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Article ; Online: Documenting the diversity of the Namibian Ju|'hoansi intestinal microbiome.

Truter, Mia / Koopman, Jessica E / Jordaan, Karen / Tsamkxao, Leon Oma / Cowan, Don A / Underdown, Simon J / Ramond, Jean-Baptiste / Rifkin, Riaan F

Cell reports

2024 Volume 43, Issue 2, Page(s) 113690

Abstract: We investigate the bacterial and fungal composition and functionality of the Ju|'hoansi intestinal microbiome (IM). The Juǀ'hoansi are a hunter-gatherer community residing in northeastern Namibia. They formerly subsisted by hunting and gathering but have ...

Abstract	We investigate the bacterial and fungal composition and functionality of the Ju\|'hoansi intestinal microbiome (IM). The Juǀ'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.
MeSH term(s)	Animals ; Humans ; Gastrointestinal Microbiome ; Prevotella ; Saccharomycetales
Language	English
Publishing date	2024-01-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2024.113690
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: 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

Cell Reports, Vol 43, Iss 2, Pp 113690- (2024)

2024

Abstract: 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 ...

Abstract	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.
Keywords	CP: Microbiology ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2024-02-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Rickettsia felis DNA recovered from a child who lived in southern Africa 2000 years ago.

Rifkin, Riaan F / Vikram, Surendra / Alcorta, Jaime / Ramond, Jean-Baptiste / Cowan, Don A / Jakobsson, Mattias / Schlebusch, Carina M / Lombard, Marlize

Communications biology

2023 Volume 6, Issue 1, Page(s) 240

Abstract: The Stone Age record of South Africa provides some of the earliest evidence for the biological and cultural origins of Homo sapiens. While there is extensive genomic evidence for the selection of polymorphisms in response to pathogen-pressure in sub- ... ...

Abstract	The Stone Age record of South Africa provides some of the earliest evidence for the biological and cultural origins of Homo sapiens. While there is extensive genomic evidence for the selection of polymorphisms in response to pathogen-pressure in sub-Saharan Africa, e.g., the sickle cell trait which provides protection against malaria, there is inadequate direct human genomic evidence for ancient human-pathogen infection in the region. Here, we analysed shotgun metagenome libraries derived from the sequencing of a Later Stone Age hunter-gatherer child who lived near Ballito Bay, South Africa, c. 2000 years ago. This resulted in the identification of ancient DNA sequence reads homologous to Rickettsia felis, the causative agent of typhus-like flea-borne rickettsioses, and the reconstruction of an ancient R. felis genome.
MeSH term(s)	Humans ; Child ; Rickettsia felis ; Africa, Southern ; DNA ; South Africa ; DNA, Ancient
Chemical Substances	DNA (9007-49-2) ; DNA, Ancient
Language	English
Publishing date	2023-03-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-023-04582-y
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Article ; Online: Human biology and ancient DNA: exploring disease, domestication and movement.

Houldcroft, Charlotte J / Rifkin, Riaan F / Underdown, Simon J

Annals of human biology

2019 Volume 46, Issue 2, Page(s) 95–98

MeSH term(s)	Archaeology ; Biological Evolution ; DNA, Ancient/analysis ; Domestication ; Genetic Predisposition to Disease/etiology ; Genetic Predisposition to Disease/history ; History, Ancient ; Human Migration/history ; Humans
Chemical Substances	DNA, Ancient
Language	English
Publishing date	2019-07-15
Publishing country	England
Document type	Editorial ; Historical Article ; Introductory Journal Article
ZDB-ID	186656-4
ISSN	1464-5033 ; 0301-4460
ISSN (online)	1464-5033
ISSN	0301-4460
DOI	10.1080/03014460.2019.1629536
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Article ; Online: The Healthy Human Blood Microbiome: Fact or Fiction?

Castillo, Diego J / Rifkin, Riaan F / Cowan, Don A / Potgieter, Marnie

Frontiers in cellular and infection microbiology

2019 Volume 9, Page(s) 148

Abstract: The blood that flows perpetually through our veins and arteries performs numerous functions essential to our survival. Besides distributing oxygen, this vast circulatory system facilitates nutrient transport, deters infection and dispenses heat ... ...

