@article {pmid42992837,
year = {2026},
author = {El-Dougdoug, NK and Magistrado, D and Perry, KI and Short, SM},
title = {Microbiota modulation impacts life history traits and mating success in male Aedes aegypti mosquitoes.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0046526},
doi = {10.1128/msphere.00465-26},
pmid = {42992837},
issn = {2379-5042},
abstract = {UNLABELLED: Aedes aegypti mosquitoes transmit multiple arboviruses, but population suppression through the mass release of sterile or incompatible male mosquitoes can effectively reduce populations. These methods depend on the reliable mass-rearing of healthy, robust males that can successfully mate with wild females. The microbiota is a critical component of the larval diet, and its modulation can dramatically influence life history traits relevant to mass-rearing and male quality. Here, we used axenic (microbe-free), monoxenic (inoculated with Escherichia coli), and "laboratory community" mosquitoes (inoculated with an undefined microbiota derived from laboratory mosquitoes) to show that longevity was significantly enhanced in axenic and monoxenic males compared to laboratory community males. Moreover, monoxenic males more efficiently obtained mates in non-competitive mating scenarios compared to laboratory community males. However, microbiota treatment had no effect on mating success when males from different treatments competed for a mate. Our findings suggest that the microbiota is a key determinant of male mosquito life history, with direct implications for optimizing production of males for control programs.

IMPORTANCE: The microbes found in association with mosquitoes are crucial to mosquito development and have the capacity to influence multiple life history traits. In the current study, we comprehensively and functionally evaluate the role of the microbiota in mating success and other life history traits of male mosquitoes. Males are crucial to disease transmission, via their role in mating, and via their use in mosquito population control. By focusing on males, the understudied sex in mosquito research, we provide novel and foundational insight into how microbial communities influence male life history traits and mating success. Moreover, our findings establish a critical framework for understanding how the microbiota may affect male quality, production efficiency, and performance in vector control programs that involve mass production of adult male mosquitoes.},
}

@article {pmid42992852,
year = {2026},
author = {Morabbi, SM and Bhowmik, N and Sutherland, S and Wylie, EA and Decker, RS and Al Daerwish, A and Pérez Pérez, M and Pascual, E and Lutter, EI and Philmus, B and Stubbendieck, RM},
title = {Differential metabolite production underlies disruption of the cystic fibrosis airway microbiota by pathogens.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0115726},
doi = {10.1128/msystems.01157-26},
pmid = {42992852},
issn = {2379-5077},
abstract = {Cystic fibrosis (CF) results in accumulation of mucus in the airways that promotes pathogen colonization, leading to respiratory exacerbations, lung failure, and death. The CF airway harbors a complex microbiota, including pathogens and oropharyngeal bacteria. Here, we reanalyzed 5,260 16S rRNA gene microbiota data sets to infer associations between members of the CF microbiota. We determined that pathogens are more likely to proliferate and dominate when present, while oropharyngeal bacteria are generally present at lower abundances. We found that higher diversity and increasing numbers of pairwise associations between bacteria were positively correlated with lung function. In contrast, dominance of the microbiota by pathogens was associated with loss of lung function. We determined that pathogens are largely negatively associated with each other and oropharyngeal bacteria, suggesting they are antagonistic toward other bacteria. As a first test of this hypothesis, we cultured 1,597 isolates from 96 people with CF and performed 12,542 coculture assays against eight representative pathogens and oropharyngeal bacteria, finding 23% of interactions resulted in inhibition. Among our isolates, Pseudomonas were the most inhibitory, but we observed variable activity between different isolates. We further found Pseudomonas aeruginosa isolates, even those from the same donor and time point, exhibited significant differences in their metabolome and bioactivity profiles that correlated with acquisition of mutations. Together, our results suggest that pathogens may disrupt the CF microbiota and proliferate in part through bioactive metabolite production. Furthermore, these data highlight that characterizing multiple isolates is necessary to capture the full landscape of chemically mediated interactions within microbiomes.IMPORTANCEThe cystic fibrosis (CF) airway harbors a complex microbiota, including oropharyngeal bacteria and opportunistic pathogens that establish chronic infections. We found that microbiota diversity is correlated with health and that a pathogen-dominated microbiota is associated with low lung function. We then inferred potential microbial interactions by determining abundance associations between CF genera, which suggested that pathogens antagonize other bacteria. To test this prediction, we cultured bacteria from people with CF and performed thousands of coculture assays, finding that approximately one-quarter of interactions resulted in growth inhibition. Pseudomonas broadly inhibited other members of the CF airway microbiota. However, we observed marked variability in bioactivity and metabolite profiles of Pseudomonas aeruginosa isolates, even from the same donor at the same time. Our results suggest that pathogens disrupt the CF microbiota, possibly through bioactive metabolite production, and that characterizing multiple isolates is necessary to capture the complete picture of interactions in these communities.},
}

@article {pmid42992936,
year = {2026},
author = {Hu, Y and Sun, L and Huang, Y and Jiang, F and Tong, X and Yang, J and Ju, Y and Yang, Z and Liufu, S and Hu, Y and Ma, W and Guo, R and Li, W and Zhang, T and Zhu, X and Zhang, Z},
title = {Integrated optimization of experimental and computational workflows improves genome recovery in long-read gut metagenomics.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0113826},
doi = {10.1128/msystems.01138-26},
pmid = {42992936},
issn = {2379-5077},
abstract = {Short-read metagenomic sequencing has been widely applied in microbial research due to its high quality and decreasing cost. However, short reads are inherently fragmented, which limits assembly contiguity and the recovery of complete microbial genomes. In contrast, long-read sequencing, with significantly longer read lengths, helps overcome these limitations. Achieving complete and accurate genome recovery is the core goal of metagenomics. To address this challenge, we systematically evaluated and optimized the long-read metagenomic workflow, from sample processing to computational assembly, using the CycloneSEQ platform.IMPORTANCEOur results suggest that upstream experimental protocols are important contributors to long-read metagenomic performance within the evaluated framework. In particular, magnetic-plate DNA extraction, together with pretreatment, was associated with more favorable input and downstream sequencing-related characteristics for long-read analysis. These changes were also associated with broader microbial recovery in the evaluated data sets. Assembly benchmarking further showed that integrating matched long-read (CycloneSEQ) and short-read (DNBSEQ) data sets provided a favorable balance across multiple evaluation dimensions. In our fecal metagenomic data set, long-read-first assembly followed by short-read polishing showed strong overall performance when recovery, contiguity, and sequence accuracy were considered together, although workflow performance remained metric dependent.},
}

@article {pmid42992937,
year = {2026},
author = {Paulsen, AA and Roghair Stroud, MN and Halverson, LJ},
title = {Physiological, behavioral, and genetic factors that shape interactions in the plant growth-promoting maize rhizosphere synthetic community.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0088826},
doi = {10.1128/msystems.00888-26},
pmid = {42992937},
issn = {2379-5077},
abstract = {Profiling microbiomes is an important way to understand the function and composition of communities in the wild, but natural microbiomes are often highly complex and often unamenable to experimentation to reveal cause-and-effect relationships. By using a small group of cultivable strains to represent those found in the wild, synthetic communities are one solution to this problem. Here we describe the maize rhizosphere synthetic community (MARSc), a genome-enabled 31-member bacterial community representative of the diversity found on the roots of maize grown in Iowa soils. This community is built around Pseudomonas putida KT2440, a model maize rhizosphere colonist and synthetic biology chassis. We characterized microbe-microbe interactions and biofilm formation of MARSc members in a variety of environmental contexts, finding that both behaviors are broadly controlled by nutrient levels. Genomic analysis and microbiome profiling of these organisms revealed that annotated biofilm genes (such as surface attachment and exopolysaccharide production) were significantly correlated with rhizosphere abundance, but neither trait correlated to in vitro biofilm formation. In vitro interaction assay findings were surprisingly consistent with co-correlations of rhizosphere abundance among MARSc members on roots. Finally, we found that when applied to the roots, MARSc can increase maize biomass (dry weight) by up to 40%-50% under varying nitrogen fertilization levels. Altogether, MARSc is a useful tool for identifying some of the factors influencing rhizosphere microbiome assembly and will be a strong foundation for further work in this area.IMPORTANCEThe microbiome surrounding the roots of plants can play an integral role in plant health and growth, and it is composed of thousands of species of microbes that are specific to the plant and environment it is grown in. However, due to this complexity, little is known about the means by which microbiomes form. In this study, we developed the maize rhizosphere synthetic community (MARSc) to gain a better understanding of the formation and function of microbiomes on the roots of plants. This consortium consists of 30 bacterial isolates plus Pseudomonas putida KT2440, a model maize root colonist. In this study, we investigated the interactions between these organisms, their genomes, cultural characteristics, and growth on the roots of maize. We show that MARSc increases maize growth under low nitrogen fertilizer, suggesting it will be a useful tool for identifying the mechanisms behind microbiome formation and plant growth promotion.},
}

@article {pmid42992988,
year = {2026},
author = {Maalumi, O and Ben Moshe, Z and Blank, O and Barkan-Michaeli, R and Yona, AH and Sharabi, K},
title = {Microbiota-derived indole-3-propionic acid regulates glucose homeostasis via remodeling of hepatic mitochondrial metabolism.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2760041},
doi = {10.1080/19490976.2026.2760041},
pmid = {42992988},
issn = {1949-0984},
mesh = {Animals ; *Indoles/metabolism ; *Glucose/metabolism ; Homeostasis ; Mice ; *Liver/metabolism ; Hepatocytes/metabolism ; Gluconeogenesis ; *Gastrointestinal Microbiome ; Male ; Mice, Inbred C57BL ; *Propionates/metabolism ; *Mitochondria/metabolism ; *Mitochondria, Liver/metabolism ; },
abstract = {The gut microbiota produces metabolites that circulate to host tissues and are increasingly linked to metabolic health, yet the mechanisms by which individual microbial products regulate liver glucose metabolism remain poorly defined. Here, we identify the tryptophan-derived microbial metabolite indole-3-propionic acid (IPA) as a direct modulator of hepatic glucose production. In primary hepatocytes, a focused screen of indole metabolites revealed that several indole-containing compounds suppress glucagon-stimulated glucose output, with IPA selected for further characterization. IPA selectively reduced glucose production from mitochondrial-dependent gluconeogenic substrates while largely preserving glycerol-supported glucose production, suggesting that it does not simply shut down gluconeogenesis but instead alters how hepatocytes use metabolic fuels. Mechanistic analyzes showed that IPA redirects lactate-derived carbon away from glucose production and reshapes mitochondrial metabolism, including redox balance, ATP availability, and urea cycle-linked metabolic activity. These effects occurred without detectable disruption of proximal insulin or glucagon signaling, supporting a model in which IPA acts primarily through intracellular metabolic remodeling. In mice, endogenous IPA levels varied with nutritional state, and short-term IPA administration improved fasting glycemia and glucose handling in Western diet-fed animals. Finally, microbiome-depleted mice colonized with IPA-producing Clostridium sporogenes displayed increased circulating IPA and improved glucose tolerance compared with mice colonized with an IPA-deficient mutant C. Sporogenes strain. Together, these findings identify IPA as a microbial metabolite that directly connects gut tryptophan metabolism to hepatic mitochondrial function and systemic glucose regulation, highlighting a mechanistic gut-liver pathway with potential therapeutic relevance to metabolic disease.},
}

Animals
*Indoles/metabolism
*Glucose/metabolism
Homeostasis
Mice
*Liver/metabolism
Hepatocytes/metabolism
Gluconeogenesis
*Gastrointestinal Microbiome
Male
Mice, Inbred C57BL
*Propionates/metabolism
*Mitochondria/metabolism
*Mitochondria, Liver/metabolism

@article {pmid42993179,
year = {2026},
author = {Scranton, C and Obergh, V and Goforth, M and Ravi, K and Jayakrishna, P and Khan, A and Boone, SA and Gerba, CP and Ijaz, MK and Xu, FY and Krupp, K and Madhivanan, P and Cooper, KK},
title = {Characterization of household microbiomes from three unique cities around the world.},
journal = {Microbial genomics},
volume = {12},
number = {11},
pages = {},
pmid = {42993179},
issn = {2057-5858},
mesh = {*Microbiota/genetics ; Humans ; Metagenomics/methods ; *Bacteria/classification/genetics/isolation & purification ; India ; United Arab Emirates ; Cities ; United States ; RNA, Ribosomal, 16S/genetics ; Shotgun Sequencing ; Family Characteristics ; Metagenome ; Housing ; },
abstract = {Characterizing the household bacterial microbiome allows for a stronger understanding of the various microbes to which a person is exposed every day in their home. Exploring household microbiomes in different countries around the world increases our understanding of the impact human behaviour might have on niche microbial communities in the house. The goal of this study was to use shotgun metagenomics to characterize the microbiome from ten locations around the house in ten different houses from three countries (Mysuru, India; Dubai, United Arab Emirates (UAE); and Tucson, USA). There was a significant difference in alpha diversity between the three countries (ANOVA, P<0.001), with homes in Mysuru, India, showing significantly higher bacterial diversity compared with those in Tucson, AZ, USA and Dubai, UAE. Beta diversity analysis of the homes found that bacterial communities differed significantly by geographic location [permutational multivariate analysis of variance (PERMANOVA), P=0.001] and, within cities, by household location (PERMANOVA, P=0.001), with geographic location explaining 5.3% and household location explaining 7.3% of variation. Household location was a strong driver of diversity within each of the three cities individually, accounting for 14-18% of microbiome variation. The highest levels of bacterial diversity across the three cities were found underneath the toilet rim and within bathroom and kitchen sinks. A core microbiome of classes Actinomycetota and Gammaproteobacteria was found in all homes in all three cities. Within each city, a core microbiome was identified at the species level within specific household locations. Many bacterial taxa found in the homes were a part of the human-associated phyla Actinomycetota (e.g. genera Brevibacterium, Mycolicibacterium and Rhodococcus), Pseudomonadota (e.g. genera Acinetobacter, Moraxella, Paracoccus and Pseudomonas) and Bacillota (genus Streptococcus), which is comparable to previous studies. The household microbiome is variable across different locations within the house and on a global scale. Factors such as human activity, cultural practices, climate and surface type and use may drive this diversity. Characterizing the household microbiome on a global scale allows for a better understanding of what drives microbial diversity, increasing our understanding of how microbial communities are shaped by the environment and how humans influence their dynamics, as well as any risks to human health that the built microbiome may potentially pose.},
}

*Microbiota/genetics
Humans
Metagenomics/methods
*Bacteria/classification/genetics/isolation & purification
India
United Arab Emirates
Cities
United States
RNA, Ribosomal, 16S/genetics
Shotgun Sequencing
Family Characteristics
Metagenome
Housing

@article {pmid42993299,
year = {2026},
author = {Kaunisto, KM and Smolander, N and Tamminen, M and Stoks, R and Kylänpää, S and Sääksjärvi, IE and Vesterinen, EJ},
title = {The Invisible Web: Linking Diet and Gut Microbiota Across Time and Space in Odonates.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {42993299},
issn = {1432-184X},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Diet ; *Bacteria/classification/genetics/isolation & purification ; *Odonata/microbiology/physiology ; Finland ; Feces/microbiology ; Seasons ; RNA, Ribosomal, 16S/genetics ; Electron Transport Complex IV/genetics ; DNA Barcoding, Taxonomic ; Feeding Behavior ; },
abstract = {The complex relationship between insects and their gut microbiota has become a central theme in host-microbe ecology, revealing profound effects on host fitness and interactions. Yet, how gut microbial communities-and their primary determinant, diet-vary across space and time in natural insect populations remains largely unexplored. Understanding these dynamics is essential for linking microbial variation with host biology. We investigated bacterial gut microbiota and dietary patterns in two odonate species, Sympetrum vulgatum and Lestes sponsa, across their flight season and three locations in southern Finland. Using faecal DNA metabarcoding of the cytochrome c oxidase subunit I (COI) gene for diet and 16 S rRNA gene for gut microbiota, we examined spatiotemporal changes and their associations. Season, location, and host species affected both dietary and bacterial diversity. The observed parallel responses of dietary composition and microbial communities highlight that the same ecological factors shaping insect feeding behaviour also influence their associated microbiota, illustrating the dynamic and context-dependent nature of insect-microbe interactions in the wild and emphasizing the need for broader ecological perspectives in microbiome research.},
}

Animals
*Gastrointestinal Microbiome
*Diet
*Bacteria/classification/genetics/isolation & purification
*Odonata/microbiology/physiology
Finland
Feces/microbiology
Seasons
RNA, Ribosomal, 16S/genetics
Electron Transport Complex IV/genetics
DNA Barcoding, Taxonomic
Feeding Behavior

@article {pmid42993389,
year = {2026},
author = {Toksanbaevich, ZK and Awulibieer, M and Maidanniyati, D and Hornok, S and Rysbayuli, SA and Serik, K and Kairat, O and Zhumagadyrovish, BN and Mukhitdinovich, DV and Wang, Y and Hazihan, W},
title = {Identification of bacterial communities and tick-borne pathogens in the fowl ticks (Argas persicus) from Almaty Oblast, Turkistan Oblast, and Shymkent City of Kazakhstan.},
journal = {Experimental & applied acarology},
volume = {97},
number = {4},
pages = {},
pmid = {42993389},
issn = {1572-9702},
support = {AP23489750//the Scientific and Technical Projects for Sustainable Development of the Agro-Industrial Complex of the Republic of Kazakhstan 2024-2026,/ ; (82260399 and 81960379)//the National Natural Science Foundation of China/ ; 2025AA018//the Key Scientific & Technological Project of XPCC/ ; 2023TSYCTD0020//the Science & Technology Innovation Team Project of Tianshan Elite/ ; 2026001ZYWGHZSYJSTGXM65004985//Health Science and Technology Program of Xinjiang Uygur Autonomous Region/ ; },
mesh = {Animals ; Kazakhstan ; *Microbiota ; *Argas/microbiology/growth & development ; RNA, Ribosomal, 16S/analysis ; *Bacteria/isolation & purification/classification ; Coxiella/isolation & purification ; Chickens ; RNA, Bacterial/analysis ; Poultry Diseases/parasitology/microbiology ; },
abstract = {Argas persicus (the fowl tick) is native to Central Asia. In this study, a total of 671 soft ticks were collected from chickens in three sampling sites (Bakanas District, Almaty Oblast; Sayram District, Turkistan Oblast; Shymkent City), Kazakhstan. A total of 16 tick pools (10 ticks per pool) were used for 16 S rRNA gene-based microbiome profiling by sequencing the V3-V4 region. Subsequently, seven genetic markers were amplified for molecular detection of Anaplasma, Rickettsia and Coxiella. Alpha and beta diversity analyses revealed that A. persicus ticks in Bakanas District had the highest microbial richness and diversity, while the ticks in Shymkent City and Sayram District exhibited highly similar microbial community compositions. The microbiome was predominated by Proteobacteria, specifically the genera Rickettsia and Coxiella, especially in Sayram District and Shymkent City, and the relative abundance of the top 30 bacterial components differed among sampling sites. Three pathogens including unclassified Anaplasma sp., Rickettsia hoogstraalii and Coxiella burnetii were detected for the first time in A. persicus ticks in Kazakhstan. The unclassified Anaplasma sp. was prevalent in ticks associated with domestic poultry and migratory birds, while Rickettsia hoogstraalii tended to parasitize seabird-related ticks with high prevalence. In addition, Coxiella burnetii infection prevalence was higher in pastoral areas than in urban areas, and birds act as secondary transmission vectors. These findings reveal that tick-borne pathogens harbored by avian soft ticks deserve close attention, especially in Central Asia.},
}

Animals
Kazakhstan
*Microbiota
*Argas/microbiology/growth & development
RNA, Ribosomal, 16S/analysis
*Bacteria/isolation & purification/classification
Coxiella/isolation & purification
Chickens
RNA, Bacterial/analysis
Poultry Diseases/parasitology/microbiology

@article {pmid42993715,
year = {2026},
author = {Mennen, MC and Zulu, MZ and Mabatha, KC and Baguma, R and Skelem, S and Mbundwini, NN and Aremu, OO and Adriaanse, M and van Dijk, D and Pillay, P and Africa, S and Jones, E and Setshedi, M and Brink, A and Burgers, WA and Ntusi, NAB},
title = {Protocol for investigating the association between Helicobacter pylori exposure, antigen-specific serological responses, and resistant versus non-resistant hypertension in a South African cohort.},
journal = {PloS one},
volume = {21},
number = {11},
pages = {e0362215},
pmid = {42993715},
issn = {1932-6203},
mesh = {Humans ; *Helicobacter pylori/immunology ; South Africa/epidemiology ; *Hypertension/microbiology/immunology/blood ; *Helicobacter Infections/complications/immunology/microbiology ; Cross-Sectional Studies ; *Antigens, Bacterial/immunology ; Adult ; Female ; Male ; Middle Aged ; Bacterial Proteins/immunology ; },
abstract = {BACKGROUND: Hypertension is a leading contributor to cardiovascular morbidity and mortality, with poor control in low- and middle-income countries. Helicobacter pylori (H. pylori) has been associated with hypertension through inflammatory, endothelial, metabolic and immune pathways, but data from sub-Saharan Africa, particularly in resistant hypertension, are limited.

METHODS: This cross-sectional observational study will enrol 200 adults aged ≥18 at a tertiary academic hospital in Cape Town, South Africa: 80 with resistant hypertension, 80 with non-resistant hypertension and 40 with normotension. Participants will undergo standardised clinical assessment, blood pressure measurement, and collection of blood, urine and saliva. H. pylori exposure will be assessed using the Pylori DuoTect® point-of-care assay, which detects antibodies to CagA and FliD. Laboratory analyses will include lipid profile, inflammatory and nitric oxide-related markers, homocysteine, insulin indices, complete blood count, ghrelin, multiplex cytokine profiling and flow cytometric immunophenotyping. PAXgene® blood RNA samples will be retained for future exploratory analyses. Saliva will undergo exploratory H. pylori antigen testing using CerTest® kits, which are validated for stool rather than saliva. Saliva analysis will be exploratory, and results will not define the primary H. pylori exposure variable. Remaining saliva will be kept for potential future oral microbiome analyses not defined in this protocol. Multivariable logistic regression will evaluate associations between H. pylori exposure and hypertension phenotype, adjusting for demographic, lifestyle, and clinical covariates.

DISCUSSION: To our knowledge, this will be the first African study to integrate point-of-care H. pylori serology with detailed clinical, inflammatory, metabolic, and immunological profiling across resistant hypertension, non-resistant hypertension and normotension. Findings may clarify biological pathways linking H. pylori exposure to blood pressure dysregulation and inform future mechanistic and interventional studies.},
}

Humans
*Helicobacter pylori/immunology
South Africa/epidemiology
*Hypertension/microbiology/immunology/blood
*Helicobacter Infections/complications/immunology/microbiology
Cross-Sectional Studies
*Antigens, Bacterial/immunology
Adult
Female
Male
Middle Aged
Bacterial Proteins/immunology

@article {pmid42993867,
year = {2026},
author = {Chakraborty, T and Kashyap, SJ and Chetia, PD and Purkayastha, S},
title = {The carcinogenic transition: toxicological, metabolic, and microbiome consequences of Westernized high-heat culinary practices in Asian populations.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-21},
doi = {10.1080/10408398.2026.2756028},
pmid = {42993867},
issn = {1549-7852},
abstract = {Colorectal and prostate cancer incidence has risen rapidly in several industrializing Asian populations. Dietary-pattern explanations focus on macronutrients, but cooking method is rarely examined. We discuss a "carcinogenic transition" hypothesis, in which a shift from moist-heat cooking (≤100 °C) toward dry-heat techniques (≥150 °C) increases formation of heterocyclic amines (HCAs) and polycyclic aromatic hydrocarbons (PAHs) in food. We examine three components (the "Triple Threat" framework) that may be relevant to some populations: (1) dietary HCA/PAH exposure; (2) host variation in xenobiotic metabolism, including N-acetyltransferase 2 (NAT2), cytochrome P450 1A2 (CYP1A2), and aldehyde dehydrogenase 2 (ALDH2) variants, which may alter bioactivation or clearance; and (3) diet-associated gut microbiome activity, including β-glucuronidase (GUS)-mediated deconjugation of excreted metabolites, supported by in vitro data with unquantified human magnitude. The framework rests on epidemiological associations and experimental mechanisms, not established causation. Confounding by obesity, alcohol, screening, and acculturation cannot be excluded, and trials isolating cooking method are needed. We also discuss practical food-preparation strategies, including lower-temperature cooking and antioxidant-rich marinades. Support comes from food-chemistry experiments and small urinary biomarker studies; effects on cancer incidence remain untested.},
}

@article {pmid42993877,
year = {2026},
author = {Zhang, Y and Teh, CE and Slaney, CY and Darcy, PK and Chong, MMW},
title = {Regulatory T Cell Interventions to Boost Anti-tumor Immune Responses.},
journal = {Cancer research},
volume = {},
number = {},
pages = {},
doi = {10.1158/0008-5472.CAN-26-0789},
pmid = {42993877},
issn = {1538-7445},
abstract = {FOXP3-expressing regulatory T cells (Tregs) are a specialized subset of T lymphocytes that are crucial for maintaining immune homeostasis and preventing autoimmunity. However, their pervasive presence and potent immunosuppressive functions within the tumor microenvironment (TME) are a barrier to anti-tumor immunity, presenting a major challenge for cancer immunotherapy. In this review, we discuss strategies for the therapeutic modulation of Tregs. Current and emerging promising technological approaches include antibody-based approaches, small molecule inhibitors, engineered Tregs, microbiome modulation, and Treg survival manipulations. Additionally, existing and promising combinatorial therapies integrate Treg cell targeting with complementary treatment strategies. The goal of this review is to spotlight how Treg-targeted interventions can overcome immune escape and ultimately enhance immunotherapy efficacy to improve clinical outcomes in cancer patients.},
}

@article {pmid42993880,
year = {2026},
author = {Ding, X and Du, Q and Ji, C and Chen, G and Li, J and Hu, W},
title = {Bacterial signals and mechanisms linked to the microbiota in calcium oxalate urolithiasis: Evidence boundaries and translational implications.},
journal = {Science progress},
volume = {109},
number = {4},
pages = {368504261506690},
doi = {10.1177/00368504261506690},
pmid = {42993880},
issn = {2047-7163},
mesh = {Humans ; *Calcium Oxalate/metabolism/chemistry ; *Urolithiasis/microbiology/metabolism ; Animals ; Oxalobacter formigenes/metabolism ; *Microbiota ; *Bacteria/metabolism ; Gastrointestinal Microbiome ; Crystallization ; },
abstract = {Calcium oxalate (CaOx) urolithiasis is traditionally interpreted through urinary supersaturation and metabolic risk, but emerging evidence suggests that bacterial signals and microbiota-derived metabolites may also influence crystal behavior, tubular epithelial injury, and stone-related host responses. This narrative review examines evidence from stone, urine, gut, and experimental studies, with emphasis on mechanistic evidence, compartment-specific findings, and the limits of current evidence. Human studies have detected bacterial signatures and cultivable organisms in CaOx-associated samples, but reported taxa and functional patterns vary across stone material, bladder urine, renal pelvis urine, voided urine, and stool, precluding a reproducible microbial profile. Experimental studies indicate that intact bacteria and bacterial products can modulate CaOx crystallization, crystal growth, aggregation, crystal-cell adhesion, epithelial injury, inflammation, and regulated cell-death pathways. Studies of the gut microbiota further implicate Oxalobacter formigenes-associated oxalate handling and microbiota-derived metabolites. However, direct pure-CaOx human evidence remains limited, and many mechanistic claims rely on mixed-calcium or preclinical contexts. Current evidence supports biological plausibility but not human causality, a universal microbial signature, or validated microbiota-targeted therapy. Future studies should prioritize standardized sampling, well-characterized CaOx cohorts, longitudinal validation, and clinically relevant recurrence endpoints.},
}

