@article {pmid41863002,
year = {2026},
author = {Wang, Y and Ling, W and Ouyang, L and Zhang, S and Zhou, H and Luo, T and Liu, S and Tang, J and Zhou, Z and Tang, L and Wang, Z and Wei, F and Huang, G},
title = {A lagging recovery: the delayed restoration of gut microbial diversity in Rhinolophus sinicus post-hibernation.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {41863002},
issn = {2524-4671},
support = {32192420//National Natural Science Foundation of China/ ; 32322015//National Natural Science Foundation of China/ ; 20233ACB209001//Natural Science Foundation of Jiangxi Province/ ; 2023SSY02081//Jiangxi Provincial Key Laboratory of Conservation Biology/ ; },
abstract = {BACKGROUND: Hibernation enables animals to survive extreme environments, yet gut microbiome dynamics across the full hibernation cycle remain poorly understood, particularly in chiropterans with unique physiological traits. This study aimed to precisely characterize seasonal microbial succession in wild Rhinolophus sinicus using 16S rRNA gene sequencing across 6 physiological stages, with a focus on taxonomic and functional shifts linked to hibernation-associated fasting and post-hibernation activity.

RESULTS: Alpha diversity followed a pronounced V-shaped trajectory, declining during hibernation and recovering only gradually—remaining suppressed in the early active stage and rebounding markedly by mid–late active stages. Beta diversity revealed a clear separation between hibernation and active phases, with physiological stage explaining 34.9% of community variation. At the phylum level, Pseudomonadota was the dominant taxon during hibernation, while Bacillota became the most abundant phylum in the active period. At the genus level, Yokenella was the core genus in the hibernation stage, and Lactococcus was the dominant genus in the active period. Functional predictions showed enrichment of lipid and amino acid metabolism during hibernation, supporting energy maintenance under fasting, while active-phase microbiota were oriented toward carbohydrate metabolism, matching increased energy demands.

CONCLUSIONS: Our findings demonstrate that hibernation drives directional restructuring of the gut microbiota in R. sinicus, offering new insights into microecological strategies underlying bat survival under extreme conditions.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00552-x.},
}

@article {pmid41864867,
year = {2026},
author = {Ma, W and Bai, B and Liu, M and Sheng, P and Bao, J and Song, C and Liu, J and Ma, H and Du, S and Ge, G and Jia, Y and Wang, Z},
title = {Synergistic effects of cellulase and lactic acid bacteria(Pediococcus pentosaceus and Levilactobacillus brevis) on alfalfa silage fermentation and microbial dynamics.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41864867},
issn = {1471-2180},
support = {(2025YFHH0210)//Research and Demonstration of High-Quality Forage Supply and Efficient Breeding Technology System for Dairy Cows/ ; },
abstract = {UNLABELLED: This study evaluated the effects of Lactic acid bacteria and cellulase, individually and in combination, on fermentation quality and microbial community dynamics of alfalfa silage. Six treatments were tested, including control, cellulase alone and two lactic acid bacteria species (Pediococcus pentosaceus, Levilactobacillus brevis) applied individually or in combination with cellulase. The results showed that Levilactobacillus brevis in combination with cellulase, producing higher lactic acid concentrations, lower pH (< 4.2) to the other treatments. The microbiome analysis revealed that Lactiplantibacillus was dominant, while undesirable bacterium Achromobacter was suppressed. Functional prediction of microbial communities analysis indicated a higher predicted abundance of sequences associated with pyruvate metabolism, glycolysis/gluconeogenesis and starch and sucrose metabolism pathways. These findings provide insights into optimizing alfalfa silage quality through synergistic use of cellulase and lactic acid bacteria silage inoculants with high metabolic stability.

GRAPHICAL ABSTRACT: [Image: see text]},
}

@article {pmid42010622,
year = {2026},
author = {Goldstein, C and Lavy, I and Sun, T and Ennis, D and Shreffler, WG and Yuan, Q and Virkud, YV and Martin, VM and Yassour, M},
title = {Strain-level microbial signatures and inferred functional alterations in infants with food protein-induced allergic proctocolitis.},
journal = {Genome medicine},
volume = {18},
number = {1},
pages = {},
pmid = {42010622},
issn = {1756-994X},
support = {1685-3680//Gerber Foundation/ ; 230465//Demarest Lloyd Jr Foundation/ ; 229711//the Food Allergy Science Initiative/ ; K23AI151555//National Institute of Allergy and Infectious Diseases of the US/ ; K23AI130408//Artificial Intelligence/Machine Learning Consortium to Advance Health Equity and Researcher Diversity/ ; },
abstract = {BACKGROUND: The complex relationship between the gut microbiome and immune system development during infancy is considered a key factor in the rising rates of pediatric allergic diseases. Food protein-induced allergic proctocolitis (AP), the earliest identified form of non-IgE-mediated food allergy in infants, occurs at the mucosal surface where dietary proteins, intestinal microbes, and immune cells directly interact, and increases the risk for life threatening IgE-mediated food allergy, making it an important model for understanding early food allergic disease development. The question of how specific microbial compositions and functional pathways contribute to AP development and progression remains poorly understood.

METHODS: We performed metagenomic sequencing on 740 longitudinal stool samples from 163 infants (84 with AP, 79 without AP) enrolled in the prospective GMAP cohort. Taxonomic profiling, functional pathway analysis, strain-level characterization, and machine learning-based classification were applied to identify microbial differences across disease stages.

RESULTS: Here we show that infants with AP exhibit different microbial compositions, characterized by enrichment of Escherichia coli and Bifidobacterium bifidum during early life, including pre-symptomatic stages, while species like Bifidobacterium breve and Klebsiella species are more abundant in infants without AP. These findings suggest the presence of microbial signatures that may be detectable before clinical symptoms emerge, and demonstrate that strain-level differences within E. coli populations may represent AP-associated lineages with distinct gene content profiles that were not previously recognized. For example, biofilm formation and cell adhesion genes in E. coli were particularly enriched in AP-associated clades. Short chain fatty acid (SCFA) and other functional pathways were also associated with AP, including reduced SCFA production during the symptomatic phase, and then a potentially compensatory increased production following AP resolution.

CONCLUSIONS: Our results provide the first comprehensive strain-level characterization of the gut microbiome in AP, and functional implications, and generate new hypotheses to be tested regarding candidate microbial features associated with AP for future biomarker discovery and/or intervention targets. This work advances our understanding of how specific microbial taxa and functional pathways may contribute to non-IgE-mediated food allergies and opens new avenues for microbiome-targeted therapeutic approaches as well as novel prevention targets for IgE-mediated food allergies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13073-026-01646-6.},
}

@article {pmid42049742,
year = {2026},
author = {Guarino-Vignon, P and Louis, E and Pham, HP and Orianne, G and Tkacz, E and Brot, L and Mazzetti, E and Sedda, D and Ruffié, P and Rolhion, N and D'Haens, G and Hadida, B and Langella, P and Sokol, H},
title = {Faecalibacterium prausnitzii EXL01 for the Maintenance of Steroid-induced Clinical Response or Remission in Patients with Crohn's Disease: a first in human trial.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-72375-y},
pmid = {42049742},
issn = {2041-1723},
abstract = {A marked decrease in Faecalibacterium prausnitzii is a hallmark of Crohn's disease (CD)-associated dysbiosis and predicts disease relapse. Here, we present the development and first-in-human evaluation of F. prausnitzii strain EXL01 for CD treatment. The EXL01-strain demonstrates anti-inflammatory effects in four models of colitis in rodents. A first-in-human, open-label, single-arm study of oral EXL01 was conducted in eight adult participants with mild to moderate CD, following corticosteroids-induced clinical response or remission. The primary endpoint was safety, and secondary endpoints included clinical, endoscopic, histological, molecular, and microbiome assessments. Exploratory endpoints included mucosa transcriptome and cytokine levels. EXL01 is well-tolerated with no treatment-related adverse events. Six participants completed the study; two discontinued treatment due to disease flare. While gut microbiota composition remains largely stable, transcriptomic analyses reveal distinct changes in ileal gene expression following EXL01 treatment, notably modulation of immune-related genes and upregulation of energy metabolism pathways. Compared to participants who remained in remission, those who flared show higher baseline systemic inflammation markers and innate immunity gene expression. These findings demonstrate that oral administration of EXL01 is feasible and well tolerated and establishes proof-of-concept for F. prausnitzii as a first-in-class live biotherapeutic for CD. ClinicalTrials.gov registration: NCT05542355.},
}

@article {pmid42050189,
year = {2026},
author = {Mesnage, R and Ferguson, S and Nechalioti, PM and Cercelaru, L and Hbous, MA and Docea, AO and Tsatsakis, A and Kouretas, D and Antoniou, MN},
title = {Impact of glyphosate and its mixture with 2,4-D and dicamba on gut biochemical function, intestinal barrier integrity and microbiome composition in adult rats with prenatal commencement of exposure.},
journal = {Archives of toxicology},
volume = {},
number = {},
pages = {},
pmid = {42050189},
issn = {1432-0738},
support = {26/53/2/31.05.2022//Universitatea de Medicină şi Farmacie din Craiova/ ; },
}

@article {pmid42050215,
year = {2026},
author = {Seneff, S and Boros, LG},
title = {The essential role of hydrogen gas recycling by gut microbes in reducing deuterium load in host mitochondria: is trimethylamine oxide a deuterium sensor?.},
journal = {Metabolomics : Official journal of the Metabolomic Society},
volume = {22},
number = {3},
pages = {},
pmid = {42050215},
issn = {1573-3890},
mesh = {*Methylamines/metabolism ; *Gastrointestinal Microbiome/physiology ; Humans ; Animals ; *Deuterium/metabolism ; *Mitochondria/metabolism ; *Hydrogen/metabolism ; Mice ; },
abstract = {BACKGROUND: The human gut microbiome plays many essential roles, but an often-overlooked role is to maintain an abundant supply of deuterium depleted (deupleted) nutrients to fuel the host mitochondria. Excess deuterium (heavy hydrogen) damages mitochondrial ATP synthase nanomotors, leading to a decrease in matrix water production with increased reactive oxygen species (ROS) and inefficient ATP production. A microbial metabolite, trimethylamine N-oxide (TMAO) is a powerful signaling molecule whose plasma levels are high in association with many chronic diseases, including diabetes, fatty liver disease, and atherosclerosis, as well as cancer and dementia. Thus, TMAO is an important gut-host signaling molecule that serves as a marker for an imbalanced microbiome that is unable to fully metabolize trimethylamine (TMA), an important step in maintaining a deupleted nutrient supply.

AIM OF REVIEW: In this paper, we present a hypothesis that TMAO is a marker for deuterium overload in the methylation pathway, in addition to its role as an indicator of a disrupted gut microbiome. The original study that brought attention to TMAO involved feeding mice synthetic choline with fully deuterated methyl groups. Fully deuterated TMAO was subsequently detected in the plasma. By contrast, a diet rich in eggs, a natural source of choline (a precursor to TMAO), does not raise TMAO levels. Many of the pathologies that are linked to elevated TMAO can also be viewed as strategies to promote the supply of deupleted water to the mitochondria, systemically.

KEY SCIENTIFIC CONCEPTS: The mantra that "food is medicine" is well supported by the powerful role that gut dysbiosis plays in influencing human health and disease.},
}

*Methylamines/metabolism
*Gastrointestinal Microbiome/physiology
Humans
Animals
*Deuterium/metabolism
*Mitochondria/metabolism
*Hydrogen/metabolism
Mice

@article {pmid42050221,
year = {2026},
author = {Izah, SC and Ogwu, MC and Alum, EU},
title = {Innovative approaches to mitigating persistent toxic substances and their impacts on soil health and human well-being.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {5},
pages = {},
pmid = {42050221},
issn = {1573-2959},
mesh = {*Soil Pollutants/analysis ; Humans ; *Environmental Monitoring/methods ; *Soil/chemistry ; *Environmental Restoration and Remediation/methods ; Agriculture ; *Hazardous Substances/analysis ; Environmental Pollution/prevention & control/statistics & numerical data ; },
abstract = {Persistent toxic substances (PTS), including heavy metals, persistent organic pollutants (POPs), and persistent, mobile, and toxic/very persistent and very mobile (PMT/vPvM) substances present an increasing menace to soil health, alimentary systems, atmospheric cleanliness as well as human health. Despite the large amount of literature on each of the individual groups of contaminants, there is still no unified model that connects the dynamics of the soil-atmosphere environment, bioaccumulation in the food chain, new detection techniques, and policy measures. This review presents an interdisciplinary synthesis of dynamics in the PTS in the agricultural environment, explicitly incorporating (i) historic contaminants and emerging PMT/vPvM chemicals, (ii) soil-crop-livestock-human transfer pathways, and (iii) the state-of-the-art remediation and monitoring technologies into a single management framework. We critically evaluated conventional remediation methods alongside next-generation methods, such as engineered consortia of microorganisms, synergistic phytotransformation of plants and microbes, biochar-assisted immobilization, nanosensor-based detection, IoT-based soil sensing, precision agriculture, machine-learning-driven risk prediction, and blockchain-based traceability. Contrary to the previous reviews, which only take into account the remediation, detection, and policy separately, this study presents a systems-based approach, which integrates technological innovation, sustainable agronomic practices, and multilayered governance tools (such as the Stockholm Convention, REACH, and national soil action plans). We highlight the fact that the combination of smart agricultural technology and regenerative land management will help reduce the accumulation of PTS and maintain productivity, especially in resource-scarcity settings. The review outlines the research gaps, including contaminant-microbiome interactions, longitudinal deterioration of ecosystem services, and socioeconomic barriers to technology adoption. We propose a transdisciplinary roadmap that aligns environmental toxicology, soil science, public health, and policy innovation to mitigate PTS and safeguard food security. This integrative approach provides a strategic framework for advancing sustainable management of persistent toxic substances in agricultural systems.},
}

*Soil Pollutants/analysis
Humans
*Environmental Monitoring/methods
*Soil/chemistry
*Environmental Restoration and Remediation/methods
Agriculture
*Hazardous Substances/analysis
Environmental Pollution/prevention & control/statistics & numerical data

@article {pmid42050297,
year = {2026},
author = {Park, SH and Park, SB and Kang, J and Shin, S and Kim, GY and Bong, Y and Gu, M and Lee, YS and Bin, G and Seo, W},
title = {Multiomics characterization of an alcohol-induced hepatocellular carcinoma mouse model.},
journal = {Lab animal},
volume = {},
number = {},
pages = {},
pmid = {42050297},
issn = {1548-4475},
support = {2018R1A5A2025286//National Research Foundation of Korea (NRF)/ ; 2021R1A6C101A442//National Research Foundation of Korea (NRF)/ ; 2021R1C1C1009445//National Research Foundation of Korea (NRF)/ ; RS-2024-00404418//National Research Foundation of Korea (NRF)/ ; RS-2024-00439963//National Research Foundation of Korea (NRF)/ ; NIAAA, BG//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; },
abstract = {Hepatocellular carcinoma (HCC) is a major global health problem, ranking as the sixth most frequently diagnosed cancer and the third leading cause of cancer-related mortality worldwide. Although the incidence of viral infection-mediated HCC has decreased in recent years, the incidence of alcohol- and metabolic dysfunction-associated HCC has increased, driven by changes in lifestyle and diet. Excessive alcohol consumption contributes to advanced liver diseases, including liver fibrosis, cirrhosis and HCC. Despite the clinical relevance of alcohol-associated HCC, there are no suitable animal models that adequately reflect the pathophysiological features of alcohol-associated HCC in humans. Here, to address this limitation, we established a mouse model of alcohol-associated HCC through the combined administration of N-diethylnitrosamine and carbon tetrachloride (CCl4), followed by administration of an alcohol-containing Lieber-DeCarli diet. The results indicated that chronic alcohol exposure in the presence of N-diethylnitrosamine and CCl4 substantially accelerated HCC development, which was characterized by increased oxidative stress, inflammation and severe fibrosis. Furthermore, we found that chronic ethanol consumption disrupted hepatic immunity, characterized by natural killer/natural killer T cell depletion, increased PD1[+]CD8[+] cells, reduced cytotoxicity and elevated inflammation. We also observed marked alterations in the gut microbiome following chronic alcohol administration. These immunological and microbiome alterations fostered an immunosuppressive microenvironment that accelerated HCC progression. Our newly developed mouse model induced liver tumorigenesis within a relatively short timeframe and recapitulated the clinical and pathological features of alcohol-associated HCC. The model therefore represents a valuable tool for studying the mechanisms underlying alcohol-associated HCC and related chronic liver diseases.},
}

@article {pmid42050317,
year = {2026},
author = {Lima, ALA and Costa, SS and do Socorro Dos Reis, R and de Souza, DC and Baião, GC and Moreira, RG and Rogez, HLG and das Graças, DA and Viana, RB and Marques, JM},
title = {Age Influences the Bacterial Composition of Samples From Buffaloes in the Marajó Archipelago, Pará, Brazilian Amazon.},
journal = {Environmental microbiology reports},
volume = {18},
number = {3},
pages = {e70330},
pmid = {42050317},
issn = {1758-2229},
support = {88887.633228/2021-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
mesh = {Animals ; *Buffaloes/microbiology ; Brazil ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Feces/microbiology ; *Milk/microbiology ; *Microbiota ; Cattle ; Female ; Age Factors ; Soil Microbiology ; },
abstract = {Buffalo milk stands out for its nutritional qualities and is mainly produced in Brazil in the Amazon region, particularly in the Marajó Archipelago, State of Pará. In this context, the milk microbiome is an intriguing and underexplored research topic. This study tested the hypothesis that the buffalo milk microbiome could share taxa with faeces, pasture soil and calf spittle. A possible correlation between generations was also explored. Samples of milk, faeces, spittle and pasture soil were analysed using a 16S rRNA metabarcoding approach, revealing significant phylogenetic and ecological differences among matrices. Beta-diversity analysis showed clustering between milk samples from heifers and cows, as well as proximity between soil and buffalo samples (milk and faeces). Relative abundance analysis identified shared taxa between buffaloes and their calves, though no clustering was observed between generations. A total of 15 bacterial families were found across all matrices, with Staphylococcaceae, Planococcaceae and Enterobacteriaceae being the most prominent. The milk microbiota was similar among animals of different ages. The grouping pattern varied depending on the animal and matrix, but not on the maternal relationship. Despite compositional differences, the shared taxa reinforce the idea of interaction among the studied microbial communities.},
}

Animals
*Buffaloes/microbiology
Brazil
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Phylogeny
Feces/microbiology
*Milk/microbiology
*Microbiota
Cattle
Female
Age Factors
Soil Microbiology

@article {pmid42050358,
year = {2026},
author = {Zhu, F and Wang, T and Wang, Z and Shan, Y and Ren, P and Bie, X and Wang, D and Gao, Z and Guan, Q and Ge, L and Chen, Y},
title = {Bacillus cereus T146 Enhances Wheat Salt Tolerance by Restructuring the Rhizosphere Microbiome and Activating TaPIN1-Dependent Auxin Transport.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70567},
pmid = {42050358},
issn = {1365-3040},
support = {2024CXPT072//Key R&D Program of Shandong Province/ ; ZR2025QC186//Shandong Provincial Natural Science Foundation/ ; ZR2023QC067//Shandong Provincial Natural Science Foundation/ ; },
abstract = {Salinity stress disrupts rhizosphere homoeostasis and inhibits root development. Although PGPR are known to alleviate such stress, critical knowledge gaps remain regarding the specific mechanisms by which they enhance tolerance under moderate to high salinity, particularly within the wheat rhizosphere -root interface. Here, we show that Bacillus cereus T146, isolated from saline-alkali soil, enhances wheat salt tolerance through two integrated mechanisms. Metagenomic and culturomic analyses further revealed that T146 enriches IAA-producing Pseudomonas in the rhizosphere, and co-inoculation experiments demonstrated that these recruited bacteria contribute synergistically to salt tolerance. On the host side, transcriptomic and cell biological analyses demonstrated that T146 reactivates salt-suppressed auxin pathways. Specifically, inoculation upregulates key regulators of lateral root development (PLT3, PLT7, GLV6) and increases PIN1, PIN2, and PIN3 abundance, leading to elevated auxin accumulation as indicated by DR5::GFP signals. Importantly, silencing TaPIN1 largely compromised T146-induced tolerance and transcriptional reprogramming, demonstrating a functional interplay between microbiome modulation and host hormonal regulation. These results reveal that T146 synergistically promotes salinity resilience by coordinating rhizosphere microbiome remodelling with auxin-mediated root development, offering a mechanistic framework for microbiome-based strategies to improve crop stress tolerance.},
}

@article {pmid42050578,
year = {2026},
author = {Srisanoi, K and Curado, TFF and Leles, C and Egli, A and Rooney, AM and Srinivasan, M},
title = {From culture-based to 16S sequencing approaches: oral microbiota changes in aging, frailty, and oral hypofunction - a systematic review.},
journal = {BMC oral health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12903-026-08387-3},
pmid = {42050578},
issn = {1472-6831},
}

@article {pmid42050719,
year = {2026},
author = {Yang, D and Yang, L and Yang, J and Wang, G},
title = {Beyond the known: prospective research directions for the gut-brain axis in obesity and type 1 diabetes mellitus.},
journal = {Diabetology & metabolic syndrome},
volume = {18},
number = {1},
pages = {},
pmid = {42050719},
issn = {1758-5996},
abstract = {BACKGROUND: This letter engages with the seminal review by Argyrakopoulou et al. Obesity and the Gut-Brain Axis in Type 1 Diabetes Mellitus: Terra Incognita? Curr Obes Rep, https://doi.org/10.1007/s13679-025-00654-8IF:11.0Q1B1 . on the putative role of the gut-brain axis in the rising prevalence of obesity within type 1 diabetes mellitus (T1DM).

OBJECTIVE: We aim to commend the authors while proposing key future research avenues to advance the field from correlation to causation and therapeutic application. We also seek to integrate recent high-impact evidence to contextualize our perspectives.

MAIN POINTS: First, we emphasize the need for deep mechanistic studies using gnotobiotic models and targeted metabolomics to delineate the causal role of specific microbial metabolites, informed by recent concepts of host genetic regulation of the gut-liver axis (e.g., via p53/PI3K/AKT/Wnt signaling) and microbiota composition in metabolic disease pathophysiology (1, 2). Second, we highlight the imperative for longitudinal cohort studies to determine the temporal relationship between gut dysbiosis, autoimmunity, and subsequent metabolic complications. Finally, we discuss the promising intersection of microbiome science with emerging therapeutics, including next-generation probiotics and GLP-1 receptor agonists, whose efficacy may be partly mediated through the gut-brain axis.

