Microbiome

Early-life gut microbial colonization is an important process shaping host physiology, immunity and long-term health outcomes in humans and other animals. However, our understanding of this dynamic process remains poorly investigated in wild animals, where developmental mechanisms can be better understood within ecological and evolutionary relevant contexts. Using 16s rRNA amplicon sequencing on 525 fecal samples from a large cohort of infant and juvenile geladas (Theropithecus gelada), we characterized gut microbiome maturation during the first three years of life and assessed the role of maternal effects in shaping offspring microbiome assembly. Microbial diversity increased rapidly in the first months of life, followed by more gradual changes until weaning. As expected, changes in gut microbiome composition and function with increasing age reflected progressive dietary transitions: in early infancy when infants rely heavily on their mothers milk, microbes that facilitate milk glycans and lactose utilization dominated, while later in development as graminoids are progressively introduced into the diet, microbes that metabolize plant complex polysaccharides became dominant. Furthermore, the microbial community of nursing infants born to first-time (primiparous) mothers was more "milk-oriented" compared to similarly-aged infants born to experienced (multiparous) mothers. Comparisons of matched mother-offspring fecal samples to random dyads did not support vertical transmission as a conduit for these maternal effects, which instead could be explained by slower phenotypic development (and associated slower gut microbiome maturation) in infants born to first-time mothers. Together, our findings highlight the dynamic nature of gut colonization in early life and the role of maternal effects in modulating this trajectory in a wild primate.

BackgroundThe murine CBA/J mouse model widely supports immunology and enteric pathogen research. This model has illuminated Salmonella interactions with the gut microbiome since pathogen proliferation does not require disruptive pretreatment of the native microbiota, nor does it become systemic, thereby representing an analog to gastroenteritis disease progression in humans. Despite the value to broad research communities, microbiota in CBA/J mice are not represented in current murine microbiome genome catalogs. ResultsHere we present the first microbial and viral genomic catalog of the CBA/J murine gut microbiome. Using fecal microbial communities from untreated and Salmonella-infected, highly inflamed mice, we performed genomic reconstruction to determine the impacts on gut microbiome membership and functional potential. From high depth whole community sequencing (~42.4 Gbps/sample), we reconstructed 2,281 bacterial and 4,129 viral draft genomes. Salmonella challenge significantly altered gut membership in CBA/J mice, revealing 30 genera and 98 species that were conditionally rare and unsampled in non-inflamed mice. Additionally, inflamed communities were depleted in microbial genes that modulate host anti-inflammatory pathways and enriched in genes for respiratory energy generation. Our findings suggest decreases in butyrate concentrations during Salmonella infection corresponded to reductions in the relative abundance in members of the Alistipes. Strain-level comparison of CBA/J microbial genomes to prominent murine gut microbiome databases identified newly sampled lineages in this resource, while comparisons to human gut microbiomes extended the host relevance of dominant CBA/J inflammation resistant strains. ConclusionsThis CBA/J microbiome database provides the first genomic sampling of relevant, uncultivated microorganisms within the gut from this widely used laboratory model. Using this resource, we curated a functional, strain-resolved view on how Salmonella remodels intact murine gut communities, advancing pathobiome understanding beyond inferences from prior amplicon-based approaches. Salmonella-induced inflammation suppressed Alistipes and other dominant members, while rarer commensals like Lactobacillus and Enterococcus endure. The rare and novel species sampled across this inflammation gradient advance the utility of this microbiome resource to benefit the broad research needs of the CBA/J scientific community, and those using murine models for understanding the impact of inflammation on the gut microbiome more generally.