Humans
*Calcium Oxalate/metabolism/chemistry
*Urolithiasis/microbiology/metabolism
Animals
Oxalobacter formigenes/metabolism
*Microbiota
*Bacteria/metabolism
Gastrointestinal Microbiome
Crystallization

@article {pmid42994040,
year = {2026},
author = {He, T and Alai, W and Yang, Y and Hou, K and Ji, M and Han, Y and Yi, X and Zhou, N and Zhang, H},
title = {Microbiome-mediated regulation of growth and steroidal saponin biosynthesis in Paris species: Roles of endophytes and arbuscular mycorrhizal fungi.},
journal = {Microbiological research},
volume = {315},
number = {},
pages = {128810},
doi = {10.1016/j.micres.2026.128810},
pmid = {42994040},
issn = {1618-0623},
abstract = {Paris species (Paris spp., Liliaceae) are important medicinal plants whose therapeutic value is largely attributed to their bioactive steroidal saponins. However, their slow growth, prolonged cultivation cycles, depletion of wild resources, and susceptibility to continuous-cropping problems constrain sustainable production and the improvement of medicinal quality. Elucidating the biological and environmental factors governing steroidal saponin accumulation is therefore essential for optimizing Paris cultivation and enhancing medicinal quality. This review focuses on the roles of endophytes and arbuscular mycorrhizal fungi (AMF) in regulating the growth and medicinal quality of Paris species. First, the biosynthetic pathways and spatiotemporal accumulation patterns of major steroidal saponins in Paris species are summarized, together with the effects of environmental factors on their accumulation. The diversity, distribution, and identification of microorganisms associated with Paris species are then reviewed, followed by a synthesis of the mechanisms through which these microorganisms regulate plant growth and steroidal saponin biosynthesis. These mechanisms encompass modulation of photosynthetic performance and phytohormone signaling, enhancement of stress tolerance and mineral nutrient acquisition, remodeling of the rhizosphere environment, regulation of heavy metal accumulation, microbial induction of secondary metabolism, and modulation of key genes involved in steroidal saponin biosynthesis. Finally, the potential applications of beneficial microorganisms in the development of microbial inoculants and the alleviation of continuous-cropping problems are discussed.},
}

@article {pmid42994041,
year = {2026},
author = {Li, W and Zhu, Q and Wu, Y and Zhu, J and Zhu, X and Li, L and Lin, F and Su, Z},
title = {A new species in the Magnaporthiopsis genus from wild rice enhances rice yield and disease resistance by restructuring the microbiome.},
journal = {Microbiological research},
volume = {315},
number = {},
pages = {128816},
doi = {10.1016/j.micres.2026.128816},
pmid = {42994041},
issn = {1618-0623},
abstract = {Wild rice serves as a rich reservoir of beneficial endophytic fungi. However, the diversity and functional potential of these endophytes remain largely unexplored, limiting their utilization in sustainable rice production. In this work, we isolated and identified a novel endophytic fungus, Magnaporthiopsis oryzae (coded MB-9-27), from wild rice, Oryza granulata, and demonstrated that it directly promotes rice growth (yield increased by 12.66%) and enhances resistance to rice blast (disease rate decreased by 45.51%) in the field. Furthermore, MB-9-27 inoculation reshaped the rice microbiome, simplifying microbial interaction networks while significantly enriching beneficial bacteria (Methylobacterium sp., Sphingomonas sp.) and fungi (Mortierella sp., Rhizophagus sp., Mollisia sp., and Coniothyrium sp.). Among 75 fungi isolated from MB-9-27-treated rice plants, five representative strains (F14: Mortierella sp., F25: Trichoderma sp., F27: Clonostachys sp., F29: Podospora sp., and F30: Pseudeurotium sp.) corresponded to taxa ranked among the top 150 dominant fungal members identified through microbiome analysis. Functional screening revealed that Mortierella sp. (coded F14) markedly promoted rice growth, increasing shoot and root development by 55.8% and 51.6%, respectively, and reducing rice blast severity by 18.2%, indicating its dual role in promoting growth and suppressing disease. Metabolomic profiling of the rice-F14 holobiont identified significant accumulation of several metabolites, including Indole-3-glycerol phosphate (IGP), Adenine, and S-lactoylglutathione (SLG), suggesting alterations in pathways related to tryptophan metabolism, cellular metabolism, and redox homeostasis. Targeted LC-MS analysis further confirmed the production of IGP by F14. Bioassays demonstrated that IGP significantly promoted rice growth, supporting a potential role of tryptophan-derived metabolites in the plant growth-promoting activity of F14. Collectively, our findings demonstrated that MB-9-27 functions not only as a growth-promoting and disease-suppressive endophyte but also as a driver of beneficial microbiota assembly. Our results highlighted the potential of wild rice-derived endophytic fungi and their associated microbiota as valuable resources for microbial-assisted sustainable rice production.},
}

@article {pmid42994147,
year = {2026},
author = {Furtado, MM and Margalho, LP and Amorim-Neto, DP and Lemos Junior, WJF and Duarte, VS and Garcia, MV and Santos, AFM and Rodrigues, DP and Copetti, MV and Sant'Ana, AS},
title = {Bacterial and fungal community dynamics in black pepper (Piper nigrum) across different processing plants using culture-based and amplicon sequencing approaches.},
journal = {International journal of food microbiology},
volume = {464},
number = {},
pages = {112149},
doi = {10.1016/j.ijfoodmicro.2026.112149},
pmid = {42994147},
issn = {1879-3460},
abstract = {Black pepper (Piper nigrum) is among the most commercially relevant spices worldwide, yet its microbial ecology throughout processing remains insufficiently understood, particularly in relation to food safety. Despite being a low-water-activity product, black pepper may harbor diverse bacterial and fungal communities, including spoilage microorganisms, mycotoxigenic fungi, and foodborne pathogens. In this study, we investigated the dynamics of bacterial and fungal communities along the black pepper processing chain in three distinct processing plants. A total of 154 samples were collected from processing plants A, B, and C in São Mateus, Espírito Santo, Brazil. Culture-dependent analyses included enumeration of aerobic mesophilic bacteria, Enterobacteriaceae, lactic acid bacteria, total fungi, and xerophilic fungi; fungal isolation and identification; and Salmonella detection and confirmation. Culture-independent profiling was performed by amplicon sequencing targeting the V3-V4 region of the 16S rRNA gene and the V9 region of the 18S rRNA gene. Microbial counts increased throughout processing, indicating that post-drying operations represent critical contamination points. Fungal isolation revealed genera of hygienic and toxicological relevance, including Aspergillus, Fusarium, Penicillium, and Cladosporium. Salmonella was detected in 14.3% of the samples, comprising nine serotypes, with the highest occurrence after drying. Amplicon sequencing identified 5 phyla and 85 genera in the fungal community, whereas for the bacterial community, 24 phyla and 475 genera were identified, with Ascomycota, Proteobacteria and Firmicutes predominating across samples. Alpha and beta diversity analyses demonstrated significant differences among processing plants and confirmed processing as a major driver of microbial community assembly. Collectively, these findings reveal processing-associated microbial shifts and underscore the urgent need for improved hygienic practices, targeted monitoring, and effective decontamination strategies for black pepper.},
}

@article {pmid42994148,
year = {2026},
author = {Myung, GE and Min, SC},
title = {L-arginine supplementation in plasma-activated water (PAW) enhances the efficacy of PAW treatment for microbial inactivation and storage stability of grape tomatoes.},
journal = {International journal of food microbiology},
volume = {464},
number = {},
pages = {112135},
doi = {10.1016/j.ijfoodmicro.2026.112135},
pmid = {42994148},
issn = {1879-3460},
abstract = {This study investigated the antimicrobial efficacy of L-arginine-supplemented plasma-activated water (Arg-PAW) against Escherichia coli O157:H7 and Listeria monocytogenes inoculated onto grape tomatoes, as well as its effects on indigenous microbial growth, microbial community composition, and nutritional attributes, including lycopene and ascorbic acid, during storage. PAW and Arg-PAW were generated by treating 1 L of distilled water or L-arginine (L-Arg) solution (1 mg/mL), respectively, for 60 min using surface dielectric barrier discharge (SDBD) atmospheric cold plasma, with electrodes positioned above the liquid surface. Individual grape tomatoes were immersed without agitation in 500 mL of DW, L-Arg, PAW, or Arg-PAW at 23.0 °C for 5 min. L-Arg supplementation increased the nitrite, nitrate, and hydrogen peroxide concentrations in PAW from 25.3, 419.5, and 1.4 μM to 59.2, 1091.9, and 46.2 μM, respectively, while reducing the ozone concentration from 208.8 to 60.0 μM. Arg-PAW exhibited a higher pH and oxidation-reduction potential but lower electrical conductivity than PAW, with values of 3.0, 610.5 mV, and 1066.2 μS/cm, respectively. Arg-PAW achieved 3.8- and 3.2-log CFU/g reductions in E. coli O157:H7 and L. monocytogenes, respectively, slightly exceeding PAW, and showed lower Ascomycota and Pseudomonas abundances and Shannon diversity on day 3. During 14 days at 4 °C, Arg-PAW maintained lower indigenous mesophilic bacterial populations without adversely affecting color or pH. Lycopene remained stable, firmness was highest with Arg-PAW, and ascorbic acid increased during storage (p < 0.05). These findings indicate that L-Arg supplementation modified the PAW reactive-species profile and modestly improved microbial control while maintaining tomato quality.},
}

@article {pmid42994308,
year = {2026},
author = {Shen, D and Lv, Y and Wu, W},
title = {Bidirectional association and mechanisms between periodontitis and inflammatory bowel disease: A systematic review.},
journal = {International immunopharmacology},
volume = {191},
number = {Pt 1},
pages = {117639},
doi = {10.1016/j.intimp.2026.117639},
pmid = {42994308},
issn = {1878-1705},
abstract = {Periodontitis and inflammatory bowel disease are bidirectionally associated, yet the molecular mechanisms linking the two mucosal sites have not been systematically integrated. This systematic review synthesized these bidirectional pathways and identified core immunological hubs, following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 guidelines. Mechanistic studies formed the core evidence, supplemented by population-based epidemiological and Mendelian Randomization studies; evidence strength was graded using a prespecified scoring system with a sensitivity analysis. Thirty-nine studies were included. Most mechanistic evidence derived from dextran sulfate sodium-induced (ulcerative colitis-like) colitis models, whereas validation in Crohn's disease-relevant models was limited. In the forward direction (periodontitis to inflammatory bowel disease), mechanisms comprised microbial translocation, metabolic disturbance, immune cell gut homing, and intestinal barrier disruption. The reverse direction was supported exclusively by preclinical models and is presented as a hypothesis. T helper 17 and regulatory T cell imbalance and dysregulated macrophage polarization constituted two shared hubs, interconnected via interleukin-1 beta and interleukin-17 A crosstalk. Macrophage polarization was the only hub with evidence in both directions, whereas Th17/Treg imbalance was robust only in the forward direction; however, a quality-restricted sensitivity analysis downgraded macrophage polarization to insufficiently supported. Preclinical modulation of either hub concurrently improved colitis and periodontitis, but clinical efficacy remains unestablished. These findings support a bidirectional association with mechanistic plausibility, although definitive causality is unproven. An asymmetrical dual-hub model is proposed for oral-gut axis research, predominantly in ulcerative colitis-like models; extrapolation to Crohn's disease requires independent validation.},
}

@article {pmid42994432,
year = {2026},
author = {Kohli, A and Hron, BM and Ebbeling, CB and Reyes, MM and Quealy, M and Gurry, T and Nguyen, LTT and Alm, EJ and Ludwig, DS and Zhang, YJ},
title = {Effects of dietary carbohydrate-to-fat ratio on the gut microbiome following weight loss.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {103137},
doi = {10.1016/j.xcrm.2026.103137},
pmid = {42994432},
issn = {2666-3791},
abstract = {Reducing dietary carbohydrates can improve metabolic health, yet the precise influence of carbohydrate restriction on the gut microbiome remains uncertain. Here, we report an ancillary study to the Framingham State Food Study, or FS(2), a controlled, randomized feeding trial involving adults with overweight and obesity. After a calorie-restriction phase to induce weight loss, we randomized participants to diets varying in energy from carbohydrate and fat (low-carb: 20% carb, 60% fat; moderate-carb: 40% carb, 40% fat; high-carb: 60% carb, 20% fat) for weight-loss maintenance for 20 weeks. Weight loss results in significant microbiome shifts, mirroring known associations. We do not detect compositional changes in the microbiome when diets vary carbohydrate-to-fat ratio, while controlling for other potentially confounding dietary factors. Changes in Shuttleworthia abundance correlate positively with maintenance of total energy expenditure following weight loss, suggesting a link between the gut microbiome and energy metabolism.},
}

@article {pmid42994532,
year = {2026},
author = {Wang, H and Shu, Z and Xie, Y and Zhang, L and Li, Q and Hu, Y and Gui, MY and Wang, M and Gu, MR and Zhu, L and Zhao, Y and Zhang, Y},
title = {Cord-serum Organophosphate Flame Retardants and Childhood Allergic Rhinitis: Multi-omics Insights.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2026.10.022},
pmid = {42994532},
issn = {1097-6825},
abstract = {BACKGROUND: Prenatal exposure to organophosphate flame retardants (OPFRs) may influence childhood allergic rhinitis (AR), but the potential involvement of the early-life gut microbiome and metabolome remains unclear.

OBJECTIVE: To evaluate associations between cord-serum OPFR concentrations and childhood AR and explore correlated microbial and metabolic pathways underlying these associations.

METHODS: OPFR-AR associations were evaluated in 1,255 children from the Shanghai Maternal-Child Pairs Cohort (MCPC), including 457 AR cases and 798 controls. Microbiome, metabolome, and exploratory correlated parallel-mediator analyses were conducted in a nested propensity-score-matched sub-study of 400 case-control pairs. Multiplicity was controlled within prespecified analysis-specific testing families using the Benjamini-Hochberg false-discovery-rate (BH-FDR) procedure.

RESULTS: Higher cord-serum concentrations of Tris (2-butoxyethyl) phosphate (TBEP) (adjusted odds ratio, OR=1.84, 95% CI: 1.63-2.09), tris(2-chloro-1-(chloromethyl) ethyl) phosphate (TDCPP) (OR=1.33, 95% CI: 1.04-1.70), and tri-m-cresyl phosphate (TMCP) (OR=1.05, 95% CI: 1.03-1.08) were associated with greater odds of childhood AR after multiple-testing correction. OPFR exposure and AR were also associated with bacterial genera and fecal metabolic features involving acetate and several tryptophan-related metabolites. Among 20 selected genus-metabolite models, 11 joint indirect associations met the full prespecified prioritization criteria.

CONCLUSION: Selected cord-serum OPFR concentrations were associated with childhood AR. Exploratory multi-omics analyses identified correlated bacterial and metabolic features consistent with potential indirect involvement in the OPFR-AR association.},
}

@article {pmid42994691,
year = {2026},
author = {Moran-Ramos, S and Alvarado-Calderon, J and Cerqueda-Garcia, D and Lopez-Contreras, BE and Villamil-Ramirez, H and Leon-Mimila, P and Aguilar-Salinas, C and Garcia, OP and Canizales-Quinteros, S},
title = {Children at risk of vitamin A deficiency exhibit taxonomic dysbiosis and functional remodeling of the gut microbiome: a matched case-control study.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101933},
doi = {10.1016/j.tjnut.2026.101933},
pmid = {42994691},
issn = {1541-6100},
abstract = {BACKGROUND: Vitamin A deficiency is one of the most prevalent micronutrient deficiencies worldwide. This condition increases susceptibility to infections and due to its role in intestinal barrier integrity, it has been suggested that it could predispose to gut dysbiosis.

OBJECTIVE: The aim of the study was to identify whether the gut microbiome of school-aged children at risk of vitamin A deficiency is associated with a dysbiotic state.

METHODS: This 1:2 matched case-control study for children at risk of vitamin A deficiency included thirteen school-aged children (6-9 years old) at risk of VAD and 26 with adequate vitamin A levels (VAA) from the ORSMEC cohort. Habitual diet was determined with a FFQ, plasma retinol levels were determined through HPLC, and gut microbial characterization was performed through shotgun sequencing.

RESULTS: In the present study, children at risk of VAD showed significantly higher levels of serum CRP (P=0.026). Although taxonomic gut microbial characterization showed no differences in alpha or beta diversity among groups, children at risk of VAD showed an enrichment of some facultative anaerobes, proposed to be established pathogens mainly from Streptococcus and Enterococcus genera (PFDR<0.1). At a functional level vitamin A status explained 7.09% of the variation in gut microbial functionality, when evaluated with the Bray-Curtis dissimilarity metric (P=0.008). Specifically, pathways related to pathogenicity such as O-antigen biosynthesis, heme biosynthesis and ethanolamine utilization were significantly enriched in children at risk of VAD (PFDR<0.1). In contrast, abundance of pathways related to B vitamins metabolism such as folate transformations, the super pathway for Coenzyme A biosynthesis and its precursor phosphopantothenate (vitamin B5) were depleted (PFDR<0.1).

CONCLUSION: Overall, our study showed that in school-aged children, being at risk of vitamin A deficiency is associated with an enrichment of potential pathobionts and a shift in gut microbial functionality that could be related to greater pathogenicity.},
}

@article {pmid42994723,
year = {2026},
author = {Agrawal, A and Lee, S and Chediak, A and Azizi, J and Labib, ME and Kulkarni, K and Gavette, M and White, J and Basile, R and Elson, N and Scott Phillips, K},
title = {Three-hospital study of endoscope protein contamination and microbiome.},
journal = {American journal of infection control},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajic.2026.11.001},
pmid = {42994723},
issn = {1527-3296},
abstract = {BACKGROUND: Over 15 million colonoscopies and 7 million upper-GI endoscopies are performed annually in the United States, requiring reprocessing after each use to reduce infection risk. Methods for endoscope quality control are limited and require rapid turnover and high sensitivity/specificity.

METHODS: Here we explore two novel approaches to measure protein soil on endoscopes: turbulent fluid flow (TFF) extraction and extractionless assay for quick check of endoscope reprocessing (QC-ER). Microbial strains in extracted samples are characterized with Next-gen sequencing and PCR.

RESULTS: Both methods are suitable for clinical use. For TFF, 68 samples across three hospitals had an average pre-cleaning protein mass of 541±342µg and post-cleaning mass of 59±57 µg. For QC-ER, 63 samples across three hospitals had an average pre-cleaning mass of 66±52µg and post-cleaning mass of 28±33µg. None of 60 samples tested positive for microbes after high-level disinfection.

DISCUSSION: In method validation, both high level disinfection exposure and clinical sample matrices interfered with protein quantification by the bicinchoninic acid (BCA) assay. TFF and QC-ER detected soil that remained after simple rinsing. Differences in clinical results for pre-cleaning were likely due to post-procedure protocols. All levels were below consensus thresholds.

PRINCIPAL CONCLUSIONS: The amount of protein on endoscopes in healthcare facilities was quantified by these methods and fell within the expected range, with variations by type and age of endoscope.},
}

@article {pmid42994767,
year = {2026},
author = {May, L and Bajaj, JS and Wolstenholme, JT},
title = {The Gut-Liver-Brain-Lung Axis in Alcohol Use Disorder: Mechanisms and Therapeutic Implications.},
journal = {Alcohol (Fayetteville, N.Y.)},
volume = {},
number = {},
pages = {107470},
doi = {10.1016/j.alcohol.2026.107470},
pmid = {42994767},
issn = {1873-6823},
abstract = {Alcohol use disorder (AUD) is a multi-organ disease associated with an increased risk of severe pneumonia and acute respiratory distress syndrome (ARDS). While alcohol-related lung disease has often been attributed to ethanol-mediated injury to the alveolar epithelium, new evidence suggests a more broad and integrated model in which pulmonary vulnerability arises as a consequence of dysregulation in the gut-liver-brain axis. This review proposes a framework to explain how chronic alcohol consumption induces dysregulation in the gut-liver-brain axis and subsequently primes the lung for failure when a secondary hit, such as sepsis or infection, occur. Drawing on human observations and mechanistic studies in experimental preclinical models, we outline four candidate pathways that may link alcohol-related gut, hepatic, and neuroimmune changes to pulmonary vulnerability: 1) alcohol induces gut barrier disruption and dysbiosis, leading to the escape of lipopolysaccharides (LPS) into circulation; 2) the liver transitions to an amplifier of inflammation, releasing inflammatory signals into systemic circulation; 3) simultaneously, neuroimmune circuits such as the vagal cholinergic anti-inflammatory pathway and the hypothalamic-pituitary-adrenal axis are disrupted by chronic alcohol exposure, resulting in delays in resolving inflammatory responses; and 4) the lungs receive these inputs on a background of glutathione depletion and innate immune dysfunction, resulting in an environment that may appear normal at baseline but is primed to fail. Recognizing alcohol-related lung disease as a potential consequence of altered gut-liver-brain signaling in the context of chronic alcohol use could provide a foundation for developing targeted therapeutic strategies for ARDS in individuals with AUD.},
}

@article {pmid42994768,
year = {2026},
author = {Blinchevsky, N and Weed, M and Liangpunsakul, S and Llorente, C and Melamed, E},
title = {Vagus Nerve Stimulation as a Potential Therapeutic Strategy for Alcohol Use Disorder.},
journal = {Alcohol (Fayetteville, N.Y.)},
volume = {},
number = {},
pages = {107469},
doi = {10.1016/j.alcohol.2026.107469},
pmid = {42994768},
issn = {1873-6823},
abstract = {Alcohol use disorder (AUD) contributes to approximately 3 million deaths worldwide each year and leads to substantial emotional, financial, and social implications for individuals and their families. AUD leads to multi-system damage, including the immune system, gut microbiome, neuroendocrine pathways, and the brain. Current treatments for AUD, focused primarily on behavioral and pharmaceutical interventions, insufficiently address alcohol's extensive impact on multiple body systems. Vagus nerve stimulation (VNS) has shown therapeutic benefits across a spectrum of neurological conditions, including epilepsy, depression, and addictive disorders. More recently, VNS is being investigated as a potential promising adjunctive treatment for AUD, which may complement currently used treatments by targeting many of the body systems dysregulated in AUD. Preclinical and clinical models have evaluated different VNS paradigms, including invasive, noninvasive, and minimally invasive approaches targeting motor and cognitive rehabilitation, withdrawal symptoms, and relapse during abstinence. However, while VNS has many promising potential benefits for improving AUD outcomes, direct evidence that VNS reduces alcohol consumption, alcohol seeking, or craving in AUD remains limited, and there are several logistical and ethical considerations that researchers, clinicians, and policymakers should evaluate before VNS is considered standard of care. Additionally, optimization of VNS parameters, modality (implanted versus noninvasive or minimally invasive), and development of responder biomarkers could better inform patient selection for VNS. Although significant work remains before transitioning VNS into clinical practice, VNS offers an exciting opportunity for adjunctive treatment in AUD that could potentially target multi-system AUD dysfunction.},
}

@article {pmid42994801,
year = {2026},
author = {Salas-Salvadó, J and García-Gavilán, J and Ni, J and Hernández-Cacho, A and Plaza-Diaz, J},
title = {Perspective. Precision Nutrition at a Crossroads: From Biological Prediction to Contextual Implementation.},
journal = {Advances in nutrition (Bethesda, Md.)},
volume = {},
number = {},
pages = {100764},
doi = {10.1016/j.advnut.2026.100764},
pmid = {42994801},
issn = {2156-5376},
abstract = {Precision nutrition has substantially reshaped nutritional science by demonstrating that individuals can respond differently to identical dietary exposures. Advances in genomics, metabolomics, proteomics, microbiome research, wearable technologies, digital health, and artificial intelligence have improved our ability to characterize biological heterogeneity and predict individual responses to diet. However, demonstrating such variability does not necessarily result in nutritional strategies that provide clinically meaningful benefits beyond established evidence-based care. A critical distinction should therefore be made between precision nutrition as a discovery science, which has convincingly established interindividual heterogeneity in dietary responses, and precision nutrition as an intervention science, which must demonstrate meaningful incremental value over dietary approaches already supported by clinical evidence. Despite increasingly sophisticated technologies and predictive models, evidence of consistent improvements in long-term health outcomes, cost-effectiveness, scalability, and equity remains limited. In this Perspective, we argue that precision nutrition has reached a critical crossroads. We distinguish prediction of individual responses, which is only one route to precision nutrition, from treatment-effect heterogeneity, treatment selection and clinical utility. We then propose contextual precision nutrition as a translational framework that integrates biological responsiveness with the behavioral, psychological, social, cultural, economic, and environmental determinants of dietary behavior. Rather than claiming novelty for these components, the framework integrates them into a decision logic that asks whether biological information improves the selection of a dietary strategy beyond routine information and established care, and how that strategy can be delivered and sustained. It complements population-based dietary recommendations by refining their implementation and maximizing adherence and real-world effectiveness. Ultimately, the success of precision nutrition will be determined not by the sophistication of its predictions but by its ability to translate biological knowledge into interventions that are clinically effective, scalable, equitable, and sustainable, thereby improving both individual and population health.},
}

@article {pmid42994968,
year = {2026},
author = {Yuan, X and Wu, L and Wang, Y and Zhao, Y and Zhou, L and Zhao, J},
title = {From systemic to oral: Unifying immunological mechanisms via the gut microbiome axis.},
journal = {Virulence},
volume = {17},
number = {1},
pages = {2750615},
doi = {10.1080/21505594.2026.2750615},
pmid = {42994968},
issn = {2150-5608},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Animals ; Intestinal Barrier Function ; Dysbiosis/immunology/microbiology ; *Mouth Diseases/immunology/microbiology ; Fecal Microbiota Transplantation ; Probiotics ; Immunity, Mucosal ; Mouth/immunology/microbiology ; },
abstract = {While the gut microbiome regulates host homeostasis and systemic disease via the gut-immune axis, its potential role in regulating oral diseases remains underexplored. This review examines how established gut microbiome-immune mechanisms may contribute to oral inflammation and their therapeutic potential. Gut microbiome dysbiosis may influence oral diseases through microbial metabolites, intestinal barrier dysfunction, inflammatory signaling, and immune regulation. Evidence from systemic diseases supports these mechanisms and provides a rationale for microbiome-targeted approaches, including probiotics, dietary interventions, and fecal microbiota transplantation. However, direct clinical evidence in oral diseases remains limited and heterogeneous. Future research should clarify bidirectional gut-oral interactions, standardize microbiome assessment and clinical outcomes. Well-designed clinical studies are needed to address these limitations and translate the gut-oral axis into meaningful interventions.},
}

