Intermittent hypoxia and hypercapnia (IHC), a hallmark of obstructive sleep apnea (OSA), accelerates atherosclerosis, yet the underlying mechanisms remain unclear. The gut microbiota and metabolites, specifically bile acids, change with IHC and thus the bile acid receptor farnesoid X receptor (FXR) might mediate IHC-induced atherosclerosis. In this study, ApoE -/- and ApoE -/- FXR -/- mice were exposed to IHC or room air and fed with a high-fat, high-cholesterol diet for 10 weeks. Markers of atherosclerosis, fecal microbiome, and metabolome were then examined via Sudan IV staining, absolute abundance shotgun metagenomics, and untargeted liquid chromatography tandem mass spectrometry (LC-MS/MS). IHC markedly increased aortic atherosclerosis in ApoE -/- mice, an increase that was abolished by FXR deficiency. In addition, IHC reshaped gut microbial composition, promoting enrichment of bile acid-modifying taxa and increasing levels of microbial hydroxysteroid dehydrogenase ( hsdh ). The bile acid pool was also remodeled and associated with aortic atherosclerosis via FXR-dependent metabolic signals in ApoE -/- mice. Knockout of FXR disrupted microbiome shift under IHC and uncoupled microbial bile acid metabolism from vascular lesion development, thereby protecting against aortic atherosclerosis. These findings show that FXR has a central role in linking IHC, microbial bile acid metabolism, and cardiovascular pathology.

The microbial and biochemical landscape of clinically normal-appearing skin in individuals with acne remains uncharacterized. Here, we performed longitudinal multi-omics profiling of facial skin from 10 moderate acne patients and 10 healthy controls, integrating 16S rRNA gene sequencing, shotgun metagenomics, and untargeted metabolomics across lesional and non-lesional sites. Compositional tensor factorization revealed that non-lesional acne skin occupies a distinct intermediate state between healthy and lesional skin in both the microbiome and the metabolome. Machine learning models distinguished healthy from non-lesional acne skin with 70% accuracy, demonstrating that molecular dysbiosis occurs in skin without visible lesions. Non-lesional sites exhibited reduced microbial diversity, strain-level shifts in Corynebacterium and Lawsonella correlating with disease severity, and metabolic alterations, including elevated lipids and perturbed amino acid and dipeptide profiles. Microbe–metabolite co-occurrence network analyses revealed that healthy skin is enriched for protective metabolites such as urocanic acid, while acne-associated skin shows distinct co-occurrence patterns. These findings establish acne as a field effect disorder, with molecular alterations extending beyond visible lesions across the entire facial skin ecosystem. This molecular signature of pre-lesional skin provides potential biomarkers for early intervention and suggests that effective acne treatment may require holistic approaches targeting the broader skin environment rather than individual lesions.

Maternal intrapartum antibiotic prophylaxis (IAP) and postpartum maternal antibiotic usage are increasingly common and have been linked to altered growth and immune development in offspring. However, the mechanisms underlying these effects, particularly those arising from indirect early-life exposure to antibiotics, remain poorly understood. Here, using a preclinical murine model, we examined the impact of in vivo antepartum and postpartum maternal ampicillin administration on the maternal fecal microbiome and metabolome. Ampicillin treatment resulted in a significant depletion of bacterial species belonging to the Muribaculaceae family, including Muribaculum intestinale and Duncaniella dubosii, accompanied by a cohort-dependent enrichment of Enterococcus and Prevotella species. These microbial shifts coincided with substantial and reproducible metabolic remodeling, including elevated fecal acylcarnitines and altered bile acid profiles. Notably, we identified two previously uncharacterized trihydroxylated bile acids conjugated to a hexose moiety, which we annotated as cholic acid-galactose and taurocholic acid-galactose and synthesized. These metabolites were consistently associated with antibiotic exposure across public metabolomics data repositories. Finally, alterations in the maternal fecal microbiome and metabolome were associated with increased weight gain in offspring, suggesting potential pathways by which maternal antibiotic exposure may influence early developmental outcomes. These findings highlight microbial and metabolic signatures linked to perinatal antibiotic use and underscore the need to balance infection control with long-term infant health considerations.

