genomics/methods ; Machine Learning ; }, abstract = {Understanding microbial phenotypes from genomic data is crucial for studying co-evolution, ecology, and pathology. This study presents a scalable approach that integrates literature-extracted information with genomic data, combining natural language processing and functional genome analysis. We applied this method to publicly available data, providing novel insights into predicting microbial phenotypes. We fine-tuned transformer-based language models to analyze 3.83 million open-access scientific articles, extracting a phenotypic network of bacterial strains. This network maps relationships between strains and traits such as pathogenicity, metabolism, and biome preference. By annotating their reference genomes, we predicted key genes influencing these traits. Our findings align with known phenotypes, reveal novel correlations, and uncover genes involved in disease and host associations. The network's interconnectivity provides deeper understanding of microbial communities and allowed identification of hub species through inferred trophic connections that are difficult to infer experimentally. This work demonstrates the potential of machine learning for uncovering cross-species gene-phenotype patterns. As microbial genomic data and literature expand, such methods will be essential for extracting meaningful insights and advancing microbiology research. In summary, this integrative approach can accelerate discovery and understanding in microbial genomics. Ultimately, such techniques will facilitate the study of microbial ecology, co-evolutionary processes, and disease pathogenesis to an unprecedented depth.}, }
@article {pmid41472773, year = {2025}, author = {Charoenwai, O and Tanpichai, P and Sukkarun, P and Jeon, HJ and Kim, B and Han, JE and Piamsomboon, P}, title = {Emergence of decapod hepanhamaparvovirus genotype V and its co-infection with Enterocytozoon hepatopenaei in cultured Penaeus vannamei in Thailand: Evidence from epidemiological, pathogenicity, and microbiome analyses.}, journal = {Veterinary world}, volume = {18}, number = {11}, pages = {3496-3508}, pmid = {41472773}, issn = {0972-8988}, abstract = {BACKGROUND AND AIM: Growth retardation syndrome in cultured Penaeus vannamei has been associated with Enterocytozoon hepatopenaei (EHP) and a recently identified decapod hepanhamaparvovirus (DHPV) genotype V. However, data on its prevalence, pathogenicity, and interaction with the shrimp hepatopancreatic microbiome in Thailand remain limited. This study aimed to determine the incidence and co-infection rate of DHPV genotype V with EHP, evaluate its pathogenic potential, and explore microbiome alterations associated with infection.<br><br>MATERIALS AND METHODS: Between 2022 and 2023, 1,270 shrimp from 127 grow-out ponds across 46 farms in eastern Thailand and post-larvae 12 from five hatcheries in the south were screened for DHPV and EHP by polymerase chain reaction. Six representative isolates underwent phylogenetic analysis based on non-structural protein 1 (NS1) and NS2 genes. Pathogenicity was evaluated by immersion challenge bioassays in specific pathogen-free P. vannamei. Hepatopancreatic microbiomes of naturally infected and healthy shrimp were compared using 16S ribosomal RNA gene sequencing and Quantitative Insights Into Microbial Ecology 2-based analysis.<br><br>RESULTS: DHPV was detected in 54.33% (69/127) of ponds and 4% (1/25) of hatchery tanks. Co-infection with EHP occurred in 40.16% of ponds. Phylogenetic analysis showed 97.99%-98.82% similarity with DHPV genotype V from South Korea, confirming transboundary genetic relatedness. Experimental infection caused low mortality (20%) but resulted in viral replication (10[1]-10[3] copies/&#x3bc;L) and characteristic intranuclear inclusion bodies in hepatopancreatic cells. DHPV-infected shrimp exhibited distinct microbiome profiles with elevated Firmicutes, Planctomycetota, and Actinobacteriota abundances, supporting a pathobiome shift during infection.<br><br>CONCLUSION: This is the first report of DHPV genotype V in P. vannamei from Thailand and its frequent co-infection with EHP. Despite its low experimental virulence, the widespread occurrence and microbiome dysbiosis suggest that it may have subclinical impacts that could exacerbate growth retardation. Routine molecular screening in hatcheries and farms, coupled with integrated viral-microbiome surveillance, is essential for sustainable aquaculture biosecurity and aligns with the United Nations Sustainable Development Goal 14 (Life Below Water) by promoting resilient aquatic food systems.}, }
@article {pmid41472186, year = {2025}, author = {Lu, Y and Li, Z and Yang, Z and Zhu, R and Yan, M and Liu, Z and Liu, M and Wang, Y and Wang, J and Wang, Q and Liu, J and Zhang, C and Wang, X and Cui, H}, title = {Effects of Combined Oregano Essential Oil and Macleaya cordata Extract on Growth, Antioxidant Capacity, Immune Function, and Fecal Microbiota in Broilers.}, journal = {Veterinary sciences}, volume = {12}, number = {12}, pages = {}, pmid = {41472186}, issn = {2306-7381}, support = {YJ2023038&#xff1b;246Z6604G&#xff1b;HBCT2024270204&#xff1b;CARS-41-13&#xff1b;KY2024006//This research was funded by the special project of introducing talents for scientific research in Hebei Agricultural University&#xff1b;Central government guided local science and technology development fund projects&#xff1b;Hebei Agriculture Research System&#xff1b;China Agricu/ ; }, abstract = {With the growing demand for antibiotic-free and sustainable poultry production, plant-derived antimicrobials have emerged as promising alternatives. However, a systematic understanding of the combined effects of oregano essential oil (OEO) and Macleaya cordata extract (MCE) on the broiler gut microbiome remains lacking. This study employed an integrated "structure-function-phenotype" framework to investigate the individual and combined (OMS) effects of OEO and MCE on gut microecological remodeling and its coupling with host growth, metabolic, and immune phenotypes. A total of 960 one-day-old broiler chicks were individually weighed and then randomly allocated to four treatments using body-weight-stratified randomization, with 6 replicate pens per treatment and 40 birds per pen, to ensure similar initial body weight across groups. Over a 42-day trial, we evaluated growth performance, serum biochemistry, antioxidant status, and immune parameters. Compared to the control, the OMS treatment significantly enhanced average daily feed intake (ADFI) and average daily gain (ADG), increased serum total protein (TP), and decreased blood urea nitrogen (BUN), triglycerides (TG), total cholesterol (TC), and alkaline phosphatase (ALP). However, the feed-to-gain ratio (F/G) was also higher in the OMS group, indicating that the improvement in growth rate did not translate into enhanced feed efficiency but was primarily driven by increased feed consumption. OMS also improved overall antioxidant capacity and key enzyme activities, elevated immunoglobulin levels, and reduced pro-inflammatory cytokines. Notably, OMS maintained Lactobacillus dominance, enriched Bacteroides, Enterococcus, and Butyricicoccus, and reduced Escherichia-Shigella. Functional predictions via PICRUSt2 suggested enhanced metabolic pathways related to antioxidant and immune functions; however, these results represent inference-based predictions and should be interpreted cautiously. Overall, the combination of OEO and MCE exerted synergistic benefits on growth, physiological health, and gut microbiota, supporting its potential as a phytogenic strategy for antibiotic-free broiler production.}, }
@article {pmid41472031, year = {2025}, author = {Yuan, W and Shang, Y and Bai, M and Sun, M and Su, Z and Yang, X and Riaz, L and Guo, Y and Lu, J}, title = {Occurrence and Distribution of Antibiotics and Antibiotic Resistance Genes in the Water and Sediments of Reservoir-Based Drinking Water Sources in Henan, China.}, journal = {Microorganisms}, volume = {13}, number = {12}, pages = {}, pmid = {41472031}, issn = {2076-2607}, support = {241111320200//the Key R&amp;D projects in Henan Province/ ; 42407404//the National Natural Science Foundation of China/ ; }, abstract = {The improper use of antibiotics accelerates the emergence of resistance via environmental selection pressures, jeopardizing public health and ecosystems by promoting the worldwide dissemination of antibiotic resistance genes (ARGs). Reservoirs, as crucial water supplies, have been recognized as primary reservoirs of ARGs, particularly those that originate from the Yellow River, necessitating further investigation. This study analyzed 9 ARGs, 3 mobile genetic elements (MGEs), 16 antibiotics, and 10 heavy metals in water/sediments from three reservoirs originating from the Yellow River in Henan Province, China. The findings indicated that antibiotic concentrations in water exceeded those in sediment, with quinolones detected at 100% frequency (5.47-116.03 ng/L) and enrofloxacin predominating (3.36-107.71 ng/L). Redundancy analysis revealed that MGEs exert greater control over ARG dissemination than antibiotics, with intI1 showing strong positive correlations with sul1 (p < 0.05). Conversely, heavy metals (Zn, As, Cd) suppress ARG proliferation through negative selection pressures. A network study indicated Mycobacterium, Pseudarthrobacter, and Massilia as critical hosts for ermB, tetA, and qnrA, respectively. Of the three reservoirs, Jian'gang Reservoir, driven by synergistic effects of unique microbial ecology, water self-purification capacity, and flow dynamics, exhibited the best removal effectiveness of ARGs from input to outflow, with 71.75% in the water and 97.91% in the sediment. These findings provide critical insights into the prevalence, migration, and self-purification processes of ARGs in reservoirs originating from the Yellow River, integrating environmental factors and microbial data to clarify the complex dynamics affecting ARG behavior and inform targeted pollution control strategies.}, }
@article {pmid41472029, year = {2025}, author = {Dhakal, R and Guo, W and Vieira, RAM and Guan, L and Neves, ALA}, title = {Advances in Lignocellulose-Degrading Enzyme Discovery from Anaerobic Rumen Fungi.}, journal = {Microorganisms}, volume = {13}, number = {12}, pages = {}, pmid = {41472029}, issn = {2076-2607}, abstract = {Anaerobic fungi (phylum Neocallimastigomycota) play a crucial role in degrading forages and fibrous foods in the gastrointestinal tract of mammalian herbivores, particularly ruminants. Currently, they are classified into twenty-two genera; however, recent research suggests the occurrence of several novel taxa that require further characterization. Anaerobic rumen fungi play a pivotal role in lignocellulose degradation due to their unique enzymatic capabilities. This review explores the enzymatic systems of rumen anaerobic fungi, highlighting their ability to produce a diverse array of carbohydrate-active enzymes (CAZymes), such as cellulases, hemicellulases, and pectinases. These enzymes facilitate the breakdown of complex plant polymers, making anaerobic fungi essential contributors to fiber degradation in the rumen ecosystem and valuable resources for biotechnological applications. This review summarizes the structural and functional diversity of fungal CAZymes, and the mechanical disruption of plant cell walls by fungal rhizoidal networks is discussed, showcasing the ability of fungi to enhance substrate accessibility and facilitate microbial colonization. Recent studies using genomic, transcriptomic, and biochemical approaches have uncovered several novel CAZymes in anaerobic fungi, including multifunctional xylanases, β-glucosidases, and esterases. These findings highlight the continued expansion of fungal enzyme repertoires and their potential for biotechnology and feed applications. Continued research in this field will enhance our understanding of microbial ecology and enzyme function, paving the way for applications that address global challenges in energy, food security, and environmental sustainability.}, }
@article {pmid41472008, year = {2025}, author = {Leal, G and Canals, JM and Beltran, G and Peña-Neira, &#xc1; and Jara, C and Romero, J and Ramírez, C and Sanz, R}, title = {From Soil to Wine: Influence of Vegetative Covers on Microbial Communities and Fermentative Dynamics in Cabernet Sauvignon.}, journal = {Microorganisms}, volume = {13}, number = {12}, pages = {}, pmid = {41472008}, issn = {2076-2607}, abstract = {The implementation of vegetative cover crops in vineyards is a sustainable alternative to chemical weed control, potentially influencing both soil fertility and grape-associated microbiota. This study evaluated the impact of six groundcover management strategies under vines-white clover (Trifolium repens), red clover (Trifolium pratense), burr medic (Medicago polymorpha), lupine (Lupinus albus), spontaneous weeds, and an herbicide-treated control-on the microbial dynamics and physicochemical properties of Cabernet Sauvignon must and wine from the Maipo Valley, Chile. Amplicon sequencing of bacterial (16S rRNA) and fungal (ITS) communities was combined with spontaneous fermentation trials and chemical analyses of must and wine. Fungal and bacterial communities on grape surfaces were dominated by Ascomycota and Proteobacteria, respectively, with no significant compositional differences among treatments. During fermentation, Metschnikowia and Tatumella were the most abundant non-Saccharomyces and bacterial genera, respectively, showing dynamic shifts across fermentation stages. Legume-based covers, particularly red clover, increased wine total acidity and polyphenol index while reducing pH. Correlation analyses revealed associations between specific microbial taxa (Metschnikowia, Cohnella, Saliterribacillus) and key enological parameters. Overall, these findings demonstrate that leguminous cover crops subtly modulate vineyard microbial ecology and fermentation outcomes, offering an environmentally sustainable pathway to enhance enological differentiation in semi-arid viticultural regions.}, }
@article {pmid41471996, year = {2025}, author = {Zhang, X and Mao, G and Pei, Z and Sun, Y and Cen, J and Zhang, S and Li, S and Meng, W and Xiao, K and Xu, Q and Sun, M}, title = {Microbial Ecology of Sulfur Mustard Toxicity: From Dysbiosis to Restoration.}, journal = {Microorganisms}, volume = {13}, number = {12}, pages = {}, pmid = {41471996}, issn = {2076-2607}, support = {82103885//National Natural Science Foundation of China/ ; 82273672//National Natural Science Foundation of China/ ; 20ZR1470300//Natural Science Foundation of Shanghai Municipality/ ; 21ZR1477700//Natural Science Foundation of Shanghai Municipality/ ; GWV-10.2-YQ48//Shanghai Municipal Health Commission-Outstanding Youth Foundation of Public Health/ ; }, abstract = {Sulfur mustard (SM) causes multi-organ toxicity, yet its impact on intestinal tissue and the associated gut microbiota remains poorly characterized. This study demonstrates that in a mouse model of SM exposure, gut microbial ecological collapse occurs, characterized by depletion of protective taxa (Bifidobacteriales, Gordonibacter, and Lachnospiraceae UCG010) while promoting a 302-fold expansion of inflammation-associated Escherichia/Shigella. Mendelian randomization analysis established causal relationships between these SM-perturbed taxa and human inflammatory bowel disease. Fecal microbiota transplantation effectively restored microbial diversity (Simpson index: 0.85 to 0.95), suppressed Escherichia/Shigella by 97.4%, and ameliorated intestinal pathology. Longitudinal tracking revealed persistent vulnerability of Bifidobacteriales compared to other depleted taxa. Our findings establish the gut microbiota as a key mediator in SM intestinal toxicity and provide new insights for microbiota-targeted interventions against chemical injuries.}, }
@article {pmid41469005, year = {2025}, author = {Cao, ZW and Zhang, LK and Fang, B and Zhang, X}, title = {[Risk management and clinical strategies for early enamel demineralization in orthodontic patients].}, journal = {Zhonghua kou qiang yi xue za zhi = Zhonghua kouqiang yixue zazhi = Chinese journal of stomatology}, volume = {61}, number = {1}, pages = {30-38}, doi = {10.3760/cma.j.cn112144-20251020-00418}, pmid = {41469005}, issn = {1002-0098}, support = {2022YFC2405900, 2022YFC2405902//National Key Research and Development Program of China/ ; 82171007//National Natural Science Foundation of China/ ; }, abstract = {Early enamel demineralization, one of the common side effects of orthodontic treatment, occurs when dental plaque accumulation disrupts the balances of demineralization-remineralization and the oral microbial ecology. Clinically, the existence of orthodontic appliances can make oral hygiene more challenging. At the same time, patient adherence to oral hygiene appointments may be inconsistent. The combination of these factors often leads to inadequate plaque control and increases the risk of enamel demineralization. Presently, there is a lack of standardized guidelines for the clinical intervention and management for early enamel demineralization. Moreover, the associated risk assessment and prevention systems require further improvement. This article provides a review of the etiology, risk factors, and preventive and treatment strategies for managing early enamel demineralization in orthodontic patients. The aim is to provide references for clinicians to promote the early detection, early intervention, and standardized management of early enamel demineralization, thereby effectively controlling the incidence and progression of these lesions during orthodontic treatment.}, }
@article {pmid41468165, year = {2025}, author = {Benner, SA and Schulze-Makuch, D and Spacek, J and Abraham, C}, title = {Viking Mars, Now 50 Years Old, Still Needs a Scientific Analysis.}, journal = {Astrobiology}, volume = {}, number = {}, pages = {}, doi = {10.1177/15311074251404929}, pmid = {41468165}, issn = {1557-8070}, abstract = {A scientific back-and-forth, a half century overdue, is needed to develop an understanding of the possibility of life on the near surface of Mars before crewed missions complicate the search for indigenous extant martian life.}, }
@article {pmid41466397, year = {2025}, author = {Alimata, B and Ablassé, R and Moussa, C and Eli, C and Leila, KWME and Noufou, O and Emmanuelle, HA and Martin, K and Marie-Geneviève, DF}, title = {Anti-biofilm, anti-quorum sensing potential, cytotoxicity, and UPLC-UV/DAD-MS/MS/QTOF profiling of Prosopis Africana (Guill. &amp; Perr.) Taub. leaves and stems extracts: benefits of a traditional medicine in dental care.}, journal = {BMC complementary medicine and therapies}, volume = {25}, number = {1}, pages = {445}, pmid = {41466397}, issn = {2662-7671}, abstract = {BACKGROUND: Prosopis africana is traditionally used in folk medicine in Burkina Faso for oral diseases. Leaves and stems are used in rural areas to treat dental caries, and the bark is used to treat green diarrhea in infants. In the context of a better understanding of Prosopis africana’s bioactivity and toxicity, the present study deals with the chemical profiling of the different botanical parts of P. Africana used in phytomedicine. The impact of herbal medicine on various factors contributing to oral infections and caries, specifically with its anti-biofilm and anti-quorum sensing properties have been little investigated.<br><br>METHODS: The anti-biofilm effect of methanolic extracts of leaves and stems of P. africana was evaluated on Streptococcus mutans, Staphylococcus aureus, and Pseudomonas aeruginosa by using the crystal violet assay. The anti-quorum sensing effect on Chromobacterium CV026 and Pseudomonas aeruginosa was assessed spectrophotometrically by using the violacein, rhamnolipids and pyocyanin quantification assay. The cytotoxicity of the leaves and stems extracts was also evaluated by using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide method. The chemical composition of the extracts was characterized by UPLC-UV/DAD-MS[2]/ESI-QTOF analysis.<br><br>RESULTS: The extracts (100&#xa0;&#xb5;g/ml), without affecting cells viability, significantly reduced the biofilm formation of S. mutans with the best inhibition rates of 56.7% and 47.6% for stem and leaf extracts respectively. In Chromobacterium CV026, the violacein inhibition rate was 37.9&#x2009;&#xb1;&#x2009;3.7% for leaves methanol extract and 42.6&#x2009;&#xb1;&#x2009;1.4% for the stem methanol extract. In P. aeruginosa inhibition rates of 49.03%, 40.2%, and 46.7% were obtained for pyocyanin, elastase, and rhamnolipids respectively, with leaf extracts. UPLC-UV-MS[2] analysis identified sixteen compounds which are mainly polyphenols and alkaloids. They could be related to the activities.<br><br>CONCLUSION: The present study provides evidence of the efficacy and basic scientific justification for the traditional uses of P. africana in the treatment of dental caries.}, }
@article {pmid41465800, year = {2025}, author = {Messina, BM and Polizzi, A and Panuzzo, C and Belmonte, A and Angjelova, A and Fuochi, V and Annunziata, M and Isola, G}, title = {Impact of Periodontal Host-Modulation Therapies on Oral-Gut Microbiome Axis in Periodontitis Patients with Hematological Diseases: A Narrative Review.}, journal = {Life (Basel, Switzerland)}, volume = {15}, number = {12}, pages = {}, doi = {10.3390/life15121862}, pmid = {41465800}, issn = {2075-1729}, abstract = {Host-modulating therapies and oral microbiome-targeted approaches are emerging options in periodontal care and are especially relevant for patients undergoing immunotherapy for hematologic malignancies. Immune dysregulation induced by immune checkpoint inhibitors or CAR-T cell therapy may worsen periodontal inflammation and alter the composition and functions of the oral microbiota. Beyond these, other immunomodulatory treatments commonly employed in hematologic malignancies-including monoclonal antibodies (e.g., rituximab, daratumumab), immunomodulatory drugs (e.g., lenalidomide, thalidomide), cytokine-based therapies (e.g., interferon-α), and targeted small-molecule inhibitors (e.g., BTK inhibitors, JAK inhibitors) may also influence periodontal homeostasis and oral microbial ecology by altering neutrophil function, cytokine profiles, and mucosal immune surveillance. The oral microbiota is functionally connected with the intestinal microbial ecosystem through the oral-gut axis, by periodontal pathogens may colonize the gut and modulate systemic immune responses, with potential repercussions on the efficacy and safety of immunotherapy. This narrative review examines the mechanisms and clinical applicability of host-modulating therapies, including subantimicrobial-dose doxycycline, omega-3 fatty acids, and microbiome-targeted interventions, such as oral probiotics, prebiotics and other antimicrobials in patients treated with immunotherapy.}, }
@article {pmid41465447, year = {2025}, author = {Duda-Madej, A and Viscardi, S and Łabaz, JP and Topola, E and Szewczyk, W and Gagat, P}, title = {Berberine in Bowel Health: Anti-Inflammatory and Gut Microbiota Modulatory Effects.}, journal = {International journal of molecular sciences}, volume = {26}, number = {24}, pages = {}, doi = {10.3390/ijms262412021}, pmid = {41465447}, issn = {1422-0067}, mesh = {*Berberine/pharmacology/therapeutic use ; Humans ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Anti-Inflammatory Agents/pharmacology/therapeutic use ; *Inflammatory Bowel Diseases/drug therapy/microbiology ; }, abstract = {Disruption of the gut-microbiome-brain axis contributes to the development of chronic inflammation, impaired intestinal barrier integrity, and progressive tissue damage, ultimately reducing quality of life and increasing risk of comorbidities, including neurodegenerative diseases. Current therapies are often limited by adverse effects and insufficient long-term efficacy, highlighting the need for more comprehensive therapeutic approaches. Berberine (BRB), a plant-derived isoquinoline alkaloid, has attracted growing attention due to its pleiotropic immunomodulatory, neuroprotective, and gut-homeostasis-modulating properties, which involve reshaping the gut microbiota and underscore its therapeutic relevance within the gut-microbiome-brain axis. The aim of this review is to synthesize current scientific evidence regarding the anti-inflammatory mechanisms of BRB in inflammatory bowel disease (IBD). We compare its activity with first-line therapies and discuss its impact on microbial composition, including the bidirectional regulation of specific bacterial taxa relevant to intestinal and systemic disorders that originate in the gut. Furthermore, we emphasize that gut bacteria convert BRB into bioactive metabolites, contributing to its enhanced intraluminal activity despite its low systemic bioavailability. By integrating molecular and microbiological evidence, this review fills a critical knowledge gap regarding the comprehensive therapeutic potential of BRB as a promising candidate for future IBD interventions. The novelty of this work lies in unifying fragmented findings into a framework that explains how BRB acts simultaneously at the levels of host immunity, microbial ecology, and neuroimmune communication-thus offering a new conceptual model for its role within the gut-microbiome-brain axis.}, }
@article {pmid41463564, year = {2025}, author = {Zi, Y and Yang, Y and Li, M and Li, Y and An, Z and Liu, M and Ma, C and Gao, F and Li, C}, title = {Rumen Microbial Diversity and Metabolome Analysis Reveals the Effects of Alkaline Metal Ion Complexes on Muscle Quality of Lambs.}, journal = {Biology}, volume = {14}, number = {12}, pages = {}, doi = {10.3390/biology14121791}, pmid = {41463564}, issn = {2079-7737}, support = {CARS38//China Agriculture Research System/ ; BRS231402//Interdisciplinary Research Fund of Inner Mongolia Agricultural University/ ; }, abstract = {This study investigated the effects of dietary supplementation with an alkaline metal ion complex (AMIC) on growth performance, meat quality, rumen microbiota, and metabolome in Hu lambs. Fifty lambs were randomly assigned to either a control group (basal diet) or an AMIC group (basal diet + 0.15% AMIC) for 60 days. The results showed that AMIC significantly increased carcass weight, Longissimus dorsi area, crude protein, intramuscular fat, ash content, and meat luminosity (L*). Amino acid profiles and key flavor compounds were elevated, while off-flavor hydrocarbons were reduced. 16S rRNA sequencing revealed that AMIC altered rumen microbiota composition, enriching butyrate-producing genera such as Butyrivibrio and Saccharofermentans. Metabolomic analysis identified 398 differentially expressed metabolites, with upregulated pathways including butanoate metabolism and xylene degradation. Correlation analyses indicated strong associations between specific microbial taxa, metabolites, and meat quality traits. These findings suggest that AMIC enhances meat quality by modulating rumen microbial ecology and metabolic pathways, leading to improved nutrient deposition and flavor development. This study provides novel insights into the microbe-metabolite-muscle axis in ruminants and supports the use of AMIC as a dietary strategy for quality lamb production.}, }
@article {pmid41463403, year = {2025}, author = {Sun, X and Li, P and Chen, B and Chen, C and Zhao, J and Sun, S}, title = {Fucoidan Therapy for Extraintestinal Diseases: Targeting the Microbiota-Gut-Organ Axes.}, journal = {Biomolecules}, volume = {15}, number = {12}, pages = {}, doi = {10.3390/biom15121750}, pmid = {41463403}, issn = {2218-273X}, support = {82374218//National Natural Science Foundation of the People's Republic of China/ ; 82405310//National Natural Science Foundation of the People's Republic of China/ ; 2023DYPLHGG-09//The First Batch of Joint Research Projects of the China Association of Traditional Chinese Medicine/ ; MS2021002//Jiangsu Province Traditional Chinese Medicine Science and Technology Development Project/ ; 1020241792//Natural Science Foundation of the Jiangsu Higher Education Institutions of China/ ; }, mesh = {*Polysaccharides/therapeutic use/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Humans ; Animals ; Prebiotics ; Obesity/drug therapy/microbiology ; }, abstract = {The microbiota-gut-organ axis is widely recognized as a pivotal mediator of systemic health, primarily through gut-derived immune, metabolic, and inflammatory signaling. Fucoidans, a class of fucose-containing sulfated polysaccharides predominantly composed of L-fucose and exclusively found in brown seaweeds, have been demonstrated to modulate gut microbiota composition and function, resulting in the enrichment of beneficial bacteria and the suppression of harmful species. They enhance the production of beneficial metabolites, such as short-chain fatty acids and specific bile acids, while suppressing harmful metabolites, including lipopolysaccharide, thereby ameliorating organ damage via key mechanisms such as the mitigation of oxidative stress and inhibition of inflammatory responses. Furthermore, fucoidan supplementation was found to restore intestinal barrier integrity. Using disease models including Parkinson's disease, alcoholic liver disease, diabetic kidney disease, and obesity, the mechanisms through which fucoidans ameliorate extraintestinal diseases via the microbiota-gut-organ axis were elucidated. Microbiota-dependent mechanisms have been confirmed via experimental approaches such as fecal microbiota transplantation and specific bacterial strain supplementation. Fucoidans represent promising prebiotic agents for the restoration of microbial ecology and the treatment of extraintestinal diseases, highlighting the need for further clinical investigation.}, }
@article {pmid41462375, year = {2025}, author = {Zhang, Y and Zhou, K and Chen, X and Zhang, H and Han, J and Ning, K}, title = {A temporal-aware machine learning framework enables microbial community dynamics prediction with personalized precision.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {261}, pmid = {41462375}, issn = {2049-2618}, support = {Grant No. 2023YFA1800900 and 2018YFC0910502//National Key R&amp;D Program of China/ ; Grant Nos. 32071465, 31871334, 81827901//the National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Machine Learning ; *Precision Medicine/methods ; *Gastrointestinal Microbiome ; *Microbiota ; Infant ; Bacteria/classification/genetics ; }, abstract = {BACKGROUND: Accurately forecasting the dynamic behavior of microbial communities from sparse longitudinal data remains a critical challenge for microbiome-based precision medicine and ecological monitoring. Most existing models depend on data interpolation and assume population-level dynamics, which limits their ability to capture personalized microbial changes in real-world scenarios.<br><br>RESULTS: We propose MicroProphet, a personalized temporal-aware framework capable of accurately forecasting microbial abundance trajectories from incomplete longitudinal observations without requiring data imputation. Powered by a time-aware Transformer architecture, MicroProphet reconstructs subject-specific microbial trajectories using only the initial 30% of observed time points, capturing critical transitional states through an attention mechanism. We demonstrated its robust cross-ecosystem generalizability across synthetic communities, human gut microbiomes, infant gut development, and corpse decomposition. The framework consistently achieves high predictive accuracy and biological interpretability. In clinical contexts, the framework enables early detection of disease-associated microbial shifts and supports timing optimization for microbiome-targeted interventions. In forensic settings, it accurately infers decomposition timelines from early microbial signals.<br><br>CONCLUSIONS: By transforming incomplete, noisy microbiome data into actionable, individualized forecasts, MicroProphet lays the foundation for a new class of temporal-aware systems in microbial ecology and precision health.}, }
@article {pmid41461510, year = {2026}, author = {Chen, B and Hao, Z and Luo, L and Wu, N and Liu, W and Zhu, D and Ge, Y and Chen, W and Jiao, W and Zhang, X and Liu, S and Shen, J and Xiao, KQ and Fu, W and Wu, S and Zhu, YG}, title = {Soil science research in Research Center for Eco-Environmental Sciences: Review and outlook.}, journal = {Journal of environmental sciences (China)}, volume = {161}, number = {}, pages = {64-74}, doi = {10.1016/j.jes.2025.09.065}, pmid = {41461510}, issn = {1001-0742}, mesh = {*Soil/chemistry ; *Environmental Science ; Soil Microbiology ; Ecosystem ; China ; Soil Pollutants/analysis ; Environmental Monitoring ; Environmental Pollution ; Research ; }, abstract = {Soil science research involves the composition, properties, processes, and functions of soil under natural conditions and anthropogenic utilization, and provides scientific basis for the utilization, protection, and sustainable management of soil resources. This review summarizes the significant contributions of Research Center for Eco-Environmental Sciences (RCEES), Chinese Academy of Sciences, to the advances of soil science. Over past decades, RCEES has conducted innovative research in areas such as soil pollution and remediation, biogeochemical cycling of macro and trace elements and soil microbial ecology. Groundbreaking discoveries have been achieved in research directions such as metal transformation and translocation in the soil-plant continuum, soil microbial diversity and biogeography, and the environmental and health risk of soil contamination. In recent years, on-going projects also involves cutting-edge hotspots, including the environmental behavior of emerging pollutants, and soil organic matter dynamics. The soil lab in RCEES has undertaken important research projects and trained a group of dynamic young scientists, and has also been instrumental in establishing international collaborations, enhancing its global impact through participation in global soil research initiatives and conferences. Concurrently, soil science at RCEES is moving forward to the resilience of soil ecosystems to global changes, integrating soil health into the One Health framework, and sustainable soil management practices. RCEES remains a key player in shaping the future of soil science, contributing to both scientific advances and the sustainable management of soil resources in China.}, }
@article {pmid41461285, year = {2025}, author = {Bharathi, S and Soundara Rajan, YAPA and Prakash, S and Immanuel, G and Ramasubburayan, R}, title = {Pathobionts in the microbiome: Drivers of disease and targets for treatment.}, journal = {Microbial pathogenesis}, volume = {211}, number = {}, pages = {108268}, doi = {10.1016/j.micpath.2025.108268}, pmid = {41461285}, issn = {1096-1208}, abstract = {Pathobionts are commensal inhabitants of the human microbiome that can transition to a pathogenic state under specific genetic or environmental conditions. They have recently gained attention for their impact on various clinical conditions. This review discusses the key factors behind pathobiont emergence, including microbial dysbiosis, antibiotic use, dietary influences, immune dysfunction and host genetics. It provides a comprehensive overview of pathobionts associated with the gut, oral cavity, and vaginal microbiomes highlighting their roles in disease pathogenesis. A significant focus is also placed on the involvement of pathobiont in immune-related disorders. Furthermore, current and advanced therapeutic strategies aimed at mitigating the effects of pathobionts, such as faecal microbiota transplantation, phage therapy, probiotics and prebiotics, along with their advantages and limitations, were highlighted. Thus, the integrated perspective combining microbial ecology, host immunity, and therapeutic strategies outlines the need for targeted, microbiome-based interventions to address the complex behaviour of pathobionts.}, }
@article {pmid41460347, year = {2025}, author = {Zhang, Y and Zheng, C and Wang, S and Zhu, F}, title = {Variations in Nodule Microbial Communities and Their Association with Root-Colonizing Arbuscular Mycorrhizal Fungi in Medicago Sativa.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02687-x}, pmid = {41460347}, issn = {1432-184X}, support = {2022YFF1302801//National Key Research and Development Program of China/ ; 2022YFD1900301//National Key Research and Development Program of China,China/ ; }, abstract = {Alfalfa (Medicago sativa L.), known as "Queen of forages", is valued to its high-nutritional quality and is a key member of Leguminosae family. Its productivity is largely attributed to mutualistic symbioses with arbuscular mycorrhizal fungi (AMF) and rhizobia, which facilitate nutrient exchange and plant growth. However, the coexistence and mutualistic interactions between rhizobia and AMF across alfalfa genotypes with differing yields in native soil remain poorly understood. In this study, we investigated the community composition of rhizobia and AMF colonizing alfalfa roots across different-yield varieties. Our results showed variations in dominant microbial taxa and the structural complexity of root-associated microbial networks among genotypes. Moreover, rhizobia exhibited no significant associations with AMF on genus level, however, negative correlations were observed among genera within the AMF community, and a comparable trend was identified among rhizobial taxa. In summary, our findings offer new insights into how native soil microbiota influence the dual symbiotic relationships of alfalfa, with implications for leveraging native microbial communities to enhance sustainable forage production.}, }
@article {pmid41459044, year = {2025}, author = {Wu, X and Shao, T and Huang, Y and Cui, X and Luo, Y and Ji, Q and Hu, Z and Teng, S and Bao, G and Liu, Y}, title = {Effects of dietary nisin supplementation on the growth performance, serum biochemistry, digestive enzyme activities, intestinal morphology, and intestinal microbiota in rabbits.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1726365}, pmid = {41459044}, issn = {2297-1769}, abstract = {INTRODUCTION: This study evaluated the impact of dietary supplementation with varying doses of nisin (NI) on the growth performance, serum biochemical parameters, intestinal digestive enzyme activity, short-chain fatty acid (SCFA) profiles, mucosal morphology, and the cecal microbiota composition in rabbits.<br><br>METHODS: Healthy female New Zealand white rabbits (5 weeks old; n = 90) of comparable body weight were randomly allocated to five groups: a positive control (PC) group receiving a basal diet supplemented with kitasamycin (300 mg/kg), three NI groups supplemented with nisin at 600 (NI600), 800 (NI800), or 1,000 (NI1000) mg/kg, and a negative control (NC) group receiving the basal diet without additives. Each treatment was comprised of three replicates (n = 6 per replicate), and the trial lasted 42 days.<br><br>RESULTS: The results showed that the rabbits administered NI displayed significantly enhanced final body weights as compared to the NC group (P < 0.05), with a dose-dependent effect. Notably, the NI800 and NI1000 groups exhibited a superior average daily gain (ADG) and average daily feed intake (ADFI). Serum analyses showed improved lipid profiles and elevated antioxidant enzyme activities concomitant with reduced lipid peroxidation in the NI-supplemented groups. Enzymatic assays indicated elevated duodenal a-amylase activity in the NI800 group as compared to the PC (P < 0.05) and enhanced ileal trypsin activity in the NI800 as compared to NI1000 and PC (P < 0.05). Histological evaluation confirmed that the NI800 group displayed optimal intestinal villi morphology, characterized by increased density, height, and structural integrity relative to the PC and NC controls. Metagenomic analysis of the cecal microbiota further revealed dose-dependent shifts in the diversity and composition of the microbiota, with the NI800 group exhibiting pronounced restructuring. Enriched functional pathways in the NI groups, including cofactor/vitamin metabolism, amino acid biosynthesis, energy homeostasis, and environmental adaptation.<br><br>DISCUSSION: Collectively, these findings highlight that NI supplementation enhances digestive efficiency, augments systemic antioxidant defenses, fortifies intestinal barrier function, and modulates microbial ecology and SCFA production, there by promoting growth and metabolic health in rabbits. Nisin, especially at 800 mg/kg, demonstrates significant potential as an antibiotic alternative.}, }
@article {pmid41458128, year = {2025}, author = {Qin, Y and Wang, Y and Huang, Y and Chen, H and Zhuang, Y and Liu, Q and Soteyome, T and Zhu, B and Brennan, C}, title = {Antimicrobial EU@Ag-MOF/PLA composite films enhance postharvest quality of strawberries by mitigating oxidative stress and modulating microbial communities.}, journal = {Food chemistry: X}, volume = {32}, number = {}, pages = {103377}, pmid = {41458128}, issn = {2590-1575}, abstract = {Strawberries are highly perishable fruits susceptible to rapid postharvest deterioration. This study investigated the efficacy of EU@Ag-MOF/PLA composite films for postharvest strawberry preservation. The 3EU@Ag-MOF/PLA formulation demonstrated optimal performance in maintaining physicochemical properties, reducing reactive oxygen species accumulation, and enhancing antioxidant enzyme activities. Notably, this composite film suppressed hydrogen peroxide, superoxide anion, and malondialdehyde content by 28.44 %, 37.33 %, and 29.91 %, respectively, compared to control packaging after 10 days. Pathogen challenge studies with Botrytis cinerea and Rhizopus stolonifer revealed that this composite effectively balances reactive oxygen species production and scavenging mechanisms during storage. High-throughput sequencing showed that 3EU@Ag-MOF/PLA packaging preserved more balanced microbial community structures and dramatically reduced the relative abundance of pathogenic fungi by day 10. These findings demonstrate that 3EU@Ag-MOF/PLA composite film represent a promising active packaging solution for extending the shelf life of highly perishable fruits by simultaneously addressing fungal proliferation, oxidative stress, and microbial ecology.}, }
@article {pmid41457489, year = {2025}, author = {Silbiger, NJ and Fields, JB and Nelson, CE and Kelly, LW}, title = {Foundation Species Modulate Microbial Benthic-Pelagic Coupling in the Rocky Intertidal.}, journal = {Ecology letters}, volume = {28}, number = {12}, pages = {e70301}, doi = {10.1111/ele.70301}, pmid = {41457489}, issn = {1461-0248}, support = {2044837//NSF Biological Oceanography/ ; 2513325//NSF Biological Oceanography/ ; COAST-GDP-2020-006//Council on Ocean Affairs Science and Technology, California State University/ ; //Uehiro Foundation on Ethics and Education/ ; }, mesh = {Animals ; *Ecosystem ; Oregon ; *Bacteria/growth &amp; development ; *Bivalvia/physiology ; Nitrogen/metabolism ; Seawater/microbiology ; }, abstract = {Benthic-pelagic coupling, the reciprocal exchange of materials between benthic and pelagic habitats, has traditionally emphasised pelagic influences on benthic systems. Yet, the role of benthic biological processes in shaping pelagic microbial dynamics remains underexplored. We investigated how surfgrass and mussels regulate nitrogen and dissolved organic matter (DOM) cycling and their cascading effects on heterotrophic bacteria in Oregon tide pools. We quantified biogeochemical fluxes and bacterial responses before and after foundation species removal during contrasting upwelling regimes. Mussel-dominated pools released high concentrations of ammonium and nitrate, while surfgrass pools transformed DOM that fueled bacterial growth; upwelling intensified these benthic-pelagic linkages. Removing foundation species dampened nutrient release in mussel pools and reduced DOM-fueled bacterial growth in surfgrass pools, ultimately decoupling benthic productivity from pelagic microbial growth. Our results demonstrate the critical role of foundation species to pelagic microbial processes and underscore the vulnerability of coastal microbial dynamics to their global decline.}, }
@article {pmid41457317, year = {2025}, author = {Anbo, M and Otani, S and Ivanova, M and Nielsen, HN and Jensen, JD and Svendsen, CA and Pang, C and Aarestrup, FM}, title = {Contrasting pH optima of β-lactamases CTX-M and CMY influence Escherichia coli fitness and resistance ecology.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0177525}, doi = {10.1128/aem.01775-25}, pmid = {41457317}, issn = {1098-5336}, abstract = {Antimicrobial resistance is one of the largest and most pressing global health threats. This is not only a huge burden on the global economy but also a growing threat to animal, environmental, plant, and human health, and new strategies are needed to avoid resistance and improve treatment. Novel antimicrobial resistance genes are normally first detected once they cause problems in clinical infections, and we have limited knowledge on their evolutionary trajectories. Current antimicrobial susceptibility testing and research have a limited focus on key environmental factors in pathogen-reservoir-host interactions, possibly leading to inaccurate results that do not reflect the in vivo conditions. Focusing on differences in pH, we determined the MIC of a panel of isogenic strains expressing CTX-M-15 and CMY-2 β-lactamases. We found that pH has a large impact on the activity of β-lactamases, and treatment of these resistant isolates could be possible if the pH of the environment is modified. We verified this using enzyme kinetics, co-cultures, and growth experiments, suggesting that exposure to different environmental conditions may lead to distinct evolutionary trajectories for specific β-lactamases. Exploring the effect of different temperatures, we also observed a differential effect of avian and mammal host temperatures. Environmental factors such as pH and temperature may have a large unnoticed effect on antimicrobial resistance, and we might use this knowledge to renew and extend the use of old antibiotics for certain infections.IMPORTANCEAntimicrobial resistance is a huge burden to global health and economy. We need new options for avoiding selection of resistance and improved treatment. Overlooked aspect: current susceptibility testing does not take pH into account. With this study, we show that pH and temperature can have large and contrasting effects on the activity (and therefore MIC) of specific β-lactamases. This might help to explain the phenomenon of bacteria often harboring multiple β-lactamases seemingly with the same function as well as be utilized to enable treatment of genotypically resistant strains under very specific conditions, that is, treatment of CTX-M-15, the most prevalent ESBL in healthcare, under alkaline conditions.}, }
@article {pmid41456824, year = {2025}, author = {Quan, H and Ouyang, J and Fu, X and Lin, D and Wu, Q and Li, D and Li, Y and Yang, F and Wu, S and Li, C and Mao, W}, title = {Elucidating the Therapeutic Mechanism of Orthosiphon aristatus in Hyperuricemic Nephropathy: An Integrated Microbiome-Metabolomics Approach.}, journal = {Journal of ethnopharmacology}, volume = {}, number = {}, pages = {121115}, doi = {10.1016/j.jep.2025.121115}, pmid = {41456824}, issn = {1872-7573}, abstract = {Hyperuricemic nephropathy (HN) remains challenging to treat due to the limitations, including variable efficacy and side effects, of conventional drugs. Orthosiphon aristatus (O. aristatus), used for over 2000 years in Dai medicine to treat kidney disorders by "clearing heat and promoting diuresis," shows strong potential for HN management. However, its mechanisms of action against HN remain unclear.<br><br>AIM OF THE STUDY: This study aimed to elucidate the nephroprotective effects and underlying mechanisms of O. aristatus against HN using an integrated strategy focusing on the gut-kidney axis.<br><br>METHODS: A rat model of HN was established by combined oral administration of potassium oxonate (750 mg/kg) and uric acid (300 mg/kg) daily for 7 weeks. Model rats were treated with a low- or high-dose aqueous extract of O. aristatus (3.125 or 6.25 g/kg/day), using allopurinol (5 mg/kg/day) as a positive control. Renal function was assessed by measuring serum levels of uric acid, creatinine, and urea nitrogen. Renal pathological injury and fibrosis were evaluated through histopathological examination (H&amp;E and Masson's trichrome staining), immunohistochemistry (&#x3b1;-SMA, vimentin), and transmission electron microscopy. To elucidate the underlying mechanisms, an integrated multi-omics approach was employed: gut microbiota composition was profiled by metagenomic sequencing, and metabolic alterations in cecal content and kidney tissue were characterized using UPLC-MS-based metabolomics. Furthermore, the protein expression of key targets involved in intestinal barrier function (Occludin, Claudin-1) and the IDO1/AhR signaling pathway was validated by Western blot analysis.<br><br>RESULTS: O. aristatus treatment significantly ameliorated renal dysfunction and pathological injury, as demonstrated by marked reductions in serum uric acid (sUA), creatinine (Scr), and blood urea nitrogen (BUN) levels (all p < 0.001), alongside attenuated tubular injury and fibrosis. Concurrently, it restored gut microbiota diversity (e.g., increased Shannon index, p < 0.05) and composition, characterized by an enrichment of beneficial Prevotella and a reduction in Bacteroides. Integrated metabolomics analysis further linked these effects to the rectification of tryptophan metabolism, manifested by decreased renal kynurenine levels (p < 0.01) and enhanced intestinal barrier integrity (e.g., elevated Occludin and Claudin-1, p < 0.05). Collectively, our results delineate that the renoprotective effect of O. aristatus is mediated through the suppression of the renal IDO1/kynurenine/AhR pro-fibrotic signaling axis, unveiling a novel gut microbiota-metabolite-kidney interaction mechanism.<br><br>CONCLUSION: This study elucidates that the renoprotective effect of O. aristatus against HN is mediated through modulation of the gut-kidney axis, by restoring microbial ecology, reprogramming host tryptophan metabolism, and subsequently inhibiting the IDO1/kynurenine/AhR pro-fibrotic pathway.}, }
@article {pmid41455542, year = {2025}, author = {Mariën, Q and Regueira, A and Petrognani, C and Scarborough, M and Ganigué, R}, title = {Enhancing carbon capture and utilization: mixotrophic growth of Clostridium luticellarii using methanol and hydrogen for efficient CO2 reduction.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133886}, doi = {10.1016/j.biortech.2025.133886}, pmid = {41455542}, issn = {1873-2976}, abstract = {Carbon capture and utilization remains a major challenge in mitigating climate change. Carbon dioxide (CO2) fixing microorganisms offer promising routes to convert CO2 emissions into valuable products. Clostridium luticellarii is a recently discovered acetogen capable of converting CO2 to acetic, butyric and isobutyric acids using H2 or methanol as electron donors. Both routes can use renewable electricity as primary energy input, but each has its limitations: While H2-based processes suffer from poor gas-to-liquid mass transfer and low product selectivity beyond acetic acid, methanol requires a preliminary energy-intensive catalytic reduction of CO2. This study investigated the growth of C. luticellarii on both substrates to compensate their respective drawbacks. Combining methanol and H2 resulted in mixotrophic growth and enhanced CO2 assimilation up to four-fold compared to conversion of methanol alone, while producing similar product spectra. Thermodynamic pathway analysis suggested that high H2 pressures inhibit the H2-producing formate oxidation, while pathways with alternative electron carriers remain favorable. Subsequently, a metabolic model of the one-carbon catabolism was constructed and used to perform flux balance analysis. This revealed that H2 oxidation during mixotrophic growth augments the intracellular pool of reducing equivalents, reducing the need for methanol oxidation and increasing net CO2 assimilation into products. These findings highlight the potential of combining methanol and H2 as electron donors to improve CO2 conversion efficiency for the sustainable production of butyric and isobutyric acids.}, }
@article {pmid41455317, year = {2025}, author = {Caly-Simbou, E and Ramin-Mangata, S and Poussier, S and Pecrix, Y}, title = {Bacteriocins in plant pathology: current knowledge, application, challenges and perspectives.}, journal = {Biochemical and biophysical research communications}, volume = {797}, number = {}, pages = {153203}, doi = {10.1016/j.bbrc.2025.153203}, pmid = {41455317}, issn = {1090-2104}, abstract = {To address the growing emergence of multi-resistant phytopathogenic bacteria, innovative solutions are being explored in the field of plant health. Among them, bacteriocins, antimicrobial peptides or proteins secreted by bacteria, characterized by a highly specific spectrum of activity and involved in intra-specific competition, are gaining increasing interest. Bacteriocins can confer a positive selective advantage in both natural and agricultural environments, thereby contributing to microbiome modulation. Bacteriocin-producing rhizobacteria and lactic acid bacteria are already used as biocontrol agents against phytopathogenic bacteria, as well as plant growth stimulators. Bacteriocins can be produced in situ by using avirulent strains, or ex situ through industrial synthesis and applied as biopesticides. Nowadays, genetic engineering enables production of chimeric bacteriocins and their direct production in transgenic plants, avoiding the need for repeated treatments and limiting emergence of resistances. The selection of promising bacteriocins can be guided by omics-based approaches, notably metagenomics, which involve the direct extraction and sequencing of DNA from environmental samples and provides access to the genetic diversity in complex soil or plant-associated microbiomes. Combined with open-access databases and recently developed integrated tools, this approach not only facilitates the identification of known structures of bacteriocins, but also enables the prediction of potentially active peptides even those never experimentally characterized. Bacteriocin-based strategies, at the crossroads of molecular biology, microbial ecology and agronomy, hold significant potential for promoting sustainable agriculture through highly specific pathogen targeting. However, their large-scale implementation still faces several challenges, including standardization of strain screening protocols, compliance with regulatory frameworks and farmer acceptance.}, }
@article {pmid41455041, year = {2025}, author = {Sarkar, P and Das, S and Bandyopadhyay, S and Gopi, P and Biswas, S and Tribedi, P and Pandya, P and Mandal, S and Bhadra, K}, title = {Beta Carboline Alkaloid Harmine as Biofilm Inhibitor: In vitro, in Silico and in Vivo Studies Suppressing Growth and Virulence-Related Factors Against Resistant Staphylococcus Aureus.}, journal = {Applied biochemistry and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {41455041}, issn = {1559-0291}, support = {2025-2026//PRG University of Kalyani/ ; 2025-2026//DST PURSE/ ; }, abstract = {Screening plant-based alkaloids is one of the alternate therapeutic approaches to control antibiotic-resistant micro-pathogens. Our research highlighted beta carboline alkaloids as one of the most promising small molecules to established anti-virulent and anti-biofilm efficacy to regulate resistant bacterial infection. In vitro, in vivo assay and molecular docking were employed. Result Among six different bacterial strains, harmine showed 160 ± 2.07 µg/ml as the minimum inhibitory concentrations (MIC), followed by harmalol (190 ± 2.46) and harmaline (270 ± 3.04) against Staphylococcus aureus 96 (SA 96). Methicillin-resistant Staphylococcus aureus MRSA strain also showed inhibition of growth (MIC) by harmine, harmalol and harmaline at 250 ± 3.10, 320 ± 3.39 and 390 ± 4.90 µg/ml, respectively. MRSA is a prominent source of nosocomial infections, forming biofilms. The growth of biofilm got decreased with exposure to the sub-MIC concentrations (60, 80 and 100 µg/mL) of harmine, suppressing protein, targeting EPS and inhibiting extracellular protease. Harmine promote biofilm cell detachment by targeting cell surface hydrophobicity. Harmine causes depolarization of bacteria's cell membrane. Bacterial cell viability was further studied by propidium iodide (PI), DNA leakage and Acridine Orange (A/O)-Ethidium Bromide (EtBr) assay. Harmine treatment leads to increased reactive oxygen species (ROS) levels in biofilm cells. The binding affinities by molecular docking and dynamics indicated highest affinity with AgrC (-6.17 kcal/mol). Harmine treatment (32.0 mg/ kg bw, IP for five days) further recovered MRSA infected lungs in BALB/c mice. The findings revealed that among the three beta carboline alkaloids, harmine might be employed as a potential antibiofilm and antimicrobial agent for successful control of clinical S. aureus infection.}, }
@article {pmid41454163, year = {2025}, author = {Bovio-Winkler, P and Orellana, E and Campanaro, S and de Jesús Montoya-Rosales, J and Fuess, LT and Carrillo-Reyes, J and Castelló, E and Muñoz-Páez, KM and Moreno-Andrade, I and Buitrón, G and Razo-Flores, E and Etchebehere, C}, title = {Unraveling the biological mechanisms of biohydrogen production through dark fermentation using assembled genomes from metagenomic data.}, journal = {Bioprocess and biosystems engineering}, volume = {}, number = {}, pages = {}, pmid = {41454163}, issn = {1615-7605}, support = {project A1-S-37174//Fondo Sectorial SEP-CONACYT/ ; }, abstract = {Dark fermentation represents a sustainable and promising approach for biohydrogen generation. However, achieving high yields depends on understanding the complex microbial interactions driving the process. This study used genome-centric metagenomics to analyze microbial communities from 11 hydrogen-producing reactors. In total, 44 metagenome-assembled genomes (MAGs) were analyzed in detail. High-yield reactors demonstrated a strong synergy between hydrogen-producing bacteria (HPB) and lactic acid bacteria (LAB), particularly Clostridium butyricum and Clostridium beijerinckii. These species encode the electron-transferring flavoprotein-lactate dehydrogenase complex (EtfAB-ldh complex), enabling hydrogen production from lactic acid. In contrast, reactors with lower hydrogen yields exhibited a higher prevalence of hydrogenotrophic microorganisms, including homoacetogens and methanogens, which redirected electron flow toward competing pathways, thereby decreasing hydrogen output. These results emphasize the importance of promoting HPB while suppressing hydrogen consumers to maintain an optimal microbial community. By linking community composition with metabolic potential, this study provides a framework for improving reactor performance, increasing hydrogen yields, and advancing sustainable hydrogen production from organic waste streams.}, }
@article {pmid41452003, year = {2025}, author = {Sun, B and Sun, T and Ji, K and Yang, Z and Wang, J and Zhao, Y and Yu, X and Tang, X and Xiao, H}, title = {Effects of the tidal dehydration stress on epiphytic bacterial community of the intertidal macroalga Sargassum thunbergii.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0194825}, doi = {10.1128/spectrum.01948-25}, pmid = {41452003}, issn = {2165-0497}, abstract = {UNLABELLED: Intertidal macroalgae and their epiphytic bacteria experience periodic dehydration-rehydration cycles due to tidal fluctuations. The influence of tidal dehydration on algal epiphytic bacteria remains poorly understood. This study investigated the effect of tidal dehydration on epiphytic bacterial communities of macroalga Sargassum thunbergii. While tidal dehydration had a small impact on the composition of the epiphytic bacterial community of S. thunbergii, it significantly influenced community diversity, abundance of dominant taxa, and some predicted functional genes. Specifically, the abundance of Proteobacteria and Granulosicoccus increased markedly, whereas that of Cyanobacteria, Litoreibacter, and Sva0996_marine_group decreased significantly. The abundance of Marinomonas exhibited a trend of initial decrease, followed by subsequent increase. Predictive functional analysis suggested that the bacterial community adapted to dehydration stress by regulating genes involved in energy, nitrogen, and sulfur metabolism. The shifts in the bacterial community following dehydration stress may result from the inherent differential stress tolerance among bacterial taxa and host-mediated facilitation through algal metabolic adjustments that selectively favored specific groups. This study revealed the structural and functional response of the epiphytic bacterial community of macroalgae in intertidal zones to dehydration stress.<br><br>IMPORTANCE: The adaptive mechanisms of the intertidal macroalgal-epiphytic bacterial symbiotic system to periodic tidal dehydration stress play a crucial role in maintaining coastal ecosystem stability. Although numerous studies have investigated the effects of tidal dehydration on intertidal macroalgae, the impact of dehydration on the epiphytic bacteria has received much less attention. Our investigation revealed that tidal dehydration stress significantly alters both the community structure and metabolic functions of the epiphytic bacteria on Sargassum thunbergii. Notably, dehydration stress selectively enriched stress-tolerant bacterial taxa and induced metabolic reprogramming, particularly in energy, nitrogen, and sulfur cycling pathways. These microbial responses demonstrate not only bacterial stress adaptation strategies but also suggest potential host-mediated regulation within the algal-bacterial symbiotic system. These findings provide novel insights into the ecological adaptability mechanisms of intertidal ecosystems under environmental stress.}, }
@article {pmid41450949, year = {2025}, author = {Perzon, O and Ilan, Y}, title = {Understanding gut microbial diversity using systems based on the Constrained-Disorder Principle provides a novel approach to targeting gut microbiome therapies.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1713775}, pmid = {41450949}, issn = {1664-302X}, abstract = {BACKGROUND/AIMS: The diverse composition of the gut microbiome is vital for human health, influencing digestion, immune regulation, and disease resistance. While higher diversity is generally associated with resilience, reduced and excessive diversity can lead to health issues.<br><br>METHODS: This paper introduces the Constrained Disorder Principle (CDP) as a new framework for understanding microbial diversity.<br><br>RESULTS: The CDP emphasizes the significance of maintaining variability within certain boundaries to sustain ecosystem stability and promote health. It considers intra- and inter-individual variability, illustrating how microbial ecosystems adapt throughout different life stages, genetic backgrounds, and environmental exposures. Integrating CDP-based artificial intelligence systems may enable the establishment of personalized diversity thresholds, predict dysbiosis, and refine interventions such as probiotics, prebiotics, fecal microbiota transplantation, and customized dietary strategies. CDP-driven platforms enhance therapeutic precision by utilizing variability induction, feedback loops, and microbial signature analysis to optimize diversity goals and identify actionable biomarkers.<br><br>CONCLUSION: This platform can pave the way for adaptive, individualized disease prevention and treatment strategies, bridging the gap between microbial ecology and precision medicine. It provides a powerful tool for harnessing the therapeutic potential of gut microbial diversity to enhance human health.}, }
@article {pmid41445807, year = {2025}, author = {Wang, XW and Wang, T and Liu, YY}, title = {Artificial Intelligence for Microbiology and Microbiome Research.}, journal = {ArXiv}, volume = {}, number = {}, pages = {}, pmid = {41445807}, issn = {2331-8422}, abstract = {Advancements in artificial intelligence (AI) have transformed many scientific fields, with microbiology and microbiome research now experiencing significant breakthroughs through machine learning applications. This review provides a comprehensive overview of AI-driven approaches tailored for microbiology and microbiome studies, emphasizing both technical advancements and biological insights. We begin with an introduction to foundational AI techniques, including primary machine learning paradigms and various deep learning architectures, and offer guidance on choosing between traditional machine learning and sophisticated deep learning methods based on specific research goals. The primary section on application scenarios spans diverse research areas, from taxonomic profiling, functional annotation \&amp; prediction, microbe-X interactions, microbial ecology, metabolic modeling, precision nutrition, clinical microbiology, to prevention \&amp; therapeutics. Finally, we discuss challenges in this field and highlight some recent breakthroughs. Together, this review underscores AI's transformative role in microbiology and microbiome research, paving the way for innovative methodologies and applications that enhance our understanding of microbial life and its impact on our planet and our health.}, }
@article {pmid41443232, year = {2025}, author = {Dissanayaka, S and Jayasingh, T and Sohrabi, HR and Rainey-Smith, SR and Scott, K and Martins, RN and Fernando, WMADB and , }, title = {Basic Science and Pathogenesis.}, journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association}, volume = {21 Suppl 1}, number = {Suppl 1}, pages = {e105512}, doi = {10.1002/alz70855_105512}, pmid = {41443232}, issn = {1552-5279}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; *Alzheimer Disease/metabolism/microbiology ; Aged ; *Cognitive Dysfunction/metabolism/microbiology ; *Fatty Acids, Volatile/metabolism ; Feces/microbiology/chemistry ; Amyloid beta-Peptides/metabolism ; Brain/metabolism ; Positron-Emission Tomography ; Aged, 80 and over ; Middle Aged ; }, abstract = {BACKGROUND: Gut microbiota and their metabolites, particularly short-chain fatty acids (SCFAs), play a vital role in the gut-brain axis, and have been associated with neurodegenerative diseases like Alzheimer's disease (AD). However, the changes in gut microbiota composition and SCFA levels during the progression of AD are not yet well understood. This study seeks to investigate these variations to gain deeper insights into their potential role in disease development.<br><br>METHOD: This study examined changes in gut microbiota and SCFA across three groups; Cognitively unimpaired individuals with low amyloid-beta ((CU) A&#x3b2; Low (n&#xa0;=&#xa0; 71)), CU A&#x3b2; High (n&#xa0;=&#xa0; 19), and those diagnosed with mild cognitive impairment (MCI) or AD (Disease Group (DG), n = 10). Participants were selected from well characterised cohorts and underwent Pittsburg compound B-positron emission tomography to determine cerebral amyloid status. Faecal microbiota composition was assessed using shotgun metagenomics, while faecal SCFA concentrations were quantified via Gas Chromatography-Mass Spectrometry (GC-MS). Associations between taxa and SCFAs were assessed using Spearman correlation and MaAsLin2.<br><br>RESULT: Firmicutes, Proteobacteria, and Bacteroidetes exhibited significant correlations with SCFAs across all groups. In the CU A&#x3b2; Low and Disease Group (DG), Firmicutes showed Positive correlations with butyric acid. Group-specific patterns included negative correlations between Bacteroidetes and propionic acid in the DG group, a positive correlation between Firmicutes and total SCFAs in the CU A&#x3b2; Low group, and a positive correlations between Proteobacteria and Actinobacteria with butyric acid in the CU A&#x3b2; High group, alongside notable interactions with isovaleric acid. Furthermore, specific taxa such as Corynebacterium falsenii (Phylum: Actinobacteria), Ruthenibacterium lactatiformans (Phylum: Firmicutes), and Streptomyces capitiformicae (Phylum: Actinobacteria) showed significant associations with SCFAs, particularly propionic acid and butyric acid.<br><br>CONCLUSION: These findings suggest that changes in gut bacteria and their metabolites vary at different stages of AD. Key results show that certain bacteria, such as Firmicutes, Bacteroidetes, and Proteobacteria, are linked to SCFAs, especially butyric acid, which plays a role in gut and brain health. This suggests that modifying gut bacteria could help regulate SCFA levels and potentially slow the progression of AD. However, more research is needed to fully understand this connection.}, }
@article {pmid41441004, year = {2025}, author = {Alabi, JO and Kholif, AE and Ike, KA and Okedoyin, DO and Adelusi, OO and Wuaku, M and Anotaenwere, CC and Enikuomehin, JM and Oderinwale, OA and Adebayo, JO and Gentry-Apple, AR and Anele, UY}, title = {Rumen Fluid Metabolomics and Microbiome Profiling of Dairy Cows Fed Combinations of Prebiotics, Essential Oil Blend, and Onion Peel Using the RUSITEC System.}, journal = {Metabolites}, volume = {15}, number = {12}, pages = {}, pmid = {41441004}, issn = {2218-1989}, support = {NC.X338-5-21-120-1//United States Department of Agriculture/ ; }, abstract = {BACKGROUND AND OBJECTIVES: Dairy products provide vital energy, high-quality protein, and micronutrients for over six billion people worldwide, with dairy cows contributing nearly 81% of global milk production. Sustainable strategies to enhance productivity are therefore critical. Feed additives such as essential oil blends (EOB), onion peel (OPE), and prebiotics including mannan oligosaccharides (MOS) and galacto-oligosaccharides (GOS) have been proposed to improve rumen fermentation, modulate microbial ecology, and mitigate greenhouse gas emissions. This study evaluated the combined effects of EOB, OPE, MOS, and GOS on rumen metabolism using the rumen simulation technique (RUSITEC).<br><br>MATERIALS AND METHODS: Rumen inoculum from three cannulated Holstein Friesian cows was incubated across 16 vessels (four treatments &#xd7; four replicates) for nine days. Treatments included a control (CON; TMR only), GEO (TMR + GOS + EOB + OPE), MEO (TMR + MOS + EOB + OPE), and OLEO (TMR + a 1:1 mixture of GOS and MOS + EOB + OPE). Additives were included at 3 &#xb5;L/g TMR for EOB and 30 mg/g TMR (3% w/w) for OPE, GOS, MOS, or OLG. Rumen effluents were collected for untargeted metabolomic profiling by liquid chromatography-mass spectrometry, identifying 661 metabolites.<br><br>RESULTS: Partial least squares-discriminant analysis revealed clear separation between CON and additive groups, confirming distinct metabolic shifts. GEO primarily enhanced tryptophan, tyrosine, and purine metabolism; MEO stimulated phosphonate and pyrimidine pathways and bile acid biosynthesis; OLEO promoted phosphonate, nicotinamide, and taurine metabolism. Microbial analysis showed enrichment of taxa such as Lachnospira, Succinivibrionaceae, Macellibacteroides, Lysinibacillus, and Christensenellaceae, indicating complementary effects on fermentation and microbial stability.<br><br>CONCLUSIONS: These results demonstrate that dietary supplementation with GEO, MEO, or OLEO modulates rumen metabolism and microbial ecology without impairing fermentation, supporting improved nutrient utilization, antioxidant defenses, and metabolic resilience in dairy cows, with potential benefits for productivity and sustainability.}, }
@article {pmid41439189, year = {2025}, author = {Ghotbi, M and Ghotbi, M and D'Agostino, E and Kanitz, M and Needham, DM}, title = {From microscale to microbial insights: validating high-throughput microvolume extraction (HiMEx) methods for marine microbial ecology.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf218}, pmid = {41439189}, issn = {2730-6151}, abstract = {Extracting and directly amplifying DNA from small-volume, low-biomass samples would enable rapid, ultra-high-throughput analyses, facilitating the study of microbial communities where large-volume sample collection is challenging. This can aid where 'conventional' filtrater-based methods miss capturing smaller microbes, or where microscale variability matters, such as the ocean. Here, we develop and validate physical and chemical-based DNA extractions from microvolumes with universal rRNA gene amplicons and metagenomic sequencing of all domains and viruses, on natural surface seawater and experimentally manipulated marine waters. Compared to 500-mL filter-based extraction, direct PCR of 3 μL of lysate from seawater microvolume extractions ranging from 100-1000 μL consistently captured comparable microbial community composition and diversity, with reliable amplification and little to no contamination. Metagenomic results of 10 μL lysates from 15 microvolume samples (100 μL) captured 83 high- and draft-quality, diverse bacterial genomes and 430 complete, high and medium quality viral contigs. Our approach enables scaling of rRNA gene sequencing and metagenomic library prep for high-throughput experimentation for a fraction of the cost of conventional methods and builds upon existing microvolume approaches by removing unnecessary expenses, like excess plasticware and expensive bead clean-up. The method expands opportunities for more comprehensive microbial community monitoring and controlled laboratory experiments by facilitating higher sample numbers and lowering sample volume needs. However, its potential bias against Gram-positive bacteria should be considered when applying to environments where these taxa are abundant.}, }
@article {pmid41439181, year = {2025}, author = {Yang, M and He, T and Moukarzel, R and Li, M and Li, M and Zhang, Z and He, Y and Liu, Y and Yu, L and Zhu, S and Du, F}, title = {Phyllosphere microbiome responses to nano-berberine and chemical fungicides in powdery mildew infected strawberry.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1712123}, pmid = {41439181}, issn = {1664-462X}, abstract = {Strawberry powdery mildew, caused by the obligate biotroph Podosphaera aphanis, is a major threat to commercial strawberry production, reducing both yield parameters and fruit quality. While chemical fungicides remain a standard control method, their non-target effects on phyllosphere microbial communities have raised important ecological and environmental concerns. Nano-pesticides are increasingly applied in plant disease management, however, their influence on the composition and functional potential of phyllosphere microbial communities remains poorly understood. The nano-berberine formulation (BBR-M) used in this study was provided by a collaborative group, with synthesis and physicochemical characteristics consistent with those previously reported for this material. In this study, we compared the field-level effects of a nano-berberine formulation (BBR-M) and conventional chemical fungicides (e.g., bupirimate) on the strawberry phyllosphere microbiota using high-throughput sequencing, bioinformatics analysis, and microbial isolation techniques. The results showed that nano-fungicide application significantly reduced the disease index of powdery mildew and markedly decreased its incidence in field-grown strawberries, ultimately lowering leaf disease incidence to 5.06% with a control efficacy of 96.81%. Furthermore, nano-fungicides and conventional chemical fungicides treatments were associated with distinct impacts on the phyllosphere microenvironment of strawberry. Application of BBR-M was associated with a more structured and potentially stable microbial community, characterized by increased fungal diversity and higher modularity in co-occurrence networks. In contrast, bupirimate treatment increased microbial complexity but coincided with reduced network stability. A strain of Bacillus siamensis-a genus identified as a core taxon within the BBR-M phyllosphere network-was subsequently isolated from nano-berberine-treated leaves and exhibited strong antagonistic activity against Colletotrichum nymphaeae. Field assays showed that this strain effectively suppressed strawberry powdery mildew with 98.18% control efficacy. Collectively, these findings provide important insights into the ecological safety and functional implications of novel pesticide technologies, underscoring the potential of nano-fungicides and native biocontrol agents for sustainable strawberry disease management.}, }
@article {pmid41438540, year = {2025}, author = {Zhou, L and Lin, X and Guo, R and Li, T and Brennan, C and Fu, X and Liu, RH}, title = {Phytochemical compounds, antioxidant activity, and antiproliferative activity of sesame seeds as affected by simulated digestion.}, journal = {Food chemistry: X}, volume = {32}, number = {}, pages = {103317}, pmid = {41438540}, issn = {2590-1575}, abstract = {Antioxidant and antiproliferative activities in white and black sesame seeds were investigated during a simulated in vitro digestion. The levels of phenolic compounds, flavonoids and oxygen radical absorbance capacity (ORAC) values of sesame seeds increased by over 50 % after simulated stomach, small and large intestine digestion. A higher cellular antioxidant activity (CAA) and a higher inhibition of HepG2 cell proliferation were found in the extract from small intestine digestion phase. In comparison with Aijiao Bawangbian (white color), the phenolics, flavonoids, ORAC values, CAA values and antiproliferative activity of Changzhi II (black color) were higher both before and after simulated digestion. In tested phenolics, sesamol and ferulic acid showed better antioxidant and antiproliferative activities than pinoresinol diglucoside, pinoresinol, sesamolin, and sesamin in cellular level. Sesame seed has considerable cellular antioxidant and antiproliferative activities both before and after simulated digestion, which merits further investigation in vivo studies.}, }
@article {pmid41438070, year = {2025}, author = {Brandt, A and Yergaliyev, T and Halibasic, E and Cyba, A and Jaeger, JW and Gong, R and Hernández-Arriaga, A and Schneider, CV and Sjöland, W and Molinaro, A and Trauner, M and Trautwein, C and Camarinha-Silva, A and Bergheim, I and Schneider, KM}, title = {Fiber enrichment is not superior to dietary monitoring in MASLD: A dual-center, double-blind, placebo-controlled trial.}, journal = {iScience}, volume = {28}, number = {12}, pages = {114019}, pmid = {41438070}, issn = {2589-0042}, abstract = {Dietary fiber enrichment may modulate intestinal microbiota and positively impact metabolic dysfunction-associated steatotic liver disease (MASLD). This randomized, double-blind, placebo-controlled dual-center study evaluated the effects of dietary fiber (oat bran and spelt bran) on MASLD. After a 3-week Run-in phase during which dietary intake was assessed, 48 patients (CAP >280 dB, no fibrosis) were assigned to oat bran (4.5 g oat β-glucan, total fiber 11.7 g/day), spelt bran (11.7 g fiber/day), or placebo (2.1 g fiber/day) for 12 weeks. During the Run-in phase, dietary assessment alone significantly decreased BMI and liver enzymes (ALT, AST, γ-GT) while increasing microbiota diversity. Improvements were maintained in all three intervention groups. However, no significant changes were observed in hepatic steatosis (CAP), overall microbiota composition, and serum bile acid profiles. Dietary assessment alone improved MASLD biomarkers, with the fiber supplementation offering no additional benefit. This highlights the importance of dietary counseling in MASLD management. (clinical trials: NCT03897218).}, }
@article {pmid41436102, year = {2025}, author = {Hild, K and Kwarkye, N and Huang, C and Harms, H and Chatzinotas, A and Ritschel, T and Totsche, KU and Wick, LY}, title = {Transport and Survival of Marine Tracer Phages in Topsoil at Field Conditions.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c12252}, pmid = {41436102}, issn = {1520-5851}, abstract = {Phages are ubiquitous in soil, shaping microbial diversity and nutrient cycling. Phage replication requires maintaining infectivity and finding the right host. Yet, there are limited data on phage persistence and transport in soil under field conditions. The potential presence of hosts enabling phage replication impedes the assessment of the mobility of autochthonous phages in soils. In lysimeters installed in forest and pasture topsoil, we elucidated the transport of the tailed marine Pseudoalteromonas phage HS2 in comparison to deuterium. Transport of infectious phages as well as numbers of tracer phage genomes and tracer capsid-bound genomes were quantified to account for phage retention and inactivation. Phages were transported up to 4 times faster than the simultaneously applied deuterium tracer, which was attributed to pore size exclusion. Retention in immobile regions and remobilization during precipitation caused pronounced tailing in tracer breakthroughs. High phage survival in pasture soil resulted in mass recoveries of infectious phages that were up to 6 times higher than those in forest soil. However, long-term observations showed that the infectivity was also preserved in forest soil, enabling event-driven remobilization. This remobilization underscores the importance of distinguishing between phage retention and inactivation, which is crucial for accurately predicting phage transport dynamics and their ecological impact in terrestrial environments.}, }
@article {pmid41435658, year = {2025}, author = {Ho, L and Pham, K and Debognies, A and Bodé, S and Vermeir, P and Boeckx, P and De Vrieze, J and Goethals, P}, title = {Unveiling the important roles of sludge worms (Tubifex tubifex) in wetland carbon and nitrogen cycling: Implications for greenhouse gas emissions in a warming climate.}, journal = {Water research}, volume = {291}, number = {}, pages = {125230}, doi = {10.1016/j.watres.2025.125230}, pmid = {41435658}, issn = {1879-2448}, abstract = {Wetland greenhouse gas (GHG) emissions represent a major component of global climate feedbacks, driven by complex biogeochemical processes that regulate carbon and nitrogen cycling. However, how bioturbating invertebrates, such as sludge worms (Tubifex tubifex), regulate these underlying microbial and physicochemical mechanisms remains poorly understood. Here, we conducted controlled microcosm incubations at 15, 25, and 35°C to examine how increasing temperatures modulate the influence of these sludge worms on wetland carbon and nitrogen cycling, combining biogeochemical flux measurements with microbial functional gene analysis. We discovered four synergistic mechanisms by which T. tubifex influences wetland biogeochemistry: 1) physical bioturbation creating distinct biogeochemical conditions; 2) respiratory and feeding activities modifying redox conditions; 3) specialized gut microbiomes directly producing GHGs; and 4) continuous microbial inoculation of sediments through excretion. These mechanisms collectively enhanced CH4 and N2O emissions, with N2O fluxes showing a fourfold increases at elevated temperatures. Worm gut microbiomes were primarily regulated by temperature, organic matter, and nitrogen compounds, with the main controlling factors shifting from nutrient availability at lower temperatures to direct thermal stress effects at higher temperatures. Strong metabolic intensity of worm gut microbiomes, with gene expression-to-abundance ratios being up to 2000 times higher than in sediment communities, resulted in their indirect impacts on wetland GHG emissions. At cooler temperatures (15°C), denitrifier genes (nirK and nirS) prevailed in worm guts, whereas higher temperatures (35°C) favored nitrifier genes (amoA AOA and amoA AOB). These findings provide the first comprehensive framework revealing previously underappreciated mechanisms by bioturbating invertebrates amplifying wetland GHG emissions under warming, creating overlooked positive feedback loops in wetland ecosystems.}, }
@article {pmid41432929, year = {2025}, author = {Garcia, M and Sadler, NC and Stohel, I and Zhao, S and Krishnamoorthy, S and Farris, Y and Reichart, NJ and Bagwell, CE and Zambare, N and McClure, R}, title = {Community Dynamics Drive Calcium Carbonate Production in an Enriched Consortium of Soil Microbes.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02632-y}, pmid = {41432929}, issn = {1432-184X}, abstract = {Recently, there has been a focus on using soil microbes as a means to store carbon in the soil in the form of calcium carbonate, outcomes of which include soil stabilization and biocementation. The molecular processes involved in microbially induced calcium carbonate formation are known, but there is still a significant knowledge gap regarding how community interactions, emergent processes that are distinct from the roles of individual members, may drive the formation of carbonate. To answer these questions, we describe the development and application of a consortium of soil microbes consisting of one species each of the Rhodococcus, Microbacterium, and Curtobacterium genera and two species from the Bacillus genus. We term these five species cultivated together carbon storing consortium A (CSC-A). Growth assays show that only a subset of CSC-A members produces CaCO3 with Rhodococcus producing the most CaCO3 but the complete CSC-A produces significantly higher amounts of CaCO3 compared to the sum total carbonate produced by all member species. The development of CSC-A shows that CaCO3 production may be as much a community process as it is the contribution of individual species, requiring us to move beyond single species analysis to fully understand carbonate formation by microbial communities in nature. CSC-A will allow the scientific community to ask and answer key questions about the molecular interactions surrounding inorganic carbon formation in soil, an important knowledge gap that must be filled if we wish to stabilize soils and harness microbial processes for materials production.}, }
@article {pmid41432792, year = {2025}, author = {Basile, A and Spagoni, L and Visaggio, D and Riggio, FP and Bologna, MA and Mancini, E and Visca, P and Riccieri, A}, title = {The Putative Involvement of Bacterial Symbionts in Cantharidin Biogenesis: An Explorative Study in Meloidae Insects.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02683-1}, pmid = {41432792}, issn = {1432-184X}, abstract = {Insect-microbes holobionts integrate host and microbial functions, with symbionts supporting nutrition, immunity, and defence, while producing metabolites, including beetle-derived compounds with therapeutic potential. Cantharidin is a toxic terpene produced by blister beetles (Coleoptera: Meloidae), endowed with defensive and pharmacological properties. Male insects produce and contain cantharidin in large quantities and transfer it to females upon mating. This study is aimed to gain information about the involvement of insect-associated bacteria in cantharidin biogenesis. To support the possibility that bacteria participate in cantharidin biogenesis, cantharidin antibacterial activity was assessed against six reference strains of representative species of Bacillota and Pseudomonadota from publicly available culture collections. All bacterial strains tolerated concentrations up to 600 µg/ml cantharidin in a standard antibacterial susceptibility test. To identify candidate bacterial lineages, 16S rRNA metataxonomic profiling of the V5-V6 region was performed in males and females from different Meloidae subfamilies and tribes. Analysis of the insect-associated microbiomes of the five cantharidin-producing species (Lydus trimaculatus, Meloe proscarabaeus, Mylabris variabilis, Hycleus polymorphus, Zonitis flava) revealed communities dominated by Pseudomonadota, with secondary contributions from Actinomycetota in Z. flava and M. proscarabaeus and Cyanobacteriota in the other host insects. Although overall community structure and composition did not differ significantly between sexes, a few taxa displayed consistent male-associated patterns, with Staphylococcus, Cutibacterium and one Enterobacteriaceae ASV resulting more abundant in males across all species. The intrinsic bacterial resistance to cantharidin, with both quantitative and qualitative differences in microbiome structure between male and female insects, makes the hypothesis of a putative involvement of bacteria in cantharidin biogenesis still viable.}, }
@article {pmid41432418, year = {2025}, author = {Weiss, AS and Santos-Santiago, JA and Keenan, O and Smith, AB and Knight, M and Zackular, JP and Tamayo, R}, title = {Enterococcus faecalis modulates phase variation in Clostridioides difficile.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {e0037425}, doi = {10.1128/jb.00374-25}, pmid = {41432418}, issn = {1098-5530}, abstract = {To adapt and persist in the gastrointestinal tract, many enteric pathogens, including Clostridioides difficile, employ strategies such as phase variation to generate phenotypically heterogeneous populations. Notably, the role of the gut microbiota and polymicrobial interactions in shaping population heterogeneity of invading pathogens has not been explored. Here, we show that Enterococcus faecalis, an opportunistic pathogen that thrives in the inflamed gut during C. difficile infection, can impact the phase-variable CmrRST signal transduction system in C. difficile. The CmrRST system controls multiple phenotypes, including colony morphology, cell elongation, and cell chaining in C. difficile. Here, we describe how interactions between E. faecalis and C. difficile on solid media lead to a marked shift in C. difficile phenotypes associated with phase variation of CmrRST. Specifically, E. faecalis drives a switch of the C. difficile population to the cmr-ON state, leading to chaining and a rough colony morphology. This phenomenon is most pronounced with E. faecalis, as other enterococcal species and select Gram-negative enteric bacteria do not show a similar effect. These results suggest that the composition of the polymicrobial environment in the gut is critical to influencing C. difficile population heterogeneity. Our findings shed light on the complex role that microbial ecology and polymicrobial interactions can have in the phenotypic heterogeneity of invading pathogens.IMPORTANCEClostridioides difficile is an enteric pathogen with critical implications for public health. The microbial ecosystem in which C. difficile resides shapes the behavior and fitness of C. difficile; however, the mechanisms underlying these interactions are not well defined. Here, we demonstrate that Enterococcus faecalis, an opportunistic pathogen known to co-colonize the gut with C. difficile, influences phase variation and downstream growth phenotypes in C. difficile. This phenomenon represents a new paradigm by which co-residing bacteria can modulate phase variation dynamics in C. difficile or other enteric pathogens. Understanding factors that influence C. difficile behavior may elucidate new therapeutic strategies, especially in complex polymicrobial infections.}, }
@article {pmid41432242, year = {2025}, author = {Xie, X and Chen, L and Yuan, J and Zheng, H and Zhang, L and Yu, X and Liu, X and Wei, C and Qiu, G}, title = {Metagenomic characterization of the metabolism, evolution, and global distribution of Candidatus Accumulibacter members in wastewater treatment plants.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf278}, pmid = {41432242}, issn = {1751-7370}, abstract = {Deciphering the genomic basis of ecological diversification in activated sludge microbiomes is essential for optimizing treatment technology and advancing microbial ecology. Here, we present a global genome-resolved investigation of Candidatus Accumulibacter, the primary functional agent of enhanced biological phosphorus removal, based on 828 metagenomes from wastewater treatment plants across six continents. We recovered 104 high-quality Candidatus Accumulibacter metagenome-assembled genomes, discovering a new clade (Clade IV), substantially expanding the known phylogenetic diversity and revealing a ubiquitous yet geographically heterogeneous global distribution. Phylogenomic and pangenome analyses uncovered extensive clade-specific gene gain and loss, particularly in nitrogen metabolism, suggesting divergent evolutionary trajectories shaped by relaxed selection and niche adaptation. Genome-wide patterns of convergent streamlining and enriched antiviral defense systems indicate selective pressures from strong competition and viral predation. Constraint-based metabolic modeling revealed pervasive amino acid autotrophies and metabolic complementarity, coupled with distinct carbon utilization strategies that support ecological specialization across operational settings. Experimental validation reconciled model-phenotype discrepancies, highlighting the importance of transporter promiscuity and gene regulation in carbon substrate assimilation. Collectively, our findings redefine Candidatus Accumulibacter as a dynamic model of microbial genome plasticity, metabolic adaptation, and ecological resilience, providing an insight for understanding how microbial communities adapt and respond under engineered environmental conditions.}, }
@article {pmid41430825, year = {2025}, author = {Gao, ZL and Li, JJ and Ai, BQ}, title = {Activity-driven demixing and sustained temperature gradients in inertial active-passive mixtures.}, journal = {Physical review. E}, volume = {112}, number = {5-1}, pages = {054103}, doi = {10.1103/5lm1-h83g}, pmid = {41430825}, issn = {2470-0053}, abstract = {While traditional thermodynamic equilibrium requires uniform temperature across coexisting phases, underdamped active matter systems can sustain nonequilibrium hot-cold coexistence through motility-induced phase separation. We investigate particle demixing and emergent temperature gradients in binary mixtures of inertial active and passive particles. Remarkably, within specific parameter ranges of intermediate particle inertia and self-propulsion strength, the system simultaneously achieves pronounced particle demixing and sustains significant hot-cold coexistence. Activity differences drive rapid species separation, which is further enhanced over time by persistent rotational diffusion. The synergy between inertia and activity significantly amplifies temperature differences both between particle species and across coexisting gas-liquid phases. These temperature disparities originate from inertia-enabled energy storage, collision-mediated energy transfer, propulsion-driven acceleration, and weakened liquid-phase cohesion. Unlike equilibrium systems, active-passive mixtures circumvent thermal homogenization by maintaining kinetic temperature gradients through continuous energy injection and dissipation. These findings elucidate fundamental principles of nonequilibrium self-organization in hybrid systems, with implications for bio-inspired materials, microbial ecology, and energy transport in active composites.}, }
@article {pmid41430013, year = {2025}, author = {Wolfgang, A and Temme, N and Tilcher, R and Schumann, M and Berg, G}, title = {Wireworm-Associated Microbial Communities and their Implications on Biological Control.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02672-4}, pmid = {41430013}, issn = {1432-184X}, abstract = {Wireworms (larvae of different click beetles, Elateridae) are significant soil-borne pest species that can cause severe crop losses. They are difficult to control, and biocontrol using entomopathogenic fungi (EPF) display variable field efficacy. To understand microbial interactions and improve biological control, we studied the interplay between insect and soil microbiota in four wireworm species (Agriotes spp.) at temporal and spatial scales. We found that microbiota associated with wireworms are species-specific and primarily soil-derived. Our results further indicate that ectosymbiotic bacterial community composition on wireworm cuticles is relatively stable over time in specimens not deceasing from spontaneous entomopathogen infection. Therefore, successful microbiome homeostasis on cuticles appears to be correlated with long-term survival of wireworms in soil. Interestingly, EPF were prevalent but low-abundant in all wireworm species as well as in soils. Therefore, we analyzed immune priming effects by low-abundant EPF in soil. Mortality was higher in naïve wireworms than in wireworms pre-exposed to EPFs, and molting frequency increased, indicating both developmental adaptations and immune priming as strategies for EPF avoidance in wireworms. This work disentangles the key components of wireworm microbiomes and highlights the importance of microbial interactions for biocontrol. Biocontrol of wireworms could be improved by considering their species-dependency in microbiome homeostasis as well as physiological and behavioral adaptations to soil-borne pathogens. The potential functional synergies between EPF and soil microbes need further exploration.}, }
@article {pmid41429876, year = {2025}, author = {Galbán, S and Almela, P and Quesada, A and Justel, A}, title = {Exploring local and regional contribution to airborne bacterial communities in the Antarctic Peninsula.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-025-32162-z}, pmid = {41429876}, issn = {2045-2322}, support = {PIPF-2022/ECO-25833//Comunidad de Madrid/ ; CTM2016-79741-R//European Regional Development Fund/ ; CTM2016-79741-R//European Regional Development Fund/ ; PID2020-116520RB-I00//Agencia Estatal de Investigaci&#xf3;n/ ; }, abstract = {Understanding microbial dispersion in the atmosphere is essential for studying microbial biogeography and ecosystem dynamics under global change. Airborne bacterial communities, shaped by exchanges between atmosphere and Earth's surface, can originate from diverse sources and vary with meteorological conditions and air mass trajectories. In this study, we assessed airborne microbial communities in Antarctica at regional and local scales. Air samples were collected during the austral summer at two Antarctic Specially Protected Areas (ASPAs): Byers Peninsula (Livingston Island, South Shetland Islands) and Avian Island (Marguerite Bay). Bacterial composition was analysed through 16S rRNA gene sequencing using amplicon sequence variants (ASVs). Additionally, back-trajectories of the sampled air parcels were simulated with HYSPLIT. A core community was identified in 80% of Byers Peninsula samples, representing 57.91% of total ASVs. Notably, 79.4% of ASVs matched soil bacteria from the same location, suggesting a strong influence of local sources. Communities from Byers Peninsula and Avian Island showed low overall similarity. However, one sample from Byers resembled the Avian sample, likely due to similar air mass back-trajectories. These findings suggest that airborne bacterial communities are shaped by both local ecosystems, and broader regional or continental processes, such as long-range trajectories carrying microorganisms from distant locations.}, }
@article {pmid41427997, year = {2025}, author = {Lebrun, S and Crevecoeur, S and Taminiau, B and Everaert, N and Marzorati, M and Leenders, J and de Tullio, P and Korsak, N and Daube, G and Stiernon, B and Delcenserie, V and Gonza, I}, title = {Gut Microbiota Modulation by Pomegranate Extract: Insights from a Controlled Supplementation Study.}, journal = {Plant foods for human nutrition (Dordrecht, Netherlands)}, volume = {81}, number = {1}, pages = {5}, pmid = {41427997}, issn = {1573-9104}, support = {NUTRIGUTIOR under grant convention 6918//Walloon Agri-Food innovation cluster Wagralim/ ; NUTRIGUTIOR under grant convention 6918//Walloon Agri-Food innovation cluster Wagralim/ ; NUTRIGUTIOR under grant convention 6918//Walloon Agri-Food innovation cluster Wagralim/ ; NUTRIGUTIOR under grant convention 6918//Walloon Agri-Food innovation cluster Wagralim/ ; NUTRIGUTIOR under grant convention 6918//Walloon Agri-Food innovation cluster Wagralim/ ; NUTRIGUTIOR under grant convention 6918//Walloon Agri-Food innovation cluster Wagralim/ ; NUTRIGUTIOR under grant convention 6918//Walloon Agri-Food innovation cluster Wagralim/ ; }, mesh = {*Pomegranate/chemistry ; *Gastrointestinal Microbiome/drug effects ; *Plant Extracts/pharmacology ; Humans ; *Dietary Supplements ; Male ; Fatty Acids, Volatile/metabolism ; Colon/microbiology/drug effects/metabolism ; Polyphenols/pharmacology ; Adult ; Female ; Lactic Acid/metabolism ; Bacteria/metabolism/drug effects ; Fruit/chemistry ; }, abstract = {Regular consumption of pomegranate, a polyphenol-rich fruit, is associated with multiple health benefits. As polyphenols reach the colon, they interact with the gut microbiota, influencing both its composition and metabolic activity. This study investigated the impact of a one-week supplementation with two doses of the commercial pomegranate extract Oxylent[®] (1.3 and 2.6 g/day) on gut microbiota and metabolite production using the SHIME[®] system. Bacterial metabolite production, including short-chain fatty acids (SCFA), urolithins, succinate, and lactate, was assessed using chromatographic and enzymatic assays. The bacterial composition across colonic sections, represented by different fermenters in the SHIME, was investigated using 16 S rRNA amplicon sequencing. Pomegranate extract did not significantly alter SCFA or succinate levels, but reduced L- and D-lactate in the transverse colon; the higher dose (2.6 g/day) also decreased D-lactate in the ascending colon. Microbiota profiling revealed a higher bacterial diversity following pomegranate extract supplementation. However, Prevotella abundance decreased in the ascending and transverse colonic sections, potentially explaining the reduced propionate levels observed in the transverse colon with 2.6 g/day of pomegranate extract. Interestingly, contrasting effects were noted for Mitsuokella genus, which decreased in the descending colon at 1.3 g/day but increased at 2.6 g/day in the transverse and descending colons. Furthermore, the higher dose reduced Enterocloster abundance in the descending colon. Overall, Oxylent[®] pomegranate extract influenced both microbial composition and metabolite production, particularly taxa associated with health-related metabolites. These results highlight the potential of pomegranate compounds to beneficially influence the gut microbiota, supporting their role in promoting intestinal health.}, }
@article {pmid41427744, year = {2025}, author = {Burnside, M and Helliwell, E and Treerat, P and Rozendal, T and Merritt, J and Baker, JL and Kreth, J}, title = {Comparative characterization reveals conserved and divergent ecological traits of oral corynebacteria.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0297325}, doi = {10.1128/spectrum.02973-25}, pmid = {41427744}, issn = {2165-0497}, abstract = {Corynebacteria are abundant members of the oral microbiome and increasingly recognized as key structural organizers of supragingival biofilms. Despite their prevalence, the ecological roles and phenotypic traits of many oral corynebacterial species remain poorly defined. Here, we isolated and characterized two new strains, Corynebacterium durum JJ2 and Corynebacterium argentoratense MB1, and compared them with previously characterized and published Corynebacterium durum JJ1 and reference strain Corynebacterium matruchotii ATCC 14266. Phenotypic assays revealed that C. durum strains displayed robust aggregation, thick biofilm formation, and extensive extracellular polymeric substance (EPS) networks, whereas C. argentoratense MB1 and C. matruchotii ATCC 14266 formed thinner biofilms with minimal EPS production. All four strains secreted extracellular membrane vesicles capable of inducing chain elongation in Streptococcus sanguinis, underscoring a conserved interspecies signaling function. Genomic analysis demonstrated close relatedness between C. durum and C. matruchotii, while C. argentoratense MB1 was more distantly related, with a reduced genome, fewer metabolic pathways, and the absence of nitrate reductase genes, consistent with its inability to grow under anaerobic conditions. These findings suggest that C. argentoratense MB1 may represent a less specialized or transient inhabitant of the oral cavity, whereas C. durum and C. matruchotii are well adapted to the oral niche. Together, this study expands our understanding of phenotypic diversity, metabolic capacity, and interspecies interactions among selected oral corynebacteria, highlighting their potential importance as biofilm organizers and contributors to oral microbial ecology.IMPORTANCEOral corynebacteria contribute to the structural and ecological stability of supragingival communities. Yet, their species-level functions remain poorly defined. By isolating and characterizing new strains of Corynebacterium durum and Corynebacterium argentoratense, and comparing them with reference strains including Corynebacterium matruchotii, we provide new insight into their phenotypic diversity, metabolic capacity, and ecological roles. Our results demonstrate that C. durum strains form robust biofilms enriched in extracellular polymeric substances, while C. argentoratense produces thinner biofilms and lacks the genomic features required for anaerobic growth, suggesting a less specialized or transient role in the oral cavity. Importantly, we show that extracellular membrane vesicles secreted by all tested strains promote chain elongation in Streptococcus sanguinis, highlighting a conserved mechanism of interspecies communication. These findings advance our understanding of how oral corynebacteria contribute to biofilm organization and microbial homeostasis and position them as critical but understudied players in oral microbial ecology.}, }
@article {pmid41424705, year = {2025}, author = {Charria Girón, E and Toshe, R and Khonsanit, A and Kobmoo, N and Kwanthong, P and Gorelik, TE and Luangsa-Ard, JJ and Ebada, SS and Stadler, M}, title = {Chemical clues to infection: A pilot study on the differential secondary metabolite production during the life cycle of selected Cordyceps species.}, journal = {IMA fungus}, volume = {16}, number = {}, pages = {e172651}, pmid = {41424705}, issn = {2210-6340}, abstract = {Cordyceps species are widespread entomopathogens and promising biocontrol agents that produce diverse secondary metabolites, yet the roles of these molecules during the infection process remain unclear. To interpret how fungal chemistry contributes to host colonization, we compared the metabolomes and virulence traits of two strains of phylogenetically distinct Cordyceps species (C. javanica and C. blackwelliae) and assessed their effects on beet armyworms (fungiSpodoptera exigua). Virulence assays revealed species-dependent pathogenicity, with C. javanica showing the highest virulence. Combining untargeted metabolomics, feature-based molecular networking (FBMN), 3D electron-diffraction crystallography and comprehensive 1D/2D NMR, we gained insights into their metabolomic traits. For instance, C. javanica displayed notable beauveriolide diversity, including three previously undescribed derivatives (1-3), while C. blackwelliae produced mainly diketopiperazines in vitro. The FBMN results revealed putative beauveriolide analogs in the C. blackwelliae extracts, unlike the cadaver analysis, revealing beauvericins in infected corpses. Remarkably, the crude extracts obtained from authentic insect cadavers contained beauveriolides and beauvericins, providing in vivo chemical evidences of their production during infection for the first time. Moreover, bioassays with purified compounds showed that insecticidal activity cannot be attributed across all beauveriolides but depends on amino-acid composition, implying multifunctional roles beyond direct toxicity. Altogether, these results reveal context-dependent metabolic reprogramming and species-specific chemical strategies in entomopathogenic fungi, with implications for microbial ecology, host specificity, and the rational development of fungal biocontrol agents. The results of this study also give rise to the need for more intensified study on the chemical composition of the insect cadavers that are colonized by other entomopathogens.}, }
@article {pmid41422804, year = {2025}, author = {Tabuteau, S and Hervé, V and Irlinger, F and Monnet, C}, title = {Metagenomic Profiling and Genome-Centric Analysis Reveal Iron Acquisition Systems in Cheese-Associated Bacteria and Fungi.}, journal = {Environmental microbiology}, volume = {27}, number = {12}, pages = {e70218}, doi = {10.1111/1462-2920.70218}, pmid = {41422804}, issn = {1462-2920}, support = {//ABIES Doctoral School/ ; //MICA Department of INRAE/ ; }, mesh = {*Cheese/microbiology ; *Iron/metabolism ; Siderophores/biosynthesis/metabolism/genetics ; Metagenomics ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; *Fungi/genetics/metabolism/classification/isolation &amp; purification ; *Metagenome ; Genome, Bacterial ; }, abstract = {Cheese microbial communities are composed of diverse interacting microorganisms, including both inoculated and non-inoculated strains. One limiting factor for microbial growth on cheese surfaces is iron availability. To better understand the role of iron acquisition in cheese microbial ecology, we investigated the diversity and distribution of iron uptake systems across a wide range of cheeses. We analysed 136 metagenomes and 1400 genomes and Metagenome-Assembled Genomes (MAGs) from 44 French Protected Designation of Origin (PDO) cheeses. Using an updated set of Hidden Markov Models targeting iron acquisition genes, we identified a wide diversity of iron uptake systems. Siderophore biosynthesis and import systems were more prevalent in surface-associated species than in those from the cheese core. About 20 different siderophore biosynthesis pathways were detected, with desferrioxamine and enterobactin-type being the most prevalent. Genomic analyses revealed the main bacterial and fungal producers, including Glutamicibacter, Corynebacterium, Staphylococcus, and Penicillium. While siderophore biosynthesis pathways were found in a minority of MAGs, iron/siderophore import systems were widespread, suggesting the potential for cross-feeding interactions involving siderophores. These findings enhance our understanding of microbial interactions in cheese and open perspectives for improving ripening cultures by considering iron acquisition traits.}, }
@article {pmid41422362, year = {2025}, author = {Kuuri-Riutta, O and Palacios Ganoza, B and Ylänne, H and Mitchell, EAD and Väliranta, MM and Tuittila, ES}, title = {Assessing the Value of Testate Amoebae and their Functional Traits in Detecting Climate Change-Induced Peatland Drying.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02682-2}, pmid = {41422362}, issn = {1432-184X}, support = {00240717//Suomen Kulttuurirahasto/ ; 20230925//OLVI-S&#xe4;&#xe4;ti&#xf6;/ ; 3825//Maj ja Tor Nesslingin S&#xe4;&#xe4;ti&#xf6;/ ; 338631//Research Council of Finland/ ; 30840//Research Council of Finland/ ; }, }
@article {pmid41422133, year = {2025}, author = {Chang, CY and Topping-Brown, T and Rud, JL and Calvert, MB and Bencosme, G and Wood, CW}, title = {Biogeographic and Genomic Signatures of Thermal Adaptation in Facultative Symbionts.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02678-y}, pmid = {41422133}, issn = {1432-184X}, support = {The Data-Driven Discovery Postdoctoral fellowship//University of Pennsylvania/ ; DEB2118397//National Science Foundation/ ; DEB2118397//National Science Foundation/ ; DEB2118397//National Science Foundation/ ; DEB2118397//National Science Foundation/ ; DEB2118397//National Science Foundation/ ; DEB2118397//National Science Foundation/ ; }, }
@article {pmid41421681, year = {2025}, author = {Fu, Q and Shi, JS and Lai, JL and Zhang, Y and Huang, Y and Luo, XG}, title = {Maize adaptation to low-dose nanoplastic-lead co-contamination: Foliar metabolic reprogramming and phyllospheric microbiome restructuring.}, journal = {NanoImpact}, volume = {}, number = {}, pages = {100606}, doi = {10.1016/j.impact.2025.100606}, pmid = {41421681}, issn = {2452-0748}, abstract = {Nanoplastics (NPs) and lead (Pb), as emerging environmental pollutants, have been rarely studied in terms of their combined effects on crop growth and metabolic processes under low-dose co-exposure conditions. This study simulated rain-mediated co-exposure of maize seedlings to NPs and Pb at environmentally relevant concentrations (400 μg/L) to elucidate the metabolic responses in leaves and the dynamics of phyllosphere microbial communities. Short-term exposure (45 days) to NPs and Pb did not significantly impair maize seedling growth; however, it induced the accumulation of essential macronutrients in leaves. The metabolic adaptation of maize leaves to NPs and Pb exposure was characterized by a reduction in carbon metabolic flux coupled with an enhancement in lipid metabolic flux. Furthermore, plants responded to co-exposure by activating key metabolic pathways such as those involving ABC transporters, nucleotide metabolism, and amino acid metabolism. Concurrently, the phyllosphere microbiome exhibited structural reorganization, with enrichment of stress-tolerant microbial taxa (e.g., Acidobacteria, Chloroflexi), activation of microbial redox systems, and enhanced capacity of the leaf microbiota to adapt to NPs and Pb exposure. The findings offer theoretical insights into assessing agricultural environmental impacts associated with combined exposure to emerging pollutants, phyllosphere microbial ecology, and plant stress resistance.}, }
@article {pmid41421210, year = {2025}, author = {De Munck, J and Grootaert, C and Magdalenic, K and Deveci, D and Gansemans, Y and Van Nieuwerburgh, F and Boon, N and Skirtach, A and Rajkovic, A and D'hooghe, M and Van Camp, J}, title = {Curcumin-based benzothiazepane analogues exhibit selective anti-cancer activity in HCT-116 cells via precipitated particle formation and internalisation.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {194}, number = {}, pages = {118926}, doi = {10.1016/j.biopha.2025.118926}, pmid = {41421210}, issn = {1950-6007}, abstract = {Despite extensive investigation into the anti-cancer activity of the natural polyphenol curcumin, its therapeutic application is restricted by its inherent physicochemical properties. Synthetic curcumin analogues, however, offer a promising strategy to improve the drug-like potential of curcumin. In this study, we evaluated three curcumin-based benzothiazepane analogues for their ability to selectively target colon cancer cells. Their cytotoxicity was assessed on intestinal cancerous HCT-116 and non-cancerous IPEC-J2 cells using cell viability assays and microscopic imaging. Two analogues, AT007 and AT096, demonstrated enhanced anti-cancer selectivity compared to curcumin. Interestingly, this effect correlated with the aggregation of these compounds in cell medium, which was influenced by compound concentration and medium composition (particularly the presence of albumin). Confocal microscopy confirmed the presence of particles up to 12 µm inside both cell lines, yet downstream metabolic and transcriptomic responses revealed distinct coping mechanisms that may underlie the higher survival of IPEC-J2 cells. Rather than direct molecular interactions typical of soluble compounds, the observed selectivity appears to result from indirect, particle-driven physical effects, potentially involving (intracellular) membrane disruption. Our findings suggest that aggregation behaviour can be a key determinant in improving the potency and selectivity of bioactive compounds, opening new opportunities for the design and screening of more selective anti-cancer therapeutics.}, }
@article {pmid41420099, year = {2025}, author = {Stansfield, AR and Booth, RK and Nelson, DM and Johnson, J}, title = {Recent Changes in the Use of Phototrophy by a Mixotrophic Testate Amoeba Inferred from δ[13]C Measurements from an Arctic Peat Core.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02681-3}, pmid = {41420099}, issn = {1432-184X}, support = {College of Arts &amp; Sciences Dean's Research Fellowship//Lehigh University/ ; DEB-1802810//Division of Environmental Biology/ ; }, abstract = {High-latitude ecosystems are undergoing rapid ecological changes in response to climate warming. While some changes are well studied, the responses of microbial communities remain less understood. Testate amoebae, shell-producing protists well preserved in peat, provide a means to reconstruct past microbial dynamics. Mixotrophic taxa such as Archerella flavum host algal endosymbionts (zoochlorellae), allowing both heterotrophic and phototrophic energy acquisition. Previous work has demonstrated that these pathways result in different δ[13]C values. We applied a novel stable isotope approach to a peat core from the North Slope of Alaska to reconstruct changes in phototrophy by Archerella flavum. δ[13]C values were measured on Archerella flavum tests (i.e. shells) and Sphagnum, and a two-endmember mixing model was used to estimate relative usage of phototrophy through time. δ[13]C values were compared with testate amoeba community composition, test size, vegetation, and historical climate. Archerella flavum δ[13]C values were consistently more positive than Sphagnum δ[13]C values in the peat core, and patterns indicated greater phototrophy use after the late 1980s CE. This shift was followed by expansion of Archerella flavum populations and a trend of decreasing test length in several testate amoeba taxa. Increased phototrophy was associated with higher peat C:N ratios, indicating more oligotrophic conditions. From 2007 to 2019 CE, the length of the snow-free growing season was correlated with estimates of phototrophy usage, with more phototrophy during longer growing seasons. δ[13]C analyses of mixotrophic testate amoebae are a powerful tool for reconstructing microbial nutritional strategies and responses to past environmental change.}, }
@article {pmid41416826, year = {2025}, author = {Wang, B and Zhu, C and Wang, X and Yang, T and Zhang, B and Hu, Y}, title = {The assembly of microbial communities on red sandstone surfaces was shaped by dispersal limitation and heterogeneous selection.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0160025}, doi = {10.1128/msystems.01600-25}, pmid = {41416826}, issn = {2379-5077}, abstract = {Understanding the role of microbiota on stone surface is essential for developing effective grottoes conservation strategies. However, the ecological feature of microbial communities on stone surfaces has been rarely investigated systematically. In this study, we explored diversity, assembly, and functional profiles of microbial communities on the red sandstone surface of the Leshan Giant Buddha from a microbial ecology perspective. The results show that Proteobacteria, Actinobacteria, Cyanobacteria, and Ascomycota are the dominant phyla. Fundamental metabolic pathways are maintained during the formation of visually distinguishable microbial communities, but gene profiles vary across microbial communities of different colors. Ecological modeling suggests that selective pressure from the harsh stone surface environment fostered the interplay of dispersal limitation and heterogeneous selection during community assembly. The assembly of visually distinct microbial communities is linked to a narrower ecological niche, a higher proportion of habitat specialists, and a sparser network structure. Microbial-mediated ammonium assimilation and nitrogen mineralization might be the two prominent processes that contribute to stone biodeterioration. This study deepens our understanding of the assembly mechanisms and functional potentials of microbial communities on stone cultural heritage surfaces, provides microbial ecological insights for the conservation of these cultural treasures.IMPORTANCEMinimal systematic research on the ecological interpretation of stone biodeterioration. This study reports dispersal limitation and heterogeneous selection shape the microbial community assembly responsible for the biodeterioration of red sandstone. Furthermore, fundamental metabolic processes of microbial communities, such as ammonium assimilation and nitrogen mineralization, are identified as contributors to stone biodeterioration. This study improves our understanding of microbial community assembly and their functional roles, providing a microbial ecological basis for developing effective strategies for the conservation of stone cultural heritage.}, }
@article {pmid41413692, year = {2025}, author = {Carrascosa-Robles, &#xc1; and Pascual, JA and Trinchera, A and Testani, E and Fontaine, S and Sanchez-Moreno, S and Supronienė, S and Sail, S and Rasmussen, J and Hanegraaf, M and Ros, M}, title = {The Influence of Agroecological Intensification on Dominant and Rare Microbial Communities Across Diverse European Countries.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02655-5}, pmid = {41413692}, issn = {1432-184X}, }
@article {pmid41410463, year = {2025}, author = {Xie, Y and Cidan, Y and Cisang, Z and Ciwang, R and Liu, G and Wu, D and Cideng, D and Chilie, J and Kang, J and Zhu, Y and Basang, W}, title = {Effect of altitudes on serum parameters, metabolome, and gut microbiota in yaks on the Qinghai-Tibet Plateau.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0254925}, doi = {10.1128/spectrum.02549-25}, pmid = {41410463}, issn = {2165-0497}, abstract = {Yaks (Bos grunniens), native to the Qinghai-Tibet Plateau, have evolved extraordinary physiological resilience to chronic hypoxia, cold, and nutritional scarcity. However, the integrated metabolic and microbial mechanisms underlying these adaptations remain poorly defined. Here, a comprehensive multi-omics analysis was performed on thirty grazing heifer yaks (2.5 years old) from three altitudes-3,600 m (low altitude [LA]), 4,000 m (middle altitude [MA]), and 4,500 m (high altitude [HA])-to investigate how altitude affects host physiology, metabolism, and gut microbial ecology. Increasing altitude significantly reduced serum total protein, globulin, blood urea nitrogen, and alkaline phosphatase, indicating suppressed anabolic metabolism and nitrogen-sparing strategies. Antioxidant capacity (total superoxide dismutase, total antioxidant capacity) and pro-inflammatory cytokines (interleukin-2 [IL-2], IL-6, tumor necrosis factor-α, interferon-γ) increased (P < 0.05), while glutathione peroxidase, IL-4, IL-10, growth hormone, insulin-like growth factor-1, and growth hormone-releasing hormone declined (P < 0.05), reflecting energy reallocation from growth toward antioxidation and immune maintenance under hypoxia. Plasma metabolomics revealed distinct altitude-dependent reprogramming, with enrichment of retinol metabolism at 4,000 m and α-linolenic acid metabolism, tricarboxylic acid (TCA) cycle, and branched-chain amino acid biosynthesis at 4,500 m. These pathways link lipid remodeling, oxidative balance, and oxygen utilization. The gut microbiota displayed altitude-specific shifts, characterized by enrichment of Christensenellaceae_R-7_group and Monoglobus and reduced UCG-005 and Rikenellaceae_RC9_gut_group, accompanied by lower fecal volatile fatty acids (P < 0.05). Correlation analyses confirmed tight associations between fermentative taxa and volatile fatty acids production. Collectively, our results establish a serum-metabolome-microbiota axis as a central mechanism supporting yak adaptation to high altitude.IMPORTANCEThis study demonstrates that the gut microbiota plays a crucial role in how yaks adapt to high-altitude hypoxia. Rising altitude not only alters the composition of gut microbes but also shifts their metabolic activity toward improving fermentation efficiency and antioxidant capacity. These microbial changes are closely linked with host metabolism, forming a coordinated serum-metabolome-microbiota network that helps maintain energy balance and immune stability when oxygen is limited. The enrichment of retinol and α-linolenic acid metabolism as altitude-responsive pathways further highlights the metabolic interplay between host and microbes in supporting physiological resilience. Overall, our findings show that microbial flexibility and metabolic cooperation are key factors enabling ruminants to survive in extreme environments, providing a scientific basis for microbiome-informed strategies to enhance yak health and productivity on the Qinghai-Tibet Plateau.}, }
@article {pmid41410364, year = {2025}, author = {Mancini, L and Saliekh, L and Claydon, R and Kotar, J and Bernadett Benyei, E and A Munro, C and N Shendruk, T and Brown, A and Welch, M and Cicuta, P}, title = {Hyphal growth determines spatial organization and coexistence in a pathogenic polymicrobial community in a spatially structured environment.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf279}, pmid = {41410364}, issn = {1751-7370}, abstract = {The bodies of macroorganisms host microbes living in multi-species communities. Sequencing approaches have revealed that different organs host different microbiota and tend to be infected by different pathogens, drawing correlations between environmental parameters at the organ level and microbial composition. However, less is known about the microscale dimension of microbial ecology, particularly during infection. In this study, we focus on the role of microscale spatial structure, studying its influence on the ecology of a polymicrobial infection of P. aeruginosa, S. aureus, and C. albicans. Although these pathogens are commonly found together in the lungs of chronically ill patients, it is unclear whether they coexist or compete and segregate in different niches. We find that, whereas P. aeruginosa quickly outcompetes C. albicans and S. aureus on large surfaces, robust spatial organization and coexistence emerges in spatially structured microenvironments. In confined spaces, slowly growing C. albicans is able to leverage rapid radial hyphal growth to conquer boundaries, where it establishes itself displacing the other pathogens. Similar outcomes are observed when the P. aeruginosa strain carries mexT-inactivating mutations, which are often found in clinical isolates. The observed spatial organization enables coexistence and potentially determines infection severity and outcomes. Our findings reveal a previously unrecognized role of mechanical forces in shaping infection dynamics, suggesting that microenvironmental structure might be a critical determinant of pathogen coexistence, virulence, and treatment outcomes. Because adaptations, such as changes in morphology, are widespread among microbes, these results are generalizable to other ecologies and environments.}, }
@article {pmid41410209, year = {2025}, author = {Vidal, E and Lindsay, MR and Bradley, JA and Osburn, MR and Ruff, SE}, title = {Subsurface Life on Earth as a Key to Unlock Extraterrestrial Mysteries.}, journal = {Microbial biotechnology}, volume = {18}, number = {12}, pages = {e70286}, doi = {10.1111/1751-7915.70286}, pmid = {41410209}, issn = {1751-7915}, support = {https://doi.org/10.52044/HFSP.RGEC342023.pc.gr.168586//Human Frontier Science Program/ ; https://doi.org/10.52044/HFSP.RGY00582022.pc.gr.153592//Human Frontier Science Program/ ; ANR23-CPJ1-0172-01//Agence Nationale de la Recherche/ ; 101115755/ERC_/European Research Council/International ; //CIFAR Earth 4D/ ; 80NSSC23K1355//NASA Exobiology/ ; EAR-2042249//National Science Foundation/ ; EAR-2120912//National Science Foundation/ ; OCE-1450528//National Science Foundation/ ; //United States Science Support Program/ ; //David and Lucile Packard Foundation/ ; }, mesh = {*Earth, Planet ; *Extraterrestrial Environment ; *Exobiology/methods ; Bacteria/metabolism/genetics ; }, abstract = {The first forms of life on Earth were microbial, preceding the evolution of multicellular life by more than two billion years. Based on our current understanding of the origin of life, it is likely that the first life forms on any extraterrestrial world would also be microbial. Due to the extreme temperatures, radiation or aridity on most planetary surfaces, such extraterrestrial microbes would most likely dwell in subsurface environments. Earth's subsurface features a wide range of environments, including deep marine sediments, crustal aquifers, rock fracture fluids, hydrocarbon reservoirs, caves and permafrost soils. These environments are known to host an immense diversity of life forms, predominantly microbes that survive or even thrive under extreme conditions and energy scarcity. Life's ability to endure and possibly evolve in Earth's subsurface lends credence to the possible existence of life beyond our planet and provides a blueprint for the extraterrestrial life forms and biosignatures we might expect. The exploration of space via extraterrestrial samples analysed on Earth, in situ extraterrestrial analyses, and remote sensing continue to advance our search for and understanding of potential biosignatures on other planetary bodies. But by investigating Earth's deep, dark and isolated ecosystems, we not only broaden our understanding of life's adaptability but also refine our strategies and technologies for detecting life on other planets and moons. Subsurface exploration is not just a frontier of Earth science-it is a cornerstone of astrobiology and in the pursuit of understanding the multitude of processes that could create and sustain life anywhere. In this opinion article, we discuss the latest highlights in subsurface research and technology, how Earth's subsurface environments serve as models for potential environments on other planetary bodies, why insights into subsurface microbiomes inform the search for life elsewhere, and which technologies and developments will advance the field in the future.}, }
@article {pmid41408796, year = {2025}, author = {Rojas-Preciado, N and Stockmans, I and Everaert, EA and De Jonghe, K and Wauters, A and Lievens, B and Jacquemyn, H}, title = {Incidence and environmental drivers of beet mild yellowing virus, beet chlorosis virus and beet yellows virus in sugar beet fields in Flanders.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-08-25-1626-RE}, pmid = {41408796}, issn = {0191-2917}, abstract = {Since the ban on neonicotinoids, aphid-transmitted yellowing viruses have increasingly reduced sugar beet yields, leading to substantial economic losses. With limited sustainable alternatives, understanding virus incidence and its drivers is essential for effective disease prevention. This study examined the prevalence and incidence of major yellowing viruses in sugar beet crops across Flanders and assessed the influence of aphid abundance and environmental factors to identify key drivers of infection. We evaluated the incidence of beet mild yellowing virus (BMYV), beet chlorosis virus (BChV), and beet yellows virus (BYV) in 25 sugar beet fields and investigated the influence of aphid abundance, soil nutrients, weather conditions, and landscape features on virus incidence. BMYV was the most prevalent virus detected. Higher incidences of BMYV and BYV were associated with earlier sowing dates and increased early-season abundance of Myzus persicae. BMYV incidence increased under warmer, wetter conditions, while BYV showed the opposite trend. Incidences of BChV and BYV increased in areas dominated by sugar beet cultivation. Elevated soil concentrations of phosphorus and potassium were only associated with higher BMYV incidence. The incidence of yellowing viruses in Flanders was primarily driven by early-season aphid pressure and environmental conditions that facilitate virus transmission and establishment. The increasing occurrence of yellowing viruses poses a significant threat to sugar beet production and calls for better insights into the factors driving virus infection and spread. Effective preventive management strategies should integrate pest dynamics, weather forecasting, landscape structure, and soil health into informed decision-making to limit further spread of yellowing viruses.}, }
@article {pmid41408749, year = {2025}, author = {Zuccaro, A}, title = {Effector biology and immunometabolic (re)programming: microbial strategies for compatibility.}, journal = {Molecular plant}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.molp.2025.12.016}, pmid = {41408749}, issn = {1752-9867}, abstract = {Root immunometabolism: balancing defense and accommodation Plant health depends on balanced immune defense and microbial accommodation. As constant contact zones, roots must exclude pathogens while fostering beneficial symbionts. Classical, leaf-based immunity models fail to capture the spatial and metabolic complexity of roots, which contain functionally distinct zones and cell types with diverse immune sensitivities and responses (Tsai et al., 2023). Unlike broad immune responses in leaves, root defense is often confined to a few neighboring cells where cellular damage signals coincide with microbial cues. This localized activation likely prevents excessive immunity that could disrupt root development or beneficial colonization (Tsai et al., 2023), shaping microbiome assembly by determining which taxa persist in specific root niches. Beyond immunity, metabolic cues also influence niche formation, collectively defining the physicochemical landscape that selects specific microbial consortia (Loo et al., 2024). Microbial effector proteins from both pathogens and mutualists act individually or cooperatively to reprogram host immune and metabolic pathways, modulating compatibility and plant health. This integrated regulation, known as immunometabolism, is well established in animals, where defined metabolic pathways govern immune cell fate and function. In plants, immunometabolic control is emerging as a conceptual frontier, with host transporters, receptors, and microbial effectors increasingly recognized as key modulators along the mutualism-pathogenesis continuum. Central to this molecular dialogue are extracellular and intracellular signaling metabolites, or infochemicals, produced by both plants and microbes. These small molecules coordinate immune-metabolic states and shape community composition, with purine-derived signals and iron-mediated redox exchanges representing conserved regulatory axes across plant and animal systems (Dangol et al., 2019; Dunken et al., 2024). Together, these cross-kingdom principles offer conceptual and practical leverage for predictive microbiome engineering. Because this opinion piece spans immunity, metabolism, and microbial ecology, INFOBOX 1 defines key terms to establish a shared conceptual framework.}, }
@article {pmid41408715, year = {2025}, author = {Pérez-Lorente, AI and Molina-Santiago, C and Vela-Corcía, D and Stincone, P and Hierrezuelo, J and Grifé, M and Pakkir Shah, AK and de Vicente, A and Petras, D and Romero, D}, title = {Offensive role of the Bacillus extracellular matrix in driving metabolite-mediated dialogue and adaptive strategies with the fungus Botrytis.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf277}, pmid = {41408715}, issn = {1751-7370}, abstract = {Bacterial-fungal interactions have traditionally been attributed to secondary metabolites, but the role of the bacterial extracellular matrix in shaping these relationships has remained unclear. Here, we demonstrate that the extracellular matrix protein TasA is a key mediator in the antagonistic interaction between Bacillus subtilis and Botrytis cinerea. TasA enables Bacillus to tightly adhere to fungal hyphae, disrupts the β-glucan layer, and compromises fungal cytoskeletal integrity synergistically with fengycin, which causes cytological damage. Additionally, TasA acts as a carrier for bacillaene, amplifying its fungistatic activity. In response, Botrytis mounts a multifaceted defense, enzymatically degrading fengycin, producing antibacterial oxylipins, and activating adaptive programs such as hyphal branching and chlamydospore formation. Our findings reveal the previously unrecognized role of extracellular matrix components in fungal suppression and the modulation of fungal adaptive responses. This study reveals the complex interplay between microbial aggression and defense, providing new insights into the ecological dynamics of microbial competition and coexistence.}, }
@article {pmid41407993, year = {2025}, author = {Cota Ortega, LE and Quiroz-Guzmán, E and Balcázar, JL}, title = {Ecological Drivers of Plasmid-Mediated Antimicrobial Resistance in Aquaculture.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02684-0}, pmid = {41407993}, issn = {1432-184X}, abstract = {Antimicrobial resistance (AMR) is a growing global challenge that compromises the effectiveness of disease control and increases risks for both human and animal health. Aquaculture systems are particularly vulnerable, as extensive and often inappropriate antimicrobial use has driven the emergence and persistence of multidrug-resistant bacteria. This mini-review summarizes the ecological and genetic mechanisms underlying AMR in aquaculture, with emphasis on plasmid-mediated resistance and its role in horizontal gene transfer. It also addresses the broader environmental and public health implications of these processes and calls for sustainable management, enhanced surveillance, and coordinated international policies to curb resistance dissemination and safeguard global food security.}, }
@article {pmid41405607, year = {2025}, author = {Satterwhite, RS and Bergelson, J}, title = {Adaptation without Dominance in Pseudomonas syringae Pathovars.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02675-1}, pmid = {41405607}, issn = {1432-184X}, support = {Hutchinson Fund//University of Chicago Department of Ecology and Evolution/ ; NSF MCB 0603515//National Science Foundation, United States/ ; }, abstract = {Understanding local adaptation of phytopathogens has significant practical and economic implications. The opportunistic pathogen Pseudomonas syringae exemplifies this challenge, causing regular epidemics in diverse host plants. Many pathogenic microbes, including P. syringae, are divided into intraspecific lineages, or pathovars, based on their host-of-isolation. However, whether pathovar classifications reflect adaptation of the pathogen to the host (local adaptation) or a competitive advantage of the pathogen in the host (local dominance), often goes untested. In this study, we performed in vitro growth assays and factorial controlled infections to test whether a suite of five P. syringae pathovars are locally adapted to, and/or locally dominant in, their hosts-of-isolation. We found evidence of local adaptation in three of five pathogens, only one of which was also locally dominant. Several strains performed as well or better than the locally adapted strain in that strain's host-of-isolation, consistent with cost-free generalism. Thus, pathovar designations do not reliably delineate pathogenic phenotypes. Moreover, we found that in vitro growth was not predictive of in planta growth. To contextualize phenotypes, we compared pathogen gene content, identifying unique phytotoxins, secreted effectors, and general virulence factors. In all, we found that local adaptation is common but not universal, and that locally adapted strains are not necessarily constrained from performing competitively in multiple hosts. Thus, neither host-of-isolation nor in vitro performance is reliable for strain classification. Our findings highlight the vast intraspecific variation in P. syringae, and the coexistence of multiple successful adaptive strategies.}, }
@article {pmid41404415, year = {2025}, author = {Sakarika, M and Brancart, J and Gujar, SA and De Meester, S and Allegue, LD and Bastiaens, L and Ragaert, P and Vlaeminck, SE and De Wever, H and Rabaey, K}, title = {Microbial protein-derived bioplastics from renewable substrates: pathways, challenges, and applications in a circular economy.}, journal = {Environmental science and ecotechnology}, volume = {28}, number = {}, pages = {100635}, pmid = {41404415}, issn = {2666-4984}, abstract = {Microbial protein (MP)-the protein-rich biomass derived from recovered or virgin resources-is attracting interest as a source of food and feed. However, its potential as a feedstock for protein-based bioplastics remains underexplored. Proteins offer desirable properties, including superior oxygen-barrier capabilities and complete biodegradability, making them ideal for applications from food packaging to agricultural mulches. Currently, most protein-based bioplastics derive from crops such as wheat, restricting applications and competing with food production. MP can overcome these limitations by supplying diverse proteins from various inputs, including CO2, biomass, and liquid side-streams. In this review, we evaluate bioprocessing pathways for producing MP from renewable and waste-derived substrates from an interdisciplinary viewpoint. We also examine the technical, regulatory, market, and environmental factors to address, delineating the pathway from substrate to MP-based plastics and highlighting key challenges throughout the production chain. Novel strategies-such as efficient co-recovery of proteins with other cellular products like polyhydroxyalkanoates or direct use of microbial biomass without extraction-are essential to maximize environmental and economic sustainability. Carefully chosen processing methods for recovered proteins, including wet and dry blending or extrusion with other biopolymers, can yield diverse products. Concurrently, policy and market developments are vital for adopting MP-based bioplastics. Addressing these challenges will enable MP-based bioplastics to propel the shift toward a circular economy, diminishing dependence on fossil-derived plastics and alleviating plastic pollution.}, }
@article {pmid41403705, year = {2025}, author = {Paccagnella, D and Bağcı, C and Gavriilidou, A and Ziemert, N}, title = {PanBGC: a pangenome-inspired framework for comparative analysis of biosynthetic gene clusters.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf225}, pmid = {41403705}, issn = {2730-6151}, abstract = {Bacterial secondary metabolites are a major source of therapeutics and play key roles in microbial ecology. These compounds are encoded by biosynthetic gene clusters (BGCs), which show extensive genetic diversity across microbial genomes. While recent advances have enabled clustering of BGCs into gene cluster families (GCFs), there is still a lack of frameworks for systematically analysing their internal diversity at a population scale. Here, we introduce "PanBGC", a pangenome-inspired framework that treats each GCF as a population of related BGCs. This enables classification of biosynthetic genes into core, accessory, and unique categories and provides openness metrics to quantify compositional diversity. Applied to over 250 000 BGCs from more than 35 000 genomes, PanBGC maps biosynthetic diversity of more than 80 000 GCFs. Our analysis reveals that gene composition reshuffling, rather than acquisition of new genes, is the dominant driver of diversity within GCFs, with most families exhibiting closed gene repertoires but high compositional variability. Additionally, transporter-related domains were commonly identified among core genes, reflecting the fundamental importance of compound export in BGC function. To facilitate exploration, we present PanBGC-DB (https://panbgc-db.cs.uni-tuebingen.de), an interactive web platform for comparative BGC analysis. PanBGC-DB offers gene- and domain-level visualizations, phylogenetic tools, openness metrics, and custom query integration. Together, PanBGC and PanBGC-DB provide a scalable framework for exploring BGCs at population resolution and for contextualizing newly discovered BGCs within the global landscape of secondary metabolism.}, }
@article {pmid41402555, year = {2025}, author = {Lakhlifi, T and El Oirdi, S and Kaddouri, AC and Belhaj, A}, title = {Factors influencing antifungal activity of selected lactic acid bacteria strains and characterization of their active compounds.}, journal = {Antonie van Leeuwenhoek}, volume = {119}, number = {1}, pages = {13}, pmid = {41402555}, issn = {1572-9699}, support = {PPR2/2016/07//Centre National pour la Recherche Scientifique et Technique/ ; }, mesh = {*Antifungal Agents/pharmacology/metabolism/chemistry ; *Lactobacillales/chemistry/metabolism ; Hydrogen-Ion Concentration ; Temperature ; Carbon/metabolism ; Culture Media/chemistry ; Microbial Sensitivity Tests ; }, abstract = {Lactic acid bacteria (LAB) are known to possess potent antifungal activity; however, the factors that affect this activity remain poorly investigated. In this study, we explored the influence of physicochemical and nutritional factors on the antifungal activity of five LAB strains namely Lactiplantibacillus pentosus 22B, Leuconostoc mesenteroides 8C2, Lactiplantibacillus plantarum 21B, Enterococcus faecium LC2V5 and Enterococcus faecium LC2P8. These factors included incubation period, medium initial pH, incubation temperature, long-term storage and carbon source. Results showed that these factors significantly influenced the antifungal activity of the studied LAB strains (p < 0.0001). The optimal conditions yielding the most potent inhibition (21 ± 0.4 mm to 19 ± 0.4 mm) were identified. Specifically, maximum activity was achieved after a 48-h incubation (late stationary phase), at 25-30 °C, an initial pH of 3-4, and with sucrose, galactose, or mannose as the carbon source, depending on the strain. Moreover, long-term storage at - 80 °C led to complete loss of activity in two strains (8C2 and LC2P8), while the other three remained stable. Furthermore, HPLC and GC-MS analyses were used to identify the antifungal compounds produced by these three stable strains. The results revealed the presence of various organic acids (lactic, acetic, formic, malic, and fumaric acids) and fatty acids, such as 9-octadecenoic acid, 11-dodecenoic acid, 10-hydroxy. Scanning electron microscopy confirmed that these compounds caused significant structural damage to fungal mycelia, supporting their demonstrated fungicidal effects. This study improves our understanding of the key factors and mechanisms underlying LAB antifungal activity, contributing to the optimization of their use as natural antifungal agents.}, }
@article {pmid41402426, year = {2025}, author = {Wauquier, F and Chavanelle, V and Bouchard-Mercier, A and Boutin-Wittrant, L and Otero, YF and Krisa, S and Valls, J and Le Joubioux, F and Pereira, B and Roux, V and Macian, N and Pickering, G and Sapone, V and Cazaubiel, M and Bron, A and Peltier, S and Blanquet, S and Sirvent, P and Wittrant, Y}, title = {Bioavailable human metabolites from TOTUM-448 (plant-based formulation) maintain liver cell functionality in a hyperlipidic context that drives MASLD onset.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-025-32556-z}, pmid = {41402426}, issn = {2045-2322}, support = {Labcom MIMETiv (ANR, ANR-22-LCV1-0003-01)//Agence Nationale de la Recherche/ ; Labcom MIMETiv (ANR, ANR-22-LCV1-0003-01)//Agence Nationale de la Recherche/ ; Labcom MIMETiv (ANR, ANR-22-LCV1-0003-01)//Agence Nationale de la Recherche/ ; Labcom MIMETiv (ANR, ANR-22-LCV1-0003-01)//Agence Nationale de la Recherche/ ; Labcom MIMETiv (ANR, ANR-22-LCV1-0003-01)//Agence Nationale de la Recherche/ ; Labcom MIMETiv (ANR, ANR-22-LCV1-0003-01)//Agence Nationale de la Recherche/ ; Labcom MIMETiv (ANR, ANR-22-LCV1-0003-01)//Agence Nationale de la Recherche/ ; Labcom MIMETiv (ANR, ANR-22-LCV1-0003-01)//Agence Nationale de la Recherche/ ; Labcom MIMETiv (ANR, ANR-22-LCV1-0003-01)//Agence Nationale de la Recherche/ ; Labcom MIMETiv (ANR, ANR-22-LCV1-0003-01)//Agence Nationale de la Recherche/ ; Labcom MIMETiv (ANR, ANR-22-LCV1-0003-01)//Agence Nationale de la Recherche/ ; Labcom MIMETiv (ANR, ANR-22-LCV1-0003-01)//Agence Nationale de la Recherche/ ; Labcom MIMETiv (ANR, ANR-22-LCV1-0003-01)//Agence Nationale de la Recherche/ ; Pack Ambition Recherche 2021 MICROMETiv//R&#xe9;gion Auvergne-Rh&#xf4;ne-Alpes/ ; Pack Ambition Recherche 2021 MICROMETiv//R&#xe9;gion Auvergne-Rh&#xf4;ne-Alpes/ ; Pack Ambition Recherche 2021 MICROMETiv//R&#xe9;gion Auvergne-Rh&#xf4;ne-Alpes/ ; Pack Ambition Recherche 2021 MICROMETiv//R&#xe9;gion Auvergne-Rh&#xf4;ne-Alpes/ ; Pack Ambition Recherche 2021 MICROMETiv//R&#xe9;gion Auvergne-Rh&#xf4;ne-Alpes/ ; Pack Ambition Recherche 2021 MICROMETiv//R&#xe9;gion Auvergne-Rh&#xf4;ne-Alpes/ ; Pack Ambition Recherche 2021 MICROMETiv//R&#xe9;gion Auvergne-Rh&#xf4;ne-Alpes/ ; Pack Ambition Recherche 2021 MICROMETiv//R&#xe9;gion Auvergne-Rh&#xf4;ne-Alpes/ ; Pack Ambition Recherche 2021 MICROMETiv//R&#xe9;gion Auvergne-Rh&#xf4;ne-Alpes/ ; Pack Ambition Recherche 2021 MICROMETiv//R&#xe9;gion Auvergne-Rh&#xf4;ne-Alpes/ ; ANR11-INBS-0010//Bordeaux Metabolome Facility and the MetaboHUB/ ; ANR11-INBS-0010//Bordeaux Metabolome Facility and the MetaboHUB/ ; }, abstract = {Lipotoxic and inflammatory environment drives metabolic dysfunction-associated steatotic liver disease (MASLD) onset. As most conventional treatments present adverse side effects, alternative options such as preventive nutritional interventions have been developed, though further clinical validation is needed. In this study, we conducted an innovative ex vivo clinical investigation to examine how circulating metabolites generated after oral intake of TOTUM-448 (a plant-based, polyphenol-rich formulation) may influence hepatocyte function. UHPLC-MS/MS analysis confirmed and characterized the bioavailable polyphenol metabolites present in human serum. This metabolite-enriched serum was further used to treat HepG2 hepatocytes, with or without palmitate pretreatment (250 µM). The effects of TOTUM-448-derived metabolites on hepatocytes were evaluated by monitoring cell viability, lipid metabolism, inflammation, oxidative stress, and endoplasmic reticulum (ER) stress, all of which are central features of MASLD. Treated hepatocytes exhibited resistance to palmitate-induced lipotoxic stress, showing reduced intracellular lipid accumulation. TOTUM-448-derived metabolites also prevented the palmitate-induced upregulation of inflammatory gene expression. Additionally, while palmitate strongly upregulated CHOP and XBP1 mRNA expression as well as ATF6 and Caspase-3 activities, the presence of TOTUM-448-derived metabolites restored these ER stress markers to normal levels.}, }
@article {pmid41400860, year = {2025}, author = {Zander, S and von Friesen, LW and Gonçalves-Araujo, R and Grosso, O and Benavides, M and Granskog, MA and Riemann, L}, title = {Contrasting Nitrogen Fixation Between Arctic and Atlantic Waters in the Fram Strait.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02673-3}, pmid = {41400860}, issn = {1432-184X}, support = {730965//European Union H2020/ ; NE/W004933/1//Natural Environment Research Council/ ; 2032-00001B//Danmarks Frie Forskningsfond/ ; 6108-00013//Danish Council for Independent Research/ ; }, abstract = {Nitrogen availability limits primary production in the Arctic Ocean, making it vital to understand its sources and sinks to predict future productivity. Although nitrogen fixation has been reported in the Arctic Ocean, data remain scarce, especially in the Atlantic sector. Here, we measured nitrogen fixation rates and examined diazotroph community composition across the Fram Strait, targeting Polar waters in the East Greenland Current, Atlantic waters in the West Spitsbergen Current, and their frontal zone. Nitrogen fixation was mainly low (< 1 nmol N L[-1] d[-1]) in Polar waters, however, elevated at the one station in the Atlantic water sector (up to 10.15 nmol N L[-1] d[-1]). Rates were only detectable in the epipelagic layer (0-100 m) across the strait and positively correlated with temperature, primary production, and chlorophyll-a fluorescence, and negatively correlated with coloured dissolved organic matter and silicate. The diazotrophs were dominated by non-cyanobacterial diazotrophs (NCDs; 77% of nifH amplicon reads), with an Arctic Betaproteobacterial group (order Rhodocyclales) accounting for 11% of sequence reads. This group was quantifiable (up to 6700 nifH gene copies L[-1]) within the West Spitsbergen Current and the frontal zone, where the highest nitrogen fixation and primary production occurred, and its prevalence was positively correlated with temperature. We propose that temperature and freshly produced dissolved organic matter influence the NCD-dominated nitrogen fixation in Fram Strait. Our study suggests that NCDs are key diazotrophs in Fram Strait, and that nitrogen fixation rates and their potential importance for primary production vary across the contrasting water masses entering and exiting the Arctic Ocean. We encourage future studies to quantify these nitrogen fluxes and evaluate their importance for productivity in the Arctic Ocean.}, }
@article {pmid41400345, year = {2025}, author = {Yuan, W and Xu, EG and Zhu, D and Zhang, W and Liu, W and Abdolahpur Monikh, F and Lin, L and Li, L and Grossart, HP and Yang, Y and Rillig, MC and Peijnenburg, WJGM}, title = {Nanoplastics in Duckweed: Single-Cell Responses and Recovery.}, journal = {ACS nano}, volume = {}, number = {}, pages = {}, doi = {10.1021/acsnano.5c15989}, pmid = {41400345}, issn = {1936-086X}, abstract = {Micro- and nanoplastics have emerged as critical contaminants in aquatic ecosystems due to their small size, persistent nature, and potential for bioaccumulation. Nanoplastics are particularly concerning because they can be widespread in aquatic environments and ingested by aquatic organisms, posing potential risks to ecological health and environmental sustainability. However, the response and recovery of aquatic plants to nanoplastics, as well as the cell-specific molecular mechanisms underlying these processes, remain unclear. By integrating single-cell transcriptomics, enzymatic assays, and europium-doped nanoplastic tracing, we comprehensively investigated the response of duckweed to polystyrene nanoplastics at environmentally relevant and high doses over exposure and recovery phases. Nanoplastics exposure reduced plant reproduction and root length by inducing oxidative damage, with partial recovery after removal. Single-nucleus RNA sequencing revealed cell-type-specific responses of duckweed to nanoplastics, particularly in mesophyll, mestome sheath, epidermis, and parenchyma cells. Interestingly, recovery triggered a greater number of differentially expressed genes mechanistically linked to carbon metabolism, membrane transport, and stress-responsive pathways. Nanotracer quantification demonstrated root/frond absorption and 36.8-51.4% postrecovery excretion. These multiscale lines of evidence decipher the molecular strategies of duckweed to nanoplastics at single-cell resolution, providing mechanistic insights into the interactions between aquatic plants and nanoplastics contamination.}, }
@article {pmid41398214, year = {2025}, author = {Sari, SP and Soylu, A and Peker, KD and Adas, G and Akgul, O and Sapmaz, B and Oner, YA and Mayda, PY and Caliskan, R}, title = {Comparative gastric microbiota profiles in non-ulcer dyspepsia and peptic ulcer patients.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-025-04607-y}, pmid = {41398214}, issn = {1471-2180}, support = {Project number: 2018/05//Istanbul Ayd&#x131;n University Scientific Research Projects Coordination Unit/ ; }, abstract = {BACKGROUND: Recent evidence suggests that the human stomach hosts a diverse microbiota beyond Helicobacter pylori, and that shifts in microbial composition may influence gastric health. In particular, oral-origin bacteria may dominate the gastric niche in the absence of H. pylori, yet their specific roles in different gastroduodenal disorders remain unclear. This study aimed to profile and compare the gastric microbiota composition in Turkish patients with non-ulcer dyspepsia (NUD) and peptic ulcer disease (PUD), in order to better understand microbial profiles potentially associated with gastroduodenal disease.<br><br>METHODS: Ninety-eight patients underwent endoscopic evaluation and were divided into two groups according to the presence or absence of ulcers. Group 1 (n&#x2009;=&#x2009;52) included individuals with NUD, while Group 2 (n&#x2009;=&#x2009;46) comprised patients with PUD. Gastric biopsy samples from both groups were analyzed for the relative abundance of H. pylori using quantitative real-time PCR (qPCR), and next-generation sequencing was employed for a comprehensive analysis of the gastric microbiota.<br><br>RESULTS: In total, H. pylori DNA was detected in 71.4% (70/98) of the samples, with a significantly higher prevalence in PUD patients (82.6%) compared to NUD patients (61.5%) (p&#x2009;=&#x2009;0.02). Distinct microbial profiles were observed based on H. pylori status. In NUD patients, Alloprevotella showed significantly higher relative abundance in H. pylori-negative samples (p&#x2009;<&#x2009;0.05). Among PUD patients, the absence of H. pylori was associated with increased levels of Porphyromonas and Neisseria compared to NUD patients without H. pylori (p&#x2009;<&#x2009;0.05). These genera, typically associated with the oral cavity, appeared to expand opportunistically when H. pylori was absent.<br><br>CONCLUSIONS: The absence of H. pylori in gastric disorders was linked to a notable shift in microbiota composition, with increased representation of oral-origin bacteria such as Alloprevotella, Porphyromonas, and Neisseria. These findings, observed in a Turkish patient cohort, may reflect a potentially compensatory or opportunistic microbial shift in H. pylori-negative gastroduodenal disease. As exploratory findings, this study represents the first analysis from T&#xfc;rkiye comparing gastric microbiota profiles in NUD and PUD patients and provides novel regional insight into gastric microbial ecology.}, }
@article {pmid41398058, year = {2026}, author = {}, title = {Microbial ecology and evolution in the genomics era.}, journal = {Nature reviews. Genetics}, volume = {27}, number = {1}, pages = {1-2}, pmid = {41398058}, issn = {1471-0064}, }
@article {pmid41396129, year = {2025}, author = {Timmis, K and Baquero, F and Lal, R and Amorim, LRP and Nikel, PI and Kaur, J and Sood, U and Lata, P and Singh, S and Robinson, JM and Chavarria, M and Verstraete, W and Bernal, P and Banciu, H and Steward, K and Frey, J and Danchin, A and Karnkowska, A and Kotsyurbenko, O and Pereira, CS and Boyd, ES and Hallsworth, JE and Nunes, O and Udaondo, Z and Huang, W and Wang, Y and Karahan, ZC and Junier, P and Ron, E and Ramos, JL}, title = {Scientists' Warning to Humanity: The Need to Begin Teaching Critical and Systems Thinking Early in Life.}, journal = {Microbial biotechnology}, volume = {18}, number = {12}, pages = {e70270}, doi = {10.1111/1751-7915.70270}, pmid = {41396129}, issn = {1751-7915}, mesh = {Humans ; Decision Making ; }, abstract = {We live in a time of global crises: a deteriorating environment that is struggling to provide all the resources and services we demand of it, changing climate and its consequences for the biosphere, its habitats, inhabitants and biodiversity, conflicts-divisive ideologies-competition for resources, increasing societal inequalities and human deprivations, and a youth mental health pandemic, to name but just a few. Most of these crises are self-made, the result of human decisions, and their acceptance/toleration by society. Policies and practices at all levels of society that created, exacerbate and launch new crises are, at worst, self-serving and, at best, faulted through a lack of understanding. In democracies, citizens can hold decision-makers to account but, to do this, they must understand the issues and be able to imagine better policies. We also live in a digital world in which a flood of mostly inconsequential information and misinformation pollutes our brains, enhancing pre-existing biases and creating new ones, and numbing our mental ability to think clearly and reach sensible decisions. But sensible decisions are urgently needed at all levels to fix problems and reduce future self-harm. Sensible decisions require sourcing the best available relevant information, and a process to convert information into understanding, understanding into clear decision options, and the choice of a decision option that leads to an action that represents best practice. Critical thinking is the enabling cognitive process of this decision pathway, because it selects the best available information through demanding evidence-basing, seeks critical discourse between experts and stakeholders that agnostically explores solution space to find plausible options, and whittles down options inter alia through plausibility, due diligence, bottleneck analysis, cost-benefit analysis, and benchmarking filtering. Crucially, it rejects biases, influencing factors, and other constraints on options, and is an effective barrier to the information flood. The problem is that critical thinking capacity is not widely available among either decision makers or stakeholders. There is an urgent need to rapidly roll out effective education programmes in which critical thinking teaching is solidly embedded. Since biases accumulate with age, the teaching of critical thinking must begin with the very young. However, the very young are not able to comprehend the complex abstract issues underpinning critical thinking. Embedding the teaching of critical thinking in a suitable educational context, and integrating it into curricula, is another challenge. To address these two challenges, the International Microbiology Literacy Initiative is developing a storytelling programme for children, called the Critical Thinking MicroChats Gallery, within the curriculum of societally relevant microbiology it is creating. MicroChats illustrate the principal practical elements of critical thinking, like bottlenecks, cost: benefit, benchmarking, the need for discussions and other points of view, employing readily relatable, relevant microbially centric scenarios. MicroChats suggest class discussion topics to encourage children to imagine the application of each element in other contexts to reinforce principles and hone critical thinking skills. Critical thinking, and especially the cultivation of the habit of asking 'why' and requiring plausible justification for policies/actions, is a shield against bias, prejudice, propaganda, misinformation and the incessant pressures of social media. It promotes a healthy mind and the attainment of the developmental potential of individuals. Increasing critical thinking in society will raise the quality of decision making at all levels and thereby improve sustainability/reduce the human footprint on our planet, and promote the individual sense of responsibility and global citizenship necessary for the improvement of the condition of humanity and its relationship with Planet Earth.}, }
@article {pmid41395947, year = {2025}, author = {Bouchali, R and Sentenac, H and Bates, KA and Fisher, MC and Schmeller, DS and Loyau, A}, title = {Unraveling the disease pyramid: the role of environmental micro-eukaryotes in amphibian resistance to the deadly fungal pathogen Batrachochytrium dendrobatidis.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0143625}, doi = {10.1128/msystems.01436-25}, pmid = {41395947}, issn = {2379-5077}, abstract = {The disease pyramid conceptualizes the predictors of host infection risk, linking the host, the pathogen, environmental conditions, and both host and environmental microbiomes. However, the importance of the interaction between environmental and host-associated microbiomes in shaping infectious disease dynamics remains poorly understood. While the majority of studies have focused on bacteria, the role of micro-eukaryotes has been seldom investigated. Here, we explore three axes of the disease pyramid using an 18S rRNA gene metabarcoding approach to analyze the micro-eukaryotic assemblages of biofilm, water, and skin samples from three European amphibian species. Skin bacterial communities of the investigated amphibian populations have already been shown to be impacted by the presence of the lethal fungal pathogen Batrachochytrium dendrobatidis (Bd), with a higher abundance of protective bacteria in infected populations and a greater environmental microbial contribution to the skin microbiota in Bd-positive lakes. Here, we explored the relationships between the micro-eukaryotic skin communities of these tadpole populations with their surrounding environment. Tadpoles were sampled at 22 mountain lakes located in the Pyrenees (France), 8 of which harbored amphibian populations infected by Bd. We found that biofilms from Bd-negative lakes had higher environmental micro-eukaryotic diversity and a greater abundance of putative anti-Bd fungi, both in the environment and on the skin microbiota of Bufo spinosus and Rana temporaria, but not of Alytes obstetricans. Bayesian SourceTracker analysis further showed that the environmental contribution from biofilms to amphibian skin micro-eukaryotic assemblages was higher in Bd-positive lakes for B. spinosus and R. temporaria, but not for A. obstetricans.IMPORTANCEResearch on host-associated microbiomes and infectious diseases has mostly focused on bacteria, overlooking the potential contributions of micro-eukaryotes to infection dynamics. Here, we show that environmental and skin-associated micro-eukaryotes-especially putative anti-Batrachochytrium dendrobatidis (Bd) fungi-differ between Bd-positive and Bd-negative amphibian populations in mountain lakes. Our results suggest that micro-eukaryotes influence disease resistance and microbiome assembly, similarly to bacteria. Importantly, environmental reservoirs of micro-eukaryotes appear to contribute differently across infection contexts. These findings demonstrate the importance of adopting a broader microbiome perspective that includes micro-eukaryotes when investigating the ecological mechanisms underlying infectious disease risk.}, }
@article {pmid41395872, year = {2025}, author = {Mason, AR and Taylor, LS and Gilbert, NE and Wilhelm, SW and DeBruyn, JM}, title = {Soil Microbial Gene Expression Over One Year of Human Decomposition.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf126}, pmid = {41395872}, issn = {1574-6941}, abstract = {During terrestrial vertebrate decomposition, host and environmental microbial communities work together to drive biogeochemical cycling of carbon and nutrients. These mixed communities undergo dramatic restructuring in the resulting decomposition hotspots. To reveal the succession of the active microbes (bacteria, archaea, and fungi) and the metabolic pathways they use, we generated metatranscriptomes from soil samples collected over one year from below three decomposing human bodies. Soil microbes increased expression of heat shock proteins in response to decomposition products changing physiochemical conditions (i.e. reduced oxygen, high salt). Increased fungal lipase expression identified fungi as key decomposers of fat tissue. Expression of nitrogen cycling genes was phased with soil oxygen concentrations: during hypoxic soil conditions, genes catalyzing N-reducing processes (e.g. hydroxylamine to nitric oxide and nitrous oxide to nitrogen gas during reduced oxygen conditions) were increased, followed by increased expression of nitrification genes once oxygen diffused back into the soil. Increased expression of bile salt hydrolases implicated a microbial source for the high concentrations of taurine typically observed during vertebrate decomposition. Collectively, microbial gene expression profiles remained altered even after one year. Together, we show how human decomposition alters soil microbial gene expression, revealing both ephemeral and lasting effects on soil microbial communities.}, }
@article {pmid41395225, year = {2025}, author = {Mortier, L and Vanhoomissen, R and Davies, L and Kirk, PM and Maciá-Vicente, JG and Piepenbring, M and Haelewaters, D}, title = {The first checklist of fungi known for Honduras: revealing taxonomic, geographical, and functional trends.}, journal = {MycoKeys}, volume = {126}, number = {}, pages = {93-117}, pmid = {41395225}, issn = {1314-4049}, abstract = {Fungi play pivotal roles in ecosystem functioning and the provision of ecosystem services. Despite their ecological importance, fungal research remains limited, particularly in tropical regions. Many tropical countries, including Honduras, still lack a comprehensive fungal checklist. To address this gap, we compiled the first fungal checklist for Honduras by collating data from Index Fungorum, MyCoPortal, the Kew Data Portal, and published literature. The resulting dataset contains 1365 species across 4011 records, of which 96.6% are true fungi and 3.4% are fungus-like organisms. Among the true fungi, 69.8% belong to Basidiomycota and 29.4% to Ascomycota. A large percentage of the records refer to plant pathogens (42.4%), reflecting a relatively high number of phytopathological studies and a focus on fungal associations with plant species. Species accumulation curves indicate that all administrative divisions (departments) of Honduras remain understudied, as none have reached saturation. This checklist is a fundamental resource tool for fungal identification and conservation planning and contributes to a broader understanding of fungal biodiversity in the region.}, }
@article {pmid41394253, year = {2025}, author = {Fadum, J and Sun, X and Zakem, E}, title = {Redox-constrained microbial ecology dictates nitrogen loss versus retention.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf219}, pmid = {41394253}, issn = {2730-6151}, abstract = {Microorganisms drive biogeochemical cycling. Therefore, examining environmental change through the lens of microbial ecology is particularly useful for developing a mechanistic understanding of the biogeochemical consequences and feedbacks of perturbations to ecosystems. When aquatic systems with deep anoxic waters undergo eutrophication, the resulting surface productivity impacts the anaerobic microbial community below. The increase in sinking organic carbon can shift the anaerobic community function from inorganic nitrogen (N) loss to N retention, amplifying eutrophication as a positive feedback. However, we lack a mechanistic understanding of this transition, which is critical for anticipating these impacts in aquatic environments where microbial community composition is unknown. Here, we provide a first-principles, quantitative model of this transition from N loss to retention by linking ecological dynamics to the energetics underlying microbial metabolisms. We develop and analyze an ecosystem model in which redox chemistry constrains the traits of key anaerobic N-cycling microbial functional types: denitrification, dissimilatory nitrate reduction to ammonium, and anaerobic ammonium oxidation (anammox). The model captures the transition from N loss to N retention with increasing organic carbon supply, consistent with observations for specific systems and species. Results identify characteristics of the microbial community composition at the "net zero N loss" point at which N loss balances N retention, providing testable hypotheses for sequencing data and other observations. By tying microbial ecological dynamics to environmental chemical potential, results provide a broadly applicable framework for better predicting the biogeochemical impacts of eutrophication, deoxygenation, and other perturbations.}, }
@article {pmid41393217, year = {2025}, author = {Xu, Z and Premarathna, M and Li, Y and Yin, X and Soteyome, T and Liu, J and Seneviratne, G}, title = {Current knowledge on the polymicrobial interaction and biofilm between Saccharomyces and Lactobacillaceae: regulatory mechanisms and applications.}, journal = {Biofilm}, volume = {10}, number = {}, pages = {100336}, pmid = {41393217}, issn = {2590-2075}, abstract = {The family Lactobacillaceae plays a crucial role in food fermentation and probiotic applications, and exhibiting metabolic versatility and adaptability to diverse nutrient-rich environments. They are abundant in nutrient-rich environments like fermented food, vegetables, and the vaginal and gastrointestinal tracts of animals, where they metabolize carbohydrates to produce lactic acids. They also produce bioactive compounds and exhibit anti-inflammatory, antibacterial, and antifungal properties. Saccharomyces yeasts are also widely applied in food, medicine, and biofuel industries. Some species, such as S. boulardii, are recognized for their probiotic benefits, particularly in promoting gut health and alleviating intestinal disorders. This review focuses on the polymicrobial interactions between Lactobacillaceae and Saccharomyces species, highlighting their synergistic roles in improving fermentation efficiency, product quality, and microbial stability through mechanisms such as biofilm formation, metabolic exchange, and nutrient sharing. We also discuss competitive interactions observed in certain systems, such as sugarcane fermentation, which demonstrate the complexity of microbial ecology and the need for precise microbial management strategies. By synthesizing current research, this review aims to provide a comprehensive understanding of how microbial interactions influence fermentation outcomes, and to identify existing knowledge gaps and future directions for optimizing industrial applications.}, }
@article {pmid41392918, year = {2025}, author = {Cianetti, S and Marchianò, S and Wijeratne, DF and Carino, A and Biagioli, M and Bordoni, M and Roselli, R and Di Giorgio, C and Bellini, R and Valenti, C and Coniglio, M and Lomurno, G and Lomurno, AP and Pagano, S}, title = {Analysis of Oral and Gut Microbiota Composition in Children with Dental Caries by NGS Approaches.}, journal = {Recent advances in inflammation &amp; allergy drug discovery}, volume = {19}, number = {3}, pages = {413-427}, doi = {10.2174/0127722708335159241117062704}, pmid = {41392918}, issn = {2772-2716}, mesh = {Humans ; *Dental Caries/microbiology ; *Gastrointestinal Microbiome ; Male ; Female ; *Mouth/microbiology ; Child ; *Probiotics/administration &amp; dosage/therapeutic use ; Feces/microbiology ; High-Throughput Nucleotide Sequencing ; Child, Preschool ; Streptococcus salivarius ; Saliva/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {OBJECTIVES: This study aimed to characterize oral and gut microbiota of children with high dmft index and caries-free children at phylum, family and species levels as well as to evaluate the effect of Streptococcus salivarius M18 DSM 14685 (Carioblis) administration on microbiota composition of caries active children.<br><br>MATERIALS AND METHODS: Ten children with active caries and nine caries-free children have been recruited. Four samples from different oral niches and stools were collected from each patient for the NGS sequencing of 16s Microbiota rDNA by S5 Ion Torrent.<br><br>RESULTS: Our results revealed modifications in the microbiota composition of teeth, saliva and vestibular regions of the oral cavity and faecal samples in the presence of dental caries. These changes were evident at the family and species levels, with no significant differences found at the phylum composition level. In particular, Streptococcaceae were positively correlated to the high degree of caries in all niches, and the analysis at the species level led to the identification of 39 bacterial species significantly modulated in the analyzed groups. The use of probiotic seemed to exert beneficial effects on oral but not on faeces dysbiosis. The intestinal tract was confirmed to have a different microbiota composition compared to the oral cavity.<br><br>CONCLUSION: Dental caries mainly lead to modifications in the oral microbiota composition. Streptococcus salivarius M18 DSM 14685 administration determines a shift in the oral microbiota composition towards a healthier state. Concerning the gastrointestinal tract, our study found for the first time that caries cause the increase of two bacterial species, related to other disorders: Bifidobacterium adolescentis and Ruminococcus torques.}, }
@article {pmid41391312, year = {2025}, author = {Wang, T and Roschke, C and Sánchez, N and Duncan, AH and Namayandeh, A and Fendorf, S and da Rocha, UN and Muehe, EM}, title = {Temporal decoupling of metal(loid) binding and microbial adaptation in arsenic and cadmium contaminated soils under changing climates.}, journal = {Journal of hazardous materials}, volume = {501}, number = {}, pages = {140787}, doi = {10.1016/j.jhazmat.2025.140787}, pmid = {41391312}, issn = {1873-3336}, abstract = {Soil contamination with metals and metalloids is a growing environmental concern, impacting soil ecosystems. Exogenous metal(loid)s are retained in the soil matrix via adsorption, structural incorporation, and precipitation, imposing stress on soil microbiomes, potentially influenced by climate. It remains unclear whether introduced metal(loid)s bind similarly to native ones and how quickly soil microbiomes adapt under today's and future climate conditions. We incubated soils spiked with 0.7 mg kg[-1] cadmium or 15 mg kg[-1] arsenic under today's and future climate scenarios (IPCC SSP 3-7.0: +400 ppmv CO2, +4°C). After 38 days, spiked As and Cd did not integrate into soil minerals like native counterparts but preferentially associated with more reactive minerals. Spiked As became more recalcitrant over time, an effect enhanced under future conditions. Spiked Cd remained reactive during incubation, independent of climate conditions. Prokaryotic abundances increased faster in metal(loid)-spiked soil under future conditions with distinct soil prokaryotic community structures emerging in response to metal(loid)s and climate. Despite this, key functions like Fe(III) reduction were maintained. Communities nearly stabilized within 38 days across climate conditions. These findings suggest that exogenous metal(loid)s may require years to achieve native-level binding, while soil microbes adapt functionally within weeks, even under climate change.}, }
@article {pmid41391222, year = {2025}, author = {García-Carmona, M and Sulbaran-Bracho, Y and Marín, C and Maldonado, JE and García-Orenes, F and Rojas, C}, title = {Organic amendments as a tool to restore soil microbial diversity after wildfires in native Mediterranean forests.}, journal = {Journal of environmental management}, volume = {397}, number = {}, pages = {128261}, doi = {10.1016/j.jenvman.2025.128261}, pmid = {41391222}, issn = {1095-8630}, abstract = {Wildfires are intensifying under climate change and increasingly compromising the resilience of Mediterranean ecosystems. Soil restoration through organic amendments has been proposed as an effective tool to mitigate soil degradation after fires, yet there is limited knowledge on how different typologies of organic amendments influence soil microbial communities and the recovery of microbial-mediated functions. This study evaluated contrasting organic amendments-straw mulch, compost, and fresh swine and poultry manures-on soil microbial diversity and enzymatic activity in burned native sclerophyllous, Mediterranean forest in central Chile, the earliest in its type experiencing effects of climate change. The study took place six months after amendment application and two years after a wildfire occurrence. Enzyme activities showed different responses according to organic amendments type: while manures strongly stimulate enzymes (urease, glucosidase, and phosphatase activities), compost and mulch promoted a gradual effect on nutrient cycling. Fungal biomass, reduced by fire, recovered best under compost and swine manure. However, organic amendments significantly reduced eukaryotic alpha diversity and differentiated communities from unburned soils and burned soils with no amendment. In contrast, only manures reduced alpha diversity in prokaryotes, while beta diversity analyses revealed that compost amended soils maintained communities closer to reference conditions. Overall, manures provided short-term functional improvements in burned soils, but compost supported a more balanced recovery, preserving microbial communities closer to unburned soils. Therefore, the compost amendment can represent a practical and ecologically safer strategy to accelerate post-fire soil restoration. Targeted application, for example through "fertile islands" in the most degraded areas, may enhance soil resilience while minimizing ecological risks in fire-sensitive landscapes.}, }
@article {pmid41389787, year = {2025}, author = {Pei, J and Gong, J and Liu, Z and Jin, W and Hou, M and Abd El-Aty, AM and Deng, Q}, title = {High-throughput sequencing reveals microbial transitions in refrigerated sturgeon meat: Implications for quality assurance.}, journal = {International journal of food microbiology}, volume = {448}, number = {}, pages = {111542}, doi = {10.1016/j.ijfoodmicro.2025.111542}, pmid = {41389787}, issn = {1879-3460}, abstract = {This study investigated the microbially driven spoilage mechanism of sturgeon (Acipenser baerii) under refrigerated (4 °C) aerobic storage. High-throughput sequencing analysis revealed that Pseudomonas and Shewanella dominated late-stage spoilage, which was strongly positively correlated with volatile base nitrogen (VBN) accumulation and microbial metabolic shifts toward amino acid degradation pathways. By applying machine learning (random forest coupled with SHAP analysis, AUROC = 0.96) and graph neural networks (GAT, recall = 89.7 %), we pinpointed key spoilage-associated taxa and their interaction dynamics. Furthermore, numerous chemical descriptors have revealed that spoilage-associated enzymes present elevated molecular electrostatic potential (MEPs >25 kcal/mol), which facilitates the nucleophilic attack of amino acids and accelerates spoilage reactions. Time series forecasting (multivariate Prophet model) accurately predicted critical spoilage thresholds (96.5 ± 4.2 h postprocessing) with high accuracy (MAPE = 12.3 %). Additionally, metabolic modeling has demonstrated microbial cold-adapted energy strategies, including a significant increase in succinate fermentation flux (3.8 ± 0.5 mmol·g[-1] DW·h[-1]) and the suppression of TCA cycle activity. This study establishes a multiscale framework linking microbial ecology, enzymatic quantum mechanics, and metabolic dynamics, offering mechanistic insight into spoilage and providing a foundation for precise sturgeon preservation strategies in cold chain logistics.}, }
@article {pmid41389460, year = {2025}, author = {Balaberda, AL and Escolástico-Ortiz, D and Martineau, C and Heshka, NE and Lindsay, MBJ and Degenhardt, D}, title = {Biogeochemical characterization of froth treatment tailings.}, journal = {Chemosphere}, volume = {394}, number = {}, pages = {144800}, doi = {10.1016/j.chemosphere.2025.144800}, pmid = {41389460}, issn = {1879-1298}, abstract = {Froth treatment tailings (FTT) are byproducts of bitumen extraction at oil sands mines in northern Alberta. Produced during froth treatment, where diluent such as naphtha is added to separate bitumen from water and solids, FTT contain residual hydrocarbons and sulfide minerals like pyrite, potentially posing reclamation challenges. This study investigated the spatial and vertical distribution of hydrocarbons and microbial communities across a transect of an FTT deposit at Syncrude's Mildred Lake Settling Basin. Residual naphtha and petroleum hydrocarbon (PHC) concentrations reflected deposition history, with higher concentrations near the pond and in deeper, older tailings at the dyke. Microbial diversity was lower in FTT than in underlying coarse tailings, with the lowest diversity observed at ∼30 m depth, likely due to moderate to high PHC concentrations, anoxic conditions, and nutrient limitations. Microbial community composition varied with depth, material type, and location, and FTT were enriched in taxa involved in hydrocarbon degradation (Pseudomonas), sulfur cycling (Thiobacillus, Desulfovibrio, Desulfotomaculales), and methanogenesis (Methanosaeta). Among hydrocarbons, toluene and ethylbenzene were strong predictors of microbial variation. Pyrite content also emerged as an important driver, likely due to its role in redox processes. These results highlight the close links between residual diluent, tailings geochemistry, and microbial ecology, emphasizing the importance of accurate FTT characterization to support closure landform design and inform future reclamation monitoring.}, }
@article {pmid41389450, year = {2025}, author = {Mittal, A and Sharma, S}, title = {Gut microbiota and nutritional interventions in alcohol-associated liver disease: Mechanisms and therapeutic advances.}, journal = {Nutrition research (New York, N.Y.)}, volume = {145}, number = {}, pages = {8-24}, doi = {10.1016/j.nutres.2025.11.004}, pmid = {41389450}, issn = {1879-0739}, abstract = {Alcohol-associated liver disease (ALD) is a leading cause of liver-related morbidity and mortality worldwide. Despite growing awareness of its burden, treatment options remain limited, with abstinence as the only widely accepted intervention. Recent research underscores the critical role of the gut-liver axis and nutritional status, particularly dietary protein, in modulating ALD pathogenesis and progression. This review aims to integrate current knowledge on the interplay between gut microbiota, dietary protein, and alcohol-induced liver injury, and to evaluate microbiota-targeted therapeutic strategies, including fecal microbiota transplantation (FMT), within this context. We examine how chronic alcohol intake reshapes the gut microbiome, impairs barrier function, and alters microbial metabolism. We discuss how dietary protein, based on source, quantity, and amino acid composition, influences microbial ecology and metabolite profiles, with plant and dairy proteins emerging as beneficial. The review also highlights advances in FMT, which shows promise in improving outcomes in severe alcoholic hepatitis. However, its efficacy is modulated by donor microbial composition and recipient compatibility, both of which may be influenced by diet. Furthermore, we address emerging evidence on the role of fungal and viral communities, which remain understudied contributors to ALD. Despite substantial progress, significant knowledge gaps persist. These include the need for clinical validation of preclinical findings, deeper exploration of nonbacterial microbiota, and a lack of personalized, nutrition-based interventions. Addressing these gaps through integrative, multiomic approaches will be essential to advancing precision therapeutics in ALD.}, }
@article {pmid41388438, year = {2025}, author = {Chiriac, MC and Layoun, P and Fernandes, C and Szőke-Nagy, T and Kasalicky, V and Okazaki, Y and Woodhouse, JN and Grossart, HP and Piwosz, K and Znachor, P and Sonntag, B and Callieri, C and Orlić, S and Sommaruga, R and Lepère, C and Biderre-Petit, C and Tammert, H and Herlemann, DPR and Ślusarczyk, M and Bednarska, A and Banciu, HL and Zalewski, M and Woźniczka, A and Ghai, R and Salcher, MM and Haber, M}, title = {Ecological success in freshwater lakes: insights from novel cultivated lineages of the abundant Nanopelagicales order.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-025-02272-x}, pmid = {41388438}, issn = {2049-2618}, support = {24-12912M//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 22-03662S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 22-33245S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 20-12496X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 21-21990S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 022/2019/P//Grant Agency of the University of South Bohemia/ ; 017/2022/P//Grant Agency of the University of South Bohemia/ ; JPMJFR2273//JST FOREST/ ; 25K18161//Japan Society for the Promotion of Science/ ; GR1540/37-1//Leibniz-Institut f&#xfc;r Gew&#xe4;sser&#xf6;kologie und Binnenfischerei/ ; KK.01.1.1.01.0003//European Regional Development Fund - the Operational Programme Competitiveness/ ; HRZZ IP-2020-02-9021//Croatian Science Foundation/ ; 760010/30.12.2022//Ministerul Cercet&#x103;rii &#x15f;i Inov&#x103;rii/ ; }, abstract = {BACKGROUND: The order Nanopelagicales is the most abundant bacterioplankton lineage in freshwater lakes and exhibits typical streamlined genomic characteristics such as small cell volumes (<0.1 μm[3]), reduced genome sizes (<1.5 Mbp), and low GC content. These characteristics reflect adaptations to a free-living life strategy in oligotrophic environments. While many Nanopelagicales metagenome-assembled genomes and single-amplified genomes are available in public databases, strain-level microdiversity within this lineage remains poorly understood. This is mainly attributed to the incomplete nature of these genomes and the difficulty in isolating and maintaining pure cultures, with only 20 genome-sequenced cultures available to date.<br><br>RESULTS: Here, we report the isolation and genome analysis of 72 new Nanopelagicales strains, including members of Planktophila and a novel, previously uncultured genus, Aquilimus. High interspecific diversity and microdiversity were observed in the&#xa0;genus Planktophila, which likely facilitates the coexistence of closely related species within the same habitats by allowing fine-scale niche partitioning. The unusually high diversity of transporters for small organic compounds, along with carbohydrate-active enzymes, suggests that Planktophila members can degrade plant and algal polymers and import the resulting products to support growth. A notable finding is the repeated, independent loss of the oxidative phase of the pentose phosphate pathway in abundant Nanopelagicales species, which may represent an energy-saving adaptation in oligotrophic waters. Two species (Planktophila vernalis and Nanopelagicus abundans) seem to be equally abundant on a global scale, with water pH likely being the most significant factor influencing the predominance of one group over the other in different water bodies. Additionally, P. vernalis may tolerate periods of anoxia due to genomic encoding of respiratory nitrate reductase and nitrate/nitrite antiporters.<br><br>CONCLUSIONS: In conclusion, this work increased to a great degree the cultivated diversity of the abundant Nanopelagicales order. Analysis of over 1700 metagenomes showed that only a few cultivated species are globally dominant, and time-series analyses revealed consistent spring and autumn peaks. Key metabolic adaptations, such as loss of the oxidative phase of the pentose phosphate pathway and a high microdiversity of genes involved in cell surface biosynthesis and modifications, are likely to help these species survive periods of starvation and avoid predation. These findings highlight the ecological importance of Nanopelagicales and suggest that microdiversity underpins their adaptability. This work lays a foundation for studying their physiology, ecology, and strain-specific functional variation. Video Abstract.}, }
@article {pmid41388368, year = {2025}, author = {Chen, Y and Nguyen, AD and Lunjani, N and Ndhlovu, G and Kaul, D and De Pessemier, B and Nakatsuji, T and Madzinga, M and Sovershaeva, E and Hlela, C and Levin, M and Mankahla, A and Hightower, G and Callewaert, C and Knight, R and Gallo, RL and Dupont, CL and Dube, F}, title = {Environmental and skin-nasal microbiome variation in South African children with atopic dermatitis.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-025-04589-x}, pmid = {41388368}, issn = {1471-2180}, support = {HREC/REF: 451/2014/GF/NIH HHS/United States ; }, abstract = {BACKGROUND: Atopic dermatitis (AD) in early childhood is associated with microbial dysbiosis. Skin and nasal microbiomes have been linked to AD severity; this relationship has not yet been studied in an African cohort. Here, we aimed to explore how urban and rural stratification, disease severity, and inter-site bacterial overlap shape the skin and nasal microbiomes of South African children with AD.<br><br>METHODS: Children were recruited from urban Cape Town (CT) and rural Umtata (UM), South Africa. We profiled the skin and nasal microbiomes of 183 children (84 healthy controls and 99 with AD; ages 9-37 months), totaling 462 samples, including both lesional and non-lesional skin sites in children with AD, in a cross-sectional study design. Using 16S rRNA V4-V5 sequencing for its accessibility, we applied random forest (RF) models to classify AD status based on amplicon sequence variants (ASVs) and analyzed microbiome composition and diversity by region.<br><br>RESULTS: We found that RF models could predict AD status using both skin and nasal microbiomes (AUCs: skin&#x2009;=&#x2009;0.69-0.79; nasal&#x2009;=&#x2009;0.65), strongly driven by both Streptococcus and Staphylococcus. The correlations between skin and nasal microbiomes were significantly stronger in children with AD compared to controls, with higher correlations observed in rural UM (healthy r&#x2009;=&#x2009;0.45 to AD r&#x2009;=&#x2009;0.67) compared to urban CT (healthy r&#x2009;=&#x2009;0.27 to AD r&#x2009;=&#x2009;0.65). The skin microbiome diversity was higher in children from rural UM with healthy skin than in those from urban CT (p&#x2009;=&#x2009;0.004). However, children with AD in both groups showed significant alterations in their microbiome, with those in rural UM exhibiting greater beta diversity changes (p&#x2009;=&#x2009;0.001-0.002) than their urban CT counterparts (p&#x2009;=&#x2009;0.002-0.349).<br><br>CONCLUSION: In South African children with AD, skin-nasal microbiomes reflect shared reservoirs, and differences in the AD microbiome were observed between environmental regions. These findings highlight the need for geographically diverse studies incorporating skin and mucocutaneous sampling to better understand pediatric AD.}, }
@article {pmid41387715, year = {2025}, author = {Fundora, MP and Dressner, L and Calamaro, C and Brown, AM and John, AS and Keiffer, R and Alexander, N and Huang, H and Gillespie, S and Denning, PW and Sanders-Lewis, K and Bai, J}, title = {Association between the gut microbiome and neurodevelopmental outcomes in infants with congenital heart disease: A prospective cohort study.}, journal = {JPEN. Journal of parenteral and enteral nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1002/jpen.70038}, pmid = {41387715}, issn = {1941-2444}, support = {UL1-TR002378//The Imagine, Innovate and Impact (I3) Award from the Emory University School of Medicine, Georgia CTSA NIH award/ ; }, abstract = {BACKGROUND: Children with congenital heart disease are at risk for poor neurodevelopment. The gut microbiome may influence neurodevelopmental outcomes through the gut-brain axis. This study investigated the association of early-life gut microbiome with neurodevelopmental outcomes.<br><br>METHODS: A prospective cohort study was conducted in the cardiac intensive care unit. Fecal samples were collected before surgery, after surgery, and before discharge. Neurodevelopmental testing used Bayley Scales of Infant and Toddler Development between 9 and 12 months. Microbial data of the 16S ribosomal RNA V4 region were processed. Microbiome data were analyzed using Quantitative Insights Into Microbial Ecology 2 and MicrobiomeAnalyst 2.0.<br><br>RESULTS: Twenty-four patients were analyzed: 15 (62.5%) were male and 12 (50%) were White. Children with lower cognitive (Chao1 P&#x2009;=&#x2009;0.024) and language scores (Chao1 P&#x2009;=&#x2009;0.018) had lower alpha diversity; beta diversity showed marginally significant dissimilarities (Jaccard P&#x2009;=&#x2009;0.102 and P&#x2009;=&#x2009;0.051, respectively). Lower cognitive scores were associated with less Parabacteroides (P&#x2009;=&#x2009;0.031), Bacteroides (P&#x2009;=&#x2009;0.041), and Bifidobacterium (P&#x2009;=&#x2009;0.047), and lower language scores were associated with less Bifidobacterium (P&#x2009;=&#x2009;0.044) and Enterococcus (P&#x2009;=&#x2009;0.024). Lower motor scores were associated with less Rothia (P&#x2009;=&#x2009;0.017) but a higher abundance of Serratia (P&#x2009;<&#x2009;0.001), Acinetobacter (P&#x2009;=&#x2009;0.016), and Proteus (P&#x2009;=&#x2009;0.013).<br><br>CONCLUSION: Children with congenital heart disease with lower cognitive and language scores had lower diversity and less anti-inflammatory flora (eg, Bifidobacterium), whereas those with lower motor scores had a higher abundance of pro-inflammatory flora (eg, Serratia, Acinetobacter, and Proteus). Further studies are needed to understand the longitudinal effect of gut microbial dysbiosis on neurodevelopment in children with congenital heart disease.}, }
@article {pmid41387646, year = {2025}, author = {Crucitti, D and Carimi, F and Caruso, T and Pacifico, D}, title = {Microbial Allies in the Olive Canopy: Endophyte Composition, Drivers, and their Role in Plant Protection.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02676-0}, pmid = {41387646}, issn = {1432-184X}, abstract = {The olive tree (Olea europaea L.) hosts diverse endophytic microbial communities that contribute to its resilience, productivity, and adaptation to environmental stressors. Since the temperature increases caused by global climate change primarily affects the aerial part of the plant, this review synthesizes current knowledge on the diversity, composition, and ecological drivers of olive phyllosphere endophytes, with a focus on bacterial and fungal communities. We highlight the role of host-related factors-including plant genotype, organ specificity, age, and phenological stage-in shaping microbiota structure across spatial and temporal scales. Genotype consistently emerges as a major determinant of microbial composition, while leaves and twigs harbor distinct yet overlapping communities. Geographic location, environmental variables, and seasonal shifts significantly influence microbial assemblages, with closer sites often supporting more similar communities. We also discuss the impact of agricultural practices and biotic and abiotic stressors on microbiota stability and function. Notably, several cultivable taxa-including Bacillus, Paenibacillus, Pantoea, Aureobasidium, and Penicillium-exhibit antagonistic activity against key olive pathogens, underscoring their potential as biological control agents. We conclude by emphasizing the need for functional studies to elucidate the roles of keystone endophytes and to inform microbiome-based strategies for sustainable olive cultivation.}, }
@article {pmid41387206, year = {2025}, author = {Wang, Z and Li, Q and Shi, M and Leite, MFA and Chen, X and Kuramae, EE and Cordovez, V and Cao, T and Zhu, C and Zhou, L and Yu, W and Tang, Z and Peng, C and Song, X}, title = {Compartmentalized Homeostasis Drives High Bamboo Forest Productivity under Nutrient Imbalance.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e17442}, doi = {10.1002/advs.202517442}, pmid = {41387206}, issn = {2198-3844}, support = {32125027//National Natural Science Foundation of China/ ; 32361143866//National Natural Science Foundation of China/ ; 32401673//National Natural Science Foundation of China/ ; LQ23C030005//Natural Science Foundation of Zhejiang Province/ ; }, abstract = {Stoichiometric homeostasis, the ability to maintain internal nutrient balance, is central to plant fitness under soil nutrient variability. While traditionally viewed as static, emerging theory posits that it is a conditionally flexible trait, though empirical evidence is scarce. Through large-scale field investigations, nutrient additions, and data synthesis, this study shows that Moso bamboo (Phyllostachys edulis), a fast-growing plant species, employs a unique compartmentalized homeostasis strategy by decoupling nitrogen (N) and phosphorus (P) regulation across tissues. It achieves strict N:P homeostasis in leaves while allowing P flexibility in woody tissues to serve as reservoirs that buffer leaves from soil P limitation and microbial competition. This mechanism, consistently observed in bamboo across wide geographical and soil nutrient gradients, yields lower leaf N:P variability than 75 out of 91 co-occurring tree species, can be one of the critical factors for sustaining ≈25% higher annual productivity than other forests (including evergreen-broadleaf, deciduous-broadleaf, and coniferous forests). These findings reconcile classical views of stoichiometric homeostasis and plasticity by demonstrating a flexible, compartmentalized mechanism that resolves growth-stability conflicts. Recognizing such flexible strategy advances the understanding of eco-evolutionary feedbacks in ecosystem stoichiometry and improves predictions of species adaptability, nutrient cycling, and carbon sequestration under global change.}, }
@article {pmid41387111, year = {2025}, author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW}, title = {Root-driven microbiome memory enhances plant disease resistance.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2025.12.002}, pmid = {41387111}, issn = {1878-4372}, abstract = {Root-driven microbiome memory imprints biological and chemical legacies in soil, boosting plant disease resistance across generations. In a recent study, Wu et al. found flavonoids acting as key mediators, recruiting protective microbes and lowering pathogen severity beyond one crop cycle. Here, we highlight this concept, its limitations, and opportunities for sustainable disease resistance in agriculture.}, }
@article {pmid41386888, year = {2025}, author = {Wu, Q and Su, S and Han, Y and Deng, S and Wang, B and She, Y and Zhang, F}, title = {Full genome sequences of two strains of Pseudomonas stutzeri isolated from oil reservoirs and their adaptation mechanisms to harsh environments.}, journal = {Journal, genetic engineering &amp; biotechnology}, volume = {23}, number = {4}, pages = {100623}, doi = {10.1016/j.jgeb.2025.100623}, pmid = {41386888}, issn = {2090-5920}, abstract = {Pseudomonas stutzeri is a type of microorganism widely present in nature, particularly in petroleum-contaminated environments, where it exhibits a high capacity for biodegradation. In this study, two strains of Pseudomonas stutzeri 1W1-1A and DW2-1A, were isolated from oil-water samples from Dagang Oilfield and their whole genomes were sequenced. The whole genome of 1W1-1A is 4,454,378 bp in size, with a GC content of 64.23 % in its single circular chromosome; the whole genome of DW2-1A is 3,967,155 bp in size, with a GC content of 62.98 % in its single circular chromosome. Comparing these two strains with Pseudomonas sp. in the NCBI database, we counted the strains with genes related to hydrocarbon oxidation, nitrate, sulfite, and oxygen reduction in the genome and their global distribution. Genes related to hydrocarbon oxidation, nitrate, sulfite, and oxygen reduction were found in the genome, revealing the survival strategies and adaptation mechanisms of Pseudomonas in extreme oil reservoir environments, including its genomic characteristics, functional gene distribution, and tolerance to different environmental conditions. These findings enrich our understanding of the ecological adaptability and functional evolution of Pseudomonas, providing a new perspective for research in microbial ecology and environmental microbiology. The results of this study offer new strain resources and a scientific basis for microbial enhanced oil recovery (MEOR). Utilizing the hydrocarbon degradation capabilities and biosurfactant production characteristics of these strains is of great significance for microbial industrial applications such as MEOR and the remediation of petroleum-contaminated environments.}, }
@article {pmid41386516, year = {2025}, author = {Drabesch, S and Mueller, S and Leon Ninin, JM and Planer-Friedrich, B and Kappler, A and Muehe, EM}, title = {Rising temperature and atmospheric CO2 combine to antagonistically alter Cd mobility and biogeochemistry in an agricultural soil.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {127508}, doi = {10.1016/j.envpol.2025.127508}, pmid = {41386516}, issn = {1873-6424}, abstract = {Soil cadmium (Cd) contamination threatens ecosystems and crop safety. Understanding how individual climate change factors influence soil Cd bioavailability is essential for mechanistic understanding and future risk assessments. This study examined individual and combined effects of elevated temperature (+4°C) and doubled atmospheric CO2 (800 ppmv) on soil Cd bioavailability, biogeochemistry, and greenhouse gas emissions in agricultural soils with native (0.13 mg Cd kg-[1]) and high Cd (1.5 mg Cd kg[-1]). Elevated temperature increased porewater Cd up to 50% relative to ambient, while doubled atmospheric CO2 did not alter porewater Cd. Combined future conditions increased porewater Cd by 30% relative to ambient indicating an antagonistic interaction. Doubled atmospheric CO2 enhanced microbial nitrogen fixation and reduced ammonium oxidation, increasing ammonium concentrations up to 10-fold relative to ambient. Elevated temperature stimulated microbiome activity and ammonium oxidation, leading to 1.7-fold more CO2 and 5.5-fold more N2O compared to ambient, both exceeding levels observed under combined future climate. These contrasting single-factor responses highlight the non-additive nature of combined climate factor effects. Warming alone overestimated and CO2 alone underestimated the combined impact on Cd mobility and soil biogeochemistry. Simulating multiple climate drivers is therefore essential for accurate environmental prediction and sustainable Cd management under climate change.}, }
@article {pmid41385904, year = {2025}, author = {Pan, X and Elsayed, SS and van Wezel, GP and Raaijmakers, JM and Carrión, VJ}, title = {Disentangling the molecular mechanisms of disease suppression by endophytic Flavobacterium sp. 98.}, journal = {Microbiological research}, volume = {304}, number = {}, pages = {128415}, doi = {10.1016/j.micres.2025.128415}, pmid = {41385904}, issn = {1618-0623}, abstract = {Endophytic microorganisms colonize internal plant tissues and enhance host resistance to pathogens. We previously showed that endophytic Flavobacterium sp. 98 (Fl98) protects sugar beet against the fungal root pathogen Rhizoctonia solani via biosynthetic gene cluster 298 (BGC298). However, the molecular mechanisms underlying this protection remained poorly understood. Here, comparative metabolomic analyses revealed that knockout of BGC298 led to reduced production of the antifungal compound 5,6-dimethylbenzimidazole (DMB) in Fl98. We hypothesized that BGC298 is involved in regulating DMB biosynthesis and therefore contributes to Fl98's disease suppression as a novel protective mechanism. Subsequent site-directed mutagenesis of the DMB-synthase gene bluB abolished DMB production by Fl98, and both ΔBGC298 and ΔbluB mutants were compromised in protecting sugar beet seedlings in greenhouse bioassays. Bioinformatic analyses further indicated that bluB is widespread across Flavobacterium, while BGC298 is limited to a small subset of plant-associated strains. Together, our findings highlight the pivotal role of BGC298 and DMB biosynthesis in plant protection by endophytic Flavobacterium sp. 98.}, }
@article {pmid41384736, year = {2025}, author = {Madrid-Restrepo, MA and León-Inga, AM and Peñuela-Martínez, AE and Cala, MP and Reyes, A}, title = {Metagenomic, metabolomic, and sensorial characteristics of fermented Coffea arabica L. var. Castillo beans inoculated with microbial starter cultures.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0136425}, doi = {10.1128/msystems.01364-25}, pmid = {41384736}, issn = {2379-5077}, abstract = {UNLABELLED: Coffee is one of the most important and widely consumed drinks around the world, and fermentation plays a pivotal role in shaping its quality. This research explores the impact of co-fermentation with "starter cultures" on the sensory and metabolic profiles, as well as on the dynamics of microbial communities involved in coffee processing. Freshly harvested Arabica coffee beans were subjected to two wet-fermentation processes, one inoculated with a microbial starter culture and the other undergoing spontaneous fermentation. Quantitative descriptive analysis revealed that the inoculated coffee outperformed the spontaneous fermentation in all sensory attributes, boasting higher sweetness, reduced acidity and bitterness, and the presence of consumer-preferred notes. Untargeted metabolomic analysis identified over a hundred differential metabolites distinguishing both fermentation processes in green and roasted beans. Inoculated coffee displayed elevated levels of compounds such as sucrose, mannitol, methyl phenylacetate, and organic acids like malic, citric, and quinic acid, compounds likely associated with improved sensory perception. The inoculated process was characterized by shifts in the abundance of lactic acid bacteria and Kazachstania yeasts, groups linked to desirable metabolites such as lactic, acetic, isobutyric, and hexanoic acids. Our results strongly suggest that the use of starter cultures can enhance coffee beverage quality, as reflected by standardized cupping, metabolic profiles, and microbial community dynamics. Future studies should focus on disentangling microbial contributions and metabolite pathways to inform the design of commercially viable starter cultures for coffee fermentation.<br><br>IMPORTANCE: Our study demonstrates that inoculating coffee fermentation alters the sensory qualities of coffee and reshapes the dynamics of bacterial and fungal communities during this process. We identified distinct changes in microbial diversity and metabolite composition associated with inoculation, which correlated with improved sensory attributes. In addition, we detected aminophenol and phenol at higher levels in spontaneously fermented coffees, compounds that are likely responsible for phenolic defects. To our knowledge, this is the first report directly linking these compounds to defective flavor notes in coffee. Together, these findings show that inoculation not only enhances desirable flavor profiles but may also serve as a strategy to reduce the risk of cup defects by modulating the fermentation microbiota. Our work advances the understanding of community-level microbial processes in coffee fermentation and opens opportunities for developing techniques to produce coffee with unique, high-quality, and reproducible sensory characteristics.}, }
@article {pmid41383741, year = {2025}, author = {Song, J and He, Q and Cao, K and Song, X and Zeng, Q}, title = {Effects of continuous cropping on soil metabolomics and rhizosphere bacterial communities in Panax quinquefolius L.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1698779}, pmid = {41383741}, issn = {1664-302X}, abstract = {INTRODUCTION: Continuous cropping obstacles (CCOs) due to long-term monoculture have emerged as a pervasive challenge in contemporary agriculture worldwide. The practices of CCOs are the primary causes of restraining the Panax quinquefolius L. (P. quinquefolius) growth, whereas its underlying microbial mechanisms have not been fully elucidated.<br><br>METHODS: We investigated the effects of CCOs on soil physicochemical properties, enzyme activities, microbial community composition, and metabolite profiles in the rhizosphere of P. quinquefolius cultivated continuously for one, two, three, and four consecutive years (designated as CC1, CC2, CC3, and CC4, respectively) without crop rotation. Rhizosphere soil samples were collected from fields with different years of CCOs and analyzed for physicochemical properties and enzyme activities. Microbial community composition was assessed using Illumina high-throughput sequencing, and metabolite profiles were analyzed using non-targeted metabolomics (UPLC-MS/MS).<br><br>RESULTS: Significant decreases were observed in soil pH (12.2-28.0%), cation exchange capacity (42.6-65.5%), organic matter (8.7-27.3%), total nitrogen (7.6-27.8%), and ammonium (NH4 [+]) content (16.9-56.6%) with an increasing number of continuous cropping years. Enzymatic activities, including urease, invertase, alkaline phosphatase, catalase, protease, and polyphenol oxidase, were also reduced. The occurrence of CCOs decreased bacterial richness and number but increased bacterial diversity. Key microbial biomarkers were shifted from Gemmatimonadota, Actinobacteriota, and Proteobacteria to Acidobacteriota, Chloroflexi, and WPS-2 with P. quinquefolius CCOs. Consequently, the number of beneficial microorganisms decreased, whereas the number of pathogenic microorganisms increased. Non-targeted metabolomic profiling showed significant enantioselectivity in phenylpropanoid biosynthesis and pyrimidine metabolism. Time-series analysis revealed a decrease in metabolites classified as lipids and lipid-like molecules and an increase in organic acids, derivatives, phenylpropanoids, and polyketides with continuous cropping. Partial least squares-path modeling identified reduced soil enzymatic activity due to CCOs as the primary factor regulating soil bacterial communities and metabolites.<br><br>SIGNIFICANCE: These findings offer new insights into the microecological mechanisms of CCOs in P. quinquefolius, aiding in controlling pathogenic bacteria and maintaining soil health in agricultural systems.<br><br>CONCLUSION AND PROSPECTS: P. quinquefolius CCOs significantly alter soil physicochemical properties, microbial community structure, and metabolite profiles, leading to reduced soil fertility and increased prevalence of soil-borne diseases. Future research should focus on exploring sustainable agricultural practices, such as crop rotation and soil amendments, to mitigate these adverse effects and improve the long-term viability of P. quinquefolius cultivation.}, }
@article {pmid41383635, year = {2025}, author = {Zhu, W and Ni, R and Cai, B and Ma, S and Jiang, J and Wang, B}, title = {In-situ diet-microbiota associations across taxonomic scales in desert-dwelling amphibians and reptiles.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf213}, pmid = {41383635}, issn = {2730-6151}, abstract = {Understanding how host and environmental factors shape gut microbiota is central to microbial ecology and evolution. However, the extent to which gut microbes covary with diet and how such variation reflects host phylogeny, remains unclear under natural conditions. Here, we used DNA metabarcoding of gut contents to analyze the dietary arthropod composition and gut microbiota of four amphibian and three reptile species from the Tarim Desert, Xinjiang, China. These species showed pronounced differences in both diet and microbial profiles. Dominant dietary arthropod families exhibited generally low overlap among species, and dietary variation did not align with host phylogeny. Interestingly, Bufotes pewzowi (amphibian) and Teratoscincus przewalskii (reptile)-the most common species in their respective groups-both primarily consumed ants (Formicidae). Conversely, gut microbial composition more closely reflected host phylogeny than diet, with a clear separation between amphibians and reptiles, particularly in the relative abundances of Bacteroidetes and the genera Bacteroides and Blautia. These findings suggest that the previously reported phylosymbiosis in these species is not primarily driven by dietary overlap. Significant diet-microbiota correlations were observed across all species and within each taxonomic class but were largely absent within species. This highlights taxonomic-level differences in the diet-microbiota relationship, indicating that diet-microbiota covariation is more pronounced over evolutionary timescales than in response to real-time dietary variation. Taken together, our results show that gut microbiota and diet exhibit distinct phylogenetic patterns, with microbiota showing both associations with diet and resilience to short-term dietary changes, underscoring the importance of considering timescales in diet-microbiota studies.}, }
@article {pmid41381925, year = {2025}, author = {González-Villalobos, E and Aranda, A and de Almeida, ACM and Balcázar, JL}, title = {Global Transcriptomic Profiling Reveals Conserved and Phage-specific Responses to Phage Infection in Escherichia Coli.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02665-3}, pmid = {41381925}, issn = {1432-184X}, support = {792686//EU Horizon 2020 Programme (Marie Sk&#x142;odowska-Curie)/ ; }, abstract = {Although phages shape bacterial evolution and physiology, the specificity of host transcriptomic responses to phage infection remains incompletely understood. Here, we performed global transcriptomic profiling of Escherichia coli exposed to two lytic phages, ΦX174 and T4, and the temperate phage λ, to explore both conserved and phage-specific host responses. All infections induced stress-related genes, including SOS and general stress pathways, along with repression of anabolic processes such as purine and amino acid biosynthesis, suggesting a metabolic shift to conserve resources. Notably, ΦX174 strongly activated the phage shock protein operon, while both ΦX174 and λ selectively induced soxS, a regulator of oxidative stress. Despite infecting the same host, each phage triggered distinct transcriptional signatures. These findings highlight the complexity of bacterial responses and the value of transcriptomics in decoding host-phage interactions, offering insights into resistance, survival, and co-evolution.}, }
@article {pmid41381498, year = {2025}, author = {Dong, Z and Zhou, H and Cao, R and Zhang, O and Zhao, S and Lyu, P and Alcalde, R and Yang, C}, title = {Analytic Fourier ptychotomography for aberration-free and high-resolution volumetric refractive index imaging.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-025-67460-7}, pmid = {41381498}, issn = {2041-1723}, abstract = {Three-dimensional (3D) refractive index tomography offers label-free quantitative volumetric imaging. However, existing tomography approaches are limited by optical aberrations, limited resolution, and computational complexity. To overcome these issues, we propose Analytic Fourier Ptychotomography (AFP), a computational microscopy technique that analytically reconstructs aberration-free, complex-valued 3D refractive index distributions without iterative optimization or axial scanning. AFP employs a unique prior based on the finite sample thickness to recast the inverse scattering problem into analytically solvable linear equations. Unlike iterative methods, AFP does not require parameter tuning and computationally intensive optimizations, and can achieve efficient, robust, and generalizable image reconstructions across diverse samples and systems. We experimentally demonstrated that AFP greatly enhanced image quality and resolution under various aberration conditions across a range of applications. AFP corrected aberrations associated with 25 Zernike modes (with maximal phase difference of 2.3π and maximal Zernike coefficient value of 4), extended the synthetic numerical aperture from 0.41 to 0.99, and provided a two-fold resolution enhancement in all directions. With its simplicity, robustness, and broad applicability, AFP offers a user-friendly imaging platform for quantitative 3D analysis in biology, microbial ecology, and clinical science.}, }
@article {pmid41378987, year = {2025}, author = {Niu, S and Al, MA and Zhang, D and Ming, Y and Liu, H and Zhu, W and Li, M and Yu, X and Niu, M and Wu, K and Xie, W and He, Z and Yan, Q}, title = {Assembly and interactions of denitrifying and anammox communities in a typical eutrophic lake.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnaf139}, pmid = {41378987}, issn = {1574-6968}, abstract = {Nitrogen removal is crucial for controlling nitrogen levels in eutrophic lakes and depends on the high transformation capacity of nitrogen-cycling microorganisms. However, the assembly mechanisms and interactions of nitrogen removal microbial communities in lake water remain unclear. This study aimed to clarify how nitrogen levels influence the diversity, interactions, and assembly of denitrifying and anaerobic ammonia oxidation (anammox) communities. We collected lake water from different areas in a typical eutrophic lake and investigated the nitrogen removal bacterial communities by high-throughput sequencing of two representative functional genes (nirS and hzsB). Our results indicated that the α-diversity of anammox bacteria was higher in sites with high concentration of nitrogen (> 1.5 mg/L) than in sites with low concentration of nitrogen (< 1.5 mg/L). Anammox bacteria in high-nitrogen sites were dominated by the potential keystone taxon Candidatus Brocadia. Co-occurrence network analysis revealed that low-nitrogen sites had more negative connections between denitrifying and anammox communities. Moreover, total nitrogen and electrical conductivity were key factors determining community structure. Microbial community assembly analysis indicated that both denitrifying and anammox communities were primarily governed by stochastic processes across different nitrogen levels. This study enhanced our understanding of microbial community dynamics in nitrogen removal processes in eutrophic lakes.}, }
@article {pmid41377758, year = {2026}, author = {Benjamin, K and Yuan, Q and Boyer, J}, title = {Increased gut Saccharomyces and decreased pathogenic fungi associated with food protein-induced enterocolitis syndrome resolution.}, journal = {The journal of allergy and clinical immunology. Global}, volume = {5}, number = {1}, pages = {100598}, pmid = {41377758}, issn = {2772-8293}, abstract = {BACKGROUND: Food protein-induced enterocolitis syndrome (FPIES) is a non-IgE-mediated allergy, primarily affecting infants and children, with potentially severe gastrointestinal impacts. As with other allergic diseases, the cause of FPIES is unknown. Preliminary research suggests that the gut microbiome may play a role in FPIES, as well as other allergy, yet data on the mycobiome are limited.<br><br>OBJECTIVE: We sought to examine the role of the gut mycobiome in FPIES by comparing the stool mycobiome of children with FPIES to that of children who have outgrown FPIES.<br><br>METHODS: Caregivers of children with FPIES and children who had outgrown FPIES completed a demographic and lifestyle survey. DNA was extracted and sequenced from stool samples of 23 children with FPIES and 17 children with resolved FPIES. Fungal diversity and composition between the 2 groups were compared using QIIME2 (Quantitative Insights Into Microbial Ecology 2).<br><br>RESULTS: Children with resolved FPIES had significantly more Saccharomyces than children with current FPIES. Children with current FPIES had significantly more diverse samples and included opportunistic pathogens, such as Candida spp. Children with resolved FPIES reported significantly less infant antibiotic usage and proton pump inhibitor usage.<br><br>DISCUSSION: This study identified distinct mycobiome profiles in children with current versus resolved FPIES. Resolved FPIES was associated with Saccharomyces enrichment, whereas children with current FPIES had more diverse, opportunistic pathogen-associated communities and greater infant antibiotic and proton pump inhibitor usage. Although these associations do not establish causality, they underscore the need for larger, longitudinal studies to determine whether the mycobiome and early-life exposures influence FPIES outcomes, because it could have implications for treatment and prevention.}, }
@article {pmid41376875, year = {2026}, author = {Yadav, BNS and Sharma, P and Maurya, S and Yadav, A and Tiwari, N and Reddy, MS and Yadav, RK}, title = {Spatial and seasonal variations of active micro-eukaryotic community structure in heavy metal-contaminated soils.}, journal = {3 Biotech}, volume = {16}, number = {1}, pages = {6}, pmid = {41376875}, issn = {2190-572X}, abstract = {UNLABELLED: Heavy metal contamination of soil poses a significant hazard to the environment. However, numerous eukaryotic microbes can sustain themselves and thrive in such polluted soils, playing a pivotal role in transforming heavy metal contaminants into more stable and less toxic forms. This study employed an amplicon-based metatranscriptomic approach to investigate the active micro-eukaryotic community structure in heavy metal-contaminated soils across two locations in India, KJ (Jajmau) and UZ (Zawar Mines), during two different seasons (spring and autumn). The diversity assessment targeted the V4 hypervariable region of the 18S rRNA gene, amplified from reverse-transcribed RNA. The supergroup Opisthokonta was found to be dominant across all soil samples, constituting a significant proportion of the eukaryotic community. The microbial communities exhibited clear seasonal variation. In UZ, the genera Aplanochytrium and Colpoda dominated in spring, whereas Hypocreales prevailed in autumn. In KJ, Chlorella, Acari, and Colpoda dominated in spring, while Acari remained dominant in autumn. Regardless of seasonal or spatial fluctuations, 44 genera were found to be common across all samples. Alpha and beta diversity measures, along with hierarchical clustering, network analysis, heatmap visualization, and Principal Component Analysis (PCA), provided strong support for the variations in biodiversity and community organization across the datasets. The ecological significance of these findings lies in demonstrating how micro-eukaryotic communities reorganize spatially and seasonally to maintain resilience in contaminated soils. Such adaptive associations highlight their potential role in natural attenuation and provide a foundation for developing targeted bioremediation strategies by leveraging stress-adapted micro-eukaryotes.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04605-x.}, }
@article {pmid41373555, year = {2025}, author = {Zhang, J and Shen, J and Ji, L and Tan, P and Liu, C and Zhang, X and Ma, X}, title = {Lacticaseibacillus rhamnosus MS27 Potentially Prevents Ulcerative Colitis Through Modulation of Gut Microbiota.}, journal = {International journal of molecular sciences}, volume = {26}, number = {23}, pages = {}, doi = {10.3390/ijms262311397}, pmid = {41373555}, issn = {1422-0067}, mesh = {Animals ; *Colitis, Ulcerative/prevention &amp; control/microbiology/chemically induced ; *Gastrointestinal Microbiome/drug effects ; *Lacticaseibacillus rhamnosus/physiology/isolation &amp; purification ; *Probiotics/pharmacology/therapeutic use ; Mice ; RNA, Ribosomal, 16S/genetics ; Disease Models, Animal ; Dextran Sulfate ; Male ; }, abstract = {(1) This study explored Lacticaseibacillus rhamnosus MS27, a newly isolated strain, as a potential probiotic candidate for alleviating the onset and severity of ulcerative colitis (UC). (2) L. rhamnosus MS27 was isolated and subjected to biochemical identification, antibiotic sensitivity testing, and antibacterial activity assessment. Dextran sulfate sodium (DSS) colitis model mice were used to evaluate its alleviating effects. In this study, 16S rRNA microbiome and eukaryotes reference transcriptome analyses were conducted to investigate its impact on intestinal microbial ecology and potential molecular mechanisms. (3) L. rhamnosus MS27 exhibits high acid tolerance at pH 3.23 and maintains a high viable bacterial count for 24 h. It can utilize sucrose, lactose, maltose, inulin, esculin, salicin, and mannitol but not raffinose, and it is sensitive to carbenicillin, erythromycin, tetracycline, chloramphenicol, clindamycin, and penicillin. It effectively increases the abundance of beneficial microbes, particularly Akkermansia, Muribaculaceae, and Limosilactobacillus reuteri (p < 0.05), while significantly reducing microorganisms linked to human pathogens causing diarrhea and gastroenteritis (p < 0.05). Transcriptomic analysis demonstrated that the expression levels of Igkv16-104 and C1qtnf3 were significantly downregulated in the presence of L. rhamnosus MS27 treatment compared to DSS treatment alone (p < 0.05). Further analysis revealed significant differences in genes related to immune functions, antigen presentation, and immune cell markers, indicating potential protein-protein interaction networks, particularly among genes of the major histocompatibility complex (MHC). (4) L. rhamnosus MS27, as a novel strain, demonstrates a significant capacity to alleviate inflammatory phenotypes. L. rhamnosus MS27 exhibits distinctive metabolic characteristics in lactic acid utilization, acetic acid and oleic acid production. Furthermore, it contributes to systemic homeostasis regulation by modulating Turicibacter to link intestinal microbiota composition with host immune function.}, }
@article {pmid41373452, year = {2025}, author = {Mehelleb, D and Ghidouche, A and Baldi, S and Djoudi, F and Bertorello, S and Di Gloria, L and Ramazzotti, M and Niccolai, E and Madaoui, M and Takbou, I and Tliba, S and Amedei, A}, title = {Specific Intratumoral Microbiome Signatures in Human Glioblastoma and Meningioma: Evidence for a Gut-Brain Microbial Axis.}, journal = {International journal of molecular sciences}, volume = {26}, number = {23}, pages = {}, doi = {10.3390/ijms262311290}, pmid = {41373452}, issn = {1422-0067}, support = {THE-Tuscany Health Ecosystem-ECS00000017-CUP B83C22003920001; #NEXTGENERA-TIONEU (NGEU)//European Union/ ; National Recovery and Resilience Plan (NRRP), project MNESYS (PE0000006) - A Multiscale in-tegrated approach to the study of the nervous system in health and disease (DR. 1553 11.10.2022)//Ministero dell'universit&#xe0; e della ricerca/ ; }, mesh = {Humans ; *Meningioma/microbiology/pathology ; *Glioblastoma/microbiology/pathology ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; *Brain Neoplasms/microbiology/pathology ; *Meningeal Neoplasms/microbiology ; Aged ; Adult ; Bacteria/genetics/classification ; Case-Control Studies ; }, abstract = {Brain tumors (BTs), including glioblastoma (GBM) and meningioma (MGM), contribute significantly to the global cancer burden. The microbiome has been implicated in carcinogenesis, yet its role in BTs remains underexplored. We performed 16S rRNA gene sequencing of the gut microbiota (GM) and intratumoral microbiome (ItM) from fresh tissue samples of 9 patients with GBM and 18 with MGM. 12 age- and sex-matched healthy controls (HCs) were also enrolled. GM profiling revealed reduced alpha diversity and distinct microbial communities in BT patients versus HCs. Notably, Verrucomicrobiota and Synergistaceae were enriched, while Lachnospiraceae, Peptostreptococcaceae, and Muribacter spp. were depleted. GBM patients showed reductions in Peptostreptococcaceae and the Eubacterium hallii group, while MGM patients had increased Synergistia and Erysipelatoclostridium. Compared with MGM, GBM patients were enriched in Peptostreptococcales-Tissierellales, Coprobacillus, and Peptoniphilus but depleted in Weissella. Venn analysis revealed 176 genera shared across groups with unique taxa distinguishing tumor patients and HCs. ItM profiling revealed enrichment of Proteobacteria, Actinomycetota, and Campylobacterota in GBM, while MGM contained higher levels of Bacillota and Bacteroidota. GBM tissues harbored Burkholderia-Caballeronia-Paraburkholderia, Helicobacter, and Leifsonia, whereas MGM tissues were dominated by Bacteroides and Blautia. Notably, stool and tumor samples shared 91 genera in GBM and 105 in MGM. This study provides novel insights by (i) characterizing ItM from fresh samples, (ii) comparing ItM profiles of GBM and MGM, (iii) linking GM and ItM within the same patients, and (iv) suggesting potential clinical implications for BT management.}, }
@article {pmid41369196, year = {2025}, author = {Gundrum, J and Ramirez-Puebla, ST and Mark Welch, JL and Borisy, GG}, title = {Slicing overcomes the bacterial cell wall barrier to fluorescence in situ hybridization.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0200125}, doi = {10.1128/spectrum.02001-25}, pmid = {41369196}, issn = {2165-0497}, abstract = {UNLABELLED: Simultaneous visualization of all bacterial species in a polymicrobial biofilm by fluorescence in situ hybridization (FISH) remains a challenge because bacterial taxa respond differently to the hybridization procedure. This heterogeneity is due, in part, to the cell wall barrier of Gram-positive taxa. Enzymatic procedures required to permeabilize the cell walls of Gram-positive microbes can result in the disruption or loss of Gram-negative bacteria. Here, we demonstrate a procedure that enables the hybridization of difficult-to-hybridize bacteria while preserving the microarchitecture of all bacteria within a biofilm. The key feature of the procedure is to physically cut through the cell wall, thus allowing probe entry. We first embed the sample in a covalently crosslinked, glycol methacrylate resin to preserve the structure of the biofilm. Embedment is followed by sectioning and hybridization of material with the methacrylate still in place. We tested the procedure on common oral species, including difficult Gram-positive taxa, and found marked improvement in hybridization; both average signal intensity and homogeneity of hybridization were improved as compared to standard whole cell mount procedures. Our results confirm that the cell wall is the major barrier preventing efficient hybridization in whole mount samples. By physically overcoming the cell wall barrier, our protocol provides a universal procedure to visualize all bacteria in a polymicrobial community.<br><br>IMPORTANCE: It has long been recognized that the major barrier to efficient in situ hybridization of bacteria is the cell wall, with Gram-positive bacteria generally being the most problematic. Because enzymatic methods that facilitate hybridization of Gram-positive bacteria can result in the loss of Gram-negative bacteria, visualization of both kinds of bacteria simultaneously is often not feasible. In this study, we use embedding and sectioning to establish a universal approach for the simultaneous visualization of all bacteria within a microbial community while preserving its microarchitecture. We show that the mechanism underlying the approach is the physical slicing of the bacterial cell, thus obviating the barrier posed by the cell wall. These findings will benefit researchers within the microbiology community interested in complex microbial communities.}, }
@article {pmid41368505, year = {2025}, author = {Di Leo, D and Nilsson, E and Krinos, A and Pinhassi, J and Lundin, D}, title = {The Nextflow nf-core/metatdenovo pipeline for reproducible annotation of metatranscriptomes, and more.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e20328}, pmid = {41368505}, issn = {2167-8359}, mesh = {*Software ; Reproducibility of Results ; Workflow ; *Transcriptome ; *Computational Biology/methods ; *Molecular Sequence Annotation/methods ; *Metagenomics/methods ; }, abstract = {Metatranscriptomics-the sequencing of community RNA-has become a popular tool in microbial ecology, proving useful for both in situ surveys and experiments. However, annotating raw sequence data remains challenging for many research groups with limited computational experience. Standardized and reproducible analyses are important to enhance transparency, comparability across studies, and long-term reproducibility. To simplify metatranscriptome processing for biologists, and to promote reproducible analyses, we introduce nf-core/metatdenovo, a Nextflow-based workflow. Nextflow pipelines run on different computing platforms, from standalone systems to high-performance computing clusters and cloud platforms (e.g., AWS, Google Cloud, Azure) and use container technology such as Docker or Singularity to reproducibly provision software. Biologists can access the pipeline using either the command line or the Seqera platform, which provides a web browser-based interface to Nextflow pipelines. Collaborating with nf-core ensures high-quality, documented, reproducible workflows. Our nf-core/metatdenovo pipeline adheres to these established standards, enabling FAIR metatranscriptome de novo assembly, quantification, and annotation.}, }
@article {pmid41367422, year = {2025}, author = {Yu, H and Guo, Y and Li, J and Fu, R and Zhang, Y and Guo, W}, title = {Disruption of the gut bile acid-microbiota axis precedes severe bronchopulmonary dysplasia in preterm infants.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1705965}, pmid = {41367422}, issn = {1664-302X}, abstract = {BACKGROUND: Bronchopulmonary dysplasia (BPD) remains a major cause of morbidity in preterm infants, yet current diagnostic criteria are delayed and underlying mechanisms are incompletely defined. Evidence suggests that intestinal dysbiosis may influence pulmonary outcomes via the gut-lung axis, but the metabolic mediators of this interaction remain unclear.<br><br>METHODS: We conducted a prospective cohort study of 50 preterm infants (&#x2264; 32 weeks gestation), stratified by BPD severity at 36 weeks. Stool samples collected on postnatal day 7 underwent 16S rRNA sequencing and targeted bile acid metabolomics. Differential features were identified via multivariate statistics and LEfSe. Spearman correlation analysis explored bile acid-microbiota interactions. An interpretable machine learning model (XGBoost) incorporating bile acid and microbial features was developed and validated using five-fold cross-validation and an independent test set.<br><br>RESULTS: Infants with severe BPD showed significantly reduced levels of 16 bile acids-including primary, secondary, and sulfated species-compared to non-BPD controls. Gut microbiome &#x3b2;-diversity differed significantly among groups, with enrichment of opportunistic Proteobacteria (e.g., Brevundimonas) in severe BPD. Negative correlations were observed between depleted bile acids and enriched bacterial genera. The XGBoost model predicted BPD severity with 80% accuracy (AUC = 0.91), leveraging key features such as chenodeoxycholic acid (CDCA), hyocholic acid (HCA), and Brevundimonas.<br><br>CONCLUSIONS: Preterm infants who develop severe BPD exhibit early disruption of the bile acid-microbiota axis, characterized by reduced bile acid levels and enrichment of opportunistic taxa. Integrating these features within interpretable machine-learning models enables accurate early risk stratification and provides mechanistic insights beyond traditional inflammation-based frameworks. Validation in larger, multicenter cohorts is warranted to refine biomarker panels and explore targeted interventions that modulate bile acid signaling or microbial ecology to prevent or attenuate BPD.}, }
@article {pmid41366526, year = {2025}, author = {Zhang, Y and Zhou, J and Wu, M and Wang, Z and Zhang, N and Wang, W}, title = {Impact of Different Aquaculture Densities on the Growth Performance and Intestinal Health of Triploid Rainbow Trout (Oncorhynchus mykiss) Fry in High-altitude Environments.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02653-7}, pmid = {41366526}, issn = {1432-184X}, abstract = {The high-altitude regions of the Tibet Autonomous Region possess abundant cold-water resources, with annual average water temperatures suitable for culturing triploid rainbow trout. However, environmental challenges-including low atmospheric pressure, hypoxic water conditions, and significant diurnal temperature fluctuations-necessitate precise optimization of stocking density. Inadequate densities result in suboptimal resource utilization, whereas excessive densities induce chronic stress, leading to suppressed growth, reduced survival, and intestinal microbiota dysbiosis. Currently, research on appropriate stocking densities under these specific conditions remains limited. This study investigated the effects of stocking density on growth performance, intestinal microbiota, and tissue health of triploid rainbow trout, to identify the optimal density to support sustainable aquaculture in high-altitude plateau areas. Three stocking densities were tested over a 60-day culture period in 0.25 m[3] cylindrical tanks (radius 0.45 m, water depth 0.45 m, adjusted for internal volume): Low-Density (LD, 100 fish/barrel), Medium-Density (MD, 200 fish/barrel), and High-Density (HD, 300 fish/barrel). Results demonstrated that the final body weight (Wt) and specific growth rate (SGR) in the LD treatment were significantly higher than those in the HD group (Wt: P ≤ 0.009; SGR: P ≤ 0.019). Survival rate was also significantly greater in the LD treatment compared to HD (P < 0.036), with values of 84.67%, 80.83%, and 72.67% for LD, MD, and HD, respectively. Alpha diversity of both water and gut microbial communities varied with stocking density. Principal component analysis (PCA) revealed differentiated clustering of microbial communities in water and the intestine across density treatments (Water: P = 0.35; intestinal microbiota: P = 0.7). The dominant phyla in aquatic and intestinal microbiomes were Proteobacteria, Firmicutes, and Bacteroidetes. In intestinal samples, the genus Pseudomonas was significantly more abundant in the HD and MD treatments than in the LD treatment. Co-occurrence network analysis revealed a higher average degree in LD and MD treatments, suggesting enhanced stability of microbial ecosystems in both the intestine and water under these conditions. In conclusion, low and medium stocking densities are more suitable for cultivating triploid rainbow trout in high-altitude plateau environments. These findings provide a scientific basis for ecologically sound, efficient, and healthy aquaculture practices for this species in alpine regions.}, }
@article {pmid41365804, year = {2025}, author = {Thompson, AR and Adams, BJ and Hogg, ID and Yooseph, S}, title = {Evidence for Trace Gas Metabolism and Widespread Antibiotic Synthesis in an Abiotically Driven, Antarctic Soil Ecosystem.}, journal = {Environmental microbiology reports}, volume = {17}, number = {6}, pages = {e70249}, doi = {10.1111/1758-2229.70249}, pmid = {41365804}, issn = {1758-2229}, support = {ANT 2133685//National Science Foundation/ ; OPP-2224760//National Science Foundation/ ; DBI-2400009//National Science Foundation/ ; OAC-2408259//National Science Foundation/ ; OPP-1043681//National Science Foundation/ ; OPP-1559691//National Science Foundation/ ; OPP-2129685//National Science Foundation/ ; //Antarctica New Zealand (Event K024)/ ; //New Zealand Antarctic Research Institute (Event K024)/ ; //Monte L. Bean Life Science Museum, the Department of Biology, Brigham Young University/ ; //Kravis Department of Integrated Sciences, Claremont McKenna College/ ; }, mesh = {Antarctic Regions ; *Soil Microbiology ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Metagenome ; *Anti-Bacterial Agents/biosynthesis ; Ecosystem ; Soil/chemistry ; *Gases/metabolism ; }, abstract = {The McMurdo Dry Valleys (MDVs) of Antarctica are a uniquely pristine, low-biodiversity model system for understanding fundamental ecological phenomena, the impact of a warming climate on ecosystem functioning, community structure and composition and the dynamics of adaptation. Despite the scientific value of this system, we still know little about the functional ecology of its biota, especially the bacteria. Here, we analysed the bacterial taxonomic and functional diversity of 18 shotgun metagenomes using the VEBA metagenome processing pipeline. We recovered 701 medium-to-high quality metagenome-assembled genomes (MAGs) (≥ 50% completeness and contamination < 10%) and 201 high-quality MAGs (≥ 80% completeness and < 10% contamination), almost 50% more than found in similar sites previously. We found that: (1) community composition shifts along environmental gradients correlated with soil moisture, elevation and distance to the coast; (2) many MDV bacteria are capable of performing trace gas metabolism; (3) genes associated with antibiotic-mediated competitive interactions (e.g., antibiotic biosynthesis and antibiotic resistance genes) are widespread; and (4) MDV bacteria employ survival strategies common to bacteria in similarly extreme environments. This study provides novel insight into microbial survival strategies in extreme environments and lays the groundwork for a more comprehensive understanding of the autecology of MDV bacteria.}, }
@article {pmid41364266, year = {2025}, author = {Carrasco, N and Miranda, MH and Aristimuño Ficoseco, C and Nader-Macías, MEF and LeBlanc, JG}, title = {Lactic acid bacteria: potentials in canine formulas for puppies.}, journal = {Veterinary research communications}, volume = {50}, number = {1}, pages = {70}, pmid = {41364266}, issn = {1573-7446}, support = {PICT 2018-00473//MINCYT-ANPCYT:/ ; 2019-00942 and 2021-00071//Mincyt-Anpcyt/ ; }, mesh = {Animals ; Dogs/microbiology ; *Probiotics ; *Animal Feed/microbiology/analysis ; *Lactobacillales/physiology ; }, abstract = {The use of probiotics and natural nutraceuticals with demonstrated therapeutic effects for companion animals is becoming increasingly popular in the veterinary community. Probiotics are alternative to antibiotics, which produce adverse effects, such as promoting bacterial resistance and altering the intestinal microbial ecology and in turn affecting the animal's health. In this study, the in vitro safety and technological characteristics of previously isolated beneficial canine strains were evaluated for the design of a probiotic formulation for dogs. The screening of inhibitory substances production was performed in 100 isolates by plate diffusion technique. 30 strains were pre-selected to evaluate their in vitro safety and innocuity by phenotypic and genotypic antibiotic resistance and expression of pathogenicity enzymes related to virulence factors. Finally, 10 were selected to assay their tolerance to gastrointestinal conditions and stress situations such as high temperatures and solute concentrations by microplate assays. Compatibility between the selected strains was also determined in order to include them in a probiotic multi-strain formulation for canines. According to the results obtained, some strains showed inhibitory activity against common pathogens, and 38% were able to produce H2O2. Antibiotic resistance genes were detected in only one of the selected strains, none evidenced gelatinase or lecithinase activity and most isolates showed alpha and gamma hemolysis. Resistance to gastrointestinal tract and stress conditions was strain dependent. The compatible strains with complementary beneficial characteristics were: Lactobacillus johnsonii 67, Lactiplantibacillus plantarum 74, Ligilactobacillus salivarius 84 and Pediococcus acidilactici 81 and are being included in the design of a probiotic formulas to be evaluated in small dogs.}, }
@article {pmid41364243, year = {2025}, author = {Xie, T and Lin, Y and Jia, P and Li, X}, title = {Warming Promotes Deterministic Assembly of Bacterial and Fungal Communities in Drylands.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02668-0}, pmid = {41364243}, issn = {1432-184X}, support = {32061123006//National Natural Science Foundation of China/ ; }, abstract = {Warming is altering the functioning of desert ecosystems in global drylands. Microbial communities are crucial for maintaining these ecosystems, yet how their co-occurrence networks and assembly mechanisms respond to warming remains unclear. Using 16 S and ITS rRNA amplicon sequencing, we examined bacterial and fungal community composition and structure. Further, we investigated cross-trophic bacterial-fungal interactions via inter-domain ecological network analysis. Warming significantly altered the diversity, composition, and structure of both bacterial and fungal communities. It increased bacterial network complexity but simplified the fungal network. Notably, warming enhanced cross-trophic interactions between bacteria and fungi, facilitating the maintenance of microbial hierarchical interactions, particularly bacterial network complexity. However, microbial keystone taxa declined dramatically under warming, 41.18% of these belonged to Ascomycota. Neutral community models and normalized stochastic ratio-based analyses revealed that deterministic processes dominated community assembly, with warming increasing their relative importance by 8-46%. This suggests a potential deterministic environmental filtering induced by warming. Collectively, these findings advance our understanding of the ecological mechanisms and microbial interactions underpinning rhizospheric communities in drylands under future climate change.}, }
@article {pmid41363836, year = {2025}, author = {Wang, B and Zhang, J and Zhu, X and Wang, Y and Teng, HH}, title = {Mineral substrates as evolutionary drivers of soil microbial diversity through the rare biosphere.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0201125}, doi = {10.1128/aem.02011-25}, pmid = {41363836}, issn = {1098-5336}, abstract = {UNLABELLED: Minerals are fundamental yet underappreciated drivers of microbial ecology. Traditionally viewed as passive nutrient sources or inert scaffolds, their broader ecological roles remain poorly defined. This study investigates the evolutionary influence of substrates (minerals and rocks) on soil bacterial communities through serial passage evolution experiments. Soil-derived microbial consortia from three distinct locations were exposed to nutritive (olivine, granite, diorite) and non-nutritive (quartz, kaolinite, montmorillonite) substrates under nutrient-rich conditions to isolate substrate-specific effects. Results revealed systemic variations of community structure across all treatments, characterized by elevated Firmicutes/Bacteroidetes ratio and taxonomic changes predominantly driven by rare taxa. These discoveries indicate that, under the influence of substrates, the communities shifted toward ones that preferentially utilize more labile carbon. Crucially, the acute responsiveness of rare taxa to mineral-induced environmental selection suggests that, although abundant taxa appeared to maintain core community functions, the rare biosphere facilitated niche specialization and functional diversification. These findings position minerals as dynamic drivers of microbial ecology and evolution, highlighting the mineralosphere as a critical microhabitat where abiotic properties govern biodiversity, functional redundancy, and evolutionary innovation in soil ecosystems.<br><br>IMPORTANCE: Even under nutrient-rich conditions, non-nutritive and chemically inert minerals, exemplified by quartz, actively reshape microbial community assembly. Through controlled serial-passage experiments, we show that distinct substrates selectively enrich rare biosphere members that expand functional potential and seed adaptation, while dominant taxa sustain core processes. These results reveal that mineral surface properties and physical interfaces, rather than nutrient supply, govern microbial diversification and evolutionary trajectories. Accordingly, the mineralosphere emerges as a dynamic microhabitat where abiotic complexity regulates biodiversity, metabolism, and long-term community succession. This reframes minerals and rocks as active ecological and evolutionary agents, bridging geomicrobiology and evolutionary ecology, with implications for soil health, biogeochemical cycling, and the origin and maintenance of microbial diversity.}, }
@article {pmid41363449, year = {2025}, author = {Meyer, KM and Lindow, SE}, title = {Microbial dispersal from surrounding vegetation influences phyllosphere microbiome assembly of corn and soybean.}, journal = {mBio}, volume = {}, number = {}, pages = {e0333525}, doi = {10.1128/mbio.03335-25}, pmid = {41363449}, issn = {2150-7511}, abstract = {Non-crop plants surrounding agricultural fields provide numerous ecological services to crops but have rarely been considered a source of microorganisms during the early stages of crop growth. In this study, we test whether crops in close proximity to surrounding woodland habitat fragments develop a denser microbiome that more closely resembles the microbiome composition of the surrounding vegetation than plants farther away. We sampled epiphytic bacteria from corn and soybean plants weekly for 4 (corn) and 3 (soybean) weeks during early development using a spatially explicit design, and on the final time point, we sampled additional cohorts of younger leaves. To contextualize the source strength of the surrounding vegetation, we also sampled soil at each sampling location. Both crop species exhibited a microbiome density gradient and a decay of microbiome similarity to the surrounding vegetation over a distance of 100 m from the vegetation at many time points. Phyllosphere microbiome similarity to the soil tended to increase into the field interior. The strength of host microbiome filtering also depended on the proximity to the surrounding vegetation, with intermediate to most distant locations exhibiting the highest values of host filtering. Last, the microbiomes of younger leaves tended to more closely resemble those of the older surrounding conspecific leaves than the soil or surrounding woodland vegetation. Overall, our study demonstrates that dispersal of bacteria from nearby leaves can shape the abundance and composition of developing crop phyllosphere microbiomes and highlights the diminishing role that soil plays when plant sources are closer or more abundant.IMPORTANCEA central concern in microbial ecology is understanding the sources of microbial colonists and how proximity to such sources impacts community assembly. This area of research is especially important for plants during early stages of development, where the arrival of leaf-specialized bacteria plays an influential role in priming plant immunity and consequently promoting disease resistance. In this study, we test the effect of dispersal from surrounding vegetation on the phyllosphere assembly of corn and soybean using a time series over the early stages of growth. Our work demonstrates that at these early developmental stages, non-crop vegetation surrounding croplands acts as a meaningful source of phyllosphere microorganisms. We further show that the influence of soil on the phyllosphere depends on host proximity to surrounding vegetation and that microbiomes of young leaves emerging on more mature plants tend to be more influenced by older surrounding crop leaves than soil or non-crop leaves.}, }
@article {pmid41359884, year = {2025}, author = {Zhang, Q and Zhou, Z and Cheung, YM and Yeung, HW and Li, M and He, C and Tian, XY and Li, C and Wong, WT}, title = {Hydroxylation-Driven Microbial and Metabolic Reshaping: Coumarin Derivatives as Novel Prebiotics for Aging Gut Health.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c10344}, pmid = {41359884}, issn = {1520-5118}, abstract = {This study aimed to investigate the therapeutic potential of three naturally occurring coumarin derivatives─coumarin, umbelliferone, and esculetin, which exhibit distinct hydroxylation patterns in mitigating age-related gut dysbiosis through in vitro colonic fermentation models. By integrating antioxidant profiling, short-chain fatty acid (SCFA) profiling, 16S rRNA sequencing, and metabolomics, we assessed their structural specificity in modulating microbial ecology and metabolic pathways. Results demonstrated a hydroxylation-dependent hierarchy in antioxidant capacity and differential regulation of SCFA production. Coumarin partially enriched g__Turicimonas but showed limited SCFA induction, whereas umbelliferone selectively enhanced butyrate synthesis and enriched g__Bacteroides. Esculetin exhibited the broadest impact, characterized by both increased acetate and propionate levels and the concurrent enrichment of g__Ileibacterium and g__Enterococcus. Metabolomic profiling further revealed that three coumarins released antioxidant metabolites, correlating with microbiota-driven detoxification. These findings highlight hydroxylated coumarins as promising prebiotics that counter age-related dysbiosis via multitarget microbiota-metabolite modulation, providing a mechanistic basis for antiaging strategies.}, }
@article {pmid41359033, year = {2025}, author = {ElKhouri-Vidarte, N and Useros, F and Lara, E}, title = {Beneath the Cedars: Exploring the Water-Energy Balance on Arcellinida Biodiversity in Lebanon's Cedar Forests.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02666-2}, pmid = {41359033}, issn = {1432-184X}, abstract = {The distribution of diversity in function of climate has been largely studied in plants and animals, leading to a large body of literature on macroecological rules applied to large geographic scales. However, the applicability of these rules to microbes has almost never been tested at local scales. Arcellinida are a diverse group of protists known to be narrow ecological specialists and constitute therefore an excellent group to test general rules validated on "macrobes", like the water-energy balance that stipulates that biodiversity peaks with humidity and temperature. In order to test that hypothesis, we collected 122 samples from four cedar forests situated along an elevation gradient in Lebanon, spanning different local climates. We evaluated their diversity using an Arcellinida-specific metabarcoding approach based on the cytochrome oxidase subunit I gene. Our study shows that Arcellinida richness and phylogenetic diversity follow a unimodal distribution, peaking at mid-elevations. β-diversity was chiefly the product of turnover, illustrating the high spatial heterogeneity of the forests. Precipitation and actual evapotranspiration were identified as key drivers of diversity, thus supporting the water-energy balance hypothesis. Communities situated at higher or lower elevation were, to a large extent, subsets of more diverse mid-elevation assemblages, which designates the latter as biodiversity sources. These results suggest that, under the increasing aridification of the Middle East due to climate change, Arcellinida communities will lose diversity and will undergo a process of homogenisation, with possible consequences on ecosystem functioning.}, }
@article {pmid41358850, year = {2025}, author = {Winther-Have, CS and Rasmussen, JA and Zhai, X and Nielsen, DS and Sicheritz-Pontén, T and Gopalakrishnan, S and Clokie, MRJ and Middelboe, M and Limborg, MT}, title = {Ecological strategies of bacteria shape inherent phage diversity in Atlantic salmon gut microbiomes.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf272}, pmid = {41358850}, issn = {1751-7370}, abstract = {Understanding host-specific phage diversity is essential for deciphering the complex dynamics shaping microbial ecology and evolution. However, the lack of inherent host associations between uncultivated bacteria and their viruses remains a major limitation to understanding the drivers of viral diversity and its role in bacterial ecology, particularly given the intricate specificity of phage-host interactions. The naturally low complexity of the gut microbiota within piscivorous fish, such as Atlantic salmon (Salmo salar), makes it a valuable model for unravelling ecological patterns of viral diversity in the context of a limited bacterial species composition, and to explore the impact of an invading pathogen on the "steady-state" viral community. The intestinal microbiota of the salmon studied here, was in some cases dominated by a salmon-associated Mycoplasma or increasing levels of an opportunistic Aliivibrio, the latter observed in response to a disease outbreak. The two bacteria are distinctively different in their ecological strategies and their overall genomic and functional properties. A pronounced difference was observed in the gut viral communities and diversity, depending on whether it was dominated by a commensal or an invading bacterial species. Samples dominated by Mycoplasma sp. had few to no viruses, whereas samples dominated by Aliivibrio sp. had viral communities comprising up to 22 viral taxonomic operational units. This study provides unique insights into the significance of bacterial ecological trade-offs linked to niche adaptation and how these affect the associated viral communities in a natural host-controlled environment.}, }
@article {pmid41358825, year = {2025}, author = {Kumar, C and Bertani, I and Chaouachi, M and Myers, MP and Garbeva, P and Bez, C and Venturi, V}, title = {AHL quorum sensing regulates T6SS and volatiles production in rice root-colonizing Enterobacter asburiae AG129.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf120}, pmid = {41358825}, issn = {1574-6941}, abstract = {Pseudomonadota (formerly Proteobacteria) commonly use a contact independent cell-cell communication system known as quorum sensing (QS) mediated by N-acyl-homoserine lactone (AHL) signal molecules. The canonical AHL QS system involves a luxI-family gene which encodes an AHL synthase, and a luxR-family gene, which encodes a transcriptional regulator responsive to the cognate AHL(s). This study involves the AHL QS system of Enterobacter asburiae AG129, a root associated strain isolated from rice (Oryza sativa). E. asburiae AG129 produces the N-butanoyl homoserine lactone (C4-AHL) signal molecule. Genome sequencing of strain AG129 revealed the presence of a canonical AHL QS system, comprising genetically adjacent easI-like and easR-like genes. A genomic easI knockout mutant was no longer able to produce AHLs, but the in-trans complementation with a plasmid carrying the easI gene restored the AHL production. QS mediated by AHLs in AG129 was found to influence rice root colonization, and secretome analysis highlighted a significant regulatory role in the expression of Type VI secretion system (T6SS) proteins. GC-MS analysis identified sixteen volatile organic compounds (VOCs) that were more abundantly emitted by the wild-type strain compared to the easI mutant. Overall, our findings suggest that AHL-based QS in E. asburiae AG129 positively regulates T6SS expression and VOC production, while negatively affecting root colonization. This study is among the first to explore the role of QS signaling in a bacterial root-endophyte, providing evidence of a connection between QS activity and the ability of the bacterium to inhabit, compete and colonize the plant endosphere.}, }
@article {pmid41358465, year = {2025}, author = {Tang, X and Wang, R and Yang, S and Wang, G and Luo, J and Peng, S and Liang, K and Yang, J}, title = {Species-Specific Antibacterial Materials: From Design to Application.}, journal = {Small (Weinheim an der Bergstrasse, Germany)}, volume = {}, number = {}, pages = {e07114}, doi = {10.1002/smll.202507114}, pmid = {41358465}, issn = {1613-6829}, support = {SKLOD-2025RD002//State Key Laboratory of Oral Diseases/ ; 2023YFSY0048//Sichuan Science and Technology Program/ ; 82170949//National Natural Science Foundation of China/ ; 82270970//National Natural Science Foundation of China/ ; 82470967//National Natural Science Foundation of China/ ; 51903169//National Natural Science Foundation of China/ ; }, abstract = {Traditional broad-spectrum antibacterial strategies are known to contribute to the increase in drug-resistant microorganisms and the disruption of microbial ecological balance. To break this stalemate, researchers have begun to explore selective antibacterial strategies that minimize the impact on normal flora and maintain microbial ecological balance. Species-specific antibacterial materials, which can target particular bacterial species or even specific strains, offer innovative perspectives and methodologies for the prevention and treatment of infectious diseases. This review first explores the selective mechanisms that underpin species-specific antibacterial strategies, summarizes the main classifications of species-specific antibacterial strategies, investigates the engineering techniques employed in the development of such materials, and emphasizes the importance of structure-activity relationships in the design of species-specific antibacterial materials. It explores techniques like peptide modification, nanoparticle engineering, and genetic manipulation, highlighting that a thorough understanding of the structure and function of antibacterial materials is essential for improving their efficacy and specificity. Ultimately, it anticipates the potential applications of species-specific antibacterial materials in disease diagnosis and treatment, while addressing the challenges associated with clinical translation. It is expected that this comprehensive review will offer novel perspectives for the development of species-specific antibacterial materials.}, }
@article {pmid41358355, year = {2025}, author = {Shen, S and Xu, Y and Liu, Z and Luo, Y and Wang, R and Li, G and Liu, Y}, title = {Combined application of biochar and halophyte intercropping enhances cucumber yield and quality by ameliorating soil properties in a continuous cropping system.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1711099}, pmid = {41358355}, issn = {1664-462X}, abstract = {Biochar amendment and halophyte intercropping are viable strategies for alleviating soil degradation in greenhouse systems, specifically the secondary salinization and autotoxicity induced by continuous cropping. Nevertheless, the potential synergistic effects of combining these practices remain poorly understood. This study investigated their synergistic effects on soil properties, microbial communities, and cucumber performance. A pot experiment was conducted with the following treatments: soil without amendment (CK), biochar (B), Paspalum vaginatum intercropping (S), and biochar combined with Paspalum vaginatum intercropping. The results showed that BS treatment led to the highest increases in soil organic carbon content, pH, total nitrogen content, available phosphorus content, and available potassium content compared to CK (p<0.05). Concurrently, BS significantly reduced available nitrogen, electrical conductivity, Na[+], SO4 [2-], and Cl[-] levels, while total phosphorus remained unaffected. Cucumber yield increased significantly by 11.50% and 27.12% under B and BS treatments, respectively, whereas S showed no significant effect. BS also achieved the highest fruit quality enhancement, followed by B and S. Notably, B and S treatments displayed the highest and lowest K[+], Ca[2+]and Mg[2+] accumulation, respectively, whereas the BS treatment led to K[+] and Ca[2+] concentrations that were significantly lower than those in the B treatment. Soil bacterial diversity was significantly enhanced under BS. The PLS-PM identified the alleviation of soil salinity and acidity, along with improved nutrient availability, as the primary drivers for enhanced crop performance, with soil bacterial diversity playing a secondary yet significant role. These findings suggest that biochar combined with intercropping (BS) effectively mitigates continuous cropping obstacles in greenhouse systems by synergistically improving soil health and microbial ecology.}, }
@article {pmid41358162, year = {2025}, author = {Nicolas-Asselineau, L and Speth, DR and Zeller, LM and Woodcroft, BJ and Singleton, CM and Liu, L and Dueholm, MKD and Milucka, J}, title = {Occurrence and temporal dynamics of denitrifying protist endosymbionts in the wastewater microbiome.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf209}, pmid = {41358162}, issn = {2730-6151}, abstract = {Effective wastewater treatment is of critical importance for preserving public health and protecting natural environments. Key processes in wastewater treatment, such as denitrification, are performed by a diverse community of prokaryotic and eukaryotic microbes. However, the diversity of the microbiome and the potential role of the different microbial taxa in some wastewater treatment plant setups is not fully understood. We aimed to investigate the presence and diversity of denitrifying bacteria of the candidate family Azoamicaceae that form obligate symbioses with protists in wastewater treatment plants. Our analyses showed that denitrifying endosymbionts belonging to the Ca. Azoamicus genus are present in 20%-50% of wastewater treatment plants worldwide. Time-resolved amplicon data from four Danish WWTPs showed high temporal fluctuations in the abundance and composition of the denitrifying endosymbiont community. Twelve high-quality metagenome-assembled genomes of denitrifying endosymbionts, four of which were circular, were recovered. Genome annotation showed that a newly described, globally widespread species, Ca. Azoamicus parvus, lacked a nitrous oxide reductase, suggesting that its denitrification pathway is incomplete. This observation further expands the diversity of metabolic potentials found in denitrifying endosymbionts and indicates a possible involvement of microbial eukaryote holobionts in wastewater ecosystem dynamics of nitrogen removal and greenhouse gas production.}, }
