Suguru Nishijima

Analyses disentangling the role of the gut microbiome in linking lifestyle factors to health outcomes remain limited. Here, using fecal shotgun metagenomics from 6,803 adults in the Japanese 4D cohort, we identified two opposing microbiome-mediated axes linking lifestyle to health and 15 diseases. A health-associated axis enriched in microbial metabolism of dietary components was linked to plant-based, soy and dairy intake. In contrast, a disease-associated axis, enriched in oral-derived bacteria and pathobionts, was linked to refined carbohydrates and sedentary behavior. Starter culture microorganisms used to ferment foods did not show statistically significant mediation of the observed health effects. Alcohol was associated with both health- and disease-oriented mediation patterns involving microbial host-glycan utilization. Microbiome-defined health- and disease-oriented mediator axes were supported by fecal short-chain fatty acids and plasma cytokines from >1,700 individuals, revealing butyrate-associated anti-inflammatory and pro-inflammatory host profiles, respectively. Microbiome-based prediction (MADE) scores captured lifestyle-microbiome-disease mediation patterns and distinguished individual diseases across 13 independent external cohorts from the United States, China, Sweden, Russia and Australia. We identify the gut microbiome as a key mediator linking lifestyle to health and disease, providing a framework for microbiome-based assessment to guide lifestyle interventions for health promotion and disease prevention.

Industrialization has profoundly reshaped the structure and function of the human gut microbiome, yet our current knowledge of its diversity remains heavily biased toward industrialized populations. Here, we performed an integrated analysis of a large-scale metagenomic dataset (n = 41,471) to systematically characterize the gut microbiome across the African continent. We show that sub-Saharan African populations harbor gut microbiome structures that are distinct not only from industrialized populations but also from other non-industrialized populations. Notably, we identify a strong enrichment of Gastranaerophilales, a poorly characterized lineage of non-photosynthetic Cyanobacteria, in sub-Saharan African populations. Comparative genomic analyses reveal that this lineage encodes distinctive functional features, including motility-related genes, vitamin biosynthesis pathways, and specialized carbohydrate transport systems. Furthermore, we show that this lineage is widely distributed across non-human primates, supporting an evolutionarily conserved host association predating modern humans. Together, our findings identify Gastranaerophilales as a potential ancestral gut symbiont that has been markedly reduced in industrialized societies but retained within African populations, highlighting a major but previously underappreciated component of the human gut microbiome.

Metagenomics has become a powerful approach for deciphering the structure and function of the human gut microbiome, a complex microbial ecosystem in the gut. The human gut microbiome plays a crucial role in health and disease through multifaceted interactions with various factors, including age, diet, lifestyle, and medications. This review summarizes key advances in gut microbiome research over the past two decades and presents several topics from a recent large-scale, data-driven study, specifically a cohort-based initiative, the Japanese 4D microbiome project. These include a population-level characterization of the Japanese gut microbiome in a global context through comparison with 31,695 gut metagenomes from 37 countries, as well as an extensive analysis of the effects of medications. This review provides new insights into the ecology and uniqueness of the Japanese gut microbiome and highlights the importance of large-scale, well-phenotyped cohorts in advancing microbiome science.

Viruses are the most abundant biological entities on Earth, yet their global diversity remains largely unexplored. Here, we present VIRE, a comprehensive resource comprising over 1.7 million high- and medium-quality viral genomes recovered from >100 000 publicly available metagenomes derived from samples that cover diverse ecosystems, including host-associated, aquatic, terrestrial, and anthropogenic environments. Using a unified and scalable pipeline, we systematically assembled viral genomes and provided detailed information on genome completeness, taxonomic classification, predicted lifestyle, and host assignment based on CRISPR spacer matches. VIRE contains >89 million predicted viral open reading frames, as well as detailed functional annotations derived from multiple databases. Importantly, VIRE is seamlessly integrated with related microbiome resources such as SPIRE (https://spire.embl.de) and Metalog (https://metalog.embl.de), enabling users to jointly explore viral genomes, metagenome-assembled genomes, and associated environmental or clinical metadata. Accessible at https://vire.embl.de, VIRE provides an open-access, scalable platform for investigating viral diversity, evolution, and ecology on a planetary scale.

Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data is deposited in public databases, the associated contextual data is often not complete and needs to be retrieved from primary publications. This lack of access to sample-level metadata like clinical data or in situ observations impedes cross-study comparisons and meta-analyses. We therefore created the Metalog database, a repository of manually curated metadata for metagenomics samples across the globe. It contains 80 423 samples from humans (including 66 527 of the gut microbiome), 10 744 animal samples, 5547 ocean water samples, and 23 455 samples from other environmental habitats such as soil, sediment, or fresh water. Samples have been consistently annotated for a set of habitat-specific core features, such as demographics, disease status, and medication for humans; host species and captivity status for animals; and filter sizes and salinity for marine samples. Additionally, all original metadata is provided in tabular form, simplifying focused studies e.g. into nutrient concentrations. Pre-computed taxonomic profiles facilitate rapid data exploration, while links to the SPIRE database enable genome-based analyses. The database is freely available for browsing and download at https://metalog.embl.de/.

Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals and the environment. While sequencing data is deposited in public databases, the associated contextual data is often not complete and needs to be retrieved from primary publications. This lack of access to sample-level metadata like clinical data or in situ observations impedes cross-study comparisons and meta-analyses. We therefore created the Metalog database, a repository of manually curated metadata for metagenomics samples across the globe. It contains 73,082 samples from humans (including 58,506 of the gut microbiome), 10,703 animal samples, 5,146 ocean water samples, and 21,802 samples from other environmental habitats such as soil, sediment, or fresh water. Samples have been consistently annotated for a set of habitat-specific core features, such as demographics, disease status and medication for humans, host species and captivity status for animals, and filter sizes and salinity for marine samples. Additionally, all original metadata is provided in tabular form, simplifying focused studies e.g. into nutrient concentrations. Pre-computed taxonomic profiles facilitate rapid data exploration, while links to the SPIRE database enable genome-based analyses. The database is freely available for browsing and download at https://metalog.embl.de/ .

