Nav: Home

Microbiome diversity is influenced by chance encounters

March 03, 2017

CAMBRIDGE, MA 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.

A new study of the microbe populations of worms offers another factor that may contribute to this variation: chance.

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.

"This study shows that you can have heterogeneity that's driven by the randomness of the initial colonization event. That's not to say the heterogeneity between any two individuals has to be driven by that, but it's a potential source that is often neglected when thinking about this variation," says Jeff Gore, the Latham Family Career Development Associate Professor of Physics at MIT.

Gore is the senior author of the study, which appears in the March 3 issue of the journal PLOS Biology. The paper's lead author is MIT postdoc Nicole Vega.

A simple model

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.

"We know that gut communities are different within different individuals, and that this could have really important implications for health and disease, but it's often difficult to figure out the origin of this diversity between different individuals," Gore says.

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.

"What you would like to do is take a bunch of identical individuals, place them in identical environments, and then look to see whether the microbial communities are the same or different. That's a very difficult experiment to do with people, but with model organisms it's feasible," Gore says.

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.

"Whichever color bacteria is lucky and happens to survive getting eaten and sticks to the gut, this bacterium starts growing, and it can grow to dominate the gut community," he says.

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.

An overlooked source

The researchers also found the same effect when they fed the worms two different species of bacteria: Enterobacter aerogenes and Serratia marcescens.

Gore says that 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, he says.

"I don't believe that stochastic colonization is the only or dominant source of heterogeneity between individuals, but I think it's a source of heterogeneity that is often overlooked," Gore says.

His lab is now studying many different pairs of bacterial species in the worm gut to see if the outcome of competition between two species can be used to predict the outcome when three or more species are competing.
-end-
The research was funded by the National Institutes of Health, the National Science Foundation, a Pew Fellowship, and a Sloan Foundation Fellowship.

Massachusetts Institute of Technology

Related Bacteria Articles:

Conducting shell for bacteria
Under anaerobic conditions, certain bacteria can produce electricity. This behavior can be exploited in microbial fuel cells, with a special focus on wastewater treatment schemes.
Controlling bacteria's necessary evil
Until now, scientists have only had a murky understanding of how these relationships arise.
Bacteria take a deadly risk to survive
Bacteria need mutations -- changes in their DNA code -- to survive under difficult circumstances.
How bacteria hunt other bacteria
A bacterial species that hunts other bacteria has attracted interest as a potential antibiotic, but exactly how this predator tracks down its prey has not been clear.
Chlamydia: How bacteria take over control
To survive in human cells, chlamydiae have a lot of tricks in store.
More Bacteria News and Bacteria Current Events

Best Science Podcasts 2019

We have hand picked the best science podcasts for 2019. Sit back and enjoy new science podcasts updated daily from your favorite science news services and scientists.
Now Playing: TED Radio Hour

Teaching For Better Humans
More than test scores or good grades — what do kids need to prepare them for the future? This hour, guest host Manoush Zomorodi and TED speakers explore how to help children grow into better humans, in and out of the classroom. Guests include educators Olympia Della Flora and Liz Kleinrock, psychologist Thomas Curran, and writer Jacqueline Woodson.
Now Playing: Science for the People

#535 Superior
Apologies for the delay getting this week's episode out! A technical glitch slowed us down, but all is once again well. This week, we look at the often troubling intertwining of science and race: its long history, its ability to persist even during periods of disrepute, and the current forms it takes as it resurfaces, leveraging the internet and nationalism to buoy itself. We speak with Angela Saini, independent journalist and author of the new book "Superior: The Return of Race Science", about where race science went and how it's coming back.