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, Zimbabwe
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, USA
​7. Jose Clemente, Clemente Lab, Ichan School of Medicine at Mount Sinai, USA

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



AMI Affiliation

African Microbiome Institute, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University​

​​Publication list

  • Moodley, S, Kroon, E, Naidoo, CC, et al. 2024. Latent Tuberculosis Infection Is Associated with an Enrichment of Short-Chain Fatty Acid-Producing Bacteria in the Stool of Women Living with HIV. Microorganisms. doi:10.3390/microorganisms12061048
  • Ramaboli MC, Ocvirk S, Khan Mirzaei M, et al. 2024. Diet Changes due to Urbanization in South Africa are Linked to Microbiome and Metabolome Signatures of Westernization and Colorectal Cancer. Nature Communications. doi: 10.1038/s41467-024-46265-0. PMID: ​38643180​.
  • Eribo OA, Naidoo CC, Theron G, et al. 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.
  • Nel Van Zyl K, Whitelaw AC, Hesseling AC, et al. 2022. Fungal diversity in the gut microbiome of young South African children. BMC Microbiology 22:201. doi :10.1186/s12866-022-02615-w. PMID: 35978282​.
  • Nyawo G, Naidoo CC, Wu B, et al. 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, et al. 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.
  • Nel Van Zyl K, Matukane SR, Hamman BL, et al. 2022. The effect of antibiotics on the human microbiome: a systematic review. International Journal of Antimicrobial Agents 59:106502. doi: 10.1016/j.ijantimicag.2021.106502. PMID: 34929293.
  • Eberhart BL 2nd, Wilson AS, O'Keefe SJD, et al. 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
  • Nel Van Zyl K, Whitelaw AC, Hesseling AC, et al. 2021. Association between clinical and environmental factors and the gut microbiota profiles in young South African children. Scientific Reports 11:15895. doi: 10.1038/s41598-021-95409-5. PMID: 34354176.​
  • Wilson AS, Koller KR, Ramaboli MC, et al. 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, et al. 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​