Your microbiome shapes your life, but where does it come from?

Collaborative research led by Carnegie's William Ludington has revealed key details of how the bacterial communities that make up each of our individual gut microbiomes are acquired
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The findings, published in the Proceedings of the National Academy of Sciences, have important implications for treatments such as fecal transplants and probiotic management

Ludington explained: "There are huge differences in the composition of the microbiome between individuals
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For example, if you look at the sum of all the bacterial species that are adapted to live in the human gastrointestinal system, most people do not have these bacteria

A combination of factors, including genetics, diet, and the environment, contribute to the differences between our microbiomes
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However, there is no direct link between these inputs and the species that successfully occupy our guts

Although many researchers have studied microbial community composition in natural populations, few have attempted to use controlled environments to uncover the processes by which new species successfully join the gut microbial ecosystem
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Ludington and his collaborators -- Eric Jones and David Sivak of Simon Fraser University and Jean Carlson of the University of California, Santa Barbara -- have developed a new ecological model to understand how we obtain specific combinations of microbes that are responsible for Our specific gut flora is individual

Studies in the relatively uncomplicated microbial community of Drosophila have shown that exposure to a microbial species does not guarantee its successful integration into the microbial community ecosystem
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They found that the state of the microbiome, as well as interactions between existing microbiome member species, determined whether newly encountered bacteria were added to the mix

"Even among genetically identical flies, living in the same housing and eating the same food, we saw changes in the composition of the microbiome," Sivak said
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The researchers then used these results to build mathematical models that could explore increasingly complex scenarios through which new microbial community species could be obtained, giving them a breakthrough understanding of the community factors that shape microbial community ecosystem membership
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"Think of the composition of the microbiome as a large gathering, where social dynamics determine who leaves early and stays until dawn," Ludington said
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Jones, lead author of the paper, added: "Bacterial colonization depends on complex factors that we are just beginning to understand
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For example, we found that some groups of species promote colonization of each other and are therefore more likely to coexist

These intergroup interactions have exciting implications for how the microbiome spreads between individuals, including how medical professionals can push a person's microbiome toward a desired composition

"The beauty of the mathematical approach we took is that it acknowledges that colonization is a dice, but we are now able to attribute the weight of the dice to biological interactions, the molecular basis that has been honed by evolution," Fraser said

The team's findings provide a framework for quantitatively studying the mechanisms upon which therapies such as fecal transplants and probiotics rely, moving toward the ultimate goal of personalized microbiome medicine

Stochastic microbiome assembly depends on context Proceedings of the National Academy of Sciences