@article {pmid42771999,
year = {2026},
author = {Fang, Y and Ma, W and Liu, WT and Ye, L},
title = {Artificial intelligence-enhanced machine learning model improves microbial community analysis of anaerobic digestion systems.},
journal = {Water research},
volume = {308},
number = {Pt B},
pages = {126978},
doi = {10.1016/j.watres.2026.126978},
pmid = {42771999},
issn = {1879-2448},
abstract = {An integrative framework combining a large language model (LLM) with sequence-based machine learning was developed and applied to 16S rRNA gene-based microbial analyses in anaerobic digestion (AD) systems that constantly receive wasted biomass from upstream activated sludge (AS) processes. Using ChatGPT API, all genus-level microbes in the MiDAS 16S rRNA gene database for wastewater microbiome were annotated according to their environmental preferences (aerobic, anaerobic, or facultative) and categorized into four groups: AS-specific, AD-specific, both AS and AD, and unsure. The results were subsequently paired with full-length 16S rRNA gene sequences for training a random forest classifier based on DNA k-mer frequency patterns. The resulting model demonstrated strong predictive performance across multiple sequence types, achieving 98.76% accuracy on full-length taxonomically classified sequences, 78.87% accuracy on full-length taxonomically unclassified sequences, and over 94% accuracy on partial amplicon sequences. When applied to datasets from previous laboratory-scale and full-scale AD studies, the model successfully identified AS-specific sequences from AD samples, substantially reducing biological noise and revealing clearer beta-diversity clustering. Overall, this study establishes a scalable LLM-enhanced machine learning framework for microbial functional inference directly from 16S rRNA gene sequences, with broad potential applicability to microbial community analyses in a wide range of biological processes.},
}

@article {pmid42772031,
year = {2026},
author = {Chen, L and Bian, C and Zhu, Y and Liu, Q and Li, X and Xie, A and Fang, R and Hu, X and Gele, S and Zhang, L and Liu, G and Su, X and Gao, G},
title = {Gut microbiota, metabolome and hormone profiles associate with pregnancy-related biomarkers in sheep with frozen embryo transfer.},
journal = {Theriogenology},
volume = {267},
number = {},
pages = {118197},
doi = {10.1016/j.theriogenology.2026.118197},
pmid = {42772031},
issn = {1879-3231},
abstract = {Recipients' gut microbiota and serum metabolites are linked to pregnancy outcomes in frozen embryo transfer (FET), but the underlying integrative mechanisms remain unclear. Here we compared the gut microbiome, serum metabolome, and reproductive hormones between pregnant (P group) and non-pregnant (N group) Small-Tailed Han ewes at three time points: prior to oestrus detection (1st), prior to embryo transfer (2nd), and prior to pregnancy diagnosis (3rd). Of 55 recipients, 24 became pregnant (43.6%). Beta-diversity of the gut microbiota partially separated P from N at 1st (R[2] = 0.0597, P = 0.159), 2nd (R[2] = 0.0330, P = 0.293), and 3rd (R[2] = 0.0062, P = 0.405). On the day of oestrus detection, Prevotellaceae UCG-001 was more abundant in the P group than in the N group (P < 0.05). On the day of embryo transfer, the opportunistic pathogen Escherichia-Shigella was enriched in the N group (P < 0.05). On the day of pregnancy diagnosis, the probiotic Lactobacillus was higher in the P group. Untargeted metabolomics identified 24, 24, and 33 stage-specific differential metabolites. Glycerophospholipid metabolism was consistently enriched across all stages. Notably, oleoyltaurine was a differential metabolite at both 2nd and 3rd (FC = 2.11 and 3.60, respectively; both P < 0.05). At oestrus, serum luteinizing hormone (LH) and prostaglandin E2 (PGE2) were significantly higher in the P group than in the N group (P < 0.05 for both). On the day of embryo transfer, cortisol and prostaglandin F2α (PGF2α) were markedly elevated in the N group (P < 0.01 for both). Microbiota-metabolite integration revealed that oleoyltaurine correlated negatively with Escherichia-Shigella (r = -0.51, P < 0.05) and positively with Lactobacillus (r = 0.64, P < 0.05). Adequate LH/PGE2 priming at oestrus was associated with a receptive peri-transfer period in ovine FET. This endocrine profile aligns with a distinct gut microbial succession and a systemic metabolomic signature, with oleoyltaurine emerging as a candidate metabolite putatively linking gut microbial shifts with systemic metabolic changes. These findings offer a basis for developing multi-target candidate biomarkers to improve recipient selection in sheep FET.},
}

@article {pmid42772141,
year = {2026},
author = {Poudel, S and Zelaya, FAC and Guzman, EGG and Rahman, FA and Naeem, M and Adhikari, Y and Manjankattil, S and Pacheco, W and Hauck, R and Bourassa, D and Macklin, K},
title = {Machine learning identifies key microbial signatures for Salmonella enteritidis colonization and persistence in broiler ceca.},
journal = {Poultry science},
volume = {105},
number = {12},
pages = {107753},
doi = {10.1016/j.psj.2026.107753},
pmid = {42772141},
issn = {1525-3171},
abstract = {Non-typhoidal Salmonella is a leading cause for bacterial foodborne illnesses in humans, and contaminated poultry products are considered a major source of transmission. Therefore, reducing Salmonella contamination in poultry products is needed to reduce human salmonellosis. This study examined the effects of organic acid (OA) supplementation and Salmonella persistence/cleared in cecal microbiome of Ross YP × Ross 708 male broilers. A total of 900 1-day-old male broilers were randomly distributed to three treatments Control (CN), acetic, lactic and propionic acid blend (ALP), and citric acid (CA); 12 replicate pens/treatment and 25 birds/pen. All birds were challenged with 10[6] Cfu of Salmonella Enteritidis at d 7. Birds other than in control received continuous supplementation of OA via drinking water. Cecal samples (n = 12/treatment) were collected on d 41; genomic DNA was extracted; and full-length 16S rRNA was sequenced using MinIon (Oxford Nanopore). Organic acid supplementation did not significantly affect alpha and beta diversity indexes, indicating no major changes in overall microbial diversity and community structure. Birds were categorized into Salmonella persistence or clearance groups based on detection of genus Salmonella in 16S rRNA sequence results. Salmonella detection status (persistence vs clearance) did not significantly alter diversity metrics. However, shared and unique bacterial analysis revealed that control birds harbored more unique bacterial species than organic-acid supplemented and Salmonella-clearance birds harbored higher unique bacterial species than Salmonella-persistence birds. These findings suggest that, despite stable diversity indices, compositional shifts occurred in response to organic acid supplementation as well as presence of Salmonella. Using random forest-based machine learning approach, Escherichia coli, Shigella dysenteriae, and Shigella flexneri were identified to be positively correlated to Salmonella, while Romboutsia timonensis was negatively correlated with Salmonella-presence. In conclusion, this study identifies bacterial species associated with persistence or clearance of Salmonella and identifies a promising candidate that could potentially competitive exclude Salmonella colonization and proliferation in ceca.},
}

@article {pmid42772256,
year = {2026},
author = {Perea, J and Spinelli, A},
title = {Molecular surgery in colorectal cancer: Integrating genomics into operative decision-making.},
journal = {European journal of surgical oncology : the journal of the European Society of Surgical Oncology and the British Association of Surgical Oncology},
volume = {52},
number = {12},
pages = {112130},
doi = {10.1016/j.ejso.2026.112130},
pmid = {42772256},
issn = {1532-2157},
abstract = {Colorectal cancer (CRC) surgery has traditionally been planned on the basis of anatomy and histopathology, with relatively standardised procedures applied across biologically heterogeneous disease. In contrast, systemic treatment has progressively incorporated molecular stratification into routine practice, including mismatch repair deficiency, microsatellite instability, germline susceptibility, and circulating tumour DNA (ctDNA). This divergence has created a growing disconnect between operative and systemic oncology, whereby surgical indications, timing, extent of resection, and postoperative surveillance remain largely anatomy-based despite major advances in tumour biology. In this Review, we propose the concept of molecular surgery in CRC, defined as the integration of genomic, germline, immunologic, and liquid-biopsy-derived information into surgical decision-making. We present a practical framework structured around four key domains: indication, timing, extent, and surveillance/reintervention. Within this framework, we discuss organ preservation and the transition from clinical to molecular complete response in rectal cancer, genotype-guided extent of surgery in hereditary CRC syndromes such as Lynch syndrome and familial adenomatous polyposis, the impact of neoadjuvant immunotherapy on surgical sequencing in dMMR/MSI-high disease, and the role of ctDNA-defined molecular residual disease in postoperative management. We also examine emerging tools, including multi-omic profiling, microbiome research, and artificial intelligence, as enabling technologies for future biology-informed surgical care. Finally, we address the educational, infrastructural, and ethical challenges of implementing molecular surgery in routine practice. CRC provides a timely model in which surgery is increasingly shaped not only by anatomical resectability, but also by tumour biology and treatment response. We argue that molecular data should be considered more systematically when defining surgical strategy in contemporary CRC care.},
}

@article {pmid42772323,
year = {2026},
author = {Li, SS and Niu, YH and Yu, HJ},
title = {A retrospective metagenomic analysis of fecal microbiota transplantation donors from five countries: Safety considerations for donor screening and core microbiome profiles of qualified donors.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {64},
number = {9},
pages = {e2604010},
doi = {10.71150/jm.2604010},
pmid = {42772323},
issn = {1976-3794},
support = {//Shanghai Engineering Research Center of Innovative Probiotic Drugs/ ; },
mesh = {Humans ; Retrospective Studies ; *Fecal Microbiota Transplantation/adverse effects ; *Metagenomics ; *Feces/microbiology ; *Bacteria/genetics/classification/isolation & purification ; Canada ; New Zealand ; Netherlands ; China ; United States ; *Tissue Donors ; *Donor Selection ; Virulence Factors/genetics ; *Metagenome ; *Gastrointestinal Microbiome/genetics ; *Microbiota/genetics ; },
abstract = {Fecal microbiota transplantation (FMT) has been successfully applied on clinical aspects, but its clinical outcomes remain unpredictable due to inconsistent donor screening protocols across hospitals, institutions, and countries. Hence, a retrospective analysis of metagenomic data from published studies on FMT donors via a unified bioinformatics workflow might contribute to the understanding of the safety considerations for donor screening and the fecal microbial profiles of qualified donors. In this study, we reanalyzed metagenomic data of 475 screened donor fecal samples from 24 studies spanning China, the USA, Canada, New Zealand, and the Netherlands. The genomic safety risks were evaluated by profiling antibiotic resistance genes (ARGs) and virulence factors (VFs), the results of which showed that no major toxin-associated virulence genes, such as Shiga toxin, Shiga-like toxin, or botulinum neurotoxin (BoNTs) genes harbored in the detected Escherichia coli, Clostridium butyricum, and Streptococcus pneumoniae, but several high-risk ARGs remained insufficiently addressed. The distribution of ARG-harboring bacteria in eligible FMT donors was country-specific. The alpha-diversity and microbial community structure were comparable between donor fecal samples from China and the USA. Interestingly, the core microbiome in fecal samples from Canada, the Netherlands, and New Zealand formed a single guild, while that from China and the USA formed two guilds, with predominantly positive intra-guild and negative inter-guild correlations, indicating that the co-abundance patterns of the core microbiome were conserved among certain countries. Furthermore, an exploratory retrospective classifier was developed based on core microbiome profiles to distinguish eligible FMT donors from general healthy individuals. These results provide evidence for integrating metagenomic sequencing into future FMT donor screening strategies.},
}

Humans
Retrospective Studies
*Fecal Microbiota Transplantation/adverse effects
*Metagenomics
*Feces/microbiology
*Bacteria/genetics/classification/isolation & purification
Canada
New Zealand
Netherlands
China
United States
*Tissue Donors
*Donor Selection
Virulence Factors/genetics
*Metagenome
*Gastrointestinal Microbiome/genetics
*Microbiota/genetics

@article {pmid42772353,
year = {2026},
author = {Yu, M and Hou, D and Wang, Z and Cui, Y and Wang, Y and Lou, Y and Han, G and Zhang, X and Gregorini, P},
title = {Precipitation gradients restructure rhizosphere and bulk soil microbial communities and potential nitrogen-cycling gene profiles in a desert steppe.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125706},
doi = {10.1016/j.envres.2026.125706},
pmid = {42772353},
issn = {1096-0953},
abstract = {Precipitation change can restructure microbially mediated soil nitrogen (N) cycling in water-limited grasslands, yet whether rhizosphere and bulk soils respond differently remains unclear. An in situ precipitation-gradient experiment in the desert steppe of Inner Mongolia combined soil physicochemical measurements, shotgun metagenomic sequencing, and piecewise structural equation modelling. Treatments included 50% reduced precipitation (W-50%), ambient precipitation (CK), 50% increased precipitation (W+50%), and 100% increased precipitation (W+100%). Soil water content was 37.2% higher under W+100% than under W-50%, whereas NO3[-]-N was 55.5% lower under W+50% than under W-50%. Microbial α-diversity showed a significant treatment × soil compartment interaction, whereas N-cycling functional α-diversity did not differ significantly among precipitation treatments or soil compartments. Precipitation treatment explained 48.35% of microbial community variation and 38.41% of N-cycling gene variation, while soil compartment explained 8.88% and 11.16%, respectively. From W-50% to W+50%, Sphingomonas increased from 2.93% to 13.66% in bulk soil and from 5.14% to 16.87% in rhizosphere soil. Relative to CK, W-50% increased the relative abundances of narZ and norB by 152.5% and 46.6% but decreased those of nrfC and gltD by 27.2% and 7.9%. W+50% increased the relative abundance of ureC by 23.1% while decreasing those of amoB, nirD, and nirK by 56.9%, 31.3%, and 17.8%, respectively. Compared with bulk soil, rhizosphere soil had higher relative abundances of nrfA, ureB, gltB, and nifD. Piecewise SEM explained 86.8% of the variation in N-cycling functional profiles, with microbial community composition showing the strongest association (β = 0.710, P < 0.001). These findings show that precipitation gradients primarily reorganize microbial community composition and potential N-cycling functions, with distinct N-cycling gene profiles between rhizosphere and bulk soils.},
}

@article {pmid42772392,
year = {2026},
author = {Kumar, N and Lakshmi, S and Sebastian, A and Westphal, A and Schroers, VJ and Adamek, M and Elumalai, P},
title = {Evaluation of the efficacy of lectin-adjuvanted Bivalent oral vaccine against Aeromonas veronii and Streptococcus iniae in Nile tilapia (Oreochromis niloticus).},
journal = {Fish & shellfish immunology},
volume = {},
number = {},
pages = {111735},
doi = {10.1016/j.fsi.2026.111735},
pmid = {42772392},
issn = {1095-9947},
abstract = {Aeromonas veronii and Streptococcus iniae are emerging pathogens that cause co-infections and have been a significant threat to the productivity of Nile tilapia, causing high mortality. Vaccination is a promising strategy to prevent bacterial infectious diseases. Coinfection with these bacterial pathogens is widespread in Nile tilapia culture, highlighting the need to develop a bivalent vaccine. This study explores an innovative oral bivalent vaccination approach using a lectin (Concanavalin A from Canavalia ensiformis) adjuvant to combat A. veronii and S. iniae in Nile tilapia (Oreochromis niloticus). The vaccinated group fed with lectin-adjuvanted bivalent oral vaccine exhibited significantly higher levels of lysozyme, myeloperoxidase, and superoxide dismutase compared to the control group (p < 0.05). Furthermore, increased levels of specific antibody (IgM) in the vaccinated group, with notable differences between the prime and booster vaccinations against both antigens. Upregulation of the adaptive immune genes on the 56 days post vaccination (Dpv) in the spleen was observed, and the vaccinated group fed with the lectin-adjuvanted bivalent oral vaccine demonstrated high survival rates, with relative percent survival of 66.6% against A. veronii and 62.1% against S. iniae at 76 DPV. Furthermore, gut microbiome analysis of post-vaccinated and post-challenged fish revealed improved gut health in the vaccinated group, underscoring the protective and immunomodulatory potential of the vaccine. These findings highlight the potential of a lectin-based oral bivalent vaccine system as a novel and effective approach for aquaculture. This strategy could also be adapted for the development of vaccine against bacterial infections and therapeutics in aquatic species.},
}

@article {pmid42772429,
year = {2026},
author = {Siddiqua, KS and Farooqui, SA and Zhang, Y and Wang, L and Zhang, G and Jiang, F and Wen, T},
title = {Nanoparticle Pharmacomicrobiomics: Reprogramming the Microbiome-Immune Axis for Cancer Immunotherapy.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {108481},
doi = {10.1016/j.phrs.2026.108481},
pmid = {42772429},
issn = {1096-1186},
abstract = {The composition and functional activity of the gut microbiome are important host-associated factors that influence the efficacy and responsiveness of cancer immunotherapy. Traditional microbiome modulation methods lack precision, consistency, and extensive clinical applicability. Engineered nanoparticles (NPs) represent an emerging platform for investigating more controllable approaches to microbiome-associated therapeutic modulation. NPs possess physicochemical characteristics that can influence the gut microbial ecosystem. This review introduces the concept of "nanoparticle pharmacomicrobiomics" as an emerging framework that links NP design to defined microbial shifts and their potential pharmacological and immunological consequences. Through integrated literature synthesis, bibliometric co-occurrence analysis, clinical trial synthesis, and mechanistic interpretation, we develop a conceptual framework that describes potential relationships among NP properties, microbial ecology, metabolite signalling, immune modulation, and cancer immunotherapy. We emphasize the integration of nanomaterials, microbiome science, and immunology as an emerging interdisciplinary direction in oncology. This framework provides a conceptual basis that may facilitate the development of future strategies that integrate nanotechnology with microbiome and immune modulation to improve precision cancer immunotherapy.},
}

@article {pmid42772460,
year = {2026},
author = {Upadhyay, SK},
title = {Rhizosphere engineering 2.0: Predictive microbiome design for climate-resilient agriculture, sustainable food production, and global food security.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {373},
number = {},
pages = {113469},
doi = {10.1016/j.plantsci.2026.113469},
pmid = {42772460},
issn = {1873-2259},
abstract = {The rhizosphere is a dynamic interface among plant roots, soil, and microbiota, where the resident microbial community shapes plant health, ecosystem resistance and resilience, nutrient cycling, and sustainable crop production. Yet the limited efficacy of conventional microbial inoculants under field conditions - reflecting poor persistence of introduced microorganisms, incomplete mechanistic understanding of plant-microbiome signalling, and high context-dependence across soils and climates - has created a need for predictive, rather than empirical, microbiome engineering. To close this gap, we introduce Rhizosphere Engineering 2.0 (RE 2.0), defined here as a predictive, systems-level framework that integrates systems biology, multi-omics, ecological network analysis, synthetic biology, artificial intelligence (AI), and precision agriculture to forecast and design microbiome composition and function before field deployment, rather than selecting inoculants by trial and error. We review the biological underpinnings of RE 2.0 - the plant-soil-microbiome holobiont, root-exudate-driven microbiome assembly, interkingdom communication, and ecological network organisation - that govern nutrient uptake, disease resistance, carbon sequestration and ecosystem stability. We then evaluate the engineering strategies that operationalise this framework, including synthetic microbial communities (SynComs), root exudate engineering, biochar-assisted microbiome engineering, regenerative soil management, CRISPR-based microbiome editing, and AI- and digital-twin-guided microbiome prediction, for improving nutrient-use efficiency, crop productivity, climate resilience and soil restoration. Key translational challenges are critically examined, including ecological complexity, poor field persistence of introduced microorganisms, incomplete mechanistic understanding, and biosafety and regulatory constraints. We conclude by outlining a research and implementation roadmap through which the integrated RE 2.0 approach can advance sustainable agricultural intensification, climate resilience, soil restoration and global food security.},
}

@article {pmid42772552,
year = {2026},
author = {Jung, H and Youn, DH and Kang, HJ and Im, SW and Shin, SH and Park, G and Han, SW and In, YH and Lee, JJ and Jeon, JP and Hong, JY},
title = {Intratracheal Neomycin Attenuates TBI-induced Secondary Brain Injury via Modulation of Lung Dysbiosis and Inhibition of the NLRP3 Inflammasome.},
journal = {Translational research : the journal of laboratory and clinical medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.trsl.2026.09.014},
pmid = {42772552},
issn = {1878-1810},
abstract = {This study is the first to investigate whether modulation of the lung microbiome after traumatic brain injury (TBI) can reduce secondary brain injury and promote neurological recovery. Moderate TBI was induced in adult male Sprague-Dawley rats, which were assigned to normal, TBI, or TBI with intratracheal neomycin treatment for three days. Bronchoalveolar lavage fluid (BAL) and lung tissues were collected on day 3, and brain neuropathology, neuroinflammation, and cognition were assessed on day 7. TBI induced marked neutrophil infiltration and alveolar interstitial edema, accompanied by elevated IL-6 and NOS2 expression in BAL fluid and increased Acinetobacter abundance (LEfSe, LDA score > 3, p < 0.05). Intratracheal neomycin treatment after TBI corrected lung dysbiosis, significantly reduced Acinetobacter abundance, and suppressed IL-6, RAGE, and NLRP3 inflammasome components (NLRP3, ASC, caspase-1, and IL-1β) in lung tissues. In the brain, neomycin improved novel object recognition, reduced IL-6, IL-1β, and NLRP3 inflammasome activation, attenuated GFAP and Iba-1 activation, decreased FJB- and TUNEL-positive cells, preserved blood-brain barrier integrity, and prevented synaptic injury. Serum IL-1β levels peaked on day 3 after TBI, but this elevation was substantially attenuated in neomycin-treated rats. Furthermore, restoration of viable Acinetobacter baumannii largely reversed the neuroprotective effects of neomycin, supporting a causal role for lung Acinetobacter in secondary brain injury after TBI. These findings suggest that early intratracheal neomycin instillation following TBI mitigates lung dysbiosis and NLRP3-mediated inflammation in both lung and brain, thereby reducing secondary brain injury via the lung-brain axis, highlighting translational therapeutic potential.},
}

@article {pmid42772575,
year = {2026},
author = {Yano, T and Ohta, H and Namba, T and Kawabe, H and Okumura, N and Fujitani, N and Mitsui, R},
title = {Development of a qPCR-based method for absolute quantification of facial skin bacteria considering DNA extraction efficiency.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107723},
doi = {10.1016/j.mimet.2026.107723},
pmid = {42772575},
issn = {1872-8359},
abstract = {The skin microbiome differs with age, and understanding the relationship between the microbial balance and skin health is valuable in skin healthcare. In this study, we developed a quantitative real-time PCR (qPCR) method using TaqMan MGB probes to measure the abundance of indigenous skin bacteria. Representative facial skin bacteria (Cutibacterium acnes, Staphylococcus epidermidis, and Staphylococcus aureus) were detected and quantified with high sensitivity using specific primer sets and probes. C. acnes was divided into two groups for qPCR analysis: Group 1, which included major acne-associated types, and Group 2, which included C. acnes subsp. defendens, which is predominant in healthy skin. Cell suspensions of each bacterial species, for which the total cell numbers were assessed, were subjected to DNA extraction with lytic enzyme treatment. The purified DNA enabled the accurate calculation of the extraction efficiency. The DNA extraction efficiency of the targeted skin bacteria ranged from 30% to 100%, indicating a species-dependent variation. The established method enabled stable quantification over a bacterial concentration range of 10[4]-10[8] cells/mL. The qPCR results using DNA extracted from mixed bacterial suspensions were generally consistent with the expected genomic DNA copy numbers after correcting for species-specific DNA extraction efficiencies. The established extraction efficiency-corrected qPCR method provides improved quantification of bacterial abundance on facial skin.},
}

@article {pmid42772775,
year = {2026},
author = {Van Malderen, J and De Boeck, I and van den Broek, MFL and Hiel, M and Jörissen, J and Tuyaerts, I and Bakelants, S and Spacova, I and Vanderveken, OM and Boudewyns, AN and Lebeer, S},
title = {Potential transfer of orally administered probiotics to the upper respiratory tract in children with otitis media with effusion.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-13},
doi = {10.1163/18762891-bja00130},
pmid = {42772775},
issn = {1876-2891},
abstract = {The upper respiratory tract (URT) microbiome is increasingly recognised as a key determinant of airway health, yet the potential of probiotics to beneficially modulate these communities remains largely unexplored, despite the high burden of URT infections such as otitis media (OM). This randomised controlled trial investigated the migration of two model probiotic strains, Lacticaseibacillus rhamnosus GG and Bifidobacterium animalis subsp. lactis BB-12, to different URT niches in 37 children with otitis media with effusion (OME) treated daily with oral oil drops for one month. URT samples from the adenoids, and nasopharynx were analysed with species-specific qRT-PCR and 16S amplicon sequencing. L. rhamnosus GG-like bacteria were detected in 4/19 of treated patients compared to 0/18 in the control group. Probiotic treatment with oral oil droplets modestly increased the prevalence of L. rhamnosus GG-like bacteria in the nasopharynx and adenoids (from 0% to 16.67% and 15.79% respectively), and a slight positive association was observed with the abundance of Dolosigranulum pigrum (effect size = 0.13). Interestingly, other factors, such as maternal antibiotic use after birth, were associated with a notable higher abundance of Moraxella catarrhalis/nonliquefaciens (Maaslin effect size = 5.10), and a lower abundance of Streptococcus pneumoniae/pseudopneumoniae (Maaslin effect size = -2.27). In conclusion, this study suggests that oral probiotics might modulate the URT microbiome in ways relevant to OM, although the magnitude and direction of effects likely depend on the specific strains used. The trial was registered at ClinicalTrials.gov under B300201731908.},
}

