A new perspective piece in mSystems by TMC director Cathy Pfister et al looks at different 'microbe' or 'environment' first approaches to studying the microbiome in different habitats, be it the human gut or coastal wetlands. Co-authors include Sam Light, Assistant Prof in Microbiology, and former UChicago PhD students Katrine Whiteson and Suzanne Devkota. The advent of DNA sequencing methods and culturing techniques has allowed the identification of microbes prior to understanding their metabolic roles, whether they are free living or host associated. Prior to this, the relative abundance of electron donor/acceptors and elements was used to predict their presence. The article discusses the complementary advantages of both approaches.
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.
Reference
Pfister, C. A., Light, S. H., Bohannan, B., Schmidt, T., Martiny, A., Hynson, N. A., Devkota, S., David, L., & Whiteson, K. (2022). Conceptual Exchanges for Understanding Free-Living and Host-Associated Microbiomes. MSystems. https://doi.org/10.1128/msystems.01374-21