Infant antibiotic treatment is associated with increased risk of developing non-communicable diseases, potentially through disruption of the gut microbiome. However, the impact of indirect antibiotic exposure via human milk remains largely unexplored. Here, we investigate a cohort (n=80) of antibiotic-treated breastfeeding mother-infant dyads and untreated matching controls using integrative multi-omics analyses of fecal, milk, and skin samples (n=1,455). Maternal antibiotic treatment was associated with different infant fecal microbiome and metabolome profiles, including lower abundance of Bacteroides, Lactobacillus, and Bifidobacterium, and higher levels of antimicrobial resistance gene reads. Further, fecal metabolic alterations associated with indirect antibiotic exposure were exacerbated by formula milk supplementation. In a subset of infants (n=61), indirect exposure was associated with higher body mass index (BMI). These findings suggest that maternal antibiotic treatment during lactation may influence the early-life infant gut microbiome with potential long-term implications.

Microbial metabolites play a critical role in regulating ecosystems, including the human body and its microbiota. However, understanding the physiologically relevant role of these molecules, especially through liquid chromatography tandem mass spectrometry (LC-MS/MS)-based untargeted metabolomics, poses significant challenges and often requires manual parsing of a large amount of literature, databases, and webpages. To address this gap, we established the Collaborative Microbial Metabolite Center knowledgebase (CMMC-KB), a platform that fosters collaborative efforts within the scientific community to curate knowledge about microbial metabolites. The CMMC-KB aims to collect comprehensive information about microbial molecules originating from microbial biosynthesis, drug metabolism, exposure-related molecules, food, host-derived molecules, and, whenever available, their known activities. Molecules from other sources, including host-produced, dietary, and pharmaceutical compounds, are also included. By enabling direct integration of this knowledgebase with downstream analytical tools, including molecular networking, we can deepen insights into microbiota and their metabolites, ultimately advancing our understanding of microbial ecosystems.

The etiology of Alzheimer's disease (AD) remains unclear but is likely driven by gene-environment interactions. We present a multi-organ untargeted metabolomics atlas (n = 2,271) paired with metagenomics data (n = 666) from two AD transgenic mouse models (3xTg and 5xFAD) under colonized and germ-free conditions. Systems-level analyses revealed clusters of dysregulated molecules across tissues, including carnitines, bile acids, B vitamins, neurotransmitters, and N-acyl lipids. Metabolic shifts were associated with the depletion of Akkermansia muciniphila and enrichment of Mucispirillum schaedleri in the 3xTg model. We identify previously unexplored carnitines linked to microbial metabolism of phenylalanine. Using tissueMASST-a mass spectrometry search tool we developed to translate animal-model findings into a human clinical context-we trace phenylacetyl-carnitine in human plasma and serum samples (n = 1,470) from independent cohorts, revealing associations with aging, cognitive impairment, and diminished memory performance. This public resource and associated tools will aid future research in AD etiology.

Emerging studies suggest that antibiotics can disrupt the gut microbiome and alter vaccine-induced immune responses. However, the specific consequences of early-life exposure on neonatal immune development remain poorly understood. Here, we examined how two antibiotics frequently used in perinatal care, broad-spectrum ampicillin (AMP) and the extended-spectrum combination amoxicillin/clavulanate (AMOX/CLAV), administered during gestation and lactation, influence neonatal gut microbiome composition, fecal metabolome profiles, and responses to the 20-valent pneumococcal conjugate vaccine (PCV20). Maternal treatment with AMOX/CLAV, but not AMP, significantly reduced PCV-specific IgG titers at 4 and 6 weeks post-prime immunization compared to untreated controls. Exclusive exposure to AMOX/CLAV also impaired neutrophil-mediated opsonophagocytic killing, indicating reduced antibody functionality. These effects were transient, with immune parameters normalizing by 8 weeks post-prime immunization. Metabolomic and microbiome profiling revealed that maternal AMP and AMOX/CLAV differentially perturbed specific metabolite classes, including bile acids, N-acyl lipids, and indole derivatives. Key commensal taxa, including Bacteroidales and Coriobacteriales were also impacted within the gut microbiota. Together, these findings reveal a previously underappreciated maternal-offspring route of antibiotic influence that is transiently associated with neonatal vaccine responsiveness and microbiome and metabolome alterations. These results highlight maternal antibiotic exposure as a possible modifiable factor shaping early-life immunity.

