Microbiome diversity is influenced by chance encounters

Within the human digestive tract, there are trillions of bacteria, and these communities contain hundreds or even thousands of species. The makeup of those populations can vary greatly from one person to another, depending on factors such as diet, environmental exposure, and health history. Variations in the human gut microbiome have been shown to contribute to gastrointestinal disorders such as colitis and Crohn's disease, and studies suggest that microbiome composition can also influence diabetes, heart disease, and cancer.

A new study of the microbe populations of worms offers another factor that may contribute to this variation: chance. Here MIT researchers found that when they put genetically identical worms into identical environments and fed them the same diet, the worms developed very different populations of bacteria in their gut, depending on which bacteria happened to make it there first.

The researchers chose to study the worm C. elegans because it is among the simplest animals with a digestive tract colonized by bacteria, offering a way to model what might be happening in the human gut. C. elegans consume bacteria as part of their normal diet, so the researchers first fed a group of genetically identical worms a mix of six different species of bacteria. When the experiment began, the worms had no bacteria in their digestive tracts, but after being exposed to the identical bacterial diet, the worms each generated very different microbe populations in their guts.

The researchers explored this further by feeding the worms a mix of only two types of bacteria, making it easier to study their interactions. In this scenario, all of the bacteria were E. coli, but half were engineered to produce a green fluorescent protein and the other half produced a red fluorescent protein.

After a week of this diet, each worm had about 30,000 bacteria in its digestive tract. However, these populations were not evenly divided between red and green. Instead, each population was dominated by one or the other. This happens, Gore says, because the initial colonization of the gut is a rare event, so whichever microbe makes it there first tends to dominate the entire population.

This randomness tends to prevail when the colonization rate is low. When the researchers fed the worms larger amounts of bacteria, the colonization rate went up and the researchers found much less variation among individuals' microbe populations. The researchers also found the same effect when they fed the worms two different species of bacteria: Enterobacter aerogenes and Serratia marcescens.

This random variability may contribute to the differences in microbe populations seen in the human gut as well, since usually only a small fraction of bacteria consumed by humans and other animals survives the digestion process. However, many other factors such as environmental exposure also play roles.

See:

Nicole M. Vega, Jeff Gore. Stochastic assembly produces heterogeneous communities in the Caenorhabditis elegans intestine. PLOS Biology, 2017; 15 (3): e2000633 DOI: 10.1371/journal.pbio.2000633



Posted by Dr. Tim Sandle