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.

Viral discovery in the ‘realm’ of COVID‐19

“…From this dataset, Nayfach et al . (2020) were able to predict putative hosts for >81 000 viral sequences and link multiple viral clades. Further high‐throughput discovery of RNA viruses and investigation of their ecology is just beginning.…”

“…This taxonomic organization may guide our understanding of shared ecological, epidemiological, or evolutionary traits, such as broad predictions of host (e.g. DJR; Nayfach et al ., 2020), disease emergence, or infection dynamics in marine ecosystems. Though forecasting power is currently low, these genomic tools ‐ when paired with sufficient data of disease‐eliciting environmental conditions ‐ may provide a starting point for pathogen diagnostics, particularly in non‐multifactorial marine EIDs.…”

“…Geering et al, 2014;Moniruzzaman et al, 2020) through integrations in a germline sequence in a eukaryote, somewhat analogous to components of sequence-dependent defence systems such as CRISPR, though not always in a functional capacity. As it stands, 85% of viral sequences are affiliated with a predicted host (Roux et al, 2020), and a database of more than 700 000 nonretroviral endogenized genes have provided insight into the history of infection in mammals (Nakagawa and Takahashi, 2016).…”

Degradation of terrestrial organic matter by aquatic microbial genomes in the Amazon River

“…In addition, PGs may reveal metabolic adaptations or speci c gene arrangements [32,33], being also important to predict the ecological roles played by uncultured microorganisms. PGs have been retrieved from diverse environments [23][24][25][26][27][28][29]34], leading to important ndings, such as novel clades [23] as well as new insights on light-harvest mechanisms, nutrients uptake and nitrogen xation in freshwater microbes [24,30,31]. However, to our knowledge, no previous study has extracted PGs from the Amazon River in order to connect them with major biogeochemical cycles, such as the carbon cycle.…”

Synthetic biology 2020–2030: six commercially-available products that are changing our world

“…Soil, water, and animals harbor complex microbial communities into which there is the potential to add beneficial functions, or remove harmful ones, from these ecosystems [58][59][60] . Doing this by introducing a new strain can be challenging as the microbiome environment is poorly characterized, dynamic and ecologically rich 61 .…”