Mediterranean grasslands, vital natural and agricultural ecosystems, experience seasonal variation in water content that likely affect microbial activity. We used metagenomics-informed stable isotope probing to investigate how the activities of microorganisms in Angelo Reserve (2160 mm rainfall) and Hopland (956 mm rainfall) soil change over depth and the seasons. At both sites, we find that the relative abundances of organisms in shallow soil changes relatively little but the most abundant organisms vary greatly with soil depth. Notably the highest levels of isotope incorporation, indicative of growth, occurs in deep soils. The active part of the 0-10 cm soil community varies over time, especially in Hopland soils during the fall rewetting. We defined a large, novel clade of Actinomycetota with notable capacity for thiosulfate oxidation whose representatives are prevalent and active in deep soils (>20 cm) across both ecosystems. Active Saccharibacteria unexpectedly encode nucleotide synthesis genes that enabled isotope incorporation while growing in shallow Angelo soils over all time periods. In contrast to predicted episymbiotic lifestyles of Saccharibacteria, other highly active bacteria are predicted predators. Obligately predatory Pseudobdellovibrio are active in intermediate depth Hopland soils whereas bacteria of the order Haliangiales are active in shallow Angelo soils. Supporting predatory lifestyles of Haliangiales, we used in silico structure prediction to assemble a large protein complex that we identify as a contractile injection system. Overall, the results indicate the potential for active carbon turnover in deep grassland soil and strong seasonal changes in the active members of microbial communities, despite relatively minor shifts in community composition.

Soil organic matter (SOM) decomposition by microorganisms represents one of the largest uncertainties in predicting terrestrial carbon-atmosphere feedbacks. Yet we lack systematic understanding of the microbial taxa that drive decomposition of chemically distinct carbon pools and of the metabolic pathways they employ across environmental gradients. Here, we address this critical gap using the first continental-scale soil dataset pairing shotgun metagenomes with high-resolution molecular characterization of SOM chemistry. We use data from 47 standardized soil cores - selected using microbial respiration rates from 106 soils across the United States - to assemble 0.76 terabases (Tbs) of prokaryotic metagenome-assembled genomes (828 MAGs) and identify 66,727 distinct SOM molecules. Integrating these datasets revealed widespread microbial potential for depolymerizing chemically-recalcitrant carbon compounds previously considered stable. Notably, we uncover complementary metabolic specialization between genera affiliated with two abundant bacterial orders, Rhizobiales and Chthoniobacterales, and an archaeal order, Nitrososphaerales. This metabolic partitioning is consistent across soil depths and activity levels, suggesting coordinated decomposition of chemically-complex carbon through distinct but complementary biochemical strategies. The metabolic potential for depolymerization of chemically-recalcitrant compounds is supported by the abundance of these molecules across the soils, as indicated by Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR-MS), and by flux balance analysis of metabolic models. Our continental-scale integration of microbial genotypes with their chemical substrates reveals that a substantial fraction of SOM that is considered to be relatively stable harbors decomposition potential that current Earth system models fail to capture. These findings provide mechanistic insight for incorporating microbial metabolic pathways into carbon cycle predictions and highlight an underappreciated vulnerability of soil carbon to environmental variability.

Gut bacterial symbionts can support animal nutrition by facilitating digestion and providing valuable metabolites. While the composition of gut symbiont communities shifts with host development in holometabolous insects, changes in symbiotic roles between immature and adult stages are not well documented, especially in ants. Here, we explored the metabolic capabilities of microbiomes sampled from herbivorous turtle ant (Cephalotes sp.) larvae and adult workers through genomic and metagenomic screenings and targeted in vitro metabolic assays. We reveal that larval guts harbor bacterial symbionts from the Enterobacteriales, Lactobacillales and Rhizobiales orders, with impressive metabolic capabilities, including catabolism of plant and fungal recalcitrant fibers common in turtle ant diets, and energy-generating fermentation. Additionally, several members of the specialized turtle ant adult gut microbiome, sampled downstream of an anatomical barrier that dams large food particles, show a conserved potential to depolymerize many dietary fibers and other carbohydrates. Symbionts from both life stages have the genomic capacity to recycle nitrogen, synthesize amino acids and B-vitamins, and perform several key aspects of sulfur metabolism. We also document, for the first time in ants, an adult-associated Campylobacterales symbiont with an apparent capacity to anaerobically oxidize sulfide, reduce nitrate, and fix carbon dioxide. With help of their gut symbionts, including several bacteria likely acquired from the environment, turtle ant larvae appear as an important component of turtle ant colony digestion and nutrition. In addition, the conserved nature of the digestive, energy-generating, and nutritive capacities among adult-enriched symbionts suggests that nutritional ecology of turtle ant colonies has long been shaped by specialized, behaviorally-transferred gut bacteria with over 46 million years of residency.