@article {pmid42772828,
year = {2026},
author = {Basu, S},
title = {Biofilms and beyond: The impact of Porphyromonas gingivalis on oral squamous cell carcinoma.},
journal = {Progress in molecular biology and translational science},
volume = {224},
number = {},
pages = {169-193},
doi = {10.1016/bs.pmbts.2026.08.001},
pmid = {42772828},
issn = {1878-0814},
mesh = {Humans ; *Porphyromonas gingivalis/physiology ; *Carcinoma, Squamous Cell/microbiology/pathology ; *Mouth Neoplasms/microbiology/pathology ; *Biofilms/growth & development ; Animals ; Epithelial-Mesenchymal Transition ; },
abstract = {Oral squamous cell carcinoma (OSCC) appears as a very common type of head and neck cancer across the world in the recent past. The widespread use of contemporary diagnostic and prognostic methods, a low rate of survival (approximately five-year), a relatively higher chances towards recurrence, and a wide range of malignancy along with metastases are still caused by delayed diagnosis and treatment resistance. There is growing evidence that oral microbiome bacteria, including the Gram-negative anaerobic Porphyromonas gingivalis, may be important in the development of OSCC by causing periodontitis. In fact, the activity of a dysbiotic microbiota has been linked to the epithelial-to-mesenchymal transition (EMT) and dysregulated immune response. Conversely, organisms that are typically thought of as oral commensals, including streptococci from the mitis group, are frequently negatively correlated and have anticancer qualities in vivo. This chapter summarizes the role of P. gingivalis in OSCC initiation, progression, invasion, and metastatic dissemination, highlighting its contribution to microbial dysbiosis, immune modulation, epithelial-mesenchymal transition, and tumor microenvironment remodelling. Several reports have showed a positive correlation exist between the bacteria present in the periodontal part along with oral carcinoma. This would in turn pave the way for future researchers to target P. gingivalis as a potential therapeutic cornerstone to combat the life-threatening diseases.},
}

Humans
*Porphyromonas gingivalis/physiology
*Carcinoma, Squamous Cell/microbiology/pathology
*Mouth Neoplasms/microbiology/pathology
*Biofilms/growth & development
Animals
Epithelial-Mesenchymal Transition

@article {pmid42772829,
year = {2026},
author = {Mazumder, S and Bhattacharya, D and Maity, S and Dutta, T and Chatterjee, S},
title = {Microbial allies in malignancy: Role of Porphyromonas gingivalis and Candida biofilms in oral squamous cell carcinoma.},
journal = {Progress in molecular biology and translational science},
volume = {224},
number = {},
pages = {195-223},
doi = {10.1016/bs.pmbts.2026.07.009},
pmid = {42772829},
issn = {1878-0814},
mesh = {Humans ; *Biofilms/growth & development ; *Porphyromonas gingivalis/physiology ; *Mouth Neoplasms/microbiology/pathology ; *Carcinoma, Squamous Cell/microbiology/pathology ; *Candida/physiology ; Animals ; },
abstract = {Oral squamous cell carcinoma (OSCC) is the most common type of oral cancer, and it is becoming clear that it is a multifactorial disease condition that is affected by microbial dysbiosis. Porphyromonas gingivalis and Candida spp. are keystone periodontal pathogens that have become key disease initiators and progressors in the formation of polymicrobial biofilms in periodontal disease. The biofilms are hyper-virulent, resistant, and cooperate metabolically, leading to chronic inflammation and epithelial remodelling. P. gingivalis, in a mechanistic way, regulates host signaling pathways such as NF- kB, PI3K/Akt, and MAPK to induce anti-apoptotic and proliferative responses, and Candida biofilms trigger carcinogenesis by producing acetaldehyde, disrupting the epithelial barrier, and activating oncogenic pathways. This interaction between bacteria and fungal elements is further synergistic and leads to immune evasion, redox dysbalance, and chronic inflammation, which form a tumor-promoting microenvironment. The implication of emerging evidence also includes the effects of microbial metabolites, quorum sensing, and biofilm architecture in determining the OSCC niche. Notably, such polymicrobial interactions offer new therapeutic avenues, such as anti- biofilm therapy, modulation of microbiomes, and targeted molecular therapy. This chapter thoroughly addresses the mechanistic contributions of P. gingivalis and Candida biofilms to OSCC pathogenesis with a specific focus on their synergistic contribution and potential translational implications in diagnosis, prevention, and treatment.},
}

Humans
*Biofilms/growth & development
*Porphyromonas gingivalis/physiology
*Mouth Neoplasms/microbiology/pathology
*Carcinoma, Squamous Cell/microbiology/pathology
*Candida/physiology
Animals

@article {pmid42773020,
year = {2026},
author = {Nunner, R and Veloso, V and Ramos-Rojas, J and Karki, S and Wollmann, M and Shin, J and Sprenger, A and Kuper, P and Hasenpusch, C and Skiba, EM and Sieferle, K and Ávila-Oliver, C and Rada, G and Apfelbacher, C},
title = {[Allergy Prevention L·OVE: Development of a structured, publicly accessible evidence repository for allergy prevention].},
journal = {Zeitschrift fur Evidenz, Fortbildung und Qualitat im Gesundheitswesen},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.zefq.2026.07.006},
pmid = {42773020},
issn = {2212-0289},
abstract = {BACKGROUND: The prevention of allergic diseases has been addressed by numerous systematic reviews. However, the evidence landscape is fragmented due to heterogeneous populations, interventions, outcomes, and dynamically evolving research approaches. Structured and continuously updated evidence resources are therefore needed to support guideline development, healthcare decision-making, and public health. Against this background, the Allergy Prevention Living Overview of Evidence (L·OVE) was developed as a freely accessible, continuously updated evidence repository for allergy prevention. The aim of this study is to describe the conceptual and methodological development of the repository as well as selected preliminary findings.

METHODS: A systematic search was conducted in the Epistemonikos database for systematic reviews. In order to structure the evidence, a hierarchical taxonomy was developed covering the dimensions population, intervention, contextual dimensions, and outcome. Systematic reviews on primary preventive interventions aiming to prevent the development of allergic diseases or allergic sensitization were included. Relevant evidence was identified using an automated, platform-supported classification and identification workflow validated through a relative recall approach; included reviews were subsequently screened and taxonomically classified manually by two independent reviewers. Disagreements were resolved through discussion and, if necessary, by consultation with a third reviewer.

RESULTS: As of 18 November 2025, the repository included 245 systematic reviews that met the inclusion criteria after a systematic search and multi-stage selection process. Nutrition- and microbiome-related interventions dominated the available evidence base, whereas nature-based, behavioral, and environmentally oriented prevention strategies were comparatively rarely addressed in systematic reviews. The automated, platform-supported identification strategy achieved a sensitivity of 96.49% compared with 92.98% for a Boolean search strategy, while also reducing the manual screening workload.

DISCUSSION: The findings indicate an uneven distribution of systematically synthesized evidence across different prevention domains and highlight potential research gaps. At the same time, the approach shows that systematic reviews in allergy prevention can be organized and continuously updated using structured taxonomies and automated, platform-supported identification procedures. The repository does not perform evidence synthesis itself, but rather supports the structured retrieval, classification, and contextualization of existing evidence.

CONCLUSION: The Allergy Prevention L·OVE provides a structured, freely accessible, and continuously updatable evidence repository for allergy prevention. By combining automated evidence identification, a structured taxonomy, and expert curation, it can support researchers, guideline groups, and stakeholders in healthcare and public health in identifying systematic reviews more efficiently, recognizing evidence gaps, and making more transparent use of the existing evidence base.},
}

@article {pmid42773061,
year = {2026},
author = {Yie, GE and Kim, E and Pham, DD and Lee, CE and Song, H and Kim, YK and Kang, CS and Kwon, HS and Song, WJ and Cho, YS and Lee, SW and Ban, GY and Lee, T and Kim, MH and Ahn, KM and Lee, SM and Bhavsar, PK and Adcock, IM and Chung, KF and Won, S and Kim, TB},
title = {Stool and Airway Microbiome Signatures Associated With Treatment Response to Dupilumab in Severe Asthma: Findings From the PRISM Study.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70524},
pmid = {42773061},
issn = {1398-9995},
support = {RS-2024-00403700//Korea Health Industry Development Institute/ ; },
abstract = {BACKGROUND: Severe asthma is characterized by persistent airway inflammation and heterogeneous responses to biologic therapies. Growing evidence implicates the gut-lung axis in asthma pathophysiology; however, few studies have concurrently characterized gut and airway microbiomes in relation to treatment response in severe asthma.

METHODS: We profiled microbiomes of stool bacteria (STB), stool-derived extracellular vesicles (STE), and exhaled breath condensate (EBC) from 48 patients with severe asthma receiving dupilumab. Microbial composition, alpha diversity, and predicted functional profiles were compared across sample types and longitudinally according to treatment response. Associations between microbial features and asthma-related clinical markers were also evaluated.

RESULTS: Distinct taxonomic and predicted functional signatures were identified across biological compartments. EBC samples were enriched in Proteobacteria, including Pseudomonas, and exhibited a higher predicted abundance of pathways related to two-component systems and bacterial secretion systems. EBC microbial diversity was positively associated with baseline sputum eosinophil levels (p = 0.018), whereas stool microbial richness demonstrated a time-dependent association with blood eosinophil counts after treatment (p for interaction = 0.023). Treatment responders exhibited lower abundances of Lachnospira (STB q = 0.046; STE q = 0.042) and Escherichia-Shigella (STE q = 0.038), and a higher relative abundance of the Oscillospiraceae NK4A214 group (STB q = 5.5 × 10[-7], STE q = 1.4 × 10[-8]) in stool-derived profiles.

CONCLUSION: Gut and airway-derived microbiomes appear to play complementary roles in severe asthma. Stool-derived microbial features may reflect systemic inflammatory signals associated with treatment response, whereas airway-derived microbial profiles reflect local airway inflammation. Integrating multi-compartment microbiome data may improve the understanding of heterogeneity in biologic treatment response among patients with severe asthma.},
}

@article {pmid42773092,
year = {2026},
author = {Le Berre, C and Rezazadeh Ardabili, A and Czepielewski, R and Cices, A and Mehandru, S and Colombel, JF},
title = {Revisiting the role of lymphatics in Crohn's disease.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izag187},
pmid = {42773092},
issn = {1536-4844},
support = {//French network of University Hospitals HUGO/ ; //"Hôpitaux Universitaires du Grand Ouest"/ ; //Société Nationale Française de Gastro-Entérologie (SNFGE)/ ; //Fondation SantéDige/ ; },
abstract = {BACKGROUND: Early pathological observations consistently highlighted the involvement of the intestinal lymphatic system in Crohn's disease (CD), although this remains underappreciated in current conceptual models of disease pathogenesis. This narrative review synthesizes evidence supporting lymphatic dysfunction as a key contributor of CD pathogenesis, and discusses its therapeutic potential.

METHODS: We searched PubMed to identify relevant studies on lymphatic biology in CD, including pathological, clinical, and experimental data.

RESULTS: Lymphatic obstruction, lymphangitis, and lymphangiectasia are early, widespread features of CD; structural remodeling coexists with compensatory lymphangiogenesis, suggesting a bidirectional relationship in which lymphatic dysfunction both drives and is sustained by intestinal inflammation. Peyer's patches, closely integrated with the lymphatic network, may represent a portal of entry for luminal pathogens. CD susceptibility genes impair microbial handling at this interface, potentially enabling translocation into the lymphatics, endothelial injury, and the granulomatous lymphangitis hallmark of CD. Experimental models reinforce this framework: pathogens such as Yersinia or norovirus can induce lymphangitis preceding overt intestinal inflammation. Metastatic cutaneous CD, a rare extraintestinal manifestation involving lymphatic vessels characterized by granulomatous dermal inflammation at sites anatomically discontinuous from the gut, may provide a unique window into lymphatic pathology independent of the intestinal microbiome.

CONCLUSIONS: These observations support an alternative view of CD in which intestinal lymphatic dysfunction plays an under-recognized role in both promoting and sustaining inflammation. This framework may explain disease features (patchy distribution, transmural inflammation, mesenteric hypertrophy) and positions the lymphatic system as a therapeutic target to restore drainage and modulate immune-lymphatic crosstalk.},
}

@article {pmid42773364,
year = {2026},
author = {Xu, R and Shi, Y and Liao, L and Yin, Z and Li, Q and Qu, G and Zhang, Y and Yin, C and Tian, Y},
title = {Efficacy of Fe/Mn (hydro)oxide-phosphate composites for synergistic immobilization of Cd, Pb, Cu, and Zn and microecological regulation in mining soils.},
journal = {Environmental geochemistry and health},
volume = {48},
number = {15},
pages = {},
pmid = {42773364},
issn = {1573-2983},
support = {52400167//National Natural Science Foundation of China/ ; 2022NK2057//Key Research and Development Program of Hunan Province of China/ ; },
mesh = {*Soil Pollutants/chemistry ; Mining ; *Metals, Heavy/chemistry ; *Soil Microbiology ; *Phosphates/chemistry ; *Environmental Restoration and Remediation/methods ; Soil/chemistry ; *Oxides/chemistry ; Cadmium/chemistry ; Microbiota ; Zinc/chemistry ; Copper/chemistry ; *Manganese Compounds/chemistry ; },
abstract = {In situ stabilization is a practical strategy for mitigating multi-metal contamination while restoring soil ecological functions. In this study, Fe/Mn (hydr)oxide-phosphate composites (FMPs) were synthesized and applied to highly Cd-Pb-Cu-Zn co-contaminated mining soil. After 60 days of FMPs application (5 wt.%), DTPA-extractable Cd, Pb, Cu, and Zn were effectively reduced by 70.10%, 99.82%, 68.30%, and 75.05%, respectively, successfully transforming target metals from labile (F1/F2) to stable (F3/F4) fractions. Physicochemically, FMPs applications elevated soil pH and essential nutrients (TP, AP, NH4[+]-N), which directly correlated with the significant enhancement of soil enzymatic activities (S_ACP, S_CL and S_CAT). High-throughput sequencing further revealed that FMPs reconstructed the soil microbiome. While overall bacterial diversity decreased and fungal diversity increased, ecologically beneficial and metal-resistant taxa, including Chloroflexi, Bacteroidota and Pseudaleuria were significantly enriched. Moreover, molecular ecological network (MEN) analysis indicated that FMPs induced more tightly connected and stable bacterial networks while simplifying fungal networks, with low-abundance taxa primarily acting as keystone connectors. Furthermore, neutral community model (NCM) predictions verified that stochastic processes dominantly governed the assembly mechanisms of both bacterial and fungal communities during the restoration process. These multidimensional results systematically demonstrate that FMPs not only achieve highly efficient chemical stabilization of multiple heavy metals but also facilitate robust ecological restoration by optimizing microbial community.},
}

*Soil Pollutants/chemistry
Mining
*Metals, Heavy/chemistry
*Soil Microbiology
*Phosphates/chemistry
*Environmental Restoration and Remediation/methods
Soil/chemistry
*Oxides/chemistry
Cadmium/chemistry
Microbiota
Zinc/chemistry
Copper/chemistry
*Manganese Compounds/chemistry

@article {pmid42773439,
year = {2026},
author = {He, T and Fu, M and Wang, M and Yang, M and Li, M and Du, R and Lin, R and Deng, W and Yang, M and Li, A and Zhu, S and Du, F},
title = {Hydrophobic nano-calcium superphosphate enhances leaf disease resistance via coordinated physical, biochemical, and phyllosphere responses.},
journal = {Journal of nanobiotechnology},
volume = {24},
number = {1},
pages = {},
pmid = {42773439},
issn = {1477-3155},
support = {32360712//National Natural Science Foundation of China/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202305AF150129//The Expert Workstation Project in Yunnan Province/ ; },
mesh = {*Plant Leaves/microbiology/drug effects/metabolism ; *Vitis/microbiology/drug effects/metabolism ; *Plant Diseases/microbiology/prevention & control ; *Disease Resistance/drug effects ; Hydrophobic and Hydrophilic Interactions ; *Calcium Phosphates/pharmacology/chemistry ; Microbiota/drug effects ; *Nanoparticles/chemistry ; },
abstract = {Hydrophobic nano-calcium superphosphate (NPS1) is a novel nano-fertilizer that has shown great potential for enhancing plant growth and suppressing foliar diseases. However, the mechanisms underlying these effects remain unclear. We investigated the responses of grape leaves and phyllosphere microbiota to NPS1 under both open-field and rain-shelter cultivation systems. NPS1 application significantly reduced leaf wetness duration and the disease severity of downy and powdery mildew, increased leaf-associated phosphorus retention, which remained elevated at later sampling stages, while enhancing vine growth, increasing SOD and POD activities, and inhibits several grape pathogens in vitro. Integrated transcriptomic and metabolomic analyses identified substantial changes in gene expression and metabolite accumulation following NPS1 treatment, characterized by the upregulation of stress-responsive genes (WRKY41, PEROXIDASE, and EREBP) and enrichment of pathways related to phenylpropanoid and secondary metabolite biosynthesis. Exogenous validation experiments indicated that coumaric acid and lignin were associated with enhanced seedling growth and restricted pathogen growth in vitro. Furthermore, amplicon sequencing revealed significant shifts in the composition, diversity, and co-occurrence patterns of phyllosphere microbial communities, accompanied by reduced relative abundances of pathogen-associated taxa (e.g., Erysiphe and oomycetes). Notably, representative beneficial isolates (e.g., Sphingomonas spp. and Bacillus spp.) exhibited stronger pathogen inhibition when combined with NPS1 than when applied alone. Collectively, these findings indicate that NPS1 alters the leaf surface conditions through reduced leaf wetness, associated with coordinated changes in plant physiological responses, metabolite accumulation, and phyllosphere microbial communities, which may be linked to reduced disease severity and improved grapevine performance.},
}

*Plant Leaves/microbiology/drug effects/metabolism
*Vitis/microbiology/drug effects/metabolism
*Plant Diseases/microbiology/prevention & control
*Disease Resistance/drug effects
Hydrophobic and Hydrophilic Interactions
*Calcium Phosphates/pharmacology/chemistry
Microbiota/drug effects
*Nanoparticles/chemistry

@article {pmid42773529,
year = {2026},
author = {Mkilima, T},
title = {Electroactive Microbiomes: Electron Transfer Mechanisms and Environmental Biotechnology Applications.},
journal = {Environmental microbiology reports},
volume = {18},
number = {5},
pages = {e70419},
doi = {10.1111/1758-2229.70419},
pmid = {42773529},
issn = {1758-2229},
mesh = {Electron Transport ; *Bioelectric Energy Sources/microbiology ; Biofilms/growth & development ; *Biotechnology/methods ; *Microbiota/physiology ; Electrodes/microbiology ; Bacteria/metabolism ; Oxidation-Reduction ; },
abstract = {Electroactive microbiomes are mixed microbial communities in which one or more members exchange electrons with extracellular minerals, redox-active compounds, electrodes, or partner organisms and in which community interactions materially influence net electron flow. This review develops a mechanism-interface-function-readiness framework that connects extracellular electron transfer (EET) with biofilm ecology, microbiome-electrode organisation, environmental process performance, and translational maturity. Direct transfer through multiheme cytochromes and conductive structures, mediated transfer through soluble redox shuttles, and interspecies electron transfer are evaluated as system-dependent pathways rather than universally ranked mechanisms. Particular emphasis is placed on wastewater treatment and resource recovery, anaerobic digestion, pollutant and metal transformation, soil and sediment bioelectrochemistry, carbon conversion, microbial fuel cells, microbial electrolysis cells, electro-fermentation, and microbial electrosynthesis. Multi-omics, metabolic modelling, synthetic biology, advanced materials, and artificial intelligence are examined according to the strength of their direct evidence in electroactive systems. Across applications, performance depends strongly on reactor configuration, electrode properties, inoculum, biofilm architecture, mass and charge transport, substrate loading, and normalisation basis, making unqualified cross-study numerical comparison inappropriate. Major barriers are long-term stability, mechanistic attribution in mixed communities, standardisation, scale-up, energy and mass balances, biosafety, techno-economic feasibility, and regulatory compatibility.},
}

Electron Transport
*Bioelectric Energy Sources/microbiology
Biofilms/growth & development
*Biotechnology/methods
*Microbiota/physiology
Electrodes/microbiology
Bacteria/metabolism
Oxidation-Reduction

@article {pmid42773683,
year = {2026},
author = {Conti, DE and Debarbieux, L and Henrot, C},
title = {The OMM[12] mice: a decade of dissecting host-microbiome interactions.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2725332},
doi = {10.1080/19490976.2026.2725332},
pmid = {42773683},
issn = {1949-0984},
mesh = {Animals ; Mice ; *Host Microbial Interactions ; Germ-Free Life ; Bacteria/genetics/classification/metabolism ; *Gastrointestinal Microbiome ; Bacteriophages/physiology ; Mice, Inbred C57BL ; Humans ; *Microbiota ; },
abstract = {Humans and their associated microbes form a multifaceted ecosystem. Gaining mechanistic insight into this system necessitates reductionist models integrating ecological and immunological dimensions. Over the past decade, the gnotobiotic Oligo-Mouse-Microbiota (OMM[12]) mouse line has exemplified this approach, pairing a standardized consortium of 12 bacterial strains representative of the five major phyla of the mouse microbiota, with the most widely used host background, C57bl/6 mice, in microbiome research. Across numerous studies, this reproducible and experimentally tractable model has enabled the identification of molecular mechanisms underlying colonization resistance, pathogen virulence, microbiota-dependent metabolic and immune pathways, as well as bacterial and bacteriophage dynamics. The modular ability/nature of the OMM[12] model may now be further leveraged and refined in different host and microbial dimensions to address remaining gaps in translational microbiome research, positioning it as a reference framework for mechanistic investigations.},
}

Animals
Mice
*Host Microbial Interactions
Germ-Free Life
Bacteria/genetics/classification/metabolism
*Gastrointestinal Microbiome
Bacteriophages/physiology
Mice, Inbred C57BL
Humans
*Microbiota

@article {pmid42774018,
year = {2026},
author = {Enoma, E and Adu-Gyamfi, A and Carter, J and Wu, S and Nemesure, B and Williams, JL},
title = {Allostatic load as a framework for understanding early-onset colorectal cancer: current biomarker evidence and future directions.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1823995},
pmid = {42774018},
issn = {2234-943X},
abstract = {INTRODUCTION: Colorectal cancer incidence rates have been on the decline over the past 50 years due to increased screening and diagnostic tools. Over the past 32 years (since 1994), there has been a rise in colorectal cancer for those under 50 years old. This trend has been designated as early-onset colorectal cancer (EOCRC) and is in direct opposition to the decline seen in those over 50 years of age; designated as late onset colorectal cancer (LOCRC). The rise in EOCRC has been attributed to various factors such as environmental, modern diet and lifestyle.

METHODS: The paper includes a comprehensive search of both cohort and case-control studies that were designed to investigate the association between EOCRC and allostatic load (AL) using two databases: MEDLINE PubMed and Stony Brook University Libraries Database.

RESULTS: 12 studies were included in this paper. These papers varied on how many used biomarkers that are measured in allostatic load. Out of the 12 studies, only 3 had direct measurements of AL such as metabolic and cardiovascular, 9 measured indirect biomarkers such as inflammatory pathways and epigenetics.

CONCLUSION: The purpose of this paper is to change the current paradigm focus of the causation of EOCRC being associated with a single factor and instead study factors together using allostatic load. Although none of the papers measured AL and EOCRC directly, they each used a direct or indirect measurement of AL when studying EOCRC. We believe that AL should be the next focus for future research of EOCRC to better understand how all these factors contribute to disease progression.},
}

@article {pmid42774052,
year = {2026},
author = {Yin, X and Du, S and Wan, J},
title = {Oral microbiome and lesion-associated microbiological findings in medication-related osteonecrosis of the jaw: a systematic review and evidence map.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1923000},
pmid = {42774052},
issn = {2235-2988},
mesh = {Humans ; *Microbiota ; *Mouth/microbiology ; Biofilms/growth & development ; *Bisphosphonate-Associated Osteonecrosis of the Jaw/microbiology ; Actinomyces ; Bacteria/classification/isolation & purification ; },
abstract = {BACKGROUND: Medication-related osteonecrosis of the jaw (MRONJ) may involve microbial colonization, anaerobic organisms, and biofilm formation, but whether it has a reproducible microbial signature remains unclear. We mapped the human microbiological evidence in MRONJ.

METHODS: The protocol was registered in PROSPERO (CRD420261432571). Reporting followed PRISMA 2020, PRISMA-S, and Synthesis Without Meta-analysis guidance. Six sources were searched from inception in two waves through 25 July 2026, supplemented by citation searching. Original human microbiological studies of MRONJ were eligible. Community-level evidence was classified as core, other MRONJ microbiological evidence as supportive, and evidence from related jawbone conditions as contextual. Five prespecified domains included explicit MRONJ-specific Actinomyces events and denominators, strict-anaerobe evidence, and direct biofilm evidence. Design-specific JBI checklists and STORMS-informed reporting items were applied. Meta-analysis was conditional on prespecified compatibility criteria.

RESULTS: Of 4,044 records, 71 reports representing 67 independent studies were included: 51 MRONJ studies, comprising 13 core and 38 supportive studies, and 16 contextual studies. Community-level findings were not sufficiently comparable for pooling. Among the 51 MRONJ studies, criteria were met by 19 for strict-anaerobe evidence, seven for viral evidence, six for explicit Actinomyces events and denominators, three for direct biofilm evidence, and two for fungal evidence; 32 contributed to at least one domain. Nine method-specific Actinomyces observations from six studies reported raw detection proportions of 5.1%-65.7% by culture, 82.9%-96.4% by PCR or quantitative PCR, and 36.4%-100.0% by histology, using patient- or specimen-level denominators. Diagnostic criteria, antibiotic timing, negative controls, and data availability were inconsistently reported. No domain met the compatibility criteria for meta-analysis.

