@article {pmid41874457,
year = {2026},
author = {Mohr, AE and Berryman, CE and Harris, MN and Lawrence, AB and Chakraborty, N and Campbell, R and Dimitrov, GI and Gautam, A and Hammamieh, R and Lieberman, HR and Rood, JC and Pasiakos, SM and Karl, JP},
title = {Testosterone administration partially modulates gut microbiota responses to severe energy deficit.},
journal = {American journal of physiology. Endocrinology and metabolism},
volume = {330},
number = {5},
pages = {E606-E626},
doi = {10.1152/ajpendo.00291.2025},
pmid = {41874457},
issn = {1522-1555},
support = {W81XWH-14-1-0335//DOD | OSD | Defense Technical Information Center (ADD)/ ; W81XWH-17-2-0026//DOD | OSD | Defense Technical Information Center (ADD)/ ; Joint Program Committee-5//Military Operational Medicine Research Program (MOMRP)/ ; //DOE | Oak Ridge Institute for Science and Education (ORISE)/ ; T32DK137525//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; *Testosterone/pharmacology/analogs & derivatives/administration & dosage ; *Energy Metabolism/drug effects ; Adult ; Fatty Acids, Volatile/metabolism ; Feces/chemistry/microbiology ; Young Adult ; Exercise/physiology ; *Androgens/pharmacology/administration & dosage ; Energy Intake/drug effects ; Double-Blind Method ; },
abstract = {Severe diet- and exercise-induced energy deficit (SED) suppresses androgen production in healthy men, altering metabolism and driving muscle loss. The gut microbiota modulates host metabolism, yet the community's response to SED and any role of androgen hormones are unclear. Herein, healthy, physically active men were randomized to receive 200 mg/wk testosterone enanthate (n = 24) or placebo (n = 26) during a 28-day residential intervention that restricted energy intake and increased energy expenditure inducing a ∼2,000 kcal/day SED. Multiomic analyses revealed altered gut microbiota composition, reduced fecal short-chain fatty acids (SCFA), and shifts in bacterial metabolic pathways toward lipid utilization and mucin degradation during SED, suggesting adverse effects of SED on gut microbiota metabolic functions. Testosterone administration preserved certain SCFA-producing taxa and bioenergetic pathways without fully counteracting the effects of SED indicating a limited but potentially important interplay between androgen status and the gut microbiota under conditions of SED.NEW & NOTEWORTHY This study is the first to demonstrate that testosterone administration partially preserves gut microbiota composition and metabolic function during severe energy deficit in healthy men. Using a multiomic approach, we show that testosterone modulates short-chain fatty acid-producing taxa and microbial pathways linked to host energy metabolism. These findings reveal a novel role for androgens in shaping host-microbiome interactions during catabolic stress and may inform strategies to maintain metabolic resilience.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Male
*Testosterone/pharmacology/analogs & derivatives/administration & dosage
*Energy Metabolism/drug effects
Adult
Fatty Acids, Volatile/metabolism
Feces/chemistry/microbiology
Young Adult
Exercise/physiology
*Androgens/pharmacology/administration & dosage
Energy Intake/drug effects
Double-Blind Method

@article {pmid41959403,
year = {2026},
author = {Maier, J and Gin, C and Rabasco, J and Bass, A and Spencer, W and Duerkop, BA and Callahan, B and Kleiner, M},
title = {TrIdent - An R package to automate transductomics analysis of virus-like particle mediated DNA mobilization.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41959403},
issn = {2692-8205},
support = {R01 AI171046/AI/NIAID NIH HHS/United States ; R35 GM138362/GM/NIGMS NIH HHS/United States ; },
abstract = {BACKGROUND: Transduction is a form of horizontal gene transfer in which bacterial DNA is packaged and transferred by virus-like particles (VLPs). Transductomics is a sequencing-based method used to detect DNA carried by VLPs. During transductomics analysis, reads from a sample's ultra-purified VLPs are mapped to metagenomic contigs assembled from the same sample's whole-community. The read mapping produces coverage patterns that require a time-consuming manual inspection and classification process which makes the method's use unfeasible for datasets with many samples.

RESULTS: We developed a novel algorithm, TrIdent (Transduction Identification), that uses pattern-matching to automate the transductomics data analysis and that is available as an R package (https://jlmaier12.github.io/TrIdent/). There is no software equivalent to TrIdent so we compared TrIdent's classifications of transductomics datasets to classifications made by human classifiers. TrIdent's classifications were generally comparable to the manual classifications on a previously generated, manually classified transductomics dataset. When applied to newly generated transductomics data from the murine microbiota, TrIdent agreed with two independent human classifiers as much as the two independent human classifications agreed with each other. TrIdent classified transductomics datasets in a fraction of the time needed by human classifiers, and the classifications produced by TrIdent are fully reproducible. We used TrIdent to explore three murine gut transductomes and found that bacterial DNA associated with the Oscillospiraceae and Turicibacteraceae families was highly enriched in the DNA packaged by VLPs as compared to the whole community metagenomes.

CONCLUSIONS: The TrIdent software is a more accessible, more efficient, and more reproducible alternative to the manual inspection of read coverage patterns previously required for transductomics data analysis. To demonstrate the application of TrIdent, we analyzed transductomics datasets from murine fecal pellets and showed that specific low abundance bacterial families appear to be heavily involved in transduction.},
}

@article {pmid42000489,
year = {2026},
author = {Della-Negra, O and Bru-Adan, V and Patureau, D and Ait-Mouheb, N and Wéry, N},
title = {Tracking antibiotic resistance genes and microbiome shifts under reclaimed wastewater irrigation: Root-associated selective modulation.},
journal = {Journal of environmental management},
volume = {405},
number = {},
pages = {129707},
doi = {10.1016/j.jenvman.2026.129707},
pmid = {42000489},
issn = {1095-8630},
abstract = {The reuse of treated wastewater (TWW) for crop irrigation reduces pressure on freshwater resources but may also disseminate antimicrobial resistance (AMR) through the presence of antibiotics, resistant bacteria and antibiotic resistant genes (ARGs). While many studies have examined the impact of water quality on dissemination of AMR in soils, the role of plants in filtering or accumulating AMR within the soil-plant continuum remains unclear. Here, we investigated the influence of irrigation water quality, plant species, and microbial compartments (soil, rhizosphere, roots) on bacterial communities and selected ARGs under controlled mesocosm conditions. Lettuce and leek were irrigated over two consecutive years with drinking water (DW), TWW, or raw wastewater (RWW). We monitored the abundance of ARGs sul1, ermB, and intI1 and characterized bacterial community composition by 16S rRNA sequencing. Soil microbiomes were influenced by water type and probably irrigation volume, and bacterial enrichment associated with DW, TWW, and RWW were identified. Plant-specific effects on soil microbiome were observed but were minor compared to the effect of water quality. Root microbiomes appeared more resilient than soils, as most taxa enriched in TWW- or RWW-irrigated soils were less or not amplified in roots, suggesting a potential barrier effect or at least selective processes at the root interface. Only Tahibacter and Rhodanobacteraceae increased in roots, while RWW irrigation also promoted the growth of the plant-pathogen Rhizorhapis. ARGs rose significantly in soils under TWW and RWW irrigation, with distinct year-to-year dynamics, but these shifts were not observed in root communities. Overall, our results indicate that root-associated compartments may contribute to modulate the dissemination of sul1, ermB, and intI1 ARGs in the plants irrigated with TWW.},
}

@article {pmid42000492,
year = {2026},
author = {Zhao, X and Zhang, S and Lai, X and Shi, D and Yang, C and Yu, H},
title = {Natural recovery trajectory of soil chemistry and microbiome after low-temperature thermal desorption remediation.},
journal = {Journal of environmental management},
volume = {405},
number = {},
pages = {129700},
doi = {10.1016/j.jenvman.2026.129700},
pmid = {42000492},
issn = {1095-8630},
abstract = {Urban soil contamination from historical industrial activities hinders sustainable redevelopment. Low-temperature thermal desorption is a common soil remediation strategy, offering efficient removal of volatile pollutants while limiting soil disruption. However, its ecological legacy and the potential for natural microbial recovery remain poorly understood. We tracked chemical and microbial recovery in an isolated urban brownfield for two years following remediation. Soil chemistry improved naturally over time: pH decreased from 9.1 to 8.2, total organic carbon rose from 2.3 to 5.4 g kg[-1], and carbon-to-nitrogen ratio increased from year 1 to year 2 post-remediation, although all remained below nearby urban greenspace soil (city park) soil levels. In contrast, salinity emerged as a new stressor in year 2, with electrical conductivity rising to 1.13 mS cm[-1], higher than both year 1 (0.41 mS cm[-1]) and the park (0.21 mS cm[-1]), likely due to the gradual weathering of quicklime additives applied during the thermal desorption process to enhance organic pollutant volatilization. Microbial abundance, measured by qPCR of total 16S rRNA genes, remained three orders of magnitude lower in remediated soils than park soils, but the microbial communities increased in diversity and network complexity. Functional annotations revealed a trajectory from mainly chemoheterotrophy in year 1 to a broader suite of metabolisms in year 2, though still distinct from park soils with substantially more nitrifying taxa. Collectively, these findings show that although qPCR-based microbial abundance suggests non appreciable recovery at first glance, the underlying communities exhibited clear post-remediation restructuring over two years. Persistent salinity and carbon limitation remain barriers, offering opportunities for targeted interventions-organic carbon replenishment, salinity management, and nitrogen-cycling taxa stimulation-to accelerate convergence toward resilient, multifunctional urban soils.},
}

@article {pmid42000498,
year = {2026},
author = {Wu, F and Deng, Y and Wu, Q and Chen, H and Mu, J and Zhang, Y and Meng, W and Li, N and Xie, L},
title = {Heteroaggregation with microalgae masks charge-dependent accumulation but amplifies charge-dependent toxicity of nanoplastics in mussels.},
journal = {Journal of hazardous materials},
volume = {510},
number = {},
pages = {142121},
doi = {10.1016/j.jhazmat.2026.142121},
pmid = {42000498},
issn = {1873-3336},
abstract = {In natural waters, nanoplastics (NPLs) often form heteroaggregates (HAs) with microalgae. Despite surface charge being a primary driver of NPL behavior, its role in governing HA toxicokinetics and impacts in bivalves remains largely unknown. Here, the effects of positively charged polystyrene NPLs (NPL+), their negative charged counterparts (NPL-), and the pre-formed HAs (HA+ and HA-) with the microalga Chlorella salina were evaluated in the green mussel (Perna viridis) during a 21-day exposure followed by 7-day elimination. HA+ and HA- enhanced NPL uptake in digestive gland and peripheral tissues, with uptake rate constants 1.5 - 4.0 times those of NPLs alone. Although 70 - 95% of accumulated NPLs were eliminated within 24 h, higher initial burdens under HA+ and HA- produced greater residual levels. NPL+ showed stronger uptake than NPL- due to greater electrostatic affinity with negatively charged epithelial surfaces. However, this charge-related uptake advantage was attenuated in HAs, concurrent with algal-like ζ-potentials of the heteroaggregates. Biological responses paralleled toxicokinetics, with HA+ inducing the strongest effects, including hemocyte dysfunction, oxidative stress, and fungal community disruption. Overall, HAs and surface charge jointly regulated NPL accumulation and toxicity in P. viridis, highlighting the need for ecological risk assessments to consider charge effects and HA formation to avoid underestimating NPLs hazards in filter-feeding bivalves.},
}

@article {pmid42000502,
year = {2026},
author = {Wang, Z and Wang, P and Yin, B and Gao, R and Dai, P and Lin, X and Sun, C},
title = {Enantioselective alteration of soil bacterial community assembly and keystone taxa under chiral triadimefon stress.},
journal = {Journal of hazardous materials},
volume = {510},
number = {},
pages = {142063},
doi = {10.1016/j.jhazmat.2026.142063},
pmid = {42000502},
issn = {1873-3336},
abstract = {Triadimefon, a representative chiral triazole fungicide, is ubiquitously applied as a racemic mixture and exhibits negative effects on microbiome in agroecosystems. However, its enantioselective effects on soil microbial community structure and assembly processes remain undefined. In this study, we investigated how bacteriome assembly responds to triadimefon at the enantiomeric level. It was found that the R- and S-enantiomers exerted distinct effects on bacterial diversity and community structure. Furthermore, deterministic processes dominated bacterial community assembly under chiral triadimefon. Co-occurrence network analysis revealed a distinct shift in microbial network across the chiral triadimefon treatments, revealing enantiomeric disparity in network organization to different enantiomers. Importantly, we identified 12 and 6 distinct key amplicon sequence variants (ASVs), respectively, selected by R- and S-enantiomers. These stereoselective key taxa are closely associated with bacterial community recombination trajectories. Overall, our research provides novel insights into understanding the enantioselective response of microbiome under chiral triadimefon and ideal targets to manipulate for contaminated situations. SYNOPSIS: Soil microbial community assembly exhibited striking differences in response to the R- and S-enantiomers of triadimefon, which are governed by the stereospecific selection imposed on the keystone taxa.},
}

@article {pmid42000515,
year = {2026},
author = {Qiu, Y and Yang, Y and Li, N and Li, X and Lu, Z and Zhou, Z and Feng, S and Liu, Y},
title = {Secondary chlorination enhanced the role of pipe materials in shaping chlorine-resistant microbiome and antibiotic resistome in secondary water supply systems.},
journal = {Journal of hazardous materials},
volume = {510},
number = {},
pages = {142114},
doi = {10.1016/j.jhazmat.2026.142114},
pmid = {42000515},
issn = {1873-3336},
abstract = {Secondary chlorination is often strategically applied in secondary water supply systems (SWSSs) with insufficient disinfectant residuals to suppress microbial regrowth. However, the associated risks posed by chlorine-resistant bacteria (CRB) and antibiotic resistance genes (ARGs) remain unclear. Herein, simulated SWSSs with different pipe materials and chlorine levels were operated for 220 days. Biomass in biofilms and bulk water was markedly reduced following chlorination, and extracellular polymeric substances responded more strongly in stainless steel (SS) pipes, with polysaccharides (70.28%) exhibiting a greater reduction than proteins (37.44%). Meanwhile, chlorination reduced bacterial diversity and reshaped community structure, boosting the contributions of biofilm and particulate phases to waterborne bacteria by 11.47%-15.60% and 17.52%-22.82%, respectively. Chlorination promoted the CRB enrichment (e.g., Nevskia and Sphingomonas), with higher relative abundance in polyvinyl chloride (PVC) pipes and more taxa in SS pipes. The decline in Legionella mitigated potentially pathogenic risks, particularly in chlorinated PVC pipes, despite nine of 13 potential pathogens being chlorine-resistant. Moreover, chlorination generally reduced the ARG absolute abundance but increased their relative abundance, with sulfonamide- and multidrug-ARGs being predominant. Regarding the ARG bacterial hosts, potential pathogens (e.g., Pseudomonas and Enterobacter) posed the highest risk, followed by non-pathogenic CRB (e.g., Herbaspirillum and Sediminibacterium) and chlorine-sensitive bacteria (e.g., Runella and Isosphaera). Vertical gene transfer dominated ARG transmission, while horizontal gene transfer occurred more readily in the water phase and was promoted in chlorinated PVC pipes. These findings provide novel insights into the microbial risk and antibiotic resistome, and may guide pipe material selection and disinfection optimization within SWSSs.},
}

@article {pmid42000726,
year = {2026},
author = {Zhou, X and Zhou, D and Pu, Y and Kim, H and Sun, Z and Qi, W and Jin, J and Zhang, W and Xia, M and Wang, C and Hong, S and Nguyen, LH and Jiao, N and Zheng, Y and Liu, T},
title = {Multi-kingdom profiling reveals altered gut phage-bacteria-metabolite interactions in MASLD.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71981-0},
pmid = {42000726},
issn = {2041-1723},
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is increasingly linked to gut microbial dysbiosis, but most studies have focused on bacteria, neglecting viruses and fungi, and their interactions. Here we show that MASLD is characterized by coordinated disruption of bacterial, viral and fungal communities and by a disturbed phage-bacteria-metabolite axis associated with disease-related bile acid changes. Integrating shotgun metagenomics, fungal ITS2 sequencing, fecal metabolomics and clinical profiling in 210 patients with MASLD and 210 age- and gender-matched healthy controls, we find reduced microbial diversity and extensive remodeling of cross-kingdom ecological networks in MASLD. Ruminococcus gnavus emerges as an enriched central hub, while Faecalibacterium prausnitzii and its associated bacteriophages are depleted. Phage-host analyses further reveal reduced lytic activity against R. gnavus and loss of sulfur amino acid metabolism-related auxiliary metabolic genes, which may impair F. prausnitzii fitness. Diminished phage control may facilitate R. gnavus expansion, alongside increased fecal isodeoxycholic acid, a secondary bile acid implicated in hepatic steatosis. A diagnostic classifier integrating bacterial and viral features with clinical parameters distinguish MASLD from controls in our cohort and maintain predictive performance in two external datasets. Together, these findings uncover a disrupted phage-bacteria-metabolite axis in MASLD and provide a multi-kingdom framework for non-invasive biomarker discovery and microbiome-targeted therapies.},
}

@article {pmid42000796,
year = {2026},
author = {Xu, P and Chen, J and Lu, X and Luo, H},
title = {Exploring the characteristics of gut microbiome changes in lung cancer patients and healthy controls.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-48560-w},
pmid = {42000796},
issn = {2045-2322},
abstract = {Lung cancer is among the most prevalent and lethal malignant neoplasms worldwide. Although the role of the pulmonary microbiome in the pathogenesis of lung cancer has been examined, the structure, diversity, and composition of the gut microbiome in lung cancer remain largely unclear. The present study is chiefly concerned with the analysis of the characteristics and alterations of the gut microbiome in lung cancer patients and healthy individuals, and with the exploration of potential characteristic gut microbiome in lung cancer patients. Stool samples were collected from 40 patients with lung cancer and 20 healthy controls at the Lung Cancer Center of West China Hospital, Sichuan University. The samples were analysed using 16S rRNA gene amplicon sequencing to investigate differences in the relative and absolute abundance, diversity, and functionality of the gut microbiome between the two groups. The predominant gut microbiome communities in lung cancer patients and healthy controls were found to comprise Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria. The F/B (Firmicutes/Bacteroidetes) ratio in the lung cancer group (0.73) was lower than that in the healthy control group (0.96). We found that there was no significant difference in α-diversity between LC patients and the control group (p > 0.05), whereas β-diversity of the gut microbiome revealed differences in microbial community structure between the patient and control groups (stress < 0.2). The healthy controls exhibited higher abundances of Bacteroidetes and Firmicutes as dominant bacterial groups, whereas the characteristic bacterial groups in lung cancer patients were the Ruminococcus_gnavus_group and the Prevotellaceae NK3B31 group. Studies have demonstrated that the gut microbiome of patients with lung cancer patients undergoes changes, and characteristic gut microbiome profiles may serve as potential diagnostic markers for lung cancer. Furthermore, we have revealed that impairments in normal gut microbiome function may be associated with the development and progression of lung cancer, providing valuable insights for the early prevention, diagnosis, and targeted intervention of lung cancer.},
}

@article {pmid42001039,
year = {2026},
author = {Li, S and White, JF and Zhai, Y and Li, X and Wang, K},
title = {Study on the diversity, structure, and function of endophytic bacteria in seeds of genuine medicinal plants in gansu province.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-08767-5},
pmid = {42001039},
issn = {1471-2229},
support = {25YFFA043//Gansu Provincial Key Research and Development Program/ ; },
}

@article {pmid42001079,
year = {2026},
author = {Yang, Y and Kang, C and Pang, R and Huang, S and He, X and Gou, X and Yang, Y and Yan, Y and Ma, X},
title = {Dihydromyricetin exerts neuroprotective effects in acute spinal cord injury by inhibiting NLRP3/Caspase-1 inflammasome through gut microbiome modeling.},
journal = {Journal of inflammation (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12950-026-00499-5},
pmid = {42001079},
issn = {1476-9255},
support = {2024060//Chengdu Municipal Health Commission Medical Research Project/ ; 25MSZX488//Sichuan Provincial Administration of Traditional Chinese Medicine Research Project/ ; },
}

@article {pmid42001152,
year = {2026},
author = {Leroy, M and Cyriaque, V and Rattei, T and Laurion, I and Comte, J},
title = {Microbiome and plasmidome shifts drive carbon, nitrogen, and greenhouse gas dynamics within transitioning permafrost.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00892-w},
pmid = {42001152},
issn = {2524-6372},
support = {2021-PR-284297//Fonds de recherche du Québec - Nature et technologie/ ; RGPIN-2020-06876//Natural Sciences and Engineering Research Council - Discovery and Northern Research Programs/ ; RGPIN-2020-06874//Natural Sciences and Engineering Research Council - Discovery and Northern Research Programs/ ; 2021-PR-284297//Fonds de recherche du Québec - Nature et technologies/ ; },
abstract = {Thermokarst lakes contribute to greenhouse gas emissions but often experience constraints on available nitrogen. However, the interactions between carbon and nitrogen cycles in these systems, especially along the terrestrial-aquatic continuum, remain poorly understood. The increased soil-water connectivity in those systems affects organic matter processing, nutrient availability, and microbial transport. In Nunavik (Quebec, Canada), we sampled along a transect from a palsa (permafrost remnant) through an emerging thermokarst lake to peatland soils and mature lake. Using hybrid metagenome co-assemblies with gene-, plasmid-, and genome-centric approaches, we explored key biogeochemical cycles and the role of plasmids in microbial adaptation along the transect. Gene annotation, metagenome-assembled genome (MAG) reconstruction, and network analysis revealed a shift from potential for anaerobic ammonium oxidation (anammox) in palsa and emerging lake to potential for nitrification in mature lake. Potential for methanogenesis transitions from hydrogenotrophic in the palsa to methylotrophic in lakes, likely driven by a bacterial consortium degrading aromatic, peat-derived compounds. Sediments may support methane production via both hydrogenotrophic and acetoclastic potential for methanogenesis, partially fueled by the action of polysaccharide lyases. Anaerobic methane oxidation (AOM) potential seems important in both peat and the mature lake; and can be coupled with nitrification and sulfate-reducing partners through extracellular electron transfer, with cytochromes playing a central role. Notably, plasmidome shifts preceded metagenomic changes, especially in genes related to carbon and methane cycling, suggesting a role for plasmids in microbial adaptation to permafrost thaw. These findings highlight the complex microbial and plasmid dynamics that drive carbon, nitrogen, and greenhouse gas cycles in permafrost ecosystems.},
}

