Changes in the genetic requirements for microbial interactions with increasing community complexity
- University of California, San Diego, United States
Abstract
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. E. coli's 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.
Data availability
The Pseudomonas psychrophila JB418 genome is publicly available at https://img.jgi.doe.gov/ (IMG Genome ID 2751185442).
Article and author information
Author details
Funding
David and Lucile Packard Foundation (#2016-65131)
- Rachel J Dutton
Pew Charitable Trusts (Pew Scholar in Biomedical Sciences)
- Rachel J Dutton
National Institutes of Health (P50 GM068763)
- Rachel J Dutton
CJS INRA/INRIA
- Manon Morin
National Institutes of Health (5 T32 GM 7240-40)
- Emily C Pierce
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2018, Morin et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Changes in the genetic requirements for microbial interactions with increasing community complexity
eLife 7:e37072.
https://doi.org/10.7554/eLife.37072