Bdellovibrio and like organisms (BALOs) are obligate bacterial predators that shape microbial communities by promoting species diversity, yet they have long been considered irrelevant to the human gut due to their presumed obligate aerobic lifestyle. Here, we challenge this view through a combined meta-analytic, experimental, and conceptual investigation of BALOs in human microbiomes. Reanalyzing 168,000 consistently processed samples from the Human Microbiome Compendium spanning 482 studies, we detected BALOs in more than 80 studies and across multiple body sites worldwide, with a gut prevalence of 2.4%, a finding confirmed by reanalysis of the PRIME database for 16S rRNA microbiome data. Strikingly, BALO presence was consistently associated with higher microbial alpha-diversity across body sites and disease contexts. Biopsy-derived samples showed a substantially higher prevalence than fecal samples, suggesting a mucosa-proximal niche. Our laboratory experiments showed that multiple Bdellovibrio strains can delay the loss of microbial diversity in vitro and remain active under gut-relevant conditions, including 37C, pH 6.5, and in the presence of mucus. Genomic analyses further revealed terminal reductases, including nitrite reductases, in several BALO genomes, indicating the capacity for anaerobic or microaerobic respiration, consistent with persistence in mucosal microenvironments. Notably, the metabolic and ecological profiles of cultured BALOs closely match those of facultative anaerobes, which constitute their preferred prey and are central drivers of dysbiosis in inflammatory bowel disease, diabetes, colorectal cancer, and chronic kidney disease. Building on these findings, we propose a conceptual framework in which BALOs contribute to gut homeostasis by controlling the expansion of facultative anaerobes under inflammatory conditions, thereby facilitating the restoration of fermentative, butyrate-producing communities. Together, our results establish BALOs as consistent, functionally relevant members of the human microbiome and a promising natural candidate for therapeutic strategies targeting chronic gut disease.

The surface of fresh vegetable leaves harbors diverse microorganisms with the potential to influence human health through the microbiome-food-gut axis. We investigated the ecology of the bacterial and fungal microbiota on green and red lettuces (n=143) for a 12-month period using high-throughput amplicon sequencing, and assessed the potential transfer of these microbiota to the human gut. Lettuce-associated fungal and bacterial microbiota exhibited substantial temporal variation, converging into two distinct seasonal cycles: early-season (S1) and late-season (S2). Seasonal progression from S1 to S2 increased species richness in season-specific fungal and bacterial taxa, while inducing abundance shifts in persistent fungal taxa and compositional shifts in persistent bacterial taxa. These seasonal dynamics resulted in more complex and stable microbial networks, in which potentially pathogenic fungi were less frequently enriched. Comparative analyses with gut microbiota datasets from 2,831 (fungal) and 3,254 (bacterial) individuals revealed that lettuce-associated fungi and bacteria were widely detected in the human gut, with bacteria detected more frequently than fungi. Season-specific taxa were detected more frequently than persistent taxa, and microbial assembly in the gut was shaped by both neutral and deterministic processes. Notably, lettuce-associated bacteria predominantly co-occurred with non-plant glycan-degrading commensal bacteria in a season-dependent manner, and enrichment of these co-occurring taxa correlated positively with gut microbiota richness and composition. Our findings provide insights into the ecological linkages between fresh vegetable microbiota and the human gut microbiota through the food-gut axis.

BackgroundFunctional or compositional perturbations of the microbiome can occur at different sites of the body and this dysbiosis has been linked to various diseases. Changes in the nasopharyngeal microbiome are associated to patients susceptibility to multiple viral infections, including COVID-19, supporting the idea that the nasopharynx may be playing an important role in health and disease. Most studies on the nasopharyngeal microbiome have focused on a specific component in the lifespan, such as infanthood or the elderly, or have other limitations such as low sample sizes. Therefore, detailed studies analyzing the age- and sex-associated changes in the nasopharyngeal microbiome of healthy people across their whole life are essential to understand the relevance of the nasopharynx in the pathogenesis of multiple diseases, particularly viral infections such as COVID-19. Results120 nasopharyngeal samples from healthy subjects of all ages and both sexes were analyzed by 16s rRNA sequencing. Nasopharyngeal bacterial alpha diversity did not vary in any case between age or sex groups. Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were the predominant phyla in all the age groups, with several sex-associated differences probably due to the different levels of sex hormones between both sexes. Acinetobacter, Brevundimonas, Dolosigranulum, Finegoldia, Haemophilus, Leptotrichia, Moraxella, Peptoniphilus, Pseudomonas, Rothia, and Staphylococcus were the only 11 bacterial genera that presented significant age-associated differences. Other bacterial genera such as Anaerococcus, Burkholderia, Campylobacter, Delftia, Prevotella, Neisseria, Propionibacterium, Streptococcus, Ralstonia, Sphingomonas, and Corynebacterium appeared in the population with a very high frequency, suggesting that their presence might be biologically relevant. ConclusionsIn contrast to other anatomical areas such as the gut, bacterial diversity in the nasopharynx of healthy subjects remains very stable and resistant to perturbations throughout the whole life and in both sexes. Age-associated changes in taxonomic composition were observed at phylum, family, and genus levels, as well as several sex-associated changes probably due to the different levels of sex hormones present in both sexes at certain ages. Our results provide a complete and valuable dataset that will be useful for future research aiming for studying the relationship between changes in the nasopharyngeal microbiome and susceptibility to or severity of multiple diseases, including COVID-19.

