Ecological and Evolutionary Science

The Composition of a Human Infant’s Gut Microbiome Can Predict Cognitive Development by Age 2

Infants with relatively high levels of the bacterial genus Bacteriodes and less diverse gut microbiomes had better cognitive scores at age 2 than infants without high levels of Bacteriodes and diverse gut microbiomes say researchers at the University of North Carolina at Chapel Hill.

“This is the first study to show that [human] cognitive development is associated with the [gut] microbiome and so it’s the very first step,” said Alexander Carlson, first author of the study.  “We’re not really at the point where we can say, ‘Let’s give everyone a certain probiotic’ but we did have a few big takeaways from what we found.  One was that, when measuring the microbiome at age one, we already see the emergence of adult-like gut microbiome communities, which means that the ideal time for intervention would be before age one.”

The surprise was that children with less diverse microbiomes did better on cognitive tests at age two than children with more diverse microbiomes, because low diversity in the gut microbiome in infancy is associated with Type 1 diabetes, asthma, and other negative health outcomes.

“Our work suggests that an ‘optimal’ microbiome for cognitive and psychiatric outcomes may be different than an optimal microbiome for other outcomes,” said Dr. Rebecca Knickmeyer, the study’s senior author.

The team, which did its work in Knickmeyer’s lab, collected fecal samples from 89 typically developing one-year olds.  They analyzed the samples and formed three different groups based on similarities in their microbial communities.  The children’s cognitive development was assessed at age two with the Mullen Scales of Early Learning that examine fine and gross motor skills, perceptual abilities, and language development.  They also looked at the brain volumes of the participants at one and two years of age using structural MRIs and found no significant differences between the groups.

The study raised as many questions as it answered.  Are the bacteria actually communicating with the developing brain?  Are signaling pathways involved?  Is the bacterial community just representing another process that influences brain development, like diet?  Are other aspects of child development reflected in the gut microbiome, such as the emergence of social skills and anxiety?  The team will orient its future research to address these topics.

For more information, go to Biological Psychiatry; DOI:

Original Article can be found here:


1 Comment

Alexandra Linz

2017-07-20 11:16:05

This looks like another case of overselling the microbiome to me. The paper itself states "This study does not attempt to address a causative role in the observed relationships, but is an important translational starting point." It is very possible that there are other variables leading both to decreased fecal microbiome diversity and increased performance on the Mullen Scales of Early Learning - for example, variables found to co-vary with diversity and intelligence in Fig 3 include having older siblings, parental ethnicity, sex, maternal education, paternal age, twin status, and income. Another thing to note is that microbiome Cluster 2, the one associated with low diversity and high intelligence, contained more infants who were breastfed and had white parents compared to the other clusters. This suggests that socioeconomic factors may be contributing the observed trends in both microbiome diversity and performance on intelligence tests. This, combined with the difficulty of measuring intelligence in adults, let alone 2 year olds (are you truly measuring intelligence or something else, such as the ability/willingness of a child to sit still and focus or their desire to please adults?), makes me skeptical of a direct link between gut microbiome diversity and intelligence.