Distinct Difference between microbiome of rural and urban population in Lagos State, Nigeria

Background: The human gut microbiome differs among populations and also varies with diet, genetic and geographic locations. The diet in Nigeria is changing to a more western diet with extra sugar and processed food. There is a need to investigate dietary pattern and impact on gut microbiome in health and in diseases. Aim: We determined the impact of diet on the microbiome of Yoruba ethnic group living in rural and urban areas. Methodology: We characterized bacterial species present in faecal samples obtained from 20 Yoruba; Ten from each site, matched by age and sex. A universal primer set was used to amplify the V3–V4 region for faecal microbial 16S rRNA sequences. The resultant data was compared between the rural and urban diet and to those from other nations. Results: The composition of the Yoruba gut microbiome of both rural and urban were mainly organisms from the phylum Bacteroidetes Actinobacteria, and Firmicutes, particularly the genus Prevotella, Bifidobacteria, and Faecalibacterium. In the urban population, Bifidobacterium, Prevotella and Faecalibacterium species were the predominant organisms while Prevotella and Faecalibacterium species predominated in the rural population. There were similarities between the microbiomes found in rural Nigerians with those from Africans with similar diets. The diversity of core gut microbiome in Nigeria differs between diets. Conclusion: The urban region of Lagos seems to have transitioned towards a diet pattern typical of ‘Westernized’ societies and this may have contributed to the variations in microbiomes of those of similar ethnicity, living in the rural region. Further studies needs to be conducted in a larger population to fully ascertain this relationship. Keywords: Prevotella, Bifidobacterium, Faecalibacterium, Gut microbiome, Urban, Rural, Next Generation Sequencing, Nigeria AbstraitContexte: Le microbiome intestinal humain differe d’une population a l’autre et varie egalement en fonction du regime alimentaire, des emplacements genetiques et geographiques. Le regime au Nigeria est en train de passer a un regime plus occidental avec un supplement de sucre et des aliments transformes. Il est necessaire d’etudier les habitudes alimentaires et l’impact sur le microbiome intestinal dans la sante et les maladies. Objectif: Nous avons determines l’impact de l’alimentation sur le microbiome du groupe ethnique Yorouba vivant dans les zones rurales et urbaines. Methodologie: Nous avons caracterise les especes bacteriennes presentes dans les echantillons fecaux obtenus a partir de 20 Yoroubas ; Dix de chaque site, apparie par âge et sexe. Un ensemble d’amorce universel a ete utilise pour amplifier la region V3 – V4 pour les sequences 16S ARNr microbiennes fecales. Les donnees resultantes ont ete comparees entre le regime alimentaire rural et urbain et celui des autres pays. Resultats : La composition de l’intestin microbiome Yorouba des localites rurale et urbaine etaient principalement des organismes du phylum Bacteroidetes Actinobacteries et Firmicutes, en particulier du genre Prevotella, bifidobacteries, et Faecalibacterium. Dans la population urbaine, les especes Bifidobacterium , Prevotella et Faecalibacterium etaient les organismes predominants tandis que les especes Prevotella et Faecalibacterium predominaient dans la population rurale. Il y avait des similitudes entre les microbiomes trouves dans les Nigerians ruraux avec ceux des Africains avec regimes similaires. La diversite du microbiome intestinal de base au Nigeria differe selon les regimes. Conclusion : Les regions urbaines de Lagos semble avoir fait la transition vers un modele de regime typique des societes ‘Occidentalises’ et cela peut avoir contribue aux variations des microbiomes de ceux d’origine ethnique similaire, vivant dans la region rurale. Des etudes complementaires doivent etre menees dans une population plus large pour verifier pleinement cette relation . Mots cles: Prevotella , Bifidobacterium , Faecalibacterium, Microbiome intestinal, Urbain, Rural, Sequencage de nouvelle generation, Nigeria Correspondence: Dr. Francisca Nwaokorie, Department of Medical Laboratory Science, Faculty of Basic Medical Science, College of Medicine, University of Lagose, Nigeria. E-mail: fnwaokorie@unilag.edu.ng