@article {pmid41975402,
year = {2026},
author = {Zhu, Y and Xiao, C and Zhang, Z and Zhou, Y and Xu, L and Zhang, L and Qu, K and Yu, B and Yan, H},
title = {Association between oral microbiota and suicidal ideation among vocational high school students in China.},
journal = {BMC oral health},
volume = {26},
number = {1},
pages = {},
pmid = {41975402},
issn = {1472-6831},
support = {82204073//the National Natural Science Foundation of China/ ; 22YJC840037//the Ministry of Education of Humanities and Social Science project/ ; WY22B09//the Wuhan Health Science Research Funding/ ; },
abstract = {OBJECTIVE: To investigate the association between oral microbiome characteristics and suicidal ideation (SI) in vocational high school students.

METHODS: The oral microbiota composition and abundance of the SI group (N = 45) and the matched healthy control group (N = 45) were analyzed using 16S rRNA sequencing. Demographic variables and SI assessments (measured by the Columbia Suicide Severity Rating Scale) were obtained. Bioinformatics analyses (e.g., alpha and beta diversity indices, PCoA, NMDS, and LEfSe) were performed to compare oral microbiota characteristics between the SI group and the control group.

RESULTS: The vocational high school students with SI exhibited significantly lower alpha diversity indices in oral microbiota compared to the control group, including PD whole tree (20.56 [19.45, 21.38] vs. 21.37 [20.17, 23.27]), Chao1 (621.82 ± 66.99 vs. 672.24 ± 68.52), and observed species (426.91 ± 54.59 vs. 466.42 ± 69.75) (all p values < 0.01). Beta diversity analysis revealed distinct microbial composition between groups (p < 0.05), with greater homogeneity in the SI group. LEfSe analysis identified increased abundances of Enterobacter, Escherichia_Shigella, and Parabacteroides in the SI group, while controls showed enrichment of Rikenellaceae and Alistipes.

CONCLUSION: A decrease in oral microbiota diversity and alterations in the abundance of specific bacterial genera (Enterobacter, Escherichia_Shigella, and Parabacteroides) are associated with SI among vocational high school students. Longitudinal studies are needed to elucidate the underlying mechanisms and potential health impacts.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12903-026-08317-3.},
}

@article {pmid42254517,
year = {2026},
author = {Liu, S and Luo, X and Zhou, J and Wang, L and Li, R and Luo, Z and Li, N and Xiao, S and Zhang, P},
title = {A comparative study of the gut microbiome and fecal metabolome in hypertensive patients from middle-temperate and tropical cities of China: Daqing and Haikou.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1801806},
pmid = {42254517},
issn = {1664-302X},
abstract = {BACKGROUND: Geographic variations in climate and lifestyle may be associated with hypertension (HTN) through alterations in the gut microbiota and its metabolites. This study aimed to comparatively analyze the gut microbiome and fecal metabolome of hypertensive patients from two Chinese cities characterized by distinct climatic conditions: Daqing (middle-temperate climate) and Haikou (tropical climate). The objective was to identify gut microbial and metabolic characteristics associated with geographic differences and to provide insights into HTN prevention and management.

METHODS: A cross-sectional study was conducted between May and December 2024, involving hypertensive patients from Daqing and Haikou. Fecal samples were collected from 28 hypertensive patients in Daqing (DQ group) and 32 in Haikou (HK group), and analyzed using shotgun metagenomic sequencing and untargeted metabolomics.

RESULTS: Differences in microbial composition and metabolite profiles were observed between the two groups. Using ALDEx2 analysis at the genus level, 34 genera were identified as differentially abundant between the DQ and HK groups. After adjusting for potential confounding variables, including age, body mass index, smoking, and drinking status, 6 genera remained significantly associated with geographic grouping. A logistic regression model based on these genera achieved an area under the curve (AUC) of 0.8069, with Pseudescherichia showing the highest individual discriminatory performance (AUC = 0.7925). Functional analysis suggested that pathways such as xylene degradation and biofilm formation were relatively reduced in the DQ group. Metabolomic analysis identified 38 differentially abundant metabolites, including 15-hydroxyeicosatetraenoic acid (15-HETE), 7α,25-dihydroxycholesterol, the putative metabolite (3-hydroxypentadecanoyl) lysine, and ginsenoside Rg3. Dysregulated pathways were mainly involved in glycerophospholipid metabolism, ABC transporters, and choline metabolism. Correlation analysis revealed potential associations between differential microbes and metabolites.

CONCLUSION: Distinct gut microbiome and metabolome profiles were observed between hypertensive patients from the two geographic regions. These findings suggest potential associations between environmental factors and host-microbiome-metabolite interactions.},
}

@article {pmid42254525,
year = {2026},
author = {Chen, J and Zhou, Q and Cao, X and Jin, S and Wu, Y and Ren, T and Xu, C and Chen, H and Zhang, H and Zhang, Y and Liu, J},
title = {The outcome of Infliximab induction in patients with severe ulcerative colitis may be related to intestinal microbiota.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1779143},
pmid = {42254525},
issn = {1664-302X},
abstract = {BACKGROUND AND OBJECTIVE: Although infliximab (IFX) is endorsed for induction therapy in severe ulcerative colitis (SUC), its therapeutic response remains heterogeneous. We conducted a comprehensive analysis of fecal and mucosal microbiota, coupled with targeted metabolomics, to delineate microbial and metabolic signatures predictive of IFX induction efficacy and to explore mechanistic pathways underlying differential treatment responses.

METHODS: This study was a prospective cohort study (clinical study registration number: ChiCTR2300071816). It enrolled adult patients aged ≥ 18 years who were first diagnosed with SUC at the First Affiliated Hospital of Nanjing Medical University and Northern Jiangsu People's Hospital between February 2022 and December 2023. None of these patients had received any medication for UC, including antibiotics. Clinical data, fecal samples, and rectal mucosal samples were collected for analysis. High-throughput sequencing of the 16S rRNA gene and non-targeted metabolomics analysis were performed on both fecal and rectal mucosal samples. All patients underwent IFX (5 mg/kg) induced remission therapy at weeks 0, 2, and 6. Based on their clinical response at week 14, they were categorized into two groups: response and unresponse. Significant differences in bacterial composition between the two groups were identified by screening fecal and mucosal samples. The gut microbiota of feces and intestinal mucosa were combined with clinical data to create four prediction models and conduct comparisons. Furthermore, different metabolites from fecal and mucosal samples of the two groups were screened and compared with KEGG and PubChem databases to identify metabolic pathways associated with the efficacy of IFX-induced therapy.

RESULTS: Compared with non-responders, IFX responders harbor distinct gut microbiota. Clinical indices alone poorly forecast induction response (AUC 0.6429). Augmenting clinical variables with fecal or mucosal microbiota improves prediction to AUC 0.795 and 0.900, respectively; combining both compartments further elevates performance to AUC 0.964, indicating that integrated microbiome profiling is essential for optimal IFX response prediction. IFX responders and non-responders differ metabolically, with more discriminatory features in mucosa than feces. The most enriched differential pathways in feces included nicotinate and nicotinamide metabolism, butyrate metabolism, biosynthesis of valine, leucine, and isoleucine, pantothenate and coenzyme A biosynthesis, histidine metabolism, and alanine, aspartate, and glutamate metabolism. In mucosa, the most enriched differential pathways included alanine, aspartate, and glutamate metabolism, sphingolipid metabolism, ascorbate and aldarate metabolism, tryptophan metabolism, and D-glutamine and D-glutamate metabolism. The common pathway enriched in both feces and mucosa was alanine, aspartate, and glutamate metabolism.

CONCLUSION: The intestinal microbiota may be a predictive factor for IFX induction outcome in patients with SUC. The metabolic pathway of alanine, aspartate, and glutamate may be associated with the 14-week clinical response to IFX treatment in SUC.},
}

@article {pmid42254837,
year = {2026},
author = {Schmelz, P and Eckensperger, S and Osvatic, J and Séneca, J and Alzubaidy, H and Petersen, JM},
title = {Host depletion kits improve microbiome analyses in environmental samples: seagrass as a test case.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag082},
pmid = {42254837},
issn = {2730-6151},
abstract = {All plants and animals associate with specific communities of symbiotic microorganisms. Characterizing the diversity and functions of these communities is essential for understanding their roles in host health; however, such efforts are often hindered by the dominance of host-derived material in, e.g. DNA extractions. Although various commercial host DNA depletion kits have been developed to overcome these challenges, they have not yet been systematically tested on environmental samples. We used Zostera marina, globally the most widespread seagrass species, as a test case to assess the effectiveness of three different commercially available host DNA depletion kits: QIAamp DNA Microbiome Kit, HostZero Microbial Enrichment Kit, and NEBNext Microbiome DNA Enrichment Kit, when compared to the widely used DNeasy PowerSoil Pro Kit. All three host depletion kits substantially reduced the relative proportion of host DNA, as assessed by 16S rRNA gene amplicon sequencing, and enriched previously identified seagrass-associated bacteria. Furthermore, in metagenomes, only samples processed with host depletion methods allowed for the assembly of metagenome-assembled genomes with high completeness and low contamination. Metagenomic analysis further enabled the recovery of seagrass root core microbiome members, including previously undetected members of the family Sedimenticolaceae, highlighting the value of these techniques for uncovering novel host-associated microbial diversity in environmental samples such as marine plants.},
}

@article {pmid42254838,
year = {2026},
author = {Kobayashi, R and Shiba, T and Nagai, T and Komatsu, K and Matsumura, S and Watanabe, T and Nemoto, T and Takada, K and Takeuchi, Y and Iwata, T},
title = {Metatranscriptomic insights into microbial network modulation and pathogen dynamics underlying healing outcomes in non-surgical periodontal treatment.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag092},
pmid = {42254838},
issn = {2730-6151},
abstract = {Gingivitis and periodontitis are caused by oral microbiome dysbiosis. Post-treatment alterations in bacterial community structure are uncharacterized in situ, including how these alterations may differ between resolved and unresolved disease states. Understanding these treatment-induced microbial shifts and identifying prognostic markers in situ associated with favorable or unfavorable outcomes are crucial for developing diagnostic tools and refining therapeutic strategies. Therefore, we performed metatranscriptomic analysis on subgingival plaque samples from the anterior teeth of individuals, including healthy, gingivitis, and periodontitis sites, before and after non-surgical treatment in 28 patients. We revealed a new bacteriological characteristic of periodontitis, where periodontal pathogens emerge within the bacterial network alongside excessive and skewed associations among bacterial taxa, such as those in the Streptococcus and Actinomyces genera. Furthermore, these imbalances were found improvable through non-surgical treatment. However, even in clinically resolved gingivitis or periodontitis, the bacterial networks did not fully revert to the state observed in healthy sites. This was due to the persistence of periodontal pathogens, absent in the networks at healthy sites. By comparing groups in which periodontitis resolved and those in which it did not, specific bacterial taxa, such as Neisseria elongata and Rothia aeria, were suggested to play a role in the periodontitis healing process, while increases in genes related to glycine degradation and bacterial adhesion, including glycine dehydrogenase β-subunit and cleaved adhesin domain were implicated in inhibiting the healing process. These findings provide insights for the development of treatment strategies targeting specific bacteria and functional genes involved in the resolution of periodontitis.},
}

@article {pmid42254885,
year = {2026},
author = {Targino, AJM and da Silva Vilarinho, JLP and Carneiro, VMA and Greggianin, BF and Guimarães, MDCM},
title = {Periodontal Ecosystem and Clinical Implications of the Oral Microbiome: A Narrative Review.},
journal = {International journal of dentistry},
volume = {2026},
number = {},
pages = {1479982},
pmid = {42254885},
issn = {1687-8728},
abstract = {BACKGROUND: Periodontal disease, although widely documented, remains one of the leading causes of tooth loss worldwide. This situation can be attributed to patients' difficulty in following treatment protocols and to an incomplete understanding of the disease's mechanisms, which could be explored to develop new therapies.

OBJECTIVE: The present study aimed to summarize the main advances in understanding the periodontal microbiome, especially concerning the development of genetic sequencing technologies and metabolite analysis, as well as new treatment methods that have emerged from these innovations.

METHODS: A narrative literature review was conducted through searches in the PubMed, Scopus, Web of Science, and SciELO databases, prioritizing publications from the past 15 years while also including classic and foundational studies relevant to the theoretical framework.

CONCLUSIONS: Periodontal microbiome results from the synergistic interaction among different microorganisms, rather than just the sum of their individual metabolites. This synergy can create structural microarrangements that resist biofilm disruption, such as fungal barriers surrounding Gram-negative bacteria. Innovative treatments-such as host response modulation with resolvins and oral microbiome modulation, particularly using prebiotics derived from plant extracts (nitrate metabolism)-offer promising prospects. However, limitations remain regarding their clinical use and the challenge of managing refractory cases, highlighting the need for further research to support these findings.},
}

@article {pmid42254896,
year = {2026},
author = {Vaggi, C and Vötterl, JC and Lerch, F and Yosi, F and Koger, S and Ricci, S and Verhovsek, D and Metzler-Zebeli, BU},
title = {Characterization of fecal bacterial microbiomes according to fecal color, consistency, and sample type in piglets before and after weaning.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1815748},
pmid = {42254896},
issn = {2297-1769},
abstract = {Fecal samples are widely used as a proxy for the large intestinal microbiota; however, phenotypic characteristics (e.g., color and consistency) may be associated with divergent microbial profiles, especially around weaning, when diet and physiological adaptation rapidly alter gut function. The relationship between fecal phenotype, sample type, and piglet gut microbiota under physiological conditions remains poorly understood. This study investigated the bacterial communities in different fecal phenotypes of piglets shortly before and immediately after weaning. The fecal consistency of 192 piglets across two replicate batches was scored daily from day of life (DoL) 28 to 36, and fecal or rectal swab samples were collected at DoL28 and DoL33. The samples were classified by type (feces/swab), color (brown/yellow), and consistency (balls/liquid). DNA was extracted for quantification of total bacterial gene copies and 16S rRNA gene sequencing, and microbial composition was analyzed using Quantitative Insights Into Microbial Ecology 2 (QIIME2), Statistical Analysis System (SAS), and R. Fecal consistency changed markedly over time, shifting from predominantly ball-shaped on DoL28-32 to softer feces thereafter (p < 0.001). Age strongly influenced microbiota structure, with marked increases in relative abundance of Prevotella and Alloprevotella from DoL28 to DoL33, whereas the abundance of Escherichia, Methanobrevibacter, and Fusobacterium declined. Microbial communities differed between sample types, with swabs potentially reflecting mucosa-associated taxa more closely than fecal samples. Shannon and Simpson indices indicated reduced diversity in yellow and liquid feces on DoL28 (p < 0.001). Swabs and yellow liquid feces on DoL28 showed higher relative abundances of Escherichia, Bacteroides, and Fusobacterium, whereas brown ball-shaped feces were enriched in Lachnospiraceae, Prevotella, and Lactobacillus on both sampling days (p < 0.05). Overall, each fecal phenotype exhibited a distinct bacterial signature, and the sample type influenced the composition of the captured community. Monitoring fecal phenotypes alongside selecting appropriate sample types may enhance the interpretation of microbiome data and offer a practical, non-invasive approach to assess gut health during the critical weaning period.},
}

@article {pmid42254901,
year = {2026},
author = {Adegbeye, MJ and Sadarman, S and Poonooru, R and Alvarado-Ramírez, ER and Widiawati, Y},
title = {Editorial: Natural compounds/products and livestock productivity: enhancing antioxidant levels, gut health, mitigating greenhouse gas emissions, and disease control, volume II.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1867705},
pmid = {42254901},
issn = {2297-1769},
}

@article {pmid42254910,
year = {2026},
author = {Al-Ardhi, SA and Al-Waeli, SK and Osman, MA and Al-Shahari, EA and Siddig, NH and Ahmed, AE and Hazzazi, Y and Sumayli, M and Al-Rasheed, M and Alanazi, IMM},
title = {Modeling of growth performance, physiological response, and intestinal microbiota shift in growing Japanese quail fed olive leaf powder.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1824857},
pmid = {42254910},
issn = {2297-1769},
abstract = {INTRODUCTION: Due to the anti-inflammatory, antioxidant, and antibacterial properties of olive leaf powder (OLP), it may serve as a beneficial feed supplement for birds. This study aimed to evaluate the effect of adding OLP to feed on growth efficiency, carcass traits, blood parameters, antioxidant activity, and cecal microbial load in growing Japanese quail.

METHODS: Three hundred and seventy-five one-day-old quail chicks were randomly assigned to five experimental groups, each containing five replicates of 15 birds: a control group fed a basal feed and four experimental groups given 3, 4, 5, and 6% OLP per kg of quail diets for the 6 weeks.

RESULTS: The results showed a significant (P < 0.05) improvement in growth performance, with increased live body weight (LBW) and an insignificantly improved feed conversion ratio in the 6% OLP group. Carcass yield and total edible meat also substantially improved (P < 0.05). Blood parameters showed improved (P < 0.05) protein and lipid levels and increased liver enzyme activity; moreover, the use of the OLP led to a decrease in TC, TG, LDL, and VLDL levels, as well as an increase in HDL. Additionally, the activity of antioxidant enzymes increased (P < 0.001), along with higher levels of GSH and SOD activity. All meat quality attributes, including cooking loss %, water-holding capacity, PH values, and meat color, improved (P < 0.05) with the use of OLP. Furthermore, intestinal microbiota analysis showed a significant improvement in Lactobacillus count and a decrease in pathogenic bacteria (total bacterial count, coliforms, E. coli, and Salmonella). However, the Bacillus count was not significantly affected by OLP supplementation.

DISCUSSION: The findings of this study demonstrate that OLP is a promising natural feed additive for growing Japanese quail, enhancing growth performance and the gut microbiome, thereby establishing it as a safe and natural growth promoter.},
}

@article {pmid42255244,
year = {2026},
author = {Saadatkhah, A and Nicholson, L and Buchholz, TA and Hong, L},
title = {Beyond the tumor: the role of the gut microbiome in triple-negative breast cancer.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1832176},
pmid = {42255244},
issn = {2234-943X},
abstract = {The gut microbiome, a metabolically active community of microorganisms in the gastrointestinal tract, regulates host immunity, metabolism, and inflammation. Dysbiosis, or disruption of this ecosystem, has been linked to cancer initiation, progression, and therapy resistance. Triple-negative breast cancer (TNBC) accounts for 10-15% of breast cancers and is managed primarily with chemotherapy and immune checkpoint inhibitors; however, treatment responses remain variable and these patients are at higher risk of cancer recurrence compared to patients with hormone receptor-positive or HER2-positive breast cancer. Emerging evidence suggests that the gut microbial composition and its diversity can influence outcomes and therapeutic efficacy of systemic treatments in TNBC. We review the current epidemiologic, mechanistic, and clinical evidence on how the gut microbiome influences TNBC biology, with particular attention to the tumor immune microenvironment and response to therapy. We highlight protective and pro-tumorigenic microbial signatures, the impact of antibiotics and obesity, and emerging strategies, such as dietary modulation and microbiome-targeted interventions, that may ultimately be used to optimize TNBC management and improve patient outcomes.},
}

@article {pmid42255295,
year = {2026},
author = {Ranjan, P and Das, D and Bundela, V and Ramesh, A and Verma, RK and Nargund, R and Manandhar, U and Drijber, R and Upadhyay, RK and Sharma, MP},
title = {Role of rhizosphere specific microbiome in enhancing soybean productivity across contrasting soil and crop management systems.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1830235},
pmid = {42255295},
issn = {1664-462X},
abstract = {Soybeans are a globally significant legume and oilseed crop with a diverse rhizospheric microbiome that can enhance sustainable agriculture by reducing the need for chemical fertilizers. These microbes can potentially impact plant growth and development through symbiotic (rhizobium and mycorrhizae) and non-symbiotic (plant growth-promoting rhizobacteria and fungi) interactions with soybean roots under optimal crop and soil management practices. During the production of soybeans, practices such as excessive use of fertilizers and pesticides, mono-cropping, and intensive tillage are often employed to achieve higher yields. However, these practices can alter the rhizomicrobiome communities and their interactions with soybean crops. Implementing optimal soil and crop management techniques can create a more favorable environment for rhizomicrobial communication with soybean roots, ultimately enhancing nutrient uptake for the soybean plants. In this review, we address how the soil rhizomicrobiome communicates with soybean roots, its role in promoting plant health and yield, and approaches to enhance soil rhizomicrobiome diversity and function through improved crop and soil management practices. Herein we synthesize current literature on soybean-microbe interactions, including both symbiotic and non-symbiotic relationships with an emphasis on how plant-microbe interactions within soybean cropping systems are influenced by agricultural practices such as crop rotation, intercropping, integrated nutrient management, and no-tillage. Greater understanding of the complexity underlying rhizosphere microbiome relationships will enable design of local cropping systems enhancing soybean yield along with improving soil health.},
}

@article {pmid42255425,
year = {2026},
author = {Hu, R and Deng, J and Tu, L and Jiang, T and Xu, J},
title = {Integration of tongue image features and tongue coating microbiome for differentiating dampness patterns in MASLD.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1851610},
pmid = {42255425},
issn = {1664-2392},
abstract = {BACKGROUND: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a prevalent metabolic disorder that can progress to hepatic fibrosis, cirrhosis, and hepatocellular carcinoma. Traditional Chinese medicine (TCM) has therapeutic effects in MASLD. In TCM, dampness patterns predominate in MASLD and are further classified into damp heat (DH) and cold dampness (CD) subtypes based on distinct pathogenic mechanisms. However, the characteristics of the tongue image and tongue coating microbiome across different dampness patterns and their associations with clinical features remain poorly understood.

MATERIALS AND METHODS: This study enrolled 320 participants, including 214s dampness patterns patients with MASLD, further classified into DH pattern (n = 110) and CD pattern(n = 104), along with 106 healthy controls. Tongue images and tongue coating samples were collected; tongue image segmentation was performed using a customized Tongue-InSPyReNet framework and extract quantitative features, while tongue coating microbiota were profiled using 16S rRNA gene sequencing. To distinguish between patterns, five machine learning models were developed and evaluated based on integrated tongue image features and microbiome data.

RESULTS: Significant differences in tongue features and microbial composition were observed between groups. The DH pattern was characterized by a red-crimson tongue with yellow coating and enrichment of Prevotella (P < 0.05). In contrast, the CD pattern more frequently exhibited a pale tongue with petechiae and higher abundances of Streptococcus and Rothia (P < 0.05). Integration of tongue image features and tongue coating microbiome effectively distinguished DH and CD patterns, achieving an AUC of 0.871 and an accuracy of 79.1%.

CONCLUSION: Our study highlights the contributions of tongue image features and the tongue coating microbiome to differentiating two TCM patterns in MASLD, and may provide the rationale for adopting different treatment strategies for different TCM syndromes of MASLD in the future.},
}

@article {pmid42255437,
year = {2026},
author = {Shi, S and Song, W and Wu, Z and Cheng, Y and Liu, H and Tian, F and Li, X},
title = {Multi-omics Mendelian randomization integrating metabolism, microbiome and immunity supports a putative gut-immune-pelvic pathway in deep infiltrating endometriosis.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1827134},
pmid = {42255437},
issn = {1664-2392},
abstract = {BACKGROUND: Deep infiltrating endometriosis (DIE) is a highly fibrotic and deeply invasive subtype of endometriosis that causes severe pelvic pain, infertility and marked impairment of quality of life. Metabolic, microbial and immune disturbances have been reported in women with endometriosis, but whether these systemic perturbations causally contribute to DIE and which lesion-level molecular mediators connect them to pelvic pathology remains unknown.