@article {pmid42001319,
year = {2026},
author = {Romandini, M and Hajishengallis, G and Curtis, M and Baima, G},
title = {Periodontal Medicine Rewired: Mechanisms Linking Periodontitis to Systemic Diseases.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.70099},
pmid = {42001319},
issn = {1600-0765},
abstract = {Periodontitis is now recognized not merely as a localized oral condition but as a systemic disease linked to over 70 communicable and non-communicable conditions. This Review explores the key mechanistic pathways-or "gum-shots"-underpinning the systemic impact of periodontitis. Seven interwoven mechanisms are identified. The first, microbial translocation, involves oral pathobionts and virulence factors breaching anatomical barriers and gaining systemic access via hematological, respiratory, and enteral routes, contributing to tissue damage at extra-oral sites. The second, systemic (meta)inflammation, implicates both the spillover of inflammatory mediators from periodontal tissues into circulation and the immune response to translocated pathogens, fueling pro-inflammatory processes. The third, maladaptive myelopoiesis, involves the periodontitis-associated maladaptive trained immunity and aging-related clonal hematopoiesis of indeterminate potential in the bone marrow, leading to myeloid cells with heightened proinflammatory potential. The fourth, immune players trafficking, centers on the systemic repercussions of periodontally generated autoantibodies, translocated orally primed inflammatory cells, and other local immune events. The fifth, masticatory dysfunction-mediated dietary alterations, involves compromised chewing efficiency that alters dietary intake, resulting in nutritional and metabolic imbalances. The sixth, functional dysregulation of the oral microbiome, describes how periodontitis alters the metabolic activity of this densely populated microbial "superorganism", with downstream effects on both oral and systemic physiology. The final mechanism, shared underlying vulnerabilities, refers to background entities-such as biological aging, oxidative stress, psychosocial stress, (epi)genetic predispositions, certain viral infections, and potentially other as-yet-unknown contributors-that drive multi-morbidity, including periodontitis. By dissecting these interconnected pathways, this critical Review challenges the traditional dichotomy of direct versus indirect mechanisms, revealing a more intricate and dynamic interplay.},
}

@article {pmid42001402,
year = {2026},
author = {Boroumand, B and Jaberi, A and Zamani, G and Zandi, E and Zare, F and Vahedinezhad, M and Abdollahi, E and KarkonShayan, S and GhazanfarAhari, S and Sattar, M},
title = {Therapeutic Remodeling of the Gut Microbiome as a Strategy to Restore Immune Tolerance in Autoimmunity.},
journal = {MicrobiologyOpen},
volume = {15},
number = {2},
pages = {e70294},
pmid = {42001402},
issn = {2045-8827},
mesh = {*Gastrointestinal Microbiome/immunology ; Humans ; *Autoimmune Diseases/therapy/immunology/microbiology ; *Dysbiosis/immunology/therapy/microbiology ; *Immune Tolerance ; *Autoimmunity ; Animals ; },
abstract = {Autoimmune diseases happen when the immune system, which is supposed to defend the body from infections and other harmful things, starts to attack the body's own cells by mistake. In the last few years, they seem to be getting more public, and the reasons are quite complicated. It is usually not just one factor, but a mix of genes and environmental influences, such as diet, infections, or even stress. The gut microbiome, the vast community of bacteria and other tiny organisms living in our intestines, plays an important role in shaping how the immune system behaves. When this gut microbiota becomes unstable (a state called dysbiosis), it can be associated with the onset or worsening of various autoimmune diseases. In this review, we discuss the close relationship between the gut microbiome and autoimmune disorders and focus on how the microbiome can affect immune activation, immune tolerance, and inflammation at the molecular level. The general idea is that, if we understand these interactions better, we might be able in the future to design new ways to manage autoimmune diseases earlier and maybe in a more personalized way. In the end, the review suggests that if we understand better how the microbiome is involved in autoimmune diseases, it might be possible in the future to design more personalized therapies that change gut bacteria in a smart way and hopefully improve patient outcomes.},
}

*Gastrointestinal Microbiome/immunology
Humans
*Autoimmune Diseases/therapy/immunology/microbiology
*Dysbiosis/immunology/therapy/microbiology
*Immune Tolerance
*Autoimmunity
Animals

@article {pmid42001407,
year = {2026},
author = {Zhao, B and Li, D and Yang, Y and Hou, T and Hu, L},
title = {DRHIN: An Integrated and Interactive Web Server for Drug Repositioning.},
journal = {Journal of chemical information and modeling},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jcim.6c00311},
pmid = {42001407},
issn = {1549-960X},
abstract = {Drug repositioning (DR) identifies new therapeutic uses for approved drugs, reducing development burdens and offering safer treatment options for patients. While high-throughput technologies generate complex, large-scale multiomics data, existing DR tools struggle to comprehensively analyze the resulting biological networks. To address this challenge, we present DRHIN, an integrated, interactive web server for DR over heterogeneous information networks (HINs) using advanced deep learning techniques. DRHIN integrates transcriptomics, proteomics, and microbiome data, incorporating eight biological entities and 19 association types to build diverse HINs and elucidate the underlying molecular mechanisms. It includes 19 state-of-the-art graph representation algorithms, enabling flexible training, comparison, and evaluation of heterogeneous network data. The platform provides a code-free portal supporting three key predictive tasks: discovering drug-disease associations, repurposing existing drugs for new indications, and identifying potential therapies for specific diseases, making analyses accessible and reproducible. Leveraging high-performance computing, DRHIN efficiently processes million-scale networks, ensuring practical applicability in real-world scenarios. The web server is freely accessible at http://drhin.tianshanzw.cn.},
}

@article {pmid42001412,
year = {2026},
author = {Maria Lewis, B and Prashanth, A and Ramachandran, N and Sabat, S},
title = {Mutation studies on degradation of 3-phenoxybenzoic acid by Lacticaseibacillus paracasei - human gut microbiome in controlling risk for Parkinson's disease using molecular simulation dynamics.},
journal = {Journal of biomolecular structure & dynamics},
volume = {},
number = {},
pages = {1-28},
doi = {10.1080/07391102.2026.2653065},
pmid = {42001412},
issn = {1538-0254},
abstract = {Parkinson's disease (PD) is a debilitating neurodegenerative disease affecting millions worldwide, especially the elderly. Pesticides, particularly pyrethroids like Cypermethrin, have been linked to the development of PD. Cypermethrin, when ingested, is broken down into 3-phenoxybenzoic acid (3PBA), which can lead to the dysfunction or death of dopaminergic neurons. Catechol-2,3-dioxygenase is an enzyme that breaks down 3PBA into catechol, that can further be processed and excreted by the human body. This enzyme is produced by the bacteria Lacticaseibacillus paracasei, a naturally present human gut microbe. Mutation studies were done to study the potential of the human gut microbiome in pesticide degradation improve the activity of the wild-type enzymes in degrading pesticides. The mutations were induced in two subunits of Catechol-2,3-dioxygenase using the WGS sequence of the gene coding for the same. Two subunits of the same protein i.e. Catechol-2,3-dioxygenase and NAD(+) reductase, were subjected to mutations using PyMol v3.1.0, and the crystal structures of the wild-type and mutant were docked against the ligand, 3-Phenoxybenzoic acid, using PyRx v0.8, and visualised using BIOVIA Discovery Studio Visualiser v24.1.0.23298, PyMol v3.1.0 and LigPlot + v2.2.9. The effects of mutation were further studied by analyzing the results of the molecular dynamics simulations conducted using the GROMACS software. Simulation trajectories like RMSD, RMSF, Inter and Intramolecular H-bonds, SASA, RG, PCA, FEL and FEP, all indicated better binding of the ligand (3PBA) to the active site.},
}

@article {pmid42001450,
year = {2026},
author = {Yao, J and Fei, C and Wu, H and Zhang, Z and Jiang, Z},
title = {Characterization of the Oral Bacteria in Patients With Neuroendocrine Tumors of the Pancreas.},
journal = {Cancer medicine},
volume = {15},
number = {4},
pages = {e71840},
doi = {10.1002/cam4.71840},
pmid = {42001450},
issn = {2045-7634},
support = {YKK20108//Nanjing health science and technology development special fund project plan/ ; NMUB2019134//Science and Technology Development Project of Nanjing Medical University/ ; },
mesh = {Humans ; Male ; *Pancreatic Neoplasms/microbiology ; Female ; *Neuroendocrine Tumors/microbiology/diagnosis ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; *Dysbiosis/microbiology ; *Microbiota ; *Bacteria/genetics/classification/isolation & purification ; Adult ; *Saliva/microbiology ; Aged ; Case-Control Studies ; Prognosis ; *Mouth/microbiology ; },
abstract = {The primary objective of this study was to investigate dysbiosis in the oral microbiota of patients with pancreatic neuroendocrine tumors (pNETs) and to identify potential biomarkers for clinical diagnosis and prognostic evaluation of pNETs. Healthy controls and pNETs patients were recruited from our hospital. Salivary flora were profiled in healthy subjects (HS group) and pNETs patients (PS group) using 16S rRNA gene sequencing. Microbial diversity was assessed by α-diversity (Tukey test) and β-diversity (Partial Least Squares Discriminant Analysis, PLS-DA). Taxonomic differences between groups were evaluated using linear discriminant analysis effect size (LEfSe). The salivary microbiota of pNETs patients showed higher abundance and diversity compared to healthy controls. Dominant bacterial phyla in both groups include Proteobacteria, Firmicutes, Bacteroidota, Actinobacteriota, Fusobacteriota, Cyanobacteria, and Campilobacterota. At the genus level, Leptotrichia, Actinobacillus, and Granulicatella were more abundant in the PS group. LEfSe analysis further indicated a greater abundance of Rothia, Chloroplast, Leptotrichia, Actinomyces, and Granulicatella in the PS group. Our findings offer initial evidence suggesting a potential link between oral microbiome dysbiosis and pNETs, and identify microbial features that could be evaluated in future studies as potential biomarkers for clinical diagnosis and prognosis.},
}

Humans
Male
*Pancreatic Neoplasms/microbiology
Female
*Neuroendocrine Tumors/microbiology/diagnosis
Middle Aged
RNA, Ribosomal, 16S/genetics
*Dysbiosis/microbiology
*Microbiota
*Bacteria/genetics/classification/isolation & purification
Adult
*Saliva/microbiology
Aged
Case-Control Studies
Prognosis
*Mouth/microbiology

@article {pmid42001830,
year = {2026},
author = {Vijayakumar, V and Rathinam, T and Deenadhayalan, SS and Edwin, ER},
title = {Human microbiome influence on head and neck cancer.},
journal = {Cancer treatment and research communications},
volume = {47},
number = {},
pages = {101218},
doi = {10.1016/j.ctarc.2026.101218},
pmid = {42001830},
issn = {2468-2942},
abstract = {Recent breakthroughs in microbiome research have identified the gut microbiota as an important regulator of systemic immunity, inflammation, and carcinogenesis. Although established risk factors for head and neck cancer (HNC) include tobacco use, alcohol use, and human papillomavirus (HPV) infection, growing data suggest that gut microbial dysbiosis may also play a role in its etiology. Changes in gut microbiota composition can have a distal influence on the head and neck region by modulating immune function, producing microbial metabolites, and disrupting epithelial barrier integrity, influencing tumor initiation, development, and therapeutic response. New research suggests that the gut microbiome plays an important role in regulating the success and toxicity of traditional HNC treatments such as chemoradiation and immunotherapy. This review focuses on current evidence linking alterations in the gut microbiome to HNC development and progression, emphasizing underlying mechanisms, diagnostic potential, and emerging microbiome-based therapeutic strategies.},
}

@article {pmid42001862,
year = {2026},
author = {Özcan, F and Arserim, NB},
title = {Antibacterial immunity in teleost fish: Integrating innate and adaptive responses for sustainable aquaculture.},
journal = {Veterinary immunology and immunopathology},
volume = {297},
number = {},
pages = {111113},
doi = {10.1016/j.vetimm.2026.111113},
pmid = {42001862},
issn = {1873-2534},
abstract = {Bacterial infections are currently the most significant hindrance to the worldwide adoption of sustainable aquaculture, causing unprecedented economical losses and challenges to food security. Teleosts have an extremely well-developed innate and adaptive immune system, but the functional integrity of these immune systems is adversely affected under universal aquaculture-related stress factors. The current review critically and comprehensively synthesizes the two most important challenges, addressing immune resilience, which include: (1) the complex functional interactions between innate and adaptive immune mechanisms, and (2) the combined modulation of these immune mechanisms under environmental factors mentioned above. Our focus primarily centers on the role of major stressors such as temperature change, water quality measures, (physiological) chronic stressing, and microbiome diversity on innate host immunity and resistance to bacterially infected diseases. Finally, we not only conclude the current state regarding the latest research progress on the role and mechanisms utilized in the transition phase from the latent to chronic infection phase based on autophagy-related responses but also emphasize the need to adopt an integrated research area named 'Eco-Immunology' to measure and develop effective interventions against fish diseases. It is the prime requirement to improve the host's resistance to diverse farming conditions to develop sustainable and effective aquaculture. This review uniquely integrates innate-adaptive immune crosstalk with environmentally driven immune reprogramming and autophagy-mediated control of chronic bacterial infections, framing teleost antibacterial immunity within an eco-immunological perspective relevant to sustainable aquaculture.},
}

@article {pmid42002154,
year = {2026},
author = {Dang, CP and Chen-Liaw, A and Xue, M and Luchak, A and Mu, K and Li, Q and Ren, MY and Lee, SH and Moayyedi, P and Griffiths, AM and Deslandres, C and Murthy, SK and Steinhart, AH and Otley, A and Dieleman, LA and Jacobson, K and Rubin, DT and Panaccione, R and Feagan, BG and Streutker, C and Mogno, I and Britton, GJ and Faith, JJ and , and Croitoru, K and Turpin, W},
title = {Pre-Crohn's Disease Stool from Discordant Siblings Promotes the Development of Colitis in Germ-Free Mice.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2026.03.023},
pmid = {42002154},
issn = {1528-0012},
abstract = {BACKGROUND AND AIMS: The gut microbiome is implicated in Crohn's disease (CD) development. However, human microbiome studies need experimental evidence to demonstrate if specific microbial differences promote CD pathogenesis. This study aims to determine if the gut microbiome from individuals who later developed CD promotes colitis in germ-free recipient mice.

METHODS: Germ-free mice were colonized with fecal samples from 12 pairs of discordant siblings: where one sibling later developed CD (pre-CD), while the other remained a healthy matched control (HMC). After colonization, colitis was induced by T-cell transfer to assess effect of stool on multiple measures of colitis severity. Comparative analysis with human donor metadata explored transferred pathogenic traits.

RESULTS: Mice receiving pre-CD stool exhibited increased weight loss, fecal lipocalin-2, and intestinal histological damage compared to mice receiving HMC stool. Fecal metabolomic analysis revealed differences in 40 metabolites between pre-CD and HMC colonized mice. Furthermore, two metabolic pathways were shared between pre-CD participants and mice. Notably, sphingolipids showed a positive correlation between humans and mice, associated with increased colitis in mice.

CONCLUSION: This study functionally demonstrates that the stool microbiome of individuals susceptible to CD is altered years before diagnosis, exhibiting greater inflammatory potential when transferred to susceptible mice.},
}

@article {pmid42002159,
year = {2026},
author = {Liu, X and Li, S and Huang, C and Liu, Y and Dong, Y and Gong, H and Zhou, G},
title = {Iron plaque on wetland plant roots serves as a hotspot at the rhizosphere and a barrier within the endosphere for antibiotic resistance gene dissemination.},
journal = {Bioresource technology},
volume = {453},
number = {},
pages = {134648},
doi = {10.1016/j.biortech.2026.134648},
pmid = {42002159},
issn = {1873-2976},
abstract = {The iron plaque (IP) on wetland plant roots provides a crucial microenvironment for pollutant transport and transformation, yet its influence on the migration and dissemination of antibiotic resistance genes (ARGs) remains unexplored. Plasmid conjugation greatly contributes to ARG spreads. This study investigated the effect of IP formation on the plasmid-mediated ARG transfer across rhizosphere-iron plaque-root endosphere continuum and identified the key factors driving this process. Both the quantification of target genes and visual evidence demonstrated that conjugation frequencies within IP increased in a dose-dependent manner with the amount of IP formed on the root surface. In contrast, conjugation frequencies in the endosphere declined significantly as IP increased. The elevated IP content enhanced cell membrane permeability, raised reactive oxygen species (ROS) levels, and increased the activities of antioxidant enzymes including superoxide dismutase (SOD) and catalase (CAT). A significant positive correlation was observed between ROS levels and conjugation frequencies, as well as between the activities of antioxidant enzymes (SOD and CAT) and IP formation. The bacterial community structure was significantly shaped in root compartments. The transconjugal pool was phylogenetically constrained, dominated by Gammaproteobacteria such as Escherichia and Pseudomonas, which accounted for over 70% of transfer events despite representing less than 3% of the total bacterial community. Our findings imply that IP functions as both a hotspot for ARG transfer on root surfaces and a barrier against their entry into the root interior, which guide and optimize the application of IP in the phytoremediation of emerging contaminants including ARGs.},
}

@article {pmid42002228,
year = {2026},
author = {Liu, S and Huang, Z and Guo, Z},
title = {Fecal Microbiota Transplantation for gastrointestinal complications after Allogeneic Hematopoietic Cell Transplantation: a systematic review and narrative synthesis.},
journal = {Transplantation and cellular therapy},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtct.2026.04.016},
pmid = {42002228},
issn = {2666-6367},
abstract = {BACKGROUND: Following allogeneic hematopoietic stem cell transplantation (allo-HSCT), patients frequently develop gastrointestinal complications, including microbiota dysbiosis, infectious syndromes, and graft-versus-host disease (GVHD), which remain major contributors to post-transplant morbidity and mortality. In recent years, several studies have explored microbiome-based interventions, particularly fecal microbiota transplantation (FMT), as a therapeutic strategy for these complications in this highly immunocompromised population. However, substantial variability exists across studies with respect to clinical indications, FMT protocols, and reported outcomes.

OBJECTIVES: To systematically evaluate the reported clinical use of FMT for gastrointestinal complications following allo-HSCT, including microbiota dysbiosis, infectious complications, and GVHD. The aim was to characterize study populations, treatment protocols, and reported clinical outcomes, and to synthesize evidence regarding efficacy and safety, with a focus on indication-specific patterns and potential translational relevance for patient management in this highly immunocompromised population.

STUDY DESIGN: We conducted a PRISMA-compliant systematic review of studies evaluating FMT as a treatment in patients after allo-HSCT. PubMed, Embase, Web of Science, and the Cochrane Library were searched through October 2025. Eligible studies included randomized controlled trials, cohort studies, and prospective or retrospective single-arm studies reporting clinical outcomes following FMT. Given the marked heterogeneity in clinical indications, FMT administration strategies, and outcome definitions, study findings were synthesized using a structured narrative approach, with quantitative data summarized descriptively where appropriate.

RESULTS: Twenty studies including patients after allo-HSCT were analyzed. FMT demonstrated high and consistent response rates in non-GVHD indications, whereas GVHD cohorts exhibited more variable responses, with median CR and ORR ranging 50-55% in steroid-refractory cases. One-year overall survival was generally favorable in dysbiosis and infection groups (>70%), but more heterogeneous in GVHD. FMT was well tolerated, with predominantly mild gastrointestinal adverse events; serious events were infrequent and mostly disease-related.

