Changes in the genetic requirements for microbial interactions with increasing community complexity

• DOI: 10.7554/elife.37072
• Publication Date: 2018-09-13T12:00:17Z
• Authors: Manon Morin; Emily C Pierce; Rachel J Dutton
• Keywords: 0301 basic medicine; 570; QH301-705.5; infectious disease; Science; microbiome; cheese; 03 medical and health sciences; Genetics; Escherichia coli; DNA Barcoding, Taxonomic; Biology (General); transposon sequencing; cross-feeding; Ecosystem; 2. Zero hunger; species interactions; Microbiology and Infectious Disease; Microbiota; microbiology; Human Genome; Q; E. coli; R; Taxonomic; High-Throughput Nucleotide Sequencing; DNA Barcoding; 3. Good health; DNA Transposable Elements; higher-order interactions; Medicine; Microbial Interactions; Biochemistry and Cell Biology

Microbial community structure and function rely on complex interactions whose underlying molecular mechanisms are poorly understood. To investigate these interactions in a simple microbiome, we introduced E. coli into an experimental community based on a cheese rind and identified the differences in E. coli’s genetic requirements for growth in interactive and non-interactive contexts using Random Barcode Transposon Sequencing (RB-TnSeq) and RNASeq. Genetic requirements varied among pairwise growth conditions and between pairwise and community conditions. Our analysis points to mechanisms by which growth conditions change as a result of increasing community complexity and suggests that growth within a community relies on a combination of pairwise and higher-order interactions. Our work provides a framework for using the model organism E. coli as a readout to investigate microbial interactions regardless of the genetic tractability of members of the studied ecosystem.