METHODS: We performed two-sample Mendelian randomization (MR) to assess the causal effects of circulating metabolites, gut microbiota (GM) traits and immune cell phenotypes on DIE risk using genome-wide association data from FinnGen and large exposure GWAS. Bayesian colocalization was applied to identify protein-coding genes with shared causal variants between exposures and DIE. Colocalized genes were integrated with RNA-sequencing data from GSE141549 (normal endometrium, n = 43; DIE lesions, n = 88) to evaluate differential expression and immune-cell associations inferred by CIBERSORT-like deconvolution. Machine-learning-based feature selection was used to derive a multigene logistic model, and protein expression of feature genes was validated by immunohistochemistry in independent specimens.

RESULTS: MR revealed putative causal associations between multiple circulating metabolites, GM taxa and immune phenotypes and DIE susceptibility, including risk-increasing bile acid-related and acylcarnitine species, specific bacterial taxa, and monocytic/dendritic-cell traits, and protective lipid species, short-chain-fatty-acid-linked genera and CD45RA[-]CD4[+] T-cell subsets. Colocalization identified 324 protein-coding genes, of which 42 were differentially expressed between DIE and controls and enriched in inflammatory and extracellular matrix remodeling pathways. A five-gene panel-HDC, GADD45B, CDK5, AHNAK and RASGRP2-was prioritized, showed structured correlations with B-cell, NK-cell and CD4[+] memory T-cell subsets, and showed excellent within-cohort discrimination between DIE lesions and normal endometrium (AUC = 0.999). Immunohistochemistry confirmed upregulation of HDC, GADD45B, AHNAK and RASGRP2 and downregulation of CDK5 in DIE lesions.

CONCLUSION: This multi-omics MR framework supports a putative gut-immune-pelvic pathway in DIE and identifies a biologically plausible five-gene tissue-level signature consistent with lesion-associated fibrotic and immune-inflammatory remodeling.},
}

@article {pmid42255668,
year = {2026},
author = {An, Z and Xin, Y and Wang, Y and Wang, T and Niu, J and Hu, X and Li, X and Jin, W},
title = {Lanzhou Lily (Lilium davidii var. unicolor) Extract Alleviates Chronic Stress-Induced Mood Disturbances by Suppressing Neuroinflammation and Modulating the Gut-Brain Axis in Mice.},
journal = {Food science & nutrition},
volume = {14},
number = {6},
pages = {e71914},
pmid = {42255668},
issn = {2048-7177},
abstract = {Chronic stress is a major contributor to mood disturbances through dysregulation of the gut-brain axis and neuroinflammatory responses. Lilium davidii var. unicolor (Lanzhou lily), a traditional medicinal and edible plant, contains bioactive compounds with anti-inflammatory potential. This study investigated the effects of Lanzhou lily extract (LLE) on chronic restraint stress (CRS)-induced behavioral and physiological changes in mice. LLE improved CRS-induced anxiety- and depression-like behaviors, reduced microglial activation in the hippocampus, and suppressed TLR4/MyD88/NF-κB signaling and downstream cytokine release (TNF-α, IL-6, IL-1β). LLE also restored intestinal barrier integrity, decreased serum LPS levels, and modulated gut microbiota composition by enriching Ligilactobacillus murinus and Muribaculum intestinale while reducing Prevotella abundance. Correlation analysis linked microbial restoration with barrier protection and reduced neuroinflammation. UHPLC-Q-Exactive Orbitrap-MS/MS analysis tentatively identified multiple constituents of LLE, including dioscin, matrine, timosaponin AIII, and catechin. Previous studies have suggested that some of these compounds may possess neuroprotective or antidepressant-related activities. These findings suggest that Lanzhou lily extract may modulate the gut-brain axis and exert antidepressant-like effects in a preclinical stress model, warranting further investigation in clinical studies.},
}

@article {pmid42255680,
year = {2026},
author = {Luo, T and Zhu, Y and Xu, F and Xie, J and Chen, H and Qin, L and Ren, T},
title = {Hydroxy-α-Sanshools From Zanthoxylum bungeanum Maxim. Alleviate Obesity in Mice via the Regulation of Appetite and Gut Microbiota.},
journal = {Food science & nutrition},
volume = {14},
number = {6},
pages = {e71952},
pmid = {42255680},
issn = {2048-7177},
abstract = {To explore whether hydroxy-alpha-sanshool (HAS) prevents obesity by modulating appetite and the gut microbiome, an obesity model was established using mice fed a high-fat diet. The food intake, body mass, feed efficiency and organ index of the mice were recorded, and the serum levels of GLP-1 and PYY were measured. The mRNA and protein expression of appetite-related genes in the small intestine and brain tissue were detected by real-time quantitative PCR and Western blotting, and the intestinal flora was analyzed by 16S rRNA gene sequencing. The results revealed that the body weight, food intake and feed efficiency of the mice were significantly reduced (4.28%, 14.46%, and 25.33%, respectively) and that the levels of GLP-1 and PYY were significantly increased (p < 0.05) (9.11% and 5.49%, respectively) by the HAS intervention. The relative mRNA expression of NPY and AGRP in the small intestine decreased significantly (39.62%, 21.95%) (p < 0.05); the relative mRNA levels of CART, GLP-1R, NPY2R and GLP-1 in the brain tissue increased significantly; and those of NPY and AGRP decreased significantly (p < 0.05). The protein expression of POMC and GLP-1 increased significantly (p < 0.05), whereas the protein expression of NPY and AGRP decreased significantly (p < 0.05). The diversity of intestinal flora in the cecal contents and the relative abundance of probiotics among the dominant flora increased. In conclusion, HAS could modulate the expression of appetite-related factors and the composition of intestinal microbiota in mice fed with a high-fat diet by regulating food intake and maintaining energy homeostasis, which is consistent with the involvement of the gut-brain axis in this regulatory mechanism.},
}

@article {pmid42255811,
year = {2026},
author = {Tiwari, S and Kaur, U and Kaur, N and Alauddin, W and Khairnar, S and Bala, R and Kaushal, V and Mishra, M},
title = {The Gut-Brain-Immune Axis: Role of Microbiota Dysbiosis and Autonomic Nervous System in Infectious Diseases.},
journal = {Cureus},
volume = {18},
number = {5},
pages = {e108276},
pmid = {42255811},
issn = {2168-8184},
abstract = {The human gastrointestinal tract harbors a complex microbial ecosystem that plays a fundamental role in maintaining immune balance and defending against infectious diseases. Disruption of this ecosystem, known as dysbiosis, has been increasingly associated with impaired immune responses and heightened susceptibility to infections. Emerging evidence highlights the importance of the gut-brain-immune axis, particularly the role of the autonomic nervous system (ANS), in regulating these interactions. This systematic review aimed to examine the relationship between gut microbiota dysbiosis and infectious diseases, with specific emphasis on the influence of autonomic dysfunction on disease susceptibility and outcomes. A comprehensive search of PubMed/Medical Literature Analysis and Retrieval System Online (MEDLINE), Scopus, and Google Scholar was conducted to identify relevant observational studies published between 2000 and 2025. Data extraction and quality assessment were performed using standardized tools, including the Newcastle-Ottawa Scale (NOS). A total of 11 studies were included in the qualitative synthesis. The included studies consistently demonstrated that dysbiosis is associated with reduced microbial diversity and loss of beneficial taxa, which in turn were linked to increased infection risk and disease severity. Additionally, autonomic imbalance, reflected by increased sympathetic activity and reduced parasympathetic (vagal) tone, was frequently associated with impaired immune regulation. Reduced heart rate variability was commonly reported, suggesting a potential link between microbial alterations and neuroimmune dysfunction. Overall, the findings suggest that gut microbiota dysbiosis may be associated with infectious disease outcomes, with ANS dysfunction acting as a potential modulatory pathway. These findings should be interpreted with caution, as the included studies are predominantly observational and mechanistic. The results are therefore hypothesis-generating rather than practice-changing, and further high-quality studies are required to establish causal relationships.},
}

@article {pmid42255976,
year = {2026},
author = {Lu, Z and Zhang, L and Zhang, Q and Duan, Q and Liu, X and Deng, X and Chen, D and Chen, X},
title = {Genetically Predicted Gut Microbiota in Correlation with the Risk of Head and Neck Cancer.},
journal = {Cancer informatics},
volume = {25},
number = {},
pages = {11769351261457904},
pmid = {42255976},
issn = {1176-9351},
abstract = {BACKGROUND: Existing evidence supports observational associations between the gut microbiome composition and susceptibility to extraintestinal cancers; however, the causal relationship between gut microbiome composition and the risk of developing head and neck cancer (HNC) remains uncertain. Therefore, we conducted a two-sample Mendelian randomization (MR) analysis using publicly available genome-wide association study (GWAS) data to investigate the potential causal link between gut microbiome composition and HNC.

METHODS AND ANALYSIS: Relevant investigations were conducted to examine the casualties of exposures and outcomes, using inverse variance weighted (IVW), weighted median (WM) and the MR-Egger method. Sensitivity analyses, including the MR-Egger intercept test, Cochran's Q test, and leave-one-out analysis, were used to assess pleiotropy and heterogeneity. In addition, the Steiger directionality test was applied to exclude studies with potential directional biases.

RESULTS: Our study identified 16 causal relationships between the genetically predicted abundances of gut microbiota and the risk of developing HNC. After sensitivity analysis on these identified relationships, 10 [class (Actinobacteria, Betaproteobacteria), order Bacillales, family (Ruminococcaceae), genus (Eubacterium_ventriosum_group, Coprococcus2, Coprococcus3, Desulfovibrio, Howardella, Subdoligranulum, Veillonella, Victivallis)] out of the initially identified 16 causal relationships were ultimately validated as being associated with HNC tumors. Steiger directionality test indicated that the MR estimate of causal direction was accurate (All p < 0.05).

CONCLUSION: Our MR analysis revealed that the gut microbiome composition was causally associated with the risk of developing HNC and could serve as a new biomarker for preventive and therapeutic strategies for HNC.},
}

@article {pmid42256174,
year = {2026},
author = {Powell, ME and Solomon, SL and Schoepf, V and Castillo, KD},
title = {Stress-Resistant Symbiodiniaceae and Diverse Bacterial Communities Promote Coral Persistence in Variable, Multi-Stressor Environments.},
journal = {Ecology and evolution},
volume = {16},
number = {6},
pages = {e73783},
pmid = {42256174},
issn = {2045-7758},
abstract = {Coral holobionts maintain complex symbioses, which can be influenced by global and local stressors. However, the role of coral-associated bacterial and algal (Symbiodiniaceae) communities in facilitating coral persistence in variable and extreme, multi-stressor environments is not fully understood. Multi-stressor environments, such as semi-enclosed inland bays, provide natural laboratories to study potential coral holobiont responses to future ocean conditions in situ. We investigated the role of Symbiodiniaceae and bacterial communities in coral holobiont persistence across habitats and dry versus wet seasons. We collected three Caribbean coral species (Siderastrea siderea, Siderastrea radians, and branching Porites sp.) from two semi-enclosed inland bays and two nearby fringing reefs in Curaçao across three seasonal timepoints. We show that all coral species hosted high proportions of stress-tolerant Symbiodiniaceae in inland bays, likely facilitating the survival of their coral hosts in these turbid and highly variable and extreme environments. We also observed distinct differences in bacterial community composition across habitats, sites, and seasons in S. siderea and S. radians but not branching Porites sp. Bacterial communities of S. siderea and S. radians contained higher proportions of bacteria with the potential for diverse metabolisms, such as sulfur and nitrogen cycling, in inland bays and during wet seasons. Environmental conditions therefore strongly influence bacterial community composition, and bacterial diversity and metabolic flexibility are likely critical for coral holobiont success across environments and seasons. Our findings show how Caribbean coral holobionts persist in multi-stressor environments and may respond as anthropogenic climate change continues to exacerbate and intensify these stressors.},
}

@article {pmid42256181,
year = {2026},
author = {Worsley, SF and Crighton, Z and Lee, CZ and Burke, T and Komdeur, J and Dugdale, HL and Richardson, DS},
title = {Gut Microbiome Communities Vary Across Translocated Populations of the Seychelles Warbler.},
journal = {Ecology and evolution},
volume = {16},
number = {6},
pages = {e73750},
pmid = {42256181},
issn = {2045-7758},
abstract = {Conservation translocations are an increasingly common tool used to help combat species extinction and global biodiversity loss. However, their success is dependent on a wide range of abiotic and biotic factors. To date, the potential role of host-associated microbiomes in translocation success has been overlooked despite their fundamental contribution to host health and fitness. Here, we use faecal samples to evaluate how gut microbiome communities vary across the last remnant (source) population, and all four translocated populations (established between 1988 and 2011), of the Seychelles warbler (Acrocephalus sechellensis). Gut microbiome alpha diversity was lower in all translocated populations compared to the source population on Cousin Island. Gut microbiome composition also varied, with several short-chain fatty acid producing bacterial families being lost from the core microbiome in some translocated populations; such taxa have been shown to play an important role in maintaining host metabolic health. Furthermore, the two translocated populations that were established the longest time ago, and with the fewest individuals, had reduced inter-individual gut microbiome variability compared to the source population. While it was not possible to directly assess the specific drivers of these differences due to samples being collected after the translocation event, it is likely that the size of the founding population, subsequent loss of host genetic variation and environmental factors all contribute to shaping gut microbiome variation amongst these populations. Future work should assess whether taxonomic variation translates into differences in gut microbiome function and the possible consequences for host population health and long-term resilience to environmental change.},
}

@article {pmid42256221,
year = {2026},
author = {Giju, JK and John, S and Sivadas, A and Prabhakar, M and K, K and Sunilkumar, D and Nair, BG and Pal, S and Prakash, V},
title = {From dysbiosis to precision medicine: targeting the microbial-metabolic axis in IBD management.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1826972},
pmid = {42256221},
issn = {2235-2988},
abstract = {Inflammatory bowel disease (IBD) is a chronic relapsing inflammatory condition that has a rapidly changing global epidemiology. IBD has been traditionally viewed as a primary immune system dysfunction, but emerging evidence more accurately describes IBD as a perturbance of the intricate balance between host immunity, the intestinal microbiome, and intestinal metabolism. Although genetic and environmental components have long been recognized as contributors, accumulating evidence increasingly highlights the pivotal role of microbial dysbiosis in the pathogenesis of IBD. In patients with IBD, intestinal dysbiosis, which is often characterized by reduced Firmicutes and increased pro-inflammatory bacteria, triggers a cascade of pathogenic events. These pathogenic events include impaired epithelial barrier function, dysregulated immune activation against luminal antigens, and immune reprogramming. Central to these processes are functional changes in microbial metabolism, particularly in pathways involving short-chain fatty acids (SCFAs), bile acids, and redox homeostasis, which critically contribute to the development of chronic mucosal inflammation. The current therapeutic backbone of IBD-including aminosalicylates, biologics, and immunomodulators-largely targets the inflammatory response. However, the challenges such as primary non-response, secondary loss of response, and systemic side effects are often problematic. Consequently, there is an urgent need to develop novel therapeutic and preventive strategies that target the underlying microbial and metabolic causes of the disease rather than modulating immune responses. This review integrates the pathomechanistic implications of the microbiome-metabolic axis in the maintenance of gut homeostasis and its disruption in IBD, with particular emphasis on the global epidemiology of the disease. We further evaluate emerging therapeutic and preventive strategies aimed at restoring the microbiome-metabolic axis, including fecal microbiota transplantation (FMT), probiotic therapy, bacteriophage therapy, and helminth-based therapies. In addition, we explore the potential of advanced approaches such as microbiome engineering and precision genome editing to enable highly personalized therapeutic paradigms. By bridging microbial ecology with clinical pathology, this review highlights the transformative potential of targeting the host-microbiota interface to achieve improved long-term outcomes in IBD.},
}

@article {pmid42256227,
year = {2026},
author = {Feng, J and He, X and Li, R and Chen, C and Yu, Z and Zhang, L},
title = {Trends and hotspots in gut microbiota and neonatal necrotizing enterocolitis: a bibliometric analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1684491},
pmid = {42256227},
issn = {2235-2988},
abstract = {BACKGROUND: Neonatal necrotizing enterocolitis (NEC) is one of the most life-threatening gastrointestinal emergencies in preterm infants. Accumulating evidence has identified gut microbiota dysbiosis as a key driver of NEC pathogenesis. Probiotics/prebiotics and bioactive components in breast milk can reduce NEC risk by modulating microbiota balance. With microbial intervention strategies becoming a research hotspot, publications in this field have surged over the past 5 years. However, no studies have yet systematically mapped its knowledge evolution and collaboration networks.

OBJECTIVE: This study pioneers the use of bibliometric methods to systematically analyze global research trends, core contributors (countries, institutions, authors), and emerging frontiers in gut microbiota and NEC research from 2005 to 2024, aiming to provide strategic guidance for future translational studies.

METHODS: A total of 1,011 English-language articles were screened from the Web of Science Core Collection. Software tools, including VOSviewer, CiteSpace, and Pajek, were employed to analyze publication trends, country/region and institution collaboration networks, journal co-citations, keyword clustering, and keyword bursts.

RESULTS: Annual publications increased from 5 in 2005 to a peak of 120 in 2023, with cumulative citations reaching 52,330 and an h-index of 115. The United States led in output (424 publications, 41.9%) and total citations (30,446). China ranked second in publications (158 articles) but exhibited lower average citations per article (22.65). The University of California System (65 publications) and the State University System of Florida (51 publications) were the most productive institutions. Mark A. Underwood (31 publications) focused on multi-omics mechanisms, while Josef Neu achieved the highest average citations per article (107.88) for his work on microbe-host interactions. "Nutrients" published the most articles (49), while "Microbiome" (impact factor 12.7) demonstrated the highest influence. Research hotspots evolved from early-stage microbiota composition analysis to mid-phase mechanism exploration and probiotic intervention evidence synthesis, shifting recently toward clinical translation, intestinal barrier repair, and stem cell therapy.

CONCLUSION: Research on gut microbiota and NEC shows sustained growth, with trends shifting from microbiota structure description to multi-omics mechanistic exploration and accelerating clinical translation.},
}

@article {pmid42256231,
year = {2026},
author = {Gomez-Ramirez, U and De La Torre-González, C and Villamor, P and Huante Guido, M and Contreras-Rodríguez, A and Velázquez-Guadarrama, N},
title = {Recolonization dynamics of the middle ear microbiota following MESNA-assisted dissection in pediatric cholesteatomatous chronic otitis media.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1830192},
pmid = {42256231},
issn = {2235-2988},
abstract = {INTRODUCTION: Cholesteatomatous chronic otitis media (CCOM) remains a clinical challenge due to its high recurrence rates despite surgical intervention. Sodium 2-mercaptoethanesulphonate (MESNA) is used to assist dissection, yet its impact on the middle ear microbiome and ecological recovery remains poorly understood. The aim of this study is to characterize the microbiota of paediatric CCOM and evaluate the ecological shifts induced by MESNA-assisted surgery.

METHODS: We analyzed 16S rRNA gene sequences (V3-V4) from middle ear tissue of paediatric patients with CCOM (CCOM Before MESNA, n = 13; CCOM After MESNA, n = 13) and healthy controls (n = 11). Bioinformatic processing was performed via QIIME2 and DADA2. We employed a Compositional Data Analysis (CoDA) framework, centering on Aitchison distances, ALDEx2 for differential abundance, and consensus co-occurrence networks (SparCC, SPIEC-EASI, and CLR-Pearson). Functional potential was inferred using PICRUSt2.

RESULTS: CCOM was associated with a marked reduction in microbial network connectivity, decreasing from 185 edges in healthy controls to only two total edges in the CCOM Before MESNA stage. Cutibacterium emerged as a candidate keystone pathobiont, exhibiting profound ecological isolation and predicted metabolic shifts toward lipid catabolism and biofilm formation in dysbiotic states. MESNA application disrupted the disease-associated community equilibrium, initiating secondary succession. However, post-treatment recovery was marked by taxonomic homogenization and the expansion of Pseudomonas in several patients.

DISCUSSION: Our findings identify network fragmentation and functional dysbiosis as the ecological signatures of pediatric CCOM. While MESNA disrupts the dysbiotic equilibrium, it does not fully restore a healthy stable climax community within the studied timeframe, as defined in ecological succession theory. These results support a paradigm shift from simple pathogen eradication toward ecological restoration as a strategy to prevent disease recurrence in CCOM patients.},
}

@article {pmid42256254,
year = {2026},
author = {Zhang, A and Du, R and Lei, L and Liu, J and Sun, G and Wang, R and Hu, T and Cheng, R},
title = {Fibrinogen was associated with subgingival microbiome in periodontal diseases: a pilot study.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2681264},
pmid = {42256254},
issn = {2000-2297},
abstract = {BACKGROUND: Periodontal diseases are associated with complex interactions among inflammatory responses, microbial dysbiosis, and clinical periodontal parameters. However, the relationships among inflammatory biomarkers, microbial biomarkers, and clinical parameters in gingival crevicular fluid (GCF) remain to be further clarified.

OBJECTIVE: To explore the interactions among inflammatory biomarkers, microbial biomarkers, and clinical parameters in gingival crevicular fluid in periodontal diseases.

DESIGN: In this cross-sectional study, GCF and subgingival plaque were collected from healthy, gingivitis, and periodontitis participants. Levels of fibrinogen, fibrin (measured as fibrin degradation products (FDP)), Interleukin (IL)-1β, IL-17, Matrix metallopeptidase (MMP)8, and MMP9 were measured by enzyme-linked immunosorbent assay. The subgingival microbiome was analyzed using 16S rRNA gene sequencing.

RESULTS: Among all biomarkers, fibrinogen was the most sensitive biomarker detected in GCF. Levels of fibrinogen were higher in the gingivitis (p = 0.024) and periodontitis (p = 0.002) groups than in the healthy group. Positive correlations were found between fibrinogen and numerous subgingival microorganisms, such as Tannerella forsythia, Treponema denticola, Porphyromonas gingivalis, and Filifactor alocis. Fibrinogen was the only GCF marker that could differentiate between healthy and gingivitis individuals. Fibrinogen and its combination with specific subgingival microorganisms may be potential markers indicating gingivitis and periodontitis.

CONCLUSIONS: Compared with IL-1β, IL-17, MMP8 and MMP9, fibrinogen in GCF demonstrated distinct associations with clinical parameters and subgingival microbiome in periodontal diseases.},
}

@article {pmid42256255,
year = {2026},
author = {Wu, X and Xiao, H and Chen, Y and Wu, C and Xie, Q and Gu, Y and Qin, X},
title = {Blueberry leaf polyphenols suppress biofilm formation and restore oral microbial homeostasis for caries control.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2681284},
pmid = {42256255},
issn = {2000-2297},
abstract = {BACKGROUND: Dental caries is a dysbiotic biofilm-induced disease driven by Streptococcus mutans (S. mutans). Blueberry leaf polyphenols (BLP) are plant-derived polyphenols exhibiting antimicrobial properties. However, their effects on S. mutans remain incompletely understood.

