Recruiting Human Microbiome Shotgun Data to Site-Specific Reference Genomes

The human body consists of innumerable multifaceted environments that predispose colonization by a number of distinct microbial communities, which play fundamental roles in human health and disease. In addition to community surveys and shotgun metagenomes that seek to explore the composition and diversity of these microbiomes, there are significant efforts to sequence reference microbial genomes from many body sites of healthy adults. To illustrate the utility of reference genomes when studying more complex metagenomes, we present a reference-based analysis of sequence reads generated from 55 shotgun metagenomes, selected from 5 major body sites, including 16 sub-sites. Interestingly, between 13% and 92% (62.3% average) of these shotgun reads were aligned to a then-complete list of 2780 reference genomes, including 1583 references for the human microbiome. However, no reference genome was universally found in all body sites. For any given metagenome, the body site-specific reference genomes, derived from the same body site as the sample, accounted for an average of 58.8% of the mapped reads. While different body sites did differ in abundant genera, proximal or symmetrical body sites were found to be most similar to one another. The extent of variation observed, both between individuals sampled within the same microenvironment, or at the same site within the same individual over time, calls into question comparative studies across individuals even if sampled at the same body site. This study illustrates the high utility of reference genomes and the need for further site-specific reference microbial genome sequencing, even within the already well-sampled human microbiome.人体拥有无数复杂多元的微环境，这些微环境易被多种不同的微生物群落定植，而这些群落对人类健康与疾病发挥着关键作用。除了旨在探究这些微生物组（microbiome）组成与多样性的群落调查与霰弹枪宏基因组（shotgun metagenome）研究之外，学界正大力开展针对健康成年人多个身体部位的参考微生物基因组（reference microbial genome）测序工作。为阐明参考基因组（reference genome）在研究更为复杂的宏基因组（metagenome）时的应用价值，本研究对从5大身体部位（含16个子部位）选取的55份霰弹枪宏基因组样本所产生的序列读段（sequence reads）开展了基于参考基因组的分析。值得注意的是，这些霰弹枪序列读段中有13%至92%（平均62.3%）可比对至当时完整收录的2780个参考基因组，其中包含1583个人类微生物组参考基因组。然而，并未有任何一个参考基因组可在所有身体部位中被普遍检测到。针对任意一份宏基因组样本，源自与样本同一身体部位的部位特异性参考基因组，平均占已映射序列读段的58.8%。尽管不同身体部位的优势菌属存在差异，但彼此邻近或对称的身体部位的微生物组特征最为相似。无论是同一微环境下不同个体之间，还是同一个体同一部位随时间推移所产生的差异，其程度之大使得即便在同一身体部位取样的跨个体比较研究也受到了质疑。本研究证实了参考基因组的极高应用价值，同时表明即便在已被充分采样的人类微生物组领域，仍需开展更多针对特定身体部位的参考微生物基因组测序工作。