Due to technical limitations, most gut microbiome studies have focused on prokaryotes, overlooking viruses. Phanta, a virome-inclusive gut microbiome profiling tool, overcomes the limitations of assembly-based viral profiling methods by using customized k-mer-based classification tools and incorporating recently published catalogs of gut viral genomes. Phanta’s optimizations consider the small genome size of viruses, sequence homology with prokaryotes and interactions with other gut microbes. Extensive testing of Phanta on simulated data demonstrates that it quickly and accurately quantifies prokaryotes and viruses. When applied to 245 fecal metagenomes from healthy adults, Phanta identifies ~200 viral species per sample, ~5× more than standard assembly-based methods. We observe a ~2:1 ratio between DNA viruses and bacteria, with higher interindividual variability of the gut virome compared to the gut bacteriome. In another cohort, we observe that Phanta performs equally well on bulk versus virus-enriched metagenomes, making it possible to study prokaryotes and viruses in a single experiment, with a single analysis.

由于技术限制，大多数肠道微生物组研究都集中在原核生物上，而忽略了病毒。Phanta 是一种包含病毒组的肠道微生物组分析工具，通过使用定制的k-克服了基于组装的病毒分析方法的局限性基于 mer 的分类工具，并结合最近发布的肠道病毒基因组目录。Phanta 的优化考虑了病毒的小基因组大小、与原核生物的序列同源性以及与其他肠道微生物的相互作用。Phanta 对模拟数据的广泛测试表明，它可以快速准确地量化原核生物和病毒。当应用于来自健康成年人的 245 个粪便宏基因组时，Phanta 在每个样本中识别出约 200 种病毒，比标准的基于组装的方法多约 5 倍。我们观察到 DNA 病毒和细菌之间的比例约为 2:1，与肠道细菌组相比，肠道病毒组的个体间变异性更高。在另一个队列中，我们观察到 Phanta 在批量宏基因组和富含病毒的宏基因组上表现同样出色，这使得在单个实验中研究原核生物和病毒成为可能，