@article {pmid41357478, year = {2025}, author = {Ni, J and Tang, Y and Zhou, F and Hu, Y and Liu, L and Huang, M and Ouyang, H and Xie, C}, title = {Association between serum total cholesterol levels and Crohn's clinical disease severity: a retrospective cross-sectional study.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1708838}, pmid = {41357478}, issn = {2296-858X}, abstract = {BACKGROUND: This retrospective cross-sectional study aimed to investigate the relationship between serum total cholesterol (TC) levels and the clinical activity of Crohn's disease (CD).<br><br>METHODS: One hundred and four patients with Crohn's disease (CD) and twenty healthy volunteers were included in the analysis. Serum uric acid (SUA) levels and indicators related to lipid metabolism were measured within 1 week before undergoing endoscopic and CT enterography (CTE) examinations. Patients were divided into groups based on their Crohn's Disease Activity Index (CDAI) scores.<br><br>RESULTS: Patients were categorized into mild and moderate groups, with no patients meeting the criteria for severe CD. The serum uric acid (SUA) and triglyceride (TG) levels were similar between CD patients and the control group (p > 0.05). However, the levels of total cholesterol (TC), apolipoprotein A1 (apo A1), apolipoprotein B (apo B), high-density lipoprotein cholesterol (HDL-C), and low-density lipoprotein cholesterol (LDL-C) were higher in the control group (p < 0.05). The TC and LDL-C levels were lower in the moderate patients compared to those in mild group (p < 0.05). TC &#x2264; 3.5 mmol/L was identified as an independent risk factor for more severe disease (OR = 4.50, 95%CI 1.612-12.561, p = 0.004). TC levels were correlated to both CRP and CDAI scores negatively (p < 0.05).<br><br>CONCLUSION: TC may serve as a potential supplementary marker for clinical disease activity in CD, but further research, including longitudinal studies, is needed to confirm its reliability.}, }
@article {pmid41356477, year = {2025}, author = {Chakraborty, A and Roy, A and He, S and Castellano-Hinojosa, A and Asiegbu, FO and Coutinho, TA}, title = {Editorial: Forest microbiome: dynamics and interactions in the anthropocene era.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1729625}, pmid = {41356477}, issn = {1664-302X}, }
@article {pmid41356467, year = {2025}, author = {Castelli, L and García-Amado, MA and Rudolf, CA and Contreras, M and Espinosa-Blanco, AS and Godoy-Vitorino, F}, title = {Microbial diversity in the critically endangered Orinoco crocodile (Crocodylus intermedius): influence of body site and Helicobacter spp. on microbiota composition.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1697111}, pmid = {41356467}, issn = {1664-302X}, abstract = {INTRODUCTION: The Orinoco crocodile (Crocodylus intermedius), a critically endangered species from Colombia and Venezuela Llanos, continues to face significant threats despite existing legal protections. Understanding the microbial diversity associated with this species, particularly in captive populations, can offer valuable insights into its health status and inform conservation strategies. In this study, we characterized the bacterial microbiota of C. intermedius, focusing on the influence of body site and the presence of Helicobacter spp. on microbial diversity.<br><br>METHODS: We collected oral and cloacal samples from five captive C. intermedius individuals and analyzed their bacterial microbiota using high-throughput sequencing techniques. The study specifically investigated how microbial diversity varies by body site and how the presence of Helicobacter spp. influences community structure and composition.<br><br>RESULTS: Oral samples exhibited higher microbial diversity compared to cloacal samples. This difference is likely attributable to greater environmental exposure and dietary variation affecting the oral cavity. The presence of Helicobacter spp. was associated with a marked reduction in bacterial richness and significant shifts in community composition. Samples positive for Helicobacter spp. were notably enriched in potentially pathogenic genera, including Campylobacter and Escherichia, suggesting a dysbiotic effect on the microbiota.<br><br>DISCUSSION: Our findings indicate that both body site and Helicobacter spp. presence play significant roles in shaping the microbial communities of C. intermedius. These results have important implications for reptile health management and zoonotic disease surveillance, as dysbiosis could compromise host health and facilitate pathogen transmission. Furthermore, this study underscores the role of reptiles as potential reservoirs for Campylobacter spp. and Helicobacter spp., highlighting the need for continued research into the microbial ecology of endangered species to guide conservation strategies and inform public health policies.}, }
@article {pmid41356191, year = {2026}, author = {Xiao, Y and Li, X and Fang, Y and Guo, M and Shui, M and Zhong, G and Zhou, H and Lin, C and Sun, B and Wang, S}, title = {Berberine suppresses colon inflammation via integrated modulation of host metabolism, microbial ecology, and innate immune signaling.}, journal = {Theranostics}, volume = {16}, number = {4}, pages = {2019-2036}, pmid = {41356191}, issn = {1838-7640}, mesh = {*Berberine/pharmacology ; Animals ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Immunity, Innate/drug effects ; *Colitis/drug therapy/chemically induced/microbiology ; RNA, Ribosomal, 16S/genetics ; Mice, Inbred C57BL ; Signal Transduction/drug effects ; Metabolomics ; *Anti-Inflammatory Agents/pharmacology ; Fatty Acids, Volatile/metabolism ; Male ; Inflammation/drug therapy ; Colon/drug effects/pathology ; Single-Cell Analysis ; Disease Models, Animal ; Dextran Sulfate ; Energy Metabolism/drug effects ; Interleukin-1beta/metabolism ; }, abstract = {Background: Berberine, a natural compound with unique bioactivity, has been widely used in the treatment of gastrointestinal inflammatory diseases. Despite its well-documented anti-inflammatory properties, the system-level regulatory network underlying its multifaceted mechanisms remains poorly understood. Methods: In this study, we employed a multi-level analytical approach, integrating single-cell RNA sequencing, targeted metabolomics, 16S rRNA gene sequencing, and drug-target analysis, to elucidate the integrative effects of berberine on gut microbiota-metabolism-immune interactions. Results: Single-cell RNA sequencing revealed that berberine enhances energy metabolism in intestinal cells of DSS-induced mice, thereby maintaining normal physiological functions. Targeted metabolomics analysis of short-chain fatty acids, combined with 16S rRNA gene sequencing, demonstrated that berberine supplementation significantly increases short-chain fatty acid (SCFA) levels in the intestinal environment and selectively enriches the abundance of Akkermansia. Furthermore, single-cell RNA sequencing data indicated that berberine inhibits fibroblast-to-lymphatic transformation and suppresses the expression of interleukin-1β, leading to reduced immune activation in innate immune cells. Drug-target analysis identified shared molecular targets between berberine and various immunotherapeutic agents. Conclusion: This study provides a comprehensive understanding of berberine's multi-target mechanisms and highlights its potential as a therapeutic agent for inflammatory diseases through the modulation of gut microbiota, host metabolism, and immune responses.}, }
@article {pmid41356074, year = {2025}, author = {Tsuji, K and Yoshida, H and Saba, M and Terauchi, Y and Kawauchi, M and Honda, Y and Tanaka, C and Yoshimi, A}, title = {Hydrophobins in Bipolaris maydis do not contribute to colony hydrophobicity, but their heterologous expressions alter colony hydrophobicity in Aspergillus nidulans.}, journal = {Frontiers in fungal biology}, volume = {6}, number = {}, pages = {1604903}, pmid = {41356074}, issn = {2673-6128}, abstract = {Hydrophobins are small amphiphilic proteins secreted by filamentous fungi. These proteins confer hydrophobic properties to the hyphae and conidia. Bipolaris maydis is the causal agent of southern corn leaf blight; the biological function of its hydrophobins is not clear. In the present study, we focused on the broad function of hydrophobins in the life cycle of this fungus. We found that the B. maydis genome encodes four hydrophobins-Hyp1 of class I, and Hyp2, Hyp3 and Hyp4 of class II-and all of them are expressed. We generated single disruptants of each gene, as well as triple and quadruple disruptants. No differences were detected between the wild type and any of disruptants in mycelial growth, conidiation, stress tolerance, virulence, or sexual reproduction. The colony hydrophobicity of all disruptant strains was similar to that of the wild-type strain. Complementation of a null Aspergillus nidulans mutant of dewA, which showed a significantly reduced colony hydrophobicity, with each of the four B. maydis hydrophobin genes restored the hydrophobic phenotype, although the degree of hydrophobicity varied among them. Despite the absence of any significant phenotypic changes in the B. maydis mutants generated, results strongly suggest that all four hydrophobins have retained their function in hydrophobicity. Furthermore, the results of this study suggest that the role of hydrophobins might change depending on the fungal species.}, }
@article {pmid41355978, year = {2025}, author = {Oporto-Llerena, R and Huerto-Huánuco, R and Quispe-Hualpa, Y and Palomino-Kobayashi, LA and Soza, G and Rojas-Jaimes, J and Gonzales, P and Pollack, L and Gomez, AC and Salvador-Luján, G and Cuaresma, E and Luque, N and Casapia, M and Arteaga-Livias, K and Sáenz, Y and Pons, MJ and Ruiz, J}, title = {bla OXA-51-Negative Acinetobacter calcoaceticus-baumannii Complex as a Cause of Human Infection in Peru.}, journal = {Journal of tropical medicine}, volume = {2025}, number = {}, pages = {8851906}, pmid = {41355978}, issn = {1687-9686}, abstract = {BACKGROUND: Common identification techniques do not differentiate among members of the Acinetobacter calcoaceticus-baumannii (ACB) complex, and the presence of non-baumannii Acinetobacter is often misinterpreted. The bla OXA-51 gene is located within the chromosome of Acinetobacter baumannii. Despite its plasmid dissemination to other members of the genus, it may be considered in initial species screening. Thus, this study aimed to determine the presence of bla OXA-51-negative Acinetobacter spp. as a cause of infection in Peru.<br><br>METHODS: Two hundred ninety-eight ACB complex isolates from different regions of Peru were isolated between January 2018 and March 2024. Of these, 272 and 25 were confirmed as hospital-acquired and community infections, respectively. The presence of bla OXA-51 was determined by polymerase chain reaction, and the susceptibility levels to 12 antimicrobial agents were determined.<br><br>RESULTS: The results showed that 38 (12.7%) isolates were bla OXA-51-negative. These isolates were frequent among community infections (13/25, p < 0.0001), often causing urine infections. They showed significantly lower levels of resistance to almost all antimicrobial agents tested, and most of them were recovered from regions outside metropolitan Lima.<br><br>CONCLUSION: A relevant number of infections by non-baumannii Acinetobacter species in Peru is suggested, highlighting the need for systematic identification of these species in the country.}, }
@article {pmid41355197, year = {2025}, author = {Yi, F and Shao, L and Wu, S and Cheng, K and Zhang, Z and Li, Y and Hu, S and Wan, J and Liu, Q and Guo, L and Zhang, X and Shang, B and Yu, J and Zheng, H and Liu, J and Cai, Y and Zhang, X}, title = {Cotton gland formation genes GbCGF2/3 positively regulate Verticillium wilt resistance through modulating suberin biosynthesis.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.70809}, pmid = {41355197}, issn = {1469-8137}, support = {2022YFD1200303//National Key Research and Development Program of China/ ; 251111113800//Key Research and Development Project of Henan Province/ ; 32070262//National Natural Science Foundation of China/ ; 32401779//National Natural Science Foundation of China/ ; CB2024A16//State Key Laboratory of Cotton Bio-breeding and Integrated Utilization Open Fund/ ; CB2024A23//State Key Laboratory of Cotton Bio-breeding and Integrated Utilization Open Fund/ ; CB2023A14//State Key Laboratory of Cotton Bio-breeding and Integrated Utilization Open Fund/ ; CB2023A11//State Key Laboratory of Cotton Bio-breeding and Integrated Utilization Open Fund/ ; CB2025A26//State Key Laboratory of Cotton Bio-breeding and Integrated Utilization Open Fund/ ; 2024M760773//China Postdoctoral Science Foundation/ ; 234400510004//Project of Zhongyuan Scholars Workstation/ ; }, abstract = {Verticillium wilt, caused by Verticillium dahliae, is a serious vascular wilt disease in cotton (Gossypium spp.). However, the roles and mechanisms of cotton gland formation (CGF) genes in regulating cotton V. dahliae resistance remain elusive. Virus-induced gene silencing or CRISPR-/Cas9-mediated knockdown or knockout of GbCGF2/3 decreases cotton resistance to Verticillium wilt. RNA-sequencing (RNA-seq) shows lower transcript levels of the suberin biosynthetic gene fatty acyl-coenzyme A reductase 3.1 (FAR3.1) in GbCGF2/3-silenced cotton plants. Silencing or knocking out GbFAR3.1 impairs cotton resistance to V. dahliae and decreases suberin compositional monomer fatty acids (C16-C24) contents. GbCGF2/3 positively regulates GbFAR3.1 expression by binding to its promoter. Suberin deposition in the lamellae layer of the root cell wall decreases significantly in GbCGF2/3 Cas9-mediated knockout and GbFAR3.1-silenced cotton plants. Additionally, the expression of gossypol biosynthetic genes and defense-related genes PDF1.2 and PR4 in the phytohormone jasmonic acid (JA) pathway is also downregulated in GbCGF2/3-silenced or Cas9-mediated knockout plants. In conclusion, GbCGF2/3 positively regulates Verticillium wilt resistance through promoting suberin biosynthesis, gossypol accumulation and expression of JA signaling defense-related genes, providing a novel insight and strategy for breeding cotton cultivars resistant to Verticillium wilt.}, }
@article {pmid41353943, year = {2025}, author = {Zheng, Y and Zhou, X and Deng, S and Zhao, H}, title = {Spatial pattern of spring dissolved organic matter and microbial communities under dual anthropogenic-natural forcing in a tropical semi-enclosed bay.}, journal = {Marine environmental research}, volume = {214}, number = {}, pages = {107739}, doi = {10.1016/j.marenvres.2025.107739}, pmid = {41353943}, issn = {1879-0291}, abstract = {Coastal zones serve as vital interfaces between continental and oceanic ecosystems, where anthropogenic inputs strongly influence dissolved organic matter (DOM) and associated microbial processes. However, the response of DOM-microbe interactions to various human activities remains inadequately understood. In this study, we examined physicochemical parameters, DOM optical properties, and microbial community structures in surface waters of Zhanjiang Bay, which is influenced by agricultural runoff, sewage, and industrial effluent. This pattern could be attributed to the impact of agricultural runoff and sewage input. Nutrient-rich terrestrial inputs were associated with enhanced humic-like and protein-like fluorescent DOM (FDOM) and high-molecular-weight, aromatic chromophoric DOM (CDOM), accompanied by the enrichment of Cyanobacteria and Thermoplasmatota. In contrast, in the lower bay, industrial activities, particularly effluent from a steel plant, resulted in an increased humic-like and protein-like FDOM alongside low-aromatic CDOM. Additionally, an increase in Verrucomicrobiota and humification index indicated that DOM may undergo decomposition processes in addition to in situ production. Multivariate analyses (PCA, RDA) confirmed strong correlations between physicochemical parameters, DOM properties, and microbial community composition. Collectively, these findings demonstrate that anthropogenic activities primarily shape DOM characteristics, which in turn structure microbial communities, highlighting the cascading effects of anthropogenic activities in regulating coastal biogeochemistry. This study elucidates the mechanistic pathway through which anthropogenically altered DOM composition shapes microbial community assembly, providing insights into the coupling between DOM dynamics and microbial ecology in anthropogenically impacted coastal ecosystems.}, }
@article {pmid41353355, year = {2025}, author = {Todorović, I and Abrouk, D and Kyselková, M and Rey, M and López-Mondéjar, R and Raičević, V and Jovičić-Petrović, J and Moënne-Loccoz, Y and Muller, D}, title = {Fluorescent Pseudomonas spp. from suppressive and conducive soils share genomic and functional traits relevant to Fusarium graminearum disease suppression.}, journal = {BMC genomics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12864-025-12374-3}, pmid = {41353355}, issn = {1471-2164}, support = {grant numbers 670-00-573/1/372/2019-04, 670-00-2590/1/304/2020-04, 670-00-2551/1/298/2021-04 and 670-00-1/1/317/2022-01//Ministry of Youth and Sports, Belgrade, Serbia/ ; grant numbers 964308G, 972203C and 103939T//Campus France/ ; PHC DANUBE 2020: 45296XM//Programme for Multilateral Scientific and Technological Cooperation in the Danube Region/ ; Ministry of Education, Youth and Sports of the Czech Republic, project number 8X20052//Programme for Multilateral Scientific and Technological Cooperation in the Danube Region/ ; Ministry of Education, Youth and Sports of the Czech Republic, project number 8X20052//Programme for Multilateral Scientific and Technological Cooperation in the Danube Region/ ; The Ministry of Education, Science, and Technological Development of the Republic of Serbia, project number: 451-03-01086/2020-09/07//Programme for Multilateral Scientific and Technological Cooperation in the Danube Region/ ; PHC DANUBE 2020: 45296XM//Programme for Multilateral Scientific and Technological Cooperation in the Danube Region/ ; PHC DANUBE 2020: 45296XM//Programme for Multilateral Scientific and Technological Cooperation in the Danube Region/ ; SuppressSOIL ANR-19-EBI3-0007//BiodivERsA3 ERA-Net COFUND programme/ ; SuppressSOIL ANR-19-EBI3-0007//BiodivERsA3 ERA-Net COFUND programme/ ; SuppressSOIL ANR-19-EBI3-0007//BiodivERsA3 ERA-Net COFUND programme/ ; SuppressSOIL ANR-19-EBI3-0007//BiodivERsA3 ERA-Net COFUND programme/ ; project number CZ.02.01.01/00/22_008/0004635//the Ministry of Education, Youth and Sports of the Czech Republic/ ; The Ministry of Education, Science, and Technological Development of the Republic of Serbia, project number: 451-03-01086/2020-09/07//Programme for Multilateral Scientific and Technological Cooperation in the Danube Region, The Ministry of Education/ ; grant number 451-03-137/2025-03/200116//The Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; }, abstract = {BACKGROUND: Soils suppressive to fungal pathogens harbor microbiomes that can inhibit disease development despite the presence of virulent pathogens and susceptible hosts. Fluorescent Pseudomonas are often implicated in such suppressiveness, but their genomic determinants and distribution in suppressive vs. non-suppressive (i.e., conducive) soils remain unclear.<br><br>RESULTS: We investigated the taxonomic and functional diversity of Pseudomonas populations from wheat rhizospheres in four agricultural soils with contrasting suppressiveness to Fusarium graminearum-induced seedling disease. rpoD-based metabarcoding and culture-dependent isolation revealed distinct Pseudomonas community structures linked to soil suppressiveness. However, major phylogenetic groups were shared across soils. From 406 isolates, 29 representative strains spanning seven subgroups of the P. fluorescens group were selected for whole-genome sequencing. Comparative genomics revealed 14 putative novel Pseudomonas genomospecies (dDDH&#x2009;<&#x2009;70% with closest described type strains). Genomic screening revealed wide distribution of genes linked to biocontrol and plant-growth promotion, including siderophore biosynthesis, hormone modulation, phosphate solubilization, and production of antimicrobial compounds. Biosynthetic genes for phenazine and pyrrolnitrin were detected exclusively in P. chlororaphis strains isolated from suppressive soils, and rpoD alleles corresponding to these strains were not found in conducive soils within our metabarcoding dataset. Other traits such as hydrogen cyanide, ACC deaminase, and auxin biosynthesis were broadly distributed across isolates from all soils. Functional assays demonstrated variable expression of predicted traits, indicating regulatory or environmental influence. Several strains inhibited F. graminearum mycelial growth via volatile organic compounds, while two strains also reduced conidia germination, including isolates from both suppressive and conducive soils.<br><br>CONCLUSIONS: This study demonstrates that Pseudomonas genomic traits important for biocontrol are not restricted to suppressive soils, and that functional redundancy and context-dependent expression may shape the contribution of Pseudomonas to disease suppression. Our results highlight the need for integrative analyses combining community profiling, genome-based prediction, and phenotyping to better understand microbiome-mediated plant protection. The identification of novel genomospecies and lineage-specific biosynthetic traits advances our knowledge of Pseudomonas diversity in agricultural soils and supports future development of targeted microbial consortia.}, }
@article {pmid41353279, year = {2025}, author = {Stuehrenberg, J and Kitzinger, K and von Arx, JN and Graf, JS and Lavik, G and Littmann, S and Milucka, J and Orsi, WD and Schorn, S and Speth, DR and Vuillemin, A and Wu, S and Marchant, HK and Kuypers, MMM}, title = {Urea use drives niche separation between dominant marine ammonia oxidizing archaea.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-025-67048-1}, pmid = {41353279}, issn = {2041-1723}, support = {EXC-2077-390741603//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, abstract = {Ammonia-oxidizing archaea (AOA) are among the most abundant microorganisms in the ocean and play a critical role in marine nitrogen cycling. Recently, urea has been shown to serve as an additional substrate for marine AOA, with substantial urea use in the ammonium-depleted open-ocean. Yet, the mechanisms that control urea use and potentially maintain high AOA abundances remain unclear. Here, we investigate urea and ammonia use by AOA in three contrasting marine environments, from coastal, ammonium-rich to open-ocean, ammonium-poor waters. Our combined results indicate that distinct substrate utilization strategies of Nitrosopumilus and Nitrosopelagicus control their environmental distribution. The more coastal AOA genus, Nitrosopumilus, primarily uses ammonium. In contrast, enhanced urea utilization in ammonium-limited waters is linked to the activity and growth of Nitrosopelagicus. Thus, the use of urea, and potentially other organic-N compounds by Nitrosopelagicus plays a major role in fueling open-ocean nitrification and sustaining primary productivity in these vast regions.}, }
@article {pmid41352799, year = {2026}, author = {Cheng, W and Jiang, C and Pan, T and Zhu, Q and Liu, G and Li, N and Wu, Z and Li, X}, title = {Effects of quinoa addition on physicochemical properties, microbiome profiles, and volatile organic compounds in medium-temperature Daqu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {223}, number = {Pt 1}, pages = {117868}, doi = {10.1016/j.foodres.2025.117868}, pmid = {41352799}, issn = {1873-7145}, mesh = {*Volatile Organic Compounds/analysis ; *Chenopodium quinoa/chemistry ; *Microbiota ; Fermentation ; Food Microbiology ; Food Handling/methods ; Temperature ; }, abstract = {The selection of raw materials plays a pivotal role in shaping the microbial ecology and metabolic functions of Daqu, a fermentation starter widely used in Baijiu production. Quinoa (Chenopodium quinoa Willd.), a pseudocereal rich in proteins, polyphenols, and bioactive compounds, has recently gained attention as a functional food ingredient. In this study, Quinoa was used to replace a certain proportion of wheat and incorporated into the making process of medium-temperature Daqu (MTD), and its effects on the physicochemical properties, microbial community dynamics, and volatile organic compound (VOC) were investigated. Compared with traditional MTD, quinoa-supplemented Daqu (L-MTD) exhibited significantly higher starch (increased by 8.4 %), reducing sugar (increased by 12.7 %), and acidity (increased by 15.3 %) levels (p < 0.05), along with enhanced esterification and fermentation power of its central part (increased by 10.2 % and 9.5 %, respectively, p < 0.05). High-throughput sequencing revealed that quinoa addition reshaped the microbial community by enriching beneficial lactic acid bacteria (e.g., Lactobacillus and Weissella) and reducing potential spoilage fungi (e.g., Aspergillus and Rhizopus). In addition, Lactobacillus and Saccharomycopsis showed strong correlations with the accumulation of esters and aromatic compounds, including ethyl lactate, phenethyl acetate, DL-(-)-pantoyl lactone, and benzyl alcohol. Redundancy analysis (RDA) indicated strong correlations between Lactobacillus and Saccharomycopsis with the accumulation of esters (such as ethyl acetate and ethyl lactate) and aromatic compounds (such as benzyl alcohol and phenethyl acetate), providing a research basis for identifying functional microbial strains in MTD and conducting subsequent micro-fermentation experiments. These findings highlight the potential of quinoa as a functional additive that modulates the microbial ecology and enhances the aroma complexity of Daqu, thereby offering a novel strategy for improving the quality and potential health value of traditional fermented products.}, }
@article {pmid41352467, year = {2025}, author = {Nalladiyil, A and Khuntia, HK and Chanakya, HN and Babu, GLS}, title = {Treatment of ultra-high-strength compost leachate using an anaerobic biomass biofilm reactor.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133774}, doi = {10.1016/j.biortech.2025.133774}, pmid = {41352467}, issn = {1873-2976}, abstract = {Leachate produced during the composting of the organic fraction of municipal solid waste (OFMSW) is highly concentrated and acidic (chemical oxygen demand (COD) -125 g/L, pH 3-5). Its recalcitrant nature necessitates long hydraulic retention times for effective digestion, which, in turn, leads to high organic loads and, consequently, large reactor footprints. This study evaluated the treatment performance, bioenergy potential, and microbial ecology of the Anaerobic Biomass Biofilm Reactor (ABBR) for ultra-high strength leachate treatment. The reactor employed lignocellulosic wastes such as coir, ridge gourd, and dried acacia leaves as natural biofilm supports. Operated over 180 days with a gradually increasing organic loading rate from 1.1 to 11.2 kg COD/m[3]/d, the reactor achieved 92.9 % COD removal and a methane yield of 0.357 NL/g COD removed at the maximum loading rate. Moreover, the reactor also exhibited exceptionally high space utilization efficiency (3.5-4 L CH4/L/d), highlighting its enhanced volumetric productivity and effectiveness in treating high-strength leachate. Metagenomic analysis revealed a diverse microbial community, with Methanospirillum (3 %) and Methanosaeta (2.6 %) identified as dominant archaea contributing to methanogenesis. The high moisture content of OFMSW, coupled with tropical climatic conditions, leads to rapid fermentation and the generation of large volumes of leachate. Therefore, the ABBR represents a sustainable and high-rate alternative to conventional anaerobic systems, enabling efficient leachate treatment and enhanced bioenergy recovery in windrow composting facilities.}, }
@article {pmid41351873, year = {2025}, author = {Pan, X and Hageman, JJ and Weits, DA and Caldas, L and Elsayed, SS and Bayona, LM and van Wezel, GP and Berendsen, RL and Carrión, VJ and Raaijmakers, JM}, title = {Hypoxia Induces Phenotypic and Metabolic Shifts in Endophytic Flavobacterium sp. 98.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf269}, pmid = {41351873}, issn = {1751-7370}, abstract = {Oxygen plays a crucial role in shaping microbial physiology, functions, and behavior. Endophytic bacteria, residing within plant tissues, inhabit microenvironments where oxygen availability can be limited. However, the magnitude of hypoxic conditions in the endosphere and how these affect functional microbial traits is largely unknown. Here, we showed with a microsensor that oxygen levels in roots of sugar beet seedlings drop drastically to variable, low oxygen levels when going from epidermal to endodermal root tissue into the vasculature. Subsequently, we investigated phenotypic and metabolic responses of endophytic Flavobacterium sp. 98 at oxygen levels of 100 ppm. Under these oxygen conditions, Flavobacterium sp. 98 showed reduced growth, enhanced motility, and an altered extracellular metabolite profile. Flavobacterium sp. 98 colonies spread out in response to oxygen limitation and more effectively restricted hyphal growth of the sugar beet root pathogen Rhizoctonia solani than Flavobacterium sp. 98 grown at ambient oxygen conditions. Exometabolome analysis revealed enhanced accumulation of lysophosphatidylethanolamine (lysoPE) and N-acetyl-phenylalanine under low-oxygen conditions, along with a reduced level of the antifungal compound 5,6-dimethylbenzimidazole. These responses reflect physiological and metabolic plasticity of Flavobacterium sp. 98, highlighting significant changes in the expression of specific traits under hypoxic conditions. Our findings provide insights into niche-adaptive strategies of endophytic bacteria and pinpoint functional traits in microbe-plant interactions operating inside plant tissue.}, }
@article {pmid41351708, year = {2025}, author = {Campbell, KL and Armitage, AR and Labonté, JM}, title = {Microbial Communities Display Key Functional Differences between Reference and Restored Salt Marshes.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02661-7}, pmid = {41351708}, issn = {1432-184X}, abstract = {Salt marshes, despite their ecological importance (i.e., carbon sequestration) and rapid decline due to climate change and sea-level rise. Salt marsh ecosystems provide essential services such as removal of pollutants, carbon sequestration, and protection of coastal lands from storm surges. These services are strongly influenced by plant productivity, which is closely linked to microbial processes such as biogeochemical cycling of carbon, nitrogen, and sulfur. To retain carbon sequestration and other ecological functions, substantial efforts are currently directed towards coastal marsh restoration. Restoration efforts often lack comprehensive assessments of ecosystem functioning. Here, in an effort to assess ecosystem functions, we compared the microbial and viral community composition, as well as the genetic potential between reference and 10-year-old restored marshes in Galveston Bay, TX, USA. Duplicate bulk surface sediment in stands of Spartina alterniflora were sampled for metagenomic analysis. Metagenome assembled genomes analysis showed that while the microbial community composition was largely similar among sites, the overall metabolic potential was dissimilar. Restored sites displayed a higher abundance of carbon and nitrogen cycling functions compared to reference sites, which mainly consisted of sulfur cycling. Although the restored sites developed sediment microbial communities that approached reference microbial composition, the differences in the metabolic functions suggest that even after 10 years, the restored sites were still in a transitional stage of development. The differences between the reference and restored sites were even more differentiated in the viral community's predicted host composition. Additionally, viruses potentially play a variety of roles within the sediment community, including population control and biogeochemical cycles participation through auxiliary metabolic genes. These results highlight the prolonged timeline of functional development in restored salt marshes and highlight the need to develop approaches to boost the development of soil microbial communities in newly created habitats.}, }
@article {pmid41350753, year = {2025}, author = {Kim, K and Park, S and Jinno, C and Ji, P and Liu, Y}, title = {Impact of dietary supplementation of Bacillus subtilis on the metabolic profiles and microbial ecology of weanling pigs experimentally infected with a pathogenic Escherichia coli.}, journal = {Journal of animal science and biotechnology}, volume = {16}, number = {1}, pages = {167}, pmid = {41350753}, issn = {1674-9782}, abstract = {BACKGROUND: Our previous study demonstrated that dietary supplementation of Bacillus subtilis enhanced growth performance and intestinal integrity in weaned pigs challenged with enterotoxigenic Escherichia coli (ETEC). Therefore, this study aimed to explore the impact of Bacillus subtilis on gut health and its role in modulating host-microbe interactions in post-weaning pigs.<br><br>RESULTS: ETEC infection disrupted key metabolic pathways in distal colon, including glutathione, beta-alanine, and pyrimidine metabolism, indicating increased oxidative stress, impaired nucleotide balance, and amino acid catabolic stress. Bacillus subtilis supplementation induced distinct metabolomic and microbiome profiles in colon digesta of weaned pigs challenged with ETEC. Bacillus subtilis-treated pigs under ETEC challenge exhibited significant enrichment in amino acid- and energy-related pathways such as arginine biosynthesis, phenylalanine metabolism, pantothenate and CoA biosynthesis. ETEC infection induced microbial dysbiosis in the distal colon, resulting in decrease (P < 0.05) in abundance of Streptococcaceae and Enterobacteriaceae compared to healthy controls. Bacillus subtilis supplementation mitigated the ETEC-induced disruptions by increasing the relative abundance of beneficial bacterial families, including Lachnospiraceae and Bacteroidaceae.<br><br>CONCLUSION: Supplementation of Bacillus subtilis improves intestinal health and resilience against ETEC challenge by mitigating infection-induced metabolic disruptions and gut dysbiosis in weaned pigs.}, }
@article {pmid41350118, year = {2025}, author = {Fukase, S and Kouketsu, A and Tamahara, T and Saito, T and Ito, A and Higashi, Y and Kajita, T and Kurobane, T and Miyakoshi, M and Iikubo, M and Shimizu, R and Takahashi, T and Yamauchi, K and Sugiura, T}, title = {Differences in the Oral Microbiome Between Patients With and Without Oral Squamous Cell Carcinoma.}, journal = {Journal of oral pathology &amp; medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jop.70099}, pmid = {41350118}, issn = {1600-0714}, abstract = {BACKGROUND: Although studies have demonstrated a relationship between pathogenic microorganisms and oral cancer, no study has demonstrated a relationship between changes in bacterial flora and oral squamous cell carcinoma (OSCC). Therefore, we investigated the association between oral microbiota and oral squamous cell carcinoma using metagenomic analysis.<br><br>METHODS: Saliva samples from 64 patients with OSCC and 50 healthy controls who visited the Department of Oral Surgery, Tohoku University Hospital, were collected, and bacterial genomic DNA was extracted using polymerase chain reaction amplification. Single-end sequencing was performed using the Illumina MiSeq platform, and sequence data were analyzed using the Quantitative Insights Into Microbial Ecology 2 platform. The Steel-Dwass test was used for between-group comparisons, and Analysis of Compositions of Microbiomes with Bias Correction was used to detect significant differences in microbiome composition.<br><br>RESULTS: Significant differences were observed in alpha-diversity indices of bacterial flora (richness, Faith- phylogenetic diversity, Shannon index) in the OSCC group compared to those in the control group. Among the OSCC group, patients with larger tumor diameters and lymph node metastases (T3/T4, N1 or greater) formed independent clusters in the beta diversity analysis of the bacterial flora. Bacteria of the Actinomycetia phylum, such as Actinomyces and Rothia, were significantly reduced in patients with higher stage and pathological grade. Conversely, bacteria of the phylum Spirochaetia and Proteobacteria, particularly those of the genus Treponema, were significantly elevated in advanced cancer cases.<br><br>CONCLUSIONS: Our results suggest that changes in the oral microbiota may play a role in OSCC development and progression.}, }
@article {pmid41348832, year = {2025}, author = {Cervantes-Echeverría, M and Jimenez-Rico, MA and Manzo, R and Hernández-Reyna, A and Cornejo-Granados, F and Bikel, S and González, V and Hurtado Ramírez, JM and Sánchez-López, F and Salazar-León, J and Pedraza-Alva, G and Perez-Martinez, L and Ochoa-Leyva, A}, title = {Human-derived fecal virome transplantation (FVT) reshapes the murine gut microbiota and virome, enhancing glucose regulation.}, journal = {PloS one}, volume = {20}, number = {12}, pages = {e0337760}, doi = {10.1371/journal.pone.0337760}, pmid = {41348832}, issn = {1932-6203}, mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; Mice ; *Fecal Microbiota Transplantation/methods ; *Virome ; Male ; Diet, High-Fat/adverse effects ; Obesity/therapy/microbiology ; *Feces/virology ; Mice, Inbred C57BL ; *Glucose/metabolism ; Metabolic Syndrome/therapy/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; }, abstract = {The gut microbiome, comprising bacteria, viruses, archaea, fungi, and protists, plays a crucial role in regulating host metabolism and health. This study explored the effects of fecal virome transplantation (FVT) from healthy human donors on metabolic syndrome (MetS) in a diet-induced obesity (DIO) mouse model, without diet change. Mice received a single oral dose of human-derived virus-like particles (VLPs) and continued on a high-fat diet (HFD) for 17 weeks. Despite persistent dietary stress, FVT significantly improved glucose tolerance. Longitudinal profiling by virome shotgun metagenomics and bacterial 16S rRNA sequencing revealed marked, durable shifts in both viral and bacterial community composition. Notable bacterial changes included a decrease in Akkermansia muciniphila and Peptococcaceae and increases in Allobaculum and Coprococcus; A. muciniphila positively correlated with glucose levels and negatively correlated with body weight. Together, these results suggests that human-derived virome can durably reshape gut microbial ecology and improve glucose metabolism in mice with obesity, even without dietary modification, offering a novel avenue for developing phage-based therapies. This proof-of-concept study provides foundational observations for using human-derived VLPs for FVT in standard laboratory mouse models, and provides a foundation for elucidating bacteria-phage interactions and their role in host metabolic health.}, }
@article {pmid41348222, year = {2025}, author = {Soto-Pozos, &#xc1;F and Rebollar, EA and Rovito, SM and Parra-Olea, G}, title = {Imprints of Land Use History on the Cutaneous Microbiota of Mexican Cloud Forest Salamanders.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02671-5}, pmid = {41348222}, issn = {1432-184X}, support = {CF-2019/373914//Secretar&#xed;a de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n del Distrito Federal/ ; IN208024//Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; }, abstract = {The cloud forest harbors the highest amphibian diversity in Mexico, particularly among plethodontid salamanders. However, the expansion of agricultural and cattle ranching activities has significantly impacted this ecosystem and their native species. Beyond direct effects on cloud forest-dwelling species, effects of land-use change on free-living and salamander skin associated bacterial assemblages are underexplored in the cloud forest and in plethodontid salamanders specifically. This study examines how historical land-use changes may influence environmental and salamander skin bacterial communities, focusing on two types of previous land-use and six sympatric plethodontid salamanders from the cloud forest. Furthermore, we explored the presence of the pathogenic fungus Batrachochytrium dendrobatidis (Bd), due to its potential interaction with salamander skin bacterial communities. We found that skin bacterial communities varied with land-use history: in habitats formerly used for agriculture salamanders exhibited higher bacterial diversity, and communities' dispersion varied depending on the previous land-use. We found a very low Bd prevalence throughout the study area. Our findings suggest that bacterial communities associated with the skin of plethodontid salamanders may be influenced by land-use history in cloud forest fragments.}, }
@article {pmid41345535, year = {2025}, author = {Guijosa-Ortega, JL and Romaní, AM and Grau, O and Pla-Rabés, S and Margalef, O and Salminci, JG and Zarroca, M and Pastor, A}, title = {Effects of Acid Rock Drainage on Microbial Communities in Alpine Streams of the Pyrenees.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02667-1}, pmid = {41345535}, issn = {1432-184X}, abstract = {Weathering of sulphur-bearing rocks leads to acid rock drainage (ARD), which decreases water pH, mobilizes heavy metals, and forms coloured coatings of metal precipitates on riverbeds. This study assessed the effects of ARD on microbial biofilm biodiversity and community structure in alpine streams across two Pyrenean regions (Núria and Chistau). Biofilms were sampled from acidic (pH < 5.5) and non-acidic (pH > 6.5) streams, and at their confluence, where metal precipitates occur (white-coated streams). We characterised bacterial and eukaryote communities by molecular tools and specifically analysed the diatom communities by morphology approach. Their respective community composition varied with stream category for both bacteria and eukaryotes, but only bacteria exhibited a loss in diversity in acidic and white-coated streams. Diatom communities and diversity differences were driven mainly by region. In acidic and white-coated streams, bacteria which can use metals and sulphurs in their metabolic processes increased, together with fungi and some photosynthetic groups (Chlorophyta, Streptophyta) among eukaryotes. Amplicon Sequence Variants (ASVs) assigned to acidophilic and psychrotolerant bacteria were highly associated with acidic streams, and Cyanophyceae ASVs were highly associated with white-coated ones. As for eukaryotes, ASVs of Chrysophyceae were associated with both acidic and white-coated streams. Nonetheless, the regional factor remained consistently significant across microbial communities. This study indicates that ARD-affected streams can support microbial communities adapted to their extreme conditions, with the communities in white-coated rivers differing markedly from those in acidic rivers.}, }
@article {pmid41345364, year = {2025}, author = {Zhai, L and Yang, J and Lu, M and Sun, T and Wang, Y and Tang, G and Wu, D and Xu, L}, title = {Effects of Leaf Structure, Physiological Characteristics, and Chemical Properties on Phyllosphere Microorganisms Associated with Four Forage Crops in Fallow Land.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02638-6}, pmid = {41345364}, issn = {1432-184X}, support = {2023//Xingzhao Talent Support Program/ ; QKHJCQN[2025]265//Guizhou Provincial Basic Research Program (Natural Sciences) Youth Guidance Project/ ; 52020-2024-PT-02//Liupanshui Municipal-Level Science and Technology Innovation Platform Construction Project/ ; LPSSYKYJJ202306//High-Level Talents Introduction Project of Liupanshui Normal University/ ; }, abstract = {Phyllosphere microorganisms promote plant health, facilitate plant growth, and support ecosystem function. In this study, we compared the effects of leaf anatomy, physiological properties, and chemical composition on the diversity and abundance of epiphytic microorganisms across four forage species: wheat (Triticum aestivum), rye (Secale cereale), barley (Hordeum vulgare), and Italian ryegrass (Lolium multiflorum). The results showed that crop type significantly influenced microbial abundances on leaf surfaces and in whole leaves (P < 0.05). Specifically, wheat exhibited higher abundances of aerobic bacteria, lactic acid bacteria, molds, and yeasts in whole leaves and on leaf surfaces than those of the other three forage species. Microbial abundance on leaf surfaces was lower than that in whole leaves among the four crops. The stomatal density on the abaxial leaf surface was significantly higher than that on the adaxial surface (P < 0.0001) among the four crops. The main drivers of whole-leaf microbial abundance included soluble sugars, stomatal density, intercellular CO2 concentration, and total water vapor conductance. Conversely, the key factors influencing surface microbial abundance were reducing sugars (affecting lactic acid bacteria and molds) and stomatal density on the adaxial surface (affecting yeasts). In conclusion, the morphology, physiology, and chemical composition of forage leaves collectively shape the colonization patterns and abundance of epiphytic microorganisms. Wheat exhibited larger microbial numbers than those of the other three forages. Soluble sugars and stomatal density emerged as key determinants of microbial community structure, whereas epidermal structure influenced the formation of specific functional microbial communities through a dual mechanism of physical selection and microenvironmental regulation.}, }
@article {pmid41345336, year = {2025}, author = {Antoł, W and Surmacz, B and Ostap-Chec, M and Stec, D and Miler, K}, title = {Do Shifts in Honeybee Crop Microbiota Enable Ethanol Accumulation? A Comparative Analysis of Caged and Foraging Bees.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02627-9}, pmid = {41345336}, issn = {1432-184X}, support = {Sonata 17 grant 2021/43/D/NZ8/01044//National Science Center in Poland/ ; }, abstract = {Honeybees encounter low environmental doses of ethanol, primarily through fermenting nectar, which can have both beneficial and detrimental effects on their functioning. Yet, ethanol traces can also be detected in the crop of caged bees with no access to environmental food sources. This raises the possibility that endogenous ethanol accumulation could occur under restricted conditions, with microbial contributions as a potential mechanism. The crop microbiota, although less diverse than that in other gut segments, plays important roles in food fermentation and pathogen defense. We hypothesized that captivity-induced shifts in crop microbiota may facilitate fermentation, resulting in measurable ethanol. To test this, we compared the crop contents of naturally foraging hive bees and caged bees reared without access to the natural environment. Ethanol levels were low in both groups and did not differ significantly, but non-zero measurements were more frequently observed in caged bees. Microbial community structure differed strongly in α- and β-diversity. Caged bees showed reduced abundance of nectar-associated genera (e.g., Apilactobacillus) and an increase in genera that include known ethanol-producing strains, such as Gilliamella and Bifidobacterium. While we did not directly assess metabolic activity, our results suggest that captivity alters microbial communities in ways that may influence ethanol levels. This raises broader questions about how microbe-host interactions modulate host phenotypes under different environmental conditions.}, }
@article {pmid41345266, year = {2025}, author = {Zhao, Z and Klawonn, I and Baltar, F and Grossart, HP}, title = {Size-fractionated fungal communities in the sunlit ocean.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-025-09314-y}, pmid = {41345266}, issn = {2399-3642}, abstract = {Marine fungi play key roles in organic matter cycling, yet their distribution across particle size fractions remains understudied. We analyze 18S rDNA data from four size fractions (0.8-5, 5-20, 20-180, and 180-2000 μm) collected across the global sunlit ocean. Here, we show fungal diversity and relative abundance decline with increasing particle size. Fungal community structure is influenced by eukaryotic diversity and chlorophyll levels. Fungi co-occur with other eukaryotes, especially zooplankton, hinting at potential predator-prey interactions. Generalist fungi dominate smaller fractions, while specialists dominate larger fractions, likely due to stronger microenvironmental selection. Co-occurrence networks are dominated by positive interactions and driven by fungal specialists. Dispersal limitation emerges as the main ecological process shaping community assembly. Our findings reveal strong niche differentiation among marine fungi along the particle continuum and emphasize the role of particle size and biological interactions in structuring fungal diversity and biogeography.}, }
@article {pmid41345123, year = {2025}, author = {Tucker, SJ and Füssel, J and Freel, KC and Kiefl, E and Freel, EB and Ramfelt, O and Sullivan, CES and Gajigan, AP and Mochimaru, H and de Souza, MR and Quinn, M and Ratum, C and Tran, LL and Sobczyk, M and Miller, SE and Trigodet, F and Lolans, K and Morrison, HG and Fallon, B and Huettel, B and Pan, T and Rappé, MS and Eren, AM}, title = {A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1913}, pmid = {41345123}, issn = {2052-4463}, support = {687269//Simons Foundation/ ; 989028//Simons Foundation/ ; 989028//Simons Foundation/ ; 2019589//NSF | GEO | Division of Ocean Sciences (OCE)/ ; }, mesh = {*Metagenome ; Pacific Ocean ; *Transcriptome ; *RNA, Transfer/genetics ; *Seawater/microbiology ; Ecosystem ; Microbiota ; }, abstract = {The roles of marine microbes in ecosystem processes are inherently linked to their ability to sense, respond, and ultimately adapt to environmental change. Capturing the nuances of this perpetual dialogue and its long-term implications requires insight into the subtle drivers of microbial responses to environmental change that are most accessible at the shortest scales of time. Here, we present a multi-omics dataset comprising surface ocean metagenomes, metatranscriptomes, tRNA transcripts, and biogeochemical measurements, collected every 1.5 hours for 48 hours at two stations within coastal and adjacent offshore waters of the tropical Pacific Ocean. We expect that this integrated dataset of multiple sequence types and environmental parameters will facilitate novel insights into microbial ecology, microbial physiology, and ocean biogeochemistry and help investigate the different mechanisms of adaptation that drive microbial responses to environmental change.}, }
@article {pmid41344775, year = {2026}, author = {Zhu, J and Liao, Y and Zhao, Y and Liu, J and Li, Z and Kong, X and Zhang, S and Song, C and Fu, Q and Wang, X and Xue, R and Shi, X and Tian, Y and Cao, R and You, J and Li, L}, title = {Functional division of labor within defined yeast consortia drives flavor formation during early solid-state fermentation of sichuan shai vinegar.}, journal = {Food microbiology}, volume = {135}, number = {}, pages = {104983}, doi = {10.1016/j.fm.2025.104983}, pmid = {41344775}, issn = {1095-9998}, mesh = {*Acetic Acid/metabolism/analysis ; Fermentation ; *Flavoring Agents/metabolism ; Saccharomyces cerevisiae/metabolism ; Taste ; *Microbial Consortia ; Pichia/metabolism ; Saccharomycetales/metabolism ; *Yeasts/metabolism/classification ; Ethanol/metabolism ; Fermented Foods/microbiology/analysis ; Food Microbiology ; Brettanomyces ; }, abstract = {Sichuan Shai vinegar (SSV) is a traditional fermented product with complex microbial ecology. This study elucidated the functional division of labor within the yeast microbiota during the early stage (days 1-5) of solid-state fermentation in SSV. Investigating of four key yeast strains (Saccharomyces cerevisiae, Pichia kudriavzevii, Kazachstania humilis, and Brettanomyces bruxellensis) via co-culturing, metabolomics, and simulated fermentation revealed distinct roles: Pichia kudriavzevii dominated ester synthesis, Brettanomyces bruxellensis primarily produced characteristic flavor compounds (e.g., acetaldehyde, 4-ethylguaiacol), Kazachstania humilis efficiently produced acids accelerating acidification, and Saccharomyces cerevisiae produced ethanol, which served as a precursor for ester synthesis by other yeasts. The triple-strain combination of Pichia kudriavzevii, Kazachstania humilis, and Brettanomyces bruxellensis exhibited optimal synergy, achieving peak total acid (10.96 g/100 g DW) and acetic acid (3.54 g/100 g DW) content while significantly enhancing characteristic flavor profiles. Untargeted metabolomics indicated that this combination efficiently regulated multiple flavor biosynthesis pathways through pyruvate-mediated metabolic hubs. This systematic clarification of functional roles within the yeast community provides an experimental foundation for designing synthetic microbial starters to modulate flavor profiles and advance the standardization of fermented food production.}, }
@article {pmid41344333, year = {2025}, author = {Cao, Y and Bowker, MA and Feng, Y and Delgado-Baquerizo, M and Xiao, B}, title = {The Great Wall of China harbors a diverse and protective biocrust microbiome.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2025.10.087}, pmid = {41344333}, issn = {1879-0445}, abstract = {The Great Wall of China, one of the most emblematic human heritage sites ever built, is largely covered by a living skin that has a potentially distinct microbiome compared with bare wall surfaces. However, the structure and function of this microbiome remain virtually unknown, which hampers any effort to understand the impacts of this microbiome on the long-term conservation of the Great Wall. Here, we investigated the microbiome of the Great Wall at six sampling sites along a 600-km section, which stretches across arid and semiarid climates and is covered by a mosaic of biological soil crusts (biocrusts) and exposed wall surfaces. We hypothesized that these biocrusts could establish a unique microhabitat and support a microbiome with a community structure and function potentially distinct from those on bare walls, thereby modulating the biodeterioration processes affecting the Great Wall. Our findings revealed that biocrust-covered sections exhibited a 12%-62% increase in abundance, diversity, and co-occurrence network complexity for bacterial and fungal communities compared with bare walls. Further metagenomic analyses indicated that the biocrust cover enhanced the abundance of overall functional genes and stress-resistance pathways within the microbiome by 4%-15%, while decreasing the metabolic pathways linked to heritage biodeterioration. Aridity was an additional determinant of the microbiome. Our work serves as a critical step toward understanding the microbiome of the Great Wall, which contributes to conserving this unparalleled human monument for future generations.}, }
@article {pmid41344264, year = {2025}, author = {Li, C and Li, S and Ma, L and Wang, H and Li, X and Li, M and Yang, Q}, title = {Allantoin enhances growth and nutrient accumulation in Dioscorea opposita under saline-alkali stress through regulation of ion homeostasis and antioxidant capacity.}, journal = {Plant physiology and biochemistry : PPB}, volume = {229}, number = {Pt E}, pages = {110819}, doi = {10.1016/j.plaphy.2025.110819}, pmid = {41344264}, issn = {1873-2690}, abstract = {Saline-alkali stress (SAS) significantly impairs crop growth, yield and quality, while allantoin plays a crucial role in enhancing plant tolerance to this stress. Yam (Dioscorea opposita Thunb.) has substantial nutritional and medicinal value. However, the regulatory mechanism of allantoin in regulating yam growth and nutritional quality under SAS remains largely unclear. In this study, we found that SAS severely inhibited the growth and root development of yam bulbil seedlings. Specifically, in leaves, the contents of osmotic regulators (e.g., proline, soluble sugar) and malondialdehyde (MDA), along with the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), were significantly increased. Additionally, leaf Na[+] content was increased, K[+] content was decreased, and the Na[+]/K[+] ratio was significantly elevated. Meanwhile, the contents of allantoin, diosgenin, and polysaccharides in tubers were significantly increased. Overexpression of the allantoin synthase gene DoAS in Arabidopsis thaliana further enhanced its tolerance to SAS. Furthermore, compared with the SAS-only group, allantoin treatment significantly improved yam seedling growth, reduced leaf proline and MDA contents, enhanced SOD and POD activities, decreased the Na[+]/K[+] ratio, increased tuber yield and contents of major active components, and lowered tuber Na[+] content. Taken together, allantoin significantly improves ionic balance and antioxidant capacity in yam bulbil seedlings under SAS, thereby promoting seedling growth and nutrient accumulation in tubers. This study thus highlights the critical role of allantoin in regulating the growth and nutrient accumulation in tuber crops under SAS.}, }
@article {pmid41342921, year = {2025}, author = {Taurozzi, D and Scalici, M}, title = {Regional γ Diversity of Diatoms in Mediterranean and Alpine Temporary Ponds.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02670-6}, pmid = {41342921}, issn = {1432-184X}, abstract = {Temporary ponds, characterized by periodic or intermittent hydroperiods, are globally widespread in all the biogeographical regions and host peculiar biotic communities. Here we investigated shifts in diatom community assemblages across two contrasting biogeographical regions in Italy, the Mediterranean and the Alpine. The study focused on 24 temporary ponds, with 12 ponds sampled at Castelporziano (CP) and 12 at Campo Imperatore (GS). Our results highlighted that γ diversity varied significantly between the two study sites, indicating a notably greater species richness in GS compared to CP. In GS, functional richness values were generally higher, whereas no significant differences were detected for functional distance and functional divergence. Species composition differed significantly between CP and GS indicating that the two sites host distinct communities, with species turnover (0.904) which contributed most to total beta diversity (0.926), while nestedness (0.021) was negligible. CP communities were characterized by pronounced functional clustering in specific sites while GS exhibited both clustering and slight overdispersion. However, although GS communities occupy slightly larger trait space, both regions shared most functional strategies, reflecting substantial redundancy in functional traits across the two environments. Overall, diatom communities in the GS were characterized by higher frequencies of small, mobile, low-profile, and mucilaginous-tube taxa, whereas CP ponds displayed relatively higher representation of larger or motile forms. Although our study is a starting point, large-scale analyses of diatom communities are crucial, as climate change may rapidly and irreversibly alter taxonomic and functional diversity, profoundly affecting the ecology of these temporary habitats and surrounding landscapes.}, }
@article {pmid41342600, year = {2025}, author = {Bauchinger, F and Berry, D}, title = {Metatranscriptomic-driven insights into mucosal glycan degradation by the human gut microbiota.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf118}, pmid = {41342600}, issn = {1574-6941}, abstract = {The secreted mucus layer in the human gastrointestinal tract constitutes both a protective boundary between gut lumen and epithelium as well as an important nutrient source for members of the gut microbiota. While many gut microbes possess the genetic potential to degrade mucin it is still unclear which species transcribe the respective genes. Here, we systematically analyzed publicly available metagenome and metatranscriptome datasets to characterize the gut microbial community involved in mucosal glycan degradation. We utilized co-occurrence network analysis and linear regression to elucidate the ecological strategies of, and relationship between, mucus degraders. We found that although approximately 60% of species carrying genes encoding for mucosal-glycan-degrading enzymes have detectable transcription of these genes, only 21 species prevalently transcribe more than 1 gene. Furthermore, the transcription of individual genes was frequently dominated by single species in individual samples. Transcription patterns suggested the presence of competitive mucosal glycan degraders characterized by abundance-driven transcription that were negative predictors for the transcription of other degraders as well as opportunistic species with decoupled abundance and transcription profiles. These findings provide insights into the ecology of the mucosal glycan degradation niche in the human gut microbiota.}, }
@article {pmid41341498, year = {2025}, author = {Sun, D and Šmilauer, P and Pjevac, P and Rozmoš, M and Forczek, ST and Kotianová, M and Hršelová, H and Bukovská, P and Jansa, J}, title = {Arbuscular mycorrhiza suppresses microbial abundance, and particularly that of ammonia oxidizing bacteria, in agricultural soils.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1671859}, pmid = {41341498}, issn = {1664-302X}, abstract = {Interactions between arbuscular mycorrhizal (AM) fungi and ammonia-oxidizing (AO) microorganisms, two important microbial guilds contributing to soil-plant mineral nutrient cycling, are complex, given the high variability of soil biological, physical, and chemical properties. In addition, AO microorganisms are generally slow growing and require ample time to establish. Their communities are thus difficult to reconstruct under laboratory conditions, for example after soil sterilization. Therefore, in this study, we investigated quantitative and compositional responses of indigenous microorganisms occurring in 50 different field soils (collected from grasslands and arable fields) to actively growing mycelium of the AM fungus Rhizophagus irregularis. To this end, we quantified the abundance of various microbial guilds including AO bacteria (AOB), AO archaea (AOA), and comammox Nitrospira in pot-incubated soils exposed or not to actively growing AM fungus. Across the variety of soils, we observed systematic suppression by the AM fungus of different microbial groups including bacteria, protists, and fungi. The strongest suppression was noted for AOB and comammox Nitrospira, whereas the abundance and community structure of AOA remained unaffected by the AM fungal activity. Mycorrhizal suppression of AOB abundance was accompanied by changes in AOB community structure and correlated with soil pH. Contrary to the expected competition between AM fungus and AO microorganisms for available ammonium (NH4 [+]) in the soil solution, the presence of the actively growing AM fungus significantly increased soil NH4 [+] levels as compared to the non-mycorrhizal control, at least upon the final destructive harvest. Thus, the interaction between the AM fungi and AO microorganisms likely goes beyond the simple competition for the free ammonium ions and might involve microorganisms active in other pathways of soil nitrogen cycle (e.g., mineralization) or temporarily different trajectories of nutrient use in mycorrhizal vs. non-mycorrhizal systems. Alternatively, elusive biological nitrification inhibitors may have contributed to the observed effect, produced by the AM fungus or its host plant, and subsequently transported to the root-free soil via the AM fungal hyphae.}, }
@article {pmid41339548, year = {2025}, author = {Singleton, CM and Jensen, TBN and Delogu, F and Knudsen, KS and Sørensen, EA and Jørgensen, VR and Karst, SM and Yang, Y and Sereika, M and Petriglieri, F and Knutsson, S and Dall, SM and Kirkegaard, RH and Kristensen, JM and Overgaard, CK and Woodcroft, BJ and Speth, DR and Aroney, STN and ,  and Wagner, M and Dueholm, MKD and Nielsen, PH and Albertsen, M}, title = {The Microflora Danica atlas of Danish environmental microbiomes.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {41339548}, issn = {1476-4687}, abstract = {Over the past 20 years, there have been considerable advances in revealing the microbiomes that underpin processes in natural and human-associated environments. Recent large-scale metagenome surveys have recorded the variety of microbial life in the oceans[1], in the human gut[2] and on Earth[3], with compilations encompassing thousands of public datasets[4,5]. However, despite their broad scope, these studies often lack functional information, and their sample locations are frequently sparsely distributed, limited in resolution or lacking metadata. Here we present Microflora Danica-an atlas of Danish environmental microbiomes encompassing 10,683 shotgun metagenomes and 450 nearly full-length 16S and 18S rRNA datasets, linked to a five-level habitat classification scheme. We show that although human-disturbed habitats have high alpha diversity, species reoccur, revealing hidden homogeneity. This underlines the role of natural systems in maintaining total species (gamma) diversity and emphasizes the need for national baselines for tracking microbial responses to land-use and climate change. Consequently, we focused our dataset exploration on nitrifiers, a functional group closely linked to climate change and of major importance for Denmark's primary land use: agriculture. We identify several lineages encoding nitrifier key genes and reveal the effects of land disturbance on the abundance of well-studied, as well as uncharacterized, nitrifier groups, with potential implications for N2O emissions. Microflora Danica offers an unparalleled resource for addressing fundamental questions in microbial ecology about what drives microbial diversity, distribution and function.}, }
@article {pmid41338824, year = {2025}, author = {Guo, M and Chen, C and Wang, W and Zhang, C and Ma, J and Sadike, M and Niyazi, M and Feng, X and Zhu, K}, title = {Research on the relationship between HPV infection and alterations in vaginal microbial ecology.}, journal = {Enfermedades infecciosas y microbiologia clinica (English ed.)}, volume = {43}, number = {10}, pages = {688-697}, doi = {10.1016/j.eimce.2025.07.006}, pmid = {41338824}, issn = {2529-993X}, mesh = {Female ; Humans ; *Vagina/microbiology/virology ; Adult ; *Papillomavirus Infections/microbiology ; *Microbiota ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {OBJECTIVE: To investigate the changes in vaginal microbiota under different HPV infection statuses and explore the correlation between vaginal microbiota alterations and HPV infection.<br><br>METHODS: 151 cervical samples from gynecological outpatients were grouped into HPV-negative (HN, N=51), transient infection (HTI, N=42), and persistent infection (HPI, N=58). Vaginal secretions were collected to assess microecology (pH, vaginal cleanliness, hydrogen peroxide, leukocyte esterase) via genital secretion analyzer. 16S ribosomal RNA (rRNA) sequencing analyzed vaginal microbiota characteristics, community state types (CST), richness, diversity, and biomarkers.<br><br>RESULTS: 16S rRNA sequencing identified 5 CST II, 52 CST III, and 94 mixed CST IV samples, showing diverse microbiota. Compared with HN, HTI and HPI had lower vaginal cleanliness, higher sialidase activity, elevated pH, and fewer Lactobacilli (P<0.05). Lactobacillus iners dominated all groups, while Sneathia amnii was significantly higher in HPI (P<0.05). HPV infection increased vaginal microbiota richness (HPI>HTI/HN, P<0.05), with distinct group compositions (P<0.05). Linear Discriminant Analysis Effect Size identified Lactobacillus gasseri, Atopobium vaginae, and Lactobacillus jensenii as biomarkers.<br><br>CONCLUSION: This study found significant differences in microbial community characteristics under different HPV infection statuses. The identification of biomarkers in vaginal microbiota under different infection statuses could provide new targets for clinical screening and prevention of cervical cancer.}, }
@article {pmid41335295, year = {2025}, author = {Jayanandan, M and Veeraraghavan, VP and Govindarajan, S and Mariyappa Subramani, S}, title = {Development of oral dysbiosis following use of antimicrobial mouthwashes: a systematic review.}, journal = {Odontology}, volume = {}, number = {}, pages = {}, pmid = {41335295}, issn = {1618-1255}, abstract = {The oral microbiome maintains the oral and systemic health. The extensive use of antimicrobial mouthwashes to control biofilm-related diseases has increased the concerns about their effect on microbial ecology. Specific formulations may cause microbial shifts which influences both the oral and systemic physiology in an individual. This systematic review evaluates the oral dysbiosis development after antimicrobial mouthwash use and correlates the microbial changes with clinical and systemic outcomes. A comprehensive search in various databases like PubMed, Scopus, etc. (till March 2025) was done. It identified 14 relevant studies from a total of 681 screened records. Risk of bias was assessed using ROB2, ROBINS-I, CRIS, and NOS tools, with data extracted on microbial diversity, taxonomic changes, nitrate reduction capacity, and antibiotic resistance. The findings showed that chlorhexidine caused the greatest dysbiosis and reduces the microbial diversity by 40-60%, with increasing Streptococcus spp. two-to-threefold, and elevating antibiotic resistance gene prevalence. Cetylpyridinium chloride and polyhexamethylene biguanide showed milder effects, thus preserving 70-80% of commensals, while herbal and plant-based rinses (o-cymen-5-ol, StellaLife®, Rosella) reduced pathogens by 25-40% without disrupting the balance. Fluoride-arginine formulations promote beneficial bacteria by 30-50% but marginally upregulated resistance genes, whereas mechanical hygiene methods maintained over 90% microbial diversity. Suppression of nitrate-reducing bacteria was associated with reduced nitric oxide bioavailability, potentially increasing vascular and cognitive risks. Hence, antimicrobial mouthwashes especially chlorhexidine induces significant dysbiotic shifts, while herbal, postbiotic, and mechanical alternatives demonstrate safer, microbiome thereby preserving the effects which is suitable for long-term oral health maintenance.}, }
@article {pmid41333479, year = {2025}, author = {Ni, Z and Zhou, W and Gao, Y}, title = {A social-architecture perspective on gut microbiota dynamics and host physiology.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1642080}, pmid = {41333479}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology/immunology ; Animals ; *Host Microbial Interactions ; Homeostasis ; }, abstract = {The human gut microbiota, a dynamic consortium of trillions of microorganisms, is increasingly recognized not merely as a metabolic entity but as a structured "microbial society" exhibiting hierarchical organization, cooperative networks, and competitive exclusion. This hypothesis posits that gut microbiota communities operate under principles analogous to social structures, with emergent behaviors that directly impact host health. By integrating recent advances in microbial ecology, spatial omics, and neurogastroenterology, this paper proposes those microbial social dynamics-such as division of labor, territorial specialization, and collective decision-making-mediate critical host functions, including immune regulation, metabolic homeostasis, and cognitive processes. In research or therapy targeting the gut microbiota, safeguard the stability of the microbial society and eschew simplistic, blunt approaches. In short, the gut microbiota behaves like a collective mind, showing tight unity and rapid, fine-tuned adaptation to external cues. Its imbalance breeds disease; its vigor enhances human life.}, }
@article {pmid41330424, year = {2025}, author = {Zöhrer, J and Ascher-Jenull, J and Prem, EM and Wagner, AO}, title = {State-Specific Extraction of Environmental DNA: Spike-and-Recovery Controls to Validate and Optimise Extraction Protocols.}, journal = {Environmental microbiology}, volume = {27}, number = {12}, pages = {e70209}, doi = {10.1111/1462-2920.70209}, pmid = {41330424}, issn = {1462-2920}, support = {P36711//Austrian Science Fund/ ; }, mesh = {*DNA, Environmental/isolation &amp; purification ; *DNA, Bacterial/isolation &amp; purification ; *Bacteria/genetics/isolation &amp; purification/classification ; Polymerase Chain Reaction ; *Environmental Microbiology ; }, abstract = {Getting insights into the quantitative and qualitative contribution of different DNA states, i.e., extracellular (exDNA) and intracellular DNA (iDNA), to the total environmental DNA (eDNA) pool requires reliable methods for their separation. Even though a multitude of respective extraction protocols has been published, their validation is often missing. Here, we selected four protocols for the state-specific extraction of eDNA and traced the separation of exDNA and iDNA within natural environments using previously designed spike-and-recovery controls. Besides accounting for the different eDNA states, the spike-ins also distinguished different bacterial origins (gram-positive, gram-negative). Following their quantification by digital PCR, the recovery of exDNA and iDNA spike-ins in both the target as well as nontarget eDNA states differed among the selected extraction protocols and environmental matrices, albeit the effect of the former was far more decisive. While the recovery of exDNA spike-ins was mainly affected by the chemical composition of the washing buffer and the duration of each washing step, the lysis method determined the recovery of spiked iDNA. These aspects were further combined within an optimised protocol, providing a valuable step towards a more concise understanding of factors governing the state-specific extraction of eDNA and hence their relevance in molecular microbial ecology.}, }
@article {pmid41325059, year = {2025}, author = {Zhang, Y and Walker, RW and Kaplan, RC and Qi, Q}, title = {Added sugars, gut microbiota, and host health.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2592431}, doi = {10.1080/19490976.2025.2592431}, pmid = {41325059}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Animals ; Bacteria/classification/metabolism/genetics/isolation &amp; purification ; *Dietary Sugars/adverse effects/metabolism ; Fatty Acids, Volatile/metabolism ; Obesity/microbiology ; }, abstract = {Excessive intake of added sugars is a global public health concern, given its established links with cardiometabolic disease and other chronic conditions. Emerging evidence suggests that the gut microbiota might mediate the harms of high sugar intake. In this review, we summarize evidence from animal and human studies regarding the impact of added sugar intake on gut microbiota diversity and composition, and discuss potential mechanisms linking sugar-induced microbial changes to health outcomes. Added sugars, including glucose, fructose, and sucrose, can alter gut microbial diversity, enrich sugar-utilizing taxa, and deplete short-chain fatty acid-producing bacteria. These microbial changes may impair gut barrier integrity, increase luminal oxygen and alternative electron acceptors under inflammatory conditions, reduce short-chain fatty acid production, alter bile acid and amino acid metabolism, and promote translocation of endotoxin across the gut barrier into the bloodstream. Collectively, these pathways may link added sugar intake to irritable bowel syndrome, obesity, liver steatosis, diabetes, and cardiovascular diseases. However, inconsistent results on alterations in the gut microbiota related to added sugar intake were observed across studies, which may be due to differences in sugar dose and form (liquid vs. solid), as well as population variation in background diet, host genetics, and gut microbial ecology. Future research should focus on mechanistic investigations, characterization of inter-individual variability in response to added sugar intake, and clinical studies to assess whether dietary or therapeutic interventions can reverse sugar-induced gut microbial changes and improve host health outcomes.}, }
@article {pmid41321823, year = {2025}, author = {Zheng, Z and Xie, D and Han, Y and Li, G and Wang, S and Zhang, X and Huang, T and Xu, W and Wu, G}, title = {Deciphering the urinary microbiome and urological cancers: from correlation to mechanisms and treatment.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1699308}, pmid = {41321823}, issn = {1664-302X}, abstract = {Given that the sterility of urine and the urinary tract has been questioned by research, urinary microbiome dysbiosis has been recognized as one of the potential cancer-promoting factors. The composition of the urinary microbial community in healthy individuals has a relatively high similarity at the phylum level, with factors like age and gender influencing the expression and distribution. In contrast, the urinary microbiome of patients with urologic cancers shows significant variability and diversity depending on the type of cancer. Most of the early studies focused on the distribution, aggregation, and expression of microbiota in urologic cancers, warranting advanced studies on the causal relationship between microbes and urologic cancers. Bladder and prostate cancer tumorigenesis and progression can be influenced by microbes through chronic inflammatory or immunomodulatory pathways making them cancer models strongly associated with the urinary microbiome. Here, we summarize the expression characteristics of the microbiomes associated with these cancers and analyze the pathophysiological mechanisms and signaling pathways of the microbiome in the tumor promotion or suppression. By examining the role played by the urinary microbiome in the pathogenesis of urologic cancers, we assess the potential of specific microbial groups as biomarkers for diagnosis and surveillance. Additionally, involving the microbiome or using adjunctive participation in tumor therapy is becoming an emerging cancer treatment option. Improving urinary microbial homeostasis in urinary cancers by direct treatment with microbial products, microbial co-immunotherapy, probiotic-assisted therapy, and fecal microbial transplantation may broaden the scope of therapy and enhance the efficacy of conventional medicines.}, }
@article {pmid41321415, year = {2025}, author = {Horstmann, L and Lipus, D and Bartholomäus, A and Oses, R and Kitte, A and Friedl, T and Wagner, D}, title = {Microbial ecology of subsurface granitic bedrock: a humid-arid site comparison in Chile.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf199}, pmid = {41321415}, issn = {2730-6151}, abstract = {Subsurface microorganisms face extreme challenges such as anoxic, xeric, and oligotrophic conditions. In igneous systems, nutrient limitation is critical, as biomass input relies on surface-derived fluids via tectonic fractures. Despite growing interest in subsurface habitats, little is known about ecosystems beneath arid landscapes, where surface water input is limited by the low annual precipitation. This study compares granitic subsurface environments beneath arid and humid surface ecosystems, highlighting the link between surface climate and subsurface biodiversity. DNA was extracted from granitic subsurface rocks recovered from two endmember sites along a north-south climate gradient in Chile's Coastal Cordillera. Microbial communities inhabiting down to 55 m deep subsurface rocks were characterized using 16S rRNA amplicon and shotgun metagenomic sequencing. We identified an abundant and potentially active subsurface community below both climates dominated by heterotrophic bacteria, including Pseudarthrobacter, Janthinobacterium, and Pseudomonas. However, rare taxa affiliated with common chemolithoautrophs, e.g. Thiobacillus, Sulfuriferula, and Sulfuricurvum, were only observed in the arid subsurface, indicating increased oligotrophic conditions and reliance on inorganic electron donors in the deeper subsurface of the desert. Functional analysis revealed sulphur, hydrogen, and carbon monoxide as potential inorganic electron donors. These findings expand the current understanding of microbial life in the subsurface of granite rocks showing the influence of surface climate on nutrient conditions in the deeper subsurface, providing new insights into the extent and functional capacity of terrestrial subsurface habitats and their role in global biogeochemical processes.}, }
@article {pmid41320393, year = {2026}, author = {Wang, S and De Paepe, K and Onyango, SO and Zhang, B and Huang, Q and Wang, S and Van de Wiele, T}, title = {Starch-entrapped microspheres selectively promote propionate or butyrate production through individual-specific modulation of the human fecal microbiome.}, journal = {Carbohydrate polymers}, volume = {373}, number = {}, pages = {124614}, doi = {10.1016/j.carbpol.2025.124614}, pmid = {41320393}, issn = {1879-1344}, mesh = {Humans ; *Starch/chemistry/pharmacology ; *Feces/microbiology ; *Microspheres ; Prebiotics ; *Butyrates/metabolism ; *Propionates/metabolism ; *Gastrointestinal Microbiome/drug effects ; Adult ; Male ; Zea mays/chemistry ; Female ; Inulin/chemistry ; Fermentation ; Young Adult ; }, abstract = {Starch microspheres encapsulated with chitosan synergistically and beneficially modulate the microbiota composition and metabolic activity of a pooled fecal slurry compared to starch, suggesting a superior prebiotic potential. Interindividual differences in prebiotic potential are, however, unexplored. Therefore, we incubated starch-entrapped microspheres (MS), high amylose maize starch (HAMS) and the reference prebiotic inulin with the separate fecal microbiota derived from six healthy individuals. The variation in microbial community composition was largely driven by inter-individual variability (effect size of 71.7 %). Despite the inter-individual variability, the different prebiotic substrates significantly affected the microbiota composition (effect size of 9.5 %) and metabolic activity over the course of fermentation. MS delayed the fermentation and reduced the gas production and acidification in all donors compared to HAMS and inulin. Furthermore, compared to HAMS, MS more effectively promoted propionate or butyrate production in a donor-dependent manner. MS increased butyrate levels with 0.1 ± 0.72 mM per unit of starch across all donors. Additional, MS increased the propionate production with 0.52 ± 0.71 mM per unit of starch in donors 1, 2, 4, 6. The donor-specific propiogenic and butyrogenic effects of MS were linked to the enrichment of Bacteroides and Agathobacter species. Our findings confirm the superior prebiotic effect of MS and provide directions for the design and manufacture of starch-based functional foods to enhance gut health.}, }
@article {pmid41318730, year = {2025}, author = {González-Pimentel, JL and Cuecas, A and Álvarez, C and Mariscal, V}, title = {Soil Bacteriome Shifts along a Cultivation Gradient in Southwestern Spanish Wetlands.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02660-8}, pmid = {41318730}, issn = {1432-184X}, abstract = {Understanding how long-term agricultural practices affect soil bacteriome is essential for sustainable land management. In the Guadalquivir Marshes of southwestern Spain, which encompass both Doñana National Park and one of Europe's most productive rice cultivation areas, decades of rice farming have transformed natural wetlands into artificial agroecosystems. Although bacterial degradation in cultivated soils has been previously suggested, comparative analyses between rice paddies and adjacent natural wetlands remain scarce.Here, we characterized the soil bacteriome across a cultivation gradient by comparing undisturbed natural marshes, within Doñana National Park, with rice fields cultivated for 25 years (Cantarita) and 80 years (Mínima 2). Using full 16S rRNA gene via long-read metabarcoding and standardized soil physicochemical assays, we analysed taxonomic composition, environmental associations, and predicted functional profiles.Our results reveal a progressive restructuring of bacterial communities with increased cultivation time, notably a significant enrichment of Chloroflexota (especially Anaerolineae) and a decline in Actinomycetota and Planctomycetota in paddy soils. Functional predictions indicated a higher potential for denitrification in cultivated soils-likely involving Chloroflexota taxa-compared to more diverse nitrogen pathways in natural sites. These shifts were strongly associated with changes in pH, electrical conductivity, calcium carbonate, and nitrate levels. Remarkably, most bacterial differences were already evident within the first 25 years of cultivation, underscoring the rapid ecological impact of intensive rice cultivation.Notably, we identified specific bacterial groups (Anaerolineae and Nocardioides in paddy soils; Euzebya, Rubrobacter, and Planctomycetota in natural wetlands), whose enrichment was associated with soil type. This approach highlights the value of integrating bacterial-based assessments into sustainable wetland management strategies.}, }
@article {pmid41318612, year = {2025}, author = {Rivera, DS and Beltrán, V and Hoepfner, C and Del Pilar Fernández, M and Oliva, CA and Vera, MJ and Farías, C and Valenzuela, R and Pérez, I and Correa, LA and Urbina, F}, title = {Nutritional modulation of host physiology, behavior, and gut microbiome in the captive rodent Octodon degus.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-025-26991-1}, pmid = {41318612}, issn = {2045-2322}, support = {11190603//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; }, abstract = {Diet is a key determinant of health by affecting nutrient metabolism, energy balance, body weight regulation, and mental health. The gut-brain axis is a critical pathway through which dietary factors influence cognitive function and behavior via microbial metabolites. While this relationship has been extensively studied in traditional laboratory models, diet-microbiome-cognition interactions remain largely unexplored in Octodon degus, an emerging model for aging, neurodegeneration, and cognitive research. Here, we compared two widely used rodent diets-LabDiet and Champion-to evaluate their effects on digestive efficiency, behavior, and gut microbiome composition. We also examined the relationships between these variables using piecewise structural equation modeling (pSEM). Our results indicated that LabDiet-fed degus exhibited enhanced nutrient absorption, higher fecal acetic acid levels, and a higher abundance of Actinobacteria (particularly Bifidobacterium), likely driven by its vitamin C supplementation. These animals also showed improved working memory and social motivation, but they displayed increased anxiety-like behavior. In contrast, Champion-fed degus, which consumed a more fiber-diverse, plant-based diet, showed lower anxiety traits and significantly greater gut microbial richness, with higher abundance of Bacteroidota and Tenericutes. Innate behaviors, such as burrowing and nesting, remained unaffected by the diet. SEM analysis revealed that diet explained most of the variance in microbial activity and identified a positive association between acetic acid levels and cognitive performance. This emphasizes a strong relationship among diet, microbiome, and brain function. Overall, our results suggest that dietary composition is a key factor influencing experimental outcomes in degus, with important implications for physiology, cognition, and microbial ecology. Standardizing dietary inputs is essential to ensure reproducibility in behavioral and biomedical studies using this model. Additionally, our results reinforce the microbiome's role as a mediator of diet-driven brain function via SCFAs, underscoring degus as a powerful system for investigating diet-microbiome-neurobehavioral interactions relevant to aging and mental health.}, }
@article {pmid41317466, year = {2025}, author = {Belarbi, H and Kebede, F and De Leyn, I and Van Bockstaele, F and Van De Wiele, T and Lambrecht, F and Cakmak, I and Du Laing, G}, title = {Enhancing iodine delivery through sourdough wheat bread: influence of biofortified flour and iodized salt on iodine concentration and bioaccessibility.}, journal = {Food chemistry}, volume = {498}, number = {Pt 2}, pages = {147232}, doi = {10.1016/j.foodchem.2025.147232}, pmid = {41317466}, issn = {1873-7072}, abstract = {Iodine deficiency remains a critical health concern, particularly in populations with limited access to iodized salt or shifting dietary patterns. This study assessed the impact of iodine-biofortified wheat flour (IBF), alone or combined with iodized salt (IS), on iodine content and bioaccessibility in sourdough bread. In vitro digestion showed that IBF increased iodine content to 158 μg/kg, and to 340 μg/kg with IS, compared to 1.63 μg/kg in control bread. This corresponds to an estimated intake of 68 μg/day. The IBF + IS formulation demonstrated the highest iodine bioaccessibility (224 μg/kg; 65 %). Interestingly, while iodine-fortified breads showed reduced values for selenium, potassium, and calcium, breads made with plain salt exhibited higher bioaccessibility for these minerals. These findings confirm the efficacy of IBF in enhancing iodine intake and its potential as an alternative or complement to salt iodization. They also indicate the importance of fortification approaches, considering the broader nutritional matrix over individual nutrients.}, }
@article {pmid41315866, year = {2025}, author = {Engelberts, JP and Tyson, GW}, title = {Understanding microbial ecology and evolution with single-cell genomics.}, journal = {Nature reviews. Genetics}, volume = {}, number = {}, pages = {}, pmid = {41315866}, issn = {1471-0064}, }
@article {pmid41315055, year = {2025}, author = {Gallardo-Becerra, L and Cornejo-Granados, F and Bikel, S and Arenas, I and López-Leal, G and Alvarado-Gonzalez, C and Sánchez-López, F and Manzo, R and Corzo, G and Espino-Solis, GP and Canizales-Quinteros, S and Ochoa-Leyva, A}, title = {Bioactive Plasmid- and Phage-Encoded Antimicrobial Peptides (AMPs) in the Human Gut: A Metatranscriptome-Virome Profiling Reveals Exploratory Links to Metabolic Human Diseases.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02620-2}, pmid = {41315055}, issn = {1432-184X}, abstract = {Microbe-derived antimicrobial peptides (AMPs) can shape gut community structure; however, their contribution to disease-associated dysbiosis remains poorly understood. We assembled fecal metatranscriptomes from individuals with normal weight (NW), obesity (O), and obesity with metabolic syndrome (OMS), yielding 51,087 non-human transcripts. We screened 1,095 small open reading frames (smORFs) using AMP-prediction algorithms combined with stringent post-hoc bioinformatics filters identifying 51 high-confidence AMP candidates. Most matched bacterial homologs, predominantly Faecalibacterium prausnitzii, while eight mapped to plasmids or bacteriophages. Differential expression identified two and four AMPs overexpressed in O and OMS, respectively. Two of them were originated from chromosomes, three from phages, and one from plasmid. Notably, the over-expression of these AMPs was negatively correlated with healthy-associated bacteria and positively correlated with obesity-enriched taxa. Furthermore, these AMPs were broadly detectable across 372 external gut metatranscriptomes (prevalence up to 94% of the samples) indicating conservation within the human gut microbiome and highlighting mobile elements as an overlooked reservoir of transcriptionally active AMPs. Using DNA virome sequencing and prophage analyses, we suggested phage origin of the transcribed AMPs. We further synthesized a phage-encoded AMP (AMP-3020), demonstrating broad-spectrum activity against Gram-positive and Gram-negative bacteria, without detectable cytotoxicity toward human immune T cells. This supports the idea that phages could encode functional AMPs capable of shaping gut community structure by suppressing diverse bacteria without harming host immune cells. Our gut metatranscriptome-virome profiling revealed a conservative core of actively transcribed, plasmid- and phage-encoded AMPs with exploratory associations to obesity/MetS. These findings support mobile-element AMPs as candidate ecological regulators and motivate validation in larger cohorts and mechanistic models.}, }
@article {pmid41314076, year = {2025}, author = {Md Ali, SA and Saito, S and Nishiyama, M and Phung, LD and Watanabe, T}, title = {Composted sewage sludge reshapes soil resistome connectivity and enhances antibiotic resistance gene dissemination in paddy fields.}, journal = {The Science of the total environment}, volume = {1009}, number = {}, pages = {181049}, doi = {10.1016/j.scitotenv.2025.181049}, pmid = {41314076}, issn = {1879-1026}, abstract = {The reuse of organic waste streams, such as composted sewage sludge (CSS), provides agronomic benefits, but also represents a critical pathway for the environmental dissemination of antibiotic resistance genes (ARGs). The consequences of CSS application for soil resistome dynamics and microbial ecology remain insufficiently understood. Here, we investigated paddy soils in Tsuruoka, Japan, under three fertilization treatments: CSS, chemical fertilizer (CF), and their combination (CSS + CF). Quantitative PCR targeted total bacterial (16S rRNA), fecal indicators (E. coli, Enterococcus spp.), mobile genetic element (MGE) (inlt1), and five ARGs (sul1, blaTEM, blaCTX-M Groups 1, 2, and 9). CSS amended soils showed elevated levels of intI1, sul1, and blaTEM in 2023, with blaTEM persisting into 2024. Although both E. coli and Enterococcus spp. showed weak correlations with ARGs, only Enterococcus spp. (ρ = 0.37, p < 0.05) showed statistically significant associations with intI1. Network analysis demonstrated that CSS fostered a highly interconnected resistome with sul1 emerging as a central hub linking multiple bacterial families. In contrast, CF maintained a sparse modular structure while CSS + CF generated an intermediate network. Collectively, these results demonstrate that CSS amplifies the potential for ARG dissemination by fostering a highly connected resistome, whereas co-application with chemical fertilizers partially disrupts this connectivity, thereby reducing dissemination risk in the soil environment. Our findings provide field-based evidence of the environmental impacts of waste-derived fertilization and underscore the need for integrated fertilization strategies and ARG surveillance to promote sustainable soil management and safeguard environmental health.}, }
@article {pmid41313007, year = {2025}, author = {Fletcher, JR and Hansen, LA and Hoyser, JR and Hanna, AE and Martinez, R and Freeman, CD and Thorns, NT and Penningroth, MR and Villarreal, AR and Vogt, GA and Tyler, MA and Hines, KM and Hunter, RC}, title = {Commensal-derived short-chain fatty acids disrupt lipid membrane homeostasis in Staphylococcus aureus.}, journal = {mBio}, volume = {}, number = {}, pages = {e0139225}, doi = {10.1128/mbio.01392-25}, pmid = {41313007}, issn = {2150-7511}, abstract = {The role of commensal anaerobic bacteria in chronic respiratory infections is unclear, yet they can exist in abundances comparable to canonical pathogens in vivo. Their contributions to the metabolic landscape of the host environment may influence pathogen behavior by competing for nutrients and creating inhospitable conditions via toxic metabolites. Here, we show that the anaerobe-derived short-chain fatty acids (SCFAs) propionate and butyrate negatively affect Staphylococcus aureus physiology by disrupting branched-chain fatty acid (BCFA) metabolism. In turn, alterations to BCFA abundance impair S. aureus growth, compromise membrane integrity, diminish expression of the accessory gene regulator quorum-sensing system, and increase sensitivity to membrane-targeting antimicrobials. Disrupted BCFA metabolism also reduced S. aureus fitness in competition with Pseudomonas aeruginosa, suggesting that airway microbiome composition and the metabolites they exchange can directly impact pathogen succession over time. The pleiotropic effects of SCFAs on S. aureus fitness and their ubiquity as metabolites in the human host also suggest that they may be effective as adjuvants to traditional antimicrobial agents when used in combination.IMPORTANCEStaphylococcus aureus is a primary pathogen of chronic airway disease yet is also found in the upper airways of 30%-50% of the population to no obvious detriment. Thus, identifying the host and/or microbial factors that tip the balance between its commensal and pathogenic states may be key to its control. Here, we reveal that short-chain fatty acids produced by commensal microbiota promote a marked remodeling of the S. aureus lipid membrane that, in turn, sensitizes the pathogen to antimicrobials, disrupts accessory gene regulator quorum signaling, and reduces its competitive fitness. Altogether, these data suggest that co-colonizing microbiota and the metabolites they exchange with S. aureus may be key players in the microbial ecology of airway disease.}, }
@article {pmid41311479, year = {2025}, author = {Gao, Y and Zhang, L and Zhang, Y and Huang, J and Wu, C and Zhou, R}, title = {Synthetic microbial community SMC-L1 optimizes flavor chemistry in reduced salt soy sauce via targeted metabolic reprogramming.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1701479}, pmid = {41311479}, issn = {1664-302X}, abstract = {The high sodium content in traditional soy sauce presents significant public health concerns, particularly related to hypertension and cardiovascular diseases. However, reducing salt content often disrupts microbial ecology and impairs flavor formation during fermentation. To overcome this challenge, we developed synthetic microbial communities (SynMCs) for reduced-salt (13% NaCl) moromi fermentation under traditional sun-brewing conditions. Using integrated multi-omics analyses, we identified an optimal consortium (SMC-L1) incorporating Tetragenococcus halophilus T10 as a key lactic acid bacterium alongside functional yeast strains. This defined community maintained fermentation stability while significantly enhancing flavor-relevant biochemical profiles. SMC-L1 inoculation markedly improved key quality parameters, increasing total nitrogen by 40.8% and amino acid nitrogen by 56.7%. Furthermore, it elevated critical metabolites including organic acids, particularly succinate, free amino acids, and short-chain esters. Network analysis revealed robust ecology-metabolite relationships: Tetragenococcus abundance correlated with succinate production and ester synthesis, while Aspergillus dynamics corresponded with free amino acid accumulation. These findings highlight how targeted microbial consortia can reprogram metabolic networks under salt-reduced conditions. From a food microbiology perspective, this study demonstrates that rational design of microbial communities can effectively decouple salt reduction from flavor deterioration in fermented foods. The metabolic pathways observed, particularly the anaerobic TCA cycle activity connecting Tetragenococcus to succinate accumulation, provides mechanistic insights into microbial adaptation to reduced-salt environments. This approach offers a viable strategy for developing healthier fermented products without compromising their sensory characteristics, advancing both fundamental knowledge and practical applications in food biotechnology.}, }
@article {pmid41307726, year = {2025}, author = {Ferreira, CM and de Affonseca, DB and Barbosa, FAS and Campos, AB and Menezes, R and Brait, L and Viana, PAB and Trindade-Silva, AE and Loiola, M and Azevedo, AR and Coutinho, FH and Assis, APA and Bruce, T and Ramos, PIP and Ara, A and Brouns, R and Andrade, RFS and Guimarães, PR and Meirelles, PM}, title = {Rare Phyla, Such as CPR and DPANN, Shape Ecosystem-Level Microbial Community Structure Dissimilarities.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {135}, pmid = {41307726}, issn = {1432-184X}, support = {88887-468244-2019-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 114693/2022-6//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; RYC2022-037094-I//Ministerio de Ciencia e Innovaci&#xf3;n/ ; Serra-1709-17818//Instituto Serrapilheira/ ; }, mesh = {*Bacteria/classification/genetics/isolation &amp; purification ; *Archaea/classification/genetics/isolation &amp; purification ; *Microbiota ; *Ecosystem ; Metagenome ; Biodiversity ; Phylogeny ; Soil Microbiology ; }, abstract = {Rare microbial lineages, such as members of the candidate phyla radiation (CPR) bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) archaea, are increasingly recognized as key components of microbial communities in natural systems. Yet, their global distribution, biogeographic patterns, and broader role in shaping microbial community structure across diverse ecosystems remain poorly characterized. Here, we analyzed 2860 metagenomes spanning nine ecosystems using a curated reference database and a bias-aware taxonomic filtering approach to quantify the richness, relative abundance, and structural influence of low-abundance microbial taxa on community structure across a wide range of ecosystems. Our findings reveal that rare taxa, primarily CPR and DPANN, disproportionately shape microbial community dissimilarities across global ecosystems. We observed that the richness of these two groups, that drives community structure variation, increases with latitude, peaking in temperate regions, thereby contrasting classical latitudinal diversity patterns and suggesting unique biogeographic drivers. CPR and DPANN were predominantly enriched in free-living environments, particularly groundwater and soil, then in host-associated habitats, consistent with niche specialization shaped by environmental filtering and dispersal constraints. These findings challenge abundance-centric assumptions in microbial ecology and highlight the need to integrate low-abundance taxa into macroecological frameworks. Fully resolving their ecological functions, however, will require targeted experimental and multi-omics investigations.}, }
@article {pmid41304320, year = {2025}, author = {Tawidian, P and Tucker, BJ and Zembsch, TE and Ip, HS and Bartholomay, LC}, title = {Infection-Mediated Shifts in the Microbial Communities of Deer-Fed Ixodes scapularis Ticks.}, journal = {Microorganisms}, volume = {13}, number = {11}, pages = {}, pmid = {41304320}, issn = {2076-2607}, support = {cooperative agreement U01CK000505/CC/CDC HHS/United States ; G21AC10134//United States Department of Agriculture/ ; }, abstract = {The holobiont of the blacklegged tick (Ixodes scapularis) includes maternally inherited rickettsial endosymbionts and environmentally acquired microbes that may influence tick fitness and vector competence. While previous studies have focused on characterizing the microbiota of I. scapularis ticks, less is known about the influence of tick infection status on microbial assemblages. Here, we collected engorged female I. scapularis ticks from hunter-harvested white-tailed deer (Odocoileus virginianus) across 11 counties in Wisconsin during fall 2022. The ticks were maintained in laboratory conditions for oviposition and then frozen for nucleic acid extraction. The infection status of each tick was determined using qPCR, targeting Borrelia spp., Babesia spp., and Powassan virus. Bacterial and fungal communities were characterized through amplicon-based sequencing targeting the 16S rRNA gene and ITS2 region, respectively. Our targeted pathogen testing revealed that 14.1% of the collected ticks were infected with Babesia odocoilei and 23.3% with Borrelia burgdorferi. The microbial community composition of ticks was significantly influenced by infection status and pathogen identity. Notably, Borrelia-infected ticks exhibited distinct microbiota profiles and increased microbial network connectivity. These findings provide new insights into the microbial ecology of deer-fed I. scapularis ticks and highlight the role of infection in shaping both microbiota and mycobiota communities.}, }
@article {pmid41304309, year = {2025}, author = {Paoli, JE and Thongthum, T and Bassett, M and Beardsley, J and Tagliamonte, MS and Cash, MN and Spertus Newman, J and Smith, LM and Anderson, BD and Salemi, M and Subramaniam, K and von Fricken, ME and Braun de Torrez, E and Mathis, V and Mavian, CN}, title = {Virome and Microbiome of Florida Bats Illuminate Viral Co-Infections, Dietary Viral Signals, and Gut Microbiome Shifts.}, journal = {Microorganisms}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/microorganisms13112625}, pmid = {41304309}, issn = {2076-2607}, support = {Department of Pathology EPIG RAS 2021-2022//University of Florida/ ; Florida Informatics Institute SEED 2022-2023//University of Florida/ ; Biodiversity Institute SEED 2022-2023//University of Florida/ ; }, abstract = {Florida's bat virome remains poorly characterized despite the state's high bat species diversity and conservation importance. We characterized viral metagenomes from rectal tissues, anal swabs, and feces of Myotis austroriparius and Tadarida brasiliensis sampled across north Florida. We recovered a near-complete Hubei virga-like virus 2 (HVLV2) genome from T. brasiliensis feces, a finding consistent with an arthropod-derived dietary signal rather than active bat infection. An Alphacoronavirus (AlphaCoV) was detected in two M. austroriparius specimens, including one with a putative co-infection involving an Astrovirus (AstV), the first detection of AstV in Florida bats to date. Parallel profiling of the M. austroriparius gut microbiome highlighted compositional differences in the co-infected individual relative to AlphaCoV-only and virus-negative bats, suggestive of potential associations between viral detection and gut microbial shifts. Our study expands the known viral diversity in Florida bat populations, and demonstrates how metagenomics can simultaneously illuminate host diet, viral exposure, and gut microbial ecology. This approach provides a scalable framework for monitoring how diet, microbiome composition, and environmental pressures shape the bat virome, and inform conservation and zoonotic risk assessments.}, }
@article {pmid41304257, year = {2025}, author = {Ma, R and Chen, Y and Chen, X and Zhang, J and Liu, C and Yang, L and Song, Y and Sun, Z and Lin, X and Ai, T and Ren, D and Chen, S}, title = {The Dominant Role of Dietary Differences in Shaping the Intestinal Microbial Communities of Grass Carp, Carp, and Crucian Carp in a Saline-Alkali Lake in Xinjiang During Winter.}, journal = {Microorganisms}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/microorganisms13112572}, pmid = {41304257}, issn = {2076-2607}, support = {Grant No. 2023YFD2401000;Grant No.2023TSYCCX0128;2024AB019;Grant No. XJARS-08-14//The Key R &amp; D plan of Ministry of Science and Technology;The Tianshan Talent Training Project of Xinjiang;The Key Scientific and Technological Research Projects of Xinjiang Production and Construction Corps;Xinjiang Agriculture Research System/ ; }, abstract = {In this study, gut microorganisms of herbivorous grass carp, omnivorous carp, crucian carp, and aquatic microorganisms were collected from natural salt-alkali lakes and ponds in Xinjiang in winter to analyze their community structures. We sequenced 16S rRNA amplicons to investigate the composition and function of the microorganisms in the gut. PCoA analysis revealed that the gut microbiota of herbivorous and omnivorous fish formed two distinct clusters. Proteobacteria, Actinobacteria, Desulfobacterota, Firmicutes, and Chloroflexia are the dominant bacteria in the gut of fish. Proteobacteria, Bacteroidetes, Actinobacteria, Cyanobacteria, and Gram-negative bacteria are the dominant bacteria in the water. Carbohydrate- and protein-degrading bacteria, such as Desulfofustis, Lactiplantibacillus, and Vibrio, were predominant in omnivorous fish (CC and GRC), while cold-resistant bacteria, such as Shewanella and Psychromonas, were colonized in grass carp. This suggests that the same environment does not lead to similar gut bacteria, and that specific endogenous factors play a far more important role in shaping the microbiota composition than environmental factors.}, }
@article {pmid41304168, year = {2025}, author = {Ouyang, H and Grześkowiak, &#x141; and Vahjen, W and Zentek, J and Martínez-Vallespín, B}, title = {Effects of Fibrous By-Products on Growth Performance, Ileal Nutrient Digestibility, Intestinal Morphology, and Microbiota Composition in Weaned Piglets.}, journal = {Microorganisms}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/microorganisms13112482}, pmid = {41304168}, issn = {2076-2607}, abstract = {Three fibrous by-products were evaluated over a 35-day feeding period in 64 weaned piglets, randomly assigned to four groups: a control without by-products (CON) and three others with diets containing 8% carrot pomace (CRT), 8% brewers' spent grain (BSG), or 8% carob pods (CRB). The growth performance, feed intake, feed conversion ratio, and apparent ileal digestibility of protein and amino acids were not affected. The jejunal and colonic morphology showed no statistical differences, although small numerical increases in the villus height and villus height-to-crypt ratio were noted with the by-products. Total short-chain fatty acid concentrations were stable, but their profile shifted: acetate increased in CRT and CRB (p < 0.001) mainly at the expense of propionate (p = 0.005). The microbiota composition in the proximal colon showed modest changes, with the highest Bifidobacterium spp. abundance in CRT and lowest in CRB (p = 0.042), reduced Ruminococcaceae UCG 005 with all the by-products (p = 0.008), and greater microbial richness in CRB (p = 0.009). These results suggest that a moderate inclusion of fibrous by-products may influence intestinal microbial ecology and fermentation patterns without negatively affecting performance or nutrient digestibility in weaned piglets, with no source appearing superior, thereby highlighting their potential as sustainable feed ingredients.}, }
@article {pmid41304165, year = {2025}, author = {Tong, F and Feng, X and Yuan, H and Chen, Y and Chen, P}, title = {Oyster Aquaculture Impacts on Environment and Microbial Taxa in Dapeng Cove.}, journal = {Microorganisms}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/microorganisms13112480}, pmid = {41304165}, issn = {2076-2607}, support = {SML2023SP237//Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)/ ; 2023TD06//Central Public-interest Scientific Institution Basal, Research Fund, CAFS/ ; 2024YFD2401405; 2024YFB4206600//National Key Research and Development Program of China/ ; }, abstract = {Environmental physicochemical factors and microorganisms play critical roles in the health of oysters. However, the impact of high-density oyster farming-a highly efficient filter-feeding bivalve system-on environmental conditions and microbial community structure and function remains poorly understood. This study conducted four-season monitoring of the water and sediment parameters in a semi-enclosed bay commercial oyster aquaculture (OA) system and a control area (CT), coupled with 16S rRNA amplicon sequencing of the environmental microbiota. Oyster aquaculture caused negligible disruption to water column parameters but significantly increased the concentrations of total organic carbon (TOC, annual mean OA vs. CT:1.15% vs. 0.56%), sulfides (annual mean OA vs. CT:67.72 vs. 24.99 mg·kg[-1]), and heavy metals (Cd, Pb, Cu, Zn, and Cr) in the sediment. α-diversity (Shannon and Chao indices) exhibited minimal overall perturbation, with significant inter-regional differences observed only in winter for both water and sediment. The bacterial community structure of the water column was significantly altered only in winter, whereas sediment communities showed structural shifts in spring, summer, and autumn. Water microbiota were primarily influenced by turbidity, dissolved oxygen, salinity, the Si/N ratio, and silicates. Sediment microbiota were correlated with Pb, Cu, Zn, TOC, Cr, and sediment particle size. Water bacterial functions displayed only four significantly divergent biogeochemical processes annually (sulfur compound respiration; OA vs. CT). In contrast, sediment bacteria exhibited 29 significantly disrupted functions annually, with the greatest seasonal divergence in winter (11/67 functions). Spring, summer, and autumn sediment functions showed distinct patterns. Understanding these environmental-microbial interactions is essential for sustainable oyster aquaculture and ecological optimization.}, }
@article {pmid41304129, year = {2025}, author = {Zhong, Y and Wu, C and E, J and Gu, Y and Chi, H and Du, X}, title = {Bioavailability, Ecological Risk, and Microbial Response of Rare Earth Elements in Sediments of the Remediated Yitong River: An Integrated DGT and Multi-Parameter Assessment.}, journal = {Microorganisms}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/microorganisms13112443}, pmid = {41304129}, issn = {2076-2607}, abstract = {The expanding use of rare earth elements (REEs) in high-tech industrials has increased their environmental release, raising concerns about their ecological risks. This study employed the Diffusive Gradients in Thin Films (DGT) technique to assess REE bioavailability, spatial distribution, and ecological risks of REEs in sediments of the Yitong River, a historically polluted urban river in Changchun, China. Sediment characteristics (organic matter, pH, salinity), nutrient dynamics (N, P), and metal concentrations (Fe, Mn, As, etc.) were analyzed alongside REEs to evaluate their interactions and environmental drivers. Results revealed that REE concentrations (0.453-1.687 μg L[-1]) were dominated by light REEs (50.1%), with levels an order of magnitude lower than heavily industrialized regions. Ecological risk quotients (RQ) for individual REEs were below thresholds (RQ < 1), indicating negligible immediate risks, though spatial trends suggested urban runoff influences. Probabilistic risk assessment integrating DGT data and species sensitivity distributions (SSD) estimated a low combined toxic probability (2.26%) for REEs and nutrients. Microbial community analysis revealed correlations between specific bacterial (e.g., Clostridium, Dechloromonas) and fungal genera (e.g., Pseudeurotium) with metals and REEs, highlighting microbial sensitivity to pollutant shifts. This study provides a multidimensional framework linking REE bioavailability, sediment geochemistry, and microbial ecology, offering insights for managing REE contamination in urban riverine systems.}, }
@article {pmid41304117, year = {2025}, author = {Guo, M and Liu, D and Xia, Z and Xie, T and Su, L and Pérez-Moreno, J and Yu, F}, title = {Geographic Provenances Outweigh Tissue Compartments in Bacteriome Assembly of the Ectomycorrhizal, Edible, and Hallucinogenic if Undercooked, Lanmoa asiatica (Boletaceae, Boletales) Mushroom from Yunnan China.}, journal = {Microorganisms}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/microorganisms13112431}, pmid = {41304117}, issn = {2076-2607}, support = {KCXFZJ-DDBF-202403//Designated Support Project of Chinese Academy of Sciences/ ; Guike AB22080097//the Key Research and Development Program of GuangXi/ ; 202205AD160036//the Yunnan Technology Innovation Program/ ; }, abstract = {Ectomycorrhizal fungal sporomes represent complex microuniverses harboring structurally and functionally eclectic microbiomes with significant ecological roles and potential anthropogenic applications. Nevertheless, the factors governing the assembly of these microbial communities remain poorly understood, and numerous fungal taxa, including many ectomycorrhizal species, remain uninvestigated. This study characterizes the bacteriome of the socioculturally and economically important yet hallucinogenic-if-raw ectomycorrhizal bolete Lanmoa asiatica. We analyzed 36 basidiomata from four geographic locations within China, partitioning each into pileus, stipe, and hymenophore tissues, and sequenced the V5-V7 region of the bacterial 16S rRNA gene. Proteobacteria dominated (>85%), with Pantoea, Sphingomonas, and the Burkholderia complex identified as core genera. Contrary to expectations, α-diversity was highest in the stipe (Chao1 index up to 1934) rather than the exposed hymenophore. PERMANOVA indicated that geographic origin (R[2] = 0.46, p < 0.001) was a stronger structuring force than tissue type (R[2] = 0.28, p < 0.01). Functional prediction via PICRUSt2 revealed enrichments in lipid metabolism, antimicrobial resistance, and apoptosis pathways across sites, while tissue-specific functions involved carbohydrate and nitrogen metabolism. These findings support a hierarchical model of bacteriome assembly where broad-scale environmental filters override micro-niche differentiation, providing a biogeographic framework for the conservation of this highly valued edible mushroom.}, }
@article {pmid41301533, year = {2025}, author = {Sabharwal, A and Haase, EM and Scannapieco, FA}, title = {Amylase Binding to Oral Streptococci: A Key Interaction for Human Oral Microbial Ecology, Adaptation and Fitness.}, journal = {Biomolecules}, volume = {15}, number = {11}, pages = {}, doi = {10.3390/biom15111616}, pmid = {41301533}, issn = {2218-273X}, support = {1R01DE022673-01/NH/NIH HHS/United States ; 1C06DC022673-18/NH/NIH HHS/United States ; }, mesh = {Humans ; *Mouth/microbiology ; *Streptococcus/metabolism/enzymology ; Biofilms/growth &amp; development ; *Amylases/metabolism ; Bacterial Adhesion ; Adaptation, Physiological ; Microbiota ; }, abstract = {The interaction between human salivary alpha-amylase (HSAmy) and amylase-binding oral streptococci (ABS) helps determine the bacteria that colonize the oral cavity by establishing dental biofilms. Streptococci are important pioneer species of the oral cavity and influence oral health as well as common diseases such as dental caries. Various oral streptococcal species express distinct amylase-binding proteins, among which amylase-binding protein A (AbpA), encoded by the abpA gene in Streptococcus gordonii and several other species, which is the most extensively studied. Amylase binding facilitates microbial adhesion to host surfaces and biofilm formation and enables bacteria to harness the host's amylase enzymatic activity at their cell surface, enhancing their capacity to metabolize dietary starch for nutritional gain. Additionally, amylase binding may also influence bacterial cell division and stress tolerance by engaging novel bacterial signaling pathways. From an evolutionary perspective, both Neanderthals and modern humans exhibit functional adaptations in nutrient metabolism, including selection for salivary amylase-binding oral streptococci, highlighting the importance of microbial co-adaptation in response to host diet. Further research is warranted to elucidate the broader roles of amylase binding to bacteria in host-bacterial signaling, bacterial cell division and fitness and the evolutionary trajectory of the oral microbiome.}, }
@article {pmid41301495, year = {2025}, author = {Teslya, AV and Stepanov, AA and Poshvina, DV and Petrushin, IS and Vasilchenko, AS}, title = {From Lab to Field: Context-Dependent Impacts of Pseudomonas-Produced 2,4-Diacetylphloroglucinol on Soil Microbial Ecology.}, journal = {Biomolecules}, volume = {15}, number = {11}, pages = {}, doi = {10.3390/biom15111578}, pmid = {41301495}, issn = {2218-273X}, support = {19-76-30005//Russian Science Foundation/ ; FEVZ-2024-0005//The Ministry of Science and Higher Education of the Russian Federation/ ; }, mesh = {*Soil Microbiology ; *Phloroglucinol/analogs &amp; derivatives/pharmacology/metabolism ; *Pseudomonas/metabolism ; Fungi/drug effects/genetics ; Bacteria/drug effects/genetics ; Microbiota/drug effects ; }, abstract = {The secondary metabolite 2,4-diacetylphloroglucinol (2,4-DAPG), which is produced by Pseudomonas bacteria, is a potent antimicrobial agent with well-documented properties that suppress phytopathogens. However, its broader ecological impact on soil microbial communities is not understood. Through a combination of controlled microcosm and field trials, we have demonstrated that the effects of 2,4-DAPG are highly context-dependent. Laboratory exposure (10 mg kg[-1]) altered the abundance of 8.53% of bacterial and 6.91% of fungal amplicon sequence variants, and simplified the bacterial co-occurrence networks (reduced number of nodes and links). In contrast, field conditions amplified bacterial sensitivity (the Shannon index decreased from 4.77 to 4.17, p < 0.05) but maintained fungal stability (Shannon index varied from 3.93 to 3.97, p > 0.05); these conditions affected a smaller proportion of fungal ASVs (4.23%). Taxonomic analysis revealed consistent suppression of fungi of the Mucoromycota (e.g., Mortierella) and context-dependent shifts in bacteria, with an enrichment of Bacillota (e.g., Bacillus, Paenibacillus) in the laboratory but not in the field. Enzymatic responses revealed a dose-dependent activation of the C-cycle, with up to 7.4-fold increases in the laboratory and up to a 10.5-fold increase in the field. P- and N- cycles showed more complex dynamics, with acid phosphatase activity increasing 3.8-fold in laboratory conditions and recovering from initial suppression to an increase of 144% in field conditions, while N-acetylglucosaminidase activity increased and L-leucine aminopeptidase decreased under laboratory conditions. Our results suggest that the response of microorganisms to 2,4-DAPG in natural soils is reduced, probably due to functional redundancy and pre-adaptation to abiotic stresses. This difference between laboratory and field studies warns against extrapolating data from controlled experiments to predict outcomes in agricultural ecosystems, and emphasizes the need for a context-specific evaluation of biocontrol agents.}, }
@article {pmid41301464, year = {2025}, author = {Cai, Y and Zhao, F and Cheng, X}, title = {Gut Microbiota and Ferroptosis in Colorectal Cancer: A Comprehensive Review of Mechanisms and Therapeutic Strategies to Overcome Immune Checkpoint Resistance.}, journal = {Biomolecules}, volume = {15}, number = {11}, pages = {}, doi = {10.3390/biom15111546}, pmid = {41301464}, issn = {2218-273X}, mesh = {Humans ; *Ferroptosis/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Colorectal Neoplasms/microbiology/immunology/therapy/drug therapy/pathology/metabolism ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Animals ; *Drug Resistance, Neoplasm ; }, abstract = {Colorectal cancer (CRC) remains a leading cause of cancer-related mortality worldwide. Although immune checkpoint inhibitors (ICIs) have achieved striking clinical efficacy in the subset of CRCs with mismatch repair deficiency/high microsatellite instability (dMMR/MSI-H), the vast majority of patients-those with proficient mismatch repair/microsatellite-stable (pMMR/MSS) tumors-derive little benefit from current immunotherapies. Ferroptosis, an iron-dependent form of regulated cell death driven by lethal accumulation of lipid peroxides, has emerged as a promising antitumor mechanism that can interact with and modulate antitumor immunity. Concurrently, the gut microbiota exerts powerful control over host metabolism and immune tone through microbial community structure and metabolite production; accumulating evidence indicates that microbiota-derived factors can either sensitize tumors to ferroptosis (for example, via short-chain fatty acids) or confer resistance (for example, indole-3-acrylic acid produced by Peptostreptococcus anaerobius acting through the AHR→ALDH1A3→FSP1/CoQ axis). In this review we synthesize mechanistic data linking microbial ecology, iron and lipid metabolism, and immune regulation to ferroptotic vulnerability in CRC. We discuss translational strategies to exploit this "microbiota-ferroptosis" axis-including precision microbiome modulation, dietary interventions, pharmacologic ferroptosis inducers, and tumor-targeted delivery systems-and we outline biomarker frameworks and trial designs to evaluate combinations with ICIs. We also highlight major challenges, such as interindividual microbiome variability, potential collateral harm to ferroptosis-sensitive immune cells, adaptive antioxidant compensation (e.g., NRF2/FSP1 activation), and safety/regulatory issues for live biotherapeutics. In summary, this review highlights that targeting the microbiota-ferroptosis axis may represent a rational and potentially transformative approach to reprogramming the tumor microenvironment and overcoming immune checkpoint resistance in pMMR/MSS colorectal cancer; however, further research is essential to validate this concept and address existing challenges.}, }
@article {pmid41300079, year = {2025}, author = {Guo, X and Lin, M and Le, TN and Zhou, Z and Zhao, M and Cai, H}, title = {Impact of Aspergillus Species on Microbial Community Dynamics and Their Associations with Fermentation Properties in Fermented Walnut-Based Soy Sauce.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {22}, pages = {}, doi = {10.3390/foods14223921}, pmid = {41300079}, issn = {2304-8158}, support = {32172214, 31972079//National Natural Science Foundation of China/ ; }, abstract = {This study investigated microbial community dynamics and their links to fermentation traits in solid-state fermentation of walnut -based soy sauce (WSS) using walnut meal-soybean meal mixtures. Via 16S rRNA sequencing and molecular docking, it analyzed the effects of three distinct starter culture treatments-Aspergillus oryzae (AO), Aspergillus niger (AN), and mixed starter culture (A. oryzae + A. niger, ON)-as well as fermentation duration on microbial diversity and physicochemical properties, aiming to clarify microbial-driven quality mechanisms. Physicochemical analysis demonstrated superior fermentation performance in the AO group, showing significantly higher amino nitrogen (NH3-N) accumulation (0.23 g/100 mL) and protease activity (30.5 U/mL) compared to the AN group, with the mixed inoculation group (ON) exhibiting intermediate results, indicating A. oryzae's dominant role in mixed fermentation. Via PCA and Shannon index, microbial diversity analyses revealed starter cultures shaped microbial community structure: Enterococcus and Staphylococcaceae were enriched by AO starter, and Klebsiella dominated in AN group. Additionally, temporal succession of the microbiota occurred during post-fermentation of WSS, with Lactobacillales, Staphylococcus, and special flavor-producing functional flora dominating early, middle, and later stages, respectively. Staphylococcus positively correlated with protease activity and amino nitrogen, critical for quality. Molecular docking showed major walnut polyphenols significantly affected protease activity, aiding process optimization. This research provides theoretical foundations for improving WSS production and enriches understanding of solid-state fermentation microbial ecology.}, }
@article {pmid41299791, year = {2025}, author = {Cheng, Q and Ma, J and Yang, Y and Ma, J and Grossart, HP and Xu, L and Lin, H}, title = {Enrichment of vitamin B12-producing Porphyrobacter in the phycosphere microbiome promotes microalgal stress adaptation to antibiotic exposure.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {240}, pmid = {41299791}, issn = {2049-2618}, support = {42207285//National Natural Science Foundation of China/ ; 42177002//National Natural Science Foundation of China/ ; LMS25C150001//Natural Science Foundation of Zhejiang Province/ ; 2021R52045//Leading talents in scientific and technological innovation, high-level Talents of Zhejiang Special Support Program/ ; 202204T14//Key Scientific Research and Development Program of Hangzhou/ ; }, mesh = {*Vitamin B 12/biosynthesis/metabolism ; *Microalgae/drug effects/microbiology/growth &amp; development/physiology ; *Anti-Bacterial Agents/pharmacology ; *Microbiota ; Stress, Physiological ; Adaptation, Physiological ; }, abstract = {BACKGROUND: Planktonic microalgae deploy multifaceted responsive and adaptive strategies against anthropogenic pollutants; however, current understanding of antibiotic resistance mechanisms remains predominantly focused on intrinsic physiological adaptations. While microalgae maintain intimate relationships with the phycosphere microbiome, the ecological roles of these associated microbes in mediating host adaptation to polluted environments are inadequately characterized.<br><br>RESULTS: We identified a phycosphere microbiome-involved antibiotic resistance mechanism in Dictyosphaerium sp., a pollution-tolerant Chlorophyta microalgae exhibiting remarkable enrofloxacin (ENR) tolerance. Microalgal growth displayed initial inhibition followed by significant promotion under 5&#xa0;mg/L ENR exposure. This resilience was associated with the restructuring of phycosphere microbiome, characterized by Porphyrobacter enrichment and functional enhancement of algal fitness-promoting pathways, including upregulation of cobalamin biosynthesis genes (log2FC&#x2009;=&#x2009;7.76) and a 33.3-fold increase in extracellular B12 accumulation. Consequently, we isolated the ENR-selected microbial taxa to elucidate their roles in microalgal stress adaptation. Co-culturing axenic Dictyosphaerium sp. with Porphyrobacter enhanced microalgal growth by 36.5% after 8-day ENR exposure, whereas non-dominant bacteria exhibited negligible effects. Based on the transcriptomic and metabolomic analyses of the algal system when Porphyrobacter was dominant, we subsequently compared the growth of axenic microalgae with and without B vitamin (B1, B6, B7, B12) supplementation. Experimental validation demonstrated the pivotal role of B12-producing Porphyrobacter in enhancing microalgal ENR adaptation through (i) stimulating extracellular polymeric substances production and subsequently enhancing ENR removal via EPS-mediated adsorption and (ii) alleviating intracellular oxidative stress via elevating superoxide dismutase and peroxidase activities and reducing malondialdehyde levels. Additionally, this B12-producing bacteria/B12-mediated adaptability exhibited cross-species conservation, improving ENR resistance in Chlorella vulgaris and Scenedesmus quadricauda, with analogous protection observed under ciprofloxacin and norfloxacin exposures.<br><br>CONCLUSION: Collectively, our findings establish stress-induced enrichment of B12-producing Porphyrobacter within the phycosphere microbiome as a pivotal mechanism underlying microalgal antibiotic adaptation. This insight facilitates the rational development of microalgae-microbiome systems for enhanced wastewater treatment and sustainable bioproduction, with applications in aquatic feed supplementation, biofuel production, and biofertilizer development. Video Abstract.}, }
@article {pmid41299662, year = {2025}, author = {Jiménez, DJ and Jamil, T and Miliotis, G and Schultz, J and Patel, N and Aldakheel, L and Kontis, N and García, FC and Villela, HDM and Duarte, GAS and Barno, AR and Farran, A and Alsaggaf, A and Santoro, &#xc9;P and Tumeo, A and Page, A and Wong, S and Kabza, A and Putra, A and Park, C and Angelov, A and Driguez, P and Peixoto, RS and Green, SJ and Tighe, S and Rosado, AS and Venkateswaran, K}, title = {Microbial community characterization in Red Sea-derived samples using a field-deployable DNA extraction system and nanopore sequencing.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-025-00819-x}, pmid = {41299662}, issn = {2524-6372}, support = {BAS/1/1096-01-0//King Abdullah University of Science and Technology/ ; }, abstract = {BACKGROUND: In this study, xTitan, a field-deployable, automated, and versatile nucleic acid extraction system was employed to characterize microbial communities in Red Sea-derived samples, including coral colonies, mangrove sediments, and seawater. The use of the xTitan in the field was intended to minimize sample transport bias, obtaining data that may be closer to "ground truth" for microbial diversity. The observed microbial communities from DNA extracted in the field using the xTitan system were compared to DNA extractions performed in a laboratory setting using both xTitan and a standard commercial kit (Qiagen) after approximately 24 h of sample transfer and storage.<br><br>RESULTS: Microbial community analyses conducted on DNA extracted using the xTitan system and the Qiagen kit yielded similar alpha diversity metric values, with a trend toward higher diversity observed in most samples extracted with the xTitan. The microbial community structure in samples from a Pocillopora verrucosa colony, mangrove sediments, and seawater was affected by the DNA extraction system. In the P. verrucosa colony, 16S rRNA gene sequences affiliated to Endozoicomonas acroporae were preferentially abundant when DNA was extracted in the field with the xTitan system rather than in the lab. In mangrove sediments, significant differences (P-value&#x2009;<&#x2009;0.05) in beta diversity and functional gene profiles were observed when comparing in-field to in-lab xTitan DNA extracts. In seawater, a pronounced decrease in the relative abundance of cyanobacterial populations was observed when DNA was extracted with both methods after samples were transported to the lab on ice. In addition, hundreds of species in mangrove-associated samples were differentially abundant when DNA was extracted on-site with the xTitan system compared to in-lab extractions. Balneolaceae was one of the most abundant taxa in mangrove sediments and several genera from this family were detected in all replicates across all DNA extraction systems.<br><br>CONCLUSIONS: The usability of different field-deployable instruments for microbial community characterization in marine-derived samples was demonstrated. Moreover, differences in beta diversity were observed when DNA was extracted in-field versus in-lab using the xTitan system, particularly for mangrove-associated samples. These results highlight the value of on-site nucleic acid extraction for enhancing the detection of microbial taxa that can be sensitive to cold storage. This study enabled the testing of the xTitan on Red Sea-derived samples, generating comprehensive information on the effects of DNA extraction systems and transportation of samples on coral and mangrove-associated microbiomes.}, }
@article {pmid41299176, year = {2025}, author = {Wirbel, J and Hickey, AS and Chang, D and Enright, NJ and Dvorak, M and Chanin, RB and Schmidtke, DT and Bhatt, AS}, title = {Long-read metagenomics reveals phage dynamics in the human gut microbiome.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {41299176}, issn = {1476-4687}, abstract = {Gut bacteriophages profoundly impact microbial ecology and health[1-3]; yet, they are understudied. Using deep long-read bulk metagenomic sequencing, we tracked prophage integration dynamics in stool samples from six healthy individuals, spanning a 2-year timescale. Although most prophages remained stably integrated into their hosts, approximately 5% of phages were dynamically gained or lost from persistent bacterial hosts. Within a sample, we found that bacterial hosts with and without a given prophage coexisted simultaneously. Furthermore, phage induction, when detected, occurred predominantly at low levels (1-3× coverage compared to the host region), in line with theoretical expectations[4]. We identified multiple instances of integration of the same phage into bacteria of different taxonomic families, challenging the dogma that phages are specific to a host of a given species or strain[5]. Finally, we describe a new class of 'IScream phages', which co-opt bacterial IS30 transposases to mediate their mobilization, representing a previously unrecognized form of phage domestication of selfish bacterial elements. Taken together, these findings illuminate fundamental aspects of phage-bacterial dynamics in the human gut microbiome and expand our understanding of the evolutionary mechanisms that drive horizontal gene transfer and microbial genome plasticity.}, }
@article {pmid41299132, year = {2025}, author = {Zhang, J and Zhou, X and Rong, X and Salem, H and Zhang, J and Yin, B and Guo, X and Zhang, Y}, title = {Effects of Plant Phylogeny and Traits on the Composition of Phyllosphere Microbial Communities in a Typical Temperate Desert in Central Asia.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02635-9}, pmid = {41299132}, issn = {1432-184X}, support = {2022D01A351//The Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; Non//The Tianchi Talent Introduction Project of Xinjiang Uygur Autonomous Region/ ; 2022D01D083//The Key Project of Xinjiang Uygur Autonomous Region Natural Science Foundation/ ; 2022TSYCLJ0058//The Leading Talents in Sci-Technological Innovation Project of "Tianshan Talent" Training Plan of Xinjiang Uygur Autonomous Region/ ; }, abstract = {Phyllosphere microorganisms play a vital role in supporting host plant health and adaptability. Although previous research on the effects of host performance and their phylogenetic associations on phyllosphere microbial communities has predominantly focused on tropical, subtropical, and temperate forestry ecosystems, the responses of these microbial communities to plant phylogeny and functional traits in temperate desert environments remains poorly understood. In this study, we conducted a quantitative analysis of bacterial and fungal community structures in the phyllosphere of 39 plant species from the Gurbantunggut Desert, a typical temperate desert in Central Asia. Variation partitioning analysis revealed that plant phylogeny, leaf physicochemical properties, and leaf morphological characteristics collectively explained the variation in phyllosphere microbial communities. Specifically, these factors accounted for 19.26%, 14.53%, and 2.32% of the variance in bacterial communities, and 11.55%, 8.36%, and 2.19% of the variance in fungal communities, respectively. A significant hierarchical pattern emerged: plant phylogeny > leaf physicochemical properties > leaf morphological characteristics, highlighting the dominant role of plant filtering effects in community assembly. Linear mixed-effects model analysis further confirmed the significant influence of multiple plant attributes, including phylogeny and functional traits, on microbial community structure. Plant-microbe interaction analysis revealed distinct host preferences of microbial taxa across different plant taxonomic levels. Co-evolutionary analysis also indicated a significant phylogenetic association between host plants and their phyllosphere amplicon sequence variants (ASVs). Overall, our findings demonstrate that plant attributes, particularly plant phylogeny and functional traits, are key factors driving the assembly of phyllosphere microbial communities in deserts. This study provides new insights into species coexistence mechanisms in fragile habitats and enhances our understanding of plant-microbe interactions in global desert ecosystem.}, }
@article {pmid41297120, year = {2025}, author = {Rajbhandari, RM and Shrestha, S and Manandhar, P and Napit, R and Sadaula, A and Chaudhary, A and Raut, R and Gortázar, C and Alves, PC and de la Fuente, J and Queirós, J and Forcina, G and Karmacharya, D}, title = {Comparing the respiratory tract microbiome in captive elephants and humans in Chitwan National Park: Implications for conservation medicine.}, journal = {Comparative immunology, microbiology and infectious diseases}, volume = {125}, number = {}, pages = {102422}, doi = {10.1016/j.cimid.2025.102422}, pmid = {41297120}, issn = {1878-1667}, abstract = {The study of gut microbiome in both animals and humans living in proximity has proven crucial in understanding their coevolution, the potential for microbial transfer and the dynamics behind various diseases. Similarly, the investigation of respiratory microbiomes has been gaining popularity due to its significance and impact on respiratory health. Here, we use 16S rRNA metabarcoding to explore the respiratory microbiome of captive Asian elephants (Elephas maximus) and their mahouts (i.e., trainers and handlers) in Chitwan National Park (Nepal), with local villagers residing out of the protected area acting as control. Sputum samples were collected to characterize their bacterial composition, while its functional profile was inferred with PICRUSt2. Additionally, the occurrence of genera hosting potentially pathogenic ESKAPE-E species was evaluated. Our findings revealed high similarity in the bacterial and functional composition of the respiratory microbiome of elephants and mahouts, with Bacillota and Pseudomonadota emerging as the most abundant phyla across all host categories and the controls displaying the highest diversity. A striking difference was observed in relation to the family Bacillaceae that dominated the microbial composition of both mahouts and elephants but not controls. Genera hosting potentially pathogenic ESKAPE-E bacteria were found in all host categories, which underscores the need for in-depth analyses to identify the species involved. Our study delivers valuable insights in the respiratory microbial community of both Asian elephants and humans, thus laying the basis for further investigations on their diversity and function, unveiling their role in respiratory health of both host species.}, }
@article {pmid41296916, year = {2025}, author = {Rettura, F and Lambiase, C and Bottari, A and Filippini, F and Giacomelli, L and Pistello, M and Bellini, M}, title = {Gut Virome: What's the Role in Irritable Bowel Syndrome?.}, journal = {Reviews in medical virology}, volume = {35}, number = {6}, pages = {e70080}, doi = {10.1002/rmv.70080}, pmid = {41296916}, issn = {1099-1654}, support = {2022FRE3RH//Italian Ministry of University and Research/ ; CUP I53D23000480006//National Recovery and Resilience Plan/ ; }, mesh = {Humans ; *Irritable Bowel Syndrome/virology/microbiology/therapy ; *Virome ; *Gastrointestinal Microbiome ; Bacteriophages/physiology ; Dysbiosis/virology ; Animals ; }, abstract = {The gut virome, an integral but still poorly understood component of the gut microbiota, is emerging as an important player in the pathophysiology of irritable bowel syndrome (IBS). Recent evidence suggests that alterations in virome diversity and phage-bacteria interactions contribute to gut dysbiosis, immune modulation and gut barrier dysfunction in IBS. This review summarises current knowledge on virome alterations in IBS and emphasises the role of bacteriophages in shaping microbial ecology and host responses. Different virome signatures in the different subtypes of IBS highlight the potential of the virome for disease stratification and personalised therapeutic strategies. In addition, we discuss the analytical challenges in virome research and explore novel virome-targeted interventions, including phage therapy and dietary modulation. A deeper understanding of virome dynamics in the gut could open new avenues for precision medicine approaches to treat IBS.}, }
@article {pmid41296063, year = {2025}, author = {Guo, M and Zhou, Z and Zheng, Y and Fu, D and Hou, L and Zhu, R}, title = {Ubiquity and Dominance of Comammox Over AOB and AOA and their Links To ARGs in Antarctic Lake Sediments.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02664-4}, pmid = {41296063}, issn = {1432-184X}, support = {2022YFF0801101//National Key Research and Development Program of China/ ; 42576267//National Natural Science Foundation of China/ ; }, abstract = {Complete ammonia oxidizers (comammox), oxidizing ammonia to nitrate directly, have been found to exist widely in multiple environments, but their distribution patterns are still under-explored in Antarctic environments. For the first time, the sediments were collected from West Antarctic lakes to investigate distribution patterns and community structure for comammox, ammonia oxidizing archaea (AOA) and bacteria (AOB), and nitrite-oxidizing bacteria (NOB), as well as the associations between ammonia oxidizers and antibiotic resistance genes (ARGs). Comammox clade B and AOB were dominant ammonia oxidizers, with the abundances of (1.62 ± 0.10) × 10[2] - (5.21 ± 0.74) × 10[6] and (0.17 ± 0.05) × 10[5] - (4.79 ± 0.65) × 10[5] copies g[- 1] sediment, respectively. Comammox clade B, instead of clade A, occurred in all sediments, exhibiting higher abundances than AOB and AOA in most of the sediments. The abundances for comammox clade B demonstrated significant positive correlation (p < 0.01) with NH4[+]-N levels, but negative correlation (p < 0.05) with C: N ratios. The coexistence of ammonia oxidizers in lake sediments was jointly structured by niche differentiation and environmental variables, and pH, modulated by penguin guano input, was found to be the most crucial factor in shaping their community structure. Co-occurrence network analyses revealed strong synergistic interactions between comammox and AOB, AOA, NOB, which played a critical role in nitrification processes. Our results further confirmed that comammox could act as important hosts for ARGs, hence stimulated their transmission and proliferation in the sediments. This study presented novel insights into the distribution patterns for ammonia oxidizers, their niche differentiation and the associations with ARGs in natural lake sediments of West Antarctica.}, }
@article {pmid41295040, year = {2025}, author = {Abdul Rahiman, S and Qiblawey, H}, title = {Anammox-MBR Technology: Breakthroughs and Challenges in Sustainable Nitrogen Removal from Wastewater.}, journal = {Membranes}, volume = {15}, number = {11}, pages = {}, doi = {10.3390/membranes15110337}, pmid = {41295040}, issn = {2077-0375}, support = {QUHI-CENG-25/26-747//Qatar University/ ; }, abstract = {Wastewater nitrogen pollution is a serious environmental problem, and traditional treatment techniques are frequently constrained by their high energy requirements and operational complexity. The anaerobic ammonium oxidation (anammox) process combined with membrane bioreactor (MBR) technology (anammox-MBR) offers a practical and energy-efficient solution for the sustainable removal of nitrogen, further enhanced by its potential to minimize emissions of nitrous oxide (N2O), a potent greenhouse gas with a global warming potential nearly 300 times that of carbon dioxide. This review outlines the most recent advancements in anammox-MBR systems, highlighting their ability to achieve nitrogen removal efficiencies of more than 70-90% and, in integrated systems with reverse osmosis, to recover up to 75% of the inflow as high-quality reusable water. Significant advancements such as high-rate activated sludge coupling, reverse osmosis integration, microaeration methods, and membrane surface modifications have decreased membrane fouling, accelerated startup times, and enhanced system stability. Despite these achievements, there are still issues that hinder widespread use, such as membrane fouling exacerbated by hydrophobic anammox metabolites, sensitivity to low temperatures (≤10 °C), and the persistent challenge of suppressing nitrite-oxidizing bacteria (NOB), which compete for the essential nitrite substrate. To enable cost-effective, energy-efficient, and environmentally sustainable large-scale applications, future research directions will focus on creating cold-tolerant anammox strains, advanced anti-fouling membranes, and AI-driven process optimization.}, }
@article {pmid41294522, year = {2025}, author = {Špiljak, B and Andabak Rogulj, A and Lončar Brzak, B and Brailo, V and Škrinjar, I and Ozretić, P and Vidović Juras, D}, title = {Desquamative Gingivitis and the Oral Microbiome: Insights into Immune-Microbial Interactions in Mucosal Inflammation.}, journal = {Dentistry journal}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/dj13110541}, pmid = {41294522}, issn = {2304-6767}, abstract = {Desquamative gingivitis (DG) is a clinical presentation characterized by erythema, epithelial desquamation, and mucosal fragility, commonly associated with immune-mediated diseases such as oral lichen planus (OLP), mucous membrane pemphigoid (MMP), and pemphigus vulgaris (PV). While traditionally viewed as a manifestation of immune dysregulation, growing evidence suggests that the oral microbiome may modulate disease onset, persistence, and severity. This review summarizes current knowledge on the oral microbiota in DG and its underlying diseases, explores mechanistic links between dysbiosis and immune activation, and discusses clinical and research implications. A narrative literature review was conducted using PubMed and Scopus, focusing on studies analyzing the oral microbiome in OLP, MMP, and PV. Emphasis was placed on molecular microbiology techniques, immune profiling, and functional or longitudinal approaches. In OLP, microbial dysbiosis is consistently reported, including reduced diversity and increased abundance of pro-inflammatory genera such as Fusobacterium, Prevotella, and Capnocytophaga. These shifts correlate with epithelial barrier disruption and inflammatory cytokine production. Although data on MMP and PV are limited, early findings suggest microbial involvement in sustaining inflammation, delaying healing, and possibly amplifying autoimmune responses. Dysbiosis may activate Toll-like receptors, skew T cell responses, and contribute to the breakdown of immune tolerance. DG may reflect a dynamic interplay between immune mechanisms and microbial ecology. While evidence is strongest for OLP, preliminary data suggest broader microbial contributions across DG-associated diseases. Microbiome-informed approaches could enhance diagnostic accuracy and support the development of adjunctive therapies.}, }
@article {pmid41293856, year = {2025}, author = {Schäfer, RB and Baikova, D and Bayat, HS and Beermann, AJ and Berger, SA and Boenigk, J and Brauns, M and Burfeid-Castellanos, A and Cardinale, BJ and David, GM and Feckler, A and Feld, CK and Fink, P and Gessner, MO and Hadziomerovic, U and Hering, D and Le, TTY and Macaulay, SJ and Madariaga, GM and Serge Mayombo, NA and Pimentel, IM and Orr, JA and Osakpolor, S and Schlenker, A and Sures, B and Vermiert, AM and Vos, M and Weitere, M and Schürings, C}, title = {Effects of Biodiversity Loss on Freshwater Ecosystem Functions Increase With the Number of Stressors.}, journal = {Global change biology}, volume = {31}, number = {11}, pages = {e70617}, doi = {10.1111/gcb.70617}, pmid = {41293856}, issn = {1365-2486}, support = {426547801//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Biodiversity ; *Fresh Water ; *Ecosystem ; *Stress, Physiological ; Biomass ; }, abstract = {A multitude of anthropogenic stressors drive biodiversity loss and alter ecosystem functioning. Freshwaters, which contribute disproportionally to global biodiversity and biogeochemical cycles, are particularly threatened. Although the relationship between biodiversity and ecosystem functions (BEF) is generally well-established, especially in terrestrial ecosystems, the role of multiple, co-occurring stressors in modulating the relationship remains unclear. We conducted a meta-analysis to address this knowledge gap by assessing the effect of multiple stressors on the relationship between taxon richness and four measures of ecosystem function. The relationship was generally positive, with the slope becoming steeper as the number of stressors increased, suggesting that exposure to multiple stressors exacerbates impacts of biodiversity loss on ecosystem function. Multiple stressor effects on both taxon richness and ecosystem functions were largely predictable from individual stressor effects, although antagonistic effects on ecosystem functions emerged in 14% of the considered cases. The type of stressor and ecosystem function, along with taxonomic group, exerted no influence on the BEF relationship, contrary to our expectations. Microbial production and biomass declined most strongly in response to stressors, despite notable variability. Overall, our findings imply that functional consequences of freshwater biodiversity loss are more severe under multifaceted environmental change than previously assumed.}, }
@article {pmid41292685, year = {2025}, author = {O'Brien, JM and Blais, ND and Holland-Moritz, H and Shek, KL and Douglas, TA and Barbato, RA and Ernakovich, JG}, title = {Consistent microbial responses during the aerobic thaw of Alaskan permafrost soils.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1654065}, pmid = {41292685}, issn = {1664-302X}, abstract = {Arctic systems are warming at four times the global average, causing permafrost-permanently frozen soil, ice, organic matter, and bedrock-to thaw. Permafrost thaw exposes previously unavailable soil carbon and nutrients to decomposition-a process mediated by microbes-which releases greenhouse gases such as carbon dioxide and methane into the atmosphere. While it is well established that thaw alters the composition and function of the permafrost microbiome, patterns revealing common responses to thaw across different permafrost soil types have not yet emerged. In this study, we address how permafrost thaw impacts microbiome diversity, alters species abundance, and contributes to carbon flux in the Arctic. We sampled peat-like, mineral, and organic-mineral permafrost from three locations in central and northern Alaska. We assessed their abiotic soil properties and microbiome characteristics before and after a 3-month laboratory microcosm incubation. Across all sites, prokaryotic biomass increased following thaw, measured as 16S rRNA gene copy number. This change in biomass was positively correlated with cumulative respiration, indicating an increase in microbial activity post-thaw. We evaluated the thaw response of microbial taxa across three sites, identifying taxa that significantly increased in abundance post-thaw. Common responders shared across all sites belonged to the families Beijerinckiaceae, Burkholderiaceae, Clostridiaceae, Oxalobacteraceae, Pseudomonadaceae, and Sporichthyaceae, indicating a common set of taxa that consistently respond to thaw regardless of site-specific conditions. Alpha diversity decreased with thaw across all sites, likely reflecting the increased dominance of specific thaw-responsive taxa that may be driving post-thaw biogeochemistry and increased respiration. Taken together, we deepen the understanding of different permafrost microbiomes and their response to thaw, which has implications for the permafrost-climate feedback and enables more accurate predictions of how Arctic ecosystem structure and function respond to change.}, }
@article {pmid41291355, year = {2025}, author = {Han, H and Luo, Z and Pei, X and Xie, Y and Zhu, Y and Li, J and Zou, T and Wang, Z and Su, C}, title = {Microbial-Plant Interaction: Bacillus subtilis-Driven Gravel Soil Improvement and Growth Promotion of Festuca arundinacea.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02634-w}, pmid = {41291355}, issn = {1432-184X}, abstract = {The rapid expansion of tunnel engineering in China has led to extensive excavation of gravelly soils, resulting in significant land occupation that threatens the ecological environment and surrounding biota. As a result, there is an increasing need for effective ecological restoration of nutrient-poor gravelly soils, where challenges in vegetation establishment and sustainable soil management persist. This study evaluates the potential of Bacillus subtilis to promote the growth of Festuca arundinacea in engineered gravel soils through a controlled greenhouse experiment, examining its effects on plant growth, soil nutrient dynamics, and microbial community structure. The results showed that, compared to the control group (CK), neither the Bacillus subtilis treatment group (Bs) nor the nutrient application treatment group (LB) significantly altered the soil bacterial species composition at the phylum level. However, at the genus level, Azotobacter dominated the LB group, while Sphingomonas was the predominant genus in both the CK and Bs groups. Additionally, Bacillus subtilis significantly increased bacterial diversity relative to the nutrient application treatment, leading to substantial changes in microbial community composition. Furthermore, Bacillus subtilis notably enhanced both aboveground and belowground biomass, improved nutrient uptake, and increased the availability of phosphorus and potassium. It also stimulated soil enzymatic activities involved in carbon, nitrogen, and phosphorus cycling, emphasizing its critical role in nutrient cycling. Thus, Bacillus subtilis-driven soil enhancement offers a promising solution for ecological restoration in nutrient-poor gravelly soils, where conventional amendments are often ineffective. These findings underscore the potential of microbial-plant synergies to improve soil fertility and support sustainable vegetation restoration.}, }
@article {pmid41291216, year = {2025}, author = {Jurado, J and Garcia-Vega, A and Vasquez, Y and Villegas-Plazas, M and Roldan, F}, title = {Field-Scale AMD Remediation: Microbial Community Dynamics and Functional Insights in Biochemical Passive Reactors.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02628-8}, pmid = {41291216}, issn = {1432-184X}, abstract = {Acid mine drainage (AMD) generated during coal mining activities is characterized by low pH, high concentrations of dissolved metals and metalloids, and elevated sulfate levels, all of which significantly impact surrounding ecosystems. Scaling up biochemical passive reactor (BPR) systems represents a promising approach for the in situ bioremediation of AMD. While numerous laboratory-scale studies have described the taxonomic and functional composition of microbial communities in BPRs, typically dominated by (ligno)cellulolytic organisms and sulfate-reducing bacteria (SRB), it remains unclear whether this composition is maintained at the field-pilot scale under environmental conditions. To address this gap, 16S rRNA gene metabarcoding and shotgun metagenomics analyses were performed to characterize the taxonomic and functional diversity of microbial communities in the BPRs within a multi-unit field-pilot system. The results revealed that bioremediation effectiveness was driven by syntrophic interactions among hydrolytic, fermentative, and sulfate-reducing bacteria, aligning with laboratory-scale observations. While community composition shifts altered specific taxa, core operational dynamics remained preserved.}, }
@article {pmid41291200, year = {2025}, author = {Zha, Y and Fan, L and Shen, T and Zhang, Y and Ren, H}, title = {Triptolide ameliorates LPS-induced acute lung injury in Balb/c mice through gut-lung axis-mediated regulation of bile acid metabolism and gut microbiota.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-025-29758-w}, pmid = {41291200}, issn = {2045-2322}, support = {PW2022A-21//the Scientific Research Program of Shanghai Pudong New Area Health Commission/ ; }, abstract = {Acute lung injury (ALI) associated with pulmonary edema is a severe clinical condition characterized by acute inflammation, disrupted lung barrier function, and high mortality. Current therapeutic strategies remain limited, highlighting the need for exploring novel agents and their underlying mechanisms. Triptolide (TP), an active component derived from Tripterygium wilfordii, has shown anti-inflammatory and tissue-protective properties[1,2], but its specific role in alleviating ALI and the involvement of the lung-gut axis in metabolic regulation remain poorly understood. This study aims to investigate the therapeutic effects of TP on LPS-induced ALI, focusing on its impact on pulmonary edema and inflammatory injury. By analyzing the lung-gut axis using multi-omics approaches, we seek to clarify the metabolic network regulatory mechanisms through which TP exerts its effects. LPS-induced ALI model was established in Balb/c mice, with TP administered as the therapeutic intervention. Histopathological examination of lung tissues and detection of pro-inflammatory cytokines were performed to assess lung injury. Untargeted metabolomics via LC-MS/MS was used to identify differential metabolites in lung tissues and serum, while metagenomic sequencing analyzed changes in gut microbiota composition. Integrated multi-omics analysis was applied to explore associations between gut microbiota alterations, serum metabolites, and pulmonary bile acid levels. TP administration significantly reduced histopathological damage in lung tissues of ALI mice and decreased pro-inflammatory cytokine levels. Metabolomics profiling revealed distinct changes in key metabolites, including bile acids, amino acid derivatives, and energy metabolism intermediates, in both lung tissues and serum after TP treatment. Metagenomic analysis showed that TP restructured gut microbiota composition, with functional enrichment in glycolysis and thiamine metabolism pathways. Integrated analysis confirmed strong correlations between dynamic microbiota changes, serum metabolite profiles, and pulmonary bile acid levels, indicating a regulatory role of the lung-gut axis. This study demonstrates that TP alleviates pulmonary edema and inflammatory injury in ALI by modulating gut microbial ecology and function, which drives bile acid metabolic reprogramming and regulates metabolite interactions within the lung-gut axis. These findings provide novel insights into TP's therapeutic mechanism and support its potential application in ALI treatment.}, }
@article {pmid41291153, year = {2025}, author = {Joshi, H and Caprio, M and Reon, L and Fan, P}, title = {Rumen Microbiota-Based Machine Learning Approach for Predicting Heat Stress and Identifying Associated Microbes.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02656-4}, pmid = {41291153}, issn = {1432-184X}, abstract = {Heat stress poses a significant global challenge to sustainable livestock production, leading to detrimental impacts on animal production and welfare. Reduced appetite and increased body temperature further disrupt the gastrointestinal microbial ecosystem of heat-stressed animals, altering nutrient digestion and affecting host production. However, reported heat-stress-associated microbes have varied across studies, partly due to inconsistencies in microbiota analysis pipelines and taxonomic levels reported. In this study, to identify consistent rumen microbial taxa influenced by heat stress and evaluate potential of rumen microbiota in heat stress prediction, we collected publicly available raw 16S rRNA gene amplicon sequencing data of rumen fluid samples from lactating Holstein cattle housed in thermoneutral or heat stress condition from eight studies, analyzed their microbial composition using a consistent bioinformatic pipeline, and built machine learning models with the rumen microbiota profile to predict heat stress. Important rumen microbial taxa were selected using Boruta (a feature selection algorithm to identify important features) as potential biomarkers to predict heat stress, such as lactate-producing bacteria Lactobacillales, fiber-degrading bacteria Ruminococcaceae UCG-001, and methanogenic archaea Methanomicrobium. Additionally, the random forest model using the available animal factors and relative abundance of rumen microbial taxa showed a much higher performance for heat stress prediction, compared to the model without rumen microbiota profile (Area Under the Curve: 0.851 vs. 0.440). This study confirmed a distinct rumen microbiota signature in heat-stressed lactating Holstein cattle and identified specific rumen microbial taxa as potential biomarkers that could be targeted to mitigate heat-stress responses in dairy cows.}, }
@article {pmid41291109, year = {2025}, author = {Cohen, DD and Faigenboim, A and Elingold, I and Sher, Y and Galpaz, N and Minz, D}, title = {Dynamics in Microbial Communities Associated with the Development of Soil Fatigue in Banana.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02637-7}, pmid = {41291109}, issn = {1432-184X}, abstract = {Soil fatigue, well documented in various crops, presents a significant challenge to banana production by causing fast and then gradual declines in plant growth and yield over years of cultivation. Despite its impact on profitability, the underlying mechanisms driving soil fatigue remain poorly understood; however, a strong link to shifts in the soil microbiome has been suggested. We investigated the dynamics of microbial communities in relation to soil fatigue, using a novel semi-controlled outdoor experimental system. Soil at different stages of fatigue (0 to 42 months of banana cultivation) was generated in large containers filled with initially healthy soil. Banana plants grown in these soils were replaced with new plants which showed soil age-dependent growth. Three months postplanting, soil and root samples were collected for analyses of soil parameters and microbial community composition using bacterial (16S) and fungal (ITS) amplicon sequencing. We identified minor age-related shifts in mainly pH, potassium, and organic matter in the soil. While alpha diversity remained unchanged, significant shifts in bacterial and fungal community composition were observed in fatigued soils. Notably, the relative abundance of bacterial families such as Flavobacteriaceae, Pseudomonaceae, and Acidibacter increased, as did some fungal taxa (many from groups with known pathogens)-Ceratobasidiaceae (including Rhizoctonia), Dothideomycetes, and Stachybotryaceae. Simultaneously, the relative abundance of bacterial families with known beneficial members, including Gemmatimonadaceae, Moraxellaceae, Sphingomonadaceae, and Azospirillaceae, as well as symbiotic fungal taxa such as Glomeraceae and Lasiosphaeriaceae, declined. Thus, soil fatigue may be correlated to the proliferation of pathogenic populations and a loss of beneficial microorganisms.}, }
@article {pmid41291103, year = {2025}, author = {Katanić, Z and Ćurković-Perica, M and Idžojtić, M and Boljevac, K and Krstin, L}, title = {Status of Dutch Elm Disease Fungus Ophiostoma novo-ulmi and Assessment of Its Temporal Variability in Croatia.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02601-5}, pmid = {41291103}, issn = {1432-184X}, abstract = {Dutch elm disease (DED) was originally caused by the ascomycete Ophiostoma ulmi, which has been replaced by a more virulent species, O. novo-ulmi, divided into subsp. novo-ulmi and subsp. americana. Permeable reproductive barriers, a period of co-occurrence of O. ulmi and O. novo-ulmi, and the current overlap of O. novo-ulmi subspecies have been important in shaping the present O. novo-ulmi populations in Europe, which were initially clonal, predominantly of the MAT-2 type. This study confirmed the persistence of O. novo-ulmi in Croatia over the years, although at some forest sites, the diseased elms were not detected. The methodology used to assess changes in O. novo-ulmi populations was based on the col1 and cu genes, which have subspecies-specific nucleotide differences, analysis of MAT idiomorphs, and temperature-growth responses. The col1 and cu gene sequencing did not reveal a change in the number of isolates with the recombinant col1/cu genotype over 10 years (2012-2022). At both sampling times, approximately one-fourth of all analyzed isolates had recombinant col1/cu genotypes. However, the frequency of MAT-1 isolates, which all have MAT-1 genes originating from O. ulmi, increased during this period. Differences in growth rate at 20, 26, and 30 °C revealed variations in the temperature response of isolates, which were affected by sampling time and mating type. The MAT-1 isolates were shown to grow more slowly than MAT-2 at the three temperatures tested. The advantage of MAT-2 was reflected in temporal differences in growth rate at resampled sites, particularly at lower temperatures. These results suggest that changes in the frequency of mating types in Croatia occurred between 2012 and 2022, accompanied by modifications in the pathogen's response to temperature at the population level.}, }
@article {pmid41291089, year = {2025}, author = {Calbet, A}, title = {Pelagic Shuttles of Antibiotic Resistance Genes: Zooplankton as Overlooked Vectors Across Space and Food Webs.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02669-z}, pmid = {41291089}, issn = {1432-184X}, abstract = {Antibiotic resistance genes (ARGs) accumulate in aquatic environments, where they create reservoirs and transmission pathways that can undermine antimicrobial treatments and alter the microbial community structure in ways that ultimately affect human and animal health. However, the contribution of zooplankton in these pathways remains critically overlooked. Emerging evidence shows that compared with surrounding water, copepods and cladocerans accumulate ARG loads that are one to two orders of magnitude greater, acting as microbial hotspots that disperse resistant bacteria across seasons and depths. Inside protistan vacuoles, densely packed prey cells undergo conjugation, rapidly accelerating horizontal ARG transfer. Long-term archives reveal persistent ocean-wide dissemination of the class-1 integron integrase (intI1) and sul2 genes since at least the 1970s. Here, I synthesize mechanistic and field evidence, pinpoint knowledge gaps, and recommend priorities: integrate zooplankton into routine ARG surveillance, quantify biofilm-mediated exchanges, and mitigate contamination from coselective pollutants to curb zooplankton-driven ARG propagation. By framing zooplankton-associated ARG dynamics within the broader community ecology of antimicrobial resistance, this mini-review highlights how aquatic food-web processes feed back into the emergence, evolution, and transmission of resistance that concerns for One Health outcomes beyond the clinic.}, }
@article {pmid41290433, year = {2025}, author = {Ishibashi, S and Susukida, S and Muto, K and Miyazawa, K and Zhang, S and Yoshimi, A and Tabata, E and Abe, K}, title = {Using pure oxygen aeration to increase recombinant protein production by an Aspergillus oryzae hyphal dispersion strain.}, journal = {Journal of bioscience and bioengineering}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jbiosc.2025.10.011}, pmid = {41290433}, issn = {1347-4421}, abstract = {A high growth rate is essential for increasing protein production efficiency in liquid fermentation of filamentous fungi, such as Aspergillus oryzae. However, the increase in culture viscosity due to fungal growth constrains the overall yield. We have demonstrated that culture viscosity is lower in A. oryzae AGΔ-GAGΔ strains, which are deficient in the cell surface polysaccharides α-1,3-glucan (AG) and galactosaminogalactan (GAG), than in the wild-type (WT) strains. Nevertheless, even in aerated fermentation, an increase in AGΔ-GAGΔ viscosity results in oxygen depletion, which limits fungal growth and enzyme production. In this study, we investigated viscosity dynamics and protein production during high-cell-density fermentation of AGΔ-GAGΔ under pure oxygen aeration. Fed-batch cultivation of the WT and AGΔ-GAGΔ strains, expressing recombinant xylanase (XynF1), was used to compare the effects of air and pure oxygen aeration at the same flow rate. At 60 h, AGΔ-GAGΔ under pure oxygen aeration showed higher cell density (1.2× WT under pure oxygen aeration, 2.1× AGΔ-GAGΔ under air aeration) and XynF1 activity (1.8× WT under pure oxygen aeration, 2.3× AGΔ-GAGΔ under air aeration). Under pure oxygen aeration, AGΔ-GAGΔ showed lower viscosity (0.32×) and mixing time (0.50×) than WT. At 60 h, fine mycelial pellets (micropellets; 200-700 μm) were clearly observed in AGΔ-GAGΔ under pure oxygen but not under air aeration. These findings suggest that oxygen enrichment during AGΔ-GAGΔ cultivation mitigated the increase in viscosity, thereby promoting higher cell density and protein production. The formation of micropellets in AGΔ-GAGΔ likely contributed to a reduction in culture viscosity.}, }
@article {pmid41289323, year = {2025}, author = {Li, C and Urem, M and Kotsogianni, I and Lau, J and Du, C and Elsayed, SS and Martin, NI and McNae, IW and Voskamp, P and Mayer, C and Rigali, S and Pannu, N and Abrahams, JP and Schada von Borzyskowski, L and van Wezel, GP}, title = {The novel GlcNAc 6-phosphate dehydratase NagS governs a metabolic checkpoint that controls nutrient signaling in Streptomyces.}, journal = {PLoS biology}, volume = {23}, number = {11}, pages = {e3003514}, doi = {10.1371/journal.pbio.3003514}, pmid = {41289323}, issn = {1545-7885}, abstract = {Streptomyces bacteria are renowned for their multicellular lifestyle and as Nature's medicine makers, producing the majority of the clinical antibiotics. A landmark event during early development is the lytic dismantling of the substrate mycelium. Degradation of the hyphal cell-wall leads to the accumulation of N-acetylglucosamine (GlcNAc) in the colonies, which is a metabolic checkpoint during the onset of development and antibiotic production. Here, we show that GlcNAc sensing requires a toxicity pathway dependent on the enzyme GlcNAc-6P dehydratase (NagS). Dehydration of GlcNAc-6P by NagS to 6P-chromogen I is an unprecedented reaction in central metabolism that is highly conserved in - and limited to - the Streptomycetaceae. 6P-chromogen I is metabolized into a structural analogue of ribose by a promiscuous activity of GlcNAc-6P deacetylase NagA. Toxicity is relieved by supplementing the growth media with ribose. Structure-function analysis of NagS not only highlighted key residues in the active site of the enzyme in interaction with its substrate GlcNAc-6P, but also revealed 6-phosphogluconate as its catalytic inhibitor. Our work uncovers a conserved metabolic toxicity pathway in Streptomyces that revolves around a novel enzyme that plays a key role in nutrient signaling.}, }
@article {pmid41288749, year = {2025}, author = {Ndabankulu, KP and Zama, N and Suinyuy, TN and Magadlela, A}, title = {Soil Microbe Interaction and Extracellular Enzyme Activity Mediated by Encephalartos villosus in KwaZulu-Natal Scarp Forest Ecosystems.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {132}, pmid = {41288749}, issn = {1432-184X}, support = {129403//National Research Foundation, South Africa/ ; 138091//National Research Foundation/ ; }, mesh = {*Soil Microbiology ; South Africa ; Soil/chemistry ; Forests ; *Bacteria/classification/enzymology/genetics/isolation &amp; purification/metabolism ; Rhizosphere ; Symbiosis ; Ecosystem ; Microbiota ; }, abstract = {Cycads are ancient gymnosperms that play a crucial role in the soil health of scarp forests through their symbiotic associations with nutrient-cycling bacteria. However, the abundance of cycads in scarp forests has been decreasing at an alarming rate, highlighting the importance of determining the role of these species in nutrient cycling, microbial dynamics, and soil health. This study examined soil nutrient and microbial dynamics associated with Encephalartos villosus across four scarp forest sites in KwaZulu-Natal, South Africa. Soil samples were collected from the rhizosphere and non-rhizosphere zones (3-5 m away from the canopy) of mature plants. Results show that collection point did not influence soil nutrient and properties statistically; however, site-level variation was evident, with Hlathikhulu showing higher pH and nutrient concentrations, while Vernon Crookes exhibited lower pH and nutrient availability. Rhizosphere soils supported a greater diversity of nutrient-cycling bacteria, particularly taxa from the genera Bacillus, Burkholderia, Enterobacter, Luteibacter, and Pseudomonas with N-fixing, P-solubilizing, and N-cycling functions. Non-metric multidimensional scaling (NMDS) revealed that site differences, mainly driven by Mg, Ca, K, Zn, pH, and total cations, were stronger predictors of soil nutrient and microbial community variation than collection point alone. Enzyme assays showed that glucosaminidase and acid phosphatase were associated with community differences. These findings indicate that E. villosus enhances soil nutrient enrichment and microbial functional diversity in scarp forests, although the strength of these effects depends on local site conditions. Conservation of E. villosus is therefore critical, not only for species survival but also for sustaining soil fertility and ecosystem functioning in nutrient-limited scarp forest habitats.}, }
@article {pmid41288747, year = {2025}, author = {Kim, J and Cui, Y and Nam, KH and Lee, JW and Kim, JG and Chun, SJ}, title = {Effects of CP4-EPSPS-Containing Brassica juncea Hybrids on the Gut and Fecal Microbiota of the Terrestrial Decomposer Armadillidium vulgare.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {131}, pmid = {41288747}, issn = {1432-184X}, support = {NIE-A-2025-04; NIE-A-2025-06//Ministry of Environment (MOE) of the South Korea/ ; }, mesh = {*Mustard Plant/genetics ; *Feces/microbiology ; *Gastrointestinal Microbiome ; *Plants, Genetically Modified/genetics ; Animals ; Bacteria/classification/genetics/isolation &amp; purification ; Fungi/classification/genetics/isolation &amp; purification ; Republic of Korea ; Plant Leaves ; }, abstract = {The unintended spread of genetically modified (GM) crops and introgression into wild relatives raises concerns about ecological impacts. In South Korea, CP4-EPSPS-containing Brassica juncea hybrids (GM-hybrid B. juncea) have been detected in natural ecosystems. However, the impact of these GM crops on ecology remains unclear. In this study, we aimed to investigate the potential effects of GM-hybrid B. juncea on the gut and fecal microbiomes of Armadillidium vulgare, a dominant decomposer in natural habitats and an ideal model organism for assessing the ecological impact of GM plant material. Leaf litter from wild-type and GM-hybrid B. juncea was collected from the field, and feeding experiments were conducted using A. vulgare under controlled conditions. Although no significant differences in survival rates or growth were observed between groups, microbiome analysis revealed significant changes in both bacterial and fungal community composition and functional profiles in the gut and feces of the GM-hybrid-fed group. Specifically, in the GM-hybrid-fed group, the proportion of intestinal Plectosphaerella (Glomerellales) increased. Additionally, the bacterial Shannon index decreased, whereas the fungal Shannon index increased. Microbial network analysis revealed distinct interaction patterns and GM-hybrid-specific modules. GM-hybrids may influence decomposer-associated microbiomes through indirect pathways. Such influences could affect ecosystem-level processes such as decomposition and nutrient cycling. This experimental framework can be extended to other crop-derived hybrids or applied to different ecological contexts, providing a valuable basis for future assessments of transgene impacts on ecosystem functions.}, }
@article {pmid41288715, year = {2025}, author = {Yang, W and Deng, Z and Blair, D and Hu, W and Yin, M}, title = {Heavy-metal Pollution Affects Daphnia Fitness by Altering Diversity of the Gut Microbiota.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {130}, pmid = {41288715}, issn = {1432-184X}, support = {32271690//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Daphnia/drug effects/microbiology/genetics/physiology ; *Gastrointestinal Microbiome/drug effects ; *Nickel/toxicity ; *Metals, Heavy/toxicity ; *Water Pollutants, Chemical/toxicity ; Bacteria/classification/genetics/drug effects ; Germ-Free Life ; *Genetic Fitness/drug effects ; }, abstract = {The role of gut microbiota in shaping host fitness is already well established. However, it remains unclear to what extent the gut microbiota influences host fitness in the presence of environmental stressors. Here, we tested the hypothesis that responses of water flea Daphnia to the heavy metal nickel are mediated by gut microbiota. Germ-free D. magna exhibited somewhat lower fitness than did those with gut microbiota transplant. Among germ-free Daphnia, those that were exposed to heavy metals did not differ in fitness from unexposed Daphnia. In contrast, when incubated with their donors' gut microbiota, initially germ-free D. magna continuously exposed to nickel for 21 days showed a significantly lower survival rate than those not exposed to nickel. We detected a reduced set of microbes in the formerly germ-free Daphnia in the presence of nickel. Transcriptomic analysis of Daphnia showed that expression/regulation of genes related to oxygen transport, chitin metabolism, and detoxification changed in response to the reduced gut microbiomes acquired in the presence of nickel. Our findings show that the toxic effects of heavy metal led to a reduced diversity of gut microbiota in Daphnia and can thus affect host fitness.}, }
@article {pmid41288688, year = {2025}, author = {Wardhani, R and Shin, J and Lee, S and Lee, J and Nam, YH and Lee, MH and Han, KL and Ahn, H}, title = {Evaluation of Aquamicrobium lusatiense NLF 2-7 as a Biocontrol Agent in Manure Composting: Effects on Odorous Compounds and Microbial Community Under Mesophilic Conditions.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {129}, pmid = {41288688}, issn = {1432-184X}, support = {NNIBR20253108//Nakdonggang National Institute of Biological Resources/ ; RS-2021-IP321088//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry/ ; }, mesh = {*Composting/methods ; *Manure/microbiology ; *Odorants/prevention &amp; control/analysis ; Hydrogen Sulfide/metabolism/analysis ; *Soil Microbiology ; *Bacteria/classification/metabolism/genetics ; Biodegradation, Environmental ; Sulfides/metabolism/analysis ; Soil/chemistry ; *Biological Control Agents ; Microbiota ; }, abstract = {Microbial inoculation is a commonly applied approach in composting to enhance organic matter biodegradation and reduce odor emissions. However, the different characteristics of bacteria in terms of temperature can be considered to optimize their effect during different phases of composting. A mesophilic bacterium, namely Aquamicrobium lusatiense NLF 2-7, was evaluated to mitigate odor emissions and enhance the bacterial community under mesophilic composting. Two different treatments were designed: treatment 1 with a single inoculation on the initial day and treatment 2 with split inoculation at the initial and after 2 weeks. Results show that the treatments improve organic matter decomposition by 17.7-28.6% and significantly reduce volatile sulfur compound emissions, especially dimethyl sulfide (DMS) and hydrogen sulfide (H2S) during the initial phase of composting. DMS emissions were mostly emitted in the first week, with reduction rates of 60.3% and 61.5% in both treatments, respectively. Additionally, mean phenol emissions were reduced by 7.9% in treatment 1 and 11.7% in treatment 2. The dominant bacterial phyla during composting were Bacillota, Pseudomonadota, Bacteroidota, and Actinomycetota, comprising 74 to 95% of the total population. This experiment suggests that A. lusatiense NLF 2-7, which is known for reducing sulfur emissions, can also enhance organic matter decomposition. Split inoculation appears more beneficial, with an initial inoculation managing sulfur emissions early on, followed by a second inoculation after the thermophilic phase to control phenol emissions throughout the composting process.}, }
@article {pmid41288389, year = {2025}, author = {Taheri, S and Schwarzkopf, E and Berman, HL and Brandt, N and McNeill, J and Sevier, N and Ruffieux, M and Dunn, RR and Smukowski Heil, C}, title = {The role of flour type and feeding schedule on the sourdough microbiome.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0238025}, doi = {10.1128/spectrum.02380-25}, pmid = {41288389}, issn = {2165-0497}, abstract = {Sourdough starters are fermentations of various grains by bacteria and yeast and are of worldwide economic and cultural importance. Sourdoughs are sometimes spontaneously inoculated, and their resident microbial communities are in part shaped by environmental factors, potentially including flour, water, air, human microbiota, equipment, geography, and temperature. The number of different genera of bacteria and yeast found in sourdoughs is large; however, only a handful of species typically dominate an individual sourdough starter. Understanding how and why certain species form a mature climax community in a particular environment is a key question in microbial ecology. To investigate this question, we used a meta-barcoding approach and tested whether different baking flours (all-purpose, bread, and whole wheat) and frequency of feeding, also known as backslopping, shape the sourdough starter microbial community over the course of one month. We found that the yeast genus Kazachstania rapidly rose in frequency and became the most abundant yeast in all starters, regardless of flour type or feeding schedule. In contrast, flour type did affect the bacterial community. Mature sourdoughs all contained the bacterial genera Companilactobacillus, Levilactobacillus, Lactiplantibacillus, Furfurilactobacillus, and Acetobacter, with Companilactobacillus detected at higher relative abundance in whole wheat flour and Levilactobacillus detected at higher relative abundance in bread flour. We conclude that flour can shape the microbial community of sourdough and has potential implications for functional traits.IMPORTANCEHow organisms disperse and colonize new environments is central to our understanding of biodiversity. Sourdough, the often spontaneously inoculated fermentation of grains by bacteria and yeast, represents a great system to test and observe how microorganisms come to inhabit a particular niche. In our study, we investigate how environmental parameters such as flour type and feeding frequency influence the microbial community. We find that the common sourdough yeast genus Kazachstania is most abundant in all starters regardless of treatment, but we also find a significant effect of flour type on the lactic acid bacteria composition of the sourdough starters. This work shows how the environment can impact the presence and abundance of particular microorganisms and prompts future studies to test how particular lactic acid bacteria species can specialize on certain resources.}, }
@article {pmid41286473, year = {2025}, author = {Wang, H and Yang, Y and Zhang, H and Chen, X and Zhang, R and Hou, W and Zhang, G}, title = {Symbiotic N-Fixing Bacteria in the Root and Leaf of Typical Alpine Grassland Plants.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {127}, pmid = {41286473}, issn = {1432-184X}, mesh = {Grassland ; *Plant Roots/microbiology ; *Symbiosis ; *Plant Leaves/microbiology ; RNA, Ribosomal, 16S/genetics ; Tibet ; *Nitrogen-Fixing Bacteria/classification/genetics/isolation &amp; purification/physiology ; Nitrogen Fixation ; Phylogeny ; DNA, Bacterial/genetics ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Soil Microbiology ; }, abstract = {Alpine plants in nitrogen-deficient environments can acquire nitrogen by associating with endophytic nitrogen-fixing microorganisms that inhabit their roots and leaves to form symbiotic relationships. However, research is limited on nitrogen-fixing bacterial communities in the roots and leaves of alpine grassland plants, especially regarding the differences between various plant parts. In this study, we compared the root and leaf bacterial communities of four alpine plant families (Asteraceae, Leguminosae, Poaceae, and Rosaceae) in the alpine meadow ecosystem of Naqu, Tibet, using culture-based methods, 16S rRNA, and nifH gene pyrosequencing. The results showed greater bacterial diversity in the root compared to the leaf, and Fabaceae plants harbored a higher abundance of nitrogen-fixing bacteria. Interestingly, the roots and leaves of non-Fabaceae plants (Kobresia, Festuca ovina, and Leontopodium) also harbored abundant nitrogen-fixing communities such as Microbacterium, Curtobacterium, and Rhodococcus. Compared with subtropical environments, Cyanobacteria are important symbiotic nitrogen-fixing bacteria in plants of alpine ecosystems. These findings indicate that plant species and plant parts strongly influence the selection of bacterial populations. Understanding these microbial ecological functions in alpine grasslands provides scientific insights for optimizing agricultural practices and ecosystem management.}, }
@article {pmid41286374, year = {2025}, author = {Jones, AK and Jordan, HR and Wolff, CL and Lashley, MA and Barton, BT}, title = {Lasting Effects of Different Scaled Mass Mortality Events on Soil Microbial Communities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02625-x}, pmid = {41286374}, issn = {1432-184X}, abstract = {Death is a natural process present in all ecosystems; however, mass mortality events are instances of larger than average numbers of animals dying in a relatively short period of time. These events are increasing in frequency and magnitude, and the effects of mass mortalities - especially their long-term effects - are understudied. To better understand the long-term effects of mass mortalities in terrestrial ecosystems, we conducted experimental mass mortality events to determine if key ecosystem properties remained affected after 4 years. The experiment crossed three types of input treatments (control, carrion, and nutrient additive) with scavenger access (open plots versus fenced plots). To evaluate how increasing carrion biomass affected the ecosystem, sites were randomly assigned biomass (25, 59, 182, 363, 726 kg total (20m[2] plots)). Biomasses consisted of feral swine carcasses or the equivalent amount of N, phosphorus, and K nutrients. After 4 years, we found that while soil N did not differ among treatments, soil K and Ca significantly increased with biomass. Microbial communities significantly differed at the 182 kg biomass treatments compared to others and indicated significant effects between carrion and nutrient additive treatments. These results demonstrate that large die-offs, such as mass mortality events, can have long-lasting effects on soil composition through increased soil nutrients and alter soil microbial community (i.e., reduced Bacilliaceae, etc.). These long-lasting impacts can permanently alter the soil community, which can lead to cascading bottom-up effects that can alter the entire ecosystem structure.}, }
@article {pmid41286365, year = {2025}, author = {Bondarenko, S and Obiol, A and Casamayor, EO and Massana, R}, title = {Non-Dikarya Fungal Clades Are Everywhere: What 18S rRNA Gene Metabarcoding Reveals About Cross-System Distribution of Fungi.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02642-w}, pmid = {41286365}, issn = {1432-184X}, support = {2020 BP 00293//Ag&#xe8;ncia de Gesti&#xf3; d'Ajuts Universitaris i de Recerca (AGAUR), Generalitat de Catalunya/ ; PID2021-127701NB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2019-108457RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, abstract = {Non-Dikarya fungi remain poorly characterized due to their cryptic morphology, cultivation difficulties, and limited representation in reference databases. To investigate their diversity and environmental distribution at a global scale, we reanalyzed over 6000 environmental samples using metabarcoding targeting the V4 region of the 18S rRNA gene, encompassing marine, freshwater, soil, hypersaline, polar, and other habitats. We constructed reference phylogenetic trees based on near full-length 18S rRNA gene sequences to enable accurate placement of short-read amplicon sequence variants (ASVs). This approach yielded robust classification at the phylum level and provided finer-scale clade resolution within major non-Dikarya groups. We delineated precise clades within Chytridiomycota, Microsporidia, Rozellida, and Aphelidea, and unveiled several novel ones. Our results show strong ecological structuring of fungal communities across habitats, with inland systems harboring greater fungal abundance and broader phylogenetic diversity than marine systems. Non-Dikarya fungi were consistently detected across diverse environments, including extreme habitats such as hypersaline lakes, deep sediments, and polar regions, where they were often the dominant fungal taxa. Although most ASVs tended to occur in a limited number of ecologically related habitats, phylogenetically related ASVs within the same clade were often adapted to different environments, indicating ecological diversity within clades. Our findings underscore both the ecological relevance and the cryptic diversity of non-Dikarya fungi in globally distributed environments, including extreme ones. Improved taxonomic resolution and broader reference dataset coverage are required to fully integrate these newly characterized lineages into fungal systematics and environmental surveys.}, }
@article {pmid41286193, year = {2025}, author = {García-Gutiérrez, L and Mellado, E and Martin-Sanchez, PM}, title = {Contribution of DNA Metabarcoding to the Environmental Fungal Assessments in Hospitals.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02626-w}, pmid = {41286193}, issn = {1432-184X}, support = {PID2021-123184OA-I00//Agencia Estatal de Investigaci&#xf3;n/ ; }, abstract = {Hospitals are particularly sensitive environments where immunosuppressed patients might acquire invasive fungal infections. Therefore, it is necessary to carry out periodical environmental microbiological assessments that evaluate the fungal bioburden in air and surfaces from different hospital zones. Current microbiological monitoring protocols at healthcare settings are mostly based on cultivation, while environmental DNA (eDNA) assessments are still scarce and should be further evaluated. To fill this gap, this study combines a large sampling scheme, comprising > 200 samples (air, surface, dust and soil) collected from four zones at three Spanish hospitals in two campaigns (winter and autumn), with two eDNA approaches (DNA metabarcoding and quantitative PCR) to characterize the hospital mycobiomes (diversity, community composition and airborne load), compared to a parallel culture-dependent study. DNA metabarcoding revealed a much more comprehensive inventory of hospital fungi compared to culturing; however, both approaches found similar dominant taxa including a variety of potentially opportunistic human pathogens. Hospital mycobiomes were affiliated to 4 phyla (mostly Ascomycota and Basidiomycota), 35 classes, 114 orders, 305 families, 643 genera and 535 species. The dominant genera, in both air and surfaces from the three hospitals, were Cladosporium, Alternaria, Aureobasidium, Penicillium, Neodidymelliopsis, Aspergillus, Pseudopithomyces and Stemphylium. The yeasts Candida and Clavispora were particularly abundant on high-touch surfaces indoors. The most important explanatory factors for the variance in community composition were the hospital and zone where samples were collected, the type of sample and the sampling campaign. DNA metabarcoding can assist hospital managers by providing an in-depth characterization of the baseline hospital mycobiome during normal operating conditions, as well as identifying and controlling community imbalances and associated health risks under demanding situations such as construction works or reported clinical outbreaks.}, }
@article {pmid41286179, year = {2025}, author = {Sultanova, Z and Dönertaş, HM and Hita, A and Aguilar, P and Dag, B and Lucas-Lledo, JI and Latorre, A and Carazo, P}, title = {Age-Dependent Gut Microbiota Dynamics and Their Association with Male Life-History Traits in Drosophila melanogaster.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02640-y}, pmid = {41286179}, issn = {1432-184X}, support = {ECF-2022-214//Leverhulme Trust/ ; P2021-00-007//Carl-Zeiss-Stiftung/ ; CGL2014-58722-P//Spanish Ministry of Economy and Competitivity/ ; PGC2018-099344-B-I00//Spanish Ministry of Economy and Competitivity/ ; }, abstract = {Growing evidence suggests that the gut microbiota is closely intertwined with life-history evolution in a wide range of species, including well-studied model organisms like Drosophila melanogaster. Although recent studies have explored the relationship between gut microbiota and female life-history, the link between gut microbiota and male life-history remains relatively unexplored. In this study, we investigated how gut microbiota changes with male age as well as the associations between gut microbiota composition and male life-history traits in D. melanogaster. Using 22 isolines from the Drosophila melanogaster Genetic Reference Panel (DGRP), we measured lifespan, early/late-life reproduction, and early/late-life physiological performance. We characterized the gut microbiota composition in young (5 days old) and old (26 days old) flies using 16S rDNA sequencing. We observed substantial variation in both male life-history traits and gut microbiota composition across isolines and age groups. Using machine learning, we show that gut microbiota composition could predict the chronological age of the organisms with high accuracy. The most important species contributing to machine learning prediction belonged to the Acetobacter and Ralstonia genera. Associations between gut microbiota and life-history traits were also notable, particularly involving different species from the Acetobacter genus. Our findings suggest that taxa such as Acetobacter may be relevant to the evolutionary ecology of host-microbe interactions in male fruit flies.}, }
@article {pmid41286138, year = {2025}, author = {Liu, XQ and An, XP and He, WX and Xu, XH and Hashem, A and Abd-Allah, EF and Wu, QS}, title = {Hairy Vetch Intercropping Attenuates Mycorrhizal Benefits to Walnut Growth and Soil Organic Carbon Sequestration via Glomalin.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {128}, pmid = {41286138}, issn = {1432-184X}, support = {SCXX-XZCG-22016//Hubei Province '14th Five-Year' Major Science and Technology Aid Tibet Project/ ; ORF-2025-356//Ongoing Research Funding program, King Saud University, Riyadh, Saudi Arabia/ ; }, mesh = {*Juglans/growth &amp; development/microbiology ; *Mycorrhizae/physiology/growth &amp; development ; *Soil/chemistry ; Soil Microbiology ; *Carbon Sequestration ; Plant Roots/microbiology/growth &amp; development ; Carbon/metabolism/analysis ; Biomass ; *Agriculture/methods ; *Fungal Proteins/metabolism ; *Glycoproteins/metabolism ; }, abstract = {Intercropping is a prevalent soil management strategy within walnut orchards, while its impacts on the functionality of arbuscular mycorrhizal fungi (AMF) in walnuts (Juglans regia) remain unclear, especially concerning soil carbon (C) sequestration via glomalin-related soil protein (GRSP). This study aimed to explore the effects of inoculation with the AMF species Diversispora spurca and intercropping with hairy vetch (Vicia villosa) on walnut biomass accumulation, soil water-stable aggregate (WSA) stability, leaf and root C (Cleaf and Croot) content, soil organic carbon (SOC), GRSP, and GRSP-contained C (CGRSP), in addition to the contribution rate of CGRSP to SOC. The intercropping treatment significantly inhibited root mycorrhizal colonization rate, soil hyphal length, and spore density in AMF-inoculated walnut plants. Individual AMF inoculation, rather than individual intercropping, significantly promoted shoot and root biomass accumulation, WSA stability, SOC, Cleaf and Croot, the levels of purified easily extractable (EEG), difficultly extractable (DEG), and total GRSP (TG), as well as their C contents. The combination treatment (AMF inoculation + intercropping) displayed limited benefits, improving just WSA stability without yielding synergistic advantages over individual treatments. Arbuscular mycorrhizal fungal inoculation significantly increased CGRSP, especially CDEG, while individual intercropping resulted in a reduction of CDEG. The combination treatment elevated both CDEG and CTG, albeit to a lesser extent than AMF alone. The contribution rates of CEEG, CDEG, and CTG to SOC were 0.33% - 0.53%, 1.16% - 1.78%, and 1.49% - 2.31%, respectively. Although AMF inoculation significantly increased the contribution rates of CDEG and CTG to SOC, this effect was diminished when combined with intercropping. Notably, CDEG, rather than CEEG, exhibited a significantly positive correlation with SOC and WSA stability. The findings provide new insights into the mechanisms of SOC sequestration in walnuts grown in controlled environments and offer a theoretical basis for the application of AMF in walnut cultivation.}, }
@article {pmid41284260, year = {2025}, author = {Song, H and Dowdell, K and Delafont, V and Skerlos, S and Raskin, L}, title = {The Neglected Role of Heterotrophic Protists in Engineered Water Systems.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c04958}, pmid = {41284260}, issn = {1520-5851}, abstract = {Heterotrophic protists can be considered the dark matter of microbial communities in engineered water systems. They are ubiquitous and ecologically significant yet remain largely overlooked. Although a growing body of research demonstrates their pivotal roles (e.g., predation, symbiosis, and nutrient cycling) in microbial communities in natural ecosystems, their functions in engineered water systems are poorly characterized, and heterotrophic protists are frequently excluded from microbial analyses. This is largely due to methodological constraints that have only recently been overcome. Recent advances in imaging, high-throughput sequencing, and meta-omics approaches, combined with expanding reference databases, have revolutionized studies of protist diversity and functions in a wide range of natural environments. Drawing on research from the fields of protistology, microbial ecology, and environmental microbiology, this review explores how the well-documented ecological roles of heterotrophic protists in natural environments translate to engineered ecosystems, offering insights into their functions in water treatment. We critically evaluate recent literature to synthesize both beneficial roles and potential risks of heterotrophic protists in various water treatment systems, while identifying key knowledge gaps and proposing directions for future research. We advocate for a shift in perspective that recognizes heterotrophic protists as important players and call for their integration into microbial community characterization and ecological frameworks in microbial ecology studies of engineered water systems. This integration will transform our understanding of microbial communities in engineered water systems, ultimately enabling novel, mechanistic, and ecologically informed management strategies.}, }
@article {pmid41280504, year = {2025}, author = {Ganguly, D and Roy, R and Mondal, P and Chakraborty, P and Paul, P and Das, S and Mallik, M and Maity, A and Trivedi, S and Tribedi, P and Sarkar, S}, title = {Nisin, a promising antimicrobial peptide, forestalls the methicillin-resistant Staphylococcus aureus biofilm network via reactive oxygen species generation.}, journal = {3 Biotech}, volume = {15}, number = {12}, pages = {428}, pmid = {41280504}, issn = {2190-572X}, abstract = {UNLABELLED: Staphylococcal infections have been reported to be a significant global threat to the effective management of public healthcare due to their drug resistance property. This attribute has further been complicated by their robust biofilm-forming potential. This escalating threat of biofilm-associated infections necessitates innovative and promising therapeutic strategies. Hence, in the present study, the biofilm threat of methicillin-resistant Staphylococcus aureus (MRSA) has been challenged by Nisin, a natural lantibiotic produced by Lactococcus lactis. This compound showed a promising antibacterial effect with minimum inhibitory concentrations (MICs) of 150 µg/ml against MRSA. Furthermore, a series of experiments has been conducted to confirm the antibiofilm potential of Nisin against MRSA. Towards this direction, the sub-MIC dose of Nisin (40 µg/mL) was found to inhibit biofilm formation by ~ 51% for MRSA. To support this finding, extracellular polymeric substance (EPS) was measured under the Nisin-treated and untreated conditions of MRSA. It was observed that Nisin could destabilise the MRSA biofilm by reducing the EPS production to an extent of ~ 55%. Mechanistic studies further demonstrated that Nisin was found to increase the intracellular accumulation of reactive oxygen species (ROS), which could lead to the alteration of cell membrane permeability. Additionally, Nisin attenuated staphyloxanthin production (~ 54%), hemolytic ability (~ 26%), and fibrinogen clumping ability (~ 27%) of MRSA, suggesting its interference in the virulence profile of MRSA. Collectively, these findings suggest Nisin's dual role as a promising Staphylococcal biofilm inhibitor and virulence factor suppressor, making it a viable option for the treatment of MRSA-linked infections.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04597-8.}, }
@article {pmid41278148, year = {2025}, author = {Dely, A and Racicot, R and Samples, R and Giddings, LA}, title = {Draft genome sequence and metabolomics data for Streptomyces sp. ADLamb9 isolated from the rhizosphere of Lavandula dentata.}, journal = {Data in brief}, volume = {63}, number = {}, pages = {112199}, pmid = {41278148}, issn = {2352-3409}, abstract = {Iron-chelating molecules or siderophores play pivotal roles in soil ecosystems, particularly in facilitating plant iron uptake as well as the phytoremediation of metal-polluted environments. Lavandula dentata, commonly referred to as French Lavender, is a valuable species for siderophore production due to its ability to thrive in iron-deficient Mediterranean soils by forming symbiotic relationships with siderophore-producing rhizosphere microbes. Here, we used a Chrome Azurol S (CAS) overlay assay to isolate a yellow-pigmented L. dentata rhizosphere siderophore-producing bacterium. This isolate also demonstrated antibacterial and antifungal activities against Bacillus subtilis and Aspergillus flavus, respectively. Genomic sequencing revealed that the isolate was Streptomyces sp. ADLamb9 with a genome size of 8.2 Mb and 71.77% GC content. antiSMASH analysis of the Streptomyces sp. ADLamb9 genome identified four putative siderophore biosynthetic gene clusters as well as the catecholate siderophore mirubactin. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) masses consistent with desferrioxamine B (561.3604 m/z), IC202C (517.3342 m/z), mirubactin (605.2207 m/z), as well as previously unreported desferrioxamine A1C. Notably, the presence of the rare earth element cerium differentially affected the accumulation of catecholate and hydroxamate siderophores, highlighting our incomplete understanding of the complex regulation and relationship between siderophore biosynthesis genes. These datasets, deposited at NCBI under the BioProject accession number PRJNA1224804, contribute to the broader scientific understanding of metabolite diversity and genomic features of Streptomyces sp. ADLamb9, providing insight into its use in bioremediation, especially in the presence of rare earth elements.}, }
@article {pmid41277839, year = {2025}, author = {Qian, M and Zhu, D and Yao, K-y and Liu, S-y and Li, M-k and Ye, M and Zhu, Y-g}, title = {Coexistence of virome-encoded health-associated genes and pathogenic genes in global habitats.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0150125}, doi = {10.1128/aem.01501-25}, pmid = {41277839}, issn = {1098-5336}, abstract = {UNLABELLED: Viral remnants constitute approximately 8% of the human genome, reflecting extensive historical gene exchange between viruses and their hosts. Some viral genomes harbor genes acquired through horizontal gene transfer that are associated with potential benefits to human health, alongside genes associated with pathogenicity. However, their global distribution, functional characteristics, and coexistence patterns remain poorly understood. Here, using the Integrated Microbial Genomes and Virome (IMG/VR v4) database, we identified 4,556 viruses carrying gene segments associated with human health across eight habitat types spanning 13 regions and 76 countries worldwide. Among viruses with identifiable hosts, those distributed in humans (478) accounted for the highest proportion. The viral genes associated with human health included BCO1 (beta-carotene oxygenase 1), bioB (biotin synthase), COQ2 (4-hydroxybenzoate polyprenyltransferase), GPX1 (glutathione peroxidase 1), GSTs (glutathione transferases), GSTT1 (glutathione S-transferase theta 1), GULO (L-gulonolactone oxidase), and menA (1,4-dihydroxy-2-naphthoate polyprenyltransferase). These genes not only associate with human health but also function as auxiliary metabolic genes in viral genomes. Notably, four pathogenic genes were found in viral sequences carrying health-associated genes, with potential for transcription and expression, indicating functional interactions. Experimental transduction of the viral bioB gene into Escherichia coli altered the expression of host pathogenic genes GCH1 (GTP cyclohydrolase IA) and UGDH (UDP-glucose 6-dehydrogenase), supporting potential cross-regulatory interactions. Overall, this study incorporates health-associated genes into viral genomics, highlighting their coexistence with pathogenic genes, and provides new insights into virus-host coevolution and potential biotechnological applications.<br><br>IMPORTANCE: Viruses are the most abundant biological entities on Earth and key drivers of microbial evolution through horizontal gene transfer. While often studied for their pathogenic effects, viruses can also carry genes that influence host metabolism and health. Genes associated with human health have been identified in viral genomes, yet their global distribution, functions, and coexistence with pathogenic genes remain largely unexplored. This study integrates datasets of health-associated genes into viral genomic analyses, revealing for the first time the coexistence of viral health-associated genes with those linked to pathogenicity. This dual genetic potential is observed across diverse habitats, highlighting viruses as multifaceted reservoirs of both beneficial and harmful genes. The study findings advance understanding of viral functional diversity and open new avenues for exploring viral roles in microbial ecology, biotechnology, and human health.}, }
@article {pmid41277251, year = {2025}, author = {Bron, A and Beltramo, C and Durif, C and Arora, T and Deschamps, C and Couturier, I and Domingo-Almenara, X and Otero, YF and Denis, S and Van de Wiele, T and Blanquet-Diot, S}, title = {Small intestine is not colon: a new in vitro model of the human ileum microbiome integrating the mucosal microenvironment and feeding status.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2579353}, doi = {10.1080/19490976.2025.2579353}, pmid = {41277251}, issn = {1949-0984}, mesh = {Humans ; *Ileum/microbiology ; *Gastrointestinal Microbiome/physiology ; *Colon/microbiology ; Adult ; *Intestinal Mucosa/microbiology ; Fatty Acids, Volatile/metabolism ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Fermentation ; Male ; Feces/microbiology ; Models, Biological ; Female ; Bile Acids and Salts/metabolism ; }, abstract = {The small intestinal microbiota plays a key role in human health but is understudied due to the invasiveness of sampling. There is no available model of the human ileal microbiome simulating the key nutritional and physicochemical parameters shaping this ecosystem, which has been fully validated based on in vivo data. Here, the Mucosal Artificial Ileum (M-ARILE) was set up to reproduce the pH, transit time, anoxic conditions, dynamics of feeding and microenvironments (luminal versus mucosal) found in a healthy human mid-ileum. To validate the newly developed in vitro system, nine-day fermentations were performed under either ileal or colonic conditions using the same fecal inoculum (n = 3 adult volunteers). The gut microbiota composition and metabolic activities were monitored daily. Distinct microbial signatures and metabolite profiles were obtained between in vitro ileum and colon conditions. In accordance with in vivo data, Peptostreptococcaceae, Clostridiaceae and Enterococcaceae were enriched in the ileum and associated with lower short-chain fatty acid production but higher O2 percentages. Interestingly, the abundances of key populations, such as Akkermansiaceae, and bile acid profiles were dependent on the feeding status of the M-ARILE. This new model provides a powerful platform for mechanistic studies on the role of ileal microbes in human nutrition and health considering inter-individual variabilities.}, }
@article {pmid41275375, year = {2025}, author = {Su, Z and Zhang, X and Wang, Q and Tang, Q and Yang, D and Liu, Y}, title = {amplysis: an R package for microbial composition and diversity analysis using 16S rRNA amplicon data.}, journal = {Briefings in functional genomics}, volume = {24}, number = {}, pages = {}, pmid = {41275375}, issn = {2041-2657}, support = {//Guangxi Education Agency/ ; //Guangxi Province Talent Project/ ; 42377012//National Natural Science Foundation of China/ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; *Software ; *Microbiota/genetics ; *Computational Biology/methods ; Biodiversity ; Bacteria/genetics/classification ; }, abstract = {The downstream analysis of 16S rRNA sequencing data remains a significant challenge for researchers lacking extensive bioinformatics expertise, often requiring proficiency in diverse tools and methodologies. To address this, we present amplysis, an R package designed to streamline the analysis and visualization of 16S rRNA amplicon sequencing data through an intuitive, code-light workflow. amplysis integrates data importing, processing, statistical analysis, and visualization into a unified framework. Key features include data normalization, microbial composition profiling, alpha/beta diversity analysis, ordination methods (e.g. Principal Component Analysis), and publication-ready visualization tools. The package's utility was demonstrated through three case studies, one of which analyzed microbial community responses to hexachlorocyclohexane (HCH) degradation in groundwater environments. Using amplysis, we efficiently generated phylum/genus-level abundance plots, alpha-diversity indices, and Principal Coordinates Analysis ordination, revealing significant shifts in community structure and diversity under HCH stress. The other case studies utilized publicly available data from published studies by other researchers. These results underscore the package's ability to simplify complex analyses while ensuring reproducibility and high-quality output. By integrating modular, user-friendly functions, amplysis lowers the barrier to robust microbiome data exploration. The package is available on GitHub (https://github.com/min-perilla/amplysis), offering a valuable resource for researchers in microbial ecology and environmental genomics.}, }
@article {pmid41275050, year = {2025}, author = {Naziębło, A and Pytlak, A and Furtak, A and Dobrzyński, J}, title = {Advances and Hotspots in Research on Verrucomicrobiota: Focus on Agroecosystems.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02657-3}, pmid = {41275050}, issn = {1432-184X}, support = {2021/41/B/NZ9/03130//Narodowe Centrum Nauki/ ; 2021/41/B/NZ9/03130//Narodowe Centrum Nauki/ ; }, abstract = {Members of the phylum Verrucomicrobiota are abundant yet relatively understudied soil bacteria that play key roles in biogeochemical cycling and plant-microbe interactions. They participate in the carbon (C) and nitrogen (N) cycles through the degradation of complex organic polymers such as cellulose, pectin, and starch - via the production of hydrolytic enzymes (e.g., cellulases, xylanases, chitinases), and through nitrogen transformations including denitrification, ammonification, and nitrogen fixation. Methanotrophic representatives (Methylacidiphilum, Methylacidimicrobium) oxidise methane under acidic or thermophilic conditions, thereby contributing to greenhouse gas mitigation. The ecological distribution and activity of Verrucomicrobiota are strongly influenced by nutrient availability, particularly of C, N, phosphorus (P), and potassium (K). Their variable responses to these elements reflect diverse life-history strategies, encompassing both copiotrophic (r-strategist) and oligotrophic (K-strategist) taxa. While Spartobacteria (e.g., Ca. Udaeobacter) are typically oligotrophic, classes such as Opitutia and Verrucomicrobiae exhibit mixed strategies. Beyond nutrient cycling, several members of the phylum function as plant growth-promoting and stress mitigating bacteria. They produce phytohormones (e.g., indole-3-acetic acid) and siderophores, increase the availability of nitrogen and solubilise phosphate. Some taxa exhibit antioxidant activity and can suppress phytopathogens such as Fusarium oxysporum through secondary metabolite production. These traits suggest a significant potential in soil health improvement. Overall, Verrucomicrobiota represent a functionally diverse and ecologically significant bacterial phylum whose metabolic versatility, adaptive life strategies, and plant-associated traits underscore their central role in sustainable agricultural ecosystems.}, }
@article {pmid41274594, year = {2025}, author = {Zou, H and Ying, W and Mafla Endara, PM and Klinghammer, F and Bai, J and Kang, H and Hammer, EC}, title = {Deep learning-driven investigation of nanoplastic impacts on soil protist behavior in soil chips.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {127414}, doi = {10.1016/j.envpol.2025.127414}, pmid = {41274594}, issn = {1873-6424}, abstract = {Nanoplastics are emerging environmental contaminants that increasingly threaten soil ecosystems, yet their effects on microbial behavior remain poorly understood. This is mainly due to the lack of experimental tools capable of directly observing microbial dynamics in situ under realistic soil-like conditions. Here, we present a proof-of-concept system that enables real-time, high-throughput monitoring of soil protists within microfluidic soil chips under nanoplastic exposure. Using microscopy video analysis integrated with a deep learning-based detection model and a transformer-based trajectory reconstruction algorithm, we quantitatively measured the movement of morpho-/locomotion type groups flagellates, ciliates, and amoebae across a gradient of nanoplastic concentrations (0, 2, and 10 mg/L). Our results showed reduced movement velocities for the groups of flagellates and ciliates under high nanoplastic conditions with a 24%-30% reduction in speed, while affect on amoebae was not detected. The trajectory data also provides novel insights into how protists navigate soil-like structures. Beyond these specific findings, our approach establishes a transformative framework for observing microbial life directly in its microenvironment, comparable to how animal behavior is monitored in ecological studies. By bridging real-time imaging and artificial intelligence, this method offers a new angle to study protist-environment interactions without the need for culture extraction. It opens the door to rethinking how microbial ecology, soil contamination, and biotic responses to environmental stressors are investigated, advancing opportunities from static, population-level measurements to dynamic, behavioral-level understanding within realistic habitats.}, }
@article {pmid41273983, year = {2025}, author = {Wu, YX and Wang, HY and Chu, WC and Gao, YY and Xia, MQ and Liu, FF}, title = {Ecological implications of biodegradable and conventional microplastics: Dissolved organic matter bioavailability and microbial response in marine systems.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140526}, doi = {10.1016/j.jhazmat.2025.140526}, pmid = {41273983}, issn = {1873-3336}, abstract = {The increasing accumulation of microplastics (MPs) in marine environments raises concerns about their ecological impacts, particularly through the release of dissolved organic matter (DOM). However, the bioavailability and ecological effects of MPs-derived DOM (MPs-DOM) remain poorly understood. In this study, we systematically investigated the leaching characteristics and microbial bioavailability of DOM derived from three biodegradable MPs (BMPs) including polylactic acid (PLA), polycaprolactone (PCL), polybutylene adipate terephthalate (PBAT) and two conventional MPs (CMPs, PE: polyethylene, PET: polyethylene terephthalate) under simulated photoaging. Our results demonstrated that BMPs released significantly more dissolved organic carbon (DOC) than CMPs, with PBAT showing the highest yield (40.77 vs. PE: 11.63 mg-DOC g-C[-1]). Optical analyses revealed that BMPs-DOM contained more protein-like fluorescent components, with higher fluorescence index and biological index, indicating greater lability. BMPs-DOM stimulated microbial growth more efficiently, with PBAT supporting the highest bacterial concentrations (∼52 ×10[3] cells mL[-1]) and DOC utilization (76.39 %). 16S rRNA sequencing revealed that MPs-DOM exposure reduced community richness, reshaped microbial communities through selective enrichment of copiotrophic and plastic-degrading taxa (e.g., Pseudomonas, Bacteroidota), and promoted stochastically driven assembly with specialized functional modules. Our study highlights that while BMPs may alleviate particulate plastic accumulation, their labile DOM release warrants careful evaluation for potential impacts on marine microbial ecology.}, }
@article {pmid41273632, year = {2025}, author = {Bi, J and Li, J and Rahman, SU and Long, Y and Hui, N and Romantschuk, M and Zheng, J and Zhang, X and Hou, D and Tan, J and Bi, Q and Xia, H and Yu, X and Luo, L and Liu, X}, title = {Balancing water efficiency and crop productivity: rhizosphere microbiome shifts in drought-resistant rice.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {12}, pages = {469}, pmid = {41273632}, issn = {1573-0972}, }
@article {pmid41272024, year = {2025}, author = {Khatbane, M and Mangavel, C and Borges, F and Aridhi, S and Toussaint, Y}, title = {Knowledge graph embedding for predicting and analyzing microbial interactions.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-025-27591-9}, pmid = {41272024}, issn = {2045-2322}, support = {R31PNCVX//ML4Community Project/ ; R31PNCVX//ML4Community Project/ ; R31PNCVX//ML4Community Project/ ; R31PNCVX//ML4Community Project/ ; R31PNCVX//ML4Community Project/ ; }, abstract = {Interactions between microorganisms play a major role in shaping the structure and function of microbial communities, yet their prediction remains a challenge in microbial ecology. While currently available machine learning methods have shown promising performance, they often rely on extensive input features that are obtained from labor-intensive experiments. Here, we propose a new framework to predict pairwise interactions that minimizes the need for in vitro experimentation. Our approach is based on knowledge graph embedding, which learns the representation of microorganisms and their interactions in an embedding space. Using a dataset of interactions between 20 soil bacterial strains cocultured in 40 different carbon source environments, we demonstrate the effectiveness of our framework in accurately predicting pairwise interactions. Notably, we show that our model can predict interactions involving strains with missing culture data. We additionally show that the obtained embeddings can reveal similarities between carbon source environments, enabling the prediction of interactions in one environment based on the outcomes in a similar environment between the same pair of microorganisms. Furthermore, our approach allows the design of a recommendation system that can be used to guide microbial community engineering. These findings demonstrate that knowledge graph embedding is a promising modeling strategy in microbial ecology.}, }
@article {pmid41271578, year = {2025}, author = {Man, M and Castañeda-Gómez, L and Moisan, MA and Gagné, P and Martineau, C and Ghosh Biswas, R and Knorr, MA and Frey, SD and Cadotte, MW and Nadelhoffer, KJ and Lajtha, K and Simpson, AJ and Simpson, MJ}, title = {Deciphering the Complex Interactions between Litter Inputs and Microbial Responses in Modulating Long-Term Soil Organic Matter Dynamics.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c08706}, pmid = {41271578}, issn = {1520-5851}, abstract = {Natural climate solutions that focus on increasing carbon in forests rely on the potential for additional carbon that may be incorporated into soil organic matter (SOM). The fate of soil carbon in temperate forests remains uncertain due to the complex role of microbes and their regulation of carbon flows in soils, especially with the addition of extra litter. We identified comprehensive molecular-level evidence that revealed shifts in SOM composition and microbial communities after 30 years of added litter in a temperate deciduous forest. Chronic litter addition failed to add new soil carbon after 30 years and correlated with reorganization in microbial community composition and altered carbon use. Excluding detrital inputs decreased soil carbon content, resulting in enhanced SOM decomposition and shifts toward specific bacterial groups (such as oligotrophs) that can utilize less energetically favorable carbon substrates that are typically more recalcitrant. Collectively, we found that microbial communities shifted in composition and altered carbon use strategies and traits, which aligned with changes to the molecular composition of SOM. Finally, this work demonstrates that in mesic temperate forests, decadal increases in litterfall, resulting from increased ecosystem productivity or management, may not offset soil carbon losses from climate change nor enhance carbon sequestration.}, }
@article {pmid41270014, year = {2025}, author = {Madsusan, A and Krainara, S and Suksong, W and Sudchoo, K and Tohmoh, N and Jonggrijug, P and Maipunklang, C and Chadaram, C and Samaeng, K and Kurdthongmee, P and Noosab, U and Nakapong, A and Udomsri, Y and Kanaso, S and Sakorn, N and Guan, NY and Sangkhano, S}, title = {Impact of a tropical monsoon climate on formaldehyde exposure and microbial contamination in anatomy dissection hall.}, journal = {PloS one}, volume = {20}, number = {11}, pages = {e0337238}, doi = {10.1371/journal.pone.0337238}, pmid = {41270014}, issn = {1932-6203}, mesh = {*Formaldehyde/analysis/adverse effects ; Humans ; *Occupational Exposure/analysis ; *Tropical Climate ; *Dissection ; Thailand ; *Air Pollution, Indoor/analysis ; *Anatomy/education ; Microbiota ; }, abstract = {Gross anatomy dissection is an essential component of medical and health science education, yet it presents notable occupational hazards, particularly from formaldehyde (FA) exposure and microbial contamination. These risks may be intensified in anatomy dissection halls located in tropical monsoon (Am) climates, where elevated humidity and temperature promote both chemical volatility and microbial persistence. This study assessed the combined effects of such climatic conditions on FA concentrations and microbial ecology within a naturally ventilated dissection hall in southern Thailand. FA levels were measured through personal and area air sampling across seven anatomical regions, while microbial contamination on cadaver-contact surfaces was evaluated using culture-based methods and high-throughput sequencing. Functional prediction of microbial communities was performed using PICRUSt2 to assess their metabolic adaptation to environmental stressors. The results revealed that both personal and indoor FA concentrations (mean 1.17 ± 0.39 ppm and 1.09 ± 0.45 ppm, respectively) exceeded several international occupational exposure limits, with the highest levels observed during dissections involving deep or adipose-rich anatomical regions. Microbial analyses identified stress-tolerant and potentially pathogenic genera, including Bdellovibrio, Aequorivita, and Aspergillus spp., along with enriched pathways involved in aromatic compound degradation and environmental resilience. These findings highlight the limitations of natural ventilation in controlling occupational exposures and microbial contamination in Am climate anatomy laboratories. The study supports the implementation of climate-responsive engineering controls and laboratory management strategies that address chemical safety, thermal regulation, and biosafety to promote healthier and more sustainable dissection environments in similar high-risk settings.}, }
@article {pmid41269303, year = {2025}, author = {Xin, H and He, L and Zhu, B}, title = {Ecological Insights into Gut Microbiota Networks Across Cognitive States in Alzheimer's Disease.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02662-6}, pmid = {41269303}, issn = {1432-184X}, support = {No. 202212691//Jiangxi Provincial Health Commission/ ; }, abstract = {The ecological mechanisms governing gut microbial community stability during Alzheimer's disease (AD) progression remain poorly understood. This study employed an ecological network to investigate microbial interactions and stability across cognitively normal controls (CK), individuals with mild cognitive impairment (MCI), and AD patients. We observed a stepwise decline in network complexity across groups, characterized by reduced clustering coefficients and average degree, from CK to AD. While the MCI group exhibited intermediate structural complexity, it displayed the highest vulnerability and lowest robustness, indicating a critical transitional state. Keystone taxa analysis revealed a significant shift in microbial community, with the CK network was enriched with diverse, potentially beneficial keystone taxa, whereas the AD network retained only connector species, and the MCI network showed a complete absence of keystone taxa. Cohesion analysis revealed a non-linear trajectory of microbial interactions, with negative cohesion peaking in MCI. Our findings demonstrate that cognitive decline is associated with a fundamental reorganization of the gut microbial ecosystem. This reorganization pattern reveals a resilient state in health, a vulnerable phase in MCI, and a stable yet dysbiotic configuration in AD, with keystone taxa serving as pivotal regulators of community stability. Community assembly analysis showed a shift from deterministic to stochastic processes during cognitive decline, with weakened host regulatory mechanisms. These findings advance our understanding of the gut microbial ecology in neurodegenerative disease and reveal the mechanism by which microbial communities reorganize network to maintain stability in different cognitive states.}, }
@article {pmid41268901, year = {2025}, author = {Zhao, Y and Zhao, Y and Dong, Y and Sun, X and Zhang, W and Zhao, L and Grégori, G}, title = {Biogeography of Virioplankton Abundance and Subcluster Patterns in the Northwest Pacific: A Large-Scale Perspective.}, journal = {MicrobiologyOpen}, volume = {14}, number = {6}, pages = {e70161}, doi = {10.1002/mbo3.70161}, pmid = {41268901}, issn = {2045-8827}, support = {//This study was financially supported by the National Natural Science Foundation of China (No. 42076139), National Key Research and Development Program of China (No. 2024YFE0114300), and the Sino-French International Research Project (CNRS-CAS) Dynamics and Function of Marine Microorganisms (IRP-DYF2M): insight from physics and remote sensing./ ; }, mesh = {Pacific Ocean ; *Seawater/virology ; *Plankton/virology/classification ; *Viruses/classification/isolation &amp; purification/genetics ; Flow Cytometry ; Phylogeography ; Biodiversity ; }, abstract = {Marine virioplankton, the most abundant biological entities in the ocean, play essential roles in microbial ecology and biogeochemical cycling. This study investigates their biogeography in the Northwest Pacific using enhanced-resolution flow cytometry and phenotypic diversity analyses. By resolving four consistent viral subclusters across oceanic and coastal waters and detecting a fifth subcluster in the Yellow Sea, we revealed previously unrecognized patterns of viral community structures. Viral abundances ranged from 3.69 × 10[6] to 17.09 × 10[6] particles/mL, showing clear coastal-oceanic differentiation. Environmental gradients, particularly temperature, chlorophyll, and picoplankton abundance, emerged as the primary drivers of virioplankton community structure. These findings underscored the tight coupling between viral populations and their microbial hosts across contrasting marine environments. Phenotypic diversity analysis revealed distinct viral communities in the Luzon Strait, despite comparable abundance patterns to adjacent regions, demonstrating the method's sensitivity in detecting subtle community shifts. This study advances understanding of marine viral biogeography and introduces a robust framework for investigating viral community dynamics. The approach enables high-throughput screening across large spatial scales while maintaining sensitivity to fine-scale community variations, offering new possibilities for monitoring viral responses to environmental change in marine ecosystems.}, }
@article {pmid41268888, year = {2025}, author = {Trivedi, S and Roy, R and Naskar, A and Das, B and Chakraborty, P and Paul, P and Das, S and Malik, M and Tribedi, P}, title = {Cuminaldehyde Potentiates the Antimicrobial and Antibiofilm Activity of Vancomycin: A Biochemical Study to Manage the Threats of Methicillin Resistant Staphylococcus aureus (MRSA).}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {133}, number = {11}, pages = {e70087}, doi = {10.1111/apm.70087}, pmid = {41268888}, issn = {1600-0463}, support = {TNU/R&amp;D/MG/24/02//The Neotia University/ ; TNU/R&amp;D/MG/24/04//The Neotia University/ ; }, mesh = {*Methicillin-Resistant Staphylococcus aureus/drug effects/physiology ; *Vancomycin/pharmacology ; *Biofilms/drug effects ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; Drug Synergism ; Humans ; Oxidative Stress/drug effects ; Bacterial Adhesion/drug effects ; Reactive Oxygen Species/metabolism ; *Benzaldehydes/pharmacology ; Staphylococcal Infections/microbiology/drug therapy ; Virulence Factors/metabolism ; }, abstract = {Methicillin-resistant Staphylococcus aureus (MRSA) is reported to cause serious health issues in humans by exploiting its biofilm network. To combat this global concern, the combined efficacy of cuminaldehyde (a bioactive phytochemical) and vancomycin (an antibiotic) was tested against MRSA strains. While both compounds exhibited independent antibacterial activity, their combination revealed improved efficacy against MRSA through additive interactions. Response surface methodology (RSM)-generated quadratic models optimized the combinatorial doses, revealing significant microbial growth inhibition of the MRSA strains (p < 0.05). Furthermore, the combined application of cuminaldehyde and vancomycin at sub-MIC doses could inhibit biofilm formation by lowering bacterial adhesion, extracellular polysaccharide (EP) synthesis and the extent of biofilm-associated proteins. Additionally, the mechanistic studies revealed that the said combination (cuminaldehyde and vancomycin) was found to accumulate oxidative stress with a ~2.5-fold increase in intracellular reactive oxygen species (ROS) and a ~2.3-fold reduction in membrane integrity. In view of the same, this combination attenuated key virulence factors (protease, hemolysin, and coagulase) and metabolic activity of MRSA. Hence, the combinations involving cuminaldehyde and vancomycin could potentially enhance the antimicrobial and antibiofilm efficacy, presenting a promising approach to combat the escalating crisis linked with MRSA-associated threats.}, }
@article {pmid41268502, year = {2025}, author = {Fu, Y and Dou, Q and Wang, F and Virta, M and Zhang, T and Elsner, M and Amelung, W and Jiang, X and Tiedje, JM}, title = {A flowing database: Harnessing sewage-based surveillance for antimicrobial resistance.}, journal = {Innovation (Cambridge (Mass.))}, volume = {6}, number = {11}, pages = {100977}, pmid = {41268502}, issn = {2666-6758}, }
@article {pmid41267490, year = {2025}, author = {Sharma, P and Dagariya, S and Sharma, S and Singh, M}, title = {Uncovering the nexus of human health hazards of nanoplastics, gut-dysbiosis and antibiotic-resistance.}, journal = {Journal of environmental science and health. Part C, Toxicology and carcinogenesis}, volume = {}, number = {}, pages = {1-60}, doi = {10.1080/26896583.2025.2578871}, pmid = {41267490}, issn = {2689-6591}, abstract = {Nanoplastics (1-1000 nm) (NPs) represent a novel and insidious class of emerging contaminants with the potential to profoundly disrupt gut microbial ecology and accelerate the spread of antibiotic resistance two critical and converging threats to global health. While prior studies have examined the toxicokinetics of NPs and their general microbial interactions, this review provides the first comprehensive synthesis specifically focused on the nexus between NPs, gut dysbiosis, and the propagation of antibiotic resistance genes (ARGs). This review highlights how NPs alter gut microbiota composition, suppressing beneficial microbes while fostering opportunistic pathogens and how such imbalances may contribute to human health issues. Importantly, emerging evidence also suggests that NPs may serve as unrecognized vectors for horizontal gene transfer (HGT), enabling the rapid dissemination of ARGs via conjugation, transformation, transduction, and extracellular vesicles within the gastrointestinal tract. In addition, this review also identifies urgent methodological gaps in detecting NPs in biological matrices and the environment, as well as assessing their mechanistic impacts, calling for innovation in analytical approaches. By presenting an interdisciplinary perspective that bridges nanotoxicology, microbiome science, and antimicrobial resistance, this article sheds light on an underexplored yet urgent frontier in environmental health, offering novel insights to guide future research, risk assessment, and policy development.}, }
@article {pmid41266882, year = {2025}, author = {Hu, H and Zhang, Y and Liu, Z and Han, Y and Luo, Y and Zhang, C and Yu, Y and Wang, J and Li, B and Su, S}, title = {Microbial Diversity Affects the Cold Tolerance of Red Swamp Crayfish (Procambarus clarkii) by Regulating Histamine Metabolism.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02659-1}, pmid = {41266882}, issn = {1432-184X}, support = {No. 2025JBFR03//Central Public-interest Scientific Institution Basal Research Fund, Freshwater Fisheries Research Center, CAFS/ ; No. 2025JBFR03//Central Public-interest Scientific Institution Basal Research Fund, Freshwater Fisheries Research Center, CAFS/ ; No. 2025JBFR03//Central Public-interest Scientific Institution Basal Research Fund, Freshwater Fisheries Research Center, CAFS/ ; No. 2025JBFR03//Central Public-interest Scientific Institution Basal Research Fund, Freshwater Fisheries Research Center, CAFS/ ; No. 2025JBFR03//Central Public-interest Scientific Institution Basal Research Fund, Freshwater Fisheries Research Center, CAFS/ ; DTYZ2024003//"Soil Transplantation" Team Project of Panjin Talent Program/ ; DTYZ2024003//"Soil Transplantation" Team Project of Panjin Talent Program/ ; DTYZ2024003//"Soil Transplantation" Team Project of Panjin Talent Program/ ; DTYZ2024003//"Soil Transplantation" Team Project of Panjin Talent Program/ ; DTYZ2024003//"Soil Transplantation" Team Project of Panjin Talent Program/ ; DTYZ2024003//"Soil Transplantation" Team Project of Panjin Talent Program/ ; JBGS [2021]123//"JBGS" Project of Seed Industry Revitalization in Jiangsu Province/ ; JBGS [2021]123//"JBGS" Project of Seed Industry Revitalization in Jiangsu Province/ ; JBGS [2021]123//"JBGS" Project of Seed Industry Revitalization in Jiangsu Province/ ; 2023TD39//Central Public-Interest Scientific Institution Basal Research Fund, CAFS/ ; 2023TD39//Central Public-Interest Scientific Institution Basal Research Fund, CAFS/ ; }, abstract = {The red swamp crayfish (Procambarus clarkii) is one of the important freshwater aquaculture species in China, but its growth and development are greatly affected by temperature, which makes it difficult to expand its aquaculture range to the northern regions of China. The composition of gut microbes plays a vital role in resisting environmental pressure, and is also an important driving factor for amino acid metabolism in the body. However, little is known about the relationship between microorganisms, metabolism, and cold-resistance ability of P. clarkii. In this study, we performed the cold-resistance and antioxidant ability test, gut microbiota diversity analysis, quantitative analysis of histamine, and bioinformatics analysis of histamine receptor (HR) family on P. clarkii. The results showed that the cold-resistance crayfish exhibited high antioxidant ability and low gut microbiota diversity after acute cold stress. Next, we also found that there was significant correlation between the Lactobacilli genus and histamine abundance, indicating that the excellent cold tolerance ability of crayfish may stem from the degradation of histamine by Lactobacilli. Finally, it was revealed that HR genes had considerable quantity of gene copies, conservative evolution in crustacean lineages and expression differences in low-temperature tolerant populations. These results suggested that the diversity of Lactobacillus mediated changes in histamine metabolism affect antioxidant capacity, which is one of the reasons why P. clarkii exhibits cold resistance ability. This finding provided a theoretical basis for understanding the microorganism-histamine regulation mechanism of red swamp crayfish under cold stress, promoting the breeding and healthy culture of cold-resistance strain.}, }
@article {pmid41266660, year = {2025}, author = {Caroppo, C and Caruso, G and Bergamasco, A and Decembrini, F}, title = {Phytoplankton diversity and size structure in the Central-Southern Tyrrhenian Sea: implications for microbial functioning.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02650-w}, pmid = {41266660}, issn = {1432-184X}, abstract = {Microbial community dynamics in relation to mesoscale hydrographical features are almost unknown particularly in the pelagic Central-Southern Tyrrhenian Sea. To get a more comprehensive view of phytoplankton community structure and microbial community functioning, datasets of phytoplankton abundance, composition and some microbial enzyme activities (leucine aminopeptidase, LAP, beta-glucosidase, GLU and alkaline phosphatase, AP) from six cruises carried out twenty years ago were analyzed. Hydrographic characteristics identified the presence of both Atlantic Waters (AW) and Tyrrhenian Intermediate Waters (TIW). Size structure of phytoplankton biomass showed an unexpected high contribution of the pico-phytoplankton to the total primary production (> 60%) determining a predominant microbial food web. Phytoplankton distribution patterns varied more significantly on a seasonal rather than spatial scale. Autumn assemblages were characterized by the highest abundance and carbon content, with species mainly belonging to dinoflagellates whose growth was supported by intense microbial activities. In contrast, in the summer diatoms developed in unstable TIW where microbial activity was declining. Enzymatic activities varied in the different water masses and seasons, with high LAP activity in summer AW (s-AW) as well as in deep TIW (d-TIW), while AP and GLU reached their maximum in autumn AW (a-AW), suggesting quick organic matter recycling. Coupled primary production and hydrolysis in mixed AW (m-AW) and in a-AW indicated synchronized autotrophic and heterotrophic processes, while in TIW organic matter was only partially recycled. Overall, microbial metabolism was closely shaped by hydrographic and seasonal dynamics, confirming its key role in biogeochemical cycles. Our data could provide a baseline study for future research dealing with the microbial functioning in this Mediterranean region.}, }
@article {pmid41074769, year = {2025}, author = {Tucker, SJ and Freel, KC and Eren, AM and Rappé, MS}, title = {Habitat-specificity in SAR11 is associated with a few genes under high selection.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf216}, pmid = {41074769}, issn = {1751-7370}, support = {#989028//Simons Postdoctoral Fellowship in Marine Microbial Ecology/ ; NA20NOS4200123//National Science Foundation Graduate Research/ ; 1842402//National Science Foundation Graduate Research/ ; #687269//Simons Foundation/ ; }, mesh = {*Ecosystem ; Phylogeny ; *Selection, Genetic ; *Seawater/microbiology ; Metagenome ; *Alphaproteobacteria/genetics/classification/isolation &amp; purification ; Metagenomics ; Genome, Bacterial ; Pacific Ocean ; Genetic Variation ; }, abstract = {The order Pelagibacterales (SAR11) is the most abundant group of heterotrophic bacteria in the global surface ocean, where individual sublineages likely play distinct roles in oceanic biogeochemical cycles. Yet, understanding the determinants of niche-partitioning within SAR11 has been a formidable challenge due to the high genetic diversity within individual SAR11 sublineages and the limited availability of high-quality genomes from both cultivation and metagenomic reconstruction. Through an integrated metapangenomic analysis of 71 new SAR11 isolate genomes and a time-series of metagenomes from the prominent source of isolation, we reveal an ecological and phylogenetic partitioning of metabolic traits across SAR11 genera. We resolve distinct habitat-preferences among genera for coastal or offshore environments of the tropical Pacific and identify a handful of genes involved in carbon and nitrogen metabolisms that appear to contribute to these contrasting lifestyles. Furthermore, we find that some habitat-specific genes experience high selective pressures, indicating that they are critical determinants of SAR11 fitness and niche differentiation. Together, these insights reveal the underlying evolutionary processes shaping niche-partitioning within sympatric and parapatric populations of SAR11 and demonstrate that the immense genomic diversity of SAR11 bacteria naturally segregates into ecologically and genetically cohesive units, or ecotypes, that vary in spatial distributions in the tropical Pacific.}, }
@article {pmid41265332, year = {2025}, author = {Mol, Z and Segers, L and Van Langenhove, H and Vandermarliere, T and De Gusseme, B and Walgraeve, C and Demeestere, K}, title = {Pressure-induced taste and odour deviations within the high-pressure drinking water distribution system.}, journal = {Water research}, volume = {289}, number = {Pt B}, pages = {124965}, doi = {10.1016/j.watres.2025.124965}, pmid = {41265332}, issn = {1879-2448}, abstract = {Taste and odour (T&amp;O) issues in tap water decrease the willingness of consumers to drink it. Production and/or release of odour compounds during drinking water distribution should be avoided as the water is directly delivered to consumers without further treatment. Odours can be caused by leaching of compounds from pipe materials, microbial metabolism, disinfection reactions, or diffusion of odour compounds or precursors from external sources. Increasing knowledge of T&amp;O origins is needed to better solve future problems. Therefore, this research focuses on odour linked to changes in pressure because of maintenance work at the high-pressure (HP) drinking water distribution system. A trace analytical method targeting 45 T&amp;O compounds is further optimized by including derivatisation to improve halophenol detection. Next, in a field section of a real HP pipe (± 3 km), three scenarios were systematically investigated. Lowering the overpressure in the HP pipe from 10 to 5 bar resulted in an observed bitumen/asphalt odour, that further increased in intensity after a subsequent sudden pressure drop to 2 bar. Based on the odour threshold and profile, two halophenols were detected that may have contributed to this odour observation. When the section was partially emptied, 6 halophenols and 5 other T&amp;O compounds were identified. Our results indicate that pressure changes induce the leaching of T&amp;O compounds from sealing materials connecting the 6m-pipe sections. This is further supported by the detection of similar T&amp;O compounds in a water extract of the sealing materials and in an odorous household sample collected after maintenance work in the HP-network.}, }
@article {pmid41264968, year = {2025}, author = {Yang, C and Bao, L and Shi, Z and Xv, X and Li, J and Jiang, D and You, L}, title = {Jingning formula alleviates ADHD by restoring gut microbiota dysbiosis and tryptophan metabolic dysfunction.}, journal = {Journal of pharmaceutical and biomedical analysis}, volume = {269}, number = {}, pages = {117256}, doi = {10.1016/j.jpba.2025.117256}, pmid = {41264968}, issn = {1873-264X}, abstract = {Jingning Fang (JNF), a clinically used herbal medicine for attention deficit hyperactivity disorder (ADHD), demonstrates significant efficacy in alleviating core symptoms such as hyperactivity and impulsivity in pediatric patients. To systematically investigate its therapeutic mechanisms, we implemented an integrated approach encompassing UPLC-Q-TOF/MS-based untargeted metabolomics profiling of brain, serum, and fecal specimens, targeted quantification of tryptophan pathway metabolites across these biological compartments, and gut microbiome characterization via 16S rRNA sequencing. Our analysis revealed a prominently dysregulated metabolic pathway in ADHD, characterized by perturbations in tryptophan metabolism that were particularly pronounced in feces (P < 0.05). Notably, the kynurenic acid (KYNA)/quinolinic acid (QUINA) ratio, a pivotal indicator of kynurenine pathway homeostasis, exhibited robust correlations with both behavioral manifestations and gut microbial ecology. These findings provide a mechanistic basis for JNF's clinical efficacy in ADHD management by highlighting its role in restoring gut microbiome balance and tryptophan metabolic homeostasis.}, }
@article {pmid41264852, year = {2025}, author = {Kosmopoulos, JC and Anantharaman, K}, title = {Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises.}, journal = {Biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.biochem.5c00349}, pmid = {41264852}, issn = {1520-4995}, abstract = {Viruses are the most abundant biological entities on Earth and play central roles in shaping microbiomes and influencing ecosystem functions. Yet, most viral genes remain uncharacterized, comprising what is commonly referred to as "viral dark matter." Metagenomic studies across diverse environments consistently show that 40-90% of viral genes lack known homologues or annotated functions. This persistent knowledge gap limits our ability to interpret viral sequence data, understand virus-host interactions, and assess the ecological or applied significance of viral genes. Among the most intriguing components of viral dark matter are auxiliary viral genes (AVGs), including auxiliary metabolic genes (AMGs), regulatory genes (AReGs), and host-physiology-modifying genes (APGs), which may alter host function during infection and contribute to microbial metabolism, stress tolerance, or resistance. In this Review, we explore recent advances in the discovery and functional characterization of viral dark matter. We highlight representative examples of novel viral proteins across diverse ecosystems, including human microbiomes, soil, oceans, and extreme environments, and discuss what is known and still unknown about their roles. We then examine the bioinformatic and experimental challenges that hinder functional characterization and present emerging strategies to overcome these barriers. Finally, we highlight both the fundamental and applied benefits that multidisciplinary efforts to characterize viral proteins can bring. By integrating computational predictions with experimental validation and fostering collaboration across disciplines, we emphasize that illuminating viral dark matter is both feasible and essential for advancing microbial ecology and unlocking new tools for biotechnology.}, }
@article {pmid41264018, year = {2025}, author = {Villalón, A and Rodríguez Alonso, &#xc1; and Carballo, J and Rodríguez López, LA and Pérez, MJ}, title = {Diversity of Bacteria and Yeasts Present in an Automobile Treatment System.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02651-9}, pmid = {41264018}, issn = {1432-184X}, abstract = {The formation of biofilms in industrial environments poses a significant challenge because of their ability to degrade materials, contaminate products, and harbour pathogenic microorganisms. In the automotive industry, surface treatment systems (STS) used to prepare car bodies can provide a favourable environment for microbial development, driven by the presence of water, organic matter, and variable physicochemical conditions. In this context, the microbial diversity present in the different STS baths of an automotive plant, as well as in the process water, was analysed. Through culture-based methods and molecular analysis, 33 bacterial and 6 yeast species were identified. The results revealed a constant presence of bacteria at all sampling points, whereas yeasts were detected less frequently and in more localized areas (Industrial and Dechromatized Water, E2, Conversion stage, E4 and Passivation stage). This study underscores the importance to enhance cleaning and disinfection protocols in STS, as high bacterial counts persisted even after rinsing stages, in order to prevent economic losses, product degradation and health risks. Furthermore, it highlights the potential use of certain microorganisms in biotechnology and bioremediation applications.}, }
@article {pmid41263569, year = {2025}, author = {Ding, W and Ling, Z and Liu, X and Zhang, J and Cheng, Y and Zhu, Z and Wu, L and Xu, X and Gao, Y and Hu, X}, title = {Impact of carbapenem-resistant Klebsiella pneumoniae infection on gut microbiota and host immunity: a case-control study.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0297525}, doi = {10.1128/spectrum.02975-25}, pmid = {41263569}, issn = {2165-0497}, abstract = {Carbapenem-resistant Klebsiella pneumoniae (CRKP) represents a critical global health threat with limited treatment options. While the gut microbiota is a reservoir for opportunistic pathogens and a regulator of host immunity, the reciprocal impact of systemic CRKP infection on gut microbial ecology and immune responses remains poorly defined. In a prospective case-control study, 38 patients with confirmed CRKP infection and 38 matched hospitalized controls without CRKP were enrolled. Fecal samples underwent 16S rRNA gene sequencing to characterize microbial profiles, and serum cytokine levels were quantified using multiplex immunoassays. CRKP infection was associated with significantly reduced microbial diversity and a distinct shift in community structure, characterized by depletion of beneficial commensals (Bacteroides, Faecalibacterium, Roseburia) and enrichment of pathobionts (Klebsiella, Enterococcus). Enterotype analysis revealed a predominance of a Klebsiella/Enterococcus-dominated enterotype in CRKP patients. Functional predictions indicated impaired carbohydrate and butyrate metabolism alongside increased virulence- and resistance-associated pathways. Systemically, patients exhibited elevated pro-inflammatory cytokines (IL-6, TNF-α, IFN-γ) and chemokines (IP-10, MCP-1, RANTES). Correlation analyses linked opportunistic taxa with heightened inflammatory markers, while beneficial short-chain fatty acid producers showed inverse associations. Systemic CRKP infection is associated with profound gut dysbiosis and a hyper-inflammatory immune response. The strong microbiota-immune correlations suggest that the gut microbiota may serve as a biomarker and a potential therapeutic target for mitigating CRKP-associated immune dysfunction, though the directional relationship (cause vs. consequence) between dysbiosis and CRKP infection remains to be elucidated.IMPORTANCECarbapenem-resistant Klebsiella pneumoniae (CRKP) is a critical global threat with limited therapeutic options. This study reveals that systemic CRKP infection is associated with profound gut dysbiosis-characterized by loss of beneficial commensals (e.g., Faecalibacterium) and expansion of pathobionts (e.g., Klebsiella, Enterococcus)-as well as a hyperinflammatory immune response. We demonstrate strong correlations between specific microbial taxa and host cytokines, suggesting that the gut microbiome may hold potential as a biomarker and therapeutic target. These findings enhance our understanding of host-microbe interactions in CRKP infection and support the exploration of microbiota-based therapies. However, further studies, including longitudinal and animal models, are needed to clarify whether gut dysbiosis directly influences CRKP outcomes or is a secondary consequence.}, }
@article {pmid41263391, year = {2025}, author = {Gilbert, JA and Scholz, AH and Dominguez Bello, MG and Korsten, L and Berg, G and Singh, BK and Boetius, A and Wang, F and Greening, C and Wrighton, K and Bordenstein, SR and Jansson, J and Lennon, JT and Souza, V and Allard, SM and Thomas, T and Cowan, D and Crowther, TW and Nguyen, N and Harper, L and Haraoui, LP and Ishaq, SL and McFall-Ngai, M and Redford, KH and Peixoto, R}, title = {Safeguarding microbial biodiversity: microbial conservation specialist group within the species survival commission of the International Union for Conservation of Nature.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf239}, pmid = {41263391}, issn = {1751-7370}, }
@article {pmid41263344, year = {2025}, author = {Gilbert, JA and Scholz, AH and Dominguez Bello, MG and Korsten, L and Berg, G and Singh, BK and Boetius, A and Wang, F and Greening, C and Wrighton, K and Bordenstein, SR and Jansson, J and Lennon, JT and Souza, V and Allard, SM and Thomas, T and Cowan, D and Crowther, TW and Nguyen, N and Harper, L and Haraoui, LP and Ishaq, SL and McFall-Ngai, M and Redford, KH and Peixoto, R}, title = {Safeguarding microbial biodiversity: microbial conservation specialist group within the species survival commission of the International Union for Conservation of Nature.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {12}, pages = {}, doi = {10.1093/femsec/fiaf107}, pmid = {41263344}, issn = {1574-6941}, support = {//Gordon and Betty Moore Foundation/ ; }, }
@article {pmid41263324, year = {2025}, author = {Gilbert, JA and Scholz, AH and Dominguez Bello, MG and Korsten, L and Berg, G and Singh, BK and Boetius, A and Wang, F and Greening, C and Wrighton, K and Bordenstein, SR and Jansson, J and Lennon, JT and Souza, V and Allard, SM and Thomas, T and Cowan, D and Crowther, TW and Nguyen, N and Harper, L and Haraoui, L-P and Ishaq, SL and McFall-Ngai, M and Redford, KH and Peixoto, R}, title = {Safeguarding microbial biodiversity: microbial conservation specialist group within the species survival commission of the International Union for Conservation of Nature.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0150525}, doi = {10.1128/msystems.01505-25}, pmid = {41263324}, issn = {2379-5077}, }
@article {pmid41262936, year = {2025}, author = {Postec, A and Yumoto, I and Morales-Barrera, L and Gessesse, A and McMillan, DGG}, title = {Editorial: Microbial ecology and biotechnological potential of alkaline environments.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1726999}, pmid = {41262936}, issn = {1664-302X}, }
@article {pmid41262263, year = {2025}, author = {Bautista, J and López-Cortés, A}, title = {Chronobiome medicine: circadian regulation of host-microbiota crosstalk in systemic physiology.}, journal = {Frontiers in endocrinology}, volume = {16}, number = {}, pages = {1691172}, pmid = {41262263}, issn = {1664-2392}, mesh = {Humans ; *Circadian Rhythm/physiology ; *Gastrointestinal Microbiome/physiology ; Animals ; }, abstract = {Circadian rhythms, governed by central and peripheral clocks, orchestrate nearly all aspects of human physiology, including metabolism, endocrine function, neuroimmune activity, and behavior. Emerging evidence reveals that these oscillations are closely intertwined with the gut microbiota, which itself displays diurnal fluctuations in composition and metabolite production. This bidirectional regulation establishes a dynamic circadian-microbiota axis that synchronizes nutrient processing, hormonal secretion, immune surveillance, and neural signaling. Disruption of this temporal alignment, through genetic, environmental, or lifestyle factors, precipitates systemic dysregulation, fostering metabolic syndrome, endocrine imbalance, immune dysfunction, neuropsychiatric vulnerability, cardiovascular alterations, and carcinogenesis. Mechanistic studies highlight that microbial-derived metabolites such as short-chain fatty acids, bile acids, and indoles act as circadian cues, while host clock genes modulate microbial ecology and intestinal barrier integrity. These insights underscore the translational potential of circadian precision medicine, in which time-restricted feeding, probiotics, prebiotics, and chronotherapy restore synchrony between microbial and host clocks. This review synthesizes current knowledge on circadian modulation of microbiota-mediated crosstalk across metabolic, neural, immune, and endocrine pathways, emphasizing its implications for health, disease, and novel therapeutic strategies.}, }
@article {pmid41260033, year = {2025}, author = {Zhang, Q and Zhang, S and Cao, X and Zhi, Y and Guo, Y}, title = {The gut microbiota in post-stroke depression: A systematic review of microbial mechanisms and therapeutic targeting of neuroinflammation.}, journal = {Microbiological research}, volume = {303}, number = {}, pages = {128391}, doi = {10.1016/j.micres.2025.128391}, pmid = {41260033}, issn = {1618-0623}, abstract = {Post-stroke depression (PSD), a frequent and debilitating complication after stroke, severely hinders rehabilitation. Emerging evidence underscores the role of neuroinflammation and the gut microbiota in PSD pathogenesis. This review systematically elaborates the mechanisms by which gut dysbiosis contributes to PSD-related neuroinflammation via immune cell regulation (e.g., Treg/Th17 balance), microbial metabolites (e.g., SCFAs, tryptophan derivatives), and neural pathways (vagus nerve, HPA axis). A key focus is the comparative analysis of the gut microbiota in PSD against major depressive disorder (MDD) and Alzheimer's disease (AD), revealing a unique, stroke-induced microbial signature characterized by a loss of protective symbionts and a bloom of pro-inflammatory taxa. We further discuss the translational potential of microbiota-targeted interventions (e.g., probiotics, prebiotics) for PSD. By integrating clinical microbial ecology with mechanistic insights, this review synthesizes evidence suggesting that the gut microbiome may represent a promising diagnostic and therapeutic target for PSD, offering a distinct perspective from previous literature.}, }
@article {pmid41259914, year = {2025}, author = {Yang, W and Wang, X}, title = {Transmission mechanisms and risk tracing of antibiotic resistance genes in rivers driven by wastewater inputs.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140523}, doi = {10.1016/j.jhazmat.2025.140523}, pmid = {41259914}, issn = {1873-3336}, abstract = {Aquatic environments are critical for ARG dissemination, yet contributions from different wastewater sources, dominant HGT mechanisms, and residual risks in natural waters remain unclear. Based on 863 metagenomic samples across China, we systematically analyzed wastewater inputs, HGT mechanisms, and risks of riverine ARGs. Wastewater treatment plants were the primary source, contributing about 50 % of riverine ARGs. Conjugation dominated ARG transfer, primarily via F-type type IV secretion systems. High-transmission plasmids were widespread. Although phage-mediated transduction represented only 3 % of HGT, it facilitated cross-environmental spread of clinically significant blaGES-18. Metagenome-assembled genomes revealed 78 % of resistant bacteria belonged to Pseudomonadota; 42 % co-harbored virulence factors. Phylogenetic analysis showed high inter-generic mobility of sul1/sul2, explaining their environmental persistence. Overall risk in rivers decreased by 44 % - 93 % compared to wastewaters. However, Acinetobacter carrying blaOXA and Cellvibrio sp002483145 carrying blaKHM-1 were phylogenetically close to Acinetobacter baumannii and Pseudomonas aeruginosa, indicating potential pathways toward key pathogens. Our study identifies wastewater as the main source of riverine ARGs, reveals conjugation as the primary transmission mechanism with transduction playing a secondary role, and demonstrates that high-risk ARGs can still spread to pathogenic bacteria in rivers. These findings are crucial for developing effective strategies to mitigate ARG risks.}, }
@article {pmid41259520, year = {2025}, author = {Usman, H and Molaei, M and House, SD and Haase, MF and Dennis, CL and Niepa, THR}, title = {Magnetically responsive nanocultures for direct microbial assessment in soil environments.}, journal = {Science advances}, volume = {11}, number = {47}, pages = {eady2654}, doi = {10.1126/sciadv.ady2654}, pmid = {41259520}, issn = {2375-2548}, mesh = {*Soil Microbiology ; *Soil/chemistry ; Bioreactors ; Magnetic Iron Oxide Nanoparticles/chemistry ; }, abstract = {Cultivating microorganisms in native-like conditions is vital for bioprospecting and accessing now unculturable species. However, there remains a gap in scalable tools that can both mimic native microenvironments and enable targeted recovery of microbes from complex settings. Such approaches are essential to advance our understanding of microbial ecology, predict community functions, and discover previously unidentified biotherapeutics. We present magnetic nanocultures-a high-throughput microsystem for isolating and growing environmental microbes under near-native conditions. These nanoliter-scale bioreactors are encapsulated in semipermeable membranes that form magnetic polymeric microcapsules using iron oxide nanoparticles within polydimethylsiloxane-based shells. This design offers mechanical stability and magnetic actuation, enabling efficient retrieval from soil-like environments. The nanocultures are optimized for optical and biological properties to support microbial encapsulation, growth, and sorting. Our study demonstrates the feasibility of using magnetically responsive microenvironments to cultivate elusive microbes, offering a promising platform for bioprospecting previously uncultured or unknown microbial species.}, }
@article {pmid41258716, year = {2025}, author = {Marsh, CC and Nel Van Zyl, K and Babalola, OO and Böhmer, R and Cowan, DA and Moganedi, KLM and Moroenyane, I and Naidoo, J and Nieves Delgado, A and Posma, JM and Segal, LN and Setati, ME}, title = {From description to implementation: key takeaways from the 3rd African Microbiome Symposium.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0068325}, doi = {10.1128/msphere.00683-25}, pmid = {41258716}, issn = {2379-5042}, abstract = {The 3rd African Microbiome Symposium was held in Cape Town, South Africa, from 20 to 22 November 2024. The symposium featured a diverse range of local and international microbiome research and provided a platform for 79 researchers, students, and industry members to engage in discussions on the microbiome within an African context and focusing on translational research. This meeting review shares highlights, findings, and recommendations derived from the event. Insights from two panel discussions revealed key barriers to microbiome research in Africa, including limited funding, infrastructure gaps, and a shortage of trained local scientists. Recommendations centered on increased investment, institutional training, adherence to ethical guidelines, and the fostering of equitable global partnerships.}, }