Establishing the biological context of microbial metabolites remains a major challenge. We present microbiomeMASST, a metadata-driven network graph that maps metabolites across 467 available datasets with 144,424 mass spectrometry files from humans, animals, and microbial culture systems. MicrobiomeMASST integrates monocultures, synthetic communities, and host-associated samples across multiple body sites and plants. MS/MS spectra can be queried to trace occurrence across hosts, experimental conditions, and interventions, enabling cross-study integration. We demonstrate this framework by contextualizing microbial-conjugated bile acids and interrogating microbiome-mediated drug metabolism. Screening gut bacteria revealed deprolylation of the angiotensin-converting enzyme (ACE) inhibitor prodrug enalapril. Using microbiomeMASST, we traced this metabolite across human cohorts, microbial isolates, environmental samples, and in Gorilla gorilla . Structural modeling and enzymatic assays showed that microbial deprolylation abolishes ACE inhibition, thereby inactivating its therapeutic effect. Together, microbiomeMASST links MS/MS spectra to biological context, converting isolated observations into an interpretable microbiome map for cross-study analysis.

Searching and learning from aggregated public metabolomics data spanning thousands of studies remained largely inaccessible. Here we present StructureMASST, a web-based application enabling scalable, structure-centric searches across public metabolomics repositories using molecule names or chemical representations. It queries a precomputed knowledgebase of 2.19 billion spectral matches and 420 million metadata links, supports modification-tolerant and mass-shift searches, and maps chemical structures across taxonomy, biological context and environmental conditions to accelerate discovery.

Untargeted metabolomics is a powerful approach for exploring the chemical diversity and dynamics of biological systems. However, the types of questions that can be addressed depend not only on experimental design but also on the data processing and analysis workflows employed, many of which require advanced computational expertise. GNPS1, now transitioning to its second major implementation (GNPS2), has evolved into an expandable platform that supports the integration of modular web applications designed to simplify and enhance downstream analysis. These apps, named MetaboApps, facilitate the post-processing of outputs of several GNPS workflows and help make repository-scale metabolomics knowledge and other areas of metabolomics more accessible to a broader community.

Bacteroides fragilis, a key member of the human gut microbiota, contributes to host health by maintaining intestinal homeostasis. Yet, it is also the most frequently isolated anaerobe in clinical infections. These contrasting roles raise questions about the genetic and ecological factors that explain why this common symbiont is disproportionately linked to infection. We analyzed 813 Division I B. fragilis genomes, including 147 new isolates from intestinal and extra-intestinal sites. Infection-associated isolates spanned all phylogroups, indicating no pathogenic lineage. We identified 16 phylogroups, distinguished by genes associated with capsule biosynthesis and interbacterial competition. Additionally, differential metabolomic analysis identified 12 metabolites associated with isolation source, while a microbial genome-wide association study uncovered 44 genes enriched in isolates from extra-intestinal sites, providing the first population-scale markers tied to clinical recovery sites. These results do not implicate a pathogenic lineage; instead, they point to associational links between accessory modules and recovery from extra-intestinal sites under permissive host conditions. This work underscores how genomic diversity and ecological context may jointly shape the clinical impact of gut commensals.IMPORTANCEBacteroides fragilis, a human gut resident, is paradoxically one of the most frequent anaerobes recovered from bloodstream and abscess infections. The genetic features that enable frequent recovery from extra-intestinal sites remain poorly defined. Using comparative genomic and metabolomic analyses of strains from intestinal and extra-intestinal sources, we show that strains isolated from infections are phylogenetically dispersed rather than restricted to a single lineage. We observe lineage-linked differences in capsule loci and competition systems, which suggests constrained gene flow and lineage-specific adaptation within the gut. Additionally, a subset of genes and metabolites is enriched among extra-intestinal isolates. Together, these findings suggest that extra-intestinal survival among B. fragilis strains reflects the interplay between species-wide genomic diversity and permissive host conditions, rather than the emergence of a single pathogenic lineage.