METHODS: The composition of BLP was determined by ultrahigh-pressure liquid chromatography-triple quadrupole tandem mass spectrometer (UPLC-MS/MS). The minimum inhibitory concentration (MIC) and acid suppression activity were determined. In addition, the effect on biofilm was investigated by adhesion and aggregation assay, crystal violet assay, glycosyltransferases (GTF) activity, extracellular polysaccharides (EPS) quantification, scanning electron microscope (SEM) images and qRT-PCR. Furthermore, we carried out a rat caries model, and microbiome analyzes were performed by 16S rRNA sequencing.

RESULTS: UPLC-MS/MS analysis identified a range of compounds in BLP, including quercetin and chlorogenic acid. The MIC of BLP was 500 μg/mL, and it inhibited the acid production of S. mutans. Importantly, BLP decreased the sucrose-dependent adhesion and its auto-aggregation, inhibited the activity of GTF, resulting in reduced EPS and down-regulated genes like gtfB, comA and gbpB. In addition, it inhibited dental caries in rats and ameliorated the microbiota dysbiosis associated with caries.

CONCLUSIONS: BLP combats caries by inhibiting S. mutans growth, biofilm formation and restoring the oral microbiota.},
}

@article {pmid42256259,
year = {2026},
author = {Dewan, A and Mascellino, MT},
title = {Computational and multi-omics systems biology for precision microbiome therapeutics.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1842701},
pmid = {42256259},
issn = {2813-4338},
abstract = {The human gut microbiome represents a complex and dynamic therapeutic target whose effective interrogation requires system-level analytical approaches beyond single-omics or reductive methods. This mini-review synthesizes recent advances in computational modeling and multi-omics integration relevant to the development of predictive, patient-tailored microbiome therapies. We critically assess the analytical strengths and limitations of genome-scale metabolic models (GEMs); generalized Lotka-Volterra and ODE-based community models; agent-based simulations; and statistical machine-learning frameworks and examine how their integration with metagenomics, metatranscriptomics, metaproteomics, and metabolomics can help bridge microbial functional potential with clinically relevant phenotypes. Representative applications-including MintTea for disease module identification, gNOMO2 for integrative microbiome profiling, and AGORA-based community metabolic modeling-illustrate the translational scope of these frameworks across inflammatory, metabolic, and infectious disease contexts. Hybrid ML-GEM frameworks have not yet been directly applied to FMT outcome prediction; however, the mechanistic principles underlying both approaches - metabolic compatibility modeling and data-driven responder stratification - suggest a compelling direction for future investigation, contingent on prospective validation in adequately powered and independent clinical cohorts. Persistent methodological challenges-such as data heterogeneity, batch effects across sequencing platforms, incomplete multi-omics coverage, and limited interpretability of complex machine-learning models-are being actively addressed through standardized preprocessing pipelines, explainable Artificial intelligence (AI) strategies, and federated analytics. While federated approaches enable privacy-preserving, multi-institutional model training, they introduce additional constraints related to non-identically distributed data, communication overhead, and uneven computational capacity. Overall, the convergence of mechanistic modeling, data-driven learning, and distributed analytical infrastructures may assist in advancing microbiome research from a largely correlational perspective toward mechanistic and ultimately prescriptive frameworks for precision microbiome medicine.},
}

@article {pmid42256281,
year = {2026},
author = {Yang, J and Liu, Y and Li, B and Zhang, T and Yan, L and Zhang, K and Xu, F and Wang, Z and Liu, Y and Lin, B and Wang, J and Wei, Y},
title = {A tumor-resident Staphylococcus epidermidis strain exhibits genomic and metabolic traits driving hepatocellular carcinoma progression.},
journal = {iScience},
volume = {29},
number = {6},
pages = {116084},
pmid = {42256281},
issn = {2589-0042},
abstract = {Although bacteria have been detected in hepatocellular carcinoma (HCC), the low microbial biomass has hindered isolation of viable intratumoral strains and evaluation of their functional relevance. Intratumoral microbiota profiling by 5R 16S rRNA sequencing, together with a stringent contamination-controlled workflow, identified enrichment of Staphylococcus in advanced-stage (Barcelona Clinic Liver Cancer [BCLC] C) HCC and enabled isolation of a viable S. epidermidis strain, GX3-2, from HCC tissue. GX3-2 promoted HCC cell proliferation and migration in vitro and was associated with accelerated xenograft growth in a pilot intratumoral inoculation model. Multi-omics analyses linked GX3-2 to distinct metabolic features, including adenosine and 2-phenylethylamine (2-PEA), together with host transcriptional programs related to cell cycle and epithelial-mesenchymal transition. These findings provide proof-of-concept evidence that a tumor-derived S. epidermidis isolate may modulate malignant phenotypes in HCC.},
}

@article {pmid42256599,
year = {2026},
author = {Keum, HL and Sul, WJ and Kim, HS},
title = {Comparison of skin microbiota profiles in chronic scratch lesions using tape strip and swab sampling.},
journal = {JAAD international},
volume = {27},
number = {},
pages = {19-20},
pmid = {42256599},
issn = {2666-3287},
}

@article {pmid42257352,
year = {2026},
author = {Guiot, J and Gester, F and Frix, AN and Denis, A and Corhay, JL and Louis, R},
title = {[Environmental exposome and interstitial lung diseases].},
journal = {Revue medicale de Liege},
volume = {81},
number = {5-6},
pages = {327-333},
pmid = {42257352},
issn = {0370-629X},
abstract = {Interstitial lung diseases (ILDs) encompass a heterogeneous group of pulmonary disorders whose prevalence is increasing, partly driven by the environmental exposome. Fine particulate matter (PM2.5), air pollutants, bioaerosols, and occupational exposures (such as silica, asbestos, and organic dust) play a major role in the initiation, progression, and exacerbations of ILDs. These agents induce oxidative stress, inflammation, and fibrotic activation. Conditions such as asbestosis, anthracosilicosis, idiopathic pulmonary fibrosis, sarcoidosis, and hypersensitivity pneumonitis illustrate the interaction between individual susceptibility and environmental factors. Infections and the lung microbiome also contribute to pathophysiology and may act as disease triggers in at-risk populations. The exposome concept provides an integrative framework to understand these complex interactions. Despite recent advances, uncertainties remain, particularly regarding the long-term effects of inhaled ultrafine particles.},
}

@article {pmid42257359,
year = {2026},
author = {Delahaye, T and Absil, G and Damsin, T and Libon, F and Nikkels, A},
title = {[Climate change and skin].},
journal = {Revue medicale de Liege},
volume = {81},
number = {5-6},
pages = {373-379},
pmid = {42257359},
issn = {0370-629X},
mesh = {Humans ; *Skin Diseases/etiology/epidemiology ; *Climate Change ; Ultraviolet Rays/adverse effects ; },
abstract = {Climate change, pollution, extreme weather events, and ecosystem disruption cause a wide range of consequences for the skin and dermatologic diseases, affecting epidemiology, disease behaviour, and therapeutic response. Some inflammatory dermatoses are worsened by ultraviolet radiation, such as cutaneous lupus and Darier disease. In addition, UV radiation is responsible for most skin cancers. Humidity favours skin infections, particularly fungal infections. Pollution exacerbates atopic dermatitis. Rising temperatures increase sweating, an aggravating factor for fungal infections, Darier disease, and hidradenitis suppurativa. Even some drug-related cutaneous adverse effects are modulated by weather conditions. Several aspects of the dermatological activity contribute to pollution and climate changes, by, for instance, packaging, metabolites and conservatives, UV filters and waste generated by dermatological surgery.},
}

Humans
*Skin Diseases/etiology/epidemiology
*Climate Change
Ultraviolet Rays/adverse effects

@article {pmid42257498,
year = {2026},
author = {Bi, R and Zhang, Y and Zhang, W and Shi, C and Qiao, Z and Quan, R and Sun, Y and Chen, J and Wang, R and Ren, F and Li, Y},
title = {Lactobacillus paracasei L9 Ameliorates Pulmonary Fibrosis in Aged Mice via Gut-Lung Axis-Mediated Regulation of Immune Cell Migration.},
journal = {Aging cell},
volume = {25},
number = {6},
pages = {e70576},
doi = {10.1111/acel.70576},
pmid = {42257498},
issn = {1474-9726},
support = {2022QNRC001//Young Elite Scientist Sponsorship Program by CAST/ ; B18053//111 Project of the Education Ministry of China/ ; },
abstract = {Age-related pulmonary fibrosis (PF) imposes a growing global burden with limited therapies. This study explored the role of Lactobacillus paracasei L9 (L9) in alleviating PF in C57BL/6J mice and its mechanisms. Nine-month oral administration of L9 (4 × 10[9] CFU/mL) suppressed collagen (Col-) I deposition in aged mice, with no significant effect on Col-III. Mechanistically, L9 inhibited the JNK-HSF1 signaling pathway, thereby resulting in a 61% decrease in HSP47 expression, which is crucial for Col-I synthesis. L9 reshaped the gut microbiota by increasing short-chain fatty acid (SCFA)-producing bacteria (e.g., Blautia), leading to a 97% increase in serum propionic acid and 193% increase in butyric acid; notably, the levels of SCFAs in the lungs were below the limit of detection. In L9-treated mice, pulmonary IL-17A levels and Th17 cell populations were reduced. In vitro, SCFAs directly inhibited Th17 cell differentiation and IL-17A secretion, and IL-17A was confirmed to promote Col-I synthesis via the JNK-HSF1 pathway in pulmonary fibroblasts. Consequently, L9 modulates the gut microbiota to produce SCFAs, which regulate naïve CD4[+] T cell differentiation and migration via the gut-lung axis. This reduces pulmonary Th17 cells and IL-17A, thereby suppressing Col-I synthesis in pulmonary fibroblasts and ultimately alleviating age-related PF. In conclusion, this study highlights L9 as a microbiome-targeted precision nutrition strategy for the adjuvant therapy of age-related PF via the novel gut-lung axis mechanism.},
}

@article {pmid42257537,
year = {2026},
author = {Yu, J},
title = {Gut microbiome: an emerging player and therapeutic target in cancer.},
journal = {Cancer biology & medicine},
volume = {23},
number = {5},
pages = {},
doi = {10.20892/j.issn.2095-3941.2026.0349},
pmid = {42257537},
issn = {2095-3941},
}

@article {pmid42257577,
year = {2026},
author = {Amenta, E and Grigoryan, L and Laytner, L and Olmeda, K and Paasche-Orlow, MK and Trautner, BW},
title = {Lack of knowledge of antibiotic risks among outpatients is associated with intention to use antibiotics without a prescription.},
journal = {Expert review of anti-infective therapy},
volume = {},
number = {},
pages = {1-7},
doi = {10.1080/14787210.2026.2683611},
pmid = {42257577},
issn = {1744-8336},
abstract = {BACKGROUND: Antimicrobial resistance is a major public health issue. Little is known about patients' understanding of the risks associated with antibiotic use or antimicrobial resistance. We conducted a survey in Houston, Texas among ethnically and racially diverse patients to identify factors associated with knowledge of antibiotic risks and to determine whether knowledge of antibiotic risks impacts patients' intention to use antibiotics without a prescription.

METHODS: A survey was conducted between January 2020 and June 2021 among adult patients in waiting rooms at six public clinics and two private emergency rooms in Houston, Texas. Univariate and multivariate analyses were performed to identify independent risk factors associated with the intention to use non-prescription antibiotics.

RESULTS: Surveys were collected among 564 individuals, of which 62% knew about any risks (individual or public health) associated with antibiotics, 19% had some knowledge of antibiotic resistance, and 6% had knowledge about microbiome effects. Knowledge gaps, younger age, receiving care in public rather than private healthcare setting were independent predictors of intention to use non-prescription antibiotics in the future.

CONCLUSIONS: Improving knowledge regarding antibiotic risks may reduce the use of antibiotics without a prescription.},
}

@article {pmid42257587,
year = {2026},
author = {Tai, D and Latif, K and Shah, P and Sittambalam, G and Demisse, R and Sekaran, K and Gong, J and Figueiredo, JC and Liu, L},
title = {Ultra-Processed Foods and Gastrointestinal Cancer: Epidemiologic Evidence, Mechanistic Pathways, and Clinical Implications.},
journal = {Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology},
volume = {},
number = {},
pages = {},
doi = {10.1158/1055-9965.EPI-26-0417},
pmid = {42257587},
issn = {1538-7755},
abstract = {Ultra-processed foods (UPFs), which NOVA classification defines as industrial formulations composed largely of refined ingredients and additives, now account for a majority of caloric intake in many high-income countries. Epidemiologic evidence suggests high UPF consumption may contribute to gastrointestinal (GI) malignancies independent of traditional nutrient-based dietary metrics. This review examines associations between UPF intake and colorectal, gastric, esophageal, and pancreatic cancers, integrating mechanisms supporting biological plausibility. The association between UPF consumption and colorectal cancer is the most consistent, with 10-30% increased risk among individuals with the highest intake. Evidence also suggests associations with non-cardia gastric cancer and esophageal adenocarcinoma, although data remain limited. Findings for pancreatic cancer are inconclusive. Mechanistically, ultra-processing may promote carcinogenesis through multiple pathways. Disruption of the food matrix and rapid glycemic absorption may activate insulin and insulin-like growth factor signaling. Low fiber content and additive exposure may alter the gut microbiome, reduce short-chain fatty acid production, impair intestinal barrier integrity, and promote chronic inflammation. Nitrates, nitrites, and emulsifiers in UPFs demonstrate pro-inflammatory and carcinogenic effects in experimental models. Although observational design limits causal inference, the consistency of epidemiologic associations, dose-response relationships, and supporting mechanistic data suggest UPF reduction may represent a potential GI cancer prevention strategy.},
}

@article {pmid42257736,
year = {2026},
author = {Di Nezio, F and Di Cesare, A and García-Cobo, M and Brankovits, D and Sabatino, R and Borgomaneiro, G and Fresno-López, Z and Neunschwander Kurtz, M and Boulamail, S and Cozzoli, F and Fumarola, L and Gonzalez, BC and Roldán, A and Camacho, C and García-Herrero, A and Moro, L and Valdivia, C and Mateo-Mederos, E and García-Gómez, G and Fontaneto, D and Corno, G and Eckert, EM and Martínez, A},
title = {Multilayered Human Activities Shape the Microbial Communities of Groundwater-Dependent Ecosystems on an Arid Oceanic Island.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02797-0},
pmid = {42257736},
issn = {1432-184X},
abstract = {Island coastal aquifers, though spatially limited, sustain key ecosystem functions linked to locally critical provisioning, maintenance and cultural ecosystem services. These functions are largely dependent on the presence of highly adapted biological communities, whose microbial components remain poorly understood. Here, we describe bacterial communities across groundwater-dependent ecosystems on Lanzarote (Canary Islands, Spain), spanning habitats with contrasting environmental conditions and degrees of human influence, using 16 S rRNA gene amplicon sequencing. We then infer the processes shaping community variation by integrating diversity partitioning, indicator species analysis, and machine-learning classification. Bacterial taxonomic diversity varied significantly among habitats, with community composition primarily structured by turnover, consistent with environmental filtering. In contrast, predicted human-associated and potentially pathogenic taxa showed patterns dominated by nestedness, indicating localized enrichment linked to anthropogenic inputs. Caves, enclosed marine bays, and hypersaline systems hosted the most compositionally distinct microbial communities, whereas wells and anchialine pools showed greater overlap in community composition. Together, our results suggest that groundwater microbial communities are influenced by the interplay between environmental filtering and anthropogenic inputs, and that coastal aquifers can act simultaneously as reservoirs of natural biodiversity and sinks of human-associated bacteria. These findings highlight the need for integrative monitoring and conservation strategies that incorporate both hydrological and biological components to safeguard groundwater-dependent ecosystems on oceanic islands.},
}

@article {pmid42257753,
year = {2026},
author = {Rajan, H and Devipriya, SP and Bhat, SG},
title = {Integrative frameworks for plastic biodegradation in insect-microbiome systems: mechanistic insights, emerging multi-omics and enzyme engineering perspectives.},
journal = {Biodegradation},
volume = {37},
number = {4},
pages = {},
pmid = {42257753},
issn = {1572-9729},
support = {NTA Ref. No. 211610151053//University Grants Commission/ ; BT/PR48086/BCE/8/1804/2023//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
abstract = {Plastic pollution remains a major global environmental challenge due to the persistence and recalcitrance of synthetic polymers, particularly polyolefins such as polyethylene and polypropylene. Conventional management strategies, including landfilling, incineration, and chemical recycling, are energy-intensive and often fail to achieve complete degradation. Biological approaches offer a promising alternative, yet microbial systems alone are frequently limited by low degradation efficiency, incomplete mineralization, and challenges in scalability. In this context, insect-microbiome systems have emerged as integrated biological platforms in which host physiology and gut microbial communities interact to facilitate polymer transformation. This review synthesizes current knowledge on plastic degradation in insect larvae, with a focus on mechanistic insights into host-microbe interactions. Evidence suggests a multi-step process involving mechanical fragmentation, oxidative modification of polymer chains, microbial depolymerization, and metabolic processing of intermediates. However, the relative contributions of host-derived enzymes and gut microbiota, as well as the extent of true biodegradation versus partial transformation, remain incompletely resolved. Advances in multi-omics approaches have provided important insights into these systems by linking physicochemical changes in polymers to underlying molecular and metabolic processes. At the same time, these data are largely correlative, and direct experimental validation of specific enzymatic roles remains limited. Building on these insights, emerging enzyme engineering and synthetic biology strategies aim to replicate the coordinated, multi-step processes observed in insect systems for improved degradation efficiency. This review highlights insect-microbiome systems as valuable models for understanding complex biodegradation mechanisms and guiding the development of integrated, enzyme-based strategies for sustainable plastic waste management.},
}

@article {pmid42257798,
year = {2026},
author = {Zhou, AN and Liu, L and Huang, MM and Yang, S and Fei, H},
title = {The microbiota-gut-immunity axis in teleost fish: dual regulatory mechanisms of viral infections and prospects for microbiome-based antiviral strategies.},
journal = {Fish physiology and biochemistry},
volume = {52},
number = {3},
pages = {},
pmid = {42257798},
issn = {1573-5168},
abstract = {Bacteria and viruses engage in complex synergistic and antagonistic interactions with profound implications for host health, particularly through functional modulation by intestinal and other mucosal (e.g., skin, gill) microbiota. In teleost models, intestinal microbiota demonstrates dual regulatory capacities-either potentiating or suppressing viral infections. However, the mechanistic underpinnings of these interactions remain inadequately explored in aquatic species. This review systematically delineates the dual regulatory pathways (facilitative vs. inhibitory) through which the gut microbiota modulates viral infections in fish. Based on these mechanisms, we propose a novel microbiota-gut-immunity axis framework-defined as the bidirectional communication network linking gut microbial communities, intestinal barrier function, and host systemic immunity-for the development of integrated antiviral interventions. Furthermore, we critically evaluate emerging strategies-including probiotics, prebiotics, postbiotics, synbiotics, fecal microbiota transplantation (FMT), microalgae, seaweed, and phytoactive compounds-to develop preventive and therapeutic countermeasures. Based on mechanistic insights, probiotics and prebiotics emerge as the most promising candidates for large-scale application, as they directly reshape gut microbial composition and enhance host immunity along the microbiota-gut-immunity axis. In contrast, FMT and herbal medicines, while acting on multiple nodes of the axis, currently face safety and standardization challenges, positioning them as adjunctive therapies. Importantly, these mechanistic insights reveal evolutionarily conserved immune pathways with significant translational potential for human virology.},
}

@article {pmid42257872,
year = {2026},
author = {Martins, FMT and de Azevedo, CS and Rocha, DG and de Melo, DHA and Ribeiro, MC and de Moura, SAL},
title = {Biases and blind spots in the global research agenda on metallic pollution and bees.},
journal = {Die Naturwissenschaften},
volume = {113},
number = {4},
pages = {},
pmid = {42257872},
issn = {1432-1904},
abstract = {Metallic pollution is an emerging and underappreciated stressor contributing to global bee declines, yet the evidence base remains fragmented across metals, taxa, endpoints, and geographic regions. Here, we provide the first hypothesis-driven scientometric synthesis of the global literature on metallic pollutants and bees. Using Web of Science records, we compiled 154 experimental and field-based studies and quantitatively tested five predictions regarding taxonomic, methodological, and thematic biases. Publication output increased sharply after 2013, with China, the United States, and Brazil leading research activity. Research effort was disproportionately concentrated on managed honey bees (Apis mellifera and Apis cerana), adult workers, and dietary exposure pathways, while larvae, wild bee taxa, and environmentally mediated exposures were less examined. Physiological, behavioural and mortality endpoints dominated the literature, whereas reproductive and microbiome impacts remained major blind spots. Adverse outcomes predominate across metals, although essential elements (Zn, Cu, Se) tended to produce less severe effects than non-essential toxic metals (Cd, Pb, Hg), this difference disappeared when exposure concentration and duration were considered. Experimental concentrations varied significantly among metals in food-based exposure studies, indicating substantial heterogeneity in dosing regimes across the literature. Multi-metal studies were not statistically underrepresented, although only a narrow subset of metal combinations has been repeatedly tested. Overall, this synthesis highlights strong structural biases in current knowledge production and identifies priorities for future research, including broader taxonomic coverage, inclusion of early life stages, standardised field-realistic exposures, and integration of chronic, sublethal, and multi-stressor scenarios. Expanding evidence toward more ecologically representative designs will be essential for robust risk assessment of metallic contamination in pollinator communities.},
}

@article {pmid42258061,
year = {2026},
author = {Wu, K and Yang, LX and Chen, ZJ and Du, Y},
title = {Exploring the oral microbiome diversity and genus signatures associated with a novel non-invasive metabolic indicator: a cross-sectional study.},
journal = {The Saudi dental journal},
volume = {38},
number = {6},
pages = {},
pmid = {42258061},
issn = {1013-9052},
abstract = {PURPOSE: To examine the associations between oral microbiome diversity and genus composition with the Zhejiang University Index (ZJU Index) and clinical biomarkers.

METHODS: We included 2,490 eligible participants from the U.S. National Health and Nutrition Examination Survey (NHANES). Oral microbiome diversity was assessed using alpha and beta diversity, and genus-level analyses were based on abundance transformed using the centered log-ratio (CLR) method to account for compositionality. Weighted logistic regression models were used to assess the corresponding associations. Beta diversity disparities were evaluated through Principal Coordinate Analysis (PCoA) and Permutational Multivariate Analysis of Variance (PERMANOVA).

RESULTS: Alpha diversity metrics were positively correlated with the ZJU Index in males aged 30-44 years (Faith's Phylogenetic Diversity: unadjusted: β = 0.05, 95% CI: 0.006 to 0.094, p = 0.033; Model 1: β = 0.058, 95% CI: 0.011 to 0.104, p = 0.026; Model 2: β = 0.076, 95% CI: 0.032 to 0.120, p = 0.005; Model 3: β = 0.081, 95% CI: 0.035 to 0.128, p = 0.008) and in females aged 60-69 years (Observed ASVs: β = 1.242, 95% CI: 0.345 to 2.139, p = 0.042; Faith's Phylogenetic Diversity: β = 0.097, 95% CI: 0.025 to 0.168, p = 0.045). Significant differences in beta diversity metrics were observed among ZJU Index-defined subgroups (p < 0.05), confirmed with age- and sex-stratified analyses. Genera including Bulleidia, Senegalimassilia, Fretibacterium, and Hungatella exhibited significant associations with the ZJU Index and with clinical biomarkers (triglycerides, low-density lipoproteins (LDL), high-density lipoproteins (HDL), insulin, and testosterone).

