StrainR2能够准确地解析合成微生物群落中菌株水平的丰度。

StrainR2 accurately deconvolutes strain-level abundances in synthetic microbial communities.

作者信息

Heber Kerim, Tian Shuchang, Betancurt-Anzola Daniela, Koo Heejung, Bisanz Jordan E

机构信息

Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, United States.

One Health Microbiome Center, Huck Life Sciences Institute, University Park, PA 16802, United States.

出版信息

Bioinformatics. 2025 Aug 2;41(8). doi: 10.1093/bioinformatics/btaf440.

DOI:10.1093/bioinformatics/btaf440

PMID:40794845

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12377904/

Abstract

MOTIVATION

Synthetic microbial communities offer an opportunity to conduct reductionist research in tractable model systems. However, deriving abundances of highly related strains within these communities is currently unreliable. 16S rRNA gene sequencing does not resolve abundance at the strain level and other methods such as quantitative polymerase chain reaction (qPCR) scale poorly and are resource prohibitive for complex communities. We present StrainR2, which utilizes shotgun metagenomic sequencing to provide high accuracy strain-level abundances for all members of a synthetic community, provided their genomes.

RESULTS

Both in silico, and using sequencing data derived from gnotobiotic mice colonized with a synthetic fecal microbiota, StrainR2 resolves strain abundances with greater accuracy and efficiency than other tools utilizing shotgun metagenomic sequencing reads. We demonstrate that StrainR2's accuracy is comparable to that of qPCR on a subset of strains resolved using absolute quantification.

AVAILABILITY AND IMPLEMENTATION

Software is available at GitHub and implemented in C, R, and Bash. Software is supported on Linux and MacOS, with packages available on Bioconda or as a Docker container. The source code at the time of publication is also available on figshare at the doi: 10.6084/m9.figshare.29420780.

摘要

动机

合成微生物群落为在易于处理的模型系统中进行简化研究提供了机会。然而，目前在这些群落中推导高度相关菌株的丰度是不可靠的。16S rRNA基因测序无法在菌株水平上解析丰度，而其他方法，如定量聚合酶链反应（qPCR），扩展性较差，并且对于复杂群落来说资源消耗过大。我们提出了StrainR2，它利用鸟枪法宏基因组测序为合成群落的所有成员提供高精度的菌株水平丰度，前提是已知它们的基因组。