Lifestyle and the presence of helminths is associated with gut microbiome composition in Cameroonians

• Published in: Genome Biology Vol. 21; no. 1; p. 122
• Main Authors: Rubel, Meagan A., Abbas, Arwa, Taylor, Louis J., Connell, Andrew, Tanes, Ceylan, Bittinger, Kyle, Ndze, Valantine N., Fonsah, Julius Y., Ngwang, Eric, Essiane, André, Fokunang, Charles, Njamnshi, Alfred K., Bushman, Frederic D., Tishkoff, Sarah A.
• Format: Journal Article
• Language: English
• Published: England BioMed Central 25.05.2020; BMC
• Subjects: agropastoralism; Animals; Ascaris lumbricoides; Bacteria; Blood; Cameroon; coevolution; Colonization; Cytokines; data collection; Diet, Paleolithic; Digestive system; ethnic differences; Farmers - statistics & numerical data; Feces; Galactose; Gastrointestinal Microbiome; genome; Genomics; Gut microbiome; Gut microbiota; Helminths; HIV; Host-Parasite Interactions - immunology; Human immunodeficiency virus; Humans; Hunter-gatherers; Immune response; Industrialization; Infections; Inflammation; Intestinal microflora; intestinal microorganisms; Lactose; Life Style; lifestyle; Lifestyles; Lipid metabolism; Lymphocytes T; Machine Learning; metabolism; Metagenome; Metagenomics; Microbiomes; Microbiota; Microscopy; milk; multicultural diversity; Necator americanus; Nematoda - physiology; Parasite Load; Parasites; Parasitic diseases; Pathogens; phenotype; Phenotypes; Phylogenetics; Physiology; RNA, Ribosomal, 16S - genetics; rRNA 16S; Strongyloides stercoralis; Trichuris trichiura; Variables; Cameroon; United States > US; Industrialization; Lactose; Diet; HIV; Hunter-gatherers; Parasites; Gut microbiome; Helminths; Metagenomic sequencing; TH2
• ISSN: 1474-760X; 1474-7596; 1474-760X
• DOI: 10.1186/s13059-020-02020-4

African populations provide a unique opportunity to interrogate host-microbe co-evolution and its impact on adaptive phenotypes due to their genomic, phenotypic, and cultural diversity. We integrate gut microbiome 16S rRNA amplicon and shotgun metagenomic sequence data with quantification of pathogen burden and measures of immune parameters for 575 ethnically diverse Africans from Cameroon. Subjects followed pastoralist, agropastoralist, and hunter-gatherer lifestyles and were compared to an urban US population from Philadelphia. We observe significant differences in gut microbiome composition across populations that correlate with subsistence strategy and country. After these, the variable most strongly associated with gut microbiome structure in Cameroonians is the presence of gut parasites. Hunter-gatherers have high frequencies of parasites relative to agropastoralists and pastoralists. Ascaris lumbricoides, Necator americanus, Trichuris trichiura, and Strongyloides stercoralis soil-transmitted helminths ("ANTS" parasites) significantly co-occur, and increased frequency of gut parasites correlates with increased gut microbial diversity. Gut microbiome composition predicts ANTS positivity with 80% accuracy. Colonization with ANTS, in turn, is associated with elevated levels of TH1, TH2, and proinflammatory cytokines, indicating an association with multiple immune mechanisms. The unprecedented size of this dataset allowed interrogation of additional questions-for example, we find that Fulani pastoralists, who consume high levels of milk, possess an enrichment of gut bacteria that catabolize galactose, an end product of lactose metabolism, and of bacteria that metabolize lipids. These data document associations of bacterial microbiota and eukaryotic parasites with each other and with host immune responses; each of these is further correlated with subsistence practices.