Humans
*Gastrointestinal Microbiome/immunology
Animals
Intestinal Barrier Function
Dysbiosis/immunology/microbiology
*Mouth Diseases/immunology/microbiology
Fecal Microbiota Transplantation
Probiotics
Immunity, Mucosal
Mouth/immunology/microbiology

@article {pmid42995195,
year = {2026},
author = {Qi, W and Chen, X and Guo, H and Zhu, S and Zhou, Z and Xu, L and Yan, Q and Gu, FF and Liu, JX and Sun, HZ},
title = {Microbiome-derived proline dipeptides underpin improved nitrogen utilization efficiency in dairy cattle.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42995195},
issn = {2041-1723},
support = {no. 32322077//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; Cattle ; *Dipeptides/metabolism ; *Nitrogen/metabolism ; *Proline/metabolism ; Rumen/microbiology/metabolism ; Female ; Fermentation ; Milk/metabolism ; *Microbiota ; Dairying ; Metagenomics ; Metabolomics ; *Gastrointestinal Microbiome ; },
abstract = {Dairy production is constrained by low nitrogen utilization efficiency (NUE; milk N/intake N), leading to nitrogen losses and environmental pollution. Although the rumen microbiome is central to nitrogen turnover, the role of small peptides, a critical nitrogen pool, remains poorly understood. Here, we constructed a genome-resolved atlas of predicted small-peptide metabolism and integrated high-performance chemical isotope-labeling metabolomics with metagenomics in 30 dairy cows. Among 349 detected small peptides, proline-containing dipeptides were associated with higher NUE, together with an S15 peptidyl-peptidase with Xaa-Pro dipeptide-generating activity. In vitro rumen fermentation, metatranscriptomics and targeted quantification showed that proline-dipeptide accumulation coincided with transcriptional patterns consistent with nitrogen assimilation and amino acid biosynthesis. Bacterial incubation and heterologous expression confirmed that S15.001 hydrolyzed Xaa-Pro substrates. These findings identify a microbial proline-dipeptide axis associated with NUE and provide a basis for precision nutrition strategies targeting ruminal peptide metabolism.},
}

Animals
Cattle
*Dipeptides/metabolism
*Nitrogen/metabolism
*Proline/metabolism
Rumen/microbiology/metabolism
Female
Fermentation
Milk/metabolism
*Microbiota
Dairying
Metagenomics
Metabolomics
*Gastrointestinal Microbiome

@article {pmid42995217,
year = {2026},
author = {Brodeur, GM and MacFarland, SP and Brodeur, GC and Porter, CC and Villani, A and Malkin, D},
title = {Emerging strategies for paediatric cancer predisposition: detection, surveillance and prevention.},
journal = {Nature reviews. Clinical oncology},
volume = {},
number = {},
pages = {},
pmid = {42995217},
issn = {1759-4782},
abstract = {A substantial proportion of childhood cancers occur in children who are genetically predisposed to develop that cancer. Close surveillance of children with cancer predisposition syndromes enables early cancer detection and results in better survival outcomes and less therapy-related toxicity, although many more predisposition syndromes are likely to exist and remain undetected. Building on conventional clinical surveillance protocols, new approaches are being explored, including liquid biopsy, molecular or metabolic biomarkers, enhanced imaging and microbiome profiling for the purposes of both improved surveillance and the discovery of additional predisposing factors. Knowing the specific genes, expressed proteins and biological pathways associated with a specific cancer predisposition syndrome might permit the use of targeted agents or vaccines, as well as the introduction of lifestyle changes to delay, reduce or even eliminate the development of cancer. Preclinical studies investigating the risks and benefits of preventive interventions would be greatly aided by the identification or development of animal models that faithfully recapitulate human syndromes. The incorporation of artificial intelligence to complement the clinical and experimental assessment of cancer risk based on the syndrome, genotype, modifier genes, family history, environmental exposures and other factors will undoubtedly improve the management and, ultimately, the outcomes of children with an increased genetic risk of cancer. In this Perspective, we discuss strategies to identify new cancer predisposition genes, developing approaches to cancer surveillance, emerging efforts for cancer prevention in high-risk patients, and the role of artificial intelligence in improving data analysis and optimizing medical decision-making.},
}

@article {pmid42995255,
year = {2026},
author = {Winkler, MKH and Ash, SR and Barraclough, KA and Bluechel, C and Ferrell, N and Fissell, W and Freedman, BS and Gerritsen, KGF and Hassan, HA and Hentschel, DM and Hestekin, J and Hughes, A and Johnson, DG and Krendel, M and Li, Z and Locke, JE and Montserrat, N and Nishinakamura, R and Plisiewicz, A and Ratner, BD and Roberts, GV and Roy, S and Sirich, TL and Subramanya, AR and Wasse, H and Wiener, S and Wieringa, F and Wolf, K and Himmelfarb, J},
title = {An integrative roadmap for a new era of kidney replacement therapies.},
journal = {Nature reviews. Nephrology},
volume = {},
number = {},
pages = {},
pmid = {42995255},
issn = {1759-507X},
abstract = {Innovation in kidney replacement is entering a transformative era. Although precision medicine has driven major breakthroughs in disease-specific therapies, progress in translating next-generation kidney replacement strategies into practice has lagged. This updated Roadmap highlights a shift toward bold, integrative approaches that merge engineering, biology and patient-centred design. Emerging directions include reimagining filtration and tubular function through biomimetic membranes, cellular systems and organ-on-chip technologies, and simultaneously exploring microbiome modulation and sorbent-based strategies to reduce the uraemic toxin burden. Beyond improving survival, new solutions are being shaped by priorities of mobility, sustainability and quality of life, pointing toward wearable and implantable systems that move care beyond the clinic. Biologic frontiers such as xenotransplantation and stem cell regeneration are opening pathways to potentially curative therapies, although challenges in safety, equity and scalability remain. Central to these efforts is the need to embed patient perspectives and ensure that innovations align with lived experiences. This integrative approach calls for renewed investment, regulatory clarity and cross-sector collaboration to accelerate translation of advances into equitable therapies redefining the future of kidney health.},
}

@article {pmid42995260,
year = {2026},
author = {Morris, LM and Boucher, M and Service, C and Anderson, JT and Rainwater, TR and Parrott, BB and Goffredi, SK},
title = {Microbiome Diversity, Persistence, and Potential Symbiont Dynamics in Placobdella Leeches from American Alligators.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {42995260},
issn = {1432-184X},
support = {2030763//National Science Foundation/ ; SC-1700590//United States Department of Agriculture's National Institute of Food and Agriculture/ ; DE-EM0004391//U.S. Department of Energy/ ; },
mesh = {Animals ; *Symbiosis ; *Leeches/microbiology/physiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Alligators and Crocodiles/parasitology ; *Bacteria/classification/genetics/isolation & purification ; Phylogeny ; },
abstract = {Placobdella leeches are common ectoparasites of reptiles that rely on microbial symbionts to supplement the nutritional limitations of blood feeding. Although the primary symbiont Reichenowia is documented, little is known about the broader microbial community or ecological factors that influence Placobdella microbiome assembly. Here, we characterized the whole-body microbiomes of seven Placobdella clades from American alligators (Alligator mississippiensis) across the southeastern United States. Sampling revealed four Placobdella lineages not previously reported from alligators, including several undescribed species. Placobdella microbiomes, based on 16S rRNA gene sequencing, were dominated by Actinobacteriota, Alphaproteobacteria, Bacteroidota, and Pseudomonadota (the former Betaproteobacteria). Although microbiome composition was not strongly structured by leech clade, geography, or habitat type, location-specific bacterial signatures were observed. Captivity experiments resulted in significant declines in microbial diversity, and persistence of four bacterial taxa. Comparisons between leech microbiomes and microbial communities on alligator skin revealed limited overlap. Additionally, while a distinct Reichenowia lineage was generally associated with each Placobdella species, multiple low-abundance Reichenowia variants were detected within individuals, and an identical Reichenowia variant occurred in sympatric Placobdella species. Together, these results identify a conserved candidate core microbiome in Placobdella and demonstrate that microbiome assembly in blood-feeding leeches reflects persistent symbiotic interactions and ongoing environmental acquisition.},
}

Animals
*Symbiosis
*Leeches/microbiology/physiology
RNA, Ribosomal, 16S/genetics
*Microbiota
*Alligators and Crocodiles/parasitology
*Bacteria/classification/genetics/isolation & purification
Phylogeny

@article {pmid42995425,
year = {2026},
author = {Fay, BP and Tam, J and Wrobel, JA and Huang, G and Chou, WE and Sheikh, SZ and Furey, TS and Sartor, RB and Guo, H and Ting, JP},
title = {The role of NLRC5 in human inflammatory bowel diseases and murine experimental colitis.},
journal = {Journal of immunology (Baltimore, Md. : 1950)},
volume = {215},
number = {11},
pages = {},
doi = {10.1093/jimmun/vkag263},
pmid = {42995425},
issn = {1550-6606},
support = {P01 DK094779/DK/NIDDK NIH HHS/United States ; R01 DK138462//NIH/NIDDK/ ; R01 DK136262//NIH/NIDDK/ ; T32-CA009156//UNC-ITCMS/ ; //P40 OD010995/ ; //Crohn's and Colitis Foundation/ ; },
mesh = {Animals ; Humans ; *Intracellular Signaling Peptides and Proteins/genetics/metabolism/immunology ; Mice ; *Colitis/immunology/chemically induced/metabolism ; *Inflammatory Bowel Diseases/immunology/metabolism ; Disease Models, Animal ; Gastrointestinal Microbiome/immunology ; Mice, Knockout ; },
abstract = {Nucleotide-binding, leucine-rich repeat-containing (NLR) innate immune proteins have been implicated in inflammatory bowel diseases (IBD). NLRC5 is a key trans-activator of class I MHC (MHC-I) genes, but it is also found to regulate cytokines and cell death. Meta-analysis of 14 different human RNAseq or microarray data (total n = 1,093) revealed a consistent and strong association between IBD and heightened NLRC5 expression, suggesting a role for NLRC5 across diverse IBD patients. Furthermore, these data show a strong correlation of NLRC5 with inflammation and STAT1 signatures, suggesting that its role in human IBD may extend beyond its canonical role as a regulator of MHC-I, or that its expression is controlled by inflammation/STAT1. However, in the dextran sulfate sodium (DSS)-induced colitis mouse model, Nlrc5 protected against colitis, which mimicked B2m-/- mice lacking MHC-I. This Nlrc5-associated protection has been consistent across hundreds of mice over a decade in the hands of several investigators. Microbiome study found significant alterations in the microbiota in overall composition and strain-specific differences over time, suggesting a dynamic relationship between microbiome dysbiosis and Nlrc5. To resolve these issues, we studied germ-free (GF) wild-type and Nlrc5-/- mice. Surprisingly, GF mice showed that Nlrc5 exacerbated instead of protected against DSS-induced colitis. A major difference between GF and conventionally-raised mice is that DSS reduced Nlrc5/ 2m expression in GF mice, while it did the opposite in SPF mice. These data highlight the complex role of Nlrc5 and the microbiome in the pathogenesis of IBD, as well as the necessity of complementary mouse models.},
}

Animals
Humans
*Intracellular Signaling Peptides and Proteins/genetics/metabolism/immunology
Mice
*Colitis/immunology/chemically induced/metabolism
*Inflammatory Bowel Diseases/immunology/metabolism
Disease Models, Animal
Gastrointestinal Microbiome/immunology
Mice, Knockout

@article {pmid42995442,
year = {2026},
author = {Yin, C and He, Y and Wang, P and Xu, Z},
title = {Hypersensitivity Pneumonitis: Clinical Paradigm Evolution, Immune-Driven Mechanisms, and Fibrotic Progression.},
journal = {Journal of immunology research},
volume = {2026},
number = {1},
pages = {},
doi = {10.1155/jimr/1288887},
pmid = {42995442},
issn = {2314-7156},
support = {82570097//National Natural Science Foundation of China/ ; 7262089//Natural Science Foundation of Beijing Municipality/ ; ZC201906243//Integrated Research Funding for Accumulated Projects of Peking Union Medical College Hospital/ ; },
mesh = {Humans ; *Alveolitis, Extrinsic Allergic/diagnosis/immunology/etiology/therapy/pathology ; Disease Progression ; Animals ; Idiopathic Pulmonary Fibrosis/immunology ; Adaptive Immunity ; Gene-Environment Interaction ; },
abstract = {Hypersensitivity pneumonitis (HP) is a complex immune-mediated interstitial lung disease (ILD) triggered by inhaled antigens in genetically susceptible individuals. Recent diagnostic paradigms have shifted from exposure-centric empiricism to fibrosis-based stratification and, most recently, separation of etiology from morphology, with fibrotic HP (FHP) now recognized as a progressive fibrotic phenotype distinct from yet overlapping with idiopathic pulmonary fibrosis (IPF). Mechanistically, HP progression reflects a sequential cascade involving gene-environment interactions, dysregulated innate and adaptive immunity, and maladaptive repair. Early disease is characterized by Th1/Th17-driven granulomatous inflammation, whereas chronic FHP exhibits Th2/M2 polarization, tertiary lymphoid structures, B-cell dysregulation, cellular senescence, lung microbiome dysbiosis, and persistent fibroblast activation, ultimately leading to progressively less reversible remodeling. Despite shared terminal pathways with IPF (e.g., extracellular matrix (ECM) deposition, EndoMT, and SASP), FHP may be conceptualized as predominantly inflammation-driven or "top-down," whereas IPF is often viewed as predominantly epithelial injury-driven or "bottom-up"; however, these heuristic models are not mutually exclusive and do not establish a discrete mechanistic transition or a uniform therapeutic window. Antigen avoidance remains the cornerstone of management; immunomodulatory treatment may be considered in selected inflammation-predominant phenotypes, whereas antifibrotic treatment may be considered when FHP meets criteria for progressive pulmonary fibrosis. The role of combined therapy remains uncertain, and strategies targeting IL-17, IL-6, or JAK-STAT remain investigational in HP. Early diagnosis is hindered by occult antigens and nonspecific presentations. Future advances will depend on multiomics integration, novel antigen-detection tools, and biomarkers that may help characterize the proposed transition from predominantly antigen-responsive inflammation toward fibrosis-dominant remodeling. Resolving whether a clinically meaningful transition exists may support a more mechanism-informed approach to HP. Unlike previous reviews focusing on diagnostic criteria, this review integrates our interpretation of the morphology-etiology distinction emphasized by the 2025 ERS/ATS classification update with single-cell-resolved immune evidence and uses the "immunofibrotic switch" as an integrative hypothesis rather than an established biological transition.},
}

Humans
*Alveolitis, Extrinsic Allergic/diagnosis/immunology/etiology/therapy/pathology
Disease Progression
Animals
Idiopathic Pulmonary Fibrosis/immunology
Adaptive Immunity
Gene-Environment Interaction

@article {pmid42995531,
year = {2026},
author = {Jentzsch, J and Wirtz, S and Brunner, M and Ribback, S and Kneis, B and Weber, K and Denz, A and Grützmann, R and Schierwagen, R and Tyc, O and Trebicka, J and Kersting, S and Langheinrich, M},
title = {Longitudinal gut microbiome dynamics in rectal cancer: associations with neoadjuvant therapy and tumor regression.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42995531},
issn = {1471-2180},
mesh = {Humans ; *Rectal Neoplasms/microbiology/therapy ; *Neoadjuvant Therapy ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Female ; Male ; Prospective Studies ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Longitudinal Studies ; Middle Aged ; Aged ; Treatment Outcome ; },
abstract = {BACKGROUND: The gut microbiome has emerged as a key modulator of colorectal cancer biology, influencing tumor progression and therapeutic response. However, most existing studies analyze colorectal cancer as a single entity despite biological and therapeutic differences between colon and rectal cancer. Consequently, longitudinal data linking microbiome dynamics to treatment response, particularly in rectal cancer, remain limited.

METHODS: In this prospective cohort study, 31 patients with rectal cancer were included, of whom 17 received neoadjuvant therapy and 14 underwent primary surgery. A total of 110 stool and tissue samples were collected at defined time points before, during, and after treatment. Microbial composition and diversity were analyzed using 16S rRNA gene sequencing. Alpha and beta diversity metrics, differential abundance analyses, and longitudinal comparisons were performed to assess treatment-related microbiome alterations.

RESULTS: Distinct microbial communities were observed between stool and tissue samples, with stool samples enriched in Bacteroidetes and tissue samples dominated by Firmicutes, Actinobacteria, and Verrucomicrobia. Neoadjuvant therapy was associated with a marked reduction in microbial diversity with no recovery before surgery, and community composition shifted significantly over the treatment course (patient-constrained PERMANOVA, p = 0.0016), with Clostridium XIVa becoming the dominant genus before surgery. Longitudinal analyses further revealed exploratory differences between patients with complete and incomplete tumor regression. Between diagnosis and surgery, patients achieving complete tumor regression (Dworak TRG 4) showed an increase in the propionate-producing genus Phascolarctobacterium, the only genus significant after correction for multiple testing, together with an exploratory rise in the butyrate-producing genus Roseburia. Higher Bacteroides in patients with incomplete regression was a descriptive observation that was not statistically significant (p = 0.35, q = 0.71). No genus-level differences between response groups were detected at baseline after correction for multiple testing; however, the small sample size limits the ability to exclude baseline differences.

CONCLUSIONS: Rectal cancer treatment induces distinct and time-dependent alterations in the gut microbiome. Complete tumor regression was associated with an increase in short-chain fatty acid-producing taxa, led by the propionate producer Phascolarctobacterium, whereas higher Bacteroides in incomplete responders was a non-significant, exploratory observation. Given the growing role of organ-preserving strategies such as watch-and-wait, in which reliable identification of complete response is critical, these exploratory patterns warrant validation in larger cohorts.},
}

Humans
*Rectal Neoplasms/microbiology/therapy
*Neoadjuvant Therapy
*Gastrointestinal Microbiome/genetics
RNA, Ribosomal, 16S/genetics
Female
Male
Prospective Studies
Feces/microbiology
*Bacteria/classification/genetics/isolation & purification
Longitudinal Studies
Middle Aged
Aged
Treatment Outcome

@article {pmid42995617,
year = {2026},
author = {Swift, JF and Trello, GE and Harris, ZN and Migicovsky, Z and Miller, AJ},
title = {Conserved rhizosphere microbiomes and metabolic functions across diverse grapevine rootstocks: implications for plant elemental composition.},
journal = {Environmental microbiome},
volume = {21},
number = {1},
pages = {},
pmid = {42995617},
issn = {2524-6372},
support = {2305703//National Science Foundation/ ; 1546869//National Science Foundation/ ; CRC-2021-00314//Natural Sciences and Engineering Research Council/ ; },
abstract = {BACKGROUND: While grapevine rootstocks are essential to commercial viticulture, researchers still lack a complete understanding of how these root systems and their associated microbiomes influence the vine's mineral nutrition. Previous research has shown that rootstocks with similar pedigrees, reflecting the limited number of parental genotypes in the breeding pool, affect both the vine's elemental profile and microbiome composition. Here, we extend this work by surveying a broader diversity of rootstock genotypes representing distinct parentage groups across multiple scions and by assessing both functional and taxonomic correlations between the rhizosphere metagenome and vine elemental composition.

RESULTS: We used a rootstock diversity trial with ten rootstock genotypes grafted to one of two scions to simultaneously characterize the rhizosphere metagenome and elemental composition of both berries and roots. We found that elemental composition varied strongly among vine compartments, while scion and rootstock had comparatively minor effects. Berries of 'Cabernet Sauvignon' contained higher concentrations of boron, potassium, and phosphorus than those of 'Chardonnay'. Only three elements in root tissues differed among rootstock genotypes, and these differences were unrelated to genetic relatedness among rootstocks. Rhizosphere microbiome composition was also conserved across rootstocks, suggesting that diverse genotypes recruit a consistent microbial community with similar functional potential. By linking rhizosphere microbiome profiles with root elemental composition, we found that Streptomyces and Mesorhizobium were significantly associated with elemental patterns, showing negative correlations with a principal component heavily loaded for molybdenum, cadmium, potassium, and iron.

CONCLUSIONS: Our findings suggest that vine compartment is a dominant influence on elemental composition, while rootstock genotypes have comparatively modest effects. Despite the overall conservation of the rhizosphere microbiome, specific microbial taxa were associated to elemental variation, highlighting potential microbe-element correlations that may influence nutrient dynamics in the grapevine rhizosphere. These results provide a step towards disentangling how root-associated microbes contribute to vine mineral nutrition, or vice versa, across diverse rootstock genotypes.},
}

@article {pmid42995884,
year = {2026},
author = {Karstens, L and Lamp, B and Kudrick, J and Siddiqui, N},
title = {Advances in 16S Taxonomic Classification: Impacts on Species-Level Resolution of Female Bladder Microbiota.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.16.759675},
pmid = {42995884},
issn = {2692-8205},
abstract = {Bacteria are present in the human urinary bladder, even in the absence of infection. These bacteria comprise the urinary microbiome, or urobiome, and have the potential to promote bladder health or contribute to pathology. Despite its importance, studying the urobiome remains challenging given the high proportion of host to bacterial cells and low microbial biomass. The leading method for studying the urobiome has been 16S rRNA amplicon sequencing. This culture-independent approach provides a cost-effective method for identifying bacteria, but taxonomic classification accuracy depends on three key factors: 1) the variable region targeted; 2) the reference database; and 3) the classification algorithm. In 2021, Hoffman et al. demonstrated that species-level classification of bladder microbiota was possible and that the database used was the most important factor, followed by the variable region. Here, we provide an updated analysis evaluating classification schemes using updated taxonomic databases, most notably GreenGenes2, and expand the analysis to full length 16S gene sequencing. We show that updated taxonomic reference databases improve the ability to identify bladder microbiota at the species level and that long-read sequencing of the full length 16S rRNA gene further improves species identification. These innovations may allow for enhanced discoveries when studying bladder bacteria in the context of bladder disorders.},
}

@article {pmid42995906,
year = {2026},
author = {Leon, F and Shih, JB and Keller, LE and Palaniappan, S and Degaetano, L and Nine, GA and Lind, AL},
title = {A novel clonal and axenic isolation pipeline for the human gut protist Blastocystis reveals within-subtype strain coexistence.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.19.760120},
pmid = {42995906},
issn = {2692-8205},
abstract = {UNLABELLED: Blastocystis is the most prevalent protist in the human gut microbiome, but its study is impeded by limitations in existing cultivation methods that hinder routine axenic and clonal isolation. These barriers have left open the question of whether multiple strains of a protist species can coexist within a single host, as observed within the bacterial gut microbiota. To address this, we introduce egg-based monophasic (EBM) medium, a novel optically clear liquid medium that supports exponential growth of Blastocystis from low inoculum densities in standard tissue-culture plates and flasks, a capability not supported by existing media formulations tested here. Using EBM medium, we established a modular axenization and clonal isolation pipeline and recovered axenic and clonally isolated cultures representing Blastocystis subtypes 1-4 from human and non-human primate hosts. To investigate within-host strain diversity, we sequenced a subtype 1 culture before and after clonal isolation. The non-clonal culture yielded a 21 Mb assembly with gene copy distribution and allelic polymorphism patterns consistent with multiple strains, whereas its clonal derivative yielded a 15 Mb assembly with patterns consistent with a single strain. These results indicate that the original culture contained multiple closely related strains co-colonizing one host. We identified the same genomic signature in published xenic cultures established from single human donors, supporting the presence of strain-level diversity within Blastocystis subtypes. Our pipeline provides a scalable platform for Blastocystis cultivation, imaging, and clonal isolation, enabling investigation of strain-level diversity that may be obscured in non-clonal cultures.

