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

ELife
Manon MorinRachel J Dutton

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. 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.

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Citations

Feb 11, 2019·Molecular Oral Microbiology·Robert C Shields, Paul A Jensen
Oct 23, 2019·Environmental Microbiology·Henriette L RøderMette Burmølle
Aug 21, 2019·Proceedings of the National Academy of Sciences of the United States of America·Gina R LewinMarvin Whiteley
Apr 26, 2020·Applied and Environmental Microbiology·Breah LaSarreJames B McKinlay
Jul 17, 2020·FEMS Microbiology Reviews·Christina C SaakRachel J Dutton
Jun 13, 2020·Annual Review of Microbiology·Connor R FitzpatrickJeffery L Dangl
Aug 1, 2020·Nature Communications·Cristal ZuñigaKarsten Zengler
Sep 23, 2020·Proceedings of the National Academy of Sciences of the United States of America·Lara Labarta-BajoElina I Zúñiga
Feb 21, 2019·Journal of Bacteriology·Clay FuquaKaren L Visick
Jan 6, 2021·Nature Reviews. Gastroenterology & Hepatology·Maria L MarcoRobert Hutkins
Jan 6, 2021·Nature Ecology & Evolution·Daniel MachadoKiran R Patil
Nov 4, 2020·Nature Microbiology·Emily C PierceRachel J Dutton
Oct 19, 2019·Current Opinion in Microbiology·Casey M Cosetta, Benjamin E Wolfe
Oct 15, 2020·MBio·Deepika SundarramanRaghuveer Parthasarathy

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Datasets Mentioned

BETA
2751185442

Methods Mentioned

BETA
RNAseq
PCR
Illumina sequencing
scraping
BarSeq
Assay

Software Mentioned

Geneious
BarSeqTest
RB
GenomicRanges
DesignRandomPool
Rsamtool
GenomeInfoDb
RNASeq
R
MapTnSeq

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