Transductomics: sequencing-based detection and analysis of transduced DNA in pure cultures and microbial communities

Manuel Kleiner,Lora V Hooper,Brian Bushnell,Kenneth E Sanderson,Breck A Duerkop

doi:10.1186/s40168-020-00935-5

Abstract

BackgroundHorizontal gene transfer (HGT) plays a central role in microbial evolution. Our understanding of the mechanisms, frequency, and taxonomic range of HGT in polymicrobial environments is limited, as we currently rely on historical HGT events inferred from genome sequencing and studies involving cultured microorganisms. We lack approaches to observe ongoing HGT in microbial communities.ResultsTo address this knowledge gap, we developed a DNA sequencing-based “transductomics” approach that detects and characterizes microbial DNA transferred via transduction. We validated our approach using model systems representing a range of transduction modes and show that we can detect numerous classes of transducing DNA. Additionally, we show that we can use this methodology to obtain insights into DNA transduction among all major taxonomic groups of the intestinal microbiome.ConclusionsThe transductomics approach that we present here allows for the detection and characterization of genes that are potentially transferred between microbes in complex microbial communities at the time of measurement and thus provides insights into real-time ongoing horizontal gene transfer. This work extends the genomic toolkit for the broader study of mobile DNA within microbial communities and could be used to understand how phenotypes spread within microbiomes.D6q6rZAK8CpuN3-AyzxibTVideo

Highlights

The importance of horizontal gene transfer (HGT) as a driver of rapid evolution and adaptation in microbial communities and host-associated microbiomes has become increasingly recognized [1, 2]
One subsample is directly used for whole community DNA extraction, the other subsample is subjected to ultra-purification of virus-like particles (VLPs) using a combination of filtration, DNAse digestion, and CsCl density gradient centrifugation as previously described [24] followed by DNA extraction from the purified VLPs
Our results show that packaging of host DNA by the gene transfer agents (GTAs)-like PBSX element of B. subtilis produces a distinct and non-random sequencing coverage pattern that bears similarities to the read coverage pattern produced by the generalized transducing phage P1 (Fig. 3c)

Summary

Introduction

The importance of horizontal gene transfer (HGT) as a driver of rapid evolution and adaptation in microbial communities and host-associated microbiomes has become increasingly recognized [1, 2]. There are several known types of transduction including classic specialized and generalized transduction, and more recently discovered types, including gene transfer agents (GTAs), lateral transduction, and hijacking of bacteriophage (phage) particles by genomic islands [10,11,12]. Non-random pieces of the host bacterial genomic DNA or plasmids get packaged at low frequency into phage particles when a lytic phage infects and replicates in a bacterial cell or upon induction of lysogens. This non-random packaging is mediated by genomic features that resemble the packaging site (pac site) on the phage genome, which is used by the phage particle packaging machinery as the start site of phage DNA packaging into the capsid [13]. We lack approaches to observe ongoing HGT in microbial communities

Methods

Results

Conclusion