African Microbiome Institute
Welcome to Stellenbosch University

The Af​rican Microbiome Institute (AMI)


Local and International collaborators ​

1. University of Pittsburgh, USA
    Stephen O'Keefe, Research in Nutritional Gastroenterology 
    Alison Morris & Barbara Methe, Center for Medicine and the Microbiome

​2. James Kinross, Imperial College, London, UK 
3. ​TROPGAN (Tropical Gastroenterology & Nutrition group)​ resources and facilities, University of Zambia, Lusaka, Zambia
​4. Leolin Katsidzira, University of Zimbabwe College of Health Sciences
5​. Rina Swart, Department of Dietetics and Nutrition, University of the Western Cape, RSA

6. ​Leopoldo Segal, Segal Lab, New York University School of Medicine
​7. Jose Clemente, Clemente Lab, Ichan School of Medicine at Mount Sinai 

​8. Sören Ocvirk, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Germany



  • Ramaboli MC, Ocvirk S, Khan Mirzaei M, Eberhart BL 2nd, Valdivia-Garcia M, Metwaly A, Neuhaus K, Barker G, Ru J, Nesengani L, Wilson S, Joni S, Layman D, Zheng J, Mandal R, Chen Q, Perez M, Fortuin S, Gaunt B, Wishart D, Methe B, Haller D, Li J, Deng Li, Swart R, Mahdi-Joest D, O'Keefe SJD. In press February 2024. Diet Changes due to Urbanization in South Africa are Linked to Microbiome and Metabolome Signatures of Westernization and Colorectal Cancer. Nature Communications.
  • Eribo OA, Naidoo CC, Theron G, Walzl G, du Plessis N, Chegou NN. 2023. An Archetypical Model for Engrafting Bacteroides fragilis into Conventional Mice Following Reproducible Antibiotic Conditioning of the Gut Microbiota. Microorganisms. doi: 10.3390/microorganisms11020451. PMID: 36838416.
  • Nyawo G, Naidoo CC, Wu B, Sulaiman I, Clemente J, Li Y, Minnies S, Reeve B, Moodley S, Rautenbach C, Wright C, Singh S, Whitelaw A, Schubert P, Warren R, Segal L, Theron G. 2022. More than Mycobacterium tuberculosis: site-of-disease microbial communities, and their functional and clinical profiles in tuberculous lymphadenitis. Thorax. doi: 10.1136/thorax-2022-219103. PMID: 36598079.
  • Ramaboli M, Nesengani L, Katsidzira L, Haller D, Kinross J, Ocvirk S, O'Keefe SJD; and the African Microbiome International Consortium. 2022. Interactions between the environmental and human microbiota in the preservation of health and genesis of disease: symposium report. Current Opinion in Gastroenterology. doi: 10.1097/mog.0000000000000817. PMID: 35098936.
  • Eberhart BL 2nd, Wilson AS, O'Keefe SJD, Ramaboli MC, Nesengani LT. 2021. A simplified method for the quantitation of short-chain fatty acids in human stool. Analytical Biochemistry. doi: 10.1016/j.ab.2020.114016. PMID: 33188741
  • Wilson AS, Koller KR, Ramaboli MC, Nesengani LT, Ocvirk S, Chen C, Flanagan CA, Sapp FR,  Merritt ZT, Bhatti F, Thomas TK, O'Keefe SJD. 2020. Diet and the Human Gut Microbiome: An International Review. Digestive Diseases and Sciences doi: 10.1007/s10620-020-06112-w. PMID: 32060812
  • Naidoo CC, Nyawo GN, Wu B, Walzl G, Warren RM, Segal LN, Theron G. 2019. The microbiome and tuberculosis: state of the art, potential applications, and defining the clinical research agenda. The Lancet Respiratory Medicine. doi: 10.1016/S2213-2600(18)30501-0. PMID: 30910543​