Background: Alcohol overuse disrupts liver function and alters microbial gut communities, with alcohol-related liver disease (ALD) accounting for half of all liver-related deaths worldwide. Bile acids (BAs) regulate liver and gut function, but their metabolism becomes disrupted in ALD. While it is known that gut microbes transform primary to secondary BAs, which are subsequently reabsorbed via the enterohepatic circulation, BA metabolism during ALD progression remains poorly understood. Methods: We investigated BA co-metabolism in a cross-sectional cohort of individuals with ALD (n=462) and healthy controls (n=148). We validated key findings in two independent ALD cohorts (n=34 and n=52). We integrated BA concentrations, measured by targeted mass spectrometry in feces and plasma, with liver proteomics, and gut microbiome profiles derived from metagenomic and metatranscriptomic sequencing of fecal samples. Results: Advanced fibrosis was associated with decreased hepatic BA synthesis and impaired BA transport. Despite this, disease progression corresponded with increased levels of primary and secondary BAs in plasma and feces. The abundance of microbial secondary BA dehydroxylation and epimerization pathways in the gut microbiome changed with disease severity. Genes encoding early steps in the multi-step dehydroxylation pathway increased, whereas those involved in later steps were depleted, indicating a community-level microbial imbalance. In ALD, we identified Eggerthella lenta as a key mediator of BA dehydroxylation, while Mediterraneibacter torques and Bacteroides thetaiotaomicron facilitated most of the BA epimerization as a detoxification mechanism. Conclusion: Fibrotic ALD is characterized by disrupted primary BA synthesis and transport, leading to BA accumulation in the gut and blood circulation. Altered microbial secondary BA metabolism reflects a compensatory mechanism that becomes impaired at advanced fibrosis stages. Our findings highlight the gut-liver axis as an important factor influencing ALD progression. Impact and Implications: With the progression of alcohol-related liver disease (ALD), levels of bile acids (BA) in serum and feces increase, but BA production and transport are impaired in the liver. Secondary microbial BA metabolism, particularly epimerization and dehydroxylation, increases in ALD. However, a key enzyme, baiN, is depleted, illustrating a microbial community-level metabolic dysbiosis. The main contributing microbial species were, among others, Mediterraneibacter torques , Bacteroides thetaiotaomicron , and Eggerthella lenta , which could serve as potential targets for future microbial-targeted interventions. Lay summary: Alcohol-related liver disease (ALD) from long-term alcohol overuse affects how the liver and gut interact, especially in handling bile acids (BAs), which are molecules produced by the liver and transformed by gut bacteria. Our study found that in people with ALD, the liver produces fewer BAs, but BAs accumulate in the gut and blood because their transport is impaired. We also observed that bacterial transformations of these BA change as the disease progresses, most likely due to an imbalance in the gut microbiome. For the first time, we identify specific bacterial species that strongly influence BA levels in ALD. Abstract Figure: Figure 0: Graphical

The integrative multi-kingdom interaction of the gut microbiome in ulcerative colitis (UC) and Crohn’s disease (CD) remains underinvestigated. Here, we perform shotgun metagenomic sequencing of feces from patients with UC and CD, and healthy controls in the Japanese 4D cohort, profiling bacterial taxa, gene functions, and antibacterial genes, bacteriophages, and fungi. External metagenomic datasets from the US, Spain, the Netherlands, and China were analyzed to validate our multi-biome findings. We found that Enterococcus faecium and Bifidobacterium spp. were enriched in both diseases. Enriched Escherichia coli was characteristic of CD and was linked to numerous antibiotic resistance genes involved in efflux pumps and adherent-invasive Escherichia coli virulence factors. Virome changes correlated with shifts in the bacteriome, including increased abundances of phages encoding pathogenic genes. Saccharomyces paradoxus and Saccharomyces cerevisiae were enriched in UC and CD, respectively. Saccharomyces cerevisiae and Escherichia coli had negative associations with short-chain fatty acid (SCFA)-producing bacteria in CD. Multi-biome signatures and their interactions in UC and CD showed high similarities between Japan and other countries. Since bacteria, phages, and fungi formed multiple hubs of intra- or trans-kingdom networks with SCFA producers and pathobionts in UC and CD, an approach targeting the interaction network may hold therapeutic promise.

Summary: Background: Enterotypes describe human fecal microbiomes grouped by similarity into clusters of microbial community composition, often associated with disease, medications, diet, and lifestyle. Numbers and determinants of enterotypes have been derived by diverse frameworks and applied to cohorts that often lack diversity or inter-cohort comparability. Results: To overcome these limitations, we selected 16,772 fecal metagenomes collected from 38 countries to revisit the enterotypes using state-of-the-art fuzzy clustering and found robust clustering regardless of underlying taxonomy, consistent with previous findings. Quantifying the strength of enterotype classifications enriched the enterotype landscape, also reflecting some continuity of microbial compositions. As the classification strength was associated with the patient’s health status, we established an “Enterotype Dysbiosis Score” (EDS) as a latent covariate for various diseases. Conclusion: This global study confirms the enterotypes, reveals a dysbiosis signal within the enterotype landscape, and enables robust classification of metagenomes with an online “Enterotyper” tool, allowing reproducible analysis in future studies. Graphical