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By combining microbial culture experiments with genomic approaches, researchers from Wellcome Trust Sanger Institute and their colleagues have now shown that, contrary to the widely held assumption that most bacteria are “unculturable,” most known gut microbial species can be grown and preserved in vitro. The results, published in Nature, reveal that many “unculturable” gut bacteria belong to novel groups, and nearly 60 percent of them form spores in order to survive outside the human body.
To assess how much of the human gut microbiota could be cultured, the Sanger Institute’s Trevor Lawley and colleagues began with fresh fecal samples from six healthy individuals. The researchers sequenced the samples to identify bacterial diversity, grew bacteria from the samples on plates containing a broad-range growth medium called YCFA, and then compared the genomic data from the original samples to that from species that grew in the petri dishes.
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The two shared 72 percent of their genomic sequences, and sequences from the cultured bacterial colonies represented 39 percent of the genes present in a larger database of gut microbiomes of 318 individuals, the team reported. But the researchers found that to match the species detection levels possible by sequencing a fecal sample directly, more than 8 million bacterial colonies would have to be picked off plates.
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