Abstract	The blood that flows perpetually through our veins and arteries performs numerous functions essential to our survival. Besides distributing oxygen, this vast circulatory system facilitates nutrient transport, deters infection and dispenses heat throughout our bodies. Since human blood has traditionally been considered to be an entirely sterile environment, comprising only blood-cells, platelets and plasma, the detection of microbes in blood was consistently interpreted as an indication of infection. However, although a contentious concept, evidence for the existence of a healthy human blood-microbiome is steadily accumulating. While the origins, identities and functions of these unanticipated micro-organisms remain to be elucidated, information on blood-borne microbial phylogeny is gradually increasing. Given recent advances in microbial-hematology, we review current literature concerning the composition and origin of the human blood-microbiome, focusing on bacteria and their role in the configuration of both the diseased and healthy human blood-microbiomes. Specifically, we explore the ways in which dysbiosis in the supposedly innocuous blood-borne bacterial microbiome may stimulate pathogenesis. In addition to exploring the relationship between blood-borne bacteria and the development of complex disorders, we also address the matter of contamination, citing the influence of contaminants on the interpretation of blood-derived microbial datasets and urging the routine analysis of laboratory controls to ascertain the taxonomic and metabolic characteristics of environmentally-derived contaminant-taxa.
MeSH term(s)	Bacteria/classification ; Bacteria/genetics ; Blood/microbiology ; Blood-Borne Pathogens/classification ; Dysbiosis ; Humans ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2019-05-08
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2619676-1
ISSN	2235-2988 ; 2235-2988
ISSN (online)	2235-2988
ISSN	2235-2988
DOI	10.3389/fcimb.2019.00148
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Article: The Role of aDNA in Understanding the Coevolutionary Patterns of Human Sexually Transmitted Infections.

Pimenoff, Ville N / Houldcroft, Charlotte J / Rifkin, Riaan F / Underdown, Simon

Genes

2018 Volume 9, Issue 7

Abstract: Analysis of pathogen genome data sequenced from clinical and historical samples has made it possible to perform phylogenetic analyses of sexually transmitted infections on a global scale, and to estimate the diversity, distribution, and coevolutionary ... ...

Abstract	Analysis of pathogen genome data sequenced from clinical and historical samples has made it possible to perform phylogenetic analyses of sexually transmitted infections on a global scale, and to estimate the diversity, distribution, and coevolutionary host relationships of these pathogens, providing insights into pathogen emergence and disease prevention. Deep-sequenced pathogen genomes from clinical studies and ancient samples yield estimates of within-host and between-host evolutionary rates and provide data on changes in pathogen genomic stability and evolutionary responses. Here we examine three groups of pathogens transmitted mainly through sexual contact between modern humans to provide insight into ancient human behavior and history with their pathogens. Exploring ancient pathogen genomic divergence and the ancient viral-host parallel evolutionary histories will help us to reconstruct the origin of present-day geographical distribution and diversity of clinical pathogen infections, and will hopefully allow us to foresee possible environmentally induced pathogen evolutionary responses. Lastly, we emphasize that ancient pathogen DNA research should be combined with modern clinical pathogen data, and be equitable and provide advantages for all researchers worldwide, e.g., through shared data.
Language	English
Publishing date	2018-06-25
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2527218-4
ISSN	2073-4425
ISSN	2073-4425
DOI	10.3390/genes9070317
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Article: Ancient oncogenesis, infection and human evolution.

Rifkin, Riaan F / Potgieter, Marnie / Ramond, Jean-Baptiste / Cowan, Don A

Evolutionary applications

2017 Volume 10, Issue 10, Page(s) 949–964

Abstract: The recent discovery that malignant neoplastic lesions date back nearly 2 million years ago not only highlights the antiquity of cancer in the human lineage, but also provides remarkable insight into ancestral hominin disease pathology. Using these Early ...

Abstract	The recent discovery that malignant neoplastic lesions date back nearly 2 million years ago not only highlights the antiquity of cancer in the human lineage, but also provides remarkable insight into ancestral hominin disease pathology. Using these Early Pleistocene examples as a point of departure, we emphasize the prominent role of viral and bacterial pathogens in oncogenesis and evaluate the impact of pathogens on human evolutionary processes in Africa. In the Shakespearean vernacular "what's past is prologue," we highlight the significance of novel information derived from ancient pathogenic DNA. In particular, and given the temporal depth of human occupation in sub-Saharan Africa, it is emphasized that the region is ideally positioned to play a strategic role in the discovery of ancient pathogenic drivers of not only human mortality, but also human evolution. Ancient African pathogen genome data can provide novel revelations concerning human-pathogen coevolutionary processes, and such knowledge is essential for forecasting the ways in which emerging zoonotic and increasingly transmissible diseases might influence human demography and longevity in the future.
Keywords	covid19
Language	English
Publishing date	2017-07-11
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2405496-3
ISSN	1752-4563 ; 1752-4571
ISSN (online)	1752-4563
ISSN	1752-4571
DOI	10.1111/eva.12497
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Article ; Online: Migrating microbes: what pathogens can tell us about population movements and human evolution.

Houldcroft, Charlotte J / Ramond, Jean-Baptiste / Rifkin, Riaan F / Underdown, Simon J

Annals of human biology

2017 Volume 44, Issue 5, Page(s) 397–407

Abstract: Background: The biology of human migration can be observed from the co-evolutionary relationship with infectious diseases. While many pathogens are brief, unpleasant visitors to human bodies, others have the ability to become life-long human passengers. ...

