Prediction of functional proteins associated with the gut microbiome of an adult population in Lagos State, Nigeria
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Date
2022-11-22
Authors
Francisca Obiageri Nwaokoriea , Uwem Okon Edet b , Akaninyene Paul Josephc , Kanki Phylis d, Ogunsola Folasade.
Journal Title
Journal ISSN
Volume Title
Publisher
Elsevier B.V
Abstract
The human gut microbiome is implicated in health and disease. Yet, its func tions in healthy adults from a divergent population like those seen in Africa are quite un clear. We set to reveal the roles of the gut microbiome of a healthy rural and urban Yoruba
population of Lagos State.
Methodology: Sociodemographic and clinical data, and fecal samples were obtained from
rural (n = 10) and urban (n = 10) participants. fecal DNA extraction was done using ZR Fecal
DNA MiniPrepTM D6010 and metagenomic next generation sequencing performed on Illu mina Miseq platform. Functional roles prediction and antibiotics resistance genes (ARGs)
were done using the Clusters of Orthologous Groups (COG) and Comprehensive Antibiotic
Resistance Database (CARD) tools, respectively. The potential link between phenotypes and
COG abundance were inferred using principal component analysis (PCA).
Results: We found 12 (urban) and 11 (rural) COG classes of proteins from the gut mi crobes. Class E protein which denotes amino acid transport and metabolism was unique
to urban respondents and was dominated by 5-enolpyruvylshikimate-3-phosphate syn thase (45%) and asparagine synthase (30%), implying a high protein-based diet. Class S
was found in both groups. COG families of proteins revealed the presence of exo-beta-1,3-
glucanase (31%), pyruvate-decarboxylase, and thiamine pyrophosphate-requiring enzymes
(22%) among the rural respondents’ indicative of carbohydrate-rich diets. In addition, un characterized protein linked to hypothetical functions was found in both. The COG proteins
clustered with female sex, BMI (body mass index) and BP (blood pressure) for urban while
for the rural populace, it clustered with height, BMI, and BP. CARD analysis showed ARGs in
both groups (urban 90%; rural 10%) and all were Escherichia coli 16S rRNA (rrsB) mutation
conferring resistance to streptomycin with gene variant model A523C n/a to aminoglyco side antibiotics.