The human gut microbiome exhibits reproducible configurations, yet the ecological forces connecting them to health remain unclear. Here, using enterosignature-based stratification of 5,170 individuals from the Le French Gut cohort, we identified hydrogen disposal as a key determinant of population-scale microbiome configurations, independently replicated in a meta-cohort (n = 5,107). Microbial configurations followed a continuum of hydrogen recycling capacity and redox-associated functions, aligned with dietary patterns and health indicators. Methanogenesis-dominant partitions were associated with more favorable health profiles, whereas acetogenesis-enriched partitions exhibited features of low-grade inflammation, and increased digestive symptoms, perceived stress and antidepressant use. Experimental characterization of mucin profiles highlighted differences across partitions and alterations in Bacteroides-enriched configurations. Together, our findings support an ecological host-microbiome framework linking hydrogen metabolism, redox ecology, and host health, offering microbiome-informed targets for precision intervention. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=128 SRC="FIGDIR/small/722951v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@e7b8d1org.highwire.dtl.DTLVardef@116ab09org.highwire.dtl.DTLVardef@136f1f8org.highwire.dtl.DTLVardef@480097_HPS_FORMAT_FIGEXP M_FIG C_FIG

BackgroundMetformin is the cornerstone therapy for type 2 diabetes, but gastrointestinal intolerance commonly limits dose escalation and long-term adherence. In the ProGasMet trial, multi-strain probiotic supplementation improved metformin tolerability. However, the underlying microbiome-metabolome mechanisms remain unclear. Methods and analysisWe performed an exploratory multi-omics analysis using Period 1 of a randomized, double-blind, placebo-controlled trial. Participants with metformin intolerance received a multi-strain probiotic or placebo for 12 weeks. Paired stool samples collected at baseline (Visit 2) and end of treatment (Visit 5) were available from 34 participants (68 samples). We integrated shotgun metagenomic species profiles, predicted gut metabolic modules, and untargeted faecal LC-MS metabolomics using multi-block sparse PLS (DIABLO), complemented by longitudinal feature-level analyses and associations with gastrointestinal symptom burden (QACSMI and a simplified GI score). ResultsMulti-omics integration showed moderate concordance across taxonomic, functional, and metabolomic blocks and separated probiotic from placebo profiles at 12 weeks. Bile acid-related metabolites were among the strongest contributors to group separation, with hyodeoxycholic acid and related compounds enriched in the probiotic arm. Global biodiversity and community-wide turnover did not differ materially between groups. Feature-level analyses suggested modest, directionally coherent changes in selected taxa, functional modules, and metabolites. Higher hyodeoxycholic acid concentrations at Visit 5 were associated with lower gastrointestinal symptom burden in probiotic-treated participants, a pattern not observed under placebo; statistical support was exploratory. ConclusionProbiotic supplementation may be associated with coordinated microbiome-metabolome shifts in metformin-intolerant type 2 diabetes, highlighting bile acid remodelling, particularly hyodeoxycholic acid, as a plausible mechanistic candidate for improved tolerability.

