Dataset Information

A genomic catalog of Earth's microbiomes.

ABSTRACT: The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth's continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.

SUBMITTER: Nayfach S

PROVIDER: S-EPMC8041624 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature

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A genomic catalog of Earth's microbiomes.

Nayfach Stephen S Roux Simon S Seshadri Rekha R Udwary Daniel D Varghese Neha N Schulz Frederik F Wu Dongying D Paez-Espino David D Chen I-Min IM Huntemann Marcel M Palaniappan Krishna K Ladau Joshua J Mukherjee Supratim S Reddy T B K TBK Nielsen Torben T Kirton Edward E Faria José P JP Edirisinghe Janaka N JN Henry Christopher S CS Jungbluth Sean P SP Chivian Dylan D Dehal Paramvir P Wood-Charlson Elisha M EM Arkin Adam P AP Tringe Susannah G SG Visel Axel A Woyke Tanja T Mouncey Nigel J NJ Ivanova Natalia N NN Kyrpides Nikos C NC Eloe-Fadrosh Emiley A EA

Nature biotechnology 20201109 4

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth's continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This compre ...[more]

PMID: 33169036

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Project description:Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure and function of microbial communities across multiple habitats on a planetary scale. Here we present a multi-omics analysis of a diverse set of 880 microbial community samples collected for the Earth Microbiome Project. We include amplicon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry). We used standardized protocols and analytical methods to characterize microbial communities, focusing on relationships and co-occurrences of microbially related metabolites and microbial taxa across environments, thus allowing us to explore diversity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of an evolving community resource. We demonstrate the utility of this database by testing the hypothesis that every microbe and metabolite is everywhere but the environment selects. Our results show that metabolite diversity exhibits turnover and nestedness related to both microbial communities and the environment, whereas the relative abundances of microbially related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner. We additionally show the power of certain chemistry, in particular terpenoids, in distinguishing Earth's environments (for example, terrestrial plant surfaces and soils, freshwater and marine animal stool), as well as that of certain microbes including Conexibacter woesei (terrestrial soils), Haloquadratum walsbyi (marine deposits) and Pantoea dispersa (terrestrial plant detritus). This Resource provides insight into the taxa and metabolites within microbial communities from diverse habitats across Earth, informing both microbial and chemical ecology, and provides a foundation and methods for multi-omics microbiome studies of hosts and the environment.

Project description:While considerable progress has been made in understanding the complex relationships between gut microbiomes and their hosts, especially in mammals and humans, the functions of these microbial communities in avian species remain largely unexplored. This gap in knowledge is particularly notable, given the critical roles gut microbiomes are known to play in facilitating crucial physiological functions, such as digestion, nutrient absorption, and immune system development. Corvidae birds are omnivorous and widely distributed across various habitats, exhibiting strong adaptability and often displaying the traits of accompanying humans. However, to date, information on species composition, sequenced genomes, and functional characteristics of crow gut microbes is lacking. Herein, we constructed the first relatively comprehensive crows gut microbial gene catalog (2.74 million genes) and 195 high-quality and medium-quality metagenome-assembled genomes using 53 metagenomic samples from five typical crow species (Pyrrhocorax pyrrhocorax, Corvus dauuricus, Corvus frugilegus, Corvus macrorhynchos, and Corvus corax) on the Qinghai-Tibetan Plateau. The species composition of gut microbiota at the phylum and genus levels was revealed for these five crow species. Simultaneously, numerous types of prevalent pathogenic bacteria were identified, indicating the potential of these crows to transmit diseases within the local community. At the functional level, we annotated a total of 356 KEGG functional pathways, six CAZyme categories, and 3607 virulence factor genes in the gut microbiomes of the crows. The gut microbiota of five distinct crow species underwent a comparative analysis, which uncovered significant differences in their composition, diversity, and functional structures. Over 36% of MAGs showed no overlap with existing databases, suggesting they might represent new species. Consequently, these findings enriched the dataset of microbial genomes associated with crows' digestive systems. Overall, this study offers crucial baseline information regarding the gut microbial gene catalog and genomes in crows, potentially aiding microbiome-based research, as well as an evaluation of the health risks to humans from the bacterial pathogens transmitted by wild birds.

Dataset Information

A genomic catalog of Earth's microbiomes.

Publications

A genomic catalog of Earth's microbiomes.

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