In MicrobiomeNet, the term “context” or “ecological context" , which differs from “study context", refers to the natural habitat or biological environment in which a microbe typically exists and performs its metabolic functions. Examples include human gut, oral cavity, and other host-associated niches, as well as soil, marine, and other environmental habitats.
The context assigned to each microbe in MicrobiomeNet comes from a structured annotation process performed during the GEM collection. Specifically, each microbe’s context was identified based on the following sources:
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AGORA publications and metadata: All models in AGORA v1 represent human gut microbes. The v2 release provides additional metadata and supplementary tables that classify microbes into broader ecological groups.
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Public databases: We also manually consulted authoritative microbial resources such as BacDive, NCBI, GTDB, and EMP to determine isolation sources and habitat information.
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Published literature: For many microbes, we also relied on published papers, such as the Unified Human Gut Genome Catalog for human gut species, along with other ecological and cultivation studies describing microbial origins and habitats (Thompson et al., 2017; The Human Microbiome Project Consortium, 2012; Noah Fierer 2017, etc).
This multi-source approach helps provide as accurate and consistent an ecological labeling as possible for the microbes included in MicrobiomeNet. A detailed list of microbes and their assigned contexts is available for download on the “Resource” page.