Antibiotic resistance is increasing among bacterial pathogens, posing one of the most severe threats to future public health. A major contributor to the increasing resistance is the dissemination of mobile antibiotic resistance genes (ARGs) among bacterial communities. These genes are ubiquitously present in various environments and are especially diverse in the human gut and wastewater. Despite this, the clinical implications of the prevalence of ARGs in these bacterial communities remain unclear. In this study, we aimed to investigate how the prevalence of ARGs in human gut and wastewater microbiomes reflects their dissemination among important bacterial pathogens. To do this, we estimated the prevalence of >30,000 ARGs, including both well-known (established) and computationally predicted (latent) genes, in >6,000 metagenomic samples. From their prevalence in the human gut and wastewater, we identified four categories of ARGs: co-promoted, human gut (HG)-promoted, wastewater (WW)- promoted, and non-promoted. Our results showed that co-promoted ARGs were by far the most promiscuous, being more frequently found across multiple bacterial phyla, and more often co-localized with broad host range conjugative elements. Co-promoted ARGs were also found to be overrepresented among genes identified in multiple pathogenic species and exhibited an overall higher genetic compatibility with both pathogens and other typical residents of the human gut and wastewater microbiomes. Taken together, our results highlight the link between the promotion of ARGs in the human gut and wastewater microbiomes and their presence in human pathogens, and, thereby, the genes potential risk to human health.

AimsThe gut microbiome has been implicated in type 2 diabetes progression, but reproducible biomarkers across studies remain limited due to technical and population heterogeneity. This study investigated whether specific gut microbiome shifts occur progressively across stages of type 2 diabetes. MethodsWe systematically reanalysed 16S rRNA datasets from 12 published studies (n=1,247 samples) after quality control, examining five groups (healthy controls, prediabetes (PD), new-onset type 2 diabetes, established type 2 diabetes, and type 2 diabetes with complications. Sequencing reads were quality-filtered, denoised, and resolved into amplicon sequence variants with genus-level taxonomic assignments using the SILVA database. Centered log-ratio (CLR)-transformed abundance data were analysed using PERMANOVA, meta-analysis with leave-one-study-out validation, differential abundance testing (Wilcoxon and ANCOM), and Random Forest classification. Eligible studies were identified through comprehensive searches of PubMed, Ovid Medline and Web of Science from June 2010 - June 2025 using predefined inclusion and exclusion criteria following PRISMA 2020 guidelines. Studies were investigated by two independent reviewers and included if they provided 16S rRNA data on adults across diabetes stages. Study quality was assessed based on metadata completeness and raw data availability. This systematic review and meta-analysis was registered in the Open Science Framework (OSF; registration https://osf.io/eth7a; embargoed until October 2026) and conducted according to PRISMA guidelines. ResultsEarly disease transitions showed minimal microbiome alterations, with only 4 genera, (notably enrichment of Allisonella and Escherichia-Shigella) were significantly different between healthy and PD (q < 0.05), and no significant genera between PD and new-onset type 2 diabetes. Advanced disease exhibited robust dysbiosis, with 9 genera differentially abundant in type 2 diabetes vs complicated type 2 diabetes and 5 genera in healthy vs complicated type 2 diabetes comparisons. Complicated type 2 diabetes was characterised by enrichment of Hungatella and [Clostridium] innocuum group and depletion of Faecalibacterium and compared to both uncomplicated type 2 diabetes and healthy controls. Random Forest classification achieved poor performance for early contrasts (AUC [&le;] 0.79) but strong discrimination for advanced disease (type 2 diabetes vs complicated type 2 diabetes: AUC = 0.89; Healthy vs complicated type 2 diabetes: AUC = 0.96). ConclusionGut microbiome alterations are subtle and inconsistent in early dysglycemia but become pronounced and reproducible with diabetic complications, suggesting microbiome-based biomarkers may be most clinically useful for identifying disease progression rather than early detection. Limitations include heterogeneity of sequencing methods and reliance on 16S rRNA data, which may restrict taxonomic and functional resolution. To our knowledge, this is the first meta-analysis to systematically evaluate gut microbiome alterations across multiple clinical stages of type 2 diabetes progression.