CONCLUSIONS: The MRONJ microbiological evidence is methodologically heterogeneous and dominated by observational, lesion-derived studies. Detection proportions varied substantially with method and denominator unit, limiting their interpretation as prevalence estimates. Repeated reports of anaerobic organisms and Actinomyces, together with sparse direct biofilm evidence, describe lesion-associated findings of undetermined specificity rather than a reproducible MRONJ-specific signature. Standardized comparators and sampling, explicit denominators, contamination controls, extractable numerical results, and accessible sequence data are needed for future synthesis and clinical evaluation.

https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD420261432571, identifier CRD420261432571.},
}

Humans
*Microbiota
*Mouth/microbiology
Biofilms/growth & development
*Bisphosphonate-Associated Osteonecrosis of the Jaw/microbiology
Actinomyces
Bacteria/classification/isolation & purification

@article {pmid42774064,
year = {2026},
author = {Bae, S and Avila-Pacheco, J and Clay, SL and Bang, S and Scott, MC and Andreeva, N and Michaud, M and Fonseca-Pereira, D and Chun, E and Cao, YG and Zhang, Y and Bhosle, A and Perez, RM and Pishchany, G and Vlamakis, H and El Tekle, G and Morgan, XC and Chen, SP and Glickman, JN and Xavier, RJ and Graham, DB and Clish, CB and Clardy, J and Franzosa, EA and Huttenhower, C and Garrett, WS},
title = {Microbial-associated acylated putrescines as immunomodulatory molecules in inflammatory bowel diseases.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.08.24.746719},
pmid = {42774064},
issn = {2692-8205},
abstract = {UNLABELLED: The gut microbiota profoundly shapes intestinal immunity through the production of small-molecule metabolites; yet in inflammatory bowel diseases (IBD), where the microbial metabolome is substantially altered, the identities and immunological functions of most disease-associated metabolites remain unknown. Here, we integrate untargeted fecal metabolomics from two independent IBD patient cohorts with gnotobiotic mouse metabolomic data to identify N-acyl putrescines as a class of microbiome-associated metabolites consistently enriched in both Crohn's disease (CD) and ulcerative colitis (UC). Among these, N-oleoylputrescine (NOP) induces potent and selective transcriptional responses in bone marrow-derived dendritic cells (BMDCs) and colonic organoids, establishing it as the primary immunomodulatory candidate in this metabolite class. Enterocloster species harboring nonribosomal peptide synthetase (NRPS) biosynthetic gene clusters produce NOP via conjugation of oleic acid with putrescine, confirmed by isotope-tracing in vitro and germ-free mouse mono-colonization in vivo. NOP suppresses five core IBD-associated inflammatory pathways in mouse dendritic cells and human monocytes, reduces gene signatures of histologic inflammation and IBD therapy non-response, and ameliorates colitis in four murine models. NOP dampens NF-κB activation and iNOS expression in myeloid cells and suppresses type 1 immune responses through a T cell-intrinsic mechanism. The enrichment of NOP in IBD despite its anti-inflammatory activity supports a holobiont defense hypothesis: that the gut microbiota mounts a compensatory metabolic response to intestinal inflammation that may contribute to the restoration of organismal homeostasis.

IN BRIEF: Bae et al. identify N-acyl putrescines as gut microbiota-associated metabolites enriched in IBD and demonstrate that N-oleoylputrescine (NOP), produced by Enterocloster species via NRPS biosynthetic machinery, broadly suppresses innate and adaptive inflammatory programs and ameliorates colitis in mice, supporting a holobiont defense hypothesis for microbiota-mediated immunomodulation.

HIGHLIGHTS: N-acyl putrescines are microbiome-associated metabolites enriched in IBD feces across two independent human cohorts Enterocloster species harboring NRPS biosynthetic gene clusters produce NOP via oleic acid- putrescine conjugation NOP suppresses NF-κB, iNOS, and IBD therapy non-response gene signatures in mouse and human myeloid cellsNOP ameliorates colitis in four distinct murine models and suppresses type 1 immunity via a T cell-intrinsic mechanism.},
}

@article {pmid42774080,
year = {2026},
author = {Butler, CA and Brown, AC},
title = {Editorial: Women in oral microbes and host: 2025.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1968328},
doi = {10.3389/fcimb.2026.1968328},
pmid = {42774080},
issn = {2235-2988},
}

@article {pmid42774306,
year = {2026},
author = {Zhang, R and Chen, Y and Meng, H and Jia, A and Fu, D and Lin, X and Wang, J and He, J and Zhou, Y and Li, Y},
title = {Gut microbiota and metabolomics reveal the combined effects of Alpinia oxyphylla fructus polysaccharide and nootkatone on chronic kidney disease via the "gut-kidney" axis.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1904155},
pmid = {42774306},
issn = {1663-9812},
abstract = {BACKGROUND: Chronic kidney disease (CKD) imposes a substantial burden on healthcare systems worldwide. Traditional Chinese medicine has gained attention as a complementary and alternative selection given the limitations of current CKD management. Although the renoprotective potential of Alpinia oxyphylla fructus has been reported, existing studies mainly focus on crude extracts or individual metabolites, leaving interactions among metabolites unexplored. This study investigated the individual and combined effects of A. oxyphylla fructus polysaccharide (AOP) and nootkatone (NKT) in CKD.

METHODS: The protective effects of AOP and NKT on CKD were evaluated using an adenine-induced mouse model. Renal and colonic injuries were assessed by plasma biochemistry, histopathological analysis, and inflammation-related gene expression. Plasma metabolic profiles were characterized by untargeted metabolomics. Intestinal microbiota structure was analyzed by microbial diversity sequencing. Fecal short-chain fatty acids (SCFAs) were quantified by gas chromatography, and intestinal barrier-related gene and protein expression levels were examined by RT-qPCR and immunohistochemistry, respectively.

RESULTS: Combined intervention exerted stronger protective effects than either intervention administered alone. It markedly reduced plasma urea nitrogen and creatinine levels, alleviated renal inflammation and fibrosis, and improved metabolic dysregulation with reduced uremic toxin accumulation. Key regulated pathways included pyrimidine, purine, and ascorbate and aldarate metabolism. The combined intervention also ameliorated gut microbiota dysbiosis, preserved SCFA levels, and maintained intestinal barrier integrity.

CONCLUSION: The combination of AOP and NKT exhibited combined effects through modulation of the plasma metabolic profile and the gut microenvironment, suggesting its potential protective role against CKD via the gut-kidney axis. These findings provide new insights into the combined effects of multiple bioactive metabolites from traditional Chinese medicine.},
}

@article {pmid42774612,
year = {2026},
author = {McGillivray, E and Kane, S and Saadatkhah, A and Yeung, KT},
title = {Emerging biomarkers of immune checkpoint inhibitor toxicity in triple-negative breast cancer: a mini-review.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1950429},
pmid = {42774612},
issn = {1664-3224},
mesh = {Humans ; *Triple Negative Breast Neoplasms/drug therapy/immunology ; *Immune Checkpoint Inhibitors/adverse effects/therapeutic use ; *Biomarkers, Tumor ; Female ; },
abstract = {Immune checkpoint inhibitors (ICI) have revolutionized the treatment of TNBC, leading to durable responses and improved survival. With the adoption of immunotherapy into high-risk early-stage and selected metastatic triple-negative breast cancer (TNBC), clinicians' ability to recognize and treat immune-related adverse events has become increasingly important. There is no prospectively validated or FDA-approved predictive biomarker of toxicity; however, candidate biomarkers involving circulating blood counts, immune-cell phenotypes, cytokines, transcriptomics, immune age, germline genetics, human leukocyte antigen genotypes, autoantibodies, and the gut microbiome have been described, with many more currently under investigation. Most evidence remains exploratory and is derived from non-TNBC populations. Going forward, incorporating these investigational tools within prospective TNBC trials and validating them in real-world, multicenter TNBC cohorts are critical to ensure these predictive biomarkers translate into clinically useful tools for risk-adapted monitoring. This mini-review highlights the current landscape of predictive biomarkers of ICI toxicity, with a focus on TNBC.},
}

Humans
*Triple Negative Breast Neoplasms/drug therapy/immunology
*Immune Checkpoint Inhibitors/adverse effects/therapeutic use
*Biomarkers, Tumor
Female

@article {pmid42774746,
year = {2026},
author = {Obeagu, EI},
title = {Engineering probiotic consortia to improve chemotherapy tolerance and reduce toxicity in breast cancer patients: a new frontier in supportive precision oncology.},
journal = {Oncology reviews},
volume = {20},
number = {},
pages = {1909404},
pmid = {42774746},
issn = {1970-5565},
abstract = {Chemotherapy is a cornerstone of breast cancer treatment but is often limited by systemic toxicities, gastrointestinal mucositis, immunosuppression, and treatment interruptions, which compromise patient outcomes. Emerging evidence highlights the gut microbiome as a central mediator of chemotherapy tolerance and toxicity. Cytotoxic regimens induce dysbiosis, characterized by depletion of beneficial commensals, expansion of pathobionts, and impaired microbial metabolic function, exacerbating mucosal injury, inflammation, and systemic side effects. Engineered probiotic consortia-rationally designed multi-strain microbial communities-offer a novel strategy to restore microbial balance, reinforce epithelial barrier function, modulate immune responses, and enhance chemotherapy tolerance. Preclinical and emerging clinical studies demonstrate that multi-strain consortia can increase short-chain fatty acid production, reduce pro-inflammatory signaling, preserve mucosal integrity, and improve patient resilience during treatment. Advances in synthetic biology and microbiome engineering enable precise design of microbial consortia with complementary functions and ecological stability. This review provides a comprehensive overview of the mechanistic rationale, preclinical and clinical evidence, technological strategies, and translational implications of engineered probiotic consortia, highlighting their potential to transform supportive care in breast cancer therapy.},
}

@article {pmid42774761,
year = {2026},
author = {MacInnis, EM and Ebbeskotte, T and AbdelKhalek, A and Nieforth, LO},
title = {The microbiome and non-occupational human-animal interactions: a scoping review.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1938888},
pmid = {42774761},
issn = {2296-2565},
mesh = {Humans ; *Microbiota/physiology ; Animals ; *Human-Animal Interaction ; },
abstract = {Human-animal interactions may impact the composition of the human microbiome. This can then influence human physical, mental, and social wellbeing. This scoping review synthesizes the literature on the impacts of intentional, non-occupational human-animal interactions on the human microbiome. Six databases (PubMed, CINAHL, PsycINFO, Web of Science, CAB Abstracts, and ProQuest Dissertations and Theses) were searched using keywords for human-animal interactions and microbiomes. Database searching resulted in 2,946 publications. Publications were screened according to the following inclusion criteria: (1) published in English, (2) peer-reviewed article or dissertation presenting empirical data, (3) studies humans engaging in intentional, non-occupational interaction with animals, and (4) compares human microbiome composition before and after human-animal interactions or compares humans that interact with animals to humans that do not interact with animals. Screening resulted in 30 relevant publications. Of these, 24 reported a significant effect of human-animal interactions on microbiome composition. However, there were notable gaps in the reporting of demographics and methodology, such as length of human-animal interaction, species of animal, and variable 16S regions of focus. To better understand the impacts of human-animal interactions on the human microbiome, future studies should include detailed reporting of both human-animal interactions and microbiome analysis methods.},
}

Humans
*Microbiota/physiology
Animals
*Human-Animal Interaction

@article {pmid42774854,
year = {2026},
author = {Wei, X and Pei, X and Yu, S},
title = {Tertiary lymphoid structures in urothelial carcinoma: bridging spatial architecture with therapeutic vulnerability in the post-BCG era.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1853633},
pmid = {42774854},
issn = {1664-3224},
mesh = {Humans ; *Tertiary Lymphoid Structures/immunology/pathology ; Tumor Microenvironment/immunology ; Non-Muscle Invasive Bladder Neoplasms ; Animals ; *BCG Vaccine/therapeutic use/administration & dosage ; *Urinary Bladder Neoplasms/immunology/pathology/therapy ; Immunotherapy/methods ; *Carcinoma, Transitional Cell/immunology/pathology/therapy ; Biomarkers, Tumor ; },
abstract = {Urothelial carcinoma (UC) remains a persistent clinical challenge in the post-Bacillus Calmette-Guérin (BCG) era, particularly because a substantial proportion of patients with high-risk non-muscle-invasive bladder cancer (NMIBC) experience recurrence or progression despite standard intravesical immunotherapy. Although immune checkpoint inhibitors (ICIs) and antibody-drug conjugates (ADCs) have expanded the therapeutic armamentarium, widely studied biomarkers such as tumor mutational burden (TMB) and PD-L1 expression show limited and inconsistent predictive performance in UC, which may partly reflect their inability to capture the spatial organization and functional states of the tumor immune microenvironment (TIME). Tertiary lymphoid structures (TLS), ectopic lymphoid aggregates that develop in non-lymphoid tissues at sites of chronic inflammation or cancer, have emerged as candidate mediators and spatial markers of local adaptive immunity. In UC, TLS appear to exhibit spatial heterogeneity and may exist across a maturation continuum from early, disorganized lymphoid aggregates to mature, germinal center-containing follicles; their localization within the lamina propria, tumor stroma, or invasive front may be associated with distinct immune contexts and clinical outcomes. This review provides a urology-centric perspective on TLS biology in UC, emphasizing how the anatomical and immunological niche of the bladder, including urinary exposure, the urinary microbiome, BCG-associated inflammation, and stromal remodeling, may shape the conditions under which TLS develop and function. We critically discuss TLS maturation status as a potential spatial biomarker, while emphasizing that its relationship with BCG failure and subsequent response to PD-1/PD-L1 blockade or enfortumab vedotin (EV)-based therapy remains largely correlative and requires prospective validation. Furthermore, we explore emerging strategies that may modulate TLS-associated immune architecture, including STING agonist instillation and LTβR pathway modulation, and discuss how TLS could be tested as an adjunctive biomarker in future bladder-preservation studies for high-risk T1 disease. By synthesizing current evidence and methodological advances in spatial transcriptomics, we underscore the translational imperative of viewing UC as a malignancy with heterogeneous local immune architecture, including candidate tertiary lymphoid structures. At present, TLS should not be used as a stand-alone biomarker for selecting bladder preservation, radical cystectomy, intravesical therapy continuation, or systemic treatment switching.},
}

Humans
*Tertiary Lymphoid Structures/immunology/pathology
Tumor Microenvironment/immunology
Non-Muscle Invasive Bladder Neoplasms
Animals
*BCG Vaccine/therapeutic use/administration & dosage
*Urinary Bladder Neoplasms/immunology/pathology/therapy
Immunotherapy/methods
*Carcinoma, Transitional Cell/immunology/pathology/therapy
Biomarkers, Tumor

@article {pmid42775021,
year = {2026},
author = {Chakraborty, A and Roy, A and He, S and Castellano-Hinojosa, A and Asiegbu, FO},
title = {Editorial: Forest microbiome: dynamics and interactions in the Anthropocene era, volume II.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1974582},
pmid = {42775021},
issn = {1664-302X},
}

@article {pmid42775036,
year = {2026},
author = {Wathore, N and Kumbam, S and Ibikunle, D and Abdelrahman, MU and Kalakonda, CM and Ejimgini, GP and Azhar, R and Khanam, S and Ali, AB},
title = {Short-Chain Fatty Acids in Blood Pressure Management: A Systematic Review of Clinical Effects, Delivery Strategies, and Translational Barriers.},
journal = {Cureus},
volume = {18},
number = {8},
pages = {e115011},
pmid = {42775036},
issn = {2168-8184},
abstract = {Short-chain fatty acids (SCFAs) have been proposed as mediators of the relationship between the intestinal microbiome and blood pressure (BP), but their therapeutic relevance in humans remains uncertain. This systematic review evaluated the effects of direct SCFA administration and interventions modifying endogenous fecal or circulating SCFAs on BP in adults. MEDLINE via PubMed, Scopus, and Web of Science Core Collection were searched for randomized controlled trials published from January 1, 2022, through May 31, 2026. The review was reported in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 statement, with study selection, data extraction, and risk-of-bias assessment performed independently by two reviewers. Six randomized controlled trials were included and synthesized narratively because of substantial clinical and methodological heterogeneity. Three trials evaluated direct butyrate administration, while three assessed exercise, plant-derived, dietary, prebiotic, or physical therapy interventions that modified endogenous SCFAs. Direct administration produced inconsistent effects. Conventional oral butyrate increased daytime systolic and diastolic BP relative to placebo in adults with hypertension, whereas acute colon-targeted delivery reduced daytime systolic BP relative to a lower concentration in a small crossover trial. A further oral trial in type 2 diabetes mellitus reported within-group BP reductions without a demonstrated between-group effect. Indirect interventions generally increased plasma or fecal SCFAs alongside improvements in selected BP outcomes, but their multicomponent effects and the absence of formal mediation analyses precluded attributing these responses specifically to SCFAs. Fecal and circulating measurements also showed different relationships with BP, indicating that these compartments are not biologically interchangeable. One study was judged at low risk of bias, two had some concerns, and three were at high risk. Current evidence does not demonstrate a uniform antihypertensive effect of increasing SCFA availability or a reproducible dose-response relationship. Future trials should compare oral and colon-targeted formulations, measure fecal and circulating SCFAs concurrently, use 24-hour ambulatory BP monitoring as the primary outcome, and evaluate whether treatment responses vary by exposure and cardiometabolic phenotype.},
}

@article {pmid42775139,
year = {2026},
author = {Wang, K and Tang, Q and Fan, W and Su, Q},
title = {Gut-prostate axis in prostate cancer: microbiome signatures, mechanistic insights, and therapeutic opportunities.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1882172},
pmid = {42775139},
issn = {2235-2988},
mesh = {Humans ; Male ; *Prostatic Neoplasms/therapy/microbiology/metabolism/pathology ; *Gastrointestinal Microbiome/physiology ; *Prostate/microbiology/pathology/metabolism ; Signal Transduction ; Fecal Microbiota Transplantation ; Animals ; Probiotics/therapeutic use ; Androgens/metabolism ; },
abstract = {Prostate cancer (PCa) is one of the most common malignant tumors in men, and its onset and progression may be closely associated with an imbalance in the gut microbiota. Existing studies indicate that PCa patients exhibit reduced fecal microbiota diversity and altered microbiota composition, with the abundance of certain bacterial genera correlated with disease risk and progression. Mechanistically, the gut microbiota may regulate signaling pathways such as IGF-1, MAPK/PI3K, and NF-κB through metabolites including short-chain fatty acids, bile acids, and microbiota-derived androgens, thereby potentially contributing to tumor proliferation, inflammatory responses, and immune evasion. Androgen deprivation therapy (ADT) can also reshape the gut microbiota; certain bacterial populations may contribute to the development of castration resistance through androgen metabolism, while changes in bacteria such as Akkermansia muciniphila are associated with treatment response. Currently, strategies such as dietary interventions, probiotics, and fecal microbiota transplantation have shown some promise; however, most existing studies are small-sample or cross-sectional in nature, and causal relationships remain unclear. Future studies should combine multicenter longitudinal cohorts with multi-omics technologies to further elucidate the translational value of the gut microbiota in PCa screening, risk stratification, prognostic assessment, treatment-response prediction, toxicity monitoring, and personalized microbiome-targeted interventions.},
}

Humans
Male
*Prostatic Neoplasms/therapy/microbiology/metabolism/pathology
*Gastrointestinal Microbiome/physiology
*Prostate/microbiology/pathology/metabolism
Signal Transduction
Fecal Microbiota Transplantation
Animals
Probiotics/therapeutic use
Androgens/metabolism

@article {pmid42775205,
year = {2026},
author = {Yang, Y and Liu, X and Wang, M and Zhu, X and Yang, B and Cao, J and Song, Y and Jiang, G},
title = {The Human Microbiome in Airborne Particulate Matter-Associated Aging-Related Chronic Diseases: An Evidence-Stratified Review.},
journal = {Environment & health (Washington, D.C.)},
volume = {4},
number = {9},
pages = {1856-1876},
pmid = {42775205},
issn = {2833-8278},
abstract = {Airborne particulate matter (PM) exposure is increasingly recognized for its profound impact on human health. Emerging evidence highlights the human microbiome as a plausible intermediary between environmental exposures and host physiological responses. While current research largely focuses on PM's direct toxicological effects, the role of microbiome disruption in mediating aging-related chronic diseases remains underexplored. This review integrates epidemiological data, animal models, and multiomics approaches to examine the impact of PM exposure on microbial communities across the respiratory, gut, and skin microbiomes, with a particular focus on the gut microbiome's role in aging phenotypes. We propose an evidence-stratified PM Exposure-Microbiome-Aging framework, in which the microbiome is considered a plausible exposure-sensitive interface linking environmental exposure to health outcomes, with the gut microbiota representing the most mechanistically developed interface in the current literature. By synthesizing current evidence on microbiome-linked pathways relevant to PM-associated chronic disease risk, this review provides a structured framework to guide future mechanistic and translational research.},
}

@article {pmid42775265,
year = {2026},
author = {Alqahtani, S},
title = {Nano-enabled disruption of bacterial virulence and communication in plant pathosystems: emerging strategies for sustainable disease management.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1924185},
pmid = {42775265},
issn = {1664-462X},
abstract = {Bacterial diseases are a major cause of crop losses worldwide, threatening food security and the sustainability of agricultural production. Traditional management practices heavily rely on antibiotics, resistant strains and copper-based compounds but their continued efficiency is hampered by antimicrobial resistance, ecological issues and rapid evolution of pathogens. Nano-enabled anti-virulence strategies offer a novel approach that specifically targets bacterial virulence instead of the killing of the pathogens alone, which can potentially reduce the pressure for resistance development. This review rigorously investigates mechanistic basis of nano-facilitated interference in bacterial communication and pathogenicity in the plant pathosystems. We evaluated the impact of metallic, metal oxide, silica-based, carbon-based and polymeric nanomaterials on quorum sensing (QS), biofilm formation, extracellular polysaccharide synthesis, motility, secretion pathways, phytotoxin production and host colonization. Particular emphasis is placed on nanoparticle-pathogen interactions, nano-enabled delivery of quorum quenchers, RNA molecules and biological agents, microbiome compatibility, and the integration of these processes within a mechanistic anti-virulence framework. Current evidence indicates that nanomaterial efficacy is strongly influenced by physicochemical properties, target virulence mechanisms, delivery efficiency, and environmental conditions; therefore, no single nanoplatform is universally optimal across plant-pathogen systems. Although smart delivery systems provide opportunities to simultaneously interfere with interconnected virulence pathways, their practical application remains constrained by field stability, biosafety, non-target effects, scalability, and regulatory uncertainty. Overall, advancing nano-enabled anti-virulence technologies from laboratory efficacy toward sustainable crop protection will require mechanism-guided nanomaterial design, microbiome-compatible formulations, rigorous field validation, and comprehensive environmental risk assessment.},
}

@article {pmid42775651,
year = {2026},
author = {Tan, Y and Jiang, X and Ran, J and Gao, Y and Li, Z and Xie, X and Wang, L and Wang, Y and Ou, X and Kang, C and Guo, L and Huang, L and Zhou, T and Yuan, QS},
title = {Light Modulates Growth-Resistance-Quality Trade-Offs in Pseudostellaria Heterophylla via a Light-Induced Microbiota-Root-Shoot Axis.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70897},
pmid = {42775651},
issn = {1365-3040},
support = {2023YFC3503803//National Key R&D Programme of China/ ; 32460079//National Natural Science Foundation of China/ ; QiankexieKJLYRC-[2026]145//the Guizhou High-level Talents Training Support Program/ ; },
abstract = {Plants rely on plant-microbiota interactions to balance growth, defence, and metabolism under stress. Still, the mechanisms governing growth-resistance-quality trade-offs in the shade-tolerant medicinal herb Pseudostellaria heterophylla in understory cultivation systems remain unclear. Here, we integrated phenotypic/photosynthetic/quality assays, rhizosphere microbiome sequencing, leaf transcriptomics, and plant-microbe co-culture experiments to study responses to graded shading. Shading enhanced yield and disease resistance, reshaped the microbiome (enriching beneficial taxa, suppressing pathogenic Alternaria), and induced transcriptional reprogramming-upregulating starch-sucrose/glycerophospholipid metabolism and downregulating flavonoid biosynthesis genes (CHI/CHS) to reduce root-exuded flavonoids that inhibit beneficial bacteria. Functional assays confirmed that these bacteria promote growth and suppress Alternaria-mediated disease under low light. Our findings demonstrate trade-offs in shading coordinates along a bidirectional microbiota-root-shoot axis, establishing a framework for sustainable understory medicinal plant cultivation.},
}

@article {pmid42775881,
year = {2026},
author = {Shahrizal, S and Aazmi, MS and Lim, YAL and Muslim, A},
title = {Parasite-associated microbiomes in Ascaris and Trichuris nematodes: current evidence, challenges, and future directions.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0056926},
doi = {10.1128/msystems.00569-26},
pmid = {42775881},
issn = {2379-5077},
abstract = {Soil-transmitted helminth (STH) parasites, particularly Ascaris lumbricoides and Trichuris trichiura, co-exist and co-evolve with a complex human microbiota within the gut ecosystem. Most research has focused on how parasitic nematodes affect the host gut microbial structure and its consequences. In contrast, studies on the parasites' own associated microbiota remain underexplored. Understanding this gap is crucial, as it adds another layer of complexity to holobiont-holobiont interactions. Driven by the Parasite Microbiome Project, this review summarizes current evidence on Ascaris- and Trichuris-associated microbiomes from both natural and experimental studies, with a focus on their compositions, potential functional roles, challenges, and future directions. Existing findings are largely based on microbiomes associated with the gut of the parasites and are often characterized by transient, host-derived communities acquired through horizontal transmission, which may contribute to parasite survival and host interaction. We therefore emphasize the need to expand investigations to other specific tissues, particularly reproductive organs, as potential sites of a stable and conserved microbiota in STH parasites. Understanding this aspect is essential for advancing our knowledge of parasite-microbiome-host interactions in STH infections and may uncover the potential of microbiome-based therapeutic interventions for STH control and prevention.},
}

@article {pmid42775892,
year = {2026},
author = {Wang, Y-H and Yuan, B-J and Meng, Y and Xu, H-T and Gao, X-Y and Liu, L and Tian, H-D and Wang, X and Zhang, X-H and Zhu, S-L and Johnston, RN and Tang, L and Liu, G-R and Liu, S-L},
title = {A novel human Streptomyces strain redresses malignancy by inducing apoptosis and regaining gut homeostasis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0052826},
doi = {10.1128/msystems.00528-26},
pmid = {42775892},
issn = {2379-5077},
abstract = {UNLABELLED: Colorectal cancer is among the deadliest malignancies globally. The modern therapies do not lead to ideal outcomes due mostly to drug resistance and recurrence. Previously, we treated cancer patients by ameliorating the gut microbiome and achieved curative effects. We hypothesize that anticancer bacteria might be ubiquitous in the gut but suppressed under certain conditions, pointing to a possibility that an ameliorated gut ecology may help regain the abundance or functions of the hypothetical anticancer bacteria. Here, we show our successful isolation and polyphasic characterization of a gut bacterial strain, CGMCC 17111, which exhibited potent suppressive effects on colorectal cancer. CGMCC 17111 belongs to Streptomyces and is most closely related to the type strain of Streptomyces albidoflavus, DSM 40455[T]. However, DSM 40455[T] does not show any appreciable anticancer effects. Genetic, phenotypic, and functional analyses established CGMCC 17111 as representing a novel gut bacterial species with peculiar activities to redress malignancy without eliciting violent inflammatory reactions in the host.

