采用正交试验设计和蛋白组学评价肠道菌群的体外培养基

Title：
Evaluating in Vitro Culture Medium of Gut Microbiome with Orthogonal Experimental Design and a Metaproteomics Approach

DOI：
10.1021/acs.jproteome.7b00461

Abstract：
In vitro culture based approaches are time- and cost-effective solutions for rapidly evaluating the effects of drugs or natural compounds against microbiomes. The nutritional composition of the culture medium is an important determinant for effectively maintaining the gut microbiome in vitro. This study combines orthogonal experimental design and a metaproteomics approach to obtaining functional insights into the effects of different medium components on the microbiome. Our results show that the metaproteomic profile respond differently to medium components, including inorganic salts, bile salts, mucin, and short-chain fatty acids. Multifactor analysis of variance further revealed significant main and interaction effects of inorganic salts, bile salts, and mucin on the different functional groups of gut microbial proteins. While a broad regulating effect was observed on basic metabolic pathways, different medium components also showed significant modulations on cell wall, membrane, and envelope biogenesis and cell motility related functions. In particular, flagellar assembly related proteins were significantly responsive to the presence of mucin. This study provides information on the functional influences of medium components on the in vitro growth of microbiome communities and gives insight on the key components that must be considered when selecting and optimizing media for culturing ex vivo microbiotas.

All Authors：
Leyuan Li, Xu Zhang, Zhibin Ning, Janice Mayne, Jasmine I Moore, James Butcher, Cheng-Kang Chiang, David R Mack, Alain Stintzi, Daniel Figeys

First Authors：
Leyuan Li, Xu Zhang

Correspondence：
Alain Stintzi, Daniel Figeys

内容要点：

本研究采用正交实验设计与蛋白组学分析的方法，发现不同培养基成分（包括无机盐、胆汁盐、粘蛋白以及短链脂肪酸）下，蛋白组学特征不同。多因素方差分析显示无机盐、胆汁酸以及粘蛋白与肠道菌群的不同功能蛋白组之间有显著的相互作用。培养基成分对基础代谢通路有广泛的调节作用。不同的培养基成分对细胞壁、细胞膜、包膜生物合成、细胞功能性迁移等也有调节作用，尤其是鞭毛合成相关蛋白对黏蛋白的存在有显著响应。