IMPORTANCE: Blastocystis is the most prevalent protist in the human gut, yet experimental investigation remains limited by a difficulty in obtaining single-microbe and genetically defined cultures. Existing methods make it difficult to separate the protist from associated bacteria or recover individual lineages from mixed cultures. We developed a liquid growth medium compatible with standard tissue culture plates, live-cell imaging, and a modular workflow for producing axenic and clonal isolates. We use this pipeline to create axenic and clonal isolates across four common subtypes. Applying this workflow exposed a mixture of closely related strains in a single-subtype culture, a finding supported by analyses of independent published cultures. This culturing pipeline enables controlled investigation of strain-level diversity, and provides a new experimental framework for the study of Blastocystis biology and its interactions with the gut microbiome.},
}

@article {pmid42995909,
year = {2026},
author = {Schiro, G and Patel, A and Tierney, E and Pasch, B and Upham, NS and Suzuki, TA},
title = {Conserved patterns of mammal-microbe codiversification and interspecific bacterial sharing.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.16.759742},
pmid = {42995909},
issn = {2692-8205},
abstract = {What determines whether a gut microbial lineage has fidelity to one host species or is shared freely across multiple species? Factors that predict microbial community composition, including host species, diet, and environmental variation, have been well documented in wild animals. However, the eco-evolutionary processes maintaining host species- or population-specific microbial lineages remain unresolved. Here, we analyze 519 gut microbiome samples collected from 15 species of wild rodents across two mountains in the Madrean Sky Islands of southeastern Arizona using full-length 16S rRNA sequencing. This montane system provides a natural experiment in which adjacent replicated elevational gradients bring different combinations of rodent species into sympatry, allowing host evolutionary history to be disentangled from shared environmental effects. We find that host phylogeny, rather than environment, is the primary driver of microbial strain sharing across host species. We recover replicated signatures of codiversification on both mountains, indicating shared evolutionary history between hosts and their microbes, despite ample opportunities for cross-species environmental transmission. This evolutionary coupling is associated with predicted differences in bacterial oxygen tolerance and optimal growth temperature: codiversifying lineages are predominantly obligate anaerobes with optimal growth near host body temperature, suggesting more limited out-of-host persistence than non-codiversifying taxa. This pattern mirrors findings from the human gut microbiome, suggesting conserved constraints on microbial dispersal across mammalian hosts. The cost-effectiveness of long-read amplicon sequencing for phylogenetic inference within bacterial species opens new opportunities for large-scale evolutionary and ecological studies of host-microbe interactions in wildlife.},
}

@article {pmid42995936,
year = {2026},
author = {Schedler, A and McCollough, K and Rogers, F and Macomb, K and Song, MJ and Ekwealor, JTB},
title = {Epiphytic cryptogam communities differ little despite strong variation in coastal fog exposure.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.16.759761},
pmid = {42995936},
issn = {2692-8205},
abstract = {Because mosses and lichens obtain water directly from their surroundings, coastal fog is expected to strongly influence epiphytic cryptogam communities during the long summer droughts of Mediterranean-climate ecosystems. We examined epiphytic mosses and lichens on coyote brush (Baccharis pilularis) across coastal and inland transects on San Bruno Mountain, California, where marine-layer exposure produces a sharp local microclimate gradient. We surveyed coyote brush availability, sampled standardized branches, monitored temperature and relative humidity, and quantified cryptogam occurrence, diversity, morphology, and reproduction. Morphological and chemical identifications were supplemented with molecular markers, while bacterial 16S sequencing was used to characterize cryptogam-associated microbiomes across host taxa and, for the dominant moss Pulvigera pringlei , across transects. Coastal microsites were cooler and more humid, whereas inland microsites experienced substantially greater daytime atmospheric drying demand. Despite this pronounced environmental contrast, cryptogam abundance, reproduction, and visible community composition differed little between transects, although branch-level genus diversity was modestly higher on the coastal transect. Macrolichen lobe or branch length and cryptogam patch area were greater inland in pooled comparisons, but these differences weakened after accounting for taxonomic composition. Bacterial communities differed strongly among cryptogam host taxa, but the P. pringlei microbiome showed no detectable difference in diversity or composition between coastal and inland transects. The broad similarity of cryptogam communities across a strong fog gradient is consistent with buffering of epiphytic cryptogams against fine-scale variation in marine-layer exposure. For the predominantly green-algal lichens in this community, the ability to absorb water vapor from humid air may reduce dependence on direct fog wetting, while host-associated bacterial communities may be structured more strongly by host identity than by local microclimate. Together, our results show that epiphytic cryptogam communities and microbiomes can remain remarkably similar across pronounced microclimatic variation despite modest morphological shifts.},
}

@article {pmid42995949,
year = {2026},
author = {Turabi, K and Sardarni, UK and Ankenbauer, KE and Torbit, SM and Taranto, CP and Dash, S and Meade, A and Cephas, AT and Klute, KA and Pasca di Magliano, M and McFall, T and DelGiorno, KE and Bailey-Lundberg, JM},
title = {Oncogenic KRAS-MAPK signaling sustains a CD73 dependent therapeutic vulnerability in pancreatic cancer.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.20.760559},
pmid = {42995949},
issn = {2692-8205},
abstract = {Pancreatic ductal adenocarcinoma (PDAC) is predominantly driven by oncogenic KRAS signaling and sustained by a desmoplastic, immunosuppressive microenvironment limiting therapeutic response. CD73-mediated adenosine signaling supports this immune-excluded, tumor-supportive microenvironment. Whether dual targeting of KRAS-MAPK and CD73 signaling creates a therapeutic opportunity to improve tumor control remains unexplored. Analysis of KRAS -mutant cancer cell lines revealed increased expression of NT5E and adenosine receptor ADORA2B . Pharmacologic and genetic suppression of oncogenic KRAS inhibited CD73 expression through a MAPK-dependent program. In syngeneic KPC tumors, conversely, CD73 inhibition with quemliclustat increased ERK phosphorylation in vivo , suggesting adaptive MAPK activation following CD73 blockade. Combined CD73 and RAS(ON) inhibition in vivo produced the strongest antitumor response, reducing endpoint tumor volume beyond either monotherapy. This combination significantly suppressed tumor proliferation and αSMA-positive stroma and resulted in a substantial reduction in CD163-positive macrophage infiltration. RAS-MAPK targeted therapy was also associated with increased CD8α-positive T cell infiltration and granzyme B-positive staining. As therapeutic responses in PDAC have been linked to the gut microbiome, we further examined treatment-associated changes in the microbiome. RAS-MAPK inhibition produced the most pronounced microbial alterations, which correlated with tumor volume and immune markers. Together, these findings identify KRAS-MAPK driven CD73 signaling as a therapeutic vulnerability in PDAC and support combined CD73 and RAS(ON) inhibition as a strategy to suppress tumor growth, remodel stroma, and alleviate tumor-associated immune suppression.},
}

@article {pmid42996130,
year = {2026},
author = {Vega-Rodríguez, J and Saraiva, FS and Silva, TAE and da Cunha, OT and Iniguez, E and Alvarenga, P and Barletta, A and Kudyba, H and Minai, M and Suzuki, M and Tolosano, E and Alves, D and Valenzuela, J and Barillas-Mury, C and Kamhawi, S},
title = {Mammalian Hemopexin Protects Blood-Feeding Dipterans from Heme Toxicity and Promotes Parasite Transmission.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-10295862/v1},
pmid = {42996130},
issn = {2693-5015},
abstract = {Blood feeding exposes arthropod vectors and the pathogens they transmit to toxic heme released during hemoglobin digestion. Although mammalian blood proteins can cross the mosquito midgut into the hemolymph, whether they remain biologically active within the vector is unknown. Proteomic analysis of Anopheles gambiae hemolymph identified mammalian proteins enriched by Plasmodium infection, including several involved in heme and iron metabolism. This enrichment was dependent on parasite invasion of the midgut epithelium. We show that mammalian hemopexin, a high-affinity heme scavenger, retains its heme-binding activity within mosquito tissues, where it mitigates heme toxicity, preserves midgut barrier integrity and microbiome homeostasis, and promotes Plasmodium development. These protective effects were lost with recombinant hemopexin unable to bind heme, establishing heme scavenging as the underlying mechanism. Hemopexin also promoted Leishmania parasite development in the sand fly and supported the fitness of Aedes aegypti and sand flies. Thus, parasite induced-redistribution of host hemopexin establishes a functional link between mammalian heme homeostasis, vector physiology, microbiome homeostasis and pathogen development, revealing a previously unrecognized host-vector-pathogen interaction and a potential vulnerability for transmission-blocking interventions.},
}

@article {pmid42996160,
year = {2026},
author = {Yao, Y and Yang, Y and Song, J and Wu, L and Xu, M and Liu, H and Liou, YC and Xia, L},
title = {Intratumoral microbiota stratifies glioma malignancy and patient survival through metabolic associations.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1940097},
pmid = {42996160},
issn = {2235-2988},
mesh = {Humans ; *Glioma/microbiology/pathology/mortality/metabolism ; RNA, Ribosomal, 16S/genetics ; Female ; Prognosis ; *Microbiota/genetics ; Male ; Retrospective Studies ; Middle Aged ; *Brain Neoplasms/microbiology/pathology/mortality ; Tumor Microenvironment ; *Bacteria/classification/genetics/isolation & purification ; Survival Analysis ; },
abstract = {BACKGROUND: Glioma is the most common primary malignant tumor of the central nervous system, and its clinical outcomes remain highly heterogeneous despite advances in molecular classification and therapeutic strategies. Emerging evidence suggests that the intratumoral microbiome may influence tumor progression and the tumor microenvironment; however, its role in glioma malignancy stratification and prognosis remains poorly understood. This study aimed to characterize the intratumoral microbiota of glioma tissues and investigate its associations with tumor grade, overall survival, and potential metabolic regulatory mechanisms.

METHODS: A total of 107 treatment-naïve glioma patients were retrospectively enrolled, and tumor tissue samples were subjected to 16S rRNA gene sequencing to profile intratumoral microbial communities. Microbial sequence processing and taxonomic annotation were performed using QIIME2 and DADA2 pipelines. Microbial diversity and compositional differences were evaluated using alpha diversity analysis, Bray-Curtis distance-based principal coordinate analysis (PCoA), and differential abundance analysis. Kaplan-Meier survival analysis, univariate Cox regression, random forest feature selection, and multivariate prognostic modeling were performed to identify microbiome-associated survival indicators. Bootstrap optimism correction was performed with 1,000 resamples. PICRUSt2 was used to predict microbial functional profiles.

RESULTS: We found that intratumoral microbiota composition was significantly associated with WHO grade and overall survival. Positively associated taxa, including Firmicutes and Clostridia, were enriched in low-grade gliomas and favorable-prognosis groups, whereas negatively associated taxa such as Enterobacterales and Porphyromonas gingivalis predominated in high-grade gliomas and poor-survival patients. The model based on WHO grade-associated microbiota achieved optimism-corrected AUCs of 0.71, 0.86, and 0.88 at 1, 2, and 3 years, respectively. Functional prediction suggested differences in microbial pathways related to nucleotide biosynthesis and amino acid metabolism between groups.

CONCLUSIONS: Collectively, these findings suggest associations of intratumoral microbial signatures with glioma malignancy and prognosis, alongside differences in predicted microbial functional profiles. These exploratory observations warrant independent validation to clarify their biological and potential clinical relevance.},
}

Humans
*Glioma/microbiology/pathology/mortality/metabolism
RNA, Ribosomal, 16S/genetics
Female
Prognosis
*Microbiota/genetics
Male
Retrospective Studies
Middle Aged
*Brain Neoplasms/microbiology/pathology/mortality
Tumor Microenvironment
*Bacteria/classification/genetics/isolation & purification
Survival Analysis

@article {pmid42982526,
year = {2026},
author = {Mulligan, RJ and Cotobal Martin, C and Allerton, DM and Strickland, M and Bibby, I and Fachal, L and Watson, H and Bates, G and Beck, LC and Ahmad, T and Blackwell, J and Dart, RJ and Dong, C and Doona, M and Doyle, J and Fouweather, T and Gemmell, E and Hall, R and Irving, PM and Jacques, K and Kennedy, NA and King, AT and Lee, JC and Lees, CW and Lees, RD and Lindsay, JO and Masi, AC and Palmer-Jones, C and Parkes, GC and Parkes, M and Patel, KV and Povlsen, S and Powell, N and Prichard, J and Raine, T and Roberts, C and Samuel, E and Speight, RA and Subramanian, S and Reis, P and Vayreda, E and Wyatt, NJ and , and Stewart, CJ and Young, GR and McGregor, N and Anderson, CA and Lamb, CA},
title = {Open-IBD: protocol for a longitudinal multi-omics inception cohort in inflammatory bowel disease.},
journal = {BMJ open gastroenterology},
volume = {13},
number = {1},
pages = {},
pmid = {42982526},
issn = {2054-4774},
abstract = {INTRODUCTION: The clinical course of inflammatory bowel disease (IBD) is highly heterogeneous, yet the biological mechanisms underlying this variability, along with robust predictive biomarkers of disease course and treatment response, remain elusive. Most existing multi-omic cohorts recruit patients after IBD diagnosis and following therapeutic exposure, limiting the ability to distinguish between primary disease biology and downstream consequences of chronic inflammation and/or treatment. There is, therefore, a critical unmet need for large-scale, treatment-naïve inception cohorts integrating deep clinical phenotyping with longitudinal multi-omic profiling from the point of IBD diagnosis.

METHODS AND ANALYSIS: Open-IBD is a prospective, multicentre UK inception cohort study recruiting up to 2000 adults referred with suspected IBD, prior to diagnosis and initiation of IBD-specific therapy. Baseline assessment includes detailed clinical metadata collection, patient-reported outcome measures and collection of blood, stool and intestinal biopsy samples. 1000 participants subsequently diagnosed with IBD will be followed for up to 48 months, with repeated clinical assessments, questionnaires and biosampling. Participants not diagnosed with IBD will form a symptomatic control cohort with longitudinal clinical record review. Multi-omic analyses will include human genetics, single-cell transcriptomics of blood and intestinal tissue, stool and intestinal mucosal microbiome characterisation, metabolomics and proteomics. Integrated longitudinal clinical and multi-omic datasets will be generated to characterise early-stage treatment-naïve IBD, identify biomarkers associated with long-term outcomes and nominate causal factors driving IBD pathophysiology.

ETHICS AND DISSEMINATION: Ethical approval has been obtained from the Wales Research Ethics Committee 1 (24/WA/0338). All participants provide informed consent before enrolment. Recruitment is ongoing. Study findings will be disseminated through peer-reviewed publications, presentations at scientific meetings and lay summaries.

STUDY REGISTRATION NUMBER: ISRCTN15535639.},
}

@article {pmid42985524,
year = {2026},
author = {Bai, L and Zhang, Q and Zhu, J and Zhang, W and Cui, Z and Jia, T and Li, C and Guo, Z},
title = {Preventive effects of compound probiotics supplementation on migraine: Mendelian randomization analysis and experimental evidence.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1939532},
pmid = {42985524},
issn = {1664-302X},
abstract = {INTRODUCTION: Migraine imposes a substantial economic and societal burden. The microbiota-gut-brain axis (MGBA) has emerged as a key potential mechanism, yet its causal relationships with migraine and the underlying pathways remain unclear.

METHODS: We performed Mendelian randomization (MR) to assess the causal effects of gut microbiota on migraine, and further conducted mediation analysis to identify key mediating brain regions. In addition, we performed in vivo mouse experiments, in which we induced migraine-like pain via nitroglycerin (NTG) and investigated changes in gut microbiota, mechanical pain threshold, and regional brain activation following pretreatment with composite probiotics.

RESULTS: MR analysis identified eight gut microbial taxa causally associated with migraine and its subtypes. Mediation analysis suggested that the association between genetically predicted Paraprevotella abundance and migraine risk was partially mediated by ICVF in the posterior insular cortex. In NTG-induced migraine mice, composite probiotics ameliorated gut dysbiosis and maintained Paraprevotella abundance, while elevating mechanical pain thresholds in both periorbital and hind paw region. Probiotics intervention also suppressed c-Fos expression in the pIC, Sp5c, PVT, and mPFC. Additionally, it specifically decreased CGRP immunoreactivity in the Sp5c.

CONCLUSION: This study provides genetic and experimental evidence supporting a potential role of the gut microbiome in migraine and the potential of microbiome-based strategies for migraine prevention.},
}

@article {pmid42985593,
year = {2026},
author = {Hoza-Frederick, E and Martínez-Campos, S and Barber, PH and Vasquez, MI and Fotopoulos, V and Antoniou, C and Drakou, K and Godoy-Vitorino, F and Chiquillo, KL},
title = {Better together? Microbial communities associated with enhanced growth of the invasive seagrass Halophila stipulacea when mixed with a native Mediterranean seagrass Cymodocea nodosa.},
journal = {Frontiers in Marine Science},
volume = {13},
number = {},
pages = {1871379},
pmid = {42985593},
issn = {2296-7745},
support = {P20 GM103475/GM/NIGMS NIH HHS/United States ; },
abstract = {INTRODUCTION: Microorganisms are increasingly recognized as important contributors to the invasion success of introduced species into new environments. The globally invasive seagrass Halophila stipulacea flourishes in mixed species assemblages with native seagrasses, where it exhibits enhanced growth, while, in contrast, native seagrasses in mixed environments experience reduced growth. Here, we hypothesize that microbes may support the success of invasive seagrass in mixed Mediterranean environments.

METHODS: We analyzed 16S rRNA genes to characterize phyllosphere microbial diversity associated with the Mediterranean-native seagrass Cymodocea nodosa and the invasive H. stipulacea when grown alone or together, alongside biochemical, morphological, and sediment nutrient measurements.

RESULTS: Overall, C. nodosa in monoculture harbored a microbiome exhibiting higher ASV richness and a distinct community composition than H. stipulacea. Variation in bacterial diversity associated with hydrogen peroxide (H2O2) and internode length suggests that microbial communities of the native seagrass might be shaped by its stress-related physiological condition. Conversely, H. stipulacea's microbiome was most abundant in mixed environments, with bacteria significantly reduced in monoculture, and bacterial diversity loosely associated with growth, suggesting that bacterial diversity patterns associated with H. stipulacea vary across competition contexts and may be associated with differences in performance in mixed environments.

DISCUSSION/CONCLUSION: Our findings suggest that invasive H. stipulacea in the Mediterranean Sea is capable of harboring distinct bacterial assemblages that may be associated with growth patterns observed when co-occurring with the native seagrass C. nodosa. Future work should center on the mechanisms driving H. stipulacea bacterial communities and investigating whether H. stipulacea actively determines its own microbiome, or whether it passively acquires its microbiome by environmental variables.},
}

@article {pmid42985619,
year = {2027},
author = {Kreimeyer, H and Gonzalez, C and Fondevila, MF and , and Canbay, A and Stärkel, P and Gonzalez, DJ and Schnabl, B},
title = {DUF6383-domain containing protein from Parabacteroides distasonis predicts survival in patients with alcohol-associated hepatitis.},
journal = {Gut microbes reports},
volume = {4},
number = {1},
pages = {2728306},
pmid = {42985619},
issn = {2993-3935},
support = {R01 AA020703/AA/NIAAA NIH HHS/United States ; K12 GM068524/GM/NIGMS NIH HHS/United States ; I01 BX004594/BX/BLRD VA/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R01 AA024726/AA/NIAAA NIH HHS/United States ; R01 AA031710/AA/NIAAA NIH HHS/United States ; P50 AA011999/AA/NIAAA NIH HHS/United States ; U01 AA026939/AA/NIAAA NIH HHS/United States ; },
abstract = {Intestinal dysbiosis is a hallmark of alcohol-associated liver disease (ALD) characterized by a higher abundance of unfavorable species and a reduction of beneficial species. In this study, we aimed to analyze the bacterial proteome of stool samples from patients with alcohol-associated hepatitis (AH) (n = 80), alcohol use disorder (AUD; n = 20), and controls (n = 19) from an international multicenter cohort using quantitative tandem mass tag (TMT)-based metaproteomic profiling. We validated our results in an independent multicenter cohort of 72 patients with AH at the genomic level using qPCR. We detected 2,364 bacterial proteins and identified distinct metaproteomic signatures separating controls, patients with AUD, and AH. Patients with AUD and AH were characterized by depletion of Firmicutes-derived proteins and enrichment of proteins from Bacteroidetes, Proteobacteria, and Actinobacteria. Eighteen bacterial proteins increased with disease severity, many with multifunctional "moonlighting" roles, including enolase and hexokinase. DUF6383 domain-containing protein from Parabacteroides distasonis is correlated with histological injury, inflammatory cell infiltration, and is linked to neutrophil degranulation in the host. Patients with a high abundance of DUF6383 domain-containing protein had significantly lower 90-day survival, and this association was validated by qPCR at the genomic level in a second cohort. Our findings show that microbial proteins are associated with disease severity and progression, and that DUF6383 domain-containing protein from P. distasonis is a potential prognostic biomarker for AH.},
}

@article {pmid42985998,
year = {2026},
author = {Yang, T and Li, M and Wu, X},
title = {Mechanistic Insights Into How Acupuncture Modulates Host Immunity via the Gut Microbiota-Macrophage Axis.},
journal = {Immunity, inflammation and disease},
volume = {14},
number = {11},
pages = {},
pmid = {42985998},
issn = {2050-4527},
support = {//Jiangsu Road Sub-district Community Health Service Center, Shinan District, Qingdao/ ; },
mesh = {Humans ; Animals ; *Gastrointestinal Microbiome/immunology ; *Macrophages/immunology ; *Acupuncture Therapy ; },
abstract = {BACKGROUND: Acupuncture is proposed to operate within the neuro-endocrine-immune network. Its therapeutic efficacy is proposed to be partly mediated through the gut microbiota-macrophage axis. This proposal is based primarily on preclinical findings. This axis may act as a biological transducer that helps sustain systemic homeostasis[1]. This review synthesizes current evidence on how acupuncture may orchestrate a top-down regulation of the intestinal microenvironment through somato-vagal circuits, particularly those involving PROKR2-expressing sensory fibers.

MATERIALS AND METHODS: This narrative review examined recent preclinical and clinical literature on acupuncture, gut microbiota, metabolites, and macrophage polarization. Studies were selected by relevance and expert judgment. Evidence was organized around the proposed gut microbiota-macrophage axis.

RESULTS: In preclinical rodent models and some human studies, acupuncture has been reported to suppress pathogens such as Proteobacteria. It may also promote symbionts like Akkermansia muciniphila and butyrate-producing taxa. Butyrate promotes anti-inflammatory M2 macrophage polarization via histone deacetylase (HDAC) inhibition and G-protein-coupled receptor signaling. In rodent models, acupuncture has been shown to strengthen barrier integrity. It may upregulate tight junction proteins. It may also prevent lipopolysaccharide (LPS) translocation and suppress M1-driven cascades. These effects extend distally via the gut-lung and gut-brain axes.

DISCUSSION: It is important to note that this proposed cascade is primarily derived from preclinical rodent models, and direct evidence in humans that confirms all steps from vagal activation to macrophage reprogramming remains incomplete. Ultimately, acupuncture may serve as a potential eco-immunological therapy that restores balance between the microbiome and innate immunity. This framework provides a preliminary conceptual basis for the eventual development of personalized, biomarker-driven protocols for chronic inflammatory diseases, although this hypothesis requires rigorous causal validation.},
}

Humans
Animals
*Gastrointestinal Microbiome/immunology
*Macrophages/immunology
*Acupuncture Therapy

@article {pmid42986106,
year = {2026},
author = {Izquierdo, VS and Sousa, LM and Brauner, C and Berwanger, J and Vendramini, JMB and Ashrafi, N and Mimi, RA and Graham, SF and Cappellozza, BI and Moriel, P},
title = {Fecal microbiome and plasma metabolome responses to Bacillus-based direct-fed microbial supplementation in cow-calf pairs from late gestation through weaning.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skag353},
pmid = {42986106},
issn = {1525-3163},
abstract = {This study evaluated the effects of supplementation of a Bacillus-based direct-fed microbial (DFM) on the plasma metabolome and fecal microbiome of multiparous beef cow-calf pairs. On day 0 (94 ± 19 days prepartum), 296 Brangus crossbred beef cows were randomly assigned to treatments consisting of free-choice access to a trace mineral supplement alone (CON) or combined (BAC) with Bacillus subtilis 810 and B. licheniformis 809 (3 g/head/day; 6.6 × 109 CFU/head/day) from day 0 to 330 (weaning). Blood was collected from cows on days 0, 30, and 60, and from calves at birth, day 150, and day 330 for targeted metabolomics. Fecal samples were collected from cows on days 0, 60, 150, and 330, and from calves on days 150 and 330 for 16S rRNA gene sequencing. On day 30, BAC cows had greater (P ≤ 0.05) plasma concentrations of seven conjugated bile acids and two ceramides, but reduced (P ≤ 0.05) isoleucine, 3-indoleacetic acid, and indoxyl sulfate, with 12 pathways upregulated and 3 downregulated. On day 60, BAC cows had greater (P ≤ 0.05) total diacylglycerol and select diacylglycerol and triacylglycerol species, but reduced (P ≤ 0.05) eicosapentaenoic acid (EPA) and polyunsaturated phosphatidylcholines, with 11 pathways downregulated. Treatment effects were not detected (P ≥ 0.14) for fecal bacterial phyla, genera, or alpha diversity in cows, except for greater (P ≤ 0.04) Clostridium butyricum and C. alkalicellulosi relative abundances in BAC vs. CON cows at weaning. In calves, 103 metabolic pathways were impacted at birth (P ≤ 0.05), with the most upregulated being alanine, aspartate, and glutamate metabolism pathways; BAC calves also had greater (P ≤ 0.04) plasma alanine, aspartate, proline, and EPA concentrations at birth. At day 150, BAC calves exhibited greater total triacylglycerol concentrations (P = 0.01) across 48 individual species and upregulation of MIF-mediated immune regulation pathways. At weaning (day 330), BAC calves had greater (P ≤ 0.05) plasma anserine and select triacylglycerols, but reduced (P ≤ 0.05) ceramides and tended to have reduced (P ≤ 0.10) branched-chain amino acids, with 17 metabolic pathways downregulated. These findings indicate that gestation-to-weaning Bacillus-based DFM supplementation altered the plasma metabolome of beef cow-calf pairs, with limited effects on the fecal microbiome, and these changes coincided with the previously reported improvements in calf preweaning growth, post-weaning immune response, and carcass quality.},
}

@article {pmid42986108,
year = {2026},
author = {Xu, Y and Zhang, C and Wu, Y and Zhuo, J and Shen, X and Zhou, Y and Jin, J},
title = {Metagenomic insights into the avian gut microbiome: novel viruses, antimicrobial resistance, and beyond.},
journal = {mBio},
volume = {},
number = {},
pages = {e0234326},
doi = {10.1128/mbio.02343-26},
pmid = {42986108},
issn = {2150-7511},
abstract = {Birds play crucial roles in shaping ecosystems, and their gut microbiomes significantly influence host physiology and pathology. Understanding the composition, functions, and dynamics of avian gut microbiomes is therefore essential. Recent advances in metagenomic and metatranscriptomic sequencing have greatly increased our ability to characterize the avian gut microbiome. This review presents a systematic summary of the current knowledge regarding the composition of the avian gut microbiome as revealed through high-throughput sequencing technologies. It provides a statistical overview of the predominant bacterial and viral taxa present in the gut microbiomes of 195 bird species, revealing a persistent trend toward the discovery of novel viruses, and gives insight into the gene functions of these taxa. Interestingly, in terms of both antimicrobial resistance and multidrug resistance, wild birds harbor a greater diversity of resistance types than poultry. This review also presents a discussion of the relationships of avian life stages and the living conditions of birds with the gut microbiome and highlights practical applications of microbiome regulation in poultry production. Building on this foundation, future research priorities are outlined, such as the study of archaea, fungi, protists, and novel viruses, ways of improving methods to reduce costs and standardize protocols, and the development of more extensive metagenomic and metatranscriptomic data resources. Ultimately, these efforts could provide a holistic understanding of the avian gut microbiome.},
}

@article {pmid42986189,
year = {2026},
author = {Tytgat, B and Seppey, C and De Maeyer, L and Frossard, A and Velazquez, D and Karsten, U and Frey, B and Quesada, A and Vyverman, W and Svenning, MM and Verleyen, E},
title = {Differential effects of moisture on surface versus mineral soil microbial communities in the High-Arctic.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag126},
pmid = {42986189},
issn = {1574-6941},
abstract = {Microorganisms play key roles in nutrient/carbon cycling and greenhouse gas fluxes in High-Arctic soils. However, the influence of soil conditions on tundra microbiomes remains poorly understood. Using high-throughput sequencing, we studied bacterial, fungal and micro-eukaryotic communities in surface soil-biocrust matrices and the underlying mineral soil along two environmental gradients in Svalbard. Both layers harboured highly different communities. Gravimetric water content and pH were the most important factors in explaining the variation in surface communities. Cyanobacteriota were the dominant phototrophs in wetter tundra soils, while Chlorophyta dominated drier ones. In mineral soils, soil texture explained community structure for all three groups, together with carbon-content and carbon: nitrogen-ratio for micro-eukaryotes and bacteria. Chloroflexota and Spirotrichea dominated mineral soils with high clay content, Actinobacteriota positively correlated with sand content. The effects of soil texture and water content were also reflected in co-occurrence networks. Surface communities split into two network clusters linked to either drier or wetter tundra. The mineral soil network was much less coherent, and clustering was related to soil texture. Our findings revealed the important interplay between soil layer, toposequence and soil microbiome in the High-Arctic. As precipitation patterns shift, the impact of topography on tundra microbial communities is likely to intensify.},
}

