Quantification of bacterial strain count in the human gut microbiome in health and disease

健康和疾病中人体肠道微生物组中细菌菌株计数的量化

• 批准号: 10387448
• 负责人: Alice Yulan Chen-Liaw
• 金额: $ 4.95万
• 依托单位: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-12-23 至 2025-12-22
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10387448
• 关键词: Address; Affect; Algorithms; Architecture; Bacterial Genome; Bacteroides fragilis; Clostridium difficile; Colitis; Communities; Crohn' s disease; Cross-Sectional Studies; Culture Techniques; Diet; Disease; Feces; Functional disorder; Genome; Genomics; Gnotobiotic; Health; Human; Immune; Individual; Inflammatory; Inflammatory Bowel Diseases; Investigation; Learning; Measures; Mediating; Metagenomics; Methods; Modeling; Mus; Pathogenicity; Pattern; Physiology; Play; Process; Research; Resolution; Role; Severities; Severity of illness; Structure; T-Lymphocyte; Time; Ulcerative Colitis; Variant; Work; base; commensal bacteria; dysbiosis; fecal transplantation; genome sequencing; gut bacteria; gut colonization; gut microbiome; gut microbiota; microbial; microbial colonization; microbiome; microbiome alteration; microbiome composition; microbiota; microorganism; mouse model; success; transplantation therapy; whole genome

PROJECT SUMMARY In Inflammatory Bowel Disease (IBD), the gut microbiome demonstrates reduced species diversity that can then be reversed following FMT. However, no study has identified a common pattern of microbiome alteration that is causally related to IBD nor has any study elucidated the mechanisms underlying FMT success in the subset of individuals with IBD that respond. In FMT, both species and strain diversity are increasing but currently studies only track changes in species diversity, resulting in a fundamental feature of the microbiome that is changing but not measured in trials or in cross sectional studies of comparing with healthy and IBD microbiomes. Thus, it is unclear whether it is the increase in species or strain diversity that is critical to FMT success or if there are unique differences in the strain-level structure of the IBD microbiome. Since microbial functional variation is found at the strain level, a functional understanding of microbiome composition in IBD may lie at the strain level. However, no studies so far have systematically characterized the strain-level microbiome structure in health or disease. This proposal aims to define strain count—the number of unique strains each bacterial species stably maintains in an individual—in healthy and IBD microbiomes and to further investigate the functional impact of strain count in disease. We will quantify strain count by employing a high- throughput culturing technique to isolate and sequence thousands of gut bacterial isolates for all culturable species in a breadth-focused manner and validate our breadth-focused quantifications by using a depth- focused approach to intensely sequence more genomes from ten of the most common gut species. For our depth-sequencing, we will use gnotobiotic mice fed different diets to enrich for low abundance strains. This experimental approach allows us to increase the efficiency by which we capture the strains of a particular species and achieve a more accurate quantification of strain count. Aim 1—Based on our preliminary findings, we anticipate that there is a limited number of strains each species can maintain in the gut microbiota and that our method sequences a sufficient number of genomes to quantify strain count. We aim to define strain count in healthy and IBD microbiomes which will allow for higher resolution, functional investigations into microbiome composition in disease. In Aim 2—we will investigate the effect of increasing strain count on colitis severity. We will combine defined communities of strains isolated from an IBD and healthy microbiota in a gnotobiotic T cell transfer colitis model. The defined communities will allow us to specifically increase strain count while holding species diversity stable. By studying the functional role of strain count, we can uncover the potential contributions of microbiome strain-level architecture to the disease process and identify appropriate targets for optimizing FMT for the treatment of IBD.

项目概要 在炎症性肠病 (IBD) 中，肠道微生物组表现出物种多样性减少， 然而，尚无研究发现微生物组改变的常见模式。 与 IBD 有因果关系，也没有任何研究阐明 FMT 成功的机制 对 FMT 做出反应的 IBD 个体的子集，物种和品系多样性都在增加，但 目前的研究仅追踪物种多样性的变化，从而得出微生物组的基本特征 正在发生变化，但在与健康人和 IBD 比较的试验或横断面研究中未进行测量 因此，尚不清楚物种或菌株多样性的增加对于 FMT 至关重要。 成功或 IBD 微生物组的菌株水平结构是否存在独特差异。 在菌株水平上发现功能变异，这是对 IBD 微生物组组成的功能性理解 可能存在于应变水平上，然而，迄今为止还没有研究系统地表征应变水平。 该提案旨在定义健康或疾病中的微生物组结构——独特的数量。 每个细菌物种在健康和 IBD 微生物组中稳定维持在个体体内，并进一步 研究菌株计数对疾病的功能影响我们将通过采用高通量来量化菌株计数。 通量培养技术可对数千种肠道细菌分离株进行分离和测序，以获取所有可培养的细菌 以广度为中心的方式来分析物种，并通过使用深度来验证我们以广度为中心的量化 重点方法对十种最常见肠道物种的更多基因组进行密集测序。 通过深度测序，我们将使用喂食不同饮食的无菌小鼠来富集低丰度菌株。 实验方法使我们能够提高捕获特定菌株的效率 目标 1——根据我们的初步发现， 我们预计每个物种在肠道微生物群中可以维持的菌株数量有限，并且 我们的方法对足够数量的基因组进行测序以量化菌株计数。 对健康和 IBD 微生物群进行计数，这将有助于进行更高分辨率的功能研究 在目标 2 中，我们将研究增加菌株的影响。 我们将结合从 IBD 和健康人群中分离出的确定的菌株群落。 无菌 T 细胞转移结肠炎模型中的微生物群定义的群落将使我们能够专门进行研究。 增加菌株计数，同时保持物种多样性稳定通过研究菌株计数的功能作用，我们。 可以揭示微生物组菌株水平结构对疾病过程的潜在贡献， 确定优化 FMT 治疗 IBD 的适当目标。