SEARCH · Search PubMed

Results for “human microbiome”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 163 records · Page 9Linked to original sources

PubMed2025

Controlled human infection model of Neisseria lactamica in late pregnancy investigating mother-to-infant transmission in the UK: a single-arm pilot trial.

BACKGROUND: The infant respiratory microbiome is derived largely from the mother and is associated with downstream health and disease. Manipulating maternal respiratory flora peripartum to influence the infant microbiome has not previously been investigated. Neisseria lactamica is a harmless pharyngeal commensal that correlates inversely with Neisseria meningitidis carriage and disease. Intranasal N lactamica inoculation is a safe and well characterised controlled human infection model (CHIM) in non-pregnant healthy adults. We hypothesised that N lactamica inoculation in pregnancy induces mother-to-infant N lactamica transmission postnatally. METHODS: In this single-arm trial, 21 healthy pregnant female participants aged 18 years or older were inoculated at 36-38 weeks' gestation with 105 colony-forming units of N lactamica Y92-1009 at University Hospital Southampton Clinical Research Facility, Southampton, UK. N lactamica selective culture, genome sequencing, and serological testing were performed on maternal and infant oral, nasopharyngeal, breastmilk, and serum samples over 15 weeks postpartum. Seven female participants naturally colonised with N lactamica at baseline were followed up, but not inoculated. Oral samples were obtained from 12 cohabiting siblings younger than 5 years. The primary endpoint was infant N lactamica colonisation. This study was registered with ClinicalTrials.gov, NCT04784845, and is now complete. FINDINGS: Between Oct 25, 2021, and March 7, 2022, 31 adult female participants (median age 33·5 years [range 23·1-39·9]; 26 [84%] were White, British) were screened and enrolled, of whom seven were already colonised with N lactamica. After exclusion of three participants, 21 participants were inoculated, of whom 15 (71%) became N lactamica-colonised, and no sustained N lactamica Y92-1009 transmission to their infants was observed. Conversely, non-Y92-1009 N lactamica strain sharing was observed in four (57%) of seven uninoculated mother-sibling pairs, and Moraxella catarrhalis strain sharing in nine (38%) of 24 mother-infant pairs completing the study. Anti-N lactamica serum IgG titres increased in seven (88%) of eight N lactamica Y92-1009-colonised female participants, but none of their infants (where paired sera were available). There were no serious adverse reactions to the inoculum. INTERPRETATION: As the world's first perinatal CHIM, this trial demonstrates that this model in pregnancy is feasible, and that N lactamica Y92-1009 can safely and efficiently colonise pregnant individuals. Lack of sustained mother-to-infant N lactamica transmission, despite evidence supporting mother-to-infant M catarrhalis and sibling-to-mother N lactamica transmission, challenges conventional perceptions of infants as passive recipients of maternal microbes, suggesting that respiratory commensal transmission is selective and microbe-specific. FUNDING: Medical Research Council and National Institute for Health Research Southampton Biomedical Research Centre.

Adult↗

PubMed2025

The gut's hidden arsenal: A genomics-guided atlas of class II bacteriocins.

Unmodified class II bacteriocins promise precision antimicrobials that spare bystander microbes. Zhang and colleagues introduce IIBacFinder, a genomics-guided pipeline that detects precursor and context genes with a curated pHMM library, infers leader-peptide cleavage, and triages candidates by meta-omics signals. The authors apply it across bacterial genomes, including an atlas of ∼280,000 human-gut genomes, and recover a vast reservoir of narrow-spectrum peptides and prioritize gut-resident candidates for synthesis. Of the 26 synthesized, 16 display activity in vitro, largely via membrane perturbation and with additive effects alongside vancomycin, while ex vivo assays show minimal compositional disruption of fecal communities compared with antibiotic controls. These results position unmodified class II bacteriocins as tractable, microbiome-sparing agents and illustrate how genome-scale mining coupled to meta-omics can bridge sequence to function in complex ecosystems.

Bacteriocins↗

PubMed2006

Ecological and evolutionary forces shaping microbial diversity in the human intestine.

The human gut is populated with as many as 100 trillion cells, whose collective genome, the microbiome, is a reflection of evolutionary selection pressures acting at the level of the host and at the level of the microbial cell. The ecological rules that govern the shape of microbial diversity in the gut apply to mutualists and pathogens alike.