BackgroundViruses are the most abundant microbial entity on the planet, impacting microbial community structure and ecosystem services. Despite outnumbering Bacteria and Archaea by an order of magnitude, viruses have been comparatively underrepresented in reference databases. Metagenomic examinations have illustrated that viruses of Bacteria and Archaea have been specifically understudied in engineered environments. Here we employed metagenomic and computational biology methods to examine the diversity, host interactions, and genetic systems of viruses predicted from 27 samples taken from three municipal landfills across North America. ResultsWe identified numerous viruses that are not represented in reference databases, including the third largest bacteriophage genome identified to date ([~]678 kbp), and note a cosmopolitan diversity of viruses in landfills that are distinct from viromes in other systems. Host-virus interactions were examined via host CRISPR spacer to viral protospacer mapping which captured hyper-targeted viral populations and six viral populations predicted to infect across multiple phyla. Virally-encoded auxiliary metabolic genes (AMGs) were identified with the potential to augment hosts methane, sulfur, and contaminant degradation metabolisms, including AMGs not previously reported in literature. CRISPR arrays and CRISPR-Cas systems were identified from predicted viral genomes, including the two largest bacteriophage genomes to contain these genetic features. Some virally encoded Cas effector proteins appear distinct relative to previously reported Cas systems and are interesting targets for potential genome editing tools. ConclusionsOur observations indicate landfills, as heterogeneous contaminated sites with unique selective pressures, are key locations for diverse viruses and atypical virus-host dynamics.

Anthropogenic pressures are increasingly reshaping wildlife habitats worldwide. These transformations reduce natural areas, but also create new ecological niches, food resources, and environmental stressors, with potential consequences for wildlife behavior, physiology, and morphology. These changes may affect the gut microbiome, a critical component of host health, yet such effects are often inconsistent across species, particularly in wild non-human primates, and remain poorly understood. Here, we investigated how the gut microbiome of chacma baboons (Papio ursinus ursinus), an ecologically flexible generalist, responds to an anthropization gradient. We analyzed 512 fecal samples collected from 33 wild troops across a broad range of anthropogenic environments in the Western Cape, South Africa. Using a multi-metric approach including the Human Footprint Index, land-use variables and dietary proxies derived from stable isotopes, we assessed gut microbial diversity and composition based on 16S rRNA gene (V4) sequencing. Human-altered environments characterized by high Human Footprint and built-up areas were associated with reduced microbial diversity, and compositional and functional shifts, including decline in fiber-degrading taxa and increase in bacteria associated with simple carbohydrate and dairy metabolism. In contrast, highly cultivated areas showed no diversity difference and distinct microbial assemblages, while dietary variation had weaker effects, primarily altering rare taxa. Our results demonstrate that different components of anthropogenic pressure exert contrasting effects on the baboon gut microbiome, reflecting multiple ecological pathways extending beyond diet alone. Microbiome shifts may have implications for host health, potentially increasing susceptibility to pathogens or inflammatory diseases, with consequences for wildlife populations.

Beetles (order Coleoptera) are a diverse insect group whose associated microbial communities remain understudied despite their ecological, commercial, and biotechnological importance. Larvae of the darkling beetle species Tenebrio molitor (mealworms) and Zophobas atratus (superworms) have gained attention for their reported ability to ingest and possibly degrade plastics such as polyethylene and polystyrene. This degradation is believed to be mediated by enzymes from their gut microbiota, yet the underlying microbial mechanisms remain unclear. Using deep shotgun metagenomics, we generated comprehensive gut metagenomes for mealworms and superworms, recovering 53 and 100 high-quality metagenome-assembled genomes (MAGs), respectively. We found that the gut microbiomes of both insect species are dominated by bacteria from the phyla Bacillota and Pseudomonadota, with superworms trending towards greater bacterial diversity than mealworms. Comparing gut bacterial communities of insects fed polyethylene or polystyrene versus controls revealed no clear plastic ingestion effects beyond those attributable to starvation. On the other hand, insect cohort contributed substantially to variation in bacterial community composition, explaining 23% and 33% of the total variation in mealworms and superworms, respectively. Finally, we computationally identified numerous secreted proteins with sequence similarity to enzymes previously implicated in polyethylene and polystyrene degradation, and we provide support for dye decolorizing peroxidase (DyP)-type peroxidases as being the enzyme class mostly likely to initiate plastic oxidation in the digestive tracts of mealworms and superworms. Overall, this study provides high-quality metagenomes and MAGs for mealworms and superworms, revealing substantial under-explored microbial biodiversity, and highlighting DyP-type peroxidases as promising targets for future plastic biodegradation studies.