CONCLUSION: By addressing these priorities and integrating recent knowledge, the scientific community can translate this compelling paradigm into tangible clinical benefits for patients with T1DM.},
}

@article {pmid42050755,
year = {2026},
author = {Russnak, V and Koll, R and Keuter, S and Sanders, T and Dähnke, K},
title = {The Elbe Estuary Microbiome Shifts With Salinity and Discharge and Depends on Fresh Organic Matter and Nutrient Availability.},
journal = {Environmental microbiology reports},
volume = {18},
number = {3},
pages = {e70349},
pmid = {42050755},
issn = {1758-2229},
support = {03F0864C//Bundesministerium für Bildung und Forschung/ ; 407270017/RTG2530//Deutsche Forschungsgemeinschaft/ ; 496691966/FA 1568//Deutsche Forschungsgemeinschaft/ ; MOSES//Helmholtz Association/ ; 101000518//European Commission/ ; },
mesh = {*Estuaries ; *Salinity ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; Seasons ; RNA, Ribosomal, 16S/genetics ; Germany ; Nutrients/analysis ; *Seawater/microbiology/chemistry ; Biodiversity ; Nitrogen/analysis ; },
abstract = {The Elbe Estuary (Germany) stretches 142 km from the weir in Geesthacht to the North Sea. It is classified as mesotidal, partially mixed and heavily impacted by anthropogenic activities and modifications. Despite well-documented changes in ecosystem status, little is known about the microbial community in its surface water. In this study, we used 16S rDNA sequencing to characterise bacterial communities in surface water of the Elbe Estuary. Samples were collected across three seasons (winter, spring, and summer) in 2021 and 2022, to assess the relationship between environmental factors and bacterial community structure. Our analyses revealed that bacterial community diversity and composition varied seasonally and along the estuary stretch and were closely linked to physicochemical properties. Alpha diversity was highest in winter and in oligohaline samples. Distance-based redundancy analysis showed that salinity, discharge, temperature, inorganic nitrogen (NO2), and silicate are key factors in shaping the bacterial community compositions. Although spatial differences were observed, seasonal variation was the main determinant of bacterial diversity and community structure. Overall, our results show that anthropogenic pressures and seasonal changes are reflected in a dynamic microbial community with metabolic functions strongly shaped by human activity.},
}

*Estuaries
*Salinity
*Microbiota
*Bacteria/classification/genetics/isolation & purification
Seasons
RNA, Ribosomal, 16S/genetics
Germany
Nutrients/analysis
*Seawater/microbiology/chemistry
Biodiversity
Nitrogen/analysis

@article {pmid42050886,
year = {2026},
author = {Fatima, R and Ud Din Shah, S and Hameed, A and Ditta, A and Saleemi, MK and Gill, A and Tarique, H},
title = {Microbiome-host interactions driving the transition from non-pregnant to pregnant states in a goat model.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skag144},
pmid = {42050886},
issn = {1525-3163},
abstract = {Pregnancy in goats involves complex hormonal, metabolic, and immune shifts, and growing evidence suggests that the gut microbiome plays a key regulatory role in these physiological transitions, yet its specific role in guiding the shift from non-pregnant to pregnant states is still not clearly defined. This study investigated dynamic changes in the microbial community, biochemical markers, and metabolic profile shifts that influence host physiology during the transition from non-pregnant to pregnant states. The results revealed that significant changes in the abundance of microbial genera such as Ruminococcus, Bacteroides, and Lactobacillus were observed across groups. Alpha diversity metrics (Chao1, Shannon, Sobs) indicated substantial differences between groups, while Simpson diversity remained unaffected. Beta diversity analysis (PCoA, NMDS) revealed clear group separation, and pairwise PERMANOVA tests confirmed significant differences (P < 0.05). Heatmap and box plot analyses revealed distinct clustering of microbial profiles, and showed significant differences in genus abundance, including Bacteroides, Christensenella, and Prevotella_7 (P < 0.05). Moreover, significant variations in hematological parameters (RBC, HGB, MCV, MCH, MCHC, PLT, WBC) were noted, with distinct patterns between groups (P < 0.05). Correlation analysis identified strong associations between microbiota taxa (Lachnospira, p < 0.01; Oscillibacter, P < 0.001) and hematological markers. In addition, progesterone and estrogen hormones significantly increased in G1, G2 and G3 groups in response to control group (P < 0.01). Furthermore, antioxidant markers (SOD, CAT) were significantly elevated in G3 group, with a marked decrease in TAC as compared to control group (P < 0.05). FTIR analysis of plasma biomolecules revealed distinct functional group variations across the phases, indicating alterations in key metabolic components. LEfSe analysis identified microbial biomarkers specific to each group, with distinct taxa associated with each pregnancy stage. KEGG pathway analysis showed significant functional shifts, particularly in carbohydrate, amino acid, and energy metabolism. These findings suggest that microbial shifts, metabolic changes, and hormonal fluctuations are intricately linked and play a pivotal role in the reproductive transitions of Beetal goats. The study underpins the potential of microbiome analysis as a tool for improving reproductive health management in livestock.},
}

@article {pmid42050950,
year = {2026},
author = {Jia, Q and Jin, KJ and Liu, SQ and Zhang, YM and Meng, YL and Nie, H and Hu, S and Yang, F and Zhao, XC and Ye, J},
title = {[Research Progress on the Methodological System for Decomposition Stage Classification in Forensic Medicine].},
journal = {Fa yi xue za zhi},
volume = {42},
number = {1},
pages = {34-42},
doi = {10.12116/j.issn.1004-5619.2025.450906},
pmid = {42050950},
issn = {1004-5619},
mesh = {Humans ; *Postmortem Changes ; Algorithms ; *Forensic Medicine/methods ; Machine Learning ; *Forensic Pathology/methods ; Microbiota ; Metabolomics ; },
abstract = {Accurate classification of postmortem decomposition stages is a critical step in estimating the postmortem interval (PMI) and tracing the initial decomposition environment. Research on the decomposition staging methodological system is gradually shifting from empirical observation to the establishment of systems based on multidimensional quantitative indicators. This paper focuses on two key pathways, "macroscopic morphological evolution" and "microscopic molecular succession", and systema-tically reviews the evolutionary patterns and applicability of the decomposition staging system in three typical environmental media: surface exposure, burial, and aquatic systems. It also summarizes research progress in constructing stage classification models utilizing microbiome and metabolomic features. Furthermore, it highlights the integrated application of decomposition characteristic quantification techniques, multi-omics data integration, and machine learning algorithms in decomposition analysis systems. It analyzes the prospects and challenges of applying these approaches to build a standardized and practical decomposition staging system, aiming to provide theoretical support for establishing a decomposition staging system with high accuracy and strong adaptability to different environments.},
}

Humans
*Postmortem Changes
Algorithms
*Forensic Medicine/methods
Machine Learning
*Forensic Pathology/methods
Microbiota
Metabolomics

@article {pmid42051014,
year = {2026},
author = {Memon, FU and Ahmad, S and Mo, Q and Liu, S and Xie, X and Nabi, F and Huang, Z and Tettamanti, G and Tian, L},
title = {Probiotic-based fermentation of watermelon waste: Effects on bioconversion efficiency, microbial shifts, and expression profiles of black soldier fly larvae.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.70280},
pmid = {42051014},
issn = {1744-7917},
support = {//Guangxi Key Laboratory of Sericulture Ecology and Applied Intelligent Technology/ ; //Special Project of Guangxi Collaborative Innovation Center of Modern Sericulture and Silk/ ; //Natural Science Foundation of Guangdong Province/ ; },
abstract = {Insects such as black soldier fly larvae (Hermetia illucens, BSFL) are efficient bioconverters whose growth and physiological performance are strongly influenced by diet composition, gut microbiota, and the molecular regulation. This study investigated how a probiotic-based fermentation strategy modulates larval physiology, microbiome dynamics, and gene expression when BSFL are reared on fermented watermelon waste. Watermelon waste was fermented for 14 d using a consortium of Bacillus subtilis, Enterococcus faecalis, and Aspergillus oryzae, resulting in a nutritionally enhanced substrate. BSFL fed on fermented diet exhibited significantly increased growth performance, biomass yield, and nutritional content of the insect biomass. Metagenomic analysis revealed marked enrichment of gut microbes belonging to genera known to include beneficial and commensal species (Enterococcus, Vagococcus, Carnobacterium, Tetragenococcus, and Blautia) along with a reduction in genera containing species previously associated with opportunistic or pathogenic traits (Mycobacterium, Pseudomonas, Morganella, Pedobacter, and Serpula), indicating diet-induced modulation of host-microbe interactions. Transcriptomic profiling highlighted an upregulation of key genes involved in growth and development (CK1, HIB, and PDK1), protein and fat biosynthesis (DVL, GSK3, and Lpin), and immune defense (PGRP-SA, Spz, Toll, and Cactus). Functional enrichment analysis further confirmed their participation in critical signaling pathways, including Hedgehog, Wnt, mTOR, Toll and Imd, and MAPK. Overall, this study demonstrates that probiotic fermentation improves nutrient utilization, regulates host-microbe interactions, and activates molecular pathways associated with growth and immune resilience in BSFL, providing new insights into the physiological and molecular basis of dietary adaptation in insects.},
}

@article {pmid42051097,
year = {2026},
author = {Kasthuri, S and Padmavathi, S and Jeevitha, M and Rajangam, J},
title = {Therapeutic Innovations in Parkinson's and Alzheimer's Disease: Molecular Mechanisms and Emerging Strategies.},
journal = {CNS & neurological disorders drug targets},
volume = {},
number = {},
pages = {},
doi = {10.2174/0118715273445849260403045802},
pmid = {42051097},
issn = {1996-3181},
abstract = {Parkinson's Disease (PD) and Alzheimer's Disease (AD) are still significant neurodegenerative disorders that have few disease-modifying therapies. In this review, recent advances are assessed based on the strength of evidence for major molecular targets and the therapeutic approaches that have been developed around those targets. Alpha-synuclein is a key target in PD, as indicated by genetic correlations, pathological distribution, and experimental evidence supporting its involvement in neuronal injury. Initial trials of alpha-synuclein antibodies and vaccines show evidence of target engagement, with yet-to-be-determined clinical outcomes. Interventions targeting gene-based dopamine synthesis restoration using AADC or multi-enzyme vectors have shown consistent biological effects, with clinical variability, and determining optimized delivery and patient selection is necessary. In AD, amyloid-beta- and tau-directed interventions have produced measurable changes in biomarkers, and some agents have demonstrated a slight deceleration of deterioration at an early stage of the disease. The experience with previous BACE inhibitors also demonstrates that excellent mechanistic rationale does not always translate into clinical efficacy in the case of interference with critical physiological processes by target modulation. Regenerative methods, such as stem-cell-based neuronal grafts in PD and neurotrophic factor gene delivery in AD, show potential to repair network function, but still pose issues regarding long-term stability, integration, and the complexity of the procedures. Lifestyle-driven interventions, control of the gut microbiome, and neuromodulation methods also remain of interest and can be included in the list of supportive strategies offered to complement molecular therapies. AI-based analytics and digital tools are helpful in the earlier detection, monitoring, and trial stratification. Taken together, existing evidence suggests that authenticated protein targets, neurotransmitter-targeted remedial strategies, and technology-enabled accuracy methods are the most promising approaches for the development of disease-modifying therapies in PD and AD.},
}

@article {pmid42051198,
year = {2026},
author = {Pan, Y and Xu, JF},
title = {Microbiome and its role in bronchiectasis.},
journal = {Therapeutic advances in respiratory disease},
volume = {20},
number = {},
pages = {17534666261444168},
doi = {10.1177/17534666261444168},
pmid = {42051198},
issn = {1753-4666},
mesh = {Humans ; *Bronchiectasis/microbiology/therapy/physiopathology/diagnosis ; *Dysbiosis/microbiology ; *Microbiota ; *Lung/microbiology/physiopathology ; *Gastrointestinal Microbiome ; Prognosis ; Severity of Illness Index ; Animals ; Mouth/microbiology ; Disease Progression ; },
abstract = {Bronchiectasis (BE) is a chronic respiratory disease characterized by damage to the bronchial wall structure and permanent dilation of the bronchi. The symptoms include a persistent cough, excessive production of purulent sputum, and recurrent hemoptysis. Dysbiosis of the microbiome plays a crucial role in the progression of BE. An increased abundance of pathogenic bacteria, along with viral and fungal infections, is closely associated with disease severity and clinical outcomes. Next-generation sequencing technology has significantly enhanced the sensitivity and resolution of the airway microbiome, providing powerful tools for a more detailed characterization of the microecology of BE. However, certain challenges still exist in clinical applications of this technology. In addition, extra-airway microbiomes, such as the gut and oral microbiome, may participate in airway inflammation and immune regulation through the gut-lung axis and oral-lung axis. In this review, we summarize the characteristics of microbiome dysbiosis in BE and highlight the potential value of related biomarkers in disease classification, severity assessment, and prognosis. We also provide an overview of recent treatment advancements. A deeper understanding of the microbiome's role in BE may facilitate early diagnosis and the optimization of individualized treatment strategies.},
}

Humans
*Bronchiectasis/microbiology/therapy/physiopathology/diagnosis
*Dysbiosis/microbiology
*Microbiota
*Lung/microbiology/physiopathology
*Gastrointestinal Microbiome
Prognosis
Severity of Illness Index
Animals
Mouth/microbiology
Disease Progression

@article {pmid42051260,
year = {2026},
author = {Liu, YN and Jia, SY and Zhou, LS and Tang, XJ and Ming, Z and Su, Y and Lin, JY},
title = {Paeoniflorin as a candidate disease-modifying therapy for diabetic peripheral neuropathy: mechanisms, exposure challenges, and translational priorities.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1751578},
pmid = {42051260},
issn = {1663-9812},
abstract = {Diabetic peripheral neuropathy (DPN) is the most common chronic complication of diabetes and remains largely treated with symptomatic analgesics (e.g., pregabalin, duloxetine) that do not reverse nerve fiber loss or demyelination, underscoring the need for disease-modifying therapies. Paeoniflorin (PF), a plant-derived monoterpene glycoside metabolite from Paeonia spp., shows multitarget activity relevant to DPN pathophysiology in preclinical studies, including activation of Nrf2/HO-1 antioxidant signaling, suppression of TLR4/NF-κB-driven neuroinflammation, support of neurotrophic/repair pathways (e.g., BDNF/TrkB) for axonal regeneration and remyelination, and modulation of microvascular pathways (e.g., HIF-1α/VEGF) linked to endoneurial perfusion. We critically appraise this evidence and highlight key translational constraints: very low oral bioavailability and poor intestinal permeability, extensive presystemic biotransformation (microbiome-mediated hydrolysis and CYP-mediated metabolism) with unresolved "active species" (parent PF versus metabolites), and limited DPN-relevant pharmacokinetics, particularly the lack of peripheral nerve/DRG exposure measurements aligned with pharmacodynamic endpoints. Although formulation and delivery approaches may improve exposure, PF-specific validation in DPN models is currently limited and should be distinguished from platform-level concepts. Finally, because DPN patients frequently experience polypharmacy, a clinically meaningful safety narrative requires systematic assessment of CYP/transporter-mediated drug-drug interaction potential. Priority next steps include integrated PK-PD studies with nerve/DRG distribution, metabolite-resolved exposure-activity linkage, PF-specific delivery validation using disease-modifying endpoints beyond pain behavior, and standardized DDI screening to support trial design.},
}

@article {pmid42051286,
year = {2026},
author = {Zeng, Y and Yang, L and Liu, H and Liao, H and Zhou, Y and Liu, J},
title = {Gut-Brain Connection: Deciphering Causal Pathways Between Gut Microbiota and Neuroimaging Profiles Through Mendelian Randomization.},
journal = {Food science & nutrition},
volume = {14},
number = {},
pages = {e71820},
pmid = {42051286},
issn = {2048-7177},
abstract = {Recent research on the gut-brain axis (GBA) indicates that the gut microbiome can significantly influence brain structural and functional connectivity. However, the specific causal relationships between the gut microbiome and brain imaging-derived phenotypes (IDPs) of functional/structural connectivity, as well as how the gut microbiota influences mood and cognition, remain unclear. This study utilizes data from large-scale genome-wide association studies (GWAS) and employs a bidirectional Mendelian randomization (MR) approach to evaluate the causal effects between the gut microbiome and brain connectivity. We obtained data on 196 gut microbiome taxa from the MiBioGen consortium and acquired IDPs for seven resting-state networks (RSNs) from the UK Biobank (UKB). Subsequently, we conducted bidirectional MR analyses to explore their causal relationships. In the forward MR analysis, Ruminococcus torques, Eubacterium fissicatena, and Coprobacter exerted positive effects on the default mode network (DMN), whereas Terrisporobacter influenced the structural connectivity of the dorsal attention network (DAN). Conversely, Gammaproteobacteria inhibited the functional connectivity of the ventral attention network (VAN). Additionally, reverse MR analysis revealed that increased functional connectivity of the DAN was positively associated with the abundance of Alloprevotella. The enhanced functional connectivity of the VAN negatively impacted Alloprevotella, Catenibacterium, and Methanobacteria. Furthermore, the structural connectivity of the frontoparietal network (FPN) and somatomotor network (SMN) significantly reduced the abundance of Bacilli and Intestinibacter, respectively. This study utilized a bidirectional MR approach to establish causal evidence for the relationship between the gut microbiome and brain network connectivity, and support the bidirectional regulatory pattern of the GBA. These findings provide new insights into the potential roles of gut microbiota in emotional regulation, cognitive function, and neurodevelopment, and offer a theoretical basis for microbiome-based intervention strategies.},
}

@article {pmid42051335,
year = {2026},
author = {Li, B and Ren, Z and Li, H and Li, M and Zhong, H and Nie, Q and Chen, J and Wu, R and Zheng, JS and Deng, K and Cai, Y},
title = {Microbiota-metabolites interaction associated with glycemic improvement following a dietary herbal intervention in type 2 diabetes.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1793130},
pmid = {42051335},
issn = {2296-861X},
abstract = {BACKGROUND: Type 2 diabetes (T2D) is a global metabolic disorder characterized by chronic hyperglycemia and disruption of the gut microbiome. Nutritional and microbiota-targeted interventions have emerged as promising strategies for glycemic management, yet longitudinal clinical evidence integrating microbial and metabolic mechanisms remains limited. This study investigated microbiota-metabolites alterations during a standardized dietary herbal intervention (QingYun7, QY7) and explored their relationship with glycemic regulation across both animal study and clinical settings.

METHODS: The metabolic and microbial effects of QY7 were first evaluated in diabetic rats through measurements of blood glucose, and gut microbiota composition. Subsequently, a prospective cohort of 385 patients with T2D received QY7, with longitudinal monitoring of fasting, random, and 2-h postprandial glucose, gut microbiota, and serum metabolites across multiple time points. Fecal microbiota transplantation (FMT) from patients before and after intervention into antibiotic-treated mice was performed to evaluate the causal contribution of the gut microbiome to glycemic improvement. Mediation analyses were conducted to delineate potential pathways linking gut microbes, serum metabolites, and glucose outcomes.

RESULTS: In diabetic rats, QY7 administration significantly reduced blood glucose, and restored gut microbial composition. In the clinical cohort, the intervention was associated with rapid and sustained reductions in fasting, random, and postprandial glucose levels, accompanied by consistent remodeling of the gut microbiome and serum metabolite profile. FMT experiments demonstrated that microbiota derived from post-intervention patients conferred improved glycemic responses in recipient mice, supporting a causal role of gut microbiota in metabolic regulation. Serum metabolomic profiling revealed significant alterations, including enrichment of branched-chain amino acid related pathways. Mediation analyses identified key metabolites, phenyllactic acid, 3-methyl-2-oxobutanoic acid, and anandamide, as mediators linking specific bacterial taxa (Alistipes shahii and Limosilactobacillus mucosae) to fasting and postprandial glucose levels.

CONCLUSION: This study provides translational evidence that a dietary herbal intervention associated with glycemic improvement in T2D through microbiota-mediated metabolic reprogramming. Gut microbiome alterations induced by the intervention exerted causal effects on blood glucose regulation, with serum metabolites acting as potential key intermediaries. These findings highlight the mechanistic insight in nutrition-based microbiome modulation strategy in T2D.},
}

@article {pmid42051338,
year = {2026},
author = {Shahzad, M and Saidal, A and Ismail, M and Tariq, K and Melhem, AL and Iqbal, K and Khattak, MI and Ahmad, HA and Saeed, M and Ghani, M and Al Nabhani, Z and Andrews, SC},
title = {Dietary intake, nutritional status and healthcare characteristics of mothers and newborn infants in a prospective cohort study (CHAMP) from a malnutrition-endemic region of Pakistan.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1785862},
pmid = {42051338},
issn = {2296-861X},
abstract = {BACKGROUND: Dietary intake, nutritional status, healthcare access, and early-life exposures play a critical role in shaping infant growth and development. Recent evidence suggests that the impact is largely mediated by gut microbiome. The Child Health, Nutrition and Microbiome in Pakistan (the CHAMP study) is a longitudinal cohort study aiming to assess the bidirectional relationship between gut microbiome and infant growth and development in a cohort of children residing in malnutrition endemic areas of Pakistan.

OBJECTIVES: The current study report the baseline sociodemographic, dietary, healthcare, and nutritional characteristics of mother-infant dyads participating in the CHAMP study.

METHODS: Baseline data were collected from 70 mothers and 72 newborn infants recruited from rural communities in District Swat, Pakistan. Information on household socioeconomic status, maternal dietary intake, antenatal, delivery and postnatal care, infant feeding practices, morbidity, and anthropometric measurements was obtained using validated tools. Descriptive and sex-stratified analyses were conducted.

RESULTS: Households were socioeconomically disadvantaged, with low parental education, large family size, and mean household income substantially below the national minimum wage. Maternal utilization and quality of antenatal and postnatal care were suboptimal, including limited completion of recommended antenatal visits. Dietary quality was also poor, and none of the mothers met the recommended minimum dietary diversity for women. Among infants, morbidity was common, with nearly half experiencing diarrheal illness or respiratory infections. Exclusive breastfeeding reported only in 43.1% of infants. Anthropometric assessment revealed evidence of early growth faltering, with 35.4% of infants were low-length-for-age with higher prevalence among females.

CONCLUSION: These baseline findings highlight substantial socioeconomic vulnerability, poor maternal diet quality, gaps in maternal and infant healthcare, and early-life undernutrition in this rural Pakistani cohort. The study finding provides foundation for longitudinal analyses examining how these factors interact with gut microbiome development and child growth, informing and cost effective and culturally relevant intervention strategies.},
}

@article {pmid42051340,
year = {2026},
author = {Lee, S and Dubrof, S and Ahmed, I and Zhao, Q and Callaway, TR and Lourenco, J and Park, HJ},
title = {Maternal docosahexaenoic acid supplementation shapes offspring gut microbiota to modulate the gut-brain axis in a sow-piglet model.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1776896},
pmid = {42051340},
issn = {2296-861X},
abstract = {INTRODUCTION: Modification of maternal nutrition during the perinatal period represents an important window that may influence offspring neurodevelopment. Docosahexaenoic acid (DHA), a key omega-3 polyunsaturated fatty acid found in the brain, is reported to have beneficial effects on cognitive outcomes of infants. However, its specific effects on the shaping of gut microbiota to influence the piglet gut-brain axis remain to be elucidated.

METHODS: Using a sow-piglet model, this study aimed to investigate changes in offspring gut microbiota, intestinal barrier integrity, and their correlations with brain resting-state functional connectivity following maternal supplementation of DHA.

RESULTS: Piglets born to DHA-supplemented sows showed significant differences in microbial alpha- and beta-diversity compared to control piglets. Jejunal claudin-1 expression was upregulated in DHA piglets, and tight junction protein levels were positively correlated with specific microbial taxa. Furthermore, gut microbial diversity and specific taxa were significantly associated with functional brain networks.

DISCUSSION: Our findings demonstrate the role of maternal DHA supplementation in shaping offspring gut microbiome and gut integrity, potentially altering offspring brain function networks. Furthermore, these results underscore the importance of gut microbiota shaping through perinatal nutritional interventions as a means of programming the gut-brain axis in the early stages of life.},
}

@article {pmid42051348,
year = {2026},
author = {Liu, B and Zhang, Y and Deng, W and Zhou, YN and Cao, Y and Xiong, L and Shen, R and Lee, SM and Bian, J and Bian, Y},
title = {Dietary restriction as a potential neuroprotective intervention: a narrative review of its impact on neuroinflammation across neurodegenerative diseases and other neurological disorders.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1731416},
pmid = {42051348},
issn = {2296-861X},
abstract = {Dietary restriction (DR) involving chronic or intermittent calorie/nutrient reduction without malnutrition, delays neurological disease progression. Decades of research across in vitro models, animal studies, and clinical trials provide preclinical evidence for a potential role of DR in modulating multiple mechanisms underlying CNS disorders. Interactions between caloric intake, meal frequency, diet composition, and the gut microbiome regulate specific metabolic pathways governing cellular, tissue, and organ homeostasis as well as inflammatory processes during neurodegenerative and neurological diseases. In this review, we synthesize evidence on the role of DR in modulating neuroinflammation and related mechanisms within a selected set of neurodegenerative and neurological disorders, aims to provide a consolidated evidence base and perspective on the potential of DR as an adjunctive strategy for the future therapeutic investigations.},
}

@article {pmid42051417,
year = {2026},
author = {Stokes, CS and Türk, T and Lammert, F and Appenrodt, B},
title = {Comparison of Mucosal and Faecal Microbiomes in Patients With Cirrhosis.},
journal = {Gastroenterology research and practice},
volume = {2026},
number = {},
pages = {6847983},
pmid = {42051417},
issn = {1687-6121},
abstract = {OBJECTIVE: The colonic sigmoid mucosal microbiome is reportedly different from the faecal microbiome in patients with cirrhosis. This exploratory study is aimed at comparing the luminal and mucosal microbiome in patients with cirrhosis, with a specific focus on the proximal intestine.

METHODS: Mucosal and faecal samples were obtained from 12 patients with cirrhosis. The microbiome was quantified with V4 16S rRNA gene sequencing. Relative abundance, alpha and beta diversity were calculated, compared between the mucosal and faecal samples and correlated with stage of cirrhosis.

RESULTS: Faecal samples displayed lower microbial diversity than mucosal samples (Shannon diversity, p = 0.025) and the microbiome profiles differed significantly: Operational taxonomic units primarily of the phyla Firmicutes and Actinobacteria were more abundant in faecal samples, whereas biopsy samples contained units spanning all six phyla. Microbial composition of faecal samples were more similar to faecal samples from other patients rather than to the individual's corresponding biopsy sample (principal coordinate analysis, p = 0.004). At the family level, Lachnospiraceae, Erysipelotrichaceae and Enterobacteriaceae were significantly more abundant in faecal samples, whereas biopsy samples contained more Streptococcaceae (p = 0.011) and Prevotellaceae (p = 0.031). Faecal samples from patients in Child-Pugh Stage C contained less Bacteroidetes but significantly more Streptococcaceae than Stage B samples (p = 0.04); however, biopsy samples did not differ significantly.

