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

The INBUGS-NG cohort enrolled 90 mother-infant dyads between February and July 2024 at a tertiary hospital in Kano city, Nigeria.

• Enrollment occurred over approximately 6 months, from February to July 2024.
• The study is a prospective longitudinal cohort design.
• Follow-ups were scheduled at 10 time points: days 0, 1, 3, 5, 7, 14, 28, 90, 180 and 365.
• Stool sampling was intensified after infant antibiotic administration to enable dense early-life sampling.

The cohort has generated a total of 1772 biological samples across multiple sample types.

• 480 infant stool samples were collected.
• 232 maternal rectal swabs were collected.
• 254 breast milk samples were collected.
• 806 environmental samples were collected.
• Socio-demographic, clinical and cultural data were collected using Research Electronic Data Capture (REDCap) and household visit diaries.

The vast majority of mothers (93.3%) received postpartum antibiotics.

• 84 out of 90 mothers (93.3%) received postpartum antibiotics.
• This high rate of postpartum antibiotic use represents a key exposure variable for the study.
• This is reported as baseline data from the cohort.

More than one quarter of infants (28.9%) received antibiotics within the first 3 months of life.

• 26 out of 90 infants (28.9%) received antibiotics within the first 3 months of life.
• This early antibiotic exposure is a primary exposure of interest for resistome dynamics analyses.
• This is reported as baseline data from the cohort.

Exclusive breastfeeding rates were very low (8%), with early water supplementation being common.

• Only 8% of infants were exclusively breastfed.
• Early water supplementation was described as common in the cohort.
• Feeding practices are one of the primary exposures being investigated for their effect on gut microbiome development.

Caesarean deliveries accounted for 25% of births, and the mean gestational age was 38.5 weeks.

• 25% of births were by caesarean section.
• The mean gestational age was 38.5 weeks.
• Delivery mode is one of the primary factors under investigation for shaping gut microbiome development.

The study uses shotgun long-read metagenomic sequencing (Oxford Nanopore Technology) to enable strain-level and plasmid-level profiling of microbial communities and antibiotic resistance genes.

• Oxford Nanopore long-read sequencing was selected to generate a unique long-read metagenomic resource from an African infant population.
• Planned analyses include associations between early-life exposures and resistome dynamics.
• Cross-cohort comparisons with a parallel study in Pakistan are planned.
• Analyses are described as ongoing at the time of publication.
• Follow-up will continue through 12 months.