Animals↗

PubMed2026

Synthesis and Application of a Suite of 2,5-Aryl Tetrazole Photoaffinity-Based Probes for Profiling Microbial Carbohydrate and Mucin Metabolism in Gut Microbiota.

Photoaffinity-based chemoproteomics provides a strategy for interrogating protein engagement and networks within complex biological systems. In the context of carbohydrate metabolism, however, linking the probe structure to glycan-processing networks remains challenging due to the diversity and redundancy of carbohydrate-active enzymes (CAZymes). Here, we employ 2,5-tetrazoles as photoreactive groups to develop a suite of monosaccharide-bearing probes designed to capture carbohydrate-associated protein environments in gut microorganisms. Across defined bacterial cultures and human fecal lysates, tetrazole probes enriched glycoside hydrolases (GHs) and additional carbohydrate-associated proteins, including transporters and regulatory elements. Notably, enrichment profiles were functionally biased toward glycan-processing modules, despite minimal shifts in global protein abundance under different growth conditions. These findings demonstrate that tetrazole chemoproteomics complements abundance-based proteomics by reporting on glycan-associated protein engagement and organization. Together, this probe suite provides a substrate-centric approach to studying carbohydrate-processing networks in defined microbes and complex microbiomes.

Tetrazoles↗

PubMed2025

Genetics of Anorexia Nervosa: Translation to Future Personalized Therapies.

Anorexia nervosa (AN) is a debilitating and often refractory eating disorder that is unique among psychiatric disorders insofar as nutrition is key to recovery. Treatment options and efficacy are limited with no approved medications for AN. Genetic studies are clarifying the etiology of AN, with the goal of eventually informing the development of innovative personalized pharmacologic, nutritional, microbial, and behavioral interventions. We present the current state of genome-wide and epigenome-wide association studies, gut microbiome research, and functional genomics investigations and discuss translating this knowledge into clinical practice.

Humans↗

PubMed2026

Indole-3-acetic acid production is rare among gut bacteria and reflects OFOR-driven amino acid oxidation in acetogens.

Indole-3-acetic acid (IAA) is a tryptophan-derived gut microbial metabolite with reported anti-inflammatory activities, but the organisms and anaerobic pathways that support robust production remain unclear. Screening 206 human gut bacterial isolates by LC-MS revealed that IAA production is rare: only five strains exceeded the limit of quantitation, and high-capacity production was confined to the acetogens Blautia hydrogenotrophica and Intestinibacter bartlettii. Across growth conditions, IAA was a minor product that rose alongside carbohydrate-sensitive, OFOR-linked catabolism of multiple amino acids, generating abundant branched-chain and aromatic organic acids. In gnotobiotic mice mono-colonized with I. bartlettii, these metabolites were produced in vivo but showed distinct host handling, with branched-chain fatty acids largely extracted between portal and peripheral plasma, whereas aromatic acids and their glycine conjugates appeared in plasma and urine. Genomic analyzes and heterologous enzyme assays identified expanded repertoires of 2-oxoacid:ferredoxin oxidoreductases (OFORs) with activities spanning pyruvate/oxaloacetate, branched-chain, and aromatic 2-oxoacids, including indolepyruvate conversion to indoleacetyl-CoA, a putative intermediate en route to IAA. Finally, position-specific 13C tracing showed that CO2 released during amino acid oxidation is reassimilated into acetate via reductive acetogenesis, indicating that gut acetogens can maintain redox balance without fermenting partner strains. Together, these findings show that high IAA output is restricted to select gut acetogens and linked to a broader OFOR-driven anaerobic metabolism that generates additional metabolites that are absorbed by the host.

Indoleacetic Acids↗

PubMed2026

A 2-step, 2-sample Mendelian randomization study of gut microbiota, blood metabolites and dry age-related macular degeneration.