IMPORTANCE: The human gut bacterial strain Streptomyces sp. CGMCC 17111 represents a genetically distinct gut-derived Streptomyces lineage that exhibited antitumor activity in both in vitro and in vivo experimental models. As a resident member of the human gut microbiota, CGMCC 17111 may contribute to host-microbiota interactions that influence tumor-associated biological processes. The findings of this study provide a foundation for future research into gut-derived microbial products and their potential applications in cancer therapy while preserving host physiological homeostasis.},
}

@article {pmid42776010,
year = {2026},
author = {Shen, ZQ and Thuy, TTD and Lu, CK and Nguyen, TS and Tung, CY and Kao, CY and Tsai, TF},
title = {A probiotic Bifidobacterium pseudocatenulatum converts hesperidin to bioactive hesperetin and improves metabolic dysfunction in aging mice.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2736902},
doi = {10.1080/19490976.2026.2736902},
pmid = {42776010},
issn = {1949-0984},
mesh = {*Hesperidin/metabolism ; Animals ; *Probiotics/administration & dosage ; *Aging/metabolism ; Mice ; *Bifidobacterium pseudocatenulatum/metabolism ; Mice, Inbred C57BL ; Male ; Energy Metabolism ; Biotransformation ; },
abstract = {Dietary flavonoids often require microbial metabolism to generate bioactive metabolites that influence host physiology. Hesperidin, a citrus flavanone glycoside, exhibits limited intestinal absorption and depends on gut microbial biotransformation to yield its active aglycone, hesperetin. Hesperetin activates CDGSH iron-sulfur domain 2 (CISD2), a pro-longevity gene whose expression declines with age, and its pharmacological activation has emerged as a strategy to promote healthy aging. Here, we identified a probiotic strain, Bifidobacterium pseudocatenulatum CL256B, that efficiently converts hesperidin to hesperetin via coordinated α-L-rhamnosidase and β-glucosidase activities, achieving ~90% bioconversion efficiency. In naturally aging mice challenged with a Western diet, six-month treatment with probiotic-derived hesperetin significantly improved age-associated metabolic phenotypes, including reduced body weight and adiposity, increased lean mass, enhanced muscle integrity and grip strength, and attenuation of hepatic steatosis. In addition, glucose tolerance, insulin sensitivity, and whole-body energy metabolism were improved. Transcriptomic analyses revealed activation of SIRT1 and HNF4α signaling in the liver and restoration of ribosome homeostasis in skeletal muscle. These findings support a microbiome-enabled strategy in which probiotic-assisted hesperetin bioconversion activates the CISD2 longevity pathway to improve metabolic health during aging.},
}

*Hesperidin/metabolism
Animals
*Probiotics/administration & dosage
*Aging/metabolism
Mice
*Bifidobacterium pseudocatenulatum/metabolism
Mice, Inbred C57BL
Male
Energy Metabolism
Biotransformation

@article {pmid42776130,
year = {2026},
author = {Saqib, U and Ratlamwala, S and Pandey, M and Hajela, K},
title = {Gut feeling: Microbes at the heart of cancer therapy.},
journal = {Oncotarget},
volume = {17},
number = {1},
pages = {430-433},
doi = {10.18632/oncotarget.28919},
pmid = {42776130},
issn = {1949-2553},
}

@article {pmid42776291,
year = {2026},
author = {Mody, S and Laxer, A and Gandhi, J},
title = {Small Intestinal Bacterial Overgrowth in the Pediatric Population: A Review of Pathophysiology, Diagnosis, and Management.},
journal = {Current gastroenterology reports},
volume = {28},
number = {1},
pages = {},
pmid = {42776291},
issn = {1534-312X},
mesh = {Humans ; Child ; *Intestine, Small/microbiology/physiopathology ; Anti-Bacterial Agents/therapeutic use ; *Blind Loop Syndrome/diagnosis/therapy/physiopathology ; Gastrointestinal Microbiome ; },
abstract = {PURPOSE OF REVIEW: Small intestinal bacterial overgrowth (SIBO) remains a significant diagnostic and therapeutic challenge in pediatric gastroenterology. This review summarizes the epidemiology, pathophysiology, diagnosis, and management of SIBO in children, with emphasis on recent advances in microbiome science, evolving diagnostic paradigms, and pediatric-specific clinical considerations.

RECENT FINDINGS: SIBO is increasingly recognized across a broad range of pediatric conditions, including intestinal failure, motility disorders, disorders of gut-brain interaction, and systemic diseases associated with gastrointestinal dysmotility. Diagnosis remains challenging as currently available tests have important limitations and pediatric-specific diagnostic standards are lacking. Management requires a multifaceted approach that combines antimicrobial therapy, correction of underlying anatomic abnormalities or treatment of dysmotility, nutritional support, and emerging microbiome-directed strategies. Future research should focus on validating pediatric-specific diagnostic criteria, defining optimal treatment regimens, and advancing precision approaches to microbiome characterization and modulation.},
}

Humans
Child
*Intestine, Small/microbiology/physiopathology
Anti-Bacterial Agents/therapeutic use
*Blind Loop Syndrome/diagnosis/therapy/physiopathology
Gastrointestinal Microbiome

@article {pmid42776350,
year = {2026},
author = {Yang, S and Huang, Z and Lu, W and Wang, W and Wu, S and Wang, Y and Huang, L and Chen, L and Chen, R and Liang, F},
title = {Beyond Pleasure: Unraveling the Multifaceted Role of Dopamine in Obesity and Metabolic Regulation.},
journal = {Current obesity reports},
volume = {15},
number = {1},
pages = {},
pmid = {42776350},
issn = {2162-4968},
support = {No. 2024AFD238//the Key Project of the Innovation and Development Joint Fund of the Natural Science Foundation of Hubei Province/ ; No. 82274634//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Obesity/metabolism/physiopathology ; *Dopamine/metabolism ; *Energy Metabolism/physiology ; Animals ; Feeding Behavior ; *Dopaminergic Neurons/metabolism ; Reward ; Signal Transduction ; Receptors, Dopamine/metabolism ; Brain/metabolism ; Pleasure ; },
abstract = {PURPOSE OF REVIEW: Obesity is a heterogeneous chronic disease involving dysregulated energy intake and expenditure. Dopamine (DA) has traditionally been recognized as a key regulator of reward-driven feeding. However, accumulating evidence indicates that its functions extend beyond hedonic eating. This review examines the central and peripheral actions of DA in obesity. It focuses on neuronal and receptor diversity, DA-related circuits, metabolic interactions, and responses to anti-obesity interventions.

RECENT FINDINGS: DA neurons and receptor subtypes exhibit substantial molecular, anatomical, and functional diversity. Obesity-related alterations in DA release, receptor function, and downstream signaling vary across brain regions and metabolic contexts. DA regulates food reward, feeding, physical activity, and thermogenesis through VTA-centered reward circuits, hypothalamus-centered feeding circuits, and central-peripheral metabolic pathways. These circuits interact with neuropeptides, neurotransmitter and neuromodulatory systems, and metabolic hormones. In peripheral tissues, local DA signaling regulates gastrointestinal motility, pancreatic hormone secretion, adipose tissue function, and skeletal muscle glucose utilization. Dietary adjustment, exercise, microbiome interventions, bariatric surgery, glucagon-like peptide-1 receptor (GLP-1R) agonists, and other DA-modulating agents may alter these pathways. However, direct evidence that DA modulation mediates their clinical effects remains limited. Current evidence does not support a uniform pattern of dopaminergic (DAergic) dysfunction or a generalized reward-deficiency model in obesity. DA alterations vary across neural circuits, receptor subtypes, tissues, metabolic states, and feeding phases. Most human findings are associative, whereas mechanistic evidence is derived largely from animal models. It remains unclear whether DA alterations precede obesity or result from dietary exposure and metabolic dysfunction. The coordination between central and peripheral DA systems is also poorly defined. Longitudinal and mechanistically informed human studies are needed to identify clinically relevant DAergic biomarkers and therapeutic targets.},
}

Humans
*Obesity/metabolism/physiopathology
*Dopamine/metabolism
*Energy Metabolism/physiology
Animals
Feeding Behavior
*Dopaminergic Neurons/metabolism
Reward
Signal Transduction
Receptors, Dopamine/metabolism
Brain/metabolism
Pleasure

@article {pmid42776402,
year = {2026},
author = {Iswahyudi, I and Garfansa, MP},
title = {Biological degradation of macroplastics and microplastics by greater wax moth larvae (Galleria mellonella): evidence, gut microbiome, and proposed mechanisms.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {42776402},
issn = {1614-7499},
abstract = {Plastic pollution, encompassing macroplastics and microplastics, is an increasing global environmental problem that remains difficult to address using conventional methods. Larvae of the greater wax moth, Galleria mellonella, have attracted attention as a biological model for investigating plastic consumption and transformation. This review synthesizes evidence concerning their interactions with polyethylene, polystyrene, polypropylene, polyvinyl chloride, bioplastics, and complex plastic waste. The reviewed studies used heterogeneous substrates, including macroplastic films, sheets, foams, and fragments, as well as powders and microplastic particles. These categories require distinction because particle size and geometry influence surface-area-to-volume ratio, larval mastication and ingestion, microbial colonization, analytical recovery, and apparent degradation kinetics. Evidence obtained from macroplastic substrates therefore cannot be directly extrapolated to microplastic degradation. Reported consumption and transformation efficiencies varied according to polymer type, substrate form and dimensions, exposure duration, feeding regime, larval density, pretreatment, and analytical method. Gut-associated taxa, including Bacillus, Pseudomonas, Enterococcus, and Enterobacter, were recurrently reported; however, their detection or enrichment indicates association with plastic exposure rather than definitive evidence of direct degradation. Chemical, metabolomic, microbiome, and proteomic findings support proposed oxidative and downstream metabolic pathways, although complete depolymerization, bioassimilation, and mineralization remain insufficiently demonstrated across polymers and size classes. Despite inconsistent experimental designs and variable substrate characterization, G. mellonella remains valuable for identifying candidate enzymes, microorganisms, and host-microbiome interactions. Future studies should use chemically characterized substrates with defined size classes, appropriate controls, molecular-weight analysis, and isotope tracing to distinguish fragmentation from chemical transformation, bioassimilation, and mineralization.},
}

@article {pmid42776412,
year = {2026},
author = {Mello, MJB and Fonseca, BR and Saceloti, GC and de Carvalho, LD and Tonucci, BL and Soares, SMA and Medeiros, JD and Machado, ABF and Gameiro, J},
title = {Extracellular Vesicles from Lactic Acid Bacteria: Emerging Postbiotic Effectors in Host-Microbe Crosstalk.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42776412},
issn = {1867-1314},
abstract = {This article addresses extracellular vesicles derived from lactic acid bacteria (LAB-EVs), which have become fundamental mediators of host-microbe communication, yielding new insights about the molecular mechanisms underlying probiotic and postbiotic activity. The review integrates current evidence on the biogenesis, structural characteristics, and functional roles of LAB-EVs, stressing their capacity to transport bioactive cargos - including proteins, nucleic acids, and metabolites - to host cells. We highlight how LAB-EVs interact with the intestinal epithelial barrier, modulate innate and adaptive immune responses, and contribute to the maintenance of mucosal homeostasis. Particular attention is given to signaling pathways mediated by pattern recognition receptors, macrophage polarization, and the regulation of tight junction proteins, which collectively sustain barrier integrity and immune tolerance. Furthermore, we discuss the therapeutic implications of LAB-EVs in inflammatory bowel disease, epithelial repair, and systemic tissue regeneration. Despite these promising findings, significant obstacles remain in standardizing isolation methods, characterizing vesicle heterogeneity, and developing regulatory systems for clinical translation. Conquering these technical and safety barriers will be essential to consolidate LAB-EVs as safe and effective postbiotic tools in microbiome-based therapies. This review provides a discerning perspective on the current state of LAB-EVs research and describes future directions for their use in human health.},
}

@article {pmid42776479,
year = {2026},
author = {Granata, G and Petrosillo, N and Taglietti, F},
title = {Novel options for the management of C. difficile: a look into the future.},
journal = {Expert review of anti-infective therapy},
volume = {},
number = {},
pages = {},
doi = {10.1080/14787210.2026.2739273},
pmid = {42776479},
issn = {1744-8336},
abstract = {INTRODUCTION: Clostridioides difficile infection (CDI) remains one of the leading causes of healthcare-associated diarrhea; additionally, evidence suggests a growing incidence of community-acquired CDI worldwide. CDI is characterized by substantial morbidity, mortality, and risk of recurrence. CDI underdiagnosis and recurrent CDI represent a major unmet clinical need, highlighting the need for innovative diagnostic, preventive and therapeutic strategies.

AREAS COVERED: This perspective article summarizes emerging approaches that may shape the future management of CDI, including novel microbiome-sparing antimicrobials, fecal microbiota transplantation (FMT), live biotherapeutic products, C. difficile vaccines, bacteriophage-derived therapies, CRISPR-Cas technology and artificial intelligence (AI) applications.

EXPERT OPINION: Future CDI management is expected to evolve toward precision medicine focused on microbiome preservation, prevention of recurrence, and individualized patient care. Novel antimicrobials such as ibezapolstat and CRS3123, phage-derived approaches, and CRISPR-guided antimicrobials may provide highly targeted alternatives to conventional treatments. Microbiota-based therapies will evolve to assume an increasingly central role in reducing microbiota disruption. Simultaneously, advances in diagnostics, vaccine development, and AI-driven predictive tools may improve risk stratification, therapeutic selection, and infection prevention and control. All these innovative strategies have the potential to redefine CDI prevention and treatment, although robust clinical validation and long-term safety data remain essential.},
}

@article {pmid42776568,
year = {2026},
author = {Yang, Z and Shen, X and Lai, Y and Liu, T and Yue, Z and Huang, L and Sun, S and Chen, Y and Qiao, X and Wu, T and Jiang, M and Jiao, Z and Yang, A and Miao, Y and Liu, W and Chen, C},
title = {A Comparative Analysis of Tissue and Digestive Microbiota Composition in Patients With Oral Squamous Cell Carcinoma.},
journal = {Technology in cancer research & treatment},
volume = {25},
number = {},
pages = {15330338261465540},
doi = {10.1177/15330338261465540},
pmid = {42776568},
issn = {1533-0338},
mesh = {Humans ; Female ; *Mouth Neoplasms/microbiology/pathology ; Male ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; *Gastrointestinal Microbiome ; Aged ; Retrospective Studies ; *Carcinoma, Squamous Cell/microbiology/pathology ; *Bacteria/genetics/classification ; Dysbiosis/microbiology ; *Microbiota ; },
abstract = {IntroductionAs the most prevalent malignant tumor in oral cancer, oral squamous cell carcinoma (OSCC) remains incompletely understood, especially its complex interactions with microbiota. This study investigated microbial signatures across tumor tissue and digestive tract niches in patients with OSCC.MethodsThis retrospective cohort study included 28 patients with OSCC who underwent surgical treatment at a tertiary cancer center between 2019 and 2022, along with 14 healthy controls. 16S rRNA gene sequencing was performed to characterize microbial profiles in tumor tissues, as well as oral and gut samples.ResultsTumor tissues exhibited largely similar microbial compositions to adjacent tissues and lymph nodes. However, tumor tissues showed a relatively higher abundance of Fusobacterium and a depletion of Streptococcus. Gut microbiota in patients exhibited dysbiosis, characterized by enrichment of Prevotella, Klebsiella, Lactobacillus, and Streptococcus, while oral microbiota showed enrichment of Streptococcus and Haemophilus. In addition, increased abundance of Lactobacillus in the gut and Bacteroidales in the oral cavity was associated with adverse clinical outcomes (ACO) in OSCC patients.ConclusionThe tissues and digestive microbiota of OSCC patients exhibit heterogeneity. These findings suggest that specific microbial signatures may serve as potential biomarkers for disease detection and progression; however, these associations should be interpreted cautiously and require validation in larger cohorts and mechanistic studies.},
}

Humans
Female
*Mouth Neoplasms/microbiology/pathology
Male
RNA, Ribosomal, 16S/genetics
Middle Aged
*Gastrointestinal Microbiome
Aged
Retrospective Studies
*Carcinoma, Squamous Cell/microbiology/pathology
*Bacteria/genetics/classification
Dysbiosis/microbiology
*Microbiota

@article {pmid42776851,
year = {2026},
author = {Zamir, H and Rauf, F and Jamali, ZH and Khan, S and Zulfiqar, U and Alotaibi, MS and Muminov, M and Abdusamatov, S and Gururani, MA and Korai, SK},
title = {Responses of arbuscular mycorrhizal wheat to salinity: from symbiotic signaling to stress adaptation.},
journal = {Plant signaling & behavior},
volume = {21},
number = {1},
pages = {2733240},
doi = {10.1080/15592324.2026.2733240},
pmid = {42776851},
issn = {1559-2324},
mesh = {*Mycorrhizae/physiology ; *Triticum/microbiology/physiology ; *Symbiosis ; *Signal Transduction ; *Salinity ; *Adaptation, Physiological ; *Stress, Physiological ; },
abstract = {Salinity is a major constraint to wheat productivity, imposing osmotic stress, ionic imbalance, and oxidative pressure that compromise growth and yield. Arbuscular mycorrhizal fungi can improve wheat performance under salinity through effects extending beyond nutrient acquisition. This review examines the context-dependent symbiosis between wheat and arbuscular mycorrhizal fungi, in which reciprocal signaling and resource exchange influence stress adaptation. Direct studies, particularly in durum and bread wheat, indicate that AM colonization can improve K[+]/Na[+] balance, nutrient acquisition, water relations, membrane stability, antioxidant regulation, osmoprotectant metabolism, and stress-responsive gene expression. By contrast, detailed mechanisms of presymbiotic communication, fungal-signal perception, nuclear Ca[2+] decoding, transcriptional accommodation, arbuscule development, and plant-to-fungus lipid transfer have been characterized mainly in AM model plants and other cereals. These conserved pathways provide a mechanistic framework for interpreting, rather than presuming, their operation in salt-stressed wheat. Integrating these evidence levels indicates that AM-associated benefits arise from coordination among ion and water transport, reactive oxygen species and redox regulation, hormonal crosstalk, carbon allocation, and arbuscule-mediated nutrient exchange rather than from enhancement of a single protective trait. The magnitude and nature of these benefits are context-dependent, influenced by wheat genotype, fungal identity, salinity intensity, nutrient status, and carbon cost-benefit trade-offs. We identify priorities for wheat-specific functional validation, spatial and temporal analysis of Ca[2+], reactive oxygen species, hormones, and transport processes, genotype-fungus matching, and multi-environment field assessment. This evidence-aware framework can support microbiome-informed breeding, targeted inoculant development, and integrated management of wheat in salt-affected agroecosystems.},
}

*Mycorrhizae/physiology
*Triticum/microbiology/physiology
*Symbiosis
*Signal Transduction
*Salinity
*Adaptation, Physiological
*Stress, Physiological

@article {pmid42766739,
year = {2026},
author = {Tolman, NJ and Choi, W and Coulter, R and Snyder, ME and Sharma, L and Qin, S and Morrell, ED and Mikacenic, C and Alder, JK and Wang, X and Tabary, M and Zhang, Y and Inman, K and Britton, N and Methe, B and Benos, PV and Bon, J and Robinson, K and Dela Cruz, C and Nguyen, MH and Morris, A and Biswas, PS and Bain, W and Kitsios, GD},
title = {Candida in the lower respiratory tract induces barrier disruption in mice and predicts poor outcomes in mechanically ventilated humans.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {39},
pages = {e2608378123},
doi = {10.1073/pnas.2608378123},
pmid = {42766739},
issn = {1091-6490},
support = {R01 HL176668//HHS | NIH (NIH)/ ; IK2 BX004886//United States Department of Veterans Affairs Biomedical Laboratory R&D Services/ ; R38 HL150207//HHS | NIH (NIH)/ ; T32 HL110849//HHS | NIH (NIH)/ ; R01 HL164177//HHS | NIH (NIH)/ ; R01 DK104680//HHS | NIH (NIH)/ ; R01 HL169265//HHS | NIH (NIH)/ ; R01 HL149676//HHS | NIH (NIH)/ ; S10OD028483//HHS | NIH (NIH)/ ; },
mesh = {Animals ; Humans ; Mice ; *Candida albicans/pathogenicity ; *Respiration, Artificial/adverse effects ; *Candidiasis/microbiology ; Male ; Disease Models, Animal ; Neutrophils ; Female ; *Lung Injury/microbiology ; Mice, Inbred C57BL ; Lung/microbiology ; },
abstract = {Candida albicans (Calb) in the lower respiratory tract (LRT) is considered a rare cause of pneumonia, yet its frequent recovery from LRT secretions of mechanically ventilated patients associates with poor clinical outcomes. To determine whether Calb contributes to lung injury, we conducted a translational investigation spanning two independent, prospective human cohorts, murine models of lung injury, and in vitro assays. In critically ill patients, Calb was the most abundant fungus in LRT specimens, and its detection associated with increased markers of lung injury, prolonged mechanical ventilation, and increased mortality. In a murine model, intratracheal Calb was sufficient to disrupt the air-blood barrier and recruit neutrophils, effects markedly attenuated with heat-killed Calb. Neutrophil depletion led to uncontrolled fungal growth, systemic dissemination and mortality, with surviving mice exhibiting worsened barrier disruption, demonstrating that neutrophils support pathogen control while lung injury is driven by the live organism. Calb induced lung epithelial cytotoxicity as well as barrier disruption in human alveolar epithelial cells at air liquid interface. Yeast-locked mutants without hyphal morphogenesis demonstrated attenuated barrier disruption in human alveolar cells and diminished lung injury in mice, despite higher fungal burden. In human cohort data, LRT microbiome profiles with high Calb abundance and codominant bacterial pathogens predicted worse mortality, and mouse models confirmed that Calb amplifies lung barrier disruption when followed by Pseudomonas aeruginosa inoculation, an effect requiring hyphal morphogenesis. These findings establish that LRT Calb causes direct air-blood barrier disruption through hyphal morphogenesis and amplifies bacterial lung injury, challenging the prevailing view of Candida as an innocent respiratory bystander.},
}

Animals
Humans
Mice
*Candida albicans/pathogenicity
*Respiration, Artificial/adverse effects
*Candidiasis/microbiology
Male
Disease Models, Animal
Neutrophils
Female
*Lung Injury/microbiology
Mice, Inbred C57BL
Lung/microbiology

@article {pmid42766821,
year = {2026},
author = {Hogan, R and Chuntova, N and Ait Abdelmalek, I and Lavallée-Rodrigue, K and Thériault, ER and Guenoun, Z and Boulette, J and Coveny, V and Castillo-Nehme, A and Massicotte, S and Gauthier, L and Savard, D and Tunc, A and Leclair, JL and Mechawar, F and Cotocea, I and Jacmin-Park, S and Borduas-Pagé, S and Juster, RP},
title = {Stress and Resilience Study (STARS) Protocol: A Multimethod Investigation of Minority Stress, Allostatic Load and Cognition in LGBTQ+ Adults.},
journal = {Biopsychosocial science and medicine},
volume = {},
number = {},
pages = {},
doi = {10.1097/PSY.0000000000001528},
pmid = {42766821},
issn = {2998-8756},
support = {FRN 171374//Canadian Institutes of Health Research Sex and Gender Science Chair/ ; },
abstract = {BACKGROUND: Lesbian, gay, bisexual, transgender, and queer (LGBTQ+) people face significant stigma, a structural and social determinant of health that contributes to persistent health disparities. Minority stress theory proposes that both proximal and distal stressors adversely impact health and well-being, while protective factors act as buffers. This study aims to identify mechanisms through which minority stress and protective factors influence physical and mental health in LGBTQ+ adults and to determine whether these processes differ across subgroups as well as in comparison to cisgender heterosexual adults. We hypothesize that greater levels of minority stress will be linked to increased AL, decreased microbiota diversity, and diminished cognitive performance. We further hypothesize that protective factors will moderate these associations.

METHODS: The cross-sectional design aims to recruit a minimum of 360 participants, including diverse LGBTQ+ and cisgender heterosexual subgroups. Data collection will include psychosocial questionnaires, biomarkers assayed from saliva, blood, and stool samples, and a semi-structured interview assessing medical and health history.

