Documenting the diversity of the Namibian Ju|’hoansi intestinal microbiome
Mia Truter,
Jessica E. Koopman,
Karen Jordaan,
Leon Oma Tsamkxao,
Don A. Cowan,
Simon J. Underdown,
Jean-Baptiste Ramond,
Riaan F. Rifkin
Affiliations
Mia Truter
Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield 0028, South Africa; Scientific Computing Research Unit, Department of Chemistry, University of Cape Town, Rondebosch 7700, South Africa
Jessica E. Koopman
Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield 0028, South Africa
Karen Jordaan
Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield 0028, South Africa
Leon Oma Tsamkxao
Juǀʼhoan Traditional Authority (JUTA), Tsumkwe, Otjozondjupa Region, Namibia
Don A. Cowan
Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield 0028, South Africa
Simon J. Underdown
Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield 0028, South Africa; Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford OX3 0BP, UK
Jean-Baptiste Ramond
Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield 0028, South Africa; Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford OX3 0BP, UK; Extreme Ecosystem Microbiomics & Ecogenomics (E2ME) Lab., Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
Riaan F. Rifkin
Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield 0028, South Africa; Juǀʼhoan Traditional Authority (JUTA), Tsumkwe, Otjozondjupa Region, Namibia; Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford OX3 0BP, UK; Corresponding author
Summary: We investigate the bacterial and fungal composition and functionality of the Ju|’hoansi intestinal microbiome (IM). The Juǀʼhoansi are a hunter-gatherer community residing in northeastern Namibia. They formerly subsisted by hunting and gathering but have been increasingly exposed to industrial dietary sources, medicines, and lifestyle features. They present an opportunity to study the evolution of the human IM in situ, from a predominantly hunter-gatherer to an increasingly Western urban-forager-farmer lifestyle. Their bacterial IM resembles that of typical hunter-gatherers, being enriched for genera such as Prevotella, Blautia, Faecalibacterium, Succinivibrio, and Treponema. Fungal IM inhabitants include animal pathogens and plant saprotrophs such as Fusarium, Issatchenkia, and Panellus. Our results suggest that diet and culture exert a greater influence on Ju|’hoansi IM composition than age, self-identified biological sex, and medical history. The Ju|’hoansi exhibit a unique core IM composition that diverges from the core IMs of other populations.