CONCLUSIONS: Current evidence indicates that FMT has been explored as a context-dependent therapy for selected gastrointestinal complications following allo-HSCT, particularly in patients with aGVHD. Nevertheless, substantial heterogeneity in study design, clinical indications, and outcome assessment limits definitive conclusions regarding efficacy. Well-designed prospective studies with standardized treatment indications, outcome measures, and careful consideration of concurrent immunosuppressive therapies are required to better define the optimal role, timing, and patient selection for FMT in the post-transplant treatment setting.},
}

@article {pmid42002296,
year = {2026},
author = {Yang, X and Zhang, L and Zhou, S and Wang, Z and Lv, Q and Zhao, M and Wang, C},
title = {Mechanisms Underlying Bioactive Compounds Decline in Medicinal Blaps rhynchopetera During Artificial Rearing.},
journal = {Environmental microbiology},
volume = {28},
number = {4},
pages = {e70304},
doi = {10.1111/1462-2920.70304},
pmid = {42002296},
issn = {1462-2920},
support = {2022YFC2602500//National Key Research and Development Program of China/ ; JiaoWaiSiYa[2020]619//Lancang-Mekong Cooperation Special Fund Projects/ ; SAJC202402//Chinese Academy of Sciences/ ; 2025YKZY002//Yunnan Characteristic Plant Extraction Laboratory/ ; 202449CE340005//Yunnan Provincial Science and Technology Department/ ; 202305AH340007//Yunnan Provincial Science and Technology Department/ ; },
mesh = {Animals ; *Coleoptera/microbiology/metabolism/growth & development ; *Gastrointestinal Microbiome ; Bacteria/metabolism/genetics/classification/isolation & purification ; Metabolome ; Biological Products/metabolism ; },
abstract = {Artificial rearing is essential for sustainable utilization of medicinal insects, yet its impact on bioactive compound production remains poorly understood. Here we provide preliminary evidence that rearing of the medicinal beetle Blaps rhynchopetera reshapes its gut microbiota and metabolome, beyond mere environmental effects. Metabolomic analysis revealed 727 significantly altered metabolites, with 436 compounds, many linked to analgesic and anti-inflammatory activities, markedly reduced under rearing. Network pharmacology analysis suggested that this metabolic remodelling alters the overall regulatory landscape, with reduced network complexity compared to wild counterparts. Metagenomic profiling uncovered a decline in Pseudomonadota, a phylum positively correlated with multiple bioactive metabolites. Preliminary reintroduction of four Pseudomonadota strains suggested their potential involvement in terpenoid backbone biosynthesis, a key pathway for natural product synthesis. These findings reveal an intrinsic trade-off between rearing-driven microbial homogenization and preservation of medicinal potency, highlighting the need for microbiome-informed rearing strategies.},
}

Animals
*Coleoptera/microbiology/metabolism/growth & development
*Gastrointestinal Microbiome
Bacteria/metabolism/genetics/classification/isolation & purification
Metabolome
Biological Products/metabolism

@article {pmid42002330,
year = {2026},
author = {Zhao, Y and Qiao, M and Ma, C and Hou, Q and Hu, J and Yang, J},
title = {A fructan-type polysaccharide from Lycium ruthenicum attenuates liver fibrosis via microbiota-dependent ferroptosis inhibition.},
journal = {Carbohydrate polymers},
volume = {382},
number = {},
pages = {125243},
doi = {10.1016/j.carbpol.2026.125243},
pmid = {42002330},
issn = {1879-1344},
mesh = {Animals ; *Liver Cirrhosis/drug therapy/metabolism/pathology/chemically induced ; *Gastrointestinal Microbiome/drug effects ; *Lycium/chemistry ; *Ferroptosis/drug effects ; Mice ; Male ; *Polysaccharides/pharmacology/chemistry ; Mice, Inbred C57BL ; *Fructans/pharmacology/chemistry ; Liver/drug effects/metabolism/pathology ; Oxidative Stress/drug effects ; },
abstract = {Plant-derived polysaccharides represent promising candidates for hepatic fibrosis (HF) therapy through the gut-liver axis. This study investigated the structural characteristics, anti-fibrotic efficacy, and mechanisms of LRMP1, a novel polysaccharide from Lycium ruthenicum Murr. LRMP1 was identified as a homogeneous inulin-type fructan (3.055 kDa) with a → 1)-β-D-Fruf-(2 → backbone terminated by α-D-Glcp-(1 → 2)-β-D-Fruf linkages (DP 4-20). Integrated multi-omics analysis combining hepatic transcriptomics, serum metabolomics, and gut microbiome profiling revealed that LRMP1 ameliorates HF via a gut microbiota-postbiotics-ferroptosis regulatory axis. In both CCl4-induced and MCD diet-induced chronic fibrosis models, LRMP1 significantly attenuated liver injury, fibrosis, inflammation, and oxidative stress, while restoring intestinal barrier integrity. These protective effects correlated with enrichment of beneficial bacteria (Akkermansia muciniphila, Lactobacillus spp.) and pathogen depletion. Mechanistically, LRMP1 suppressed TGF-β signaling and inhibited hepatocyte ferroptosis by restoring the GPX4/SLC7A11 antioxidant system and reducing lipid peroxidation. Serum metabolomics further revealed elevated anti-ferroptotic metabolites and suppressed pro-inflammatory lipids. Crucially, antibiotic depletion abolished LRMP1's efficacy, whereas fecal microbiota transplantation and fermentation supernatant experiments confirmed that microbiota-derived postbiotics selectively protect hepatocytes from ferroptosis. These findings establish LRMP1 as a promising microbiota-targeted polysaccharide for HF intervention through the gut-liver axis.},
}

Animals
*Liver Cirrhosis/drug therapy/metabolism/pathology/chemically induced
*Gastrointestinal Microbiome/drug effects
*Lycium/chemistry
*Ferroptosis/drug effects
Mice
Male
*Polysaccharides/pharmacology/chemistry
Mice, Inbred C57BL
*Fructans/pharmacology/chemistry
Liver/drug effects/metabolism/pathology
Oxidative Stress/drug effects

@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 & 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 {pmid42002490,
year = {2026},
author = {Liao, B and Chen, L and Ruan, J and Wang, R and Hu, B and Long, R and Li, Y and Zhang, G and Yu, J and Ming Zhang, and Zhang, Y and Liao, S},
title = {Corrigendum to "Microbiome and gartynecologic cancer" [Cancer Lett. 636 (2026) 217940].},
journal = {Cancer letters},
volume = {},
number = {},
pages = {218519},
doi = {10.1016/j.canlet.2026.218519},
pmid = {42002490},
issn = {1872-7980},
}

@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//Secretaría de Ciencia, Humanidades, Tecnología e Innovación/ ; PAPIIT IN224716//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; },
}

@article {pmid42002801,
year = {2026},
author = {Luo, J and Wang, X and Ju, Y and Ji, Q and Li, R and Ruan, Y and Zhao, J and Long, Q and Shang, Y and Li, P and Cao, M and Chen, X},
title = {Dietary N-acetylcysteine enhances sperm motility by remodeling the rumen microbiome and its metabolic axis in goats.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42002801},
issn = {1674-9782},
support = {2021YFD1200403//National Key Research and Development Program/ ; GZNYJGHX-2023006//Guizhou Province Mountainous Agriculture Key Research Program/ ; Qian Kehe Platform Talent-CXTD[2023]025//Guizhou Province Mutton Sheep Genetic Improvement and Innovative Utilization Science and Technology Innovation Talent Team Project/ ; GCC[2022]021-1//Guizhou Province High-level Innovative"Hundred" Level Talent Project/ ; },
abstract = {BACKGROUND: Enhancing sperm motility is crucial for improving male fertility in ruminants. The rumen microbiota, central to nutrient metabolism of ruminants, represents a promising yet underexplored target for dietary intervention. This study investigated whether N-acetylcysteine (NAC) improves sperm motility via modulating the rumen microbiota-metabolite axis.

RESULTS: Dietary NAC supplementation significantly enhanced sperm motility in goats (P < 0.05), with the optimal effect observed at 0.3%, which coincided with improvements in sperm membrane integrity, antioxidant capacity, and mitochondrial function. Functional analysis revealed that NAC-induced microbial remodeling enriched KEGG pathways involved in antioxidant, energy, and lipid metabolism. Correspondingly, beneficial bacteria such as Pediococcus pentosaceus, Bacteroides acidifaciens, and Akkermansia, among others, were significantly enriched (P < 0.05). Notably, metabolic alterations in these pathways were consistently reflected in both the rumen fluid and plasma metabolomes, as evidenced by 25 conserved pathways and 2 overlapping metabolites. Collectively, these metabolic alterations ultimately enhanced sperm motility by improving sperm antioxidant status, energy supply, and lipid homeostasis.

CONCLUSIONS: Our study thus reveals that NAC enhances sperm motility via a rumen microbiome-mediated "rumen-plasma-sperm" axis. This novel insight broadens the understanding of how NAC-and potentially other antioxidants-regulates sperm motility, highlighting the promise of NAC-based dietary interventions for improving reproductive performance.},
}

@article {pmid42002816,
year = {2026},
author = {Jiang, H and Cui, Y and Lei, J},
title = {Global research on the crosstalk between microbiota - intratumoral microorganisms and liver cancer: a visualization analysis.},
journal = {Infectious agents and cancer},
volume = {21},
number = {1},
pages = {},
pmid = {42002816},
issn = {1750-9378},
support = {2020-XG-40//Lanzhou Science and Technology Bureau Project, 2020-XG-40: Development of an Intelligent Image-Assisted Diagnosis System for Early Detection and Quantitative Assessment of Therapeutic Efficacy in COVID-19 Using Deep Learning Technology and Its Clinical Application./ ; },
abstract = {BACKGROUND: In the past few decades, the field of microbiota research has experienced rapid development and growth. We have employed bibliometric methods to comprehensively visualize and analyze the global knowledge and hotspots in the field of microbiome-intratumoral microbiota in liver cancer.

METHOD: The relevant literature in this field from 2009 to 2025 was extracted from the Web of Science Core Collection Database. After the data was extracted, it was analyzed and visualized using CiteSpace, VOSviewer and R (bibliometrix) software.

RESULT: A total of 1001 publications on microbiome - intratumoral microbiota and liver cancer were published during the period 2009–2025. Among these, China had the highest number of publications (n = 495). The most prolific institution publishing on microbiome - intratumoral microbiota and liver cancer was Huazhong University of Science and Technology, China (n = 29). The author with the most publications on this topic was Yu, Jun (n = 14, 1.4%). The journal with the highest number of publications on this subject was Cancers (n = 41, 4.1%). The top seven keywords with a frequency of 100 or more include: gut microbiota, hepatocellular carcinoma, nonalcoholic fatty liver disease, fatty liver disease, cancer, inflammation, bile acids, liver cancer, cell, and insulin resistance. Recent emerging topics include “intratumoral microbiota” (since 2024) and “tumor microenvironment.”

CONCLUSION: Current research in this field primarily investigates the mechanistic associations between gut microbiota and hepatic malignancies, with particular emphasis on hepatocellular carcinoma. The scientific frontier has progressively evolved to encompass the exploration of intratumoral microbiota and its multifaceted interactions within the tumor microenvironment.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13027-026-00750-x.},
}

@article {pmid42002835,
year = {2026},
author = {Morineau, N and Tessoulin, B and Guimard, T and Papin, M and Roquilly, A and Le Gouill, S and Montassier, E},
title = {Longitudinal gut microbiome dynamics are associated with clinical outcome and toxicity during ibrutinib therapy.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2659397},
doi = {10.1080/19490976.2026.2659397},
pmid = {42002835},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Piperidines/adverse effects/therapeutic use ; *Adenine/analogs & derivatives/adverse effects/therapeutic use ; Male ; Female ; Middle Aged ; Aged ; Longitudinal Studies ; *Bacteria/classification/genetics/isolation & purification/metabolism/drug effects ; Feces/microbiology ; Treatment Outcome ; *Antineoplastic Agents/adverse effects/therapeutic use ; Adult ; },
abstract = {Accumulating evidence indicates that the gut microbiome influences therapeutic efficacy and toxicity across cancer treatments; however, its longitudinal dynamics during targeted therapies remain poorly characterized. Here, we performed whole-genome shotgun metagenomic sequencing of 291 longitudinal stool samples collected over one year from 30 patients with hematologic malignancies treated with ibrutinib. Overall gut microbial diversity remained stable at the population level but exhibited markedly divergent temporal trajectories according to clinical outcome, with progressive recovery in responders and blunted or delayed restoration in non-responders. Longitudinal modeling revealed distinct species- and pathway-level microbial dynamics between patients with treatment response or nonresponse, including enrichment of saccharolytic, short-chain fatty acid-associated taxa and metabolic pathways in responders, and expansion of bile acid-modifying, proteolytic, and inflammation-associated microbial features in non-responders. Functional profiling further demonstrated opposing temporal trends in pathways related to carbohydrate fermentation, amino-acid metabolism, and secondary bile acid synthesis. In addition, both baseline microbiome composition and longitudinal remodeling were associated with the development of ibrutinib-associated diarrhea. Together, these findings reveal coordinated, outcome-specific remodeling of the gut microbiome during ibrutinib therapy and highlight longitudinal microbiome trajectories, rather than static baseline features, as potential biomarkers of treatment response and toxicity, as well as targets for microbiome-directed interventions. In conclusion, our findings highlight a potential role of gut microbiome dynamics in modulating response to BTK inhibition and support the need for larger, prospective studies to validate these observations.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Piperidines/adverse effects/therapeutic use
*Adenine/analogs & derivatives/adverse effects/therapeutic use
Male
Female
Middle Aged
Aged
Longitudinal Studies
*Bacteria/classification/genetics/isolation & purification/metabolism/drug effects
Feces/microbiology
Treatment Outcome
*Antineoplastic Agents/adverse effects/therapeutic use
Adult

@article {pmid42002973,
year = {2026},
author = {Nam, K and Choi, JH and Kim, YS and Lee, S and Park, JH and Kim, H and Lee, S and Lee, Y and Lee, D and Ryou, S and Shin, JE},
title = {Impact of Portulaca oleracea L. extract in patients with irritable bowel syndrome.},
journal = {Intestinal research},
volume = {},
number = {},
pages = {},
doi = {10.5217/ir.2025.00200},
pmid = {42002973},
issn = {1598-9100},
abstract = {BACKGROUND/AIMS: Portulaca oleracea is known to have anti-inflammatory and immunoregulatory effects, and also showed positive effect on complete spontaneous bowel movement and bowel symptoms in patients with chronic constipation in a previous study. Thus, we aimed to investigate the impact of P. oleracea in patients with irritable bowel syndrome (IBS).

METHODS: Patients with IBS defined by ROME IV criteria were enrolled between July 2022 and April 2023. Patients were randomly assigned to P. oleracea or placebo group and took drugs for 8 weeks. Clinical data including gastrointestinal and IBS symptoms, laboratory tests including inflammatory and immunologic laboratory markers, and stool tests including fecal calprotectin and stool microbial analysis were evaluated at the baseline, week 4, and week 8.

RESULTS: A total of 108 patients were initially enrolled and 101 patients were finally included in the analysis. There was significant improvement during 8 weeks in P. oleracea group compared to placebo group in the aspect of gastrointestinal and IBS-related bowel symptoms (Gastrointestinal Symptom Rating Scale total score: from 44.1 to 31.7 vs. from 41.4 to 39.9; IBS-Symptom Severity Score total score: from 232.0 to 120.6 vs. from 202.7 to 178.2), especially in the aspect of abdominal pain. Interleukin-6 (IL-6) was significantly decreased during 8 weeks in P. oleracea group, although there was no significant difference between 2 groups. In addition, increase in IL-6 during study period was significantly associated with dysbiosis in stool microbial analysis. There was no significant adverse event.

CONCLUSIONS: P. oleracea has positive impact in patients with IBS showing improvement of immunologic cytokine and stool microbiome.},
}

@article {pmid42003036,
year = {2026},
author = {Ganamurali, N and Sabarathinam, S},
title = {Resveratrol as a Multi-Domain Modulator of Oxidative Stress, Gut Dysbiosis, and Epigenetic Remodeling in Obesity: A Systems Biology Interpretation.},
journal = {Journal of biochemical and molecular toxicology},
volume = {40},
number = {5},
pages = {e70846},
doi = {10.1002/jbt.70846},
pmid = {42003036},
issn = {1099-0461},
mesh = {*Resveratrol/pharmacology/therapeutic use ; *Obesity/drug therapy/metabolism/genetics/microbiology/pathology ; Humans ; *Epigenesis, Genetic/drug effects ; *Oxidative Stress/drug effects ; *Dysbiosis/drug therapy/metabolism ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Systems Biology ; },
abstract = {Obesity is increasingly recognized as a chronic inflammatory redox disorder sustained by gut dysbiosis and maladaptive epigenetic programming. A "lock-in" model describes how gut dysbiosis induced reactive oxygen species (ROS) stabilize inflammatory signaling and establish epigenetic metabolic scars in adipose tissue, thereby perpetuating obesity even after the initial triggers subside. Resveratrol, a dietary stilbenoid, acts as a tri-axis therapeutic candidate by: (1) Restoring redox balance via Nrf2 activation and SIRT1 signaling, (2) Reshaping the gut microbiota to enhance SCFA production and barrier integrity, and (3) Reprogramming obesity-associated epigenetic alterations, including DNA methylation and miRNA dysregulation. By targeting oxidative, microbial, and epigenetic dimensions simultaneously, resveratrol offers a novel strategy to erase metabolic memory and disrupt obesity chronicity.},
}

*Resveratrol/pharmacology/therapeutic use
*Obesity/drug therapy/metabolism/genetics/microbiology/pathology
Humans
*Epigenesis, Genetic/drug effects
*Oxidative Stress/drug effects
*Dysbiosis/drug therapy/metabolism
*Gastrointestinal Microbiome/drug effects
Animals
*Systems Biology

@article {pmid42003076,
year = {2026},
author = {Malik, JA},
title = {Lactobacillus plantarum as a Novel Modulator of Immune and Behavioral Recovery in Substance Use Disorders: A Hypothesis.},
journal = {Current drug research reviews},
volume = {},
number = {},
pages = {},
doi = {10.2174/0125899775442579260409073358},
pmid = {42003076},
issn = {2589-9783},
abstract = {Substance Use Disorders (SUDs) are increasingly recognized as conditions driven by neuroimmune dysfunction, leading to neuroinflammation and immune dysregulation. Growing evidence highlights the microbiota-gut-brain axis as a critical regulator of central nervous system activity, particularly through the modulation of glial cells such as microglia and astrocytes. The gut microbiome provides key immunomodulatory signals, and its therapeutic exploitation through probiotics offers a promising avenue. In this study, we hypothesize that supplementation with Lactobacillus plantarum can attenuate neuroinflammation and improve immune tolerance in SUDs by restoring microbial balance and modulating neuroimmune activity via the gut-brain axis. Using an established animal model of SUD, we propose to investigate the impact of L. plantarum on gut microbial composition, systemic and central inflammatory markers, glial cell activation, and behavioral outcomes. We further suggest that probiotics containing Lactobacillus species, including L. plantarum, could serve as a transformative approach not only for SUD-associated neuroinflammation but also for other neurological disorders. Such interventions may represent a breakthrough in non-drug discovery strategies by reducing reliance on conventional pharmacological treatments. Importantly, probiotic-based therapies could enhance overall survival and quality of life in individuals with SUDs, as Lactobacillus species have been shown to suppress inflammatory pathways from early developmental stages. Lactobacillus species could regulate the gut-brain axis and impact neurodegenerative diseases. If validated, this work could position L. plantarum and related probiotic strains as novel microbiome-based adjuncts for managing SUDs and open broader therapeutic possibilities for neuropsychiatric and neurodegenerative conditions.},
}

@article {pmid42003095,
year = {2026},
author = {Aru, N and Chen, Y and Li, T and Liu, J},
title = {Metabolites and Polycystic Ovarian Syndrome: A Mendelian Randomization Study.},
journal = {Current medicinal chemistry},
volume = {},
number = {},
pages = {},
doi = {10.2174/0109298673408216260414174125},
pmid = {42003095},
issn = {1875-533X},
abstract = {INTRODUCTION: Polycystic ovarian syndrome (PCOS) is a common reproductive disorder that affects a considerable number of women worldwide. Nevertheless, the causal relationship between metabolites and PCOS remains undetermined.

METHODS: We utilized a comprehensive two-sample Mendelian randomization (MR) analysis, a genetic epidemiological approach that uses genetic variants as instrumental variables to assess causal relationships between exposures and outcomes, to examine the causal link between 1352 metabolites and PCOS. We employed complementary MR methods, such as the inverse-variance weighted (IVW) method, and conducted sensitivity analyses to evaluate the reliability of the outcomes. Reverse MR analysis was performed to evaluate the possibility of reverse causation.

RESULTS: Five metabolites were identified to be significantly associated with PCOS risk: Methionine sulfoxide levels (IVW: OR [95%]: 1.549[1.274 to 1.883], p = 1.154E-5), Theophylline levels (IVW: OR [95%]: 0.725[0.589 to 0.890], p = 0.002), 4-hydroxycoumarin levels (IVW: OR [95%]: 0.786[0.658 to 0.940], p = 0.008), Tyramine O-sulfate levels (IVW: OR [95%]: 0.699[0.568 to 0.862], p = 0.0008), and Sulfate of piperine metabolite C16H19NO3 (3) levels (IVW: OR [95%]: 1.296[1.064 to 1.579], p = 0.009). We found PCOS was significantly associated with decreased Tyramine O-sulfate levels using the IVW method (OR [95%]: 0.953[0.917 to 0.991], p = 0.015) in the reverse MR analysis. The results of the sensitivity analyses were consistent with the main findings.

DISCUSSION: This study establishes causal relationships between specific metabolites and PCOS, highlighting the significant roles of oxidative stress (methionine sulfoxide), dietary components (theophylline, piperine metabolite), and gut microbiome-derived metabolites. These findings provide novel insights into PCOS pathogenesis and identify potential targets for prevention and treatment. However, the study's limitation to European populations necessitates further validation in diverse ethnic groups.

CONCLUSION: Our MR analysis provides strong evidence supporting a causal association between metabolites and the susceptibility of PCOS.},
}

@article {pmid42003340,
year = {2026},
author = {Tong, Y and Marcelino, VR and Turnbull, R and Verbruggen, H},
title = {ChloroScan: Recovering Plastid Genome Bins From Metagenomic Data.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70143},
doi = {10.1111/1755-0998.70143},
pmid = {42003340},
issn = {1755-0998},
support = {2023.06155//Fundação para a Ciência e a Tecnologia/ ; DE220100965//Australian Research Council/ ; RYC2023-042907-I//Ministerio de Ciencia e Innovación/ ; //The University of Melbourne's Research Computing Services/ ; },
mesh = {*Metagenomics/methods ; *Computational Biology/methods ; *Genome, Plastid ; *Eukaryota/genetics/classification ; *Software ; Phylogeny ; Metagenome ; },
abstract = {Genome-resolved metagenomics has contributed greatly to discovering prokaryotic genomes. When applied to microscopic eukaryotes (protists), challenges such as the high number of introns and repeat regions found in nuclear genomes have hampered the mining and discovery of novel protistan lineages. Organellar genomes are simpler, smaller, have higher abundance than their nuclear counterparts and contain valuable phylogenetic information, but are yet to be widely used to identify new protist lineages from metagenomes. Here we present "ChloroScan", a new bioinformatics pipeline to extract eukaryotic plastid genomes from metagenomes. It incorporates a deep learning contig classifier to identify putative plastid contigs and an automated binning module to recover bins with guidance from a curated marker gene database. Additionally, ChloroScan summarizes the results in different user-friendly formats, including annotated coding sequences and proteins for each bin. We show that ChloroScan recovers more high-quality plastid bins than MetaBAT2 for simulated metagenomes. The practical utility of ChloroScan is illustrated by recovering 16 medium to high-quality metagenome assembled genomes (MAGs) from four protist-size-fraction metagenomes, with several bins showing high taxonomic novelty. The ChloroScan code (v0.1.7) is available at https://github.com/Andyargueasae/chloroscan/tree/release_v0.1.7 under Apache-2.0 licence.},
}

*Metagenomics/methods
*Computational Biology/methods
*Genome, Plastid
*Eukaryota/genetics/classification
*Software
Phylogeny
Metagenome

@article {pmid42003351,
year = {2026},
author = {Tahlan, S and Singh, S and Dey, H and Kaira, M and Pandey, KC},
title = {Molecular strategies for heterocyclic frameworks in antidiabetic drug discovery: a vision from 2020-2024.},
journal = {Future medicinal chemistry},
volume = {},
number = {},
pages = {1-24},
doi = {10.1080/17568919.2026.2658007},
pmid = {42003351},
issn = {1756-8927},
abstract = {Diabetes mellitus represents a global health crisis requiring innovative therapeutic strategies beyond traditional treatments. This comprehensive review analyzes heterocyclic frameworks developed between 2020-2024 for antidiabetic drug discovery, highlighting structure-activity relationships (SAR), molecular docking insights, and therapeutic mechanisms. Key scaffold classes emerged as potent antidiabetic agents, with benzimidazoles and triazoles demonstrating dual α-amylase/α-glucosidase inhibition (IC50 values 1.20-22.46 µg/mL), thiazolidinediones and quinazolines showing PPAR-γ agonism with improved insulin sensitivity and reduced cardiovascular risks, DPP-4 inhibitory scaffolds (pyrrolidines, pyrimidines) achieving IC50 values as low as 0.021 µM, and SGLT2-targeting heterocycles exhibiting glucose-lowering effects with cardio-renal protection. Major findings revealed that electron-donating groups (methoxy, hydroxyl) consistently enhanced binding affinity across multiple targets, halogen substitutions (fluoro, chloro, bromo) improved metabolic stability and selectivity, hybrid molecules combining multiple pharmacophores achieved superior multi-target effects, and natural product-derived heterocycles (flavonoids, coumarins, alkaloids) showed IC50values 10-100× better than acarbose. Emerging frontiers include multi-agonist therapies (GLP-1/GIP, dual SGLT1/SGLT2 inhibitors), glucokinase activators for insulin-independent glucose control, microbiome-targeting agents, and AI-driven rational drug design integrating SAR, docking, and ADMET prediction. This review provides a strategic framework for developing safer, more selective antidiabetic agents through systematic exploitation of heterocyclic chemistry, advancing toward personalized diabetes management.},
}