CONCLUSIONS: This exploratory study in a small sample of patients with cirrhosis observed significant differences in the microbial signature of faecal versus biopsy samples from the proximal intestine. Future studies are needed to further investigate the relationship between different gastrointestinal microbial sites and cirrhosis.},
}

@article {pmid42051455,
year = {2026},
author = {Du, X and Su, H and Huang, Y and Liu, J and Li, Q and Yang, X and Tao, X and Li, R},
title = {Gut microbiome dysbiosis in PCOS: from pathogenesis to microbiome-targeted therapies.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1747766},
pmid = {42051455},
issn = {1664-2392},
mesh = {Humans ; *Polycystic Ovary Syndrome/microbiology/therapy/etiology/pathology ; *Dysbiosis/microbiology/therapy/complications ; *Gastrointestinal Microbiome/physiology ; Female ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; },
abstract = {(PCOS), one of the most common endocrine and metabolic disorders in women of reproductive age, has a complex pathogenesis that continues to be unraveled by ongoing research. The condition is defined by three key features: hyperandrogenemia, ovulatory dysfunction, and insulin resistance. Recent studies have highlighted the gut microbiome and its metabolites as crucial regulators in PCOS development. Evidence suggests that gut dysbiosis and intestinal barrier dysfunction play a pivotal role in the onset and progression of PCOS. This review comprehensively examines the central role of gut microbiota in PCOS pathogenesis, including shifts in microbial communities such as bacteria, fungi, and viruses, and their impact on critical metabolites like short-chain fatty acids, bile acids, and tryptophan metabolites, which modulate host metabolism and reproductive function. Furthermore, based on mechanistic insights, the review explores targeted gut microbiota interventions, systematically evaluating clinical evidence for dietary modifications, probiotic/prebiotic supplementation and fecal microbiota transplantation. These approaches provide novel perspectives for precision medicine in PCOS treatment. The findings not only deepen our understanding of PCOS pathogenesis but also establish a strong theoretical foundation for innovative microbiome-based therapeutics.},
}

Humans
*Polycystic Ovary Syndrome/microbiology/therapy/etiology/pathology
*Dysbiosis/microbiology/therapy/complications
*Gastrointestinal Microbiome/physiology
Female
Fecal Microbiota Transplantation
Probiotics/therapeutic use

@article {pmid42051461,
year = {2026},
author = {Wang, Q and Zhou, Z and Pang, L and Du, Y and Li, X and Dai, L},
title = {Gut microbiota in chronic kidney disease-mineral and bone disorder: shared mechanisms, disease-specific signatures, and therapeutic prospects.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1802845},
pmid = {42051461},
issn = {1664-2392},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/microbiology ; *Chronic Kidney Disease-Mineral and Bone Disorder/microbiology/therapy/metabolism/pathology ; Fibroblast Growth Factor-23 ; Animals ; *Renal Insufficiency, Chronic/microbiology ; },
abstract = {Chronic Kidney Disease-Mineral and Bone Disorder (CKD-MBD) is a systemic syndrome characterized by mineral metabolism disorders and impaired bone homeostasis. Recent studies have indicated that gut microbiota dysbiosis is a key regulatory factor driving the development and progression of this disease. This review systematically summarizes the mechanisms by which gut microbiota acts in CKD-MBD through the "gut-kidney-bone axis": dysbiosis drives chronic low-grade inflammation by impairing the intestinal barrier and promoting endotoxin translocation; alterations in its metabolites (e.g., reduced short-chain fatty acids, accumulation of uremic toxins) and dysregulation of endocrine pathways (e.g., FGF23-Klotho axis, PTH) collectively exacerbate renal injury and abnormal bone metabolism. Additionally, in diseases such as CKD, rheumatoid arthritis (RA), osteoarthritis (OA), and osteoporosis (OP), gut microbiota exhibits the coexistence of "shared dysbiosis" and "disease-specific characteristics," which collectively contribute to chronic inflammation and metabolic disorders. Interventional strategies targeting gut microbiota have demonstrated the potential to regulate this axis and improve bone health, marking that the management of metabolic bone diseases and chronic kidney disease is entering the "era of microbiome medicine." This review aims to provide new insights into understanding the comorbidity mechanisms of the aforementioned diseases and lay a theoretical foundation for the development of microbiota-targeted therapeutic strategies.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Dysbiosis/microbiology
*Chronic Kidney Disease-Mineral and Bone Disorder/microbiology/therapy/metabolism/pathology
Fibroblast Growth Factor-23
Animals
*Renal Insufficiency, Chronic/microbiology

@article {pmid42051499,
year = {2026},
author = {Lee, AR and Choi, H and Lee, SY and Kang, HY and Moon, YM and Nam, SW and Lee, BI and Cho, ML},
title = {Overexpression of mitochondrial STAT3 protein improves colonic inflammation and fibrosis in inflammatory bowel disease by enhancing mitochondrial function.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1728341},
pmid = {42051499},
issn = {1664-3224},
mesh = {*STAT3 Transcription Factor/genetics/metabolism ; Animals ; *Inflammatory Bowel Diseases/metabolism/pathology/genetics ; Mice ; *Mitochondria/metabolism/genetics ; Fibrosis ; *Colon/pathology/metabolism/immunology ; Disease Models, Animal ; *Colitis/metabolism/pathology/genetics ; Gastrointestinal Microbiome ; Male ; Mice, Inbred C57BL ; Cytokines/metabolism ; *Mitochondrial Proteins/genetics/metabolism ; Inflammation ; },
abstract = {INTRODUCTION: The STAT3 protein is involved in mitochondrial functions such as the respiratory electron transport chain, regulation of cellular metabolism, and scavenging of reactive oxygen species. Inflammatory bowel disease (IBD) is associated with damaged intestinal cells and mitochondrial dysfunction due to the inflammatory environment of the intestine. Here, we studied the potential use of the Stat3 gene to induce STAT3 expression in mitochondria to help treat IBD.

METHODS: We transferred the Stat3 gene and examined its effects on the expression of proinflammatory cytokines and fibrosis markers, and mitochondrial function, in intestinal tissues via immunohistochemistry. The microbiomes of mice were also analyzed.

RESULTS: The gene increased the expression of mitochondrial STAT3 (mtSTAT3), which reduced the levels of iNOS and fibrosis factors (aSMA, COL1A1) as well as proinflammatory cytokines (IL-17, IL-6) in the colon. It also enhanced mitochondrial function in the colon, and in immune cells, and led to higher levels of the beneficial bacteria Lactobacillus reuteri and Akkermansia muciniphila in the intestine. Taken together, these changes helped alleviate colitis and protected against intestinal damage.

DISCUSSION: Stat3 gene transfer targeting mtSTAT3 expression ameliorates colitis, enhances mitochondrial function in the colon, and reduces inflammation via inhibition of the inflammatory response and necroptosis, offering a potential treatment for IBD.},
}

*STAT3 Transcription Factor/genetics/metabolism
Animals
*Inflammatory Bowel Diseases/metabolism/pathology/genetics
Mice
*Mitochondria/metabolism/genetics
Fibrosis
*Colon/pathology/metabolism/immunology
Disease Models, Animal
*Colitis/metabolism/pathology/genetics
Gastrointestinal Microbiome
Male
Mice, Inbred C57BL
Cytokines/metabolism
*Mitochondrial Proteins/genetics/metabolism
Inflammation

@article {pmid42051509,
year = {2026},
author = {Ali, S and Kuang, R and Abdelkarim, OF and Nawaz, AH and Rahim, MF and Wang, D and Asif, A and Zhu, M},
title = {Integrative transcriptome and microbiome analysis reveals ferroptosis-driven duodenal damage caused by Ochratoxin A in mice.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1804647},
pmid = {42051509},
issn = {1664-3224},
mesh = {Animals ; *Ferroptosis/drug effects/genetics ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Duodenum/drug effects/pathology/metabolism/microbiology ; *Ochratoxins/toxicity ; *Transcriptome ; Male ; Gene Expression Profiling ; Intestinal Mucosa/metabolism/drug effects/pathology ; Mice, Inbred C57BL ; },
abstract = {Ochratoxin A (OTA), a prevalent mycotoxin produced by fungal contaminants, poses a significant threat to intestinal health. That can induce ferroptosis, a regulated iron-dependent cell death by disrupting duodenal epithelium and gut microbiota homeostasis. We exposed mice to OTA (2 mg/kg body weight/day) for seven days and assessed duodenal damage using histological analysis, transmission electron microscopy (TEM), transcriptomics, quantitative real-time PCR (qRT-PCR), Western blotting, immunofluorescence, biochemical assays, and 16S rRNA sequencing of cecal contents. OTA markedly reduced body weight from day 2 onwards and significantly elevated serum lipopolysaccharides (LPS) (P<0.05), duodenal malondialdehyde (MDA), and iron levels compared to the control group. OTA significantly diminished duodenal antioxidant defenses, including glutathione, SOD, CAT, and total antioxidant capacity (T-AOC), and caused villus atrophy, crypt hyperplasia, and mitochondrial shrinkage with cristae loss, which are the hallmarks of ferroptosis. Transcriptomic analysis revealed 769 differentially expressed genes (DEGs), including 134 upregulated and 635 downregulated genes, with 26 overlapping ferroptosis-regulating genes (FerroDb). Among these, four key genes SLC7A11, GSTM1, CP, and SLC40A1 were downregulated, which are major regulators of redox and iron homeostasis, and were enriched in ROS/lipid metabolism pathways. Microbiome profiling showed augmented diversification, altered Bacteroidota abundance and enrichment of pathogenic microbiota (e.g., Oscillibacter and Barnesiella), linking ferroptosis with dysbiosis. These findings demonstrate that OTA induces duodenal ferroptosis through dual microbiota-duodenum axis, where microbial dysbiosis amplifies redox imbalance and iron homeostasis. Ferroptotic inhibitors may preserve the gut health in animals and humans exposed to fungal contaminants.},
}

Animals
*Ferroptosis/drug effects/genetics
Mice
*Gastrointestinal Microbiome/drug effects
*Duodenum/drug effects/pathology/metabolism/microbiology
*Ochratoxins/toxicity
*Transcriptome
Male
Gene Expression Profiling
Intestinal Mucosa/metabolism/drug effects/pathology
Mice, Inbred C57BL

@article {pmid42051515,
year = {2026},
author = {Zheng, QX and Wang, HW and Ge, L and Lin, Y and Gao, X and Zhu, Y and Huang, L and Jiang, XM},
title = {Influences of dietary intake on Chinese women with gestational diabetes mellitus by inhibiting gut microbiome on plasma metabolome.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1745459},
pmid = {42051515},
issn = {1664-3224},
mesh = {Humans ; Female ; Pregnancy ; *Gastrointestinal Microbiome ; *Diabetes, Gestational/microbiology/blood/metabolism ; Adult ; *Metabolome ; China ; *Diet ; Prospective Studies ; Dysbiosis ; East Asian People ; },
abstract = {BACKGROUND: Lines of evidence indicate that microbiome and its derived metabolites are implicated in gestational diabetes mellitus (GDM) etiology through the regulation of insulin resistance and inflammatory responses, and pregnant women with GDM have significant gut dysbiosis and metabolic disturbance. Although the gut microbiota and gut metabolites in pregnant women with GDM are extensively studied, the trilateral relationship between diet, gut microbiota, and plasma metabolites in patients with GDM remains unclear. Therefore, the aim of this study was to systematically analyze the associations between diet, gut microbiome, and plasma metabolome among Chinese pregnant healthy controls and patients with GDM.

METHODS: The study is a prospective cohort study conducted at two maternal and child hospitals in China from 8 October 2021 to 31 December 2022. We compared the daily dietary intake, microbial compositions, and plasma metabolic signatures of 173 patients with GDM and 47 pregnant healthy individuals. A food frequency questionnaire was used to investigate the dietary intake of pregnant healthy controls and patients with GDM. 16S rRNA sequencing and liquid chromatography-tandem mass spectrometry (LC-MS/MS) were used to sequence the gut microbiome and plasma metabolome, respectively.

RESULTS: We found that women with GDM had higher intakes of whole grains, red meat, poultry, and eggs compared with normal pregnant women. Women with GDM had lower amounts of Klebsiella, Lactiplantibacillus, and Sphingomonas, and higher amounts of Desulfovibrio; they also had higher amounts of D-mannose, D-ribose, homo-L-arginine, and norophthalmic acid in plasma. Moreover, whole grains negatively influenced Sphingomonas, Klebsiella, and Lactiplantibacillus; red meat had a negative influence on Sphingomonas; and eggs had a positive impact on Desulfovibrio; these gut microbiota affected D-mannose, D-ribose, homo-L-arginine, and norophthalmic acid.

CONCLUSION: Overall, this study provided information about the influences of dietary intake on Chinese women with GDM by inhibiting gut microbiome on plasma metabolome, and their interactions play vital roles in GDM pathogenesis. These findings may be useful for patients with GDM in terms of dietary counseling and glucose control during pregnancy.},
}

Humans
Female
Pregnancy
*Gastrointestinal Microbiome
*Diabetes, Gestational/microbiology/blood/metabolism
Adult
*Metabolome
China
*Diet
Prospective Studies
Dysbiosis
East Asian People

@article {pmid42051550,
year = {2026},
author = {Chakraborty, DK and Roy, T and Ngo, ST and Al-Chalabi, A and Al Khleifat, A},
title = {Gut microbiota and ALS: cause, consequence or correlation? - a systematic review.},
journal = {Frontiers in neuroscience},
volume = {20},
number = {},
pages = {1774417},
pmid = {42051550},
issn = {1662-4548},
abstract = {BACKGROUND: Gut microbiome disturbances have been proposed as contributors to amyotrophic lateral sclerosis (ALS), a multisystem neurodegenerative disorder characterised by motor neuron loss, extra-motor symptoms, and rapid progression. Mechanistic links between dysbiosis, epithelial and blood-brain barrier dysfunction, metabolic imbalance, and immune activation have been suggested, but causality remains unresolved. We conducted a systematic review to evaluate the evidence supporting microbiome involvement in ALS pathogenesis.

METHODS: We searched PubMed, Medline, Embase, Scopus, Semantic Scholar, and Google Scholar (Nov 23, 2025) for human and ALS-relevant animal studies assessing bacterial microbiota, gut or blood-brain barrier integrity, microbial metabolites, or immune pathways. No language or date restrictions were applied. Studies were screened according to predefined criteria, and quality was assessed using QUADAS-2. Owing to the heterogeneity of study designs and sequencing approaches, findings were synthesised narratively.

FINDINGS: 61 of 2,397 studies met inclusion criteria. Across human cohorts, ALS was consistently associated with reduced microbial diversity, shifts in key taxa, and disruption of microbial pathways regulating short-chain fatty acids, nicotinamide metabolism, and inflammatory signalling. Several mechanistic animal studies demonstrated that microbiota manipulation, through antibiotics, faecal microbiota transfer, or supplementation with protective taxa, modulated motor function, microglial activation, gut permeability, and survival, indicating that dysbiosis can influence disease trajectories. Conversely, longitudinal human data showed that dysbiosis often emerged alongside worsening physical function, gastrointestinal dysmotility, weight loss, and changes in dietary intake, suggesting secondary effects of disease progression. Integrative multi-omics studies linked microbial alterations with systemic cytokine profiles, metabolic stress pathways, and CNS immune phenotypes, reinforcing a bidirectional gut-brain axis. However, the predominance of cross-sectional designs and small sample sizes substantially limits causal inference.

INTERPRETATION: Current evidence supports a model in which gut dysbiosis interacts with ALS via barrier failure, metabolic disruption, and immune dysregulation, but does not establish dysbiosis as a primary cause of disease. Preclinical findings highlight microbiome-derived mechanisms with disease-modifying potential, yet human data largely indicate association rather than initiation. Clarifying temporal relationships will require longitudinal, multi-modal studies, integration with pre-symptomatic cohorts, and controlled interventional trials. Microbiome-targeted therapies remain a promising but unproven avenue for ALS.},
}

@article {pmid42051692,
year = {2026},
author = {Wang, LM and Chen, C and Danzheng, JC and Zhao, J},
title = {Gut microbiome in sepsis: from dysbiotic biomarker to precision and palliative decision-making.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1811304},
pmid = {42051692},
issn = {2296-858X},
abstract = {Sepsis is a major cause of mortality in critically ill patients, necessitating improved early detection, risk stratification, and individualized clinical decision-making. The gut microbiome actively regulates host immunity, metabolism, and barrier function, engaging in bidirectional interactions with sepsis progression. Evidence suggests that gut dysbiosis not only accompanies sepsis but may also accelerate it. Characteristic shifts, including reduced microbial diversity, expansion of opportunistic pathogens, and decreased short-chain fatty acid production, could offer early prognostic signals prior to clinical decline. Advances in multi-omics and computational analytics are enabling the translation of microbial signatures into actionable clinical insights, supporting phenotype-specific stratification in sepsis. Emerging microbiome-targeted interventions such as next-generation probiotics, synbiotics, metabolite supplementation, and fecal microbiota transplantation show potential for modulating host responses in a stage-specific manner. Within a precision medicine framework, microbiome-derived biomarkers may refine both critical care management and palliative decision-making. In advanced or refractory sepsis, these insights could help tailor treatment intensity, prioritize symptom control, and avoid non-beneficial therapeutic escalation. Realizing this potential will require prospective validation and standardized approaches to integrate microbiome data into personalized, goal-concordant sepsis care.},
}

@article {pmid42051745,
year = {2026},
author = {Urrutia, ÍM and Plaza, N and Moraga, F and Griffiths-Sanhueza, C and Pérez-Reytor, D and Karahanian, E and Ramírez-Araya, S and Kinkead, A and Gómez, MP and Garcia, K},
title = {High intellectual ability and the gut-brain-sex steroids axis: a perspective on cognitive and emotional diversity.},
journal = {Frontiers in physiology},
volume = {17},
number = {},
pages = {1791778},
pmid = {42051745},
issn = {1664-042X},
abstract = {The gut-brain axis is a bidirectional communication network integrating neural, endocrine, immune, and metabolic signals that regulate neurodevelopment, cognition, and emotion. It contributes to neurotransmitter production, inflammatory regulation, and the microbial metabolism of sex steroids, processes that have been shown to modulate synaptic plasticity and emotional behavior in experimental and clinical contexts, although their specific relevance to high intellectual ability remains unknown. In this perspective, we propose that high intellectual ability could be explored as a heterogeneous construct, within which some individuals identified as having HIA may exhibit responses potentially associated with differential sensitivity to gut-brain-sex hormone interactions. We discuss that microbial modulation of steroid bioavailability and neuroactive metabolites may represent one hypothetical pathway through which variations in steroid bioavailability and neuroactive metabolites could intersect with cognitive performance and emotional intensity, traits frequently described in some individuals with HIA. Integrating evidence from neuroendocrinology, microbiome science, and cognitive neuroscience, we outline a conceptual framework linking microbial, hormonal, and neural processes. This model aims to stimulate empirical research examining how physiological variation across the gut-brain-sex hormone axis may underlie cognitive and emotional diversity in gifted subpopulations. Importantly, this framework is conceptual and extrapolates from converging evidence in microbiome science and neuroendocrinology, as direct empirical studies in high intellectual ability are currently lacking.},
}

@article {pmid42051940,
year = {2026},
author = {Sandra, F and Scania, AE and Dewi, NM and Ranggaini, D and Halim, J and Pakpahan, A and Lee, KH},
title = {Coevolution of Human Diet and Gut Microbiome: Implications for Nutrigenomics and Cross-Population Health.},
journal = {International journal of microbiology},
volume = {2026},
number = {},
pages = {5597426},
pmid = {42051940},
issn = {1687-918X},
abstract = {The coevolution of the human diet and gut microbiome has played a pivotal role in shaping metabolic, immune, and epigenetic functions across human history. Dietary transitions from high-fiber ancestral patterns to modern ultraprocessed diets have markedly influenced microbial diversity and functionality, contributing to the emergence of chronic diseases such as obesity, Type 2 diabetes, and inflammatory conditions. Recognizing the significance of gut microbial patterns in humans, this review explores the coevolution of diet and gut microbiota, especially on how gut microbiota influences human gene regulation, and the implications of these interactions for personalized nutrition and global health strategies. Comparative insights across populations in different periods reveal that geography, dietary practices, and host genetics interact to shape distinct microbiome configurations and disease susceptibility. Therefore, implementing a nutrigenomics and nutrigenetics approach might provide a molecular framework to understand these interactions and to develop personalized nutrition strategies. Though several clinical implementations utilizing genomic data have been embedded in several countries, global implementation remains challenging due to population-specific genetic variability, cultural dietary preferences, cost limitations, and ethical considerations. Integrating microbiome and genetic data into clinical practice and public health policy offers a promising path to mitigate diet-related health disparities that is tailored to individual and population-level needs.},
}

@article {pmid42052124,
year = {2026},
author = {Liao, X and Liu, J and Pang, Z and Li, X and Jiang, D and Wang, J and Sun, Y and Pang, B},
title = {Pharmacodynamic Material Basis of the Components of Four Epimedium Species with Activities Against Hepatocellular Carcinoma Based on Biological Target Networks and Multi-Omics Analysis.},
journal = {Journal of hepatocellular carcinoma},
volume = {13},
number = {},
pages = {578719},
pmid = {42052124},
issn = {2253-5969},
abstract = {AIM: Epimedium plants are used in traditional Chinese medicine due to their medicinal properties and can be clinically used for the treatment of liver cancer.Using network pharmacology and HPLC, we identified a key anti-HCC complex, CMPLX (containing icariin and kaempferol), from four Epimedium species. In vitro and in vivo studies demonstrated that CMPLX suppresses HCC proliferation by downregulating p-Akt, p-PI3K, and Bcl-2 expression. Untargeted metabolomics and gut microbiome analysis revealed significant negative correlations between serum levels of lignin/kaempferol derivatives and Escherichia coli abundance. These findings highlight CMPLX as a promising candidate for HCC drug development.

PURPOSE: Investigate the pharmacodynamic material basis of the components of four Epimedium species with activities against hepatocellular carcinoma based on biological target networks and multi-omics analysis.

MATERIALS AND METHODS: We first screened four Epimedium extracts for anti-HCC activity using HepG2 cells. Shared bioactive compounds were identified through network pharmacology and HPLC, defining core target AKT1 and key complex CMPLX (icariin and kaempferol). Molecular docking/dynamics simulations confirmed CMPLX-AKT1 binding. In vitro assays (CCK-8, wound healing, colony formation, Annexin V/PI, Western blot) demonstrated CMPLX inhibits proliferation, migration, and induces apoptosis via PI3K/AKT/Bcl-2 pathway. In vivo validation in H22 tumor-bearing mice showed tumor suppression, corroborated by histology, serum metabolomics and gut microbiota analysis.

RESULTS: CMPLX suppressed hepatocellular carcinoma proliferation in vitro and in vivo. Mechanistically, it downregulated p-Akt, p-PI3K, and Bcl-2 expression, inhibiting growth and promoting apoptosis in HepG2 cells. Integrated multi-omics revealed CMPLX treatment elevated flavonoid/kaempferol derivatives while reducing Enterobacteriaceae_A/Escherichia abundance, with Marinifilaceae dominating the gut microbiota. Crucially, lignan/kaempferol derivatives showed significant negative correlation with Escherichia levels.

CONCLUSION: CMPLX demonstrated synergistic anti-HCC efficacy in vitro and in vivo. Multi-omics analysis revealed its modulation of tumor-related pathways and gut microbiota composition, collectively contributing to tumor suppression.},
}

@article {pmid42052326,
year = {2026},
author = {Shabibi, A and Basati, G and Zarif, BR and Davari, K and Rangin, A},
title = {Laboratory Analysis of Fecal Lactobacillus Strains and pH in Tobacco Smokers: A Comparative Study From a Developing Country.},
journal = {Health science reports},
volume = {9},
number = {5},
pages = {e72348},
pmid = {42052326},
issn = {2398-8835},
abstract = {BACKGROUND AND AIMS: Tobacco smoking is a major cause of preventable mortality globally, disproportionately impacting developing countries. While its systemic health effects are well-known, the influence of tobacco on gut microbiota-especially beneficial Lactobacillus species-remains poorly explored in resource-limited settings.

METHODS: This study examined fecal Lactobacillus composition and stool pH among 200 participants from western Iran, including cigarette smokers, hookah users, combined users, and non-smoking controls. Standard microbiological methods were employed: stool pH measurement, anaerobic culture on MRS agar, Gram staining, biochemical tests, phenotypic assays (acid/bile resistance, antibiotic susceptibility), and PCR sequencing of the 16S rRNA gene for species identification.

RESULTS: Results showed significantly elevated stool pH in tobacco users, particularly hookah smokers (p = 0.001). Lactobacillus prevalence was markedly lower in all smoker groups compared to controls (p < 0.001). Dominant species identified were L. casei, L. plantarum, and L. acidophilus, with control strains exhibiting greater acid and bile tolerance (p < 0.05). Antibiotic resistance was common, notably to vancomycin (75%) and ampicillin (67%).