DISCUSSION: STARS and the resulting biobank are among the first to integrate psychosocial, cognitive, and multi-system biological measures within LGBTQ+ health research. We will analyze LGBTQ+ subgroups separately rather than as a single heterogeneous population, allowing identification of subgroup-specific risk and protection. Findings are expected to inform the development of targeted, biologically grounded interventions to reduce health disparities in LGBTQ+ communities.},
}

@article {pmid42767039,
year = {2026},
author = {Zheng, B and Hu, Y and Saiqin, G and Zheng, B and Xiang, X},
title = {Aquatic-derived bioactive peptides: molecular mechanisms, digestive fate, and precision nutrition.},
journal = {Food chemistry},
volume = {530},
number = {},
pages = {151204},
doi = {10.1016/j.foodchem.2026.151204},
pmid = {42767039},
issn = {1873-7072},
abstract = {Aquatic-derived peptides (ADPs) are bioactive peptides from fish, shellfish, algae, and aquatic by-products. Reported biochemical activities include antioxidant, ACE-inhibitory, and mineral-binding properties, with immunomodulatory and metabolic functions reported. However, an integrated understanding linking peptide structure, bioavailability, and systemic functions remains incomplete. This review summarizes advances from 2020 to 2026 across in silico, in vitro, animal, and human studies, integrating peptidomics, molecular simulations, transport biology, and multi-omics. Particular attention is given to potential pathways through which ADPs may influence the gut-brain, gut-liver, gut-bone, and gut-skin axes. Emerging delivery strategies, including nanoencapsulation, hydrogel-based carriers, and targeted-release systems, are discussed for peptide stability and gastrointestinal delivery. Finally, we summarize challenges in structural standardization, human mechanistic validation, and regulatory considerations, and discuss future directions including AI-assisted peptide design and precision nutrition. Overall, current evidence supports sequence-dependent bioactivity and selected digestive and transport effects, whereas causal multi-organ and individualized responses remain insufficiently validated in humans.},
}

@article {pmid42767075,
year = {2026},
author = {Arachchilage, PW and Tao, W},
title = {Sustaining thermo-alkaline anaerobic digestion at high organic loading rates by ammonia recovery in a high-rate recirculation line.},
journal = {Water research},
volume = {308},
number = {Pt B},
pages = {126957},
doi = {10.1016/j.watres.2026.126957},
pmid = {42767075},
issn = {1879-2448},
abstract = {Thermophilic anaerobic digestion at high organic loading rates (OLRs) may be inhibited by ammonia. This study coupled thermophilic co-digestion of food waste and sludge with vacuum stripping of ammonia in a recirculation line. OLR increased stepwise from 0.7 to 7.0 g VS/Lreactor/d over 223 d of semi-continuous operation at 55 °C. Starting at OLR 4.0 g/L/d, 25% of working volume in three digesters was replaced once a day with vacuum-stripped digestate having pH 9.80 ± 0.09. Digestate replacement immediately decreased ammonia concentration but resulted in robust alkaline conditions at OLR 5.0-7.0 g/L/d. Methane production in the controls without vacuum stripping stabilized around 2.40 L/L/d for 46 d at OLR 5.0 g/L/d, then began to collapse when total ammonia nitrogen exceeded 1983-2273 mg/L, followed by sharp accumulation of volatile fatty acids to 95.9-308 mmol/L and pH drop to 5.51-5.77. The treatment digesters maintained total ammonia nitrogen below 1018-1085 mg/L while methane production rate increased from 2.83 L/L/d at OLR 5.0 g/L/d to 3.34 L/L/d at OLR 6.5 g/L/d. The treatment digesters became unstable upon daily shocks of pH 8.52-8.64 at OLR 7.0 g/L/d. Digestate microbiome was dominated by fermentative bacteria in genus Defluviitoga and ammonia-tolerant hydrogenotrophic Methanothermobacter. These anaerobic thermophiles were viable upon 5-h vacuum stripping of digestate boiling at pH 9.22-9.80, 65 °C and 25-27 kPa. Methanothermobacter had a strong syntrophic association with Defluviitoga. The interwoven effect of OLR, pH and concentrations of acetic acid, propionic acid and ammonia drove microbial community restructuring and process failure.},
}

@article {pmid42767102,
year = {2026},
author = {Motamedi, H and Derakhshan-Sefidi, M and Kuhestani-Dehaghi, B},
title = {Gut microbiota regulation of the IL-6/STAT3 pathway: Linking hematopoiesis to colorectal cancer progression.},
journal = {International immunopharmacology},
volume = {189},
number = {},
pages = {117452},
doi = {10.1016/j.intimp.2026.117452},
pmid = {42767102},
issn = {1878-1705},
abstract = {BACKGROUND AND AIM: Chronic gut microbiota-driven inflammation fuels colorectal cancer (CRC) progression, but how microbial signals influence systemic immunity and tumor growth remains poorly defined. This review synthesizes evidence on gut microbiota regulation of the interleukin-6 (IL-6)/signal transducer and activator of transcription 3 (STAT3) pathway as the central mechanistic link connecting intestinal dysbiosis, altered hematopoiesis, and CRC progression. Other inflammatory pathways and therapies are discussed only as they intersect with this core axis.

METHODS: A structured search of PubMed, Web of Science, and Scopus (January 2015-December 2024) was performed using CRC, microbiota, IL-6, and STAT3 terms. Included studies provided direct evidence from human CRC tissues, CRC cell lines, or relevant animal models.

RESULTS: Pathobionts such as Fusobacterium nucleatum and enterotoxigenic Bacteroides fragilis directly activate STAT3, whereas beneficial commensals like Clostridium butyricum suppress IL-6/STAT3 signaling. Microbial metabolites-including tryptophan derivatives, short-chain fatty acids, and 4-hydroxybenzeneacetic acid-fine-tune STAT3 activation via host receptors (e.g., aryl hydrocarbon receptor, GPR43). Beyond local effects, chronic IL-6/STAT3 signaling systemically reprograms hematopoiesis: gut-derived inflammatory signals reach the bone marrow, activating STAT3 in hematopoietic stem and progenitor cells and skewing differentiation toward myeloid lineages. This drives expansion of immunosuppressive polymorphonuclear myeloid-derived suppressor cells that infiltrate tumors, inhibit cytotoxic T cell and natural killer cell activity, and enable immune evasion.

CONCLUSION: The microbiota-IL-6/STAT3 interface establishes a gut-bone marrow-tumor axis linking dysbiosis to altered hematopoiesis and CRC progression. Integrative strategies targeting this axis hold promise but require further safety evaluation.},
}

@article {pmid42767106,
year = {2026},
author = {Oliveira, JAVC and Moreira, MIS and Coelho, CPES and Belmok, A and Cena, JA and Dame-Teixeira, N},
title = {Ammonia-oxidizing archaea in host-associated environments and the oral microbiome: Ecological evidence and molecular detection.},
journal = {Archives of oral biology},
volume = {192},
number = {},
pages = {106769},
doi = {10.1016/j.archoralbio.2026.106769},
pmid = {42767106},
issn = {1879-1506},
abstract = {OBJECTIVE: Ammonia-oxidizing archaea (AOA) are key contributors to environmental nitrogen cycling. Reliable detection methods are needed to investigate these low-abundance microorganisms. This review aims to: (1)synthesize and contextualize the evidence on AOA, with an emphasis on the oral microbiome; and (2)evaluate primer sets targeting the amoA gene (encoding ammonia monooxygenase) to support the selection of molecular markers for future investigations of AOA in oral samples.

DESIGN: A narrative review with an exploratory in silico primer analysis was performed. Evidence of AOA detection across environmental and host-associated microbiomes was synthesized, including AOA findings in oral microbiome studies. Published amoA-targeting primer pairs developed for environmental communities were evaluated against reference genomes representing AOA lineages reported in human-associated samples. Reference amoA coding sequences were retrieved from genomes and aligned with each primer pair to compare primer-template compatibility, annealing characteristics, and sequence mismatches across AOA representatives.

RESULTS: AOA was predominantly detected in the oral microbiome based on molecular detection and does not yet distinguish active oral residents from transient organisms or environmental exposure. AOA-related sequences, including signatures assigned to Nitrososphaerota, have been found in oral and caries-associated samples. Although their residency is plausible, stability and metabolic activity still have to be studied. For that, an exploratory analysis showed good performance of four primers, but also the need of more reference sequences to have definitive information.

CONCLUSIONS: Current evidence remains insufficient to define the ecological or functional role of AOA in the oral microbiome. Broader in silico assessment and experimental validation in oral samples are required before specific primer sets can be recommended.},
}

@article {pmid42767155,
year = {2026},
author = {Xu, P and Li, L and Zhang, Y and Jiang, Q and Zhang, Y and Wu, X and Xu, Y},
title = {Threshold effects of organic amendment on acidic red soil remediation: Community assembly and core microbiome-mediated metabolic coupling.},
journal = {Journal of environmental management},
volume = {417},
number = {},
pages = {130999},
doi = {10.1016/j.jenvman.2026.130999},
pmid = {42767155},
issn = {1095-8630},
abstract = {To identify the ecological threshold and microbial mechanisms underlying organic amendment (OA)-mediated remediation of acidic red soils, pak choi was employed as a model plant, and a gradient of digestate-derived OA from 0% to 25% was established. This study integrated soil-plant assessment, community assembly modeling, metagenome-assembled genomes (MAGs), and metabolic network analysis. Both soil functioning and plant growth exhibited nonlinear responses. The optimal OA rate was found to be 15%, which increased the soil quality index and pak choi biomass by 92% and more than 13-fold compared to the control group. In contrast, a 25% OA rate elevated electrical conductivity, induced secondary salinity stress, and reduced productivity and economic returns. Under the 15% OA treatment, the microbial community showed the strongest deviation from neutral community model predictions, indicating that neutral processes had limited explanatory power for community assembly, while deterministic processes associated with altered soil conditions may have played a more important role in community reorganization. Accordingly, core functional MAGs (e.g., MAG302, MAG299, MAG321) were significantly enriched under this treatment, with a total relative abundance 17.3 times that of the control group. These MAGs harbored key genes involved in C, N, P, and S cycling (bglB, atoB, narG, nirK, nosZ, gcd, pst, sqr), suggesting functional complementarity in organic matter degradation, denitrification, phosphorus mobilization, and sulfide oxidation, thereby supporting efficient nutrient turnover and system function. Deviation from this threshold resulted in reduced core MAG enrichment and metabolic network synergy. Overall, this study provides genome-resolved targets for functional strain isolation and synthetic community construction, as well as a mechanistic basis for optimizing OA rates and developing microbiome-based precision remediation strategies.},
}

@article {pmid42767176,
year = {2026},
author = {Delican, D and Kılıçkaya, O and Ozden, O and Ensari, Y},
title = {Novel L-Asparaginases from the human gut microbiome: Genome mining, biochemical characterization, and in vitro anti-leukemic activity.},
journal = {Bioorganic chemistry},
volume = {182},
number = {},
pages = {110550},
doi = {10.1016/j.bioorg.2026.110550},
pmid = {42767176},
issn = {1090-2120},
abstract = {L-asparaginase is essential for acute lymphoblastic leukemia treatment; however, current Escherichia coli and Erwinia chrysanthemi formulations face significant limitations, including immunogenicity, glutaminase-associated toxicity, and short plasma half-life. The human gut microbiome represents an unexplored reservoir of therapeutic enzymes that may offer superior biocompatibility due to host-commensal co-evolution. We employed a systematic genome-mining approach to screen human gut metagenomic data for novel L-asparaginase candidates. Five candidate enzymes from the genera Bacteroides, Ruminococcus, Clostridium, and Prevotella were identified using virtual screening. These enzymes were subsequently codon-optimized and heterologously expressed in E. coli, thereby validating our computational selection strategy. Biochemical characterization revealed optimal activity at alkaline pH (8.0-9.0), robust performance at physiological temperature (37 °C), and excellent storage stability. Ruminococcus_seq7 exhibited exceptional kinetic properties (Km = 0.53 ± 0.19 mM; Vmax = 78.6 ± 5.59 U/mg), whereas Bacteroides_seq104 showed intermediate kinetics (Km = 2.04 ± 0.57 mM; Vmax = 75.4 ± 5.75 U/mg). These lead candidates demonstrated complementary anti-leukemic profiles: Ruminococcus_seq7 showed broad-spectrum activity against T-cell leukemias (IC50: 5.1-8.6 U/mL for Jurkat, MOLT-4, and THP-1), while Bacteroides_seq104 exhibited remarkable potency against THP-1 cells (IC50 = 0.9 U/mL) and successfully overcame resistance in REH cells (IC50 = 36.9 U/mL). Both enzymes maintained >95% viability in healthy HUVEC cells. This study provides proof-of-concept for the discovery of therapeutic enzyme from the human gut microbiome. The identified L-asparaginases exhibited favorable biochemical properties, potent and selective anti-leukemic activity, and enhanced safety profiles. The absence of glutaminase activity and high biocompatibility position these gut microbiome-derived enzymes as promising biotherapeutic scaffolds for next-generation leukemia treatment, pending further optimization of substrate affinity to meet clinical standards.},
}

@article {pmid42767184,
year = {2026},
author = {Zhang, K and Gong, Z and Chen, M and Arain, MA and Zohaib, M and Zhang, L},
title = {Ellagic acid in poultry nutrition: emerging roles in gut health, immunity, and sustainable production.},
journal = {Poultry science},
volume = {105},
number = {12},
pages = {107792},
doi = {10.1016/j.psj.2026.107792},
pmid = {42767184},
issn = {1525-3171},
abstract = {Ellagic acid (EA), is a naturally occurring polyphenolic compound abundant in pomegranate, berries, walnuts, and various agro-industrial by-products, and has attracted increasing interest as a potential phytogenic feed additive for poultry. Its importance arises from the need for effective natural alternatives to antibiotic growth promoters that can simultaneously support bird health, productivity, and production sustainability. This review synthesizes evidence from peer-reviewed studies identified through systematic searches of major scientific databases using combinations of keywords related to EA, poultry, gut health, immunity, oxidative stress, inflammation, growth performance, meat quality, and sustainable production. Relevant peer-reviewed studies were selected based on their direct relevance to EA-mediated physiological, intestinal, immunological, and productive responses in poultry. Literature indicates that EA exerts antioxidant, anti-inflammatory, antimicrobial, and immunomodulatory activities through regulation of oxidative stress responses, inflammatory signaling, intestinal barrier function, and gut microbial communities. Emerging evidence further suggests potential benefits for growth performance, feed efficiency, meat quality, and product stability, while nutrigenomic studies indicate that EA can modulate genes involved in immunity, metabolism, antioxidant defense, and intestinal function. However, its practical application is constrained by limited bioavailability, variable responses, dose optimization, and insufficient long-term evidence. Therefore, this review aims to critically evaluate the mechanistic basis and poultry-specific evidence for EA as a phytogenic feed additive, with particular emphasis on gut-microbiota interactions, immune regulation, oxidative stress and inflammation, productive performance, and highlights the prospects and limitations for sustainable poultry production.},
}

@article {pmid42767274,
year = {2026},
author = {Su, JB},
title = {Letter to the Editor: The Gut Microbiome-Endocrine Axis in Obesity: Mechanisms and Therapeutics.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.70772},
pmid = {42767274},
issn = {1440-1746},
abstract = {Obesity therapeutics is rapidly evolving, and mechanistic frameworks linking the gut microbiome to systemic metabolism are essential for clinical translation. In this letter, I commend the invited review by Mao et al., which elegantly integrates mechanistic insights across the gut-brain, gut-adipose, and gut-pancreas axes, and we propose three extensions to strengthen its clinical relevance. First, I highlight the bidirectional interplay between GLP-1 receptor agonists (GLP-1 RAs)-now first-line obesity pharmacotherapy-and the gut microbiome: GLP-1 RAs enrich Akkermansia muciniphila and short-chain-fatty-acid-producing taxa, while baseline microbiome composition modulates individual drug responsiveness. Second, I argue for greater attention to upper gastrointestinal microbial niches and synthetic biology approaches, including engineered Clostridium butyricum strains that secrete GLP-1 locally within the intestinal lumen. Third, I emphasize the circadian dimension of the gut-endocrine axis-time-restricted feeding restores microbial diurnal oscillations-and its integration with phenotype-guided precision medicine (e.g., "hungry gut," "hungry brain," and "emotional hunger" subtypes). Incorporating these perspectives would transform the review into a practical roadmap for personalized obesity intervention.},
}

@article {pmid42767300,
year = {2026},
author = {Ding, MQ and Zhang, ZR and Wang, JY and He, L and Ding, J and Zhang, LY and Zhao, L and Ren, NQ and Wu, WM and Yang, SS},
title = {Corn Straw Co-Feeding Enhances Polystyrene Biotransformation in Mealworms through Redox Regulation and Gut Microbiota-Host Interactions.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125731},
doi = {10.1016/j.envres.2026.125731},
pmid = {42767300},
issn = {1096-0953},
abstract = {Plastic-degrading insects ("plastivores") have emerged as promising biological systems for mitigating plastic pollution, yet the mechanisms linking dietary supplementation, gut microbiota, and host physiology remain poorly understood. Here, we investigated the effects of corn straw (CS) co-feeding on the biotransformation of polystyrene (PS) microplastics (Mw 142.6 kDa) versus PS plus natural lignocellulose-containing diet CS at a 4:1 (w/w) ratio versus CS as sole at 25.0 ±0.5 °C for 32 days by yellow mealworms (Tenebrio molitor). Compared with a PS-only diet, CS co-feeding increased PS removal efficiency from 47.3% to 58.5% and enhanced the specific PS consumption rate by 38%. Stable-isotope analysis (with a Δδ[13]C of 1.60‰), gel permeation chromatography (GPC), and Fourier transform infrared spectroscopy (FTIR) confirmed enhanced PS depolymerization and biotransformation. CS co-feeding elevated gut ROS levels by approximately 30% while maintaining antioxidant homeostasis. Integrated metabolomic, microbiome, metatranscriptomic, and host transcriptomic analyses revealed coordinated shifts in redox metabolism, microbial activity, and host signaling pathways. The results suggest that redox regulation and gut microbiota-host interactions jointly contribute to enhanced PS biotransformation during CS co-feeding.},
}

@article {pmid42767344,
year = {2026},
author = {Gruber, I and Edinger, M and Poeck, H and Meedt, E and Holler, E and Herr, W and Koelbl, O and Wolff, D and Weber, D},
title = {Early Broad-Spectrum Antibiotic Exposure Is Associated with Increased Relapse after Myeloablative TBI-Based Allogeneic Hematopoietic Cell Transplantation.},
journal = {Transplantation and cellular therapy},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtct.2026.09.037},
pmid = {42767344},
issn = {2666-6367},
abstract = {BACKGROUND: Broad-spectrum antibiotics are frequently administered during the peri-transplant period in patients undergoing allogeneic hematopoietic cell transplantation (allo-HCT). Antibiotic exposure can disrupt the intestinal microbiota and may influence immune recovery and post-transplant outcomes. However, the impact of antibiotic timing on relapse risk after myeloablative total body irradiation (TBI)-based conditioning remains poorly defined.

OBJECTIVE: To investigate whether the timing of therapeutic antibiotic exposure is associated with relapse and other transplantation outcomes in adults undergoing myeloablative TBI-based allo-HCT.

STUDY DESIGN: We retrospectively analyzed 160 adults with acute myeloid leukemia (n = 59) or acute lymphoblastic leukemia (n = 101) undergoing first allo-HCT following myeloablative TBI (8 or 12 Gy). Therapeutic antibiotic exposure was classified as early (initiation before stem cell infusion on Day 0; observed range, Day -20 to -1) or non-early (initiation on Day 0 or thereafter during the initial hospitalization for allo-HCT, or no systemic therapeutic antibiotic exposure during this hospitalization). Endpoints were cumulative incidence of relapse (CIR) and non-relapse mortality (NRM). Associations were evaluated using multivariable models adjusted for disease status, age, diagnosis, and TBI dose. Fine-Gray regression was used for relapse and NRM and Cox regression for OS and PFS. Sensitivity analyses included adjustment for calendar year, ATG use, gut decontamination strategy, and institutional antibiotic protocol era, landmark analyses at Days +30 and +60, and assessment of interactions between early antibiotic exposure and clinically relevant factors.

RESULTS: Median follow-up was 9.8 years. Forty-five patients (28.1%) received early and 115 (71.9%) non-early therapeutic antibiotics. Baseline characteristics were broadly comparable between groups. Early antibiotic exposure was associated with a higher unadjusted CIR than non-early exposure (1-year: 40% vs. 17%; 2-year: 45% vs. 23%; Gray's test P = .006), whereas unadjusted NRM was similar (2-year: 16% vs. 15%; Gray's test P = .690). In multivariable Fine-Gray analyses, early antibiotic exposure was associated with a higher subdistribution hazard of relapse (SDHR 2.00, 95% CI, 1.16-3.43; P = .013), but not with NRM or GVHD. No statistically significant interactions between early antibiotic exposure and disease status, diagnosis, age, or TBI dose were observed. Cause-specific Cox regression confirmed the association between early antibiotic exposure and relapse (CSHR 2.06, 95% CI, 1.20-3.56; P = .009). The association remained consistent after adjustment for calendar year, gut decontamination strategy, ATG use, and the institutional antibiotic protocol era and in landmark analyses at Days +30 and +60. Early antibiotic exposure was associated with inferior OS (HR 1.66, 95% CI, 1.05-2.62; P = .030) and PFS (HR 1.75, 95% CI, 1.12-2.75; P = .014).

CONCLUSION: In adults with acute leukemia undergoing myeloablative TBI-based allo-HCT, early therapeutic antibiotic exposure was associated with increased relapse incidence and inferior survival, without detectable associations with GVHD or NRM. These observational findings support an association between antibiotic timing and leukemia control but do not establish causality or justify withholding clinically indicated antibiotic therapy. Prospective studies integrating detailed antibiotic exposure data, immune reconstitution analyses, and microbiome profiling are needed to determine whether antibiotic timing contributes to post-transplant relapse risk.},
}

@article {pmid42767355,
year = {2026},
author = {Zhang, W and Yu, Y and He, L and Gong, C and Zha, S and Yao, H and Yu, H and Shi, W and Dong, Y and Liu, G},
title = {Bioaccumulation of Three Typical Antibiotics in the Edible Bivalve Tegillarca granosa: Potential Mechanisms and Human Health Implications.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {129194},
doi = {10.1016/j.envpol.2026.129194},
pmid = {42767355},
issn = {1873-6424},
abstract = {Marine bivalves may be exposed to various terrigenous antibiotics, while empirical evidence supporting antibiotic accumulation and potential health risks remains limited. Thus, the accumulation of three typical antibiotics, ciprofloxacin (CIP), erythromycin (ERY), and oxytetracycline (OTC), in an edible bivalve species, blood clam (Tegillarca granosa), was measured in this study. Moreover, microbiological target hazard quotients (mTHQs) and dietary exposure doses of the human gut microbiota (DEGMs) were estimated to assess food safety risks to consumers. Furthermore, the detoxification processes, oxidative status, and energy metabolism in the gill and hepatopancreas were analyzed to explore their potential associations with antibiotic accumulation. Obtained data demonstrated that 28 days of exposure to environmentally realistic levels resulted in significant antibiotic accumulation in blood clams. Fortunately, the mTHQs of antibiotics were far below the critical value, suggesting a low likelihood of direct inhibition of the human intestinal microbiota. Nevertheless, as the DEGM value exceeded the lower boundary of the minimal selective concentration, consuming CIP-contaminated clams may pose a potential concern about antibiotic resistance selection in the intestinal microbiome. Additionally, the contents (or activity) of detoxification enzymes, the expressions of detoxification genes, and the levels of oxidative stress of detoxification organs were all notably altered by antibiotic exposure. Moreover, significant shifts in energy supply were also detected in antibiotic-treated clams. Overall, these findings suggest that antibiotic accumulation in blood clams mag be associated with alterations in detoxification, oxidative status, and energy metabolism, providing insights into the potential toxicological and food safety implications of antibiotic exposure in bivalves.},
}

@article {pmid42767827,
year = {2026},
author = {Nikitina, D and Suk, KT and Torre, A and Idilman, R and Alvares-da-Silva, MR and Lauridsen, MM and Fagan, AC and Kreivenaite, E and Sharma, SP and Nielsen, EJ and Turan, D and Jahagirdar, V and Michalczuk, MT and Khoruts, A and Bojja, SH and Lee, HW and Skieceviciene, J and Sikaroodi, M and Kupcinkas, J and Gillevet, PM and Bajaj, JS},
title = {Hospitalisation in cirrhosis is linked to distinct gut microbiome structural and functional profiles: a multinational metagenomic study.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2026-339378},
pmid = {42767827},
issn = {1468-3288},
abstract = {BACKGROUND: Hospitalisations represent major clinical events in cirrhosis, yet prediction based on clinical variables alone remains limited.

OBJECTIVE: Given the role of the gut microbiome in disease progression, we evaluated whether gut metagenomic profiles are associated with 90-day hospitalisation and provide additional prognostic information beyond clinical features in a multinational outpatient cirrhosis cohort.

DESIGN: We enrolled 679 outpatients with cirrhosis from seven countries and performed stool metagenomic profiling, including taxonomic, functional pathway and antibiotic resistance gene (ARG) analyses, with 90-day follow-up. Machine learning models were developed using clinical and microbiome features for predicting non-elective hospitalisations.

RESULTS: 25% of patients required hospitalisation within 90 days. Hospitalised patients had more advanced cirrhosis, lower microbial diversity which was consistent across countries despite marked variation in microbial composition. Diet had a modest influence on microbiome structure. After adjustment for country, disease severity, cirrhosis aetiology and treatment, 19 bacterial species remained independently associated with hospitalisation, including enrichment of Enterococcus faecium and Veillonella rogosae and depletion of multiple commensal taxa. Functional profiling demonstrated coordinated taxonomic-functional alterations focusing on complex carbohydrate degradation pathways, glycan biosynthesis, lipid and nucleotide salvage pathways and association with antimicrobial resistance mechanisms. The combined clinical-microbiome model significantly outperformed both the clinical-only (area under the curve (AUC) 0.79) and microbiome-only (AUC 0.74) models, achieving an AUC of 0.84.