Dry age-related macular degeneration (dAMD) is the leading cause of blindness among elderly people in developed countries. The main objective of this study is to investigate the causal relationship between gut microbiota (GM), blood metabolites, and dAMD among European participants. Based on the genome-wide association analysis database, double sample Mendelian randomization (MR) analysis was performed on GM, blood metabolites, and dAMD. The inverse-variance weighted method is used to estimate the causal relationship between GM, blood metabolites, and dAMD, while multiple methods are employed to eliminate pleiotropy and heterogeneity. A 2-step MR analysis quantitatively assessed the effect of metabolite-mediated GM on dAMD. In MR analysis, 15 GM were found to be associated with increased or decreased risk of dAMD, and 18 blood metabolites were found to be associated with increased or decreased risk of dAMD. Our research also found that the potential association between GM and dAMD may be mediated by blood metabolite levels, specifically, ADpSGEGDFXAEGGGVR levels accounted for 38.9% of the causal pathway from genus Parasutterella to dAMD. Our research findings indicate that certain GM and blood metabolites can affect the onset of dAMD, and increasing the abundance of genus Parasottella can increase the risk of dAMD through the mediation of ADpSGEGDFXAEGGGVR levels.

Humans↗

PubMed2026

Role of CD25hi CD45RA+ CD4 not Treg %T cell in mediating the effect of pyruvate fermentation to acetone on intrahepatic cholangiocarcinoma.

This study aimed to elucidate the potential correlation between gut microbiota and intrahepatic cholangiocarcinoma (ICC) by investigating their causal relationship, while also exploring the possible role of immune cells as mediators in this association. We first identified gut microbiota based on phylum, class, order, family, and genus level information. Using summary-level data from a Genome-Wide Association Study (GWAS), we performed a 2-sample Mendelian randomization (MR) analysis of ICC and gut microbiota. Furthermore, we used 2-step MR to quantify the proportion of the effect of immune cell-mediated gut microbiota on ICC. MR analysis identified pyruvate fermentation to acetone (PFA) as predicting ICC risk reduction. There was no strong evidence that genetically predicted ICC had an effect on PFA risk. Furthermore, the proportion of genetically predicted PFA mediated by CD25hi CD45RA+ CD4 not Treg %T cell (CCCTT) was 3% (95% CI: 0.93-5.03%). In conclusion, our study established a causal relationship between PFA and ICC. We observed that a minor fraction of this effect was mediated by CCCTT, while the majority of the impact exerted by PFA on ICC remains elusive. However, further investigations are warranted to elucidate the mechanisms underlying the influence of gut microbiota on ICC development.

Cholangiocarcinoma↗

PubMed2026

Gut microbiota-derived metabolites target C5AR1/KDM2A/HCAR3 axis in inflammatory bowel disease: a multi-machine learning algorithms and molecular docking study.

BACKGROUND: Inflammatory bowel disease (IBD) is a chronic recurrent disorder. Gut microbiota-derived metabolites regulate intestinal homeostasis, but their molecular mechanisms in IBD remain unclear. Current studies lack systematic "microbiota-metabolite-target" network mining with multi-method validation. This study integrates network pharmacology, three machine learning algorithms, and molecular docking to construct this regulatory network in IBD. METHODS: Transcriptome data were obtained from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified using limma (p < 0.05, |log2FC| > 0.5). Weighted gene co-expression network analysis (WGCNA) with an optimal soft threshold of β = 7 was performed to identify key module genes. Candidate genes were obtained by intersecting DEGs, gut microbiota-associated genes from the gutMGene database, and WGCNA module genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted to explore the functional roles of candidate genes. Core genes were identified using three machine learning algorithms (LASSO, Boruta, and SVM-RFE), followed by protein-protein interaction (PPI) network analysis. Molecular docking was performed to assess the binding affinities between hub proteins and gut microbiota-derived metabolites. RESULTS: A total of 885 DEGs were identified between the IBD and control groups, including 463 upregulated and 422 downregulated genes. WGCNA identified 280 key module genes from the purple and yellow modules. The intersection of DEGs, gut microbiota-associated genes, and WGCNA module genes yielded 19 core candidate genes. PPI network analysis combined with three machine learning algorithms jointly identified C5AR1, KDM2A, and HCAR3 as core hub genes. ROC curve analysis demonstrated that all three hub genes achieved AUC values greater than 0.7 in both the training and validation sets, indicating excellent diagnostic performance for IBD. Enrichment analysis revealed significant associations with the TNF, NF-κB, and IL-17 signaling pathways. Molecular docking confirmed stable binding of C5AR1 with 1,3-Diphenylpropan-2-Ol (-7.87 ± 0.83 kcal·mol-¹) and HCAR3 with 3-Indolepropionic Acid (-6.35 ± 0.70 kcal·mol-¹), both below -5.0 kcal·mol-¹. CONCLUSION: This study first constructs a "gut microbiota-metabolite-hub gene" axis in IBD, providing a computational framework for microbiota-targeted precision therapy, and identifying C5AR1/KDM2A/HCAR3 as computationally predicted diagnostic biomarkers and 1,3-Diphenylpropan-2-Ol/3-Indolepropionic Acid as candidate intervention molecules that warrant further experimental validation.

