Human biology and ancient DNA: exploring disease, domestication and movement

No abstract available.http://www.tandfonline.com/loi/iahb202020-07-15hj2019BiochemistryGeneticsMicrobiology and Plant Patholog

Migrating microbes : what pathogens can tell us about population movements and human evolution

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.CJH was funded by the University of Cambridge. JBR was funded by the University of Pretoria and the South African National Research Foundation (ERTTG 2016 grant UID 105197). RFR was funded by the National Geographic Society/Waitt Fecundation Scientific Exploration Grant (Nr. W420-15) and the University of Pretoria. SJU was funded by Oxford Brookes University.http://www.tandfonline.com/loi/iahb202018-06-30hj2017Genetic

Rickettsia felis DNA recovered from a child who lived in southern Africa 2000 years ago

DATA AVAILABILITY : Raw reads from Ballito Bay A samples are available under the NCBI BioProject PRJEB22660. The R. felis BBayA mapped reads and the metagenome-assembled genome are available under the NCBI BioProject PRJNA930765. The NCBI WGS accession number is JAQQRK000000000.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.A National Geographic Society Scientific Exploration Grant, the Oppenheimer Endowed Fellowship in Molecular Archaeology, the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme and the Knut and Alice Wallenberg Foundation.https://www.nature.com/commsbiohj2023BiochemistryGeneticsMicrobiology and Plant Patholog

Ancient oncogenesis, infection and human evolution

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.National Research Foundation South Africa, National Geographic Society, Grant/Award Number: W420-15, Waitt Foundation, University of Pretoria.http://www.wileyonlinelibrary.com/journal/evaam2018Genetic

The healthy human blood microbiome : fact or fiction?

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.An NRF career advancement fellowship, an MRC self-initiated research grant, a National Geographic Society Scientific Exploration Grant and the University of Pretoria.http://www.frontiersin.org/Cellular_and_Infection_Microbiologyam2020BiochemistryGeneticsMicrobiology and Plant Patholog