Mapping the bacterial metabolic niche space

Details

• Journal Title:
  Nature Communications
• Personal Author:
  Fahimipour, Ashkaan K. ; Gross, Thilo
• NOAA Program & Office:
  NMFS (National Marine Fisheries Service) ; SWFSC (Southwest Fisheries Science Center)
• Description:
  The rise in the availability of bacterial genomes defines a need for synthesis: abstracting from individual taxa, to see larger patterns of bacterial lifestyles across systems. A key concept for such synthesis in ecology is the niche, the set of capabilities that enables a population's persistence and defines its impact on the environment. The set of possible niches forms the niche space, a conceptual space delineating ways in which persistence in a system is possible. Here we use manifold learning to map the space of metabolic networks representing thousands of bacterial genera. The results suggest a metabolic niche space comprising a collection of discrete clusters and branching manifolds, which constitute strategies spanning life in different habitats and hosts. We further demonstrate that communities from similar ecosystem types map to characteristic regions of this functional coordinate system, permitting coarse-graining of microbiomes in terms of ecological niches that may be filled.
• Source:
  Nat Commun. 2020 Sep 28;11(1):4887.
• DOI:
  https://doi.org/10.1038/s41467-020-18695-z
• Pubmed ID:
  32985497
• Pubmed Central ID:
  PMC7522980
• Document Type:
  Journal Article
• Rights Information:
  CC BY
• Compliance:
  PMC
• Download URL:
  https://repository.library.noaa.gov/view/noaa/27515/noaa_27515_DS1.pdf
• File Type:
  [PDF - 22.11 MB]
• Collection(s):
  National Marine Fisheries Service (NMFS)
• Main Document Checksum:
  urn:sha256:4fdace15047fb02d3f376d2aeac1852929c848421e52d943a0487f8a1a513ac4