CONCLUSION: These findings indicate tobacco-associated gut dysbiosis characterized by increased stool pH and diminished Lactobacillus viability, potentially impairing gut barrier integrity. The study highlights the importance of clinical microbiological evaluation of smoking-related microbiota alterations, especially in populations with limited probiotic access.},
}

@article {pmid42052329,
year = {2026},
author = {Brar, GS and Sharma, A and Siddiqui, AJ and Sharma, L},
title = {Emerging Microbiome-Based Therapies for Skin Infections: From Probiotics and Prebiotics to Synthetic Microbiome Engineering.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {592685},
pmid = {42052329},
issn = {1178-6973},
abstract = {Skin infections are a major global health burden, made worse by the quick development of antimicrobial resistance (AMR) and the poor effectiveness of traditional antibiotic treatments for chronic and recurring diseases. The importance of the skin microbiome in preserving cutaneous homeostasis, pathogen exclusion, and immunological modulation is becoming more and more clear. Many infectious and inflammatory skin conditions have been linked to dysbiosis of the skin microbiota, which has led to a strategic reorientation from pathogen control to microbiome regulation. Probiotics, prebiotics, postbiotics, bacteriophages, microbiome transplants, and new methods in synthetic microbiome engineering are just a few of the recent advances in microbiome-based therapies in skin diseases that are covered in detail in this review. We go into the clinical effectiveness, safety issues, regulatory obstacles, and molecular underpinnings of various therapies. The promise of microbiome-based treatments to lower AMR, improve long-term effectiveness, and restore microbial balance is highlighted by comparison with traditional antibiotics. Lastly, future possibilities are examined that highlight the translational potential of microbiome-centred techniques in dermatology treatments, such as multi-omics integration, artificial intelligence-guided customisation, or synthetic microbial consortia.},
}

@article {pmid42052390,
year = {2026},
author = {Guo, Z and Feng, Y and Ren, Z and Wang, W and Huang, R and Zhao, J},
title = {Neurotransmitter-mediated gut-brain axis: a bibliometric analysis of research trends and knowledge structure.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1771169},
pmid = {42052390},
issn = {1664-302X},
abstract = {INTRODUCTION: The gut-brain axis constitutes a bidirectional network linking the gastrointestinal tract and central nervous system through neural, endocrine, metabolic, and immune pathways. Neurotransmitters play a central role in mediating this crosstalk, serving as intermediates through which the gut microbiota influences brain function. Although important mechanistic advances have been made, research on the neurotransmitter-mediated gut-brain axis remains fragmented across disciplines. This study aimed to provide a comprehensive bibliometric overview of this field.

METHODS: We conducted a bibliometric analysis of 788 publications retrieved from Web of Science, Scopus, and PubMed between 2005 and 2025. Using VOSviewer, CiteSpace, and Pajek, we analyzed publication trends, geographic distribution, institutional and author contributions, journal co-citations, and keyword evolution to characterize the knowledge structure and emerging themes of the field.

RESULTS: The results revealed three developmental phases: an exploratory phase (2005-2016) with limited output, a developmental phase (2017-2019) with moderate growth, and a rapid expansion phase (2020-2025) marked by exponential increases in publications driven by advances in microbiome and neurotransmitter research. China led in publication volume, while the United States and Ireland served as major hubs of collaboration. University College Cork showed the highest citation impact, with 10,935 citations from 28 publications (average citations per document = 390.54). John F. Cryan, Timothy G. Dinan, and Gerard Clarke were among the leading contributors, with Cryan ranking first in both publication output and citation count. Keyword and thematic analyses identified gut microbiota, serotonin, short-chain fatty acids, depression, and inflammatory bowel disease as core topics, reflecting a shift from mechanistic studies to disease-specific and neurotransmitter-targeted research. Highly cited studies focused on microbial regulation of neurotransmitters, neuroimmune signaling, and their implications for neurodevelopmental and neurodegenerative disorders.

DISCUSSION: This study provides the first comprehensive bibliometric overview of neurotransmitter-mediated gut-brain axis research, offering a macroscopic perspective on its evolution, core knowledge base, and emerging frontiers. Future research should integrate multidisciplinary approaches, apply omics technologies, and develop precision interventions targeting neurotransmitter pathways while considering individual microbial profiles, in order to translate mechanistic insights into therapeutic strategies for neuropsychiatric disorders.},
}

@article {pmid42052395,
year = {2026},
author = {Banerjee, A and Gupta, N and Koley, A and Kumar, MS and Saha, S and Balachandran, S},
title = {Microbial contamination and microbiome composition of fresh edible mushrooms: a critical review.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1757755},
pmid = {42052395},
issn = {1664-302X},
abstract = {Fresh edible mushrooms have gained popularity as valuable dietary components, with global consumption steadily increasing due to their high nutritional and functional benefits. However, their constitutional characteristics make them especially vulnerable to microbial spoilage, potentially harming the fruiting bodies during cultivation and creating major challenges in harvesting, handling, and storage after harvest. This review highlights the types, sources, and impacts of microbial contamination in fresh edible mushrooms, with a focus on spoilage organisms. It explores the emerging field of mushroom microbiome research, highlighting the composition, diversity, and functional roles of microbial communities associated with 4 edible mushroom species (Agaricus sp., Pleurotus sp., Lentinula sp., and Flammulina sp). Studies employing high-throughput sequencing technologies to explore the microbial associations of edible mushrooms are discussed, providing deeper insights into these complex microbial ecosystems and their impacts on mushroom quality, shelf life, and safety. Bibliometric studies using VOSviewer over a 10-year period have uncovered global research trends, emerging focus areas, and identified gaps in the field. This review also discusses post-harvest control strategies and microbiome-targeted interventions to enhance microbial safety and extend shelf life. Edible mushrooms also contribute to the circular bioeconomy by converting agricultural residues into nutritious food. However, microbial contamination can compromise product quality and safety within this sustainable production system. Persistent knowledge gaps in understanding microbial dynamics and mushroom-microbiota interactions must be addressed to develop innovative, sustainable approaches to mushroom preservation and food safety management.},
}

@article {pmid42052398,
year = {2026},
author = {Crippen, TL and Kim, D and Swiger, SL and Anderson, RC and Arsenault, RJ},
title = {Capturing the fungal diversity in manure, lagoons, troughs, and flies at a commercial dairy.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1794875},
pmid = {42052398},
issn = {1664-302X},
abstract = {The microbiomes within dairy facilities that could serve as reservoirs for beneficial and pathogenic fungi have not been extensively explored. Though fungi can cause food safety and animal health issues, they also represent species contributing to bovine digestion and environmental nutrient cycling. This study investigated whether fungal communities from specific elements at a working dairy differed between cross-vent or flow-through, free stall barn management systems and defined the possible pathogen locations. Shotgun metagenomics was carried out on manure, lagoons, troughs, and fly samples from the barns. The diversity of species was not significantly affected by management systems, except between lagoon communities. Flies carried the highest number of unique fungal species and the most abundant potential mammalian pathogens, but there was a lack of overlapping pathogen profiles between flies and the other dairy components. Thus, it remains unclear whether the species are being efficiently exchanged between these different components of the dairy environment, mechanically or biologically. Manure harbored the most opportunistic pathogenic species, lagoons harbored the most plant pathogens and beneficial species, and troughs had the most innocuous or understudied species. The results allow dairy managers to consider advantageous management systems and focus on fungal mitigation efforts at appropriate locations within the dairy.},
}

@article {pmid42052400,
year = {2026},
author = {Xie, J and Zhang, J and Zhang, L and Chen, X},
title = {Exercise prescription for mood and cognition: targeting the microbiota-gut-brain axis through short-chain fatty acids.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1740680},
pmid = {42052400},
issn = {1664-302X},
abstract = {Scientific study has extensively corroborated the advantageous impacts of exercise on mood, cognitive function, and stress resilience. Nonetheless, the fundamental biological mechanisms underpinning these effects have yet to be thoroughly integrated. This review advocates for and substantiates an integrated model focused on the "Exercise-Gut Microbiome-Short-Chain Fatty Acids (SCFAs)-Brain Function" axis. Consistent physical exercise alters the gut microbiota, enhancing Short-Chain Fatty Acid (SCFA)-producing populations, which is associated with markedly elevated bioavailability of key metabolites (acetate, propionate, and butyrate). Rather than detailing exhaustive molecular pathways here, we emphasize that these SCFAs facilitate gut-brain communication through multiple synergistic routes, including receptor-mediated neuroendocrine signaling, epigenetic modulation of neuroplasticity, and the attenuation of systemic neuroinflammation. Current human observational and interventional data strongly support an associative link between exercise-induced SCFA fluctuations and improved mental health outcomes. Crucially, we propose the novel "Exercise × Fiber Synergy" hypothesis: exercise primes the intestinal ecological niche for efficient substrate-utilizing bacteria, while adequate fermentable dietary fiber provides the necessary raw materials. Synergistically, this combination optimizes SCFA production to maximize cognitive and emotional benefits. To transition this framework into clinical practice, future research must prioritize 2 × 2 factorial designs (Exercise × Fiber) with dynamic kinetic measurements, paving the way for microbial phenotype-oriented precision exercise and personalized nutritional interventions to enhance public mental health.},
}

@article {pmid42052590,
year = {2026},
author = {Alebouyeh, M and Aminzadeh, M and Pourmand, MR and Bahiraee, M and Mirbagheri, SZ and Bakhtiari, R},
title = {Culturable bacteria in the gastric tissue and diversity of antimicrobial resistance in adults with gastritis.},
journal = {Caspian journal of internal medicine},
volume = {17},
number = {1},
pages = {143-151},
pmid = {42052590},
issn = {2008-6164},
abstract = {BACKGROUND: Despite growing knowledge in microbiome studies data about the diversity of cultivable bacteria and their drug resistance patterns in patients with gastritis are scant.

METHODS: Two gastric biopsies of 171 symptomatic patients were collected and examined by histological and microbiological methods. Viable bacteria were characterized using conventional techniques, and antimicrobial susceptibility of the isolates was detected.

RESULTS: Acute gastritis, chronic gastritis, and peptic ulcers were detected in 3.5%, 86.5%, and 5.8% of the patients, respectively. Culturable bacteria were isolated from 71.3% of the patients, including Helicobacter pylori (H. pylori) (26.9%), Staphylococcus epidermidis (19.8%), Micrococcus (1.1%), Streptococcus viridans (S. viridans) (13.4%), Enterococcus faecalis (E. faecalis) (4.6%), Staphylococcus aureus (S. aureus) (1.7%), and Group D Streptococcus (7.1%). Single infection and coexistence of two and three types of bacteria were detected in 43.2%, 15.2%, and 5.2% of the patients, respectively. An odd ratio of 4.4 was measured for Staphylococcus spp. in patients with acute gastritis (P-value = 0.08). E-test results showed intermediate resistance to penicillin in 66.6% of the S. aureus isolates, while resistance to vancomycin was detected only in the S. viridans (30.4%). Resistance to linezolid was detected in 100%, 17.4%, and 16.7% of E. faecalis, S. viridans, and group D Streptococci isolates, respectively. A high frequency of resistance to penicillin, clindamycin, linezolid, erythromycin, and tetracycline was detected in S. epidermidis strains.

CONCLUSION: Our results highlighted the importance of Gram-positive bacteria in the etiology of gastritis. Resistance of these bacteria to different classes of antibiotics should be considered in the clinical setting.},
}

@article {pmid42052722,
year = {2026},
author = {Qiao, S and Fan, S and Xu, J and Xu, Z and Peng, C and Qu, J and Bing, Z and Zhou, S and Shen, S and Xu, G and Zhao, Y and Wang, T},
title = {Gut Mycobiota-Associated Tryptophan Catabolites Protect Against Metabolic Dysfunction-Associated Steatotic Liver Disease.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e14830},
doi = {10.1002/advs.202514830},
pmid = {42052722},
issn = {2198-3844},
support = {T2341015//National Natural Science Foundation of China/ ; 32271182//National Natural Science Foundation of China/ ; 82273011//National Natural Science Foundation of China/ ; 82302934//National Natural Science Foundation of China/ ; 2024300382//Fundamental Research Funds for the Central Universities/ ; },
abstract = {Accumulating evidence suggests that the intestinal microbiota participates in the progression of metabolic dysfunction-associated steatotic liver disease (MASLD) through microbiota-host interaction. However, the beneficial role of commensal mycobiota in MASLD progression remains poorly understood. By comparing the gut microbiome differences, we demonstrated that the deficiency of Caspase Recruitment Domain-containing protein 9 (CARD9), an adaptor protein for a microbiota recognition receptor, exacerbated high-fat diet (HFD)-induced MASLD in a gut fungi-dependent manner. CARD9 deficiency reduced the abundance of Saccharomyces cerevisiae (S. cerevisiae), which was a probiotic alleviating MASLD progression. S. cerevisiae promoted a significantly greater abundance of 5-hydroxyindoleacetic acid (5-HIAA) in the intestine through Toll-like receptor 1 (TLR1), which reduced body weight in mice and alleviated MASLD phenotypes via the "gut-liver" axis. Particularly, 5-HIAA directly binds to aryl-hydrocarbon receptor (AhR) and stimulates its nuclear translocation, subsequently inducing fatty acid oxidation via carnitine palmitoyltransferase 1A (CPT1A) and acyl-CoA oxidase 1 (ACOX1) transactivation. MASLD patients exhibited decreased levels of S. cerevisiae and 5-HIAA, and S. cerevisiae effectively reduced hepatic steatosis and improved glucose homeostasis in patients with MASLD. In summary, our findings identified a novel pathway of fungi-S. cerevisiae stimulating intestinal 5-HIAA production and indicated that S. cerevisiae and 5-HIAA might alleviate MASLD progression, highlighting that the mycobiota-dependent gut-liver axis was a promising target for the prevention of MASLD.},
}

@article {pmid42052831,
year = {2026},
author = {Li, Y and Gao, H and Liao, Z and Chen, Z and Song, Z and Xiong, W and Dai, Y and Li, W and Luan, S},
title = {Metagenomic Analysis Reveals Gut Microbiota Features in Membranous Nephropathy.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {31},
number = {4},
pages = {48982},
doi = {10.31083/FBL48982},
pmid = {42052831},
issn = {2768-6698},
support = {JCYJ20240813153002004//Shenzhen Foundation of Science and Technology/ ; JCYJ20250604191024032//Shenzhen Foundation of Science and Technology/ ; 2025A1515012512//Guangdong Basic and Applied Basic Research Foundation/ ; 2022041//Shenzhen Longhua District Healthcare Institutions Scientific Research Project/ ; //Key Medical Discipline Construction Fund of Shenzhen Longhua District/ ; JZ2025107//Guangdong Yiyang Healthcare Charity Foundation/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Glomerulonephritis, Membranous/microbiology ; *Metagenomics/methods ; Male ; Female ; Middle Aged ; Feces/microbiology ; Adult ; *Bacteria/genetics/classification ; Case-Control Studies ; },
abstract = {BACKGROUND: Membranous nephropathy (MN) is one of the most common forms of primary glomerulonephritis worldwide and is closely associated with immune dysregulation. Increasing evidence suggests that the gut microbiota plays a critical role in regulating renal disease through the gut-renal axis. However, the use of metagenomic sequencing to analyze changes in the gut microbiota in patients with MN has not yet been reported.

METHODS: This study employed a metagenomic approach to comprehensively analyze the gut microbiota in patients with MN (n = 10) and normal controls (NCs; n = 10). Shotgun metagenomic sequencing was performed on fecal samples. Microbial diversity, taxonomic composition, and functional pathways were assessed, followed by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. In addition, correlations between gut microbial characteristics and clinical indicators were also evaluated.

RESULTS: The gut microbial community in the MN group showed distinct differences from the control group, particularly with an increased abundance in phylum: Proteobacteria, Firmicutes_C, and Cyanobacteria; the genera Dialister, Selenomonadales, Clostridium, Bacillus, Megamonas, Romboutsia, and Inesitibacter; the species Bilophila_wadsworthia, Enterococcus_C, Megamonas funiformis, and Clostridium_perfringens. Furthermore, Bacillus_A showed a significant positive correlation with both serum creatinine and the protein-to-creatinine ratio. Conversely, higher levels of Victivallis were associated with lower blood urea nitrogen, while increased Fusicatenibacter was correlated with lower phospholipase A2 receptor levels. KEGG analysis indicated that the MN gut microbiota was enriched for pathways related to tryptophan metabolism, oxidative phosphorylation, and pathogenic Escherichia coli infection. Additionally, receiver operating characteristic analysis revealed that a four-genus model comprising enriched Dialister, Enterococcus_C, and Clostridium_P, and reduced Fusicatenibacter yielded an area under the curve of 0.90 ± 0.12, suggesting promising discriminatory potential that warrants further validation.

CONCLUSION: These findings demonstrate alterations in the composition and functional potential of the gut microbiota in patients with MN compared with the control group. Given the cross-sectional design of this study, these observations should be interpreted as associative, and further studies are required to validate these findings and explore any associated biological relevance.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Glomerulonephritis, Membranous/microbiology
*Metagenomics/methods
Male
Female
Middle Aged
Feces/microbiology
Adult
*Bacteria/genetics/classification
Case-Control Studies

@article {pmid42052832,
year = {2026},
author = {Byun, AS and Kwok, PCL and Chan, HK and Vitetta, L},
title = {The Gut-Lung Axis, Epigenetics and Respiratory Disease.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {31},
number = {4},
pages = {48743},
doi = {10.31083/FBL48743},
pmid = {42052832},
issn = {2768-6698},
mesh = {Humans ; *Epigenesis, Genetic ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology ; *Lung/microbiology ; Prebiotics ; Probiotics/therapeutic use ; Animals ; *Respiratory Tract Diseases/microbiology ; },
abstract = {The first and second phases of the human microbiome project provided a view of mucosal surfaces and the skin of humans that mapped an abundant and complex ecosystem (microbiota) that is composed of bacteria (bacteriobiota), fungi (mycobiota), viruses (virobiota), enteric phages, archaea, protists, and helminths. Intestinal dysbiosis describes an adverse shift in microbial homeostasis in the gut that enhances intestinal epithelial permeability, translocating toxins that may lead to endotoxemia. Numerous intestinal and extra-intestinal illnesses have been linked to gut dysbiosis, including inflammatory bowel disease, infections, food allergies, asthma, diabetes, obesity, multiple sclerosis, autism, periodontitis, and colorectal cancer. The gut-lung axis is a bidirectional communication network between the lungs and the intestines mediated by bacterial elaborated products (e.g., butyrate), immune cells and neural pathways influencing health and disease at both sites. This review has focused on the gut-lung axis and the role that probiotics, prebiotics and postbiotics may play on the amelioration of respiratory symptoms that may result from viral and/or bacterial lung infections. Clinicians have for some time focused on treating inflammatory lung disorders such as asthma and chronic obstructive pulmonary disease by encouraging beneficial effects on the intestinal microbiome through the gut-lung axis with orally administered probiotics and pre- and/or postbiotics. The purpose is to restore gut microbial homeostasis. Developing novel delivery platforms to administer probiotics directly to the airways or as adjunctive systemic modulators is a plausible and increasingly supported hypothesis, with careful strain selection, formulation to preserve viability, targeted delivery, and rigorous safety and efficacy testing before clinical use. It is posited that such adjunctive treatments may significantly influence the lung microbiota epigenome by positively impacting the balance of microorganisms within the lung, restoring eubiosis and consequently health.},
}

Humans
*Epigenesis, Genetic
*Gastrointestinal Microbiome
Dysbiosis/microbiology
*Lung/microbiology
Prebiotics
Probiotics/therapeutic use
Animals
*Respiratory Tract Diseases/microbiology

@article {pmid42052843,
year = {2026},
author = {Yusuf, K and Attard, TM and Al-Kasspooles, M and Umar, S},
title = {An Emerging Approach to IBD Treatment: Personalized Nutrition Through Gut Microbiome Optimization.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {31},
number = {4},
pages = {47779},
doi = {10.31083/FBL47779},
pmid = {42052843},
issn = {2768-6698},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/diet therapy/microbiology/therapy ; *Precision Medicine/methods ; Diet ; },
abstract = {Inflammatory bowel disease (IBD) is a chronic inflammatory disorder of the gastrointestinal tract characterized by relapsing and remitting disease activity. Despite decades of research, a definitive cure for IBD remains elusive, as cycles of remission and flare-ups mark the disease course and often relies on long-term pharmacologic and supportive strategies. Increasing evidence indicates that diet and nutrition play an important role in modulating the outcomes of IBD. Although a wide range of dietary interventions has been explored, no universally effective approach has been established. Investigations have also proven that different dietary interventions can significantly affect clinical outcomes by altering gut microbial composition. This review explores a novel approach to IBD management by integrating gut microbiome modulation into personalized patient diets. The review examines various dietary interventions commonly used in IBD treatment and their impact on the gut microbiome composition. Furthermore, the study proposes a framework for creating personalized nutrition based on individual microbiome profiles. Finally, the review discusses the potential of personalized nutrition as a long-term therapeutic strategy for IBD management, offering insights into its feasibility and implications for patient care.},
}

Humans
*Gastrointestinal Microbiome
*Inflammatory Bowel Diseases/diet therapy/microbiology/therapy
*Precision Medicine/methods
Diet

@article {pmid42053308,
year = {2026},
author = {Bojang, E and Sheriff, L and Morris, E and Rouvray, S and Fu, MS and Wellings, C and Abdissa, K and Stavrou, V and Clark, C and Southam, AD and Dunn, WB and Bending, D and Hombrebueno, JR and Jacobsen, I and Dimeloe, S and Hall, RA and Drummond, RA},
title = {Vancomycin disrupts mitochondrial morphology and function and impairs macrophage fungal killing.},
journal = {mBio},
volume = {},
number = {},
pages = {e0058026},
doi = {10.1128/mbio.00580-26},
pmid = {42053308},
issn = {2150-7511},
abstract = {Vancomycin is a widely prescribed antibiotic used in the treatment of gram-positive bacterial infections. We previously showed that this antibiotic disrupted protective antifungal immune responses via microbiome dysbiosis, enhancing susceptibility to invasive candidiasis. Antibiotics are an independent risk factor for developing this life-threatening fungal infection, but whether microbiota-independent mechanisms also drive this association is not clear. Here, we show that vancomycin directly impairs macrophage responses to Candida albicans, the main causative agent of invasive candidiasis. Vancomycin-treated macrophages were less able to kill C. albicans despite normal phagocytosis rates and were hyper-inflammatory and more likely to die during infection. Using a fluorescently labeled vancomycin, we observed vancomycin uptake by macrophages in vivo and within close proximity to the mitochondrial outer membrane. Vancomycin treatment led to a significant depolarization, reduced respiratory capacity, and a hyper-fragmented morphology of mitochondria, as well as increased cellular ROS production. Taken together, this work demonstrates direct effects of vancomycin on mammalian immune cells, helping us to understand the pro-inflammatory effects of this drug and how it promotes susceptibility to life-threatening fungal infection.IMPORTANCEAntibiotics are widely prescribed drugs used to treat bacterial infections; however, their use may increase the likelihood of developing life-threatening fungal infections in vulnerable patients. Candida albicans is a commensal fungus in humans but may cause serious disease in patients with defined risk factors, including antibiotic exposure. We find that the antibiotic vancomycin significantly impairs the ability of macrophages to kill C. albicans yeast. Vancomycin-induced defects in fungal killing were associated with changes to mitochondria in antibiotic-exposed macrophages, which also exhibited enhanced oxidative stress and reduced survival during fungal infection. This work identifies a direct mechanism by which antibiotics may impair antifungal immunity.},
}

@article {pmid42053319,
year = {2026},
author = {Fulcher, MR and Tritz, A and Beauchamp, V and Wu, CA},
title = {Wavyleaf basketgrass (Oplismenus undulatifolius) invasion is associated with changes in soil microbial communities.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0089525},
doi = {10.1128/msphere.00895-25},
pmid = {42053319},
issn = {2379-5042},
abstract = {UNLABELLED: Introduced invasive plants can alter the composition of resident soil microbial communities, which may disrupt ecosystem function and facilitate continued invasion success. Wavyleaf basketgrass (Oplismenus undulatifolius) is a high-risk, non-native invasive plant currently confined to the Mid-Atlantic United States but with the potential to colonize forest understory across the eastern United States. In this study, we characterized soil microbial communities from locations spanning the invaded range using amplicon sequencing to understand the impacts of wavyleaf basketgrass establishment on resident soil microbiomes. We compared the diversity and structure of microbial communities from invaded and uninvaded forest soils, as well from wavyleaf basketgrass rhizospheres. Invasion by wavyleaf basketgrass was associated with an increase in fungal diversity within sampling locations but a decrease in diversity across sampling locations. Changes in the relative abundance of specific sequence variants indicated a small number of resident microbes may be amplified in wavyleaf basketgrass rhizospheres. Finally, fungal alpha diversity was correlated with soil chemistry variables in uninvaded plots but not in invaded plots, and increased plant ground cover attributed to wavyleaf basketgrass invasion was positively correlated with fungal diversity. Together, these patterns suggest that wavyleaf basketgrass recruits diverse microbial associates from the environment, homogenizes soil microbiomes across invaded locations, and overrides existing environmental selection pressures exerted by soil chemistry profiles. Ongoing expansion of the species' invaded range may produce similar impacts in new environments.