Molecular Docking Simulation↗

PubMed2026

Brucellar spondylitis is associated with disturbance in gut microbiota and histamine metabolism associated inflammation.

BACKGROUND: The pathogenesis of brucellar spondylitis (BLS) has traditionally been considered to be primarily limited to local osteoarticular lesions. With the proposal of the "gut-spine axis" concept, the role of intestinal microecological dysbiosis in inflammatory spinal diseases has attracted in an increase of attention. The overactivated inflammatory cytokine network not only mediates bone destruction and intervertebral disc damage, but also forms a bidirectional interaction with gut microbiota dysbiosis through the "gut-spine axis," collectively driving disease progression. However, the inflammatory mechanism by which gut microbiota participates in the pathological process of BLS remains largely unclear. METHODS: This study recruited 20 BLS patients and 20 healthy donors. Multi-omics analysis including metagenomics, untargeted metabolomics, and targeted short-chain fatty acids (SCFAs) analysis, were used to compare the structural differences in gut microbiota between the two groups and screen for signature differential bacterial species. Plasma levels of histamine and histidine decarboxylase were measured by ELISA to clarify the role of differential histidine metabolic pathway in the disease. Additionally, plasma levels of lipopolysaccharide (LPS) and inflammatory cytokines (IL-1β, IL-6, IL-10, IL-17A, TNF-α) were detected by ELISA. The correlation between gut microbiota and inflammatory indicators was further analyzed. RESULTS: Compared to the healthy control group, the α-diversity of the gut microbiota in BLS patients was significantly reduced, with the microbial community structure exhibiting increased homogeneity. Beta diversity analysis revealed significant differences, suggesting that disease progression is associated with an overall imbalance in the gut microbiota and the deterioration of its specific structural composition. At the phylum level, the abundances of Actinomycetota, unclassified_d_Viruses, and Fusobacteriota were significantly increased in the gut microbiota of BLS patients compared to the control group, while the abundances of Bacillota and Pseudomonadota were significantly decreased. Further analysis revealed that, compared to the control group, the generic abundance of Enterococcus was significantly increased, while the proportions of Blautia, Faecalibacterium, Ruminococcus, Agathobacter, Roseburia, Clostridium, Eubacterium, Alistipes and Anaerobutyricum were significantly decreased. At the species level, the abundances of Enterococcus sp and Enterococcus-faecium were increased, whereas Blautia sp, Ruminococcus sp, Faecalibacterium sp, Faecalibacterium prausnitzii, Agathobacter rectalis, Eubacterium sp, Agathobacter sp, and Roseburia sp were decreased. Furthermore, untargeted metabolomics revealed that metabolites were enriched in the histidine metabolic pathway, and the levels of SCFAs including butyrate, isobutyrate, valerate, and 4-methylvalerate in the intestinal contents were reduced in BLS. Functional KEGG profiling revealed that key KOs involved in butyrate synthesis (e.g., K00074, K00172, K01640) and transport were globally downregulated in the patient group, whereas histidine decarboxylase KOs (K01693, K11755, K19787) that convert histidine to pro-inflammatory histamine were significantly enriched. The loss of butyrate-producing symbionts led to SCFAs deficiency and mucosal barrier disruption, creating ecological niches for facultatively anaerobic Enterococcus, which further exacerbated local inflammation via proteolytic fermentation and histamine production. Compared with the control group, BLS patients showed decreased plasma levels of IL-10, while levels of IL-1β, IL-6, IL-17A, and TNF-α were increased, and LPS levels were elevated. In addition, significantly elevated plasma pro-inflammatory LPS levels in patients with BLS suggest disruption of intestinal integrity and permeability. Correlation analysis indicated a close relationship between gut microbiota and inflammation. CONCLUSION: BLS is associated with gut microbiota dysbiosis and alterations in microbial metabolites, which may be linked to inflammatory responses and histamine metabolism. The differential microbial taxa identified in this study could be developed into a stool-based non-invasive diagnostic panel to facilitate early differentiation of BLS from other spinal disorders. Furthermore, restoring gut microbial balance through probiotic supplementation or dietary modulation may represent a promising adjunctive strategy to enhance the efficacy of standard antibiotic therapy and reduce disease recurrence.