@article {pmid42986545,
year = {2026},
author = {Chamekh, A and Fersi, C and Souguir, D and Chouari, R},
title = {Impact of treated wastewater irrigation on soil pollution-induced community tolerance and microbiome dynamics.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {11},
pages = {},
pmid = {42986545},
issn = {1573-0972},
mesh = {*Soil Microbiology ; *Agricultural Irrigation ; *Bacteria/classification/genetics/isolation & purification/drug effects ; *Microbiota/drug effects/genetics ; RNA, Ribosomal, 16S/genetics ; Metals, Heavy/analysis ; *Soil Pollutants/analysis ; Soil/chemistry ; *Wastewater/chemistry/microbiology ; Agriculture ; },
abstract = {The reuse of treated wastewater (TWW) for agriculture is widespread in arid regions, but its comparative short- and long-term impacts on soil and microbiome remain poorly understood. This study aims to evaluate the short-term (4-5 years) and long-term (20-25 years) effects of TWW irrigation on soil physico-chemical properties, bacterial community structure, and emergence of contaminant tolerance in Cebala Borj Touil (Tunisia). Samples from irrigated and non-irrigated control soils (n = 4) were analyzed using physico-chemical characterization, 16S rRNA amplicon sequencing, and pollution-induced community tolerance (PICT) via [[3]H]leucine incorporation after exposure to Cu, Zn, Pb and tetracycline. Long-term irrigation led to a drop in pH with a significant increase in salinity, organic matter, and heavy metal concentrations (reaching, on average, 55, 120, and 63 mg/kg for Cu, Zn, and Pb), accompanied by a significant increase in PICT tolerance indices compared to control soils and in the short term. 16S sequencing revealed changes in alpha diversity (Chao1, ACE), with short-term irrigation showing the highest bacterial richness, while long-term exposure induced a profound community reshuffling with the dominant emergence of specific genera such as Defluviococcus, Pseudarthrobacter, Nocardioides and Gaiella. In conclusion, the prolonged irrigation by TWW selects a microbial community tolerant to chemical constraints and enriched in key taxa, which are promising bio-indicators for environmental monitoring of contaminated agricultural soils.},
}

*Soil Microbiology
*Agricultural Irrigation
*Bacteria/classification/genetics/isolation & purification/drug effects
*Microbiota/drug effects/genetics
RNA, Ribosomal, 16S/genetics
Metals, Heavy/analysis
*Soil Pollutants/analysis
Soil/chemistry
*Wastewater/chemistry/microbiology
Agriculture

@article {pmid42986679,
year = {2026},
author = {Maloney, S and Folliard, NT and Karakaya, G and Waters, SM},
title = {Importance of rumen ciliated protozoa and current research techniques for their analysis.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {11},
pages = {},
pmid = {42986679},
issn = {1465-2080},
mesh = {Animals ; *Rumen/parasitology/microbiology ; *Ciliophora/genetics/classification/isolation & purification/physiology ; Ruminants/parasitology ; Methane/metabolism ; Microbiota ; RNA, Ribosomal, 18S/genetics ; },
abstract = {Rumen protozoa are an integral component of the ruminant foregut microbiome, with a profound influence on feed digestion, microbial ecosystem dynamics and enteric methane emissions. Although they represent only a small proportion of species richness, protozoa contribute significantly to microbial biomass and functions in fibre degradation, volatile fatty acid production, microbial protein turnover, pH modulation and hydrogen-mediated methanogenesis. In addition to highlighting their importance to rumen function, this review summarizes classical and contemporary methodologies for enumerating, identifying and characterizing rumen protozoa. These methodologies include microscopy, fluorescent staining, flow cytometry and molecular approaches such as 18S rRNA, ITS and 28S rRNA amplicon sequencing. All major rRNA primers widely used over the last two decades are catalogued and their coverage is evaluated against current databases, highlighting the superior taxonomic resolution provided by ITS-based markers. The integration of single-cell sequencing and long-read platforms with multi-omics approaches (metagenomics, metatranscriptomics and metaproteomics) and advanced bioinformatic tools enables genome-resolved and functionally informed analyses of rumen protozoa. Methodological advances are integrated with functional insights to elucidate the contributions of protozoa to rumen ecology, feed efficiency and methane output. Key research gaps are also identified, including the need for improved microscopy techniques, automated image analysis, optimized cryopreservation protocols and robust culturing systems. This synthesis provides a comprehensive resource for researchers in microbial ecology, animal nutrition and environmental science, enabling precise protozoal profiling and informing strategies to enhance livestock productivity while mitigating environmental impacts.},
}

Animals
*Rumen/parasitology/microbiology
*Ciliophora/genetics/classification/isolation & purification/physiology
Ruminants/parasitology
Methane/metabolism
Microbiota
RNA, Ribosomal, 18S/genetics

@article {pmid42986703,
year = {2026},
author = {Guo, K and Golob, J and Berinstein, J and Sheehan, J and Chey, WD and Higgins, PDR and Young, V and Rao, K and Singh, P and Bishu, S and Lee, A},
title = {Mucosal transcriptomic and fecal microbiome signatures associated with persistent symptoms in quiescent Crohn's disease.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izag244},
pmid = {42986703},
issn = {1536-4844},
support = {//IBD Plexus program of the Crohn's & Colitis Foundation/ ; //The Leona M. and Harry B. Helmsley Charitable Trust/ ; DK124567/NH/NIH HHS/United States ; DK139095/NH/NIH HHS/United States ; HS027431/NH/NIH HHS/United States ; T32-DK062708/NH/NIH HHS/United States ; R01-DK125687/NH/NIH HHS/United States ; R01-DK118154/NH/NIH HHS/United States ; AI182787/NH/NIH HHS/United States ; DK123403/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: Persistent symptoms in quiescent Crohn's disease (qCD + S) lack clear mechanistic explanations. Building on prior evidence linking qCD + S to sulfidogenic microbial metabolism, this study characterizes the underlying site-specific mucosal transcriptional programs and host-microbe interactions associated with qCD + S.

METHODS: We integrated paired metagenomic and transcriptomic data from a cross-sectional cohort of patients with qCD. Host-microbe interactions in the ileum and rectosigmoid colon were analyzed using differential expression, penalized regression, and sparse canonical correlation analysis.

RESULTS: qCD + S was associated with transcriptional differences in separate analyses of ileal and rectosigmoid samples. The ileum showed reduced expression of genes related to immune surveillance, whereas the rectosigmoid colon exhibited reduced chemokine-related and increased ribosomal gene expression. Multi-omic integration identified associations between previously identified sulfidogenic microbes and mucosal genes related to mitochondrial metabolism, epithelial homeostasis, and neurosensory signaling. Exploratory sparse canonical correlation analysis identified multivariate patterns involving oral-associated taxa and mucosal genes related to B-cell receptor signaling and RNA-processing.

CONCLUSIONS: Persistent symptoms in qCD are mucosal transcriptional differences and fecal microbial features. These findings suggest a model in which altered immune regulation, microbial sulfur metabolism, and downstream epithelial and metabolic stress pathways contribute to symptom persistence despite quiescent inflammation, but this model requires mechanistic validation.},
}

@article {pmid42986715,
year = {2026},
author = {Kozłowska, P and Borowiecka, A and Strzemkowska, M and Jaworska, Z and Nowak-Arkusz, M and Skrypnik, D},
title = {How Plants Feed Our Microbes: Plant-Based Diets and Gut Microbiota Modulation-A Systematic Review.},
journal = {Nutrition reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/nutrit/nuag157},
pmid = {42986715},
issn = {1753-4887},
support = {//Department of Family Medicine/ ; JAK0000049//Poznan University of Medical Sciences/ ; },
abstract = {CONTEXT: Diet is a key factor shaping gut microbiota composition and function, with important implications for human health. The growing popularity of plant-based dietary patterns has increased interest in their effects on the gut microbiota.

OBJECTIVE: This systematic review examines specific changes in gut microbiota among individuals following a plant-based diet (PBD), as well as shifts occurring after transitioning from an omnivorous diet.

DATA SOURCES: PubMed and Google Scholar were searched for articles reporting original English-language human and animal studies investigating the effects of PBDs on gut microbiota composition or function. Studies published from 2015 onward were primarily considered, with most included articles published during 2020-2024.

DATA EXTRACTION: Four reviewers independently screened records according to eligibility criteria and extracted data on study characteristics, populations, dietary patterns, and outcomes related to gut microbiota composition and function.

DATA ANALYSIS: A total of 37 studies met the inclusion criteria. A PBD appeared to promote the growth of short-chain fatty acid-producing and probiotic bacteria, which help maintain intestinal integrity and support carbohydrate metabolism and may offer protection against certain diseases. A PBD was also reported to encourage the growth of beneficial taxa such as Roseburia spp., Akkermansia muciniphila, Clostridium symbiosum, and Faecalibacterium prausnitzii, which are considered indicators of a healthy microbiome. An increased Bacteroidetes/Firmicutes ratio, which was found to be a common occurrence in study participants following a PBD, correlated with a lower body mass index (BMI) and a more favorable metabolic profile, supporting healthy weight maintenance. In addition, PBDs were also associated with improvements in alpha- and beta-diversity compared with omnivorous diets.

CONCLUSIONS: This review indicates that PBDs appear to beneficially influence the gut microbiota and may have positive effects on human health. Nonetheless, not all studies agree on the extent or direction of microbiota changes associated with dietary patterns.

PROSPERO registration No. [CRD420251229407]; link: https://www.crd.york.ac.uk/PROSPERO/view/CRD420251229407.},
}

@article {pmid42986980,
year = {2026},
author = {},
title = {Erratum for the Report "Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors".},
journal = {Science (New York, N.Y.)},
volume = {394},
number = {6824},
pages = {eaen6718},
doi = {10.1126/science.aen6718},
pmid = {42986980},
issn = {1095-9203},
}

@article {pmid42987300,
year = {2026},
author = {H, B and Sahu, S and Balakrishnan, D and Ramadass, B},
title = {Effects of Lactobacillus crispatus-Containing Probiotics and Metformin on Insulin Resistance, Inflammation, and Gut Microbiome in Polycystic Ovary Syndrome: Protocol for an Open-Label Randomized Controlled Trial.},
journal = {JMIR research protocols},
volume = {15},
number = {},
pages = {e102121},
pmid = {42987300},
issn = {1929-0748},
mesh = {Female ; *Metformin/therapeutic use/pharmacology ; *Polycystic Ovary Syndrome/drug therapy ; Humans ; *Insulin Resistance/physiology ; *Probiotics/therapeutic use/pharmacology/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; *Inflammation/drug therapy ; *Lactobacillus crispatus ; India ; Adult ; },
abstract = {BACKGROUND: Polycystic ovary syndrome (PCOS) affects 9% to 12% of reproductive-age women worldwide, with higher prevalence reported in India. Its pathophysiology involves insulin resistance, hyperandrogenism, and chronic low-grade inflammation, increasingly linked to gut dysbiosis and lipopolysaccharide-driven toll-like receptor 4 signaling. Elevated calprotectin and suppressed acylated ghrelin (AGH) reflect this inflammatory-metabolic disruption. While metformin remains standard therapy, it does not address underlying gut dysbiosis. Lactobacillus crispatus, with its antibacterial and immunomodulatory properties, is a promising but untested gut-targeted adjunct. This trial evaluates whether combining metformin with L. crispatus supplementation improves metabolic and inflammatory outcomes beyond either therapy alone.

OBJECTIVE: This study aims to compare probiotic, metformin, and combination therapy for reducing insulin resistance in PCOS over 12 weeks and assess their effects on gut barrier integrity, microbiome composition, hyperandrogenemia, glycemic control, and clinical outcomes.

METHODS: This open-label randomized, hospital-based trial at the All India Institute of Medical Sciences, Bhubaneswar, will assess the effects of probiotic and/or metformin therapy in women aged 18 to 40 years diagnosed with PCOS per Rotterdam criteria. A total of 135 participants will be randomized equally into 3 groups: probiotics only, metformin only, and combination therapy. The 3-month intervention includes metformin (1000 mg per day) and a specified L. crispatus-containing probiotic (2 capsules per day). The primary outcome is the change in Homeostatic Model Assessment for Insulin Resistance (HOMA-IR). Key secondary outcomes include changes in serum and fecal calprotectin, AGH, total testosterone, and fecal microbiome profile.

RESULTS: Participant recruitment began in January 2026. As of August 30, 2026, 26 of the planned 135 participants had been enrolled. Enrollment and data collection are projected to conclude by December 2026; statistical analysis will begin after database lock, with study completion anticipated by June 2027 and publication targeted for mid- to late 2027.

CONCLUSIONS: This trial will provide critical, mechanistic evidence on whether the targeted action of L. crispatus can work additively with metformin to heal the intestinal mucosal barrier, arrest systemic endotoxemia, and rescue disrupted gut-brain-endocrine signaling. By validating this novel metabolic-inflammatory regimen against localized (calprotectin) and systemic (AGH and HOMA-IR) end points, this study intends to establish a highly integrated, microbiome-targeted therapeutic strategy capable of optimizing long-term metabolic and reproductive health outcomes in women with PCOS.},
}

Female
*Metformin/therapeutic use/pharmacology
*Polycystic Ovary Syndrome/drug therapy
Humans
*Insulin Resistance/physiology
*Probiotics/therapeutic use/pharmacology/administration & dosage
*Gastrointestinal Microbiome/drug effects
*Inflammation/drug therapy
*Lactobacillus crispatus
India
Adult

@article {pmid42987457,
year = {2026},
author = {Nazario, C and Solari, L and Sciara, M and de la Vega Elena, CD},
title = {Exploring normality: Mapping the endometrial microbiome in healthy reproductive-aged women from Argentina.},
journal = {Revista Argentina de microbiologia},
volume = {59},
number = {1},
pages = {100763},
doi = {10.1016/j.ram.2026.100763},
pmid = {42987457},
issn = {0325-7541},
abstract = {The human microbiome varies according to individual and geographic characteristics. The endometrial microbiome plays a relevant role in reproductive physiology; however, data from healthy South American populations remain scarce. This prospective observational study aimed to characterize the endometrial microbiome in healthy reproductive-aged women from Rosario, Argentina and to establish a regional baseline for future research. A total of 100 healthy women aged 22-50 years from Rosario, Argentina, were included. Endometrial samples were obtained by aspiration biopsy during the follicular phase of the menstrual cycle or under hormonal contraception. Microbiome analysis was performed using 16S rRNA gene sequencing targeting the V4 region on the Illumina NextSeq 500/550 platform (2×150bp). Bioinformatic analysis was carried out in QIIME2. Of the 98 samples successfully amplified, 86 met quality criteria and were included in the final analysis. The endometrial microbiome was predominantly composed of Firmicutes, particularly members of the Lactobacillaceae family. The most abundant species were Lactobacillus iners and Lactobacillus helveticus/crispatus. No significant differences in alpha diversity were observed among age groups; however, a progressive increase in Gardnerella, Prevotella, and Megasphaera was detected with advancing age. This study provides the first regional characterization of the normal endometrial microbiome in healthy Argentine women and establishes a reference framework for future studies addressing endometrial dysbiosis and reproductive disorders.},
}

@article {pmid42987462,
year = {2026},
author = {Song, W and Wei, Y and Tang, L and Wong, FL and Lam, HM and Prasad, R and Zhang, S},
title = {Exploring the wild soybean derived cross-kingdom SynCom for mitigating continuous cropping obstacles: potential links to fungus-associated bacterial dispersal and root exudate reprogramming.},
journal = {Plant physiology and biochemistry : PPB},
volume = {240},
number = {},
pages = {111928},
doi = {10.1016/j.plaphy.2026.111928},
pmid = {42987462},
issn = {1873-2690},
abstract = {Continuous cropping obstacles severely constrain global soybean productivity, yet scalable biological solutions remain limited. While continuous monoculture typically causes yield decline in cultivated soybean, its wild relative persists in the same soils for decades without apparent decline, suggesting the presence of a protective native rhizosphere. By integrating long-term field surveys, metagenomic profiling, and stress-directed cultivation, we established a multi-tiered rational design framework to construct a functionally complementary, cross-kingdom synthetic community from wild soybean rhizospheres. Using a reductionist hydroponic model to isolate direct microbial effects from the complexities of the soil matrix, a simplified bacterial-fungal consortium successfully mitigated CCO-associated stresses. Specifically, SSC mitigated the growth inhibition caused by continuous cropping obstacles, enhanced disease resistance, and reduced the accumulation of phenolic autotoxins in the rhizosphere. Regarding the mechanism of action, compartmentalized experiments suggest that fungal hyphae can act as bacterial carriers, facilitating bacterial dispersal and increasing the accumulation of beneficial bacteria in the plant rhizosphere, thereby promoting rapid root colonization. SSC reprograms root exudates, significantly upregulating the biosynthesis of flavone and flavonol biosynthesis, which may act as chemotactic inducers to recruit beneficial microorganisms to soybean roots. Our research reveals that the wild soybean microbiome is an exploitable reservoir, providing a practical framework for translating the resilience of the native microbiome into sustainable agricultural solutions.},
}

@article {pmid42987531,
year = {2026},
author = {von Hellfeld, R and Gade, C and Williams, RS and Derous, D},
title = {Lessons learned from model species: Molecular markers for anthropogenic pollutant toxicity in cetaceans.},
journal = {Marine pollution bulletin},
volume = {234},
number = {Pt 1},
pages = {120546},
doi = {10.1016/j.marpolbul.2026.120546},
pmid = {42987531},
issn = {1879-3363},
abstract = {The planet is currently facing a triple crisis driven by climate change, biodiversity loss, and pollution. While the effects of environmental contaminants on reproduction, neurological function, and immune processes are well established in model species, far less is known about their impacts on marine sentinels such as cetaceans. Although contaminant burdens can be quantified, there is a lack of validated biomarkers that reliably capture molecular and cellular effects, limiting robust impact assessment and conservation strategies. Cetaceans exhibit unique physiological and metabolic adaptations, including specialised lipid dynamics and life-history traits, complicating direct extrapolation from model organisms. Here, we review current knowledge of biomarkers associated with three major contaminant classes: persistent organic pollutants (POPs), heavy metals, and microplastics. Candidate biomarkers such as cytochrome P4501A1, acetylcholinesterase, and metallothioneins are well characterised in experimental systems but show inconsistent responses in cetaceans, influenced by ecological, physiological, and methodological factors. Emerging evidence indicates that microplastics may drive gut inflammation, microbiome disruption, and systemic stress responses, although validated biomarkers remain scarce. Overall, we highlight the limitations of single-marker approaches and the need for integrative frameworks capturing complex, multi-stressor responses across biological scales. Future efforts should prioritise robust, early-warning biomarkers that account for species-specific physiology, trophic ecology, and cumulative exposure. Progress will require cross-disciplinary collaboration, integration of multi-omics tools, and improved standardisation of methods. Strengthening biomarker frameworks in cetaceans is essential for advancing marine conservation and understanding shared risks to ocean and human health.},
}

@article {pmid42987833,
year = {2026},
author = {Cho, J and Danner, R and Kim, WS and Lopez, L and Williams, J and Singh, A and Han, JA and Van Vranken, JG and Walker, AS and Rhoads, TW and Chaudhari, SN},
title = {Microbial metabolism of methotrexate produces a STAT3 signaling molecule that alleviates gut inflammation.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.10.005},
pmid = {42987833},
issn = {1934-6069},
abstract = {Methotrexate (MTX) is a gold standard therapy for inflammatory diseases but has mixed therapeutic success in inflammatory bowel disease (IBD). The gut microbiota impact MTX efficacy and toxicity by metabolizing MTX and altering its bioavailability, yet how inflammation alters this metabolism, and how the resulting metabolites act on the host, remain poorly understood. Here, we find that gut microbes, notably Clostridium asparagiforme, metabolize MTX via carboxypeptidase G2 (CPDG2) to produce deoxyaminopteroic acid (DAMPA). In intestinal epithelial cells, DAMPA preserves mitochondrial health through mitochondrial signal transducer and activator of transcription 3 (STAT3) signaling and enhances mitophagy. DAMPA administration attenuates intestinal inflammation in vivo, and remodels colonic mitochondrial pathways. IBD mouse models show reduced microbial CPDG2 and DAMPA, while patients with IBD show reduced CPDG2 gene abundance and suppressed DAMPA-enriched mitochondrial pathways, potentially explaining MTX outcomes in IBD. Together, these findings reframe microbial MTX metabolism from passive drug detoxification to active regulation of host mitochondrial and inflammatory homeostasis.},
}

@article {pmid42988189,
year = {2026},
author = {Luque, MVS and Moreno, ASA and Angarita-Planchez, ME and Múnera-Rodríguez, AM and López-Enríquez, S and Casado-Jurado, D and de Miguel, M and Palomares, F},
title = {Hypoxia Orchestrates the Natural History of Inflammatory Bowel Disease: Mechanisms and Therapeutic Opportunities.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {109736},
doi = {10.1016/j.phrs.2026.109736},
pmid = {42988189},
issn = {1096-1186},
abstract = {Inflammatory bowel disease (IBD) arises from a dynamic interplay between epithelial dysfunction, immune activation, microbial dysbiosis and tissue remodelling. Although hypoxia was initially regarded as a consequence of intestinal inflammation, it is now recognized as an active regulator of epithelial, immune and stromal responses that coordinate disease progression. Here, we propose that hypoxia acts as a biological organizer linking oxygen sensing to the transition from intestinal homeostasis to chronic inflammation and structural tissue damage. We use this term in a mechanistic rather than a hierarchical sense: oxygen availability is a shared upstream constraint on epithelial, immune, microbial and stromal programmes, not a single initiating event. This review integrates evidence connecting oxygen sensing with epithelial barrier integrity, immunometabolism, microbial ecology and stromal remodelling, with emphasis on advances in single-cell transcriptomics, spatial biology and microbiome research. Physiological low-oxygen gradients support epithelial metabolism, barrier integrity and immune tolerance, whereas persistent inflammatory hypoxia drives oxidative stress, metabolic reprogramming and maladaptive epithelial-immune-microbial interactions. Hypoxia also contributes to spatially distinct epithelial, immune and stromal niches that may sustain chronic inflammation and fibrotic progression. Microbial metabolites, including short-chain fatty acids and succinate, together with iron metabolism and ferroptosis, further link oxygen sensing to tissue injury, adaptation and repair. These findings position hypoxia-responsive signalling as a pharmacologically actionable network rather than a downstream consequence of inflammation. Targeting selected components may promote mucosal healing and limit structural disease progression, although successful translation will require cell- and isoform-selective modulation, adequate tissue exposure and careful assessment of long-term safety.},
}

@article {pmid42988284,
year = {2026},
author = {Pourbozorg, G and Heckmann, ND and Mont, MA and Lieberman, JR and Parvizi, J},
title = {Can We Target the Microbiome to Improve Outcomes in Osteoarthritis and Arthroplasty?.},
journal = {The Journal of arthroplasty},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.arth.2026.10.044},
pmid = {42988284},
issn = {1532-8406},
abstract = {Osteoarthritis (OA) is the most prevalent degenerative joint disease and a leading cause of pain, disability, and joint arthroplasty worldwide. Despite advances in surgical technique and perioperative care, periprosthetic joint infection (PJI) remains a devastating complication associated with substantial morbidity, mortality, and healthcare costs. Increasing evidence suggests that the gut microbiome plays a central role in regulating systemic inflammation, immune competence, metabolic homeostasis, and intestinal barrier integrity, biological processes relevant to both OA progression and postoperative infection risk. Preclinical and emerging clinical studies support the existence of a gut-joint axis, whereby alterations in gut microbial composition and microbial metabolites, such as short-chain fatty acids (SCFAs), bile acids, lipopolysaccharides, tryptophan-derived metabolites, and other immunomodulatory compounds, influence joint inflammation, cartilage degeneration, and host immune responses. Experimental models demonstrate that dysbiosis exacerbates OA-related joint damage, while targeted modulation of the gut microbiome can attenuate inflammation, reduce oxidative stress, and preserve cartilage integrity. Importantly, perioperative factors such as surgical stress, antibiotic exposure, and nutritional changes may further disrupt gut microbial homeostasis, potentially impairing immune resilience and increasing susceptibility to PJI. Microbiome-targeted strategies, including dietary modification, probiotics, prebiotics, and physical activity, have shown promise in restoring microbial balance and supporting immune regulation in arthritic populations. Although most evidence remains preclinical or observational, these findings suggest that modulation of the gut microbiome represents a biologically plausible adjunctive approach for both osteoarthritis management and perioperative optimization. This review summarizes current evidence linking the gut microbiome to OA pathophysiology and surgical outcomes and evaluates the potential role of microbiome modulation in joint health optimization and PJI risk reduction. Although biologically compelling, current evidence remains largely preclinical and observational, and prospective clinical trials are required before routine implementation.},
}

@article {pmid42988299,
year = {2026},
author = {Hua, J and Pi, X and Zhang, J and Tian, J and Sun, X and You, X and Sun, C and Li, Y and Li, M and Liu, Q and Liu, L and Liu, R and Luo, X and Li, F and Zheng, H},
title = {Feedstock-specific biochar attenuates brominated flame retardant transfer to cherry radish: Links to rhizosphere microbiome reassembly and dietary exposure reduction.},
journal = {Environmental research},
volume = {},
number = {},
pages = {126113},
doi = {10.1016/j.envres.2026.126113},
pmid = {42988299},
issn = {1096-0953},
abstract = {Brominated flame retardants (BFRs) are emerging contaminants in agricultural soils that threaten food safety and human health. Although biochar can remediate contaminated soils, its performance and mechanisms in soil-root vegetable systems remain unclear. Herein, the effects of biochars from pig manure (PHC), peanut shell (FSC), corn straw (STC), and bamboo (BBC) on soil-to-food transfer and dietary exposure of decabromodiphenyl ether (BDE-209) and pentabromotoluene (PBT) were investigated in a 48-day pot experiment with bacterial and fungal community analyses. PHC, FSC, and BBC reduced BDE-209 and PBT accumulation in cherry radish by 60.1-78.3% and 34.1-89.4%, respectively, relative to the control. These biochars enriched putative BFR-attenuating taxa (Pseudomonas, Sphingomonas, and Humicola); enrichment of oxygen-containing functional groups (C=O and O-C=O) and dissolved organic matter in these biochars may have provided high-affinity niches that selectively recruited these taxa, potentially contributing to lower BFR accumulation. PHC, FSC, and BBC also promoted deterministic fungal assembly and more complex, stable networks. Overall, BFR transfer to cherry radish was associated with feedstock-dependent biochar properties, plant performance, and rhizosphere community assembly, providing an integrated basis for selecting biochars for contaminated agricultural soils. These findings link soil, rhizosphere, and food exposure and support feedstock-specific biochar use to reduce contaminant transfer while improving rhizosphere ecological health.},
}

