Molecular Characterization of the Gut Microbiota of Nigerian Children over 12 months based on Mode of delivery and Diet

The gut microbiota plays an important role in health and different factors contribute to infant gut colonization which includes gestational age, mode of delivery, diet and antibiotic treatment. Many studies in Western countries have reported the effect of these factors on the gut microbiota of children but there are no studies in Nigeria where prenatal and postnatal care is quite different. We investigated the changes in the gut microbiota of Nigerian children from birth to 12 months based on mode of delivery and diet.One hundred and seventy two fecal samples were collected monthly from twenty eight infants from birth till 12 months with some attrition. Metagenomics DNA extraction and characterization of the gut microbiota were done through amplification of the V1-V2 region of the 16S rRNA gene using 27_Miseq primer sequences set and the amplicons were sequenced using Illumina MiSeq v3 flowcell. Sequences were analysed using DADA2 software (version 1.3.1). Diversity analysis was performed using QIIME (version 1.9.0). LefSE analysis was done to identify taxonomic biomarkers that drive differences between sample groups.Eleven phyla were identified, the phylum Actinobacteria is the most abundance (45.95 ± 2.12; Mean ± SEM), Firmicutes (36.73 ± 1.78), Proteobacteria (12.96 ± 1.47), Bacteroidetes (4.30 ± 0.57), Fusobacteria (0.05 ± 0.03) and Others (0.01 ± 0.00) respectively. At genus level, Bifidobacterium is the most abundance (41.07 ± 3.96).There is no significant difference in the microbiota between normal birth and caesarean section. Bifidobacterium have higher abundance in mixed fed samples and Bacteroidales in breast-fed samples. The most prevalent bacterial groups preweaning and weaning, were also different. The introduction of local solid foods had a specific effect, with significant biomarkers, Lactobacillus, Dorea, Enterococcus casseliflavus, Roseburia, Blautia, Clostridiaceae, Bacteroidaceae.This study shows that the infant's gut microbiota has a lower but stable diversity between 1-6 months and sample richness increases particularly when weaning starts, from 7-12 months with significant signatures that depicts a healthy gut composition. The local cereals typical to Nigeria encourage the growth of beneficial bacterial in the gut.