Changes in the genetic requirements for microbial interactions with increasing community complexity
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.
Metrics
-
- 6,940
- views
-
- 960
- downloads
-
- 76
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.