Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue

Metagenomic sequencing has contributed important new knowledge about the microbes that live in a symbiotic relationship with humans. With modern sequencing technology it is possible to generate large numbers of sequencing reads from a metagenome but analysis of the data is challenging. Here we present the bioinformatics pipeline MEDUSA that facilitates analysis of metagenomic reads at the gene and taxonomic level. We also constructed a global human gut microbial gene catalogue by combining data from 4 studies spanning 3 continents. Using MEDUSA we mapped 782 gut metagenomes to the global gene catalogue and a catalogue of sequenced microbial species. Hereby we find that all studies share about half a million genes and that on average 300 000 genes are shared by half the studied subjects. The gene richness is higher in the European studies compared to Chinese and American and this is also reflected in the species richness. Even though it is possible to identify common species and a core set of genes, we find that there are large variations in abundance of species and genes.

宏基因组测序（Metagenomic Sequencing）为解析与人类共生的微生物提供了关键性新认知。依托现代测序技术，可从宏基因组中获取海量测序读段，但相关数据分析仍颇具挑战。本研究推出一款名为MEDUSA的生物信息学流程，可实现基因与分类学水平下的宏基因组读段分析。本研究还整合了覆盖三大洲的4项研究数据，构建了全球人类肠道微生物基因目录。借助MEDUSA流程，本研究将782个肠道宏基因组比对至上述全球基因目录以及已测序微生物物种目录。分析结果显示，所有研究共共享约50万个基因，且平均有30万个基因为半数研究受试者所共有。相较于中国与美国的研究队列，欧洲队列的基因丰富度更高，这一差异在物种丰富度层面亦有所体现。尽管可识别出共通的微生物物种与核心基因集，但研究发现物种与基因的丰度仍存在显著差异。