Humans↗

PubMed2026

Long-read sequencing reveals putatively mobilizable resistance genes and multi-drug resistance plasmids underestimated by short-read metagenomics.

While shotgun metagenomics is often used to profile antibiotic resistome in gut microbial communities, few studies have investigated if the choice of sequencing platform and assembly strategy affect what mobile genetic elements and antimicrobial resistance genes are recovered. In this study, we compared three platforms (Illumina, Oxford Nanopore, and PacBio HiFi) and seven assembly strategies on gut metagenomes from cattle, pig, and human as case studies. Long-read assemblies recovered 5- to 7-fold more plasmid sequence than Illumina in cattle and pig (mean 17.0 Mb vs. 3.1 Mb), while Illumina performed comparably in the less diverse human gut where high per-species coverage enabled effective short-read plasmid assembly. Long reads also detected more resistance genes on plasmid contigs. Hybrid assembly results depended on the algorithm: scaffolding-based OPERA-MS preserved long-read contiguity and recovered more plasmid-borne resistance genes, while the short-read-centric metaSPAdes hybrid mode produced fragmented assemblies. After collapsing haplotype redundancy, PacBio HiFi identified 2 and 49 unique multi-drug resistance plasmid lineages in cattle and pig, respectively. On the other hand, only 2 and 4 were identified from Illumina. Long reads also placed far more ARGs in a putative mobilization context (50-73%) compared to 14-21% for short reads. Platform and assembly strategy are thus key variables in mobilome and resistome characterization and should be accounted for in antimicrobial resistance surveillance.

Animals↗

PubMed2026

High dietary fiber is associated with improved outcomes in patients with melanoma and sarcoma treated with immunotherapy regardless of gut microbiome dysbiosis and social vulnerability.

BACKGROUND: Social vulnerability, dietary fiber, and the gut microbiome have been individually implicated in clinical outcomes for melanoma and sarcoma patients. This study hypothesized that increasing social vulnerability is associated with insufficient dietary fiber intake and negatively associated with microbiome composition and clinical outcomes. METHODS: Clinicopathologic data, baseline fiber intake, and gut microbiome profiles were assessed in 153 patients with melanoma or sarcoma treated with immune checkpoint blockade (ICB) and prospectively followed. Patients' social vulnerability index (SVI) and fiber intake were evaluated for associations with microbiome composition, treatment response, and overall survival (OS). RESULTS: SVI percentile was 0.4 (interquartile ratio [IQR], 0.2-0.7), and median dietary fiber intake was 17 (IQR, 15-20) g/day. SVI was inversely correlated with dietary fiber intake (r, -0.18, p = .0398). Gut microbiome analyses revealed community and compositional differences by SVI, including inverse associations with α-diversity and the relative abundance of favorable bacteria such as Bifidobacterium longum (p < .001), contrasting the positive associations observed between fiber and these microbial markers. Increased dietary fiber intake was associated with measurable response to ICB. A difference in OS was not observed in more socially vulnerable patients (SVI, not reached vs. 81.7 months), however, a survival advantage was evident with higher dietary fiber intake (not reached, 58.9 months). CONCLUSIONS: Increased social vulnerability was associated with a less favorable gut microbiome composition but not worse OS among melanoma and sarcoma patients treated with ICB. Consistent with prior findings, high dietary fiber intake emerged as a potentially modifiable pathway to improve outcomes in patients initiating ICB, particularly those with increased SVI.

