How genetics and environment could influence gut microbiome “signature”

The gut microbiome, though an intricate web of forces, plays a vital role in keeping people healthy. An individual’s genetics and birthplace could determine the makeup of the microbial community in their gut, according to research by a team of scientists from the Department of Energy's Pacific Northwest National Laboratory (PNNL) and Lawrence Berkeley National Laboratory.

Early life history and genetics both play a role in building the gut microbiome, says Janet Jansson, director of biological sciences at PNNL and co-author of the study. In its findings, scientists linked the specific genes in an animal—a mouse, in this case—to the presence and abundance of specific microbes in its gut. The group determined that both genetics and early environment play a strong role in determining an organism's microbiome.

Some genes in mice are very similar to humans, in particular those that are involved in development of chronic diseases, such as arthritis, colon cancer, and diabetes. Additionally, the researchers found indications that moderate shifts in diet play a role in determining exactly what functions the microbes carry out in the gut.

Researchers initially studied more than 50,000 genetic variations in mice and identified more than 100 factors that affect the population of microbes in the gut. They focused on 30 strains of the mice, to capture the genetic variation in human populations, which were housed in two facilities with different environments for four weeks after they were born. The researchers took fecal samples from the mice to analyze their gut microbiomes before transferring them to a third facility.

The microbiome retained a clear microbial signature formed where the mice were first raised, which scientists referred to as their “hometown.” Further, the microbial trait carried over to the next generation.

The first dose of microbes ones gets comes from the mom, and that remains a strong influence for a lifetime. The early life environment was found to significantly affect the formation of an individual’s microbiome.

The abundance of a probiotic strain of Lactobacillales, in particular, was affected by several host genes and was linked to higher levels of helper T cells. These results support the role of the microbiome in the body’s immune response and the possibility that controlling the microbes in the gut could influence an individual’s immune system and disease vulnerability.

The microbiome is thought to help fight infections, says Antoine Snijders, research scientist in biological systems and engineering at Berkeley Lab. The level of helper T cells in the blood of mice is connected to the level of Lactobacillales in the gut, which is in the same family of bacteria found in yogurt and is often used as a probiotic.

In the future, people could have specific diets optimized according to their genes and their microbiome, says Jasson. This could allow individuals to digest foods more effectively or to modulate their susceptibility to disease.