Limits...
Mining microbial metatranscriptomes for expression of antibiotic resistance genes under natural conditions.

Versluis D, D'Andrea MM, Ramiro Garcia J, Leimena MM, Hugenholtz F, Zhang J, Öztürk B, Nylund L, Sipkema D, van Schaik W, de Vos WM, Kleerebezem M, Smidt H, van Passel MW - Sci Rep (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.

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.

No MeSH data available.


Related in: MedlinePlus

Relative cumulative expression of antibiotic resistance genes in different ecological niches.The relative expression is based on the total of number of reads that aligned to genes of the RED-DB, and calculated as a percentage of the non-ribosomal RNA reads. Error bars represent one standard deviation.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4495384&req=5

f1: Relative cumulative expression of antibiotic resistance genes in different ecological niches.The relative expression is based on the total of number of reads that aligned to genes of the RED-DB, and calculated as a percentage of the non-ribosomal RNA reads. Error bars represent one standard deviation.

Mentions: Reads from metatranscriptome datasets from seven different ecological niches (human, mouse and pig intestinal microbiota, sea bacterioplankton, a marine sponge, forest soil and sub-seafloor sediment) were compared with genes from the resistance determinants database (RED-DB, www.fibim.unisi.it/REDDB) using megaBLAST. Per niche, a cumulative total was obtained for reads mapping to the different resistance genes, with the requirement that ≥3 reads aligned per gene. In order to allow for comparison of gene expression in different datasets, we determined the relative abundance of resistance gene transcripts as a percentage of the total number of non-ribosomal RNA reads. Expression of resistance genes was detected in all seven ecological niches (Fig. 1), of which only the pig microbiota was knowingly exposed to antibiotics (i.e. a mixture of neomycin and procaine benzylpenicilline) approximately two to four weeks prior to taking the samples used for RNA extraction. Highest relative expression levels were observed in the sea bacterioplankton sample (0.7%), whereas resistance gene transcripts comprised less than 0.06% of the reads in the other investigated niches. For human adults and pigs relative abundance of resistance gene transcripts was in the same order of magnitude (0.009% ± 0.014 and 0.028% ± 0.012 [s.d.], respectively), whereas it was more than 15-fold lower in mice (4.4 × 10−4% ± 6.8 × 10−4) and the human infant (5.7 × 10−4%).


Mining microbial metatranscriptomes for expression of antibiotic resistance genes under natural conditions.

Versluis D, D'Andrea MM, Ramiro Garcia J, Leimena MM, Hugenholtz F, Zhang J, Öztürk B, Nylund L, Sipkema D, van Schaik W, de Vos WM, Kleerebezem M, Smidt H, van Passel MW - Sci Rep (2015)

Relative cumulative expression of antibiotic resistance genes in different ecological niches.The relative expression is based on the total of number of reads that aligned to genes of the RED-DB, and calculated as a percentage of the non-ribosomal RNA reads. Error bars represent one standard deviation.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4495384&req=5

f1: Relative cumulative expression of antibiotic resistance genes in different ecological niches.The relative expression is based on the total of number of reads that aligned to genes of the RED-DB, and calculated as a percentage of the non-ribosomal RNA reads. Error bars represent one standard deviation.
Mentions: Reads from metatranscriptome datasets from seven different ecological niches (human, mouse and pig intestinal microbiota, sea bacterioplankton, a marine sponge, forest soil and sub-seafloor sediment) were compared with genes from the resistance determinants database (RED-DB, www.fibim.unisi.it/REDDB) using megaBLAST. Per niche, a cumulative total was obtained for reads mapping to the different resistance genes, with the requirement that ≥3 reads aligned per gene. In order to allow for comparison of gene expression in different datasets, we determined the relative abundance of resistance gene transcripts as a percentage of the total number of non-ribosomal RNA reads. Expression of resistance genes was detected in all seven ecological niches (Fig. 1), of which only the pig microbiota was knowingly exposed to antibiotics (i.e. a mixture of neomycin and procaine benzylpenicilline) approximately two to four weeks prior to taking the samples used for RNA extraction. Highest relative expression levels were observed in the sea bacterioplankton sample (0.7%), whereas resistance gene transcripts comprised less than 0.06% of the reads in the other investigated niches. For human adults and pigs relative abundance of resistance gene transcripts was in the same order of magnitude (0.009% ± 0.014 and 0.028% ± 0.012 [s.d.], respectively), whereas it was more than 15-fold lower in mice (4.4 × 10−4% ± 6.8 × 10−4) and the human infant (5.7 × 10−4%).

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.

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.

No MeSH data available.


Related in: MedlinePlus