Co-development of gut microbial metabolism and visual neural circuitry over human infancy

Infancy is a time of elevated neuroplasticity supporting rapid brain and sensory development. The gut microbiome, also undergoing extensive developmental changes in early life, may influence brain development through metabolism of neuroactive compounds. Here, we leverage longitudinal data from 194 infants across the first 18 months of life to show that microbial genes encoding enzymes that metabolize molecules playing a key role in modulating early neuroplasticity are associated with visual cortical neurodevelopment, measured by the Visual-Evoked Potential (VEP). Neuroactive compounds included neurotransmitters GABA and glutamate, the amino acid tryptophan, and short-chain fatty acids involved in myelination, including acetate and butyrate. Microbial gene sets around 4 months of age were strongly associated with the VEP from around 9 to 14 months of age and showed more associations than concurrently measured gene sets, suggesting microbial metabolism in early life may affect subsequent ..., Stool Samples
We collected stool and the visual evoked potential (VEP) in a longitudinal cohort of 194 children in South Africa during the first 18 months of life (visit 1, N = 119, age 3.7 ± 0.9 months, visit 2, N = 144, age 8.6 ± 1.5 months, and visit 3, N = 130, age 14.1 ± 1.0 months).
Stool samples (n = 315) were collected in the clinic by the research assistant directlyfrom the diaper, transferred to Zymo DNA/RNA ShieldTM Fecal collection Tubes (#R1101, Zymo Research Corp., Irvine, USA), and immediately frozen at −80 ˚C. Stool samples were not collected if the participant had taken antibiotics within the 2 weeks prior to sampling.
DNA extraction was performed at Medical Microbiology, University of Cape Town, South Africa, from stool samples collected in DNA/RNA Shield Fecal collection tube using the Zymo Research Fecal DNA MiniPrep kit (# D4300, Zymo Research Corp., Irvine, USA) following the manufacturer’s protocol. To assess the extraction process’s quality, ZymoBIOMICS Microbial..., # Co-development of gut microbial metabolism and visual neural circuitry over human infancy

Dataset DOI: [10.5061/dryad.rn8pk0pq2](10.5061/dryad.rn8pk0pq2)

## Description of the data and file structure

Data collected for *Codevelopment of gut microbial metabolism and visual neural circuitry over human infancy,* to be published in mBio ([https://doi.org/10.1128/mbio.00835-25](https://doi.org/10.1128/mbio.00835-25), preprint link: [https://www.medrxiv.org/content/10.1101/2024.07.24.24310884](https://www.medrxiv.org/content/10.1101/2024.07.24.24310884)).

## Files and variables

### Subject metadata and VEP features

The `allmeta.csv` file contains subject- and sample-specific metadata for all subjects and visits included in the study. There is one header row and 487 data rows. Columns names and contents are described below. Cells where data is missing contain no text.

The following columns are included:

* `subject_id`: type `String` - a unique identifier for the child participating i..., Study procedures were offered in English or Xhosa depending on the language preference of the
mother. This study was approved by the relevant university Health Research Ethics Committees
(University of Cape Town study number: 666/2021). Informed consent was collected from mothers on
behalf of themselves and their infants.

All data is de-identified and does not contain any personally identifiable information.