Rumen Plasmids

Kav, Aya Brown; Benhar, Itai; Mizrahi, Itzhak

doi:10.1007/978-1-4614-7780-8_5

Cited by 3 publications

(2 citation statements)

References 74 publications

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“…More generally, ruminants, such as cattle, host diverse microbial communities, particularly in the rumen. Rumen microbes allow cattle to digest otherwise indigestible plant matter [26,27]. While research on plasmids traditionally focused on those that are clinically relevant [28], advances in metagenomics and sequencing technology have enabled the exploration of the plasmidome, all plasmids within a given sampled environment, including the bovine rumen [29,30].…”

Section: Introductionmentioning

confidence: 99%

Multilayer networks of plasmid genetic similarity reveal potential pathways of gene transmission

et al. 2023

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Antimicrobial resistance (AMR) is a significant threat to public health. Plasmids are principal vectors of AMR genes, significantly contributing to their spread and mobility across hosts. Nevertheless, little is known about the dynamics of plasmid genetic exchange across animal hosts. Here, we use theory and methodology from network and disease ecology to investigate the potential of gene transmission between plasmids using a data set of 21 plasmidomes from a single dairy cow population. We constructed a multilayer network based on pairwise plasmid genetic similarity. Genetic similarity is a signature of past genetic exchange that can aid in identifying potential routes and mechanisms of gene transmission within and between cows. Links between cows dominated the transmission network, and plasmids containing mobility genes were more connected. Modularity analysis revealed a network cluster where all plasmids contained a mobM gene, and one where all plasmids contained a beta-lactamase gene. Cows that contain both clusters also share transmission pathways with many other cows, making them candidates for super-spreading. In support, we found signatures of gene super-spreading in which a few plasmids and cows are responsible for most gene exchange. An agent-based transmission model showed that a new gene invading the cow population will likely reach all cows. Finally, we showed that edge weights contain a non-random signature for the mechanisms of gene transmission, allowing us to differentiate between dispersal and genetic exchange. These results provide insights into how genes, including those providing AMR, spread across animal hosts.

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Section: Introductionmentioning

confidence: 99%

Multilayer networks of plasmid genetic similarity reveal potential pathways of gene transmission

et al. 2023

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“…Livestock can be important reservoirs of plasmids containing genes for AMR [22–25]. More generally, ruminants, such as cattle, host diverse microbial communities, particularly in the rumen, which allow them to digest otherwise indigestible plant matter [26, 27]. While research on plasmids traditionally focused on those that are clinically relevant [28], advances in metagenomics and sequencing technology have allowed for the exploration of the plasmidome, all plasmids within a given sampled environment, including the bovine rumen [29, 30].…”

Section: Introductionmentioning

confidence: 99%

Multilayer Networks of Plasmid Genetic Similarity Reveal Potential Pathways of Gene Transmission

Shapiro

Zorea

Kav

et al. 2022

Preprint

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Antimicrobial resistance (AMR) is a major threat to public health. Plasmids are principal vectors of antimicrobial resistance genes, greatly contributing to their spread and mobility across hosts. Nevertheless little is known about the dynamics of plasmid genetic exchange across animal hosts. The cow rumen ecosystem is an excellent model system because it hosts diverse plasmid communities which interact and exchange genes. Here, we use theory and methodology from network and disease ecology to investigate the potential of gene transmission between plasmids using a data-set of 21 plasmidomes from a single dairy cow population. We constructed a multilayer network based on pairwise genetic similarity between plasmids serving as a signature for past genetic exchange to identify potential routes and mechanisms of gene transmission within and between cows. The transmission network was dominated by links between cows. Modularity analysis unraveled a major cross-cow transmission pathway with additional small pathways. Plasmid functions influenced network structure: plasmids containing mobility genes were more connected; those with the same AMR genes formed their own modules. We find signatures of gene superspreading in which a few plasmids and cows are responsible for most gene exchange. An agent-based transmission model showed that a new gene invading the cow population is likely to reach all cows. Finally, we showed that link weights contain a non-random signature for the mechanisms of gene transmission allowing us to differentiate between dispersal and genetic exchange. These results provide insights into the mechanisms by which genes, including those providing AMR, spread across animal hosts.

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Unravelling plasmidome distribution and interaction with its hosting microbiome

Kav

Rozov

Bogumil

et al. 2019

Environmental Microbiology

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SummaryHorizontal gene transfer via plasmids plays a pivotal role in microbial evolution. The forces that shape plasmidomes functionality and distribution in natural environments are insufficiently understood. Here, we present a comparative study of plasmidomes across adjacent microbial environments present in different individual rumen microbiomes. Our findings show that the rumen plasmidome displays enormous unknown functional potential currently unannotated in available databases. Nevertheless, this unknown functionality is conserved and shared with published rat gut plasmidome data. Moreover, the rumen plasmidome is highly diverse compared with the microbiome that hosts these plasmids, across both similar and different rumen habitats. Our analysis demonstrates that its structure is shaped more by stochasticity than selection. Nevertheless, the plasmidome is an active partner in its intricate relationship with the host microbiome with both interacting with and responding to their environment.

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Rumen Plasmids

Cited by 3 publications

References 74 publications

Multilayer networks of plasmid genetic similarity reveal potential pathways of gene transmission

Multilayer networks of plasmid genetic similarity reveal potential pathways of gene transmission

Multilayer Networks of Plasmid Genetic Similarity Reveal Potential Pathways of Gene Transmission

Unravelling plasmidome distribution and interaction with its hosting microbiome

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