GUT MICROBIOME OF DIARRHOEIC UNDER-FIVE CHILDREN IN LAGOS AND OGUN STATES, NIGERIA

UGBOKO, HARRIET UNUAGBON and Covenant University, Theses (2021) GUT MICROBIOME OF DIARRHOEIC UNDER-FIVE CHILDREN IN LAGOS AND OGUN STATES, NIGERIA. ["eprint_fieldopt_thesis_type_phd" not defined] thesis, COVENANT UNIVERSITY.

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Abstract

Diarrhoea is a major cause of morbidity and mortality in young children. This study aimed to investigate the gut microbiome of under-five diarrhoeic children in Lagos and Ogun States. Hospital records were obtained from the four healthcare facilities used. Ethical approval was obtained from two tertiary institutions. A total of 180 stool samples were taken from underfive diarrhoeic and non-diarrhoeic children from two states in approximately a ratio of four to one (4:1). Samples were analysed using standard, cultural and biochemical techniques. Isolates were further identified using the API 20E test. An Antibiogram profile of the pure isolates was conducted using the disks diffusion technique. Amplicon-based metagenomic analyses were carried out on DNA isolates obtained from stool samples of diarrhoeic and healthy children. The species richness and species abundance were determined using the Microbial Genomics Module version 4.0 (Qiagen). Data obtained from the questionnaires, hospital records, and antibiogram were analysed using logistic regression, Chi-square and student t-tests. This study showed an overall prevalence rate of 11.1% for diarrhoea in Lagos and Ogun States. Mother’s educational status (OR= 11.459, P= 0.0001), mother’s employment status (OR= 2.082, P= 0.025) and family income (OR= 7.613, P=0.0001), were the factors significantly associated with diarrhoea. A total of 279 isolates obtained were predominantly members of the Enterobacteriaceae. Others include Pseudomonas, Staphylococcus, Bacillus, Acinetobacter, and Alcaligenes. Most of the bacteria isolated from the diarrhoeic children were resistant to multiple class of antibiotics; Penicillins, Sulonamides, Tetracyclines, and Cefuroxime in a decreasing order. The isolates were more resistant to Ampicillin (83.4%), Augmentin (79.6%), Trimethoprim-Sulphamethoxazole 70.5%), and Tetracycline (65.6%) and more sensitive to Nitrofurantoin (68.9%), Gentamycin 67.2%), Ofloxacin (65.9%), and Ciprofloxacin (61.8%). The phylogenetic diversity revealed six bacterial phyla which include Firmicutes (51.7%), Bacteroidetes (9.1%), Proteobacteria (27.1%), Actinobacteria (11.5%), Fusobacteria (0.5%), and Verrucomicrobia (0.1%). The major classes in the Firmicutes were Bacilli (71%) and Clostridia 24%. The classes under Proteobacteria were mainly Gammaproteobacteria (99.9%) whil Alphaproteo bacteria occurred (0.1%). The two classes, Actinobacteria (50%) and Coriobacteriia (50%), in the phylum Actinobacteria, were represented equally. The phyla Bacteroidetes, Fusobacteria and Verrucomicrobia were represented by a single class each which is: Bacteroidia (100%), Fusobacteriia (100%) and Verrucomicrobiae (100%), respectively. The predominant phyla detected among the diarrhoeic samples were Firmicutes (50.4%) and Proteobacteria (37.2%). There was a remarkable increase in the abundance of Proteobacteria in the diarrhoeic group (37.2%), compared to the healthy group (6.5%) at p<0.0001. The total number of different species presented decreased in the diarrhoeic children (341, 31%) and increased in the non-diarrhoeic children (774, 69%). Also, the proportion of Escherichia coli, Shigella, Staphylococcus and Klebsiella were in abundance in the diarrhoeic group. In contrast, Bifidobacterium, Faecalibacterium, Lactobacillus, Clostridium (sensu stricto), and Bacteroides significantly decreased in the diarrhoeic group. This suggests that diarrhoeal diseases thrive in the dysbiotic gut, which is characterised by the depletion of beneficial microbes and increased pathogens in the gut.

Item Type:	Thesis (["eprint_fieldopt_thesis_type_phd" not defined])
Uncontrolled Keywords:	Bacteria, Children, Diarrhoea, Gut Microbiome, Metagenome
Subjects:	Q Science > Q Science (General) Q Science > QH Natural history > QH301 Biology
Divisions:	UNSPECIFIED
Depositing User:	Mrs Hannah Akinwumi
Date Deposited:	01 Sep 2021 11:39
Last Modified:	01 Sep 2021 11:39
URI:	http://eprints.covenantuniversity.edu.ng/id/eprint/15334

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