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

Contexte: Le microbiome intestinal humain diffère d’une population à l’autre et varie également en fonction du régime alimentaire, des emplacements génétiques et géographiques. Le régime au Nigéria est en train de passer à un régime plus occidental avec un supplément de sucre et des aliments transformés. Il est nécessaire d’étudier les habitudes alimentaires et l’impact sur le microbiome intestinal dans la santé et les maladies.

Objectif: Nous avons détermines l’impact de l’alimentation sur le microbiome du groupe ethnique Yorouba vivant dans les zones rurales et urbaines.

Méthodologie: Nous avons caractérisé les espèces bactériennes présentes dans les échantillons fécaux obtenus à partir de 20 Yoroubas ; Dix de chaque site, apparié par âge et sexe. Un ensemble d’amorce universel a été utilisé pour amplifier la région V3 – V4 pour les séquences 16S ARNr microbiennes fécales. Les données résultantes ont été comparées entre le régime alimentaire rural et urbain et celui des autres pays.

Résultats : La composition de l’intestin microbiome Yorouba des localités rurale et urbaine étaient principalement des organismes du phylum Bacteroidetes Actinobactéries et Firmicutes, en particulier du genre Prevotella, bifidobactéries, et Faecalibacterium. Dans la population urbaine, les espèces Bifidobacterium , Prevotella et Faecalibacterium étaient les organismes prédominants tandis que les espèces Prevotella et Faecalibacterium prédominaient dans la population rurale. Il y avait des similitudes entre les microbiomes trouvés dans les Nigérians ruraux avec ceux des Africains avec régimes similaires. La diversité du microbiome intestinal de base au Nigéria diffère selon les régimes.

Conclusion : Les régions urbaines de Lagos semble avoir fait la transition vers un modèle de régime typique des sociétés ‘Occidentalisés’ et cela peut avoir contribué aux variations des microbiomes de ceux d’origine ethnique similaire, vivant dans la région rurale. Des études complémentaires doivent être menées dans une population plus large pour vérifier pleinement cette relation .

Mots clés: Prevotella , Bifidobacterium , Faecalibacterium, Microbiome intestinal, Urbain, Rural, Séquençage de nouvelle génération, Nigéria

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



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