@article {pmid42003595,
year = {2026},
author = {Williams, MR and Rowe, HM},
title = {Bacterial alteration of redox stressors impacts environmental stability of influenza A virus.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0012526},
doi = {10.1128/msphere.00125-26},
pmid = {42003595},
issn = {2379-5042},
abstract = {Influenza A virus (IAV) causes annual morbidity and mortality and remains a constant pandemic threat due to the emergence of novel strains. Therefore, understanding the factors important in host-to-host transmission of IAV is a key control point for protecting individual and public health. Transmission is highly heterogeneous with viral factors and host inflammatory and immune factors being implicated. Also implicated is the upper respiratory microbiome. While typically thought to act indirectly on viral pathogenesis, in an immunomodulatory capacity to enhance or reduce susceptibility to viral infection, recent studies on the pathogenesis of IAV have identified direct interactions between the virus and upper respiratory pathobiont bacteria. We hypothesize that the bacterial cells and their metabolites co-shed into respiratory droplets with IAV particles alter the viability of the IAV particles in the environment, therefore altering the capacity for host-to-host transmission. In this investigation, we utilize a simplified model of fomite transmission in the absence of confounding host factors and demonstrate how oxidative stress from both the environment and the metabolic activity of Streptococcus pneumoniae contributes to the killing of IAV, while catalase or the metabolic activity of Staphylococcus aureus can protect IAV from environmental or pneumococcally produced reactive oxygen species. These findings support a mechanism for bacterial modulation of viral transmission where bacterial metabolic products present in the respiratory droplet are capable of stabilizing and destabilizing viral particles during environmental transit and therefore modulating viral transmissibility.IMPORTANCEInfluenza A virus is a major cause of illness and death every year. A key knowledge gap exists in understanding what factors modulate viral transmission. One potential mediator of viral transmission is the bacteria that are found in the human nasopharynx. However, the mechanisms responsible for bacterial modulation of viral transmission are unclear. Here, we utilize a simplified model of environmental survival where we expose viral particles to indoor environmental conditions in the presence of bacterial cells. We demonstrate that hydrogen peroxide produced by Streptococcus pneumoniae reduces viral environmental survival, while incubation with catalase or viable Staphylococcus aureus cells can protect viral particles from S. pneumoniae-mediated viability loss. This supports a model of trans-kingdom bacterial-viral interactions where bacterial metabolites produced in the respiratory droplet are capable of modulating viral environmental survival and therefore transmission.},
}

@article {pmid42003615,
year = {2026},
author = {Yamada, K and Koroleva, A and Tirkkonen, H and Siitonen, V and Laughlin, M and Moglia, A and Matroodi, S and Akhgari, A and Mazurier, G and Niemi, J and Metsä-Ketelä, M},
title = {Facultative predation expands the ecological repertoire of Streptomyces.},
journal = {mBio},
volume = {},
number = {},
pages = {e0056326},
doi = {10.1128/mbio.00563-26},
pmid = {42003615},
issn = {2150-7511},
abstract = {Microbial predators obtain energy from killing other living cells. Streptomyces are soil bacteria that are known to produce numerous catabolic enzymes and antimicrobial compounds to defend against competing organisms. Here, we demonstrate that Streptomyces are predatory bacteria that prey on Saccharomyces cerevisiae. Time-lapse fluorescence microscopy and scanning electron microscopy revealed that predation is initiated by physical contact between Streptomyces lavendulae YAKB-15 and yeast cells. Comparative transcriptomics indicated that the interaction triggered the production of numerous extracellular catabolic enzymes and natural products, while delaying morphological development. Proteomics and enzyme assays confirmed co-culture-dependent production of carbohydrate-active enzymes (CAZymes), including various glucanases, mannosidases, and chitinases, which degraded the yeast cell wall. Streptomyces lavendulae YAKB-15 destabilized yeast cell membranes through the production of two polyene antifungal agents, pentamycin and filipin III. We found that the bioactivity was enhanced by cell-associated cholesterol oxidase ChoD, putatively by modulating sterol extraction kinetics. Metabolomic analyses suggest Streptomyces assimilates yeast cell sterols as nutrients. Furthermore, we observed the depletion of yeast-derived phosphatidylcholine and phosphatidylethanolamine lipids, which points to their consumption. We show that yeast predation is a common phenomenon in Streptomyces, which changes the paradigm of how these bacteria should be considered in the soil microbiome ecosystem.IMPORTANCESoil is a rich environment for microbes, where they compete for space and resources. Streptomyces bacteria are well known for their ability to synthesize natural products, particularly antibiotics, that are used in chemical defense against competing microbes. Here, we show that Streptomyces are, in fact, predatory bacteria. Upon encountering yeast cells, Streptomyces initiate the production of numerous enzymes that digest the cell wall and cell membrane. In addition, the interaction triggers the production of natural products that destabilize the yeast cell membrane. Collectively, these actions lead to the death of yeast cells and release of cellular building blocks that Streptomyces can use as nutrients. The work fundamentally shifts the paradigm of how Streptomyces are perceived within the soil microbiome ecosystem.},
}

@article {pmid42003642,
year = {2026},
author = {Krausfeldt, LE and Subramanian, P and Doan, D and McCauley, K and Dolan, M and Hurt, DE},
title = {DiscoVir: an automated, web-based pipeline for viral metagenomics.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0008526},
doi = {10.1128/mra.00085-26},
pmid = {42003642},
issn = {2576-098X},
abstract = {DiscoVir is an automated pipeline for viral metagenomics available in National Institute of Allergy and Infectious Diseases (NIAID)'s free web application for microbiome analysis, Nephele. DiscoVir makes viral discovery, taxonomic and functional annotation, host predictions, and diversity analyses of the virome easily accessible to researchers at all levels of expertise.},
}

@article {pmid42003650,
year = {2026},
author = {Huedo, P and Astó, E and Perez, M and Rodriguez-Palmero, M and Espadaler-Mazo, J},
title = {Draft genome sequences of Lactiplantibacillus plantarum strains KABP062 and KABP063 isolated from human feces.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0019626},
doi = {10.1128/mra.00196-26},
pmid = {42003650},
issn = {2576-098X},
abstract = {We present the draft genome sequences of Lactiplantibacillus plantarum strains KABP062 and KABP063, two fecal isolates with probiotic potential.},
}

@article {pmid42003651,
year = {2026},
author = {Kocakahya, İ and Şahin, G and Büyükkahraman, E and Arıkan, M},
title = {Metagenome-assembled genomes from urban pigeon feces in Istanbul, Türkiye.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0140525},
doi = {10.1128/mra.01405-25},
pmid = {42003651},
issn = {2576-098X},
abstract = {We report herein about 101 metagenome-assembled genomes (MAGs) obtained from pigeon fecal samples collected in 2025 from the Beyazıt, Kadıköy, and Beşiktaş squares of Istanbul. The MAGs were predominantly composed of members of the phyla Firmicutes, Actinobacteria, and Proteobacteria, with a lower representation of Campylobacterota and Patescibacteriota.},
}

@article {pmid42003736,
year = {2026},
author = {Xue, H and Diao, F and Yu, Q and Zhu, X and Zhong, T and Wang, L and Zhang, K and Li, D and Ji, J and Luo, J and Cui, J and Gao, X},
title = {Cotton Recruits Soil-Derived Delftia tsuruhatensis to Suppress Aphid Detoxification Via Salicylic Acid-Mediated Defense.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e75321},
doi = {10.1002/advs.75321},
pmid = {42003736},
issn = {2198-3844},
support = {2022YFF1001400//National Key Research and Development Program of China/ ; 262300421139//Natural Science Foundation of Henan Province/ ; Y2023QC23//Youth Innovation Program of Chinese Academy of Agricultural Sciences/ ; CARS-15-21//China Agriculture Research System/ ; 2022QNRC001//Young Elite Scientists Sponsorship Program by CAST/ ; //Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences/ ; },
abstract = {The synergistic defense between microorganisms and plants holds significant ecological importance in resisting pest attacks. Herbivorous insects pose a significant threat to global agriculture. While plants deploy defense hormones like jasmonic acid (JA) and salicylic acid (SA), the role of beneficial microbes in enhancing these defenses remains underexplored. This study unveils a novel tripartite interaction in which cotton actively mobilizes the soil-derived bacterium Delftia tsuruhatensis to roots and leaves upon aphid attack, reshaping its microbiome for defense. Following aphid infestation, the abundance of D. tsuruhatensis was increased significantly in both roots and leaves. Inoculation of cotton with D. tsuruhatensis significantly reduced aphid fitness, inhibiting phloem feeding, decreasing survival, prolonging nymphal development, and impairing reproduction. Mechanistically, we found that D. tsuruhatensis activates the host plant's SA signaling pathway. This plant-mediated response, in turn, effectively suppresses the expression of a key aphid detoxification gene, UGT2B17 (UDP-glucosyltransferase 2B17), compromising the insect's ability to metabolize plant defenses. Furthermore, the combination of D. tsuruhatensis and RNAi-mediated silencing of UGT2B17 synergistically enhanced aphid mortality. Our results elucidate a sophisticated defense strategy wherein the host plant leverages a beneficial microbe to augment its innate immunity through cross-kingdom gene regulation, ultimately disarming the pest's detoxification system.},
}

@article {pmid42003748,
year = {2026},
author = {Fletcher Wheeler, L and Lehmann, M and Melo-Narvaez, MC},
title = {Mechanistic Advances and Emerging Technologies Redefining Lung Aging Research.},
journal = {American journal of physiology. Cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpcell.00912.2025},
pmid = {42003748},
issn = {1522-1563},
support = {512453064//Deutsche Forschungsgemeinschaft (DFG)/ ; 71_0011//Von-Behring-Röntgen-Stiftung (Von Behring-Röntgen-Foundation)/ ; LOEWE Habitat//Hessisches Ministerium für Wissenschaft und Kunst (Hessian Ministry for Science and Art)/ ; //Deutsches Zentrum für Lungenforschung (DZL)/ ; 5/2026 MR//Uniklinikum Giessen und Marburg (UKGM)/ ; 73_0031//Von-Behring-Röntgen-Stiftung (Von Behring-Röntgen-Foundation)/ ; },
abstract = {As the population ages, defining how biological processes change over the lifetime has become increasingly important. Acute and chronic lung diseases are more prevalent in older adults and emerging research is beginning to uncover the mechanistic and cellular pathways that link aging to conditions such as pneumonia and COPD. Additional mechanisms, particularly those involving extracellular vehicles (EVs), the microbiome, and sex differences, are now recognized as potential contributors to age-related changes in lung health yet remain underexplored. Advances in experimental models and analytical tools have accelerated progress in the field. Three-dimensional lung models such as organoids, precision cut lung slices, ECM scaffolds, and lung-on-a-chip systems offer more physiologically relevant systems than traditional two-dimensional cultures, improving translatability to in vivo biology. Meanwhile, the expansion of genomics, transcriptomics, proteomics, and metabolomics has enabled comprehensive, multi-omics approaches for mapping disease mechanisms, and such datasets are increasingly available. However, deeper integration with patient metadata and spatially resolved methods are still needed to advance precision medicine approaches to exploit aging mechanisms in chronic lung diseases. In this review, we highlight the importance of investigating EVs, the microbiome, and sex differences and their contribution of age-associated mechanism in the context of pneumonia and COPD and discuss how innovations in 3D lung models and omics technologies are reshaping our understanding of the pathological mechanisms that underlie these diseases.},
}

@article {pmid42003783,
year = {2026},
author = {Krueger, Q and Phippen, B and Reitzel, AM},
title = {Unique Transcriptional Responses by the Sea Anemone Nematostella vectensis to Individual Bacteria: Roles for Bacterial Species, Secreted Products and the Microbiome.},
journal = {Molecular ecology},
volume = {35},
number = {8},
pages = {e70339},
doi = {10.1111/mec.70339},
pmid = {42003783},
issn = {1365-294X},
support = {2044826//Division of Environmental Biology/ ; },
mesh = {Animals ; *Sea Anemones/microbiology/genetics/immunology ; *Microbiota/genetics ; Vibrio ; *Bacteria/genetics ; Transcriptome ; },
abstract = {Animal responses to bacteria, viruses and other microorganisms are important for understanding how host-microbe interactions lead to divergent molecular responses by the host and the assembly of the holobiont. The immune system of the animal and the resident microbial community are critical factors in the response, or lack thereof, by a host to a newly encountered microbe. Here, we describe the transcriptional response of the model cnidarian Nematostella vectensis when exposed to three Live Cell (LC) isolates (Bacillus velezensis, Pseudoalteromonas spiralis and Vibrio diabolicus) or their Cell Free Supernatants (CFS) with and without the native microbiome. Gene expression revealed large variation in the overall response ranging from 829 differentially expressed genes (DEGs) for antibiotically treated anemones exposed to B. velezensis to 49 DEGs in xenic individuals inoculated with V. diabolicus. The anemone's response similarly varied widely if the exposure was to live bacteria or the secreted products, especially for B. velezensis. Genes associated with the RIG-I-like immune pathway showed large differences in expression whereas the transcriptional variation for NF-kB and toll-like receptor were not significantly different. The response to each gram-negative bacteria differed from a purified bacterial ligand (lipopolysaccharide). Together, these results support the hypothesis that N. vectensis mounts unique transcriptional responses to individual bacterial species and their products, which are dependent on the presence of the native microbiome. The complexity of this molecular response further highlights the dynamic interplay between cnidarians and microbes in the assembly and maintenance of the holobiont.},
}

Animals
*Sea Anemones/microbiology/genetics/immunology
*Microbiota/genetics
Vibrio
*Bacteria/genetics
Transcriptome

@article {pmid42003978,
year = {2026},
author = {Oda, Y and Miyake, M and Nishimura, N and Shimizu, T and Owari, T and Iida, K and Nakai, Y and Tanaka, N and Fujimoto, K},
title = {Changes of urinary immunity and microbiome after intravesical BCG therapy and their association with outcomes in NMIBC.},
journal = {Exploration of targeted anti-tumor therapy},
volume = {7},
number = {},
pages = {1002365},
pmid = {42003978},
issn = {2692-3114},
abstract = {AIM: Intravesical Bacillus Calmette-Guérin (BCG) is the standard therapy for non-muscle invasive bladder cancer (NMIBC); however, many patients experience recurrence or progression. We examined how urinary immune signals and the urinary microbiome change across BCG and are related to outcomes.

METHODS: In this single-center prospective cohort study, adults with NMIBC underwent transurethral resection of bladder tumor (TURBT), followed by BCG induction. Urine was collected before TURBT, before BCG, after BCG induction, and three months later. Urine sediment mRNA (PD-L1, PD-L2, CD33, and CD204) was quantified using TaqMan ΔCt. The urinary microbiome was profiled using 16S rRNA gene sequencing, and diversity, composition, and taxon balance were evaluated using nonparametric tests, PERMANOVA, repeated-measures correlations, and mixed-effects models. We analyzed the relationship between the urinary microbiome and prognosis.

RESULTS: Twenty-three patients were analyzed; ten recurrences, eight progressions, and three deaths were observed. Relative to baseline, CD33 increased after BCG and after three months; PD-L2 increased immediately after BCG and returned to baseline by three months; PD-L1 and CD204 increased after BCG. Shannon alpha-diversity was unchanged, but total read count was higher at three months, with stable beta-diversity and dispersion. Higher PD-L1 expression was associated with lower Actinobacteria abundance in the bladder cancer microenvironment. A higher post-BCG Firmicutes/Bacteroidetes ratio was associated with worse prognosis, with the clearest signal for progression-free survival (PFS) observed in the univariate Cox models. Higher post-BCG Corynebacterium and Enterobacteriaceae abundance was associated with better PFS.

CONCLUSIONS: BCG was associated with higher urinary PD-L1/PD-L2 and myeloid marker transcripts, while overall community structure remained stable. These exploratory data support that pre-BCG microbial features may be related to early response, and post-BCG profiles may reflect durability and survival. Urine immune-microbiome profiling could be a feasible, noninvasive adjunct for monitoring and risk stratification in NMIBC.},
}

@article {pmid42003997,
year = {2026},
author = {Nto, NJ and Pirovano, W and Nel Van Zyl, K and Malan-Müller, S and Koch, E and Ramaboli, M and Madikgetla, D and de Leeuw, C and Lowry, CA and Hemmings, SMJ},
title = {The role of gut microbiome in the pathophysiology of PTSD, depression, and anxiety disorders.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2654224},
pmid = {42003997},
issn = {2993-3935},
abstract = {Posttraumatic stress disorder (PTSD), depression, and anxiety disorders are prevalent and often overlapping mental health conditions with complex, multifactorial etiologies. Growing evidence implicates the gut microbiome in their pathophysiology through immune modulation, neurotransmitter regulation, and bidirectional gut-brain signaling. Findings remain fragmented and difficult to reconcile due to differences in study populations, clinical contexts, and analytic methods. This structured narrative review synthesizes current evidence on gut microbial alterations in PTSD, depression, and anxiety, while examining methodological sources of heterogeneity. We searched four databases: PubMed, Scopus, Web of Science, and PsycINFO, and identified 64 eligible studies assessing the gut microbiome composition in these disorders. Sample sizes ranged from small, exploratory cohorts (≈20 participants) to large population-based datasets (>1000 participants), with most studies conducted in China. Stool sampling and DNA extraction protocols varied widely, although 16S rRNA gene amplicon sequencing of the V3-V4 region on Illumina platforms predominated. Alpha-diversity results were inconsistent, whereas beta-diversity analyses distinguished cases from controls. Across these disorders, alterations in microbial composition was observed, including enrichment of proinflammatory and depletion of beneficial bacterial taxa. The current findings indicate that that the gut microbiome represents a promising avenue for biomarker discovery and therapeutic innovation.},
}

@article {pmid42004001,
year = {2026},
author = {Yuan, Y and Ou, J and Fu, X and Tang, Y and Chen, Y and Deng, Q and Deng, Y and Sun, Y},
title = {A global-scale framework for quantifying the gut microbiome's mediating role in environmental and personal determinants of health.},
journal = {Eco-Environment & Health},
volume = {5},
number = {2},
pages = {100236},
pmid = {42004001},
issn = {2772-9850},
abstract = {The human gut microbiome mediates health risks from the exposome, but research focuses on diet and lifestyle, leaving the impact of environmental characteristics unclear. Furthermore, the microbiota's quantitative, mediating role in linking the full exposome to disease is poorly understood. We conducted a global-scale association and mediation analysis of 13,463 American Gut Project participants, linking 128 environmental/personal factors to 10 gut microbial indices. We identified 390 significant but moderate associations (R[2] < 0.03, FDR < 0.05) between exposome factors and the microbiota, revealing it is influenced by numerous small, cumulative effects. Our analysis confirmed expected patterns, such as reduced gut diversity with antibiotic use and exposure to pollutants like PM2.5 and SO2. However, it also revealed counterintuitive findings, notably that several hazardous exposures, including alcohol, airborne persistent organic pollutants (POPs), and mycotoxin deoxynivalenol, were associated with increased alpha diversity (FDR < 0.05). Our mediation analysis linking these factors to 24 self-reported health outcomes identified 1129 significant pathways (p < 0.05), confirming established links such as antibiotic-associated risk for irritable bowel syndrome (IBS) and the protective effects of vegetable consumption on allergies. Our analysis also revealed striking paradoxes: exposure to POPs increased inflammatory bowel disease (IBD) risk, partly via an increase in gut alpha diversity (1.5%-15.7% mediated effect), directly challenging the "higher diversity is better" paradigm. Our global-scale analysis provides the first comprehensive map of the gut microbiome's mediating role in the human exposome, establishing a methodological blueprint for assessing the microbial contribution to the global burden of environmental disease.},
}

@article {pmid42004003,
year = {2026},
author = {Wang, B and Zhou, H and Yang, J and Fang, Y and Zi, Y and Zhang, L and Wang, J and Wang, L and He, Y and Ji, R and Lyu, T},
title = {Metabolomic and microbial responses of multilevel aquatic organisms to antibiotics in freshwater microcosm: The uniformity and specificity.},
journal = {Eco-Environment & Health},
volume = {5},
number = {2},
pages = {100231},
pmid = {42004003},
issn = {2772-9850},
abstract = {The widespread presence of antibiotics in aquatic environments raises concerns about their ecological impacts. However, the molecular-level effects of antibiotics and the underlying mechanisms, particularly the responses across aquatic species, remain unclear. We established a freshwater microcosm including duckweeds (Salvinia natans), snails (Cipangopaludina cathayensis), and fish (Danio rerio) to investigate their uniform and specific responses to antibiotics (sulfamethoxazole, ciprofloxacin, oxytetracycline, and azithromycin), each at 1, 10, and 100 μg/L for 45 days. Antibiotic exposure diminished chlorophyll content in duckweeds, increased soluble sugar levels, elevated triglyceride levels in snails, and raised total bile acid concentrations in fish. Metabolomic analysis revealed that both duckweeds and fish tended to store energy to defend against antibiotic-induced stress, but through different pathways. Duckweeds accumulated sugar metabolites and downregulated antioxidants, while fish consumed primary sugars and converted them into lipid metabolites. Microbiome analysis indicated a self-coordination of gut bacteria in both snails and fish exposed to 1 and 10 μg/L of antibiotics, while dysbiosis occurred in snails at 100 μg/L, marked by increased pernicious bacteria abundance. In contrast, the abundance of probiotic bacteria increased in the fish gut due to microbial resistance to antibiotics, which played a crucial role in bile acid metabolism and positively influenced hepatic lipid metabolism via the gut-liver axis. This study uncovered the uniform and specific defense and dysregulation behaviors of multilevel aquatic organisms in response to antibiotic exposure, providing valuable insights into the selection of molecular-level endpoints for water quality benchmark development to safeguard aquatic life from antibiotic pollution.},
}

@article {pmid42004015,
year = {2026},
author = {Graham, NJ and Slavov, G and Wakelin, SA and Klápště, J and Day, NJ},
title = {Heritability of the Pinus radiata root microbiome.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1793374},
pmid = {42004015},
issn = {1664-462X},
abstract = {INTRODUCTION: Both evolutionary history and recent breeding selections can influence plant microbiomes, with closely-related individuals often having more similar microbiomes. Pinus radiata D.Don is an emerging conifer model species for investigating tree-microbiome interactions. However, little is known about how the P. radiata microbiome covaries with host genotype, especially beyond the seedling stage.