CONCLUSION: Gut microbiome composition and function are associated with short-term hospitalisation risk and provide additional prognostic information beyond clinical variables in a multicountry cohort. Hospitalisation, regardless of country, is characterised by loss of short-chain fatty acid-producing taxa, functional shifts, ARG and pathway changes.},
}

@article {pmid42767852,
year = {2026},
author = {Crossley, P and Feehily, C},
title = {The who, how, and when of mother-infant microbial sharing.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.07.015},
pmid = {42767852},
issn = {1878-4380},
abstract = {The establishment of the infant gut microbiome is strongly linked to health outcomes throughout life. Recently, Mueller et al. reported that the majority of strains shared between a mother and an infant are gut-derived, as opposed to vaginally derived, and strain sharing could be observed into the second year of life.},
}

@article {pmid42767975,
year = {2026},
author = {Burge, K and Velsko, IM and Salazar-García, DC and Uriarte, MH and Lomba Maurandi, J and Warinner, C},
title = {Comparing the Performance of Double-Stranded and Single-Stranded DNA Libraries for Ancient Oral Microbiome Reconstruction.},
journal = {Molecular ecology resources},
volume = {26},
number = {7},
pages = {e70201},
pmid = {42767975},
issn = {1755-0998},
support = {//Werner Siemens-Stiftung/ ; 390713860//Deutsche Forschungsgemeinschaft/ ; //National Science Foundation/ ; },
mesh = {Animals ; *Microbiota ; *Mouth/microbiology ; *Gene Library ; Humans ; *DNA, Ancient ; Sequence Analysis, DNA ; DNA, Single-Stranded/genetics ; Neanderthals ; *Metagenomics/methods ; },
abstract = {DNA library construction methods can affect the recovery of ancient DNA, thus influencing downstream analyses. While single-stranded library preparation (ssLib) has been shown to outperform double-stranded (dsLib) for highly degraded vertebrate host DNA, especially for samples older than 40,000 years, few studies have examined how library protocols shape ancient microbial community reconstruction. Here, we compare the sequencing output of paired ssLib and dsLib dental calculus libraries generated from 12 Neanderthals and two Chalcolithic humans, prepared using implementations of the Gansauge et al. and Meyer and Kircher protocols, respectively, and sequenced with identical Illumina chemistry. We compared read length and GC%, read duplication and taxonomic profiles across normalization strategies to assess protocol-specific biases. Double-stranded libraries retained a significantly higher proportion of sequenced reads throughout data processing (dsLib 72.1%, ssLib 37.9%), a higher proportion of oral reads (dsLib 9.78%, ssLib 6.75%), significantly longer median oral DNA read lengths (dsLib 57.5 bp, ssLib 50.5 bp) and more GC-rich fragments (dsLib 60.5% GC, ssLib 52.5% GC). In contrast, ssLibs exhibited slightly higher Shannon diversity and a greater proportion of unique reads. Despite these differences, species richness and overall community composition was not significantly different between protocols, with individual and preservation status explaining the most variance. Stratifying reads by length (< 50 bp vs. ≥ 50 bp) resulted in different classification rates but only had minor effects on diversity estimates. Together, these results demonstrate that dsLib and ssLib protocols impose distinct trade-offs and library choice should be guided by study-specific goals.},
}

Animals
*Microbiota
*Mouth/microbiology
*Gene Library
Humans
*DNA, Ancient
Sequence Analysis, DNA
DNA, Single-Stranded/genetics
Neanderthals
*Metagenomics/methods

@article {pmid42768105,
year = {2026},
author = {Dong, D and Walsh, AM and Vatanen, T and Weingart, G and Khdhiri, M and Stampfer, MJ and Vehik, K and Franzosa, EA and Huttenhower, C and Wang, DD and , },
title = {Gut microbiome maturation in early childhood interacts with host genetics to predict type 1 diabetes risk.},
journal = {Nature metabolism},
volume = {},
number = {},
pages = {},
pmid = {42768105},
issn = {2522-5812},
abstract = {Prospective evidence linking early-life microbiome development and host genetics with type 1 diabetes (T1D) risk is limited. Here, we describe how gut microbiome maturation and host genetics influence T1D risk in the TEDDY study. We analysed 12,151 longitudinal metagenomes and host genetic data from 887 children at high genetic risk for T1D followed for up to 6 years. We identify three microbiome maturational patterns: Early Matured, Late Matured and Early Plateaued, driven primarily by non-linear changes in species from the Bifidobacterium and Ruminococcus genera. The Early Matured pattern is enriched in galactose metabolism and exhibits higher production of aromatic amino acids and B-group vitamins at early follow-ups, whereas the Early Plateaued pattern has increased microbial production of branched-chain amino acids. Notably, the Early Plateaued pattern is associated with a threefold elevated risk of T1D, whereas other patterns are not associated with T1D risk. Furthermore, we find that host genetic variants related to antimicrobial and antiviral immune responses modify the association between the Late Matured pattern and T1D risk. These findings highlight the role of early microbial exposures and host genetics in T1D susceptibility.},
}

@article {pmid42768289,
year = {2026},
author = {DeVito, A and Kimm-Drapeau, AL and Higgins, WJ and Montecillo, M and Bernstein, MN and Wright, S and Li, C and Bal, I and Dadhania, DM and Selbach, F and Lee, JR},
title = {Serial Blood Microbiome Profiles in Kidney Transplant Recipients Reveal Evidence of Circulating Gut and Non-Gut Derived Microbial DNA.},
journal = {Transplant infectious disease : an official journal of the Transplantation Society},
volume = {},
number = {},
pages = {e70323},
doi = {10.1111/tid.70323},
pmid = {42768289},
issn = {1399-3062},
support = {R21 AI 173849/NH/NIH HHS/United States ; R01DK139249/NH/NIH HHS/United States ; R01AI184528/NH/NIH HHS/United States ; UL1TR002384//National Center for Advancing Translational Sciences of the National Institutes of Health/ ; 539291308//German Research Foundation/ ; },
abstract = {BACKGROUND: In this study, we sought to investigate the utility of 16S rRNA gene sequencing of whole blood in kidney transplant recipients and to assess a link between the gut microbiota and the blood microbiota.

METHODS: We recruited 63 kidney transplant recipients who provided 163 whole blood specimens over the first 140 days after transplantation. We profiled the blood microbiome using 16S rRNA gene sequencing of the V4-V5 hypervariable region. We additionally evaluated the gut microbiota via metagenomic sequencing in a subset of kidney transplant recipients who had matched blood specimens.

RESULTS: We generated a median of 19 959 sequences per blood specimen. We discovered that most whole blood microbiome profiles consisted of mitochondrial DNA (mean relative blood abundance greater than 99%) with minimal microbial DNA detected. Out of the 163 blood specimens, 83 (51%) had detectable microbial 16S rRNA sequences and there were 92 distinct taxa detected at the genus level. Among the 51 kidney transplant recipients, blood microbial 16S sequences were persistently detected in 10 kidney transplant recipients over time, intermittently detected in 29 kidney transplant recipients over time, and not detected in 12 kidney transplant recipients over time. Among 76 matched blood-fecal specimens, 9 blood specimens had detectable gut microbial 16S sequences, which were also detected in 3 of the 9 fecal specimens.

CONCLUSION: Our study finds minimal detection of bacterial DNA in the blood microbiome in kidney transplant recipients and evidence of gut bacterial DNA in the bloodstream of kidney transplant recipients.},
}

@article {pmid42768305,
year = {2026},
author = {Avershina, E and Birkeland, EE and Bucher-Johannessen, C and Rounge, TB},
title = {CRISPR-Cas immune repertoires as an ecological record of bacterial interactions with mobile genetic elements in the human gut.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2734649},
pmid = {42768305},
issn = {1949-0984},
mesh = {Humans ; *Interspersed Repetitive Sequences ; *Bacteria/genetics/classification/immunology/isolation & purification/virology ; *Gastrointestinal Microbiome/genetics ; *CRISPR-Cas Systems ; Plasmids/genetics ; Feces/microbiology ; Middle Aged ; Metagenome ; Norway ; Female ; Diet ; Bacteriophages/genetics ; Gastrointestinal Tract/microbiology ; },
abstract = {Bacteria in the human gut influence host physiology and disease risk, but their ecology is strongly shaped by mobile genetic elements (MGEs) such as phages and plasmids. Past interactions between bacteria and MGEs can be inferred from CRISPR-Cas cassettes, which contain short DNA fragments derived from invading elements. To lay the groundwork for research on the impact of such interactions on the human host, we constructed an extended microbiome resource comprising 1.7 K prokaryotic mOTUs, 19.5 K viral vOTUs, and 24.2 K plasmid PTUs, using fecal shotgun metagenomes from 1034 adults over 55 y of age residing in South-East Norway. We also recovered 74.2 K unique CRISPR-Cas cassettes to map past bacteria-MGE interactions and assessed their associations with the human diet and lifestyle factors. CRISPR-Cas spacers, and which viruses and plasmids they targeted, varied substantially within bacterial species, but were predominantly directed towards cohort-specific MGEs. Moreover, bacteria were more likely to target MGEs present in the same sample, consistent with local exposure. Plasmid MGEs were more often targeted by Type II CRISPR-Cas cassettes, whereas viruses were more likely to be targeted by Type I CRISPR-Cas cassettes. Bacteria also shared more targets within taxonomic families than across families, where mobilizable plasmids were more frequent among the targets. CRISPR-Cas cassettes mirrored microbiome associations to human demographic and lifestyle factors and enabled the recovery of dairy-associated B. animalis. Together, this research provides a large-scale resource and a structured analysis of bacteria-MGE interactions in the gut microbiome and their contribution to microbial ecosystem dynamics.},
}

Humans
*Interspersed Repetitive Sequences
*Bacteria/genetics/classification/immunology/isolation & purification/virology
*Gastrointestinal Microbiome/genetics
*CRISPR-Cas Systems
Plasmids/genetics
Feces/microbiology
Middle Aged
Metagenome
Norway
Female
Diet
Bacteriophages/genetics
Gastrointestinal Tract/microbiology

@article {pmid42768312,
year = {2026},
author = {Rosenn, EH and Zuniga, M and Lipshitz, M and Fox, E and Engel, M and Pasinetti, GM},
title = {The cervicovaginal gut microbiota axis as a key determinant of systemic physiology.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2726648},
pmid = {42768312},
issn = {1949-0984},
mesh = {Humans ; Female ; *Vagina/microbiology/immunology ; *Gastrointestinal Microbiome/physiology ; Dysbiosis/microbiology ; *Cervix Uteri/microbiology ; *Microbiota ; },
abstract = {The gut and vaginal microbiomes are both essential to human health, yet they have largely been studied in isolation. Gut microbiota are central to host metabolism, immunity, and the gut-brain axis, while the vaginal microbiome, typically dominated by Lactobacillus species, protects against infection and shapes reproductive outcomes. Although dysbiosis at either site has been linked to systemic disease, the possibility that these communities are interrelated and that the vaginal microbiome could serve as a clinically accessible proxy for systemic microbial states remains underexplored. This represents a clear gap in the literature. In this review, we examine physiological connections between digestive and genitourinary systems, explore how endocrine and immune networks exert dual control across compartments, and analyze correlations between dysbiosis and disease states. We then consider emerging technologies for microbiome analysis and their clinical and translational implications, including the potential for vaginal microbiome profiling to function as a diagnostic surrogate for the gut and as a complementary biomarker platform for prediction of neurologic disease risk. By building a systems-level understanding of the joint immuno-microbial interactome, evaluating advances in computational and omics-based technologies, and situating these tools within emerging healthcare frameworks, we argue that the cervicovaginal-gut microbiota axis is a unique and understudied source for medical discovery.},
}

Humans
Female
*Vagina/microbiology/immunology
*Gastrointestinal Microbiome/physiology
Dysbiosis/microbiology
*Cervix Uteri/microbiology
*Microbiota

@article {pmid42768338,
year = {2026},
author = {Torki, S and Qorbani, M and Ejtahed, HS and Etebarian, A},
title = {Alterations of oral microbiome in oral potentially malignant disorders: a systematic review.},
journal = {BMC oral health},
volume = {26},
number = {1},
pages = {},
pmid = {42768338},
issn = {1472-6831},
mesh = {Humans ; *Microbiota ; *Mouth Neoplasms/microbiology ; *Mouth/microbiology ; Leukoplakia, Oral/microbiology ; Lichen Planus, Oral/microbiology ; *Precancerous Conditions/microbiology ; Oral Submucous Fibrosis/microbiology ; },
abstract = {BACKGROUND AND OBJECTIVES: Oral potentially malignant disorders (OPMDs), including conditions such as Oral lichen planus, Oral leukoplakia, Proliferative verrucous leukoplakia and Oral submucous fibrosis are associated with an increased risk of oral squamous cell carcinoma. Emerging evidence suggests that alterations in the oral microbiome may contribute to the pathogenesis of these disorders and their malignant transformation. This systematic review aimed to synthesize current evidence on oral microbiome composition and diversity in patients with OPMDs.

METHODS: A comprehensive literature search of PubMed, Scopus, Web of Science, and Google Scholar was conducted to identify eligible human studies published through August 2025. Studies evaluating oral microbiome profiles in patients with clinically and/or histopathologically diagnosed oral potentially malignant disorders (OPMDs) were included. Data on study characteristics, sampling and analytical methods, microbial diversity, and differentially abundant taxa were extracted independently by two reviewers. Risk of bias was assessed using the Newcastle-Ottawa Scale. Owing to substantial clinical and methodological heterogeneity, findings were synthesized qualitatively.

RESULTS: A total of 56 studies were included, comprising 30 studies of Oral lichen planus, 9 of Oral leukoplakia, and 17 examining other OPMDs. 16srRNA sequencing was mostly used and whole unstimulated saliva was the most frequently collected specimen. The most prevalent microbial phyla identified in OPMD patients included Firmicutes, Proteobacteria, and Fusobacteria, but the direction and magnitude of changes varied across OPMD subtypes and sampling methods. Several studies reported an increase in pathogenic species such as Porphyromonas and Prevotella, while commensal bacteria like Streptococcus were less abundant. Findings concerning microbial richness and diversity were inconsistent.

CONCLUSIONS: Oral microbial dysbiosis is a common feature of oral potentially malignant disorders; however, a reproducible microbial signature has not yet been established. Substantial heterogeneity in study design, sampling strategies, and analytical approaches limits causal inference and clinical applicability. Future standardized longitudinal studies are needed to clarify the role of the oral microbiome in malignant transformation and its potential utility as a prognostic biomarker.

TRIAL REGISTRATION: Prospero registration number: CRD42024516735.},
}

Humans
*Microbiota
*Mouth Neoplasms/microbiology
*Mouth/microbiology
Leukoplakia, Oral/microbiology
Lichen Planus, Oral/microbiology
*Precancerous Conditions/microbiology
Oral Submucous Fibrosis/microbiology

@article {pmid42768386,
year = {2026},
author = {Pateriya, D and Tanwar, A and Sharma, VK},
title = {Insights into the dynamics of antibiotic resistance genes in the human gut microbiome across populations.},
journal = {Gut pathogens},
volume = {18},
number = {1},
pages = {},
pmid = {42768386},
issn = {1757-4749},
support = {INSACOG//Biotechnology Industry Research Assistance Council/ ; BT/PR50613/MED/32/981/2023//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
abstract = {The human microbiome serves as a reservoir of antibiotic resistance genes (ARGs), collectively known as the resistome, which has crucial implications for human health. However, the distribution of ARGs across diverse bacterial taxa and their variation across populations, disease states, and body sites remain less well understood. Here, we comprehensively profiled the human resistome using genomic and metagenomic data. Our analysis included 4,744 species-representative gut bacterial genomes and 452 oral bacterial genomes, along with gut metagenomic data from 10,230 individuals across 58 studies encompassing 5,388 healthy and 4,842 disease-associated samples, including underexplored non-Western cohorts. Our analysis revealed variation in the gut resistome across population groups and countries. The oral microbiome exhibited a distinct resistome profile with lower ARG prevalence compared to the gut. Across multiple datasets, ARG abundance was generally higher in inflammatory bowel disease samples compared to healthy samples. Pathogenic taxa such as Enterobacter, Citrobacter, Escherichia, and Klebsiella carried the highest number of ARGs, including clinically relevant ARGs, whereas abundant commensals like Bacteroides and Prevotella contributed to the baseline resistome. Notably, population-level differences in ARG composition appeared to be linked to microbial community structure. Shared ARGs between commensal and pathogenic bacteria provided clues to horizontal gene transfer. These findings provide crucial insights into the ecological and population-level factors shaping the gut resistome, highlighting the roles of both pathogens and commensals in the maintenance and dissemination of antimicrobial resistance.},
}

@article {pmid42768390,
year = {2026},
author = {Macey, MC and Ilieva, V and Stephens, BP and Tatton, B and Balcha, E and Schwenzer, SP and McGenity, TJ and Miruts, H and Gomez, F and Cavalazzi, B and Olsson-Francis, K},
title = {Metagenomic insights into the taxonomic and metabolic diversity of the microbiome of Lake Karum in the Danakil Depression, Ethiopia.},
journal = {Environmental microbiome},
volume = {21},
number = {1},
pages = {},
pmid = {42768390},
issn = {2524-6372},
support = {Grant agreement No 871149//Europlanet 2024 RI project - Expert Exchange/ ; Grant Agreement No 654208//Europlanet 2020 RI project - Transnational Access/ ; Expanding Excellence in England, grant number 124.18//Research England/ ; },
abstract = {BACKGROUND: Hypersaline environments are dynamic ecosystems, the chemistry of which is significantly influenced by climate change, which in turn impacts the microbiota and biogeochemical processes. This study investigates the microbiome of Lake Karum, a hypersaline lake in the Danakil Depression, Ethiopia, with a particular focus on genome-based potential of climate-relevant biogeochemical processes.

RESULTS: The microbiomes of Lake Karum sediments and waters were dominated by halophilic Archaea (Halobacteriota) and Bacteria (Bacteroidota, Pseudomonadota, and Cyanobacteriota), with significant variation in community composition among sites, reflecting geochemical heterogeneity. Despite these taxonomic differences, sediment and water metagenomes exhibited broadly overlapping functional gene profiles. Genes involved in denitrification, carbon monoxide oxidation, osmotic stress tolerance, and utilisation of osmolytes were widespread and predominantly affiliated with Halobacteriales, indicating their pivotal role in nitrogen and carbon cycling. Genome‑resolved analyses revealed substantial intrageneric variation in metabolic potential within dominant halobacterial lineages as well as bacterial candidate phyla, including Candidatus Bipolaricaulota and Candidatus Salsurabacteriota, which encode genes linked to trace-gas metabolism and nitrogen cycling. Notably, a high‑quality metagenome‑assembled genome assigned to the Candidatus Salsurabacteriota was recovered that possesses novel combinations of functional genes not previously reported for this lineage.

CONCLUSION: This study provides a comprehensive genome‑resolved assessment of the taxonomic and functional diversity of the Lake Karum microbiome and identifies microbial taxa with the potential to drive key carbon, nitrogen, and sulfur cycling processes in a hypersaline lake. By revealing previously unrecognised metabolic capabilities within bacterial candidate phyla and highlighting intrageneric functional heterogeneity among dominant halophilic Archaea, this work advances understanding of how hypersaline microbial communities contribute to biogeochemical cycling in extreme environments.},
}

@article {pmid42768438,
year = {2026},
author = {Melby, MC and Timlin, CL and McCracken, FB and Rojas, CA and Carchedi, C and White, B and Cassibry, L and Blake, A and Coon, CN},
title = {Impacts of a fresh-frozen dog food on fecal consistency and microbiome in colony dogs.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skag303},
pmid = {42768438},
issn = {1525-3163},
abstract = {Fresh-frozen dog diets are becoming increasingly popular among pet owners, but little is known regarding the impact of this diet on canine gut health and the microbiome. This study evaluated the impacts of a fresh-frozen versus an extruded kibble diet on the fecal consistency, metabolites, and microbiome in 16 adult Labrador Retrievers (average age 4.2 ± 0.26 years; average weight: 25.7 kg ± 3.18 kg) over the course of 6 months. Dogs were randomly assigned to one of the two diets in a parallel design. Feces were collected at baseline, 3 months, and 6 months for short-chain fatty acid, ammonia, and microbiome analyses. An additional sample was collected at 1 month for microbiome analysis. Fecal microbiome was analyzed via 16S rRNA gene sequencing. Fecal consistency scores were recorded daily, and body weights and body condition scores were recorded weekly. Data were analyzed across time and treatments using a repeated measures ANOVA. Results showed that fecal consistency was improved in the dogs fed the fresh diet, with differential changes detected shortly after the transition phase onto the test diets (P < 0.01). Fecal butyrate concentrations were greater in the fresh group (P < 0.01), and fecal valerate concentrations fluctuated more in the kibble group while the fresh group remained more consistent over time (P = 0.05). No differences were observed in fecal moisture, pH, ammonia, or other fecal short-chain or branched-chain fatty acids. General dog health was not negatively impacted by either diet, as observed through weight maintenance and veterinary wellness exams. Diet type impacted fecal microbiome composition, as shown by differences in beta diversity between the fresh and kibble groups (P < 0.01). Additionally, microbiomes of dogs fed a fresh diet were enriched in short-chain fatty acid producers such as Turicibacter sanguinis, Ruminococcus, and Clostridium compared to dogs fed kibble. Overall, the fresh diet increased fecal consistency and fecal butyrate, though other fecal parameters were not different.},
}

@article {pmid42768445,
year = {2026},
author = {Due, EM and Munezero, O and Burrough, ER and Burkey, TE and Fernando, SC and Gabler, NK},
title = {Effect of dietary fiber and tributyrin on nursery pig health, performance, bacteriome, and volatile fatty acid concentration.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skag302},
pmid = {42768445},
issn = {1525-3163},
abstract = {Dietary fiber and volatile fatty acid (VFA) metabolites have been shown to improve intestinal health and reduce post-weaning diarrhea in pigs. Therefore, the current study was conducted to evaluate the impact of insoluble and soluble dietary fiber sources and butyrate on the intestinal health and growth performance of nursery pigs. It was hypothesized that insoluble and soluble dietary fiber sources or butyrate supplementation would improve nursery pig performance and enteric health. Over two replicates, a total of 610 weaned pigs were assigned to one of five dietary treatments (n = 17 pens/treatment): 1) control diet (CON), 2) wheat bran (WB), 3) beet pulp (BP), 4) corn distiller's dried grains with solubles (DDGS), and 5) CON plus 0.20% tributyrin. Diets were fed in two phases (14 and 28 days). Pigs were confirmed positive for rotavirus A, B, and C and F18 enterotoxigenic Escherichia coli (E. coli). There was no effect of dietary fiber or tributyrin on the proportion of pigs with normal, soft, or liquid fecal consistency in weeks 1, 2, or 3 of the study (P > 0.10). There were no significant differences in average daily gain (ADG), average daily feed intake (ADFI), or gain-to-feed ratio (G:F) among treatments in phase 1 (P > 0.10). Tributyrin tended to increase ADFI in phase 2 compared to CON and BP (P = 0.063), and increased ADFI overall compared to CON (P = 0.031), but had no significant effect on final body weight (P > 0.10). Dietary treatment did not affect ileal, colonic, or fecal VFA concentrations on days 7, 10, or 42. However, on day 22, CON pigs had greater fecal acetate, propionate, valerate, and total VFA concentrations than one or more fiber treatments (P < 0.05), with butyrate tending to be greater than WB (P = 0.080). Bacterial community analysis revealed no effect of dietary fiber treatment on alpha diversity, except for DDGS, where day 14 and day 42 communities differed (P = 0.014). Beta-diversity analysis identified distinct clustering between time points (P = 0.001) and between treatments (P = 0.024) using the Bray Curtis dissimilarity matrix. Overall, although bacterial community composition was affected, the inclusion of wheat bran, beet pulp, corn DDGS, or tributyrin did not significantly impact intestinal health, pathogen load, VFA concentration, or growth performance in nursery pigs.},
}

@article {pmid42768897,
year = {2026},
author = {Watson, CD and Lem, AJ and Bissett, A and Cando-Dumancela, C and Gardner, MG and Hodgson, RJ and Liddicoat, C and Peddle, SD and Breed, MF},
title = {Restoration Plantings Promote Functional Recovery of Soil Fungi.},
journal = {Molecular ecology},
volume = {35},
number = {18},
pages = {e70552},
pmid = {42768897},
issn = {1365-294X},
support = {LP240100073//Australian Research Council/ ; UOWX2101//Ministry of Science and Innovation, New Zealand/ ; //Australian Government under the National Environmental Science Program's Resilient Landscapes Hub/ ; },
mesh = {*Soil Microbiology ; *Fungi/genetics/classification ; Soil/chemistry ; Biodiversity ; Ecosystem ; *Environmental Restoration and Remediation ; Phosphorus/analysis ; },
abstract = {The global scale of biodiversity loss and land degradation has prompted the establishment of ambitious international restoration agreements, with the goal of returning biodiverse and functional ecosystems. Restoration interventions are often vegetation focused, and while they yield positive, measurable outcomes, they do not always lead to whole ecosystem recovery. Although soil microbiota such as fungi are integral ecosystem components (e.g., as symbionts, decomposers and drivers of nutrient cycling), they are largely absent from restoration planning and monitoring. Therefore, how fungi respond to ecosystem restoration, especially over longer time scales, is largely unknown. Here, we show trends of reduced dominance of soil fungal pathotrophs across a restoration chronosequence 6 years after initial sampling. This decline in soil fungal pathotrophs is consistent with continued functional recovery, despite little evidence of additional whole-community fungal recovery. Fungal community composition was also strongly associated with soil properties, particularly phosphorus, consistent with persistent land-use legacies constraining further recovery. The observed change in fungal functional composition is consistent with previous studies reporting higher relative abundance of pathotrophic fungi in ecologically degraded sites. Our study provides valuable insights into how soil fungal communities respond to restoration plantings and highlights the importance of repeated sampling. Our findings also demonstrate the value of considering both taxonomic and functional indicators when assessing ecosystem recovery.},
}

*Soil Microbiology
*Fungi/genetics/classification
Soil/chemistry
Biodiversity
Ecosystem
*Environmental Restoration and Remediation
Phosphorus/analysis

@article {pmid42768967,
year = {2026},
author = {Kang, L and Jia, YJ and Jiang, N and Hu, DM and Mao, JF},
title = {Weed control, maize (Zea mays L.) metabolism, and rhizosphere microbiome of hollow mesoporous silica nanoparticles loaded with S-metolachlor and ZnO quantum dots.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.71268},
pmid = {42768967},
issn = {1526-4998},
support = {//the Excellent Postdoctoral Program of Xinjiang Uygur Autonomous Region/ ; },
abstract = {BACKGROUND: Conventional pesticide formulations employ large amounts of organic solvents, raising concerns regarding their environmental contamination, pesticide residues, and potential toxicity to non-target organisms. Hollow mesoporous silica nanoparticles (HMSNs) are non-toxic to both animals and plants, making them a suitable candidate for pesticide loading and delivery studies.

RESULTS: HMSNs with an average particle size of 165 nm were synthesized using a self-template method. Fluorescein isothiocyanate was successfully conjugated to the HMSNs to enable the investigation of their transport and distribution in maize. The S-metolachlor (S-met) loading efficiencies of HMSN and HMSN@ZnO quantum dots (QDs) carriers were 18.7% and 10.7%, respectively. Application of nanocarriers did not adversely affect weed control efficacy, maize growth, or plant antioxidant enzymatic activity. No detrimental effect of the nanocarriers was observed on crop and weed control, and no clear differences were observed in metabolites and soil microbial dynamics. HMSN@S-met@ZnO QDs treatment increased the proportions of lysobacter and blastococcus compared to the control, whereas the EC treatment exhibited a relatively different distribution pattern for sphingobacterium and pseudomonas. Actinophytocola algeriensis and sphingomicrobium were selectively enriched in nanocarriers-based treatments relative to the control and conventional S-met EC treatment. The active microbial community was predominantly composed of species affiliated with entotheonella and pseudomonas based on the metatranscriptomic species profiling.

