Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok, Thailand.
Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand.
PLoS Comput Biol. 2021 Jan 6;17(1):e1008487. doi: 10.1371/journal.pcbi.1008487. eCollection 2021 Jan.
Investigating metabolic functional capability of a human gut microbiome enables the quantification of microbiome changes, which can cause a phenotypic change of host physiology and disease. One possible way to estimate the functional capability of a microbial community is through inferring metagenomic content from 16S rRNA gene sequences. Genome-scale models (GEMs) can be used as scaffold for functional estimation analysis at a systematic level, however up to date, there is no integrative toolbox based on GEMs for uncovering metabolic functions. Here, we developed the MetGEMs (metagenome-scale models) toolbox, an open-source application for inferring metabolic functions from 16S rRNA gene sequences to facilitate the study of the human gut microbiome by the wider scientific community. The developed toolbox was validated using shotgun metagenomic data and shown to be superior in predicting functional composition in human clinical samples compared to existing state-of-the-art tools. Therefore, the MetGEMs toolbox was subsequently applied for annotating putative enzyme functions and metabolic routes related in human disease using atopic dermatitis as a case study.
研究人类肠道微生物组的代谢功能能力可以量化微生物组的变化，从而导致宿主生理学和疾病的表型变化。一种估计微生物群落功能能力的可能方法是通过从 16S rRNA 基因序列推断宏基因组内容。基因组规模模型 (GEM) 可以用作功能估计分析的系统级支架，但是到目前为止，还没有基于 GEM 的综合工具箱用于揭示代谢功能。在这里，我们开发了 MetGEMs（宏基因组规模模型）工具箱，这是一种从 16S rRNA 基因序列推断代谢功能的开源应用程序，旨在通过更广泛的科学界来促进人类肠道微生物组的研究。所开发的工具箱使用 shotgun 宏基因组数据进行了验证，并显示在预测人类临床样本中的功能组成方面优于现有的最先进工具。因此，MetGEMs 工具箱随后被应用于注释与特应性皮炎等人类疾病相关的假定酶功能和代谢途径。
