Using DNA sequencing to assess dietary species richness

使用 DNA 测序评估饮食物种丰富度

• 批准号: 10686098
• 负责人: Lawrence Anthony David
• 金额: $ 54.38万
• 依托单位: DUKE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-01 至 2026-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10686098
• 关键词: African American; African ancestry; Age; Animals; Benchmarking; Biochemical; Biodiversity; Biological Markers; Biometry; Cardiometabolic Disease; Clinical; Communication; Complex; Consumption; Country; DNA; DNA Sequence; DNA sequencing; Data; Development; Diet; Diet Habits; Diet Research; Diet Surveys; Dietary Assessment; Dietary Practices; Dietary intake; Digestion; Eating; Education; Enrollment; Ethnic Origin; Feces; Food; Genomics; Geography; Goals; Health; High-Throughput DNA Sequencing; Hispanic; Human; Individual; Intake; Link; Longitudinal cohort; Low income; Measures; Metabolic Diseases; Minority Groups; Modeling; Monitor; Nature; Nutritional; Organism; Outcome; Participant; Patient Self-Report; Physical activity; Plants; Population; Predisposition; Process; Protocols documentation; Public Health; Reaction Time; Sampling; Standardization; Surveys; Sustainable Development; Systematic Bias; Techniques; Testing; Time; Time trend; United Nations; Wild Animals; Work; Youth; cohort; dietary; disorder risk; economic determinant; experimental study; feeding; genomic biomarker; improved; indexing; insight; lower income families; nutritional epidemiology; obesity treatment; repository; socioeconomics; specific biomarkers; stool sample

ABSTRACT: Valid measures of diet are essential for monitoring and improving human health. One simple measure is dietary diversity (i.e., the number of different foods eaten over a period of time), which can serve as a marker of nutritional inadequacies. Surveys of dietary diversity, however, are limited by current assessment techniques that rely on dietary self-report. Another approach to surveying dietary diversity would be to use biomarkers or biochemical indicators of diet. However, a dietary biomarker that specifically captures overall dietary diversity has yet to be developed. Here, we will develop and validate a new technique, known as DNA metabarcoding, for enumerating the number of dietary plant and animal species individuals consume (dietary species richness). Our approach builds on a conceptual insight made by ecologists studying complex feeding practices in wild animal populations, which is that dietary DNA survives digestion and can be detected in stool using high-throughput DNA sequencing. Our preliminary studies support the promise of this approach: we have successfully amplified and sequenced more than a hundred dietary species from over a thousand human stool samples collected across multiple countries. Our pilot work has also shown significant correlations between the number of dietary species captured by DNA metabarcoding and survey-based indices of dietary diversity and quality. To further establish DNA metabarcoding as a reliable and useful marker of dietary diversity, our team of experts in fecal genomics, nutritional epidemiology, and biostatistics will pursue two Specific Aims. First, we will optimize DNA metabarcoding for assessing intake of dietary animal species. This Aim will build on our existing protocols for metabarcoding analysis of dietary plants. We will perform bench-top experiments under well- controlled lab settings using mixtures of intact and processed foods. We will then test our most promising protocols using a repository of stool samples collected from human cohorts undergoing controlled feeding. Second, we will test the validity and utility of measuring dietary diversity using DNA metabarcoding. This Aim will apply the technique to: 1) a cohort of primarily African-American/Hispanic youth from low-income families enrolled in a study of obesity treatment; and, 2) a cohort of 1,000 individuals of African descent from five countries with varying dietary habits and cardiometabolic disease risk. We will use these studies to validate that metabarcoding species richness reflects existing measures of dietary diversity measured by recall-based surveys of dietary intake. These real-world cohorts will further allow us to integrate metabarcoding data into models of metabolic disease risk, examine temporal trends in metabarcoding results, and identify potential geographic and socioeconomic determinants of dietary species richness.

摘要：有效的饮食措施对于监测和改善人类健康至关重要。一个简单 度量是饮食多样性（即，在一段时间内食用的不同食物的数量），可以用作 营养不足的标志。但是，饮食多样性的调查受到当前评估的限制 依靠饮食自我报告的技术。调查饮食多样性的另一种方法是使用 饮食的生物标志物或生化指标。但是，专门捕获总体的饮食生物标志物 饮食多样性尚未开发。在这里，我们将开发并验证一种新技术，称为DNA metabarcoding，用于列举饮食动植物的数量和动物种子的消费（饮食 物种丰富度）。我们的方法建立在研究复杂饲料的生态学家做出的概念见解的基础上 野生动物种群的实践，即饮食DNA可以存活消化，可以在粪便中检测到 使用高通量DNA测序。我们的初步研究支持这种方法的希望：我们有 从一千多个人的粪便中成功放大并测序了一百多种饮食物种 在多个国家 /地区收集的样品。我们的飞行员工作也显示了 通过DNA元法编码和基于调查的饮食多样性指数捕获的饮食物种数量 质量。为了进一步建立DNA metabarcoding作为饮食多样性的可靠且有用的标志，我们的团队 粪便基因组学，营养流行病学和生物统计学专家将追求两个具体目标。首先，我们会的 优化DNA metabarcoding，以评估饮食动物物种的摄入量。这个目标将基于我们现有的 用于饮食植物的元编码分析的方案。我们将在井下进行基准实验 使用完整和加工食品的混合物受控的实验室设置。然后，我们将测试我们最有前途的 使用经受受控喂养的人群收集的粪便样品存储库的协议。 其次，我们将使用DNA元编码测量饮食多样性的有效性和实用性。这个目标 将技术应用于：1）低收入家庭的主要是非裔美国人/西班牙裔青年 参加了肥胖治疗研究； 2）来自五个国家的1,000个非洲血统的人群 具有不同的饮食习惯和心脏代谢疾病风险。我们将使用这些研究来验证 元编码物种丰富度反映了通过基于召回的饮食多样性的现有措施 饮食摄入量的调查。这些现实世界的同伙将使我们能够将元法编码数据集成到 代谢疾病风险的模型，检查元法编码结果的时间趋势，并确定潜力 饮食物种丰富度的地理和社会经济决定因素。