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.
Highlights
Antibiotic resistance genes are found in a broad range of ecological niches associated with complex microbiota
Expression of resistance genes was detected in all seven ecological niches (Fig. 1), of which only the pig microbiota was knowingly exposed to antibiotics approximately two to four weeks prior to taking the samples used for RNA extraction
Our explorative metatranscriptome analysis showed that antibiotic resistance genes are present, and expressed in a broad variety of natural environments, exemplified here by samples derived from the intestinal tract of humans, mice, as well as from sea bacterioplankton, a marine sponge, forest soil and sub-seafloor sediment
Summary
Antibiotic resistance genes are found in a broad range of ecological niches associated with complex microbiota. Resistance gene expression could result from the presence of natural antibiotics in the environment, we could not link it to expression of corresponding secondary metabolites biosynthesis clusters. Metagenomic studies have revealed the presence of resistance determinants in environments as different as soil, gut, seawater, caves and glaciers[2,3,4,5,6,7,8]. Bacterial communities in these and other ecological niches contain particular subsets of antibiotic resistance determinants, and can be seen as natural reservoirs from where they can theoretically spread into other environments and previously non-resistant microbial www.nature.com/scientificreports/. We investigated the expression levels and richness of genes conferring resistance against ten types of antibiotics, and assessed local production of these antibiotics by investigating the expression of relevant secondary metabolite gene clusters
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