Petrone Brianna L, Bartlett Alexandria, Jiang Sharon, Korenek Abigail, Vintila Simina, Tenekjian Christine, Yancy William S, David Lawrence A, Kleiner Manuel
Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
Medical Scientist Training Program, Duke University School of Medicine, Durham, NC, USA.
Food Funct. 2025 Jan 2;16(1):282-296. doi: 10.1039/d4fo02656j.
Objective biomarkers of food intake are a sought-after goal in nutrition research. Most biomarker development to date has focused on metabolites detected in blood, urine, skin, or hair, but detection of consumed foods in stool has also been shown to be possible DNA sequencing. An additional food macromolecule in stool that harbors sequence information is protein. However, the use of protein as an intake biomarker has only been explored to a very limited extent. Here, we evaluate and compare measurement of residual food-derived DNA and protein in stool as potential biomarkers of intake. We performed a pilot study of DNA sequencing-based metabarcoding and mass spectrometry-based metaproteomics in five individuals' stool sampled in short, longitudinal bursts accompanied by detailed diet records ( = 27 total samples). Dietary data provided by stool DNA, stool protein, and written diet record independently identified a strong within-person dietary signature, identified similar food taxa, and had significantly similar global structure in two of the three pairwise comparisons between measurement techniques (DNA-to-protein and DNA-to-diet record). Metaproteomics identified proteins including myosin, ovalbumin, and beta-lactoglobulin that differentiated food tissue types like beef from dairy and chicken from egg, distinctions that were not possible by DNA alone. Overall, our results lay the groundwork for development of targeted metaproteomic assays for dietary assessment and demonstrate that diverse molecular components of food can be leveraged to study food intake using stool samples.
食物摄入量的客观生物标志物是营养研究中一个备受追求的目标。迄今为止，大多数生物标志物的开发都集中在血液、尿液、皮肤或头发中检测到的代谢物上，但通过DNA测序也已证明在粪便中检测所摄入的食物是可行的。粪便中另一种携带序列信息的食物大分子是蛋白质。然而，蛋白质作为摄入量生物标志物的应用仅在非常有限的程度上得到探索。在这里，我们评估并比较了粪便中残留的食物来源DNA和蛋白质作为摄入量潜在生物标志物的测量方法。我们对五名个体的粪便进行了一项初步研究，采用基于DNA测序的宏条形码技术和基于质谱的宏蛋白质组学技术，在短时间内进行纵向采样，并伴有详细的饮食记录（共27个样本）。粪便DNA、粪便蛋白质和书面饮食记录提供的饮食数据独立地识别出了个体内部强烈的饮食特征，识别出了相似的食物种类，并且在测量技术之间的三次两两比较中的两次（DNA与蛋白质以及DNA与饮食记录）中具有显著相似的整体结构。宏蛋白质组学鉴定出了包括肌球蛋白、卵清蛋白和β-乳球蛋白在内的蛋白质，这些蛋白质区分了不同的食物组织类型，如牛肉与乳制品、鸡肉与蛋类，而仅靠DNA是无法做到这些区分的。总体而言，我们的研究结果为开发用于饮食评估的靶向宏蛋白质组学检测方法奠定了基础，并表明可以利用食物的多种分子成分，通过粪便样本研究食物摄入量。
