Gut Microbiome Speedometers

S. C.P. Williams 09/21/2015

BioTechniques Newsletter (http://www.biotechniques.com/news/)

A new method can detect the growth rates of gut bacteria using a single metagenomics sample, allowing researchers to show that growth rates are even better predictors of disease than bacterial abundance...

By comparing the abundance of different fragments of DNA in a metagenomics sample, researchers have discovered a new way to calculate the growth rate of any given bacterial species. Moreover, they’ve shown that the growth rate of species in the gut microbiome—not just the species’ prevalence—is correlated with disease conditions, including diabetes and inflammatory bowel disease.

“I think having another lens through which we can focus and look at metagenomics samples, beyond just their composition, is going to be very beneficial,” said Eran Segal of the Weizmann Institute, one of the senior authors of the new study published in Science. While mapping genes from metagenomics samples, Segal and his colleagues noticed a sinusoidal shape in prevalence patterns of genes in some organisms. The pattern, they realized, reflected replicating DNA, with the peak of the curve—where gene material was most prevalent—representing the origin of replication for the bacterial genome.

The researchers then determined that the origin of replication—previously unknown for some species—wasn’t the only information they could get out of these prevalence curves. By calculating the ratio of the peak of the curve to the tail ends, they could determine the exact growth rate of the bacterial strain at the time the single metagenomic snapshot was taken. “The ratio of the peak and the terminus really varied between people, so that was an indication that the same bacteria might be growing at different rates between people,” said Segal. Indeed, when his group looked more closely at the growth rates, they found that they differed in people with diabetes or inflammatory bowel disease, and changed in mice after doses of antibiotics.

“What was interesting for these bacteria was that prevalence wasn’t associated with the disease phenotype, but the growth rate was,” said Segal. Why isn’t the growth rate simply reflected in the abundance of a species? Some bacteria may be growing fast but are outcompeted by another bacteria growing even faster, Segal point out. And other bacteria may be dying.

Segal and his colleagues created software for calculating growth rates and made it available online for other researchers. They are planning to use it to follow up on the utility of growth rate as a diagnostic or prognostic tool in clinical settings.

Ref

Korem et al. 2015. Growth dynamics of gut microbiota in health and disease inferred from single metagenomics sample. Science doi: 10.1126/science.aac4812