Culturing Ancient Bacteria Carrying Resistance Genes from Permafrost and Comparative Genomics with Modern Isolates
International audience Long considered to be a consequence of human antibiotics use by deduction, antibiotic resistance mechanisms appear to be in fact a much older phenomenon as antibiotic resistance genes have previously been detected from millions of year-old permafrost samples. As these specimen...
Published in: | Microorganisms |
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Main Authors: | , , , , , , , , , , |
Other Authors: | , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
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HAL CCSD
2020
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Subjects: | |
Online Access: | https://amu.hal.science/hal-03141648 https://amu.hal.science/hal-03141648/document https://amu.hal.science/hal-03141648/file/microorganisms-08-01522-v2.pdf https://doi.org/10.3390/microorganisms8101522 |
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Open Polar |
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Institut national des sciences de l'Univers: HAL-INSU |
op_collection_id |
ftinsu |
language |
English |
topic |
culturomics Siberian permafrost resistance genes genomic evolution [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases |
spellingShingle |
culturomics Siberian permafrost resistance genes genomic evolution [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases Afouda, P Dubourg, Gregory Levasseur, Anthony Fournier, Pierre-Edouard Delerce, Jeremy Mediannikov, Oleg Diene, S.M. Nahon, D. Bourles, D.L. Rolain, Jean-Marc Raoult, Didier Culturing Ancient Bacteria Carrying Resistance Genes from Permafrost and Comparative Genomics with Modern Isolates |
topic_facet |
culturomics Siberian permafrost resistance genes genomic evolution [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases |
description |
International audience Long considered to be a consequence of human antibiotics use by deduction, antibiotic resistance mechanisms appear to be in fact a much older phenomenon as antibiotic resistance genes have previously been detected from millions of year-old permafrost samples. As these specimens guarantee the viability of archaic bacteria, we herein propose to apply the culturomics approach to recover the bacterial content of a Siberian permafrost sample dated, using the in situ-produced cosmogenic nuclide chlorine36 (36 Cl), at 2.7 million years to study the dynamics of bacterial evolution in an evolutionary perspective. As a result, we cultured and sequenced the genomes of 28 ancient bacterial species including one new species. To perform genome comparison between permafrost strains and modern isolates we selected 7 of these species (i.e., Achromobacter insolitus, Bacillus idriensis, Brevundimonas aurantiaca, Janibacter melonis, Kocuria rhizophila, Microbacterium hydrocarbonoxydans and Paracoccus yeei). We observed a high level of variability in genomic content with a percentage of shared genes in the core genomes ranging from 21.23% to 55.59%. In addition, the Single Nucleotide Polymorphism (SNP) comparison between permafrost and modern strains for the same species did not allow a dating of ancient strains based on genomic content. There were no significant differences in antibiotic resistance profiles between modern and ancient isolates of each species. Acquired resistance to antibiotics was phenotypically detected in all gram-negative bacterial species recovered from permafrost, with a significant number of genes coding for antibiotic resistance detected. Taken together, these findings confirm previously obtained data that antibiotic resistance predates humanity as most of antimicrobial agents are natural weapons used in inter-microbial conflicts within the biosphere. |
author2 |
Microbes évolution phylogénie et infections (MEPHI) Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS) Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille) Vecteurs - Infections tropicales et méditerranéennes (VITROME) Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées Brétigny-sur-Orge (IRBA) Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE) Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) ANR-10-IAHU-0003,Méditerranée Infection,I.H.U. Méditerranée Infection(2010) |
format |
Article in Journal/Newspaper |
author |
Afouda, P Dubourg, Gregory Levasseur, Anthony Fournier, Pierre-Edouard Delerce, Jeremy Mediannikov, Oleg Diene, S.M. Nahon, D. Bourles, D.L. Rolain, Jean-Marc Raoult, Didier |
author_facet |
Afouda, P Dubourg, Gregory Levasseur, Anthony Fournier, Pierre-Edouard Delerce, Jeremy Mediannikov, Oleg Diene, S.M. Nahon, D. Bourles, D.L. Rolain, Jean-Marc Raoult, Didier |
author_sort |
Afouda, P |
title |
Culturing Ancient Bacteria Carrying Resistance Genes from Permafrost and Comparative Genomics with Modern Isolates |
title_short |
Culturing Ancient Bacteria Carrying Resistance Genes from Permafrost and Comparative Genomics with Modern Isolates |
title_full |
Culturing Ancient Bacteria Carrying Resistance Genes from Permafrost and Comparative Genomics with Modern Isolates |
title_fullStr |
Culturing Ancient Bacteria Carrying Resistance Genes from Permafrost and Comparative Genomics with Modern Isolates |
