Browsing by Author "Rifkin, Riaan F."

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    Documenting the diversity of the Namibian Ju|'hoansi intestinal microbiome
    (2024) Truter, Mia; Koopman, Jessica E.; Jordaan, Karen; Tsamkxao, Leon Oma; Cowan, Don A.; Underdown, Simon J.; Ramond, Jean-Baptiste; Rifkin, Riaan F.
    We investigate the bacterial and fungal composition and functionality of the Ju|'hoansi intestinal microbiome (IM). The Ju|'hoansi 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.
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    Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the ‘ancestral’ sub-Saharan African intestinal microbiome.
    (2020) Rifkin, Riaan F.; Ramond, Jean-Baptiste.; Vikram, Surendra.; Rey-Iglesia, Alba.; Brand, Tina B.; Porraz, Guillaume.; Val, Aurore.; Hall, Grant.; Woodborne, Stephan.; Le Bailly, Matthieu.
    Abstract Background The archaeological incidence of ancient human faecal material provides a rare opportunity to explore the taxonomic composition and metabolic capacity of the ancestral human intestinal microbiome (IM). Here, we report the results of the shotgun metagenomic analyses of an ancient South African palaeo-faecal specimen. Methods Following the recovery of a single desiccated palaeo-faecal specimen from Bushman Rock Shelter in Limpopo Province, South Africa, we applied a multi-proxy analytical protocol to the sample. The extraction of ancient DNA from the specimen and its subsequent shotgun metagenomic sequencing facilitated the taxonomic and metabolic characterisation of this ancient human IM. Results Our results indicate that the distal IM of the Neolithic ‘Middle Iron Age’ (c. AD 1460) Bantu-speaking individual exhibits features indicative of a largely mixed forager-agro-pastoralist diet. Subsequent comparison with the IMs of the Tyrolean Iceman (Ötzi) and contemporary Hadza hunter-gatherers, Malawian agro-pastoralists and Italians reveals that this IM precedes recent adaptation to ‘Western’ diets, including the consumption of coffee, tea, chocolate, citrus and soy, and the use of antibiotics, analgesics and also exposure to various toxic environmental pollutants. Conclusions Our analyses reveal some of the causes and means by which current human IMs are likely to have responded to recent dietary changes, prescription medications and environmental pollutants, providing rare insight into human IM evolution following the advent of the Neolithic c. 12,000 years ago. Video Abtract.