Humans↗

PubMed2026

Microbiome features associated with persistent intestinal carriages of Escherichia coli ST131 in a Southeast Asian cohort study.

Escherichia coli sequence-type 131 (ST131) is the dominant global extraintestinal pathogen capable of asymptomatic intestinal carriage and sustained household transmission, challenging infection control. Despite its clinical significance, the ecological determinants of gut persistence remain poorly understood. We performed shotgun metagenomics on fecal samples to investigate gut microbiome features associated with ST131-positive samples, distinct host carrier statuses (persistent, intermittent and non-carriers) and household risks in a study of a Southeast Asian cohort. Here, we show that ST131 carriage was associated with compositional shifts without reducing species alpha-diversity. Regression analyses identified depletion of commensal taxa and the 1,5-anhydrofructose degradation pathway in ST131-positive samples. Persistent carriers exhibited highly perturbed microbiome enriched with pathobionts, aerobactin- and lipopolysaccharide (LPS)-biosynthesis pathways. Comparing household risk groups to control, revealed that biotin biosynthesis and 1,5-anhydrofructose degradation may influence ST131 co-colonization through both direct and indirect mechanisms. Machine learning analyses identified metabolic pathways as stronger discriminators of persistent carriage than taxonomic features. Genomic-resolved analysis of clinical ST131 isolates revealed conserved genes for iron-acquisition, LPS and antibiotic resistance determinants. Overall, while commensals and metabolism may influence initial ST131 colonization, persistent carriage is associated with specific microbial and metabolic adaptations, providing potential targets to limit intestinal ST131 persistence.

Humans↗

PubMed2026

Commensal Dysbiosis Alters Primary Bile Acid Signaling to Drive Mammary Gland Inflammation and Breast Tumor Dissemination.

UNLABELLED: Breast cancer is the most commonly diagnosed malignancy and a leading cause of cancer-related mortality. Hormone receptor-positive (HR+) tumors represent the most prevalent metastatic subtype, and early dissemination remains a major clinical challenge. Commensal dysbiosis, defined as an inflammatory gut microbiome with low biodiversity, promotes metastasis by inducing mammary gland inflammation. In this study, we investigated systemic mechanisms governing dysbiosis-induced metastasis. Metabolomic profiling revealed elevated primary bile acids (BA) in the dysbiotic fecal microbiome. Sequestration and supplementation approaches demonstrated that beyond driving metabolic disease and mammary gland inflammation, primary BAs orchestrated enhanced HR+ tumor dissemination via a prostaglandin E2 (PGE2)-dependent pathway. Analysis of The Cancer Genome Atlas showed that BA, insulin resistance, and PGE2 gene signatures are associated with reduced survival in patients with HR+ tumors. In complementary analyses using the Epic Cosmos electronic health record database, BA sequestrant use was associated with longer restricted mean survival time among patients with metastatic disease. Together, these findings reveal that commensal dysbiosis-associated loss of microbial BA metabolism elevates primary BAs and promotes HR+ metastatic progression through PGE2 signaling. SIGNIFICANCE: Dysbiosis-induced bile acids drive systemic and mammary tissue-specific inflammation that promotes HR+ breast tumor metastasis, supporting the development of strategies targeting microbiome-derived metabolites to reduce metastatic risk in vulnerable populations.

Female↗

PubMed2026

Integrated metagenomic and metabolomic analysis identifies severity-specific inflammatory and metabolic signatures in post-stroke depression.

