Gut metagenome associations with extensive digital health data in a volunteer-based Estonian microbiome cohort

Microbiome research is starting to move beyond the exploratory phase towards interventional trials and therefore well-characterized cohorts will be instrumental for generating hypothesis and providing new knowledge. As part of the Estonian Biobank (EstBB), we established the Estonian Microbiome Cohort (EstMB) which includes stool, oral and plasma samples from 2,509 participants and is supplemented with multi-omic measurements, questionnaires, and regular linkages to national electronic health records (EHRs). In this study, we analyzed stool data from deep metagenomic sequencing together with rich phenotyping, including 71 diseases, 136 medications, 21 dietary questions, 5 procedures, and 19 other factors. The data revealed numerous relationships (n = 3262) with different microbiome features. Additionally, we present that long-term antibiotic usage, independent from recent administration, has a significant impact on the microbiome composition, partly explaining the common associations between diseases. Overall, this study extends the understanding of microbiome–host interactions and facilitates the development of microbiome-related studies.

Post-weaning shifts in microbiome composition and metabolism revealed by over 25 000 pig gut metagenome-assembled genomes

Using a previously described metagenomics dataset of 27 billion reads, we reconstructed over 50 000 metagenome-assembled genomes (MAGs) of organisms resident in the porcine gut, 46.5 % of which were classified as >70 % complete with a <10 % contamination rate, and 24.4 % were nearly complete genomes. Here, we describe the generation and analysis of those MAGs using time-series samples. The gut microbial communities of piglets appear to follow a highly structured developmental programme in the weeks following weaning, and this development is robust to treatments including an intramuscular antibiotic treatment and two probiotic treatments. The high resolution we obtained allowed us to identify specific taxonomic ‘signatures’ that characterize the gut microbial development immediately after weaning. Additionally, we characterized the carbohydrate repertoire of the organisms resident in the porcine gut. We tracked the abundance shifts of 294 carbohydrate active enzymes, and identified the species and higher-level taxonomic groups carrying each of these enzymes in their MAGs. This knowledge can contribute to the design of probiotics and prebiotic interventions as a means to modify the piglet gut microbiome.

HumGut: a comprehensive human gut prokaryotic genomes collection filtered by metagenome data

Background A major bottleneck in the use of metagenome sequencing for human gut microbiome studies has been the lack of a comprehensive genome collection to be used as a reference database. Several recent efforts have been made to re-construct genomes from human gut metagenome data, resulting in a huge increase in the number of relevant genomes. In this work, we aimed to create a collection of the most prevalent healthy human gut prokaryotic genomes, to be used as a reference database, including both MAGs from the human gut and ordinary RefSeq genomes. Results We screened > 5,700 healthy human gut metagenomes for the containment of > 490,000 publicly available prokaryotic genomes sourced from RefSeq and the recently announced UHGG collection. This resulted in a pool of > 381,000 genomes that were subsequently scored and ranked based on their prevalence in the healthy human metagenomes. The genomes were then clustered at a 97.5% sequence identity resolution, and cluster representatives (30,691 in total) were retained to comprise the HumGut collection. Using the Kraken2 software for classification, we find superior performance in the assignment of metagenomic reads, classifying on average 94.5% of the reads in a metagenome, as opposed to 86% with UHGG and 44% when using standard Kraken2 database. A coarser HumGut collection, consisting of genomes dereplicated at 95% sequence identity—similar to UHGG, classified 88.25% of the reads. HumGut, half the size of standard Kraken2 database and directly comparable to the UHGG size, outperforms them both. Conclusions The HumGut collection contains > 30,000 genomes clustered at a 97.5% sequence identity resolution and ranked by human gut prevalence. We demonstrate how metagenomes from IBD-patients map equally well to this collection, indicating this reference is relevant also for studies well outside the metagenome reference set used to obtain HumGut. All data and metadata, as well as helpful code, are available at http://arken.nmbu.no/~larssn/humgut/.