Multiple sclerosis (MS) is an autoimmune disease of the central nervous system (CNS) driven by genetic and environmental determinants. The gut microbiome of people with MS (pwMS) is distinct and influences disease through immunomodulatory metabolite production. Circulating metabolites are altered in pwMS, but identifying microbial-metabolic drivers remains challenging. We previously showed that colonization by the gut commensal Limosilactobacillus reuteri (L. reuteri) exacerbates disease in the experimental autoimmune encephalomyelitis (EAE) model of MS, in a tryptophan-dependent manner. Here, we integrated microbiomic and metabolomic datasets from a longitudinal EAE study utilizing high and low tryptophan diets in mice colonized or not with L. reuteri. Gut microbiome dynamics under short- and long-term alterations in tryptophan bioavailability, were affected by diet, microbiome context, or disease. During short-term dietary intervention, L. reuteri colonization exerted a greater impact on microbiome composition than tryptophan bioavailability. With longer dietary exposure and EAE progression, high dietary tryptophan and L. reuteri colonization synergized to elicit profound microbiota changes, including alterations in Lachnospiraceae, Blautia, and Akkermansia. Integration of metabolomic and microbiomic datasets using joint Robust Aitchison PCA revealed clusters of associated metabolites and microbiota enriched for functional pathways, including bile acid and tryptophan metabolism. Metabolites outperformed microbiota in predicting EAE severity, identifying p-cresols and indoles as top disease-associated metabolites. Treatment with p-cresol or 3-indoleglyoxylic acid exacerbated EAE, enhanced proinflammatory T cell responses, and increased cerebellar pathology. These data demonstrate that dietary responses are shaped by gut microbiome composition and that integrated microbiomic-metabolomic analyses can identify drivers of disease worsening in MS. IMPORTANCEMS is a multifactorial disease influenced not only by genetics but also by environmental factors, potentially including diet and the composition of the gut microbiome. We show that interactions between diet and commensal gut microbiota profoundly impact levels of immunomodulatory systemic metabolites, including several that are associated with disease in pwMS. Importantly, we demonstrate that individual gut microbiota produced metabolites are sufficient to worsen disease in a mouse model of MS. Integration of gut microbiome and blood metabolite datasets combined with subsequent predictive modeling, may bolster biomarker identification and the capacity to predict disease severity in pwMS, as compared to performance of individual datasets alone. These findings highlight metabolites as key mediators linking diet and the gut microbiota to neuroinflammation. Importantly, this work suggests that targeting microbial metabolites or modifying diet-microbiome interactions may represent new strategies to reduce disease activity in MS and related autoimmune disorders.

Despite the recognized role of the gut microbiome in modulating immune checkpoint inhibitor (ICI) efficacy, the ecological principles governing this relationship remain elusive. Moving beyond cataloging specific bacteria, we investigated whether general ecosystem properties determine clinical outcome. Through genome-resolved metagenomic analysis, we constructed a comprehensive catalog from 951 stool metagenomes and subsequently analyzed a curated subset of 624 samples from 11 multi-cancer cohorts. Our catalog comprises 3,816 non-redundant metagenome-assembled genomes (MAGs) and reveals key ecological determinants of ICI response. We found that clinical benefit is associated with an ecosystem dominated by prevalent, autochthonous taxa. A taxons prevalence in the population positively correlated with its association with positive outcome. Functionally, responder-associated microbes were enriched in genomic capacity for complex carbohydrate metabolism (including specialized mucin degradation) and amino acid biosynthesis. In contrast, non-response was characterized by enrichment of low-prevalence, exogenous (oral and food-derived) bacteria and a functional shift toward nucleoside metabolism, indicative of a dysbiotic state focused on replication. A log-ratio biomarker capturing this ecological shift provided generalizable predictive value across independent cohorts (mean AUC = 0.67 {+/-} 0.13). Our results support an ecological interpretation of the "Anna Karenina principle" in microbiomes: response is linked to a stable, functionally coherent microbial community, whereas non-response represents a destabilized state with high individual variability. This reframes the search for biomarkers from individual taxa to the assessment of ecosystem stability and metabolic competence, providing a foundation for microbiome-targeted strategies to improve cancer immunotherapy outcomes. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/652660v2_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@f0c9edorg.highwire.dtl.DTLVardef@591c6eorg.highwire.dtl.DTLVardef@59863forg.highwire.dtl.DTLVardef@17c934d_HPS_FORMAT_FIGEXP M_FIG C_FIG

