MetaGenomic Species (MGS:351) from Distal Human Gut Microbiota (MetaHit), Sample V1.CD41-0. Sutterella sp. CAG:351

Metagenomic data acquired by deep sequencing is immensely complex, lacks apparent structure and is typically dominated by unknown species. Using an abundance co-variance strategy, we group highly co-varying genes into MetaGenomic Species, which represent a wide range of biological entities: bacterial genomes, plasmids, genomic islands, clonal variation and bacteriophages. Applying this concept to a new 3.9 million microbial gene catalogue derived from 396 human stool samples we identified 7,381 such MetaGenomic Species. They range in size from 3 to 6,319 genes, with 741 MetaGenomic Species resembling bacterial genomes in number of genes contained. The Meta-Genomic Species displays remarkable consistency in taxonomy and GC content. 247 of the MetaGenomic Species assemblies even pass the HMP high quality draft genome criteria. A large proportion (73%) of the MetaGenomic Species displays no sequence similarity to any previously sequenced organism. Smaller MetaGenomic Species are enriched for genes characteristic for bacteriophages and functions important for biotic interactions and show strong dependencies to gene-rich MetaGenomic Species. We present the first unsupervised structuring of a highly complex series of metagenomic samples into biological entities, including a global analysis of the genetic interdependencies between bacteria, plasmids, phages and genetic islands in the human distal gut.

通过深度测序（Deep Sequencing）获取的宏基因组数据（Metagenomic Data）复杂度极高，缺乏明确的结构特征，且通常以未知物种为主导。我们采用丰度共变异策略（Abundance Co-variance Strategy），将高度共变异的基因聚类为宏基因物种（MetaGenomic Species），这类实体涵盖了多样化的生物类群：细菌基因组（Bacterial Genomes）、质粒（Plasmids）、基因组岛（Genomic Islands）、克隆变异（Clonal Variation）以及噬菌体（Bacteriophages）。我们将该思路应用于由396份人类粪便样本（Human Stool Samples）构建的全新390万微生物基因目录（Microbial Gene Catalogue），共识别出7381个此类宏基因物种。这些宏基因物种的基因数量跨度为3至6319个，其中741个宏基因物种的基因数量与细菌基因组的规模相仿。宏基因物种在分类学特征与GC含量（GC Content）上表现出显著的一致性。其中247个宏基因物种的组装结果甚至达到了人类微生物组计划（Human Microbiome Project, HMP）的高质量草图基因组标准。高达73%的宏基因物种与任何已测序生物（Previously Sequenced Organism）均未检测到序列相似性（Sequence Similarity）。小型宏基因物种富含噬菌体特征基因以及参与生物交互（Biotic Interactions）的关键功能基因，且与基因丰富型宏基因物种存在显著的依赖关系。本研究首次通过无监督结构化（Unsupervised Structuring）方法，将一系列高度复杂的宏基因组样本拆解为各类生物实体，并对人类远端肠道（Human Distal Gut）内细菌、质粒、噬菌体以及基因组岛之间的遗传互作关系进行了全局性分析。