Flavonoid-modifying capabilities of the gut microbiome – an in silico study

Flavonoids are a major group of dietary plant polyphenols and have a positive health impact, but their modification and degradation in the human gut is still widely unknown. Due to the rise of human gut metagenome data and the assembly of hundreds of thousands of bacterial metagenome-assembled genomes (MAGs), large-scale screening for potential flavonoid-modifying enzymes is now feasible. With sequences from characterized flavonoid-transforming enzymes as queries, the Unified Human Gastrointestinal Protein catalog was analyzed and quantification of putative flavonoid-modifying enzymes was carried out. The results revealed that flavonoid-modifying enzymes are often highly abundant in bacteria hitherto not considered as flavonoid-modifying gut bacteria. The enzymes for the physiologically important daidzein to equol conversion, well studied in Slackia isoflavoniconvertens, were encoded only to a low extent in Slackia MAGs, but more abundant in Adlercreutzia equolifaciens and an uncharacterizedEggerthellaceae species. In addition, a high abundance of genes with a similarity of only about 35% in uncultivated Collinsella species suggest a hitherto uncharacterized Daidzein-to-equol potential in these bacteria. Of all potential flavonoid modification steps, O-deglycosylation (including derhamnosylation) was by far the most abundant in this analysis. In contrast, enzymes putatively involved in C-deglycosylation were detected less often in human gut bacteria and mainly found in Agathobacter faecis (formerly Roseburia faecis). Phloretin hydrolase, flavanonol/flavanone-cleaving reductase and flavone reductase (all three most abundant in Flavonifractor plautii) and O-demethylase (Intestinibacter bartlettii) homologs were of intermediate prevalence (several hundreds of MAGs). This first comprehensive insight into the black box of flavonoid modification in the human gut highlights many hitherto overlooked and uncultured bacterial genera and species as key organisms in flavonoid modification by the human gut microbiota. This could lead to a significant contribution to future biochemical-microbiological investigations on gut bacterial flavonoid transformation. In addition, our results are important for individual nutritional recommendations and for biotechnological applications which rely on novel enzymes catalyzing potentially useful flavonoid modification reactions.

Comprehensive mouse gut metagenome catalog reveals major difference to the human counterpart

Mouse is the most used model for studying the impact of microbiota on its host, but the repertoire of species from the mouse gut microbiome remains largely unknown. Here, we construct a Comprehensive Mouse Gut Metagenome (CMGM) catalog by assembling all currently available mouse gut metagenomes and combining them with published reference and metagenome-assembled genomes. The 50’011 genomes cluster into 1’699 species, of which 78.1% are uncultured, and we discovered 226 new genera, 7 new families, and 1 new order. Rarefaction analysis indicates comprehensive sampling of the species from the mouse gut. CMGM enables an unprecedented coverage of the mouse gut microbiome exceeding 90%. Comparing CMGM to the human gut microbiota shows an overlap 64% at the genus, but only 16% at the species level, demonstrating that human and mouse gut microbiota are largely distinct.

Enhanced Intestinal Protein Fermentation Correlates With Severe Psychiatric Symptoms of Schizophrenia

Emerging findings highlighted the associations of mental illness to nutrition and dysbiosis in the intestinal microbiota, but the underlying mechanisms, especially in schizophrenia (SZ), remain unclarified. Here we conducted a case-control study of SZ by performing gut metagenome, fecal and plasma non-targeted metabolome, short-, medium-, and long-chain fatty acids, and targeted metabolite analysis. The results uncovered an apparent contradiction in SZ patients between inadequate protein intake and protein-fermentation-dominated intestinal microbial metabolism, which shifted from carbohydrate fermentation and protein synthesis in healthy conditions. Moreover, the extent of protein fermentation represented as the abundance of related enzymes and fecal levels of related products, usually nitrogenous and neurologically active, correlated with the severity of psychiatric symptoms. These findings provide a previously uncharacterized pathophysiological process in SZ related to the dysbiosis of gut microbiota and dysregulation in macronutrient metabolism, highlighting the importance of nutrition care and the potentials for developing microbiota-targeted therapeutics in SZ.

