Pei Zhangming, Liu Yufei, Chen Yutao, Pan Tong, Sun Xihao, Wang Hongchao, Ross R Paul, Lu Wenwei, Chen Wei
State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, P. R China.
School of Food Science and Technology, Jiangnan University, Wuxi, P. R China.
Gut Microbes. 2024 Jan-Dec;16(1):2309684. doi: 10.1080/19490976.2024.2309684. Epub 2024 Feb 1.
Prophages, which are an existing form of temperate phages that integrate into host genomes, have been found extensively present in diverse bacterial species. The human gut microbiome, characterized by its complexity, dynamism, and interconnectivity among multiple species, remains inadequately understood in terms of the global landscape of bacterial prophages. Here, we analyzed 43,942 human gut-derived bacterial genomes (439 species of 12 phyla) and identified 105,613 prophage regions in ~ 92% of them. 16254 complete prophages were distributed in ~ 24% of bacteria, indicating an extremely uneven prophage distribution across various species within the human gut. Among all identified prophages, ~4% possessed cross-genera (2-20 genera) integration capacity, while ~ 17% displayed broad infection host ranges (targeting 2-35 genera). Functional gene annotation revealed that antibiotic-resistance genes and toxin-related genes were detected in ~ 2.5% and ~ 5.8% of all prophages, respectively. Furthermore, through sequence alignments between our obtained prophages and publicly available human gut phageome contigs, we have observed that ~ 72% of non-redundant prophages are previously unreported genomes, and they illuminate ~ 6.5-9.5% of the individual intestinal "viral dark matter". Our study represents the first comprehensive depiction of human gut-derived prophages, provides a substantial collection of reference sequences for forthcoming human gut phageome-related investigations, and potentially enables better risk assessment of prophage dissemination.
原噬菌体是整合到宿主基因组中的温和噬菌体的一种存在形式，已被广泛发现存在于多种细菌物种中。人类肠道微生物群具有复杂性、动态性和多种物种间的相互关联性，就细菌原噬菌体的全球格局而言，人们对其了解仍不充分。在此，我们分析了43942个源自人类肠道的细菌基因组（12个门的439个物种），并在其中约92%的基因组中鉴定出105613个原噬菌体区域。16254个完整原噬菌体分布在约24%的细菌中，这表明人类肠道内不同物种间原噬菌体分布极不均衡。在所有鉴定出的原噬菌体中，约4%具有跨属（2 - 20个属）整合能力，而约17%表现出广泛的感染宿主范围（针对2 - 35个属）。功能基因注释显示，在所有原噬菌体中，分别有约2.5%和5.8%检测到抗生素抗性基因和毒素相关基因。此外，通过将我们获得的原噬菌体与公开可用的人类肠道噬菌体组重叠群进行序列比对，我们观察到约72%的非冗余原噬菌体是以前未报道的基因组，它们揭示了约6.5 - 9.5%的个体肠道“病毒暗物质”。我们的研究首次全面描绘了源自人类肠道的原噬菌体，为即将开展的人类肠道噬菌体组相关研究提供了大量参考序列集合，并有可能对原噬菌体传播进行更好的风险评估。