@article {pmid42988334,
year = {2026},
author = {Dong, Z and Ye, Q and See, WC and Oo, A and Pan, M},
title = {Advances in engineering strategies for manipulating insect antiviral immunity.},
journal = {Current opinion in insect science},
volume = {},
number = {},
pages = {101648},
doi = {10.1016/j.cois.2026.101648},
pmid = {42988334},
issn = {2214-5753},
abstract = {Insect immunity primarily relies on a highly developed innate immune system to defend against viral invasion. Research on insect immunity has gained considerable traction in recent years, with major progress in elucidating the underlying immune and defense mechanisms and developing improved pest-control strategies. Collectively, these advancements have paved a translational pathway toward the close application of insect immunology in fields such as medicine, agriculture, and ecology. This review systematically discusses current progress in genetic engineering-based strategies for modulating insect antiviral immunity, specifically transgenic, antimicrobial peptides, gene-editing gene drives, and microbiome regulation. The review also outlines the implications of regulating insect immunity for enhancing genetic traits, preventing disease, controlling vectors, and modifying pathogenic microorganisms.},
}

@article {pmid42988415,
year = {2026},
author = {Leung, JM},
title = {Unravelling the mysteries of long COVID: what the microbiome can tell us.},
journal = {The European respiratory journal},
volume = {68},
number = {5},
pages = {},
doi = {10.1183/13993003.01419-2026},
pmid = {42988415},
issn = {1399-3003},
}

@article {pmid42988675,
year = {2026},
author = {Kuribayashi, R and Nakano, A and Kawasaki, M and Hariu, A and Sakurai, A},
title = {Regulatory science for microbiome-based medicines: lessons from Pharmaceuticals and Medical Devices Agency initiatives.},
journal = {Trends in biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibtech.2026.10.007},
pmid = {42988675},
issn = {1879-3096},
abstract = {Recent Pharmaceuticals and Medical Devices Agency initiatives for live biotherapeutic products, fecal microbiota transplantation, and phage therapy medicinal products illustrate a dialog-driven regulatory approach for microbiome-based medicines. We compare this strategy with evolving Food and Drug Administration and European Medicines Agency frameworks and identify priorities for future regulatory development and international alignment.},
}

@article {pmid42988683,
year = {2026},
author = {Brown, BRP and Dahlquist, SE and Miranker, AD},
title = {Microbiome sharing and the shift to relational privacy.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.09.007},
pmid = {42988683},
issn = {1878-4380},
abstract = {Concerns about big data privacy are growing. While much of the current privacy framework focuses on individuals, protections must also account for relational risks. In this article, we use the microbiome as an example to demonstrate the limitations of applying existing individual-centered privacy frameworks to biological data that can reveal information about interacting individuals.},
}

@article {pmid42988772,
year = {2026},
author = {Asoudeh-Fard, A and Barzegari, A and Maghsoodi, M and Gholami, A},
title = {Harnessing Nanotechnology and Microbiome Interactions to Enhance Therapeutic Outcomes in GI Cancers.},
journal = {Expert reviews in molecular medicine},
volume = {},
number = {},
pages = {1-53},
doi = {10.1017/erm.2026.10087},
pmid = {42988772},
issn = {1462-3994},
}

@article {pmid42988933,
year = {2026},
author = {Nap, B and Hensen, T and Barton, W and Sheehy, A and Widder, J and Chenna, S and Thiele, I},
title = {Personalization and evaluation of human whole-body metabolic models and community microbiome models using Persephone.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {42988933},
issn = {1750-2799},
abstract = {Human metabolism and human gut microbiome co-metabolism can be difficult to investigate in vivo owing to the complexity of the systems involved. Genome-scale metabolic modeling with human whole-body metabolic models (WBMs) offers a computational approach to address this challenge. However, personalization and analysis of WBMs requires comprehensive knowledge of metabolic modeling, which can be daunting for beginners. To reduce the computational expertise required and to standardize the process of working with and analyzing WBMs, we present Persephone: a personalization and evaluation pipeline for human WBMs. Persephone has functionalities to create community microbiome models from raw sequencing data or taxonomy-assigned read tables, use physiological and metabolomic data to create personalized WBMs, combine community microbiome models with WBMs or personalized WBMs to create community microbiome (personalized) WBMs, optimize WBMs according to user-defined metabolic reactions, perform statistical analyses to describe the data, and visualize significant results in various figures. Persephone saves intermediate results as well as a log file with all changes made to the model, data and any warnings encountered during the various steps. Persephone is designed for use by anyone with basic research-computing experience and access to modest computer hardware. Applications include the investigation of human-microbiome co-metabolism and the evaluation of the effects of various physiological parameters, such as weight, on human metabolism. Using a dataset of 100 metagenomic samples, it can take several days to a week to run Persephone on a single computer, depending on the number of reactions optimized and whether taxonomic assignment is performed.},
}

@article {pmid42988934,
year = {2026},
author = {Nagata, N and Wei, R and Kaneko, G and Nishijima, S and Aoki, R and Kojima, Y and Tamura, Y and Sugiyama, M and Hamabata, T and Nakagawa, T and Ueki, K and Ohsugi, M and Nakanishi, Y and Ito, A and Asami, S and Suzuki, R and Kuhn, M and Bork, P and Hattori, M and Ohno, H and Uemura, N},
title = {Opposing microbiome-mediated axes link modifiable lifestyles to health and chronic diseases.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {42988934},
issn = {1546-170X},
support = {28-2401, 19A1011, 24A1010//National Center for Global Health and Medicine (NCGM)/ ; 24A1010//National Center for Global Health and Medicine (NCGM)/ ; 28-2401//National Center for Global Health and Medicine (NCGM)/ ; NA//Smoking Research Foundation (SRF)/ ; NA//Takeda Science Foundation/ ; JP22fk0410051, JP22fk0108538, JP25ck0106061//Japan Agency for Medical Research and Development (AMED)/ ; },
abstract = {Analyses disentangling the role of the gut microbiome in linking lifestyle factors to health outcomes remain limited. Here, using fecal shotgun metagenomics from 6,803 adults in the Japanese 4D cohort, we identified two opposing microbiome-mediated axes linking lifestyle to health and 15 diseases. A health-associated axis enriched in microbial metabolism of dietary components was linked to plant-based, soy and dairy intake. In contrast, a disease-associated axis, enriched in oral-derived bacteria and pathobionts, was linked to refined carbohydrates and sedentary behavior. Starter culture microorganisms used to ferment foods did not show statistically significant mediation of the observed health effects. Alcohol was associated with both health- and disease-oriented mediation patterns involving microbial host-glycan utilization. Microbiome-defined health- and disease-oriented mediator axes were supported by fecal short-chain fatty acids and plasma cytokines from >1,700 individuals, revealing butyrate-associated anti-inflammatory and pro-inflammatory host profiles, respectively. Microbiome-based prediction (MADE) scores captured lifestyle-microbiome-disease mediation patterns and distinguished individual diseases across 13 independent external cohorts from the United States, China, Sweden, Russia and Australia. We identify the gut microbiome as a key mediator linking lifestyle to health and disease, providing a framework for microbiome-based assessment to guide lifestyle interventions for health promotion and disease prevention.},
}

@article {pmid42989114,
year = {2026},
author = {Saha, P and Böttcher, L and Gonze, D and Zhou, X and Bernaerts, K and Faust, K},
title = {Effects of common antibiotics on representative gut bacterial strains associated with inflammatory bowel disease.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42989114},
issn = {1471-2180},
support = {G046721N//Fonds Wetenschappelijk Onderzoek/ ; 1140026N//Fonds Wetenschappelijk Onderzoek/ ; },
mesh = {*Anti-Bacterial Agents/pharmacology ; Humans ; *Inflammatory Bowel Diseases/microbiology ; Escherichia coli/drug effects/growth & development ; *Bacteria/drug effects/growth & development ; *Gastrointestinal Microbiome/drug effects ; Bacteroides fragilis/drug effects/growth & development ; Microbial Sensitivity Tests ; },
abstract = {BACKGROUND: Inflammatory Bowel Disease (IBD), a group of multifactorial diseases marked by chronic inflammation of the gastrointestinal tract, is characterized by an altered gut microbial community composition that is enriched in opportunistic and pathogenic species, such as Bacteroides fragilis and adherent-invasive Escherichia coli strains. To better understand the consequences of using antibiotics to suppress these harmful species, we quantified the response of three bacterial species representative of a healthy gut microbiome, as well as two species typically enriched in IBD to five selected antibiotics that are widely employed against anaerobes.

RESULTS: We found that the adherent-invasive Escherichia coli LF82 strain and the type strains of the opportunistic Bacteroides species B. fragilis and B. thetaiotaomicron are resistant to even high doses of several of the tested antibiotics whereas the type strains of the probiotic butyrate producer Roseburia intestinalis and the acetogen Blautia hydrogenotrophica are sensitive to the majority of the tested antibiotics at low concentrations. We performed a Bayesian parameter estimation of a parsimonious mechanistic growth model. The effects of the antibiotics on lag phase, growth rate, and death rate varied across compounds in a manner consistent with their modes of action. For example, metronidazole, which inhibits DNA synthesis, reduced the growth rate, whereas meropenem, which inhibits cell wall synthesis, increased the death rate in several cases. In contrast, eravacycline, piperacillin/tazobactam and rifampin exhibited variable and species-dependent effects on the growth dynamics.

CONCLUSION: The observation that opportunistic strains in monoculture are resistant to several tested antibiotics in contrast to commensals questions the use of broad-spectrum antibiotics for microbiome modulation in gastrointestinal diseases and motivates the need for targeted strategies to reshape dysbiotic microbial communities.},
}

*Anti-Bacterial Agents/pharmacology
Humans
*Inflammatory Bowel Diseases/microbiology
Escherichia coli/drug effects/growth & development
*Bacteria/drug effects/growth & development
*Gastrointestinal Microbiome/drug effects
Bacteroides fragilis/drug effects/growth & development
Microbial Sensitivity Tests

@article {pmid42989121,
year = {2026},
author = {Suchet, M and Pannetier, P and Danion, M and Braunbeck, T and Alves Gomes, P and Cachot, J and Bellec, L},
title = {Long-term intermittent exposure to fluoride and tebuconazole alters gill, skin and gut microbiomes in rainbow trout (Oncorhynchus mykiss).},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42989121},
issn = {1471-2180},
support = {ANSES-22-EST-050//French National Research Program for Environmental and Occupational Health of ANSES/ ; },
mesh = {Animals ; *Oncorhynchus mykiss/microbiology ; *Gills/microbiology/drug effects ; *Triazoles/toxicity/adverse effects/pharmacology ; *Fluorides/adverse effects/pharmacology ; *Bacteria/classification/genetics/drug effects/isolation & purification ; *Gastrointestinal Microbiome/drug effects ; RNA, Ribosomal, 16S/genetics ; Skin/microbiology/drug effects ; *Water Pollutants, Chemical ; Skin Microbiome ; *Microbiota/drug effects ; },
abstract = {BACKGROUND: Fluoride and tebuconazole are two compounds widely used in industrial processes and agriculture, respectively, and are regularly detected in surface waters. Therefore, there is an urgent need to characterise their effects on aquatic organisms. In this context, adopting a holistic approach that integrates the host and its associated microbiomes, the holobiont, is particularly relevant. In this study, rainbow trout were exposed from 6 days post-fertilisation for 7 months to a daily 7-hour pulsed regime of two concentrations of fluoride (6.8 or 24.7 mg/L, representing environmentally relevant levels for contaminated hotspots), to tebuconazole (51.7 µg/L, within the range of agricultural runoff peaks), or maintained in control conditions. At the end of the exposure period, gill, skin and intestine microbiomes were characterized using 16 S rRNA gene metabarcoding.

RESULTS: Fluoride and tebuconazole significantly affected the bacterial alpha diversity in gill and skin tissues. Beta diversity was significantly affected in gill and skin tissues, whereas the intestine exhibited a weak overall treatment effect without significant pairwise differences. If compared to the control treatment, fluoride exposure altered microbial co-occurrence networks, affecting bacterial interconnections in a tissue-specific manner, with reduced interconnections in gills and increased interconnections in skin and intestine compared to the control treatment. Shifts in taxonomical composition were present following exposure to both pollutants, and notably increases in the relative abundance of fish pathogens such as Candidatus Piscichlamydia, Flavobacterium and Aeromonas were observed. Increased abundance of Aeromonas (gill, skin and intestine) and Acidovorax (gill), along with functional predictions, suggested potential alterations in pathways related to antibiotic resistance, warranting further metagenomic investigation.

CONCLUSIONS: These results highlight alterations of gill, skin and intestine microbiomes in the rainbow trout following chronic exposure to fluoride and tebuconazole, with distinct and tissue-specific microbial responses. Beyond taxonomical shifts, the observed alterations of bacterial co-occurrence networks, enrichment of pathogenic bacteria, and antibiotic-resistant taxa, indicating that the fish microbiome is a sensitive bioindicator of chronical chemical stress. Whether these microbial shifts translate into adverse host health outcomes remains to be investigated in future studies.},
}

Animals
*Oncorhynchus mykiss/microbiology
*Gills/microbiology/drug effects
*Triazoles/toxicity/adverse effects/pharmacology
*Fluorides/adverse effects/pharmacology
*Bacteria/classification/genetics/drug effects/isolation & purification
*Gastrointestinal Microbiome/drug effects
RNA, Ribosomal, 16S/genetics
Skin/microbiology/drug effects
*Water Pollutants, Chemical
Skin Microbiome
*Microbiota/drug effects

@article {pmid42989307,
year = {2026},
author = {Jacot, W and Cayrefourcq, L and Dunyach-Remy, C and Jarlier, M and Lossaint, G and D'Hondt, V and Pastre, T and Garima, F and Massemin, B and Guiu, S and Dupuy, AMG and Cristol, JP and Lavigne, JP and Alix-Panabières, C},
title = {Circulating blood microbiome biomarkers as liquid biopsy in breast cancer.},
journal = {Journal of experimental & clinical cancer research : CR},
volume = {45},
number = {1},
pages = {},
pmid = {42989307},
issn = {1756-9966},
support = {No. 25014115//FEDER/ ; No. 115749//CANCER-ID program/ ; Recherche Tremplin' initiative//Centre Hospitalier Régional Universitaire de Montpellier/ ; },
mesh = {Humans ; Female ; *Breast Neoplasms/blood/pathology/microbiology ; Liquid Biopsy/methods ; *Biomarkers, Tumor/blood ; Prognosis ; Middle Aged ; Neoplastic Cells, Circulating/pathology ; *Microbiota ; Adult ; Aged ; },
abstract = {BACKGROUND: Circulating tumor material can already be used to help in cancer management, but host-microbiota interactions may add complementary value. This study evaluated a "liquid microbiopsy", combining cell-free microbial DNA (cf-mbDNA) with host biomarkers of microbial translocation/permeability (LBP, sCD14, I-FABP), to refine staging and prognosis in breast cancer.

METHODS: We analyzed 136 individuals: 58 metastatic breast cancer (MBC), 58 early breast cancer (EBC), and 20 healthy donors. Plasma cf-mbDNA was quantified by 16S rRNA qPCR with extraction/run negative controls; LBP, sCD14, I-FABP by ELISA; and CRP by immunoturbidimetry. Circulating tumor cells (CTCs) and PD-L1 on CTCs were assessed by CellSearch® and immunostaining. Diagnostic performance was assessed by area under the ROC curve. In MBC, progression-free survival (PFS) and overall survival (OS) were analyzed using Kaplan-Meier and Cox models.

RESULTS: LBP discriminated EBC from MBC with an AUC 0.92, with a slight improvement in the 3- or 5-marker models (AUC 0.936-0.939). For EBC vs healthy donors, CRP showed modest performance (AUC 0.73), and marker combinations offered no improvement.. In MBC (median follow-up 77.5 months), median PFS and OS were 4.5 and 14.5 months, respectively. In univariate analysis, shorter PFS was associated with tumor subtype, > 3 prior treatments, > 2 metastatic sites, CTCs ≥ 5, and PD-L1-positive CTCs detection. In multivariate analysis, sCD14 and I-FABP independently predicted PFS, while sCD14 was independently associated with OS.

CONCLUSIONS: A measurable host-microbiota-barrier axis (LBP, sCD14, I-FABP) provided stage-related and prognostic information complementary to CTC/PD-L1 status, whereas cf-mbDNA load alone showed limited discriminative value. These findings support liquid microbiopsy as a complementary extension of liquid biopsy but must be considered as exploratory, and warrant multicenter validation in larger independent cohorts with standardized pre-analytics and low-biomass controls.

TRIAL REGISTRATION: NCT03449264; NCT02866149.},
}

Humans
Female
*Breast Neoplasms/blood/pathology/microbiology
Liquid Biopsy/methods
*Biomarkers, Tumor/blood
Prognosis
Middle Aged
Neoplastic Cells, Circulating/pathology
*Microbiota
Adult
Aged

@article {pmid42989337,
year = {2026},
author = {Barón, MD and Martín-Vivaldi, M and Martínez-Renau, E and Arlettaz, R and Engelbrecht, D and Enkvist, C and van Rensburg, ELJ and Zhang, L and Martín-Platero, A and Martínez-Bueno, M and Martínez-García, Á and Ruiz-Castellano, C and Schaub, M and Stanback, M and van de Ven, TMFN and Videvall, E and Liang, W and Soler, JJ},
title = {Functional phylosymbiosis in birds: phylogeny and antimicrobial properties of bacterial symbionts in Bucerotiformes.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {42989337},
issn = {2524-4671},
abstract = {Bacterial symbionts and their animal hosts differ in the strength and type of selection pressures that promote their evolution and, as some host traits are phylogenetically conserved, their symbiotic bacterial communities could also exhibit greater similarity than expected by chance; a pattern known as phylosymbiosis. This might result from differences in bacterial assemblages across species-specific habitats, and/or from natural selection favouring host traits that allow harbouring functional species-specific bacteria (functional phylosymbiosis). We explored these patterns in eight Bucerotiformes taxa, including hoopoes, woodhoopoes, and hornbills, of which hoopoes and woodhoopoes harbour antibiotic-producing symbionts in their uropygial gland. We characterised uropygial secretion bacterial communities using high-throughput 16S-rRNA gene sequencing and analysed its association with avian phylogeny. Furthermore, we quantified antimicrobial activity of bacterial isolates, and explored its relationship with host phylogenetic distances and bacterial community composition. We found a significant correlation between avian phylogeny and bacterial community dissimilarities, supporting phylosymbiosis. Moreover, antimicrobial activity was significantly predicted by bacterial community composition and the relative abundance of particular strains in hoopoes and woodhoopoes. These findings suggest that antimicrobial properties of symbionts could be responsible for the detected phylosymbiosis and that natural selection may favour uropygial gland features allowing hosts to harbour specific antimicrobial-producing symbionts.},
}

@article {pmid42989368,
year = {2026},
author = {Ma, B and Xiao, J and Xu, Y and Chen, T and Liu, S and Zou, S and Gao, D and Zhuang, Y and Li, M and Wang, W and Li, S and Cao, Z},
title = {Multi-omics analysis reveals microbial and metabolic signatures associated with neutral detergent fiber digestibility in dairy cattle.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42989368},
issn = {1674-9782},
support = {No: 2025-JSGG-048//National Technology Innovation Center for Dairy/ ; No: 2024BBF01006//Key R&D Programme of Ningxia/ ; },
abstract = {BACKGROUND: The rumen microbiome is central to fiber degradation in dairy cows, yet the precise functional and metabolic networks driving variations in neutral detergent fiber (NDF) digestibility remain poorly understood. Elucidating these microbiome-host interactions is critical for improving forage utilization and advancing sustainable dairy production.

RESULTS: Employing an integrative metagenomics-metabolomics approach, we characterized the rumen microecology of lactating dairy cows exhibiting high and low NDF digestibility phenotypes (n = 10/group). Metagenomic profiling revealed a significant enrichment of fibrolytic taxa (Prevotella sp., Lachnospiraceae bacterium) and carbohydrate-active enzymes in the high-NDF group (HI). In addition, species-level differential abundance testing showed that Methanobrevibacter spp. was more abundant in the low-NDF group (LO) than in the HI group, whereas no archaeal differences were detected at the phylum or genus levels. Functional and metabolomic analyses indicated broader enrichment of amino acid degradation functions and higher concentrations of major volatile fatty acids (VFAs) in HI cows, consistent with stronger overall ruminal fermentation activity. Furthermore, VFAs and microbial composition explained 54.3% and 43.0% of the variation in NDF digestibility, respectively. An exploratory machine learning model based on selected annotated metabolite features showed moderate discriminatory performance, with an out-of-bag accuracy of 77.19%.

CONCLUSIONS: Our findings suggest that coordinated shifts in rumen microbial composition, amino acid metabolism, and VFA production are associated with variation in NDF digestibility in dairy cattle. These results provide a basis for future studies aimed at improving fiber utilization through microbiome-informed nutritional or breeding strategies.},
}

@article {pmid42989377,
year = {2026},
author = {Lad, H and Shah, A and Thompson, ER and Javid, S and Chee, RH and Zaransky, S and Dhanda, A and Mudhar, A and Lamichhane, S and Chua, AT and Bono, K and Bono, J and Kaye, R and Johnson, WE and Cugini, C and Yan, K},
title = {Laryngeal Cancer Microbiome Study Reveals Parvimonas and Campylobacter as Potential Therapy Targets.},
journal = {The Laryngoscope},
volume = {},
number = {},
pages = {},
doi = {10.1002/lary.71027},
pmid = {42989377},
issn = {1531-4995},
support = {PC 162-25//New Jersey Health Foundation/ ; },
abstract = {OBJECTIVE: Laryngeal cancer accounts for 40% of head and neck malignancies and 1% of all cancer-related deaths worldwide. We evaluated the laryngeal cancer microbiome to identify cancer-specific genera as potential treatment targets.

METHODS: A prospective study was conducted using 57 laryngeal mucosal samples from 24 treatment-naive laryngeal cancer patients and 33 patients who were undergoing otolaryngological surgery unrelated to oral or laryngeal diseases (01/2023-09/2025). DNA was extracted and amplified in triplicate, targeting the V3/V4 region of the 16S rRNA gene, followed by paired-end 2 × 300 bp sequencing on the Illumina NextSeq 2000. Amplicon sequence variants were identified via DADA2 and assigned to genera using a naive Bayes classifier. Two samples with zero classified read pairs were excluded.

RESULTS: Most patients were male (87.5% cancer, 66.7% controls) and smokers (83.3% cancer, 54.5% controls). Cancer patients' core laryngeal microbiomes uniquely contained Parvimonas (3.67%; 95% CI: 0.70%-6.64%), and Campylobacter (1.12%; 95% CI: 0.60%-1.63%), while control patients' uniquely contained Corynebacterium (2.97%; 95% CI: 0.00%-7.67%) and Alloprevotella (1.34%; 95% CI: 0.64%-2.04%). Cancer samples were significantly enriched in 19 genera, notably Peptococcus (2.93, q = 0.0003), Campylobacter (1.68, q = 0.009), and Parvimonas (2.02, q = 0.03), compared to controls.

CONCLUSIONS: Laryngeal cancer patients' samples displayed microbial dysbiosis, with enrichment of microbes present in gastrointestinal cancers, cervical cancer, and inflammatory states; they also exhibited loss of immunoprotective taxa. These findings support that microbiome profiling can distinguish malignant mucosa and guide future studies targeting genera increased in cancer, including Parvimonas and Campylobacter.},
}

@article {pmid42989406,
year = {2026},
author = {Shen, H and Ma, L and Li, J and Hu, Y and Peng, N and Zhao, S},
title = {Microbial drivers of high aquaculture productivity: decoupling of taxonomic and functional profiles enables efficient nitrogen cycling in greenhouse shrimp farming.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {42989406},
issn = {2524-4671},
support = {NWZZJ2025-2027-05//Major Project of Hubei Agricultural Microbial Industry Development-Innovative Bio-feed Development and Demonstration of Straw-Based Feed Utilization/ ; },
abstract = {As a global cornerstone of animal protein, farmed shrimp production in China has been revolutionized by the Greenhouse Shrimp Farming Model (GSFM). However, the microbial mechanisms underpinning the productivity and biosafety of this intensive paradigm remain poorly understood. Through a large-scale metagenomic survey of 90 standardized aquaculture units in the core GSFM production regions of China, spanning a 15-degree latitudinal gradient, we deciphered the functional architecture of the GSFM microbiome. Our results reveal a striking functional convergence despite geographic taxonomic variation: while microbial compositions shifted across regions, the core metabolic pathways-particularly those governing nutrient cycling-remained conserved. High-productivity systems, notably in southern provinces (Guangxi and Guangdong), were characterized by a specialized microbial repertoire that optimized water chemistry through efficient nitrogen processing. We identified a sophisticated spatial division of labor, where the gut microbiota acts as a specialized nitrite detoxification unit, while the water column microbiota serves as the primary engine for ammonia assimilation. Furthermore, we characterized a diverse antibiotic resistome and utilized host-tracking to evaluate the ecological costs of intensification. These findings shift the focus from microbial identity to functional niche partitioning, providing a mechanistic blueprint for the sustainable intensification of aquaculture through targeted microbiome management.},
}

@article {pmid42989411,
year = {2026},
author = {Jahnke, TT and Holschuh, C and Schlattmann, P},
title = {Mediterranean diet and risk of prostate cancer: a systematic review and meta-analysis of observational studies.},
journal = {BMC nutrition},
volume = {12},
number = {1},
pages = {},
pmid = {42989411},
issn = {2055-0928},
abstract = {BACKGROUND: Prostate cancer is the most common malignancy among men worldwide. In addition to non-modifiable risk factors, modifiable lifestyle factors are increasingly recognized in prevention. The Mediterranean diet (Med Diet), characterized by high intake of plant-based foods, unsaturated fatty acids, and antioxidant micronutrients, has been proposed as a protective dietary pattern.

METHODS: A systematic search was conducted in PubMed, Web of Science, and Scopus examining associations between Mediterranean diet adherence and prostate cancer risk. Fourteen studies met eligibility criteria. Meta-analysis was performed in R applying a random-effects model (REML estimation; Hartung-Knapp adjustment). Heterogeneity was assessed with I² and τ²; publication bias was evaluated using a funnel plot, contour-enhanced funnel plot, and Egger's test.

RESULTS: Based on a random effects model, we did not find a statistically significant difference in risk of prostate cancer in men with high versus low Mediterranean diet adherence (RR = 0.98; 95% CI: 0.93-1.04). Heterogeneity was moderate (Q = 19.95, I² = 34.8%). Although Egger's regression test did not indicate statistically significant publication bias (p = 0.115), complementary analyses (Q-Q plot and limit meta-analysis) suggested a possible small-study effect, warranting cautious interpretation.

