Humans and nonhuman primates (NHPs) harbor complex gut microbial communities that affect phenotypes and fitness. The gut microbiotas of wild NHPs reflect their hosts’ phylogenetic histories and are compositionally distinct from those of humans, but in captivity the endogenous gut microbial lineages of NHPs can be lost or replaced by lineages found in humans. Despite its potential contributions to gastrointestinal dysfunction, this humanization of the gut microbiota has not been investigated systematically across captive NHP species. Here, we show through comparisons of well-sampled wild and captive populations of apes and monkeys that the fraction of the gut microbiota humanized by captivity varies significantly between NHP species but is remarkably reproducible between captive populations of the same NHP species. Conspecific captive populations displayed significantly greater than expected overlap in the sets of bacterial 16S rRNA gene variants that were differentially abundant between captivity and the wild. This overlap was evident even between captive populations residing on different continents but was never observed between heterospecific captive populations. In addition, we developed an approach incorporating human gut microbiota data to rank NHPs’ gut microbial clades based on the propensity of their lineages to be lost or replaced in captivity by lineages found in humans. Relatively few microbial genera displayed reproducible degrees of humanization in different captive host species, but most microbial genera were reproducibly humanized or retained from the wild in conspecific pairs of captive populations. These results demonstrate that the gut microbiotas of captive NHPs display predictable, host-species specific responses to captivity.

中文翻译：

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圈养灵长类动物肠道微生物群的可预测和宿主物种特异性人源化

人类和非人类灵长类动物 (NHP) 拥有影响表型和适应性的复杂肠道微生物群落。野生 NHP 的肠道微生物群反映了它们宿主的系统发育历史，并且在组成上与人类不同，但在人工饲养中，NHP 的内源性肠道微生物谱系可能会丢失或被人类中发现的谱系所取代。尽管它可能导致胃肠道功能障碍，但尚未对圈养的 NHP 物种系统地研究肠道微生物群的这种人性化。在这里，我们通过比较采样良好的野生和圈养类人猿和猴子种群，表明因圈养而人性化的肠道微生物群的比例在 NHP 物种之间存在显着差异，但在同一 NHP 物种的圈养种群之间具有显着的可重复性。同种圈养种群在圈养和野生之间差异丰富的细菌 16S rRNA 基因变异组中显示出明显大于预期的重叠。这种重叠甚至在居住在不同大陆的圈养种群之间也很明显，但从未在异种特异性圈养种群之间观察到。此外，我们开发了一种方法，结合人类肠道微生物群数据，根据 NHP 的谱系在圈养中被人类谱系丢失或取代的倾向对 NHP 的肠道微生物进化枝进行排名。相对较少的微生物属在不同圈养宿主物种中表现出可重复的人源化程度，但大多数微生物属在圈养种群的同种对中可重复地人源化或从野外保留下来。