Post-stroke depression (PSD) is a common complication that significantly impacts patient prognosis. This study aimed to systematically characterize the associations among gut microbial ecology, metabolic profiles, and inflammatory responses across different severities of PSD. We conducted metagenomic sequencing, non-targeted metabolomics, and serum cytokine analysis (IL-1β, IL-6, IL-10, IL-18, TNF-α, IFN-γ, and CRP) in 91 patients with varying degrees of PSD and non-PSD controls. Bioinformatics analyzes were employed to construct multi-omics association networks and machine learning models. Results indicated that PSD patients exhibited significantly increased gut microbiota alpha-diversity, suggesting dysbiosis. Mild depression was characterized by compensatory neural signaling activation, whereas the moderate depression group exhibited abnormalities in tryptophan/indole metabolism, oxidative stress-related metabolic imbalances, and functional decompensation. Further analyzes suggested that Alistipes, Blautia_A, Evtepia gabavorous, and Lachnospira were associated with inflammatory features, GABA-related metabolic alterations, aromatic amino acid/indole metabolism, and lipid-amino acid metabolism, respectively. Under a more rigorous 10-fold cross-validation framework, the performance of different multi-omics combination models showed heterogeneity; however, some combinations still demonstrated superior discriminatory ability compared to single-omics approaches. This study provides multi-omics clues suggesting associations between different PSD severity levels and features such as increased Alistipes abundance, reduced antioxidant capacity, and altered tryptophan metabolism. It provides candidate biomarker combinations that may be useful for PSD stratification and suggests that the gut microbiome may represent a potential target for future PSD intervention. In summary, PSD may be associated with dynamic alterations along the "gut-brain-inflammation-metabolism" axis. These findings provide integrated evidence for microbial, metabolic, and inflammatory abnormalities across different PSD severity levels, but still require validation in larger samples, longitudinal cohorts, and mechanistic studies.

Humans↗

PubMed2025

Survival and safety evaluation of Bifidobacterium longum subsp. longum ZS-8 in healthy adults, determined using PMAxx-qPCR and amplicon sequencing.

UNLABELLED: Species-level quantitative PCR (qPCR) provides in-depth knowledge of oral probiotics in the human gastrointestinal tract (GIT). However, it lacks the capability to differentiate exogenous strains from native microbiota, nor can it distinguish between live and dead bacteria. In this study, we employed improved propidium monoazide (PMAxx)-qPCR to evaluate the survival and colonization of Bifidobacterium longum subsp. longum ZS-8 (designated ZS-8) on the strain level in the GIT and its impact on human gut microbiota. By spiking in live and dead ZS-8, we demonstrated that strain-level PMAxx-qPCR could identify and quantify the viable ZS-8 in fecal samples accurately. Using this method, we found that, in healthy humans, oral administration of ZS-8 can transiently survive in the GIT, and multi-layer seamless capsules (MLSC) significantly improve the gastrointestinal tolerance and survivability of ZS-8 compared to its powder form. Furthermore, through selective cultivation and PMAxx-microbiome sequencing, we investigated the response of gut viable microbiome to ZS-8. Results showed that, while the microbiota diversity and total viable counts of Bifidobacterium and Lactobacillus remained stable, certain indigenous species of Bifidobacterium and Lactobacillus increased in abundance, confirming ZS-8's probiotic potential in healthy individuals. Overall, our study demonstrates the effectiveness of combining strain-specific comparative genomics with PMAxx-qPCR for evaluating probiotic survival and colonization in the human gut and highlights the safety of ZS-8 oral administration in healthy individuals. IMPORTANCE: The survival and colonization of probiotics in the gut are critical for their functional efficacy, yet conventional species-level quantitative PCR (qPCR) fails to distinguish exogenous strains from native microbiota or differentiate live from dead bacteria. By integrating strain-specific comparative genomics with propidium monoazide (PMAxx)-qPCR, we precisely quantified the viability of Bifidobacterium longum ZS-8 at the strain level in the human gut after its oral administration. Our study demonstrated that 1.53-6.90% of cells surviving transit and multi-layer seamless capsules (MLSC) significantly enhanced the gastrointestinal tolerance of ZS-8. While ZS-8 administration did not alter gut microbiota diversity or total viable counts of Bifidobacterium and Lactobacillus, it selectively increased the abundance of specific indigenous beneficial species. This method overcomes the dual limitations of traditional techniques (strain-level specificity and viability discrimination), providing a robust tool for probiotic research. Furthermore, our findings confirm the safety of ZS-8 in healthy individuals and its potential to modulate gut ecology, offering a scientific foundation for personalized probiotic development and clinical translation.

Humans↗

PubMed2026

Identifying fundamental gaps in functional metagenomics: a step towards unlocking microbiome research potential.