IMPORTANCE: Understanding whether and how microbial communities are altered by plant invasion provides important information about the impact of introduced species on natural resources, nutrient cycling, and biodiversity that influence subsequent land management and ecosystem restoration decisions. We document biotic homogenization of resident soil microbes across geographically disparate locations following a relatively recent plant invasion. We further provide evidence suggesting microbial community changes are linked to the enrichment of specific taxa from the invasive plant's rhizosphere and possible buffering of these communities against other environmental selective pressures.},
}

@article {pmid42053321,
year = {2026},
author = {Okyere, L and Di Fulvio, A and Gaulke, CA},
title = {Long-term culture of germ-free zebrafish using gamma-irradiated feeds.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0035326},
doi = {10.1128/msystems.00353-26},
pmid = {42053321},
issn = {2379-5077},
abstract = {Host-associated microbiota play important roles in modulating key host functions, including digestion, nutrient acquisition, immunity, and xenobiotic metabolism. Disruption of these communities is linked to numerous diseases and health defects, though causal mechanisms underpinning these associations remain unclear in most cases. Gnotobiotic zebrafish provide a scalable low-cost in vivo model that is increasingly used to resolve causality in host-microbiota interactions. However, reliance on live diets and autoclaved diets limits the use of gnotobiotic zebrafish to early life stages where body systems and microbial communities are incompletely developed. As a result, many important host-microbiota interactions may be unable to be studied in this model system. Here, we tested a simple method for long-term husbandry of gnotobiotic zebrafish using gamma-irradiated chow diets and evaluated effects on growth, gene expression, and microbial community composition. In conventionally reared animals, gamma-irradiated diets did not affect growth or survival and only modestly impacted microbial community composition and diversity. In contrast, germ-free zebrafish maintained on sterile irradiated diets for 55 days post-fertilization were smaller, weighed less, and exhibited aberrant gene expression profiles relative to controls. These genes were enriched for pathways related to immune response, xenobiotic metabolism, organ development, liver function, and lipid metabolism, with many expression patterns linked to the abundance of specific microbial taxa. Together, these findings establish a practical protocol for long-term maintenance of gnotobiotic zebrafish and extend the utility of this model to study microbiome-dependent effects on host physiology and development beyond early larval stages of life.IMPORTANCEWhile the gnotobiotic zebrafish have been a powerful model for interrogation of host-microbiota interactions, their use has been limited to early life stages due to complications of long-term husbandry. To address this limitation, we developed a simple protocol that enables rearing germ-free zebrafish well beyond larval stages. Germ-free fish exhibit physiological and developmental defects that mirror those described in mammalian counterparts supporting a conserved role for microbiota in vertebrate development and physiology. Our protocol provides a method to investigate microbial influences on adaptive immunity, metabolism, and chronic disease processes in zebrafish not possible with current methodologies. Given the rapid and simple methods for gnotobiotic derivation and the large number of transgenic animal lines available for zebrafish, we anticipate this model will accelerate mechanistic discovery of microbial impacts on host health.},
}

@article {pmid42053337,
year = {2026},
author = {Wutke-Ostręga, J and Szul, M and Pluta, D},
title = {Eradicating hyperandrogenism? Hormonal changes following Helicobacter pylori eradication in women with polycystic ovary syndrome: an observational case series.},
journal = {Endokrynologia Polska},
volume = {77},
number = {2},
pages = {107-111},
doi = {10.5603/ep.110428},
pmid = {42053337},
issn = {2299-8306},
mesh = {Humans ; Female ; *Polycystic Ovary Syndrome/complications/blood ; Adult ; *Helicobacter Infections/drug therapy/complications/blood ; *Hyperandrogenism/blood/drug therapy/complications ; *Helicobacter pylori ; Sex Hormone-Binding Globulin/metabolism/analysis ; Testosterone/blood ; Young Adult ; Androgens/blood ; Dehydroepiandrosterone Sulfate/blood ; Anti-Mullerian Hormone/blood ; },
abstract = {INTRODUCTION: Polycystic ovary syndrome (PCOS) is a heterogeneous endocrine disorder in which hyperandrogenism represents a centralpathophysiological feature. Increasing attention has been directed toward chronic inflammatory factors that may modulate androgenexcess. Helicobacter pylori (H. pylori) infection is a prevalent chronic bacterial infection associated with systemic low-grade inflammation.However, its potential relationship with androgen-related hormonal parameters in PCOS remains poorly explored.

MATERIAL AND METHODS: This observational mini case series included seven women with PCOS diagnosed according to the Rotterdam criteriaand confirmed active H. pylori infection. Hormonal parameters including total testosterone, androstenedione, dehydroepiandrosteronesulfate (DHEAS), sex hormone-binding globulin (SHBG), anti-Müllerian hormone (AMH), and free androgen index (FAI) were assessedduring active infection and after confirmed eradication. No hormonal contraception, antiandrogens, metformin, incretin-based therapies,or inositol supplements were used during the study period.

RESULTS: Following successful H. pylori eradication, consistent changes in androgen-related parameters were observed. Median DHEAS,androstenedione, and total testosterone concentrations decreased, while SHBG levels increased. Consequently, the free androgen indexdecreased in all patients. AMH levels showed a downward trend after eradication. Due to the descriptive nature of the study, no inferentialstatistical analyses were performed.

CONCLUSIONS: In this observational case series, H. pylori eradication was associated with coherent changes in androgen-related hormonal parameters and reduced androgen bioavailability in women with PCOS. Although causality cannot be established, these findings suggestthat chronic infection-related inflammation may influence the androgenic milieu in PCOS.},
}

Humans
Female
*Polycystic Ovary Syndrome/complications/blood
Adult
*Helicobacter Infections/drug therapy/complications/blood
*Hyperandrogenism/blood/drug therapy/complications
*Helicobacter pylori
Sex Hormone-Binding Globulin/metabolism/analysis
Testosterone/blood
Young Adult
Androgens/blood
Dehydroepiandrosterone Sulfate/blood
Anti-Mullerian Hormone/blood

@article {pmid42053342,
year = {2026},
author = {Mehta, N and Guzzetta, V and Liu, KH and Webster, AS and Adelman, MW and Fitts, EC and Jones, DP and Kraft, CS and Woodworth, MH and Collins, JM},
title = {High-resolution metabolomic analysis of stool reveals expanded biomarkers of C. difficile colitis and insights into pathophysiology.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0282625},
doi = {10.1128/spectrum.02826-25},
pmid = {42053342},
issn = {2165-0497},
abstract = {Clostridioides difficile infection (CDI) is facilitated by gut microbiome disruption and associated metabolic disturbances. While many prior studies have focused on the microbial composition of CDI stool, fewer have explored the fecal metabolome using untargeted high-resolution metabolomics (HRM). To characterize the metabolic phenotype of CDI, we performed untargeted HRM on stool samples from 55 CDI patients and 72 healthy controls. CDI was associated with marked alterations in stool metabolites, mapping to 14 significantly dysregulated pathways, including tryptophan metabolism, bile acid metabolism, short-chain fatty acid metabolism, and fatty acid oxidation. These findings suggest that CDI is associated with a distinct fecal metabolic milieu that may promote inflammation, impair colonization resistance, and facilitate C. difficile replication. Our results corroborate previous studies and support further investigation of the role of microbial and immune signaling in CDI as well as metabolic biomarkers and therapeutic targets.IMPORTANCEAs we learn more about the essential role of gut microbes in human health and disease, there is an effort to identify and characterize stool biomarkers that distinguish patients with microbiome-associated disease from healthy individuals. Clostridioides difficile infection contributes to excess healthcare burden and is tightly linked to disruption of the gut microbiome (usually by use of antimicrobials). We compared the metabolome of healthy stool and C. difficile-infected stool to identify metabolites that correlate with disease and may support the development of improved diagnostic tests for C. difficile infection. In comparing these two groups, we found chemical pathways that strongly correlate with disease and others more associated with healthy stool, including bile acid biosynthesis, tryptophan metabolism, and carnitine activation.},
}

@article {pmid42053606,
year = {2026},
author = {Koch, H and Lessard, B and Escobar-Correas, S and Thurman, JH and Paten, AM and Morgan, MJ},
title = {A Comparative Survey of Soldier Fly (Stratiomyidae) Larval Gut Microbiomes Across Five Subfamilies Reveals Novel Bacterial Diversity and a "Wild Core" in Hermetia illucens.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02760-z},
pmid = {42053606},
issn = {1432-184X},
}

@article {pmid42053608,
year = {2026},
author = {Çağatay, NS and Dageri, A and Saruhan, I and Tuncer, C and Guz, N},
title = {Diversity and Composition of the Microbiome Associated with Adult of the Green Shield Bug Palomena prasina (Hemiptera: Pentatomidae).},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02779-2},
pmid = {42053608},
issn = {1432-184X},
support = {Project number: 116O328//Türkiye Bilimsel ve Teknolojik Araştırma Kurumu/ ; },
}

@article {pmid42053737,
year = {2026},
author = {Jasrotia, P and Chandra, P and Singh, A and Kashyap, PL and Sharma, SK},
title = {Symbiont dominance and microbiome dysbiosis in wheat-aphid revealed through 16 S rRNA gene amplicon sequencing analysis.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {5},
pages = {},
pmid = {42053737},
issn = {1573-0972},
mesh = {*Triticum/parasitology/microbiology ; Animals ; *Aphids/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification ; Phylogeny ; *Symbiosis ; *Dysbiosis/microbiology ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Biodiversity ; },
abstract = {Insect herbivory represents a major biotic stress that leads to significant losses in crop yield and quality worldwide. Aphids, in particular, damage wheat (Triticum aestivum L.), a staple crop that provides nearly 20% of the global protein and caloric intake, and also harbor diverse bacterial symbionts that can influence plant health. In this study, 16 S rRNA gene amplicon sequencing was used to characterize the bacterial communities associated with healthy and aphid-infested wheat plants. Alpha-diversity indices, including Simpson, Shannon, Chao1, and ACE, revealed statistically significant variation (P < 0.05) in bacterial richness and diversity across the samples. Richness estimates ranged from 101.25 to 137.2 (Chao1) and 106.04 to 139.37 (ACE), while diversity metrics ranged from 0.428 to 1.243 for the Shannon index, with Faith's phylogenetic diversity varying from 1.27 to 1.48 and Pielou's evenness from 0.626 to 0.740. In healthy wheat plants, Spirodela accounted for approximately 4% of the bacterial community, whereas about 95% of taxa remained unclassified. In contrast, aphid-infested wheat plants contained 3% Spirodela, 7% Buchnera, and 89% unclassified taxa. The aphid microbiome itself was strongly dominated by Buchnera (86%), followed by Pseudomonas (2%) and other minor taxa (1%), with approximately 10% remaining unclassified. The pronounced abundance of Buchnera in both aphids and infested wheat plants highlights its essential nutritional role and its long-standing obligate endosymbiotic association with aphids. Overall, these findings provide new insights into wheat-aphid-microbiome interactions and establish a foundation for developing microbiome-informed pest management strategies.},
}

*Triticum/parasitology/microbiology
Animals
*Aphids/microbiology
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Bacteria/genetics/classification/isolation & purification
Phylogeny
*Symbiosis
*Dysbiosis/microbiology
Sequence Analysis, DNA
DNA, Bacterial/genetics
Biodiversity

@article {pmid42053754,
year = {2026},
author = {Goyal, O and Aggarwal, A and Goyal, MK and Mehta, V and Mahajan, R and Gupta, Y and Singh, A and Sood, A},
title = {Prevalence, clinical significance and predictors of small intestinal bacterial overgrowth and elevated fecal calprotectin in refractory irritable bowel syndrome: Insights from a prospective cross-sectional study.},
journal = {Indian journal of gastroenterology : official journal of the Indian Society of Gastroenterology},
volume = {},
number = {},
pages = {},
pmid = {42053754},
issn = {0975-0711},
abstract = {BACKGROUND: Irritable bowel syndrome (IBS) is a common disorder with multi-factorial pathophysiology. Emerging evidence suggests a role of low-grade mucosal inflammation in IBS. Small intestinal bacterial overgrowth (SIBO), which has symptoms similar to IBS, may be misdiagnosed as IBS. Data on the prevalence of SIBO and elevated fecal calprotectin (FCP) levels in IBS patients remains sparse and conflicting. We aimed at determining the prevalence and clinical significance of SIBO and elevated FCP in patients with refractory IBS.

METHODS: This prospective cross-sectional study enrolled refractory IBS patients (Rome-IV criteria). SIBO was diagnosed using the glucose hydrogen breath test and FCP levels ≥ 50 μg/g were considered elevated. Clinical evaluation was performed using standardized questionnaires: IBS Symptom Severity Scale (IBS-SSS) and IBS Quality of Life (IBS-QoL).

RESULTS:  Of 209 patients screened, 148 with refractory IBS were enrolled (mean age 35.8 ± 11.9 years; 66.1% male). SIBO was detected in 46 (31.1%) and elevated FCP in 41 (27.7%) patients, with the highest prevalence in the IBS-D group (37.1% and 33.3%, respectively). Patients who were SIBO and/or FCP-positive had a longer duration of symptoms, higher IBS symptom burden and poorer QoL. Multi-variate analysis identified bloating (aOR = 4.59) and the IBS-SSS (aOR = 1.20) as independent predictors of SIBO.

CONCLUSIONS: Approximately one-third of patients with refractory IBS, particularly those with IBS-D, have SIBO and/or elevated FCP. This subset of patients demonstrates a higher symptom burden and poorer QoL, emphasizing the crucial need for accurate diagnosis and personalized treatment. Incorporating non-invasive biomarkers (SIBO testing and FCP) into the management of refractory IBS may optimize patient care.},
}

@article {pmid42053842,
year = {2026},
author = {Sysak, A and Górska, S},
title = {Extracellular Vesicles in Allergy: From Cellular Communication to Clinical Implications.},
journal = {Clinical reviews in allergy & immunology},
volume = {69},
number = {1},
pages = {},
pmid = {42053842},
issn = {1559-0267},
support = {2021/43/I/NZ7/00693//National Science Centre of Poland/ ; },
abstract = {Extracellular vesicles (EVs) are lipid bilayer-enclosed particles released by both eukaryotic and prokaryotic cells and represent an evolutionarily conserved system of intercellular communication. By transporting bioactive cargo, including proteins, lipids, microRNAs, EVs enable the transfer of molecular signals between cells, thereby regulating immune homeostasis and inflammatory responses. In allergic diseases, EVs have emerged as key mediators linking epithelial barriers, immune cells, and the microbiome. EVs derived from epithelial, immune, and microbiota-associated cells may contribute to the initiation, amplification, and persistence of allergic inflammation by modulating barrier integrity, immune cell polarization, and cytokine signaling pathways. Disease-specific alterations in EV cargo reflect underlying pathogenic mechanisms, positioning EVs as promising non-invasive biomarkers for disease diagnosis, stratification, and monitoring. In parallel, accumulating experimental evidence highlights the therapeutic potential of EVs as cell-free immunomodulatory agents capable of suppressing allergic inflammation and promoting immune tolerance. This review synthesizes current knowledge on extracellular vesicles across three major allergic diseases: asthma, atopic dermatitis, and food allergy, integrating mechanistic insights with diagnostic and therapeutic advances. By incorporating highly recent literature and covering a broad spectrum of EV sources and engineered vesicle-based strategies, the review provides a comprehensive overview of how EV-mediated cellular communication translates into clinically relevant applications in allergy.},
}

@article {pmid42053902,
year = {2026},
author = {Dai, T and Chen, AX and Chow, EWL and Pang, LM and Li, J and Verma, CS and Oehlers, SH and Wang, Y and Li, N},
title = {A Cationic Supramolecule With Potent Antifungal Activity, Single-Species Selectivity, and Strong Synergy With Echinocandins.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e75480},
doi = {10.1002/advs.75480},
pmid = {42053902},
issn = {2198-3844},
support = {//A*STAR Infectious Diseases Labs/ ; OFYIRG24jan-0051//National Medical Research Council Open-Fund Young Individual Research Grant/ ; C233312014//A*STAR Career Development Fund/ ; SRIS_JRG_2001//Skin Research Institute of Singapore Joint Research Grant (SRIS_JRG_2001)/ ; },
abstract = {Claiming 3.8 million lives annually, fungal pathogens represent a major health threat, where Candida species are the leading cause with >40% mortality rates. Despite rising prevalence of life-threatening fungal species/strains, progress in developing new antifungal agents remains limited. Here, we report a new synthetic membrane-active cationic supramolecule Gua-SMACS-16 that exhibits high antifungal potency and selectivity for Candida tropicalis (MIC = 0.4-0.8 µM) without affecting other phylogenetically close species in the Candida genus, non-Candida fungal, or common opportunistic bacterial species in the human microbiome. Gua-SMACS-16 exerts its activity by disrupting the cytoplasmic membrane, while its C. tropicalis selectivity is attributed to the species' low cell wall β-glucan level, which fails to block the supramolecule entry. It also exhibits minimal toxicity to mammalian cells and zebrafish embryos, suggesting a high clinical translation potential. Moreover, an ultra-strong synergy was observed between Gua-SMACS-16 and caspofungin, a clinical antifungal drug inhibiting 1,3-β-glucan synthase, reducing their MICs by orders of magnitude against all tested Candida species including the intractable C. auris. Together, this work highlights the importance of cell wall glucan for membrane-active antifungal amphiphiles, provides a novel design principle for species-specific antifungal agents, and uncovers a new approach to developing synergizers for combination antifungal therapy.},
}

@article {pmid42054100,
year = {2026},
author = {Mellor, SA and Bloomfield, SJ and Palau, R and Savva, GM and Wain, J and Mather, AE},
title = {Metagenomic analysis of UK retail foods finds limited evidence for associations between food production method and antimicrobial resistance gene burden.},
journal = {Microbial genomics},
volume = {12},
number = {4},
pages = {},
doi = {10.1099/mgen.0.001705},
pmid = {42054100},
issn = {2057-5858},
mesh = {Animals ; *Metagenomics/methods ; *Food Microbiology ; Chickens/microbiology ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Drug Resistance, Bacterial/genetics ; *Meat/microbiology ; Cattle ; Sheep ; Salmon/microbiology ; United Kingdom ; Microbiota/genetics ; Anti-Bacterial Agents/pharmacology ; Swine ; },
abstract = {Food is produced by a range of methods including extensive (organic and free range), intensive (conventional) and wild-caught production systems. Antimicrobial use varies between different food production systems, which may affect the microbial populations as well as the prevalence and diversity of antimicrobial resistance genes (ARGs) found on food at retail. In this study, shotgun metagenomics was used to investigate the microbial and ARG composition of 25 pork, 33 beef, 33 lamb, 60 chicken, 31 salmon and 41 leafy green samples collected in Norfolk, England, and labelled as extensive, wild caught or intensive. Food microbiomes consisted predominantly of spoilage-associated organisms including Pseudomonas, Lactococcus and Psychrobacter. Significant differences in bacterial diversity were found between intensive and extensive systems on chicken, and 22 differentially abundant genera were identified between production systems across beef, chicken and salmon. Genes conferring resistance to tetracyclines and beta-lactams comprised the majority of the food resistome across all commodities. Across most measures used to compare food resistomes between production methods, no significant differences were detected, except on chicken and salmon where differences in beta-diversity between production methods were detected, albeit with low effect sizes. Overall, these results suggest that differently produced foods, at least when tested at retail and in this region, may present a similar risk of antimicrobial resistance across the commodities investigated within this study. However, specific associations were identified with the microbial composition across chicken, beef and salmon, suggesting that production method may drive some variation in the microbial population structure on food products. Additional work at the farm or food processing levels is required to identify the drivers of these differences between production systems.},
}

Animals
*Metagenomics/methods
*Food Microbiology
Chickens/microbiology
*Bacteria/genetics/classification/drug effects/isolation & purification
*Drug Resistance, Bacterial/genetics
*Meat/microbiology
Cattle
Sheep
Salmon/microbiology
United Kingdom
Microbiota/genetics
Anti-Bacterial Agents/pharmacology
Swine

@article {pmid42054198,
year = {2026},
author = {Côrtes, J and Trindade Filho, JCS and Rogatto, SR},
title = {The emerging role of the microbiome in bladder cancer: prognostic implications and treatment response.},
journal = {Brazilian journal of medical and biological research = Revista brasileira de pesquisas medicas e biologicas},
volume = {59},
number = {},
pages = {e15526},
pmid = {42054198},
issn = {1414-431X},
mesh = {Humans ; *Urinary Bladder Neoplasms/microbiology/therapy/pathology ; *Microbiota/physiology ; Prognosis ; Risk Factors ; },
abstract = {Bladder cancer (BCa) is a histologically and molecularly heterogeneous disease and is one of the leading causes of cancer death globally. The main risk factors are sex (with incidence 3 to 4 times higher in men), tobacco usage, occupational exposure to carcinogens, and persistent infections, such as those caused by Schistosoma haematobium. Urine and the bladder were recently confirmed to be non-sterile, prompting investigations into the urinary and intratumoral microbiomes and their roles in tumor stage, prognosis, and therapy response. In this context, the role of the urinary and intratumoral microbiome in bladder carcinoma is among the most promising areas in translational uro-oncology. Recent evidence demonstrates the presence and diversity of microbial communities in both urine and bladder cancer tissue, with patterns associated with tumor stage and prognosis. Chronic inflammation, genotoxin production, altered carcinogen metabolism, and modulation of the immune microenvironment are biological processes that provide a rationale for the functional role of these microorganisms in the bladder. Furthermore, microbial profiles have been correlated with responses to intravesical therapies (such as BCG - Bacillus Calmette-Guérin) and, potentially, with systemic immunotherapies. The microbiome can help identify predictors of treatment response and potential adjuvant interventions, and offers a non-invasive, translational pathway for diagnosis and surveillance. This review summarizes current evidence on the microbiome in bladder cancer patients and its prognostic and therapeutic potential.},
}

Humans
*Urinary Bladder Neoplasms/microbiology/therapy/pathology
*Microbiota/physiology
Prognosis
Risk Factors

@article {pmid42054627,
year = {2026},
author = {Braun, AE and Hesami, H and Deng, M and Hasler, JS and Bukavina, L and Handorf, E and Abbosh, PH},
title = {Association Between Antibiotic Therapy and Treatment Effectiveness in Patients With Renal Cell Carcinoma Receiving Immune Checkpoint Inhibitors or Tyrosine Kinase Inhibitors.},
journal = {JCO oncology practice},
volume = {},
number = {},
pages = {OP2500963},
doi = {10.1200/OP-25-00963},
pmid = {42054627},
issn = {2688-1535},
abstract = {PURPOSE: It has been theorized that antibiotic therapy (ABT) affects response to immune checkpoint inhibition (ICI) by inducing dysbiosis of the gut microbiome (GM). To investigate the association between ABT and real-world overall survival (rwOS)/progression-free survival (rwPFS) in patients with metastatic renal cell carcinoma (mRCC) receiving ICI versus tyrosine kinase inhibitors (TKIs).

METHODS: In total, 5,237 patients with mRCC from a nationwide electronic health record-derived deidentified database who received ICI or TKI first-line after diagnosis were included. ABT exposure was stratified by exposure (yes or no), timing (before v after treatment initiation v none), excretion modes (hepatic v renal excretion v none), and administration routes (oral v intravenous v none). Three-month landmark Kaplan-Meier estimation and log-rank tests were used to compare rwOS/rwPFS among ABT groups. Multivariable Cox proportional hazards models with time-varying coefficients investigated the association between rwPFS, rwOS, ABT, and treatment modality.

RESULTS: ABT exposure was negatively associated with rwOS/rwPFS in both ICI (rwOS [23.9 v 33.6 months, P = .029]; rwPFS [8.8 v 11.6 months, P < .001]) and TKI (rwOS [17.4 v 26.2 months, P < .001]; rwPFS [8.0 v 9.7 months, P < .001]) recipients. For ICI patients only, a negative correlation between ABT after treatment initiation (rwOS, P = .003, rwPFS <0.001) and oral administration route (rwOS P = .004, rwPFS P = .001) was identified. In time-varying Cox proportional models, the effect of ABT on rwPFS beyond 12 months was only statistically significant in ICI patients (ICI, hazard ratio [HR], 1.67, P = .013; TKI, HR, 0.95; P = .7).