Studies using Alzheimer’s disease (AD) models suggest that gut bacteria contribute to amyloid pathology and systemic inflammation. Further, gut-derived metabolites serve critical roles in regulating cholesterol, blood-brain barrier permeability, neuroinflammation, and circadian rhythms. Recent studies from the Alzheimer’s Disease Neuroimaging Initiative have shown that serum-based gut-derived metabolites are associated with AD biomarkers and cognitive impairment. We recently reported a time-restricted feeding (TRF) intervention that restored brain transcription, increased Aβ clearance, reduced amyloid deposition, and improved memory deficits in AD mice (PMID:37607543). Here we investigated gut microbiome alterations in the APP23 mouse stool and terminal ileum and evaluated the role of the microbiome and metabolome in the beneficial effects of TRF. Adult male and female APP23 transgenic (TG) and littermate non-transgenic (NTG) mice (n = 3-4/sex/genotype/condition) underwent ad libitum feeding (ALF) or a TRF protocol consisting of 6-hours of active-phase feeding followed by 18-hours fasting for 3-months. Metabolomics, metagenomics and metatranscriptomics were performed on ileum and stool (collected every 4-hours for 24-hours) from mice used in our TRF intervention study. Metagenomic analyses revealed that the stool microbiome composition and genomic functions were altered in APP23 TG compared to NTG mice and were further uniquely modulated in TG mice on TRF. Notably, stool metabolites relating to metabolism and neuroimmune function were differentially abundant in TG mice and partially restored by TRF. The stool microbiome and metabolome presented distinct diurnal cycling dynamics. TG mice showed a significant loss of rhythmic genomes which were markedly increased by TRF, indicative of broad entrainment of microbial rhythmicity. Ileal diurnal dynamics further differentiated TG mice on TRF. Ileal metatranscriptomic analysis revealed that TRF also reversed bacterial compositional and functional alterations in TG mice, including the attenuation of elevated inflammation-related bacterial transcripts. TG mice showed alterations in microbiome composition, function, and rhythmicity. The unique microbiome induced by TRF regulated functions and metabolites implicated in AD and may represent one of the pathways by which TRF rescued pathology and cognition in AD mice.

Indirect exposure to antibiotics during early life, via maternal intrapartum antibiotic prophylaxis (IAP) or postpartum maternal antibiotic usage, is increasingly common and has been epidemiologically linked to altered growth and immune developmental trajectories in offspring. Nevertheless, the underlying mechanisms remain poorly understood. Here, we explored the effects of antepartum and postpartum maternal ampicillin administration on the dams' fecal microbiome and metabolic profiles in vivo. Ampicillin caused a reproducible depletion of beneficial bacterial species belonging to the Muribaculaceae family, including Muribaculum intestinale and Duncaniella dubosii, and led to cohort-dependent enrichments of Enterococcus and Prevotella species. These microbial alterations were accompanied by substantial metabolic remodeling, characterized by elevated fecal acylcarnitines and dysregulation of the bile acids profile. Intriguingly, we identified two previously uncharacterized trihydroxylated bile acids conjugated to a hexose moiety, which appeared to be associated with antibiotic exposure across public metabolomics repositories. These alterations in the fecal maternal microbiome and metabolome coincided with increased weight gain in offspring, suggesting a possible role for maternal antibiotic exposure in shaping early developmental trajectories. Further studies are warranted to elucidate the long-term implications of these changes in infant health.

Early life is a critical period for immune and metabolic development, but these patterns remain underexplored in populations from low- and middle-income countries. Here, we profile the microbiome and metabolome of 55 Bangladeshi mother-infant dyads over the first 6 months of life. Importantly, we observe an increase in microbially derived bile amidates and N-acyl lipids with age in conjunction with reads matching the bile salt hydrolase/transferase (bsh) gene. Although microbial source tracking confirms maternal fecal seeding, a substantial environmental contribution is also highlighted. Differences in infant fecal metabolic profiles are associated with delivery mode, maternal milk composition, household assets, and household-level water treatment. Cesarean section (C-section) delivery and untreated drinking water are linked to transient metabolic differences, including increases in bile amidates, N-acyl lipids, and other host-microbe co-metabolic products, including acylcarnitines. Multi-omics analysis reveals specific microbial-metabolite relationships, highlighting how early environmental and maternal living circumstances influence gut metabolic development through the microbiome.

