title: Mining microbial metatranscriptomes for expression of antibiotic resistance genes under natural conditions.
abstract: Antibiotic resistance genes are found in a broad range of ecological niches associated with complex microbiota. Here we investigated if resistance genes are not only present, but also transcribed under natural conditions. Furthermore, we examined the potential for antibiotic production by assessing the expression of associated secondary metabolite biosynthesis gene clusters. Metatranscriptome datasets from intestinal microbiota of four human adults, one human infant, 15 mice and six pigs, of which only the latter have received antibiotics prior to the study, as well as from sea bacterioplankton, a marine sponge, forest soil and sub-seafloor sediment, were investigated. We found that resistance genes are expressed in all studied ecological niches, albeit with niche-specific differences in relative expression levels and diversity of transcripts. For example, in mice and human infant microbiota predominantly tetracycline resistance genes were expressed while in human adult microbiota the spectrum of expressed genes was more diverse, and also included β-lactam, aminoglycoside and macrolide resistance genes. Resistance gene expression could result from the presence of natural antibiotics in the environment, although we could not link it to expression of corresponding secondary metabolites biosynthesis clusters. Alternatively, resistance gene expression could be constitutive, or these genes serve alternative roles besides antibiotic resistance.
authors.affiliation: Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
authors.forename: Dennis
authors.initials: D
authors.lastname: Versluis
authors.affiliation: Department of Medical Biotechnologies, University of Siena, Italy.
authors.forename: Marco Maria
authors.initials: MM
authors.lastname: D'Andrea
authors.affiliation: 1] Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands [2] Top Institute Food and Nutrition, Wageningen, The Netherlands.
authors.forename: Javier
authors.initials: J
authors.lastname: Ramiro Garcia
authors.affiliation: 1] Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands [2] Top Institute Food and Nutrition, Wageningen, The Netherlands.
authors.forename: Milkha M
authors.initials: MM
authors.lastname: Leimena
authors.affiliation: 1] Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands [2] Top Institute Food and Nutrition, Wageningen, The Netherlands [3] Netherlands Consortium for Systems Biology, University of Amsterdam, The Netherlands.
authors.forename: Floor
authors.initials: F
authors.lastname: Hugenholtz
authors.affiliation: Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
authors.forename: Jing
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
authors.forename: Başak
authors.initials: B
authors.lastname: Öztürk
authors.affiliation: 1] Functional Foods Forum, University of Turku, Turku, Finland [2] Department of Veterinary Biosciences, University of Helsinki, Finland.
authors.forename: Lotta
authors.initials: L
authors.lastname: Nylund
authors.affiliation: Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
authors.forename: Detmer
authors.initials: D
authors.lastname: Sipkema
authors.affiliation: Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
authors.forename: Willem
authors.initials: W
authors.lastname: van Schaik
authors.affiliation: 1] Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands [2] Department of Veterinary Biosciences, University of Helsinki, Finland [3] Department of Bacteriology and Immunology, Haartman Institute, University of Helsinki, Finland.
authors.forename: Willem M
authors.initials: WM
authors.lastname: de Vos
authors.affiliation: 1] Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands [2] Top Institute Food and Nutrition, Wageningen, The Netherlands [3] NIZO Food Research B.V., Ede, The Netherlands [4] Host-Microbe Interactomics Group, Wageningen University, Wageningen, The Netherlands.
authors.forename: Michiel
authors.initials: M
authors.lastname: Kleerebezem
authors.affiliation: 1] Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands [2] Top Institute Food and Nutrition, Wageningen, The Netherlands.
authors.forename: Hauke
authors.initials: H
authors.lastname: Smidt
authors.affiliation: 1] Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands [2] National Institute for Public Health and the Environment, Bilthoven, The Netherlands.
authors.forename: Mark W J
authors.initials: MW
authors.lastname: van Passel
mesh_terms: D000328:Adult; D000617:Aminoglycosides / Q000378:metabolism; D000818:Animals; D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D001419:Bacteria / Q000235:genetics / Q000378:metabolism; D001688:Biological Products / Q000494:pharmacology; D024881:Drug Resistance, Bacterial / Q000235:genetics*; D041981:Gastrointestinal Tract / Q000382:microbiology; D005798:Genes, Bacterial; D006801:Humans; D007223:Infant; D051379:Mice; D064307:Microbiota; D005810:Multigene Family; D061065:Polyketides / Q000378:metabolism; D013552:Swine; D013753:Tetracycline Resistance / Q000235:genetics; D059467:Transcriptome / Q000187:drug effects
chemical_list: D000617:Aminoglycosides; D000900:Anti-Bacterial Agents; D001688:Biological Products; D061065:Polyketides