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Race-Linked Microbiome Changes Detected in Babies

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A new study from Washington University in St. Louis investigated the racial differences in gut microbiome composition in children from birth to 12 years of age. The research has been published in PLOS Biology.

Racial differences in the human gut microbiome

The gut microbiome consists of all the microorganisms that exist within the gastrointestinal tract. Heavily implicated in human health, this large community has been associated with various diseases, including arthritis, Alzheimer’s disease and cancer.

Development of the gut microbiome occurs throughout an individual's life, influenced by genetic and environmental factors. Rapid development can be observed during the first two years of a person's life and this period is vital for setting up microbiome composition in adulthood, says first author Dr. Elizabeth Mallott, adding that, “it could be setting people up for various diseases.”

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In the United States (US), the composition of the adult gut microbiome has been found to correlate with race and ethnicity, despite there being no genetic or biological reason for this. “The age at which microbiome variability emerges between these groups remains a central gap in knowledge,” said Mallott.

The researchers set out to investigate at what point during a child’s development are disparities in microbiome diversity detectible.

The critical window occurs at three months of age

The researchers gathered datasets from 8 previous studies that had obtained 2756 gut microbiome samples from 729 US children.

All eight datasets included 16S rRNA sequencing data for the samples, and race and ethnicity metadata. Machine learning approaches were utilized to analyze the data.

Mallott and the research team discovered that variations “are not present at birth, or even shortly after”, but appear to arise at three months of age and persist throughout childhood.


Only 2 of the 82 microbes that were defined as differing due to race or ethnicity were maternally transmitted, suggesting that “the vast majority are all microbes that we acquire from the environment,” the researchers say. These results point towards the many socioeconomic differences between races seen in the US such as culture, diet and access to health care and education as contributing factors.

“A lot happens in the life of a child between 3 and 9 months,” Mallott said. “If kids are going to go into group daycare settings, that’s usually when it starts. That’s also when we typically start introducing solids into children’s diets. There could be differences in how, when and why different solid foods are introduced.”

“Even outside of day care, beyond 3 months is when a child starts being integrated into their communities,” she added. “There are differences in how many family members, friends and caregivers a child is in contact with. And this is when infants start to become more mobile and explore their environments.”

Early life experiences impact future health

The research demonstrates the impact of a child’s environment on their long-term health and well-being and how this may cause health disparities between races during adulthood.


Further studies are needed to understand the effects of gut microbiome variations and how we can utilize this information to provide better care for children of all races and ethnicities. Dr Seth Bordenstein, corresponding author, commented, “We want to eventually translate diverse microbiome discoveries into shaping the future of health precision, policy and equity across the diversity of all of us.”

Reference: Mallott EK, Sitarik AR, Leve LD, Cioffi C, Camargo CA, Jr, Hasegawa K, et al. Human microbiome variation associated with race and ethnicity emerges as early as 3 months of age. PLoS Biol. 2023. 21(8): e3002230. doi: 10.1371/journal.pbio.3002230

This article is a rework of a press release issued by Washinton University in St. Louis. Material has been edited for length and content.