Abstract
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
Abstrait
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
References
Sender R, Fuchs S and Milo R. Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLoSBi. 2016: l14:e1002533.
Rinninella E, Raoul P, and Cintoni M. et al. What is the Healthy Gut Microbiota Composition? A Changing Ecosystem across Age, Environment, Diet, and Diseases. Microorganisms. 2019: 7:14.
Rothschild D, Weissbrod O, Barkan E. et al., Environment dominates over host genetics in shaping human gut microbiota. Nature. 2018: 8(555):210-215.
Thomas S, Izard J, Walsh E. et al. The Host Microbiome Regulates and Maintains Human Health: A Primer and Perspective for Non-Microbiologists. Cancer Res. 2017: 77:1783-1812.
Round JL and Mazmanian Sk. The gut microbiota shapes intestinal immune responses during health and disease. Nature Rev Immunol. 2009: 313–323.
O’Callaghan A. van Sinderen D. Bifidobacteria and Their Role as Members of the Human Gut Microbiota. Fr Microbiol. 2016;7: 925.
Fukuda S, Toh H and Hase K. Bifidobacteria can protect from enteropathogenic infection through production of acetate Nature. 2011;469:543–547.
Pianta A, Arvikar S. Strle K et al. Evidence of the Immune Relevance of Prevotella copri, a Gut Microbe, in Patients with Rheumatoid Arthritis. Arth Rheumatol. 2017;69:964–975.
Nishijima1 S, Suda W. Oshima K. et al. The gut microbiome of healthy Japanese and its microbial and functional uniqueness. DNA Res. 2016;23: 125–133.
Qin J, Li R. Raes J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464:59–65.
De Filippo C, Cavalieri D, Di Paola M. et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci USA. 2010; 107:14691-14696.
Yadav D, Ghosh TS, Mande SS. Global investigation of composition and interaction networks in gut microbiomes of individuals belonging to diverse geographies and age-groups. Gut Pathog. 2016; 8:17.
Yatsunenko T, Rey FE, Manary MJ. et al. Human gut microbiome viewed across age and geography. Nature. 2012; 9486: 222-227.
Jha AR, Davenport ER, Gautam Y1. et al. Gut microbiome transition across a lifestyle gradient in Himalaya. PLOS Biology. 2018; 16:e2005396.
Tito RY, Knights D, Metcalf J. Insights from characterizing extinct human gut microbiomes. PLoSOne. 2012;7: e51146-2210.
Liao M1, Xie Y, Mao Y. et al. Comparative analyses of fecal microbiota in Chinese isolated Yao population, minority Zhuang and rural Han by 16sRNA sequencing. Sci Rep. 2018; 18:1142.
Tandon D, Haque MM, Shaikh SPS. et al. Snapshot of gut microbiota of an adult urban population from Western region of India. PloS one 2018; 13; e0195643.
Silveira-Nunes G, Durso DF, Alves de Oliveira LR Jr et al. Hypertension is Associated with Intestinal Microbiota Dysbiosis and Inflammation in a Brazilian Population. Front. Pharmacol. 2020; 11:258.doi: 10.3389/fphar.2020.00258.18.
Brennan C.A. and Garrett, W.S. Gut microbiota, inflammation, and colorectal cancer. Annu. Rev. Microbiol. 2016; 70, 395–411.
De Angelis M., Ferrocino I, Calabrese F.M. et al. Diet influences the functions of the human intestinal microbiome. Sci Rep 2020; 10, 4247.
Hills RD, Pontefract BA, Mishcon HR. et al. Black CA, Sutton SC, and Cory R. Theberge CR. Gut Microbiome: Profound Implications for Diet and Disease. Nutrients. 2011; 19: 1613 29-40.
Oleskin AV and Shenderov BA. Neuromodulatory effects and targets of the SCFAs and gasotransmitters produced by the human symbiotic microbiota. Microb Ecol Health Dis 2016; 27:30971. https ://doi.org/10.3402/mehd.v27.3097120
Mohajeri, MH, Brummer, RJM and Rastall RA. 2018: 57 (1):S1 S14.https://doi.org/10.1007/s00394-018-1703-1704.
Kandala N and Stranges S. Geographic Variation of Overweight and Obesity among Women in Nigeria: A Case for Nutritional Transition in Sub-Saharan Africa. PLoS ONE. 2014; 9: e101103.
Magoc T and. Salzberg S. FLASH (Fast Length Adjustment of Short reads). Bioinformatics. 2011, 27:21 2957-2963.
Kuczynski J, Stombaugh J, Walters WA. et al. Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Curr. Protoc. Microbiol. 2012; C1:1E 5.
Ayeni FA, Biagi E, Rampelli S et al. Infant and Adult Gut Microbiome and Metabolome in Rural Bassa and Urban Settlers from Nigeria. Cell Rep. 2018; 23:3056–3067.
Cockx L, Colen L, DeWeerdt J. From corn to popcorn? Urbanization and food consumption in sub-Saharan Africa: Evidence from rural-urban migrants in Tanzania. LICOS Discussion Paper Series. 2017; 390/2017.
Arboleya S, Watkins C and Stanton C. Gut Bifidobacteria Populations in Human Health and Aging. Front. Microbiol. 2016; 7:1204.
Rautava S. Early microbial contact, the breast milk microbiome and child health. J Dev Orig Health Dis. 2016; 7:5–14.
Dillon S. M., Lee EJ, Donovan AM. et al. Enhancement of HIV-1 infection and intestinal CD4+ T cell depletion ex vivo by gut microbes alered during chronic HIV-1 infection. Retrovirol. 2016; 13: 5.
Zhang M, Zhou L, Wang Y. et al. Faecalibacterium prausnitzii produces butyrate to decrease c-Myc-related metabolism and Th17 differentiation by inhibiting histone. deacetylase 3, Intern. Immunol. 2019;dxz022, https://doi.org/10.1093/intimm/dxz022.
Yooseph S, Kirkness EF, Tran TM. et al. Stool microbiota composition is associated with the prospective risk of Plasmodium falciparum infection. BMC Genom. 2015: 16631.