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RefSoil+: a Reference Database for Genes and Traits of Soil Plasmids.
Taylor K Dunivin1,2, Jinlyung Choi3, Adina Howe3
1Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA.
Msystems
|March 6, 2019
Summary
Environmental plasmids in soil carry transferable genes. A new database, RefSoil+, reveals soil plasmids are larger and may limit antibiotic resistance gene spread to clinical strains.
Area of Science:
- Microbiology
- Genomics
- Environmental Science
Background:
- Plasmids are key vectors for gene transfer in microbial communities, including antibiotic resistance genes.
- Environmental plasmids, particularly from soils, pose a potential risk for spreading antimicrobial resistance to clinical pathogens.
- Studying soil plasmids is challenging due to high microbial diversity and plasmid variability.
Purpose of the Study:
- To create a comprehensive database of soil plasmid sequences to enhance understanding of their characteristics and functional genes.
- To investigate the relationship between genomic traits (chromosome size, plasmid size, plasmid number) in soil microorganisms.
- To compare the distribution of antibiotic resistance genes on plasmids and chromosomes in soil versus non-soil microorganisms.
Main Methods:
- Development of RefSoil+, a database containing plasmid sequences from 922 soil microorganisms.
- Analysis of plasmid and chromosome sizes and numbers in soil microbial genomes.
- Comparative analysis of antibiotic resistance gene content in soil-associated plasmids and chromosomes versus other microbial plasmids and chromosomes.
Main Results:
- Soil plasmids were found to be larger than other described plasmids, suggesting higher mobility.
- Genomic traits like chromosome size and plasmid characteristics showed weak or no correlation in soil microbes.
- Soil-associated plasmids contained fewer antibiotic resistance genes compared to non-soil microorganisms, suggesting limited transfer potential.
Conclusions:
- The RefSoil+ database provides a valuable resource for studying soil plasmid diversity, composition, and host associations.
- Soils may present a limited pathway for the plasmid-mediated transfer of currently known antibiotic resistance genes to clinical settings.
- This study enhances the understanding of soil plasmids and provides a reference for tracking antimicrobial resistance gene dynamics between environmental and clinical niches.
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