Cultured microorganisms have been the source of almost all characterized antibiotic-resistance genes. Yet these microorganisms represent only a tiny fraction of microbial diversity, limiting access to the potentially vast reservoir of undiscovered antibiotic-resistance determinants harboured by uncultured bacteria. A report published in Environmental Microbiology describes the use of metagenomic analysis to explore this reservoir in uncultured soil bacteria — an analysis that has revealed the presence of antibiotic-resistance genes considerably different from previously reported sequences.

The approach adopted by Jo Handelsman and colleagues was to isolate DNA directly from soil samples, clone the DNA and select for expressed antibiotic resistance in Escherichia coli. Four libraries were constructed containing 4.1 gigabases of cloned soil DNA and, from analysis of these libraries and two previously reported libraries, ten clones expressing antibiotic resistance were identified. From preliminary screening of these clones and subsequent sequence analysis, the authors identified nine aminoglycoside-resistance genes and one gene encoding a tetracycline-efflux protein. The sequence analysis also revealed that the resistance mechanisms used by these proteins included the inactivation of aminoglycoside antibiotics by phosphorylation and acetylation, as well as the efflux of tetracycline. Interestingly, nine out of the ten resistance proteins identified were found to have less than 60% identity to previously published sequences, clearly suggesting that soil microorganisms harbour antibiotic-resistance genes with significantly more genetic diversity than indicated by previous studies.

The study of Riesenfeld et al. provides an insightful snapshot of the power of metagenomic analysis in unlocking the biological potential of the uncultivatable bacterial community. Harnessing that potential in the search for new antibiotic entities remains the ongoing goal.