Incomplete functional annotation limits biological interpretation in microbiome studies and their translational potential. Poor annotation arises from multiple causes, with incomplete gene-protein-reaction mapping being one tractable yet under-examined contributor. We address this gap by developing a comprehensive hierarchical framework that systematically integrates gene families in UniRef, proteins in UniProt, and metabolic reactions in MetaCyc and BioCyc through UniProtKB accession, EC number, and Pfam-domain matching. Applied to a human gut metagenome dataset via HUMAnN3, our MetaCyc-based mapping recovers up to 2.3-fold more unique reaction identifiers than the default pipeline and increases reaction prevalence across samples from ≈32% to 52% core reactions, addressing the data sparsity that limits statistical and machine-learning applications in microbiome research. Biological plausibility for the tested functions was supported by positive and negative controls: gut-microbial hormone-metabolism reactions previously linked to this dataset were recovered, while vertebrate-specific hormone-metabolism reactions remained correctly undetected. These gains derive from systematic database integration alone, without predictive algorithms, indicating that a tractable, mapping-related component of functional dark matter and data sparsity in microbiome studies is directly addressable. Because Pfam- and BioCyc-derived mappings trade specificity for coverage, confidence in any individual reaction assignment depends on the supporting evidence tier and source database.

Humans↗

PubMed2025

The Effect of Colesevelam on the Microbiome in Postoperative Crohn's Disease.

BACKGROUND: While surgery plays a pivotal role in the management of ileal Crohn's disease, the risk of endoscopic recurrence following an ileocaecal resection can be greater than 65% within 12 months of surgery. More than 90% of patients with Crohn's disease have a concomitant diagnosis of bile acid diarrhea following an ileal resection. This pilot study aimed to assess whether the use of bile acid sequestrants in patients with Crohn's disease who have undergone a primary terminal ileal resection with concomitant bile acid diarrhea can alter the microbiome and prevent disease recurrence. METHODS: Patients with Crohn's disease who underwent a primary terminal ileal resection and had symptoms of diarrhea within 1-3 months of surgery underwent 75SeHCAT testing for bile acid diarrhea. If positive (75SeHCAT ≤ 15%), patients were treated with colesevelam and stool samples were collected at 4 weeks, 8 weeks, and 6-12 months posttreatment. If negative (75SeHCAT > 15%), treatment was not given and were reviewed in the clinic as per local guidelines. All patients underwent a 6-12 month postoperative colonoscopy where further stool samples and mucosal biopsies were taken. Disease activity was established using the endoscopic Rutgeert's score, with disease remission defined as Rutgeert's score <i2 and disease recurrence ≥i2. 16S ribosomal RNA gene analysis was undertaken for the collected fecal and mucosal samples to assess α/β-diversity and microbial composition. RESULTS: A total of 14 patients who completed the study, 10 of whom had a 75SeHCAT positive diagnosis of bile acid diarrhea and were started on treatment with colesevelam. Four patients did not require treatment as 3 were asymptomatic and 1 had a negative 75SeHCAT scan. Three of the fourteen patients had disease recurrence at their 6-12 month postoperative colonoscopy assessment, of which 1 patient was taking colesevelam and 2 patients were not taking colesevelam. A total of 44 fecal samples and 44 mucosal biopsies underwent 16S ribosomal RNA gene analysis to assess α/β-diversity and microbial composition. In the colesevelam treated patients there was no significant difference in α/β-diversity pre- and posttreatment. Pretreatment, the 3 most abundant bacterial classes in all patients were Bacteroidia, Clostridia, and Gammaproteobacteria. Following 6-12 months of treatment, out of the 9 patients on colesevelam, 5/9 (55.6%) had a reduction in Bacteroidia, 9/9 (100%) had an increase in Clostridia, and 7/9 (77.8%) had a reduction in Gammaproteobacteria. Of the 2 patients not given colesevelam, one showed a reduction in Bacteroidia, increase in Clostridia and a reduction in Gammaproteobacteria. CONCLUSIONS: This small pilot study demonstrated that patients who were given colesevelam, were more likely to be in disease remission at their 6-12 months colonoscopy review compared with those not treated. Furthermore, treatment with colesevelam may have a role in altering the microbiome to help maintain remission states in postoperative Crohn's disease. Larger mechanistic studies are now needed to confirm these findings and demonstrate statistical significance as well as investigate whether this benefit may be present even in those patients with 75SeHCAT negative disease.

Humans↗