Data from: Gut-resident microorganisms and their genes are associated with cognition and neuroanatomy in children

The gastrointestinal tract, its resident microorganisms, and the central
nervous system are connected by biochemical signaling, also known as the
”microbiome-gut-brain-axis.” Both the human brain and the gut microbiome
have critical developmental windows in the first years of life, raising
the possibility that their development is co-occurring and likely
co-dependent. Emerging evidence implicates gut microorganisms and
microbiota composition in cognitive outcomes and neurodevelopmental
disorders (e.g., autism and anxiety), but the influence of gut microbial
metabolism on typical neurodevelopment has not been explored in detail. We
investigated the relationship of the microbiome with the neuroanatomy and
cognitive function of 381 healthy children, demonstrating that differences
in gut microbial taxa and gene functions are associated with overall
cognitive function and with differences in the size of multiple brain
regions. Using a combination of multivariate linear and machine learning
(ML) models, we showed that many species, including Alistipes obesi and
Blautia wexlerae, were associated with higher cognitive function, while
some species such as Ruminococcus gnavus were more commonly found in
children with low cognitive scores after controlling for sociodemographic
factors. Microbial genes for enzymes involved in the metabolism of
neuroactive compounds, particularly short-chain fatty acids such as
acetate and propionate, were also associated with cognitive function. In
addition, ML models were able to use microbial taxa to predict the volume
of brain regions, and many taxa that were identified as important in
predicting cognitive function also dominated the feature importance metric
for individual brain regions, and for specific subscales of cognitive
function. For example, B. wexlerae was the most important species in
models predicting the size of the parahippocampal region in both the left
and right hemispheres and was among the top predictors of gross motor and
expressive language performance. Several species from the phylum
Bacteroidetes, including GABA-producing Bacteroides ovatus, were important
for predicting the size of the left accumbens area, but not the right.
These findings provide potential biomarkers of neurocognition and brain
development and may lead to the future development of targets for early
detection and early intervention.