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

Abstract

Both the brain and microbiome of humans develop rapidly in the first years of life, enabling extensive signaling between the gut and central nervous system (dubbed the “microbiome-gut-brain axis”). Emerging evidence implicates gut microorganisms and microbiota composition in cognitive outcomes and neurodevelopmental disorders (e.g., autism), 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 281 healthy children in a cross-sectional analysis and demonstrated that differences in gut microbial taxa and gene functions are associated with the size of brain regions and with overall cognitive function. Many species, including Eubacterium eligens and Roseburia hominis, were associated with higher cognitive function, while some species such as Ruminococcus gnavus was more commonly found in children with low cognitive scores. Microbial enzymes involved in the metabolism of neuroactive compounds such as glutamate and GABA, were also associated with structure of the brain, including the first brain regions to develop such as the cerebellum, and with overall cognitive function.

Targeted High-Resolution Taxonomic Identification of Bifidobacterium longum subsp. infantis Using Human Milk Oligosaccharide Metabolizing Genes

“…Finally, we used the five HMO-metabolizing gene clusters to distinguish B. infantis from the rest of the B. longum subspecies in the gut microbiomes of human children using fecal samples in the RESONANCE cohort of young, healthy children [ 40 ]. We applied the specificity of this HMO-metabolizing cluster to identify B. infantis from metagenomic analysis of 1092 fecal samples.…”

“…Metagenome data were deposited in NCBI’s Sequence Read Archive (SRA), under BioProject PRJNA695570 and accession numbers SAMN17618458-9435. Code for data analysis, statistics, and figures generated for this manuscript is available on OSF.io [ 40 ].…”

Targeted High-Resolution Taxonomic Identification of Bifidobacterium longum subsp. infantis Using Human Milk Oligosaccharide Metabolizing Genes

“…Finally, we used the five HMO-metabolizing gene clusters to distinguish B. infantis from the rest of the B. longum subspecies in the gut microbiomes of human children using fecal samples in the RESONANCE cohort of young, healthy children (Bonham et al, 2020). We applied the specificity of this HMO-metabolizing cluster to identify B. infantis from metagenomic analysis of our samples.…”

“…Data Availability Statement: Metagenome data were deposited in NCBI's Sequence Read Archive (SRA), under BioProject PRJNA695570 and accession numbers SAMN17618458-9435. Code for data analysis, statistics, and figures generated for this manuscript is available on OSF.io [40].…”

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

“…Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. Taxonomic and functional microbial profiles, as well as subject demographics necessary for statistical analyses and machine learning, are available on the Data Dryad (81). Data processing, generation of summary statistics, and generation of plots were performed using the julia programming language and third-party packages (74,75,(82)(83)(84)(85)(86).…”