METHODS: We sampled the root microbiome of 528 individual P. radiata trees (age = 9 yrs), comprising four clonal copies each of 132 host genotypes from 28 full-sib families, from a clonal breeding trial in New Zealand. We determined whether variations in the bacterial and fungal root microbiomes were associated with host ancestry (i.e., provenance), family, and genotype.

RESULTS: Host family was associated with fungal but not bacterial root microbiome composition, whereas broader ancestry and individual genotype within families had no detectable effect on either bacterial or fungal microbiome composition. While core (in ≥80% samples) amplicon sequence variants (ASVs) typically had negligible heritability, the relative abundances of 83 bacterial and 13 fungal non-core ASVs had low to moderate broad-sense heritabilities (0.2 to 0.46). Host genetic effects associated with abundances of heritable ASVs were primarily non-additive and likely involve complex gene interactions.

DISCUSSION: Our study revealed subtle host family effects for the root fungal microbiome of P. radiata, with several heritable bacterial and fungal ASVs. This study broadens our understanding of host genetic influences on the composition of the root microbiome of P. radiata and indicates there are both opportunities and challenges for including microbiome-related traits in tree breeding programmes.},
}

@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 {pmid42004633,
year = {2026},
author = {Monjardino, P and Azevedo, AR and Mendonça, D and Pozsgai, G and Borges, PAV and Frias, J and Toubarro, D},
title = {Metagenomic survey of fungal communities in compost from dairy plant wastewater sludge and garden trimmings.},
journal = {Biodiversity data journal},
volume = {14},
number = {},
pages = {e174893},
pmid = {42004633},
issn = {1314-2828},
abstract = {BACKGROUND: Composting converts organic residues into stable organic matter and nutrients under aerobic conditions, improving soil properties and microbiome balance, while mitigating environmental impacts. Although microbiomes of various compost types have been studied, information is still fragmented and often not tailored to specific raw material combinations. In particular, little is known about the fungal communities involved in composting dairy plant wastewater sludge mixed with garden trimmings. This data paper contributes to filling that gap by providing a comprehensive taxonomic inventory.

NEW INFORMATION: We provide a fungus-focused dataset from 18 compost samples generated from a 1:1 (w/w) mix of garden trimmings and dairy plant wastewater sludge, collected at three process stages (thermophilic start/end; mid-cooling and maturation) under two turning regimes. Shotgun metagenomes were taxonomically annotated against NCBI taxonomy (accessed 19 Feb 2025). Only Fungi were detected within Eukarya, spanning nine phyla; Ascomycota (60.8%), Mucoromycota (17.76%), Basidiomycota (8.50%) and Chytridiomycota (7.21%) comprised 94.27% of the taxonomic features. We report 417 genera (13 >1% relative abundance each); top: Aspergillus (17.93%), Rhizopus (8.61%), Chaetomium (4.83%), Aureobasidium (3.09%), Madurella (2.85%), Paramicrosporidium (2.71%), Rhizophagus (1.88%), Rasamsonia (1.81%), Hyaloraphidium (1.39%), Thermochaetoides (1.31%), Talaromyces (1.19%), Trichoderma (1.15%), Podospora (1.06%) comprised 49.81% of the taxonomic feature abundance. Overall 663 taxa were identified (578 species, 416 genera, 230 families, 106 orders, 48 classes and 9 phyla). The dataset (DwCA; 663 occurrences) is intended to serve as a reference for compost mycobiomes and will be available via GBIF (DOI 10.15468/nmpzwr).},
}

@article {pmid42004820,
year = {2026},
author = {Finkelstein, S and Frishman, S and Turjeman, S and Shtossel, O and Tikhonov, E and Nuriel-Ohayon, M and Pinto, Y and Popova, P and Tkachuk, AS and Vasukova, EA and Anopova, AD and Agay-Shay, K and Pustozerov, EA and Pervunina, TM and Grineva, EN and Hod, M and Schwartz, B and Hadar, E and Koren, O and Louzoun, Y},
title = {Early pregnancy is characterized by a significant decrease in the diversity of the oral microbiome and strong associations with lifestyle and conception method.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2657139},
pmid = {42004820},
issn = {2000-2297},
abstract = {BACKGROUND: Most studies of the oral microbiome during pregnancy have focused on the second and third trimesters (T2, T3, respectively). To date, no large-scale longitudinal study has examined oral microbiome development across all three trimesters, leaving early gestational dynamics largely unexplored.

METHODS: We conducted a longitudinal analysis of 346 pregnant Israeli women, validated in an independent cohort of 154 Russian women. In Israel, saliva samples were collected during T1 (11-14 weeks), T2 (24-28 weeks), and T3 (32-38 weeks); in Russia, samples were collected during T2 and T3 at similar gestational ages. Microbial profiles were analyzed for differential abundance and associations with maternal nutrition and lifestyle.

RESULTS: Significant shifts in oral microbial composition were observed as early as the transition from T1 to T2. Alpha diversity decreased progressively across pregnancy. Taxonomic changes included a reduction in Verrucomicrobiota and an increase in Synergistota. Gluten-free diet showed the strongest associations with microbiome composition across all trimesters, followed by smoking history and conception method.

CONCLUSIONS: This study provides the first large-scale evidence of significant oral microbiome changes beginning in early-mid pregnancy, characterized by reduced diversity and a directional shift toward inflammation-associated communities. Strong associations between gluten consumption and smoking suggest a lifestyle effect on the oral microbiome.},
}

@article {pmid42004950,
year = {2026},
author = {Suarez, LJ and Vargas-Sanchez, PK and Angelov, N and Mylonakis, E and Arce, RM},
title = {Host-pathogen interactions in periodontitis: an integrative interkingdom perspective.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1797726},
pmid = {42004950},
issn = {1664-3224},
mesh = {Humans ; *Periodontitis/microbiology/immunology ; *Host-Pathogen Interactions/immunology ; Microbiota/immunology ; Dysbiosis/microbiology/immunology ; Biofilms/growth & development ; Animals ; Bacteria/immunology ; },
abstract = {Periodontitis is an infectious, inflammatory, non-communicable disease characterized by tissue destruction driven by host responses to dysbiotic shifts in oral microbial communities. The subgingival microbiome constitutes a complex ecosystem in which bacteria, fungi, viruses, and archaea interact via interkingdom communication to modulate the inflammatory response through molecular mechanisms that remain largely unknown. This narrative review aims to understand how functional imbalances within the microbiome alter the microenvironment and promote uncontrolled inflammation responsible for periodontal tissue damage, with implications for systemic disease. The search strategy was conducted according to the PRISM-S extension, to include studies evaluating interkingdom host-pathogen interactions at the gingiva interphase leading to microbial and immune dysbiosis. The discovery of fungi acting as opportunistic pathogens highlights their role in enhancing biofilm virulence and exacerbating host responses, contributing to the total inflammatory burden. Similarly, viruses and archaea influence bacterial metabolism through mechanisms including lysis, nutrient recycling, horizontal gene transfer, and interspecies hydrogen transfer. This interkingdom crosstalk disrupts symbiosis, facilitating enhanced biofilm formation, increased production of virulence factors, and antibiotic resistance. A better understanding of the interkingdom perspective necessitates a comprehensive polymicrobial approach to diagnosis and treatment that extends beyond simply controlling bacteria to include the modulation of interkingdom communication systems. Developing new therapeutic alternatives that address these complex interactions is essential for improving outcomes achieved with mechanical therapy and managing the interrelationships between periodontitis and other systemic diseases.},
}

Humans
*Periodontitis/microbiology/immunology
*Host-Pathogen Interactions/immunology
Microbiota/immunology
Dysbiosis/microbiology/immunology
Biofilms/growth & development
Animals
Bacteria/immunology

@article {pmid42004962,
year = {2026},
author = {Li, J and Chen, X and Xie, X},
title = {Mechanistic insights into gut microbiota-driven autoimmunity in rheumatoid arthritis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1812972},
pmid = {42004962},
issn = {1664-3224},
mesh = {Humans ; *Arthritis, Rheumatoid/immunology/microbiology/therapy ; *Gastrointestinal Microbiome/immunology ; *Autoimmunity ; Animals ; Dysbiosis/immunology ; },
abstract = {Rheumatoid arthritis (RA) is a systemic autoimmune disease whose pathogenic drivers and initiating immune events remain incompletely understood. Increasing evidence implicates the gut-joint axis in RA, yet the mechanisms by which intestinal microbiota contribute to disease development still require integrative clarification. This review summarizes current experimental and clinical evidence on the role of gut dysbiosis in promoting autoimmunity in RA. We discuss alterations in microbial composition and their links to barrier dysfunction, immune-cell polarization, microbial metabolites, and antigen-specific immune responses. Human cohort studies and arthritis models suggest that reduced microbial diversity, loss of short-chain fatty acid (SCFA)-producing commensals, and expansion of taxa such as Prevotella copri and Collinsella are associated with impaired epithelial integrity, enhanced Th17/Tfh differentiation, reduced regulatory T- and B-cell activity, and increased autoantibody production. Mechanistic studies further support roles for molecular mimicry, microbially derived citrullinated antigens, and metabolite-mediated signaling in the breakdown of immune tolerance and persistence of synovial inflammation. We also discuss emerging microecology-based interventions, including probiotics, prebiotics, postbiotics, and fecal microbiota transplantation, together with their translational potential and current limitations. Overall, available evidence places gut microbiota-mediated immune remodeling at the center of RA pathogenesis and supports precision microbiome modulation as a promising adjunctive strategy for disease prevention and treatment.},
}

Humans
*Arthritis, Rheumatoid/immunology/microbiology/therapy
*Gastrointestinal Microbiome/immunology
*Autoimmunity
Animals
Dysbiosis/immunology

@article {pmid42005042,
year = {2026},
author = {Dalamaga, M and Liu, J},
title = {Metabolic advances in 2025: from clinical breakthroughs to molecular reprogramming.},
journal = {Metabolism open},
volume = {29},
number = {},
pages = {100442},
pmid = {42005042},
issn = {2589-9368},
abstract = {The year 2025 represented a turning point in metabolic research, marked by advances that combined unprecedented clinical efficacy with deep mechanistic insight. Landmark obesity trials redefined therapeutic expectations, with head-to-head and combination studies showing that the depth and distribution of weight loss are critical determinants of metabolic benefit across obesity and type 2 diabetes. In parallel, gene-editing studies crossed a translational threshold, showing that durable modification of metabolic pathways in humans is feasible, from bespoke correction of inborn errors to population-scale lipid lowering. Mechanistic investigations challenged long-standing assumptions about metabolic regulation. Experimental work revealed that mitochondrial electron transport functions as a dynamic redox regulator rather than a passive energy conduit, linking coenzyme Q imbalance and reverse electron transport to hepatic steatosis and metabolic dysfunction. Other studies reframed nutrient exposure and endogenous metabolites, demonstrating that non-nutritive sweeteners and cyanide exert context-dependent metabolic effects through regulated endocrine and redox pathways. At the systems level, multi-omics analyses defined reproducible microbiome-metabolome signatures associated with impaired glucose regulation, while artificial intelligence and continuous glucose monitoring exposed dynamic glycemic phenotypes invisible to conventional biomarkers. Precision-nutrition studies further showed that selective manipulation of sulfur amino acid availability can program thermogenic and metabolic responses. Collectively, these studies illustrate how metabolism in 2025 was approached as a modifiable, programmable system, shaped by clinical intervention, molecular control, and data-driven phenotyping, and point toward an era of increasingly precise and integrated metabolic medicine.},
}

@article {pmid42005241,
year = {2026},
author = {Flores Rodríguez, JC and Morán Ortega, MJ and Jimenez Ordoñez, AC and Rojas López, AK and Leyva, MC and Romero, HV},
title = {Postbiotics in Dermatology: A Literature Review of Emerging Topical Therapies for Acne, Rosacea, and Eczema.},
journal = {Cureus},
volume = {18},
number = {3},
pages = {e105440},
pmid = {42005241},
issn = {2168-8184},
abstract = {Postbiotics, defined as non-viable microbial cells and their metabolites, have emerged as topical therapies for inflammatory dermatoses and provide more clinical benefits than live postbiotics by eliminating infection risk and stability. This literature review aims to generalise existing knowledge about the effectiveness and mechanisms of action of first-line topical postbiotic treatments for acne, rosacea, and eczema. Search terms included "postbiotics" and keywords that represented the dermatological conditions of interest. Thematic synthesis was performed on the systematically extracted data. After screening, 16 studies were included in the review. Postbiotic preparations showed significant reductions in Scoring Atopic Dermatitis (SCORAD) and pruritus and improved barrier function in the skin, as well as longer remissions (p < 0.001). In acne vulgaris, postbiotics decreased inflammatory lesions by 50% to 70%, suppressed sebum secretion (42% to 72%), and stopped the growth of Cutibacterium acnes. The study concluded that topical postbiotics, reported to be effective in atopic dermatitis and acne vulgaris, have favourable safety profiles and can be integrated into treatment regimens for the aforementioned diseases. However, no interventional studies have examined rosacea, and the evidence is limited to narrative reviews in which microbiome disequilibrium remains undetermined despite a lack of clinical efficacy. Therefore, a lack of clinical trials for rosacea is a high research priority, given the substantial mechanistic rationale for this absence of high-quality pragmatic evidence.},
}

@article {pmid42005542,
year = {2026},
author = {Canha-Gouveia, A and Tenorio, CM and Rööp, T and Kõljalg, S and Smidt, I and Sepp, E and Štšepetova, J and Saare, M and Vela, S and Pérez-Prieto, I and Vargas, E and Mozas, J and Clavero, A and Sola-Leyva, A and Salumets, A and Mändar, R and Altmäe, S},
title = {Assessing endometrial microbiota in endometriosis: culturomics and sequencing analysis of receptive-phase tissue.},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100593},
pmid = {42005542},
issn = {2666-5174},
abstract = {Endometriosis has been associated with alterations in the reproductive tract microbiota, yet studies focusing on the endometrial microbiome remain inconsistent, partly due to the low-biomass nature of this niche and methodological heterogeneity. In this prospective pilot study, we investigated whether the receptive-phase endometrial microbiota differs between women with and without endometriosis using a combined culturomics and 16S rRNA gene sequencing approach. Endometrial samples were collected from 20 women undergoing fertility assessment, including 10 women with a previous diagnosis of endometriosis and 10 controls with male factor infertility. Biopsies were used for culturomics and Tao brush samples for sequencing, both obtained during the mid-secretory phase. Viable bacterial growth was recovered from 19 of 20 biopsies, yielding approximately 2500 colonies corresponding to 40 non-redundant species. Direct plating and aerobic pre-incubation shared around 45% of detected species, with pre-incubation enhancing species recovery but limiting quantitative comparisons. Bacterial load estimated from direct cultures showed wide inter-individual variability and no significant differences between groups, consistent with 16S rRNA gene sequencing results, which also revealed no clear differences in microbial diversity or overall community composition within this cohort. Only a limited overlap was observed between taxa detected by culture and sequencing, highlighting the complementarity and methodological biases of each approach. Overall, this study demonstrates the feasibility of recovering viable bacteria from receptive-phase endometrial samples and supports the combined use of culturomics and sequencing as complementary tools for studying microbiota in low-biomass uterine environments. These findings should, however, be interpreted considering the exploratory design and limited sample size.},
}

@article {pmid42005840,
year = {2026},
author = {Zhgun, AA and Khomutov, MA and Avdanina, DA and Troyan, E and Dumina, MV and Ermolyuk, AA and Simonenko, N and Shumikhin, K and Khurs, EN and Zhuikova, Y and Varlamov, VP and Shitov, MV and Khomutov, AR},
title = {H-phosphinic analogs of natural amino acids: a novel and efficient treatment for preventing biodeterioration of treasured painted artworks.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1677277},
pmid = {42005840},
issn = {1664-302X},
abstract = {INTRODUCTION: Microorganisms can destroy various materials that make up objects of cultural heritage. In particular, ancient tempera paintings are made with egg yolk, animal glue, and a number of other organic materials, which serve as a good breeding ground for the development of microorganisms. Recently, the range of traditional antiseptics used to protect tempera paintings from biodeterioration has been significantly reduced because of undesirable properties associated with their interaction with painting materials and toxicity. Therefore, it is necessary to develop a new generation of antiseptics that can effectively protect paintings from destructive microorganisms.

METHODS: To solve this challenging task and protect paintings from fungal damage, we used H-phosphinic analogs of natural amino acids. Twelve different H-phosphinic analogs of natural amino acids were screened on Czapek-Dox agar medium against 11 mold fungi belonging to the genera Aspergillus, Penicillium, Simplicillium, Microascus, Cladosporium, and Ulocladium. These mold fungi are responsible for the biodegradation of tempera paintings and are the dominant representatives of the microbiome of the State Tretyakov Gallery in Russia.

RESULTS: All the studied compounds at concentrations of 0.7-2.5 mM inhibited the mycelial growth of mold fungi. The supplementation of H-phosphinic analogs of alanine, aspartate, and valine resulted in the loss of characteristic pigmentation of Penicillium chrysogenum, which may be associated with inhibition of Ac-CoA and malonyl-CoA biosynthesis. The H-phosphinic analog of methionine protected mock layers with sturgeon glue more effectively than the other H-phosphinates and standard antiseptics, such as benzalkonium chloride or sodium pentachlorophenolate. The addition of H-phosphinic amino acid analogs to sturgeon glue did not significantly affect the spectral and surface properties of the glue applied on the layout but effectively inhibited the growth of the studied mold fungi on mock-up layers during long-term storage.

CONCLUSION: Our data provide the first evidence of the successful use of nontoxic H-phosphinic analogs of natural amino acids for protecting paintings from biodeterioration.},
}

@article {pmid42005845,
year = {2026},
author = {Berg, G and Antonietti, M and Egamberdieva, D and Korsten, L and Wicaksono, WA},
title = {Correction: Microbiome-inspired solutions to save human and planetary health.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1831892},
doi = {10.3389/fmicb.2026.1831892},
pmid = {42005845},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2026.1744452.].},
}

@article {pmid42006274,
year = {2026},
author = {Saravinovska, K and Santi, D and Costantino, F and Prete, A and Šojat, AS and Spaggiari, G and Ivović, M and Lambrinoudaki, I and Armeni, E and Jurišić, A and Mihajlović, S and Vujović, S and Marina, LV},
title = {The impact of estrogen status on the gut microbiome: a systematic review and meta-analysis.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1780806},
pmid = {42006274},
issn = {1664-2392},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Female ; *Estrogens/metabolism ; Postmenopause ; *Primary Ovarian Insufficiency/microbiology/metabolism ; Premenopause ; },
abstract = {BACKGROUND: Estrogens have been proposed as modulators of gut microbiome (GM) composition, yet evidence from observational studies remains inconsistent.

OBJECTIVE: This meta-analysis aimed to systematically summarise existing evidence on GM alterations in hypoestrogenic women - post-menopausal or premature ovarian insufficiency (POI) - compared to euestrogenic pre-menopausal controls.

METHODS: PubMed, SCOPUS and Embase were searched through December 2024 for studies comparing GM characteristics between hypoestrogenic and pre-menopausal women. Primary outcome was α-diversity (Shannon index). Secondary outcomes included relative abundances of Bacteroidetes, Firmicutes, and the Bacteroidetes to Firmicutes ratio. Random-effects models were used for data synthesis.

RESULTS: Out of 1092 studies screened, 7 met the inclusion criteria (n = 45 women with POI, n = 1222 post-menopausal women, n = 463 eustrogenic controls). No significant differences were observed in α-diversity (p=0.990), Bacteroidetes (p=0.440), or Firmicutes abundance (p=0.110) between hypoestrogenic and euestrogenic groups, irrespective of POI or postmenopause. Similarly, the Bacteroidetes to Firmicutes ratio showed no significant difference between the groups (p=0.400). Study heterogeneity was high (I² 61-99%).

CONCLUSION: Current evidence does not support consistent differences in GM diversity or major bacterial phyla between hypoestrogenic and euestrogenic women. Given the substantial heterogeneity, limited control of confounding factors, and variability in methodological quality, these findings should be interpreted with caution. High-quality, well-controlled studies are needed to better define the relationship between estrogen status and the GM.},
}

Humans
*Gastrointestinal Microbiome/physiology
Female
*Estrogens/metabolism
Postmenopause
*Primary Ovarian Insufficiency/microbiology/metabolism
Premenopause

@article {pmid42006291,
year = {2026},
author = {He, H and Liu, S and Han, H and Zhou, H and Chen, Y and Tian, H and Chen, M and Wei, W},
title = {Microbial transmission among giant panda, sympatric wildlife, and domesticated animals.},
journal = {iScience},
volume = {29},
number = {4},
pages = {115276},
pmid = {42006291},
issn = {2589-0042},
abstract = {The gut microbiome of wild animals is subject to complex influences, including cross-species transmission that risks host and environmental health. This study used 16S rRNA sequencing to profile microbial communities in giant pandas (GPs), sympatric wildlife, domesticated animals, and environmental samples from panda habitats. Results revealed significant differences in microbial community structure at both phylum and genus levels. Source Tracker analysis indicated that red pandas (RPs) serve as the primary potential microbial source for GPs (72.17%). However, the two species exhibited distinct patterns in acquiring microbes from other groups: GPs were more susceptible to potential transmission by aerobic and facultative anaerobic bacteria compared to RPs. Water and soil showed distinct microbial assembly patterns as sinks, reflecting their divergent physicochemical properties. These findings demonstrate that dietary specialization and environmental exposure collectively shape the gut microbiome, offering insights for managing microbial interactions and habitats.},
}

@article {pmid41994262,
year = {2026},
author = {Li, CM and Kenéz, Á},
title = {Effects of dietary black soldier fly larvae meal inclusion on the serum metabolome of Silkie crossbreed chickens.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1803699},
pmid = {41994262},
issn = {2297-1769},
abstract = {INTRODUCTION: Black soldier fly larvae (BSFL; Hermetia illucens) meal, an alternative to conventional dietary protein sources, such as soybean meal, is rich in medium-chain fatty acids, antimicrobial peptides and other bioactive components. These components may modulate the composition and function of the gut microbiota or, after absorption, affect host metabolic pathways. We hypothesised that the functional effects of BSFL meal would be reflected in alterations in the serum metabolite profile of Silkie crossbreed chickens.

