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

Abstract
Data availability
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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).

The following data sets were generated

1. Pierce EC
2. Dutton RJ
(2017) Pseudomonas psychrophila JB418
IMG Genome ID 2751185442.

https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=2751185442

Article and author information

Author details

Manon Morin

Division of Biological Sciences, University of California, San Diego, La Jolla, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-2158-0473
Emily C Pierce

Division of Biological Sciences, University of California, San Diego, La Jolla, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-9960-0270
Rachel J Dutton

Division of Biological Sciences, University of California, San Diego, La Jolla, United States

For correspondence
rjdutton@ucsd.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-2944-2182

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

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.