Widespread extinctions of co-diversified primate gut bacterial symbionts from humans

生物 克莱德 基因组 灵长类动物 进化生物学 系统发育学 系统发育树 人科 动物 自然选择 寄主(生物学) 厚壁菌 生态学 遗传学 基因 选择(遗传算法) 生物进化 16S核糖体RNA 人工智能 计算机科学
作者
Jon G. Sanders,Daniel D. Sprockett,Yingying Li,Deus Mjungu,Elizabeth V. Lonsdorf,Jean-Bosco N. Ndjango,Alexander V. Georgiev,John Hart,Crickette Sanz,David Morgan,Martine Peeters,Beatrice H. Hahn,Andrew H. Moeller
出处
期刊:Nature microbiology [Nature Portfolio]
卷期号:8 (6): 1039-1050 被引量:29
标识
DOI:10.1038/s41564-023-01388-w
摘要

Humans and other primates harbour complex gut bacterial communities that influence health and disease, but the evolutionary histories of these symbioses remain unclear. This is partly due to limited information about the microbiota of ancestral primates. Here, using phylogenetic analyses of metagenome-assembled genomes (MAGs), we show that hundreds of gut bacterial clades diversified in parallel (that is, co-diversified) with primate species over millions of years, but that humans have experienced widespread losses of these ancestral symbionts. Analyses of 9,460 human and non-human primate MAGs, including newly generated MAGs from chimpanzees and bonobos, revealed significant co-diversification within ten gut bacterial phyla, including Firmicutes, Actinobacteriota and Bacteroidota. Strikingly, ~44% of the co-diversifying clades detected in African apes were absent from available metagenomic data from humans and ~54% were absent from industrialized human populations. In contrast, only ~3% of non-co-diversifying clades detected in African apes were absent from humans. Co-diversifying clades present in both humans and chimpanzees displayed consistent genomic signatures of natural selection between the two host species but differed in functional content from co-diversifying clades lost from humans, consistent with selection against certain functions. This study discovers host-species-specific bacterial symbionts that predate hominid diversification, many of which have undergone accelerated extinctions from human populations.
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