Gut Bacteria Variation Among Human Social Groups Emerges by 3 Months of Age

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UNIVERSITY PARK, Pa. — Bacteria and other microorganisms that live within the human digestive tract — the gut microbiome — differ with parent-reported race and ethnicity as early as 3 months of age, according to a new study co-led by Penn State. The gut microbiome can influence health and disease risk, the researchers said, so understanding when and how variations arise could help science and medicine work for a much wider range of people. The study, led by a team of researchers from Penn State, Washington University in St. Louis and Vanderbilt University, appeared today (Aug. 17) in the open access journal PLOS Biology.

The gut microbiome contains a community of often-beneficial microorganisms that impacts a person’s health throughout their life. Penn State researchers previously reported that the diversity of bacterial species within the gut microbiome consistently correlates with self-reported race and ethnicity in adults in the United States. The evidence, researchers said, suggests this correlation is due to lived experiences with environmental or social factors rather than genetic or biological differences. According to the new study, those lived experiences could begin to influence the gut microbiome in early infancy.

“In the United States, social constructs such as race and ethnicity are a proxy for a variety of other factors, such as environmental exposures, stress, socioeconomic differences, culture, diet, and access to healthcare and education,” said Seth Bordenstein, Huck Chair in Microbiome Sciences, director of the One Health Microbiome Center at Penn State, and corresponding author of the new study. “Inequitable social and environmental influences due to structural racism are known to negatively impact health across the country. With this study, we set out to better understand when and how microbiome variations arise so that we can diversify the research, connect with social scientists, and in the long-term better mitigate potential health disparities.”

The research team analyzed 2,756 gut microbiome samples from 729 children between birth and 12 years of age, data collated from eight previous studies comprising the broadest representation of children’s microbiomes in the United States to date. They found that gut microbiome variation associated with parent-reported identities arises after 3 months of age and persists through childhood. These differences were not present at birth or shortly after. 

Although some bacteria within the gut microbiome can be acquired during birth or through close contact with the mother, such as breastfeeding, many others are accumulated as a person interacts with the world around them. Their life experiences dictate which bacteria species they encounter and, of those species, which remain a long-term part of their microbial community. The researchers found two microbial species that differed with either race or ethnicity came from the mother, but the majority were acquired from the environment.

“Microbiome composition early in life sets up composition in adulthood, so it could be setting people up for various diseases,” said Elizabeth Mallott, an assistant professor of biology in the College Arts and Sciences at Washington University and first author of the study. “Now that we know when the variation is occurring, we can look for the specific factors driving it and think about early interventions.”

Early life experiences can add up and result in tangible impacts to health, including changes to human physiology that contribute to health disparities. How the gut microbiome develops, the researchers said, is known to be associated with immune system development, metabolic programming, and antibiotic resistance as well as risk of asthma, allergic and autoimmune diseases. According to the researchers, clarifying the timing of when the variations emerge is important to understanding how the microbiome contributes to adult health and health disparities.

“Many changes occur in a child’s life between 3 and 9 months of age,” Bordenstein said. “They typically start to eat solid foods. They become more mobile and may start to attend group daycare and have more contact with family members, friends and caregivers. The nuances of when and how all of this occurs may ultimately lead to changes in the microbiome.”

The researchers found that both race and ethnicity account for small but statistically significant proportions of the variation in the composition of species within the gut microbiome. They also found that the abundance of multiple bacteria varied between self-reported racial and ethnic categories, several of which are also known to vary in adults. Of the 57 types of bacteria that varied in abundance between children of differing racial categories identified by their parents, 19 were previously identified as variable between adults.

“The analysis presented in this paper highlights that human microbiome studies have an urgent imperative to prioritize diversity and the social sciences in research from early life onward,” Bordenstein said. “We want to eventually translate microbiome discoveries into shaping the future of health precision, policy and equity across the diversity of all of us.”

In addition to Bordenstein and Mallott, the research team includes Alexandra Sitarik at Henry Ford Health; Leslie Leve and Camille Cioffi at the University of Oregon; and Carlos Camargo Jr. and Kohei Hasegawa at the Harvard Medical School. This work was supported by the Vanderbilt Microbiome Innovation Center, the One Health Microbiome Center in the Huck Institutes of the Life Sciences at Penn State, the National Institutes of Health, and University of Oregon College of Education.

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