Culture-enriched human gut microbiomes reveal core and accessory resistance genes
Abstract Background Low-abundance microorganisms of the gut microbiome are often referred to as a reservoir for antibiotic resistance genes. Unfortunately, these less-abundant bacteria can be overlooked by deep shotgun sequencing. In addition, it is a challenge to associate the presence of resistanc...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-04-01
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| Series: | Microbiome |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s40168-019-0669-7 |
| _version_ | 1811287681621032960 |
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| author | Frédéric Raymond Maurice Boissinot Amin Ahmed Ouameur Maxime Déraspe Pier-Luc Plante Sewagnouin Rogia Kpanou Ève Bérubé Ann Huletsky Paul H. Roy Marc Ouellette Michel G. Bergeron Jacques Corbeil |
| author_facet | Frédéric Raymond Maurice Boissinot Amin Ahmed Ouameur Maxime Déraspe Pier-Luc Plante Sewagnouin Rogia Kpanou Ève Bérubé Ann Huletsky Paul H. Roy Marc Ouellette Michel G. Bergeron Jacques Corbeil |
| author_sort | Frédéric Raymond |
| collection | DOAJ |
| description | Abstract Background Low-abundance microorganisms of the gut microbiome are often referred to as a reservoir for antibiotic resistance genes. Unfortunately, these less-abundant bacteria can be overlooked by deep shotgun sequencing. In addition, it is a challenge to associate the presence of resistance genes with their risk of acquisition by pathogens. In this study, we used liquid culture enrichment of stools to assemble the genome of lower-abundance bacteria from fecal samples. We then investigated the gene content recovered from these culture-enriched and culture-independent metagenomes in relation with their taxonomic origin, specifically antibiotic resistance genes. We finally used a pangenome approach to associate resistance genes with the core or accessory genome of Enterobacteriaceae and inferred their propensity to horizontal gene transfer. Results Using culture-enrichment approaches with stools allowed assembly of 187 bacterial species with an assembly size greater than 1 million nucleotides. Of these, 67 were found only in culture-enriched conditions, and 22 only in culture-independent microbiomes. These assembled metagenomes allowed the evaluation of the gene content of specific subcommunities of the gut microbiome. We observed that differentially distributed metabolic enzymes were associated with specific culture conditions and, for the most part, with specific taxa. Gene content differences between microbiomes, for example, antibiotic resistance, were for the most part not associated with metabolic enzymes, but with other functions. We used a pangenome approach to determine if the resistance genes found in Enterobacteriaceae, specifically E. cloacae or E. coli, were part of the core genome or of the accessory genome of this species. In our healthy volunteer cohort, we found that E. cloacae contigs harbored resistance genes that were part of the core genome of the species, while E. coli had a large accessory resistome proximal to mobile elements. Conclusion Liquid culture of stools contributed to an improved functional and comparative genomics study of less-abundant gut bacteria, specifically those associated with antibiotic resistance. Defining whether a gene is part of the core genome of a species helped in interpreting the genomes recovered from culture-independent or culture-enriched microbiomes. |
| first_indexed | 2024-04-13T03:23:30Z |
| format | Article |
| id | doaj.art-57fe01188d7f48308ee8ff5134f4b1e0 |
| institution | Directory Open Access Journal |
| issn | 2049-2618 |
| language | English |
| last_indexed | 2024-04-13T03:23:30Z |
| publishDate | 2019-04-01 |
| publisher | BMC |
| record_format | Article |
| series | Microbiome |
| spelling | doaj.art-57fe01188d7f48308ee8ff5134f4b1e02022-12-22T03:04:43ZengBMCMicrobiome2049-26182019-04-017111310.1186/s40168-019-0669-7Culture-enriched human gut microbiomes reveal core and accessory resistance genesFrédéric Raymond0Maurice Boissinot1Amin Ahmed Ouameur2Maxime Déraspe3Pier-Luc Plante4Sewagnouin Rogia Kpanou5Ève Bérubé6Ann Huletsky7Paul H. Roy8Marc Ouellette9Michel G. Bergeron10Jacques Corbeil11École de nutrition, Faculté des sciences de l’agriculture et de l’alimentation, Université LavalCentre de Recherche en Infectiologie de l’Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université LavalCentre de Recherche en Infectiologie de l’Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université LavalCentre de Recherche en Infectiologie de