CONCLUSION: In our observational study, we identified a potential unique and complex association between ABT and rwOS/rwPFS in patients with mRCC receiving ICI. We found a negative correlation between ABT use after treatment initiation or via the oral route on oncologic outcomes in ICI patients. Moreover, there appears to be an ICI-specific negative association of ABT on rwPFS beyond 1 year. Our findings are associative, but they emphasize the importance of antibiotic stewardship in this space.},
}

@article {pmid42054761,
year = {2026},
author = {Liu, Y and He, P and He, P and Li, X and Ahmed, A and Tang, G and Tang, P and Di, Y and Zhou, Y and Hu, D and Li, Y and Wu, Y and Munir, S and He, Y},
title = {Cross-kingdom synthetic microbial consortium controls citrus Huanglongbing and root rot by modulating the rhizosphere microbiome and plant defense.},
journal = {Microbiological research},
volume = {309},
number = {},
pages = {128528},
doi = {10.1016/j.micres.2026.128528},
pmid = {42054761},
issn = {1618-0623},
abstract = {The synergistic occurrence of citrus Huanglongbing (HLB) caused by Candidatus Liberibacter asiaticus (CLas) and root rot severely threatens the global citrus industry. In this study, field surveys were conducted across nine major citrus-producing regions in seven provinces of China. Highly pathogenic strains, Phytophthora nicotianae CR62 and Fusarium solani CR15, were selected as targets for screening Trichoderma strains for mycoparasitic activity. Compatibility and metabolic cross-feeding with the HLB-controlling strain Bacillus subtilis L1-21 enabled the construction of a cross-kingdom SynCom. Pot experiments evaluated plant growth promotion and root rot control, while high-throughput sequencing (16S rRNA/ITS) elucidated the regulatory mechanisms of rhizosphere microbiomes. The results showed that HLB and root rot co-occurred widely in the field, with oomycetes (Phytophthora spp. and Pythium spp.) accounting for 65.22% of root rot pathogens. P. nicotianae and F. solani exhibited the highest pathogenicity, whereas no significant correlation was detected between the root rot disease index and CLas titer. Targeted screening showed that T. asperellum NY-1 exerted more than 60% inhibition against root rot pathogens and exhibited high compatibility with B. subtilis L1-21. Moreover, the cell-free filtrate of NY-1 significantly reshaped the global metabolic profile of L1-21, primarily by modulating amino acid and energy metabolism, as well as ABC transporter pathways, thereby comprehensively altering its cellular metabolic activities. Importantly, the SynCom NL significantly promoted plant growth and increased rhizosphere urease and sucrase activities after 90 days of treatment. SynCom NL enriched beneficial microbes (Bacillus, Sphingomonas, Trichoderma, Humicola), suppressed pathogens (Fusarium, Penicillium, Neocosmospora), and activated root defense enzymes (SOD, CAT, PAL, PPO), boosting root protection and achieving 92.86 ± 8.25% root rot control. Overall, the Trichoderma-Bacillus cross-kingdom SynCom targeting the HLB-root rot disease complex provides a technical foundation for integrated biocontrol and sustainable citrus production.},
}

@article {pmid42043192,
year = {2026},
author = {Knap-Wielgus, W and Knap, A and Pietrzak, B and Suchońska, B and Wielgoś, M},
title = {A Role of the Lower Genital Tract Microbiome in Promoting Cervical Intraepithelial Neoplasia: A Premalignant Precursor of Cervical Cancer-A Literature Review.},
journal = {Viruses},
volume = {18},
number = {4},
pages = {},
pmid = {42043192},
issn = {1999-4915},
mesh = {Humans ; Female ; *Microbiota ; *Uterine Cervical Dysplasia/microbiology/virology/pathology ; *Uterine Cervical Neoplasms/microbiology/virology/pathology ; Papillomavirus Infections/complications/virology/microbiology ; Dysbiosis/microbiology ; *Vagina/microbiology/virology ; Papillomaviridae ; Lactobacillus ; },
abstract = {The cervicovaginal microbiome (CVMB) is pivotal in maintaining the homeostasis of the lower female genital tract and has emerged as a significant modulator of cervical carcinogenesis. Although persistent infection with high-risk human papillomavirus (HR-HPV) is a prerequisite for the development of cervical intraepithelial neoplasia (CIN) and subsequent cervical carcinoma, it remains insufficient alone to drive oncogenesis. Accumulating evidence suggests that alterations in the CVMB composition profoundly impact HPV persistence, local immune responses, and disease progression. A vaginal microbiota dominated by Lactobacillus species, most notably Lactobacillus crispatus, correlates with low microbial diversity, robust immune regulation, and facilitated HPV clearance. Conversely, microbial dysbiosis-characterized by Lactobacillus depletion and a concomitant proliferation of anaerobic taxa, typical of Community State Type (CST) IV and Lactobacillus iners-dominated profiles-is strongly associated with chronic inflammation, oxidative stress, epithelial barrier compromise, and an elevated risk of CIN progression. This review synthesizes current evidence regarding the multifaceted interactions among the cervicovaginal microbiome, HPV pathogenesis, immune dysregulation, and oxidative stress in the etiology of CIN. Elucidating these intricate host-microbiome dynamics may precipitate the discovery of novel microbiome-derived biomarkers, ultimately informing innovative prophylactic and therapeutic interventions for cervical cancer.},
}

Humans
Female
*Microbiota
*Uterine Cervical Dysplasia/microbiology/virology/pathology
*Uterine Cervical Neoplasms/microbiology/virology/pathology
Papillomavirus Infections/complications/virology/microbiology
Dysbiosis/microbiology
*Vagina/microbiology/virology
Papillomaviridae
Lactobacillus

@article {pmid42043303,
year = {2026},
author = {Böswald, LF and Zeyner, A and Santo, MM and Wensch-Dorendorf, M and Sünder, A and Popper, B and Siegert, W},
title = {Feeding Laboratory Mice: Comparing a Standard Versus a Purified Diet - Marked Effects on Digestive Physiology.},
journal = {Journal of animal physiology and animal nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpn.70063},
pmid = {42043303},
issn = {1439-0396},
abstract = {Diet composition and processing have a major impact on its utilisation by the animal, as is known from farm and pet animal species. This includes effects on energy and nutrient digestibility, the intermediary metabolism, and the intestinal microbiome, with all the resulting impacts. For laboratory animals, data is scarce on influencing factors on diet digestibility. In experiments using special diets, either standard diets are used for the control group, or purified control diets. The aim of the present study was to compare a standard diet and a purified control diet (both pelleted) fed ad libitum to C57BL/6J mice and to investigate the potential effect on body weight development, feed conversion, energy and nutrient digestibility and indicators of intestinal fermentation (pH, short-chain fatty acids). Thus, 21 mice each were fed the standard diet (STD) and the purified diet (PD). Results showed a significantly higher apparent digestibility of gross energy and the crude nutrients in group PD (p < 0.001). The weight of the filled cecum and colon was significantly lower in group PD than STD (p < 0.001; p < 0.01). The pH of ingesta was significantly higher in stomach, cecum and colon of group PD (p < 0.0001), likely influenced by the significantly lower concentration of total short-chain fatty acids measures in cecum and colon of PD mice. The high apparent digestibility of the PD implied a lower influx of fermentable substrate into the hindgut, resulting in lower concentrations of microbial metabolites and altered pH milieu.},
}

@article {pmid42043563,
year = {2026},
author = {Chatterjee, S and Dutta, S and Ghosh, J and Saha, S and Mondal, M and Sarkar, J and Mondal, N and Ghosh, W},
title = {Warming responses, antibiosis potentials, and ecological implications of cryo-adapted copiotrophs from a Trans-Himalayan lake-desert ecosystem.},
journal = {Archives of microbiology},
volume = {208},
number = {7},
pages = {},
pmid = {42043563},
issn = {1432-072X},
support = {Intramural Faculty Grant//Bose Institute/ ; },
}

@article {pmid42043564,
year = {2026},
author = {Niu, YJ and Liu, LB and Yang, ZD and Xu, CJ and Zhao, TK and Chen, LL and Wang, QQ and Sun, B and Kim, S},
title = {The antimicrobial arsenal of endophytes in Lilium pumilum: active components of Fusarium tricinctum and antifungal mechanisms.},
journal = {Archives of microbiology},
volume = {208},
number = {7},
pages = {},
pmid = {42043564},
issn = {1432-072X},
support = {No. 22267011//National Natural Science Foundation of China/ ; 2023-RC-43//The project of the Bureau of Science and Technology of Lanzhou/ ; Y20220198//The Science and Technology Plan Project of Wenzhou, China/ ; 2025CXZX-608//The Gansu Provincial Department of Education: Graduate Student 'Innovation Star' Project/ ; No. 2022CYZC-29//The Industrial Support Plan Project of Colleges and Universities in Gansu Province/ ; },
mesh = {*Fusarium/isolation & purification/metabolism/physiology/chemistry ; Botrytis/drug effects ; *Endophytes/isolation & purification/metabolism/chemistry/physiology ; *Lilium/microbiology ; Plant Diseases/microbiology/prevention & control ; Rhizoctonia/drug effects ; *Antifungal Agents/pharmacology ; Soil Microbiology ; Rhizosphere ; Ascomycota/drug effects ; Antibiosis ; Hypocreales ; },
abstract = {The microbiome of Lilium pumilum represents a valuable resource for developing sustainable biocontrol strategies. This study investigated the potential of these microorganisms to serve as major plant pathogen-antagonistic strains. In this study, 38 strains (18 fungi and 20 actinobacteria) were isolated from L. pumilum and its rhizosphere soil. Among these, the endophytic fungus Z-SD-LJ-2 (Fusarium tricinctum) exhibited remarkable broad-spectrum antifungal activity against five tested plant pathogens, with inhibition rates of 68.07-89.42% and half maximal effective concentration (EC50) values of 16.58-30.97 µg mL[- 1]. Notably, its performance surpassed the commercial fungicide azoxystrobin against Fusarium oxysporum and Botrytis cinerea. Concurrently, the rhizosphere-derived strain Z-SDTR-2 (Purpureocillium lilacinum) demonstrated potent inhibition against Rhizoctonia solani, Sclerotinia sclerotiorum, and Botrytis cinerea, with all inhibition rates exceeding 80% and EC50 values of 17.17-21.80 µg mL[- 1]. Activity-guided isolation from Z-SD-LJ-2 led to the identification of enniatin B as the most active compound, exhibiting EC50 values of 13.78-26.81 µg mL[- 1]. Further studies revealed that enniatin B induces apoptosis in the pathogens by triggering reactive oxygen species (ROS) accumulation and causing mitochondrial dysfunction. In pot experiments, the fermentation broth of Z-SD-LJ-2 (2 × 10[3] mg L[- 1]) effectively controlled lily wilt, reducing the disease index to 30% (14.3% lower than azoxystrobin) and achieving a preventive efficacy of 72.6% (18% higher than the control). Additionally, the treatment promoted lily growth, increasing plant height by 4.4% and stem thickness by 8.71% compared to the control, underscoring its dual-function potential as a novel, effective biopesticide for sustainable agricultural practices.},
}

*Fusarium/isolation & purification/metabolism/physiology/chemistry
Botrytis/drug effects
*Endophytes/isolation & purification/metabolism/chemistry/physiology
*Lilium/microbiology
Plant Diseases/microbiology/prevention & control
Rhizoctonia/drug effects
*Antifungal Agents/pharmacology
Soil Microbiology
Rhizosphere
Ascomycota/drug effects
Antibiosis
Hypocreales

@article {pmid42043853,
year = {2026},
author = {Pucci, N and Mende, DR},
title = {bifidoAnnotator: fine-grained annotation of bifidobacterial glycoside hydrolases for human milk glycan utilization.},
journal = {Microbial genomics},
volume = {12},
number = {4},
pages = {},
pmid = {42043853},
issn = {2057-5858},
mesh = {Humans ; *Milk, Human/metabolism/microbiology ; *Glycoside Hydrolases/genetics/metabolism ; *Polysaccharides/metabolism ; *Bifidobacterium/genetics/enzymology/metabolism ; *Molecular Sequence Annotation/methods ; Bacterial Proteins/genetics/metabolism ; Software ; },
abstract = {Human milk glycan (HMG) metabolism, especially by bifidobacteria, is crucial for infant gut colonization and healthy microbiome development. Bifidobacterial species and even strains are highly variable in their ability and in their enzymatic repertoire for HMG metabolism. The enzymes involved in HMG metabolism often have many non-HMG-related homologues, necessitating fine-grained annotation for accurate assessment of bifidobacterial HMG metabolic capabilities. However, current annotation tools provide only broad glycoside hydrolase (GH) (sub)family classifications. Here, we present bifidoAnnotator, a tool for fine-grained annotation and visualization of bifidobacterial GH genes involved in HMG utilization. bifidoAnnotator leverages MMseqs2 (Many-against-Many sequence searching) to map protein sequences against a manually curated database of over 22,000 bifidobacterial GH proteins, organized into 13 families and 108 functional clusters, each assigned a validation status (i.e. experimentally validated, putative or hypothetical). The tool performs hierarchical annotation at family and cluster levels, identifying consistently annotated protein variants rather than just broad family assignments, and generates publication-ready heatmaps for comparative analysis. Benchmarking on a gold standard dataset demonstrated that bifidoAnnotator has superior performance (95.9% precision, 100% recall) compared with six established tools and is an order of magnitude faster than the most accurate competitor. bifidoAnnotator's superior performance and computational efficiency represent a meaningful advance in high-throughput genomic annotation workflows, enabling detailed characterization of strain-level functional diversity in bifidobacterial HMG metabolism.},
}

Humans
*Milk, Human/metabolism/microbiology
*Glycoside Hydrolases/genetics/metabolism
*Polysaccharides/metabolism
*Bifidobacterium/genetics/enzymology/metabolism
*Molecular Sequence Annotation/methods
Bacterial Proteins/genetics/metabolism
Software

@article {pmid42043859,
year = {2026},
author = {Patel, RA and Harke, SN},
title = {A decade of evidence linking gut microbiome dysbiosis to depression: a computational meta-analysis of mechanistic pathways: 2014-2024.},
journal = {The world journal of biological psychiatry : the official journal of the World Federation of Societies of Biological Psychiatry},
volume = {},
number = {},
pages = {1-28},
doi = {10.1080/15622975.2026.2660311},
pmid = {42043859},
issn = {1814-1412},
abstract = {OBJECTIVES: The gut microbiome-gut-brain axis (MGBA) has been associated in the pathophysiology of depression; however, the expanding literature remains fragmented across metabolic signalling, immune-inflammatory pathways, stress physiology and dysbiosis outcomes.

METHODS: Abstracts were retrieved from bibliographic databases (Lens.org, PubMed, DOAJ, Europe PMC) for studies published between 2014 and 2024 investigating associations between the gut microbiome and depression using 16S rRNA sequencing. Following text preprocessing, Latent Dirichlet Allocation (LDA) was applied to identify latent thematic topics. Topic proportions were subsequently embedded using principal component analysis (PCA), t-distributed stochastic neighbour embedding (t-SNE), and uniform manifold approximation and projection (UMAP).

RESULTS: Topic modelling revealed distinct interconnected thematic domains within the gut microbiome depression literature, encompassing metabolic and short chain fatty acid pathways, immune inflammatory mechanisms, stress and hypothalamic pituitary adrenal (HPA) axis regulation, probiotic and interventional work, microbial diversity and compositional metrics, neurochemical and neuroplasticity, developmental cohorts, and sequencing- or methodology-focused research.

CONCLUSIONS: Computational synthesis indicates that research on the gut microbiome depression axis is structured around multiple convergent mechanistic themes. This thematic landscape highlights dominant areas of mechanistic focus, providing a conceptual framework to guide future experimental design, mechanistic validation and translational research.},
}

@article {pmid42043941,
year = {2026},
author = {Qu, W and Shi, X and Xu, X and Liu, C and Ding, L and Song, M and Xu, Z and Xu, Y and Mo, F and Ruan, J and Timko, MP and Fan, L and Zheng, S and Jiang, W and Wang, Y and Shen, Y},
title = {BACON: decoding the dynamic social networks of complex microbial communities at single-cell resolution.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {2},
pages = {},
pmid = {42043941},
issn = {1477-4054},
support = {82402729//National Natural Science Foundation of China/ ; 32200073//National Natural Science Foundation of China/ ; 32250710678//National Natural Science Foundation of China/ ; LQ23H200003//Zhejiang Provincial Natural Science Foundation of China/ ; 2021R01012//Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang/ ; 2024C03005//Pioneer' R&D programs of Zhejiang Province/ ; 2024SSYS0022//Key Research and Development Program of Zhejiang/ ; LR23H200002//Zhejiang Provincial Natural Science Foundation for Distinguished Young Scholar/ ; },
mesh = {*Quorum Sensing ; Humans ; *Single-Cell Analysis ; *Gastrointestinal Microbiome ; *Microbiota ; Escherichia coli/genetics ; Bacillus subtilis/genetics ; *Computational Biology/methods ; Pseudomonas aeruginosa/genetics ; },
abstract = {Microbial communities function as dynamic societies where intercellular communication governs collective behaviors. However, mapping these interaction networks has remained a fundamental challenge in microbiology. This study aims to decode the social networks of complex bacterial communities at single-cell resolution by developing BACON, a computational framework that infers quorum sensing-mediated communication from single-microbe transcriptomic data. The approach combines a curated database of signaling systems with a statistical model that quantifies communication strength through coordinated expression of signal synthesis and receptor genes. Validation in model systems demonstrated BACON's precision in reconstructing density-dependent communication trajectories in Bacillus subtilis and capturing rapid network reorganization in Escherichia coli under antibiotic stress, revealing distinct sender-receiver subpopulations. Applied to human gut microbiomes, BACON unveiled diurnal fluctuations in cross-species signaling that transcend enterotype boundaries and uncovered conserved metabolic specialization in signal-responsive bacteria. In a clinical context, analysis of an ICU patient's gut microbiome revealed how Pseudomonas aeruginosa establishes a self-reinforcing communication circuit that upregulates virulence pathways. This work provides a unified framework for analyzing bacterial social interactions across diverse ecosystems. It opens new avenues for understanding microbial sociology, combating antimicrobial resistance, and engineering synthetic communities.},
}

*Quorum Sensing
Humans
*Single-Cell Analysis
*Gastrointestinal Microbiome
*Microbiota
Escherichia coli/genetics
Bacillus subtilis/genetics
*Computational Biology/methods
Pseudomonas aeruginosa/genetics

@article {pmid42044092,
year = {2026},
author = {Bloemendaal, M and Mulder, D and Gudden, J and Heikamp-de Jong, I and Ioannou, A and Belzer, C and Emile Natasha, E and Edwin Thanarajah, S and Aatsinki, AK and van Gelder, MMHJ and Arias Vasquez, A},
title = {Development of the gut microbiota throughout the first year of life and its association with socio-emotional development into childhood.},
journal = {Developmental neuroscience},
volume = {},
number = {},
pages = {1-27},
doi = {10.1159/000552189},
pmid = {42044092},
issn = {1421-9859},
abstract = {Introduction Early life is a critical window for the development of many bodily systems, including the gut microbiota and the central nervous system, that are inter-connected through the gut-brain-axis. These early life gut-brain-axis connections are often studied through cross-sectional cohorts, limiting insights into temporal developmental trajectories. This longitudinal cohort study assessed whether gut microbial development over the first year of life is associated with socio-emotional development into childhood. Methods The PRIDE (PRegnancy and Infant DEvelopment) BIOME study (n=81, n=42 males) is a focus cohort within the larger prospective PRIDE Study. Gut microbiome was measured 5 times throughout the first year of life (at 2, 4, 6, 9 and 12 months through V4 16S rRNA sequencing) and socio-emotional development 8 times over 4.5 years, between 6 months and 5 years through the Ages and Stages Questionnaire: Social-Emotional (ASQ-SE). We related the development of the gut microbiota of infants throughout their first year of life with their socio-emotional development into childhood, the latter modelled as a slope per individual (ASQ slope). We assessed effects of time, ASQ slope and its interaction with time on microbial community measures alpha and beta diversity, as well as taxonomy, using linear mixed-effects models and PERMANOVA, correcting for sex, birth weight, gestational age and sequencing depth. Results Expected developmental patterns on the gut microbiota over the first year of life were observed, including increased alpha diversity and clustering of beta diversity before and after solid food introduction. Interestingly, ASQ slope was a significant predictor of beta diversity (F(1,394)=25.90, p=0.001) and Bifidobacterium abundance across the first year of life (b= -0.745, SE= 0.24, pFDR= 0.023). Moreover, we observed a temporal association between ASQ slope and Eggerthella abundance (ASQ slope × timepoint interaction, b=0.709, SE=0.21, pFDR=0.009). That is, Eggerthella abundance decreased across the group, but not in "late concern" infants, with concern about socio-emotional development at more recent timepoints. Discussion This study shows that genera Bifidobacterium and Eggerthella, known to be altered in mental health conditions such as autism spectrum disorder and depression, are already linked to socio-emotional development during early life. Hence, this work contributes to the identification of gut microbial candidates relevant for preventive screening of healthy gut-brain development and microbiota-targeted interventions.},
}

@article {pmid42044128,
year = {2026},
author = {Zhou, Y and Trujillo-González, A and Nicol, S and Huerlimann, R and Sarre, SD and Gleeson, D},
title = {Diet and gut microbiome of skipjack tuna (Katsuwonus pelamis) as indicators of environmental changes.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0346882},
pmid = {42044128},
issn = {1932-6203},
mesh = {Animals ; *Tuna/microbiology/physiology ; *Gastrointestinal Microbiome ; *Diet ; Pacific Ocean ; *Climate Change ; Ecosystem ; Food Chain ; },
abstract = {Understanding the relationship between environmental changes and marine ecosystem dynamics is crucial, especially under the influence of climate events such as the El Niño Southern Oscillation (ENSO). The diet and gut microbiome of marine predators have the potential to efficiently, timely, and reliably indicate impacts of environmental and ecosystem changes, especially with the assistance of high-throughput sequencing (HTS) technology. This study investigated the gut content and microbiome of skipjack tuna (Katsuwonus pelamis) collected in the central Pacific Ocean during a transitional period of ENSO phases, shifting from a strong La Niña phase to a weak El Niño phase, aiming to evaluate the impacts of ENSO and other environmental factors on marine food webs and microbiome dynamics of skipjack tuna. While prey diversity was unaffected by ENSO events, skipjack tuna exhibited high diversity and opportunistic foraging patterns, with fish as the primary prey. In contrast, gut microbiome diversity was affected by ENSO events and Southern Oscillation Index (SOI). Five microbiome families (Fusobacteriaceae, Bacillaceae, Propionibacteriaceae, Beijerinckiaceae, and Comamonadaceae), which are associated with immune system functionality and nutritional provisioning of the host, displayed the most significant abundance changes between ENSO phases. A random forest model showed potential for ENSO phase classification based on the abundances of these five families, achieve high accuracy in internal validation, though the performance of external validation was mixed due to storage and sampling period differences. This study highlights the potential of skipjack tuna gut microbiome as indicators of rapid environmental changes, while acknowledging that the short sampling period requires longer-term validation across multiple ENSO cycles.},
}

Animals
*Tuna/microbiology/physiology
*Gastrointestinal Microbiome
*Diet
Pacific Ocean
*Climate Change
Ecosystem
Food Chain

@article {pmid42044527,
year = {2026},
author = {Rabasco, JT and Bolyen, E and Caporaso, JG and Sapers, H and Callahan, BJ},
title = {Identify contaminants with decontam on the QIIME 2 Framework.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0126125},
doi = {10.1128/mra.01261-25},
pmid = {42044527},
issn = {2576-098X},
abstract = {Here, we present the integration of the decontam method for contaminant identification and a supplemental approach for identifying the source of contaminants in sequencing data within the QIIME 2 Framework for microbiome data science. We demonstrate its use in a tutorial based on the QIIME 2 "Moving Pictures Tutorial" data.},
}

@article {pmid42044645,
year = {2026},
author = {Shoemark, A and Johnson, ED and Shuttleworth, M and Schwiening, M and Hull, R and Stobo, J and Abo-Leyah, H and Finch, S and Pollock, J and Huang, JTJ and Richardson, H and Perea, L and McIntosh, E and Cant, E and Galloway, R and Choi, H and de Soyza, A and Spinou, A and Ringshausen, FC and Lorent, N and Mallia, P and Johnston, SL and Gierlinski, M and Goeminne, P and Loebinger, MR and Hua Gao, Y and Chotirmall, SH and Dhar, R and Haworth, C and Altenburg, J and Blasi, F and Polverino, E and Shteinberg, M and Strickson, S and Cipolla, D and Teper, A and Fernandez, C and Shih, VH and Mange, K and Singanayagam, A and Aliberti, S and Sibila, O and Long, MB and Chalmers, JD},
title = {Azurocidin-1 as a mediator of bronchiectasis severity, epithelial defence, and target of dipeptidyl peptidase-1 inhibition: an international, multicohort study.},
journal = {The Lancet. Respiratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/S2213-2600(25)00334-0},
pmid = {42044645},
issn = {2213-2619},
abstract = {BACKGROUND: Dipeptidyl peptidase-1 (DPP1) inhibitors prevent the activation of neutrophil serine proteases and reduce exacerbations in people with bronchiectasis. We previously identified a novel effect of DPP1 inhibitors in reducing the neutrophil pseudoenzyme azurocidin-1 (AZU1). The aim of this study was to investigate the role of AZU1 in the pathophysiology of bronchiectasis.

