Large scale capsid-mediated mobilisation of bacterial genomic DNA in the gut microbiome

Tatiana Borodovich; Jason S. Wilson; Pavol Bardy; Muireann Smith; Conor Hill; Ekaterina Khokhlova; Bianca Govi; Paul C.M. Fogg; Colin Hill; Andrey N. Shkoporov

doi:10.1101/2024.11.15.623857

Large scale capsid-mediated mobilisation of bacterial genomic DNA in the gut microbiome

Tatiana Borodovich, Jason S. Wilson, Pavol Bardy, Muireann Smith, Conor Hill, Ekaterina Khokhlova, Bianca Govi, Paul C.M. Fogg, Colin Hill, Andrey N. Shkoporov

Research output: Working paper › Preprint

Abstract

Here, we present a novel approach to study packaging and mobilisation of bacterial DNA in complex microbial communities, such as the human gut microbiome, by viral or virus-like capsids.Transducing bacteriophage (phage) particles and gene transfer agents (GTAs) are constrained by their capsids’ structural properties in the length of host DNA they can package. This results in a narrow distribution of DNA fragment lengths associated with a given viral carrier. Single molecule nanopore sequencing of intact capsid-packaged single DNA molecules with full genome-sized reads can be used to establish the precise lengths and identity of individual packaged DNA molecules and their association with specific bacterial hosts and virus-like agents. The approach developed in this study was validated using a selection of well-characterised transducing phages and a GTA-like element, and then applied to study bacterial DNA encapsidation in the faecal microbiomes from three healthy human donors.Bacterial DNA encapsidation by viruses and virus-like particles appears to be widespread in the microbiome with up to 5.4% of capsid-packaged DNA in the gut virome being of bacterial (non- prophage) origin. Generalised transduction and GTA activity are especially prevalent in the families Ospillospiraceae and Ruminococcaceae (genera Faecalibacterium, Gemmiger, Onthomonas), whereas an example of lateral transduction was observed in genus Bacteroides. In addition to that, induction of prophages in a variety of highly prevalent anaerobic bacteria was observed.Further work will be needed to understand biological significance of capsid-mediated DNA packaging in the gut microbiome and its role in community structure, evolution on ecological timescales, spread of beneficial and detrimental genes, as well as its possible role in gastrointestinal disease.Competing Interest StatementThe authors have declared no competing interest.

Original language	English
Publisher	biorxiv
Pages	2024.11.15.623857
DOIs	https://doi.org/10.1101/2024.11.15.623857
Publication status	Published - 21 Nov 2024

Publication series

Name	bioRxiv
Publisher	Cold Spring Harbor Laboratory Press
ISSN (Print)	2692-8205

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10.1101/2024.11.15.623857Licence: CC BY

http://biorxiv.org/content/early/2024/11/16/2024.11.15.623857.abstractLicence: CC BY

Cite this

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title = "Large scale capsid-mediated mobilisation of bacterial genomic DNA in the gut microbiome",

abstract = "Here, we present a novel approach to study packaging and mobilisation of bacterial DNA in complex microbial communities, such as the human gut microbiome, by viral or virus-like capsids.Transducing bacteriophage (phage) particles and gene transfer agents (GTAs) are constrained by their capsids{\textquoteright} structural properties in the length of host DNA they can package. This results in a narrow distribution of DNA fragment lengths associated with a given viral carrier. Single molecule nanopore sequencing of intact capsid-packaged single DNA molecules with full genome-sized reads can be used to establish the precise lengths and identity of individual packaged DNA molecules and their association with specific bacterial hosts and virus-like agents. The approach developed in this study was validated using a selection of well-characterised transducing phages and a GTA-like element, and then applied to study bacterial DNA encapsidation in the faecal microbiomes from three healthy human donors.Bacterial DNA encapsidation by viruses and virus-like particles appears to be widespread in the microbiome with up to 5.4% of capsid-packaged DNA in the gut virome being of bacterial (non- prophage) origin. Generalised transduction and GTA activity are especially prevalent in the families Ospillospiraceae and Ruminococcaceae (genera Faecalibacterium, Gemmiger, Onthomonas), whereas an example of lateral transduction was observed in genus Bacteroides. In addition to that, induction of prophages in a variety of highly prevalent anaerobic bacteria was observed.Further work will be needed to understand biological significance of capsid-mediated DNA packaging in the gut microbiome and its role in community structure, evolution on ecological timescales, spread of beneficial and detrimental genes, as well as its possible role in gastrointestinal disease.Competing Interest StatementThe authors have declared no competing interest.",

