As Constant As A Colon

The massive community of microbes in our guts can be shaken up by assaults of antibiotics or drastic changes in diet. But what happens during peacetime? If you fast-forward through the years of a healthy adult, what happens to their resident microbes? At one level, the answer appears to be: surprisingly little. Over at The Scientist, I’ve written about a new study showing that gut bacteria communities are remarkably stable over time.  Here’s a taster:

We all have trillions of microbes inside our guts, which outnumber our own cells by a factor of 10. Now, a team from Washington University School of Medicine in St. Louis (WUSTL) has shown that this microscopic community is extraordinarily stable. In healthy people, once these microbes are established in the gut early in life, presumably due to contact from close family members, most strains are unwavering in their presence, staying in the gut for decades or longer.

“We have this part of ourselves that’s assembled from outside but stays inside for decades and decades, and it contributes to our uniqueness as individuals and our health,” said WUSTL’s Jeffrey Gordon who led the study.

Although the team only studied healthy adults, their results have big implications for our understanding of disease, Gordon added. Many studies have shown that conditions such as obesity or autoimmune disorders are associated with dramatic changes in the gut microbiota.  But, Gordon said, “if we don’t know what the normal variations are in healthy people, we can’t tell how an individual with disease deviates.”

If these communities are usually steady, it may be possible to monitor a person’s health by analyzing stool samples each year, said Jacques Ravel, a microbiologist from the University of Maryland School of Medicine who was not involved in the study. “This is the future of medicine: a genome once and a microbiome at each annual exam.”

Head over there for the full details:

Meanwhile, on Twitter, a few scientists has concerns with how some of the results have been interpreted. David Baltrus from the University of Arizona, who studies microbial evolution, sent me an email last night outlining his views. “It’s a good paper; details are messy. What slightly gets me about this article is the term ‘stability’,” he says, which risks portraying the bacterial communities in the guts as unchanging. However, lab experiments tell us that even in constant environments, individual strains of bacteria can evolve over time and do dramatically different things—consider Richard Lenski’s long-term evolution experiment, which I’ve written about before.

Even changing a single nucleotide (DNA letter) can dramatically alter a bacterium’s collection of traits—its phenotype. The change could turn off important genes, or make a strain resistant to antibiotics. “The term strain is used kind of loosely all the time, but if two nearly identical isolates have different phenotypes, I’d say they were different,” says Baltrus. On top of that, the team’s methods may have missed important genetic events that can have similarly big effects, like the movement of jumping genes.

“The whole genomes [of microbes] from a single individual are very similar over time, but there are still many regions that change,” says Baltrus. “Strains change over time when you focus on the trees in the forest, but stable if you see the forest instead of the trees.”

I asked Jeremiah Faith (the study’s first author) about this critique. “I again agree with this point,” he says. “It could be that over time your microbes would mutate to provide you with a different perturbation to your physiology.  But the evolution of a bacterial strain’s genome is most likely far less of a perturbation than the removal of that strain and replacement with a strain of the same species, which would probably have 1000 genes that are different.”