CONCLUSION: In this meta-analysis, no protective effect of the Mediterranean diet against prostate cancer was found. Nevertheless, biological plausibility and inconsistent epidemiological trends suggest that further research using standardized dietary assessments and incorporating genetic and microbiome-related factors is needed.

TRIAL REGISTRATION: The review protocol was not prospectively registered.},
}

@article {pmid42989617,
year = {2026},
author = {Sommer, AJ and Kiudeliene, E and Lauridsen, M and Torre, A and Fagan, A and Skieceviciene, J and Jonasson, E and Obolewicz, H and Sikaroodi, M and Kupcinskas, J and Khoruts, A and Gillevet, PM and Bajaj, JS},
title = {Gut‒liver‒brain axis signature of cirrhosis-related cognitive impairment is consistent across multi-national cohorts.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2753908},
doi = {10.1080/19490976.2026.2753908},
pmid = {42989617},
issn = {1949-0984},
mesh = {Humans ; Female ; Middle Aged ; *Liver Cirrhosis/complications/microbiology/psychology ; Male ; Hepatic Encephalopathy/microbiology ; *Gastrointestinal Microbiome ; *Cognitive Dysfunction/microbiology/etiology/physiopathology ; *Liver/metabolism/microbiology/physiopathology ; *Brain/metabolism/physiopathology ; Lithuania ; Mexico ; United States ; Denmark ; Feces/microbiology ; Aged ; Cohort Studies ; Bacteria/classification/isolation & purification/genetics ; *Brain-Gut Axis ; },
abstract = {Cognitive impairment in cirrhosis is associated with an altered gut‒liver‒brain axis, but geographic variations in diet and clinical practices may limit generalizability. We investigated consistency of microbial signatures for cirrhosis-related cognitive impairment across four countries. We enrolled outpatients with cirrhosis from USA, Denmark, Lithuania, and Mexico who underwent Psychometric Hepatic Encephalopathy Score (PHES) testing for covert hepatic encephalopathy (CHE), and stool shotgun metagenomic sequencing. Taxonomic and functional associations with PHES were evaluated after adjustment for MELD, country, demographics, sex, proton pump inhibitor (PPI), lactulose, and rifaximin use. We enrolled 221 patients (median age 58 y, 57.9% men, median MELD 12). Cognitive performance varied by country despite adjustment for clinical covariates. Lithuania demonstrated greater microbial richness and better cognition despite higher MELD, accompanied by distinct dietary patterns including greater yogurt and tea consumption. In the entire cohort, increasing MELD was associated with reduced microbial richness and depletion of commensals. Worse PHES performance, however, showed a distinct microbiome signature with increased Streptococcus abundance independent of MELD, country, PPI use, and HE therapies. Twenty-two microbial pathways were associated with PHES, mostly related to amino-acid biosynthesis and nitrogen metabolism. Of these, ornithine degradation and heme B biosynthesis II were uniquely enriched with worse PHES and CHE, which mapped onto Enterobacteriaceae. We conclude that across four geographically and culturally disparate countries, cirrhosis-related cognitive impairment was associated with consistent microbial compositional and functional alterations distinct from advancing liver disease. These findings support a consistent gut‒liver‒brain axis signature involving oral-gut translocation and altered nitrogen metabolism.},
}

Humans
Female
Middle Aged
*Liver Cirrhosis/complications/microbiology/psychology
Male
Hepatic Encephalopathy/microbiology
*Gastrointestinal Microbiome
*Cognitive Dysfunction/microbiology/etiology/physiopathology
*Liver/metabolism/microbiology/physiopathology
*Brain/metabolism/physiopathology
Lithuania
Mexico
United States
Denmark
Feces/microbiology
Aged
Cohort Studies
Bacteria/classification/isolation & purification/genetics
*Brain-Gut Axis

@article {pmid42989696,
year = {2026},
author = {Pai, N and Nicholson, M and Rich, S and Conrad, MA},
title = {Fecal microbiota transplantation and microbiota-based therapeutics in pediatric clinical practice: Current status and emerging indications.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpn3.70633},
pmid = {42989696},
issn = {1536-4801},
support = {//None/ ; },
abstract = {Fecal microbiota transplantation (FMT) is a safe and effective treatment for recurrent or refractory Clostridioides difficile infection (rCDI) in children and adults. This review outlines the evidence behind FMT for rCDI, considerations in special pediatric populations, and limitations in current practice due to FMT access for patients under the age of 18.},
}

@article {pmid42989733,
year = {2026},
author = {Mu, K and Dang, CP and Xue, M and Li, Q and Huynh, HQ and Griffiths, AM and Turner, D and Moayyedi, P and Steinhart, AH and Dieleman, LA and Deslandres, C and Bitton, A and Mack, DR and Jacobson, K and Cino, M and Aumais, G and Panaccione, R and Bressler, B and Lee, SH and Crohn's And Colitis Canada Genetic Environment Microbial Gem Project Research Consortium, and Croitoru, K and Turpin, W},
title = {Fecal neuraminidase correlates with inflammatory signatures and microbiome shifts in preclinical Crohn's disease.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2755166},
doi = {10.1080/19490976.2026.2755166},
pmid = {42989733},
issn = {1949-0984},
mesh = {Humans ; *Crohn Disease/microbiology/enzymology/immunology ; *Neuraminidase/analysis/metabolism ; *Feces/enzymology/chemistry/microbiology ; Female ; Male ; Prospective Studies ; Adult ; *Gastrointestinal Microbiome ; Inflammation ; Bacteria/classification/genetics/isolation & purification/enzymology ; RNA, Ribosomal, 16S/genetics ; Leukocyte L1 Antigen Complex/analysis ; Biomarkers/analysis ; },
abstract = {The mucus layer, rich in mucin glycoproteins, serves as a critical barrier to microbial invasion. Neuraminidases cleave terminal sialic acids from mucin glycans, a process that may influence mucus integrity, epithelial exposure to microbial antigens, and mucosal immune responses, making fecal neuraminidase activity a biologically relevant functional readout of host-microbe interactions in the context of Crohn's disease (CD) pathogenesis. We evaluated whether fecal neuraminidase activity is associated with future CD risk and examine its relationships with inflammatory and microbial signatures relevant to early disease development. Within the prospective GEM cohort, 69 individuals who later developed CD were matched to 69 healthy first-degree relative controls. Fecal neuraminidase activity was measured using a fluorometric assay. Conditional logistic regression assessed its association with future CD risk. Partial Spearman correlations evaluated relationships with 446 serum proteins (OLINK), followed by pathway enrichment analysis, and with fecal calprotectin (FCP) and gut microbial composition (16S rRNA sequencing). Fecal neuraminidase activity was positively associated with future CD (OR = 1.541; 95% CI: 1.05-2.25; p = 0.026). Proteins correlated with neuraminidase activity were enriched in immune and inflammatory pathways. Neuraminidase activity was positively correlated positively with FCP (p ≤ 0.05), and its association with future CD was attenuated after adjustment for FCP. Fourteen microbial taxa were significantly correlated with neuraminidase activity (q ≤ 0.05). Fecal neuraminidase activity's relationships with inflammatory markers and microbial taxa support its potential relevance as a functional marker of host-microbe alterations during preclinical CD.},
}

Humans
*Crohn Disease/microbiology/enzymology/immunology
*Neuraminidase/analysis/metabolism
*Feces/enzymology/chemistry/microbiology
Female
Male
Prospective Studies
Adult
*Gastrointestinal Microbiome
Inflammation
Bacteria/classification/genetics/isolation & purification/enzymology
RNA, Ribosomal, 16S/genetics
Leukocyte L1 Antigen Complex/analysis
Biomarkers/analysis

@article {pmid42989912,
year = {2026},
author = {Pluer, B and Travis, J},
title = {Links Between Environmental Quality, Gut Microbiota, and Host Performance in Nutrient-Impacted Springs.},
journal = {Environmental microbiology},
volume = {28},
number = {11},
pages = {},
doi = {10.1111/1462-2920.70471},
pmid = {42989912},
issn = {1462-2920},
support = {G2020031598770049//Sigma Xia/ ; //Florida State University/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Nutrients/analysis ; Florida ; *Natural Springs/chemistry/microbiology ; RNA, Ribosomal, 16S/genetics ; Female ; *Bacteria/classification/genetics/isolation & purification ; Male ; Ecosystem ; *Fundulidae/microbiology/physiology/growth & development ; Reproduction ; Symbiosis ; Fresh Water/chemistry ; },
abstract = {Microbial symbionts may enhance adaptation to environmental stress, yet their role in nutrient-enriched freshwater habitats remains unclear. We conducted a full-factorial laboratory experiment with least killifish, Heterandria formosa, manipulating water chemistry from four Florida springs and gut microbiota inoculations from conspecifics at those sites. Sequencing of 16S rRNA revealed that gut microbial richness was higher in fish reared in less nutrient-loaded waters, but inoculation treatments, if successful, did not produce significant shifts in composition. Gut communities consistently differed from ambient water, with enrichment of Pseudomonadota and Planctomycetota. Females grew more slowly in the most polluted water. In a parallel result, males displayed higher mass-specific metabolic rates in the most nutrient-loaded water. Reproductive output per female nearly doubled when experimental microbiota and water originated from the same site, despite stable microbial diversity, though parentage and inoculation success were not verified; therefore, these results should be interpreted cautiously. These results indicate that environmental quality shapes gut microbiota and host performance, and that matching microbial communities to habitat conditions can boost reproduction. Such interactions may contribute to freshwater fish resilience and merit integration into conservation strategies.},
}

Animals
*Gastrointestinal Microbiome
*Nutrients/analysis
Florida
*Natural Springs/chemistry/microbiology
RNA, Ribosomal, 16S/genetics
Female
*Bacteria/classification/genetics/isolation & purification
Male
Ecosystem
*Fundulidae/microbiology/physiology/growth & development
Reproduction
Symbiosis
Fresh Water/chemistry

@article {pmid42989938,
year = {2026},
author = {Birabaharan, M and Immer, A and Gomez, AN and Valdes, D and Smith, DM},
title = {Mapping HIV reservoir geography: lessons for cure from the Last Gift rapid autopsy cohort.},
journal = {Current opinion in HIV and AIDS},
volume = {},
number = {},
pages = {},
pmid = {42989938},
issn = {1746-6318},
abstract = {PURPOSE OF REVIEW: Deep tissue reservoirs remain a major barrier to HIV cure. Their anatomical distribution and connectivity are difficult to study in living people. We examine how the Last Gift rapid-autopsy cohort clarifies reservoir connectivity, persistence behind anatomical barriers, and variation within organs, and consider the implications for cure.

RECENT FINDINGS: Tissue studies reveal HIV reservoirs that are interconnected across yet differ between and within anatomical sites. Viral sequence analyses suggest that blood links tissue reservoirs, with gut and lymphoid tissues acting as hubs of viral dispersal. Recovery of replication-competent HIV from brain microglia during suppressive antiretroviral therapy (ART) provides direct evidence of a resident brain reservoir. Even within the gastrointestinal tract, HIV DNA burden and transcriptions vary by region, with different microbiome associations in the small and large bowel.

SUMMARY: HIV reservoir geography supports durable ART-free remission as a practical goal. Achieving this goal will likely require combination therapies with complementary functions and tissue access. Because tissue heterogeneity limits what negative biopsies can establish, remission should be assessed through carefully monitored analytical treatment interruption and long-term follow up.},
}

@article {pmid42989971,
year = {2026},
author = {Chai, X and Yan, W and Wei, L and Ning, L and Gao, C and Zhang, Y and Cuo, P and Wang, R and Yang, M and Wang, H},
title = {Multi-Omics Reveals Divergent Gut Microbiome-Metabolome Associations Between High-Altitude Snowcock and Low-Altitude Pheasant.},
journal = {Animal genetics},
volume = {57},
number = {6},
pages = {},
doi = {10.1002/age.70231},
pmid = {42989971},
issn = {1365-2052},
support = {31802256//National Natural Science Foundation of China/ ; 25JRRA653//Natural Science Foundation of Gansu Province/ ; //Gansu Province's Longyuan Young Talents/ ; 2025KJZC00020//Science and Technology Support Special Project of Lanzhou Chengguan District/ ; GSJKKY2025-01//Disease Prevention and Control Research Project of Gansu Province/ ; },
mesh = {Animals ; *Altitude ; *Metabolome ; *Galliformes/microbiology/metabolism/genetics ; Multiomics ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Metabolomics ; Bacteria/classification/genetics ; },
abstract = {The gut microecological differences associated with high-altitude habitats remain poorly understood. The Snowcock (Tetraogallus tibetanus), a high-altitude bird endemic to the Qinghai-Xizang Plateau, and the low-altitude Pheasant (Phasianus colchicus) differ strikingly in habitat elevation and diet, providing an ideal comparative model. Fecal samples from six Snowcocks and six Pheasants were analyzed using 16S rRNA gene sequencing and UPLC-MS/MS untargeted metabolomics. Multi-omics integration was performed via Procrustes analysis, correlation networks, and random forest classification. Snowcocks displayed significantly lower alpha diversity and distinct beta diversity clustering compared with Pheasants. The Snowcock microbiota was dominated by Actinobacteriota and enriched in cold-tolerant genera such as Psychrobacillus. In contrast, the Pheasant microbiota showed higher diversity and was dominated by Firmicutes and Bacteroidota. Metabolomics revealed that differential metabolites enriched in Pheasants were predominantly mapped to amino acid metabolism and terpenoid biosynthesis pathways, while those enriched in Snowcocks were linked to glycerophospholipid and sphingolipid metabolism. Multi-omics integration demonstrated a significantly correlated microbiome-metabolome association, and the random forest model discriminated the two species in this dataset. The Snowcock microbiota was simplified and enriched with psychrophilic genera, and its fecal metabolome showed specific glycerophospholipid signatures. These features may reflect microecological divergence associated with the harsh plateau environment. Our findings provide multi-omics insights into high-altitude divergence in wild birds.},
}

Animals
*Altitude
*Metabolome
*Galliformes/microbiology/metabolism/genetics
Multiomics
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Metabolomics
Bacteria/classification/genetics

@article {pmid42990048,
year = {2026},
author = {Syed, RA and Ahmed, A and Hayat, U and Qazi, J},
title = {Targeting the Skin Microbiome in Dermatology: Translational Hype or Emerging Therapeutic Modality?.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {21},
pages = {},
doi = {10.1096/fj.202602650RR},
pmid = {42990048},
issn = {1530-6860},
mesh = {Humans ; *Skin Microbiome ; *Skin Diseases/microbiology/therapy ; *Dysbiosis/microbiology/therapy ; Translational Research, Biomedical ; *Dermatology/methods ; *Skin/microbiology ; Probiotics/therapeutic use ; Animals ; *Microbiota ; Prebiotics ; Antimicrobial Peptides ; },
abstract = {The human skin microbiome is a complex network of microorganisms, including bacteria, fungi, viruses, and archaea, that exist in a mutualistic relationship with the host. These microorganisms play important roles in maintaining skin homeostasis, defense against pathogens, regulation of immune response, and antimicrobial peptide synthesis. Dysbiosis, defined as an imbalance of microbial communities, has been linked to dermatological conditions including atopic dermatitis (AD), acne, psoriasis, and chronic wounds. Despite compelling mechanistic insights, the translation of microbiome science into clinically effective therapies remains inconsistent and prematurely optimistic. Emerging therapeutic strategies aim to restore and modulate the skin microbiome with precision, thereby moving beyond conventional broad-spectrum antimicrobial approaches. These encompass probiotics, prebiotics, synbiotics, live biotherapeutic products (LBPs), bacteriophage therapy, microbiome engineering, postbiotics, microbial consortia treatment, and antimicrobial peptides that selectively target microbial communities instead of eliminating them. While these strategies are biologically plausible and have initial-phase evidence, their clinical stability, reproducibility, and scalability are uncertain. Major limitations include inter-individual variability of microbiomes, transient colonization, methodological limitations in functional profiling, and regulatory uncertainties surrounding them. This review article critically evaluates microbiome-directed dermatologic therapies at the crossroads of real therapeutic potential and translational overextension. The field is not just hype; its clinical application has advanced more rapidly than the supporting evidence base justifies. Progress in this domain requires a shift from descriptive and associative research toward mechanism-driven, precision-based interventions. Such interventions must be validated against robust clinical endpoints. By critically assessing biological plausibility, clinical evidence, and translational barriers, this review provides a balanced perspective on the field and outlines realistic pathways for its evolution into a viable therapeutic paradigm.},
}

Humans
*Skin Microbiome
*Skin Diseases/microbiology/therapy
*Dysbiosis/microbiology/therapy
Translational Research, Biomedical
*Dermatology/methods
*Skin/microbiology
Probiotics/therapeutic use
Animals
*Microbiota
Prebiotics
Antimicrobial Peptides

@article {pmid42990228,
year = {2026},
author = {Ferrer, DM and Holton, M and Yang, M and Villamil, I and Urtecho, G},
title = {Culturomics-Guided Precision FMT Enables Stable Antibiotic-Independent Engraftment via Metabolic Niche Targeting.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.25.761671},
pmid = {42990228},
issn = {2692-8205},
abstract = {The gut microbiome's functional architecture can be conceptualized as a network of metabolic niches, yet clinical approaches to fecal microbiota transplantation (FMT) do not leverage niche - level information to guide engraftment. Here, we present a culturomics-based framework that profiles the metabolic niche landscape of individual microbiomes to enable targeted, antibiotic-independent FMT. Using a panel of 60 diverse media conditions, we show that gut communities from genetically identical mice harboring distinct microbiomes exhibit reproducible, vendor - specific niche-occupancy profiles, with each condition selecting for compositionally distinct niche-associated communities (NACs). We demonstrate that antibiotic pretreatment prior to FMT compromises community resilience, yielding communities that lose donor taxa more rapidly and recover less taxonomic diversity after secondary perturbation compared to untreated recipients. By comparing donor and recipient niche profiles, we identify vacant metabolic niches in recipient microbiomes and show that NACs targeting these vacancies achieve stable engraftment persisting for over 72 days without antibiotic pretreatment, whereas NACs targeting occupied niches fail to colonize. Furthermore, complex NACs not only fill vacant niches but reshape the surrounding native community, while simpler NACs engraft with minimal collateral impact. This culturomics-guided framework provides a scalable, mechanistic approach for rational donor-recipient matching that could advance personalized microbiome-based therapies.},
}

@article {pmid42990330,
year = {2026},
author = {Glesener, H and Dorn, N and Cheng, Q and Voth-Gaeddert, LE and Krajmalnik-Brown, R},
title = {Human Gut Microbiota of Healthy Individuals Show Resilience to Acute Aflatoxin B1 Exposure Despite Solvent-Driven Community Shifts.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.26.760590},
pmid = {42990330},
issn = {2692-8205},
abstract = {UNLABELLED: Aflatoxin B1 (AFB1) is a potent mycotoxin linked to severe systemic health issues and gut microbiome disruption in in vivo models. However, it remains unclear whether AFB1 directly impairs human gut microbial composition and function or if observed dysbiosis is host-mediated. The objective of this work was to investigate the direct impact of acute AFB1 exposure on human gut microbiota from healthy individuals using anaerobic batch bioreactors. Fecal inoculum from 17 healthy adults was exposed to AFB1 concentrations ranging from 1,000 to 5,000 ppb, delivered in two solvents (ethanol and corn oil) under conditions simulating the large intestine. Metabolic activity was assessed via short-chain fatty acid (SCFA) and gas production measurements, while community structure was assessed using 16S rRNA gene amplicon sequencing. AFB1 concentrations remained stable throughout the incubations, indicating no significant microbial degradation of AFB1. Results showed that AFB1 did not significantly alter microbial SCFA output or community composition compared to solvent-only controls. Observed shifts in microbial profiles were primarily driven by the solvents used to bring AFB1 into solution rather than by the toxin. These findings demonstrate that healthy human gut microbial communities are resilient to direct, acute AFB1 exposure even at concentrations exceeding typical dietary levels. This suggests that microbiome disruption reported in vivo may be an indirect consequence of host-mediated factors, such as reactive metabolites or systemic immune responses, rather than direct toxicity by the parent compound.

IMPORTANCE: Aflatoxin B1 is a major global health threat, particularly in regions with high dietary exposure, where it is associated with liver cancer and childhood growth stunting. While research has linked aflatoxin exposure to changes in the gut microbiome, the mechanisms driving this "dysbiosis" are not known. This work provides evidence that the parent aflatoxin molecule does not directly affect healthy human gut microbes, even at very high concentrations. The observed resilience of these microbial communities suggests that the damage reported in living organisms is likely caused by host-specific responses to the toxin or by toxic byproducts created during liver detoxification. Furthermore, microbially driven detoxification of the parent aflatoxin molecule was not observed. Distinguishing between direct and indirect toxicity is essential for developing effective strategies and medical interventions to mitigate the health impacts of aflatoxin exposure worldwide.},
}

@article {pmid42990373,
year = {2026},
author = {Noyes, H and Anika, NE and Combs, J and Khan, T and Just, J and Fitzpatrick, S and Angelini, RG and Angelini, DR},
title = {Host specificity, seasonality, and urbanicity shape the gut microbiome of a synanthropic insect.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.28.762591},
pmid = {42990373},
issn = {2692-8205},
abstract = {The soapberry bug Jadera haematoloma is a classic model of rapid adaptive evolution, with a well-documented host shift from native herbaceous sapinds to the introduced goldenrain tree (Koelreuteria spp.). This host shift has facilitated the insect's spread into novel anthropogenic urban habitats. Microbial associations are often critical to insect environmental adaptation. Here, we characterize the gut microbiota of J. haematoloma across native and introduced host plants, seasonal transitions, and a gradient of urbanicity. Our findings indicate that the soapberry bug gut microbiome is highly specialized, with a small number of core bacterial amplicon sequence variants (ASVs) primarily from the families Rhizobiaceae, Streptococcaceae, Enterobacteriaceae, and Lactobacillaceae. While traits such as sex and wing morph do not correlate with microbiome structure, the host plant acts as the primary determinant of community composition. Bugs feeding on the ancestral host plant maintain a more diverse and even microbial community featuring Enterobacteriaceae, whereas the gut environment of bugs on the introduced host is overwhelmingly dominated by a single unclassified Rhizobiaceae ASV. Furthermore, seasonal transitions drive significant turnover among accessory microbial taxa. Finally, we demonstrate that urbanization introduces a distinct ecological effect on the insect's microbiome. While the degree of local green space does not systematically alter within-host taxonomic richness, it is associated with modest change in mean community composition and significantly disrupts microbial community variance. Increased urbanization correlates with significantly higher beta dispersion, indicating that anthropogenic environments lead to more stochastic microbiomes, which may be an indicator of environmental stress. Together, these results illustrate how rapid dietary host shifts and the ecological pressures of urbanization interact to shape the microbiome of a synanthropic insect.},
}

@article {pmid42990397,
year = {2026},
author = {Zandi, E and Medetgul-Ernar, K and Lenz, HJ and Alishahi, F},
title = {Dense Longitudinal Multi-Omics Reveals Microbial-Metabolic-Immune Succession During Immune Checkpoint Therapy.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.24.26366392},
pmid = {42990397},
abstract = {Immune checkpoint inhibitors (ICIs) can induce durable clinical responses, yet relationships among the gut microbiome, microbial function, intestinal metabolism, and host immunity remain incompletely resolved. We performed dense longitudinal multi-omics profiling of a single patient with colorectal cancer metastatic to the liver during ICI therapy and sustained tumor regression. Eleven serial stool samples spanning approximately 7.3 months were analyzed by 16S rRNA sequencing, microbial metatranscriptomics, metabolomics, lipidomics, and stool host-RNA immune profiling and aligned with serial clinical imaging. A major intestinal ecosystem transition accompanied the emergence of clinical response. Microbial abundance and transcriptional activity were frequently discordant, demonstrating that compositional profiling alone incompletely captured microbial dynamics. Taxon-resolved functional analysis revealed sequential microbial states rather than a single responder-associated configuration. Loss of early Bacteroides/Fusobacterium-associated functions accompanied purine/sphingolipid remodeling and changes in myeloid-associated immune signatures. At T5, a transient Bifidobacterium carbohydrate/fermentation program coincided with lactate/indole-3-lactate remodeling and broad adaptive T-cell, memory/regulatory, mucosal, and B-cell immune changes. At T6, marked Clostridium transcriptional emergence and lipid/coenzyme-A pathway activation coincided with fatty-acid/lysophospholipid remodeling and a distinct immune configuration. Historical HUMAnN reconstruction using original UniRef90 and MetaCyc resources confirmed taxon-specific, reaction-associated gene-family support for prioritized functional programs. These findings define a temporally ordered microbial-metabolic-immune succession during ICI response. Although this N-of-1 design cannot establish population generalizability, dense within-person multi-omics resolves transient functional states obscured by cross-sectional analyses and generates testable hypotheses for larger prospective cohorts and personalized studies of ICI response.},
}

@article {pmid42990531,
year = {2026},
author = {Li, R and Fan, X and Kang, J and Huang, X and Shi, Y and Chen, X},
title = {Harnessing metatranscriptomics to unveil the metabolic landscape of microbiota in traditional fermented foods.},
journal = {Current research in food science},
volume = {13},
number = {},
pages = {101601},
pmid = {42990531},
issn = {2665-9271},
abstract = {Traditional fermented foods are widely consumed and valued for their distinctive sensory properties and potential health benefits. These foods contain complex microbiota whose interactions and metabolic activities shape biochemical transformations relevant to product quality, safety, and functionality. Metatranscriptomics provides a culture-independent means of profiling community RNA and examining changes in microbial gene expression during fermentation. However, most fermented-food microbiome studies continue to infer function from community composition or genomic potential rather than from in situ gene expression. Existing metatranscriptomic applications also differ substantially in sampling, RNA processing, sequencing, and data analysis, limiting comparisons across food systems. This review examines the metatranscriptomic workflows applied to fermented foods, including sample preparation, sequencing strategies, and bioinformatic analysis. It identifies practical requirements for reproducible RNA-based studies in complex food matrices and compares transcriptionally represented taxa and pathways across fermentation systems. The review also distinguishes gene expression from realized metabolic activity, an important boundary when interpreting transcript annotations and reconstructed pathways. We further assess the strengths and limitations of metatranscriptomics, both alone and in combination with complementary omics, for resolving microbiota structure-function relationships. Key challenges include data integration, evidence interpretation, and the recovery of biologically meaningful information from complex transcriptomic datasets. When combined with complementary omics and experimental validation, metatranscriptomics can help relate expressed genes and pathways to fermentation phenotypes. These insights may guide the experimental evaluation of starter cultures and the development of more precise fermentation-control strategies.},
}

@article {pmid42990555,
year = {2026},
author = {Sommer, AJ and Sikaroodi, M and Fagan, A and Davis, BC and Khoruts, A and Gillevet, PM and Bajaj, JS},
title = {Global Carriage of Antimicrobial Resistance Genes and Virulence Factors Among Physicians in Cirrhosis Care.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-11319770/v1},
pmid = {42990555},
issn = {2693-5015},
abstract = {Cirrhosis patients are at high risk for drug-resistant infections, which may be transmitted between patients and healthcare providers. In this study, we used shotgun metagenomics to characterize the fecal microbiome of physicians in cirrhosis care (n = 55) across 9 countries. Our results indicate physicians from low- or middle-income countries carry greater antimicrobial resistance gene (ARG) diversity corresponding to increased taxonomic richness. Physicians carried a low prevalence of clinically relevant ARGs or virulence factors (VFs), regardless of country of practice or patient exposure. Further comparison of fecal microbiomes between a subset of cirrhosis patients and physicians' fecal samples collected from the same medical facility in the United States indicated that cirrhosis patients carried a far greater burden of high-risk VFs and ARGs. Collectively, this study provides evidence that most physicians in cirrhosis care are unlikely to be a primary reservoir of drug-resistant pathogens, although further surveillance of healthcare workers is warranted.},
}

@article {pmid42990654,
year = {2026},
author = {Moglowsky, H and Reynolds, C and Lovasz, J and Mir, FM and Shah, M and Varadhan, A and von Dohlen, G and Wall, N and Mahalaha, SA and Blackmon, L and Ringold, SM and Ejaz, FK and Stein, EA},
title = {Evaluation of a Targeted Oral Microbiome Treatment in an Older Adult Population.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.27.26366652},
pmid = {42990654},
abstract = {Gingivitis is highly prevalent among older adults and is associated with systemic diseases. Accessible and effective interventions are needed, particularly for underserved populations facing barriers to conventional dental care, such as older adults. This study evaluated the efficacy of a novel, multi-component lozenge (PTx800) designed to modulate the oral environment through blockade of sugar-to-acid and sugar-to-biofilm production of the oral microbiota. A six-week, double-blind, randomized, active placebo-controlled pilot trial was conducted with older adults (final sample n=20) residing in Cleveland, Ohio. Participants were randomized to receive either PTx800 or an active placebo lozenge containing sugar alcohols, used three times daily. Primary outcomes included Modified Gingival Index (MGI), Plaque Index (PI), Bleeding on Probing (BOP), Periodontal Probing Depth (PPD), and changes in oral pathogen load assessed by quantitative PCR. The PTx800 group demonstrated a 100% reduction in BOP, achieving complete resolution of bleeding sites, compared to an 82% reduction in the active placebo group. PPD was stabilized in the PTx800 group and slightly worsened in the control group. Microbiological analysis revealed a significant reduction in the total bacterial load in the PTx800 group, with pronounced decreases in key red complex periodontal pathogens, including Porphyromonas gingivalis (Pg), Tannerella forsythia (Tf), and Treponema denticola (Td). PTx800 lozenges significantly improved clinical and microbiological measures of gingival health in older adults compared to active placebo. These findings suggest that PTx800 is a promising, non-antibiotic approach for managing oral inflammation and dysbiosis in aging populations, with potential implications for reducing oral pathogens strongly linked to systemic diseases.},
}

@article {pmid42991003,
year = {2026},
author = {Sharma, K and Bhushan, I and Sistla, S},
title = {Predictors of Psychological Stress and Infertility Among Reproductive-Age Women in Jammu and Kashmir: A Cross-Sectional Study.},
journal = {Health science reports},
volume = {9},
number = {11},
pages = {e73482},
pmid = {42991003},
issn = {2398-8835},
abstract = {BACKGROUND AND AIMS: Infertility affects nearly one in six individuals globally, with a substantial proportion of cases remaining idiopathic. Emerging evidence suggests that psychological stress may influence reproductive outcomes through neuroendocrine and immune pathways, potentially influencing the vaginal microbiome and the reproductive microenvironment. This study aimed to assess the prevalence of stress and infertility and examine their association among women of reproductive age in Jammu and Kashmir.