@article {pmid41258518, year = {2025}, author = {Cong, D and Liu, J and Yu, S and Wu, P and Qin, M}, title = {Assessment of Anthropogenic Impacts on Water Quality and Microbial Communities in the Heilongjiang Maolan Gou National Nature Reserve.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02645-7}, pmid = {41258518}, issn = {1432-184X}, abstract = {Freshwater ecosystems within protected areas play a vital role in maintaining biodiversity and ecological stability, yet they are increasingly threatened by anthropogenic disturbances such as agriculture and tourism. Understanding the impacts of human activities on water quality and microbial community dynamics is essential for the effective conservation and management. This study investigates the spatial variability of water quality and microbial communities across the core, buffer, and experimental zones of the Heilongjiang Maolan Gou National Nature Reserve. Twelve water samples were collected and analyzed for key physicochemical parameters (turbidity, electrical conductivity (EC), chemical oxygen demand (COD), biochemical oxygen demand (BOD), NH4[+], PO4[3-] and heavy metals). The core zone exhibited excellent water quality with low turbidity (0.4-0.5 NTU), EC (45-130 µS/cm), COD (8-10 mg/L), BOD (1.5-2.2 mg/L). In contrast, the experimental zone showed significant contamination due to agriculture and tourism, with high COD (up to 35 mg/L), BOD (up to 6.5 mg/L), NH4[+] (0.18-0.35 mg/L), and PO4[3-] (0.008-0.035 mg/L). Heavy metal concentrations, particularly Cd (up to 0.24 µg/L), were elevated in the experimental zone, correlating with higher Pollution and Water Quality Indices (HPI up to 96.4, WQI up to 61.28). According to standard classifications, HPI values > 100 indicated heavy pollution and WQI scores between 50 and 100 denoted moderate to poor water quality, highlighting degraded conditions in the experimental zone. Microbial analysis revealed distinct community structures across zones, with enhanced pollutant-degrading taxa such as Pseudomonas (noted for aromatic hydrocarbon degradation) and members of Bacteroidota (associated with organic matter breakdown) in the experimental zone. These findings highlight the need for sustainable management to mitigate human impacts and preserve ecological health within the reserve.}, }
@article {pmid41258495, year = {2025}, author = {Gutiérrez-Sarmiento, W and Fosado-Mendoza, M and Lozano-Flores, C and Varela-Echavarría, A}, title = {The Body Wall Microbiome of the Terrestrial Slug Deroceras laeve Reveals Potential Endosymbionts and Shares Core Organisms with Other Mollusks.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02652-8}, pmid = {41258495}, issn = {1432-184X}, support = {CBF2023-2024-834//SECIHTI/ ; IN211322//DGAPA-UNAM PAPIIT/ ; }, abstract = {The marsh slug Deroceras laeve is an invasive mollusk found in gardens, field crops, and wetlands. It lacks a protective shell, suggesting that microbial communities are associated with its adaptability to the environment. Here, we used a whole shotgun metagenomic approach to analyse the complex microbiome of D. laeve and compared it to that of other mollusks. This demonstrated the presence in D. laeve of bacteriophages such as Erwinia phage, Certrevirus, and Machinavirus, which target plant pathogen bacteria. In the Archaea domain the halophilics Halovivax and Halobaculum predominated, but also present were the methanogens Methanobacterium, Methanobrevibacter, Methanocaldococcus, Methanococcus, and Methanosarcina, involved in phosphate solubilization and methanogenesis during decomposition of organic matter. The Bacteria domain was dominated by γ-Pseudomonadota such as Buttiauxella, Citrobacter, Enterobacter, Klebsiella, Kluyvera, Leclercia, and Pseudomonas which are producers of enzymes that degrade biomass and complex carbohydrates. Regarding the fungal community, filamentous or yeast ascomycetes predominated such as Debaryomyces, Puccina, and Pyricularia known as plant pathogens or associated with decaying organic matter. Consistent with these findings, functional analysis revealed enrichment in genes involved in fermentation and carbohydrate metabolism. Remarkably, regardless of species, ecosystem, and tissue type, we found that the core microbiome of the mollusks in this study is mainly structured by the Phyla Uroviricota, Euryarchaeaota, Pseudomonadota, and Ascomycota, with diversity at the genus level. This suggests ancient symbiotic interactions of these mollusks with specific types of microbes which may have been critical for adaptability to their environment.}, }
@article {pmid41258437, year = {2025}, author = {Romaní, AM and Núria, P and Marta, P and Giulia, G}, title = {Drought Drives Extracellular Polymeric Substances Accumulation and Functional Shifts in Streambed Biofilm Communities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02649-3}, pmid = {41258437}, issn = {1432-184X}, abstract = {This study investigates the adaptive response of streambed microbial biofilms to water scarcity, focusing on the role of extracellular polymeric substances (EPS) production across a gradient of hydrological conditions. Sediment samples from 37 streams in the north-eastern Iberian Peninsula, encompassing both permanent and intermittent flow regimes, were analysed for EPS-polysaccharide content, microbial biomass, chlorophyll-a, and biofilm function (carbon substrate utilization profiles). Drought conditions were characterized based on the number of dry days over the eight months preceding sampling. Results revealed that EPS production increased significantly in intermittent streams, particularly under long-term drought, reaffirming that EPS synthesis is a key microbial strategy to mitigate desiccation stress. Notably, when normalized to prokaryotic density, EPS content exhibited a significant positive correlation with drought duration, emphasizing the dominant role of heterotrophic bacteria over algae in EPS secretion. However, EPS content alone was not a universal indicator of water scarcity, which showed a large variability in permanently flowing streams. Functional profiling showed clear shifts in carbon substrate utilization associated with stream hydrology. Intermittent streams exhibited a broader metabolic range, and particularly a capacity to use phenolic compounds, suggesting an adaptation to terrestrial organic matter inputs. Contrary to expectations, functional diversity increased in drier conditions, challenging assumptions derived from controlled experiments and underscoring the resilience of Mediterranean microbial biofilm communities to drought. These findings provide empirical support for EPS-mediated drought adaptation in natural biofilms and highlight functional diversity as a potential mechanism maintaining ecosystem processes under increasing aridity due to climate change.}, }
@article {pmid41258129, year = {2025}, author = {Cabrerizo, MJ and González-Olalla, JM and Medina-Sánchez, JM and Vila-Duplá, M and Carrillo, P}, title = {Warming Fluctuations Strengthen the Photo-Phagotrophic Coupling in Mixoplanktonic Protists.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02658-2}, pmid = {41258129}, issn = {1432-184X}, support = {PID2022-136280NA-I00//MICIN/AEI/10.13039/501100011033 and the European Regional Development Fund/ ; RYC2023-042504-I//MICIU/AEI/10.13039/501100011033 and the European Social Fund plus (ESF+)/ ; DGP-POST-2024-00283//Junta de Andaluc&#xed;a/ ; TED2021-131262B-I00//MCIN/AEI/10.13039/501100011033 and by the European Union NextGeneration EU/PRTR/ ; FPU19/05924//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-118872RB-I00//MICIN/AEI/10.13039/501100011033 and the European Regional Development Fund (ERDF)/ ; }, abstract = {Mixoplankton, a major trophic group in aquatic ecosystems, are being affected by global warming. However, most studies on temperature effects use constant mean conditions, overlooking how short-term thermal fluctuations could deviate from climate projections and impact this group. We experimentally quantified how increasing amplitudes of warming fluctuation (± 1, 3, and 5 °C) alter carbon-specific electron transport (ETR[c]), net photosynthesis (P[c]), respiration (R[c]), phagotrophy (Ph[c]), carbon use efficiency (CUE), and growth (µ) in four protist species (three mixoplanktonic and one strict phototroph). We observed a consistent positive link between photosynthetic efficiency (P[c]:ETR[c] ratio) and Ph[c], and a shift towards a strengthening of the Ph[c] (P[c]:ETR[c] / Ph[c] ratio) with greater thermal fluctuation. A potential explanation is a selective behavior aimed to increase phagotrophy to obtain inorganic nutrients through ingested prey internal re-cycling rather than relying on the environment, to support an enhanced photosynthetic efficiency and growth. An enhanced, coupled photo-phagotrophy activity could boost mixoplankton competitiveness compared to phytoplankton. Our findings underscore the need to incorporate trophic flexibility and its interaction with environmental variability into trait-based models to better predict community dynamics, biogeochemical cycling, and food web structure in aquatic ecosystems.}, }
@article {pmid41254852, year = {2025}, author = {Alster, CJ and Schipper, LA and Bååth, E}, title = {Thermal Adaptation of Bacterial and Fungal Growth in a Geothermally Influenced Soil Transect.}, journal = {Global change biology}, volume = {31}, number = {11}, pages = {e70605}, doi = {10.1111/gcb.70605}, pmid = {41254852}, issn = {1365-2486}, support = {MFP-UOW1904//Marsden Fund/ ; }, mesh = {*Soil Microbiology ; New Zealand ; *Fungi/growth &amp; development ; *Bacteria/growth &amp; development ; Temperature ; *Soil/chemistry ; }, abstract = {Numerous studies have investigated microbial adaptation to increasing soil temperature, but limitations in experimental design hinder comprehensive understanding. These include short-term laboratory studies with constant environmental conditions and field studies with few distinct temperature treatments. Here, we utilized a long-term natural soil geothermal gradient in Aotearoa, New Zealand, ranging in mean annual soil temperature (MAT) from 17°C to 42°C to explore thermal adaptation of microbial growth rates. We collected soil from 28 locations along the gradient and measured bacterial growth rate (via leucine incorporation) at eight temperatures (4°C-45°C) and fungal growth rate (via Ac-in-ergosterol) at two temperatures (16°C and 39°C). We then fit Macromolecular Rate Theory and the Ratkowsky equation to estimate the temperature minimum (T min $$ {T}_{min} $$), optimum (T opt $$ {T}_{opt} $$), and inflection point (T inf $$ {T}_{inf} $$) for bacterial growth, and a temperature sensitivity index to compare relative fungal and bacterial growth rates. We found predictable changes in thermal adaptation of bacterial growth along the geothermal gradient with temperature response curves shifting 0.22°C-0.27°C per 1°C increase in MAT regardless of the temperature metric (i.e., T min $$ {T}_{min} $$ , T opt $$ {T}_{opt} $$ , and T inf $$ {T}_{inf} $$) used. Thermal adaptation of bacterial and fungal growth increased roughly in parallel. We also compared the bacterial growth results to published temperature response data of microbial respiration (with added glucose) from this geothermal gradient. Rates of thermal adaptation for bacterial growth and microbial respiration were similar, suggesting synchronicity across microbial processes. The less than 1°C change in all measured temperatures metrics per degree increase in MAT resulted in microbial growth and activity closer to in situ temperatures at high soil temperatures and lower than in situ temperatures under non-elevated soil temperatures. Overall, our results highlight the use of geothermal gradients and appropriate temperature models in studying thermal adaptation of soil microbial processes; the predictability of results also underscores potential for incorporating microbial thermal adaptation into soil carbon modeling efforts.}, }
@article {pmid41254344, year = {2025}, author = {Distante, A and Garino, D and Cerrato, C and Perez-Ardavin, J and Flores, FQ and Lopetuso, L and Mir, MC}, title = {The role of the human microbiome in prostate cancer: a systematic review from diagnosis to treatment.}, journal = {Prostate cancer and prostatic diseases}, volume = {}, number = {}, pages = {}, pmid = {41254344}, issn = {1476-5608}, abstract = {BACKGROUND: Prostate cancer (PC) heterogeneity and treatment resistance remain major clinical challenges, with emerging evidence implicating the microbiome as a key modulator of disease pathogenesis. While microbial dysbiosis has been linked to PC diagnosis, progression, and therapeutic outcomes, the mechanisms underlying these associations are poorly understood. This review synthesizes current evidence on the diagnostic, prognostic, and therapeutic potential of the microbiome in PC.<br><br>METHODS: A systematic search of PubMed, Embase, and Cochrane Central Register of Controlled Trials (through April 2024) was conducted following PRISMA guidelines (PROSPERO: CRD42024534899). Controlled and observational studies investigating microbial roles in PC diagnosis (e.g., ISUP grading group), prognosis, or treatment response were included. Data extraction and quality assessment used the QUIPS tool. From 810 screened records, 42 studies met inclusion criteria.<br><br>RESULTS: Distinct microbial profiles differentiated PC from controls, with Mycoplasma genitalium and Staphylococcus spp. enriched in prostate tumors (3.1- and 2.7-fold, respectively) and correlated with inflammation (IL-6: r&#x2009;=&#x2009;0.38, p&#x2009;=&#x2009;0.002). Urinary microbiota showed diagnostic potential (sensitivity: 58-82%), though sampling methods influenced variability. Prognostically, Betaproteobacteria gut enrichment predicted earlier castration-resistant progression (5.2 months; HR 1.8, 95% CI 1.3-2.5), while ADT-induced dysbiosis (e.g., Klebsiella overgrowth) accelerated resistance (2.1-fold risk). Therapies altered microbial ecology: radiotherapy depleted Bacteroides (linked to proctitis; OR 3.1), and immunotherapy responders harbored higher Akkermansia muciniphila. Microbial androgen synthesis and endotoxin production emerged as resistance mechanisms.<br><br>CONCLUSIONS: The microbiome influences PC detection, aggressiveness, and treatment efficacy through direct (tissue-resident) and indirect (gut-derived) mechanisms. Standardized profiling and microbiome-modulating strategies (e.g., probiotics during ADT) may personalize management. Prospective trials are needed to validate causality and translate microbial biomarkers into clinical practice.}, }
@article {pmid41252854, year = {2025}, author = {Chen, X and Huang, Y and Zhu, X and Gan, C and An, W and Liu, Y and Zhou, S and Xu, M}, title = {Global biogeographic patterns and assembly processes of landfill leachate microbiomes.}, journal = {Water research}, volume = {289}, number = {Pt B}, pages = {124922}, doi = {10.1016/j.watres.2025.124922}, pmid = {41252854}, issn = {1879-2448}, abstract = {Approximately 95 % of municipal solid waste is disposed of in landfill globally, generating leachate that is known as a complex mixture of biodegradable and persistent toxic compounds. Microbes are main forces for tackling the toxic leachate but the patterns of microbial assembly in such treatments are largely unknown, limiting the proper optimization of leachate treatment efficiency. This study, for the first time, presents a global-scale analysis involving 151 landfill leachate treatment samples for uncovering mechanisms of microbial assembly from an ecological perspective. The information of microbiome from 97 treatments in Asia, 41 treatments in Europe, and 13 treatments in North America were collected. The results revealed pronounced biogeographic divergence, with Asian samples (particularly those from India) exhibiting lower microbial diversity and richness compared to Europe and North America counterparts. Geographical-climatic and socio-economic factors significantly influenced microbial composition, with elevation and per capita GDP being primary drivers. Further, the community assembly was predominantly governed by deterministic processes. Co-occurrence network analyses demonstrated distinct microbial interaction patterns across continents, with Asian networks being more vulnerable to collapse under external disturbances. This study provides critical insights into the global microbial ecology of landfill leachate treatment, offering a foundation for developing targeted bioremediation strategies.}, }
@article {pmid41251823, year = {2025}, author = {Della Mónica, IF and Godeas, AM and Scervino, JM}, title = {Hyphosphere interactions: P-solubilizing fungi modulate AMF phosphatase activity and mycorrhizal symbiosis via exudate-mediated communication.}, journal = {Mycorrhiza}, volume = {35}, number = {6}, pages = {66}, pmid = {41251823}, issn = {1432-1890}, support = {UBACyT 20020220400300BA//Secretar&#xed;a de Ciencia y T&#xe9;cnica, Universidad de Buenos Aires/ ; PIBAA 28720210100694CO//Consejo Nacional de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas/ ; PICT 01283-2021//Agencia Nacional de Promoci&#xf3;n de la Investigaci&#xf3;n, el Desarrollo Tecnol&#xf3;gico y la Innovaci&#xf3;n/ ; PINI 04/B253//Fundaci&#xf3;n de la Universidad Nacional del Comahue para el Desarrollo Regional/ ; }, mesh = {*Mycorrhizae/physiology/enzymology ; *Symbiosis ; Plant Roots/microbiology ; *Phosphorus/metabolism ; Acid Phosphatase/metabolism ; *Phosphoric Monoester Hydrolases/metabolism ; Daucus carota/microbiology ; *Glomeromycota/physiology/enzymology ; *Phosphates/metabolism ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) form symbiotic associations with plant roots, enhancing water and nutrient absorption. Phosphate-solubilizing fungi (PSF) can solubilize and mineralize phosphorus, an essential nutrient with low bioavailability, and eventually interact with AMF. However, the understanding of how they interact in the hyphosphere, where root influence is absent, remains limited. Furthermore, the effect of PSF on the phosphatase activity of AMF, related to the P efficiency in acquisition and utilization, within the hyphosphere and mycorrhizosphere zones, remains unclear. Therefore, this study aimed to assess the effect of three different PSF (Talaromyces flavus, T. helicus, and T. diversus) exudates on extracellular acid phosphatases and alkaline phosphatases associated with intra- and extraradical AMF structures in the hyphosphere and mycorrhizosphere, in vitro. To achieve this aim, the AMF Rhizophagus intraradices was cultured with Ri T-DNA transformed carrot roots in a system using Petri dishes that mimicked the hyphosphere (with 2 sections: (a) with roots and AMF, and (b) with only AMF) and the mycorrhizosphere (with roots and AMF in the same place). Different concentrations of PSF exudates were placed in either the hyphosphere or the mycorrhizosphere, and at the end of the experiment (8 weeks), the phosphatase activity of the AMF was measured. This research highlights that the enzymatic activity of AMF is modulated by PSF exudates, depending on whether these exudates are present in the hyphosphere or the mycorrhizosphere. Exudates in the hyphosphere, where PSF are directly associated with AMF hyphae, have a more pronounced effect on AMF extraradical alkaline phosphatases than acid phosphatases, and promote symbiosis efficiency. In contrast, PSF exudates in the mycorrhizosphere had a neutral or negative effect on symbiosis efficiency, improving the extraradical alkaline phosphatases of AMF and the acid phosphatases of the roots. Also, the effect depends on the fungal identity. AMF act as mediators in this context, improving communication between the roots and the hyphosphere microbiome. When exploring the soil, the hyphae encounter compounds produced by microorganisms, thus establishing a complex network of interactions. These interactions enhance the symbiotic efficiency of AMF, modulating the host plant without direct contact. These results show that microbial interactions not only influence the efficiency of phosphorus transfer to plants but also have broader implications for soil health and fertility management.}, }
@article {pmid41251489, year = {2025}, author = {Ye, H and Šlipogor, V and Hanson, BT and Séneca, J and Hausmann, B and Herbold, CW and Pjevac, P and Bugnyar, T and Loy, A}, title = {Associations between gut microbiota and personality traits: insights from a captive common marmoset (Callithrix jacchus) colony.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0044325}, doi = {10.1128/spectrum.00443-25}, pmid = {41251489}, issn = {2165-0497}, abstract = {Recent studies have suggested associations between consistent inter-individual behavioral variation (i.e., animal personality) and gut microbiota. Non-human primates living under controlled conditions are valuable models to investigate diet-independent microbiome-host interactions. In this study, we investigated associations between specific gut microbiota members and personality traits, as well as group membership, sex, age class, breeding status, and relatedness of 26 captive common marmosets (Callithrix jacchus), maintained under the same diet and housing conditions. Personality was assessed using an established testing battery in repeated tests. Then, we collected a total of 225 fecal samples during the summers of 2017 and 2019 from five marmoset social groups for 16S rRNA gene amplicon sequencing. Within-individual microbiota variance was smaller than that between group members. Group members also exhibited more similar gut microbiota than individuals from different groups in each sampling year. Beta diversity of the gut microbiota was linked with personality traits, age class, sex, and breeding status, but not with genetic relatedness. We identified specific bacterial taxa associated with personality traits. In particular, members of the sulfite-reducing genus Desulfovibrio were enriched in more avoidant marmosets. Amplicon sequencing of the dissimilatory sulfite reductase gene dsrB confirmed this pattern, yet additionally revealed an unknown uncultured bacterium that was the predominant sulfite-reducing bacterium in the fecal samples and was linked to more explorative individuals. These findings highlight specific association patterns between identified microbial taxa and personality traits in captive common marmosets.IMPORTANCEThis study provides valuable insights into the intricate relationship between gut microbiota and host personality traits, using captive common marmosets as a model. By controlling for diet and housing conditions, it probes key host factors such as personality, age, sex, and social group membership, offering a robust framework for understanding microbiome-host interactions. The discovery of specific microbial taxa associated with personality traits, particularly the enrichment of sulfite-reducing genera in more avoidant individuals, underscores the potential of the gut microbiome to reflect or be associated with personality differences. These findings advance our understanding of microbiome-host dynamics and pave the way for future research on the mechanistic links between behavior and gut microbiota in other animal models and across broader ecological contexts.}, }
@article {pmid41251323, year = {2025}, author = {Ferreira, J and Lievens, B and Rediers, H}, title = {Development of a spore-based confrontation assay to screen for biocontrol organisms with antagonistic activity against oomycete and fungal pathogens.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxaf286}, pmid = {41251323}, issn = {1365-2672}, abstract = {AIMS: Screenings for biocontrol organisms against fungal and oomycete pathogens are typically performed on mycelium. While this allows for high-throughput screenings, it omits a major actor in pathogenicity, i.e. the spores. This study aims to improve the screening strategy using a spore-based confrontation assay (SBCA), as well as comparing its performance to the traditional mycelium-based confrontation assay (MBCA) and microscopy analyses of spore germination.<br><br>METHODS AND RESULTS: The SBCA was used to screen for 38 candidate biocontrol bacteria against two relevant broad-spectrum phytopathogens, Botrytis cinerea and Phytophthora cactorum. The performance of the SBCA was benchmarked to the traditional mycelium-based confrontation assay and microscopy observations for spore germination inhibition. The SBCA demonstrated a higher hit rate and reproducibility than its counterparts. The bacteria tested exhibited diverse traits in vitro such as production of lytic enzymes, biosurfactant, bioactive volatile organic compounds, and cell-free extracts. These characteristics suggest potential biocontrol modes of action, such as antibiosis (via diffusible metabolites and enzymes) or competition for nutrients and space. For two Pseudomonas strains, the biocontrol activity against P. cactorum was confirmed in planta in a detached leaf assay.<br><br>CONCLUSIONS: This study showcases a versatile and robust spore-based screening that outperforms conventional screening methods. Through the use of the SBCA, two promising biocontrol strains with antagonistic activity against P. cactorum in strawberry were identified.}, }
@article {pmid41250675, year = {2025}, author = {Gao, Y and Bai, J and Zhou, F and He, Y and Wang, Y and Huang, X}, title = {ICCTax: a hierarchical taxonomic classifier for metagenomic sequences on a large language model.}, journal = {Bioinformatics advances}, volume = {5}, number = {1}, pages = {vbaf257}, pmid = {41250675}, issn = {2635-0041}, abstract = {MOTIVATION: Metagenomic data increasingly reflect the coexistence of species from Archaea, Bacteria, Eukaryotes, and Viruses in complex environments. Taxonomic classification across the four superkingdoms is essential for understanding microbial communities, exploring genomic evolutionary relationships, and identifying novel species. This task is inherently imbalanced, uneven, and hierarchical. Genomic sequences provide crucial information for taxonomy classification, but many existing methods relying on sequence similarity to reference genomes often leave sequences misclassified due to incomplete or absent reference databases. Large language models offer a novel approach to extract intrinsic characteristics from sequences.<br><br>RESULTS: We present ICCTax, a classifier integrating the large language model HyenaDNA with complementary-view-based hierarchical metric learning and hierarchical-level compactness loss to identify taxonomic genomic sequences. ICCTax accurately classifies sequences to 155 genera and 43 phyla across the four superkingdoms, including unseen taxa. Across three datasets built with different strategies, ICCTax outperforms baseline methods, particularly on Out-of-Distribution data. On Simulated Marine Metagenomic Communities datasets from three oceanic sites, DairyDB-16S rRNA, Tara Oceans, and wastewater metagenomic datasets, it demonstrates strong performance, showcasing real-world applicability. ICCTax can further support identification of novel species and functional genes across diverse environments, enhancing understanding of microbial ecology.<br><br>Code is available at https://github.com/Ying-Lab/ICCTax.}, }
@article {pmid41249638, year = {2025}, author = {Tinning, Z and Kaestli, M and Nowland, SJ and Siboni, N and Seymour, JR and Gibb, KS and Padovan, AC}, title = {Dynamics of Bacterial and Vibrio Communities in Blacklip Rock Oysters in the Seasonal Tropics.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {125}, pmid = {41249638}, issn = {1432-184X}, support = {2020-043//Fisheries Research and Development Corporation/ ; Discovery Project DP240100370//Australian Research Council/ ; }, mesh = {Animals ; *Vibrio/isolation &amp; purification/genetics/classification ; *Ostreidae/microbiology ; Seasons ; Aquaculture ; Seawater/microbiology ; *Microbiota ; Australia ; Tropical Climate ; Shellfish/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Humans ; }, abstract = {Cultivation of the tropical Blacklip Rock Oyster (BRO) (Saccostrea spathulata) is an emerging Indigenous-led aquaculture industry in the seasonal tropics of northern Australia. However, little is currently known about the potential for pathogen outbreaks in this species. We conducted a year-long study to establish a microbial baseline to identify potential oyster and human health risks to inform future food safety decision making in this nascent industry. In healthy oysters, we identified both the core microbiome of this oyster species and the presence of potential oyster and human pathogens. The core bacteriome comprised nine bacterial families, while the core vibriome comprised the animal pathogens Vibrio harveyi and V. owensii. The potential human pathogen V. parahaemolyticus was detected in some oysters during the wet season, during periods of increased rainfall, turbidity and total nitrogen. The bacteriome and vibriome of oysters were significantly different to the adjacent seawater and therefore we concluded that seawater is not an appropriate surrogate for pathogen risk surveillance in this developing industry. These results provide new knowledge on the microbiology of a previously understudied oyster species and will inform monitoring methods, harvesting and shellfish quality compliance in this emerging Indigenous-led industry.}, }
@article {pmid41249586, year = {2025}, author = {Zhou, S and Bi, J and Zhou, S and Luo, L and Yan, X and Zou, J and Ji, Y and Zhao, S and Qiu, J and Liu, Z and Jiang, J and Wang, B and Liu, X}, title = {Community Assembly Mechanisms Underlying Divergent Responses of Indica and Japonica Rice Rhizosphere Microbiota to Drought Stress.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {126}, pmid = {41249586}, issn = {1432-184X}, support = {2022YFD2300302//National Key Research and Development Program of China/ ; 42277304//National Natural Science Foundation of China/ ; 42407399//National Natural Science Foundation of China/ ; XUEKEN2022003//Fundamental Research Funds for the Central Universities/ ; BX20240168//National Postdoctoral Program for Innovative Talents/ ; BK20241558//Natural Science Foundation of Jiangsu Province/ ; 2024ZB624//Jiangsu Funding Program for Excellent Postdoctoral Talent/ ; }, mesh = {*Oryza/microbiology/growth &amp; development/physiology/genetics/classification ; *Rhizosphere ; *Droughts ; *Microbiota ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Stress, Physiological ; Agricultural Irrigation ; }, abstract = {Drought stress markedly reduces rice yield, with notable genotypic variation in drought tolerance. While the rhizosphere microbiome is regarded as the second genome of plants, how the indica and japonica rice rhizosphere microbial communities respond to deficit irrigation and their relationship with yield remain to be elucidated. Here, we conducted field experiments using 12 indica and 12 japonica rice varieties under full and deficit irrigation regimes. Yield-related traits, including filled grain number, seed setting rate, two-plant yield, and thousand grain weight, were measured, and the rhizosphere microbial communities were characterized by 16S rRNA gene sequencing. In line with previous studies, japonica varieties showed superior drought resistance in terms of yield performance. Both rice genotype and irrigation regime significantly influenced the composition and functional potential of the rhizosphere microbiome. Compared to indica rice, the japonica rice rhizosphere was enriched with more beneficial microorganisms. Enrichment of nitrogen‑metabolism‑related groups, such as Microvirga and Nitrososphaeraceae, may contribute to rhizosphere nitrogen cycling and support nitrogen availability for the rice. Similarly, higher abundance of Streptomyces in japonica varieties under drought conditions may be associated with improved drought tolerance. These microbial genera were closely associated with rice yield. Moreover, the japonica rhizosphere microbiome was less disturbed by water limitation, showing higher stability. Overall, the rhizosphere microbiome of japonica rice exhibited functional optimization under drought stress by promoting the enrichment of beneficial and nitrogen-cycling microbes, thereby enhancing drought resistance and yield stability. This study demonstrated a significant correlation between rhizosphere microbial communities and rice yield, providing fundamental insights that may contribute to future strategies for optimizing crop productivity through microbiome management in sustainable agriculture.}, }
@article {pmid41248576, year = {2025}, author = {Zhou, Y and Chang, L and Sun, H and Li, W and Ao, T and Lin, J}, title = {Evaluation of reclaimed treated wastewater on soil quality, microbial community and function in urban greening irrigation.}, journal = {Journal of environmental management}, volume = {395}, number = {}, pages = {127958}, doi = {10.1016/j.jenvman.2025.127958}, pmid = {41248576}, issn = {1095-8630}, abstract = {Reclaimed treated wastewater (TWW) offers a sustainable irrigation alternative for urban greening amid freshwater scarcity. However, its impact on soil quality and microbial ecology in urban landscapes remains underexplored. This study assessed the effects of three TWW types and one TWW-purified water mixture on soil properties, heavy metal accumulation, enzyme activity and microbial community dynamics in Common Nandina (Nandina domestica Thunb.) systems over three- and five-month in Nanjing, China, using a metagenomic approach. The results showed that TWW irrigation significantly increased soil nitrogen, phosphorus content and pH (P < 0.05), with stronger effects observed at three-month (P < 0.05). Soil heavy metal content varied, with Cr and As exhibiting potential accumulation. Enzyme activity (N-acetyl-glucosaminidase and phosphatase) was positively influenced by TWW irrigation at three-month. Metagenomic analysis revealed significant shifts in microbial community composition, particularly fungi, with Mucoromycota increasing and Ascomycota decreasing under TWW. The Normalized Stochasticity Ratio indicated increased stochasticity in microbial assembly under TWW irrigation (P < 0.05). Functionally, TWW increased abundance of functional genes related to amino acid metabolism and peroxisomes (P < 0.05), but decreased degradation genes for aromatic compounds. TWW also increased the abundance of antibiotic resistance genes (ARGs), particularly those related to triclosan and glycopeptide, and plant pathogenic genera like Aspergillus and Fusarium. The findings suggest that while TWW irrigation improves certain soil properties and microbial functions in the short term, it may pose ecological risks from heavy metal and microbial contamination, offering key insights for sustainable urban irrigation strategies.}, }
@article {pmid41247962, year = {2025}, author = {Wei, D and Hu, S and Tang, T and Yang, Y and Meng, F and Peng, Y}, title = {Confinement Reduces Surface Accumulation of Swimming Bacteria.}, journal = {Physical review letters}, volume = {135}, number = {18}, pages = {188401}, doi = {10.1103/dvc8-tlh1}, pmid = {41247962}, issn = {1079-7114}, mesh = {*Models, Biological ; Hydrodynamics ; *Bacterial Physiological Phenomena ; Movement ; *Escherichia coli/physiology ; }, abstract = {Many swimming bacteria naturally inhabit confined environments, yet how confinement influences their swimming behaviors remains unclear. Here, we combine experiments, continuum modeling, and particle-based simulations to investigate near-surface bacterial swimming in dilute suspensions under varying confinement. Confinement reduces near-surface accumulation and facilitates bacterial escape. These effects are quantitatively captured by models incorporating the force quadrupole, a higher-order hydrodynamic singularity, that generates a rotational flow reorienting bacteria away from surfaces. Under strong confinement, bacterial trajectories straighten due to the balancing torques exerted by opposing surfaces. These findings highlight the role of hydrodynamic quadrupole interactions in near-surface bacterial motility, with implications for microbial ecology, infection control, and industrial applications.}, }
@article {pmid41247508, year = {2025}, author = {Wenten, IG}, title = {Rethinking Biofilm Engineering and Fouling Resistance in Membrane Bioreactors.}, journal = {Langmuir : the ACS journal of surfaces and colloids}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.langmuir.5c03864}, pmid = {41247508}, issn = {1520-5827}, abstract = {Membrane bioreactors (MBRs) are increasingly recognized as a key technology in sustainable wastewater treatment, offering a high effluent quality through the integration of biological degradation and membrane filtration. Among the critical factors influencing their performance are biofilm dynamics and membrane fouling. This article critically examines recent advances in biofilm engineering and antifouling strategies for MBRs, with an emphasis on microbial community modulation, quorum quenching, and hydrodynamic control to improve biofilm stability. In parallel, the review examines material-based and biological methods to mitigate membrane fouling, emphasizing multifunctional surfaces and emerging biocontrol strategies. Key operational challenges, such as energy consumption, cleaning frequency, and membrane aging, are evaluated alongside future research directions in materials design, microbial ecology, and real-time system optimization. The integration of these innovations is essential for advancing MBR technologies that are robust, resource-efficient, and aligned with circular economy principles.}, }
@article {pmid41247324, year = {2025}, author = {Weagley, JS and Cárdenas, LAC and Romani, A and Sullender, ME and Aggarwal, S and Makimaa, H and Hogarty, MP and Rodgers, R and Kennedy, EA and Foster, L and Schriefer, LA and Baldridge, MT}, title = {Differential Microbial Community Assembly Following Co-housing versus Microbiota Transplant.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf256}, pmid = {41247324}, issn = {1751-7370}, abstract = {Mouse models are vital tools for discerning the relative contributions of host and microbial genetics to disease, often requiring the transfer of microbiota between different mouse strains. Transfer methods include antibiotic treatment of recipients and colonization using either co-housing with donors or the transplantation of faecal or caecal donor material. However, the efficiency and dynamics of these methods in reconstituting recipients with donor microbes is not well understood. We thus directly compared co-housing, faecal transplantation, and caecal transplantation methods. Donor mice from Taconic Biosciences, possessing distinct microbial communities, served as the microbial source for recipient mice from Jackson Laboratories, which were treated with antibiotics to disrupt their native microbiota. We monitored bacterial and viral populations longitudinally over the course of antibiotics treatment and reconstitution using 16S rRNA gene sequencing, quantitative PCR, and shotgun sequencing of viral-like particles. As expected, antibiotic treatment rapidly depleted microbial biomass and diversity, with slow and incomplete natural recovery of the microbiota in non-transfer-recipient control mice. Although all transfer methods reconstituted recipient mice with donor microbiota, co-housing achieved this more rapidly for both bacterial and viral communities. Overall, faecal and caecal transplant resulted in highly similar colonization processes with some minor variation in enrichment for two specific bacterial families. This study provides valuable insights into microbial ecology, as well as the dynamics underlying experimental microbial transfer methods, enhancing reproducibility and informing best practices for microbiota transfer in mouse models.}, }
@article {pmid41247030, year = {2025}, author = {Van Beek, JM and Robles, G and Mewalal, R and Blaby, I and Hatzenpichler, R}, title = {A collection of archaeal 16S rRNA Clone-FISH cultures for probe validation in fluorescence in situ hybridization experiments.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0113125}, doi = {10.1128/mra.01131-25}, pmid = {41247030}, issn = {2576-098X}, abstract = {We present a collection of 30 Escherichia coli cultures (Clone-FISH cultures), each carrying a plasmid for the heterologous expression of a (near) full-length 16S rRNA gene from 1 of 30 lineages of archaea, including 17 yet uncultured ones. We make these clones available for use as controls in fluorescence in situ hybridization experiments.}, }
@article {pmid41247018, year = {2025}, author = {Xiong, M and Kuang, W and Liu, Z and Tong, R and Deng, X and Wang, N and Wan, X and Feng, M and Luo, Y and Zhang, B and Zhang, Z and Zheng, F}, title = {Quercetin alleviates ulcerative colitis via regulating gut microbiota and tryptophan metabolism.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0070325}, doi = {10.1128/msystems.00703-25}, pmid = {41247018}, issn = {2379-5077}, abstract = {UNLABELLED: Quercetin, a natural flavonoid in traditional Chinese medicinal plants, has shown promise in alleviating ulcerative colitis symptoms despite uncertainties about its exact mode of action. This study explored how quercetin influences tryptophan breakdown and gut bacterial populations in mice with chemically induced colitis. The treatment demonstrated measurable improvements-normalizing body weight, reducing spleen enlargement, lowering clinical severity scores, preserving colon structure, and healing tissue damage. Through advanced microbiome profiling and metabolic analysis, researchers observed increased populations of helpful gut microbes alongside higher concentrations of tryptophan byproducts. These biochemical shifts stimulated the aryl hydrocarbon receptor system, which plays a key role in restoring gut lining integrity. The collective evidence points to quercetin's therapeutic potential through its dual action on microbial ecology and tryptophan-derived signaling pathways.<br><br>IMPORTANCE: Ulcerative colitis is a chronic inflammatory disease with limited effective therapeutic options. In this study, quercetin-a flavonoid commonly found in traditional Chinese medicinal herbs-was shown to relieve colitis symptoms by reshaping gut microbiota and restoring tryptophan metabolism. Notably, the increase in indolelactic acid, a key microbial metabolite, led to activation of the aryl hydrocarbon receptor, which supports intestinal barrier integrity and dampens inflammation. These findings reveal a gut microbiota-derived metabolite-host signaling axis as a central mechanism of action, highlighting the potential of quercetin as a microbiota-targeted therapeutic approach for UC.}, }
@article {pmid41246320, year = {2025}, author = {Dey, P}, title = {Genes, guts, and microbes: decoding host-driven microbial regulation using intestine-specific conditional knockouts.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1674913}, doi = {10.3389/fimmu.2025.1674913}, pmid = {41246320}, issn = {1664-3224}, mesh = {Animals ; *Gastrointestinal Microbiome/immunology/genetics ; Humans ; Dysbiosis ; Mice, Knockout ; *Intestines/microbiology/immunology ; *Intestinal Mucosa/metabolism/microbiology/immunology ; *Host Microbial Interactions/genetics ; Mice ; }, abstract = {This narrative review underscores the influence of host genetics in actively regulating gut microbiota composition and function, highlighting the distinctive advantages of intestine-specific conditional knockout (cKO) models in gut microbiome research. In contrast to whole-body knockouts or germ-free animals, these precision models, enabled by Cre-loxP technology, eliminate confounding systemic effects to elucidate how localized host genes within intestinal cells regulate the gut microbial ecology. The review identifies three fundamental host-driven regulatory mechanisms through the analysis of specific gene deletions: (1) barrier integrity (e.g., mucus and junction proteins), (2) immune defenses (e.g., antimicrobial peptides and glycan synthesis), and (3) metabolic signaling (e.g., bile acid receptors and glucose transporter). These pathways jointly impose microbial symbiosis, and their disruption leads to dysbiosis characterized by increased abundance of pathobionts (e.g., Escherichia, Proteobacteria), directly connecting host genetics to inflammatory and metabolic disorders. This host-centric viewpoint emphasizes the gut as an active regulator, rather than a passive microenvironment for the microbiota, providing significant insights for creating tailored therapeutics that focus on host pathways to restore microbial balance in disorders such as inflammatory bowel diseases.}, }
@article {pmid41246283, year = {2025}, author = {Phoo, MTP and Dechathai, T and Singkhamanan, K and Chusri, S and Pomwised, R and Wonglapsuwan, M and Morikawa, K and Surachat, K}, title = {Pseudomonas aeruginosa affects Acinetobacter baumannii's growth, gene expression and antibiotic resistance in in vitro co-culture system.}, journal = {Current research in microbial sciences}, volume = {9}, number = {}, pages = {100499}, doi = {10.1016/j.crmicr.2025.100499}, pmid = {41246283}, issn = {2666-5174}, abstract = {Pseudomonas aeruginosa and Acinetobacter baumannii are opportunistic pathogens co-isolated frequently in the same infection sites. In this study, we aimed to elucidate the interaction between P. aeruginosa and A. baumannii in in vitro co-culture system. Growth analysis showed that P. aeruginosa PA01 unilaterally exerts a negative effect on the growth of A. baumannii SK005. A. baumannii alone exhibited an altered transcriptome pattern, especially in the genes for metabolic pathways. Strong upregulation of genes in iron acquisition systems (acinetobactin, baumannoferrin, 2,3-dihydroxybenzoic acid synthesis cluster, and Feo iron transport system) and downregulation of iron-storage genes (bacterioferritin) were the most prominent changes. In terms of antibiotic resistance, we observed the downregulation of the fosfomycin resistance gene fosB. Strikingly, the phenotypic analysis demonstrated that A. baumannii in co-culture is more vulnerable to fosfomycin than in monoculture conditions, while it is more resistant to cefoxitin and imipenem. This study broadens our understanding of microbial ecology in co-infection settings by highlighting the fact that mixed pathogens do not always undergo interaction to a mutually equivalent extent.}, }
@article {pmid41244671, year = {2025}, author = {Zhang, Z and Jia, L and Liu, B and Liu, Y and Zhao, J and Wang, Y and Zhang, M and Qiao, W and Yang, B and Luo, L and Chen, L}, title = {Maternal gut microbiota and placenta-derived tissues microbes are important for initial gut microbial colonization in infants.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1631590}, doi = {10.3389/fmicb.2025.1631590}, pmid = {41244671}, issn = {1664-302X}, abstract = {BACKGROUND: Early infant gut microbiota colonization, influenced by various factors, significantly affects future growth and development. However, results related to how the initial microbial ecology is established in the infant gut remain inconsistent.<br><br>RESULTS: In this study, we collected maternal and infant feces, vaginal secretions, placental tissues, breast milk, amniotic membrane tissues, umbilical cord blood, and breast skin for homology comparisons and for exploring the main sources of infant intestinal microbiota. Our results revealed that early infant gut microbiota originated mainly from the vertical transmission of maternal microbiota, and that vaginal microbiota did not affect infant gut microbiota colonization. Microbiota was detected in the placenta, supporting the idea that the uterus is not sterile. Moreover, we verified microbial composition-related similarities in the amniotic tissues and umbilical cord blood, further validating our hypothesis that gut microbiota in the early stages of infancy are mainly vertically transmitted from the mother and placenta-derived tissues also play a significant role in the formation of the infant's initial gut microbiota. Notably, none of the hereby-mentioned influences (i.e., gender, delivery mode, feeding mode, and Hepatitis B virus) affected significantly infant gut microbiota colonization.<br><br>CONCLUSION: This study demonstrated that infant intestinal microbiota resulted from microbiotic co-provision from multiple maternal sites. In addition to the maternal gut microbiota, the placenta-derived tissues is the relevant contributor to initial infant gut microbiota, providing strong evidence for the source colonization of the infant gut microbiota.}, }
@article {pmid41244624, year = {2025}, author = {Addo, SO and Addo, M and DeWitt, ME and Tawiah-Mensah, CNL and Amoah, S and Obuam, PK and Unicorn, NM and Kyeremateng, ET and Desewu, G and Larbi, JA}, title = {Knowledge, Attitude and Practices of Abattoir Workers in Kumasi Towards Ticks and Tick-Borne Pathogens.}, journal = {Public health challenges}, volume = {4}, number = {4}, pages = {e70167}, doi = {10.1002/puh2.70167}, pmid = {41244624}, issn = {2769-2450}, abstract = {The high dependence on livestock in Ghana comes with the risk of zoonotic tick-borne pathogen infection. Abattoir workers are especially at risk due to their frequent contact with livestock that are infested with ticks and tick-borne pathogens. This study sought to assess the knowledge, attitude and practices of abattoir workers in Kumasi towards ticks and tick-borne pathogens. A total of 130 workers were recruited from the Kumasi abattoir (92), Suame abattoir (24) and Akwatia Line slaughter slab (14). The respondents were males, mostly aged between 46 and 55 years (36.2%), had no form of education (43.8%) and had >10 years (68.5%) of working experience. Given that a significant number of the workers handled live animals (95.4%) or dead animals or animal parts (87.7%), were involved in slaughtering (69.2%) and had experienced tick bites (81.5%), there was a risk of tick-borne pathogen infection. However, only 35.4% thought humans can get diseases from tick bites, and 58.5% of the respondents believed tick bites lead to the development of a tick-borne disease. It was observed that education (p = 0.008) had a significant influence on the risk of zoonotic tick-borne pathogen infection, with 52% of the respondents with no education believing humans cannot get infections from ticks. The findings of this study indicate that the abattoir workers are at risk of zoonotic tick-borne infections, and there is a need for frequent education as well as the adoption of effective tick control and preventive measures.}, }
@article {pmid41242981, year = {2025}, author = {Andonotopo, W and Bachnas, MA and Dewantiningrum, J and Adi Pramono, MB and Bernolian, N and Yeni, CM and Putra Wiradnyana, AAG and Hariyasa Sanjaya, IN and Akbar, MIA and Darmawan, E and Sulistyowati, S and Stanojevic, M and Kurjak, A}, title = {The fetal exposome and Preterm Birth: a systematic synthesis of environmental exposures and multi-omics evidence.}, journal = {Journal of perinatal medicine}, volume = {}, number = {}, pages = {}, pmid = {41242981}, issn = {1619-3997}, abstract = {OBJECTIVES: Preterm birth (PTB), defined as delivery before 37 weeks of gestation, is a leading cause of neonatal mortality and long-term developmental impairment. Its complex etiology, spanning environmental, genetic, psychosocial, and socio-economic domains, limits effective prediction and prevention. We systematically synthesized evidence on how environmental exposures influence PTB risk through multi-omic disruptions within a fetal exposome framework.<br><br>METHODS: A comprehensive literature search was conducted in major biomedical databases, following PRISMA guidelines. Ninety-five human studies published through May 2025 were included, encompassing exposures such as ambient air pollution, endocrine-disrupting chemicals, maternal stress, nutrition, occupational hazards, climate variability, and microbiome alterations. Two reviewers independently extracted data (exposure type, omics platform, biospecimen, PTB subtype) with inter-rater reliability assessment, and study quality was evaluated using the Newcastle-Ottawa Scale. Findings were narratively stratified by exposure category, study design, and spontaneous vs. indicated PTB.<br><br>RESULTS: Environmental exposures were consistently associated with disruptions in oxidative stress, inflammation, immune regulation, hormonal signaling, placental aging, and microbial ecology, mediated by multi-omic signatures in maternal, placental, and fetal tissues. Candidate biomarkers show promise for early risk stratification but lack validation and population-level predictive performance due to heterogeneous exposure assessment and study design.<br><br>CONCLUSIONS: Integrating fetal exposome concepts with multi-omics enhances mechanistic insight into PTB risk and may support biomarker discovery and precision-guided prenatal interventions. Clinical translation requires standardized exposure measurement, biomarker validation, and equity-focused implementation.}, }
@article {pmid41242561, year = {2025}, author = {Gloria, LD and Lotti, T and van Loosdrecht, MC and Ramazzotti, M}, title = {Who calls granules "home"? Domain-spanning meta-analysis charting microbial ecosystems underlying aerobic granular sludge reactors.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133657}, doi = {10.1016/j.biortech.2025.133657}, pmid = {41242561}, issn = {1873-2976}, abstract = {The theatre of activity of complex microbial communities underpins the Aerobic Granular Sludge (AGS) systems, resulting in efficient wastewater treatment. Here, we present the first meta-analysis of DNA sequencing data from both published and newly generated AGS samples, aiming to define the "core microbiota" of AGS reactors, consisting of bacteria, archaea, eukaryotes and DNA viruses consistently featured and shared across different scales and operational settings. Briefly, the results indicated that a sequencing depth of at least 10 GB is required to profile the majority of the AGS community, revealed the core taxa, detected the recurrent presence of the uncultured genus ADurb.Bin028 in full-scale reactors and identified Rotaria and Diploscapter, as well as the sessile ciliates Stentor and Thuricola, as the most abundant eukaryotes in AGS. In conclusion, this work provided a taxonomic overview of AGS' common microbes and addressed potential technical caveats, aiming to establish a reference for future studies.}, }
@article {pmid41240073, year = {2025}, author = {Berkhout, MD and de Ram, C and Boeren, S and Plugge, CM and Belzer, C}, title = {Probiotic Engraftment of Akkermansia muciniphila in an In Vitro Synthetic Microbial Community.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {123}, pmid = {41240073}, issn = {1432-184X}, support = {0.24.002.002//Ministerie van Onderwijs, Cultuur en Wetenschap/ ; }, mesh = {*Probiotics ; *Gastrointestinal Microbiome ; Humans ; Mucins/metabolism ; *Verrucomicrobia/physiology ; Akkermansia ; Polysaccharides/metabolism ; Bacteroides thetaiotaomicron ; }, abstract = {Akkermansia muciniphila is a specialist mucin glycan-degrader that is common in the human gut. A. muciniphila is associated with host health and therefore proposed as a next-generation probiotic. However, it is unknown if consumption of live and active A. muciniphila will be effective in terms of survival and engraftment in the gut microbiome. Furthermore, it is of interest whether introduction of A. muciniphila would influence the resident mucosal microbiota. To this end, we investigate the addition of live A. muciniphila to a stable in vitro microbial mucin glycan-degrading synthetic community. A. muciniphila engrafted in this synthetic community and actively degraded mucin using essential mucin glycan-degrading enzymes. Addition of A. muciniphila did not induce major compositional changes, except that Bacteroides thetaiotaomicron increased in relative abundance at the expense of Bacteroides caccae. At the metaproteomic level, community function was not significantly affected, as peptidase, fucosidase, galactosidase and sulfatase expression remained stable. However, sialidase was significantly enriched after A. muciniphila addition, which can be explained by the relative increase of generalist glycan-degrader B. thetaiotaomicron. Overall, we show that a community without A. muciniphila still harbours a niche for this bacterium, but that A. muciniphila did not induce major changes in the in vitro mucosal synthetic community. This suggests that A. muciniphila applied as a probiotic can engraft and exert its beneficial effects on the host, without major impact on the human gut mucosal microbiota composition and function and warrants further research into A. muciniphila engraftment in vivo.}, }
@article {pmid41240069, year = {2025}, author = {Cambronero-Heinrichs, JC and Pepori, AL and Pecori, F and Santoiemma, G and Cavaletto, G and Santini, A and Rassati, D}, title = {Microbial Interactions Support the Role of Ambrosia Beetles as Potential Vectors of Dutch Elm Disease.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {124}, pmid = {41240069}, issn = {1432-184X}, support = {National Recovery and Resilience Plan (NRRP), Mission 4, Component 2, project: "Ulmus glabra protection in Italian peninsula - MONTANA", CUP:C53D23003510006//European Union - NextGenerationEU/ ; }, mesh = {Animals ; *Plant Diseases/microbiology ; *Ulmus/microbiology/parasitology ; Symbiosis ; *Coleoptera/microbiology ; *Microbial Interactions ; Female ; *Insect Vectors/microbiology ; Ophiostoma/physiology ; *Weevils/microbiology ; }, abstract = {Dutch elm disease (DED) has caused devastating pandemics in natural elm populations across Europe, North America, and Asia. The primary vectors of DED are native elm-associated bark beetles of the genus Scolytus. However, there is evidence suggesting that ambrosia beetles may also carry Ophiostoma novo-ulmi and potentially transmit it to elm trees. In this study, we explored microbial interactions and host selection mechanisms that could support the role of ambrosia beetles as vectors of O. novo-ulmi. Our study showed that females of Anisandrus dispar, Xyleborinus saxesenii, Xylosandrus crassiusculus, and Xylosandrus germanus emerging from both DED-infected and healthy elm logs carried O. novo-ulmi DNA. Furthermore, we showed that none of the tested ambrosia beetle fungal symbionts was adversely affected by O. novo-ulmi, while Dryadomyces spp. and the bacterial symbiont Erwinia sp. 1C4 partially restricted or inhibited O. novo-ulmi growth without fully suppressing it. Overall, these findings provide additional evidence supporting the potential role of ambrosia beetles as vectors of DED and emphasize the need for further research on this understudied insect-pathogen relationship.}, }
@article {pmid41239036, year = {2025}, author = {Casanova-Hernández, D and Pinacho-Pinacho, CD and Calixto-Rojas, M and Rubio-Godoy, M and Hernández-Velázquez, IM and Guevara-Avendaño, E and Méndez, O and Velázquez-Velázquez, E and Zamora-Briseño, JA}, title = {Challenging the paradigm: the Asian fish tapeworm (Schyzocotyle acheilognathi, Yamaguti 1934) lacks an intrinsic symbiotic bacterial community.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {41239036}, issn = {1618-1905}, abstract = {Schyzocotyle acheilognathi is an invasive generalist cestode with a high capacity for adaptation to multiple hosts and freshwater environments. Recent reports suggest that this parasite possesses an intrinsic symbiotic microbiota distinct from that of its fish hosts, and its presence induces gut dysbiosis in the host. In this study, we reassessed these ideas. For this, we collected naturally parasitized fish specimens from different locations in Mexico, encompassing different host species, including Cyprinus carpio, Pseudoxiphophorus bimaculatus, Tlaloc hildebrandi, and Vieja hartwegi. We also tested whether this parasite induces a dysbiotic process in the gut bacterial community of Tlaloc hildebrandi. Parasites were identified based on morphological and molecular criteria, and their bacterial communities were characterized using metataxonomy. Our results revealed that S. acheilognathi does not harbor a consistent microbial community among the different host species surveyed. We also did not detect any dysbiotic effect on the gut microbiota of Tlaloc hildebrandi. These findings contradict previous data and provide evidence of the loose relationship between this parasite and bacteria, which we propose could be a part of its successful generalist strategy. The results presented herein offer a novel perspective on the quest for understanding the microbial ecology in generalist cestodes of freshwater fish.}, }
@article {pmid41239026, year = {2025}, author = {Cao, D and Huang, W and Pang, M and Li, J and Huang, H and Ma, H and Li, D and Qin, Y and Peng, X and Fan, H}, title = {Investigation of the Alterations in the Gut Microbiota and Intestinal Mucosa in Mice Infected with Echinococcus multilocularis.}, journal = {Acta parasitologica}, volume = {70}, number = {6}, pages = {211}, pmid = {41239026}, issn = {1896-1851}, support = {No. 2020-ZJ-Y01//Key Laboratory Project of the Science and Technology Department of Qinghai Province/ ; Qinghai[2023]-125//The National Clinical Key Specialty Construction Project of Hepatobiliary Surgery (Hydatidosis) at Qinghai University Affiliated Hospital/ ; Qinghai Research Key Laboratory for Echinococcosis//The 2022 Science and Technology Plan Project of Qinghai Department of Science and Technology/ ; }, mesh = {Animals ; *Echinococcus multilocularis/physiology ; *Gastrointestinal Microbiome ; Mice ; *Intestinal Mucosa/pathology/microbiology/parasitology ; RNA, Ribosomal, 16S/genetics ; *Echinococcosis/parasitology/pathology ; Disease Models, Animal ; Feces/microbiology/parasitology ; Female ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {PURPOSE: Alveolar echinococcosis (AE), a zoonotic parasitic disease caused by the larval metacestode of Echinococcus multilocularis (E. multilocularis), primarily affects the liver and can invide other organs. Given its extremely poor prognsis, witha 10-year mortality rate exceeding 90% in untreated cases, this study aimed to investigate the characteristics and compositional alterations of the intestinal microbiota in AE-infected hosts and evaluate associated intestinal mucosal damage.<br><br>METHODS: We established a mouse model of AE for analysis. Fecal samples were collected from 12 AE-infected mice and 12 age-matched healthy controls at 3 and 6 months post-infection. Gut microbiota composition was assessed by 16S rRNA gene sequencing. Intestinal tissues were subjected to histopathological exnamination using hematoxylin-eosin staining (H&amp;E staining), Alcian blue-glucogen staining (AB-PAS staining), and Lendrum's fluorescent peach red staining, to evaluate mucosal structural integrity and quantify the Paneth and goblet cells.<br><br>RESULTS: The analysis revealed significant alterations in intestinal microbiota diversity and composition in AE-infected mice compared with controls, with changes becoming more pronounced as the infection progressed. Minimal disruption in microbial ecology was observed at 3&#xa0;months, whereas substantial reductions in alpha diversity and distinct shifts in beta diversity emerged after 6&#xa0;months of chronic infection. Phylum-level analysis showed an early increase in Verrucomicrobiota, Bacteroidota, and Campylobacterota at 3&#xa0;months, followed by a marked enrichment of Verrucomicrobiota and Actinobacteriota at 6&#xa0;months when compared with controls. At the genus level, AE infection led to a rapid depletion of Ligilactobacillus and Lactobacillus between 3 and 6&#xa0;months, while Akkermansia abundance significantly increased. Histopathological examination of intestinal tissue further demonstrated severe mucosal damage, including villous atrophy, reduced crypt depth, a pronounced decrease in Paneth cell density (P&#x2009;<&#x2009;0.01), and reduced goblet cell counts (P&#x2009;<&#x2009;0.05), collectively indicating compromised intestinal barrier integrity.<br><br>CONCLUSION: AE infection induces progressive gut microbiota dysbiosis and compromises intestinal barrier integrity. The specific microbial shifts, particularly the depletion of Ligilactobacillus and enrichment of Akkermansia, represent promising diagnostic biomarkers and potential targets for probiotic supplementation or microbial modulation. To further clarify their roles, future research should incorporate multi-omics strategies, including metagenomics and metabolomics, within larger cohorts to better characterize microbiota-host metabolic interactions and to validate stage-specific microbial biomarkers in AE.}, }
@article {pmid41237939, year = {2025}, author = {Devarajan, B and Sharma, S and Mills, B and Prajna, L and Venkatesh, PN and Dharmalingam, K}, title = {Dysbiosis of Bacterial and Fungal Microbiomes Affects the Disease Process and Treatment Outcome in Fungal Keratitis.}, journal = {Experimental eye research}, volume = {}, number = {}, pages = {110745}, doi = {10.1016/j.exer.2025.110745}, pmid = {41237939}, issn = {1096-0007}, abstract = {Fungal keratitis (FK) is a severe eye infection mainly caused by Aspergillus flavus and Fusarium solani. We examined the changes in bacterial and fungal microbiome profiles over a week of disease progression, treatment, and clinical status using targeted next-generation sequencing (NGS). Samples were collected from infected and healthy contralateral eyes of 25 FK patients and one eye of 10 healthy, non-infected cataract controls. QIIME (Quantitative Insights into Microbial Ecology) and MicrobiomeAnalyst were utilised for the data analysis. There was a reduction in beneficial bacteria like Prevotella, Lactobacillus, and Leuconostoc in FK patients compared to the control samples. On the other hand, opportunistic bacteria including Clostridium, Bifidobacterium, and Pseudomonas increased in FK patients. Aspergillus, Colletotrichum, and Basidiobolus were more abundant in keratitis patients, whereas Malassezia and Trichoderma were less abundant. This dysbiosis was also evident in the uninfected contralateral eyes of FK patients. Treatment resulted in significant changes in bacterial genera like Dolosigranulum, Sutterella, and Akkermansia, and fungal genera such as Myrothecium, Corynespora, and Penicillium. Further, treatment returned them to the control group levels, except for Akkermansia and Corynespora. Among the treated patients, a large subset remains nonresponsive to treatment. This treatment outcome, responder versus non-responder, was reflected in the abundance of bacterial genera such as Tannerella, Sutterella, Odoribacter, and fungal genera such as Coprinellus and Volutella. This study highlights the clinical relevance of microbiome signatures in FK, demonstrating bilateral dysbiosis, integrated bacterial-fungal profiling, and correlations with treatment outcomes. These findings suggest potential for microbiome-informed diagnostics, prognostic biomarkers, and risk stratification.}, }
@article {pmid41236361, year = {2025}, author = {Markfeld, M and Titcomb, G and Randriamoria, TM and Sehgal, G and Baksh, N and Kerrigan, A and Soarimalala, V and Nunn, CL and Pilosof, S}, title = {Differential Assembly of Core and Non-Core Host-Microbe Network Structures Along a Land-Use Change Gradient.}, journal = {Ecology letters}, volume = {28}, number = {11}, pages = {e70255}, doi = {10.1111/ele.70255}, pmid = {41236361}, issn = {1461-0248}, support = {1281/20//Israel Science Foundation/ ; 2308460//National Science Foundation/ ; R01-TW011493//NIH-NSF-NIFA Ecology and Evolution of Infectious Diseases program/ ; 2022721//United States-Israel Binational Science Foundation/ ; Provost's Collaboratory Award//Duke University/ ; RGY0064/2022//Human Frontier Science Program/ ; //Duke Lemur Center/ ; }, mesh = {Animals ; Rats/microbiology ; Madagascar ; *Microbiota ; *Host Microbial Interactions ; }, abstract = {Microbial communities are fundamental to host health, yet their assembly dynamics under environmental change remain poorly understood. We analysed individual-level host-microbe networks in the non-native wild black rats (Rattus rattus) across a land-use gradient in Madagascar. By applying a moving prevalence threshold, we distinguished between core and non-core microbes and compared the assembly drivers shaping their network structures. Non-core microbes formed fragmented, modular networks shaped mainly by heterogeneous selection, reflecting environmental filtering. In contrast, core microbes exhibited stable, less modular networks driven primarily by stochastic ecological drift. These distinct assembly processes persisted across thresholds, highlighting fundamental differences in microbial structuring. Land-use change significantly influenced the modular structure of non-core microbes but had minimal effects on core microbes, demonstrating the differential sensitivity of microbial groups to environmental variation. This study advances our understanding of host-microbe interactions and provides a framework for assessing microbiome assembly under anthropogenic change.}, }
@article {pmid41236145, year = {2025}, author = {Maillard, F and Klinghammer, F and Beatty, BH and Zou, H and Lara, E and Hammer, EC and Tunlid, A and Kennedy, PG}, title = {Keystone protist suppression triggers mesopredator release and biotic homogenization in complex soil microbial communities.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf253}, pmid = {41236145}, issn = {1751-7370}, abstract = {The keystone species concept holds that certain members of an ecological community, despite their low abundance, exert disproportionately large effects on species diversity and composition. In microbial ecology, experimental validation of this concept has been limited because targeted removal of individual species remains technically challenging. Here, we developed a procedure to test the keystone species concept within a soil microbial food web by selectively suppressing a protist predator at the microscale via UV-induced phototoxicity in a microfluidic soil chip system. We targeted a hypotrich ciliate (subclass Hypotrichia), and combined microscopy with high-throughput amplicon sequencing of microbial taxonomic markers to assess, across multiple trophic levels, how its suppression affected microbial community abundance, diversity, and composition. Over the 20-day incubation, the chip system supported complex communities of bacteria, fungi, and protists. Following Hypotrichia suppression, two distinct ecological responses were observed: first, an increase in the relative abundance of flagellates, consistent with mesopredator release, accompanied by a significant rise in overall protist diversity; second, a convergence in protist community composition, indicative of biotic homogenization. Bacterial community abundance, richness, and composition remained unchanged, likely due to compensatory predation from a relative increase in bacterivorous flagellates. In contrast, fungal diversity decreased, presumably because the altered protist community favored facultative fungal consumers. Collectively, these findings provide direct experimental evidence that low abundance microbial predators can function as keystone species, modulating predator community composition and diversity, and exerting cascading effects on lower trophic levels within microbial brown food webs.}, }
@article {pmid41234770, year = {2025}, author = {Wang, IC and Swanson, JL and Waters, JL and Kochukov, MY and Buffington, SA and Dooling, SW and Arenkiel, BR and Costa-Mattioli, M}, title = {Alteration of gut microbial ecology by the direct activation of the brain: Inverse gut-microbiome-brain dynamics.}, journal = {iScience}, volume = {28}, number = {11}, pages = {113709}, pmid = {41234770}, issn = {2589-0042}, abstract = {The gut-microbiome-brain axis is a bidirectional communication system influencing host physiology and overall fitness. While "bottom-up" effects-where gut microbes influence brain function and behavior-are well established, direct evidence for "top-down" modulation-where the brain shapes the gut microbial ecology-remains elusive. Here, we show that the selective expression of the bacterial ion channel mNaChBac in glutamatergic lateral habenula (LHb) neurons increases their bursting activity and leads to endophentypes associated with depression. Importantly, this chronic activation leads to changes in the gut microbiome composition over time, as reflected by shifts in alpha-diversity and alterations in specific microbial taxa. These findings provide direct evidence that the persistent activation of the brain acts as a selective pressure that affects the stability and diversity of the gut microbiome, providing a new dimension by which gut-microbiome-brain interactions may cooperate to modulate host physiology and health.}, }
@article {pmid41233937, year = {2025}, author = {Zhang, P and Roque, B and Romero, P and Shapiro, N and Eloe-Fadrosh, E and Kebreab, E and Diamond, S and Hess, M}, title = {Red seaweed supplementation suppresses methanogenesis in the rumen, revealing potentially advantageous traits among hydrogenotrophic bacteria.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {231}, pmid = {41233937}, issn = {2049-2618}, mesh = {Animals ; *Rumen/microbiology/metabolism ; *Methane/metabolism/biosynthesis ; Cattle ; *Seaweed ; *Dietary Supplements ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Animal Feed/analysis ; *Gastrointestinal Microbiome ; Fermentation ; Metagenome ; Metagenomics ; Hydrogen/metabolism ; }, abstract = {BACKGROUND: Macroalgae belonging to the genus Asparagopsis have shown to reduce methane (CH4) production during rumen fermentation, while increasing feed efficiency when added to the feed of cattle. However, little is known about how the rumen microbiome responds to Asparagopsis supplementation, and how changes in the microbiome may contribute to changes in rumen function and host phenotype. Here, we generated and analyzed metagenomic and metatranscriptomic data from the rumen microbiome from cows receiving (treatment) and not receiving (control) an Asparagopsis armata supplemented diet.<br><br>RESULTS: Using a combination of metatranscriptome and metagenome analysis, we found that reduction of CH4 emission from animals receiving A. armata was coupled to a significant reduction in the transcription of methanogenesis pathways. Additionally, a significant decrease in the transcription of genes for carbon catabolism and a reorganization of carbon catabolic gene expression occurred at the species level within the rumen microbiome of animals that received red seaweed with their diet. Increased H2 production, a consequence of methanogenesis suppression, was coupled to a significant increase in the transcription of hydrogenases that mediate hydrogenotrophic metabolism in the treatment group. Metatranscriptome analysis identified a single metagenome assembled genome (MAG) of a Duodenibacillus sp., a hitherto uncultured hydrogenotrophic bacterial species, as the dominant driver of this transcriptional change.<br><br>CONCLUSIONS: Comparative genomic analysis between the Duodenibacillus sp. and other hydrogenotrophic rumen organisms revealed metabolic traits that may provide Duodenibacillus sp. with a competitive advantage in H2 scavenging. Our findings provide an initial understanding of how the rumen microbiome responds to a promising CH4 reducing feed additive and serve as a model for alternative stable rumen microbiome states that produce less methane and increase animal productivity. Ultimately, insights from the work presented here might enable the development of advanced microbiome-based strategies to reduce enteric methane production.}, }
@article {pmid41233936, year = {2025}, author = {Modolon, F and N Garritano, A and J Hill, L and Duarte, G and Bendia, A and de Moura, R and Pellizari, V and Thomas, T and Peixoto, RS}, title = {Putative promiscuous symbionts in deep-sea corals and crinoids may contribute to nitrogen cycling.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {234}, pmid = {41233936}, issn = {2049-2618}, support = {141954/2019-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; ANP 21005-4//Shell, Brazil/ ; BAS/1/1095-01-01 and FCC/1/1976-40-01//KAUST/ ; }, mesh = {*Anthozoa/microbiology ; Animals ; *Symbiosis ; *Nitrogen Cycle ; Metagenomics/methods ; Microbiota ; Brazil ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; In Situ Hybridization, Fluorescence ; }, abstract = {BACKGROUND: Crinoids (feather stars) are frequently found in association with corals, yet the physiological and microbial interactions between these organisms remain poorly understood. Both corals and crinoids host symbiotic microorganisms, but the functional roles of these symbionts, particularly in deep-sea environments, are largely unexplored. This study characterizes the microbiomes of the deep-sea corals Desmophyllum pertusum and Solenosmilia variabilis and their associated crinoid Koehlermetra sp. (Thalassometridae) from the Campos Basin, Brazil, to investigate potential cross-host microbial interactions and their ecological implications. We used multiple approaches for this investigation, including amplicon sequencing surveys, genome-resolved metagenomics, and fluorescence in situ hybridization.<br><br>RESULTS: We found that the same endosymbiotic members of the families Endozoicomonadaceae and Nitrosopumilaceae inhabit both corals and the crinoids, suggesting promiscuity in host-symbiont relationships. Metagenomic analysis revealed a novel and dominant Endozoicomonas species (E. promiscua sp. nov.), whose genome encodes pathways for dissimilatory nitrate reduction to ammonia (DNRA). This metabolic capability could provide a substrate for ammonia-oxidizing archaea (Nitrosopumilaceae), indicating a potential cross-host nitrogen-cycling network. Shared microbial taxa between corals and crinoids further support the hypothesis of symbiont promiscuity, where metabolic redundancy may facilitate colonization across species.<br><br>CONCLUSIONS: Our findings suggest that nitrogen cycling plays a key role in structuring microbial symbioses in deep-sea coral-crinoid holobionts. The promiscuous distribution of symbionts across hosts implies that metabolic interactions, such as DNRA-driven ammonia provisioning, could underpin resilience in nutrient-limited environments. This study highlights the importance of microbial versatility in deep-sea ecosystems and provides new insights into how cross-host symbiosis may contribute to biogeochemical cycling in the ocean. Video Abstract.}, }
@article {pmid41233829, year = {2025}, author = {Sieders, M and Candry, P and El Aidy, S}, title = {Hydrogel-based experimental models of the gastrointestinal tract.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {233}, pmid = {41233829}, issn = {2049-2618}, abstract = {The gut microbiome plays a pivotal role in human health, yet its complexity has long eluded detailed study under physiologically relevant conditions. Hydrogel-based models are revolutionizing microbiome research by bridging the gap between traditional in vitro systems and the complexity of in vivo environments. These advanced systems replicate key physical and biochemical features of the gastrointestinal tract, offering unprecedented opportunities to study microbial behavior, adaptation, and interactions within three-dimensional, tunable architectures. Unlike suspension cultures, hydrogels provide porous, mucosa-like environments that enable the cultivation of mucosa-associated microbes, co-culturing with human cells, and mimicking healthy and disease-related states. This review explores the transformative potential of hydrogel matrices in unveiling the spatial organization, nutrient gradients, and community communication that define microbial ecosystems. By integrating the benefits of in vitro and in vivo models, hydrogel-based platforms promise to accelerate discoveries in microbiome science, with far-reaching implications for understanding human health and developing targeted therapeutics. Video Abstract.}, }
@article {pmid41231796, year = {2025}, author = {Baral, T and Maile, A and Adimurthy, NH and Saravu, K and Kudru, CU and Singh, J and Mukhopadhyay, C and Rao, M and Manu, MK and Sekhar Miraj, S}, title = {Exploring gut microbiota and its predicted functions in pulmonary tuberculosis: A multi-regional study using public 16S datasets.}, journal = {PloS one}, volume = {20}, number = {11}, pages = {e0336337}, doi = {10.1371/journal.pone.0336337}, pmid = {41231796}, issn = {1932-6203}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics/drug effects ; *Tuberculosis, Pulmonary/microbiology/drug therapy ; Phylogeny ; *RNA, Ribosomal, 16S/genetics ; Antitubercular Agents/therapeutic use ; Male ; Female ; Mycobacterium tuberculosis/genetics ; Middle Aged ; Adult ; }, abstract = {BACKGROUND: Pulmonary tuberculosis, caused by the bacillus Mycobacterium tuberculosis, remains a major global health challenge, particularly in developing countries. In this study, we analyzed publicly available 16S amplicon sequencing datasets from four geographical locations using a single workflow.<br><br>METHODS: We employed Quantitative Insights Into Microbial Ecology v.2 for microbial diversity analysis and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States v.2 for functional pathway predictions of the gut microbiota in patients with PTB and antitubercular therapy.<br><br>RESULTS: Our analysis revealed statistically significant alpha diversity differences in West Africa with decreased microbial diversity in pulmonary tuberculosis patients after two months of antitubercular therapy. Additionally, there were no statistically significant differences observed in pairwise comparisons within the same location or in the aggregate beta diversity of the datasets. The predicted microbial metabolic pathways related to vitamin biosynthesis, amino acid synthesis, and energy production were depleted in pulmonary tuberculosis patients following antitubercular therapy.<br><br>CONCLUSIONS: The observed alterations of gut microbial diversity and predicted functional profile underscores the influence of antitubercular therapy on gut health, suggesting that longer treatment durations may aggravate these alterations in gut microbial function. Moreover, geographical location exerts a more significant impact on microbial diversity than the disease state in a specific location, highlighting the potential for precision medicine to tailor interventions based on individual or regional microbiome characteristics.}, }
@article {pmid41230548, year = {2025}, author = {Mukherjee, A and Tan, BH and Swarup, S}, title = {In Silico Prediction and In Vitro Validation of Bacterial Interactions in the Plant Rhizosphere Using a Synthetic Bacterial Community.}, journal = {Bio-protocol}, volume = {15}, number = {21}, pages = {e5496}, pmid = {41230548}, issn = {2331-8325}, abstract = {The rhizosphere, a 2-10 mm region surrounding the root surface, is colonized by numerous microorganisms, known as the rhizosphere microbiome. These microorganisms interact with each other, leading to emergent properties that affect plant fitness. Mapping these interactions is crucial to understanding microbial ecology in the rhizosphere and predicting and manipulating plant health. However, current methods do not capture the chemistry of the rhizosphere environment, and common plant-microbe interaction study setups do not map bacterial interactions in this niche. Additionally, studying bacterial interactions may require the creation of transgenic bacterial lines with markers for antibiotic resistance/fluorescent probes and even isotope labeling. Here, we describe a protocol for both in silico prediction and in vitro validation of bacterial interactions that closely recapitulate the major chemical constituents of the rhizosphere environment using a widely used Murashige &amp; Skoog (MS)-based gnotobiotic plant growth system. We use the auto-fluorescent Pseudomonas, abundantly found in the rhizosphere, to estimate their interactions with other strains, thereby avoiding the need for the creation of transgenic bacterial strains. By combining artificial root exudate medium, plant cultivation medium, and a synthetic bacterial community (SynCom), we first simulate their interactions using genome-scale metabolic models (GSMMs) and then validate these interactions in vitro, using growth assays. We show that the GSMM-predicted interaction scores correlate moderately, yet significantly, with their in vitro validation. Given the complexity of interactions among rhizosphere microbiome members, this reproducible and efficient protocol will allow confident mapping of interactions of fluorescent Pseudomonas with other bacterial strains within the rhizosphere microbiome. Key features • This method builds upon the widely used MS-based gnotobiotic system for growing plants and a synthetic bacterial community (SynCom) for plant-microbe interaction studies. • It considers the chemical composition of plant growth media (MS) and root exudates to map bacterial interactions. • It provides a method to both predict and validate interactions of fluorescent Pseudomonas with other strains within a SynCom. • This method is scalable for any bacterial pair with distinguishing markers (e.g., fluorescence, antibiotic resistance).}, }
@article {pmid41229186, year = {2025}, author = {Park, JW and Park, JS and Kook, PR and Cho, YH and Park, SK and Lee, JH and Kang, SK and Kim, SW and Kim, SR}, title = {Impact of Artificial Diet Versus Mulberry Leaves on Silkworm Growth, Nutrient Composition, and Gut Microbiota.}, journal = {Archives of insect biochemistry and physiology}, volume = {120}, number = {3}, pages = {e70113}, doi = {10.1002/arch.70113}, pmid = {41229186}, issn = {1520-6327}, support = {PJ01721401.//This study was supported by the 2025 RDA Fellowship Program of the National Institute of Agricultural Science./ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Morus/chemistry ; *Bombyx/growth &amp; development/microbiology/metabolism ; Plant Leaves/chemistry ; Larva/growth &amp; development/microbiology ; *Diet ; *Animal Feed/analysis ; Nutrients/analysis ; RNA, Ribosomal, 16S ; }, abstract = {Silkworms (Bombyx Mori) are traditionally reared on mulberry leaves; however, artificial diets have been developed to enable year-round rearing and automation. The physiological performance and cocoon yield of silkworms fed artificial diets remain inferior to those reared on mulberry leaves. We compared growth and nutrient composition in larvae reared on mulberry leaves (ML) and antibiotic-free artificial diet (ADS), and profiled gut microbiota in ML, ADS, and antibiotic-supplemented artificial diet (ADSA) to assess dietary effects on host physiology and microbial ecology. Proximate analysis revealed that protein accumulation was greater in ML-fed larvae, while ADS-fed larvae showed relatively higher fat content at the late fifth instar. Amino acid profiling showed consistently higher silk-related residues (Gly, Ala, Ser) and the derived Silk Amino Acid Index in ML-fed larvae, indicating enhanced fibroin synthesis potential. Microbiome analysis using 16S rRNA amplicon sequencing demonstrated dominance of Enterococcus mundtii in ADS groups, resulting in reduced alpha diversity and uneven community structure. In contrast, ML-fed larvae harbored diverse taxa, including Methylorubrum and Methylobacterium, while ADSA groups exhibited intermediate profiles with occasional dominance of Bacillus cereus. These findings highlight that artificial diet alters host nutrient metabolism and drives dysbiosis of gut microbiota, underscoring the need for optimized formulations and microbiome-stabilizing strategies, such as probiotics or prebiotics.}, }
@article {pmid41228488, year = {2025}, author = {Yin, C and Liu, X and Fang, W and Meng, Q and Feng, X and Zhang, W and Dang, G and Zhong, R and Chen, L and Wang, Z and Zhang, H}, title = {Hyocholic Acid Species as the Key Modulator for Cecal Epithelial Homeostasis in Low-Birth-Weight Piglets.}, journal = {Nutrients}, volume = {17}, number = {21}, pages = {}, doi = {10.3390/nu17213415}, pmid = {41228488}, issn = {2072-6643}, support = {32202709//National Natural Science Foundation of China/ ; U22A20515//National Natural Science Foundation of China/ ; Y2023QC09//Youth Innovation of Chinese Academy of Agricultural Sciences/ ; }, mesh = {Animals ; *Cecum/microbiology/drug effects/metabolism ; Swine ; *Homeostasis/drug effects ; Gastrointestinal Microbiome/drug effects ; *Intestinal Mucosa/metabolism/drug effects ; Bile Acids and Salts ; Animals, Newborn ; Birth Weight ; Dietary Supplements ; *Cholic Acids/pharmacology ; Dysbiosis ; }, abstract = {Background: Low birth weight (LBW) is correlated with gut microbiota dysbiosis and intestinal barrier function disruption, increasing susceptibility to enteric diseases. These alterations underscore the critical need to identify key regulators of gut homeostasis, among which bile acids are increasingly recognized as pivotal for barrier integrity, microbial ecology, and host metabolism. Methods: Eight pairs of LBW (the initial BW was 0.850 ± 0.053 kg) and normal-birth-weight (NBW; 1.488 ± 0.083 kg) piglets were compared to evaluate cecal morphology and bile acid profiles. Subsequently, sixteen LBW piglets and eight NBW piglets were allocated into three groups: NBW (1.563 ± 0.052 kg), LBW control (LBW-CON; 0.950 ± 0.120 kg), and LBW with bile acid supplementation (LBW-bile powder; 0.925 ± 0.116 kg). Piglets in the LBW-bile powder group received 25 mg/kg BW of bile powder (hyodeoxycholic acid-enriched) by daily oral gavage for 14 days. Results: LBW piglets exhibited retarded cecal development and lower abundance of hyocholic acid species (p = 0.006). Importantly, bile powder supplementation significantly improved cecal length (p = 0.009) and mucosal thickness (p = 0.020) compared with LBW-CON piglets. Microbial analysis showed that the microbial dysbiosis index was restored to near-normal levels. Transcriptomic analysis revealed impaired extracellular matrix structure and mucus secretion in LBW piglets. Notably, bile powder supplementation markedly upregulated the protein expression of WNT8B (p < 0.001) and the bile acid receptors (i.e., GPBAR1 and FXR), alongside enhanced tight junctions and the goblet cell marker mucin-2 expression (p < 0.05). Conclusions: These findings suggest that specific bile acid supplementation improves gut barrier function and partially supports cecal development in LBW piglets.}, }
@article {pmid41227744, year = {2025}, author = {Fu, Y and Wang, Y and Zhang, J and Ren, J and Fang, B}, title = {Prebiotic Structural Diversity Shapes Gut Microbial Diversity, Community Composition, and Metabolic Activity In Vitro.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {21}, pages = {}, pmid = {41227744}, issn = {2304-8158}, support = {81770558//National Natural Science Foundation of China/ ; 3502Z20149031//Xiamen Joint Projects for Major Diseases/ ; 22278343//National Natural Science Foundation of China/ ; }, abstract = {Prebiotics are selectively utilized substrates that modulate gut microbiota and host health, yet different prebiotic structures may elicit distinct ecological and metabolic responses. In this study, we investigated the effects of five structurally diverse prebiotics-isomaltooligosaccharides (IMO), arabinogalactans (AG), pectin, inulin, and stachyose-on human gut microbiota via a 24 h in vitro anaerobic culture with healthy donors' gut microbiota. Microbial community dynamics were profiled by 16S rRNA gene sequencing, and short-chain fatty acids (SCFAs) production was analyzed. All treatments resulted in decreased α-diversity compared with baseline, with pectin most effectively preserving microbial richness and evenness, whereas stachyose led to the greatest reduction. Community composition and functional profiles shifted in a substrate-specific manner, with AG promoting Bacteroidaceae, IMO stimulating Lachnospiraceae and Faecalibacterium, and pectin supporting balanced microbial structures and SCFA production. Pectin, IMO, and inulin enhanced butyrate levels, whereas AG and pectin promoted propionate formation. These findings demonstrate that prebiotic structural differences strongly shape gut microbial ecology and metabolism, providing a mechanistic basis for rationally selecting and combining prebiotics to beneficially modulate the gut microbiota.}, }
@article {pmid41227660, year = {2025}, author = {Alfonzo, A and Gaglio, R and Alongi, D and Franciosi, E and Perricone, G and Garofalo, G and Prestianni, R and Naselli, V and Pirrone, A and Francesca, N and Moschetti, G and Settanni, L}, title = {Polyphasic Characterisation of Microbiota Associated with Sant'Agostino Table Olives Flavoured with Foeniculum vulgare.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {21}, pages = {}, pmid = {41227660}, issn = {2304-8158}, support = {B7521002300001//Ministry of University and Research in Italy/ ; B73C23000060001//European Union/ ; }, abstract = {Sant'Agostino green table olives, traditionally processed in Apulia and flavoured with Foeniculum vulgare, represent a niche product whose microbial ecology remains largely unexplored. This study aimed to characterise the microbiota of the final product (both brine and fruit) after six months of storage with wild fennel. Four production batches were analysed using a combined culture-dependent and culture-independent approach. Microbiological counts revealed variable levels of aerobic mesophilic microorganisms, yeasts, lactic acid bacteria (LAB), and staphylococci, with yeasts and LAB being predominant. Ten LAB strains were identified, including Enterococcus faecium, Leuconostoc mesenteroides subsp. jonggajibkimchii, Leuconostoc mesenteroides subsp. cremoris, Leuconostoc pseudomesenteroides, Lactiplantibacillus plantarum, and Lactiplantibacillus pentosus. Yeast isolates belonged to Candida tropicalis, Torulaspora delbrueckii, and Saccharomyces cerevisiae. Amplicon sequencing (MiSeq Illumina) revealed distinct bacterial profiles between fruit and brine samples, with taxa from Actinobacteria, Bacteroidetes, Enterococcus, Lactobacillus, Leuconostoc, Alphaproteobacteria, Enterobacteriaceae, and other Gammaproteobacteria. Enterococcus and Leuconostoc were consistently detected, while Lactobacillus sensu lato appeared only in one fruit and one brine sample. These findings provide new insights into the microbial diversity of Sant'Agostino olives and contribute to the understanding of their fermentation ecology and potential for quality and safety enhancement.}, }
@article {pmid41227479, year = {2025}, author = {Chessari, G and Tumino, S and Castiglioni, B and Biscarini, F and Bordonaro, S and Avondo, M and Marletta, D and Cremonesi, P}, title = {Girgentana's Goat Milk Microbiota Investigated in an Organic Farm During Dry Season.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {21}, pages = {}, pmid = {41227479}, issn = {2076-2615}, support = {Agritech National Research Center and received funding from the European Union Next-GenerationEU (National Recovery and Resilience Plan (NRRP), Mission 4, Component 2, Investment 1.4-D.D. 1032 17/06/2022, CN00000022//Agritech National Research/ ; }, abstract = {Milk microbiota is a complex microbial ecosystem with implications for product quality, safety, and animal health. However, limited data exist on goat milk microbiota, particularly in local breeds. This study provides the first detailed characterization of the milk microbiota of Girgentana goats, a resilient Sicilian breed valued for high-quality dairy products. Illumina NovaSeq sequencing was used to analyze the 16S rRNA V3-V4 regions of 44 individual and 3 bulk milk samples. Briefly, 16S rRNA-gene sequencing produced a total of 8,135,944 high-quality reads, identifying 1134 operational taxonomic units (OTUs) across all individual samples. On average, each sample showed 864 OTUs with counts > 0. Alpha diversity metrics, based on richness estimators (Chao1: 948.1; ACE: 936.3) and diversity indices (Shannon: 4.06; Simpson: 0.95; Fisher: 118.5), indicated a heterogeneous community with both common and low-abundance taxa. Firmicutes (51%) and Proteobacteria (27%) were the predominant phyla, with Lactobacillaceae (54%) and Bifidobacteriaceae (22%) dominating at the family level. Notably, farm bulk milk profiles closely mirrored individual samples. These results establish a milk microbiota baseline for the Girgentana breed and offer valuable insights into microbial ecology in traditional dairy systems, supporting future comparisons across breeds and farming practices.}, }
@article {pmid41222858, year = {2025}, author = {Dvořák, P and Skoupý, S and Stanojković, A and Johansen, JR and Villanueva, C and Jung, P and Briegel-Williams, L and Laughinghouse, HD and Lefler, FW and Berthold, DE and Kaštovský, J and Hurley, AC and Casamatta, DA}, title = {A hitchhiker's guide to modern, practical cyanobacterial taxonomy.}, journal = {Journal of phycology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jpy.70102}, pmid = {41222858}, issn = {1529-8817}, support = {23-06507S//Grant Agency of the Czech Republic/ ; }, abstract = {There has been an explosion of new Cyanobacterial taxa described within the last two decades. Cyanobacteria exhibit incredible ecological versatility and morphological variability, and thousands of species have already been described using "traditional" approaches (e.g., morphological features). However, DNA sequencing and other molecular tools have provided extensive evidence that the diversity of cyanobacteria is not necessarily congruent with morphology, as many morphological genera (e.g., Phormidium, Leptolyngbya, and Nostoc) are polyphyletic, and species within the genera are often morphologically indistinguishable, thus cryptic. Further confounding systematic assessments, newly erected taxa are often based on a single strain with one or two 16S rRNA gene sequences, may have incomplete formal descriptions, and lack indication of the employed species concepts. Here we have proposed a set of guidelines for cyanobacterial taxonomists. We have focused on the whole process of erecting new taxa: sampling, sequencing (including genomes), phylogenetic inference, phenotype characterization, species concepts, formal descriptions, and codes of nomenclature. Our hope is that these guidelines will help with the laborious but ever-rewarding task of identifying and describing the taxa within the world of cyanobacteria.}, }
@article {pmid41221507, year = {2025}, author = {Clinton, CK and Jackson, FLC}, title = {Persistent human-associated microbial signatures in burial soils from the 17th and 18th century New York African burial ground.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf181}, pmid = {41221507}, issn = {2730-6151}, abstract = {Understanding the long-term persistence of human-associated microbial signatures in burial soils offers a untapped insights into historical human health, decomposition, and ecological transformation. This study investigates whether centuries-old burial soils retain distinguishable microbial evidence of human decomposition using 16S rRNA gene sequencing on 81 samples from the New York African Burial Ground (NYABG), a 17th and 18th century cemetery for free and enslaved Africans. Comparative analyses against six control soils from nearby urban parks were conducted using QIIME2, ALDEx2, and ANCOM. Burial soils exhibited significantly greater alpha diversity (Faith's PD, Shannon, observed ASVs; P < .01) and distinct beta diversity patterns (Bray-Curtis, UniFrac; PERMANOVA P = .001). Enrichment of Firmicutes, Actinobacteriota, and gut-associated genera such as Bacillus and Ruminococcus characterized burial soils, whereas oligotrophic taxa dominated controls. Tentative identifications of human-associated pathogenic genera (e.g. Fusobacterium periodonticum, Prevotella pleuritidis) were observed exclusively in burial soils, suggesting their origin from the interred individuals but requiring further validation. These findings demonstrate that soil microbiomes reflect host-associated microbial communities long after decomposition, providing a scalable, nondestructive approach for reconstructing ancient microbial communities and host-associated health signatures. This work establishes the NYABG burial soil microbiome as a valuable model for microbial archaeology and introduces a replicable framework for integrating environmental microbiology, bioarchaeology, and historical epidemiology through the lens of postmortem microbial ecology.}, }
@article {pmid41220415, year = {2025}, author = {Moseeb, HM and Aizaz, MM and Aiza, K and Hafsa, TH and Sania, M and Kamran, Z and Shamama, ZT and Usama, AM and Maroof, QP and Feroze, F and Ahmed, R and Ammara, N and Mahima, G}, title = {From obesity to cancer: Gut microbiome mechanisms, biomarkers, and U.S. public health strategies.}, journal = {Oncoscience}, volume = {12}, number = {}, pages = {175-188}, pmid = {41220415}, issn = {2331-4737}, abstract = {BACKGROUND: Obesity, metabolic syndrome, and colorectal cancer (CRC) remain major public health challenges in the United States, collectively driving substantial morbidity, mortality, and economic burden. Beyond diet and genetics, the gut microbiome has emerged as a pivotal determinant of host metabolism, immunity, and carcinogenesis, influenced by both environmental and behavioral factors.<br><br>OBJECTIVE: This review synthesizes current evidence linking gut microbial dysbiosis to obesity, metabolic syndrome, and CRC, emphasizing mechanistic pathways, environmental modifiers, and translational opportunities relevant to U.S. public health and precision medicine.<br><br>METHODS: Comprehensive searches of PubMed and Scopus (2000-2025) identified large epidemiologic studies, mechanistic experiments, and clinical trials, prioritizing research from U.S. populations and nationally representative databases including NHANES, SEER, and the Nurses' Health Study.<br><br>RESULTS: Microbial alterations such as enrichment of Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis, and colibactin-producing Escherichia coli contribute to CRC initiation and progression. In obesity and metabolic syndrome, shifts in Firmicutes-to-Bacteroidetes ratios, altered short-chain fatty acid metabolism, and endotoxin-mediated inflammation disrupt metabolic homeostasis. Environmental and lifestyle exposures, including air pollutants, smoking, and Westernized diets, modulate microbial ecology across the aerodigestive tract, affecting disease susceptibility. The emerging discipline of Molecular Pathological Epidemiology (MPE) integrates lifestyle, microbiome, and biomarker data to elucidate exposure-outcome relationships, enabling personalized prevention and therapeutic strategies.<br><br>CONCLUSIONS: The gut microbiome functions as both a biomarker and therapeutic target across metabolic and neoplastic diseases. Integrating microbiome science with environmental epidemiology and MPE frameworks offers transformative potential for precision prevention and equitable public health strategies in the U.S.}, }
@article {pmid41219483, year = {2025}, author = {Han, J and Fang, Q and Hao, Y and Huang, X and Kong, F and Chen, H and Liu, Y}, title = {Diversity of Yeast and Drosophila Species Associated with Grape Sour Rot in China.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {121}, pmid = {41219483}, issn = {1432-184X}, support = {2022E02073//Special Regional Collaborative Innovation Project of Xinjiang Uygur Autonomous Region (Science and Technology Aid Xinjiang Program)/ ; 32272550//National Natural Science Foundation of China/ ; CARS-29-bc-5//Agriculture Research System of China/ ; 202305AF150129//Expert Workstation Project in Yunnan Province/ ; }, abstract = {Sour rot is a complex disease of grapes, primarily caused by the synergistic effects of yeast and Drosophila species, leading to fruit decay, poor quality, and significant economic losses. The lack of information on species distribution and diversity of these organisms in China limits the efficacy of control strategies. In this study, we sequenced the 26S rRNA D1/D2 region in yeasts and the COI region in Drosophila. Nine yeast genera were identified. Hanseniaspora spp. (45.76% of total) were the most abundant, followed by Starmerella spp. (23.62%) and Saccharomyces spp. (17.34%). At the species level, 14 yeast species were identified. Starmerella bacillaris (23.62%), Saccharomyces cerevisiae (17.34%), H. opuntiae (17.34%), and H. uvarum (15.13%) predominated. Of the five species of Drosophila present, Drosophila melanogaster (63.16%) was the dominant species. This study is the first to characterize the diversity of yeasts and Drosophila across major grape-producing regions in China. The findings provide a scientific foundation for elucidating the key drivers of sour rot and designing targeted control strategies.}, }
@article {pmid41219454, year = {2025}, author = {Zhang, C and Zhang, X and Wang, F and Li, G and Ding, J and Cao, Y and Wang, H and Wu, S and Shang, X and Wei, K and Yang, L}, title = {Integrated Multi-Omics Analysis Reveals Microbial Community Restructuring and its Role in Key Carbohydrate Metabolic Pathways During Tobacco Leaf Curing.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {122}, pmid = {41219454}, issn = {1432-184X}, support = {1102022202016 / 110202201019 (LS-03)//Science and Technology Project of China Tobacco General Corporation/ ; QKHJC-ZK [2022] YB288//Science and Technology Project of Guizhou Provincial Department of Science and Technology/ ; 2022XM17//Science and Technology Project of Guizhou Tobacco Industry Technology Center/ ; 202111/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Plant Leaves/microbiology/metabolism/chemistry ; *Nicotiana/microbiology/metabolism/chemistry ; *Microbiota ; *Fungi/metabolism/genetics/classification/isolation &amp; purification ; *Carbohydrate Metabolism ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Metabolic Networks and Pathways ; Temperature ; Metabolomics ; Multiomics ; }, abstract = {Microorganisms play a significant role in improving the flavor and quality of plant products. Analyzing how tobacco processing affects the microbial community structure is essential. Understanding the synergistic mechanisms of microorganisms during this process can help optimize the flavor and quality of plant products. In this study, samples were collected from four processing stages (T1: fresh leaves, T2: 42 °C, T3: 54 °C, T4: 68 °C), and metabolite and Phylloplane microbial data of tobacco leaves were generated. A comprehensive multi-omics analysis was conducted. The study shows that the increase in temperature and the decrease in humidity during the processing lead to the reorganization of the microbial community. Brevibacterium, Staphylococcus, Aspergillus, and Ganoderma were identified as core biomarkers. Bacteria dominate in the initial degradation of starch, while fungi promote the accumulation of soluble sugars through the transformation of intermediate products. This study deepens our understanding of the role of microorganisms and their carbohydrate metabolism in the tobacco leaf processing process and proposes a new strategy for constructing regulatory models by integrating multi-omics.}, }
@article {pmid41218435, year = {2025}, author = {Ren, J and Wang, J and Dong, Y and Xiao, L and Wang, L and Ji, J and Liu, Y}, title = {Microbial community dynamics and its relationship with biogeochemical processes under geochemical perturbations.}, journal = {Water research}, volume = {289}, number = {Pt B}, pages = {124889}, doi = {10.1016/j.watres.2025.124889}, pmid = {41218435}, issn = {1879-2448}, abstract = {Environmental microbial communities are crucial in regulating ecosystem functions and are increasingly affected by human-induced geochemical perturbations. While microbial communities are known to shift under such perturbations, the explicit link between these shifts and corresponding biogeochemical processes remains unclear. Here, we conducted time-series sediment incubation experiments under elevated nitrate conditions, combining 16S rRNA gene sequencing, qPCR, and metagenomics to track microbial taxonomic and functional dynamics. We further developed a gene-centric, process-based biogeochemical model to quantitatively connect microbial community structure to geochemical reaction kinetics. Our results revealed that functional metagenomics provided a broader view of functional diversity than qPCR and enabled detailed analysis of gene co-occurrence. Through modeling, we uncover a quantitative coupling between functional gene abundance and reaction rates under geochemical perturbations. However, this relationship can be obscured by redox-driven abiotic processes affected by perturbations and the nonlinear nature of enzyme-mediated reactions, making it difficult to resolve using standard statistical approaches. Together, these findings improve our understanding of the linkage between microbial function and biogeochemical processes, and underscore the value of gene-centric, process-based models for predicting ecosystem behavior under geochemical stress.}, }
@article {pmid41217184, year = {2025}, author = {Creagh, JW and Rolfsmeier, M and Evans, KJ and Bizarria, R and Reetz, DC and Badigian, TJ and Fredericks, LR and Hasenoehrl, AM and Brown, AP and Graves, BM and Alexander, CK and Rodrigues, A and Stoffregen, EP and Patel, JS and Ytreberg, FM and Rowley, PA}, title = {The Saccharomyces killer toxin K62 is a protein of the aerolysin family.}, journal = {mBio}, volume = {}, number = {}, pages = {e0142525}, doi = {10.1128/mbio.01425-25}, pmid = {41217184}, issn = {2150-7511}, abstract = {UNLABELLED: K62 is an antifungal killer toxin produced by Saccharomyces paradoxus, encoded by a double-stranded RNA satellite. The toxin exhibits a unique antifungal activity but lacks sequence homology to other killer toxins, and its antifungal mechanism of action remains unknown. To understand the function of K62, its tertiary structure was predicted using AlphaFold, followed by molecular dynamics simulations to create high-confidence molecular models. These analyses revealed that K62 monomers closely resemble the five-beta-strand domain found in pore-forming aerolysin toxins. Models of K62 oligomers yielded a circular complex and beta-barrel with structural and biochemical similarities to aerolysin-family pre-pores and pores. Consistent with the formation of aerolysin-like pores, recombinant K62 assembled into membrane-associated high molecular weight oligomers (>250 kDa) that were heat- and detergent-resistant. K62 has more than 1,000 uncharacterized sequence homologs, which were mostly found in fungi of the Ascomycota, as well as in the Chytridiomycota, Basidiomycota, plants, and bacteria, with evidence of extensive horizontal gene transfer. Homologs were also identified in pathogenic fungal species, including human and plant pathogens from the Candida and Fusarium genera, but unlike aerolysins, K62 appeared to be non-toxic to higher eukaryotes. K62 is the first aerolysin family protein discovered in yeasts, revealing a likely role in fungal niche competition and establishing an entirely new, expansive family of aerolysin-like proteins.<br><br>IMPORTANCE: Pore-forming toxins are potent biological weapons used across nature, from virulence factors to immune defense proteins. This study identifies K62, a little-known antifungal toxin produced by a wild yeast, as a structural and functional relative of the aerolysin family, which is well-known for forming damaging pores in cell membranes. Using structure prediction, molecular simulations, and biochemical analysis, we show that K62 assembles into large, stable pore-like complexes. Remarkably, K62 is just one member of a large and previously unrecognized family of similar toxin-like proteins found in fungi, plants, and bacteria, including pathogens that affect humans and crops. These findings uncover an unexpected evolutionary link across kingdoms, suggesting that pore-forming toxins may play a widespread role in fungal pathogenesis and microbial warfare. This work lays the foundation for understanding a new group of antifungal molecules and their potential impacts on health, agriculture, and microbial ecology.}, }
@article {pmid41216320, year = {2025}, author = {González-Rosales, C and Rezaei Somee, M and Buck, M and Bertilsson, S and Mehrshad, M and Dopson, M}, title = {A global deep terrestrial biosphere core microbiome.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf176}, pmid = {41216320}, issn = {2730-6151}, abstract = {The deep biosphere encompasses life beneath the Earth's surface and constitutes a substantial portion of the planet's microbial biomass. This study analyzed nucleic acid datasets from low-carbon and low-energy deep terrestrial subsurface groundwaters across four continents and revealed four core global populations. These populations exhibited metabolic strategies and adaptations reflecting depth and environmental constraints. Erythrobacter featured heterotrophic metabolism; Thiobacillus demonstrated sulfur oxidation coupled to denitrification along with carbon and nitrogen fixation; Methanobacteriaceae were methanogenic autotrophs using the Wood-Ljungdahl pathway (WL); and Candidatus Desulforudis audaxviator functioned as a sulfate-reducer also encoding the WL pathway. Depth-related adaptations suggested heterotrophic dominance at shallower depths with increasing contributions from autotrophy with depth. Finally, comparative genomics revealed minimal evolutionary changes among these populations, suggesting functional conservation since diverging from their ancestral lineages. These findings underscore a global deep biosphere core community.}, }
@article {pmid41215682, year = {2025}, author = {Alonso, C and Zanetti, J and Griffero, L and Pereira-Flores, E and González, B and Lescano, C and Pérez-Parada, A and Crisci, C and Amann, R}, title = {Marine Bacterioplankton Composition Predicts Oxygen Consumption During Dissolved Organic Matter Degradation Experiments.}, journal = {Environmental microbiology}, volume = {27}, number = {11}, pages = {e70197}, doi = {10.1111/1462-2920.70197}, pmid = {41215682}, issn = {1462-2920}, support = {ANII_MPI_ID_2017_1_1007663//Agencia Nacional de Investigaci&#xf3;n e Innovaci&#xf3;n/ ; Grupos I+D 2022//Comisi&#xf3;n Sectorial de Investigaci&#xf3;n Cient&#xed;fica/ ; }, abstract = {Microbial communities play pivotal roles in ocean biogeochemistry, yet linking their composition to ecosystem functions remains a significant challenge. In this study, we demonstrate the predictive power of bacterioplankton taxonomic composition in explaining oxygen consumption during dissolved organic matter (DOM) degradation. Using 4 years of experimental data, we integrated 'omics with statistical modeling, applying feature selection and dimensionality reduction to develop high-performance linear regression models with strong predictive accuracy. Our framework also identifies key microbial groups driving oxygen consumption, including taxa known for their differential capabilities in DOM processing and recently shown to exhibit distinct respiration rates. Flavobacteriales emerge as central contributors to oxygen consumption, underscoring their ecological importance in nutrient-rich, highly productive coastal systems often referred to as 'green seas'. Their consistent dominance across varying oxygen consumption categories highlights their pivotal role in sustaining ecosystem functions in these environments. Beyond oxygen consumption, this framework provides a versatile tool for investigating microbially driven biogeochemical processes. By linking community composition with ecosystem functions, our study advances predictive microbial ecology. These findings deepen our understanding of microbial contributions to the ocean's carbon and oxygen cycles, improving our ability to anticipate their responses to environmental change.}, }
@article {pmid41215000, year = {2025}, author = {Graça, JS and Sachinelli, LDS and Tobar, N and Guadagnini, D and Cabral, L and Noronha, MF and Coutinho, LL and Cazarin, CBB and Bogusz-Junior, S and Belangero, WD and Brunetto, SQ and Pimentel, TC and Saad, MJA and Sant'Ana, AS}, title = {Fermented probiotic dairy products with buriti and orange byproducts enhance gut and bone health.}, journal = {Food research international (Ottawa, Ont.)}, volume = {221}, number = {Pt 3}, pages = {117364}, doi = {10.1016/j.foodres.2025.117364}, pmid = {41215000}, issn = {1873-7145}, abstract = {The integration of functional ingredients and probiotics in dairy matrices is a promising strategy to nehance bone and intestinal health and preventing the onset of diseases. This study aimed to evaluate the impact of fortification of fermented dairy products (yogurt and fermented milk) with buriti pulp or orange bagasse added, added or not of a probiotic strain L. acidophilus DSM 13241 (Nu-trish® LA-5®) (Chr. Hansen, Hoersholm, Denmark) (yogurt and fermented milk) on bone and intestinal health of Wistar rats. The experimental design consisted of male Wistar rats (n = 6/group) that received supplementation daily for 60 days. The parameters assessed included the quantification of minerals (Ca, P, and Mg) in the products and femurs, the biomechanical and densitometric parameters, the fecal microbiota composition through the sequencing analysis of the 16S rRNA gene, the short-chain fatty acid (SCFA) content, and the permeability of the intestinal barrier. It was observed that the consumption of buriti pulp was responsible for the bone strength and stiffness of the femurs. The consumption of buriti pulp increased the bone strength and stiffness of the femurs and the relative abundance of the Lachnospiraceae NK4A136 group. The fortification of probiotic yogurt with buriti pulp led to an increase in the production of SCFA (acetic acid) and the daily intake of Ca, Mg, and P. The consumption of orange bagasse increased the magnesium mineral content in the femur and serum calcium values. The consumption of orange bagasse increased the Mg content in the femur and serum values of Ca, improved the permeability of the intestinal barrier (reducing serum levels of lipopolysaccharide), and positively impacted the fecal composition (increases in the relative abundance of Lactobacillus and Muribaculaceae). The concentration of acetic and propionic acid increased after consumption of the two fermented milk formulations containing orange bagasse (LA OB and LA OX OB). The groups that consumed yogurt containing buriti pulp (Y BP) and yogurt containing L. acidophilus DSM 13241 (Nu-trish® LA-5®) and buriti pulp (Y LA BP) presented higher concentrations of acetic acid in the feces compared to the group that consumed only yogurt (Y). The consumption of all fermented products containing the probiotic L. acidophilus DSM 13241 (Nu-trish® LA-5®) (fermented milk or natural yogurts and yogurts fortified with buriti pulp and orange pulp: LA, LA OB, LA OX OB, Y LA, and Y LA BP) increased the abundance of the Lachnospiraceae family NK4A136 group. The findings of this study indicate that fruit byproducts and probiotic fermented dairy products exert synergistic effects on bone and gut microbial ecology health in growing rats. These results support the use of sustainable functional ingredients in food innovation to promote systemic health benefits.}, }
@article {pmid41212898, year = {2025}, author = {Mihajlovic, L and Hofacker, LM and Lindner, F and Jayakumar, P and Diepold, A and Huwiler, SG}, title = {A molecular toolbox to modulate gene expression and protein secretion in the bacterial predator Bdellovibrio bacteriovorus.}, journal = {PLoS genetics}, volume = {21}, number = {11}, pages = {e1011935}, doi = {10.1371/journal.pgen.1011935}, pmid = {41212898}, issn = {1553-7404}, abstract = {The predatory bacterium Bdellovibrio bacteriovorus kills and consumes other bacteria, thrives in diverse environments and holds great potential to address major challenges in medicine, agriculture, and biotechnology. As a bacterial predator it represents an alternative to traditional antimicrobial strategies to combat multidrug-resistant bacterial pathogens and prevent food waste, while the multitude of predatory enzymes it produces have potential for biotechnological applications. However, while a limited set of genetic tools exist, the lack of secretion assays and fine-tuning of secretion constrain both fundamental studies and bioengineering of B. bacteriovorus. Here, we present a molecular toolbox for B. bacteriovorus by systematically tuning gene expression and secretion of a reporter protein. Building on functional native and synthetic promoters from the Anderson library with varying expression levels of fluorescent reporter protein mScarletI3, we evaluated different ribosomal binding sites (RBS) to fine-tune gene expression. To examine secretion, we established a novel protocol to quantify extracellular release of a Nanoluc luciferase reporter protein in B. bacteriovorus using different native Sec-dependent signal sequences. We anticipate that the newly developed genetic toolkit and techniques will advance research on this fundamental predator-prey system, laying the foundation for its broader application and future bioengineering efforts. This work will pave the way for tailored applications of B. bacteriovorus in microbial ecology, agriculture, biotechnology, and medicine.}, }
@article {pmid41212266, year = {2025}, author = {Malassigné, S and Valiente Moro, C and Luis, P}, title = {Microbial Volatiles from Human Skin and Floral Nectar: Insufficiently Understood Adult Feeding Cues To Improve Odor-Based Traps for Aedes Vector Control.}, journal = {Journal of chemical ecology}, volume = {51}, number = {6}, pages = {108}, pmid = {41212266}, issn = {1573-1561}, abstract = {Mosquitoes of the genus Aedes, including the invasive Aedes albopictus, are responsible for the transmission of arboviruses such as dengue, chikungunya, and Zika. Their global expansion has intensified public health concerns, while the efficacy of insecticide-based control is declining due to resistance and environmental risks. These limitations have increased interest in odor-baited traps as complementary tools for surveillance and population reduction. Yet, their performance in the field remains inconsistent, largely because lures rely on a restricted set of human skin microbial volatiles and capture mainly host-seeking females. This review highlights the contribution of microorganisms inhabiting human skin and floral nectar to mosquito feeding ecology. Skin microbiota shape odor profiles by producing volatile organic compounds that mediate host attractiveness and species-specific mosquito responses. Likewise, nectar-dwelling yeasts and bacteria alter nectar chemistry and floral scent, generating volatiles that influence insect foraging, although their role in Aedes attraction remains poorly studied. By integrating data from Aedes and other insect models, we highlight microbial semiochemicals with demonstrated or potential roles in guiding blood- and sugar-feeding behaviors. We further discuss how microbial ecology, compound concentration, and chemical interactions drive variability in mosquito responses, raising both opportunities and challenges for trap design. Expanding research to nectar-associated microbial cues, while considering ecological specificity and possible non-target effects, could help create more versatile lures that attract both sexes and multiple feeding stages. This review advances our understanding of microbial-associated cues as critical drivers of mosquito behavior and outlines future directions to improve odor-based surveillance and control of Aedes vectors.}, }
@article {pmid41211947, year = {2025}, author = {Calvez, E and Quétel, I and Saint-Alban, L and Gutiérrez-Bugallo, G and Dollin, C and Ramdini, C and Vega-Rúa, A}, title = {Contrasted impacts of commercial diets and rearing water on Aedes aegypti fitness and microbiota.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0054325}, doi = {10.1128/msphere.00543-25}, pmid = {41211947}, issn = {2379-5042}, abstract = {Mosquito rearing optimization in laboratory conditions is crucial for both vector research and control. Although the addition of nutrients is important for Aedes aegypti development from immature stages to adult mosquitoes, little is known about the nutrient composition of commercial diets used for mosquito rearing and their influence on Ae. aegypti life traits. Here, we evaluated the influence of four commercial diets commonly used to rear Ae. aegypti in the laboratory on its fitness, lifespan, and microbiota. We also compared the effect of these diets on this mosquito when combined with two different rearing waters (laboratory versus field-collected waters). Our investigations demonstrated that higher levels of protein and lipid in commercial diets promote better Ae. aegypti development, lifespan, and size in both water. Metagenomic analysis revealed specific modulations of adult microbiota composition according to both diet and rearing water. Chryseobacterium dominated the microbiota of female mosquitoes reared in laboratory water, except for yeast condition, where a more diverse microbiota was observed. When reared in larval site water, the microbiota diversity was overall higher despite diet addition, except for fish food, which promoted Sphingobacterium dominance. Given the pivotal influence of diet addition during the larval stage on Ae. aegypti microbiota and life traits, rearing conditions should be carefully chosen according to the goals of the research (i.e., vectorial capacity estimations) or vector control intervention.IMPORTANCEAedes aegypti is the main vector of arbovirus, such as dengue, yellow fever, and chikungunya viruses. Vector research and control are primarily carried out in laboratories, with larval stage rearing conducted using commercial diet. If many nutrients are essential for Ae. aegypti development, gaining insight into the influence of these diets and their nutrient levels is important to promote optimized rearing worldwide. In this study, our results indicated a significant impact of commercial diet on Ae. aegypti development, lifespan, size, and microbiota related to contrasted protein, lipid, and carbohydrate levels in these diets. This study will help people working with Ae. aegypti raise awareness in staff working with Ae. aegypti to select optimized diets for their specific purpose.}, }
@article {pmid41210076, year = {2025}, author = {Bayer, B and Kitzinger, K and Paul, NL and Albers, JB and Saito, MA and Wagner, M and Carlson, CA and Santoro, AE}, title = {Minor contribution of ammonia oxidizers to inorganic carbon fixation in the ocean.}, journal = {Nature geoscience}, volume = {18}, number = {11}, pages = {1144-1151}, pmid = {41210076}, issn = {1752-0894}, abstract = {Ammonia-oxidizing archaea are the most abundant chemolithoautotrophs in the ocean and are assumed to dominate carbon fixation below the sunlit surface layer. However, the supply of reduced nitrogen delivered from the surface in sinking particulate organic matter is insufficient to support the amount of nitrification required to sustain measured carbon fixation rates in the dark ocean. Here we attempt to reconcile this observed discrepancy by quantifying the contribution of ammonia oxidizers to dark carbon fixation in the eastern tropical and subtropical Pacific Ocean. We used phenylacetylene-a specific inhibitor of the ammonia monooxygenase enzyme-to selectively inhibit ammonia oxidizers in samples collected throughout the water column (60-600 m depth). We show that, despite their high abundances, ammonia oxidizers contribute only a small fraction to dark carbon fixation, accounting for 4-25% of the total depth-integrated rates in the eastern tropical Pacific. The highest contributions were observed within the upper mesopelagic zone (120-175 m depth), where ammonia oxidation could account for ~50% of dark carbon fixation at some stations. Our results challenge the current view that carbon fixation in the dark ocean is primarily sustained by nitrification and suggest that other microbial metabolisms, including heterotrophy, might play a larger role than previously assumed.}, }
@article {pmid41209725, year = {2025}, author = {Wang, F and Li, S and Li, P and Feng, C and Zhao, Z and Yang, Y and Han, F and Xue, A and Li, Z and Han, P}, title = {The assembly processes and network characteristics of bacterial, fungal and archaeal communities in the middle Yangtze River and river-connected lakes.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1701799}, pmid = {41209725}, issn = {1664-302X}, abstract = {Despite the crucial ecological roles of bacterial, fungal and archaeal communities in rivers and lakes, their interactions and dynamic changes in large, hydrologically-connected river-lake systems remain poorly understood. This study investigated the biogeographic patterns, assembly processes and co-occurrence network characteristics of bacterial, fungal and archaeal communities in the middle reaches of Yangtze River (MYR) and its two largest connected lakes, Dongting Lake (DTL) and Poyang Lake (PYL). Our results revealed significant spatial heterogeneity in microbial diversity and composition, with higher sedimentary microbial diversity in lakes than in the river. Stochastic processes, particularly dispersal limitation, dominated community assembly across all habitats. β-NRI analysis showed that deterministic processes were more influential for planktonic bacterial and archaeal communities in the lakes. Co-occurrence network analysis demonstrated that inter-domain cooperation was prevalent in PYL, whereas intra-domain interactions were more common in MYR and DTL, reflecting distinct hydrological connectivity. Keystone taxa differed between rivers and lakes, with rare taxa prevailing in MYR and both rare and abundant taxa contributing in lakes. Our findings highlight how connectivity and flow dynamics fundamentally shape microbial ecology, providing insights into for the management and conservation of large river-lake ecosystems.}, }
@article {pmid41207985, year = {2025}, author = {Mei, J and Li, L and Ma, ZS}, title = {Unraveling the Ecological Mechanisms Influencing the Structure and Composition of Lung Cancer Microbiomes.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {119}, pmid = {41207985}, issn = {1432-184X}, abstract = {This study investigates the ecological mechanisms governing the structure and composition of lung microbiome communities within tumor tissue from lung cancer patients. While this field has attracted increasing research attention, the ecological and etiological mechanisms driving microbial community assembly in this environment remain poorly characterized. To address this gap, we applied Sloan's near neutral model, Ning et al.'s normalized stochasticity ratio framework and Harris et al.'s multi-site neutral model to evaluate the influences of stochastic and deterministic factors at species, community and metacommunity levels, respectively. Our findings include: (i) Stochastic drift exhibited predominant influence at both species and community levels in normal adjacent tissue (NT), exceeding its effects in LUAD (lung adenocarcinoma) and LUSC (lung squamous cell carcinoma). (ii) At the metacommunity level, neutrality was not rejected at the metacommunity or local community levels, which is consistent with the previous finding (i). (iii) Elevated metacommunity biodiversity (θ) and immigration rates (m) in LUAD/LUSC compared to NT (observed in ∼50% of cases) suggest that tumor occurrence/progression may actively promote microbial recruitment to tumor microenvironments. We propose three non-exclusive mechanistic interpretations: (i) Tumor-mediated immune modulation creates permissive ecological niches; (ii) structural remodeling of tissue enhances microbial colonization potential; (iii) selective enrichment of opportunistic taxa (e.g., Streptococcus) through tumor-specific microenvironmental changes. Our results demonstrate that LUAD and LUSC microbiomes are shaped by deterministic tumor-driven selection, in contrast to the predominantly stochastic assembly observed in NT microbiomes. These findings reveal substantial reorganization of tumor-associated microbial communities, warranting further biomedical investigation and clinical validation.}, }
@article {pmid41207977, year = {2025}, author = {Oliveira-Pinto, PR and Oliveira-Fernandes, J and Gramaje, D and Santos, C}, title = {Metabarcoding Profiling Reveals Microbiome Structure and Predicts Functional Shifts in Grapevines Challenged by Phyllosticta ampelicida.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {120}, pmid = {41207977}, issn = {1432-184X}, abstract = {Black rot disease (BRD), caused by the still understudied Phyllosticta ampelicida, is spreading across several grape producing countries, posing a growing threat to the agroindustry. The role of the grapevine microbiome in defending against this pathogen, particularly in terms of microbiota structure and community homeostasis, remains unclear. In this study, we aimed to characterize the epiphytic phyllosphere microbiota of grapevines and identify shifts in microbial genetic structure associated with BRD symptoms. We sampled three vineyards of the cultivar "Touriga Nacional" in the Douro region (Portugal), collecting 20 leaves from (a) five healthy and (b) five BRD-symptomatic grapevines. The presence of P. ampelicida was confirmed in all symptomatic samples. Epiphytic bacterial DNA was extracted and sequenced using next-generation sequencing (NGS). Results indicate that although overall the diversity and richness indexes were not different in diseased plants compared to healthy ones, there was a reduction in OTU richness in black rot-affected grapevines. Diseased plants exhibited significant shifts in microbial network assemblages and showed an increased relative abundance of certain taxa, such as Acinetobacter, suggesting a possible recruitment of beneficial bacteria in response to biotic stress. Additionally, we observed a higher abundance of antibiotic resistance-related KEGG Orthologues (KOS) in symptomatic plants, raising potential concerns for human health. This study presents the first characterization of the grapevine phyllosphere epiphytic bacterial microbiota and its structural shifts in response to BRD.}, }
@article {pmid41206559, year = {2025}, author = {Fournier, P and Pellan, L and Aubert, J and This, P and Vacher, C}, title = {A new scenario of pathogen-microbiota interactions involving the oomycete Plasmopara viticola.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf111}, pmid = {41206559}, issn = {1574-6941}, abstract = {A key question in microbial ecology is how the microbiota regulates host invasion by pathogens. Several ecological theories link the diversity, abundance and assembly processes of the microbiota with its resistance to invasion, but the specific properties of microbial communities that confer protection to the host are poorly understood. We addressed this question for the oomycete Plasmopara viticola, the causal agent of grapevine downy mildew. Using state-of-the-art microbial ecology methods, we compared microbial communities associated with asymptomatic and symptomatic leaf tissues to elucidate pathogen-microbiota interactions. Despite visible symptoms, P. viticola infection induced only subtle changes in microbial community composition. Symptomatic tissues showed enrichment in basidiomycete yeasts and Bacillus species, both known for their biocontrol activity, and exhibited a higher degree of determinism in community assembly processes. Asymptomatic tissues hosted more diverse microbiota, but lacked consistent associations with known biocontrol agents. Instead, they were often associated with other airborne grapevine pathogens. These findings suggest a novel interaction scenario: upon infection, P. viticola reshapes locally the leaf microbiota, excluding other pathogens and selecting for beneficial microbes. Although further studies are needed to uncover the underlying mechanisms, these findings underscore the relevance of targeting disease lesions in the search for protective microbial consortia.}, }
@article {pmid41204663, year = {2025}, author = {Budziak, M and Ilicic, D and Grossart, HP and Krztoń, W and Walusiak, E and Fyda, J and Wilk-Woźniak, E}, title = {Phytoplankton Under Pressure: Temperature, Precipitation and Cyanobacterial Blooms as Drivers of Chytrid Infections.}, journal = {Environmental microbiology reports}, volume = {17}, number = {6}, pages = {e70224}, doi = {10.1111/1758-2229.70224}, pmid = {41204663}, issn = {1758-2229}, support = {Statutory funds//Institute of Nature Conservation Polish Academy of Sciences/ ; GR 1540/48-1//German Research Foundation (DFG)/ ; COST Action ParAqua CA20125//European Cooperation in Science and Technology/ ; life17 env/lt/000407//European Union (EU) Life programme/ ; }, mesh = {Temperature ; *Cyanobacteria/growth &amp; development ; *Phytoplankton/microbiology/growth &amp; development ; Seasons ; Fresh Water/microbiology ; Ecosystem ; Rain ; Diatoms/microbiology ; *Chytridiomycota/isolation &amp; purification ; Chlorophyta/microbiology ; Eutrophication ; }, abstract = {The area of fungal parasitism is attracting growing attention because of its great importance for aquatic organisms and their community dynamics. Despite increasing interest in this area, few studies have addressed baseline data on occurrence and environmental factors associated with chytrid parasite infections in natural ecosystems. This work provides insights into occurrence, prevalence, and dynamics of parasitic infections by studying three freshwater reservoirs over a period of 6 years. Chytrid infections were detected in each of the studied water bodies, infecting species of cyanobacteria, green algae and diatoms. However, recurring and prevalent infections were observed in only one water body, which is classified as a natural aquatic ecosystem. The recorded infection prevalence (IPC) ranged between 0% and 20%, while the mean infection severity remained low. Infection rates were highest in summer and most prominent during cyanobacterial blooms. Yet, the most infected group of phytoplankton consisted of green algae. GLM revealed a significantly positive correlation between IPC and water temperature and precipitation. Overall, these results demonstrate the dynamic nature of chytrid infections, which are shaped by multiple environmental factors across space and time.}, }
@article {pmid41204024, year = {2025}, author = {Mileng, K and Mani, S and Bezuidenhout, JJ and Mokgokong, PS and Ramatla, TA and Thekisoe, OMM and Lekota, KE}, title = {Bacterial Communities Harboured by Amblyomma Hebraeum Infesting Small Stock in Mahikeng city, South Africa.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {118}, pmid = {41204024}, issn = {1432-184X}, support = {GUN: CSUR23030681021//National Research Foundation/ ; }, mesh = {Animals ; South Africa ; *Bacteria/classification/genetics/isolation &amp; purification ; Goats/parasitology/microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Sheep/parasitology ; *Amblyomma/microbiology ; *Tick Infestations/veterinary/parasitology/epidemiology ; *Goat Diseases/parasitology/microbiology/epidemiology ; Phylogeny ; *Sheep Diseases/parasitology/microbiology/epidemiology ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; }, abstract = {Ticks are important vectors of pathogens affecting livestock productivity and public health, yet their bacterial communities remain poorly characterized in many parts of South Africa. This study investigated the bacterial diversity and potential pathogenic bacterial etiology associated with Amblyomma hebraeum ticks collected from sheep and goats in Mahikeng, North West province. A total of 168 adult ticks were sampled across four villages. Microbiome profiling was performed using high-throughput sequencing of the V3-V4 hypervariable regions of the 16S rRNA gene on the Illumina MiSeq platform. High-throughput 16S rRNA sequencing revealed 16,193 ASVs in goat-derived ticks and 16,510 ASVs in those from sheep. Proteobacteria emerged as the dominant phylum across all samples, with ticks collected from goats showing a particularly high dominance of Rickettsia spp. (51.64% relative abundance), suggesting potential zoonotic risks. In contrast, ticks from sheep harboured significantly more diverse and evenly distributed bacterial communities, as indicated by Shannon (p = 0.0138) and Simpson (p = 0.0233) diversity indices, despite comparable species richness. A core microbiome comprising 1,374 ASVs (32.3%) was shared across all ticks, alongside 1,504 and 1,372 unique ASVs in goat- and sheep-derived ticks, respectively. Notably, several medically and veterinary-relevant genera, including Coxiella, Ehrlichia, Staphylococcus, Bacillus, Acinetobacter, Corynebacterium, and Streptococcus, were detected across both host groups. While total species richness was comparable between hosts, alpha diversity indices that account for evenness revealed host-based differences, and beta diversity patterns further showed clear separation of bacterial communities by host species. This study indicates that the host plays a crucial role as an ecological driver affecting the diversity of microbial communities associated with ticks. This study improves our understanding of the diversity, composition, and abundance of tick-associated microbiomes and pathogens in South African small ruminants. These insights support the development of microbiome-targeted strategies for detecting and controlling tick-borne diseases.}, }
@article {pmid41203821, year = {2025}, author = {Young, JD and Pinnell, LJ and Wolfe, CA and Scott, MA and Lawrence, TE and Cavasin, JP and Ellis, JA and Langsten, KL and Richeson, JT and Morley, PS}, title = {Microbial communities and tight junction protein expression in the gastrointestinal tract of feedlot cattle.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {39055}, pmid = {41203821}, issn = {2045-2322}, mesh = {Animals ; Cattle ; *Tight Junction Proteins/metabolism/genetics ; *Gastrointestinal Microbiome ; *Gastrointestinal Tract/microbiology/metabolism ; RNA, Ribosomal, 16S/genetics ; Rumen/microbiology/metabolism ; Male ; Tight Junctions/metabolism ; Bacteria/genetics/classification ; }, abstract = {The gastrointestinal tract (GIT) of cattle plays a vital role in nutrient absorption, immune function, and microbial homeostasis. While the importance of the GIT microbiome and epithelial barrier integrity has been increasingly recognized, the typical composition of microbial communities and the expression of tight junction proteins (TJPs) in feedlot cattle remains poorly characterized. We investigated microbial community structure and TJP expression at three GIT sites: the rumen (RU), small intestine (SI), and large intestine (LI) in 21 finish-fed feedlot steers sourced from 21 commercial feedyards in the Texas Panhandle. Samples of luminal contents and GIT tissue were collected from each region, as well as feces and liver abscess material. Microbial communities were characterized using 16S rRNA gene sequencing. TJP gene expression was quantified by RT-qPCR using synthetic standards, and protein expression was evaluated by immunohistochemistry (IHC) with both computer-generated and pathologist-generated scoring. Microbial community structures varied primarily by GIT region rather than by individual animals raised at different locations. Nine bacterial families were identified as core microbiome members, with Lachnospiraceae being the most abundant across the GIT. TJP gene expression varied considerably by site, with RU having significantly lower Claudin 1, Claudin 2, and E-Cadherin expression than the SI and LI. IHC results paralleled qPCR findings, with region-specific patterns of protein localization and intensity. Computerized and pathologist-generated H-scores showed moderate agreement but differed notably between epithelial and lamina propria regions. This study provides a comprehensive baseline of microbial and host factors associated with gut health in a uniquely diverse population of feedlot cattle. The identification of regional microbial communities and distinct TJP expression patterns offers foundational insights into gastrointestinal physiology and barrier function. This work establishes baseline data to support future investigations into the relationships among microbial ecology, epithelial barrier function, and cattle health and productivity.}, }
@article {pmid41202998, year = {2025}, author = {Kuang, B and Yang, W and Li, C and Lee, CW and Liu, BY and Bong, CW and Wang, W and Chen, S}, title = {Long-Term Oral Administration of Inactivated Vibrio harveyi Vaccine Triggers Immunosuppression in Penaeus vannamei.}, journal = {Fish &amp; shellfish immunology}, volume = {}, number = {}, pages = {110983}, doi = {10.1016/j.fsi.2025.110983}, pmid = {41202998}, issn = {1095-9947}, abstract = {This study investigated optimal oral vaccination strategies to enhance Vibrio resistance in Penaeus vannamei by comparing two feeding regimens: continuous administration of inactivated Vibrio harveyi (IVH) (CF group) and intermittent IVH feeding (7-day IVH followed by 7-day commercial feed, IF group). Results demonstrated that 7-day IVH feeding effectively induced anti-Vibrio immunity. The IF group maintained >60% relative percent survival (RPS) during challenge tests at 14, 21 and 28 days post-immunization, whereas the CF group exhibited a sharp RPS decline to -22.73% at day 14, with persistently low values thereafter. Specific growth rates were significantly reduced in the CF group compared to controls. Immune enzymatic activity analysis at day 14 revealed sustained high levels in the IF group but marked declines in the CF group. Histopathological examination confirmed severe cellular necrosis in intestinal and hepatopancreatic tissues of the CF group at day 14. Gut microbiota analysis indicated comparable dominant taxa between groups at day 14, while the IF group exhibited higher proportions of Ruegeria genera. Proteomic profiling identified distinct expression patterns between groups, with the CF group displaying significant downregulation of proteins associated with energy metabolism, immune responses, metabolic pathways, and cell/tissue maintenance. These data demonstrated that continuous IVH feeding elicited substantial physiological stress, leading to cellular and tissue damage and consequent immunosuppression in P. vannamei, whereas intermittent feeding mitigated immune impairment and conferred V. harveyi resistance. This study highlights the critical need for temporally optimized vaccination protocols in shrimp aquaculture.}, }
@article {pmid41202458, year = {2025}, author = {Biswas, A and Saini, N and Chivukula, N and Samal, A and Jansari, MR and Bhadury, P and Darbha, GK}, title = {The dawn of a new air pollutant: inhalable microplastics as emerging vectors of hazardous contaminants and their implications for human health.}, journal = {Environment international}, volume = {205}, number = {}, pages = {109897}, doi = {10.1016/j.envint.2025.109897}, pmid = {41202458}, issn = {1873-6750}, abstract = {This study presents the first comprehensive research on inhalable microplastics (iMPs, <10 μm), a notorious subset of airborne microplastics (AMPs). To identify human health risk, ambient iMPs concentrations were assessed at human breathing height across the markets of four major Indian cities. With winter evening being the highest iMPs concentration, in Kolkata (14.23 µg/m[3]), followed by Delhi (14.18 µg/m[3]), linked to the highest footfalls, use of synthetic clothing, and poor waste management. Coastal cities (Chennai: 4 µg/m[3], and Mumbai: 2.65 µg/m[3]) showed lower levels, likely due to improved air circulation, less winter, and reduced apparel, confirmed by Principal Component Analysis. Py-GC-MS quantified 11 polymers, with PET (Polyester) from textiles as the most abundant, followed by PE and SBR from single-use plastics, packaging, vehicles, and footwear. Urban areas in India show an average iMPs concentration of 8.8 µg/m[3], translating to a lifetime lung load of ∼2.9 g/person. Furthermore, this investigation highlights the risks of iMPs-associated tracers such as diethyl phthalates and lead. This pioneering research is the first-ever study to explore AMPs carrier capabilities for ultrafine particulate matter, PTEs, POPs, PPCPs, and microbes. During peak exposure periods like autumn festivals, AMPs harbored diverse microbial communities, including pathogenic (Aspergillus fumigatus) and new strains of bacteria/fungi with antibiotic resistance and virulence factor genes. This suggests that microbes carried by iMPs possess enhanced pathogenicity and resistance against broad-spectrum drugs like tetracycline and are more likely to be multidrug-resistant. Cross-referencing toxicological databases revealed that exposure to AMPs-linked modern-day contaminants elevates the risk of cancer, gastrointestinal, endocrine, breast, and respiratory diseases.}, }
@article {pmid41201519, year = {2025}, author = {López-Sandoval, DC and Fernández-González, C and González-García, C and Marañón, E}, title = {Warming Accelerates Phytoplankton Bloom Dynamics and Differentially Affects the Fluxes of Carbon, Nitrogen, and Oxygen Through a Coastal Microbial Community.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {117}, pmid = {41201519}, issn = {1432-184X}, support = {Project POLARIS (PGC2018-094553-B-I00)//Spanish Ministry of Science and Innovation/ ; }, mesh = {*Nitrogen/metabolism ; *Carbon/metabolism ; *Phytoplankton/growth &amp; development/metabolism ; *Oxygen/metabolism ; *Microbiota/physiology ; Seawater/microbiology/chemistry ; Biomass ; *Eutrophication ; Carbon Cycle ; Ecosystem ; Global Warming ; Hot Temperature ; }, abstract = {Marine heatwaves affect the abundance and community structure of microbial plankton, with implications for food web and ecosystem processes, but their impact on microbially mediated elemental cycling remains poorly constrained. To determine the biogeochemical effects of increased temperature, we conducted an experiment in September 2023 in which a plankton community from a coastal, productive ecosystem (Ría de Vigo, NW Iberia) was exposed to a warming of + 2 °C and + 4 °C under unamended and nutrient-enriched conditions. The response of microbial plankton was characterized in terms of organic matter production, carbon fixation, nitrogen uptake, and oxygen net production. We found that warming caused increased nutrient consumption and biomass production, as well as faster bloom dynamics, both in unamended and nutrient-enriched treatments, indicating that the community was robust to thermal perturbation. Accelerated nutrient depletion under warming gave way to an earlier decrease in carbon fixation and nitrate uptake rates, together with a shift towards a negative or less positive metabolic balance. Carbon fixation was less sensitive than nitrate uptake to the different temperature and nutrient scenarios, leading to wide changes in the carbon-to-nitrogen uptake ratio, while respiration increased non-linearly with temperature. Overall, the investigated microbial fluxes were more responsive to nutrient availability than to temperature. Our results show that microbially driven ecosystem services in coastal waters have the potential to be enhanced during short-term warming events.}, }
@article {pmid41199522, year = {2025}, author = {Chen, HJ and Liu, Y and Zhong, YS and Li, MZ and Lai, JJ and Luo, YY and Huang, SL and Liu, SQ and Yu, GH and Sun, YH and Shao, MW}, title = {Modulating Surfactin Biosynthesis in Bacillus subtilis R31 Enhances Behavioural Traits and Biocontrol Efficacy Against Banana Fusarium Wilt.}, journal = {Microbial biotechnology}, volume = {18}, number = {11}, pages = {e70261}, doi = {10.1111/1751-7915.70261}, pmid = {41199522}, issn = {1751-7915}, support = {202206010083//Guangzhou Municipal Science and Technology Project/ ; 2021ZDJS002//Guangdong Province Key Discipline Research Capacity Enhancement Project/ ; 32302450//National Natural Science Foundation of China/ ; 22-035-31-23KF03//Guangxi Key Laboratory of Crop Pest Biology Foundation/ ; 2023B0202010012//Guangdong Province Key Area Research and Development Program/ ; }, mesh = {*Fusarium/growth &amp; development/drug effects/physiology ; *Bacillus subtilis/genetics/metabolism/physiology ; *Plant Diseases/microbiology/prevention &amp; control ; *Musa/microbiology ; *Lipopeptides/biosynthesis/pharmacology ; *Peptides, Cyclic/biosynthesis ; RNA, Ribosomal, 16S/genetics ; Metabolic Engineering ; Quorum Sensing ; Rhizosphere ; Biofilms/growth &amp; development ; Bacterial Proteins/genetics/metabolism ; DNA, Ribosomal/chemistry/genetics ; }, abstract = {Surfactin, a lipopeptide antibiotic and quorum-sensing (QS) mediator from Bacillus subtilis, has dual functions in microbial ecology and plant disease suppression. This study engineered B. subtilis R31 to overproduce comK and phrC, key regulators of surfactin biosynthesis, increasing surfactin yield by 45% compared to the WT strain. While elevated surfactin enhanced antimicrobial potential, comK-mediated overproduction impaired biofilm formation and swarming motility, but rhizosphere colonisation was mostly unaffected. 16S rRNA sequencing of banana rhizospheres showed that surfactin selectively shaped the microbial community by enriching beneficial Bacillus species. Mechanistic studies confirmed surfactin's dual role as an antimicrobial and an intercellular signalling molecule for coordinated development in Bacillus populations. These results reveal the molecular mechanisms of R31-mediated suppression of banana Fusarium wilt and offer a strategy for engineering synthetic microbial consortia by manipulating metabolic signalling pathways.}, }
@article {pmid41197919, year = {2025}, author = {Mohit,  and Verma, S and Venkatesh, V and Nityanand, S}, title = {Immuno-Microbial Crosstalk in Aplastic Anemia: Role of Gut and Viral Triggers.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {108158}, doi = {10.1016/j.micpath.2025.108158}, pmid = {41197919}, issn = {1096-1208}, abstract = {Aplastic anemia (AA) is a rare but life-threatening hematological disorder, manifested in bone marrow failure and pancytopenia, which occurs worldwide due to the preferential immune mediated destruction of hematopoietic stem and progenitor cells. Despite the autoimmune etiology of AA, recent findings emphasize the key role of microbial and viral factors in the pathogenesis of AA by driving the host immune dysregulation. We delve into the immune-microbial crosstalk that is relevant in AA pathogenesis to provide novel insights related to gut microbial ecology, microbial metabolites, viral infections mediated inflammation and cytotoxicity against bone marrow components. Additionally, providing the roadmap of current knowledge for immune-mediated bone marrow failure focusing on activated cytotoxic T cells, altered regulatory T cells and proinflammatory cytokines. Imbalanced immune activation via defects in gut barrier function which promotes pathogen-associated molecular patterns (PAMPs) signaling through Toll-like receptors (TLRs) and other innate sensors. Considering the role of viral trigger such as Parvovirus B19, Epstein-Barr and Hepatitis as inducers of dysregulated immunity and their ability to affect antigen presentation, T cell receptor repertoires, and interferon pathways. We also delineate the potential of targeting the gut-immune axis for personalized AA therapy, including potential microbiome-directed interventions, antiviral and anti-cytokine approaches, as promising complement lines for standard immunosuppression therapy in AA. This cited approach will provide the advanced and novel clinical paradigm for the interconnected immune-microbial signals in pathogenesis of AA which promotes the host immune surveillance and also lead to precision medicine in AA treatment.}, }
@article {pmid41197741, year = {2025}, author = {Chen, Y and Chen, Y and Hu, C and Xing, X and Zhang, S and Zeng, K and Yin, Z and Meng, C and Situ, F and Li, J and Chen, C and Ma, K and Chen, J and Li, F}, title = {Simultaneous control of disinfection by-products, opportunistic pathogens, and antibiotic resistance genes in drinking water based on a novel advanced treatment process consisting of Fenton-like reaction and biological activated carbon.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133602}, doi = {10.1016/j.biortech.2025.133602}, pmid = {41197741}, issn = {1873-2976}, abstract = {Disinfection by-products (DBPs), opportunistic pathogens (OPs), and antibiotic resistance genes (ARGs) are typical drinking water quality risks today, and the synchronous control of these factors has always been an important challenge. Herein, a novel drinking water treatment process (Fe3C-NC/PMS-BAC) consisting of Fe3C-NC Fenton-like reaction and biological activated carbon (BAC) was established in this study. Fe3C-NC/PMS caused the decomposition of high molecular weight organic matter into low molecular weight organic matter, which was efficiently biodegraded in the subsequent BAC biofilter (PBAC). In addition, the suspended extracellular polymeric substances (EPS) in the effluent of PBAC contained only a small amount of polysaccharides, markedly weakening the biofilm stability and its protective effect against OPs. The changes in organic matter and EPS ultimately led to the reduction of DBPs precursors. More importantly, the Fe3C-NC/PMS treatment remarkably changed the microbial ecology in subsequent PBAC, including shaping the microbial community, regulating EPS characteristics, weakening quorum sensing, and even inhibiting microbial activities, contributing to the inhibition of horizontal gene transfer of ARGs. Therefore, the Fe3C-NC/PMS-BAC is a promising alternative to BAC treatment for future applications, providing new ideas for the collaborative removal of chemical and microbial water quality risks in drinking water.}, }
@article {pmid41194431, year = {2025}, author = {Truant, A and Giacometti, F and Losasso, C and Peruzzo, A and Petrin, S and Zancato, I and Di Leva, V and Giaccone, V}, title = {First Metataxonomic Characterisation of Gut Microbiota of Swordfish (Xiphias gladius).}, journal = {Environmental microbiology reports}, volume = {17}, number = {6}, pages = {e70199}, doi = {10.1111/1758-2229.70199}, pmid = {41194431}, issn = {1758-2229}, mesh = {Animals ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Perciformes/microbiology ; Phylogeny ; *Fishes/microbiology ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Biodiversity ; }, abstract = {Swordfish (Xiphias gladius) is a large, migratory apex predator with a carnivorous diet, occupying a top position in the marine food chain. Although it is a valuable teleost pelagic fish with a significant commercial value, its gut microbiota has never been studied. The gut microbiota of 100 individuals was characterised by sequencing the V3-V4 region of the bacterial 16S rRNA gene. Gut microbiota findings were classified with consideration to diversity, taking into account their weight (10-20; 21-30; over 31 kg) and the FAO fishing areas in which they were caught (FAO 27, 34, 37.1.1 areas). Significant differences in the alpha diversity were observed among the weight categories for all metrics examined (except for the evenness index) and only by Shannon's index among the FAO fishing areas. Beta-diversity analysis revealed no significant differences. The phylum Pseudomonadota dominated the swordfish gut microbiota, followed by Fusobacteriota. Photobacterium was the most abundant genus across all weight categories and FAO fishing areas. Smaller fishes showed a less rich and diverse gut microbiota, dominated almost exclusively by Photobacterium. Conversely, Pseudoalteromonas, Psychrobacter, Psychrilyobacter, and Cetobacterium appeared to increase in abundance with fish weight. Although Photobacterium was dominant across the different FAO fishing areas, distinctive microbial community compositions were observed: Cetobacterium was more prevalent in FAO 27, while Pseudoalteromonas was more prevalent in the other areas. Unlike the gut microbiota of other marine fish species, Vibrio and Lactobacillus were largely absent. This study represents the first metataxonomic characterisation of the gut microbiota of swordfish using next-generation sequencing.}, }
@article {pmid41193960, year = {2025}, author = {Van Goethem, MW and Vikram, S and Cowan, DA and Makhalanyane, TP}, title = {Comparative genomics reveals adaptive traits in novel Antarctic lithic cyanobacteria.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {994}, pmid = {41193960}, issn = {1471-2164}, }
@article {pmid41193926, year = {2025}, author = {Wei, N and Nakaji-Conley, M and Tan, J}, title = {Contrasting Diversity and Network Dynamics of Soil Fungal Functional Groups in the Plant Rhizosphere.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {116}, pmid = {41193926}, issn = {1432-184X}, support = {2300058//Directorate for Biological Sciences/ ; 2300057//Directorate for Biological Sciences/ ; E455990101//Wuhan Botanical Garden, Chinese Academy of Sciences/ ; }, mesh = {*Rhizosphere ; *Soil Microbiology ; *Fungi/classification/genetics/isolation &amp; purification/physiology ; Mycorrhizae/genetics/classification/isolation &amp; purification ; *Biodiversity ; *Plants/microbiology ; Microbiota ; Soil/chemistry ; Plant Roots/microbiology ; }, abstract = {Soil microbiomes, critical for plant productivity and ecosystem functioning, mediate essential functions such as pathogenesis, mutualism, and decomposition through different fungal functional groups. Yet, our understanding of the dynamics of co-existing soil fungal functional groups in the rhizosphere remains limited. By leveraging urban farming-featuring fields of different ages and multiple genotypes-we tracked the relative abundance, richness, and microbial networks of putative plant pathogenic fungi, mycorrhizal fungi, and saprotrophic fungi across fields over two years. We observed an increase in the relative abundance of putative plant pathogenic fungi in the rhizosphere in older fields relative to younger fields, supporting the prediction of pathogen accumulation over time. In contrast, there was a decrease in the relative abundance of mycorrhizal fungi in older fields. The relative abundance of saprotrophic fungi remained similar between younger and older fields. While the richness of putative plant pathogenic fungi and saprotrophic fungi was similar across the examined fields, the community structure of both groups differed between younger and older fields. For mycorrhizal fungi, the richness declined in older fields and over the two years. These dynamics led to distinct microbial networks, with decreased network links for mycorrhizal fungi and increased links for saprotrophic fungi in older fields, whereas the links for plant pathogenic fungi remained similar across fields. Our study reveals contrasting dynamics of essential soil fungal functional groups in the rhizosphere and provides predictive insight into the potential shifts in soil function and their impact on plant productivity.}, }
@article {pmid41193719, year = {2025}, author = {Sugden, S and Davis, CL and Quinn, MW and Whyte, LG}, title = {Current and projected effects of climate change in cryosphere microbial ecosystems.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, pmid = {41193719}, issn = {1740-1534}, abstract = {Cold environments, including glaciers, ice sheets, permafrost soils and sea ice, are common across the surface of the Earth. Despite the challenges of life at subzero temperatures, the global cryosphere hosts diverse microbial communities that support biogeochemical cycling and ecosystem functioning in areas where few other organisms can survive. However, the composition and function of cryosphere microbial communities, and the continued existence of cryosphere habitats, are threatened by ongoing climate change, which has disproportionate impacts in polar regions. In this Review, we survey the breadth of cryosphere habitats and the composition, function and unique adaptations of the microbial communities that inhabit them. We outline how climate change can affect these communities and the ecosystem services they provide through short-term changes in substrate availability, enzyme activity and redox potentials as well as longer-term changes in community composition. We also explore the wide-ranging consequences these changes may have for local ecosystems, human communities and the global climate. Finally, we outline the knowledge gaps in cryosphere microbial ecology that contribute to uncertainties about the future of these ecosystems in a warming world.}, }
@article {pmid41192073, year = {2025}, author = {McDonagh, F and Kovarova, A and Tumeo, A and O'Connor, A and McEvoy, N and Lonappan, AM and Venkateswaran, K and Murray, EK and Hallahan, B and Miliotis, G}, title = {Complete genome and comparative genomic analysis of cefpodoxime resistant Pantoea septica strain GABEPS69 isolated from saliva of a patient diagnosed with treatment resistant schizophrenia.}, journal = {International journal of medical microbiology : IJMM}, volume = {321}, number = {}, pages = {151681}, doi = {10.1016/j.ijmm.2025.151681}, pmid = {41192073}, issn = {1618-0607}, abstract = {OBJECTIVES: This study aims to generate the first complete genome of Pantoea septica and provide a thorough genomic characterisation of this under-documented species. The study seeks to enhance understanding of P. septica, clarifying features relevant to opportunistic infection in vulnerable cohorts.<br><br>METHODS: P. septica GABEPS69 was an opportunistic coloniser isolated from the saliva of a patient prescribed the antipsychotic clozapine, leading to a dysbiotic oral microbiome. A hybrid sequencing approach yielded a closed genome comprising a 4.1&#x202f;Mb chromosome and six plasmids. Phenotypic susceptibility was determined by disk-diffusion and minimum inhibitory concentration (MIC) assays. Its chromosomal and plasmidic content was bioinformatically analysed alongside all canonical GenBank available P. septica genomes and the type strains of taxonomic neighbours Pantoea piersonii and "Pantoea latae", with focus on virulence-factors (VFs), antimicrobial-resistance-genes (ARGs), metal-resistance-genes (MRGs) and biosynthetic gene clusters.<br><br>RESULTS: GABEPS69 exhibited a narrow resistance spectrum, displaying resistance to the third-generation cephalosporin cefpodoxime. Plasmid pGABEPS69_1 harboured an aerobactin pathogenicity island homologue; a locus implicated in enhanced virulence, that was also identified across most other P. septica genomes and in the closely related human-pathogen Pantoea piersonii. A conserved chromosomal class-A &#x3b2;-lactamase homologue was also identified. Additionally, a universal presence of bioactive thiopeptide biosynthetic-gene-clusters was observed in P. septica genomes, suggesting a potential role in microbiome modulation.<br><br>CONCLUSION: This study presents a first complete genome of P. septica, revealing its genomic architecture, resistance, and virulence potential. Detailed plasmid analysis and comparative genomics enhance our understanding of the species clinical relevance and microbiome-modulating capacity. These findings motivate surveillance of transient oral microbiota in at-risk populations, including patients receiving clozapine.}, }
@article {pmid41191617, year = {2025}, author = {Rivas-Santisteban, J and Fernández-González, N and Laso-Pérez, R and Tamames, J and Pedrós-Alió, C}, title = {Picoplankton nitrogen guilds in the tropical and subtropical oceans: From the surface to the deep.}, journal = {PloS one}, volume = {20}, number = {11}, pages = {e0335222}, doi = {10.1371/journal.pone.0335222}, pmid = {41191617}, issn = {1932-6203}, mesh = {*Nitrogen/metabolism ; Oceans and Seas ; Ecosystem ; *Nitrogen Cycle ; Tropical Climate ; *Plankton/metabolism ; Seawater/microbiology ; *Phytoplankton/metabolism ; }, abstract = {Ecological guilds quantify the incidence and extent of resource transformation functions, irrespective of the species involved. Therefore, tackling the microbial nitrogen guilds is key to our understanding of the oceanic nitrogen cycle, but quantitative estimates of guild contribution across varying depths and under specific environmental conditions have yet to be accomplished. In this study, we examine the main picoplankton guilds participating in nitrogen cycling within the low and mid-latitude ocean ecosystems, from the surface down to 4000 m, using data obtained from 75 samples belonging to 11 stations in the Malaspina dataset. In particular, we used a quantitative approach to investigate the stability of nitrogen acquisition and nitrogen-redox guilds separately. Our results showed that nitrogen acquisition guilds are more stable and redundant than nitrogen-redox guilds across depths and site specific conditions. For example, differential conditions such as nitrogen depletion and oxygen availability affected the two groups of guilds in different ways. These findings have implications for the understanding of global nitrogen fluxes and the biosphere's functional diversification.}, }
@article {pmid41188621, year = {2025}, author = {Kwon, SL and Seo, CW and Kwon, H and Cho, M and Yoo, Y and Lee, SH and Kwon, DY and Lee, YM and Heo, YM and Kim, GH and Lim, YW and Lee, D and Choi, YS and Lee, H and Kim, JJ}, title = {Exploring Multifaceted Roles of Bambusicolous Apiospora in Phyllostachys bambusoides.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {115}, pmid = {41188621}, issn = {1432-184X}, support = {2021R1A2C1011894//National Research Foundation of Korea/ ; PN24120//Korea Polar Research Institute/ ; }, mesh = {*Endophytes/genetics/physiology/classification/isolation &amp; purification ; Symbiosis ; *Ascomycota/genetics/physiology/classification/isolation &amp; purification ; Plant Diseases/microbiology ; Mycobiome ; Soil Microbiology ; Phylogeny ; *Cyperaceae/microbiology ; Plant Roots/microbiology ; }, abstract = {Bamboo plays a crucial role in mitigating climate change. Among various microorganisms inhabiting bamboo, Apiospora is a common bambusicolous fungus that induces black spots, functioning either as a saprobe or as a plant pathogen. However, the diversity and ecological roles of Apiospora as an endophyte in bamboo remain poorly understood. This study explored the diversity and ecological functions of bambusicolous Apiospora in Phyllostachys bambusoides forests. Bamboo samples representing different stages-young (1-year-old, without black spots), mature (aged 3 years, few black spots), and dead (with many black spots)-were collected. Mycobiome analyses across different tissues (culm, leaf, root) and environmental samples (forest soil) revealed diverse Apiospora species throughout the bamboo lifecycle. Notably, Apiospora hysterina emerged as a prevalent endophyte, inhabiting not only mature but also younger, healthier bamboo stages. Biological activity assays, including antioxidant, antifungal, and plant hormone tests, indicated that A. hysterina exhibits potential mutualistic interactions beneficial to bamboo. Conversely, genomic analyses of carbohydrate-active enzyme profiles, effector/virulence factors, and putative biosynthetic gene clusters suggested potential pathogenic capabilities that may involve secondary metabolites, though functional validation is required. These findings reveal the widespread presence of Apiospora species as endophytes from the early to senescent bamboo stages, highlighting A. hysterina's dual capacity as a symbiont and pathogen. Our study underscores the complexity of bambusicolous Apiospora's ecological roles, emphasizing the need for further investigation into its interactions with bamboo ecosystems.}, }
@article {pmid41188517, year = {2025}, author = {Hettiarachchi, A and Tuerlings, T and Weekers, T and Marshall, L and Leclercq, N and Wood, TJ and Cejas, D and Gerard, M and Vereecken, NJ and Michez, D and Smagghe, G and Joossens, M and Vandamme, P}, title = {The Gut Microbial Community of Solitary Bees is Acquired through Host and Location Filtering.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {114}, pmid = {41188517}, issn = {1432-184X}, support = {3094785//Fonds Wetenschappelijk Onderzoek/ ; 3094785//Fonds De La Recherche Scientifique - FNRS/ ; }, mesh = {Animals ; Bees/microbiology/physiology ; *Gastrointestinal Microbiome ; *Fungi/classification/isolation &amp; purification/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Europe ; Biodiversity ; }, abstract = {Species traits and environmental conditions are among the many factors that shape bee communities. Their effective conservation is currently challenged due to global changes. The gut microbiome likely contributes to bee plasticity and resilience but is largely understudied in solitary bees. A stable core microbiome in social bees has been identified to be important for health and survival in changing environmental conditions, but knowledge on a host-specific core microbiome in solitary bees is very scarce. In the present study, we analyzed the gut bacterial and fungal communities of eight solitary bee species commonly found in apple orchards along a latitudinal gradient throughout Europe. We aimed to understand the intra- and interspecific variations in the gut microbial communities and the extent to which host species and local environment shape the solitary bee gut microbiota. The bacterial community showed strong host effects, with each bee species having a distinct core bacterial community that was mostly stable across locations. The fungal community was most strongly influenced by the local environment, while different environmental variables were responsible for the variation in bacterial and fungal communities. Our study demonstrated that the examined solitary bee species harbor a distinct microbial diversity and composition, which undergoes host- and location-specific filtering.}, }
@article {pmid41059692, year = {2025}, author = {Bedi de Silva, A and Polson, SW and Schvarcz, CR and Steward, GF and Edwards, KF}, title = {Genomic diversity and global distribution of four new prasinoviruses from the tropical north Pacific.}, journal = {Microbiology spectrum}, volume = {13}, number = {11}, pages = {e0258324}, pmid = {41059692}, issn = {2165-0497}, support = {1559356, 2129697, 1736030//National Science Foundation/ ; Investigator Award in Marine Microbial Ecology and Evolution//Simons Foundation/ ; }, mesh = {*Genome, Viral/genetics ; Phylogeny ; Pacific Ocean ; *Genetic Variation ; Phytoplankton/virology ; Seawater/virology ; *Chlorophyta/virology ; *Phycodnaviridae/genetics/classification/isolation &amp; purification ; *DNA Viruses/genetics/classification/isolation &amp; purification ; }, abstract = {Viruses that infect phytoplankton are an integral part of marine ecosystems, but the vast majority of viral diversity remains uncultivated. Here, we introduce four near-complete genomic assemblies of viruses that infect the widespread marine picoeukaryote Micromonas commoda, doubling the number of reported genomes of Micromonas dsDNA viruses. All host and virus isolates were obtained from tropical waters of the North Pacific, a first for viruses infecting green algae in the order Mamiellales. Genome length of the new isolates ranges from 205 to 212 kb, and phylogenetic analysis shows that all four are members of the genus Prasinovirus. Three of the viruses form a clade that is adjacent to previously sequenced Micromonas viruses, while the fourth virus is relatively divergent from previously sequenced prasinoviruses. We identified 61 putative genes not previously found in prasinovirus isolates, including a phosphate transporter and a potential apoptosis inhibitor novel to marine viruses. Forty-eight genes in the new viruses are also found in host genome(s) and may have been acquired through horizontal gene transfer. By analyzing the coding sequences of all published prasinoviruses, we found that ~25% of prasinovirus gene content is significantly correlated with host genus identity (i.e., Micromonas, Ostreococcus, or Bathycoccus), and the functions of these genes suggest that much of the viral life cycle is differentially adapted to the three host genera. Mapping of metagenomic reads from global survey data indicates that one of the new isolates, McV-SA1, is relatively common in multiple ocean basins.IMPORTANCEThe genomes analyzed here represent the first viruses from the tropical North Pacific that infect the abundant phytoplankton order Mamiellales. Comparing isolates from the same location demonstrates high genomic diversity among viruses that co-occur and presumably compete for hosts. Comparing all published prasinovirus genomes highlights gene functions that are likely associated with adaptation to different host genera. Metagenomic data indicate these viruses are globally distributed, and one of the novel isolates may be among the most abundant marine viruses.}, }
@article {pmid41187907, year = {2025}, author = {Marrec, L and Bank, C}, title = {Drivers of diversity within and between microbial communities during stochastic assembly.}, journal = {Journal of the Royal Society, Interface}, volume = {22}, number = {232}, pages = {20250329}, doi = {10.1098/rsif.2025.0329}, pmid = {41187907}, issn = {1742-5662}, support = {//HORIZON EUROPE European Innovation Council/ ; //Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, mesh = {*Microbiota/physiology ; *Models, Biological ; Stochastic Processes ; *Biodiversity ; }, abstract = {No two microbial communities share the same species richness and abundance profiles. Experiments have shown that the assembly of new microbial communities from the same environmental pool is sufficient to generate diversity within and between communities: when microbial dispersal is slower than division, communities exhibit low richness but high between-community dissimilarity; when dispersal is faster, richness increases while dissimilarity decreases. Here, we study a minimal stochastic model that recovers these empirically observed assembly regimes. Our mathematical framework yields explicit expressions for the abundance fluctuation distributions across low-, intermediate- and high-dispersal regimes, providing a quantitative lens on microbiome assembly. We derive analytical predictions for the bimodality coefficient that quantifies the transition between assembly regimes, which appears as a robust metric to predict community richness and dissimilarity. Additionally, we highlight the mean relative abundance as a complementary metric sensitive to differences in microbial traits (e.g. dispersal or division rates). Applying these metrics to experimental data indicates their practical value for the rapid identification of assembly regimes and trait asymmetries. Overall, our study provides general predictions about how stochasticity, timescales and microbial traits influence both within-community diversity (richness) and between-community diversity (dissimilarity) during the assembly of new microbial communities. Our work thus contributes to a better understanding of the factors driving variation in microbiome formation.}, }
@article {pmid41185310, year = {2025}, author = {Wu, S and Li, Y and Zhang, H and Pan, Y and Yang, H and Tan, Y}, title = {Microbial community reshaping: Calcium chloride-heat treatment synergy in fresh-cut jackfruit preservation via antagonistic yeast enrichment.}, journal = {Food research international (Ottawa, Ont.)}, volume = {221}, number = {Pt 4}, pages = {117558}, doi = {10.1016/j.foodres.2025.117558}, pmid = {41185310}, issn = {1873-7145}, mesh = {*Calcium Chloride/pharmacology ; *Food Preservation/methods ; *Hot Temperature ; *Food Microbiology/methods ; *Fruit/microbiology ; *Artocarpus/microbiology ; Penicillium/drug effects/growth &amp; development ; *Yeasts/drug effects/growth &amp; development ; Antibiosis ; }, abstract = {Fresh-cut jackfruit is highly susceptible to microbial contamination and rapid spoilage due to mechanical damage and its nutrient-rich substrate. We evaluated calcium chloride combined with heat treatment (CH, 2 % CaCl2 - 55 °C) for controlling spoilage and preservation of fresh-cut jackfruit. The results identified Gilbertella hainanensis, Penicillium kongii, and P. citrinum as the dominant spoilage fungi in fresh-cut jackfruit. CH inhibited these fungi with in vitro inhibition rates of 80.14 %, 43.75 %, and 52.94 %, and corresponding in vivo rates of 83.1 %, 77.9 %, and 83.7 %, respectively. In vitro assays indicated CH compromises fungal membrane integrity, causing leakage of cellular contents. Further analysis revealed that CH markedly increased the relative abundance of the antagonistic yeast Meyerozyma guilliermondii (42.82 %, 8.13-fold vs. control) and was associated with reduced relative abundance of plant pathogenic and saprotrophic fungi. Correlation analysis linked dominant yeast genera to higher total phenolic content and reduced weight loss and other quality deterioration. Overall, CH treatment effectively delayed spoilage and preserved fruit physicochemical and nutritional quality, likely via direct antifungal effects and beneficial reshaping of the surface microbiome. These findings advance understanding of jackfruit postharvest microbial ecology and CH as a promising preservation strategy for fresh-cut jackfruit fruit.}, }
@article {pmid41184333, year = {2025}, author = {Ghosh, A and Maile, A and Nagarajaram, HA}, title = {Prokaryotic co-occurrence patterns in diverse Indian mangrove ecosystems.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {38283}, pmid = {41184333}, issn = {2045-2322}, mesh = {India ; *Wetlands ; Biodiversity ; *Bacteria/genetics/classification/isolation &amp; purification ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Ecosystem ; Phylogeny ; Soil Microbiology ; }, abstract = {Mangrove ecosystems are unique coastal zones known to harbour a rich biodiversity of flora and fauna, including microbial communities. These microorganisms play a crucial role in nutrient cycling and sustain the primary productivity driven by plants within this ecosystem. Recent advancements in microbial ecology research emphasise that microbial community structure and composition are critical for an ecosystem to thrive. Studies have focused on the microbial diversity within Indian mangrove forests; however, there is a limited understanding of the co-occurrence patterns and functional roles of microbial communities in these ecosystems. This study explores prokaryotic diversity, primarily focusing on community interactions across three major Indian mangrove forests: the Bhitarkanika mangrove forest in Odisha, the Goan mangroves, and the Sundarbans in West Bengal. By analysing the publicly available 16 S rRNA amplicon datasets of the Indian mangrove microbiomes and performing co-occurrence network analysis on these datasets, we identified positively correlated genera and their predicted functional roles. Furthermore, the findings revealed the co-occurrence of several pathogenic bacteria in two of the mangrove ecosystems. Overall, our study highlights the shared functional roles adopted by co-occurring microbes in three major Indian mangrove ecosystems and suggests the need for large-scale studies in these understudied Indian ecosystems.}, }
@article {pmid41183683, year = {2025}, author = {Ali, S and Burke, LP and Fitzpatrick, F and Fitzgerald-Hughes, D}, title = {A Scoping Review of Disinfection Strategies for Carbapenemase-Producing Enterobacterales (CPE) in Hospital Water Systems.}, journal = {The Journal of hospital infection}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jhin.2025.10.021}, pmid = {41183683}, issn = {1532-2939}, abstract = {BACKGROUND: Carbapenemase-producing Enterobacterales (CPE) pose a global health crisis. Their resistance to conventional antimicrobials and many disinfectants, increases the healthcare costs of treatment and risk mitigation. Hospital water systems are reservoirs for CPE, necessitating targeted infection prevention and control (IPC) strategies.<br><br>OBJECTIVE: To review and consolidate current evidence of disinfection strategies for CPE in hospital water systems, focusing on practical application, challenges and IPC integration.<br><br>METHODOLOGY: A scoping review was conducted following PRISMA guidelines, encompassing studies from 1[st] December 2014 to 31[st] December 2024. Of 1,188 records screened, 22 met inclusion criteria. Thematic analysis categorised findings into chemical, physical and integrative strategies.<br><br>KEY FINDINGS: Sodium hypochlorite and hydrogen peroxide reduced contamination temporarily but were poorly effective against biofilms, while acetic acid showed consistent efficacy with regular use. Quaternary ammonium compounds proved effective but required standardised protocols. Physical interventions, such as steam cleaning and drain covers, reduced contamination; and plumbing modifications minimised biofilm formation. Resource-intensive measures, like removing contaminated sinks or adopting water-free environments were also effective. Integrative approaches combining chemical disinfection, infrastructural upgrades and enhanced sink protocols demonstrated the most sustained outcomes, with novel technologies like UV light and biofilm-targeting foams showing great promise.<br><br>CONCLUSION: Effective CPE control in hospital water systems requires multidisciplinary action addressing biofilm-protected reservoirs. Regular application of proven disinfectants, tailored to specific contexts, coupled with infrastructural upgrades and comprehensively implemented IPC strategies, offers the most promising outcomes. Novel technologies and updated guidelines are essential to standardising practices and mitigating the broader threat of antimicrobial resistance.}, }
@article {pmid41180493, year = {2025}, author = {Choi, JM and Wu, X and Zhang, L}, title = {FastST: an efficient tool for inferring decomposition and directionality of microbial communities.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e20161}, pmid = {41180493}, issn = {2167-8359}, mesh = {*Microbiota ; Humans ; Bayes Theorem ; Computer Simulation ; *Software ; *Computational Biology/methods ; }, abstract = {Microbiomes play crucial roles in human health, disease development, and global ecosystem functioning. Understanding the origins, movements, and compositions of microbial communities is essential for unraveling the principles governing microbial ecology. Microbial source tracking (MST) approaches have emerged as valuable tools for quantifying the proportions of different microbial sources within target communities, enabling researchers to track transmissions between hosts and environments, identify similarities between microbiome samples, and determine sources of contamination in various settings. Current MST methods like SourceTracker2 and FEAST have advanced the field by employing Bayesian and expectation-maximization approaches, respectively, but are limited by computational inefficiency with high-dimensional data and inability to infer directionality in source-sink relationships. This study presents a novel computational framework for microbial source tracking called FastST. FastST infers the relative contributions of source environments to sink microbiomes while also determining directionality when source-sink relationships are not predefined. Through extensive simulation studies with varying numbers of sources and complexity, FastST demonstrates superior performance in both accuracy and computational efficiency compared to FEAST and SourceTracker2, maintaining consistent execution times even as the number of source environments increases. Furthermore, the proposed method achieved over 90% accuracy in directionality inference across all tested scenarios, even when multiple major sources are present, broadening its applicability in practical microbiome research and environmental monitoring. FastST and data simulation codes are publicly available at https://github.com/joungmin-choi/FastST.}, }
@article {pmid41178963, year = {2025}, author = {Whitehead, K and Eppinger, J and Srinivasan, V and Ugalde, JA}, title = {Microbial cross contamination in household laundering and microbial ecology of household washing machines.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1667606}, pmid = {41178963}, issn = {1664-302X}, abstract = {Household washing machines host diverse microbial communities that may include opportunistic pathogens, potentially impacting laundry hygiene and human health. However, our understanding of these communities and their transfer abilities remains limited. We examined microbial communities from 10 household washing machines (five front-load and five top-load) using surface swabs from specific hotspots and sterile sentinel washcloths. Samples were analyzed using culture-based methods and 16S rRNA/ITS metabarcoding. We tested microbial transfer during washing cycles with and without clothing and evaluated the effects of machine drying on this transfer. Front-load machines had significantly higher microbial loads than top-load machines (average bacterial counts: 6.50 ± 2.46 Log10/swab vs. 3.79 ± 1.73 Log10/swab). The microbial community composition was mainly shaped by the machine user rather than the machine type or sampling location. The dominant bacterial genera included Pseudomonas, Micrococcus, and Sphingomonas, while Aspergillus, Cladosporium, and Penicillium dominated the fungal communities. Opportunistic microorganisms were identified, but no highly pathogenic species (pathogenicity score 3) were found. Machine drying did not significantly decrease microbial loads, whereas the presence of soiled clothing impacted community composition. Household washing machines host user-specific microbial communities, including potential opportunistic pathogens. Current laundry practices may be inadequate for the complete elimination of pathogens, especially in immunocompromised individuals. These results support the need for additional household laundry sanitization strategies.}, }
@article {pmid41177050, year = {2025}, author = {Su, F and Li, Y and Zhu, C and Gurmesa, GA and Fang, Y}, title = {Impact of freeze-thaw cycle on metagenomics in subsurface wastewater infiltration systems: Ecological implications for greenhouse gas emissions.}, journal = {Journal of environmental management}, volume = {395}, number = {}, pages = {127839}, doi = {10.1016/j.jenvman.2025.127839}, pmid = {41177050}, issn = {1095-8630}, abstract = {Nitrous oxide (N2O) is a potent greenhouse gas, with a global warming potential 273 times that of carbon dioxide (CO2) and is a significant byproduct of wastewater treatment. Subsurface wastewater infiltration systems (SWIS) effectively treat nitrate-rich wastewater but can also contribute to N2O emissions, particularly during freeze-thaw cycles. This study used metagenomics and [15]N isotope tracing to investigate the impacts of freeze-thaw on microbial ecology and nitrogen transformation in SWIS. Results show that freeze-thaw significantly increased abundances of denitrifying bacteria (Bradyrhizobium, Streptomyces and Nocardioides), on average, by 16-63 %. Denitrification genes (nirK and norB) were also increased by 40 ± 16 % and 22 ± 5 %, while the N2O reductase gene (nosZ) decreased by 19 ± 0.46 %. These impacts collectively increased N2O emissions by more than 20 %. During freezing, about one-third of the added [15]NO3[-]-N was recovered as gas (25 % as N2O and 13 % as N2), increasing to 43 % during thawing (29 % N2O and 15 % N2). This study underscores the need for targeted strategies N2O emission in SWIS, particularly under freeze-thaw conditions, to maximize their sustainability in wastewater treatment.}, }
@article {pmid41175425, year = {2025}, author = {Awasthi, A and Sandal, A and Mahajan, R and Kaundal, R and Sharma, N and Sharma, S}, title = {Fermentation induced changes in physicochemical properties, antioxidant activity, total sugars, and comprehensive polyphenolic profiles of the Rhododendron-infused wine blends.}, journal = {Food chemistry}, volume = {496}, number = {Pt 2}, pages = {146743}, doi = {10.1016/j.foodchem.2025.146743}, pmid = {41175425}, issn = {1873-7072}, abstract = {This study evaluated the sensory, physicochemical, and functional attributes of seven experimental wine formulations incorporating apple juice, ginger, honey or sucrose, and varying levels of Rhododendron arboreum flower juice. Sensory scores revealed significant improvements in color, aroma and sweetness in rhododendron-enriched blends, with Treatment T7 (apple + honey + ginger + R. arboreum) achieving the highest overall acceptability. Physicochemical analyses showed variations in titratable acidity (0.19-0.51 %), alcohol (9.50-11.97 %), and ascorbic acid (4.76-8.53 mg/100 mL), influenced by substrate composition and sweetener type. Inclusion of R. arboreum substantially enhanced total phenolic (up to 19.78 mg GAE/mL) and flavonoid levels (25.84 mg QE/mL) alongside targeted compounds such as quercetin and caffeic acid. Antioxidant assays also confirmed superior radical scavenging activity. Multivariate analyses highlighted strong correlations between polyphenolic content and antioxidant performance. Overall, R. arboreum addition improved both sensory appeal and functional properties, supporting its potential in functional wine development.}, }
@article {pmid41174663, year = {2025}, author = {Waclawiková, B and Schwalbe, M and Ilyaskina, D and Toptas, S and Thome, NU and Du, C and Elsayed, SS and de Jong, A and van Wezel, GP and El Aidy, S}, title = {Serotonin modulation of metabolism and stress response in Pseudomonas fluorescens.}, journal = {BMC biology}, volume = {23}, number = {1}, pages = {330}, pmid = {41174663}, issn = {1741-7007}, mesh = {*Pseudomonas fluorescens/metabolism/physiology/genetics ; *Serotonin/metabolism/analogs &amp; derivatives ; Oxidative Stress ; *Stress, Physiological ; }, abstract = {BACKGROUND: Pseudomonas fluorescens is a Gram-negative bacterium with a remarkable metabolic and physiological versatility that enables it to adapt and colonize diverse ecological niches, including the human small intestine. While serotonin is primarily found in high concentrations in gut tissue, its levels in the lumen can be elevated in conditions such as celiac disease, where P. fluorescens is also found in increased abundance. The potential effects of serotonin on P. fluorescens in such contexts remain unclear.<br><br>RESULTS: We demonstrate that P. fluorescens metabolizes serotonin primarily into 5-hydroxyindole-3-acetic acid (5-HIAA) and, to a lesser extent, into 5-hydroxytryptophol and N-acetylserotonin. Gene expression analysis revealed significant changes in oxidative stress-related pathways over time, and proteomic analysis confirmed the shifts seen particularly in amino acid catabolic pathways. Serotonin metabolism also enhanced bacterial resistance to oxidative stress, suggesting a protective role.<br><br>CONCLUSIONS: The findings reveal a novel mechanism by which serotonin modulates the metabolism and stress responses of P. fluorescens. This study provides insight into how P. fluorescens adapts to serotonin-rich environments, such as in celiac disease, and may inform future research on microbial interactions with host-derived metabolites in disease contexts.}, }
@article {pmid41174295, year = {2025}, author = {Afonso, AC and Simões, M and Saavedra, MJ and Simões, L and Lema, JM and Trueba-Santiso, A}, title = {Physicochemical, Structural, and Proteomic Insights into Drinking Water-Isolated Acinetobacter calcoaceticus Aggregation and Biofilm Dynamics.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {113}, pmid = {41174295}, issn = {1432-184X}, mesh = {*Biofilms/growth &amp; development ; Proteomics ; Bacterial Proteins/metabolism/genetics ; *Acinetobacter calcoaceticus/physiology/isolation &amp; purification/genetics ; *Drinking Water/microbiology ; *Bacterial Adhesion ; Proteome ; }, abstract = {Acinetobacter calcoaceticus, a ubiquitous Gram-negative bacterium, exhibits remarkable adaptability across diverse environments, including drinking water distribution systems (DWDS), where its biofilm-forming and coaggregation capabilities pose significant public health challenges. This study integrates physicochemical, structural, and proteomic analyses to elucidate the mechanisms underlying A. calcoaceticus aggregation and biofilm dynamics. Surface characterization through contact angle measurements, zeta potential, and co-adhesion energy assessments revealed a predominantly hydrophilic surface with strong electron donor properties and a highly negative charge, promoting intercellular adhesion. Transmission electron microscopy unveiled dense cellular aggregates with extracellular filamentous structures, indicative of enhanced cell-to-cell interactions and potential extracellular polymeric substance involvement. Proteomic profiling identified 2593 differentially expressed proteins between aggregation stages, highlighting metabolic shifts, stress response activation, and upregulation of biofilm-associated proteins, including chaperones and quorum-sensing regulators. Our multidisciplinary approach emphasizes the importance of surface characterization in understanding bacterial community and underscores the critical role of physicochemical properties and proteomic flexibility in A. calcoaceticus biofilm and aggregation ability.}, }
@article {pmid41174268, year = {2025}, author = {Almansour, A and Akkaya, SN and Akbulut, S and Adiguzel, G and Yilmaz, B and Adiguzel, A}, title = {Biogenic Amine Degradation by Lactic Acid Bacteria Isolated from Home-Made White Cheese: Molecular and HPLC-Based Assessment.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41174268}, issn = {1867-1314}, abstract = {Due to the potential health risks to humans associated with biogenic amines (BAs) accumulation in cheeses and other foods, this study is the first of its kind on Erzurum home-made white cheese to investigate the presence of BA-degrading lactic acid bacteria (LAB). Polymerase chain reaction (PCR) was applied for all putative LAB strains to detect the presence of (hdcA, cadA, tdcA, and odc) genes responsible for BA formation (histamine, cadaverine, tyramine, and putrescine, respectively). Only 72% of all strains showed amplicons for hdcA and tdcA, and no strains were found to have cadA, ldc, and odc genes. High-performance liquid chromatography (HPLC) analysis confirmed these findings. Furthermore, 12% of BA-nonproducing LAB have the sufI gene responsible for Multicopper Oxidases (MCOs) production. HPLC analysis was then applied to these strains to investigate their ability to degrade BAs. Nine strains were found to have degradation abilities with optimal conditions at pH 4.5-5.5 and 32-37 °C. Importantly, analysis of twenty home-made white cheeses revealed that the levels of BAs were within safe limits. This research provides valuable insights into the microbial ecology of these cheeses and highlights the potential of utilizing indigenous LAB for controlling BA formation and improving cheese quality.}, }
@article {pmid41171124, year = {2025}, author = {Lv, J and Ma, S and Ma, C and Liu, F and Duan, X and Huang, X and Geng, Q and Liu, F and Li, G and Li, Y and Wang, J and Li, C and Zheng, H and Zhang, Y and Sun, Z and Wang, J and Fan, G and Huang, S and Zhang, L and Bao, Z and Wang, S}, title = {Ocean-M: an integrated global-scale multi-omics database for marine microbial diversity, function and ecological interactions.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkaf1098}, pmid = {41171124}, issn = {1362-4962}, support = {2024YFC2816000//National Key Research and Development Program of China/ ; LSKJ202202804//Marine S&amp;T Fund of Shandong Province for Laoshan Laboratory/ ; 2025B1111180001//Guangdong Provincial Key Areas R&amp;D Program Project/ ; SOLZSKY2025013//Hainan Province Science and Technology Special Fund/ ; 32573498//Natural Science Foundation of China/ ; 32222085//Natural Science Foundation of China/ ; QDLYY-2024011//Blue Seed Industry Science and Technology Innovation Project/ ; GZB20250215//Postdoctoral Fellowship Program of CPSF/ ; }, abstract = {Multi-omics analyses have significantly advanced the understanding of complex marine microbial communities and their interactions. Despite notable progress from recent large-scale ocean meta-analysis efforts, the effective integration and accessibility of these diverse datasets remain challenging. To address this, we introduce Ocean-M (http://om.qnlm.ac), a comprehensive and publicly accessible platform for marine microbial multi-omics data integration, analysis, and visualization. Ocean-M provides a systematic view of 54 083 high-quality metagenome-assembled genomes, including genome assembly statistics, genome clustering, gene annotation, and interactive tools for global-scale taxonomic profiling. The platform also incorporates microbial community networks, host-microbiome interactions, and environmental DNA datasets to support an integrated ecological framework for studying microbial interactions and ecosystem functions. Additionally, Ocean-M enables large-scale mining of ecologically and biotechnologically important genes, with curated catalogs of 151 798 biosynthetic gene clusters, 52 699 antibiotic resistance genes, and millions of carbohydrate-active enzymes and plastic-active enzymes. By combining multi-omics data with environmental metadata, Ocean-M serves as a valuable resource for advancing marine microbial ecology, global biogeography, and functional gene discovery.}, }
@article {pmid41169038, year = {2025}, author = {Buccola, MJ and Satheesh Babu, AK and Paz, HA and Porter, ND and Srinivasan, H and Ricks, RL and Rosquist, K and Torres, JL and Zhong, Y and Jalili, T and Wankhade, UD and Anandh Babu, PV}, title = {Dietary Prebiotics Modulate Omeprazole-Induced Alterations in the Gut Microbial Signature.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e70307}, doi = {10.1002/mnfr.70307}, pmid = {41169038}, issn = {1613-4133}, abstract = {Proton pump inhibitors (PPIs) are commonly used to treat heartburn and acid-related disorders. However, their misuse and prolonged use contribute to gut dysbiosis. This study investigated whether well-known prebiotic dietary sources, blueberries or strawberries, can reverse PPI (omeprazole) induced dysbiosis and gut inflammation by modulating gut microbes. Male C57BL/6J mice (7 weeks old) were fed a diet with or without omeprazole (40 mg/kg diet), blueberry (3.7% in the diet; ∼1.5 human servings) or strawberry (2.35% in the diet; ∼2 human servings) for 12 weeks. Metabolic parameters, gut microbes (in the cecum and colon), and inflammatory markers were assessed. In this study, no changes were observed in metabolic parameters in mice fed a diet supplemented with omeprazole or berries. Second, blueberry or strawberry supplementation at nutritional dosages improved alterations in gut microbial ecology induced by omeprazole, with effects varying between the cecum and colon. Third, strawberry supplementation reduced omeprazole-induced gut inflammation. Fourth, selected genera were either positively or negatively associated with markers of gut inflammation, suggesting that dietary berries can ameliorate inflammatory signaling through modifications in the gut microbiome. Dietary berries represent a potential nutritional strategy for improving PPI-induced gut dysbiosis and inflammation.}, }
@article {pmid41168937, year = {2025}, author = {Brangarí, AC and Knorr, MA and Frey, SD and Rousk, J}, title = {Shifts in Microbial Thermal Traits Mitigate Heat-Induced Carbon Losses in Soils.}, journal = {Global change biology}, volume = {31}, number = {11}, pages = {e70579}, doi = {10.1111/gcb.70579}, pmid = {41168937}, issn = {1365-2486}, support = {2022-01478//Svenska Forskningsr&#xe5;det Formas/ ; CTS 22: 2131//Carl Tryggers Stiftelse f&#xf6;r Vetenskaplig Forskning/ ; KAW 2022.0175//Knut och Alice Wallenbergs Stiftelse/ ; KAW 2023.0384//Knut och Alice Wallenbergs Stiftelse/ ; DEB-1832110//National Science Foundation/ ; DEB-1456610//National Science Foundation/ ; }, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Hot Temperature ; *Carbon/metabolism/analysis ; *Global Warming ; *Carbon Cycle ; Carbon Dioxide/metabolism ; Forests ; }, abstract = {Global warming is expected to transfer carbon from soil organic matter to atmospheric CO2, with microbial communities playing a crucial role in regulating this exchange. While the immediate impact of temperature on microbial functions is well understood and causes soil carbon losses, the long-term response remains unclear, with losses stabilising over time, reducing the overall effect of chronic warming on soil organic carbon (SOC) stocks. Here, we examined the temperature dependence of microbial respiration and growth after 9 years of +5°C warming in a temperate forest. Using these temperature dependences and field temperature data, we modelled in situ carbon fluxes and changes in SOC stocks. Results showed that the direct effect of temperature initially increased respiration and growth, projecting a potential 31% SOC stock loss if the trend had persisted. However, the gradual optimisation of microbial traits to warming balanced the direct temperature effects, enhanced carbon use efficiency and offset CO2 emissions. Together, these microbial trait shifts limited the heat-induced SOC loss to 15%, closely aligning with empirical observations. These findings suggest that microbial trait optimisation can moderate carbon emissions, providing a parsimonious mechanistic explanation for observations worldwide and underscoring the need to integrate microbial dynamics into models.}, }
@article {pmid41168882, year = {2025}, author = {Bowers, RM and Bennett, S and Riley, R and Villada, JC and Da Silva, IR and Woyke, T and Frank, AC}, title = {Host species and geographic location shape microbial diversity and functional potential in the conifer needle microbiome.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {222}, pmid = {41168882}, issn = {2049-2618}, support = {10.46936/10.25585/60000936//U.S. Department of Energy/ ; DEB-1442348//Directorate for Biological Sciences/ ; }, mesh = {*Microbiota/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics/methods ; *Tracheophyta/microbiology ; Metagenome ; Phylogeny ; *Plant Leaves/microbiology ; Pinus/microbiology ; }, abstract = {BACKGROUND: The aerial surface of plants, known as the phyllosphere, hosts a complex and dynamic microbiome that plays essential roles in plant health and environmental processes. While research has focused on root-associated microbiomes, the phyllosphere remains comparatively understudied, especially in forest ecosystems. Despite the global ecological dominance and importance of conifers, no previous study has applied shotgun metagenomics to their phyllosphere microbiomes.<br><br>RESULTS: This study uses metagenomic sequencing to explore the microbial phyllosphere communities of subalpine Western conifer needle surfaces from 67 trees at six sites spanning the Rocky Mountains, including 31 limber pine, 18 Douglas fir, and 18 Engelmann spruce. Sites span&#x2009;~&#x2009;1,075&#xa0;km and nearly 10&#xb0; latitude, from Glacier National Park to Rocky Mountain Biological Laboratory, capturing broad environmental variation. Metagenomes were generated for each of the 67 samples, for which we produced individual assemblies, along with three large coassemblies specific to each conifer host. From these datasets, we reconstructed 447 metagenome-assembled genomes (MAGs), 417 of which are non-redundant at the species level. Beyond increasing the total number of extracted MAGs from 153 to 294, the three coassemblies yielded three large MAGs, representing partial sequences of host genomes. Phylogenomics of all microbial MAGs revealed communities predominantly composed of bacteria (n&#x2009;=&#x2009;327) and fungi (n&#x2009;=&#x2009;117). We show that both microbial community composition and metabolic potential differ significantly across host tree species and geographic sites, with site exerting a stronger influence than host.<br><br>CONCLUSIONS: This dataset offers new insights into the microbial communities inhabiting the conifer needle surface, laying the foundation for future research on needle microbiomes across temporal and spatial scales. Variation in functional capabilities, such as volatile organic compound (VOC) degradation and polysaccharide metabolism, closely tracks shifts in taxonomic composition, indicating that host-specific chemistry, local environmental factors, and regional microbial source pools jointly shape ecological roles. Moreover, the observed patterns of mobile genetic elements and horizontal gene transfer suggest that gene exchange predominantly occurs within microbial lineages, with occasional broader transfers dispersing key functional genes (e.g., those involved in polysaccharide metabolism), which may facilitate microbiome adaptation.}, }
@article {pmid41168506, year = {2025}, author = {Martinez-Urtaza, J}, title = {From clonality to complexity: a journey through microbial ecology and evolution.}, journal = {Nature reviews. Genetics}, volume = {}, number = {}, pages = {}, pmid = {41168506}, issn = {1471-0064}, }
@article {pmid41165314, year = {2025}, author = {Nauwynck, W and Sakarika, M and Faust, K and Boon, N}, title = {Differential recovery of chain-elongating bacteria: comparing droplet, plating, and dilution-to-extinction methods.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0135625}, doi = {10.1128/msystems.01356-25}, pmid = {41165314}, issn = {2379-5077}, abstract = {Microbial chain elongation via reverse β-oxidation offers a more sustainable route to produce medium-chain fatty acids like caproate, commodity chemicals typically produced via (petro)chemical processes. Thermophilic anaerobic microbiomes allow production at a high rate and selectivity but remain poorly understood due to the limited cultivability of their members. To better access functional taxa from a thermophilic chain-elongating reactor community, we applied multiple isolation strategies: conventional anaerobic plating, dilution-to-extinction (DTE), droplet-based microfluidics, and fluorescence-activated cell sorting (FACS). We evaluated the taxonomic range and cultivation success of each method using 16S rRNA gene sequencing. Each method yielded a distinct subset of microbial taxa. While Clostridium acetireducens-related strains were consistently isolated across all strategies, key thermophilic chain elongators (e.g., Thermocaproicibacter melissae-like organisms) only appeared in DTE. Droplet microfluidics enriched the most unique taxa in total, mostly rare taxa, including Caproicibacter and Thermoanaerobacterium spp. Plating yielded the lowest diversity, recovering only dominant taxa. FACS-based approaches failed to yield isolates, likely due to stress during processing. Comparing droplet-based isolation to DTE revealed critical insights: although droplets offer higher throughput, which intrinsically increases the chance of capturing rare taxa, not all DTE-cultivated organisms grew in droplets. This suggests additional contributing factors (apart from an increased throughput), such as encapsulation stress and droplet-specific microenvironments. These findings clarify the advantages and limitations of droplet cultivation strategies, allowing a more informed application of these techniques to access the so-called "microbial dark matter."IMPORTANCEMany environmentally and industrially relevant microbes remain uncultured, limiting our ability to understand and use them. This is especially true in thermophilic anaerobic microbiomes, which are promising systems for producing sustainable chemicals from organic waste streams. In this study, we explored how different cultivation strategies influence which microbes can be isolated from a thermophilic chain-elongating reactor. By comparing traditional and novel methods, including droplet microfluidics, we showed that each method recovers a unique set of microbes. While droplet-based methods enable high sampling depth with minimal effort and excel at isolating rare microbes, we found that they also introduce clear biases, as certain organisms recovered by other methods did not grow in droplets. Our work highlights the importance of the cultivation method in isolation success and helps shine a light on the selective forces at play in droplet-based microbial isolation.}, }
@article {pmid41165014, year = {2025}, author = {Freudenthal, J and Schlegel, M and Bonkowski, M and Dumack, K}, title = {A Novel Protistan Trait Database Reveals Functional Redundancy and Complementarity in Terrestrial Protists (Amoebozoa and Rhizaria).}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e70064}, doi = {10.1111/1755-0998.70064}, pmid = {41165014}, issn = {1755-0998}, support = {221301018//Deutsche Forschungsgemeinschaft/ ; 447013012//Deutsche Forschungsgemeinschaft/ ; SPP 1991//Deutsche Forschungsgemeinschaft/ ; }, abstract = {The inclusion of functional traits of protists in environmental sequencing surveys, in addition to the traditional taxonomic framework, is essential for a better understanding of their roles and impacts on ecosystem processes. We provide a database of functional traits for a widespread and important clade of protists-the Amoebozoa-based on extensive literature research in eight trait categories: Habitat, locomotion, nutrition, morphology, morphotype, size, spore formation, and disease-relatedness. The comparison of community traits of the Amoebozoa with sympatric but highly divergent Cercozoa (Rhizaria) revealed both convergent evolution of morphology or locomotion and distinct differences in habitat preference and feeding selectivity. Amoebozoa seem to be rather unselective in their prey choice compared to Cercozoa. Indeed, the feeding preferences of Amoebozoa appeared to be related to cell size, whereas Cercozoa selectively feed on prey. Applications to metatranscriptomic data from soil, litter, and bark surfaces revealed differences in the average community trait compositions and ecosystem functioning, such as an increased proportion of disease-related Amoebozoa in soil or different proportions of nutrition types of Amoebozoa and Cercozoa on bark. This database will facilitate ecological analyses of sequencing data and improve our understanding of the diversity of adaptations of Amoebozoa to the environment and their functional roles in ecosystems.}, }
@article {pmid41164406, year = {2025}, author = {Sierra, AM and Escolástico-Ortiz, DA and Zartman, CE and Derome, N and Lovejoy, C and Villarreal A, JC}, title = {Assembly and co-occurrence networks of nitrogen-fixing bacteria associated with epiphyllous liverworts in fragmented tropical forests.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf173}, pmid = {41164406}, issn = {2730-6151}, abstract = {Understanding the spatial dynamics of plant-associated microbial communities is increasingly urgent in the context of habitat loss and the biodiversity crisis. However, the influence of reduced habitat size and connectivity on the assembly mechanisms underlying microbial associations is fundamental to advancing microbial ecology and conservation. In the Brazilian Amazon, we investigated nitrogen-fixing (diazotrophic) bacterial communities associated with two epiphyllous liverworts, Cololejeunea surinamensis and Radula flaccida, across 11 forest sites within the Biological Dynamics of Forest Fragments Project landscape. Using amplicon sequencing targeting the nitrogenase gene (nifH), we characterized diazotroph community diversity, inferred assembly mechanisms through null models, and analyzed co-occurrence network structure. Host-specific associations were evident: C. surinamensis predominantly hosted Hassallia, while R. flaccida was primarily associated with Fischerella. Despite habitat fragmentation, diazotrophic richness and composition remained similar across habitats of different sizes, consistent with strong homogenizing dispersal. Network analyses revealed that smaller fragments harbored more modular communities with fewer module hubs, pronounced shifts in key species relative abundance, and reduced network robustness. Our findings underscore the influence of habitat size on the stability of liverwort-associated diazotrophs, with smaller fragments exhibiting lower key species specificity and disruption of microbe-microbe interactions. Our results emphasize the importance of conserving large, connected forest habitats to maintain the functional integrity of phyllosphere N-fixing microbiota.}, }
@article {pmid41164176, year = {2025}, author = {Cai, S and Lin, L and Cai, Y and Wang, C and Lin, Y and Zhou, J and Zhou, F and Chen, M}, title = {Correction: Phase angle associates with severity and mortality in acute-on-chronic liver failure.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1695643}, doi = {10.3389/fmed.2025.1695643}, pmid = {41164176}, issn = {2296-858X}, abstract = {[This corrects the article DOI: 10.3389/fmed.2025.1541795.].}, }
@article {pmid41164007, year = {2025}, author = {Lerner, H and Eck, M and Link, C and Witt, T and Battagliarin, G and Mecking, S and Schleheck, D}, title = {Thermomonospora spp. are implicated in the biodegradation of long-chain aliphatic polyester bioplastics during thermophilic composting.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1671731}, pmid = {41164007}, issn = {1664-302X}, abstract = {Biodegradable plastics are an important component for achieving a circular polymer economy. To be considered biodegradable at the regulatory level, plastics must pass standardized tests, for example under industrial composting conditions at 58 °C (ISO 14855-1). Although such tests are frequently applied, little is known about the microorganisms catalyzing these degradation processes. Recently, bioplastics with properties similar to polyethylene, Long-Chain Aliphatic Polyesters (LCAP), for example polyester 1,18-octadecanediol-alt-1,18-octadecanedioic acid (abbreviated PE-18,18), were shown to biodegrade under industrial composting conditions. In this work, we analyzed the microbial communities that had developed in the compost treatments at the end of the biodegradation test for three different LCAPs (PE-18,18, PE-12,12 and PE-2,18) relative to the untreated controls, via amplicon-sequencing of bacterial 16S and fungal ITS2 rDNA. This revealed significant treatment-induced shifts in the bacterial communities (p < 0.05), with Pseudonocardia and Thermomonospora ASVs enriched in all LCAP-treated samples compared to the controls (p ≤ 0.0001), while no pronounced shifts were observed for the fungal community. Thermomonospora sequences showed high similarity to T. curvata DSM43183, which encodes the known polyester hydrolase Tcur1278, and the presence of gene tcur1278 was confirmed in LCAP-treated samples via PCR. Enzyme assays with heterologously expressed and partially purified Tcur1278 demonstrated its activity on PE-2,18 LCAP, releasing up to 230 μmol of soluble monomers over 48 h at 50 °C. Hence, our study implicated Thermomonospora species in LCAP degradation during thermophilic composting, based on taxonomic enrichment, and provided evidence linking the detected phylotypes to Tcur1278, the first bacterial enzyme demonstrated to depolymerize LCAP. It thereby is the first evidence for an ecological relevance of Tcur1278-encoding Thermomonospora phylotypes for bioplastic degradation in situ.}, }
@article {pmid41162221, year = {2025}, author = {Hodžić, A}, title = {The contribution of the Midichloria mitochondrii endosymbiont to Borrelia infection dynamics.}, journal = {Trends in parasitology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pt.2025.10.003}, pmid = {41162221}, issn = {1471-5007}, abstract = {Recent studies have revealed a positive correlation between the presence of the Midichloria mitochondrii endosymbiont and Borrelia species in the tick vector, suggesting potential interactions that may influence pathogen infection and the transmission dynamics of Lyme borreliosis. This article discusses the possible mechanistic pathways underlying these interactions.}, }
@article {pmid41160321, year = {2025}, author = {de Azevedo, CS and Schork, IG and Passos, LF and Goodhead, I and Young, RJ}, title = {The domestic cat microbiome: mapping knowledge gaps through scientometric analysis in feline microbial research.}, journal = {Veterinary research communications}, volume = {50}, number = {1}, pages = {6}, pmid = {41160321}, issn = {1573-7446}, mesh = {Animals ; Cats/microbiology ; *Microbiota ; *Gastrointestinal Microbiome ; }, abstract = {In this study, we present the first comprehensive scientometric analysis of research on the domestic cat microbiome, providing a transparent and data-driven overview of the field. We examined 282 publications on the microbiome of domestic cats (Felis catus) to uncover dominant research themes, methodological patterns, microbial niches, and knowledge gaps. Our results reveal a sharp rise in publications since 2012, with a peak in 2024, where most work is concentrated in high-income countries and driven by a small number of academic institutions. Current efforts are heavily focused on the bacterial gut microbiome, typically using genomic tools for taxonomic profiling in comparative designs. In contrast, research on other microbial communities (e.g., oral or skin), non-bacterial taxa, functional analyses, and behavioural outcomes remains scarce, with behavioural studies virtually absent. Although some studies report health-related effects, mainly positive or neutral, the functional roles of the microbiota and their possible influence on feline behaviour remain largely unexplored. By mapping these trends and gaps, our study provides a strategic framework for advancing microbiome research in domestic cats. These findings highlight priority areas and methodological opportunities that can guide future investigations, foster interdisciplinary collaboration, and ultimately deepen our understanding of the intricate links between microbial ecology, feline health, and behaviour. Studies connecting the microbiome with feline diseases, behaviour, and diet are strongly encouraged, given their high applicability to everyday animal care and management. Such research has the potential to improve both feline health and welfare, while also strengthening the human-cat bond.}, }
@article {pmid41159880, year = {2025}, author = {,  and Cuthbertson, BH and Billot, L and Campbell, MK and Daneman, N and Davis, JS and Delaney, A and Devaux, A and Ferguson, ND and Finfer, SR and Fowler, R and Gordon, AC and Hammond, NE and Klein, G and Li, Q and Marshall, J and Micallef, S and Murthy, S and Mysore, J and Naik, C and Patel, C and Pinto, R and Rose, L and Seppelt, IM and Venkatesh, B and Young, PJ and Myburgh, JA}, title = {Selective Decontamination of the Digestive Tract during Ventilation in the ICU.}, journal = {The New England journal of medicine}, volume = {}, number = {}, pages = {}, doi = {10.1056/NEJMoa2506398}, pmid = {41159880}, issn = {1533-4406}, support = {1084244//National Health and Medical Research Council/ ; MYG-151210/CAPMC/CIHR/Canada ; PJT-153367/CAPMC/CIHR/Canada ; }, abstract = {BACKGROUND: Whether selective decontamination of the digestive tract (SDD) reduces mortality among patients undergoing mechanical ventilation and whether it adversely affects microbial ecology in the intensive care unit (ICU) remain unclear. In an earlier analysis of data from Australia, SDD did not result in a lower incidence of in-hospital death than standard care, but data from the full international trial are needed.<br><br>METHODS: We randomly assigned ICUs in Australia and Canada to use SDD or to continue standard care for two 12-month periods in patients undergoing mechanical ventilation. Patients in the SDD group received specific oral and gastric antimicrobial interventions for the duration of ventilation and an intravenous antibiotic agent for the first 4 days after enrollment. All other patients in the ICU were included in an observational ecologic assessment. Previously reported data from Australia are now combined with data from Canada. The primary outcome was in-hospital death from any cause at 90 days. The secondary clinical outcomes, assessed at 90 days, were death in the ICU and the number of days alive and free of mechanical ventilation, ICU admission, and hospitalization. Microbiologic secondary outcomes included new positive cultures for bloodstream infections and antibiotic-resistant organisms. For the ecologic assessment, the microbiologic outcomes were tested for noninferiority (noninferiority margin, 2 percentage points).<br><br>RESULTS: In this trial involving 20,000 patients in 26 ICUs, 9289 patients were enrolled in the randomized trial and 10,711 were included in the ecologic assessment. At 90 days, 1175 of 4215 patients (27.9%) in the SDD group and 1494 of 5065 (29.5%) in the standard-care group had died before hospital discharge (odds ratio, 0.93; 95% confidence interval [CI], 0.84 to 1.05; P&#x2009;=&#x2009;0.27). New bloodstream infections occurred in 4.9% of the patients in the SDD group and in 6.8% of those in the standard-care group (adjusted mean difference, -1.30 percentage points; 95% CI, -2.55 to -0.05); antibiotic-resistant organisms were cultured in 16.8% and 26.8%, respectively (adjusted mean difference, -9.60 percentage points; 95% CI, -12.40 to -6.80). In the ecologic assessment, noninferiority of SDD was not confirmed for the development of new antibiotic-resistant organisms. Adverse events considered to be related to SDD or standard care were reported in 12 patients (0.3%) in the SDD group and in no patients in the standard-care group. Serious adverse events occurred in 47 patients (1.1%) and 59 patients (1.2%), respectively.<br><br>CONCLUSIONS: Among critically ill patients undergoing mechanical ventilation, SDD did not result in a lower incidence of in-hospital death than standard care. (Funded by the National Health and Medical Research Council of Australia and the Canadian Institutes of Health Research; ClinicalTrials.gov number, NCT02389036.).}, }
@article {pmid41159723, year = {2025}, author = {Duan, Z and Yang, R and Lai, T and Jiang, W and Zhang, J and Chen, B and Liao, L}, title = {Development of a CRISPR/Cas9-induced gene editing system for Pseudoalteromonas fuliginea and its applications in functional genomics.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0177125}, doi = {10.1128/aem.01771-25}, pmid = {41159723}, issn = {1098-5336}, abstract = {Pseudoalteromonas has been used as a model system to study cold adaptation and is of widespread interest in biotechnology and ecology. To explore its physiological responses to extreme cold, uncover functional genes, and clarify their ecological roles, efficient genetic tools are essential. However, existing genetic manipulation methods in Pseudoalteromonas rely on traditional homology-based recombination, which is laborious and time-consuming in this bacterial system. Consequently, improving editing efficiency is crucial for advancing both basic research and applied potential. Here, we established a CRISPR/Cas9 system in Pseudoalteromonas and carried out an extensive investigation of the Type II CRISPR/Cas9 platform for gene editing in Pseudoalteromonas fuliginea, a representative species thriving in the frigid polar oceans. To validate the feasibility of the CRISPR/Cas system in P. fuliginea, multiple genes were selected as targets, and the gene editing effects were confirmed through phenotypic changes or gene expression. We have successfully achieved both gene knockouts and insertions in P. fuliginea, encompassing the deletion of genes such as fliJ, indA, and genes encoding Pf sRNAs, as well as the in vivo insertion of 3×FLAG and the gfp gene. The average CRISPR/Cas9 gene editing efficiency in P. fuliginea exceeded 70%. In summary, we developed an efficient CRISPR/Cas9-based editing system in P. fuliginea, which can be utilized to accelerate the development of Pseudoalteromonas as a model system for addressing fundamental questions related to extreme environmental adaptation and to fulfill its potential biotechnological applications.IMPORTANCEPseudoalteromonas fuliginea is a marine bacterium with great potential for ecological and biotechnological research, yet its genetic manipulation has long been a technical challenge. In this study, we developed a gene editing system based on CRISPR technology that enables efficient and precise genome modification in this organism. Using this system, we successfully deleted, inserted, and tagged multiple genes, including regulatory and non-coding elements, with high success rates. Notably, several of these genes are linked to key traits such as motility and stress response, which contribute to microbial adaptation in polar environments. This tool allows researchers to directly test gene function and study microbial adaptation in cold marine environments. The ability to perform reliable genetic edits in P. fuliginea opens new possibilities for its use as a model organism and will support future advances in microbial ecology, environmental microbiology, and marine biotechnology.}, }
@article {pmid41159286, year = {2025}, author = {Shirani, K and Mottaghi, A and Shabani, M}, title = {Honey as a Functional Food: Evaluating Its Antimicrobial Properties and Bacterial Safety Concerns.}, journal = {Foodborne pathogens and disease}, volume = {}, number = {}, pages = {}, doi = {10.1177/15353141251392181}, pmid = {41159286}, issn = {1556-7125}, abstract = {Honey is increasingly recognized as a functional food with intrinsic antimicrobial properties. Its complex chemical makeup, high sugar content, low water activity, acidic pH, hydrogen peroxide generation, and a spectrum of bioactive phytochemicals create a multifaceted defense against microbial growth, yet honey also harbors diverse microorganisms, including potential pathogens, underscoring the need for robust quality control and safety considerations across production, processing, and storage. This study synthesizes current evidence on the antimicrobial mechanisms of honey and evaluates bacterial safety concerns, with emphasis on probiotic potential and risks associated with pathogens such as Clostridium botulinum, to inform safe use and innovative functional food applications. A comprehensive review of existing literature and honey-specific data was conducted to collate chemical, microbiological, and safety-related parameters. Key antimicrobial mechanisms (osmotic pressure, acidic environment, hydrogen peroxide production, and bioactive compounds such as methylglyoxal in certain varieties) were mapped to their effects on diverse microbes. Safety considerations, contamination pathways, and regulatory frameworks were qualitatively assessed to identify critical control points. Honey's antimicrobial activity arises from synergistic interactions among sugars, pH, hydrogen peroxide, enzymes, and phytochemicals, yielding broad-spectrum inhibition. Beneficial lactic acid bacteria from honey and bees contribute probiotic potential, while the risk of contamination by pathogens necessitates stringent hygiene, processing controls, and adherence to quality standards. Processors can leverage nonthermal and thermal reduction methods to balance safety with the preservation of bioactive components. Honey remains a robust functional food with antimicrobial advantages and probiotic opportunities, provided that meticulous quality control and regulatory compliance are maintained to mitigate safety risks for vulnerable populations. Future work should optimize honey-based probiotic formulations and establish standardized safety protocols across the supply chain.}, }
@article {pmid41158777, year = {2025}, author = {Skoog, EJ and Cutts, E and Bosak, T}, title = {Linking microbial ecology to the cycling of neutral and acidic polysaccharides in pustular mats from Shark Bay, Western Australia.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1684648}, pmid = {41158777}, issn = {1664-302X}, abstract = {Cyanobacteria and other microbes in peritidal microbial mats have produced extracellular polymeric substances (EPS) for more than two billion years. The production and degradation of EPS contributes to the biogeochemical cycling of carbon and carbonate precipitation within modern microbial mats, but key microbes involved in the cycling of EPS remain unidentified. Here, we investigate the cycling of EPS in the peritidal pustular mats of Shark Bay, Western Australia. We characterize the chemical composition of EPS produced by cyanobacterial enrichment cultures under natural and UV-stress conditions and link these findings to the metabolic potential for EPS production and degradation encoded in 84 metagenome-assembled genomes (MAGs) from the mat community. We further identify the key microbial degraders of specific acidic and neutral polysaccharides in this community by cultivating enrichment cultures on seven commercially available polysaccharides representative of those present in the mats and assessing the dominant taxa. All sequenced Cyanobacteria MAGs have the potential to synthesize mannose, fucose, glucose, arabinose, rhamnose, galactose, xylose, N-acetylglucosamine, galacturonic acid and glucuronic acid. Biochemical analyses confirm the presence of nearly all these monosaccharides in the hydrolysates of EPS extracted from UV- and non-UV exposed cyanobacterial enrichments. Ultraviolet radiation influences the structure and composition of EPS by reducing the hydration, potentially due to cross-linking among polymers in EPS and increasing the relative abundances of uronic acids and xylose in polysaccharides. Analyses of carbohydrate-active enzymes (CAZymes) in the MAGs and of 16S rRNA sequences from experimental polysaccharide enrichments point to major roles for Bacteroidetes, Planctomycetes, and Verrucomicrobia in the cycling of acidic EPS. These experiments reveal a complex interplay among microbial community composition, CAZyme diversity, environmental stressors, and EPS cycling, which together shape carbon flow and biomineralization in pustular mats in Shark Bay.}, }
@article {pmid41156863, year = {2025}, author = {Rajput, AP and Sun, D and Zhou, S and Meegaskumbura, M}, title = {Distinct Gut and Skin Microbiomes of a Carnivorous Caecilian Larva (Ichthyophis bannanicus) Show Ecological and Phylogenetic Divergence from Anuran Tadpoles.}, journal = {Microorganisms}, volume = {13}, number = {10}, pages = {}, doi = {10.3390/microorganisms13102405}, pmid = {41156863}, issn = {2076-2607}, support = {Guangxi University's startup-funding to Madhava Meegaskumbura;Postdoctoral Project funding to Amrapali Prithvisingh Rajput//Guangxi University/ ; }, abstract = {The amphibian microbiome plays a vital role in host health, yet the bacterial communities of caecilians (Order: Gymnophiona) remain largely uncharacterised. We investigated this by providing the first characterisation of the gut and skin microbiome of larval Ichthyophis bannanicus, a carnivorous caecilian, using 16S rRNA gene metabarcoding. Our analyses show distinct communities between the faecal samples and skin, with significant enrichment of Laribacter in faeces and Flavobacterium on skin. Despite significant variation in their community structures, the core genera Escherichia-Shigella were shared between both regions, suggesting similar microbial exchange in the aquatic environments. Skin bacterial diversity exhibited relatively higher richness, but lower evenness than that of faeces. Further, the skin bacterial community exhibited more complex interactions, suggesting stronger resilience to changes. The relationships and interactions of skin and faecal bacterial communities suggest their interactive effects on the host's overall health. Compared with anuran tadpoles, the I. bannanicus larval microbiome showed taxonomic overlap, but possessed certain unique core bacteria. This work on an understudied amphibian lineage is foundational, highlighting how diet, phylogeny, and aquatic environment shape microbial communities and informing future research into amphibian health and disease.}, }
@article {pmid41156709, year = {2025}, author = {Liu, X and Zhao, G and Bai, J and Qu, X and Chai, J and Lin, D}, title = {Pediococcus pentosaceus OL77 Enhances Oat (Avena sativa) Silage Fermentation Under Cold Conditions.}, journal = {Microorganisms}, volume = {13}, number = {10}, pages = {}, doi = {10.3390/microorganisms13102248}, pmid = {41156709}, issn = {2076-2607}, support = {32160810//National Natural Science Foundation of China/ ; }, abstract = {Ensiling forage under low-temperature conditions often leads to poor fermentation and nutrient losses. This study evaluated the effects of a cold-tolerant Pediococcus pentosaceus OL77 strain on oat silage. Silages were prepared with or without Pediococcus pentosaceus inoculation (1 × 10[5] cfu/g FM). After 90 days, OL77-treated silage showed markedly higher lactic acid (45.83 vs. 30.51 g/kg DM), lower pH (3.88 vs. 4.443), and better preservation of WSC (64.68 vs. 47.60 g/kg DM) and crude protein (89.26 vs. 65.52 g/kg DM) than the control. Microbial analysis revealed accelerated colonization by Pediococcus, reduced bacterial diversity, and faster stabilization of the fermentation process. Functional predictions indicated enhanced carbohydrate and energy metabolism. These findings demonstrate that OL77 can effectively improve fermentation quality and nutrient preservation of oat silage under low-temperature conditions, offering a practical inoculant option for cold regions.}, }
@article {pmid41151518, year = {2025}, author = {Ouyang, S and Zhao, HP and Lai, CY}, title = {Propane-driven efficient BPA degradation in groundwater: Transformation pathways, microbial ecology and enzymatic mechanisms in a membrane biofilm reactor.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140214}, doi = {10.1016/j.jhazmat.2025.140214}, pmid = {41151518}, issn = {1873-3336}, abstract = {The widespread occurrence of bisphenol A (BPA) in groundwater has raised growing concern due to its endocrine-disrupting effects. This study demonstrates for the first time that a propane-fed membrane biofilm reactor (C3H8-MBfR) achieved efficient BPA degradation, with rates up to 1157.8 ± 42.7 μg·L[-1]·d[-1]. In-situ withdrawal experiments confirmed that propane is essential for maintaining degradation performance. Transformation products (TPs) analysis revealed hydroxylation, oxidative skeletal rearrangement, ipso substitution, and ring-cleavage steps consistent with stepwise detoxification. ECOSAR-based toxicity predictions indicated that BPA degradation potentially leads to a reduced overall ecological risk, although minor toxic TPs might still pose residual risks. Multi-omic profiling identified a metabolically diverse microbial consortium dominated by J033 sp., Methyloversatilis discipulorum (M. discipulorum), Macondimonas, and Gemmobacter sp., which expressed key oxidative enzymes including cytochrome P450 (CYP450), particulate methane monooxygenase (pMMO), and propane monooxygenase (PrMO). Enzymatic inhibition assays supported their crucial roles in BPA transformation. The generated intermediates were subsequently transformed by these upstream oxidizers together with downstream degraders, such as M. discipulorum. These findings reveal a previously unrecognized, enzyme-driven network for BPA degradation in the C3H8-fed biofilm, offering a sustainable strategy for mitigating endocrine disrupting compounds from groundwater.}, }
@article {pmid41151427, year = {2025}, author = {Hernández-Villamor, D and Jeaidi, A and Boydens, R and Rabaey, K and Van de Wiele, T and Prévoteau, A}, title = {Mediated electron transfer in five prevalent human oral microbial species.}, journal = {Bioelectrochemistry (Amsterdam, Netherlands)}, volume = {168}, number = {}, pages = {109149}, doi = {10.1016/j.bioelechem.2025.109149}, pmid = {41151427}, issn = {1878-562X}, abstract = {An increasing number of microbial species within the human body, many of which are pathogenic, are being reported as "electroactive". However, the mechanisms and kinetics of extracellular electron transfer (EET) and its putative ecological relevance remain understudied. We utilized rotating disk electrodes (RDEs) to assess mediated electron transfer (MET) in five oral species via their ability to reduce riboflavin and ferricyanide. The use of both mediators was confirmed in Streptococcus mutans, Fusobacterium nucleatum, Aggregatibacter actinomycetemcomitans and Porphyromonas gingivalis, while A. viscosus only reduced riboflavin. Kinetics of EET (turnover rate per cell) were slow with riboflavin (kcat, RF< 10[4] s[-1]) in all species but F. nucleatum, whereas ferricyanide resulted in fast kinetics (kcat, Ferri(app)> 10[4] s[-1]) in all but S. mutans. Due to its central role in oral biofilms and association to systemic diseases, MET was further characterized in F. nucleatum. Apparent Michaelis-Menten kinetics showed Km values of (0.57 ± 0.16 and 10.43 ± 0.91) μM for ferricyanide and riboflavin. The presence of mediators enhanced acetate production compared to mediator-free controls; when ferricyanide was used, butyrate and formate production was triggered only after its depletion. Finally, the putative molecular mechanisms enabling MET in F. nucleatum are discussed.}, }
@article {pmid41146339, year = {2025}, author = {Barker, EM and Small, CM and Bassham, S and Beck, EA and Currey, MC and Healey, HM and Johnson, BD and Cresko, WA and Jones, AG}, title = {Signatures and likely sources of the male pregnancy microbiome in wild bay pipefish (Syngnathus leptorhynchus).}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {112}, pmid = {41146339}, issn = {2524-4671}, abstract = {BACKGROUND: Understanding the origin and structure of microbiomes and their associations with ecologically significant host traits is essential for understanding the evolution of host-microbe interactions. These interactions support a wide range of physiological processes important for development, survival, and reproduction. Syngnathid fishes (seahorses, pipefish, and seadragons) represent a compelling system for investigating host-microbiome interactions due to their unique evolution of male pregnancy. Males harbor a fitness-critical brood pouch that provides embryos with protection, osmoregulation, and nutrient exchange through a placenta-like structure, all while requiring the male to modulate his immune system to accommodate developing offspring. These features create a tightly regulated internal environment where microbial interactions could be especially influential to supporting a successful pregnancy. While we have some understanding of the physiological and genetic factors underlying brood pouch development and maintenance, the role of the microbiome and host-microbe interactions in male pregnancy has remained underexplored across the broader diversity of Syngnathidae species and geographic regions. To investigate this relationship further, and for the first time sampling microbiota from a wild syngnathid population, we characterized microbiomes of the bay pipefish (Syngnathus leptorhynchus) using high-throughput 16S rRNA gene sequencing. We quantified microbial community diversity and composition across the brood pouch, embryos, ovaries, gills, intestines, and outer skin body tissues, focusing on sex-specific (brood pouch, embryo, ovary) and sex-shared (gill, intestine, skin) tissues, and variation in pregnancy stage (non-pregnant, early, mid, and late pregnancy).<br><br>RESULTS: We found that the male brood pouch microbiome was distinct from all other body sites (ovaries, embryos, gills, intestines, and outer skin) in community composition, and in that it exhibited the highest richness and phylogenetic diversity of microbes of any site on average, possibly supporting a specialized environment for embryonic development. Moreover, we found that microbial diversity was lower in non-pregnant brood pouches compared to each pregnancy stage (non-pregnant, early, mid, and late pregnancy) but found no significant differences among the pregnancy stages. Female ovaries had the lowest microbial richness and phylogenetic diversity compared to nonpregnant brood pouches, pregnant brood pouches, and embryos. Source tracking analysis using fast expectation-maximization for microbial source tracking (FEAST) indicated that the male outer skin serves as a significant microbial source for both the pregnant brood pouch and developing embryos, establishing a strong paternal influence on the offsprings&#x2019; microbial communities. Overall, we identified Proteobacteria, Bacteroidota, Cyanobacteria, Planctomycetota, and Actinobacteriota as the dominant phyla spanning all surveyed bay pipefish tissue sites, consistent with previous teleost fish microbiome studies. Analysis of core microbiome and indicator species further revealed that sequences classified as Methylotenera_A_557637 (two species), GCA-2862085 sp., Yoonia_491068 sp., Pla163 sp007750655, and Roseibacillus_B sp. show relatively high abundance and specificity with respect to the male brood pouch, suggesting that these taxa may have functional connections to the biology of male pregnancy.<br><br>CONCLUSIONS: These findings reveal insights into the microbial ecology of a unique reproductive system in its natural environment, highlighting the paternal microbiome&#x2019;s potential functional role in shaping the developing offspring. Our results also indicate a likely influence of both environmental and host-specific factors in shaping the bay pipefish microbiome, but there is need for future research on the functional implications of these microbial communities, especially in the brood pouch during pregnancy, and with respect to offspring viability and fitness.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-025-00476-y.}, }
@article {pmid41149922, year = {2025}, author = {Blanchette, RA and Held, BW and Chemello, C and Mardikian, P}, title = {Evaluation of Wood Decay and Identification of Fungi Found in the USS Cairo, a Historic American Civil War Ironclad Gunboat.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {11}, number = {10}, pages = {}, doi = {10.3390/jof11100732}, pmid = {41149922}, issn = {2309-608X}, support = {no number//US National Park Service/ ; Hatch project MIN22-089//USDA/ ; }, abstract = {Studies of microbial degradation of historic woods are essential to help protect and preserve these important cultural properties. The USS Cairo is a historic Civil War gunboat and one of the first steam-powered and ironclad ships used in the American Civil War. Built in 1861, the ship sank in the Yazoo River of Mississippi in 1862 after a mine detonated and tore a hole in the port bow. The ship remained on the river bottom and was gradually buried with sediments for over 98 years. After recovery of the ship, it remained exposed to the environment before the first roofed structure was completed in 1980, and it has been displayed under a tensile fabric canopy with open sides at the Vicksburg National Military Park in Vicksburg, Mississippi. Concerns over the long-term preservation of the ship initiated this investigation to document the current condition of the wooden timbers, identify the fungi that may be present, and determine the elemental composition resulting from past wood-preservative treatments. Micromorphological characteristics observed using scanning electron microscopy showed that many of the timbers were in advanced stages of degradation. Eroded secondary cell walls leaving a weak framework of middle lamella were commonly observed. Soft rot attack was prevalent, and evidence of white and brown rot degradation was found in some wood. DNA extraction and sequencing of the ITS region led to the identification of a large group of diverse fungi that were isolated from ship timbers. Soft rot fungi, including Alternaria, Chaetomium, Cladosporium, Curvularia, Xylaria and others, and white rot fungi, including Bjerkandera, Odontoefibula, Phanerodontia, Phlebiopsis, Trametes and others, were found. No brown rot fungi were isolated. Elemental analyses using induced coupled plasma spectroscopy revealed elevated levels of all elements as compared to sound modern types of wood. High concentrations of boron, copper, iron, lead, zinc and other elements were found, and viable fungi were isolated from this wood. Biodegradation issues are discussed to help long-term conservation efforts to preserve the historic ship for future generations.}, }
@article {pmid41148908, year = {2025}, author = {Zhang, X and Wang, Z and Feng, G and Xiao, Q and Tang, M}, title = {Temporal Dynamics of Bacterial Communities in Ectropis grisescens Following Cryogenic Mortality.}, journal = {Insects}, volume = {16}, number = {10}, pages = {}, doi = {10.3390/insects16101040}, pmid = {41148908}, issn = {2075-4450}, support = {31700613 and CAAS-ASTIP-TRICAAS//the National Natural Science Foundation of China and the Innovative Program of the Chinese Academy of Agricultural Sciences/ ; }, abstract = {Ectropis grisescens (Lepidoptera: Geometridae) is a destructive pest in tea plantations, leading to significant economic losses through defoliation. Existing control strategies, including chemical insecticides and biological agents, are often limited by environmental concerns, resistance, and variable efficacy. Recent evidence suggests that bacteria influence insect physiology and could be leveraged for pest management, but the postmortem microbial ecology of E. grisescens remains uncharacterized. In this study, we employed 16S rRNA sequencing to investigate temporal changes in the bacterial communities of E. grisescens cadavers at 0, 7, and 21 days following cryogenic mortality. Our results indicate a time-dependent decline in microbial diversity, while species richness initially increased before subsequent reduction. The dominant endosymbiont Wolbachia gradually diminished after host death, whereas Enterobacter remained abundant. Notably, non-dominant genera including Lysinibacillus and Sporosarcina exhibited a transient increase in abundance at day 7 before reverting to control levels by day 21. This study presents the first comprehensive analysis of postmortem microbial succession in a lepidopteran system, highlighting dynamic shifts in bacterial composition and offering potential avenues for microbiome-based pest management strategies.}, }
@article {pmid41147699, year = {2025}, author = {Bick, B and Lumpi, T and Lindström, ES and Langenheder, S}, title = {Linking nutrient availability and community size to stochasticity in microbial community assembly.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf110}, pmid = {41147699}, issn = {1574-6941}, abstract = {Both deterministic (e.g. species-environment interactions) and stochastic processes (e.g. random birth and death events) shape communities, but it remains poorly understood which environmental conditions promote stochasticity. Here we investigated interactive effects of nutrient availability and community size on stochasticity in order to predict how eutrophication and biomass loss shift the balance between predictable and random community dynamics. For this, we used freshwater bacterial communities in a microcosm experiment where communities were diluted to varying sizes and exposed to low, intermediate and high nutrient concentrations. Stochasticity was estimated with null modelling and as beta-diversity among replicate communities. At low nutrient concentrations, deterministic processes dominated, especially in smaller communities, which had the lowest diversity and abundance. In contrast, higher nutrient concentrations increased stochasticity. In contrast to theoretical predictions, this was particularly the case in larger communities with the highest diversity and abundance, likely due to stochastic initial growth. The findings underline how nutrient availability and community size jointly influence stochastic assembly processes, with important consequences for bacterial diversity and ecosystem functioning under environmental change.}, }
@article {pmid41144669, year = {2025}, author = {Tao, A and Fu, S and Zhang, R and Yuan, J}, title = {Flagellar location determines the stability of bacterial surface entrapment.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {44}, pages = {e2506380122}, doi = {10.1073/pnas.2506380122}, pmid = {41144669}, issn = {1091-6490}, support = {12090053//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Flagella/physiology ; *Pseudomonas aeruginosa/physiology ; Escherichia coli/physiology ; }, abstract = {Surface interactions play a crucial role in shaping the motility patterns and ecological adaptations of swimming bacteria. Previous studies have primarily focused on peritrichous bacteria like Escherichia coli, whose multiple flagella form a bundle during swimming, allowing them to remain trapped at surfaces for extended periods. However, this surface entrapment phenomenon varies significantly among different bacterial species, despite all fitting into the simplified theoretical models of pusher-type bacteria, suggesting that key factors remain unidentified. Here, we demonstrate that flagellar location is a critical determinant of surface entrapment stability in pusher-type bacteria. Using fluorescently labeled Pseudomonas aeruginosa, we show that cells with a single lateral flagellum exhibit substantially longer surface residence times compared to those with a single polar flagellum, despite similar cell morphology and swimming speeds. Through direct visualization of bacterial orientation angles relative to surfaces, we reveal that this difference results from the distinct bending directions of the flagellar hook-the flexible joint connecting the rigid filament to the cell body. The hook-generated torque resists reorientation differently depending on flagellar location, facilitating surface escape for polar-flagellated bacteria while enhancing entrapment for lateral-flagellated bacteria. Our findings highlight the previously overlooked importance of flagellar placement in bacterial surface interactions, providing insights for understanding microbial ecology and designing biomimetic microswimmers.}, }
@article {pmid41140797, year = {2025}, author = {Zöchling, A and Séneca, J and Pjevac, P and Auñon-Lopez, A and Zebeli, Q and Pignitter, M and Duszka, K}, title = {Comparative analysis of dietary fiber impact on bile acid metabolism and gut microbiota composition in mice.}, journal = {Npj gut and liver}, volume = {2}, number = {1}, pages = {26}, pmid = {41140797}, issn = {3004-9806}, abstract = {Dietary fiber is essential for health but remains under-consumed in Western diets. Fiber types differ in their physicochemical properties, which influence gastrointestinal function, bile acid (BA) metabolism, and gut microbiota composition. C57Bl/6 mice were fed control or 10% (w/w) fiber diets containing cellulose, chitin, resistant starch, pectin, inulin, β-glucan, psyllium, dextrin, or raffinose. All fibers reduced bacterial diversity, while most increased Akkermansia muciniphila abundance. Cellulose/chitin and inulin/β-glucan/raffinose formed distinct microbiome clusters. Rikenellaceae correlated positively with taurine-conjugated BAs levels. BA concentrations were reduced across tissues. Taurine conjugates showed inverse liver-intestine distribution. Inulin and β-glucan resulted in the highest taurine conjugate levels and reduced intestinal taurine-conjugated BAs concentrations, suggesting enhanced bile salt hydrolase (BSH) activity. Resistant starch had a minimal effect. Psyllium most strongly impacted BA- and taurine-related gene expression, cecum size and weight loss. Dietary fibers distinctly modulate BA metabolism and gut microbiota, with implications for metabolic health and targeted therapies.}, }
@article {pmid41140306, year = {2025}, author = {Merges, AK and Manning, P and Baulechner, D and John, K and Zaitsev, A and Wolters, V and Baranski, D and Grossart, HP and Woodhouse, J and Schneider, C and Bálint, M}, title = {StrataSeq: A Workflow for Rapid Development of Molecular Databases for Hard-To-Identify Species.}, journal = {Ecology and evolution}, volume = {15}, number = {10}, pages = {e72375}, pmid = {41140306}, issn = {2045-7758}, abstract = {Biodiversity loss necessitates improved monitoring of small, species-rich taxa, such as protists, phyto- and zooplankton and terrestrial invertebrates. Traditional biomonitoring is often infeasible for these taxa due to complex morphology and few taxonomists. DNA-based approaches offer promising solutions by enabling rapid species identification. However, the effectiveness of these methods depends on the completeness of molecular reference databases, which remain incomplete, particularly for remote and biodiverse regions. To address this, we propose the StrataSeq workflow, a systematic approach to optimise the generation of DNA reference databases for hard-to-identify taxa. Reference sequences allow us to connect molecular operational taxonomic units to a wealth of information available for many described taxa. StrataSeq consists of four key steps: (1) Habitat-stratified sample subsetting selects a minimal but ecologically representative sample set by stratifying along key environmental gradients. (2) Prioritising morphospecies involves sorting specimens into morphospecies and ranking them based on their occurrence across samples, prioritising common taxa for detailed identification. (3) Detailed morphological identification focuses on common morphospecies to maximise taxonomic coverage while minimising effort. (4) Reference DNA sequence generation targets taxa lacking molecular references, with sequenced specimens deposited as museum vouchers. We benchmarked the StrataSeq workflow using two datasets of Collembola from grassland soils in Germany. In comparison with a species list generated by a more labour-intensive traditional approach (identification of randomly selected individuals from all samples), the StrataSeq workflow captured 69% of species but required only 22% of the effort. StrataSeq is adaptable to various organism groups and environmental settings, including both spatial and temporal gradients. The workflow enhances the cost-effectiveness of generating reference DNA databases, supporting improved biodiversity monitoring and ecological research. StrataSeq offers a scalable solution to accelerate the completion of molecular databases, thereby improving biomonitoring and ecosystem assessments under global change pressures.}, }
@article {pmid41139509, year = {2025}, author = {Roy, R and Gogoi, UR and Das, M and Paul, P and Chakraborty, P and Das, S and Sarkar, S and Gupta, AD and Malik, M and Sarker, RK and Tribedi, P}, title = {Optimization of Doses of Antibiotics and Cuminaldehyde to Combat Methicillin-Resistant Staphylococcus aureus (MRSA): A Study With Machine Learning.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {133}, number = {10}, pages = {e70076}, doi = {10.1111/apm.70076}, pmid = {41139509}, issn = {1600-0463}, support = {TNU/R&amp;D/M P/2021/008//The Neotia University/ ; TNU/R&amp;D/M/12//The Neotia University/ ; }, mesh = {*Methicillin-Resistant Staphylococcus aureus/drug effects/physiology ; *Anti-Bacterial Agents/pharmacology/administration &amp; dosage ; Biofilms/drug effects ; *Machine Learning ; Tobramycin/pharmacology/administration &amp; dosage ; Humans ; Microbial Sensitivity Tests ; Gentamicins/pharmacology/administration &amp; dosage ; Staphylococcal Infections/drug therapy/microbiology ; *Benzaldehydes/pharmacology/administration &amp; dosage ; }, abstract = {Methicillin-resistant Staphylococcus aureus (MRSA), a drug-resistant organism, can cause a spectrum of infections in the human host involving biofilm. Therefore, novel therapeutic approaches need to be explored to mitigate this persistent infection. This study investigated a combinatorial approach that incorporates cuminaldehyde (a phytochemical) alongside aminoglycoside antibiotics (gentamicin and tobramycin) to improve antibiofilm efficacy by addressing multiple targets. In this regard, to achieve precise dosing of the chosen compounds for effective biofilm management, different machine learning models, namely multiple linear regression (MLR), polynomial regression (PR), artificial neural network regression (ANNR), and support vector regression (SVR), were employed. The results suggested that ANNR exhibited a strong association between the predicted and experimental observations (R[2] = 98.07). Furthermore, the ANNR model, followed by genetic algorithm (GA), recommended that the combinatorial doses of the selected compounds [cuminaldehyde (40 μg/mL); gentamicin (0.5 μg/mL); and tobramycin (0.035 μg/mL)] could show the highest antibiofilm activity against MRSA. Additionally, this study revealed that the combination of the mentioned compounds at their recommended doses not only accumulated intracellular reactive oxygen species (ROS) but also increased the cell membrane permeability of MRSA. Thus, this study provides a promising foundation for developing novel therapeutic strategies against MRSA biofilm through an AI-driven approach.}, }
@article {pmid41135758, year = {2025}, author = {Declerck, L and Bouchon, F and Demeester, W and Guidi, C and De Mey, M}, title = {Accelerated adaptive laboratory evolution: A tool for evolutionary biotechnology.}, journal = {Biotechnology advances}, volume = {}, number = {}, pages = {108741}, doi = {10.1016/j.biotechadv.2025.108741}, pmid = {41135758}, issn = {1873-1899}, abstract = {Adaptive laboratory evolution (ALE) is a powerful strategy for enhancing microbial traits by harnessing the principles of natural selection in controlled environments. It has enabled significant advances in microbial growth, stress tolerance, and product yield across a variety of organisms, while also providing insight into evolutionary mechanisms. However, the traditional ALE workflow is time- and resource-intensive, relying on prolonged cultivation to allow beneficial mutations to emerge and be maintained in the population. To improve this, a range of evolutionary engineering tools have been developed to accelerate ALE by increasing mutation rates and genetic diversity in evolving strains. In this review, we explore the core parameters that shape ALE, such as selection pressure, transfer method, and passage size, and provide a comprehensive overview of both established and emerging acceleration methods. These techniques are categorized based on portability (applicability across different microorganisms), genomic targetability (specificity of mutagenesis), and reliability (minimal off-target mutations and mutational reproducibility), with the resulting framework for selecting the most suitable approach summarized in Table 3 at the end of the review. We highlight the growing potential of accelerated ALE and outline future directions, including the integration of genome-wide and targeted mutagenesis, computational modeling, laboratory automation, and broader application beyond model organisms. This review aims to streamline the use of accelerated ALE, unlocking its true potential for advancing microbial strain engineering.}, }
@article {pmid41135394, year = {2025}, author = {Khalil, S and Ugolini, V and Forsbacka, J and Karlsson, M and Vetukuri, RR and Lai, FY}, title = {Could extracts from spent mushroom materials transform reclaimed water quality? - A pilot study on pathogen suppression, antimicrobial chemical removal, and plant growth enhancement.}, journal = {Journal of environmental management}, volume = {395}, number = {}, pages = {127688}, doi = {10.1016/j.jenvman.2025.127688}, pmid = {41135394}, issn = {1095-8630}, }
@article {pmid41135049, year = {2025}, author = {Zhang, X and Guo, Y and Shi, J and Zang, Q and Li, Y}, title = {Exclusive Effects of Moxibustion on Gut Microbiota: Protocol for a Focused Systematic Review and Meta-Analysis.}, journal = {JMIR research protocols}, volume = {14}, number = {}, pages = {e73317}, doi = {10.2196/73317}, pmid = {41135049}, issn = {1929-0748}, mesh = {*Moxibustion/methods ; *Gastrointestinal Microbiome/physiology ; Humans ; Meta-Analysis as Topic ; Systematic Reviews as Topic ; Animals ; Research Design ; }, abstract = {BACKGROUND: The gut microbiota (GM) plays a critical role in systemic health, influencing immune, metabolic, and neurological functions. There is emerging evidence suggesting that moxibustion, a traditional thermal therapy, may modulate the GM to restore microbial homeostasis, yet its exclusive effects remain undifferentiated from those of combined therapies such as acupuncture. Previous meta-analyses lack mechanistic specificity, necessitating a focused evaluation of moxibustion's impact on microbial ecology.<br><br>OBJECTIVE: This systematic review and meta-analysis aims to quantify moxibustion-induced changes in GM diversity, taxonomic composition, and functional metabolites (eg, short-chain fatty acids).<br><br>METHODS: We will systematically search the PubMed, Web of Science, Cochrane Library, China National Knowledge Infrastructure, Wanfang, and VIP databases from inception to December 31, 2024, using keywords such as "moxibustion," "gut microbiota," and "intestinal flora." Eligible preclinical (animal) and clinical (human) studies evaluating stand-alone moxibustion interventions on the GM will be included. Primary outcomes include microbial &#x3b1; diversity indexes (Shannon and Simpson) and relative abundance of key taxa (eg, Firmicutes and Bacteroidetes). Risk of bias will be assessed using the Systematic Review Center for Laboratory Animal Experimentation risk-of-bias tool for animal studies and the modified Collaborative Approach to Meta-Analysis and Review of Animal Data from Experimental Studies criteria for human trials. Pooled effect estimates for continuous outcomes (eg, diversity indexes and taxa ratios) will be calculated using the ratio of means with 95% CIs. Statistical analyses will be conducted in RevMan (version 5.4) and R (metafor package), with data archived on Figshare for reproducibility.<br><br>RESULTS: As of March 2025, the literature search and screening have been completed, and 31 studies meeting the inclusion criteria have been identified. The comprehensive analysis is scheduled to be completed by October 2025, with results anticipated to be published in late 2025. On the basis of previous work, an anticipated result is that moxibustion may reduce pathogenic genera such as Ruminococcus while enhancing beneficial genera, effects that are expected to be associated with improved intestinal barrier integrity and anti-inflammatory responses.<br><br>CONCLUSIONS: This protocol provides a rigorous framework to evaluate moxibustion's unique role in GM modulation, bridging traditional medicine with microbiome science. The results will inform optimized, nonpharmacological strategies for managing microbiome-associated chronic diseases and guide future research priorities.}, }
@article {pmid41131424, year = {2025}, author = {Aidarova, A and Carels, M and Haegman, M and Driege, Y and Timmermans, S and Van Damme, E and Aguilera-Lizarraga, J and Viola, MF and de Cássia Collaço, R and Manils, J and Ley, SC and Bosmans, F and Van de Wiele, T and Boeckxstaens, G and Libert, C and Beyaert, R and Afonina, IS}, title = {CARD14 signaling in intestinal epithelial cells induces intestinal inflammation and intestinal transit delay.}, journal = {EMBO molecular medicine}, volume = {}, number = {}, pages = {}, pmid = {41131424}, issn = {1757-4684}, support = {G035517N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; 3G0I1422//Fonds Wetenschappelijk Onderzoek (FWO)/ ; G000220N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; 12Z3922N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; G0A7T24N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; 3G086521//Fonds Wetenschappelijk Onderzoek (FWO)/ ; 3S003122//Strategic Basic Research grants from FWO/ ; 3179K5620//Strategic Basic Research grants from FWO/ ; 01G00419//Ghent University grant GOA/ ; 01M00121//Methusalem/ ; 2024/01/511//Universiteit Gent (UGent)/ ; 365C06721//Stichting Tegen Kanker (Fondation Contre le Cancer)/ ; 222487/Z/21/Z//Wellcome Trust Investigator/ ; }, abstract = {CARD14 is an intracellular NF-κB signaling mediator in the skin, and rare CARD14 variants have been associated with psoriasis and atopic dermatitis. CARD14 is also expressed in intestinal epithelial cells (IEC). However, its function in the intestine remains unknown. We demonstrate here that transgenic mice expressing the psoriasis-associated gain-of-function human CARD14(E138A) mutant specifically in IEC show mild intestinal inflammation, without epithelial damage. Moreover, CARD14(E138A)[IEC] mice show a drastic reduction in intestinal motility, often associated with rectal prolapse. Enteric neuronal survival and functionality are unaffected in CARD14(E138A)[IEC] mice. Transcriptome analysis of IEC from CARD14(E138A)[IEC] mice reveals decreased expression of antimicrobial peptides by Paneth cells, accompanied by microbial dysbiosis and increased susceptibility to enteric bacterial infection. Our findings suggest that gain-of-function CARD14 mutations may not only predispose patients to psoriasis but also mild intestinal inflammation, reduced intestinal motility, and increased sensitivity to intestinal infection. CARD14(E138A)[IEC] mice are also a valuable tool for further investigation of IEC-intrinsic molecular processes involved in intestinal inflammation and motility disorders.}, }