CONCLUSION: The nanocarrier formulations were safe for maize and maintained effective weed control, and significantly modulated metabolites of maize plants and the microbial community composition in the soil. © 2026 Society of Chemical Industry.},
}

@article {pmid42768978,
year = {2026},
author = {Boettcher, SR and Kenney, RM and Everson, NA and Kashat, I and Soyad, A and Tengler, G and Ramesh, M and Veve, MP},
title = {Clinical Experience with Oral Fecal Microbiota Spores (Vowst®) in a Health System Specialty Pharmacy.},
journal = {American journal of health-system pharmacy : AJHP : official journal of the American Society of Health-System Pharmacists},
volume = {},
number = {},
pages = {},
doi = {10.1093/ajhp/zxag293},
pmid = {42768978},
issn = {1535-2900},
abstract = {PURPOSE: To describe clinical experience and patient outcomes with orally administered fecal microbiota spore (FMS) capsules, live-brpk, for prevention of recurrent Clostridioides difficile infection (rCDI) after workflow implementation into a local health-system specialty pharmacy (HSSP) model.

SUMMARY: rCDI carries substantial morbidity, and the approval of orally administered FMS capsules introduced a novel prevention option with new challenges in medication access, prior authorization, and cost. To meet this need, an HSSP workflow was adapted to support acquisition of FMS for adults receiving a prescription order. Over the period from June 1, 2023, through December 31, 2024, a total of 72 FMS prescriptions were generated for 50 patients, of which 29 (58%) ultimately obtained the medication. Patients reflected a real-world population, the median (IQR) age was 70 (55-79) years, 55% were men, the median (IQR) number of previous CDI episodes (including the proximal episode) was 2 (1-3), and 25% were immunocompromised. Among patients who received FMS, rCDI occurred in 2 (7%) patients at eight weeks. Of the 21 prescriptions obtained through the HSSP, 62% required a single prior authorization (PA) attempt, and the median (IQR) time to dispensing from prescription generation was 16 (12-20) days. Copayments ranged from $0 to >$2,500, with most patients (18, 86%) receiving FMS for less than $6.

CONCLUSION: Implementation of an adapted HSSP FMS medication workflow resulted in medication access for more than half of patients and offers a practical, adaptable model for integrating high-cost microbiome therapies into specialty pharmacy practice.},
}

@article {pmid42769362,
year = {2026},
author = {McKelvey, MC and Einarsson, GG and Carson, J and Kadoom, A and Brown, RR and Campbell, C and Jackson, A and McDowell, C and Clarke, M and Copeland, F and Ferguson, K and McLeese, RH and Convery, R and Hill, AT and De Soyza, A and Shahidi, M and Kelly, M and Carroll, M and Gatheral, T and Anwar, M and Duckers, J and Flight, W and Hurst, JR and Ionescu, AA and Loebinger, MR and Sullivan, AL and Chalmers, JD and Downey, DG and Tunney, MM and O'Neill, B and McAuley, DF and Elborn, JS and Bradley, JM and Taggart, CC},
title = {Effects of hypertonic saline and/or carbocisteine on sputum rheology in bronchiectasis: CLEAR-EME.},
journal = {ERJ open research},
volume = {12},
number = {5},
pages = {},
pmid = {42769362},
issn = {2312-0541},
abstract = {BACKGROUND: Mucoactives such as hypertonic saline (HTS) and carbocisteine are widely used in the treatment of bronchiectasis, though there is insufficient evidence to support their use. The aim of this mechanistic sub-study, embedded within the CLEAR trial, was to characterise the properties of sputum from patients with bronchiectasis and to assess whether treatment with HTS and/or carbocisteine altered these properties.

METHODS: In CLEAR, patients were randomised to receive HTS, carbocisteine, HTS plus carbocisteine or standard care, and sputum samples were collected at randomisation (baseline) and at 2 and 8 weeks post-randomisation. Sputum viscoelasticity was determined by rotational plate rheometry. Biomarkers were quantified by ELISA and microbiome composition was assessed by next-generation sequencing. The primary outcome was differences in sputum viscoelasticity between groups at 2 weeks following the commencement of treatment.

RESULTS: Sputum viscoelastic properties were not reduced by 2 or 8 weeks of treatment with HTS and/or carbocisteine (n=6-15 per group). Sputum biomarker levels and bacterial community composition were similar across groups at 2 or 8 weeks. At baseline, viscoelasticity (crossover point σc) was positively correlated with interleukin-8 (r=0.49, p=0.012) and greater relative bacterial dominance (r=0.35, p=0.041).

CONCLUSIONS: These data do not support the use of HTS or carbocisteine to alter sputum viscoelasticity, inflammatory marker levels or bacterial community composition in patients with bronchiectasis.},
}

@article {pmid42769424,
year = {2026},
author = {Yang, Y and Jia, W and Xie, J and Qiu, J and Li, C and He, C and Luo, M and Zhao, L and Wang, Y},
title = {Microbiome network remodeling is associated with soil lipid metabolism in safflower under different cropping system-location combinations: an omics-based dissection.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1898896},
pmid = {42769424},
issn = {1664-302X},
abstract = {This study investigated differences in safflower rhizosphere soil microbiota and metabolic functions among three planting pattern-location combinations (PLMEs): soybean-safflower rotation at Chenghai (CH), tobacco-safflower rotation at Longpan (ZYHY), and apple orchard intercropping at Lijiang (LJ). Each PLME comprised 6 plots. Bacterial α-diversity was significantly higher in the CH system, whereas fungal α-diversity peaked under the ZYHY system. Correlation analysis showed that bacterial α-diversity was negatively correlated with available potassium, while fungal α-diversity was negatively correlated with catalase activity. Microbial community structures significantly varied among the different PLMEs, with redundancy analysis indicating that bacterial variation was mainly explained by electrical conductivity, while fungal variation was mainly explained by available phosphorus. Under the adopted network-construction procedure, sample-specific subnetwork analysis suggested that the bacterial subnetworks in CH were more topologically complex and stable, while the fungal subnetworks in ZYHY were more complex than those in other treatments; no marked differences in fungal subnetwork stability were observed. These findings remain exploratory. Although dominant microbial taxa were unchanged, their relative abundances varied notably. Non-targeted metabolomics analysis identified significant shifts in glycerophospholipid metabolism, with five key metabolites, including L-serine, phosphatidylethanolamine, and lecithin, serving as biomarkers strongly correlated with genera such as Gaiella, Microlunatus, and Mortierella. An exploratory structural equation modeling analysis revealed significant positive associations of bacterial α-diversity and bacterial network complexity with glycerophospholipid metabolism, and a significant negative association of fungal network complexity with glycerophospholipid metabolism. Overall, our results suggest that the CH system is associated with higher bacterial diversity, greater microbial network stability, and alterations in key metabolic pathways. Future studies involving direct measurements of plant growth, yield, and disease incidence are required to validate whether such rhizosphere changes are associated with agronomic benefits.},
}

@article {pmid42769442,
year = {2026},
author = {Xu, J and Mei, W and Shi, J and Li, J and Liu, M and Yang, Z and Tian, N and Hu, Y},
title = {Rhizosphere microbial diversity analysis reveals enrichment of biocontrol taxa in healthy tobacco plants and yields novel antagonists against Phytophthora nicotianae.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1889242},
pmid = {42769442},
issn = {1664-462X},
abstract = {INTRODUCTION: Tobacco black shank (TBS), caused by Phytophthora nicotianae, is a devastating disease. Current control relies heavily on chemical pesticides, which pose risks of resistance and environmental pollution. Biological control using rhizosphere microorganisms offers a sustainable alternative. However, the relationship between the composition of the rhizosphere microbiome and its suppressive activity against P. nicotianae has not yet been systematically elucidated.

METHODS: High-throughput sequencing was used to compare the differences in rhizosphere microbiota of healthy and diseased plants from multiple field sites in Yunnan, China, combined with culture-dependent isolation and screening of antagonistic microorganisms against P. nicotianae.

RESULTS: No significant differences in bacterial or fungal diversity were found between healthy and diseased rhizosphere soils. Despite this overall similarity in diversity, healthy rhizosphere soil was significantly enriched in biocontrol genera, including Pseudomonas, Paenibacillus, and Massilia. A total of 204 bacterial and 95 fungal strains were isolated, among which 64 bacteria and 41 fungi exhibited antagonistic activity against P. nicotianae. Four strains (710, 733, 1088, and 1145) showed the strongest inhibitory effects and were identified as Bacillus amyloliquefaciens, Yokenella sp., Metapseudomonas resinovorans, and Bacillus subtilis, respectively. Moreover, the soluble metabolites and volatile metabolites produced by these strains also inhibited P. nicotianae. Notably, this study provides the first evidence that Y. regensburgei and M. resinovorans function as biocontrol agents against P. nicotianae, with mycelial inhibition rates reaching 72.29% and 38.96%, respectively.

DISCUSSION: These results reveal the enrichment of specific biocontrol taxa in healthy tobacco rhizosphere and identify Y. regensburgei and M. resinovorans as novel antagonists against P. nicotianae. This study expands the strain library for TBS biological control and provides promising candidates for developing green management strategies.},
}

@article {pmid42769480,
year = {2026},
author = {Zhang, X and Sun, C and Yang, B},
title = {Microbiome-based nutrition and the gut-muscle axis: emerging perspectives for athletic performance and recovery.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1927715},
pmid = {42769480},
issn = {2296-861X},
abstract = {The gut microbiota has emerged as a significant regulator of exercise adaptation, recovery, and skeletal-muscle function, giving rise to the idea of the gut-muscle axis as a potential target in sports nutrition. This review summarizes current data on how microbiome-targeted nutritional approaches, such as probiotics, prebiotics, synbiotics, post-biotics, and polyphenol-rich dietary interventions, effect physiological processes related to athletic performance. Human research suggests that certain therapies may enhance endurance capacity, recuperation, gastrointestinal health, immunological function, and body composition, however, these advantages are typically strain-, formulation-, and population-specific. Further experimental evidence indicates that microbial metabolites, especially urolithins and short-chain fatty acids, may control anabolic signaling, inflammatory responses, mitochondrial function, and redox balance via pathways involving AMPK, PGC-1α, and associated molecular networks. However, there is still no direct validation of these pathways in human athletes, and the majority of mechanistic information comes from cellular and animal models. The translation of existing findings into evidence-based sports nutrition recommendations is further constrained by significant variation in study design, intervention characteristics, participant populations, and outcome measures. More robust longitudinal human investigations incorporating strain-resolved microbiome profiling, microbial metabolomics, and standardized physiological and performance outcomes are needed in order to identify effective intervention strategies and establish causal mechanisms.},
}

@article {pmid42769587,
year = {2026},
author = {Pourbahrighesmat, S and Tojjari, A and Laliotis, G and Saeed, A},
title = {Interkingdom microbiome physiology in colorectal cancer: barrier dysfunction, immune-metabolic signaling, and therapeutic resistance.},
journal = {Frontiers in physiology},
volume = {17},
number = {},
pages = {1922297},
pmid = {42769587},
issn = {1664-042X},
abstract = {Colorectal cancer develops within a physiologically altered intestinal ecosystem. Epithelial barrier disruption, chronic inflammatory signaling, immune remodeling, and metabolic rewiring reshape host-microbial interactions in this niche. Although most colorectal cancer microbiome reviews have emphasized bacterial taxa, the gut ecosystem is inherently multi-kingdom, comprising bacteria, fungi, bacteriophages, and other viral elements that interact with one another and with the host. In this review, we propose that the clinically relevant unit of the colorectal cancer microbiome is often not a single organism but a configured interkingdom whose functional output depends on local physiology. Throughout, we distinguish human observational associations from mechanisms demonstrated in experimental models and from prospectively validated clinical effects. We synthesize evidence linking the bacteriome, mycobiome, and phageome to colorectal carcinogenesis, immune modulation, metabolic signaling, and therapeutic response. We highlight context-dependent mechanisms, including the paradoxical effects of Fusobacterium nucleatum, fungal regulation of myeloid and inflammasome pathways, phage-mediated control of bacterial virulence, and cross-kingdom metabolic circuits involving butyrate, succinate, bile acids, lactate, and arginine. We further propose, as a conceptual framework requiring longitudinal validation, that therapeutic resistance may sometimes reflect a treatment-selected ecological state rather than the action of a single resistance-conferring microbe. Finally, we address the reproducibility challenges raised by low-biomass intratumoral microbiome studies and outline minimum methodological standards for future multi-kingdom investigations. A framework centered in physiology, attentive to contamination, and organized around interactions may improve biomarker development and support rational microbiome-directed strategies in colorectal cancer.},
}

@article {pmid42769625,
year = {2026},
author = {Baram, S and Sarathi, A and Bakke, M and Arumugam, M and Pedersen, AML},
title = {Oral health and oral microbiota composition in patients with Parkinson's disease: a case‒control study.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2726612},
pmid = {42769625},
issn = {2000-2297},
abstract = {INTRODUCTION: Parkinson's disease (PD) is associated with motor and non-motor dysfunctions that may influence oral homeostasis. An altered microbiota has been linked to PD, yet oral microbial changes remain poorly characterized. This case‒control study aimed to determine if the oral microbiota, the oral health status, and salivary secretion differ between patients with PD and matched controls.

MATERIALS AND METHODS: Forty participants (20 with PD and 20 controls) underwent standardized oral examinations, neurological scoring (Hoehn & Yahr; UPDRS II-III), and measurements of unstimulated (UWS) and stimulated whole saliva (SWS) flow rates. Microbial profiling of SWS samples and dorsal tongue scrapes was performed using long-read 16S rRNA gene sequencing (V1-V8). Alpha/beta diversity and differential abundance analyses were performed.

RESULTS: Patients with PD exhibited significantly lower UWS flow rates, higher plaque scores, and higher prevalence of xerostomia and drooling. Dental status and gingival inflammation did not differ between the groups. Microbial richness and Shannon diversity were lower in tongue scrapes from the PD group, but not in saliva samples. Veillonella, Prevotella and Streptococcus dominated the microbiota in both groups. Fusobacterium periodonticum and pseudoperiodonticum were consistently more enriched in both saliva and tongue microbiota of patients with PD.

CONCLUSION: Patients with PD have lower UWS flow rates and a shift toward a more anaerobic, biofilm-adapted oral ecosystem, particularly on the tongue. The tongue microbiome may potentially serve as a sensitive biomarker of PD-related dysbiosis.},
}

@article {pmid42769647,
year = {2026},
author = {Zhao, X and Wang, H and Liu, Y and Cao, L},
title = {Beyond the tumor microenvironment: a hierarchical immune-circuit model of immune checkpoint blockade resistance.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1919294},
pmid = {42769647},
issn = {2234-943X},
abstract = {Immune checkpoint blockade (ICB) produces durable tumor control in a subset of patients, yet resistance is usually interpreted through tumor-intrinsic lesions or suppression within the tumor microenvironment (TME). We propose that ICB resistance can also be organized as failure of a multiscale antitumor immune circuit comprising local immune execution, regional immune education in tumor-draining lymph nodes (TDLNs), and systemic immune calibration by the host. In this model, "hierarchical" denotes nested functional dependence rather than one-way anatomical control: local killing depends probabilistically on antigen visibility, access, and a renewable supply of tumor-reactive cells; nodal priming depends on competent dendritic-cell licensing and host immune fitness; and reciprocal feedback can propagate or repair failure across compartments. We first define the canonical CD8-dominant substrate that ICB can amplify, including cross-presentation, costimulation, progenitor-exhausted T-cell maintenance, trafficking, and target-cell recognition, while retaining alternative CD4, natural killer, intratumoral antigen-presenting-cell, and tertiary lymphoid routes. We then evaluate local, regional, and systemic resistance mechanisms, four directional feedback axes, and context-dependent patterns in pancreatic cancer, melanoma, non-small-cell lung cancer, microsatellite-stable colorectal cancer, hepatocellular carcinoma, and prostate cancer. Evidence from animal perturbation, human spatial and clonal studies, and clinical trials supports individual circuit components but remains heterogeneous. Randomized perioperative regimens demonstrate disease- and setting-specific benefit, whereas negative randomized results and mixed or limiting early-phase signals across innate agonism, stromal or metabolic targeting, radiotherapy combinations, and systemic conditioning constrain therapeutic extrapolation. We therefore present compartment-resolved biomarkers and adaptive trial designs as research hypotheses, not a validated classifier or standard-care algorithm. The framework will be useful only if prespecified multiscale measurements improve prediction beyond tumor-only models and if mechanism-matched interventions produce the expected pharmacodynamic repair before clinical benefit is attributed to the circuit.},
}

@article {pmid42769662,
year = {2026},
author = {Goodall, T and Jones, B and Thorpe, AC and Griffiths, RI and Gweon, HS and Read, DS and Pywell, R and Busi, SB},
title = {Antimicrobial resistance as a signature of soil restoration across a 143-year chronosequence.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag250},
pmid = {42769662},
issn = {2730-6151},
abstract = {Restoring agriculturally degraded habitats to species-rich grasslands is a vital conservation objective. During restoration, how the soil resistome matures alongside microbial community composition and function remains unclear. Here, we tested two competing hypotheses: whether the soil resistome co-occurs through a microbial structural maturation, in which soil restoration is associated with higher-order biotic interactions, or whether antimicrobial resistance (AMR) is instead associated with the competitive pressures and high bacterial taxonomic richness found in disturbed, eutrophic arable land. Using a unique land-use chronosequence on Salisbury Plain, UK, we investigated the trajectory of ecosystem reassembly following the cessation of agricultural activity. Our results demonstrate that AMR abundance increases significantly with restoration age, reaching a maximum in >143-year-old soils. The strongest predictor of this rise in AMR abundance was an increasing microbial eukaryotic signature rather than increasing microbial density, suggesting that resistome expansion is not associated with generalized spatial competition, but rather, co-occurs with structural maturation of the microbiome. We observed an order of magnitude increase in antibiotic biosynthetic potential, dominated by the emergence of streptomycin clusters. Microbial reorientation during soil maturation mirrors the expansion of a core resistome comprised of ancient, intrinsic mechanisms, such as Major Facilitator Superfamily (MFS) efflux pumps and RNA Polymerase-Binding Protein A (RbpA) target protection, in older soils. We demonstrate that endogenous AMR is a hallmark of healthy, restored soil ecosystems rather than a marker of anthropogenic soil degradation.},
}

@article {pmid42769680,
year = {2026},
author = {Zelca, E and Gudra, D and Karklina, D and Ustinova, M and Lunge, M and Fridmanis, D and Rumba-Rozenfelde, I and Daugule, I},
title = {New Insights into the Composition of the Early-Life Gut Microbiome: A Metagenomic Analysis of Fecal Samples in Children Up to 18 Months of Age.},
journal = {Pediatric gastroenterology, hepatology & nutrition},
volume = {29},
number = {5},
pages = {359-373},
pmid = {42769680},
issn = {2234-8646},
abstract = {PURPOSE: To determine the gut microbiome composition and associated factors in infants.

METHODS: Cross-sectional study was conducted in primary healthcare centers including healthy children up to 18 months of age. Parents of children answered a questionnaire and bring a fecal sample of their child. Fecal samples were analyzed using shotgun sequencing. The relative abundances of taxonomic profile were detected and compared with associated factors.

RESULTS: In the study were included 91 children. The most abundant taxonomic units belonged to phyla: Bacillota, Bacteroidota, Actinobacteria. In contrast, the most abundant species were Bifidobacterium longum and Bifidobacterium breve, demonstrating an age-appropriate microbial composition. The viral fraction mainly consisted of bacteriophages, with the most abundant viral family being Tospoviridae. Nevertheless, more than 50 rather new taxonomic entities were observed to cause shifts in the taxonomic units of the infant gut microbiome in association with perinatal antibacterial therapy, type of delivery, feeding type in the first 6 months of life. Higher relative abundance of Kitasatospora spp. MMS16 BH015 was associated with C-section and antibacterial treatment during delivery. A total of 302 antimicrobial resistance genes were identified, the most frequently encountered genes were associated with glycopeptide antibiotic resistance: vanG, vanT, vanW, vanY and adeF. The distribution of ARGs did not differ among different age groups.

CONCLUSION: Metagenomic sequencing provides broader insights into the composition of the gut microbiome, emphasizing the presence of unusual species associated with environmental and perinatal factors. Perinatal antibacterial treatment may have a greater impact on the infant microbiome than was previously estimated.},
}

@article {pmid42769727,
year = {2026},
author = {González, M and Galarza-Arévalo, GE and Garzón-Romero, C and Romero, MP},
title = {Antimicrobial Strategies for Chronic Cutaneous Ulcers: From Preclinical Nanotechnology to Clinical Practice.},
journal = {International journal of nanomedicine},
volume = {21},
number = {},
pages = {624310},
pmid = {42769727},
issn = {1178-2013},
mesh = {Humans ; Chronic Disease ; Biofilms/drug effects ; Wound Healing/drug effects ; *Skin Ulcer/therapy/microbiology/drug therapy ; Animals ; Nanotechnology/methods ; Nanomedicine ; *Anti-Infective Agents/therapeutic use ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {Chronic cutaneous ulcers represent a growing global public health challenge, affecting an estimated 1-2% of the population in high-income countries and imposing a substantial socioeconomic burden through prolonged hospitalizations, repeated outpatient visits, increased risk of amputation, and significant impairment of patients' quality of life. Standard wound care centered on debridement, moisture-balancing dressings, and systemic antibiotics fails to resolve a large proportion of cases, particularly those complicated by polymicrobial biofilm infection and antimicrobial resistance, underscoring an urgent need for more effective therapeutic strategies. Despite the growing body of work on individual therapeutic modalities, no prior review has jointly evaluated clinically validated adjunct therapies and preclinical nanoplatform evidence for chronic cutaneous ulcers within a single, biofilm-ecology-centered framework, the gap this review addresses. This review critically evaluates current clinical and preclinical advances in the treatment of chronic cutaneous ulcers, with a focus on novel therapeutic modalities and emerging nanotechnology-based approaches. Clinically, the available evidence indicates that low-intensity ultrasound, electrical microcurrent therapy, photodynamic therapy, regenerative biomaterials, oxygen-based interventions, and advanced topical therapies may improve wound contraction, reduce microbial burden, relieve pain, and enhance tissue repair when used as adjuncts to standard care. At the preclinical level, metallic, polymeric, inorganic, and hybrid nanoplatforms can simultaneously target resistant bacteria and biofilms, stimulate angiogenesis, regulate inflammatory signaling, and support extracellular matrix remodeling. Recent advances in ulcer therapy are moving the field beyond passive wound coverage toward mechanism-driven treatments that actively modulate the chronic wound microenvironment. Despite this progress, current clinical evidence remains inconsistent and is often limited by small patient cohorts and non-standardized protocols. This highlights the pressing need for rigorous translational research to incorporate multifunctional bioactive platforms into well-supported, ulcer-specific therapeutic strategies.},
}

Humans
Chronic Disease
Biofilms/drug effects
Wound Healing/drug effects
*Skin Ulcer/therapy/microbiology/drug therapy
Animals
Nanotechnology/methods
Nanomedicine
*Anti-Infective Agents/therapeutic use
Anti-Bacterial Agents/therapeutic use

@article {pmid42769745,
year = {2026},
author = {Ratnadewi, N and Husin, F and Mose, JC and Syamsunarno, MRAA and Irianti, S},
title = {Gut and Gastric Dysbiosis in Hyperemesis Gravidarum: A Scoping Review of Microbiome-Targeted Evidence and Translational Pathways.},
journal = {International journal of women's health},
volume = {18},
number = {},
pages = {632969},
pmid = {42769745},
issn = {1179-1411},
abstract = {BACKGROUND: Hyperemesis gravidarum (HG) is defined by severe nausea and/or vomiting beginning in early pregnancy, impaired ability to eat or drink normally, and a marked restriction of daily activities. Although gastrointestinal dysbiosis has been proposed in HG, its role remains uncertain within the emerging growth differentiation factor 15 (GDF15)-centered model of susceptibility.

METHODS: Guided by PRISMA-ScR, this scoping review searched PubMed/MEDLINE, Scopus, Web of Science, publisher websites, and reference lists for contemporary evidence published between 1 January 2021 and 2 May 2026. Pre-2021 foundational publications were excluded from the charted evidence map and included-study count and were cited only as methodological or biological background.

RESULTS: Thirty-six sources of evidence were synthesized across five thematic domains. Direct human studies identified associations between HG and altered microbial diversity or composition, as well as gastric Helicobacter pylori exposure, but taxonomic findings were inconsistent and no reproducible diagnostic signature emerged. Mendelian randomization implicated Coprococcus 2, Ruminococcus, and Turicibacter, whereas observational studies could not resolve whether dysbiosis preceded symptoms or followed vomiting, dietary restriction, medication exposure, or hospitalization. Pregnancy-context and mechanistic studies supported plausible pathways involving bile acids, short-chain fatty acids, intestinal barrier function, inflammation, and gut-brain signaling, but these remain indirect for HG. GDF15-centered endocrine susceptibility had the strongest mechanistic support. Pregnancy probiotic and prebiotic studies provided safety and proof-of-concept data, while HG-specific efficacy evidence remained insufficient.