author = "Tatiana Borodovich and Wilson, {Jason S.} and Pavol Bardy and Muireann Smith and Conor Hill and Ekaterina Khokhlova and Bianca Govi and Fogg, {Paul C.M.} and Colin Hill and Shkoporov, {Andrey N.}",

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AU - Khokhlova, Ekaterina

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N2 - Here, we present a novel approach to study packaging and mobilisation of bacterial DNA in complex microbial communities, such as the human gut microbiome, by viral or virus-like capsids.Transducing bacteriophage (phage) particles and gene transfer agents (GTAs) are constrained by their capsids’ structural properties in the length of host DNA they can package. This results in a narrow distribution of DNA fragment lengths associated with a given viral carrier. Single molecule nanopore sequencing of intact capsid-packaged single DNA molecules with full genome-sized reads can be used to establish the precise lengths and identity of individual packaged DNA molecules and their association with specific bacterial hosts and virus-like agents. The approach developed in this study was validated using a selection of well-characterised transducing phages and a GTA-like element, and then applied to study bacterial DNA encapsidation in the faecal microbiomes from three healthy human donors.Bacterial DNA encapsidation by viruses and virus-like particles appears to be widespread in the microbiome with up to 5.4% of capsid-packaged DNA in the gut virome being of bacterial (non- prophage) origin. Generalised transduction and GTA activity are especially prevalent in the families Ospillospiraceae and Ruminococcaceae (genera Faecalibacterium, Gemmiger, Onthomonas), whereas an example of lateral transduction was observed in genus Bacteroides. In addition to that, induction of prophages in a variety of highly prevalent anaerobic bacteria was observed.Further work will be needed to understand biological significance of capsid-mediated DNA packaging in the gut microbiome and its role in community structure, evolution on ecological timescales, spread of beneficial and detrimental genes, as well as its possible role in gastrointestinal disease.Competing Interest StatementThe authors have declared no competing interest.

AB - Here, we present a novel approach to study packaging and mobilisation of bacterial DNA in complex microbial communities, such as the human gut microbiome, by viral or virus-like capsids.Transducing bacteriophage (phage) particles and gene transfer agents (GTAs) are constrained by their capsids’ structural properties in the length of host DNA they can package. This results in a narrow distribution of DNA fragment lengths associated with a given viral carrier. Single molecule nanopore sequencing of intact capsid-packaged single DNA molecules with full genome-sized reads can be used to establish the precise lengths and identity of individual packaged DNA molecules and their association with specific bacterial hosts and virus-like agents. The approach developed in this study was validated using a selection of well-characterised transducing phages and a GTA-like element, and then applied to study bacterial DNA encapsidation in the faecal microbiomes from three healthy human donors.Bacterial DNA encapsidation by viruses and virus-like particles appears to be widespread in the microbiome with up to 5.4% of capsid-packaged DNA in the gut virome being of bacterial (non- prophage) origin. Generalised transduction and GTA activity are especially prevalent in the families Ospillospiraceae and Ruminococcaceae (genera Faecalibacterium, Gemmiger, Onthomonas), whereas an example of lateral transduction was observed in genus Bacteroides. In addition to that, induction of prophages in a variety of highly prevalent anaerobic bacteria was observed.Further work will be needed to understand biological significance of capsid-mediated DNA packaging in the gut microbiome and its role in community structure, evolution on ecological timescales, spread of beneficial and detrimental genes, as well as its possible role in gastrointestinal disease.Competing Interest StatementThe authors have declared no competing interest.

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