意大利特伦托大学Nicola Segata研究小组近日取得一项新成果。经过不懈努力，他们利用MetaPhlAn 4对未表征物种的宏基因组分类学分析进行了扩展和改进。这一研究成果发表在2023年2月23日出版的国际学术期刊《自然—生物技术》上。

研究人员研发了MetaPhlAn 4，它整合了宏基因组组装和微生物分离基因组信息，以进行更全面的宏基因组分类分析。从1.01兆原核参考和宏基因组组装基因组的精选集合中，研究人员确定了26，970个物种级基因组的独特标记基因，其中有4，992个未在物种水平分类学上被鉴定。MetaPhlAn 4发现了约20%国际人类肠道微生物组和大于40%罕见环境种的微生物例如瘤胃微生物组，并且在综合评估中证明比可用的替代方案更准确，同时还可靠地量化了没有培养分离株的生物体。

将该方法应用于24，500个宏基因组，研究发现了以前未检测到强生物标志物，其与人类和小鼠微生物组中宿主条件和生活方式有关，并表明即使是以前未表征的物种也可以在单一微生物菌株分辨率下进行遗传分析。

据悉，宏基因组组装能够从微生物群落中发现新的物种，但它只能从大多数宏基因组中发现少量的新物种。

附：英文原文

Title: Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4

Author: Blanco-Mguez, Aitor, Beghini, Francesco, Cumbo, Fabio, McIver, Lauren J., Thompson, Kelsey N., Zolfo, Moreno, Manghi, Paolo, Dubois, Leonard, Huang, Kun D., Thomas, Andrew Maltez, Nickols, William A., Piccinno, Gianmarco, Piperni, Elisa, Punoch, Michal, Valles-Colomer, Mireia, Tett, Adrian, Giordano, Francesca, Davies, Richard, Wolf, Jonathan, Berry, Sarah E., Spector, Tim D., Franzosa, Eric A., Pasolli, Edoardo, Asnicar, Francesco, Huttenhower, Curtis, Segata, Nicola

Issue&Volume: 2023-02-23

Abstract: Metagenomic assembly enables new organism discovery from microbial communities, but it can only capture few abundant organisms from most metagenomes. Here we present MetaPhlAn 4, which integrates information from metagenome assemblies and microbial isolate genomes for more comprehensive metagenomic taxonomic profiling. From a curated collection of 1.01M prokaryotic reference and metagenome-assembled genomes, we define unique marker genes for 26,970 species-level genome bins, 4,992 of them taxonomically unidentified at the species level. MetaPhlAn 4 explains ~20% more reads in most international human gut microbiomes and >40% in less-characterized environments such as the rumen microbiome and proves more accurate than available alternatives on synthetic evaluations while also reliably quantifying organisms with no cultured isolates. Application of the method to >24,500 metagenomes highlights previously undetected species to be strong biomarkers for host conditions and lifestyles in human and mouse microbiomes and shows that even previously uncharacterized species can be genetically profiled at the resolution of single microbial strains.

DOI: 10.1038/s41587-023-01688-w

Source: https://www.nature.com/articles/s41587-023-01688-w