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.

项目总结 在炎症性肠病(IBD)中，肠道微生物群显示出物种多样性降低，这可能 然后在FMT后逆转。然而，还没有研究确定微生物群改变的共同模式。 这与IBD有因果关系，也没有任何研究阐明FMT成功的机制。 有反应的IBD患者的子集。在FMT中，物种和菌株的多样性都在增加，但 目前的研究只跟踪物种多样性的变化，从而导致微生物组的一个基本特征 这种情况正在改变，但没有在与健康和IBD进行比较的试验或横断面研究中进行测量 微生物群。因此，目前还不清楚是物种或菌株多样性的增加对fmt至关重要。 成功与否取决于IBD微生物群的菌株水平结构是否存在独特的差异。由于微生物 在菌株水平上发现了功能变异，这是对IBD微生物组组成的功能理解 可能处于紧张的水平。然而，到目前为止，还没有研究系统地描述这种应变水平 健康或疾病中的微生物组结构。这项提议旨在定义菌株计数-唯一的 每种细菌在个体中稳定保持的菌株-在健康和IBD微生物群中，并进一步 研究细菌计数在疾病中的功能影响。我们将通过使用高密度的 用于所有可培养的数千个肠道细菌分离和测序的生产能力培养技术 以广度为重点的物种，并通过使用深度来验证我们以广度为重点的量化 集中测序十种最常见的肠道物种的更多基因组。为我们的 通过深度测序，我们将使用饲喂不同饲料的灵芝小鼠来丰富低丰度菌株。这 实验方法使我们能够提高捕获特定菌株的效率 并实现了更准确的菌株计数的量化。目标1-根据我们的初步调查结果， 我们预计，每个物种在肠道微生物区系中可以保持的菌株数量有限，而且 我们的方法对足够数量的基因组进行测序，以量化菌株数量。我们的目标是定义菌株 在健康和IBD微生物群中进行计数，将允许进行更高分辨率的功能研究 转化为疾病中的微生物群组成。在目标2中，我们将研究增加应变的影响 要看结肠炎的严重程度。我们将把从IBD分离的菌株和健康的菌株组合在一起 诺生菌T细胞转移性结肠炎模型中的微生物区系。定义的社区将使我们能够具体地 在保持物种多样性稳定的同时增加菌株数量。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 确定适当的目标，以优化治疗IBD的FMT。