CONCLUSIONS: Higher oral microbiome alpha diversity was associated with higher ZJU Index in certain populations. Beta diversity demonstrated that ZJU Index-defined subgroups differed in oral microbial composition. Specific genera were identified to be significantly associated with the ZJU Index and clinical biomarkers.},
}

@article {pmid42258064,
year = {2026},
author = {Wei, Q and Ding, D and Zhong, J and Liu, R},
title = {MNRS: Multi-Factor Network-Based Ranking Score for Detecting Critical Transitions of Complex Diseases Using Gut Microbial Data.},
journal = {Bulletin of mathematical biology},
volume = {88},
number = {7},
pages = {},
pmid = {42258064},
issn = {1522-9602},
support = {42450084//National Natural Science Foundation of China/ ; T2341022//National Natural Science Foundation of China/ ; 12401630//National Natural Science Foundation of China/ ; },
abstract = {Disease progression is not always gradual and may instead involve abrupt deterioration, with a critical threshold separating pre-deterioration and post-deterioration states. Detecting such pre-disease states is of major importance because they often precede catastrophic transitions. Increasing evidence suggests that the onset and progression of many diseases, including type 1 diabetes, celiac disease, and colorectal cancer, are closely associated with the gut microbiome. Although transcriptome-based approaches, particularly those relying on gene expression data, have been widely used to identify critical states in biological systems, they are often not well suited to gut microbiome data because of its sparsity, compositionality, and substantial noise. Here, we propose a novel computational framework, termed multi-factor network-based ranking score (MNRS), for detecting pre-disease states from gut microbiome data. MNRS infers perturbed microbial networks and quantifies dynamic alterations in species- or genus-level associations, thereby enabling the detection of early-warning signatures of critical transitions. Analyses of both simulated data and multiple real-world datasets show that MNRS accurately identifies pre-disease states and outperforms existing methods in both robustness and detection performance. In addition, MNRS reveals sensitive "dark species" overlooked by conventional differential abundance analyses but potentially important in disease deterioration.},
}

@article {pmid42258075,
year = {2026},
author = {Shah, TM and Pandit, R and Bhure, M and Nehra, C and Chavda, P and Patil, NV and Patel, AK and Kachhawaha, S and Kumawat, RN and Bhatt, V and Joshi, M and Joshi, C},
title = {Unravelling the effect of moringa supplemented diet on goat gastrointestinal microbiota and metabolic potential.},
journal = {AMB Express},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13568-026-02079-5},
pmid = {42258075},
issn = {2191-0855},
support = {BT/AQ/1/SP41105/2020//Department of Biotechnology, Ministry of Science and Technology, India/ ; BT/AQ/1/SP41105/2020//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
abstract = {Goat is an important livestock species that contribute significantly to global food supply by converting complex plant biomass into animal protein, depending on the gut commensal microbiota for digestion of complex plant biomass. Gastrointestinal tract (GIT) microbiome manipulation using natural plant-based feed supplement is one of the promising strategies for improving livestock performance and mitigating enteric biogases. Moringa oleifera improves animal performance, yet its effects on microbiota structure and functional remodelling across GIT remain poorly understood. Here, we investigated the impact of moringa supplementation on microbiota structure and functional remodelling across the gut in goats. We show that moringa induces microbiota restructuring associated with metabolic output in terms of body weight gain in goat. The forestomach (FS) and large intestine (LI) showed specific enrichment of efficient fibre utilizing and fermentative microbial community, particularly Ruminococcus flavefaciens, Sodaliphilus sp., Prevotella sp., Treponema bryantii, Faecousia sp., and Phocaeicola sp., whereas small intestine exhibited greater abundance of lactate producing microbes such as Rombustia hominis. These spatial patterns reflect alternative metabolic pathways across the GIT driven by nutrient availability. Moringa supplementation selectively enriched microbial genes involved in the metabolic cascades such as production of butyrate and propionate via succinate pathway in FS, while reductive acetogenesis via Wood-Ljungdahl pathway in LI. Decreased abundance of Entodinium and increased abundance of Prevotella were observed in moringa supplemented diet. Our findings provide mechanistic insight into how diet modulates gut microbial ecosystems, demonstrating that a plant-based feed supplement intervention can restructure microbial composition and functional potential along the GIT.},
}

@article {pmid42258100,
year = {2026},
author = {Zahran, E and Elbahnaswy, S and Karam, R and ElBanna, NI and El Sebaei, MG},
title = {The multifaceted challenge of viral nervous necrosis in fish farming: a review of current knowledge and control.},
journal = {Veterinary research communications},
volume = {50},
number = {5},
pages = {},
pmid = {42258100},
issn = {1573-7446},
support = {Grant No. KFU260316.//The Deanship of Scientific Research, Vice Presidency for Graduate Studies and Scientific Research, King Faisal University, Saudi Arabia/ ; },
abstract = {Viral nervous necrosis (VNN), caused by the nervous necrosis virus (NNV) of the genus Betanodavirus, is a significant threat to global aquaculture, resulting in substantial economic losses in both marine and freshwater fish farming. The virus demonstrates considerable genetic diversity, encompassing multiple genotypes and reassortant strains that affect host susceptibility and disease severity across a wide array of fish species. Environmental factors strongly influence viral transmission and outbreak dynamics. Advances in diagnostic methodologies have enhanced the speed and sensitivity of detection. Although commercial vaccines are available for selected host species and production settings, their availability remains limited across fish species, viral genotypes, geographic regions, and early developmental stages. This review summarizes the current knowledge on Betanodavirus virology, host tropism, epidemiology, molecular diagnosis, microbiome, and control. Furthermore, it focuses on advanced disease manipulation via the microbiome and emerging molecular diagnostic platforms.},
}

@article {pmid42258155,
year = {2026},
author = {Chapman, O},
title = {Intraspecific Trait Variation in the Mammalian Gastrointestinal Tract: A Digestive Dive and Systematic Literature Review.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icag070},
pmid = {42258155},
issn = {1557-7023},
abstract = {The gastrointestinal tract (GIT) represents the functional link between food and energy for organisms. It also harbors the gut microbiome, protects against toxins, and eliminates waste, all of which mediate individual health and fitness. The form and function of the GIT can be dynamic, allowing organisms to respond to-and buffer against-rapid changes in their environment and energetic demands. However, knowledge of intraspecific trait variation (ITV) in the GIT is sparse among different taxa and traits (e.g., microstructural traits and physiology). Additionally, the actual mechanics of how these changes occur (e.g., cell proliferation, cellular redistribution) remain largely unknown. This systematic review summarizes the current state of knowledge on mammalian GIT ITV at multiple levels (macroscopic, microstructural, and physiological), speculates as to how global change drivers will affect ITV, and suggests new directions for future work. A comprehensive list of mammal species heretofore examined for GIT morphology and ITV from a total of 260 journal articles or book chapters identified 824 mammal species with quantitative GIT traits available (12% of all mammal species), but only 79 species (1.1%) investigated for GIT ITV. This highlights the increased need to preserve and collect trait data in standardized ways for mammalian GITs, a series of organs typically discarded or unused during specimen preparation. Understanding how wild species utilize GIT ITV to cope with energetic costs will be crucial to predicting how species may fare under rapidly changing environments.},
}

@article {pmid42258310,
year = {2026},
author = {Mehboob, AA and Fatima, R and Kanwal, S and Ali, M and Karim, M and Fatima, S},
title = {Exploring the gut-lung axis in post-liver transplant acute lung injury: A multi-omics approach.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {},
number = {},
pages = {},
doi = {10.1556/030.2026.02911},
pmid = {42258310},
issn = {1588-2640},
abstract = {Acute lung injury (ALI) is a significant post-operative complication of liver transplant (LT), with mounting evidence suggesting a role for the gut-lung axis. However, the mechanistic link between gut microbiota dysbiosis and ALI pathogenesis in LT recipients remains poorly understood. This hybrid translational investigation integrates transcriptomic profiling (bulk and single-cell RNA-seq), immune infiltration analysis, fecal microbiota composition (16S rRNA), and predictive functional profiling in ALI vs. non-ALI (NALI) LT patients. Machine learning algorithms (LASSO, SVM-RFE, Random Forest) were used to identify key gene biomarkers. Microbiota-host gene correlations and canonical correspondence analysis (CCA) were performed to evaluate multi-omic relationships. ALI patients exhibited reduced gut microbial diversity and increased abundance of Enterococcus and Escherichia-Shigella, alongside a depletion of beneficial taxa (Faecalibacterium, Bacteroides). CXCL3, CD48, and IRAK3 were identified as robust ALI biomarkers (Area Under the Curve >0.83), validated in both serum and Bronchoalveolar Lavage Fluid. These genes correlated positively with pro-inflammatory microbes and immune cell infiltration. Functional prediction revealed enrichment in lipopolysaccharide biosynthesis, Toll-like receptor signaling, and bacterial chemotaxis. CCA confirmed that microbiota variation significantly explained host transcriptomic variance. Our study uncovers a functional gut-lung immunological axis in post-LT ALI. Gut dysbiosis modulates immune gene expression and lung inflammation, suggesting that the microbiome serves as a potential source of diagnostic biomarkers and therapeutic targets in transplant-associated lung injury.},
}

@article {pmid42258623,
year = {2026},
author = {Mosquera, RA and Magana-Ceballos, IG and De Jesus Rojas, W and Huang, X and Koochak, H and Tellez, ME and Castillo-Moguel, JA and Bishehsari, F and Mahdavinia, M and Ramos-Benitez, MJ and Harris, T and Yadav, A and Owens, K and Lemus-Rangel, R and Romero, M and Zuleta, S and Luz, A and Baltazar-Fernandez, A and McBeth, KE and Hashmi, S and Rosario Ortiz, G and Santoyo-Rios, J and Loyo-Rodriguez, JF and Colasurdo, GN},
title = {Multi-Omics Analysis Defines Endotypes and Systemic Inflammation in Primary Ciliary Dyskinesia: A Comparison with Healthy Controls.},
journal = {Annals of the American Thoracic Society},
volume = {},
number = {},
pages = {},
doi = {10.1093/annalsats/aaoag152},
pmid = {42258623},
issn = {2325-6621},
abstract = {INTRODUCTION: Primary ciliary dyskinesia (PCD) is a rare genetic disorder characterized by chronic airway inflammation and progressive lung injury. The inflammatory profile and systemic involvement remain poorly defined. We applied integrated multi omics (transcriptomics, proteomics, and metagenomics) to characterize inflammatory signatures and explore saliva as a noninvasive marker of systemic inflammation. These findings may support improved disease characterization and inform therapy and monitoring.

METHODS: This cross sectional, multicenter study included participants with PCD and healthy controls from Houston, Texas; Puerto Rico; and Mexico. Demographic and clinical data were collected in the absence of acute infection. Oral swabs underwent a bulk inflammatory transcriptomic profiling of 590-genes using NanoString nCounter® and microbiome evaluation via metagenomic sequencing. High sensitivity NULISA™ proteomic profiling of 250-proteins was performed on both saliva and plasma, with results correlated across omic layers. Pathway and gene set analyses were conducted using nSolver Advanced Analysis.

RESULTS: Seventy-six participants were enrolled: 51 with PCD and 25 healthy controls. PCD patients, especially those older than 10 years and those with microtubular defects, showed markedly elevated inflammatory gene and protein expression in saliva and plasma. Five inflammatory endotypes were identified: Neutrophilic protease dominant, Dipeptidyl Peptidase 1(DPP‑1) profile (78%); neutrophilic recruiting, high‑Th17 (71%); eosinophilic dominant, high‑Th2 (51%); Th2/Th17‑high (47%), and Th2/Th17‑low (25%). PCD demonstrated increased neutrophil, and CD45‑related gene expression and activation of ten inflammatory pathways, including NF‑κB, oxidative stress, T‑cell-receptor, TREG, Th17, TNF, Th1, Th2, TGF-B signaling, and TLR (P < .01). Saliva and plasma showed strong molecular concordance. Microbiome analysis revealed significant shifts in diversity and abundance linked to inflammatory pathways.

DISCUSSION: These findings show that PCD is characterized by baseline inflammatory activity with marked endotypic heterogeneity, most frequently involving neutrophilic-immune pathways driven by DPP1-associated protease activity and Th17-mediated neutrophil recruitment, while a distinct subset of patients demonstrates a Th2-predominant inflammatory endotype. Salivary inflammatory profiling, which closely mirrors plasma, may offer a practical, non-invasive approach to capturing this patient-level heterogeneity and monitoring systemic immune activity and treatment response, especially with the new anti-inflammatory medications for bronchiectasis.},
}

@article {pmid42258717,
year = {2026},
author = {Wang, Y and Chang, HW and Barratt, MJ and Gordon, JI},
title = {Reply to Wang et al.: Linking microbial metabolites and gut epithelial responses to microbiome-directed therapeutic foods.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {24},
pages = {e2613406123},
doi = {10.1073/pnas.2613406123},
pmid = {42258717},
issn = {1091-6490},
}

@article {pmid42258719,
year = {2026},
author = {Wang, Z and Xie, J and Liu, S and Han, M and Wang, L},
title = {Regulation of gut epithelial barrier and tuft/goblet cell responses by microbiome repair: Opportunities and future directions.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {24},
pages = {e2535289123},
doi = {10.1073/pnas.2535289123},
pmid = {42258719},
issn = {1091-6490},
}

@article {pmid42252506,
year = {2026},
author = {Galtier, A and Warinner, C and Velsko, IM},
title = {Ancient species diversity and niche adaptation in Tannerella and Porphyromonas revealed through pangenomics.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evag136},
pmid = {42252506},
issn = {1759-6653},
abstract = {De novo assembly of ancient and modern bacterial metagenomes can shed light on evolution and ecology of bacterial species that are challenging to culture. Tannerella and Porphyromonas are bacterial genera linked to periodontal disease, and understanding their evolution may reveal insights into their role in oral disease development. We performed pangenomic and phylogenetic analyses on a global set of isolates and metagenome-assembled genomes of the genera Tannerella (n=238) and Porphyromonas (n=976), including 66 genomes from ancient dental calculus samples (up to 14,800 years old), and modern oral samples from present-day living populations. We identify a novel species of oral Tannerella in modern and ancient humans, which we call Ca. Tannerella abscondita, that is related to and often mistaken for Tannerella forsythia but differs in its virulence repertoire. We reveal distinct niche tropism in Tannerella species and Porphyromonas pasteri, but not Porphyromonas gingivalis. There is limited phylogeographic structuring, and virulence genes are homogeneously distributed across continents and oral niches. Saliva-derived strains of T. forsythia and P. gingivalis from Oceania and T. serpentiformis and P. pasteri from Asia show enrichment of pseudogenes related to ecological niche transitions. A phylogenetic analysis of the P. gingivalis major fimbrial protein gene fimA reveals the genes cluster by genotypes, and that no ancient genes are found in genotypes I and Ib. Using de novo assembly for bacterial pangenomics improves the representation of oral genera found in reference databases and enhances our ability to study the evolutionary history of these taxa.},
}

@article {pmid42252693,
year = {2026},
author = {Jourdain, L and Leininger, A and Pacheco, AR and Gu, W},
title = {Environmental selection constrains metabolic network architecture despite taxonomic turnover in anaerobic digestion communities.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag145},
pmid = {42252693},
issn = {1751-7370},
abstract = {Microbial ecosystems often sustain stable metabolic functions despite pronounced taxonomic turnover, yet the mechanisms underlying such reproducible functional states remain poorly understood. Here, we investigated how physicochemical constraints shape functional convergence in anaerobic digestion communities using replicated serial enrichments seeded from four distinct inocula. Across three pH levels and six substrate regimes, replicate communities from different inocula consistently converged toward reproducible metabolite profiles, with pH emerging as the dominant organizing factor. Community composition became progressively environment-driven over time, and after 30 generations, pH explained the largest fraction of compositional variance (PERMANOVA R2 = 0.21, P = 0.001), followed by substrate. Genome-resolved metagenomics revealed that convergence was accompanied by strong pH-dependent structuring of redox-balancing and terminal electron-sink pathways, whereas upstream carbohydrate-entry pathways were conserved. Taxonomic convergence was incomplete and scale-dependent: the ability to correctly assign communities to their inoculum declined from 75% at the genus level to 53% at the phylum level, indicating increasing similarity across inocula at coarser taxonomic resolution despite persistent fine-scale variability. Despite this taxonomic flexibility, communities assembled under identical conditions consistently recruited similar sets of metabolic pathways organized into comparable network architectures. Functional redundancy analyses showed high redundancy and flexible taxonomic implementation for upstream fermentative processes, contrasted with lower redundancy and stronger convergence for terminal methanogenic functions. Together, these results demonstrate that reproducible metabolic function in AD emerges from environmentally constrained assembly of shared metabolic network architectures, rather than deterministic fixation of species composition, highlighting environmental control of metabolic organization as a central principle governing microbiome function.},
}

@article {pmid42252762,
year = {2026},
author = {Ahsan, M and Afzoon, S and Nandni, and Ahmed, A and Mubashirah, and Priyanka, and Rahman, HU and Arif, AR and Faiz, A and Mirza, I and Bhatt, N},
title = {Chronic Kidney Disease and the Gut Microbiota: An Expanding Confluence in the Development of the Disease.},
journal = {Comprehensive Physiology},
volume = {16},
number = {3},
pages = {e70192},
doi = {10.1002/cph4.70192},
pmid = {42252762},
issn = {2040-4603},
abstract = {PURPOSE: Chronic kidney disease (CKD) remains a major global health burden despite advances in conventional therapies. This review synthesizes current clinical and experimental evidence on the bidirectional relationship between CKD and gut microbial dysbiosis, emphasizing mechanisms, measurable outcomes, and therapeutic interventions.

METHODS: A narrative review of recent clinical and experimental studies was conducted to explore alterations in gut microbial composition, generation of uremic toxins, and the impact of CKD therapies on microbial balance. Emerging microbiota-targeted interventions were also examined.

RESULTS: Studies consistently report reduced microbial diversity, loss of short-chain fatty acid (SCFA)-producing taxa, and enrichment of proteolytic, toxin-producing bacteria in CKD. Gut-derived metabolites such as indoxyl sulfate (IS), p-cresyl sulfate (pCS), and trimethylamine N-oxide (TMAO) are linked to oxidative stress, RAAS activation, and fibrogenesis. In human trials, microbiota-directed therapies show modest biochemical benefits: a meta-analysis of 21 randomized studies reported mean reductions in serum BUN (8.5 mg/dL) and CRP (1.4 mg/L) with probiotic or synbiotic supplementation, while inulin (10 g/day) in stage 3-4 CKD reduced serum pCS by 25% and increased fecal butyrate by 40%. However, most mechanistic data derive from animal and in vitro models, and human evidence remains heterogeneous and underpowered. Stage-specific differences are evident-early CKD shows subtler dysbiosis, while advanced CKD and dialysis populations exhibit profound microbial shifts and variable responsiveness.

CONCLUSION: The gut microbiota is a promising, modifiable contributor to CKD pathophysiology. Stage-stratified longitudinal studies are needed to establish causality and therapeutic efficacy.},
}

@article {pmid42252802,
year = {2026},
author = {Stang, A and Illig, T and Hiller, K and Weilert, H and Schmidt, R and Gronauer, R and Seifert, M},
title = {Lowered Abundance of Gut Bacteriophage Species Is Associated With Human Cancer Cachexia.},
journal = {Journal of cachexia, sarcopenia and muscle},
volume = {17},
number = {3},
pages = {e70324},
doi = {10.1002/jcsm.70324},
pmid = {42252802},
issn = {2190-6009},
support = {3465//Asklepios Proresearch, Asklepios Hospitals Hamburg, Germany/ ; },
abstract = {BACKGROUND: Cancer cachexia exemplifies a high medical need condition without effective treatment. Recent studies implicated bacterial gut microbiome alterations to cancer cachexia. Whether the gut bacteriophage profile, an important microbiome component for health and disease, is also related to cancer cachexia remains unknown. We aimed to profile gut microbiome alterations in human cancer cachexia with attention on bacteriophages.

METHODS: We performed shotgun metagenomic sequencing in stool samples from 78 cachectic and 42 noncachectic patients (53% male, mean age 67 ± 8 years) with newly diagnosed, advanced-stage (UICC IV) gastrointestinal cancers. Cachexia was defined according to the main criterion agreed upon international consensus (weight loss [WL] adjusted to body mass index [BMI]). Obtained DNA short-reads were used for k-mers-based, phage-inclusive matching with reference databases, de novo phage assembly and inferring microbiome-encoded functions. We replicated significance-based statistical and prediction-oriented machine-learning analyses in 2022 and 2025 generated metagenome datasets to incorporate the recent change by the International Committee on Taxonomy of Viruses (ICTV) from morphology-based (valid until 2022) to revised genome-based phage taxonomy into microbiome findings of cachexia.

RESULTS: Cachectic and noncachectic patients differed significantly regarding BMI (mean 20.9 vs. 26.4 kg/m2), WL (mean -6.5 vs. -0.2 kg), survival (median 5 vs. 13 months) and clinical cachexia domains (e.g., C-reactive proteine and appetite loss) (all p < 0.001) but not for other clinical covariables (e.g., cancer type) (all p > 0.05). Read-based mapping (2022/2025) identified 1.312/1.513 species (74/39 phage species), and de novo assembly resulted in 4.184/4.209 contigs (corresponding to 65/39 phage species). Concordantly, both analyses (2022 and 2025) showed that prevalent cachexia associated significantly with beta-diversity (Bray-Curtis distance, PERMANOVA, p < 0.05), but not to alpha-diversity (Shannon-Index, ANOVA, p > 0.05), reduced microbiome-encoded detoxification functions (e.g., enriched microbial β-glucuronidase and depleted bacterial efflux pumps) and lowered abundance of bacterial species with false-discovery-rate (FDR)-corrected p < 0.05 (2022: Faecalibacterium prausnitzii, Roseburia intestinalis, Streptococcus species and Lachnospiraceae species; 2025: Faecalibacterium species, Ruminococcus gauvreauii and Intestinibacter bartlettii). Further, lowered abundance of bacteriophages associated with cachexia, predominantly affecting double-stranded (2022: Caudovirales, Siphoviridae, FDR-corrected p < 0.05; 2025: Myoviridae, Siphoridae, p < 0.05) but also single-stranded (2022: Inoviridae, Microviridae, p < 0.05; 2025: Inoviridae; p < 0.05) DNA phage species. In machine-learning models, bacteriophages were top-ranked cachexia predictors (2022: Caudovirales, Siphoviridae; 2025: Myoviridae, Siphoridae). Accuracy was highest when only phage contigs were taken into account (correctly classified instances: 75.0%-85.8%; AUC: 0.703-0.916).

CONCLUSIONS: The previously unknown link between gut bacteriophages and human cancer cachexia expands the scope for basic, translational and clinical microbiome-targeted research in an area of significant unmet medical need.

