Sequencing unculturable bacteria

The birth of microbiology as we understand it arises from the ability to grow organisms under reasonably reproducible laboratory conditions – “culturing” them in the laboratory. If you can’t grow it, you can’t study it (Growing unculturable bacteria. (2012) Journal of Bacteriology, 194(16), 4151-4160).

The media today is reporting a new paper which describes single cell sequencing of 201 bacterial genomes from a range of environments, thus removing the need to be able to culture the organism before its genome can be sequenced:

Sequencing unculturable bacteria

This is good stuff. But the BBC News report of this story is dreadful – it makes it sound as if sequencing bacterial genomes is new in some way. Some credit to the BBC – for once the online item contains a direct link to the actual Nature paper (which you probably can’t read unless you work in a scientific organisation with a Nature subscription).

The Nature News report is a little better, but still fails to clarify the concept that many if not most bacterial species may be unculturable, reporting the article as Researchers glimpse microbial ‘dark matter, pissing at least one commenter off by over-dramatising the subject (Nature News items generate so few comments that if someone does comment, you know they’re angry).

So interesting science, bad media coverage. I guess you’ll have to read the paper for yourself (if you’re luck enough to have a a Nature subscription). And of course, keep reading specialist microbiology blogs if you want to really understand the significance of current scientific research in a larger context.


Insights into the phylogeny and coding potential of microbial dark matter. (2013) Nature doi:10.1038/nature12352
Genome sequencing enhances our understanding of the biological world by providing blueprints for the evolutionary and functional diversity that shapes the biosphere. However, microbial genomes that are currently available are of limited phylogenetic breadth, owing to our historical inability to cultivate most microorganisms in the laboratory. We apply single-cell genomics to target and sequence 201 uncultivated archaeal and bacterial cells from nine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life, so-called ‘microbial dark matter’. With this additional genomic information, we are able to resolve many intra- and inter-phylum-level relationships and to propose two new superphyla. We uncover unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the three domains of life. These include a novel amino acid use for the opal stop codon, an archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea similar to those in Bacteria. The single-cell genomes also served to phylogenetically anchor up to 20% of metagenomic reads in some habitats, facilitating organism-level interpretation of ecosystem function. This study greatly expands the genomic representation of the tree of life and provides a systematic step towards a better understanding of biological evolution on our planet.


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