Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3.
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3.
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DOI：
10.7554/elife.65088
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发表时间：
2021-05-04
期刊：
影响因子：
7.7
通讯作者：
Segata N
中科院分区：
文献类型：
--
作者：
Beghini F;McIver LJ;Blanco-Míguez A;Dubois L;Asnicar F;Maharjan S;Mailyan A;Manghi P;Scholz M;Thomas AM;Valles-Colomer M;Weingart G;Zhang Y;Zolfo M;Huttenhower C;Franzosa EA;Segata N
在过去十年中，微生物群落的不依赖培养的分析取得了巨大进展，特别是由于鸟枪法宏基因组学的生物分析方法的进步。随着对多组学、微生物参考基因组和菌株水平多样性的更多获取，改进的机会不断增加。为了利用这些优势，我们推出了bioBakery 3，这是一套用于宏基因组的分类学、菌株水平、功能和系统发育分析的综合改进方法，它是在现有的最大参考序列集的基础上新开发的。与当前的替代方法相比，MetaPhlAn 3提高了分类学分析的准确性，HUMAnN 3提高了功能潜力和活性分析的准确性。这些方法在应用于结直肠癌（1262个宏基因组）和炎症性肠病（1635个宏基因组和817个宏转录组）时发现了新的疾病 - 微生物组关联。使用StrainPhlAn 3和PanPhlAn 3对另外4077个宏基因组进行菌株水平分析，揭示了常见肠道微生物瘤胃球菌（Ruminococcus bromii）的系统发育和功能结构，此前仅由15个分离基因组描述过。通过开源实现和可在云端部署的可重复工作流程，bioBakery 3平台可以帮助研究人员提高微生物群落研究中多组学分析的分辨率、规模和准确性。
Culture-independent analyses of microbial communities have progressed dramatically in the last decade, particularly due to advances in methods for biological profiling via shotgun metagenomics. Opportunities for improvement continue to accelerate, with greater access to multi-omics, microbial reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set of integrated, improved methods for taxonomic, strain-level, functional, and phylogenetic profiling of metagenomes newly developed to build on the largest set of reference sequences now available. Compared to current alternatives, MetaPhlAn 3 increases the accuracy of taxonomic profiling, and HUMAnN 3 improves that of functional potential and activity. These methods detected novel disease-microbiome links in applications to CRC (1262 metagenomes) and IBD (1635 metagenomes and 817 metatranscriptomes). Strain-level profiling of an additional 4077 metagenomes with StrainPhlAn 3 and PanPhlAn 3 unraveled the phylogenetic and functional structure of the common gut microbe Ruminococcus bromii, previously described by only 15 isolate genomes. With open-source implementations and cloud-deployable reproducible workflows, the bioBakery 3 platform can help researchers deepen the resolution, scale, and accuracy of multi-omic profiling for microbial community studies.