@article {pmid41131131, year = {2025}, author = {Corduneanu, A and Bendjeddou, ML and Sándor, AD and Mihalca, AD and Hornok, S and Péter, &#xc1; and Khelfaoui, F and Aželytè, J and Obregon, D and Mateos-Hernández, L and Maitre, A and Abuin-Denis, L and Wu-Chuang, A and Kratou, M and Ben Said, M and Cabezas-Cruz, A}, title = {Microbial network assembly in bat flies with differing host specificity from North Africa.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {41131131}, issn = {1618-1905}, support = {14/2022-2024//Ministerul Cercet&#x103;rii &#x15f;i Inov&#x103;rii/ ; 1500107//Hungarian Research Network/ ; NTP-NFT&#xd6;-20-B-0094//Hungarian Ministry of Human Resources, Hungary/ ; SGCE - RAPPORT No 0300//Collectivit&#xe9; de Corse/ ; ANR-10-LABX-62-IBEID//Agence Nationale de la Recherche/ ; }, abstract = {The study investigates the microbial composition of bat flies (Diptera: Nycteribiidae) collected from Myotis punicus in Algeria, focusing on the diversity and dynamics of their microbiota through network analysis. The analysis targets two genera, Nycteribia and Penicillidia, comparing oioxenous and stenoxenous species to understand host specificity's influence on microbial communities. Utilizing 16S rRNA sequencing, alpha and beta diversity metrics, and co-occurrence networks, the study assesses microbial diversity, community composition, and the impact of specific bacteria (endosymbionts, commensals, and pathogens) on network stability. Results reveal significant microbial community variations between genera and species, with N. latreillii exhibiting the most complex network. We showed that host specificity and feeding strategies significantly influence microbial diversity and interactions within bat flies. Robustness analysis through node removal simulations identifies the roles of key bacteria, such as Wolbachia, Arsenophonus, and Bartonella, in maintaining network stability. Findings highlight the complex interplay between these microorganisms and their hosts, offering insights into microbial ecology and vector-pathogen dynamics. The research underscores the importance of bat flies in shaping pathogen transmission networks, contributing valuable knowledge to wildlife ecology, disease control, and conservation strategies.}, }
@article {pmid41129402, year = {2025}, author = {Kovács, E and Szűcs, C and Juhász-Erdélyi, A and Bagi, Z and Kovács, KL}, title = {Anaerobic fungi - effective warriors in lignocellulosic biomass degradation and fermentation.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf108}, pmid = {41129402}, issn = {1574-6941}, abstract = {The significant advancements in understanding the roles of anaerobic fungi within microbial ecology have opened numerous avenues for biotechnological exploitation, particularly in enhancing the productivity of livestock. The efficient, unique, and complex enzyme systems of anaerobic fungi play a determining role in the metabolic conversion of lignocellulosic plant matter into animal products such as milk and meat by mammalian herbivores. Mitigation of methane emissions through microbial or dietary strategies in ruminants is a major environmental climate change issue. In turn, controlled management of the inter-kingdom syntrophic interactions among the eukaryotic anaerobic fungi, prokaryotic bacteria and archaea can lead to the production of valuable biofuels, (biomethane, biohydrogen, bioethanol), and organic acids. These products can also serve as building blocks in numerous processes to generate high value chemicals in circular bioeconomy.}, }
@article {pmid41128906, year = {2025}, author = {Ma, Z and Wang, J and Huang, C and Cao, Y and Sun, Y and Hu, Y and Basit, MF and Huang, J}, title = {Effects of Facility Cultivation Shaping Soil Microbial Community Structure in Jujube Orchard.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {112}, pmid = {41128906}, issn = {1432-184X}, support = {2019YFD1001605//National Key Research and Development Program of China/ ; 2019YFD1001605//National Key Research and Development Program of China/ ; 2019YFD1001605//National Key Research and Development Program of China/ ; 2019YFD1001605//National Key Research and Development Program of China/ ; 2019YFD1001605//National Key Research and Development Program of China/ ; 2019YFD1001605//National Key Research and Development Program of China/ ; 2019YFD1001605//National Key Research and Development Program of China/ ; 2019YFD1001605//National Key Research and Development Program of China/ ; 31870584//National Natural Science Foundation of China/ ; 31870584//National Natural Science Foundation of China/ ; 31870584//National Natural Science Foundation of China/ ; 31870584//National Natural Science Foundation of China/ ; 31870584//National Natural Science Foundation of China/ ; 31870584//National Natural Science Foundation of China/ ; 31870584//National Natural Science Foundation of China/ ; 31870584//National Natural Science Foundation of China/ ; XJCYTX-01//Xinjiang Jujube Industrial Technology System/ ; XJCYTX-01//Xinjiang Jujube Industrial Technology System/ ; XJCYTX-01//Xinjiang Jujube Industrial Technology System/ ; XJCYTX-01//Xinjiang Jujube Industrial Technology System/ ; XJCYTX-01//Xinjiang Jujube Industrial Technology System/ ; }, mesh = {*Soil Microbiology ; *Ziziphus/microbiology/growth &amp; development ; *Bacteria/classification/genetics/isolation &amp; purification ; Soil/chemistry ; *Mycorrhizae/classification/genetics/isolation &amp; purification ; *Microbiota ; Nitrogen/analysis ; *Agriculture/methods ; Carbon/analysis ; Hydrogen-Ion Concentration ; Biodiversity ; }, abstract = {Facility cultivation systems provide protection for jujube (Ziziphus jujuba) against rain-induced fruit cracking during the maturation and regulate the fruit ripening process. Prolonged cultivation within these controlled environments may alter the soil microbial community structure, potentially detrimentally affecting plant growth and fruit quality. There is a lack of information regarding the arbuscular mycorrhizal fungi (AMF) and bacterial communities in orchards under facility conditions. This study compared the soil bacterial and AMF communities in jujube orchards under greenhouse and rain shelter conditions. Greenhouse cultivation significantly increased soil organic carbon (SOC), total nitrogen (TN), and electrical conductivity, while it decreased soil pH compared to rain shelters. These changes were associated with reduced α-diversity indices in both bacterial and AMF communities. Non-metric multidimensional scaling analysis demonstrated distinct differences between bacteria and AMF communities under the two cultivation types. The phyla Actinobacteria, Gemmatimonadetes, and Rokubacteria were identified as key contributors to the observed alterations in the bacterial community, while variations in the genus Glomus and Paraglomus were responsible for changes in the AMF communities between the two cultivation types. Redundancy analysis revealed that pH was the primary factor shaping microbial community structure across the two cultivation types. Using a Zi-Pi plot, we identified several keystone ASVs, which showed a positive correlation with pH, SOC, and TN. The findings highlight the significant impact of cultivation type on soil microbial community structure and function, which has important implications for optimizing cultivation practices and ensuring sustainable jujube production.}, }
@article {pmid41127647, year = {2025}, author = {von Friesen, LW and Farnelid, H and von Appen, WJ and Benavides, M and Grosso, O and Laber, CP and Schüttler, J and Sundbom, M and Torres-Valdés, S and Bertilsson, S and Peeken, I and Snoeijs-Leijonmalm, P and Riemann, L}, title = {Nitrogen fixation under declining Arctic sea ice.}, journal = {Communications earth &amp; environment}, volume = {6}, number = {1}, pages = {811}, pmid = {41127647}, issn = {2662-4435}, abstract = {With climate change-induced sea ice decline in the Arctic Ocean, nitrogen is expected to become an increasingly important determinant of primary productivity. Nitrogen fixation is the conversion of molecular nitrogen to bioavailable ammonium by microorganisms called diazotrophs. Here, we report nitrogen fixation rates, diazotroph composition, and expression under different stages of declining sea ice in the Central Arctic Ocean (multiyear ice, five stations) and the Eurasian Arctic (marginal ice zone, seven stations). Nitrogen fixation in the Central Arctic Ocean was positively correlated with primary production, ranging from 0.4 ± 0.1 to 2.5 ± 0.87 nmol N L[-1] d[-1]. Along two transects across the marginal ice zone, nitrogen fixation varied between days and ice regime from below detection up to 5.3 ± 3.65 nmol N L[-1] d[-1] associated with an ice-edge phytoplankton bloom. We show nitrogen fixation in sea ice-covered waters of the Arctic Ocean and provide insight into present and active non-cyanobacterial diazotrophs in the region.}, }
@article {pmid41127399, year = {2025}, author = {Guo, Y and Ouyang, H and Su, J and Zhong, M and Huang, W and Huang, M and Xie, C}, title = {Developing and validating a nomogram for predicting endoscopic hemostasis failure in cirrhotic patients with esophageal variceal bleeding.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1670759}, pmid = {41127399}, issn = {2296-858X}, abstract = {BACKGROUND AND AIMS: This study aimed to create and validate a model to predict the failure of endoscopic hemostasis in Chinese cirrhosis patients with acute esophagogastric variceal bleeding (EGVB), enabling early identification of high-risk individuals.<br><br>METHODS: A retrospective study analyzed 296 cirrhotic patients with EGVB who received emergency endoscopic therapy from January 2020 to February 2025. Patients were divided into success (n = 273) and failure (n = 23, defined as bleeding recurrence within 5 days) groups. LASSO regression optimized variable selection, and multivariate logistic regression identified independent predictors to create a nomogram. Internal validation used Bootstrap resampling (500 iterations). Model performance was assessed using ROC curves, calibration plots, and decision curve analysis (DCA), and compared with CTP (Child-Turcotte-Pugh), MELD (Model for End-Stage Liver Disease), and Rockall scores.<br><br>RESULTS: The cumulative incidence of endoscopic failure was observed to be 7.8%. Independent predictors identified included a shock index (SI) > 1.2 (OR = 5.447), the presence of a red color (RC) sign (OR = 10.005), active bleeding observed during endoscopy (OR = 5.962), and the CTP (OR = 1.584). The nomogram exhibited superior discriminatory power with an AUC of 0.890 (95% CI: 0.820-0.960), outperforming the CTP (AUC = 0.771, 95% CI: 0.656-0.886; P < 0.001), MELD (AUC = 0.733, 95% CI: 0.616-0.849; P < 0.001), and Rockall (AUC = 0.656, 95% CI: 0.545-0.768; P < 0.001). Calibration was satisfactory as indicated by the Hosmer-Lemeshow test (&#x3c7;[2] = 10.021, P = 0.263). DCA demonstrated a clinical net benefit across a broad range of thresholds.<br><br>CONCLUSION: A validated nomogram that integrates the SI, RC sign, active bleeding, and CTP provides an effective prediction of the risk of endoscopic hemostasis failure in patients with cirrhotic EGVB, thereby facilitating timely intervention.}, }
@article {pmid41126179, year = {2025}, author = {Heuberger, M and Wehrkamp, CM and Pfammatter, A and Poretti, M and Graf, JP and Herger, A and Isaksson, J and Schlagenhauf, E and Honegger, R and Wicker, T and Sotiropoulos, AG}, title = {A reference metagenome sequence of the lichen Cladonia rangiformis.}, journal = {BMC biology}, volume = {23}, number = {1}, pages = {319}, pmid = {41126179}, issn = {1741-7007}, support = {310030_212428//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, mesh = {*Lichens/genetics/microbiology ; *Metagenome ; Symbiosis/genetics ; *Genome, Fungal ; *Ascomycota/genetics ; Chlorophyta/genetics ; }, abstract = {BACKGROUND: Lichens are an ancient symbiosis comprising the thalli of lichen-forming fungi, their photoautotrophic partners, and their microbiome. So far, they were poorly studied at the genome sequence level. Here, we present a reference metagenome for the holobiont of Cladonia rangiformis, aiming to illuminate the genomic complexity and evolutionary interactions within lichen symbioses.<br><br>RESULTS: Using long-read sequences from an entire symbiotic complex, plus short-read libraries from 28 additional diverse European lichen samples, we were able to separate genome sequences of 20 individual species. We constructed chromosome-scale assemblies of the C. rangiformis fungus and its trebouxioid green algal photobiont Asterochloris mediterranea. The genome of the fungus comprises&#x2009;~&#x2009;22% transposable elements and is highly compartmentalized into genic regions and large TE-derived segments which show extensive signatures of repeat-induced point mutations (RIP). We found that A. mediterranea centromeres are predominantly derived from two interacting retrotransposon families. We also identified strong candidates for genes that were horizontally transferred from bacteria to both alga and fungus. Furthermore, we isolated 18 near-complete bacterial genomes, of which 13 are enriched in the lichen compared to surrounding soil. Analysis of gene content in fungus, algae, and bacteria identified 22 distinct biosynthetic gene cluster categories for known secondary metabolites.<br><br>CONCLUSIONS: Our findings revealed that the thalli of C. rangiformis have a highly complex microbiome, comprising a mix of species that may include opportunists, ecologically obligate symbionts and possibly even lichen-beneficial bacteria. This study provides the first chromosome-scale genomic framework for a lichen holobiont, offering a foundational resource for future research into metagenomics, symbiosis, and microbial ecology in lichens.}, }
@article {pmid41124090, year = {2025}, author = {Ahumada, D and Schwob, G and Osorio, M and Astorga, MS and Lavergne, C and Olgun, N and Thalasso, F and Poulin, E and Orlando, J and Cabrol, L}, title = {Higher variability of bacterial communities across space than over time in Antarctic lakes, and contrasting assembly processes.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0107925}, doi = {10.1128/aem.01079-25}, pmid = {41124090}, issn = {1098-5336}, abstract = {As sentinels of environmental changes, Antarctic lakes are ideal systems for studying the temporal and spatial dynamics of microbial communities. However, the relative magnitude and underlying mechanisms driving these variations remain poorly understood. Studying the spatiotemporal variation of microbial communities is crucial to provide a robust baseline for predicting ecosystem responses to global changes. Here, we investigated the spatial and inter-annual variation of bacterial community structure and their underlying assembly processes across sediment and water habitats in 11 lakes on the Fildes Peninsula, Maritime Antarctica, sampled during austral summers from 2017 to 2023, using 16S rRNA gene sequencing. The communities primarily clustered by habitat, with higher diversity in sediment (characterized by Rhodoferax, Intraporangiaceae, and Vicinamibacterales) compared to water (characterized by Polaromonas, Flavovacterium, and Sporichthyaceae). Spatial turnover of communities dominated over inter-annual variation in both habitats. Accordingly, the temporal core microbiome showed greater stability than the spatial core. The conserved bacterial communities (core communities) over time and across space exhibited a strikingly similar taxonomic composition. Community assembly processes differed between habitats, with a stronger contribution of dispersal limitation in sediment, versus ecological drift in water, as expected from the differences in connectivity within each habitat. Spatial and temporal variations in sediment were driven by globally similar assembly processes. In contrast, in water communities, different assembly processes explained the spatial and temporal variation. These insights emphasize the need to consider both spatial and temporal scales and various habitat types when predicting future bacterial dynamics in Antarctic lakes in a changing environment.IMPORTANCEUnderstanding the inherent baseline microbial dynamics in Antarctic lakes is crucial for predicting their responses to environmental changes. Our findings underscore the predominance of spatial (rather than inter-annual) factors in shaping bacterial communities and highlight the slightly higher contribution of stochastic processes in sediment compared to water habitats. The stochastic processes differed considerably among habitats. The greater stability of the temporal core microbiome suggests a certain degree of resilience toward possible seasonal fluctuations between the inter-annual sampling dates. In water, dispersal limitation and homogeneous selection played a greater role in the spatial than in the temporal turnover of communities, whereas environmental filtering exerted a stronger influence over time. Future studies should integrate both spatial and temporal dimensions in evaluating microbial community variability to improve forecasting of ecosystem shifts in response to global change and thus provide a better baseline for Antarctic biodiversity conservation and management.}, }
@article {pmid41124050, year = {2025}, author = {Zhu, J and Chen, C and Zhang, Y and Li, C}, title = {Impact of ecological restoration on the soil microbial communities during the restoration of damaged Mountain Slope in China's Heilong River Basin.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxaf262}, pmid = {41124050}, issn = {1365-2672}, abstract = {AIMS: This study aimed to elucidate the dynamics of soil microbial communities during ecological restoration on degraded mountain slopes, specifically comparing the impacts of two common strategies: aggregate spray-seeding and planted forest establishment, against undisturbed natural slopes, and assessing key drivers of microbial recovery.<br><br>METHODS AND RESULTS: Soil microbial community composition (bacteria and fungi), diversity, and co-occurrence network structure were analyzed seven years after restoration initiation. Both restoration approaches facilitated microbial community recovery, with restored slope compositions converging towards natural slope baselines. Fungal communities exhibited greater OTU diversity than bacteria, attributed to engineered substrates and rapid vegetation stabilization from spray-seeding. Crucially, restoration successfully increased microbial network complexity. Spray-seeding specifically achieved network stability comparable to natural ecosystems. Significant environmental relationships were identified: soil water content (SWC) showed negative correlations with fungal richness and composition, while below-ground biomass (BGB) positively correlated with bacterial composition.<br><br>CONCLUSIONS: Restoration effectively promotes soil microbial community recovery towards natural ecosystem states, albeit with distinct dynamics for bacteria and fungi. Fungal communities are particularly responsive to restoration techniques like spray-seeding. Soil properties (SWC) and plant development (BGB) are pivotal drivers shaping microbial assemblage during restoration.}, }
@article {pmid41123377, year = {2025}, author = {Piccolo, BD and Chen, M-H and Lan, RS and Moody, B and Yao, T and Huang, T-Y and Pack, L and Adams, SH and Lindemann, SR}, title = {Xenometabolomics reveals metabolic functional guilds unique to specific inulin subtypes in human gut microbiota cultures.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0103125}, doi = {10.1128/msystems.01031-25}, pmid = {41123377}, issn = {2379-5077}, abstract = {UNLABELLED: Dietary fibers promote positive health outcomes that are generally attributed to large bowel bacterial fermentation and associated bioactive metabolites. Historically, studies of the latter have focused on short-chain fatty acids such as butyrate. The gastrointestinal microbiota generate thousands of xenometabolites (microbe-derived, "non-host" metabolites). Most remain uncharacterized for composition and potential bioactivity, and little is known about the impact of fiber structure on the xenometabolome. Using LC/MS, we characterized culture supernatant metabolite profiles in human stool lineages derived from three healthy adult donors and six inulins covering a range of degrees of polymerization (DPs): chicory-derived Frutalose L90 (L90; DP ~ 3), Alfa Aesar (AA; DP ~ 5), Frutafit CLR (CLR; DP ~ 8), Frutafit IQ (IQ; DP ~ 12), Frutafit TEX (TEX; DP > 23), and the highly branched Frutafit agave inulin (AGA). Of the 1,219 LC/MS detected metabolites included in the final data analysis, concentrations of 704 were statistically significant (FDR < 0.1; Kruskal-Wallis test). Of these, 15 metabolites had a structural annotation, highlighting the large number of "unknown" xenometabolites associated with inulin substrates. Each fiber type led to distinct metabolite signatures, despite lineages displaying highly disparate microbial community structures within and across donors. This illustrates that fiber-specific metabolic functional guilds manifest despite highly diverse human gut bacteria communities. While speculative, these metabolic functional guilds could help explain why health effects of dietary fibers are prevalent across the population despite highly disparate gut microbiota patterns. The results also reinforce that fiber structures have a profound effect on the xenometabolome.<br><br>IMPORTANCE: Dietary fibers can convey positive health effects, but the full suite of mechanisms and fiber type differences remains to be elaborated. Historically, most discussions have focused on the impact of fibers in promoting lower gut bacterial fermentation, leading to the generation of short-chain fatty acids (especially butyrate) and promoting growth of specific microbes. That said, health effects associated with dietary fiber are generally shared across diverse individuals harboring disparate gut microbial species, and it is increasingly appreciated that xenometabolites derived from microbial metabolism number in the thousands. In the current report, we applied metabolomics characterization to human stool cultures incubated with six structurally distinct inulin fibers. The results indicate that distinct, fiber-specific metabolite signatures manifest despite quite diverse bacterial community structures across donors. Such outcomes point to the existence of metabolic functional guilds that shape the metabolite landscape-and likely the unique bioactive characteristics-across dietary fiber types.}, }
@article {pmid41123360, year = {2025}, author = {Campbell, KD and Bohannan, BJM and Adair, KL}, title = {Assembly of skin microbiomes is more neutral than gut microbiomes in multiple animal species.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0222325}, doi = {10.1128/spectrum.02223-25}, pmid = {41123360}, issn = {2165-0497}, abstract = {The gut and external tissues of most animals are colonized by communities of microorganisms that can influence the health, development, and fitness of the host. The composition of these communities can vary greatly between individuals within a host species, and both selective factors (e.g., host immune response) and neutral processes (e.g., random loss of microbial cells) have been shown to contribute to this variation. Although it is known that microbiome composition differs between tissues within an individual host, less is known about the ecological processes that underlie these differences. To address this, we investigated whether the contribution of neutral ecological processes to microbiome assembly differs between external (skin and scale) and internal (gut) host tissues for a diverse panel of animal hosts. To do this, we fit a neutral ecological model to microbial communities from external and internal tissues across a variety of animal hosts. Strikingly, we discovered that the neutral model was equally or a better fit to skin or scale microbial communities across all hosts, suggesting that neutral processes play a larger role in the assembly of skin or scale microbiomes compared with gut microbiomes. Furthermore, we observed that this trend is robust to different definitions of the metacommunity (i.e., the microbial taxa available to colonize a host). Finally, we leveraged a simulation framework to compare the model fits of empirical versus simulated microbial communities. We found that neutral model fits to empirical communities can differ from simulated communities, emphasizing the importance of temporal sampling in profiling animal microbiomes.IMPORTANCEAnimal microbiomes are complex assemblages of microorganisms that influence a wide variety of host phenotypes. Despite their importance, we lack a thorough understanding of the processes that guide the formation of microbiomes (i.e., microbiome assembly). Understanding how microbiomes assemble is essential to managing microbiomes for host health, conservation, and other goals. Our work highlights the relatively underappreciated role of neutral ecological processes (the random loss or gain of microbial cells) in the assembly of animal microbiomes. We document a potentially general trend: the microbiomes of external tissues (i.e., skin or scales) tend to be more neutrally assembled than those of internal tissues (i.e., guts). This observation suggests that the commonly reported differences in microbiome composition of external and internal animal tissues may be due in part to different assembly processes. Our work also highlights the dynamic nature of microbiomes and the importance of longitudinal sampling when studying animal microbiomes.}, }
@article {pmid41123190, year = {2025}, author = {Dieter, C and Lemos, NE and Girardi, E and Massignam, ET and Kowalski, TW and Recamonde-Mendoza, M and Puñales, M and Assmann, TS and Crispim, D}, title = {Expression of long noncoding RNAs in peripheral blood mononuclear cells of patients with type 1 diabetes mellitus: potential biomarkers for disease onset.}, journal = {Archives of endocrinology and metabolism}, volume = {69}, number = {6}, pages = {e240496}, doi = {10.20945/2359-4292-2024-0496}, pmid = {41123190}, issn = {2359-4292}, mesh = {Humans ; *Diabetes Mellitus, Type 1/genetics/blood/diagnosis ; *RNA, Long Noncoding/genetics/blood/metabolism ; *Leukocytes, Mononuclear/metabolism ; Female ; Male ; Biomarkers/blood ; Adult ; Case-Control Studies ; Young Adult ; Up-Regulation ; Adolescent ; Glycated Hemoglobin/analysis ; }, abstract = {OBJECTIVE: Long non-coding RNAs (lncRNAs) do not encode proteins and are transcripts longer than 200 nucleotides. The precise involvement of lncRNAs in type 1 diabetes mellitus (T1DM) pathogenesis remains unclear. Therefore, this study aimed to analyze the expressions of five lncRNAs in peripheral blood mononuclear cells of individuals with T1DM and without DM.<br><br>MATERIALS AND METHODS: This study comprised 27 patients with T1DM (cases) and 13 individuals without DM (controls). The case group was divided into two subgroups based on T1DM duration: < 5 years of diagnosis group and long-term diabetes group (&#x2265;5 years). LncRNA expression was evaluated by qPCR.<br><br>RESULTS: MALAT1 and TUG1 were upregulated in patients within the first five years of diagnosis of T1DM compared to the other groups. MEG3 was upregulated in the case group of < 5 years of diagnosis compared to controls. TUG1 and MALAT1 levels were negatively correlated with the duration of T1DM, while TUG1 and MEG3 were positively correlated with glycated hemoglobin levels. Bioinformatics analysis revealed that MALAT1, MEG3, and TUG1 regulate and interact with protein-codifying genes and microRNAs involved in T1DM-related pathways.<br><br>CONCLUSION: Our study revealed MALAT1, MEG3, and TUG1 upregulation in patients within the first five years of diagnosis of T1DM.}, }
@article {pmid41118732, year = {2025}, author = {Zahn, G and Amend, A and Gladfelter, A}, title = {Mycology: The rising tide of marine fungal research.}, journal = {Current biology : CB}, volume = {35}, number = {20}, pages = {R946-R948}, doi = {10.1016/j.cub.2025.09.024}, pmid = {41118732}, issn = {1879-0445}, mesh = {*Fungi/physiology ; *Seawater/microbiology ; *Carbon Cycle ; Biomass ; Oceans and Seas ; }, abstract = {A new study provides a robust global estimate of pelagic fungal biomass. Their findings reveal fungi as ecologically significant components of the ocean carbon cycle, marking a turning point for integrating fungi into marine microbial ecology.}, }
@article {pmid41118316, year = {2025}, author = {Liang, B and Pu, M and Xu, YN and Li, Y and Sun, JN and Zhu, Y and Doraiswamy, C and Dadd, T and Chu, CC}, title = {Dandruff scalp microbiome exhibits flake severity and sex-related differences.}, journal = {The British journal of dermatology}, volume = {193}, number = {Supplement_2}, pages = {ii32-ii39}, doi = {10.1093/bjd/ljaf099}, pmid = {41118316}, issn = {1365-2133}, support = {//Unilever Global R&amp;D/ ; }, mesh = {Humans ; Female ; Male ; *Microbiota/genetics ; *Dandruff/microbiology/pathology ; *Scalp/microbiology ; Adult ; Severity of Illness Index ; Sex Factors ; Middle Aged ; *Dysbiosis/microbiology ; RNA, Ribosomal, 16S ; Young Adult ; }, abstract = {BACKGROUND: Dandruff is a prevalent scalp condition characterized by flakiness and itchiness. Its severity can be assessed clinically based on the grade of flakes and coverage area of flakes adhering to the scalp. Dysbiosis of the scalp microbiome is a key factor associated with dandruff, as revealed by studies comparing healthy individuals with those with dandruff.<br><br>OBJECTIVES: This study further investigated the interplay between microbiome alterations and dandruff severity, and whether these changes are consistent across different sexes.<br><br>METHODS: Dandruff condition was assessed using the Total Weighted Head Score for Adherent Flakes (TWHS AF). Male and female participants with lower dandruff severity (TWHS AF = 32-40 inclusive) and higher dandruff severity (TWHS AF &#x2265; 44) were recruited following ethical clearance of the study and obtaining informed consent. Scalp bacterial composition was investigated by 16S rRNA amplicon sequencing. The absolute abundance of key scalp microbes was quantified by quantitative polymerase chain reaction.<br><br>RESULTS: Notable microbiome compositional differences were observed between scalps with lower and higher dandruff severity. More severe dandruff exhibited a significantly reduced abundance of Cutibacterium acnes and elevated levels of Staphylococcus capitis and Corynebacterium spp. The absolute numbers of Malassezia restricta significantly increased with increased dandruff severity, while M. globosa remained similar. Additionally, distinctive scalp microbial profiles were observed between female and male participants with dandruff, even with the same levels of severity. Interestingly, beta diversity analysis revealed that the microbiomes from male participants with less severe dandruff clustered closely with those of male and female participants with more severe dandruff. Similarly, microbiome metabolic pathway profiles indicated that metabolic alteration in male participants with less severe dandruff was more similar to male and female participants with more severe dandruff.<br><br>CONCLUSIONS: Our findings underscored significant severity-associated variations in microbial ecology. For the first time, we unveiled sex-related differences in microbiome profiles among individuals with dandruff, with male profiles resembling a severe dandruff dysbiosis state. These results highlight a progressive development of microbiome dysbiosis with dandruff severity and suggest potential mechanistic differences between male and female dandruff conditions, which may require different intervention strategies.}, }
@article {pmid41117697, year = {2025}, author = {Li, Z and Kuang, X and Ling, J and Shen, T and Shan, G and Wu, J}, title = {Mouse chymase mast cell protease-4 facilitates blood feeding of Aedes aegypti (Diptera: Culicidae) mosquitoes.}, journal = {Journal of medical entomology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jme/tjaf137}, pmid = {41117697}, issn = {1938-2928}, support = {24 3505 Pj//Swedish Cancer Society/ ; //Guizhou High-level Innovative Talents Training Program (Qiankehe Platform Talents-GCC[2022]033-1)/ ; //Science and Technology Innovation Talent Team of Guizhou Province (Qian Ke He Platform Talent-CXTD [2022]004)/ ; ZK[2021]430]//Guizhou Provincial Basic Research Program (Natural Science)/ ; 21NSFCP29//Incubation Funding of Guizhou Medical University National Natural Science Foundation/ ; }, abstract = {Aedes aegypti (Linnaeus) are rapidly spreading across the globe. Evidence suggests that a Type I hypersensitivity reaction, characterized by IgE-mediated mast cell degranulation, may enhance the blood-feeding behavior of Ae. aegypti. Chymases, the mast cell-specific proteases, may play a critical role in this process. To investigate the role of mouse chymase mast cell protease-4 (mMCP-4) on mosquito blood feeding, we incubated bone marrow-derived mast cells with serum from mice sensitized by female Ae. aegypti bites and subsequently challenged the cells with salivary gland proteins (SGPs) from female mosquito. And the degradation of SGPs by mMCP-4 was assessed. Then, the MCP-4 deficient mice were sensitized twice by Ae. aegypti, the first bite on day 0 and the second on day 3. Throughout these experiments, we recorded the total blood meal duration, probing time, and blood feeding of the mosquitoes and analyzed the cutaneous microbiota. We discovered that serum from sensitized mice enhanced mast cell degranulation and chymase release. And mMCP-4 degraded some SGPs, in particular, potentially cleaving the blood-feeding-related salivary protein D7. Mcpt-4 deficiency resulted in prolonged blood-feeding duration during the second exposure, without affecting initial probing behavior. Moreover, Mcpt-4-deficient mice exhibited a reduced proportion of mosquitoes achieving rapid engorgement. Skin microbiome profiling revealed that Mcpt-4 deficiency attenuated the bite-induced expansion of potentially harmful bacterial taxa, including the dominant genus Corynebacterium (Mycobacteriales: Corynebacteriaceae). These findings identify mMCP-4 as a critical mediator of mosquito blood-feeding behavior and a modulator of skin microbial ecology in response to Ae. aegypti bites.}, }
@article {pmid41117590, year = {2025}, author = {Guo, X and Yang, C and Fu, Q and Li, H and Fang, J and Zheng, R}, title = {Impact of yak excreta on soil bacterial community in alpine marsh under warming conditions.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0149325}, doi = {10.1128/aem.01493-25}, pmid = {41117590}, issn = {1098-5336}, abstract = {Livestock excreta and climate warming are two main disturbances of wetlands embedded in grazing lands, resulting in long-lasting changes in soil microorganisms. However, the impact of livestock excreta on the soil bacteria community in wetlands with climate warming has not been elucidated. In the current study, a laboratory culture experiment was designed to investigate how yak excreta, temperature, and their interaction regulate the soil bacterial community in an alpine marsh. The results show that yak dung increased soil moisture, pH, total organic carbon (TOC), and available phosphorus (AP), but decreased NO3[-]-N (P < 0.05). Yak urine increased soil moisture, NH4[+]-N, and NO3[-]-N (P < 0.05). Warming decreased soil moisture and pH of marsh soil (P < 0.05). Warming increased the alpha-diversity of the bacterial community in marsh soil; yak dung had an opposite effect, while yak urine exerted almost a negligible effect. In comparison with warming, yak excreta was the main cause of changing the bacterial community in marsh soil. Yak dung altered more bacterial genera of marsh soil than yak urine. Moreover, yak dung obviously strengthened the bacterial association interaction in marsh soil, while yak urine had the opposite trend. Yak excreta and temperature altered the bacterial community by regulating NO3[-]-N, AP, pH, TOC, and moisture of marsh soil. This study confirms the different influences of yak dung and urine on the bacterial community of marsh soil under warming conditions and highlights that the impacts of yak excreta on the bacterial community are sensitive to climate warming.IMPORTANCEInvestigating the response of the bacterial community in marsh soil to external disturbances is an important but poorly elucidated topic in microbial ecology. In this study, we evaluated the impacts of yak excreta, temperature, and their interaction on the bacterial community in alpine marsh soil. Our results showed that yak excreta exhibited a stronger influence on the bacterial community of marsh soil than temperature. The response of the bacterial community of marsh soil to yak dung is more sensitive than to yak urine. Yak excreta and temperature significantly altered the bacterial community by regulating NO3[-]-N, AP, pH, TOC, and moisture of marsh soil. Understanding the impact of yak excreta on soil bacterial community under warming conditions is extremely significant for managing grazing and maintaining a healthy alpine marsh ecosystem.}, }
@article {pmid41117558, year = {2025}, author = {Maltz, MR and Topacio, TM and Lo, DD and Zaza, M and Freund, L and Botthoff, J and Swenson, M and Cocker, D and Biddle, T and Yisrael, K and Del Castillo, D and Drover, RW and Aronson, E}, title = {Lung microbiomes' variable responses to dust exposure in mouse models of asthma.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0020925}, doi = {10.1128/msphere.00209-25}, pmid = {41117558}, issn = {2379-5042}, abstract = {UNLABELLED: Inhalation of dust is significant and relevant to health effects. As pollution and climate change worsen in dryland regions, wind currents entrain loose sediment and dust. This potentially disperses toxic geochemical and microbial burdens throughout the region. When inhaled environmental dust and host-associated microbiomes mingle, they pose exposure risks to host respiratory health. The Salton Sea, California's largest lake, is shrinking, thus exposing nearby communities to playa dust. Therefore, we analyze the effect of Salton Sea dust exposure in murine models to relate lung microbial communities and respiratory health. We used an environmental chamber to expose mice to dust filtrate or ambient air and examined the effects of those exposures on lung microbiomes. We found that lung microbial composition varied by dust exposure. Furthermore, dust elicited neutrophil recruitment and immune responses more than mice exposed to ambient air. Sources of dust differentially affected the composition of the lung core microbiome. Lung microbial diversity correlated with neutrophil recruitment as lungs associated with inflammatory responses harbored more diverse microbiomes. Although Salton Sea dust influences dust microbiomes and prevalent taxa, these responses are variable. The composition of lungs exposed to dust collected further from the Salton Sea was more similar to lungs from ambient air exposures; in contrast, dust collected near the Salton Sea yielded lung microbiomes that clustered further from lungs exposed to ambient air. As lakes continue to dry out, we expect greater public health risks in proximal dryland regions, which may correlate with dust microbial dispersal-related changes to lung microbiomes.<br><br>IMPORTANCE: Dust inhalation can lead to health effects, especially when toxic chemicals and microbes mix in with the dust particles. As California's Salton Sea dries up, it exposes lake bottom sediments to wind, which disperses the dried sediments. To mimic the effect of inhaling Salton Sea dust, we collected and filtered airborne dust to use in exposure experiments with mice in environmental chambers. We predicted that inhaling small dust particles, chemicals, and microbial residues found in this dust would affect mouse respiratory health or change the microbes found inside their lungs. We found that inhaling dust led to lung inflammation, and the dust source influenced the type of microbes found inside mouse lungs. As lakes continue to dry out, we expect greater health risks and changes to lung microbiomes.}, }
@article {pmid41117325, year = {2025}, author = {Kaundal, R and Parkash, V and Paul, S and Thapa, M}, title = {Heavy metal stress alters soil microbial structure and diversity in the BBN industrial corridor, Himachal Pradesh, India.}, journal = {International journal of phytoremediation}, volume = {}, number = {}, pages = {1-13}, doi = {10.1080/15226514.2025.2572305}, pmid = {41117325}, issn = {1549-7879}, abstract = {Soil microorganisms are essential to ecosystem functioning, yet their communities are highly susceptible to environmental disturbances such as heavy metal contamination from industrial activities. This study investigates the impact of heavy metal pollution on soil bacterial and fungal communities in the Baddi-Barotiwala-Nalagarh (BBN) Industrial Corridor, Himachal Pradesh, India. Soil samples were analyzed for physicochemical properties and heavy metal content, i.e., cadmium (Cd), iron (Fe), copper (Cu), arsenic (As), lead (Pb), chromium (Cr), zinc (Zn), and manganese (Mn), followed by the isolation and characterization of culturable bacterial and fungal communities. Microbial profiling indicated significant variations in community composition, diversity, and abundance across industrial sites. Firmicutes (Bacillota) and Proteobacteria emerged as dominant bacterial phyla, while the fungal communities were predominantly composed of Ascomycota. Although overall microbial richness and diversity declined with increasing heavy metal concentrations, several isolates exhibited key plant growth-promoting (PGP) traits, including phosphate solubilization, siderophore production, indole-3-acetic acid (IAA) synthesis, ammonia production, and nitrate reduction. Pearson correlation analysis demonstrated a relation between microbial community structure and multiple environmental variables, including heavy metals and key soil physicochemical properties. The findings highlight the dual role of soil microbes as indicators of environmental stress and as potential agents for microbe-assisted bioremediation.}, }
@article {pmid41114872, year = {2025}, author = {Dyczko, D and Hałupka, L and Czyż, B and Czułowska, A and Kiewra, D}, title = {Ticks on migrating birds in southwestern Poland: occurrence of Ixodes ricinus and the first Polish record of Haemaphysalis concinna on birds.}, journal = {Experimental &amp; applied acarology}, volume = {95}, number = {4}, pages = {46}, pmid = {41114872}, issn = {1572-9702}, mesh = {Animals ; Poland/epidemiology ; *Bird Diseases/parasitology/epidemiology ; Nymph/physiology/growth &amp; development/genetics ; *Tick Infestations/veterinary/parasitology/epidemiology ; Larva/growth &amp; development/physiology/genetics/classification ; *Ixodidae/physiology/growth &amp; development/genetics/classification/anatomy &amp; histology ; Animal Migration ; Ixodes/physiology/growth &amp; development ; *Songbirds ; Female ; Male ; Animal Distribution ; }, abstract = {During ornithological research conducted at the Milicz Fishponds Nature Reserve (Barycz Valley Landscape Park, southwestern Poland) from May to July 2024, a total of 245 birds were captured. Four ticks were collected: two Ixodes ricinus larvae and two Haemaphysalis concinna nymphs. We present the first confirmed record of H. concinna parasitising a great reed warbler (Acrocephalus arundinaceus) in Poland. Identification of H. concinna was based on both morphological identification keys and molecular analysis of the COI gene. This finding expands current knowledge on the biodiversity of ticks parasitising birds in Poland and highlights the need for further research on the role of migratory birds in the dispersal of ticks across Central Europe.}, }
@article {pmid41114853, year = {2025}, author = {de Scally, SZ and McDonald, MJ}, title = {Evolution of One Species Increases Resistance to Invasion in a Simple Synthetic Community.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {110}, pmid = {41114853}, issn = {1432-184X}, support = {CE230100001//Australian Research Council/ ; }, mesh = {*Escherichia coli/genetics/growth &amp; development/physiology ; *Saccharomyces cerevisiae/genetics/growth &amp; development/physiology ; *Biological Evolution ; Models, Biological ; Ecosystem ; Introduced Species ; }, abstract = {The species that make up a microbial community determine its potential function. A major goal of microbial ecology is to make assemblages of microbes - synthetic communities - with targeted applications. Replacing a dysfunctional community with a synthetic microbial community can have transformative impacts upon a host or ecosystem, yet the introduced community may be outcompeted by local species or communities, resulting in transient effects. Here, we study a simple synthetic community comprised of two species - E. coli and S. cerevisiae - that have coevolved for either 0, 1000 or 4000 generations, and evaluate the potential for 12 bacterial strains, from five species, to invade. We find that the dominant species (E. coli) in the community protects the less dominant species from being outcompeted during an invasion, and that this effect is strengthened by longer periods of coevolution. Using a mathematical model, we show how prolonged co-evolution leads to protective effects for a community member sensitive to displacement.}, }
@article {pmid41114740, year = {2025}, author = {Hopton, CM and Cockell, CS}, title = {Spatiotemporal Impacts of Enceladus- and Earth-relevant Ammonia Gas On Cultivation of Extremophile Halomonas meridiana.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {111}, pmid = {41114740}, issn = {1432-184X}, support = {NE/S007407/1//Natural Environment Research Council/ ; ST/V000586/1//Science and Technology Facilities Council/ ; }, mesh = {*Ammonia/metabolism ; *Halomonas/growth &amp; development/metabolism/drug effects ; Volatilization ; }, abstract = {One underexplored aspect of microbial growth is the impact of toxic gases transported through the atmosphere. Ammonia is a gas that can supply essential nitrogen but also exert cellular toxicity. Ammonia volatilized from a concentrated source into surrounding environments is therefore a crucial consideration when assessing the capacity of environments to support life, such as within terrestrial environments polluted with ammonia, or the ice crusts above ammonia-water oceans of icy moons. We cultivate Halomonas meridiana proximal to an ammonia source and examine the impact of ammonia volatilization on growth. Lower cell densities (OD600 = 0-1) occurred nearest the ammonia source. At 24 h, wells exhibiting an OD600 = 0-0.5 were evident when ammonia concentrations were ≥ 0.5 M. H. meridiana in proximity to 0 M, 0.1 M, 0.25 M, 0.5 M, and 1 M ammonia exhibited OD600 > 2 in 89.86%, 57.97%, 37.32%, 30.07%, and 18.48% of culture wells at 48 h, respectively. Alteration to growth kinetics and viability of H. meridiana cultivated adjacently to an ammonia source ("adjacently exposed") were not as severe compared to direct culture in ammonia ("directly exposed"). Compared to control, adjacent exposure to 0.1 M ammonia exerted no significant detrimental effect on growth kinetics and enhanced cell density, but adjacent exposure to ≥ 0.5 M ammonia greatly extended lag time, doubling time, reduced cell density, and reduced viability. Ammonia volatilized from 0.1 M sources may thus minimally affect, if not improve, habitability, whereas environments exposed to ammonia volatilized from sources at ≥ 0.5 M could constrain habitability.}, }
@article {pmid41114647, year = {2025}, author = {Basso, TO and Venturini, AM and Ceccato-Antonini, SR and Gombert, AK}, title = {Microbial Ecology Applied to Fuel Ethanol Production from Sugarcane.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf100}, pmid = {41114647}, issn = {1574-6941}, abstract = {The production of fuel ethanol in sugarcane biorefineries is a non-aseptic industrial operation, which employs cell recycling and the use of adapted Saccharomyces cerevisiae strains. Microbial contaminants are present and, depending on the conditions, may lead to process performance deterioration. Past studies have identified the main microbial species present in this environment, using culture-dependent techniques. A few recent studies started to deploy culture-independent techniques to better understand this microbiota and its dynamics. In both cases, lactic acid bacteria have been identified as the main contaminating microorganisms. Less than a handful of reports are available on the interactions between yeast and contaminating bacteria, using synthetic microbial communities, proposing that interactions are not necessarily always detrimental. The present mini-review aims at systematizing the current knowledge on the microbiota present in the alcoholic fermentation environment in sugarcane biorefineries and setting the ground and claiming the need for a microbial ecology perspective to be applied to this system, which in turn might lead to future process improvements.}, }
@article {pmid41114112, year = {2025}, author = {Yang, YQ and Li, N and Liu, S and Yu, YW}, title = {Uridine diphosphate-glucose 6-dehydrogenase-mediated glucuronidation and its emerging role in gut-liver immune regulation.}, journal = {World journal of gastrointestinal oncology}, volume = {17}, number = {10}, pages = {110464}, pmid = {41114112}, issn = {1948-5204}, abstract = {This editorial builds on a recent study by Cao et al, which identified uridine diphosphate-glucose 6-dehydrogenase (UGDH) as a pro-tumorigenic enzyme in hepatocellular carcinoma (HCC). UGDH, a key catalyst in glucuronidation, promotes tumor growth and correlates with immunosuppressive features in the HCC microenvironment. Expanding on these findings, we explore broader implications of UGDH within the gut-liver axis. We propose that UGDH regulates immune tone not only through detoxification of bile acids and microbial products, but also by maintaining intestinal barrier integrity. Its dysregulation may impair glucuronidation, leading to bile acid accumulation, increased gut permeability, and microbial translocation, collectively promoting hepatic immune tolerance. Additionally, emerging evidence suggests that gut microbiota-derived metabolites can modulate hepatic UGDH expression, forming a bidirectional feedback loop between microbial ecology and liver metabolism. In this context, UGDH may act as a metabolic immune checkpoint, linking metabolic dysfunction with immune escape mechanisms such as programmed cell death ligand 1 upregulation and cyclic guanosine monophosphate-adenosine monophosphate synthase-stimulator of interferon genes pathway activation. Targeting UGDH could therefore help restore gut-liver immune balance and delay gastrointestinal cancer progression, especially in metabolic HCC. This editorial integrates metabolic, microbial, and immunological perspectives to support a novel translational framework.}, }
@article {pmid41114005, year = {2025}, author = {Sun, R and Xu, W and Xu, Y and Xu, Z and Tan, Y and Li, J and Liu, H and Yung, CCM}, title = {Environmental gradients shape viral-host dynamics in the Pearl River estuary.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf164}, pmid = {41114005}, issn = {2730-6151}, abstract = {Marine viruses play critical roles in shaping microbial communities and driving biogeochemical cycles, yet their dynamics in estuarine systems are not well characterized. Here, we conducted a comprehensive metagenomic analysis of viral communities and virus-host interactions across the Pearl River estuary, a dynamic subtropical estuary in southern China. Using 24 metagenomic libraries from eight sampling sites, we identified 29,952 viral populations, with Uroviricota and potential Uroviricota accounted for 80.48% of taxa, underscoring their ecological importance. A key finding of our integrated analysis is the unexpectedly high abundance of nucleocytoplasmic large DNA viruses in offshore waters, which suggests a more significant role for eukaryotic viruses in coastal ecosystems than previously acknowledged and correlates with elevated levels of their eukaryotic hosts. Environmental variables, particularly salinity and nutrient availability, emerged as key drivers of viral and host distribution patterns. By linking environmental gradients to distinct community "envirotypes" and their underlying genomic features, we revealed novel virus-host interactions and highlighted the impact of environmental gradients on microbial ecology. Additionally, viral auxiliary metabolic genes linked to phosphorus and nitrogen metabolism suggest critical roles in modulating host metabolic pathways and influencing nutrient cycling. Our findings demonstrate how spatial heterogeneity and environmental gradients shape viral and microbial ecology in estuarine ecosystems. Our findings provide a holistic, multi-domain view of microbial and viral ecology, demonstrating how integrating prokaryotic, eukaryotic, and viral community analyses offers a more complete understanding of ecosystem function in these critical transition zones.}, }
@article {pmid41113651, year = {2025}, author = {Lan, R and De Paula Ramos, L and Chen, Z and Carrouel, F}, title = {Editorial: Exploring the oral-gut microbiome interactions: pathways to therapeutic strategies and implications for systemic health.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1691238}, pmid = {41113651}, issn = {1664-302X}, }
@article {pmid41112761, year = {2025}, author = {Lestin, L and Villemur, R}, title = {Modulation of carbon-to-nitrogen ratio shapes the microbial ecology in a methanol-fed recirculating marine denitrifying reactor.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e20129}, pmid = {41112761}, issn = {2167-8359}, mesh = {*Denitrification ; *Methanol/metabolism ; *Bioreactors/microbiology ; *Nitrogen/metabolism/analysis ; Biofilms/growth &amp; development ; *Carbon/metabolism/analysis ; Piscirickettsiaceae/metabolism/genetics ; Nitrates/metabolism ; Water Purification/methods ; }, abstract = {BACKGROUND: Nitrate (NO3 [-]) can accumulate in closed-circuit ecosystems to a toxic level. Adding heterotrophic denitrification process to the water treatment is a strategy to reduce this level. This type of process usually requires the addition of a carbon source. Carbon-to-nitrogen ratio (C/N) is a key parameter known to influence both the function and the activity of microbial communities in bioprocesses. Few studies have examined the influence of C/N on denitrification systems operated under methylotrophic and marine conditions. Here we assessed the influence of C/N (methanol and NO3 [-]) on the performance of a laboratory-scale, recirculating denitrifying reactor operated under marine conditions. We monitored the evolution of the bacterial community in the biofilm to assess its stability during the operating conditions. Finally, the relative gene expression profiles of Methylophaga nitratireducenticrescens strain GP59, the main denitrifier in the denitrifying biofilm, were determined during the operating conditions and compared with those of GP59 planktonic pure cultures.<br><br>METHODOLOGY: A 500-mL methanol-fed recirculating denitrification reactor operated under marine conditions and colonized by a naturally occurring multispecies denitrifying biofilm was subjected to eight different C/N. We monitored several physico-chemical parameters (denitrifying activities, methanol consumption, CO2 production) throughout the operating conditions. The evolution of the bacterial community in the biofilm during these conditions was determined by 16S rRNA gene amplicon sequencing. Metatranscriptomes were derived from the biofilm to determine (1) the relative gene expression profiles of strain GP59, and (2) the functional diversity of the active microorganisms in the biofilm.<br><br>RESULTS: Changes in C/N did not correlate with the denitrification dynamics (NO3 [-] and NO2 [-] reduction rates, NO2 [-] and N2O dynamics), but did correlate with the methanol consumption rates, and the CO2 production rates. Throughout the operating conditions, nitrite and N2O appeared transiently, and ammonium was not observed. The bacterial community in the reactor increased in diversity with biofilm aging, especially among heterotrophic bacteria, at the expense of methylotrophic bacteria. The relative expression profiles of strain GP59 in the biofilm are distinct from those of planktonic pure cultures of strain GP59, and that the expression of several riboswitches and xoxF would be involved in these differences.<br><br>CONCLUSIONS: When the biofilm community is well established in the reactor, it can withstand changes in C/N with limited impact on the denitrification performance. The increase in the proportion of heterotrophs would allow the reactor to be more flexible regarding carbon sources. This knowledge can be useful for improving the efficiency of denitrification system treating close circuit systems such as marine recirculating aquaculture wastewater or seawater aquarium.}, }
@article {pmid41112022, year = {2025}, author = {Gao, J and Zhang, J and Wang, J and Chang, Y and Qin, Z and Sun, L and Li, M and Yang, Q}, title = {Intraspecific Genetic Diversity Analyses of Yam (Dioscorea polystachya Turcz.) Based on DUS Traits and SSR Molecular Markers.}, journal = {Ecology and evolution}, volume = {15}, number = {10}, pages = {e72295}, pmid = {41112022}, issn = {2045-7758}, abstract = {Yam (Dioscorea polystachya Turcz.) is an asexually reproduced food and traditional Chinese medicinal crop with extensive genomic variability. However, the detailed characterization of genetic diversity among different yam germplasm samples is still insufficient. This study evaluated the genetic divergence and genetic structure of 113 D. polystachya accessions collected from 17 provinces in China based on 50 distinctness, uniformity, and stability (DUS) traits and 19 simple sequence repeat (SSR) markers. All the selected varieties were categorized into three groups based on morphological characteristics and further validated by principal component analysis. Furthermore, 14 core traits, including 6 leaf traits, 4 tuber traits, 3 bulbil traits, and 1 stem trait, were selected to increase field inspection efficiency. SSR fingerprinting, utilizing 19 highly polymorphic markers, successfully distinguished all 113 yam varieties, revealing relatively high levels of genetic variation. Interestingly, the optimal genetic structure defined three groups, whereas a finer-scale model consistently classified the varieties into five groups, corroborating the genotypic cluster analysis. Furthermore, this study preliminarily identified 10 groups of potential heterotypic synonyms and 13 groups of potential homonyms among the yam accessions. These results demonstrate that the 19 selected SSR markers, in conjunction with DUS traits, can effectively discriminate the 113 D. polystachya varieties. Our findings provide critical insights for the conservation of pure breeds and the utilization of Dioscorea germplasm resources.}, }
@article {pmid41109620, year = {2025}, author = {Rojas Oñate, D and Opazo Capurro, A and González Rocha, G and Zornoza, R and Torres Bustos, C and Hasbún, R and Bucarey, B and Osman, JR and Schoebitz, M}, title = {Plastisphere and the occurrence of antibiotic resistance in a 40-year-old abandoned coastal landfill site in Chile.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {127280}, doi = {10.1016/j.envpol.2025.127280}, pmid = {41109620}, issn = {1873-6424}, abstract = {Plastispheres are microbial communities that inhabit plastic surfaces and have been extensively studied in aquatic environments. However, little is known about their occurrence in landfills. We investigated plastisphere communities in a 40-year-old coastal abandoned landfill in Rocuant-Andalién, Chile, and aimed to characterize landfill plastisphere communities and assess their potential role as reservoirs of antibiotic resistance genes (ARGs). High-density polyethylene was the predominant plastic type (56 %). Microscopy revealed diverse bacterial morphotypes, including bacilli, cocci, and filamentous forms, forming clusters on plastic surfaces. 16S rRNA gene sequencing revealed that Actinobacteria, Firmicutes, and Proteobacteria dominated most samples, with high overall diversity and richness. Beta diversity analysis indicated significant variation in bacterial communities among sites but not among polymer types. Notably, the intI1 gene, associated with the spread of antibiotic resistance, was detected at 67 % of the sampled sites. These findings reveal that landfills act as reservoirs for a wide range of bacteria, some of which may have clinical significance, highlighting their ecological and public health impact. Furthermore, plastics are likely to transport resistance genes originating from human activities, spreading them into nearby ecosystems, such as wetlands and oceans, where they interact with wildlife.}, }
@article {pmid41107717, year = {2025}, author = {Khan, MSI and Wu, J and Hou, S and Ji, S and Li, H and Chang, Y and Sui, B and Tan, D and Yin, J}, title = {Bile modulates phage-host interactions in multidrug-resistant Pseudomonas aeruginosa.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {666}, pmid = {41107717}, issn = {1471-2180}, support = {2021-243//People's Government of Dalian Municipality/ ; 2021-243//People's Government of Dalian Municipality/ ; 2021-243//People's Government of Dalian Municipality/ ; 2021-243//People's Government of Dalian Municipality/ ; 2021-243//People's Government of Dalian Municipality/ ; 2021-243//People's Government of Dalian Municipality/ ; 2021-243//People's Government of Dalian Municipality/ ; }, mesh = {*Pseudomonas aeruginosa/virology/drug effects/genetics/physiology ; *Bile/metabolism ; *Drug Resistance, Multiple, Bacterial ; Biofilms/growth &amp; development/drug effects ; *Pseudomonas Phages/physiology ; Lipopolysaccharides/biosynthesis ; Pseudomonas Infections/microbiology ; *Host-Pathogen Interactions ; }, abstract = {Biliary tract infections (BTIs) arise within a bile-rich environment that profoundly shapes microbial ecology and pathogen adaptation. Pseudomonas aeruginosa, a major opportunistic pathogen in nosocomial settings, exhibits remarkable physiological plasticity, that enable persistence in such challenging niches. However, the influence of bile on P. aeruginosa's adaptive responses and phage-host interactions remains largely unexplored. Here, we demonstrate that ox-bile imposes concentration-dependent stress on P. aeruginosa strain ZS-PA-35, indicative of host-derived selective pressure. Notably, ox-bile enhances biofilm formation and promotes swarming and twitching motilities while concurrently suppressing swimming motility. Moreover, ox-bile modulates phage susceptibility, likely through altered receptor expression: exposure to ox-bile sensitizes P. aeruginosa to the type IV pili (T4P)-dependent phage phipa2, whereas susceptibility to the lipopolysaccharide (LPS)-targeting phage phipa10 remains unchanged. Genome-wide mutagenesis identified resistance-conferring mutations affecting T4P structures, LPS biosynthesis, and associated regulatory pathways. Among these, phage-resistant mutants ΔpilT and ΔgalU retained high fitness under ox-bile stress, accompanied by enhanced swarming and swimming motilities. Furthermore, in a lysogenic context, ox-bile markedly suppressed prophage accumulation in the T4P-dependent strain ZS-PA-05. These findings reveal that bile acts as a critical environmental cue shaping both adaptive physiology and phage susceptibility in P. aeruginosa, with broad implications for microbiome dynamics and the development of phage-based therapies targeting bile-impacted infections.}, }
@article {pmid41107300, year = {2025}, author = {Urrutia-Angulo, L and Ocejo, M and Yergaliyev, T and Oporto, B and Aduriz, G and Camarinha-Silva, A and Hurtado, A}, title = {Exploring colostrum microbiota and its influence on early calf gut microbiota development using full-length 16S rRNA gene metabarcoding.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {36350}, pmid = {41107300}, issn = {2045-2322}, support = {PRE2020-096275//MICIU/AEI/10.13039/501100011033 and ESF Investing in your future/ ; }, mesh = {*Colostrum/microbiology ; Animals ; Cattle ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; Feces/microbiology ; DNA Barcoding, Taxonomic/methods ; Female ; Phylogeny ; }, abstract = {The early gut microbiota of calves is seeded by colostrum and shaped by diet, environment, disease, and antibiotic treatments. This study analyzed the colostrum microbiota of 42 cows and tracked their calves' gut microbiota during early life (days d1, d16, and d57), assessing the impact of antimicrobial dry cow therapy and infection treatments. The full-length 16S rRNA gene was sequenced using Oxford Nanopore, enabling taxonomic classification down to species level. Microbial richness and diversity were lowest at d1 and increased afterwards. Beta diversity analysis showed that d16 samples had microbial profiles intermediate to those of d1 and d57. The most abundant phyla (Pseudomonadota, Bacillota, and Bacteroidota) were common to all sample categories, while genus-level composition showed greater variability. Colostrum was dominated by Paraclostridium, Romboutsia, and Staphylococcus, while Escherichia/Shigella and Clostridium were more abundant in d1 feces, later replaced by Succinivibrio and Faecalibacterium at d16 and d57. Notably, 56.2% of species in d1 feces were also present in colostrum, and 37.4% of colostrum species persisted in feces at d57, highlighting colostrum´s role in bacterial gut colonization. Interindividual variability in gut microbiota decreased over time as richness and diversity increased. Antimicrobial treatments did not significantly alter microbiota diversity or composition, suggesting a limited long-term impact.}, }
@article {pmid41106786, year = {2025}, author = {Guo, M and Zhao, H and Song, N and Huang, P and Li, M and Han, L and Zeng, KW and Lu, Z}, title = {Shenmai injection attenuates sepsis-associated acute lung injury by remodeling gut microbiota and restoring steroid hormone biosynthesis.}, journal = {Fitoterapia}, volume = {}, number = {}, pages = {106935}, doi = {10.1016/j.fitote.2025.106935}, pmid = {41106786}, issn = {1873-6971}, abstract = {Sepsis-associated acute lung injury (SA-ALI), a critical complication of sepsis, is characterized by immune dysregulation-induced pulmonary dysfunction. Shenmai Injection (SMI) is a standardized herbal preparation consisting of Panax ginseng C.A.Mey (Hongshen) and Ophiopogon japonicus (Thunb.) Ker Gawl (Maidong), traditionally used for qi-replenishing, collapse-stabilizing, and lung-moistening therapy. Although clinically utilized in the management of SA-ALI, the specific mechanisms by which it acts against SA-ALI necessitate further investigation. The present study endeavors to comprehensively determine the therapeutic efficacy of SMI against SA-ALI through an integrated approach combining network pharmacology, metabolomics, metagenomic sequencing, and experimental validation. In this study, murine SA-ALI was established using lipopolysaccharide (LPS) and Poly(I:C). Results indicated that SMI administration significantly attenuated pulmonary inflammation, restored blood-gas barrier integrity, reduced serum pro-inflammatory cytokines and suppressed NF-κB pathway activation in SA-ALI mice. Network pharmacology elucidated the multi-targeted mechanism of SMI in modulating steroid hormone biosynthesis. Integrated metabolomics and target analysis revealed that ophiopogonin A/B and luteolin in SMI alleviates metabolic dysregulation by targeting key enzymes, including AKR1C3, HSD17B1/2, and SULT1E1. Metagenomic profiling demonstrated SMI-mediated gut microbiota remodeling, marked by suppression of pathogenic Chlamydiaceae (particularly Chlamydia abortus) and enrichment of commensal Lactobacillaceae. Correlation analysis showed that intestinal androstenedione and androsterone levels during SMI treatment recovery were negatively correlated with Chlamydia abortus abundance. In conclusion, SMI enhances the recovery from sepsis-associated SA-ALI by dual modulation of gut microbial ecology and host metabolic homeostasis, thereby establishing its potential as a multi-mechanistic therapeutic candidate for sepsis-related organ injury.}, }
@article {pmid41106598, year = {2025}, author = {Khan, KS and Alam, T and Fiaz, S and Azim, R and Qadeer, A and Iqbal, R and Li, L}, title = {Hyphosphere Fungi-Bacteria-Plant Interactions Regulate Phosphorus Tradeoffs in the Soil Plant System.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {}, number = {}, pages = {112819}, doi = {10.1016/j.plantsci.2025.112819}, pmid = {41106598}, issn = {1873-2259}, abstract = {Tripartite interactions among arbuscular mycorrhizal fungi (AMF), phosphorus-solubilizing bacteria (PSB), and terrestrial plants are pivotal in plant stress resistance, nutritional cycling, and soil-microbe ecological functions. The convoluted association between AMF and PSB may play a significant role in the decomposition and absorption of soil organic phosphorus (P), because AMF dynamically secretes carbon-containing compounds from extraradical hyphae (ERH) to stimulate PSB growth rate and activities. PSB are the main contributors of plant nutrition and could play a pivotal role in making soluble P available to plants. In this context, this comprehensive review critically examined the AMF-PSB interactions in soil P mobilization, with a focus on soil biochemical dynamics, microbial ecology, physiological mechanisms, biochemical pathways, and gene expression. While the explored studies emphasize the role of AMF-PSB interactions in P mobilization, it is important to consider that many experiments used root-free compartments, potentially overestimating mycorrhizal contributions relative to root pathways. Future research should integrate root-inclusive systems to provide a more comprehensive understanding of P acquisition dynamics by regulating indigenous AMF in terrestrial ecosystems.}, }
@article {pmid41106329, year = {2025}, author = {Hill, RC and Pieńkowska, A and Merbach, I and Reitz, T and Muehe, EM and Vengosh, A}, title = {Impacts of fertilization on metal(loid) transfer from soil to wheat in a long-term fertilization experiment - using [87]Sr/[86]Sr isotopes as metal(loid) tracer.}, journal = {Environment international}, volume = {205}, number = {}, pages = {109851}, doi = {10.1016/j.envint.2025.109851}, pmid = {41106329}, issn = {1873-6750}, abstract = {Fertilizers are widely used to sustain food production but can alter soil chemistry and potentially contribute toxic metal(loid)s to agricultural systems. For the first time, this study examined the occurrence of select metal(loid)s (Zn, Sr, V, As, Cd, Pb, and U) alongside the [87]Sr/[86]Sr isotope ratio in agricultural soil- both total and mobile pools- and wheat grain. Samples were collected from one of four fertilization treatments- mineral (NPK), organic (manure), combined mineral+organic, and unfertilized controls- within the 120-year Static Fertilization Experiment in Bad Lauchstädt, Germany. Fertilization treatments altered soil pH and organic carbon resulting in mineral fertilization lowering pH and increasing cation mobility (Cd, Zn, Sr), whereas organic fertilization increased pH and enhanced the mobility of non-cationic elements (V, As). These effects translated into higher Cd in mineral-fertilized wheat grain and higher As in mineral+organic wheat grain. Fertilization shifted the [87]Sr/[86]Sr ratios in soils and wheat grains toward that of the applied fertilizers, with mineral and mineral+organic wheat grains inheriting the triple super phosphate signature (0.70778) and organic wheat grains matching manure (0.70883). The [87]Sr/[86]Sr ratio in the mobile soil pool was correlated with mobile As, V, and P, demonstrating that the [87]Sr/[86]Sr ratio reflects both fertilizer source and the mobility of select co-occurring metal(loid)s. Overall, this study demonstrates metal(loid) enrichment in soil and wheat from fertilization and establishes [87]Sr/[86]Sr ratio as a robust tracer of fertilizer impacts. These findings underscore the need for targeted fertilization strategies to reduce contaminant accumulation in agroecosystems.}, }
@article {pmid41106081, year = {2025}, author = {Krimech, A and Sbahi, S and Cherifi, O and Hejjaj, A and Mugani, R and Ouazzani, N and Kerner, M and Oudra, B and Mandi, L}, title = {Seasonal effects on Chlorella sorokiniana UCAM 001 growth and physiology in flat-plate photobioreactors in Morocco's arid climate.}, journal = {European journal of protistology}, volume = {101}, number = {}, pages = {126171}, doi = {10.1016/j.ejop.2025.126171}, pmid = {41106081}, issn = {1618-0429}, abstract = {This study aims to investigate the seasonal variation in growth and physiology of Chlorella sorokiniana UCAM 001 strain using annual optimization monitoring with a groundwater medium in two outdoor flat-plate photobioreactors (PBRs), which were first scaled up at the Faculty of Sciences Semlalia (Marrakech, Morocco). The culture medium was adjusted to ensure non-limiting nutrient concentrations (10 mg·L[-1] and 100 mg·L[-1] of additional phosphorus and nitrate, respectively). Temperature, light, and algal growth were monitored daily. Proline, glycine betaine, and catalase levels were measured every four days to assess the degree of algal stress. Biomass productivity increased during spring, reaching 30 mg·L[-1]·day[-1] with a specific growth rate of 0.73 day[-1]. However, no growth was observed during the summer. Physiological analysis revealed increased proline and glycine betaine levels during autumn and winter due to temperatures as low as 13 °C. In contrast, catalase concentration peaked in spring. Pearson correlation analysis indicated that nutrient limitation, together with temperature and light intensity, induced stress in C. sorokiniana, stimulating catalase production. Algal growth efficiently removed nutrients from the medium, achieving removal rates of 97 % for total phosphorus and 87 % for total nitrogen. Optimized cooling systems will improve PBR efficiency and support algal growth under extreme summer conditions.}, }
@article {pmid41105271, year = {2025}, author = {Castellano-Hinojosa, A and Llodrà-Llabrés, J and Ramos-Rodríguez, E and Smol, JP and Meyer-Jacob, C and Sigro, J and Pérez-Martínez, C}, title = {Temporal succession of bacterial and archaeal communities in a Mediterranean high-mountain lake over the last 430 years using sedimentary DNA.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {107}, pmid = {41105271}, issn = {1432-184X}, support = {LACEN (OAPN 2403-S/2017)//Ministry of Ecological transition in their National Park Autonomous Agency/ ; LifeWatch-2019-10-UGR-01//Ministry of Science and Innovation through the FEDER funds from the Spanish Pluriregional Operational Program 2014-2020 (POPE), LifeWatch-ERIC action line/ ; BIOD22_001//Consejer&#xed;a de Universidad, Investigaci&#xf3;n e Innovaci&#xf3;n and Gobierno de Espa&#xf1;a and Uni&#xf3;n Europea - NextGenerationEU/ ; }, mesh = {*Lakes/microbiology/chemistry ; *Archaea/classification/genetics/isolation &amp; purification ; *Geologic Sediments/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Climate Change ; Spain ; Microbiota ; DNA, Archaeal/genetics ; Biodiversity ; Ecosystem ; DNA, Bacterial/genetics ; Nitrogen/analysis ; DNA, Ancient/analysis ; Temperature ; }, abstract = {Despite the known influence of climate change on high-altitude ecosystems, the long-term response of prokaryotic communities in Mediterranean high-mountain lakes remains poorly understood. Here, we investigate the temporal dynamics of prokaryotic communities over the past ~ 430 years in a Mediterranean high-mountain lake, utilizing sedimentary ancient DNA (sedDNA). By examining a sediment core from Borreguil Lake in the Sierra Nevada (Spain), we evaluated bacterial and archaeal abundance, diversity, and community composition (β-diversity) in relation to paleoenvironmental and climate data. Our findings revealed a significant restructuring of prokaryotic communities, particularly since ca. 1960. A Random Forest model identified dissolved organic carbon, organic nitrogen, Saharan atmospheric dust inputs, and temperature as key drivers of the abundance, diversity, and composition of prokaryotic communities, particularly in the modern era. Notably, the abundance and diversity of bacterial communities increased in response to increased dissolved organic carbon, elevated temperatures, and dust deposition, while archaea demonstrated a more nuanced response linked to organic nitrogen availability and dust inputs. The temporal shifts in microbial community composition point to broader ecological changes within the lake, shaped by climate-driven environmental variations. For example, the increased relative abundance of Cyanobacteria and other taxa linked to higher nutrient availability indicates ongoing eutrophication processes, likely intensified by climate warming. This study highlights the importance of high-mountain lakes as indicators of climate change, contributing valuable insights into microbial ecology's response to long-term environmental change. Our findings offer a foundational understanding for predicting microbial responses in sensitive ecosystems under future climate scenarios.}, }
@article {pmid41105270, year = {2025}, author = {Gamoń, F and Ćwiertniewicz-Wojciechowska, M and Muszyński-Huhajło, M and Miodoński, S and Ziembińska-Buczyńska, A and Cema, G and Tomaszewski, M}, title = {Low-Temperature Anammox Supported by Zero-Valent Iron (ZVI): Microbial and Physicochemical Changes during Treatment of Synthetic and Municipal Wastewater.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {108}, pmid = {41105270}, issn = {1432-184X}, support = {UMO-2017/25/N/NZ9/01159//Narodowe Centrum Nauki/ ; }, mesh = {*Iron/metabolism/chemistry ; *Wastewater/microbiology/chemistry ; Oxidation-Reduction ; Bioreactors/microbiology ; Anaerobiosis ; *Ammonium Compounds/metabolism ; *Bacteria/metabolism/classification/genetics ; *Waste Disposal, Fluid/methods ; Cold Temperature ; }, abstract = {The anaerobic ammonium oxidation (anammox) process offers a sustainable and energy-efficient alternative for nitrogen removal in wastewater treatment, but its performance at low temperatures remains a major challenge. This study investigated the role of zero-valent iron (ZVI) in enhancing anammox activity across a temperature range of 10-30 °C using both synthetic and municipal wastewater (MWW). Short-term batch tests demonstrated that low-dose ZVI (5-10 mg/L) stimulated specific anammox activity (SAA) particularly at 13-20 °C, while ZVI increasing concentration (1-10 mg/L) enhanced the enzymatic activity of HDH and decreased NIR activity, as well as modulated oxidative stress (ROS and GSH balance). In contrast, the long-term operation of the anammox process in sequencing batch reactors (SBR) showed that while ZVI (5 mg/L) improved SAA and microbial stability under synthetic conditions at 13 °C in compared to control (without ZVI), these benefits diminished once real municipal wastewater was introduced, most likely due to biomass stress and organic load. Metataxonomic analysis confirmed that ZVI selectively promoted genera such as Candidatus Brocadia, Denitratisoma, Micavibrionales_unclassified, while reducing overall microbial diversity. These results indicate that low-dose ZVI can temporarily enhance anammox resilience at suboptimal temperatures. However, its long-term application in MWW requires further optimization to mitigate potential inhibitory effects and iron passivation.}, }
@article {pmid41105260, year = {2025}, author = {Phauk, S and Assentato, L and Sin, S and Uk, O and Hap, S and Terenius, O}, title = {Symbiont Diversity of Rice-Associated Leafhoppers (Cicadellidae) in the Tropical Floodplains of the Tonle Sap Lake, Cambodia.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {109}, pmid = {41105260}, issn = {1432-184X}, mesh = {Animals ; *Hemiptera/microbiology/physiology/classification ; *Symbiosis ; *Oryza/parasitology ; Cambodia ; Female ; Lakes/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Male ; Biodiversity ; Microbiota ; Phylogeny ; }, abstract = {Rice-associated leafhoppers (Cicadellidae) play a significant role in rice agroecosystems, contributing not only to direct crop damage but also to the transmission of plant pathogens. This study investigates the symbiont diversity of seventeen leafhopper species from the tropical floodplains of Tonle Sap Lake (TSL), Cambodia. The dominant symbiont across most species was Candidatus (Ca.) Karelsulcia muelleri, an obligate primary endosymbiont essential for nutrient synthesis. The co-obligate symbiont Ca. Nasuia deltocephalinicola was also consistently detected, particularly in Deltocephalinae hosts. In addition, several secondary symbionts, including Sodalis, Arsenophonus, Diplorickettsia, Rickettsia, Wolbachia, and Ca. Lariskella, were identified, showing species-specific associations and potential roles in host fitness and pathogen transmission. Variations in symbiont diversity were observed across cicadellid species, geographic origins, and between sex-associated symbionts, with notable differences in the bacterial composition of Nephotettix virescens. While geographical differences (Battambang vs. Kampong Thom) did not strongly affect microbial composition, sex-associated variations were evident in N. virescens. Females exhibited a higher abundance of Karelsulcia and Nasuia, suggesting possible microbial adaptation related to reproduction. This study highlights the complex and dynamic nature of cicadellid hosts-symbiont interactions and suggests that microbial communities are primarily structured by host species. While geographic distance can influence these communities, this effect is not the same for every species. These findings provide critical insights into the microbial diversity of rice-associated leafhoppers and their potential for ecological roles in rice farming systems. Further studies, including functional analysis and host-symbiont interactions, are crucial to understanding the ecological roles and evolutionary dynamics of these microbial communities.}, }
@article {pmid41105100, year = {2025}, author = {Arellano, AA and Prack, JL and Coon, KL}, title = {Host-mediated niche construction of bacterial communities in an aquatic microecosystem.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf233}, pmid = {41105100}, issn = {1751-7370}, abstract = {Microbes coordinate homeostasis in host-associated and environmental ecosystems alike, but the connectivity of these biomes is seldom considered. Hosts exert controls on the composition and function of their internally associated symbionts, but an underappreciated modality of microbiome curation is external to the host through changes to the environmental species pool from which they recruit microbial symbionts. Niche construction theory describes how organisms alter their environment and the selective landscape of their offspring and conspecifics. We hypothesize that host-driven manipulation of environmental microbial communities is an underexplored form of this concept. Using the pitcher plant mosquito (Wyeomyia smithii) as a model, we tested how hosts shape microbial communities across developmental stages and gradients of pre-existing community complexity. We report three lines of evidence supporting host-mediated niche construction, leveraging amplicon sequencing and microbiota manipulation experiments with germ-free (axenic) and selectively recolonized (gnotobiotic) mosquitoes. First, single female egg-laying assays showed repeatable adult inoculation of sterile water with beneficial bacteria capable of sustaining robust larval development. Second, increasing larval density in assays inoculated with complex, field-derived microbial communities selected for environmental and host-associated bacteria that correlated with increased larval fitness. Finally, exposing axenic larvae to mixtures of parentally and environmentally derived microbiota demonstrated that prior conditioning by conspecifics enhanced offspring fitness. Although the bacterial taxa associated with mosquito structuring varied, members of the Actinobacteriota and Acetobacteraceae were consistently associated with increased fitness. Overall, our results provide an example of host-mediated niche construction to favor environmental microbial communities that positively impact host fitness.}, }
@article {pmid41104934, year = {2025}, author = {Ryan, D}, title = {Gene regulation in Bacteroides fragilis: adaptive control in a dynamic host environment.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {}, number = {}, pages = {e0022525}, doi = {10.1128/mmbr.00225-25}, pmid = {41104934}, issn = {1098-5557}, abstract = {SUMMARYBacteroides fragilis occupies a dynamic position within the human gut. Though it comprises a relatively minor fraction of the gut microbiota, it is disproportionately enriched at extraintestinal sites of infection. This ability to survive in contrasting host environments pivots on a regulatory framework that is both modular and highly plastic. Rather than deploying a suite of hierarchical global regulators, B. fragilis employs numerous operon-embedded transcriptional switches, including site-specific DNA inversions, phase-variable epigenetic systems, extracytoplasmic function sigma/anti-sigma factor pairs, and hybrid two-component systems. These networks are further complemented by cis-regulatory elongation checkpoints and post-transcriptional control by small RNAs. This review explores the full spectrum of these regulatory mechanisms, highlighting how they facilitate niche adaptation, surface variation, immune evasion, and metabolic prioritization. It also explores intraspecies variation focusing on glycan metabolism, antibiotic resistance, and virulence. Additionally, it outlines recombination-driven regulation, alongside extracytoplasmic function sigma factor diversification, flexible promoter architecture, and elongation checkpoints, each contributing to the evolution of transcriptional control in B. fragilis. Finally, it outlines unanswered questions, including the largely unexplored sRNA regulon, the coordination of DNA inversions, elongation control, and phase-variable methylation, and proposes experimental strategies to investigate the integration of these regulatory systems during environmental transitions. Taken together, B. fragilis emerges as a model bacterium for studying decentralized gene regulation in complex microbial ecosystems, with implications for both microbial ecology and therapeutic targeting of the gut microbiota.}, }
@article {pmid41104481, year = {2025}, author = {}, title = {Laila P. Partida-Martínez.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.70665}, pmid = {41104481}, issn = {1469-8137}, abstract = {Laila P. Partida-Martínez, Cinvestav-Irapuato (Mexico).}, }
@article {pmid41104383, year = {2025}, author = {Kumar, P and Chitara, D and Sengupta, S and Banerjee, P and Rai, SN}, title = {Microbial consortia in biotechnology: applications and challenges in industrial processes.}, journal = {3 Biotech}, volume = {15}, number = {11}, pages = {386}, pmid = {41104383}, issn = {2190-572X}, abstract = {Microbial consortia, dynamic communities of interacting microorganisms, outperform single-species cultures in industrial biotechnology by overcoming metabolic bottlenecks and degrading complex compounds. These consortia are vital in bioremediation, bioenergy, bioproduction, agriculture, and wastewater treatment. In bioremediation, they efficiently break down persistent pollutants like polycyclic aromatic hydrocarbons. For bioenergy, they convert organic waste into biofuels such as methane and ethanol through multi-step metabolic processes unachievable by single microbes. They also enable sustainable synthesis of bioplastics, antibiotics, and other high-value compounds while enhancing agricultural productivity through improved nutrient availability and biocontrol of plant pathogens. Consortia degrade complex organic contaminants in wastewater treatment, ensuring cleaner effluents and environmental protection. The industrial application faces challenges, including ensuring microbial community stability, optimising performance, and scaling processes from laboratory to industrial scale. The intricate interactions within consortia complicate control, predictability, and real-time monitoring, while intellectual property and regulatory frameworks pose additional barriers. Limitations include gaps in understanding long-term ecological impacts and scalability in diverse environments. Advancements in microbial ecology, systems biology, and bioprocess engineering are crucial to address these issues. Prospects involve using CRISPR and AI to design robust consortia, improve predictive modelling, and foster interdisciplinary collaborations for sustainable applications. Overcoming these challenges will unlock the full potential of microbial consortia, revolutionise industrial processes, and advance sustainable biotechnology.}, }
@article {pmid41104112, year = {2025}, author = {Hayes, A and Zhang, L and Snape, J and Feil, E and Kasprzyk-Hordern, B and Gaze, WH and Murray, AK}, title = {Common non-antibiotic drugs enhance selection for antimicrobial resistance in mixture with ciprofloxacin.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf169}, pmid = {41104112}, issn = {2730-6151}, abstract = {Antimicrobial resistance (AMR) is a major health concern, and a range of antibiotic and non-antibiotic agents can select for AMR across a range of concentrations. Selection for AMR is often investigated using single compounds, however, in the natural environment and the human body, pharmaceuticals will be present as mixtures, including both non-antibiotic drugs (NADs), and antibiotics. Here, we assessed the effects of one of three NADs in combination with ciprofloxacin, a commonly used antibiotic that is often found at concentrations in global freshwaters sufficiently high to select for AMR. We used a combination of growth assays and qPCR to determine selective concentrations of mixtures and used metagenome sequencing to identify changes to the resistome and community composition. The addition of the three NADs to ciprofloxacin altered the selection dynamics for intI1 compared to the ciprofloxacin alone treatments, and sequencing indicated that mixtures showed a stronger selection for some AMR genes such as qnrB. The communities exposed to the mixtures also showed changed community compositions. These results demonstrate that NADs and ciprofloxacin are more selective than ciprofloxacin alone, and these mixtures can cause distinct changes to the community composition. This indicates that future work should consider combinations of antibiotics and NADs as drivers of AMR when considering its maintenance and acquisition.}, }
@article {pmid41103765, year = {2025}, author = {Li, M and Bi, J and Wang, X and Li, H}, title = {The hidden nitrogen nexus: stochastic assembly and linear gene synergies drive urban park microbial networks.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1652652}, pmid = {41103765}, issn = {1664-302X}, abstract = {Urban parks play a significant role in environmental greening, cultural heritage, and recreational activities. The diversity and distribution of park environmental microbiota have become a hot focus of microbial ecology. However, there has been limited attention on the functional attributes of microbial communities, highlighting the importance of studying the distribution and diversity of functional genes in urban parks. Here, we employed metagenomic sequencing and binning to explore the diversity, assembly, and functional synergy of nitrogen cycling genes from the grassland soil and water in urban parks. Our results showed that glutamate metabolism and assimilatory nitrate reduction are the predominant nitrogen cycling pathways in both the soil and water. The diversity of nitrogen cycling genes in water was more abundant than in soil. The assembly of nitrogen cycling genes in both the soil and water was primarily driven by stochastic processes. Nutrient factors (such as total sulfur) were the most significant influencers of nitrogen cycling genes in park soil, while bacterial communities were the most critical determinants in water. The gene narH, involved in multiple nitrogen cycling metabolic pathways, was identified as an important marker of nitrogen storage in both soil and water. Through metagenomic binning, we discovered linear arrangements of multiple nitrogen cycling genes, such as narG-narH-narJ-narI, which collectively participate in the reduction of nitrate to nitrite, demonstrating the synergy, functional redundancy, and complementarity among nitrogen cycling genes. Our study holds significant implications for the biochemical cycling and the management of nitrogen pollution in urban parks.}, }
@article {pmid41100058, year = {2025}, author = {Duncan, AH and Armenta, N and Garcia-Ledezma, F and Heck, CA and Hafner, S and Planer-Friedrich, B and Fendorf, S}, title = {Alternate Wetting and Drying Limits Arsenic in Porewater and Rice Grain under Severe Future Climate Conditions.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c03552}, pmid = {41100058}, issn = {1520-5851}, abstract = {Climate change, coupled with widespread soil arsenic (As) contamination, is expected to decrease rice yields and increase grain As, threatening food security. One promising mitigation strategy is alternate wetting and drying (AWD) irrigation. However, AWD has not previously been tested under potential future climate conditions. Using rhizoboxes to visualize the rhizosphere, we evaluated the efficacy of AWD for limiting porewater and grain As under both current (daily high of 33 °C and 420 ppmv CO2) and severe warming conditions (daily high of 38 °C and 850 ppmv CO2). Compared to continuous flooding, AWD decreased cumulative As exposure 10 cm below the surface by 8.2× under a 33 °C climate and by 15.9× under a 38 °C climate. Grain total As concentrations decreased by 1.5× with AWD under a 33 °C climate and by 1.3× under a 38 °C climate. Porewater cadmium (Cd) concentrations often increased following drainage but never exceeded 1 μg L[-1], and grain Cd concentrations were 14.7× to 119.7× lower than grain As concentrations. Both AWD and the 38 °C and 850 ppmv CO2 climate conditions enhanced root growth. Our findings indicate that AWD may still be an effective As mitigation strategy under severe future climate conditions.}, }
@article {pmid41099815, year = {2025}, author = {Price, A and Mog, SYA and Dubach, J and Billington, C and Larsen, P}, title = {Microbiomes of 2024's Periodical Cicada Brood XIII Vary By Species and Location.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {105}, pmid = {41099815}, issn = {1432-184X}, support = {2216567 &amp; 1912104//National Science Foundation (NSF)/ ; }, mesh = {Animals ; *Microbiota ; *Hemiptera/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; Illinois ; Male ; Female ; }, abstract = {The 17-year Periodical cicadas (Magicicada spp.) are long-lived insects that emerge in mass synchronized events after 17 years underground. Their survival and ecological success depend heavily on their microbiomes, which include obligate bacterial symbionts essential for nutrient acquisition, as well as occasional pathogens such as the behavior-altering fungus Massospora cicadina. While the periodical cicada lifecycle is well studied, little is known about how cicada microbiomes vary across species and environments during a single emergence event. During the 2024 emergence of Brood XIII in northern Illinois, 17-year cicadas were sampled from four ecologically distinct forest preserves. Cicadas were identified by species and sex; their microbiomes were assayed using 16S rRNA gene sequencing and tested for the presence of the fungal pathogen M. cicadina DNA in asymptomatic individuals. Sampling sites were characterized by plant community composition, historical disturbance, and potential presence of the antifungal compound juglone. Microbiome composition differed significantly by cicada species and site, but not by sex. The obligate symbionts Hodgkinia cicadicola and Sulcia muelleri dominated microbiome profiles, though other bacteria-including Pantoea agglomerans, a potential pheromone producer-were variably abundant. Cicada species distributions were non-random across sites and correlated with local plant diversity. M. cicadina DNA was detected in 23% of otherwise asymptomatic cicadas, with infection rates varying by location and negatively correlated with microbiome diversity. This study highlights complex interactions between cicada species, their microbial communities, and environmental variables such as plant diversity, soil chemistry, and land use history.}, }
@article {pmid41099800, year = {2025}, author = {Zhang, W and Yang, C and Zhao, K and Jin, M and Han, K and Wang, Y and Jiang, Z}, title = {Endophytic bacterial diversity of Vicatia thibetica collected from Xizang and the association with flavonoid accumulation.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {106}, pmid = {41099800}, issn = {1432-184X}, support = {82260759//National Natural Science Foundation of China/ ; }, mesh = {*Flavonoids/metabolism/analysis ; Plant Roots/microbiology/chemistry ; Rhizosphere ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Endophytes/classification/genetics/isolation &amp; purification/metabolism ; *Soil Microbiology ; China ; Biodiversity ; }, abstract = {Vicatia thibetica de Boiss is a unique medicinal and edible plant endemic to Xizang, China. It is one of the five primary root medicines in Tibetan medicine due to its high content of flavonoids. However, the community composition of endophytic bacteria in its various tissues and their potential role in flavonoid accumulation remain unclear. We employed high-throughput sequencing to compare the diversity of endophytic bacteria in the rhizosphere soil and various tissues of V. thibetica collected from three sampling sites in Nyingchi, Xizang. Concurrently, we assessed the types and concentrations of flavonoids present in the roots. Finally, we investigated the relationship between root endophytic bacteria and flavonoid accumulation through correlation analysis. The results indicated that the diversity and abundance of bacterial communities in the rhizosphere soil exceeded those of the endophytic bacterial communities of V. thibetica. Proteobacteria is the dominant phylum, and Sphingomonas is the dominant genus. Each tissue of a plant exhibits its dominant genus. PICRUSt predictive analysis revealed that RNA processing and modification were the predominant functions among related species. Targeted metabolomics analysis has revealed that the roots of the plants contain 14 flavonoid compounds. Correlation analysis revealed that the concentrations of flavonoids in the roots, including apigenin, rutin, astragalin, quercetin 3-glucoside, L-epicatechin, kaempferol, and luteolin, are associated with the distribution and abundance of specific bacterial genera, such as Lactobacillus, Kurthia, Bradyrhizobium, Phenylobacterium, Novosphingobium, and Mycobacterium, among others. This finding suggests that these bacterial genera may directly influence the production and accumulation of flavonoids in the plant. Our findings will enhance the understanding of plant-microbe interactions and provide crucial insights into the role of endophytes in the production of V. thibetica and its significant secondary metabolites.}, }
@article {pmid41099526, year = {2025}, author = {Lami, R}, title = {From biocides to biology: multispecies biofilms as a sustainable, self-regenerating, and effective antifouling strategy.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0160925}, doi = {10.1128/aem.01609-25}, pmid = {41099526}, issn = {1098-5336}, abstract = {Finding antifouling strategies that are effective and environmentally safe remains a central challenge for maritime operations and ecosystem protection. Amador et al.'s article in Applied and Environmental Microbiology (91:e01392-25, 2025, https://doi.org/10.1128/aem.01392-25) proposes a bioinspired, applied-microbial-ecology solution: deliberately shaping pioneer biofilm communities, so they form a physical barrier against macrofouler settlement, avoiding biocides and low-adhesion inert coatings. Though focused on the ocean, this paradigm could inform broader anti-biofilm interventions across microbiology, reframing control as ecological steering rather than chemical suppression or materials-based design.}, }
@article {pmid41096495, year = {2025}, author = {Phutthaphol, R and Bunchasak, C and Loongyai, W and Rakangthong, C}, title = {Effects of Vitamin D3 and 25(OH)D3 Supplementation on Growth Performance, Bone Parameters and Gut Microbiota of Broiler Chickens.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {19}, pages = {}, doi = {10.3390/ani15192900}, pmid = {41096495}, issn = {2076-2615}, support = {//Huvepharma (Thailand) Co., Ltd./ ; }, abstract = {Broiler chickens are commonly reared in closed housing systems with limited exposure to sunlight, thereby relying entirely on dietary sources of vitamin D. The hydroxylated metabolite 25-hydroxycholecalciferol [25(OH)D3] has been proposed as a more potent form than native vitamin D3 (cholecalciferol). This study evaluated the effects of dietary supplementation with vitamin D3 alone or in combination with 25(OH)D3 on growth performance, bone characteristics, and cecal microbiota in Ross 308 broilers. A total of 952 one-day-old male chicks were allocated to four treatments: a negative control (no vitamin D3), a positive control (vitamin D3 according to Ross 308 specifications), and a positive control supplemented with 25(OH)D3 at 1394 or 2788 IU/kg, in a randomized design with 17 replicates per treatment and 14 birds per replicate. Over a 40-day feeding trial, diets containing vitamin D3 (positive control) or supplemented with 25(OH)D3 significantly improved final body weight, weight gain, average daily gain, and feed conversion ratio compared with the negative control (p < 0.01), with no significant differences among the positive control and 25(OH)D3-supplemented groups, with a clear linear dose-dependent response. Although tibia ash and bone-breaking strength were not significantly affected, linear responses indicated a slight numerical trend toward improved skeletal mineralization with increasing 25(OH)D3. Microbiota analysis indicated that 25(OH)D3 affected cecal microbial ecology: low-dose inclusion showed reduced species richness and evenness, whereas high-dose inclusion restored richness to levels comparable to the positive control and enriched taxa associated with fiber fermentation and bile acid metabolism while reducing Lactobacillus dominance. In conclusion, supplementation with 25(OH)D3 in addition to vitamin D3 enhanced growth performance and selectively shaped the cecal microbiota of broilers, with suggestive benefits for bone mineralization. These findings highlight 25(OH)D3 as a more potent source of vitamin D than cholecalciferol alone and support its practical use in modern broiler nutrition to improve efficiency, skeletal health, and microbial balance.}, }
@article {pmid41092097, year = {2025}, author = {Almeida-Silva, F and Van de Peer, Y}, title = {Gene expression divergence following gene and genome duplications in spatially resolved plant transcriptomes.}, journal = {The Plant cell}, volume = {}, number = {}, pages = {}, doi = {10.1093/plcell/koaf243}, pmid = {41092097}, issn = {1532-298X}, abstract = {Gene and genome duplications expand genetic repertoires and facilitate functional innovation. Segmental or whole-genome duplications generate duplicates with similar and somewhat redundant expression profiles across multiple tissues, while other modes of duplication create genes that show increased divergence, leading to functional innovations. How duplicates diverge in expression across cell types in a single tissue remains elusive. Here, we used high-resolution spatial transcriptomic data from Arabidopsis thaliana, Glycine max, Phalaenopsis aphrodite, Zea mays, and Hordeum vulgare to investigate the evolution of gene expression following gene duplication. We found that genes originating from segmental or whole-genome duplications display increased expression levels, expression breadths, spatial variability, and number of coexpression partners. Duplication mechanisms that preserve cis-regulatory landscapes typically generate paralogs with more preserved expression profiles, but such differences generated by mode of duplication fade or disappear over time. Paralogs originating from large-scale (including whole-genome) duplications display redundant or overlapping expression profiles, indicating functional redundancy or subfunctionalization, while most small-scale duplicates diverge asymmetrically, consistent with neofunctionalization. Expression divergence also depends on gene functions, with dosage-sensitive genes displaying highly preserved expression profiles, and genes involved in more specialized processes diverging more rapidly. Our findings offer a spatially resolved view of expression divergence following duplication, elucidating the tempo and mode of gene expression evolution, and helping understand how gene and genome duplications shape cell identities.}, }
@article {pmid41089691, year = {2025}, author = {Li, W and Lu, K and Tang, J and Chen, Y and Lu, Y and Hu, X and Zhu, H and Feng, Y}, title = {The alterations of airway and intestine microbiota in asthma: a systematic review and meta-analysis.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1675124}, pmid = {41089691}, issn = {1664-3224}, mesh = {Humans ; *Asthma/microbiology/immunology ; *Gastrointestinal Microbiome/immunology ; *Respiratory System/microbiology/immunology ; }, abstract = {BACKGROUND: Emerging evidence highlights notable differences in microbial ecology between individuals with asthma and healthy controls (HC). This meta-analysis aims to compile data on microbial diversity indices in the airway and intestinal microbiota of both groups for comparative analysis.<br><br>METHODS: We conducted a thorough systematic search of literature in PubMed, Embase, the Web of Science, and the Cochrane Library to find English-language studies focused on airway and intestinal microbiota in asthma, published from May 16, 2020 to May 16, 2025. We extracted data regarding microbial diversity indices to facilitate comparisons between the asthma group and HC.<br><br>RESULTS: 26 studies were included in this systematic review. Our analysis revealed no significant differences in alpha diversity between the two participant groups; however, beta diversity exhibited significant differences in 9 of the studies reviewed.<br><br>CONCLUSION: Our meta-analysis did not confirm the hypothesis that asthma shows lower alpha diversity than HC. To enhance understanding and inform future diagnostic and therapeutic approaches, further studies should be conducted with larger sample sizes and more robust methodologies.<br><br>https://www.crd.york.ac.uk/prospero/, identifier CRD420251113790.}, }
@article {pmid41088478, year = {2025}, author = {Chen, X and Ma, X and Liu, Z and Gu, H and Fang, H and Shen, Z and Zhang, H and Wan, S and Li, W and Hao, X and Clarke, NJ and Liu, J}, title = {Organic fertilizers increase microbial community diversity and stability slowing down the transformation process of nutrient cycling.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {130}, pmid = {41088478}, issn = {2524-6372}, support = {07//the Straw Returning Project/ ; 07//the Straw Returning Project/ ; 07//the Straw Returning Project/ ; 07//the Straw Returning Project/ ; CHN-2152, 22/0013 SINOGRAIN III//Norwegian Ministry of Foreign Affairs/ ; CHN-2152, 22/0013 SINOGRAIN III//Norwegian Ministry of Foreign Affairs/ ; CX25PT02-01-04//Agricultural Science and Technology Innovation Project of Heilongjiang Province/ ; CX25PT02-01-04//Agricultural Science and Technology Innovation Project of Heilongjiang Province/ ; CX25PT02-01-04//Agricultural Science and Technology Innovation Project of Heilongjiang Province/ ; CX25PT02-01-04//Agricultural Science and Technology Innovation Project of Heilongjiang Province/ ; }, abstract = {BACKGROUND: Soil microbes play a central role in nutrient recycling in soils: however, the genetic mechanisms governing their responses to long-term fertilization remain poorly understood. While the agronomic benefits of long-term fertilization are well-documented, the genetic mechanisms and ecological processes underlying microbial community responses to different fertilization regimes remain poorly understood, particularly in unique soil systems such as black soils (Mollisols), which are critical for global food security. A deeper insight into how organic and inorganic fertilizers influence microbial assembly, functional potential, and community stability is essential for developing sustainable soil management practices.<br><br>RESULTS: This study deciphers microbial assembly mechanisms, functional gene dynamics, and community restructuring in black soils subjected to&#xa0;44&#xa0;years of chemical fertilizer (CF), manure amendment (M), and integrated chemical fertilizer with manure (CFM) treatments. Results revealed that CF significantly enhances functional gene abundance related to carbon (C) degradation (e.g., starch, cellulose, chitin and lignin) and nitrification, accelerating the conversion of recalcitrant C to labile C pools and ammonium to nitrate. Conversely, M and CFM treatments promote microbial diversity and stability while decelerating nutrient transformation processes. In addition, microbial assembly mechanisms shift from stochastic to deterministic processes with long-term fertilizer application in CF. The structural equation modeling (SEM) indicated that soil chemical properties shape both the diversity and composition of taxonomic and functional gene communities which subsequently regulate microbial -mediated nutrient cycling processes and crop yield.<br><br>CONCLUSIONS: Our findings highlight the trade-offs between microbial functional potential and community stability under contrasting fertilization strategies, emphasizing the need to integrate microbial metrics into sustainable land management frameworks.}, }
@article {pmid41086300, year = {2025}, author = {Peterson, BD and Poulin, BA}, title = {Illuminating the Black Box: Trace Element Biogeochemistry from a Microbial Perspective.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c06816}, pmid = {41086300}, issn = {1520-5851}, abstract = {Microbial processes are central to the transformation and fate of trace elements in the environment (e.g., mercury (Hg), arsenic (As)), but the complexities underlying microbial transformation rates and the influence of human impacts present considerable hurdles to developing conceptual and quantitative models of these processes. This perspective highlights processes that govern microbial activity in the environment as it pertains to trace elements, including redox, energy generation, resource limitation, and ecology and evolution. In this context, we compare and contrast the microbial-driven processes of Hg and As cycling, two elements with a genetic basis for microbial transformations (e.g., hgcAB, mer, arsH) that are used for microbial (i) metabolism (e.g., conversion of arsenate to arsenite), (ii) detoxification (e.g., reduction of divalent Hg(II) to volatile Hg(0)), (iii) warfare (e.g., conversion of arsenite to highly toxic trivalent methylated As(III)), or (iv) reasons not yet known (e.g., methylation of Hg(II) to toxic methylmercury). We argue for experimental approaches that quantify contaminant transformation(s) of interest in parallel with relevant metrics of microbial community activity. This microbe-centric framework may catalyze advancement that facilitates microbial integration into conceptual and quantitative models used to forecast environmental and human exposure to contaminants.}, }
@article {pmid41085588, year = {2025}, author = {Purohit, HV and Chakraborty, J}, title = {Metagenomic approaches for studying ubiquitous yet diverse nucleoid associated proteins in microbial communities: challenges and advances.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {10}, pages = {383}, pmid = {41085588}, issn = {1573-0972}, }
@article {pmid41085259, year = {2025}, author = {Li, S and Ye, X and Luo, K and Yu, L and Shen, Z and Yi, T and Wang, M and Gu, Q}, title = {High-Throughput Absolute Quantification Sequencing Advances Characterisation of Microbial Community Ecology.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e70139}, doi = {10.1111/mec.70139}, pmid = {41085259}, issn = {1365-294X}, support = {2023YFD2400902//National Key Research and Development Program of China/ ; 31800388//National Natural Science Foundation of China/ ; 41601203//National Natural Science Foundation of China/ ; 2019JJ50314//Natural Science Foundation of Hunan Province, China/ ; kq2208163//Natural Science Foundation of Changsha, China/ ; 23B0073//Scientific Research Foundation of Hunan Provincial Education Department/ ; 2108085ME186//Anhui Provincial Natural Science Foundation/ ; }, abstract = {High-throughput sequencing has been extensively used in microbial ecology research, but this technology typically generates semi-quantitative relative abundance data. The discrepancies of community dynamics delivered by relative and absolute abundances have long been recognised by microbial ecologists. However, few studies have considered the discrepancies and their potential effects on related ecological interpretations. Here, the absolute copy numbers (absolute abundances) of taxa were quantified using a 'spike-in' based 16S absolute quantification sequencing to investigate the dynamics, co-occurrence patterns, and ecological assembly processes of microbial community in the river-connected Lake Dongting, Hunan province, China. Routine sequencing data analysis based on relative abundance was also obtained for comparison. The results indicated that outcomes based on relative and absolute abundances were comparable at the community level but differed significantly at the population level when dynamics and interactions of specific taxa were of interest. Specifically, at the population level, the dynamics of individual taxa were usually masked by their relative abundances, particularly for abundant taxa. The correlation-based co-occurrence network constructed from relative abundance largely underestimated the importance of rare taxa, consisted of massive false negative connections, and was less stable than the one constructed using absolute abundance. At the community level, the diversity and composition of microbial communities in Lake Dongting exhibited significant temporal rather than spatial variations, and temperature was determined to be the most important factor shaping microbial community composition and assembly processes, regardless of which abundance data were used. Nonetheless, relative abundance data yielded stronger environmental and deterministic effects on microbial assembly than absolute abundance. In summary, our study highlights the importance of incorporating absolute quantification to unveil the underlying microbial ecological patterns masked by relative abundance.}, }
@article {pmid41082055, year = {2025}, author = {Aderolu, AZ and Salam, LB and Lawal, MO and Kabiawu-Mutiu, LF and Bassey, ME and Shobande, MA}, title = {Microbial ecology and functional landscape of black soldier fly larval bioconversion of orange waste: A metataxonomic perspective.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {10}, pages = {377}, pmid = {41082055}, issn = {1573-0972}, mesh = {Animals ; Larva/microbiology/metabolism ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Gastrointestinal Microbiome/genetics ; *Simuliidae/microbiology ; *Citrus sinensis/metabolism ; *Diptera/microbiology ; Nigeria ; Metagenome ; Metagenomics ; Phylogeny ; }, abstract = {The accumulation of citrus waste, particularly orange waste (OW), presents significant environmental and economic challenges in Nigeria and worldwide. This study presents the first high-resolution, species-level metataxonomic analysis of OW bioconversion mediated by black soldier fly larvae (BSFL) in a West African context, addressing a critical gap in region-specific microbial ecology. Using long-read PacBio 16S rRNA sequencing and PICRUSt2-based functional prediction, microbial communities were profiled across three ecologically distinct substrates: untreated OW, BSFL gut microbiota (OW-BSFL), and post-digestion frass (OWF). Results revealed a dramatic microbial shift driven by host filtering: the OW-BSFL metagenome was overwhelmingly dominated (> 96%) by Lysinibacillus and Cytobacillus, while OWF exhibited markedly higher diversity (263 species), including Mycolatisynbacter and Sphingobacterium. Functional analysis revealed a significant enrichment of genes associated with carbohydrate (e.g., COG2814, COG0726) and amino acid metabolism (e.g., COG1173, COG0444) in the BSFL gut, indicating an elevated enzymatic processing capacity during waste digestion. In contrast, OWF displayed unique enrichment in genes associated with residual carbohydrate turnover and environmental colonization. This microbial succession highlights the selective enrichment and functional specialization that occur across the substrate-gut-frass continuum. By elucidating keystone taxa and metabolic signatures, the study not only advances understanding of insect-microbiome symbiosis but also provides a microbial blueprint for optimizing waste-to-value strategies. The findings support the deployment of BSFL bioconversion as a scalable, sustainable solution for organic waste valorization and biofertilizer production in sub-Saharan Africa's circular bioeconomy.}, }
@article {pmid41081862, year = {2025}, author = {Bandyopadhyay, A and Sarkar, D and Das, A and Das, A}, title = {Intersections of ABO blood group, secretor status, and the gut microbiome: implications for disease susceptibility and therapeutics.}, journal = {Archives of microbiology}, volume = {207}, number = {11}, pages = {296}, pmid = {41081862}, issn = {1432-072X}, mesh = {Humans ; *ABO Blood-Group System/genetics/metabolism ; *Gastrointestinal Microbiome ; Disease Susceptibility ; Galactoside 2-alpha-L-fucosyltransferase ; Bacteria/classification/genetics/isolation &amp; purification ; Probiotics ; }, abstract = {The human gut microbiome is a dynamic ecosystem. It is shaped by host factors, including genetic traits such as ABO blood type and associated secretor status (FUT2 gene). In secretor individuals (~ 80% of the population), ABO antigens are expressed on the gut mucosal surfaces. These antigens serve as adhesion sites and nutrient substrates for select microorganisms. Evidence links blood groups to gut microbial ecology, with taxa such as Bacteroidessp., Eubacteriumsp., and Faecalibacterium sp. exhibiting preferential colonization patterns influenced by mechanisms including mucin glycan foraging, pathogen adhesion, and competitive exclusion. ABO blood type further modulates susceptibility to infectious, metabolic, and autoimmune diseases by affecting microbiome composition. Secretor status impacts microbiota diversity and probiotic colonization Non-secretors exhibit altered Bifidobacterium sp. profiles and reduced norovirus adhesion. These insights suggest possible avenues for tailoring microbiome-based interventions; however, current evidence remains preliminary and requires validation through controlled clinical studies. We outline a conceptual model linking host genetics, microbial ecology, and health outcomes, recognizing that these associations are still being mapped. The idea of incorporating blood type and secretor status into precision microbiome approaches remains exploratory and requires rigorous validation.}, }
@article {pmid41081374, year = {2025}, author = {Hoshyaripour, S and Mauri, M and Hobbs, JK and Foster, SJ and Allen, RJ}, title = {Cell wall mechanical stress could coordinate septal synthesis and scission in Staphylococcus aureus.}, journal = {mBio}, volume = {}, number = {}, pages = {e0172825}, doi = {10.1128/mbio.01728-25}, pmid = {41081374}, issn = {2150-7511}, abstract = {Staphylococcus aureus divides by building a septum and then splitting into two daughter cells. Scission should be coordinated with septum completion to avoid cell lysis; however, it is not known how this is achieved, or what the relative roles of mechanical forces and the activity of peptidoglycan hydrolase enzymes are. Here, we show using thin-shell mechanics that septum formation causes a localized decrease in mechanical stress at the cell's equator. We propose that this local decrease in stress could act as a mechanical trigger for hydrolase activity, leading eventually to splitting. This mechanical trigger model can explain observed cell division defects, including premature splitting and failure to initiate splitting. The model also shows how cell size, turgor pressure, cell wall thickness and stiffness, and the relative rates of synthesis and hydrolysis combine to determine cell cycle timing and the outcome of antibiotic exposure. Bacterial cell division requires dynamic orchestration of molecular players, in concert with cell wall mechanics. Our work suggests how mechanical forces could coordinate with enzyme activity in the control of this complex process.IMPORTANCEStaphylococcus aureus is a major threat due to its ability to generate antibiotic-resistant strains. Understanding S. aureus division is therefore of great importance, but we do not know how septum formation is coordinated with cell scission. Previous works have shown that both mechanical stress and autolysin activity play key roles in scission, but it is unclear how mechanical and biochemical cues work together. Here, we propose a "mechanical trigger" model for the interplay between mechanical stress and autolysin activation. We use mathematical modeling to show that stress decreases in the S. aureus cell wall close to the division site as the septum is formed, and we propose that this could trigger autolysin activity. Our model explains reports of diverse division outcomes in the presence of mutations and antibiotics and points to a general link between cell geometry and antibiotic resistance.}, }
@article {pmid41080577, year = {2025}, author = {Wang, Z and Yu, J and Liu, Y and Gong, J and Hu, Z and Liu, Z}, title = {Role of the microbiota-gut-lung axis in the pathogenesis of pulmonary disease in children and novel therapeutic strategies.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1636876}, pmid = {41080577}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Child ; *Lung/immunology/microbiology/metabolism ; *Lung Diseases/therapy/microbiology/immunology/etiology/metabolism ; Dysbiosis ; Animals ; Fatty Acids, Volatile/metabolism ; }, abstract = {Emerging evidence highlights the microbiota-gut-lung axis (MGLA) as a pivotal regulator of pediatric respiratory health, yet mechanistic insights are lacking and therapeutic applications remain unclear. This review synthesizes cutting-edge findings to delineate how gut microbiota-derived metabolites, particularly short-chain fatty acids (SCFAs), orchestrate pulmonary immunity and disease pathogenesis in children. Leveraging multi-omics integration (metagenomics, metabolomics, transcriptomics), emerging studies have uncovered novel microbe-host interactions driving immune dysregulation in asthma, pneumonia, and cystic fibrosis. A comprehensive map of gut-lung crosstalk has been established across these conditions. Current studies suggest that early-life gut dysbiosis, shaped by delivery mode, antibiotics, and diet, disrupts SCFA-mediated immune homeostasis, amplifying T-helper 2 cell inflammation and impairing alveolar macrophage function. Crucially, we identified disease-specific microbial signatures (e.g., depletion of Lachnospira and Faecalibacterium in asthma) and demonstrated that fecal microbiota transplantation and probiotic interventions restore microbial balance, attenuating airway inflammation in preclinical models. This work pioneers the translation of MGLA insights into precision medicine strategies, highlighting dietary modulation and microbial therapeutics as viable alternatives to conventional treatments. By bridging microbial ecology and immune dynamics, our findings provide actionable biomarkers for early diagnosis and personalized interventions, addressing critical gaps in pediatric respiratory disease management. The integration of multi-omics frameworks not only advances mechanistic understanding but also positions the MGLA as a transformative target in reducing global childhood morbidity. Future research must prioritize longitudinal studies and clinical trials to validate these innovations, ultimately redefining therapeutic paradigms for GLA-driven pathologies.}, }
@article {pmid41079626, year = {2025}, author = {Papadopoulou, K&#x39a; and Chatzinotas, A and Diaz-Otero, BG and Brader, G and Karpouzas, DG and Garces Ruiz, M and Alonso Prados, JL and Declerck, S and Kellari, LM and Sessitsch, A}, title = {Benefits and challenges of upcoming microbial plant protection applications sustaining planetary health.}, journal = {iScience}, volume = {28}, number = {10}, pages = {113557}, pmid = {41079626}, issn = {2589-0042}, abstract = {Plant disease outbreaks pose severe risks to global food security. Due to climate change, new diseases are expected to emerge, and the current use of chemical pesticides poses risks to environmental and human health. In the last decade, alternative plant protection agents of microbial origin have been developed, which also raise great expectations in the industry. Current products primarily represent individual microbial strains, either fungi or bacteria, which occasionally fail under field conditions due to various factors while their regulatory status differs globally. Recently, more diverse applications have started to emerge, ranging from microbial consortia, phages and protists to microbiome modulation or soil translocation. Integrated solutions, incorporating artificial intelligence are also proposed. In this review, we discuss the opportunities and challenges of these solutions, providing specific examples and discuss the regulatory needs for their market entry as well as their relevance for improving food security and planetary health.}, }
@article {pmid41078603, year = {2025}, author = {Otto, JFM and Pohnert, G and Wichard, T and Bauer, M and Busch, A and Ueberschaar, N}, title = {Global DNA-methylation in quantitative epigenetics: orbitrap mass spectrometry.}, journal = {Frontiers in molecular biosciences}, volume = {12}, number = {}, pages = {1681568}, pmid = {41078603}, issn = {2296-889X}, abstract = {DNA methylation is the most common epigenetic modification in both prokaryotic and eukaryotic genomes. Here we present a method based on highly efficient acid-hydrolysis of DNA, liquid chromatography, and detection by mass spectrometry to accurately quantify cytosine methylation in highly methylated DNA samples. This approach enables direct, rapid, cost-efficient, and sensitive quantification of the methyl-modified nucleobase 5-methylcytosine and 6-methyl adenine, along with their unmodified nucleobases. In contrast to standard sequencing techniques, our method only gives quantitative information on the overall degree of methylation, but it requires only small amounts of DNA and is not dependent on lengthy bioinformatic analyses. Our method allows rapid, global methylome analysis and quantifies a central epigenetic marker. In a proof-of-principle study, we show that it can also be extended to the monitoring of other DNA modifications, such as methylated adenine. Uncomplicated data analysis facilitates a quick and straightforward comparison of DNA methylation across biological contexts. In a case study, we also successfully identified changes in methylation signatures in the marine macroalga Ulva mutabilis "slender". The advantage of global methylation analysis compared to sequencing allows for generating fast prior knowledge on which sample sequencing is senseful. The great benefit of the presented method is the speed and accuracy of the global methylation analysis, which is independent of the total methylation rate and gives accurate results, whereas competitive based on enzymatic digestion might fail.}, }
@article {pmid41078307, year = {2025}, author = {He, H and Xiao, M and Song, L and Tian, Y and Jia, Y}, title = {Lipidome-microbiome crosstalk as an outer niche in the skin: regulatory networks in health and disease.}, journal = {The British journal of dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1093/bjd/ljaf353}, pmid = {41078307}, issn = {1365-2133}, support = {//Beijing Technology and Business University/ ; //Beijing Municipal Education Commission/ ; 32100254//National Science Foundation of China/ ; }, abstract = {The skin is the outermost barrier to organisms from the external environment. This natural role, endowed by evolution, results in a nutrient-poor skin surface that enables microbial nutrition-dependent lipids to shape microbial ecology by survival pressure and nutrient preference. In turn, the skin microbiota produce microorganism-metabolized bioactive molecules (MBMs) to increase molecular diversity. This crosstalk functions as a crucial component of niche-regulating skin properties via multiple mechanisms. Furthermore, the local and remote effects of different barrier sites provide a more comprehensive explanation for the crosstalk from a global perspective. The variable function and mechanism of crosstalk may represent an evolutionary means by which the skin uses fluctuating commensal signals - the highly dynamic MBMs - to calibrate skin status and provide heterologous protection against invasive pathogens. Elucidating the reasons for the differing selectivity and catalytic efficiency of lipid-metabolizing enzymes in microorganisms and revealing the biologic processes and regulatory mechanisms of the 'co-metabolic systems' on the skin will advance diagnostic and therapeutic strategies for local cutaneous disorders and comorbid diseases of distant organs.}, }
@article {pmid41069707, year = {2025}, author = {Rubio-Portillo, E and Arias-Real, R and Rodríguez-Pérez, E and Bañeras, L and Antón, J and de Los Ríos, A}, title = {Short-term virus-host interactions and functional dynamics in recently deglaciated Antarctic tundra soils.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf157}, pmid = {41069707}, issn = {2730-6151}, abstract = {Long-term chronosequence studies have shown that, as glaciers retreat, newly exposed soils become colonized through primary succession. To determine the key drivers of this process and their vulnerability to climate change, the short-term responses of these pioneering microbial communities also need to be elucidated. Here, we investigated how the taxonomic and functional structure of microbial communities, including viruses, changed over a 7-year period in an Antarctic glacier forefield. Using metagenomics and metatranscriptomics we assessed the influence of both abiotic and biotic factors on these communities. Our results revealed a highly heterogeneous bacteria-dominated microbial community, with Pseudomonas as the most abundant genus, followed by Lysobacter, Devosia, Cellulomonas, and Brevundimonas. This community exhibited the capacity for aerobic anoxygenic phototrophy, carbon and nitrogen fixation, and sulfur cycling, processes vital for survival in nutrient-poor environments. 52 high-quality metagenome-assembled genomes (MAGs) were recovered, representing both transient and cosmopolitan taxa, some of which were able to rapidly respond to environmental changes. A diverse and highly dynamic collection of lytic and temperate viruses was identified across all samples, with high clonal viral genomes typically detected in only one of the eight samples analyzed. Metatranscriptomic analyses confirmed the activity of lytic viruses, while prophage genomes featured much lower expression levels. Prophages appeared to influence host fitness through the expression of genes encoding membrane transporters. Additionally, the abundance of genes linked to antimicrobial compound synthesis and resistance, along with antiphage defense systems, highlights the importance of biotic interactions in driving microbial community succession and shaping short-term responses to environmental fluctuations.}, }
@article {pmid41069527, year = {2025}, author = {Jiang, W and Gu, S}, title = {Editorial: The oral microbiome and its impact on systemic health: from disease development to biomaterials development.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1697069}, pmid = {41069527}, issn = {2235-2988}, }
@article {pmid41066956, year = {2025}, author = {Huang, P and Zhou, R and Huang, Z and Wu, C}, title = {Deciphering the environmental response and assembly of rare and abundant taxa in zaopei employing daqu produced by different pressing patterns.}, journal = {International journal of food microbiology}, volume = {445}, number = {}, pages = {111471}, doi = {10.1016/j.ijfoodmicro.2025.111471}, pmid = {41066956}, issn = {1879-3460}, abstract = {Baijiu fermentation relies on complex microbial communities within zaopei, which are significantly shaped by the microbial starter daqu. This study investigated the rare and abundant taxa composition, and flavor characteristics of zaopei (fermented grains) employing Nongxiangxing daqu produced by different pressing patterns (mechanically pressed, artificially pressed) from microbial ecology perspective. Then, the origin, environmental response, assembly patterns and driving factors of rare and abundant taxa were revealed. The results indicated that both Lactobacillus and Acetobacter consistently dominated in rare bacteria and abundant bacteria of zaopei, the dominant abundant fungi were Thermoascus and Issatchenkia, while the dominant rare fungi were Aspergillus and Pichia. The microbial community of zaopei was significantly influenced by fungi originating from daqu, according to Fast expectation-maximization microbial source tracking (FEAST) analysis. Moreover, daqu significantly influenced the assembly process of abundant fungi taxa in zaopei, with the mechanically pressed daqu (MDQ) increased the proportion of heterogeneous selection. Moreover, water, starch and ethanol contents were important factors driving the rare bacteria assembly. Co-occurrence network analysis indicated that artificially pressed daqu (ADQ) enhanced microbial interactions in zaopei, which were closely related to rare bacteria. Meanwhile, Spearman's correlation between microorganisms and differential flavor compounds showed that fungal taxa (abundant Clavispora, rare Pichia and rare Issatchenkia) played a dominant role in flavor synthesis. These results contributed to a better understanding of the functional contributions of rare and abundant taxa in baijiu fermentation and provided theoretical support and technical guidance for regulating baijiu quality.}, }
@article {pmid41065083, year = {2025}, author = {Cantoran, A and Maillard, F and Bermudez, R and Stefanski, A and Reich, PB and Kennedy, PG}, title = {Warming and Reduced Rainfall Alter Fungal Necromass Decomposition Rates and Associated Microbial Community Composition and Functioning at a Temperate-Boreal Forest Ecotone.}, journal = {Global change biology}, volume = {31}, number = {10}, pages = {e70536}, doi = {10.1111/gcb.70536}, pmid = {41065083}, issn = {1365-2486}, support = {DE-FG02-07ER64456//Biological and Environmental Research/ ; NSF-DBI-2021898//Division of Biological Infrastructure/ ; }, mesh = {*Rain ; *Soil Microbiology ; *Climate Change ; Minnesota ; *Microbiota ; Soil/chemistry ; *Fungi/metabolism ; Taiga ; *Global Warming ; }, abstract = {Changes in temperature and rainfall associated with altered climatic conditions are likely to significantly alter rates of soil organic matter decomposition. To determine how the combined effects of warming and drought impact the decomposition of fungal necromass, a large and fast-cycling portion of the global soil organic carbon (C) pool, we incubated Hyaloscypha bicolor necromass under both ambient and altered conditions (+3.3°C air and soil warming and ~40% reduced rainfall) at the B4Warmed experiment in Minnesota, USA. We conducted two multi-week incubations, one assessing mass loss and microbial community composition on decaying necromass after 1, 2, 7, and 14 weeks and the second characterizing the substrate utilization capacities of necromass-associated microbial communities after Weeks 1 and 7. Warming and reduced rainfall accelerated the initial rate of necromass decay by ~20%, yet slowed overall mass loss by ~6% at the end of the 14-week incubation. These different rates of decay over time paralleled shifting abiotic conditions, with altered plots experiencing warmer and relatively moist conditions early, but hotter and drier conditions later. The microbial community composition also varied by treatment and time, with warming and reduced rainfall stimulating fast-growing fungi as well as fungal relative to bacterial growth overall. Additionally, the functional capacity of the microbial community also changed over time, having a higher metabolic capability to utilize C and N substrates in the altered plots early in decomposition but a lower capability later in decay. Collectively, our findings highlight a dynamic, stage-dependent response of fungal necromass decomposition to altered climate regimes. By linking these decay dynamics to shifts in environmental conditions as well as microbial community composition and function, our study highlights the critical roles of both abiotic and biotic changes in mediating decomposition responses to climate change.}, }
@article {pmid41064756, year = {2025}, author = {Lofgren, L and Maillard, F and Michaud, T and Gredeby, A and Tunlid, A and Kennedy, PG}, title = {Diverse nitrogen acquisition strategies of conifer-associated ectomycorrhizal fungi shape unique responses to changing nitrogen regimes.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1666003}, pmid = {41064756}, issn = {1664-462X}, abstract = {Ectomycorrhizal fungi are critical mediators of nitrogen acquisition in forest ecosystems, exhibiting variation in both host association and metabolic traits that mediate differential responses to forest nitrogen availability. However, how nitrogen acquisition strategies vary among closely related fungal species, how these patterns manifest in conifer-associated ECM fungi, and whether they persist over changing nitrogen regimes, remains poorly understood. Using an integrative approach combining in silico genomic analysis, in vitro growth assays, and isotopic analysis of in situ specimens spanning six decades, we provide the first comprehensive examination of nitrogen assimilation in congeneric conifer-associated ectomycorrhizal fungi using six Suillus species. We found highly conserved genes for inorganic nitrogen assimilation across species, but striking interspecific variation in the genetic capacity for organic nitrogen metabolism. Interspecific differences were also observed in fungal growth on varying nitrogen substrates in the growth assays, as well as in the isotopic signatures of historical specimens. For the latter, carbon isotopic patterns showed divergent temporal trends among Suillus species, suggestive of differential N use over time. Collectively, these genomic, physiological, and isotopic findings support the presence of notable interspecific diversity in ectomycorrhizal fungal nitrogen acquisition and suggest that coniferous forests and their fungal symbionts exhibit distinct responses to shifts in nitrogen availability compared to broadleaf forests. The ability of even closely related ectomycorrhizal fungi to employ diverse nitrogen acquisition strategies has important implications for forest ecosystem resilience, as different species may provide complementary services to host trees under varying environmental conditions, potentially reducing competition, and influencing forest responses to altered nutrient availability.}, }
@article {pmid41064004, year = {2025}, author = {Pérez-Ramos, DW and Caragata, EP}, title = {Fungal communities in Florida salt marsh mosquito midguts vary between species and over time but have low structure.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1648091}, pmid = {41064004}, issn = {1664-3224}, mesh = {Animals ; *Fungi/genetics/classification ; *Mycobiome ; *Culicidae/microbiology ; Florida ; Wetlands ; *Aedes/microbiology ; Species Specificity ; *Culex/microbiology ; *Gastrointestinal Microbiome ; }, abstract = {INTRODUCTION: Microorganisms are intrinsically tied to the developmental and reproductive success of mosquitoes, can influence their ability to resist insecticides, and can strongly influence their ability to harbor and transmit pathogens of medical importance. Although mosquito-associated fungi have oben been overlooked at the expense of bacteria, several different fungal taxa are known to modulate interactions between mosquitoes and pathogens, while others have potential applications as biopesticides due to their entomopathogenic activity. Accordingly, understanding how and why different fungi associate with mosquito tissues is an important step toward elucidaUng the impact the diverse kingdom of microorganisms has on mosquito biology and mosquito- borne disease.<br><br>METHODS: In this study, we used Illumina Mi-Seq profiling of the internal transcribed spacer gene to characterize the midgut mycobiota of field collected adult mosquitoes from three species: Aedes taeniorhynchus, Anopheles atropos, and Culex nigripalpus, at two different collection times.<br><br>RESULTS: We observed that all mosquito specimens carried high loads of Rhodotorula lamellibrachiae, a common environmental yeast that is known to be involved in nitrogen fixation, although its role in mosquito biology is not clear. We also find that the mycobiome is strongly influenced by mosquito species, that few fungi have both high abundance and prevalence, and that few fungi consistently co- associate across time and host species.<br><br>DISCUSSION: These findings suggest that there is limited structure to mosquito associated fungal communities, implying that their assembly may be more driven by stochastic than deterministic processes. Our findings highlight the influence of key variables on mosquito fungal diversity and help facilitate understanding of how and when mosquitoes acquire fungi and the roles that fungi play in mosquito biology.}, }
@article {pmid41063836, year = {2025}, author = {Chen, X and Ye, L and Zou, X and Zhou, Y and Peng, C and Huang, R}, title = {The role of gut microbiota in myocardial ischemia-reperfusion injury.}, journal = {Frontiers in cardiovascular medicine}, volume = {12}, number = {}, pages = {1625299}, pmid = {41063836}, issn = {2297-055X}, abstract = {Myocardial ischemia-reperfusion injury denotes the pathological damage resulting from the restoration of blood flow and oxygen supply following acute coronary artery occlusion. Myocardial ischemia-reperfusion injury is commonly seen in acute coronary syndromes and is an important factor in the development of ischemic cardiomyopathy, which severely affects the prognosis of coronary heart disease. The gut microbiota, a complex ecosystem with multifaceted functions, plays a crucial role in host health. Dysregulation of the gut microbiota exerts substantial effects on the onset and progression of cardiovascular diseases, including myocardial ischemia-reperfusion injury. This review elucidates the mechanisms underlying myocardial ischemia-reperfusion injury and the involvement of the gut microbiota in this process, encompassing aspects such as intestinal barrier integrity, microbial dysbiosis, inflammatory responses, oxidative stress, mitochondrial dysfunction, and metabolic alterations. Additionally, we investigate various interventions that modulate myocardial ischemia-reperfusion injury by influencing the gut microbiota. Maintaining a healthy intestinal barrier and a stable microbial ecology is paramount in preventing myocardial ischemia-reperfusion injury. High-fiber diets, probiotic consumption, short-chain fatty acids supplementation, and Traditional Chinese Medicine, can safeguard the heart against myocardial ischemia-reperfusion injury by regulating gut microbiota through diverse mechanisms. As the role of gut microbiota in myocardial ischemia-reperfusion injury continues to be investigated, it provides important therapeutic targets and drug development opportunities for the prevention and treatment of myocardial ischemia-reperfusion injury. However, further in-depth and comprehensive studies are required to fully realize these potentials.}, }
@article {pmid41063423, year = {2025}, author = {Bartz, PM and Grullón-Penkova, IF and Cavaleri, MA and Reed, SC and Shahid, S and Wood, TE and Bachelot, B}, title = {Experimental warming alters free-living nitrogen fixation in a humid tropical forest.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.70592}, pmid = {41063423}, issn = {1469-8137}, support = {1754713//Division of Environmental Biology/ ; 2120085//Division of Environmental Biology/ ; 89243018S-SC-000014//Basic Energy Sciences/ ; 89243018S-SC-000017//Basic Energy Sciences/ ; 89243021S-SC-000076//Basic Energy Sciences/ ; DE-SC-0011806//Basic Energy Sciences/ ; DE-SC-0018942//Basic Energy Sciences/ ; DE-SC0012000//Basic Energy Sciences/ ; DE-SC0022095//Basic Energy Sciences/ ; }, abstract = {Microbial nitrogen (N) fixation accounts for c. 97% of natural N inputs to terrestrial ecosystems. These microbes can be free-living in the soil and leaf litter (asymbiotic) or in symbiosis with plants. Warming is expected to increase N-fixation rates because warmer temperatures favor the growth and activity of N-fixing microbes. We investigated the effects of warming on asymbiotic components of N fixation at a field warming experiment in Puerto Rico. We analyzed the function and composition of bacterial communities from surface soil and leaf litter samples. Warming significantly increased asymbiotic N-fixation rates in soil by 55% (to 0.002 kg ha[-1] yr[-1]) and by 525% in leaf litter (to 14.518 kg ha[-1] yr[-1]). This increase in N fixation was associated with changes in the N-fixing bacterial community composition and soil nutrients. Our findings suggest that warming increases the natural N inputs from the atmosphere into this tropical forest due to changes in microbial function and composition, especially in the leaf litter. Given the importance of leaf litter in nutrient cycling, future research should investigate other aspects of N cycles in the leaf litter under warming conditions.}, }
@article {pmid41062579, year = {2025}, author = {Wang, Y and Wang, Y and Hou, L and Zhong, L and Yang, H and Kang, X and Zhou, Y and Pan, J}, title = {Assessment of airborne and surface microbes on leather cultural relics in museums of arid regions represented by xinjiang, China.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {35107}, pmid = {41062579}, issn = {2045-2322}, support = {2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; }, mesh = {China ; *Museums ; *Air Microbiology ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects ; Microbiota ; }, abstract = {This study investigates the airborne microbial contamination in three museums located in the dry region of Xinjiang region, China-Bayingolin, Hami, and Turpan. Airborne microbial concentrations in these museums were found to be relatively low, ranging from 7.5 to 38.3 CFU/m[3], which is advantageous for the preservation of cultural relics, especially in comparison to humid regions where higher microbial concentrations have been reported. The microbial communities were dominated by bacteria, with Firmicutes being the most abundant phylum, followed by Proteobacteria and Bacteroidetes. Notably, Pseudomonas sp., Bacillus sp., and Staphylococcus hominis were identified as potential threats to the degradation of leather cultural relics. Additionally, Mycobacterium sp., Pantoea sp., and Priestia aryabhattai were first identified in the context of cultural heritage conservation. Metagenomic sequencing revealed a significant presence of salt-tolerant, spore-forming bacteria, which are characteristic of dry environments. Antibacterial tests showed that 0.5% K100 exhibited the best antimicrobial effect. This study provides valuable insights into the microbial ecology of museums in rid climates and suggests the need for targeted preservation strategies to mitigate microbial-induced biodeterioration, particularly through the use of antimicrobial agents and environmental management.}, }
@article {pmid40981661, year = {2025}, author = {Pearl Mizrahi, S and Lee, H and Goyal, A and Owen, E and Gore, J}, title = {Structured interactions explain the absence of keystone species in synthetic microcosms.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf211}, pmid = {40981661}, issn = {1751-7370}, support = {//Schmidt Science Polymath award/ ; 542385//Simons Foundation Principles of Microbial Ecology Collaboration/ ; LT000378/2018//HSFP Long-term fellowships/ ; GBMF4513//Gordon and Betty Moore Foundation/ ; T32GM087237//NIH Training/ ; /GM/NIGMS NIH HHS/United States ; }, mesh = {*Ecosystem ; *Bacteria/growth &amp; development/classification ; *Microbial Interactions ; *Extinction, Biological ; }, abstract = {In complex ecosystems, the loss of certain species can trigger a cascade of secondary extinctions and invasions. However, our understanding of the prevalence of these critical "keystone" species and the factors influencing their emergence remains limited. To address these questions, we experimentally assembled microcosms from 16 marine bacterial species and found that multiple extinctions and invasions were exceedingly rare upon removal of a species from the initial inoculation. This was true across eight different environments with either simple carbon sources (e.g. glucose) and more complex ones (e.g. glycogen). By employing a generalized Lotka-Volterra model, we could reproduce these results when interspecies interactions followed a hierarchical pattern, wherein species impacted strongly by one species were also more likely to experience strong impacts from others. Such a pattern naturally emerges due to observed variation in carrying capacities and growth rates. Furthermore, using both statistical inference and spent media experiments, we inferred interspecies interaction strengths and found them consistent with structured interactions. Our results suggest that the natural emergence of structured interactions may provide community resilience to extinctions.}, }
@article {pmid41061000, year = {2025}, author = {Cummings, CL and Landreville, KD and Kuzma, J}, title = {Public perceptions and support for introduced microbes to combat hospital-acquired infections and antimicrobial resistance.}, journal = {PloS one}, volume = {20}, number = {10}, pages = {e0332578}, doi = {10.1371/journal.pone.0332578}, pmid = {41061000}, issn = {1932-6203}, mesh = {Humans ; *Cross Infection/prevention &amp; control/microbiology ; Female ; Adult ; Male ; Middle Aged ; *Microbiota ; *Public Opinion ; Surveys and Questionnaires ; Aged ; Young Adult ; *Drug Resistance, Microbial ; Adolescent ; United States ; }, abstract = {Hospital-acquired infections and antimicrobial resistance (AMR) remain major global health threats, prompting interest in microbiome-based interventions that introduce beneficial microbes or genetic interventions to control pathogens and reduce AMR genes in hospital environments. Microbiome engineering, which can use advanced biotechnology, genetics, and microbial ecology principles to restructure microbial communities, is a rapidly growing field with applications in infection control. As researchers explore deploying beneficial microbes and other genetic interventions in clinical settings like hospital sinks, public perception becomes critical to responsible implementation. This study addresses how U.S. adults perceive microbiome evaluation, and education. Drawing on a nationally representative survey (N = 1,000), we conducted hierarchical ordinary least squares regression modeling to assess predictors of support across three domains: implementation of introduced microbiomes (IM), rigorous testing, and education for healthcare stakeholders. Results demonstrate that support for IM in hospital sinks is shaped less by demographic traits and more by emotional responses, trust in institutional efficacy, belief in intervention benefits, and a desire to learn about microbiome science. These findings advance previous knowledge by distinguishing cognitive, affective, and contextual predictors across distinct types of support. Contrary to expectations, prior familiarity and information-seeking were negatively associated with IM support, suggesting that some engagement or exposure to risk-framing may drive skepticism. Meanwhile, emotional reactions and perceived efficacy consistently predicted support for IM, testing, and education (i.e., across all dependent variables), underscoring the need to address affective and trust-based components of public engagement. This research contributes to an emerging empirical foundation for responsible microbiome innovation by grounding the analysis in the Responsible Research and Innovation (RRI) framework. With the technology still in early development, these insights provide critical guidance for biotechnology developers, policymakers, and hospital leaders seeking to align microbiome engineering with societal values through transparent communication, rigorous oversight, and inclusive education.}, }
@article {pmid41057344, year = {2025}, author = {Sun, X and Frey, C and McCoy, D and Spieler, MBA and Kelly, CL and Maloney, AE and Garcia-Robledo, E and Lehmann, MF and Ward, BB and Zakem, EJ}, title = {Mechanistic understanding of nitrate reduction as the dominant production pathway of nitrous oxide in marine oxygen minimum zones.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {8916}, pmid = {41057344}, issn = {2041-1723}, mesh = {*Nitrous Oxide/metabolism ; *Nitrates/metabolism ; *Oxygen/metabolism ; Oxidation-Reduction ; *Seawater/microbiology/chemistry ; Ecosystem ; Denitrification ; Nitrites/metabolism ; Bacteria/metabolism ; }, abstract = {Nitrous oxide (N2O), a potent greenhouse gas and ozone-depleting agent, is produced intensely in oxygen minimum zones (OMZs) predominantly through nitrate reduction NO 3 - → N 2 O . However, mechanisms and controls of this pathway remain unclear. Here, we investigate the microbial ecology governing this pathway using experiments and an ecosystem model. We experimentally confirm a critical hypothesis: most NO 3 - → N 2 O denitrifiers do not utilize extracellular nitrite, an intermediate of the pathway. Model results demonstrate that the NO 3 - → N 2 O pathway is compatible with oxygen, and that its response to oxygen is heterogeneous because it is governed by niche partitioning of distinct microbial types and thus may not follow a smooth curve. Lastly, experiments demonstrate that this pathway is sensitive to the type of organic matter, its electron acceptor, in addition to organic matter availability. These findings advance our mechanistic understanding of the primary N2O production pathway, necessary for predictions of marine N2O emissions.}, }
@article {pmid41057270, year = {2025}, author = {Hallett, EN and Comte, J}, title = {Identification and Global Distribution of a Core Microbiome From High-Arctic Lakes.}, journal = {Environmental microbiology}, volume = {27}, number = {10}, pages = {e70182}, doi = {10.1111/1462-2920.70182}, pmid = {41057270}, issn = {1462-2920}, support = {RGPIN-2020-06874//Natural Sciences and Engineering Research Council of Canada/ ; RGPNS-2020-06874//Natural Sciences and Engineering Research Council of Canada/ ; //Natural Resources Canada/ ; }, mesh = {*Lakes/microbiology ; Arctic Regions ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; DNA, Bacterial/genetics ; Biodiversity ; High-Throughput Nucleotide Sequencing ; }, abstract = {Arctic lakes are sentinels of climate change, yet their microbial community structure and functioning remain poorly understood. This study analysed the genetic content of clear-water Arctic lakes and their surroundings using high-throughput amplicon sequencing of the 16S rRNA gene to identify their core microbiome and its contribution to the overall taxonomy pool. To assess geographical constraints and oligotrophic conditions, these results were compared with a latitudinally diverse multi-basin oligotrophic lake in a temperate climate. Arctic and temperate lakes exhibited different assemblages, but both showed similar transitional gradients of microbial community composition from upstream soils/inlets through the lake system to the outlet, driven mainly by the dissolved organic matter (DOM) characteristics. Distinct core microbiomes were identified for temperate and Arctic lakes, with Arctic lakes appearing more diverse. A limited shared core microbiome was observed between the two regions, composed mostly of typical freshwater bacteria. While core taxa identities differed between regions, most exhibited characteristics of generalist bacteria with a strong global presence. These results provide key insights into the structure of remote high Arctic lakes, contributing to our understanding of aquatic microbial ecology in a transitioning Arctic and identifying microbial communities and individual taxa of interest for further study on oligotrophy.}, }
@article {pmid41056783, year = {2025}, author = {Guo, H and Lu, Y and Bulok, Y and Huang, W and Liu, Y}, title = {Advances and challenges of anammox-based PN/A and PD/A coupled processes in treating diverse wastewater qualities: A review.}, journal = {Journal of environmental management}, volume = {394}, number = {}, pages = {127484}, doi = {10.1016/j.jenvman.2025.127484}, pmid = {41056783}, issn = {1095-8630}, abstract = {The anammox process is critical for sustainable nitrogen removal, yet widespread use faces operational, environmental and microbial challenges. This review evaluates recent advances in anammox-based coupled processes, particularly PN/A and PD/A, highlighting their adaptation to varied wastewater types. PN/A has been extensively validated at full scale for high-ammonia wastewaters, including sludge digestion liquor, landfill leachate, and industrial effluents, and is now being extended to mainstream municipal applications. However, persistent barriers such as NOB suppression, sensitivity to low temperature, and heterotrophic competition under high C/N conditions continue to limit its performance. In contrast, successful PD/A deployment in mainstream wastewater depends on innovative solutions to temperature-related constraints, including biofilm buffering, metabolic adaptation, and kinetic optimization. The performance of both PN/A and PD/A systems is closely tied to wastewater composition (e.g. such as salinity, organic load, and the presence of toxic compounds) and its influence on microbial kinetics. Emerging innovations, including EPS-enriched biofilms, granular sludge, quorum sensing microbial regulation, and AI-driven controls have enhanced system resilience. Furthermore, integrated approaches enabling simultaneous nitrogen and phosphorus removal and novel reactor configurations are expanding the practical applicability of anammox processes, supporting resource recovery goals. This review synthesizes mechanistic insights, highlights full-scale implementation cases, and outlines emerging frontiers such as nanotechnology-enhanced biofilms and digital twin modelling for process optimization. By bridging microbial ecology with advanced process engineering, this work provides strategic direction for scaling up anammox-based systems in pursuit of energy-neutral and sustainable wastewater treatment under tightening environmental regulations.}, }
@article {pmid41054273, year = {2025}, author = {Wang, S and Bao, Z and Li, Z and Zhao, M and Wang, X and Liu, F}, title = {The impact of very-low-calorie ketogenic diets on gut microbiota in individuals with obesity: a systematic review and meta-analysis.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2566305}, doi = {10.1080/19490976.2025.2566305}, pmid = {41054273}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Diet, Ketogenic ; *Obesity/microbiology/diet therapy ; Bacteria/classification/genetics/isolation &amp; purification ; Body Mass Index ; *Caloric Restriction ; }, abstract = {OBJECTIVE: This study aimed to systematically review and meta-analyze the effects of very-low-calorie ketogenic diets (VLCKD) on gut microbiota in individuals with obesity.<br><br>METHODS: A comprehensive literature search was conducted across four electronic databases-PubMed, EBSCOhost, Cochrane Library, and Web of Science-up to June 2025. Outcomes included changes in gut microbial diversity and the relative abundance of key taxa. Subgroup analyses were performed based on body mass index (BMI), age, and intervention duration.<br><br>RESULTS: A total of 14 studies were included. Random-effects meta-analysis revealed that VLCKD interventions significantly improved gut microbial &#x3b1;-diversity, as indicated by increased Shannon index (SMD: 0.54, 95% CI: 0.03 to 1.04, P&#x2009;=&#x2009;0.0378) and Faith's Phylogenetic Diversity (PD) index (SMD: 0.77, 95% CI: 0.36 to 1.18, P&#x2009;=&#x2009;0.0002). In addition, VLCKD significantly increased the abundance of Akkermansia (SMD: 1.76, 95% CI: 0.48 to 3.03, P&#x2009;=&#x2009;0.0069) and the Firmicutes-to-Bacteroidetes (F/B) ratio (SMD: 1.01, 95% CI: 0.67 to 1.34, P < 0.0001), while significantly reducing the probiotic genus Bifidobacterium (SMD: -1.23, 95% CI: -1.81 to -0.64, P < 0.0001). Subgroup analyses indicated that the increase in Shannon index was more pronounced in participants with BMI&#x2009;&#x2264;&#x2009;30 kg/m&#xb2; and age >30 years. Akkermansia showed a greater increase in those with BMI 30-35 kg/m&#xb2;, age >40 years, and intervention duration &#x2264;6 weeks. Conversely, Bifidobacterium abundance declined significantly in individuals with BMI 30-35 kg/m&#xb2;, age >40 years, and within an intervention period &#x2264;12 weeks.<br><br>CONCLUSION: VLCKD appears to be a promising dietary intervention for modulating gut microbiota in individuals with obesity. However, its bidirectional effects on microbial ecology warrant caution. Future studies should further investigate its long-term safety and explore personalized strategies for microbiota-targeted interventions.}, }
@article {pmid41053793, year = {2025}, author = {Ou, HX and Chen, Y and Zheng, DL and Lu, YG and Gan, RH}, title = {Evaluating microbial regulation as a preventive strategy for radiation-related caries: A review.}, journal = {Head &amp; face medicine}, volume = {21}, number = {1}, pages = {67}, pmid = {41053793}, issn = {1746-160X}, support = {2022J01270//Fujian provincial Natural Science Foundation of China/ ; 2021GGA055//Fujian Provincial Health Technology Project/ ; }, mesh = {Humans ; *Dental Caries/prevention &amp; control/microbiology/etiology ; *Microbiota/radiation effects ; *Head and Neck Neoplasms/radiotherapy ; Probiotics/therapeutic use ; *Radiation Injuries/prevention &amp; control/microbiology ; Squamous Cell Carcinoma of Head and Neck/radiotherapy ; }, abstract = {Radiotherapy is a crucial treatment for head and neck squamous cell carcinoma but is associated with several complications, particularly the onset of radiation-related caries (RRC), which severely compromises patients' oral health and quality of life. Most studies have focused on the direct effects of radiation on host organs. Such as radiotherapy/Concurrent Chemoradiotherapy (CCRT) contributing to RRC primarily by inducing salivary gland hypofunction and directly damaging tooth structure. However, emerging evidence implicates additional mechanisms including dietary modifications and oral microbial dysbiosis in driving pathogenic microbial shifts characterized by cariogenic bacterial/fungal proliferation, thereby exacerbating RRC progression. In particular, changes in common cariogenic bacteria/fungi after radiotherapy remain poorly understood. Furthermore, clinical translation of microbial ecology principles into effective RRC prevention strategies remains underexplored. This review centers on radiation-induced oral microbiota alterations, critically analyzing documented microbial shifts characterized by marked proliferation of cariogenic taxa including Streptococcus mutans, Lactobacillus, Prevotella melaninogenica, Veillonella, and Actinomyces, alongside fungal overgrowth of Candida albicans. We propose a dual-focused intervention protocol: initiating probiotic supplementation at radiotherapy commencement to stabilize microbial ecology and preserve salivary function, combined with standardized oral care encompassing mechanical plaque removal, fluoride therapy, and natural anticariogenic agents. While mechanistically plausible, this paradigm requires rigorous validation through multicenter randomized controlled trials assessing ecological stability maintenance and caries incidence reduction.}, }
@article {pmid41051094, year = {2025}, author = {Cheng, Z and Xia, W and McKelvey, S and He, Q and Chen, Y and Yuan, H}, title = {Building Predictive Understanding of the Activated Sludge Microbiome by Bridging Microbial Growth Kinetics and Microbial Population Dynamics.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c05925}, pmid = {41051094}, issn = {1520-5851}, abstract = {Modeling microbiomes can provide predictive insights into microbial ecology, but current modeling approaches suffer from inherent limitations. In this study, a novel modeling approach was developed based on the intrinsic connection between the growth kinetics of guilds and the dynamics of microbial populations. To implement this approach, 466 samples from four full-scale activated sludge systems were retrieved. The raw samples were processed using a data transformation method that tripled the data set size and enabled quantification of population dynamics. Of the 42 family level core populations, 36 showed overall dynamics statistically close to zero (within ± 0.05 d[-1]). Bayesian networks were built to classify the core populations into heterotrophic and autotrophic guilds. Topological data analysis was applied to identify keystone populations and time-dependent microbial interactions. The data-driven inferences were validated directly using the Microbial Database for Activated Sludge (MiDAS) and indirectly by predicting community structure using artificial neural networks. The Bray-Curtis similarity between predicted and observed communities was higher with microbial kinetic parameters than without these parameters (0.70 vs 0.66, t test, p < 0.05). Owing to the flexibility of the modeling framework, this proposed hybrid approach might potentially be adapted to time-dependent data from natural systems for predictive understanding of the involved microbiomes.}, }
@article {pmid41049421, year = {2025}, author = {Yan, J and Zhao, J and Naizemuding, P and Zhao, W and Sun, J and Wang, Y and Yang, J and Li, D and Zhang, F and Cao, H}, title = {Unraveling the Anti-Obesity Potential of White Kidney Bean α-Amylase Inhibitors: Mechanistic Insights From Enzyme Kinetics to Gut Microbiota Modulation.}, journal = {Food science &amp; nutrition}, volume = {13}, number = {10}, pages = {e71043}, pmid = {41049421}, issn = {2048-7177}, abstract = {The global rise in obesity, driven largely by excessive carbohydrate consumption, highlights the demand for innovative dietary interventions targeting starch digestion. This study investigates the anti-obesity effects of α-amylase inhibitors (α-AI) extracted from white kidney beans, employing a multidisciplinary strategy encompassing botanical screening, enzyme kinetics, clinical trials, and gut microbiota profiling. Among 10 varieties evaluated, the A10 strain from Jilin Province demonstrated the highest α-AI activity, characterized by noncompetitive inhibition that remains effective across varying starch concentrations. In an 8-week randomized controlled trial, α-AI supplementation significantly reduced body weight, BMI, waist circumference, and hip circumference compared to placebo. Further, 16S rRNA sequencing revealed dual mechanisms: enrichment of SCFA-producing bacteria (e.g., Bifidobacterium and Bacteroides ovatus) and modulation of microbial lipid metabolic pathways. These results highlight α-AI as a dual-action anti-obesity agent, combining direct enzymatic inhibition with microbiome-mediated metabolic effects. By bridging phytochemical characterization with clinical outcomes, this work proposes a novel therapeutic approach that simultaneously targets carbohydrate absorption and gut microbial ecology, supporting the development of standardized α-AI formulations as potential nutraceuticals for metabolic syndrome.}, }
@article {pmid41048979, year = {2025}, author = {Nurhazli, NAA and Tan, JH and Kamaroddin, MF and Shamsir, MS and Yaakop, AS and Goh, KM}, title = {Microbial Community Profiles of Biofilms from Hot Springs: 16S and 18S rRNA Amplicon Sequencing Data.}, journal = {Data in brief}, volume = {62}, number = {}, pages = {112093}, pmid = {41048979}, issn = {2352-3409}, abstract = {This article presents microbial diversity data from biofilms collected from the sides or outflows of several Malaysian hot springs, with temperatures ranging from 38 to 56 °C and pH values between 7.1 and 8.7. Genomic DNA was extracted from the biofilms and subjected to 16S V3-V4 and 18S V4 amplicon sequencing using the Illumina NovaSeq 6000 platform. Reads were processed with various bioinformatic tools including QIIME2, and eventually, amplicon sequence variants (ASVs) were identified. In almost all analyzed biofilms, approximately 50% of the total ASVs belonged to Cyanobacteriota and Chloroflexota, except for one biofilm, labeled DTO, which was dominated by Pseudomonadata and Cyanobacteriota. Besides bacteria, the data also suggest the presence of various eukaryotic organisms, including small animals such as nematodes, rotifers, and arthropods; fungi and fungus-like organisms such as Ascomycota, Zoopagomycota, Oomycota, and Cryptomycota; as well as photosynthetic eukaryotes from the Viridiplantae group. This dataset serves as a valuable resource for microbial ecology studies in hot spring biofilms and is openly available for reuse, providing a foundation for future research on microbial diversity and functional roles in geothermal ecosystems.}, }
@article {pmid41048492, year = {2025}, author = {Chen, X and Yu, D and Yan, Y and Yuan, C and He, J}, title = {Soil viruses drive carbon turnover during subtropical secondary forest succession.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1633379}, pmid = {41048492}, issn = {1664-302X}, abstract = {INTRODUCTION: Soil viruses are increasingly recognized as key regulators of microbial ecology and ecosystem function, yet their roles in forest ecosystems, particularly during natural secondary succession, remain largely unexplored.<br><br>METHODS: We examined soil viral communities across five successional stages of secondary forests to investigate their taxonomic dynamics and functional potential. Using high-throughput viral metagenomics, we characterized viral community structure, abundance, and auxiliary metabolic gene content.<br><br>RESULTS: Our results demonstrate that soil viral abundance and community composition shift significantly with forest stand age. Viral richness increased during succession, with compositional transitions observed across stages; however, tailed bacteriophages consistently dominated. Structural equation modeling and linear mixed-effects analysis identified soil pH and bacterial diversity as primary environmental determinants of viral diversity. Functionally, soil viruses harbored auxiliary metabolic genes related to carbohydrate metabolism, indicating their potential involvement in modulating host metabolic processes. Successional trends in viral functional profiles revealed a transition from carbon assimilation to carbon release pathways, suggesting viral mediation of carbon turnover. Notably, the enrichment of glycoside hydrolase and glycosyl transferase genes across forest ages implies a role for viruses in shaping microbial carbon processing capacities through carbohydrate-active enzyme contributions.<br><br>DISCUSSION: These findings provide novel evidence that soil viruses actively participate in ecosystem succession by influencing microbial functional potential and biogeochemical cycling. This study underscores the ecological importance of soil viral communities in regulating carbon dynamics during secondary forest development.}, }
@article {pmid41048389, year = {2025}, author = {Kong, S and Abrams, E and Binik, Y and Cappelli, C and Chu, M and Cornett, T and Culbertson, I and Garcia, E and Henry, J and Lam, K and Lampman, DB and Morenko, G and Rivera, I and Swift, T and Torres, I and Velez, R and Waxman, E and Wessely, S and Yuen, A and Lardner, CK and Weissman, JL}, title = {Metagenomes and metagenome-assembled genomes from tidal lagoons at a New York City waterfront park.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e20081}, pmid = {41048389}, issn = {2167-8359}, mesh = {New York City ; *Metagenome ; *Parks, Recreational ; Metagenomics ; Humans ; *Seawater/microbiology ; Microbiota/genetics ; *Water Microbiology ; }, abstract = {New York City parks serve as potential sites of both social and physical climate resilience, but relatively little is known about how microbial organisms and processes contribute to the functioning of these deeply human-impacted ecosystems. We report the sequencing and analysis of 15 shotgun metagenomes, including the reconstruction of 129 high-quality metagenome-assembled genomes, from tidal lagoons and bay water at Bush Terminal Piers Park in Brooklyn, NY sampled from July to September 2024. Our metagenomic database for this site provides an important baseline for ongoing studies of the microbial communities of public parks and waterfront areas in NYC. In particular, we provide rich functional and taxonomic annotations that enable the use of these metagenomes and metagenome-assembled genomes for a wide variety of downstream applications.}, }
@article {pmid41047820, year = {2025}, author = {Lu, Q and Feng, Y and Wang, H and Zhu, K and Teng, L and Yue, M and Li, Y}, title = {Gut microbiota as a regulator of vaccine efficacy: implications for personalized vaccination.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2563709}, doi = {10.1080/19490976.2025.2563709}, pmid = {41047820}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Vaccine Efficacy ; *Precision Medicine ; Vaccination ; Immunity, Innate ; *Vaccines/immunology ; Animals ; Adaptive Immunity ; }, abstract = {Vaccines are one of the most significant achievements in global health, as they have substantially reduced morbidity and mortality from infectious diseases. However, the vaccine efficacy varies markedly across different populations, particularly among infants, older adults, and people living in low- and middle-income countries. Host-intrinsic factors, such as sex, age, and genetic predisposition, contribute to these heterogeneities. However, accumulating data indicate that the gut microbiota also plays a pivotal role in modulating vaccine efficacy. This review summarizes current knowledge, demonstrating that vaccine efficacy is shaped not only by host biology but also by a dynamic, bidirectional interplay between the gut microbiota and immune system. We discuss how the microbiota influences vaccine outcomes through several mechanisms, including priming the innate immune response, regulating adaptive responses through metabolites, and facilitating antigen cross-reactivity. Furthermore, we examine the potential for microbiota-informed precision vaccinology, which integrates multiomics profiling and artificial intelligence to predict and improve vaccine performance. These advancements establish a framework for personalized vaccine development based on microbial ecology.}, }
@article {pmid41046701, year = {2025}, author = {Yao, H and Yu, J and Yang, X and Xu, J}, title = {Mechanisms of disruption of the gut-brain axis by environmental endocrine disruptors.}, journal = {Ecotoxicology and environmental safety}, volume = {304}, number = {}, pages = {119124}, doi = {10.1016/j.ecoenv.2025.119124}, pmid = {41046701}, issn = {1090-2414}, abstract = {Environmental endocrine disruptors (EEDs) are exogenous chemicals that impair physiological health by disrupting endocrine function. The gut-brain axis represents a complex bidirectional communication network integrating the gut microbiome, immune system, neural signaling, and endocrine pathways to maintain systemic homeostasis. Within this interconnected system, gut microbiota influence mood regulation, immune activity modulates neural processes, and neural signaling governs circadian and sleep cycles. This review explores the multi-system impacts of EEDs across four key physiological domains: (1) gut microbial ecology, (2) immune function, (3) neuroendocrine regulation, and (4) developmental processes. Evidence indicates that EED exposure disrupts intestinal microbial composition, leading to dysbiosis marked by the depletion of beneficial taxa and the expansion of pathogenic species. Concurrently, EEDs impair gut-associated immune cell populations (T cells, B cells, and macrophages), undermining mucosal immunity and increasing susceptibility to inflammatory bowel disease, autoimmune conditions, and gastrointestinal malignancies. At the endocrine level, EEDs interfere with the hypothalamic-pituitary-adrenal and hypothalamic-pituitary-gonadal axes, contributing to hormonal imbalances and impaired reproductive development. Neurochemically, they disrupt the synthesis, release, and degradation of key neurotransmitters, including norepinephrine, dopamine, and serotonin, while exerting direct neurotoxic effects such as cerebrovascular abnormalities and delayed cerebellar myelination. In summary, this review delineates the mechanistic pathways through which EEDs perturb gut-brain axis homeostasis. These insights provide a scientific basis for designing targeted therapeutic interventions and shaping evidence-based public health policies.}, }
@article {pmid41044018, year = {2025}, author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW}, title = {Soil microbes: below-ground defenders against desertification.}, journal = {Trends in ecology &amp; evolution}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tree.2025.09.014}, pmid = {41044018}, issn = {1872-8383}, abstract = {Soil microbes act as below-ground defenders against desertification by several mechanisms, such as rhizosheath formation, necromass accumulation, biological soil crusts, exopolysaccharide (EPS) production, hyphal networks, and calcium carbonate precipitation. Here, we discuss how soil microbes drive ecosystem recovery in drylands, offering promising, nature-based strategies for restoring soils in the face of desertification.}, }
@article {pmid41041139, year = {2025}, author = {Berlanga, M and Martín-García, A and Guerrero, R and Riu-Aumatell, M and López-Tamames, E}, title = {Changes in healthy Wistar rat gut microbiome by short-term dietary cava lees intervention.}, journal = {Frontiers in nutrition}, volume = {12}, number = {}, pages = {1641612}, pmid = {41041139}, issn = {2296-861X}, abstract = {INTRODUCTION: The gut microbiome plays a crucial role in host health through complex host-microbe interactions. Beta-glucans, structural polysaccharides found in yeast cell walls, have emerged as promising modulators of immune function and microbial ecology. Cava lees, a by-product of sparkling wine production composed of Saccharomyces cerevisiae cell walls, represent a rich source of beta-glucans that could be upcycled for nutritional and therapeutic applications.<br><br>METHODS: Twenty-four Wistar rats (12 males, 12 females) were randomly divided into control and treatment groups. The treatment group received daily doses of 2,000&#x202f;mg lees/kg body weight for 14&#x202f;days. Shotgun metagenomic analysis was performed to assess microbial composition and functional changes.<br><br>RESULTS: A 14-day cava lees supplementation study revealed significant shifts in gut microbiota composition and function. Baseline microbiota was dominated by Bacillota (64-72%) and Bacteroidota (23-32%) with sex-specific differences at the family level. Post-supplementation analysis showed increased Shannon diversity across both sexes, with beneficial enrichment of Bifidobacteriaceae and Rikenellaceae families and reduction of Eubacteriaceae. While global metabolic profiles remained stable, targeted functional pathways were significantly changed, including butyrate production genes. Females exhibited particularly elevated secondary bile acid modification genes (Mann-Whitney-Wilcoxon test p&#x202f;=&#x202f;0.032), and male oxidative stress response pathways (Mann-Whitney-Wilcoxon test p&#x202f;=&#x202f;0.016) showing both a potentially sex-dependent responses to dietary intervention.<br><br>CONCLUSION: Working with healthy individuals provides a clear understanding of the normal, baseline microbiota composition and function before any intervention. These findings suggest a degree of plasticity of the gut microbiome and its responsiveness to dietary modifications. Beta-glucans from cava lees appear to create a favorable environment for beneficial bacteria, with sex-specific changes of certain bacterial families and functions. These findings provide a foundation for future translational research in humans. Nonetheless, to establish their true impact on human health, these observations in rodent models must be validated through appropriately designed human clinical studies.}, }
@article {pmid41039213, year = {2025}, author = {IJdema, F and Arias-Giraldo, LM and Vervoort, E and Struyf, T and Van den Ende, W and Raaijmakers, JM and Lievens, B and De Smet, J}, title = {Metagenome-based identification of functional traits of the black soldier fly gut microbiome associated with larval performance.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {612}, pmid = {41039213}, issn = {1471-2180}, support = {S008519N//ENTOBIOTA/ ; IMP20028//KU Leuven Impuls grant/ ; C3/22/041//KU Leuven CHITINERY grant/ ; G0C4622N//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {Animals ; Larva/microbiology/growth &amp; development ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Metagenome ; *Diptera/microbiology/growth &amp; development ; Animal Feed/analysis ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Diet ; Phylogeny ; Chickens ; }, abstract = {BACKGROUND: The relationship between microbiomes and their hosts has been the subject of intensive study in recent years. For black soldier fly larvae (BSFL) (Hermetia illucens L., Diptera: Stratiomyidae), correlations between shifts in its microbial gut community composition and its health and performance suggest that the BSFL gut microbiome encodes important functions that complement the insect's own immune system and metabolism. To date, most BSFL microbiome studies have been based on 16S rRNA sequencing data. Because this approach derives a lot of information from very short sequencing reads, it was hypothesized that more insight into bacterial functionality could be generated using more extensive sequencing technologies. Here, whole genome shotgun (WGS) metagenomic sequencing was employed to investigate which microbiome-associated taxa and functions were associated with increased performance of larvae reared on a chicken feed (CF) or artificial supermarket food waste (SFW) based diet.<br><br>RESULTS: Taxonomic and functional profiling of the BSFL gut microbiome revealed a significant shift in response to diet, where bacterial genes encoding specific metabolic functions, such as the metabolism of sorbitol, were significantly enriched in the microbiome of larvae reared on SFW-diet. This indicates that the nutritional composition of the substrate alters the gut bacterial composition by providing competitive benefits or new niches for specific bacteria that can utilise these compounds. Moreover, specific microbial functions, such as cobalamin synthesis, appear to be correlated with larval performance. Aside from metabolic functions, biosynthetic gene cluster analysis revealed potential antimicrobial competition and protective functions among bacterial species. Improved taxonomic resolution provided by WGS led to the identification of several metagenome assembled genomes (MAGs), including a potentially novel BSFL-associated Scrofimicrobium species. Furthermore, there were differences in larval performance between rearing diets, and larval growth was correlated with high abundance of several MAGs.<br><br>CONCLUSIONS: Variation in the nutritional and bacterial load of a diet can result in functional shifts in the gut microbiome of the larvae. Analysis of the BSFL metagenome identified several bacteria that are positively correlated with larval performance, which could potentially provide beneficial metabolic functions for the host that should be further explored.}, }
@article {pmid41037135, year = {2025}, author = {Cárdenas, P and Carpio-Arias, V and Chávez, M and Benítez, AD and Baldeón, AD and Suárez-Jaramillo, A and Fornasini, M and Robles, J and Loza, G and Baldeón, ME}, title = {Nutritional Status and Fecal Microbiota in School Children from the Galapagos and the Andean Region.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {103}, pmid = {41037135}, issn = {1432-184X}, support = {I+D+I-XVII-2022-03//This work was supported by the Ecuadorian Consortium for the Development of Advanced Internet (CEDIA) and Universidad Internacional del Ecuador, Universidad San Francisco de Quito, and Escuela Superior Politecnica del Chimborazo./ ; }, mesh = {Humans ; Ecuador/epidemiology ; *Feces/microbiology ; *Nutritional Status ; Child ; Male ; Female ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; Intestinal Diseases, Parasitic/epidemiology/microbiology ; }, abstract = {Schoolchildren from the Galapagos and the Andean region present the worst indices of malnutrition in Ecuador and are exposed to distinctive food and water insecurity. We compared the nutritional status, the fecal microbiota composition of schoolchildren from the Galapagos (n = 51; 8.88 ± 2.15 years) and the Andean region (n = 114; 8.69 ± 1.83 years). Children had a nutritional evaluation and provided fecal samples for microbiota analysis by 16S rRNA gene sequencing. Excess weight was more prevalent in Galapagos (41.18%) than in the Andes (24.5%). Additionally, intestinal parasitosis was more prevalent in children from the Andes (76.4%) than in Galapagos (13.0%). Species richness was lower in fecal samples of children from the Galapagos than those from the Andes (Chao1 index p = 0.001). Beta-diversity metrics also showed significant differences between these samples. Bacteroidota and Proteobacteria were enriched in the microbiota of Galapagos children, whereas Firmicutes A and Cyanobacteria were enriched in the Andean children. At the genus level, the top 3 genera present in schoolchildren from the Galapagos were Bacteroides, Phocaeicola, and Escherichia, while in children from the Andes were Cryptobacteroides, Prevotella, and Clostridium. Cyanobacteria were inversely associated with BMI z-score in the Galapagos region (q = 0.009), while, Firmicutes D had a direct relationship with BMI z-score in children from the Andes (q = 0.05). At the genus level, only Butyrivibrio was inversely associated with BMI z-score in children of the Galapagos (q = 0.04). We conclude that schoolchildren with different degrees of malnutrition from two distinct geographical areas have dissimilar fecal microbiota characteristics.}, }
@article {pmid41037127, year = {2025}, author = {Arunrat, N and Mhuantong, W and Sereenonchai, S}, title = {Land-use legacies shape soil microbial communities and nutrient cycling functions in rotational shifting cultivation fields of Northern Thailand.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {102}, pmid = {41037127}, issn = {1432-184X}, support = {MU-SRF-RS-21 B/67//Mahidol University (Strategic Research Fund: 2024)/ ; }, mesh = {*Soil Microbiology ; Thailand ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Soil/chemistry ; *Microbiota ; Nitrogen/metabolism ; Nitrification ; *Agriculture/methods ; Nitrogen Fixation ; Nitrogen Cycle ; }, abstract = {How land-use history-particularly in contrasting systems such as rotational shifting cultivation (RSC) and continuously fallow (CF) fields-influences soil microbial communities and their biogeochemical functions remains insufficiently understood. In this study, shotgun metagenomic sequencing was used to compare the taxonomic composition and functional gene profiles of soils under RSC and CF systems in Northern Thailand. The results revealed distinct microbial assemblages and metabolic potentials shaped by land-use legacy. RSC soils were characterized by a higher abundance of nitrifiers and nitrogen-fixing taxa, including Nitrosocosmicus and Streptomyces, along with enriched genes involved in nitrification (e.g., amoC_B, nxrB) and nitrogen fixation (nifD, nifK), reflecting an enhanced potential for nitrogen acquisition and retention. In contrast, CF soils showed enrichment in Bradyrhizobium, Halobaculum, and Russula, and exhibited higher expression of denitrification-related genes (norB, narJ), suggesting increased nitrogen loss via gaseous emissions. Functional genes related to phosphate metabolism (phoX, glpQ) and nutrient signal transduction were more abundant in RSC soils, indicating active nutrient cycling in response to recent disturbance. Conversely, CF soils demonstrated broader metabolic capabilities, including genes for sulfur oxidation and redox regulation, suggesting microbial adaptation to more stable but nutrient-limited conditions. These findings demonstrate that land-use legacies strongly influence microbial composition and function, with important implications for nutrient cycling and soil fertility restoration in shifting cultivation landscapes.}, }
@article {pmid41037066, year = {2025}, author = {Scott, CM and Holman, DB and Gzyl, KE and Ibe, A and Taheri, AE}, title = {Production Systems and Age Influence Fecal Mycobiota Diversity and Composition in Swine.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {104}, pmid = {41037066}, issn = {1432-184X}, mesh = {Animals ; *Feces/microbiology ; Swine/microbiology ; *Fungi/classification/genetics/isolation &amp; purification ; *Animal Husbandry/methods ; *Gastrointestinal Microbiome ; *Mycobiome ; Biodiversity ; DNA, Fungal/genetics ; Age Factors ; Female ; }, abstract = {The gut microbiome is an important factor in animal health and can be influenced by factors such as age, diet, stress, environmental conditions, and farming practices. Bacterial communities of the gut microbiome in many species have been extensively studied, but research on the fungal microbiota remains limited and underrepresented in the literature. The objective of this study was to characterize the fecal mycobiota of swine raised under two different production systems: outdoor pasture-based or conventional indoor systems. Fecal samples from nursery, growing-finishing, and sow pigs from both farming systems were collected, and the mycobiota was profiled using PCR amplification and sequencing of the universal fungal internal transcribed spacer 1 (ITS1) region. A significant difference in fungal community structure was observed between the conventionally raised and pasture-raised pigs, as well as among all three production phases. Four species, Arthrographis kalrae, Enterocarpus grenotii, Pseudallescheria angusta, and Sagenomella oligospora, were differentially abundant between the two farms, all of which had higher relative abundance in the pasture-raised pigs. Additionally, pasture-raised pigs hosted a more diverse fungal community with higher species richness in their gastrointestinal tract. In summary, farming practices and pig age influenced the pig fecal mycobiota.}, }
@article {pmid41036845, year = {2025}, author = {Du Plessis, I and Snyder, H and Calder, R and Rolando, JL and Kostka, JE and Weitz, JS and Dominguez-Mirazo, M}, title = {Viral community diversity in the rhizosphere of the foundation salt marsh plant Spartina alterniflora.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0023425}, doi = {10.1128/msphere.00234-25}, pmid = {41036845}, issn = {2379-5042}, abstract = {Viruses of microorganisms impact microbial population dynamics, community structure, nutrient cycling, gene transfer, and genomic innovation. In wetlands, root-associated microbial communities mediate key biogeochemical processes important for plants involved in ecosystem maintenance. Nonetheless, the presence and role of microbial viruses in salt marshes remain poorly understood. In this study, we analyzed 24 metagenomes retrieved from the root zone of Spartina alterniflora, a foundation plant in salt marshes of the eastern and Gulf coasts of the U.S. The samples span three plant compartments-bulk sediment, rhizosphere, and root-and two cordgrass plant phenotypes: short and tall. We observed differentiation between phenotypes and increased similarity in viral communities between the root and rhizosphere, indicating that plant compartment and phenotype shape viral community composition. The majority of viral populations characterized are novel at the genus level, with a subset predicted to target microorganisms known to carry out key biogeochemical functions. The findings contribute to ongoing efforts to understand plant-associated viral diversity and community composition and to identify potential targets for exploring viral modulation of microbially mediated ecosystem functioning in intertidal wetlands.IMPORTANCESalt marshes are vital coastal ecosystems. Microbes in these environments drive nutrient cycling and support plant health, with Spartina alterniflora serving as a foundation species. This study explores viral communities associated with S. alterniflora, revealing how plant compartments and phenotypes shape viral composition. The discovery of numerous novel viruses, some potentially influencing microbes involved in key biogeochemical processes, highlights their ecological significance. Given the increasing pressures on coastal ecosystems, understanding virus-microbe-plant interactions is essential for predicting and managing ecosystem responses to environmental change.}, }
@article {pmid41033533, year = {2025}, author = {Kim, YJ and Jung, DH and Jung, JH and Seo, DH and Kim, JS and Park, CS}, title = {Genomic and functional characterization of carbohydrate-active enzymes from Ruminococcoides bili FMB-CY1 reveals modular strategy for resistant starch degradation in the human gut.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {147957}, doi = {10.1016/j.ijbiomac.2025.147957}, pmid = {41033533}, issn = {1879-0003}, abstract = {Ruminococcoides bili FMB-CY1, a human gut bacterium, exhibits strong resistant starch (RS)-degrading ability. To elucidate its RS-degradation strategy, we performed comprehensive genomic annotation and biochemical characterization of 19 encoded carbohydrate-active enzymes (CAZymes). Genome analysis revealed glycoside hydrolases (GH13, GH31, GH77), glycosyltransferase (GT35), carbohydrate-binding modules (CBMs), and domains associated with amylosome-like multienzyme complexes, including dockerin and cohesin motifs. All 19 CAZyme genes were heterologously expressed in Escherichia coli, and their enzymatic properties were systematically characterized. Most α-amylases exhibited extracellular activity against raw RS granules, particularly those harboring CBMs. Hydrolysis profiling revealed distinct substrate preferences, leading to functional reannotation of four enzymes. Domain analyses further suggested that select CAZymes form a surface-associated complex analogous to the amylosome. Together, these enzymes suggest a putative RS-degradation system, in which extracellular α-amylases initiate starch breakdown and are followed by pullulanases, glucosidases, and transferases that complete RS degradation. The released sugars support microbial cross-feeding and potentially contribute to host energy metabolism. The study provides molecular insight into RS utilization by Rc. bili FMB-CY1 and identifies enzymatic features relevant to gut microbial ecology and functional food applications targeting RS metabolism.}, }
@article {pmid41031660, year = {2025}, author = {Wick, LY}, title = {Rebuttal to Correspondence on "DC Electric Fields Promote Biodegradation of Waterborne Naphthalene in Biofilter Systems".}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c12499}, pmid = {41031660}, issn = {1520-5851}, }
@article {pmid41029470, year = {2025}, author = {Cutajar, S and Braglia, C and Alberoni, D and Mifsud, M and Baffoni, L and Spiteri, J and Di Gioia, D and Mifsud, D}, title = {Gut microbiome of Vespa orientalis: functional insights and potential honey bee pathogen dynamics.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {95}, pmid = {41029470}, issn = {2524-4671}, support = {TESS 2022//Tertiary Education Scholarships Scheme by the Ministry for Education, Sport, Youth, Research and Innovation in Malta (TESS 2022)./ ; CN00000022//European Union Next-GenerationEU, PIANO NAZIONALE DI RIPRESA E RESILIENZA (PNRR) - MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4 - D.D. 1032 17/06/2022/ ; CN00000022//European Union Next-GenerationEU, PIANO NAZIONALE DI RIPRESA E RESILIENZA (PNRR) - MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4 - D.D. 1032 17/06/2022/ ; }, abstract = {Vespa orientalis, the oriental hornet, is an emerging predator of honey bees whose ecological impact and microbial ecology remain poorly understood. Here, we present the first detailed characterisation of its gut microbiota by integrating 16S rRNA gene sequencing, predicted microbial function, pathogen screening, and a three-year beekeeper survey across urban and rural sites in Malta. Hornets were sampled from four locations and classified by observed foraging behaviour, either predation on honey bees or scavenging on cat food.Survey data confirmed consistent V. orientalis sightings and seasonal colony losses, particularly during peak foraging months. Microbiome analysis revealed a conserved core community dominated by Spiroplasma, Arsenophonus, and Rosenbergiella, with overall diversity stable across sites and diets. However, specific taxa varied with foraging behaviour. For example, Arsenophonus was enriched in bee-predating hornets, while Enterobacter and Serratia were more common in scavenging individuals, suggesting environmental and dietary influences on microbiota composition. Predicted functional profiles remained broadly conserved, reflecting robust nutrient metabolism and potential detoxification capabilities, with some variations related to the diet behaviour.Pathogen screening detected Nosema ceranae and Crithidia bombi in a substantial proportion of hornets, including those not observed feeding on bees. Although our findings do not demonstrate pathogen transmission, they support the hypothesis that V. orientalis may act as a transient carrier, potentially contributing to pathogen persistence via environmental exposure.Together, these results reveal the dietary flexibility and microbial flexibility within the gut microbiome of V. orientalis, and highlight its potential involvement in pollinator pathogen dynamics.}, }
@article {pmid41028416, year = {2025}, author = {Sidharthan, VK and Patel, R and Thiyaharajan, M and Krishnappa, C and Pattanaik, S and Kumar, A}, title = {Metabarcoding reveals unique rhizospheric microbiomes of Rhizophora in Indian Mangroves.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {41028416}, issn = {1874-9356}, support = {IFB/T-1/WME/23-1//Indian Council of Forestry Research and Education/ ; }, abstract = {Rhizophora species are ecologically significant true mangroves with a broad tropical distribution. We examined the rhizospheric microbiomes of dominant Rhizophora species from two contrasting Indian mangrove ecosystems-Coringa and Pichavaram-using high-throughput metabarcoding. Soil properties differed significantly between sites: Pichavaram exhibited higher electrical conductivity (24.53 dS/m), organic carbon (1.70%), sodium (8811.86 ppm), sodium adsorption ratio (220.15), and exchangeable sodium percentage (64.27%), while Coringa soils showed higher pH (8.01). Sequencing generated 1.31, 1.24, and 1.22 million high-quality reads for archaea, bacteria, and fungi, respectively. Taxonomic profiling revealed Nitrososphaeria (62.3-91.9%), Gammaproteobacteria (16.8-25.1%), and Sordariomycetes (18.6-27.8%) as dominant classes. Core taxa across both sites included Candidatus Nitrosopumilus, Woeseia, and Aspergillus. Alpha diversity indices (Chao1, Shannon, Simpson) indicated significantly higher bacterial richness and evenness in R. apiculata at Coringa (P < 0.001), while archaeal and fungal diversity showed no marked differences. Beta diversity analysis (PCoA, PERMANOVA) revealed distinct community compositions between Coringa and Pichavaram, with stronger segregation in archaeal and bacterial assemblages than in fungi. Differential abundance analysis identified nine archaeal, fifty-nine bacterial, and three fungal genera enriched between sites, with methanogens (Methanosarcina, Methanocella) predominant in Coringa and halophiles (Halococcus, Haloferax) in Pichavaram. Redundancy analysis showed sodium adsorption ratio as the key determinant of microbial assemblages, while electrical conductivity significantly shaped archaeal and fungal communities. These findings provide the first baseline dataset of the Coringa rhizospheric microbiome and new insights into the microbial ecology of Indian mangroves, with implications for ecosystem functioning, methane emissions, and conservation strategies.}, }
@article {pmid41026240, year = {2025}, author = {Abdelali, SK and Aissaoui, L and Cano-Argüelles, AL and Piloto-Sardiñas, E and Abuin-Denis, L and Maitre, A and Foucault-Simonin, A and Mateos-Hernández, L and Kratou, M and Wu-Chuang, A and Obregon, D and Cabezas-Cruz, A}, title = {Seasonal Variations in the Microbiome of Hyalomma excavatum Ticks in Algeria.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {96}, pmid = {41026240}, issn = {1432-184X}, mesh = {Animals ; *Seasons ; Algeria ; *Microbiota ; *Ixodidae/microbiology ; Female ; *Bacteria/classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 16S/genetics ; Rickettsia/isolation &amp; purification/genetics ; Biodiversity ; }, abstract = {Ticks are key vectors of zoonotic diseases, with their microbiomes playing a critical role in tick physiology, survival, and vector competence. This study presents the first investigation of the microbiome in Hyalomma excavatum ticks from Algeria, focusing on seasonal variations in bacterial diversity, community composition, and pathogen interactions. Using next-generation sequencing (NGS), the microbiome of 21 female ticks collected during spring, summer, and autumn was analyzed. Beta diversity analysis revealed significant seasonal shifts in microbial community structure, while alpha diversity metrics showed no significant differences in richness and evenness. Co-occurrence network analysis demonstrated seasonal shifts in microbial interactions, particularly between symbionts and pathogens, highlighting Francisella as a key taxon in tick survival and pathogen dynamics. Rickettsia presence varied by season, influencing microbial network stability. These findings underscore the ecological determinants shaping the microbiome and its potential role in pathogen transmission. Understanding seasonal microbiome shifts provides valuable insights for managing tick-borne diseases and could inform the development of targeted, season-specific vector control strategies.}, }
@article {pmid41026216, year = {2025}, author = {Martin-Pozas, T and Fernandez-Cortes, A and Calaforra, JM and Sanchez-Moral, S and Saiz-Jimenez, C and Jurado, V}, title = {Aerobiology and Environmental Zonation in Gypsum Caves: A Comparative Study of Culturing and NGS Approaches.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {95}, pmid = {41026216}, issn = {1432-184X}, support = {PID2020-114978GB-I00 and PDI2023-146299OB-C22//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, mesh = {*Caves/microbiology ; *Calcium Sulfate/analysis ; *Bacteria/genetics/classification/isolation &amp; purification/growth &amp; development ; High-Throughput Nucleotide Sequencing/methods ; *Air Microbiology ; *Microbiota ; Spain ; *Fungi/isolation &amp; purification/genetics/classification ; Geologic Sediments/microbiology ; Phylogeny ; Biodiversity ; }, abstract = {Classical aerobiological studies commonly use high-volume air samplers to quantify and identify cultivable airborne bacteria and fungi. However, this approach introduces a significant bias, as it overlooks the non-cultivable fraction, which likely constitutes a major component of the airborne microbiome. The advent of next-generation sequencing (NGS) has addressed this limitation, enabling a more comprehensive characterization of the cave aerobiome. This study analyzes both cultivable and non-cultivable airborne bacteria from Covadura and C3 caves, located in the Gypsum Karst of Sorbas (SE Spain). A total of 24 bacterial genera were identified using culture-based methods, whereas NGS revealed 749 genera. Culture-based methods using the surface air system (SAS) predominantly recovered Gram-positive spore-forming bacteria from the phyla Bacillota and Actinomycetota, which were largely absent or present in low relative abundances in the NGS datasets. In contrast, NGS revealed a broader diversity, including numerous Gram-negative and rare airborne bacteria not detected by culture. The NGS results from airborne samples showed greater similarity to the microbial communities found in cave biofilms and sediments, suggesting that a portion of airborne bacteria originates from within the cave and is influenced by microclimatic conditions such as ventilation and air stagnation. Although the short-read sequencing approach used in this study has limitations, such as reduced taxonomic resolution compared to the culture-based approach, it remains the most effective tool for capturing the diversity and ecological patterns of airborne microorganisms. The integration of gas tracers and other environmental data allowed the identification of zones within the cave with different ventilation patterns and degrees of isolation, which corresponded to different spatial distributions of airborne bacteria. Our findings underscore that reliable aerobiological studies in caves require the combination of non-culture dependent-based sequencing approaches and environmental monitoring to fully understand the origin, diversity, and ecological dynamics of airborne microbial communities.}, }
@article {pmid41026209, year = {2025}, author = {Gutiérrez-Pavón, AJ and Pereyra, MM and Chacón, FI and Monroy-Morales, E and Rebollar, EA and Dib, JR and Serrano, M and Romero-Contreras, YJ}, title = {Bacteria from the Amphibian Skin Inhibit the Growth of Phytopathogenic Fungi and Control Postharvest Rots.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {101}, pmid = {41026209}, issn = {1432-184X}, support = {PICT-2021-GRF-TII-0020//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; N203023//Programa de Apoyo a Proyectos de Investigaci&#xf3;n e Innovaci&#xf3;n Tecnol&#xf3;gica/ ; }, mesh = {Animals ; *Plant Diseases/microbiology/prevention &amp; control ; Botrytis/growth &amp; development ; *Skin/microbiology ; Penicillium/growth &amp; development ; *Antibiosis ; *Bacteria/isolation &amp; purification/metabolism ; Fruit/microbiology ; *Biological Control Agents ; Solanum lycopersicum/microbiology ; Alternaria/growth &amp; development ; *Anura/microbiology ; Citrus/microbiology ; *Fungi/growth &amp; development ; Volatile Organic Compounds/pharmacology ; Aspergillus niger/growth &amp; development ; Pest Control, Biological ; }, abstract = {Postharvest diseases caused by phytopathogenic fungi represent one of the main challenges in the agricultural industry, leading to significant losses in fruit production. Although chemical treatments have been widely used for the control of these pathogens, the emergence of resistant strains and concerns regarding food safety and environmental impact have driven the search for novel effective and eco-friendly alternatives, such as the use of biological control agents (BCAs). Previously, we demonstrated that bacteria isolated from frog skin inhibit the growth of the phytopathogenic fungus Botrytis cinerea. Based on these findings, in this study we aimed to investigate the biocontrol potential of three bacterial isolates obtained from the skin of the frog Craugastor fitzingeri. Dual culture assays showed that these bacteria strongly inhibited the mycelial growth of several postharvest fungal phytopathogens, including Penicillium digitatum, P. italicum, Alternaria alternata, Aspergillus niger, and Alternaria solani. This antagonistic activity was further confirmed through assays using bacterial filtrates (BFs) and volatile organic compounds (VOCs), effectively delaying or suppressing fungal development under in vitro conditions. Additionally, in vivo experiments on citrus fruits, tomato, and blueberry demonstrated that treatments with bacterial cell suspensions or BFs significantly reduced disease incidence caused by P. digitatum, A. alternata, and B. cinerea. However, no inhibitory effects were observed against Geotrichum citri-aurantii, Fusarium sp., Fusarium oxysporum, and Phytophthora capsici, suggesting a degree of specificity. Our findings highlight the potential of frog skin-associated bacteria as a novel source of BCAs for the sustainable management of postharvest diseases in fruits.}, }
@article {pmid41026187, year = {2025}, author = {Cheng, P and Liu, F and Li, L and Wu, S and Xiao, W and Zong, Q and Liu, T and Peng, Y}, title = {Impact of Tebuconazole On the Development and Symbiotic Microbial Communities of Pardosa Pseudoannulata.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {97}, pmid = {41026187}, issn = {1432-184X}, mesh = {*Triazoles/toxicity ; *Symbiosis/drug effects ; Animals ; *Microbiota/drug effects ; Bacteria/drug effects/classification/genetics/isolation &amp; purification ; *Fungi/drug effects/classification/genetics ; *Fungicides, Industrial/toxicity ; *Spiders/microbiology/drug effects/growth &amp; development/physiology ; RNA, Ribosomal, 16S/genetics ; Animals, Poisonous ; }, abstract = {Tebuconazole is a widely used triazole fungicide to control fungal diseases. While there have been reported side effects on non-target arthropods, its ecological risks to natural enemies remain poorly understood. In this study, we evaluated the developmental toxicity and symbiotic microorganism responses of the wolf spider Pardosa pseudoannulata, an important predator in rice ecosystems, following exposure to tebuconazole. The results indicated that tebuconazole did not significantly increase the mortality rate of spiderlings; however, it did lead to a significant decrease in spiderling body weight, as well as the length and width of the carapace. High-throughput sequencing of the 16S rRNA gene V3-V4 regions and the ITS region revealed that tebuconazole significantly reduced bacterial diversity indices in the short term, with a gradual recovery over time. In contrast, the impact on the fungal community was continuous and irreversible, with a significant decrease in the Shannon index observed after 15 days. At the genus level, the relative abundances of Cupriavidus and Staphylococcus in the bacterial community decreased significantly after tebuconazole exposure, while Stenotrophomonas increased. In the fungal community, Fungi_gen_Incertae_sedis decreased significantly, and Simplicillium increased. Our findings highlight the ecological risks of fungicide exposure to beneficial predators and underscore the importance of considering symbiotic microbiota in pesticide risk assessments.}, }
@article {pmid41026185, year = {2025}, author = {Borja-Martínez, G and de León-Lorenzana, A and Yanez-Montalvo, A and Hernández-Canchola, G and Falcón, LI and Vázquez-Domínguez, E}, title = {Evolutionary and Ecological Drivers of Gut Microbiota in Wild Rodent Species from the Yucatán Peninsula.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {100}, pmid = {41026185}, issn = {1432-184X}, support = {887756//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as (CONAHCyT)/ ; IV200421//Programa de Apoyo a Proyectos de Investigaci&#xf3;n e Innovaci&#xf3;n Tecnol&#xf3;gica-DGAPA/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Mexico ; *Rodentia/microbiology/classification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Biological Evolution ; Biodiversity ; Symbiosis ; }, abstract = {The host-microbiome association is considered a coevolutionary process, in which the microbiome provides important functions for host development, physiology and health. However, the ecological and evolutionary forces shaping the diversity and structure of the bacterial communities that form the microbiome are still being elucidated. We assessed the composition of gut microbiota in six rodent species from three geographic regions across the Yucatán peninsula, Mexico. We evaluated the contribution of host species identity, phylogenetic relationships, and geography to the rodents' gut microbiota, using 16S rRNA V4 sequences. We performed a comprehensive set of analytical approaches, including Hill numbers, machine learning, and phylogenetic comparative frameworks. Our results show that phylosymbiosis is one of the main mechanisms driving microbiota dissimilitude across species and specific microbiota diversity traits. Additionally, the microbial pool in each region was geographically differentiated, shaped by the rodent community ensemble, while ecological filtering rendered a microbial pool characteristic of each species. The environment also played a significant role for some species like Heteromys gaumeri, while dietary habits showed a stronger signal for Oryzomys couesi. Rodents with more specialized habits like Ototylomys phyllotis (semi-arboreal, folivorous) had higher bacterial diversity. The abundance of eight bacterial families determined key differences of the gut microbiota which, in addition to phylogeny and geography, are associated with distinct diet and metabolic functions among rodents. Distinct metabolic functions were related, among others, to toxins metabolism and digestion of complex food components. Overall findings show that both evolutionary and ecological drivers influence these rodents gut microbial structure and composition.}, }
@article {pmid41026172, year = {2025}, author = {Gao, H and Ma, X and Lu, M and Wang, Y and Liu, H and Hu, X and Nie, Y}, title = {Population and Spatial Features Impact the Gut Phageome-Bacteriome Structure and Interactions in a Mammal Species Living in Fragmented Habitats.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {98}, pmid = {41026172}, issn = {1432-184X}, support = {32225033//National Natural Science Foundation of China/ ; 2022YFF1301500//Ministry of Science and Technology of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Bacteriophages/genetics/classification/physiology/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification/virology ; *Ecosystem ; RNA, Ribosomal, 16S/genetics ; *Antelopes/microbiology/virology ; Metagenome ; Feces/microbiology ; }, abstract = {The mammalian gut microbiome composition has been shown to promote host adaptation to ecological environments. However, the variation in the gut phageome and bacteriome composition at both the population level and spatial scale in wild animals has not been well investigated. Here, we used viral metagenomes and 16S rRNA gene sequencing to explore how these characteristics affect the gut microbiome of Przewalski's gazelle, an endangered group-living ungulate that lives in several fragmented habitats due to anthropogenic activities. The results revealed that population and habitat geographic characteristics collectively explained much more of the variation in phageome and bacteriome compositions than did host-associated factors. Both gut phage and bacterial diversity were positively associated with population size, and differentiation in gut microbiome diversity increased with geographic distance among populations. Additionally, the gut phage and the bacterial hosts displayed similar patterns in composition across habitats, indicating that the microbiome may exhibit complex interactions in response to the environment. For the first time, our study reveals the important roles of population and habitat geographic characteristics in driving spatial patterns of gut microbiome structures in wild animals and highlights the interactions between gut phages and the bacteriome in adaptation to living environments under the influence of human disturbances.}, }
@article {pmid41026164, year = {2025}, author = {Yeo, IC and Shim, KY and Min, JO and Kim, JH and Ha, SY and Jeong, CB}, title = {Vertical Structure and Functional Diversity of Microbial Communities in the Ross Sea, Antarctica.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {99}, pmid = {41026164}, issn = {1432-184X}, support = {KIMST RS-2022-KS221661//Korea Institute of Marine Science and Technology promotion/ ; NRF-2022R1C1C1010575//National Research Foundation of Korea/ ; }, mesh = {Antarctic Regions ; *Seawater/microbiology/chemistry ; *Microbiota ; *Biodiversity ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; }, abstract = {The Ross Sea, Antarctica, encompasses distinct water masses, each characterized by unique physicochemical conditions influencing microbial community composition and functional diversity. This study examined microbial communities across five stations covering various water masses, including Antarctic Surface Water (AASW), Circumpolar Deep Water (CDW), and Shelf Water (SW). Despite limited horizontal variability, significant vertical structuring was observed, potentially driven by vertical microbial dispersal from surface waters. Surface communities exhibited lower alpha diversity due to abundant labile organic matter favoring fast-growing heterotrophic taxa, whereas deeper communities displayed increased microbial richness, reflecting adaptation to more refractory organic matter. Functional diversity revealed distinct depth-related patterns, with metabolic pathways associated with organic matter predominantly enriched in surface layers. Concurrently, rare taxa became more abundant with depth, emphasizing their potential role as keystone organisms in deep-ocean nutrient cycling. These findings highlight the critical role of vertical microbial connectivity and organic matter composition in shaping microbial community structure and functional specialization, contributing significantly to our understanding of microbial-mediated biogeochemical processes in polar marine ecosystems.}, }
@article {pmid41025798, year = {2025}, author = {Damashek, J and Sheik, CS and Petro, C and Reeder, CF and Chowdhury, S and Kramer, BJ and DeVilbiss, SE and Pierella Karlusich, JJ and Marks, JC and Valdespino-Castillo, PM and Furey, PC and Berberich, ME and Marcarelli, AM and Scott, JT and Fulweiler, RW}, title = {DiazoTIME: a metabolically-resolved reference database of nitrogen-fixing microbial genomes.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0089725}, doi = {10.1128/mra.00897-25}, pmid = {41025798}, issn = {2576-098X}, abstract = {Microbial nitrogen fixation (diazotrophy) is a critical ecological process. We curated DiazoTIME (Diazotroph Taxonomic Identity and MEtabolism), a comprehensive database of diazotroph genomes including taxonomic annotation and metabolic prediction. DiazoTIME is unique among databases for classifying diazotrophs because it resolves both taxonomy and metabolic functionality.}, }
@article {pmid41025789, year = {2025}, author = {Hodgskiss, LH and Kerou, M and Luo, Z-H and Bayer, B and Maier, A and Weckwerth, W and Nägele, T and Schleper, C}, title = {Metabolic response of a chemolithoautotrophic archaeon to carbon limitation.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0073225}, doi = {10.1128/msystems.00732-25}, pmid = {41025789}, issn = {2379-5077}, abstract = {The ubiquitously distributed ammonia-oxidizing archaea generate energy from ammonia and build cell mass from inorganic carbon sources, thereby contributing to both the global nitrogen and carbon cycles. However, little is known about the regulation of their predicted core carbon metabolism. A thermodynamic model for Nitrososphaera viennensis was developed to estimate the consumption of inorganic carbon in relation to ammonia consumed for energy and was tested experimentally by growing cells in carbon-limited and excess conditions. A combined proteomic and metabolomic approach to the experimental conditions revealed distinct metabolic adaptation depending on the amount of carbon supplied, either in a catalase or pyruvate background as a reactive oxygen species scavenger. Integration of protein and metabolite dynamics revealed a cellular strategy under carbon limitation to maintain a pool of amino acids and an upregulation of proteins necessary for translation initiation to stay primed for protein synthesis. The combination of modeling and functional genomics fills gaps in the understanding of the central metabolism and its regulation in a chemolithoautotrophic, ammonia-oxidizing archaeon, even in the absence of available genetic tools.IMPORTANCELittle is known about the regulation of carbon metabolism within ammonia-oxidizing archaea (AOA), a widespread clade that plays a critical role in the global nitrogen cycle while also fixing inorganic carbon. To address this missing knowledge, the soil AOA Nitrososphaera viennensis was subjected to various levels of inorganic carbon and analyzed via a systems biology approach to better understand how its core metabolism is regulated. The results demonstrate a strong dependence on the carbon fixation cycle and highlight key connection points between the core metabolic pathways. The analysis additionally revealed tight control on translational processes and elucidated unique cellular responses when the organism was exposed to either exogenous catalase or pyruvate to relieve oxidative stress from reactive oxygen species. The presented data highlight metabolic responses of N. viennensis and provide a better understanding of how the organism, and likely other AOA, respond to various environmental conditions.}, }
@article {pmid41024334, year = {2025}, author = {Zhan, J and Zhang, L and Lai, S and Guo, J and Lin, T and Liu, G and Rensing, C and Liu, X and Zhou, S}, title = {Fe(III)-dependent Nrf activity determines nitrate reduction partitioning in nitrate-reducing communities.}, journal = {mBio}, volume = {}, number = {}, pages = {e0222025}, doi = {10.1128/mbio.02220-25}, pmid = {41024334}, issn = {2150-7511}, abstract = {Identifying the factors that affect the nitrate reduction partitioning between dissimilatory nitrate reduction to ammonium (DNRA) and denitrification is crucial for mitigating nitrogen loss in ecosystems. Conventionally, the nutrient status of the environment (e.g., the carbon-to-nitrogen ratio) is recognized as the key determinant of nitrogen conversion pathways. Here, we report that the availability of Fe(III) regulates the nitrate reduction partitioning in Geobacter metallireducens and Alcaligenes faecalis co-culture. We controlled the availability of Fe(III) in the coculture medium and tracked nitrogen conversion dynamics and community composition. The results demonstrated that the coculture performed DNRA, contributed mainly by G. metallireducens under Fe(III)-replete conditions, while performing interspecies synergistic denitrification between both species under Fe(III)-depleted conditions. Nitrate/nitrite reductase activity calculations and mutation analyses indicated that nitrate reduction partitioning in the coculture was governed by the nitrite reductase (Nrf) activity of G. metallireducens, which was Fe(III)-dependent. Further validation in urban river water confirmed that Fe(III) supplementation significantly enhances DNRA activity. Our findings establish Fe(III) as a previously unrecognized regulator of microbial nitrogen retention, showing insights into strategies for managing nitrogen fluxes in agricultural and aquatic systems.IMPORTANCENitrogen is essential for life, but its loss from ecosystems through microbial processes like denitrification harms agricultural productivity and contributes to greenhouse gas emissions. Retaining nitrogen as ammonium via microbial dissimilatory nitrate reduction to ammonium (DNRA) could mitigate these issues, but the factors governing microbial prioritization of DNRA over denitrification remain unclear. Our study reveals that Fe(III) plays a critical, previously unrecognized role in steering this process. We show that Fe(III) availability determines whether the nitrate-reducing community conserves nitrogen as ammonium or releases it as gas, with implications for managing nitrogen in soils and waterways. By demonstrating Fe(III)'s ability to enhance nitrogen retention in environmental systems like urban rivers, our findings offer a new lever for sustainable agriculture and pollution control. This work bridges microbial ecology and environmental management, highlighting how trace metals shape nutrient cycles in ways that can be harnessed to protect ecosystem health.}, }
@article {pmid41023320, year = {2025}, author = {Musiałowski, M and Mierzwa-Hersztek, M and Gondek, K and Dębiec-Andrzejewska, K}, title = {A novel two-step metabarcoding approach improves soil microbiome biodiversity assessment.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {33697}, pmid = {41023320}, issn = {2045-2322}, support = {LIDER/13/0051/L-11/NCBR/2020//Narodowe Centrum Bada&#x144; i Rozwoju,Poland/ ; LIDER/13/0051/L-11/NCBR/2020//Narodowe Centrum Bada&#x144; i Rozwoju,Poland/ ; }, mesh = {*Soil Microbiology ; *Biodiversity ; *DNA Barcoding, Taxonomic/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; High-Throughput Nucleotide Sequencing ; *Bacteria/genetics/classification ; Phylogeny ; }, abstract = {The foundation of microbial ecology research is Next-Generation Sequencing (NGS), which allows for reconstruction of the soil microbiome taxonomical structure and the calculation of biodiversity metrics. However, obtaining reliable data on soil biodiversity poses several challenges, with accurate primer selection being one of the most critical. While 16S rDNA primers are widely used for their ability to broadly target bacterial communities, they can introduce biases. These primers may preferentially amplify certain bacterial groups, leading to a skewed representation of the microbial diversity in soil samples. To overcome the bias, we developed a novel, Two-Step Metabarcoding (TSM) approach to obtain more accurate and detailed data on soil microbiome structure and biodiversity. The first step involved sequencing of amplicons generated using universal 16S rDNA primers, provided an initial overview of the microbial community, and allowed the identification of key taxonomical groups. In the second step, we employed sequencing of amplicons generated with taxa-specific primers designed for the most abundant phyla in the community. We used the obtained data for a more reliable reconstruction of microbiome taxonomic structure and biodiversity. This two-step approach ensures a thorough exploration of the soil microbiome and promises to enhance our understanding of soil microbial dynamics and ecology.}, }
@article {pmid41018004, year = {2025}, author = {Neilson, R and King, D and Giles, ME}, title = {The microbiome associated with Trichodorus primitivus is enriched with Janthinobacterium compared to soil.}, journal = {Journal of nematology}, volume = {57}, number = {1}, pages = {20250043}, pmid = {41018004}, issn = {0022-300X}, abstract = {Although soil biota mediates many key processes that deliver multiple environmental benefits, interactions between soil biota are not well characterized. In an ecological context, studies to date on the associations between nematodes and bacteria have mostly focused on either intracellular bacteria or bacteria that have a potential role in crop pathogenesis by endoparasitic nematode species, that is, those species that have a component of their life cycle within the plant host. Moreover, evolutionary studies have utilized the model nematode species, Caenorhabditis elegans, for studies on survival, behavior, and fecundity. In this study, we characterize the bacterial communities associated with an ectoparasitic nematode species, Trichodorus primitivus, whose complete life cycle is external to the plant host. Compared to the soil from which the nematodes were extracted, the diversity of bacterial communities associated with T. primitivus was reduced. By contrast, the nematode-associated bacterial community was significantly enriched with Janthinobacterium, a known antagonist of soilborne pathogens. This study advances knowledge on the interactions between bacteria and ectoparasitic nematodes, which could help inform the future development of novel strategies for nematode control.}, }
@article {pmid41017558, year = {2025}, author = {Han, P and Liu, C and Abdal-Hay, A and Reed, S and Liaw, A and Wang, J and Ning, Y and Ivanovski, S}, title = {Proteome and microbiome profiles of polymicrobial salivary biofilms on 3D MEW fibrous scaffolds: biomimetic ECM-inspired structures.}, journal = {Journal of materials chemistry. B}, volume = {}, number = {}, pages = {}, doi = {10.1039/d5tb01410g}, pmid = {41017558}, issn = {2050-7518}, abstract = {Replicating the structural complexity of polymicrobial oral biofilms in vitro remains a significant challenge in biomaterials research. Nevertheless, developing clinically relevant biofilm models is crucial for advancing our understanding of biofilm-host interactions and elucidating how biomaterials influence microbial composition, behaviour, and overall biofilm dynamics. In this work, 3D biomimetic fibrous scaffolds made from medical-grade polycaprolactone (mPCL) were fabricated using the melt electrowriting (MEW) technique. The effects on biofilm viability, activity, microbiome, and proteome profiles were assessed on 3D fibrous scaffolds and conventional 2D tissue culture plates (TCP). Human saliva was cultured on MEW mPCL (3D BF) and TCP (2D BF) for 4 days, followed by microbiome profiling via 16S rRNA sequencing and proteomic analysis using LC-MS/MS, SWATH with GO and KEGG pathway enrichment. The results demonstrated that 3D MEW mPCL scaffolds enhanced biofilm biomass, thickness, and viability. Microbiome analysis revealed that 3D BF was enriched with both commensals and pathogens, including Veillonella, Peptostreptococcus, Porphyromonas gingivalis, and Treponema denticola, alongside probiotic species like Lactobacillus acidophilus. Pooled proteomic data from three technical repeats, along with GO and KEGG analyses, revealed a functionally dynamic biofilm ecosystem characterised by elevated expression of proteins involved in glycolysis, the TCA cycle, and nucleotide metabolism, highlighting pathways essential for biofilm survival, stress adaptation, and host interaction. These 'proof-of-concept' findings highlight the potential of 3D MEW fibrous mPCL scaffolds as a biomimetic 3D platform capable of accurately recapitulating the dynamic spatial and metabolic complexity of oral biofilms, thereby facilitating innovative investigations into microbial ecology, host-pathogen interactions, and the accelerated development of targeted antimicrobial therapies.}, }
@article {pmid41016925, year = {2025}, author = {Li, C and Wu, M and Tang, W and Yu, B and Saiz-Lopez, A and Poulain, A and Bank, MS and Zhou, Q and Bodelier, PLE and Yan, Z and Frey, B and Hu, H and Chen, J and Jiang, Y and Zhong, H}, title = {Aligning global mercury mitigation with climate action.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {7826}, pmid = {41016925}, issn = {2041-1723}, support = {42107223//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41673075//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Mercury/analysis/toxicity ; *Climate Change ; Greenhouse Gases/metabolism/analysis ; Humans ; *Environmental Pollution/prevention &amp; control ; Microbiota/drug effects ; *Environmental Pollutants/analysis ; }, abstract = {Environmental mercury (Hg) pollution affects microbial community structure and functions. Yet, whether and how this influence cascades through microbe-mediated cycling of major greenhouse gases (GHGs) remains poorly understood. This Perspective synthesizes emerging evidence on the Hg-microbe-GHG nexus, exploring the possibility that global Hg emission reductions, while critical for human and planetary health, may cause alterations to microbe-mediated GHG fluxes. Significant knowledge gaps persist, however, regarding the Hg-microbe-GHG nexus, particularly concerning the magnitude and direction of the nexus's net impact on climate and global environmental change. To bridge these gaps, we propose a three-step roadmap aimed at disentangling the potential impacts of global Hg emission mitigation strategies on microbial communities, associated GHG emissions, and subsequent climate change. Collectively, these joint efforts from scientists, industry, community stakeholders, and policymakers are critical to harmonizing global Hg mitigation efforts with climate action and to ensuring a sustainable future for Earth systems and their inhabitants.}, }
@article {pmid41016813, year = {2025}, author = {Lee, HH}, title = {Iodine Biogeochemical Cycle and Microbial Bioremediation of Radioactive Iodine-129.}, journal = {Journal of microbiology and biotechnology}, volume = {35}, number = {}, pages = {e2508018}, doi = {10.4014/jmb.2508.08018}, pmid = {41016813}, issn = {1738-8872}, mesh = {*Biodegradation, Environmental ; *Iodine Radioisotopes/metabolism ; *Bacteria/metabolism ; *Iodine/metabolism ; Oxidation-Reduction ; Humans ; Hydrocarbons, Iodinated ; }, abstract = {Iodine is an essential biophilic element that plays pivotal roles in both environmental systems and human physiology, particularly as a key constituent of thyroid hormones and a regulator of atmospheric ozone. In contrast, its radioactive isotope, iodine-129 (I-129), predominantly generated through anthropogenic nuclear activities, represents a persistent environmental and public health concern. With an exceptionally long half-life of approximately 15.7 million years and high environmental mobility, especially in groundwater, combined with a strong tendency to bioaccumulate in the human thyroid, I-129 poses a disproportionate and long-term radiological hazard in contaminated sites. The biogeochemical cycling of iodine involves intricate interconversions among multiple oxidation states and phases across the lithosphere, hydrosphere, atmosphere, and biosphere. Microorganisms are central to these processes, mediating oxidation, reduction, methylation, accumulation, and sorption. While microbial methylation can increase I-129 mobility via the production of volatile methyl iodide, other microbial pathways, notably biosorption and binding to organic matter, provide promising mechanisms for immobilization and natural attenuation. Microbial bioremediation offers a sustainable and cost-effective alternative or complement to conventional physicochemical methods for managing radioactive contaminants. Strategies such as bioreduction, biosorption, bioaccumulation, and biomineralization exploit the metabolic versatility of microorganisms to alter radionuclide speciation, solubility, and mobility. However, practical application to I-129 remains challenging due to its extreme persistence, environmental variability, and uncertainties in predicting its long-term geochemical fate. Effective management of I-129 contamination will require an integrated, multidisciplinary approach that combines advanced microbial ecology insights, optimized biotechnological processes, and long-term monitoring frameworks.}, }
@article {pmid41016251, year = {2025}, author = {Schubert, K and Shosanya, T and García-Bayona, L}, title = {The role of mobile genetic elements in adaptation of the microbiota to the dynamic human gut ecosystem.}, journal = {Current opinion in microbiology}, volume = {88}, number = {}, pages = {102675}, doi = {10.1016/j.mib.2025.102675}, pmid = {41016251}, issn = {1879-0364}, abstract = {The human intestinal microbiota is a dynamic ecosystem shaped by extensive horizontal gene transfer, particularly in individuals from industrialized populations. In this review, we discuss recent advances in our understanding of how mobile genetic elements (MGEs) contribute to microbial ecology and evolution in this diverse community, focusing on MGEs carrying fitness-conferring genes. Bacteroidales species can colonize individuals for decades and serve as major hubs for MGE exchange. Most MGEs are highly variable across individuals and geographies. Occasionally, conserved MGEs can spread across geography and lifestyles. Functional characterizations of MGEs reveal their roles in antibiotic resistance, interbacterial antagonism, biofilm formation, immune evasion, and nutrient acquisition, among others. Substantive progress in our understanding of MGEs in the gut microbiome offers promising avenues for therapeutic microbiome interventions. However, major challenges remain in functional prediction, host-MGE linkage, and experimental characterization.}, }
@article {pmid41013679, year = {2025}, author = {Ramljak, A and Jurburg, S and Chatzinotas, A and Lučić, M and Žižek, M and Babić, I and Udiković-Kolić, N and Petrić, I}, title = {Identifying the drivers of microbial community changes and interactions in polluted coastal sediments.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {117}, pmid = {41013679}, issn = {2524-6372}, support = {IP-2020-02-6510//Hrvatska Zaklada za Znanost/ ; IP-2020-02-6510//Hrvatska Zaklada za Znanost/ ; IP-2020-02-6510//Hrvatska Zaklada za Znanost/ ; IP-2020-02-6510//Hrvatska Zaklada za Znanost/ ; }, abstract = {Despite over three decades of research into the composition and distribution of microbial communities, gaps remain in our mechanistic understanding of microbial community assembly processes, especially in benthic communities in coastal zones continuously exposed to anthropogenic pressures. We analyzed the microbial communities (prokaryotes, fungi, and protists) in sediment samples from ports and bays located along the Adriatic coast chronically exposed to chemical and nutrient pollution, and explored how selective pressures (pollutants, nutrients, and environmental conditions) and dispersal shape these communities. We found that biogeographic factors (i.e. location) play a key role in structuring microbial communities, with benthic fungi also being shaped by the presence of pollutants and nutrients. Strong correlations between nutrient loads and pollutants were observed, along with weakened interactions between microbial communities, particularly between prokaryotes and protists, in the presence of specific pollutants (bismuth, cadmium, copper, zinc, mercury). These results are an important step in disentangling the complex interactions between pollutants and microbial community dynamics in aquatic ecosystems. Further research is needed to assess how these shifts in microbial community dynamics may affect ecosystem services in vulnerable coastal zones.}, }
@article {pmid41012703, year = {2025}, author = {Johnson, ML and Boezen, D and Grum-Grzhimaylo, AA and van der Vlugt, RAA and de Visser, JAGM and Zwart, MP}, title = {Living Together Apart: Quantitative Perspectives on the Costs and Benefits of a Multipartite Genome Organization in Viruses.}, journal = {Viruses}, volume = {17}, number = {9}, pages = {}, doi = {10.3390/v17091275}, pmid = {41012703}, issn = {1999-4915}, support = {016.VIDI.171.061/NWO_/Dutch Research Council/Netherlands ; }, mesh = {*Genome, Viral ; *Plant Viruses/genetics/physiology ; Host Specificity ; Metagenomics ; Plant Diseases/virology ; Plants/virology ; }, abstract = {BACKGROUND: Multipartite viruses individually package their multiple genome segments into virus particles, necessitating the transmission of multiple virus particles for effective viral spread. This dependence poses a cost in the form of reduced transmission compared to monopartite viruses, which only have a single genome segment. The notable cost of a multipartite genome organization has spurred debate on why multipartite viruses are so common among plant viruses, including a search for benefits associated with this organizational form.<br><br>METHODS: We investigated the costs and benefits of multipartite viruses with three approaches. First, we reanalyzed dose-response data to measure the cost of multipartition to between-host transmission for multipartite viruses. Second, we developed a simulation model to explore when the sharing of viral gene products between cells is beneficial. Third, we tested whether multipartite viruses have a broad host range by estimating the host range for plant viruses using metagenomics data.<br><br>RESULTS: We find that the observed cost to transmission exceeds theoretical predictions. We predict that a virus gene-product-sharing strategy only confers benefits under limited conditions, suggesting that this strategy may not be common. Our results suggest that multipartite and segmented viruses have broader host ranges than monopartite viruses.<br><br>CONCLUSIONS: Our analyses also suggest there is limited evidence for the costs and benefits of a multipartite organization, and we argue that the diversity of multipartite virus-host systems demands pluralistic explanatory frameworks.}, }
@article {pmid41011533, year = {2025}, author = {Dai, X and He, Y and Su, Y and Mo, H and Li, W and Li, W and Zi, S and Liu, L and Di, Y}, title = {Pathogen Identification, Antagonistic Microbe Screening, and Biocontrol Strategies for Aconitum carmichaelii Root Rot.}, journal = {Microorganisms}, volume = {13}, number = {9}, pages = {}, doi = {10.3390/microorganisms13092202}, pmid = {41011533}, issn = {2076-2607}, support = {202403AP140013//The Sino-Vietnamese International Joint Laboratory for Characteristic &amp; Cash Crops Green De-velopment of Yunnan Province/ ; Yunnan Academic Degrees Committee Document [2024] No. 19//The Construction Project for Postgraduate Tutor Team of Yunnan Province in 2024/ ; 2024J0486//Scientific Research Fund of the Educational Department of Yunnan Province/ ; }, abstract = {The undefined microbial ecology of Aconitum carmichaelii root rot in western Yunnan constrains the advancement of eco-friendly control strategies. The identification of potential pathogenic determinants affecting A. carmichaelii growth is imperative for sustainable cultivation and ecosystem integrity. High-throughput sequencing was employed to profile microbial communities across four critical niches, namely rhizosphere soil, tuberous root epidermis, root endosphere, and fibrous roots of healthy and diseased A. carmichaelii. The physicochemical properties of corresponding rhizosphere soils were concurrently analyzed. Putative pathogens were isolated from diseased rhizospheres and tubers through culturing with Koch's postulates validation, while beneficial microorganisms exhibiting antagonism against pathogens and plant growth-promoting (PGP) traits were isolated from healthy rhizospheres. Highly virulent strains (2F14, FZ1, L23) and their consortia were targeted for suppression. Strain DX3, demonstrating optimal PGP and antagonistic capacity in vitro, was selected for pot trials evaluating growth enhancement and disease control efficacy. Significant disparities in rhizosphere soil properties and bacterial/fungal community structures were evident between healthy and diseased cohorts. Fifteen putative pathogens spanning eight species across four genera were isolated: Fusarium solani, F. avenaceum, Clonostachys rosea, Mucor racemosus, M. irregularis, M. hiemalis, Serratia liquefaciens, and S. marcescens. Concurrently, eight PGP biocontrol strains were identified: Bacillus amyloliquefaciens, B. velezensis, B. subtilis, B. pumilus, and Paenibacillus polymyxa. Pot trials revealed that Bacillus spp. enhanced soil physiochemical properties through nitrogen fixation, phosphate solubilization, potassium mobilization, siderophore production, and cellulose degradation, significantly promoting plant growth. Critically, DX3 inoculation elevated defense-related enzyme activities in A. carmichaelii, enhanced host resistance to root rot, and achieved >50% disease suppression efficacy. This work delineates key pathogenic determinants of Yunnan A. carmichaelii root rot and identifies promising multifunctional microbial resources with dual PGP and biocontrol attributes. Our findings provide novel insights into rhizosphere microbiome-mediated plant health and establish a paradigm for sustainable disease management.}, }
@article {pmid41011501, year = {2025}, author = {Dai, L and Hao, X and Niu, T and Liu, Z and Wang, Y and Geng, X and Cai, Q and Wang, J and Ren, Y and Liu, F and Liu, H and Li, Z}, title = {Analysis of Microbial Community Structure and Diversity in Different Soil Use Types in the Luo River Basin.}, journal = {Microorganisms}, volume = {13}, number = {9}, pages = {}, doi = {10.3390/microorganisms13092173}, pmid = {41011501}, issn = {2076-2607}, support = {30803302//Henan Provincial Finance Forest and Grass Science and Technology (Intermediate Trial) Promo-tion Demonstration Project "Introduction and Cultivation of desia polycarpa Maxim. 'Yulu/ ; 2025-2627//Henan Province Science and Technology Research Project "Innovative Utilization of Germplasm Resources and Breeding of Excellent New Varieties of desia polycarpa Maxim."/ ; }, abstract = {The Luohe River boasts a profound historical heritage. Due to long-term impacts of human activities along its banks, significant variations in soil environmental conditions may exist across different land use types within the region. This study focused on four land use types (farmland, bamboo forest, grassland, and abandoned land) in Luoning County of the Luohe River Basin and employed high-throughput sequencing technology to analyze the characteristics of soil microbial communities and differences in soil nutrients. The results showed the following: There were significant differences in soil nutrients and microbial diversity among different land use types. Specifically, the organic matter content in farmland was significantly higher than that in bamboo forests (p < 0.05), and the available phosphorus content in farmland was significantly higher than that in abandoned land (p < 0.05); the abandoned land had a significant advantage in alkali-hydrolyzable nitrogen and available potassium contents (p < 0.05) but the lowest soil water content (p < 0.05). Microbial diversity indices indicated that Pielou's evenness index (Pieloue) in farmland was significantly higher than that in grassland. The bacterial community was dominated by Acidobacteria, Proteobacteria, and Actinobacteria. At the genus level, available potassium was the key factor affecting the top 20 dominant bacterial genera. Redundancy Analysis (RDA) showed that pH was the core environmental variable driving the variation of bacterial community structure. Metabolic pathway analysis revealed that biosynthetic metabolism was the main pathway, and grassland exhibited outstanding performance in the secondary metabolite synthesis pathway. The results of this study fill the gap in soil microbial ecology research in this region and provide a theoretical basis for the sustainable utilization of land resources and agricultural ecological management in the Luohe River Basin.}, }
@article {pmid41011387, year = {2025}, author = {Wang, Y and Deng, C and Sui, M and Wei, P and Duan, B and Li, Z and Zou, F}, title = {Acute Toxoplasma gondii Infection Drives Gut Microbiome Dysbiosis and Functional Disruption in Mice as Revealed by Metagenomic Sequencing.}, journal = {Microorganisms}, volume = {13}, number = {9}, pages = {}, doi = {10.3390/microorganisms13092056}, pmid = {41011387}, issn = {2076-2607}, support = {202449CE340019//the Yunnan Key Laboratory of Veterinary Etiological Biology/ ; U2202201//the NSFC-Yunnan Joint Fund/ ; 202401AT070440//the Yunnan Fundamental Research Projects/ ; 2024Y339//the Scientific Research Fund of Education Department of Yunnan Province/ ; No.XXX//the Yunnan Provincial University Key Industry Service Science and Technology Program/ ; }, abstract = {Toxoplasma gondii is a widely distributed intracellular parasite that disrupts host immune and metabolic homeostasis. Although accumulating evidence highlights the role of gut microbiota in parasitic infections, the effects of acute T. gondii infection on host gut microbial ecology remain poorly understood. In this study, metagenomic sequencing technology was used to systematically analyze the composition and functional alterations of the ileal microbiota in BALB/c mice on day 10 post-infection. Compared to uninfected controls, T. gondii infected mice exhibited a significant reduction in microbial diversity and a pronounced shift in community structure. Notably, there was an expansion of Proteobacteria, particularly the Enterobacteriaceae family, alongside a marked decline in beneficial taxa such as Actinobacteria and Bacillota. Functional annotation using the KEGG and CAZy databases revealed enrichment of metabolic pathways related to glycolysis/gluconeogenesis, O-antigen nucleotide sugar biosynthesis, bacterial secretion systems, and biofilm formation-Escherichia coli in the infected microbiota. These findings provide novel insights into the dysbiosis of gut microbiota and host-microbe interactions during acute T. gondii infection.}, }
@article {pmid41010480, year = {2025}, author = {Duysburgh, C and Fiore, W and Marzorati, M}, title = {Survival and Impact on Microbial Diversity of Lacticaseibacillus paracasei DG in a Simulation of Human Intestinal Microbial Ecosystem.}, journal = {Nutrients}, volume = {17}, number = {18}, pages = {}, doi = {10.3390/nu17182952}, pmid = {41010480}, issn = {2072-6643}, support = {N/A//Alfasigma S.p.A./ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Probiotics ; *Lacticaseibacillus paracasei/physiology/growth &amp; development/metabolism ; Microbial Viability ; Hydrogen-Ion Concentration ; Fatty Acids, Volatile/metabolism ; Colon/microbiology ; Lactic Acid/metabolism ; Feces/microbiology ; }, abstract = {Background/Objectives: The probiotic Lacticaseibacillus paracasei DG (LpDG) has shown promising results for various gastrointestinal diseases. This study evaluated the survival, metabolic activity, and impact on colonic microbiota of LpDG in an in vitro gastrointestinal tract simulation. Methods: Encapsulated LpDG was tested under simulated fed, fasted, and shortened fasted conditions compared with a blank control in a modified Simulator of the Human Intestinal Microbial Ecosystem (SHIME[®]) reactor. Capsule integrity, and cell culturability and viability were assessed at the end of each digestion phase. Metabolic activity (pH, total gas production, and concentrations of short-chain fatty acids, lactate, and ammonium) was assessed after a 24 h colonic incubation with a faecal inoculum. The impact of LpDG on the colonic microbial community was analysed by quantitative polymerase chain reaction and shallow shotgun sequencing. Results: The capsule was completely degraded at the end of the jejunum under all conditions. A low pH had a minimal impact on LpDG culturability and viability. Compared with blank control, LpDG remained metabolically active in the microbial community following a 24 h colonic incubation (LpDG [0-24 h] vs. blank control [0-24 h]: ΔpH, decreased [0.29-0.38 vs. 0.12-0.34]; Δlactic acid, decreased [1.52-1.69 mM vs. 0.13-0.21 mM]; and Δbutyrate, increased [7.49-10.52 mM vs. 5.19-7.76 mM]). Under fed conditions, treatment with LpDG compared with blank control significantly decreased levels of Escherichia coli and Blautia wexlerae and increased Clostridiaceae, Eubacteriaceae, and Lachnospiraceae. Conclusions: LpDG remains viable and metabolically active in the gastrointestinal tract, positively affecting intestinal microbiota and metabolite production.}, }
@article {pmid41009926, year = {2025}, author = {Dealis Gomes, ML and Afonso, L and Basso, KR and Alves, LC and Macías, EJN and Yamada-Ogatta, SF and Guidi, AC and de Mello, JCP and Andrade, FG and Cabeça, LF and Cely, MVT and Andrade, G}, title = {Liposomal Fluopsin C: Physicochemical Properties, Cytotoxicity, and Antibacterial Activity In Vitro and over In Vivo MDR Klebsiella pneumoniae Bacteremia Model.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {9}, pages = {}, doi = {10.3390/antibiotics14090948}, pmid = {41009926}, issn = {2079-6382}, support = {439754/2018-6 (AMR MCTIC)//Brazilian National Council for Scientific and Technological Development (CNPq)/ ; 406016/2022-4, PPSUS-Aracauria Foundation-PR//Brazilian National Council for Scientific and Technological Development (CNPq)/ ; }, abstract = {Introduction: Antimicrobial resistance has become a global concern, and few new antimicrobials are currently being developed. Fluopsin C has proven broad-spectrum activity, being a promising candidate for new antimicrobial development. To optimize antimicrobial activity, this research aimed at fluopsin C (Flp) encapsulation in liposomes to achieve controlled release and reduce cytotoxicity. Methods: Liposomal formulations were prepared by extruding formulations based on soy phosphatidylcholine (SPC) or poly (ethylene glycol)-distearoylphosphatidylethanolamine (DSPE-PEG) plus cholesterol, and were characterized by their size, polydispersity index, zeta potential, encapsulation efficiency, shelf-life stability, in vitro release profile, cytotoxicity, and antimicrobial activity against Klebsiella pneumoniae in vitro and in vivo. Results: The results indicated that the DSPE-PEG DMSO+Flp formulation presented superior physicochemical stability and unaltered antimicrobial activity. In vitro, CC50 decreased by 54%. No lethal dose was obtained in mice within the concentration range tested. The most effective doses in vivo were 2 × 2 mg/kg for free fluopsin C and 1 × 2 mg/kg for DSPE-PEG DMSO+Flp, resulting in a 40% reduction in mortality from bacteremia. Only discrete inflammatory infiltration was detected in the liver, while kidney necrosis ranged from discrete to moderate. Encapsulation of fluopsin C in liposomes showed promising features supporting to use against infections by MDR K. pneumoniae.}, }
@article {pmid41009119, year = {2025}, author = {Kiewra, D and Ojrzyńska, H and Czułowska, A and Dyczko, D and Jawień, P and Plewa-Tutaj, K}, title = {Dermacentor reticulatus (Fabricius, 1794) in Southwestern Poland: Changes in Range and Local Scale Updates.}, journal = {Insects}, volume = {16}, number = {9}, pages = {}, doi = {10.3390/insects16090935}, pmid = {41009119}, issn = {2075-4450}, abstract = {The ornate dog tick Dermacentor reticulatus is a key vector of several pathogens and has been expanding its range across Europe, raising concerns about the associated veterinary and public health risks. This study aimed to assess the current distribution and local-scale expansion of D. reticulatus in southwestern Poland, particularly in and around the city of Wrocław. In 2024, host-seeking ticks were collected using the flagging method at 80 sites, including 30 previously monitored locations and 50 newly designated ones, selected based on land cover analysis and field verification. Spatial statistics and kriging method were applied to evaluate changes in the tick's range compared to data from 2014-2019. The presence of D. reticulatus was confirmed at 68 sites, including 13 located beyond the previously estimated range. A shift in the mean center of tick occurrence toward the southeast was observed, along with an increase in the compact area of occurrence. The results indicate a continued expansion of D. reticulatus in the region, with urbanization and landscape structure likely influencing its spread. These findings underscore the importance of local-scale surveillance and spatial modeling in assessing the risk of tick-borne diseases.}, }
@article {pmid41006295, year = {2025}, author = {van Galen, LG and Smith, GR and Margenot, AJ and Waldrop, MP and Crowther, TW and Peay, KG and Jackson, RB and Yu, K and Abrahão, A and Ahmed, TA and Alatalo, JM and Anslan, S and Anthony, MA and Araujo, ASF and Ascher-Jenull, J and Bach, EM and Bahram, M and Baker, CCM and Baldrian, P and Bardgett, RD and Barrios-Garcia, MN and Bastida, F and Beggi, F and Benning, LG and Bragazza, L and Broadbent, AAD and Cano-Díaz, C and Cates, AM and Cerri, CEP and Cesarz, S and Chen, B and Classen, AT and Dahl, MB and Delgado-Baquerizo, M and Eisenhauer, N and Evgrafova, SY and Fanin, N and Fornasier, F and Francisco, R and Franco, ALC and Frey, SD and Fritze, H and García, C and García-Palacios, P and Gómez-Brandón, M and Gonzalez-Polo, M and Gozalo, B and Griffiths, R and Guerra, C and Hallama, M and Hiiesalu, I and Hossain, MZ and Hu, Y and Insam, H and Jassey, VEJ and Jiang, L and Kandeler, E and Kohout, P and Kõljalg, U and Krashevska, V and Li, X and Lu, JZ and Lu, X and Luo, S and Lutz, S and Mackie-Haas, KA and Maestre, FT and Malmivaara-Lämsä, M and Mangelsdorf, K and Manjarrez, M and Marhan, S and Martin, A and Mason, KE and Mayor, J and McCulley, RL and Moora, M and Morais, PV and Muñoz-Rojas, M and Murugan, R and Nottingham, AT and Ochoa, V and Ochoa-Hueso, R and Oja, J and Olsson, PA and Öpik, M and Ostle, N and Peltoniemi, K and Pennanen, T and Pescador, DS and Png, GK and Poll, C and Põlme, S and Potapov, AM and Priemé, A and Pritchard, W and Puissant, J and Rocha, SMB and Rosinger, C and Ruess, L and Sayer, EJ and Scheu, S and Sinsabaugh, RL and Slaughter, LC and Soudzilovskaia, NA and Sousa, JP and Stanish, L and Sugiyama, SI and Tedersoo, L and Trivedi, P and Vahter, T and Voriskova, J and Wagner, D and Wang, C and Wardle, DA and Whitaker, J and Yang, Y and Zhong, Z and Zhu, K and Ziolkowski, LA and Zobel, M and van den Hoogen, J}, title = {A global database of soil microbial phospholipid fatty acids and enzyme activities.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1568}, pmid = {41006295}, issn = {2052-4463}, support = {DEB-1845544//National Science Foundation (NSF)/ ; DEB-1926335//National Science Foundation (NSF)/ ; DGE 1450271//National Science Foundation (NSF)/ ; QUEX-CAS-QP-RD-18/19//Qatar Petroleum (QP)/ ; QUEX-CAS-QP-RD-18/19//Qatar Petroleum (QP)/ ; 305069/2018-7//Ministry of Science, Technology and Innovation | Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (National Council for Scientific and Technological Development)/ ; I989-B16//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; I989-B16//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; I989-B16//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; CZ.02.01.01/00/22_008/0004635//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy (Ministry of Education, Youth and Sports)/ ; NE/N009452/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/N009452/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/I027037/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/I027037/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/N009452/1//RCUK | Natural Environment Research Council (NERC)/ ; PICT 2014-2838//Ministry of Science, Technology and Productive Innovation, Argentina | Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica (National Agency for Science and Technology, Argentina)/ ; 315260_149807//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; BIPD_01_2021_FCT-PTDC/BIA-CBI/2340/2020, UIDB/05937/2020, UIDP/05937/2020//NOVA | Faculdade de Ci&#xea;ncias e Tecnologia, Universidade Nova de Lisboa (FCT/UNL)/ ; UID/EMS/00285/2020//NOVA | Faculdade de Ci&#xea;ncias e Tecnologia, Universidade Nova de Lisboa (FCT/UNL)/ ; UID/EMS/00285/2020//NOVA | Faculdade de Ci&#xea;ncias e Tecnologia, Universidade Nova de Lisboa (FCT/UNL)/ ; DFG- FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG- FZT 118, 202548816, Ei 862/29-1 and Ei 862/31-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG- FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 192626868-SFB 990//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 316045089//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 192626868-SFB 990//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 315415//Academy of Finland (Suomen Akatemia)/ ; PTDC/BIA-CBI/2340/2020//Ministry of Education and Science | Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia (Portuguese Science and Technology Foundation)/ ; ANR; MIXOPEAT; ANR-17-CE01-0007//Agence Nationale de la Recherche (French National Research Agency)/ ; 31872994//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41922056//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32101286//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32061143027//National Natural Science Foundation of China (National Science Foundation of China)/ ; CIDEGENT/2018/041//Generalitat Valenciana (Regional Government of Valencia)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; NE/T012226//National Eye Research Centre (NERC)/ ; PRG1065, PRG1789, PSG784//Ministry of Education and Research | Estonian Research Competency Council (Research Competency Council)/ ; 2021M693360//China Postdoctoral Science Foundation/ ; }, mesh = {*Soil Microbiology ; *Phospholipids ; *Fatty Acids ; *Databases, Factual ; *Enzymes ; Soil/chemistry ; Ecosystem ; }, abstract = {Soil microbes drive ecosystem function and play a critical role in how ecosystems respond to global change. Research surrounding soil microbial communities has rapidly increased in recent decades, and substantial data relating to phospholipid fatty acids (PLFAs) and potential enzyme activity have been collected and analysed. However, studies have mostly been restricted to local and regional scales, and their accuracy and usefulness are limited by the extent of accessible data. Here we aim to improve data availability by collating a global database of soil PLFA and potential enzyme activity measurements from 12,258 georeferenced samples located across all continents, 5.1% of which have not previously been published. The database contains data relating to 113 PLFAs and 26 enzyme activities, and includes metadata such as sampling date, sample depth, and soil pH, total carbon, and total nitrogen. This database will help researchers in conducting both global- and local-scale studies to better understand soil microbial biomass and function.}, }
@article {pmid41005096, year = {2025}, author = {Wang, J and Hao, J and Jing, W and Gao, Y and Qiu, S}, title = {Effects of polyethylene terephthalate microplastics on performance of sequencing-batch membrane bioreactor for simulated municipal wastewater treatment.}, journal = {Journal of hazardous materials}, volume = {498}, number = {}, pages = {139956}, doi = {10.1016/j.jhazmat.2025.139956}, pmid = {41005096}, issn = {1873-3336}, abstract = {Municipal wastewater treatment plants (WWTPs) are recognized as key recipients of microplastics (MPs), with polyethylene terephthalate (PET) being among the most prevalent types in sewage. However, the systemic impact of PET MPs on integrated biological-membrane systems-especially their role in microbial ecology and membrane fouling-remains poorly understood. Therefore, the influence of PET MPs on the performance, microbial community and membrane fouling in a sequencing-batch membrane bioreactor (SMBR) was evaluated in this study. Based on the results, adding PET MPs decreased the MLSS from around 5000 mg/L to 4500 mg/L whereas the MLVSS/MLSS remain basically consistent. The SV30 and SVI increased rapidly to 76 % and 173.2 mL/g on the 3rd day (from 64 % and 128.3 mL/g on the 1st day) of adding PET MPs, however, they could be restored in the following days. For pollutants removal, the COD and NH4[+]-N removal were initially negatively affected but gradually recovered after several days of operation. The addition of PET MPs enhanced denitrification, resulting in a decrease in the effluent TN concentration from 15.1 ± 4.9 mg/L to 10.4 ± 4.4 mg/L. PET MPs changed microbial community structure and decreased the abundance of dominant bacteria and species diversity in activated sludge. Arenimonas and Sphingopyxis had strong relationships with PET MPs addition. PET MPs addition exacerbated membrane biofouling, and the microbial diversity on membrane at was basically consistent with activated sludge whereas the abundance changed significantly. This research provides a comprehensive understanding of how PET MPs affect the performance of integrated biological-membrane systems.}, }
@article {pmid41000638, year = {2025}, author = {Flores, C and Seekatz, AM}, title = {Reduced carbohydrate complexity alters gut microbial structure independent of total carbohydrate intake.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.09.20.677466}, pmid = {41000638}, issn = {2692-8205}, abstract = {Dietary habits have dramatically altered over recent decades, yet the impact of simplified carbohydrate intake on the gut microbiome's complexity and function remains poorly understood. This study investigates how the variety of dietary carbohydrates - not just their amount - shapes gut microbial diversity and resilience in C57BL/6 mice. Over eight weeks, mice consumed diets varying in carbohydrate complexity but matched for total carbohydrate content. Using 16S rRNA sequencing, we found that reduced carbohydrate diversity led to significant declines in microbial diversity and taxonomic redundancy among important bacterial groups, such as unclassified Lachnospiraceae, Ruminococcaceae, and Muribaculaceae, despite no immediate changes in host physiology. Concurrently, Akkermansia increased under low-complexity diets, suggesting a shift toward mucin degradation when complex polysaccharides are scarce. These changes indicate that loss of carbohydrate complexity narrows microbial niches, potentially disrupting metabolic interactions and functional stability of the gut ecosystem. Given the widespread adoption of processed, low-fiber diets in modern societies, these findings emphasize the importance of macronutrient complexity in maintaining gut microbial health. While short-term host effects were minimal, the microbial shifts observed could presage long-term consequences for gut resilience and disease susceptibility. This study underscores the need to consider carbohydrate diversity in dietary recommendations and microbial ecology research to safeguard gut health in the face of global dietary simplification.}, }
@article {pmid41000006, year = {2025}, author = {Hodgson, RJ and Cando-Dumancela, C and Davies, T and Dinsdale, EA and Doane, MP and Edwards, RA and Liddicoat, C and Peddle, SD and Ramesh, SA and Robinson, JM and Breed, MF}, title = {Contrasting Microbial Taxonomic and Functional Colonisation Patterns in Wild Populations of the Pan-Palaeotropical C4 Grass, Themeda triandra.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.70205}, pmid = {41000006}, issn = {1365-3040}, support = {//This metagenomics sequencing for this project was supported by the Flinders University Accelerator for Microbiome Exploration. We also received funding from the Holsworth Wildlife Research Endowment with the Ecological Society of Australia, the Conservation Biology Grant 2022 with the Biological Society of South Australia and Nature Conservation Society of South Australia and the Lirabenda Wildlife Research Fund from the Field Naturalists Society of South Australia. We also received support from the Australian Research Council (grant numbers LP190100051 and LP190100484) and the New Zealand Ministry of Business Innovation and Employment (grant UOWX2101)./ ; }, abstract = {The interactions between native plants and soil microbiota are not well characterised, despite growing recognition of their importance for host plant fitness and ecological functioning. We used shotgun metagenomics to examine microbial taxonomic and functional colonisation patterns in wild populations of the pan-palaeotropical C4 grass, Themeda triandra, across a globally representative aridity gradient (aridity index 0.318-0.903). We investigated these patterns through the two-step selection process whereby microbes are recruited from bulk soils into rhizospheres (soil on the root surface), and root interiors (endospheres). We provide clear evidence of this process through decreasing microbial taxonomic diversity from bulk soil to T. triandra roots. Surprisingly, microbial functional potential showed the opposite trend: the diversity of potential functions (exponent of Shannon's diversity) increased from bulk soil to the rhizosphere and endosphere, but functional richness did not. Finally, we found that increasing aridity was associated with rhizospheres that were more compositionally similar, yet remained highly diverse in functional potential. Overall, aridity is strongly associated with the root-associated microbiome of T. triandra, selecting for microbiota that likely support plant resilience under dry conditions. Furthermore, microbial functional potential closely tracks taxonomic composition and aridity trends, highlighting how native plants can shape their microbial communities.}, }
