Kropochev Andrew I, Lashin Sergey A, Matushkin Yury G, Klimenko Alexandra I
Institute of Cytology and Genetics, Novosibirsk 630090, Russia.
Kurchatov Genomic Center of ICG SB RAS, Novosibirsk 630090, Russia.
Biology (Basel). 2023 Jan 11;12(1):115. doi: 10.3390/biology12010115.
We propose the trait-based method for quantifying the activity of functional groups in the human gut microbiome based on metatranscriptomic data. It allows one to assess structural changes in the microbial community comprised of the following functional groups: butyrate-producers, acetogens, sulfate-reducers, and mucin-decomposing bacteria. It is another way to perform a functional analysis of metatranscriptomic data by focusing on the ecological level of the community under study. To develop the method, we used published data obtained in a carefully controlled environment and from a synthetic microbial community, where the problem of ambiguity between functionality and taxonomy is absent. The developed method was validated using RNA-seq data and sequencing data of the 16S rRNA amplicon on a simplified community. Consequently, the successful verification provides prospects for the application of this method for analyzing natural communities of the human intestinal microbiota.
我们提出了一种基于宏转录组数据量化人类肠道微生物群中功能组活性的基于特征的方法。它使人们能够评估由以下功能组组成的微生物群落的结构变化：丁酸盐产生菌、产乙酸菌、硫酸盐还原菌和黏蛋白分解菌。这是另一种通过关注所研究群落的生态水平来对宏转录组数据进行功能分析的方法。为了开发该方法，我们使用了在精心控制的环境中以及从合成微生物群落中获得的已发表数据，在这些数据中不存在功能与分类学之间的模糊性问题。所开发的方法使用RNA测序数据和简化群落上16S rRNA扩增子的测序数据进行了验证。因此，成功的验证为该方法应用于分析人类肠道微生物群的自然群落提供了前景。