Abstract	Background: The biology of human migration can be observed from the co-evolutionary relationship with infectious diseases. While many pathogens are brief, unpleasant visitors to human bodies, others have the ability to become life-long human passengers. The story of a pathogen's genetic code may, therefore, provide insight into the history of its human host. The evolution and distribution of disease in Africa is of particular interest, because of the deep history of human evolution in Africa, the presence of a variety of non-human primates, and tropical reservoirs of emerging infectious diseases. Methods: This study explores which pathogens leave traces in the archaeological record, and whether there are realistic prospects that these pathogens can be recovered from sub-Saharan African archaeological contexts. Results: Three stories are then presented of germs on a journey. The first is the story of HIV's spread on the back of colonialism and the railway networks over the last 150 years. The second involves the spread of Schistosoma mansoni, a parasite which shares its history with the trans-Atlantic slave trade and the origins of fresh-water fishing. Finally, we discuss the tantalising hints of hominin migration and interaction found in the genome of human herpes simplex virus 2. Conclusions: Evidence from modern African pathogen genomes can provide data on human behaviour and migration in deep time and contribute to the improvement of human quality-of-life and longevity.
Language	English
Publishing date	2017-08
Publishing country	England
Document type	Journal Article
ZDB-ID	186656-4
ISSN	1464-5033 ; 0301-4460
ISSN (online)	1464-5033
ISSN	0301-4460
DOI	10.1080/03014460.2017.1325515
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Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

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Article ; Online: The Role of aDNA in Understanding the Coevolutionary Patterns of Human Sexually Transmitted Infections

Ville N. Pimenoff / Charlotte J. Houldcroft / Riaan F. Rifkin / Simon Underdown

Genes, Vol 9, Iss 7, p

2018 Volume 317

Abstract	Analysis of pathogen genome data sequenced from clinical and historical samples has made it possible to perform phylogenetic analyses of sexually transmitted infections on a global scale, and to estimate the diversity, distribution, and coevolutionary host relationships of these pathogens, providing insights into pathogen emergence and disease prevention. Deep-sequenced pathogen genomes from clinical studies and ancient samples yield estimates of within-host and between-host evolutionary rates and provide data on changes in pathogen genomic stability and evolutionary responses. Here we examine three groups of pathogens transmitted mainly through sexual contact between modern humans to provide insight into ancient human behavior and history with their pathogens. Exploring ancient pathogen genomic divergence and the ancient viral-host parallel evolutionary histories will help us to reconstruct the origin of present-day geographical distribution and diversity of clinical pathogen infections, and will hopefully allow us to foresee possible environmentally induced pathogen evolutionary responses. Lastly, we emphasize that ancient pathogen DNA research should be combined with modern clinical pathogen data, and be equitable and provide advantages for all researchers worldwide, e.g., through shared data.
Keywords	evolutionary medicine ; sexually transmitted infections ; papillomaviruses ; herpesviruses ; ectoparasites ; virus-host coevolution ; divergence ; host-switch ; Hominin evolution ; Genetics ; QH426-470
Subject code	630
Language	English
Publishing date	2018-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Assessing the photoprotective effects of red ochre on human skin by in vitro laboratory experiments

Riaan F. Rifkin / Francesco d'Errico / Laure Dayet-Boulliot / Beverley Summers

South African Journal of Science, Vol 111, Iss 3/4, Pp 1-

2015 Volume 8

Abstract: Archaeological indicators of cognitive complexity become increasingly prevalent during the African Middle Stone Age, with the habitual exploitation of red ochre widely viewed as a key feature of the emergence of modern human behaviour. Given that some of ...

Abstract	Archaeological indicators of cognitive complexity become increasingly prevalent during the African Middle Stone Age, with the habitual exploitation of red ochre widely viewed as a key feature of the emergence of modern human behaviour. Given that some of the uses of ochre remain ambiguous, we present the preliminary results of an ongoing study in which we explore the efficacy of red ochre as a photoprotective device or sunscreen. The capacity of ochre to inhibit the susceptibility of humans to the detrimental effects of ultraviolet radiation was confirmed through the in vitro calculation of the sun protection factor values of samples derived from the Kunene Region in Namibia and the Bokkeveld Group deposits, Western Cape Province, South Africa. Visible spectroscopy was employed to determine colourimetric parameters of samples and assess the correlation between ochre colour and sun protection factor. The possible role of ochre as a sunscreen agent for hominin populations, including modern humans, during the Middle Stone Age in Africa is explored. We conclude that the habitual use of red ochre as a photoprotective agent likely played a role in the ability of prehistoric humans to adapt to novel environmental circumstances.
Keywords	red ochre ; Ovahimba ; Middle Stone Age ; UVR ; sunscreen ; Science ; Q ; Science (General) ; Q1-390 ; Social Sciences ; H ; Social sciences (General) ; H1-99
Subject code	930
Language	English
Publishing date	2015-03-01T00:00:00Z
Publisher	Academy of Science of South Africa
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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