Virus hotspot: the human gut

Australian and US researchers have identified 54,118 viruses in human poo samples, 92% of which weren’t described in existing databases.

Most of the viruses are harmless to humans, with 75% of them being “phages” – viruses that infect bacterial cells, not human cells.

“The most intensively studied ecosystem on the planet is our own gut,” says Phil Hugenholtz, a professor of microbiology and microbial evolution at the University of Queensland (UQ), and co-author on a paper, published in Nature Microbiology, describing the research.

“What’s really emerging in the last five to 10 years in particular, is that the microorganisms in our gut are really essential to our health and wellbeing, [and] there have been tens of thousands of stool samples which have been analysed.

“So we have a ton of data, but mostly what’s been looked at up until this point are bacteria. We know that there’s a bunch of viral diversity, but that hasn’t really been looked at in huge detail.”

The researchers created a “metagenomic catalogue” from 11,810 human stool samples in public databases.

Metagenomics is a method of sequencing and identifying environmental DNA from a range of organisms, rather than isolating and identifying the DNA from one thing at a time.

Though less precise, it’s a faster way to find new species because it dodges the “cultivation bottleneck” – the lab work required to grow a single type of virus or bacterium.

“We expected that there would be a bunch of species we’ve never seen before,” says Hugenholtz.

The UQ researchers assisted scientists from the Joint Genome Institute in the US with the sorting and identification of the viral DNA.

“Our specific involvement in the paper was to classify these hundreds of thousands of viruses that had been mined out of the public faecal metagenome database,” says Hugenholtz.

“The current classification system is based on features that are not good markers of evolution, so we were interested to try to use the genomes of the viruses in order to classify them more accurately.”

He says the new viral catalogue is more than just a “stamp-collecting exercise”: the viruses revealed could be useful in fighting antibiotic resistance.

Most of the viruses found were phages, which have been proposed as a way to fight bacterial infections for more than a century, but haven’t until now been as effective as antibiotics.

“Phage therapy has come back into vogue, because we’re getting a lot of antibiotic-resistant microbes,” says Hugenholtz.

“Think of it like the difference between a homing missile and napalm. Antibiotics napalm the whole forest, and this is more like a targeted missile that will go in and take out a particular organism.”

This article written by Cosmos is published under a Creative Commons license and can be republished online or in print for free with or without modification, provided you credit the authors (Cosmos).

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