Micro-engineered capsules for spatial sampling of microbiome in vivo

用于体内微生物组空间采样的微工程胶囊

基本信息

批准号：
10269448
负责人：
Sameer R Sonkusale
金额：
$ 15.99万
依托单位：
TUFTS UNIVERSITY MEDFORD
依托单位国家：
美国
项目类别：
财政年份：
2020
资助国家：
美国
起止时间：
2020-02-01 至 2024-01-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10269448
关键词：
3D Print Address Administrative Supplement Animal Model Animals Antibiotics Ascending colon Autopsy Award Budgets Cells Cellulose Charge Chronic Disease Color Complementary DNA Complex Custom DNA Data Diet Dietary Fiber Dietary Intervention Ecosystem Engineering Enterocytes Epithelial Cells Escherichia coli Exploratory/Developmental Grant for Diagnostic Cancer Imaging Family suidae Feces Funding Gastrointestinal tract structure Gene Expression Generations Genes Genetic Transcription Goals Health High-Throughput Nucleotide Sequencing Human In Situ Inflammatory Intestines Inulin Knowledge Laboratories Link Location Metagenomics Methods Modeling Motor Organ Parents Pectins Physiological Population Postdoctoral Fellow Pump RNA Research Research Personnel Research Proposals Risk Rodent Running Sampling Structure Suspensions Technology Testing Training Weaning body system capsule colon microbiota cost design dietary dietary control dietary supplements dysbiosis experimental study feasibility testing graduate student gut microbiome gut microbiota ileum improved in vitro testing in vivo insoluble fiber intestinal epithelium jejunum magnetic field microbial microbiome microbiota motor control novel pandemic disease parent project prebiotics prototype rRNA Genes response soluble fiber transcriptome transcriptome sequencing

项目摘要

ABSTRACT OF SUPPLEMENTAL RESEARCH This proposal is submitted in response to PA-20-227 (Administrative Supplements for Research on Dietary Supplements). The Specific Aims of parent award R21 AI144521 are (1) to design, fabricate and test micro- engineered ingestible capsules for sampling the gastro-intestinal tract; (2) to test the capsules in pigs. The parent project seeks to demonstrate the feasibility of non-invasively sampling the gastro-intestinal tract in a realistic animal model and to validate the ingestible capsule technology. Non-invasive sampling of the gastro-intestinal tract will advance the study of the intestinal microbiome and its beneficial functions. We are seeking supplemental funding to leverage research conducted under the parent award to study the effect of dietary supplements on the bacterial microbiota populating the gastro-intestinal tract. Although the intestinal microbiota's response to various perturbations, like diet, antibiotics or inflammatory conditions has been studied, the bulk of this research has been conducted in humans and rodents. For obvious reasons, most of these studies rely on the analysis of fecal DNA and fecal metabolites, which do not closely mirror changes in more proximal sections of the GI tract, like the jejunum, ileum and ascending colon. Supplemental funding would allow us to: 1) increase the number of pigs to study the effect of 3 commonly used prebiotic supplements (inulin, pectin, cellulose) on the microbiota populating different organs of the GI tract, 2) expand the scope of the project beyond the bacterial microbiota to the intestinal epithelium and its transcriptional response to diet. To non-invasively investigate the response of the intestinal epithelium to changes in diet, we are proposing to use RNA-Seq to analyze the "exfoliome", i.e., the transcriptome of exfoliated epithelial cells excreted in feces. To assess the quality of the exfoliome, we will compare exfoliome RNA-Seq data with RNA- Seq data obtained from epithelial cells collected directly from different GI organs after the animal has been sacrificed. The analysis of the pig intestinal exfoliome seeks to evaluate whether changes in enterocyte gene expression are detectable non-invasively by sequencing fecal cDNA. Although supplementary experiments expand the scope of the parent award to include dietary intervention, this research is not dependent on the optimization of the ingestible capsule. Pigs used for testing the capsules will be leveraged to investigate the following Supplemental Specific Aims: 1) to assess the impact of inulin, pectin and cellulose on the bacterial microbiota sampled in vivo using an ingestible capsule and collected post-mortem from different GI organs; 2) to apply RNA-Seq to evaluate the feasibility of characterizing the transcriptome of exfoliated enterocytes from pigs fed control and test diet. Thus, supplemental experiments will use a well-defined dietary intervention to expand the scope of the parent award in two directions; 1) to assess the effect of diet on commensal bacterial which are not present in fecal DNA; 2) to test the feasibility of non- invasively characterizing the enterocyte transcriptome and its response to dietary perturbation.

补充研究摘要该建议是根据PA-20-227提交的（饮食研究的行政补充剂补充）。父级奖R21 AI144521的具体目的是设计，制造和测试Micro- 设计的可植入的胶囊，用于对胃肠道进行采样；（2）测试猪中的胶囊。父项目旨在证明非侵入性采样胃肠道的可行性逼真的动物模型，并验证可观的胶囊技术。非侵入性抽样胃肠道将推进对肠道微生物组及其有益功能的研究。我们是寻求补充资金来利用父母奖项进行的研究来研究细菌菌群的饮食补充剂，胃肠道的植物群。虽然肠道微生物群对各种扰动的反应，例如饮食，抗生素或炎症状况研究了，这项研究的大部分是在人类和啮齿动物中进行的。出于明显的原因，大多数这些研究依赖于粪便DNA和粪便代谢产物的分析，这些分析并不能紧密地反映出的变化胃肠道的近端部分，例如空肠，回肠和上升结肠。补充资金将允许我们：1）增加研究3种常用益生元的影响的猪数量 gi道的不同器官的微生物群上的补充剂（肌蛋白，果胶，纤维素），2）膨胀细菌菌群超出肠上皮及其转录的项目范围对饮食的反应。为了非侵入性研究肠上皮对饮食变化的反应，我们提议使用RNA-Seq分析“去角质组”，即去角质上皮细胞的转录组排出粪便。为了评估去角质组的质量，我们将比较exfoliome RNA-seq数据与RNA- 从动物后直接从不同的胃gorgan收集的上皮细胞获得的SEQ数据已是牺牲了。对猪肠exfoliome的分析旨在评估肠细胞基因的变化是否变化通过测序粪cDNA，可以非侵入性地检测到表达。虽然补充实验将父母奖的范围扩大到包括饮食干预的范围，这项研究不依赖于可观胶囊的优化。用于测试胶囊的猪将被利用以研究以下补充特定目的：1）评估菊粉，果胶和纤维素对细菌微生物群在体内采样，并使用可摄取的胶囊，并从不同的gi器官； 2）应用RNA-Seq评估表征转录组的可行性来自猪的去角质肠上皮细胞喂养控制和测试饮食。因此，补充实验将使用定义明确的饮食干预措施将父母奖的范围扩大到两个方向上； 1）评估饮食对粪便DNA中不存在的共生细菌的影响； 2）测试非 - 侵入性地表征了肠上皮细胞转录组及其对饮食扰动的反应。