Conceptual Exchanges for Understanding Free-Living and Host-Associated Microbiomes
Catherine A. Pfister,
Samuel H. Light,
Brendan Bohannan,
Thomas Schmidt,
Adam Martiny,
Nicole A. Hynson,
Suzanne Devkota,
Lawrence David,
Katrine Whiteson
Affiliations
Catherine A. Pfister
Department of Ecology & Evolution and The Microbiome Center, University of Chicago, Chicago, Illinois, USA
Samuel H. Light
Department of Microbiology & Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
Brendan Bohannan
Environmental Studies and Biology, University of Oregon, Eugene, Oregon, USA
Thomas Schmidt
Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
Adam Martiny
Earth System Science & Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA
Nicole A. Hynson
Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, Hawaii, USA
Suzanne Devkota
Microbiome Research, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
Lawrence David
Molecular Genetics & Microbiology, Duke University, Durham, North Carolina, USA
Katrine Whiteson
Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California, USA
ABSTRACT 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.