@article {pmid40999741, year = {2025}, author = {Sun, J and Huang, H and Li, J and Xu, J and Jia, J and Li, W and Cheng, J and Zhu, D and Liu, M and Yuan, M and Xiao, S and Xue, C}, title = {Mitochondrial iron transporter ClMrs3/4 regulates iron homeostasis to modulate nitric oxide balance facilitating appressorial development in Curvularia lunata.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.70594}, pmid = {40999741}, issn = {1469-8137}, support = {2024YFD1400304//National Key Research &amp; Development Program of China/ ; 2023JH101300163/2022JH2/101300168//Liaoning Provincial Applied Basic Research Program/ ; 2024JH1/11700007-3//Liaoning Provincial Key Projects of Science and Technology/ ; JYTYB2024053//Basic Research Project of the Department of Education of Liaoning Province/ ; }, abstract = {Iron is indispensable for the vast majority of organisms, and iron homeostasis plays a pivotal role in both the physiology and pathogenesis of fungal pathogens. However, the underlying mechanisms by which iron homeostasis modulates fungal pathogenesis remain to be fully elucidated. We therefore focused on investigating the functions of mitochondrial iron transporter ClMrs3/4 in virulence. We conducted targeted gene deletions, expression analyses, biochemistry, and pathogenicity assays, demonstrating that ClMrs3/4 regulates appressorial development via maintenance of cellular iron balance in Curvularia lunata. ClMrs3/4 modulates virulence by influencing appressorial development in C. lunata, which is dependent on iron homeostasis. ClMrs3/4 controls nitric oxide (NO) balance via the nitrate (NO3 [-]) assimilation pathway by modulating cytoplasmic iron levels, a process crucial for turgor pressure accumulation within the appressoria independent of mitochondrial and cytoplasmic Fe-S cluster biosynthesis. Our findings underscore the conserved role of Mrs3/4 in iron homeostasis among pathogenic fungi and propose a novel mechanism by which iron homeostasis regulates virulence, particularly through the NO3 [-] assimilation pathway mediated by cytoplasmic iron levels to regulate appressorial development.}, }
@article {pmid40998779, year = {2025}, author = {Li, Y and Sun, M and Raaijmakers, JM and Mommer, L and Zhang, F and Song, C and Medema, MH}, title = {Predicting rhizosphere-competence-related catabolic gene clusters in plant-associated bacteria with rhizoSMASH.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {8400}, pmid = {40998779}, issn = {2041-1723}, support = {24.004.014//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; }, mesh = {*Rhizosphere ; *Bacteria/genetics/metabolism/classification ; *Plant Roots/microbiology ; Soil Microbiology ; Microbiota/genetics ; *Multigene Family ; *Plants/microbiology ; Machine Learning ; Algorithms ; }, abstract = {Plants release a substantial fraction of their photosynthesized carbon into the rhizosphere as root exudates that drive microbiome assembly. Deciphering how plants modulate the composition and activities of rhizosphere microbiota through root exudates is challenging, as no dedicated computational methods exist to systematically identify microbial root exudate catabolic pathways. Here, we integrate published information on catabolic genes in bacteria that contribute to their rhizosphere competence and develop the rhizoSMASH algorithm for genome-synteny-based annotation of rhizosphere-competence-related catabolic gene clusters (rCGCs) in bacteria with 58 curated detection rules. Our analysis reveals heterogeneity in rCGC prevalence both across and within plant-associated bacterial taxa, indicating extensive niche specialization. Furthermore, we demonstrate the predictive value of the presence or absence of rCGCs for rhizosphere competence in machine learning with two case studies. rhizoSMASH provides an extensible framework for studying rhizosphere bacterial catabolism, facilitating microbiome-assisted breeding approaches for sustainable agriculture.}, }
@article {pmid40997605, year = {2025}, author = {Wu, G and Ding, Z and Wang, J and Xie, J}, title = {Frontier research on the risk of spoilage microorganisms in refrigerated marine fish: From regional to global perspectives.}, journal = {International journal of food microbiology}, volume = {444}, number = {}, pages = {111465}, doi = {10.1016/j.ijfoodmicro.2025.111465}, pmid = {40997605}, issn = {1879-3460}, abstract = {Microbial spoilage is creating safety risks and significant wastage of refrigerated marine fish. Spoilage microorganisms possess distinct physiological adaptations that enable them to contribute to the spoilage of refrigerated marine fish, thereby complicating the accuracy of microbial risk predictions and the efficacy of control strategies. This review integrates research findings from diverse geographical regions to elucidate mechanisms of microbial spoilage and underscores the ongoing challenges in cross-regional collaborative studies. Omics serve as guiding tools for elucidating the molecular mechanisms by which metabolite mediate spoilage microorganisms-induced deterioration of flavor, texture, and safety. Quantitative Microbial Risk Assessment (QMRA) provides a critical framework for risk prediction, with its future development being intrinsically linked to the integration of omics data, rapid fluorescence sensing, and artificial intelligence (AI) for enhanced prediction and modeling. In conclusion, this review underscores the critical role of spoilage microorganisms in the deterioration of refrigerated marine fish, highlights the complex interplay between microbial ecology, cold adaptation, and spoilage potential, and emphasizes the necessity for collaborative global efforts. Advancing research on native microbial communities, molecular spoilage mechanisms, and AI-powered QMRA frameworks is paramount for reducing food waste, enhancing food safety risk assessment, and the sustainable development of preservation technology.}, }
@article {pmid40996662, year = {2025}, author = {Rév, A and Parádi, I and Füzy, A and Juhász, P and Kocsis, K and Cseresnyés, I and Takács, T}, title = {Improvement of soil fertility and enzymatic activity by wastewater sludge compost and arbuscular mycorrhizal fungi in giant reed's rhizosphere.}, journal = {Biologia futura}, volume = {}, number = {}, pages = {}, pmid = {40996662}, issn = {2676-8607}, support = {SA-26/2021//E&#xf6;tv&#xf6;s Lor&#xe1;nd Research Network/ ; }, abstract = {The effect of low-dose, commercially available wastewater sludge compost (WSC; 15 t ha[-1]) treatment was examined with or without arbuscular mycorrhizal fungal (AMF) inoculation on the nutritional status, heavy metal (HM) concentration and the rhizosphere activity of giant reed (Arundo donax L. var. BL clone (Blossom)) plants. Funneliformis mosseae (BEG12; AMF1), F. geosporum (BEG11; AMF2) or their combination (AMFmix) were applied as AMF treatments in a short-term pot experiment. The physiological and growth parameters of the host plants, the AMF root colonization and the microbiological enzyme activity of the mycorrhizosphere were examined. We assumed that the combined treatment (WSC + AMF) enhances the fertility of low-fertility acidic sandy soil. Neither the WSC treatment nor the AMF inoculations changed the extent of root colonization. Based on the results of root electrical capacitance and the phosphorous uptake, plant nutritional status was improved by WSC addition, without any negative impacts among the measured parameters. AMF treatments increased the enzyme activity in the soil and decreased the concentrations of the potentially toxic HMs (Cu, Mn, Pb, Zn) in roots, but that mitigation of Cu and Zn was compensated in shoots. According to the results of MicroResp™ measurements, the catabolic activity profile of the soil microbial community was changed in case of the AMF2 treatment. The efficient regulatory mechanism of giant reed might be able to adjust optimal/maximal colonization rate, and to select the preferential AMF partners, this supposed mechanism might be responsible for its invasiveness and tolerance to a wide range of environmental conditions.}, }
@article {pmid40996559, year = {2025}, author = {Han, SI and Kim, JO and Lee, YR and Ekpeghere, KI and Koh, SC and Whang, KS}, title = {Correction: Denitratimonas tolerans gen. nov., sp. nov., a denitrifying bacterium isolated from a bioreactor for tannery wastewater treatment.}, journal = {Antonie van Leeuwenhoek}, volume = {118}, number = {10}, pages = {157}, doi = {10.1007/s10482-025-02169-7}, pmid = {40996559}, issn = {1572-9699}, }
@article {pmid40995846, year = {2025}, author = {Stephenson, T and Crowder, DW and Osburn, E and Strickland, M and Jones, M and Bartel, S and Kittipalawattanapol, K and Cunningham, CX and Hudiburg, T and Storfer, A and Piaskowski, J and Lynch, L}, title = {Apex Scavenger Declines Have Cascading Effects on Soil Biogeochemistry and Ecosystem Processes.}, journal = {Global change biology}, volume = {31}, number = {9}, pages = {e70520}, doi = {10.1111/gcb.70520}, pmid = {40995846}, issn = {1365-2486}, support = {DEB-2054716//National Science Foundation/ ; }, mesh = {Animals ; *Soil/chemistry ; *Soil Microbiology ; *Food Chain ; *Marsupialia/physiology ; *Ecosystem ; Seasons ; Microbiota ; }, abstract = {Global apex scavenger declines strongly alter food web dynamics, but studies rarely test whether trophic downgrading impacts ecosystem functions. Here, we leverage a unique, disease-induced gradient in Tasmanian devil (Sarcophilus harrisii) population densities to assess feedbacks between carcass persistence, subordinate scavenger guilds, and biogeochemical cycling. We further explored interkingdom and seasonal interactions by manipulating carcass access and replicating experiments in warmer, drier summer versus cooler, wetter winter periods. We show Tasmanian devil declines significantly extend carcass persistence and increase the flux of carcass-derived nutrients belowground (e.g., by 18-134-fold for ammonium). Greater nutrient availability reduces soil microbiome diversity by up to 26%, increasing the relative abundance of putative zoonotic pathogens. Nutrient subsidies also shift microbial communities toward faster-growing taxa that invest less energy in resource acquisition, with implications for soil carbon sequestration. Rates of carcass decomposition were reduced in the winter, dampening soil biogeochemical responses and interkingdom competition. Notably, while less efficient scavenger guilds clearly facilitate carcass consumption, they were not able to fill the functional role of apex scavengers. Our study illustrates how trophic downgrading effects can ripple across all levels of ecological organization.}, }
@article {pmid40993772, year = {2025}, author = {Dubey, JP and Alić, A and Hodžić, A and Lopez-Flores, J and Baneth, G}, title = {Hepatozoon infections in domestic and wild Carnivora: etiology, prevalence, clinical disease, diagnosis and treatment, and redescription of Hepatozoon silvestris, H. martis, and H. ursi.}, journal = {Parasites &amp; vectors}, volume = {18}, number = {1}, pages = {391}, pmid = {40993772}, issn = {1756-3305}, mesh = {Animals ; Prevalence ; *Coccidiosis/veterinary/diagnosis/epidemiology/parasitology/drug therapy/therapy ; *Eucoccidiida/classification/isolation &amp; purification ; *Carnivora/parasitology ; Animals, Wild/parasitology ; Animals, Domestic/parasitology ; Life Cycle Stages ; }, abstract = {Hepatozoon spp. are common pathogens in dogs and other Carnivora in many parts of the world, especially in the tropics. There is considerable taxonomic debate concerning the Hepatozoon species infecting Carnivora. Morphological descriptions of several Hepatozoon species are inadequate and their validity is questionable. Additionally, different terminology has been used for the description of life cycle stages. Here, we provide a comprehensive review of the Hepatozoon species in the Carnivora, using a uniform terminology. Worldwide prevalence of clinical and subclinical Hepatozoon infections for the past century is tabulated and critically evaluated. We also review the epizootiology, clinical signs, diagnosis, and treatment of hepatozoonosis in the Carnivora. The morphology and life cycles of seven valid species with known merogonic stages (Hepatozoon americanum, H. canis, H. felis, H. martis, H. rufi, H. silvestris, H. ursi) are summarized in a table using standard terminology. Additional information on H. apri, H. martis, and H. silvestris life cycle stages is provided. Information lacking for H. procyonis, H. luiperdjie and H. ingwe is discussed. The relevance of H. mustelis, H. banethi and H. ewingi is discussed and they are considered as invalid species. For the benefit of future researchers, worldwide reports of prevalence, clinical disease, diagnosis, and treatment of Hepatozoon infections in domestic and wild Carnivora for the past century are summarized in tables alphabetically and chronologically for each country. Co-infections of H. canis, H. americanum, H. felis, and H. silvestris are summarized and discussed. The role of Hepatozoon infections causing clinical illness in wild Carnivora is discussed, particularly for red foxes, coyotes, and mustelids.}, }
@article {pmid40993491, year = {2025}, author = {Sun, S and Qiao, Z and Tikhonenkov, DV and Gong, Y and Li, H and Li, R and Sun, K and Huo, D}, title = {Temporal Dynamics and Adaptive Mechanisms of Microbial Communities: Divergent Responses and Network Interactions.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {94}, pmid = {40993491}, issn = {1432-184X}, support = {24-44-00093//Russian Science Foundation/ ; 32361133561//National Natural Science Foundation of China/ ; 2021M703430//China Postdoctoral Science Foundation/ ; }, mesh = {*Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; Ecosystem ; *Rivers/microbiology ; *Eukaryota/genetics/classification/physiology ; Water Microbiology ; High-Throughput Nucleotide Sequencing ; }, abstract = {Microbial communities are vital to aquatic ecosystems, driving biogeochemical cycles, nutrient recycling, and overall ecosystem functioning. However, their instant feedback, particularly in response to environmental fluctuations, remain insufficiently understood. In this study, we investigated the interaction of prokaryotic and eukaryotic microbial communities in riverine ecosystems under temporal dynamics using high-throughput sequencing and co-occurrence network analysis. We observed distinct patterns, with eukaryotic communities showing a consistent increase in alpha diversity, while prokaryotic communities exhibited more variable and directional shifts over time. Two key phases were identified: a dynamic phase characterized by rapid changes in both alpha and beta diversity and a stabilization phase where community composition became more stable, with increased evenness. Co-occurrence network analysis revealed a transition from a modular structure in the dynamic phase to a more centralized and highly connected network in the stabilization phase. While modularity can enhance stability by localizing perturbations within distinct subnetworks, increased centralization and connectivity may weaken this stabilizing effect, potentially making the network less resilient to environmental fluctuations. Our findings provide new insights into the adaptive mechanisms that sustain microbial community stability and resilience in dynamic aquatic ecosystems, emphasizing the importance of diversity and network structure in maintaining ecological stability.}, }
@article {pmid40991823, year = {2025}, author = {Lennon, JT and Bittleston, LS and Chen, Q and Cooper, VS and Fernández, J and Gilbert, JA and Häggblom, MM and Harper, LV and Jansson, JK and Jiao, N and Kuurstra, EM and Peixoto, RS and Rappuoli, R and Schembri, MA and Ventosa, A and Vullo, DL and Zhang, C and Nguyen, NK}, title = {Microbes without borders: uniting societies for climate action.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf199}, pmid = {40991823}, issn = {1751-7370}, }
@article {pmid40991432, year = {2025}, author = {van Gestel, J and Koo, BM and Stürmer, VS and Garriga-Canut, M and Wagner, J and Zanon, A and Gross, CA}, title = {Bacillus subtilis in defense mode: Switch-like adaptations to protistan predation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {39}, pages = {e2518989122}, doi = {10.1073/pnas.2518989122}, pmid = {40991432}, issn = {1091-6490}, support = {101116560//EC | ERC | HORIZON EUROPE European Research Council (ERC)/ ; P400PB_186789//Swiss National Science Foundation (Postdoc.Mobility)/ ; R35GM118061//HHS | National Institutes of Health (NIH)/ ; }, mesh = {*Bacillus subtilis/genetics/physiology/growth &amp; development ; *Dictyostelium/physiology ; *Adaptation, Physiological ; Bacterial Proteins/metabolism/genetics ; Phenotype ; }, abstract = {Single-cell eukaryotic predators in the soil are a primary cause of bacterial cell death. Yet, most functional genomic studies on soil bacteria have been performed without predation, thereby selecting for phenotypes impacting growth rather than survival and biasing our view on the ecological factors driving genomic evolution. Here, we study how predation by the ubiquitous amoebal predator Dictyostelium discoideum affects Bacillus subtilis' growth and survival using both a genome-scale mutant screen and de novo evolution of resistance. We show that predation-related genes (many not previously identified) promote survival by enabling filament or aggregate formation, thereby outsizing D. discoideum and slowing or preventing ingestion. Importantly, we find that predation resistance is costly, causing a trade-off between growth and survival. B. subtilis navigates this trade-off through switch-like adaptations, where cells switch back-and-forth between a slow-growing resistant state and a fast-growing susceptible state. These behaviors are controlled through both genotypic and phenotypic switches, with a central role for the Spo0A phosphorylation cascade, whose ancestral function may have been to evade or slow predation. Taken together, we uncover how the antagonist selection pressure imposed by predation is an important ecological driver of phenotypic heterogeneity in B. subtilis.}, }
@article {pmid40990948, year = {2025}, author = {Basu, A and Mondal, S and Roy, A and Tewari, S and Chattopadhyay, S and Ghosh, A and Sil, AK}, title = {Paraclostridium sp. AKS46 vesicles facilitate extracellular electron transport.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxaf239}, pmid = {40990948}, issn = {1365-2672}, abstract = {AIMS: Paraclostridium sp. AKS46 was shown to have high exoelectrogenic activity. The current study investigated whether membrane vesicles (MVs) contribute to this electrogenic activity of this organism.<br><br>METHODS AND RESULTS: To examine the contribution of MVs to electrogenic activity, formation of MVs was first investigated by microscopic analyses of AKS46 cells at different time points of growth. The results showed increasing MV formation with time, especially in electrode-attached cells. To test electrogenic activity, the redox property and the electrochemical activity of the vesicles were examined. To this end, purified AKS46 vesicles demonstrated robust redox activities, and cyclic voltammetry and electrochemical impedance spectroscopy revealed high electrochemical properties of purified vesicles. Furthermore, proteomic analysis of the vesicles identified the presence of redox-active proteins, particularly flavoproteins, which might significantly contribute to electron carrier properties. AKS46 MVs also harbour enzymes involved in CO2 and nitrogen fixation, suggesting their roles in nutrient cycling and maintaining microbial ecology.<br><br>CONCLUSION: The exoelectrogenic gram-positive bacteria Paraclostridium sp. AKS46 produces extracellular vesicles packed with electron-rich molecules and thus, these vesicles act as electron transporters. The work highlights a vesicle-mediated mechanism for energy harvesting from waste degradation in microbial fuel cells.}, }
@article {pmid40990516, year = {2025}, author = {Wang, Y and Xu, J and Liu, Y and Liu, L and Xiao, S and Wang, X and Zhang, J and Huang, S and Zheng, Q}, title = {Ocean currents and environmental gradients shape prokaryotic community structure and function in the South China Sea.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0102025}, doi = {10.1128/spectrum.01020-25}, pmid = {40990516}, issn = {2165-0497}, abstract = {UNLABELLED: The South China Sea (SCS) is characterized by complex hydrodynamic conditions that influence the structure and function of prokaryotic microbial communities. This study conducted a comprehensive analysis of prokaryotic diversity, community assembly, and functional potential across various water masses within the SCS. Using 16S rRNA gene sequencing and co-occurrence network analyses, we found that geographic distance and environmental gradients, particularly temperature and nutrient levels, significantly impacted community composition. Our findings indicate that ecological drift is the primary mechanism governing community assembly, with spatial turnover primarily driven by the dispersal of microorganisms facilitated by ocean currents. Distinct modules in co-occurrence networks were associated with specific environmental factors, reflecting potential environmental selection processes along the SCS current. Keystone species and biomarkers identified through network analysis and random forest modeling exhibited varying associations with environmental variables, highlighting their adaptability to changing conditions. This work underscores the importance of ocean currents and environmental factors in shaping prokaryotic community dynamics and provides insights into microbial biogeography and ecosystem function in the SCS.<br><br>IMPORTANCE: Microorganisms, especially prokaryotes, are fundamental in sustaining marine ecosystems through nutrient cycling and organic matter decomposition. However, understanding what shapes their diversity and distribution remains challenging. Our study highlights the significant role ocean currents and environmental conditions play in influencing prokaryotic communities in the South China Sea-a critical marine environment due to its dynamic currents and ecological complexity. We found that currents facilitate microbial dispersal, shaping community composition over vast areas, while temperature gradients act as key selective pressures, determining which species thrive. Additionally, we reveal that both predictable environmental selection and random ecological drift significantly contribute to community structuring. By identifying keystone microbes and biomarkers sensitive to environmental change, our work offers essential insights into marine microbial ecology. These findings are crucial for predicting how microbial communities, and thus ocean health and productivity, respond to ongoing environmental changes.}, }
@article {pmid40989908, year = {2025}, author = {Lopez-Alforja, X and Sà, EL and Quiroga, MV and Pernice, MC and Cardelús, C and Balagué, V and Gasol, JM and Coutinho, FH and Massana, R and Vaqué, D}, title = {Long-term decline of marine viruses associated with warming and oligotrophication at a NW Mediterranean coastal site.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf150}, pmid = {40989908}, issn = {2730-6151}, abstract = {Viruses play key roles in controlling microbial abundance and community composition, nutrient cycling, and productivity in marine systems. Rising ocean temperatures, alongside increasing oligotrophy, are expected to alter the availability of inorganic nutrients and oxygen-key environmental factors that shape microbial community structure and virus-host interactions. While many studies have investigated viral abundances and community structure across spatial gradients, less is known about their long-term temporal variations, which is particularly relevant in the current context of global change. To address this gap, we analyzed two decades of surface water data from the Blanes Bay Microbial Observatory, located at the North-Western Mediterranean, to describe how biotic and abiotic variables influence temporal dynamics of viral abundances and community composition. Statistical tools for time series, including GAMMs, anomaly analysis, and neural networks, allowed us to demonstrate that viral abundance follows strong seasonality and a clear decrease starting midway (ca. 2011) through the sampled period (2005-2022). Fingerprint analysis evidenced that viral community composition was significantly influenced by seasonality and some environmental and biotic factors, with strong differences in viral communities between summer and winter months. Our analyses revealed that over the last 18 years, the abundance of most microbial groups, including viruses and their potential hosts, has declined, coinciding with an increase in seawater temperature and transparency, as well as a notable decrease in nutrient concentrations and phytoplankton biomass. We identified the ongoing shift toward more oligotrophic conditions as a potential driver of the observed decline in viral abundance, particularly in the last decade.}, }
@article {pmid40989192, year = {2025}, author = {Alfahl, Z and O'Connor, L and Morris, D and Smith, TJ and O'Dwyer, J and Hynds, PD and Cormican, M and Burke, LP}, title = {A novel enrichment-free, low-volume filtration and rapid lysis (ELR) method in combination with real-time PCR for detection of Shiga toxin-producing Escherichia coli (STEC) in water.}, journal = {Access microbiology}, volume = {7}, number = {7}, pages = {}, pmid = {40989192}, issn = {2516-8290}, abstract = {Consequences of Shiga toxin-producing Escherichia coli (STEC) infection can range in severity from asymptomatic infection to haemolytic uraemic syndrome, renal failure and death. Groundwater-derived drinking water is an important route for STEC transmission. Detection of STEC in water is crucial for timely response and public health interventions; however, currently used culture-based methods are time-consuming and laborious. Therefore, there is a need for rapid methods that maintain high sensitivity and specificity [1]. We describe a novel, sensitive, enrichment-free water filtration method using a convenient sample volume (100 ml) to detect DNA markers of STEC serogroups and virulence factors within 6 h. Quantitative real-time PCR (qPCR) was used to detect and quantify the most common STEC infection-associated serogroups globally, O157 and O26. Real-time PCR was used to detect genetic determinants of STEC virulence (stx1, stx2 and eae genes) and specific marker genes for the clinically relevant serogroups O111, O103, O145 and O104. Results showed that the novel method can detect as low as 5 c.f.u. ml[-1] of STEC in water. The limit of detection for O157 and O26 qPCR assays was two and six copies, respectively. Groundwater and surface water samples (n=28) were collected and processed using the novel method. STEC O157 and O26 serogroups were detected in 23 out of 28 (82.1%) samples (mean 5.2×10[4] copies/reaction) and 19 out of 28 (67.9%) samples (mean 7.83×10[4] copies/reaction), respectively. Shiga toxin genes stx1 or stx2 were detected in 15 out of 28 (53.6%) and 9 out of 28 (32.1%) samples, respectively. The virulence factor intimin gene eae was detected in 24 out of 28 (85.7%) samples. STEC serogroups O111, O103, O145 and O104 were detected in 15 out of 28 (53.6%), 10 out of 28 (35.7%), 11 out of 28 (39.3%) and 15 out of 28 (53.6%) samples, respectively. This novel method reproducibly detects low copies of STEC in low-volume fresh water and has the potential to be used for the detection and quantification of waterborne bacterial pathogens.}, }
@article {pmid40987850, year = {2025}, author = {Laso-Pérez, R}, title = {Deep-mining the archaeal proteome for antibiotics.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {40987850}, issn = {2058-5276}, }
@article {pmid40987416, year = {2025}, author = {Liaqat, F and Khazi, MI and Ismail, W}, title = {Microbial transport systems of organic sulfur compounds: Diversity and implications for biocatalysis, healthcare, and environmental biotechnology.}, journal = {Biotechnology advances}, volume = {}, number = {}, pages = {108718}, doi = {10.1016/j.biotechadv.2025.108718}, pmid = {40987416}, issn = {1873-1899}, abstract = {The global sulfur cycle plays a vital role in human health, global warming and biogeochemistry. Organic sulfur compounds constitute a substantial sulfur reservoir and serve as an energy and/or carbon source for prokaryotes. In addition, microbial interactions with organic sulfur compounds are pivotal for several biotechnological applications in petroleum biorefining, industrial biocatalysis, bioremediation, healthcare, and plant growth promotion. Microbial degradation of organic sulfur compounds is hindered by slow degradation rates, substrate specificity, toxicity of by-products, and challenges in scalability and efficiency. While degradation pathways of some organic sulfur compounds have been elucidated, transport systems involved in their uptake and efflux remain less explored. Regulating the uptake and efflux of organic sulfur compounds in microorganisms can help overcome several of the limitations associated with their transformation. Membrane transporters are not only crucial for uptake and efflux of organic sulfur compounds but also play a key role in stress tolerance by facilitating the excretion of toxic metabolites. Understanding the intricacies of these transporters provides valuable insights into microbial ecology and the development of strategies for harnessing microbial sulfur metabolism for important biotechnological applications. This review systematically presents the diversity, mechanisms, and potential evolution pathways of microbial membrane transporters involved in organic sulfur compounds acquisition. Furthermore, it highlights and discusses advances in the characterization of transporter systems and current limitations in using transporter systems for fuel biodesulfurization and organic sulfur compound degradation. Eventually, we explore the implications of organic sulfur compounds transporters in biotechnology and identify future research directions toward leveraging the biotechnological potential of microbial sulfur metabolism, fueled by advanced techniques of systems microbiology, metabolic engineering, as well as artificial intelligence.}, }
@article {pmid40986398, year = {2025}, author = {Lennon, JT and Bittleston, LS and Chen, Q and Cooper, VS and Fernández, J and Gilbert, JA and Häggblom, MM and Harper, LV and Jansson, JK and Jiao, N and Kuurstra, EM and Peixoto, RS and Rappuoli, R and Schembri, MA and Ventosa, A and Vullo, DL and Zhang, C and Nguyen, NK}, title = {Microbes without borders: uniting societies for climate action.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {10}, pages = {}, doi = {10.1093/femsec/fiaf084}, pmid = {40986398}, issn = {1574-6941}, }
@article {pmid40985999, year = {2025}, author = {Lennon, JT and Bittleston, LS and Chen, Q and Cooper, VS and Fernández, J and Gilbert, JA and Häggblom, MM and Harper, LV and Jansson, JK and Jiao, N and Kuurstra, EM and Peixoto, RS and Rappuoli, R and Schembri, MA and Ventosa, A and Vullo, DL and Zhang, C and Nguyen, NK}, title = {Microbes without borders: uniting societies for climate action.}, journal = {mBio}, volume = {}, number = {}, pages = {e0213625}, doi = {10.1128/mbio.02136-25}, pmid = {40985999}, issn = {2150-7511}, abstract = {The climate crisis is one of the greatest challenges of our time, yet the role of microorganisms remains underrecognized in climate science and policy. Microbes are highly sensitive to environmental change and regulate essential biogeochemical processes, while also offering solutions for reducing emissions, restoring ecosystems, and enhancing resilience. Microbiology societies from five continents recently convened in Washington, DC, for the inaugural Global Strategy Meeting on Microbes and Climate Change. The gathering launched a global alliance to position microbial science as a pillar of climate action and identified four priorities: building a coalition, embedding microbes in climate frameworks, transforming communication, and advancing real-world demonstration projects. This initiative marks the beginning of coordinated global action to harness microbial life for climate solutions.}, }
@article {pmid40985636, year = {2025}, author = {Grosso Giordano, F and Mariën, Q and De Belie, N and Rodriguez-Navarro, C and Boon, N}, title = {Characterization of isolates used in bacterial-based strategies for accelerated carbonation of lime mortars.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0068325}, doi = {10.1128/aem.00683-25}, pmid = {40985636}, issn = {1098-5336}, abstract = {Portland cement largely replaced hydraulic lime over the past century because of its rapid hardening. Achieving earlier hardening in lime through faster carbonation is thus essential to help overcome one of lime's limiting qualities. Here, we isolated two alkaliphilic bacteria, Shouchella clausii and Shouchella patagoniensis, from a lime mortar wall. S. clausii was then further grown in high pH (>11) by adaptive laboratory evolution to acclimate a third isolate. Bacterial suspensions of all three isolates were followed for 14 days in serum bottles at pH 11, and gas composition of the headspace, intact/damaged cell populations, and pH were measured. In parallel, lime mortar samples were incubated in a closed environment with bacterial suspension of the isolates and analyzed with thermogravimetric analysis after 7 and 14 days to quantify carbonation. S. patagoniensis produced more CO2, close to the estimated maximum CO2 uptake rate of lime, and carbonated the lime mortars to a larger extent than the other isolates. Finally, the bacterial suspensions were directly mixed with lime. A linear and homogeneous carbonation of the paste samples was measured compared to water-based pastes, and the development of Liesegang patterns was observed upon phenolphthalein spreading. All this indicated that the organic addition altered the carbonation dynamics of the material, although bacteria did not accelerate carbonation relative to media alone and inhibited it relative to water-based paste. Still, a relationship between bacterial activity, CO2 emission, and carbonation rate was established, but practical aspects of bacterial delivery into lime must be addressed.IMPORTANCEPortland cement is the dominant binder used in most construction today, but until last century, lime was the ubiquitous construction material. The increase in use of cement has sprung from its higher strength and faster hardening; yet, lime still remains a relevant material, particularly in masonry structures and the built heritage. As such, novel lime materials are necessary to tackle some of the current limitations of lime, such as earlier hardening, which would not only make lime easier to work with but would also limit failure due to environmental conditions. As existing strategies to speed up lime hardening have had limited uptake due to their reliance on expensive and often toxic chemicals, the need for novel solutions is in place. We show that bacterial-based strategies could be a viable option to go beyond the limitations of current strategies, but limitations are in place.}, }
@article {pmid40985445, year = {2025}, author = {Shen, K and Tang, Y and Shi, J and Hu, Z and He, M and Li, J and Wang, Y and Shao, M and Liu, H}, title = {Relationship Between Aquatic Fungal Diversity in Surface Water and Environmental Factors in Yunnan Dashanbao Black-Necked Crane National Nature Reserve, China.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {11}, number = {7}, pages = {}, doi = {10.3390/jof11070526}, pmid = {40985445}, issn = {2309-608X}, support = {2024//Yunnan Provincial Department of Education Scientific and Technological Innovation Team for Development and Utilization of Gastrodia Resources/ ; 202110BA070001-059//Special Basic Cooperative Research Programs of Yunnan Provincial Undergraduate Universities' Association/ ; 2023-3//Zhaotong "Xingzhao Talent Support Program" Team Project/ ; }, abstract = {Aquatic fungi serve as core ecological engines in freshwater ecosystems, driving organic matter decomposition and energy flow to sustain environmental balance. Wetlands, with their distinct hydrological dynamics and nutrient-rich matrices, serve as critical habitats for these microorganisms. As an internationally designated Ramsar Site, Yunnan Dashanbao Black-Necked Crane National Nature Reserve in China not only sustains endangered black-necked cranes but also harbors a cryptic reservoir of aquatic fungi within its peat marshes and alpine lakes. This study employed high-throughput sequencing to characterize fungal diversity and community structure across 12 understudied wetland sites in the reserve, while analyzing key environmental parameters (dissolved oxygen, pH, total nitrogen, and total phosphorus). A total of 5829 fungal operational taxonomic units (OTUs) spanning 649 genera and 15 phyla were identified, with Tausonia (4.17%) and Cladosporium (1.89%) as dominant genera. Environmental correlations revealed 19 genera significantly linked to abiotic factors. FUNGuild functional profiling highlighted saprotrophs (organic decomposers) and pathogens as predominant trophic guilds. Saprotrophs exhibited strong associations with pH, total nitrogen, and phosphorus, whereas pathogens correlated primarily with pH. These findings unveil the hidden diversity and ecological roles of aquatic fungi in alpine wetlands, emphasizing their sensitivity to environmental gradients. By establishing baseline data on fungal community dynamics, this work advances the understanding of wetland microbial ecology and informs conservation strategies for Ramsar sites.}, }
@article {pmid40983756, year = {2025}, author = {Dong, S and Wang, S and Li, L and Yu, J and Zhang, Y and Xue, JY and Chen, H and Ma, J and Zeng, Y and Cai, Y and Huang, W and Zhou, X and Wu, J and Li, J and Yao, Y and Hu, R and Zhao, T and Villarreal A, JC and Dirick, L and Liu, L and Ignatov, M and Jin, M and Ruan, J and He, Y and Wang, H and Xu, B and Rozzi, R and Wegrzyn, J and Stevenson, DW and Renzaglia, KS and Chen, H and Zhang, L and Zhang, S and Mackenzie, R and Moreno, JE and Melkonian, M and Wei, T and Gu, Y and Xu, X and Rensing, SA and Huang, J and Long, M and Goffinet, B and Bowman, JL and Van de Peer, Y and Liu, H and Liu, Y}, title = {Bryophytes hold a larger gene family space than vascular plants.}, journal = {Nature genetics}, volume = {}, number = {}, pages = {}, pmid = {40983756}, issn = {1546-1718}, abstract = {After 500 million years of evolution, extant land plants compose the following two sister groups: the bryophytes and the vascular plants. Despite their small size and simple structure, bryophytes thrive in a wide variety of habitats, including extreme conditions. However, the genetic basis for their ecological adaptability and long-term survival is not well understood. A comprehensive super-pangenome analysis, incorporating 123 newly sequenced bryophyte genomes, reveals that bryophytes possess a substantially greater diversity of gene families than vascular plants. This includes a higher number of unique and lineage-specific gene families, originating from extensive new gene formation and continuous horizontal transfer of microbial genes over their long evolutionary history. The evolution of bryophytes' rich and diverse genetic toolkit, which includes new physiological innovations like unique immune receptors, likely facilitated their spread across different biomes. These newly sequenced bryophyte genomes offer a valuable resource for exploring alternative evolutionary strategies for terrestrial success.}, }
@article {pmid40981669, year = {2025}, author = {Riisgaard-Jensen, M and Valença, RM and Peces, M and Nielsen, PH}, title = {Sewer microbiomes shape microbial community composition and dynamics of wastewater treatment plants.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf213}, pmid = {40981669}, issn = {1751-7370}, abstract = {The link between the sewer microbiome and microbial communities in activated sludge wastewater treatment plants is currently poorly understood despite the systems being directly interconnected. Microbial immigration from wastewater has been identified as a key factor determining activated sludge community assembly. Here, we present the first comprehensive study of the sewer microbiome and hypothesize that it harbors a process-critical activated sludge microbes, thus critical for activated sludge community assembly and performance. We integrated species-level microbial analyses of biofilm, sediment, and sewer wastewater in domestic gravity and pressure sewers in Aalborg, Denmark, with samples from influent wastewater and activated sludge from two downstream wastewater treatment plants. By tracing the sources of incoming bacteria and determining their growth fate in the activated sludge, we confirmed the hypothesis that most activated sludge process-critical bacteria were part of the sewer microbiome. Within the sewer system, a gradient was observed, from dominance of gut-bacteria in the wastewater upstream to prevalence of biofilm and sediment bacteria downstream at the wastewater treatment plants inlet, with the relative ratio strongly affected by rain events. A holistic understanding of the sewer system and activated sludge is essential, as the sewers hold massive amounts of active biomass serving as a major microbial source for community composition and dynamics in wastewater treatment plants. Sewer systems should be recognized as a crucial environmental filtration step, and the sewer microbiome as an important source community for activated sludge, helping to explain the observed regional and global differences in activated sludge community structure.}, }
@article {pmid40981467, year = {2025}, author = {Qiao, Y and Wang, L and Wang, S and Li, S and Wang, F and Wang, B and Lin, S and Liu, Y}, title = {Bacterial generalists and fungal specialists play important roles in maintaining community stability and regulating microbial diversity of the algae-associated microbiome throughout the growth cycle of Alexandrium pacificum.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0135925}, doi = {10.1128/aem.01359-25}, pmid = {40981467}, issn = {1098-5336}, abstract = {The algae-associated microbiome represents a consortium that has been chronically domesticated by specific algae, maintaining a close relationship with the host population. Although the microbes associated with dinoflagellates have garnered significant attention in recent years, the interactions and contributions of microbial generalists and specialists through the growth cycle of a bloom-forming dinoflagellate remain largely unexplored. Herein, the ecological and evolutionary characteristics of free-living generalists and specialists within bacterial and fungal communities were investigated during the growth process of Alexandrium pacificum cultured in the laboratory for years without antibiotic treatment. From an ecological perspective, bacterial generalists and fungal specialists dominated the community, indicating different microbial niche patterns between the bacterial and fungal consortia. Furthermore, microbial specialists were more susceptible to disturbance from algal proliferation, as evidenced by greater community dissimilarity and determinacy-dominated assembly processes. Compared with their counterparts, the molecular networks of bacterial generalists and fungal specialists were more complex and robust, suggesting that they significantly contributed to resistance to environmental stress and functional maintenance. Evolutionarily speaking, bacterial generalists and fungal specialists showed much higher diversification potential, and others featured higher extinction rates. Despite these differences, a continuous transition from the former two to their counterparts was observed, alleviating the "Matthew effect" in the biological world for ecological trade-offs. Collectively, these findings emphasize that bacterial generalists and fungal specialists play important roles in maintaining community stability and regulating microbial diversity during the growth process, which expands the current understanding of the maintenance mechanisms of the diversity and community of phytoplankton-associated microbes in the face of disturbance from bloom-forming dinoflagellates.IMPORTANCELike the microbes residing in the rhizosphere and human gut, bacteria that coexist chronically with microalgae exemplify a relationship, forming potentially intimate partnerships with the host. However, studies on the ecological significance of algae-associated microbiomes with different niches under the interference of bloom-forming species are still lacking. This work investigated the ecological interactions and contributions of generalists and specialists within algae-associated bacterial and fungal communities across the growth cycle of Alexandrium pacificum for the first time. These results increase the understanding of the microbial ecology of algae-associated microbes in the context of interference from the proliferation of harmful algal bloom species.}, }
@article {pmid40981420, year = {2025}, author = {Wing, AJ and Hegarty, B and Bastien, GE and Denef, VJ and Evans, J and Dick, GJ and Duhaime, MB}, title = {Tracking putative Microcystis viruses and virus-host associations across distinct phases of a Microcystis-dominated bloom.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0057525}, doi = {10.1128/msystems.00575-25}, pmid = {40981420}, issn = {2379-5077}, abstract = {Viruses significantly impact microbial community composition and function. Yet their role in the fate of freshwater cyanobacterial harmful algal blooms (cHABs), an increasing threat to freshwater systems, remains poorly understood. Here, we address this with a metagenomic analysis of viruses of bloom-forming Microcystis aeruginosa through a seasonal cHAB in the western basin of Lake Erie. We identified globally distributed Microcystis viruses in Lake Erie based on sequence homology to well-studied isolates. A machine-learning model was then used to predict associations between uncharacterized viral populations and the Microcystis and non-Microcystis hosts of the cHAB. Size fractionation of water samples allowed us to identify significant fraction-specific trends in Microcystis viral diversity that corresponded with Microcystis genetic diversity. Viral diversity was highest in the non-colony-associated fraction and lowest in the colony-associated fraction, suggesting that colony formation may lead to bottlenecks in viral diversity in cHABs. Significant turnover of predicted Microcystis virus populations was observed through time, but not between stations miles apart. The virus-host networks revealed extensive interconnectivity and the potential for virus-mediated cross-species genetic exchange. The networks predicted that Lake Erie Microcystis viruses infect hosts spanning phyla, in agreement with lab studies in other systems but challenging previous notions of "narrow" host-virus associations in this genus. Abundant Microcystis virus genes revealed a potential role in key metabolic pathways and host adaptation. These findings advance our understanding of Microcystis viruses and their potential influence on host metabolism, species interactions, and coevolution in Microcystis-dominated cHABs.IMPORTANCEUnderstanding associations between viruses, their hosts, and environmental factors is key for identifying the mechanisms behind the rise and fall of cyanobacterial harmful algal blooms. This study explores the diversity and host ranges of viruses predicted to infect Microcystis, reporting how these properties vary over time, across sample stations in western Lake Erie, and among different filter size fractions. We found that Microcystis virus diversity is highest in non-colony-associated fractions and the lowest in colony-associated fractions, suggesting a link between Microcystis colony formation and reduced viral diversity. We identify abundant genes belonging to predicted Microcystis viruses and their potential roles in key metabolic pathways and adaptation to environmental changes. These findings enhance our understanding of the interplay among viruses, Microcystis, and co-occurring bacteria in cHABs, offering insights into the mechanisms driving bloom dynamics, species interactions, and coevolutionary processes.}, }
@article {pmid40980873, year = {2025}, author = {Lai, W and Alberdi, A and Leu, A and de Leon, AVP and Kobel, CM and Aho, VTE and Roehe, R and Pope, PB and Hvidsten, TR}, title = {Metabolic capabilities of key rumen microbiota drive methane emissions in cattle.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0060125}, doi = {10.1128/msystems.00601-25}, pmid = {40980873}, issn = {2379-5077}, abstract = {UNLABELLED: The rumen microbiome plays a critical role in determining feed conversion and methane emissions in cattle, with significant implications for both agricultural productivity and environmental sustainability. In this study, we applied a hierarchical joint species distribution model to predict directional associations between biotic factors and abundances of microbial populations determined via metagenome-assembled genomes (MAGs). Our analysis revealed distinct microbial differences, including 191 MAGs significantly more abundant in animals with a higher methane yield (above 24 g/kg dry matter intake [DMI]; high-emission cattle), and 220 MAGs more abundant in low-emission cattle. Interestingly, the microbiome community of the low-methane-emission rumen exhibited higher metabolic capacity but with lower functional redundancy compared to that of high-methane-emission cattle. Our findings also suggest that microbiomes associated with low methane yields are prevalent in specific functionalities such as active fiber hydrolysis and succinate production, which may enhance their contributions to feed conversion in the host animal. This study provides an alternate genome-centric means to investigate the microbial ecology of the rumen and identify microbial and metabolic intervention targets that aim to reduce greenhouse gas emissions in livestock production systems.<br><br>IMPORTANCE: Ruminant livestock are major contributors to global methane emissions, largely through microbial fermentation in the rumen. Understanding how microbial communities vary between high- and low-methane-emitting animals is critical for identifying mitigation strategies. This study leverages a genome-centric approach to link microbial metabolic traits to methane output in cattle. By reconstructing and functionally characterizing hundreds of microbial genomes, we observe that a low-methane-emission rumen harbors well-balanced, "streamlined" microbial communities characterized by high metabolic capacity and minimal metabolic overlap across populations (low functional redundancy). Our results demonstrate the utility of genome-level functional profiling in uncovering microbial community traits tied to climate-relevant phenotypes.}, }
@article {pmid40980756, year = {2025}, author = {Kosmopoulos, JC and Anantharaman, K}, title = {Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises.}, journal = {ArXiv}, volume = {}, number = {}, pages = {}, pmid = {40980756}, issn = {2331-8422}, abstract = {Viruses are the most abundant biological entities on Earth and play central roles in shaping microbiomes and influencing ecosystem functions. Yet, most viral genes remain uncharacterized, comprising what is commonly referred to as "viral dark matter." Metagenomic studies across diverse environments consistently show that 40-90% of viral genes lack known homologs or annotated functions. This persistent knowledge gap limits our ability to interpret viral sequence data, understand virus-host interactions, and assess the ecological or applied significance of viral genes. Among the most intriguing components of viral dark matter are auxiliary viral genes (AVGs), including auxiliary metabolic genes (AMGs), regulatory genes (AReGs), and host physiology-modifying genes (APGs), which may alter host function during infection and contribute to microbial metabolism, stress tolerance, or resistance. In this review, we explore recent advances in the discovery and functional characterization of viral dark matter. We highlight representative examples of novel viral proteins across diverse ecosystems including human microbiomes, soil, oceans, and extreme environments, and discuss what is known, and still unknown, about their roles. We then examine the bioinformatic and experimental challenges that hinder functional characterization, and present emerging strategies to overcome these barriers. Finally, we highlight both the fundamental and applied benefits that multidisciplinary efforts to characterize viral proteins can bring. By integrating computational predictions with experimental validation, and fostering collaboration across disciplines, we emphasize that illuminating viral dark matter is both feasible and essential for advancing microbial ecology and unlocking new tools for biotechnology.}, }
@article {pmid40980429, year = {2025}, author = {Rahman, MS and Chlingaryan, A and Thomson, PC and Islam, MR and Lees, AM and Gregorini, P and Pereira, FC and Clark, CEF}, title = {In vitro simulation of drinking events in cattle.}, journal = {MethodsX}, volume = {15}, number = {}, pages = {103593}, pmid = {40980429}, issn = {2215-0161}, abstract = {Drinking causes a rapid decline in reticulorumen temperature (RT) followed by an exponential recovery, which may potentially impact the reticulorumen ecosystem. However, the nexus between drinking events and their effects on ruminal fermentation and microbial diversity has not yet been studied, either in vitro or in vivo. Although artificial (in vitro) rumen systems are widely used in ruminant research to simulate the reticulorumen environment, no such simulation has been described to consider the impact of drinking events on the reticulorumen environment. Therefore, we have developed a method for the in vitro simulation of drinking events in the fermentation jar where the jar temperature was considered a proxy for RT is reduced by adding a measured amount of cold water to the water bath, and the subsequent recovery period is achieved following a temperature profile regulated by a heating immersion circulator. This method enables the replication of RT fluctuations from drinking events, allowing for the monitoring of their impact on fermentation characteristics and microbial ecology in future research. The features of this method are: Creation of a hypothetical drinking event Estimation of volume and temperature of cold water for a drinking event Establishing a temperature profile to regulate the recovery period.}, }
@article {pmid40978322, year = {2025}, author = {Phonlamai, A and Khetkorn, W and Thongpool, V and Panyachanakul, T and Suriyachadkun, C and Kitpreechavanich, V and Sakdapetsiri, C and Lomthong, T}, title = {Profiling of the bacterial community and the degradative capability of newly isolated poly(lactic acid) (PLA)- and poly(butylene succinate) (PBS)-degrading bacteria from coastal samples.}, journal = {3 Biotech}, volume = {15}, number = {10}, pages = {352}, pmid = {40978322}, issn = {2190-572X}, abstract = {UNLABELLED: The coastal area of Thailand is a tropical marine environment with high microbial diversity, providing favorable conditions for microorganisms capable of degrading bioplastics. The current study aimed to investigate the bacterial community profiling of four samples collected from a coastal area in Thailand and to isolate the potential thermophilic bacteria with the ability to produce bioplastic-degrading enzymes. Our analysis revealed site-specific predominant genera: Brevibacillus in seawater (64.34 ± 0.27%), Pseudomonas in plastic waste (39.69 ± 3.77%), Pseudoalteromonas in soil (54.83 ± 2.40%), and Psychrobacter in moss rock (41.01 ± 1.67%). The thermophilic bacteria, including 6 poly(lactic acid) (PLA)- and 3 poly(butylene succinate) (PBS)-degrading bacteria, were isolated using a two-step technique in an emulsified polymer medium. These nine isolates were classified into five species across four genera: Brevibacillus gelatini, Microbispora rosea, Actinomadura keratinilytica, Paenibacillus thermoaerophilus, and P. ginsengihumi. Among these, Actinomadura keratinilytica LDF1 and M. rosea BS2-4 exhibited the highest enzymatic activities for PLA and PBS degradation (0.87 ± 0.11 U/mL and 0.31 ± 0.03 U/mL, respectively). Scanning electron microscopy confirmed the degradation capabilities of these strains in culture medium. Crude enzyme from the LDF1 strain demonstrated versatility in degrading various types of PLA, including PLA film, PLA powder, commercial cup, and commercial cutlery, while the strain BS2-4 enzyme effectively degraded PBS in film, powder, commercial cup, and commercial drinking straw. These findings advance our understanding of coastal microbial ecology and also highlight the potential of indigenous bacteria for bioplastic waste management, contributing to sustainable environmental solutions.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04521-0.}, }
@article {pmid40976393, year = {2025}, author = {Cui, J and Dörmann, P}, title = {Microbial degradation of hydrocarbons from petroleum assisted by biosurfactants: pathways and bioremediation potential.}, journal = {Biochimie}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.biochi.2025.09.011}, pmid = {40976393}, issn = {1638-6183}, abstract = {Petroleum pollution from oil extraction, transportation, and industrial activities poses significant threats to marine ecosystems and socioeconomic stability due to the high toxicity of alkanes and polycyclic aromatic hydrocarbons (PAHs) to many organisms. Traditional remediation methods, including physical removal and chemical oxidation, are often costly and ecologically disruptive. Microbial degradation, facilitated by hydrocarbonoclastic bacteria like Pseudomonas aeruginosa and Alcanivorax borkumensis, offers a sustainable alternative by converting hydrocarbons into non-toxic CO2 and water. This review examines the degradation pathways of aliphatic and aromatic hydrocarbons by these bacteria, highlighting key enzymatic mechanisms and the pivotal role of biosurfactants-specifically rhamnolipids, and glycine-glucolipid-in enhancing hydrocarbon bioavailability. It also delves into the biosynthesis of these biosurfactants, along with the involvement of non-ribosomal peptide synthetases (NRPS) in producing lipopeptide biosurfactants such as surfactin. Additionally, the review addresses the challenges associated with scaling up biosurfactant production for bioremediation applications. Through a synopsis of recent research, this work proposes strategies to optimize biosurfactant efficacy, contributing to environmental sustainability and advancing the field of microbial ecology.}, }
@article {pmid40976174, year = {2025}, author = {Allouche, M and Bouzidi, I and Lassoued, A and Sellami, B and Derguini, A and Idres, T and Badraoui, R and Ben Hamadi, N and Chaudhary, AA and Bendif, H and Pacioglu, O and Abd-Elkader, OH and Boufahja, F and Plavan, G}, title = {How do polyethylene microplastics, ibuprofen, and sediment mud levels influence meiobenthic features and their interactions with CeO2-doped ZnO nanoparticles? Answers through nematode taxon/functional traits, allometry of Metoncholaimus pristiurus, and computational analyses.}, journal = {Marine environmental research}, volume = {212}, number = {}, pages = {107564}, doi = {10.1016/j.marenvres.2025.107564}, pmid = {40976174}, issn = {1879-0291}, abstract = {Microplastic pollution and pharmaceutical contaminants represent growing environmental threats, particularly in aquatic ecosystems. This research examines the individual and combined effects of polyethylene microplastics, sediment particles, and ibuprofen on meiobenthic species, specifically free-living nematodes. Abundance changes, species diversity, and functional characteristics were monitored during a 30-day microcosm experiment. The binding affinities and molecular interactions of both contaminants with germ-line development protein 3 (GLD-3) and sex-determining protein (SDP) have been assessed using computational modeling assays. The results indicate that contamination significantly alters nematode communities, with pronounced declines in sensitive species such as Dorylaimopsis timmi and Halalaimus longicaudatus. At the same time, opportunistic taxa like Paramonhystera pellucida and Parodontophora beviseta exhibited increased abundance, resulting in a worldwide reduction of nematofauna (432 individuals in controls compared to 233-322 individuals in treated communities). The experimental results and computational assays supported each other. Furthermore, the strongest negative effects were observed in combined polyethylene-ibuprofen treatments, suggesting a synergistic interaction that enhances toxicity. Polyethylene microplastics appear to modulate the bioavailability and toxicity of ibuprofen, potentially exacerbating its impact on benthic communities. According to regressions linking body dimensions, the combination of polyethylene microplastics and ibuprofen with ZnO-CeO2 (slopes: 0.53629 and 0.31718, respectively) nanoparticles enhanced the growth rate of the nematode Metoncholaimus pristiurus, compared to the control group (slopes: 0.05775).}, }
@article {pmid40976099, year = {2025}, author = {Saci, S and Nabti, EH and Sebbane, H and Issad, HA and Boufahja, F and De Martino, L and Nocera, FP and Bendif, H and Derguini, A and Hamadi, NB and Chaudhary, AA and Rebai, A and Cruz, C and Idres, T and Houali, K}, title = {Exploring Thymus vulgaris Extract as a Phytotherapeutic Agent: A Multifaceted Approach to tackle Avian Colibacillosis and Drug Resistance.}, journal = {Poultry science}, volume = {104}, number = {11}, pages = {105794}, doi = {10.1016/j.psj.2025.105794}, pmid = {40976099}, issn = {1525-3171}, abstract = {Avian colibacillosis remains a major threat to poultry production and food security, whereas its antibiotic-based control accelerates antimicrobial resistance. This study investigated the antibacterial potential of the hydroethanolic extract of Thymus vulgaris, alone and in combination with antibiotics, against avian pathogenic Escherichia coli (APEC). The phytochemical composition of the extract was analyzed by HPLC, while its antibacterial activity was assessed using agar diffusion and minimum inhibitory concentration (MIC) assays. Antibiotic-extract interactions were evaluated by the checkerboard method, and mechanisms of action were explored through assays targeting membrane permeability, proton pump inhibition, catalase inhibition, oxidative stress, and biofilm formation. Its antioxidant, anti-inflammatory, and cytotoxic activities were also evaluated. HPLC analysis revealed 16 phenolic compounds, including rosmarinic, ferulic, and salicylic acids, as well as flavonoids such as quercetin and luteolin, with an extraction yield of 15% ± 0.55. The extract displayed significant antibacterial activity (MIC: 5.46-10.93 mg/ml, p < 0.05). In synergy tests, the extract enhanced ampicillin efficacy 4-8-fold and showed additive effects with ciprofloxacin and tetracycline (2-4-fold). Mechanistic assays demonstrated disruption of bacterial membranes (32.66% electrolyte leakage, p < 0.05), inhibition of H[+]-ATPase proton pumps (p < 0.05), catalase activity reduction by 79.2% (p < 0.05), >50% decrease in cell hydrophobicity, and inhibition of biofilm formation (49.07-72.47%), alongside eradication of mature biofilms (41.89-64.67%) (p < 0.05). Beyond antimicrobial effects, the extract exhibited notable antioxidant capacity. In DPPH radical scavenging, the extract showed an IC50 of 9.76 ± 0.228 μg/ml (p < 0.05), while in the TAC assay, it reached 467.25 ± 1.889 μg/ml (p < 0.05), and it reduced ampicillin-induced lipid peroxidation by 42.85% (p < 0.05). Anti-inflammatory testing revealed inhibition of protein denaturation (4.95-52.48% at 15-2000 µg/ml, p < 0.05), although weaker than aspirin. Hemolysis assays confirmed the extract was non-hemolytic at concentrations up to 11 mg/ml (p < 0.05). In conclusion, Thymus vulgaris extract demonstrated safe, multi-target bioactivity, supporting its potential as a promising alternative to combat avian colibacillosis and antimicrobial resistance.}, }
@article {pmid40975416, year = {2025}, author = {Bi, Z and Wang, X and Fu, H and Huang, Y}, title = {Carbon source shaped microbial ecology, metabolism and performance in biofilm system for simultaneous phosphorus recovery and nitrogen removal.}, journal = {Environmental research}, volume = {}, number = {}, pages = {122800}, doi = {10.1016/j.envres.2025.122800}, pmid = {40975416}, issn = {1096-0953}, abstract = {The application of biofilm-based phosphorus enrichment technology has been hampered by the limited information on the performance, microbial interactions and metabolic patterns of dominant functional bacteria, especially those fed with complex carbon sources conditions. In this study, three representative carbon sources contained in real sewage, i.e., volatile fatty acids (VFAs), glucose, and amino acids were selected as the complex carbon sources. The comparison in phosphorus removal/enrichment performance, carbon utilization, and metabolic characteristics were performed during the biofilm system changed the sole carbon source (acetate sodium) feeding to complex carbon source feeding gradually. The performance reduction and instability were observed in initial stage of complex carbon source feeding, while the phosphorus removal/enrichment efficiency improved significantly after long-term acclimation by extending the anaerobic HRT. The concentration of phosphorus enrichment solution exceeded 50 mg/L, meanwhile the total nitrogen and total phosphorus removal efficiencies over 82% and 97%, respectively. Intriguing, intracellular organic phosphorus (OP) contents fluctuated with phosphorus uptake and release, which may be a hint of the important role of OP in PAOs energy conversion. Complex carbon sources induced the succession of biofilm community, especially the enrichment of hydrolytic fermentation bacteria, and a more intricate microbial interaction network among functional microbiota. The co-occurrence of the EMP and ED pathways during glycolysis implied more extensive carbon utilization pathways, and amino acids was speculated to complement intracellular energy metabolism via the tricarboxylic acid cycle (TCA). This study demonstrated that the biofilm systems have great potential to simultaneously achieve phosphorus removal and enrichment by using complex carbon sources in sewage wastewater.}, }
@article {pmid40972460, year = {2025}, author = {Arulananthan, A and Scholz, B and Karsten, U and Grossart, HP and Sigurbjörnsdóttir, A and Rolfsson, &#xd3; and Joerss, H and Duarte, B and Vilhelmsson, O&#xde;}, title = {Arctic and sub-Arctic marine diatom responses to PFAS exposure: Understanding physiological changes and resilience.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {289}, number = {}, pages = {107562}, doi = {10.1016/j.aquatox.2025.107562}, pmid = {40972460}, issn = {1879-1514}, abstract = {Per- and polyfluoroalkyl substances (PFAS) are persistent organic pollutants widely detected across diverse ecosystems. Despite regulatory bans on several PFAS compounds, PFAS remain prevalent in remote areas like the Arctic, raising significant ecological health concerns. This study addresses a critical knowledge gap regarding the effects of PFAS on unicellular primary producers, with a focus on diatom physiology and fitness. Two ecologically important Arctic and sub-Arctic diatom species, Cylindrotheca closterium and Thalassiosira pseudonana, as well as legacy long-chain PFAS, and two emerging PFAS replacements were investigated. Exposures were conducted for 10 days at three concentrations (100 mg/L, 1 mg/L, and 0.9 ng/L). Following the 10 d (short-term) toxicity assessment, one PFAS mixture was exposed for 28 days (long-term) at an environmentally relevant concentration of 0.9 ng/L. Physiological and biochemical responses, including growth, photosynthetic capacity, stress biomarkers, and metabolic changes, were assessed. Results revealed distinct impacts of PFAS on individual PFAS and their mixtures. Perfluorooctane sulfonic acid (PFOS), perfluorooctanoic acid (PFOA), perfluorononanoic acid (PFNA), perfluorododecanoic acid (PFDoA), perfluorotridecanoic acid (PFTrDA), and perfluorotetradecanoic acid (PFTeDA) often exhibited the most detrimental effects on both species relative to controls. PFAS mixtures exhibited synergistic impacts, with increasing effects as the number of PFAS compounds increased. Both diatoms exhibited significant reductions in growth and photochemical efficiency of photosystem II, along with elevated proline and total antioxidant activity, during short-term exposure to PFAS. During the long-term experiment, after the exponential growth phase (after 14 d), growth rates were not significantly different from those of the controls, suggesting potential compensatory responses over time. Despite the mild growth inhibition, enhanced biochemical activity relative to controls indicates sustained metabolic adjustment under prolonged PFAS exposure. These findings emphasize the potential impacts of PFAS, specially in mixtures, on disrupting primary producers in cold marine ecosystems, highlighting the need to assess the cumulative effects of pollutants on foundational Arctic biota.}, }
@article {pmid40972045, year = {2025}, author = {Feliu-Paradeda, L and Puig, S and Bañeras, L}, title = {Electron conductive compounds alter fermentative pathways and cooperation in Clostridium carboxidivorans and Clostridium acetobutylicum in co-culture.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf090}, pmid = {40972045}, issn = {1574-6941}, abstract = {The addition of conductive materials promotes interactions between bacteria as they facilitate the exchange of reducing equivalents among cells. In this work, the impact of electron conductive compounds (magnetite, activated carbon or iron salts) was investigated on a Clostridium acetobutylicum/Clostridium carboxidivorans co-culture. Co-culturing both species with soluble iron salts or magnetite significantly improved carbon recovery in liquid end-products (75-85% of added carbon) compared to control and activated carbon supplementation (50-55% of added carbon). The addition of magnetite enhanced the production of longer-chain acids and alcohols (C4 and C6) when compared to all other treatments and reached the highest production after 44 h of fermentation. This effect was not observed in C. carboxidivorans nor in C. acetobutylicum pure cultures, advocating for a cooperation between the two species. Among comparisons to the behaviour observed in pure cultures, we suggest magnetite was first used as a sink of reduced equivalents produced by C. carboxidivorans and later as a source of energy for C. acetobutylicum for the production of elongated short-chain fatty acids and alcohols. We propose that adding magnetite (iron) could be an effective strategy to enhance alcohol production in synthetic clostridia consortia.}, }
@article {pmid40970936, year = {2025}, author = {Uddin, MR and Saifullah, S}, title = {Type II toxin-antitoxin systems as stress-responsive survival circuits in archaea and bacteria.}, journal = {Archives of microbiology}, volume = {207}, number = {11}, pages = {269}, pmid = {40970936}, issn = {1432-072X}, support = {23-FoBST-02//Research Cell, JUST/ ; }, mesh = {*Toxin-Antitoxin Systems/genetics ; *Archaea/genetics/physiology/metabolism ; *Bacteria/genetics/metabolism ; *Stress, Physiological ; Bacterial Proteins/genetics/metabolism ; DNA Repair ; Phylogeny ; *Antitoxins/genetics/metabolism ; Bacterial Toxins/genetics/metabolism ; Biofilms/growth &amp; development ; }, abstract = {Simple early lifeforms with relatively small genomes were evolved with certain genetic circuitry to better their stress-response mechanism which significantly enhances their survival during stress, hypothetically. In this review, we conducted a comprehensive investigation to identify survival-focused genetic circuitry in microorganisms, focusing on type II toxin-antitoxin (TA) systems, particularly sought after due to their ubiquitousness in nature, composed of two functionally coordinated genes: one that transiently inhibits reproduction during stress and another that represses this inhibition under normal conditions, while simultaneously promoting DNA repair under stress. Our comprehensive analysis of 22 type II TA systems reveals diverse roles, including dormancy induction, biofilm formation, pathogenicity and DNA repair. While canonical modules such as HigAB and RelBE are well-characterized, others like ParDE, Kid-Kis, and YafO-YafN remain understudied in the context of dormancy or biofilm involvement. Additionally, systems such as DarT-DarG, YafQ-DinJ and CcdB-CcdA have been implicated in DNA repair pathways, suggesting broader functional repertoires beyond growth inhibition. Phylogenetic analyses further reveal that TA systems such as VapC-VapB and MazF-MazE are widely distributed among bacteria, archaea, and cyanobacteria, including lineages thriving in extreme environments like deep-sea hydrothermal vents, which are considered potential sites for the emergence of early life. The presence of TA loci in ancient microorganisms like Methanocaldococcus jannaschii and Microcystis aeruginosa hints at their ancient origin and possible role in microbial survival on early Earth. This review synthesizes current knowledge on type II TA systems as stress-responsive survival circuits and highlights their significance in microbial ecology, evolution, and adaptation.}, }
@article {pmid40970741, year = {2025}, author = {Lee, W and Kim, G and Park, T}, title = {Refining microbial biomarker identification in rumen microbiome studies: a viability PCR-based approach.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0142925}, doi = {10.1128/aem.01429-25}, pmid = {40970741}, issn = {1098-5336}, abstract = {The rumen microbiome significantly affects host performance, influencing feed efficiency, nitrogen utilization, and methane emission. However, conventional DNA-based marker gene sequencing cannot distinguish between viable and non-viable microbes, leading to inaccurate microbiota analyses. Viability PCR (v-PCR) with propidium monoazide (PMA) can inhibit DNA amplification from membrane-compromised cells, allowing the detection of viable microbes in rumen cultures. Therefore, this study aims to identify conditions for applying PMA in rumen culture experiments using qPCR and to examine its effect on the rumen microbial community using 16S rRNA gene sequencing in standard in vitro experiments. PMA treatment conditions were applied using a fivefold inoculum dilution, 100 µM PMA concentration, 30 min dark incubation, and 20 min light exposure, validated by a decrease in absolute abundance in heat-treated samples. When applied to in vitro rumen experiments, PMA treatment reduced bacterial evenness and induced shifts in key bacterial and archaeal taxa. Additionally, it affected major functional profiles of the microbiota. PMA treatment increased the relative abundance of Ruminobacter [log fold change (LFC) = 0.52] and Succinivibrio (LFC = 0.68) at 0 h (no incubation), along with Ruminobacter (LFC = 0.83) after 24 h of incubation, while decreasing that of Xylanibacter (LFC = -0.39) at 24 h. These shifts align with those of RNA-based studies showing higher Succinivibrionaceae abundance than Prevotellaceae, supporting the effectiveness of PMA in capturing active microbial dynamics. PMA-based v-PCR offers a reliable alternative to RNA-based methods, improving microbial community assessments and facilitating the identification of viability-associated microbial biomarkers in rumen studies.IMPORTANCEThis study identifies the optimal conditions for applying propidium monoazide (PMA) in in vitro rumen experiments to selectively amplify DNA from viable microorganisms while suppressing amplification from nonviable ones. PMA-based viability PCR (v-PCR) improves the accuracy of microbial community analysis by selectively detecting viable microorganisms, addressing the limitations of conventional DNA-based methods. Additionally, this approach provides a potential cost-effective alternative to RNA-based analyses, offering a practical tool for studying rumen microbial ecology.}, }
@article {pmid40970700, year = {2025}, author = {Havlena, ZE and Lucero, K and Graham, HV and Stern, JC and Wankel, SD and Mainiero, M and Jones, DS}, title = {Microbial ecology of acidic, biogenic gypsum: community structure and distribution of extremophiles on freshly formed and relict sulfate deposits in a hydrogen sulfide-rich cave.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0139725}, doi = {10.1128/aem.01397-25}, pmid = {40970700}, issn = {1098-5336}, abstract = {UNLABELLED: Sulfate minerals are abundant on the Martian surface, and many of these evaporite deposits are thought to have precipitated from acidic fluids. On Earth, gypsum (CaSO4•2H2O) and other sulfates sometimes form under acidic conditions, so exploring the extremophilic life that occurs in these mineral environments can help evaluate the astrobiological potential of acid sulfate depositional settings. Here, we characterized the microbial communities associated with acidic gypsum deposits in a sulfuric acid cave, where sulfate precipitation is driven by sulfide-oxidizing bacteria and archaea. We used 16S rRNA gene sequencing and cell counts to characterize gypsum-associated microorganisms in freshly formed and relict deposits throughout the cave, to test how microbial community composition and abundance would vary with distance from the sulfidic water table and with the concentration of H2S(g) and other gases in the cave atmosphere. We found that actively forming gypsum in the lower cave levels was colonized by low-diversity communities that have few cells compared to other environments in the cave. The most abundant taxa were Acidithiobacillus, Metallibacterium, Mycobacteria, and three different Thermoplasmatales-group archaea, which occupied distinct niches based on proximity to sulfidic streams and the concentration of gases in the cave air. By contrast, deposits in older cave levels had more diverse communities that were distinct from those associated with freshly formed gypsum and likely represent a community reliant on different energy resources. These findings show that acidic sulfate deposits serve as habitats for extremophilic microorganisms and broaden our knowledge of the life associated with terrestrial sulfates.<br><br>IMPORTANCE: Gypsum and other sulfate salts are common on Mars, and many of these deposits are thought to have formed from acidic fluids early in the planet's history. Understanding the life that survives and thrives in similar environments on Earth is therefore crucial for evaluating whether these Martian sulfates are or ever were habitable. One such environment where acidic gypsum occurs is in sulfuric acid caves, where extremophilic microorganisms drive the precipitation of sulfate minerals by oxidizing hydrogen sulfide gas from the cave atmosphere. Here, we characterized the communities of microorganisms on freshly formed and ancient gypsum in the Frasassi Caves and found that the gypsum deposits hosted microbial communities that changed based on chemical energy availability and the age of the gypsum. Our findings underscore the importance of chemical and microbiological interactions in shaping habitable niches and provide context for searching for past or present life in acidic Martian sulfates.}, }
@article {pmid40969862, year = {2025}, author = {Wang, H and Lindemann, E and Liebmann, P and Varsadiya, M and Svenning, MM and Waqas, M and Petters, S and Richter, A and Guggenberger, G and Barta, J and Urich, T}, title = {Methane-cycling microbiomes in soils of the pan-Arctic and their response to permafrost degradation.}, journal = {Communications earth &amp; environment}, volume = {6}, number = {1}, pages = {748}, pmid = {40969862}, issn = {2662-4435}, abstract = {The methane-cycling microbiomes play crucial roles in methane dynamics. However, little is known about their distributions on a pan-Arctic scale as well as their responses to the widespread permafrost degradation. Based on 621 datasets of 16S rRNA gene amplicons from intact permafrost soils across the pan-Arctic, we identified only 22 methanogen and 26 methanotroph phylotypes. Their relative abundances varied significantly between sites and soil horizons. Only four methanogen phylotypes were detected at all locations. Remarkably, the permafrost soil methane filter was almost exclusively dominated by some obligate methanotroph (Methylobacter-like) phylotypes. However, a case study in Alaska suggests that atmospheric methane oxidizing bacteria (Methylocapsa-like phylotypes) dominated methanotrophs in a drier condition after permafrost degradation. These findings point towards a few key microbes particularly relevant for future studies on Arctic methane dynamics in a warming climate and that under future dry conditions, increased atmospheric methane uptake in Arctic upland soils may occur.}, }
@article {pmid40968530, year = {2025}, author = {Popov, IV and Chikindas, ML and Venema, K and Ermakov, AM and Popov, IV}, title = {KEGGaNOG: A Lightweight Tool for KEGG Module Profiling From Orthology-Based Annotations.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e70269}, doi = {10.1002/mnfr.70269}, pmid = {40968530}, issn = {1613-4133}, support = {23-14-00316//Russian Science Foundation/ ; }, abstract = {Functional interpretation of bacterial genomes and metagenomes is essential for applications ranging from microbial ecology to probiotic development. KEGGaNOG is a lightweight and scalable Python tool that enables pathway-level profiling by translating orthology-based annotations into KEGG module completeness scores. KEGGaNOG accepts input from eggNOG-mapper annotations and supports both individual genome and multi-sample analyses. It calculates completeness scores for KEGG modules using internally integrated KEGG-Decoder logic and offers a suite of visualization options, including heatmaps, grouped summaries, barplots, radar plots, and correlation networks. We demonstrate its use on 11 well-characterized bacterial genomes, including several probiotic strains. KEGGaNOG accurately captured core biosynthetic capabilities and highlighted functionally informative differences across samples, such as vitamin biosynthesis, stress-response pathways, and transport systems. KEGGaNOG provides a practical framework for high-throughput functional annotation and comparative metabolic profiling in bacterial genomics and microbiome research. It is particularly well suited for preliminary analysis of novel or uncharacterized strains and is applicable to both isolate and metagenome-derived data. In the context of probiotic research, KEGGaNOG supports mechanistic exploration and strain selection by linking genomic content to functional capacity in a reproducible and interpretable manner.}, }
@article {pmid40968492, year = {2025}, author = {Dong, X and Chu, Y and Tong, Z and Yi, X and Sun, M and Meng, D and Gao, T and Wang, M and Duan, J}, title = {The adsorption mechanism of tembotrione on modified biochar and its impact on soil microbial communities.}, journal = {Pest management science}, volume = {}, number = {}, pages = {}, doi = {10.1002/ps.70225}, pmid = {40968492}, issn = {1526-4998}, support = {2023YFD1400900//National Key Research and Development Program of China/ ; 32372609//National Natural Science Foundation of China/ ; 32302414//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Tembotrione, a triketone herbicide with high mobility and persistence, poses significant environmental risks by disrupting soil microbial ecology and threatening crop rotation systems. This study investigates the adsorption mechanism and ecological benefits of hydrogen peroxide-modified biochar (HPBC-700) for mitigating tembotrione contamination in soil environments.<br><br>RESULTS: The oxidative modification introduces abundant oxygen-containing functional groups, including hydroxyl, carboxyl, and carbonyl, which substantially enhance the biochar's adsorption capacity and surface reactivity. Density Functional Theory (DFT) calculations and non-covalent interaction analyses reveal that hydrogen bonding and &#x3c0;-&#x3c0; stacking are the dominant adsorption mechanisms. Among the functional groups, carboxyl contributes the strongest binding due to its ability to form dual hydrogen-bond interactions. In addition to physically immobilizing the herbicide, HPBC-700 improves soil microbial diversity and enriches degradation-related functional taxa, particularly Proteobacteria and Acinetobacter, thereby alleviating pesticide-induced ecological stress.<br><br>CONCLUSION: These findings highlight the dual function of HPBC-700 as both an efficient adsorbent and a regulator of soil microbiomes, providing a sustainable strategy for pesticide remediation and agroecosystem restoration. This work advances the understanding of biochar-pesticide interactions and offers new insights into integrating chemical immobilization with ecological recovery for effective soil pollution control. &#xa9; 2025 Society of Chemical Industry.}, }
@article {pmid40968405, year = {2025}, author = {Trubl, G and Probst, AJ}, title = {Clarifying Terminology in Microbial Ecology: A Call for Precision in Scientific Communication.}, journal = {Environmental microbiology}, volume = {27}, number = {9}, pages = {e70177}, doi = {10.1111/1462-2920.70177}, pmid = {40968405}, issn = {1462-2920}, support = {SCW1632//U.S. Department of Energy Office of Biological and Environmental Research through the Genomic Science Program and the Lawrence Livermore National Laboratory/ ; CRC 1439/1//Deutsche Forschungsgemeinschaft/ ; CRC 1439/2//Deutsche Forschungsgemeinschaft/ ; 426547801//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Terminology as Topic ; *Ecology ; *Microbiota ; *Microbiology ; Communication ; }, abstract = {The rapid evolution of microbiology as a field of research has led to the introduction of new terminology and the adaptation of existing terms. However, inconsistencies in the use of these terms, including variations across different scientific disciplines, can lead to confusion and miscommunication within the scientific community. This article discusses the importance of precise terminology in microbiome research, highlighting examples where terms have been misused or redefined without clear justification. We also present a list of frequently used terms in microbial ecology along with their specific definitions. We argue that the misuse of terminology can hinder scientific progress by creating ambiguity and misunderstanding. To address this, we propose a set of guidelines for the consistent use of key terms and provide clear definitions for some of the most commonly misused or newly introduced terms in the field. The definitions provided herein will also function as a guide for young researchers new to the field of microbial ecology. Accurate and consistent use of terminology is crucial for effective communication and collaboration in microbiology research. By adhering to standardised definitions, researchers can ensure that their work is clearly communicated and contributes meaningfully to the progress of science.}, }
@article {pmid40967376, year = {2025}, author = {Huang, M and Lian, Y and Xie, C}, title = {A rare case of recurrent abdominal pain with facial edema.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2025.09.019}, pmid = {40967376}, issn = {1528-0012}, }
@article {pmid40969174, year = {2024}, author = {Matz, LM and Shah, NS and Porterfield, L and Stuyck, OM and Jochum, MD and Kayed, R and Taglialatela, G and Urban, RJ and Buffington, SA}, title = {Gut pathobiont enrichment observed in a population predisposed to dementia, type 2 diabetics of Mexican descent living in South Texas.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {}, pmid = {40969174}, issn = {2813-4338}, abstract = {Type 2 diabetes (T2D) is a common forerunner of neurodegeneration and accompanying dementia, including Alzheimer's Disease (AD), yet the mechanisms underlying this comorbidity remain unresolved. Individuals of Mexican descent living in South Texas have increased prevalence of comorbid T2D and early onset AD, despite low incidence of the APOE-ε4 risk variant among the population and an absence of a similar predisposition among relatives residing in Mexico - suggesting a role for environmental factors in coincident T2D and AD susceptibility. We therefore sought to test if differences in gut community structure could be observed in this population prior to any AD diagnosis. Here, in a small clinical trial (ClinicalTrials.gov Identifier NCT04602650), we report evidence for altered gut microbial ecology among subjects of Mexican descent living in South Texas with T2D (sT2D) compared to healthy controls without T2D (HC), despite no differences in expressed dietary preferences. We performed metataxonomic 16S rRNA gene amplicon sequencing of study participant stool samples. Although no significant decrease in microbial alpha diversity was observed between sT2D gut communities versus those of HC, body mass index was identified as a driver of gut community structure. Intriguingly, we observed a significant negative association of Faecalibacterium with T2D and an increase in the abundance of pathobionts Escherichia-Shigella, Enterobacter, and the erysipelotrichial species Clostridia innocuum among sT2D gut microbiota, as well as differentially abundant gene and metabolic pathways. Future large-scale, longitudinal sequencing efforts of the gut microbiome of individuals with T2D who go onto develop AD might identify key actors among "disease state" microbiota that contribute to increased susceptibility to comorbid dementia among type 2 diabetics. Finally, we identified candidate microbiome-targeted approaches for the treatment of T2D.}, }
@article {pmid40966281, year = {2025}, author = {Dai, J and Chen, C and Zhai, ZQ and Gao, AX and Johnson, DR and Kopittke, PM and Zhao, FJ and Wang, P}, title = {The balance between microbial arsenic methylation and demethylation in paddy soils underpins global arsenic risk and straighthead disease in rice.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {38}, pages = {e2508311122}, doi = {10.1073/pnas.2508311122}, pmid = {40966281}, issn = {1091-6490}, support = {42325701 W2411035//National natural science foundation of china/ ; }, mesh = {*Oryza/microbiology/metabolism ; *Arsenic/metabolism/toxicity ; *Soil Microbiology ; Methylation ; Soil/chemistry ; *Plant Diseases/microbiology ; *Soil Pollutants/metabolism ; Bacteria/metabolism/genetics ; Cacodylic Acid/metabolism ; Food Contamination/analysis ; }, abstract = {Arsenic contamination in rice poses a global challenge to food safety and agricultural productivity, as toxic methylated arsenic species-dimethylarsinic acid (DMA) and its highly toxic derivative, methylated monothioarsenate (DMMTA)-accumulate in rice grains. These arsenic species endanger human health and trigger rice straighthead disease, a crop disorder that drastically reduces yields. However, the microbial ecological processes driving arsenic speciation in paddy soils, and their link to striking geographic disparities in rice arsenic speciation profiles and disease prevalence, remain poorly understood. Here, we integrate soil chronosequences spanning 1 to 2,000 y of rice cultivation, a global metagenomic survey of 801 paddy soils, controlled incubations, and field surveys to demonstrate that the balance between arsenic-methylating and arsenic-demethylating microbes is the key determinant of rice grain arsenic speciation and straighthead disease susceptibility. We show that young and moderate-age paddy soils (<700 y), common in regions such as the Americas and Europe, are enriched in arsenic-methylating bacteria, leading to elevated DMA and DMMTA in soils and rice grains. In contrast, ancient paddies in Southeast Asia harbor robust populations of DMA-demethylating methanogenic archaea that effectively mitigate the buildup of these toxic arsenic species. We identify core microbial taxa whose abundances serve as predictive biomarkers and construct a global risk map linking a high methylator-to-demethylator ratio in soils with increased straighthead disease incidence. These findings advance our understanding of arsenic biogeochemistry in agroecosystems and establish a predictive framework for identifying regions at elevated risk of arsenic-induced crop disorders and food contamination.}, }
@article {pmid40965595, year = {2025}, author = {Nieto, EE and Ghanem, N and Cammarata, RV and Borim Corrêa, F and Coppotelli, BM and Chatzinotas, A}, title = {Effects of a novel Paraburkholderia phage IPK on the phenanthrene degradation efficiency of the PAH-degrading strain Paraburkholderia caledonica Bk.}, journal = {Biodegradation}, volume = {36}, number = {5}, pages = {86}, pmid = {40965595}, issn = {1572-9729}, mesh = {*Phenanthrenes/metabolism ; Biodegradation, Environmental ; *Polycyclic Aromatic Hydrocarbons/metabolism ; *Bacteriophages/genetics/isolation &amp; purification/physiology/metabolism ; Soil Pollutants/metabolism ; *Burkholderiaceae/virology/metabolism ; Genome, Viral ; Soil Microbiology ; }, abstract = {Phages are a major cause of bacterial mortality, affecting bacterial diversity and ecosystem functioning. However, the impact of phage-host interactions in contaminated environments and their role in pollutant biodegradation have largely been overlooked. We isolated and characterized a novel phage that infects the PAH-degrading bacterium Paraburkholderia caledonica Bk from a polycyclic aromatic hydrocarbon (PAH)-contaminated soil and investigated the effect of different multiplicity of infection (MOI) ratios on the degradation efficiency of phenanthrene. The phage IPK is a temperate phage with a wide pH and temperature tolerance and a burst size of 80 PFU ml[-][1]. The phage was classified as a member of the Caudoviricetes and is related to Pseudomonas and Burkholderia phages. However, its low intergenomic similarity indicates that it is a new species. Three auxiliary metabolic genes (AMGs) related to amino acid metabolism and to bacterial growth regulation were identified in the phage genome. The highest multiplicity of infection (MOI 10) showed a rapid recovery of the host density and greater phenanthrene degradation than MOIs ranging from 0.01 to 1. This work highlights the important role of phage-host interactions in modulating the efficiency of pollutant degradation, which could be a key for improving the establishment of inoculants in bioremediation processes.}, }
@article {pmid40965271, year = {2025}, author = {Dell'Acqua, AN and Scicchitano, D and Simoncini, N and Mercanti, I and Leuzzi, D and Turroni, S and Corlatti, L and Rampelli, S and Colonna, M and Corinaldesi, C and Candela, M and Palladino, G}, title = {Ski Tourism Shapes the Snow Microbiome on Ski Slopes in the Italian Central Alps.}, journal = {Environmental microbiology reports}, volume = {17}, number = {5}, pages = {e70195}, doi = {10.1111/1758-2229.70195}, pmid = {40965271}, issn = {1758-2229}, mesh = {Italy ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; *Skiing ; *Snow/microbiology/virology ; RNA, Ribosomal, 16S/genetics ; *Tourism ; Humans ; Viruses/classification/genetics/isolation &amp; purification ; Metagenomics ; Seasons ; }, abstract = {Winter sports exert significant anthropogenic pressures on the snow microbiome, affecting the entire alpine ecosystem. The massive usage of artificial snow, human occupation, and the release of xenobiotics like microplastics or ski wax components on ski tracks can profoundly alter snow microbial ecology. Here, we reconstructed the temporal dynamics of the snow microbiome at three sites in the Italian Alps: inside and outside a ski track at the impacted site of Santa Caterina Valfurva and near Cancano lake as an unimpacted control. Using epifluorescence microscopy, 16S rRNA amplicon sequencing, and inferred metagenomics, we found that the snow microbiome inside the track presented a higher load of prokaryotes and viruses. Notably, N2-fixing microorganisms from cryospheric environments and host-associated taxa, like Terrisporobacter, Clostridium sensu stricto, Enterococcus, and Muribaculaceae, and the opportunistic pathogen Citrobacter characterised the impacted site. These microorganisms could originate from the river water used to produce artificial snow during winter. Our findings highlight the complexity and multifunctionality of the snow microbiome, where microorganisms with different ecological propensities can coexist, and the detectable impact of ski tourism, which enriches host-associated and xenobiotic-degrading microorganisms. This underscores the need for systematic monitoring and protection of the snow microbiome in the Alpine environment from anthropogenic threats.}, }
@article {pmid40965193, year = {2025}, author = {Armin, G and Boros, G and Kis, M and Burányi, M and Horváth, H and Krassován, K and Masuda, T and Bernát, G and Inomura, K}, title = {The effect of temperature on phytoplankton physiology: a mesocosm and modeling study.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0045725}, doi = {10.1128/spectrum.00457-25}, pmid = {40965193}, issn = {2165-0497}, abstract = {Strategies that focus on reducing nutrient loading to freshwater lakes have historically been successful in improving water quality by curbing large phytoplankton blooms. However, as waters warm, little is known about the resultant phytoplankton physiology and ensuing perturbations in the food web that may occur. Here, we designed a mesocosm experiment to investigate the impact of warming water on phytoplankton physiology and further validate a previously developed, coarse-grained model that predicts the key aspects of phytoplankton physiology, including elemental stoichiometry and macromolecular allocation, across varying temperatures. We found that higher temperatures double the maximum cellular density (cells L[-1]) of phytoplankton, suggesting that high temperature stimulates cell division over maximizing carbon storage. Also, the cells in warmer waters dedicate fewer resources to proteins and RNA production, leading to higher fractions of carbon allocated to storage. This work illustrates the potential impact warming waters may have on the ecosystem, as higher fractions of carbohydrates are often associated with less nutritious food for higher trophic levels.IMPORTANCEWe take a novel approach to investigating the impact of warming on phytoplankton physiology by utilizing mesocosms and a coarse-grained cellular model. Previous work in this field tends to use idealized laboratory experiments, mesocosms, or models alone. By synthesizing model and mesocosm results, we test the model's ability to capture physiology in semi-natural environments. We conducted this experiment under phosphorus limitation and saw high cell densities in the heated, treatment tanks. Thus, warming waters may negate some successful management practices that curb eutrophication. With increased temperatures, we also observed increased N:P values in both the experimental and model results, which may be due to the combined effects of a lack of P storage, fewer enzymes required, and a corresponding decrease in RNA production. Our model predictions closely aligned to mesocosm observations, suggesting the capability of our model to represent lower trophic organisms in ecosystem models.}, }
@article {pmid40965139, year = {2025}, author = {Kim, M and Kamagata, Y and Park, S-J}, title = {Genomics and physiological characterizations of an acidotolerant nitrite-oxidizing Nitrospira enriched from freshwater pond.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0152225}, doi = {10.1128/aem.01522-25}, pmid = {40965139}, issn = {1098-5336}, abstract = {Nitrite-oxidizing bacteria (NOB) play a crucial role in global nitrogen cycling, yet their presence and adaptations in acidic environments remain poorly understood. This study unveils the cultivation and characterization of a novel acid-tolerant NOB, NS4 culture, affiliated with lineage II (Nitrospira_D) within the genus Nitrospira. Enriched and isolated from a freshwater pond sediment, NS4 culture exhibits remarkable physiological and genomic traits that shed light on NOB survival strategies in low pH conditions. NS4 culture demonstrates the optimal growth at pH 6 and 0.5 mM nitrite concentration, with a maximum growth rate of 0.62 day[-1]. Kinetic analyses reveal a high affinity for nitrite (Km(app) = 4.02 µM), suggesting adaptation to oligotrophic environments. Phylogenomic and genomic-relatedness analyses position NS4 culture as a novel member within the genus Nitrospira, for which we propose as "Candidatus Nitrospira acidotolerans." Genomic investigations indicate the presence of a complete reductive tricarboxylic acid cycle and genes for nitrite oxidation, confirming its chemolithoautotrophic lifestyle. Intriguingly, NS4 genome lacks complete pathways for cobalamin biosynthesis, implying a potential dependence on symbiotic partners for this essential cofactor. The NS4 genome harbors genes associated with acid resistance, including chaperones, transporters, and amino acid metabolism, suggesting a genetic potential for adaptation or resistance to low pH conditions. This discovery expands our understanding of NOB diversity and adaptability, offering insights into nitrogen cycling in acid-impacted ecosystems. The physiological and genomic traits of this acid-tolerant NOB open new insights for exploring the ecological significance of NOB in previously overlooked acidic habitats.IMPORTANCENitrite-oxidizing bacteria (NOB) are integral to the global nitrogen cycle, yet their adaptations to acidic environments remain poorly understood. This study introduces Candidatus Nitrospira acidotolerans, an acid-tolerant NOB highly enriched from freshwater pond sediment. By combining physiological and genomic analyses, this work reveals unique adaptations that enable survival and nitrite oxidation under low pH conditions. Notably, the NS4 culture demonstrates high nitrite affinity and resistance to acidic stress, suggesting its ecological significance in acid-impacted ecosystems. Additionally, NS4 genomic traits reveal genetic potential of metabolic dependencies, including reliance on symbiotic partners for cobalamin synthesis. These findings expand our understanding of NOB diversity and their role in nitrogen cycling under extreme conditions, offering novel insights into microbial ecology and potential applications in managing nitrogen processes in acidic environments.}, }
@article {pmid40961788, year = {2025}, author = {Kotowska, D and Báldi, A and Dobosy, P and Felföldi, T and Garamszegi, LZ and Horváth, Z and Kröel-Dulay, G and Ódor, P and Valkó, O and Batáry, P}, title = {Aligning land use with sustainability: Context-sensitive pathways forward.}, journal = {Journal of environmental management}, volume = {394}, number = {}, pages = {127252}, doi = {10.1016/j.jenvman.2025.127252}, pmid = {40961788}, issn = {1095-8630}, abstract = {The concept of sustainable development states that economic, social, and technological progress needs to be harmonised with nature. However, with the rate of global environmental deterioration now higher than at any time in human history and an ever-increasing human population, sustainability slips out of reach. One of the central processes and key issues in attaining sustainability is human use of and interaction with land resources. These can be described by two main processes that often go hand in hand: land conversion and land-use intensification. As these two phenomena accelerate, the level of disturbance in the environment increases, transforming natural ecosystems into altered, novel ecosystems or intensively used ecosystems. Depending on the degree of human-induced land alterations, different actions are needed to achieve and maintain sustainability. Conservation and prevention are necessary in natural areas with a low level of anthropogenic pressures. In areas that have already been disturbed by humans, sustainable management allows for a harmonious coexistence between humans and nature. Restoration and mitigation can help address the negative impacts of the most altered habitats. Sustainability, however, is not a fixed target but a dynamic condition shaped by evolving local contexts and global drivers. We advocate for transformative change grounded in flexible, context-sensitive land-use strategies that integrate ecological resilience, participatory governance, and institutional adaptability. With such systemic shifts, land systems can become catalysts for long-term sustainability.}, }
@article {pmid40832858, year = {2025}, author = {Gregor, R and Vercelli, GT and Szabo, RE and Gralka, M and Reynolds, RC and Qu, EB and Levine, NM and Cordero, OX}, title = {Vitamin auxotrophies shape microbial community assembly on model marine particles.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf184}, pmid = {40832858}, issn = {1751-7370}, support = {542395//Simons Collaboration on Principles of Microbial Ecosystems/ ; 653410//Simons Postdoctoral Fellowship in Marine Microbial Ecology/ ; OCE-2019589//Center for Chemical Currencies of a Microbial Planet Postdoctoral Fellowship/ ; #031//NSF Center for Chemical Currencies of a Microbial Planet/ ; }, mesh = {*Seawater/microbiology/chemistry ; *Bacteria/metabolism/classification/isolation &amp; purification/genetics ; *Vitamins/metabolism ; Polysaccharides/metabolism ; *Microbiota ; }, abstract = {Microbial community assembly is governed by the flow of carbon sources and other primary metabolites between species. However, central metabolism represents only a small fraction of the biosynthetic repertoire of microbes: metabolites such as antimicrobial compounds, signaling molecules, and co-factors are underexplored in their potential to shape microbial communities. Here, we focus on B vitamin exchange in marine bacterial communities that degrade polysaccharides, a key component of particulate organic matter. We found that in a screen of 150 natural isolates, almost a third were auxotrophs for one or more B vitamins. By measuring physiological parameters such as uptake affinities and comparing those to ambient seawater concentrations, we showed that marine bacteria live at the edge of vitamin limitation in the environment. To understand how auxotrophs survive in the open oceans, we used our experimental data to model vitamin cross-feeding on particles through both secretion and lysis. Our results highlight the importance of vitamin auxotrophies in shaping microbial community assembly and succession, adding another layer of complexity to the trophic structure of particle-associated communities.}, }
@article {pmid40959279, year = {2025}, author = {Liu, X and Chen, Z and Lin, J and Lian, Y and Gan, W and Liu, H and Huang, X and Mei, J and Ma, T and Lu, Z and Zeng, W and Gong, Y and Chen, S and He, W}, title = {DLGAP5 Promotes Acute Liver Injury via Hepatocyte Pyroptosis-Driven Macrophage Metabolic Reprogramming and M1 Polarization.}, journal = {International journal of biological sciences}, volume = {21}, number = {12}, pages = {5563-5585}, pmid = {40959279}, issn = {1449-2288}, mesh = {Animals ; *Pyroptosis/physiology/genetics ; *Hepatocytes/metabolism ; Mice ; *Macrophages/metabolism ; Methyltransferases/metabolism/genetics ; Mice, Inbred C57BL ; Mice, Knockout ; Male ; NLR Family, Pyrin Domain-Containing 3 Protein/metabolism/genetics ; Inflammasomes/metabolism ; Metabolic Reprogramming ; }, abstract = {Pyroptosis is a novel programmed cell death that exists in inflammatory diseases and methyltransferase-like 3 (METTL3) is a core N6-methyladenosine (m6A) modified methyltransferase that has been shown to regulate cell fate. However, the role of pyroptosis in acute liver injury (ALI) is still unknown and whether it is regulated by m6A modification needs to be elucidated. Here, Mettl3 mutant and Nlrp3 knockout mouse were constructed, CCl4- and TAA-induced ALI models were established and primary cells were isolated, and cell pyroptosis and m6A modification were evaluated. We found that hepatocyte pyroptosis is a key characteristic of ALI, and METTL3-mediated m6A modification was upregulated in hepatocytes during ALI. Inhibition of METTL3-mediated m6A modification alleviated hepatocyte pyroptosis and ALI. Through MeRIP-seq analysis and verification, Dlgap5 was determined as the target of METTL3-mediated m6A modification, which was regulated in an IGF2BP2-dependent manner. Mechanistically, METTL3 can bind to DLGAP5, and then DLGAP5 promoted pyroptosis through NF-κB-dependent NLRP3 inflammasome activation and direct potentiation of inflammasome structure formation and assembly. Mettl3 mutation or AT9283-mediated DLGAP5 inhibition alleviated pyroptosis and ALI. The effects of hepatocyte pyroptosis on cell interaction were then explored and we revealed that NLRP3 inflammasome and interleukin releasing by the GSDMD-N-dependent membrane pores from pyroptotic hepatocytes activated macrophage metabolic reprogramming and M1 polarization, further exacerbating ALI. Nlrp3 deficiency alleviated ALI by suppressing hepatocyte pyroptosis and blocking communication between macrophages and hepatocytes. Our findings indicate the potential mechanisms of ALI from an intercellular communication perspective, and targeted-inhibition of DLGAP5 and -blockade of hepatocyte-macrophage interaction provide promising strategies for ALI treatment.}, }
@article {pmid40958166, year = {2025}, author = {Ghaly, TM and Rajabal, V and Russell, D and Colombi, E and Tetu, SG}, title = {EcoFoldDB: Protein Structure-Guided Functional Profiling of Ecologically Relevant Microbial Traits at the Metagenome Scale.}, journal = {Environmental microbiology}, volume = {27}, number = {9}, pages = {e70178}, doi = {10.1111/1462-2920.70178}, pmid = {40958166}, issn = {1462-2920}, support = {CE200100029//ARC Centre of Excellence in Synthetic Biology/ ; //Macquarie University Research Fellowship/ ; }, mesh = {*Metagenome ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism ; Soil Microbiology ; Phylogeny ; *Microbiota/genetics ; Computational Biology/methods ; *Bacterial Proteins/genetics/chemistry ; *Databases, Protein ; Protein Conformation ; }, abstract = {Microbial communities are fundamental to planetary health and ecosystem processes. High-throughput metagenomic sequencing has provided unprecedented insights into the structure and function of these communities. However, functionally profiling metagenomes remains constrained due to the limited sensitivity of existing sequence homology-based methods to annotate evolutionarily divergent genes. Protein structure, more conserved than sequence and intrinsically tied to molecular function, offers a solution. Capitalising on recent breakthroughs in structural bioinformatics, we present EcoFoldDB, a database of protein structures curated for ecologically relevant microbial traits, and its companion pipeline, EcoFoldDB-annotate, which leverages Foldseek with the ProstT5 protein language model for rapid structural homology searching directly from sequence data. EcoFoldDB-annotate outperforms state-of-the-art sequence-based methods in annotating metagenomic proteins, in terms of sensitivity and precision. To demonstrate its utility and scalability, we performed structure-guided functional profiling of 32 million proteins encoded by 8000 high-quality metagenome-assembled genomes from the global soil microbiome. EcoFoldDB-annotate could resolve the phylogenetic partitioning of important nitrogen cycling pathways, from taxonomically restricted nitrifiers to more widespread denitrifiers, as well as identifying novel, uncultivated bacterial taxa enriched in plant growth-promoting traits. We anticipate that EcoFoldDB will enable researchers to extract ecological insights from environmental genomes and metagenomes and accelerate discoveries in microbial ecology.}, }
@article {pmid40957333, year = {2025}, author = {Sánchez, N and Merbach, I and Drabesch, S and Blagodatskaya, E and Jamoteau, F and Keiluweit, M and Bachelder, J and Tarkka, M and Muehe, EM}, title = {Bioavailability and phyto-extractability of metals in a peat-amended agricultural soil under climate stress.}, journal = {Journal of environmental management}, volume = {394}, number = {}, pages = {127167}, doi = {10.1016/j.jenvman.2025.127167}, pmid = {40957333}, issn = {1095-8630}, abstract = {Climate-induced mobilization of harmful metals in soils with a pH below 7 threatens food safety through plant uptake. While organic amendments like peat are known to immobilize metals, it remains unclear how their immobilization effectiveness changes under future climate scenarios and whether there is an optimal amendment threshold before immobilization turns into re-mobilization. This study assessed how varying peat input levels (3, 5 and 8 %) and projected climatic conditions (+4 °C, +320 ppmv CO2) affect metal fractionation, bioavailability, and uptake by a metal-tolerant plant in historically contaminated soils. Intermediate 5 % peat levels enhanced metal immobilization via organic matter complexation, reducing exchangeable Zn and Cd ∼2-fold compared to 3 % peat, despite acidification. At high 8 % peat input, a 0.65-unit pH decline and increased dissolved organic matter reversed this trend, increasing exchangeable Zn and Cd > 2-fold relative to 5 % peat. Chemical equilibrium modeling (WHAM VII) confirmed greater metal complexation with dissolved organic matter at higher 5-8 % peat levels. Under future climatic conditions-elevated temperature and CO2-metal immobilization improved at low 3 % peat input, likely due to stable organic matter and functional group buffering. Nevertheless, metal re-mobilization occurred at higher peat inputs, likely due to enhanced peat decomposition. Despite these variations, plant Cd uptake remained low across peat and climate treatments. This emphasizes peat's protective role against Cd while maintaining the plant's nutritional status for Zn. This study highlights the dual effects of peat amendments: intermediate levels optimize metal immobilization, but excessive amendments may destabilize harmful metals, especially under future conditions.}, }
@article {pmid40954372, year = {2025}, author = {Jauri, PV and Silva, C and Massa, AM}, title = {Early shifts in soil microbial community structure and functions upon application of a biofertilizer in a kaki (Diospyros kaki) orchard.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {40954372}, issn = {1874-9356}, abstract = {Biofertilizers are key tools for sustainable agriculture and soil health Maintenance, yet their specific effects on soil functions and microbiota remain unclear. In order to address this, we aimed to evaluate how a biofertilizer alters soil microbial communities, physicochemical properties, and functions after 18 months of periodical use in a kaki monoculture. We found that the biofertilizer indirectly reshaped microbial community structure-especially bacterial diversity-likely through interactions with the native microbiome. Functional changes included increased microbial biomass, nitrogen mineralization, and dehydrogenase activity, with reduced acid phosphatase activity. The composition of bacterial and fungal communities exhibited significant differences between biofertilizer-treated soils and control soils across most evaluated taxonomic levels. Biodiversity was altered with biofertilizer application in bacterial communities, while fungal communities were less affected. Microbial co-occurrence networks differed between the two soil treatments, although a few patterns were consistent among treated and control soils. A novel contribution of this work is the integration of co-occurrence network analysis with microbial functional traits, revealing that core microbial networks linked to nitrogen and phosphate cycling persist despite disturbance. These findings highlight the role of microbial biodiversity and community assembly in sustaining soil functions under biofertilizer application.}, }
@article {pmid40952163, year = {2025}, author = {Nir, I and Armoza-Zvuloni, R and Barak, H and De Los Ríos, A and McKay, CP and Kushmaro, A}, title = {The Biology, Microclimate, and Geology of a Distinctive Ecosystem Within the Sandstone of Hyper-Arid Timna Valley, Israel.}, journal = {Environmental microbiology reports}, volume = {17}, number = {5}, pages = {e70188}, doi = {10.1111/1758-2229.70188}, pmid = {40952163}, issn = {1758-2229}, support = {PID2023-147027NB-I00B//Agencia Estatal de Investigaci&#xf3;n. Write: Agencia Estatal de Investigacion (AEI), MICINN/ ; EXO-92-4//NASA AMES/ ; 3-17370//Minstry of Science and Technology (MOST), Israel/ ; }, abstract = {Microbial endolithic communities in the sandstone rocks of the southern Negev Desert, particularly in Timna Park, were initially discovered by Imre Friedmann and Roseli Ocampo-Friedmann in their pioneering study about 50 years ago. Nonetheless, this harsh microecosystem, dominated by cyanobacterial taxa, raises questions about the adaptive mechanisms that enable the survival of these microorganisms. The present study provides comprehensive data, including extensive precipitation records for the Timna Valley, and multi-year microclimatic data from a colonised site. It includes examinations of rock structure, as well as microscopic and metagenomic analysis. Our findings point to a distinct bacterial endolithic population dominated by the cyanobacterial genus Chroococcidiopsis. Although the taxa are well known, we show here how their exclusive persistence is driven by the sandstone's fine porosity and thermal properties, combined with rare, low-volume precipitation. This highly selective microenvironment highlights how specific rock and climate interactions can filter microbial diversity in hyper-arid deserts. Additionally, it demonstrates an adaptation strategy based on both short-term and decadal-scale dormancy. Thus, it offers new insights for the survival of these unique ecosystems and provides valuable perspectives for astrobiology and the search for evidence of microbial life on Mars.}, }
@article {pmid40951970, year = {2025}, author = {Guan, Y and Berne, E and Hennessy, RC and Garbeva, P and Nicolaisen, MH and Bak, F}, title = {NRPS gene dynamics in the wheat rhizoplane show increased proportion of viscosin NRPS genes of importance for root colonization during drought.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0085224}, doi = {10.1128/msphere.00852-24}, pmid = {40951970}, issn = {2379-5042}, abstract = {Secondary metabolites are bioactive compounds, diverse in structure, with versatile ecological functions, including key roles in mediating interactions between microorganisms and plants. Importantly, these compounds can promote the colonization of plant surfaces, such as roots, or modulate root exudates to enhance microbial recruitment and establishment. However, owing to the vast diversity of secondary metabolites, their importance in plant root colonization-particularly under stress conditions, such as drought-remains unclear. To determine the involvement of some of these secondary metabolites in root colonization, we used amplicon sequencing targeting the adenylation domain of the non-ribosomal peptide synthases (NRPSs) and the 16S rRNA gene from the rhizoplane of wheat grown in soil under normal and drought stress conditions. Results showed that drought transiently affected the bacterial community composition and the NRPS composition in the rhizoplane. We observed that drought selected for distinct groups of siderophores from different taxonomical groups, enriching for Streptomyces and depleting Pseudomonas siderophores. In addition, drought enriched Pseudomonas-derived NRPS genes encoding viscosin, a cyclic lipopeptide with biosurfactant properties, indicating that compounds linked to motility and colonization provide a competitive advantage during rhizoplane colonization under drought stress conditions. This observation was experimentally confirmed using the viscosin-producing P. fluorescens SBW25 and its viscosin-deficient mutant. A higher abundance of SBW25 colonized the roots under drought stress conditions compared to the viscosin-deficient mutant. In summary, our work demonstrates the potential for amplicon sequencing of NRPS genes, coupled with in planta experiments, to elucidate the importance of secondary metabolites in root colonization.IMPORTANCETo harness beneficial plant-microbe interactions for improved plant resilience, we need to advance our understanding of key factors required for successful root colonization. Bacterial-produced secondary metabolites are important in plant-microbe interactions; thus, targeting these genes generates new knowledge that is essential for leveraging bacteria for sustainable agriculture. We used amplicon sequencing of the NRPS A domain on the rhizoplane of wheat exposed to drought stress to identify important secondary metabolites in plant-microbe interactions during drought. We show that the siderophores respond differently to drought stress depending on taxonomic affiliation and that the potential to synthesize viscosin increases root colonization. Importantly, this study demonstrates the potential of amplicon sequencing of NRPS genes to reveal specific secondary metabolites involved in root colonization, particularly in relation to drought stress, and highlights how the resolution provided by this approach can link specific compounds to a specific stress condition in a soil system.}, }
@article {pmid40951136, year = {2025}, author = {Al Harrasi, RJ and Al Balushi, AY and Al Kindi, FI and Al Kindi, NA and Kamel, AH}, title = {Potential Role of Oral Microbiota in Medication-Related Osteonecrosis of the Jaw in Cancer Patients: A Narrative Review.}, journal = {Cureus}, volume = {17}, number = {8}, pages = {e89943}, pmid = {40951136}, issn = {2168-8184}, abstract = {Medication-related osteonecrosis of the jaw (MRONJ) is a severe complication frequently observed in cancer patients undergoing antiresorptive therapies, such as bisphosphonates and denosumab. Emerging evidence suggests that dysbiosis of the oral microbiota plays a pivotal role in the pathogenesis of MRONJ. The complex interplay between microbial communities, host immune responses, and the effects of cancer treatments creates an environment conducive to pathogenic colonization, chronic inflammation, and impaired bone healing, which are the key hallmarks of MRONJ. Chemotherapy, radiotherapy, and antiresorptive agents significantly disrupt oral microbiota homeostasis, reducing microbial diversity and the overgrowth of opportunistic pathogens. These alterations exacerbate the inflammatory responses, accelerate bone resorption, and impede tissue repair. The identification of specific microbial biomarkers associated with MRONJ could facilitate early detection and targeted interventions, such as antimicrobial and probiotic therapies, to restore the microbial balance and mitigate the risk of MRONJ. Furthermore, the implementation of personalized preventive protocols, including rigorous oral hygiene and multidisciplinary collaboration among oncologists, dentists, and microbiologists, is critical for reducing the incidence and severity of MRONJ in high-risk populations. Future research should focus on elucidating the mechanisms by which microbial dysbiosis contributes to MRONJ, validating microbiome-based diagnostic tools, and optimizing therapeutic strategies to preserve oral and systemic health in patients with cancer. Integrating microbial ecology into the MRONJ management framework offers a promising avenue for addressing this challenging condition and improving the outcomes for vulnerable individuals.}, }
@article {pmid40950580, year = {2025}, author = {Panteleev, V and Kulbachinskiy, A and Gelfenbein, D}, title = {Evaluating phage lytic activity: from plaque assays to single-cell technologies.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1659093}, pmid = {40950580}, issn = {1664-302X}, abstract = {Bacteriophages are the most abundant biological entities on Earth, playing critical roles in microbial ecology, evolution, and horizontal gene transfer. Since the discovery of bacteriophages in the early 20th century, a wide range of techniques has been developed to study their lytic activity. This review provides a perspective on the wide range of methods for studying phage-bacteria interactions, spanning classical bulk-culture techniques and modern single-cell and high-throughput approaches. The first section covers solid culture methods relying on plaque formation phenomenon, which allow for quantification of infectious viruses, phage host-range establishment, and analysis of certain phage traits, now augmented by robotic high-throughput screening. The second section focuses on liquid culture approaches, utilizing optical density measurements, quantitative PCR, metabolic assays and cell damage assays to measure the infection dynamics. The third section details single-cell techniques, which help to dissect the heterogeneity of infection within cell populations, using microscopy, microfluidics, next-generation sequencing, and Hi-C methods. The integration of these diverse methods has greatly advanced our understanding of the molecular mechanisms of phage infection, bacterial immunity, and facilitated phage therapy development. This review is dedicated to the 110th anniversary of phage discovery and is aimed to guide researchers in selecting optimal techniques in the fast-growing field of phage biology, phage-host interactions, bacterial immunity, and phage therapy.}, }
@article {pmid40950160, year = {2025}, author = {Pratyush, MR and Prentice, JA and Eutsey, RA and Mikheyeva, I and Hiller, NL and Bridges, AA}, title = {Label-free microscopy enables high-throughput identification of genes controlling biofilm development.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.09.02.673883}, pmid = {40950160}, issn = {2692-8205}, abstract = {The biofilm mode of growth plays a critical role in microbial ecology and in the persistence of human pathogens. Yet, much remains unknown regarding the molecular determinants of biofilms in human pathogens. In this study, we present label-free analysis of biofilms (LFAB), an imaging approach that combines time-lapse, low-magnification brightfield microscopy with regional optical density measurements to quantify biofilm biomass. Unlike other approaches to biofilm biomass quantification, LFAB enables real-time, non-perturbative, and high-throughput monitoring of biofilms. We validated LFAB in diverse microbes and found that our measurements strongly correlate with traditional biofilm assays. We then used LFAB to identify and characterize critical factors mediating biofilm formation in Streptococcus pneumoniae , a major human pathogen whose biofilm lifecycle is known to be intimately related to colonization and infection. Initial characterization revealed that S. pneumoniae microcolonies form by radial expansion of attached cells, displaying reproducible morphology and growth dynamics. Screening of a transposon mutant library revealed that genes spanning carbohydrate metabolism, signaling, surface binding, cell wall synthesis, and adhesion impinge on the biofilm lifecycle of S. pneumoniae . We performed follow-up investigations of choline binding protein A (CbpA) and its adjacently encoded two-component system regulator, which we find are critical for the dynamics of microcolony biofilms in S. pneumoniae . Overall, this work establishes LFAB as a powerful approach for identifying and characterizing biofilm determinants across bacteria and uncovers key regulators of the biofilm lifecycle in a major human pathogen.}, }
@article {pmid40949998, year = {2025}, author = {Garabello, E and Yoon, H and Reid, MC and Giometto, A}, title = {Tunable Low-Rate Genomic Recombination with Cre-lox in Escherichia coli : A Versatile Tool for Environmental Biosensing and Synthetic Biology.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.10.02.616356}, pmid = {40949998}, issn = {2692-8205}, abstract = {UNLABELLED: The ability to induce heritable genomic changes in response to environmental cues is valuable for environmental biosensing, for experimentally probing microbial ecology and evolution, and for synthetic biology applications. Site-specific recombinases provide a route to genetic memory via targeted DNA modifications, but their high specificity and efficiency are offset by leaky expression and limited tunability in prokaryotes. We developed a tightly regulated, titratable Cre recombinase system for Escherichia coli that achieves low recombination rates and minimal basal activity. Implemented on both plasmids and the chromosome, the latter showed superior retention of genetic memory across generations. These features make the system broadly useful for environmental biosensing and other applications. To demonstrate applicability to environmental biosensing, we developed a whole-cell recombination-based biosensor for arsenite, a toxic and ubiquitous pollutant that is primarily mobilized in anoxic environments such as flooded soils, sediments, and aquifers. However, existing arsenite whole-cell biosensors face limitations in sensitivity and workflow in anaerobic settings. Our biosensor reliably recorded anoxic arsenite exposure as a stable genetic memory for delayed fluorescence readout in aerobic conditions, with detection sensitivity comparable to conventional wet chemical methods. By decoupling exposure from measurement, this approach offers a foundation for arsenite biosensing under field-relevant conditions, including redox variability and other physicochemical gradients, without the constraints of anoxic measurement. More broadly, the ability to induce low-rate, heritable genetic changes expands the genetic toolkit for environmentally responsive systems, with applications in environmental monitoring, bioproduction, bioengineering, as well as experimental studies of microbial ecology, evolution, and host-microbe interactions.<br><br>IMPORTANCE: Arsenic is a toxic and globally prevalent pollutant, mobilized primarily under anoxic conditions where detection is challenging. Whole-cell biosensors offer a promising route for monitoring bioavailable arsenic in situ , but their development has largely focused on aerobic conditions, with anoxic assays limited by sensitivity and workflow constraints. Genetic tools that enable heritable, low-frequency genomic changes in bacteria can expand biosensor capabilities by recording transient exposures and supporting applications in environmental monitoring, synthetic biology, and quantitative microbial population dynamics research. Here, we developed a tightly regulated, chemically inducible Cre- lox system in Escherichia coli that enables recombination at low, tunable rates. We demonstrate its utility by constructing an arsenite biosensor that reliably detects low concentrations and records exposures under both aerobic and anoxic conditions. This approach is broadly applicable for biosensors designed for field deployment and for experiments investigating microbial ecology and evolution, where controllable genetic diversification may be desirable.}, }
@article {pmid40945448, year = {2025}, author = {Pei, T and Liu, X and Xu, G and Xin, T and Wu, G and Ma, B and Liu, X and Zhang, H}, title = {Hydraulic regimes-driven microbial community assembly and network stability in drinking water distribution systems: Mechanistic linkages with transport distance and stagnation effects.}, journal = {Journal of hazardous materials}, volume = {498}, number = {}, pages = {139825}, doi = {10.1016/j.jhazmat.2025.139825}, pmid = {40945448}, issn = {1873-3336}, abstract = {Hydraulic regimes within drinking water distribution system (DWDS) critically alter water quality and microbial communities, posing significant public health risks. However, how hydraulic regimes modify microbial (bacteria and fungi) assembly and network stability in DWDS remains poorly understood. This study investigated spatiotemporal dynamics of water quality and microbial succession across a full-scale DWDS, focusing on hydraulic regimes (transport distance (1-5 km) and stagnation) effects. Results indicated that increasing transport distance and hydraulic stagnation led to water quality deterioration, while concurrently amplifying microbial diversity and triggering community structural reorganization. Transport distance predominantly influenced microbial diversity during summer, whereas stagnation dominated community succession in winter. Besides, microbial species richness was greater in the 5 km tap water in summer, while higher species evenness was observed in winter. Integrated neutral community modeling and null model analysis (βNTI and RCbray metrics) demonstrated that a deterministic to stochastic transition in microbial assembly mechanisms - from niche-based selection at treatment plants to increasing stochastic dominance along distribution networks (|βNTI| < 2). Hydraulic regimes enhanced microbial stability and complexity, evidenced by elevated graph density and natural connectivity, conferring rapid resilience to bacterial and fungal communities. These findings establish a hydraulic-microbial ecology coupling framework within DWDS, proposing operational strategies for hydraulic regime optimization management in drinking water management.}, }
@article {pmid40945439, year = {2025}, author = {Wang, W and Yang, W and Jiang, L and Yao, C and Zhang, Z and Xu, M and Yan, X and Qian, X}, title = {Applications of Oxford Nanopore Technology in the analysis of antibiotic resistance genes: A review.}, journal = {Journal of hazardous materials}, volume = {498}, number = {}, pages = {139824}, doi = {10.1016/j.jhazmat.2025.139824}, pmid = {40945439}, issn = {1873-3336}, abstract = {Antibiotic misuse has led to the rapid expansion of the antibiotic resistance gene (ARGs) pool, making antimicrobial resistance (AMR) a major global health threat. The efficient identification of ARGs and the development of strategies to control AMR have become research hotspots. However, the Next-generation sequencing (NGS) has many limitations in ARGs identification, hindering our understanding of their genetic context. This review uses Oxford Nanopore Technology (ONT) as an example to summarize the advantages and application prospects of the third-generation sequencing technologies in the migration and transmission of ARGs. By analyzing 12 sets of NGS - ONT datasets, this review demonstrates the strengths and limitations of ONT from multiple perspectives, including the identification of ARGs, key pathogens, plasmids, viruses, and horizontal gene transfer events, and provides detailed analytical workflows. It offers comprehensive analytical approaches and application insights for ARGs research based on ONT, highlighting the importance and necessity of the third-generation sequencing technologies in studying the prevalence and transmission of ARGs in complex environments.}, }
@article {pmid40945060, year = {2025}, author = {Zhang, M and Zhao, C and Zhang, W and Guo, Y and Han, F and Li, Y and Zhou, W}, title = {Stable ammonium assimilation mediates the metabolic adaptation of halophilic microbiome to hypo-osmotic stress in wastewater treatment.}, journal = {Water research}, volume = {288}, number = {Pt A}, pages = {124572}, doi = {10.1016/j.watres.2025.124572}, pmid = {40945060}, issn = {1879-2448}, abstract = {Salinity barrier shapes distinct microbial ecology on earth, and applications of microbiomes are frequently hindered by trans-osmotic challenges. As a central nutrient metabolism, nitrogen transformations may contribute to conquering osmotic perturbations in microbiomes, and thus understanding the nitrogen metabolic responses to non-isosmotic exposure is crucial. Here we uncover that ammonium assimilation mediates the maintenance of physicochemical properties in a marine-derived halophilic microbiome when adapting to hypo-osmotic stress from salinity of 3 % to 0.5 %. An adaptive threshold at salinity approximately around 1 % is observed that reducing osmotic gradients disrupt ammonium assimilation and microbial community stability with decreasing specific ammonium assimilation rates from 2.34 to 0.62 mg-N/(g MLSS h). Multi-omics analysis demonstrates that enhancing ammonium-assimilating function prevents nitrogen metabolic differentiation and promotes production of amino acids and their derivatives recognized as osmoprotectants. Genes coding for transporter systems and mechanosensitive channels are also up-regulated. The results of this study suggest that maintaining stable ammonium assimilation could enhance the amino acid metabolism and subsequent osmoprotectant production, thus improving the metabolic adaptation of the halophilic microbiome to hypotonic conditions. Our findings provide insights into the adaptation of microbiomes to osmotic alterations, and highlight the importance of enhancing ammonium assimilation in engineering microbiomes under environmental stress.}, }
@article {pmid40941211, year = {2025}, author = {Yu, Z and Zhao, H and Ma, T and Zhang, X and Yan, Y and Zhu, Y and Yu, Y}, title = {Insights into the Composition and Function of Virus Communities During Acetic Acid Fermentation of Shanxi Aged Vinegar.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {17}, pages = {}, doi = {10.3390/foods14173095}, pmid = {40941211}, issn = {2304-8158}, support = {2023M741438//China Postdoctoral Science Foundation/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; }, abstract = {Viruses play a regulatory role in microbial ecology. Traditional fermented foods have complex fermentation environments with abundant viral participation, yet current research on viral communities in fermented foods remains insufficient. Traditional, manually produced solid-state fermented vinegar serves as an excellent model for studying the role of viral communities in fermented foods. Using metagenomic approaches, this study investigates the structure and dynamics of viral communities during the acetic acid fermentation process of Shanxi aged vinegar. All identified viruses were bacteriophages, and the dominant families were identified as Herelleviridae, Autographiviridae, and Stanwilliamsviridae. The richness and diversity of viral communities exhibited significant variations during acetic acid fermentation. Furthermore, correlation analysis revealed a strong association (p < 0.01) between core bacteria and core viruses. Functional annotation revealed the presence of viral genes associated with amino acid and carbohydrate metabolism. Notably, abundant auxiliary carbohydrate-active enzyme (CAZyme) genes were identified in viruses, with glycoside hydrolases (GHs), glycosyltransferases (GTs), and carbohydrate-binding modules (CBMs) demonstrating particularly high abundance. Additionally, several antibiotic resistance genes were detected in viruses. This study elucidates the impact of viral communities on microbial dynamics during food fermentation, advancing our understanding of viral roles in traditional fermented food ecosystems.}, }
@article {pmid40940565, year = {2025}, author = {Gilbert, JA and Peixoto, RS and Scholz, AH and Dominguez Bello, MG and Korsten, L and Berg, G and Singh, B and Boetius, A and Wang, F and Greening, C and Wrighton, K and Bordenstein, S and Jansson, JK and Lennon, JT and Souza, V and Thomas, T and Cowan, D and Crowther, TW and Nguyen, N and Harper, L and Haraoui, LP and Ishaq, SL and Redford, K}, title = {Launching the IUCN Microbial Conservation Specialist Group as a global safeguard for microbial biodiversity.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {40940565}, issn = {2058-5276}, }
@article {pmid40935756, year = {2025}, author = {Ledford, SM and Geffre, P and Marschmann, GL and Karaoz, U and Brodie, EL and Meredith, LK}, title = {Volatile traits expand the microbial playbook.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2025.08.001}, pmid = {40935756}, issn = {1878-4380}, abstract = {Microbial metabolic functions are increasingly conceptualized as fitness-regulating traits. However, volatile compounds (the volatilome), despite their key roles in metabolism and ecology, are often overlooked in trait-based frameworks. We propose that volatile traits not only reflect ecological strategies but also shape them by mediating responses to selection pressures. Their volatility affects diffusion, substrate access, and interactions across space, conferring selective advantages as resources or waste products. We outline approaches to incorporate volatile traits into predictive models to improve understanding of microbial selection and community dynamics. This integration enables a more holistic view of microbial life by accounting for the ecological and evolutionary consequences of volatile-mediated processes.}, }
@article {pmid40934885, year = {2025}, author = {Kujawska, M and Seki, D and Chalklen, L and Malsom, J and Kiu, R and Goatcher, S and Christoforou, I and Mitra, S and Crouch, L and Hall, LJ}, title = {Host-specific microbiome and genomic signatures in Bifidobacterium reveal co-evolutionary and functional adaptations across diverse animal hosts.}, journal = {Cell host &amp; microbe}, volume = {33}, number = {9}, pages = {1502-1517.e13}, doi = {10.1016/j.chom.2025.08.008}, pmid = {40934885}, issn = {1934-6069}, abstract = {Animals harbor divergent microbiota, including various Bifidobacterium species, yet their evolutionary relationships and functional adaptations remain understudied. Using samples from insects, reptiles, birds, and mammals, we integrated taxonomic, genomic, and predicted functional annotations to uncover how Bifidobacterium adapts to host-specific environments. Host phylogeny is a major determinant of gut microbial composition. Distinct microbiota in mammalian and avian hosts reflect evolutionary adaptations to dietary niches, such as carnivory, and ecological pressures. At a strain-resolved level, Bifidobacterium and their hosts exhibit strong co-phylogenetic associations, driven by vertical transmission and dietary selection. Functional analyses highlight striking host-specific adaptations in Bifidobacterium, particularly in carbohydrate metabolism and oxidative stress responses. In mammals, Bifidobacterium strains are enriched in glycoside hydrolases tailored to complex carbohydrate-rich diets, including multi-domain GH13_28 α-amylases associated with degradation of resistant starch. Together, these findings deepen our understanding of host-microbe co-evolution and the critical role of microbiota in shaping animal health and adaptation.}, }
@article {pmid40931664, year = {2025}, author = {Krespach, MKC and Rosin, M and Scherlach, K and Stroe, MC and Hertweck, C and Brakhage, A}, title = {The Linear Arginoketides Neotetrafibricin A, B, and C have Algicidal and Signal Function in Microbial Interactions.}, journal = {Chembiochem : a European journal of chemical biology}, volume = {}, number = {}, pages = {e202500479}, doi = {10.1002/cbic.202500479}, pmid = {40931664}, issn = {1439-7633}, support = {239748522-CRC 1127//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Soils harbor some of the most diverse microbiomes on Earth. Interactions within these microbial communities are often mediated by natural products, many functioning as chemical signals. Specialized metabolites known as arginoketides, or arginine-derived polyketides, have been linked to mediate these interactions. However, the effect of linear arginoketides on soil microalgae has not yet been investigated. Here, we report that Streptomyces mashuensis DSM40221 produces the linear arginoketide neotetrafibricin A, and show that it exhibits algicidal activity against the green alga Chlamydomonas reinhardtii and induces production of orsellinic acid and derivatives encoded by the silent ors biosynthetic gene cluster (BGC) in the fungus Aspergillus nidulans. Thus, neotetrafibricin serves as an inter-kingdom signaling molecule. Genome mining identified the neotetrafibricin BGC in S. mashuensis. Disrupting the first polyketide synthase gene abolished neotetrafibricin production. Further mutational studies identified two neotetrafibricin congeners, including the novel neotetrafibricin C, which contains a terminal guanidino group. Structure-activity relationship analyses revealed that neither the terminal amino group nor the sugar moiety is essential for its algicidal activity or the induction of the ors BGC in the fungus. These findings expand the understanding of linear arginoketides in microbial ecology and highlight their potential as multifunctional signaling compounds in soil environments.}, }
@article {pmid40931662, year = {2025}, author = {Bains, JS and Baggaley, AW and Croze, OA}, title = {Drift velocity of bacterial chemotaxis in dynamic chemical environments.}, journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences}, volume = {383}, number = {2304}, pages = {20240261}, pmid = {40931662}, issn = {1471-2962}, support = {//EPSRC/ ; }, mesh = {*Chemotaxis/physiology ; *Models, Biological ; Computer Simulation ; *Bacterial Physiological Phenomena ; Monte Carlo Method ; Chemotactic Factors ; Bacteria ; }, abstract = {Chemotaxis allows swimming bacteria to navigate through chemical landscapes. To date, continuum models of chemotactic populations (e.g. Patlak-Keller-Segel models) have considered bacteria responding only to spatial chemical gradients. In these models, chemotactic advection is modelled through a drift velocity proportional to the spatial chemical gradient. In nature and industry, however, bacterial populations experience dynamic, spatio-temporally varying chemical environments, such as the neighbourhood of lysing phytoplankton cells. Recent analyses have shown how temporal gradients can 'confuse' individual bacteria, impacting the precision of their gradient estimation. However, very few studies have considered how temporal gradients influence the chemotactic drift velocity of whole populations. Here, we use Monte Carlo simulations to infer the drift velocity of a population when both spatial and temporal gradients are present. We propose an ansatz for the drift velocity, which fits the simulations well. This ansatz allows us to account for how temporal gradients can significantly impact chemotaxis of bacterial populations up a spatial gradient. We explore the consequences of this new effect through a Patlak-Keller-Segel type model applied to single decaying and oscillating pulses of chemoattractant. Finally, we discuss possible biological consequences of our results and extensions of our modelling framework.This article is part of the theme issue 'Biological fluid dynamics: emerging directions'.}, }
@article {pmid40930771, year = {2025}, author = {Feng, L and Loi, JX and Séneca, J and Pjevac, P and Adnan, FH and Ngoh, GC and Khor, BC and Aris, AM and Oshiki, M and Daims, H and Chua, ASM}, title = {Nitrifying Communities in Biological Nitrogen Removal Processes at Tropical Municipal Wastewater Treatment Plants.}, journal = {Microbes and environments}, volume = {40}, number = {3}, pages = {}, doi = {10.1264/jsme2.ME25036}, pmid = {40930771}, issn = {1347-4405}, mesh = {*Nitrification ; *Wastewater/microbiology/chemistry ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Nitrogen/metabolism ; RNA, Ribosomal, 16S/genetics ; Ammonia/metabolism ; *Archaea/classification/genetics/metabolism/isolation &amp; purification ; Malaysia ; Sewage/microbiology ; Phylogeny ; Tropical Climate ; Water Purification ; Oxidoreductases/genetics ; Oxidation-Reduction ; In Situ Hybridization, Fluorescence ; }, abstract = {Nitrifying communities in activated sludge play a crucial role in biological nitrogen removal processes in municipal wastewater treatment plants. While extensive research has been conducted in temperate regions, limited information is available on nitrifiers in tropical regions. The present study investigated all currently known nitrifying communities in two full-scale municipal wastewater treatment plants in Malaysia operated under low-dissolved oxygen (DO) (0.2-0.7‍ ‍mg‍ ‍DO‍ ‍L[-1]) or high-DO (2.0-5.5‍ ‍mg‍ ‍DO‍ ‍L[-1]) conditions at 30°C. The core nitrifiers in the municipal wastewater treatment plants were Nitrosomonas (ammonia-oxidizing bacteria, AOB), Nitrospira (nitrite-oxidizing or complete ammonia-oxidizing, comammox, bacteria), and ammonia-oxidizing archaea (AOA) as identified by a 16S rRNA gene amplicon sequencing ana-lysis and corroborated by 16S rRNA-targeted fluorescence in situ hybridization. A quantitative polymerase chain reaction (qPCR) targeting ammonia monooxygenase subunit A (amoA) genes revealed stable populations of comammox Nitrospira and AOB in both wastewater treatment plants. AOA were detected in only one of the plants and their population sizes fluctuated, with higher temporary abundance under high-DO conditions. These results provide important insights into the composition and dynamics of nitrifying communities in tropical municipal wastewater treatment plants.}, }
@article {pmid40928120, year = {2025}, author = {Lauwens, K and Saghi, M and Germonpré, PJ and Zayed, N and Boon, N and Bernaerts, K and Teughels, W and Van Holm, W}, title = {Can We Combine Mouthrinses With Probiotics? An Evaluation of Their Compatibility and Combined Therapy on Oral Biofilms.}, journal = {Journal of periodontal research}, volume = {}, number = {}, pages = {}, doi = {10.1111/jre.70033}, pmid = {40928120}, issn = {1600-0765}, abstract = {AIM: Multiple oral pathologies requiring antiseptic mouthrinses for prevention or treatment. However, nonselective elimination of the microbes may also harm beneficial commensal, healthy bacteria. Promicrobial strategies, such as probiotics, aim to rebalance the oral microbiome rather than eradicate it; however, we hypothesised that their incorporation might be challenged due to the microbiome's inherent resistance to outsiders. In this study, their combined effect on an in vitro oral biofilm model was assessed. Instead of comparing mouthrinses to probiotics, could they be combined to obtain the best of both worlds?<br><br>METHODS: The compatibility of two commonly used Limosilactobacillus reuteri strains with 13 commercially available mouthrinses was tested by evaluating probiotic survival in the mouthrinses and their combined effect on a multispecies in&#xa0;vitro biofilm model.<br><br>RESULTS: Differences in compatibility were observed. Several mouthrinses showed moderate compatibility and improved the probiotics incorporation into biofilms. One mouthrinse (O7 Active Oxygen) demonstrated the most favourable compatibility, enabling abundant probiotic incorporation and beneficial biofilm composition changes.<br><br>CONCLUSION: The combination of mouthrinses and probiotics has the potential to improve the treatment of oral pathologies and promote a healthier oral microbiome, although compatibility varies.}, }
@article {pmid40927988, year = {2025}, author = {Veresoglou, SD}, title = {Mycorrhizal ecology: In the land of the one-eyed king.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/eraf399}, pmid = {40927988}, issn = {1460-2431}, abstract = {Unlike most of the other disciplines in microbial ecology, a substantial fraction of the theory on mycorrhizal ecology originates from times when assaying microbes was laborious and inefficient. Most of those hypotheses target, as a result, the plant partner of the symbiosis, or at best treat the two mycorrhizal partners as a unified organism, a holobiont. I here address the legacy of this era of mycorrhizal ecology, as a means of systematizing our understanding of the discipline, but also identifying gaps of knowledge. First, I pair and review hypotheses that align with the holobiont concept with complementary hypotheses that explicitly consider the fitness of the mycorrhizal fungus. Second, I generate a hierarchy of hypotheses in mycorrhizal ecology to showcase the high potential for classifying theory that the distinction between hypotheses considering mycorrhiza as either a holobiont or an association of two individual partners maintains. Third, I identify settings that might dictate when to better abstract mycorrhizas into holobionts and when to consider all their partners individually to foster research progress. I conclude the review with suggestions on how to further unify expectations in mycorrhizal ecology.}, }
@article {pmid40926344, year = {2025}, author = {Sarango Flores, S and Cordovez, V and Oyserman, BO and Arias Giraldo, LM and Stopnisek, N and Raaijmakers, JM and van 't Hof, P}, title = {Microbiome-Mediated Resistance of Wild Tomato to the Invasive Insect Prodiplosis longifila.}, journal = {Environmental microbiology reports}, volume = {17}, number = {5}, pages = {e70190}, doi = {10.1111/1758-2229.70190}, pmid = {40926344}, issn = {1758-2229}, support = {024.004.014/NWO_/Dutch Research Council/Netherlands ; CZ07-000440-2018//SENESCYT scholarship/ ; 10093//Chancellor Research Grant/ ; }, mesh = {*Solanum lycopersicum/microbiology/parasitology/immunology ; Animals ; *Microbiota ; *Soil Microbiology ; *Diptera/physiology ; Ecuador ; Plant Roots/microbiology/parasitology ; Introduced Species ; Bacteria/classification/genetics/isolation &amp; purification ; Plant Leaves/parasitology ; }, abstract = {Plant roots are colonised by diverse communities of microorganisms that can affect plant growth and enhance plant resistance to (a) biotic stresses. We investigated the role of the indigenous soil microbiome in the resistance of tomato to the invasive sap-sucking insect Prodiplosis longifila (Diptera: Cecidomyiidae). Native and agricultural soils were sampled from the Andes in Southern Ecuador and tested, in greenhouse bioassays, for leaf tissue damage caused by P. longifila on domesticated Solanum lycopersicum cv. Moneymaker and wild tomato S. pimpinellifolium. We observed no significant differences in insect damage between domesticated and wild tomatoes grown in live native or agricultural soils. However, when grown in sterilised native and agricultural soils, wild tomato was more severely affected by the insect than the domesticated tomato. Microbiome analyses revealed that soil sterilisation impacted overall rhizobacterial diversity and abundance in wild tomato. Particularly, Actinoplanes abundance was reduced upon sterilisation, which significantly correlated with loss of insect resistance. Metagenome analyses and genome assembly of Micromonosporaceae (Actinoplanes family) suggested a putative association between motility, chemotaxis, membrane transport, chorismate, and lanthipeptide biosynthesis and insect resistance. This indicates that wild S. pimpinellifolium, in contrast to domesticated S. lycopersicum, relies on specific members of the root-associated microbiome for P. longifila protection.}, }
@article {pmid40925292, year = {2025}, author = {Sumana, SL and Tarawallie, S and Osei, SA and Kamara, AM and Xiaofei, Y and Mansaray, A and Zhang, J}, title = {Chemical interactions between filter-feeding mussels and Ulvaprolifera: The role of dissolved organic matter and secondary metabolites in growth promotion and competition inhibition of algal species.}, journal = {Marine environmental research}, volume = {212}, number = {}, pages = {107529}, doi = {10.1016/j.marenvres.2025.107529}, pmid = {40925292}, issn = {1879-0291}, abstract = {This review examines the chemical and ecological interactions between filter-feeding mussels and the green macroalga Ulva prolifera in integrated multi-trophic aquaculture (IMTA) systems. Mussels are crucial for nutrient recycling, as they filter water and release bioavailable compounds such as ammonium (NH4[+]), urea (CO(NH2)2), and dissolved organic matter (DOM). These compounds promote Ulva growth and enhance microbial activity. In turn, U. prolifera produces sulfated polysaccharides, phenolics, and halogenated metabolites that can influence microbial communities, suppress competitors, and potentially affect mussel physiology at high concentrations. The review emphasizes the interconnectedness of nutrient exchange, DOM cycling, and microbial genes such as pmoA and mcrA, highlighting the novelty of integrating microbial ecology with biogeochemical cycles and ecosystem outcomes, illustrating both the synergies and risks present in co-culture systems. While moderate production of metabolites helps control biofouling and maintain ecosystem stability, excessive DOM or allelochemical accumulation can hinder mussel filtration and lead to hypoxia. Maintaining specific thresholds, such as DOM concentrations below 5 mg C/L and labile-to-refractory DOM ratios above 1:1, is essential for balance. This synthesis integrates microbial ecology, metabolite feedbacks, and biogeochemical processes to provide a framework for resilient IMTA design. It also emphasizes practical strategies like adjusting stocking densities, optimizing water exchange, and employing microbial monitoring tools to promote sustainable IMTA practices. By linking molecular interactions to ecosystem-scale outcomes, the review offers guidance for sustainable aquaculture systems that enhance productivity, minimize environmental risks, and improve resilience in the face of climate stress.}, }
@article {pmid40923842, year = {2025}, author = {Alteio, LV and Spiegel, F and Rychli, K and Wagner, M}, title = {Nevertheless, they persist: addressing the stalemate of persistence in food-associated Listeria monocytogenes research.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-21}, doi = {10.1080/1040841X.2025.2555938}, pmid = {40923842}, issn = {1549-7828}, abstract = {Foodborne illness is a critical food safety and public health concern, often resulting from contamination events by resident pathogens in food processing environments (FPEs). Listeria monocytogenes, the causative agent of listeriosis, can persist in FPEs over long time periods. Despite rigorous research on the phenotypic and genotypic traits of L. monocytogenes, no clear pattern has arisen to explain why some strains are able to persist. Researchers face definitional and methodological challenges, which influence identification and comparison of persistent and non-persistent strains. Moreover, only weak associations between persistence and gene-level patterns have been detected, necessitating new perspectives. In this review, we synthesize years of research based on whole genome sequencing, highlighting sequence-type and gene-level patterns linked to persistence. As these patterns do not robustly explain persistence, we critically assess how applied definitions and methodological approaches have shaped, and potentially biased, our current understanding. We evaluate existing hypotheses on persistence and suggest future research directions, integrating insights from ecology, evolution, and predictive modeling to disentangle factors and mechanisms that enable L. monocytogenes to persist in food processing environments.}, }
@article {pmid40923499, year = {2025}, author = {Van Hecke, T and Jakobsen, LMA and Tian, X and Van Pee, J and Elias Masiques, N and Vermeersch, AS and Deforce, D and Van Nieuwerburgh, F and Van Royen, G and De Vrieze, J and Bertram, HC and De Smet, S}, title = {Metabolic consequences and gut microbiome alterations in rats consuming pork or a plant-based meat analogue.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d5fo02197a}, pmid = {40923499}, issn = {2042-650X}, abstract = {It is unknown how human health is affected by the current increased consumption of ultra-processed plant-based meat analogues (PBMA). In the present study, rats were fed an experimental diet based on pork or a commercial PBMA, matched for protein, fat, and carbohydrate content for three weeks. Rats on the PBMA diet exhibited metabolic changes indicative of lower protein digestibility and/or dietary amino acid imbalance, alongside increased mesenteric (+38%) and retroperitoneal (+20%) fat depositions despite lower food and energy intake. In contrast, rats on the pork diet demonstrated signs of a disturbed gut-liver axis with increased liver weight (+15%) and blood low-density lipoprotein (+86%), which may have been facilitated by gut microbial changes. The colon of rats on the PBMA diet was characterized by an outgrowth of bacterial groups including Muribaculaceae, Roseburia and various Eubacterium spp. known to improve cholesterol metabolism, whereas a remarkable outgrowth of Akkermansia, Oscillospiraceae and Desulfovibrionaceae in rats on the pork diet may be conducive to colon mucin degradation. Effects on oxidative stress parameters were equivocal, with increased lipid oxidation (+27%) in the colon mucosa of PBMA-fed rats, whereas lower blood levels of the endogenous antioxidant glutathione (-30%) were found in pork-fed. Overall, the present rat study reveals major differences in the physiological and microbiota-related responses to diets containing either conventional pork or PBMA, which could have implications for human health.}, }
@article {pmid40919941, year = {2025}, author = {Bodelier, PL}, title = {Expansion of aerobic methanotrophy to the phylum of Actinomycetota and its environmental implications.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0133425}, doi = {10.1128/aem.01334-25}, pmid = {40919941}, issn = {1098-5336}, abstract = {For over a century, taxonomically validated pure cultures of aerobic methanotrophs belonged to Pseudomonadota, or since 2007, Verrucomicrobiota. A recent article published in Applied and Environmental Microbiology by H. Kambara, T. Kawamoto, S. Matsushita, T. Kindaichi, et al. (91:e00796-25, 2025, https://doi.org/10.1128/aem.00796-25) expands the phylogenetic radiation of aerobic methanotrophs to the Actinomycetota with the description of Ca. Mycobacterium methanica MM1. This isolate confirms and strengthens the position of the genus Mycobacterium as methanotrophs displaying a wide pH and ammonia tolerance and expanding the habitat range for methane capture.}, }
@article {pmid40919204, year = {2025}, author = {Shukla, A and Goswami, D and Jha, CK}, title = {Editorial: Navigating challenges and innovations in antimicrobial resistance, environmental microbiology, and industrial solutions (ARTEMIS).}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1677866}, doi = {10.3389/fmicb.2025.1677866}, pmid = {40919204}, issn = {1664-302X}, }
@article {pmid40916293, year = {2025}, author = {Ma, J and Yin, Z and Zhang, K and Zhang, X and Ye, L}, title = {Concentration-specific effects of micropollutants on microbial communities and antibiotic resistance genes in activated sludge systems.}, journal = {Journal of hazardous materials}, volume = {497}, number = {}, pages = {139720}, doi = {10.1016/j.jhazmat.2025.139720}, pmid = {40916293}, issn = {1873-3336}, abstract = {Micropollutants are widespread in wastewater systems and can impact microbial communities and the transfer of antibiotic resistance genes (ARGs). Nevertheless, the specific concentration thresholds for these effects under environmental conditions remain largely unknown. This study evaluated six micropollutants at five environmentally relevant concentrations (0.1-500 μg/L) to clarify the concentration-dependent effects on microbial ecology and ARG dynamics. The results showed micropollutant exposure generally reduced microbial diversity. Most micropollutants, except triclosan (TCS), influenced microbial community structure and ARG profiles at even 0.1-1 μg/L, indicating a close association between taxonomic shifts and resistome changes. In contrast, low concentration TCS (0.1-1 μg/L) affected ARG dynamics without altering community composition. Moreover, ARG abundance generally increased with micropollutant concentration. Nevertheless, the acetaminophen and naproxen posed lower horizontal transfer risks despite ARG elevation. In contrast, diclofenac and TCS markedly enhanced ARG transfer at ≥ 10 and 1 μg/L, respectively. Network analysis identified high-risk ARG hosts (e.g., Burkholderiales, Rhodocyclaceae) and highlighted mobile genetic elements involved in replication/recombination/repair. These findings demonstrate that micropollutant-induced resistance dissemination is both concentration-specific and compound-specific, guiding ARG management in wastewater.}, }
@article {pmid40915198, year = {2025}, author = {Zhai, Y and Chen, G and Xiao, Y and Tian, H and Liu, G and Li, X and Bai, J and Cui, B}, title = {Urbanization cast a shadow over bacterial community in river sediment: Insights from community diversity, assembly processes and network interactions.}, journal = {Journal of environmental management}, volume = {393}, number = {}, pages = {127190}, doi = {10.1016/j.jenvman.2025.127190}, pmid = {40915198}, issn = {1095-8630}, abstract = {Rivers reflect natural-anthropogenic interactions, yet how urbanization affects riverine bacterial communities along rural-urban gradients is poorly understood. This study examined bacterial diversity and assembly mechanisms along such a gradient of river sediments. Results showed that bacterial diversity significantly decreased with increasing urban influence. Community assembly shifted from stochastic processes dominating in rural zones to environmental selection prevailing in urban zones. The rural-urban transition caused bacterial network instability, potentially reducing resilience. The participation of prevalent taxa decreased but the rare taxa related to chitinolysis and nitrate/nitrite denitrification were selectively enriched along with rural-urban gradient, suggesting rapid functional recruitment to exploit dissolved organic nitrogen and nitrate pulses typical of urban runoff. Our findings underscore that urbanization's influence on bacterial communities is more pronounced than the river's inherent natural characteristics. These insights highlight the profound ecological consequences of urbanization on river microbiomes, informing protection and restoration strategies.}, }
@article {pmid40914221, year = {2025}, author = {Geng, J and Zhang, W and Christie-Oleza, JA and Abdolahpur Monikh, F and Yang, Q and Yang, Y}, title = {Succession-driven potential functional shifts in microbial communities in the Tire-plastisphere:Comparison of pristine and scrap tire.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {127074}, doi = {10.1016/j.envpol.2025.127074}, pmid = {40914221}, issn = {1873-6424}, abstract = {Tire microplastics (TMPs) represent a major contributor to microplastic pollution, posing threats to aquatic ecosystems. As carbon-rich substrates, TMPs influence microbial colonization and ecological functions. This study investigates the impacts of pristine (P-TMPs) and scrap (S-TMPs) TMPs from the same brand on microbial communities within the tire-plastisphere. We incubated wood particles, P-TMPs, and S-TMPs in situ in a lake environment for 60 days. Utilizing amplicon and metagenome sequencing, we analyzed structural and potential functional changes in microbial communities across five colonization time points. Our findings reveal that TMPs establish distinct ecological niches, functioning as hotspots of microbial activity in aquatic environments. Both niche specificity and colonization time significantly shape microbial community structure. During the early adaptation stage, we observed clustering patterns in both microbial composition and functional genes associated with the particles. Over time, divergent succession in community composition and potential function emerged, primarily driven by differences in substrate availability between niches. Notably, the substrate availability of S-TMPs promoted microbial community shifts, whereas the P-TMPs posed challenges to microbial adaptation. This study elucidates the long-term adaptive processes exhibited by microbial communities when colonizing the contrasting ecological niches represented by these two TMP states (pristine vs. scrap), documenting the progression from community structural change to functional adaptation. The results underscore the complexity of TMP impacts on microbial ecology and highlight the critical need for long-term monitoring to fully understand their environmental implications.}, }
@article {pmid40914115, year = {2025}, author = {Ho, L and Pham, K and Debognies, A and Bodé, S and Vermeir, P and Boeckx, P and De Vrieze, J and Goethals, P}, title = {Interplay between temperature and redox conditions regulates wetland biogeochemistry and greenhouse gas emissions.}, journal = {The Science of the total environment}, volume = {1000}, number = {}, pages = {180413}, doi = {10.1016/j.scitotenv.2025.180413}, pmid = {40914115}, issn = {1879-1026}, abstract = {Wetlands play a crucial role in global greenhouse gas (GHG) dynamics, yet their response to climate change is not yet fully understood. Here, we investigate how increasing temperature and oxygen availability interact to regulate wetland GHG emissions through combined analysis of biogeochemical and functional gene measurements. We found distinct temperature-dependent shifts in carbon emission pathways, with CO2 emissions unexpectedly declining as temperature rose from 15 to 25 °C, while increasing consistently at higher temperatures (25-35 °C), reflecting a transition to more thermally-driven processes. Conversely, CH4 production exhibited exceptionally high temperature sensitivity in the lower range (Q10 = 32.3 ± 2.4 in oxic conditions) before normalizing at higher temperatures (Q10 = 4.1 ± 2.2), suggesting a fundamental shift from aerobic respiration to methanogenesis dominance when temperature increases. Similarly, N2O production pathways transitioned from nitrification-dominated at lower temperatures to denitrification-dominated at higher temperatures, supported by substantial changes in ammonia-oxidizing (amoA AOA and amoA AOB) and denitrifying (nirK, nirS, and nosZ) gene expression. We observed unexpectedly high CH4 production and denitrification activity under oxic conditions, particularly at elevated temperatures, suggesting that anoxic microsites play a crucial role in wetland GHG dynamics. These findings reveal the complex interactions between temperature, oxygen availability and microbial processes in the wetland ecosystem, which underscores the need for incorporating pathway-specific temperature sensitivities into climate models to better predict wetland responses to global change.}, }
@article {pmid40913309, year = {2025}, author = {Harris, KJ and Bennett, AE}, title = {Exploring Bacterial Interactions Under the Stress Gradient Hypothesis in Response to Selenium Stress.}, journal = {Environmental microbiology reports}, volume = {17}, number = {5}, pages = {e70191}, doi = {10.1111/1758-2229.70191}, pmid = {40913309}, issn = {1758-2229}, support = {//Ohio State University/ ; }, mesh = {*Selenium/metabolism/toxicity ; *Bacteria/metabolism/drug effects/growth &amp; development ; *Stress, Physiological ; *Microbial Interactions ; Oxidative Stress ; Metals, Heavy/metabolism/toxicity ; *Bacterial Physiological Phenomena ; }, abstract = {The Stress Gradient Hypothesis (SGH) predicts that interspecific interactions shift from competition under low stress to facilitation under high stress. Historically, this framework has been extensively studied in plants, but its application to microbial communities remains underexplored. Here, we review literature to examine bacterial interactions under heavy metal stress, using selenium (Se) stress as a model for heavy metal-induced environmental pressures. Se, a naturally occurring and anthropogenic metalloid contaminant, provides oxidative stress on bacteria, which will modify competitive and facilitative behaviours under the SGH framework. At low Se concentrations, bacterial interactions are predominantly competitive, driven by resource competition and antimicrobial strategies. However, as Se stress increases, we predict facilitative interactions to increase, including detoxification mechanisms that reduce toxicity for Se intolerant species. We discuss methodologies to measure bacterial competition and facilitation, propose experimental approaches to identify the transition between these interaction modes, and explore the implications of species richness in microbial stress resilience. Understanding these interactions provides insights into microbial ecology, biogeochemical cycling and potential applications in bioremediation.}, }
@article {pmid40913044, year = {2025}, author = {Müller, MC and Wissink, M and Mukherjee, P and Von Possel, N and Laso-Pérez, R and Engilberge, S and Carpentier, P and Kahnt, J and Wegener, G and Welte, CU and Wagner, T}, title = {Atomic resolution structures of the methane-activating enzyme in anaerobic methanotrophy reveal extensive post-translational modifications.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {8229}, pmid = {40913044}, issn = {2041-1723}, support = {101125699//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; WA 4053/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; VI.Vidi.223.012//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; }, mesh = {*Methane/metabolism ; Anaerobiosis ; *Protein Processing, Post-Translational ; *Oxidoreductases/metabolism/chemistry/genetics ; *Archaeal Proteins/metabolism/chemistry/genetics ; Oxidation-Reduction ; *Archaea/enzymology/metabolism ; Phylogeny ; Methanosarcinales/enzymology/metabolism ; Models, Molecular ; Catalytic Domain ; }, abstract = {Anaerobic methanotrophic archaea (ANME) are crucial to planetary carbon cycling. They oxidise methane in anoxic niches by transferring electrons to nitrate, metal oxides, or sulfate-reducing bacteria. No ANMEs have been isolated, hampering the biochemical investigation of anaerobic methane oxidation. Here, we obtained the true atomic resolution structure of their methane-capturing system (Methyl-Coenzyme M Reductase, MCR), circumventing the isolation barrier by exploiting microbial enrichments of freshwater nitrate-reducing ANME-2d grown in bioreactors, and marine ANME-2c in syntrophy with bacterial partners. Despite their physiological differences, these ANMEs have extremely conserved MCR structures, similar to homologs from methanogenic Methanosarcinales, rather than the phylogenetically distant MCR of ANME-1 isolated from Black Sea mats. The three studied enzymes have seven post-translational modifications, among them was a novel 3(S)-methylhistidine on the γ-chain of both ANME-2d MCRs. Labelling with gaseous krypton did not reveal any internal channels that would facilitate alkane diffusion to the active site, as observed in the ethane-specialised enzyme. Based on our data, the methanotrophic MCRs should follow the same radical reaction mechanism proposed for the methane-generating homologues. The described pattern of post-translational modifications underscores the importance of native purification as a powerful approach to discovering intrinsic enzymatic features in non-isolated microorganisms existing in nature.}, }
@article {pmid40911620, year = {2025}, author = {Yuen, ELH and Savage, Z and Pražák, V and Liu, Z and Adamkova, V and King, F and Vuolo, C and Ibrahim, T and Wang, Y and Jenkins, S and Zhou, Y and Tumtas, Y and Erickson, JL and Prautsch, J and Balmez, AI and Stuttmann, J and Duggan, C and Rivetti, F and Molinari, C and Gaboriau, DCA and Carella, P and Zhuang, X and Schattat, M and Bozkurt, TO}, title = {Membrane contact sites between chloroplasts and the pathogen interface underpin plant focal immune responses.}, journal = {The Plant cell}, volume = {}, number = {}, pages = {}, doi = {10.1093/plcell/koaf214}, pmid = {40911620}, issn = {1532-298X}, abstract = {Communication between cellular organelles is essential for mounting effective innate immune responses. The transport of organelles to pathogen penetration sites and their assembly around the host membrane, which delineates the plant-pathogen interface, are well-documented. However, whether organelles associate with these specialized interfaces, and the extent to which this process contributes to immunity, remain unknown. Here, we discovered defense-related membrane contact sites (MCS) comprising a membrane tethering complex between chloroplasts and the extrahaustorial membrane (EHM) surrounding the haustorium of the pathogen Phytophthora infestans in Nicotiana benthamiana. The assembly of this complex involves association between the chloroplast outer envelope protein CHLOROPLAST UNUSUAL POSITIONING 1 (CHUP1) and its plasma membrane-associated partner KINESIN-LIKE PROTEIN FOR ACTIN-BASED CHLOROPLAST MOVEMENT 1 (KAC1). Our biochemical assays revealed that CHUP1 and KAC1 interact, and infection cell biology assays demonstrated their co-accumulation in foci where chloroplasts contact the EHM. Genetic depletion of CHUP1 or KAC1 reduces the focal deposition of callose around the haustorium without affecting other core immune processes. Our findings suggest that the chloroplast-EHM attachment complex promotes plant focal immunity, revealing key components and their potential roles in the deposition of defense materials at the pathogen interface. These results advance our understanding of organelle-mediated immunity and highlight the significance of MCS in plant-pathogen interactions.}, }
@article {pmid40911039, year = {2025}, author = {Dagenais Roy, M and Déziel, E}, title = {Microbial Primer: Biosurfactants - the ABCs of microbial surface-active metabolites.}, journal = {Microbiology (Reading, England)}, volume = {171}, number = {9}, pages = {}, doi = {10.1099/mic.0.001604}, pmid = {40911039}, issn = {1465-2080}, mesh = {*Surface-Active Agents/metabolism/chemistry ; *Fungi/metabolism/genetics ; *Bacteria/metabolism/genetics ; Biosynthetic Pathways ; Yeasts/metabolism ; Biosurfactants ; }, abstract = {Microbial surfactants (biosurfactants) are low-molecular-weight amphiphilic secondary metabolites synthesized by a wide range of micro-organisms, including bacteria, yeasts and fungi. These compounds reduce surface and interfacial tension, promote emulsification and self-assemble into supramolecular structures such as micelles. Their remarkable structural diversity reflects the metabolic complexity of their microbial producers. In this primer, we outline shared features across biosurfactant-producing organisms, focusing on biosynthetic pathways, biological functions and regulatory mechanisms. The study of biosurfactants lies at the intersection of ecological, biotechnological and medical research, offering valuable insights into microbial ecology and promising avenues for sustainable innovation.}, }
@article {pmid40908830, year = {2025}, author = {Yamlahi, YE and Remmal, I and Maurady, A and Britel, MR and Bakali, AH and Mokhtar, NB and Galiatsatos, I and Stathopoulou, P and Tsiamis, G}, title = {Characterization of the olive fly (Bactrocera oleae) microbiome across diverse geographic regions of Morocco.}, journal = {Insect science}, volume = {}, number = {}, pages = {}, doi = {10.1111/1744-7917.70126}, pmid = {40908830}, issn = {1744-7917}, support = {22662//International Atomic Energy Agency/ ; }, abstract = {The olive fruit fly (Bactrocera oleae) is a significant pest threatening olive production worldwide. Bactrocera oleae relies on symbiotic bacteria for nutrition, development, and adaptation to its environment. Among these, Candidatus Erwinia dacicola is the most dominant symbiont and plays a key role in the fly's physiology and ecological adaptation. Understanding the dynamics between B. oleae, Ca. E. dacicola, and other components of the B. oleae microbiome is essential for developing effective targeted area-wide pest management strategies. This study aims to leverage full 16S rRNA gene sequencing to enhance the characterization of microbiome diversity in wild B. oleae populations from different regions in Morocco: Ouezzane, Rabat, Tanger, Errachidia, and Beni-Mellal. The results revealed distinct microbiome compositions influenced by geographic locations, with Candidatus Erwinia dacicola as the dominant symbiont, followed by Erwinia persicina as a secondary contributor. Other bacterial taxa, including Asaia bogorensis, were also identified, highlighting the functional diversity within the olive fly microbiome. These findings provide insights into the microbial ecology of B. oleae, contributing to the development and enhancement of sustainable pest control strategies.}, }
@article {pmid40908508, year = {2025}, author = {Boden, L and Bludau, D and Sieber, G and Deep, A and Baikova, D and David, GM and Hadžiomerović, U and Stach, TL and Buchner, D and Boenigk, J}, title = {Varying Responses to Heat Stress and Salinization Between Benthic and Pelagic Riverine Microbial Communities.}, journal = {Environmental microbiology}, volume = {27}, number = {9}, pages = {e70173}, doi = {10.1111/1462-2920.70173}, pmid = {40908508}, issn = {1462-2920}, support = {CRC 1439/1//Deutsche Forschungsgemeinschaft/ ; //Open Access Publication Fund of the University of Duisburg-Essen/ ; }, abstract = {Microbial communities play a crucial role in the functioning of freshwater ecosystems but are continuously threatened by climate change and anthropogenic activities. Elevated temperatures and salinisation are particularly challenging for freshwater habitats, but little is known about how microbial communities respond to the simultaneous exposure to these stressors. Here, we use mesocosm experiments and amplicon sequencing data to investigate the responses of pelagic and benthic microbial communities to temperature and salinity increases, both individually and in combination. Our results highlight the varying responses of freshwater microbial communities, with sediment communities exhibiting greater stability in response to environmental changes compared to water column communities, and salinisation having a more pronounced impact on microeukaryotes compared to prokaryotes. Simultaneous exposure to elevated temperature and salinity reduced the impact of salinisation on prokaryotes, while microeukaryotes were similarly affected by the combined treatments and salinisation alone. These findings emphasise the complexity of microbial responses to single and multiple stressors, underscoring the need to consider both individual and interactive effects when predicting ecosystem responses to environmental changes.}, }
@article {pmid40907150, year = {2025}, author = {Prósperi de Oliveira Paula, M and Wurdig Roesch, LF and Coutinho Ramos, A and Tótola, MR and Satler Pylro, V}, title = {Bacterial consortia enhance glyphosate breakdown and drive soil microbial dynamics.}, journal = {Chemosphere}, volume = {387}, number = {}, pages = {144677}, doi = {10.1016/j.chemosphere.2025.144677}, pmid = {40907150}, issn = {1879-1298}, abstract = {This study assessed the bioremediation potential of four microbial consortia in soil microcosms contaminated with glyphosate, focusing on their metabolic activity and impact on microbial diversity. Among the tested consortia, Con_CC-G-isolated from Conilon Coffee soil that had remained glyphosate-free for three years-demonstrated the most pronounced effects. Microbial metabolic activity was quantified using respirometry, which tracked CO2 production over 140 h in both inoculated and control soils. Changes in microbial community composition were analyzed using 16S rRNA gene metataxonomics. The results revealed that glyphosate exposure stimulated respiratory activity, particularly in inoculated treatments. Differential abundance analysis revealed significant increases in Achromobacter and Serratia in inoculated microcosms, as well as in other key herbicide-degrading genera. Complementary HPLC-DAD analyses confirmed glyphosate degradation, with Con_CC and Con_CC-G achieving the highest removal efficiencies under both carbon- and phosphorus-limited conditions. These findings provide direct evidence of glyphosate biodegradation and highlight the strong bioremediation potential of Con_CC-G for soils contaminated with this herbicide. Further research must assess its environmental impact and safety before field-scale application.}, }
@article {pmid40906125, year = {2025}, author = {Basit, A and Haq, IU and Hyder, M and Humza, M and Younas, M and Akhtar, MR and Ghafar, MA and Liu, TX and Hou, Y}, title = {Microbial Symbiosis in Lepidoptera: Analyzing the Gut Microbiota for Sustainable Pest Management.}, journal = {Biology}, volume = {14}, number = {8}, pages = {}, doi = {10.3390/biology14080937}, pmid = {40906125}, issn = {2079-7737}, support = {National Natural Science Foundation of China (U22A20489; 32361143791).//National Natural Science Foundation of China (U22A20489; 32361143791)./ ; }, abstract = {Recent advances in microbiome studies have deepened our understanding of endosymbionts and gut-associated microbiota in host biology. Of those, lepidopteran systems in particular harbor a complex and diverse microbiome with various microbial taxa that are stable and transmitted between larval and adult stages, and others that are transient and context-dependent. We highlight key microorganisms-including Bacillus, Lactobacillus, Escherichia coli, Pseudomonas, Rhizobium, Fusarium, Aspergillus, Saccharomyces, Bifidobacterium, and Wolbachia-that play critical roles in microbial ecology, biotechnology, and microbiome studies. The fitness implications of these microbial communities can be variable; some microbes improve host performance, while others neither positively nor negatively impact host fitness, or their impact is undetectable. This review examines the central position played by the gut microbiota in interactions of insects with plants, highlighting the functions of the microbiota in the manipulation of the behavior of herbivorous pests, modulating plant physiology, and regulating higher trophic levels in natural food webs. It also bridges microbiome ecology and applied pest management, emphasizing S. frugiperda as a model for symbiont-based intervention. As gut microbiota are central to the life history of herbivorous pests, we consider how these interactions can be exploited to drive the development of new, environmentally sound biocontrol strategies. Novel biotechnological strategies, including symbiont-based RNA interference (RNAi) and paratransgenesis, represent promising but still immature technologies with major obstacles to overcome in their practical application. However, microbiota-mediated pest control is an attractive strategy to move towards sustainable agriculture. Significantly, the gut microbiota of S. frugiperda is essential for S. frugiperda to adapt to a wide spectrum of host plants and different ecological niches. Studies have revealed that the microbiome of S. frugiperda has a close positive relationship with the fitness and susceptibility to entomopathogenic fungi; therefore, targeting the S. frugiperda microbiome may have good potential for innovative biocontrol strategies in the future.}, }
@article {pmid40906100, year = {2025}, author = {Li, W and Yang, L and Cong, X and Mao, Z and Zhou, Y}, title = {Distribution Patterns and Assembly Mechanisms of Rhizosphere Soil Microbial Communities in Schisandra sphenanthera Across Altitudinal Gradients.}, journal = {Biology}, volume = {14}, number = {8}, pages = {}, doi = {10.3390/biology14080944}, pmid = {40906100}, issn = {2079-7737}, support = {2025NC-YBXM-059//the Shaanxi Provincial Department of Science and Technology Key Research and Development Program-General Project/ ; }, abstract = {To investigate the characteristics of rhizosphere soil microbial communities associated with Schisandra sphenanthera across different altitudinal gradients and to reveal the driving factors of microbial community dynamics, this study collected rhizosphere soil samples at four elevations: 900 m (HB1), 1100 m (HB2), 1300 m (HB3), and 1500 m (HB4). High-throughput sequencing and molecular ecological network analysis were employed to analyze the microbial community composition and species interactions. A null model was applied to elucidate community assembly mechanisms. The results demonstrated that bacterial communities were dominated by Proteobacteria, Acidobacteriota, Actinobacteriota, and Chloroflexi. The relative abundance of Proteobacteria increased with elevation, while that of Acidobacteriota and Actinobacteriota declined. Fungal communities were primarily composed of Ascomycota and Basidiomycota, with both showing elevated relative abundances at higher altitudes. Diversity indices revealed that HB2 exhibited the highest bacterial Chao, Ace, and Shannon indices but the lowest Simpson index. For fungi, HB3 displayed the highest Chao and Ace indices, whereas HB4 showed the highest Shannon index and the lowest Simpson index. Ecological network analysis indicated stronger bacterial competition at lower elevations and enhanced cooperation at higher elevations, contrasting with fungal communities that exhibited increased competition at higher altitudes. Altitude and soil nutrients were negatively correlated with soil carbon content, while plant nutrients and fungal diversity positively correlated with soil carbon. Null model analysis suggested that deterministic processes dominated bacterial community assembly, whereas stochastic processes governed fungal assembly. These findings highlight significant altitudinal shifts in the microbial community structure and assembly mechanisms in S. sphenanthera rhizosphere soils, driven by the synergistic effects of soil nutrients, plant growth, and fungal diversity. This study provides critical insights into microbial ecology and carbon cycling in alpine ecosystems, offering a scientific basis for ecosystem management and conservation.}, }
@article {pmid40905693, year = {2025}, author = {González-Marín, C and García-Botero, C and Metaute-Molina, E and Caraballo-Rodríguez, AM and Dorrestein, PC and Villegas-Escobar, V}, title = {Bacillus spp. Antibacterial Activity Induced by Triphenyl Tetrazolium Chloride against Ralstonia solanacearum: Oxidative Stress Response and Metabolome Changes.}, journal = {ACS chemical biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acschembio.5c00171}, pmid = {40905693}, issn = {1554-8937}, abstract = {High salt concentrations affect the electron transport chain of bacterial cells, leading to an oxidative stress response that encompasses the formation of reactive oxygen species (ROS). The salt 2,3,5-triphenyltetrazolium chloride (TTC) triggers antibacterial activity against the phytopathogen Ralstonia solanacearum in Bacillus species; however, the underlying mechanisms remain unknown. Here, we tested the hypothesis that TTC-inducible activity is related to the formation of ROS and its metabolites. We found that l-ascorbic acid, superoxide dismutase, and catalase counteracted TTC-inducible activity in various Bacillus species. Furthermore, R. solanacearum exhibited a higher susceptibility to H2O2 than Bacillus spp. Genomic analysis showed differences in stress-related genes, with Bacillus strains containing the ROS scavengers bacillithiol and bacillibactin, while glutathione inR. solanacearum. Multivariate analysis indicated that the Bacillus species and TTC influence Bacillus metabolome, resulting in higher levels of quinazoline alkaloids, with potential antibacterial activity against R. solanacearum. Results suggest that TTC induces the production of O2[•-] and H2O2 and metabolites that arrest R. solanacearum growth.}, }
@article {pmid40904889, year = {2025}, author = {Lv, J and Zhao, HP and Yu, Y and Wang, JH and Zhang, XJ and Guo, ZQ and Jiang, WY and Wang, K and Guo, L}, title = {From gut microbial ecology to lipid homeostasis: Decoding the role of gut microbiota in dyslipidemia pathogenesis and intervention.}, journal = {World journal of gastroenterology}, volume = {31}, number = {30}, pages = {108680}, pmid = {40904889}, issn = {2219-2840}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Dyslipidemias/microbiology/therapy/metabolism/etiology ; Homeostasis ; *Lipid Metabolism ; Animals ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; Prebiotics/administration &amp; dosage ; Dysbiosis/microbiology/therapy ; }, abstract = {Dyslipidemia, a complex disorder characterized by systemic lipid profile abnormalities, affects more than half of adults globally and constitutes a major modifiable risk factor for atherosclerotic cardiovascular disease. Mounting evidence has established the gut microbiota (GM) as a pivotal metabolic modulator that is correlated with atherogenic lipid profiles through dietary biotransformation, immunometabolic regulation, and bioactive metabolite signaling. However, the host-microbe interactions that drive dyslipidemia pathogenesis involve complex gene-environment crosstalk spanning epigenetic modifications to circadian entrainment. Mechanistically, GM perturbations disrupt lipid homeostasis via lipopolysaccharide-triggered hepatic very low-density lipoprotein overproduction, short-chain fatty acid-G protein-coupled receptor 43/41-mediated adipocyte lipolysis, bile acid-farnesoid X receptor/Takeda G protein-coupled receptor 5 axis dysfunction altering cholesterol flux, microbial β-oxidation intermediates impairing mitochondrial energetics, and host-microbiota non-coding RNA crosstalk regulating lipogenic genes. This comprehensive review systematically examines three critical dimensions, including bidirectional GM-lipid axis interactions, molecular cascades bridging microbial ecology to metabolic dysfunction, and translational applications of GM modulation through precision probiotics, structure-specific prebiotics, and a metabolically optimized fecal microbiota transplantation protocol. Notwithstanding these advances, critical gaps persist in establishing causal microbial taxa-pathway relationships and optimal intervention timing. Future directions require longitudinal multi-omic studies, gnotobiotic models for mechanistic validation, and machine learning-driven personalized microbiota profiling. This synthesis provides a framework for developing microbiota-centric strategies targeting dyslipidemia pathophysiology, with implications for precision dyslipidemia management and next-generation cardiovascular disease prevention.}, }
@article {pmid40904105, year = {2025}, author = {Elliott, JFK and Cozens, K and Cai, Y and Waugh, G and Watson, BN and Westra, E and Taylor, TB}, title = {Phage susceptibility to a minimal, modular synthetic CRISPR-Cas system in Pseudomonas aeruginosa is nutrient dependent.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {380}, number = {1934}, pages = {20240473}, pmid = {40904105}, issn = {1471-2970}, support = {//UK Government's Horizon Europe funding guarantee/ ; //Royal Society/ ; //Philip Leverhulme Prize/ ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Pseudomonas aeruginosa/virology/genetics ; *CRISPR-Cas Systems ; *Pseudomonas Phages/physiology/genetics ; *Nutrients/metabolism ; *Bacteriophages/physiology ; }, abstract = {CRISPR-Cas systems can provide adaptive, heritable immunity to their prokaryotic hosts against invading genetic material such as phages. It is clear that the importance of acquiring CRISPR-Cas immunity to anti-phage defence varies across environments, but it is less clear if and how this varies across different phages. To explore this, we created a synthetic, modular version of the type I-F CRISPR-Cas system of Pseudomonas aeruginosa. We used this synthetic system to test CRISPR-Cas interference against a panel of 13 diverse phages using engineered phage-targeting spacers. We observed complete protection against eight of these phages, both lytic and lysogenic and with a range of infectivity profiles. However, for two phages, CRISPR-Cas interference was only partially protective in high-nutrient conditions, yet completely protective in low-nutrient conditions. This work demonstrates that nutrient conditions modulate the strength of CRISPR-Cas immunity and highlights the importance of environmental conditions when screening defence systems for their efficacy against various phages.This article is part of the discussion meeting issue 'The ecology and evolution of bacterial immune systems'.}, }
@article {pmid40904103, year = {2025}, author = {Le Roux, F}, title = {The ecology and evolution of microbial immune systems: a look on the wild vibrio side.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {380}, number = {1934}, pages = {20240078}, pmid = {40904103}, issn = {1471-2970}, support = {/ERC_/European Research Council/International ; //Canada Excellence Research Chairs Program/ ; //Agence Nationale de la Recherche/ ; }, mesh = {*Bacteriophages/physiology/genetics ; *Vibrio/virology/immunology/genetics ; *Biological Evolution ; Host Specificity ; Interspersed Repetitive Sequences ; Animals ; }, abstract = {Natural populations of vibrio beyond the well-studied pandemic strains of Vibrio cholerae, provide a powerful model for investigating the eco-evolutionary dynamics of microbial immune systems. Their genetic diversity, ecological versatility, ease of culturability and the availability of time-series data enable detailed studies of phage-host interactions in natural contexts. This review synthesizes recent advances in vibriophage research, highlighting key findings and emerging tools. High-throughput assays and genomic tools have offered new perspectives on phage specificity, host range and the evolutionary pressures shaping these interactions. Theoretical frameworks, such as arms race and fluctuating selection dynamics, are informed by empirical data from vibrio-phage systems, with time-series sampling providing crucial insights into their temporal and spatial dynamics. A major finding is the role of mobile genetic elements (MGEs) in encoding bacterial defence systems, which shape phage-host coevolution. Discoveries like the phage satellite PICMI illustrate how MGEs facilitate the transfer of antiviral systems, influencing ecological and evolutionary dynamics. The paradox of generalist vibriophages, rare despite their broad host ranges, is also explored. By integrating experimental approaches with field observations, vibriophage research advances microbial ecology and informs sustainable applications in aquaculture and phage therapy, reinforcing vibrios as a versatile model system.This article is part of the discussion meeting issue 'The ecology and evolution of bacterial immune systems'.}, }
@article {pmid40904102, year = {2025}, author = {Pons, BJ and Łapińska, U and Lopes-Domingues, I and Chisnall, MAW and Westra, ER and Pagliara, S and van Houte, S}, title = {Phage provoke growth delays and SOS response induction despite CRISPR-Cas protection.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {380}, number = {1934}, pages = {20240474}, pmid = {40904102}, issn = {1471-2970}, support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /MRC_/Medical Research Council/United Kingdom ; //UK Government's Horizon Europe funding guarantee/ ; //Leverhulme Trust/ ; }, mesh = {*Pseudomonas aeruginosa/virology/growth &amp; development/genetics ; *CRISPR-Cas Systems ; *Pseudomonas Phages/physiology ; *SOS Response, Genetics ; *Bacteriophages/physiology ; }, abstract = {Bacteria evolve resistance against their phage foes with a wide range of resistance strategies whose costs and benefits depend on the level of protection they confer and on the costs for maintainance. Pseudomonas aeruginosa can evolve resistance against its phage DMS3vir either by surface mutations that prevent phage binding or through CRISPR-Cas immunity. CRISPR immunity carries an inducible cost whose exact origin is still unknown, and previous work suggested it stems from the inability of the CRISPR-Cas system to completely prevent phage DNA injection and subsequent gene expression before clearing the phage infection. However, the bacterial processes involved are still unknown, and we hypothesize that CRISPR-immunity-associated costs could come from increased mortality rate or reduced growth ability compared with surface-resistant bacteria. To tease apart these two mechanisms with divergent ecological consequences, we use a novel microfluidics-based single-cell approach combined with flow cytometry methods to monitor the effects of phage exposure on the survival and growth of its host. We observed that while CRISPR immunity protects from phage-induced lysis, it cannot prevent phage-induced division lag, filamentation and SOS response activation in a subpopulation of the host bacteria. These results suggest that the costs associated with CRISPR immunity at the population level are caused by heterogeneity in phage-induced growth defects.This article is part of the discussion meeting issue 'The ecology and evolution of bacterial immune systems'.}, }
@article {pmid40902774, year = {2025}, author = {Azeem, M and Han, R and Liu, S and Jacques, KJ and Abdelrahman, H and Kazmi, SSH and Kareem, A and Khan, ZH and Rafiq, N and Li, H and Kuzyakov, Y and Qin, K}, title = {Biochar-derived dissolved organic matter induced changes in the bacterial communities structure and metabolic functions in As and Cd contaminated soil.}, journal = {Environmental research}, volume = {}, number = {}, pages = {122749}, doi = {10.1016/j.envres.2025.122749}, pmid = {40902774}, issn = {1096-0953}, abstract = {This study investigates the effects of pyrolytic temperature and feedstock type on the release of biochar-derived dissolved organic matter (BDOM) and its impact on the soil bacterial community and the composition of soil dissolved organic matter (SDOM). The BDOM was extracted from biochars produced from sheep bones, rice husk, and rabbit manure, prepared at low (400 °C, LPT) or high (700 °C, HPT) pyrolytic temperatures. The BDOM was then applied at a concentration of 2.5% (w/w). LPT-BDOM produced higher contents of BDOM (up to 1440±43 mg kg[-1]), resulting in higher SDOM (up to 78%, compared with control soil) after application and higher availability of nutrients (Ca, Mg, and P) and toxic metalloids (TMs; As and Cd) in soil. The addition of BDOM altered the bacterial community composition, with increased bacterial richness and diversity observed in the HPT-BDOM compared to the control. The community shift was linked with higher levels of volatile organic compounds and increased nutrient availability compared with HPT. The increase in fluorescence (up to 54%), freshness (up to 29%), biological (up to 112%), and humification (up to 52%) indices was associated with LPT-derived BDOM, particularly with sheep bone-BDOM. Manure-LPT and sheep bone-HPT enhanced hydrocarbon degradation, while rice husk-LPT enriched taxa related to nitrogen fixation and nitrate reduction. LPT treatments favored cellulolysis and fermentation, whereas HPT treatments promoted methylotrophy, aligning with their contrasting carbon lability. These findings highlight the dual role of biochar's labile fraction in shaping carbon availability, influencing SDOM dynamics, nutrient and total metals (TMs) bioavailability, and microbial ecology, underscoring the need for feedstock- and temperature-specific selection in environmental applications.}, }
@article {pmid40901853, year = {2025}, author = {Gómez-Palacio, A and Junca, H and Vivero-Gomez, RJ and Suaza, J and Moreno-Herrera, CX and Cadavid-Restrepo, G and Pieper, DH and Uribe, S}, title = {Metagenomic profiling of the insect-specific virome in non-urban mosquitoes (Culicidae: Culicinae) from Colombia's Northern inter-Andean valleys.}, journal = {PloS one}, volume = {20}, number = {9}, pages = {e0331552}, doi = {10.1371/journal.pone.0331552}, pmid = {40901853}, issn = {1932-6203}, mesh = {Animals ; Colombia ; *Virome/genetics ; *Culicidae/virology ; *Metagenomics/methods ; *Metagenome ; Phylogeny ; *Insect Viruses/genetics/classification ; }, abstract = {Hematophagous mosquitoes are major vectors of diverse pathogens and serve as bioindicators in tropical ecosystems, yet their virome in non-urban Neotropical regions remains poorly characterized. We analyzed the virome of 147 mosquitoes from two natural ecosystems in Colombia using a hybrid viral identification approach, combining high-confidence and less stringent methods. Most high-confidence viral contigs remained unclassified or unknown, as expected for metagenomic surveys in novel ecosystems. However, members for the Magrovirales and Ortervirales, and other six orders were detected at lower abundance. Using a complementary, less stringent approach, we identified 168 viral species from 68 genera and 22 families across four mosquito tribes (Aedini, Culicini, Orthopodomyiini, Sabethini), with dominance of Metaviridae, Retroviridae, Iridoviridae, and Poxviridae, though many sequences could not be taxonomically assigned. Insect-specific viruses predominated, while no medically relevant arboviruses were detected. Both methods consistently identified Trichoplusia ni TED virus, Cladosporium fulvum T-1 virus, Lymphocystis disease viruses, and Oryctes rhinoceros nudivirus among the most abundant and frequently detected taxa across samples. Alpha diversity indices revealed the highest virome diversity in Sabethini, followed by Orthopodmyiini, and substantially lower richness and diversity in Aedini and Culicini. These results provide a baseline for virome characterization in sylvatic mosquitoes from Colombia and highlight the need for further research on the ecological roles of the mosquito virome in pathogen transmission and microbiome evolution.}, }
@article {pmid40901273, year = {2025}, author = {Worsley, SF and Lee, CZ and Versteegh, MA and Burke, T and Komdeur, J and Dugdale, HL and Richardson, DS}, title = {Gut microbiome communities demonstrate fine-scale spatial variation in a closed, island bird population.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf138}, doi = {10.1093/ismeco/ycaf138}, pmid = {40901273}, issn = {2730-6151}, abstract = {Environmental variation is a key factor shaping microbial communities in wild animals. However, most studies have focussed on separate populations distributed over large spatial scales. How ecological factors shape inter-individual microbiome variation within a single landscape and host population remains poorly understood. Here, we use dense sampling of individuals in a natural, closed population of Seychelles warblers (Acrocephalus sechellensis) on Cousin Island (<0.7 km diameter, 0.34 km[2] total area) to determine whether gut microbiome communities exhibit high-resolution spatial variation over fine scales (average territory area is 0.0023 km[2]). We identified a small but highly significant quadratic relationship between geographic distance and gut microbiome beta diversity across the island. Microbiome composition initially diverged with increasing geographic distance between territories. However, after ca. >300 m, microbiome composition became increasingly similar amongst individuals situated on different sides of the island. This relationship was robust to the effects of host relatedness, age, and sex. Further analysis showed that microbiome composition differed between individuals inhabiting coastal and inland territories. Warblers in coastal territories harboured greater abundances of marine bacteria and lower abundances of anaerobic taxa commonly linked to host metabolic health, suggesting that exposure to different environmental microbes and variation in host condition (which is lower in coastal territories) could drive spatial patterns of gut microbiome variation across the island. This work demonstrates that host-microbe interactions can be labile even at very fine spatial scales. Such variability may have implications for how species respond to anthropogenic disturbance in wild habitats.}, }
@article {pmid40900750, year = {2025}, author = {Li, Y and Zhang, S and Guo, Y and Xu, K and Zhang, X and Pan, M and Sun, Q and Zhang, Y and Fan, Y}, title = {Analysis of microbial diversity and functions in sediments and overlying water of the Shiliu River.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19979}, pmid = {40900750}, issn = {2167-8359}, mesh = {*Rivers/microbiology ; *Geologic Sediments/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; *Fungi/genetics/classification/isolation &amp; purification ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; *Water Microbiology ; *Microbiota ; }, abstract = {BACKGROUND: With the acceleration of urbanization, urban rivers have become a significant component of the urban ecosystem, attracting considerable attention regarding their ecological status and biodiversity. This study focuses on the Shiliu River, aiming to analyze the microbial diversity and functions present in the overlying water and sediments of severely polluted areas.<br><br>METHODS: This study investigated the Shiliu River. In August 2024, sediment and overlying water samples were collected from its severely polluted reaches. The NextSeq 2000 PE300 platform was employed for sequencing to detect bacterial and fungal taxa abundances. PICRUSt and FUNGuild predicted sample functional abundances using bacterial 16S rRNA and fungal internal transcribed spacer (ITS) gene sequences, respectively.<br><br>RESULTS: The findings demonstrate that sediments exhibit higher bacterial and fungal richness than overlying water, with significant discrepancies in bacterial and fungal community compositions. Dominant taxa differ at both phylum and genus levels: in sediments, the predominant bacterial phylum is Proteobacteria and genus norank_Anaerolineaceae, while the dominant fungal phylum is Rozellomycota and genus unclassified_Rozellomycota. In overlying water, the bacterial phylum remains Proteobacteria but the dominant genus shifts to Acinetobacter, whereas fungal phyla and genera (Rozellomycota and unclassified_Rozellomycota) are consistent with sediments. Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotation identifies 25 metabolic pathways, with amino acid metabolism-related genes showing the highest abundance in both environments. Clusters of Orthologous Genes (COG) annotation reveals the highest abundance of [R] General function prediction in both sample groups, and FUNGuild analysis indicates that Animal Endosymbiont-Animal Pathogen-Plant Pathogen-Undefined Saprotroph is the most prevalent functional category in both sediments and overlying water. This study provides a microbiological foundation by clarifying microbial community structures (dominant phyla, functional taxa), decoding pollutant-degrading metabolic potentials (N/C cycling pathways), and identifying river health ecological indicators. This enables targeted bioremediation strategies (e.g., sediment microbial consortia for nutrient removal) and integrates microbial ecological data into urban river restoration.<br><br>CONCLUSIONS: This study reveals the microbial community structures in the sediments and overlying water of the polluted Shiliu River, finding diverse patterns with higher richness in sediments, Proteobacteria and Ascomycota as dominants. Shared taxa have different abundances, indicating niche differentiation. Sediments have enriched nitrogen/carbon cycling pathways for pollutant degradation. These results offer a microbiological basis for urban river restoration, identify bioremediation-target taxa, and stress the integration of microbial ecology into pollution management.}, }
@article {pmid40388809, year = {2025}, author = {Mijatović Scouten, J and Hsieh, SC and Sung, LK and Wen, YV and Kuo, CH and Lai, EM and Chang, JH}, title = {Function, Evolution, and Ecology of Type VI Secretion Systems of Plant-Associated Bacteria.}, journal = {Annual review of phytopathology}, volume = {63}, number = {1}, pages = {333-356}, doi = {10.1146/annurev-phyto-121423-084620}, pmid = {40388809}, issn = {1545-2107}, mesh = {*Type VI Secretion Systems/genetics/metabolism/physiology ; *Plants/microbiology ; *Bacteria/genetics/metabolism/pathogenicity ; Biological Evolution ; *Plant Diseases/microbiology ; Virulence ; Bacterial Proteins/metabolism/genetics ; }, abstract = {Intense competition for resources among microorganisms imposes strong selective pressure for traits that provide a competitive advantage, including traits that harm others. The type VI secretion system (T6SS) is a versatile contractile injection apparatus encoded by many Gram-negative bacteria. This system is best known for its lethal use in deploying effectors toxic to neighboring bacteria. However, T6SSs can also be used to secrete effectors into the environment to influence nutrient acquisition. Additionally, for some bacteria, T6SSs deploy effectors toxic to eukaryotic hosts and are involved in virulence, which, however, has not been demonstrated for plant-associated bacteria. Here, we review the diverse functions and evolutionary basis of T6SSs. We discuss the potential ecological impacts of T6SSs in plant-associated communities. Understanding outcomes is important for finding the best approaches for using bacteria in sustainable management of plant agricultural systems.}, }
@article {pmid40896518, year = {2025}, author = {Elias Masiques, N and Vermeiren, S and De Vrieze, J and Gansemans, Y and Deforce, D and Van Nieuwerburgh, F and De Smet, S and Van Hecke, T}, title = {Food hydrocolloids κ-carrageenan and xanthan gum in processed red meat modify gut health in rats.}, journal = {Current research in food science}, volume = {11}, number = {}, pages = {101162}, doi = {10.1016/j.crfs.2025.101162}, pmid = {40896518}, issn = {2665-9271}, abstract = {The food hydrocolloids κ-carrageenan and xanthan gum, used in processed foods including meat products, have unclear effects on gut health. This study investigated the effects of incorporating 1 % κ-carrageenan or xanthan gum into pork on protein digestibility, gut microbiota, oxidative stress, and gene expression using both in vitro gastrointestinal digestion/fermentation and an in vivo rodent model. In vitro, xanthan gum reduced protein digestibility (-11 %) in the simulated small intestine, thus elevating protein fermentation metabolites (up to 4-fold), but this was not observed in vivo. Consumption of a low-fiber pork diet without hydrocolloids promoted Akkermansia (29.5 % median abundance) and Tannerellaceae (24.7 %) growth in the colon, whereas κ-carrageenan increased Desulfovibrio (7.95 %) and Alistipes (6.14 %), and xanthan gum enhanced unclassified Muribaculaceae (14.8 %) and Bacteroides (12.1 %). Unexpectedly, transcriptomic analysis revealed a down-regulation of gut inflammatory pathways, accompanied by lower fecal calprotectin levels, in rats consuming pork with hydrocolloids. While κ-carrageenan notably reduced lipid oxidation in stomach contents, only xanthan gum lowered plasma and colonic oxidative stress. These findings highlight the potential of hydrocolloids to modulate dietary responses, suggesting a role in influencing gut health following high processed meat consumption.}, }
@article {pmid40894307, year = {2025}, author = {van den Bergh, SG and Chardon, I and Meima-Franke, M and Pérez, G and Rocha, GS and Brenzinger, K and Korthals, GW and Mayer, J and Cougnon, M and Reheul, D and de Boer, W and Bodelier, PLE}, title = {Improved methane mitigation potential and modulated methane cycling microbial communities in arable soil by compost addition.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf139}, doi = {10.1093/ismeco/ycaf139}, pmid = {40894307}, issn = {2730-6151}, abstract = {The global atmospheric concentration of the potent greenhouse gas methane (CH4) is rising rapidly, and agriculture is responsible for 30%-50% of the yearly CH4 emissions. To limit its global warming effects, strong and sustained reductions are needed. Sustainable agricultural management strategies, as the use of organic amendments like compost, have previously proven to have a potent CH4 mitigation effect in laboratory experiments. Here we investigated, using an extensive field study, the effect of organic amendments on the CH4 mitigation potential and CH4 cycling microbial communities of arable soils. Organic-amended soils had higher potential CH4 uptake rates and an improved potential to oxidize CH4 to sub-atmospheric concentrations. Also, we showed for the first time that the methanotrophic and methanogenic microbial communities of arable soils were unequivocally altered after organic amendment application by increasing in size while getting less diverse. Compost-amended soils became dominated by the compost-originating methanotroph Methylocaldum szegediense and methanogen Methanosarcina horonobensis, replacing the indigenous methane cycling community members. However, multivariate analyses didn't point out type Ib methanotrophs like M. szegediense as significant driving factors for the observed improved soil CH4 uptake potential. Conventional type IIa methanotrophs like Methylocystis sp. also had higher differential abundances in organic-amended soils and are speculated to contribute to the improved CH4 uptake potential. Altogether, the results showed that compost serves as a vector for the introduction of CH4 cycling microbes and improves the soil's CH4 uptake potential, which emphasizes the potential of organic fertilization with compost to contribute to CH4 mitigation in agricultural soils.}, }
@article {pmid40892732, year = {2025}, author = {Yssel, J and Everaerts, V and Van Hemelrijk, W and Bylemans, D and Setati, ME and Lievens, B and Blancquaert, E and Crauwels, S}, title = {Assessing the potential of seaweed extracts to improve vegetative, physiological and berry quality parameters in Vitis vinifera cv. Chardonnay under cool climatic conditions.}, journal = {PloS one}, volume = {20}, number = {9}, pages = {e0331039}, pmid = {40892732}, issn = {1932-6203}, mesh = {*Vitis/drug effects/growth &amp; development/physiology ; *Seaweed/chemistry ; *Fruit/drug effects/growth &amp; development/physiology ; Ascophyllum/chemistry ; Plant Leaves/drug effects/growth &amp; development ; Climate ; }, abstract = {Seaweed extracts are promising plant biostimulants for viticulture, but their effects on white winegrape cultivars grown under cool climates remain fairly undocumented. Furthermore, information is limited on the biostimulant potential of some brown seaweed species like Ecklonia maxima. This study evaluated the impact of two commercial extracts (derived from Ascophyllum nodosum and Ecklonia maxima) on Vitis vinifera cv. Chardonnay in Belgium during the 2021 and 2022 growing seasons. The extracts, alongside a water‑control and an NPK‑reference (NPK‑Ref) treatment (with nitrogen, phosphorus, and potassium levels comparable to the extracts), were applied as foliar sprays five times at regular intervals, from flowering to ripening. In 2021 and 2022, A. nodosum significantly increased individual leaf area (+12% and +15%), while in 2021 A. nodosum‑treated vines had an increased chlorophyll content index (+12% CCI) and photosystem II (PSII) reaction centre density (+6%) relative to control vines. This corresponded with a small, but significant, improvement (+1.5%) in PSII maximum quantum yield (Fv∕Fm), whereas PSII electron transport efficiency (ΦE0) remained unchanged. Furthermore, increased berry size, mass, and sugar content were observed in A. nodosum‑treated vines during ripening in 2022, comparable to NPK‑Ref vines. Conversely, the E. maxima extract had limited effects on vegetative growth, physiology, and subsequent berry development. Yield increase from 2021 to 2022 varied by treatment, with a significant increase observed for E. maxima (+60%) and NPK‑Ref vines (+80%), relative to control vines. Our results indicate that seaweed extracts, specifically A. nodosum‑based, can enhance grapevine leaf area, CCI, and Fv∕Fm under cool climatic conditions. A. nodosum treatment was also associated with increased berry size and sugar content, while E. maxima treatment was associated with increased yield in the subsequent, warmer season. Altogether, our study highlights that the differential effects of seaweed extracts on grapevine development are modulated by species and environmental conditions.}, }
@article {pmid40892071, year = {2025}, author = {Gordon, DAR and Burke, DJ and Carrino-Kyker, SR and Bashian-Victoroff, C and Mabrouk, AI and Van Stan, JT}, title = {Community Composition of Microbial Eukaryotes Transported by Stemflow from Fagus grandifolia Ehrh. (American Beech) Trees in Northeastern Ohio (USA).}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {93}, pmid = {40892071}, issn = {1432-184X}, support = {DEB-2213623//Division of Environmental Biology/ ; }, mesh = {Ohio ; *Fagus/microbiology ; Fungi/genetics/classification/isolation &amp; purification ; *Eukaryota/classification/genetics/isolation &amp; purification ; *Rain ; RNA, Ribosomal, 18S/genetics ; Seasons ; Trees/microbiology ; Biodiversity ; Forests ; *Microbiota ; }, abstract = {Stemflow, the concentrated fraction of rainfall that drains down tree trunks, can translocate canopy biota to the forest floor, but its eukaryotic composition remains uncharacterized via eDNA methods. We collected stemflow from 18 Fagus grandifolia (American beech) trees during ten storms in northeastern Ohio (USA) and analyzed 18S rRNA eDNA to resolve transported microbial-eukaryote communities. Over 12 million reads (83 samples) revealed 920 zero-radius OTUs spanning fungi, algae, protists, and metazoans. Community composition differed significantly among storm events (PERMANOVA F = 3.6, r[2] = 0.31, p < 0.001) and among NOAA HYSPLIT modeled air-mass back-trajectories (F = 8.9, r[2] = 0.36, p < 0.001). Summer storms were dominated by fungal taxa (Entomophthoromycota, Basidiomycota, and Ascomycota comprised up to 90% of reads), whereas late-autumn and winter storms carried mainly algal stramenopiles (Ochrophyta). Large storms (> 60 mm event[-1]) mobilized conspicuously higher relative abundances of larger metazoans (tardigrades and arthropods). We infer from stemflow eDNA that (i) seasonal resource shifts in tree canopies favor parasitic fungi in summer and saprotrophic fungi in autumn; (ii) northerly winter storms entrain Great Lakes aerosol algae that deposit onto canopies; (iii) rainfall intensity and duration jointly control the detachment of well-attached canopy eukaryotes. Together, our results establish stemflow eDNA as a non-invasive window into storm-mediated linkages between above- and below-ground biodiversity, offering new scope for monitoring canopy microbiomes under intensifying hydro-climatic regimes.}, }
@article {pmid40886609, year = {2025}, author = {Wen, C and Dai, Z and Cheng, F and Cheng, H and Zha, X and Dai, H and Lu, X}, title = {Partially water-level-fluctuating strategy enhances rural greywater treatment in vertical flow constructed wetlands.}, journal = {Water research}, volume = {287}, number = {Pt B}, pages = {124484}, doi = {10.1016/j.watres.2025.124484}, pmid = {40886609}, issn = {1879-2448}, abstract = {Vertical flow constructed wetlands (VFCWs) represent a cost-effective and eco-friendly solution for sustainable wastewater management in rural areas. However, their limited capacity to tolerate influent fluctuations constrains their reliability in practical applications. This study aims to enhance the efficiency and reliability of rural greywater treatment by developing a new partially water-level-fluctuating strategy (PFCW) in VFCWs. The performance of PFCW was systematically evaluated and compared with conventional unsaturated (USCW) and partially saturated (PSCW) strategies under field conditions with varying hydraulic and pollutant loads. Results showed that PFCW significantly improved oxygen transfer and utilization, consistently achieving high removal efficiencies for COD (> 93 %) and NH4[+]-N (> 92 %). Weibull reliability analysis confirmed that PFCW maintained 100 % treatment reliability with discharge standards under all tested conditions, whereas others did not. Microbial analysis revealed that the dynamic water-level fluctuations in PFCW balanced anaerobic and aerobic conditions, promoting a stable and interconnected microbial community, which significantly enhanced key metabolic pathways associated with organic and nitrogen removal, thereby supporting high performance and contributing to long-term stability. Overall, this study demonstrates how water level management strategies shape microbial ecology and functional metabolism in VFCWs, offering a reliable, simple, and cost-efficient solution for greywater treatment in resource-constrained rural areas.}, }
@article {pmid40885026, year = {2025}, author = {Bajić, D and van Oort, M and Gabriëls, M and Gojković, U}, title = {Structuring complexity by mapping the possible in microbial ecosystems.}, journal = {Current opinion in microbiology}, volume = {88}, number = {}, pages = {102658}, doi = {10.1016/j.mib.2025.102658}, pmid = {40885026}, issn = {1879-0364}, abstract = {Microbial ecosystems consist of many interacting components that integrate through stochastic and highly dynamic processes across multiple scales. Yet, despite this complexity, microbial communities exhibit remarkably robust patterns and reproducible functions. This apparent paradox reflects the role of constraints, whether physical, physiological, or evolutionary, that channel stochasticity into structured outcomes. Due to the limited knowledge of the nature of these constraints, models in ecology have traditionally relied on stochastic exploration under minimal mechanistic assumptions. Now, advances in data availability and computational methods increasingly allow us to construct models that incorporate explicit mechanistic constraints. In this review, we synthesize emerging modeling approaches that explore the space of ecological possibility in microbial ecosystems under realistic constraints, such as those imposed by metabolic stoichiometry, thermodynamics, or the structure of ecological interaction networks. We argue that integrating such constraints can significantly improve the predictive resolution of models, helping us build a much needed bridge between theory and data. We further discuss how novel statistical approaches are revealing simple, low-dimensional patterns in microbial communities, offering empirical clues for identifying the underlying constraints. Together, these developments suggest a path toward a data-driven and mechanistically informed theory in microbial ecology.}, }
@article {pmid40884577, year = {2025}, author = {Kumar, V and Sandil, S and Verma, P and Ameen, F}, title = {Decoding microbial ecology and functions: metagenomic profiling of activated sludge contaminated with chlorolignin compounds in a pulp-paper mill treatment system.}, journal = {Archives of microbiology}, volume = {207}, number = {10}, pages = {247}, pmid = {40884577}, issn = {1432-072X}, support = {ORF-2025-364//The authors extend their appreciation to the ongoing research funding program, (ORF-2025-364), King Saud University, Riyadh, Saudi Arabia./ ; }, mesh = {*Sewage/microbiology/chemistry ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; Metagenomics ; *Water Pollutants, Chemical/analysis ; Microbiota ; Metals, Heavy/analysis ; Industrial Waste/analysis ; }, abstract = {This study aimed to profile the dynamics of indigenous bacterial communities in activated sludge, assess the pollutant load, and unlock the functional genes involved during the activated sludge treatment process. The physicochemical analyses of activated sludge revealed high amounts of phosphate, sulfate, chloride, and lignin, along with heavy metals like Fe, Zn, Cu, Ni, and Pb. Simultaneously, the GC-MS/MS technique identified decane, 1 bromo-2-methyl, pentadecanoic acid, methyl ester, benzene dicarboxylic acid, stigmasterol, borinic acid, diethyl, 2-hydroxymethyl cyclopropane, 2-methoxy-4-ethyl-phenol, 3,4,5-trichlorophenol, octadecanoic acid, and tetracosanic acid as major compounds. Furthermore, taxonomic classification of operational taxonomic unit (OTU) data revealed that Proteobacteria was the most abundant phylum, comprising 44.54% of the microbial community. In addition, other phyla, such as Bacteriodetes, Acidobacteria, Planctomycetes, Chlorolfexi, Actinobacteria, and Verrucomicrobia were also recorded within a range between 13.27 and 4.1% in the sludge. At the genus and species levels, the dominant organisms were unclassified (3.62%) and belonged to the family Rhodospirillacea. Further, PICRUSt2-based KEGG Orthology (KO) analysis showed enriched energy metabolism as the most abundant category, driven by oxidative phosphorylation and the TCA cycle. Furthermore, the MetaCyc analysis revealed a robust and adaptable microbial community with the dominant pathways of aerobic respiration I (cytochrome c) and fatty acid biosynthesis pathways, such as cis-vaccenate biosynthesis. The EC assignments highlighted a broad range of enzymatic functions, with a strong emphasis on oxidoreductases and transferases involved in energy production and biosynthesis. This research offers valuable insights into microbial community dynamics in wastewater treatment processes and identifies their functional role in a chlorolignin waste-polluted environment.}, }
@article {pmid40883892, year = {2025}, author = {Kanaan, G and Deming, JW}, title = {Multiple roles of DNA methylation in sea-ice bacterial communities and associated viruses.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf198}, pmid = {40883892}, issn = {1751-7370}, abstract = {Despite growing evidence for the role of DNA methylation in bacterial acclimation to environmental stress, this epigenetic mechanism remains unexplored in sea-ice microbial communities known to tolerate multiple stressors. This study presents a first analysis of DNA methylation patterns in bacterial communities and associated viruses across the vertical thickness of sea ice. Using a novel stepped-sackhole method, we collected sea-ice brines from distinct horizons of an Arctic ice floe, capturing microbial communities that had been exposed to different environmental conditions. Through Oxford Nanopore sequencing, we characterized methylation patterns in bacterial and associated viral DNA, analysing for methylation motifs and differences between ice horizons. We identified 22 unique bacterial methylation motifs and 27 viral motifs across three nucleotide methylation types (5mC, 6mA, and 4mC), with evidence of differential methylation between upper and lower ice. Analysis of metagenome-assembled genomes revealed the regulatory potential of methylation in both ice-adapted (Psychromonas and Polaribacter) and non-adapted bacteria (Pelagibacter); e.g., in Pelagibacter, differential methylation of the GANTC motif between upper and lower ice affected genes involved in core cellular processes. Viral methylation patterns showed evidence of recent infection. We also identified orphan methyltransferases in sea-ice phages, suggesting a mechanism for bypassing host restriction-modification systems and regulating host genes. Our findings reveal that DNA methylation serves functions in sea ice beyond traditional restriction-modification systems that protect against foreign DNA, opening new avenues for research on the role of epigenetic mechanisms not only in acclimation to the cryosphere but also more generally in microbial ecology and evolution.}, }
@article {pmid40883737, year = {2025}, author = {Feng, C and Shou, Y and Wu, S and Mo, H and Mao, X and Huang, H and Lu, Q and Xia, L and Lu, L and Su, Z and Guo, H and Huang, Z}, title = {Sea cucumber polypeptide ameliorates aging properties via the brain-gut axis in naturally aging mice.}, journal = {Chinese medicine}, volume = {20}, number = {1}, pages = {136}, pmid = {40883737}, issn = {1749-8546}, support = {GUIKE AB22080063//Guangxi Key Research and Development Program/ ; }, abstract = {BACKGROUND: Sea cucumber has been recognized as a traditional nutraceutical in Chinese medicine for millennia, with its derived polypeptide (SCP) demonstrating diverse bioactive properties. Nevertheless, the molecular mechanisms underlying SCP's potential geroprotective effects remain insufficiently characterized.<br><br>METHODS: We systematically evaluated SCP's impact on neuromotor function and cognitive performance in physiologically aged C57BL/6&#xa0;J mice models using a behavioral test battery comprising open field, Y-maze, and Barnes maze paradigms. Complementary multi-omics approaches were employed to interrogate age-related perturbations in gut microbial ecology (16S rRNA sequencing) and systemic metabolism (untargeted LC-MS).H&amp;E and immumohistochemical staining was used to evaluate the pathological features of mice brain tissues and intestinal tissue. Bulk RNA-sequencing was used to detect gene expression profiles in mice brain tissue.<br><br>RESULTS: Behavioral assessments (open field, Y-maze, Barnes maze) demonstrated that SCP intervention effectively delayed the decline in exercise, learning and memory abilities in aging mice. SCP administration enhanced cerebral organosomatic indices and hepatic functional markers while reducing neuronal senescence biomarkers. Furthermore, SCP improved intestinal mucosal barrier function in aging mice restored gut microbial diversity metrics, effectively counteracting age-associated dysbiosis. Mechanistically, SCP induced taxonomic restructuring characterized by increased abundance of neuroprotective Eubacterium_brachy_group and Prevotellaceae genera, concomitant with suppression of dementia-linked Dubosiella. Metabolomic integration revealed SCP-mediated upregulation of steroidogenic pathways correlating with cognitive enhancement. Multi-omics validation through integrated transcriptomic profiling and immunohistochemical quantification corroborated these physiological improvements.<br><br>CONCLUSION: Our findings propose a mechanism whereby SCP might exert geroprotective effects through multimodal regulation of the gut-brain axis and systemic metabolic homeostasis, establishing mechanistic foundations for its translational potential in healthy longevity promotion.}, }
@article {pmid40881287, year = {2025}, author = {Pluym, T and Waegenaar, F and Dejaeger, K and Dhoore, M and Mestdagh, E and Cornelissen, E and Boon, N and De Gusseme, B}, title = {Membrane filtration reduces nutrient availability and invasion potential in drinking water systems, without affecting mature biofilms.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1622038}, doi = {10.3389/fmicb.2025.1622038}, pmid = {40881287}, issn = {1664-302X}, abstract = {Ensuring biostable drinking water is a growing priority for drinking water utilities, especially in non- or minimally chlorinated distribution systems where microbial regrowth is controlled through nutrient limitation. In this study, we evaluated the efficacy of ultrafiltration (UF) and nanofiltration (NF) in reducing total organic carbon (TOC) and their impact on the microbiology in a pilot-scale drinking water distribution system over 7 weeks. NF achieved significantly higher TOC removal (75.4%) compared to UF (25.4%), with high performance size exclusion chromatography revealing almost complete removal of all molecular weight fractions in NF-treated water. When introduced into the pilot system, NF-, UF-treated water, and untreated tap water supported similar increasing bulk cell concentrations, but exhibited distinct bacterial community compositions, with NF-treated water showing the most divergent microbiome. Despite these differences in the bulk water, the mature biofilm community (~2 years old) remained stable, underscoring it resilience to changes in nutrient conditions. An invasion assay demonstrated that decay rates of unwanted microorganisms increased with decreasing organic carbon content. For example, decay rates for the introduced microorganism Pseudomonas putida in NF-, UF- treated water, and untreated tap water were respectively, -0.18 h[-1], -0.143 h[-1], and -0.089 h[-1], indicating enhanced biostability in membrane-treated systems.}, }
@article {pmid40879794, year = {2025}, author = {Sun, X and Xia, R and Xie, J and Duan, K and Xun, W and Zhang, N and Huang, G and Zhang, R and Shen, Q and Wu, K and Xu, Z}, title = {Cooperative Interactions Between Bacillus and Lysobacter Enhance Consortium Stability and Fusarium Wilt Suppression in Cucumber.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {92}, pmid = {40879794}, issn = {1432-184X}, support = {42307173//National Natural Science Foundation of China/ ; 2023M747140//China Postdoctoral Science Foundation/ ; GZB20230309//Postdoctoral Fellowship Program of CPSF/ ; 2023ZB250//Excellent Postdoctoral Program of Jiangsu Province/ ; 2024YFD1701002//National Key Research and Development Program of China/ ; 2023WPY00002//Rural Revitalization Strategy Project Seed Industry Vitalization Action Project of Guangdong Province/ ; }, mesh = {*Cucumis sativus/microbiology ; *Fusarium/physiology ; *Bacillus/physiology ; *Plant Diseases/microbiology/prevention &amp; control ; Rhizosphere ; Soil Microbiology ; *Lysobacter/physiology ; *Microbial Consortia/physiology ; Microbial Interactions ; Biofilms/growth &amp; development ; }, abstract = {The rhizosphere microbiome plays a pivotal role in plant health by mediating interactions between hosts, beneficial microbes, and pathogens. However, the ecological mechanisms underlying microbial consortia that suppress soil-borne diseases remain largely unexplored. In this study, we investigated how the biocontrol bacterium Bacillus velezensis SQR9 influences the assembly of the cucumber rhizosphere bacterial community in the presence of the pathogenic fungus Fusarium oxysporum f. sp. cucumerinum (FOC). Inoculation with B. velezensis SQR9 significantly enriched the genus Lysobacter, a known biocontrol taxon. Meta-analysis revealed a positive correlation between Bacillus and Lysobacter abundances in healthy plant rhizospheres-a relationship absent in Fusarium wilt-diseased soils-suggesting a conserved ecological association linked to disease suppression. Mechanistic assays demonstrated that Lysobacter enzymogenes XL8, an antifungal bacterium isolated from the cucumber rhizosphere, formed synergistic biofilms with B. velezensis SQR9. Spent medium growth assays indicated that strain SQR9 facilitated the growth of L. enzymogenes XL8 through metabolic interactions. Targeted RT-qPCR and UHPLC-MS/MS analyses confirmed that treatment with spent medium of the partner strain enhanced the expression and production of antifungal metabolites bacillomycin D and heat-stable antifungal factor (HSAF), both antagonistic to F. oxysporum. Greenhouse trials confirmed that this dual-species consortium more effectively suppressed Fusarium wilt than single-species inoculations, as evidenced by reduced pathogen abundance and enhanced plant growth. Together, our findings underscore the importance of microbial metabolic cooperation and biofilm-mediated coexistence in shaping rhizosphere community assembly and function, providing ecological insights for the development of synthetic microbial consortia aimed at sustainable plant disease management.}, }
@article {pmid40879396, year = {2025}, author = {Li, D and Li, Y and Xu, H and Wu, J}, title = {Nonlinear response of soil microfauna network complexity and stability to multilevel warming in an old-growth subtropical forest.}, journal = {mBio}, volume = {}, number = {}, pages = {e0015625}, doi = {10.1128/mbio.00156-25}, pmid = {40879396}, issn = {2150-7511}, abstract = {The influence of climate warming on soil microbes and the mechanisms underlying these effects have become the subject of intense focus in microbial ecology and climate change research. However, it is largely unknown how warming affects soil microfauna network complexity and stability or how warming-induced changes may affect ecosystem functioning in old-growth forests. Here, we conducted a 3-year multilevel warming experiment in an old-growth subtropical forest using infrared heating with five treatments: ambient soil temperature and 0.8°C, 1.5°C, 3.0°C, and 4.2°C above ambient soil temperature. We found that soil microfauna network complexity and stability and multinutrient cycling were significantly higher under warming and showed similar hump-shaped trends across rising temperatures. The nonlinear responses of soil microfauna network complexity and stability were primarily linked to soil temperature, moisture, organic carbon, and microbial biomass. Importantly, we found that soil multinutrient cycling was positively influenced by microfauna network complexity and stability. Consequently, our findings provide insights into the key role of soil microfauna network structure in regulating soil multinutrient cycling, highlighting the need to consider soil organisms' potential interactions and that it is crucial to preserve soil microfauna "interactions" for ecosystem management in forests under global change.IMPORTANCEIt is largely unknown how warming affects soil microfauna network complexity and stability or how warming-induced changes may affect ecosystem functioning in old-growth forests. We conducted a 3-year multilevel warming experiment in an old-growth subtropical forest using infrared heating. We found that soil microfauna network complexity and stability were significantly higher under warming treatments and displayed nonlinear responses to different warming levels. Soil multinutrient cycling was positively and significantly influenced by microfauna network complexity and stability. Given that complex interconnections between soil microfauna are critical for sustaining ecosystem functioning, protecting microfauna "interactions" may be critical to mitigating the adverse impacts of warming-induced biodiversity reduction on ecosystem functioning.}, }
@article {pmid40875436, year = {2025}, author = {Maguire, M and Serna, C and Delgado-Blas, JF and Clarke, C and DeLappe, N and Cormican, M and Coughlan, SC and Miliotis, G and Gonzalez-Zorn, B and Burke, LP}, title = {Healthcare-related transmission of mobile genetic elements co-carrying bla NDM and 16S rRNA methyltransferase genes in multiple Enterobacterales.}, journal = {Microbial genomics}, volume = {11}, number = {8}, pages = {}, doi = {10.1099/mgen.0.001473}, pmid = {40875436}, issn = {2057-5858}, mesh = {*beta-Lactamases/genetics ; *Methyltransferases/genetics ; *Interspersed Repetitive Sequences ; *Enterobacteriaceae/genetics/drug effects/isolation &amp; purification ; Humans ; Ireland ; Plasmids/genetics ; RNA, Ribosomal, 16S/genetics ; Anti-Bacterial Agents/pharmacology ; *Enterobacteriaceae Infections/microbiology/transmission ; Bacterial Proteins/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; }, abstract = {Aminoglycosides are used in the treatment of serious infections with Gram-negative bacteria, especially those resistant to beta-lactams and carbapenems. 16S rRNA methyltransferases (16S-RMTase) are capable of conferring resistance to nearly all aminoglycosides. They are sometimes detected in combination with bla NDM. This study describes the mobile genetic elements associated with bla NDM and 16S-RMTase (co-)carriage in Enterobacterales from Ireland in the period 2019-2023. All isolates (n=58) carrying both bla NDM and a 16S-RMTase gene between 2019 and 2023 were obtained from the CPE National Reference Laboratory Service. Short-read sequences were generated for all isolates, and long-read sequences were generated for a subset of isolates (n=27). MOB-recon was used to distinguish plasmid-derived contigs from draft assemblies. The containment distance and DCJ-indel distance were used to find clusters of related plasmids. Isolates carrying bla NDM-1 were associated with armA (n=31) but also rmtC (n=6) carriage. These genes were co-localized most frequently on IncFIB/HI1B (n=12), IncM2 (n=10) and IncC (n=8) plasmids. Closely related plasmids were identified in multiple species (range: 2-5) and at different sites around Ireland; however, the IncM2 plasmids were largely associated with a single hospital. Isolates carrying bla NDM-5 were associated with rmtB1 (n=28) carriage. The majority (n=15) were carried on a diverse range of mosaic IncF-type plasmids. Two discrete clusters of IncM1 (n=3) and IncFII (n=4) type plasmids were also detected. The study highlights the diverse plasmids co-carrying carbapenem and aminoglycoside resistance genes in Ireland. Detection of plasmids across multiple species and hospitals suggests dissemination driven by antimicrobial selective pressure and environmental reservoirs within healthcare networks. The co-dissemination of these genes on highly mobile plasmids poses a significant public health concern and emphasizes the need for greater awareness that chains of transmission of antimicrobial resistance in the healthcare setting may involve multiple species.}, }
@article {pmid40875044, year = {2025}, author = {Shao, Q and Yang, Q and Xu, Y and Zhang, L and Ding, M and Li, F and He, C}, title = {The Impact of Artificial Water Diversion-induced Algal Blooms on Carbon Balance in a Semi-enclosed Bay.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {91}, pmid = {40875044}, issn = {1432-184X}, support = {2022J195//Ningbo Natural Science Foundation/ ; 2022S116//Ningbo Public Welfare Science and Technology Project/ ; SS//K.C. Wong Magna Fund in Ningbo University/ ; }, mesh = {*Phytoplankton/growth &amp; development/metabolism/classification ; *Eutrophication ; *Bays/microbiology/chemistry ; *Carbon/metabolism ; Diatoms/growth &amp; development/metabolism ; Ecosystem ; Seasons ; *Carbon Cycle ; Dinoflagellida/growth &amp; development ; Seawater/chemistry ; }, abstract = {Artificial water diversion is widely used to address water security; yet, its impacts on phytoplankton communities and coastal carbon balance remain poorly understood. Using a seasonal diversion project in a semi-enclosed bay as a case study, we analyzed phytoplankton composition via morphological methods and assessed carbon balance through simultaneous measurements of primary production (P), ecosystem respiration rate (R), and production-to-respiration (PP/R) ratio. Our results showed that artificial water diversion activities during the wet month enhanced hydrological connectivity and phytoplankton homogeneity, triggering a mixed diatom-dinoflagellate bloom. Phytoplankton abundance during the wet month increased by sevenfold (surface layer) and 26.5-fold (bottom layer) compared to dry month values. This simultaneously resulted in the PP value of the wet month being more than twice that of the dry month. Although R rose with increasing phytoplankton abundance, no significant correlation was observed between them. Instead, dry-month R was primarily driven by pH and dissolved organic carbon, whereas wet-month R showed minimal environmental linkages. PP/R ratios of surface and bottom layers were always less than 1, implying Meishan bay was a net heterotrophic ecosystem, despite significant changes in phytoplankton community structure induced by artificial water diversion and associated algal bloom. Furthermore, our results strongly suggest that changes in PP, but not in R, control the PP/R ratio of Meishan bay. This study offers valuable guidance for the ecological management of artificial water diversions and can serve as a reference for similar water diversion projects in other semi-enclosed bays.}, }
@article {pmid40871342, year = {2025}, author = {Touati, A and Ibrahim, NA and Tighilt, L and Idres, T}, title = {Anti-QS Strategies Against Pseudomonas aeruginosa Infections.}, journal = {Microorganisms}, volume = {13}, number = {8}, pages = {}, doi = {10.3390/microorganisms13081838}, pmid = {40871342}, issn = {2076-2607}, support = {IMSIU-DDRSP2501//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)./ ; }, abstract = {Pseudomonas aeruginosa poses significant health threats due to its multidrug-resistant profile, particularly affecting immunocompromised individuals. The pathogen's ability to produce virulence factors and antibiotic-resistant biofilms, orchestrated through quorum-sensing (QS) mechanisms, complicates conventional therapeutic interventions. This review aims to critically assess the potential of anti-QS strategies as alternatives to antibiotics against P. aeruginosa infections. Comprehensive literature searches were conducted using databases such as PubMed, Scopus, and Web of Science, focusing on studies addressing QS inhibition strategies published recently. Anti-QS strategies significantly attenuate bacterial virulence by disrupting QS-regulated genes involved in biofilm formation, motility, toxin secretion, and immune evasion. These interventions reduce the selective pressure for resistance and enhance antibiotic efficacy when used in combination therapies. Despite promising outcomes, practical application faces challenges, including specificity of inhibitors, pharmacokinetic limitations, potential cytotoxicity, and bacterial adaptability leading to resistance. Future perspectives should focus on multi-target QS inhibitors, advanced delivery systems, rigorous preclinical validations, and clinical translation frameworks. Addressing current limitations through multidisciplinary research can lead to clinically viable QS-targeted therapies, offering sustainable alternatives to traditional antibiotics and effectively managing antibiotic resistance.}, }
@article {pmid40871329, year = {2025}, author = {McKay, S and Churchill, H and Hayward, MR and Klein, BA and Van Meulebroek, L and Ghyselinck, J and Marzorati, M}, title = {Effects of cRG-I Prebiotic Treatment on Gut Microbiota Composition and Metabolic Activity in Dogs In Vitro.}, journal = {Microorganisms}, volume = {13}, number = {8}, pages = {}, doi = {10.3390/microorganisms13081825}, pmid = {40871329}, issn = {2076-2607}, abstract = {Low-dose carrot rhamnogalacturonan-I (cRG-I) has shown consistent modulatory effects on the gut microbiota and immune function in humans. In this study we investigated its effects on the microbial composition and metabolite production of the gut microbiota of small (5-10 kg), medium-sized (10-27 kg), and large (27-45 kg) dogs, using inulin and xanthan as comparators. Fecal samples from six dogs of each size group were evaluated. Overall microbiome composition, assessed using metagenomic sequencing, was shown to be driven mostly by dog size and not treatment. There was a clear segregation in the metabolic profile of the gut microbiota of small dogs versus medium-sized and large dogs. The fermentation of cRG-I specifically increased the levels of acetate/propionate-producing Phocaeicola vulgatus. cRG-I and inulin were fermented by all donors, while xanthan fermentation was donor-dependent. cRG-I and inulin increased acetate and propionate levels. The responses of the gut microbiota of different sized dogs to cRG-I were generally consistent across donors, and interindividual differences were reduced. This, together with the significant increase in P. vulgatus during fermentation in both this study and an earlier human ex vivo study, suggests that this abundant and prevalent commensal species has a core capacity to selectively utilize cRG-I.}, }
@article {pmid40870599, year = {2025}, author = {Guo, H and Wang, Y and Guo, Y and Liu, X and Gui, T and Ling, M and Qian, H}, title = {Correlation of Midgut Microbiota and Metabolic Syndrome-Related Lipids in Hemolymph Between Obese and Lean Silkworm Strains.}, journal = {Insects}, volume = {16}, number = {8}, pages = {}, doi = {10.3390/insects16080798}, pmid = {40870599}, issn = {2075-4450}, support = {No. CARS-18//The present study was supported by the China Agriculture Research System (Sericulture industry, No. CARS-18)/ ; }, abstract = {Metabolic syndrome is a global health crisis. However, there are no effective therapeutic strategies for metabolic syndrome. Therefore, this study was conducted to find out a novel silkworm-based metabolic syndrome model that bridges microbial ecology and metabolic dysregulation by integrating hemolymph lipids and midgut microbiota. Our results showed that the levels of HDL-C in the hemolymph of the lean silkworm strain were significantly higher than that in the obese silkworm strain. Furthermore, correlation analysis revealed that Lactococcus and Oceanobacillus were positively related to HDL-C levels, while SM1A02 and Pseudonocardia were negatively associated with HDL-C levels. These relationships between the identified bacteria in the midgut and HDL-C, known as the "good" lipid, in the hemolymph could help guide the development of new treatments for obesity and metabolic problems like high cholesterol in humans. Overall, our results not only established a framework for understanding microbiota-driven lipid dysregulation in silkworms but also offered potential probiotic targets and a bacterial biomarker for obesity and metabolic dysfunction intervention in humans.}, }
@article {pmid40869967, year = {2025}, author = {Fu, Y and Bonifacio-Mundaca, J and Desterke, C and Casafont, &#xcd; and Mata-Garrido, J}, title = {Genomic Alterations and Microbiota Crosstalk in Hepatic Cancers: The Gut-Liver Axis in Tumorigenesis and Therapy.}, journal = {Genes}, volume = {16}, number = {8}, pages = {}, doi = {10.3390/genes16080920}, pmid = {40869967}, issn = {2073-4425}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Liver Neoplasms/genetics/microbiology/therapy/pathology ; *Carcinoma, Hepatocellular/genetics/microbiology/therapy/pathology ; *Carcinogenesis/genetics ; Liver/pathology/metabolism/microbiology ; *Cholangiocarcinoma/genetics/microbiology/therapy ; Mutation ; Epigenesis, Genetic ; Animals ; }, abstract = {Background/Objectives: Hepatic cancers, including hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA), are major global health concerns due to rising incidence and limited therapeutic success. While traditional risk factors include chronic liver disease and environmental exposures, recent evidence underscores the significance of genetic alterations and gut microbiota in liver cancer development and progression. This review aims to integrate emerging knowledge on the interplay between host genomic changes and gut microbial dynamics in the pathogenesis and treatment of hepatic cancers. Methods: We conducted a comprehensive review of current literature on genetic and epigenetic drivers of HCC and CCA, focusing on commonly mutated genes such as TP53, CTNNB1, TERT, IDH1/2, and FGFR2. In parallel, we evaluated studies addressing the gut-liver axis, including the roles of dysbiosis, microbial metabolites, and immune modulation. Key clinical and preclinical findings were synthesized to explore how host-microbe interactions influence tumorigenesis and therapeutic response. Results: HCC and CCA exhibit distinct but overlapping genomic landscapes marked by recurrent mutations and epigenetic reprogramming. Alterations in the gut microbiota contribute to hepatic inflammation, genomic instability, and immune evasion, potentially enhancing oncogenic signaling pathways. Furthermore, microbiota composition appears to affect responses to immune checkpoint inhibitors. Emerging therapeutic strategies such as probiotics, fecal microbiota transplantation, and precision oncology based on mutational profiling demonstrate potential for personalized interventions. Conclusions: The integration of host genomics with microbial ecology provides a promising paradigm for advancing diagnostics and therapies in liver cancer. Targeting the gut-liver axis may complement genome-informed strategies to improve outcomes for patients with HCC and CCA.}, }
@article {pmid40868890, year = {2025}, author = {Zhang, M and Zhang, Y and Zhao, Z and Deng, F and Jiang, H and Liu, C and Li, Y and Chai, J}, title = {Bacterial-Fungal Interactions: Mutualism, Antagonism, and Competition.}, journal = {Life (Basel, Switzerland)}, volume = {15}, number = {8}, pages = {}, doi = {10.3390/life15081242}, pmid = {40868890}, issn = {2075-1729}, abstract = {The interaction between bacteria and fungi is one of the key interactions of microbial ecology, including mutualism, antagonism, and competition, which profoundly affects the balance and functions of animal microbial ecosystems. This article reviews the interactive dynamics of bacteria and fungi in more concerned microenvironments in animals, such as gut, rumen, and skin. Moreover, we summarize the molecular mechanisms and ecological functions of the interaction between bacteria and fungi. Three major bacterial-fungal interactions (mutualism, antagonism, and competition) are deeply discussed. Understanding of the interactions between bacteria and fungi allows us to understand, modulate, and maintain the community structure and functions. Furthermore, this summarization will provide a comprehensive perspective on animal production and veterinary medicine, as well as guide future research directions.}, }
@article {pmid40866705, year = {2025}, author = {Chen, SC and Li, XM and Battisti, N and Guan, G and Montoya, MA and Osvatic, J and Pjevac, P and Pollak, S and Richter, A and Schintlmeister, A and Wanek, W and Mussmann, M and Loy, A}, title = {Microbial iron oxide respiration coupled to sulfide oxidation.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41586-025-09467-0}, pmid = {40866705}, issn = {1476-4687}, abstract = {Microorganisms have driven Earth's sulfur cycle since the emergence of life[1-6], yet the sulfur-cycling capacities of microorganisms and their integration with other element cycles remain incompletely understood. One such uncharacterized metabolism is the coupling of sulfide oxidation with iron(III) oxide reduction, a ubiquitous environmental process hitherto considered to be strictly abiotic[7,8]. Here we present a comprehensive genomic analysis of sulfur metabolism across prokaryotes, and reveal bacteria that are capable of oxidizing sulfide using extracellular solid phase iron(III). Based on a phylogenetic framework of over hundred genes involved in dissimilatory transformation of sulfur compounds, we recorded sulfur-cycling capacity in most bacterial and archaeal phyla. Metabolic reconstructions predicted co-occurrence of sulfur compound oxidation and iron(III) oxide respiration in diverse members of 37 prokaryotic phyla. Physiological and transcriptomic evidence demonstrated that a cultivated representative, Desulfurivibrio alkaliphilus, grows autotrophically by oxidizing dissolved sulfide or iron monosulfide (FeS) to sulfate with ferrihydrite as an extracellular iron(III) electron acceptor. The biological process outpaced the abiotic process at environmentally relevant sulfide concentrations. These findings expand the known diversity of sulfur-cycling microorganisms and unveil a biological mechanism that links sulfur and iron cycling in anoxic environments, thus highlighting the fundamental role of microorganisms in global element cycles.}, }
@article {pmid40864652, year = {2025}, author = {Rigou, S and Schmitt, A and Moreno, AB and Lartigue, A and Danner, L and Mayer, L and Giry, C and Trabelsi, F and Belmudes, L and Olivero-Deibe, N and Le Guenno, H and Couté, Y and Berois, M and Legendre, M and Jeudy, S and Abergel, C and Bisio, H}, title = {Evolutionarily conserved grammar rules viral factories of amoeba-infecting members of the hyperdiverse Nucleocytoviricota phylum.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {35}, pages = {e2515074122}, doi = {10.1073/pnas.2515074122}, pmid = {40864652}, issn = {1091-6490}, support = {101160452//EC | European Research Council (ERC)/ ; 832601//EC | European Research Council (ERC)/ ; ANR-10-INBS-08//Agence Nationale de la Recherche grant ProFI/ ; ANR-17-EURE-0003//Chemistry Biology Health (CBH) Graduate School of University Grenoble Alpes grant/ ; }, abstract = {Despite sharing fewer than 10 core genes, the hyperdiverse Nucleocytoviricota phylum (ranging from poxviruses to giant viruses) universally assembles viral factories (VFs) resembling biomolecular condensates. Regardless, it is unclear how these viruses achieve such a level of functional conservation without clear conserved genetic information. We demonstrate that the VFs produced by amoeba-infecting viruses have liquid-like properties and identify a conserved molecular grammar governing viral factory scaffold protein: charge-patterned intrinsically disordered regions that drive phase separation independently of sequence homology. This grammar predicts functional scaffold proteins across the 15 viral families, revealing evolutionary constraints invisible to sequence or structural analysis. Strikingly, VFs exhibit subcompartmentalization analogous to nuclei, segregating transcription and mRNA processing (inner condensates) from replication (interphase zones) and translation (host cytoplasm). Our work establishes phase separation as a fundamental organizational principle bridging extreme genomic diversity, explaining how biological complexity emerges without gene conservation. This grammar is likely also conserved in non-amoeba-infecting members of the phylum and thus may represent a primordial solution for organelle-like organization, with broad implications for antiviral targeting.}, }
@article {pmid40863168, year = {2025}, author = {Buckley, AM and Zaidan, S and Sweet, MG and Ewin, DJ and Ratliff, JG and Alkazemi, A and Davis Birch, W and McAmis, AM and Neilson, AP}, title = {Choline Metabolism to the Proatherogenic Metabolite Trimethylamine Occurs Primarily in the Distal Colon Microbiome In Vitro.}, journal = {Metabolites}, volume = {15}, number = {8}, pages = {}, pmid = {40863168}, issn = {2218-1989}, support = {N/A/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; N/A//OIRC INFORM hub/ ; N/A/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; N/A//North Carolina Agricultural Research Service/ ; N/A//Applied Microbiology International/ ; N/A//Hatch program, USDA/ ; }, abstract = {BACKGROUND/OBJECTIVES: Gut microbial metabolism of choline and related quaternary amines to trimethylamine (TMA) is the first step in the production of trimethylamine N-oxide (TMAO), a circulating metabolite that contributes to the development of atherosclerosis and other forms of cardiovascular disease (CVD). No data exist on regional differences in TMA production within the colon due to difficulties studying gut regions in vivo. A better understanding of TMA production by gut microbiota is needed to develop strategies to limit TMA production in the gut and TMAO levels in circulation with the goal of reducing CVD risk.<br><br>METHODS: We employed our novel three-compartment MiGut in vitro model, which establishes three distinct microbial ecologies mimicking the proximal, mid, and distal colon, to study conversion of choline to TMA by human gut microbiota using isotopically labelled substrate.<br><br>RESULTS: Choline-d9 was almost completely converted to TMA-d9 in vessels 2-3 (mimicking the mid and distal colon) within 6-8 h, but little conversion occurred in vessel 1 (mimicking the proximal colon). Abundance of cutC, part of the cutC/D gene cluster responsible for choline conversion to TMA, was highest in vessel 1 vs. 2-3, suggesting that its expression or activity may be suppressed in the proximal colon. Another possibility is that the viability/activity of bacteria expressing cutC could be suppressed in the same region.<br><br>CONCLUSIONS: This novel finding suggests that while bacteria capable of converting choline to TMA exist throughout the colon, their activity may be different in distinct colon regions. The regional specificity of TMA production, if confirmed in vivo, has implications for both basic microbial ecology related to CVD and the development of strategies to control TMA and TMAO production, with the goal of lowering CVD risk. These findings warrant further study in vitro and in vivo.}, }
@article {pmid40862636, year = {2025}, author = {Modin, O}, title = {From ecology to engineering: the role of myxobacteria in recirculating aquaculture systems.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0137625}, doi = {10.1128/aem.01376-25}, pmid = {40862636}, issn = {1098-5336}, abstract = {Open microbial communities play vital roles in many engineered systems, providing essential ecosystem services but also posing operational challenges. In recirculating aquaculture systems (RASs), microbial activity is crucial for water purification, yet it can also lead to the accumulation of taste-and-odor compounds that compromise fish quality. In a recent study, Södergren et al. (Appl Environ Microbiol 91:e00757-25, 2025, https://doi.org/10.1128/aem.00757-25) report the first successful isolation of myxobacteria from RAS and demonstrate their ability to produce geosmin and other volatile organic compounds under various nutrient conditions, including in real RAS water. This work provides foundational insights into the ecological roles of myxobacteria and their contributions to off-flavor formation in aquaculture environments. In this commentary, I reflect on the broader significance of microbial ecology in environmental biotechnology and discuss how the findings of Södergren et al. may inform future strategies for managing microbial communities in RAS to improve system performance and product quality.}, }
@article {pmid40862349, year = {2025}, author = {Benot, AO and Waldschmidt, G and Tiyapun, C and Okyere, IJ and Goff, JL}, title = {Metagenomic characterization of fire-adapted soil microbiomes in the Albany Pine Bush Preserve.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0066425}, doi = {10.1128/mra.00664-25}, pmid = {40862349}, issn = {2576-098X}, abstract = {The Albany Pine Bush Preserve's documented fire history enables a unique study of fire-dependent ecosystems. We identified 94 unique bacterial and archaeal metagenome-assembled genomes spanning 27 classes, providing genomic insights into microbial nutrient cycling in these systems.}, }
@article {pmid40862159, year = {2025}, author = {Wang, Y and Jiang, L and Zhou, F and Zhang, Y and Fine, RD and Li, M}, title = {The hidden dancers in water: the symbiotic mystery of Legionella pneumophila and free-living amoebae.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1634806}, pmid = {40862159}, issn = {1664-302X}, abstract = {Legionella pneumophila, a Gram-negative bacillus, is the primary etiological agent of Legionnaires' disease, a severe respiratory infection. The symbiotic relationship between L. pneumophila and free-living amoebae (FLAs), particularly Acanthamoeba spp., represents a critical intersection of microbial ecology and human pathogenesis. This symbiosis provides Legionella with a protective intracellular niche, enhancing its resistance to biocides, increasing its pathogenicity, and facilitating horizontal gene transfer. These interactions not only boost the environmental persistence and dissemination of L. pneumophila but also elevate the risk of human exposure through contaminated drinking water systems. This review delves into the sophisticated survival strategies employed by L. pneumophila within host cells, including evasion of endocytic pathways, inhibition of phagosome maturation and acidification, and prevention of phagosome-lysosome fusion. By elucidating these mechanisms, we underscore the critical need for in-depth research into the Legionella-amoebae symbiosis and its broader implications for public health. Additionally, we address the challenges and strategies for mitigating environmental risks, emphasizing the importance of innovative approaches to ensure water system safety and prevent pathogen transmission.}, }
@article {pmid40860928, year = {2025}, author = {Šikić, A and Gagović, E and Rojas, A and Sindičić, M and Žilić, DJ and Naletlić, &#x160; and Balić, D and Hodžić, A and Beck, R}, title = {First molecular identification of Spirometra mansoni in the golden jackal (Canis aureus) in Croatia.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1629099}, pmid = {40860928}, issn = {2297-1769}, abstract = {This study presents the first molecularly confirmed identification of the cestode Spirometra mansoni in the golden jackals (Canis aureus) in Croatia, and possibly the first such report in Europe. Of 198 jackals examined between 2020 and 2025, adult Spirometra worms were recovered from three individuals. The morphological characteristics of these specimens were consistent with S. mansoni, and their identity was confirmed by PCR and sequencing of the mitochondrial cox1 and nad1 genes. Phylogenetic analysis grouped the obtained sequences within the S. mansoni clade, with strong posterior probability support. This finding expands the known host range and geographic distribution of S. mansoni and underscores the importance of integrating molecular diagnostics in parasitological surveys. Further research is needed to assess the role of golden jackals and other wildlife in the epidemiology of Spirometra spp. in Europe.}, }