Honeybees (Apis mellifera) rely on a specialized gut microbiome shaped by climate, flora, agrochemicals, and dietary supplements. Yet, how these factors alter microbiome composition and function remains unclear. We integrated 16S rRNA and shotgun metagenomics data from eight published studies across six regions, alongside newly generated 16S data from Armenia, to assess how environmental and agrochemical factors influence the honeybee gut microbiome. We also introduced a novel co-abundance and functional analysis pipeline to identify treatment-affected bacterial networks and associated pathways. We observed a stable core of six to twelve phylotypes in amplicon and metagenomic datasets respectively. However, we note significant geographic variation in relative abundances, likely reflecting differences in diet, climate, and local flora. Armenian data revealed distinct seasonal shifts, particularly elevated Commensalibacter in autumn and minor urban-rural differences. Pesticide treatments elicited varying responses: oxalic acid drove pronounced beta-diversity shifts; neonicotinoids had subtler effects, both primarily impacting opportunistic pathogens; and glyphosate disrupted core taxa with stronger effects in newly emerged bees under prolonged exposure. Co-abundance network analysis highlighted that the pesticide-associated community was enriched in adaptive pathways, including potential glyphosate degradation by Pseudomonas, biofilm formation, and aromatic amino acid synthesis. These findings reaffirm the stability of the honeybee core microbiome yet underscore that environmental and anthropogenic stressors induce distinct compositional and functional shifts. We emphasize the need for longitudinal metagenomic approaches that enable high-resolution functional profiling and co-abundance network analysis to clarify how these microbiome shifts impact bee health and colony sustainability.

Revegetation is a key strategy for restoring degraded lands globally. While this process can reshape belowground microbial communities, the extent to which such changes restore soil ecosystem functions, and whether different microbial traits recover synchronously or on distinct timescales remains less clear. Understanding this is essential for evaluating restoration success, as different microbial traits underpin distinct ecosystem services, from carbon storage to plant growth promotion, and the sequence in which these are restored can inform restoration targets and provide meaningful indicators of long-term ecological recovery. To address this, we applied deep metagenomic sequencing to characterise soil microbial responses following revegetation (spanning 1-31 years prior to sampling) on grazing agricultural lands. We find that revegetation following grazing cessation drove significant and sequential shifts in dominant microbial functions and life-history strategies. Functional changes occurred in distinct phases: an early, rapid restructuring of core soil health processes, detectable as early as three years, including enrichment of nutrient retention and carbon fixation pathways, followed by a more gradual development of plant growth-promoting traits as the plant community matures. Genome-resolved analyses of nearly 500 metagenome-assembled genomes revealed a fundamental shift in dominant microbial life history strategies: from a resource-scavenging and stress tolerance profile in grazing soils to strategies that prioritise biosynthesis and growth yields in revegetated soils. These lifestyle shifts have important implications for enhancing the microbial biomass and carbon sink potential of soils. Together, these findings show that microbial functional shifts following revegetation are temporally structured -- informing expectations for when key restoration targets may be achieved, and providing a practical framework for monitoring ecosystem recovery.

Winter carbon loss in northern ecosystems is estimated to be greater than the average growing season carbon uptake. However, most ecosystem carbon measurements neglect winter months since carbon losses (primarily driven by microbial decomposers) are assumed to be negligible at low temperatures. We used stable isotope probing (SIP) targeted metagenomics to reveal the genomic potential of active soil microbial populations under winter conditions, with an emphasis on viruses and virus-host dynamics. Peat soils from the Bonanza Creek LTER site in Alaska were incubated under subzero anoxic conditions with H218O for 184 and 370 days. We identified 46 bacterial populations (MAGs; spanning 9 bacterial phyla) and 243 viral populations (vOTUs) that actively took up 18O and produced significant CO2 throughout the incubation. Active hosts, predicted for 33% of the active vOTUs, were some of the most abundant MAGs and capable of fermentation and organic matter degradation. Approximately three-quarters of the active vOTUs carried auxiliary metabolic genes that spanned five functional categories, including carbon utilization, highlighting the potential impact of viruses in this peat soils microbial biogeochemistry. These results illustrate significant bacterial and viral activity and interactions occur in frozen soils, revealing viruses are a major community-structuring agent throughout winter months.