METHODS: Serum samples from chickens fed a control soybean-based diet or a diet containing 150 g/kg partially defatted BSFL meal were analysed using untargeted liquid chromatography-mass spectrometry.

RESULTS AND DISCUSSION: A total of 3304 metabolite features were detected, of which 1341 were annotated, with 777 retained for statistical analysis. Principal component analysis and PERMANOVA revealed a clear separation between dietary groups (p = 0.001). Forty metabolites were significantly altered (FDR ≤ 0.05), with 31 more abundant and nine less abundant in the BSFL group. These shifts were characterised mainly by increased lipid-related metabolites, including medium-chain fatty acids (MCFAs) and phospholipids, indicating alterations in lipid metabolism. In addition, changes in amino acid derivatives and energy-related metabolites suggested the modulation of amino acid and energy metabolic pathways. Several metabolites with putative microbial origin were elevated, consistent with indirect host-microbiome metabolic interactions. These metabolic changes showed correlations with significantly higher average daily gain (p = 0.02), numerically greater final live weight, and a reduced feed conversion ratio in BSFL-fed chickens (p = 0.07 and p = 0.08, respectively). Overall, dietary inclusion of 150 g/kg BSFL meal modified systemic metabolism without detectable negative effects on performance or serum biomarkers, suggesting that this level of BSFL inclusion can be beneficial for slow-growing Silkie chickens.},
}

@article {pmid41994270,
year = {2026},
author = {Albarracín, VH and Gámez-Espinosa, E and Bingjie, M and Gomez de Saravia, SG and Jroundi, F},
title = {Editorial: Microbes and cultural heritage: from biodiversity to applications.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1829794},
doi = {10.3389/fmicb.2026.1829794},
pmid = {41994270},
issn = {1664-302X},
}

@article {pmid41994275,
year = {2026},
author = {Yu, T and Yu, Y and Zhao, J and Li, H and Lu, H and Li, Y and Peng, Y and Wang, S and Wei, W and Cheng, X},
title = {Qifuyin improves physiological frailty by regulating the intestinal flora in 3xTg-AD mice.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1753643},
pmid = {41994275},
issn = {1664-302X},
abstract = {OBJECTIVE: Alzheimer's disease (AD) is often accompanied by motor dysfunction, impaired limb strength, and gut microbiota disturbances. This study aimed to evaluate the effects of Qifuyin (QFY), a traditional Chinese medicine formula, on motor deficits, limb strength, aging, and gut microbiota composition in 3xTg-AD mice, a widely used model of AD.

METHODS: Male and female 3xTg-AD mice were administered QFY at low, medium, or high doses. Motor function was assessed using grip strength and rotarod tests. Aging was evaluated through aging scores. Gut microbiota composition was analyzed at the phylum, family, genus, and species levels. Functional profiling of microbiota was performed using KEGG, eggNOG, and carbohydrate-active enzyme (CAZyme) databases. Pearson correlation analyses were conducted to explore relationships between microbiota composition and motor performance.

RESULTS: QFY treatment significantly improved both absolute and normalized grip strength in male and female 3xTg-AD mice. Similarly, motor coordination, as assessed by latency to fall on the rotarod, was significantly enhanced in the groups of QFY. Aging scores were significantly reduced after the treatment of QFY. Microbiome analysis revealed that QFY treatment restored species diversity and improved the overall composition of gut microbiota, with significant increases in Muribaculaceae and decreases in Alcaligenaceae, Rhodanobacteraceae, and Spirochaetaceae. Principal component analysis (PCA) indicated that the gut microbiota composition of the QFY group resembled that of the control (Con) group. Functional analyses showed that treatment of QFY restored microbial pathways related to metabolism and genetic information processing, with significant correlations between microbial alterations and improved motor outcomes. Additionally, QFY modulated the abundance of key carbohydrate-active enzymes, including GH43 and GH35, which were positively correlated with grip strength and rotarod performance.

CONCLUSION: Qifuyin improves motor function, reduces aging-related deficits, and restores gut microbiota homeostasis in 3xTg-AD mice. These findings suggest that QFY may offer therapeutic potential for addressing frailty and motor dysfunction in AD, in association with alterations in gut microbiota composition and predicted microbial functions.},
}

@article {pmid41994282,
year = {2026},
author = {Wang, X and Wei, M and Yi, Y and An, J and Wang, J and Zhao, R and Su, Z and Ji, G and Zhang, X and Liu, X},
title = {Elephant-derived Bacillus licheniformis modulates immune cells shedding light on cancer resistance.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1753410},
pmid = {41994282},
issn = {1664-302X},
abstract = {INTRODUCTION: Colorectal cancer (CRC) is currently a leading cause of cancer-related morbidity and mortality globally, underscoring the need for innovative therapeutic strategies. Probiotic treatment is increasingly appreciated as an innovative method for ameliorating inflammation and modulating the tumor microenvironment, especially in gastrointestinal diseases. Many bacterial species isolated from human and animal sources are proven effective in potential disease treatments. Elephants, renowned for their exceptional resistance to cancer, have traditionally been linked to their TP53 gene multiplicity. However, the potential contribution of their evolutionarily-refined gut microbiota to their remarkable cancer resistance remained largely unexplored.

METHODS: Here, we investigated this underexplored avenue by analyzing the elephant gut microbiome and isolating a probiotic bacterium. We utilized whole genome sequencing (WGS) to assess its genomic profile. The in vivo efficacy was evaluated in mouse models of gut inflammation and colorectal tumors. Underlying mechanisms were investigated using transcriptomic analysis, flow cytometry, and integrative metabolomics. Finally, in vitro experimental validations were conducted on mouse and human CRC cell lines using the bacterial culture supernatant.

RESULTS: We found that elephants possess a highly specialized gut microbiome finely tuned to metabolize complex polysaccharides. WGS of the isolated Bacillus licheniformis revealed its metabolic and functioning roles and confirmed the absence of virulence factors. We demonstrated that this elephant-derived strain effectively alleviated gut inflammation and suppressed the progression of colorectal tumors in mouse models. Transcriptomic analysis and flow cytometry revealed that B. licheniformis remodeled the immune microenvironment, specifically activating tumor-infiltrating T cell response and cell cytotoxicity. Integrative metabolomics identified several key metabolites as potential soluble mediators correlated with tumor regression. Furthermore, the supernatant of B. licheniformis culture significantly enhanced cytotoxicity and upregulated p53 expression in CRC cell lines in vitro.

DISCUSSION: Collectively, these findings unveil previously unrecognized therapeutic potentials inherent in elephant-derived probiotics, suggesting a mechanism of functional immune regulation for CRC prevention.},
}

@article {pmid41994290,
year = {2026},
author = {Li, J and Xu, L and Ding, X and Qiu, N and Yue, J},
title = {Gut and skin microbial dysbiosis correlate with systemic inflammation and pruritus in immunological non-responders.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1758111},
pmid = {41994290},
issn = {1664-302X},
abstract = {INTRODUCTION: Among people living with human immunodeficiency virus (PLWH), those who exhibit immunological non-responders (INR) are highly susceptible to developing pruritus. The aim of this study was to examine the relationships among pruritus, alteration of the gut and skin microbiomes, and systemic inflammation in PLWH with INR.

METHODS: Thirty-three PLWH with INR were enrolled and divided into Pruritus (n = 18) and Control (n = 15) groups. All participants met the defining criterion of a low CD4+ T cell count (≤ 350 cells/μl). We performed 16S rRNA gene sequencing of fecal and skin samples, and measured plasma IL-1β and IL-10 levels.

RESULTS: Microbiome analysis revealed specific, bidirectional patterns of microbial dysbiosis. Specifically, the skin microbiome of the Pruritus Group exhibited significantly greater microbial richness (Chao1 and Faith's Phylogenetic Diversity indices, P < 0.01), coupled with significantly lower representation of the potentially protective genus Bacillus (adjusted P<0.05), compared with that of the INR Control Group. Conversely, the gut microbiome of the Pruritus Group exhibited significantly lower alpha diversity (adjusted P<0.05). Furthermore, we identified a significant positive correlation between levels of plasma pro-inflammatory cytokine IL-1β and the relative abundance of the opportunistic gut genus Veillonella (adjusted P<0.05).

CONCLUSIONS: Pruritic PLWH-INRs exhibit skin microbial hyper-richness, Bacillus depletion, and reduced gut diversity, suggesting a systemic inflammatory basis linked to gut-skin dysbiosis. These findings provide new insights into the pathological process, offering a potential foundation for future microbiome-targeted therapeutic strategies as novel management avenues.},
}

@article {pmid41994309,
year = {2026},
author = {Sarkar, P and Sarkar, S and Unnisa, M and Singh, AP and Inavolu, P and Rughwani, H and Jakkampudi, A and Jaggaiahgari, S and Reddy, DN and Talukdar, R},
title = {The Jejunal Microbiota in Patients With Chronic Pancreatitis: Results From a Pilot Study.},
journal = {Gastro hep advances},
volume = {5},
number = {5},
pages = {100907},
pmid = {41994309},
issn = {2772-5723},
abstract = {BACKGROUND AND AIMS: Chronic pancreatitis (CP) is associated with several systemic metabolic abnormalities including diabetes. While the colonic microbiota and its association with diabetes in CP have been reported, the specific composition of the small intestinal microbiota and its function in CP remains poorly understood. In this pilot study, we primarily aimed to characterize the jejunal microbiota in patients with CP and explore potential associations with diabetes.

METHODS: Jejunal aspirates were collected in a RNAlater-containing sterile container from 29 patients with CP and 10 controls. The samples were then snap lysed followed by metagenomic DNA extraction. Next-generation sequencing was performed for the variable region 3-4 of the 16SrDNA in Illumina MiSeq. After quality control, microbial profiling and functional analysis were conducted using standard bioinformatics pipelines. We also evaluated tight junction integrity in jejunal biopsy samples using immunofluorescence. Furthermore, we assessed for plasma and stool metabolites.

RESULTS: Patients with CP exhibited higher abundances of Prevotella vespertina, Prevotella oris, and Prevotella salivae, while controls demonstrated higher abundances of Prevotella scopos, Veillonella, Rothia, and Lachnospiraceae. Immunofluorescence showed decreased expression of the tight junction protein occludin in the jejunal mucosa of CP diabetic (CPD) patients compared to endoscopic controls (EC) (p.corr. CPD-EC = 0.012). No differences were seen between CP nondiabetic and endoscopic controls, and between the CP subgroups (CPND-EC = 0.29 and CPD-CPND = 1 respectively). Overall, there were significant plasma metabolomic abnormalities in patients with CP and a trend toward reduction of butyrate in the stool samples of the CP patients with diabetes.

CONCLUSION: Our observations suggest alterations in the jejunal microbiota and mucosal barrier function in CP. These were associated with lower fecal butyrate. This may contribute to the pathogenesis of associated metabolic complications in CP. Further large-scale longitudinal and mechanistic studies are needed to validate our findings.},
}

@article {pmid41994453,
year = {2026},
author = {Zhang, W and Zhang, K and Liao, Y and Yang, Z and Xia, Z and Ke, X and Zhang, D and Chen, J and Wu, H and Hong, Y and Wang, H and Liu, Z and Suo, L and Zhang, Y and Zhang, C},
title = {Characterization of the aqueous humor microbiome in Posner-Schlossman syndrome: an exploratory metagenomic sequencing study.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1780981},
pmid = {41994453},
issn = {2296-858X},
abstract = {OBJECTIVE: This study aims to characterize the aqueous humor (AH) microbiome in Posner-Schlossman syndrome (PSS) patients and evaluate its potential as a diagnostic and therapeutic target.

METHODS: Metagenomic next-generation sequencing (mNGS) was performed on 59 AH samples from patients diagnosed with PSS (n = 28) and myopia patients who underwent intraocular lens (ICL) implantation (n = 31). Taxonomic profiling and diversity analyses were conducted to characterize the microbial communities. Interactions among microbial community members were evaluated using correlation analyses.

RESULTS: Key findings revealed that intraocular microbiomes existed in both normal and diseased eyes; however, PSS patients exhibited lower microbial diversity (Shannon index, p = 0.066; Simpson index, p = 0.065) and distinct community structures (PERMANOVA, p = 0.05). Disease-specific microbial signatures were identified: Paeniglutamicibacter was uniquely enriched in the PSS group, whereas Escherichia coli dominated in the ICL group. Moreover, ecological network analysis demonstrated contrasting interaction patterns. The microbiomes in the PSS group formed stable, tightly connected networks with balanced positive/negative correlations, whereas those in the ICL group exhibited antagonistic relationships, suggesting competitive exclusion. These results challenge the traditional view of ocular sterility and reveal dynamic microbiome shifts associated with PSS pathogenesis. The enrichment of Paeniglutamicibacter in PSS may represent an associated microbial signature that could potentially reflect compensatory responses to chronic inflammation, although experimental validation is needed to confirm this hypothesis.

CONCLUSION: Our study provides preliminary evidence supporting the concept of intraocular microbiome dysbiosis in PSS, which requires validation in future studies. These findings suggest that potential microbial biomarkers warrant further investigation for their diagnostic and therapeutic implications.},
}

@article {pmid41994836,
year = {2026},
author = {Radhika, M and Mohan, S and Singh, HJ and Kadwe, P and Prajapati, J and Mansuri, SH and Sonis, JJ},
title = {Clinical Impact of Macronutrients and Micronutrients: A Review of Nutritional Balance, Deficiency Disorders, and Therapeutic Applications.},
journal = {Cureus},
volume = {18},
number = {3},
pages = {e105305},
pmid = {41994836},
issn = {2168-8184},
abstract = {Nutrition plays a fundamental role in maintaining human health and modulating disease risk across the life course. This narrative review synthesizes contemporary evidence on the clinical significance of macronutrients, including carbohydrates, proteins, and fats, and micronutrients, including vitamins and minerals, establishing nutritional balance as a central determinant of human health, disease susceptibility, and therapeutic efficacy. These nutrient categories function within an integrated metabolic network in which macronutrients provide energy and structural substrates, while micronutrients serve as essential cofactors and regulatory agents in enzymatic, hormonal, and cellular signalling processes. The synthesis demonstrates that nutritional imbalance, arising from either deficiency, such as iron-deficiency anaemia and vitamin D insufficiency, or excess, including high intakes of refined carbohydrates and saturated fats, constitutes a major contributor to global disease burden, particularly the phenomenon described as the double burden of malnutrition. In response to these challenges, the review highlights the role of evidence-based nutritional therapy, encompassing established dietary patterns such as the Mediterranean and Dietary Approaches to Stop Hypertension (DASH) diets, as well as the clinical implementation of medical nutrition therapy in chronic disease management. It further emphasizes a paradigmatic shift from population-level dietary recommendations toward precision nutrition, an emerging framework that integrates nutrigenomics, metabolomics, and gut microbiome profiling to inform personalized dietary interventions. By conceptualizing nutrition as a dynamic and interactive system, this review offers a comprehensive perspective that integrates biochemical mechanisms with individualized clinical care, positioning nutritional balance as a foundational component of contemporary preventive and therapeutic medicine.},
}

@article {pmid41995085,
year = {2026},
author = {Cao, Y and Chen, W and Li, Q and Liao, Y and Wang, J and Pan, L},
title = {Microbiome and Metabolomics Reveal the Effect of Rhizosphere Microorganisms on Quizalofop-p-ethyl Resistance in Polypogon fugax.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c01864},
pmid = {41995085},
issn = {1520-5118},
abstract = {Plant-microbiome interactions are essential for plant health and productivity under stress; however, little is known about these interactions in response to herbicide. Here, we integrated 16S rRNA gene sequencing with nontargeted gas chromatography-mass spectrometry (GC-MS) to investigate the interactions between rhizosphere microbiomes and metabolomes in Polypogon fugax. The results indicated that quizalofop-p-ethyl-resistant (QU-resistant) P. fugax promoted microbial colonization within its microbiome, enriched the abundance of Verrucomicrobia, and increased the levels of d-proline and α,α-trehalose in the rhizosphere, potentially attracting Verrucomicrobia. Furthermore, when the rhizosphere microbiome from R3 populations was transplanted to QU-sensitive plants, the recipients exhibited enhanced antioxidant defense systems and demonstrated reduced sensitivity to QU. These results suggest that the rhizosphere microbiome of QU-resistant P. fugax contributes to its resistance against QU. Overall, our findings highlight the complex interactions among herbicide resistance mechanisms, rhizosphere microbiota, and plant responses, suggesting potential strategies for managing herbicide-resistant weed populations.},
}

@article {pmid41995217,
year = {2026},
author = {Liu, M and Yang, Z and Liu, B and Cheng, H and Qin, J and Zhang, P and Tang, T and Peng, F and Yang, J and Wei, P and Su, H},
title = {Multi-omics reveals gut microbiome- and metabolome-specific responses to sugar alcohols.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6fo00282j},
pmid = {41995217},
issn = {2042-650X},
abstract = {The impacts of sugar alcohols (SA) utilized as low-calorie sweeteners on the gut microbiome and metabolome remain undefined. Among six SAs tested, isomalt, erythritol, xylitol and sorbitol significantly lowered fasting serum insulin and hepatic lipid levels in healthy rats, while mannitol and maltitol showed no such effect. Moreover, isomalt consumption lowered body weight gain, low-density lipoprotein and tumor necrosis factor-α, while improving high-density lipoprotein concentrations. All SAs effectively regulated gut microbiota composition and functionality. Most of the microbiota enriched by isomalt were short-chain fatty acid producers, including Faecalibaculum, Bacillus, Dubosiella and Anaerostipes, which led to a significant increase in the propionate proportion in faeces. The elevated Blautia and UCG-008 and lowered Akkermansia were the key specific responders to sorbitol, mannitol and maltitol. Notably, almost all SAs showed inhibitive efficacy on opportunistic pathogens such as Streptococcus, Staphylococcus and Ruminococcus. Dietary SAs significantly shifted stool and global metabolome profiles in rats. Isomalt and maltitol activated aldosterone-regulated sodium reabsorption and suppressed steroid hormone biosynthesis. Isomalt and sorbitol induced the thyroid hormone signaling pathway. Erythritol intake expressively triggered histamine metabolism, chemical carcinogenesis-receptor activation and folate biosynthesis. Xylitol, sorbitol and mannitol robustly promoted nucleotide metabolism, lysine biosynthesis and pyrimidine metabolism. Sorbitol and mannitol administration induced arginine biosynthesis, nicotinate and nicotinamide metabolism and terpenoid backbone biosynthesis. Additionally, stool metabolome suggested that mannitol intake attenuated ferroptosis in rats. Interestingly, structurally similar SAs, e.g. sorbitol, mannitol and maltitol, showed more shared microbiota and metabolites. This systematic comparative study identifies specific microbiota and associated metabolic pathways as responders to each SA and provides novel insights for future application in functional foods.},
}

@article {pmid41995305,
year = {2026},
author = {Haag, KL and Stein, LQ and Nunes da Silva, CG and Mazel, F and Prasad, A and Engel, P},
title = {Conserved gut microbiomes with cross-species spillover between sympatric Neotropical stingless bees and honey bees.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0248325},
doi = {10.1128/aem.02483-25},
pmid = {41995305},
issn = {1098-5336},
abstract = {Stingless bees (Meliponini) are ecologically vital pollinators with deep cultural and economic importance in the Neotropics; however, the biogeographic structure of their gut microbiota and the extent of microbial exchange with managed honey bees (Apis mellifera) remain insufficiently understood. Using full-length 16S rRNA gene sequencing of individually sampled workers from 167 colonies across Brazil, we compared gut bacterial communities of Melipona quadrifasciata and Melipona mondury with those of co-occurring A. mellifera through an integrated taxonomic, phylogenetic, and community ecological framework. The core microbiota of Melipona species was dominated by Lactobacillus, Bifidobacterium, Apilactobacillus, Bombella, and Floricoccus, whose relative abundances covaried inversely with a set of low-prevalence taxa. Although the core communities of stingless bees overlapped only partially with those of honey bees, both groups displayed comparable alpha- and beta-diversity dispersion, suggesting broadly similar assembly dynamics. Notably, 6% of all amplicon sequence variants (ASVs) were shared across hosts, encompassing nearly all canonical honey bee symbionts, consistent with frequent cross-species spillover. Among these, several Snodgrassella ASVs-typically rare in these stingless bee species-reached high abundance in M. quadrifasciata and formed a deeply divergent clade (~96% 16S rRNA identity to Snodgrassella alvi). These patterns indicate that human-mediated management practices, such as mixed apiaries and artificial feeding, create ecological opportunities for interspecific microbial exchange. Overall, our results show that stingless bee gut microbiomes are compositionally stable yet ecologically permeable, shaped jointly by long-term host specificity and recent anthropogenic contact.IMPORTANCEStingless bees are key pollinators in tropical ecosystems and hold long-standing cultural significance in the Neotropics; however, their microbiomes remain far less studied than those of managed honey bees. Understanding how gut bacterial communities vary across landscapes, and whether microbes move between native and non-native hosts, is essential for predicting the ecological consequences of increasing meliponiculture and urban beekeeping. Our study reveals that stingless bee gut microbiota are generally stable and host-associated but nonetheless acquire bacterial symbionts typical of honey bees, indicating that human management practices facilitate cross-species microbial transmission. These findings broaden current knowledge of bee-microbe evolution by showing that gut symbiont boundaries are not fixed but can become permeable under anthropogenic influence. This has important implications for pollinator health, conservation, and biosecurity as managed and native bees increasingly co-occur in human-modified environments.},
}

@article {pmid41995339,
year = {2026},
author = {Ayalew, M and Hoffman, AM and Fuller, K and Kerr, J and Lee, A and Lee, J and Martinez, ES and Ulbricht, K and Xie, X},
title = {Microbiome education at under-resourced institutions: current status, barriers, and approaches to successful implementation.},
journal = {Journal of microbiology & biology education},
volume = {},
number = {},
pages = {e0028825},
doi = {10.1128/jmbe.00288-25},
pmid = {41995339},
issn = {1935-7877},
abstract = {Microbiome research offers significant promise for advancing public health, medicine, environmental science, and industry. The topic also lends itself well to engaging students and teaching a "new biology" that integrates several disciplines, including computational biology. However, access to microbiome education remains limited, particularly at under-resourced institutions. We conducted a poll showing that over 90% of faculty expressed strong interest in microbiomes; however, only 48% reported that their institutions offer related courses or modules. The most commonly cited barrier was a lack of time and/or funding for design or implementation. A secondary barrier was limited access to professional development or a supportive community of practice. Through case vignettes and reflective analysis, we explore successful efforts to incorporate microbiome education at under-resourced institutions, highlighting the role of faculty development, collaboration, curriculum design, and external funding. These cases demonstrate that implementation is possible with varying levels of investment. We conclude by emphasizing the need for innovative and collaborative strategies, along with sustained resources, to support microbiome education and empower the next generation of genomic data scientists from diverse educational backgrounds.},
}

@article {pmid41995478,
year = {2026},
author = {Conley, TE and Duncan, A and Modasia, A and Ford, AC and Pritchard, DM and Hildebrand, F and Warren, FJ and Spiller, R and Probert, CS},
title = {The Emerging Short Chain Fatty Acid Enriched Metabotype in Irritable Bowel Syndrome and Its Potential Clinical Relevance.},
journal = {Alimentary pharmacology & therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.1111/apt.70677},
pmid = {41995478},
issn = {1365-2036},
abstract = {BACKGROUND: Metabolomic analysis in irritable bowel syndrome (IBS) has identified metabotypes enriched in faecal short-chain fatty acids (SCFAs), but it remains unclear whether this reflects rapid colonic transit or if these metabolites actively contribute to pathophysiology.