METHODS: A cross-sectional study was conducted among 1068 married women aged 18-48 years in Jammu and Kashmir, including women with idiopathic infertility and fertile controls. Data on sociodemographic characteristics, perceived stress, symptoms of reproductive tract infections (RTIs), sleep patterns, and physical stress manifestations were collected using a structured interviewer-administered questionnaire. Binary logistic regression analysis was performed to identify factors associated with psychological stress and infertility.

RESULTS: Overall, 37.6% of participants reported stress, while 29.3% had infertility. Stress was significantly associated with older age groups, employment status, lower financial status, RTI symptoms, physical stress manifestations, sleep duration, and infertility. Women with infertility had markedly higher odds of stress. Infertility was significantly associated with a history of stress, age, employment status, financial status, RTI symptoms, and sleep duration.

CONCLUSION: Psychological stress is strongly associated with infertility and related health and socioeconomic factors among women in this population. These findings highlight the potential interplay between psychological, reproductive, and social factors in reproductive health. Further longitudinal studies are needed to clarify causal pathways and inform targeted interventions.},
}

@article {pmid42991011,
year = {2026},
author = {Chen, L and Cheng, J and Mao, S},
title = {Mechanisms of resistance to immune checkpoint inhibitors in renal cell carcinoma and novel treatment strategies.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1984645},
pmid = {42991011},
issn = {2234-943X},
abstract = {In recent years, immune checkpoint inhibitors (ICIs), such as nivolumab, ipilimumab, pembrolizumab, and atezolizumab have substantially improved the prognosis of patients with advanced renal cell carcinoma. These agents have greatly changed the management of advanced renal cell carcinoma, shifting the treatment paradigm from cytokine and vascular endothelial growth factor-based therapies to immunotherapy strategies. However, drug resistance limits the long-term benefit. The mechanisms of immunotherapy resistance in RCC are complex. Recently, increasing research has focused on how cancer cells evade the surveillance and attack of the immune system and identifying the molecular and cellular drivers of resistance. In response, combination regimens incorporating ICIs are being developed to alleviate drug resistance and attack cancer cells through multiple pathways. At the same time, novel targeted strategies are under investigation to develop innovative approaches to delay, partially overcome, or bypass resistance in defined clinical settings. This review outlines the mechanisms of immunotherapy resistance in RCC from three interrelated perspectives: cancer cell-intrinsic mechanisms, the tumor microenvironment, and host related factors. We also summarize current efforts to overcome resistance, including ICI combined with tyrosine kinase inhibitors, dual ICI therapy, tumor microenvironment-targeting strategies, radiotherapy combined with immunotherapy, and gut microbiota modulation. Although these new strategies have shown different therapeutic effects in clinical trials, deeper understanding of immune regulation highlights their potential. Moreover, the integration of multi-omics analysis, and microbiome regulation may increase patient choices and optimize therapeutic outcomes, but their clinical efficacy has not been fully confirmed and requires prospective, treatment defined validation. Overall, ICIs have substantially changed RCC treatment, future progress will depend on deeper biological insights, rational combination design, and validated personalized immunotherapy.},
}

@article {pmid42991063,
year = {2026},
author = {Seri, A and Yue, B and Khawaja, M and Tang, WHW and Birnbaum, Y and Lavie, CJ and Virani, SS and Strauss, M and Krittanawong, C},
title = {Cardiovascular health and longevity: where are we?.},
journal = {Frontiers in cardiovascular medicine},
volume = {13},
number = {},
pages = {1921582},
pmid = {42991063},
issn = {2297-055X},
abstract = {Cardiovascular health is a key factor in human longevity, affecting not just lifespan but also the quality of aging. We synthesize evidence across four risk factor domains: genetic and epigenetic factors (APOE, FOXO3, telomere biology, epigenetic clocks); metabolic and vascular factors (hyperglycemia, dyslipidemia, obesity, arterial stiffness); lifestyle determinants (diet, physical activity, smoking, sleep, gut microbiome); and environmental exposure (air and noise pollution, climate stressors, ionizing radiation). These factors influence various biological processes such as oxidative stress, chronic low grade inflammation (inflammaging), mitochondrial dysfunction, metabolic disturbances, and changes in telomere length and epigenetics that collectively damage the endothelium, stiffen arteries, promote atherosclerosis, and contribute to overall cardiovascular decline with age. Understanding these processes helps explain why cardiovascular aging is such a strong predictor of mortality. We further summarize the principal intervention strategies with evidence for improving cardiovascular health and longevity, such as adherence to the American Heart Association's Life's Essential 8 construct, heart-healthy dietary patterns(Mediterranean, DASH), smoking cessation, sleep optimization, and reduction of environmental exposures. This narrative review distinguishes evidence derived from model organisms, human observational cohorts, and human interventional/genetic studies, since these evidence tiers differ substantially in their support for lifespan or longevity extending claims specifically, as opposed to cardiovascular risk reduction more broadly.},
}

@article {pmid42991095,
year = {2026},
author = {Mwesige, B and Angucia, B and Mbodi, L and Mwazha, A and Niyonzima, N and Mwansa-Kambafwile, J and Breiman, RF and Zakumumpa, H and Chikandiwa, A},
title = {The cervicovaginal microbiome as a candidate correlate and potential predictor of HPV clearance and treatment response after HSIL therapy: a scoping review.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1972845},
pmid = {42991095},
issn = {2234-943X},
abstract = {BACKGROUND: Persistent high-risk human papillomavirus (hrHPV) infection causes virtually all high-grade squamous intraepithelial lesions (HSIL) and cervical cancer, but only a minority progress, implicating host and microenvironmental cofactors. The cervicovaginal microbiome (CVM), particularly Lactobacillus-dominated communities, may influence hrHPV persistence, clearance, and response to HSIL treatment.

OBJECTIVE: To map evidence linking the CVM with hrHPV clearance and outcomes after HSIL treatment, including loop electrosurgical excision procedure (LEEP) and conization, using PRISMA-ScR and Arksey and O'Malley frameworks.

METHODS: Literature on cervicovaginal microbiota, community state types (CSTs), HPV natural history, HSIL/CIN treatment, probiotics, microbiome-directed interventions, and predictive biomarkers was systematically searched and narratively synthesized using a Population-Concept-Context framework.

RESULTS: Sixty-six sources were charted. Lactobacillus crispatus-dominated communities (CST-I) were associated with hrHPV clearance and favorable post-treatment outcomes, whereas CST-IV, bacterial vaginosis, and increased alpha-diversity were associated with hrHPV persistence, greater HSIL severity, and treatment failure. Proposed mechanisms include lactic acid-mediated pH regulation, D-lactic acid signaling, and modulation of viral oncoproteins and immune responses. Excision altered the CVM, with restoration of Lactobacillus dominance accompanying viral clearance. Microbial-signature machine-learning models showed promising but preliminary predictive performance. Oral and intravaginal probiotics showed inconsistent but generally favorable trends, with strongest evidence for intravaginal L. crispatus transplantation. Gut microbiome diversity may also influence chemoradiotherapy outcomes in invasive cervical cancer.

CONCLUSION: The CVM is a promising predictor of hrHPV clearance and HSIL treatment response. However, methodological heterogeneity, small cohorts, and limited prospective evidence restrict clinical translation. Large prospective studies and rigorously designed trials are needed to validate predictive signatures and determine whether microbiome profiling or targeted modulation can improve HSIL management and outcomes.},
}

@article {pmid42991189,
year = {2026},
author = {Chakravarthy, A},
title = {Cross-cohort generalization limitations in gut microbiome-based Alzheimer's disease classifiers: evidence from four supervised cohorts with batch-correction analysis.},
journal = {Frontiers in aging neuroscience},
volume = {18},
number = {},
pages = {1918251},
pmid = {42991189},
issn = {1663-4365},
abstract = {Gut microbiome dysbiosis has been proposed as an Alzheimer's disease (AD) biomarker, but the transportability of microbiome classifiers across independent cohorts remains uncertain. We reprocessed five public 16S rRNA cohorts (509 samples, China, Kazakhstan, South Korea) with a common DADA2/genus-level pipeline and evaluated logistic regression and LightGBM classifiers using nested within-cohort cross-validation, leave-one-cohort-out (LOCO) transfer, pairwise transfer, permutational multivariate analysis of variance (PERMANOVA), batch adjustment, and out-of-fold SHapley Additive exPlanations (SHAP) analyses. Within four labeled cohorts, using strict training-only genus selection as the primary classifier-performance pipeline (Section 2.5.1), within-cohort area under the receiver operating characteristic curve (AUC-ROC) ranged from 0.611 to 0.996. The near-perfect Li 2019 result was stable across 50 repeated nested-cross-validation (CV) partitions and exceeded a 1,000-permutation label null (p = 0.000999), though a technical metadata confound cannot be excluded (Section 4.3). In LOCO evaluation, AUC ranged from 0.506 to 0.812 (mean decreases of 0.170 for logistic regression and 0.133 for LightGBM); paired bootstrap intervals excluded zero for four of eight cohort-model differences. LOCO estimates agreed closely with a fixed common-universe reference retained for secondary analyses (max |Δ| = 0.066), though one pairwise-transfer cell changed materially (Kazakhstan→Ling 2020, LightGBM: 0.58 → 0.44), reported without smoothing. In the four-cohort marginal PERMANOVA model, cohort-associated compositional variation exceeded diagnosis-associated variation (R[2] = 0.172 vs. 0.014), decreasing to 0.059 vs. 0.023 when restricted to three more technically comparable Chinese paired-end MiSeq cohorts; dispersion differed significantly among cohorts. Label-blind transductive ComBat-seq and MMUPHin adjustment changed mean LOCO AUC by at most 0.007 and did not recover transferability. Cross-cohort overlap of top predictive taxa was low: logistic regression overlap remained above a prevalence-restricted null, while LightGBM did not. A descriptive coefficient-stability screen identified eight logistic-regression genera with opposite, stable fitted-coefficient directions across cohorts. These findings demonstrate substantial, heterogeneous cross-cohort generalization limitations among the evaluated public 16S datasets and show that, under the tested label-blind transductive design, the two batch-adjustment methods did not restore transferability. Prospective validation in larger, geographically and technically diverse cohorts is needed before microbiome-based AD classifiers can be considered clinically actionable.},
}

@article {pmid42991275,
year = {2026},
author = {Zhao, M and Mo, T and Huang, X and He, H and Long, F and Wu, P and Zou, Y},
title = {Integrated microbiome and metabolome analysis reveals mechanisms of Fusarium wilt resistance in banana rhizosphere soil under different continuous cropping durations.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1853743},
pmid = {42991275},
issn = {1664-302X},
abstract = {INTRODUCTION: Fusarium fungi are the primary causal agents of banana Fusarium wilt disease. In this study, using a resistant banana line (derived from cultivar Baodao), we observed that with increasing years of continuous cropping, the incidence of Fusarium wilt disease showed a notable reduction.

RESULTS: Microbial community abundance was lower in the susceptible banana variety (V) than in the resistant variety [sampled after one (S1), two (S2), and three (S3) years of continuous cropping]. With increasing continuous cropping years (S1, S2, and S3), microbial abundance increased, while the abundance of Fusarium oxysporum significantly decreased, and these changes coincided with visually healthier plant growth compared to the susceptible variety. However, the relative abundance of Fusarium, Bisifusarium Gibellulopsis, and Rectifusarium were the highest in V. Rozellomycota sp., Trichoderma virens, Trichoderma asperellum, and Hypocreaceae sp. were also identified with high abundance in S2 and S3, but were not detected in V. In addition, using Spearman's correlation analysis and network analysis (|r| > 0.6), we found that the reduction of Fusarium pathogens was significantly correlated with the enrichment of beneficial bacteria such as Sphingomonas parvus and Rozellomycota sp. A total of 1153 metabolites were identified, including amino acids, phenolic acids, organic acids, phenolic acids, and flavonols. Among these, 79 compounds showed a significant decrease in V but increased in S1, S2, and S3; these compounds were negatively correlated with Fusarium oxysporum and positively correlated with Rozellomycota sp. Additionally, 47 compounds were associated with Sphingomonas parvus, Bryobacter and other beneficial bacteria.

CONCLUSION: These findings suggest that specific metabolic compounds are associated with the enrichment of beneficial fungi and bacteria in the banana rhizosphere soil as continuous cropping time increases.},
}

@article {pmid42991397,
year = {2026},
author = {Li, M and Pang, L and Li, Y and Shang, S and Huang, C},
title = {Multi-omics profiling identifies a putative Akkermansia-HK3-lactate immunometabolic link associated with JPZS treatment in lupus nephritis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1873518},
pmid = {42991397},
issn = {1664-3224},
mesh = {Animals ; *Lupus Nephritis/drug therapy/metabolism/immunology ; Female ; Mice ; Multiomics ; *Hexokinase/metabolism/genetics ; Mice, Inbred MRL lpr ; *Akkermansia ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Gastrointestinal Microbiome/drug effects ; *Lactic Acid/metabolism ; Kidney/metabolism/pathology/drug effects ; Disease Models, Animal ; Mice, Inbred C57BL ; Metabolomics ; },
abstract = {BACKGROUND: Lupus nephritis (LN) is associated with aberrant glycolytic reprogramming in renal immune cells, yet its relationship with gut microbial alterations remains poorly defined. Hexokinase 3 (HK3) has emerged as a candidate metabolic node in myeloid activation, while the relationship between gut Akkermansia abundance and renal HK3-associated metabolic changes in LN remains unclear. We used Qihuang Jianpi Zishen decoction (JPZS), an herbal formula used as an adjunct in clinical practice, as an experimental probe to investigate this putative gut-immunometabolic connection through integrated multi-omics.

METHODS: Female MRL/lpr mice (n = 6 per group) received JPZS (6.305, 12.61, or 25.22 g/kg/day) or vehicle for 8 weeks, with C57BL/6 mice serving as a healthy reference group. Renal function, autoantibodies, histopathology, and glomerular IgG deposition were assessed across treatment groups. Integrated multi-omics profiling-fecal 16S rRNA sequencing, untargeted plasma metabolomics, and renal RNA sequencing-was performed in the matched control, model, and high-dose JPZS groups. Renal lactate and pyruvate were quantified, and HK3 and Ldhal6b mRNA and their corresponding proteins were evaluated by qPCR and western blotting. HK3/F4/80 dual immunofluorescence was additionally performed to examine the spatial localization of HK3 relative to renal macrophages.

RESULTS: JPZS reduced proteinuria, serum creatinine, glomerular IgG deposition, and renal histopathological injury in MRL/lpr mice. Gut microbiome profiling showed marked enrichment of Akkermansia and altered community composition, without significant recovery of Chao1 or Shannon diversity, accompanied by reductions in Klebsiella and Enterococcus. Plasma metabolomics revealed remodeling of amino-acid and central carbon metabolism, while renal transcriptomics identified immune-related differences and an exploratory glycolysis/gluconeogenesis enrichment signal. JPZS reduced renal lactate accumulation and the lactate/pyruvate ratio and decreased renal HK3 expression at both the mRNA and protein levels. Dual immunofluorescence showed increased HK3 and F4/80 fluorescence in model kidneys, with overlapping signals evident in merged images; both signals were lower following JPZS-H treatment. Cross-layer correlation analyses linked gut genera, circulating metabolites, and renal gene expression; targeted assays separately characterized renal lactate/pyruvate status.

CONCLUSION: JPZS ameliorated renal injury while inducing coordinated changes in the gut microbiome, circulating metabolome, and renal immunometabolic profile in MRL/lpr mice. Integrated multi-omics and targeted validation identified a putative Akkermansia-HK3-lactate immunometabolic link associated with JPZS treatment. These findings provide a hypothesis-generating framework for gut-kidney immunometabolic crosstalk in LN and warrant future causal validation through microbiota- and HK3-targeted approaches.},
}

Animals
*Lupus Nephritis/drug therapy/metabolism/immunology
Female
Mice
Multiomics
*Hexokinase/metabolism/genetics
Mice, Inbred MRL lpr
*Akkermansia
*Drugs, Chinese Herbal/pharmacology/therapeutic use
Gastrointestinal Microbiome/drug effects
*Lactic Acid/metabolism
Kidney/metabolism/pathology/drug effects
Disease Models, Animal
Mice, Inbred C57BL
Metabolomics

@article {pmid42991468,
year = {2026},
author = {Li, X and Liu, H and Wu, J and Xi, C},
title = {Distribution and resistance-associated genomic features of Acinetobacter in an urban wastewater network.},
journal = {Current research in microbial sciences},
volume = {11},
number = {},
pages = {100673},
pmid = {42991468},
issn = {2666-5174},
abstract = {Acinetobacter spp. are important opportunistic pathogens with strong multidrug resistance potential, yet their distribution and associations with antibiotic resistance across urban wastewater systems remain poorly resolved. In this study, we characterized the spatiotemporal dynamics of Acinetobacter across an urban wastewater network including hospital, student residence hall, and wastewater treatment plant (WWTP) sites. A total of 300 wastewater samples were collected weekly over 1.5 years and analyzed by droplet digital PCR (ddPCR), with 94 samples further subjected to shotgun metagenomic sequencing. Acinetobacter was consistently detected across all sampling sites and ranked among the more abundant genera in site-pooled metagenomic community profiles. Throughout the WWTP treatment process, absolute Acinetobacter concentrations decreased by a median of 2.71 log10 units from influent to effluent, coinciding with a reduced ratio of Acinetobacter to total bacterial 16S rRNA gene copies. Cross-validated differential abundance analyses (DESeq2 and ANCOM-BC2) of the metagenomes corroborated this significant reduction in the effluent. Despite this removal efficacy, treated effluent maintained an average Acinetobacter concentration of 9.19 × 10[2] copies/100 mL, and the genus persisted as a highly abundant member of the effluent microbiome. Notably, Acinetobacter showed a positive association with 16S-normalized total antibiotic resistance gene (ARG) abundance (ρ = 0.570) that robust even remained significant after covariate adjustment (partial ρ = 0.508; 95% CI, 0.321-0.662). Genome-resolved analysis recovered 20 medium-to-high-quality Acinetobacter metagenome-assembled genomes, revealing site-specific lineage variations and identifying seven distinct OXA β-lactamase gene sequences. Although acquired ARG carriage and mobility were not established, the combined analyses support Acinetobacter as a widely detected genus associated with the wastewater resistome. From a public health perspective, tracking Acinetobacter alongside ARGs can characterize treatment-associated changes, provide bacterial-community context for resistance signals, and inform targeted genomic follow-up.},
}

@article {pmid42991495,
year = {2026},
author = {Buettner, C and Peterburs, P and Schulz-Kuhnt, A and Herrmann, L and Soeberdt, M and Abels, C},
title = {Peppermint oil exhibits antispasmodic and anti-inflammatory properties and alters gut microbial community composition and gas production in vitro.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1963380},
pmid = {42991495},
issn = {1663-9812},
abstract = {BACKGROUND: Peppermint oil (PMO) is an herbal medicinal product used for the symptomatic relief of minor spasms of the gastrointestinal tract, flatulence and abdominal pain, especially in patients with irritable bowel syndrome (IBS). To gain a more comprehensive understanding of the multimodal effects of PMO in IBS, the investigations aimed to confirm its antispasmodic and anti-inflammatory effects and assess direct effects of PMO on the human gut microbiome and microbial gas production in vitro.

METHODS: To investigate the spasmolytic activity of PMO (BNO 2910), circular smooth muscle strips from the proximal colon of five male guinea pigs were used. Its anti-inflammatory potential was evaluated using RAW 264.7 macrophages stimulated with LPS. TNF secretion and nitrite levels, as an indicator of NO production, were measured using ELISA and Griess reagent, respectively. Effects on the human gut microbiome and colonic fermentation activity were assessed in an anaerobic in vitro fermentation system inoculated with stool samples from six healthy donors using 16S rRNA gene sequencing, flow cytometry-based cell counting and gas production measurements.

RESULTS: PMO showed antispasmodic effects on isolated smooth muscle strips of guinea pig colon tissue as well as inhibition of LPS-induced TNF secretion and NO induction in RAW 264.7 macrophages. Additionally, PMO significantly reduced microbial gas production in stool samples from healthy donors, indicating reduced microbial fermentation activity under the experimental conditions, while the alpha diversity indices richness and evenness were maintained or even increased. At the genus level, PMO showed direct effects on microbiome community composition, inhibiting the growth of potential disease-related organisms (e.g., Escherichia-Shigella or Eggerthella), while maintaining or even increasing the abundance of health-related organisms (e.g., Blautia and Faecalibacterium).

CONCLUSION: Besides antispasmodic and anti-inflammatory effects, PMO exhibits direct effects on the human gut microbiome, including the modulation of microbial communities and total gas production in vitro. To determine the specific relevance of the observed microbiome-related effects of PMO in IBS further disease-specific studies are warranted.},
}

@article {pmid42991517,
year = {2026},
author = {Qi, Z and Wang, M and Li, Y and Tian, L and Liu, J},
title = {Molecular mechanisms by which the intratumoral microbiome drives pancreatic ductal adenocarcinoma progression and therapeutic response.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1970900},
pmid = {42991517},
issn = {1664-3224},
mesh = {Humans ; *Carcinoma, Pancreatic Ductal/microbiology/immunology/pathology/therapy/drug therapy ; *Pancreatic Neoplasms/microbiology/immunology/pathology/therapy/drug therapy ; Animals ; *Microbiota/immunology ; Disease Progression ; Tumor Microenvironment/immunology ; },
abstract = {Pancreatic ductal adenocarcinoma has an extremely poor prognosis. Pancreatic ductal adenocarcinoma harbors a multidomain intratumoral microbial community dominated by bacteria and also containing fungi; its composition differs fundamentally from that of normal pancreatic tissue and drives malignant progression through three major axes: inflammatory-immune signaling, metabolic-epigenetic regulation, and stromal remodeling. Gammaproteobacterial lipopolysaccharide establishes a chronic proinflammatory microenvironment through the Toll-like receptor 4-nuclear factor kappa B axis, whereas in situ gemcitabine inactivation by the long isoform of bacterial cytidine deaminase represents the best-supported microbiome-mediated mechanism of drug resistance to date. In experimental systems, Fusobacterium nucleatum has been linked to tumor-cell invasion and alternatively activated macrophage polarization. In mouse and cell models, intratumoral fungi have been implicated in immunosuppressive signaling through the C-type lectin receptor dectin-1-interleukin 33 axis and the mannose-binding lectin-complement pathway; their relevance to human pancreatic ductal adenocarcinoma remains debated. These three axes may converge on stromal activation and epithelial-mesenchymal transition and contribute to invasion and treatment resistance. Antimicrobial strategies targeting drug-resistance-associated bacteria can restore gemcitabine efficacy in animal experiments and have been explored experimentally alongside programmed cell death protein 1 blockade; the clinically appropriate patient populations and optimal sequencing of such combinations remain to be defined in prospective trials.},
}

Humans
*Carcinoma, Pancreatic Ductal/microbiology/immunology/pathology/therapy/drug therapy
*Pancreatic Neoplasms/microbiology/immunology/pathology/therapy/drug therapy
Animals
*Microbiota/immunology
Disease Progression
Tumor Microenvironment/immunology