METHODS: Sputum AZU1 concentrations were analysed in multiple cohorts. These consisted of two observational cohorts of patients with bronchiectasis (EMBARC BRIDGE cohort 1 and cohort 2) and a cohort of patients with chronic obstructive pulmonary disease (COPD; TARDIS COPD cohort) to correlate AZU1 with disease severity and exacerbations. A rhinovirus challenge study was used to investigate AZU1 concentrations during experimental exacerbation in COPD, people who smoke, and controls. A post-hoc analysis of the phase 2 WILLOW trial of brensocatib versus placebo was used to assess the effect of DPP1 inhibition on airway AZU1.

FINDINGS: Higher AZU1 sputum concentration was associated with increased bronchiectasis disease severity index (p<0·0001), decreased percentage predicted forced expiratory volume in 1 second (r=-0·4662, p<0·001), and increased exacerbation frequency (p<0·0019; EMBARC cohort 1, n=197). AZU1 was associated with radiological severity (Reiff score), symptoms (quality of life bronchiectasis respiratory symptom score), and bacterial infection (sputum microbiology and 16S microbiome alpha diversity; highest levels of AZU1 were found in airway samples with Pseudomonas aeruginosa; p<0·0001; EMBARC cohort 2, n=144). Bronchiectasis patients with bacterial and viral exacerbations had increased concentrations of AZU1 (p=0·0003; n=96). These findings were extended to COPD, in which AZU1 was related to COPD severity (COPD cohort, n=101), and in patients with COPD challenged with rhinovirus A16, AZU1 was increased at day 9 post-challenge (p<0·001; n=9). In-vitro AZU1 impaired ciliary function and epithelial integrity, suggesting a mechanism by which AZU1 drives disease pathogenesis. In a post-hoc analysis of the WILLOW trial, AZU1 was the most downregulated protein with brensocatib treatment (brensocatib 10 mg, n=71; brensocatib 25 mg, n=73; and placebo, n=71). Over 24 weeks, AZU1 was significantly reduced by DPP1 inhibition (p<0·0001).

INTERPRETATION: AZU1 was identified as a novel marker of disease severity in bronchiectasis, associated with bacterial infection and exacerbation, and targeted by DPP1 inhibition.

FUNDING: EMBARC3 and Insmed.},
}

@article {pmid42044680,
year = {2026},
author = {Maitan Santos, B and Estellé, J and Ramayo-Caldas, Y and Chadi, S and Barone, M and Chain, F and Kropp, C and Bridigi, P and Langella, P and Martín, R},
title = {Sex modulates the long-term effects of delivery mode on microbiota-gut barrier crosstalk and colitis susceptibility in mice.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2658276},
doi = {10.1080/19490976.2026.2658276},
pmid = {42044680},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Female ; Male ; Mice ; Disease Susceptibility ; *Colitis/microbiology ; Disease Models, Animal ; Mice, Inbred C57BL ; Sex Characteristics ; Sex Factors ; *Cesarean Section/adverse effects ; *Intestinal Mucosa/microbiology ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Sexual dimorphism and mode of delivery are key determinants of gut physiology and microbiota development and may differentially affect predisposition to gut-related diseases. Cesarean section delivery markedly shapes early-life microbiota, predisposing individuals to higher risk of immune and metabolic comorbidities later in life. Although both sex and delivery mode are known to influence gut barrier-microbiota crosstalk, whether delivery mode modulates or counter-regulates sex-specific features of this interaction remains, to our knowledge, largely unexplored. Here, we investigated how sex impacts gut barrier-microbiota crosstalk shaped by delivery mode across development until adulthood by reanalyzing existing data. Using a preclinical mouse model, we combined gut barrier analyses with differential abundance and co-occurrence network approaches (LinDA and NetMoss). We found that the impact of CSD on gut barrier-microbiota crosstalk is partially dependent on sex and life stage. During the first days of life, delivery mode dictates immune imprinting and microbial network topology, with only limited sex effects. However, trajectories diverged with age, with CSD males exhibiting colitis reoccurrence in adulthood. By applying integrative strategies to stratify data by sex and development, our study uncovers short- and long-term sex-dependent gut barrier and microbial signatures. These findings reveal that delivery mode might program sex-specific host-microbiota trajectories with consequences for gut health and disease susceptibility, highlighting the need to consider sex and early-life microbial imprinting in future microbiome-targeted interventions.},
}

Animals
*Gastrointestinal Microbiome/physiology
Female
Male
Mice
Disease Susceptibility
*Colitis/microbiology
Disease Models, Animal
Mice, Inbred C57BL
Sex Characteristics
Sex Factors
*Cesarean Section/adverse effects
*Intestinal Mucosa/microbiology
Bacteria/classification/genetics/isolation & purification

@article {pmid42044685,
year = {2026},
author = {Kooima, P and Oesterle, DA and Hematti, Y and Kay, DM and McFarlane, K and Roberts, JL},
title = {Gut microbiota depletion alters functional recovery and bone healing following fracture in mice.},
journal = {Bone},
volume = {},
number = {},
pages = {117907},
doi = {10.1016/j.bone.2026.117907},
pmid = {42044685},
issn = {1873-2763},
abstract = {Bone fracture pain evolves dynamically with tissue repair, yet current analgesic strategies are limited by adverse effects and concerns regarding impaired healing. The gut microbiome is an established regulator of pain and inflammation; however, its contribution to post-fracture recovery remains unclear. We tested whether antibiotic-induced microbiota depletion alters functional recovery and behavior after femoral fractures. Young female C57BL/6J mice received a broad-spectrum oral antibiotic cocktail or control water for two weeks prior to femoral fracture and were assessed longitudinally over 28 days after fracture. Microbiota depletion was associated with prolonged deficits in hindlimb loading and zone clearance performance, and continuous home-cage monitoring revealed decreased vertical rearing activity and voluntary wheel-running, collectively indicating sustained functional and motivational impairment. Despite a hypoinflammatory systemic and intestinal phenotype, microbiota-depleted mice exhibited elevated ipsilateral lumbar DRG expression of Ngf and Cxcl1 at Day 7 post-fracture alongside suppressed DRG Il10. NGF immunoreactivity was also elevated in the ipsilateral lumbar DRG of microbiota-depleted mice at the same timepoint. Microarchitectural analysis of fracture callus were suggestive of delayed secondary fracture healing. Together, these findings indicate that antibiotic-induced microbiota depletion was associated with altered inflammatory, behavioral, and skeletal responses after fracture. These results identify the gut microbiome as a potential contributor to the integrated pain-healing response to skeletal injury.},
}

@article {pmid42044842,
year = {2026},
author = {Al-Awadi, AA and Grove, JI and Bawden, S and Vijay, A and Valdes, AM and Gowland, P and Taylor, MA and Aithal, GP},
title = {The effect of a two-week low glycaemic index, higher fibre diet versus high glycaemic index diet on body composition, ectopic lipids, inflammatory biomarkers, gastrointestinal hormones and gut microbiota in Metabolic dysfunction-associated Steatotic Liver Disease (MASLD): A pilot randomized cross-over study.},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {103306},
doi = {10.1016/j.clnesp.2026.103306},
pmid = {42044842},
issn = {2405-4577},
abstract = {Metabolic dysfunction-Associated Steatotic Liver Disease (MASLD) is a global health concern. Low glycaemic index (LGI) diets, which tend to be naturally higher in dietary fibre, may reduce liver fat, blood glucose, and gut microbiota imbalance arresting MASLD progression. We hypothesized that in patients with MASLD, an LGI diet, meeting estimated energy requirements, would reduce liver fat more than a high GI (HGI) diet, despite matched energy (isoenergetic) and macronutrient content. To test this, a 2×2 randomized cross-over trial was undertaken involving 7 participants with MASLD randomised (1:1 ratio) to a 2-week either high GI (HGI) or LGI diet followed by a 4-week wash-out period and then the opposite diet. The impact of the LGI diet on liver fat content, measured using Magnetic Resonance Spectroscopy ([1]H-MRS) liver-related blood biomarkers, appetite (using subjective visual analogue scales) and gut microbiome composition was identified. Relative liver fat fraction was markedly reduced following the LGI diet (8.57%).Observations in the LGI group coincided with changes in blood glycaemic biomarkers, including a significant reduction in HOMA-IR (-1.78, p=0.043). Additionally, the LGI diet resulted in significant reductions in body weight (-1.2 kg, p=0.018) and body mass index (-0.38 Kg/m[2], p=0.017), as well as increased pre-meal appetite scores during the middle of the diet period and decreased interleukin 6; IL-6 (-0.9 pg/mL) and glucagon (-13.7 pg/mL) levels (all p<0.05). In agreement with previous work in healthy participants, this study suggests that LGI diets reduce liver fat in patients with MASLD and may be an important factor in preventative care. REGISTRATION: This trial was registered on the website of ClinicalTrials.gov, number NCT04415632.},
}

@article {pmid42044997,
year = {2026},
author = {Sanyaolu, L and Ahmed, H and Santer, M and Jones, S and Hayward, G},
title = {Update to the management of recurrent urinary tract infections in women aged 16 years and older.},
journal = {Drug and therapeutics bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1136/dtb.2025.000042},
pmid = {42044997},
issn = {1755-5248},
abstract = {Recurrent urinary tract infections (rUTIs) are a burdensome condition affecting approximately 6% or 1.7 million women in the UK. UTIs are also a common reason for antibiotic use, with UK data demonstrating that they are the second most common reason for antibiotic prescribing after respiratory tract infections. UTIs also result in significant healthcare costs, with hospital admissions alone estimated to have cost the National Health Service in England over £600 million from 2023 to 2024. This review provides an up-to-date overview of the management of rUTIs, focusing on the updated 2024 National Institute for Health and Care Excellence guidance, which recommends a stepwise approach starting with behavioural measures, then progressing to non-antibiotic and finally antibiotic prevention. It also compares the guidance with international recommendations and outlines the current evidence on pathogenesis, diagnostic approaches and treatment options, including behavioural measures, non-antibiotic interventions (eg, vaginal oestrogen and methenamine hippurate) and antibiotic prophylaxis. Key challenges in primary care are discussed, such as diagnostic uncertainty, patient dissatisfaction and antimicrobial resistance (AMR). Emerging research in point-of-care testing, the urinary microbiome and novel therapies is also highlighted. This review aims to support safe prescribing, improve patient satisfaction and mitigate AMR by promoting antimicrobial and diagnostic stewardship in the management of rUTIs.},
}

@article {pmid42045370,
year = {2026},
author = {Prasoodanan Pk, V and Maistrenko, OM and Fullam, A and Mende, DR and Kartal, E and Coelho, LP and Spang, A and Bork, P and Schmidt, TSB},
title = {Author Correction: Unbinned contigs expand known diversity in the global microbiome.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41564-026-02354-y},
pmid = {42045370},
issn = {2058-5276},
}

@article {pmid42045408,
year = {2026},
author = {Kutuzova, S and Piera Líndez, P and Danielsen, LS and Nielsen, KN and Olsen, NS and Riber, L and Gobbi, A and Forero-Junco, LM and Erdmann Dougherty, P and Westergaard, JC and Browne, PD and Christensen, S and Hestbjerg Hansen, L and Nielsen, M and Nybo Andersen, J and Rasmussen, S},
title = {Improving metagenome binning by integrating intrinsic features and taxonomy.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {42045408},
issn = {1546-1696},
support = {NF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF21SA0072102//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 7076-00129B//Innovationsfonden (Innovation Fund Denmark)/ ; },
abstract = {A common procedure for studying the microbiome is binning the sequenced contigs into metagenome-assembled genomes. State-of-the-art binning methods use coabundance and sequence-based motifs such as tetranucleotide frequencies, whereas taxonomic labels derived from alignment based classification have not been widely used. Here we propose TaxVAMB, a metagenome binning tool based on semisupervised bimodal variational autoencoders, combining tetranucleotide frequencies and contig coabundances with taxonomic information. TaxVAMB outperformed all other binners on CAMI2 human microbiome datasets, returning on average 29% more high-quality assemblies than the next best binner, and performed on par with the best binners on short-read datasets. On a human gut long-read dataset, TaxVAMB recovered 29% more high-quality bins. In a typical single-sample setup, TaxVAMB on average returns 83% more high-quality bins compared to VAMB. Lastly, TaxVAMB binned incomplete genomes better than any other tool, returning on average 300% more high-quality bins of incomplete genomes than the next best binner.},
}

@article {pmid42045433,
year = {2026},
author = {Reisinger, SN and Kong, G and van de Garde, N and Muhammad, A and Adithya, P and Lu, D and Kiridena, P and Gubert, C and Dabscheck, G and Payne, JM and Hannan, AJ},
title = {Gut microbiome alterations are sex-dependently associated with brain abnormalities in a mouse model of Neurofibromatosis type I.},
journal = {Molecular psychiatry},
volume = {},
number = {},
pages = {},
pmid = {42045433},
issn = {1476-5578},
abstract = {Neurofibromatosis type 1 (NF1) is a genetic condition presenting with variable symptomatology, however most individuals will demonstrate cognitive and behavioural difficulties, including autism. Using a heterozygous germline knockout mouse model of NF1 (Nf1 +/-), we performed in-depth behavioural evaluations encompassing learning and memory, stereotypy, social interaction, anxiety- and depression-like behaviour. Anatomical and functional studies of the brain and gastrointestinal tract were followed by the first investigation of gut microbiota composition (via full-length 16S rRNA sequencing) in a Nf1 +/- mouse model. The cognitive and autism-like behavioural phenotype seen in Nf1 +/- mice was accompanied by a striking increase in relative brain size which is highly relevant to clinical NF1. Furthermore, brain size was correlated with behaviour, supporting a potential mechanistic link. Nf1 +/- mice showed significant alterations in gut microbiota composition vs. Nf1 +/+ wild-type controls, with males additionally showing significant changes to species abundance of the Clostridium and Blautia genera, and the Lachnospiraceae family, findings which partially overlap with those in preclinical and clinical autism. Composition of associated functional pathways was not globally altered, however +/- mice showed significant changes in a pyrimidine deoxynucleotide biosynthesis pathway. In male Nf1 +/- mice, we also identified a genotype-specific host-microbial signature, pointing towards a mechanistic link between gut microbiome composition and brain size. These findings significantly expand our understanding of brain and behavioural abnormalities in this preclinical model of NF1 and, importantly, have uncovered the gut microbiome as a highly promising new area of research and a potential therapeutic target for these symptom clusters.},
}

@article {pmid42045512,
year = {2026},
author = {Moghadam, Z and Doraghi, M and Fallahizadeh, S and Badeenezhad, A and Alinehjad, N and Parseh, I},
title = {Enhanced phytoremediation of crude oil-contaminated soil using Cynodon dactylon with nutrient and mixed liquid suspended solids amendments.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-50261-3},
pmid = {42045512},
issn = {2045-2322},
support = {98065//Behbahan Faculty of Medical Sciences/ ; },
}

@article {pmid42045563,
year = {2026},
author = {Mai, H and Wang, Y and Zhu, Y and Zhao, Y and Chen, Y and Hoeher, L and Al-Maskari, R and Luo, J and Erturk, A},
title = {Whole-mouse immunolabeling at cellular resolution for comprehensive 3D atlases.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {42045563},
issn = {1750-2799},
abstract = {Mapping complex biological systems and tracking disease progression at high resolution across the entire mammalian body has remained technically challenging. Here, to address this, we present wildDISCO (immunolabeling of wild-type mice and DISCO clearing), a comprehensive protocol for whole-body immunolabeling, optical clearing and imaging of mice at cellular resolution using standard IgG antibodies. This protocol optimizes tissue permeabilization using cyclodextrin as a potent enhancer of cholesterol extraction and membrane permeabilization, enabling deep antibody penetration across all organs. We detail procedures for sample preparation, tissue decolorization and decalcification, whole-body immunostaining, clearing, and subsequent 3D imaging, virtual reality visualization and whole-mouse atlas construction. The method allows comprehensive mapping of neuronal, vascular, lymphatic and immune systems, as well as systemic studies in disease models, including cancer and microbiome-host interaction studies. We anticipate that wildDISCO will serve as a broadly applicable platform for generating whole-body cellular atlases, enabling systems-level investigations of health and disease. Only standard immunohistochemistry facilities are required, but successful implementation may require initial technical training, particularly for researchers with limited prior experience in tissue clearing or 3D imaging workflows. From start to finish, the procedure takes 4 weeks.},
}

@article {pmid42045628,
year = {2026},
author = {Snir, A and Schwarzman, P and Wainstock, T and Sheiner, E},
title = {Offspring long-term infectious morbidity following pregnancies with cervical cerclage.},
journal = {Archives of gynecology and obstetrics},
volume = {313},
number = {1},
pages = {},
pmid = {42045628},
issn = {1432-0711},
mesh = {Humans ; Female ; *Cerclage, Cervical/adverse effects/statistics & numerical data ; Pregnancy ; Retrospective Studies ; Adult ; Premature Birth/prevention & control ; Kaplan-Meier Estimate ; Proportional Hazards Models ; Infant, Newborn ; *Uterine Cervical Incompetence/surgery ; Incidence ; Young Adult ; },
abstract = {INTRODUCTION: Cervical cerclage is an acceptable procedure in women with cervical insufficiency and is known to be effective in the prevention of preterm delivery. However, limited data exist regarding long-term health outcomes among offspring exposed to cerclage during pregnancy. Since the presence of a foreign body during pregnancy may change the vaginal microbiome, we aimed to study whether a cervical cerclage is associated with long-term infectious morbidity of the offspring.

STUDY DESIGN: A retrospective population-based cohort study was performed at a tertiary medical center, including all singleton deliveries between the years 1991-2021. Long-term infectious morbidity was compared among offspring after pregnancies with and without cervical cerclage. The diagnoses of infectious morbidities were defined based on ICD-9 codes as recorded in community clinics and hospitalization files. A Kaplan-Meier survival curve was utilized to evaluate the cumulative incidence. A Cox proportional hazards model was used to control for confounders.

RESULTS: Out of 356,356 offspring included in the analysis, 0.4% (n = 1416) were following pregnancies with cervical cerclage. Unadjusted analyses demonstrated no significant difference in total infectious morbidity between the groups (OR 1.0, 95% CI 0.9-1.1; p = 0.369, Table 1). Kaplan-Meier analysis showed no difference in cumulative incidence (log-rank test P-value = 0.19, Fig. 1). In the primary analysis, cerclage was not associated with long-term infectious morbidity. However, in a secondary model, after adjustment for confounders including gestational age, obesity and diabetes, cerclage exposure was associated with a modest reduction in the risk of long-term infectious morbidity (adjusted HR 0.9, 95% CI 0.87-0.99, p = 0.036).

CONCLUSION: In this large population-based cohort, cervical cerclage was not associated with increased long-term infectious morbidity in offspring. A modest association with reduced infectious morbidity was observed after adjustment for confounding factors. These findings should be interpreted cautiously given the observational design and potential residual confounding.},
}

Humans
Female
*Cerclage, Cervical/adverse effects/statistics & numerical data
Pregnancy
Retrospective Studies
Adult
Premature Birth/prevention & control
Kaplan-Meier Estimate
Proportional Hazards Models
Infant, Newborn
*Uterine Cervical Incompetence/surgery
Incidence
Young Adult

@article {pmid42045676,
year = {2026},
author = {Wood, GV and Liddicoat, C and Robinson, JM and Breed, MF},
title = {Restoring soil and sediment microbiomes in the Anthropocene.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42045676},
issn = {1740-1534},
abstract = {Soil and sediment microbiomes have a central role in biogeochemical cycling, climate regulation and ecosystem resilience. However, they are increasingly degraded by land use change, pollution and climate change. Despite their foundational roles in ecosystems, these microbiomes remain under-represented in ecosystem restoration science, practice and policy. Improving the integration of microbiomes across the restoration science-practice-policy nexus is essential for achieving more effective and resilient restoration outcomes. Without this, global restoration risks neglecting the microbial foundations of functional ecosystems and long-term resilience. In this Review, we synthesize the current state of knowledge of soil and sediment microbiome restoration. We describe the major anthropogenic stressors that are degrading these microbiomes, highlighting the linked and context-dependent nature of these impacts, and evaluate existing strategies to restore them. To improve restoration effectiveness, we propose a research workflow that encompasses baseline establishment, degradation diagnostics, designing and testing interventions, research methodology selection and best practice principles. We also outline key theoretical frameworks and propose future research priorities to help soil and sediment microbiome restoration to move towards a predictive, theory-led discipline.},
}

@article {pmid42045695,
year = {2026},
author = {da Silva, JB and Câmara, PEAS and Rosa, LH and Oliveira, VM},
title = {Disentangling bacterial diversity and biogeography in snow-covered regions.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {5},
pages = {},
pmid = {42045695},
issn = {1573-0972},
abstract = {UNLABELLED: This study investigated the bacterial diversity of snow-inhabiting microbial communities across multiple geographic locations, including Antarctic and temperate regions. Using high-throughput sequencing of the 16S rRNA gene from Antarctic snow samples and comparisons with publicly available datasets from other cold regions worldwide, we assessed patterns of taxonomic diversity and the influence of geographic and environmental factors on snow bacterial communities. Our results revealed that bacterial communities from Martel Inlet (King George Island) exhibited lower diversity compared to other Antarctic sites, likely influenced by the geographic characteristics. In contrast, snow microbial communities from temperate regions such as Austria, Quebec, and Iceland showed higher diversity, potentially driven by overlapping environmental conditions including temperature range, snow dynamics, and seasonal variability. Network analyses revealed distinct interaction patterns among regions, with more dynamic and competitive microbial networks observed in Maritime Antarctic environments, while continental snow ecosystems exhibited more compartmentalized and stable network structures. Overall, our findings highlight the combined influence of geographic distance and environmental conditions in shaping microbial diversity and ecological interactions in snow ecosystems across different regions of the globe.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11274-026-04918-w.},
}

@article {pmid42045813,
year = {2026},
author = {Lindstrøm, JC and Gjerdrum, HSV and Brynildsrud, OB and Tannæs, TM and Kristoffersen, AB and Ricanek, P and Leegaard, TM and Bjørnholt, JV and Jørgensen, SB and Tunsjø, HS and Olbjørn, C and Detlie, TE and Jahnsen, J and Kristensen, VA and Høivik, ML and Hov, JR and Moen, AE and , },
title = {Exploring alterations in the gut resistome in medically treated inflammatory bowel disease patients.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05101-9},
pmid = {42045813},
issn = {1471-2180},
}

@article {pmid42045958,
year = {2026},
author = {Huang, J and Chen, Z and Wang, M and Yang, C and Wang, A and Chen, Y},
title = {Efficacy and safety of fecal microbiota transplantation in reducing recurrence of colorectal adenomas after endoscopic resection: study protocol for a multicenter, open-label, randomized, no-treatment-controlled trial.},
journal = {Trials},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13063-026-09740-1},
pmid = {42045958},
issn = {1745-6215},
support = {C2401027//Shenzhen Medical Research Fund/ ; },
abstract = {BACKGROUND: Endoscopic resection is the standard treatment for colorectal adenoma (CRA), a key precursor to colorectal cancer (CRC). However, a high rate of recurrence post-procedure poses a significant challenge for long-term CRC prevention. Growing evidence suggests gut microbial dysbiosis contributes to adenoma development and recurrence. This trial will test the hypothesis that restoring a healthy gut microbiome with fecal microbiota transplantation (FMT) can reduce the recurrence of CRA after endoscopic resection.

METHODS: This protocol describes a multicenter, open-label, randomized, no-treatment-controlled trial that will enroll 466 participants with CRA following endoscopic resection. Participants will be randomly assigned in a 1:1 ratio to receive either FMT or no treatment (control). The FMT intervention consists of an initial colonoscopic infusion and oral capsules, followed by oral maintenance capsules at months 3, 6, and 9. The primary outcome is the rate of CRA recurrence at the 12-month follow-up colonoscopy. Key secondary outcomes include the incidence of all polypoid lesions, changes in the gut and mucosal microbiota composition, the incidence of CRC, and a comprehensive assessment of adverse events to evaluate safety.

DISCUSSION: This trial is designed to provide high-quality evidence on the efficacy and safety of FMT for preventing CRA recurrence. The findings may support a novel, microbiome-based strategy for the secondary prevention of CRC and provide mechanistic insights into the role of the gut microbiota in colorectal carcinogenesis.