l’Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université LavalCentre de Recherche en Infectiologie de l’Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université LavalCentre de Recherche en Infectiologie de l’Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université LavalCentre de Recherche en Infectiologie de l’Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université LavalCentre de Recherche en Infectiologie de l’Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université LavalCentre de Recherche en Infectiologie de l’Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université LavalCentre de Recherche en Infectiologie de l’Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université LavalCentre de Recherche en Infectiologie de l’Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université LavalCentre de Recherche en Infectiologie de l’Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université LavalAbstract Background Low-abundance microorganisms of the gut microbiome are often referred to as a reservoir for antibiotic resistance genes. Unfortunately, these less-abundant bacteria can be overlooked by deep shotgun sequencing. In addition, it is a challenge to associate the presence of resistance genes with their risk of acquisition by pathogens. In this study, we used liquid culture enrichment of stools to assemble the genome of lower-abundance bacteria from fecal samples. We then investigated the gene content recovered from these culture-enriched and culture-independent metagenomes in relation with their taxonomic origin, specifically antibiotic resistance genes. We finally used a pangenome approach to associate resistance genes with the core or accessory genome of Enterobacteriaceae and inferred their propensity to horizontal gene transfer. Results Using culture-enrichment approaches with stools allowed assembly of 187 bacterial species with an assembly size greater than 1 million nucleotides. Of these, 67 were found only in culture-enriched conditions, and 22 only in culture-independent microbiomes. These assembled metagenomes allowed the evaluation of the gene content of specific subcommunities of the gut microbiome. We observed that differentially distributed metabolic enzymes were associated with specific culture conditions and, for the most part, with specific taxa. Gene content differences between microbiomes, for example, antibiotic resistance, were for the most part not associated with metabolic enzymes, but with other functions. We used a pangenome approach to determine if the resistance genes found in Enterobacteriaceae, specifically E. cloacae or E. coli, were part of the core genome or of the accessory genome of this species. In our healthy volunteer cohort, we found that E. cloacae contigs harbored resistance genes that were part of the core genome of the species, while E. coli had a large accessory resistome proximal to mobile elements. Conclusion Liquid culture of stools contributed to an improved functional and comparative genomics study of less-abundant gut bacteria, specifically those associated with antibiotic resistance. Defining whether a gene is part of the core genome of a species helped in interpreting the genomes recovered from culture-independent or culture-enriched microbiomes.http://link.springer.com/article/10.1186/s40168-019-0669-7MicrobiomeAntibiotic resistancePangenomeMetagenomics assembly comparative genomics |
| spellingShingle | Frédéric Raymond Maurice Boissinot Amin Ahmed Ouameur Maxime Déraspe Pier-Luc Plante Sewagnouin Rogia Kpanou Ève Bérubé Ann Huletsky Paul H. Roy Marc Ouellette Michel G. Bergeron Jacques Corbeil Culture-enriched human gut microbiomes reveal core and accessory resistance genes Microbiome Microbiome Antibiotic resistance Pangenome Metagenomics assembly comparative genomics |
| title | Culture-enriched human gut microbiomes reveal core and accessory resistance genes |
| title_full | Culture-enriched human gut microbiomes reveal core and accessory resistance genes |
| title_fullStr | Culture-enriched human gut microbiomes reveal core and accessory resistance genes |
| title_full_unstemmed | Culture-enriched human gut microbiomes reveal core and accessory resistance genes |
| title_short | Culture-enriched human gut microbiomes reveal core and accessory resistance genes |
| title_sort | culture enriched human gut microbiomes reveal core and accessory resistance genes |
| topic | Microbiome Antibiotic resistance Pangenome Metagenomics assembly comparative genomics |
| url | http://link.springer.com/article/10.1186/s40168-019-0669-7 |
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