Construction and Characterization of Synthetic Bacterial Community for Experimental Ecology and Evolution

Frontiers in Genetics
Johannes CairnsTeppo Hiltunen

Abstract

Experimental microbial ecology and evolution have yielded foundational insights into ecological and evolutionary processes using simple microcosm setups and phenotypic assays with one- or two-species model systems. The fields are now increasingly incorporating more complex systems and exploration of the molecular basis of observations. For this purpose, simplified, manageable and well-defined multispecies model systems are required that can be easily investigated using culturing and high-throughput sequencing approaches, bridging the gap between simpler and more complex synthetic or natural systems. Here we address this need by constructing a completely synthetic 33 bacterial strain community that can be cultured in simple laboratory conditions. We provide whole-genome data for all the strains as well as metadata about genomic features and phenotypic traits that allow resolving individual strains by amplicon sequencing and facilitate a variety of envisioned mechanistic studies. We further show that a large proportion of the strains exhibit coexistence in co-culture over serial transfer for 48 days in the absence of any experimental manipulation to maintain diversity. The constructed bacterial community can be a valuable resourc...Continue Reading

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Citations

Jan 31, 2019·Life·Jai A Denton, Chaitanya S Gokhale
Nov 7, 2019·Molecular Plant-microbe Interactions : MPMI·Bridget S O'BanionSarah L Lebeis
Mar 1, 2019·Life·Daniel Rodríguez Amor, Martina Dal Bello
Feb 16, 2021·Frontiers in Microbiology·Angel Rain-FrancoSara Beier
Feb 16, 2021·FEMS Microbiology Ecology·Constantinos XenophontosKirsten Küsel
Nov 23, 2021·Ecology Letters·Shane L HogleTeppo Hiltunen

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Datasets Mentioned

BETA
PRJNA476209
PRJEB21728
BN000925

Methods Mentioned

BETA
amplicon sequencing
PCR
Amplicon Analysis Sequencing

Software Mentioned

IslandViewer
CollectWgsMetrics
MAPLE
ABRicate
ResFinder
R scripts
multiQC
Roary
SPAdes
PHAge Search Tool – Enhanced Release ( PHASTER

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