Pan Sheng, Hullar Meredith A J, Lai Lisa A, Peng Hong, May Damon H, Noble William S, Raftery Daniel, Navarro Sandi L, Neuhouser Marian L, Lampe Paul D, Lampe Johanna W, Chen Ru
Institute of Molecular Medicine, the University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
Fred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA 98109, USA.
Microorganisms. 2020 Mar 7;8(3):379. doi: 10.3390/microorganisms8030379.
Although the gut microbiome has been associated with dietary patterns linked to health, microbial metabolism is not well characterized. This ancillary study was a proof of principle analysis for a novel application of metaproteomics to study microbial protein expression in a controlled dietary intervention. We measured the response of the microbiome to diet in a randomized crossover dietary intervention of a whole-grain, low glycemic load diet (WG) and a refined-grain, high glycemic load diet (RG). Total proteins in stools from 9 participants at the end of each diet period ( = 18) were analyzed by LC MS/MS and proteins were identified using the Human Microbiome Project (HMP) human gut microbiome database and UniProt human protein databases. T-tests, controlling for false discovery rate (FDR) <10%, were used to compare the Gene Ontology (GO) biological processes and bacterial enzymes between the two interventions. Using shotgun proteomics, more than 53,000 unique peptides were identified including microbial (89%) and human peptides (11%). Forty-eight bacterial enzymes were statistically different between the diets, including those implicated in SCFA production and degradation of fatty acids. Enzymes associated with degradation of human mucin were significantly enriched in the RG diet. These results illustrate that the metaproteomic approach is a valuable tool to study the microbial metabolism of diets that may influence host health.
尽管肠道微生物群与健康相关的饮食模式有关，但微生物代谢尚未得到充分表征。这项辅助研究是一项原理验证分析，用于蛋白质组学在可控饮食干预中研究微生物蛋白质表达的新应用。我们在一项全谷物、低血糖负荷饮食（WG）和精制谷物、高血糖负荷饮食（RG）的随机交叉饮食干预中，测量了微生物群对饮食的反应。在每个饮食阶段结束时，对9名参与者的粪便中的总蛋白质（ = 18）进行了液相色谱串联质谱分析，并使用人类微生物组计划（HMP）人类肠道微生物组数据库和通用蛋白质数据库（UniProt）对蛋白质进行了鉴定。使用控制错误发现率（FDR）<10%的t检验来比较两种干预之间的基因本体（GO）生物学过程和细菌酶。使用鸟枪法蛋白质组学，鉴定出了超过53,000种独特的肽段，包括微生物肽段（89%）和人类肽段（11%）。两种饮食之间有48种细菌酶存在统计学差异，包括那些与短链脂肪酸产生和脂肪酸降解有关的酶。与人类粘蛋白降解相关的酶在RG饮食中显著富集。这些结果表明，蛋白质组学方法是研究可能影响宿主健康的饮食微生物代谢的有价值工具。