TRIAL REGISTRATION: Study Box of the German Cancer Society (Registration Number ST-U069, Date: 29 May 2018).},
}

@article {pmid42252976,
year = {2026},
author = {Unno, T},
title = {16S-Pipeline: A comprehensive web-based platform for end-to-end 16S rRNA amplicon sequencing analysis.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {64},
number = {5},
pages = {e2603014},
doi = {10.71150/jm.2603014},
pmid = {42252976},
issn = {1976-3794},
support = {RS-2025-02633155//Rural Development Administration/ ; },
abstract = {16S rRNA gene amplicon sequencing is the most widely used approach for characterizing microbial communities, yet analyzing such data requires navigating a fragmented landscape of bioinformatics tools with distinct installation requirements, parameter settings, and data formats. Here we present 16S-Pipeline, an open-source, web-based platform that provides a complete workflow from raw FASTQ files to publication-ready statistical analyses. 16S-Pipeline automatically detects sequencing type (paired-end, single-end, long-read), variable region, and sequencing platform (Illumina, PacBio HiFi, Nanopore), then performs quality filtering, primer trimming, amplicon sequence variant (ASV) inference via DADA2, taxonomy assignment against SILVA v138.1, phylogenetic tree construction, and optional functional prediction via PICRUSt2. Downstream analyses include alpha and beta diversity, taxonomic composition visualization, differential abundance testing using five complementary methods (ALDEx2, DESeq2, ANCOM-BC2, LinDA, MaAsLin2) with consensus reporting, and KEGG pathway mapping. Built-in NCBI SRA integration enables downloading public datasets for re-analysis and generates submission metadata spreadsheets for data deposition. The interactive web interface built on FastAPI and Plotly Dash enables researchers to perform complex microbiome analyses without command-line expertise. 16S-Pipeline is freely available at https://github.com/tatsu1207/16S-Pipeline under the MIT License.},
}

@article {pmid42253015,
year = {2026},
author = {Wang, Z and Pu, R and Gao, B and Cai, W and Yang, G},
title = {Oral microbiota associated with tooth loss and cognitive function in older adults: Evidence from NHANES.},
journal = {Journal of periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jper.70154},
pmid = {42253015},
issn = {1943-3670},
support = {82271001//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The aim of this study is to investigate the association between tooth loss and cognitive decline and to explore the potential role of salivary microbial genera in this relationship in a nationally representative population.

METHODS: Data from 1,413 adults aged ≥ 60 years in NHANES 2011-2012 were analyzed. Cognitive function was assessed using the Consortium to Establish a Registry for Alzheimer's Disease (CERAD) Word Learning Tests, the Animal Fluency Test (AFT), and the Digit Symbol Substitution Test (DSST). Salivary microbiome profiles were obtained from a subsample of 661 participants using 16S rRNA sequencing. Complex survey regression, PERMANOVA, and multivariable microbial association analyses were applied. Mediation analyses were conducted as exploratory analyses to evaluate potential microbial pathways linking tooth loss with cognitive outcomes.

RESULTS: Moderate tooth loss was associated with higher odds of low global cognition (OR = 2.91, 95%CI: 2.01-4.23), low AFT (OR = 1.57, 95%CI: 1.03-2.39), and low DSST (OR = 2.15, 95%CI: 1.47-3.16) after adjustment. Sixteen genera were associated with at least one cognitive metric, including Prevotellaceae_NA, Phocaeicola, and Lactobacillus. In exploratory mediation analyses, three organic acid-producing genera (Lactobacillus, Lachnospiraceae_NA, and Leptotrichiaceae_NA) were identified as potential contributors to the association between tooth loss and cognition.

CONCLUSION: Tooth loss was associated with cognitive decline in older adults, and both conditions were accompanied by differences in salivary microbial composition. Exploratory mediation analyses suggested that certain organic acid-producing taxa may contribute to the observed association.

PLAIN LANGUAGE SUMMARY: Tooth loss is common in older adults and has been linked to problems with memory and thinking, but the reasons for this connection are not fully understood. In this study, we used data from a large national health survey of adults aged 60 years and older to examine tooth loss, results from several cognitive tests, and the types of bacteria found in saliva. We found that older adults with more missing teeth were more likely to perform poorly on tests measuring memory, attention, and processing speed. We also observed that some types of oral bacteria were related to both tooth loss and cognitive performance. In exploratory analyses, several groups of bacteria that produce organic acids were linked to the relationship between tooth loss and cognitive outcomes. These findings suggest that differences in the oral microbial community may be one of several biological pathways connecting oral health and cognitive function. Understanding how oral health, diet, and oral bacteria interact may help researchers better understand factors related to cognitive aging and to identify potential targets for future research and prevention strategies.},
}

@article {pmid42253256,
year = {2026},
author = {Suchday, P and Dhabuwala, A and Adrejiya, P and Bajpai, P and Shingala, TS and Prajapati, K and Patel, V and Nunna, K and Desai, R},
title = {The Role of Firmicutes in Coronary Artery Disease: A Taxonomic-Level Meta-Analysis of Mendelian Randomization Studies.},
journal = {Current cardiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.2174/011573403X432303260316044935},
pmid = {42253256},
issn = {1875-6557},
abstract = {INTRODUCTION/OBJECTIVE: The Gut Microbiome (GM) plays a critical role in cholesterol metabolism through the production of metabolites such as trimethylamine N-oxide and shortchain fatty acids, contributing to inflammation, endothelial dysfunction, and host gene regulation. This study aims to taxonomically characterize gut microbial profiles, evaluate their association with coronary artery disease, and explore the potential therapeutic implications of microbiome- mediated cardiometabolic pathways.

METHODS: We pooled data from six Mendelian Randomization studies that utilized the MiBio- Gen consortium and CAD, and cardiovascular risk GWAS data from CARDIoGRAMplusC4D, FinnGen, and UK Biobank databases. Within the phylum Firmicutes, inverse variance weighted analysis was used to estimate the association between: (1) protective effects of Clostridiales vadinBB60 group, Genus Butyricicoccus, Genus Ruminococcus UCG010, Coprococcus 1, Intestinibacter, Ruminiclostridium 6, Anaerotruncus, and Family Acidaminococcaceae; and (2) causative effects of Clostridium innocuum group, Genus Turicibacter, Eisenbergiella, Holdemanella, Eubacterium, Coprostanoligenes group, Ruminococcaceae UCG005, and Genus Catenibacterium on CAD.

RESULTS: Higher levels of phylum Firmicutes exhibit a statistically significant protective effect on CAD (OR: 0.880, 95% CI: 0.853-0.907), with low heterogeneity (I² = 20%, P = 0.857). Conversely, an increased abundance of Firmicutes also correlates with a higher risk of CAD (OR: 1.10, 95% CI: 1.06-1.14), showing low heterogeneity (I² = 20%, P = 0.90). Leave-one-out sensitivity analyses confirmed the robustness of these results.

DISCUSSION: The findings highlight a significant relationship between gut microbiome dysbiosis and adverse cardiometabolic outcomes, potentially mediated through inflammatory pathways, metabolic signaling, and microbial metabolite production. These results support the growing role of microbiome-targeted interventions as emerging strategies for cardiometabolic risk modification.

CONCLUSION: Firmicutes exhibit both protective and causative effects on CAD. These findings highlight the complexity of the gut microbiome's role in cardiovascular diseases. Further detailed research on the mechanisms by which specific bacteria at the lower taxonomic levels exert this effect is imperative to understand this complex relationship and its clinical implications.},
}

@article {pmid42253936,
year = {2026},
author = {Wetzel, S and Kohnert, E and Huber, R and Müller, A and Knott, A and Kousoulas, L and Kreutz, C and Badr, MT and Lederer, AK},
title = {Divergent Resilience of Bacterial and Fungal Gut Microbiota After Colorectal Surgery: Insights From a Prospective Longitudinal Cohort Study.},
journal = {MedComm},
volume = {7},
number = {6},
pages = {e70781},
pmid = {42253936},
issn = {2688-2663},
abstract = {The composition of the gut microbiota changes throughout life and is shaped by various external influences, particularly major physiological stressors such as surgery. The extent of these changes and their impact remain poorly understood. This prospective cohort study aimed to investigate changes in the gut microbiota following colorectal surgery and to identify factors that modify these alterations. Paired pre- and postoperative stool samples from 59 patients at the University Medical Centre Freiburg were analyzed using 16S rRNA and ITS2 gene sequencing. Analyses included alpha and beta diversity, LEfSe differential feature analysis, network analysis with Louvain clustering, KEGG pathway annotation, and correlation with clinical parameters. Bacterial diversity significantly decreased postoperatively (Shannon index: p < 0.001), while fungal diversity remained largely unchanged (p > 0.05). Beta diversity revealed increased inter-patient variability in bacterial communities after surgery (PERMANOVA p = 0.001). Preoperative network analyses identified 18 microbial network clusters and interkingdom associations between bacteria and fungi. KEGG pathway mapping showed cluster-specific metabolic profiles, including enrichment in degradation pathways, antimicrobial resistance mechanisms, and bacterial secretion systems. The contrasting responses of bacterial and fungal communities highlight the importance of considering the entire gut microbiome in perioperative care and suggest a central role for interkingdom interactions in maintaining gut homeostasis during surgical recovery.},
}

@article {pmid42253941,
year = {2026},
author = {Yu, R and Zhang, M and Meng, Y and Zhu, C and Zhang, W and Zhang, H and Cao, Z and Du, M and Zhao, Z and Bai, J and Han, Y and Tang, Y and Kang, W and To, KF and Jiao, S and An, L and Zhou, Z},
title = {Gastric Cancer: Pathobiology and Therapeutics.},
journal = {MedComm},
volume = {7},
number = {6},
pages = {e70772},
pmid = {42253941},
issn = {2688-2663},
abstract = {Gastric cancer (GC) remains a formidable global health challenge, characterized by pronounced molecular heterogeneity, late-stage diagnosis, and limited durable responses to existing therapies. This review synthesizes recent advances in GC research through an integrated, multidisciplinary lens, spanning tumor biology, microenvironmental dynamics, and therapeutic innovation. We first consolidate updated histopathological and molecular classification systems, highlighting oncogenic programs that underpin GC development, including Hippo-YAP signaling and emerging neural-stem cell interactions. We then examine the immunosuppressive tumor microenvironment, emphasizing the dynamic crosstalk among tumor-associated macrophages, regulatory T cells, tertiary lymphoid structures, and cancer-associated fibroblasts that collectively drive metastatic dissemination and therapeutic resistance. Emerging biomarker-guided strategies, including CLDN18.2-targeted therapies, dual immune checkpoint blockade, and engineered cellular therapies, are critically discussed alongside rational combination approaches designed to overcome resistance. Beyond canonical paradigms, we highlight transformative frontiers, such as cancer neuroscience, microbiome-driven immune modulation, and spatially resolved multiomics technologies, that enable high-resolution mapping of cellular interactions. Finally, we critically assess translational barriers, including organ-specific metastatic tropism and resistance evolution, and propose that the convergence of deep molecular profiling, neural-immune modulation, and AI-enabled computational oncology will be central to advancing precision medicine for GC. This integrated framework aims to accelerate the development of mechanism-based combination therapies.},
}

@article {pmid42253950,
year = {2026},
author = {Han, X and Guo, XL and Qiu, J},
title = {From gut-reproductive microbiota to ferroptosis: a comprehensive insight into the molecular-pathogenicity of endometriosis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1762013},
pmid = {42253950},
issn = {1664-3224},
abstract = {Endometriosis (EMS) is a highly heterogeneous chronic gynecological disease characterized by pain, infertility, and relapse, with its etiology and pathogenesis not yet fully elucidated. Traditional theories, including "retrograde menstruation," "implantation theory," and "abnormalities in immune tolerance," struggle to adequately explain the complex lesion behavior, diverse phenotypic characteristics, and accompanying immune-metabolic disorders. In recent years, the key roles of imbalances in the gut and reproductive microbiomes, abnormal iron metabolism, and the newly proposed ferroptosis in the occurrence and development of EMS have gradually gained attention, suggesting that this disease may be a systemic condition involving the interplay of microbial ecology, iron metabolism, and cell death. Existing studies indicate that the gut-reproductive microbiome profoundly influences the body's iron homeostasis and iron load by regulating mucosal immunity, systemic inflammatory responses, and metabolic environments. This, in turn, activates the ferroptosis pathway through iron-dependent lipid peroxidation and cell membrane damage, participating in the formation, maintenance, and inflammatory microenvironment shaping of ectopic lesions. Based on these findings, this article systematically reviews the interactions between gut-reproductive microbiome imbalance and iron metabolism disorders, integrating multi-omics evidence such as microbiome analysis, metabolomics, and iron metabolism/ferroptosis-related molecular markers. It proposes a new pathological mechanism framework of "dysbiosis-iron overload-ferroptosis" incorporating microecological imbalance and ferroptosis into a unified picture of the pathogenesis of EMS. Furthermore, this article discusses potential therapeutic strategies and application prospects surrounding microbiome remodeling (such as probiotics, fecal microbiota transplantation, dietary and lifestyle interventions) and pharmacological targeting of key ferroptosis-related molecules. Through a comprehensive and critical analysis of existing evidence, this review aims to provide a more systematic theoretical framework for the mechanistic research of EMS and offer ideas and directions for future clinical translation of precise classification, individualized intervention, and novel treatment plans.},
}

@article {pmid42253968,
year = {2026},
author = {Feng, P and Zhang, W and Zhao, Y and Zhao, P and Li, E},
title = {Synthetic microbial communities: a novel emerging models for dissecting gut microbiota-host interactions in neurodegenerative diseases.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1822743},
pmid = {42253968},
issn = {1664-3224},
abstract = {The gut-brain axis (GBA) has emerged as a critical regulatory pathway underlying the pathogenesis of neurodegenerative diseases (NDs) such as Alzheimer's disease and Parkinson's disease. However, the high complexity and individual variability of native gut microbiotas hinder the precise elucidation of causal relationships between specific microbial taxa, their metabolites, and host neuroinflammatory or neurodegenerative processes. Synthetic microbial communities (SynComs), consisting of defined and reproducible bacterial strains, have recently emerged as powerful experimental models to overcome these limitations. This review summarizes the applications of SynComs in dissecting GBA crosstalk in NDs, highlighting their utility in validating key microbial mediators, deciphering molecular signaling pathways (e.g., microbial metabolite-brain barrier interactions, immune cell activation), and evaluating therapeutic strategies targeting the gut microbiota. By reducing community complexity while retaining core functional traits, SynComs enable controlled in vitro and in vivo studies that bridge the gap between observational microbiome profiling and mechanistic insights. Furthermore, the customization of SynComs allows for mimicking disease-specific microbial dysbiosis, facilitating the identification of novel therapeutic targets for NDs. Collectively, SynComs represent an innovative and standardized tool to advance our understanding of gut microbiota-host interactions in neurodegeneration and accelerate the development of microbiome-based interventions.},
}

@article {pmid42254101,
year = {2026},
author = {Khan, SA and Qamar, MA and Ali, T and Omer, MH and Tahir, A},
title = {Reconsidering immunotherapy resistance: the emerging role of the tumor microbiome in head and neck and lung cancers.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {6},
pages = {3812-3814},
pmid = {42254101},
issn = {2049-0801},
abstract = {Immunotherapy with immune checkpoint inhibitors (ICIs) has revolutionized treatment for non-small cell lung cancer (NSCLC) and head and neck squamous cell carcinoma (HNSCC), yet resistance limits durable responses in many patients. Emerging evidence implicates the intratumoral microbiome - comprising bacteria, fungi, and viruses within tumor tissues - as a key modulator of tumor biology, immune infiltration, and ICI sensitivity, beyond traditional tumor-intrinsic and immune factors. In HNSCC, human papillomavirus (HPV)-negative tumors exhibit higher oncobacteria abundance than HPV-positive ones, with elevated levels linked to worse survival in HPV-positive oropharyngeal cases, suggesting an immunosuppressive tumor microenvironment that may influence ICI outcomes. In NSCLC, intratumoral taxa such as Fusobacterium nucleatum and Bacteroides fragilis promote progression and evasion via immune checkpoint modulation (PD-1/PD-L1), pro-inflammatory pathways (toll-like receptors and cytokines like interleukin-6/tumour necrosis factor-alpha), metabolic reprogramming (PI3K/AKT), and recruitment of suppressive cells (neutrophils and myeloid-derived suppressor cells). Pan-cancer studies show microbial enrichments and compositional shifts in responders versus non-responders to ICI, with metabolites (e.g., lactate and succinic acid) driving M2 macrophage polarization, T-cell suppression, and resistance. The gut-tumor axis further exacerbates refractoriness through systemic dysbiosis and immune alterations. Preclinical models indicate that targeted microbiome interventions - such as fecal microbiota transplantation, specific probiotics (e.g., Bifidobacterium spp. and Akkermansia muciniphila), or selective antibiotics - can restore antitumor immunity, enhance ICI efficacy, and minimize broad dysbiosis risks. Integrating intratumoral microbial profiling into HNSCC and NSCLC clinical trials could refine patient stratification, uncover predictive biomarkers, and accelerate microbiome-directed adjunct therapies, advancing precision oncology and expanding immunotherapy benefits.},
}

@article {pmid42254119,
year = {2026},
author = {Sanan, A and Bibi, F and Sadat, SH},
title = {Rare co-existence of rodent-borne arenavirus patterns and autoimmune-like systemic flares: novel microbiome markers for public health risk stratification.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {6},
pages = {3901-3902},
pmid = {42254119},
issn = {2049-0801},
}

@article {pmid42254157,
year = {2026},
author = {Arif, L and Abbasi, MM and Raza, AA and Samadi, A},
title = {From microbiome profiling to precision medicine: diagnostic and therapeutic potential in gastrointestinal disorders: current evidence, challenges, and future directions.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {6},
pages = {3348-3359},
pmid = {42254157},
issn = {2049-0801},
abstract = {Gastrointestinal (GI) disorders, affecting millions globally (approximately 1.5 billion people with IBS alone), impose a significant healthcare burden and remain challenging to diagnose and manage. Current approaches are often invasive or symptom based, highlighting an urgent need for more precise and personalized strategies. The gut microbiome may offer novel diagnostic biomarkers and therapeutic targets, potentially transforming patient care. It supports GI and systemic health via metabolism, immune modulation, and neurochemical signaling. The dysbiosis of the gut microbiota contributes significantly to the pathogenesis of various GI disorders, including inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), colorectal cancer (CRC), and small intestinal bacterial overgrowth. This narrative review critically evaluates the diagnostic potential of microbiome profiling and its clinical applications in developing personalized therapeutic strategies. We examine cutting-edge techniques such as 16S rRNA sequencing, metagenomics, and metabolomics, and discuss how dietary modulation, precision probiotics, and fecal microbiota transplantation are being increasingly used to reshape gut microbial composition. However, it is critical to note that while microbiome alterations show consistent associations with GI diseases, current evidence remains largely observational and associative. To date, no microbiome-based test has achieved regulatory approval or clinical validation as a standalone diagnostic tool for IBD, IBS, or CRC, and therapeutic applications remain investigational with modest clinical benefits in select conditions. Additionally, we highlight the translational challenges of integrating microbiome-based diagnostics into mainstream clinical practice and propose future research imperatives. This review provides a balanced perspective on the promise and challenges of integrating microbiome-based approaches into clinical gastroenterology, while proposing actionable research priorities to guide future investigations toward clinically validated, patient-centered diagnostic, and therapeutic solutions.},
}

@article {pmid42254190,
year = {2026},
author = {Wu, X and Cai, S and Bai, Z and Li, P and Jia, Y and Li, J},
title = {Association between the oral microbiota and hyperlipidemia: evidence from a national cross-sectional study.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {6},
pages = {3129-3141},
pmid = {42254190},
issn = {2049-0801},
abstract = {BACKGROUND: Oral and gut microbiota interact in the pathogenesis of metabolic diseases. However, the associations between the oral microbiome and host lipid metabolism remain unclear. This study aimed to explore the relationship between metabolic syndrome and the oral microbiome.

METHODS: Participants from the 2009-2012 National Health and Nutrition Examination Survey database were analyzed. Correlations between alpha diversity and hyperlipidemia, as well as blood lipid levels, were examined. Principal coordinate analysis and permutational multivariate analysis of variance were used to determine differences in microbial composition between groups. Linear discriminant analysis effect size (LEfSe) analysis identified key microbial taxa associated with hyperlipidemia. Cox regression and Kaplan‒Meier methods were applied for survival analyses. Functional Annotation of Prokaryotic Taxa and mediation analyses were used to explore the role of microbial functions in microbiome-mediated hyperlipidemia risk.

RESULTS: A total of 3104 participants were included, with 2215 diagnosed with hyperlipidemia. Multivariate linear regression revealed significant correlations between alpha diversity and total cholesterol and low-density lipoprotein levels (P < 0.017). Cox regression indicated that higher oral microbial alpha diversity was associated with a lower risk of cardiovascular mortality (P < 0.017). Beta diversity analysis revealed distinct oral microbial profiles between hyperlipidemic and non-hyperlipidemic individuals (P < 0.017). LEfSe analysis identified Prevotella and Parvimonas as key genera enriched in the oral microbiota of hyperlipidemic participants. Sulfur metabolism partially mediated the association between Parvimonas and hyperlipidemia.