TRIAL REGISTRATION: ClinicalTrials.gov NCT06205862. Registered on 16 January, 2024. https://clinicaltrials.gov/study/NCT06205862.},
}

@article {pmid42045979,
year = {2026},
author = {Deng, Y and Chen, R and Gao, X and Wu, H and He, N and Hu, N and Zhang, W and Chen, L and Zheng, X and Jiang, J},
title = {Tissue-resident Limosilactobacillus reuteri modulates intratumoral arachidonic acid metabolism to enhance CD8[+] T cell-mediated anti-PD1 response.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-08170-6},
pmid = {42045979},
issn = {1479-5876},
}

@article {pmid42046041,
year = {2026},
author = {Thomas, LF and Panaretos, C and Scott, MA and Valeris-Chacin, R and Cook, WE},
title = {Distinct host-pathogen and microbiome responses of aoudad (Ammotragus lervia) and bighorn sheep (Ovis canadensis) following exposure to Mycoplasma ovipneumoniae with or without co-exposure to leukotoxigenic Pasteurellaceae.},
journal = {BMC veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12917-026-05375-1},
pmid = {42046041},
issn = {1746-6148},
}

@article {pmid42046057,
year = {2026},
author = {Hsu, CY and Abdelgawwad El-Sehrawy, AAM and Alshkarchy, SS and Abdul, AS and Ganesan, S and Gupta, PK and Sharma, R and Nayak, PP and Ebrahimpour, A and Khazaei, Y},
title = {Innovative approaches in the treatment of hematologic malignancies: the role of CRISPR-engineered microbiomes along the gut-immune axis in immunotherapy development.},
journal = {Cancer cell international},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12935-026-04316-0},
pmid = {42046057},
issn = {1475-2867},
}

@article {pmid42046285,
year = {2026},
author = {Miyamoto, S and Yoshimoto, S and Katsumata, N and Mutoh, N and Iwabuchi, N and Odamaki, T and Asaoka, D and Machida, S},
title = {Bifidobacterium longum BB536 is associated with improvements in gastrointestinal symptoms and odor-related metabolites in microbiota-defined subgroups of male athletes consuming a high-protein diet: exploratory randomized double‑blind placebo‑controlled trial.},
journal = {Journal of the International Society of Sports Nutrition},
volume = {23},
number = {1},
pages = {2664664},
doi = {10.1080/15502783.2026.2664664},
pmid = {42046285},
issn = {1550-2783},
mesh = {Humans ; Male ; Double-Blind Method ; *Gastrointestinal Microbiome ; *Probiotics/administration & dosage ; *Bifidobacterium longum ; Adolescent ; *Odorants ; Feces/microbiology/chemistry ; *Diet, High-Protein/adverse effects ; Young Adult ; Athletes ; Volatile Organic Compounds/analysis ; *Gastrointestinal Diseases ; Whey Proteins/administration & dosage ; },
abstract = {BACKGROUND: High‑protein diets are widely used by athletes but may disturb the gut environment and increase production of odor‑related metabolites. Probiotic supplementation has been proposed as a strategy to support gastrointestinal function under such dietary stress. This study aimed to explore the effects of Bifidobacterium longum BB536 on gastrointestinal symptoms, gut microbiota, and odor‑related metabolites in male athletes consuming a high‑protein diet.

METHODS: In an exploratory, randomized, double‑blind, placebo‑controlled trial, 60 healthy male athletes (mean age: 18.62 ± 0.75 years; mean BMI: 22.35 ± 1.80 kg/m[2]) consumed a whey protein supplement (70 g/day) together with either BB536 (46 billion CFU/day, as measured at the start of the intervention) or placebo for 4 weeks. Gastrointestinal symptoms, gut microbiota composition, skin‑emitted volatile compounds, and fecal metabolites were assessed. Subgroup analyses based on responder status and baseline enterotype were conducted post hoc to generate hypotheses regarding microbiota‑dependent responses.

RESULTS: In the overall cohort, no significant between‑group differences were observed across gastrointestinal outcomes, gut microbiota indices, or metabolite profiles. Within the BB536 group, diarrhea‑related scores improved from baseline. Post hoc analyses suggested that increases in Faecalibacterium were evident among responders. Enterotype‑based patterns also emerged: individuals with Ruminococcus‑dominant microbiota showed higher skin‑emitted short‑chain fatty acids after BB536 intake, whereas those with Faecalibacterium‑dominant microbiota exhibited reductions in odor‑related metabolites, including methyl mercaptan and ammonia. Corresponding fecal metabolite shifts were modest.

CONCLUSION: BB536 supplementation was associated with improvements in diarrhea‑related symptoms and odor‑related metabolites in specific microbiota‑defined subgroups. As these findings did not extend to the full cohort, they should be interpreted as exploratory and hypothesis‑generating. Baseline gut microbiota composition may influence probiotic responsiveness, warranting confirmatory trials with prespecified endpoints.},
}

Humans
Male
Double-Blind Method
*Gastrointestinal Microbiome
*Probiotics/administration & dosage
*Bifidobacterium longum
Adolescent
*Odorants
Feces/microbiology/chemistry
*Diet, High-Protein/adverse effects
Young Adult
Athletes
Volatile Organic Compounds/analysis
*Gastrointestinal Diseases
Whey Proteins/administration & dosage

@article {pmid42046303,
year = {2026},
author = {Sun, S and He, Y and Deng, Y and Wang, J},
title = {Urinary Microbiome Characteristics in Kidney Transplant Recipients and Their Clinical Implications: A Narrative Review.},
journal = {Annals of transplantation},
volume = {31},
number = {},
pages = {e952286},
doi = {10.12659/AOT.952286},
pmid = {42046303},
issn = {2329-0358},
mesh = {Humans ; *Kidney Transplantation/adverse effects ; *Microbiota ; Dysbiosis/microbiology ; *Urinary Tract/microbiology ; Graft Rejection/microbiology ; Transplant Recipients ; Urinary Tract Infections/microbiology ; *Urine/microbiology ; },
abstract = {High-throughput sequencing has overturned the long-standing "sterile urine" paradigm and revealed a low-biomass yet clinically informative urinary tract microbiota. In kidney transplant recipients, immunosuppression, perioperative instrumentation, and antibiotic exposure can reshape urinary microbial communities; however, reported signatures remain heterogeneous across cohorts and methodologies. This narrative review synthesizes evidence on: (1) baseline urobiome patterns and major determinants of inter-individual variability, (2) post-transplant drivers of dysbiosis, and (3) associations between urobiome dynamics and key transplant outcomes, including urinary tract infection (UTI), acute rejection (AR), and chronic allograft dysfunction such as interstitial fibrosis and tubular atrophy (IF/TA). Across studies, dysbiosis commonly manifests as reduced diversity, depletion of putatively protective taxa, and enrichment of opportunistic pathogens; several longitudinal cohort studies further suggest that microbiome shifts can precede clinical events, supporting a potential window for risk stratification and early surveillance. We also summarize translational research directions, including integration of urinary microbial profiles with host biomarkers and multi-omics readouts, as well as microbiome-sparing strategies (antimicrobial stewardship, targeted probiotics/synbiotics, and dietary modulation). Finally, we highlight methodological challenges unique to low-biomass urine samples - especially contamination control, negative controls, and transparent reporting - that are essential for improving reproducibility and enabling clinical implementation. This review aims to provide an up-to-date, clinically oriented synthesis of the post-transplant urobiome and to propose methodological and translational priorities for future research and implementation.},
}

Humans
*Kidney Transplantation/adverse effects
*Microbiota
Dysbiosis/microbiology
*Urinary Tract/microbiology
Graft Rejection/microbiology
Transplant Recipients
Urinary Tract Infections/microbiology
*Urine/microbiology

@article {pmid42046343,
year = {2026},
author = {Jiang, L and Li, T and Wu, J and Lau, HCH and Wong, CC and Zhou, X and Cheung, AHK and Wei, Q and Ren, J and Zhang, X and Li, Q and Nie, Y and Yu, J},
title = {Dietary nitrate drives gastritis by modulating gastric microbiota and metabolites.},
journal = {Cancer biology & medicine},
volume = {},
number = {},
pages = {},
doi = {10.20892/j.issn.2095-3941.2025.0679},
pmid = {42046343},
issn = {2095-3941},
support = {2023ZD0501400//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; 82472896//National Natural Science Foundation of China/ ; 3133344//Strategic Seed Funding Collaboration Research Scheme CUHK/ ; 3135509//Strategic Impact Enhancement Fund CUHK/ ; 3134277//Impact Case for RAE CUHK/ ; },
abstract = {OBJECTIVE: Dietary nitrate has been increasingly recognized as a potential carcinogen associated with gastritis. In this study the mechanistic role of a high-nitrate diet (NaD) in driving gastritis was elucidated with a focus on modulation of the gastric microbiota composition and metabolomic profiles.

METHODS: Animals were randomly assigned to two dietary intervention groups using a C57BL/6 mouse model: a NaD containing 7.5% nitrate; or a standard normal diet (ND). Gastric microbiota composition was characterized based on full-length 16S rRNA sequencing and gastric metabolite profiles were analyzed using high-performance liquid chromatography-mass spectrometry (HPLC/MS). Finally, the roles of the microbiome and metabolites in gastritis development were validated using the human gastric epithelial cell line (GES-1), as well as conventional and germ-free mouse models.

RESULTS: NaD induced gastritis in conventional mice compared to ND-fed mice. In addition, NaD incited the infiltration of macrophages and neutrophils with elevated levels of inflammatory cytokine genes (IL-17a, Ccl20, Cxcl5, IL-6, and Ccl2). A significant shift in the composition of the gastric microbiota occurred with an increase in pathogenic bacteria (Enterococcus gallinarum, Prevotella timonensis, and Mycobacterium gordona) and a decrease in probiotics (Roseburia hominis, Clostriduim scindens, and Faecalibacterium prausnitzii). Furthermore, NaD induced alterations in the metabolic profile, marked by an elevated level of 5-hydroxyindoleacetate (5-HIAA), a key downstream metabolite of the tryptophan metabolic pathway. Notably, 5-HIAA also upregulated the levels of inflammatory cytokines in the human gastric epithelial GES-1 cell line. In addition, both E. gallinarum colonization and 5-HIAA exposure significantly increased inflammatory responses in conventional and germ-free mouse models.

CONCLUSIONS: NaD drives gastritis in mice by inducing gastric microbial dysbiosis and metabolomic dysregulation with elevated 5-HIAA.},
}

@article {pmid42046474,
year = {2026},
author = {Allaham, S and Mohamed, S and Yusuf, M and Abdillahi, A},
title = {Early-Life Viral Lower Respiratory Tract Infections and Their Impact on Childhood Asthma: Molecular Endotypes and Prevention Strategies.},
journal = {Pediatric allergy, immunology, and pulmonology},
volume = {},
number = {},
pages = {2151321X261445781},
doi = {10.1177/2151321X261445781},
pmid = {42046474},
issn = {2151-3228},
abstract = {Background: Early-life viral lower respiratory tract infections (LRTIs), particularly those caused by respiratory syncytial virus (RSV) and human rhinovirus (HRV), are major contributors to pediatric morbidity and are strongly linked to asthma. RSV causes about 3.6 million hospitalizations and 100,000 deaths annually in children under 5, mainly in low- and middle-income countries. RSV peaks in infancy, while HRV has more impact later in childhood. Mechanisms include viral epithelial injury, genetic susceptibility (e.g., 17q21 variants), and environmental factors (e.g., allergic sensitization). Together, these raise asthma risk. Diagnosis is difficult due to overlapping presentations and reliance on molecular tests. Preventive strategies include maternal RSV vaccination, long-acting monoclonal antibodies such as nirsevimab and palivizumab, and pediatric vaccine candidates. Strategies to limit allergic sensitization may lower HRV-related asthma risk. Long-term effects include persistent wheeze and asthma, making early life a crucial window for prevention.Methods: This review summarizes current evidence on the epidemiology, mechanisms, and long-term impact of early viral LRTIs.Results: It highlights molecular and immunological endotypes of virus-induced asthma and explores the influence of genetic, epigenetic, and microbial factors. Emerging diagnostic tools and preventive strategies-including vaccines, monoclonal antibodies, environmental interventions, and microbiome-targeted therapies-are also discussed as means to reduce the global pediatric asthma burden and improve respiratory health.},
}

@article {pmid42046516,
year = {2026},
author = {Chowdhury, I and Massay, R and Stubbs, A},
title = {Food additives, emulsifiers, microplastics, and ultra-processed foods in rheumatic disease pathogenesis.},
journal = {Current opinion in rheumatology},
volume = {},
number = {},
pages = {},
doi = {10.1097/BOR.0000000000001161},
pmid = {42046516},
issn = {1531-6963},
abstract = {PURPOSE OF REVIEW: Dietary patterns have changed significantly over time, with ultra-processed foods now comprising a large proportion of daily energy intake in many countries. Ultra-processed foods (UPFs) contain numerous additives and may also increase exposure to processing- and packaging-related contaminants that could influence immune function. This review summarizes why UPFs have drawn growing attention and evaluates their potential relevance to autoimmune inflammation, with a focus on rheumatoid arthritis (RA) and related disorders.

RECENT FINDINGS: Population studies suggest that higher UPF intake is associated with an increased risk of RA after adjustment for obesity and lifestyle factors. Experimental and translational studies suggest that components common in UPF-rich diets (e.g., emulsifiers, thickeners, synthetic colorants, added sugars, excess sodium, and some nonnutritive sweeteners), as well as microplastic exposures, may disrupt gut barrier integrity, remodel the microbiome, and promote low-grade inflammation. These mechanisms overlap with pathways implicated in RA and systemic inflammation, including dysregulation of Treg/Th17 balance, loss of mucosal tolerance, endotoxemia, and innate immune activation.

SUMMARY: Overall, evidence supports biologically plausible mechanisms and epidemiologic associations linking UPF-rich dietary patterns to immune dysregulation relevant to rheumatic disease, but direct RA-specific interventional and mechanistic clinical data remain limited. Dietary exposures may represent modifiable risks; however, stronger longitudinal studies with validated RA phenotyping and pragmatic dietary interventions are needed before firm clinical recommendations can be made.},
}

@article {pmid42046678,
year = {2026},
author = {Dayrit, G and Mabrok, M and Chaiyapechara, S and Rodkhum, C},
title = {Habitat-structured fungal mycobiomes at the water-gill interface of farmed red tilapia in Central Thailand: An internal transcribed spacer rRNA amplicon sequencing study.},
journal = {Veterinary world},
volume = {19},
number = {3},
pages = {1196-1214},
pmid = {42046678},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: Tilapia aquaculture is rapidly expanding across Southeast Asia and plays a critical role in regional food security. While bacterial microbiomes of farmed fish have been widely investigated, the fungal component of aquatic microbial communities remains poorly characterized, particularly at the biologically important interface between rearing water and fish gills. Fungi may influence fish health, environmental microbial ecology, and occupational exposure risks within aquaculture systems. This study aimed to characterize fungal mycobiomes associated with rearing water and gills of clinically healthy red tilapia (Oreochromis spp. hybrids) cultured in Central Thailand using internal transcribed spacer (ITS) rRNA amplicon sequencing and to determine how habitat type, farming system, and environmental variables shape fungal community structure.

MATERIALS AND METHODS: Samples were collected from ten tilapia farms located in five provinces of Central Thailand, representing two aquaculture systems: open river cages and closed earthen ponds. A total of 27 rearing water samples and 30 composite gill samples were analyzed. Fungal DNA was extracted and the ITS1 region was amplified and sequenced using the Illumina MiSeq platform. Sequence processing and amplicon sequence variant inference were performed in QIIME2 using the DADA2 pipeline. Alpha diversity indices and beta diversity analyses were used to evaluate community structure, while multivariate statistical approaches assessed the influence of habitat type, geographic location, farming style, and physicochemical water parameters.

RESULTS: Fungal communities displayed considerable taxonomic diversity and differed significantly between habitats. Rearing water samples exhibited significantly higher alpha diversity than gill-associated communities. Dominant genera included Cladosporium, Candida, Aspergillus, Fusarium, and Rhodotorula. Gill communities were relatively enriched in Candida and Fusarium, whereas rearing water contained higher abundances of Cladosporium and Rhodotorula. Beta diversity analyses demonstrated significant effects of sampling source, province, and farming system on fungal community composition. Environmental parameters such as pH, nitrate concentration, and ionic strength were associated with variations in fungal diversity, particularly in rearing water. Several detected genera included taxa with known opportunistic pathogenic potential for fish and humans.

CONCLUSION: This study provides the first ITS-based baseline characterization of fungal mycobiomes associated with red tilapia aquaculture systems in Central Thailand. Distinct fungal assemblages occur at the water-gill interface, with environmental conditions and aquaculture practices influencing community composition. The presence of opportunistic fungal genera highlights the importance of incorporating fungal community monitoring into aquaculture biosecurity and One Health surveillance frameworks to support sustainable fish production, environmental health, and occupational safety.},
}

@article {pmid42046684,
year = {2026},
author = {Dehghan, H and Moghaddaszadeh-Ahrabi, S and Hashemzadeh-Farhang, H and Shahbazi, P and Nobari, B},
title = {Synergistic effects of Ferula asafoetida extract and condensed tannins from raisin pomace on in vitro cecal fermentation kinetics and nutrient digestibility in horses.},
journal = {Veterinary world},
volume = {19},
number = {3},
pages = {905-919},
pmid = {42046684},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: The equine hindgut depends on microbial fermentation for efficient nutrient utilization but remains vulnerable to dysbiosis, hindgut acidosis, and suboptimal fiber digestion. Growing restrictions on antibiotic and synthetic feed additives have increased interest in natural phytogenic compounds. Medicinal plant extracts and condensed tannins are promising candidates to modulate microbial activity, improve fermentation efficiency, and enhance nutrient digestibility. This study aimed to investigate the individual and combined effects of hydroalcoholic extract of Ferula asafoetida and condensed tannins extracted from raisin pomace on equine cecal fermentation parameters and nutrient utilization using in vitro gas production and batch culture techniques.

MATERIALS AND METHODS: A 2 × 2 factorial in vitro design was used with four treatments: control (C; basal diet only), F. asafoetida extract (A; 30 mg), condensed tannins from raisin pomace (G; 50 mg), and their combination (A × G). Fecal inoculum was collected from four healthy 14-month-old Arabian geldings adapted for 14 days to a forage-based maintenance diet. Fermentation kinetics were evaluated over 120 h using the in vitro gas production technique and fitted to the Gompertz model. Parallel batch cultures measured pH, ammonia-nitrogen (NH3-N), and apparent disappearances of dry matter (DM), crude protein (CP), acid detergent fiber (ADF), and neutral detergent fiber (NDF). Data were analyzed using PROC GLM in SAS with Tukey-Kramer post-hoc tests (p < 0.05).

RESULTS: Cumulative gas production at 120 h was significantly higher in G (340.5 mL) and A × G (340.3 mL) than in C (228.8 mL) (p < 0.01), with faster fermentation rates and shorter lag times (p < 0.01). Terminal pH values remained stable (6.33-6.40) across treatments with no indication of acidosis. NH3-N concentrations were elevated in G (26.0 mg/dL) and A × G (25.5 mg/dL) compared with C (24.5 mg/dL) (p < 0.01). Apparent digestibility improved markedly: DM increased from 64.5% (C) to 70.3% (G), CP from 60.3% (C) to 66.9% (G), with parallel positive trends observed for ADF and NDF (p < 0.01).

CONCLUSION: Supplementation with F. asafoetida extract and condensed tannins from raisin pomace, especially in combination, enhanced fermentation efficiency, accelerated substrate degradation, and improved nutrient digestibility while maintaining stable pH in an in vitro equine cecal model. These findings indicate strong potential for these phytogenic compounds as sustainable natural feed additives to optimize equine hindgut function. In vivo validation, dose optimization, and long-term microbiome studies are recommended to confirm practical efficacy and safety in horses.},
}

@article {pmid42046757,
year = {2026},
author = {Gao, RY},
title = {Targeting gut immunity as a therapy for steatotic liver disease.},
journal = {eGastroenterology},
volume = {4},
number = {2},
pages = {e100404},
pmid = {42046757},
issn = {2976-7296},
}

@article {pmid42046871,
year = {2026},
author = {Yang, Y and Tan, X and Zhang, Z and Liang, L and Wu, Z and He, J and Wang, Y and Dong, M and Zheng, J and Zhang, H and Feng, S and Cheng, W and Cui, B and Wei, H and Li, Q},
title = {Metagenomic sequencing reveals high reproducibility of human donor microbiota transplanted into germ-free mice via lower gut route.},
journal = {Journal of Zhejiang University. Science. B},
volume = {27},
number = {4},
pages = {375-389},
pmid = {42046871},
issn = {1862-1783},
support = {2021YFA0805904//the National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Humans ; Mice ; Germ-Free Life ; *Fecal Microbiota Transplantation/methods ; Feces/microbiology ; *Metagenomics ; Reproducibility of Results ; High-Throughput Nucleotide Sequencing ; Male ; *Metagenome ; Mice, Inbred C57BL ; Female ; },
abstract = {Human flora-associated (HFA) mice are often used to simulate the structure of human intestinal microbiota and to study the causal relationships between diseases and gut microbiota. However, several factors affect the colonization efficiency of human microbiota in germ-free (GF) mice, and the differential effects of gavage and lower gut transplantation on colonization are still unclear. In this study, we explored the reproducibility of the recipient-to-donor gut microbiota community structure and function under different transplantation routes and the differences in microbial colonization between recipients via gavage transplantation (GT_mice group) and lower gut transplantation (LGT_mice group). High-throughput sequencing of the metagenome was performed on the feces of each subject, and the composition of microbiome of each group was analyzed. As expected, the introduction of human fecal microbiota into GF mice via lower gut transplantation had a high transfer efficiency, which was evident from the similar species community structure to that of the donor (Adonis R[2]=0.713 960 for LGT_mice group‒donor group; Adonis R[2]=0.774 095 for GT_mice group‒donor group) and a higher bacterial colonization rate. The findings provide unique insights into improving the accuracy of constructing humanized microbiota transplantation models, aiding our understanding of the relationships between the human gut microbiota and disease.},
}

Animals
*Gastrointestinal Microbiome/genetics
Humans
Mice
Germ-Free Life
*Fecal Microbiota Transplantation/methods
Feces/microbiology
*Metagenomics
Reproducibility of Results
High-Throughput Nucleotide Sequencing
Male
*Metagenome
Mice, Inbred C57BL
Female

@article {pmid42046931,
year = {2026},
author = {Zhang, F and Lard, ML and Khachatryan, L and Guo, C and Sandifer, A and Villafuerte, NM and Nde, DB and Cook, RL and Cormier, SA and Richmond-Bryant, J},
title = {Shifts in soil microbiome surrounding a thermal treatment facility for hazardous waste: the hidden impact of environmentally persistent free radicals.},
journal = {Environmental science. Processes & impacts},
volume = {},
number = {},
pages = {},
pmid = {42046931},
issn = {2050-7895},
abstract = {The disposal of hazardous materials from Superfund sites often involves thermal treatment (TT), generating environmentally persistent free radicals (EPFRs). While substantial evidence links EPFR exposure to negative health outcomes, its effects on the soil microbiome remain underexplored. Since the mid-1980s, a TT facility in Colfax, LA, has employed open-burn and open-detonation to process hazardous waste. In 2023, we collected soil samples from 13 residential sites within a 17-km radius of the TT facility and analyzed microbial communities and EPFR content. Our findings revealed a distinct microbial community near the TT facility (within 5-km), characterized by reduced bacterial abundance and increased fungal presence. Soil EPFR concentrations ranged from 0.81 × 10[16]-4.39 × 10[16] spins per g with g-factor values of 2.0033-2.0040, indicating a mixture of carbon-centered radicals with adjacent oxygen and oxygen-centered radicals. Correlation analysis identified bacterial taxa, particularly Alpha-proteobacteria and Actinobacteria, positively associated with EPFR abundance. In vitro tests showed that laboratory generated EPFRs more strongly inhibited bacterial growth than fungal growth, though some bacterial isolates from the study sites exhibited resistance to EPFR exposure. The differences in microbial responses to EPFR exposure may contribute to the shifts in microbial communities near the TT facility. Our study advances the understanding of EPFR impacts on the soil microbiome and suggests potential long-term effects on environmental and community health.},
}

@article {pmid42047038,
year = {2026},
author = {Marsh, EB and Lavretsky, H and Kasparian, NA and Pike, NA and Doyle, KP and Aggarwal, NT and Fullerton, HJ and Ivy, AS and Dlamini, N and , },
title = {Brain Health Across the Life Span: A Framework for Future Studies: A Scientific Statement From the American Heart Association.},
journal = {Stroke},
volume = {},
number = {},
pages = {},
doi = {10.1161/STR.0000000000000518},
pmid = {42047038},
issn = {1524-4628},
abstract = {The concepts of brain health (ie, optimal functioning of the brain across cognitive, emotional, and behavioral domains throughout life) and cognitive resilience (ie, the ability of the brain to recover after an insult) have become increasingly important as the population ages. Previous research has called attention to vascular risk factors underlying cerebrovascular disease, as well as modifiable variables that contribute to premature aging and cognitive dysfunction. In this scientific statement, we focus on the role of nonvascular physical and psychologic variables that affect brain health across the life span. We provide a broad overview of influences such as chronic medical conditions, inflammation, environmental exposures, and socioeconomic drivers that affect the developing brain, along with factors including sleep quality, the gut microbiome, and mental health that contribute to neurodegeneration. We also review the varying strength of evidence supporting biologic mechanisms and mitigating strategies that may help optimize resilience, with the goal of providing a framework for future studies.},
}