Resident microbial communities inhibit growth and antibiotic resistance evolution of Escherichia coli in human gut microbiome samples

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Michael Baumgartner, Florian Bayer, Angus Buckling, Alex R. Hall

bioRxiv preprint first posted online Aug. 20, 2019; doi: 

COMMENT: This work shows how the resident microbial communities can suppress the growth and colonization by focal Escherichia coli and can prevent the acquisition of antibiotic resistance after beta-lactam antibiotic exposure.

The authors use a human gut microcosm system that consists of human faecal slurry within anaerobic fermenters with the beta-lactam antibiotic ampicillin. Using this approach, bacteria can acquire resistance either chromosomally or by horizontal transfer of a beta-lactamase gene.

The authors find that stable microbial communities are able to suppress the colonization of focal Escherichia coli and also the acquisition of antibiotic resistance even with highly effective resistance plasmids in the resident bacteria. The authors identify genetic constraints in horizontal gene transfer and in conjugative transfer that can explain the lack of resistance acquisition.

This work is important because provides evidence about the possible capability of the gastrointestinal microbiota for inhibiting antibiotic resistance acquisition by pathogens.


In conclusion, we showed species-rich microbial communities sampled from human gastrointestinal tracts can suppress growth and resistance evolution of an invading lineage. Given the variety and likely common occurrence of mechanisms that can generate such suppression of invaders (e.g. resource competition), these types of effects are likely common in species-rich communities such as the mammalian gastrointestinal tract. Our other data showed, whether or not these suppressive effects are counter-balanced by beneficial horizontal gene transfer, depends on genetic and environmental constraints that can impede the spread of resistance plasmids. This has important implications for the prediction of resistance evolution from genetic and metagenomics data, such as those widely collected through surveillance efforts: identifying mobile resistance genes in a diverse community is not enough to predict resistance evolution, requiring in addition information about genetic and environmental constraints on in situ transfer dynamics.

Data availability:

Sequences have been deposited in the European Nucleotide Archive under the study accession number PRJEB32627 for the whole genome sequences of single colonies and PRJEB33429 for the 16s rRNA gene amplicon data.



Raquel Tobes