Transductomics: sequencing-based detection and analysis of transduced DNA in pure cultures and microbial communities
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RESEARCH
Open Access
Transductomics: sequencing-based detection and analysis of transduced DNA in pure cultures and microbial communities Manuel Kleiner1* , Brian Bushnell2, Kenneth E. Sanderson3, Lora V. Hooper4,5 and Breck A. Duerkop6*
Abstract Background: Horizontal 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. Results: To 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. Conclusions: The 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.
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]. Publicly available genomes and metagenomes have revealed pervasive horizontally acquired genes in almost all available genomes. A study of HGT in the human microbiome, for example, showed > 10,000 recently transferred genes in 2235 analyzed genomes [3]. HGT has been implicated in the spread of antibiotic resistance genes [4], toxin and other virulence * Correspondence: [email protected]; [email protected] 1 Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA 6 Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA Full list of author information is available at the end of the article
genes [5, 6], as well as genes that enable digestion of dietary compounds by microbes in the intestine [7], and metabolic genes that augment microbial metabolism with critical functions in environmental populations [8]. Despite its recognized importance, our understanding of the taxonomic range, frequency, and mechanisms of HGT are still limited. Most studies of HGT in microbiomes rely on analysis of microbial genomes [3, 9] and as such these methods attempt to reconstruct historical HGT. What we currently lack are methods that measure ongo
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