@article {pmid40860758, year = {2025}, author = {Tuoliu, D and Cheng, J and Xia, L and Wen, Z and Wang, M and Yang, W and Yang, Q}, title = {Bacterial microbiome and their assembly processing in two sympatric desert rodents (Dipus sagitta and Meriones meridianus) from different geographic sources.}, journal = {Current zoology}, volume = {71}, number = {4}, pages = {440-448}, pmid = {40860758}, issn = {1674-5507}, abstract = {The microbiome of mammals has profound effects on host fitness, but the process, which drives the assembly and shift of mammalian microbiome remains poorly understood. To explore the patterns of small mammal microbial communities across host species and geographical sites and measure the relative contributions of different processes in driving assembly patterns, 2 sympatric desert rodent species (Dipus sagitta and Meriones meridianus) were sampled from 2 geographically distant regions, which differed in the environment, followed by 16S rRNA gene sequencing. The microbiomes differed significantly between D. sagitta and M. meridianus, and linear mixed modeling (LMM) analysis revealed that microbial diversity was mostly affected by species rather than the environment. For each rodent species, the microbiome diversity and structure differed across geographical regions, with individuals from lower rainfall environments exhibiting greater diversity. The null modeling results suggested dispersal limitation and ecological drift rather than differential selective pressures acting on the microbiome. In addition, each group had a different core genus, suggesting that the taxonomic composition of the microbiome was shaped most strongly by stochastic processes. Our results suggest that variation in the microbiome between hosts, both within and among geographic rodent populations, is driven by bacterial dispersal and ecological drift rather than by differential selective pressures. These results elucidated the diversity patterns and assembly processes of bacterial microbiomes in small desert mammals. Deciphering the processes shaping the assembly of the microbial community is a premise for better understanding how the environment-host-microbe interactions of mammals are established and maintained, particularly in the context of increased environmental disturbances and global changes.}, }
@article {pmid40860567, year = {2025}, author = {Gavriilidou, A and Murace, M and Portoghese, M and Schouten, S and Hamidjaja, R and Escobar Doncel, &#xc1; and Boeren, S and Giesbers, M and Capoulade, J and Vignolini, S and Smidt, H and Ingham, CJ}, title = {Pseudosulfitobacter pseudonitzschiae hitchhikes on gliding colonies of Cellulophaga lytica.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf118}, pmid = {40860567}, issn = {2730-6151}, abstract = {Interspecies interactions shape microbial communities; this is central for microbial ecology. Cellulophaga lytica PlyA2 is a marine flavobacterium, which glides over surfaces and forms ordered, structurally coloured colonies, which display angle-dependent reflection of light. Pseudosulfitobacter pseudonitzschiae SW is an apparently nonmotile, nonstructurally coloured marine bacterium. Here, we aim to understand the interaction of both strains at cellular, genomic, optical, and proteomic levels. Cocultivation on agar showed that P. pseudonitzschiae uses gliding C. lytica to spread by microbial hitchhiking in which Pseudosulfitobacter appears to "surf" on basal layers of motile Cellulophaga. This dispersal mechanism was found to be often beneficial for P. pseudonitzschiae, which could maximally expand its population up to 350-fold relative to monoculture. Coculture was often of limited benefit for C. lytica, only in extended cultivation on rich medium was the presence of P. pseudonitzschiae detrimental to its viability. The proteome of P. pseudonitzschiae was strongly impacted by the association with C. lytica. Quorum-sensing signalling, potential exchange of amino acids, vitamins, and other metabolites are likely mediating this hitchhiking interaction. In contrast, C. lytica made minimal adjustments to its proteome composition in coculture. Supported by optical analysis, P. pseudonitzschiae patterned C. lytica by changing how groups of the latter organised to reflect light. Our results underscore the unusual, dynamic interplay between two bacterial species and provide insights on the mechanisms underlying this relationship.}, }
@article {pmid40860566, year = {2025}, author = {Arnau, V and Ortiz-Maiques, A and Valero-Tebar, J and Mora-Quilis, L and Kurmauskaite, V and Campos Dopazo, L and Domingo-Calap, P and Džunková, M}, title = {CleanBar: a versatile demultiplexing tool for split-and-pool barcoding in single-cell omics.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf134}, pmid = {40860566}, issn = {2730-6151}, abstract = {Split-and-pool barcoding generates thousands of unique barcode strings through sequential ligations in 96-well plates, making single-cell omics more accessible, thus advancing microbial ecology, particularly in studies of bacterial interactions with plasmids and bacteriophages. While the wet-lab aspects of the split-and-pool barcoding are well-documented, no universally applicable bioinformatic tool exists for demultiplexing single cells barcoded with this approach. We present CleanBar (https://github.com/tbcgit/cleanbar), a flexible tool for demultiplexing reads tagged with sequentially ligated barcodes, accommodating variations in barcode positions and linker lengths while preventing misclassification of natural barcode-like sequences and handling diverse ligation errors. It also provides statistics useful for optimizing laboratory procedures. We demonstrate CleanBar's performance with the Atrandi platform for microbial single-cell genomics, coupled with PacBio sequencing, to reach a cell throughput comparable with traditional bulk metagenomics, but overcoming its limitations in studying phage-bacteria interactions. In four Klebsiella strains infected with their corresponding phages and a control phage, the single-cell genomics revealed infection heterogeneity and enabled phage copy number estimation per cell. By combining efficiency, adaptability, and precision, CleanBar, when applied to the Atrandi split-and-pool barcoding platform and PacBio sequencing, serves as a powerful high-throughput tool for advancing microbial single-cell genomics and understanding microbial ecology and evolution.}, }
@article {pmid40858791, year = {2025}, author = {Tocino-Márquez, I and Zehl, M and Séneca, J and Pjevac, P and Felkl, M and Becker, CFW and Loy, A and Rattei, T and Ostrovsky, AN and Zotchev, SB}, title = {The bacterial community of the freshwater bryozoan Cristatella Mucedo and its secondary metabolites production potential.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {31456}, pmid = {40858791}, issn = {2045-2322}, support = {MetaBac Research Platform//Universit&#xe4;t Wien/ ; }, abstract = {While marine bryozoans were shown to be a promising source of bioactive compounds with the potential to be developed into drugs, their freshwater counterparts remain understudied. Considering that bioactive compounds isolated from bryozoans may originate from bacterial communities associated with the hosts, we explored the bacterial community of the freshwater bryozoan Cristatella mucedo using genomics and metabolomics. 16 S rRNA gene amplicon sequencing of the bacterial community associated with C. mucedo showed a considerable overlap with communities from surrounding water and sediment. Using different isolation approaches we retrieved a diverse collection of bacterial strains representing 26 genera, including a potentially new one. Genome sequencing and analyses of representative isolates of each genus revealed considerable potential for secondary metabolite biosynthesis. The secondary metabolomes of both mono- and co-cultures of selected isolates and enriched bryozoan-derived communities were investigated, allowing the identification of several known and potentially novel secondary metabolites. This work provides important information regarding the composition of the bacterial community associated with C. mucedo and sets the stage for its further exploration and exploitation for drug discovery.}, }
@article {pmid40858551, year = {2025}, author = {Salcher, MM and Layoun, P and Fernandes, C and Chiriac, MC and Bulzu, PA and Ghai, R and Shabarova, T and Lanta, V and Callieri, C and Sonntag, B and Posch, T and Lepori, F and Znachor, P and Haber, M}, title = {Bringing the uncultivated microbial majority of freshwater ecosystems into culture.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {7971}, pmid = {40858551}, issn = {2041-1723}, support = {19-23469S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky (Grant Agency of the Czech Republic)/ ; 22-03662S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky (Grant Agency of the Czech Republic)/ ; 25-15813S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky (Grant Agency of the Czech Republic)/ ; 20-12496X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky (Grant Agency of the Czech Republic)/ ; 21-21990S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky (Grant Agency of the Czech Republic)/ ; 022/2019/P//Jiho&#x10d;esk&#xe1; Univerzita v &#x10c;esk&#xfd;ch Bud&#x11b;jovic&#xed;ch (University of South Bohemia in &#x10c;esk&#xe9; Bud&#x11b;jovice)/ ; 017/2022/P//Jiho&#x10d;esk&#xe1; Univerzita v &#x10c;esk&#xfd;ch Bud&#x11b;jovic&#xed;ch (University of South Bohemia in &#x10c;esk&#xe9; Bud&#x11b;jovice)/ ; }, abstract = {Axenic cultures are essential for studying microbial ecology, evolution, and genomics. Despite the importance of pure cultures, public culture collections are biased towards fast-growing copiotrophs, while many abundant aquatic prokaryotes remain uncultured due to uncharacterized growth requirements and oligotrophic lifestyles. Here, we applied high-throughput dilution-to-extinction cultivation using defined media that mimic natural conditions to samples from 14 Central European lakes, yielding 627 axenic strains. These cultures include 15 genera among the 30 most abundant freshwater bacteria identified via metagenomics, collectively representing up to 72% of genera detected in the original samples (average 40%) and are widespread in freshwater systems globally. Genome-sequenced strains are closely related to metagenome-assembled genomes (MAGs) from the same samples, many of which remain undescribed. We propose a classification of several novel families, genera, and species, including many slowly growing, genome-streamlined oligotrophs that are notoriously underrepresented in public repositories. Our large-scale initiative to cultivate the "uncultivated microbial majority" has yielded a valuable collection of abundant freshwater microbes, characterized by diverse metabolic pathways and lifestyles. This culture collection includes promising candidates for oligotrophic model organisms, suitable for a wide array of ecological studies aimed at advancing our ecological and functional understanding of dominant, yet previously uncultured, taxa.}, }
@article {pmid40858256, year = {2025}, author = {Bain, JA and Ogilvie, JE and Petry, WK and CaraDonna, PJ}, title = {Nutrient niche dynamics among wild pollinators.}, journal = {Proceedings. Biological sciences}, volume = {292}, number = {2053}, pages = {20250643}, doi = {10.1098/rspb.2025.0643}, pmid = {40858256}, issn = {1471-2954}, support = {//National Science Foundation/ ; //National Science Foundation Graduate Research Fellowship Program/ ; }, mesh = {Animals ; *Pollination ; Bees/physiology ; *Pollen/chemistry ; *Nutrients ; Feeding Behavior ; Seasons ; }, abstract = {Food underpins fitness and ecological interactions, yet how nutrient availability shapes species interactions in natural communities remains poorly understood. Most nutritional ecology research focuses on laboratory or single-species systems, limiting insight into how nutrient use and nutrient niche dynamics occur in complex, multispecies assemblages in the wild. We combined long-term plant-pollinator interaction data with pollen macronutrient analyses to examine how wild bumble bees exploit macronutrients and whether they occupy distinct nutrient niches. Pollen macronutrient composition varied across plant species and over the season, with protein-rich pollen peaking in spring and lipid- and carbohydrate-rich pollen increasing by late summer. Across this nutrient landscape, bumble bee species occupied two distinct macronutrient niches: one high in protein and low in lipid and carbohydrate, and the other lower in protein but moderate in lipid and carbohydrate. Nutrient niche partitioning was associated with differences in feeding morphology and colony life stage (but not phenology). We found little evidence that nutrient niche breadth differed among species or was explained by feeding morphology or colony life stage. Our results extend nutritional ecology to a multispecies context, provide evidence for nutrient niche partitioning among wild pollinators and highlight the need to consider species-specific nutritional requirements in pollinator conservation.}, }
@article {pmid40858018, year = {2025}, author = {Xu, J and Wen, X and Wang, S and Worrich, A and Ma, B and Zou, Y and Wang, Y and Wu, Y}, title = {Identification of key species and molecular mechanisms driving conjugative transfer of antibiotic resistance genes in swine manure-derived bacterial communities.}, journal = {Journal of hazardous materials}, volume = {497}, number = {}, pages = {139638}, doi = {10.1016/j.jhazmat.2025.139638}, pmid = {40858018}, issn = {1873-3336}, abstract = {The spread of antimicrobial resistance in livestock environments poses a major public health risk. Conjugative transfer plays a key role in antimicrobial resistance transmission, but the diversity of bacterial hosts involved and the molecular mechanisms driving conjugative transfer within complex microbial communities remain poorly understood. To address this, we investigated plasmid-mediated conjugation in both a swine manure-derived bacterial community and isolated strains from manure. Our study identified 53 OTUs as plasmid recipients, with 66 % belonging to Proteobacteria. Exposure to subinhibitory doxycycline levels decreased the diversity of transconjugants, but conjugation-related gene expression was significantly upregulated, which also became apparent in a marked increase in conjugation frequency. Increased conjugation frequency correlated with increased ATP, ROS and eLDH levels both in the complex bacterial community and in pairwise strains, pointing to the physiological shifts occurring in species that engage in conjugation. Among the identified recipients, Bacillus velezensis exhibited the highest conjugation frequency, likely due to the upregulation of its two-component system, quorum sensing pathways, and strong biofilm-forming ability. Our findings provide new insights into conjugative transfer in livestock manure, identifying potential key spreaders and highlighting opportunities for targeted intervention strategies to mitigate antimicrobial resistance transmission, thereby enhancing its sustainability as a fertilizer.}, }
@article {pmid40856799, year = {2025}, author = {Pushkareva, E and Keilholz, L and Böse, J and von Berg, KL}, title = {Genetic Diversity and Potential of Cyanobacteria and Fungi Living on Arctic Liverworts.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {90}, pmid = {40856799}, issn = {1432-184X}, support = {PU867/1-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Arctic Regions ; *Hepatophyta/microbiology ; *Cyanobacteria/genetics/classification/isolation &amp; purification/physiology ; *Fungi/genetics/classification/isolation &amp; purification ; *Genetic Variation ; Symbiosis ; Soil Microbiology ; Phylogeny ; Nitrogen Fixation ; }, abstract = {Liverworts often form symbiotic associations with fungi and cyanobacteria, yet the distribution and specificity of these relationships remain largely unexplored, particularly in Arctic environments. This study used metagenomic sequencing to investigate fungal and cyanobacterial communities associated with Arctic liverworts, analyzing photosynthetic parts of gametophytes and their rhizoids with attached soil separately. The results revealed that Ascomycota dominated the fungal community. The cyanobacterial community was primarily composed of heterocytous Nostoc and non-heterocytous filamentous Leptolyngbya, with Nostoc showing evidence of nitrogen fixation, especially in gametophytes, suggesting a potential role in enhancing nitrogen availability for the host. These findings underscore the ecological significance of liverwort-associated microorganisms in Arctic ecosystems, with microbial composition differing between upper and lower parts of plants, as well as between leafy and thalloid liverworts, indicating possible functional specialization.}, }
@article {pmid40855532, year = {2025}, author = {Babalola, OO and Ogundeji, FO and Akanmu, AO}, title = {Dataset of 16S rRNA and ITS gene amplicon sequencing of celery and parsley rhizosphere soils.}, journal = {BMC genomic data}, volume = {26}, number = {1}, pages = {60}, pmid = {40855532}, issn = {2730-6844}, support = {UID123634 and UID132595//National Research Foundation/ ; }, abstract = {OBJECTIVES: This amplicon metagenomic study examines the relative abundance, taxonomic profiles and community structure of bacterial and fungal communities associated with the roots of parsley (Petroselinum crispum) and celery (Apium graveolens) under monocropping and intercropping systems. The study aims to provide a baseline understanding of how intercropping influences rhizosphere microbial dynamics.<br><br>DATA DESCRIPTION: The dataset provides insight into the effects of parsley-celery intercropping system on soil microbial richness, diversity and community structure. Amplicon metagenomic sequencing was performed on the DNA samples, targeting the 16S rRNA gene (V3-V4 region) and the ITS region for bacterial and fungal communities, respectively. The quantified libraries were pooled and sequenced using Illumina platforms, and the raw sequences were analyzed using the Quantitative Insights Into Microbial Ecology (QIIME 2 version 2019.1.) pipeline. The resulting Amplicon Sequence Variant (ASV) profiles revealed Actinobacteria and Protobacteria as the most predominant bacteria phyla, followed by Bacteroidota, Gemmatimonadota and Acidobacteriaota. The most predominant taxonomic distribution of fungi at the phylum level includes Ascomycota and Mortierellomycota. The dataset includes raw sequence reads in FASTQ format (.fastq.gz), which have been deposited in the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI) under the Bioproject Accession numbers; SRP540554 (16S rRNA) and SRP540675 (ITS).}, }
@article {pmid40854362, year = {2025}, author = {Mo, Y and Lin, J and Li, X and Grossart, HP and Lin, L and Sido, MY and Yang, J}, title = {Single brand tire wear particles promote toxin-producing of an invasive cyanobacterium.}, journal = {Environmental research}, volume = {}, number = {}, pages = {122679}, doi = {10.1016/j.envres.2025.122679}, pmid = {40854362}, issn = {1096-0953}, abstract = {Tire wear particles (TWPs), as newly emerging pollutants, frequently co-occur with potentially toxic cyanobacteria in eutrophic waters. However, it is unknown how these new pollutants affect ecology of mass bloom-forming cyanobacteria. Here, we compared single brand and mixed brand TWPs how to affect the invasive and toxic cyanobacterium Raphidiopsis raciborskii. Our results demonstrate that, in the short-term, single- and mixed-brand TWPs have no significant influence on cyanobacterial growth, whereas single-brand TWPs and large-sized mixed-brand TWPs at high doses significantly reduced photosynthetic pigments. In the long-term, mixed-brand TWPs inhibit cyanobacterial growth and photosynthetic pigments synthesis more strongly than single-brand TWPs, especially exposed to high doses of large-sized mixed-brand TWPs (growth inhibitory effect up to about 80%). In addition, prolonged exposure to high-dose single-brand TWPs resulted in a marked reduction of photosynthetic activity. Moreover, high doses of large-sized single-brand TWPs significantly promoted toxin production by R. raciborskii. In contrast, mixed-brand TWPs have no significant effect on cyanobacterial toxin production. Our findings provide novel insights into potential risks for environmental and human health via the interaction between toxigenic R. raciborskii and different types of TWPs.}, }
@article {pmid40847400, year = {2025}, author = {Wang, Y and Jiang, Y and Song, Z and Zhu, C and Tang, Y and Peng, J and Liu, P}, title = {MreB: unraveling the molecular mechanisms of bacterial shape, division, and environmental adaptation.}, journal = {Cell communication and signaling : CCS}, volume = {23}, number = {1}, pages = {377}, pmid = {40847400}, issn = {1478-811X}, support = {2424017529//Guidance Plan Project of Hengyang City, China/ ; 32370209//National Natural Science Foundation of China (NSFC)/ ; 2023JJ30503//Natural Science Foundation of Hunan Province, China/ ; 22A0297//The Scientific Research Foundation of Hunan Provincial Education Department, China/ ; }, abstract = {As a key bacterial actin-like protein, MreB plays crucial roles in maintaining cell shape, regulating peptidoglycan synthesis, and coordinating chromosome segregation, making it a promising target for novel antibiotics. This review comprehensively explores MreB’s molecular architecture, its assembly into antiparallel protofilaments, and its pivotal roles in bacterial cell morphology and division. We also delve into how MreB interacts with membrane-associated proteins such as RodZ and MreC/D to coordinate cell wall synthesis and respond to environmental signals like ion gradients and temperature changes. Furthermore, we highlight the cooperation and functional divergence between MreB and FtsZ, underscoring the evolutionary adaptability of bacterial cytoskeletal structures. The structural and functional parallels between MreB and eukaryotic cytoskeletal proteins are also examined, offering new insights into the evolution of cytoskeletal systems. By integrating insights from structural biology, synthetic biology, and microbial ecology, this review aims to provide a deeper understanding of MreB’s role in bacterial biology, its dynamic responses to environmental cues, and its implications for therapeutic innovation. This comprehensive analysis not only enhances our knowledge of bacterial self-organization mechanisms but also paves the way for the development of innovative antimicrobial strategies to address the growing challenge of antibiotic resistance.}, }
@article {pmid40850119, year = {2025}, author = {Ellwood, KM and Kramer, AE and Dutta, A}, title = {Age-driven changes in the layer hen reproductive microbiome are associated with lay performance.}, journal = {Poultry science}, volume = {104}, number = {11}, pages = {105703}, doi = {10.1016/j.psj.2025.105703}, pmid = {40850119}, issn = {1525-3171}, abstract = {Eggs are a globally important food source and integral to optimal poultry production. Understanding the microbial ecology of the hen reproductive tract is essential for improving both food safety and reproductive efficiency. While the oviduct has been shown to harbor a continuous microbial community, this study is the first to demonstrate the presence of microbiota on the hen ovary surface, suggesting that the ovary is an extension of the oviductal microbial continuum. In this study, the ovarian and oviductal microbiomes of white-leghorn hens from mid-lay (high laying) and post-lay (lower laying) cohorts were analyzed. Using 16S rRNA sequencing, we identified significant shifts in reproductive tract microbiota between 9- and 18-month-old hens, coinciding with changes in lay performance. Several differentially abundant genera, including Acinetobacter, Ligilactobacillus, Bacillus, and Akkermansia, are known to modulate steroid hormone metabolism, with age-related abundance changes suggesting potential effects on hormone-driven reproductive processes. Other genera such as Ruminococcus_torques_group, Mucispirillum, and Fusobacterium-not traditionally associated with reproductive hormone pathways-may influence laying efficiency through their roles in mucin degradation, immune modulation, and inflammation. Notably, Turicibacter, newly identified on the ovary, increased with age and negatively correlated with lay performance, raising questions about its role in bile acid metabolism and stress response within the hen reproductive tract. Collectively, these findings highlight the ovary as an active microbial niche influenced by age and suggest that both hormone-associated and mucosal-interactive microbes contribute to lay dynamics. This work opens new avenues for probiotic strategies targeting key genera to support hen fertility and egg production across the productive lifespan.}, }
@article {pmid40849283, year = {2025}, author = {Tharp, CL and Custer, GF and Castrillo, G and Dini-Andreote, F}, title = {Revisiting the cry-for-help hypothesis in plant-microbe interactions.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2025.07.015}, pmid = {40849283}, issn = {1878-4372}, abstract = {The 'cry-for-help hypothesis' (CHH) is broadly used to study how root exudate modulation under stress influences recruitment of beneficial microbes in the rhizosphere. Here, we explored common misconceptions and limitations of the CHH and advocate for the reassessment of this prevalent hypothesis to unfold the ecological complexities of plant-microbe interactions.}, }
@article {pmid40843988, year = {2025}, author = {Crocker, K and Skwara, A and Kannan, R and Murugan, A and Kuehn, S}, title = {Timescale of environmental change modulates metabolic guild cohesion in microbial communities.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf186}, pmid = {40843988}, issn = {1751-7370}, abstract = {Microbial communities experience environmental fluctuations across timescales from rapid changes in moisture, temperature, or light levels to long-term seasonal or climactic variations. Understanding how microbial populations respond to these changes is critical for predicting the impact of perturbations, interventions, and climate change on communities. Because communities typically harbor tens to hundreds of distinct taxa, the response of microbial abundances to perturbations is potentially complex. However, even though taxonomic diversity is high, in many communities taxa can be grouped into metabolic guilds of strains with similar metabolic traits. These guilds effectively reduce the complexity of the system by providing a physiologically motivated coarse-graining. Here, using a combination of simulations, theory, and experiments, we show that the response of guilds to nutrient fluctuations depends on the timescale of those fluctuations. Rapid changes in nutrient levels drive cohesive, positively correlated abundance dynamics within guilds. For slower timescales of environmental variation, members within a guild begin to compete due to similar resource preferences, driving negative correlations in abundances between members of the same guild. Our results provide a route to understanding the relationship between metabolic guilds and community response to changing environments, as well as an experimental approach to discovering metabolic guilds via designed nutrient perturbations to communities.}, }
@article {pmid40843346, year = {2025}, author = {Xia, K and Hu, Y and Cai, S and Lin, M and Lu, M and Lu, H and Ye, Y and Lin, F and Gao, L and Xia, Q and Tian, R and Lin, W and Xie, L and Tan, D and Lu, Y and Lin, X and Yang, X and Zhong, L and Xu, L and Zhang, Z and Wang, L and Ren, J and Xu, H}, title = {GastritisMIL: An interpretable deep learning model for the comprehensive histological assessment of chronic gastritis.}, journal = {Patterns (New York, N.Y.)}, volume = {6}, number = {8}, pages = {101286}, pmid = {40843346}, issn = {2666-3899}, abstract = {The comprehensive histological assessment of chronic gastritis is imperative for guiding endoscopic follow-up strategies and surveillance of early-stage gastric cancer, yet rapid and objective assessment remains challenging in clinical workflows. We propose a powerful deep learning model (GastritisMIL) to effectively identify pathological alterations on H&amp;E-stained biopsy slides, thereby expediting pathologists' evaluation and improving decision-making regarding follow-up intervals. We have trained and tested GastritisMIL by using retrospective data from 2,744 patients and evaluated discriminative performance across three medical centers (467 patients). GastritisMIL attained areas under the receiver operating curve greater than 0.971 in four tasks (inflammation, activity, atrophy, and intestinal metaplasia) and superior performance comparable to that of two senior pathologists. Specifically, interpretable attention heatmaps generated by GastritisMIL effectively assist junior pathologists in locating suspicious lesion regions across the entire field and minimizing missed diagnosis risk. Moreover, the high generalizability of this developed model across multiple external cohorts demonstrates its potential translational value.}, }
@article {pmid40842826, year = {2025}, author = {Ahadi, R and Alizadeh, A and Chenari Bouket, A and Masigol, H and Grossart, HP}, title = {Multigene phylogeny, morphology, and pathogenicity uncover two novel Globisporangium species (Oomycota) from freshwater habitats in northwestern Iran.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1615096}, pmid = {40842826}, issn = {1664-302X}, abstract = {During the study of oomycete biodiversity in aquatic environments of northwestern Iran (East Azarbaijan), four Globisporangium isolates were recovered from a river and irrigation canal. These isolates were identified based on multi-locus phylogenetic analyses (ITS, cox1, and cox2 genomic regions) and morphological features. As a result, two novel species were described, namely Globisporangium parvizense sp. nov. and G. sarabense sp. nov., both exhibiting unique sporangial structures and growth patterns. Pathogenicity assays on cucumber seedlings confirmed strains' high potential to cause root and crown rot. This research highlights the diversity of Globisporangium in Iranian freshwater habitats, providing insights into its taxonomy and phylogenetic relationships. Detailed morphological descriptions and illustrations are provided for these novel species.}, }
@article {pmid40841038, year = {2025}, author = {Tang, Z and Zhang, Y and Shangguan, H and Xie, A and Xu, X and Jiang, Y and Breed, MF and Sun, X}, title = {Urban organic manure application enhances antibiotic resistance gene diversity and potential human pathogen abundance in invasive giant African snails.}, journal = {Journal of environmental sciences (China)}, volume = {158}, number = {}, pages = {610-620}, doi = {10.1016/j.jes.2025.02.028}, pmid = {40841038}, issn = {1001-0742}, mesh = {Animals ; *Manure ; *Drug Resistance, Microbial/genetics ; *Snails/microbiology ; Humans ; Introduced Species ; Gastrointestinal Microbiome ; Soil Microbiology ; Environmental Monitoring ; RNA, Ribosomal, 16S ; Feces/microbiology ; }, abstract = {The giant African snail (Achatina fulica) is an invasive species served as potential vectors for antibiotic resistance genes (ARGs) and potential human bacterial pathogens. Currently, urban green spaces receive extensive organic manure additions as part of their management, may intensify the biological contamination potential of these snail vectors, thereby increasing the risk of biological pollution in green spaces. However, the specific impacts of this practice on the microbial ecology of these invasive species remain poorly understood. Here, we investigated the effects of organic manure application on the gut microbiome of giant African snails, focusing on ARGs, bacterial community structure, and potential human bacterial pathogens. Microcosm experiments compared snail gut microbiomes in different treatments (Soil: soil samples collected after manure amendment, before any snail exposure. Feces: fecal samples collected from snails that lived on manure-amended soil. Control: fecal samples collected from snails that lived on unamended soil) using 16S rRNA high-throughput sequencing and metagenomic analysis. Our results show that manure application significantly altered gut bacterial community structure and increased ARG diversity by enriching specific high-risk ARGs (such as sul1 and sul2 in the Feces group increased by 2.89 and 2.43 times, respectively, compared to the Control group), and the introduction of eight novel ARG subtypes, despite decreasing overall ARG abundance. Moreover, the relative abundance of potential human pathogens, particularly Pseudomonadaceae, was greatly increased by manure application. These findings reveal that organic manure application in urban green spaces can potentially enhances their role as reservoirs and vectors of ARGs and human pathogens.}, }
@article {pmid40840191, year = {2025}, author = {Vermeersch, M and Jacxsens, L and Baele, T and Van Damme, I and Verhaegen, B and Boon, N and Uyttendaele, M}, title = {Microbiological hygiene and food safety assessment of urban aquaponic farming.}, journal = {International journal of food microbiology}, volume = {442}, number = {}, pages = {111393}, doi = {10.1016/j.ijfoodmicro.2025.111393}, pmid = {40840191}, issn = {1879-3460}, abstract = {Aquaponic production presents a promising approach in developing sustainable (urban) food systems, through combined production of plants and aquatic organisms for food. A commercial aquaponic farm was subjected to a longitudinal microbiological assessment of hygiene and food safety. Foodborne pathogenic bacteria (Salmonella spp., and Listeria monocytogenes), indicator bacteria (generic E. coli, coliforms, and Enterobacteriaceae) and total plate counts were determined during two distinct two-month production periods, focused on basil production from seed to mature plant and all water streams composing the irrigation water. The results indicated no direct food safety concerns to consumers, with neither Salmonella spp., nor Listeria monocytogenes detected on the ready-to-market basil leaves. The soilless substrate and irrigation water were identified as major risk factors for introducing and spreading foodborne pathogenic bacteria within the aquaponic environment. Overall, E. coli was present (LOD 1 CFU/100 mL or 10 CFU/g) in 21.1 % of samples and Salmonella spp. was detected in 8 out of 94 analyses. Generic E. coli was not a suitable marker for Salmonella spp. presence in irrigation water within the aquaponic farm. Strong correlations were found between Enterobacteriaceae and coliforms in water samples, however, elevated levels were not linked to positive Salmonella spp. detection. To mitigate microbiological food safety risks in aquaponics, the use of fit-for-purpose water, establishing a water quality monitoring plan, implementing effective UV treatment and applying appropriate cleaning and disinfection protocols are recommended. The implementation of tailored good agricultural practices (GAP) is key to ensure safe food production within aquaponic farming.}, }
@article {pmid40840036, year = {2025}, author = {Zhu, M and Zhang, W and Zhang, F and Duan, X and Qiu, Z and Zhao, S and Gao, S and He, F}, title = {C28-aldehyde (n-octacosanal) modulates stage-specific temporal expression of effector genes in the wheat powdery mildew fungus.}, journal = {Microbiological research}, volume = {301}, number = {}, pages = {128311}, doi = {10.1016/j.micres.2025.128311}, pmid = {40840036}, issn = {1618-0623}, abstract = {The prepenetration processes of the wheat powdery mildew fungus, Blumeria graminis f. sp. tritici (Bgt), are triggered by C28 aldehyde (n-octacosanal), a component of cuticular waxes. Despite being the most severe crop disease worldwide, the underlying molecular mechanisms of the prepenetration processes remain obscure. Utilizing a Formvar®-based in vitro system, transcriptomes of Bgt conidia impacted by n-octacosanal were profiled without the effects from plant host. A total of 1354 differentially expressed genes were identified between n-octacosanal- and n-octacosane (non-chemical signal)-treated conidia. The expression of effectors, transcription factors, and HOG-MAPK pathways is specifically regulated by n-octacosanal in a developmental stage-dependent manner. Among them, 25 effectors and three transcription factors, including COD 1, VEA, and CreA, were highly expressed at all stages. While some genes of the HOG-MAPK pathway were significantly upregulated during conidial growth, other genes were downregulated. These results revealed that C28 aldehyde-triggered Bgt conidial prepenetration in the plant host might be achieved by activating specific transcription factors and differentially regulating the HOG-MAPK pathway. The genes detected by our gene expression analysis may be crucial for successful infection by Bgt and thus serve as candidates for future functional analysis of the molecular mechanisms of conidia development in powdery mildew. These findings provide new insights into the chemical-signal-orchestrated development of an important phytopathogenic fungus and will potentially support efforts for the control and management of fungal diseases in wheat.}, }
@article {pmid40838740, year = {2025}, author = {Wang, J and Hashem, I and Bhonsale, S and F M Van Impe, J}, title = {Individual-based modeling (IbM) unravels spatial and social interactions in bacterial communities.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf116}, pmid = {40838740}, issn = {1751-7370}, abstract = {Bacterial interactions are fundamental in shaping community structure and function, driving processes that range from plastic degradation in marine ecosystems to dynamics within the human gut microbiome. Yet, studying these interactions is challenging due to difficulties in resolving spatiotemporal scales, quantifying interaction strengths, and integrating intrinsic cellular behaviors with extrinsic environmental conditions. Individual-based modeling addresses these challenges through single-cell-level simulations that explicitly model growth, division, motility, and environmental responses. By capturing both the spatial organization and social interactions, individual-based modeling reveals how microbial interactions and environmental gradients collectively shape community architecture, species coexistence, and adaptive responses. In particular, individual-based modeling provides mechanistic insights into how social behaviors-such as competition, metabolic cooperation, and quorum sensing-are regulated by spatial structure, uncovering the interplay between localized interactions and emergent community properties. In this review, we synthesize recent applications of individual-based modeling in studying bacterial spatial and social interactions, highlighting how their interplay governs community stability, diversity, and resilience. By linking individual-scale interactions with the ecosystem-level organization, individual-based modeling offers a predictive framework for understanding microbial ecology and informing strategies for controlling and engineering bacterial consortia in both natural and applied settings.}, }
@article {pmid40440482, year = {2025}, author = {Zhao, L}, title = {Guild-Level Response of the Gut Microbiome to Nutritional Signals: Advancing Precision Nutrition for Metabolic Health.}, journal = {Annual review of nutrition}, volume = {45}, number = {1}, pages = {197-221}, doi = {10.1146/annurev-nutr-122424-022254}, pmid = {40440482}, issn = {1545-4312}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Precision Medicine ; Diet ; Dietary Fiber ; Animals ; Metabolic Diseases/microbiology ; Inflammation ; }, abstract = {The gut microbiome functions as a hidden organ, providing essential ecosystem services to sustain human health. By identifying stably connected bacteria, we reveal two competing guilds (TCG) as the resilient core of the microbiome: the health-promoting foundation guild (FG) and the proinflammatory pathobiont guild (PG). FG members produce short-chain fatty acids (SCFAs), enhancing gut barrier integrity and systemic resilience, while PG members disrupt metabolism through endotoxins, indoles, and hydrogen sulfide. Together, the FG and PG mediate ∼85% of ecological interactions in a dynamic, seesaw-like relationship. As evolved nutrient sensors for coping with feast-famine cycles, these guilds align host metabolism with dietary patterns. Fiber-rich diets bolster FG activity, maintaining microbial balance and metabolic health, whereas fiber-deficient diets in modern-day society favor chronic PG dominance, driving inflammation and disease. Synthesizing clinical and experimental evidence, this review positions the TCG model as a transformative framework for precision nutrition, guiding strategies to restore microbial balance and address metabolic disorders.}, }
@article {pmid40835811, year = {2025}, author = {Luzics, S and Baka, E and Otto, M and Kosztik, J and Szalontai, H and Bata-Vidács, I and Nagy, I and Tóth, &#xc1; and Táncsics, A and Pápai, M and Nagy, I and Orsini, M and Kukolya, J}, title = {High-quality de novo genome assembly and functional genomic insights into Thermobifida alba DSM43795[T], a mesophilic actinobacterium isolated from garden soil.}, journal = {Biologia futura}, volume = {}, number = {}, pages = {}, pmid = {40835811}, issn = {2676-8607}, support = {K142686//National Research, Development and Innovation Office/ ; EK&#xd6;P- 24- VI/MATE-3//Ministry for Culture and Innovation from the source of the National Research, Development and Innovation Fund/ ; EK&#xd6;P-MATE/2024/25/D//Ministry for Culture and Innovation from the source of the National Research, Development and Innovation Fund/ ; }, abstract = {Thermobifida alba DSM43795[T], a mesophilic actinobacterium isolated from garden soil, plays a vital role in lignocellulose degradation and holds biotechnological and pharmaceutical potential. We present a high-quality, complete de novo genome assembly of T. alba DSM43795[T] using combined PacBio long-read and Illumina short-read sequencing, resulting in a single circular chromosome of 4.9 Mbp with 72.1% GC content. Comparative genomics with the thermophilic relative T. fusca YX revealed 83.39% average nucleotide identity and extensive genome synteny alongside niche-specific differences. Functional annotation identified 4345 genes, including a rich complement of carbohydrate-active enzymes (CAZymes) such as glycoside hydrolases (GHs), esterases, and polysaccharide lyases, supporting versatile plant biomass degradation. GH gene sets were largely conserved between the species in both gene number and distribution, but T. alba uniquely encodes a novel GH10 endo-xylanase near a characterised palindrome regulatory sequence, indicating species-specific regulation. We hypothesise that thermophilic adaptation in T. fusca requires more proteins for ribosome integrity and amino acid metabolism, with reduced emphasis on carbohydrate metabolism and defence compared to T. alba. Moreover, T. alba harbours a broader array of defence-related genes and mobile genetic elements, including integrases and transposases. Although lacking a complete CRISPR-Cas system, two CRISPR arrays were detected, suggesting alternative immune strategies. Virulence factor homologs shared by both species likely reflect environmental survival rather than pathogenicity. This genomic characterisation elucidates T. alba's metabolic versatility and ecological adaptations, laying the groundwork for its potential applications in biomass conversion, environmental biotechnology, and drug discovery.}, }
@article {pmid40835614, year = {2025}, author = {Ma, H and Cornadó, D and Raaijmakers, JM}, title = {The soil-plant-human gut microbiome axis into perspective.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {7748}, pmid = {40835614}, issn = {2041-1723}, support = {32201402//National Natural Science Foundation of China (National Science Foundation of China)/ ; 202206205006//China Scholarship Council (CSC)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Soil Microbiology ; *Plants/microbiology ; Soil/chemistry ; Ecosystem ; Animals ; }, abstract = {Microbiomes of soil, plants, and the animal gut are pivotal for key life processes such as nutrient cycling, stress resilience, and immunity. While studies have hinted at a shared microbial reservoir connecting these environments, compelling evidence of a soil-plant-gut microbiome axis is scarce. This perspective explores the potential continuum and diversification of microbes along this axis, highlighting specific microorganisms capable of moving from soil to plants to the human gut. A conceptual framework is proposed to better understand the mechanisms driving interactions among these microbiomes. We also examine how soil, plant, and gut microbiomes may co-evolve and influence one another through reciprocal effects. We consider external environmental factors that could strengthen their interconnections, potentially creating beneficial feedback loops that impact ecosystem and human health.}, }
@article {pmid40830705, year = {2025}, author = {Oulkhir, FE and Allaoui, A and Idbella, A and Danouche, M and Bargaz, A and Biskri, L and Idbella, M}, title = {Bacillus subtilis ED24 Controls Fusarium culmorum in Wheat Through Bioactive Metabolite Secretion and Modulation of Rhizosphere Microbiome.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {89}, pmid = {40830705}, issn = {1432-184X}, mesh = {*Triticum/microbiology/growth &amp; development ; *Fusarium/growth &amp; development/drug effects/physiology ; *Bacillus subtilis/physiology/metabolism ; *Rhizosphere ; *Plant Diseases/microbiology/prevention &amp; control ; *Microbiota ; Soil Microbiology ; Plant Roots/microbiology ; Endophytes/physiology ; Fungicides, Industrial/pharmacology ; }, abstract = {Fusarium culmorum is a soil-borne fungal pathogen causing root and stem rot, seedling blight, and significant yield losses in small grain cereals, including wheat. This study aimed to evaluate the antifungal potential of Bacillus subtilis ED24, an endophytic strain isolated from Ziziphus lotus (L.) roots, and its effects on wheat growth and yield under controlled conditions. In vitro assays demonstrated that B. subtilis ED24 inhibited F. culmorum mycelial growth by up to 87%, associated with the secretion of 37 distinct secondary metabolites, predominantly involved in carbon cycling. In pot experiments, B. subtilis ED24 significantly enhanced wheat germination (85%) and growth compared to infected plants treated with the chemical fungicide tebuconazole. Although nutrient analysis showed significantly higher shoot nitrogen (32.34 mg/pot) and phosphorus (2.41 mg/pot) contents in the B. subtilis ED24 treatment compared to tebuconazole (8.11 and 0.18 mg/pot, respectively), no significant differences were observed when compared to the infected control (C-). Similarly, B. subtilis ED24 led to improved thousand grain weight (40.4 g), protein content (19.98%), and ash content (1.95%) relative to tebuconazole (29.1 g, 18.31%, and 1.74%, respectively), yet these values did not differ significantly from the infected control (C-). Notably, the number of seeds per pot was significantly increased by B. subtilis ED24 compared to the infected control (C-) (113.8 seeds/pot vs. 54.2 seeds/pot). Additionally, B. subtilis ED24 modulated the wheat rhizosphere microbiome, enriching beneficial taxa such as Eurotiomycetes fungal class and the bacterial genus Paramesorhizobium. These findings suggest that the antifungal activity and growth-promoting effects of B. subtilis ED24 are likely mediated through the synthesis of unique bioactive metabolites and microbiome modulation, offering a promising sustainable alternative to chemical fungicides in wheat production.}, }
@article {pmid40828659, year = {2025}, author = {Wang, X and Chen, Z and Liu, C and Zhang, Z and Deng, Y and Tao, L and Tiedje, JM and Deng, J}, title = {Type I-F CRISPR-associated transposons contribute to genomic plasticity in Shewanella and mediate efficient programmable DNA integration.}, journal = {Microbial genomics}, volume = {11}, number = {8}, pages = {}, doi = {10.1099/mgen.0.001476}, pmid = {40828659}, issn = {2057-5858}, abstract = {The genome plasticity of species and strains in the genus Shewanella is closely associated with the diverse mobile genetic elements embedded in its genomes. One mobile element with potential for accurate and efficient DNA insertion in Shewanella is the type I-F3 CRISPR-associated transposon (I-F3 CAST). However, relatively little is known about the distribution and ecological significance of I-F3 CASTs and whether they could be suitable as a tool for targeted genetic manipulation in situ. To better understand the distribution of I-F3 CASTs in Shewanella, we analysed 602 Shewanella genomes. We found that I-F3 CASTs were present in 12% of all genomes, although differences in both gene arrangement and integration locus were observed. These Shewanella I-F3 CASTs carried up to 89 cargo genes, which were associated with diverse functions, including defence, resistance and electron transfer, demonstrating an important role in genomic diversification and ecological adaptation. We tested whether the I-F3 CAST present in Shewanella sp. ANA-3 enhanced gene insertion, both in situ and in a heterologous host. We observed I-F3 CAST-mediated crRNA-targeted integration of the supplied genes into the pyrF locus in Shewanella sp. ANA-3. Heterologous gene insertion with high integration efficiency in Escherichia coli was also demonstrated using a simplified version of ANA-3 I-F3 CAST. Altogether, this work highlights the important role of I-F3 CASTs in promoting genomic plasticity of the Shewanella genus and demonstrates the gene-editing capability of ANA-3-CAST both endogenously and heterologously.}, }
@article {pmid40824433, year = {2025}, author = {Schneider, T}, title = {Interactions at sea: on the microbiome life-cycle and biogeochemical processes.}, journal = {History and philosophy of the life sciences}, volume = {47}, number = {3}, pages = {41}, pmid = {40824433}, issn = {1742-6316}, abstract = {The marine phycosphere is a microscale mucosal region of microbiomes surrounding a phytoplankton cell. The phycosphere (analogous to the terrestrial rhizosphere) is where microbial interactions navigate the biochemistry of the sea. The study of this microsphere deals with the causal relation enigma between two spatiotemporal scales: the micro-communal interactions and the macro-level of the biogeochemical cycles (Stocker, Science, 338(6107), 628-633, 2012); Segev et al., eLife, 5, e17473, 2016; Seymour et al., Nature Microbiology 2, Article 17065, 2017). This study of communities and ecosystems looks at metabolic interactions and interdependence relations, not focusing on biodiversity as the object of study. Following marine microbial ecology, an epistemic view of interactions and inter-communal relations seems to take the bulk of consideration. In this paper, I ask what it is about the sea that promotes an interactionist epistemic framework that is different than other fields in microbial ecology. Using Helen Longino's interactionist ontology (2020, 2021), I ask whether the sea presents a unique epistemic framework focusing on understanding interactions and interdependence. I look into the insights marine environmental studies may provide to the methodological and conceptual challenges in understanding microbial ecological stability and life cycles. By paralleling marine and soil microbial ecology, I highlight the distinct features of the water column that offer a unique epistemic and methodological framework focused on interactions and interdependence. Exploring microbial ecology at sea, I detail its epistemic advantages in shaping an interactionist theoretical and conceptual framework.}, }
@article {pmid40824088, year = {2025}, author = {Baty, JJ and Drozdick, AK and Pfeiffer, JK}, title = {Pseudomonas aeruginosa rhamnolipids stabilize human rhinovirus 14 virions.}, journal = {Journal of virology}, volume = {}, number = {}, pages = {e0093125}, doi = {10.1128/jvi.00931-25}, pmid = {40824088}, issn = {1098-5514}, abstract = {Many mammalian viruses encounter bacteria and bacterial molecules over the course of infection. Previous work has shown that the microbial ecology of the gut plays an integral role in poliovirus and coxsackievirus infection, where bacterial glycans can facilitate virus-receptor interactions, enhance viral replication, and stabilize viral particles. However, how airway bacteria alter respiratory viral infection is less understood. Therefore, we investigated whether a panel of airway bacteria affects rhinovirus stability. We found that Pseudomonas aeruginosa, an opportunistic airway pathogen, protects human rhinovirus 14 (HRV14) from acid or heat inactivation. Further investigation revealed that P. aeruginosa rhamnolipids, glycolipids with surfactant properties, are necessary and sufficient for stabilization of rhinovirus virions. However, airway bacteria did not stabilize HRV16, a distantly related rhinovirus with higher capsid stability. Taken together, this work demonstrates that specific molecules produced by an opportunistic airway pathogen can influence a respiratory virus.IMPORTANCEBacteria can enhance viral stability and infection for enteric members of the Picornaviridae, such as poliovirus and coxsackievirus; however, whether bacteria influence respiratory picornaviruses is unknown. In this study, we examined the impacts of airway bacteria on rhinovirus, a major etiological agent of the common cold. We found that Pseudomonas aeruginosa protects human rhinovirus 14 from both acid and heat inactivation through rhamnolipids. Overall, this work demonstrates bacterial effects on respiratory viruses through specific bacterial molecules.}, }
@article {pmid40821451, year = {2025}, author = {Pignon, E and Schaerli, Y}, title = {Deciphering microbial spatial organization: insights from synthetic and engineered communities.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf107}, pmid = {40821451}, issn = {2730-6151}, abstract = {Microbial communities are frequently organized into complex spatial structures, shaped by intrinsic cellular traits, interactions between community members, initial growth condition or environmental factors. Understanding the mechanisms that drive these spatial patterns is essential for uncovering fundamental principles of microbial ecology and for developing applications. Using genetic engineering and synthetic microbial communities allows us to decipher how specific parameters influence spatial organization. In this review, we highlight recent studies that leverage synthetic microbial communities to deepen our understanding of microbial spatial ecology. We begin by exploring how initial conditions, such as cell density and relative species abundance, influence spatial organization. We then focus on studies that examine the role of individual microbial traits, such as cell shape and motility. Next, we discuss the impact of contact-dependent and long-range interactions, including metabolite exchange and toxin release. Furthermore, we highlight the influence of environmental factors on spatial dynamics. Finally, we address the current limitations of synthetic approaches and propose future directions to bridge the gap between engineered and natural systems.}, }
@article {pmid40816674, year = {2025}, author = {Hou, N and Yin, X and Wang, W and Huang, X and Fang, Y and Vancov, T and Sardans, J and Tariq, A and Zeng, F and Wiesmeier, M and Peñuelas, J}, title = {Soil carbon stabilization associated with iron-aluminum complexes and microbial communities in paddy.}, journal = {Environmental research}, volume = {}, number = {}, pages = {122601}, doi = {10.1016/j.envres.2025.122601}, pmid = {40816674}, issn = {1096-0953}, abstract = {Rice paddies play a pivotal role in global carbon cycling, offering significant potential for climate change mitigation and sustainable agriculture. This study investigates the synergistic effects of long-term fertilization, iron-aluminum-soil organic carbon (Fe(Al)-SOC) complexes, and microbial communities on soil organic carbon (SOC) stabilization across major rice-growing regions. Black soils exhibited the highest SOC content (43.9 g kg[-1]), surpassing other soils by 41.6-82.6%, suggesting distinct stabilization mechanisms. Key findings include: (1) Fe(Al)-SOC complexes and aromatic carbon (20.4% in black soils) jointly enhanced long-term SOC preservation; (2) CO2 emissions were controlled by nitrogen (N) and phosphorus (P) stoichiometry and physical protection within 0.25-0.5 mm aggregates; (3) Bacterial abundance negatively correlated with SOC and light fraction organic carbon (LFOC) levels, concomitant with reduced CO2 emissions; and (4) N/P fertilization boosted carbonyl-C (recalcitrant pool) while maintaining Alkyl-C (31.7% in brick-red soils), indicating balanced C stabilization. Critically, we demonstrate that Fe/Al-microbial interactions-where Fe/Al complexes modulate microbial composition and activity-are central to SOC storage. These results provide a mechanistic framework for optimizing rice cultivation practices to maximize soil carbon storage through the synergistic management of mineral-organic complexes, microbial ecology, and fertilization strategies.}, }
@article {pmid40815158, year = {2025}, author = {Berman, HL and McKenney, EA and Roche, CE and Michalski, S and Kwon, SH and Weichel, E and Matson, A and Nichols, LM and Alvarado, S and Horvath, JE and Dunn, RR}, title = {Cooking-class style fermentation as a context for co-created science and engagement.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0266024}, doi = {10.1128/spectrum.02660-24}, pmid = {40815158}, issn = {2165-0497}, abstract = {Fermented foods have been consumed for thousands of years and have been used as a model system to study community succession and other ecological questions. Additionally, cooking classes offer opportunities to learn about food preparation and history. In the present study, scientists and chefs delivered cooking-class style workshops in which participants learned the recipes of one of three fermented foods and the microbial ecology within these foods. Participants prepared jars of chow chow, kimchi, or kombucha to set up experiments to study microbial community succession and pH changes. The fermented foods were also used to test the following hypotheses: that increasing the number of substrates results in increased alpha diversity, and that phylogenetically diverse substrates will lead to greater beta diversity among microbial communities. Microbial communities contained lactic and acetic acid bacteria described previously in fermented foods, and indicator species were identified for cabbage and radish substrates in kimchi. Finally, we qualitatively comment on the experience of developing workshops with chefs and the use of participatory science in these experiments.IMPORTANCEThe present study demonstrates the utility of using fermented foods as an inexpensive and effective tool to investigate ecological phenomena and engage the public in microbiology and ecology through cooking-class style workshops. We also model a creative, interdisciplinary collaboration between scientists and chefs.}, }
@article {pmid40812185, year = {2025}, author = {Common, JE and Payne, RP}, title = {Microbial Makeover: Skin microbiome reset after stem cell transplantation.}, journal = {Cell host &amp; microbe}, volume = {33}, number = {8}, pages = {1318-1320}, doi = {10.1016/j.chom.2025.07.014}, pmid = {40812185}, issn = {1934-6069}, abstract = {Inborn errors of immunity disrupt host-microbe interactions. In this issue of Cell Host &amp; Microbe, Che et al.[1] examine DOCK8-deficient individuals undergoing stem cell transplantation and show that immune reconstitution rebalances the skin microbiome, underscoring the central role of immunity in shaping cutaneous microbial ecology.}, }
@article {pmid40809134, year = {2024}, author = {Casey, J and Bennion, B and D'haeseleer, P and Kimbrel, J and Marschmann, G and Navid, A}, title = {Transporter annotations are holding up progress in metabolic modeling.}, journal = {Frontiers in systems biology}, volume = {4}, number = {}, pages = {1394084}, pmid = {40809134}, issn = {2674-0702}, abstract = {Mechanistic, constraint-based models of microbial isolates or communities are a staple in the metabolic analysis toolbox, but predictions about microbe-microbe and microbe-environment interactions are only as good as the accuracy of transporter annotations. A number of hurdles stand in the way of comprehensive functional assignments for membrane transporters. These include general or non-specific substrate assignments, ambiguity in the localization, directionality and reversibility of a transporter, and the many-to-many mapping of substrates, transporters and genes. In this perspective, we summarize progress in both experimental and computational approaches used to determine the function of transporters and consider paths forward that integrate both. Investment in accurate, high-throughput functional characterization is needed to train the next-generation of predictive tools toward genome-scale metabolic network reconstructions that better predict phenotypes and interactions. More reliable predictions in this domain will benefit fields ranging from personalized medicine to metabolic engineering to microbial ecology.}, }
@article {pmid40804729, year = {2025}, author = {Rezaei, Z and Amoozegar, MA and Moghimi, H}, title = {Innovative approaches in bioremediation: the role of halophilic microorganisms in mitigating hydrocarbons, toxic metals, and microplastics in hypersaline environments.}, journal = {Microbial cell factories}, volume = {24}, number = {1}, pages = {184}, pmid = {40804729}, issn = {1475-2859}, abstract = {Hypersaline environments are ecologically, industrially, and scientifically important because they host unique extremophiles used in biotechnology, bioremediation, and enzyme production. These habitats are seriously threatened by three common contaminants: hydrocarbon pollutants, toxic metals, and microplastics. In particular, the remediation of hazardous substances under extreme conditions is challenging due to limited accessibility and bioavailability of pollutants, harsh physicochemical conditions, reduced microbial abundance and diversity, and instability of enzymes. Halophiles are extremophilic microorganisms that thrive in high-salt environments, exhibiting notable metabolic diversity and resilience, and play a critical role in overcoming these challenges. Their ability to degrade recalcitrant pollutants makes them valuable for bioremediation in contaminated hypersaline ecosystems. Advancements in engineering tools and synthetic biology have revolutionized halophile-based biotechnologies. Techniques like gene editing and recombinant DNA have facilitated the precise modification of halophiles, enabling them to efficiently target and degrade toxic compounds and significantly improve their bioremediation potential. Furthermore, with the rapid progress of omics approaches, identifying new halophilic microbes, their enzymes, and their metabolic pathways is now becoming possible. Despite these advances, challenges remain in optimizing genetically tractable strains, ensuring biosafety, and understanding microbial ecology for scalable, safe, and cost-effective applications. This review provides an overview of halophilic and halotolerant microorganisms, their habitat, and their unique adaptations to saline and hypersaline environments. Key pollutants threatening extreme environments, as well as the ability of halophiles to degrade them, are also discussed. Additionally, it highlights current challenges, including the introduction of engineered halophiles into natural ecosystems, scaling up bioprocesses, cost management, and regulatory concerns, and explains future perspectives to address these issues. Ultimately, it emphasizes the need for advanced research to fully harness the potential of halophiles in sustainable bioremediation.}, }
@article {pmid40804168, year = {2025}, author = {Sun, L and Wen, X and Li, L and Li, M and Xing, X and Zhang, Z and Dong, C}, title = {Formation and sustenance mechanism of bacterial diversity in nutrient-deficient environment of indoor stadium.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {29685}, pmid = {40804168}, issn = {2045-2322}, abstract = {Bacterial diversity has been found in indoor stadiums which can be considered as a specific nutrient-deficient environment (NDE), it remains a mystery and opens to new ideas why the bacterial diversity can be formed and maintained in NDE of indoor stadiums, since it is obvious to violate the famous competitive exclusion principle (CEP) in ecology. In the article, five most common genera, Pseudomonas, Acinetobacter, Exiguobacterium, Sphingobacterium, Chryseobacterium in indoor stadiums were selected and periodically sampled to supervise the dynamic characteristics of bacterial community. Based on quorum sensing (QS) and non-monotonic interspecific interaction (NMII) in combination with microbial ecology, clustering analysis and experimental observation, a new hypothesis was put forward to elucidate QS and NMII of substrate location information (SLI) mechanism driving bacterial community succession with high diversity in NDE of indoor stadium. A valid cellular automation (CA) model was derived from assumptions directly, and the CA simulation sufficiently proved that QS and NMII of SLI can effectively weaken interspecific competition to drive the spatiotemporal succession of bacterial community in NDE of indoor stadium towards a climax community with high richness and evenness, namely bacterial diversity. The succession mechanism confirmed by CA simulation can set up a theoretical framework for comprehensive apprehension about ecological effect of QS with NMII of SLI sharing on formation and sustenance of bacterial diversity in NDE of indoor stadium.}, }
@article {pmid40802392, year = {2025}, author = {Shaikenova, K and Issabekova, S and Sadenova, M and Omarova, K and Uskenov, R}, title = {Synergistic impact of integrated mechanical, physical, and chemical disinfection on microbial ecology and morphophysiological development in dairy calves.}, journal = {Brazilian journal of biology = Revista brasleira de biologia}, volume = {85}, number = {}, pages = {e295880}, doi = {10.1590/1519-6984.295880}, pmid = {40802392}, issn = {1678-4375}, abstract = {The article presents the results of studies of the influence of the complex process of cleaning and disinfection of the dispensary using mechanical, physical and chemical methods on the growth and development of calves of the dairy period. The dispensary for calves is divided into two rooms, where there were animals of the control and experimental groups selected by the method of pairs of analogues in the same feeding and maintenance conditions. Studies before the treatment of rooms for calves showed a massive growth of bacilli and bacteria - 100%, mold fungi - 80%, yeast - 20%, actinomycetes - 80%. After processing the room for calves of the experimental group, the number of microorganisms during mechanical treatment, microbial contamination decreased by 31%, during physical treatment by 62%, and during chemical treatment by 95%. Monitoring of live weight, exterior features of calves showed that the live weight of calves of the experimental group of monthly calves averaged 58.9 kg, and the control group 58.6 kg, respectively. In the second month, the live weight of the experimental was 7.5 kg or 9.1% more than the control. And also for all body measurements, the experimental group exceeded the control group by an average of 10%. The results of the study of hematological parameters showed that in the experimental group they are all within the normal range, whereas in the control group the content of leukocytes is 13.2 * 109 liters, lymphocytes are 7.7 * 109 liters higher than normal, which indicates inflammatory processes in the body of calves.}, }
@article {pmid40795028, year = {2025}, author = {Park, HS and Chavarria, X and Shatta, A and Kang, D and Oh, S and Choi, DY and Choi, JH and Kim, M and Cho, YH and Yi, MH and Kim, JY}, title = {Distinct microbial communities of drain flies (Clogmia albipunctata) across sites with differing human influence.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnaf078}, pmid = {40795028}, issn = {1574-6968}, abstract = {Drain flies (Clogmia albipunctata) are insects that thrive in humid urban environments such as bathrooms drains and sewage systems. While their role in pathogen transmission has been suggested, little is known about their microbiome or ecology in non-clinical contexts. Using 16S rRNA gene metabarcoding, we characterized the bacterial communities of drain flies from three locations in South Korea, public bathrooms from a college in Seoul, a rural port in Ulleungdo island, and a highly frequented public park in Yeouido. In total, we obtained 221 families and 1 474 features. We found significant differences in microbiome composition and diversity as well as a small core microbiome shared among locations, with environmental bacteria such as Pseudomonas and Ralstonia being the dominant taxa across samples. The majority of the detected amplicon sequence variants (ASV) were not shared among locations. These findings suggest drain fly transport a location-specific environmental bacteria. Notably, we also identified ASVs of potential clinical relevance, including Mycobacterium, Acinetobacter baumanii, Providencia, and Nocardia. This is the first metagenomic insight into the microbiome of this species and adds to a renewed interest in the role that non-hematophagous insects play in urban microbial ecology and the spread of microbes.}, }
@article {pmid40793771, year = {2025}, author = {Bhandari, R and Wong, AC-N and Lee, JC and Boyd, A and Shelby, K and Ringbauer, J and Kang, DS}, title = {Microbiome composition and co-occurrence dynamics in wild Drosophila suzukii are influenced by host crop, fly sex, and sampling location.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0260824}, doi = {10.1128/spectrum.02608-24}, pmid = {40793771}, issn = {2165-0497}, abstract = {Microbial control of insect pests offers promising alternatives to traditional pesticides. However, the microbial communities and factors influencing these communities within insect hosts remain poorly understood. This study examined the whole-body bacterial communities in wild Drosophila suzukii, commonly known as spotted wing Drosophila (SWD). Fly samples were collected from two farms growing wild Himalayan blackberries near blueberry crops, one blackberry farm, and one elderberry farm across four locations in the United States. Our analyses showed significant differences in microbial communities in flies across various host crops and sampling locations. We identified co-occurring bacterial genera, dominated by Gluconobacter and Morganella, and the overall microbiome was distinct from those found in laboratory-grown flies. Our findings suggest that the host crop, sex of the fly, sampling location, and their interactions play a crucial role in shaping microbial communities in SWD, indicating the influence of various ecological interactions. While no significant differences in microbiome composition were observed between male and female flies, network analysis revealed distinct sex-specific microbial co-occurrence patterns. Female flies displayed a more stable and interconnected microbial network than male flies, suggesting that sex-specific factors might influence bacterial interactions. Interestingly, the most abundant microbial taxa were not necessarily the most connected in the networks, showing that less abundant taxa may also play a significant role in shaping the fly microbiome. This study underscores the complexity of microbial ecology in SWD and highlights the necessity of considering these dynamics when developing pest management strategies in agriculture.IMPORTANCEStudies on the microbiome of spotted wing Drosophila (SWD) have primarily focused on laboratory-reared flies in controlled environments and fed artificial diets. In contrast, we examined microbial communities in wild flies from various host crops across four locations in the United States. Our findings show that these communities are distinct from those of laboratory-grown flies and are influenced by the fly's sex, host crop, geographical location, and their interactions. Our study identifies several dominant bacterial genera across samples, suggesting that these may represent the core microbial communities in wild SWD. Given that microbial communities influence physiological activities in SWD, manipulating the microbiome may have either a positive or negative impact on insect fitness. This study enhances our understanding of microbial dynamics in understudied wild SWD populations, emphasizing the importance of these dynamics in effective integrated pest management strategies.}, }
@article {pmid40791242, year = {2025}, author = {Song, HC and Elsheikha, H and Yang, T and Cong, W}, title = {Global spillover of land-derived microbes to Ocean hosts: Sources, transmission pathways, and one health threats.}, journal = {Environmental science and ecotechnology}, volume = {27}, number = {}, pages = {100603}, pmid = {40791242}, issn = {2666-4984}, abstract = {Terrestrial pathogens are increasingly being detected in marine organisms, raising concerns about ecosystem sustainability, biodiversity loss, and threats to human health. Over the past two decades, reports of microbial contaminants crossing from land to sea have increased, suggesting shifts in pathogen ecology driven by environmental changes and human activities. Pathogens originating on land can spread, adapt, and persist in marine environments, infecting a wide range of hosts and potentially re-entering terrestrial environments. Despite growing recognition of this issue, a comprehensive understanding of the distribution, diversity, and transmission pathways of these pathogens in marine ecosystems remains limited. In this Review, we provide a global analysis of terrestrial pathogen contamination in marine animal populations. Drawing from pathogen detection data across 66 countries, we used phylogenetic methods to infer land-to-sea transmission routes. We identified 179 terrestrial pathogen species, including 38 bacterial, 39 viral, 80 parasitic, and 22 fungal species, in 20 marine host species. Terrestrial pathogens are not only widespread but also highly diverse in marine ecosystems, highlighting the frequency and ecological significance of cross-system microbial exchange. By revealing the scale and complexity of land-to-sea pathogen flow, we show that climate change, pollution, and other anthropogenic pressures may intensify pathogen spillover events, with potential feedback effects on terrestrial systems. This highlights the urgent need for integrated surveillance and policy frameworks acknowledging the interconnectedness of terrestrial and marine health. Our work advocates a One Health approach to microbial ecology, stressing the need to safeguard marine and human populations from emerging cross-system threats.}, }
@article {pmid40787310, year = {2025}, author = {S, S and Nayak, P and Pal, K}, title = {Exploring the Microbial Peptides Derived from the Human Gut Microbiota to Regulate Class B GPCRS Using an In Silico Approach.}, journal = {ACS omega}, volume = {10}, number = {30}, pages = {33270-33287}, pmid = {40787310}, issn = {2470-1343}, abstract = {Class B G-protein coupled receptors (GPCRs) are significant therapeutic recipients in cardiovascular, neurological, and metabolic diseases. The human gut microbiome is a complex microbial ecology recently identified as a possible source of bioactive peptides that control host physiological functions. Candidate peptides were found using advanced bioinformatics tools including sequence homology analysis, structure modeling, and molecular docking. These peptides were then evaluated for their binding affinity and potential functional regulation of the GPCR activity. Molecular dynamics simulations offered additional insights regarding the stability and interaction diversity of peptide-receptor complexes, highlighting receptor conformational state of G-protein interaction. The findings identify unique microbial peptides capable of influencing class B GPCR function, providing important insights into microbiome-host interactions and therapeutic potential. This study emphasizes the gut microbiome's previously untapped potential as a source of GPCR modulators, opening up new avenues for microbiome-driven therapy approaches for metabolic and endocrine disorders.}, }
@article {pmid40783766, year = {2025}, author = {Son, SJ and Wu, X and Roh, HW and Cho, YH and Hong, S and Nam, YJ and Hong, CH and Park, S}, title = {Distinct gut microbiota profiles and network properties in older Korean individuals with subjective cognitive decline, mild cognitive impairment, and Alzheimer's disease.}, journal = {Alzheimer's research &amp; therapy}, volume = {17}, number = {1}, pages = {187}, pmid = {40783766}, issn = {1758-9193}, support = {HR21C1003//the Ministry of Health and Welfare, Republic of Korea/ ; HR21C1003//the Ministry of Health and Welfare, Republic of Korea/ ; RS-2019-NR040055//National Research Foundation of Korea (NRF), funded by the Ministry of Science and ICT/ ; RS-2019-NR040055//National Research Foundation of Korea (NRF), funded by the Ministry of Science and ICT/ ; RS-2023-00208567//National Research Foundation of Korea (NRF), funded by the Ministry of Science and ICT/ ; }, abstract = {BACKGROUND: The gut microbiota may influence cognitive function via the gut-brain axis. This study aimed to investigate the gut microbiota profiles of 346 older Korean individuals with subjective cognitive decline but no symptoms (SCD), mild cognitive impairment (MCI), or Alzheimer’s disease (AD).<br><br>METHODS: Participants aged an average of 72.3 years underwent the profiling of cognitive function, amyloid-&#x3b2; (A&#x3b2;) deposition, apolipoprotein E (APOE) genetic variants, depression status, nutrition, and lifestyles. Human fecal bacterial FASTA/Q data (SCD, n&#x2009;=&#x2009;24; MCI, n&#x2009;=&#x2009;246; AD, n&#x2009;=&#x2009;76) were processed using Quantitative Insights Into Microbial Ecology 2 (QIIME2) tools. Operational taxonomic units (OTUs) and their counts were assigned with the National Center for Biotechnology Information Basic Local Alignment Search Tool (BLAST). Machine learning models (random forest and XGBoost) identified key bacterial taxa differentiating groups.<br><br>RESULTS: Redundancy analysis revealed associations between gut microbiota composition and cognitive function, age, gender, nutritional status, and body mass index. All three groups shared 71 common bacterial genera with distinct taxonomic profiles across cognitive states. The AD group uniquely harbored Hominisplanchenecus and Lentihominibacter, while the SCD group exclusively contained Anaerosacchariphilus and Anaerobutyricum. Phascolarctobacterium was shared between the AD and MCI groups, and Anaerostipes between the MCI and SCD groups. The SCD group showed significantly elevated Bifidobacterium catenulatum, Anaerobutyricum hallii, and Anaerostipes hadrus. Network analysis demonstrated greater microbial community complexity in the SCD group compared to the MCI and AD groups. Gut bacteria correlated with depression, A&#x3b2; deposition, APOE status, and cognitive scores.<br><br>CONCLUSIONS: This study identified distinct gut microbiota profiles associated with different stages of cognitive impairment in older Korean adults. The observed associations between gut bacterial composition and cognitive function, neurodegeneration biomarkers, and related clinical factors suggest potential relationships that warrant further investigation. These findings contribute to the growing understanding of gut-brain interactions in cognitive aging.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13195-025-01820-9.}, }
@article {pmid40781808, year = {2025}, author = {Jalili, M and Mazloomirad, F and Jalilian, FA}, title = {The effect of bacteriophage in oral health: developing microbial ecology and emerging potential therapeutic target.}, journal = {Future microbiology}, volume = {20}, number = {12}, pages = {807-816}, pmid = {40781808}, issn = {1746-0921}, mesh = {Humans ; *Bacteriophages/physiology ; *Phage Therapy/methods ; *Mouth/microbiology/virology ; *Oral Health ; Biofilms/growth &amp; development ; Microbiota ; *Bacteria/virology ; *Periodontal Diseases/therapy/microbiology ; }, abstract = {The human oral cavity provides a convenient entry point for viruses and bacteria from the environment. The role of these viral communities remains unclear; however, many of them are bacteriophages that may actively influence the ecology of bacterial communities within the oral cavity. Bacteriophages are abundant and influential components of the oral microbiome and play a crucial role in shaping microbial ecology in oral health. They dynamically interact with oral bacteria, influencing biofilm formation, bacterial population structure, antibiotic resistance, and metabolic functions, thereby affecting disease progression and microbial community dynamics. Recent advances in studies have increased our understanding of oral phages and their impact on the amelioration of oral diseases such as periodontal disease. Nowadays, phage therapy has been identified as a potential therapeutic approach for major oral pathogens. The advantages of phage therapy include low toxicity, high specificity, the ability to penetrate biofilm structures, and the ability to replicate continuously in pathogenic bacteria. Hence, the aim of this review is to provide a comprehensive study about the role of bacteriophages as potential therapeutic target in oral health. Additionally, further studies are necessary to evaluate the role of phages in oral health and to develop safe and effective clinical applications in dentistry.}, }
@article {pmid40780001, year = {2025}, author = {Grimard-Conea, M and Reyes, EV and Marchand-Senécal, X and Faucher, SP and Prévost, M}, title = {In situ dosing of monochloramine in a hospital hot water system results in drastic microbial communities changes.}, journal = {The Science of the total environment}, volume = {997}, number = {}, pages = {180204}, doi = {10.1016/j.scitotenv.2025.180204}, pmid = {40780001}, issn = {1879-1026}, abstract = {Understanding changes in microbial composition under selective pressures is crucial to assess the emergence of resistant taxa and the survival of drinking water-associated pathogens. This study evaluated the impact of in situ monochloramine disinfection in a hospital hot water system on bacterial (16S rRNA gene amplicon sequencing, 112 samples) and eukaryotic communities (18S rRNA gene amplicon sequencing, 103 samples), and on general microbial measurements (180 samples), including adenosine triphosphate (ATP) and flow cytometry counts. After the onset of treatment, ATP decreased by 1.2- and 3.5-fold, and total cell counts (TCC) dropped by 1- and 2-log at distal and system sites, respectively. During the dosage interruption (27-day), TCC rebounded to pre-treatment levels, but viability percentage decreased, indicating that cells were predominantly damaged. Low-use sites (e.g., showerheads) showed elevated ATP (>15 pg/mL) and TCC (10[5]-10[6] cells/L). Monochloramine drastically altered bacterial and eukaryotic communities. Alpha-diversity showed increased amplicon sequence variant richness during treatment, driven by new, low-abundant taxa, while Beta-diversity revealed distinct shifts in community composition over time, with tight or looser clusters corresponding to each treatment phase. Post-treatment, temporal and spatial heterogeneity was evident across distal sites, while elevated temperatures, consistent flow, and higher monochloramine concentrations in the hot water system resulted in more uniform communities at system sites. Additionally, the persistence of potential pathogenic strains belonging to Legionella and Mycobacterium genera highlights the value of comprehensive risk assessments. These findings emphasize the need to understand microbial shifts under disinfection stress and their public health implications, offering new insights into how treatment interventions shape microbial ecology and pathogen dynamics.}, }
@article {pmid40777436, year = {2025}, author = {Shrestha Gurung, BD and Rayamajhi, M and Maharjan, N and Do, T and Bhandari, D and Yadav, R and Aryal, S and Gnimpieba, EZ}, title = {Forecasting Urban Wastewater Microbiome Dynamics Using a Digital Twin Framework.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40777436}, issn = {2692-8205}, support = {P20 GM103443/GM/NIGMS NIH HHS/United States ; }, abstract = {Urban wastewater microbiomes are complex and temporally dynamic, offering valuable insight into community-scale microbial ecology and potential public health trends. However, existing wastewater-based studies often remain descriptive, lacking tools for predictive modeling. In this study, we introduce a digital twin framework that forecasts microbial abundance trajectories in urban wastewater using an interpretable generative model, Q-net. Trained on a 30-week longitudinal metagenomic dataset from seven wastewater treatment plants, the model captures temporal microbial dynamics with high fidelity (R 2 > 0.97 for key taxa; R 2 = 0.998 at the final timepoint). Beyond accurate forecasting, Q-net provides transparent model structure through conditional inference trees and enables simulation of realistic microbial trends under hypothetical scenarios. This work demonstrates the potential of digital twins to move wastewater microbiome studies from static snapshots to dynamic, predictive systems, with broad implications for environmental monitoring and microbial ecosystem modeling.}, }
@article {pmid40777262, year = {2025}, author = {Weiss, AS and Santos-Santiago, JA and Keenan, O and Smith, AB and Knight, M and Zackular, JP and Tamayo, R}, title = {Enterococcus faecalis modulates phase variation in Clostridioides difficile.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40777262}, issn = {2692-8205}, support = {R01 AI143638/AI/NIAID NIH HHS/United States ; R01 AI188648/AI/NIAID NIH HHS/United States ; }, abstract = {To adapt and persist in the gastrointestinal tract, many enteric pathogens, including Clostridioides difficile, employ strategies such as phase variation to generate phenotypically heterogeneous populations. Notably, the role of the gut microbiota and polymicrobial interactions in shaping population heterogeneity of invading pathogens has not been explored. Here, we show that Enterococcus faecalis, an opportunistic pathogen that thrives in the inflamed gut during C. difficile infection, can impact the phase variable CmrRST signal transduction system in C. difficile. The CmrRST system controls multiple phenotypes including colony morphology, cell elongation, and cell chaining in C. difficile. Here we describe how interactions between E. faecalis and C. difficile on solid media lead to a marked shift in C. difficile phenotypes associated with phase variation of CmrRST. Specifically, E. faecalis drives a switch of the C. difficile population to the cmr-ON state leading to chaining and a rough colony morphology. This phenomenon preferentially occurs with E. faecalis among the enterococci, as other enterococcal species do not show a similar effect, suggesting that the composition of the polymicrobial environment in the gut is likely critical to shaping C. difficile population heterogeneity. Our findings shed light on the complex role that microbial ecology and polymicrobial interactions can have in the phenotypic heterogeneity of invading pathogens.}, }
@article {pmid40771314, year = {2025}, author = {Wang, L and Wang, H and Wu, J and Ji, C and Wang, Y and Gu, M and Li, M and Yang, H}, title = {Gut microbiota and metabolomics in metabolic dysfunction-associated fatty liver disease: interaction, mechanism, and therapeutic value.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1635638}, pmid = {40771314}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Metabolomics ; Dysbiosis ; Liver/metabolism/pathology ; Animals ; *Fatty Liver/metabolism/therapy/microbiology ; *Non-alcoholic Fatty Liver Disease/metabolism/therapy/microbiology ; Biomarkers ; Precision Medicine ; }, abstract = {The global epidemic of Metabolic dysfunction-associated fatty liver disease (MAFLD) urgently demands breakthroughs in precision medicine strategies. Its pathogenesis centers on the cascade dysregulation of the gut microbiota-metabolite-liver axis: microbial dysbiosis drives hepatic lipid accumulation and fibrosis by suppressing short-chain fatty acid synthesis, activating the TLR4/NF-κB inflammatory pathway, and disrupting bile acid signaling. Metabolomics further reveals characteristic disturbances including free fatty acid accumulation, aberrantly elevated branched-chain amino acids (independently predictive of hepatic steatosis), and mitochondrial dysfunction, providing a molecular basis for disease stratification. The field of precision diagnosis is undergoing transformative innovation-multi-omics integration combined with AI-driven analysis of liver enzymes and metabolic biomarkers enables non-invasive, ultra-high-accuracy staging of fibrosis. Therapeutic strategies are shifting towards personalization: microbial interventions require matching to patient-specific microbial ecology, drug selection necessitates efficacy and safety prediction, and synthetically engineered "artificial microbial ecosystems" represent a cutting-edge direction. Future efforts must establish a "multi-omics profiling-AI-powered dynamic modeling-clinical validation" closed-loop framework to precisely halt MAFLD progression to cirrhosis and hepatocellular carcinoma by deciphering patient-specific mechanisms.}, }
@article {pmid40713799, year = {2025}, author = {Soleimani Samarkhazan, H and Nouri, S and Maleknia, M and Aghaei, M}, title = {"The microbiome in graft-versus-host disease: a tale of two ecosystems".}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {832}, pmid = {40713799}, issn = {1479-5876}, mesh = {*Graft vs Host Disease/microbiology/therapy ; Humans ; *Microbiota ; Hematopoietic Stem Cell Transplantation ; Animals ; *Ecosystem ; Fecal Microbiota Transplantation ; Dysbiosis ; }, abstract = {Graft-versus-host disease (GVHD), a life-threatening complication of allogeneic hematopoietic stem cell transplantation (HSCT), is shaped by a dynamic interplay between two microbial ecosystems: the recipient's disrupted microbiome and the donor's transplanted microbiota. This narrative review unravels the "tale of two ecosystems," exploring how pre-transplant chemotherapy, radiation, and antibiotics induce recipient dysbiosis-marked by loss of beneficial taxa (Clostridia, Faecalibacterium) and dominance of pathobionts (Enterococcus). These shifts impair barrier integrity, fuel systemic inflammation, and skew immune responses toward pro-inflammatory T-cell subsets, exacerbating GVHD. Conversely, emerging evidence implicates donor microbiota in modulating post-transplant immune reconstitution, though its role remains underexplored. Therapeutic strategies, including probiotics, prebiotics, and fecal microbiota transplantation (FMT), demonstrate promise in restoring microbial balance, enhancing short-chain fatty acid (SCFA)-driven immune regulation, and reducing GVHD severity. However, challenges such as strain-specific efficacy, safety in immunocompromised hosts, and protocol standardization persist. By bridging microbial ecology and immunology, this review underscores the microbiome's transformative potential in redefining GVHD management and advocates for personalized, microbiome-targeted interventions to improve HSCT outcomes.}, }
@article {pmid40704792, year = {2025}, author = {Zhang, M and Zhang, C and Ramos, A and Whitaker, RJ and Whiteley, M}, title = {Conserved cross-domain protein-to-mRNA ratios enable proteome prediction in microbes.}, journal = {mBio}, volume = {16}, number = {8}, pages = {e0141125}, pmid = {40704792}, issn = {2150-7511}, support = {GBMF9195//Gordon and Betty Moore Foundation/ ; R01 DE023193/DE/NIDCR NIH HHS/United States ; R01DE020100/DE/NIDCR NIH HHS/United States ; R01 DE020100/DE/NIDCR NIH HHS/United States ; R01DE023193/DE/NIDCR NIH HHS/United States ; }, abstract = {UNLABELLED: Microbial communities are often studied by measuring gene expression (mRNA levels), but translating these data into functional insights is challenging because mRNA abundance does not always predict protein levels. Here, we present a strategy to bridge this gap by deriving gene-specific RNA-to-protein conversion factors that improve the prediction of protein abundance from transcriptomic data. Using paired mRNA-protein data sets from seven bacteria and one archaeon, we identified orthologous genes where mRNA levels poorly predicted protein abundance, yet each gene's protein-to-RNA ratio was consistent across these diverse organisms. Applying the resulting conversion factors to mRNA levels dramatically improved protein abundance predictions, even when the conversion factors were obtained from distantly related species. Remarkably, conversion factors derived from bacteria also enhanced protein prediction in an archaeon, demonstrating the robustness of this approach. This cross-domain framework enables more accurate functional inference in microbiomes without requiring organism-specific proteomic data, offering a powerful new tool for microbial ecology, systems biology, and functional genomics.<br><br>IMPORTANCE: Deciphering the biology of natural microbial communities is limited by the lack of functional data. While transcriptomics enables gene expression profiling, mRNA levels often fail to predict protein abundance, the primary indicator of microbial function. Prior studies addressed this by calculating RNA-to-protein (RTP) conversion factors using conserved protein-to-RNA (ptr) ratios across bacterial strains, but their cross-species and cross-domain utility remained unknown. We generated comprehensive transcriptomic and proteomic data sets from seven bacteria and one archaeon spanning diverse metabolisms and ecological niches. We identified orthologous genes with conserved ptr ratios, enabling the discovery of RTP conversion factors that significantly improved protein prediction from mRNA, even between distant species and domains. This reveals previously unrecognized conservation in ptr ratios across domains and eliminates the need for paired proteomic data in many cases. Our approach offers a broadly applicable framework to enhance functional prediction in microbiomes using only transcriptomic data.}, }
@article {pmid40701356, year = {2025}, author = {Hu, L and Ye, Y and Li, Y and Tan, X and Liu, X and Zhang, T and Wang, J and Du, Z and Ye, M}, title = {Bacteria-algae synergy in carbon sequestration: Molecular mechanisms, ecological dynamics, and biotechnological innovations.}, journal = {Biotechnology advances}, volume = {83}, number = {}, pages = {108655}, doi = {10.1016/j.biotechadv.2025.108655}, pmid = {40701356}, issn = {1873-1899}, mesh = {*Biotechnology/methods ; *Microalgae/metabolism ; *Carbon Sequestration ; *Bacteria/metabolism ; Carbon Dioxide/metabolism ; Photosynthesis ; Carbon/metabolism ; }, abstract = {Rising atmospheric CO2 levels require innovative strategies to increase carbon sequestration. Bacteria-algae interactions, as pivotal yet underexplored drivers of marine and freshwater carbon sinks, involve multiple mechanisms that amplify CO2 fixation and long-term storage. This review systematically describes the synergistic effects of bacteria-algae consortia spanning both microalgae (e.g., Chlorella vulgaris and Phaeodactylum tricornutum) and macroalgae (e.g., Macrocystis and Laminaria) on carbon sequestration. These effects include (1) molecular-level regulation (e.g., signal transduction via N-acyl-homoserine lactones (AHLs), and horizontal gene transfer), (2) ecological facilitation of recalcitrant dissolved organic carbon (RDOC) formation, and (3) biotechnological applications in wastewater treatment and bioenergy production. We highlight that microbial crosstalk increases algal photosynthesis by 20-40 % and contributes to 18.9 % of kelp-derived RDOC storage. Furthermore, engineered systems integrating algal-bacterial symbiosis achieve greater than 80 % nutrient removal and a 22-35 % increase in CO2 fixation efficiency (compared with axenic algal systems), demonstrating their dual role in climate mitigation and a circular economy. This review is the first to integrate molecular mechanisms (e.g., quorum sensing), ecological carbon transformation processes (e.g., the formation of RDOC), and applications in synthetic biology (e.g., CRISPR-engineered consortia) into a unified framework. Moreover, the novel strategy "microbial interaction network optimization" for enhancing carbon sinks is proposed. However, scalability challenges persist, including light limitations in photobioreactors and the ecological risks of synthetic consortia. By bridging microbial ecology with synthetic biology, this work provides a roadmap for harnessing bacteria-algae synergy to achieve carbon neutrality.}, }
@article {pmid40695133, year = {2025}, author = {Shi, F and Fang, H and Cheng, S and Guo, Y and Wang, H and Chen, L and Pu, H and Liu, B}, title = {Cadmium accumulation suppresses rice nitrogen use efficiency by inhibiting rhizosphere nitrification and promoting nitrate reduction.}, journal = {Journal of hazardous materials}, volume = {496}, number = {}, pages = {139298}, doi = {10.1016/j.jhazmat.2025.139298}, pmid = {40695133}, issn = {1873-3336}, abstract = {Cadmium (Cd) pollution significantly disrupts paddy soil nitrogen (N) availability and impairs rice nitrogen use efficiency (NUE). However, most existing studies rely on microcosm or pot experiments, with limited field-based manipulative studies involving Cd addition. The regulatory mechanisms by which N transformation processes influence rice N utilization under Cd stress remain poorly understood. In this study, a field experiment incorporating multiple levels of Cd addition was conducted to address this gap. Plant traits, nutrient content, and microbial community characteristics in rhizosphere and bulk soils were examined through soil chemical analysis, metagenomic sequencing, and bioinformatics approaches. The results demonstrated that microbial communities, soil N transformation potential, and rice NUE responded to Cd addition in a dose-dependent manner, with rhizosphere soils exhibiting greater sensitivity than bulk soils. Cd addition reduced dissolved organic carbon (DOC), NH4[+]-N, and NO3[-]-N in rhizosphere soil, while increasing total and available phosphorus (P) contents in both rhizosphere and bulk soils. Although Cd addition enhanced aboveground biomass and total N uptake, it led to a decline in plant N concentration and NUE. Moreover, Cd accumulation markedly suppressed the abundance of nitrification genes while promoting genes involved in dissimilatory nitrate reduction to ammonium (DNRA) and denitrification. Overall, Cd stress altered microbial community structure and soil N and P availability, thereby impairing rice N uptake and NUE. These findings suggest that acute Cd exposure rapidly disrupts microbial ecology, decouples the soil N cycle, and reduces N supply potential of paddy soils and rice NUE, ultimately threatening agroecosystem stability in southern China. These impacts warrant greater consideration in future farmland management strategies.}, }
@article {pmid40603778, year = {2025}, author = {Brinck, JE and Sinha, AK and Laursen, MF and Dragsted, LO and Raes, J and Uribe, RV and Walter, J and Roager, HM and Licht, TR}, title = {Intestinal pH: a major driver of human gut microbiota composition and metabolism.}, journal = {Nature reviews. Gastroenterology &amp; hepatology}, volume = {}, number = {}, pages = {}, pmid = {40603778}, issn = {1759-5053}, abstract = {In the human gastrointestinal tract, pH is a key factor in shaping gut microbial composition and activity, while also being influenced by microbial metabolism. pH varies substantially along the gastrointestinal tract within an individual and between different individuals due to a combination of host, diet, microbial and external factors. The importance of pH on microbiota composition and metabolic response has been widely explored over the past century. Here, we review the literature to explore the major physiological and dietary factors that influence pH along the gastrointestinal tract. From a microbial ecology perspective, we discuss how gastrointestinal pH affects microbiota composition and metabolism. We explore mechanisms by which pH can influence bacterial acid response systems, gene expression and the production of microbial metabolites important for health. Finally, we review the literature regarding the potential role of gastrointestinal pH in human diseases. We propose that we can advance our understanding of the gut microbiota in health and disease by considering gastrointestinal pH. We argue that pH-mediated gut microbial metabolic variation is highly important for predicting and manipulating metabolic output relevant to human health.}, }
@article {pmid40600721, year = {2025}, author = {Peters, DI and Shin, IJ and Deever, AN and Kaspar, JR}, title = {Design, development, and validation of new fluorescent strains for studying oral streptococci.}, journal = {Microbiology spectrum}, volume = {13}, number = {8}, pages = {e0016825}, pmid = {40600721}, issn = {2165-0497}, support = {P30 CA016058/CA/NCI NIH HHS/United States ; R03 DE031766/DE/NIDCR NIH HHS/United States ; R03DE031766/DE/NIDCR NIH HHS/United States ; }, mesh = {Biofilms/growth &amp; development ; *Luminescent Proteins/genetics/metabolism ; Humans ; Streptococcus gordonii/genetics ; *Streptococcus/genetics/metabolism/physiology ; *Mouth/microbiology ; Streptococcus mutans/genetics/metabolism ; Green Fluorescent Proteins/genetics/metabolism ; Red Fluorescent Protein ; Streptococcus sanguis/genetics ; Microscopy, Confocal ; }, abstract = {Bacterial strains that are genetically engineered to constitutively produce fluorescent proteins have aided our study of bacterial physiology, biofilm formation, and interspecies interactions. Here, we report on the construction and utilization of new strains that produce the blue fluorescent protein mTagBFP2, the green fluorescent protein sfGFP, and the red fluorescent protein mScarlet-I3 in species Streptococcus gordonii, Streptococcus mutans, and Streptococcus sanguinis. Gene fragments, developed to contain the constitutive promoter Pveg, the fluorescent gene of interest, as well as aad9, providing resistance to the antibiotic spectinomycin, were inserted into selected open reading frames on the chromosome that were both transcriptionally silent and whose loss caused no measurable changes in fitness. All strains, except for sfGFP in S. sanguinis, were validated to produce a detectable and specific fluorescent signal. Individual stains, along with extracellular polymeric substances (EPS) within biofilms, were visualized and quantified through either widefield or super-resolution confocal microscopy approaches. Finally, to validate the ability to perform single-cell-level analysis using the strains, we imaged and analyzed a triculture mixed-species biofilm of S. gordonii, S. mutans, and S. sanguinis grown with and without the addition of human saliva. Quantification of the loss in membrane integrity using a SYTOX dye revealed that all strains had increased loss of membrane integrity with water or human saliva added to the growth media, but the proportion of the population stained by the SYTOX dye varied by species. In all, these fluorescent strains will be a valuable resource for the continued study of oral microbial ecology.IMPORTANCEStreptococci are among the earliest colonizers of the soft and hard tissues of the oral cavity and are contributors to the oral health status of the host, with involvement in dental caries, endodontic infections, periodontal disease, and the development of oral cancer. Strains genetically modified to produce fluorescent proteins that can be either visualized through microscopy imaging or quantified by their specific fluorescent intensity signal are critical tools toward the study of individual or mixed-species cultures. Our report here details the development and testing of several new strains of fluorescent oral streptococci that can be utilized in the study of microbial ecology, increasing both the availability of tools and documenting experimental approaches toward in vitro assay applications such as the study of intermicrobial interactions.}, }
@article {pmid40568985, year = {2025}, author = {Zhao, J and Brandt, G and Gronniger, JL and Wang, Z and Li, J and Hunt, DE and Rodriguez-R, LM and Hatt, JK and Konstantinidis, KT}, title = {Quantifying the contribution of the rare biosphere to natural disturbances.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40568985}, issn = {1751-7370}, support = {OCE 1416673 and DEB 1831582//US National Science Foundation/ ; ICER 2033934, DEB 2224819//US National Science Foundation/ ; }, mesh = {Metagenome ; *Ecosystem ; *Microbiota ; }, abstract = {Understanding how populations respond to disturbances represents a major goal for microbial ecology. While several hypotheses have been advanced to explain microbial community compositional changes in response to disturbance, appropriate data to test these hypotheses is scarce, due to the challenges in delineating rare vs. abundant taxa and generalists vs. specialists, a prerequisite for testing the theories. Here, we operationally define these two key concepts by employing the patterns of coverage of a (target) genome by a metagenome to identify rare populations, and by borrowing the proportional similarity index from macroecology to identify generalists. We applied these concepts to time-series (field) metagenomes from the Piver's Island Coastal Observatory to establish that coastal microbial communities are resilient to major perturbations such as tropical cyclones and (uncommon) cold or warm temperature events, in part due to the response of rare populations. Therefore, these results provide support for the insurance hypothesis [i.e. the rare biosphere has the buffering capacity to mitigate the effects of disturbance]. Additionally, generalists appear to contribute proportionally more than specialists to community adaptation to perturbations like warming, supporting the disturbance-specialization hypothesis [i.e. disturbance favors generalists]. Several of these findings were also observed in replicated laboratory mesocosms that aimed to simulate disturbances such as a rain-driven washout of microbial cells and a labile organic matter release from a phytoplankton bloom. Taken together, our results advance understanding of the mechanisms governing microbial population dynamics under changing environmental conditions and have implications for ecosystem modeling.}, }
@article {pmid40556886, year = {2025}, author = {Klein, ML and Erikson, CB and McCabe, CJ and Huang, L and Rodrigues, JLM and Mitloehner, FM}, title = {Limited effects of tannin supplementation on the dairy cattle fecal microbiome with modulation of metabolites.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1570127}, pmid = {40556886}, issn = {1664-302X}, abstract = {Tannins are plant secondary metabolites that bind organic carbon (C) and nitrogen (N), potentially altering substrate bioavailability for enteric fermentation in ruminants. This interaction may reduce greenhouse gas (GHG) emissions and influence nitrogen partitioning. Given tannins' resistance to ruminal degradation and persistence through the gastrointestinal tract, this study investigated the effects of a tannin-based feed additive on fecal microbial diversity, fecal chemical composition, and GHG emissions. Twenty-four early- to mid-lactation dairy cows were randomized to receive either a tannin-based feed additive (TRT; containing condensed and hydrolyzable tannins from Schinopsis quebracho-colorado [Schltdl.]) or a control diet (CON) for 64 days. Cows were blocked by parity, dry matter intake, milk yield, body weight, and days in milk. Fecal samples were collected on days 0, 16, 32, and 64 and analyzed using 16S rRNA gene amplicon sequencing. Fecal C, N, and indole-3-lactate were measured, and GHG emissions (N2O, CH4, CO2) were assessed via 14-day laboratory incubation. A total of 1,538 amplicon sequence variants were identified, with Firmicutes as the dominant phylum. Fecal phylogenetic diversity showed a significant treatment × day interaction (p < 0.01), with TRT cows exhibiting reduced microbial diversity from day 16 to 64. Fecal C and N concentrations were significantly lower (p < 0.01) in TRT cows on day 16, while indole-3-lactate levels were higher on day 64 (p = 0.02). GHG emissions did not differ significantly between treatments. The tannin-based feed additive influenced fecal microbial community structure and select chemical parameters but did not significantly affect GHG emissions from feces. These findings suggest that dietary tannins may modulate gut microbial ecology with minimal impact on downstream manure-related emissions.}, }
@article {pmid40184706, year = {2025}, author = {He, L and Li, J and Tang, L and Wang, Y and Zhao, X and Ding, K and Xu, L and Gu, L and Cheng, S and Wei, YY}, title = {Applying side-stream gas recirculation to promote anaerobic digestion of food waste under ammonia stress: Overlooked impact of gaseous atmospheres on microorganisms.}, journal = {Water research}, volume = {281}, number = {}, pages = {123571}, doi = {10.1016/j.watres.2025.123571}, pmid = {40184706}, issn = {1879-2448}, mesh = {*Ammonia ; Anaerobiosis ; Bioreactors/microbiology ; Hydrogen ; Gases ; Food Loss and Waste ; }, abstract = {High ammonia concentrations can be toxic to microorganisms, leading to the accumulation of hydrogen (H2) and acids in anaerobic digestion (AD) system. In this study, a side gas recycling strategy (SGR), coupled with a primary reactor and a small side-stream reactor, which recirculates biogas between primary reactor and side reactor was employed to mitigate ammonia inhibition. This approach enabled the mesophilic side-stream gas recirculation system (SMGR) and the thermophilic side-stream gas recirculation system (STGR) to ultimately withstand ammonia stress levels of 2.5 g/L and 3.5 g/L, respectively, while maintaining lower hydrogen partial pressures. In contrast, the control group experienced system failure at an ammonia concentration of 2 g/L. Enzyme activity, microbial community, and metaproteomic analysis indicated that the side reactor enriched microorganisms with strong hydrogen-utilizing capacity, while the primary reactor was enriched with Methanosaeta. Furthermore, key pathways related to propionate metabolism, ABC transporters, and methane production were enhanced in the primary reactor, along with increased ATPase activity. The activity of key enzymes involved in AD was also significantly enhanced. This study enhances the understanding of the impact of gas atmosphere control on the microbial ecology and metabolic characteristics of AD system, providing valuable insights and practical guidance for the development of Engineering applications in this field.}, }
@article {pmid40179787, year = {2025}, author = {Wang, Z and Tu, S and Shehzad, K and Hou, J and Xiong, S and Cao, M}, title = {Comparative study of organosilicon and inorganic silicon in reducing cadmium accumulation in wheat: Insights into rhizosphere microbial communities and molecular regulation mechanisms.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138061}, doi = {10.1016/j.jhazmat.2025.138061}, pmid = {40179787}, issn = {1873-3336}, mesh = {*Triticum/metabolism/growth &amp; development/drug effects ; *Cadmium/metabolism ; *Silicon/pharmacology/chemistry ; Rhizosphere ; *Soil Pollutants/metabolism ; Microbiota/drug effects ; Soil Microbiology ; }, abstract = {Silicon is widely used as a "quality element" and "stress resistance element" in crop production and the remediation of heavy metal-contamination soils. Compared to inorganic silicon, organosilicon has unique properties such as amphiphilicity, low surface energy and high biocompatibility. Our previous research has confirmed the effectiveness of organosilicon-modified fertilizers in inhibiting Cadmium (Cd) absorption in wheat. Therefore, it is of great importance to further explore the potential mechanisms and comprehensive benefits of organosilicon. In this study, the microbiological and molecular mechanisms by which organosilicon reduces Cd concentration in wheat compared to inorganic silicon were investigated in depth. The findings indicated that, in comparison with inorganic silicon, organosilicon exhibited a more remarkable efficacy. Specifically, it was more effective in reducing the Cd concentration in wheat grains, achieving a reduction range of 35-39 % as opposed to the 23-28 % reduction achieved by inorganic silicon. Moreover, it manifested a greater ability to mitigate health risks, with a reduction range of 33-42 % compared to the 25-30 % reduction of inorganic silicon. Furthermore, organosilicon contributed to a significant increase in wheat yield, with a growth range of 11-14 % in contrast to the 8-11 % increase from inorganic silicon. Additionally, it enhanced the quality of the grains, substantially improving the protein content and amino acid content. The comparative advantages of organosilicon over inorganic silicon would be firstly due to the reduction of the bioavailability of soil Cd by increasing the available silicon content in the soil and improving the soil microbial ecology (increasing the abundance of Bacillus, Pseudomonas, Massilia and Talaromyces and reducing the enrichment of Fusarium). Secondly, organosilicon achieved vacuolar compartmentalization of Cd by upregulating the expression of the ABC transporter gene (TaABCB7), thereby alleviating Cd toxicity and restricting Cd transport from leaves to grains. Meanwhile, organosilicon increased the wheat yield by optimizing the availability of soil nutrients and enhancing photosynthesis. These results demonstrate the immense potential of organosilicon in mitigating heavy metal contamination in crops.}, }
@article {pmid40041702, year = {2025}, author = {Xu, Z and Chen, J and Liang, W and Chen, ZL and Wu, W and Xia, X and Chen, B and He, D and Liu, H}, title = {Contrasting diversity patterns between microeukaryotic and prokaryotic communities in cold-seep sediments.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf002}, pmid = {40041702}, issn = {2730-6151}, abstract = {Cold seeps are hotspots of biodiversity. However, the quantification of the microbial diversity, particularly that of microeukaryotes, remains scarce and little is known about the active groups. In this study we investigated the diversity and activity of prokaryotes and microeukaryotes in the Haima cold seep sediments in the northern South China Sea using both DNA (whole community) and RNA (active community) signatures. We found that, in general, prokaryotes had lower diversity in the seep sediment than in non-seep regions while microeukaryotes showed the opposite pattern. This finding could be explained by the dominance of homogeneous selection in the prokaryotic community while microeukaryotic communities were less affected by environmental selection, harboring high richness of abundant groups in the seep regions. The compositional difference between DNA and RNA communities was much larger in microeukaryotes than prokaryotes, which could be reflected by the large number of inactive microeukaryotic taxa. Compared to the whole community, the seep-active groups, e.g. among microeukaryotes, Breviatea, Labyrinthulomycetes, and Apicomplexa were more sensitive to and directly influenced by environmental factors, suggesting their pivotal roles in ecosystem biodiversity and functions. This study provides insight into the distinct diversity patterns and regulating mechanisms that occur between prokaryotic and microeukaryotic communities in cold-seep sediments, deepening our understanding of microbial ecology in deep-sea extreme habitats.}, }
@article {pmid39752189, year = {2025}, author = {Bloomfield, SJ and Hildebrand, F and Zomer, AL and Palau, R and Mather, AE}, title = {Ecological insights into the microbiology of food using metagenomics and its potential surveillance applications.}, journal = {Microbial genomics}, volume = {11}, number = {1}, pages = {}, pmid = {39752189}, issn = {2057-5858}, mesh = {*Metagenomics/methods ; *Food Microbiology ; Metagenome ; Bacteria/genetics/classification/isolation &amp; purification ; Salmonella/genetics/isolation &amp; purification/classification ; Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics/isolation &amp; purification/classification ; }, abstract = {A diverse array of micro-organisms can be found on food, including those that are pathogenic or resistant to antimicrobial drugs. Metagenomics involves extracting and sequencing the DNA of all micro-organisms on a sample, and here, we used a combination of culture and culture-independent approaches to investigate the microbial ecology of food to assess the potential application of metagenomics for the microbial surveillance of food. We cultured common foodborne pathogens and other organisms including Escherichia coli, Klebsiella/Raoultella spp., Salmonella spp. and Vibrio spp. from five different food commodities and compared their genomes to the microbial communities obtained by metagenomic sequencing following host (food) DNA depletion. The microbial populations of retail food were found to be predominated by psychrotrophic bacteria, driven by the cool temperatures in which the food products are stored. Pathogens accounted for a small percentage of the food metagenome compared to the psychrotrophic bacteria, and cultured pathogens were inconsistently identified in the metagenome data. The microbial composition of food varied amongst different commodities, and metagenomics was able to classify the taxonomic origin of 59% of antimicrobial resistance genes (ARGs) found on food to the genus level, but it was unclear what percentage of ARGs were associated with mobile genetic elements and thus transferable to other bacteria. Metagenomics may be used to survey the ARG burden, composition and carriage on foods to which consumers are exposed. However, food metagenomics, even after depleting host DNA, inconsistently identifies pathogens without enrichment or further bait capture.}, }
@article {pmid39651889, year = {2025}, author = {Wang, J and Schamp, CN and Hudson, LK and Chaggar, HK and Bryan, DW and Garman, KN and Radosevich, M and Denes, TG}, title = {Whole-genome sequencing and metagenomics reveal diversity and prevalence of Listeria spp. from soil in the Nantahala National Forest.}, journal = {Microbiology spectrum}, volume = {13}, number = {1}, pages = {e0171224}, pmid = {39651889}, issn = {2165-0497}, mesh = {*Soil Microbiology ; *Listeria/genetics/classification/isolation &amp; purification ; *Metagenomics ; *Whole Genome Sequencing ; North Carolina ; *Forests ; *Genome, Bacterial ; *Phylogeny ; Humans ; Listeriosis/microbiology/epidemiology/transmission ; Listeria monocytogenes/genetics/classification/isolation &amp; purification ; Metagenome ; Prevalence ; Soil/chemistry ; }, abstract = {UNLABELLED: Listeria spp. are widely distributed environmental bacteria associated with human foodborne illness. The ability to detect and characterize Listeria strains in the natural environment will contribute to improved understanding of transmission routes of contamination. The current standard for surveillance and outbreak source attribution is whole-genome sequencing (WGS) of Listeria monocytogenes clinical isolates. Recently, metagenomic sequencing has also been explored as a tool for the detection of Listeria spp. in environmental samples. This study evaluated soil samples from four locations across altitudes ranging from 1,500 to 4,500 ft in the Nantahala National Forest in North Carolina, USA. Forty-two Listeria isolates were cultured and sequenced, and 12 metagenomes of soil bacterial communities were generated. These isolates comprised 14 distinct strains from five species, including Listeria cossartiae subsp. cayugensis (n = 8; n represents the number of distinct strains), L. monocytogenes (n = 3), "Listeria swaminathanii" (Lsw) (n = 1), Listeria marthii (n = 1), and Listeria booriae (n = 1). Most strains (n = 13) were isolated from lower altitudes (1,500 or 2,500 ft), while the L. swaminathanii strain was isolated from both higher (4,500 ft) and lower (1,500 ft) altitudes. Metagenomic analysis of soil described a reduction in both bacterial community diversity and relative abundance of Listeria spp. as the altitude increased. Soil pH and cation exchange capacity were positively correlated (P < 0.05) with the abundance of Listeria spp. as detected by metagenomics. By integrating culture-independent metagenomics with culture-based WGS, this study advances current knowledge regarding distribution of Listeria spp. in the natural environment and suggests the potential for future use of culture-independent methods in tracking the transmission of foodborne pathogens.<br><br>IMPORTANCE: As a foodborne pathogen, Listeria continues to cause numerous illnesses in humans and animals. Studying the diversity and distribution of Listeria in soil is crucial for understanding potential sources of contamination and developing effective strategies to prevent foodborne outbreaks of listeriosis. Additionally, examining the ecological niches and survival mechanisms of Listeria in natural habitats provides insights into its persistence and adaptability, informing risk assessments and public health interventions. This research contributes to a broader understanding of microbial ecology and the factors influencing foodborne pathogen emergence, ultimately enhancing food safety and protecting public health. Moreover, using a metagenomic approach provides a detailed understanding of the soil microbial ecosystems, leading to more effective monitoring and control of foodborne pathogens. This study also highlights the potential for integrating metagenomics into routine surveillance systems for food safety in the near future.}, }
@article {pmid39545729, year = {2024}, author = {Beaudry, MS and Bhuiyan, MIU and Glenn, TC}, title = {Enriching the future of public health microbiology with hybridization bait capture.}, journal = {Clinical microbiology reviews}, volume = {37}, number = {4}, pages = {e0006822}, pmid = {39545729}, issn = {1098-6618}, support = {R01 AI148667/AI/NIAID NIH HHS/United States ; 75D30118C02889, 75D30120R67837//HHS | Centers for Disease Control and Prevention (CDC)/ ; 1R01AI148667-01A1//HHS | National Institutes of Health (NIH)/ ; }, mesh = {Humans ; Bacteria/genetics/classification/isolation &amp; purification ; Fungi/classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; *Microbiological Techniques/methods/trends ; Nucleic Acid Hybridization/methods ; *Public Health ; }, abstract = {SUMMARYPublic health microbiology focuses on microorganisms and infectious agents that impact human health. For years, this field has relied on culture or molecular methods to investigate complex samples of public health importance. However, with the increase in accuracy and decrease in sequencing cost over the last decade, there has been a transition to the use of next-generation sequencing in public health microbiology. Nevertheless, many available sequencing methods (e.g., shotgun metagenomics and amplicon sequencing) do not work well in complex sample types, require deep sequencing, or have inherent biases associated with them. Hybridization bait capture, also known as target enrichment, brings in solutions for such limitations. It is an increasingly popular technique to simultaneously characterize many thousands of genetic elements while reducing the amount of sequencing needed (thereby reducing the sequencing costs). Here, we summarize the concept of hybridization bait capture for public health, reviewing a total of 35 bait sets designed in six key topic areas for public health microbiology [i.e., antimicrobial resistance (AMR), bacteria, fungi, parasites, vectors, and viruses], and compare hybridization bait capture to previously relied upon methods. Furthermore, we provide an in-depth comparison of the three most popular bait sets designed for AMR by evaluating each of them against three major AMR databases: Comprehensive Antibiotic Resistance Database, Microbial Ecology Group Antimicrobial Resistance Database, and Pathogenicity Island Database. Thus, this article provides a review of hybridization bait capture for public health microbiologists.}, }
@article {pmid39298326, year = {2024}, author = {Gordon, JI and Barratt, MJ and Hibberd, MC and Rahman, M and Ahmed, T}, title = {Establishing human microbial observatory programs in low- and middle-income countries.}, journal = {Annals of the New York Academy of Sciences}, volume = {1540}, number = {1}, pages = {13-20}, doi = {10.1111/nyas.15224}, pmid = {39298326}, issn = {1749-6632}, support = {//Fondazione Internazionale Premio Balzan/ ; //Bill and Melinda Gates Foundation/ ; /NH/NIH HHS/United States ; /NH/NIH HHS/United States ; }, mesh = {Humans ; *Developing Countries ; Global Health ; *Microbiota ; }, abstract = {Studies of the human microbiome are progressing rapidly but have largely focused on populations living in high-income countries. With increasing evidence that the microbiome contributes to the pathogenesis of diseases that affect infants, children, and adults in low- and middle-income countries (LMICs), and with profound and rapid ongoing changes occurring in our lifestyles and biosphere, understanding the origins of and developing microbiome-directed therapeutics for treating a number of global health challenges requires the development of programs for studying human microbial ecology in LMICs. Here, we discuss how the establishment of long-term human microbial observatory programs in selected LMICs could provide one timely approach.}, }
@article {pmid38965531, year = {2024}, author = {Babajanyan, SG and Garushyants, SK and Wolf, YI and Koonin, EV}, title = {Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {148}, pmid = {38965531}, issn = {1741-7007}, support = {Intramural Research Program//U.S. National Library of Medicine/ ; }, mesh = {*Gene Transfer, Horizontal ; *Microbiota/genetics ; Biodiversity ; Symbiosis/genetics ; Models, Theoretical ; Models, Biological ; }, abstract = {BACKGROUND: Microbiomes are generally characterized by high diversity of coexisting microbial species and strains, and microbiome composition typically remains stable across a broad range of conditions. However, under fixed conditions, microbial ecology conforms with the exclusion principle under which two populations competing for the same resource within the same niche cannot coexist because the less fit population inevitably goes extinct. Therefore, the long-term persistence of microbiome diversity calls for an explanation.<br><br>RESULTS: To explore the conditions for stabilization of microbial diversity, we developed a simple mathematical model consisting of two competing populations that could exchange a single gene allele via horizontal gene transfer (HGT). We found that, although in a fixed environment, with unbiased HGT, the system obeyed the exclusion principle, in an oscillating environment, within large regions of the phase space bounded by the rates of reproduction and HGT, the two populations coexist. Moreover, depending on the parameter combination, all three major types of symbiosis were obtained, namely, pure competition, host-parasite relationship, and mutualism. In each of these regimes, certain parameter combinations provided for synergy, that is, a greater total abundance of both populations compared to the abundance of the winning population in the fixed environment.<br><br>CONCLUSIONS: The results of this modeling study show that basic phenomena that are universal in microbial communities, namely, environmental variation and HGT, provide for stabilization and persistence of microbial diversity, and emergence of ecological complexity.}, }
@article {pmid38691424, year = {2024}, author = {Xiong, X and Othmer, HG and Harcombe, WR}, title = {Emergent antibiotic persistence in a spatially structured synthetic microbial mutualism.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38691424}, issn = {1751-7370}, support = {R01 GM121498/GM/NIGMS NIH HHS/United States ; R01-GM121498/NH/NIH HHS/United States ; }, mesh = {*Escherichia coli/drug effects/genetics/growth &amp; development ; *Anti-Bacterial Agents/pharmacology ; *Symbiosis ; *Salmonella enterica/drug effects/genetics ; Coculture Techniques ; Microbial Interactions ; Ampicillin/pharmacology ; Drug Resistance, Bacterial ; }, abstract = {Antibiotic persistence (heterotolerance) allows a subpopulation of bacteria to survive antibiotic-induced killing and contributes to the evolution of antibiotic resistance. Although bacteria typically live in microbial communities with complex ecological interactions, little is known about how microbial ecology affects antibiotic persistence. Here, we demonstrated within a synthetic two-species microbial mutualism of Escherichia coli and Salmonella enterica that the combination of cross-feeding and community spatial structure can emergently cause high antibiotic persistence in bacteria by increasing the cell-to-cell heterogeneity. Tracking ampicillin-induced death for bacteria on agar surfaces, we found that E. coli forms up to 55 times more antibiotic persisters in the cross-feeding coculture than in monoculture. This high persistence could not be explained solely by the presence of S. enterica, the presence of cross-feeding, average nutrient starvation, or spontaneous resistant mutations. Time-series fluorescent microscopy revealed increased cell-to-cell variation in E. coli lag time in the mutualistic co-culture. Furthermore, we discovered that an E. coli cell can survive antibiotic killing if the nearby S. enterica cells on which it relies die first. In conclusion, we showed that the high antibiotic persistence phenotype can be an emergent phenomenon caused by a combination of cross-feeding and spatial structure. Our work highlights the importance of considering spatially structured interactions during antibiotic treatment and understanding microbial community resilience more broadly.}, }
@article {pmid37970497, year = {2023}, author = {Lee, JH and Kim, S and Kim, ES and Keum, GB and Doo, H and Kwak, J and Pandey, S and Cho, JH and Ryu, S and Song, M and Cho, JH and Kim, S and Kim, HB}, title = {Comparative analysis of the pig gut microbiome associated with the pig growth performance.}, journal = {Journal of animal science and technology}, volume = {65}, number = {4}, pages = {856-864}, pmid = {37970497}, issn = {2055-0391}, abstract = {There are a variety of microorganisms in the animal intestine, and it has been known that they play important roles in the host such as suppression of potentially pathogenic microorganisms, modulation of the gut immunity. In addition, the gut microbiota and the livestock growth performance have long been known to be related. Therefore, we evaluated the interrelation between the growth performance and the gut microbiome of the pigs from 3 different farms, with pigs of varied ages ready to be supplied to the market. When pigs reached average market weight of 118 kg, the average age of pigs in three different farms were < 180 days, about 190 days, and > 200 days, respectively. Fecal samples were collected from pigs of age of 70 days, 100 days, 130 days, and 160 days. The output data of the 16S rRNA gene sequencing by the Illumina Miseq platform was filtered and analyzed using Quantitative Insights into Microbial Ecology (QIIME)2, and the statistical analysis was performed using Statistical Analysis of Metagenomic Profiles (STAMP). The results of this study showed that the gut microbial communities shifted as pigs aged along with significant difference in the relative abundance of different phyla and genera in different age groups of pigs from each farm. Even though, there was no statistical differences among groups in terms of Chao1, the number of observed operational taxonomic units (OTUs), and the Shannon index, our results showed higher abundances of Bifidobacterium, Clostridium and Lactobacillus in the feces of pigs with rapid growth rate. These results will help us to elucidate important gut microbiota that can affect the growth performance of pigs.}, }
@article {pmid37354976, year = {2023}, author = {Kable, ME and Chin, EL and Huang, L and Stephensen, CB and Lemay, DG}, title = {Association of Estimated Daily Lactose Consumption, Lactase Persistence Genotype (rs4988235), and Gut Microbiota in Healthy Adults in the United States.}, journal = {The Journal of nutrition}, volume = {153}, number = {8}, pages = {2163-2173}, doi = {10.1016/j.tjnut.2023.06.025}, pmid = {37354976}, issn = {1541-6100}, mesh = {Male ; Female ; Humans ; Adult ; United States ; Lactose ; *Lactose Intolerance/genetics ; *Gastrointestinal Microbiome/genetics ; Cross-Sectional Studies ; RNA, Ribosomal, 16S/genetics ; Dairy Products ; Lactase/genetics ; Genotype ; }, abstract = {BACKGROUND: Lactase persistence (LP) is a heritable trait in which lactose can be digested throughout adulthood. Lactase nonpersistent (LNP) individuals who consume lactose may experience microbial adaptations in response to undigested lactose.<br><br>OBJECTIVES: The objective of the study was to estimate lactose from foods reported in the Automated Self-Administered 24-Hour Dietary Assessment Tool (ASA24) and determine the interaction between lactose consumption, LP genotype, and gut microbiome in an observational cross-sectional study of healthy adults in the United States (US).<br><br>METHODS: Average daily lactose consumption was estimated for 279 healthy US adults, genotyped for the lactase gene -13910G>A polymorphism (rs4988235) by matching ASA24-reported foods to foods in the Nutrition Coordinating Center Food and Nutrient Database. Analysis of covariance was used to identify whether the A genotype (LP) influenced lactose and total dairy consumption, with total energy intake and weight as covariates. The 16S rRNA V4/V5 region, amplified from bacterial DNA extracted from each frozen stool sample, was sequenced using Illumina MiSeq (300 bp paired-end) and analyzed using Quantitative Insights Into Microbial Ecology (QIIME)2 (version 2019.10). Differential abundances of bacterial taxa were analyzed using DESeq2 likelihood ratio tests.<br><br>RESULTS: Across a diverse set of ethnicities, LP subjects consumed more lactose than LNP subjects. Lactobacillaceae abundance was highest in LNP subjects who consumed more than 12.46 g/d (upper tercile). Within Caucasians and Hispanics, family Lachnospiraceae was significantly enriched in the gut microbiota of LNP individuals consuming the upper tercile of lactose across both sexes.<br><br>CONCLUSIONS: Elevated lactose consumption in individuals with the LNP genotype is associated with increased abundance of family Lactobacillaceae and Lachnospriaceae, taxa that contain multiple genera capable of utilizing lactose. This trial was registered on clinicaltrials.gov as NCT02367287.}, }
@article {pmid37338363, year = {2023}, author = {Ye, L and Yang, X and Zhang, B and Zhou, J and Tian, H and Zhang, X and Li, X}, title = {Seasonal Succession of Fungal Communities in Native Truffle (Tuber indicum) Ecosystems.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {7}, pages = {e0019523}, pmid = {37338363}, issn = {1098-5336}, mesh = {Ecosystem ; Seasons ; *Mycobiome ; *Ascomycota ; *Mycorrhizae ; Soil ; Soil Microbiology ; }, abstract = {Truffles are a rare underground fungus and one of the most expensive, and sought-after kitchen ingredients in the world. Microbial ecology plays an important role in the annual growth cycle of truffles, but fungal communities in native truffle ecosystems are still largely unknown, especially for Tuber indicum from China. In this study, the spatial and temporal dynamics of soil physicochemical properties and fungal communities were described associated with four T. indicum-producing plots (TPPs) and one non-truffle-producing plot in four successive growing seasons. A total of 160 biological samples were collected, 80 of which were used for the determination of 10 soil physicochemical indices and 80 for Illumina-based analysis of the fungal microbiome. Soil physicochemical properties and fungal communities exhibited considerable seasonal variation. Ascomycetes, Basidiomycetes, and Mucormycoides dominated. The core microbiome work on the microecological changes in TPPs, and the identified core members contribute to the seasonal succession of communities. The genus Tuber occupies a central position in healthy TPPs. There was a strong correlation between soil physicochemical properties and fungal communities. The genus Tuber showed a positive correlation with Ca, Mg, and total nitrogen, but a negative correlation with total phosphorus and available potassium. This study describes the complex ecological dynamics of soil physicochemical indices and fungal communities occurring during the annual cycle of Tuber indicum, and highlights the succession of core communities in truffle plots, which contribute to better protection of native truffle ecosystems and control of mycorrhizal fungal contamination in artificial truffle plantations in China. IMPORTANCE The spatial and temporal dynamics of soil physicochemical properties and fungal communities associated with four Tuber indicum-producing plots and one non truffle producing plot in four different growing seasons are described. Soil physicochemical properties and fungal communities exhibited considerable seasonal variation. This study examines the complex ecological dynamics of soil physicochemical indices and fungal communities occurring during the annual cycle of Tuber indicum and highlights the succession of core communities in truffle plots, which contributes to better protection of native truffle ecosystems and control of mycorrhizal fungal contamination in artificial truffle plantations in China.}, }
@article {pmid36061686, year = {2022}, author = {Liu, B and Chen, J and Li, Y}, title = {Keystone Microorganisms Regulate the Methanogenic Potential in Coals with Different Coal Ranks.}, journal = {ACS omega}, volume = {7}, number = {34}, pages = {29901-29908}, pmid = {36061686}, issn = {2470-1343}, abstract = {Microorganisms are the core drivers of coal biogeochemistry and are closely related to the formation of coalbed methane. However, it remains poorly understood about the network relationship and stability of microbial communities in coals with different ranks. In this study, a high-throughput sequencing data set was analyzed to understand the microbial co-occurrence network in coals with different ranks including anthracite, medium-volatile bituminous, and high-volatile bituminous. The results showed similar topological properties for the microbial networks among coals with different ranks, but a great difference was found in the microbial composition in different large modules among coals with different ranks, and these three networks had three, four, and four large modules with seven, nine, and nine phyla, respectively. Among these networks, a total of 46 keystone taxa were identified in large modules, and these keystone taxa were different in coals with different ranks. Bacteria dominated the keystone taxa in the microbial network, and these bacterial keystone taxa mainly belonged to phyla Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. Besides, the removal of the key microbial data could reduce the community stability of microbial communities in bituminous coals. A partial least-squares path model further showed that these bacterial keystone taxa indirectly affected methanogenic potential by maintaining the microbial community stability and bacterial diversity. In summary, these results showed that keystone taxa played an important role in determining the community diversity, maintaining the microbial community stability, and controlling the methanogenic potential, which is of great significance for understanding the microbial ecology and the geochemical cycle of coal seams.}, }
@article {pmid35938717, year = {2022}, author = {Okazaki, Y and Nakano, SI and Toyoda, A and Tamaki, H}, title = {Long-Read-Resolved, Ecosystem-Wide Exploration of Nucleotide and Structural Microdiversity of Lake Bacterioplankton Genomes.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0043322}, pmid = {35938717}, issn = {2379-5077}, mesh = {*Lakes/microbiology ; Ecosystem ; Nucleotides ; Metagenome ; Bacteria/genetics ; *Bacteriophages/genetics ; }, abstract = {Reconstruction of metagenome-assembled genomes (MAGs) has become a fundamental approach in microbial ecology. However, a MAG is hardly complete and overlooks genomic microdiversity because metagenomic assembly fails to resolve microvariants among closely related genotypes. Aiming at understanding the universal factors that drive or constrain prokaryotic genome diversification, we performed an ecosystem-wide high-resolution metagenomic exploration of microdiversity by combining spatiotemporal (2 depths × 12 months) sampling from a pelagic freshwater system, high-quality MAG reconstruction using long- and short-read metagenomic sequences, and profiling of single nucleotide variants (SNVs) and structural variants (SVs) through mapping of short and long reads to the MAGs, respectively. We reconstructed 575 MAGs, including 29 circular assemblies, providing high-quality reference genomes of freshwater bacterioplankton. Read mapping against these MAGs identified 100 to 101,781 SNVs/Mb and 0 to 305 insertions, 0 to 467 deletions, 0 to 41 duplications, and 0 to 6 inversions for each MAG. Nonsynonymous SNVs were accumulated in genes potentially involved in cell surface structural modification to evade phage recognition. Most (80.2%) deletions overlapped with a gene coding region, and genes of prokaryotic defense systems were most frequently (>8% of the genes) overlapped with a deletion. Some such deletions exhibited a monthly shift in their allele frequency, suggesting a rapid turnover of genotypes in response to phage predation. MAGs with extremely low microdiversity were either rare or opportunistic bloomers, suggesting that population persistency is key to their genomic diversification. The results concluded that prokaryotic genomic diversification is driven primarily by viral load and constrained by a population bottleneck. IMPORTANCE Identifying intraspecies genomic diversity (microdiversity) is crucial to understanding microbial ecology and evolution. However, microdiversity among environmental assemblages is not well investigated, because most microbes are difficult to culture. In this study, we performed cultivation-independent exploration of bacterial genomic microdiversity in a lake ecosystem using a combination of short- and long-read metagenomic analyses. The results revealed the broad spectrum of genomic microdiversity among the diverse bacterial species in the ecosystem, which has been overlooked by conventional approaches. Our ecosystem-wide exploration further allowed comparative analysis among the genomes and genes and revealed factors behind microbial genomic diversification, namely, that diversification is driven primarily by resistance against viral infection and constrained by the population size.}, }
@article {pmid35134909, year = {2022}, author = {Foster-Nyarko, E and Pallen, MJ}, title = {The microbial ecology of Escherichia coli in the vertebrate gut.}, journal = {FEMS microbiology reviews}, volume = {46}, number = {3}, pages = {}, pmid = {35134909}, issn = {1574-6976}, mesh = {Animals ; Bacteria ; *Escherichia coli ; *Escherichia coli Infections/microbiology ; Symbiosis ; Vertebrates ; }, abstract = {Escherichia coli has a rich history as biology's 'rock star', driving advances across many fields. In the wild, E. coli resides innocuously in the gut of humans and animals but is also a versatile pathogen commonly associated with intestinal and extraintestinal infections and antimicrobial resistance-including large foodborne outbreaks such as the one that swept across Europe in 2011, killing 54 individuals and causing approximately 4000 infections and 900 cases of haemolytic uraemic syndrome. Given that most E. coli are harmless gut colonizers, an important ecological question plaguing microbiologists is what makes E. coli an occasionally devastating pathogen? To address this question requires an enhanced understanding of the ecology of the organism as a commensal. Here, we review how our knowledge of the ecology and within-host diversity of this organism in the vertebrate gut has progressed in the 137 years since E. coli was first described. We also review current approaches to the study of within-host bacterial diversity. In closing, we discuss some of the outstanding questions yet to be addressed and prospects for future research.}, }
@article {pmid34989745, year = {2022}, author = {Hua, Q and Han, Y and Zhao, H and Zhang, H and Yan, B and Pei, S and He, X and Li, Y and Meng, X and Chen, L and Zhong, F and Li, D}, title = {Punicalagin alleviates renal injury via the gut-kidney axis in high-fat diet-induced diabetic mice.}, journal = {Food &amp; function}, volume = {13}, number = {2}, pages = {867-879}, doi = {10.1039/d1fo03343c}, pmid = {34989745}, issn = {2042-650X}, mesh = {Animals ; Diabetes Mellitus, Experimental/*complications ; Diabetic Nephropathies/*drug therapy ; *Diet, High-Fat ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome/*drug effects ; Gene Expression Regulation/drug effects ; Hydrolyzable Tannins/*pharmacology ; Inflammation/metabolism ; Kidney/*metabolism ; Mice ; Mice, Inbred C57BL ; Pomegranate/chemistry ; }, abstract = {Diabetic renal injury was associated with dysbiosis of the gut microbiota and intestinal barrier. Punicalagin (PU) from pomegranates potentially impacts the microbial ecosystem, intestinal barrier, and renal function. Therefore, we hypothesized that PU may improve diabetic renal injury by modulating the gut-kidney axis. The present study evaluated the effect of PU on the gut-kidney axis and kidney function in a diabetic renal injury mouse model induced by a high-fat diet (HFD). Mice were fed a HFD without PU or with at doses of 50 and 100 mg kg[-1] d[-1] for 8 weeks. Targeted metabolomics by GC-MS and 16S rRNA sequencing were implemented to determine short-chain fatty acids (SCFAs) and microbes. Further RNA sequencing analyses were performed to determine which differentially expressed genes were changed by PU. Compared with the DM model group, PU supplementation improved diabetic renal injury, ameliorated kidney architecture and function, and reshaped gut microbial ecology. Additionally, PU reversed HFD-induced gut barrier dysfunction, promoted cecal SCFA concentrations and inhibited serum lipopolysaccharide (LPS) and diamine oxidase (DAO) levels. Moreover, correlation analysis found that cecal SCFAs were significantly negatively correlated with inflammation-related genes in the kidney. The present results indicated that PU, a promising bioactive polyphenol, successfully improved diabetic renal injury, most likely through the gut-kidney axis.}, }
@article {pmid34958387, year = {2022}, author = {Kable, ME and Chin, EL and Storms, D and Lemay, DG and Stephensen, CB}, title = {Tree-Based Analysis of Dietary Diversity Captures Associations Between Fiber Intake and Gut Microbiota Composition in a Healthy US Adult Cohort.}, journal = {The Journal of nutrition}, volume = {152}, number = {3}, pages = {779-788}, doi = {10.1093/jn/nxab430}, pmid = {34958387}, issn = {1541-6100}, mesh = {Adolescent ; Adult ; Aged ; Cross-Sectional Studies ; Diet ; Dietary Fiber/analysis ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Middle Aged ; RNA, Ribosomal, 16S/analysis/genetics ; Young Adult ; }, abstract = {BACKGROUND: Diet patterns are a significant and modifiable contributing factor to the composition of the human gut microbiota.<br><br>OBJECTIVES: We set out to identify reproducible relationships between diet and gut microbial community composition in a diverse, healthy US adult cohort.<br><br>METHODS: We collected 2 to 3 automated self-administered 24-hour dietary recalls over 10-14 days, together with a single stool sample, from 343 healthy adults in a cross-sectional phenotyping study. This study examined a multi-ethnic cohort balanced for age (18-65 years), sex, and BMI (18.5-45 kg/m2). Dietary data were edited to a tree format according to published methods. The tree structure was annotated with the average total grams of dry weight, fat, protein, carbohydrate, or fiber from each food item reported. The alpha and beta diversity measurements, calculated using the tree structure, were analyzed relative to the microbial community diversity, determined by a Quantitative Insights Into Microbial Ecology (QIIME) 2 analysis of the bacterial 16S ribosomal RNA V4 region, sequenced from stool samples. K-means clustering was used to form groups of individuals consuming similar diets, and gut microbial communities were compared among groups using differential expression analysis for sequence count data.<br><br>RESULTS: The alpha diversity of diet dry weight was significantly correlated with the gut microbial community alpha diversity (r&#xa0;=&#xa0;0.171). The correlation improved when diet was characterized using grams of carbohydrates (r&#xa0;=&#xa0;0.186) or fiber (r&#xa0;=&#xa0;0.213). Bifidobacterium was enriched with diets containing higher levels of total carbohydrate from cooked grains. Lachnospira, was enriched with diet patterns containing high consumption of fiber from fruits excluding berries.<br><br>CONCLUSIONS: The tree structure, annotated with grams of carbohydrate, is a robust analysis method for comparing self-reported diet to the gut microbial community composition. This method identified consumption of fiber from fruit robustly associated with an abundance of pectinolytic bacterial genus, Lachnospira, in the guts of healthy adults. This trial was registered at clinicaltrials.gov as NCT02367287.}, }
@article {pmid37938641, year = {2021}, author = {Röttjers, L and Vandeputte, D and Raes, J and Faust, K}, title = {Null-model-based network comparison reveals core associations.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {36}, pmid = {37938641}, issn = {2730-6151}, support = {STG/16/006//KU Leuven (Katholieke Universiteit Leuven)/ ; STG/16/006//KU Leuven (Katholieke Universiteit Leuven)/ ; 801747//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 801747//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 30770923//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; 30770923//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; }, abstract = {Microbial network construction and analysis is an important tool in microbial ecology. Such networks are often constructed from statistically inferred associations and may not represent ecological interactions. Hence, microbial association networks are error prone and do not necessarily reflect true community structure. We have developed anuran, a toolbox for investigation of noisy networks with null models. Such models allow researchers to generate data under the null hypothesis that all associations are random, supporting identification of nonrandom patterns in groups of association networks. This toolbox compares multiple networks to identify conserved subsets (core association networks, CANs) and other network properties that are shared across all networks. We apply anuran to a time series of fecal samples from 20 women to demonstrate the existence of CANs in a subset of the sampled individuals. Moreover, we use data from the Global Sponge Project to demonstrate that orders of sponges have a larger CAN than expected at random. In conclusion, this toolbox is a resource for investigators wanting to compare microbial networks across conditions, time series, gradients, or hosts.}, }
@article {pmid33952552, year = {2021}, author = {Tang, H and Bohannon, L and Lew, M and Jensen, D and Jung, SH and Zhao, A and Sung, AD and Wischmeyer, PE}, title = {Randomised, double-blind, placebo-controlled trial of Probiotics To Eliminate COVID-19 Transmission in Exposed Household Contacts (PROTECT-EHC): a clinical trial protocol.}, journal = {BMJ open}, volume = {11}, number = {5}, pages = {e047069}, pmid = {33952552}, issn = {2044-6055}, support = {R03 AG064260/AG/NIA NIH HHS/United States ; }, mesh = {*COVID-19 ; Double-Blind Method ; Humans ; Pandemics ; *Probiotics ; RNA, Ribosomal, 16S/genetics ; Randomized Controlled Trials as Topic ; SARS-CoV-2 ; Treatment Outcome ; }, abstract = {INTRODUCTION: The COVID-19 pandemic has proven to be an unprecedented challenge to worldwide health, and strategies to mitigate the spread and severity of COVID-19 infection are urgently needed. Emerging evidence suggests that the composition of the gut microbiome and modification of microbial ecology via probiotics can affect susceptibility to a wide range of infections, including respiratory tract infections. In this study, we aim to evaluate the effects of the probiotic Lactobacillus rhamnosus GG (LGG) versus placebo on COVID-19 infection status and the gut microbiome in subjects with a household contact who has tested positive for COVID-19.<br><br>METHODS AND ANALYSIS: In this double-blinded, randomised, placebo-controlled trial, we will randomise 1132 subjects having a household contact who has recently (&#x2264;7&#x2009;days) tested positive for COVID-19 to daily oral LGG or placebo for 28 days. We hypothesise that taking LGG as a probiotic will protect against COVID-19 infection and reduce the severity of disease in those who become infected (primary endpoint: decreased symptoms), and will be associated with beneficial changes in the composition of the gut microbiome. Stool samples and nasal swabs will be collected to evaluate the microbiome by 16S rRNA sequencing and the presence of SARS-CoV-2 by PCR, respectively. We will also conduct multivariate analysis of demographic, behavioural, temporal, and other variables that may predict development of symptoms and other outcomes.<br><br>ETHICS AND DISSEMINATION: This trial is conducted under a Food and Drug Administration Investigational New Drug for LGG, has received ethics approval by the institutional review board of Duke University and enrolment has begun. We plan to disseminate the results in peer-reviewed journals and at national and international conferences.<br><br>TRIAL REGISTRATION NUMBER: NCT04399252.}, }
@article {pmid33653941, year = {2021}, author = {Belk, AD and Duarte, T and Quinn, C and Coil, DA and Belk, KE and Eisen, JA and Quinn, JC and Martin, JN and Yang, X and Metcalf, JL}, title = {Air versus Water Chilling of Chicken: a Pilot Study of Quality, Shelf-Life, Microbial Ecology, and Economics.}, journal = {mSystems}, volume = {6}, number = {2}, pages = {}, pmid = {33653941}, issn = {2379-5077}, abstract = {The United States' large-scale poultry meat industry is energy and water intensive, and opportunities may exist to improve sustainability during the broiler chilling process. By USDA regulation, after harvest the internal temperature of the chicken must be reduced to 40°F or less within 16 h to inhibit bacterial growth that would otherwise compromise the safety of the product. This step is accomplished most commonly by water immersion chilling in the United States, while air chilling methods dominate other global markets. A comprehensive understanding of the differences between these chilling methods is lacking. Therefore, we assessed the meat quality, shelf-life, microbial ecology, and techno-economic impacts of chilling methods on chicken broilers in a university meat laboratory setting. We discovered that air chilling methods resulted in superior chicken odor and shelf-life, especially prior to 14 days of dark storage. Moreover, we demonstrated that air chilling resulted in a more diverse microbiome that we hypothesize may delay the dominance of the spoilage organism Pseudomonas Finally, a techno-economic analysis highlighted potential economic advantages to air chilling compared to water chilling in facility locations where water costs are a more significant factor than energy costs.IMPORTANCE As the poultry industry works to become more sustainable and to reduce the volume of food waste, it is critical to consider points in the processing system that can be altered to make the process more efficient. In this study, we demonstrate that the method used during chilling (air versus water chilling) influences the final product microbial community, quality, and physiochemistry. Notably, the use of air chilling appears to delay the bloom of Pseudomonas spp. that are the primary spoilers in packaged meat products. By using air chilling to reduce carcass temperatures instead of water chilling, producers may extend the time until spoilage of the products and, depending on the cost of water in the area, may have economic and sustainability advantages. As a next step, a similar experiment should be done in an industrial setting to confirm these results generated in a small-scale university lab facility.}, }
@article {pmid32546676, year = {2020}, author = {Gulino, K and Rahman, J and Badri, M and Morton, J and Bonneau, R and Ghedin, E}, title = {Initial Mapping of the New York City Wastewater Virome.}, journal = {mSystems}, volume = {5}, number = {3}, pages = {}, pmid = {32546676}, issn = {2379-5077}, abstract = {Bacteriophages are abundant members of all microbiomes studied to date, influencing microbial communities through interactions with their bacterial hosts. Despite their functional importance and ubiquity, phages have been underexplored in urban environments compared to their bacterial counterparts. We profiled the viral communities in New York City (NYC) wastewater using metagenomic data collected in November 2014 from 14 wastewater treatment plants. We show that phages accounted for the largest viral component of the sewage samples and that specific virus communities were associated with local environmental conditions within boroughs. The vast majority of the virus sequences had no homology matches in public databases, forming an average of 1,700 unique virus clusters (putative genera). These new clusters contribute to elucidating the overwhelming proportion of data that frequently goes unidentified in viral metagenomic studies. We assigned potential hosts to these phages, which appear to infect a wide range of bacterial genera, often outside their presumed host. We determined that infection networks form a modular-nested pattern, indicating that phages include a range of host specificities, from generalists to specialists, with most interactions organized into distinct groups. We identified genes in viral contigs involved in carbon and sulfur cycling, suggesting functional importance of viruses in circulating pathways and gene functions in the wastewater environment. In addition, we identified virophage genes as well as a nearly complete novel virophage genome. These findings provide an understanding of phage abundance and diversity in NYC wastewater, previously uncharacterized, and further examine geographic patterns of phage-host association in urban environments.IMPORTANCE Wastewater is a rich source of microbial life and contains bacteria, viruses, and other microbes found in human waste as well as environmental runoff sources. As part of an effort to characterize the New York City wastewater metagenome, we profiled the viral community of sewage samples across all five boroughs of NYC and found that local sampling sites have unique sets of viruses. We focused on bacteriophages, or viruses of bacteria, to understand how they may influence the microbial ecology of this system. We identified several new clusters of phages and successfully associated them with bacterial hosts, providing insight into virus-host interactions in urban wastewater. This study provides a first look into the viral communities present across the wastewater system in NYC and points to their functional importance in this environment.}, }
@article {pmid32031212, year = {2020}, author = {Fenske, GJ and Ghimire, S and Antony, L and Christopher-Hennings, J and Scaria, J}, title = {Integration of culture-dependent and independent methods provides a more coherent picture of the pig gut microbiome.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {3}, pages = {}, doi = {10.1093/femsec/fiaa022}, pmid = {32031212}, issn = {1574-6941}, mesh = {Animals ; Bacteroidetes/genetics ; *Gastrointestinal Microbiome ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Swine ; }, abstract = {Bacterial communities resident in the hindgut of pigs, have profound impacts on health and disease. Investigations into the pig microbiome have utilized either culture-dependent, or far more commonly, culture-independent techniques using next generation sequencing. We contend that a combination of both approaches generates a more coherent view of microbiome composition. In this study, we surveyed the microbiome of Tamworth breed and feral pigs through the integration high throughput culturing and shotgun metagenomics. A single culture medium was used for culturing. Selective screens were added to the media to increase culture diversity. In total, 46 distinct bacterial species were isolated from the Tamworth and feral samples. Selective screens successfully shifted the diversity of bacteria on agar plates. Tamworth pigs are highly dominated by Bacteroidetes primarily composed of the genus Prevotella whereas feral samples were more diverse with almost equal proportions of Firmicutes and Bacteroidetes. The combination of metagenomics and culture techniques facilitated a greater retrieval of annotated genes than either method alone. The single medium based pig microbiota library we report is a resource to better understand pig gut microbial ecology and function. It allows for assemblage of defined bacterial communities for studies in bioreactors or germfree animal models.}, }
@article {pmid31506516, year = {2019}, author = {Bridier, A and Le Grandois, P and Moreau, MH and Prénom, C and Le Roux, A and Feurer, C and Soumet, C}, title = {Impact of cleaning and disinfection procedures on microbial ecology and Salmonella antimicrobial resistance in a pig slaughterhouse.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {12947}, pmid = {31506516}, issn = {2045-2322}, mesh = {Abattoirs ; Animals ; Anti-Bacterial Agents/*pharmacology ; Disinfection/*methods ; *Drug Resistance, Bacterial ; Microbial Sensitivity Tests ; Salmonella/*drug effects ; Salmonella Infections, Animal/*drug therapy/epidemiology/microbiology ; Swine ; Swine Diseases/epidemiology/microbiology/*prevention &amp; control ; }, abstract = {To guarantee food safety, a better deciphering of ecology and adaptation strategies of bacterial pathogens such as Salmonella in food environments is crucial. The role of food processing conditions such as cleaning and disinfection procedures on antimicrobial resistance emergence should especially be investigated. In this work, the prevalence and antimicrobial resistance of Salmonella and the microbial ecology of associated surfaces communities were investigated in a pig slaughterhouse before and after cleaning and disinfection procedures. Salmonella were detected in 67% of samples and isolates characterization revealed the presence of 15 PFGE-patterns belonging to five serotypes: S.4,5,12:i:-, Rissen, Typhimurium, Infantis and Derby. Resistance to ampicillin, sulfamethoxazole, tetracycline and/or chloramphenicol was detected depending on serotypes. 16S rRNA-based bacterial diversity analyses showed that Salmonella surface associated communities were highly dominated by the Moraxellaceae family with a clear site-specific composition suggesting a persistent colonization of the pig slaughterhouse. Cleaning and disinfection procedures did not lead to a modification of Salmonella susceptibility to antimicrobials in this short-term study but they tended to significantly reduce bacterial diversity and favored some genera such as Rothia and Psychrobacter. Such data participate to the construction of a comprehensive view of Salmonella ecology and antimicrobial resistance emergence in food environments in relation with cleaning and disinfection procedures.}, }
@article {pmid29134738, year = {2018}, author = {Xiao, X and Liang, Y and Zhou, S and Zhuang, S and Sun, B}, title = {Fungal community reveals less dispersal limitation and potentially more connected network than that of bacteria in bamboo forest soils.}, journal = {Molecular ecology}, volume = {27}, number = {2}, pages = {550-563}, doi = {10.1111/mec.14428}, pmid = {29134738}, issn = {1365-294X}, mesh = {Biodiversity ; Carbon/metabolism ; China ; Forests ; Fungi/*growth &amp; development ; Microbiota/*genetics ; Plants/genetics/microbiology ; Sasa/genetics/*microbiology ; *Soil Microbiology ; }, abstract = {A central aim of this microbial ecology research was to investigate the mechanisms shaping the assembly of soil microbial communities. Despite the importance of bacterial and fungal mediation of carbon cycling in forest ecosystems, knowledge concerning their distribution patterns and underlying mechanisms remains insufficient. Here, soils were sampled from six bamboo forests across the main planting area of Moso bamboo in southern China. The bacterial and fungal diversities were assessed by sequencing 16S rRNA and ITS gene amplicons, respectively, with an Illumina MiSeq. Based on structural equation modelling, dispersal limitation had strongest impact on bacterial beta diversity, while the mean annual precipitation had a smaller impact by directly or indirectly mediating the soil organic carbon density. However, only the mean annual temperature and precipitation played direct roles in fungal beta diversity. Moreover, the co-occurrence network analyses revealed a possibly much higher network connectivity in the fungal network than in the bacteria. With less dispersal limitation, stronger environmental selection and a potentially more connected network, the fungal community had more important roles in the soil carbon metabolisms in bamboo forests. Fungal beta diversity and the clustering coefficient explained approximately 14.4% and 6.1% of the variation in the carbon metabolic profiles among sites, respectively, but that of bacteria only explained approximately 1.7% and 1.8%, respectively. This study explored soil microbial spatial patterns along with the underlying mechanisms of dispersal limitation, selection and connectivity of ecological networks, thus providing novel insights into the study of the distinct functional traits of different microbial taxa.}, }
@article {pmid28680053, year = {2017}, author = {Cheng, G and Sun, M and Lu, J and Ge, X and Zhang, H and Xu, X and Lou, L and Lin, Q}, title = {Role of biochar in biodegradation of nonylphenol in sediment: Increasing microbial activity versus decreasing bioavailability.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {4726}, pmid = {28680053}, issn = {2045-2322}, mesh = {Bacteria/drug effects ; Biodegradation, Environmental ; Biological Availability ; Charcoal/*chemistry ; Geologic Sediments/chemistry/*microbiology ; Oryza/chemistry ; Phenols/*chemistry/toxicity ; Soil Pollutants/chemistry ; }, abstract = {The observed strong sorption of hydrophobic organic contaminants (HOCs) to biochar presents potential implications for HOCs bioavailability and bioaccessibility in sediments, while biochar could impact sediment microbial ecology. However, the comprehensive study on the effects of biochar on HOC biodegradation coupled with bioavailability and microbial ecology are rarely documented. In this paper, the effects of biochar on the biodegradation of nonylphenol (NP) were investigated using 3 different NP concentrations (20, 50 and 500 mg/Kg) in sediments amended with different percentage of rice straw biochar (RC). Results showed that the influence of RC on NP biodegradation varied with different NP concentrations. At low NP concentrations, RC suppressed NP biodegradation by reducing NP bioavailability, while at high NP concentrations, moderate RC addition promoted biodegradation by reducing toxicity of NP to microbes. The effects of NP on microbial community structures were significant (P < 0.01), but those of RC were not significant (P > 0.05). The RC affected microorganisms through altering NP toxicity, microbial quantity and activity, but not microbial community structures. This study indicated that there could be an optimal biochar percentage in biochar-sediment systems at different HOC concentrations, which strengthened HOC biodegradation process and accelerated biodegradation rate, forming adsorption-biodegradation coupled bioremediation.}, }
@article {pmid27144092, year = {2016}, author = {Marques, C and Meireles, M and Norberto, S and Leite, J and Freitas, J and Pestana, D and Faria, A and Calhau, C}, title = {High-fat diet-induced obesity Rat model: a comparison between Wistar and Sprague-Dawley Rat.}, journal = {Adipocyte}, volume = {5}, number = {1}, pages = {11-21}, pmid = {27144092}, issn = {2162-3945}, abstract = {In the past decades, obesity and associated metabolic complications have reached epidemic proportions. For the study of these pathologies, a number of animal models have been developed. However, a direct comparison between Wistar and Sprague-Dawley (SD) Rat as models of high-fat (HF) diet-induced obesity has not been adequately evaluated so far. Wistar and SD rats were assigned for 2 experimental groups for 17 weeks: standard (St) and high-fat (HF) diet groups. To assess some of the features of the metabolic syndrome, oral glucose tolerance tests, systolic blood pressure measurements and blood biochemical analysis were performed throughout the study. The gut microbiota composition of the animals of each group was evaluated at the end of the study by real-time PCR. HF diet increased weight gain, body fat mass, mesenteric adipocyte's size, adiponectin and leptin plasma levels and decreased oral glucose tolerance in both Wistar and SD rats. However, the majority of these effects were more pronounced or earlier detected in Wistar rats. The gut microbiota of SD rats was less abundant in Bacteroides and Prevotella but richer in Bifidobacterium and Lactobacillus comparatively to the gut microbiota of Wistar rats. Nevertheless, the modulation of the gut microbiota by HF diet was similar in both strains, except for Clostridium leptum that was only reduced in Wistar rats fed with HF diet. In conclusion, both Wistar and SD Rat can be used as models of HF diet-induced obesity although the metabolic effects caused by HF diet seemed to be more pronounced in Wistar Rat. Differences in the gut microbial ecology may account for the worsened metabolic scenario observed in Wistar Rat.}, }
@article {pmid25567040, year = {2015}, author = {Huang, YJ and Boushey, HA}, title = {The microbiome in asthma.}, journal = {The Journal of allergy and clinical immunology}, volume = {135}, number = {1}, pages = {25-30}, pmid = {25567040}, issn = {1097-6825}, support = {K23 HL105572/HL/NHLBI NIH HHS/United States ; }, mesh = {Allergens ; Animals ; Asthma/*microbiology ; Environmental Exposure ; Gastrointestinal Tract/*microbiology ; Humans ; *Microbiota ; Respiratory System/microbiology ; Respiratory Tract Infections/microbiology ; Virus Diseases/microbiology ; }, abstract = {The application of recently developed sensitive, specific, culture-independent tools for identification of microbes is transforming concepts of microbial ecology, including concepts of the relationships between the vast complex populations of microbes associated with ourselves and with states of health and disease. Although most work initially focused on the community of microbes (microbiome) in the gastrointestinal tract and its relationship to gastrointestinal disease, interest has expanded to include study of the relationships of the airway microbiome to asthma and its phenotypes and to the relationships between the gastrointestinal microbiome, development of immune function, and predisposition to allergic sensitization and asthma. Here we provide our perspective on the findings of studies of differences in the airway microbiome between asthmatic patients and healthy subjects and of studies of relationships between environmental microbiota, gut microbiota, immune function, and asthma development. In addition, we provide our perspective on how these findings suggest the broad outline of a rationale for approaches involving directed manipulation of the gut and airway microbiome for the treatment and prevention of allergic asthma.}, }
@article {pmid25033448, year = {2014}, author = {Baron, JL and Vikram, A and Duda, S and Stout, JE and Bibby, K}, title = {Shift in the microbial ecology of a hospital hot water system following the introduction of an on-site monochloramine disinfection system.}, journal = {PloS one}, volume = {9}, number = {7}, pages = {e102679}, pmid = {25033448}, issn = {1932-6203}, mesh = {Actinobacteria/genetics/growth &amp; development ; Base Sequence ; Biofilms/drug effects/growth &amp; development ; Chloramines/*pharmacology ; Cyanobacteria/genetics/growth &amp; development ; DNA, Bacterial/genetics ; Disinfectants/pharmacology ; Disinfection/*methods ; Drinking Water/*microbiology ; *Hospital Distribution Systems ; Proteobacteria/genetics/growth &amp; development ; RNA, Ribosomal, 16S/genetics ; Sanitary Engineering ; Sequence Analysis, DNA ; Tertiary Care Centers ; Water Microbiology ; Water Purification/*methods ; Water Quality ; }, abstract = {Drinking water distribution systems, including premise plumbing, contain a diverse microbiological community that may include opportunistic pathogens. On-site supplemental disinfection systems have been proposed as a control method for opportunistic pathogens in premise plumbing. The majority of on-site disinfection systems to date have been installed in hospitals due to the high concentration of opportunistic pathogen susceptible occupants. The installation of on-site supplemental disinfection systems in hospitals allows for evaluation of the impact of on-site disinfection systems on drinking water system microbial ecology prior to widespread application. This study evaluated the impact of supplemental monochloramine on the microbial ecology of a hospital's hot water system. Samples were taken three months and immediately prior to monochloramine treatment and monthly for the first six months of treatment, and all samples were subjected to high throughput Illumina 16S rRNA region sequencing. The microbial community composition of monochloramine treated samples was dramatically different than the baseline months. There was an immediate shift towards decreased relative abundance of Betaproteobacteria, and increased relative abundance of Firmicutes, Alphaproteobacteria, Gammaproteobacteria, Cyanobacteria and Actinobacteria. Following treatment, microbial populations grouped by sampling location rather than sampling time. Over the course of treatment the relative abundance of certain genera containing opportunistic pathogens and genera containing denitrifying bacteria increased. The results demonstrate the driving influence of supplemental disinfection on premise plumbing microbial ecology and suggest the value of further investigation into the overall effects of premise plumbing disinfection strategies on microbial ecology and not solely specific target microorganisms.}, }
@article {pmid24704907, year = {2014}, author = {Brooks, JP and Adeli, A and McLaughlin, MR}, title = {Microbial ecology, bacterial pathogens, and antibiotic resistant genes in swine manure wastewater as influenced by three swine management systems.}, journal = {Water research}, volume = {57}, number = {}, pages = {96-103}, doi = {10.1016/j.watres.2014.03.017}, pmid = {24704907}, issn = {1879-2448}, mesh = {Animal Husbandry/*methods ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/*genetics/*isolation &amp; purification ; Bacterial Proteins/genetics/metabolism ; Drug Resistance, Bacterial/*genetics ; Manure/*microbiology ; Methicillin-Resistant Staphylococcus aureus/drug effects/genetics/isolation &amp; purification ; *Microbiota ; RNA, Ribosomal, 16S/genetics/metabolism ; Real-Time Polymerase Chain Reaction ; Southeastern United States ; Sus scrofa ; Wastewater/*microbiology ; }, abstract = {The environmental influence of farm management in concentrated animal feeding operations (CAFO) can yield vast changes to the microbial biota and ecological structure of both the pig and waste manure lagoon wastewater. While some of these changes may not be negative, it is possible that CAFOs can enrich antibiotic resistant bacteria or pathogens based on farm type, thereby influencing the impact imparted by the land application of its respective wastewater. The purpose of this study was to measure the microbial constituents of swine-sow, -nursery, and -finisher farm manure lagoon wastewater and determine the changes induced by farm management. A total of 37 farms were visited in the Mid-South USA and analyzed for the genes 16S rRNA, spaQ (Salmonella spp.), Camp-16S (Campylobacter spp.), tetA, tetB, ermF, ermA, mecA, and intI using quantitative PCR. Additionally, 16S rRNA sequence libraries were created. Overall, it appeared that finisher farms were significantly different from nursery and sow farms in nearly all genes measured and in 16S rRNA clone libraries. Nearly all antibiotic resistance genes were detected in all farms. Interestingly, the mecA resistance gene (e.g. methicillin resistant Staphylococcus aureus) was below detection limits on most farms, and decreased as the pigs aged. Finisher farms generally had fewer antibiotic resistance genes, which corroborated previous phenotypic data; additionally, finisher farms produced a less diverse 16S rRNA sequence library. Comparisons of Camp-16S and spaQ GU (genomic unit) values to previous culture data demonstrated ratios from 10 to 10,000:1 depending on farm type, indicating viable but not cultivatable bacteria were dominant. The current study indicated that swine farm management schemes positively and negatively affect microbial and antibiotic resistant populations in CAFO wastewater which has future "downstream" implications from both an environmental and public health perspective.}, }
@article {pmid24296350, year = {2013}, author = {Hannigan, GD and Grice, EA}, title = {Microbial ecology of the skin in the era of metagenomics and molecular microbiology.}, journal = {Cold Spring Harbor perspectives in medicine}, volume = {3}, number = {12}, pages = {a015362}, pmid = {24296350}, issn = {2157-1422}, support = {P30 AR057217/AR/NIAMS NIH HHS/United States ; R00 AR060873/AR/NIAMS NIH HHS/United States ; AR060873/AR/NIAMS NIH HHS/United States ; AR057217/AR/NIAMS NIH HHS/United States ; }, mesh = {Alphapapillomavirus/physiology ; Biodiversity ; Fungi/physiology ; Humans ; Malassezia/physiology ; Metagenomics/trends ; Microbiology/trends ; Microbiota/physiology ; Skin/*microbiology ; Skin Diseases, Infectious/diagnosis/*microbiology ; }, abstract = {The skin is the primary physical barrier between the body and the external environment and is also a substrate for the colonization of numerous microbes. Previously, dermatological microbiology research was dominated by culture-based techniques, but significant advances in genomic technologies have enabled the development of less-biased, culture-independent approaches to characterize skin microbial communities. These molecular microbiology approaches illustrate the great diversity of microbiota colonizing the skin and highlight unique features such as site specificity, temporal dynamics, and interpersonal variation. Disruptions in skin commensal microbiota are associated with the progression of many dermatological diseases. A greater understanding of how skin microbes interact with each other and with their host, and how we can therapeutically manipulate those interactions, will provide powerful tools for treating and preventing dermatological disease.}, }
@article {pmid23736549, year = {2013}, author = {Zhang, N and Liu, W and Yang, H and Yu, X and Gutknecht, JL and Zhang, Z and Wan, S and Ma, K}, title = {Soil microbial responses to warming and increased precipitation and their implications for ecosystem C cycling.}, journal = {Oecologia}, volume = {173}, number = {3}, pages = {1125-1142}, pmid = {23736549}, issn = {1432-1939}, mesh = {Acclimatization/*physiology ; Analysis of Variance ; Bacteria/metabolism ; Carbon Cycle/*physiology ; China ; *Ecosystem ; *Global Warming ; *Rain ; *Soil Microbiology ; }, abstract = {A better understanding of soil microbial ecology is critical to gaining an understanding of terrestrial carbon (C) cycle-climate change feedbacks. However, current knowledge limits our ability to predict microbial community dynamics in the face of multiple global change drivers and their implications for respiratory loss of soil carbon. Whether microorganisms will acclimate to climate warming and ameliorate predicted respiratory C losses is still debated. It also remains unclear how precipitation, another important climate change driver, will interact with warming to affect microorganisms and their regulation of respiratory C loss. We explore the dynamics of microorganisms and their contributions to respiratory C loss using a 4-year (2006-2009) field experiment in a semi-arid grassland with increased temperature and precipitation in a full factorial design. We found no response of mass-specific (per unit microbial biomass C) heterotrophic respiration to warming, suggesting that respiratory C loss is directly from microbial growth rather than total physiological respiratory responses to warming. Increased precipitation did stimulate both microbial biomass and mass-specific respiration, both of which make large contributions to respiratory loss of soil carbon. Taken together, these results suggest that, in semi-arid grasslands, soil moisture and related substrate availability may inhibit physiological respiratory responses to warming (where soil moisture was significantly lower), while they are not inhibited under elevated precipitation. Although we found no total physiological response to warming, warming increased bacterial C utilization (measured by BIOLOG EcoPlates) and increased bacterial oxidation of carbohydrates and phenols. Non-metric multidimensional scaling analysis as well as ANOVA testing showed that warming or increased precipitation did not change microbial community structure, which could suggest that microbial communities in semi-arid grasslands are already adapted to fluctuating climatic conditions. In summary, our results support the idea that microbial responses to climate change are multifaceted and, even with no large shifts in community structure, microbial mediation of soil carbon loss could still occur under future climate scenarios.}, }
@article {pmid1345176, year = {1992}, author = {Molin, S}, title = {Designing microbes for release into the environment.}, journal = {Science progress}, volume = {76}, number = {300 Pt 2}, pages = {139-148}, pmid = {1345176}, issn = {0036-8504}, mesh = {Bacteria/*genetics ; Containment of Biohazards ; Ecology ; *Genetic Engineering ; }, abstract = {After 20 years in which gene technology has become an important part of modern biotechnology we have seen very beneficial applications of the new techniques in the pharmaceutical industry. We are now entering a second phase involving the deliberate release of genetically engineered organisms into the environment. This next step causes concern because of a low level of predictability of their possible effects. While the risk assessment of microbial release is far from easy, the strain designers also face problems concerning optimization of performance of the organisms. The two groups of actors in this new development--the risk assessors and the strain designers--need the same platform of understanding from the field of microbial ecology, and a number of specific areas which may now be approached by modern technology deserve particular attention. An increased understanding of the activities of microbes in the environment will also allow construction of more predictable, and therefore safer, strains. Biological containment and molecular microbial ecology are two sides of the same coin in the context of release of genetically engineered microorganisms.}, }
@article {pmid40822855, year = {2025}, author = {Roman, FA and Byrne, T and Martin, RL and Mena-Aguilar, D and Smeltz, RE and Finkelstein, R and Pruden, A and Edwards, MA}, title = {Retrospective Analysis of Drinking Water Microcosm Microbiomes Reveals an Apparent Antagonistic Relationship between and.}, journal = {Environmental science &amp; technology letters}, volume = {12}, number = {8}, pages = {990-996}, doi = {10.1021/acs.estlett.5c00590}, pmid = {40822855}, issn = {2328-8930}, abstract = {(Lp) can sometimes establish in drinking water microbial communities and infect individuals inhaling contaminated aerosols. The premise plumbing portion of the drinking water distribution system is often especially vulnerable to Lp growth. Innovative approaches to intentionally manipulate the microbial ecology to control Lp have been proposed but remain elusive. Here, we retrospectively analyzed 16S rRNA gene amplicon sequences and droplet digital PCR data in samples derived from prior drinking water studies, wherein some inexplicable stochastic variations in the Lp occurrence were observed in replicate microcosms. We discovered an apparent antagonistic relationship between and . This relationship was noted across three water sources (Flint, Detroit, and Blacksburg) and was at least partially mediated by the presence of copper, through either copper pipes or a dosed range of 0-2000 μg/L total copper. The observations of this study, which was conducted under realistic drinking water conditions harboring mixed microbial communities, are consistent with recent pure culture studies reporting that amoebic uptake may be inhibited when are established as amoebal endosymbionts. The findings may help explain the apparent stochastic behavior of Lp in field and research settings and may open a door to new engineered ecological control strategies for Lp.}, }
@article {pmid40818553, year = {2025}, author = {Galinytė, D and Aroffu, M and Manconi, M and Žilius, M and Rysevaitė-Kyguolienė, K and Karosienė, J and Koreivienė, J and Briedis, V and Pauža, DH and Savickas, A and Ferrer, EE and Manca, ML and Savickienė, N}, title = {Cyano-phycocyanin loaded enriched transfersomes for enhanced topical skin delivery and antioxidant protection.}, journal = {International journal of pharmaceutics}, volume = {}, number = {}, pages = {126079}, doi = {10.1016/j.ijpharm.2025.126079}, pmid = {40818553}, issn = {1873-3476}, abstract = {This study aimed to develop and evaluate cyano-phycocyanin (C-PC)-loaded enriched transfersomes for topical application, improved skin delivery, and antioxidant protection. The main objective was to overcome the limitations associated with C-PC's instability and poor skin permeability due to its high molecular weight and hydrophilicity. Six formulations were prepared using an organic solvent-free two-step method: glycerol-enriched transfersomes (Gly-transfersomes),glycerol and cholesterol-enriched transfersomes (Gly-chol-transfersomes),hyaluronate-enriched transfersomes (Hyal-transfersomes),hyaluronate and cholesterol-enriched transfersomes (Hyal-chol-transfersomes),glycerol and hyaluronate-enriched transfersomes (Hyal-gly-transfersomes), anda combination of all three (Hyal-gly-chol-transfersomes). Empty vesicles were prepared via direct sonication, then C-PC was gently loaded using mild sonication in a temperature-controlled ultrasonic bath. All formulations demonstrated properties suitable for skin delivery, with mean diameters <115 nm, polydispersity indexes <0.2, and zeta potential below -30 mV. Cryo- transmission electron microscopy confirmed spherical, unilamellar or oligolamellar morphology. Gly- and Gly-chol-transfersomes exhibited the highest encapsulation efficiency (∼52 %) and remained stable for up to 8 months at 4 °C. Antioxidant activity of C-PC (∼23-27 μmol TE/g of dry C-PC) was confirmed via DPPH assay. Biological tests on HaCaT cells exposed to H2O2-induced oxidative stress showed ∼80 % cell viability after treatment with C-PC formulations, compared to ∼60 % in untreated cells, indicating cytoprotective activity. Ex vivo skin penetration studies revealed significantly higher C-PC accumulation in the epidermis especially for Gly- and Gly-chol-transfersomes versus aqueous C-PC. These findings confirm the potential of enriched transfersomes as effective carriers to improve the skin delivery and bioactivity of C-PC in antioxidant skin care formulations.}, }
@article {pmid40815942, year = {2025}, author = {McDonagh, F and Ryan, K and Kovářová, A and Tumeo, A and Clarke, C and Cormican, M and Miliotis, G}, title = {Identification of blaESBL- and blaCARBA- Positive Multi-Drug Resistant Mixta calida Isolates from Distinct Human Hosts.}, journal = {International journal of medical microbiology : IJMM}, volume = {320}, number = {}, pages = {151669}, doi = {10.1016/j.ijmm.2025.151669}, pmid = {40815942}, issn = {1618-0607}, abstract = {OBJECTIVE: This study aimed to investigate the identification of blaCARBA-positive multidrug-resistant Mixta calida isolates from human hosts and to elucidate their genomic determinants in a species-wide context.<br><br>METHODS: Two carbapenemase-producing M. calida isolates were received by the Galway Reference Laboratory Service in Ireland between June and July 2024. One isolate originated from a sputum sample, while the other was recovered from a routine screening rectal swab. Initial identification was performed using MALDI-ToF mass spectrometry, with genomic confirmation via 16S rRNA sequencing, digital DNA-DNA hybridization, and Average Nucleotide Identity analysis. Antimicrobial susceptibility testing was conducted using a MicroScan panel, following EUCAST and CLSI guidelines. Whole-genome sequencing, plasmid replicon typing, and antibiotic-resistance-gene and virulence-factor profiling were employed. Comparative analysis included all additional canonical M. calida genomes from NCBI database.<br><br>RESULTS: Both Irish isolates were taxonomically placed as M. calida and exhibited multidrug resistance against penicillins, cephalosporins, monobactams and ertapenem. The acquired genes blaKPC-3, blaOXA-9, and blaTEM-122 were detected on plasmid-borne contigs, indicating horizontal acquisition. Seven plasmid replicon types were shared between the two isolates. Both plasmid replicons and acquired antimicrobial-resistance-genes (ARGs) were seldomly identified across the species. Phylogenetic inference based on core genome analysis identified a monophyletic cluster, suggesting a single introductory event.<br><br>CONCLUSION: This study documents a dual occurrence of blaCARBA-positive M. calida in human colonisation and infection. The findings highlight the potential for horizontal-gene-transfer to drive the emergence of multidrug-resistant profiles in the species, underscoring the need for enhanced surveillance, diagnostic precision, and targeted infection control strategies to mitigate public health risks.<br><br>IMPACT STATEMENT: This study reports blaESBL and blaCARBA-positive multi-drug resistant Mixta calida isolates from distinct human hosts. Genomic analysis revealed the co-occurrence of plasmid-borne resistance genes blaKPC-3, blaOXA-9, and blaTEM-122. Species-wide phylogenetic analysis grouped the two isolates into a monophyletic cluster, suggesting a single introductory event.}, }
@article {pmid40815475, year = {2025}, author = {Kondrotaite, Z and Petersen, J and Singleton, C and Peces, M and Petriglieri, F and Jensen, TBN and Sereika, M and Daugberg, AOH and Wagner, M and Dueholm, MKD and Nielsen, PH}, title = {Ecophysiology and niche differentiation of three genera of polyphosphate-accumulating bacteria in a full-scale wastewater treatment plant.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0032225}, doi = {10.1128/msystems.00322-25}, pmid = {40815475}, issn = {2379-5077}, abstract = {Polyphosphate-accumulating organisms (PAOs) are the main bacteria responsible for phosphorus removal and recovery in full-scale wastewater treatment plants (WWTPs). They encompass members of the genera Candidatus Accumulibacter, Azonexus (formerly Dechloromonas), and Candidatus Phosphoribacter (formerly Tetrasphaera), with most studies focusing on Ca. Accumulibacter, primarily using lab-scale enrichment cultures. Although members from the three genera often co-exist in full-scale WWTPs, the metabolic capabilities and traits that determine the niche differentiation of the specific species are still unknown. We retrieved 214 high-quality metagenome-assembled genomes from a full-scale plant with phosphorus removal and examined the polyphosphate-related metabolic pathways using genome-resolved metatranscriptomics in the different process tanks in situ and by using short-term incubations ex situ. We observed the co-existence of nine uncultured PAO species from the three genera with clear niche differentiation in the utilization of different carbon sources and involvement in the denitrification process. Additionally, we observed several physiological differences among species of the same genus, indicating variations in niche specialization. This suggests that biological P removal and other processes in full-scale WWTPs are carried out by a complex and diverse PAO community that together ensures stable plant performance.IMPORTANCEThe current understanding of the ecology and physiology of polyphosphate-accumulating organisms (PAOs) is mostly based on Candidatus Accumulibacter, primarily studied in enriched lab-scale studies. Recent taxonomic reclassification revealed that the most studied Ca. Accumulibacter species are either not present or present in low abundance in full-scale wastewater treatment plants (WWTPs). This raises concerns that knowledge from lab-scale studies may not apply to species in full-scale plants. Additionally, the indication of a distinct PAO physiology in Candidatus Phosphoribacter compared to Ca. Accumulibacter and the other abundant PAO Ca. Azonexus poses further questions about the accuracy of the current PAO model. Here, we show that in full-scale plant species from Ca. Accumulibacter, Ca. Azonexus, and Ca. Phosphoribacter always co-exist, and they have distinct niche separations in terms of carbon source utilization and the use of electron acceptors. This co-existence and metabolic diversity indicate that a complex microbial community is crucial for efficient phosphorus removal in full-scale WWTPs.}, }
@article {pmid40812274, year = {2025}, author = {Bermúdez, JR and Metian, M and Swarzenski, PW and Bank, MS and Bjorøy, &#xd8; and Cajas, J and Bucheli, R and González-Muñoz, R and Lynch, J and Piguave, E and Vargas, N and Vilela, K and Calle, L and Borbor-Cordova, MJ and Gaibor, N}, title = {Marine microplastics on the rise in the Eastern Tropical Pacific: Abundance doubles in 11 years and a ten-fold increase is projected by 2100.}, journal = {Marine pollution bulletin}, volume = {221}, number = {}, pages = {118437}, doi = {10.1016/j.marpolbul.2025.118437}, pmid = {40812274}, issn = {1879-3363}, abstract = {Plastic abundance in the ocean has increased systematically since the mid-20th century. Here we present a time-series dataset of microplastic abundance collected at several stations located in the Eastern Tropical Pacific Ocean off Ecuador from 2008 to 2018. The data reveals a significant and sustained increase in the abundance of microplastics over time across all sampling sites; this implies a homogeneous and sustained input, which likely also occurs at other coastal and marine ecosystems. Fiber strands were the most common microplastic observed, while polyethylene and polypropylene were the principal polymers identified by μFTIR analysis. A forecast model of the time-series data predicted that microplastics will be 3.2, 5.1 and 9.7 times more abundant in 2030, 2050 and 2100, respectively, relative to 2008 observations. These results provide insights into the decade-plus trend in microplastic abundance observed in coastal waters, which have important implications for future marine plastic pollution projections and associated ecosystem impacts.}, }
@article {pmid40812176, year = {2025}, author = {Ramirez-Villacis, DX and Leon-Reyes, A and Pieterse, CMJ and Raaijmakers, JM}, title = {Born to rewild: Reconnecting beneficial plant-microbiome alliances for resilient future crops.}, journal = {Cell host &amp; microbe}, volume = {33}, number = {8}, pages = {1241-1255}, doi = {10.1016/j.chom.2025.06.017}, pmid = {40812176}, issn = {1934-6069}, abstract = {Plant domestication is a coevolutionary process shaped by human selection, favoring traits supporting modern-day agriculture. This process has reduced genetic diversity and fixed alleles for desirable traits, coinciding with changes in agricultural practices, particularly soil tilling, crop monocultures, and the (over)use of fertilizers and pesticides. The combined effects-collectively termed "domestication syndrome"-have contributed to the homogenization of soil and plant-associated microbial communities, reducing diversity and disrupting beneficial plant-microbiome alliances. Microbiome rewilding has uncovered ecological, genetic, and molecular principles underlying these depleted plant-microbiome partnerships. Studies have revealed ancestral microbial taxa enriched in wild crop relatives, plant genes, and metabolites critical for microbial recruitment, as well as the potential of reintroducing microbes to enhance nutrient uptake, pathogen resistance, and stress tolerance. These findings offer models for restoring such interactions in modern crops. We review the current state of crop microbiome rewilding and highlight how these discoveries are instrumental for designing resilient crop systems.}, }
@article {pmid40812095, year = {2025}, author = {Rodríguez-González, L and Santás-Miguel, V and Alexandropoulou, S and Rousk, J}, title = {Effects of salinisation on Cu-contaminated vineyard soils: Assessment of changes in microbial communities and resistance to salt, Cu, and antibiotics.}, journal = {Ecotoxicology and environmental safety}, volume = {303}, number = {}, pages = {118838}, doi = {10.1016/j.ecoenv.2025.118838}, pmid = {40812095}, issn = {1090-2414}, abstract = {Climate change increases the risk of soil salinisation in Southern European vineyards. In this study, six of those soils were experimentally salinised, half of which were contaminated with Cu, a widely used fungicide. Changes in soil microbiota were assessed, including bacterial and fungal growth, respiration, carbon use efficiency calculation, and microbial community phospholipid fatty acids composition. The study also investigated whether salinisation induced a shift in the bacterial community toward increased tolerance to salt, Cu, and the antibiotics tetracycline and vancomycin. Results showed that experimental salinisation decreased bacterial growth and respiration, increased fungal growth, and limited fungal, bacterial, and microbial biomass. These effects were strongest in soils with high initial Cu content. In such soils, tolerance to salt stress was more pronounced, and salt-induced tolerance to vancomycin was observed. In contrast, tolerances to Cu and tetracycline antibiotic were not significantly increased by either Cu or salt. Subsequently, the soils underwent leaching, and analyses were repeated. Most changes in microbial parameters and tolerances were reversed, with soil texture being a particularly influential factor. However, leaching caused Cu tolerance in soils that had been salinised and had high Cu content to be greater than in soils that had not been salinised, regardless of whether they had high or low Cu content. After leaching, vancomycin tolerance also became positively correlated with soil Cu content in soils with low Cu levels. This preliminary study explored salinisation effects on soils, revealing possible bacterial resistance linked to past conditions and microbial shifts. Further research is needed to broaden the dataset and explore the underlying mechanisms and microbial species involved.}, }
@article {pmid40811531, year = {2025}, author = {Guo, D and Liu, Z and Raaijmakers, JM and Xu, Y and Yang, J and Erb, M and Zhang, J and Zhu, YG and Xu, J and Hu, L}, title = {Linalool-triggered plant-soil feedback drives defense adaptation in dense maize plantings.}, journal = {Science (New York, N.Y.)}, volume = {389}, number = {6761}, pages = {eadv6675}, doi = {10.1126/science.adv6675}, pmid = {40811531}, issn = {1095-9203}, abstract = {High planting density boosts crop yields but also heightens pest and pathogen risks. How plants adapt their defenses under these conditions remains unclear. In this study, we reveal that maize enhances its defense in high-density conditions through a plant-soil feedback mechanism triggered by the leaf volatile linalool. Linalool activates jasmonate signaling in neighboring plants and promotes root exudation of benzoxazinoids, especially 2-(2-hydroxy-4,7-dimethoxy-1,4-benzoxazin-3-one)-β-d-glucopyranose (HDMBOA-Glc). These exudates in turn reshape the rhizosphere microbiome composition to favor growth of specific bacterial taxa that trigger broad-spectrum resistance, albeit at the cost of maize growth. This microbiome-driven feedback loop is governed by salicylic acid signaling. Our findings uncover intricate chemical signaling in high-density cropping, which is instrumental for improving soil health and designing sustainable strategies that balance the trade-off between plant growth and defense.}, }
@article {pmid40810014, year = {2025}, author = {Fischer, MH and Rzepczynska, A and Kjøller, R}, title = {Taxonomic diversity in the global wheat phyllosphere mycobiome - a meta analysis.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1597807}, pmid = {40810014}, issn = {1664-462X}, abstract = {Wheat (Triticum aestivum L.) is a major crop grown on all continents. Due to environmental concerns, it is desirable to reduce the inputs of both chemical pesticides and inorganic fertilizers. However, yield reduction must be expected when switching to low-input systems. To mitigate such losses, the use of natural or introduced microbiomes may provide the key to maintaining sustainable yield. Phyllosphere fungi, both endophytic and phylloplane-associated, colonize aboveground plant structures, some of which have the potential to mitigate biotic and abiotic stressors. A first step toward realizing the potential of the wheat microbiome is to map the current knowledge on wheat phyllosphere fungi. This meta-analysis aims to map the diversity and abundance of fungal taxa associated with the wheat phyllosphere across global wheat-producing areas. To this end, we searched previous published literature and retrieved fungal community data from relevant studies. Retrieved studies included both culturing-based and metabarcoding amplicon sequence-based studies. We retrieved and analyzed 33 studies from five regions across the world, which differed greatly in their taxonomic composition. Across all regions, we found that while the majority of identified genera were unique to individual studies, some genera occurred across all five wheat growing regions, specifically Alternaria, Aspergillus, Bipolaris, Candida, Chaetomium, Cladosporium, Epicoccum, Fusarium, Nigrospora, Penicillium, Pyrenophora, Stemphylium and Trichoderma. Furthermore, we identified that while community composition differed between wheat growing regions, the identification method used was the most significant factor determining the depiction of community composition. We also highlight a lack of research in important wheat growing regions that are important for global wheat production. These considerations and other knowledge gaps are used to pinpoint future research.}, }
@article {pmid40809124, year = {2024}, author = {Trego, A and Palmeiro-Sánchez, T and Graham, A and Ijaz, UZ and O'Flaherty, V}, title = {First evidence for temperature's influence on the enrichment, assembly, and activity of polyhydroxyalkanoate-synthesizing mixed microbial communities.}, journal = {Frontiers in systems biology}, volume = {4}, number = {}, pages = {1375472}, pmid = {40809124}, issn = {2674-0702}, abstract = {Polyhydroxyalkanoates (PHA) are popular biopolymers due to their potential use as biodegradable thermoplastics. In this study, three aerobic sequencing batch reactors were operated identically except for their temperatures, which were set at 15 °C, 35 °C, and 48 °C. The reactors were subjected to a feast-famine feeding regime, where carbon sources are supplied intermittently, to enrich PHA-accumulating microbial consortia. The biomass was sampled for 16S rRNA gene amplicon sequencing of both DNA (during the enrichment phase) and cDNA (during the enrichment and accumulation phases). All temperatures yielded highly enriched PHA-accumulating consortia. Thermophilic communities were significantly less diverse than those at low or mesophilic temperatures. In particular, Thauera was highly adaptable, abundant, and active at all temperatures. Low temperatures resulted in reduced PHA production rates and yields. Analysis of the microbial community revealed a collapse of community diversity during low-temperature PHA accumulation, suggesting that the substrate dosing strategy was unsuccessful at low temperatures. This points to future possibilities for optimizing low-temperature PHA accumulation.}, }
@article {pmid40804956, year = {2025}, author = {Idres, T and Ibrahim, NA and Lamara, A and Boudjellaba, S and Derguini, A and Basher, NS and Temim, S and Aleissa, MS and Chebloune, Y}, title = {Epidemiological Insights into Maedi-Visna Virus in Algeria: First National Seroprevalence Survey and Risk Factor Profiling in Sheep Herds.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {15}, pages = {}, pmid = {40804956}, issn = {2076-2615}, support = {IMSIU- DDRSP2502//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)/ ; }, abstract = {Maedi-visna virus (MVV), a small ruminant lentivirus causing chronic multisystemic disease in sheep, poses significant economic burdens due to reduced productivity and a lack of effective treatments. Despite its worldwide prevalence, epidemiological data from Algeria remain absent. This first national seroprevalence study aimed to elucidate MVV distribution, risk factors, and transmission dynamics in Algerian sheep herds. A cross-sectional survey of 1400 sheep across four regions (East, Center, West, South) was conducted, with sera analyzed via indirect ELISA (IDvet). Risk factors (geography, age, sex, breed, farming system) were evaluated using chi-square tests and Cramer's V. Overall seroprevalence was 9.07% (95% CI: 7.57-10.57), with significant variation by sex (females: 20.44% vs. males: 3.68%; p < 0.05), age (1-5 years: 6.86% vs. <1 year: 0.29%; p = 0.01), and region (Central: 3.36% vs. Eastern: 0.86%; p < 0.05). Notably, no association was found with breed or farming system (p ≥ 0.08), contrasting prior studies and suggesting region-specific transmission dynamics. Females exhibited heightened seropositivity, implicating prolonged herd retention and vertical transmission risks. Geographic disparities highlighted industrialized farming in central Algeria as a potential transmission amplifier. Strikingly, seronegative animals in high-prevalence herds hinted at genetic resistance, warranting further investigation. This study provides foundational insights into MVV epidemiology in North Africa, underscoring the need for targeted surveillance, ewe-focused control measures, and genetic research to mitigate transmission. The absence of prior national data elevates its significance, offering actionable frameworks for resource-limited settings and enriching the global understanding of SRLV heterogeneity.}, }
@article {pmid40803134, year = {2025}, author = {Wu, F and Campbell, BC and Greenfield, P and Hose, GC and Midgley, DJ and George, SC}, title = {There and back again: Genomic insights into microbial life in a recirculating petroleum refinery wastewater biotreatment system.}, journal = {Microbiological research}, volume = {301}, number = {}, pages = {128299}, doi = {10.1016/j.micres.2025.128299}, pmid = {40803134}, issn = {1618-0623}, abstract = {Petroleum refinery wastewater biotreatment relies on microbes to remediate carbon, nitrogen, and sulfur compounds, yet their life strategies and ecological roles remain unclear. This study characterises the ecological functions of 20 metagenome-assembled genomes (MAGs) from a full-scale petroleum refinery wastewater treatment plant in southern China. The taxonomic identity, nutrient metabolism genes (including C/N/S cycling), carbohydrate-active enzymes, and CRISPR-Cas systems of these MAGs were analysed. The recovered MAGs represented bacteria primarily from the Pseudomonadota and Bacteroidota phyla. The major carbon sources for the represented organisms are likely aromatic and aliphatic compounds, as well as carbohydrates including peptidoglycan, chitin, and starch. Almost all MAGs contained genes for nitrate or nitrite reduction, while metabolic pathways for sulfur metabolism were generally less prevalent. Meiothermus sp. bin.89 was the most metabolically versatile MAG. This organism possessed genes that allowed it to recycle biomass, break down aliphatic and monoaromatic compounds, and perform anaerobic respiration using nitrate. However, it was likely the most susceptible to viral predation, as indicated by the high abundance of CRISPR spacers. Overall, the results revealed that stress-tolerant ecological traits were common among organisms in this microbiome, showcasing the ability of the microbes to obtain carbon from aromatic and aliphatic compounds. This study provides a substantial contribution towards future efforts in optimising microbiome stability for pollutant removal in petroleum refinery wastewater biotreatment systems.}, }
@article {pmid40800619, year = {2025}, author = {van Eijnatten, AL and van Zon, L and Manousou, E and Bikineeva, M and Wubs, ERJ and van der Putten, WH and Morriën, E and Dutilh, BE and Snoek, LB}, title = {SpeSpeNet: an interactive and user-friendly tool to create and explore microbial correlation networks.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf036}, pmid = {40800619}, issn = {2730-6151}, abstract = {Correlation networks are commonly used to explore microbiome data. In these networks, nodes are microbial taxa and edges represent correlations between their abundances. As clusters of correlating taxa (co-abundance clusters) often indicate a shared response to environmental drivers, network visualization contributes to the system understanding. Currently, most tools for creating and visualizing co-abundance networks from microbiome data either require the researcher to have coding skills or are not user-friendly, with high time expenditure and limited customizability. Furthermore, existing tools lack a focus on the association between environmental drivers and the structure of the microbiome, even though many edges in correlation networks can be understood through a shared association of two taxa with the environment. For these reasons, we developed SpeSpeNet (Species-Species Network, https://tbb.bio.uu.nl/SpeSpeNet), a practical and user-friendly R-shiny tool to construct and visualize correlation networks from taxonomic abundance tables. The details of data preprocessing, network construction, and visualization are automated, require no programming ability for the web version, and are highly customizable, including associations with user-provided environmental data. Here, we present the details of SpeSpeNet and demonstrate its utility using three case studies.}, }
@article {pmid40800617, year = {2025}, author = {Fuschi, A and Merlotti, A and Remondini, D}, title = {Microbiome data: tell me which metrics and I will tell you which communities.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf125}, pmid = {40800617}, issn = {2730-6151}, abstract = {In microbial community studies, analyzing diversity is crucial for uncovering ecological complexity. However, the intrinsic characteristics of Next-gen sequencing data challenge the use of Euclidean metrics for estimating proximity and correlation. Consequently, a variety of distance measures have been developed within ecological frameworks. In this study, we compare several of these metrics-including Bray-Curtis, Canberra, Jensen-Shannon, Hellinger, Euclidean, and Aitchison distances-demonstrating how the choice of metric can significantly influence the interpretation of microbial community structures. Among these, Aitchison distance specifically defined for compositional data shows markedly different behavior from the others, highlighting different features related to the data. We consider two real-world examples: the human gut microbiome sampled using 16S rRNA sequencing with multiple measurements for different patients (G-HMP2) and urban sewage environmental metagenomes collected over time at different sites through shotgun sequencing (E-WADES). We show that, for the same dataset-independently on the sequencing technique or on the sampling context-the community structure depends strongly on the choice of specific metrics. This can be explained by the mathematical properties of the chosen metrics and the specific characteristics of microbiome data, namely their high heterogeneity in species abundance. This provides clear insights into how distance metrics influence interpretation and assists in choosing the most appropriate one for the study objectives.}, }
@article {pmid40799503, year = {2025}, author = {Parret, L and Simoens, K and De Vrieze, J and Smets, I}, title = {BIO-SPEC: An open-source bench-top parallel bioreactor system.}, journal = {HardwareX}, volume = {23}, number = {}, pages = {e00670}, pmid = {40799503}, issn = {2468-0672}, abstract = {The BIO-SPEC is an open-source, cost-effective, and modular bench-top bioreactor system designed for batch, sequencing batch, and chemostat cultivation. Featuring thermoelectric condensers to eliminate the need for a chiller, it ensures stable long-term operation. Controlled by a Raspberry Pi, the BIO-SPEC offers flexibility in headplate design, gas supply, and feeding strategies, making it a versatile alternative to high-cost commercial systems. This paper details the design, construction, and validation of the BIO-SPEC system, demonstrating its potential to advance microbiology and bioprocessing research through accessible and reliable hardware at a fraction of the cost of commercial systems.}, }
@article {pmid40797302, year = {2025}, author = {Baborski, A and Barth, SA and Jung, EM and Bloos, F and Rödel, J and Löffler, B and Bauer, M and Busch, A}, title = {Surviving antibiotic treatment as a gut bacterium: genomic characterization of an Enterobacter cloacae.}, journal = {BMC genomic data}, volume = {26}, number = {1}, pages = {56}, pmid = {40797302}, issn = {2730-6844}, abstract = {Enterobacter cloacae complex is a group of common opportunistic pathogens on intensive care units. On intensive care units sepsis is treated with high doses of antibiotics. This treatment does not only eliminate pathogenic bacteria but parts of the microbiome community as well. This leads to an imbalance of the gut microbiome. However, some bacteria can survive such treatment due to certain survival and resistance mechanisms. Not only antibiotic resistance mechanisms but also forming strong communities via biofilm formation promotes cell survival. Here, we investigated the properties of the isolate AT70PIP076 from a sepsis patient treated with piperacillin and tazobactam. After biochemical analysis and MALDI-TOF analysis, the strain was found to be Enterobacter cloacae. In addition to in vitro, antimicrobial susceptibility testing the genome was further investigated in situ regarding antibiotic resistance. Further live/dead staining was performed, and the biofilm formation was investigated using confocal laser microscopy (cLSM). The genome shows the presence of biofilm-associated genes EU554560, bcsABZC_AP010953, ehaB, KF662843, and crl. The understanding of the underlying mechanism of survival of potential pathogens might contribute to elucidate potential treatment options.ObjectivesGenomic analysis of a bacterium that can survive antibiotic treatment within the gut of an antibiotictreated patient to elucidate survival and resistance mechanisms.Data descriptionThe isolate AT70PIP076 was isolated in 2021 from feces collected from a patient treated with Piperacillin and tazobactam. Whole genome DNA was isolated using the Nextera DNA Flex microbial colony extraction protocol and the Nextera Flex DNA preparation kit according to the manufacturer's instructions. Following paired-end sequencing was performed on the MiSeq platform (Illumina, Inc., San Diego, CA, USA) using a 300-cycle MiSeq reagent kit and a read length of 151 bp. Contamination check and identification of 16 S RNA sequences was done by using ContESt16S. The genomic sequence contained 4,988,237 bp and the G + C content is represented at 54.80%. This genome and its associated data set will serve as a useful resource for further analyses.}, }
@article {pmid40797046, year = {2025}, author = {Wei, L and Chen, S and Qin, Z and Pan, N and Lan, M and Zhang, T and He, R and Liang, H and Deng, W and Mo, C and Yu, K}, title = {Responses of the Coral Symbiont Cladocopium goreaui to Extreme Temperature Stress in Relatively High-Latitude Reefs, South China Sea.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {88}, pmid = {40797046}, issn = {1432-184X}, abstract = {Global climate change has led to frequent extreme temperature events in oceans. Corals are susceptible to extreme high-temperature stress in summer and extreme low-temperature stress in winter in the relatively high-latitude reef areas of the South China Sea (SCS). The most abundant symbiotic coral Symbiodiniaceae in the higher-latitude reefs of the SCS is Cladocopium goreaui, predominantly associating with dominant coral hosts such as Acropora and Porites. However, to date, relatively few studies have focused on the response and mechanism of C. goreaui to the extreme high- and low-temperature stress. In this study, the responses and regulatory mechanisms of the dominant C. goreaui to extreme high- and low-temperature stress were investigated based on physiological indexes, transmission electron microscopy (TEM), and transcriptome analysis. The results showed that (1) under 34 °C heat stress, the disintegration of thylakoids triggered photosynthetic collapse in C. goreaui; survival is enabled through metabolic reprogramming that upregulates five protective pathways and redirects energy via pentose/glucuronate shunting to sustain ATP homeostasis, revealing a trade-off between damage containment and precision energy governance under thermal extremes. (2) Low temperature exposure induced suppression of maximum quantum yield (Fv/Fm), compounded by glutathione pathway inhibition, crippling ROS scavenging. The transcriptome results revealed that C. goreaui prioritizes gene fidelity maintenance under low temperature stress. These findings reveal that energy allocation trade-offs constitute the core strategy of C. goreaui temperature response: prioritizing energy maintenance under high-temperature stress, while safeguarding genetic fidelity at the expense of antioxidant defense under low-temperature stress.}, }
@article {pmid40796291, year = {2025}, author = {Mohr, AE and Mach, N and Pugh, J and Grosicki, GJ and Allen, JM and Karl, JP and Whisner, CM}, title = {Mechanisms underlying alterations of the gut microbiota by exercise and their role in shaping ecological resilience.}, journal = {FEMS microbiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuaf037}, pmid = {40796291}, issn = {1574-6976}, abstract = {The gut microbiota (GM) is a dynamic ecosystem intricately linked to human health, including metabolic, immune, endocrine, and gastrointestinal functions. Exercise is recognized as a significant modifier of this microbial ecosystem, yet the complexities of this relationship are underexplored. Here, we delve into the multifaceted interactions between structured physical activity and the GM, emphasizing the role of exercise-induced stressors in shaping microbial composition and function. Unique to our review, we discuss the acute effects of different forms of exercise-induced stress on the GM and explore how these responses may influence long-term adaptability, stability, and resilience. Furthermore, we address critical junctures in microbial dynamics leading to shifts between different stable states. Finally, we explore the implications of host-controlled factors such as diet, exercise training, and nutritional supplementation in modulating the microbial community in the gut to optimize athletic performance. We conclude that while the potential to harness the synergistic effects of exercise-induced stressors, dietary interventions, and microbial adaptations appears promising, current evidence remains preliminary, highlighting the need for additional targeted research to guide future strategies that manipulate the GM for optimal health and athletic performance.}, }
@article {pmid40795952, year = {2025}, author = {Pluer, BD and Travis, J}, title = {The Digestive Microbiome Diversity of the Least Killifish, Heterandria formosa, and Its Implications for Host Adaptability to Varying Trophic Levels.}, journal = {Environmental microbiology reports}, volume = {17}, number = {4}, pages = {e70164}, pmid = {40795952}, issn = {1758-2229}, support = {G2020031598770049//Sigma Xia/ ; //Florida State University/ ; }, abstract = {Symbiotic microbes, in associations with aquatic hosts, aid in the acquisition of nutrients, breakdown xenobiotics, and contribute to immune system function. If associations with microbial communities facilitate host adaptation to different ecosystems, understanding the important ecological factors that act as drivers of differences among conspecific populations' microbiomes can help conservation efforts to promote beneficial interactions between fish and their microbiome for freshwater fish species facing rapid environmental changes. Here we describe the microbial communities in the gut of a freshwater fish, Heterandria formosa, in spring habitats using 16S rRNA sequencing. We quantified microbiota composition and diversity among springs ranging from oligotrophic to near eutrophic to determine the extent to which the microbiota are associated with different environmental conditions. We found higher microbial richness at sites with lower nutrient load stress. At more eutrophic sites, we detected the potential for increased metabolic capacity for pollutant degradation in the associated microbiota. We noted greater phylogenetic similarity between more environmentally similar sites, supporting previous evidence that the microbiota of freshwater fish is influenced by site water chemistry. Our findings bring to light microbial taxa and pathways that might play critical roles in the bioremediation of stressful environmental conditions.}, }
@article {pmid40795673, year = {2025}, author = {Cano, NO and Borrego, CM and Radjenovic, J}, title = {Irreversible inactivation of multidrug-resistant Gram-positive bacteria using S-functionalized graphene sponge anode.}, journal = {Water research}, volume = {287}, number = {Pt A}, pages = {124300}, doi = {10.1016/j.watres.2025.124300}, pmid = {40795673}, issn = {1879-2448}, abstract = {Graphene sponges functionalized with sulfur were employed as anodes and coupled with N-doped graphene sponge cathodes for electrochemical inactivation of a Gram-positive multidrug-resistant bacterium Enterococcus gallinarum in drinking water. The application of 43.5 A m[-2] resulted in 2.3 log removal of E. gallinarum in one-pass, flow-through mode, at 2.7 kWh m[-3] of energy demand. In the case of non-functionalized graphene sponge electrode, 1.8 log removal of E. gallinarum required 3.8 kWh m[-3]. Moreover, no bacterial regrowth was measured in any of the experiments conducted during storage of the treated samples for 16 h. Indeed, the storage of samples led to an additional 1 log removal for the S-functionalized graphene sponge anode, somewhat higher compared with the 0.7 log removal observed for the non-functionalized electrode. To further decrease the energy consumption and exploit the capacitance of graphene, the flow-through system was operated with intermittent current. Application of 43.5 A m[-2] in an intermittent mode, led to a similar, 2.4 log removal of E. gallinarum but with a significantly reduced energy consumption, from 2.7 with continuous current to 1.8 kWh m[-3]. Scanning electron microscopy analyses of the inactivated bacteria confirmed the irreversible damage to the cell walls due to low-voltage electroporation that co-occurred with the presence of abundant cellular debris resulting from the leakage of intracellular material. Using two sequential reactors equipped with the S-doped graphene sponge anode and N-doped graphene sponge cathode operated at 43.5 A m[-2] of anodic current density resulted in an overall 5.8 log removal of E. gallinarum (including storage) from drinking water, and at the energy consumption of 5.4 kWh m[-3] (i.e., electric energy per order of 0.94 kWh m[-3]). Overall, this study demonstrated the feasibility of using an S-functionalized graphene sponge anode for chlorine-free electrochemical inactivation of a multidrug resistant Gram-positive bacterium from low conductivity drinking water.}, }
@article {pmid40795332, year = {2025}, author = {Aguilera-Campos, KI and Boisard, J and Törnblom, V and Jerlström-Hultqvist, J and Behncké-Serra, A and Cotillas, EA and Stairs, CW}, title = {Anaerobic breviate protist survival in microcosms depends on microbiome metabolic function.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf171}, pmid = {40795332}, issn = {1751-7370}, abstract = {Anoxic and hypoxic environments serve as habitats for diverse microorganisms, including unicellular eukaryotes (protists) and prokaryotes. To thrive in low-oxygen environments, protists and prokaryotes often establish specialized metabolic cross-feeding associations, such as syntrophy, with other microorganisms. Previous studies show that the breviate protist Lenisia limosa engages in a mutualistic association with a denitrifying Arcobacter bacterium based on hydrogen exchange. Here, we investigate if the ability to form metabolic interactions is conserved in other breviates by studying five diverse breviate microcosms and their associated bacteria. We show that five laboratory microcosms of marine breviates live with multiple hydrogen-consuming prokaryotes that are predicted to have different preferences for terminal electron acceptors using genome-resolved metagenomics. Protist growth rates vary in response to electron acceptors depending on the make-up of the prokaryotic community. We find that the metabolic capabilities of the bacteria and not their taxonomic affiliations determine protist growth and survival and present new potential protist-interacting bacteria from the Arcobacteraceae, Desulfovibrionaceae, and Terasakiella lineages. This investigation uncovers potential nitrogen and sulfur cycling pathways within these bacterial populations, hinting at their roles in syntrophic interactions with the protists via hydrogen exchange.}, }
@article {pmid40790855, year = {2025}, author = {Xie, R and Yu, H and Wang, Y and Leung, KY and Habimana, O}, title = {Synergistic effects of sodium acetate and calcium on structure and function in multispecies biofilms.}, journal = {Biofouling}, volume = {}, number = {}, pages = {1-16}, doi = {10.1080/08927014.2025.2545940}, pmid = {40790855}, issn = {1029-2454}, abstract = {This investigation scrutinizes the manner in which sodium acetate (SA) and calcium cations (Ca[2+]) independently and collaboratively affect biofilm development. Confocal microscopy revealed that SA (1 mM) increased biofilm biovolume (5.5-fold) and thickness by enhancing microbial growth, while Ca[2+] (1.5 mM) stabilized the matrix via EPS crosslinking. Combined, SA and Ca[2+] synergistically boosted biovolume (1.5-fold) and thickness (21.3 µm) compared to SA alone. 16S rRNA sequencing showed SA-enriched Actinobacteriota (11%) and exopolysaccharide-producing Brevifollis, whereas Ca[2+] improved surface coverage (22.3%). Functional predictions linked SA to purine degradation and Ca[2+] to fatty acid oxidation, aligning with EPS modifications. These findings highlight how carbon sources and divalent cations collaboratively shape biofilm resilience, offering insights for biofilm management in environmental, industrial, and medical settings where SA and Ca[2+] gradients exist.}, }
@article {pmid40789383, year = {2025}, author = {Rout, AK and Rout, SS and Panda, A and Tripathy, PS and Kumar, N and Parida, SN and Dey, S and Dash, SS and Behera, BK and Pandey, PK}, title = {Potential applications and future prospects of metagenomics in aquatic ecosystems.}, journal = {Gene}, volume = {}, number = {}, pages = {149720}, doi = {10.1016/j.gene.2025.149720}, pmid = {40789383}, issn = {1879-0038}, abstract = {Metagenomics plays a vital role in advancing our understanding of microbial communities and their functional contributions in various ecosystems. By directly sequencing DNA from environmental samples-such as soil, water, air, and the human body-metagenomics enables the identification of previously uncultivable or unknown microorganisms, offering key insights into their ecological functions. Beyond taxonomic classification, metagenomic analyses reveal functional genes and metabolic pathways, facilitating the discovery of enzymes, bioactive compounds, and other molecules with applications in agriculture, biotechnology, and medicine. This review discusses the wide-ranging applications of metagenomics in environmental monitoring, including sample collection, high-throughput sequencing, and data analysis and interpretation. We review different sequencing platforms, library preparation methods, and advanced bioinformatics tools used for quality control, sequence assembly, and both taxonomic and functional annotation. Special focus is given to the role of metagenomics in evaluating microbial responses to environmental stress, contaminant degradation, disease emergence, and climate change. The use of microbial bioindicators for aquatic ecosystem monitoring and toxicological assessments is also examined. A comprehensive evaluation of current bioinformatics pipelines is provided for their effectiveness in processing large-scale metagenomic datasets. As global environmental pressures intensify, integrative meta-omics approaches, including whole-genome metagenomics, will be crucial for understanding the complexity, functions, and dynamics of microbiomes in both natural and affected ecosystems.}, }
@article {pmid40788461, year = {2025}, author = {Torres, MC and Breyer, GM and da Silva, MERJ and de Itapema Cardoso, MR and Siqueira, FM}, title = {Metagenomic approaches for the quantification of antibiotic resistance genes in swine wastewater treatment system: a systematic review.}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {816}, pmid = {40788461}, issn = {1573-4978}, support = {408693/2022-3//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico,Brazil/ ; }, mesh = {Swine ; *Wastewater/microbiology ; Animals ; *Metagenomics/methods ; *Drug Resistance, Microbial/genetics ; Metagenome/genetics ; Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Water Purification/methods ; Computational Biology/methods ; Anti-Bacterial Agents/pharmacology ; }, abstract = {This systematic review aims to identify the metagenomic methodological approaches employed for the detection of antimicrobial resistance genes (ARGs) in swine wastewater treatment systems. The search terms used were metagenome AND bacteria AND ("antimicrobial resistance gene" OR resistome OR ARG) AND wastewater AND (swine OR pig), and the search was conducted across the following electronic databases: PubMed, Scopus, ScienceDirect, Web of Science, Embase, and Cochrane Library. The search was limited to studies published between 2020 and 2024. Of the 220 studies retrieved, eight met the eligibility criteria for full-text analysis. The number of publications in this research area has increased in recent years, with China contributing the highest number of studies. ARGs are typically identified using bioinformatics pipelines that include steps such as quality trimming, assembly, metagenome-assembled genome (MAG) reconstruction, open reading frame (ORF) prediction, and ARG annotation. However, comparing ARGs quantification across studies remains challenging due to methodological differences and variability in quantification approaches. Therefore, this systematic review highlights the need for methodological standardization to facilitate comparison and enhance our understanding of antimicrobial resistance in swine wastewater treatment systems through metagenomic approaches.}, }
@article {pmid40788124, year = {2025}, author = {Ferreira, J and Rediers, H}, title = {Draft genome sequences of 25 candidate biocontrol bacteria against Phytophthora cactorum.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0050225}, doi = {10.1128/mra.00502-25}, pmid = {40788124}, issn = {2576-098X}, abstract = {To provide a biocontrol solution for managing the phytopathogen Phytophthora cactorum, bacteria were tested for antagonistic activity in vitro and in planta. This paper presents the draft genomes of 25 candidate biocontrol organisms, providing a solid foundation to decipher the underlying mechanisms of their antagonistic activity.}, }
@article {pmid40781093, year = {2025}, author = {Kojima, CY and Henson, MW and Coelho, JT and Lanclos, VC and Bañuelas, D and Thrash, JC}, title = {Metagenomes and 1,313 metagenome-assembled genomes from a northern Gulf of Mexico coastal time series.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1388}, pmid = {40781093}, issn = {2052-4463}, support = {OCE-1931113//National Science Foundation (NSF)/ ; Simons Investigator in Aquatic Microbial Ecology Award//Simons Foundation/ ; Faculty Innovation Research Award//USC | Wrigley Institute for Environmental Studies, University of Southern California (USC Wrigley Institute for Environmental Studies)/ ; }, mesh = {Gulf of Mexico ; *Metagenome ; *Water Microbiology ; }, abstract = {Coastal and estuarine systems are hotspots of microbial diversity, activity, and biogeochemical cycling. Despite their importance, we have few comprehensive datasets of microbial populations across space and time from these ecosystems. To improve our understanding of these systems, we generated metagenomes averaging 46 M reads per sample (nearly 389 Gbp total) from four coastal/estuarine locations in the northern Gulf of Mexico across seven timepoints spanning nine months. Using standard methodology combined with a unique assembly and binning approach called subtractive iterative assembly (SIA), we generated 1,313 non-redundant metagenome-assembled genomes (MAGs) with 5% contamination or less and at least 75% completeness. We produced approximately a third of the MAGs through SIA. Actinobacteria and Proteobacteria were represented most. We recovered MAGs of great ecological significance including SAR11, Marine Group I (Thaumarcheaota), Marine Group II Euryarchaeota, SAR324, and Asgardarchaeota. We describe both our methodology using the SIA approach as well as the 28 metagenomes and 1,313 MAGs that provide a rich spatiotemporal dataset with which to study coastal and estuarine microbiology.}, }
@article {pmid40779244, year = {2025}, author = {Sung, J and Choi, DH and Lee, Y and Kim, JH and Shin, HH and Kim, YE and Choi, JH and Noh, JH and Gobler, CJ and Park, BS}, title = {Temperature-Driven Intraspecific Diversity in Paralytic Shellfish Toxin Profiles of the Dinoflagellate Alexandrium pacificum and Intragenic Variation in the Saxitoxin Biosynthetic Gene, sxtA4.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {87}, pmid = {40779244}, issn = {1432-184X}, support = {20163MFDS641//Ministry of Food and Drug Safety/ ; 20163MFDS641//Ministry of Food and Drug Safety/ ; 20163MFDS641//Ministry of Food and Drug Safety/ ; 20163MFDS641//Ministry of Food and Drug Safety/ ; 20163MFDS641//Ministry of Food and Drug Safety/ ; 20163MFDS641//Ministry of Food and Drug Safety/ ; 20163MFDS641//Ministry of Food and Drug Safety/ ; 20210469//Ministry of Oceans and Fisheries/ ; 20210469//Ministry of Oceans and Fisheries/ ; RS-2021-KS211530//Ministry of Oceans and Fisheries/ ; RS-2023-00209356//Ministry of Science and ICT, South Korea/ ; }, mesh = {*Dinoflagellida/genetics/metabolism/growth &amp; development ; *Saxitoxin/biosynthesis/genetics ; *Genetic Variation ; Temperature ; Harmful Algal Bloom ; Phylogeny ; }, abstract = {Alexandrium pacificum, a globally distributed dinoflagellate, is well-known for causing harmful algal blooms and producing Paralytic Shellfish Toxins (PSTs), a threat to marine life and human health. The frequency and intensity of Alexandrium blooms have increased in recent decades, driven, in some cases, by increasing temperatures. Here, we investigated the temperature-dependent (15 °C, 20 °C, 25 °C, and 30 °C) growth rates and paralytic shellfish toxin profiles of eight A. pacificum strains while concurrently examining differences in sequences of the saxitoxin biosynthetic gene, sxtA4. While maximum cell densities were lowest at 30 °C, toxin production per cell was highest at higher temperatures that inhibited growth, with greater diversity of toxin analogs peaking at 30 °C, as confirmed by the higher Shannon's diversity index obtained for the toxin profiles with the increasing temperatures. Furthermore, genetic analysis of the sxtA4 gene showed that greater genetic diversity-quantified by nucleotide diversity (π) ranging from 9.91 to 30.21 across strains-was positively correlated with this wider array of toxin analogs (Shannon's diversity index; p < 0.0001). Conserved regions within the gene were identified, suggesting that these regions may play important structural or functional roles in the saxitoxin biosynthetic pathway. These findings highlight the role of temperature, genetic diversity, and sxtA4 conserved regions in influencing toxin production and profiles in Alexandrium. Further research into the genetic mechanisms underlying saxitoxin biosynthesis will improve our understanding of Alexandrium's adaptability to changing temperatures. Such insights are essential for effective ecosystem management and safeguarding public health.}, }
@article {pmid40778431, year = {2025}, author = {Maillard, F and Beatty, BH and Geisen, S and Lara, E and Kennedy, PG}, title = {Secondary Decomposers Meet Their Predators: Decomposition Stage and Substrate Quality Jointly Structure Microbial Brown Food Webs During Fungal Necromass Decay.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e70060}, doi = {10.1111/mec.70060}, pmid = {40778431}, issn = {1365-294X}, support = {DEB #2038293//National Science Foundation/ ; }, abstract = {Mycelial residues, also known as fungal necromass, represent a substantial fraction of soil organic matter (SOM) pools in terrestrial ecosystems worldwide. Although microbial decomposers are increasingly recognised as key drivers of fungal necromass carbon stock formation, the diversity and composition of their microbial predators-and the roles these predators play in mediating fungal necromass decomposition-have not been explored to date. To address this gap, we produced fungal necromass of varying biochemical quality from Hyaloscypha bicolor and decomposed it in forest topsoil in Minnesota, USA, to investigate how microbial decomposer (bacteria and fungi) and predator (protists and nematodes) communities differ between soil and necromass. We also examined whether microbial predators influence the abundance of fungal necromass decomposers and affect necromass decomposition rates. Over two sampling times (4 and 12 weeks), necromass exhibited rapid early mass loss followed by reduced decay, with a higher stabilised mass in high melanin necromass. Microbial abundances were higher in necromass than in surrounding soil, especially in low melanin necromass. Community composition of both decomposers and their predators differed between soil and necromass and shifted markedly with necromass quality and decomposition stage. Predator community composition was linked to bacterial and fungal abundances at both early and late stages of decay and was marginally associated with decomposition rates. We conclude that fungal necromass acts as a microbial 'hotspot' not only for decomposers but also for their predators. These findings highlight the importance of microbial predator-decomposer interactions to better understand the formation of fungal-derived SOM.}, }
@article {pmid40775374, year = {2025}, author = {Krasenbrink, J and Hanson, BT and Weiss, AS and Borusak, S and Tanabe, TS and Lang, M and Aichinger, G and Hausmann, B and Berry, D and Richter, A and Marko, D and Mussmann, M and Schleheck, D and Stecher, B and Loy, A}, title = {Sulfoquinovose is exclusively metabolized by the gut microbiota and degraded differently in mice and humans.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {184}, pmid = {40775374}, issn = {2049-2618}, support = {10.55776/DOC69//Austrian Science Fund/ ; 10.55776/COE7//Austrian Science Fund/ ; 10.55776/DOC69//Austrian Science Fund/ ; 10.55776/COE7//Austrian Science Fund/ ; 10.55776/DOC69//Austrian Science Fund/ ; 10.3030/101205556//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; 395357507 "SFB1371"//Deutsche Forschungsgemeinschaft/ ; EvoGutHealth, 865615/ERC_/European Research Council/International ; 503-5-7-06.712_00 and 503-5-7-06.709_00//Germany Centre for Infection Research/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Humans ; Mice ; Mice, Inbred C57BL ; Feces/microbiology ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Male ; Hydrogen Sulfide/metabolism ; Female ; }, abstract = {BACKGROUND: Sulfoquinovose (SQ) is a green-diet-derived sulfonated glucose and a selective substrate for a limited number of human gut bacteria. Complete anaerobic SQ degradation via interspecies metabolite transfer to sulfonate-respiring bacteria produces hydrogen sulfide, which has dose- and context-dependent health effects. Here, we studied potential SQ degradation by the mammalian host and the impact of SQ supplementation on human and murine gut microbiota diversity and metabolism.<br><br>RESULTS: [13]CO2 breath tests with germ-free C57BL/6 mice gavaged with [13]C-SQ were negative. Also, SQ was not degraded by human intestinal cells in vitro, indicating that SQ is not directly metabolized by mice and humans. Addition of increasing SQ concentrations to human fecal microcosms revealed dose-dependent responses of the microbiota and corroborated the relevance of Agathobacter rectalis and Bilophila wadsworthia in cooperative degradation of SQ to hydrogen sulfide via interspecies transfer of 2,3-dihydroxy-1-propanesulfonate (DHPS). Similar to the human gut microbiome, the genetic capacity for SQ or DHPS degradation is sparsely distributed among bacterial species in the gut of conventional laboratory mice. Escherichia coli and Enterocloster clostridioformis were identified as primary SQ degraders in the mouse gut. SQ and DHPS supplementation experiments with conventional laboratory mice and their intestinal contents showed that SQ was incompletely catabolized to DHPS. Although some E. clostridioformis genomes encode an extended sulfoglycolytic pathway for both SQ and DHPS fermentation, SQ was only degraded to DHPS by a mouse-derived E. clostridioformis strain.<br><br>CONCLUSIONS: Our findings suggest that SQ is solely a nutrient for the gut microbiota and not for mice and humans, emphasizing its potential as a prebiotic. SQ degradation by the microbiota of conventional laboratory mice differs from the human gut microbiota by absence of DHPS degradation activity. Hence, the microbiota of conventional laboratory mice does not fully represent the SQ metabolism in humans, indicating the need for alternative model systems to assess the impact of SQ on human health. This study advances our understanding of how individual dietary compounds shape the microbial community structure and metabolism in the gut and thereby potentially influence host health. Video Abstract.}, }
@article {pmid40774531, year = {2025}, author = {Morales, MLP and Capurro, L and Bordert, F and Chenia, H and Alonso, C and Bentos, FR and Boccardi, L and Brugnoli, E and They, NH and Agostini, VO and Leães Pinho, GL}, title = {Evaluating macrophyte extracts as eco-friendly antifouling additives for freshwater made-man structures: a field assessment.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126952}, doi = {10.1016/j.envpol.2025.126952}, pmid = {40774531}, issn = {1873-6424}, abstract = {Biofouling on artificial aquatic surfaces yields substantial economic losses and operational challenges. Traditional antifouling strategies often rely on synthetic chemical coatings, which have harmful environmental impacts, thus environmentally sustainable solutions, such as natural antifouling compounds are increasingly being sought. Extracts derived from the aquatic macrophytes Pontederia crassipes and Typha domingensis have demonstrated potential antifouling properties in preliminary studies; however, their efficacy under natural field conditions remains unverified. This study is the first to evaluate the antifouling potential of these macrophyte extracts when incorporated with epoxy coatings in a natural freshwater environment (Salto Grande Reservoir, Uruguay River). Stainless steel substrates were treated with 2.5, 5, and 10 g L[-1] of lyophilized macrophyte extracts combined with epoxy and compared to uncoated and epoxy-coated controls. Over a 165-hour period, biofouling was assessed via chlorophyll levels, bacterial counts, macro-organism presence and attachment and taxonomic diversity. Analytical techniques, including gas and liquid chromatography, along with Fourier transform infrared spectroscopy, were employed to identify active compounds in extracts. The P. crassipes extract at 5 and 10 g L[-1] exhibited superior antifouling efficacy compared to T. domingensis. Coatings with P. crassipes significantly reduced bacterial colonization (37%), algae growth (for different photosynthetic pigments), fungal presence, and macro-organism attachment (not found), while promoting the occurrence of opportunistic taxa less conducive to fouling. The observed antifouling activity may be attributed to specific chemical compounds, including long-chain hydrocarbons and phenolic derivatives, identified in the extracts. The study findings demonstrate the field antifouling efficacy of macrophyte extracts incorporated with epoxy coatings, highlighting P. crassipes as a particularly promising, sustainable antifouling candidate. Its high biomass availability and ease of cultivation enhance its potential for industrial-scale development as natural antifouling agents. This work provides critical insights into developing eco-friendly antifouling coatings that minimize environmental impact while maintaining efficacy in biofouling control being the first study to prove in a natural environment the antifouling potential of these macrophytes.}, }
@article {pmid40770074, year = {2025}, author = {Myers, T and Song, SJ and Chen, Y and De Pessemier, B and Khatib, L and McDonald, D and Huang, S and Gallo, R and Callewaert, C and Havulinna, AS and Lahti, L and Roeselers, G and Laiola, M and Shetty, SA and Kelley, ST and Knight, R and Bartko, A}, title = {Chronological age estimation from human microbiomes with transformer-based Robust Principal Component Analysis.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {1159}, pmid = {40770074}, issn = {2399-3642}, mesh = {Humans ; *Aging ; *Biometry/methods ; *Deep Learning ; *Gastrointestinal Microbiome ; *Principal Component Analysis/methods ; *Skin Microbiome ; Software Validation ; }, abstract = {Deep learning for microbiome analysis has shown potential for understanding microbial communities and human phenotypes. Here, we propose an approach, Transformer-based Robust Principal Component Analysis(TRPCA), which leverages the strengths of transformer architectures and interpretability of Robust Principal Component Analysis. To investigate benefits of TRPCA over conventional machine learning models, we benchmarked performance on age prediction from three body sites(skin, oral, gut), with 16S rRNA gene amplicon(16S) and whole-genome sequencing(WGS) data. We demonstrated prediction of age from longitudinal samples and combined classification and regression tasks via multi-task learning(MTL). TRPCA improves age prediction accuracy from human microbiome samples, achieving the largest reduction in Mean Absolute Error for WGS skin (MAE: 8.03, 28% reduction) and 16S skin (MAE: 5.09, 14% reduction) samples, compared to conventional approaches. Additionally, TRPCA's MTL approach achieves an accuracy of 89% for birth country prediction across 5 countries, while improving age prediction from WGS stool samples. Notably, TRPCA uncovers a link between subject and error prediction through residual analysis for paired samples across sequencing method (16S/WGS) and body site(oral/gut). These findings highlight TRPCA's utility in improving age prediction while maintaining feature-level interpretability, and elucidating connections between individuals and microbiomes.}, }
@article {pmid40768991, year = {2025}, author = {Li, J and Sun, Q and Wang, S and Lei, K}, title = {Environmental gradients drive the ecological dynamics of bacterioplankton in the East China Sea based on eDNA metabarcoding.}, journal = {Marine pollution bulletin}, volume = {221}, number = {}, pages = {118539}, doi = {10.1016/j.marpolbul.2025.118539}, pmid = {40768991}, issn = {1879-3363}, abstract = {Understanding the interactions between environmental factors and ecological processes that shape bacterioplankton is a fundamental goal of microbial ecology. With increasing urbanization and environmental stress, marine coastal ecosystems necessitate careful evaluation of microbial dynamics. Environmental DNA was utilized to investigate bacterioplankton in the coastal waters of the East China Sea, revealing distinct environmental gradients that significantly shape bacterioplankton community composition. Distinct spatial differentiation of microbial assemblages was observed along these gradients, primarily driven by nitrogen-related nutrient dynamics. Furthermore, shifts in coastal habitats have driven a transition in community assembly processes from predominantly stochastic to deterministic mechanisms. Changes in environmental conditions also increase the vulnerability of offshore bacterioplankton networks, compromising their stability. These findings emphasize the critical role of environmental gradients in forming coastal microbial community composition, offering valuable insights for advancing marine ecosystem management, biodiversity conservation, and sustainable environmental policies.}, }
@article {pmid40767881, year = {2025}, author = {Fowler, AE and McFrederick, QS and Adler, LS}, title = {Correction to: Pollen Diet Diversity does not Affect Gut Bacterial Communities or Melanization in a Social and Solitary Bee Species.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {86}, doi = {10.1007/s00248-025-02573-6}, pmid = {40767881}, issn = {1432-184X}, }
@article {pmid40767488, year = {2025}, author = {Harris, JE and Bledsoe, RB and Guha, S and Omari, H and Crandall, SG and Burghardt, LT and Couradeau, E}, title = {The activity of soil microbial taxa in the rhizosphere predicts the success of root colonization.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0045825}, doi = {10.1128/msystems.00458-25}, pmid = {40767488}, issn = {2379-5077}, abstract = {UNLABELLED: Plant-beneficial microbes have great potential to improve sustainability in agriculture. Still, managing beneficial microbes is challenging because the impact of microbial dormancy on community assembly across the soil, rhizosphere, and endosphere is poorly understood. We address this gap with the first documented use of Biorthogonal Non-Canonical Amino Acid Tagging (BONCAT) to probe active microbes in the soil-to-root gradient. Using nodule-forming legume Trifolium incarnatum, we confirmed that BONCAT is suitable for labeling endospheric microbes with microscopy. Next, we coupled BONCAT to Flow Cytometer Activated Cell Sorting (FACS) and 16S rRNA amplicon sequencing to probe patterns of microbial activity and the structure of the active microbial community across the soil, rhizosphere, root, and nodule with a native soil microbial community. As expected, we found 10 times higher microbial activity in the endosphere than in the rhizosphere or bulk soil, likely due to increased plant resources. Finally, we revealed that microbial activity in the rhizosphere was significantly associated with successful endosphere colonization, more so than microbial abundance alone. This last finding has implications for the development of microbial inoculants, suggesting colonizing plant roots is linked to a microbe's ability to overcome dormancy once deployed in the soil.<br><br>IMPORTANCE: Most soil microbes are dormant, so they must exit dormancy to have the potential to carry out plant-beneficial functions. It is unclear if dormant microbes revive in proximity to plant-produced resources and if overcoming dormancy in the soil is important for successful plant colonization. We use a novel microbial activity probing technique for the first time on and in plant roots, and with it, we observe microbes increased in activity 10&#xd7; inside plant tissues compared to the soil, likely in response to plant-produced resources. In complex, native microbial communities, we observe that microbes that are active and abundant are more likely to colonize plant roots successfully than just abundant microbes. Our research shows that plants could be leveraged to promote a distinct active microbial community from the native soil, a discovery that has the potential to improve sustainability in agriculture.}, }
@article {pmid40766845, year = {2025}, author = {Zheng, N and Yu, HL and Zhang, BJ and Wang, D and Ji, YL and Dai, LL and Li, W and Li, SH and Hu, ZL and Zheng, YS}, title = {Metagenomic next-generation sequencing-based characterization of the viral spectrum in clinical pulmonary and peripheral blood samples of patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1562965}, pmid = {40766845}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; *Bronchoalveolar Lavage Fluid/virology ; *Virome/genetics ; *Viruses/genetics/classification/isolation &amp; purification ; Female ; Male ; Middle Aged ; Adult ; Aged ; *Lung/virology ; *Blood/virology ; Bacteria/classification/genetics/isolation &amp; purification ; *Virus Diseases/virology ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) enables comprehensive profiling of viral communities in clinical samples. However, comparative analyses of the virome across anatomical compartments and disease states remain limited. This study aims to characterize the virome in bronchoalveolar lavage fluid (BALF) and peripheral blood samples from patients with various clinical conditions using mNGS.<br><br>METHODS: A total of 338 clinical samples-including 240 BALF and 69 blood samples for DNA sequencing, and 18 BALF and 11 blood samples for RNA sequencing-underwent shotgun metagenomic sequencing. Following removal of host-derived reads, high-quality non-human sequences were aligned to a viral reference database. Virome composition was assessed through alpha and beta diversity metrics. Principal coordinates analysis was used to evaluate disease-related variation, and virus-bacteria associations in BALF were investigated via Spearman correlation.<br><br>RESULTS: Sequencing yielded an average of 51 million raw reads per sample, resulting in approximately 8 million non-human reads after host filtering. Distinct virome profiles were observed between BALF and blood samples. Bacteriophages dominated all groups, with Siphoviridae and Myoviridae as the most abundant families, although only 13.6% of viral abundance could be assigned to known families. Diversity analyses revealed significant differences between BALF and peripheral blood, and DNA-sequenced BALF samples showed disease-specific viral signatures in pulmonary infections. In contrast, tumor presence had no significant effect on virome composition in either BALF or blood. Network analysis identified complex virus-bacteria correlations in BALF, with genera such as Haemophilus, Megasphaera, and Treponema as key bacterial hosts.<br><br>CONCLUSIONS: This study reveals pronounced differences in virome composition between the respiratory and circulatory systems and highlights the specific influence of pulmonary disease-but not tumors-on the pulmonary virome. The observed virus-bacteria networks provide novel insights into pulmonary microbial ecology and underscore the importance of integrating host and disease context in virome studies.}, }
@article {pmid40766442, year = {2025}, author = {Rathod, D and Silverman, JD}, title = {PCR Bias Impacts Microbiome Ecological Analyses.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40766442}, issn = {2692-8205}, support = {R01 GM148972/GM/NIGMS NIH HHS/United States ; }, abstract = {Polymerase Chain Reaction (PCR) is a critical step in amplicon-based microbial community profiling, allowing the selective amplification of marker genes such as 16S rRNA from environmental or host-associated samples. Despite its widespread use, PCR is known to introduce amplification bias, where some DNA sequences are preferentially amplified over others due to factors such as primer-template mismatches, sequence GC content, and secondary structures. Although these biases are known to affect transcript abundance, their implications for ecological metrics remain poorly understood. In this study, we conduct a comprehensive evaluation of how PCR-bias influences both within-samples (α -diversity) and between-sample (β -diversity) analyses. We show that perturbation-invariant diversity measures remain unaffected by PCR bias, but widely used metrics such as Shannon diversity and Weighted-Unifrac are sensitive, with their values varying according to the true community composition. To address this, we provide theoretical and empirical insight into how PCR-induced bias varies across ecological analyses and community structures, and we offer practical guidance on when bias-correction methods should be applied. Our findings highlight the importance of selecting appropriate diversity metrics for PCR-based microbial ecology workflows and offer guidance for improving the reliability of diversity analyses.}, }
@article {pmid40765478, year = {2025}, author = {Stevens-Green, R and Chénard, C and Mordret, S and MacKinnon, J and Robicheau, BM and LaRoche, J}, title = {Organellar Genomes of Three Globally Important Nanoplanktonic Diatoms Refine Their Taxon-Specific Distribution and Succession Patterns in the Northwest Atlantic.}, journal = {The Journal of eukaryotic microbiology}, volume = {72}, number = {5}, pages = {e70033}, pmid = {40765478}, issn = {1550-7408}, support = {A1-019982//NRC-ACRD Internal Project/ ; OCN-500//NRC Ocean Program Grant and Contribution/ ; (RGPIN/04060-2021)//NSERC Discovery Grant awarded to JLR/ ; //CFREF (NWA BCP) awarded to JLR/ ; }, mesh = {*Diatoms/genetics/classification ; Atlantic Ocean ; *Genome, Mitochondrial ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Genome, Chloroplast ; *Phytoplankton/genetics/classification ; DNA Barcoding, Taxonomic ; }, abstract = {Nanoplanktonic diatoms (2-20 μm) are a significant yet historically understudied component of marine ecosystems. We investigated three recently isolated nanoplanktonic diatoms from the Northwest Atlantic Ocean (NWA): Minidiscus spinulatus, Mediolabrus comicus, and Minidiscus trioculatus. Using Oxford Nanopore sequencing, we assembled and annotated their complete chloroplast and mitochondrial genomes. Pangenome analyses revealed that Minidiscus species consistently clustered more closely with select Thalassiosira species, whereas M. comicus formed a sister clade with Skeletonema. Circularized chloroplast genomes allowed us to characterize the full-length 16S ribosomal RNAs for each isolate, thereby leading to higher resolution of these taxa in preexisting 16S metabarcoding data. During our study, M. spinulatus was primarily restricted to the Bedford Basin. In contrast, both M. trioculatus and M. comicus had larger geographic ranges extending to the Labrador Sea, and in the case of M. comicus, to the Canadian Arctic Gateway. Weekly metabarcoding from the coastal Bedford Basin, N.S., Canada (2014-2022), revealed a seasonal succession of nanoplanktonic taxa, with Minidiscus trioculatus dominating in the early months, followed by M. comicus and M. spinulatus. Our results highlight the critical value of phytoplankton isolations and organelle genomics for expanding our understanding of the diversity and biogeography of nanoplanktonic diatoms.}, }
@article {pmid40765283, year = {2025}, author = {Zhang, Y and Wu, H and Wu, X and Grossart, HP and Lorke, A}, title = {Revisiting Cyanobacteria-Temperature Dynamics: Intraspecific Competition and Trait Diversity as Keys to Predicting Harmful Algal Blooms under Climate Change.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c04849}, pmid = {40765283}, issn = {1520-5851}, abstract = {Cyanobacterial harmful algal blooms are expanding spatiotemporally, with an increasing occurrence of cold-water cyanobacterial blooms (CWCBs), intensifying ecological and water quality challenges. While abiotic drivers have been identified as contributors to CWCBs, the role of biotic factors─particularly the adaptation induced by the shifts in intraspecific trait distributions─in this process remains largely unexplored. Here, we tested the hypothesis that the thermal history of cyanobacteria affects their thermal adaptations by reshaping the distribution of optimum growth temperature (Topt). Using a trait-based phytoplankton model coupled with a one-dimensional lake model, we simulated cyanobacteria dynamics over 364 days in a large, eutrophic, shallow lake recently experiencing CWCBs. The model demonstrated that Topt diversification promotes cold-adapted strains, leading to CWCBs while mitigating summer blooms. This occurs because the thermal response of Topt-diverse populations depends on their Topt distribution, which is determined by past temperature sequence, allowing Topt-diverse populations to retain a 'memory' of temperatures preceding summer. Consequently, increased summer temperatures inhibit these cold-adapted populations, challenging the prevailing cyanobacteria-temperature paradigm, which suggests that high temperatures universally favor cyanobacteria. These findings reveal that models assuming fixed traits may misrepresent cyanobacterial dynamics under climate change, highlighting the necessity of incorporating trait diversity into predictive frameworks for improved forecasting and to support adaptive lake management strategies.}, }
@article {pmid40762371, year = {2025}, author = {Li, X and Chen, Y and Gao, Z and Liu, X and Song, Z and Gao, F and Wang, S and Yu, C and Sun, L and Huang, Y and Zheng, L and Wang, G and Sun, Y and Li, J and Yang, X and Bao, Y}, title = {TSP50 in Neural Stem Cells Regulates Aging-Related Cognitive Decline and Neuroinflammation by Altering the Gut Microbiota.}, journal = {Aging cell}, volume = {}, number = {}, pages = {e70188}, doi = {10.1111/acel.70188}, pmid = {40762371}, issn = {1474-9726}, support = {GZC20240236//Postdoctoral Fellowship Program of CPSF/ ; 20230204067YY//the Science and Technology Development Program of Jilin Province/ ; 135131002//Fundamental Research Funds for the Central Universities/ ; }, abstract = {Aging is a process of gradual decline in physical and cognitive function and is a major risk factor for mortality. Despite the increasing number of relevant studies, the mechanisms regulating the aging process have not been fully elucidated. Genetic factors have long been recognized as key factors in controlling the rate of aging. Testes-specific protease 50 (TSP50) has been shown to be involved in the regulation of embryonic development and intestinal homeostasis, but its role in the regulation of aging remains unclear. Here, we showed that TSP50 expression was reduced in the hippocampus of both aged humans and mice. TSP50 deficiency in neural stem cells (NSCs) drove accelerated aging in mice, characterized by exacerbated age-related cognitive impairments and significantly elevated neuroinflammation. Notably, aged mice with NSCs-specific knockout of TSP50 exhibited impaired intestinal mucosal barriers, dysbiosis of gut microbiota, and a marked reduction in the production of short-chain fatty acids (SCFAs). Restoring gut microbial ecology using fecal microbiota transplantation (FMT) and overexpressing TSP50 successfully alleviated aging-associated cognitive decline and neuroinflammation. Taken together, our study suggests that TSP50 plays a critical role in the aging process and identifies gut microbiota as a pivotal mediator of TSP50's influence on age-related cognitive decline and neuroinflammation. These findings highlight the potential therapeutic value of targeting TSP50 and gut microbiota for aging, offering insights into aging mechanisms and interventions for aging-related neurodegenerative diseases.}, }
@article {pmid40761850, year = {2025}, author = {Cai, S and Lin, L and Cai, Y and Wang, C and Lin, Y and Zhou, J and Zhou, F and Chen, M}, title = {Phase angle associates with severity and mortality in acute-on-chronic liver failure.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1541795}, pmid = {40761850}, issn = {2296-858X}, abstract = {BACKGROUND: Acute-on-chronic liver failure is characterized by acute hepatic decompensation and high short-term mortality, thereby necessitating prompt prognostic assessment. Although phase angle (PhA) has been established as a biomarker in chronic diseases, its prognostic significance in ACLF remains unclear.<br><br>METHODS: In this study, we evaluated PhA in 78 ACLF patients and compared the results with those of two control groups: 45 patients with chronic hepatitis B infection but normal liver function, and 51 patients with abnormal liver function who did not meet the ACLF criteria. Upon hospital admission, comprehensive laboratory parameters were obtained, and PhA measurements were conducted to explore the associations among PhA, organ dysfunction indices, and established prognostic scoring systems for predicting 90-days outcomes in ACLF patients.<br><br>RESULTS: Our analysis demonstrated that ACLF patients exhibited significantly lower PhA values compared with both control groups. Notably, non-survivors within 90 days had substantially lower PhA levels than survivors. Additionally, patients with complications, including hepatic encephalopathy, ascites, gastrointestinal bleeding, and infection, showed markedly lower PhA values than those without such complications. Moreover, the combination of PhA with the Chronic Liver Failure - Sequential Organ Failure Assessment (CLIF-SOFA) score enhanced the predictive accuracy of 90-days mortality in ACLF patients.<br><br>CONCLUSION: Phase angle serves as a valuable biomarker for evaluating ACLF severity and predicting short-term mortality, potentially offering a novel approach to risk stratification in ACLF management.}, }
