Bacteriophages have important roles in the ecology of the human gut microbiome but are under-represented in reference databases. To address this problem, we assembled the Metagenomic Gut Virus catalogue that comprises 189,680 viral genomes from 11,810 publicly available human stool metagenomes. Over 75% of genomes represent double-stranded DNA phages that infect members of the Bacteroidia and Clostridia classes. Based on sequence clustering we identified 54,118 candidate viral species, 92% of which were not found in existing databases. The Metagenomic Gut Virus catalogue improves detection of viruses in stool metagenomes and accounts for nearly 40% of CRISPR spacers found in human gut Bacteria and Archaea. We also produced a catalogue of 459,375 viral protein clusters to explore the functional potential of the gut virome. This revealed tens of thousands of diversity-generating retroelements, which use error-prone reverse transcription to mutate target genes and may be involved in the molecular arms race between phages and their bacterial hosts.

噬菌体在人类肠道微生物组的生态学中具有重要作用，但在参考数据库中的代表性不足。为了解决这个问题，我们组装了宏基因组肠道病毒目录，其中包含来自 11,810 个公开可用的人类粪便宏基因组的 189,680 个病毒基因组。超过 75% 的基因组代表双链 DNA 噬菌体，它们感染拟杆菌和梭状芽孢杆菌。基于序列聚类，我们确定了 54,118 个候选病毒种类，其中 92% 未在现有数据库中找到。宏基因组肠道病毒目录提高了对粪便宏基因组中病毒的检测，并且占人类肠道细菌和古细菌中发现的 CRISPR 间隔子的近 40%。我们还制作了一个包含 459,375 个病毒蛋白簇的目录，以探索肠道病毒组的功能潜力。