AIMS: We aimed to determine whether an SCFA metabotype could be identified within a cohort of patients with moderate-severe IBS-D and assess whether this metabotype associated with greater clinical severity, alterations in gut transit time and specific microbiome features.

METHODS: This was a post hoc cross-sectional exploratory analysis of baseline data from the multicentre, randomised, placebo-controlled trial of ondansetron in IBS-D (TRITON: ISRCTN17508514). Faecal volatile organic compounds were profiled by GC-MS. The microbiome was characterised by whole-genome shotgun metagenomic sequencing. Unsupervised hierarchical clustering was used to identify an SCFA-enriched metabotype and non-negative matrix factorisation (NMF) enabled the derivation of complementary metabosignatures by assessing continuous gradients in metabolite composition.

RESULTS: A SCFA-enriched metabotype was identified in 20/63 participants (31.7%). This metabotype was associated with more severe abdominal pain, urgency, increased stool frequency and faster whole-gut transit. NMF identified three metabosignatures: S3 was typified by a high proportion of SCFAs and captured the SCFA-enriched metabotype, while S1 and S2 corresponded to the non-SCFA ("Other") metabotype. SCFA relative abundance positively correlated with symptom severity and inversely correlated with transit time. The Other metabotype and S1/S2 signatures were enriched in taxa linked to slower transit, whereas S3 showed no overlapping taxa with the SCFA metabotype.

CONCLUSION: A faecal metabotype enriched in SCFAs associated with an IBS-D phenotype characterised by pain, urgency, rapid transit and higher stool frequency.},
}

@article {pmid41995603,
year = {2026},
author = {Pu, P and Wang, Y and Liu, X and Pang, Y and Qiang, L and Wang, W},
title = {The ecological dynamics of skin microbiota in skin health and diseases.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0030525},
doi = {10.1128/cmr.00305-25},
pmid = {41995603},
issn = {1098-6618},
abstract = {SUMMARYThe skin microbiome, consisting of bacteria, fungi, viruses, and archaea, plays a crucial role in maintaining skin health by regulating immune responses, preserving barrier function, and influencing metabolic processes. Dysbiosis in the microbiome is linked to dermatological diseases such as atopic dermatitis (AD), psoriasis, and acne, with specific microbes, such as Staphylococcus aureus and Cutibacterium acnes, either promoting or protecting against disease. This review summarizes recent advances in understanding the composition and functions of the skin microbiome, its interaction with host immunity, and impact on skin health. We also discuss the implications of environmental and biological factors on microbiome stability and explore emerging therapeutic strategies targeting the skin microbiota. These insights highlight the potential of microbiome-based approaches for advancing dermatological treatment.},
}

@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 {pmid41995892,
year = {2026},
author = {Ali, M and Thakali, O and Idris, O and Sherchan, S},
title = {Comparative Evaluation of DNA Extraction Workflows for Efficient Recovery of pBI143 from Wastewater.},
journal = {Food and environmental virology},
volume = {18},
number = {2},
pages = {},
pmid = {41995892},
issn = {1867-0342},
mesh = {*Wastewater/virology ; Feces/virology ; *DNA, Viral/isolation & purification/genetics ; Workflow ; Tobamovirus/isolation & purification/genetics ; Polyethylene Glycols/chemistry ; Maryland ; },
abstract = {This study aimed to compare the performance of polyethylene glycol (PEG) precipitation, and Nanotrap[®] Microbiome magnetic particle capture workflows for recovering novel fecal marker, pBI143 from 12 wastewater samples collected across six treatment plants in Maryland, USA. Quantitative PCR (qPCR) was used to quantify marker abundance. The Nanotrap workflow yielded significantly higher concentration of pBI143 compared to PEG precipitation workflow (p < 0.05). The Nanotrap workflow used in the study utilized both magnetic nanoparticles A and B, rather than magnetic nanoparticle A alone, highlighting the necessity of optimization based on the intended targets for enhanced recovery. The extracted total nucleic acids by the Nanotrap workflow, were further analyzed to quantify other fecal markers, crAssphage, tomato brown rugose fruit virus (ToBRFV), and pepper mild mottle virus (PMMoV). No significant differences in the concentrations of pBI143, crAssphage, and ToBRFV (p > 0.05) were observed, whereas the concentration of PMMoV was significantly lower than that of the three fecal markers (p < 0.05). Based on the concentration alone, pBI143, ToBRFV, and crAssphage were found to be a better alternative to PMMoV as an endogenous fecal marker.},
}

*Wastewater/virology
Feces/virology
*DNA, Viral/isolation & purification/genetics
Workflow
Tobamovirus/isolation & purification/genetics
Polyethylene Glycols/chemistry
Maryland

@article {pmid41995913,
year = {2026},
author = {Azizan, N and Al-Maleki, AR and Karajacob, AS and Loke, MF and Goh, JPE and Kallarakkal, TG and Ho, GF and Khor, HM and Ong, HC and Tay, ST},
title = {Oral microbiome profiling of primary oral candidiasis during infection and post-antifungal therapy.},
journal = {Clinical oral investigations},
volume = {30},
number = {5},
pages = {},
pmid = {41995913},
issn = {1436-3771},
mesh = {Humans ; *Candidiasis, Oral/microbiology/drug therapy ; Male ; *Antifungal Agents/therapeutic use ; Female ; *Microbiota/drug effects ; Middle Aged ; RNA, Ribosomal, 16S ; *Mouth/microbiology ; Dysbiosis/microbiology ; Case-Control Studies ; Adult ; Aged ; },
abstract = {OBJECTIVES: Microbial dysbiosis that facilitates Candida proliferation in the oral cavity is a significant factor associated with oral candidiasis. This study aimed to gain insights into microbial dynamics of primary oral candidiasis during infection and following antifungal therapy to enhance our understanding of disease pathogenesis and treatment efficacy.

MATERIALS AND METHODS: Oral rinse samples were collected from 16 patients with primary oral candidiasis, seven of whom returned for follow-up after antifungal treatment, and from seven healthy controls. Microbiome profiling was performed using 16S rRNA gene sequencing (V3-V4 region), followed by microbial diversity and taxonomic analyses.

RESULTS: Twelve bacterial phyla and 138 genera were identified across all samples. Alpha and beta diversity analyses showed no significant differences in microbial richness or overall community structure across both infection and treatment conditions, suggesting a resilient oral microbiome. Compared to controls, oral microbiome of the patients showed a significantly higher abundance of Firmicutes and Campylobacterota, along with a lower abundance of Bacteroidota. At the genus level, Campylobacter, Staphylococcus, and lactobacilli (Lacticaseibacillus, Ligilactobacillus, and Limosilactobacillus) were present at higher abundances during oral candidiasis, while Neisseria, Prevotella, and Alloprevotella were less abundant. Following two weeks of antifungal therapy, alterations in microbial community composition and diversity were observed relative to the control group, suggesting incomplete microbiota restoration.

CONCLUSION: Microbiome analysis revealed dysbiosis with significant taxa changes during primary oral candidiasis. Clinical resolution of oral candidiasis did not correspond well with microbiota restoration, suggesting dysbiosis may persist beyond fungal clearance and contribute to delayed ecological recovery and oral homeostasis.

CLINICAL RELEVANCE: This study highlights the microbial shift during primary oral candidiasis and post-antifungal treatment. Despite clinical resolution with antifungal therapy, oral microbiome of patients with primary oral candidiasis continues to exhibit residual shifts in composition, underscoring the needs for microbiota-targeted intervention to prevent recurrence and maintain oral health. While our results provide preliminary insights into microbial dysbiosis associated with primary oral candidiasis and the effects of antifungal therapy, further validation in larger cohorts is warranted.},
}

Humans
*Candidiasis, Oral/microbiology/drug therapy
Male
*Antifungal Agents/therapeutic use
Female
*Microbiota/drug effects
Middle Aged
RNA, Ribosomal, 16S
*Mouth/microbiology
Dysbiosis/microbiology
Case-Control Studies
Adult
Aged

@article {pmid41996042,
year = {2026},
author = {Myoung, K and Kim, S and Choi, EJ and Kim, HJ and Baek, HS and Park, WS and Hwang, JS},
title = {Integrated analysis of age-related microbiome and metabolites reveals youth-associated metabolites in young Korean women's skin.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41996042},
issn = {1618-1905},
abstract = {Alterations in the composition and functional potential of the skin microbiome are closely associated with aging. Nevertheless, integrative analyses that concurrently examine microbial composition, functional gene profiles, and skin surface metabolomics remain limited, particularly among Asian populations. In this study, we performed a comprehensive multi-omics analysis integrating skin microbiome and surface metabolomic data from Korean women to explore metabolites associated with youthful skin state. Twenty-three healthy female participants in their 20s and 60s were recruited. Skin physiological parameters were assessed, and microbiome and metabolite samples were collected from the cheek area. Unsupervised clustering of microbiome functional profiles revealed three microbial community patterns that were not strictly aligned with chronological age. Based on these patterns, samples were grouped into three functional groups. The cluster enriched in participants in their 20s showed higher relative abundance of Cutibacterium and enrichment of microbial pathways related to carbohydrate and energy metabolism. Metabolomic profiling showed that phenyllactic acid (PLA) and hydroxyphenyllactic acid were more abundant in participants in their 20s and in the functionally young cluster. These metabolite patterns were accompanied by higher abundance of genes associated with phenylalanine metabolism. In vitro experiments further showed that PLA increased procollagen production and reduced the secretion of collagen-degrading enzymes in human dermal fibroblasts under inflammatory conditions. Together, these findings suggest links between microbiome functional profiles, phenylalanine-related metabolites, and skin physiology. This study provides an integrated view of microbiome-metabolite relationships in Korean skin and identifies PLA as a candidate metabolite associated with youthful skin environments.},
}

@article {pmid41996045,
year = {2026},
author = {Mohanty, A and Pavan-Kumar, A and Chaudhari, A and Kumari, K and Kumar, P and Maurye, P},
title = {Comparative performance of traditional and commercial DNA extraction methods for fish gut microbiota analysis.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {41996045},
issn = {1573-4978},
support = {FBT-PB1-01//Indian Council of Agricultural Research/ ; },
}

@article {pmid41996166,
year = {2026},
author = {Liu, L and Liu, L and Luo, X and Zhao, JL and Tan, X and Zhao, W and Huang, L and Yuan, Z and Li, F and Zheng, H and Xing, B},
title = {Novel Insights into Foodborne Microplastics-Enhanced Shoaling Behavior in Marine Korean Rockfish (Sebastes schlegelii): Energy Deficiency-Driven Gut-Brain Axis Dysregulation.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c16888},
pmid = {41996166},
issn = {1520-5851},
abstract = {Microplastics (MPs) pollution threatens ocean health, yet their impacts on fish shoaling behavior remain poorly understood. Herein, the effects of foodborne polyethylene terephthalate debris (D-PET), PET fiber (F-PET), and tire wear particles (TWPs) at environmentally relevant concentrations (0.1 and 1 mg g[-1]) on behavioral strategies and energy metabolism-mediated gut-brain axis regulation in Korean rockfish (Sebastes schlegelii) were investigated through a 50-day exposure-depuration experiment. MPs induced boldness reduction and hyperactivity, consequently intensifying shoaling behavior in an order of TWPs > F-PET > D-PET, with the interindividual distance decreased by up to 12.14 ± 0.31%. Leachable additives from TWPs, including benzothiazolone, benzothiazole, N,N'-ditolyl-p-phenylenediamine, and N-1,3-dimethylbutyl-N'-phenyl-p-phenylenediamine-quinone, were primarily responsible for the shoaling enhancement. MPs induced hepatic mitochondrial dysfunction and apoptosis that disrupted glucose homeostasis and caused systemic energy deficiency, thereby promoting shoaling as an energetically compensatory strategy. The energy imbalance subsequently triggered oxidative neurotoxicity and perturbed serotonergic, cholinergic, dopaminergic, and GABAergic pathways. Moreover, MPs disrupted the intestinal physicochemical barrier, immune function, and reshaped microbiota, exacerbating neurotransmitter disruption via the gut-brain axis. These findings demonstrate that environmentally relevant MPs exposure can enhance fish shoaling through energy deficiency-driven gut-brain axis dysregulation, revealing the mechanisms by which MPs stress can reorganize population-level behavior and thereby expand understanding of the ecological risks posed by contaminants of emerging concerns.},
}

@article {pmid41996244,
year = {2026},
author = {Liu, X and Zeng, J and Xie, P and Shen, Q and Yuan, J},
title = {Microbial damper: Rhizosphere microbiome mitigates stress-induced plant growth-defense conflicts.},
journal = {Cell reports},
volume = {45},
number = {4},
pages = {117278},
doi = {10.1016/j.celrep.2026.117278},
pmid = {41996244},
issn = {2211-1247},
abstract = {Plants face constant environmental stresses that induce conflicts between growth and defense. The rhizosphere microbiome helps resolve this conflict by enhancing nutrient-uptake efficiency and activating plant immunity simultaneously. In this review, we first outline the mechanisms and limitations of plant-intrinsic growth-defense trade-offs; we then describe the integrated support that rhizosphere microbial communities provide for plant nutrition and defense. Finally, we propose the "microbial-damper" framework and further elucidate the interactions and feedback mechanisms that constitute this system. The microbial damper is a conceptual framework describing the capacity of the rhizosphere microbiome to stabilize a plant's internal growth-defense resource allocation, which is otherwise perturbed by stresses such as nutrient imbalance and other environmental stresses. This framework highlights how the rhizosphere microbiome can reduce stress-induced plant growth-defense resource-allocation conflicts, thereby providing actionable strategies for designing sustainable agricultural systems.},
}

@article {pmid41996342,
year = {2026},
author = {Rajan, FV and Bucking, C},
title = {Effects of salinity and broad-range antibiotics on oxalate production, transport, and degradation in Poecilia latipinna.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0347147},
pmid = {41996342},
issn = {1932-6203},
mesh = {Animals ; *Salinity ; *Oxalates/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Poecilia/metabolism/microbiology ; Gastrointestinal Microbiome/drug effects ; Seawater ; Biological Transport/drug effects ; Kidney/metabolism/drug effects ; },
abstract = {Oxalate is an anion that readily binds calcium and is thought to contribute to osmoregulation. This study investigated how environmental salinity influences oxalate homeostasis in euryhaline sailfin mollies (Poecilia latipinna), with a focus on the interplay between microbial symbiosis and host transport processes. Gut microbiome profiling demonstrated regional specialization, with the posterior intestine enriched in oxalate-degrading bacterial families. Community shifts across salinities suggests functional redundancy and resilience, ensuring maintenance of oxalate-catabolizing capacity. Antibiotic treatment disrupted this system, impairing microbial degradation and causing systemic oxalate stress. Oxalate concentrations were also measured in the liver, intestine, and kidney, organs central to oxalate metabolism, under freshwater and seawater conditions. Salinity induced a redistribution of oxalate among these organs, with the gut assuming an auxiliary excretory role in seawater. This functional shift parallels mammalian colon physiology and highlights the gut's role in balancing ion and oxalate flux. Expression analyses of the oxalate transporters SLC26A3 (solute carrier family 26, member 3) and SLC26A6 (solute carrier family 26, member 6) revealed organ-specific and salinity-dependent regulation. Both transporters displayed distinct responses to seawater exposure, indicating specialized roles in oxalate handling. These patterns suggest coordinated but nonredundant mechanisms that govern absorption and secretion, linking salt transport with oxalate clearance. These findings underscore the microbial contribution to oxalate balance and reveal that osmoregulatory challenges shape gut microbial composition and function. Collectively, this study presents the first comprehensive analysis of oxalate metabolism in a euryhaline teleost and demonstrates a coordinated host-microbe system that mitigates oxalate accumulation across salinities. By integrating metabolic and osmoregulatory demands, P. latipinna reallocates excretory function from kidney to gut and leverages microbial symbiosis to preserve homeostasis. These findings expand our understanding of teleost physiology and highlight oxalate metabolism as a critical axis of environmental adaptation.},
}

Animals
*Salinity
*Oxalates/metabolism
*Anti-Bacterial Agents/pharmacology
*Poecilia/metabolism/microbiology
Gastrointestinal Microbiome/drug effects
Seawater
Biological Transport/drug effects
Kidney/metabolism/drug effects

@article {pmid41996359,
year = {2026},
author = {Li, G and Wang, Y and Zeng, S and Li, S},
title = {Shared Genetics Implicate Gut Microbiota and Immunity in Anterior Uveitis and Inflammatory Bowel Disease.},
journal = {Ocular immunology and inflammation},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/09273948.2026.2654978},
pmid = {41996359},
issn = {1744-5078},
abstract = {PURPOSE: Anterior uveitis (AU) is a common extraintestinal manifestation of inflammatory bowel disease (IBD). This study investigates the shared genetic architecture and pleiotropic loci between AU and IBD.

METHODS: Using large-scale GWAS data from European-ancestry cohorts, we performed LD score regression to assess genetic correlations, two-sample Mendelian randomization for causal inference, and PLACO analysis to identify pleiotropic loci. Multi-trait colocalization integrating 412 gut microbiome features was conducted using HyPrColoc. Functional annotation employed FUMA and ANNOVAR, gene-based analysis used MAGMA, and drug-gene interactions were explored via DrugBank.

RESULTS: AU showed significant genetic correlations with IBD (rg = 0.44, p = 2.0 × 10[-4]), ulcerative colitis (rg = 0.52, p = 6.0 × 10[-4]), and Crohn's disease (rg = 0.24, p = 0.029). Mendelian randomization supported causal effects of genetically predicted IBD and its subtypes on AU risk. We identified 62 pleiotropic risk loci, including 18 with strong colocalization evidence. Functional and pathway analyses revealed enrichment of these loci in immune and inflammatory pathways, mainly the IL-17/IL-23 axis and NOD2 signaling. Multi-trait colocalization further linked a shared AU-IBD risk locus to the gut microbial MEP pathway. Several pleiotropic genes (e.g. JAK2, STAT3) represent potential drug targets.

CONCLUSIONS: AU and IBD share pleiotropic genetic loci involved in immune regulatory pathways and gut microbiome-associated metabolic processes, revealing a potential molecular basis for their comorbidity and highlighting actionable therapeutic targets.},
}

@article {pmid41996413,
year = {2026},
author = {He, X and Yazdy, GM and Yeoman, C and Ghanem, KG and Erchick, DJ and Taylor, A and Griffin, K and Holm, J and Ravel, J and Brotman, RM and Tuddenham, S},
title = {Comparing Asymptomatic vs Symptomatic Bacterial Vaginosis: Clinical Characteristics, Vaginal Microbiota, and Lactic Acid Profiles.},
journal = {Sexually transmitted diseases},
volume = {},
number = {},
pages = {},
doi = {10.1097/OLQ.0000000000002330},
pmid = {41996413},
issn = {1537-4521},
abstract = {BACKGROUND: Irrespective of symptoms, bacterial vaginosis (BV) has been linked to increased risk of sexually transmitted infections (STI) and HIV, yet clinical guidelines recommend treatment only for symptomatic BV (sBV). We compared demographic, clinical, and vaginal microbiota factors between asymptomatic BV (aBV) and sBV.

METHODS: Data from a previously conducted vaginitis cohort study were analyzed. Participants with Amsel-BV were classified as sBV if they reported vaginal symptoms and aBV if asymptomatic. Nugent scores were assigned. Cervicovaginal lavage fluid underwent 16S rRNA gene amplicon sequencing, broad-range qPCR, and lactic acid isomer quantitative assays. Wilcoxon rank-sum, Fisher's exact, and Chi-squared tests compared factors between aBV and sBV. Taxonomic differences were evaluated using elastic net modeling and differential abundance testing.

RESULTS: Among 70 participants with sBV and 270 with aBV, clinician-assessed abnormal discharge was more common in sBV (86%) than aBV (71%). In adjusted analyses, recent use of metronidazole or clindamycin, more sex partners, and education beyond high school were associated with increased odds for sBV, and injectable contraception with aBV. No consistent differences were observed between sBV versus aBV for other Amsel's criteria, Nugent scores, or vaginal microbiota composition. D- and L-lactic acid levels were slightly higher in sBV than aBV.

CONCLUSIONS: Although some demographic, clinical, and behavioral factors differed between sBV and aBV, no consistent differences were found in vaginal microbiota composition; lactic acid isomer levels were low in both groups. Further research is needed to understand why some experience symptoms, to identify whether other biological factors differentiate aBV from sBV, and to evaluate their respective associations with adverse reproductive outcomes.},
}

@article {pmid41996830,
year = {2025},
author = {Kreimeyer, H and Fondevila, MF and Harberts, A and Raya Tonetti, F and Schöler, D and Münte, E and Hartmann, P and Llorente, C and Hube, B and LeibundGut-Landmann, S and Stärkel, P and , and Schnabl, B},
title = {Peptide YY reduces cytotoxicity of Candida albicans in alcohol-associated liver disease.},
journal = {JHEP reports : innovation in hepatology},
volume = {8},
number = {5},
pages = {101718},
doi = {10.1016/j.jhepr.2025.101718},
pmid = {41996830},
issn = {2589-5559},
abstract = {BACKGROUND & AIMS: Transitioning from yeast to hyphal morphology enables Candida albicans (C. albicans) to secrete candidalysin, invade the intestinal mucosa and translocate to the blood stream. Patients with alcohol-associated hepatitis show increased intestinal abundance of C. albicans, and the candidalysin-encoding gene is associated with reduced survival. Paneth cell-derived peptide YY (PC-PYY) inhibits hyphal growth of C. albicans. In this study, we evaluated the potential of different C. albicans strains isolated from patients with alcohol-associated hepatitis to cause systemic infections and explored the therapeutic potential of PC-PYY in ethanol-induced liver disease in mice.

