Conceptual Exchanges for Understanding Free-Living and Host-Associated Microbiomes.

Journal Article (Journal Article)

Whether a microbe is free-living or associated with a host from across the tree of life, its existence depends on a limited number of elements and electron donors and acceptors. Yet divergent approaches have been used by investigators from different fields. The "environment first" research tradition emphasizes thermodynamics and biogeochemical principles, including the quantification of redox environments and elemental stoichiometry to identify transformations and thus an underlying microbe. The increasingly common "microbe first" research approach benefits from culturing and/or DNA sequencing methods to first identify a microbe and encoded metabolic functions. Here, the microbe itself serves as an indicator for environmental conditions and transformations. We illustrate the application of both approaches to the study of microbiomes and emphasize how both can reveal the selection of microbial metabolisms across diverse environments, anticipate alterations to microbiomes in host health, and understand the implications of a changing climate for microbial function.

Full Text

Duke Authors

Cited Authors

  • Pfister, CA; Light, SH; Bohannan, B; Schmidt, T; Martiny, A; Hynson, NA; Devkota, S; David, L; Whiteson, K

Published Date

  • February 22, 2022

Published In

Volume / Issue

  • 7 / 1

Start / End Page

  • e0137421 -

PubMed ID

  • 35014872

Pubmed Central ID

  • PMC8751383

International Standard Serial Number (ISSN)

  • 2379-5077

Digital Object Identifier (DOI)

  • 10.1128/msystems.01374-21


  • eng

Conference Location

  • United States