Sturdy as a Rock

William Langhorne | January 22, 2019

Sturdy as a Rock

Scientists discover properties of stable microbiome populations

Studying the interactions within ecological communities can reveal fascinating insights into how nature is organized. At the macroscopic level, we marvel at the relationships between the flora and fauna of rainforests and coral reefs, but interactions at the microscopic level can be just as captivating.

In a paper recently published in Science, nine researchers, including Yale Professor Alvaro Sanchez, successfully observed and measured some of the fundamental quantitative principles governing the ecological architecture of microbial communities. By uncovering these rules, the researchers have taken an important step towards developing a theory of the microbiome.

The researchers began by collecting a dozen microbial communities from soil and plant samples. Each naturally-occurring microbial ecosystem was composed of unique varieties of bacterial species from many different families. The researchers then mapped the genetic makeup of these communities and placed them in a broth where their only food source was glucose sugar. After approximately 80 generations, nearly all the communities reached equilibrium. Even though the starting composition of bacteria differed, the researchers observed similar family-level community structures emerging in each community.

The researchers then reproduced this experiment with eight replicates of the original twelve microbiomes. This time, however, they provided the microbiomes with alternative carbon food sources instead of glucose. After observing the communities assemble, the researchers used machine learning to predict with 97 percent accuracy what food source the microbiomes had been raised on. This demonstrated that it was possible to quantitatively describe the development of these microbiomes.

The results raised questions about traditional consumer-resource models, which predict that when different species compete over a resource, a single species will dominate. Instead, the researchers observed competitor species coexisting on a single food source.

Professor Daniel Segrè, one of the researchers from Boston University, compared the microbiomes to factory networks that may process a single resource, like wood, to create different products. “One species will make a table, one will make tools, and so on,” Segrè said. “Then, they exchange these products with each other, and even if the initial raw material disappears each of them can survive.”

The researchers concluded that stable microbiomes, which can have multiple competitor species in coexistence, are composed of “metabolic generalists”—bacteria that can intake both the provided carbon food source and secondary secretions from other bacteria.

Determining how microbial communities stabilize could be an important step in understanding how to reduce imbalances in human gut bacteria. A disruption of microbial equilibrium in a person’s gut renders them susceptible to numerous medical conditions, including inflammatory bowel disease and irritable bowel syndrome.

Although the research did not measure how factors such as pH and more complex food sources might affect the stability of these communities, the use of mathematical modeling to unravel the intricacies of microbial ecosystems offers a promising step towards a quantitative theory of the microbiome.