BackgroundHumans have coevolved with microbial communities to establish a mutually advantageous relationship that is still poorly characterized and can provide a better understanding of the human microbiome. Comparative metagenomic analysis of human and non-human primate (NHP) microbiomes offers a promising approach to study this symbiosis. Very few microbial species have been characterized in NHP microbiomes due to their poor representation in the available cataloged microbial diversity, thus limiting the potential of such comparative approaches.ResultsWe reconstruct over 1000 previously uncharacterized microbial species from 6 available NHP metagenomic cohorts, resulting in an increase of the mappable fraction of metagenomic reads by 600%. These novel species highlight that almost 90% of the microbial diversity associated with NHPs has been overlooked. Comparative analysis of this new catalog of taxa with the collection of over 150,000 genomes from human metagenomes points at a limited species-level overlap, with only 20% of microbial candidate species in NHPs also found in the human microbiome. This overlap occurs mainly between NHPs and non-Westernized human populations and NHPs living in captivity, suggesting that host lifestyle plays a role comparable to host speciation in shaping the primate intestinal microbiome. Several NHP-specific species are phylogenetically related to human-associated microbes, such as Elusimicrobia and Treponema, and could be the consequence of host-dependent evolutionary trajectories.ConclusionsThe newly reconstructed species greatly expand the microbial diversity associated with NHPs, thus enabling better interrogation of the primate microbiome and empowering in-depth human and non-human comparative and co-diversification studies.

中文翻译：

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来自非人类灵长类肠道宏基因组的微生物基因组扩展了灵长类相关细菌生命树，包含 1000 多个新物种

背景人类与微生物群落共同进化，建立了一种互利关系，这种关系目前仍知之甚少，但可以提供对人类微生物组的更好理解。人类和非人类灵长类动物 (NHP) 微生物组的比较宏基因组分析为研究这种共生关系提供了一种有前途的方法。由于 NHP 微生物组中的微生物物种在现有编目微生物多样性中的代表性较差，因此在 NHP 微生物组中很少有微生物物种被表征，从而限制了这种比较方法的潜力。结果我们从 6 个可用的 NHP 宏基因组队列中重建了 1000 多种以前未表征的微生物物种，导致了宏基因组读数的可映射部分增加了 600%。这些新物种凸显出，几乎 90% 与 NHP 相关的微生物多样性都被忽视了。对这个新的分类群目录与来自人类宏基因组的超过 150,000 个基因组的比较分析表明，物种水平上的重叠有限，NHP 中只有 20% 的微生物候选物种也在人类微生物组中发现。这种重叠主要发生在 NHP 和非西方化人群以及圈养的 NHP 之间，这表明宿主生活方式在塑造灵长类肠道微生物组方面发挥着与宿主物种形成相当的作用。一些 NHP 特异性物种在系统发育上与人类相关微生物相关，例如 Elusimicrobia 和 Treponema，并且可能是宿主依赖性进化轨迹的结果。 结论 新重建的物种极大地扩展了与 NHP 相关的微生物多样性，从而能够更好地研究 NHP 的微生物多样性。灵长类微生物组并增强人类和非人类的深入比较和共同多样化研究。