CONCLUSION: The oral microbiota is closely associated with host lipid metabolism. Prevotella and Parvimonas exhibit higher oral abundances in hyperlipidemic individuals, with Parvimonas abundance directly correlated with blood lipids. Parvimonas may increase hyperlipidemia risk via sulfur metabolism. Further studies are needed to elucidate the underlying mechanisms, which could serve as effective targets for hyperlipidemia management.},
}

@article {pmid42254217,
year = {2026},
author = {Saad Ibrahim Abdelghany Elbeshbishy, R and Khatak, A},
title = {The skin microbiome: the overlooked axis in modern dermatology.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {6},
pages = {3045-3047},
pmid = {42254217},
issn = {2049-0801},
abstract = {The skin microbiome plays a critical role in maintaining cutaneous barrier integrity, modulating immune responses, and influencing the expression of dermatologic disease, yet its integration into clinical practice remains limited. Microbial alterations have been described in conditions such as atopic dermatitis, acne vulgaris, psoriasis, and chronic wounds; however, uncertainty regarding causality, interindividual variability, and lack of methodological standardization have hindered clinical translation. Current diagnostic frameworks rarely incorporate microbial metrics, while antimicrobial therapies remain central to management, often without consistent consideration of their ecological impact. Emerging microbiome-directed strategies, including topical probiotics, bacteriophage therapy, and microbiome-preserving approaches, show early promise but lack robust clinical validation. Advancing the role of the skin microbiome in dermatology will require standardized research methodologies, integration of multi-omics approaches, and well-designed clinical trials with clinically meaningful outcomes. This editorial highlights the need for a balanced and evidence-based framework that incorporates microbial perspectives into dermatology without overstating current evidence, advocating for a gradual integration that complements established immunologic and barrier-focused paradigms.},
}

@article {pmid42254258,
year = {2026},
author = {Panhwar, H and Panhwar, DM and Mudasir, M and Mahato, AK},
title = {Microbiome-derived metabolites as novel placental functional markers: predictive role in vasa previa.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {6},
pages = {3859-3860},
pmid = {42254258},
issn = {2049-0801},
}

@article {pmid42254377,
year = {2026},
author = {Storck-Thy, C and Krogfelt, KA and Jønsson, R},
title = {The overlooked role of the seminovaginal microbiota in infertility: a narrative mini review.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1784130},
pmid = {42254377},
issn = {2296-858X},
abstract = {Infertility affects up to 15% of couples worldwide and is influenced by complex biological, immunological, and environmental factors. While reproductive microbiome research has expanded rapidly, the majority of published studies remain largely descriptive, focusing on taxonomic profiling rather than functional or mechanistic insight. Findings from vaginal microbiome studies have been heterogeneous and strongly influenced by methodological variation, and the male genital microbiome has received comparatively less attention, particularly in a couple context. This narrative mini review provides a synthesis of studies investigating paired male and female reproductive microbiomes, emphasizing observational evidence of partner- associated microbial patterns in relation to fertility outcomes. The term 'seminovaginal' microbiota is discussed as a hypothesis describing the transient and dynamic interface arising during sexual activity. Current evidence is limited, largely associative, and constrained by insufficient standardization of sampling, sample handling and processing, data analysis, restricting causal interpretation. Addressing these gaps through coupled, longitudinal, and mechanistic study designs is essential for advancing biologically meaningful conclusions in infertility research and reproductive treatments.},
}

@article {pmid42254439,
year = {2026},
author = {Rahimah, S and Tallei, TE and Savitri, M and Yamada, C and Kim, HJ and Choi, M and Park, MN and Ophinni, Y and Kim, B},
title = {Nutraceutical Interventions in Stunting: Advances, Challenges, and Prospects.},
journal = {Food science & nutrition},
volume = {14},
number = {5},
pages = {e71910},
pmid = {42254439},
issn = {2048-7177},
abstract = {Childhood stunting remains a major global health challenge, reflecting the cumulative effects of inadequate nutrition, recurrent infection, and chronic intestinal dysfunction during early life. Beyond conventional micronutrient supplementation, nutraceutical interventions have emerged as complementary strategies to address the complex biological pathways underlying impaired linear growth. This review synthesizes current evidence on nutraceutical approaches to stunting, including improvements in macronutrient quality, bioactive food components, and microbiome-targeted strategies such as probiotics, prebiotics, synbiotics, postbiotics, and microbiota-directed foods. Evidence from clinical and preclinical studies indicates that nutraceutical effects on growth are generally modest and heterogeneous, with more consistent effects on weight gain than on height-for-age (HAZ). Variability in efficacy is strongly influenced by baseline nutritional status, environmental enteric dysfunction (EED), infection burden, dietary quality, and water, sanitation, and hygiene (WASH) conditions. Mechanistically, nutraceuticals may act through modulation of gut barrier integrity, inflammatory tone, microbial metabolism, and endocrine signaling pathways, particularly those involving the growth hormone-insulin-like growth factor-1 (GH-IGF-1) axis. Recent microbiota-directed food trials provide proof-of-concept that targeted correction of microbiome immaturity and gut dysfunction can support linear growth. Looking forward, advances in nutrigenomics, microbiome science, and epigenetics support a shift toward precision nutrition strategies that tailor interventions to biological responsiveness and context. Systems biology approaches integrating multi-omics data, network pharmacology, and interpretable artificial intelligence are expected to refine mechanistic understanding and guide intervention design. Effective translation will require rigorous trial designs, regulatory clarity, and integration of nutraceuticals within broader stunting reduction frameworks in low- and middle-income countries.},
}

@article {pmid42254500,
year = {2026},
author = {Kubota, A and Zang, L and Shinkai, T and Nakai, M and Tajima, A and Shimada, Y},
title = {Systems-level investigation of the anxiolytic gut-brain interactions induced by paraprobiotic Lactobacillus brevis SBC8803 in zebrafish.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1804536},
pmid = {42254500},
issn = {1664-302X},
abstract = {INTRODUCTION: Anxiety disorders are among the most prevalent mental health conditions worldwide, and interest in psychobiotics-live or inactivated microorganisms that beneficially modulate the microbiota-gut-brain axis-is increasing. Heat killed Lactobacillus brevis SBC8803 enhances serotonin (5 hydroxytryptamine; 5 HT) signaling and ameliorates stress-related phenotypes in mammals, although the gut-brain pathways mediating these effects remain incompletely defined. Here, we investigated the anxiolytic effects and underlying molecular mechanisms of oral SBC8803 administration in adult zebrafish.

METHODS: Adult male AB-strain zebrafish were fed a diet containing heat killed SBC8803 for 4 weeks, and anxiety-like behavior was evaluated using the novel tank test. To explore the underlying mechanisms, we performed brain RNA sequencing and V3-V4 region of 16S rRNA amplicon sequencing of intestinal contents, followed by integrative multi omics analyses, including Gene Set Variation Analysis (GSVA) combined with DIABLO-based data integration and residual correlation analysis.

RESULTS: SBC8803-treated fish exhibited a shorter latency to enter the upper half of the tank and more frequent entries into this region, consistent with reduced anxiety-like behavior. Brain transcriptomic profiling identified differentially expressed genes and enrichment of serotonin receptor, CREB, and oxytocin signaling pathways, suggesting enhanced monoaminergic and plasticity-related signaling. Microbiome functional prediction indicated SBC8803-associated shifts in lipid and vitamin metabolism, including pathways related to riboflavin (vitamin B2) and tryptophan. GSVA combined with DIABLO-based data integration revealed coordinated changes between microbial metabolic and brain signaling pathways, consistent with a vitamin B-serotonin-anti-inflammatory axis linking gut metabolism to neural regulation. Furthermore, residual correlation analysis showed innate gut-brain coordination independent of the SBC8803 effect, such as the coupling between brain arachidonic acid and gut histidine metabolism.

DISCUSSION: These findings support the biological validity of the SBC8803 administration-associated interactions observed in the multi-omics analyses. These findings suggest that the paraprobiotic SBC8803 may exert anxiolytic-like effects in zebrafish and reshape gut-brain network states at behavioral, microbial, and transcriptomic levels, providing a potential mechanistic framework for considering heat killed SBC8803 as a candidate psychobiotic for anxiety-related conditions.},
}

@article {pmid42254513,
year = {2026},
author = {Zhang, H and He, R and Xu, L and Zhou, H and Yu, R and Huang, P},
title = {A multi-omics case-control study identifying oropharyngeal microbiome-metabolite patterns that characterize secondary bacterial pneumonia among influenza patients.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1824965},
pmid = {42254513},
issn = {1664-302X},
abstract = {Secondary bacterial pneumonia is a severe complication of influenza;howeve the biological determinants that distinguish progression from uncomplicated infection remain poorly understood. We investigated the oropharyngeal microbiome and plasma metabolome as potential discriminators of pneumonia development. In this study, we report a cross-sectional case-control study conducted during the 2022-2023 influenza season to identify and internally validate a microbiome-metabolite profile that characterizes pneumonia cases from uncomplicated influenza. We enrolled 236 consecutive influenza patients from Jiangsu Province, China (October 2023-December 2024): 59 with secondary pneumonia and 177 uncomplicated controls. Oropharyngeal swabs were subjected to 16S rRNA V3-V4 sequencing; plasma metabolomics was performed by UPLC-MS/MS in both ion modes. Seven machine-learning algorithms were compared; Least Absolute Shrinkage and Selection Operator (LASSO) logistic regression was selected because it yielded the highest cross-validated discrimination. Microbial composition distinguished groups, not richness. Pneumonia cases showed enrichment of Synergistota and Bifidobacteriaceae with depletion of Bacillaceae (β-diversity p = 0.057). Controls exhibited enriched glycolysis and lipid metabolism pathways; pneumonia cases showed elevated degradation pathways (GLUCARDEG and GALLATE-DEGRADATION). Plasma metabolomics revealed a lipid depletion signature: phospholipids PC(O-16:0/0:0) and PS(14:0/18:3(9Z,12Z,15Z)) were significantly reduced (area under the (receiver operating characteristic) curves (AUCs) = 0.69-0.71). Small Molecule Pathway Database (SMPDB) pathway analysis demonstrated suppressed anabolic (tyrosine, steroid, and purine metabolism) and enhanced catabolic (beta-oxidation of very long-chain fatty acids) pathways. Machine learning identified Peptococcus as the top indicator (LASSO AUC = 0.65); Shapley Additive Explanation (SHAP) analysis revealed a monotonic risk increase with abundance. Oropharyngeal dysbiosis and systemic metabolic reprogramming characterize influenza cases that progress to secondary pneumonia. Peptococcus and four metabolites form an internally validated exploratory profile associated with secondary pneumonia; external validation and performance optimization are warranted.},
}

@article {pmid42254515,
year = {2026},
author = {Chen, H and Montero-Vale, M and Owusu-Kyei, K and Lara-Muñoz, A and Rubio-Garcia, E and de Pedro-Jové, R and Guiral, E and Chileshe, MN and Williams, J and Bofill, A and Samai, M and Casals-Pascual, C and Vila, J and Menéndez, C},
title = {Early-life carriage and antibiotic resistance of Streptococcus pneumoniae in infants from Sierra Leone.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1822296},
pmid = {42254515},
issn = {1664-302X},
abstract = {Streptococcus pneumoniae remains a major cause of child morbidity and mortality in sub-Saharan Africa, with increasing macrolide resistance mediated by erm(B) and mef(A/E/I). Integrating phenotypic and sequencing-based approaches may improve antimicrobial resistance surveillance accuracy. This study assessed nasopharyngeal carriage and macrolide resistance of S. pneumoniae among young infants in Sierra Leone (November 2022-February 2023), nested within the ICARIA trial (NCT04235816) which evaluated azithromycin for child mortality reduction. Infants aged 6-10 weeks presenting for Penta-1 immunization before trial recruitment were enrolled. Two nasopharyngeal swabs were collected per infant. S. pneumoniae was detected by lytA PCR, azithromycin minimal inhibitory concentrations (MICs) were determined by E-test, and erm(B) and mef(A/E) were identified by PCR in isolates. A subset of paired samples underwent targeted amplicon sequencing for microbiome and resistome profiling. Carriage prevalence was 17.3% (162/936; 95% CI: 14.9-19.9%), with 45.7% (74/162) of isolates resistant to azithromycin (MIC ≥ 2 μg/mL). High-level resistance (MIC ≥ 64 μg/mL) was mainly mediated by erm(B) alone (53.8%) or in combination with mef(A/E) (38.5%), whereas all 22 moderately resistant isolates (MIC 2-48 μg/mL) carried mef(A/E) only. Among susceptible isolates, 3.8% (2/52) harbored mef(A/E) despite low MICs. Microbiome sequencing showed 96% concordance with lytA PCR for S. pneumoniae detection. Normalized resistome read counts for erm(B) and mef(A/E) were significantly higher in PCR-positive samples (p = 1.98 × 10[-9] and p = 8.14 × 10[-7]). These findings provide the first estimates of nasopharyngeal S. pneumoniae carriage and macrolide resistance among infants in Sierra Leone, revealing a high prevalence of resistance. The results underscore the need to strengthen antibiotic stewardship, particularly in child survival programs with azithromycin. Large and longitudinal studies are also needed. Clinical Trial Registration: ClinicalTrials.gov, NCT04235816.},
}

@article {pmid42244577,
year = {2026},
author = {Ettinger, CL and Eisen, JA},
title = {Phoronids and their tubes harbor distinct microbiomes compared to surrounding sediment.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.05.28.596327},
pmid = {42244577},
issn = {2692-8205},
abstract = {Phoronids are a phylum of animals with only ∼12 described species, all of which are marine filter feeders that build external tubes for shelter and produce chemical deterrents against predators. Many tube-building invertebrates host distinct microbial communities and even have obligate symbionts for survival in sulfur-rich marine sediments. However, the microbiome of phoronids has only recently begun to be described. To address this, we surveyed the composition of the microbiome of the phoronid, Phoronopsis harmeri , using 16S rRNA gene amplicon and metagenomic sequencing. We found that the phoronid microbiome was dominated by members of the orders Campylobacterales, Desulfobulbales, and Desulfobacterales. We also found that the microbiomes of tubes and phoronids were less diverse than that of surrounding sediment, and that the microbiomes of phoronids, tubes and surrounding sediment were all distinctly structured. Based on analysis of metagenomic data, and even though we were only able to recover low quality MAGs of abundant taxa, we found preliminary evidence that taxa associated with phoronids and their tubes likely participate in sulfur cycling pathways. Future work should perform more robust metagenomic sequencing and chemical analysis to assess if there is a link between known phoronid chemical defenses and microorganisms. Overall, this study provides foundational insight into the microbial communities associated with phoronids and these initial findings suggest that these communities may play an important role in sulfur cycling in marine sediments.},
}

@article {pmid42244628,
year = {2026},
author = {Getange, D and Mukaratirwa, S and Chebet, D and Kabii, J and Khogali, R and Villinger, J},
title = {Ehrlichia ruminantium infection is associated with tissue-specific microbial community shifts in Amblyomma gemma ticks from cattle in Kenya.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.26.727963},
pmid = {42244628},
issn = {2692-8205},
abstract = {UNLABELLED: Tick-borne pathogens can reshape vector microbiomes in ways that influence pathogen colonisation and transmission, yet the interplay between Ehrlichia ruminantium and the microbiota of its tick vectors remains uncharacterised. We profiled bacterial communities in haemolymph, midgut, and salivary glands of infected (n = 11) and uninfected (n = 12) Am. gemma ticks, a vector of E. ruminantium in East Africa, collected from cattle in Kajiado County, Kenya, using near-full-length 16S rRNA gene amplicon sequencing on the Oxford Nanopore platform. Community composition, alpha and beta diversity, co-occurrence networks, keystone taxa, and PICRUSt2-inferred functional profiles were compared across tissue-infection status groups. We identified 226 bacterial genera dominated by Coxiella , Pseudomonas , Acinetobacter , Proteus , and Rickettsia . Infection was associated with tissue-specific shifts in community composition (PERMANOVA R [2] = 0.14, p < 0.001) and co-occurrence network structure, with midgut networks showing complete hub taxon turnover (Jaccard = 0.000, p = 0.043). Haemolymph communities converged around Luteimonas as a keystone taxon, while opportunistic Proteobacteria, including Acinetobacter and Serratia , emerged as keystones in infected midgut. Endosymbiotic Rickettsia was near-absent in infected tissues (0.3% vs 9.3% mean relative abundance in midgut), consistent with competitive exclusion. Functional inference identified FDR-significant enrichment of predicted aerobactin siderophore biosynthesis, antimicrobial efflux, and oxidative stress response gene families in infected microbiota. These findings show tissue-specific restructuring of the Am. gemma microbiome associated with E. ruminantium infection and point to candidate targets for microbiome-based interventions against heartwater.

IMPORTANCE: Heartwater, caused by the bacterium Ehrlichia ruminantium and transmitted by Amblyomma ticks, kills up to 90% of susceptible ruminants and is one of the most devastating tick-borne diseases in sub-Saharan Africa. Controlling heartwater requires understanding how the pathogen interacts with the microbial communities living inside its tick vector. In this exploratory study, we show that E. ruminantium infection is associated with tissue-specific shifts in the Amblyomma tick microbiome, including reduced abundance of beneficial symbionts, elevated representation of opportunistic bacteria among community hubs, and enrichment of iron acquisition and antimicrobial resistance functions. The midgut, the first tissue colonised during infection, showed the most marked structural reorganisation. These tissue-resolved microbiome signatures point to potential targets for novel control strategies, such as anti-microbiota vaccines or approaches that reinforce natural colonisation resistance, offering new strategies to reduce heartwater transmission and protect livestock livelihoods across Africa.},
}

@article {pmid42244638,
year = {2026},
author = {Zeng, X and Meng, X and Weakley, AM and Jarrett, KE and Higginbottom, S and Lopez, EM and Cabrera, AV and Gray, IJ and DeFelice, BC and Terasaki, M and Lai, R and Brearley-Sholto, M and Zhao, A and Hall, KR and Levia, M and Arreola, J and de Aguiar Vallim, TQ and Fischbach, MA},
title = {Ecology and engineering to modify the bile acid output of a defined microbial community.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.23.727444},
pmid = {42244638},
issn = {2692-8205},
abstract = {The bile acid pool, which is synthesized collaboratively by the host and its microbiome, impacts metabolism, immunity, and disease risk. Targeted microbiome interventions could in principle reshape the bile acid pool for therapeutic benefit, but practical strategies remain elusive. In the course of screening a complex defined community for metabolic phenotypes by dropping out individual strains, we observed that several of the single-strain dropout communities had markedly increased deoxycholic and lithocholic acid levels and a larger bile acid pool. In each of these communities, a second strain- Lactobacillus plantarum- had bloomed. The bile salt hydrolase activity of L. plantarum was necessary and sufficient to expand the size of the bile acid pool. An engineered community in which the bsh gene is overexpressed in multiple Lactobacillus strains confers on mice increased levels of secondary bile acid levels and a larger pool size. By overexpressing a different pair of bile acid metabolic genes in multiple strains of Lactobacillus -7α- and 7β-hydroxysteroid dehydrogenase-we changed the composition of the bile acid pool, enlarging it and redirecting it toward ursodeoxycholic acid. Together, these results demonstrate that fine details of the microbiome's strain composition can have a substantial effect on bile acid metabolism, and that rational manipulation of the microbiome can alter the size and composition of the bile acid pool.},
}

@article {pmid42244647,
year = {2026},
author = {Zeng, X and Meng, X and Weakley, AM and Higginbottom, S and Lopez, EM and Cabrera, AV and Gray, IJ and DeFelice, BC and Terasaki, M and Zhao, A and Hall, KR and Levia, M and Arreola, J and Fischbach, MA},
title = {A single-strain dropout screen reveals mechanistic links between microbial ecology and metabolism.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.23.727446},
pmid = {42244647},
issn = {2692-8205},
abstract = {The complexity of the gut microbiome has made it challenging to define the role of individual species in community-level function. Here, we constructed 56 single-strain dropout variants of a defined 118-member community and used each one to colonize a group of germ-free mice. In many cases, removing a single strain triggered a large reordering of a small group of species, which in turn altered the community's metabolic output. En bloc removal of the eight-strain acetogen compartment markedly reduced acetate production and caused intestinal H 2 accumulation and bloating; a specific subset of four acetogens was sufficient to relieve bloating and restore acetate production. Together, these data show that small disturbances in community composition can trigger a confined ecological reorganization with a large chemical phenotype, and they reveal novel strategies for engineering communities with altered metabolic output.},
}

@article {pmid42244659,
year = {2026},
author = {De Silva, GLSN and Vinzelj, J and Miller, SL and Jemmett, AM and Elshahed, MS and Youssef, NH},
title = {Diversity and community structure of anaerobic gut fungi in camels.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.28.728439},
pmid = {42244659},
issn = {2692-8205},
abstract = {Anaerobic gut fungi (AGF) are key members of the herbivorous gut microbiome. While AGF communities have been well-studied in foregut and hindgut fermenters, they remain poorly characterized in pseudoruminants such as camels. Here, we present a comprehensive culture-independent diversity survey of 142 fecal samples from all three extant camel species (Camelus dromedarius , Camelus bactrianus , and Camelus ferus). The AGF community in Camelus was highly diverse, with representatives of 42 AGF genera identified. However, this diversity was unevenly distributed, with three genera (Neocallimastix , Caecomyces , and Orpinomyces) accounting for 70.7% of sequences encountered, and only 12 genera exceeding 1% relative abundance in the entire dataset. While several of the genera identified as major components of the AGF community in camels are highly ubiquitous in all herbivores, others, such as Oontomyces, Aestipascuomyces , Liebetanzomyces , and the yet uncultured genera NY09, NY03, and JV-2025d are extremely rare in ruminants and hindgut fermenters, hinting at their preference and potential co-evolution with the Camelidae . Ordination approaches identified host species and biogeography as key determinants driving AGF community structure differences between various camel species. Comparative community structure analysis between AGF community in camels versus reference foregut and hindgut fermenters identified the relative enrichment of the genera Oontomyces and Aestipascuomyces in pseudoruminants datasets. Our results demonstrate a distinct AGF community composition in Camelidae , elucidate factors impacting AGF diversity and community structure variations in Camelus, and identify key distinct taxa differentially enriched in psuedoruminants compared to ruminants and hindgut fermenters. The ecological and evolutionary drivers of such patterns are discussed.},
}

@article {pmid42244690,
year = {2026},
author = {Tao, J and Gomez, D and Abu, YF and Rojas, K and Roy, S},
title = {Short-term oxycodone exposure produces delayed and persistent gut microbiome disruption in mice.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.26.727957},
pmid = {42244690},
issn = {2692-8205},
abstract = {UNLABELLED: The gut microbiome is a critical part of host homeostasis, yet its resilience following opioid exposure remains poorly understood. While opioid-induced short-term dysbiosis is well documented, the long-term recovery dynamics following oxycodone remain unclear. This study characterized the temporal dynamics of the fecal microbiota in male C57BL/6J mice following a brief 3-day oxycodone regimen (5mg/kg, BID). 16S rRNA gene sequencing was performed at baseline, day 3, 10, 17, and 70. While acute post-treatment phases (day 3 to 10) showed subtle taxonomic shifts in Clostridium_sensu_stricto_1 and Romboutsia , significant community disruption emerged later. By day 17, beta diversity significantly differed from saline controls (P =0.002). At day 70, both alpha diversity (p=0.02) and beta diversity (P=0.007) remained significantly altered, characterized by enriched Akkermansia and Marvinbryantia alongside depleted Eubacterium_xylanophilum . These findings demonstrate that even brief oxycodone exposure triggers persistent, non-recovering dysbiosis that became detectable only after treatment cessation and persisted through day 70. This suggests that the window for microbiome recovery exceeds two months in mice (equivalent to several human years), highlighting a potential long-term risk for patients prescribed short-term opioid courses.

IMPORTANCE: Short-term opioid exposure is generally assumed to cause only transient disruption of the gut microbiome. However, the duration of microbiome recovery following clinically relevant opioid treatment remains poorly defined. In this study, we show that a brief three-day course of oxycodone in mice resulted in delayed and persistent alterations in gut microbial community structure that remained detectable for at least 70 days after treatment cessation. Notably, significant divergence in microbial composition emerged weeks after exposure rather than immediately following treatment, suggesting that short-term opioid use may initiate longer-lasting remodeling of the gut microbiome than previously appreciated. These findings highlight the importance of considering extended recovery timelines when evaluating the microbiological consequences of opioid exposure.},
}

@article {pmid42244733,
year = {2026},
author = {Grossman, A and Weng, J and Silverman, AD and Bor, B},
title = {Resolving Host-Episymbiont Interaction Dynamics through Continuous Cultivation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.01.722272},
pmid = {42244733},
issn = {2692-8205},
abstract = {UNLABELLED: Patescibacteria are an elusive linage of "microbial dark matter" bacteria predicted to represent ∼25% of total bacterial diversity. Despite this abundance and ubiquity, these organisms are challenging to cultivate, resulting from their specialized episymbiotic lifestyle. All cultivated representatives to date, predominantly composed of Saccharibacteria from the oral microbiome, depend on cognate prokaryotic hosts for growth and reproduction. Studying the growth dynamics of episymbiotic bacteria and their hosts in batch cultures has suggested that many episymbionts initially reduce host populations, and that hosts eventually adapt to episymbiont stress after serial passaging. However, discontinuous batch cultures do not reflect natural interactions between these organisms due to their drastically different growth rates. An episymbiont requires several (∼2-4) serial passages alongside its host to reach the high cell densities needed to impact host growth, which complicates investigation of host inhibition and adaptation to episymbiont stress. To describe these dynamics accurately, we utilized continuous culture via small-scale Raspberry Pi powered bioreactors, called Pioreactors. Within a bioreactor, host bacteria can be cultivated at a consistent growth rate indefinitely, providing the perfect substrate for cultivation of model Saccharibacteria. Quantification of time until host crash, crash severity, time until recovery, and stable co-culture density provides mechanistic ways to describe episymbiont-host interactions. First, we used these techniques to compare episymbiont infection by three different episymbionts, revealing distinct infection patterns ranging from mild inhibition with rapid host adaptation, to rapid host collapse followed by "arms race" oscillation dynamics. Then, bioreactors were used to quantify the episymbiotic role played by a known host-binding type 4 pili (T4P-2), demonstrating that loss of long-distance host binding significantly delayed the host crash without altering general crash dynamics. These experiments reveal that episymbionts can have drastically different effects on bacterial communities and provide the tools necessary to describe strain/species differences and molecular interactions.

