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Review
. 2023 Oct;38(10):936-945.
doi: 10.1016/j.tree.2023.04.015. Epub 2023 May 24.

Into the microbial niche

Lucie A Malard  1 , Antoine Guisan  2
Affiliations
Free article
Review

Into the microbial niche

Lucie A Malard et al. Trends Ecol Evol. 2023 Oct.
Free article

Abstract

The environmental niche concept describes the distribution of a taxon in the environment and can be used to understand community dynamics, biological invasions, and the impact of environmental changes. The uses and applications are still restricted in microbial ecology, largely due to the complexity of microbial systems and associated methodological limitations. The development of shotgun metagenomics and metatranscriptomics opens new ways to investigate the microbial niche by focusing on the metabolic niche within the environmental space. Here, we propose the metabolic niche framework, which, by defining the fundamental and realised metabolic niche of microorganisms, has the potential to not only provide novel insights into habitat preferences and the metabolism associated, but also to inform on metabolic plasticity, niche shifts, and microbial invasions.

Keywords: environmental niche; metabolic niche; metagenomics; metatranscriptomics; microbial communities.

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Conflict of interest statement

Declaration of interests No interests are declared.

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