Bartlett Alexandria, Blakeley-Ruiz J Alfredo, Richie Tanner, Theriot Casey M, Kleiner Manuel
Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA.
Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA.
Proteomics. 2025 Feb 21:e202400149. doi: 10.1002/pmic.202400149.
Diet has been shown to greatly impact the intestinal microbiota. To understand the role of individual dietary components, defined diets with purified components are frequently used in diet-microbiota studies. Defined diets frequently use purified casein as the protein source. Previous work indicated that casein contains microbial DNA potentially impacting results of microbiome studies. Other diet-based microbially derived molecules that may impact microbiome measurements, such as proteins detected by metaproteomics, have not been determined for casein. Additionally, other protein sources used in microbiome studies have not been characterized for their microbial content. We used metagenomics and metaproteomics to identify and quantify microbial DNA and protein in a casein-based defined diet to better understand potential impacts on metagenomic and metaproteomic microbiome studies. We further tested six additional defined diets with purified protein sources with an integrated metagenomic-metaproteomic approach and found that contaminating microbial protein is unique to casein within the tested set as microbial protein was not identified in diets with other protein sources. We also illustrate the contribution of diet-derived microbial protein in diet-microbiota studies by metaproteomic analysis of stool samples from germ-free mice (GF) and mice with a conventional microbiota (CV) following consumption of diets with casein and non-casein protein. This study highlights a potentially confounding factor in diet-microbiota studies that must be considered through evaluation of the diet itself within a given study.
研究表明，饮食对肠道微生物群有很大影响。为了了解单个饮食成分的作用，在饮食 - 微生物群研究中经常使用含有纯化成分的特定饮食。特定饮食通常使用纯化的酪蛋白作为蛋白质来源。先前的研究表明，酪蛋白含有可能影响微生物组研究结果的微生物DNA。其他可能影响微生物组测量的基于饮食的微生物衍生分子，如通过宏蛋白质组学检测到的蛋白质，尚未针对酪蛋白进行测定。此外，微生物组研究中使用的其他蛋白质来源尚未对其微生物含量进行表征。我们使用宏基因组学和宏蛋白质组学来识别和量化基于酪蛋白的特定饮食中的微生物DNA和蛋白质，以更好地了解对宏基因组学和宏蛋白质组学微生物组研究的潜在影响。我们进一步使用综合宏基因组 - 宏蛋白质组学方法测试了六种额外的含有纯化蛋白质来源的特定饮食，发现污染的微生物蛋白质在测试组中是酪蛋白特有的，因为在其他蛋白质来源的饮食中未鉴定出微生物蛋白质。我们还通过对无菌小鼠（GF）和具有传统微生物群（CV）的小鼠在食用含有酪蛋白和非酪蛋白蛋白质的饮食后粪便样本进行宏蛋白质组分析，说明了饮食衍生的微生物蛋白质在饮食 - 微生物群研究中的作用。这项研究强调了饮食 - 微生物群研究中一个潜在的混杂因素，在给定的研究中必须通过对饮食本身的评估来加以考虑。