title_full_unstemmed |
Culturing Ancient Bacteria Carrying Resistance Genes from Permafrost and Comparative Genomics with Modern Isolates |
title_sort |
culturing ancient bacteria carrying resistance genes from permafrost and comparative genomics with modern isolates |
publisher |
HAL CCSD |
publishDate |
2020 |
url |
https://amu.hal.science/hal-03141648 https://amu.hal.science/hal-03141648/document https://amu.hal.science/hal-03141648/file/microorganisms-08-01522-v2.pdf https://doi.org/10.3390/microorganisms8101522 |
genre |
permafrost |
genre_facet |
permafrost |
op_source |
ISSN: 2076-2607 Microorganisms https://amu.hal.science/hal-03141648 Microorganisms, 2020, 8 (10), pp.1522. ⟨10.3390/microorganisms8101522⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.3390/microorganisms8101522 info:eu-repo/semantics/altIdentifier/pmid/33023015 hal-03141648 https://amu.hal.science/hal-03141648 https://amu.hal.science/hal-03141648/document https://amu.hal.science/hal-03141648/file/microorganisms-08-01522-v2.pdf doi:10.3390/microorganisms8101522 PUBMED: 33023015 WOS: 000586974100001 |
op_rights |
http://creativecommons.org/licenses/by/ info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.3390/microorganisms8101522 |
container_title |
Microorganisms |
container_volume |
8 |
container_issue |
10 |
container_start_page |
1522 |
_version_ |
1785572639371165696 |
spelling |
ftinsu:oai:HAL:hal-03141648v1 2023-12-17T10:48:28+01:00 Culturing Ancient Bacteria Carrying Resistance Genes from Permafrost and Comparative Genomics with Modern Isolates Afouda, P Dubourg, Gregory Levasseur, Anthony Fournier, Pierre-Edouard Delerce, Jeremy Mediannikov, Oleg Diene, S.M. Nahon, D. Bourles, D.L. Rolain, Jean-Marc Raoult, Didier Microbes évolution phylogénie et infections (MEPHI) Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS) Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille) Vecteurs - Infections tropicales et méditerranéennes (VITROME) Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées Brétigny-sur-Orge (IRBA) Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE) Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) ANR-10-IAHU-0003,Méditerranée Infection,I.H.U. Méditerranée Infection(2010) 2020-10 https://amu.hal.science/hal-03141648 https://amu.hal.science/hal-03141648/document https://amu.hal.science/hal-03141648/file/microorganisms-08-01522-v2.pdf https://doi.org/10.3390/microorganisms8101522 en eng HAL CCSD MDPI info:eu-repo/semantics/altIdentifier/doi/10.3390/microorganisms8101522 info:eu-repo/semantics/altIdentifier/pmid/33023015 hal-03141648 https://amu.hal.science/hal-03141648 https://amu.hal.science/hal-03141648/document https://amu.hal.science/hal-03141648/file/microorganisms-08-01522-v2.pdf doi:10.3390/microorganisms8101522 PUBMED: 33023015 WOS: 000586974100001 http://creativecommons.org/licenses/by/ info:eu-repo/semantics/OpenAccess ISSN: 2076-2607 Microorganisms https://amu.hal.science/hal-03141648 Microorganisms, 2020, 8 (10), pp.1522. ⟨10.3390/microorganisms8101522⟩ culturomics Siberian permafrost resistance genes genomic evolution [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases info:eu-repo/semantics/article Journal articles 2020 ftinsu https://doi.org/10.3390/microorganisms8101522 2023-11-22T17:37:50Z International audience Long considered to be a consequence of human antibiotics use by deduction, antibiotic resistance mechanisms appear to be in fact a much older phenomenon as antibiotic resistance genes have previously been detected from millions of year-old permafrost samples. As these specimens guarantee the viability of archaic bacteria, we herein propose to apply the culturomics approach to recover the bacterial content of a Siberian permafrost sample dated, using the in situ-produced cosmogenic nuclide chlorine36 (36 Cl), at 2.7 million years to study the dynamics of bacterial evolution in an evolutionary perspective. As a result, we cultured and sequenced the genomes of 28 ancient bacterial species including one new species. To perform genome comparison between permafrost strains and modern isolates we selected 7 of these species (i.e., Achromobacter insolitus, Bacillus idriensis, Brevundimonas aurantiaca, Janibacter melonis, Kocuria rhizophila, Microbacterium hydrocarbonoxydans and Paracoccus yeei). We observed a high level of variability in genomic content with a percentage of shared genes in the core genomes ranging from 21.23% to 55.59%. In addition, the Single Nucleotide Polymorphism (SNP) comparison between permafrost and modern strains for the same species did not allow a dating of ancient strains based on genomic content. There were no significant differences in antibiotic resistance profiles between modern and ancient isolates of each species. Acquired resistance to antibiotics was phenotypically detected in all gram-negative bacterial species recovered from permafrost, with a significant number of genes coding for antibiotic resistance detected. Taken together, these findings confirm previously obtained data that antibiotic resistance predates humanity as most of antimicrobial agents are natural weapons used in inter-microbial conflicts within the biosphere. Article in Journal/Newspaper permafrost Institut national des sciences de l'Univers: HAL-INSU Microorganisms 8 10 1522 |