Background 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. Results 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. Conclusions 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.

中文翻译：

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生活方式和蠕虫的存在与喀麦隆人的肠道微生物组成有关

背景 非洲人群提供了一个独特的机会来询问宿主-微生物共同进化及其对适应性表型的影响，因为它们的基因组、表型和文化多样性。我们将肠道微生物组 16S rRNA 扩增子和鸟枪法宏基因组序列数据与来自喀麦隆的 575 名不同种族的非洲人的病原体负荷量化和免疫参数测量相结合。受试者遵循牧民、农牧民和狩猎采集者的生活方式，并与来自费城的美国城市人口进行比较。结果我们观察到与生存策略和国家相关的不同人群肠道微生物组组成的显着差异。在这些之后，与喀麦隆人肠道微生物组结构最密切相关的变量是肠道寄生虫的存在。相对于农牧民和牧民而言，狩猎采集者的寄生虫频率较高。Ascaris lumbricoides、Necator americanus、Trichuris trichiura 和Strongyloides stercoralis 土壤传播的蠕虫（“ANTS”寄生虫）显着共同发生，并且肠道寄生虫频率的增加与肠道微生物多样性的增加相关。肠道微生物组组成以 80% 的准确率预测 ANTS 阳性。反过来，ANTS 的定植与 TH1、TH2 和促炎细胞因子水平升高有关，表明与多种免疫机制有关。该数据集前所未有的规模允许对其他问题进行询问——例如，我们发现富拉尼牧民，他们消耗大量牛奶，拥有丰富的肠道细菌，可以分解半乳糖，乳糖代谢和代谢脂质的细菌的终产物。结论 这些数据记录了细菌微生物群和真核寄生虫之间的关联以及与宿主免疫反应的关联；其中每一个都进一步与生计做法相关。