title: Functional characterization of bacteria isolated from ancient arctic soil exposes diverse resistance mechanisms to modern antibiotics.
abstract: Using functional metagenomics to study the resistomes of bacterial communities isolated from different layers of the Canadian high Arctic permafrost, we show that microbial communities harbored diverse resistance mechanisms at least 5,000 years ago. Among bacteria sampled from the ancient layers of a permafrost core, we isolated eight genes conferring clinical levels of resistance against aminoglycoside, β-lactam and tetracycline antibiotics that are naturally produced by microorganisms. Among these resistance genes, four also conferred resistance against amikacin, a modern semi-synthetic antibiotic that does not naturally occur in microorganisms. In bacteria sampled from the overlaying active layer, we isolated ten different genes conferring resistance to all six antibiotics tested in this study, including aminoglycoside, β-lactam and tetracycline variants that are naturally produced by microorganisms as well as semi-synthetic variants produced in the laboratory. On average, we found that resistance genes found in permafrost bacteria conferred lower levels of resistance against clinically relevant antibiotics than resistance genes sampled from the active layer. Our results demonstrate that antibiotic resistance genes were functionally diverse prior to the anthropogenic use of antibiotics, contributing to the evolution of natural reservoirs of resistance genes.
authors: FAS Center for Systems Biology, Harvard University, 52 Oxford Street, Cambridge, Massachusetts, 02138, United States of America; Department of Evolutionary and Organismic Biology, Harvard University, 52 Oxford Street, Cambridge, Massachusetts, 02138, United States of America; Biology Program, Bard College, 30 Campus Road, Annandale-on-Hudson, New York, 12504, United States of America.
authors: Gabriel G
authors: GG
authors: Perron
authors: Department of Natural Resource Sciences, McGill University, Macdonald Campus, 21,111 Lakeshore, Ste-Anne-de-Bellevue, Quebec, H9X 3V9, Canada.
authors: Lyle
authors: L
authors: Whyte
authors: FAS Center for Systems Biology, Harvard University, 52 Oxford Street, Cambridge, Massachusetts, 02138, United States of America; Department of Microbiology and Immunology, Hooper Foundation, University of California San Francisco, 513 Parnassus Ave, San Francisco, California, 94143, United States of America.
authors: Peter J
authors: PJ
authors: Turnbaugh
authors: Department of Natural Resource Sciences, McGill University, Macdonald Campus, 21,111 Lakeshore, Ste-Anne-de-Bellevue, Quebec, H9X 3V9, Canada.
authors: Jacqueline
authors: J
authors: Goordial
authors: Department of Epidemiology, Harvard School of Public School, 677 Huntington Avenue, Boston, Massachusetts, 02115, United States of America.
authors: William P
authors: WP
authors: Hanage
authors: Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 4444 Forest Park Avenue, St. Louis, Missouri, 63108, United States of America; Department of Pathology and Immunology, Washington University School of Medicine, 4444 Park Forest Avenue, St. Louis, Missouri, 63108, United States of America.
authors: Gautam
authors: G
authors: Dantas
authors: FAS Center for Systems Biology, Harvard University, 52 Oxford Street, Cambridge, Massachusetts, 02138, United States of America; Department of Evolutionary and Organismic Biology, Harvard University, 52 Oxford Street, Cambridge, Massachusetts, 02138, United States of America; Department of Physics, Harvard University, Cambridge, Massachusetts, 02138, United States of America.
authors: Michael M
authors: MM
authors: Desai
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D001110:Arctic Regions; D001419:Bacteria / Q000235:genetics / Q000302:isolation & purification*; D024881:Drug Resistance, Bacterial / Q000235:genetics*; D005798:Genes, Bacterial / Q000187:drug effects*; D056186:Metagenomics; D012987:Soil; D012988:Soil Microbiology
chemical_list: D000900:Anti-Bacterial Agents; D012987:Soil