IMPORTANCE: Episymbiotic Patescibacteria represent one of the largest branches of life on Earth, as well as one of the least understood. Furthermore, because Patescibacteria can manipulate their hosts growth and morphology they have immense ecological potential to be shaping the communities they occupy, both environmental and microbiome-associated. Our study highlights for the first time the potential of small-scale continuous cultivation for studying episymbiotic interactions that cannot be captured in discontinuous cultures. Herein we used these techniques to interrogate inter-species variation in host inhibition potential and to determine how loss of a long-distance episymbiosis factor mechanistically alters the cycle of episymbiont infection; however, this cultivation platform will enable researchers to answer many new questions about these ubiquitous host-episymbiont interactions.},
}

@article {pmid42244821,
year = {2026},
author = {Gao, X and Zou, Y and Fang, J and Wu, X and Zheng, W and Zhang, Y and Hao, W},
title = {The association between tongue features and tongue coating microbiota and gastrointestinal cancer: a systematic review and meta-analysis.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2681268},
pmid = {42244821},
issn = {2000-2297},
abstract = {BACKGROUND: Gastrointestinal (GI) cancers pose a significant health burden, highlighting the need for non-invasive biomarkers. Tongue inspection, a traditional diagnostic method in Chinese medicine, has been increasingly quantified via imaging and microbiome analysis.

OBJECTIVE: This review synthesizes evidence on tongue features and coating microbiota in GI cancer detection.

DESIGN: We systematically searched PubMed, EMBASE, Cochrane and Chinese databases until July 2025 for case-control or cohort studies comparing tongue characteristics or microbiota between GI cancer patients and healthy controls. Data were pooled using fixed- or random-effects models.

RESULTS: Sixteen studies (n = 4,994) were included. GI cancer patients showed significantly higher rates of abnormal tongue body morphology (OR = 5.33, 95% CI 3.26-8.72), abnormal tongue body color (OR = 17.85, 95% CI 7.01-45.54), abnormal tongue coating texture (OR = 5.98, 95% CI 4.02-8.91) and abnormal tongue coating color (OR = 3.24, 95% CI 2.00-5.26) versus controls. Although α-diversity did not differ, certain taxa (e.g. Actinobacteria, Prevotella_7) were reduced in cancer patients. Subgroup analyses by cancer type showed generally consistent directions of association for abnormal tongue manifestations in gastric, colorectal and esophageal cancers, despite significant heterogeneity.

CONCLUSION: Abnormal tongue features and specific microbial shifts are associated with GI cancers, suggesting potential non-invasive tools for early detection. However, due to heterogeneity and methodological limitations, further large-scale prospective studies are needed for validation.},
}

@article {pmid42245041,
year = {2026},
author = {Hu, S and Cheng, H and Gillenwater, L and Manpearl, K and Mandava, A and Wang, Y and Pividori, M and Stranger, B and Krishnan, A and Greene, CS and Gao, Y},
title = {Beyond Identifier Matching: An Empirical Characterization of Failure Modes in Biomedical Knowledge Graph Integration.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.26.26354182},
pmid = {42245041},
abstract = {OBJECTIVE: Biomedical knowledge graphs (KGs) such as PrimeKG, Hetionet, UMLS, and PharmGKB are increasingly used as the substrate for downstream machine-learning, retrieval-augmented generation, drug-repurposing, and electronic health record (EHR) augmentation pipelines. The dominant assumption in published work is that integrating two or more such KGs is a tractable engineering step solved by identifier (ID) matching. This paper interrogates that assumption empirically. We quantify how much concept overlap survives realistic alignment, and we characterize the new failure modes introduced by the methods that practitioners reach for when ID matching is insufficient.

MATERIALS AND METHODS: We compared four widely used biomedical KGs (PrimeKG, Hetionet v1.0, the full UMLS Metathesaurus, and PharmGKB) across eleven node types using a tiered alignment pipeline: (1) direct ID matching for nodes sharing a primary vocabulary; (2) cross-ontology bridging using standard mappings (e.g., MONDO↔DOID, HPO↔UMLS, HPO↔UMLS↔MeSH for side effects, NCBI Gene↔HGNC↔UMLS, UBERON↔FMA/SNOMEDCT_US/NCI/MeSH for anatomy); (3) ClinicalBERT cosine-similarity grouping at threshold ≥ 0.98 for over-segmented disease nodes, with a deterministic suffix-stripping canonicalizer; (4) exact name matching for ontology-poor types (anatomy, REACTOME pathways); and (5) embedding-based fuzzy matching with UMLS lookup (SapBERT and ClinicalBERT) for free-text microbiome concepts. We applied the pipeline to a 698-concept gut-microbiome benchmark spanning taxa, pathways, and disease labels, validated grouping decisions against the curated SSSOM mappings released by the MONDO project, and audited the ClinicalBERT consolidation against five clinical-genetics case studies drawn from the literature.

RESULTS: Per-type pairwise coverage was strikingly asymmetric. Genes/proteins and the three Gene Ontology categories aligned cleanly across PrimeKG and Hetionet (mutual coverage 94-99%), but disease overlap was sparse: only 0.7% of PrimeKG individual disease nodes mapped to Hetionet, rising to 2.0% after MONDO grouping (versus 78.7% and 18.4% from the Hetionet side). PrimeKG-to-UMLS coverage spanned 100% (effect/phenotype via HPO) down to 20.8% (REACTOME pathways), with drugs at 73.7% and anatomy at 58.8%. PrimeKG-to-PharmGKB drug coverage required up to two bridging hops (DrugBank → UMLS → RxNorm/ATC/MeSH). Bigger was not uniformly more complete: on a 698-concept microbiome drug benchmark, Hetionet missed 0 concepts while PrimeKG missed 16. ClinicalBERT-based grouping consolidated 22,205 raw MONDO disease nodes into 17,080 groups but introduced three reproducible failure modes documented in case studies: (i) peer over-merging: for example, all 22 osteogenesis imperfecta subtypes collapsed into a single node despite distinct severity classes; (ii) parent-child collapse: e.g. acute myeloid leukemia merged with myeloid leukemia, erasing the acute/chronic distinction that drives clinical management; and (iii) lexical false positives: neurofibromatosis and schwannomatosis grouped together despite cellular-pathology differences.

DISCUSSION: Identifier matching alone is a weak baseline for biomedical KG integration. Cross-ontology bridges and embedding-based consolidation expand coverage but do so at the cost of clinically meaningful resolution, and the resulting failures are systematic rather than random. Reporting only aggregate coverage statistics obscures these losses, which propagate silently into downstream tasks.

CONCLUSION: We provide reusable per-type coverage tables, a taxonomy of three integration failure modes, and concrete recommendations for downstream studies that depend on a unified biomedical KG. We argue that future KG integration work should report per-type coverage and per-cluster confidence rather than aggregate match rates.},
}

@article {pmid42245388,
year = {2026},
author = {Benjelloun, J and Hnini, M and Bouzroud, S and El Attar, I and Mghazli, N and Hami, A and Talbi, C and Aurag, J and Smouni, A and Guedira, A and Taha, K},
title = {Bioprospecting Cycas revoluta-associated bacterial endophytes for tomato (Solanum lycopersicum L.) growth promotion under salt stress.},
journal = {3 Biotech},
volume = {16},
number = {6},
pages = {253},
pmid = {42245388},
issn = {2190-572X},
abstract = {UNLABELLED: Twenty endophytic bacterial strains isolated from Cycas revoluta coralloid roots were characterized for their salt stress tolerance and phyto-beneficial properties, mainly indole-3-acetic acid production, siderophore secretion and phosphate solubilization under both optimal and stressful conditions. Their genetic diversity was assessed through 16 S rRNA gene sequencing. Results demonstrated a significant diversity of genera, including Agrobacterium, Pseudomonas, Pantoea, Bacillus, Peribacillus, Ochrobactrum, and Stenotrophomonas. Salt tolerance assays and PGP screening revealed the high tolerance threshold and PGP potential of two of isolated bacteria (Pantoea sp. LMR-C62 and Bacillus sp. LMR-C11). Tomato (Solanum lycopersicum L. cv Campbell 33) seeds bio-priming with these strains significantly improved germination rate (up to 75.3% at 150 mM NaCl) and decreased the mean germination time compared to non-inoculated seeds. In greenhouse trials, plantlet inoculation with these two strains led to significant improvements in root length (up to +55%), shoot dry weight (+72%), leaf area (+33%), and relative water content (+92%) under salt stress conditions. Indeed, tomato inoculation improved root development, leaf area, and plant height. At the physiological level, the results indicated positive effects of the inoculation on chlorophyll and anthocyanin contents. These findings demonstrate that Cycas revoluta-associated bacterial endophytes, particularly Panteoa sp. LMR-C62 and Bacillus sp. LMR-C11, hold robust potential as biofertilizer candidates for enhancing tomato growth and resilience under saline conditions. To our knowledge, this is the first report prospecting the unique coralloid root microbiome of Cycas revoluta for agricultural purposes, revealing novel halotolerant endophytes with notable biofertilizer potential.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material at 10.1007/s13205-026-04861-5.},
}

@article {pmid42245391,
year = {2026},
author = {Kumari, J and Das, S and Ranjan, S and Singh, S},
title = {From intake to impact: dietary modulation of the gut-brain axis across health and neurological disease.},
journal = {3 Biotech},
volume = {16},
number = {6},
pages = {247},
pmid = {42245391},
issn = {2190-572X},
abstract = {The gut-brain axis (GBA) is an intricate, bidirectional communication network linking the gastrointestinal microbiota to the central nervous system. Mounting evidence underscores its critical role in the pathogenesis of neurological and neurodegenerative disorders. Diet serves as a primary modulator of this axis, possessing the capacity to profoundly reshape microbial diversity, metabolic output, and host-microbiota interactions. This review highlights the modulatory effects of distinct dietary patterns-specifically the Western, Mediterranean, and Ketogenic diets-on GBA signaling and overall neurological health. We comprehensively analyzed how these diets alter gut microbiota composition, influence the production of neuroactive microbial metabolites, and regulate neuroimmune signaling pathways. Furthermore, the mechanistic correlations between diet-driven microbiota alterations and the pathophysiology of neurodegenerative diseases were explored. By evaluating preclinical data on the neuroprotective potential of specific dietary components, this review underscores the therapeutic promise of microbiome-targeted dietary interventions while critically addressing the translational challenges for clinical application.},
}

@article {pmid42245491,
year = {2026},
author = {León, ED and Francino, MP},
title = {Correction: Roles of secretory immunoglobulin A in host-microbiota interactions in the gut ecosystem.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1868593},
doi = {10.3389/fmicb.2026.1868593},
pmid = {42245491},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2022.880484.].},
}

@article {pmid42245495,
year = {2026},
author = {Kuźniar, A and Das, AP and Goraj, W},
title = {Editorial: Unveiling microbiome interactions and functions in soil hotspots.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1820854},
doi = {10.3389/fmicb.2026.1820854},
pmid = {42245495},
issn = {1664-302X},
}

@article {pmid42245499,
year = {2026},
author = {Wang, X and Wang, S and Chang, Z and Zhao, M and Zhang, X and Fayzullo, N and Bunyod, E and Li, S and Wang, J},
title = {A transformer based deep learning framework for accurate single nucleotide variant correction in heterogeneous samples.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1838029},
pmid = {42245499},
issn = {1664-302X},
abstract = {Profiling host genetic variations in heterogeneous host-microbiome mixtures is crucial for understanding cross-species interactions and microenvironmental dynamics. However, the variable host DNA fraction (purity) in bulk sequencing data severely compromises the performance of standard variant callers, leading to significant systematic biases in quantifying single nucleotide variants (SNVs). To address this, we developed a Transformer-based computational framework designed to model sequence context and technical artifacts in low-purity samples. The architecture employs a group-encoding mechanism to process multidimensional features-including variant allele frequency (VAF) distributions, base-level purity estimates, sequencing depth, and local genomic context (such as repeat regions and chromatin accessibility). By capturing long-range dependencies among these diverse signals, the model effectively neutralizes purity-induced biases to accurately recover the true host SNV count. We evaluated the framework using simulated sequencing data across a broad purity gradient (0.2-1.0). Our approach significantly reduced quantification errors, achieving high concordance between the corrected and actual ground-truth SNV counts. Benchmarking the corrected counts against the raw outputs of conventional callers (Mutect, Freebayes, LoFreq, and Platypus) demonstrated substantial performance gains, particularly in ultra-low purity conditions (0.2-0.3) where traditional statistical priors typically fail to provide reliable quantifications. Feature ablation and residual analyses further validated the independence of the multidimensional inputs and the unbiased, zero-centered nature of the count corrections. This deep learning pipeline provides a robust solution for the accurate quantification of host SNVs in complex biological mixtures, facilitating reliable downstream genetic analyses in highly heterogeneous microenvironments.},
}

@article {pmid42245500,
year = {2026},
author = {Dinh-Hung, N and Mohammed, H and Linh, NV and Tran, NT},
title = {Editorial: Probiotics in aquaculture: enhancing health and sustainability.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1864753},
pmid = {42245500},
issn = {1664-302X},
}

@article {pmid42245502,
year = {2026},
author = {Abdulsamad, MA and Bardaa, S and Elleuch, M and Mathlouthi, NEH and Ben Ali, M},
title = {Metagenomic characterization of infected diabetic foot ulcers in North Africa: microbial diversity, virulome, and resistome profiling.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1825173},
pmid = {42245502},
issn = {1664-302X},
abstract = {This study provides the first shotgun metagenomic characterization of infected diabetic foot ulcers (DFUs) from North Africa. We analyzed two independent datasets with distinct roles: 25 non-infected US DFUs (PRJNA506988) served as an ecological reference cohort to characterize depth-stratified microbial community patterns and pre-infection ARG ecology; 15 infected Libyan DFUs constituted the primary characterization cohort. Metagenomic sequencing, taxonomic classification, resistome and virulome profiling, and metagenome-assembled genome (MAG) reconstruction were performed. In the US reference cohort, depth-dependent community shifts were documented: Fusobacteriota predominated in deeper ulcers, while Staphylococcaceae and Pseudomonadaceae were enriched in superficial wounds. Eighty ARGs were detected across depth groups, including mecA and the mexAB-oprM efflux system, in clinically non-infected wounds. In the Libyan cohort, four major opportunistic pathogens were identified: Pseudomonas aeruginosa, Staphylococcus aureus, Acinetobacter baumannii, and Corynebacterium striatum. From sample M13, a high-quality P. aeruginosa MAG (99.68% completeness, 0.89% contamination) was reconstructed, classified as ST664 and carrying 220 virulence factors, 60 antibiotic resistance genes (all confirmed by RGI v6.0.2), and 213 mobile genetic elements. These findings represent the first genomic evidence of ST664 in a North African DFU and underscore the need for metagenomics-guided antimicrobial stewardship in chronic wound management.},
}

@article {pmid42245509,
year = {2026},
author = {Wang, Z and Li, L and Dong, Y and Zhang, Y},
title = {The microbiota-tryptophan-brain axis in neurodegenerative diseases: pathogenic mechanisms, disease-specific roles, and translational therapeutics.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1820111},
pmid = {42245509},
issn = {1664-302X},
abstract = {The pathogenesis of neurodegenerative diseases (NDDs) such as Alzheimer's disease (AD) and Parkinson's disease (PD) is very complex. Recent studies have shown that gut microbiota and their metabolites play a key role in the progression of these diseases. Tryptophan (Trp) is an essential amino acid, which mainly produces a variety of biologically active compounds in the intestine through the metabolism of indole pathway, Kynurenine pathway (KP) and serotonin pathway, including indole derivatives, Kynurenine (KYN) and serotonin (5-HT). These metabolites affect the central nervous system (CNS) through the Microbiota-gut-brain axis (MGBA) and affect CNS in a variety of mechanisms, including immune regulation, neuroprotection and maintenance of intestinal barrier function. They are involved in key pathological processes such as neuroinflammation, oxidative stress and pathological protein aggregation. This paper systematically reviews the mechanism of the role of Trp metabolites derived from gut microbiota in NDDs, and explores their specific roles in AD, PD, Amyotrophic Lateral Sclerosis (ALS) and Huntington's disease (HD), and summarizes the potential therapeutic value of the current pathway strategy. These strategies include nutritional intervention, targeted microbiome therapy [such as probiotic and fecal microbiota transplantation (FMT)], and metabolite-derived drugs. Future research must clarify its dynamic mechanism in the human body, develop relevant biomarkers, and promote personalized prevention and treatment strategies through clinical transformation, so as to provide a new direction for early intervention and treatment of NDDs.},
}

@article {pmid42245510,
year = {2026},
author = {Patel, M and Ijoma, GN and Ziarno, M},
title = {Editorial: Bifidobacteria: exploring the roles of these microbiome guardians and their effects on human health.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1861676},
doi = {10.3389/fmicb.2026.1861676},
pmid = {42245510},
issn = {1664-302X},
}

@article {pmid42245514,
year = {2026},
author = {Shen, X and Yu, FXD and Xie, S and Hsu, CD and Domingos, JA and Gibson-Kueh, S},
title = {Temporal microbiome dynamics and fish health-associated dysbiosis in freshwater aquarium systems: a case study from River Wonders Singapore.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1739391},
pmid = {42245514},
issn = {1664-302X},
abstract = {INTRODUCTION: Aquarium systems are engineered yet biologically dynamic ecosystems where microbial communities underpin nutrient cycling, organic matter decomposition and water quality regulation. These processes directly affect aquatic animal health.

METHODS: This study conducted a two-month time series analysis of waterborne microbiomes across six freshwater exhibits at River Wonders, Singapore, using 16S rRNA gene sequencing. Exhibits were categorized as "Healthy" (LM, MJ, EE) or "Stressed" (P, MJR, RG) based on fish health, and as indoor or semi-indoor/outdoor by system design.

RESULTS AND DISCUSSION: Temporal fluctuations in microbial composition and diversity were evident over time, with distinct profiles between indoor and semi-indoor/outdoor. Potential opportunistic or pathogenic genera, including Edwardsiella, Flavobacterium, Aeromonas, Pseudomonas and Mycobacterium, were consistently among the 30 most abundant taxa. The most severe dysbiosis occurred in exhibit P, characterized by a transient Pseudomonas bloom (51.4%), loss of nitrifiers (Nitrosomonas, Nitrospira) and concurrent fish health issues. MJR and RG harbored persistent polymicrobial risks, while "Healthy" exhibits maintained relatively more balanced microbial communities with lower pathogen loads. Routine husbandry interventions (e.g., partial water changes, substrate cleaning) coincided with improved microbial evenness and reductions in opportunistic taxa. These findings highlight diagnostic potential of microbiome profiling to detect early dysbiosis and support evidence-based husbandry in managed aquatic systems.},
}

@article {pmid42245662,
year = {2026},
author = {Cabanero-Navalon, MD and Carda-Diéguez, M and Mira, A and Moral Moral, P and Diaz Luna, MM and Balastegui-Martín, H and Salavert Lletí, M and Garcia-Bustos, V},
title = {Multiniche mycobiome profiling identifies distinctive fungal dysbiosis in common variable immunodeficiency.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1804724},
pmid = {42245662},
issn = {1664-3224},
abstract = {BACKGROUND: Common variable immunodeficiency (CVID) is associated with bacterial dysbiosis, particularly in patients with immune dysregulation, but the contribution of the fungal microbiome (mycobiome) remains poorly understood.

METHODS: We conducted a cross-sectional, multi-compartment study in 41 adults with CVID (24 with immune dysregulation, dCVID; 17 with infectious-only manifestations, iCVID) and 15 matched healthy controls. Saliva, sputum and stool samples were analyzed using ITS1 amplicon sequencing with amplicon sequence variant-based taxonomic assignment, followed by α/β-diversity analyses, multivariate modeling, differential abundance testing and machine learning approaches for biomarker identification.

RESULTS: Across all three niches, mycobiome composition differed significantly between CVID and controls, whereas dCVID and iCVID did not separate. Fungal richness and evenness were reduced in CVID, most prominently in respiratory and oral samples. ANCOM-BC revealed a reproducible "Candida-skewed" configuration in both phenotypes, with marked enrichment of Candida albicans in sputum, stool and saliva, accompanied by increased abundance of other opportunistic yeasts such as Nakaseomyces glabratus. In contrast, environmental or putatively commensal taxa were consistently depleted. Random forest models based on fungal profiles accurately discriminated CVID from controls, with AUC up to 0.96 (95% CI 0.91-0.99) in saliva and 0.94 (95% CI 0.88-0.99) in stool, whereas classification of dCVID versus iCVID was modest.

