Microbiome Diversity and Its Relationship to Immune Development and Infectious Disease Susceptibility in Early Childhood: Evidence from a Nigerian Birth Cohort in Rivers State, South South Nigeria

The gut microbiome plays a central role in immune system programming during the first 1,000 days of life, with early microbial colonisation patterns linked to susceptibility to infectious diseases, allergic disorders, and malnutrition. In Nigeria, the interaction between gut microbiome composition, infant feeding practices, and immune development has not been characterised in any prospective birth cohort. This study establishes the first Nigerian gut microbiome birth cohort in Rivers State, South South Nigeria, recruiting 320 mother-infant dyads at delivery from the University of Port Harcourt Teaching Hospital. Faecal samples were collected at birth, one month, three months, and six months. Microbiome composition was characterised by 16S rRNA amplicon sequencing. Immune markers including secretory IgA, plasma cytokine profiles, and CD4 to CD8 ratios were measured at three and six months. Acute infectious illness episodes were recorded monthly by structured caregiver diary. Infants delivered by caesarean section had significantly lower Bifidobacterium colonisation at one month compared to vaginally delivered infants (p less than 0.001). Exclusive breastfeeding was the strongest predictor of microbiome diversity at three months. Higher Shannon diversity at three months was inversely associated with acute respiratory infection episodes at six months (beta negative 0.38, p less than 0.01). Novel microbial taxa associated with secretory IgA levels were identified, providing candidate biomarkers for immune maturation. This study makes an original contribution to global microbiome science by characterising the Nigerian infant gut ecosystem and its immunological significance. Keywords: gut microbiome, immune development, birth cohort, Rivers State, South South Nigeria.