Identification of the Colicin V Bacteriocin Gene Cluster by Functional Screening of a Human Microbiome Metagenomic Library - PubMed (original) (raw)

Identification of the Colicin V Bacteriocin Gene Cluster by Functional Screening of a Human Microbiome Metagenomic Library

Louis J Cohen et al. ACS Infect Dis. 2018.

Abstract

The forces that shape human microbial ecology are complex. It is likely that human microbiota, similarly to other microbiomes, use antibiotics as one way to establish an ecological niche. In this study, we use functional metagenomics to identify human microbial gene clusters that encode for antibiotic functions. Screening of a metagenomic library prepared from a healthy patient stool sample led to the identification of a family of clones with inserts that are 99% identical to a region of a virulence plasmid found in avian pathogenic Escherichia coli. Characterization of the metagenomic DNA sequence identified a colicin V biosynthetic cluster as being responsible for the observed antibiotic effect of the metagenomic clone against E. coli. This study presents a scalable method to recover antibiotic gene clusters from humans using functional metagenomics and highlights a strategy to study bacteriocins in the human microbiome which can provide a resource for therapeutic discovery.

Keywords: antibiotic; bacteriocin; eDNA; metagenome; microbiome.

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Conflict of interest statement

Notes

The authors declare no competing financial interest.

Figures

Figure 1.

Figure 1.

Functional metagenomic screen for antibiotics. (A) Samples of metagenomic DNA can be isolated from any part of the human microbiome and cloned into a cosmid DNA library (B). Cosmids containing metagenomic DNA are introduced into heterologous bacterial hosts, where foreign metagenomic DNA is expressed. (C) Metagenomic clones are plated on agar and allowed to produce potential antibiotics encoded on the piece of metagenomic DNA. Indicator strains are overlaid on top of the metagenomic clones, and active metagenomic clones are identified by inhibition of growth of the indicator strain, producing a zone of clearing. Pictured is an active metagenomic clone inhibiting the growth of an E. coli indicator strain.

Figure 2.

Figure 2.

Active metagenomic clone DNA sequence. The metagenomic DNA insert contains three gene clusters with predicted virulence functions including colicin V, colicin E9, and a protease toxin. The flanking regions of the DNA contain mobile element genes. Transposon insertion sites in the genes of the colicin V cluster are pictured.

Figure 3.

Figure 3.

Spectrum of activity. E. coli expressing the colicin V gene cluster was plated on LYH-BHI agar media and overlaid with indicator strains of 20 human commensal bacteria from the four common phyla present in the human microbiome. Inhibition of the indicator strain was only observed for E. coli strains K12 and MS145–7, a strain of adherent invasive E. coli (AIEC), both indicated in red. There was no inhibition of any strains by E. coli carrying the empty vector.

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