CONCLUSION: Together, these findings provide the first integrated view of mycobiome alterations across multiple ecological niches in CVID, highlighting consistent enrichment of opportunistic yeasts over commensals. The expansion of C. albicans supports a potential pathobiont role, and the strong discriminatory performance of fungal signatures underscores their promise as non-invasive biomarkers in this immunodeficiency.},
}

@article {pmid42245783,
year = {2026},
author = {Edielu, A and Lo, CW and Mawa, PA and Webb, EL and Elliott, AM and Mugerwa, JK and Oduru, G and Nassuuna, J and Ayebazibwe, GK and Struebig, M and Friedman, JF and Bustinduy, AL and Holland, MJ},
title = {Schistosoma mansoni infection is associated with changes in gut microbiota in preschool age children in Albertine Region, Uganda.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9768290/v1},
pmid = {42245783},
issn = {2693-5015},
abstract = {Current understanding of gut microbiota alterations during helminthiasis is largely derived from experimental models, often focusing on a narrow range of metrics. This study investigates the structural and functional shifts in the gut microbiome associated with Schistosoma mansoni infection in a paediatric cohort. We conducted a cross-sectional study of preschool-aged children (12-47 months) comparing S. mansoni -infected individuals (56) to uninfected controls (57). Microbial DNA was extracted from stool samples and sequenced via the Illumina MiSeq v3 platform targeting the V4-16S rRNA region. Diversity was assessed through alpha (Chao1, Simpson, Shannon) and beta (UniFrac and Bray-Curtis distance) metrics. Functional potential was predicted using PICRUSt2 mapped against the KEGG database. The infected group (median age 36 months) exhibited significantly higher alpha diversity and species richness compared to uninfected peers (median age 26 months). Beta diversity analysis confirmed distinct microbial clustering between the two groups (p-value = 0.001). Notably, S. mansoni infection was characterized by the proliferation of pro-inflammatory taxa and a concomitant depletion of short-chain fatty acid (SCFA) producers. Functional modeling indicated a significant downregulation of metabolic pathways involved in energy metabolism and SCFA biosynthesis. S. mansoni infection is associated with profound structural and functional dysbiosis in preschool-aged children. The depletion of SCFA producers and altered metabolic pathways suggest that infection may impair host nutritional status and influence the parasite's lifecycle, necessitating further longitudinal investigation.},
}

@article {pmid42245806,
year = {2026},
author = {Cunningham, ME and Williams, MT and Spaine, KM and Marcinkowska, A and Matveyev, AV and Hur, BJ and Natterer, HO and Chatterjee, RB and Oldfield, CJ and Edupuganti, L and Zhu, B and Jefferson, KK and Iii, JFS and Olex, AL and Serrano, MG and Buck, GA},
title = {Differential Host Gene Expression Associated with Non-Lactobacillus-dominant Vaginal Microbiomes During Pregnancy.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9268667/v1},
pmid = {42245806},
issn = {2693-5015},
abstract = {Background The vaginal microbiome significantly influences gynecological and obstetric health, yet the interrelationship between host vaginal gene expression and the microbiota during pregnancy is understudied-particularly in racioethnically diverse cohorts. Here, we leveraged metatranscriptomic data from 123 participants from the Multi-Omic Microbiome Study-Pregnancy Initiative (MOMS-PI) cohort to perform a novel integrated analysis of human host gene expression and vaginal microbiota composition during pregnancy. We hypothesized that host gene expression at the vaginal-mucosal interface would exhibit distinct transcriptional profiles when colonized by bacteria commonly present in bacterial vaginosis (BV), termed BV-associated vagitypes, compared to Lactobacillus -dominated microbiomes. Such distinct host response would provide evidence linking vaginal inflammation to microbiome composition during pregnancy in a majority Black cohort. By profiling host expression with different BV-associated vagitypes, these host-microbiome signatures could inform clinically actionable biomarkers for microbiome-focused interventions during pregnancy in historically underrepresented populations. Results Host transcriptomic profiles differed significantly between BV-associated and Lactobacillus -dominated vagitypes, with this association remaining significant when analyses were restricted to Black participants. We identified 13 consistently differentially expressed genes in women with BV-associated vagitypes-vaginal microbiomes comprised of high relative abundance of either Gardnerella spp., Candidatus Lachnocurva vaginae, or a mixture of multiple anaerobic taxa-compared to women with Lactobacillus crispatus vagitypes. These differentially expressed genes are involved in host immune response (DKK1, H2BC21, ILRUN, S100A9), oxidative stress response and inflammasome activation (CSTB), transcription modulation (CLK1, PAX9), vesicle trafficking (EXPH5), ubiquitination (FBXO32), membrane integrity (PIEZO1), and ion transport (S100A16, SCNN1A, SLCO4A1). Conclusion BV-associated vagitypes are correlated with distinct host immunomodulatory gene expression profiles during pregnancy, independent of self-reported racioethnicity. We demonstrated novel molecular insights into microbiome-host interaction during pregnancy within the context of adverse cervicovaginal health.},
}

@article {pmid42245824,
year = {2026},
author = {de Azevedo-Lopes, A and Traulsen, A},
title = {Multilevel selection in multitype populations.},
journal = {PNAS nexus},
volume = {5},
number = {6},
pages = {pgag180},
pmid = {42245824},
issn = {2752-6542},
abstract = {Multilevel selection has important implications for understanding the origin, ecology, and evolution of host-associated microbiomes. Selection on the host-level can have a substantial impact on the evolution of microbial lineages, favoring microbes that are beneficial to the host. However, previous research has focused on the evolution of interactions among only two types. We alter this perspective by examining the role of multilevel selection in shaping the interaction dynamics of a population with many microbial types-a case of particular relevance for microbiomes. We ask how multilevel selection influences the selection of interactions among various microbial types, whether it promotes microbial diversity within the population, and whether it increases the likelihood of microbial lineages evolving beneficial interactions with their host and other microbes. To address these questions, we simulate a multitype population structured into groups, where individuals interact within groups through an evolutionary game that determines their fitness. We classify pairwise interactions by their dynamical outcomes: dominance, coexistence, or bistability. We find that multilevel selection reshapes interactions dynamics in complex ways, depending on the details of the population structure. We show the impact of the interaction patterns emerging in such a system.},
}

@article {pmid42246001,
year = {2026},
author = {Chen, S and Liu, J and Ni, H and Zhu, F and Liu, H and Lin, R},
title = {Gut microbiota and the kidney-gut-skin axis in chronic kidney disease-associated pruritus: mechanisms and therapeutic implications.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1811786},
pmid = {42246001},
issn = {2235-2988},
mesh = {Humans ; *Pruritus/therapy/etiology/microbiology ; *Renal Insufficiency, Chronic/complications/microbiology/therapy ; Animals ; *Gastrointestinal Microbiome/physiology ; *Skin/microbiology/pathology ; *Kidney/microbiology ; Dysbiosis ; Probiotics/therapeutic use ; },
abstract = {Chronic kidney disease-associated pruritus (CKD-aP) is a highly prevalent and debilitating symptom in patients with chronic kidney disease (CKD) and end-stage kidney disease (ESKD), severely impairing quality of life, sleep quality, mental health, and clinical outcomes. Its pathogenesis is multifactorial and remains incompletely understood, involving chronic inflammation, immune imbalance, abnormal neuro-opioid pathways, mineral metabolism disorders and skin barrier damage. The kidney-gut-skin axis has attracted increasing attention as a novel theoretical framework to elucidate the roles of gut microbiota dysbiosis, gut-derived uremic toxins, intestinal barrier impairment and systemic inflammation in the development of CKD-aP. This review summarizes the traditional pathogenic mechanisms of CKD-aP, reviews recent advances linking gut microbial alterations to pruritus-related pathways, and systematically evaluates gut-targeted and metabolism-targeted interventions, including probiotics, prebiotics, synbiotics, AST-120, fecal microbiota transplantation, phytochemicals, Uremia Clearance Granules, and vitamin D-related strategies. Current evidence is mostly associative and is mainly derived from general CKD/ESKD populations, animal models, and in vitro studies; specific clinical validation in CKD-aP cohorts remains limited. Accordingly, gut microbiome-related mechanisms and interventions remain hypothetical and adjunctive, without established causal relationships or validated standard therapies for CKD-aP. Future studies are required to identify CKD-aP-specific pathological alterations, adopt longitudinal design and multi-omics analysis, conduct mechanistic verification, and perform randomized controlled trials with pruritus as a predefined primary endpoint.},
}

Humans
*Pruritus/therapy/etiology/microbiology
*Renal Insufficiency, Chronic/complications/microbiology/therapy
Animals
*Gastrointestinal Microbiome/physiology
*Skin/microbiology/pathology
*Kidney/microbiology
Dysbiosis
Probiotics/therapeutic use

@article {pmid42246005,
year = {2026},
author = {Orcel, E and Sentausa, E and Hage, H and Louis, K and Taha, M and Bellais, S and Villain, A and Beloeil, L and Sijmons, S and Devos, N and Saliou, A},
title = {UMI-guided single locus sequence typing method for phylotyping Cutibacterium acnes from skin samples.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1807759},
pmid = {42246005},
issn = {2235-2988},
mesh = {Humans ; *Skin/microbiology ; Skin Microbiome ; DNA, Bacterial/genetics ; Phylogeny ; Sequence Analysis, DNA ; *Molecular Typing/methods ; *Propionibacteriaceae/genetics/classification/isolation & purification ; *Bacterial Typing Techniques/methods ; },
abstract = {INTRODUCTION: Cutibacterium acnes is a dominant member of the human skin microbiota and displays substantial strain-level diversity with relevance for skin health and disease. However, accurate characterization of C. acnes lineages directly from skin samples remains challenging due to low biomass, host DNA contamination, and limitations of short-read sequencing.

METHODS: Here, we present SLST-Seq, a culture-independent approach based on single-locus sequence typing (SLST), enabling strain-level profiling of C. acnes from low-input skin-strip samples. SLST-Seq adapts the LUMI-Seq® synthetic long-read sequencing technology to the C. acnes SLST marker, combining unique molecular identifier barcoding with de novo assembly to reconstruct full-length SLST sequences with high accuracy.

RESULT: Method performance was validated using single-isolate controls, defined genomic DNA mixtures, spike-in dilution series, and run-specific controls, demonstrating high specificity, quantitative accuracy across a wide range of target-to-background DNA ratios, and strong run-to-run reproducibility. Applied to skin-strip samples from healthy volunteers, SLST-Seq generated robust SLST profiles and revealed marked inter-individual variability, with donor-specific community structures largely conserved between face and back skin sites.

DISCUSSION: Overall, SLST-Seq provides a sensitive and scalable framework for in situ analysis of C. acnes population structure and supports high-resolution studies of skin microbiome composition from challenging clinical samples.},
}

Humans
*Skin/microbiology
Skin Microbiome
DNA, Bacterial/genetics
Phylogeny
Sequence Analysis, DNA
*Molecular Typing/methods
*Propionibacteriaceae/genetics/classification/isolation & purification
*Bacterial Typing Techniques/methods

@article {pmid42246191,
year = {2026},
author = {Das, D and Dixit, R and Pandey, M},
title = {The Biliary Multi-Omics Landscape: Integrating Microbiome and Metabolomics in Gallbladder Carcinogenesis.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.70462},
pmid = {42246191},
issn = {1440-1746},
abstract = {BACKGROUND: Gallbladder cancer (GBC) is a highly aggressive malignancy with a dismal prognosis, frequently diagnosed at advanced stages. While cholelithiasis is a primary risk factor, the role of the biliary microbiome and its metabolic products in driving carcinogenesis is increasingly recognized. This review synthesizes multi-omics data to elucidate the interplay between microbial dysbiosis and metabolomic shifts in GBC.

METHODS: A systematic literature search was conducted on PubMed (up to January 2026) focusing on biliary bacteria, the gut-bile axis, and multi-omics markers. A narrative synthesis integrated findings from metagenomic, metaproteomic, and metabolomic studies involving human cohorts and experimental models.

RESULTS: GBC is characterized by profound biliary dysbiosis, specifically the enrichment of Enterobacteriaceae, Streptococcus, and Helicobacter species. This taxonomic shift triggers a pro-carcinogenic metabolomic flux, where microbial 7α-dehydroxylation converts primary bile acids into secondary bile acids, such as deoxycholic acid (DCA), which induce DNA damage and promote tumor growth. Metaproteomic signatures identify bacterial proteins (e.g., QDR3, ompA) that facilitate biofilm formation and oxidative stress evasion. Furthermore, emerging paradigms like cross-species horizontal gene transfer (HGT) suggest that microbial genetic material can directly modulate host oncogenic pathways.

CONCLUSION: The GBC multi-omics landscape reveals a complex gut-bile axis where microbial and chemical factors converge. These integrated signatures offer potential as noninvasive biomarkers for early diagnosis and precision therapy.},
}

@article {pmid42246268,
year = {2026},
author = {Yun, S and Choi, KS and Min, H and Jo, YK and Jang, S},
title = {Development strategies for engineered live biotherapeutic products for metabolic diseases.},
journal = {Critical reviews in biotechnology},
volume = {},
number = {},
pages = {1-21},
doi = {10.1080/07388551.2026.2653692},
pmid = {42246268},
issn = {1549-7801},
abstract = {Metabolic diseases, such as obesity and diabetes, have risen due to lifestyle changes. Traditional treatments, including dietary modifications and pharmacological interventions, are limited by low compliance and adverse effects, highlighting the need for alternative therapeutic approaches that offer improved patient compliance and long-term effectiveness. Engineered live biotherapeutic products (eLBPs) have emerged as a promising strategy that combines bacterial chassis with synthetic genetic circuits for precise and targeted disease treatment. Unlike conventional therapeutics, eLBPs can colonize the intestinal tract and enable localized and condition-responsive therapeutic activity while offering improved safety profiles through defined mechanisms of action. This review highlights key strategies for eLBP development, particularly chassis selection and genetic circuit design. Applications in metabolic diseases, including inherited disorders such as phenylketonuria (PKU), demonstrate how engineered gene circuits can modulate specific metabolic pathways. However, several challenges remain, including genetic stability, interindividual variability, biological safety, and production scalability. In addition, further research on host-microbiota interactions is required to improve therapeutic predictability and efficacy, supporting the development of safe and effective personalized eLBP-based therapies for metabolic diseases.},
}

@article {pmid42246374,
year = {2026},
author = {Pauwels, A and Devolder, L and Falony, G and D'haeseleer, M and Nagels, G and Van Remoortel, A and Derrien, M and D'hooghe, M and Raes, J},
title = {Deconfounded, quantitative microbiome profiling identifies robust multiple sclerosis markers and clinical covariate associations.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2681876},
doi = {10.1080/19490976.2026.2681876},
pmid = {42246374},
issn = {1949-0984},
abstract = {Despite a wealth of gut microbiota studies in multiple sclerosis (MS), consistent results are lacking. Here, we study confounder effects and use of quantitative microbiome profiling (QMP) in 228 MS patients (103 untreated) and 2860 population controls (Flemish Gut Flora Project (FGFP)). Total bacterial load was lower in relapsing remitting (RR)MS, while strong fecal moisture effects, indicative of longer transit times, in MS vs. FGFP, were driven by primary progressive (PP)MS. Applying cell count and moisture in deconfounded QMP, we identified 21 differentially abundant genera in MS, with a.o. Lachnobacterium, Blautia enriched, and Clostridium, Bacteroides depleted. Deconfounded QMP across 10 published studies (1065 patients, 874 controls) did not confirm commonly detected markers (Akkermansia, Roseburia), yet lowered Bacteroides, and higher Blautia and Methanobrevibacter emerged as robust MS biomarkers. Lowered butyrate producers (Butyricicoccus, Butyricimonas) merit further investigation. Enterotype stratification linked the low cell count Bacteroides 2 enterotype to low-efficacy DMTs, and the Prevotella enterotype to lower disease severity. Serum glial fibrillary acidic protein (GFAP), a disease progression biomarker, was identified as a covariate of gut microbial variation and inversely correlated with Faecalibacterium and Roseburia abundance in PPMS. Overall, our study provides robust disease markers and emphasizes the importance of QMP and confounder control.},
}

@article {pmid42247160,
year = {2026},
author = {Palani Kumar, MK and Iyer, KS and Shahi, SK and Raygoza Garay, JA and Mangalam, A and Dayal, S},
title = {Age and sex dependent shift in murine gut microbiome reveals pathological links to host cardiovascular and metabolic pathways.},
journal = {GeroScience},
volume = {},
number = {},
pages = {},
pmid = {42247160},
issn = {2509-2723},
support = {HL168630/HL/NHLBI NIH HHS/United States ; HL007344/HL/NHLBI NIH HHS/United States ; BX007087//U.S. Department of Veterans Affairs/ ; AI162778//National Institute of Allergy and Infectious Diseases/ ; 18IPA4180014//American Heart Association/ ; P30 ES005605/ES/NIEHS NIH HHS/United States ; 1I01CX002212//Iowa City Veterans Affairs Medical Center/ ; },
abstract = {The gut microbiome undergoes dynamic, sex-dependent changes across the lifespan. However, comprehensive studies examining the combined effects of age and sex are limited. This study investigated both compositional and functional alterations in the gut microbiome of young (4 months, n = 14) and aged (20 months, n = 20) C57BL/6 J mice of both sexes using 16S rRNA gene (V3-V5) sequencing. Microbial community structure and predicted functional profiles were analyzed via QIIME2 and PICRUSt2, with pathway annotation based on MetaCyc. Compared to aged mice, young mice exhibited higher alpha diversity, with the highest increase observed in young females. This sex-specific difference was lost in aged mice. Aging was also associated with an increased Firmicutes-to-Bacteroidetes ratio, and distinct shifts in key taxa, including increased Lactobacillus and Roseburia and reduced Bacteroides and Lachnospiraceae. Functional prediction revealed substantial age-related metabolic shifts, especially in females showing alteration in 45 pathways including upregulation of branched-chain amino acid (BCAA) metabolism, uric acid metabolism, and lipopolysaccharide biosynthesis. To directly link alterations in microbial BCAA metabolism with host metabolic outcomes, fecal abundance of the bacterial BCAA aminotransferase gene (ilvE) was quantified and found to be significantly increased in aged mice. Concurrently, aged mice exhibited higher plasma levels of BCAA, insulin, and random glucose, indicating age-associated metabolic dysregulation. Fecal ilvE abundance associated positively with plasma BCAA levels, and negatively with blood glucose in aged mice, suggesting a link between microbial BCAA metabolism and host glucose homeostasis. Our findings demonstrate that gut microbiome composition and function are influenced by both age and sex. We also showed that these alterations in microbial BCAA metabolism are associated with host metabolic parameters during aging. Our findings underscore the importance of incorporating both age and sex as biological variables in microbiome research and may inform development of age- and sex-specific microbiome-targeted interventions.},
}

@article {pmid42247343,
year = {2026},
author = {Somboonna, N and Rujirawan, P and Promvaranon, T and Wongtada, C and Triwatcharikorn, J and Chottawornsak, N and Kantikosum, K and Wongsaroj, L and Parinyanitikul, N and Chongpison, Y and Chiewchengchol, D and Rerknimitr, P},
title = {Skin Barrier Dysfunction, Antimicrobial Peptide Alterations, and Microbiome Changes in Solid Cancer Patients Treated with Epidermal Growth Factor Receptor Inhibitors.},
journal = {Dermatology (Basel, Switzerland)},
volume = {},
number = {},
pages = {1-14},
doi = {10.1159/000551797},
pmid = {42247343},
issn = {1421-9832},
abstract = {INTRODUCTION: Epidermal growth factor receptor inhibitors (EGFRIs) are targeted therapies for solid cancers. Their use is associated with cutaneous adverse events (cAEs). This study aimed to investigate cAEs and changes in skin biophysics reflecting the skin barrier function, alterations in antimicrobial peptides (AMPs), and the skin microbiome in patients undergoing treatment with EGFRIs.

METHODS: A 2-year prospective cohort study was conducted involving patients receiving EGFRIs for solid cancers. cAEs and skin biophysical properties, including transepidermal water loss (TEWL), skin pH, elasticity, sebum, and pigmentation, were measured at baseline and follow-up visits up to 48 weeks. AMPs were assessed using a tape-stripping technique from the cheeks at months 0, 1, and 6, with protein assays and ELISA to determine the levels of human beta-defensin (hBD)-3 and ribonuclease (RNase)-7. Skin microbiome analysis was performed through 16S rRNA sequencing of cheek swabs collected at months 0, 1, and 6.

RESULTS: Eighty-four patients were enrolled. The cumulative incidence of cAEs was 94.05%. Skin biophysical properties showed significantly increased TEWL and pH, decreased pigmentation, and no significant changes in elasticity and sebum. AMP analysis from 15 patients revealed significant reduction of RNase-7 levels after 6 months into EGFRIs, while hBD-3 level change was insignificant. A microbiome study from 18 patients showed statistically increased Corynebacterium kroppenstedtii at months 1 and 6, while Cutibacterium acnes, Corynebacterium aurimucosum, Staphylococcus epidermidis, and Staphylococcus aureus were not significantly different among groups.

CONCLUSION: Treatment with EGFRIs compromises skin barrier function and AMP production, leading to skin microbiota changes.},
}

@article {pmid42247989,
year = {2026},
author = {Tang, Y and Qi, F and Yu, Y and Fu, Y and Zhu, P},
title = {Knowledge mapping of cholestatic liver disease and TGR5 research: A bibliometric study of trends and frontiers.},
journal = {Computational biology and chemistry},
volume = {124},
number = {Pt 1},
pages = {109158},
doi = {10.1016/j.compbiolchem.2026.109158},
pmid = {42247989},
issn = {1476-928X},
abstract = {OBJECTIVE: This study aims to provide a comprehensive bibliometric analysis of global research trends surrounding TGR5 in cholestatic liver diseases from 2006 to 2025, with the objective of elucidating publication outputs, geographic and institutional contributions, collaborative networks, journal co-citation analysis and reference co-citation mapping, key research themes, and emerging frontiers.

METHODS: Bibliographic data were retrieved from the Web of Science Core Collection (WoSCC) and supplemented by validation against Scopus and PubMed to mitigate database selection bias.Analyses were performed using CiteSpace (version 6.2.R2), VOSviewer (version 1.6.20), and the bibliometrix R package. Performance analysis was employed to evaluate productivity and impact across countries, institutions, and authors. Advanced science mapping techniques, including Thematic Map analysis, network topology metrics, and citation burst detection, were conducted to provide deeper computational and systems-level biological insights.

RESULTS: A total of 418 publications were included. Annual publications showed a steady upward trend, with the United States leading in productivity (n = 138), total citations (n = 14,638), and H-index (59), followed by China with high output but relatively lower citation impact. European countries, notably Italy and Germany, demonstrated strong collaborative networks and influence relative to output volume. Keyword and thematic analyses revealed a shift from molecular mechanisms to clinical applications and, more recently, to gut microbiota and metabolic interactions. Major research clusters encompassed bile acid receptors, gut-liver axis mechanisms, and metabolic disorders. Quantitative network analysis revealed a modularity of 0.8238 and mean silhouette of 0.96, indicating well-defined cluster structures. Although prominent research groups were identified, international collaboration remained limited.

CONCLUSION: The study illustrates the dynamic and evolving nature of TGR5 research, marked by a transition from basic science to translational and systems-level approaches. As the first comprehensive bibliometric and systems-level mapping analysis of TGR5 research in cholestatic liver diseases, this study uniquely integrates computational network analysis with microbiome-host interaction frameworks.While research productivity continues to grow, future efforts would benefit from enhanced international collaboration, microbiome engineering, systems medicine, biomarker discovery, and AI-integrated hepatology research. These findings provide valuable insights for researchers and policymakers aiming to navigate and advance this promising field.},
}

@article {pmid42248042,
year = {2026},
author = {Wang, L and Gong, X and Rao, S and Huang, L and Cheng, H and Cheng, S and Luo, J and Li, Q and Wei, Y and Xu, H},
title = {Biological effects of selenium on Hypnum plumaeforme and the underlying mechanisms mediated by physiology and microbiome.},
journal = {Ecotoxicology and environmental safety},
volume = {322},
number = {},
pages = {120341},
doi = {10.1016/j.ecoenv.2026.120341},
pmid = {42248042},
issn = {1090-2414},
abstract = {Bryophytes provide vital ecosystem services, yet the biological effects of selenium (Se) on them remain largely unknown. This study simulated ecological scenarios with different selenite exposure levels to investigate the response patterns of growth, physiology, and symbiotic bacterial communities in Hypnum plumaeforme. Overall, its inorganic, organic, and total Se content increased with increasing selenite exposure levels. At 2 mg/L, H. plumaeforme accumulated more biomass, carotenoids and selenomethionine (SeMet), but less lipid and phosphorus (P). Enhanced methylselenocysteine (MeSeCys) biosynthesis facilitated its Se detoxification. At 4 mg/L, H. plumaeforme had more photosynthetic pigments, carbohydrates and protein, but fewer chloroplasts and less P. H2O2 accumulation did not result in elevated malondialdehyde (MDA) content and growth inhibition, which was attributed to the activation of superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPX), as well as increased SeMet biosynthesis for Se detoxification. The enrichment of Variovorax and TM7a might support its starch accumulation and Se tolerance. At 8 mg/L, H. plumaeforme had more photosynthetic pigments and protein, but fewer chloroplasts and less P. Excessive SeMet synthesis induced Se toxicity. Although SOD, CAT and GPX were activated, H2O2 and MDA accumulation occurred in this bryophyte, resulting in reduced biomass and impaired nitrogen (N) uptake. The enrichment of bacterial taxa, including Alphaproteobacteria, might facilitate its antioxidant defense. This study identifies the growth-promoting, neutral, and inhibitory effects of Se on H. plumaeforme, and illustrates the underlying physiological and microbial regulatory mechanisms. These findings provide important theoretical support for bryophyte conservation and Se ecological risk assessment.},
}