In untargeted metabolomics, reference MS/MS libraries are essential for structural annotation, yet currently explain only 6.9% of the more than 1.7 billion MS/MS spectra in public repositories. We hypothesized that many unannotated features arise from simple, biologically plausible transformations of endogenous and exposure-derived compounds. To test this, we created a reference resource by synthesizing over 100,000 compounds using multiplexed reactions that mimic such biochemical transformations. 91% of the compounds synthesized are absent from existing structural databases. Through improvements in the construction of the computational infrastructure that enables pan repository-scale MS/MS comparisons, searching this biologically inspired MS/MS library increased the overall reference-based match rate by 17.4%, yielding over 60 million new matches and raising the global pan-repository MS/MS annotation rate to 8.1%. By facilitating structural hypotheses for previously uncharacterized MS/MS data, this framework expands the accessible detectable biochemical landscape across human, animal, plant, and microbial systems, revealing previously undescribed metabolites such as ibuprofen-carnitine and 5-ASA-phenylpropionic acid conjugates arising from drug-host and host-microbiome co-metabolism.

Introduction: Osteoarthritis (OA) is a chronic degenerative joint disease with limited treatment options focused primarily on symptom management. Emerging evidence suggests that dietary interventions may influence inflammation and pain through modulation of the gut microbiome and metabolome. Methods: We conducted a 4-week open-label pilot trial evaluating the effects of an anti-inflammatory dietary intervention (ITIS diet) in 20 patients with knee OA (ClinicalTrials.gov ID: NCT05559463, registered prior to enrollment; sponsor: University of California, San Diego; responsible party: Monica Guma; study start date: 1 October 2021). The following were assessed before and after the intervention: (1) clinical outcomes; (2) gut and salivary microbiomes; and (3) salivary, stool, and plasma metabolomes. Responders were defined as patients achieving ≥30% reduction in Western Ontario and McMaster Universities Arthritis Index (WOMAC) pain scores. Results: The ITIS diet was well-tolerated, with good adherence (66.2%) and a significant improvement in clinical outcomes, including reduced pain and improved overall health measured with the visual analog scale (VAS). Responders (n = 8) showed distinct gut microbiome and metabolome profiles compared to non-responders (n = 12). Notably, taxa within the Lachnospiraceae family exhibited dynamic, bidirectional shifts post-intervention: Anaerostipes and Limivivens were enriched among responders and negatively correlated with pain scores, while Oliverpabstia and Fusicatenibacter were depleted following dietary intervention. These taxa also showed strong correlations with anti-inflammatory metabolites, including hydroxydecanoic acid derivatives and pyridoxine. Furthermore, subsequent network analysis revealed more structured and selective microbiome–metabolome interactions in responders, specifically post-intervention. Conclusions: This pilot study shows that a short-term anti-inflammatory dietary intervention was associated with meaningful changes in the gut microbiome and metabolome. Members of the Lachnospiraceae family emerged as key taxa associated with pain reduction and anti-inflammatory metabolite production. Our findings suggest that specific microbial responses—rather than global diversity changes—may underlie dietary responsiveness in OA. Although exploratory and limited by sample size, our results support further investigation into personalized, microbiome-informed nutritional strategies for OA management.

Very early onset inflammatory bowel disease (VEO-IBD) is a clinically distinct form of IBD manifesting in children before the age of six years. Disease in these children is especially severe and often refractory to treatment. While previous studies have investigated changes in the fecal microbiome and metabolome in adult and pediatric IBD, insights in VEO-IBD remain limited. This multi-omics analysis reveals changes in the fecal microbiome and metabolome in children diagnosed with VEO-IBD compared with age- and sexmatched healthy controls. Untargeted metabolomics analysis identified a depletion of short-chain N-acyl lipids and an enrichment of dipeptides, tripeptides, and oxo bile acids in children with VEO-IBD. Differential abundance analysis of 16S rRNA sequencing data showed lower abundance of beneficial bacteria such as Bifidobacterium and Blautia, and higher abundance of Lachnospira, Veillonella, and Bacteroides in VEO-IBD. Multi-omics integration revealed associations between the altered gut microbiome composition and metabolic dysregulation, specifically for the N-acyl lipids. This study offers unique insight into fecal microbial and metabolic signatures in VEO-IBD, paving the way for a better understanding of disease patterns and thereby more effective treatment strategies.

