dc.description.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,
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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. |
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