CONCLUSION: Current evidence supports dysbiosis as an associated modifier, consequence, or endotype marker rather than an established independent cause of HG. Priority studies should use Windsor-compatible definitions, early longitudinal sampling, harmonized sequencing and metabolomic methods, concurrent assessment of GDF15 and nutritional status, and biologically stratified trials of confirmed H. pylori infection or reproducible functional dysbiosis.},
}

@article {pmid42769873,
year = {2026},
author = {McGovern, CJ and Tako, E},
title = {Microbial exopolysaccharides as bioactive modulators of intestinal health: a systematic review.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1885879},
pmid = {42769873},
issn = {2296-861X},
abstract = {Microbial exopolysaccharides (EPS) are secondary metabolites produced and secreted by microorganisms during fermentation. Their structure and physicochemical properties depend on the microbial strain and growth conditions, making them highly versatile for application in the food industry. Current investigations have expanded to include their use as a bioactive compound, providing health benefits to the host without the introduction of live microorganisms, as in the case with probiotics. This systematic review analyzed 28 in vivo studies to assess the effects of EPS on intestinal health. Evidence suggests that EPS modulates the gut microbiome, enhances intestinal epithelium integrity, alters inflammatory biomarkers, affects colonic morphology, and increases short-chain fatty acid (SCFA) production. Overall, this systematic review primarily focuses on colonic health, with limited consideration of the role of EPS during small intestinal digestion. The findings support the potential of microbial exopolysaccharides as bioactive macromolecules that may improve intestinal health. This systematic review has been registered with the International Prospective Register of Systematic Reviews database (PROSPERO) (ID: CRD420261292367).},
}

@article {pmid42769920,
year = {2026},
author = {Zhang, L and Yin, Y and Li, R and Wang, G and Li, L and Yu, Y and Lu, W},
title = {Space radiation health risks to hematopoietic, neural, and gastrointestinal systems in astronauts.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1926972},
pmid = {42769920},
issn = {2296-2565},
mesh = {Humans ; *Astronauts ; *Space Flight ; *Cosmic Radiation/adverse effects ; *Gastrointestinal Tract/radiation effects ; Animals ; *Hematopoietic System/radiation effects ; *Radiation Exposure/adverse effects ; *Nervous System/radiation effects ; },
abstract = {The rapid progress in global deep space exploration presents astronauts with a complex space radiation environment that substantially exceeds that of near-Earth orbit. Space radiation primarily consists of galactic cosmic rays (GCRs) and solar particle events (SPEs), which exhibit strong penetrative capability and considerable biological damaging potential. These factors may induce persistent oxidative stress, mitochondrial dysfunction, DNA double-strand breaks, and repair pathway challenges. This review examines the impacts of space radiation on the hematopoietic, neural, and gastrointestinal systems. Human spaceflight observations indicate that exposure to space radiation may be associated with bone marrow suppression, reduced lymphocyte counts, diminished thymic output, and immune dysfunction, which may heighten susceptibility to infection and inflammation. Preclinical animal model research indicates that even low doses of space-relevant radiation may induce cognitive decline, memory deficits, anxiety-like behaviors, and neurodegenerative alterations, though these findings remain to be validated in human astronauts. Proposed mechanisms include impaired hippocampal synaptic plasticity, neuroinflammatory activation, and mitochondrial energy metabolism imbalance. Radiation has been shown to compromise the intestinal epithelial barrier, induce intestinal stem cell senescence, and disturb gut microbiome equilibrium in preclinical models. These gastrointestinal alterations may potentially exacerbate neurocognitive dysfunction and promote chronic inflammation via the gut-brain axis, based on mechanistic evidence from animal studies. Currently, there remains an insufficient systematic understanding of the cumulative effects, sex differences, and individual susceptibility associated with long-term low-dose composite radiation exposure. Integrating aerospace medicine is imperative to address these knowledge gaps and safeguard astronaut health during future deep-space missions.},
}

Humans
*Astronauts
*Space Flight
*Cosmic Radiation/adverse effects
*Gastrointestinal Tract/radiation effects
Animals
*Hematopoietic System/radiation effects
*Radiation Exposure/adverse effects
*Nervous System/radiation effects

@article {pmid42769962,
year = {2026},
author = {Duraj, J and Kowalczyk, K and Żelechowska, P and Agier, J},
title = {Immune-nutritional interactions in endometriosis: current evidence and future perspectives in disease management.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1940772},
pmid = {42769962},
issn = {1664-3224},
mesh = {Humans ; Female ; *Endometriosis/immunology/diet therapy/metabolism/etiology ; Animals ; Disease Management ; *Nutritional Status ; Diet ; Gastrointestinal Microbiome ; Diet, Mediterranean ; },
abstract = {Endometriosis is a chronic estrogen-dependent inflammatory disorder affecting approximately 10% of women of reproductive age. It remains a major contributor to chronic pelvic pain, infertility, and reduced quality of life. Despite considerable advances in elucidating its genetic, hormonal, and immunological basis, current therapeutic strategies frequently provide incomplete symptom relief, may be associated with adverse effects, and fail to prevent disease recurrence. Therefore, increasing attention has been directed toward modifiable environmental factors, particularly nutrition, as supplementary strategies for disease management. This review comprehensively examines the evidence connecting dietary patterns and bioactive food components with the immunopathogenesis of endometriosis. It explores the potential role of nutrition in modulating key biological processes involved in endometriosis pathophysiology and progression, including immune dysregulation, chronic inflammation, oxidative stress, angiogenesis, estrogen metabolism, and gut microbiota imbalance. Particular emphasis is placed on the Mediterranean diet and selected dietary components, such as omega-3 fatty acids, vitamin D, resveratrol, epigallocatechin-3-gallate, and probiotics, as well as dietary interventions like low-FODMAP and gluten-free diets. The findings are discussed in relation to mechanistic evidence and emerging observations. Substantial clinical data supporting specific dietary interventions are scarce, and most dietary guidelines are based on preliminary research. Future investigations that incorporate nutritional interventions alongside immune profiling, microbiome analysis, and multi-omics technologies may facilitate the development of individualized nutritional strategies as adjuncts within the framework of precision medicine for women affected by endometriosis.},
}

Humans
Female
*Endometriosis/immunology/diet therapy/metabolism/etiology
Animals
Disease Management
*Nutritional Status
Diet
Gastrointestinal Microbiome
Diet, Mediterranean

@article {pmid42770043,
year = {2026},
author = {Wuopio, J and Graells, T and Lin, YT and Schillemans, T and Moll, JM and Eklund, AC and Nielsen, HB and Larsson, A and Engström, G and Orho-Melander, M and Johnson, LS and Ärnlöv, J},
title = {Associations between sodium intake and gut microbiota composition.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1889723},
pmid = {42770043},
issn = {2296-861X},
abstract = {INTRODUCTION: High salt intake is associated with adverse health outcomes. Emerging evidence highlights the importance of the gut microbiome in human health, but large-scale human data on salt intake and the microbiome are limited. We examined the cross-sectional association between estimated 24-h sodium excretion (est24hNa) and the gut microbiome in a population-based cohort.

METHODS: We included 9,220 participants from the Swedish SCAPIS cohort with available shotgun metagenomic sequencing of fecal samples and urine analyses. We estimated the 24-h sodium excretion using the Kawasaki formula. Alpha diversity was assessed using the Shannon and inverse Simpson indices, and beta diversity using Bray-Curtis dissimilarity. Functional potential was evaluated using Gut Microbial Modules. Associations were analyzed using mixed linear regression models.

RESULTS: Alpha diversity was inversely associated with est24hNa, but associations were attenuated after adjustment for BMI and were not significant in fully adjusted models. Beta diversity was associated with est24hNa, although the explained variance was small (R2 < 0.001). Higher est24hNa was associated with 75 microbial species, including lower abundance of 27 species and higher abundance of oral-associated taxa such as Streptococcus spp. and Veillonella. It was also associated with increased abundance of pathways involved in microbial energy metabolism and carbohydrate fermentation.

CONCLUSION: Higher est24hNa was associated with selected gut microbiome features, including a higher abundance of several oral-associated taxa and differences in inferred functional capacity for energy metabolism and carbohydrate fermentation. These findings identify microbial patterns associated with sodium exposure that may be relevant to cardiometabolic health.},
}

@article {pmid42770647,
year = {2026},
author = {Mishra, S and Saxena, S},
title = {Probiotics as Functional Dietary Interventions for Gut Health, Immune Modulation, and Overall Well-Being: A Systematic Review.},
journal = {Clinical pediatrics},
volume = {},
number = {},
pages = {99228261480530},
doi = {10.1177/00099228261480530},
pmid = {42770647},
issn = {1938-2707},
abstract = {BACKGROUND: The pediatric gut microbiome influences immune maturation, neurodevelopment, and disease susceptibility. Probiotic supplementation has been investigated across multiple childhood conditions, yet strain-specific efficacy remains inconsistent.

OBJECTIVE: The objective of this review is to systematically evaluate strain-specific probiotic interventions in children and assess clinical efficacy, safety, and mechanistic pathways.

METHODOLOGY: A systematic review was conducted following PRISMA 2020 guidelines. PubMed, Scopus, and Web of Science were searched for studies (2006-2024).

RESULTS: Strong evidence supports Lactobacillus rhamnosus GG and Saccharomyces boulardii for acute diarrhea. Mixed strains show moderate benefit in atopic dermatitis. Adjunct probiotic therapy improves Helicobacter pylori eradication rates. Evidence in asthma and autism spectrum disorder remains preliminary.

CONCLUSION: Significant heterogeneity in strains, dosing, and study design limits generalizability. Probiotic efficacy in pediatrics is strain and condition-specific. Standardized RCTs and precision microbiome approaches are required.},
}

@article {pmid42770724,
year = {2026},
author = {Zhang, Y and Elsheikha, HM and Zheng, W-B and Nan, F-L and Liu, R and Zhang, X-X and Yang, L-H and Li, Y and Ma, H},
title = {An atlas of colonization factors in the mouse gut microbiome reveals phylogenetically structured repertoires and infection-stage-associated variation during Toxoplasma gondii infection in mice.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0194026},
doi = {10.1128/spectrum.01940-26},
pmid = {42770724},
issn = {2165-0497},
abstract = {Colonization factors (CFs) comprise CF-associated gene families related to microbial establishment, persistence, host interaction, and gut ecological fitness, but their organization and variation in the mouse gut microbiome remain poorly defined. We integrated the Mouse Gut Genome Catalogue and the Mouse Gut Protein Catalogue, clustered at 90% amino acid identity, to define CF repertoires. A total of 79 conserved CF families, comprising over 2.4 million homologs, were identified across 112,951 genomes from 2,824 microbial species. Species-level CF-associated gene profiles exhibited a clear phylogeny-associated pattern and separated microbial species into two groups with distinct genome-scale functional profiles. Across the cecum and small intestine, CF profiles differed among control, acute, and chronic infection groups in dominant CF abundance, diversity, richness, and overall composition. CF profiles were significantly concordant with taxonomic profiles and associated with microbial community variation. Differential abundance analyses identified tissue- and stage-associated CF features. Exploratory machine-learning analyses showed high classification performance across all feature sets in the cecum, with the genus-level model yielding the highest median performance, whereas species- and genus-level taxonomic profiles provided stronger discrimination than CF profiles in the small intestine. This study provides a reference-based atlas of CF-associated gene repertoires and a CF-centered framework relating these repertoires to microbial phylogeny, genome-scale functional profiles, and infection-stage-associated variation in a murine Toxoplasma gondii infection model. CF-associated gene profiles can complement taxonomic and functional descriptions of the mouse gut microbiome, although the biological roles of individual CF-associated genes require experimental validation.IMPORTANCEStudies of the mouse gut microbiome commonly emphasize taxonomic composition, whereas the ecological traits associated with microbial establishment and persistence in the murine intestine remain less well characterized. By profiling CF-associated gene repertoires across control, acute, and chronic infection groups in mice, we show that infection-stage-associated differences in murine gut microbial community structure are accompanied by differences in colonization- and fitness-associated gene profiles. CF composition was associated with microbial community structure and functional potential, and CF-based features captured intestinal-region- and infection-stage-associated variation within this mouse data set. The principal contribution of this study is a reference-based, CF-centered framework that complements conventional taxonomic and functional profiling in murine infection models and provides a foundation for future mechanistic investigations of microbial colonization.},
}

@article {pmid42770729,
year = {2026},
author = {Mao, M and Wu, Y and Ye, L and Su, X and Zhang, J and Cui, S and Wang, C and Xu, S and Jian, Y and Qin, L and Zhu, B},
title = {Impact of plant sex on endophytic microbial diversity and community assembly in dioecious species.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0097626},
doi = {10.1128/spectrum.00976-26},
pmid = {42770729},
issn = {2165-0497},
abstract = {Dioecious plants show marked sexual dimorphism in morphology, physiology, defense, and life-history allocation, yet differences in endophytic microbiomes remain understudied. We compared endophytic bacterial and fungal communities between male and female individuals of four dioecious species-Eucommia ulmoides, Taxus wallichiana var. mairei, Ginkgo biloba, and Morus alba-by high-throughput sequencing of bark (E. ulmoides and T. wallichiana var. mairei) and leaves (G. biloba and M. alba). Sex significantly influenced the assembly of bacterial and fungal communities in all species. Bacterial alpha diversity (Shannon index) was significantly higher in males than females for E. ulmoides, T. wallichiana var. mairei, and M. alba. The bacterial phylum Spirochaetota was only detected in male samples of E. ulmoides, G. biloba, and M. alba, while the fungal genera Albophoma and Striaticonidium were detected only in female samples across all four species. Acidobacteria were significantly enriched in males of E. ulmoides and T. wallichiana var. mairei, whereas the fungal genus Sporidesmium was more abundant in females of T. wallichiana var. mairei and M. alba. Despite these sex-driven differences, dominant endophytic composition was similar between sexes: Actinobacteriota and Proteobacteria were the most prevalent bacterial phyla, whereas Ascomycota and Basidiomycota were the most prevalent fungal phyla across all samples. Co-occurrence analysis indicated stronger links between Actinobacteriota or Proteobacteria and other phyla than among remaining phyla. These results enhance understanding of sex-associated endophytic communities in dioecious plants and may inform studies on plant sex differentiation and potential plant-microbiome associations.IMPORTANCEPlant sex influences physiology, defense, and resource allocation, but its effects on internal microbial communities remain poorly understood. We compared endophytic bacteria and fungi in male and female Eucommia ulmoides, Taxus wallichiana var. mairei, Ginkgo biloba, and Morus alba using high-throughput sequencing and found consistent sex-associated differences in microbial diversity and specific taxa (e.g., Spirochaetota enriched in males; Albophoma and Striaticonidium enriched in females). These results indicate that sex is a reproducible driver of endophyte community assembly across diverse hosts. Recognizing sex-specific microbiomes has practical implications for conservation, forest and crop health management, and targeted bioprospecting, and underscores the need to include host sex as a key factor in ecological, functional, and evolutionary studies of plant-microbe interactions.},
}

@article {pmid42770768,
year = {2026},
author = {Speare, L and Rosales, SM},
title = {mGem: The two-decade evolution of in vivo coral microbiome manipulations.},
journal = {mBio},
volume = {},
number = {},
pages = {e0167826},
doi = {10.1128/mbio.01678-26},
pmid = {42770768},
issn = {2150-7511},
abstract = {Over the past two decades, microbiome manipulations have emerged as a strategy to bolster coral fitness. Here, we provide a timeline of two decades of research on in vivo coral microbiome manipulation studies aimed at improving coral health. A summary of coral hosts, probiotic taxa, and how experimental design varies across studies is synthesized to identify commonly used taxa and research gaps. This review highlights methodological challenges and identifies opportunities to advance probiotic development and translate microbial interventions into practical tools for coral restoration and reef management.},
}

@article {pmid42771082,
year = {2026},
author = {Jangid, C and Kumari, K and Joshi, R and Hamza, M and Dalal, J},
title = {Characterisation of microbial succession for the estimation of PMI and PMSI in terrestrial and aquatic environments.},
journal = {Forensic science, medicine, and pathology},
volume = {},
number = {},
pages = {},
pmid = {42771082},
issn = {1556-2891},
support = {200510192313//University Grant Commission/ ; },
abstract = {Decomposition is a continuous yet environmentally friendly process, and accurate estimation of the postmortem interval (PMI) and postmortem submersion interval (PMSI) remains a major challenge in forensic investigations. Recent developments in sequencing technologies have demonstrated great potential in the use of microbial communities in determining the time since death. Here, we investigated microbial community succession in human remains via 16 S rRNA gene sequencing and estimated the potential use of bacterial succession for estimating the PMI and PMSI. Distinct temporal shifts in microbial community composition were observed during aquatic and terrestrial decomposition, indicating predictable succession patterns associated with decomposition progression. Regression modeling under leave-one-out cross-validation demonstrated encouraging predictive performance, with the aquatic PMSI model based on ridge regression achieving an R[2] of 0.861 (MAE = 2.45 days), whereas the terrestrial PMI model using random forest regression achieved an R[2] of 0.768 (MAE = 2.60 days). Integration of microbial succession data with standardized decomposition scoring systems. These findings provide preliminary proof-of-concept evidence that microbial succession patterns can support PMI and PMSI estimation in forensic investigations. To the best of our knowledge, this represents the first forensic microbiome investigation of human terrestrial and aquatic decomposition for PMI and PMSI estimation in India.},
}

@article {pmid42771917,
year = {2026},
author = {Li, D and Xie, M and Chen, X and Li, T and Wang, A and Jiang, S and Xie, X},
title = {Proteins and microorganisms reveal that feed and substrate exert different effects on the growth and development of juvenile Chinese horseshoe crabs.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {61},
number = {},
pages = {102030},
doi = {10.1016/j.cbd.2026.102030},
pmid = {42771917},
issn = {1878-0407},
abstract = {In recent years, the population of Chinese horseshoe crabs (Tachypleus tridentatus) has declined sharply. As a living fossil of the ocean, they have an extremely slow growth cycle. To protect this endangered species, research has focused on identifying the optimal conditions required for its growth and development. Previous studies have focused on analyzing the optimal feed for T. tridentatus at various life stages. However, the optimal conditions required for the growth and development of first instar juveniles remain unclear. Furthermore, there is a lack of accurate and effective knowledge regarding the cultivation of first instar juveniles in aquaculture. Therefore, this study investigates the effects of feed and substrate on juvenile growth and development. Four experimental groups were established: a no-substrate, no-feeding group (WK group), a no-substrate, oyster feeding group (WS group), a group with sandy-mud substrate but no feeding (SNK group), and a group with sandy-mud substrate and oyster feeding (SNS group). The results were analyzed based on experimental records, proteomics, and microbiomics data. The results indicated that the SNS group exhibited the highest molting rate, as well as the highest weights for both first- and second instar juvenile horseshoe crabs. This indicates that the combined effect of oysters and the substrate is far greater in molting rates than the effect of either alone. Based on the proteomic results, under sandy-mud substrate conditions, oyster feeding induced substantial accumulation of mannosyl-oligosaccharide 1,2-alpha-mannosidase IA-like and Spartin, while reducing creatinase accumulation. With oyster feeding, the addition of sandy-mud substrate led to substantial accumulation of juvenile hormone acid O-methyltransferase-like isoform X1 and thromboxane-A synthase-like. Consistent with the microbiome results, juvenile horseshoe crabs in the SNS group exhibited higher average relative abundances of intestinal bacteria including Vibrionaceae, Thalassobius, and Defluviimonas.},
}

@article {pmid42761814,
year = {2026},
author = {Meng, X and Li, L and Hao, R and Lin, Z and Liu, K and Chi, G and Ren, J and Liu, R and Gao, Y and Yu, X and Tong, X},
title = {Shared oral microbiome signatures linking periodontitis and autoimmune thyroiditis: NHANES 2009-2012.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2728750},
pmid = {42761814},
issn = {2000-2297},
abstract = {OBJECTIVE: To examine the association between periodontitis severity and autoimmune thyroiditis (AIT) in a nationally representative US sample and to explore oral microbiome features shared between the two conditions.

METHODS: We analyzed adults from NHANES 2009-2012 with complete periodontal examinations, thyroid autoantibodies, and oral microbiome data (n = 1,346). Periodontitis was classified using CDC/AAP case definitions. AIT was defined as positivity for thyroid peroxidase antibodies (TPOAb ≥ 9 IU/mL) and/or thyroglobulin antibodies (TgAb ≥ 4 IU/mL). Survey-weighted multivariable logistic regression estimated adjusted odds ratios (aORs) and 95% confidence intervals (CIs). Oral microbiome diversity and differentially abundant genera were compared between groups.

RESULTS: In the fully adjusted model, mild and severe periodontitis were associated with higher odds of AIT compared with periodontally healthy individuals (mild: aOR 2.15, 95% CI 1.20-3.84; severe: aOR 2.77, 95% CI 1.22-6.28), whereas moderate periodontitis was not significantly associated (aOR 1.47, 95% CI 0.63-3.43). Genera enriched in both AIT and periodontitis included Fusobacterium, Bergeyella, Johnsonella, and Prevotella_2. Fusobacterium abundance increased across periodontal severity categories and showed a weak inverse correlation with TPOAb, whereas TT3 and FT3 showed weak positive correlations with Fusobacterium.

CONCLUSION: Periodontitis severity was associated with AIT in this cross-sectional NHANES analysis, and Fusobacterium emerged as a shared genus associated with both periodontal status and thyroid autoimmunity. Longitudinal and interventional studies are warranted to assess causality.},
}

@article {pmid42761980,
year = {2026},
author = {Assaf, S and Lio, P},
title = {The Active Shelf: A Clinician's Guide to Active Dermatologic Care for Atopic Dermatitis.},
journal = {The Journal of clinical and aesthetic dermatology},
volume = {19},
number = {7},
pages = {33-37},
pmid = {42761980},
issn = {1941-2789},
abstract = {Key therapeutic options for dermatologic care frequently extend beyond prescription medications to include evidence-based, over-the-counter (OTC) topicals that meaningfully influence disease pathophysiology. We introduce the concept of active dermatologic care (ADC), which encompasses nonprescription topical products with biologically active compounds that support and modulate key skin disease processes and can be routinely incorporated into comprehensive dermatologic care plans. We expand upon the recent concept of categorizing OTC active ingredients for acne based on their mechanisms of action and apply it to atopic dermatitis. The pathophysiologic pillars of itch, barrier dysfunction, acid mantle disruption, dysbiosis, and inflammation are each considered as potential therapeutic targets for ADC.},
}

@article {pmid42762145,
year = {2026},
author = {Yi, TW and Kumar, P and Karwasra, R and Sharma, N and Behare, MH and Linkang, X and Abdelkarim Maki, MA and Khanna, K},
title = {Biopolymeric Approaches for Colon Cancer Treatment: A Comprehensive Review of Polysaccharide-based Delivery Systems.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {235},
pages = {},
doi = {10.3791/70872},
pmid = {42762145},
issn = {1940-087X},
mesh = {Humans ; *Polysaccharides/chemistry/administration & dosage ; *Colonic Neoplasms/drug therapy ; *Drug Delivery Systems/methods ; Animals ; *Antineoplastic Agents/administration & dosage/chemistry ; Drug Carriers/chemistry ; },
abstract = {Globally, colon cancer remains one of the leading causes of mortality. Multidrug resistance, systemic toxicity, and poor tumor selectivity significantly limit conventional chemotherapy. This review highlights the need for localized therapy to increase efficacy and minimize systemic side effects. Colon-targeted drug delivery systems (CDDS) are designed and developed to overcome these challenges. Both natural and synthetic polysaccharides act as carriers in CDDS because of their biodegradability, biocompatibility, pH- and enzyme-responsiveness, and mucoadhesive properties. Polysaccharides such as chitosan, dextran, pectin, alginate, and hyaluronic acid have been formulated into nanoparticles, microparticles, and hydrogels, enabling controlled and site-specific delivery. These carriers deliver chemotherapeutics, nucleic acids, and immunotherapeutics, as well as theranostic agents that combine imaging and therapy. Preclinical evidence demonstrates significant translational potential for polysaccharide-based CDDS. However, clinical trials remain limited, which highlights the gap between laboratory findings and clinical applications. Major challenges in colon-targeted drug delivery include variability in polysaccharide sources and quality, difficulties in large-scale manufacturing, and regulatory challenges. Addressing these challenges will be essential to move towards commercialization and clinical adoption. Personalized therapy through microbiome profiling, integration with nanotechnology and bioinformatics, and smart, biosensor-responsive carriers will be the focus going forward. Polysaccharide-based CDDS provide safer, more effective, and more personalized treatment with continued research to optimize delivery and overcome existing limitations.},
}

Humans
*Polysaccharides/chemistry/administration & dosage
*Colonic Neoplasms/drug therapy
*Drug Delivery Systems/methods
Animals
*Antineoplastic Agents/administration & dosage/chemistry
Drug Carriers/chemistry

@article {pmid42762163,
year = {2026},
author = {Silva-Magaña, MA and Mora-Flores, LP and Pita-Galeana, MA and Hernández-Lemus, E and de Anda-Jáuregui, G},
title = {A network dynamical simulation model for the study of antibiotic resistance in microbial communities.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2734703},
doi = {10.1080/19490976.2026.2734703},
pmid = {42762163},
issn = {1949-0984},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Microbiota/drug effects ; *Bacteria/drug effects/genetics ; Computer Simulation ; Models, Biological ; *Drug Resistance, Bacterial ; *Drug Resistance, Microbial ; },
abstract = {Antibiotic resistance emerges from ecological and evolutionary processes occurring within complex microbial communities. Interactions among microorganisms can shape the pathways through which resistance traits spread and persist, yet many theoretical approaches treat microbial populations as homogeneous compartments. Here we present a simulation-based network dynamical model that represents microbial communities as ecological association networks. In this formulation, nodes correspond to bacterial populations, metapopulations, or taxon-level ecological units, while resistant counterparts represent state-expanded subpopulations associated with the same ecological unit. Edges represent co-occurrence-based ecological proximity rather than direct physical contacts or confirmed horizontal gene transfer events. Using stochastic simulations across multiple network topologies, we explore how structural properties of microbial communities influence the emergence and persistence of resistance. Parameter sweeps across transmission probability, initial resistance fraction, and antibiotic intervention timing allow us to characterize regimes in which resistance either remains localized or spreads through the community. The model produces time series of resistant and susceptible states and snapshots of evolving network configurations, enabling qualitative comparison across simulation scenarios. Our results show that network structure strongly modulates resistance dynamics. Highly clustered networks tend to trap resistance within local neighborhoods, whereas heterogeneous networks with hub nodes facilitate rapid dissemination. Antibiotic perturbations can either suppress resistance or paradoxically accelerate its expansion depending on network topology and intervention timing. These findings should be interpreted as qualitative results from a minimal proof-of-concept model, not as a direct reconstruction of plasmid transfer, species replacement, or patient-specific microbiome responses.},
}

*Anti-Bacterial Agents/pharmacology
*Microbiota/drug effects
*Bacteria/drug effects/genetics
Computer Simulation
Models, Biological
*Drug Resistance, Bacterial
*Drug Resistance, Microbial