Cohort profile: Infant Gut Bacterial Study in Nigeria (INBUGS-NG)

The Infant Gut Bacterial Study in Nigeria (INBUGS-NG) investigates how delivery mode, antibiotic exposure, feeding practices and environmental factors shape gut microbiome development and acquisition of antibiotic resistance genes (ARGs) during the first year of life in northern Nigeria.

Between February and July 2024, 90 mother-infant dyads were enrolled at a tertiary hospital in Kano city, Nigeria. This was a prospective longitudinal cohort with follow-ups at 10 scheduled time points: days 0, 1, 3, 5, 7, 14, 28, 90, 180 and 365. We also intensified stool sampling after infant antibiotic administration, enabling dense early-life sampling. To date, the cohort has contributed 480 infant stool samples, 232 maternal rectal swabs, 254 breast milk samples and 806 environmental samples (total 1772). In parallel, socio-demographic, clinical and cultural data were collected using Research Electronic Data Capture (REDCap) and household visit diaries.

Baseline data show that 84/90 mothers (93.3%) received postpartum antibiotics, and 26/90 infants (28.9%) received antibiotics within the first 3 months of life. Only 8% of infants were exclusively breastfed, with early water supplementation common. Caesarean deliveries accounted for 25% of births, and the mean gestational age was 38.5 weeks. Across the cohort, high retention was achieved, and the study has generated a unique long-read metagenomic resource from an African infant population, with analyses ongoing.

Shotgun long-read metagenomic sequencing (Oxford Nanopore) will enable strain-level and plasmid-level profiling of microbial communities and ARGs. Planned analyses include associations between early-life exposures and resistome dynamics, as well as cross-cohort comparisons with a parallel study in Pakistan. Follow-up will continue through 12 months.