@article {pmid40761338, year = {2025}, author = {Zhao, Y and Chen, J and Qin, Y and Yuan, J and Yu, Z and Ma, R and Liu, F and Zhao, J}, title = {Linking Short-Chain Fatty Acids to Systemic Homeostasis: Mechanisms, Therapeutic Potential, and Future Directions.}, journal = {Journal of nutrition and metabolism}, volume = {2025}, number = {}, pages = {8870958}, pmid = {40761338}, issn = {2090-0724}, abstract = {Short-chain fatty acids (SCFAs), pivotal metabolites derived from microbial fermentation of dietary fiber, serve as critical modulators of glucose and lipid metabolism. Dysregulation of SCFA levels, often stemming from inadequate fiber intake or dysbiosis of SCFA-producing microbiota, correlates with heightened susceptibility to diverse pathologies, including autoimmune disorders, metabolic syndromes, and malignancies. Emerging evidence underscores the pleiotropic roles of SCFAs in orchestrating gut and systemic homeostasis, positioning them as novel therapeutic candidates for immune dysregulation, inflammatory conditions, and transplant rejection. This review synthesizes current knowledge on SCFA biosynthesis, absorption dynamics, and their multifaceted regulatory mechanisms, spanning epigenetic modulation, G protein-coupled receptor (GPR) signaling, and immune cell crosstalk. We further elucidate their therapeutic potential in clinical contexts, emphasizing their capacity to recalibrate immune responses, suppress chronic inflammation, and mitigate oncogenesis. By integrating recent advances in microbiome research and translational applications, this work highlights the imperative for precision interventions targeting SCFA pathways to bridge the gap between microbial ecology and clinical innovation.}, }
@article {pmid40760940, year = {2025}, author = {Petrullo, L and Webber, Q and Raulo, A and Boutin, S and Lane, JE and McAdam, AG and Dantzer, B}, title = {Social Microbial Transmission in a Solitary Mammal.}, journal = {Ecology letters}, volume = {28}, number = {8}, pages = {e70186}, pmid = {40760940}, issn = {1461-0248}, support = {//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada/ ; 0515849//Division of Environmental Biology/ ; 2010726//Division of Environmental Biology/ ; 2338394//Division of Environmental Biology/ ; }, mesh = {Animals ; *Sciuridae/microbiology/physiology ; *Social Behavior ; *Gastrointestinal Microbiome ; Territoriality ; Population Density ; Behavior, Animal ; Male ; Female ; }, abstract = {Microbial transmission is hypothesised to be a major benefit of sociality, facilitated by affiliative behaviours such as grooming and communal nesting in group-living animals. Whether microbial transmission is also present in animals that do not form groups because territoriality limits interactions and prevents group formation remains unknown. Here, we investigate relationships among gut microbiota, population density and dynamic behavioural and spatial measures of territoriality in wild North American red squirrels (Tamiasciurus hudsonicus). Periods of high population density predicted population-level gut microbial homogeneity but individual-level diversification, alongside changes in obligately anaerobic, non-sporulating taxa indicative of social transmission. Microbial alpha-diversity increased with more frequent territorial intrusions, and pairs with stronger intrusion-based social associations had more similar gut microbiota. As some of the first evidence for social microbial transmission in a solitary system, our findings suggest that fluctuations in density and territorial behaviours can homogenise and diversify host microbiomes among otherwise non-interacting animals.}, }
@article {pmid40760525, year = {2025}, author = {Deng, M and Chen, W and Wang, X}, title = {Characteristics of gut microbiota in longevity populations in China and its relationship with healthy aging.}, journal = {Medicine}, volume = {104}, number = {31}, pages = {e43633}, pmid = {40760525}, issn = {1536-5964}, support = {He Technology 202217//Hezhou Science and Technology Bureau/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; China ; *Longevity/physiology ; Male ; Middle Aged ; Female ; Aged ; Adult ; *Healthy Aging/physiology ; Feces/microbiology ; Aged, 80 and over ; Child ; Young Adult ; RNA, Ribosomal, 16S/genetics ; Cohort Studies ; }, abstract = {This study aimed to investigate the differences in gut microbiota diversity and compositional characteristics between long-lived individuals (≥90 years) and individuals at different life stages (children, young and middle-aged adults, and elderly), in order to provide a foundational basis for microbial interventions in healthy aging. An observational cohort design was adopted, recruiting healthy participants divided into 4 age groups: children, young and middle-aged adults, elderly, and long-lived individuals. Fecal samples were collected and subjected to high-throughput 16S rRNA gene sequencing. The alpha diversity, beta diversity, and community structural differences of the gut microbiota were assessed, and representative microbial taxa were identified using LEfSe analysis. The long-lived group exhibited significantly higher species richness and diversity (Chao1 and Shannon indices, P < .05), with a more balanced and stable microbial structure. At the phylum level, the long-lived group had the highest relative abundance of Firmicutes and the lowest of Bacteroidetes. At the genus level, lactic acid bacteria such as Lactobacillus were significantly enriched. LEfSe analysis indicated that lactic acid bacteria-related taxa may serve as characteristic markers of this population. The gut microbiota of long-lived individuals exhibits higher ecological stability and a distinctive composition, which may be associated with healthy aging. These findings provide preliminary evidence for the relationship between longevity and gut microbial ecology and suggest that structural characteristics of these microbial communities may be involved in the process of healthy aging, offering a basis for future exploration of microbial intervention strategies.}, }
@article {pmid40759677, year = {2025}, author = {Huang, J and Wu, F and Xiao, Y and Ye, M and Wu, X and Chen, H and Xu, Q}, title = {Deciphering nitrogen-driven microbial succession in an anaerobic membrane bioreactor-coupled A[2]/O ecological system for the remediation of industrial swine wastewater.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {28422}, pmid = {40759677}, issn = {2045-2322}, support = {2024R1031001, 2024R1031003 and 2022R1032003//Basic Public Welfare Research Program of Fujian Province of China/ ; 2024R1031001, 2024R1031003 and 2022R1032003//Basic Public Welfare Research Program of Fujian Province of China/ ; 2024R1031001, 2024R1031003 and 2022R1032003//Basic Public Welfare Research Program of Fujian Province of China/ ; 2023S0003//Fuzhou Science and Technology Bureau spark project/ ; Q20194303//Scientific Research Items Foundation of Hubei Educational Committee/ ; YY202446//Jingchu University of Technology Ph.D. Startup Fund/ ; }, mesh = {*Bioreactors/microbiology ; Animals ; *Wastewater/microbiology/chemistry ; Swine ; *Nitrogen/metabolism ; Anaerobiosis ; *Waste Disposal, Fluid/methods ; Biological Oxygen Demand Analysis ; Water Purification/methods ; Membranes, Artificial ; Phosphorus ; Industrial Waste ; Biodegradation, Environmental ; }, abstract = {Rapid expansion of industrial pig farming has intensified existing challenges in the management of nutrient-rich wastewater, characterized by high organic loads (chemical oxygen demand (COD): 15,000-30,000 mg/L) and ammonium nitrogen (NH4[+]-N): 800-2,500 mg/L) concentrations. In this study, an integrated treatment system with a combination of a high-density polyethylene (HDPE) membrane-based anaerobic membrane bioreactor and an anoxic/aerobic/oxidation pond (A[2]/O) was developed for swine wastewater remediation. The system achieved exceptional remediation efficiency, removing 99.4, 99.5, 95.4, 92.8, and 97.9% of COD, biochemical oxygen demand (BOD), NH4[+]-N, total phosphorus (TP), and suspended solids (SS), respectively, with the anoxic and aerobic (A[2]) phases contributing to removal of 62.5, 60.9, 80.9, 94.6% of COD, BOD, TP, and SS, respectively. Microbial community analysis revealed process-specific dynamics, including Firmicutes enrichment (8.52 ± 3.33 to 10.81 ± 0.39%) in anaerobic stages and Nitrosomonas dominance (2.38 ± 0.21%) during nitrification. The HDPE membrane-based bioreactor performed effectively under high organic loading rates (5-8 kg COD·m[-3]·day[-1]), whereas the A[2]/O system optimized nutrient cycling through synchronized nitrification-denitrification (dissolved oxygen: 2.0-3.5 mg/L). In this study, we establish a scalable framework for the treatment of industrial swine wastewater by combining engineered infrastructure with the principles of microbial ecology to address conventional pollutants.}, }
@article {pmid40757865, year = {2025}, author = {Södergren, J and Noguera, PM and Petersen, MA and Jørgensen, NOG and Podduturi, R and Nicolaisen, MH}, title = {Myxobacteria isolated from recirculating aquaculture systems (RAS): ecology and significance as off-flavor producers.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0075725}, doi = {10.1128/aem.00757-25}, pmid = {40757865}, issn = {1098-5336}, abstract = {Despite advances in the operation of recirculating aquaculture systems (RAS), accumulation of earthy-muddy off-flavors in the fish remains a potential risk. Myxobacteria (Myxococcota) are reported to be among the most abundant geosmin synthase-harboring groups in RAS, but previous isolation attempts have been unsuccessful, limiting the knowledge of their role in off-flavor production. For the first time, we successfully isolated two geosmin-producing myxobacteria from RAS: Myxococcus virescens AT3 and Corallococcus exiguus AT4. Cell-specific geosmin production varied with the nutrient content in different media but was highest in a low-nutrient medium and when cultivated in water from RAS. Cultivation in RAS water also stimulated the production of other volatile organic compounds (VOCs). Newly identified potential off-flavor compounds included 4-methyl-2-heptanone ("forest" odor), 3-methyl-1-butanol ("medicinal" and "chemical"), and a presumptive sesquiterpenoid described as "musty," "earthy," and "flowery." The previously known off-flavor compound dimethyl sulfide was also detected. Myxobacteria have previously been proposed as keystone bacteria in the environment due to their predatory lifestyle. In predation assays using isolated bacteria from RAS, M. virescens AT3 and C. exiguus AT4 could successfully feed on 15 of 16 tested strains, suggesting a large influence on the biology of RAS microbiomes. The combination of predatory behavior and potent production of geosmin and other VOCs underscores the ecological and sensory impact of these bacteria in RAS. Understanding their behavior and metabolic outputs is critical to developing strategies for mitigating off-flavors in RAS.IMPORTANCEIssues with off-flavored fish in recirculating aquaculture systems (RAS) due to the presence of the earthy-musty smelling compounds geosmin and 2-MIB are considered as one of the industry's most economically significant challenges. Knowledge of conditions that affect off-flavor production is essential information in the development of viable solutions for its mitigation. Little is known about the function of these microbially produced compounds or the conditions that trigger their production, especially in the underexplored myxobacteria. Investigation of natural isolates is crucial to determine the function of the genes involved and their differential expression in response to environmental cues. While myxobacteria in RAS have been previously shown to harbor the geosmin synthase gene in molecular studies, the present study is the first attempt to isolate these bacteria from RAS and quantify their geosmin production under various nutrient conditions. Through cultivation-based methods, we demonstrate their production of both known and novel compounds with earthy attributes.}, }
@article {pmid40757859, year = {2025}, author = {Adekoya, AE and West, SR and Arriaga, SK and Ibberson, CB}, title = {Infections as ecosystems: community metabolic interactions in microbial pathogenesis.}, journal = {Infection and immunity}, volume = {}, number = {}, pages = {e0053024}, doi = {10.1128/iai.00530-24}, pmid = {40757859}, issn = {1098-5522}, abstract = {Microbes rarely exist alone; instead, they live in dynamic multi-species communities with a range of metabolic capacities. To establish within a polymicrobial community, an organism must compete with the other members of the community for space and nutrients. In addition, microbes form complex metabolic interdependencies in polymicrobial environments, and these nutrient exchanges are central to overall community function. Interactions between microbial community members dictate key processes, including nutrient cycling, tolerance to disturbances, and disease progression, and these interactions are known to depend on the environment in which they are measured. Therefore, understanding these ecological interactions is fundamental to our understanding of community composition, function, and impacts on disease. In this mini-review, we will describe the mechanisms microbes use to exchange nutrients in host-associated environments, with a focus on the oral and respiratory tracts. We will particularly emphasize the environmental factors that influence community composition and how interactions between organisms, ranging from cooperation to competition, impact nutrient bioavailability and overall community function during infection.}, }
@article {pmid40756216, year = {2025}, author = {Li, M and Liu, J and Cao, D and Chen, X and Shi, J and Hu, W and Xiao, C and Fang, Y}, title = {Heavy metal pollution simplifies microbial networks and enhances modularity during tailings primary succession: divergent assembly dynamics for bacterial and fungal communities.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1566627}, pmid = {40756216}, issn = {1664-302X}, abstract = {Microbial community play a fundamental role in primary succession of tailings ecosystems. However, the influence of heavy metal pollution on microbial interactions and assembly dynamics during this process remains poorly understood. In this study, we investigated bacterial and fungal communities in tailing soil and biological soil crusts (BSCs) undergoing primary succession under varying heavy metal pollution. By integrating microbial community profiling with measurements of soil nutrients and heavy metal concentrations, we aimed to elucidate how pollution levels shape microbial composition, co-occurrence networks, and assembly processes. Our results revealed clear differences in soil physicochemical properties, microbial diversity, community structure, and ecological interactions between low and high pollution conditions. Under high contamination, Burkholderiales dominated the bacterial communities, while Saccharomycetales and Pleosporales were representative among fungi. Microbial diversity decreased with increasing pollution, accompanied by simplified co-occurrence networks and increased modularity. In highly polluted environments, both bacterial and fungal communities exhibited stronger correlations with environmental factors. Interestingly, bacterial communities were more strongly associated with soil nutrient parameters, whereas fungal communities responded more closely to heavy metal concentrations. Community assembly analysis further showed a shift toward deterministic processes in bacterial communities under high pollution, while fungal assembly remained largely stochastic. These findings highlight the differential responses of bacterial and fungal communities to heavy metal stress and underscore the critical role of pollution in shaping microbial succession in tailing ecosystems. This study provides important insights into microbial ecology under environmental stress and may inform strategies for the bioremediation and management of contaminated mine lands.}, }
@article {pmid40756212, year = {2025}, author = {Cortez-Lázaro, AA and Vázquez-Medina, PJ and Caro-Degollar, EM and García Evangelista, JV and Cortez-Lázaro, RA and Rojas-Paz, JL and Legua-Cardenas, JA and Fernandez-Herrera, F and Pesantes-Rojas, CR and Ocrospoma-Dueñas, RW and Oliva-Cruz, SM and Manes-Cangana, GA and Romero Bozzetta, JL and Leiva Espinoza, ST}, title = {Global trends in Trichoderma secondary metabolites in sustainable agricultural bioprotection.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1595946}, pmid = {40756212}, issn = {1664-302X}, abstract = {The use of Trichoderma spp. constitutes a promising biotechnological strategy for sustainable agriculture, owing to its capacity to control phytopathogens and to produce bioactive secondary metabolites. This study, one of the first of its kind, addresses the absence of a comprehensive bibliometric assessment in this field. A systematic bibliometric analysis was conducted on 235 publications indexed in Scopus (2000-2025). Advanced tools such as VOSviewer and Bibliometrix were employed to track publication trends, identify key research themes, map collaborative networks, and assess the influence of leading authors and institutions. An exponential increase in scientific output was observed, peaking in 2023. Four principal research clusters were identified: antifungal activity, gene regulation, secondary metabolite production, and biosynthesis. India and China accounted for the highest publication volume, while Italy, represented by authors such as Francesco Vinale, accounted for the greatest scientific impact. International collaboration was extensive, particularly between Asia and Europe. The analysis indicates a progression from applied biocontrol studies to research focusing on molecular and genetic mechanisms, highlighting the need for multidisciplinary approaches that integrate biotechnology, agronomy, and microbial ecology. This bibliometric study provides an overview of Trichoderma secondary metabolites in agricultural biocontrol and outlines a research agenda emphasizing field validation, interdisciplinary collaboration, and the adoption of innovative technologies to bridge the gap between research and on-farm application in sustainable agriculture.}, }
@article {pmid40755785, year = {2025}, author = {Abuassaf, RA and Al-Jamal, FF and Abusara, OH and Zihlif, M and Deeb, AA and Al-Rshaidat, MMD}, title = {Evaluating the antibacterial properties of deep-sea sponges Dactylospongia elegants, Stelletta fibrosa, and Haliclona manglaris from the Jordanian Gulf of Aqaba.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19735}, pmid = {40755785}, issn = {2167-8359}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; *Porifera/chemistry/genetics ; *Gram-Positive Bacteria/drug effects ; *Haliclona/chemistry ; *Gram-Negative Bacteria/drug effects ; Tandem Mass Spectrometry ; }, abstract = {Marine sponges are known for their rich variety of secondary metabolites, many of which show potential for pharmaceutical applications. In this study, three deep-sea sponge species-Stelletta fibrosa, Dactylospongia elegans, and Haliclona manglaris-were identified using DNA barcoding, and their ethanolic extracts were tested for antibacterial activity. The extracts were evaluated against Gram-positive (e.g., Bacillus pumilus, Staphylococcus aureus, Staphylococcus epidermidis, and methicillin-resistant Staphylococcus aureus, MRSA) and Gram-negative bacteria (e.g., Escherichia coli and Klebsiella aerogenes) using the agar well diffusion method. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were also determined. Among the extracts, D. elegans exhibited the most potent antibacterial activity, with inhibition zones ranging from six to 21 mm against gram-positive bacteria and low MIC/MBC values from 0.25 to three mg/ml. Liquid chromatography-mass spectrometry (LC-MS/MS) analysis of D. elegans revealed the presence of bioactive compounds such as gallic acid, caffeic acid, bolinaquinone, dactyloquinone, and others, which are known for their antimicrobial properties. These findings suggest that D. elegans has promising antibacterial properties that could be valuable in combating antimicrobial resistance.}, }
@article {pmid40751837, year = {2025}, author = {Cruz-Cano, R and Bretón-Deval, L and Martínez-García, M and Díaz-Jaimes, P and Kolb, M}, title = {Changes in Microbial Community Assemblages Due To Urban Pollution, Detected via rRNA Gene Amplicon Sequencing in the Magdalena River, Mexico City.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {85}, pmid = {40751837}, issn = {1432-184X}, support = {516486//Secretaria de Ciencia, Humanidades, Tecnolog&#xed;a e Innovaci&#xf3;n/ ; IN211921//UNAM-PAPIIT/ ; IN211921//UNAM-PAPIIT/ ; IN211921//UNAM-PAPIIT/ ; }, mesh = {Mexico ; *Rivers/microbiology/chemistry ; *Bacteria/genetics/classification/isolation &amp; purification ; *Microbiota/genetics ; Cities ; Environmental Monitoring ; RNA, Ribosomal, 16S/genetics ; Water Quality ; *Water Pollution/analysis ; Water Microbiology ; Water Pollutants, Chemical/analysis ; }, abstract = {As freshwater sources become increasingly polluted and depleted, the delicate balance of aquatic environments is disrupted, leading to cascading effects throughout entire ecosystems. This disruption manifests in various ways, including changes in water chemistry, temperature fluctuations, and the introduction of contaminants, all of which contribute to alterations in microbial communities. We applied eDNA metabarcoding to characterize microbial communities along an anthropogenic pollution gradient in the Magdalena River, a tropical river in Mexico City. Sampling was conducted at four sites representing different levels of human influence. Results revealed differences in both bacterial and microeukaryotic community compositions between sites. In areas with low to moderate disturbance, bacterial genera associated with nitrogen cycling and plant-microbe interactions (e.g., Rhizobacter, Rhodoferax, and Flavobacterium) were predominant, whereas in more heavily impacted sites, genera linked to enteric, nosocomial, or fecal sources (e.g., Arcobacter, Acinetobacter, and Aeromonas) dominated. Peri-urban sites exhibited higher alpha diversity at the phylum level for bacteria, and microeukaryotic communities; two phyla account for over 75% of the relative abundance throughout the year (Ciliophora &amp; Chlorophyta). Statistical analysis showed that water quality influences microbial composition in the sites. These findings demonstrate that urban influence alter microbial community composition, showing similar patterns to other studies. Our study, however, also discovered certain taxa that had not been previously recorded in tropical urban rivers, thereby broadening the existing knowledge, which has primarily been based on temperate systems. This research offers one of the initial thorough evaluations of microbial communities in urban rivers in Mexico and highlights the potential of eDNA metabarcoding as a valuable tool for environmental monitoring.}, }
@article {pmid40750488, year = {2025}, author = {Lopes, ACA and Martins, LV and Ferreira, GNC and Trivedi, P and Araujo, ASF}, title = {Do plants remember their microbial partners?.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2025.07.005}, pmid = {40750488}, issn = {1878-4372}, abstract = {Plants host dynamic microbiomes that are critical for stress resilience and productivity. Emerging evidence suggests that 'microbiome memory' enables plants to retain beneficial microbes via epigenetic mechanisms and vertical transmission. Understanding how 'microbiome memory' forms, persists, and influences plant adaptation is crucial for advancing resilient crop systems and sustainable agriculture.}, }
@article {pmid40749586, year = {2025}, author = {Li, H and Hong, L and Wang, Y and Chai, S and Huang, P and Chen, H and Liu, W and Zhu, W and Marzorati, M and Wang, H and Tian, J and Zhang, X}, title = {Origin-dependent metabolic variations: How Atractylodes macrocephalae Rhizoma extract's chemical diversity leads to stage-specific changes in simulated digestion.}, journal = {Journal of pharmaceutical and biomedical analysis}, volume = {266}, number = {}, pages = {117082}, doi = {10.1016/j.jpba.2025.117082}, pmid = {40749586}, issn = {1873-264X}, abstract = {Atractylodes macrocephalae Rhizoma (AMR), a traditional Chinese medicine, is extensively utilized in clinical practice for its pharmacological properties, including anti-inflammatory, anti-tumor, and gastrointestinal regulatory effects. Nonetheless, the intricate nature of traditional Chinese medicine extracts has resulted in few studies into the effects of compositional variations in Atractylodes macrocephalae Rhizoma extracts (AMRE) from diverse sources on gastrointestinal metabolic processes. This study developed an integrated in vitro and in vivo compound analysis strategy utilizing Ultrahigh-performance liquid chromatography Quadrupole-Orbitrap tandem mass spectrometry (UHPLC-Q-Orbitrap-MS/MS) and the Simulator of Human Intestinal Microbial Ecosystem (SHIME) to examine the metabolic alterations caused by variations in the chemical constituents of AMRE from diverse sources. A total of 117 chemical constituents were found, primarily classified as terpenoids, organic acids, alkaloids, coumarins, and phenylpropanoids. 51 prototype components and 79 metabolites were identified. The metabolic processes were predominantly observed among terpenoids, with reaction types encompassing hydroxylation, oxidation, hydrogenation, methylation, glucuronidation, and sulfonation. Analysis of dynamic changes revealed that the majority of the prototype components underwent a considerable reduction in the colon, while the metabolites were markedly enriched in both the small intestine and colon. Differential analysis showed that AMRE3 contained the highest number of terpenoid compounds, AMRE1 exhibited the highest average content of chemical constituents, and AMRE2 had the lowest. These disparities were consistently observed in both prototype components and metabolic behaviors, thereby affirming the robust correlation between metabolite distribution and chemical constituents. This study elucidates, for the first time, the variations in the chemical constituents of AMRE from diverse sources and the metabolic characteristics and discrepancies they elicit in the human gastrointestinal tract (GI tract), offering a viable strategy for further clarifying the material basis of its pharmacological effects and clinical applications.}, }
@article {pmid40748243, year = {2025}, author = {Portal-Gonzalez, N and Wang, W and He, W and Santos-Bermudez, R}, title = {Engineering Plant Holobionts for Climate-Resilient Agriculture.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf158}, pmid = {40748243}, issn = {1751-7370}, abstract = {The plant holobiont-an integrated unit of the host and its microbiome-has co-evolved through ecological and genetic interactions. Microbiome engineering offers a promising route to enhance resilience in response to climate stress, soil degradation, and yield stagnation. This review presents an integrated framework combining microbial ecology, synthetic biology, and computational modeling to rationally design synthetic microbial communities (SynComs) for agriculture. We outline ecological principles-priority effects, keystone taxa, and functional redundancy-that shape microbiome assembly and guide SynCom design. Strategies like CRISPR interference, biosensor circuits, and quorum-sensing modules enable programmable microbial functions. We also highlight the predictive potential of in silico modeling-including genome-scale metabolic models, dynamic flux balance analysis, and machine learning-to simulate interactions, optimize SynCom composition, and enhance design accuracy. To bridge lab and field, we discuss native microbial chassis, encapsulation, and precision delivery as tools for scalable, ecosystem-integrated deployment. We introduce the concept of the programmable holobiont: an engineered plant-microbe partnership capable of dynamic feedback, interkingdom signaling, and ecological memory. This systems-level perspective reframes plants as designable ecosystems. By synthesizing cross-disciplinary advances, we offer a roadmap for climate-resilient agriculture, where engineered microbiomes improve sustainability, yield stability, and environmental adaptation.}, }
@article {pmid40743118, year = {2025}, author = {Ozturk, S and Ekmen, FG and Ekmen, H and Ünal, EM and Er, A and Keskin, E and Arbuckle, BS}, title = {Decoding past microbial life and antibiotic resistance in İnonü Cave's archaeological soil.}, journal = {PloS one}, volume = {20}, number = {7}, pages = {e0326358}, pmid = {40743118}, issn = {1932-6203}, mesh = {*Soil Microbiology ; *Archaeology ; *Bacteria/genetics/classification/drug effects ; *Caves/microbiology ; RNA, Ribosomal, 16S/genetics ; Humans ; *Drug Resistance, Microbial/genetics ; Microbiota/genetics ; Turkey ; }, abstract = {This study, which bridges the disciplines of archaeology and microbiology, examines the ancient bacterial communities and antibiotic-resistance genes in soil samples collected from İnönü Cave in Zonguldak, Turkiye. Our aim is to provide a comprehensive understanding of historical human activities and their influence on microbial communities. Soil samples were gathered from four distinct cultural levels from the Chalcolithic Age to the Early Iron Age. The microbial communities were characterized, and antibiotic-resistance genes were identified using high-throughput sequencing of 16S rRNA genes and metagenomic studies. This interdisciplinary approach not only enriches our understanding of ancient microbial communities but also opens up new avenues for research and collaboration. The results of our study showed a wide range of microorganisms, including prominent bacterial groups such as Acidobacteriota, Actinobacteriota, Bacteroidota, Chloroflexi, Cyanobacteria, Firmicutes, Myxococcota, and Proteobacteria. The study identified the presence of the tetracycline resistance gene tetA in Chalcolithic samples, the class 1 integron intl1 in Early Bronze Age samples, and the oxacillinase gene OXA58 in Late Bronze Age samples. These findings underscore the long-term impact of human activities on microbial communities, as antibiotic-resistance genes have been present and have remained over various historical periods, perhaps influenced by both human activities and environmental variables. This knowledge is crucial for understanding the resilience and adaptability of microbial communities in the face of human-induced changes. The coexistence of these resistance genes and alterations in the microbial population suggest substantial connections between human activities and soil microbiota. This study, which draws on the fields of archaeology, microbiology, and environmental science, offers valuable insights into the ancient microbial ecology and underscores the enduring presence of antibiotic resistance. It emphasizes the necessity of a comprehensive, interdisciplinary approach, spanning multiple fields, to comprehend microbial communities' evolution and resistance mechanisms in archaeological settings.}, }
@article {pmid40742751, year = {2025}, author = {Fischer, MT and Xue, KS and Costello, EK and Dvorak, M and Raboisson, G and Robaczewska, A and Caty, SN and Relman, DA and O'Connell, LA}, title = {Effects of parental care on skin microbial community composition in poison frogs.}, journal = {eLife}, volume = {14}, number = {}, pages = {}, pmid = {40742751}, issn = {2050-084X}, support = {DP2 HD102042/HD/NICHD NIH HHS/United States ; DP2HD102042/NH/NIH HHS/United States ; Erwin Schroedinger Stipend J-4526B//Austrian Science Fund/ ; }, mesh = {Animals ; *Skin/microbiology ; *Microbiota ; *Anura/microbiology/physiology ; Larva/microbiology ; Female ; Male ; *Bacteria/classification/isolation &amp; purification/genetics ; Poison Frogs ; }, abstract = {Parent-offspring interactions constitute the first contact of many newborns with their environment, priming community assembly of microbes through priority effects and shaping host health and disease. Microbe acquisition during parental care is well studied in humans and agriculturally relevant species but remains poorly understood in other vertebrate groups, such as amphibians. Here, we investigate vertical transmission of skin microbiota in poison frogs (Dendrobatidae), where fathers transport tadpoles piggyback-style from terrestrial clutches to aquatic nurseries. We found that substantial bacterial colonization of embryos begins after hatching, suggesting that the vitelline envelope acts as a microbial barrier. A cross-foster experiment demonstrated that poison frogs performing tadpole transport serve as a source of skin microbes for tadpoles on their back. To study how transport impacts skin communities of tadpoles in an ecologically relevant setting, we sampled sympatric species that do or do not exhibit tadpole transport in their natural habitat. We did not find a higher degree of similarity between microbial communities of tadpoles and adults in species that transport their offspring compared to those that do not. Similarly, communities of tadpoles were no more similar to their caregiver than to unrelated adults, indicating that most caregiver-associated microbes do not remain in tadpole communities long-term. Nonetheless, some taxa persisted on tadpoles over development. This study is the first to demonstrate that offspring transport facilitates transmission of parental skin microbes in anurans.}, }
@article {pmid40742667, year = {2025}, author = {Liang, M and Wu, WJ and Li, L and Qin, H and Li, SN and Zheng, GL and Hou, DM and Huang, Q and Cheng, L and Jie, HQ and Lu, JR and He, JC and Yang, J and Wei, W}, title = {Characteristics of the microbiota in the nasopharynx and nasal cavity of healthy children before and during the COVID-19 pandemic.}, journal = {World journal of pediatrics : WJP}, volume = {}, number = {}, pages = {}, doi = {10.1007/s12519-025-00953-z}, pmid = {40742667}, issn = {1867-0687}, support = {81800903//National Natural Science Foundation of China/ ; 82171135//National Natural Science Foundation of China/ ; 82371140//National Natural Science Foundation of China/ ; 81970881//National Natural Science Foundation of China/ ; 82271160//National Natural Science Foundation of China/ ; 21Y31900504//Science and Technology Innovation Plan Of Shanghai Science and Technology Commission/ ; 2024YFC2511100//National Key R&amp;D Program of China/ ; }, abstract = {BACKGROUND: Microbial colonization in the nasopharynx and nasal cavity plays a defensive role in children. The coronavirus disease 2019 (COVID-19) pandemic may have an influence on the nasopharynx and nasal cavity microbiota. This study aimed to identify and compare the microbiota in the nasopharynx and nasal cavity before and during the COVID-19 pandemic in a healthy pediatric population.<br><br>METHODS: Separate mucosal swabs were collected from the nasopharynx and nasal cavity of healthy children before and during the COVID-19 pandemic. A 16S ribosomal RNA-based metagenomic approach was employed to characterize and analyze alterations in the nasopharyngeal and nasal microbiota to determine whether isolation measures, such as mask wearing, influence microbial ecology.<br><br>RESULTS: The richness and diversity of the nasopharyngeal and nasal microbiota decreased during the COVID-19 pandemic compared with before the pandemic. Firmicutes and Proteobacteria were the most abundant phyla in the nasopharyngeal and nasal microbiota, respectively, both before and during the pandemic. Corynebacterium and Moraxella were the dominant genera in the nasopharyngeal and nasal microbiota during the COVID-19 pandemic, whereas Pseudomonas and Corynebacterium were dominant before the pandemic. Compared with pre-pandemic conditions, microbial colonization differed significantly for Cyanobacteria/Chloroplast and Bacteroidetes in the nasopharynx and for Planctomycetes in the nasal cavity during the COVID-19 pandemic.<br><br>CONCLUSIONS: This study revealed a lower microbiota diversity during COVID-19, possibly accompanied by microbiota dysbiosis, increased risk of respiratory infections and inflammatory responses in healthy children. This study underscores the importance of reestablishing microbiota balance and highlights the need for personalized treatment and prophylactic strategies in routine public health practice. Supplementary file3 (MP4 150533 KB).}, }
@article {pmid40742453, year = {2025}, author = {Lezcano, M&#xc1; and Carrizo, D and Lominchar, M&#xc1; and Sánchez-García, L and Quesada, A and Parro, V}, title = {Temperature-Sensitive Lipids Reveal Intraspecific Diversity in Bacteria Isolated from an Ancient Antarctic Microbial Mat.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {84}, pmid = {40742453}, issn = {1432-184X}, support = {FJC2018-037246-I//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2022-140180OB-C21//Ministerio de Ciencia e Innovaci&#xf3;n/ ; RYC2018-023943-I//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2021-126746NB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, mesh = {Antarctic Regions ; *Bacteria/genetics/classification/isolation &amp; purification/chemistry/metabolism ; RNA, Ribosomal, 16S/genetics ; Fatty Acids/analysis ; *Lipids/analysis/chemistry ; Temperature ; Phylogeny ; *Geologic Sediments/microbiology ; }, abstract = {Ancient Antarctic microbial mats harbour viable bacteria that have been exposed to extreme cold and arid conditions for hundreds of years. To delve into the molecular mechanisms underlaying their survival, we isolated 12 bacterial strains from a 1,000-year-old desiccated microbial mat from the McMurdo Ice Shelf and studied their lipid composition as a function of temperature. Six of the bacterial strains were classified as Paenisporosarcina macmurdoensis, and the other six as Arthrobacter sp., according to 16S rRNA gene analyses. Two strains of each taxon were incubated at their minimum and maximum growth temperatures, and the changes in their lipid profiles were analyzed. The proportion of major fatty acids (saturated, unsaturated, and iso- and anteiso-) remained relatively constant across temperature in the four strains, but the composition of hydrocarbons and alcohols differed between taxa (e.g., presence of unsaturated alkenes in Arthrobacter sp., or unidentified isoprenoid alcohols in P. macmurdoensis). This highlights the diagnostic value of non-fatty acid lipids and revealed a taxon-dependent lipid composition. Despite the taxon-associated lipid profile, incubation temperature also influenced lipid composition in both taxa, with higher temperature correlating with greater lipid richness. Interestingly, the two P. macmurdoensis strains showed distinct lipid profiles at 20°C, suggesting that intraspecific lipid diversity reflects within-species physiological variability with potential relevance for adaptation to temperature fluctuations in the mat. Therefore, assessing the influence of temperature on bacterial lipids is crucial for understanding their adaptation and survival in extreme environments, as well as for expanding species lipid inventories for biological interpretations of ancient samples.}, }
@article {pmid40742287, year = {2025}, author = {Zhang, Y and Sun, H and Huang, Q and Zhang, L and Zou, X and Liu, Y}, title = {Anaerobic Digestion Performance and Microbial Community Structures in a Pilot-Scale Up-Flow Anaerobic Sludge Blanket (UASB) Treating Distillery Wastewater.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {97}, number = {8}, pages = {e70153}, pmid = {40742287}, issn = {1554-7531}, support = {//Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant/ ; //NSERC Alliance/ ; //Alberta Distillers Limited/ ; //Alberta Innovates/ ; //City of Calgary/ ; //Canada Research Chair (CRC) in Future Water Services/ ; //China Scholarship Council (CSC) PhD Scholarship/ ; }, mesh = {Anaerobiosis ; *Waste Disposal, Fluid/methods ; *Bioreactors/microbiology ; Pilot Projects ; *Sewage/microbiology ; *Wastewater/microbiology ; *Industrial Waste ; Bacteria/metabolism ; Methane ; }, abstract = {Anaerobic digestion (AD) is a promising technology for treating high-strength industrial wastewater while recovering biogas as a renewable energy source. In this study, a pilot-scale up-flow anaerobic sludge blanket (UASB) reactor, with a working volume of 225 L, was operated for 130 days to treat raw distillery wastewater. Three different types of distillery wastewater, including centrate, spent caustic, and other low-strength process wastewater generated during operations (e.g., condensation water), were mixed to balance extreme pH levels and create conditions more suitable for AD. The UASB reactor demonstrated stable performance at an organic loading rate (OLR) of 10.0 kg COD/m[3]/day, achieving a COD removal efficiency of 86%. Average methane yield was more than 71% throughout the operation. Microbial community analysis revealed a significant increase in key syntrophic bacteria and methanogens, with Methanobacterium accounting for 55.8% of the archaeal population. Network and Mantel analyses indicated that syntrophic partnerships play a crucial role in enhancing AD of distillery wastewater under high OLR conditions. Overall, the UASB reactor exhibited high process stability, highlighting its potential for large-scale application in distillery wastewater treatment.}, }
@article {pmid40742109, year = {2025}, author = {Jones, KR and Song, Y and Rinaldi, SS and Moran, NA}, title = {Effects of priority on strain-level composition of the honey bee gut community.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0082825}, doi = {10.1128/aem.00828-25}, pmid = {40742109}, issn = {1098-5336}, abstract = {Host-associated microbiomes are complex communities shaped by interactions between members. The type VI secretion system (T6SS), among other bacterial weapons, allows gram-negative bacteria to deliver toxic effectors into competitors. In this study, we investigated the impact of differential colonization timing on the competitive advantage associated with T6SS possession using Snodgrassella alvi, a core symbiont of the honey bee gut microbiome. Following a timeline based on the natural establishment window of the gut microbiome, we sequentially inoculated newly emerged bees with fluorescently labeled strains that differed in presence of the T6SS-1. When inoculated simultaneously, the T6SS-1-possessing strain (wkB2) consistently excluded the T6SS-1-lacking strain (wkB332); however, when given a 5-day advantage, the second strain was consistently excluded regardless of strain identities. With a 1-day advantage, the effect of priority was weakened, but wkB332 was able to persist following introduction of wkB2. Utilizing a wkB2 T6SS-1 knockout strain, we repeated our 24 hour priority experiments and found that the T6SS-1 contributes to invasion outcomes along with other mechanisms of competition. Through fluorescent microscopy, we explored how coexisting strains in these experimental scenarios organize spatially within the bee ileum. Our results demonstrate that colonization timing can have lasting consequences for strain composition of the established microbiome. These findings illustrate the influence of stochastic processes in microbial community assembly and emphasize that differences in colonization timing may alter competitive outcomes between taxa, impacting taxon coexistence.IMPORTANCEThe bacterial gut communities of honey bees possess considerable strain-level diversity between hives, between individual bees, and within individual bees. However, the factors underlying strain coexistence are unclear. Here, we provide support for timing of colonization, or priority effects, as one factor driving this strain-level diversity. Our results show that priority inoculation can prevent colonization by subsequent competing bacterial strains and mitigate advantages conferred through bacterial weaponry. Further, a brief window of priority can facilitate the coexistence of strongly and weakly competitive strains within single bees. These results add to our understanding of the impacts of priority effects in host-associated microbial communities. Such an understanding can aid the development of future probiotic strategies aimed at improving honey bee health.}, }
@article {pmid40740319, year = {2025}, author = {Siceloff, AT and Waltman, D and Gunning, CE and Nolan, SP and Rohani, P and Shariat, NW}, title = {Longitudinal study highlights patterns of Salmonella serovar co-occurrence and exclusion in commercial poultry production.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1570593}, pmid = {40740319}, issn = {1664-302X}, abstract = {Recent advances in next-generation sequencing approaches have revealed that Salmonella often exists in multiserovar populations, with important implications for public health as time and resource constraints limit serovar characterization by colony-based isolation methods. It is important to characterize Salmonella population dynamics to then understand how the microbial ecology influences serovar evolution and thus, animal and human health outcomes. Chicken remains the leading source of foodborne Salmonella outbreaks in the U. S., despite reductions in contamination at the product level, underscoring the need for targeted control strategies. This study aimed to survey multiserovar Salmonella populations in broiler breeder flocks and monitor fluctuations throughout production. Deep serotyping was performed on environmental breeder samples collected over 2 years as part of a surveillance program. About 18% (104/568) of samples contained multiple serovars, with serovar Kentucky negatively associated with other serovars, often excluding them. Longitudinal sampling across two commercial complexes over 65 weeks included pullet and breeder farms. Environmental samples were collected via pre-moistened boot socks and rodent bait boxes, with on-farm rodents captured. Salmonella prevalence in pullet flocks was 17% (11/64), while 41% (135/330) of breeder samples were positive, peaking at 38 weeks of age. Rodents showed 35% (17/49) positivity in gastrointestinal samples and 9% (3/33) in bait station swabs, with six serovars identified, three of which were shared with flocks. Our cross-sectional and longitudinal Salmonella surveillance highlights the complexity of serovar interactions with further work required to elucidate the mechanisms of competitive exclusion.}, }
@article {pmid40739711, year = {2025}, author = {Xu, Y and Zhu, Y and Wu, X and Peng, W and Zhong, Y and Cai, Y and Chen, W and Liu, L and Tan, B and Chen, T}, title = {Gut Microbiota-Derived Acetate Ameliorates Endometriosis via JAK1/STAT3-Mediated M1 Macrophage Polarisation.}, journal = {Microbial biotechnology}, volume = {18}, number = {8}, pages = {e70202}, pmid = {40739711}, issn = {1751-7915}, support = {8216140922//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Female ; *Endometriosis/therapy/microbiology/metabolism ; Mice ; Humans ; Fecal Microbiota Transplantation ; *STAT3 Transcription Factor/metabolism ; *Janus Kinase 1/metabolism ; *Macrophages/metabolism/immunology ; Disease Models, Animal ; *Acetates/metabolism ; Signal Transduction ; Feces/microbiology/chemistry ; }, abstract = {Endometriosis (EMs) is a common inflammatory disorder in women of reproductive age, severely impacting patients' quality of life and fertility. Current hormonal therapies offer limited efficacy, and surgical interventions often fail to prevent recurrence. Recent studies suggest a close association between gut microbiota and the pathophysiology of EMs, though the precise mechanisms remain unclear. To investigate the influence of gut microbiota on EMs, this study established an EMs mouse model and performed faecal microbiota transplantation (FMT) using samples from healthy donors (AH group) and EMs patients (AE group) into the model mice. Results demonstrated that compared to the model group (M group), FMT from healthy donors (AH group) significantly reduced ectopic lesion volume (658.3 ± 116.1 vs. 167.2 ± 112.8 mm[3], p < 0.01) and weight (0.7420 ± 0.1233 vs. 0.1885 ± 0.1239 mg, p < 0.01). Conversely, FMT from EMs patients exacerbated disease progression. Mechanistic studies revealed that healthy donor FMT attenuated EMs by remodelling the gut microbial composition (enhancing α-diversity and Lactobacillus abundance while suppressing Bacteroidetes), significantly elevating acetate levels in faeces and ectopic lesions, activating the JAK1/STAT3 signalling pathway within lesions, and thereby driving macrophage polarisation toward the M1 phenotype (by increased iNOS/CD86 expression and decreased Arg1/CD206 expression). Simultaneously, healthy donor FMT enhanced intestinal barrier integrity by upregulating tight junction proteins (ZO-1, Occludin, Claudin-1/5) and reducing levels of intestinal permeability markers (DAO, IFABP). In contrast, AE group FMT disrupted gut microbial ecology, reduced acetate production, failed to activate the JAK1/STAT3 pathway, promoted M2 macrophage polarisation and impaired intestinal barrier function. Collectively, this study elucidates for the first time that acetate, as a key gut microbiota metabolite, exerts anti-EMs effects by activating the JAK1/STAT3 signalling pathway to drive macrophage reprogramming toward the M1 phenotype, thereby positioning gut microbiota reconstruction as a novel therapeutic strategy for endometriosis.}, }
@article {pmid40736560, year = {2025}, author = {Braglia, C and Cutajar, S and Magagnoli, S and Asciano, D and Burgio, G and Di Gioia, D and Baffoni, L and Alberoni, D}, title = {The Ground Beetle Poecilus (Carabidae) Gut Microbiome and Its Functionality.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {83}, pmid = {40736560}, issn = {1432-184X}, support = {ALMAIDEA-2018//University of Bologna/ ; ALMAIDEA-2018//University of Bologna/ ; ALMAIDEA-2018//University of Bologna/ ; ALMAIDEA-2018//University of Bologna/ ; ALMAIDEA-2018//University of Bologna/ ; }, mesh = {Animals ; *Coleoptera/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Nosema/isolation &amp; purification/genetics ; High-Throughput Nucleotide Sequencing ; DNA, Bacterial/genetics ; Solanum lycopersicum ; }, abstract = {Ground beetles of the genus Poecilus (Carabidae) play key ecological roles in pest control and soil health. However, their gut microbiome remains largely unexplored despite increasing interest in insect-associated microbiota and its environmental implications. This study used next-generation sequencing and qPCR to characterise the gut microbiome of Poecilus beetles collected from organic and conventional tomato fields. Core microbiota were identified through prevalence-abundance filtering, revealing dominant genera including Gilliamella, Weissella, Enterobacter, and Enterococcus, alongside several low-abundance but consistently present taxa. Notably, Carnobacterium was detected for the first time in an insect host, and Nosema ceranae was identified for the first time in Carabidae, expanding the known host range of this microsporidian pathogen. Functional predictions based on 16S rRNA data and comparative genomic analysis showed enrichment in pathways related to amino acid synthesis, protein degradation, and monosaccharide metabolism. Significant inter-individual variation in microbial diversity and predicted functionality was observed, with lowest diversity and metabolic potential in beetles from conventionally managed fields, potentially indicating dysbiosis and environmental stress. The detection of Nosema and Serratia pathogens in some individuals adds new insights into pathogen dynamics within carabid beetles. Our findings reveal that the gut microbiome of Poecilus may be shaped by environmental factors and agricultural practices, influencing host health and ecological performance. These insights support the use of Poecilus as a bioindicator for soil ecosystem health and highlight the potential of microbiome-based metrics in agroecological monitoring.}, }
@article {pmid40732998, year = {2025}, author = {Herrera, M and Byerley, LO}, title = {Dietary Nitrogen and Its Role in the Gut Microbiome and Inflammatory Bowel Disease: A Narrative Review.}, journal = {Nutrients}, volume = {17}, number = {14}, pages = {}, pmid = {40732998}, issn = {2072-6643}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Inflammatory Bowel Diseases/microbiology/metabolism ; *Nitrogen/metabolism ; *Diet ; Dysbiosis ; Animals ; }, abstract = {In recent years, gut microbiota has emerged as a critical regulator of gastrointestinal health and disease, with its role in inflammatory bowel disease (IBD)-including Crohn's disease and ulcerative colitis-being particularly significant. Among the many factors influencing the gut microbiota, dietary components such as fibers, fats, and polyphenols have received substantial attention. However, nitrogen-containing compounds, such as amino acids, nitrates, urea, and even nucleic acids, such as purines, remain underexplored despite their integral role in shaping microbial ecology, host metabolism, and immune responses. Some of these compounds are metabolized by gut bacteria into bioactive molecules such as short-chain fatty acids, ammonia, and nitric oxide, which exert diverse effects on mucosal integrity and inflammation. IBD pathophysiology is characterized by chronic inflammation, microbial dysbiosis, and compromised epithelial barriers. Nitrogen metabolism contributes significantly to these processes by influencing microbial composition, metabolite production, and host immune pathways. The breakdown of various nitrogen-containing compounds in the body leads to the production of byproducts, such as ammonia and hydrogen sulfide, which have been implicated in mucosal damage and immune dysregulation. At the same time, nitrogen-derived molecules, such as short-chain fatty acids and nitric oxide, exhibit protective effects, underscoring the dual role of dietary nitrogen in health and disease. This narrative review highlights the complex interactions between dietary nitrogen sources, gut microbiota, and IBD pathogenesis. We summarize the mechanisms by which nitrogen compounds influence microbial dynamics, identify their contributions to inflammation and barrier dysfunction, and explore their therapeutic potential. Multidisciplinary approaches integrating clinical, metabolomic, and microbiome research are essential to unravel the full scope of nitrogen's role in gut health and identify novel therapeutic targets.}, }
@article {pmid40732683, year = {2025}, author = {Lin, H and Zeng, Z and Zhang, H and Jia, Y and Pang, J and Chen, J and Zhang, H}, title = {Gut-Vaginal Microbiome Crosstalk in Ovarian Cancer: Implications for Early Diagnosis.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {7}, pages = {}, pmid = {40732683}, issn = {2076-0817}, support = {2021YFH0189//Sichuan International Science and Technology Innovation Cooperation/HongKong/Macao/Taiwan Science and Technology Innovation Cooperation Project/ ; 2022NSFSC1363//the Sichuan International Science Foundation Project/ ; 2021HXFH065//the project for disciplines of excellence-Clinical Research Incubation Project, West China Hospital, Sichuan University/ ; }, mesh = {Humans ; Female ; *Ovarian Neoplasms/diagnosis/microbiology ; *Vagina/microbiology ; *Gastrointestinal Microbiome ; Early Detection of Cancer/methods ; Dysbiosis/microbiology ; }, abstract = {Ovarian cancer remains a formidable global health burden, characterized by frequent late-stage diagnosis and elevated mortality rates attributable to its elusive pathogenesis and the critical lack of reliable early-detection biomarkers. Emerging investigations into the gut-vaginal microbiome axis have unveiled novel pathogenic mechanisms and potential diagnostic targets in ovarian carcinogenesis. This comprehensive review systematically examines the compositional alterations in and functional interplay between vaginal and intestinal microbial communities in ovarian cancer patients. We elucidate three principal mechanistic pathways through which microbial dysbiosis may drive oncogenesis: (1) estrogen-mediated metabolic reprogramming via β-glucuronidase activity; (2) chronic activation of pro-inflammatory cascades (particularly NF-κB and STAT3 signaling); (3) epigenetic silencing of tumor suppressor genes through DNA methyltransferase modulation. We propose an integrative diagnostic framework synthesizing multi-omics data-incorporating microbial profiles, metabolic signatures, pathway-specific molecular alterations, established clinical biomarkers, and imaging findings-within a multifactorial etiological paradigm. This innovative approach aims to enhance early-detection accuracy through machine learning-enabled multidimensional pattern recognition. By bridging microbial ecology with tumor biology, this review provides novel perspectives for understanding ovarian cancer etiology and advancing precision oncology strategies through microbiome-targeted diagnostic innovations.}, }
@article {pmid40732215, year = {2025}, author = {Bodkhe, GA and Kumar, V and Li, X and Pei, S and Ma, L and Kim, M}, title = {Biosensors in Microbial Ecology: Revolutionizing Food Safety and Quality.}, journal = {Microorganisms}, volume = {13}, number = {7}, pages = {}, pmid = {40732215}, issn = {2076-2607}, support = {RS-2025-00515546//National Research Foundation (NRF) of Korea grant funded by the Korea Government (MIST)/ ; RS-2020-NR049591//National Research Foundation of Korea/ ; }, abstract = {Microorganisms play a crucial role in food processes, safety, and quality through their dynamic interactions with other organisms. In recent years, biosensors have become essential tools for monitoring these processes in the dairy, meat, and fresh produce industries. This review highlights how microbial diversity, starter cultures, and interactions, such as competition and quorum sensing, shape food ecosystems. Diverse biosensor platforms, including electrochemical, optical, piezoelectric, thermal, field-effect transistor-based, and lateral flow assays, offer distinct advantages tailored to specific food matrices and microbial targets, enabling rapid and sensitive detection. Biosensors have been developed for detecting pathogens in real-time monitoring of fermentation and tracking spoilage. Control strategies, including bacteriocins, probiotics, and biofilm management, support food safety, while decontamination methods provide an additional layer of protection. The integration of new techniques, such as nanotechnology, CRISPR, and artificial intelligence, into Internet of Things systems is enhancing precision, particularly in addressing regional food safety challenges. However, their adoption is still hindered by complex food matrices, high costs, and the growing challenge of antimicrobial resistance. Looking ahead, intelligent systems and wearable sensors may help overcome these barriers. Although gaps in standardization and accessibility remain, biosensors are well-positioned to revolutionize food microbiology, linking ecological insights to practical solutions and paving the way for safer, high-quality food worldwide.}, }
@article {pmid40731978, year = {2025}, author = {Garcia, M and Bruna, P and Duran, P and Abanto, M}, title = {Cyanobacteria and Soil Restoration: Bridging Molecular Insights with Practical Solutions.}, journal = {Microorganisms}, volume = {13}, number = {7}, pages = {}, pmid = {40731978}, issn = {2076-2607}, abstract = {Soil degradation has been accelerating globally due to climate change, which threatens food production, biodiversity, and ecosystem balance. Traditional soil restoration strategies are often expensive, slow, or unsustainable in the long term. In this context, cyanobacteria have emerged as promising biotechnological alternatives, being the only prokaryotes capable of performing oxygenic photosynthesis. Moreover, they can capture atmospheric carbon and nitrogen, release exopolysaccharides (EPSs) that stabilize the soil, and facilitate the development of biological soil crusts (biocrusts). In recent years, the convergence of multi-omics tools, such as metagenomics, metatranscriptomics, and metabolomics, has advanced our understanding of cyanobacterial dynamics, their metabolic potential, and symbiotic interactions with microbial consortia, as exemplified by the cyanosphere of Microcoleus vaginatus. In addition, recent advances in bioinformatics have enabled high-resolution taxonomic and functional profiling of environmental samples, facilitating the identification and prediction of resilient microorganisms suited to challenging degraded soils. These tools also allow for the prediction of biosynthetic gene clusters and the detection of prophages or cyanophages within microbiomes, offering a novel approach to enhance carbon sequestration in dry and nutrient-poor soils. This review synthesizes the latest findings and proposes a roadmap for the translation of molecular-level knowledge into scalable biotechnological strategies for soil restoration. We discuss approaches ranging from the use of native biocrust strains to the exploration of cyanophages with the potential to enhance cyanobacterial photosynthetic activity. By bridging ecological functions with cutting-edge omics technologies, this study highlights the critical role of cyanobacteria as a nature-based solution for climate-smart soil management in degraded and arid ecosystems.}, }
@article {pmid40731225, year = {2025}, author = {Sharma, P and Muehe, EM}, title = {Metal-tainted soils: a hidden threat to agriculture and health.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2025.07.004}, pmid = {40731225}, issn = {1878-4372}, abstract = {Hou et al. have revealed widespread metal contamination in agricultural soils, threatening food security, food quality, and human health. We propose climate-informed risk mapping of the mobile metal pool aligned with crop production mapping, followed by risk management strategies through engineered crops, metal-remediating plants, and targeted organic and microbial amendments.}, }
@article {pmid40730873, year = {2025}, author = {Roegiers, I and Gheysens, T and Minsart, M and De Clercq, P and Vanbeversluys, K and Rać, N and Stroka, G and de Croock, J and Van de Wiele, T and Dubruel, P and Arroyo, MC}, title = {Author Correction: GelMA as scaffold material for epithelial cells to emulate the small intestinal microenvironment.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {27634}, doi = {10.1038/s41598-025-13398-1}, pmid = {40730873}, issn = {2045-2322}, }
@article {pmid40728944, year = {2025}, author = {Lange-Enyedi, NT and Tóth, E and Abbaszade, G and Németh, P and Garvie, LAJ and Wolf, J and Neumann-Schaal, M and Khayer, B and Sipos, G and Makk, J}, title = {Pseudogemmobacter sonorensis sp. nov., a new alphaproteobacterium isolated from the slime flux of a tree (Populus fremontii) in the Sonoran Desert (Arizona, USA).}, journal = {International journal of systematic and evolutionary microbiology}, volume = {75}, number = {7}, pages = {}, doi = {10.1099/ijsem.0.006859}, pmid = {40728944}, issn = {1466-5034}, mesh = {RNA, Ribosomal, 16S/genetics ; *Phylogeny ; Bacterial Typing Techniques ; Fatty Acids/chemistry/analysis ; Base Composition ; DNA, Bacterial/genetics ; Desert Climate ; Sequence Analysis, DNA ; Ubiquinone/chemistry/analogs &amp; derivatives/analysis ; *Populus/microbiology ; Phospholipids/analysis ; Nucleic Acid Hybridization ; *Methylobacteriaceae/classification/isolation &amp; purification/genetics ; *Soil Microbiology ; Trees/microbiology ; }, abstract = {The bacterial strain PA1-206B[T] is a Gram-stain-negative, aerobic, non-motile and non-spore-forming bacterium with an irregular rod shape. It was isolated from a tree wound exudate of the Populus fremontii trunk in the Sonoran Desert (USA), and its taxonomic position was investigated by a polyphasic approach. Strain PA1-206B[T] grew optimally at 28-30 °C and from pH 6 to 10 without NaCl. Based on 16S rRNA gene sequence analysis, this isolate showed only 96.0% sequence similarity to the type strain of Pseudogemmobacter hezensis and similarity of 94.4-95.7% to other species of the genus. Phylogenetic analysis based on whole-proteome comparisons placed strain PA1-206B[T] within the genus Pseudogemmobacter but, on a distinct branch, clearly separated from its closest relatives. The major isoprenoid quinone of the strain was ubiquinone Q-10. The predominant fatty acids (>5%) were C18:1 ω7c, C16:0 and 11-methyl-C18:1 ω7c. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid and two unidentified phospholipids were present. The assembled draft genome of strain PA1-206B[T] had 115 contigs with a total length of 4.5 Mb and a G+C content of 67.4 mol%. The overall genome-related indices (average nucleotide identity <80.4%, average amino acid identity <70.6%, digital DNA-DNA hybridization <21.6%) with respect to close relatives were below the corresponding threshold to demarcate bacterial species. Strain PA1-206B[T] (=DSM 115559[T]=NCAIM B.02680[T]) is suggested as the type strain of a novel Pseudogemmobacter species, for which the name Pseudogemmobacter sonorensis sp. nov. is proposed.}, }
@article {pmid40727685, year = {2025}, author = {Webb, H and Fuchs, M and Abbott, BW and Douglas, TA and Elder, CD and Ernakovich, JG and Euskirchen, ES and Göckede, M and Grosse, G and Hugelius, G and Jones, MC and Koven, C and Kropp, H and Lathrop, E and Li, W and Loranty, MM and Natali, SM and Olefeldt, D and Schädel, C and Schuur, EAG and Sonnentag, O and Strauss, J and Virkkala, AM and Turetsky, MR}, title = {A Review of Abrupt Permafrost Thaw: Definitions, Usage, and a Proposed Conceptual Framework.}, journal = {Current climate change reports}, volume = {11}, number = {1}, pages = {7}, pmid = {40727685}, issn = {2198-6061}, abstract = {PURPOSE OF REVIEW: We review how 'abrupt thaw' has been used in published studies, compare these definitions to abrupt processes in other Earth science disciplines, and provide a definitive framework for how abrupt thaw should be used in the context of permafrost science.<br><br>RECENT FINDINGS: We address several aspects of permafrost systems necessary for abrupt thaw to occur and propose a framework for classifying permafrost processes as abrupt thaw in the future. Based on a literature review and our collective expertise, we propose that abrupt thaw refers to thaw processes that lead to a substantial persistent environmental change within a few decades. Abrupt thaw typically occurs in ice-rich permafrost but may be initiated in ice-poor permafrost by external factors such as hydrologic change (i.e., increased streamflow, soil moisture fluctuations, altered groundwater recharge) or wildfire.<br><br>SUMMARY: Permafrost thaw alters greenhouse gas emissions, soil and vegetation properties, and hydrologic flow, threatening infrastructure and the cultures and livelihoods of northern communities. The term 'abrupt thaw' has emerged in scientific discourse over the past two decades to differentiate processes that rapidly impact large depths of permafrost, such as thermokarst, from more gradual, top-down thaw processes that impact centimeters of near-surface permafrost over years to decades. However, there has been no formal definition for abrupt thaw and its use in the scientific literature has varied considerably. Our standardized definition of abrupt thaw offers a path forward to better understand drivers and patterns of abrupt thaw and its consequences for global greenhouse gas budgets, impacts to infrastructure and land-use, and Arctic policy- and decision-making.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s40641-025-00204-3.}, }
@article {pmid40725499, year = {2025}, author = {Saint-Jean, M and Claisse, O and Marrec, CL and Samot, J}, title = {Structural and Genetic Diversity of Lysis Modules in Bacteriophages Infecting the Genus Streptococcus.}, journal = {Genes}, volume = {16}, number = {7}, pages = {}, pmid = {40725499}, issn = {2073-4425}, mesh = {*Streptococcus/virology/genetics ; *Genetic Variation ; *Genome, Viral ; *Streptococcus Phages/genetics ; *Bacteriophages/genetics ; Endopeptidases/genetics ; Phylogeny ; Viral Proteins/genetics ; *Bacteriolysis/genetics ; }, abstract = {Background/Objectives: Bacteriophages infecting the genus Streptococcus play a crucial role in microbial ecology and have potential applications in biotechnology and medicine. Despite their importance, significant gaps remain in our understanding of their lysis modules. This study aims to address these deficiencies by analyzing the genomic diversity and lysis module organization in Streptococcus phages. Methods: A search was conducted in the NCBI RefSeq database to identify phage genomes infecting Streptococcus. A representative panel was selected based on taxonomic diversity. Lysis modules were annotated and visualized, functional domains in endolysins were identified, and holins were characterized. Results: A total of 205 phage genomes were retrieved from the NCBI RefSeq database, of which 185 complete genomes were analyzed. A subset of 34 phages was selected for in-depth analysis, ensuring the representation of taxonomic diversity. The lysis modules were annotated and visualized, revealing five distinct organizations. Among the 256 identified endolysins, 25 distinct architectural organizations were observed, with amidase activity being the most prevalent. Holins were classified into 9 of the 74 families listed in the Transporter Classification Database, exhibiting one to three transmembrane domains. Conclusions: This study provides insights into the structural diversity of lysis modules in Streptococcus phages, paving the way for future research and potential biotechnological applications.}, }
@article {pmid40725462, year = {2025}, author = {Ait Zenati, F and Baldi, S and Di Gloria, L and Djoudi, F and Bertorello, S and Ramazzotti, M and Niccolai, E and Amedei, A}, title = {Compositional and Functional Disparities in the Breast Oncobiome Between Patients Living in Urban or Rural Areas.}, journal = {Genes}, volume = {16}, number = {7}, pages = {}, pmid = {40725462}, issn = {2073-4425}, support = {2020-WIDE SPREAD-05-2020-Twinning Grant Agreement, No. 952583//European Commission/ ; }, mesh = {Humans ; *Breast Neoplasms/microbiology/genetics/epidemiology/pathology ; Female ; *Microbiota/genetics ; Rural Population ; Middle Aged ; Urban Population ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Adult ; Aged ; }, abstract = {Background/Objectives: Breast cancer (BC) is the leading cause of cancer incidence and mortality among women and the recent identification of a resident mammary microbiota has highlighted its potential role in breast carcinogenesis. Given that environmental and socioeconomic factors influence both BC prevalence and tumor-associated bacterial composition, this study aimed to evaluate the compositional and functional features of the mammary microbiota in cancerous (oncobiome) and adjacent healthy BC tissues from patients living in urban and rural areas. Methods: Microbiota composition in both the oncobiome and adjacent healthy BC tissues was analyzed using 16S rRNA sequencing. Results: Significant variations in breast oncobiome composition were observed among BC patients from urban and rural areas. A statistically significant β dispersion among breast oncobiome of patients from urban or rural areas was highlighted. Specifically, the genera Selenomonas, Centipeda, Leptotrichia, Neisseria and Porphyromonas were found exclusively in BC tissues of patients from rural areas. Additionally, bacteria from the Neisseriaceae, Porphyromonadaceae, and Selenomonadaceae families, as well as the Selenomonas genus, were significantly enriched in the oncobiome of rural BC patients. Furthermore, the results of the PICRUSt2 (phylogenetic investigation of communities by reconstruction of unobserved states) revealed a significant increase in phospholipid biosynthesis pathways in breast oncobiome of patients from rural areas compared to those from urban areas. Conclusions: This study provides evidence of distinct compositional and functional differences in the breast oncobiome between BC patients from rural and urban areas. These findings suggest that environmental factors influence local microbiome composition, potentially contributing to BC development and/or progression.}, }
@article {pmid40724585, year = {2025}, author = {Liu, W and Zhang, C and Kuang, X and Zeng, X and Zhang, J and Wang, Q and Yang, H}, title = {Effects of Dietary Calcium and Phosphorus Levels on Growth Performance, Calcium-Phosphorus Homeostasis, and Gut Microbiota in Ningxiang Pigs.}, journal = {Life (Basel, Switzerland)}, volume = {15}, number = {7}, pages = {}, pmid = {40724585}, issn = {2075-1729}, support = {2021YFD1300402//Key National Research and Development Program projects/ ; 24A0044//Hunan Provincial Department of Education key project/ ; }, abstract = {Optimal dietary calcium (Ca) and phosphorus (P) requirements remain undetermined for Ningxiang pigs, a valuable indigenous Chinese breed. This study conducted a continuous feeding trial with two growth phases (grower: 30-50 kg; finisher: 50-80 kg) using fixed Ca/P ratios to systematically evaluate the effects of Ca/P levels on growth performance and mineral metabolism. A total of 180 pigs per phase were allocated to four Ca/P levels. During the grower phase, a dietary regimen of 0.83% Ca/0.67% P significantly increased the average daily feed intake (ADFI), average daily gain (ADG), and apparent total tract digestibility (ATTD) of energy and P. In the finisher phase, 0.60/0.48% Ca/P showed optimal growth performance, upregulated jejunal mineral transporters (CaSR and SLC34A2), enhanced bone mineralization (metatarsal ash content), and improved intestinal morphology (duodenal and jejunal villus height, jejunal villus surface area). This regimen also selectively enriched Peptostreptococcaceae abundance, indicating improved host-microbe interactions. Based on these findings, stage-specific nutritional strategies were recommended: 0.83% Ca/0.67% P during the grower phase and 0.60% Ca/0.48% P during the finisher phase. These protocols synergistically improve microbial ecology, intestinal function, and bone metabolism, thereby maximizing the growth potential of Ningxiang pigs.}, }
@article {pmid40723916, year = {2025}, author = {Wei, M and Liu, H and Hu, Z and Wen, P and Ye, Y and Chamba, Y and Zhang, H and Shang, P}, title = {A Mechanistic Approach to Replacing Antibiotics with Natural Products in the Treatment of Bacterial Diarrhea.}, journal = {Biomolecules}, volume = {15}, number = {7}, pages = {}, pmid = {40723916}, issn = {2218-273X}, support = {533325001//Xizang agriculture and Aninal Husbandry University Doctoral Progran in forestry (Fhase I) funded by Grant/ ; XZ202501ZY0147//Sxpported by Science and Technology Projects of Xizang Axtonomoxs Region, China/ ; 2023YFD1801304//National Key Research and Development Program/ ; }, mesh = {*Biological Products/therapeutic use/pharmacology ; *Diarrhea/drug therapy/microbiology ; Humans ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Gastrointestinal Microbiome/drug effects ; Animals ; Bacteria/drug effects ; *Bacterial Infections/drug therapy/microbiology ; }, abstract = {Natural products have emerged as potential alternatives to antibiotics in the treatment of bacterial diarrhea, due to their multi-targeting effects, low potential for inducing resistance, and favorable safety profiles. Currently, the search for natural product-based therapies has become an emerging focus in medical research. This growing interest is driven by the increasing awareness that the widespread and irrational use of antibiotics has contributed to the alarming rise in antibiotic-resistant bacterial strains, which in turn diminishes the efficacy of conventional drugs. Among these concerns, the limitations of antibiotics in managing bacterial diarrhea and the potential mechanisms by which natural products exert therapeutic effects are the main focus of this paper. Natural products, containing a wide array of bioactive compounds, can not only directly inhibit the growth of pathogenic bacteria, disrupt bacterial membrane synthesis, and reduce toxin production, but also modulate inflammatory responses, enhance immune function, repair intestinal barriers, and restore gut microbial ecology-highlighting their systemic and multi-targeted therapeutic potential. Therefore, this paper will elaborate on how natural products combat bacterial diarrhea from three aspects: the pathogen and pathogenesis of bacterial diarrhea, natural product-based therapeutic studies, and the underlying mechanisms of action, thereby proposing natural products as viable alternatives to antibiotics.}, }
@article {pmid40723361, year = {2025}, author = {Jiang, J and Zhang, H and Hussain, M and Abdullah,  and Feng, F and Guan, R and Zhong, H}, title = {Novel Approaches in Glucose and Lipid Metabolism Disorder Therapy: Targeting the Gut Microbiota-Bile Acid Axis.}, journal = {Biology}, volume = {14}, number = {7}, pages = {}, pmid = {40723361}, issn = {2079-7737}, support = {32402088//National Natural Science Foundation of China/ ; 2024C04012//"Pioneer" and "Leading Goose" R&amp;D Program of Zhejiang Province/ ; LQ23C200011//Zhejiang Provincial Natural Science Foundation of China/ ; KYY-HX-20230084, KYY-HX-20240810//Zhejiang University of Technology - Company Crosswise Project/ ; }, abstract = {Metabolic dysregulation involving glucose and lipids is closely associated with chronic diseases such as type 2 diabetes mellitus. Emerging evidence highlights the regulatory role of bile acid (BA)-gut microbiota interactions in these metabolic disorders. The gut microbiota orchestrates the biotransformation of primary BAs into bioactive secondary BAs, which function as endocrine signaling molecules by activating the nuclear farnesoid X receptor (FXR) and G protein-coupled membrane receptor (TGR5), forming a communication network essential for metabolic homeostasis. BAs also reciprocally modulate gut microbiota composition. This BA-gut microbiota co-metabolism has emerged as a promising therapeutic target for lipid metabolism disorders. This comprehensive review examines the bidirectional interplay between gut microbiota and BA metabolism, focusing on microbial transformation of BAs, host-microbial co-regulatory pathways and mechanisms of BA metabolism, and the therapeutic implications of modulating the gut microbiota-BA axis in addressing glucose and lipid metabolism disorders. The synthesis of current evidence aims to elucidate the intricate crosstalk between microbial ecology and host metabolism mediated by BA signaling pathways, thereby exploring novel therapeutic intervention strategies.}, }
@article {pmid40722002, year = {2025}, author = {Jordan, S and Pothier, JF and de Maayer, P and Broders, K and Kvitko, BH and Coutinho, TA and Smits, THM}, title = {Design of genus-specific semi-nested primers for simple and accurate identification of Enterobacter strains.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {456}, pmid = {40722002}, issn = {1471-2180}, support = {310030L_204333//Swiss National Science Foundation (SNSF)- South-African National Research Foundation (NRF) Lead Agency project/ ; 2019-51181-30013//USDA NIFA SCRI/ ; }, mesh = {*Enterobacter/genetics/classification/isolation &amp; purification ; *Polymerase Chain Reaction/methods ; *DNA Primers/genetics ; DNA, Bacterial/genetics ; Phylogeny ; }, abstract = {BACKGROUND: The genus Enterobacter, in the family Enterobacteriaceae, is of both clinical and environmental importance. This genus has undergone frequent taxonomic changes, making it challenging to identify taxa even at genus level. This study aimed to design Enterobacter genus-specific primers that can be used for simple PCR identification of large sets of putative Enterobacter isolates.<br><br>RESULTS: Comparative genomic approaches were employed to identify genes that were universally present on Enterobacter genomes but absent from the genomes of other members of the family Enterobacteriaceae, based on an initial set of 89 genomes. The presence of these genes was further confirmed in 4,276 Enterobacter RefSeq genomes. While no strictly genus-specific genes were identified, the hpaB gene demonstrated a restricted distribution outside of the genus Enterobacter. Semi-nested primers were designed for hpaB and its flanking gene hpaC (hpaBC) and evaluated on 123 strains in single-tube PCR reactions. All taxa showing positive reactions belonged to the genus Enterobacter. For Enterobacter strains the PCR yielded two amplicons at 110&#xa0;bp and at 370&#xa0;bp, while strains only displaying the 110&#xa0;bp amplicon were classified as Leclercia pneumoniae. A blind-test on 120 strains accessioned as Enterobacter sp. from the USDA-ARS culture collection (NRRL), revealed that one third of the strains had an incorrect genus assignment. Comparison of gene trees of the hpaBC fragment sequences with marker genes frequently used for single-gene barcoding or multi-locus sequence analysis (MLSA) further demonstrated its potential for preliminary species identification.<br><br>CONCLUSIONS: The nested PCR assay represents a rapid and cost-effective approach for preliminary identification of Enterobacter species. As the primer design was based on large-scale genomic comparison, including currently undescribed species clades, it will remain valid even after taxonomic changes within the genus.}, }
@article {pmid40721486, year = {2025}, author = {de Aviz, RO and Campos, JR and Silva, DEO and Barbosa, LMP and Costa, RM and Borges, JF and Leite, MRL and Rocha, SMB and Morais, PGC and Dauala, GA and Pereira, APA and de Medeiros, EV and Araujo, ASF}, title = {Microbial biomass and enzymatic activity in the rhizosphere of prickly-pear cactus genotypes inoculated with Bacillus subtilis and Paenibacillus Sp.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {27415}, pmid = {40721486}, issn = {2045-2322}, mesh = {*Rhizosphere ; *Paenibacillus/physiology ; *Bacillus subtilis/physiology ; Biomass ; Genotype ; Soil Microbiology ; *Cactaceae/microbiology/genetics ; }, abstract = {Some bacterial taxa, such as Bacillus and Paenibacillus, are known to colonize the rhizosphere and promote plant growth. However, little is known about their effect on microbial biomass and enzymatic activity in the rhizosphere of plants under semi-arid conditions. This field study assessed the effects of B. subtilis and Paenibacillus sp. in the rhizosphere of two prickly-pear cactus genotypes on microbial biomass of C, N, and P, and on enzymatic activity during early and late growth stages. The analysis of variance showed that microbial biomass and enzymatic activity were significantly influenced by the interaction between PGPB taxa (B. subtilis and Paenibacillus sp.), prickly-pear cactus genotypes ('Baiana' and 'Doce'), and plant growth stage (90 and 270 days). Specifically, PGPB inoculation increased microbial biomass P, β-glucosidase, and acid phosphatase, while microbial biomass of C and N were primarily driven by differences between cactus genotypes 'Baiana' and 'Doce'. At the early growth stage (90 days), the highest values of microbial biomass C, P, and acid phosphatase were observed, whereas N biomass was higher at the later stage (270 days). B. subtilis increased microbial biomass P in the 'Doce' genotype and acid phosphatase in 'Baiana,' while Paenibacillus sp. increased β-glucosidase in 'Baiana.' The combination of the 'Doce' genotype with B. subtilis enhanced phosphorus availability, suggesting that specific plant-microbe interactions may benefit nutrient acquisition in arid, nutrient-poor soils; however, further research is needed to confirm whether this effect extends to other genotypes.}, }
@article {pmid40719475, year = {2025}, author = {Fan, X and Guo, X and Qi, Q and Gui, H and Li, Y and Yang, Y and He, J-S and Wu, L}, title = {Long-term elevated precipitation promotes an acid metabolic preference in soil microbial communities in a Tibetan alpine grassland.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0047025}, doi = {10.1128/msystems.00470-25}, pmid = {40719475}, issn = {2379-5077}, abstract = {Alpine ecosystems store vast amounts of soil organic carbon but are highly sensitive to climate change. Despite this, the response of in situ soil microbial metabolic processes, especially carbon substrate utilization, to climatic shifts remains underexplored. Here, we assessed microbial activity by metatranscriptomics in a Tibetan alpine grassland after a decade of experimental warming (+2°C) and altered precipitation (+50% and -50% of ambient precipitation). The experiment revealed that altered precipitation, rather than warming, shaped the active microbial community. Altered precipitation and warming had significant interactions: warming combined with increased precipitation generally suppressed microbial carbohydrate metabolism and methane oxidation, while warming with decreased precipitation enhanced these processes. Notably, increased precipitation induced a shift in microbial communities towards acid metabolism over sugar metabolism, predominantly driven by taxa such as Betaproteobacteria. This metabolic shift corresponded with an increased emission ratio of methane (CH4) to carbon dioxide (CO2), a change primarily driven by CH4, underscoring the critical role of microbial carbon metabolic preferences in regulating greenhouse gas emissions. Our findings highlight the necessity of integrating microbial carbon metabolic preferences and their interactions with climatic factors into models to accurately predict carbon-climate feedbacks.IMPORTANCEMicrobes have specific preferences for different carbon substrates, but their responses to climate change remain unclear. Our study, conducted through a long-term climate manipulation experiment in a Tibetan alpine grassland, reveals that increased precipitation leads soil microbial communities to favor acid metabolism over sugar metabolism. This shift significantly affects greenhouse gas emissions by increasing the CH4/CO2 ratio, which has important implications for global warming. These findings are crucial for accurately forecasting carbon-climate feedbacks and managing alpine ecosystems as climate change progresses.}, }
@article {pmid40715283, year = {2025}, author = {Tan, JH and Liew, KJ and Sani, RK and Samanta, D and Pointing, SB and Chan, KG and Goh, KM}, title = {Microbial diversity and metabolic predictions of high-temperature streamer biofilms using metagenome-assembled genomes.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {27297}, pmid = {40715283}, issn = {2045-2322}, mesh = {*Biofilms/growth &amp; development ; *Hot Springs/microbiology ; *Metagenome ; Hot Temperature ; *Bacteria/genetics/metabolism/classification ; Microbiota ; Phylogeny ; Biodiversity ; Genome, Bacterial ; Metagenomics/methods ; Malaysia ; }, abstract = {High-temperature streamer biofilm communities (SBCs) are often dominated by Aquificota, which can comprise over 90% of the microbial population in shallow water channels, such as those found at Mammoth hot springs of Yellowstone National Park and the Rehai hot springs in China. This study examines SBCs from the Dusun Tua (DT) hot spring in Malaysia (75 °C, pH 7.6), where Aquificota accounted for only ~ 35% of the total amplicon sequence variants. Amplicon and hybrid metagenomic sequencing revealed a more balanced microbial community, co-dominated by Aquificota, Chloroflexota, Desulfobacterota, Bacteroidota, Deinococcota, and Candidatus Hydrothermae, along with Thermoproteota and Micrarchaeota. To our knowledge, the co-dominance of Aquificota and Chloroflexota in SBCs has not been previously reported. The unexpected abundance of Chloroflexota may stem from dispersal from upstream Cyanobacteriota-Chloroflexota biofilms, contributing to community diversification. Genome-resolved analyses identified more than 60 medium- to high-quality metagenome-assembled genomes (MAGs), suggesting that biofilm formation was initially driven by chemoautotrophic sulfur oxidation and CO2 fixation, followed by the gradual integration of heterotrophic taxa. Nitrogen cycling and hydrogen oxidation are likely to contribute additional sources of energy. The presence of diverse CAZymes suggests that plant litter may serve as an additional carbon source. Genome-centric analyses across multiple phyla indicated that extracellular polymeric substances (EPS), curli fibers, and other matrix components contribute to the biofilm matrix, enhancing structural resilience and supporting persistence under harsh conditions. Overall, this study highlights the distinct microbial ecology of the DT SBC and broader metabolic roles beyond Aquificota dominance. The genes identified in this study may hold biotechnological potential and serve as a valuable resource for future enzyme discovery and functional screening.}, }
@article {pmid40711892, year = {2025}, author = {Turner, D and Adriaenssens, EM and Amann, RI and Bardy, P and Bartlau, N and Barylski, J and Błażejak, S and Bouzari, M and Briegel, A and Briers, Y and Carrillo, D and Chen, X and Claessen, D and Cook, R and Crisci, MA and Dechesne, A and Deptula, P and Dutilh, BE and Ely, B and Fieseler, L and Fogg, PCM and Fukudome, A and Ganjoor, MS and Gientka, I and Holmfeldt, K and Kalatzis, PG and Kauffman, KM and Kempff, A and Knezevic, P and Koonin, EV and Kropinski, AM and Krupovic, M and Kurtböke, I and Lambon, K and Lavigne, R and Lehman, SM and Liu, HT and Lood, C and Lurz, R and Mäntynen, S and Matrishin, CB and Middelboe, M and Millard, AD and Moraru, C and Nielsen, DS and Nobrega, FL and Nunoura, T and Oksanen, HM and Ongenae, V and Parra, B and Pas, C and Pogliano, J and Poranen, MM and Potipimpanon, S and Prichard, A and Pye, HV and Rothschild-Rodriguez, D and Rozen, DE and Santini, JM and Sha, Y and Shymialevich, D and Sokołowska, B and Soleimani-Delfan, A and Średnicka, P and Tavares, P and Telatin, A and Tolstoy, I and Urayama, SI and van Neer, V and Vogensen, FK and Wen, Q and Wichels, A and Wójcicki, M and Ictv Taxonomy Summary Consortium,  and , }, title = {Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) from the Bacterial Viruses Subcommittee, 2025.}, journal = {The Journal of general virology}, volume = {106}, number = {7}, pages = {}, doi = {10.1099/jgv.0.002111}, pmid = {40711892}, issn = {1465-2099}, mesh = {*Viruses/classification/genetics ; *Bacteria/virology ; Phylogeny ; *Classification/methods ; }, abstract = {This article summarises the activities of the International Committee on Taxonomy of Viruses Bacterial Viruses Subcommittee, detailing developments in the classification of bacterial viruses. We provide here an overview of all new, abolished, moved and renamed taxa proposed in 2024, approved by the Executive Committee, and ratified by membership vote in 2025. Through the collective efforts of 74 international contributors of taxonomy proposals in this round, 43 ratified proposals have led to the creation of one new phylum, one class, four orders, 33 families, 14 subfamilies, 194 genera and 995 species. These proposals mark significant progress in refining the taxonomy of bacterial viruses. Key updates include the creation of new orders and families that include existing taxa to better reflect genomic and evolutionary relationships. As sequencing and bioinformatics approaches continue to advance, further expansion and refinements in viral taxonomy can be anticipated in the coming years.}, }
@article {pmid40711674, year = {2025}, author = {Xiong, Q and Wang, R and Lai, D and Cai, S and Wang, H and Zhou, N}, title = {Metagenomic Insights into the Root‒Soil Response Mechanisms of Indica and Japonica Rice Under Nitrogen Deficiency and High-Efficiency Nitrogen Compensation.}, journal = {Rice (New York, N.Y.)}, volume = {18}, number = {1}, pages = {72}, pmid = {40711674}, issn = {1939-8425}, support = {32101816//National Natural Science Foundation of China/ ; 2021M702768//China Postdoctoral Science Foundation/ ; 2021K292B//Jiangsu Province Postdoctoral Research Funding/ ; 2021KY47//Jiangxi Province Postdoctoral Scientific Research Funding/ ; 202425YBKT17//Jiangxi Provincial Water Resources Department Science and Technology Project/ ; 20242BAB20263//Natural Science Foundation of Jiangxi Province/ ; PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; }, abstract = {Nitrogen (N) dynamics critically regulate rice productivity through root-mediated absorption and assimilation processes. This study investigates the differential responses of japonica (Suxiu 867) and indica (Yangxianyou 918) rice to N deficiency and subsequent high-efficiency compensation, integrating metagenomic analysis with physiological assessments of N metabolism. Building on an established high-efficiency N compensation period (18 days after tillering for japonica and 12 days for indica), we demonstrate that optimized N compensation significantly enhances dry matter accumulation and yield in both subspecies through distinct biological mechanisms. Compensation treatment elevated key metabolic indicators including soluble protein content (Cpr), glutamine synthetase (GDH) activity, soil urease (S-UE) activity, glutamate synthase (GOGAT) activity, and glutamine synthetase (GS) activity, collectively enhancing N assimilation efficiency. Rhizosphere microbiome restructuring showed subspecies-specific patterns, with Chloroflexi and Betaproteobacteria abundance positively correlating with N metabolic enzymes in indica, versus Actinomycetia, Deltaproteobacteria associations in japonica. Functional microbial analysis revealed divergent keystone taxa, with Noviherbaspirillum (indica) and Bacillus (japonica) driving N conversion efficiencies through niche-specific community synergies. Notably, indica rice presented a relatively high N absorption capacity and conversion efficiency, while japonica rice presented relatively stable N absorption and distribution mechanisms, and relatively high N fertilizer application significantly increased the abundance of specific microbial communities in japonica rice. These findings elucidate how subspecies-specific root physiology coordinates with rhizosphere microbial ecology to optimize N utilization, providing actionable insights for precision N management strategies tailored to rice genetic types.}, }
@article {pmid40711470, year = {2025}, author = {Lera-Lozano, D and Ruiz-Toquica, JS and Kratman, SA and Holt, MW and McIntyre, CA and Jones, EK and Lopez-Victoria, M and Ritchie, KB and Medina, M and González-Pech, RA}, title = {Genomic potential of crustose coralline algae-associated bacteria for the biosynthesis of novel antimicrobials.}, journal = {Microbial genomics}, volume = {11}, number = {7}, pages = {}, doi = {10.1099/mgen.0.001456}, pmid = {40711470}, issn = {2057-5858}, mesh = {*Bacteria/genetics/metabolism/isolation &amp; purification/classification ; *Rhodophyta/microbiology ; Biosynthetic Pathways/genetics ; *Anti-Bacterial Agents/biosynthesis ; Multigene Family ; *Anti-Infective Agents/metabolism ; Genome, Bacterial ; Animals ; *Anthozoa/microbiology ; Genomics ; Microbiota/genetics ; Phylogeny ; }, abstract = {The global rise of antimicrobial resistance has intensified efforts in bioprospecting, with researchers increasingly exploring unique marine environments for novel antimicrobials. In line with this trend, our study focused on bacteria isolated from the unique microbiome of crustose coralline algae (CCA), which has yet to be investigated for antimicrobial discovery. In the present work, bacteria were isolated from a CCA collected from Varadero Reef located in Cartagena Bay, Colombia. After performing antimicrobial assays against antibiotic-resistant human and marine pathogens, three isolates were selected for genome sequencing using the Oxford Nanopore technology. Genome mining of the high-quality assemblies revealed 115 putative biosynthetic gene clusters (BGCs) and identified genes in relevant biosynthetic pathways across the three genomes. Nonetheless, we hypothesize that the biosynthesis of antimicrobial compounds results from the expression of undescribed BGCs. Further analysis revealed the absence of genes pertaining to the synthesis of coral larvae settling molecule tetrabromopyrrole, commonly produced by CCA-associated bacteria. We also discuss how differential representation of gene functions between the three isolates may be attributed to the distinct ecological niches they occupy within the CCA. This study provides valuable resources for future research aimed at the discovery of novel antimicrobials, particularly in the face of the antibiotic-resistance global crisis, and highlights the potential of specialized marine environments like CCA.}, }
@article {pmid40709922, year = {2025}, author = {Li, H and Li, W and Liu, X and Zhang, J and Lin, C and Ji, S and Jiang, H and Wang, T and Su, Z}, title = {The gut microbiota features and the application value in predicting recurrent risks for gallstone patients who underwent laparoscopic cholecystectomy.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0176024}, doi = {10.1128/msystems.01760-24}, pmid = {40709922}, issn = {2379-5077}, abstract = {Gut microbiota is associated with gallstone occurrence and recurrence. But whether they can predict post-cholecystectomy choledocholithiasis recurrence needs to be investigated. From September 2020 to June 2021, a total of 100 symptomatic gallstone patients scheduled for laparoscopic cholecystectomy were enrolled in the Disease group in the Department of Hepatobiliary Surgery at Quanzhou First Hospital. Meanwhile, a total of 50 age- and sex-matched healthy controls were included in the Control group. Fecal specimens were collected from both groups and subjected to 16S rDNA sequencing (V3V4 region) for microbiologic analysis. After laparoscopic cholecystectomy, patients were followed up, and recurrent cases were recorded. Finally, a nomogram for predicting recurrent risks was built. The gut microbial diversity in the Disease group was significantly lower than that of the Control group (all P < 0.05). The Chao1 index of the recurrent group was remarkably lower than the control group (P < 0.05). Linear discriminant analysis (LDA) effect size (LEfSe) analysis showed that Phocaeicola dorei (LDA score = 4.2, P < 0.05) was the feature microbiota in the recurrent group. Logistic regression analysis showed that the composition of stones, the high abundances of P. dorei and Fusobacterium necrogenes were potential risk factors for recurrent choledocholithiasis, and a nomogram based on these factors demonstrated high accuracy and excellent calibration. This study has identified potential risk factors for recurrent choledocholithiasis and built a nomogram that can well predict recurrent risks for patients who undergo cholecystectomy, which might serve as a useful tool for patients' stratification and post-surgery management.IMPORTANCEThis study identifies specific gut microbiome signatures of gallstone patients and indicates that reduced diversity and high abundances of Phocaeicola dorei and Fusobacterium necrogenes might be potential predictors for choledocholithiasis recurrence after cholecystectomy. By demonstrating a link between gut microbiota composition and post-surgical recurrence risk, it advances our understanding beyond simple association with predictive capability. The development of a nomogram incorporating these microbial markers provides a novel, clinically applicable tool for accurate risk stratification of patients undergoing cholecystectomy, therefore bridging the gap between microbial ecology and clinical practice. The significance of this study lies in that it aims to address a critical unmet need in gallstone disease management by offering a more cost-effective and non-invasive tool to improve long-term patient outcomes and pave the way for microbiome-targeted interventions.CLINICAL TRIALSThis study is registered with Chinese Clinical Trial Registry Center as ChiCTR2400090232.}, }
@article {pmid40708948, year = {2025}, author = {Zai, X and Zhu, F and Zhao, M and Diao, X and Zhang, F and Dini-Andreote, F and Melkonian, C and Medema, MH and Raaijmakers, JM and Cordovez, V and Song, C}, title = {Harnessing the phyllosphere microbiota of wild foxtail millet for designing beneficial cross-kingdom synthetic communities.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf066}, pmid = {40708948}, issn = {2730-6151}, abstract = {Understanding the interplay between mechanisms in plant microbiome assembly and functioning of wild ancestors has led to the proposal of a novel strategy to enhance resilience to the (a)biotic stresses of domesticated crops. The challenge is determining how to harness the diverse microbiota of wild crop ancestors in their natural habitats in order to design effective synthetic microbial communities (SynComs) that reconstitute specific microbiome-associated plant phenotypes. In this study, we profiled the phyllosphere microbiota of wild green foxtail collected from seven geographically diverse natural ecosystems and showed that variations in soil parameters and climatic conditions as well as plant genetic distance significantly correlated with bacterial and fungal community compositions. Environmental selection and dispersal limitation differently governed the assembly of bacterial and fungal communities with distinct habitat niche breadth. Specific bacterial and yeast genera were identified as core phyllosphere taxa of wild green foxtail millet on the basis of their abundance and prevalence across the seven sampling sites. Moreover, several genera of bacteria (Bacillus, Pantoea, Methylobacterium) and yeast (Vishniacozyma, Filobasidium, Sporobolomyces) displayed significant correlations with the abundances of one or more foliar pathogenic fungi, in particular fungi of the genus Alternaria. Subsequent isolation and characterization of these bacterial and yeast genera allowed the design of cross-kingdom SynComs that protected domesticated foxtail millet from leaf infections by Alternaria alternata. These results provide fundamental insight into the mechanisms governing the phyllosphere microbiota assembly of a wild crop ancestor across large geographic scales and a practical framework to leverage this fundamental knowledge for the design of SynComs that mitigate the biotic stress of the domesticated crop.}, }
@article {pmid40708946, year = {2025}, author = {Liu, ZQ and Yang, XY and Chen, JH and Ge, SC and Dai, SX and Zhu, SH and Xian, ZY}, title = {From dysbiosis to precision therapy: decoding the gut-bladder axis in bladder carcinogenesis.}, journal = {Frontiers in oncology}, volume = {15}, number = {}, pages = {1630726}, pmid = {40708946}, issn = {2234-943X}, abstract = {The gut-bladder axis (GBA), a bidirectional network connecting gastrointestinal and urinary systems, has recently emerged as a pivotal focus in bladder cancer research. Beyond conventional risk factors, gut dysbiosis, aberrant microbial metabolites, and neuro-immune pathway disruptions have been implicated in tumorigenesis and progression. Short-chain fatty acids (SCFAs), microbial-derived metabolites, are shown to indirectly modulate tumor behavior through immune microenvironment regulation and inflammatory response attenuation. Cross-organ crosstalk is further mediated by neural pathways (e.g., vagal signaling) and shared receptors, including the Farnesoid X Receptor (FXR) and Toll-like Receptor 4 (TLR4). Novel therapies leveraging microbial ecology principles demonstrate potential, including immune checkpoint inhibitors combined with microbiota modulation (e.g., Parabacteroides distasonis-enhanced PD-1 efficacy), probiotics to reverse chemoresistance, and microbiota reprogramming for SCFA-targeted strategies. However, molecular mechanisms underlying GBA-host interactions remain poorly characterized. Clinical translation is hindered by limited cohort sizes and interindividual heterogeneity. Current studies, while revealing partial pathways, face methodological inconsistencies, particularly in urinary microbiome profiling, and a lack of longitudinal human data. Future breakthroughs will require multi-omics integration, organoid-based models, and interdisciplinary collaboration to address these gaps.}, }
@article {pmid40708752, year = {2025}, author = {Zhang, Y}, title = {Fucoidan as a therapeutic agent for ulcerative colitis: mechanisms of action and modulation of the gut microbiota.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1626614}, pmid = {40708752}, issn = {2235-2988}, mesh = {*Polysaccharides/pharmacology/therapeutic use ; Humans ; *Gastrointestinal Microbiome/drug effects ; *Colitis, Ulcerative/drug therapy/microbiology ; Animals ; Cytokines/metabolism ; *Anti-Inflammatory Agents/pharmacology/therapeutic use ; NF-kappa B/metabolism ; Signal Transduction/drug effects ; }, abstract = {Ulcerative colitis (UC), a chronic inflammatory bowel disease driven by gut dysbiosis, immune dysregulation, and oxidative stress, lacks universally effective therapies. Fucoidan (FCD), a sulfated polysaccharide derived from brown algae, has emerged as a multifaceted therapeutic candidate due to its anti-inflammatory, antioxidant, and immunomodulatory properties. This review synthesizes FCD's mechanisms in UC pathogenesis, emphasizing its suppression of NF-κB and MAPK signaling pathways to reduce proinflammatory cytokines (e.g., IL-6, TNF-α) and regulate TLR-mediated macrophage polarization. FCD enhances intestinal barrier integrity via upregulation of tight junction proteins (Claudin-1, ZO-1) and mucin MUC2 expression, while remodeling gut microbial ecology through enrichment of SCFAs-producing bacteria (e.g., Ruminococcaceae) and suppression of pathogens (Escherichia coli, Candida albicans). Preclinical studies highlight LMWF as a superior candidate, demonstrating enhanced bioavailability and efficacy in mitigating DSS-induced colitis. Despite its promise, challenges persist in structural heterogeneity (source- and extraction-dependent), scalable production of LMWF, and insufficient pharmacokinetic data. Emerging strategies-including nanoparticle-based delivery systems and structural modifications (cross-linking, covalent bonding)-aim to overcome bioavailability limitations. This review underscores FCD's potential as a functional food or adjuvant therapy for UC, while advocating for rigorous clinical validation to bridge translational gaps, Enrichment of SCFAs-producing taxa and suppression of pathobionts (Escherichia coli, Candida albicans), mediated through prebiotic fermentation. Suppression of NF-κB activation via IκBα stabilization and inhibition of p65 nuclear translocation, and downregulation of MAPK phosphorylation (ERK1/2, JNK, p38), reducing proinflammatory cytokines (IL-6, TNF-α, IL-1β). FCD can be used as a potential treatment for UC.}, }
@article {pmid40708120, year = {2025}, author = {Perkins, AK and Grossart, HP and Rojas-Jimenez, K and Retter, A and Oakes, JM}, title = {The Functional Role of Fungi and Bacteria in Sulfur Cycling During Kelp (Ecklonia Radiata) Degradation: Unconventional Use of PiCrust2.}, journal = {Environmental microbiology reports}, volume = {17}, number = {4}, pages = {e70140}, pmid = {40708120}, issn = {1758-2229}, support = {RRF-2.3.1-21-2022-00008//National Laboratory for Water Science and Water Security, HUN-REN Balaton Limnological Research Institute/ ; DFG GR1540/47-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Sulfur/metabolism ; *Bacteria/metabolism/genetics/classification ; *Fungi/metabolism/genetics/classification ; *Kelp/microbiology/metabolism ; Metabolic Networks and Pathways ; Ecosystem ; High-Throughput Nucleotide Sequencing ; }, abstract = {Macroalgae is a major source of detritus in coastal ecosystems, contributing approximately 1521 ± 732 Tg C year[-1] to global net primary production. Fungal remineralisation of Ecklonia radiata detritus produces substantial amounts of dimethylsulfoniopropionate, total alkalinity, and dissolved inorganic carbon, supporting coastal biogeochemical cycles. To expand on the role of fungi during E. radiata degradation, we examined changes in fungal and bacterial communities at the start and after 21 days in a mesocosm, comparing microbial functional roles between blades and stipes. We employed next-generation sequencing to evaluate the potential contributions of fungi and bacteria, and additionally utilized FUNGuild, FungalTraits, and PiCrust2 databases. We cross-referenced the metabolic pathways predicted by PiCrust2 with the literature to determine whether these pathways have been documented in fungi. Of the 423 metabolic pathways identified, 342 have also been reported in fungi, including 281 redox-related pathways, 220 associated with nicotinamide adenine dinucleotide, and 194 linked to sulfur metabolism. These overlaps suggest that bacteria and fungi could play complementary roles in kelp degradation, contributing distinct yet interconnected functions. Our results highlight that these metabolic pathways cannot be attributed to bacteria alone and fungi are essential to kelp remineralisation.}, }
@article {pmid40707845, year = {2025}, author = {Jürisoo, L and Agan, A and Tedersoo, L and Witzell, J and Selikhovkin, A and Drenkhan, R}, title = {Fungal Assemblages in Northern Elms-Impacts of Host Identity and Health, Growth Environment, and Presence of Dutch Elm Disease.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {82}, pmid = {40707845}, issn = {1432-184X}, support = {PRG1615//Estonian Research Competency Council/ ; TEMTA22//the European Union and Ministry of Education and Research/ ; }, mesh = {*Plant Diseases/microbiology ; *Ulmus/microbiology/growth &amp; development/genetics ; Estonia ; Endophytes/genetics/classification/isolation &amp; purification ; *Mycobiome ; *Ophiostoma/genetics/isolation &amp; purification ; Russia ; *Fungi/classification/genetics/isolation &amp; purification ; }, abstract = {Dutch elm disease (DED), caused by the pathogenic ascomycete Ophiostoma novo-ulmi, has devastated natural elm (Ulmus spp.) populations in Europe and North America. Elm species vary in their susceptibility to this vascular disease, which may partly reflect differences in their associated mycobiomes. To investigate the diversity and composition of fungal endophyte communities in relation to host genotype, health status, and environment, we analyzed twig-associated fungi in symptomatic and asymptomatic individuals of highly susceptible U. glabra, less susceptible U. laevis, and hybrid elms growing in Estonia and Russia. Fungal communities were analyzed using PacBio long-read amplicon sequencing of the ITS1-5.8S-ITS2 gene region. Tree species exhibited distinct fungal community profiles. Ophiostoma novo-ulmi was detected exclusively in symptomatic trees and was dominant in U. glabra; it was absent in symptomatic hybrid elms. In contrast, the canker-associated pathogen Sphaeropsis ulmicola occurred in both symptomatic and asymptomatic trees, was dominant in symptomatic U. laevis, and common in symptomatic and healthy U. glabra, though less prevalent in symptomatic hybrid elms. Remarkably, S. ulmicola was associated with the highest level of damage in U. laevis while being present also in hybrid elms. While O. novo-ulmi's presence did not affect overall fungal richness, S. ulmicola was linked to higher fungal diversity. Additionally, fungal species richness was significantly greater in urban compared to rural environments. This was the first comparable analysis of fungal diversity and composition on three different Ulmus species shoots.}, }
@article {pmid40707215, year = {2025}, author = {Li-Hau, F and Nakagawa, M and Kakegawa, T and Ward, LM and Ueno, Y and McGlynn, SE}, title = {Metabolic Potential and Microbial Diversity of Late Archean to Early Proterozoic Ocean Analog Hot Springs of Japan.}, journal = {Microbes and environments}, volume = {40}, number = {3}, pages = {}, doi = {10.1264/jsme2.ME24067}, pmid = {40707215}, issn = {1347-4405}, mesh = {*Hot Springs/microbiology/chemistry ; Japan ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; *Archaea/classification/metabolism/genetics/isolation &amp; purification ; Oxidation-Reduction ; Phylogeny ; Nitrogen Fixation ; Oceans and Seas ; Iron/metabolism ; *Biodiversity ; Carbon Cycle ; RNA, Ribosomal, 16S/genetics ; Nitrogen Cycle ; Hydrogen/metabolism ; }, abstract = {Circumneutral iron-rich hot springs may represent analogues of Neoarchean to Paleoproterozoic oceans of early Earth, potentially providing windows into ancient microbial ecology. Here we sampled five Japanese hot springs to gain insights into functional processes and taxonomic diversity in these analog environments. Amplicon and metagenomic sequencing confirm a hypothesis where taxonomy is distinct between sites and linked to the geochemical setting. Metabolic functions shared among the springs include carbon fixation via the reductive pentose phosphate cycle, nitrogen fixation, and dissimilatory iron oxidation/reduction. Among the sites, Kowakubi was unique in that it was dominated by Hydrogenophilaceae, a group known for performing hydrogen oxidation, motivating a hypothesis that H2 as an electron donor may shape community composition even in the presence of abundant ferrous iron. Evidence for nitrogen cycling across the springs included N2 fixation, dissimilatory nitrate reduction to ammonia (DNRA), and denitrification. The low-salinity springs Furutobe and OHK lacked evidence for ammonium oxidation by ammonia monooxygenase, but evidence for complete nitrification existed at Kowakubi, Jinata, and Tsubakiyama. In most sites, the microaerophilic iron-oxidizing bacteria from the Zetaproteobacteria or Gammaproteobacteria classes had higher relative abundances than Cyanobacteria. Microaerophilic iron oxidizers may outcompete abiotic Fe oxidation, while being fueled by oxy-phototrophic Cyanobacteria. Our data provide a foundation for considering which factors may have controlled productivity and elemental cycling as Earth's oceans became oxygenated at the onset of the Great Oxidation Event.}, }
@article {pmid40705368, year = {2025}, author = {Duff, AM and Giles, M and Ganasamurthy, S and Santos, A and Morales, SE and Brennan, F}, title = {Counting soil microbial communities: the impact of qPCR platform and mastermix on accuracy and precision.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {8}, pages = {}, doi = {10.1093/femsec/fiaf073}, pmid = {40705368}, issn = {1574-6941}, support = {696356//European Union/ ; }, mesh = {*Soil Microbiology ; *Real-Time Polymerase Chain Reaction/methods/standards ; *Microbiota/genetics ; *Bacteria/genetics/isolation &amp; purification ; }, abstract = {Quantitative polymerase chain reaction (qPCR) is widely used in soil microbial ecology to quantify microbial communities, but its accuracy can be compromised by coextracted inhibitors. Furthermore, large-scale international studies involving multiple laboratories or meta-analyses studies can introduce variation in qPCR results when data generated from different sources are compared. This study evaluated the performance of four commercial mastermixes across different soil types, a mock community, and a positive template control against three targets on three widely used platforms. Sensitivity to inhibitors was tested, with one mastermix affected, although this was mitigated by adding 1 mg/ml bovine serum albumin. Amplification success varied by mastermix, platform, gene, and sample matrix. Most mastermix-platform combinations showed low accuracy emphasizing the need for careful pairing. Precision was primarily influenced by gene target, followed by platform, sample matrix, and mastermix, and was reduced at lower template concentrations. Only 64.67% of intraassay (within an assay) measurements meet accepted thresholds. Interassay (between platforms) quantification was unreliable due to significant variability, which increased the risk of inaccurate data interpretation. The study highlights the necessity of considering inter- and intraassay variation, assay accuracy, and inhibitors that may impact sample amplification when utilizing qPCR for quantification of microbial communities in environmental samples.}, }
@article {pmid40705167, year = {2025}, author = {Gdanetz, K and Noel, ZA and Saville, K and Marsh, T and Scribner, KT and Trail, F}, title = {Eukaryotic Microbiome of Lake Sturgeon Eggs, and Identification of Chemical Thresholds for Infection Control.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {80}, pmid = {40705167}, issn = {1432-184X}, mesh = {Animals ; *Fishes/microbiology ; *Microbiota/drug effects ; Lakes/microbiology ; *Fish Diseases/microbiology/prevention &amp; control/parasitology ; *Ovum/microbiology ; *Fungi/isolation &amp; purification/classification/drug effects/genetics ; Oomycetes/drug effects/isolation &amp; purification ; Aquaculture ; *Eukaryota/isolation &amp; purification/classification/drug effects/genetics ; }, abstract = {Eukaryotic microorganisms are an important, but understudied, component of freshwater aquatic ecosystems, and are significant sources of mortality in early life stages of fishes in natural and aquaculture systems. The eukaryotic microbiome colonizing egg surfaces of the lake sturgeon (Acipenser fulvescens) was characterized from eggs collected in natural stream habitats and a streamside hatchery in the Cheboygan River watershed in MI, USA. The taxonomic diversity of members of the Kingdoms Fungi and Stramenopile associated with infections of lake sturgeon eggs during spawning is contributing to lake sturgeon mortality in the hatchery. Characterization of the microbial communities from deposited eggs demonstrated heavy influence of spawning location on the diversity of Pythium, an Oomycete predominating in the microbiome. The Ascomycota also had a strong and distinguishing presence, with members of the Dothidiales found only on eggs from the streamside hatchery. Aureobasidium pullulans, a ubiquitous pigmented yeast, was present in the greatest numbers of egg samples, and Helotiales were found only on samples from the Black River. Independent isolates were collected from egg surfaces and tested for chemical sensitivity to the oomicides ethaboxam and mefenoxam, which are used for control of Oomycete agricultural pathogens. Ethaboxam inhibited mycelial growth almost completely for all Saprolegnia strains tested, while mefenoxam, at 20 × strength, was largely ineffective. Water prevents the natural inactivation of mefenoxam by light, thus is not advisable in aquatic systems, where it could accumulate. Alternatively, ethaboxam may be a nonpersistent, welcome control option for these fish pathogens.}, }
@article {pmid40705121, year = {2025}, author = {Martin-Pozas, T and Ghezzi, D and D'Angeli, IM and Madonia, G and Chiarini, V and Vattano, M and De Waele, J and Cappelletti, M and Saiz-Jimenez, C and Jurado, V}, title = {Microbial and Geochemical Variability in Sediments and Biofilms from Italian Gypsum Caves.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {81}, pmid = {40705121}, issn = {1432-184X}, support = {JDC2023-051909-I//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-114978GB-I00 and PDI2023-146299OB-C22//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-114978GB-I00 and PDI2023-146299OB-C22//Ministerio de Ciencia e Innovaci&#xf3;n/ ; Europlanet 2020 7-EPN3-021//European Commission/ ; }, mesh = {*Biofilms/growth &amp; development ; *Geologic Sediments/microbiology/chemistry ; *Calcium Sulfate/analysis ; *Caves/microbiology/chemistry ; *Bacteria/classification/genetics/isolation &amp; purification ; Italy ; *Archaea/classification/isolation &amp; purification/genetics ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; }, abstract = {In Europe, several gypsum karst regions occur among which the gypsum karsts located in Emilia-Romagna (UNESCO World Heritage Site since 2023) and Sicily are notable. The sediments, spring water microbial aggregates, and wall biofilms from three caves, Re Tiberio, Befana (Emilia-Romagna), and the Sicilian Santa Ninfa, have been studied from a microbiological and geochemical point of view. The samples of wall biofilms from gypsum caves were exclusively composed of Bacteria, while the sediments showed negligible abundances of Archaea. The two most abundant phyla in most sediments and biofilms were Actinomycetota and Pseudomonadota, whereas the microbial aggregates floating in the spring waters of Befana Cave showed a deviation from the typical abundance pattern as Campylobacterota replaced Actinomycetota, and the abundances of Bacteroidota and Desulfobacterota were high. The most abundant genus in the wall biofilms was Crossiella (Actinomycetota), but it was absent in the water aggregates collected in Befana Cave. The abundances of Crossiella in the cave sediments were very low. The dominant genera in Befana microbial aggregates showed different abundances and microbial composition when compared with the previously studied Frasassi and Fetida thermal sulfuric acid caves, located in Central and South Italy, respectively, suggesting that the community composition of the microbial aggregates is specific for each cave and related to the geochemistry of the sulfidic spring. Also, a different microbial community composition was found in Befana water aggregates with respect to the wall biofilms from Befana and Santa Ninfa caves. In the case of sediments, they significantly clustered together indicating that the microbial communities associated with sediments are similar, independently from the cave and possible other environmental parameters.}, }
@article {pmid40704825, year = {2025}, author = {Fang, J and Deng, Y and Liu, Z and Adams, JM}, title = {Is Everything Everywhere? Dispersal Limitation Impacts Methanotroph Community Functioning.}, journal = {Environmental microbiology}, volume = {27}, number = {7}, pages = {e70158}, doi = {10.1111/1462-2920.70158}, pmid = {40704825}, issn = {1462-2920}, support = {SBX2020010098//The Provincial Policy Guidance Program-Jiangsu "100 Foreign Experts Program"/ ; 42371135//The National Natural Science Foundation of China/ ; 41971077//The National Natural Science Foundation of China/ ; }, mesh = {*Methane/metabolism ; *Geologic Sediments/microbiology ; *Methylococcaceae/metabolism/genetics/classification/isolation &amp; purification ; Salinity ; Rivers/microbiology ; Ecosystem ; Lakes/microbiology ; China ; Oxidation-Reduction ; }, abstract = {The significance of dispersal limitation in microbial ecology and biogeography remains debated. We aimed to clarify the role of dispersal limitation in the adaptation of methanotroph communities to salt-stress, essentially testing the 'everything is everywhere' hypothesis in functional terms. Riparian sediments along the Yangtze River and lakeshore sediments at varying geographical distances inland from the river were collected. Microcosms were incubated with ~5% CH4 under three conditions: 50 g/L salinity, 50 g/L salinity plus a methanotroph community inoculum, and a control. We observed a significant delay in methane oxidation at increased salinity, but salt-tolerant methanotrophic activity persisted in riparian sediments. Using DNA-SIP, we identified halotolerant Methylobacter-taxa that possibly dispersed from the saline estuary. By contrast, in lakes/ponds inland away from the Yangtze, progressively fewer samples oxidised methane under high salinity without inoculation, until at 130 km distance, no samples could adapt. Methanotrophy was restored in every case by inoculation with propagules from the saline Yangtze Delta, confirming the impact of dispersal limitation of halotolerant Methylobacter-propagules in constraining ecosystem functional adaptation. By focusing on ecosystem functions rather than just taxonomic communities, this study uniquely tests a key paradigm in microbial ecology, suggesting that broad-scale microbial dispersal limitation can constrain ecosystem adaptation.}, }
@article {pmid40704813, year = {2025}, author = {Zeng, Q and Jian, L and Shi, S and Guo, Q and Quadri, SR and Long, L and Tian, X}, title = {Identified Neptunicella plasticusilytica sp. nov. and its novel PET-degrading enzyme derived from mangrove plastic debris.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0113625}, doi = {10.1128/aem.01136-25}, pmid = {40704813}, issn = {1098-5336}, abstract = {Mangrove ecosystems are critical for coastal protection and biodiversity but are increasingly threatened by plastic pollution, particularly polyethylene terephthalate (PET). In this study, a novel marine bacterium, strain SCSIO 80796[T], was isolated from PET debris collected from the mangrove in QiAo Island, Zhuhai, China. Using a polyphasic taxonomic approach, including 16S rRNA gene sequencing, genome-based comparisons (average nucleotide identity [ANI] 72.2%, digital DNA-DNA hybridization [dDDH] 19.0%, average amino acid identity [AAI] 70.6%), and phenotypic and chemotaxonomic analyses, the strain was classified as a novel species within the genus Neptunicella. It is proposed as Neptunicella plasticusilytica sp. nov. (type strain SCSIO 80796ᵀ = MCCC 1K08369[T] = KCTC 92826[T]). Genomic analysis revealed that strain SCSIO 80796ᵀ encodes a novel PET-degrading enzyme, NmCut, which degrades PET and yields 105-120 µM of degradation products [terephthalic acid (TPA), mono(2-hydroxyethyl) terephthalate (MHET), bis(2-hydroxyethyl) terephthalate (BHET)] within 48 h at 60°C. NmCut exhibits both structural and evolutionary novelty, featuring a unique PET-binding module (PBM) absent in known PETases. PBM is characterized by a long, positively charged α-helix enriched in aromatic residues, forming a distinct substrate-interacting surface with potential as a transferable domain to enhance the efficiency of other plastic-degrading enzymes. This study not only expands the known diversity within Neptunicella but also highlights the potential of marine-derived microbes in addressing plastic pollution through biotechnological applications.IMPORTANCEThe discovery of Neptunicella plasticusilytica sp. nov. advances marine microbial ecology by revealing a novel species in the scarcely studied genus Neptunicella, which previously contained only one cultured representative. Isolated from plastic-polluted mangroves, this bacterium exemplifies microbial adaptation to anthropogenic habitats. Its functional uniqueness is underscored by a phylogenetically distinct polyethylene terephthalate (PET)-degrading enzyme (NmCut), forming an evolutionary clade separate from all known plastic-degrading enzymes. By integrating taxonomic discovery with functional genomics, this study bridges the gap between microbial diversity and biotechnological potential. The dual novelty of N. plasticusilytica-as a taxonomic addition and a source of evolutionarily unique enzymes-highlights the importance of exploring understudied environments to address global challenges like plastic pollution.}, }
@article {pmid40704791, year = {2025}, author = {Reasoner, SA and Francis, J and Hadjifrangiskou, M}, title = {The urinary microbiome: the next frontier of bacterial ecology.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {e0010525}, doi = {10.1128/jb.00105-25}, pmid = {40704791}, issn = {1098-5530}, support = {F30 AI169748/AI/NIAID NIH HHS/United States ; P20 DK123967/DK/NIDDK NIH HHS/United States ; R01 AI168468/AI/NIAID NIH HHS/United States ; }, abstract = {The human urinary tract, once presumed to be sterile, has emerged as a new frontier of microbial ecology. Recent advancements in high-throughput sequencing technologies have revealed the complexity and diversity of microbial communities that reside within the urinary tract. This mini-review discusses the prominent bacteria identified in the urinary microbiome and their correlations with various urologic conditions. This review serves to summarize the current state of urobiome research and chart a path for ongoing discovery. Additionally, we address the methodological challenges in urinary microbiome research, emphasizing the need for standardization in study protocols and the refinement of bioinformatics tools. We highlight that although differences in urobiome composition have been described for various urologic diseases. Similarly, the pathophysiologic source and consequences of those differences remain uncertain. We outline the steps to move urobiome research from descriptive to mechanistic studies, emphasizing rigorous study design, integrating multi-omics approaches, and developing robust model systems for experimental investigation. Finally, we outline critical questions for future investigation aimed at elucidating the intricate connections between the urinary microbiome and host health.}, }
@article {pmid40704790, year = {2025}, author = {Best, MB and Kazemi Motlagh, Z and McLemore, VT and Jones, DS}, title = {Historic mine waste contains diverse microbial communities that reflect waste type and geochemistry.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0043425}, doi = {10.1128/aem.00434-25}, pmid = {40704790}, issn = {1098-5336}, abstract = {UNLABELLED: Waste rock and tailings left behind by historic mining operations can contain substantial critical mineral resources. However, over the decades and centuries, since these deposits were emplaced, microbial communities developed that can catalyze rock weathering and elemental cycling, which could have impacted the economic resources but also might be harnessed for future biomining or other metal recovery efforts. Here, we combined microbial cell counting, rRNA gene and transcript sequencing, and whole rock geochemistry to compare the composition and abundance of microbial communities from five inactive mine sites in south-central New Mexico that contain critical minerals. While acidic seeps and adits at the sites contained organisms commonly found in acid rock drainage and bioleaching operations, these organisms were only present at very low abundance in the waste rock and tailings, which were instead dominated by bacteria and archaea that are related to inorganic nitrogen- and organic carbon-oxidizing taxa. Generally, rRNA transcript libraries contain many of the same organisms as rRNA gene libraries, indicating that most of these populations are active. Differences among total and active microbial communities correspond to waste rock geochemistry, including concentrations of sulfur, iron, and other variables such as copper, lead, and rare earth elements. Nevertheless, many of the rRNA gene and transcript sequences in these deposits were from groups without cultured representatives, and these unknown microorganisms are likely important for biogeochemical cycling over the long lifetime of these waste deposits. We also discuss recommendations for microbiological assessment of similar large historic mine waste deposits.<br><br>IMPORTANCE: New Mexico has a long history of mining, with hundreds of mining districts across the state, many of which contain inactive operations with historic tailings and waste rock. Because metallurgical processing was in its infancy when most of these mines were active, they contain substantial metal resources in tailings and waste rock that could be used to support domestic demand for critical minerals. We found that microbial communities associated with these deposits do not represent typical bioleaching communities, and instead are dominated by taxa not typically associated with mine waste. However, the deposits did contain rare iron and sulfur-cycling taxa that could catalyze metal mobilization, as well as active populations of novel microorganisms that are likely important for biogeochemical cycling. These microbial communities could represent important resources for bioremediation and other biotechnological applications to recover valuable elements from these and other historic mine wastes.}, }
@article {pmid40703236, year = {2025}, author = {Žilić, DJ and Naletilić, &#x160; and Mihaljević, &#x17d; and Gagović, E and Špičić, S and Reil, I and Duvnjak, S and Tuk, MZ and Hodžić, A and Beck, R}, title = {Hemotropic pathogens in aborted fetuses of domestic ruminants: transplacental transmission and implications for reproductive loss.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1632135}, pmid = {40703236}, issn = {1664-302X}, abstract = {OBJECTIVE: Hemotropic pathogens of the genera Anaplasma, Babesia, Theileria, and hemotropic Mycoplasma are significant infectious agents in domestic ruminants, most commonly associated with vector-borne transmission. However, their potential for transplacental transmission and their contribution to reproductive disorders remains poorly understood. This study aimed to investigate the presence of hemopathogens in aborted fetuses of cattle, sheep, and goats in Croatia, and to evaluate their potential role in transplacental transmission.<br><br>METHODS: Molecular analyses were conducted on tissue samples from 651 aborted fetuses collected between 2016 and 2019 as part of national abortion surveillance programs. PCR screening followed by sequencing were used to detect Anaplasmataceae, Babesia, Theileria, and hemotropic Mycoplasma.<br><br>RESULTS: Thirteen hemopathogens were detected in 94 of 651 fetuses (14.44%), including Anaplasma marginale, Anaplasma ovis, Anaplasma phagocytophilum, Theileria orientalis, Theileria ovis, Theileria sp. OT3, Babesia ovis, Babesia canis, Babesia vulpes, Mycoplasma wenyonii, Mycoplasma haemobos, Mycoplasma ovis, and Mycoplasma haemominutum. The highest infection rates were observed in cattle (17.27%) and sheep (15.85%), while goats showed significantly lower prevalence (5.3%). A. marginale and A. ovis were the most frequently detected pathogens in bovine and ovine fetuses, respectively. Hemotropic mycoplasmas were reported for the first time in Croatia, with the first Western Balkan record of 'Candidatus M. haemobos'. Our study represents the first molecular documentation of a wide array of hemopathogens in aborted ruminant fetuses in Croatia, strongly indicating the possibility of transplacental transmission. The detection of species-specific patterns and the unexpected identification of protozoan species typically associated with canines highlight complex epidemiological dynamics.<br><br>CONCLUSION: Vertical transmission of the detected pathogens may play a role in abortion in endemic regions and should be integrated into differential diagnostic protocols for reproductive failure investigations.}, }
@article {pmid40699317, year = {2025}, author = {Mairi, A and Ibrahim, NA and Idres, T and Basher, NS and Smaili, A and Idres, T and Toutati, A}, title = {Emerging antimicrobial resistance and high prevalence of genital Mycoplasma hominis and Ureaplasma urealyticum infections among infertile women in Algeria : Implications for reproductive health.}, journal = {Wiener klinische Wochenschrift}, volume = {}, number = {}, pages = {}, pmid = {40699317}, issn = {1613-7671}, support = {IMSIU-DDRSP2501//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)./ ; }, abstract = {BACKGROUND: Genital infections caused by Mycoplasma hominis and Ureaplasma urealyticum are increasingly linked to female infertility, yet their epidemiology and resistance patterns remain poorly characterized in low-resource settings.<br><br>OBJECTIVE: This study aimed to determine the prevalence, antimicrobial resistance (AMR) profiles, and risk factors of M.&#xa0;hominis and U.&#xa0;urealyticum infections among infertile women in Akbou, Algeria.<br><br>METHODS: In this cross-sectional analysis (February-July 2024), cervicovaginal swabs from 79 infertile women were tested using the MYCOFAST&#xae; RevolutioN&#xa0;2 system. Demographic, clinical, and reproductive data were collected via structured questionnaires. Statistical analyses included &#x3c7;[2]-testsand logistic regression.<br><br>RESULTS: The overall infection prevalence was 37.9% (n&#x202f;=&#x2009;30), with U.&#xa0;urealyticum (17.7%), M.&#xa0;hominis (13.9%), and co-infections (6.3%) predominating. Infections peaked in women aged 31-35&#xa0;years (63.3%). Resistance to tetracycline was high (U.&#xa0;urealyticum: 71.4%; M.&#xa0;hominis: 54.5%), while doxycycline and clindamycin retained full efficacy. Significant risk factors included prior abortion (adjusted odds ratio, OR&#x202f;=&#x2009;4.2, p&#x202f;<&#x2009;0.001), STI history (OR&#x202f;=&#x2009;3.8, p&#x202f;<&#x2009;0.001), and artificial insemination (OR&#x202f;=&#x2009;2.9, p&#x202f;=&#x2009;0.018).<br><br>CONCLUSION: The high prevalence of genital Mycoplasma infections and emerging AMR in Algeria underscores the need for routine screening, updated treatment guidelines, and targeted antimicrobial stewardship programs to safeguard reproductive health.}, }
@article {pmid40699244, year = {2025}, author = {Bei, Q and Zhang, J and Huang, Q and Yang, C and Li, Y and Mu, R and Shu, D and Dai, Y and Megharaj, M and He, W and Tian, H}, title = {Rhizosphere Microbiome-Root Exudate Synergy in Pteris vittata: Coordinated Arsenic Speciation and Multielement Metabolic Coupling Drive Hyperaccumulation Efficiency.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {79}, pmid = {40699244}, issn = {1432-184X}, support = {2023YFD1700102//the National Key R&amp;D Program of China/ ; 2024NC-ZDCYL-02-14//the Key R&amp;D Program of Shaanxi Province/ ; 2025JC-QYCX-034//Frontier Exploration Project (Innovative Exploration Category)/ ; }, mesh = {*Arsenic/metabolism ; *Rhizosphere ; *Pteris/microbiology/metabolism ; *Plant Roots/microbiology/metabolism ; *Microbiota ; Soil Microbiology ; Bacteria/metabolism/classification/genetics/isolation &amp; purification ; *Soil Pollutants/metabolism ; Biodegradation, Environmental ; Fungi/metabolism/classification/genetics/isolation &amp; purification ; *Plant Exudates/metabolism ; Soil/chemistry ; }, abstract = {Rhizosphere microorganisms play a pivotal role in enhancing the arsenic (As) remediation efficiency of Pteris vittata. However, the interactions among rhizosphere microorganisms, root exudates, and As, as well as their influence on As uptake by Pteris vittata at different As concentrations, remain poorly understood. This study systematically elucidates the molecular-ecological mechanisms through which Pteris vittata facilitates arsenic (As) remediation within a multidimensional interaction network. It was found that the rhizosphere microbial community was dominated by Proteobacteria, Acidobacteriota, and Ascomycota, with 44 bacterial and 10 fungal genera identified as genetically conserved core microorganisms. Microbial-mediated arsenic (As) methylation and reduction processes, coupled with metabolic pathways such as carbon fixation, sulfur oxidation, and phosphorus mineralization, contribute to the formation of an "As-multielement cycling" synergy. This synergy drives As speciation transformation and enhances plant uptake. Root exudates, such as L-phenylalanine and citric acid, enhance arsenic (As) activation and detoxification by selectively recruiting functional microbes, including Sphingomonas carrying arsC. The resulting metabolite profiles exhibit soil-specific response patterns. High As stress shifted microbial community assembly from stochastic to deterministic processes while maintaining remediation efficiency through enhanced fungal network stability (increased average connectivity). These findings reveal the dual "genetic conservation-environmental adaptation" regulatory strategy of Pteris vittata, providing both theoretical and practical foundations for designing targeted rhizosphere microecological technologies to enhance the phytoremediation of arsenic (As)-contaminated soils.}, }
@article {pmid40699006, year = {2025}, author = {Nauwynck, W and Faust, K and Boon, N}, title = {Droplet microfluidics for single-cell studies: a frontier in ecological understanding of microbiomes.}, journal = {FEMS microbiology reviews}, volume = {49}, number = {}, pages = {}, pmid = {40699006}, issn = {1574-6976}, support = {11E3422N//Research Foundation Flanders/ ; G020119N//Research Foundation Flanders/ ; }, abstract = {Recent advances in single-cell technologies have profoundly impacted our understanding of microbial communities-shedding light on cell-to-cell variability in gene expression, regulatory dynamics, and metabolic potential. These approaches have shown that microbial populations are more heterogeneous and functionally complex than previously thought. However, direct probing of single-cell physiology-arguably more ecologically relevant by focusing on functional traits such as growth, metabolic activity, and enzymatic activity-remains underexplored. Droplet microfluidics provides a practical and high-throughput approach to address this gap, allowing functional characterization of individual microbial cells within complex communities and offering new opportunities to study ecological processes at high resolution. In this review, we look at the state of droplet microfluidics for single-cell microbial ecology. We revisit the fundamentals of microbial droplet workflows, we overview the current capabilities of droplet microfluidics that exist for microbial ecology and we look at the phenomena these workflows have uncovered and understanding they have generated. Finally, we integrate these capabilities to envision future droplet workflows that could enhance our understanding of single-cell physiology and discuss the fundamental limitations that go together with the droplet format.}, }
@article {pmid40698177, year = {2025}, author = {Roy, A and Ghosh, A and Yash,  and Mehra, P and Roy, S and Bhadury, P}, title = {Insights into the genome of Azotobacter sp. strain CWF10, isolated from an agricultural field in Central India.}, journal = {Access microbiology}, volume = {7}, number = {1}, pages = {}, pmid = {40698177}, issn = {2516-8290}, abstract = {Azotobacter sp. strain CWF10, an aerobic gram-negative, oval-shaped and motile bacterium, was isolated from the lateritic agricultural soil of Madhya Pradesh, India. The draft genome of the isolate is 5.7 Mb in size, consisting of 14 contigs with 65.09% G+C content. Average nucleotide identity (94.66%) and digital DNA-DNA hybridization (62%) calculation with the closest reference strains underpin the bacterium as a potential novel species. The bacterium has a plethora of plant growth-promoting genes that point towards the potential ability to enhance available nitrogen and biosynthesis of folic acid, among others. Siderophores such as vibrioferrin and crochelin A are also present in the genome and are known to regulate iron uptake. Overall, mining the genome of Azotobacter sp. strain CWF10 has revealed the potential of this strain for application in regenerative agriculture and sustaining soil health.}, }
@article {pmid40696151, year = {2025}, author = {Laso-Pérez, R}, title = {Anaerobic oxidation of methane: it takes two to tango.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, pmid = {40696151}, issn = {1740-1534}, }
@article {pmid40694412, year = {2025}, author = {Benz, BR and Lopez-Echartea, E and Whitaker, BK and Baldwin, T and Geddes, BA}, title = {Improved efficiency of two-step amplicon PCR using an acoustic liquid handler.}, journal = {Microbiology (Reading, England)}, volume = {171}, number = {7}, pages = {}, pmid = {40694412}, issn = {1465-2080}, mesh = {*Polymerase Chain Reaction/methods/instrumentation/economics ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; *Bacteria/genetics/classification/isolation &amp; purification ; Microbiota/genetics ; Gene Library ; *Acoustics/instrumentation ; DNA, Bacterial/genetics ; }, abstract = {The improvement in next-generation sequencing technologies has reduced the costs of sequencing significantly. However, library preparation costs for amplicon sequencing have remained largely unchanged - which is ultimately the cost-limiting step in processing large numbers of microbiome samples. Acoustic liquid handlers can transfer volumes as low as 2.5 nl and have been used to miniaturize several different molecular and cellular assays, including single-step PCR amplicon library preparations. However, there are no current methods available for a two-step library preparation process using an acoustic liquid handler. In this study, we tested the efficiency of an acoustic liquid handler to automate the PCRs and library quantification while also incorporating automated library bead cleanup. We compared the material usage and costs for library preparation and sequencing results of this automated method to the standard, manual method. The automated protocol was able to reduce both PCR reaction volumes fivefold and increased efficiency for library preparation by ~32% without affecting bacterial community compositions. The associated increase in the efficiency of our automated method will allow for greater throughput in sequencing hundreds of microbiome samples without affecting the quality of those sequences.}, }
@article {pmid40694117, year = {2025}, author = {Adam, MAC and Cailleau, G and Junier, P and Benrey, B}, title = {Host Diet and Species Interact to Shape the Bacterial and Fungal Microbiome in the Regurgitant of Four Spodoptera Species.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {78}, pmid = {40694117}, issn = {1432-184X}, support = {162860/SNSF_/Swiss National Science Foundation/Switzerland ; 162860/SNSF_/Swiss National Science Foundation/Switzerland ; 162860/SNSF_/Swiss National Science Foundation/Switzerland ; 162860/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {Animals ; *Spodoptera/microbiology/physiology/classification ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/isolation &amp; purification ; *Diet ; *Gastrointestinal Microbiome ; Herbivory ; Phylogeny ; *Mycobiome ; Microbiota ; }, abstract = {The gut microbiome of Lepidopteran insects is highly dynamic, influenced by both host diet and phylogeny. While microbial communities are thought to facilitate host adaptation to diverse diets and environments, the existence of a core microbiome shared among closely related herbivores remains largely untested. In this study, we examined the microbial communities in the regurgitant of four Spodoptera species (S. exigua, S. frugiperda, S. latifascia, and S. littoralis) across different diets (artificial diet, cotton, maize, and squash). Using a high-throughput sequencing, we characterized bacterial and fungal community composition and diversity. Bacterial communities were shaped by both diet and host species, indicating species-specific bacterial selection. In contrast, fungal communities were exclusively structured by diet, with lower diversity and dominance of a few key taxa. Notably, no operational taxonomic units were consistently shared across all species or diets, challenging the concept of a conserved core microbiome in these generalist herbivores. Understanding how microbial communities shape generalist herbivores' ability to feed on diverse plants may offer potential strategies for microbiome-based pest management.}, }
@article {pmid40693737, year = {2025}, author = {Kop, LFM and Koch, H and Speth, D and Lüke, C and Spieck, E and Jetten, MSM and Daims, H and Lücker, S}, title = {Comparative genome analysis reveals broad phylogenetic and functional diversity within the order Nitrospirales.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40693737}, issn = {1751-7370}, support = {DFG SP 667/11-2//Deutsche Forschungsgemeinschaft/ ; //Austrian Science Fund/ ; 016.Vidi.189.050//Netherlands Organization for Scientific Research/ ; VI.Veni.192.086//Netherlands Organization for Scientific Research/ ; 024.002.002//Gravitation Program of the Dutch Ministry of Education, Culture, and Science/ ; }, abstract = {Nitrification, a key process in the nitrogen cycle, involves the oxidation of ammonia to nitrite and nitrate by a diverse group of chemolithoautotrophic microorganisms. The order Nitrospirales (referred to in literature as the genus Nitrospira), which includes both nitrite-oxidizing and complete ammonia-oxidizing bacteria, plays a central role in this process. We sequenced the genomes of nine Nitrospirales members, incorporating genomes from previously unsequenced taxonomic Nitrospirales lineages. A comprehensive genomic analysis of these new Nitrospirales was conducted, which included an examination of their habitat distribution, phylogenetic diversity, and functional capabilities. This was complemented by the construction of and comparison to a database of 446 non-redundant, high-quality Nitrospirales genomes. Our phylogenomic analysis uncovered the presence of additional unclassified lineages and provided a comparison between genome-based and 16S rRNA gene-based taxonomies. Whereas some Nitrospirales lineages seem to exhibit habitat preferences, others are found across a wide variety of ecosystems, suggesting a broad niche spectrum. This capacity to adapt to different environmental conditions is also reflected in the high variability and modularity of the respiratory chain and nitrogen assimilation mechanisms. Additionally, we found evidence of quorum sensing systems in species beyond lineage II, implying a broader ecological role for this communication mechanism within the Nitrospirales. Finally, we identified a set of conserved genes unique to nitrite oxidoreductase-containing Nitrospirales, providing insights into the emergence of this functional group. In conclusion, our study emphasizes the adaptability of the various nitrifying classes of the order Nitrospirales to diverse environments and reveals the presence of new taxonomic lineages.}, }
@article {pmid40693139, year = {2025}, author = {Nankova, BB and Hu, F and LaGamma, EF}, title = {Early life microbiome disbalance impacts neuroendocrine outcomes in pre-pubertal mice in a sexually dimorphic manner.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1504513}, pmid = {40693139}, issn = {1664-302X}, abstract = {INTRODUCTION: Adverse exposures during perinatal development disrupt the emerging gut microbial ecology that in turn negatively influences long term health. How gut dysbiosis affects complex neurobehavioral functions or even simple reflex arcs (e.g. the amplitude of sympathoadrenal adaptive responses to hypoglycemia) in the extrauterine environment is not well understood.<br><br>METHODS: The C57Bl6 dams were given broad-spectrum antibiotics in the drinking water at parturition until weaning of their litter to perturb the normal seeding and maturation of the postnatal microbiome, control animals received sterile water. To evaluate the impact of altered postnatal flora the offspring were subjected to behavioral tests or sacrificed after exposure to insulin-induced hypoglycemia. Fecal samples were collected for microbial whole genome shotgun taxonomic profiling and predictive functionality. As an index of host sympathoadrenal capacity, individual adrenal medulla samples from each group were subjected to RNA sequencing to identify differentially expressed genes between the groups and gain insights into molecular pathways contributing to the observed outcomes. Given that several neurodevelopmental disorders in humans are biased by sex we also included it as variable in this report.<br><br>RESULTS: The offspring of control dams displayed sex-specific differences in microbiome composition, exploratory behavior, adrenal transcriptome profiles and basal urinary epinephrine levels. Maternal antibiotics during nursing caused: (1) microbial dysbiosis in the offspring as evident by markedly enlarged ceca, no detectable by-products of bacterial fermentation (sp. SCFA) and dramatic changes in microbial composition, diversity (reduced - alpha Chao1and beta Bray-Curtis, as compared to their respective controls) and predictive metabolic activity; (2) alteration in the transcriptional signature of the adrenal medullae and attenuated peripheral stress responses in male offspring, associated with gap junction signaling pathways; (3) increased anxiety-like testing metrics, and decreased locomotor activity; all in a sexually dimorphic manner.<br><br>DISCUSSION: We speculate that the observed sex differences in the gut microbiome may contribute to neurodevelopmental disorders known to have sex-related disparities and in the capacity for successful adaptation to stress. A better understanding of how microbial communities and their hosts interact during critical portions of postnatal neurobehavioral development may help personalize nutritional and therapeutic strategies to promote long term health.}, }
@article {pmid40691348, year = {2025}, author = {Almario, J}, title = {Blurred lines in the mycorrhiza world.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, pmid = {40691348}, issn = {1740-1534}, }
@article {pmid40689185, year = {2025}, author = {Li, K and Xu, J and Chen, S and Du, A and Feng, S and Yuan, S and Wu, B}, title = {Dose-dependent effects of capsaicin on intestinal morphology and microbiota composition in mice: Structural, immunohistochemical, and microbial insights.}, journal = {Veterinary world}, volume = {18}, number = {6}, pages = {1703-1714}, pmid = {40689185}, issn = {0972-8988}, abstract = {BACKGROUND AND AIM: Capsaicin (CAP), the pungent component of chili peppers, possesses diverse bioactive properties, including antioxidant, anti-inflammatory, and antimicrobial effects. However, its impact on gastrointestinal integrity and microbial ecology remains dose-dependent and incompletely understood. This study aimed to investigate the effects of varying CAP doses on intestinal morphology, tight junction protein expression, goblet cell density, mucosal injury markers, and gut microbiota composition in mice.<br><br>MATERIALS AND METHODS: Seventy-five male Kunming mice were randomly assigned to five groups (n = 15/group): Normal control, vehicle control (dimethyl sulfoxide), low-dose CAP (5 mg/kg), medium-dose (15 mg/kg), and high-dose (20 mg/kg). Mice received oral gavage every other day for 14 days. Histological assessments (H&amp;E and Alcian Blue-Periodic Acid-Schiff staining), enzyme-linked immunosorbent assays for diamine oxidase, fatty acid-binding protein 2, and plasma endotoxin as well as immunohistochemistry for ZO-1, Claudin-1, and Occludin, and 16S rRNA sequencing were employed to evaluate structural and microbial changes.<br><br>RESULTS: Low-dose CAP significantly enhanced villus height, reduced crypt depth, and elevated the villus-to-crypt ratio across all intestinal segments (p < 0.05). Tight junction protein expression and goblet cell counts were highest in the low-dose group, suggesting mucosal protection. In contrast, medium and high-dose CAP induced epithelial damage, villus atrophy, and downregulation of junctional proteins. Microbiota analysis revealed the suppression of Proteobacteria and the expansion of Firmicutes in the medium- and high-dose groups. All CAP doses stimulated microbial biosynthesis of cofactors, vitamins, and electron carriers, with enhanced alpha diversity at higher doses.<br><br>CONCLUSION: CAP exhibits a biphasic effect on intestinal physiology. While low-dose administration supports mucosal integrity and promotes beneficial microbial functions, higher doses disrupt epithelial architecture and induce dysbiosis. These findings underscore the importance of dose consideration in CAP's dietary and therapeutic applications, providing mechanistic insights into its gut-mediated effects.}, }
@article {pmid40688383, year = {2025}, author = {Liu, S and Rodriguez, JS and Munteanu, V and Ronkowski, C and Sharma, NK and Alser, M and Andreace, F and Blekhman, R and Błaszczyk, D and Chikhi, R and Crandall, KA and Della Libera, K and Francis, D and Frolova, A and Gancz, AS and Huntley, NE and Jaiswal, P and Kosciolek, T and Łabaj, PP and Łabaj, W and Luan, T and Mason, C and Moustafa, AM and Muralidharan, HS and Mutlu, O and Mansouri Ghiasi, N and Rahnavard, A and Sun, F and Tian, S and Tierney, BT and Van Syoc, E and Vicedomini, R and Zackular, JP and Zelikovsky, A and Zielińska, K and Ganda, E and Davenport, ER and Pop, M and Koslicki, D and Mangul, S}, title = {Analysis of metagenomic data.}, journal = {Nature reviews. Methods primers}, volume = {5}, number = {}, pages = {}, pmid = {40688383}, issn = {2662-8449}, support = {U01 DA053941/DA/NIDA NIH HHS/United States ; R01 AI125416/AI/NIAID NIH HHS/United States ; U19 AI174998/AI/NIAID NIH HHS/United States ; U54 AG089334/AG/NIA NIH HHS/United States ; R35 GM146980/GM/NIGMS NIH HHS/United States ; R01 GM146462/GM/NIGMS NIH HHS/United States ; R01 AI173172/AI/NIAID NIH HHS/United States ; R01 AI100947/AI/NIAID NIH HHS/United States ; R21 EB031466/EB/NIBIB NIH HHS/United States ; R01 AI151059/AI/NIAID NIH HHS/United States ; R21 AI129851/AI/NIAID NIH HHS/United States ; R35 GM138369/GM/NIGMS NIH HHS/United States ; }, abstract = {Metagenomics has revolutionized our understanding of microbial communities, offering unprecedented insights into their genetic and functional diversity across Earth's diverse ecosystems. Beyond their roles as environmental constituents, microbiomes act as symbionts, profoundly influencing the health and function of their host organisms. Given the inherent complexity of these communities and the diverse environments where they reside, the components of a metagenomics study must be carefully tailored to yield accurate results that are representative of the populations of interest. This Primer article examines the methodological advancements and current practices that have shaped the field, from initial stages of sample collection and DNA extraction to the advanced bioinformatics tools employed for data analysis, with a particular focus on the profound impact of next-generation sequencing (NGS) on the scale and accuracy of metagenomics studies. We critically assess the challenges and limitations inherent in metagenomics experimentation, available technologies and computational analysis methods. Beyond technical methodologies, we explore the application of metagenomics across various domains, including human health, agriculture and environmental monitoring. Looking ahead, we advocate for the development of more robust computational frameworks and enhanced interdisciplinary collaborations. This Primer serves as a comprehensive guide for advancing the precision and applicability of metagenomic studies, positioning them to address the complexities of microbial ecology and their broader implications for human health and environmental sustainability.}, }
@article {pmid40685652, year = {2025}, author = {Hedjem, A and Kouchkar, A and Ladjeroud, A and Zerrouki, N and Benaissa, F and Ibrahim, NA and Aleissa, MS and Basher, NS and Derguini, A and Idres, T and Houali, K}, title = {Androgen receptor expression in triple negative breast cancer: an Algerian population study.}, journal = {The Libyan journal of medicine}, volume = {20}, number = {1}, pages = {2535778}, pmid = {40685652}, issn = {1819-6357}, mesh = {Humans ; *Receptors, Androgen/metabolism ; *Triple Negative Breast Neoplasms/pathology/mortality/metabolism/genetics ; Female ; Middle Aged ; Algeria/epidemiology ; Adult ; Aged ; Biomarkers, Tumor/metabolism ; Survival Rate ; Ki-67 Antigen/metabolism ; }, abstract = {Triple-negative breast cancer (TNBC) is a molecular subtype of breast cancer characterized by the absence of estrogen and progesterone receptors and the lack of HER2 overexpression. TNBC is highly heterogeneous, complicating the identification of new therapeutic targets. However, the expression of the androgen receptor (AR) in the luminal androgen receptor (LAR TNBC) subgroup has opened the door to alternative therapeutic approaches. This study aimed to assess AR expression and correlate it with clinicopathological factors in 160 early-stage TNBC patients treated from February 2015 to February 2017. Our findings reveal that AR expression is observed in 16.87% (27/160) of ≥1% AR positivity cases. Moreover, a significant 12.5% (20/160) was found in ≥10% AR positive cases. Positive AR expression was inversely correlated with a high Ki-67 proliferation index and with the basal immunophenotype. The five-year survival rate for our cohort was 83.12%, and no significant association between AR expression and overall survival was observed (p = 0.77). The study highlights the potential role of AR expression in TNBC and its implications for therapeutic strategies, although no significant association with overall survival was found.}, }
@article {pmid40681538, year = {2025}, author = {Sedláček, I and Holochová, P and Sedlář, K and Staňková, E and Šedo, O and Kralova, S and Umair, M and Koublová, V and Švec, P}, title = {Two new psychrotolerant Massilia species inhibit plant pathogens Clavibacter and Curtobacterium.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {26134}, pmid = {40681538}, issn = {2045-2322}, support = {LM2023069//MEYS CR/ ; LM2023042//MEYS CR/ ; 101020356//Horizon 2020/ ; }, mesh = {Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Clavibacter/pathogenicity ; Antarctic Regions ; *Plant Diseases/microbiology ; }, abstract = {Three bacterial strains producing blue-violet pigmented colonies on R2A agar were isolated from a wet rock wall and lakes in the deglaciated northern part of James Ross Island, Antarctica. The isolated strains inhibited phytopathogenic Gram-positive bacteria Clavibacter spp., Curtobacterium flacumfaciens, and Paenarthrobacter ilicis. Phylogenetic analysis based on the 16S rRNA gene indicated that the isolates belonged to the genus Massilia and the closest relatives were Massilia violaceinigra B2[T], Massilia rubra CCM 8692[T], Massilia frigida CCM 8695[T], Massilia antarctica CCM 8941[T], and Massilia aquatica CCM 8693[T]. A polyphasic taxonomic study based on lepA genes sequencing, automated ribotyping, MALDI-TOF MS, chemotaxonomy analyses, extensive biotyping, average nucleotide identity, and digital DNA-DNA hybridization calculations based on whole-genome sequences proved that the isolates represent a novel Massilia species for which the names Massilia pseudoviolaceinigra sp. nov. and Massilia scottii sp. nov. are suggested, with the type strains P3689[T] (= CCM 9206[T] = LMG 33568[T]) and P5043[T] (= CCM 9029[T] = LMG 32502[T]), respectively. These two bioactive metabolite-producing species may play an important role in shaping the composition of fresh-water Antarctic microbiomes due to the inhibition of various Gram-positive bacteria.}, }
@article {pmid40681451, year = {2025}, author = {Nichols, HL and Coon, KL}, title = {Leveraging microbial ecology for mosquito-borne disease control.}, journal = {Trends in parasitology}, volume = {41}, number = {8}, pages = {670-684}, pmid = {40681451}, issn = {1471-5007}, support = {U01 AI184909/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Vector Borne Diseases/prevention &amp; control/transmission ; *Mosquito Vectors/microbiology ; *Microbiota ; *Mosquito Control/methods ; *Culicidae/microbiology ; Humans ; Mosquito-Borne Diseases ; }, abstract = {Mosquitoes transmit pathogens causing 700 000 deaths annually. Microbe-based vector control, which reduces vector populations or blocks pathogen development within vectors, offers an innovative way to lower global morbidity and mortality due to vector-borne disease. This review addresses challenges hindering the widespread adoption of microbe-based vector control in mosquitoes. We consider understudied transmission routes of mosquito-associated microbiota, factors affecting colonization and persistence of candidate microbial control agents in mosquito hosts, and the need for robust tools and methodologies to validate that observations in laboratory populations can be reliably extended to field populations. We highlight how understanding the microbial ecology underlying interactions between mosquitoes and their native microbiota can guide successful vector control efforts in these and other arthropod disease vectors.}, }
@article {pmid40679638, year = {2025}, author = {Fulke, AB and Sharma, N and Nadekar, J}, title = {Darkness to Discovery: A Comprehensive Mini-Review on Culturable and Non-Culturable Microbial Diversity from Deep Sea.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {77}, pmid = {40679638}, issn = {1432-184X}, support = {OLP2009//National Institute of Oceanography, India/ ; OLP2009//National Institute of Oceanography, India/ ; OLP2009//National Institute of Oceanography, India/ ; }, mesh = {*Seawater/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification/growth &amp; development ; *Microbiota ; *Biodiversity ; Metagenomics/methods ; Ecosystem ; Hydrothermal Vents/microbiology ; Oceans and Seas ; }, abstract = {Microorganisms are essential players in Earth's ecosystems, demonstrating remarkable adaptability to harsh conditions including arctic ice caps, deep-sea hydrothermal vents, and high-pressure oceanic zones. While the study of these extremophiles has long been constrained by challenges in culturing, recent advances in metagenomic techniques have enabled a deeper understanding of microbial diversity in these extreme habitats. This review explores both culturable and non-culturable microbial communities, focusing on the diverse strategies employed by microorganisms to thrive in harsh conditions, including high pressure, temperature, salinity, and nutrient limitations. Traditional cultivation methods often fail to capture the full spectrum of deep-sea microbiota due to the unique growth requirements of many organisms. In the omic era, however, microbial cultivation and the function of microbial resources are important. Non-culturable methods, like metagenomic studies and environmental DNA sequencing, have uncovered hitherto unknown microbial taxa and metabolic pathways, offering important new information on microbial ecology and biogeochemistry. The complex microbial interactions and adaptive methods that support these ecosystems are highlighted by case studies, including as studies on hydrothermal plumes and hadal deposits. The expanding significance of non-culturable techniques in microbial research is highlighted in this review, which also highlights how they might help us better understand microbial life in harsh conditions and how they may be used in biotechnology and environmental management.}, }
@article {pmid40678115, year = {2025}, author = {Tankova, H}, title = {Association between the severity of gingival inflammation and microbial findings in children.}, journal = {Frontiers in dental medicine}, volume = {6}, number = {}, pages = {1638435}, pmid = {40678115}, issn = {2673-4915}, abstract = {INTRODUCTION: The oral cavity is home to hundreds of distinct microbial species, and specific periodontal pathogens are isolated from different ecological niches. Present study aimed to investigate the relationship between the severity of gingival inflammation and the presence of subgingival microorganisms in children with dental biofilm induced gingivitis.<br><br>MATERIAL AND METHODS: The study included 30 children aged 12-14 years, divided into two groups based on the extent of gingival inflammation: Group I-16 children with BOP up to 30%; Group II-14 children with BOP over 30%. All children were interviewed to assess oral hygiene habits. Clinical examination was performed using an electronic periodontal probe, and the following were recorded: oral hygiene status (FMPS) and gingival status through BOP and SBI. For quantitative assessment of subgingival periodontopathogens, a genetic method - PCR-Real Time was used, and the following microorganisms were examined: Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia, Prevotella intermedia, Peptostreptococcus micros, Fusobacterim nucleatum, Eubacterium nodatum, Capnocytophaga gingivalis. The critical significance level for testing the null hypothesis was set at &#x3b1;&#x2009;=&#x2009;0.05, corresponding to a 95% confidence level.<br><br>RESULTS: The majority of children showed improper oral hygiene habits. Children with generalized gingival inflammation had significantly higher plaque accumulation index values compared to those with localized inflammation. In children with generalized gingival inflammation, the quantities of all isolated periodontopathogens were higher compared to those with localized inflammation, which was also confirmed regarding the overall microbial load. A. actinomycetemcomitans was not isolated in children with localized gingival inflammation, while T. denticola was isolated in significantly lower quantities compared to generalized inflammation. P. intermedia and P. micros were isolated in significantly higher quantities in more severe gingival inflammation. In children with localized gingival inflammation, combinations of an average of 2 microorganisms were found in microbial complexes, while in children with generalized inflammation, microorganisms were twice as many and in more complex combinations.<br><br>CONCLUSION: The microbial diversity within the subgingival biofilm significantly increases with disease severity, providing further evidence for the critical role of microbial ecology in the pathogenesis of gingival inflammation in children.}, }
@article {pmid40676356, year = {2025}, author = {Sibanyoni, NR and Piater, LA and Kerchev, P and Madala, NE and Mhlongo, MI}, title = {Metabolomic Insights into Cross-Feeding Interactions Between Priestia megaterium PM and Pseudomonas fluorescens NO4: Unveiling Microbial Communication in Plant Growth-Promoting Rhizobacteria.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {76}, pmid = {40676356}, issn = {1432-184X}, support = {TTK2404507217709//National Research Foundation/ ; }, mesh = {*Pseudomonas fluorescens/metabolism/physiology/growth &amp; development ; Metabolomics ; Rhizosphere ; *Microbial Interactions ; Soil Microbiology ; Quorum Sensing ; Plant Development ; Metabolome ; Volatile Organic Compounds/metabolism ; }, abstract = {Plant growth-promoting rhizobacteria (PGPR) engage in complex chemical exchange and signalling processes to enhance their survival, rhizosphere colonisation, and plant-beneficial roles. These microbial interactions are mediated by various chemical cues, including quorum sensing (QS) molecules, cyclic peptides, lipopeptides, nutrients, volatile organic compounds (VOC), and phytohormones. Cross-feeding, where one microorganism consumes metabolites produced by another, exemplifies direct chemical communication that shapes community dynamics and metabolic cooperation. However, the effects of cross-feeding among different PGPR strains remain insufficiently characterised. In this study, an LC-MS-based metabolomics approach, combined with multivariate statistical analysis, was employed to investigate metabolic perturbations induced by cross-feeding among PGPR strains. Growth curve analysis revealed that cross-fed PGPR exhibited growth patterns comparable to controls, with a slight reduction in biomass. Metabolic profiling indicated time-dependent shifts in the metabolic state of the cross-fed organisms, suggesting adaptive metabolic reprogramming in response to the donor-conditioned media. Multivariate analysis identified distinct metabolite alterations between cross-fed and control groups across different time points, highlighting the influence of nutrient availability on microbial growth dynamics. Notably, cross-fed groups showed decreased levels of primary metabolites such as amino acids and sugars alongside increased production of secondary metabolites, including surfactins, salicylic acid, and carboxylic acids. These secondary metabolites are implicated in plant growth promotion and defence, indicating their potential as natural biostimulants. The findings advance the understanding of PGPR interactions and chemical communication in the rhizosphere, supporting the development of sustainable agricultural practices by leveraging beneficial microbial interactions. Future research should explore these interactions within more complex microbial communities.}, }
@article {pmid40671255, year = {2025}, author = {Bartsch, S and Kreutz, C and Scholz, KJ and Kohnert, E and Hertel, J and Wolf, M and Jakubovics, N and Al-Ahmad, A and Cieplik, F}, title = {Culturomics: Deciphering the Microbial Dark Matter in the Oral Cavity.}, journal = {Journal of dental research}, volume = {}, number = {}, pages = {220345251346781}, doi = {10.1177/00220345251346781}, pmid = {40671255}, issn = {1544-0591}, abstract = {The idea of the tree of life originated in the 19th century and has steadily evolved since then. In the last 20 y, high-throughput sequencing methods have revolutionized microbial ecology and expanded our understanding of this tree of life tremendously. However, this has led to a sharp increase in what is known as microbial dark matter, consisting of bacterial and archaeal taxa that are only known by sequencing and have not yet been cultivated. The lack of ecologic information about these species poses a major challenge. This has led to the need for other approaches to supplement the DNA sequence-based findings. The term "culturomics"-which describes the large-scale isolation, culture, and identification of species from an environment-was introduced in 2012 with a focus on the human gut microbiota. The cultivation of new species, which had been neglected for many years, is now firmly back in the spotlight since strains are required for experimental studies to complement the knowledge obtained from microbial DNA sequences. Laboratory culture is essential to gain knowledge of microbial physiology, assign functions to novel genes and proteins, identify resistance profiles, and better understand the impact of different microorganisms on human health. While many culturomics studies have focused on gut microbiota, significant progress has been made in oral microbiology, with the enrichment of Candidatus Nanosynbacter lyticus representing one of the greatest achievements. This review gives a comprehensive overview of the oral microbial community regarding the microbial dark matter and summarizes the work carried out to date on the oral microbiota using culturomics. The capability and challenges of metagenomics and culturomics and the potential use of artificial intelligence are examined, with insights from extensive culturomics research on gut microbiota, which promises applicability to the field of oral microbiology.}, }
@article {pmid40670676, year = {2025}, author = {Su, J and Su, Y and Weng, Y and Ayub, G and She, C and Xiao, Y}, title = {Insights Into Proliferation Effects of Low-Dose Glyphosate on Phytoplankton Communities.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {75}, pmid = {40670676}, issn = {1432-184X}, support = {FJ2025MGCA019//Fujian Province Social Science Fund Project/ ; 2024R016//Fujian Environmental Protection Science and Technology Program/ ; DH1408//Enterprise and Public Institution Commissioned Science and Technology Project/ ; }, mesh = {Glyphosate ; *Glycine/analogs &amp; derivatives/pharmacology/toxicity ; *Phytoplankton/drug effects/growth &amp; development ; *Herbicides/pharmacology/toxicity ; Biomass ; Cyanobacteria/drug effects/growth &amp; development ; Phosphorus/metabolism ; Microcystis/drug effects/growth &amp; development ; Harmful Algal Bloom/drug effects ; Microalgae/drug effects/growth &amp; development ; *Water Pollutants, Chemical/toxicity ; Ecosystem ; }, abstract = {Glyphosate-based herbicides are among the most widely used agricultural chemicals globally, and their widespread application presents risks to environmental health and aquatic ecosystems. Continuous glyphosate inputs disrupt phytoplankton communities, potentially triggering harmful algal blooms. This study examines the proliferation of microalgal species exposed to low glyphosate concentrations (0.05 mg/L) and various phosphorus sources, with a particular focus on C-P and C-O-P bond phosphonates, which have been insufficiently studied in previous research. We hypothesized that cyanobacteria might exhibit a competitive growth advantage over other algal species when exposed to C-P bond glyphosate, especially under phosphorus-limited conditions. In monoculture experiments, Microcystis aeruginosa and Peridinium umbonatum var. inaequale significantly increased their biomass when cultured with C-P bond phosphonates, whereas Scenedesmus bijuga failed to thrive under similar conditions. Peridinium umbonatum var. inaequale also displayed increased soluble protein content in response to glyphosate stress, indicating an adaptive stress response. In co-culture experiments, M. aeruginosa demonstrated greater tolerance to glyphosate than P. umbonatum var. inaequale, though biomass increases were not significantly correlated with soluble protein or APA. Sediment-water interface experiments revealed that glyphosate exposure significantly promoted cyanobacterial biomass, which was approximately five times greater than that of the inorganic phosphorus group. Notably, when cyanobacterial biomass exceeded 20% of the total, Cyanophyta replaced Chlorophyta as the dominant group, suggesting a potential competitive advantage under low-dose glyphosate exposure. These findings highlight that glyphosate may promote cyanobacterial dominance by altering phytoplankton community composition, potentially contributing to the increased frequency of harmful algal blooms in nutrient-limited aquatic environments.}, }
@article {pmid40668425, year = {2025}, author = {Mnguni, FC and Shin, GY and du Toit, LJ and Derie, ML and Coutinho, TA}, title = {Ewingella allii sp. nov. isolated from a diseased onion plant in the Columbia Basin of Washington State, USA.}, journal = {Antonie van Leeuwenhoek}, volume = {118}, number = {8}, pages = {115}, pmid = {40668425}, issn = {1572-9699}, support = {2019-51181-3//USDA NIFA SCRI/ ; 2019-51181-3//USDA NIFA SCRI/ ; 2019-51181-3//USDA NIFA SCRI/ ; 2019-51181-3//USDA NIFA SCRI/ ; 2019-51181-3//USDA NIFA SCRI/ ; }, mesh = {Phylogeny ; Washington ; RNA, Ribosomal, 16S/genetics ; *Onions/microbiology ; *Plant Diseases/microbiology ; DNA, Bacterial/genetics ; Base Composition ; Genome, Bacterial ; Bacterial Typing Techniques ; }, abstract = {Isolation of strain 20WA0182[T] from a diseased onion plant grown in the Columbia Basin of Washington State, USA, led to preliminary identification as a member of the genus Ewingella. The strain was characterised as a Gram-stain-negative, facultative anaerobe that is rod-shaped, motile with polar flagella, catalase positive, and oxidase negative. The strain 20WA0182[T] isolated was pathogenic to yellow onion bulbs, weakly pathogenic on onion leaves of the cv. Ranchero, and caused a pathogenic response using the red onion bulb scale necrosis assay. Phylogenetic analyses using the 16S rRNA gene and four housekeeping genes, atpD, gyrB, infB, and rpoB, showed that strain 20WA0182[T] formed a branch that clustered with E. americana strains, but on a separate node, indicating it is a novel species of this genus. Whole-genome sequencing of strain 20WA0182[T] revealed a genome size of 4,604,541 nt, with 25 contigs and a G + C content of 53.8%, strain 20WA0182[T] was 99.2% complete. The average nucleotide identity of strain 20WA0182[T] compared with E. americana strains scores ranged from 92.85 to 93.96%, below the 95% threshold to classify strains as the same species. Similarly, dDDH scores were 56.0 to 56.2%, less than the 70% threshold required to delineate prokaryotes as the same species. Strain 20WA0182[T] and Ewingella sp. CoE-038-23 shared the ANI score above 97.59% and 81.0% dDDH score to be classified as a novel species of Ewingella. As the type strain 20WA0182[T] (= BD 3290[ T] = LMG 33618[ T]) was pathogenic to onion bulbs and leaves, the name Ewingella allii is proposed. GenBank accession number = JAWUDN000000000.}, }
@article {pmid40667995, year = {2025}, author = {Garin, T and Brault, A and Marais, C and Briand, M and Préveaux, A and Bonneau, S and Simonin, M and Barret, M and Sarniguet, A}, title = {T6SS-mediated competition by Stenotrophomonas rhizophila shapes seed-borne bacterial communities and seed-to-seedling transmission dynamics.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0045725}, doi = {10.1128/msystems.00457-25}, pmid = {40667995}, issn = {2379-5077}, abstract = {UNLABELLED: Seeds harbor diverse microbial communities important for plant growth and health. During germination, seed exudation triggers intense microbial competition, shaping the communities transmitted to seedlings. This study explores the role of the bacterial type VI secretion system (T6SS)-mediated interference competition in seed microbiota transmission to seedlings. The analysis of T6SS distribution within 180 genome sequences of seed-borne bacterial strains enabled the construction of synthetic communities (SynCom) with different levels of phylogenetic diversity and T6SS richness. These SynComs were inoculated with Stenotrophomonas rhizophila CFBP13503, a bacterial strain possessing an active T6SS in vitro and in planta. The impact of the T6SS on SynCom composition was assessed in vitro by comparing the CFBP13503 wild-type strain or its isogenic T6SS-deficient mutant co-inoculation. Additionally, the effects of the T6SS on bacterial community dynamics during seed-to-seedling transmission were examined following seed inoculation. The T6SS of S. rhizophila CFBP13503 targets a broad range of bacteria belonging to five different orders. The susceptibility of competing bacteria was partly explained by their phylogenetic proximity and metabolic overlap with CFBP13503. Furthermore, the T6SS modulates the relative abundance of specific bacterial taxa during seed-to-seedling transmission depending on the initial seed inoculum and plant developmental stage. Depending on the sensitivity of the co-inoculated competitors, the T6SS can provide a competitive advantage to CFBP13503, resulting in an increase in population size.<br><br>IMPORTANCE: The high prevalence of the type VI secretion system (T6SS) in seed-borne bacteria supports the importance of T6SS-mediated competition for seed microbiota assembly. In vitro, S. rhizophila CFBP13503 T6SS exerts a strong impact on bacterial community dynamics. The susceptibility to the T6SS increases with the phylogenetic and metabolic proximities of bacteria to CFBP13503, suggesting the influence of interspecies trophic patterns in T6SS-mediated competitions. In planta and in soil, CFBP13503 T6SS influences specific bacterial taxa, leading to shifts in bacterial interactions and distinct community dynamics. T6SS-mediated competition plays a pivotal role in shaping seed bacterial communities and the dynamics of seed-to-seedling transitions.}, }
@article {pmid40666882, year = {2025}, author = {Orkin, JD and Fournier, A and Young, D and Webb, SE and Cheves Hernandez, SE and Jack, KM and Campos, FA and Dufour, A and Melin, AD}, title = {Fecal proteomics of wild capuchins reveals impacts of season, diet, age, and, sex on gut physiology.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40666882}, issn = {2692-8205}, support = {R61 AG078529/AG/NIA NIH HHS/United States ; }, abstract = {Understanding how the physiology of free-ranging mammals is impacted by environmental stressors is a major focus of ecological research. However, the constraints of non-invasive sampling pose serious challenges to the acquisition of physiological data from most species of primates. As a result, little is known about how the gut responds to ecological stimuli at the cellular level in wild populations. Recent research has demonstrated that proteomics could fill this knowledge gap by sequencing and quantifying proteins directly from primate feces. In order to ascertain how the gut of free-ranging white-faced capuchin monkeys (C. imitator) is influenced by environmental heterogeneity, diet, age, and sex, we sequenced 45 fecal proteomes from 24 individuals from the Sector Santa Rosa population in Costa Rica, using liquid chromatography-tandem mass spectrometry with label-free quantification. Fecal proteins assigned to C. imitator were strongly localized to gut tissues and functionally enriched for digestive and immune functions. We identified 41 capuchin candidate proteins linked to seasonality, age, sex, and diet. We also quantified abundances of dietary fruit, dietary insects, helminth gut parasites, and gut microbes. Our results demonstrate the viability of using quantitative fecal proteomics in free-ranging populations of mammals to integrate host physiology, diet, and microbial ecology through non-invasive means.}, }
@article {pmid40662685, year = {2025}, author = {Verstraete, W and Strubbe, L and Pikaar, I and Vinestock, TW and Lee, PH and Matassa, S and Chong, J and Zhou, J and Daigger, GT and Guo, M}, title = {Escaping Historical Lock-in─Redesigning Wastewater Treatment Plants and Their Microbiomes for the 21st Century.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {29}, pages = {14862-14869}, pmid = {40662685}, issn = {1520-5851}, mesh = {*Wastewater ; *Microbiota ; *Water Purification ; *Waste Disposal, Fluid ; }, abstract = {Wastewater treatment plants (WWTPs) have gradually, over the last hundred years, been designed and extended to deal with a sequence of problems, including a) odor, b) suspended solids, c) organics, d) ammonia, e) nitrate and phosphate, and f) recalcitrant pollutants. The line of historical developments was piecemeal rather than holistic and did not focus on sustainability, resource recovery, and water reuse. On the contrary, microbial processes that accelerated the removal of nitrogen were incorporated and heralded as a positive part of the "cleanup" agenda, despite their relatively large energy consumption and substantial production of nitrous oxide, a potent greenhouse gas. The time has come to examine the historical, technological, and microbiological lock-in present in today's WWTPs, so that a more coherent integrated system can be developed for future generations. Some disruptive strategies are outlined, and a categorization of processes in terms of their potential for the future is formulated.}, }
@article {pmid40660619, year = {2025}, author = {Armstrong, R}, title = {Microbes as Teachers: Rethinking Knowledge in the Anthropocene.}, journal = {Microbial biotechnology}, volume = {18}, number = {7}, pages = {e70195}, pmid = {40660619}, issn = {1751-7915}, support = {101114746//European Innovation Council (EIC), Pathfinder Challenges/ ; }, mesh = {Humans ; Ecosystem ; *Microbiology/education ; }, abstract = {This opinion piece proposes that the environmental crises of our time arise from a failure to recognise the vital role of microbes in sustaining life on Earth, where ecosystems have been shaped for billions of years by microbial processes, including oxygen production, nutrient cycling and climate regulation. Yet the idea that microbes can 'teach' us how to navigate complexity, adapt across scales, and sustain planetary systems is still marginalised in science, policy, and education. A paradigm shift is proposed: microbes must be reframed as active collaborators in solving global challenges. This perspective is grounded in microbial ecology, Indigenous knowledge, and ethical philosophy, advocating for 'learning' through and with microbial life. To institutionalise this transition, policy and educational reforms are urged, centring microbial literacy as a foundation for ecological understanding. By integrating microbial agency into human knowledge systems, societal actions could be realigned with the biochemical and evolutionary logics that have sustained life for millennia. Ultimately, a deeper engagement with microbial knowledge is called for-one that informs a more sustainable future.}, }
@article {pmid40657876, year = {2025}, author = {Strachan, CR and Bowers, CM and Kim, BC and Movsesijan, T and Neubauer, V and Mueller, AJ and Yu, XA and Pereira, FC and Nagl, V and Faas, J and Wagner, M and Zebeli, Q and Weimer, PJ and Candry, P and Polz, MF and Lawson, CE and Selberherr, E}, title = {Distinct lactate utilization strategies drive niche differentiation between two co-existing Megasphaera species in the rumen microbiome.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40657876}, issn = {1751-7370}, support = {//Austrian Federal Ministry for Digital and Economic Affairs and the National Foundation for Research, Technology and Development, through the Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock/ ; //Austrian Federal Ministry for Climate Action, Environment, Energy, Mobility, Innovation and Technology (BMK), Austrian Federal Ministry for Digital and Economic Affairs (BMDW) and the provinces of Lower Austria and Vienna within the framework of COMET-Competence Centers for Excellent Technologies, which is handled by the Austrian Research Promotion Agency (FFG)/ ; //Sparkling Science 2.0 grant (project "Micro-Tramper") funded by the Austrian Federal Ministry of Science, Research and Economy (BMWFW)/ ; //Fellowship from the Natural Science and Engineering Council of Canada Postgraduate Scholarship-Doctoral (NSERC PGS-D)/ ; }, abstract = {Lactate utilization mitigates rumen acidosis and is associated with decreased methane production in the rumen. While several lactate utilization pathways exist across different microbial species in the rumen, how they are metabolically differentiated remains unclear. Here, we show that the key lactate-utilizing species Megasphaera hexanoica and Megasphaera elsdenii display distinct growth strategies based on their fermentative end products. This allows them to co-exist and play distinct metabolic roles, which appear particularly relevant in the early stages of rumen development, as both species are highly enriched in the calf. Specifically, M. hexanoica is more strongly associated with rumen microbiome states that involve increased lactate utilization and preferentially runs reverse beta-oxidation (termed chain elongation) to produce butyrate and medium-chain fatty acids from lactate. As M. elsdenii instead utilizes lactate via the acrylate pathway to produce propionate, we leverage Enzyme Cost Minimization to predict how this pathway relates to a distinct growth strategy. We find that M. elsdenii maximizes growth rate when lactate transiently accumulates, which contrasts M. hexanoica's invariably high-yield strategy. This trade-off, which is supported by the analysis of growth kinetics, metabolic flux, and bioreactors simulating the rumen microbiome, ultimately contributes to co-existence on lactate and may have driven niche differentiation. Lastly, we demonstrate how lactate utilization in the Megasphaera is threatened by toxins widespread in feed, which points to dietary interventions to support calf health.}, }
@article {pmid40657038, year = {2025}, author = {Ronin, D and Hansen, MF and Flaig, ML and Dahl Dueholm, MK and Hostrup Daugberg, AO and Nesme, J and Kot, W and Burmølle, M}, title = {Unfolding the collective functional potential of a synergistic multispecies community through genotypic and phenotypic analyses.}, journal = {Biofilm}, volume = {10}, number = {}, pages = {100290}, pmid = {40657038}, issn = {2590-2075}, abstract = {By studying model multispecies biofilm systems, we can further our knowledge regarding why some properties emerge solely in a multispecies setting. In this study, the model system under investigation is composed of four bacterial species: Paenibacillus amylolyticus, Microbacterium oxydans, Stenotrophomonas rhizophila and Stenotrophomonas maltophilia. This community was isolated from soil and has previously shown synergistic biofilm formation capabilities in vitro, along with other intrinsic properties, some of which could lead to potential industrial and agricultural applications. In this study, we conducted the first complete genome assemblies for these four strains and performed a manually curated annotation of the genomes to identify genomic features that could guide the selection of relevant phenotypic assays. In all four strains, we identified genes linked to interspecies communication, biofilm formation, secondary metabolite production, antibiotic resistance, enzymatic activity and metabolism of toxic xenobiotics. With metabolism being the largest gene function category identified, we then conducted growth assays on various carbon sources and relevant polysaccharides. This revealed interesting emergent behaviors - regarding growth and enzymatic activity - in the four-species community which were not seen in the monocultures. Overall, analysis of the complete genomes of this model community uncovered gene functions which could play a role in the previously observed community intrinsic properties, as well as provided insight to the positive social interactions observed in vitro.}, }
@article {pmid40655931, year = {2025}, author = {Redondo, MA and Jones, CM and Legendre, P and Guénard, G and Hallin, S}, title = {Predicting gene distribution in ammonia-oxidizing archaea using phylogenetic signals.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf087}, pmid = {40655931}, issn = {2730-6151}, abstract = {Phylogenetic conservatism of microbial traits has paved the way for phylogeny-based predictions, allowing us to move from descriptive to predictive functional microbial ecology. Here, we applied phylogenetic eigenvector mapping to predict the presence of genes indicating potential functions of ammonia-oxidizing archaea (AOA), which are important players in nitrogen cycling. Using 160 nearly complete AOA genomes and metagenome assembled genomes from public databases, we predicted the distribution of 18 ecologically relevant genes across an updated amoA gene phylogeny, including a novel variant of an ammonia transporter found in this study. All selected genes displayed a significant phylogenetic signal and gene presence was predicted with an average of >88% accuracy, >85% sensitivity, and >80% specificity. The phylogenetic eigenvector approach performed equally well as ancestral state reconstruction of gene presence. We implemented the predictive models on an amoA sequencing dataset of AOA soil communities and showed key ecological predictions, e.g. that AOA communities in nitrogen-rich soils were predicted to have capacity for ureolytic metabolism while those adapted to low-pH soils were predicted to have the high-affinity ammonia transporter (amt2). Predicting gene presence can shed light on the potential functions that microorganisms perform in the environment, further contributing to a better mechanistic understanding of their community assembly.}, }
@article {pmid40654884, year = {2025}, author = {Wirbel, J and Hickey, AS and Chang, D and Enright, NJ and Dvorak, M and Chanin, RB and Schmidtke, DT and Bhatt, AS}, title = {Discovering Broader Host Ranges and an IS-bound Prophage Class Through Long-Read Metagenomics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40654884}, issn = {2692-8205}, support = {R01 AI143757/AI/NIAID NIH HHS/United States ; R01 AI148623/AI/NIAID NIH HHS/United States ; T32 GM007276/GM/NIGMS NIH HHS/United States ; }, abstract = {Gut bacteriophages profoundly impact microbial ecology and human health, yet they are greatly understudied. Using deep, long-read bulk metagenomic sequencing, a technique that overcomes fundamental limitations of short-read approaches, we tracked prophage integration dynamics in 12 longitudinal stool samples from six healthy individuals, spanning a two-year timescale. While most prophages remain stably integrated into their host over two years, we discover that ~5% of phages are dynamically gained or lost from persistent bacterial hosts. Within the same sample, we find evidence of population heterogeneity in which identical bacterial hosts with and without a given integrated prophage coexist simultaneously. Furthermore, we demonstrate that phage induction, when detected, occurs predominantly at low levels (1-3x coverage compared to the host region). Interestingly, we identify multiple instances of integration of the same phage into bacteria of different taxonomic families, challenging the dogma that phage are specific to a host of a given species or strain. Lastly, we describe a new class of phages, which we name "IScream phages". These phages co-opt bacterial IS30 transposases to mediate their integration, representing a previously unrecognized form of phage domestication of selfish bacterial elements. Taken together, these findings illuminate fundamental aspects of phage-bacterial dynamics in the human gut microbiome and expand our understanding of the evolutionary mechanisms that drive horizontal gene transfer and microbial genome plasticity in this ecosystem.}, }
@article {pmid40650753, year = {2025}, author = {Pascual, A and Calabresi, F and de la Fuente, D and Catalano, MI and Brentassi, ME}, title = {Transcriptome Analysis of the Fat Body of the Maize Pest Delphacodes kuscheli (Hemiptera: Delphacidae) Reveals Essential Roles of Fungal Endosymbionts.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {74}, pmid = {40650753}, issn = {1432-184X}, support = {PICT 2021- 00914//Comisi&#xf3;n de Investigaciones Cient&#xed;ficas de la Provincia de Buenos Aires (CICPBA), Consejo Nacional de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas (CONICET), Universidad Nacional de La Plata (UNLP), and Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica (ANPCyT) (PICT 2021- 00914)./ ; PICT 2021- 00914//Comisi&#xf3;n de Investigaciones Cient&#xed;ficas de la Provincia de Buenos Aires (CICPBA), Consejo Nacional de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas (CONICET), Universidad Nacional de La Plata (UNLP), and Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica (ANPCyT) (PICT 2021- 00914)./ ; PICT 2021- 00914//Comisi&#xf3;n de Investigaciones Cient&#xed;ficas de la Provincia de Buenos Aires (CICPBA), Consejo Nacional de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas (CONICET), Universidad Nacional de La Plata (UNLP), and Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica (ANPCyT) (PICT 2021- 00914)./ ; PICT 2021- 00914//Comisi&#xf3;n de Investigaciones Cient&#xed;ficas de la Provincia de Buenos Aires (CICPBA), Consejo Nacional de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas (CONICET), Universidad Nacional de La Plata (UNLP), and Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica (ANPCyT) (PICT 2021- 00914)./ ; PICT 2021- 00914//Comisi&#xf3;n de Investigaciones Cient&#xed;ficas de la Provincia de Buenos Aires (CICPBA), Consejo Nacional de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas (CONICET), Universidad Nacional de La Plata (UNLP), and Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica (ANPCyT) (PICT 2021- 00914)./ ; }, mesh = {Animals ; *Symbiosis ; *Hemiptera/microbiology/genetics ; Gene Expression Profiling ; Zea mays/parasitology ; *Fat Body/microbiology/metabolism ; *Transcriptome ; *Hypocreales/genetics/physiology ; Phylogeny ; }, abstract = {The fat body of certain insects, in addition to performing essential biosynthetic and metabolic functions, harbors endosymbionts that play critical roles for their host. While knowledge of the diversity and functions of fungal endosymbionts harbored in the fat body of planthoppers is mostly limited to rice pests of Asia, our study presents a comprehensive transcriptomic analysis of the fat body of Delphacodes kuscheli (Hemiptera: Delphacidae), an important agricultural pest of maize in Argentina. The dominant fungal endosymbionts, identified as yeast-like symbionts (YLS), include members of the genera Ophiocordyceps, Cordyceps, Hirsutella, and Tolypocladium (Ascomycota: Hypocreales). Transcriptomic data reveal that the fungal endosymbionts encode genes involved in vital metabolic processes for the host, such as essential amino acid biosynthesis, nitrogen recycling, and steroid biosynthesis. The genetic contribution of these endosymbionts to nutrient provision and metabolism supports a mutualistic obligate relationship with D. kuscheli. The results presented here provide insights into the evolutionary dynamics of endosymbiosis in the Delphacidae. Furthermore, this study highlights the potential of YLS as promising targets for innovative pest control strategies.}, }
@article {pmid40650575, year = {2025}, author = {Guigard, L and Nazaret, F and Almario, J and Bertolla, F and Boubakri, H and Cantarel, AAM and Cournoyer, B and Favre-Bonté, S and Florio, A and Galia, W and Hazard, C and Henry, G and Belaroussi, AH and Chong, SKTF and Lavire, C and Lobreau, C and Luis, P and Maréchal, M and Meyer, T and Pozzi, ACM and Minard, G and Nazaret, S and Nicol, GW and Prigent-Combaret, C and Richaume, A and Rodriguez-Nava, V and Sanchez-Cid, C and Moro, CV and Vial, L and Vigneron, A and Wisniewski-Dyé, F and Shade, A}, title = {The connections of climate change with microbial ecology and their consequences for ecosystem, human, and plant health.}, journal = {Journal of applied microbiology}, volume = {136}, number = {7}, pages = {}, doi = {10.1093/jambio/lxaf168}, pmid = {40650575}, issn = {1365-2672}, support = {//Universit&#xe9; Claude Bernard Lyon 1/ ; }, mesh = {*Climate Change ; Humans ; *Ecosystem ; *Microbiota ; *Plants/microbiology ; }, abstract = {The climate crisis presents an urgent challenge for Earth's living creatures and the habitats in which they have been adapted to thrive. Climate-related stress presents risks to microorganisms, the stability of the functions they provide, and their maintenance of beneficial interactions with their hosts and ecosystems. Microbes move across the continuum of anthropogenic influence on Earth's ecosystems, from pristine to human-managed to fully urbanized environments. Because microbial feedback within and across this continuum exists at multiple, connected scales from molecules to ecosystem-level processes, predicting microbial responses to climate stress and their potentially wide-ranging consequences remains difficult. Here, we discuss the broad implications of microbial and microbiome responses to climate change as they interface with human, plant, and ecosystem health. For each section on human, plant and ecosystem health, we briefly discuss the state of knowledge for each and follow with proposed future research, including some directions that are promising but require more work to evaluate. We end by considering overarching microbial ecology research needs across these systems and microbial solutions under investigation as possible climate-resilient interventions to maintain human, plant, and ecosystem health. This work draws on diverse expertise to identify broad research directions across typically separated disciplines and builds a holistic framework for considering their interrelationships.}, }
@article {pmid40650408, year = {2025}, author = {Beau, A and Natividad, J and Benoit, B and Delerive, P and Duboux, S and Feng, Y and Jammes, M and Barnel, C and Sequino, G and Pinteur, C and Glorieux, G and Fouque, D and Vidal, H and Koppe, L}, title = {A specifically designed multi-biotic reduces uremic toxin generation and improves kidney function.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2531202}, pmid = {40650408}, issn = {1949-0984}, mesh = {Humans ; *Uremic Toxins/metabolism ; *Renal Insufficiency, Chronic/microbiology/therapy ; Animals ; *Probiotics/administration &amp; dosage ; Feces/microbiology/chemistry ; *Gastrointestinal Microbiome ; Male ; Cresols/metabolism ; *Kidney/physiology ; Prebiotics/administration &amp; dosage ; Female ; Middle Aged ; Lactobacillus/metabolism/growth &amp; development ; *Uremia ; Cellobiose/metabolism ; Rats ; Indican ; Bacteria/metabolism/genetics/classification ; Disease Models, Animal ; }, abstract = {Chronic kidney disease (CKD) is characterized by accumulation of uremic toxins (UTs), such as p-cresyl sulfate and indoxyl sulfate, generated through the transformation of tyrosine and tryptophan by the gut microbiota. Using an ex vivo Simulator of the Human Intestinal Microbial Ecosystem (SHIME) colonized with fecal samples from eight CKD patients or nine healthy volunteers, a higher bacterial generation of p-cresol and indoles post-amino acid enrichment, as well lower basal butyrate levels, in the feces of CKD patients were found. Through in silico data mining, we selected a probiotic strain lacking the capacity to produce UT, i.e. without genes for tryptophanase, tyrosinase and urease. In vitro, we confirmed the potential of cellobiose as a prebiotic supporting the growth of this strain. We further designed a novel specific multi-biotic for CKD (SynCKD) [containing a probiotic Lactobacillus johnsonii NCC533, a prebiotic (1% cellobiose), and a postbiotic (1% short and medium chain triglycerides C4-C8, a source of butyrate)]. SynCKD effectively curtailed UT precursor generation ex vivo. The in vivo efficacy of SynCKD (and the synergic effect) was established in two uremic rodent models, demonstrating lower plasma levels of UTs and enhancing kidney function after 6-8 weeks of treatment. These effects were linked to better gut microbial ecology. Metagenomic analysis revealed reduced microbial genes for tryptophan/tyrosine degradation. This study lays the foundation for SynCKD as a potential therapy to mitigate CKD progression.}, }
@article {pmid40649758, year = {2025}, author = {Hu, Q and Huang, T and Zhu, A and Anglés, A and Abdelghany, O and Ahmed, A and Fernández-Remolar, DC}, title = {Comparing Protein Stability in Modern and Ancient Sabkha Environments: Implications for Molecular Remnants on Ancient Mars.}, journal = {International journal of molecular sciences}, volume = {26}, number = {13}, pages = {}, pmid = {40649758}, issn = {1422-0067}, support = {2021YFA0716100//National Key Research and Development Program of China/ ; 2022YFF0504000//National Key Research and Development Program of China/ ; 2024YFF0807702//National Key Research and Development Program of China/ ; 0005/2020/A1//Fundo para o Desenvolvimento das Ci&#xea;ncias e da Tecnologia/ ; 0052/2024/RIA1//Fundo para o Desenvolvimento das Ci&#xea;ncias e da Tecnologia/ ; 42441801//National Natural Science Foundation of China/ ; }, mesh = {Mars ; *Proteins/chemistry ; United Arab Emirates ; Oceans and Seas ; Gas Chromatography-Mass Spectrometry ; Chromatography, High Pressure Liquid ; Proteomics ; Microbiota ; }, abstract = {Understanding the mechanisms of protein preservation in extreme environments is essential for identifying potential molecular biosignatures on Mars. In this study, we investigated five sabkha sedimentary samples from the Abu Dhabi coast, spanning from the present day to ~11,000 years before present (BP), to assess how mineralogy and environmental conditions influence long-term protein stability. Using LC-MS/MS and direct Data-independent Acquisition (DIA) proteomic analysis, we identified 722 protein groups and 1300 peptides, revealing a strong correlation between preservation and matrix composition. Carbonate- and silica-rich samples favored the retention of DNA-binding and metal-coordinating proteins via mineral-protein interactions, while halite- and gypsum-dominated facies showed lower recovery due to extreme salinity and reduced biomass input. Functional profiling revealed a shift from metabolic dominance in modern samples to genome maintenance strategies in ancient ones, indicating microbial adaptation to prolonged environmental stress. Contrary to expectations, some ancient samples preserved large, multi-domain proteins, suggesting that early mineral encapsulation can stabilize structurally complex biomolecules over millennial timescales. Taxonomic reconstruction based on preserved proteins showed broad archaeal diversity, including Thaumarchaeota and thermophilic lineages, expanding our understanding of microbial ecology in hypersaline systems. These findings highlight sabkhas as valuable analogs for Martian evaporitic environments and suggest that carbonate-silica matrices on Mars may offer optimal conditions for preserving ancient molecular traces of life.}, }
@article {pmid40649719, year = {2025}, author = {Popov, IV and Manakhov, AD and Gorobets, VE and Diakova, KB and Lukbanova, EA and Malinovkin, AV and Venema, K and Ermakov, AM and Popov, IV}, title = {Metagenomic Investigation of Intestinal Microbiota of Insectivorous Synanthropic Bats: Densoviruses, Antibiotic Resistance Genes, and Functional Profiling of Gut Microbial Communities.}, journal = {International journal of molecular sciences}, volume = {26}, number = {13}, pages = {}, pmid = {40649719}, issn = {1422-0067}, support = {23-14-00316//Russian Science Foundation/ ; 075-10-2025-017//Ministry of Science and Higher Education of the Russian Federation/ ; }, mesh = {Animals ; *Chiroptera/microbiology/virology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Drug Resistance, Microbial/genetics ; Phylogeny ; *Metagenome ; }, abstract = {Bats serve as key ecological reservoirs of diverse microbial communities, including emerging viruses and antibiotic resistance genes. This study investigates the intestinal microbiota of two insectivorous bat species, Nyctalus noctula and Vespertilio murinus, at the Rostov Bat Rehabilitation Center in Southern Russia using whole metagenome shotgun sequencing. We analyzed taxonomic composition, functional pathways, antibiotic resistance genes, and virulence factors. Densoviruses, especially those closely related to Parus major densovirus, were the most dominant viral sequences identified. Metagenome-assembled densovirus genomes showed high sequence similarity with structural variations and clustered phylogenomically with viruses from mealworms and birds, reflecting both dietary origins and the potential for vertebrate infection. Functional profiling revealed microbial pathways associated with cell wall biosynthesis, energy metabolism, and biofilm formation. A total of 510 antibiotic resistance genes, representing 142 unique types, mainly efflux pumps and β-lactamases, were identified. Additionally, 870 virulence factor genes were detected, with a conserved set of iron acquisition systems and stress response regulators across all samples. These findings highlight the ecological complexity of bat-associated microbiota and viromes and suggest that synanthropic bats may contribute to the circulation of insect-associated viruses and antimicrobial resistance in urban settings.}, }
@article {pmid40647934, year = {2025}, author = {Gao, X and Qian, H and Huang, R and He, W and Jiang, H and Shen, A and Li, Z and Hu, Y}, title = {Rhizosphere and Non-Rhizosphere Soil Microbial Communities in Alpine Desertified Grassland Affected by Vegetation Restoration.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {13}, pages = {}, pmid = {40647934}, issn = {2223-7747}, support = {41771552//National Natural Science Foundation of China/ ; 2022YFS0469//Sichuan Science and Technology Project/ ; }, abstract = {The rhizosphere serves as a critical interface for plant-soil-microorganism interactions. Rhizosphere soil refers to the soil directly adhering to root surfaces, while non-rhizosphere soil denotes the surrounding soil not in direct contact with roots. This study investigated the characteristics of soil microbial community structure, diversity, and enzyme activity dynamics in both rhizosphere and non-rhizosphere soils of Salix cupularis (shrub) across different restoration periods (4, 8, 16, and 24 years) in alpine sandy lands on the eastern Qinghai-Tibet Plateau, with unrestored sandy land as control (CK), while analyzing relationships between soil properties and microbial characteristics. Results demonstrated that with increasing restoration duration, activities of sucrase, urease, alkaline phosphatase, and catalase in Salix cupularis rhizosphere showed increasing trends across periods, with rhizosphere enzyme activities consistently exceeding non-rhizosphere levels. Bacterial Chao1 and Shannon indices followed similar patterns to enzyme activities, revealing statistically significant differences between rhizosphere and non-rhizosphere soils after 8 and 24 years of restoration, respectively. Dominant bacterial phyla ranked by relative abundance were Actinobacteria > Proteobacteria > Acidobacteria > Chloroflexi > Gemmatimonadetes. The relative abundance of Actinobacteria exhibited highly significant positive correlations with carbon, nitrogen, phosphorus, and enzyme activity indicators, indicating that Salix cupularis restoration promoted improvements in soil physicochemical properties and nutrient accumulation, thereby enhancing bacterial community diversity and increasing Actinobacteria abundance. These findings provide fundamental data for restoration ecology and microbial ecology in alpine ecosystems, offering a scientific basis for optimizing ecological restoration processes and improving recovery efficiency in alpine sandy ecosystems.}, }
@article {pmid40647139, year = {2025}, author = {Bach, LG and Braga, GZA and Bedutti, MC and Dias, LMP and Dos Santos, EAR and Tadielo, LE and Silva, ECD and Schmiedt, JA and Alves, VF and De Martinis, ECP and Possebon, FS and Barcellos, VC and Bersot, LDS}, title = {Total Culturable Microbial Diversity of Food Contact Surfaces in Poultry and Fish Processing Industries After the Pre-Operational Cleaning Process.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {13}, pages = {}, pmid = {40647139}, issn = {2304-8158}, support = {001//Coordination for the Improvement of Higher Education - CAPES/ ; Proc.# 3069982022-0//National Council for Scientific and Technological Development/ ; }, abstract = {This study assessed the viable and culturable microbial diversity that remained on equipment surfaces after hygiene procedures in Brazilian poultry and fish slaughterhouses. Food-contact surface samples were collected using sterile swabs in poultry (n = 50) and fish (Oreochromis niloticus, n = 50) slaughterhouses. The swab samples were used to prepare culture plates to recover viable and culturable cells. The grown plates were washed, and the total DNA of the cell suspension was extracted with a commercial kit. Sequencing of the total DNA extracted from cultures was targeted at the V3 and V4 regions of the 16S rRNA. DNA reads were analyzed by QIIME2 software, with results expressed in relative frequency (%RF). Alpha and beta diversity indexes were analyzed considering the spots of sample collection, type of industry, surfaces (smooth or modular), and materials (polypropylene, stainless steel, or polyurethane). The results showed that in the poultry slaughterhouse, the most abundant genera were Acinetobacter (27.4%), Staphylococcus (7.7%), and Pseudomonas (5.3%), while for the fish slaughterhouse, there was a higher abundance of Staphylococcus (27.7%), Acinetobacter (17.2%), and Bacillus (12.5%). Surface characteristics influenced the microbial diversity, with Acinetobacter spp. dominating modular surfaces and Staphylococcus spp. prevailing on smooth surfaces. The results obtained indicate there is an important resident microbiota that persists even after hygiene processes, and surface-specific cleaning strategies should be developed.}, }
@article {pmid40647044, year = {2025}, author = {Park, I and Mannaa, M}, title = {Fermented Foods as Functional Systems: Microbial Communities and Metabolites Influencing Gut Health and Systemic Outcomes.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {13}, pages = {}, pmid = {40647044}, issn = {2304-8158}, support = {2024//This work was supported by Youngsan University research fund of/ ; }, abstract = {Fermented foods represent an intricate ecosystem that delivers live microbes and numerous metabolites, influencing gut health. In this review, we explore how complex microbial communities and metabolites generated during food fermentation modulate the gut microbiome and affect human health. We discuss fermentation-induced biochemical transformations, including enhanced fiber fermentability; nutrient availability; and the synthesis of bioactive metabolites such as short-chain fatty acids, exopolysaccharides, bacteriocins, and modified polyphenols. We describe the dynamic microbial ecology of fermented foods, influenced by ingredient variations, highlighting its effect on health-related metabolic outcomes. Fermented products when consumed transiently introduce beneficial microbes and bioactive compounds into the gut, thereby boosting microbial diversity, resilience, and barrier function. We review clinical and preclinical studies to substantiate the roles of fermented foods in immune regulation, metabolic homeostasis, cognitive function, and inflammation mitigation. Individual variability in response to fermented foods has been emphasized, underscoring the potential for personalized nutrition strategies informed by advanced omics technologies. By integrating microbial ecology, metabolomics, and clinical evidence, this review positions fermented food intake as a strategic dietary intervention for microbiome modulation and health promotion.}, }
@article {pmid40643242, year = {2025}, author = {Nguyen, A and Ustick, LJ and Larkin, AA and Martiny, AC}, title = {Global phylogeography and microdiversity of the marine diazotrophic photoautotrophs Trichodesmium and UCYN-A.}, journal = {mSphere}, volume = {10}, number = {7}, pages = {e0024525}, pmid = {40643242}, issn = {2379-5042}, support = {1046297, 1559002, 1848576, 1948842, 2135035, 2137339//National Science Foundation/ ; //Peter und Traudl Engelhorn Stiftung/ ; 101813-Z7554214//National Oceanic and Atmospheric Administration/ ; T32AI141346/NH/NIH HHS/United States ; 80NSSC21K1654/NASA/NASA/United States ; T32 AI141346/AI/NIAID NIH HHS/United States ; }, mesh = {Nitrogen Fixation ; Phylogeography ; *Genetic Variation ; *Trichodesmium/genetics/classification ; Phylogeny ; *Seawater/microbiology ; Pacific Ocean ; Indian Ocean ; Nitrogenase/genetics ; Atlantic Ocean ; Biodiversity ; }, abstract = {Photoautotrophic diazotrophs, specifically the genera Trichodesmium and UCYN-A, play a pivotal role in marine nitrogen cycling through their capacity for nitrogen fixation. Despite their global distribution, the microdiversity and environmental drivers of these diazotrophs remain underexplored. This study provides a comprehensive analysis of the global diversity and distribution of Trichodesmium and UCYN-A using the nitrogenase gene (nifH) as a genetic marker. We sequenced 954 samples from the Pacific, Atlantic, and Indian Oceans as part of the Bio-GO-SHIP project. Our results reveal significant phylogenetic and biogeographic differences between and within the two genera. Trichodesmium exhibited greater microdiversity compared to UCYN-A, with clades showing region-specific distribution. Trichodesmium clades were primarily influenced by temperature and nutrient availability. They were particularly frequent in regions of phosphorus stress. In contrast, UCYN-A was most frequently observed in regions experiencing iron stress. UCYN-A clades demonstrated more homogeneous distributions, with a single sequence variant within the UCYN-A1 clade dominating across varied environments. The biogeographic patterns and environmental correlations of Trichodesmium and UCYN-A highlight the role of microdiversity in their ecological adaptation and reflect their different ecological strategies. These findings underscore the importance of characterizing the global patterns of fine-scale genetic diversity to better understand the functional roles and distribution of marine nitrogen-fixing photoautotrophs.IMPORTANCEThis study provides insights into the global diversity and distribution of nitrogen-fixing photoautotrophs, specifically Trichodesmium and UCYN-A. We sequenced 954 oceanic samples of the nifH nitrogenase gene and uncovered significant differences in microdiversity and environmental associations between these genera. Trichodesmium showed high levels of sequence diversity and region-specific clades influenced by temperature and nutrient availability. In contrast, UCYN-A exhibited a more uniform distribution, thriving in iron-stressed regions. Quantifying these fine-scale genetic variations enhances our knowledge of their ecological roles and adaptations, emphasizing the need to characterize the genetic diversity of marine nitrogen-fixing prokaryotes.}, }
@article {pmid40640502, year = {2025}, author = {Liu, L and Firrman, JA and Narrowe, AB and Mahalak, KK and Lemons, JMS and Marzorati, M and Duysburgh, C and Rotsaert, C and Van de Wiele, T}, title = {Structural and functional characterization of a porcine intestinal microbial ecosystem developed in vitro.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {24821}, pmid = {40640502}, issn = {2045-2322}, support = {8072-41000-108-00-D//USDA/ ; 8072-41000-108-00-D//USDA/ ; 8072-41000-108-00-D//USDA/ ; 8072-41000-108-00-D//USDA/ ; 8072-41000-108-00-D//USDA/ ; EOS-Homistasis project//FWO-FNR/ ; GOA-Microbes4Immunity//UGent-BOF/ ; }, mesh = {Animals ; Swine ; *Gastrointestinal Microbiome ; Metagenome ; Feces/microbiology ; *Bacteria/genetics/classification ; Metagenomics/methods ; Metabolomics ; *Intestines/microbiology ; Ecosystem ; }, abstract = {The mammalian digestive tract harbors a vast microbial community that has the potential to modulate numerous health-related processes. Multicompartment dynamic gut models have been developed to study microbial communities in a controlled environment. To verify the assumption that the experimental results produced in vitro in a mechanical device would be highly similar to those obtained from an in vivo study, in this study fecal samples from four pigs were inoculated in a simulator of the porcine intestinal microbial ecosystem (SPIME) and cultured until reaching steady state. The composition and structure of the resultant microbial communities, and the metabolites produced were compared with those harvested from the intestine of the same pigs. Taxonomic abundance identification based on shallow shotgun metagenomic sequencing revealed only 12.1% of species or 15% of metagenome-assembled genomes (MAGs) being shared across the colon compartments of the source pigs and the SPIME. Despite these overwhelming compositional shifts, higher functional conservation was indicated as measured by functional richness, MAG-level traits, CAZymes, and untargeted metabolomics. Environmental selection and bacterial functional redundancy were considered the two key elements in microbial compositional shifts and functional preservation.}, }
@article {pmid40639195, year = {2025}, author = {Estrada-Peña, A and Antunes, S and Domingos, A and Esser, H and Földvári, G and Fuehrer, HP and Gargili, A and van Gestel, M and Grandi, G and Kazimirova, M and Kiewra, D and Klemola, T and Kjær, LJ and Kjelland, V and Kubiak, K and de Meneghi, D and Mihalca, AD and Moutailler, S and Potkonjak, A and Prokop, P and Robert, K and Ranka, R and Sainz, A and Sormunen, J and Sotiraki, S and Strube, C and Stuen, S and Široký, P and Tomassone, L and Zintl, A}, title = {Living with ticks: Results of an online survey of the knowledge, attitudes and practices (KAP) regarding ticks and tick-borne pathogens in academic environments across Europe.}, journal = {Ticks and tick-borne diseases}, volume = {16}, number = {4}, pages = {102515}, doi = {10.1016/j.ttbdis.2025.102515}, pmid = {40639195}, issn = {1877-9603}, mesh = {Europe/epidemiology ; *Health Knowledge, Attitudes, Practice ; Animals ; *Tick-Borne Diseases/epidemiology/prevention &amp; control/psychology/microbiology ; Humans ; Surveys and Questionnaires ; Male ; *Ticks/physiology ; Female ; Adult ; Universities ; Tick Bites/epidemiology ; Young Adult ; Middle Aged ; }, abstract = {We prepared a digital questionnaire to capture knowledge, attitudes and practices (KAP) regarding ticks and tick-borne pathogens (TBPs) in 20 languages. The questionnaire was distributed to 21 universities and research institutions in 22 European countries and 9401 valid responses were collected. Most survey participants identified ticks correctly and regarded ticks as a serious health risk. There was also a good level of knowledge regarding tick activity, habitats and the predominant TBPs in the country or region. Moreover, most respondents were familiar with effective tick protection and removal measures. Over 75 % of respondents had been bitten by ticks and up to 12 % of participants had been diagnosed with a tick-borne infection in the past. Respondents from northern and central European countries who reported engaging in outdoor activities more frequently, reported increased frequencies of tick bites and infection with TBPs compared to respondents from southern Europe. Awareness of national information campaigns on ticks and TBPs was also greater among respondents from northern and central European countries than among Mediterranean countries. This study identified knowledge gaps among respondents from some European countries where TBPs have not been prioritised historically. These knowledge gaps should be addressed by reputable bodies to encourage personal protective behaviours without causing alarm and to forestall the spreading of incorrect and unreliable information propagated by some social media sources.}, }
@article {pmid40638961, year = {2025}, author = {Schröer, L and Balcaen, T and Folens, K and Boon, N and De Kock, T and Samari-Kermani, M and Kerckhofs, G and Cnudde, V}, title = {Contrast-Enhanced micro-computed tomography for 3D imaging of biofilms in opaque materials: Insights from water treatment plant sand filters.}, journal = {Water research}, volume = {285}, number = {}, pages = {124152}, doi = {10.1016/j.watres.2025.124152}, pmid = {40638961}, issn = {1879-2448}, abstract = {Microorganisms form biofilms in various environments, including porous media, where they alter substrate properties and fluid flow. Visualizing biofilms in 3D within the pore system is essential to understand their effect. Micro-computed tomography (µCT) is a powerful technique to visualize the pore system, but biofilms are usually invisible due to low contrast with water. Contrast-enhancing staining agents (CESAs) can improve their visibility by changing the attenuation of the biofilm or water phase. Traditional CESAs such as BaSO4, silver-coated microspheres or 1-chloronapthalene proved to be successful, but often stain the water phase and have drawbacks such as sedimentation or toxicity. After the successful use of isotonic Lugol and Hf-WD 1:2 POM on cyanobacteria at the surface, this study investigated the use of those CESAs to stain biofilms within opaque materials and, in particular, on biofilms colonizing field-derived sand filters of water treatment plants. Both CESAs increased the biofilms' visibility, including channels within the Hf-WD 1:2 POM stained biofilms and improved segmentation. Their visualization was consistent with Scanning Electron Microscopy (SEM). The CESAs quickly stained the biofilms, and their effect was stable. Isotonic Lugol enhanced the X-ray attenuation the most but might have caused shrinkage. The use of BaSO4 solution, added for comparison and positive control, was complicated due to its fast precipitation. BaSO4 was unable to visualize the isotonic Lugol-stained biofilms but corresponded with the Hf-WD 1:2 POM-stained biofilms. However, the stability and detail shown by isotonic Lugol and Hf-WD 1:2 POM make the latter two preferred. The study showed the potential of µCT and these CESAs for biofilm visualization and water research. Future research should apply these CESAs and focus on the CESA-biofilm interaction to understand the binding mechanisms and their effect on the structure.}, }
@article {pmid40638158, year = {2025}, author = {Dhara, S and Majhi, J and Mandal, B and Bhadury, P and Bhattacharya, S and Ghorai, SK}, title = {Polydendrorhynchus amaleshii sp. nov., a New Species With Branched Proboscis (Nemertea: Heteronemertea) From the North-East Coastal Bay of Bengal.}, journal = {Zoological science}, volume = {42}, number = {3}, pages = {326-334}, doi = {10.2108/zs240093}, pmid = {40638158}, issn = {0289-0003}, mesh = {Animals ; Phylogeny ; India ; *Invertebrates/classification/anatomy &amp; histology/genetics ; Bays ; Species Specificity ; Animal Distribution ; RNA, Ribosomal, 16S/genetics ; }, abstract = {A new lineid heteronemertean with a branched proboscis, Polydendrorhynchus amaleshii sp. nov., is described as the second member of the genus Polydendrorhynchus Yin and Zeng, 1986, following Polydendrorhynchus zhanjiangensis (Yin and Zeng, 1984). The description is based on specimens collected from the northeastern coastal Bay of Bengal, including the Subarnarekha Estuary and Frazerganj in the Indian Sundarbans mangrove ecosystem. The new species is distinguished from its congener by having up to 56 terminal branchlets of the proboscis and the absence of rhynchocoel compartments. In a maximum-likelihood phylogenetic analysis based on COI and 16S rRNA genes, P. amaleshii and P. zhanjiangensis formed a well-supported clade. Polydendrorhynchus amaleshii represents the ninth nemertean species recorded from India.}, }
@article {pmid40637783, year = {2025}, author = {Philippe, C and Denis, LA and Fonville, M and Devriendt, B and Dufrasne, FE and Obregon, D and Maître, A and Skičková, &#x160; and Cox, E and Sprong, H and Cruz, AC and Mori, M}, title = {Diversity of the Ixodes ricinus Microbiome Across Belgian Ecoregions and Its Association with Pathogen and Symbiont Presence.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {73}, pmid = {40637783}, issn = {1432-184X}, mesh = {*Ixodes/microbiology ; Animals ; *Microbiota ; Belgium ; *Symbiosis ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Nymph/microbiology ; Anaplasma phagocytophilum/isolation &amp; purification/genetics ; Biodiversity ; }, abstract = {Ticks are important vectors of zoonotic pathogens, and their presence can be influenced by the composition of the tick microbiome. In turn, this microbiome is shaped by environmental and ecological factors, as demonstrated in several studies conducted under controlled conditions. However, the extent of these influences under natural ecological conditions remains underexplored. In this study, we investigated the diversity of the microbiome and the prevalence of pathogens in Ixodes ricinus nymphs across three distinct Belgian ecoregions: Sandy Loam, Condroz, and Ardennes. Using real-time quantitative PCR (qPCR) and Oxford Nanopore 16S rRNA sequencing, we assessed how geography and pathogen presence influence tick-associated microbial communities. Our results revealed significant regional differences in microbiome composition and pathogen prevalence. Borrelia burgdorferi sensu lato (s.l.) was most prevalent in the Ardennes (9% (7.4-10.9) vs 3.8% (2.8-5.2) in the Condroz and 2.1% (1.4-3.2) in Sandy Loam) while Anaplasma phagocytophilum was more common in the Sandy Loam region (21.1% (18.7-23.8) vs 4% (3-5.4) in the Condroz and 3.2% (2.2-4.4) in the Ardennes). Endosymbionts such as Midichloria mitochondrii and Spiroplasma ixodetis also exhibited distinct geographic distributions. Network analysis identified potential pathogen-microbiota interactions, with certain bacterial taxa showing positive or negative associations with specific pathogens. Moreover, microbiome composition was influenced not only by ecoregion but also by microorganisms such as Rickettsia helvetica, suggesting that its colonization may actively shape microbial community structure, potentially through competition or facilitation mechanisms. Additionally, microbiome network robustness varied across ecoregions, highlighting the role of ecological context in shaping microbial interactions within ticks. These findings underscore the complex interplay between geography, pathogen presence, and microbial diversity in ticks, highlighting the importance of integrating these interactions to inform microbiome-based strategies for vector control and disease prevention.}, }
@article {pmid40636495, year = {2025}, author = {Chen, F and Cheng, M and Rong, D and Wang, Y and Liang, R and Irfan, M and Kang, Y and Cao, Y}, title = {Metagenomic insights into the microbial communities and functional traits of hot springs in Guizhou Province, China.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1615879}, pmid = {40636495}, issn = {1664-302X}, abstract = {INTRODUCTION: Hot springs were previously believed to be uninhabitable due to their hostile nature. However, recent studies have determined that hot springs not only have a rich microbiota but are also involved in various biogeochemical processes and possess unique characteristics that can be utilized for several biotechnological applications. This study aimed to determine the bacterial taxonomic diversity and functional profiles of 11 hot springs in the Guizhou Province, China.<br><br>METHODS: Illumina high-throughput sequencing was used to sequence the V3-V4 region of the 16S rRNA gene from microorganisms in samples collected from these hot springs. Software such as Mothur, the SILVA ribosomal RNA database, and Quantitative Insights into Microbial Ecology (QIIME) were utilized for taxonomic and operational taxonomic unit (OTU) analysis, while PICRUST2 was employed for functional predictions.<br><br>RESULTS: Guizhou Baili Rhododendron Hot Spring No.1 (BLDJA) had the highest diversity in terms of species richness, while Jianhe Hot Spring (YAS) had the lowest diversity. At the phylum level, the highest reported phyla included Pseudomonadota, Bacillota, Nitrospirota, Bacteroidota, and Actinomycetota, where Pseudomonadota had the highest abundance (92.094%) in Jianhe Hot Spring (YAS) and the lowest (41.238%) in Guizhou Baili Rhododendron Hot Spring No. 2 (BLDJB). Bacillota has the highest abundance (39.178%) in Guizhou Baili Rhododendron Hot Spring No. 2 (BLDJB) and the lowest (0.547%) in Jiutian Hot Spring (SNJT). The highest predicted functions were observed for amino acid metabolism, followed by carbohydrates. Predicted pathways for secondary metabolite and vitamin synthesis, along with stress-adaptation genes, underscore the biotechnological value of these habitats.<br><br>DISCUSSION: This study presents a preliminary survey of 11 hot springs in Guizhou Province, providing important insights into the origin and evolution of microorganisms. Furthermore, studying these microorganisms is crucial for understanding the adaptive mechanisms of life under extreme conditions, such as high temperatures, and for exploring the potential biotechnological applications of these microbes. An in-depth approach combining functional metagenomics and next-generation culturomics is required to fully understand the microbial flora and its potential biotechnological applications.}, }
@article {pmid40634370, year = {2025}, author = {Crombez, E and Van de Peer, Y and Li, Z}, title = {The subordinate role of pseudogenization to recombinative deletion following polyploidization in angiosperms.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {6335}, pmid = {40634370}, issn = {2041-1723}, support = {G0ADO25N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; BOF.BAF.2024.0889.01//Universiteit Gent (UGent)/ ; BOF.MET.2021.0005.01//Universiteit Gent (UGent)/ ; No. 833522//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, mesh = {*Polyploidy ; *Pseudogenes/genetics ; Genome, Plant/genetics ; *Magnoliopsida/genetics ; *Gene Deletion ; Evolution, Molecular ; Gene Duplication ; *Recombination, Genetic ; }, abstract = {Extensive gene loss is a hallmark of rediploidization following polyploidization, but its molecular basis remains unclear: whether it occurs primarily through pseudogenization or DNA deletion. Here, we examine pseudogenization in collinear segments from ancient whole-genome multiplications (WGMs) across 12 angiosperms. Although total pseudogenes are abundant, we find far fewer WGM-derived pseudogenes than expected if pseudogenization and DNA deletion contribute equally to gene loss. Simulations of neutrally evolving pseudogenes indicate that, if DNA deletion is absent, pseudogenes should be detectable for far longer than observed in the paleo-polyploid genomes, suggesting gene loss driven by DNA deletion. Analyses of three neo-autopolyploid genomes confirm this pattern: among substantial gene loss, DNA deletions occur on average 1.5 times more frequently than pseudogenization. Our findings imply that gene loss post-polyploidization primarily takes place via DNA deletion, enabled by a genomic environment with an elevated recombination rate created by WGMs. In contrast, small-scale duplications yield scattered duplicated genes, which appear less exposed to deletion and hence result in a high number of pseudogenes. This model is further reinforced by an enrichment of WGM-derived pseudogenes in high recombination regions. Moreover, some pseudogenes may govern a function, as indicated by non-neutral Ka/Ks ratios and overlap with lncRNAs.}, }
@article {pmid40633764, year = {2025}, author = {Kovarova, A and Amadasun, M and Hooban, B and McDonagh, F and Tumeo, A and Ryan, K and Clarke, C and Cormican, M and Miliotis, G}, title = {Characterisation of Citrobacter freundii and Enterobacter cloacae complex isolates co-carrying blaNDM-1 and mcr-9 from three hospitals.}, journal = {Journal of global antimicrobial resistance}, volume = {44}, number = {}, pages = {226-233}, doi = {10.1016/j.jgar.2025.07.003}, pmid = {40633764}, issn = {2213-7173}, abstract = {OBJECTIVES: Antimicrobial resistance (AMR) is a global health concern related to antimicrobial use and the subsequent emergence of resistant organisms, including carbapenemase-producing Enterobacterales (CPE). CPE isolate co-carrying blaNDM-1 and mcr-9.1 have been scarcely reported internationally. The identification of 20 such isolates, including 16 of one species, within a group of three hospitals in one region indicated potential dissemination within and between healthcare facilities.<br><br>METHODS: Twenty isolates were pseudo-anonymised and identified via MALDI-ToF MS. Antimicrobial susceptibility testing was performed by disc diffusion, and Minimal Inhibition Concentration for colistin was carried out using the UMIC system. Short-read sequencing was conducted using the Illumina MiSeq platform, and genomic analysis identified antimicrobial resistance genes, virulence factors and plasmid contigs. Taxonomic classification of draft genomes was bioinformatically assessed using Kraken2.<br><br>RESULTS: This collection comprised of Enterobacter hormaechei (n = 16), Citrobacter freundii (n = 3) and Enterobacter cloacae (n = 1) sourced from patient rectal swabs collected during routine screening (n = 13) or from healthcare-associated environmental sites (n = 7). The E. hormaechei isolates included four different ST types with one unassigned ST. Contig-based plasmid analysis identified 17 plasmid replicon types among the isolates. IncHI2A, IncHI2, and pKPCCAV1321_1 were detected in all isolates. Linked blaNDM-1 and mcr-9.1 gene spread in hospitals likely occurred via plasmid-mediated transfer rather than spread of E. hormaechei.<br><br>CONCLUSIONS: This study represents the first documented instance of blaNDM-1/mcr-9.1 co-occurrence in Europe to date. It highlights the increasing public health threat posed by antimicrobial resistance and underscores the importance of genomic surveillance and clinical screening.}, }
@article {pmid40633699, year = {2025}, author = {Sun, HJ and Zhao, X and Ding, J and Wang, YQ and Wang, WS and Feng, ZH and Zhao, S and Wang, L and Ren, NQ and Yang, SS}, title = {Unveiling dynamics of microbial communities, species interactions, and ecological assembly during low-temperature-induced sludge bulking in full-scale wastewater treatment systems.}, journal = {Bioresource technology}, volume = {435}, number = {}, pages = {132950}, doi = {10.1016/j.biortech.2025.132950}, pmid = {40633699}, issn = {1873-2976}, mesh = {*Sewage/microbiology ; *Wastewater/microbiology ; *Water Purification/methods ; *Cold Temperature ; *Waste Disposal, Fluid/methods ; *Microbiota ; }, abstract = {This study investigated the microbial community characteristics and ecological mechanisms of floating sludge and suspended sludge in a full-scale wastewater treatment plant under low-temperature conditions. Floating sludge exhibited a lower proportion of positive correlations compared to suspended sludge (56.98 % vs. 61.03 %), indicating stronger competition within the microbial community. Null model analysis revealed the roles of deterministic and stochastic processes in shaping the microbial communities, with stochastic processes being dominant. However, deterministic selection played a larger role in floating sludge, highlighting stronger influence of species interactions and temperature fluctuations. Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analysis revealed stronger energy metabolism in floating sludge, while suspended sludge microbes were more active in material transport. This study reveals distinct microbial and ecological differences between floating and suspended sludge at low temperatures, providing theoretical support for optimizing wastewater treatment and controlling sludge bulking in cold climates.}, }
@article {pmid40632216, year = {2025}, author = {Romano, F and John, U and Laval-Peuto, M and Pitta, P}, title = {Small Things that Make a Big Difference: Single-Cell Transcriptomic of Nanociliates Reveals Genes Potentially Involved in Mixotrophy.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {72}, pmid = {40632216}, issn = {1432-184X}, support = {766327//MixITiN/ ; 766327//MixITiN/ ; 766327//MixITiN/ ; }, mesh = {*Transcriptome ; Phylogeny ; *Haptophyta/genetics/classification ; Mediterranean Sea ; Photosynthesis/genetics ; Single-Cell Analysis ; Food Chain ; }, abstract = {Nanociliates play an important role in the microbial food web of oligotrophic marine systems as grazers of picoplankton on one side, and as prey for microplankton, on the other. However, knowledge on their taxonomy, phylogeny, and trophic strategies is very limited, as well as their potential role as mixotrophs. In the present study, we investigated the transcriptomes of five marine planktonic nanociliates isolated from the Eastern Mediterranean Sea. Our aim was the following: (i) to characterize the phylogenetic placement of these cells using concatenated phylotranscriptomic and (ii) to identify genes potentially involved in mixotrophy by focusing on both photosynthesis and digestion-related genes (phagosome, lysosome). Phylogenetic reconstruction revealed that two cells clustered with Tintinnida, while the other three clustered with Oligotrichida. Reciprocal best hits (RHBs) BlastP analysis indicated the presence of genes related to photosynthesis across all the transcriptomes, while the detection of genes associated with phagosome, lysosome, and generic metabolic pathways provided a more informative insight into the mechanism of mixotrophy. These findings suggest that photosynthesis-related genes alone may not be sufficient indicators of mixotrophic potential in nanociliates and highlight the importance of considering additional cellular pathways involved in phagotrophy. Moreover, these transcriptomes will help to establish a basis for the evaluation of differential gene expression in Oligotrichida, Choreotrichida, and Tintinnida, and a step stone for mixotrophic investigation.}, }
@article {pmid40630186, year = {2025}, author = {Ceretto, A and Weinig, C}, title = {A comparison of 16S rRNA-gene and 16S rRNA-transcript derived microbial communities in bulk and rhizosphere soils.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1608399}, pmid = {40630186}, issn = {1664-302X}, abstract = {Root exudates in a plant's rhizosphere alters microbial community membership and activity, which can in turn alter a plant's health and fitness. In this study we characterized bacterial community composition, using 16S rRNA-gene (DNA) sequencing to define total community membership and 16S rRNA-transcripts (RNA) to define protein synthesis potential (PSP) as a proxy of microbial activity in both rhizosphere and bulk soils of a Wyoming native plant Boechera stricta. Using PSP rather than total microbial membership reveals fine-scale differences in genera between the rhizosphere and control soil communities. This study found DNA community analysis alone disproportionately increased the importance of Saccharibacteria and Gemmatimonadetes phyla in the overall soil community profile, and underestimated the importance of several known root associates (Comamonadaceae, Rhizobacter, and Variovorax), which had elevated PSP in the rhizosphere soil. Thus, the use of DNA-vs. RNA-based community characterization reveals that community composition (DNA) may not completely capture community activity (RNA). Analysis of the PSP community profile also indicated elevated levels of proteins associated with carbohydrate and amino acid metabolism in the rhizosphere-associated bacteria, which may shed light on potential mechanisms by which root exudates shape the rhizosphere soil community.}, }
@article {pmid40626910, year = {2025}, author = {Kust, A and Zorz, J and Paniker, CC and Bouma-Gregson, K and Krishnappa, N and Liu, W and Banfield, JF and Diamond, S}, title = {Model cyanobacterial consortia reveal a consistent core microbiome independent of inoculation source or cyanobacterial host species.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf142}, pmid = {40626910}, issn = {1751-7370}, abstract = {Cyanobacteria are integral to biogeochemical cycles, influence climate processes, and hold promise for commercial applications. In natural habitats, they form complex consortia with other microorganisms, where interspecies interactions shape their ecological roles. Although in vitro studies of these consortia have significantly advanced our understanding, they often lack the biological replication needed for robust statistical analysis of shared microbiome features and functions. Moreover, the microbiomes of many model cyanobacterial strains, which are central to our understanding of cyanobacterial biology, remain poorly characterized. Here, we expanded on existing in vitro approaches by co-culturing five well-characterized model cyanobacterial strains with microorganisms filtered from three distinct freshwater sources, generating 108 stable consortia. Metagenomic analyses revealed that, despite host and inoculum diversity, these consortia converged on a similar set of non-cyanobacterial taxa, forming a 25-species core microbiome. The large number of stable consortia in this study enabled statistical validation of both previously observed and newly identified core microbiome functionalities in micronutrient biosynthesis, metabolite transport, and anoxygenic photosynthesis. Furthermore, core species showed significant enrichment of plasmids, and functions encoded on plasmids suggested plasmid-mediated roles in symbiotic interactions. Overall, our findings uncover the potential microbiomes recruited by key model cyanobacteria, demonstrate that laboratory-enriched consortia retain many taxonomic and functional traits observed more broadly in phototroph-heterotroph assemblages, and show that model cyanobacteria can serve as robust hosts for uncovering functional roles underlying cyanobacterial community dynamics.}, }
@article {pmid40626735, year = {2025}, author = {Kellom, M and Berg, M and Chen, I-MA and Chu, K and Clum, A and Huntemann, M and Ivanova, NN and Kyrpides, NC and Mukherjee, S and Reddy, TBK and Roux, S and Seshadri, R and Szabo, G and Varghese, NJ and Woyke, T and Eloe-Fadrosh, EA}, title = {Tetranucleotide frequencies differentiate genomic boundaries and metabolic strategies across environmental microbiomes.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0174424}, doi = {10.1128/msystems.01744-24}, pmid = {40626735}, issn = {2379-5077}, abstract = {UNLABELLED: Microbiomes are constrained by physicochemical conditions, nutrient regimes, and community interactions across diverse environments, yet genomic signatures of this adaptation remain unclear. Metagenome sequencing is a powerful technique to analyze genomic content in the context of natural environments, establishing concepts of microbial ecological trends. Here, we developed a data discovery tool-a tetranucleotide-informed metagenome stability diagram-that is publicly available in the integrated microbial genomes and microbiomes (IMG/M) platform for metagenome ecosystem analyses. We analyzed the tetranucleotide frequencies from quality-filtered and unassembled sequence data of over 12,000 metagenomes to assess ecosystem-specific microbial community composition and function. We found that tetranucleotide frequencies can differentiate communities across various natural environments and that specific functional and metabolic trends can be observed in this structuring. Our tool places metagenomes sampled from diverse environments into clusters and along gradients of tetranucleotide frequency similarity, suggesting microbiome community compositions specific to gradient conditions. Within the resulting metagenome clusters, we identify protein-coding gene identifiers that are most differentiated between ecosystem classifications. We plan for annual updates to the metagenome stability diagram in IMG/M with new data, allowing for refinement of the ecosystem classifications delineated here. This framework has the potential to inform future studies on microbiome engineering, bioremediation, and the prediction of microbial community responses to environmental change.<br><br>IMPORTANCE: Microbes adapt to diverse environments influenced by factors like temperature, acidity, and nutrient availability. We developed a new tool to analyze and visualize the genetic makeup of over 12,000 microbial communities, revealing patterns linked to specific functions and metabolic processes. This tool groups similar microbial communities and identifies characteristic genes within environments. By continually updating this tool, we aim to advance our understanding of microbial ecology, enabling applications like microbial engineering, bioremediation, and predicting responses to environmental change.}, }
@article {pmid40625615, year = {2025}, author = {Goodall, T and Busi, SB and Griffiths, RI and Jones, B and Pywell, RF and Richards, A and Nowakowski, M and Read, DS}, title = {Soil properties in agricultural systems affect microbial genomic traits.}, journal = {FEMS microbes}, volume = {6}, number = {}, pages = {xtaf008}, pmid = {40625615}, issn = {2633-6685}, abstract = {Understanding the relationships between bacteria, their ecological and genomic traits, and their environment is important to elucidate microbial community dynamics and their roles in ecosystem functioning. Here, we examined the relationships between soil properties and bacterial traits within highly managed agricultural soil systems subjected to arable crop rotations or management as permanent grass. We assessed the bacterial communities using metabarcoding and assigned each amplicon trait scores for rRNA copy number, genome size, and guanine-cytosine (GC) content, which are classically associated with potential growth rates and specialization. We also calculated the niche breadth trait of each amplicon as a measure of social ubiquity within the examined samples. Within this soil system, we demonstrated that pH was the primary driver of bacterial traits. The weighted mean trait scores of the samples revealed that bacterial communities associated with soils at lower pH (<7) tended to have larger genomes (potential plasticity), have more rRNA (higher growth rate potential), and are more ubiquitous (have less niche specialization) than the bacterial communities from higher pH soils. Our findings highlight not only the association between pH and bacterial community composition but also the importance of pH in driving community functionality by directly influencing genomic and niche traits.}, }
@article {pmid40624251, year = {2025}, author = {Karlsson, CJ and Gerlee, P and Rowlett, J}, title = {An adaptive dynamics framework for microbial ecology and evolution.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {24307}, pmid = {40624251}, issn = {2045-2322}, mesh = {*Biological Evolution ; Game Theory ; Models, Biological ; Biodiversity ; *Adaptation, Physiological ; }, abstract = {Adaptive dynamics describes a deterministic approximation of the evolution of scalar- and function-valued traits. We construct an evolutionary process for a game-theoretic model which may describe the evolution of microbes. In our analysis, we demonstrate the existence of solutions to the adaptive dynamics and determined their regularity. Moreover, we identify all stationary solutions and prove that these are precisely the Nash equilibria of the game theoretic model. Numerical examples are provided to highlight the main characteristics of the dynamics. The dynamics are unstable; non-stationary solutions oscillate and perturbations of the stationary solutions do not shrink. Instead, a linear type of branching may occur. This may explain the ever-increasing complexity in microbial biological systems and provide a mechanistic explanation for not only the tremendous biodiversity observed in microbe species but also for the extensive phenotypic variability within species.}, }
@article {pmid40624015, year = {2025}, author = {Wang, C and Zhang, L and Kan, C and He, J and Liang, W and Xia, R and Zhu, L and Yang, J and Jiang, X and Ma, W and Liang, Z and Xiao, Z and Zhang, J and Zhong, J and Sun, X and Chang, D and Wang, Z and Zhang, G and Li, M}, title = {Benefits and challenges of host depletion methods in profiling the upper and lower respiratory microbiome.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {130}, pmid = {40624015}, issn = {2055-5008}, support = {Z211100002121135//Beijing Nova Program/ ; 32100098//National Natural Science Foundation of China/ ; 2021097//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; KCXFZ20211020163545004//Shenzhen Scientific and Technological Foundation/ ; SZZYSM202311009//Sanming Project of Medicine in Shenzen Municipality/ ; 2022YFA1304300//National Key Research and Development Program of China/ ; }, mesh = {Humans ; Bronchoalveolar Lavage Fluid/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation &amp; purification ; *Respiratory Tract Infections/microbiology/diagnosis ; Oropharynx/microbiology ; *Respiratory System/microbiology ; }, abstract = {Metagenomic sequencing for respiratory pathogen detection faces two challenges: efficient host DNA depletion and the representativeness of upper respiratory samples for lower tract infections. In this study, we benchmarked seven host depletion methods, including a new method (F_ase), using bronchoalveolar lavage fluid (BALF), oropharyngeal swab (OP), and mock samples. All methods significantly increased microbial reads, species richness, genes richness, and genome coverage while reduced bacterial biomass, introduced contamination, and altered microbial abundance. Some commensals and pathogens, including Prevotella spp. and Mycoplasma pneumoniae, were significantly diminished. F_ase demonstrated the most balanced performance. High-resolution microbiomes profiling revealed distinct microbial niche preferences and microbiome disparities between the upper and lower respiratory tract. In pneumonia patients, 16.7% of high-abundance species (>1%) in BALF were underrepresented (<0.1%) in OP, highlighting OP's limitations as lower respiratory proxies. This study underscores both the potential and challenges of metagenomic sequencing in advancing microbial ecology and clinical research.}, }
@article {pmid40622379, year = {2025}, author = {Mars Brisbin, M and Acord, M and Davitt, R and Bent, S and Van Mooy, BAS and Flaum, E and Norlin, A and Turner, J and Krinos, A and Alexander, H and Saito, M}, title = {Exploring the Phaeosphere: Characterizing the microbiomes of Phaeocystis antarctica colonies from the coastal Southern Ocean and laboratory culture.}, journal = {Journal of phycology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jpy.70051}, pmid = {40622379}, issn = {1529-8817}, support = {874439//Simons Foundation/ ; OPP-2224611//National Science Foundation/ ; }, abstract = {Interactions between phytoplankton and bacteria play critical roles in shaping marine ecosystems. However, the intricate relationships within these communities-particularly in rapidly changing polar environments-remain poorly understood. We use targeted methods to directly characterize the microbiomes of individual colonies of Phaeocystis antarctica, a keystone phytoplankton species in the Southern Ocean, and showed that colony microbiomes were consistent across individual colonies collected 108 nautical miles apart. These results suggest that hosting specific colony microbiomes is a shared trait across colony-forming Phaeocystis species, with different species hosting colony microbiomes suited to their respective environments. The bacterial orders Alteromonadales, Oceanospirillales, and Sphingomonadales dominated the microbiomes of all field-collected P. antarctica colonies. The relative abundances of bacterial taxa comprising the majority of field-collected colony microbiomes-for example, Paraglaciecola sp. (Alteromonadales) and Nitrincolaceae (Oceanospirillales)-correlated with Phaeocystis abundance in surface waters, highlighting their potential roles in bloom dynamics and carbon cycling. After a year of laboratory culture, we observed a reduction in colony microbiome diversity, and Caulobacterales, Cellvibrionales, and Rhodobacterales dominated the cultured colony microbiomes. Notably, abundant genera in field-collected colony microbiomes that were lost in culture were psychrophiles. The shift in microbiome structure emphasizes the importance of field-based studies to capture the complexity of microbial interactions, especially for species from polar environments that are difficult to replicate in laboratory conditions. This research provides valuable insights into the ecological significance of prokaryotic interactions with a key phytoplankton species and underscores the necessity of considering these dynamics in the context of climate-driven shifts in marine ecosystems.}, }
@article {pmid40622159, year = {2025}, author = {Hernandez, JB and Hayer, SS and Alvarez, S and Fischer, A and Hassenstab, HR and Cooper, K and Alsafwani, ZW and Benson, AK and Suhr Van Haute, MJ and Izard, J and Song, H-S and Clayton, JB}, title = {Microbiome and metabolome association network analysis identifies Clostridium_sensu_stricto_1 as a stronger keystone genus candidate than Bifidobacterium in the gut of common marmosets.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0021425}, doi = {10.1128/msystems.00214-25}, pmid = {40622159}, issn = {2379-5077}, abstract = {The common marmoset (Callithrix jacchus), a nonhuman primate species, is a model organism of great interest due to its translational value in a variety of research settings, including the field of microbiomics. While the composition of the marmoset's gut microbiome has been somewhat described in captivity, little is known about how gut microbiota interact with each other over time and how they relate to metabolite production. To help answer this, we characterized interactions in the gut microbiome of the common marmoset by calculating the Spearman correlation coefficient between 16S rDNA-derived relative genera abundance data and targeted metabolomics data collected longitudinally from 10 captive marmosets. Association network graphs were used to visualize significant correlations and identify genera and metabolites that have high degree centrality, marking them as more influential within the microbiome. The genus Clostridium_sensu_stricto_1 engaged in the most metabolomic associations, indicating that it potentially plays a gatekeeping role over metabolites involved in microbial growth and signaling. Its associations with downregulated taurine and bile acids further suggest Clostridium_sensu_stricto_1 modifies bile acids to exert its influence. Flavonifractor and several Bacteroidales members had the most bacterial associations and were negatively associated with Bifidobacterium, indicating a potential competitive relationship. To further characterize microbiome interactions, we performed hierarchical clustering on significant within-dataset associations and developed a new "Keystone Candidate Score" metric that identified Clostridium_sensu_stricto_1 and Alloprevotella as the most influential bacteria (so-called candidate keystone genera) in the marmoset gut microbiome.IMPORTANCEPrevious studies have identified significant individuality within the gut microbiome of common marmosets. The reasons for this inter-subject variability and how it relates to health in captivity are poorly understood, owing to a lack of knowledge regarding dynamic interactions between specific microbiota. To that end, this study characterized significant temporal associations between the gut microbiome and metabolome of healthy captive marmosets. Our findings suggest that certain microbial taxa exert a stronger influence within the gut than others. Specifically, Bifidobacterium was the most abundant genus and primary driving force behind subject-specific microbiome differences, while Clostridium_sensu_stricto_1 and bacteria from the order Bacteroidales were the main sources, respectively, for significant bacteria-metabolite and bacteria-bacteria associations. Together, this suggests that Bifidobacterium may compete with the other taxa for resources and a metabolic niche in the marmoset microbiome.}, }
@article {pmid40621946, year = {2025}, author = {Engelberts, JP and Ye, J and Parks, DH and McMaster, ES and McInnes, AS and Woodcroft, BJ and Volmer, JG and McIlroy, SJ and Tyson, GW}, title = {GenomeFISH: genome-based fluorescence in situ hybridization for strain-level visualization of microbial communities.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40621946}, issn = {1751-7370}, support = {FT210100521//Australian Research Council Fellowships/ ; FT190100211//Australian Research Council Fellowships/ ; FL230100159//Australian Research Council Fellowships/ ; 2022-4087//Heising-Simons Foundation/ ; DP200102310//Australian Government Research Discovery Grant/ ; }, abstract = {Fluorescence in situ hybridization (FISH) is a powerful tool for visualizing the spatial organization of microbial communities. However, traditional FISH has several limitations, including limited phylogenetic resolution, difficulty visualizing certain lineages, and the design and optimization of new probes is time consuming and does not scale to the known diversity of microbial life. Here, we present GenomeFISH, a high-throughput, genome-based FISH approach that can differentiate strains within complex communities. Fluorescent probes are generated from the genomes of single cells, which are obtained from environmental or clinical samples through fluorescence activated single-cell sorting. GenomeFISH can distinguish between strains with up to 99% average nucleotide identity and was successfully applied to visualize strains in mock communities and human fecal samples. Given the superior sensitivity and specificity of GenomeFISH, we envisage it will become widely used for the visualization of complex microbial systems.}, }
@article {pmid40621919, year = {2025}, author = {Reintjes, G and Giljan, G and Fuchs, BM and Arnosti, C and Amann, R}, title = {Using phenotyping to visualize and identify selfish bacteria: a methods guide.}, journal = {Microbiology spectrum}, volume = {13}, number = {8}, pages = {e0160224}, pmid = {40621919}, issn = {2165-0497}, support = {496342779//Deutsche Forschungsgemeinschaft/ ; 840804//Horizon 2020 Framework Programme/ ; OCE-1736772//National Science Foundation/ ; OCE-2022952//National Science Foundation/ ; //Max-Planck-Gesellschaft/ ; }, mesh = {Humans ; *Bacteria/metabolism/classification/isolation &amp; purification/genetics ; Phenotype ; *Polysaccharides/metabolism ; }, abstract = {Polysaccharides are dominant components of plant and algal biomass, whose degradation is typically mediated by heterotrophic bacteria. These bacteria use extracellular enzymes to hydrolyze polysaccharides to oligosaccharides that are then also available to other bacteria. Recently, a new mechanism of polysaccharide processing-"selfish" uptake-has been recognized, initially among gut-derived bacteria. In "selfish" uptake, polysaccharides are bound at the outer membrane, partially hydrolyzed, and transported into the periplasmic space without loss of hydrolysis products, thus limiting the availability of smaller sugars to the surrounding environment. Selfish uptake is widespread in environments ranging from the ocean's cool, oxygen-rich, organic carbon-poor waters to the warm, carbon-rich, anoxic environment of the human gut. In this methods paper, we present a detailed guide to identifying selfish bacteria, including techniques for rapidly visualizing selfish uptake in complex bacterial communities, detecting selfish organisms, and distinguishing their activity from that of other community members.IMPORTANCEUnderstanding the role of heterotrophic bacteria in the degradation of organic matter is critical for comprehending carbon cycling and microbial ecology across different environments. This study highlights the significant prevalence of "selfish uptake" among bacteria-often overlooked by standard microbial activity assessments-and presents the method used to quantify and identify these "selfish" bacteria. Found in diverse habitats such as anoxic gut environments, oxygenated waters, sediments, and soils, their widespread presence underscores the necessity of revisiting current methodologies to include these crucial organisms. By identifying and studying selfish bacteria, we can gain detailed insights into how microbial communities function, how carbon flows through ecosystems, and how these processes impact global biogeochemical cycles.}, }
@article {pmid40621498, year = {2025}, author = {Chong, J and Zhou, Y and Li, Z and Li, X and Zhang, J and Cao, H and Ma, J and Ge, L and Zhong, H and Sun, J}, title = {Hyodeoxycholic acid modulates gut microbiota and bile acid metabolism to enhance intestinal barrier function in piglets.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1610956}, pmid = {40621498}, issn = {2297-1769}, abstract = {Oral bile acids, particularly hyodeoxycholic acid (HDCA), serve as critical drivers for gut microbial community maturation in mice. In the first study, Cy5-labeled HDCA combined with fluorescence imaging revealed rapid gastrointestinal transit of HDCA in piglets, contrasting with its delayed absorption observed in mice. In the second study, the effects of the oral HDCA supplementation on microbiota-host metabolic interactions were investigated using four piglet model groups: OPM-HDCA (naturally born, raised germ-free (GF), and orally administered HDCA), OPM-CON (naturally born, raised GF, and orally administered PBS), SPF-HDCA (naturally born, raised GF, and received fecal microbiota transplantation (FMT) and HDCA), and SPF-CON (naturally born, raised GF with FMT but no HDCA). The results demonstrated that HDCA administration at 0.2 mg/mL suppressed body weight gain in piglets, which was alleviated by FMT. HDCA significantly altered gut microbiota composition in SPF piglets, markedly increasing the Lactobacillus abundance (37.97% vs. 5.28% in SPF-CON) while decreasing the proportion of Streptococcus (28.34% vs. 38.65%) and pathogenic family Erysipelotrichaceae (0.35% vs. 17.15%). Concurrently, HDCA enhanced intestinal barrier integrity by upregulating tight junction proteins (ZO-1, Claudin, Occludin) and suppressing pro-inflammatory cytokines (TNF-α, IL-1β). Additionally, HDCA significantly upregulated ileal gene expression of CYP7A1 (cytochrome P450 family 7 subfamily A member 1) and TGR5 (G protein-coupled bile acid receptor 1) in both SPF-HDCA and OPM-HDCA groups compared to their respective controls (p < 0.05). These findings demonstrate that HDCA exerts microbiota-dependent effects on growth performance, intestinal barrier function, and bile acid metabolism in piglets. Although 0.2 mg/mL HDCA treatment suppressed body weight gain, it potentially enhanced intestinal barrier integrity by activating the TGR5 signaling pathway and increasing the abundance of beneficial bacteria such as Lactobacillus. These results also highlight the critical role of early-life gut microbiota in nutritional interventions, providing a basis for developing precision nutritional strategies targeting intestinal microbial ecology in piglets.}, }
@article {pmid40619451, year = {2025}, author = {Yan, F and Niu, Z}, title = {Impacts of pollution on coral bacterial and metabolites diversity across Dapeng Cove of South China sea.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {24107}, pmid = {40619451}, issn = {2045-2322}, mesh = {*Anthozoa/microbiology/metabolism ; China ; Animals ; *Bacteria/metabolism/classification/genetics ; Seawater/microbiology/chemistry ; Biodiversity ; Environmental Monitoring ; Oceans and Seas ; }, abstract = {Coastal ecosystems are increasingly threatened by anthropogenic activities, including sewage discharge and tourism-related pollution, which alter microbial diversity and biochemical cycles. This study applied molecular techniques to examine the coral microbial diversity, and metabolite composition of seawater across five sites (A-E) in Dapeng Cove, South China Sea, to assess pollution impacts. Sites A and B, within the yacht tourism area, exhibited high microbial diversity, dominated by Synechococcus and Rhodobacteraceae, with minimal pollution effects. Site C, inside a domestic drainage channel, showed moderate pollution, with elevated nitrite (NO2) and nitrate (NO3) levels, microbial taxa linked to organic matter degradation, and increased hydroxy acids and indoles. Sites D and E, located in main sewage channels, experienced severe pollution, characterized by high salinity, low dissolved oxygen, and dominance of pollution-tolerant bacteria such as Exiguobacterium and Tepidibacter. Metabolite analysis revealed elevated fatty acyls, organonitrogen compounds, and amino acids at these sites, highlighting strong anthropogenic influence. Beta diversity analysis (NMDS and ANOSIM) confirmed distinct microbial community structures, while KEGG pathway analysis indicated shifts in metabolic functions, with enrichment in xenobiotic biodegradation and anaerobic respiration in sewage-impacted areas. These findings underscore the detrimental effects of wastewater discharge on microbial ecology and biochemical functions. Urgent interventions, including improved wastewater management and regular environmental monitoring, are recommended to mitigate pollution effects. Future research integrating multi-omics approaches is necessary to evaluate the long-term ecological consequences of pollution and climate variability on coastal microbial communities.}, }
