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  • Buongermino Pereira, Mariana,1982Gothenburg University,Göteborgs universitet,CARe - Centrum för antibiotikaresistensforskning,Centre for antibiotic resistance research, CARe,Chalmers tekniska högskola,Chalmers University of Technology,University of Gothenburg (author)

A comprehensive survey of integron-associated genes present in metagenomes

  • Article/chapterEnglish2020

Publisher, publication year, extent ...

  • 2020-07-20
  • Springer Science and Business Media LLC,2020

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  • LIBRIS-ID:oai:gup.ub.gu.se/296060
  • https://gup.ub.gu.se/publication/296060URI
  • https://doi.org/10.1186/s12864-020-06830-5DOI
  • https://research.chalmers.se/publication/518274URI

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  • Language:English

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  • Subject category:ref swepub-contenttype
  • Subject category:art swepub-publicationtype

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  • BackgroundIntegrons are genomic elements that mediate horizontal gene transfer by inserting and removing genetic material using site-specific recombination. Integrons are commonly found in bacterial genomes, where they maintain a large and diverse set of genes that plays an important role in adaptation and evolution. Previous studies have started to characterize the wide range of biological functions present in integrons. However, the efforts have so far mainly been limited to genomes from cultivable bacteria and amplicons generated by PCR, thus targeting only a small part of the total integron diversity. Metagenomic data, generated by direct sequencing of environmental and clinical samples, provides a more holistic and unbiased analysis of integron-associated genes. However, the fragmented nature of metagenomic data has previously made such analysis highly challenging.ResultsHere, we present a systematic survey of integron-associated genes in metagenomic data. The analysis was based on a newly developed computational method where integron-associated genes were identified by detecting their associated recombination sites. By processing contiguous sequences assembled from more than 10 terabases of metagenomic data, we were able to identify 13,397 unique integron-associated genes. Metagenomes from marine microbial communities had the highest occurrence of integron-associated genes with levels more than 100-fold higher than in the human microbiome. The identified genes had a large functional diversity spanning over several functional classes. Genes associated with defense mechanisms and mobility facilitators were most overrepresented and more than five times as common in integrons compared to other bacterial genes. As many as two thirds of the genes were found to encode proteins of unknown function. Less than 1% of the genes were associated with antibiotic resistance, of which several were novel, previously undescribed, resistance gene variants.ConclusionsOur results highlight the large functional diversity maintained by integrons present in unculturable bacteria and significantly expands the number of described integron-associated genes.

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  • Österlund, Tobias,1984Gothenburg University,Göteborgs universitet,CARe - Centrum för antibiotikaresistensforskning,Centre for antibiotic resistance research, CARe,University of Gothenburg,Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)tobiaso (author)
  • Eriksson, Martin,1970Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences,University of Gothenburg,Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)marte (author)
  • Backhaus, Thomas,1967Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,CARe - Centrum för antibiotikaresistensforskning,Department of Biological and Environmental Sciences,Centre for antibiotic resistance research, CARe,University of Gothenburg(Swepub:gu)xbacth (author)
  • Axelson-Fisk, Marina,1972Gothenburg University,Göteborgs universitet,Institutionen för matematiska vetenskaper,Department of Mathematical Sciences,Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)marinaa (author)
  • Kristiansson, Erik,1978Gothenburg University,Göteborgs universitet,CARe - Centrum för antibiotikaresistensforskning,Institutionen för matematiska vetenskaper,Centre for antibiotic resistance research, CARe,Department of Mathematical Sciences,Chalmers tekniska högskola,Chalmers University of Technology,University of Gothenburg(Swepub:cth)erikkr (author)
  • Göteborgs universitetCARe - Centrum för antibiotikaresistensforskning (creator_code:org_t)

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  • In:BMC Genomics: Springer Science and Business Media LLC21:11471-2164

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