CHANGES IN THE GUT MICROBIOTA OF SOME NIGERIAN INFANTS WITHIN THE FIRST YEAR OF LIFE

Abstract

The gut microbiota plays an important role in health and its negative alteration can lead to different pathologies. Different factors which include birthing methods, diet and antibiotic treatment contribute to infant gut colonisation. Many studies in Western countries have reported the effect of these factors on the gut microbiota of infants but there is dearth of information in Nigeria. This study was designed to investigate the changes in the gut microbiota of some Nigerian infants within the first year of life. This was a longitudinal study of convenience sampled participants. Faecal samples were obtained monthly from 28 infants (gestational age (37.6±2.8 weeks) and birth weight (2.9±0.6 kg) within the first year (8.8±1.3 months) of life at Federal Teaching Hospital, Ido-Ekiti with ethical approval (ERC/2016/09/29/44B) and approved parental consent. The DNA from all samples was extracted with a commercial kit, followed by PCR amplification of the V1-V2 region of the 16S rRNA gene, library preparation and sequencing on Illumina MiSeq. The raw sequences generated underwent downstream bioinformatics analysis with DADA2 pipeline (quality score ≤ 2) to assign taxonomy and to compare the gut microbiota in different groups at different time points (0-4 n=28, 5-8 n=23 and 9-12 months n=13), caesarean section birth (CSB) (n=13) and vaginal birth (VB) (n=15), exclusively breastfed (n=15) and mixed fed (MF) (n=8) and then preweaning and weaning (n=23) groups. The diversity in all the groups was determined by Quantitative Insight into Microbial Ecology (QIIME). Selected antibiotic resistance genes (aac (6’ ), mef A/E, ermA, ermB, blaZ) and tetracycline’s ribosomal protection protein (tet) gene were detected in samples by PCR. Short chain fatty acids (SCFAs) present in each faecal sample were identified by gas chromatography. Alpha diversity significantly increased with infants’ age. Beta diversity showed tight clusters from birth to 4 months, revealing taxonomic similarities and dispersion at 5-8 and 9-12 months, thereby confirming the increased diversity with age. There was no statistically significant difference in the gut microbiota between the birthing methods. However, Klebsiella (33.8%) and Staphylococcus (13.5%) were most abundant in CSB, iii while Streptococcus (29.9%) and Enterococcus (20.2%) were most abundant in VB. Exclusively breastfed infants had Significant Differential Abundance (SDA) ofCollinsella, Bacteroides, Sutterella and Actinomyces while Bifidobacterium was differentially abundant in MF. Firmicutes were predominant in preweaning and weaning period. However, there was a shift from Proteobacteria to Actinobacteria as the next SDA phylum in preweaning and weaning groups respectively. The effect of antibiotics was marked with decrease in number of observed taxa at point of administration or the next time point while tet was the most prevalent (27.0%) resistance gene. Butyrate only appeared, while other SCFAs (acetate, lactate and propionate) increased during weaning indicative of complex carbohydrate metabolic functions. Observed gut microbiota taxonomic differences between preweaning and weaning in some Nigerian infantsas well as butyrate production were influenced by diet. Introduction of solid foods encouraged the colonisation and adaptation of specific marker organisms associated with carbohydrate metabolism helpful for a healthy life.