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How to train your microbe: metatranscriptomics as a care and feeding guide

If you work in microbiology, you know the statistics: as many as 99% of bacterial species have yet to succumb to science’s best efforts to cultivate them. In mBio this week, a new approach to cultivating these reluctant microbes reads the metatranscriptome – the RNA a community of bacteria makes as a blueprint for making their proteins – for guidance on what those bacteria might eat.

Bomar et al. successfully used the metatranscriptome as a care and feeding guide for a Rikenella-like bacterium that dominates the gut of a medicinal leech, Hirudo verbana. The authors focused their analysis on highly expressed genes that encode hydrolytic enzymes, binding proteins, and transporters in an attempt to discern what the dominant players in the gut might enjoy as sustenance. With this knowledge in hand, the authors created a designer medium for their target, rich with the favored substrate, mucin. As confirmed by diagnostic PCR, they were able to isolate a few strains of the Rikinella-like bacterium in pure liquid culture and as colonies on plates.

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