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.

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正交实验设计和元蛋白质组学方法评估肠道微生物组的体外培养基

基于体外培养的方法是节省时间和成本的解决方案，可用于快速评估药物或天然化合物对微生物群落的影响。培养基的营养成分是有效维持体外肠道微生物组的重要决定因素。这项研究结合了正交实验设计和元蛋白质组学方法，以获取功能性见解，以了解不同培养基成分对微生物组的影响。我们的结果表明，元蛋白质组学特征对中等成分的反应不同，包括无机盐，胆汁盐，粘蛋白和短链脂肪酸。方差的多因素分析进一步揭示了无机盐，胆汁盐和粘蛋白对肠道微生物蛋白不同功能基团的重要作用和相互作用。虽然在基本的代谢途径上观察到了广泛的调节作用，但不同的培养基成分也显示出对细胞壁，膜和包膜生物发生以及与细胞运动相关的功能的显着调节。特别地，鞭毛组装相关蛋白对粘蛋白的存在显着响应。这项研究提供了有关培养基成分对微生物组群落体外生长的功能影响的信息，并提供了在选择和优化用于培养离体微生物群的培养基时必须考虑的关键成分的见解。鞭毛组装相关蛋白对粘蛋白的存在有显着响应。这项研究提供了有关培养基成分对微生物组群落体外生长的功能影响的信息，并提供了在选择和优化用于培养离体微生物群的培养基时必须考虑的关键成分的见解。鞭毛组装相关蛋白对粘蛋白的存在有显着响应。这项研究提供了有关培养基成分对微生物组群落体外生长的功能影响的信息，并提供了在选择和优化用于培养离体微生物群的培养基时必须考虑的关键成分的见解。