Conceptual strategies for characterizing interactions in microbial communities
Sho M. Kodera,
Promi Das,
Jack A. Gilbert,
Holly L. Lutz
Affiliations
Sho M. Kodera
Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA
Promi Das
Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California San Diego, La Jolla, CA 92161, USA
Jack A. Gilbert
Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California San Diego, La Jolla, CA 92161, USA
Holly L. Lutz
Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California San Diego, La Jolla, CA 92161, USA; Negaunee Integrative Collections Center, Field Museum of Natural History, Chicago, IL 60605, USA; Corresponding author
Summary: Understanding the sets of inter- and intraspecies interactions in microbial communities is a fundamental goal of microbial ecology. However, the study and quantification of microbial interactions pose several challenges owing to their complexity, dynamic nature, and the sheer number of unique interactions within a typical community. To overcome such challenges, microbial ecologists must rely on various approaches to distill the system of study to a functional and conceptualizable level, allowing for a practical understanding of microbial interactions in both simplified and complex systems. This review broadly addresses the role of several conceptual approaches available for the microbial ecologist’s arsenal, examines specific tools used to accomplish such approaches, and describes how the assumptions, expectations, and philosophies underlying these tools change across scales of complexity.