METHODS: C. albicans strains isolated from fecal samples of patients with alcohol-associated hepatitis (n = 105) were co-cultured with intestinal epithelial Caco-2 cells to assess in vitro cytotoxicity. Caco-2 cells and primary mouse hepatocytes were incubated with C. albicans in the presence or absence of PC-PYY. Mice were subjected to a chronic plus binge ethanol-feeding model.

RESULTS: C. albicans strains isolated from stool of patients with alcohol-associated hepatitis induced significant cytotoxicity in Caco-2 cells, and high cytotoxicity was associated with worse 30-day survival (log-rank p = 0.032). This cytotoxicity was primarily mediated by the hyphal form and largely driven by candidalysin. PC-PYY significantly reduced C. albicans-induced cytotoxicity in Caco-2 cells (Wilcoxon rank-sum test, p = 0.015) and in primary mouse hepatocytes (p = 0.03) compared with a scrambled peptide control, by inhibiting hyphal morphogenesis. The peptide YY-to-chromogranin A ratio in intestinal crypts was significantly increased in ethanol-fed mice compared with both isocaloric (p = 0.005) and antifungal-treated controls (p = 0.009), indicating that fungal overgrowth stimulates PC-PYY release. In ethanol-fed mice, PC-PYY administration attenuated liver injury (p = 0.032) and steatosis (p = 0.0498) and reduced fecal hyphae formation (p = 0.0159).

CONCLUSION: PYY inhibits filamentous growth of C. albicans in vitro and alleviates ethanol-induced liver disease in mice, highlighting its potential as a therapy for patients with alcohol-associated liver disease.

IMPACT AND IMPLICATIONS: Candida albicans (C. albicans) and particularly its toxin candidalysin are associated with poor outcomes in patients with alcohol-associated hepatitis but the extent to which the cytotoxicity of individual C. albicans strains influences patient survival, and the role of Paneth cell-derived PYY (PC-PYY) in this context remains elusive. This study identifies a link between the cytotoxic effect of patient-derived C. albicans strains and survival in patients with alcohol-associated hepatitis and demonstrates that PC-PYY plays a protective role in ethanol-induced liver disease by limiting candidalysin-producing hyphae. Our work provides insight into why some patients with alcohol-associated liver disease have worse outcomes and highlights the potential of PC-PYY as a therapy for patients with alcohol-associated liver disease.},
}

@article {pmid41996860,
year = {2026},
author = {Ji, Z and Fu, Z and Miao, L and Hang, D and Gu, A},
title = {Relationship between pesticide exposure, gut microbiota, and hypertension.},
journal = {Environment international},
volume = {211},
number = {},
pages = {110250},
doi = {10.1016/j.envint.2026.110250},
pmid = {41996860},
issn = {1873-6750},
abstract = {BACKGROUND: Both pesticide exposure and gut dysbiosis have been independently linked to an elevated risk of hypertension. However, the extent of interaction between these two factors remains poorly characterized in human populations.

METHODS: In a population-based study involving 218 adults from Jiangsu Province, China, we quantified pesticides in serum using LC-MS/MS and analyzed the gut microbiome via metagenomic sequencing. An environmental risk score (ERS) was created to represent pesticide exposure. We also used Mendelian randomization (MR) to identify causal gut microbial genera, multivariable regression for associations, and mediation analysis for potential pathways. Machine learning models were applied to differentiate hypertensive from non-hypertensive individuals based on a combined set of features.

RESULTS: Fourteen pesticides, notably bentazone and perfluorohexanesulfonate, were significantly associated with increased hypertension risk, and the ERS based on these pesticides further corroborated this association. Additionally, the overall microbiota composition was significantly associated with both pesticide exposure and hypertension status. Observational and MR analyses consistently identified branches of Clostridium as potentially contributors to hypertension risk. An interaction was observed between pesticide exposure and specific bacterial taxa. Specifically, high ERS combined with high Catenibacterium (both defined using a median split) abundance increased hypertension risk nearly fourfold. A neural network model achieved the best differentiation performance (AUC = 0.897) for hypertension.

CONCLUSIONS: Exposure to specific pesticides, particularly bentazone, is associated with increased hypertension risk. This relationship is influenced by interactions with gut bacteria and partially mediated through alterations in the gut microbiota. These findings highlight the role of environmental chemicals and the gut microbiome in the development of hypertension.},
}

@article {pmid41997122,
year = {2026},
author = {Davar, D and Zarour, HM and Trinchieri, G},
title = {Improving immunotherapy in solid tumors using FMT.},
journal = {Cell},
volume = {189},
number = {8},
pages = {2214-2217},
doi = {10.1016/j.cell.2026.03.021},
pmid = {41997122},
issn = {1097-4172},
mesh = {Humans ; *Immunotherapy/methods ; *Fecal Microbiota Transplantation/methods ; *Neoplasms/therapy/immunology/microbiology ; Immune Checkpoint Inhibitors/therapeutic use ; Melanoma/therapy ; Animals ; Carcinoma, Non-Small-Cell Lung/therapy ; Clinical Trials as Topic ; },
abstract = {Recent clinical trials demonstrate that fecal microbiota transplantation (FMT) enhances first-line immune checkpoint inhibitor efficacy in renal cell carcinoma, cutaneous melanoma, and non-small cell lung cancer with acceptable safety. Benefit appears mediated by functional microbiome remodeling, depletion of deleterious taxa, and systemic immunometabolic modulation, supporting microbiome-directed therapeutic strategies for cancer immunotherapy.},
}

Humans
*Immunotherapy/methods
*Fecal Microbiota Transplantation/methods
*Neoplasms/therapy/immunology/microbiology
Immune Checkpoint Inhibitors/therapeutic use
Melanoma/therapy
Animals
Carcinoma, Non-Small-Cell Lung/therapy
Clinical Trials as Topic

@article {pmid41997160,
year = {2026},
author = {Yu, L and Peng, S and Chen, X and Wu, T and Dong, L and Luo, J and Xu, S and Zhou, J and Zhao, X and Zheng, L and Shu, G and Wang, X and Huang, L and Chen, Q and Jiang, D and Sun, LD and Hylemon, P and Wang, XY and Sun, L and Ma, L and Zuo, D},
title = {Intestinal dysbiosis exacerbates skin inflammation via microbial metabolite-driven Th2 cell differentiation.},
journal = {Immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.immuni.2026.03.019},
pmid = {41997160},
issn = {1097-4180},
abstract = {The interplay between gut microbiota and the mucosal immune system critically regulates systemic immunity and disease susceptibility. Here, we demonstrate that intestinal epithelial Toll-like receptor (TLR)4 deficiency reshaped the gut microbiome and subsequently exacerbated atopic dermatitis (AD) in mice. Mechanistically, TLR4 deficiency reduced Akkermansia muciniphila abundance and enriched choline trimethylamine-lyase (CutC)-expressing bacteria. This enhanced microbial choline-to-trimethylamine conversion and elevated circulating trimethylamine oxide (TMAO) levels. Clinically, AD patients exhibited increased plasma TMAO levels that positively correlated with disease severity and immunoglobulin E (IgE) levels. UK Biobank data also showed that higher dietary choline intake was associated with increased AD risk. TMAO promoted T helper (Th)2 differentiation by directly interacting with protein phosphatase 5 (PPP5) and enhancing PPP5-mediated dephosphorylation of PPARγ. CD4[+] T cell-specific PPARγ deletion abolished TMAO-driven skin pathology in AD mice. Our results reveal intestinal dysbiosis, as a result of innate immune deficiency, as a driver of inflammatory Th2 cells and AD pathology, highlighting a link among the gut immune environment, microbial metabolites, and skin disease.},
}

@article {pmid41997445,
year = {2026},
author = {Yu, J and Guo, C and Liu, Y and Ren, X and Guo, Y and Ran, B and Xiao, L and Kong, L and Gu, X and Jiang, C and Wu, J},
title = {The commensal microbiome in respiratory tract tumors: From oncogenic mechanisms to clinical translation.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.04.044},
pmid = {41997445},
issn = {2090-1224},
abstract = {BACKGROUND: The human commensal microbiome, commonly recognized as a "second genome", exerts a crucial regulatory role in host metabolism, immune homeostasis maintenance, and the progression of various diseases. Respiratory tract tumors remain a leading cause of global cancer-related deaths due to their high invasiveness and late-stage diagnosis. With the rapid development of high-throughput sequencing technology, the complex associations between microbial communities and respiratory tract tumors have been gradually uncovered. In lung cancer, distinct microbiota-related signatures, including tissue-specific and microbiota-derived ones have been identified, showing variations across cancer subtypes, anatomical sample sources, and patient demographics. These findings collectively lay the foundation for in-depth investigations into the interplay between the microbiome and respiratory tract tumors.

AIM OF REVIEW: This review aims to systematically synthesize the current understanding of the commensal microbiome across respiratory tract tumors, primarily taking lung cancer as the main example, with systematic extensions to other respiratory tract malignancies, including laryngeal carcinoma and nasopharyngeal carcinoma, focusing on clarifying the ecological characteristics of microorganisms, elucidating the mechanistic links between the microbiome and tumorigenesis as well as progression, and summarizing the translational value of the microbiome in clinical practice, including applications in diagnostics, therapeutics, and prognostic evaluation.

Emerging evidence highlights that the microbiome contributes to the initiation of respiratory tract tumors through multiple pathways: dysbiosis-induced chronic inflammation, immune system dysregulation, and metabolite-mediated epigenetic or functional alterations. Beyond tumorigenesis, the microbiome also plays a vital role in modulating the efficacy of cancer treatments, particularly conventional therapies and immunotherapies. Additionally, the microbiome provides novel opportunities for the development of diagnostic biomarkers and microbiome-targeted intervention strategies. Its prognostic potential in predicting recurrence, metastasis, and survival is increasingly recognized. These core scientific concepts collectively constitute the theoretical framework for exploring the microbiome's role in respiratory tract tumor research and clinical translation.},
}

@article {pmid41997470,
year = {2026},
author = {Saravanan, A and Bai, J and Bajaj, P and Khemmani, M and Rodriguez, A and Choudhury, S and Wolfe, AJ and Young, EE},
title = {Evidence for a shift towards a proinflammatory/pronociceptive signature of gut dysbiosis in patients with axial chronic low back pain: A preliminary cross-sectional analysis.},
journal = {The journal of pain},
volume = {44},
number = {},
pages = {106271},
doi = {10.1016/j.jpain.2026.106271},
pmid = {41997470},
issn = {1528-8447},
abstract = {Nonspecific or axial-chronic low back pain is not attributed to specific pathology yet accounts for 80%- 90% of all chronic low back pain cases and is a major cause of disability affecting one in four adults with treatment costs and lost wages totaling $100-200 billion. Despite its prevalence, there is a knowledge gap around the underlying mechanisms driving susceptibility to this type of chronic pain. Gut microbial colonization plays a role in shaping host physiology directly through interactions with host tissues and indirectly through the production of metabolites, but the role of the microbiome in the etiology of axial-low back pain is unclear. Using a cross-sectional design, in this preliminary study, patients with axial-chronic low back pain and healthy controls completed the NIH minimal dataset for chronic low back pain from the PROMIS short form followed by collection of rectal swabs and 16S rRNA sequencing and determination of microbiome composition differences between controls and patients. Our findings suggest a distinct pattern of altered colonization in axial-chronic low back pain, characterized by a specific pattern of increased formate- and succinate- producing bacterial abundance along with reduced abundance of key taxa associated with butyrate, propionate, and acetate production. A review of the literature available on metabolite production from differentially abundant bacteria suggests a proinflammatory/ pronociceptive shift in microbial colonization. These preliminary findings identify a gut dysbiosis pattern that may contribute to chronic low back pain through pro-inflammatory and pronociceptive mechanisms; however, larger, longitudinal, and metabolically profiled studies are needed to confirm causality. PERSPECTIVE: Chronic low back pain is associated with gut dysbiosis characterized by reduced abundance of butyrate and/or propionate producing bacteria combined with increased succinate- and formate-producing bacterial colonization. These data suggest a proinflammatory/pronociceptive microbial signature that may contribute to development and/or maintenance of chronic low back pain.},
}

@article {pmid41997773,
year = {2026},
author = {Han, VC and Bennett, SJ},
title = {When soils learn to suppress nematodes.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.04.002},
pmid = {41997773},
issn = {1878-4380},
abstract = {An evaluation of banana plantations, sown between 1 and 10 years ago, suggested that over time soils can become suppressive to root-knot nematodes. Lu et al. linked this transition to shifts in rhizosphere microbiomes, enrichment of free-living nematodes, and the emergence of a keystone Bacillus taxon, highlighting cross-kingdom interactions.},
}

@article {pmid41997906,
year = {2026},
author = {Tao, R and Liu, S and Crawford, J and Kramer, P and Bender, S and Tao, F},
title = {Single-cell multi-omics sequencing reveals cell-specific transcriptomic and chromatin accessibility profiles in gut microbiome metabolite butyrate-produced pain modulation.},
journal = {International journal of oral science},
volume = {18},
number = {1},
pages = {},
pmid = {41997906},
issn = {2049-3169},
support = {R01DE031255//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; R01DE032061//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; R03DE031822//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; },
mesh = {*Gastrointestinal Microbiome ; Animals ; *Chromatin/metabolism/genetics ; *Butyrates/metabolism/pharmacology ; *Transcriptome ; Single-Cell Analysis ; Male ; Mice ; Acetylation ; Multiomics ; Triglycerides ; },
abstract = {Pain is the most common symptom of temporomandibular joint (TMJ) disorders, which present significant clinical challenges due to their complexity and limited treatment options. Our previous study demonstrates that gut microbiome-derived butyrate is critical for the modulation of TMJ pain. In this study, we investigated its underlying mechanisms, and we found that oral administration of tributyrin, a prodrug of butyrate, not only significantly alleviated TMJ pain but also reversed the reduction in histone acetylation in the spinal trigeminal nucleus caudalis (Sp5C) under the TMJ pain condition. Using single-cell multi-omics sequencing, we profiled gene expression and chromatin accessibility in the Sp5C cells at the single-cell resolution. Bioinformatics analysis revealed that TMJ pain disrupted both the expression and chromatin accessibility of Nop14, Matk, Idh3b, Ndst2, and Tomm6 across four cell types in the Sp5C, and these alterations were reversed by tributyrin treatment. Specifically, Nop14 exhibited increased chromatin accessibility at its promoter region under TMJ pain condition, and knockdown of Nop14 in the Sp5C restored histone acetylation and alleviated TMJ pain. Together, our findings reveal cell-type-specific gene regulation that underlies butyrate-mediated epigenetic regulation of TMJ pain, which suggesting that targeting gut microbiome metabolites could develop a non-opioid novel therapy for TMJ disorders.},
}

*Gastrointestinal Microbiome
Animals
*Chromatin/metabolism/genetics
*Butyrates/metabolism/pharmacology
*Transcriptome
Single-Cell Analysis
Male
Mice
Acetylation
Multiomics
Triglycerides

@article {pmid41997944,
year = {2026},
author = {Wu, Y and Alomeir, N and Falsetta, M and Yang, R and Sun, E and Israel, AK and Fiscella, J and Wu, T and Liu, Y and Li, T and Wood, R and Kenney, M and Meng, G and Terando, S and Terio, C and Fiscella, K and Xiao, J},
title = {Cariogenic microorganisms induce oral epithelial atypia through host-microbiome-high sugar diet interactions.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00987-9},
pmid = {41997944},
issn = {2055-5008},
abstract = {Oral mucosal development during infancy is crucial because disruptions at this stage can compromise barrier function and increase susceptibility to oral diseases throughout life. The contribution of oral pathogens to oral mucosal development in infancy remains poorly understood. Here, we show that early-life co-infection with Streptococcus mutans and Candida albicans under a sucrose-enriched diet perturbs oral epithelial homeostasis and is associated with atypical hyperplasia and parakeratosis of the tongue. Using an infant rat model, we utilized OMICS data (microbiome, untargeted metabolomics, and multiplex immune profiling) together with high-dimensional mediation statistic modeling to reveal that microbial co-infection synergizes with dietary sugar to shape oral and gut microbial communities. The microbial alterations were accompanied by systemic metabolic alterations, marked by enhanced amino acid and carbohydrate metabolism, and depletion of vitamin B6 and taurine pathways. Oral microbial and metabolic changes were associated with atypical hyperplasia and parakeratosis on both dorsal and ventral surfaces of tongue mucosa. Complementary in vitro modeling revealed that sucrose-conditioned co-infection disrupted epithelial barrier integrity and orchestrated metabolic remodeling in oral epithelial cells. These findings reveal a host-microbe-diet interaction axis underlying early mucosal remodeling and provide mechanistic insight into how cariogenic microbes may influence oral mucosal disease beyond caries.},
}

@article {pmid41997961,
year = {2026},
author = {Zhao, JJ and Hu, M and Li, S and Wang, Q and Mo, Q and Yu, H},
title = {Oral microbiome signatures predict biological age and host health.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-72096-2},
pmid = {41997961},
issn = {2041-1723},
abstract = {Identifying robust, non-invasive biomarkers of biological age is key to preventive medicine. While gut aging clocks exist, the oral microbiome remains underexplored as a quantitative biomarker. Using oral microbiome data from two NHANES cohorts (N = 4,675), we identified 64 age-dependent bacterial genera and developed a machine learning model predicting chronological age, with generalizability in an independent external cohort (N = 1,293). We derived an Oral Microbiome Aging Acceleration (OMAA) Score as the residual of predicted age against chronological age. The OMAA Score independently predicted all-cause mortality (HR = 1.05, P = 0.024) and frailty (OR = 1.05, P = 0.008), correlated with impaired kidney function (lower eGFR: β = -0.066, P = 5.22×10[-4]), and enhanced risk prediction for cancer (AUC 0.70 vs. 0.67, P = 0.009) and heart attack (AUC 0.79 vs. 0.76, P = 0.016) beyond conventional risk factors. Diet and medication had minimal association. The OMAA Score offers a scalable, non-invasive tool to identify high-risk individuals for age-related morbidity and mortality.},
}

@article {pmid41997995,
year = {2026},
author = {Zhong, P and Ren, A and Cui, J and Guo, C and Zhang, Y and Diao, Q and Liu, X and Zhang, N and Tu, Y and Bi, Y},
title = {Microbial landscapes in dairy cow diseases: from localized dysbiosis to inter-organ axes.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00988-8},
pmid = {41997995},
issn = {2055-5008},
support = {32222081//National Natural Science Foundation of China/ ; },
abstract = {Dairy cow health involves host-microbiome interactions. This review characterized microbial landscapes across anatomical sites in dairy cows-including the gastrointestinal tract, respiratory system, reproductive tract, mammary gland, and skin-and examines their associations with diseases. We elucidated how site-specific dysbiosis drives systemic conditions such as mastitis and ketosis through inter-organ axes. Finally, we evaluated emerging microbiome-based modulation strategies and their application prospects in dairy farming.},
}

@article {pmid41998050,
year = {2026},
author = {Gao, Y and Kim, J and Wu, R and Chowdhury, NB and Lee, JY and Nicora, CD and Moore, RJ and Monroe, ME and Jansson, JK and Burnum-Johnson, KE},
title = {Metaproteomics uncovers the functional capacity of a soil microbiome.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-47816-9},
pmid = {41998050},
issn = {2045-2322},
support = {Early Career Research Program//U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research/ ; },
}

@article {pmid41998161,
year = {2026},
author = {Ji, S and Liu, Y and Xu, Y and Gao, J and Jin, J and Jiang, P and Li, Y and Su, D and Zhao, Y and Yang, S and Zhang, S and Shi, W and Zhou, Q and Zhang, M},
title = {Faecalibacterium prausnitzii enzyme reprograms PD-L1 trafficking and sensitizes colorectal cancer to immunotherapy in mice.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41998161},
issn = {2058-5276},
support = {82322010//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Microbiome-host interactions can influence colorectal cancer (CRC) outcomes and the effectiveness of immunotherapy treatment, but the precise mechanisms underlying this are poorly understood. Here we analyse CRC patient cohort data and observe that Facalibacterium prausnitzii abundance in faecal samples correlates with improved CRC survival outcome and immunotherapy response. In vitro assays and experiments in azoxymethane plus dextran sulfate sodium (AOM/DSS) and Apc[min/+] mouse CRC models show that F. prausnitzii extracts have anti-tumour activity. Mass spectrometry identifies F. prausnitzii phosphoribosyl pyrophosphate synthetase (fpPRPS) as a bacterial enzyme that inhibits tumour development and promotes CD8[+] T-cell responses. Mechanistically, fpPRPS depletes ATP levels in CRC cells, which then inhibits GTP-GDP exchange on Rab11a, reprogramming CRC energy metabolism. This leads to Rab11a degradation and the disruption of PD-L1 trafficking to reduce the inhibition of T-cell responses. fpPRPS inhibition of tumour progression is PD-L1-dependent. We also show that fpPRPS and anti-PD-1 treatment synergize to promote CD8[+] T-cell responses and tumour control in mice. These findings suggest fpPRPS as a potential strategy for sensitizing CRC to immunotherapy.},
}

@article {pmid41998285,
year = {2026},
author = {Mannino, P and Park, M and Wang, MC},
title = {Organellar insights in ageing and longevity.},
journal = {Nature cell biology},
volume = {},
number = {},
pages = {},
pmid = {41998285},
issn = {1476-4679},
abstract = {Metabolic processes shape ageing and longevity at multiple levels. Emerging evidence shows that many of these processes are orchestrated within and between cellular organelles. Organelles function not only as metabolic reactors but also as signalling hubs, and their coordination plays crucial roles in maintaining cellular homeostasis and promoting organismal fitness. Rather than acting in isolation, organelles engage in dynamic crosstalk through membrane contact sites, metabolite exchange and signalling interplay. In recent years, organelles have been increasingly recognized as critical regulators of ageing and longevity. Here we summarize age-related organellar changes, highlight organelle-mediated intra- and intercellular signalling communication in lifespan and healthspan regulation, and discuss the active roles of organelles in microbiome-host interactions and transgenerational inheritance in regulating longevity. We further outline how longevity-promoting interventions influence organelles, and provide perspectives on how future technological advances may further accelerate progress in this emerging research topic.},
}

@article {pmid41998361,
year = {2026},
author = {Thiyagarasaiyar, K and Paul, D and Kerttula, J and Keski-Karhu, M and Soosaar, K and Mander, Ü 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},
}