An Expanded Gene Catalog of Mouse Gut Metagenomes

ABSTRACT High-quality and comprehensive reference gene catalogs are essential for metagenomic research. The rather low diversity of samples used to construct existing catalogs of the mouse gut metagenome limits the numbers of identified genes in existing catalogs. We therefore established an expanded catalog of genes in the mouse gut metagenome (EMGC) containing >5.8 million genes by integrating 88 newly sequenced samples, 86 mouse gut-related bacterial genomes, and 3 existing gene catalogs. EMGC increases the number of nonredundant genes by more than 1 million genes compared to the so-far most extensive catalog. More than 60% of the genes in EMGC were assigned to Bacteria, with 54.20% being assigned to a phylum and 35.33% to a genus, while 30.39% were annotated at the KEGG orthology level. Nine hundred two metagenomic species (MGS) assigned to 122 taxa are identified based on the EMGC. The EMGC-based analysis of samples from groups of mice originating from different animal providers, housing laboratories, and genetic strains substantiated that diet is a major contributor to differences in composition and functional potential of the gut microbiota irrespective of differences in environment and genetic background. We envisage that EMGC will serve as a valuable reference data set for future metagenomic studies in mice. IMPORTANCE We established an expanded gene catalog of the mouse gut metagenome not only to increase the sample size compared to that in existing catalogs but also to provide a more comprehensive reference data set of the mouse gut microbiome for bioinformatic analysis. The expanded gene catalog comprises more than 5.8 million unique genes, as well as a wide range of taxonomic and functional information. Particularly, the analysis of metagenomic species with the expanded gene catalog reveals a great novelty of mouse gut-inhabiting microbial species. We envisage that the expanded gene catalog of the mouse gut metagenome will serve as a valuable bioinformatic resource for future gut metagenomic studies in mice.

You Are More Than What You Eat: Differential Enrichment of Microbiome Functions Across Bat Dietary Guilds

Animals evolved in a microbial world, and their gut microbial symbionts have played a role in their ecological diversification. While many recent studies have reported patterns of co-diversification of hosts and their gut microbes, few studies have directly examined the functional contributions of these microbes to the dietary habits of their hosts. Here, we examined functional enrichment of metabolic pathways in the gut bacteria of 545 bats belonging to 60 species and five terrestrial feeding niches. We found that hosts of different dietary guilds had differential enrichment of bacterial functions that may be adaptive to their respective diets, and that metagenome functions were highly predictive of host feeding guild. We detected little evidence of host phylogenetic effect on gut metagenome composition, suggesting that diet likely overrides host evolutionary history in structuring functional pathways in the gut metagenome. Our results further suggest that bats may have evolved to partially rely on their gut microbes to fulfill critical metabolic pathways, including essential amino acid synthesis, fatty acid biosynthesis, and the generation of cofactors and vitamins essential for proper nutrition. This work represents a comprehensive and novel insight into the contribution of gut microbes to vital metabolic processes in a diverse Order of wild mammals.

You Are More Than What You Eat: Differential Enrichment of Microbiome Functions Across Bat Dietary Guilds

Animals evolved in a microbial world, and their gut microbial symbionts have played a role in their ecological diversification. While many recent studies have reported patterns of co-diversification of hosts and their gut microbes, few studies have directly examined the functional contributions of these microbes to the dietary habits of their hosts. Here, we examined functional enrichment of metabolic pathways in the gut bacteria of 545 bats belonging to 60 species and five terrestrial feeding niches. We found that hosts of different dietary guilds had differential enrichment of bacterial functions that may be adaptive to their respective diets, and that metagenome functions were highly predictive of host feeding guild. We detected little evidence of host phylogenetic effect on gut metagenome composition, suggesting that diet likely overrides host evolutionary history in structuring functional pathways in the gut metagenome. Our results further suggest that bats may have evolved to partially rely on their gut microbes to fulfill critical metabolic pathways, including essential amino acid synthesis, fatty acid biosynthesis, and the generation of cofactors and vitamins essential for proper nutrition. This work represents a comprehensive and novel insight into the contribution of gut microbes to vital metabolic processes in a diverse Order of wild mammals.