Mapping the bacterial metabolic niche space

Fahimipour, Ashkaan K.; Gross, Thilo

doi:10.1038/s41467-020-18695-z

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Mapping the bacterial metabolic niche space

2020
By Fahimipour, Ashkaan K. ; Gross, Thilo
Source: Nat Commun. 2020 Sep 28;11(1):4887.

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Journal Title:

Nature Communications
Personal Author:

Fahimipour, Ashkaan K. ; Gross, Thilo

Fahimipour, Ashkaan K. ; Gross, Thilo Less -
NOAA Program & Office:

NMFS (National Marine Fisheries Service) ; SWFSC (Southwest Fisheries Science Center)

NMFS (National Marine Fisheries Service) ; SWFSC (Southwest Fisheries Science Center) Less -
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.
Keywords:

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Bacterial genomes
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
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CC BY
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PMC
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urn:sha256:4fdace15047fb02d3f376d2aeac1852929c848421e52d943a0487f8a1a513ac4
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https://repository.library.noaa.gov/view/noaa/27515/noaa_27515_DS1.pdf
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Mapping the bacterial metabolic niche space

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