The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
Department of Anthropology, Washington University in St. Louis, St. Louis, MO, 63130, USA.
ISME J. 2020 Jun;14(6):1584-1599. doi: 10.1038/s41396-020-0634-2. Epub 2020 Mar 20.
The gut microbiome can vary across differences in host lifestyle, geography, and host species. By comparing closely related host species across varying lifestyles and geography, we can evaluate the relative contributions of these factors in structuring the composition and functions of the microbiome. Here we show that the gut microbial taxa, microbial gene family composition, and resistomes of great apes and humans are more related by host lifestyle than geography. We show that captive chimpanzees and gorillas are enriched for microbial genera commonly found in non-Westernized humans. Captive ape microbiomes also had up to ~34-fold higher abundance and up to ~5-fold higher richness of all antibiotic resistance genes compared with wild apes. Through functional metagenomics, we identified a number of novel antibiotic resistance genes, including a gene conferring resistance to colistin, an antibiotic of last resort. Finally, by comparing our study cohorts to human and ape gut microbiomes from a diverse range of environments and lifestyles, we find that the influence of host lifestyle is robust to various geographic locations.
肠道微生物组可能因宿主生活方式、地理位置和宿主物种的差异而有所不同。通过比较生活方式和地理位置不同的密切相关的宿主物种，我们可以评估这些因素在构建微生物组的组成和功能方面的相对贡献。在这里，我们表明，与地理位置相比，人类和大型类人猿的肠道微生物类群、微生物基因家族组成和抗性组更多地受到宿主生活方式的影响。我们发现，圈养的黑猩猩和大猩猩体内富含在非西方化人群中常见的微生物属。与野生猿相比，圈养猿的微生物组中所有抗生素抗性基因的丰度高出约 34 倍，丰富度高出约 5 倍。通过功能宏基因组学，我们鉴定了一些新的抗生素抗性基因，包括一个对粘菌素（一种最后手段的抗生素）产生抗性的基因。最后，通过将我们的研究队列与来自不同环境和生活方式的人类和猿类肠道微生物组进行比较，我们发现宿主生活方式的影响在各种地理位置上都是稳健的。