Emerging studies reveal that gut microbes can conjugate diverse amino acids to bile acids, known as microbially conjugated bile acids. However, their regulation and health effects remain unclear. Here, we analyzed early-life microbially conjugated bile acid patterns and their link to islet autoimmunity. We quantified 110 microbial bile acids in 303 stool samples collected longitudinally (3-36 months) from children who developed one or more islet autoantibodies and controls who remained autoantibody-negative. We identified distinct age-dependent trajectories of these bile acid amidates and correlated them with gut microbiome composition. We found that altered levels of ursodeoxycholic and deoxycholic acid conjugates were linked to islet autoimmunity as well as modulated monocyte activation in response to immunostimulatory lipopolysaccharide and Th17/Treg cell balance. These findings suggest that microbially conjugated bile acids influence immune development and type 1 diabetes risk.

Despite extensive efforts, extracting medication exposure information from clinical records remains challenging. To complement this approach, here we show the Global Natural Product Social Molecular Networking (GNPS) Drug Library, a tandem mass spectrometry (MS/MS) based resource designed for drug screening with untargeted metabolomics. This resource integrates MS/MS references of drugs and their metabolites/analogs with standardized vocabularies on their exposure sources, pharmacologic classes, therapeutic indications, and mechanisms of action. It enables direct analysis of drug exposure and metabolism from untargeted metabolomics data, supporting flexible summarization at multiple ontology levels to align with different research goals. We demonstrate its application by stratifying participants in a human immunodeficiency virus (HIV) cohort based on detected drug exposures. We uncover drug-associated alterations in microbiota-derived N-acyl lipids that are not captured when stratifying by self-reported medication use. Overall, GNPS Drug Library provides a scalable resource for empirical drug screening in clinical, nutritional, environmental, and other research disciplines, facilitating insights into the ecological and health consequences of drug exposures. While not intended for immediate clinical decision-making, it supports data-driven exploration of drug exposures where traditional records are limited or unreliable.

Background and Aims Very early onset inflammatory bowel disease (VEO-IBD) is a clinically distinct form of IBD manifesting in children before the age of six years. Disease in these children is especially severe and often refractory to treatment. While previous studies have investigated changes in the fecal microbiome and metabolome in adult and pediatric IBD, insights in VEO-IBD remain limited. This multi-omics analysis reveals changes in the fecal microbiome and metabolome in VEO-IBD compared with healthy controls. Methods Fecal samples were collected from children diagnosed with VEO-IBD and age- and sex-matched healthy controls. Both the fecal metabolome and microbiome were profiled in each sample, using untargeted liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) and 16S rRNA gene amplicon sequencing. Results Fecal microbial and metabolic profiles in VEO-IBD were significantly different from healthy controls. Untargeted metabolomics analysis identified a depletion of short-chain N -acyl lipids and an enrichment of dipeptides, tripeptides, and oxo bile acids in VEO-IBD patients. Differential abundance analysis of the gut microbiome showed lower abundance of beneficial bacteria such as Bifidobacterium and Blautia , and higher abundance of Lachnospira, Veillonella , and Bacteroides in VEO-IBD. The joint analysis suggested a clear association between the altered gut microbiome composition and metabolic dysregulation, specifically for the N -acyl lipids. Conclusions This study offers unique insight into fecal microbial and metabolic signatures in VEO-IBD, paving the way for a better understanding of disease patterns and thereby more effective treatment strategies. ### Competing Interest Statement S.M.T. receives research funding from Veloxis Pharmaceuticals. P.C.D. is an advisor and holds equity in Cybele, Sirenas, and BileOmix, and he is a scientific co-founder, advisor, holds equity and/or receives income from Ometa, Enveda, and Arome with prior approval by UC San Diego. P.C.D. consulted for DSM Animal Health in 2023. J.A.C. is an advisor for Pharming Pharmaceuticals. All other authors declare no conflicts of interest. NICHD/NIH, , 5P30HD106451-03, sub-award 9800-VU NICHD P50, , P50HD106463