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.

Expression of eukaryotic‐like protein in the microbiome of sponges

“…These two methods have been extensively used with microbial isolates or enriched communities (e.g. He et al 2010;Yi et al 2011;Giannoukos et al 2012;Peano et al 2013;Bhagwat et al 2014), but there is little information on their performance in host-symbiont systems (Moitinho-Silva et al 2014;Versluis et al 2015).…”

The multi-omics promise in context: from sequence to microbial isolate

“…Therefore, antibiotic resistance genes are also widespread; they can be extracted from multi-omics data (Medema & Fischbach 2015) and have recently been shown to be expressed in a broad range of different natural environments (Versluis et al 2015). Often, antibiotics show poor activity against oligotrophic and slow-growing organisms (Lewis 2007), many of which are potential targets for cultivation studies.…”

Appearance of synthetic vector-associated antibiotic resistance genes in next-generation sequences

“…199' ' 200' Funding( 201' The'study'was'supported'by'internal'funding. (1) (Pridmore$1987,$Jeffrey$and$Joachim$1991,$tetracycline$resistance$ (Quigley$and$ 323$ Reeves$1987),$chloramphenicol$resistance$ (Chang$et*al.$2015),$bleomycin$ 324$ resistance$ (Austin$et*al.$1990) (Song$et*al.$ 330$ 2006,$Koncan$et*al.$2007,$Chiang$et*al.$2005,$Perron$et$al.$2006,$Furlan$et*al.$ 331$ 2017 blaTEM$ARG,$originating$in$RSF2124$and$derived$directly$from$pBR322$(Bolivar$et*al.$1977a,$ 335$ Bolivar$et*al.$1977b (Benes$et*al.$1993,$Parke$1990 ,$open$ocean$derived$sea$ 452$ phytoplankton$ $and$marine$sponges$ (Versluis$et*al.$2015).$ 453$ This$is$unexpected,$with$the$study$authors$stating$'Surprisingly,*in*sea* 454$ bacterioplankton,*the*expression*of*AR*genes*was*more*than*one*order*of* 455$ magnitude*higher*than*in*any*other*ecological*niche. *It*was*comprised*of*two* 456$ highly*similar*β4lactamase*genes,*namely*blaTEM41*and*blaTEM4116…*The* 457$ blaTEM41*gene*is*commonly*present*in*cloning*vectors,*and*therefore*lab* 458$ contamination*can*be*suspected,*however,*this*possibility*is*disputed*by*the* 459$ fact*that*the*gene*is*detected*in*two*separate*marine*metatranscriptome* 460$ datasets*that*have*been*independently*generated.…”