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Venter Introduces the Mini-metagenome

Kayt Sukel

Sequencing the genomes of rare bacteria that cannot be grown in the lab has been close to impossible, until J. Craig Venter and company took a swab at it. Find out how they did it...

They call it the “dark matter of life”—the scores of bacterial species ranging from microorganisms in the water to microbes within the body that remain an enigma to scientists because they cannot be cultured in the laboratory. While genomic techniques that amplify DNA from a single cell provide interesting information about genetic variability, they often don’t capture the full genome of a rare bacterial species.

Circular representation of the TM6SC1 genome as a pseudomolecule derived from the concatenated contigs for MDA2. Source: PNAS

But now researchers at the J. Craig Venter Institute (JCVI) have taken those advances a step further, using a mini-metagenomic approach to successfully recover an estimated 90% of the genome for a previously uncultured phylum, TM6.

“We thought if we can pool say 20 or 100 cells together, we can maybe get 3 or 4 cells of a single species and reconstruct a more complete genome,” Jeffrey McLean, staff scientist at JCVI and lead author on the study published today in the Proceedings of the National Academy of Sciences. “It’s kind of the ‘Holy Grail’ of microbiology right now—we’re trying to find ways to isolate and then sequence the genomes of these rare bacteria that we’ve had no way to culture before.”

McLean and colleagues took a swab of a biofilm from a sink drain in a hospital restroom and used an automated single cell genomics platform to sort the cells in the mix. The group then amplified the DNA of random pools of sorted cells to create what the researchers call a mini-metagenome.

“Once we amplify, we can see what’s in the well. In this case, we hit some sequences for TM6,” said McLean. “Once we saw that, we know it was very likely that we had some of the genome in there, and we did some deep sequencing after that.”

The team was then able to reconstruct approximately 90% of the genome for this rare phylum, suggesting that it is possible for researchers to use this technique to work backwards to understand more about the dark matter of life.

“This technique is a very nice bridge between single cell genomics and metagenomic techniques. We hope to capture more lower abundant species and reconstruct them better than we’ve ever had the ability to do before,” said McLean.

The group plans to test the technique in other environments—and, with luck, figure out how to culture TM6 and other rare species so that they can study them more closely in the laboratory.

“It’s exciting. This can help us to better understand the diversity of life that is present in our environment,” he said. “We’re just starting to learn about all these different bacteria we may be exposed to at a hospital or in other environments. So by doing this kind of work we may be able to identify and better understand potential emerging pathogens.”


1. McLeana, J.S., M.J. Lombardo, J.H. Badger, A. Edlund, M. Novotny, J. Yee-Greenbaum, N. Vyahhic, A.P. Hall, Y. Yang, C.L. Dupont, M.G. Zieglerd, H. Chitsaz, A.E. Allen, S. Yooseph, G. Tesler, P.A. Pevzner, R.M. Friedman, K.H. Nealson, J.C. Venter, and R.S. Lasken. 2013. Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum. PNAS. [online 10 June 2013]

Keywords:  metagenomics microbes