@article {pmid40614873, year = {2025}, author = {Lu, X and Gao, Y and Liu, X and Sun, Y and Zhen, G}, title = {Unlocking microbial community succession and key influencing factors during bioelectrocatalytically-driven simultaneous removal of ammonia nitrogen and sulfate from wastewater.}, journal = {Bioresource technology}, volume = {435}, number = {}, pages = {132934}, doi = {10.1016/j.biortech.2025.132934}, pmid = {40614873}, issn = {1873-2976}, mesh = {*Ammonia/isolation &amp; purification/metabolism ; *Wastewater/chemistry/microbiology ; *Sulfates/isolation &amp; purification/metabolism ; *Nitrogen/isolation &amp; purification ; Biofilms ; Electrodes ; Oxidation-Reduction ; Bacteria/metabolism ; *Water Purification/methods ; Electrolysis ; Catalysis ; Bioelectric Energy Sources/microbiology ; }, abstract = {Ammonia nitrogen (NH4[+]-N) and sulfate (SO4[2][-]) removal by Anaerobic ammonium oxidation (Anammox) and sulfate-reducing bacteria (SRB) was studied in dual-chamber microbial electrolysis cells (MECs). Appropriate anode potential stimulation promoted biofilm formation and enhanced extracellular polymeric substances fluorescence, facilitating electron transfer. The highest NH4[+]-N removal (81.1 %) was achieved at the anode potential of 0.6 V vs. Ag/AgCl after 50 days, coinciding with the increase in electroactive Candidatus_Brocadia from 1.1 % to 27.4 %. Simultaneously, SO4[2][-] removal reached 77.0 %, supported by cathodic biofilms dominated by SRB (Desulfofustis, Desulfomicrobium, and Desulfatirhabdium). Automated machine learning and principal co-ordinates analysis identified the anode potential as the key factor shaping microbial ecology. The appropriate anode potential (0.4-0.6 V vs. Ag/AgCl) promoted cathodic sulfidogenesis, indirectly enhancing electron flow and supporting Anammox process at the anode. These findings demonstrate that MECs hold great promise for simultaneously enhancing anaerobic ammonia oxidation bacteria and SRB activities, enabling efficient NH4[+]-N and SO4[2][-] removal.}, }
@article {pmid40614496, year = {2025}, author = {Brotto, AC and Kurt, H and Chandran, K}, title = {Impacts of intermittent and continuous aeration modes on performance, substrate dynamics, and microbial ecology of mainstream nitrification processes.}, journal = {Water research}, volume = {285}, number = {}, pages = {124123}, doi = {10.1016/j.watres.2025.124123}, pmid = {40614496}, issn = {1879-2448}, abstract = {Intermittent and continuous aeration strategies in combination with solids retention time (SRT) were investigated in terms of their impact on the performance and ecology of mainstream nitrification. Two lab-scale reactors (R1 and R2) were seeded with the same inoculum and subjected to intermittent aeration and continuous low aeration, respectively at statistically similar air-supply rates. For both reactors, SRT was progressively decreased from 8 d during Phase I to 4 and 2.5 d during Phases II and III, respectively. Compared to R2 (93 ± 4.8 %), R1 achieved more stable and higher ammonia oxidation (99 ± 0.13 %) averaged across SRTs. In R1, Nitrosospira were the dominant AOB, while in R2, AOB were a combination of Nitrosospira and Nitrosomonas. Among NOB, Nitrospira were more abundant than Nitrobacter for both R1 and R2 across SRTs. Intermittent aeration in R1 supported higher relative abundance of Comammox Nitrospira than R2. Notably, the enrichment patterns for nitrifying bacteria in the two reactors reflected distinct drivers (beyond microbial kinetics), including inoculum composition, extant oxygen or nitrogen concentrations or both. Overall, intermittent aeration strategies are integral to the design of biological nitrogen removal processes, although other considerations such as operational feasibility and process emissions might ultimately influence operating strategies.}, }
@article {pmid40614494, year = {2025}, author = {Mol, Z and Waegenaar, F and Pluym, T and Vermeir, P and Van Langenhove, H and De Gusseme, B and Boon, N and Walgraeve, C and Demeestere, K}, title = {Effect of biofilm, temperature and type of source water on the formation of haloanisoles in a pilot drinking water distribution system.}, journal = {Water research}, volume = {285}, number = {}, pages = {124078}, doi = {10.1016/j.watres.2025.124078}, pmid = {40614494}, issn = {1879-2448}, abstract = {Taste and odor deviations in tap water affect many consumers and cause a preference for bottled water. However, since tap water is more sustainable than bottled water, these issues should be solved and prevented rapidly. Haloanisoles (HAs) have a very low odor threshold concentration (sub ng.L[-1]) and are of considerable concern since they are mainly formed in drinking water distribution systems (DWDS). Understanding their formation and influencing factors is a crucial aspect of addressing these odor problems. Therefore, this study uses a DWDS pilot to closely mimic the complex situation in real DWDS and investigates the (microbial) formation of six HAs regarding biofilm cell density and composition, temperature, and type of source water. Ten to thirty times higher formation was observed when a stable biofilm (5 months, 10 times more biomass) was present, compared to a young biofilm (2 weeks). With a spiked halophenol (HP) concentration of 0.1 mg.L[-1], the HA concentrations produced by a young biofilm were already within the OTC range. The mature biofilm contained a higher variety of HA-producing microorganisms and more O-methyltransferase genes to convert the precursors (HPs) into HAs. Higher temperatures (24 °C instead of 16 °C) increased the formation of each HA by a factor of 2 to 4, although still low HP-HA conversion ratios were observed (0.2 %). Regardless of the temperature and the type of source water, a clear pattern is observed in the type of HAs formed, with 2,3,4-trichloroanisole being the most abundant. This study finally investigated the effectiveness of flushing to mitigate these odorous compounds in DWDS and concludes that their partitioning between the biofilm and water phase affects the performance of flushing procedures.}, }
@article {pmid40614303, year = {2025}, author = {Ferrocino, I and Buzzanca, D and Pagiati, L and Kazou, M and Georgalaki, M and Hatzopoulos, I and Tsakalidou, E}, title = {The microbial terroir of the Greek olive varieties.}, journal = {International journal of food microbiology}, volume = {441}, number = {}, pages = {111332}, doi = {10.1016/j.ijfoodmicro.2025.111332}, pmid = {40614303}, issn = {1879-3460}, mesh = {Greece ; *Olea/microbiology/classification ; *Fungi/classification/isolation &amp; purification/genetics ; *Bacteria/classification/isolation &amp; purification/genetics ; *Microbiota ; Food Microbiology ; Fruit/microbiology ; }, abstract = {The microbial terroir of Greek olive varieties remains underexplored. In this study, 62 samples of olive fruits, collected across the harvest period 2019-2020, were analyzed by high-throughput sequencing. The samples represented 38 olive varieties collected from geographically well distributed regions of Greece. Analysis of the bacterial composition revealed that the geographical area was a significant factor in discriminating samples. The core microbiota included Erwinia, Pseudomonas, and members of the Enterobacteriaceae family. Furthermore, a notable variation in bacterial taxa abundances associated with the geographic location was observed. The sampling area was a key discriminant factor for the mycobiota, and the core mycobiota comprised Alternaria, Taphrina, Candida, Wickerhamomyces anomalus and Penicillium. Finally, Redundancy Analysis (RDA) revealed a notable association between environmental characteristics and microbial composition. Specifically, tree age was associated with certain bacterial and fungal taxa (Pearson's correlation p-value adj.[FDR] < 0.05).}, }
@article {pmid40613821, year = {2025}, author = {Saini, N and Ghosh, A and Bhadury, P}, title = {Linking plastic degradation potential and resistance gene abundance in bacterioplankton community of the Sundarbans estuarine ecosystem.}, journal = {FEMS microbiology letters}, volume = {372}, number = {}, pages = {}, doi = {10.1093/femsle/fnaf067}, pmid = {40613821}, issn = {1574-6968}, support = {DST/SJF/E&amp;ASA-01/2017-18//Science and Engineering Research Board/ ; }, mesh = {*Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Plastics/metabolism ; Biodegradation, Environmental ; Estuaries ; *Plankton/genetics/metabolism/classification ; India ; *Microbiota/genetics ; Ecosystem ; Metagenomics ; }, abstract = {Harnessing microbial capabilities offers a promising and sustainable approach to address the global challenge of plastic waste. However, the potential of mangrove microbiomes to degrade diverse plastic polymers remains largely unexplored. In this metagenomic-based study, surface water microbiomes were analysed from the Indian Sundarbans, part of the world's largest contiguous mangrove ecosystem, revealing 748.21 hits per billion nucleotides associated with plastic-degrading enzymes (PDEs) targeting 17 different polymer types. Of these, 72.9% corresponded to synthetic polymers and 27.1% to natural polymers. The highest number of hits (223) was associated with polyethylene glycol-degrading enzymes, representing 26.7% of the total PDEs hits. Taxonomic analysis revealed Deltaproteobacteria and Gammaproteobacteria as key degraders of diverse synthetic plastic polymers, with Deltaproteobacteria emerging as a previously unreported group. This suggests that surface sediments may serve as reservoirs for novel plastic-degrading microbes. Co-occurrence network analysis indicated possible emerging co-selection or complex associations between PDEs, antibiotic resistance genes (ARGs), and metal resistance genes (MRGs). Notably, zinc resistance genes and aminoglycoside-related ARGs showed more associations with PDEs. While the presence of PDEs offers a promising avenue for bioremediation, their application may be complicated by the concurrent rise of ARGs and MRGs within PDE-harbouring microbes. Thus, it highlights the need for careful assessment when employing microbes for plastic bioremediation.}, }
@article {pmid40610473, year = {2025}, author = {Ivanova, EA and Suleymanov, AR and Nikitin, DA and Semenov, MV and Abakumov, EV}, title = {Machine learning-based mapping of Acidobacteriota and Planctomycetota using 16 S rRNA gene metabarcoding data across soils in Russia.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {23763}, pmid = {40610473}, issn = {2045-2322}, support = {24-44-00006//Russian Science Support Foundation/ ; 24-44-00006//Russian Science Support Foundation/ ; }, mesh = {*Machine Learning ; *Soil Microbiology ; *RNA, Ribosomal, 16S/genetics ; Russia ; *DNA Barcoding, Taxonomic/methods ; Soil/chemistry ; Microbiota/genetics ; *Acidobacteria/genetics/classification ; Ecosystem ; }, abstract = {The soil microbiome plays a crucial role in maintaining healthy ecosystems and supporting sustainable agriculture. Studying its biogeographical structure and distribution is essential for understanding the rates and mechanisms of microbially mediated soil ecosystem services. This study aimed to investigate the spatial distribution patterns of Acidobacteriota and Planctomycetota across soils in Russia, summarizing data from 16S rRNA gene metabarcoding of topsoils. A machine learning approach (Random Forest) was employed to generate digital distribution maps using climatic, topographic, vegetation, geological, and soil variables. Model interpration was performed using variable importance assessment and Shapley values. According to the error metrics, the Acidobacteriota model achieved a root mean squared error (RMSE) of 6.67% and an R[2] of 0.41, while the Planctomycetota model achieved an RMSE of 2.04% and an R[2] of 0.46. Both phyla exhibited similar spatial distribution patterns, with relative abundance decreasing from North to South. For Acidobacteriota, vegetation cover, surface temperature, and soil pH were significant predictors, whereas the relative abundance of Planctomycetota was mainly influenced by climatic variables. Specifically, Acidobacteriota were more abundant in areas with dense vegetation, stable surface temperatures, and acidic soils. In contrast, Planctomycetota showed reduced abundance in regions with higher levels of precipitable water vapor. These results highlight the potential of machine learning techniques to visualize predictive biogeographic patterns in soil microbial taxa abundance at the phylum level. Despite limitations related to the heterogeneous nature of source data, focusing on higher taxonomic ranks less sensitive to methodological variation enabled to identify preliminary large-scale distribution trends of microbial phyla in soils.}, }
@article {pmid40607773, year = {2025}, author = {Tao, Y and Liu, D and Shi, Q and Sun, Q and Liu, C and Zeng, X}, title = {Lead exposure in relation to gut homeostasis, microbiota, and metabolites.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {7}, pages = {e0037225}, pmid = {40607773}, issn = {1098-5336}, support = {701200E003,2024JKZKTS21//The Research Project of Zhejiang Chinese Medical University/ ; }, mesh = {*Lead/toxicity/metabolism ; *Gastrointestinal Microbiome/drug effects ; Humans ; *Homeostasis/drug effects ; *Gastrointestinal Tract/microbiology/drug effects ; Animals ; }, abstract = {Lead (Pb) is a hazardous heavy metal with no known safe threshold for exposure or consumption, posing significant risks to human health. Pb exposure can cause multiple system damage, depending on exposure levels, duration, and its high bioavailability and bioaccumulative potential. Gastrointestinal tract serves as a primary site for Pb absorption, making it particularly vulnerable to Pb-induced damage, including disruption of gut microbiota composition and metabolic function. This study briefly summarizes the detrimental effects of Pb gut homeostasis, microbial ecology, and host metabolism, which, in turn, further contribute to systemic toxicity. Notably, Pb exposure compromises intestinal barrier integrity, increasing gut permeability and facilitating the translocation of harmful biomolecules into systemic circulation, thereby exacerbating organ dysfunction. Importantly, we underscore that dietary and nutritional interventions such as fiber, probiotic, and vitamin C supplementation is a practicable and effective strategy for mitigating or preventing Pb toxicity.}, }
@article {pmid40606160, year = {2025}, author = {Al-Khlifeh, E and Khadem, S and Hausmann, B and Berry, D}, title = {Corrigendum: Microclimate shapes the phylosymbiosis of rodent gut microbiota in Jordan's Great Rift Valley.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1639190}, doi = {10.3389/fmicb.2025.1639190}, pmid = {40606160}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2023.1258775.].}, }
@article {pmid40605266, year = {2025}, author = {Herman, C and Barker, BM and Bartelli, TF and Chandra, V and Krajmalnik-Brown, R and Jewell, M and Li, L and Liao, C and McAllister, F and Nirmalkar, K and Xavier, JB and Caporaso, JG}, title = {A review of engraftment assessments following fecal microbiota transplant.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2525478}, pmid = {40605266}, issn = {1949-0984}, support = {U24 CA248454/CA/NCI NIH HHS/United States ; }, mesh = {*Fecal Microbiota Transplantation ; Humans ; *Gastrointestinal Microbiome ; *Clostridium Infections/therapy/microbiology ; Clostridioides difficile/physiology ; Animals ; Feces/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {Fecal Microbiota Transplant (FMT) is a treatment for recurrent Clostridium difficile infections and is being explored for other clinical applications, from alleviating digestive and neurological disorders, to restoring microbiomes impacted by cancer treatment. Quantifying the extent of engraftment following an FMT is important in understanding a recipient's response to treatment. Engraftment and clinical response need to be investigated independently to evaluate an FMT's role (or lack thereof) in achieving a clinical response. Standardized bioinformatics methodologies for quantifying engraftment extent would not only improve assessment and understanding of FMT outcomes, but also facilitate comparison of FMT results and protocols across studies. Here we review FMT studies, integrating three concepts from microbial ecology as framework to discuss how these studies approached assessing engraftment extent: 1) Community Coalescence investigates microbiome shifts following FMT engraftment, 2) Indicator Features tracks specific microbiome features as a signal of engraftment, and 3) Resilience examines how resistant post-FMT recipients' microbiomes are to reverting back to baseline. These concepts explore subtly different questions about the microbiome following FMT. Taken together, they provide holistic insight into how an FMT alters a recipient's microbiome composition and provide a clear framework for quantifying and communicating about microbiome engraftment.}, }
@article {pmid40602916, year = {2025}, author = {Puche, E and Roger, B and Vargas-Sánchez, M and Sánchez-Carrillo, S and Rodrigo, MA}, title = {Freshwater macrophyte type (macroalgae versus phanerogams) mainly determines detritus-derived greenhouse gases production: A microcosm experiment.}, journal = {Journal of environmental sciences (China)}, volume = {157}, number = {}, pages = {674-689}, doi = {10.1016/j.jes.2025.01.015}, pmid = {40602916}, issn = {1001-0742}, mesh = {*Greenhouse Gases/analysis/metabolism ; *Seaweed ; Ecosystem ; Methane/analysis ; Fresh Water ; Carbon Dioxide/analysis ; Eutrophication ; *Environmental Monitoring ; *Air Pollutants/analysis ; }, abstract = {Freshwater ecosystems are crucial in the global emissions of greenhouse gases (GHGs) such as CH4. Macrophytes are the main organic matter (i.e., detritus) supplier to the sediment of these systems, thus controlling CH4 production. However, species-specific differences (structure and composition) may determine contrasting patterns of detritus transformation into CH4. Furthermore, eutrophication can affect the degradation and, consequently, CH4 production. We performed a 64-day microcosm experiment with anoxic incubations of detritus from seven phylogenetically different macrophytes (two charophytes, filamentous algae -Spirogyra, Cladophora-, three submerged plants and an amphibious one), under two trophic conditions (oligo- versus eutrophic) and with/without sediment. We assessed the CH4 and CO2 production and the changes in the detritus quality at the end of the experiment. The ranking in the mean cumulative CH4 production was: Chara hispida > Nitella hyalina > Najas marina ≈ Teucrium scordium > Stuckenia pectinata ≈ Myriophyllum spicatum > filamentous algae, and it was related to the detritus quality. GHGs maximum production rates were 1.6 (N. marina)-1.2 (C. hispida) mmol CH4/(g OC·day) and 1.7 (N. marina)-1.5 (C. hispida) mmol CO2/(g OC·day). The CO2:CH4 ratio was biased towards CO2 during the first 10 days (average ratio of 200) and fell afterwards to about 1 for all macrophyte species and treatments. The sediment favored detritus decomposition (probably due to the "positive priming effect"), increasing GHGs production. The influence of nutrient enrichment was not evident. Delving into the macrophyte detritus quality-GHGs production relationship is needed to forecast the GHGs emissions in macrophyte-dominated systems.}, }
@article {pmid40602642, year = {2025}, author = {Pieńkowska, A and Fleischmann, J and Drabesch, S and Merbach, I and Wang, G and Rocha, U and Reitz, T and Marie Muehe, E}, title = {Long-term organic fertilization shields soil prokaryotes from metal stress while mineral fertilization exacerbates it.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {382}, number = {}, pages = {126747}, doi = {10.1016/j.envpol.2025.126747}, pmid = {40602642}, issn = {1873-6424}, mesh = {*Fertilizers/analysis ; *Soil Microbiology ; *Soil Pollutants/analysis/toxicity ; Soil/chemistry ; *Metals/toxicity ; Minerals ; Agriculture ; RNA, Ribosomal, 16S ; }, abstract = {Metal contamination in agricultural soils threatens prokaryote dynamics essential for soil health and crop productivity. Yet, whether fertilization in the long-run affects their resilience to metals remains unclear. This study examined the biogeochemical impacts of realistically low-dose applications of cadmium, zinc, and lead in soils subjected to 119 years of non-fertilization, mineral-fertilization (NPK), organic-fertilization (manure), or combined mineral-organic fertilization. Amended metals remained in the mobile fraction with the order: mineral < unfertilized < mineral + organic < organic, mirroring the effects on soil prokaryotes. In both unfertilized and mineral-fertilized soils, 16S rRNA gene copy numbers declined by 30 % upon metal addition, but recovery timing differed: in unfertilized soil, recovery began after three days, whereas in mineral-fertilized soil, numbers declined until day seven before recovering. This coincided with an increase in metal-resistant taxa, particularly in mineral-fertilized soil, with 10 significantly affected OTUs, and to a lesser extent in unfertilized soil, with 5 affected OTUs. Carbon-, nitrogen-, and phosphorus-mining enzyme activities increased 50-100 % in mineral-fertilized soils, suggesting enhanced nutrient acquisition to mitigate metal toxicity. In contrast, organic-fertilized soil hosted stable enzymatic activities and microbial copy numbers with minimal community shifts (1 affected OTU), indicating greater resistance to metal amendment. Combined mineral-organic fertilization stabilized copy numbers and enzymatic activity upon metal amendment, but 8 OTUs were affected, including specialized nutrient cyclers, suggesting increased availability of previously adsorbed NPK cations. Our findings indicate that organic fertilization shields prokaryotes from metal stress, while mineral fertilization exacerbates it, highlighting the benefits of organic practices for maintaining soil health and productivity.}, }
@article {pmid40602621, year = {2025}, author = {Zhang, Z and Yuan, G and Turgun, X and Turgun, Z and Hou, L and Ye, M and Wang, Y and Xu, X}, title = {Biogeographic Patterns and Ecological Roles of Microorganisms in Sediments Along an Estuarine Salinity Gradient.}, journal = {Environmental microbiology reports}, volume = {17}, number = {4}, pages = {e70139}, pmid = {40602621}, issn = {1758-2229}, support = {2023A1515110368//Guangdong Basic and Applied Basic Research Foundation/ ; XJNUZBS2423//Doctoral Research Foundation of Xinjiang Normal University/ ; 42361144846 and 42461006//National Natural Science Foundation of China/ ; //Tianchi Talents (Xinjiang) Plan Project (Young Doctor)/ ; }, mesh = {*Geologic Sediments/microbiology/chemistry ; *Salinity ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Estuaries ; China ; Biodiversity ; Microbiota ; Ecosystem ; Metagenome ; Phylogeny ; }, abstract = {The distribution patterns and driving mechanisms of microbial biogeographic patterns are fundamental questions in microbiology. This study analysed and compared the bacterial biogeographic patterns in the coastal environment, focusing on the Yangtze Estuary and its adjacent coastal zone. The purpose is to explore the driving mechanisms under spatial distribution, the community assembly processes and potential functions. Our results revealed that the sediment bacterial community structure exhibited a distinct geographical pattern and was significantly influenced by environmental factors. The microbial community displayed a non-random co-occurrence pattern, and the biogeographic patterns were shaped not only by environmental constraints (deterministic processes) but also by stochastic processes resulting from dispersal limitation. The metagenome sequencing analysis revealed a pronounced salinity gradient in the nitrogen-cycling function of the bacterial community. This functional difference appears to be driven by microbial diversity changes from the estuarine region to the ocean, highlighting the key role of microbial ecological characteristics. The findings of this study contribute to a deeper understanding of microbial ecology in estuarine environments, emphasizing the complex interplay between environmental factors and microbial community dynamics in shaping the function of estuarine sediment bacterial communities.}, }
@article {pmid40602118, year = {2025}, author = {Liu, Z and Wen, J and Liu, Z and Su, Z and Wu, Z and Shen, H and Wei, H and Zhang, J}, title = {Tire microplastics rather than polystyrene microplastics reduce soil microbial diversity and network complexity and stability, and induce microbial homogenization.}, journal = {Journal of hazardous materials}, volume = {495}, number = {}, pages = {138945}, doi = {10.1016/j.jhazmat.2025.138945}, pmid = {40602118}, issn = {1873-3336}, abstract = {Microplastics (MPs) pollution poses escalating threats to soil biodiversity, yet its impacts on microbial community structure, stability, and assembly are far from fully understood, limiting the comprehensive assessment of MPs risks. This study investigated effects of polystyrene (PS) and tire particle (TP) MPs (0, 1 %, 5 %; w/w) on soil microbial communities in a maize-planted system, evaluating shifts in diversity, network architecture, and assembly processes. Our results demonstrated that high-concentration (5 %) PS MPs significantly enhanced bacterial α-diversity by promoting some taxa (e.g., Planctomycetes, Betaproteobacteria), and increased bacterial network complexity. In contrast, 5 % TP MPs reduced bacterial and fungal diversity, destabilized bacterial networks, and induced taxonomic homogenization. TP MPs amplified deterministic assembly processes by elevating homogeneous selection contribution while reducing stochastic drift, thereby driving microbial community convergence. Bacterial and fungal community structure shifts under TP MPs correlated with soil stoichiometric alterations, including depleted nitrate nitrogen and available phosphorus, and elevated pH, contents of dissolved organic carbon, ammonium nitrogen, and total carbon. These findings highlight the divergent ecological risks posed by PS and TP MPs, and underscore the urgent need for prioritized mitigation of TP MPs pollution in agroecosystems to preserve microbial functional integrity.}, }
@article {pmid40601059, year = {2025}, author = {Chao, LL and Shih, CM}, title = {Molecular Survey and Genetic Identification of Wolbachia Endosymbionts in Dwelling-Caught Culex quinquefasciatus (Diptera: Culicidae) Mosquitoes from Taiwan.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {69}, pmid = {40601059}, issn = {1432-184X}, support = {NSTC 113-2320-B-037-010; NSTC 114-2923-B-037-001//National Science and Technology Council/ ; }, mesh = {Animals ; *Wolbachia/genetics/classification/isolation &amp; purification/physiology ; *Culex/microbiology ; Taiwan ; *Symbiosis ; Phylogeny ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; }, abstract = {The genetic identity of Wolbachia endosymbionts was determined in dwelling-caught Culex quinquefasciatus from Taiwan. A total of 370 Cx. quinquefasciatus (245 females and 125 males) was initially screened for Wolbachia infection targeting the universal 16S gene, and the positive samples were further identified their genogroup by a nested-polymerase chain reaction assay to amplify the group-specific Wolbachia surface protein (wsp) gene. In general, 44.59% of Cx. quinquefasciatus was detected with Wolbachia endosymbionts, and 43.2% (54/125) in male and 45.31% (111/245) in female. The group-specific detection was observed in 2.16% (8/370), 41.35% (153/370), and 1.08% (4/370) with groups A, B, and co-infection (A&amp;B), respectively. Phylogenetic analysis revealed that the genetic identities of these Taiwan strains were genetically similar to the groups A and B of Wolbachia with the high sequence homogeneity of 98.7-100% and 96.5-99.8%, respectively. Genetic relatedness is clearly discriminated using both methods of maximum likelihood (ML) and unweighted pair group with arithmetic mean (UPGMA). This study demonstrates the initial genetic identity of Wolbachia endosymbionts with a low prevalence (2.16%) of group A and a high prevalence (41.35%) of group B in dwelling-caught Cx. quinquefasciatus of Taiwan. Because the Cx. quinquefasciatus had been known as a vector for various viral pathogens, the possible impacts of Wolbachia endosymbionts on vector competence of Cx. quinquefasciatus in Taiwan need to be further identified.}, }
@article {pmid40601038, year = {2025}, author = {He, T and Chen, Y and Wang, Y and Peng, Z and Mou, Y and Wang, L}, title = {Responses of Microbial Community to Heterogeneous Dissolved Organic Nitrogen Constituents in the Hyporheic Zones of Treated Sewage-Dominated Rivers.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {71}, pmid = {40601038}, issn = {1432-184X}, support = {2021YFB2600200//National Key Research and Development Project of China/ ; grant number 52170159//National Natural Science Foundation of China/ ; No. BE2022601//Key Research and Development Program of Jiangsu Province/ ; 2016-JNHB-007//the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), and the Six Talent Peaks Project in Jiangsu Province/ ; }, mesh = {*Sewage/microbiology/chemistry ; *Nitrogen/metabolism/analysis ; China ; *Rivers/microbiology/chemistry ; *Microbiota ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; *Microbial Consortia ; }, abstract = {The hyporheic zone (HZ) of treated sewage-dominated rivers serves as a critical biogeochemical hotspot for dissolved organic nitrogen (DON) transformation, yet the mechanisms linking DON chemodiversity to microbial community dynamics remain poorly resolved. This study integrated spectroscopic fingerprinting, machine learning, and partial least squares path modeling (PLS-PM) to unravel the interactions between redox-stratified DON fractions and microbial consortia in two effluent-impacted rivers (Xi'an, China). The results revealed that DOM spectral parameters associated with distinct DON characteristics posed distinct effects on microbial communities, with the communities in oxic zones largely impacted by autobiogenic, aromatic, and protein-like DON, while the communities in suboxic zones were more intensely impacted by the humification degree of DON. Microbial communities exhibited redox-dependent niche differentiation; i.e., keystone taxa in oxic zones (e.g., Gamma-Proteobacteria) drove nitrogen assimilation, while suboxic taxa (e.g., Verrucomicrobia) prioritized stress-resistant D-amino acid metabolism. PLS-PM demonstrated that biomarkers exerted stronger control on nitrogen cycling (|path coefficients|> 0.6, P < 0.05) than keystone taxa, with summer communities showing higher model fit. Treated sewage-derived DON fostered specialized consortia through biochemical trade-offs, i.e., methionine recycling in oxic zones versus peptidoglycan modification in suboxic zones, thus highlighting the critical role of HZ in mitigating nitrogen pollution. These findings advance predictive modeling of DON-microbe interactions in anthropogenically perturbed aquatic ecosystems.}, }
@article {pmid40601033, year = {2025}, author = {Nariman, N and Entling, MH and Krehenwinkel, H and Kennedy, S}, title = {The Microbiome of an Invasive Spider: Reduced Bacterial Richness, but no Indication of Microbial-Mediated Dispersal Behaviour.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {70}, pmid = {40601033}, issn = {1432-184X}, mesh = {Animals ; *Spiders/microbiology/physiology ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; Introduced Species ; Symbiosis ; Europe ; Animal Distribution ; }, abstract = {Mermessus trilobatus, an invasive North American linyphiid spider, has expanded its invasion range up to 1400 km in Europe, accelerating its dispersal speed in less than 40 years. The high heritability of dispersal behaviour and the spatial sorting of high and low dispersers indicate a genetic basis of dispersal behaviour. However, microbial endosymbionts can moderate dispersal behaviour in related species (Rickettsia in Erigone atra). Hence, dispersal behaviour in M. trilobatus might also be dictated by the activity of dispersal-mediating endosymbionts. Here, we investigated the microbiome of invasive M. trilobatus spiders extracted from (1) high- and low-dispersive individuals and (2) spiders originating from locations close to the edge and core of the expansion. We examine the microbiomes for the presence of potential dispersal- and reproduction-mediating bacterial strains and compare the microbial assemblages of spiders based on their dispersal behaviour and locations of origin. The composition of microbial assemblages was similar among spiders of different geographic origins and dispersal behaviour. However, microbial richness was lower in high- than in low-dispersive individuals. Surprisingly, none of the known dispersal- or reproduction-altering endosymbionts of arthropods was identified in any tested spider. This contrasts with published results from North America, where M. trilobatus is a known host of Rickettsia and Wolbachia. Thus, the invasive European population appears to have lost its associated endosymbionts. As endosymbionts can reduce spider mobility, it is possible that their absence facilitates the spread of the invasive spider population. The absence of endosymbionts among the analysed individuals substantiates the role of genetic mechanisms behind the variable dispersal behaviour of invasive M. trilobatus in Europe.}, }
@article {pmid40600875, year = {2025}, author = {Yao, J and Wang, H and Fang, J and Shan, S and Joseph, SD and van Zwieten, L and Zhu, K and Chen, D and Jia, H}, title = {Distribution Hotspots, Formation Mechanisms, and Ecological Effects of Reactive Oxygen Species in Soil and Sediment: A Critical Review.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {27}, pages = {13551-13565}, doi = {10.1021/acs.est.5c00581}, pmid = {40600875}, issn = {1520-5851}, mesh = {*Soil/chemistry ; *Geologic Sediments/chemistry ; *Reactive Oxygen Species/analysis ; Rhizosphere ; Free Radicals/analysis ; Environmental Monitoring ; Carbon Sequestration ; Superoxides/analysis ; Hydrogen Peroxide/analysis ; Hydroxyl Radical/analysis ; Environmental Restoration and Remediation ; Ecological and Environmental Phenomena ; }, abstract = {Reactive oxygen species (ROS), including superoxide radical (O2[•-]), hydrogen peroxide (H2O2), hydroxyl radical ([•]OH), and singlet oxygen ([1]O2), are commonly present in soil and sediment, playing a crucial role in the nutrient biogeochemical cycle, pollutant transformation, and microbial ecology. Previous reviews mainly emphasized ROS toxicity and Fenton chemistry-related reactions, neglecting a comprehensive understanding of ROS distribution and hotspots, formation mechanisms, and ecological effects. Here, the most advanced in situ and ex situ detection methods of ROS in soil and sediment are first summarized to address these gaps. ROS hotspots are identified as active microinterfaces and oxic-anoxic fluctuation zones by graphing the distribution of ROS in soil and sediment. Second, ROS formation processes and mechanisms are outlined, which involve natural organic matter (NOM) and biochar (acting as electron shuttle, geobattery, geoconductor, and photosensitizer), transition metals (mainly via Fenton and Fenton-like reactions), and microbes (producing extracellular ROS and mediating NOM decomposition or metal oxides reduction). Further, as for the ecological effects of ROS, they impact the microbial community, nutrient cycle, and the transformation of organic pollutants and multivalence heavy metals. Finally, we call for more future research that focuses on developing rapid and in situ ROS detection techniques, elucidating the interactive ROS formation mechanisms by trace environmental components, analyzing ecological consequences in ROS hotspots, and practically applying ROS in soil and sediment. A comprehensive understanding of the ROS formation process in soil and sediment is crucial for the study of soil carbon sequestration and natural remediation processes in the context of global green and low-carbon development.}, }
@article {pmid40600175, year = {2025}, author = {Etesami, H}, title = {The dual nature of plant growth-promoting bacteria: Benefits, risks, and pathways to sustainable deployment.}, journal = {Current research in microbial sciences}, volume = {9}, number = {}, pages = {100421}, pmid = {40600175}, issn = {2666-5174}, abstract = {Plant growth-promoting bacteria (PGPB) are pivotal in sustainable agriculture, enhancing crop productivity and reducing reliance on chemical inputs. However, their dual role as beneficial agents and potential stressors remains underexplored. This review examines the paradoxical adverse effects of PGPB, challenging the predominantly optimistic narrative surrounding their use. At the plant level, unintended consequences include hormonal imbalances (e.g., auxin-induced root inhibition), phytotoxic metabolite production (e.g., hydrogen cyanide), and trade-offs between growth and defense mechanisms. At the soil level, risks encompass disrupted microbial diversity, altered nutrient cycling, and horizontal gene transfer that may foster pathogenicity. These outcomes are driven by environmental factors (soil pH and moisture), host-specific interactions, and application practices. Mitigation strategies emphasize rigorous strain selection, optimized dosing, and integrated soil management to balance efficacy with ecological safety. Advances in multi-omics technologies and synthetic consortia design offer predictive insights into strain behavior, while long-term ecological assessments are critical to address legacy impacts. The review underscores the necessity of a nuanced, evidence-based approach to PGPB deployment, harmonizing agricultural benefits with environmental stewardship. By addressing knowledge gaps in microbial ecology and risk assessment, this work supports strategies prioritizing both agricultural resilience and soil biodiversity to ensure PGPB contribute sustainably to global food security.}, }
@article {pmid40600142, year = {2025}, author = {Xia, Y and Lu, L and Wang, L and Qiu, Y and Liu, X and Ge, W}, title = {Multi-omics analyses reveal altered gut microbial thiamine production in obesity.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1516393}, pmid = {40600142}, issn = {1664-302X}, abstract = {OBJECTIVE: Accumulating evidence highlights the important role of B vitamins in maintaining the balance of gut microbial ecology and metabolism, however, few studies have focused on changes in B vitamins homeostasis in the gut and their associations with disease. This study aims to investigate the potential interplay between B vitamins, gut microbiota, and obesity.<br><br>METHODS: We conducted an integrated analysis of fecal shotgun metagenomics, fecal metabolome concerning B vitamins and short chain fatty acids (SCFAs), and obese phenotypes in a cohort of 63 participants, including 31 healthy controls and 32 individuals with obesity.<br><br>RESULTS: Metabolomic analysis identified significantly lower levels of fecal thiamine in individuals with obesity (P Wilcoxon < 0.001). Fecal thiamine levels exhibited a positive correlation with HDL-C and a negative correlation with BMI, DBP, fasting serum insulin, HOMA-IR, triglycerides, and propionic acid. Binary logistics regression suggested that fecal thiamine deficiency may be a potential contributor to the onset of obesity (Odds ratio: 0.295). Metagenomic analysis indicated that the microbial composition in individuals with obesity was characterized by a predominance of potential opportunistic pathogens, a loss of complexity, and a decrease in thiamine-producing bacteria. Integrated analysis indicated that thiamine deficiency was positively associated with the depletion of thiamine auxotrophic bacteria in the obese microbiome. Functional analysis revealed that KOs content for enzymes involved in the microbial production of thiamine were significantly lower in obesity, including tRNA uracil 4-sulfurtransferase (ThiI, P Wilcoxon = 0.001) and nucleoside-triphosphatase (NTPCR, P Wilcoxon = 0.006), both of which were positively associated with fecal thiamine.<br><br>CONCLUSION: Our study highlights the impairment of microbial thiamine production and its broad associations with gut microbiota dysbiosis and obesity-related phenotypes. Our findings provide a rationale for developing treatments that utilize thiamine to prevent obesity by modulating gut microbiota.}, }
@article {pmid40600059, year = {2025}, author = {Liu, J and Yao, P and Liu, J and Ren, G and Zhang, XH and Liu, J}, title = {Habitat and lifestyle affect the spatial dynamics of prokaryotic communities along a river-estuary-sea continuum.}, journal = {mLife}, volume = {4}, number = {3}, pages = {305-318}, pmid = {40600059}, issn = {2770-100X}, abstract = {Microbial biogeography and its controlling mechanisms are central themes in microbial ecology. However, we still lack a comprehensive understanding of how habitats and lifestyles affect microbial biogeography across complex environmental gradients. In this study, we investigated the planktonic (including free-living [FL] and particle-associated [PA] lifestyles) and benthic prokaryotic communities along a river-estuary-sea continuum of the Changjiang River to explore their distinct spatial dynamics. We observed greater community variability across spatial distances than between habitat and lifestyle types. Spatial variations were evident in FL, PA, and benthic communities, with the highest turnover rates observed in benthic communities, followed by PA, and the lowest turnover rates observed in FL. The replacement effect dominated PA and benthic community variations, whereas the richness effect was more significant in FL communities. Microbial assembly was primarily governed by homogeneous selection and dispersal limitation regardless of habitats/lifestyles, with their ratios decreasing as the spatial distance increased, particularly in the FL fraction. Dispersal limitation had a stronger effect on benthic communities compared to planktonic communities. While heterogeneous selection generally played a minor role, its influence became more pronounced over larger spatial distances and with increasing salinity differences. Finally, we showed that abiotic and biotic factors individually exerted a greater influence on PA communities, whereas their interactions had a stronger effect on FL communities. Our results revealed complex spatial dynamics and assembly mechanisms among microorganisms across different habitats and lifestyles, providing insights into the spatial scaling of community assembly across complex environmental gradients.}, }
@article {pmid40598447, year = {2025}, author = {Bulzu, PA and Henriques Vieira, H and Ghai, R}, title = {Lineage-specific expansions of polinton-like viruses in photosynthetic cryptophytes.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {154}, pmid = {40598447}, issn = {2049-2618}, support = {25-15920S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 24-11998S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 20-12496X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; }, mesh = {*Cryptophyta/virology/genetics ; Metagenomics ; Phylogeny ; Genome, Viral ; Photosynthesis ; *Giant Viruses/genetics/classification ; *DNA Viruses/genetics/classification ; }, abstract = {BACKGROUND: Polinton-like viruses (PLVs) are diverse eukaryotic DNA viral elements (14-40 kb) that often undergo significant expansion within protist genomes through repeated insertion events. Emerging evidence indicates they function as antiviral defense systems in protists, reducing the progeny yield of their infecting giant viruses (phylum Nucleocytoviricota) and influencing the population dynamics and evolution of both viruses and their hosts. While many PLVs have been identified within the genomes of sequenced protists, most were recovered from metagenomic data. Even with the large number of PLVs identified from metagenomic data, their host-virus linkages remain unknown owing to the scarcity of ecologically relevant protist genomes. Additionally, the extent of PLV diversification within abundant freshwater taxa remains undetermined. In order to tackle these questions, high-quality genomes of abundant and representative taxa that bridge genomic and metagenomic PLVs are necessary. In this regard, cryptophytes, which are among the most widely distributed, abundant organisms in freshwaters and have remained largely out of bounds of genomic and metagenomic approaches, are ideal candidates for investigating the diversification of such viral elements both in cellular and environmental context.<br><br>RESULTS: We leveraged long-read sequencing to recover large (200-600&#xa0;Mb), high-quality, and highly repetitive (>&#x2009;60%) genomes of representative freshwater and marine photosynthetic cryptophytes. We uncovered over a thousand complete PLVs within these genomes, revealing vast lineage-specific expansions, particularly in the common freshwater cryptophyte Rhodomonas lacustris. By combining deep sequence homology annotation with biological network analyses, we discern well-defined PLV groups defined by characteristic gene-sharing patterns and the use of distinct strategies for replication and integration within host genomes. Finally, the PLVs recovered from these cryptophyte genomes also allow us to assign host-virus linkages in environmental sequencing data.<br><br>CONCLUSIONS: Our findings provide a primer for understanding the evolutionary history, gene content, modes of replication and infection strategies of cryptophyte PLVs, with special emphasis on their expansion as endogenous viral elements (EVEs) in freshwater bloom-forming R. lacustris. Video Abstract.}, }
@article {pmid40594354, year = {2025}, author = {Flores, SS and Cordovez, V and Arias Giraldo, LM and Leon-Reyes, A and van 't Hof, P and Raaijmakers, JM and Oyserman, BO}, title = {Unveiling diversity and adaptations of the wild tomato Microbiome in their center of origin in the Ecuadorian Andes.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {22448}, pmid = {40594354}, issn = {2045-2322}, support = {CZ07-000440-2018//SENESCYT scholarship/ ; 10093//Chancellor Grant and COCIBA-USFQ/ ; 10093//Chancellor Grant and COCIBA-USFQ/ ; 024.004.014/NWO_/Dutch Research Council/Netherlands ; 024.004.014/NWO_/Dutch Research Council/Netherlands ; }, mesh = {*Solanum lycopersicum/microbiology/genetics ; *Microbiota/genetics ; Soil Microbiology ; Rhizosphere ; Ecuador ; Plant Roots/microbiology ; Biodiversity ; *Adaptation, Physiological ; Phylogeny ; }, abstract = {Microbiome assembly has been studied for many plant species and is recognized as a key driver of plant growth and plant tolerance to (a)biotic stresses. To date, assembly of the tomato rhizosphere microbiome has been investigated primarily for commercial varieties and field soils subjected to agricultural management practices, whereas the microbiome of wild tomato genotypes in their native habitats remains largely unexplored. This research focused on distinct populations of Solanum pimpinellifolium in three natural habitats in the Ecuadorian Andes to identify the taxonomic and functional diversity of their rhizosphere microbiome. The results showed that, despite genotypic differences among the wild tomato populations, different soil types and soil microbiome compositions, the rhizosphere microbiome showed strikingly compositional similarity across the three habitats. Proteobacteria, in particular taxa classified as Enterobacteriaceae, and specific unclassified fungal taxa were highly represented in the rhizosphere of S. pimpinellifolum. Metagenomic analyses suggested that the prevalence of Enterobacteriaceae on wild tomato roots may be explained by several traits, in particular nutrient competition, motility, iron acquisition, membrane transport, stress response, and plant hormone biosynthesis. These results reveal a conserved microbiome signature associated with wild tomato rhizosphere in their center of origin. Just as the genomes of wild crop ancestors provide a valuable source of beneficial traits for breeding cultivated varieties, exploring their microbiome in native environments could uncover microbial taxa and traits that similarly contribute to crop growth and health.}, }
@article {pmid40594086, year = {2025}, author = {Leifels, M and Cheng, D and Cai, J and Nadhirah, N and Mohidin, AF and Santillan, E and Woo, Y and Hill, E and Wu, SW and Boon, N and Favere, J and Whittle, AJ and Wuertz, S}, title = {Biofilm detachment significantly affects biological stability of drinking water during intermittent water supply in a pilot scale water distribution system.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {22408}, pmid = {40594086}, issn = {2045-2322}, support = {3S85419//the FWO Flanders/ ; 3S85419//the FWO Flanders/ ; S006221N//FWO-SBO Biostable project/ ; S006221N//FWO-SBO Biostable project/ ; }, mesh = {*Biofilms/growth &amp; development ; *Drinking Water/microbiology ; *Water Supply ; *Water Microbiology ; RNA, Ribosomal, 16S/genetics ; Pilot Projects ; Flow Cytometry ; Water Quality ; Bacteria/genetics/classification ; Water Purification ; }, abstract = {Intermittent service provision (IWS) in piped drinking water distribution systems is practiced in countries with limited water resources; it leads to stagnant periods during which water drains completely from de-pressurized pipes, increasing the likelihood of biofilm detachment upon reconnection when water is supplied to the consumer and thus affecting water quality. Our study examines the impact of uninterrupted or continuous water supply (CWS) and IWS on microbial communities and biofilm detachment, using data from three 30-day experiments conducted in an above-ground drinking water testbed with 90-m long PVC pipes containing residual monochloramine. Flow cytometry (FCM) revealed a significant increase in total and intact cell concentrations when water was supplied intermittently compared to CWS, and the microbial alpha-diversity was significantly higher in CWS sections by both 16S rRNA gene metabarcoding and phenotypic fingerprinting of flow cytometry data. Nitrate levels in the water were significantly higher during initial intermittent flow due to the activity of nitrifying bacteria in biofilms exposed to stagnant water in pipes. Overall, biofilm detachment significantly affects the biological stability of drinking water delivered through IWS compared to CWS. We developed a novel biofilm detachment potential index derived from FCM data to estimate the minimum amount of water needed to be discarded before microbial cell counts and community composition return to baseline levels.}, }
@article {pmid40589459, year = {2025}, author = {Ametefe, EN and Thorsen, L and Danwonno, H and Agoha, RK and Glover, RLK and Dzogbefia, VP and Jespersen, L}, title = {Molecular Characterization of Culturable Yeasts and Nonspore-Forming Bacteria Associated With Fermented Kapok Seeds (Kantong), a Traditional Food Condiment in Ghana.}, journal = {International journal of food science}, volume = {2025}, number = {}, pages = {6452183}, pmid = {40589459}, issn = {2314-5765}, abstract = {Fermented kapok seeds, known as kantong in northern Ghana, serve as a traditional food condiment which provides flavor and improves the protein content of soups. In this study, the occurrence of yeasts, lactic acid bacteria (LAB), and other nonspore-forming bacteria in kantong was investigated. Microbial enumeration and phenotypic characterizations on isolated strains were performed. Molecular methods were also employed for grouping and identification of strains, and these included random amplification of polymorphic DNA (RAPD) using Escherichia coli phage-derived M13 primer (M13-PCR typing), repetitive element PCR typing (rep-PCR), and 16S rRNA gene sequencing. After a 48-h fermentation period, microbial load ranged from 4.77 ± 0.11 to 8.9 ± 0.1 log10 CFU/g. The pH of the fermenting condiment decreased from 6.5 to 4.7 during the fermentation period. A total of 190 LAB, 53 enterobacteria, and 39 yeasts were identified at species levels using both phenotypic and molecular methods. The LAB included Pediococcus acidilactici, Weissella paramesenteroides, Pediococcus pentosaceus, Weissella confusa, and Lactiplantibacillus plantarum; the enterobacteria isolated were Acinetobacter baumannii, Klebsiella pneumoniae, Enterococcus faecium, Escherichia coli, and Enterobacter cloacae; and the yeasts identified were Nakaseomyces glabratus, Cyberlindnera fabianii, Pichia kudriavzevii, and Saccharomyces cerevisiae. This work presents fermented kapok seeds as a reservoir of microorganisms, some of which could possess some technological properties which could be harnessed to enhance the nutritional value of Ghanaian foods as well as improve gut health as probiotics. It also reveals the presence of enterobacteria in this spontaneous fermentation, thus impacting the safety of the product and the need for starter culture development.}, }
@article {pmid40589000, year = {2025}, author = {Sharma, H and Al Noman, A and Ahmad, I and Tonni, SD and Mim, TJ and Afrose, F and Sharma, PD and Parvez, A and Tamanna, S and Al Azad, M and Pathak, R}, title = {Bridging Mind and Gut: The Molecular Mechanisms of microRNA, Microbiota, and Cytokine Interactions in Depression.}, journal = {Current gene therapy}, volume = {}, number = {}, pages = {}, doi = {10.2174/0115665232361169250617192348}, pmid = {40589000}, issn = {1875-5631}, abstract = {Depression is a complex psychiatric disorder that arises from various underlying biological mechanisms. In this review, the role of microRNAs (miRNAs) in modulating gut microbiotacytokine communication and their potential to unravel the pathophysiology of depression and develop novel therapeutic strategies are discussed. MiRNAs are small non-coding RNA molecules that have emerged as key regulators in the bidirectional signaling of the gut-brain axis by modulating gene expression and fine-tuning an intricate dialogue between the microbiota, immune system, and central nervous system. Results show how gut microbiota can shape miRNA expression in brain regions involved in mood regulation; conversely, evidence is accumulating, elucidating how miRNA perturbations can shape microbial ecology. Gut bacteria-derived short-chain fatty acids (SCFAs) fuel this nexus by exerting effects on neurogenesis, neurotransmitter synthesis, neuroinflammation, affective behavior alterations, and depressive-like phenotypes. Pro-inflammatory cytokines such as IL-6, TNF-α, and IL-1β are also known to be associated with depressive symptoms related to altered expression patterns of specific miRNAs across these disorders. This review exposes the novel potential biomarkers and therapeutic targets/strategies to develop innovative methods in the diagnosis and treatment of depression by exploring bidirectional relations among miRNAs, gut microbiota, and cytokines. The knowledge of these molecular networks and pathways has provided the opportunity for designing new-generation therapeutics such as phytobiotics, probiotics, psychobiotics, diet therapies, and nanomedicine based on miRNAs from a future perspective, which will revolutionize the management of mental disorders.}, }
@article {pmid40586542, year = {2025}, author = {Bruno, JS and Heidrich, V and Restini, FCF and Alves, TMMT and Miranda-Silva, W and Knebel, FH and Cóser, EM and Inoue, LT and Asprino, PF and Camargo, AA and Fregnani, ER}, title = {Dental biofilm serves as an ecological reservoir of acidogenic pathobionts in head and neck cancer patients with radiotherapy-related caries.}, journal = {mSphere}, volume = {10}, number = {7}, pages = {e0025725}, pmid = {40586542}, issn = {2379-5042}, mesh = {Humans ; *Dental Caries/microbiology/etiology ; *Biofilms/growth &amp; development ; *Head and Neck Neoplasms/radiotherapy/complications ; Male ; Female ; *Microbiota ; Middle Aged ; Aged ; *Bacteria/classification/genetics/isolation &amp; purification ; Adult ; *Radiotherapy/adverse effects ; }, abstract = {UNLABELLED: Radiotherapy-related caries (RRC) is an aggressive and debilitating oral toxicity that affects half of the patients who undergo radiotherapy for head and neck cancer. However, the etiology of RRC is not fully established, and there are no clinically validated methods for preventing it. To gain a better understanding of the risk factors and the microbiome's role in causing RRC, we compared clinicopathological characteristics, oncological treatment regimens, oral health condition, and the oral microbiota at three different oral sites of radiotherapy-treated patients with (RRC+) and without radiotherapy-related caries (RRC-). We observed no significant differences between these groups in the clinicopathological characteristics and treatment regimens. However, RRC+ patients were older and had poorer oral health conditions at the start of the radiotherapy treatment, with a lower number of teeth and a higher proportion of rehabilitated teeth. RRC+ patients had lower microbiota diversity and the dental biofilm of RRC+ patients displayed striking alterations in microbiome composition compared to RRC- patients, including enrichment of acidogenic species and altered metabolic potential, with a higher abundance of genes linked to energy-related pathways associated with the synthesis of amino acids and sugars. We also compared the microbiota of RRC+ tissue with conventional caries tissue, revealing lower bacterial diversity and enrichment of Lactobacillaceae members in RRC+. The insights into the irradiated oral microbiota enhance the understanding of RRC etiology and highlight the potential for microbial-targeted therapies in its prevention and treatment.<br><br>IMPORTANCE: This study focuses on a dedicated collection of diverse oral sites to comprehensively investigate microbial differences between patients who develop RRC and those who do not. RRC is a severe oral disease that profoundly impacts on the oral health and overall quality of life of cancer survivors. Leveraging shotgun metagenomics, we characterize the unique microbial variations in in vivo irradiated dental biofilms, unveiling novel insights into the microbial ecology of radiotherapy-treated patients. Furthermore, this research integrates extensive data on oral health and oncological profiles, providing a comprehensive understanding of the intricate relationship between oral microbial communities and the outcomes of radiotherapy-induced toxicity.}, }
@article {pmid40586525, year = {2025}, author = {Taylor, CC and Parks, ST}, title = {There and back again: navigating the return to in-person lab work post-pandemic for the Hybrid Microbial Ecology Course-based Undergraduate Research Experience (H-ME-CURE).}, journal = {Journal of microbiology &amp; biology education}, volume = {}, number = {}, pages = {e0024924}, doi = {10.1128/jmbe.00249-24}, pmid = {40586525}, issn = {1935-7877}, abstract = {The Microbial Ecology Course-based Undergraduate Research Experience (ME-CURE) has evolved over time to accommodate student needs and experiences. Prior to the COVID-19 pandemic, the lab was fully in-person, with a shift to in silico, remote learning from 2020 to 2023. In 2024, the ME-CURE was further adapted to return to in-person learning while maintaining some of the remote learning pedagogy. Significantly, the 2024 Hybrid ME-CURE (H-ME-CURE) built upon the findings of prior iterations of the lab such that students in the 2024 cohort entered with lab isolates, primers, and pathways that were ready for testing. This novel version of the ME-CURE synthesized years of in-person and remote, in silico learning to yield a deeper understanding of microbial pathways and improved molecular data including novel gene sequences for further testing. The goal of this work is to provide the tools that were used to help build the H-ME-CURE by combining past in-person and in silico learning methods of the ME-CURE.}, }
@article {pmid40585502, year = {2025}, author = {Zhu, M and Zhang, F and Qiu, Z and Zhao, S and Gao, S}, title = {White Light Orchestrates Mycoparasitic and Infection Activities by Regulating Expression of Effectors in Trichothecium roseum.}, journal = {Food science &amp; nutrition}, volume = {13}, number = {7}, pages = {e70396}, pmid = {40585502}, issn = {2048-7177}, abstract = {The fungal developmental processes are orchestrated by white light. Despite the genome assembly of Trichothecium roseum being available, the underlying molecular mechanisms of the white light-mediated developments of T. roseum remain obscure. It was found that white light impaired mycoparasitic activities against the wheat powdery mildew fungus and infection processes on tomato fruits in T. roseum. In vitro and in vivo, white light significantly impaired colony expansion and dramatically increased conidiation of T. roseum. RNA-seq analysis of T. roseum conidia was profiled to illustrate the light-mediated expression of genes. A total of 153 and 666 differentially expressed genes were identified between conidia treated with or without white light at 48- and 96-h post inoculation (hpi). Among genome-wide identified effectors, 8 and 36 effectors were differentially regulated by white light at 48 and 96 hpi, respectively. The core effectors, Tro004101, Tro006854, Tro008316, and Tro004104 were commonly downregulated by white light. Notably, white light regulated gene expression in key metabolic pathways including tryptophan metabolism (3 genes) and tyrosine metabolism (5 genes), as well as the HOG-MAPK signaling cascade. These results demonstrated that white light-compromised T. roseum mycoparasitic and infection activities might be achieved by regulating specific effector expression and differentially modulating metabolism and HOG-MAPK pathways. The genes detected by our transcriptome analysis may be crucial for mycoparasitism and infection by T. roseum and thus serve as targets for future functional analysis. Our findings provide new insights into the white light-orchestrated developments of an important agricultural and economical fungus and will potentially support efforts for the study of fungal effectors.}, }
@article {pmid40584121, year = {2025}, author = {Barrero, MAO and Varón-López, M and Peñuela-Sierra, LM}, title = {Competing microorganisms with exclusion effects against multidrug-resistant Salmonella Infantis in chicken litter supplemented with growth-promoting antimicrobials.}, journal = {Veterinary world}, volume = {18}, number = {5}, pages = {1127-1136}, pmid = {40584121}, issn = {0972-8988}, abstract = {BACKGROUND AND AIM: The widespread use of antibiotic growth promoters (AGPs) in poultry production has been implicated in altering gut microbiota and promoting the excretion of multidrug-resistant (MDR) bacteria into the environment. Salmonella enterica serovar Infantis (Salmonella Infantis [S.I]), a prevalent zoonotic pathogen, has demonstrated increasing resistance in poultry systems. This study aimed to evaluate the efficacy of natural control microorganisms (NCM), Bacillus subtilis and Lactobacillus plantarum, in reducing the abundance of MDR S.I in fresh chicken litter from birds raised with or without AGP supplementation. It also examined how physicochemical properties and microbial dynamics influence pathogen persistence.<br><br>MATERIALS AND METHODS: Microcosms were constructed using litter from broilers raised under two dietary regimes (with and without avilamycin). Treatments included combinations of AGP, S.I, and NCM. Bacterial enumeration was performed using selective media, and whole-genome sequencing of S.I was conducted to characterize antimicrobial resistance and virulence genes. Physicochemical parameters (pH, humidity, temperature, and ammonia) were measured and correlated with microbial loads. Antagonistic activity of NCM strains was assessed using agar diffusion assays.<br><br>RESULTS: Genome analysis revealed that S.I carried multiple resistance genes (e.g., blaCTX-M-65, tet(A), and sul1) and efflux systems conferring MDR. In vitro assays showed strong antagonism by L. plantarum and moderate activity by B. subtilis. In microcosms, S.I counts significantly decreased in the presence of both AGP and NCM, indicating synergistic inhibition. Conversely, in the absence of AGP, NCM had a limited effect. Statistical analyses showed strong correlations between microbial groups and physicochemical variables, particularly during later production stages.<br><br>CONCLUSION: The application of B. subtilis and L. plantarum in chicken litter significantly reduced S.I colonization under AGP supplementation, suggesting their potential as biocontrol agents. These findings support the development of integrated litter management strategies to mitigate zoonotic and resistant pathogen dissemination, particularly in AGP-using systems. However, the effectiveness of such interventions may vary across farms due to differences in microbial ecology and environmental conditions.}, }
@article {pmid40583496, year = {2025}, author = {Crull, S and Hammer, E and Mann, AE and O'Connell, LM and Soule, A and Griffith, E and Blouin, T and Brigmon, RL and Richards, VP}, title = {Seasonal Host Shifts for Legionella Within an Industrial Water-Cooling System.}, journal = {Environmental microbiology reports}, volume = {17}, number = {4}, pages = {e70132}, pmid = {40583496}, issn = {1758-2229}, support = {89303321CEM000080//Office of Environmental Management/ ; //The Laboratory Directed Research and Development (LDRD) program within the Savannah River National Laboratory (SRNL)/ ; }, mesh = {Seasons ; *Legionella/genetics/isolation &amp; purification/physiology/classification ; RNA, Ribosomal, 16S/genetics ; *Water Microbiology ; RNA, Ribosomal, 18S/genetics ; Acanthamoeba ; Phylogeny ; }, abstract = {Legionella is a genus of environmental bacteria containing pathogenic species such as Legionella pneumophila that are responsible for Legionnaires' disease, a potentially fatal respiratory infection. Disease aetiology can involve Legionella replication intracellularly within protists and this study aimed to characterise the Legionella-protist relationship to develop novel outbreak prevention targets. Water and sediment samples were collected from a water-cooling tower in South Carolina over a 6-month period. Concomitantly, multiple environmental parameters were recorded. Bacterial and eukaryotic communities were characterised using 16S rRNA gene V4 region and a 252 bp fragment of 18S rRNA gene, respectively. Co-occurrence network analyses were performed to elucidate Legionella-protist correlations through time. We found that Legionella correlated with different protists as the seasons progressed. Acanthamoeba correlated with Legionella in early spring followed by Vannella and Korotnevella in late spring and early summer, and were joined by Echinamoeba in mid-summer. Vannella and Acanthamoeba are known potential hosts for Legionella, while Korotnevella is a potential undocumented host. Of the environmental parameters, temperature showed strong correlation with protists genera, suggesting that Legionella abundance was driven by temperature-dependent protist availability. Our results highlight ecological shifts that are associated with elevated Legionella levels, which offers potential targets to help predict and prevent disease outbreaks.}, }
@article {pmid40583058, year = {2025}, author = {Cornet, L and Zaidi, SS and Li, J and Ngapout, Y and Shakir, S and Meunier, L and Callot, C and Marande, W and Hanikenne, M and Rombauts, S and Van de Peer, Y and Vanderschuren, H}, title = {A BAC-guided haplotype assembly pipeline increases the resolution of the virus resistance locus CMD2 in cassava.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {185}, pmid = {40583058}, issn = {1474-760X}, support = {F.4515.17//Fonds De La Recherche Scientifique - FNRS/ ; 1.B456.20//Fonds De La Recherche Scientifique - FNRS/ ; 833522/ERC_/European Research Council/International ; BOF.MET.2021.0005.01//Universitair Ziekenhuis Gent/ ; }, mesh = {*Manihot/genetics/virology ; *Disease Resistance/genetics ; *Plant Diseases/genetics/virology ; *Haplotypes ; *Chromosomes, Artificial, Bacterial/genetics ; Genome, Plant ; Chromosome Mapping ; }, abstract = {BACKGROUND: Cassava is an important crop for food security in the tropics where its production is jeopardized by several viral diseases, including the cassava mosaic disease (CMD) which is endemic in Sub-Saharan Africa and the Indian subcontinent. Resistance to CMD is linked to a single dominant locus, namely CMD2. The cassava genome contains highly repetitive regions making the accurate assembly of a reference genome challenging.<br><br>RESULTS: In the present study, we generate BAC libraries of the CMD-susceptible cassava cultivar (cv.) 60444 and the CMD-resistant landrace TME3. We subsequently identify and sequence BACs belonging to the CMD2 region in both cultivars using high-accuracy long-read PacBio circular consensus sequencing (ccs) reads. We then sequence and assemble the complete genomes of cv. 60444 and TME3 using a combination of ONT ultra-long reads and optical mapping. Anchoring the assemblies on cassava genetic maps reveals discrepancies in our, as well as in previously released, CMD2 regions of the cv. 60444 and TME3 genomes. A BAC-guided approach to assess cassava genome assemblies significantly improves the synteny between the assembled CMD2 regions of cv. 60444 and TME3 and the CMD2 genetic maps. We then performed repeat-unmasked gene annotation on CMD2 assemblies and identify 81 stress resistance proteins present in the CMD2 region, among which 31 were previously not reported in publicly available CMD2 sequences.<br><br>CONCLUSIONS: The BAC-assessed approach improved CMD2 region accuracy and revealed new sequences linked to virus resistance, advancing our understanding of cassava mosaic disease resistance.}, }
@article {pmid40581745, year = {2025}, author = {Richter, I and Büttner, H and Hertweck, C}, title = {Endofungal bacteria as hidden facilitators of biotic interactions.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40581745}, issn = {1751-7370}, support = {//Deutsche Forschungsgemeinschaft/ ; 390713860//Germany's Excellence Strategy - EXC 2051/ ; 239748522//SFB 1127 ChemBioSys/ ; }, mesh = {*Symbiosis ; *Fungi/physiology ; *Bacteria/metabolism/genetics/classification ; Humans ; Plants/microbiology ; *Bacterial Physiological Phenomena ; Animals ; *Microbial Interactions ; Ecosystem ; }, abstract = {Fungi play pivotal roles in ecology and human health, driving nutrient cycling, supporting antibiotic production, and posing threats through toxin production. Less well-recognized, however, is their ability to harbour endosymbiotic bacteria. Advances in genomics and microscopy have revealed the prevalence of endofungal bacteria across diverse fungal phyla, though their functions are primarily inferred from genomic and transcriptomic studies. Recent functional research has begun to shed light on their influence on fungal pathogenicity, physiology, and ecology. These findings raise fundamental questions about the establishment and benefits of bacterial-fungal endosymbiosis, as well as the role of endosymbionts in mediating fungal interactions with other organisms. This review provides an in-depth analysis of the molecular mechanisms involved in the establishment and persistence of these symbioses. It also summarizes the current understanding of how endofungal bacteria impact fungal interactions with other organisms. For instance, endofungal bacteria contribute to the beneficial effects of fungi on plant health and fitness, protect fungal hosts from fungivorous predators, and enhance fungal virulence against plants, animals, and humans. These discoveries highlight the need for holistic investigations into bacterial-fungal endosymbiosis to fully understand their role in natural ecosystems. A deeper understanding of these multipartite partnerships offers exciting opportunities to improve ecosystem management, food safety, disease control, and crop productivity.}, }
@article {pmid40580837, year = {2025}, author = {Zhou, B and Niu, C and Mao, W and Wang, X and Wu, Z and Wang, Z}, title = {An electrochemical anaerobic dynamic membrane bioreactor for enhanced sludge digestion: Unveiling molecular interactions and microbial mechanisms.}, journal = {Water research}, volume = {285}, number = {}, pages = {124080}, doi = {10.1016/j.watres.2025.124080}, pmid = {40580837}, issn = {1879-2448}, abstract = {This study investigated the effects of stepwise external voltages on an electrochemical anaerobic dynamic membrane bioreactor (EC-AnDMBR) for anaerobic digestion of waste activated sludge. Increasing the applied voltage greatly mitigated membrane fouling, reduced the transmembrane pressure increase rate and enhanced both volatile solids digestion and biogas production. The dynamic membrane structure became looser with fewer biofouling substances, attributed to a 42.6 % increase in the sludge-membrane interaction energy barrier at higher voltages. Electrochemical analysis revealed improved electroactivity of the anaerobic sludge, as evidenced by increased conductivity and reduced internal resistance. The proton-coupled electron transfer (PCET) pathway was promoted, indicated by a significant increase in the hydrogen/deuterium kinetic isotope effect from 616 to 25,990. Molecular simulations of dissolved organic matter (DOM) showed an enrichment of amide and quinone groups, along with stronger hydrogen-bonding and π-cation interactions, which may contribute to the PCET process. Moreover, elevated voltages promoted more deterministic microbial community assembly and reduced upstream microbial immigration. Gene upregulation in organic metabolism, electron/proton transport, and methanogenesis further supported enhanced digestion performance via PCET pathway. These findings offer valuable insights into the molecular mechanisms and microbial ecology of EC-AnDMBR systems, advancing the development of more efficient and sustainable sludge treatment technologies.}, }
@article {pmid40578101, year = {2025}, author = {Liu, B and Jia, M and Nauwynck, W and Wang, J and Kundu, K and Springael, D and Boon, N}, title = {Hydrogen-powered bacteria enhance organic micropollutant degradation under starvation conditions.}, journal = {Water research}, volume = {285}, number = {}, pages = {124052}, doi = {10.1016/j.watres.2025.124052}, pmid = {40578101}, issn = {1879-2448}, abstract = {Organic micropollutants (OMPs) occur in natural aquatic environments at trace concentrations with suspected adverse effects on the ecosystem and human health. Microbial biodegradation plays a crucial role in OMP-elimination from drinking water resources. However, long-term OMP-biodegradation remains challenging since the metabolic activity of degrading strains is restricted by energy-limited conditions in treatment systems. Molecular hydrogen (H2) has been identified as a universally available energy source utilized by various bacteria under nutrient-starved conditions, and it can be hypothesized that H2 might also support OMP-degrading microbes when other energy carriers are scarce. The potential of H2 as a supporting energy source for OMP-degradation was tested by examining its effect on the biodegradation of 2,6-dichlorobenzamide (BAM) by Aminobacter niigataensis MSH1 and on the physiological status of the MSH1 cells during both nongrowth-linked (500 μg BAM/L) and growth-linked (10,000 μg BAM/L) regimes. MSH1 cells used as inoculum were either not or pre-exposed to H2 and were harvested at different growth phases. During the nongrowth-linked BAM biodegradation, MSH1 pre-exposed to H2 exhibited a 1.2 to 1.5-fold higher initial specific BAM biodegradation rate, resulting in more rapid BAM removal, likely due to the retention of more metabolically active cells, as suggested by a cell vitality assay. During the growth-linked biodegradation, MSH1 pre-exposed to H2 demonstrated accelerated growth with a 1.5-fold higher maximum specific growth rate, which coincided with an improved BAM removal. The positive effects of H2 were only evident for MSH1 cells harvested either at the stationary and/or starvation phase. Evidence of H2 metabolism was supported by H2 consumption measurements. Collectively, this study reveals that microbial H2 metabolism enables OMP-degrading bacteria to sustain metabolic activity under starvation conditions, offering a novel strategy to enhance long-term OMP-biodegradation.}, }
@article {pmid40577691, year = {2025}, author = {Quellhorst, HE and Ponce, MA and Holguin Rocha, AF and Sakka, MK and Tsintzou, G and Maille, JM and Vagelas, I and Madesis, P and Athanassiou, CG and Scully, ED and Zhu, KY and Morrison, WR}, title = {The capacity of 3 stored product insect species to vector microbes after increasing dispersal periods.}, journal = {Journal of economic entomology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jee/toaf123}, pmid = {40577691}, issn = {1938-291X}, support = {2024-67012-42439//USDA-NIFA/ ; }, abstract = {Prostephanus truncatus (Horn) (Coleoptera: Bostrichidae), Rhyzopertha dominica (F.) (Coleoptera: Bostrichidae), and Sitophilus zeamais Motschulsky (Coleoptera: Curculionidae) are 3 important stored product pests of maize, but there has been little work evaluating how they vector microbes. While there has been some work assessing the microbial ecology of S. zeamais, none has directly assessed whether they transfer microbes to new food patches. Thus, we evaluated the ability of both species to vector microbes when given the opportunity to forage on sterilized potato dextrose agar dishes after a 0, 24, or 72 h dispersal period in a sterilized container. We subsequently photographed the dishes at 3 and 5 d after introduction and quantified the microbial growth using ImageJ. In addition, we isolated unique morphotypes of fungi, extracted DNA and amplified the internal transcribed spacer 5/4 intergenic spacer region, then sequenced to determine fungal identity. We found that 3 species readily vectored several plant pathogenic microbes, including 21 taxa from more than 11 genera, notably Aspergillus spp. Increasing dispersal period (0, 24, 72 h) resulted in a third less microbial growth (mean microbial growth or mean greyscale value from 0 to 255) by S. zeamais after 72 h, while for P. truncatus it resulted in a 2.7-fold increase in microbial growth. Dispersal by S. zeamais (0, 24, 72 h) resulted in 6.6-fold more microbial growth than dispersal by P. truncatus. There was 1.5- to 3.7-fold more microbial growth after 5 d than 3 d by each species. This research has important implications for food safety in the postharvest environment, especially for maize production, storage, and processing.}, }
@article {pmid40577531, year = {2025}, author = {Duxbury, SJN and Raguideau, S and Cremin, K and Richards, L and Medvecky, M and Rosko, J and Coates, M and Randall, K and Chen, J and Quince, C and Soyer, OS}, title = {Niche formation and metabolic interactions contribute to stable diversity in a spatially structured cyanobacterial community.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf126}, pmid = {40577531}, issn = {1751-7370}, abstract = {Understanding how microbial communities maintain stable compositional diversity is a key question in microbial ecology. Studies from pairwise interactions and synthetic communities indicate that metabolic interactions and spatial organisation can influence diversity, but the relevance of these factors in more complex communities is unclear. Here we used a cyanobacterial enrichment community that consistently forms millimetre-scale granular structures, to investigate compositional diversity and its stability. Over a year of passaging in media without significant carbon source, we found stable co-existence of 17 species belonging to diverse bacterial phyla. Metagenomic analysis revealed polysaccharide breakdown genes and complementary vitamin biosynthesis pathways in these species. Supporting these findings, we show growth of several isolated species on cyanobacterial slime components and experimentally verify vitamin exchanges between two members of the community. Several species had genes for (an)oxygenic photosynthesis and sulfur cycling, the expression of which we verified via meta transcriptomics. Consistent with this, we found that the granular structures displayed oxygen gradients with anoxic interiors. Cyanobacteria and other bacteria were distributed on the periphery and insides of these structures, respectively. Perturbation of the community via glucose addition resulted in fold increases of the heterotrophs, whereas disturbing the community by continual shaking led to fold reductions in several heterotrophs, including anoxygenic phototrophs. In contrast, removal of vitamins supplementation did not consistently alter species coverages, due to predicted vitamin sharing amongst community members. Taken together, these findings indicate that spatial organisation, microenvironment niche formation and metabolic interactions contribute to community compositional diversity and stability.}, }
@article {pmid40577477, year = {2025}, author = {Li, B and Jiang, L and Johnson, T and Wang, G and Sun, W and Wei, G and Jiao, S and Gu, J and Tiedje, J and Qian, X}, title = {Global health risks lurking in livestock resistome.}, journal = {Science advances}, volume = {11}, number = {26}, pages = {eadt8073}, pmid = {40577477}, issn = {2375-2548}, mesh = {*Livestock/microbiology ; Animals ; *Global Health ; Humans ; Manure/microbiology ; Anti-Bacterial Agents/pharmacology ; Risk Assessment ; *Metagenome ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Livestock farming consumes more than 70% of global antibiotics annually, making livestock manures an important vector of anthropogenically influenced antibiotic resistance genes (ARGs). The global pattern of the livestock resistome, its driving mechanisms, and transmission potential to the clinic are not well assessed. We analyzed 4017 livestock manure metagenomes from 26 countries and constructed a comprehensive catalog of livestock ARGs and metagenome-assembled genomes. Livestock resistome is a substantial reservoir of known (2291 subtypes) and latent ARGs (3166 subtypes) and is highly connectable to human resistomes. We depicted the global pattern of livestock resistome and prevalence of clinically critical ARGs, highlighting the role of farm and human antibiotic stewardship in shaping livestock resistome. We developed a risk-assessment framework by integrating mobility potential, clinical significance, and host pathogenic relevance, and prioritized higher risk livestock ARGs, producing a predictive global map of livestock resistome risks that can help guide research and policy.}, }
@article {pmid40576334, year = {2025}, author = {Lee, EM and Srinivasan, S and Purvine, SO and Fiedler, TL and Leiser, OP and Proll, SC and Minot, SS and Djukovic, D and Raftery, D and Johnston, C and Fredricks, DN and Deatherage Kaiser, BL}, title = {Syntrophic bacterial and host-microbe interactions in bacterial vaginosis.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40576334}, issn = {1751-7370}, support = {P41 GM103493/GM/NIGMS NIH HHS/United States ; S10 OD021562/OD/NIH HHS/United States ; R01 AI061628/AI/NIAID NIH HHS/United States ; U19 AI113173/AI/NIAID NIH HHS/United States ; S10OD021562/RI/ORIP NIH HHS/United States ; R01AI061628/NH/NIH HHS/United States ; GM103493/GM/NIGMS NIH HHS/United States ; U19 AI113173/NH/NIH HHS/United States ; }, mesh = {Female ; *Vaginosis, Bacterial/microbiology ; Humans ; Vagina/microbiology ; *Host Microbial Interactions ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Formates/metabolism ; Adult ; Putrescine/metabolism ; Proteomics ; Microbiota ; Bacterial Proteins/metabolism ; }, abstract = {Bacterial vaginosis (BV) is a common, polymicrobial condition of the vaginal microbiota that is associated with symptoms such as malodor and excessive discharge, along with increased risk of various adverse sequelae. Host-bacteria and bacteria-bacteria interactions are thought to contribute to the condition, but many of these functions have yet to be elucidated. Using untargeted metaproteomics, we identified 1068 host and 1418 bacterial proteins in a set of cervicovaginal lavage samples collected from 20 participants with BV and 9 who were negative for the condition. We identified Dialister micraerophilus as a major producer of malodorous polyamines and identified a syntrophic interaction between this organism and Fannyhessea vaginae that leads to increased production of putrescine, a metabolite characteristic of BV. Although formate synthesis has not previously been noted in BV, we discovered diverse bacteria associated with the condition express pyruvate formate-lyase enzymes in vivo and confirm these organisms secrete formic acid in vitro. Sodium hypophosphite efficiently inhibited this function in multiple taxa. We also found that the fastidious organism Coriobacteriales bacterium DNF00809 can metabolize formic acid secreted by Gardnerella vaginalis, representing another syntrophic interaction. We noted an increased abundance of the host epithelial repair protein transglutaminase 3 in the metaproteomic data, which we confirmed by enzyme-linked immunosorbent assay. Other proteins identified in our samples implicate Finegoldia magna and Parvimonas micra in the production of malodorous trimethylamine. Some bacterial proteins identified represent novel targets for future therapeutics to disrupt BV communities and promote vaginal colonization by commensal lactobacilli.}, }
@article {pmid40573780, year = {2025}, author = {Zhang, S and Luo, Z and Peng, J and Wu, X and Meng, X and Qin, Y and Zhu, F}, title = {Analysis of Cadmium Accumulation Characteristics Affected by Rhizosphere Bacterial Community of Two High-Quality Rice Varieties.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {12}, pages = {}, pmid = {40573780}, issn = {2223-7747}, support = {2024YFD2301400//the National Key Research and Development Program of China/ ; 2024CX09//the Agricultural Science and Technology Innovation Project of Hunan Province, China/ ; }, abstract = {Cadmium-contaminated rice poses serious health risks through the bioaccumulation of Cd (cadmium) from soil to edible grains. Cd contamination disrupts soil microbial ecology and alters microbial diversity. However, the role of cultivar-specific rhizosphere microbial communities in modulating Cd uptake remains unclear. In this study, we aimed to elucidate the mechanism underlying variety-dependent rhizosphere microecological remodeling and Cd accumulation in two independently selected late rice varieties, Yuzhenxiang (YZX) and Xiangwanxian 12 (XWX12). Combining physiological and metagenomic analyses, we revealed variety-specific correlations between root Cd accumulation and dynamic changes in soil pH, soil available phosphorus, and rhizosphere bacteria. The key bacterial genera (Variibacter, Nitrospira) showed differential enrichment patterns under Cd stress. In contrast, Galella and Anaeromyxobacter likely reduce Cd bioavailability by modulating phosphorus availability. Overall, this study elucidates that rice cultivars indirectly shape Cd accumulation patterns via rhizosphere microbial remodeling, providing novel insights for microbial remediation strategies in Cd-contaminated farmland.}, }
@article {pmid40572127, year = {2025}, author = {Mohammadi, T and Ely, B}, title = {Dolichocephalovirinae Phages Exist as Episomal Pseudolysogens Across Diverse Soil Bacteria.}, journal = {Microorganisms}, volume = {13}, number = {6}, pages = {}, pmid = {40572127}, issn = {2076-2607}, abstract = {Interactions between bacteria and bacteriophages are important for the maintenance of soil communities. In this study, we characterized the giant bacteriophages found within diverse soil bacteria and 14 additional phages isolated directly from soil samples. Based on their genome sizes and genetic composition, we concluded that these phages belong to the Dolichocephalovirinae subfamily. In addition, we used pulsed-field gel electrophoresis to show that the genomes of these phages were present as episomal pseudolysogens in the cytoplasm of their host cells. These findings suggest that episomal phages are important components of soil microbial ecosystems. Understanding the interactions between bacteriophages and bacteria is essential for microbial ecology, as they influence nutrient cycling, community composition, and host evolution. Furthermore, these phage-bacteria dynamics offer potential applications in plant disease control, as bacteriophages could serve as biocontrol agents against soilborne pathogens, promoting sustainable agricultural practices.}, }
@article {pmid40569388, year = {2025}, author = {Dellicour, S and Gámbaro, F and Jacquot, M and Lequime, S and Baele, G and Gilbert, M and Pybus, OG and Suchard, MA and Lemey, P}, title = {Comparative performance of viral landscape phylogeography approaches.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {26}, pages = {e2506743122}, pmid = {40569388}, issn = {1091-6490}, support = {/WT_/Wellcome Trust/United Kingdom ; R01 AI153044/AI/NIAID NIH HHS/United States ; R01 AI162611/AI/NIAID NIH HHS/United States ; U19 AI135995/AI/NIAID NIH HHS/United States ; }, mesh = {Phylogeography/methods ; *RNA Viruses/genetics ; Phylogeny ; Genome, Viral ; Computer Simulation ; }, abstract = {The rapid evolution of RNA viruses implies that their evolutionary and ecological processes occur on the same time scale. Genome sequences of these pathogens therefore can contain information about the processes that govern their transmission and dispersal. Landscape phylogeographic approaches use phylogeographic reconstructions to investigate the impact of environmental factors and variables on the spatial spread of viruses. Here, we extend and improve existing approaches and develop three novel landscape phylogeographic methods that can test the impact of continuous environmental factors on the diffusion velocity of viral lineages. In order to evaluate the different methods, we also implemented two simulation frameworks to test and compare their statistical performance. The results enable us to formulate clear guidelines for the use of three complementary landscape phylogeographic approaches that have sufficient statistical power and low rates of false positives. Our open-source methods are available to the cientific community and can be used to investigate the drivers of viral spread, with potential benefits for understanding virus epidemiology and designing tailored intervention strategies.}, }
@article {pmid40569073, year = {2025}, author = {Kobiałka, M and Świerczewski, D and Walczak, M and Urbańczyk, W}, title = {Extremely distinct microbial communities in closely related leafhopper subfamilies: Typhlocybinae and Eurymelinae (Cicadellidae, Hemiptera).}, journal = {mSystems}, volume = {10}, number = {7}, pages = {e0060325}, pmid = {40569073}, issn = {2379-5077}, support = {2021/43/D/NZ8/02183//National Science Centre, Poland/ ; }, mesh = {Animals ; *Hemiptera/microbiology/classification ; *Microbiota ; Symbiosis ; In Situ Hybridization, Fluorescence ; High-Throughput Nucleotide Sequencing ; *Bacteria/classification/genetics/isolation &amp; purification ; Phylogeny ; }, abstract = {UNLABELLED: Among the Hemiptera insects, a widespread way of feeding is sucking sap from host plants. Due to their nutrient-poor diet, these insects enter into obligate symbiosis with their microorganisms involved in the synthesis of components essential for host survival. However, within the Cicadellidae family, there is a relatively large group of mesophyll feeders-Typhlocybinae-that is considered to be devoid of obligate symbiotic companions. In this work, we examine the composition of microorganisms in this subfamily and compare the results with their close relatives-the Eurymelinae subfamily. To study the microbiome, we used high-throughput next-generation sequencing (NGS, Illumina) and advanced microscopic techniques, such as transmission electron microscopy (TEM) and fluorescence in situ hybridization (FISH), in a confocal microscope. In the bodies of Typhlocybinae insects, we did not detect the presence of microorganisms deemed to be obligate symbionts. Their microbial communities consist of facultative symbionts, mainly alphaproteobacteria such as Wolbachia or Rickettsia as well as others that can be considered as facultative, including Spiroplasma, Acidocella, Arsenophonus, Sodalis, Lariskella, Serratia, Cardinium, and Asaia. On the other hand, the Eurymelinae group is characterized by a high diversity of microbial communities, both obligate and facultative, similar to other Cicadomorpha. We find co-symbionts involved in the synthesis of essential amino acids such as Karelsulcia, betaproteobacteria Nasuia, or gammaproteobacteria Sodalis. In other representatives, we observed symbiotic yeast-like fungi from the family Ophiocordycipitaceae or Arsenophonus bacteria inhabiting the interior of Karelsulcia bacteria. Additionally, we investigated some aspects of symbiont transmission and the phylogeny of symbiotic organisms and their hosts.<br><br>IMPORTANCE: The Typhlocybinae and Eurymelinae leafhoppers differ significantly in their symbiotic communities. They have different diets, as Typhlocybinae insects feed on parenchyma, which is richer in nutrients, while Eurymelinae, like most representatives of Auchenorrhyncha, consume sap from the phloem fibers of plants. Our work presents comprehensive studies of 42 species belonging to the two above-mentioned, and so far poorly known, Cicadomorpha subfamilies. Phylogenetic studies indicate that the insects from the studied groups have a common ancestor. The diet shift in the Typhlocybinae leafhoppers contributed to major changes in the composition of microorganisms inhabiting the body of these insects. Research on the impact of diet on the microbiome and the subsequent consequences on the evolution and adaptation of organisms plays an important role in the era of climate change.}, }
@article {pmid40567269, year = {2025}, author = {Mohamadi Nasrabadi, A and Eckstein, D and Mettke, P and Ghanem, N and Kallies, R and Schmidt, M and Mothes, F and Schaefer, T and Graefe, R and Bandara, CD and Maier, M and Liebert, UG and Richnow, H and Herrmann, H}, title = {A Virus Aerosol Chamber Study: The Impact of UVA, UVC, and H2O2 on Airborne Viral Transmission.}, journal = {Environment &amp; health (Washington, D.C.)}, volume = {3}, number = {6}, pages = {648-658}, pmid = {40567269}, issn = {2833-8278}, abstract = {The COVID-19 pandemic highlighted the urgent need to control airborne virus transmission, particularly in indoor environments with limited ventilation. This study evaluates the effectiveness of UVA and UVC irradiation, along with hydrogen peroxide (H2O2), in inactivating aerosolized viruses. A 19 m[3] virus aerosol simulation chamber, replicating indoor conditions, was used to simulate human respiratory emissions by aerosolizing Escherichia phage T4 (T4 phages) embedded in a pig mucin medium that mimics respiratory aerosols. Results showed a clear, dose-dependent reduction in viral genome copies with UVC exposure, where a dose of 129.9 mJ/cm[2] reduced over 99% of the viral genome copies. Although less efficient, UVA still contributed to virus inactivation, reducing detectable phages to 20% at 513.30 J/cm[2]. Mucin provided a protective effect, making virus removal more challenging. Hydrogen peroxide enhanced disinfection, with 1.6 ppm reducing viral genome copies by 78%, and higher concentrations (up to 16 ppm) achieving over 99% reduction in the dark condition. The combination of UVA/UVC with H2O2 further enhanced disinfection, eliminating detectable virus genome copies entirely. These findings underscore the potential for using combined UV light and chemical treatments to effectively mitigate airborne viral transmission in enclosed spaces.}, }
@article {pmid40566942, year = {2025}, author = {Kara, K and Yilmaz Öztaş, S and Baytok, E}, title = {In Vitro Ruminal Metagenomic Profiles and Ruminal Fermentation Variables of Aromatic Plant Pulps.}, journal = {Veterinary medicine and science}, volume = {11}, number = {4}, pages = {e70447}, pmid = {40566942}, issn = {2053-1095}, support = {TSA-2023-13007//Erciyes University Scientific Research Projects Unit/ ; }, mesh = {*Fermentation ; *Rumen/microbiology/metabolism/physiology ; Animals ; Cattle ; Metagenomics ; Animal Feed/analysis ; *Metagenome ; Gastrointestinal Microbiome ; Digestion ; }, abstract = {BACKGROUND: Aromatic plant residues remaining after aromatic oil extraction represent a promising alternative feed source due to their rich bioactive compound content and fibrous structure. However, their fermentative behaviour and microbial degradability in the rumen require evaluation.<br><br>OBJECTIVE: This study aimed to determine the nutrient composition, in vitro ruminal gas production, digestibility characteristics and fermentation end-products of aromatic plant pulps (sage, thyme, lavender and yarrow) obtained via hydrodistillation.<br><br>METHODS: Dried pulps were analysed for nutrient contents and subjected to in vitro ruminal fermentation for 24&#xa0;h. Gas production estimated metabolizable energy (ME), net energy for lactation (NEL), organic matter digestibility (OMd), ammonia nitrogen (NH3-N) and short-chain fatty acid (SCFA) profiles were evaluated. Microbial community composition was assessed via 16S rRNA-based metagenomics.<br><br>RESULTS: Yarrow pulp had the highest gas production, ME, NEL, OMd and SCFA concentrations (AA, BA, IVA, T-SCFA) (p&#xa0;<&#xa0;0.05). Thyme pulp exhibited the highest NH3-N levels (75.14&#xa0;mg/L), suggesting high rumen-degradable protein content. Sage pulp had the lowest NH3-N levels (60.93&#xa0;mg/L). Microbial composition shifted with fibre content; higher lignin (in lavender) was associated with lower Bacteroidota and higher Firmicutes abundance. Methanogenic archaea (Methanobrevibacter) were least abundant in thyme pulp (p&#xa0;<&#xa0;0.05).<br><br>CONCLUSION: Due to their fermentability and favourable microbial responses, aromatic plant pulps, particularly yarrow, show promise as functional ruminant feed ingredients. These byproducts may enhance ruminal fibre utilization while modulating microbial ecology and reducing methane-associated archaea.}, }
@article {pmid40564363, year = {2025}, author = {Luo, G and Cheng, Y and Xu, Y and Liu, J and Yang, W and Liu, J and Guo, B and Zhu, H}, title = {Monochromatic Light Impacts the Growth Performance, Intestinal Morphology, Barrier Function, Antioxidant Status, and Microflora of Yangzhou Geese.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {12}, pages = {}, pmid = {40564363}, issn = {2076-2615}, support = {32202622//National Natural Science Foundation of China/ ; 32102542//National Natural Science Foundation of China/ ; CX(24)1012//Jiangsu Agricultural Science and Technology Innovation Fund/ ; 2025SKLAB6-17//Open project of State Key Laboratory of Animal Biotech Breeding/ ; }, abstract = {This study investigates the effect of monochromatic light on the body weight (BW), melatonin concentration and its receptors expression levels, intestinal health, and gut microorganisms of Yangzhou geese. Green light (GL) significantly increased BW, melatonin and its receptor expression levels, villus height (VH) and villus height/crypt depth (VH/CD) ratio, superoxide dismutase (SOD), catalase (CAT), and total antioxidant capacity (T-AOC) activities, as well as the abundance of Synergistota and Prevotellaceae_UCG-001, compared with white light (WL). Blue light (BL) significantly increased the mRNA expression of melatonin membrane receptor 1a (Mel1a) and nuclear receptor 1α (RORα), VH and VH/CD ratio, CAT activity, cecal microbes diversity, and decreased malondialdehyde (MDA) levels. Red light (RL) significantly decreased average daily feed intake, reduced the abundances of Synergistota and Prevotellaceae_UCG-001, and increased Mel1a and RORα mRNA expression levels, MDA content, and cecum microbial diversity. Moreover, melatonin levels were significantly higher in the GL and BL groups compared to RL. Furthermore, the mRNA expression levels of Claudin-10, Occludin, and occludens-1 (ZO-1) were significantly upregulated under GL or BL exposures compared to the WL group, whereas RL only enhanced the expression levels of ZO-1. Spearman's correlation analysis revealed that the relative abundance of Prevotellaceae_UCG-001 exhibited positive correlations with BW, melatonin and its receptors expression, gut health, and antioxidant capacity. Overall, these findings suggested that GL exposure enhanced melatonin synthesis and its receptors expression, modulated intestinal homeostasis and microbial ecology, and ultimately increased goose BW.}, }
@article {pmid40562244, year = {2025}, author = {Costa, BF and Sawaya, C and Buren, JV and Smith, AL}, title = {Investigating anaerobic digestion microbiome resilience to high PFOA and PFOS mixtures during cometabolism.}, journal = {Bioresource technology}, volume = {435}, number = {}, pages = {132877}, doi = {10.1016/j.biortech.2025.132877}, pmid = {40562244}, issn = {1873-2976}, mesh = {*Fluorocarbons/metabolism ; *Alkanesulfonic Acids/metabolism ; Anaerobiosis ; *Microbiota/drug effects ; *Caprylates/metabolism ; Bioreactors/microbiology ; Methane/metabolism ; Sewage/microbiology ; Biodegradation, Environmental ; Biofuels ; }, abstract = {Anaerobic digestion (AD) is a reducing environment with high microbial diversity and potential for biotransformation of PFAS. Yet, their fate and impact on the microbial community remains poorly understood. This study evaluated the long-term impact (100 d) of perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) spiked at10 mg/L (low) and 100 mg/L (high), respectively. Although resilient to complete system failure, high PFAS concentrations disrupted AD, evidenced by 25-50 % reduction in methane content, 45 -48 % reduction in cumulative biogas production, and accumulation of butyric acid. No significant decrease in PFAS concentration was observed in the liquid fraction after 100 d relative to the kill controls, indicating PFAS adsorption behavior. However, PFAS concentrations were temporally variable. Microbial community analysis revealed enrichment of notable AD groups, such as Firmicutes, Synergistetes, and Methanomassillicoccus phyla in high PFAS reactors, which underscores the potential for the microbiome adaptation and informs future strategies for PFAS-contaminated sludge treatment.}, }
@article {pmid40561955, year = {2025}, author = {Yasin, MU and Muhammad, S and Chen, N and Hannan, F and Afzal, M and Haider, Z and Ali, B and Ahmad, I and Rehman, M and Gan, Y}, title = {Nano-engineered biochar enhances soil microbial interactions and maize transcriptomic pathways for cadmium detoxification.}, journal = {Journal of hazardous materials}, volume = {495}, number = {}, pages = {139029}, doi = {10.1016/j.jhazmat.2025.139029}, pmid = {40561955}, issn = {1873-3336}, abstract = {Cadmium (Cd) contamination threatens agroecosystems and food security by degrading soil health, inducing plant oxidative stress, and reducing crop yields. Sustainable strategies integrating biochar (BC) with nanoparticles (NPs) for Cd immobilization and soil-plant-microbe restoration remain underexplored. Here, we demonstrate the efficacy of BC, nano-silicon (nSi), and nano-iron (nFe) to immobilize Cd, improve soil health and reprogram maize stress responses in Cd-contaminated soil. Soil Cd bioavailability, microbial networks, and maize transcriptomes were analyzed under varying BC-nSi-nFe formulations. Among these formulations, the BC + 25 % nSi + 75 % nFe + Cd (T6) composite reduced bioavailable Cd by 21 %, raised soil pH from 6.21 to 6.98, and enhanced soil enzyme activities (118-139 %). T6 improved maize biomass (115-119 %), reduced shoot Cd accumulation (78 %), and suppressed oxidative stress (67-75 % ROS reduction). This study presents transcriptomic evidence showing that BC-NPs composites mitigate Cd stress and modulate maize antioxidant defense and phytohormone signaling pathways, offering new insights into the molecular mechanisms underlying improved plant resilience. Soil microbial networks shifted toward metal-resistant taxa, with enriched glutathione metabolism and nitrogen fixation. BC-NPs composites offer a multidimensional remediation strategy, integrating nanomaterial science, microbial ecology, and plant molecular biology to mitigate Cd toxicity. This approach enhances soil-plant resilience, supporting sustainable agriculture in contaminated ecosystems.}, }
@article {pmid40561631, year = {2025}, author = {Ma, X and Li, Y and Niu, L and Grossart, HP and Shang, J and Zheng, J and Wu, J}, title = {Salinity regulates nutrient cycling via top-down and bottom-up forces in artificial cut-off tidal channels: Insights from multitrophic microbiota.}, journal = {Water research}, volume = {285}, number = {}, pages = {124037}, doi = {10.1016/j.watres.2025.124037}, pmid = {40561631}, issn = {1879-2448}, abstract = {Artificial cut-off of natural tidal meanders for flood control has substantially altered microbial communities and their role in nutrient cycling, yet the lack of comprehensive investigations into these specific anthropogenic impacts introduces greater uncertainty regarding the resultant water quality of nutrient-enriched estuaries. Here, we investigated how planktonic multitrophic microbiota and their mediated nutrient cycling respond to artificial meander cut-off using the environmental DNA (eDNA) approach. Results showed that despite the decline in α diversity of multitrophic microbiota, the nutrient cycling potential of the water column was enhanced 2.91-fold in the straight tidal channel. The artificial cut-off restructured the microbial food web, with trophic transfer efficiency from basal species to protozoa increasing. Salinity was identified to be the key environmental driver, mitigating the negative impact of decreased biodiversity on estuarine nutrient cycling potential by intensifying protozoan predation on heterotrophic bacteria (top-down forces). Additionally, salinity further enhanced environmental selection (bottom-up forces), reducing heterotrophic bacterial diversity while promoting the proliferation of functional microbial taxa, such as Comamonadaceae, Chitinophagaceae, and Rhodocyclaceae. This study offers novel insights into nutrient cycling in artificial straight tidal channels and provides critical foundations for optimizing restoration and management strategies in anthropogenically modified tidal river.}, }
@article {pmid40560449, year = {2025}, author = {de Meireles, DA and Souza, T and de A A Carneiro, K and da S Fraga, V and de O Dias, B and da S Batista, D and Martins, EL and de Lima, AFL and Dos Santos Nascimento, G and Campos, MCC}, title = {Treated Wastewater Irrigation Enhances Plant Biomass, Soil Fertility, and Rhizosphere Microbial Activity in C4 and CAM species Grown on a Degraded Planosol.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {7}, pages = {804}, doi = {10.1007/s10661-025-14271-4}, pmid = {40560449}, issn = {1573-2959}, mesh = {*Wastewater/chemistry ; *Agricultural Irrigation/methods ; *Soil Microbiology ; *Soil/chemistry ; *Rhizosphere ; Biomass ; *Waste Disposal, Fluid/methods ; Brazil ; }, abstract = {The Brazilian semi-arid region, marked by erratic rainfall and severely degraded soils, presents critical challenges for sustainable agriculture. In this context, the reuse of treated domestic wastewater-collected from a septic tank and anaerobic filter system-offers a promising strategy to enhance plant productivity and rehabilitate soil conditions, particularly within the Caatinga biome. This study evaluated the long-term (four-year) effects of irrigation with pure water versus treated domestic wastewater on plant dry biomass, soil fertility, and rhizospheric microbial activity in a degraded Planosol. Two plant types were assessed: a C4 species (Mimosa caesalpiniifolia) and a CAM species (Opuntia atropes). Results demonstrated that treated wastewater irrigation significantly increased dry biomass, with a 12.18% increase in the C4 species and a 29.33% increase in the CAM species. Soil chemical fertility improved notably, with wastewater application raising soil pH by 5.0%, increasing soil organic carbon by 87.9%, and enhancing nutrient availability, including nitrogen, potassium, magnesium, and sodium. A 37.5% reduction in exchangeable aluminum further indicated mitigation of soil acidity. Microbial responses varied between species: while soil respiration increased in both rhizospheres-more prominently in CAM species-microbial biomass carbon rose significantly in the C4 rhizosphere but declined in CAM, suggesting species-specific microbial interactions. These findings support the potential of treated domestic wastewater as a nutrient-rich, low-cost irrigation alternative for improving plant performance and soil quality in semi-arid degraded lands. Nevertheless, potential risks-including salinity build-up and pathogen persistence-necessitate long-term monitoring and further environmental safety assessments. By integrating plant physiology, soil chemistry, and microbial ecology, this study offers a comprehensive approach to evaluating wastewater reuse as a sustainable agricultural and ecological restoration practice in the Caatinga biome.}, }
@article {pmid40559796, year = {2025}, author = {Popov, IV and Peshkova, DA and Lukbanova, EA and Tsurkova, IS and Emelyantsev, SA and Krikunova, AA and Malinovkin, AV and Chikindas, ML and Ermakov, AM and Popov, IV}, title = {Gut Microbiota Dynamics in Hibernating and Active Nyctalus noctula: Hibernation-Associated Loss of Diversity and Anaerobe Enrichment.}, journal = {Veterinary sciences}, volume = {12}, number = {6}, pages = {}, pmid = {40559796}, issn = {2306-7381}, support = {23-14-00316//Russian Science Foundation/ ; 075-10-2025-017//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {Hibernation in mammals entails profound physiological changes that are known to impact host-associated microbial communities, yet its effects on the gut microbiota of synanthropic bats remain underexplored. In this study, we investigated the gut bacterial composition and diversity of Nyctalus noctula before and during hibernation using high-throughput 16S rRNA amplicon sequencing. Fecal samples from individually banded bats were collected under controlled conditions at a rehabilitation center and analyzed for alpha and beta diversity, as well as differential taxonomic abundance. Hibernation was associated with a marked reduction in microbial diversity according to the Shannon and Simpson indices and a distinct restructuring of gut communities based on the Bray-Curtis dissimilarity index. Active bats exhibited a diverse microbiota enriched in facultative anaerobes, including Lactococcus, Enterococcus, and Escherichia-Shigella, while hibernating individuals were dominated by obligate anaerobes, such as Romboutsia and Paeniclostridium. These findings suggest a contraction and functional specialization of the gut microbiota during torpor, potentially reflecting adaptations to fasting, hypothermia, and reduced gut motility. Our results demonstrate that the bat's gut microbiome is highly responsive to physiological status and underscore the importance of microbial ecology for understanding the host's energy balance and health under seasonal contexts.}, }
@article {pmid40559651, year = {2025}, author = {Wimmer, BC and Dwan, C and De Medts, J and Duysburgh, C and Rotsaert, C and Marzorati, M}, title = {Undaria pinnatifida Fucoidan Enhances Gut Microbiome, Butyrate Production, and Exerts Anti-Inflammatory Effects in an In Vitro Short-Term SHIME[®] Coupled to a Caco-2/THP-1 Co-Culture Model.}, journal = {Marine drugs}, volume = {23}, number = {6}, pages = {}, pmid = {40559651}, issn = {1660-3397}, support = {n.a.//Marinova Pty Ltd., 249 Kennedy Drive, Cambridge, TAS 7170, Australia/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Polysaccharides/pharmacology/isolation &amp; purification ; *Undaria/chemistry ; *Anti-Inflammatory Agents/pharmacology ; Caco-2 Cells ; Coculture Techniques ; *Butyrates/metabolism ; THP-1 Cells ; Colon/microbiology/drug effects ; Feces/microbiology ; Cytokines/metabolism ; Adult ; Fatty Acids, Volatile/metabolism ; Edible Seaweeds ; }, abstract = {Fucoidans have demonstrated a wide range of bioactivities including immune modulation and benefits in gut health. To gain a deeper understanding on the effects of fucoidan from Undaria pinnatifida (UPF) on the colonic microbiome, the short-term Simulator of the Human Intestinal Microbial Ecosystem[®], a validated in vitro gut model, was applied. Following a three-week intervention period on adult faecal samples from three healthy donors, microbial community activity of the colonic microbiota was assessed by quantifying short-chain fatty acids while composition was analysed utilising 16S-targeted Illumina sequencing. Metagenomic data were used to describe changes in community structure. To assess the secretion of cytokines, co-culture experiments using Caco-2 and THP1-Blue™ cells were performed. UPF supplementation over a three-week period had a profound butyrogenic effect while also enriching colonic microbial diversity, consistently stimulating saccharolytic genera, and reducing genera linked with potentially negative health effects in both regions of the colon. Mild immune modulatory effects of UPF were also observed. Colonic fermentation of UPF showed anti-inflammatory properties by inducing the secretion of the anti-inflammatory cytokines IL-6 and IL-10 in two out of three donors in the proximal and distal colon. In conclusion, UPF supplementation may provide significant gut health benefits.}, }
@article {pmid40558970, year = {2025}, author = {Vieira, RIM and Peixoto, ADS and Monclaro, AV and Ricart, CAO and Filho, EXF and Miller, RNG and Gomes, TG}, title = {Fungal Coculture: Unlocking the Potential for Efficient Bioconversion of Lignocellulosic Biomass.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {11}, number = {6}, pages = {}, pmid = {40558970}, issn = {2309-608X}, support = {00193-00002388/2023-21//Foundation for Research Support of the Federal District/ ; }, abstract = {Microbial decomposition of persistent natural compounds such as phenolic lignin and polysaccharides in plant cell walls plays a crucial role in the global carbon cycle and underpins diverse biotechnological applications. Among microbial decomposers, fungi from the Ascomycota and Basidiomycota phyla have evolved specialized mechanisms for efficient lignocellulosic biomass degradation, employing extracellular enzymes and synergistic fungal consortia. Fungal coculture, defined as the controlled, axenic cultivation of multiple fungal species or strains in a single culture medium, is a promising strategy for industrial processes. This approach to biomass conversion offers potential for enhancing production of enzymes, biofuels, and other high-value bioproducts, while enabling investigation of ecological dynamics and metabolic pathways relevant to biorefinery operations. Lignocellulosic biomass conversion into fuels, energy, and biochemicals is central to the bioeconomy, integrating advanced biotechnology with sustainable resource use. Recent advancements in -omics technologies, including genomics, transcriptomics, and proteomics, have facilitated detailed analysis of fungal metabolism, uncovering novel secondary metabolites and enzymatic pathways activated under specific growth conditions. This review highlights the potential of fungal coculture systems to advance sustainable biomass conversion in alignment with circular bioeconomy goals.}, }
@article {pmid40557448, year = {2025}, author = {Lingua, MS and Sabatino, ME and Cuatrin, A and Salvucci, E and Blajman, JE and Páez, RB and Wunderlin, DA and Baroni, MV}, title = {From waste to worth: stability, bioaccessibility, and cellular antioxidant activity of microencapsulated red grape pomace phenolics.}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.70010}, pmid = {40557448}, issn = {1097-0010}, support = {//This work was supported by the National Institute of Agricultural Technology (INTA, Argentina) (Projects 2019-PD-I152-A537 and 2019-PE-I150-A5) and the National Agency of Scientific and Technological Promotion (FONCyT, Argentina), and Argentine Wine Corporation (COVIAR) (Project PICTO-COVIAR-2017-0123)./ ; }, abstract = {BACKGROUND: Red grape pomace (RGP) is a recognized winery by-product due to its phenolic profile with valuable antioxidant power and beneficial health properties. Following the latest trends in food science and technology, this study valorizes the use of RGP to obtain a food ingredient rich in antioxidant phenolics. An integrated approach was proposed, investigating the production by spray drying of easy-to-handle microparticles, rich in stable compounds with antioxidant properties demonstrated after simulated digestion using in vitro assays and Caco-2 cells. The changes in microbiota composition after fermentation were also studied.<br><br>RESULTS: Among investigated wall materials, maltodextrin/skimmed milk powder (1:1) 300&#x2009;g&#x2009;L[-1] offered the highest drying yield, appropriate moisture, solubility, and adequate microparticle morphology, as well as the best stability of polyphenols. Encapsulation improved the protection of phenolic compounds and the in vitro antioxidant capacity during 120&#x2009;days of storage at 4 and 25&#x2009;&#xb0;C, as compared to those unencapsulated. Microencapsulated polyphenols bioaccessibility was evident in 15 out of 22 compounds initially quantified, with 6.6% potentially absorbed. The polyphenols from microcapsules modulated positively the microbial ecology after colonic fermentation. Those derived from intestinal digestion demonstrated the highest capacity to reduce the reactive oxygen species under oxidative stress conditions in Caco-2 cells.<br><br>CONCLUSION: RGP could be used in the development of new food ingredients as a potential candidate for health promotion. This represents the first report on the benefits of RGP microcapsules as a food ingredient, validating its final biological effects in a cellular model considering the processing and digestion effects. &#xa9; 2025 Society of Chemical Industry.}, }
@article {pmid40556136, year = {2025}, author = {Long, Y and Li, Y and Zhang, J and Liu, J and Han, Q and Cao, Y and Jiang, Y and Liu, C and Hu, Y and Wang, G and Zhang, X and Jin, J and Semenov, M and Han, G and Liu, X and Yu, Z}, title = {Unconventional Nitrogen Fixation and Adaptive Genomics of a New Neorhizobium glycines sp. nov., A Promising Soybean Symbiont.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.70046}, pmid = {40556136}, issn = {1365-3040}, support = {//This study was funded by the National Key R &amp; D Program of China (2021YFD1500400), Strategic Priority Research Program of Chinese Academy of Sciences (XDA28020201), National Natural Science Foundation of China (32172123, 42207399)./ ; }, }
@article {pmid40555367, year = {2025}, author = {McGrath, AH and Steinberg, PD and Egan, S and Kjelleberg, S and Marzinelli, EM}, title = {Disruption of host-associated and benthic microbiota affects reproductive output and settlement of a habitat-forming macroalga.}, journal = {Proceedings. Biological sciences}, volume = {292}, number = {2049}, pages = {20250729}, pmid = {40555367}, issn = {1471-2954}, support = {//University of Sydney/ ; //Australian Research Council/ ; //Ecological Society of Australia/ ; }, mesh = {*Microbiota/drug effects ; Reproduction ; Ecosystem ; *Rhodophyta/microbiology/physiology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The reproduction and establishment of habitat-forming species are key processes affecting their persistence and associated biodiversity. In marine systems, microbial communities associated with habitat-forming macroalgae can influence various aspects of host performance; however, the role of these microorganisms in influencing macroalgal reproduction and settlement is poorly understood. Using a dominant habitat-forming macroalga on Australian rocky shores, Hormosira banksii, we manipulated host- and benthic-associated microbiota to determine the relative importance of microorganisms to reproductive output (number of viable eggs released) and settlement (settlement and morphogenesis of algal zygotes). Disruption of the host microbiota using antibiotics decreased reproductive output after 2 weeks, with the effect dependent on the type of antibiotic used. Disruption of host- and benthic-associated microbiota, in combination, caused a significant decrease in settlement of H. banksii zygotes, with the combined disruption having the greatest impact on settlement success. Our results demonstrate the importance of host-associated microbiota in macroalgal reproduction and an interactive effect of host- and benthic-associated microbiota on settlement-a key ecological process with important implications for host fitness and potentially ecosystem persistence.}, }
@article {pmid40553410, year = {2025}, author = {Bota, JL and Baum, C and Gawronski, S and Grafe, TU and Kerth, G and Schöner, MG and Schöner, CR}, title = {UV treatment of the digestive fluid of Nepenthes hemsleyana pitcher plants affects their digestive process, possibly via reducing microbial inquilines.}, journal = {Oecologia}, volume = {207}, number = {7}, pages = {108}, pmid = {40553410}, issn = {1432-1939}, support = {SCHO1740/1-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Ultraviolet Rays ; Animals ; Digestion/radiation effects ; }, abstract = {Interactions with microbes are ubiquitous, and many of them are essential for the survival and success of plants. In Nepenthes pitcher plants, they occur as part of a diverse community of organisms, so-called inquilines, that live inside the digestive fluid of the pitcher traps. However, evidence is ambiguous regarding the role of microbial inquilines: they may complement the plants' prey digestion, fix atmospheric N, act as competitors that reduce plant-available nutrients or affect the plants in other ways unrelated to the breakdown of prey. In a field experiment on Borneo, we investigated the effect of UV disinfection of the digestive fluid on prey digestion of N. hemsleyana that captures and digests insects as well as bat faeces in its pitchers. We show that in the short term, the photosynthetic performance of plants with UV-treated digestive fluids decreases compared to untreated plants, likely due to lower abundances of microbial inquilines. However, at the end of 2 months, responses of pitcher plants with UV-treated and untreated digestive fluids tend to equalise. Nutrient source, whether from insects or bat faeces, does not influence prey digestion. We expect our findings to be a starting point for unveiling the ecological role of microbial inquilines in pitcher plants and how they interact with other inquiline groups of higher trophic levels. Ultimately, this will also help to improve understanding of the functioning and evolution of convergent interactions in other carnivorous plants.}, }
@article {pmid40553254, year = {2025}, author = {Wu, BX and Ma, JY and Huang, XC and Liang, XS and Ning, BL and Wu, Q and Wang, SZ and Zhou, JH and Fu, WB}, title = {Acupuncture as A Potential Therapeutic Approach for Tourette Syndrome: Modulation of Neurotransmitter Levels and Gut Microbiota.}, journal = {Chinese journal of integrative medicine}, volume = {31}, number = {8}, pages = {735-742}, pmid = {40553254}, issn = {1993-0402}, mesh = {Animals ; *Tourette Syndrome/therapy/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Neurotransmitter Agents/metabolism ; *Acupuncture Therapy ; Male ; Mice, Inbred C57BL ; Mice ; }, abstract = {OBJECTIVE: To investigate the effects of acupuncture on the neurotransmitter levels and gut microbiota in a mouse model of Tourette syndrome (TS).<br><br>METHODS: Thirty-six male C57/BL6 mice were randomly divided into 4 groups using a random number table method: 3,3'-iminodipropionitrile (IDPN) group, control group, acupuncture group, and tiapride group, with 9 mice in each group. In the IDPN group, acupuncture group, and tiapride group, mice received daily intraperitoneal injections of IDPN (300 mg/kg body weight) for 7 consecutive days to induce stereotyped behaviors. Subsequently, in the acupuncture intervention group, standardized acupuncture treatment was administered for 14 consecutive days to IDPN-induced TS model mice. The selected acupoints included Baihui (DU 20), Yintang (DU 29), Waiguan (SJ 5), and Zulinqi (GB 41). In the tiapride group, mice were administered tiapride (50 mg/kg body weight) via oral gavage daily for 14 consecutive days. The control group, IDPN group, and acupuncture group received the same volume of saline orally for 14 consecutive days. Stereotypic behaviors were quantified through behavioral assessments. Neurotransmitter levels, including dopamine (DA), glutamate (Glu), and aspartate (ASP) in striatal tissue were measured using enzyme-linked immunosorbent assay. Dopamine transporter (DAT) expression levels were additionally quantified through quantitative polymerase chain reaction (qPCR). Gut microbial composition was analyzed through 16S ribosomal RNA gene sequencing, while metabolic profiling was conducted using liquid chromatography-mass spectrometry (LC-MS).<br><br>RESULTS: Acupuncture administration significantly attenuated stereotypic behaviors, concurrently reducing striatal levels of DA, Glu and ASP concentrations while upregulating DAT expression compared with untreated TS controls (P<0.05 or P<0.01). Comparative analysis identified significant differences in Muribaculaceae (P=0.001), Oscillospiraceae (P=0.049), Desulfovibrionaceae (P=0.001), and Marinifilaceae (P=0.014) following acupuncture intervention. Metabolomic profiling revealed alterations in 7 metabolites and 18 metabolic pathways when compared to the TS mice, which involved various amino acid metabolisms associated with DA, Glu, and ASP.<br><br>CONCLUSIONS: Acupuncture demonstrates significant modulatory effects on both central neurotransmitter systems and gut microbial ecology, thereby highlighting its dual therapeutic potential for TS management through gut-brain axis regulation.}, }
@article {pmid40548738, year = {2025}, author = {Mattelin, V and Van Landuyt, J and Kerkhof, F-M and Minnebo, Y and Boon, N}, title = {Integrating taxonomic and phenotypic information through FISH-enhanced flow cytometry for microbial community dynamics analysis.}, journal = {Microbiology spectrum}, volume = {13}, number = {8}, pages = {e0197324}, pmid = {40548738}, issn = {2165-0497}, support = {1288224N//Fonds Wetenschappelijk Onderzoek/ ; HBC.2019.2622//Agentschap Innoveren en Ondernemen/ ; BOF.BAS.2022.0014.01//Bijzonder Onderzoeksfonds UGent/ ; 30770923//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {*Flow Cytometry/methods ; *In Situ Hybridization, Fluorescence/methods ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Humans ; *Microbiota ; Phenotype ; Gastrointestinal Microbiome ; Biodiversity ; Ecosystem ; }, abstract = {UNLABELLED: Flow cytometry is a powerful tool to monitor microbial communities, as it allows tracking both changes in the subpopulations and cell numbers at high throughput and a low sample cost. This information can be combined in a phenotypic fingerprint that can be leveraged for diversity analysis. However, as isogenic individuals can manifest phenotypic diversity, for example, due to differing physiological state and phenotypic plasticity, combining the phenotypic information with taxonomic information adds an extra dimension for describing the dynamics of a microbial community. In this research, taxonomic information was incorporated in the microbial fingerprint through fluorescent in situ hybridization (FISH) at a single-cell level. To validate this concept and explore its versatility, two ecosystems with different micro-biodiversity were considered. In the first environment, marine bacteria were monitored for plastic biodegradation in a trickling filter, and in the second, an in vitro simulated human gut microbiome was followed over time. Samples were prepared using different (staining) methods, including FISH, and beta diversity analysis was used to evaluate the level of distinction between differently treated groups in both environments. As a reference to correlate increased distinction with the incorporation of taxonomic information, 16S rRNA gene sequencing was used. Finally, a predictive algorithm was trained to correctly classify samples in the differently treated groups. The results showed that the implementation of FISH in flow cytometry provides more information on a single-cell level to answer specific scientific questions, like distinguishing between phenotypically similar communities or following a specific taxonomic group over time.<br><br>IMPORTANCE: Understanding microbial communities is crucial for elucidating their role in maintaining ecosystem health and stability. Researchers are increasingly interested in studying microbial communities by looking at not just their genetic makeup but also their physical traits and functions. In our study, we used common techniques like fluorescence in situ hybridization and flow cytometry, along with advanced data analysis, to better understand these communities. This combination allowed us to gather and use data more effectively, demonstrating that these easy-to-use methods, when paired with proper analysis, can enhance our understanding of changing microbial ecosystems.}, }
@article {pmid40545777, year = {2025}, author = {VanWallendael, A and Wijewardana, C and Bonnette, J and Vormwald, L and Fritschi, FB and Boe, A and Chambers, S and Mitchell, RB and Rouquette, FM and Wu, Y and Fay, PA and Jastrow, JD and Lovell, JT and Juenger, TE and Lowry, DB}, title = {Local adaptation of both plant and pathogen: an arms-race compromise in switchgrass rust.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.70313}, pmid = {40545777}, issn = {1469-8137}, support = {DE-AC02-06CH11357//Biological and Environmental Research/ ; DE-SC0014156//Biological and Environmental Research/ ; DE-SC0017883//Biological and Environmental Research/ ; DE-SC0018409//Biological and Environmental Research/ ; 1832042//Division of Environmental Biology/ ; DE-AC02-05CH11231//Joint Genome Institute/ ; }, abstract = {In coevolving species, parasites locally adapt to host populations as hosts locally adapt to resist parasites. Parasites often outpace host local adaptation since they have rapid life cycles, but host diversity, the strength of selection, and external environmental influence can result in complex outcomes. To better understand local adaptation in host-parasite systems, we examined locally adapted switchgrass (Panicum virgatum), and its leaf rust pathogen (Puccinia novopanici) across a latitudinal range in North America. We grew switchgrass genotypes in 10 replicated multiyear common gardens, measuring rust severity from natural infection in a 'host reciprocal transplant' framework for testing local adaptation. We conducted genome-wide association mapping to identify genetic loci associated with rust severity. Genetically differentiated rust populations were locally adapted to northern and southern switchgrass, despite host local adaptation to environmental conditions in the same regions. Rust resistance was polygenic, and distinct loci were associated with rust severity in the north and south. We narrowed a previously identified large-effect quantitative trait locus for rust severity to a candidate YELLOW STRIPE-LIKE gene and linked numerous other loci to defense-related genes. Overall, our results suggest that both hosts and parasites can be simultaneously locally adapted, especially when parasites impose less selection than other environmental factors.}, }
@article {pmid40542918, year = {2025}, author = {Zhang, W and Li, XJ and Liu, F and Zhang, J and Tian, J and Gao, Y}, title = {Fungen: clustering and correcting long-read metatranscriptomic data for exploring eukaryotic microorganisms.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {40542918}, issn = {1869-1889}, abstract = {Long-read metatranscriptomics is a powerful and cost-effective technology for elucidating the genetic diversity and expression dynamics of active eukaryotic microorganisms by characterizing full-length transcripts. However, its potential has been limited by the lack of high-quality reference genomes and high sequencing error rates. We present Fungen, a reference-free tool that constructs accurate transcripts from long-read metatranscriptomic data through read clustering and error correction. Fungen achieves superior accuracy in transcript determination while significantly reducing memory usage and offering a 22 to 56-fold speed improvement over existing methods. This novel approach overcomes the challenges posed by sequence similarity among closely related species, enabling the analysis of deeply sequenced metatranscriptomes by generating reliable gene clusters and accurate sequences. Two applications showcase Fungen's capabilities to perform high-resolution taxonomic assignments and gene profiling in marine direct RNA datasets, as well as resolving reliable annotation identities in full-length rRNA targeted sequencing datasets. When applied to soil metatranscriptomic data, Fungen offers valuable insights into the in situ fungal composition and gene expression dynamics, revealing specialized life strategies of plant-pathogenic fungi in soil environments. Overall, Fungen provides a fast, scalable, and accurate solution for analyzing complex metatranscriptomic datasets, paving the way for a comprehensive understanding of eukaryotic diversity and function from long-read sequencing data.}, }
@article {pmid40542710, year = {2025}, author = {Susukida, S and Miyazawa, K and Ichikawa, H and Muto, K and Yoshimi, A and Kumagai, T and Kato, Y and Abe, K}, title = {Improved Mixing Properties of Stirred Fermentation of an Aspergillus oryzae Hyphal Dispersion Mutant.}, journal = {Biotechnology and bioengineering}, volume = {122}, number = {9}, pages = {2389-2399}, pmid = {40542710}, issn = {1097-0290}, support = {//This study was supported by the Institute for Fermentation, Grant/Award Number: L-2018-2-014; Japan Science and Technology Agency-Adaptable and Seamless Technology Transfer Program through target-driven R&amp;D, Grant/Award Number: JPMJTM19Y4; JSPS KAKENHI, Grant/Award Number: JP20H02895; and New Energy and Industrial Technology Development Organization, Grant/Award Number: JPNP20011./ ; }, mesh = {*Aspergillus oryzae/genetics/metabolism/growth &amp; development/physiology ; *Fermentation ; *Bioreactors/microbiology ; *Hyphae/genetics/metabolism/growth &amp; development ; Hydrodynamics ; }, abstract = {The complexity of mechanical and biological processes in filamentous fungal fermentation remains a major obstacle to improving product yield. We previously demonstrated that the AGΔ-GAGΔ strain of Aspergillus oryzae, lacking both α-1,3-glucan (AG) and galactosaminogalactan (GAG), had improved hyphal dispersion, reduced culture viscosity, and increased recombinant protein production. Here, we applied computational fluid dynamics (CFD) and multi-omics analysis to characterize the AGΔ-GAGΔ strain during fermentation in a stirred-tank bioreactor. CFD simulations revealed large gas cavities behind the impeller blades and severe compartmentalization in both wild-type and AGΔ-GAGΔ cultures. However, shear stress distribution was broader and gas cavity formation was lower in the AGΔ-GAGΔ strain than in the wild type. The simulation results were consistent with measurements of volumetric oxygen mass transfer coefficients (KLa) and mixing times. Transcriptome analysis revealed upregulation of TCA-cycle genes in AGΔ-GAGΔ relative to the wild type. Analysis of intracellular and extracellular metabolites indicated distinct metabolic profiles associated with oxygen availability. Our findings highlight the critical role of hydrodynamics in fungal fermentation and demonstrate the potential of strain engineering for improving mixing characteristics.}, }
@article {pmid40540980, year = {2025}, author = {Noviello, D and Amoroso, C and Vecchi, M and Facciotti, F and Caprioli, F}, title = {Curing inflammatory bowel diseases: breaking the barriers of current therapies- emerging strategies for a definitive treatment.}, journal = {Current opinion in immunology}, volume = {95}, number = {}, pages = {102593}, doi = {10.1016/j.coi.2025.102593}, pmid = {40540980}, issn = {1879-0372}, mesh = {Humans ; *Inflammatory Bowel Diseases/therapy/immunology/etiology ; Animals ; Gastrointestinal Microbiome/immunology ; Fecal Microbiota Transplantation ; Hematopoietic Stem Cell Transplantation ; Intestinal Mucosa/immunology ; }, abstract = {Chronic intestinal inflammation in inflammatory bowel diseases (IBD) reflects the interplay of genetic predisposition, immune dysregulation, microbial imbalance, and epithelial barrier defects. Current therapies for IBD primarily focus on controlling inflammation necessitating lifelong treatment and face a 'therapeutic ceiling' due to primary and secondary loss of efficacy over time. Immune-mediated approaches do not address additional pathogenic mechanisms, such as impairment of epithelial barrier and gut microbial ecology. Thus, innovative strategies are required to foster the field closer to a definitive cure. This review discusses novel strategies to overcome current therapeutic limitations, including immune reset via hematopoietic stem cell transplantation and B cell-targeted therapies, antigen-specific interventions such as chimeric antigen receptor T cells and tolerogenic vaccines, and intestinal epithelial barrier restoration. We also explore microbiota-based strategies - ranging from fecal microbiota transplantation to engineered consortia and bacteriophages - and discuss the adjunctive role of diet. Together, we outline a potential research roadmap toward a potential cure for IBD.}, }
@article {pmid40540566, year = {2025}, author = {Woods, PH and Speth, DR and Laso-Pérez, R and Utter, DR and Ruff, SE and Orphan, VJ}, title = {Identification of key steps in the evolution of anaerobic methanotrophy in Candidatus Methanovorans (ANME-3) archaea.}, journal = {Science advances}, volume = {11}, number = {25}, pages = {eadq5232}, pmid = {40540566}, issn = {2375-2548}, mesh = {*Methane/metabolism ; Anaerobiosis ; Phylogeny ; *Evolution, Molecular ; Genome, Archaeal ; *Archaea/genetics/metabolism ; Metagenomics ; Gene Transfer, Horizontal ; }, abstract = {Despite their large environmental impact and multiple independent emergences, the processes leading to the evolution of anaerobic methanotrophic archaea (ANME) remain unclear. This work uses comparative metagenomics of a recently evolved but understudied ANME group, "Candidatus Methanovorans" (ANME-3), to identify evolutionary processes and innovations at work in ANME, which may be obscured in earlier evolved lineages. We identified horizontal transfer of hdrA homologs and convergent evolution in carbon and energy metabolic genes as potential early steps in Methanovorans evolution. We also identified the erosion of genes required for methylotrophic methanogenesis along with horizontal acquisition of multiheme cytochromes and other loci uniquely associated with ANME. The assembly and comparative analysis of multiple Methanovorans genomes offers important functional context for understanding the niche-defining metabolic differences between methane-oxidizing ANME and their methanogen relatives. Furthermore, this work illustrates the multiple evolutionary modes at play in the transition to a globally important metabolic niche.}, }
@article {pmid40539105, year = {2025}, author = {Zhang, Z and Shi, Z and Zheng, L and Zhang, H}, title = {Remediation of acetochlor-contaminated maize field soil using Serratia odorifera AC-1 fertilizer: effects on soil microbial communities.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1510157}, pmid = {40539105}, issn = {1664-302X}, abstract = {Acetochlor is a chloroacetamide herbicide that is widely applied in corn fields. Nevertheless, the long-term usage of acetochlor in the soil leads to residues, which severely affect the germination of corn seeds and the growth of seedlings, and even exert an influence on the soil microbial community. Microbial degradation of acetochlor is the principal approach for restoring the soil microbial ecology. In this study, the Serratia odorifera AC-1 strain was isolated and identified from the soil for the degradation of residual acetochlor in the soil. To enhance the degradation efficiency, a solid microbial agent was prepared by using activated carbon as a carrier and the AC-1 strain at a 1:1 ratio and applied to the soil for degradation and remediation experiments. The content of the microbial cells in the solid microbial agent was 1.49 × 106 CFU/g after 120 days of preparation. The application of the AC-1 solid microbial agent significantly influenced the relative abundance of soil microbial communities (Actinobacteria, Firmicutes, and Proteobacteria), increasing the diversity of bacterial populations in the soil. The experimental results indicated that after the application of the AC-1 solid microbial agent, the plant height, stem diameter, and photosynthetic efficiency of corn seedlings under acetochlor stress were significantly elevated. When the application rate of the AC-1 solid microbial agent was 5.00 mg/kg, the stem diameter of corn increased by 56.4% compared with the control group. When the acetochlor concentration in the soil was 6.65 mg/kg, the DT50 value of the AC-1 solid microbial agent was 2.28 days. This study clarified the degradation mechanism and remediation capacity of the Serratia odorifera AC-1 strain in acetochlor-contaminated soil and proposed a new strategy to improve the stability and degradation efficiency of the microbial strain by optimizing the immobilization technology of the strain on activated carbon. This research provides a scientific basis and technical guidance for the future application of bioremediation technology in the field environment to remove pesticide residues, restore soil health, and enhance crop productivity.}, }
@article {pmid40537563, year = {2025}, author = {Embury, EL and Romero-Olivares, AL}, title = {Fungi Follow Flora, Bacteria Track the Seasons: A Tale of a Changing Landscape.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {68}, pmid = {40537563}, issn = {1432-184X}, support = {R16 GM146585/GM/NIGMS NIH HHS/United States ; 1R16GM146585//National Institute of General Medical Sciences of the National Institutes of Health/ ; 2312226//National Science Foundation Building Research Capacity in Biology/ ; }, mesh = {Seasons ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/isolation &amp; purification ; Desert Climate ; *Microbiota ; Ecosystem ; Grassland ; Soil/chemistry ; Biomass ; Biodiversity ; }, abstract = {Microbes play critical roles in dryland ecosystems, driving nutrient cycling, soil stability, and plant interactions. Despite their ecological importance, few studies have examined how microbial communities respond to vegetation changes in arid landscapes. In the northern extent of the Chihuahuan Desert, the encroachment of woody shrubs into grasslands has been occurring since the 1800s, largely driven by extensive livestock grazing and increased drought levels. In this study, we investigated how microbial communities respond to both biotic (i.e., vegetation) and abiotic (i.e., seasonality) factors, how they assemble in a changing landscape, and which taxa may be particularly responsive to shrub encroachment or even facilitating this transformation. We assessed microbial communities using soil surface samples across five distinct seasonal periods in a grassland-to-shrubland gradient in the Jornada Experimental Range in the Chihuahuan Desert through the use of phospholipid fatty-acid analysis and DNA metabarcoding techniques. Our findings reveal that bacterial and fungal biomass are significantly influenced by seasonal changes, with strong correlations to humidity and temperature fluctuations. We also found that fungal community assembly and diversity were highly impacted by vegetation whereas seasons were more impactful on bacteria. Our results support the idea that microbes may be playing a crucial role in facilitating the grassland-to-shrubland transition. Overall, our study highlights the complex interactions between microbial communities and biotic and abiotic factors in dryland systems. These findings are essential for understanding the future of dryland ecosystems undergoing shrub encroachment and provide a critical foundation for guiding restoration efforts, particularly those looking to incorporate microbial-mediated solutions.}, }
@article {pmid40536564, year = {2025}, author = {Parret, L and Simoens, K and Horemans, B and De Vrieze, J and Smets, I}, title = {Establishing a co-culture aggregate of N-cycle bacteria to elucidate flocculation in biological wastewater treatment.}, journal = {Applied microbiology and biotechnology}, volume = {109}, number = {1}, pages = {149}, pmid = {40536564}, issn = {1432-0614}, support = {C24/18/043//KU Leuven/ ; FWO-G032321N//Fonds Wetenschappelijk Onderzoek/ ; FWO- 1191022N//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {Flocculation ; *Wastewater/microbiology ; Coculture Techniques/methods ; Sewage/microbiology ; *Bacteria/metabolism/growth &amp; development ; Bioreactors/microbiology ; Alginates ; *Water Purification/methods ; *Nitrogen/metabolism ; Nitrification ; Microbial Consortia ; }, abstract = {Biological flocculation is a complex phenomenon that is often treated as a black box. As a result, flocculation problems are usually remediated without knowledge of the exact causes. We show that it is feasible to exploit a model (N-cycle) consortium with reduced complexity to fundamentally study bioflocculation. Strong nitrifier microcolonies were formed during oxic/anoxic cycles in sequencing batch reactors, using alginate entrapment as a cell retention system. After the release of these aggregates into suspension, macroclusters with flocs of the denitrifier were observed. These results suggest that a living model of a full-scale activated sludge floc can be built through the use of this bottom-up approach. By eliminating shifts in the microbial community, the applied experimental conditions have a more direct effect on the observations. Key Points ∙ Studying flocculation with a model consortium is feasible ∙ Alginate entrapment leads to strong microcolony formation of nitrifiers ∙ FISH by itself is not suitable to study aggregation of a coculture.}, }
@article {pmid40536143, year = {2025}, author = {Timmis, K and Williams, P and Karahan, ZC and López-García, P and Rainey, P and Chavarria, M and Greening, C and Steward, K and Hallsworth, JE and Pereira, CS and Giraldo, R and Verstraete, W and Jonjić, S and Ramos, JL and Nunes, O and Ventosa, A and Armstrong, R and Sessitsch, A and Ron, E and Wang, H}, title = {Journals Operating Predatory Practices Are Systematically Eroding the Science Ethos: A Gate and Code Strategy to Minimise Their Operating Space and Restore Research Best Practice.}, journal = {Microbial biotechnology}, volume = {18}, number = {6}, pages = {e70180}, pmid = {40536143}, issn = {1751-7915}, mesh = {*Periodicals as Topic/standards ; Peer Review, Research/standards ; Humans ; }, abstract = {Scientific research seeks to extend knowledge and understanding, an activity that perhaps more than any other advances society and humanity. In essence, it is the search for truth. But, because it seeks new knowledge, there is little or no benchmark for appraisal of the plausibility or validity of the immediate conclusions drawn from new information gained, no instant confirmation. For this and other reasons, the science ethos requires the highest level of rigour to ensure the highest level of probability that new findings are true, or at least the most plausible under the prevailing circumstances and state of knowledge. Research is only as good as its degree of rigour. Rigour comes through intensive and comprehensive scientific training and mentoring that teaches critical and agnostic evaluation of new results, self-scrutiny and self-criticism. Additional rigour comes via independent scrutiny and validation: peer review of results and interpretations submitted as publications, and peer repetition of key experiments. However, the current proliferation of publication vehicles whose business model is based on maximisation of papers published, and the revenue stream of article processing charges (APCs) they generate, is promoting an insidious degradation of rigour and quality standards of reviewing-editing practices. Such predatory practices result in the systematic degradation of research quality and its "truthfulness". Moreover, they undermine the science ethos and threaten to create a new generation of scientists that lack this ethos. These trends will inevitably progressively erode public trust in scientists and the research ecosystem. This Editorial is a call for action to all actors, in particular leaders, in scientific research to oppose predatory practices in science dissemination-to restrict the operational space of those responsible for such practices-in order to restore and maintain research rigour and the science ethos and to prevent a downward spiral of research quality. It proposes two linked actionable solutions to the problem, one for the "pull" element of predatory practices and one for the "push" element of research ecosystem management practices, especially those promoting the publish or perish mentality, that drive authors to publish in journals with predatory practices. To counter the "pull", we propose a solution based on the principle of prevention, rather than cure, and list a number of essential policy decisions and actions that should be taken at all levels of the science chain/cloud to achieve this. A central plank of the concept is journal accreditation, without which a journal would be ineligible for payment of APCs from public funds. For accreditation, a journal would need to convincingly demonstrate adoption of a prescribed journal code of conduct. Ideally, accreditation would also be required for inclusion in journal indexing and ranking services and bibliographic databases. To counter the "push", we propose a top-down imposition of a cultural change in science management that ensures merit-based success of scientists and their careers, research best practice, improved education and mentoring of younger scientists in the science ethos and greater support of them in their careers. This must include explicit recognition of the crucial role of peer reviewing for the good health of the research enterprise, its incentivisation and appropriate appreciation of the time and effort involved. To orchestrate this change, we propose the creation of a multi-stakeholder alliance whose brief is to develop the framework and implementation strategy for changes in the research ecosystem. This Editorial also exhorts all actors to embrace the principle of publish less, publish better and to use public funding provided by tax revenues more effectively to perpetually raise the bar of science quality, dissemination and potential to advance humanity.}, }
@article {pmid40534981, year = {2025}, author = {Hodgson, RJ and Cando-Dumancela, C and Liddicoat, C and Ramesh, SA and Edwards, RA and Breed, MF}, title = {Strong Host Modulation of Rhizosphere-to-Endosphere Microbial Colonisation in Natural Populations of the Pan-Palaeotropical Keystone Grass Species, Themeda triandra.}, journal = {Ecology and evolution}, volume = {15}, number = {6}, pages = {e71595}, pmid = {40534981}, issn = {2045-7758}, abstract = {Soil microbiota can colonise plant roots through a two-step selection process, involving recruitment of microbiota first from bulk soil into plant rhizospheres, then into root endospheres. This process is poorly understood in all but a few model species (e.g., Arabidopsis), which is surprising given its fundamental role in plant and soil ecology. Here, we examined the microbial community assembly processes across the rhizospheres and root endospheres in eight natural populations of the pan-palaeotropical C4 grass, Themeda triandra, in southern Australia. Using a space-for-time substitution approach, we assessed whether bacterial root colonisation patterns conformed to the two-step model and tested whether community assembly was driven more by deterministic or stochastic processes. Our results show that the two-step selection process shaped bacterial recruitment dynamics across these natural T. triandra populations, and we provide clear evidence that host plants influence microbial assembly via deterministic pressures that produce strong community convergence within endospheres. These findings highlight the central role of host filtering in shaping a conserved 'core' endosphere microbiome. However, limited understanding of these endosphere communities constrains efforts to harness these important relationships to, for example, improve plant propagation and revegetation practices.}, }
@article {pmid40533683, year = {2025}, author = {Rios-Reyes, A and Gonzalez-Lozano, KJ and Cabral-Miramontes, JP and Hernandez-Gonzalez, JJ and Rios-Sosa, A and Alvarez-Gutierrez, PE and Mireles-Torres, SP and Batista-García, RA and Arechiga-Carvajal, ET}, title = {Exploration of Plant and Microbial Life at "El Chichonal" Volcano with a Sustainable Agriculture Prospection.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {67}, pmid = {40533683}, issn = {1432-184X}, support = {700634//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; 2055419//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; 1081508//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; 315114//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; 252373/SEP-CONACYT//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; CBF2023-2024-3120//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; }, mesh = {*Soil Microbiology ; *Bacteria/classification/isolation &amp; purification/genetics/metabolism ; *Fungi/isolation &amp; purification/classification/genetics ; Agriculture ; Soil/chemistry ; *Volcanic Eruptions ; Bacillus cereus/isolation &amp; purification/genetics ; Plant Roots/microbiology ; Microbiota ; }, abstract = {Active volcanic environments represent extreme habitats with underexplored potential for microbial bioprospecting. This study aimed to characterize pioneer vegetation and associated microbial diversity in the crater of "El Chichonal" volcano, with an emphasis on their potential applications in sustainable agriculture. A physicochemical analysis of the soil was performed, identifying acidic and nutrient-poor conditions. Three pioneer plant species were described: Tibouchina longifolia (dominant) and Poaceae spp. (co-dominant), and Palhinhaea cernua (non-dominant). A total of 311 microorganisms were predominantly bacteria, were isolated from soil, root, stem, and water samples. Bacillus cereus and Priestia megaterium were molecularly identified, and in vitro assays demonstrated their ability to fix nitrogen, produce auxins, and antagonize fungal pathogens (Alternaria solani, Botrytis cinerea, and Colletotrichum gloeosporioides). These results suggest that microorganisms adapted to extreme volcanic environments could be promising sources of plant growth-promoting bacteria (PGPB) with application in biological control.}, }
@article {pmid40533475, year = {2025}, author = {Wollrab, S and Schmidt, SR and Woodhouse, J and Kasprzak, P and Berger, SA and Beyer, U and Bodenlos, M and Dalchow, J and Degebrodt, M and Ganzert, L and Gonsiorczyk, T and Huth, E and Kiel, C and Küchler, L and Krienitz, L and Lentz, M and Mach, E and Mallok, U and Nejstgaard, JC and Papke, M and Penske, A and Pinnow, S and Roßberg, R and Ronneberger, D and Sachtleben, M and Scheffler, A and Grossart, HP and Casper, P and Gessner, MO and Koschel, R}, title = {Fifty years of limnological data on Lake Stechlin, a temperate clearwater lake.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1028}, pmid = {40533475}, issn = {2052-4463}, abstract = {We present 50 years of monitoring data on water quality of Lake Stechlin, a deep, dimictic hardwater lake in northeastern Germany known for its exceptionally clear water. Although located in a forested catchment, the lake has undergone major changes in recent decades, including a period of massive heating of surface water when receiving cooling water from a nearby nuclear power plant (1966-1990), accompanied by a greatly shortened water residence time from more than 40 years to less than 300 days. These changes are superimposed by a long-term trend of surface water warming and a concomitant decrease in winter ice cover. Total phosphorus concentrations have quadrupled since 2010 and zones of deep-water oxygen depletion have greatly expanded. The presented dataset covers basic water-chemical and physical records taken at monthly to fortnightly intervals from 1970 to 2020, documenting limnological changes during that period. Furthermore, it serves as a valuable basis to assess and project potential consequences of climate change and other types of environmental change on deep clearwater lakes in temperate climates.}, }
@article {pmid40531665, year = {2025}, author = {Phithakrotchanakoon, C and Kitikhun, S and Siriarchawatana, P and Charoenyingcharoen, P and Jeennor, S and Nilsakha, T and Chanpet, A and Vorajinda, T and Mayteeworakoon, S and Yukphan, P and Ingsriswang, S}, title = {Flavobacterium mekongense sp. nov., isolated from the Mekong River in Thailand.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {75}, number = {6}, pages = {}, doi = {10.1099/ijsem.0.006815}, pmid = {40531665}, issn = {1466-5034}, mesh = {Thailand ; *Flavobacterium/classification/genetics/isolation &amp; purification ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Rivers/microbiology ; Fatty Acids/chemistry/analysis ; DNA, Bacterial/genetics ; Base Composition ; Bacterial Typing Techniques ; Sequence Analysis, DNA ; Vitamin K 2/analogs &amp; derivatives/chemistry/analysis ; Nucleic Acid Hybridization ; Genome, Bacterial ; Phospholipids/analysis/chemistry ; *Water Microbiology ; }, abstract = {Two Gram-stain-negative, aerobic, non-motile, non-gliding, rod-shaped bacterial strains, designated as TBRC 19031[T] and TBRC 19032, were isolated from water samples collected from the Mekong River, Thailand. Strain TBRC 19031[T] was obtained from Chiang Saen in the upstream section near the borders with China and Myanmar, while TBRC 19032 originated from Khong Chiam, in the downstream section where the river exits Thailand. Colonies of both strains were circular, smooth and deep yellow on Reasoner's 2A agar and did not produce flexirubin-type pigments. Phylogenetic analysis with 16S rRNA gene sequences placed both strains within the genus Flavobacterium, showing the highest sequence similarity to Flavobacterium cheonhonense ARSA-15[T] (98.29% for TBRC 19031[T] and 98.22% for TBRC 19032). However, whole-genome comparisons between the strains and F. cheonhonense ARSA-15[T] revealed average nt identity (89.39% and 89.29%), average aa identity (92.84% and 92.95%) and digital DNA-DNA hybridization (35.00% and 34.70%). The predominant fatty acids were iso-C15:1, iso-C15:0 and iso-C15:0 3-OH, and menaquinone MK-6 was the major respiratory quinone. The major polar lipids of both strains included phosphatidylethanolamine, steryl ester and diacylglycerol. The genome sizes were 3.02 and 3.04 Mbp, with G+C contents of 38.3% and 38.2% for TBRC 19031[T] and TBRC 19032, respectively. Comparative genomic analyses revealed the absence of genes involved in sulphate reduction and denitrification pathways and the presence of a gene encoding phosphatidylinositol synthase, distinguishing them from other Flavobacterium within the clade. Ecological profiling using public metagenomic datasets showed that both strains were associated with lotic freshwater environments. This study not only introduces Flavobacterium mekongense sp. nov. as a new species but also provides broader insights into the ecology, metabolism and environmental distribution of freshwater Flavobacterium. The genomic features identified here offer promising leads for future studies in microbial ecology, comparative genomics and functional gene mining in aquatic ecosystems. The type strain is TBRC 19031[T] (TBRC 19031[T]=NBRC 117006[T]).}, }
@article {pmid40531656, year = {2025}, author = {Bou Orm, E and Mukherjee, S and Rifa, E and Créach, A and Grec, S and Bayle, S and Benezet, JC and Bergeret, A and Malhautier, L}, title = {Enhancing Biodiversity-Function Relationships in Field Retting: Towards Key Microbial Indicators for Retting Control.}, journal = {Environmental microbiology reports}, volume = {17}, number = {3}, pages = {e70102}, pmid = {40531656}, issn = {1758-2229}, mesh = {*Biodiversity ; *Fungi/classification/genetics/enzymology/isolation &amp; purification/metabolism ; *Bacteria/classification/genetics/enzymology/isolation &amp; purification/metabolism ; *Cannabis/microbiology/metabolism ; Pectins/metabolism ; Glycoside Hydrolases/metabolism ; Microbiota ; }, abstract = {Hemp field retting is a bioprocess that facilitates fibre extraction by degrading pectin and other matrix components surrounding fibre bundles. However, traditional methods rely on empirical practices, often resulting in inconsistent fibre quality. This study investigates the biodiversity-function relationship in the hemp retting ecosystem to identify microbial and enzymatic indicators for improved process control. Over six weeks of field retting, we monitored bacterial and fungal community dynamics using high-throughput sequencing and assessed enzymatic activity profiles. Our results revealed a sequential enzymatic pattern: pectinases (e.g., polygalacturonase) dominated early stages, followed by hemicellulases (β-xylosidase, β-galactosidase), and later cellulases. These enzymatic shifts were reflected in the changes in microbial community composition, with pectinolytic bacteria (e.g., Proteobacteria) dominating the initial phases and cellulolytic fungi (e.g., Ascomycota) becoming more prevalent later. Our results identified specific microbial taxa correlated with optimal retting, suggesting their potential as bioindicators for monitoring retting. Specifically, key bacterial genera such as Pseudomonas and Sphingomonas, and fungal genera like Cladosporium, were associated with distinct enzymatic profiles. Our findings offer new insights into the microbial ecology of retting, providing both microbial and enzymatic indicators that could inform the development of monitoring strategies for process control, ultimately contributing to more consistent hemp fibre production.}, }
@article {pmid40530365, year = {2025}, author = {Akdur Öztürk, E and Guadano-Procesi, I and Figueiredo, AM and Godfrey, A and Gentekaki, E and Tsaousis, AD and Carmena, D and Dogruman-Al, F}, title = {A protocol for mapping Blastocystis epidemiology and diagnostics from One Health perspective.}, journal = {Open research Europe}, volume = {5}, number = {}, pages = {133}, pmid = {40530365}, issn = {2732-5121}, abstract = {Blastocystis is a globally prevalent gut protist colonising over a billion people worldwide, yet its epidemiology, transmission dynamics, and clinical significance remain underexplored. This protocol represents the first step of a large-scale effort to map Blastocystis epidemiology and diagnostic practices across Europe through the COST Action CA21105: Blastocystis under One Health. By assessing diagnostic methodologies across clinical, veterinary, and environmental sectors, this work sets the foundation for future research and standardisation. Here, we highlight key findings, challenges, and a roadmap for improving Blastocystis detection, ultimately influencing global health policies and microbial ecology studies.}, }
@article {pmid40530126, year = {2025}, author = {Wu, WJ and Wang, K and Yang, YV and Yang, X}, title = {Identification of neuronal synapse-related signatures and potential therapeutic drugs in colorectal cancer based on machine learning algorithms and molecular docking.}, journal = {Translational cancer research}, volume = {14}, number = {5}, pages = {2737-2757}, pmid = {40530126}, issn = {2219-6803}, abstract = {BACKGROUND: Nervous system-cancer interactions can regulate tumorigenesis, invasion, and metastasis. However, specific biomarkers for targeting neuron synapse in colorectal cancer (CRC) remain unexplored. This study aims to develop a neuronal synapse-related signature (NSRS) to predict survival in CRC patients, identify potential therapeutic drugs, and explore its clinical applications.<br><br>METHODS: We collected neuronal synapse genes (NSGs) from the Molecular Signatures Database (MSigDB) and published mass spectrometry data. Using weighted gene co-expression network analysis (WGCNA) and least absolute shrinkage and selection operator Cox regression (LASSO-Cox), we identified prognostic NSGs and constructed a NSRS through multivariate Cox regression. Functional enrichment analysis revealed the molecular characteristics of NSRS subgroups. Additionally, xCell and ESTIMATE algorithms quantified the abundance of 54 cell subtypes and assessed the tumor immune microenvironment (TIME) of the two NSRS subgroups. Finally, drug prediction and molecular docking identified candidate drugs with therapeutic potential.<br><br>RESULTS: Seven key prognostic NSGs were identified, and an independent, stable NSRS model was constructed. Kaplan-Meier survival curves indicated that the high NSRS group had poorer outcomes (log-rank test, P<0.05). Functional enrichment analysis revealed significant enrichment of epithelial-mesenchymal transition, hypoxia, and inflammation features in the high NSRS group. xCell and ESTIMATE analyses showed a more complex TIME and lower tumor purity in the high NSRS group, highlighting the role of neuro-tumor interactions in CRC. Drug prediction and molecular docking suggested alprostadil, dihydroergocristine, and nocodazole as candidate drugs for CRC treatment.<br><br>CONCLUSIONS: This is the first study to develop neuron synapse-related biomarkers from the perspective of neuron-cancer interactions using machine learning. We constructed a robust NSRS model and identified candidate drugs targeting prognostic NSGs, providing new insights into CRC prognosis and treatment.}, }
@article {pmid40529576, year = {2025}, author = {Sanz-López, C and Amato, M and Torrent, D and Borrego, M and Anza, M and Bibiso, M and Grijalva-Vallejos, N and Vilanova, C and Porcar, M and Pascual, J}, title = {Microbial ecology of selected traditional Ethiopian fermented products.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1570914}, pmid = {40529576}, issn = {1664-302X}, abstract = {The consumption of traditional fermented foods and beverages plays an important role in the diet of Ethiopia, providing significant nutritional and health benefits to the local population. The present study aimed to investigate the microbial ecology and diversity of nine types of fermented products. These include two foods (Kotcho and Injera), one food condiment (Datta), and six beverages (Tej, Tella, Cheka, Kinito, Borde, and Shamita). A combination of metataxonomic and culturomic approaches was used to achieve a comprehensive characterization of the bacterial communities, together with a thorough physicochemical characterization of the fermented products. This study provides one of the most comprehensive microbial characterizations of a wide selection of Ethiopian fermented products, highlighting that some bacterial species involved in the fermentation processes could contribute to the safety and nutritional quality of fermented foods and, based on previous studies, could also play a key role in enhancing their potential probiotic properties.}, }
@article {pmid40529573, year = {2025}, author = {Ma, R and Zhang, Z and Wang, J and Han, Y and Li, K and Hou, M and Lei, Y and Xiong, S and Yang, B and Zhi, X and Jiao, Y and Lin, T and Zhang, S and Li, Y}, title = {Mitigating gaseous nitrogen emissions in cotton fields through green manure and reduced nitrogen fertilization.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1615142}, pmid = {40529573}, issn = {1664-302X}, abstract = {Integrating green manure with reduced nitrogen (N) fertilization is a promising strategy to mitigate N emissions in intensive cotton cultivation, however, the underlying mechanisms remain poorly understood. This study investigated the effects of three green manure incorporation patterns-no green manure (NG), Orychophragmus violaceus (OVG), and Vicia villosa (VVG)-combined with four N reduction levels (100, 50, 25%, and conventional) on gaseous N emissions (NH3 and N2O), soil physicochemical properties, and bacterial community characteristics using a cotton field experiment in the Yellow River Basin. Results showed that OVG incorporation with 25% N reduction (N2 treatment) significantly reduced total gaseous N emissions by 36.07% on average during the cotton growth period, reducing NH3 and N2O emissions by 13.31-54.11% and 32.25-68.77%, respectively, compared with N2 application without OVG. OVG application also increased the relative abundance of Proteobacteria (28.10%), enhanced heterogeneous selection in bacterial community assembly (200%), and increased the complexity of co-occurrence networks, compared with NG. Compared with conventional N fertilization (N3 treatment), ≥50% N reduction significantly lowered NH3 (>25.51%) and N2O (>32.76%) emissions, reduced the relative abundance of Acidobacteria (-20.23%), simplified co-occurrence networks, and increased homogeneous selection in bacterial assembly (50.00%). Integrating green manure with 25% N reduction substantially reduced gaseous N emissions, which was associated with the enhanced microbial biomass carbon (MBC) and facilitated recruitment of key bacterial taxa (e.g., Sphingosinicella, Azohydromonas, Phototrophicus) within the microbial co-occurrence network. These findings provide insight into how green manure application coupled with N reduction can mitigate gaseous N losses and reshape soil microbial ecology, offering a theoretical basis for sustainable nutrient management during cotton production.}, }
@article {pmid40528722, year = {2025}, author = {Gao, D and Guo, X and Yang, Z and Li, H and Chen, Y and Yang, X and Song, L and Yang, X and Yang, J and Zhou, C}, title = {Effects of Sibiraea laevigate maxim polysaccharides on intestinal flora in immunosuppressed mice.}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.14433}, pmid = {40528722}, issn = {1097-0010}, support = {//The program of Science and Technology Department of Gansu Province (2024ZDPC001, 24YFFA026, 23CXGP0002)/ ; //The innovation Drive assistance project of Gansu for Science and Technology Association (GXH20240328-3)/ ; 2023QB-001//The Young Doctor Fund of Gansu Province/ ; //The youth science and technology talent innovation project of Lanzhou (2023-QN-69)./ ; //The Fundamental Research Funds for the Central Universities of Northwest Minzu University (31920240125-01)./ ; 2024RCXM45//The key talent project of Gansu Province (2024)/ ; }, abstract = {BACKGROUND: The intestinal microbial ecology plays a significant role in maintaining normal physiological function processes and significantly influences the immune system. However, research regarding its effects on gut flora and in vivo immunomodulation is insufficient.<br><br>RESULTS: In this study, cyclophosphamide was administered to mice to establish an immunosuppressed mouse model. The regulatory effects of Sibiraea laevigata maxim polysaccharides (SLMPs) on immunity and intestinal microbiota in the immunosuppressed mouse model were investigated. The results indicated that SLMPs could mitigate spleen and thymus damage, protect immune organs, increase the levels of leukocytes, lymphocytes, neutrophils and monocytes in mouse blood and upregulate the levels of IL-2, IFN-&#x3b3;, TNF-&#x3b1; and IgA in mouse serum. Furthermore, SLMPs can restore intestinal microbial imbalance and enhance the diversity of gut microorganisms in immunosuppressed mice.<br><br>CONCLUSION: The findings from this study indicated that SLMPs could enhance immunity and improve the structure and abundance of intestinal flora in mice. These results provide a theoretical basis for the further development and utilization of SLMPs in immunomodulatory adjuvants and functional foods, thereby promoting their application in these fields. &#xa9; 2025 Society of Chemical Industry.}, }
@article {pmid40528265, year = {2025}, author = {Selak, L and Meier, DV and Marinović, M and Čačković, A and Kajan, K and Pjevac, P and Orlić, S}, title = {Salinization alters microbial methane cycling in freshwater sediments.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {73}, pmid = {40528265}, issn = {2524-6372}, support = {DOK-2018-09-1550//Hrvatska Zaklada za Znanost/ ; IP-2020-02-9021//Hrvatska Zaklada za Znanost/ ; }, abstract = {Climate change-induced salinization poses a global threat to freshwater ecosystems and challenges microbial communities driving crucial biogeochemical processes, particularly methane cycling. This study examined the impact of salinization and the accompanying sulfate concentration increases on microbial community dynamics and methane cycling in coastal freshwater lake sediments. We show that sulfate enrichment in sediment profiles enables the proliferation of distinct sulfate-reducing bacteria (SRB) that reshape microbial niches by competing with methanogens and promoting sulfate-dependent anaerobic oxidation of methane (AOM). Freshwater SRB clusters, which compete with some methanogens for substrates but also degrade organic compounds into methanogenesis precursors, are replaced by the SEEP-SRB groups that form syntrophic relationships with ANME-1 in salinized sediments. As seawater intrudes and reshapes microbial communities, a methane pocket forms that escapes both aerobic and anaerobic oxidation. Underneath this methane pocket, SRB play a key role in enabling sulfate-dependent AOM, facilitating methane consumption at higher sediment depths. While all microorganisms demonstrated some physiological adaptability potential to elevated osmotic stress, SRB exhibited the highest resilience to increased salinity. These findings highlight how salinization-induced geochemical shifts, particularly sulfate enrichment, directly affect microbial community assembly and impact methane cycling in coastal freshwater ecosystems.}, }
@article {pmid40528093, year = {2025}, author = {Goswami, R and Sarkar, A and Bandyopadhyay, B and Sadhukhan, S}, title = {Exploring microbial diversity in the Kharasinpur hot spring of West Bengal, India.}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {608}, pmid = {40528093}, issn = {1573-4978}, mesh = {*Hot Springs/microbiology ; India ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/isolation &amp; purification/classification ; Phylogeny ; Biodiversity ; Water Microbiology ; Microbiota/genetics ; Hydrogen-Ion Concentration ; Iron/analysis ; }, abstract = {BACKGROUND: Hot springs are natural geothermal environments that harbour thermophilic microorganisms with significant biotechnological potential. Despite extensive studies on many Indian hot springs, Kharasinpur Hot Spring in West Bengal remains totally unexplored in terms of microbial diversity and physicochemical properties.<br><br>METHODS: A total of seven bacterial isolates were obtained from water samples collected at the Kharasinpur Hot Spring. These isolates underwent morphological, physiological, biochemical, and molecular characterization through 16S rRNA gene sequencing. Water samples were analyzed for physicochemical parameters such as temperature, pH, total hardness, iron concentration, salt content, and total dissolved solids (TDS).<br><br>RESULTS: The water temperature was recorded at 65&#xa0;&#xb0;C with a slightly alkaline pH (7.24). The 16S rRNA analysis identified isolates belonging to the phyla Pseudomonadota (e.g., Pseudomonas sp., Hydrogenophaga sp.) and Bacillota (e.g., Staphylococcus sp., Neobacillus sp.). The high iron content in the hot spring water was notable and rendered it unsafe for direct human consumption.<br><br>CONCLUSION: This study provides novel insights into the microbial diversity and physicochemical characteristics of a relatively unstudied Indian hot spring. The findings contribute to broader research efforts on hot spring ecosystems in India, enhancing our understanding of their microbial ecology and potential health implications.}, }
@article {pmid40528049, year = {2025}, author = {Blair, EM and Margalith, NJ and O'Malley, MA}, title = {Microbial Enrichments Contribute to Characterization Of Desert Tortoise Gut Microbiota.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {66}, pmid = {40528049}, issn = {1432-184X}, support = {DE-SC0020420//U.S. Department of Energy/ ; DE-SC0020420//U.S. Department of Energy/ ; DE-SC0020420//U.S. Department of Energy/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Turtles/microbiology ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Desert Climate ; Fatty Acids, Volatile/metabolism ; Lignin/metabolism ; DNA, Bacterial/genetics ; Biomass ; }, abstract = {Desert tortoises play ecologically significant roles, including plant seed dispersal and mineral cycling, and yet little is known about microbial members that are critical to their gut and overall health. Tortoises consume recalcitrant plant material, which their gut microbiota degrades and converts into usable metabolites and nutrients for the tortoise. Findings from tortoise gut microbiomes may translate well into biotechnological applications as these microbes have evolved to efficiently degrade recalcitrant substrates and generate useful products. In this study, we cultivated microbial communities from desert tortoise fecal samples following a targeted anaerobic enrichment for microbes involved in deconstruction and utilization of plant biomass. We employed 16S rRNA amplicon sequencing to compare cultivated communities to initial fecal source material and found high abundances of Firmicutes and Bacteroidota typically associated with biomass deconstruction in all cultivated samples. Significantly decreased microbial diversity was observed in the cultivated microbial communities, yet several key taxa thrived in lignocellulose enrichments, including Lachnospiraceae and Enterococcus. Additionally, cultivated communities produced short-chain fatty acids under anaerobic conditions, and their growth and metabolic output provide evidence of their viability in the initial fecal communities. Overall, this study adds to the limited understanding of reptilian herbivore microbiota, and offers a path towards biotechnological translation based on the ability of the cultivated communities to convert lignocellulose directly to acetate, propionate, and butyrate.}, }
@article {pmid40527958, year = {2025}, author = {Jendrusch, MA and Yang, ALJ and Cacace, E and Bobonis, J and Voogdt, CGP and Kaspar, S and Schweimer, K and Perez-Borrajero, C and Lapouge, K and Scheurich, J and Remans, K and Hennig, J and Typas, A and Korbel, JO and Sadiq, SK}, title = {AlphaDesign: a de novo protein design framework based on AlphaFold.}, journal = {Molecular systems biology}, volume = {}, number = {}, pages = {}, pmid = {40527958}, issn = {1744-4292}, support = {de.NBI project: 031A537B//Bundesministerium f&#xfc;r Bildung und Forschung (BMBF)/ ; contract 95826//Volkswagen Foundation (VolkswagenStiftung)/ ; 93874-1//Volkswagen Foundation (VolkswagenStiftung)/ ; COFUND grant nr. 847543//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; }, abstract = {De novo protein design is of fundamental interest to synthetic biology, with a plethora of computational methods of various degrees of generality developed in recent years. Here, we introduce AlphaDesign, a hallucination-based computational framework for de novo protein design developed with maximum generality and usability in mind, which combines AlphaFold with autoregressive diffusion models to enable rapid generation and computational validation of proteins with controllable interactions, conformations and oligomeric state without the requirement for class-dependent model re-training or fine-tuning. We apply our framework to design and systematically validate in vivo active inhibitors of a family of bacterial phage defense systems with toxic effectors called retrons, paving the way towards efficient, rational design of novel proteins as biologics.}, }
@article {pmid40525968, year = {2025}, author = {Lopez-Echartea, E and Dusek, N and Misialek, M and Mahmud-Un-Nabi, MA and Williamson, R and Marathe, K and Geddes, BA}, title = {Culturomics from field-grown crop plants using dilution to extinction, two-step library preparation and amplicon sequencing.}, journal = {Microbiology (Reading, England)}, volume = {171}, number = {6}, pages = {}, pmid = {40525968}, issn = {1465-2080}, mesh = {RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification/growth &amp; development ; *Zea mays/microbiology ; *Microbiota/genetics ; Phylogeny ; DNA, Bacterial/genetics ; Plant Roots/microbiology ; *Pisum sativum/microbiology ; *Crops, Agricultural/microbiology ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; Gene Library ; Soil Microbiology ; }, abstract = {Culturomics approaches have advanced microbial research by enabling the high-throughput isolation and characterization of a broader range of bacterial taxa, including some previously considered unculturable. Here, we present the testing and optimization of a protocol for isolating and identifying hundreds of cultivable microbes from field-grown plants. This protocol was tested and optimized using the root microbiomes of field-grown corn and pea plants under varying environmental conditions in ND, USA. By employing dilution-to-extinction culturing and a two-step barcoding PCR strategy targeting the V4 region of the 16S rRNA gene, we identified over 200 unique bacterial isolates. The optimized bioinformatic pipeline, built around the DADA2 package, ensured accurate amplicon sequence variant detection and taxonomy assignment. The resulting bacterial isolates span diverse phylogenetic groups, including plant-associated taxa known for promoting plant growth and mitigating stress. Our findings highlight the value of culturomics in generating microbial collections for synthetic community design and advancing plant-microbe interaction research. The protocol's scalability, cost-effectiveness and robust performance demonstrate its potential for widespread application in agricultural microbiome studies.}, }
@article {pmid40525847, year = {2025}, author = {Kroos, L and Wall, D and Islam, ST and Whitworth, DE and Muñoz-Dorado, J and Higgs, PI and Singer, M and Mauriello, EM and Treuner-Lange, A and Søgaard-Andersen, L and Kaimer, C and Elías-Arnanz, M and Stojković, EA and Müller, R and Volz, C and Velicer, GJ and Nan, B}, title = {Milestones in the development of Myxococcus xanthus as a model multicellular bacterium.}, journal = {Journal of bacteriology}, volume = {207}, number = {7}, pages = {e0007125}, pmid = {40525847}, issn = {1098-5530}, mesh = {*Myxococcus xanthus/physiology/genetics/growth &amp; development/cytology ; History, 20th Century ; History, 21st Century ; Models, Biological ; }, abstract = {From the humblest of beginnings (i.e. a pile of dry cow dung) over 80 years ago, the Gram-negative bacterium Myxococcus xanthus has emerged as a premier model system for studying diverse fields of bacteriology, including multicellular development, sporulation, motility, cell-envelope biogenesis, spatiotemporal regulation, signaling, photoreception, kin recognition, social evolution, and predation. As the flagship representative of myxobacteria found in varied terrestrial and aquatic environments, M. xanthus research has evolved into a collaborative global effort, as reflected by the contributions to this article. In celebration of the upcoming 50th anniversary of the International Conference on the Biology of Myxobacteria, this review highlights the historical and ongoing contributions of M. xanthus as a multifaceted model bacterium.}, }
@article {pmid40524759, year = {2025}, author = {Lacerda, AL and Proietti, MC and Kessler, F and Mendes, CR and Secchi, ER and Taylor, JD}, title = {Oceanic regions shape the composition of the Antarctic plastisphere.}, journal = {Communications earth &amp; environment}, volume = {6}, number = {1}, pages = {462}, pmid = {40524759}, issn = {2662-4435}, abstract = {Antarctica, once considered pristine, is increasingly threatened by plastic pollution, with debris found in its waters, sediments, sea ice, and biota. Here, we provide a comprehensive molecular survey of both prokaryotic and eukaryotic diversity on plastics around the Antarctic Peninsula, addressing a gap in existing research. Using eDNA metabarcoding, we identified diverse communities, with Pseudomonadota and Bacteroidota dominating prokaryotic communities, while Gyrista (mostly diatoms), Fungi and Arthropods were prevalent among eukaryotes. Geographic location significantly influenced community composition, with differences between the Bransfield Strait and the Gerlache Strait/Bellingshausen Sea. Polymer type and plastic shape did not impact species richness or community structure. These findings offer new insights into the complexity of the Antarctic plastisphere, highlighting potential impacts on biodiversity, ecosystem functions, and the broader implications of marine plastic pollution.}, }
@article {pmid40524188, year = {2025}, author = {Perillo, VL and Nute, M and Sapoval, N and Curry, KD and Golia, L and Yin, Y and Ogilvie, HA and Nakhleh, L and Segarra, S and Bhaya, D and Cuadrado, DG and Treangen, TJ}, title = {A survey of computational approaches for characterizing microbial interactions in microbial mats.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {168}, pmid = {40524188}, issn = {1474-760X}, support = {EF-2126387//National Science Foundation/ ; BBSRC-NSF/BIO #1921429//National Science Foundation/ ; NSF#2125965//National Science Foundation/ ; PICT 2020-302//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; Pampa Azul A8 Programa "Investigaci&#xf3;n//Ministerio de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n/ ; Desarrollo e Innovaci&#xf3;n en Ciencias del Mar"//Ministerio de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n/ ; Proposal 503441//Joint Genome Institute/ ; proposal: 10.46936/10.25585/60001132//Joint Genome Institute/ ; }, mesh = {*Microbial Interactions ; *Computational Biology/methods ; *Microbiota ; Ecosystem ; Bacteria/genetics/metabolism ; }, abstract = {In this review, we use microbial mat communities as a general model system to highlight the strengths and limitations of current computational methods for analyzing interactions between members of microbial ecosystems. We describe the factors that make this environment have such a high degree of interaction, and we explore different categories of both laboratory and computational tools for studying these interactions. For each tool, we describe efforts to apply them to microbial mats in the past and, in the process, argue that genome-scale metabolic models have breakthrough potential for modeling microbial interactions in microbial mats.}, }
@article {pmid40523669, year = {2025}, author = {Prakash, O and Chauhan, A and Green, SJ}, title = {The Study of Microbial Physiology Under Microoxic Conditions Is Critical but Neglected.}, journal = {Environmental microbiology reports}, volume = {17}, number = {3}, pages = {e70108}, pmid = {40523669}, issn = {1758-2229}, support = {2200615//BioXFEL Science and Technology Center/ ; DE-FE0032198//DOE's University Training &amp; Research Program University Coal Research (UCR)/ ; 0000602538//The Department of Energy/ ; //Major Research Project (MJRP) intramural grant from Symbiosis International (Deemed University)/ ; 1901371//National Science Foundation/ ; 2200615//National Science Foundation/ ; W911NF2210145//Department of Defence contract/ ; }, mesh = {Anaerobiosis ; Aerobiosis ; *Oxygen/metabolism ; *Bacteria/metabolism/genetics/growth &amp; development ; Ecosystem ; *Bacterial Physiological Phenomena ; Humans ; }, abstract = {During the early evolution of life on Earth, the environment was largely free of molecular oxygen, and only anaerobic life existed. With the subsequent oxidation of oceans and the atmosphere, a wide range of environmental niches, ranging from anoxic to microoxic/hypoxic and oxic, developed. Despite this broad range of natural environments, microbiology as a field has focused on the physiology, metabolism, and genetics of aerobic microorganisms, with less attention paid to anaerobes and much less attention paid to microaerophiles. The disparity in studies between aerobic and anaerobic conditions is rampant in host-associated systems, particularly in human health, and studies of microorganisms in intermediate oxygen conditions between fully aerobic and fully anoxic conditions are exceedingly rare. Studies on the physiological behaviour, metabolism, growth response, and drug susceptibility patterns of commensal and pathogenic organisms are almost totally neglected in microoxic conditions. Furthermore, microorganisms from microaerobic and microoxic ecosystems have been less robustly explored in terms of physiology, growth, and metabolism. In this work, we highlight the importance of understanding the physiological and metabolic behaviours of microorganisms under hypoxic or microoxic conditions.}, }
@article {pmid40522148, year = {2025}, author = {Fejes, R and Séneca, J and Pjevac, P and Lutnik, M and Weisshaar, S and Pilat, N and Steiner, R and Wagner, KH and Woodman, RJ and Bondonno, CP and Hodgson, JM and Berry, D and Wolzt, M and Neubauer, O}, title = {Increased Nitrate Intake From Beetroot Juice Over 4 Weeks Changes the Composition of the Oral, But Not the Intestinal Microbiome.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e70156}, doi = {10.1002/mnfr.70156}, pmid = {40522148}, issn = {1613-4133}, support = {//Austrian Science Fund (FWF)/ ; KLI 858//Clinical Research (KLIF) program/ ; }, abstract = {Inorganic dietary nitrate, metabolized through an endogenous pathway involving nitrate reducing bacteria, improves cardiovascular health, but its effects on the oral and intestinal microbiomes of older adults with treated hypertension are unknown. Our study investigated the effects of nitrate from beetroot juice on the oral and intestinal microbiomes of this population. A randomized, double-blind, placebo-controlled crossover trial was conducted with 15 participants (age range: 56-71 years), who consumed nitrate-rich or nitrate-depleted (placebo) beetroot juice for 4 weeks. The oral microbiome analysis revealed an increase in Neisseria and a decrease in Veillonella relative abundance (for both, PERMANOVA p < 0.001), with no significant changes in the intestinal microbiome composition. Our findings suggest that an increased dietary nitrate intake from a vegetable source may selectively modulate the oral microbiome and promote an increased abundance of nitrate-reducing species, which was previously associated with improved cardiovascular health outcomes.}, }
@article {pmid40521244, year = {2025}, author = {Addo, M and Apaame, S and Ghanney, MA and Adu, HK and DeWitt, ME and Addo, SO}, title = {Hepatitis B Infection in Outpatients and Pregnant Women Visiting a Mission Hospital in Ghana.}, journal = {Public health challenges}, volume = {4}, number = {2}, pages = {e70071}, pmid = {40521244}, issn = {2769-2450}, abstract = {Millions of individuals worldwide suffer from hepatitis B, a serious, potentially fatal liver infection brought on by the hepatitis B virus (HBV). Although vaccines are available for HBV, infections continue to persist in Ghana. This study reports the prevalence of HBV infections in outpatients and pregnant women attending antenatal care at the Seventh-day Adventist (SDA) Hospital in Gbawe, Ghana. This retrospective cohort study involved the review of de-identified medical records of outpatients and pregnant women who visited the hospital between 2022 and 2024. Data on their HBV infection status, sex and age were analysed using R version 4.4.1. A total of 531 outpatients and 768 pregnant women visited the hospital during the study period. The prevalence of HBV infection was 7.5% in outpatients and 3.9% in pregnant women. It was observed that outpatients were more likely to be hepatitis B surface antigen (HBsAg) positive (OR = 2.0, 95%CI = 1.24-3.28, p = 0.005). It was also seen that HBV prevalence increased from 2022 to 2023 and decreased in 2024. There is a need for more educational campaigns to raise awareness of HBV infections, especially in pregnant women due to the risk of mother-to-child transmission. Furthermore, vaccinations need to be made affordable and easily accessible to the general population to ensure maximum coverage within the country.}, }
@article {pmid40518732, year = {2025}, author = {Mota de Almeida, FJ and Rakhimova, O and Romani Vestman, N and Lee, NM and Brundin, M}, title = {In situ imaging and microbiome analysis of calculus-like deposits at the root apex: A case report of refractory apical periodontitis.}, journal = {International endodontic journal}, volume = {58}, number = {9}, pages = {1474-1487}, pmid = {40518732}, issn = {1365-2591}, support = {7003589//Region of V&#xe4;sterbotten (Sweden)/ ; 977100//Region of V&#xe4;sterbotten (Sweden)/ ; RV-967705//Region of V&#xe4;sterbotten (Sweden)/ ; }, mesh = {Humans ; Biofilms ; *Dental Calculus/microbiology/diagnostic imaging ; High-Throughput Nucleotide Sequencing ; In Situ Hybridization, Fluorescence ; *Microbiota ; *Periapical Periodontitis/microbiology/diagnostic imaging ; *Tooth Apex/microbiology/diagnostic imaging ; }, abstract = {AIM: This case report explored the application of next-generation sequencing (NGS) and fluorescence in situ hybridization (FISH) to visualize and characterize microbial populations in a refractory endodontic infection with apical calculus-like deposits, a rarely reported phenomenon.<br><br>SUMMARY: Histopathologic analysis revealed bacterial biofilms and calcifications on the root surface, with Gram-positive bacteria predominant in both hard and soft tissues. Microbial sequencing showed Pseudomonadota dominated hard tissues, whereas Bacillota were prevalent in soft tissues, with distinct genera like Lactibacterium and Streptococcus identified. FISH imaging confirmed spatially distributed bacterial taxa, including Actinomycetota and Chloroflexota, within the biofilm, aligning with NGS findings. Notably, Bacteroidota was exclusive to soft tissues, whereas Chloroflexota was detected only in hard tissues. The presence of extensive calculus-like deposits on the root surface provided new insights into the microbial complexity of persistent endodontic infections and their management.<br><br>KEY LEARNING POINTS: The combination of NGS and FISH provided unprecedented insights into the microbial composition of refractory endodontic infections, revealing a diverse and spatially organized ecosystem. Distinct microbial compositions in hard and soft tissues emphasize the importance of targeted therapeutic strategies for endodontic infections. The presence of unique bacterial taxa and biofilms in calculus-like deposits offers new avenues for research into the pathogenesis and persistence of endodontic infections.}, }
@article {pmid40511921, year = {2025}, author = {Mayer, L and Nikolov, G and Kunert, M and Horn, M and Willemsen, A}, title = {Mimivirus transcription and translation occur at well-defined locations within amoeba host cells.}, journal = {Journal of virology}, volume = {99}, number = {7}, pages = {e0055425}, pmid = {40511921}, issn = {1098-5514}, support = {891572//Marie Sklodowska-Curie Actions/ ; 101039843/ERC_/European Research Council/International ; 10.55776/COE7//Austrian Science Fund/ ; }, mesh = {*Mimiviridae/genetics/physiology ; Virus Replication ; *Transcription, Genetic ; *Protein Biosynthesis ; In Situ Hybridization, Fluorescence/methods ; RNA, Viral/genetics ; *Acanthamoeba/virology ; RNA, Messenger/genetics/metabolism ; *Amoeba/virology ; Cytoplasm/virology ; Genome, Viral ; }, abstract = {Many giant viruses replicate in the cytoplasm in viral factories. How exactly these viral factories are established and where the different steps of the replication cycle occur remain largely obscure. We have developed a single-molecule messenger RNA fluorescence in situ hybridization (smFISH) protocol for giant viruses in an Acanthamoeba host. Combined with other labeling techniques (FUNCAT, DiD, rRNA FISH, and DAPI), we show the Mimivirus transcription and translation sites during an infection cycle in the amoeba host cell. Although viral mRNA localization changes depend on the infection stage, transcription occurs at well-defined spots within the viral factory. The original viral cores released within the cytoplasm most likely define these spots. When transported outside of the viral factory, the translation of viral mRNA takes place in a well-defined ring surrounding it. With this study, we obtained novel insights into giant virus replication, of which the methods are widely applicable to other viruses for the visualization and quantification of RNA molecules.IMPORTANCEGiant viruses have massive particle and genome sizes, which are known to infect unicellular eukaryotes. Although most viruses replicate in the host cell's nucleus, the giant Mimivirus replicates in viral factories established in the host cell's cytoplasm. Before this study, the location of the various steps in the Mimivirus replication cycle was largely unknown. By developing new protocols to label giant virus mRNA, protein synthesis, host cell membranes and rRNA, we demonstrate that Mimivirus transcription occurs at well-defined sites within the viral factory. In contrast, translation takes place directly outside of it. This is different from other viruses known to have a cytoplasmic life cycle. These results bring us a step closer to understanding how the genome complexity of viruses influences the virus-host interactions and viral replication strategies.}, }
@article {pmid40510670, year = {2025}, author = {Barnhart, EP and Douterelo, I and Morgan, MJ and Puzon, GJ}, title = {Editorial: Microbial ecology supporting growth of free-living amoebae in natural and engineered water systems.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1620877}, doi = {10.3389/fmicb.2025.1620877}, pmid = {40510670}, issn = {1664-302X}, }
@article {pmid40509663, year = {2025}, author = {van Dijk, JR and Geelhoed, JS and Geerlings, N and Choyikutty, JA and Boschker, HTS and Verbruggen, E and Meysman, FJR}, title = {Inactive "Ghost" Cells Do Not Affect Motility and Long-Range Electron Transport in Filamentous Cable Bacteria.}, journal = {Environmental microbiology}, volume = {27}, number = {6}, pages = {e70117}, pmid = {40509663}, issn = {1462-2920}, support = {G038819N//Fonds Wetenschappelijk Onderzoek/ ; S004523N//Fonds Wetenschappelijk Onderzoek/ ; //Universiteit Antwerpen/ ; PRINGLE 101046719//HORIZON EUROPE European Innovation Council/ ; EMBO ALTF 102-2023//European Molecular Biology Organization/ ; }, mesh = {Electron Transport ; *Bacteria/metabolism/cytology ; Oxidation-Reduction ; Sulfur/metabolism ; *Bacterial Physiological Phenomena ; }, abstract = {Cable bacteria are multicellular filamentous microorganisms that perform electrogenic sulphur oxidation over centimetre-long distances. These filaments contain so-called "ghost cells", which display a highly reduced cytoplasmic content and a lack of metabolic activity. However, the origin and abundance of these ghost cells are not well understood, raising questions about their formation and potential impact on the functioning of the entire filaments. Here, we quantified the abundance of ghost cells in cable bacteria via a targeted propidium iodide staining technique and investigated their morphology and possible origin. Microscopy revealed that ghost cells are present in filaments under in situ conditions, and hence, they are not an artefact from filament sampling. Interestingly, filaments containing ghost cells retained gliding motility, as well as the capacity for long-distance electron transport, thus suggesting that the functionality of the filament as a whole remains largely unaffected by the presence of these ghost cells. Noteworthy is the higher frequency of ghost cells near the ends of filaments, and within filament fragments retrieved from oxic environments. Our findings provide new insights into the adaptive strategies of filamentous bacteria, highlighting their ability to maintain functionality at the organism level despite the fact that some individual cells are no longer metabolically active.}, }
@article {pmid40509476, year = {2025}, author = {Bemis, DH and Camphausen, CE and Liu, E and Dantus, JJ and Navarro, JA and Dykstra, KL and Paltrowitz, LA and Dzhelmach, M and Joerg, M and Tamelessio, P and Belenky, P}, title = {Nutrient Availability and Pathogen Clearance Impact Microbiome Composition in a Gnotobiotic Kimchi Model.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {11}, pages = {}, pmid = {40509476}, issn = {2304-8158}, abstract = {Kimchi is a fermented Korean food typically made with napa cabbage, garlic, radish, ginger, and chili pepper. It is becoming increasingly popular due to its flavor, high fiber content, and purported probiotic benefits. The microbial ecology of the fermentation community has been extensively studied, though what's less understood is how its microbial community changes when nutrients or pathogens are introduced. To study this, we used gnotobiotic cabbage media inoculated with a kimchi starter culture as a model system. These inoculated samples were exposed to E. coli or Bacillus cereus, with or without added nutrients in the form of tryptic soy broth (TSB). We tracked pH, colony-forming units (CFUs), and community composition over time. We also used Oxford Nanopore sequencing to analyze the 16S rRNA gene (V4-V9), followed by use of the Emu algorithm for taxonomic assignments. As expected, LABs suppressed pathogens, but this effect was weaker early on in the nutrient-rich condition. Pathogen exposure changed the overall community-Lactobacillus species became more common, and Leuconostoc mesenteroides less so. Interestingly, adding nutrients alone caused similar microbial shifts to those seen with pathogen exposure. This could suggest that nutrient levels have a larger impact on the final microbiome structure than direct microbial competition. Together, these findings suggest that monitoring total microbial composition, and not just the presence of pathogens, may be important for ensuring kimchi fermentation reproducibility.}, }
@article {pmid40507003, year = {2025}, author = {Karkala, A and Kotoulas, SC and Tzinas, A and Massa, E and Mouloudi, E and Gkakou, F and Pataka, A}, title = {The Lung Microbiome and Its Impact on Obstructive Sleep Apnea: A Diagnostic Frontier.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {15}, number = {11}, pages = {}, pmid = {40507003}, issn = {2075-4418}, abstract = {Obstructive sleep apnea (OSA), a prevalent disorder characterized by recurrent upper airway collapse, is increasingly recognized as a systemic inflammatory condition influenced by microbial dysregulation. Emerging evidence underscores the lung microbiome as a mediator in OSA pathophysiology, where dysbiotic shifts driven by intermittent hypoxia, oxidative stress and mechanical airway trauma amplify inflammatory cascades and perpetuate respiratory instability. This review synthesizes current knowledge on the bidirectional interplay between OSA and lung microbial communities. It aims to highlight how hypoxia-induced alterations in microbial ecology disrupt immune homeostasis, while inflammation-driven mucosal injury fosters pathogenic colonization. Clinical correlations between specific taxa like Streptococcus and Prevotella, and disease severity, suggest microbial signatures as novel biomarkers for OSA progression and treatment response. Furthermore, oxidative stress markers and pro-inflammatory cytokines emerge as potential diagnostic tools that bridge microbial dysbiosis with sleep-related outcomes. However, challenges persist in sampling standardization of the low-biomass lower airways, as well as in causative mechanisms linking microbial dysbiosis to OSA pathophysiology. By integrating microbial ecology with precision sleep medicine, this paradigm shift promises to transform OSA management from mechanical stabilization to holistic ecosystem restoration.}, }
@article {pmid40504771, year = {2025}, author = {Augustijn, HE and Reitz, ZL and Zhang, L and Boot, JA and Elsayed, SS and Challis, GL and Medema, MH and van Wezel, GP}, title = {Genome mining based on transcriptional regulatory networks uncovers a novel locus involved in desferrioxamine biosynthesis.}, journal = {PLoS biology}, volume = {23}, number = {6}, pages = {e3003183}, pmid = {40504771}, issn = {1545-7885}, mesh = {*Deferoxamine ; *Gene Regulatory Networks ; Gene Expression Regulation, Bacterial ; *Streptomyces coelicolor/genetics/metabolism ; *Genome, Bacterial ; Multigene Family ; Bacterial Proteins/genetics/metabolism ; Operon ; Computational Biology ; Iron/metabolism ; Data Mining ; }, abstract = {Bacteria produce a plethora of natural products that are in clinical, agricultural and biotechnological use. Genome mining has uncovered millions of biosynthetic gene clusters (BGCs) that encode their biosynthesis, the vast majority of them lacking a clear product or function. Thus, a major challenge is to predict the bioactivities of the molecules these BGCs specify, and how to elicit their expression. Here, we present an innovative strategy whereby we harness the power of regulatory networks combined with global gene expression patterns to predict BGC functions. Bioinformatic analysis of all genes predicted to be controlled by the iron master regulator DmdR1 combined with co-expression data, led to identification of the novel operon desJGH that plays a key role in the biosynthesis of the iron overload drug desferrioxamine (DFO) B in Streptomyces coelicolor. Deletion of either desG or desH strongly reduces the biosynthesis of DFO B, while that of DFO E is enhanced. DesJGH most likely act by changing the balance between the DFO precursors. Our work shows the power of harnessing regulation-based genome mining to functionally prioritize BGCs, accelerating the discovery of novel bioactive molecules.}, }
@article {pmid40504377, year = {2025}, author = {Zhang, J and Zhao, Z and Zhu, C and Wang, E and Brunel, B and Li, S and Zheng, Q and Feng, Z and Zhang, H}, title = {Diverse Peanut Bradyrhizobial Communities in Chinese Soils: Insights from Eastern, Central, and Northern Henan Province.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {65}, pmid = {40504377}, issn = {1432-184X}, support = {2024M761756//China Postdoctoral Science Foundation/ ; Yuzutong[2023]No.11//Central Plains Youth Top Talent Project/ ; Sabbatical Year SIP20200726//IPN, Mexico/ ; }, mesh = {*Arachis/microbiology ; China ; *Bradyrhizobium/genetics/classification/isolation &amp; purification ; Phylogeny ; *Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; Polymorphism, Restriction Fragment Length ; Symbiosis ; Soil/chemistry ; Root Nodules, Plant/microbiology ; Bacterial Proteins/genetics ; }, abstract = {Henan province is a major peanut-producing area in China, but research on rhizobia nodulating peanut have been limited to southern Henan, which accounts for only less than half of the province. A collection of 212 strains of peanut rhizobia was obtained from six field sites in eastern, central, and northern Henan, Central China, by using peanut as a trap host under glasshouse conditions. PCR-RFLP analysis of ribosomal IGS sequences classified the 212 strains into 28 distinct types. Phylogenetic analyses of the 16S rRNA, atpD, gyrB, dnaK, and rpoB genes from 30 representative strains of the 28 IGS types identified revealed the presence of Bradyrhizobium. liaoningense, B. yuanmingense, B. zhengyangense, and two novel Bradyrhizobium genospecies. This composition differs from the peanut rhizobia community found in southern Henan. B. liaoningense was the dominant species, covering 49% of the total isolates across the field sites, while B. zhengyangense accounting for 27%, B. yuanmingense for 7% and the two novel Bradyrhizobium genospecies for 17%. Phylogenetic analysis showed that the symbiosis-related nodC and nifH gene sequences clustered into six groups: three associated exclusively with the peanut host (symbiovar arachidis and two unnamed group), three originating from other legume hosts (sv. glycinearum, cajani and retamae). Through the principal component analysis (PCA) between IGS types or species and soil physicochemical properties and environmental factors, it showed that IGS types 1, 3, 5, 8, 9, 12, 14, 15, 18, and 21 positively correlated with AveTmax, AveTmin, AN and AP. IGS types 4, 11, 16, 17, 20, 25, and 26 were positively associated with Alt, AvePrecp, and pH. IGS types 2, 7, 10, 22, 24, and 27 correlated with AP, while remaining types exhibited correlations with OM. In addition, B. yuanmingense, B. liaoningense, and Bradyrhizobium genosp. I positively affected by AveTmax, AP, AN, and AK. Bradyrhizobium genosp. II positively correlated with AK, AN, and OM while B. zhengyangense mainly affected by AvePrecp and pH. The alkaline soil pH in this study differs greatly from the acid soils in southern Henan, explaining the inconsistency between the species of peanut rhizobia detected in southern Henan and the rest of the province. The symbiotic effect assay demonstrated that all representative strains successfully formed nodules and exhibited a significant increase in symbiotic efficiency. Representative strains revealed diverse abiotic stress tolerance to NaCl, acidity, alkalinity, temperature and drought. It conducted a comprehensive collection of peanut rhizobia in eastern, central, and northern Henan province, identifying two putative novel Bradyrhizobium species and isolating rhizobial strains with high symbiotic efficiency and robust stress tolerance. This study is a necessary basic for the producing and application of peanut rhizobial inoculant in this main agricultural province.}, }
@article {pmid40504009, year = {2025}, author = {Schroer, HW and Markland, K and Ling, F and Just, CL}, title = {Hydraulic Connectivity and Hydrochemistry Influence Microbial Community Structure in Agriculturally Affected Alluvial Aquifers in the Midwestern United States.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {24}, pages = {12279-12291}, pmid = {40504009}, issn = {1520-5851}, mesh = {*Groundwater/microbiology ; *Microbiota ; Midwestern United States ; Drinking Water ; }, abstract = {Alluvial aquifers can provide ecosystem services and drinking water, but much remains unknown about human effects on aquifer microbiomes. Therefore, we used amplicon sequencing and hydrochemical characterization to pair microbial communities with environmental conditions across 37 alluvial aquifer wells. The study region spanned eastern Iowa and southern Minnesota (USA) and contained a combination of drinking water and monitoring wells. In terms of microbial ecology, dominant phyla across the wells included Proteobacteria, Bacteroidota, Patescibacteria, Planctomycetota, and Nitrospirota. Tritium, an indicator of infiltration and surface water influence, was the highest correlated variable with the Shannon index (α-diversity) by the Spearman rank sum (ρ = 0.60) and one of only four significant environmental variables in the constrained correspondence analysis. We built random forest regression models to predict tritium concentrations from microbial family relative abundance (held-out testing coefficient of determination (R[2]) = 0.77 and mean absolute percentage error = 7%) and interpreted the models with Shapley additive explanation values. The most important families for predicting tritium concentrations were Nitrosopumilaceae and Methylomirabilaceae. Upwelling methane could contribute to the unusual coupling of ammonia oxidation by Nitrosopumilaceae with simultaneous nitrite-dependent methane oxidation by Methylomirabilaceae. Taken together, we illuminate the relationship among hydrochemistry, hydraulic connectivity, and alluvial aquifer microbiomes.}, }
@article {pmid40502102, year = {2025}, author = {Baty, JJ and Drozdick, AK and Pfeiffer, JK}, title = {P. aeruginosa rhamnolipids stabilize human rhinovirus 14 virions.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40502102}, issn = {2692-8205}, support = {R37 AI074668/AI/NIAID NIH HHS/United States ; T32 AI007520/AI/NIAID NIH HHS/United States ; }, abstract = {Many mammalian viruses encounter bacteria and bacterial molecules over the course of infection. Previous work has shown that the microbial ecology of the gut plays an integral role in poliovirus and coxsackievirus infection, where bacterial glycans can facilitate virus-receptor interactions, enhance viral replication, and stabilize viral particles. However, how airway bacteria alter respiratory viral infection is less understood. Therefore, we investigated whether a panel of airway bacteria affect rhinovirus stability. We found that Pseudomonas aeruginosa, an opportunistic airway pathogen, protects human rhinovirus 14 from acid or heat inactivation. Further investigation revealed that P. aeruginosa rhamnolipids, glycolipids with surfactant properties, are necessary and sufficient for stabilization of rhinovirus virions. Taken together, this work demonstrates that specific molecules produced by an opportunistic airway pathogen can influence a respiratory virus.}, }
@article {pmid40501655, year = {2025}, author = {Chen, J and Pfeifer, K and Steensen, K and Crooke, AM and Wolfram, M and Bobonis, J and Lopatina, A and Bartlau, N and Hussain, FA and Balskus, EP and Polz, MF and Blainey, PC}, title = {Bacterial peptide deformylase inhibitors induce prophages in competitors.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40501655}, issn = {2692-8205}, support = {R01 GM132564/GM/NIGMS NIH HHS/United States ; }, abstract = {While antibiotics mediate chemical warfare among microbes, their roles in the wild extend beyond direct growth inhibition(1). Some antibiotics have the potential to mediate interference competition by triggering a bacterial stress response that subsequently activates endogenous viruses integrated in bacterial genomes (prophages). Canonically, this activation is regulated by the SOS response upon DNA damage. Here we show that a metabolite produced by natural isolates of Vibrio ordalii circumvents the SOS response by directly triggering prophage induction in other Vibrio species, co-occurring in the same environment. While the metabolite was previously classified as a broad-spectrum antibiotic, we observe how it acts as a peptide deformylase inhibitor that specifically induces certain prophages, even when target bacterial cells carry multiple other prophages. Its biosynthetic gene cluster, or ord cluster, also encodes its own peptide deformylase (OrdE) which provides self-immunity to producer strains. Likewise, among natural Vibrio isolates that carry similar prophages, resistance against the ord metabolite was found in those that had acquired a divergent second peptide deformylase. Finally, we show that prophage induction by the ord cluster prevents slower-growing producer strains from being outcompeted by their otherwise fast-growing competitors if they carry an inducible prophage. Thus, we demonstrate how natural products play additional impactful roles in communities beyond antibiotic activity and that prophage induction serves as an interference competition strategy, sustaining community diversity.}, }
@article {pmid40500964, year = {2025}, author = {Li, S and Wang, T and Liu, M and Ma, T and Li, Y and Liu, J and Liu, Y and Shen, W and Ma, J and Wang, X and Han, X and Wang, H and Zhang, X}, title = {α-Linolenic Acid-Rich Flaxseed Oil Improves Polycystic Ovary Syndrome via Regulating Lipid Metabolism by GPR120-cAMP Pathway and Restoring Gut Microecology.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e70136}, doi = {10.1002/mnfr.70136}, pmid = {40500964}, issn = {1613-4133}, support = {82460793//National Natural Science Foundation of China/ ; 82160691//National Natural Science Foundation of China/ ; 2023AAC03216//Ningxia Natural Science Foundation, China/ ; 2023BEG02011//Key Research and Development Program of Ningxia/ ; 2022BSB03112//Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; XZ2021003//Key Laboratory of Fertility Preservation and Maintainance of Ministry of Education of Ningxia Medical University/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; }, abstract = {Polycystic ovary syndrome (PCOS) is a common endocrine disorder that affects metabolic and reproductive health in women. α-Linolenic acid (ALA)-rich flaxseed oil as a dietary food has been suggested to offer potential therapeutic benefits in managing metabolic disturbances associated with PCOS. This study investigates the effects of ALA-rich flaxseed oil on lipid metabolism and gut microecology in a PCOS rat model. The PCOS model was induced in rats using letrozole, and the animals were then administered ALA-rich flaxseed oil. Metabolomics, transcriptomics, 16S rRNA sequencing, hormonal levels, and markers of metabolic health were assessed. Results showed that ALA-rich flaxseed oil significantly improved lipid metabolism by reducing serum cholesterol and triglycerides. In addition, we found that the improvement in lipid metabolism may be associated with the activation of the GPR120-cAMP pathway. Furthermore, gut microbiota analysis revealed a restoration of gut microbial ecology, with a shift toward a more balanced and healthy microbial composition. ALA-rich flaxseed oil shows promising potential as a dietary intervention for managing metabolic disturbances in PCOS. Its effects on lipid metabolism and gut microecology highlight its nutritional relevance, offering new insights into the dietary management of PCOS and its associated metabolic disorders.}, }
@article {pmid40500753, year = {2025}, author = {Bograd, A and Oppenheimer-Shaanan, Y and Levy, A}, title = {Plasmids, prophages, and defense systems are depleted from plant microbiota genomes.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {163}, pmid = {40500753}, issn = {1474-760X}, support = {1535/20//Israeli Science Foundation/ ; 1535/20//Israeli Science Foundation/ ; 1535/20//Israeli Science Foundation/ ; 1001695377//Israeli Ministry of Innovation, Science, and Technology/ ; 1001695377//Israeli Ministry of Innovation, Science, and Technology/ ; 1001695377//Israeli Ministry of Innovation, Science, and Technology/ ; 81259//Israel Innovation Authority/ ; 81259//Israel Innovation Authority/ ; 81259//Israel Innovation Authority/ ; 12-12-0008//Ministry of Agriculture and Rural Development/ ; 12-12-0008//Ministry of Agriculture and Rural Development/ ; 12-12-0008//Ministry of Agriculture and Rural Development/ ; ZN4041//Volkswagen Stiftung/ ; ZN4041//Volkswagen Stiftung/ ; ZN4041//Volkswagen Stiftung/ ; }, mesh = {*Prophages/genetics ; *Plasmids/genetics ; *Plants/microbiology ; *Genome, Bacterial ; *Microbiota/genetics ; Metagenome ; *Bacteria/genetics/virology ; }, abstract = {Plant-associated bacteria significantly impact plant growth and health. Understanding how bacterial genomes adapt to plants can provide insights into their growth promotion and virulence functions. Here, we compare 38,912 bacterial genomes and 6073 metagenomes to explore the distribution of mobile genetic elements and defense systems in plant-associated bacteria. We reveal a consistent taxon-independent depletion of prophages, plasmids, and defense systems in plant-associated bacteria, particularly in the phyllosphere, compared to other ecosystems. The mobilome depletion suggests the presence of unique ecological constraints or molecular mechanisms exerted by plants to control the bacterial mobilomes independently of bacterial immunity.}, }
@article {pmid40500405, year = {2025}, author = {Chen, TK and Shiau, YJ}, title = {Effects of Soil Properties and Seasonal Variations on Microbial Communities in Constructed Wetlands.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {64}, pmid = {40500405}, issn = {1432-184X}, support = {110-2313-B-002-033-MY3//National Science and Technology Council/ ; }, mesh = {*Wetlands ; Seasons ; *Soil Microbiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Soil/chemistry ; Denitrification ; *Microbiota ; Biodiversity ; Nitrates/analysis ; Sulfates/analysis ; Nitrification ; }, abstract = {Constructed wetlands (CWs) are important ecosystems with numerous benefits such as wastewater treatment, wildlife habitat protection, and stormwater remediation. However, the development of soil microbial communities in CWs over time remains understudied. This study comprehensively investigates microbial diversity and community composition in three constructed wetlands, focusing on the influence of wetland age, soil depth, and environmental factors. The results indicate that both soil depth and seasonal variations significantly affect alpha diversity, particularly in surface soils. The predominant microbial communities, including nitrifying and denitrifying communities, were identified across the studied wetlands. Moreover, sulfate-rich conditions may promote sulfur autotrophic denitrification. Redundancy analysis and multiple linear regression highlighted the distinction between autotrophic and heterotrophic denitrifiers. Soluble organic carbon was identified as a major factor influencing heterotrophic denitrifying bacteria, while sulfate and nitrate levels were more closely associated with autotrophic denitrifying bacteria. Overall, these findings provide valuable insights into microbial community dynamics in CWs and can help optimize wetland management strategies for improved nutrient removal efficiency.}, }
@article {pmid40499249, year = {2025}, author = {McDonagh, F and Murray, EK and Hallahan, B and Miliotis, G}, title = {Systematic examination of off-target effects of antipsychotic medications associated with microbiome disruption and heightened bacterial infection risks.}, journal = {Journal of psychiatric research}, volume = {189}, number = {}, pages = {171-183}, doi = {10.1016/j.jpsychires.2025.05.046}, pmid = {40499249}, issn = {1879-1379}, abstract = {OBJECTIVE: This systematic review aims to critically evaluate the link between antipsychotic drugs and bacterial infection risk, emphasising antimicrobial properties of antipsychotics, and microbiome changes that might heighten susceptibility to bacterial infections.<br><br>METHODS: A systematic literature search was conducted across PubMed, Scopus, and Google Scholar, up to March 2024. Peer-reviewed articles that investigated the relationship between antipsychotics, their antimicrobial effects, microbiome alterations, and bacterial infection risk were included. Data extracted included antipsychotic type, infection risks, patient demographics, and study methodologies. Risk-of-bias assessments were performed using tools such as the Newcastle-Ottawa Scale and the SYRCLE risk-of-bias tool.<br><br>RESULTS: The review analysed twenty-six studies detailing antimicrobial properties of antipsychotics, four studies on antipsychotic-induced microbiome alterations, and thirty-one studies assessing bacterial infection risk associated with antipsychotics. First-generation antipsychotics were observed to have broad antimicrobial properties, whereas second-generation antipsychotics primarily affected commensal bacteria. At least four antipsychotics were observed to disrupt the gut microbiota. A heightened risk of infection was observed among psychiatric cohorts as well as off-label antipsychotics use, with clozapine linked to a substantial increase in respiratory infection risk.<br><br>DISCUSSION: Although antipsychotics remain indispensable in psychiatric care, their association with an increased risk of bacterial infections underscores the need for judicious prescribing and vigilant monitoring. The review identifies significant knowledge gaps attributable to inconsistent research methodologies, small study cohorts, lack of controls, and focus on a limited range of antipsychotics. Further standardised research is essential to deepen our understanding of these associations and to inform improved prescribing practices and risk mitigation strategies.}, }
@article {pmid40498465, year = {2025}, author = {Samimi, A and Hengoju, S and Martin, K and Rosenbaum, MA}, title = {Advancing droplet-based microbiological assays: optofluidic detection meets multiplexed droplet generation.}, journal = {The Analyst}, volume = {150}, number = {14}, pages = {3137-3146}, doi = {10.1039/d5an00130g}, pmid = {40498465}, issn = {1364-5528}, mesh = {*Microfluidic Analytical Techniques/instrumentation/methods ; High-Throughput Screening Assays/instrumentation ; *Microbiological Techniques/instrumentation/methods ; }, abstract = {Microbiological assays are crucial in understanding microbial ecology and developing new bioproducts. Given the significance of these assays, there is a growing interest in developing high throughput experimentation methods capable of assay multiplexing to enhance the accuracy and efficiency. In this study, we integrate a multiplexed droplet generation set-up into an optofluidic detection chip to facilitate rapid and high throughput analysis of microbiological assays. The optofluidic detection set-up at the same time enables fast and sensitive assessment of droplet condition and content, providing analysis scalability in a high throughput manner. Employing the integration, we produced unique fluorescence barcoded droplets containing defined concentrations of various carbon sources, allowing the simultaneous investigation of microbial growth and metabolic capacity under different experimental conditions. We successfully validated the robustness of the established setup in analyzing and distinguishing different fluorescence barcodes. Our findings highlight the potential of the integrated platform for a broader range of applications in high throughput drug screening, environmental monitoring, and microbiology research.}, }
@article {pmid40498364, year = {2025}, author = {Castledine, M and Esom, C and Van Nieuwenhuyse, B and Djebara, S and Merabishvili, M and Pirnay, JP and Buckling, A}, title = {Predicting clinical phage therapy outcomes in vitro: results using mixed versus single isolates from an MRSA case study.}, journal = {Journal of applied microbiology}, volume = {136}, number = {6}, pages = {}, doi = {10.1093/jambio/lxaf144}, pmid = {40498364}, issn = {1365-2672}, support = {NE/V012347/1//NERC/ ; NE/S000771/1//NERC/ ; }, mesh = {Humans ; Anti-Bacterial Agents/therapeutic use ; *Methicillin-Resistant Staphylococcus aureus/virology/isolation &amp; purification ; *Phage Therapy/methods ; *Staphylococcal Infections/therapy/microbiology ; *Staphylococcus Phages/physiology ; Treatment Outcome ; }, abstract = {AIMS: In phage therapy case studies, 1-3 bacteria isolates are typically tested against phages (phagogram). However, as bacteria populations differ in their susceptibility to phages and antibiotics, the strains selected may not represent how the infecting population will respond to treatment. Our aim was to assess whether the effects of phage on single or a mix of isolates in vitro show more comparable results to that observed during a clinical case study.<br><br>METHODS AND RESULTS: The patient presented with a methicillin resistant Staphylococcus aureus infection (MRSA). In this previously published case study, phage therapy alongside antibiotics rapidly cleared blood cultures of bacteria while localized regions, including the lungs, took longer to clear of bacteria. In this follow-up study, mixed isolates were more likely to persist than single isolates in vitro, more closely representing the lung, but not blood, infections. These results may reflect the different degrees of genetic diversity of the infecting bacteria in these sites.<br><br>CONCLUSIONS: For this patient, phage therapy predictions were significantly affected by whether we used mixed versus single isolates, but the predictive precision depended on the site of in vivo infection.}, }
@article {pmid40495815, year = {2025}, author = {Abiriga, D and Odong, R and Bakyayita, GK and Semyalo, R and Okello, W and Grossart, HP}, title = {The microbiology of Uganda's large freshwater lakes experiencing anthropogenic and climatic perturbations: why it matters-a review.}, journal = {Proceedings. Biological sciences}, volume = {292}, number = {2048}, pages = {20243072}, pmid = {40495815}, issn = {1471-2954}, mesh = {Uganda ; *Lakes/microbiology ; *Climate Change ; *Anthropogenic Effects ; *Water Microbiology ; Biodiversity ; Bacteria ; }, abstract = {Intensification of pollution of African water resources due to human activities together with climate change has serious implications for Africa's blue economy, biodiversity and human health. Despite these overwhelming threats, there is limited research as evidenced by the underrepresentation of Africa-based data in global ecological and biochemical models. This review, therefore, aims to highlight key challenges and existing research gaps, particularly in Ugandan freshwater ecosystems. We focus on lake microbiology as this scientific field has been greatly underrepresented. Aquatic microorganisms are situated at the base of lake food webs and thus play crucial roles in the evolution and maintenance of water quality, attenuation of pollutants, and control of biogeochemical cycling through the microbial loop. Until now, the microbiology of Ugandan lakes has not been systematically studied. Thus, many open fundamental microbial ecology questions need to be urgently addressed to generate valuable information to advance future research, education, management and policy in Uganda and beyond. These include, but are not limited to: identification of microbial taxa and functional genes in relation to anthropogenic and climatic influence; seasonal and spatial variation in species diversity and functions; diversity and functions of planktonic, sediment, biofilm and mat communities; antimicrobial resistance burden; plastisphere communities; and geomicrobiology.}, }
@article {pmid40493213, year = {2025}, author = {Vila Duplá, M}, title = {Advancements in Algal Microbiome Research: A Game-Changer for Climate Resilience and Invasion Success?.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {63}, pmid = {40493213}, issn = {1432-184X}, mesh = {*Microbiota ; *Climate Change ; *Seaweed/microbiology ; *Introduced Species ; }, abstract = {While marine microbiomes have been getting more attention in recent years, they remain understudied compared to those of terrestrial systems. With the refinement of molecular methods, microbiome research has extended to other key marine organisms such as macroalgae. The microbiome plays a key role in macroalgal health, adaptation to environmental conditions, and resilience to climate stressors. The main factors affecting the algal microbiome are host specificity (genetics, functional profile, phylum and species identity), life stage, morphology, thallus region, and tissue age. Other significant drivers of microbiome community structure include spatiotemporal distribution and environmental conditions, especially as global stressors intensify with climate change. The mechanisms through which the microbiome of invasive seaweeds might enhance their competitiveness over native species are still unclear. However, there is evidence that, like climate resilience, invasive potential is linked to the functional flexibility of associated microbiota, allowing the host to adapt to the new environmental conditions. The main objective of this review was to synthesize the current understanding of the macroalgal microbiome and propose future directions in microbiome research based on identified shortcomings. Based on the knowledge gaps detected, there is an urgent need for multi-factorial experimental studies that link host and microbiome gene expression through chemical signals under future climate change scenarios, standardization of analytical methods, and a focus on underrepresented geographical regions and species. While algal microbiome research holds great promise for predicting and mitigating the effects of climate change and invasive species, embracing new tools and tackling ecologically relevant mechanistic and applied questions will be essential to advancing this field.}, }
@article {pmid40492114, year = {2025}, author = {Zhang, Y and Fan, J and Zhao, J and Zhu, H and Xia, Y and Xu, H}, title = {A telomere-associated molecular landscape reveals immunological, microbial, and therapeutic heterogeneity in colorectal cancer.}, journal = {Frontiers in molecular biosciences}, volume = {12}, number = {}, pages = {1615533}, pmid = {40492114}, issn = {2296-889X}, abstract = {BACKGROUND: Colorectal cancer (CRC) ranks among the most prevalent malignancies of the gastrointestinal tract and remains a leading cause of cancer-related mortality worldwide. Although telomere biology has been increasingly implicated in immune modulation and tumor progression, its clinical significance in CRC remains poorly understood.<br><br>METHODS: We developed a telomere score, termed TELscore, by integrating transcriptomic and intratumoral microbiome profiles from publicly available colorectal cancer (CRC) cohorts. To comprehensively characterize TELscore subgroups, we performed pathway enrichment analysis, tumor immune microenvironment (TIME) profiling, and microbiome niche assessment. Whole-slide histopathological images (WSIs) and immunohistochemical (IHC) staining were utilized to visualize immune features, including tertiary lymphoid structures (TLSs), across subgroups. Patients were stratified into high and low TELscore categories, and the predictive robustness was validated across multiple independent training and validation cohorts. Chemotherapeutic drug sensitivity was evaluated using pharmacogenomic data from the Genomics of Drug Sensitivity in Cancer (GDSC) database. Furthermore, the predictive capacity of TELscore for immunotherapy response was independently assessed in an external cohort. Finally, single-cell RNA sequencing (scRNA-seq) analysis was conducted to further dissect the cellular landscape and immunological heterogeneity within the TME.<br><br>RESULTS: TELscore stratified patients into two biologically and clinically distinct subgroups. The high TELscore group, which exhibited significantly shorter DFS, showed marked enrichment of tumorigenic pathways such as EMT, along with a distinctly immunosuppressive TME. This was reflected by elevated ESTIMATE/TIDE scores and corroborated by CIBERSORT, which revealed increased infiltration of M0 macrophages and upregulation of immunosuppressive signatures. In contrast, the low TELscore group was enriched for cell cycle related pathways, including E2F targets and the G2/M checkpoint, and demonstrated higher infiltration of pro-inflammatory M1 macrophages. 16S rRNA sequencing further revealed a divergent intratumoral microbiome between subgroups, the high TELscore group harbored significantly greater relative abundance of Selenomonas and Lachnoclostridium, two pathogenic genera previously associated with colorectal tumorigenesis. Complementary histopathological assessment via WSI demonstrated a marked absence of intraTLSs in high TELscore tumors. From a therapeutic standpoint, high TELscore tumors exhibited reduced sensitivity to standard chemotherapeutic agents-including Fluorouracil, Irinotecan, Oxaliplatin, and Docetaxel-as reflected by elevated IC50 values. Conversely, these tumors demonstrated increased susceptibility to MAPK pathway inhibitors, such as Selumetinib and Trametinib. Notably, TELscore also served as a robust predictor of immunotherapy response, which was validated in the IMvigor210 cohort. Finally, scRNA analysis highlighted profound cellular and functional divergence between TELscore subgroups. We identified intensified intercellular communication between inflammatory macrophages and fibroblasts, reinforcing the presence of an immunosuppressive niche.<br><br>CONCLUSION: TELscore is a robust stratification tool that captures the interplay between tumor biology, immune characteristics, and microbial ecology in colorectal cancer. By identifying clinically relevant subtypes with distinct therapeutic vulnerabilities, TELscore offers a powerful framework to advance personalized treatment and precision oncology.}, }
@article {pmid40488407, year = {2025}, author = {Grossman, AS and Lei, L and Botting, JM and Liu, J and Nahar, N and Liu, J and McLean, JS and He, X and Bor, B}, title = {Saccharibacteria deploy two distinct type IV pili, driving episymbiosis, host competition, and twitching motility.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40488407}, issn = {1751-7370}, support = {R01 DE023810/DE/NIDCR NIH HHS/United States ; T90 DE026110-07/DE/NIDCR NIH HHS/United States ; 1S10OD034405-01/GF/NIH HHS/United States ; R01 AI087946/AI/NIAID NIH HHS/United States ; 1S10OD023603-01A1/GF/NIH HHS/United States ; R01 DE031274/DE/NIDCR NIH HHS/United States ; R01 AI152421/AI/NIAID NIH HHS/United States ; R01AI152421//National Institute of Allergy and Infectious Diseases/ ; S10 OD023603/OD/NIH HHS/United States ; T90 DE026110/DE/NIDCR NIH HHS/United States ; S10 OD034405/OD/NIH HHS/United States ; 1R01DE023810/DE/NIDCR NIH HHS/United States ; 1R01DE031274/DE/NIDCR NIH HHS/United States ; }, mesh = {*Fimbriae, Bacterial/genetics/physiology ; *Symbiosis ; In Situ Hybridization, Fluorescence ; }, abstract = {All cultivated Patescibacteria, also known as the candidate phyla radiation, are obligate episymbionts residing on other microbes. Despite being ubiquitous in many diverse environments, including mammalian microbiomes, molecular mechanisms of host identification and binding amongst ultrasmall bacterial episymbionts remain largely unknown. Type 4 pili are well conserved in this group and could potentially facilitate these symbiotic interactions. To test this hypothesis, we genetically targeted pili genes in Saccharibacteria Nanosynbacter lyticus strain TM7x to assess their essentiality and roles in symbiosis. Our results revealed that N. lyticus assembles two distinct type 4 pili: a nonessential thin pilus that has the smallest diameter of any type 4 pili and contributes to host-binding and episymbiont growth; and an essential thick pilus involved in twitching motility. To understand the role of these pili in vivo we developed Saccharibacteria competition assays and species-specific Fluorescence in situ hybridization probes. Competition between different Saccharibacteria within mock communities demonstrated consistent competitive outcomes that were not driven by priority effects but were dependent on the thin pilus. Collectively, our findings demonstrate that Saccharibacteria encode unique extracellular pili that enable their underexplored episymbiotic lifestyle and competitive fitness within a community.}, }
@article {pmid40487916, year = {2025}, author = {Okazaki, Y and Nishikawa, Y and Wagatsuma, R and Takeyama, H and Nakano, SI}, title = {Contrasting defense strategies of oligotrophs and copiotrophs revealed by single-cell-resolved virus-host pairing of freshwater bacteria.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf086}, pmid = {40487916}, issn = {2730-6151}, abstract = {Characterizing virus-host pairs and the infection state of individual cells is the major technical challenge in microbial ecology. We addressed these challenges using state-of-the-art single-cell genome technology (SAG-gel) combined with extensive metagenomic datasets targeting the bacterial and viral communities in Lake Biwa. From two water layers and two seasons, we obtained 862 single-cell amplified genomes (SAGs), including 176 viral (double-stranded DNA phage) contigs, which identified novel virus-host pairs involving dominant freshwater lineages. The viral infection rate, estimated by mapping the individual SAG's raw reads to viral contigs, showed little variation among samples (12.1%-18.1%) but significant variation in host taxonomy (4.2%-65.3%), with copiotrophs showing higher values than oligotrophs. The high infection rates of copiotrophs were attributed to collective infection by diverse viruses, suggesting weak density-dependent virus-host selection, presumably due to their nonpersistent interactions with viruses resulting from fluctuating abundance. In contrast, the low infection rates of oligotrophs supported the idea that their codominance with viruses is achieved by genomic microdiversification, which diversifies the virus-host specificity, sustained by their large population size and persistent density-dependent fluctuating selection. Notably, we discovered viruses infecting CL500-11, the dominant bacterioplankton lineage in deep freshwater lakes worldwide. These viruses showed extremely high read coverages in cellular and virion metagenomes but were detected in <1% of host cells, suggesting a low infection rate and high burst size. Overall, we revealed highly diverse virus-host interactions within and between host lineages that were overlooked at the metagenomic resolution.}, }
@article {pmid40487326, year = {2025}, author = {Bornbusch, SL and Dami, KA}, title = {Connecting microbial ecology to human fertility and reproduction: perspectives from the reproductive microbiomes of animals.}, journal = {F&amp;S reports}, volume = {6}, number = {Suppl 1}, pages = {45-49}, pmid = {40487326}, issn = {2666-3341}, abstract = {In all vertebrates, reproduction occurs in the context of host-associated microbiomes, which are increasingly recognized for their contributions to reproductive success. Although host-associated microbiomes are species specific, synthesizing patterns in microbial ecology across human and animal taxa provides perspectives for understanding the factors that shape microbial communities and their contributions to reproduction. Additionally, the fertility and reproductive physiology of animals under human care-particularly endangered species-is often meticulously monitored to maximize reproductive opportunities. In this mini-review, we examine current knowledge on reproductive microbiomes in animals, focusing, when available, on the sparse literature for wildlife species. We suggest ways in which studying animal microbial ecology may advance human fertility and reproduction by focusing on 3 microbial communities-vaginal, milk, and seminal microbiomes-which represent a large portion of literature and have clear implications for reproductive health. We identify avenues of future research that will further strengthen the linkages between reproductive research in wildlife species and humans and provide potential guidelines for practical applications of microbiome science to human reproductive health.}, }
@article {pmid40483289, year = {2025}, author = {Swain, PP and Subudhi, E and Sahoo, RK}, title = {Heavy Metals and Carbapenem-Resistant Klebsiella pneumoniae in a River System of Odisha, India: Correlation and Integrated Risk Assessment.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {62}, pmid = {40483289}, issn = {1432-184X}, support = {523/2020(BSR)//University Grants Commission/ ; }, mesh = {*Metals, Heavy/analysis ; *Rivers/microbiology/chemistry ; India ; *Klebsiella pneumoniae/drug effects/genetics/isolation &amp; purification ; Risk Assessment ; *Water Pollutants, Chemical/analysis ; *Carbapenems/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Wastewater/microbiology ; Environmental Monitoring ; Humans ; Microbial Sensitivity Tests ; }, abstract = {The unregulated release of heavy metals and antibiotics into rivers has the potential to significantly impact human health. Infections caused by healthcare-associated pathogen, carbapenem-resistant Klebsiella pneumoniae (CRKP), present a critical challenge to clinical practitioners due to its resistance to last-line antibiotics. In this study, we investigated co-contamination of heavy metals (As, Cd, Cr, Mn, and Pb) and CRKP isolates in water samples from multiple sites along the river receiving wastewater discharge from urban areas of twin-city, Odisha. We used a composite risk scoring framework integrating chemical risks (based on hazard indices (HI) of heavy metals) and biological risks (based on the proportion of CRKP isolates exhibiting multidrug-resistant phenotypes and their multiple antibiotic resistance (MAR) index. Furthermore, Spearman's correlations and redundancy analysis (RDA) were employed to assess the association between heavy metals and antibiotic resistance genes (ARGs). From the total CRKP isolates identified (n = 91), 90.1% and 9.89% exhibited multidrug resistant (MDR) and extensively drug-resistant (XDR) phenotypes, respectively. Sites D2 and C2 were flagged as high-risk sites based on their composite risk scores of 0.735 and 0.699, respectively. Positive correlations were observed between heavy metals and ARGs (blaOXA-48, blaTEM, and blaSHV). The findings raise concern regarding the potential threat of CRKP and heavy metal pollution in river water while also emphasizing the need for integrated assessment to control their release into the environment.}, }
@article {pmid40482721, year = {2025}, author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW}, title = {Root architecture and the rhizosphere microbiome: Shaping sustainable agriculture.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {359}, number = {}, pages = {112599}, doi = {10.1016/j.plantsci.2025.112599}, pmid = {40482721}, issn = {1873-2259}, mesh = {*Rhizosphere ; *Plant Roots/microbiology/anatomy &amp; histology/growth &amp; development ; *Microbiota ; Soil Microbiology ; *Crops, Agricultural/microbiology/growth &amp; development ; *Agriculture ; Plant Breeding ; }, abstract = {Understanding root architecture and exudation is fundamental for enhancing crop productivity and promoting sustainable agriculture. Historically, plant researchers have focused on above-ground traits to increase yield and reduce input dependence. However, below-ground traits, especially those related to the root system, are equally critical yet often overlooked due to phenotyping challenges. Root architecture, including some root traits, i.e., lateral root density, root hair abundance, and root tip number, plays central roles in plant establishment, stress tolerance, and the recruitment of beneficial microbes in the rhizosphere. Root exudates, a complex array of chemical compounds released by roots, vary with plant species, developmental stage, and environmental conditions. These compounds act as signals and nutrients, shaping the composition and function of rhizosphere microbial communities. In turn, the microbiome of rhizosphere contributes to plant health by facilitating nutrient uptake, enhancing stress resilience, and providing defense against pathogens. Integrating root traits into breeding programs offers promising opportunities to select for genotypes that are more efficient in recruiting beneficial microbes. Heritable root traits, such as increased branching, finer roots, and higher exudation capacity, can enhance microbiome assembly and stability. The assessment of genes can also regulate of these traits and represent targets for genomics-assisted selection. Some strategies, such as microbiome engineering, particularly through the design of synthetic microbial communities (SynComs), can be used to modulate root architecture and optimize plant-microbe interactions. Despite these promising outcomes, challenges remain in translating SynCom applications to the field due to environmental variability, native microbial competition, and limited understanding of host genetic controls. This review discusses how root architecture shapes the rhizosphere microbiome and explores strategies, such as trait-based breeding and microbiome engineering, for advancing sustainable crop production.}, }
@article {pmid40481550, year = {2025}, author = {Zhu, F and Ying, H and Siadat, SD and Fateh, A}, title = {The gut-lung axis and microbiome dysbiosis in non-tuberculous mycobacterial infections: immune mechanisms, clinical implications, and therapeutic frontiers.}, journal = {Gut pathogens}, volume = {17}, number = {1}, pages = {40}, pmid = {40481550}, issn = {1757-4749}, abstract = {Non-tuberculous mycobacteria (NTM) are emerging pathogens of global concern, particularly in regions with declining tuberculosis rates. This review synthesizes current evidence on the epidemiology, immune pathogenesis, and microbiome interactions underlying NTM infections. The rising incidence of NTM is driven by environmental factors, immunocompromised populations, and advanced diagnostics. Clinically, NTM manifests as pulmonary, lymphatic, skin/soft tissue, or disseminated disease, with Mycobacterium avium complex (MAC) and M. abscessus being predominant pathogens. Host immunity, particularly Th1 responses mediated by IL-12/IFN-γ and TLR2 signaling, is critical for controlling NTM, while dysregulated immunity (e.g., elevated Th2 cytokines, PD-1/IL-10 pathways) exacerbates susceptibility. Emerging research highlights the gut-lung axis as a pivotal mediator of disease, where microbiome dysbiosis-marked by reduced Prevotella and Bifidobacterium-impairs systemic immunity and promotes NTM progression. Short-chain fatty acids (SCFAs) and microbial metabolites like inosine modulate macrophage and T-cell responses, offering therapeutic potential. Studies reveal distinct airway microbiome signatures in NTM patients, characterized by enriched Streptococcus and Prevotella, and reduced diversity linked to worse outcomes. Despite advances, treatment remains challenging due to biofilm formation, antibiotic resistance, and relapse rates. This review underscores the need for microbiome-targeted therapies, personalized medicine, and longitudinal studies to unravel causal relationships between microbial ecology and NTM pathogenesis.}, }
@article {pmid40481438, year = {2025}, author = {Babalola, OO and Osuji, IE and Akanmu, AO}, title = {Amplicon-based metagenomic survey of microbes associated with the organic and inorganic rhizosphere soil of Glycine max L.}, journal = {BMC genomic data}, volume = {26}, number = {1}, pages = {40}, pmid = {40481438}, issn = {2730-6844}, abstract = {OBJECTIVES: The metagenomic dataset of 16S rRNA and ITS gene amplicons of DNA were obtained from the cultivated soybean rhizosphere of organic and inorganic treatments. The organic treatments consisted of poultry waste, and cow dung treatments while the inorganic consisted of samples from untreated soybean plots and the bulk. Amplicon sequencing was performed on the Illumina platform, and the raw sequence data were processed and analyzed using Quantitative Insights Into Microbial Ecology (QIIME 2 version 2019.1.).<br><br>DATA DESCRIPTION: The analysis revealed a metagenomic library from soybean rhizospheric soils, providing insights into diversity and distribution of the bacterial and fungal community diversities. The most predominant bacteria phylum taxa across the treatments were Proteobacteria, Firmicutes, Actinobacteriota and Bacteriodota, while those for fungi were Ascomycota, Basidiomycota and Glomeromycota. The dataset provides insights into how different organic fertilization sources affect the structure, composition, and diversity of the microbiome in the soybean rhizosphere. The sequences have been deposited in the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI) with assigned bioproject accession numbers; 16S rRNA (SRP540791) and ITS (SRP541849).}, }
@article {pmid40480043, year = {2025}, author = {Keating, C and Trego, A and O'Flaherty, V and Ijaz, UZ}, title = {Microbiomes of high-rate anaerobic digestors reveal 'Study'-specific factors and limitations of synthetic wastewater.}, journal = {Water research}, volume = {282}, number = {}, pages = {123931}, doi = {10.1016/j.watres.2025.123931}, pmid = {40480043}, issn = {1879-2448}, mesh = {*Wastewater/microbiology ; *Microbiota ; *Bioreactors/microbiology ; Anaerobiosis ; Archaea/genetics ; Bacteria/genetics ; Waste Disposal, Fluid ; }, abstract = {Anaerobic digestion (AD) is a key technology for the treatment of organic wastes and the production of renewable energy. The stability of the process hinges on the underlying microbial populations. Amplicon sequencing is increasingly used to characterise AD microbiomes, yet sequencing efforts have not translated to process engineering of the microbiome or prediction of failure using microbial tools. Using high-rate biofilm wastewater bioreactors as a study system, we aimed to i) discern trends in archaeal and bacterial diversity, ii) identify a core AD microbiome, iii) determine the functional stability of AD microbiomes, and iv) correlate taxa to experimental conditions. We analysed amplicon sequencing data from 32 high-rate anaerobic digestor studies (> 1258 samples) at various operational conditions and applied a suite of statistical microbiome tools. We found that taxonomic archaeal diversity was highly study dependent, while functional diversity was highly shared across studies. A core AD microbiome was identified with > 100 bacterial genera and 6 archaeal genera which were present at > 1 % relative abundance in at least 50 % of samples. Interestingly, we observed that microbiome stability was significantly impacted by the choice of real or synthetic wastewater, with synthetic wastewaters yielding a more stable and less complex microbiome. This was correlated to the abundances of 37 taxa in the synthetic wastewater, including 3 key methanogens (Methanothrix, Methanobacterium, and Methanosphaerula). This suggests that when synthetic wastewater is used in experimental studies, it may not result in an AD microbiome representative of real wastewater treatment systems.}, }
@article {pmid40476717, year = {2025}, author = {Baer, J and Little, M and Aquino, J and van der Geer, A and Sánchez-Quinto, A and Ballard, A and Lawrence, C and Carilli, J and Hartmann, A and Rohwer, F}, title = {Viralization as a microbial approach for enhancing coral reef restoration.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40476717}, issn = {1751-7370}, support = {2209377//National Science Foundation/ ; CR20-5175//United States Department of Defense Environmental Security Technology Certification Program/ ; 9207//Gordon and Betty Moore Foundation/ ; S10 OD026929/OD/NIH HHS/United States ; 2022717//National Science Foundation/ ; }, mesh = {*Coral Reefs ; Animals ; *Anthozoa/virology/growth &amp; development/microbiology ; *Viruses/isolation &amp; purification ; Seawater/chemistry/virology ; *Environmental Restoration and Remediation/methods ; }, abstract = {Coral reef ecosystems rely on microorganisms to carry out biogeochemical processes essential to the survival of corals and the reef food web. However, widespread shifts from coral to algal dominance as a result of anthropogenic pressures have promoted microbial communities that compromise reef health through deoxygenation and disease. These degraded reefs become locked in a "microbialized" state characterized by high microbial biomass, low oxygen, and heightened pathogenic activity that stymie efforts to outplant corals onto the reef, a common approach applied to restore these ecosystems. Over 18 months, we compared viral and microbial dynamics alongside physical and chemical parameters ("water quality") between two coral outplanting sites and two midwater reef mesocosms called Coral Arks. Seafloor sites exhibited microbialization, whereas Arks maintained conditions with higher viral abundances and virus-to-microbe ratios, smaller and less abundant microorganisms, and consistently higher dissolved oxygen, water flow, and light availability. These conditions, which we term "viralized", supported enhanced coral growth and survival, greater benthic diversity, increased coral recruitment, reduced turf and macroalgae, and higher fish abundance compared to outplanting sites. Despite these benefits, analysis of microbial carbon metabolism genes revealed an underlying trend towards microbialization at both sites, reflecting larger-scale regional decline. These findings emphasize that microbial and physicochemical conditions are drivers of reef restoration outcomes; to be successful, restoration strategies must target the underlying environmental factors that support coral survival and resilience. We identify key microbial and physical variables-such as oxygen levels, flow, and viral activity-associated with viralized reef states, which should serve as focal points for developing new interventions and technologies aimed at creating conditions conducive to reef recovery.}, }
@article {pmid40474779, year = {2025}, author = {Green, N and Norwood, A and Sidhe, C and Mutlow, A and Aymen, J and Stiles, R and Bushell, J and Lim, T and Culver, E and Reeder, N and Timmer, M and Connelly, F and Charbonneau, J and McCall, W and Koenig, L and Stein, M and Geist, N and Lambert, MR and Hernández-Gómez, O}, title = {Shell Lesion Prevalence and Bacteriome Associations in Threatened Western Pond Turtles (Actinemys marmorata and Actinemys pallida) in California, USA.}, journal = {Journal of wildlife diseases}, volume = {61}, number = {3}, pages = {574-586}, pmid = {40474779}, issn = {1943-3700}, mesh = {Animals ; *Turtles/microbiology ; California/epidemiology ; *Animal Shells/microbiology/pathology/injuries ; Endangered Species ; *Bacteria/isolation &amp; purification/classification ; }, abstract = {Bacteriome characterization studies can provide insights into the microbial ecology associated with disease. We collected western pond turtles (Actinemys marmorata and Actinemys pallida) from six San Francisco Bay Area, California, USA, ponds; assessed their shells for lesions; and collected shell swabs and keratin scrape samples to evaluate bacteriome differences between the whole shell (swabs) and the affected tissues (scrapes). We quantified shell lesion type and prevalence by using visual inspections of photographs collected of the plastron and carapace and then applied 16S rRNA amplicon sequencing to characterize the associated bacteriomes of shells that observed pits, ulcerations, or no lesions. We observed shell lesions at high frequencies throughout our sites, with larger individuals (>100-mm plastron length) more likely to possess injuries. We saw no differences in alpha diversities between shells presenting with lesions and those on which we did not observe lesions; however, swab samples showed higher bacterial richness than keratin scrapes. The bacterial composition within the scrapes was influenced by pond location and then lesion presence. We observed a higher relative abundance of Actinobacteriota, Bacteroidota, Cyanobacteria, and Deinococcota in the shell keratin microflora of turtles with shell lesions. Because western pond turtles are under consideration for listing under the Endangered Species Act of 1973 in the USA, understanding patterns of shell disease pathologies and the bacteria associated with disease is imperative for the management of current populations.}, }
@article {pmid40474000, year = {2025}, author = {Cottam, DE and Cosgrove, DW and Megía-Palma, R and Žagar, A and Blázquez-Castro, S and Faria, JF and Turner, AE and Silva, DO and Pie, MR}, title = {Does the Gut Microbiome of the Insular Lizard Gallotia galloti Reflect Variation in Sex, Environment, and Population Genetic Differentiation?.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {61}, pmid = {40474000}, issn = {1432-184X}, mesh = {Animals ; *Lizards/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Male ; Female ; Spain ; *Bacteria/classification/genetics/isolation &amp; purification ; Environment ; Genetic Variation ; Genetics, Population ; Sex Factors ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Despite their critical role in maintaining organismal health, the factors driving intraspecific variation in gut microbiotas in the wild are poorly understood. Gallotia galloti is a lizard endemic to the Canary Islands characterized by substantial phenotypic and genetic differentiation across populations, as well as by its ability to occur across considerably different environmental conditions. However, the extent to which such diversity is reflected in their gut microbiota is still unknown. Here, we use metabarcoding of fecal samples to explore how the gut microbiome of G. galloti reflects variation in sex, environment, human footprint, and subspecies identity. Fecal samples of 47 individuals were obtained across 13 locations to reflect the extent of intraspecific variation in the species. We found no evidence for consistent differences in microbiota richness across the studied groups, regardless of whether analyses were carried out at the genus, family, or phylum levels. Moreover, neither the richness nor composition of the microbiota was associated with variation in mean annual temperature, annual precipitation, and human footprint. Our results suggest that the generalist diet of G. galloti exposes them to a broad range of food items that provide a common template across the island, despite ecological and historical differences between populations.}, }
@article {pmid40473091, year = {2025}, author = {Santos, FSA and Corgosinho, PHC and de Abreu, FVS and Vaca-Sánchez, MS and Cuevas-Reyes, P and de Faria, ML and Valério, HM and Borges, MAZ}, title = {Assessing the impact of different scale removal methods on the geometric morphometrics of Aedes aegypti wings.}, journal = {Acta tropica}, volume = {268}, number = {}, pages = {107686}, doi = {10.1016/j.actatropica.2025.107686}, pmid = {40473091}, issn = {1873-6254}, mesh = {Animals ; *Aedes/anatomy &amp; histology ; *Wings, Animal/anatomy &amp; histology ; Sodium Hydroxide ; Glycerol ; }, abstract = {This work aimed to test different treatments for removing wing scales from Aedes aegypti, and evaluate through geometric morphometrics, if these treatments can modify the wing venation morphometric pattern. The treatments were wing agitation in mineral water and NaOH (sodium hydroxide) saline solution using a mini-ultrasound, and manual wing scales removal using a size zero (0) tip brush. We propose an alternative method for mounting wings on slides using glycerin. We conclude that glycerin use for slide mounting provides better optics and translucency, and that treatments with NaOH saline solution and water can impair morphometric analysis of wings. The size zero (0) tip brush treatment efficiently removed wing scales, improving wing structure visualization without causing significant modifications to the specimens.}, }
@article {pmid40471139, year = {2025}, author = {Gawish, R and Varada, R and Deckert, F and Hladik, A and Steinbichl, L and Cimatti, L and Milanovic, K and Jain, M and Torgasheva, N and Tanzer, A and De Paepe, K and Van de Wiele, T and Hausmann, B and Lang, M and Pechhacker, M and Ibrahim, N and De Vries, I and Brostjan, C and Sixt, M and Gasche, C and Boon, L and Berry, D and Jantsch, MF and Pereira, FC and Vesely, C}, title = {Filamin A editing in myeloid cells reduces intestinal inflammation and protects from colitis.}, journal = {The Journal of experimental medicine}, volume = {222}, number = {9}, pages = {}, pmid = {40471139}, issn = {1540-9538}, support = {57-B28//Austrian Science Fund/ ; V 1025-B//Austrian Science Fund/ ; DOC32-B28//Austrian Science Fund/ ; F8007//Austrian Science Fund/ ; P32678//Austrian Science Fund/ ; //Medical University of Vienna/ ; }, mesh = {*Filamins/genetics/metabolism ; Animals ; *Myeloid Cells/metabolism/pathology ; Humans ; *Colitis/genetics/pathology/prevention &amp; control ; *Inflammation/pathology/genetics ; Mice ; Mice, Inbred C57BL ; Neutrophils/metabolism ; *RNA Editing ; Macrophages/metabolism ; Male ; }, abstract = {Patho-mechanistic origins of ulcerative colitis are still poorly understood. The actin cross-linker filamin A (FLNA) impacts cellular responses through interaction with cytosolic proteins. Posttranscriptional A-to-I editing generates two forms of FLNA: genome-encoded FLNAQ and FLNAR. FLNA is edited in colon fibroblasts, smooth muscle cells, and endothelial cells. We found that the FLNA editing status determines colitis severity. Editing was highest in healthy colons and reduced during murine and human colitis. Mice that exclusively express FLNAR were highly resistant to DSS-induced colitis, whereas fully FLNAQ animals developed severe inflammation. While the genetic induction of FLNA editing influenced transcriptional states of structural cells and microbiome composition, we found that FLNAR exerts protection specifically via myeloid cells, which are physiologically unedited. Introducing fixed FLNAR did not hamper cell migration but reduced macrophage inflammation and rendered neutrophils less prone to NETosis. Thus, loss of FLNA editing correlates with colitis severity, and targeted editing of myeloid cells serves as a novel therapeutic approach in intestinal inflammation.}, }
@article {pmid40469738, year = {2025}, author = {Amen, R and Ganzert, L and Friedl, T and Rybalka, N and Wagner, D}, title = {From single pioneers to complex pro- and eukaryotic microbial networks in soils along a glacier forefield chronosequence in continental Antarctica.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1576898}, pmid = {40469738}, issn = {1664-302X}, abstract = {INTRODUCTION: In the extremely dry and oligotrophic soils of East Antarctica, where low temperatures and humidity result in minimal biological turnover rates, extracellular DNA (eDNA) can persist over extended timescales. Differentiating between sequences from living, potentially active cells (intracellular DNA, or iDNA) and those from ancient, non-living organisms (eDNA) is crucial for accurately assessing the current microbial community and understanding historical microbial dynamics.<br><br>METHODS: This study was conducted along a chronosequence in the Larsemann Hills, East Antarctica, where soil samples were collected from sites at varying distances from the glacier. By employing DNA separation methods, we distinguished iDNA, which represents living cells, from eDNA derived from dead organisms. High-throughput sequencing was used to characterize bacterial and eukaryotic communities across different successional stages.<br><br>RESULTS: The DNA separation approach revealed distinct bacterial and eukaryotic community structures along the glacier transect. Actinobacteria were consistently abundant across all sites, while other phyla such as Chloroflexi, Gemmatimonadetes, and Proteobacteria thrived in extreme, nutrient-poor environments. Early successional stages were characterized by the simultaneous colonization of green algae Trebouxiophyceae and cryophilic fungi, alongside nitrogen-fixing bacteria, which contributed to initial soil development. The study also identified three distinct modes of microbial distribution, reflecting varying degrees of activity and adaptability.<br><br>DISCUSSION: Our findings provide new insights into microbial dynamics in extreme habitats and propose new hypotheses for microbial colonization in newly exposed soils. Moreover, they contribute to the ongoing debate in microbial ecology regarding the viability of dormant or dead cells and emphasize the need for refining DNA-based methods and exploring functional pathways to deepen our understanding of microbial succession in polar regions.}, }
@article {pmid40469504, year = {2025}, author = {Van Den Bossche, T and Armengaud, J and Benndorf, D and Blakeley-Ruiz, JA and Brauer, M and Cheng, K and Cresk