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A reservoir of 'historical' antibiotic resistance genes in remote pristine Antarctic soils

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Bioinformatics: from nucleotids to networks (N2N)
Abstract
Background: Soil bacteria naturally produce antibiotics as a competitive mechanism, with a concomitant evolution, and exchange by horizontal gene transfer, of a range of antibiotic resistance mechanisms. Surveys of bacterial resistance elements in edaphic systems have originated primarily from human-impacted environments, with relatively little information from remote and pristine environments, where the resistome may comprise the ancestral gene diversity. Methods: We used shotgun metagenomics to assess antibiotic resistance gene (ARG) distribution in 17 pristine and remote Antarctic surface soils within the undisturbed Mackay Glacier region. We also interrogated the phylogenetic placement of ARGs compared to environmental ARG sequences and tested for the presence of horizontal gene transfer elements flanking ARGs. Results: In total, 177 naturally occurring ARGs were identified, most of which encoded single or multi-drug efflux pumps. Resistance mechanisms for the inactivation of aminoglycosides, chloramphenicol and beta-lactam antibiotics were also common. Gram-negative bacteria harboured most ARGs (71%), with fewer genes from Gram-positive Actinobacteria and Bacilli (Firmicutes) (9%), reflecting the taxonomic composition of the soils. Strikingly, the abundance of ARGs per sample had a strong, negative correlation with species richness (r=-0.49, P < 0.05). This result, coupled with a lack of mobile genetic elements flanking ARGs, suggests that these genes are ancient acquisitions of horizontal transfer events. Conclusions: ARGs in these remote and uncontaminated soils most likely represent functional efficient historical genes that have since been vertically inherited over generations. The historical ARGs in these pristine environments carry a strong phylogenetic signal and form a monophyletic group relative to ARGs from other similar environments.
Keywords
MICROBIAL COMMUNITIES, DRUG-RESISTANCE, BETA-LACTAMASES, ALASKAN SOIL, BACTERIA, RESISTOME, ENVIRONMENT, DATABASE, TOOL, BIOSYNTHESIS, Antibiotic resistance genes, Soil resistome, Antarctica, Metagenomics

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Citation

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Chicago
Van Goethem, Marc W, Rian Pierneef, Oliver KI Bezuidt, Yves Van de Peer, Don A Cowan, and Thulani P Makhalanyane. 2018. “A Reservoir of ‘Historical’ Antibiotic Resistance Genes in Remote Pristine Antarctic Soils.” Microbiome 6.
APA
Van Goethem, M. W., Pierneef, R., Bezuidt, O. K., Van de Peer, Y., Cowan, D. A., & Makhalanyane, T. P. (2018). A reservoir of “historical” antibiotic resistance genes in remote pristine Antarctic soils. MICROBIOME, 6.
Vancouver
1.
Van Goethem MW, Pierneef R, Bezuidt OK, Van de Peer Y, Cowan DA, Makhalanyane TP. A reservoir of “historical” antibiotic resistance genes in remote pristine Antarctic soils. MICROBIOME. 2018;6.
MLA
Van Goethem, Marc W, Rian Pierneef, Oliver KI Bezuidt, et al. “A Reservoir of ‘Historical’ Antibiotic Resistance Genes in Remote Pristine Antarctic Soils.” MICROBIOME 6 (2018): n. pag. Print.
@article{8558164,
  abstract     = {Background: Soil bacteria naturally produce antibiotics as a competitive mechanism, with a concomitant evolution, and exchange by horizontal gene transfer, of a range of antibiotic resistance mechanisms. Surveys of bacterial resistance elements in edaphic systems have originated primarily from human-impacted environments, with relatively little information from remote and pristine environments, where the resistome may comprise the ancestral gene diversity. 
Methods: We used shotgun metagenomics to assess antibiotic resistance gene (ARG) distribution in 17 pristine and remote Antarctic surface soils within the undisturbed Mackay Glacier region. We also interrogated the phylogenetic placement of ARGs compared to environmental ARG sequences and tested for the presence of horizontal gene transfer elements flanking ARGs. 
Results: In total, 177 naturally occurring ARGs were identified, most of which encoded single or multi-drug efflux pumps. Resistance mechanisms for the inactivation of aminoglycosides, chloramphenicol and beta-lactam antibiotics were also common. Gram-negative bacteria harboured most ARGs (71\%), with fewer genes from Gram-positive Actinobacteria and Bacilli (Firmicutes) (9\%), reflecting the taxonomic composition of the soils. Strikingly, the abundance of ARGs per sample had a strong, negative correlation with species richness (r=-0.49, P {\textlangle} 0.05). This result, coupled with a lack of mobile genetic elements flanking ARGs, suggests that these genes are ancient acquisitions of horizontal transfer events. 
Conclusions: ARGs in these remote and uncontaminated soils most likely represent functional efficient historical genes that have since been vertically inherited over generations. The historical ARGs in these pristine environments carry a strong phylogenetic signal and form a monophyletic group relative to ARGs from other similar environments.},
  articleno    = {40},
  author       = {Van Goethem, Marc W and Pierneef, Rian and Bezuidt, Oliver KI and Van de Peer, Yves and Cowan, Don A and Makhalanyane, Thulani P},
  issn         = {2049-2618},
  journal      = {MICROBIOME},
  keyword      = {MICROBIAL COMMUNITIES,DRUG-RESISTANCE,BETA-LACTAMASES,ALASKAN SOIL,BACTERIA,RESISTOME,ENVIRONMENT,DATABASE,TOOL,BIOSYNTHESIS,Antibiotic resistance genes,Soil resistome,Antarctica,Metagenomics},
  language     = {eng},
  pages        = {12},
  title        = {A reservoir of 'historical' antibiotic resistance genes in remote pristine Antarctic soils},
  url          = {http://dx.doi.org/10.1186/s40168-018-0424-5},
  volume       = {6},
  year         = {2018},
}

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