Plasmid encoded biofilm formation by the intestinal Bacteroidales and its importance in community ecology and resilience

肠道拟杆菌的质粒编码生物膜形成及其在群落生态和恢复力中的重要性

• 批准号: 10351693
• 负责人: Leonor Garcia-Bayona
• 金额: $ 9.92万
• 依托单位: UNIVERSITY OF CHICAGO
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-03-25 至 2024-02-29
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10351693
• 关键词: Adhesives; Affect; Anabolism; Antibiotic Therapy; Antibiotics; Architecture; Bacteroides; Bar Codes; Biopsy; Cells; China; Colon; Communities; Costs and Benefits; DNA; Data; Dissection; Ecology; Ecosystem; Evolution; Food; Frequencies; Genes; Gnotobiotic; Health; Health Benefit; Horizontal Gene Transfer; Human; Human Volunteers; Image; In Vitro; Individual; Inflammation; Inflammatory; Intervention; Intestines; Japanese; Knowledge; Life; Link; Location; Mediating; Mentors; Methods; Microbe; Microbial Biofilms; Microscopy; Mobile Genetic Elements; Mucous body substance; Mus; Persons; Phenotype; Physiologic pulse; Plasmids; Play; Polysaccharides; Population; Population Dynamics; Role; Sampling; Shapes; Stains; Stress; Structure; Surface; Techniques; Testing; Therapeutic Intervention; Training; cohort; cost; design; experimental study; extracellular; fitness; genetic element; gut bacteria; gut microbiome; gut microbiota; host-microbe interactions; human microbiota; human subject; improved; in vitro Assay; interest; member; microbial; microbial community; microbiome; microbiome components; microbiota; mouse model; mucosal biofilms; particle; polymicrobial biofilm; preservation; resilience; sample fixation; stressor; targeted treatment

Project Summary/Abstract The intestinal microbiota plays a major role in human health and is therefore the focus of significant interest as a target for therapeutic interventions. However, our understanding at the mechanistic level of the ecological and evolutionary forces shaping this diverse and densely colonized ecosystem is still tenuous. Notably, although we know that horizontal gene transfer is pervasive in the gut community, we understand only superficially the different roles of the majority of these exchanged genes and how this repertoire affects community dynamics. Similarly, little is known about the mechanisms underlying community resiliency. This question is particularly intriguing for the Bacteroidales, the most abundant Gram-negative gut microbiome members, which can stably colonize for decades. This proposal will investigate the importance of biofilm formation by the Bacteroidales for community ecology and resilience, focusing on the conjugative megaplasmid pMMCAT which enables biofilm formation in the strains that acquire it. This plasmid is exceptional because of the high frequency of intrapersonal transfer to multiple Bacteroidales species and its ubiquity, with conserved architecture, across global human populations. Some studies suggest that mucosal biofilms in healthy humans are rare, but there is little information about other locations or unattached biofilms. I hypothesize that this megaplasmid, shared among many species in a community, enables the formation of multi-species biofilms and plays a role in community cooperation, notably through increasing community resilience. To test this hypothesis, or otherwise understand alternative roles of pMMCAT, I will systematically characterize the phenotypes conferred by this plasmid in culture and in gnotobiotic mice in a single strain (aim 1) or in different Bacteroidales consortia where some strains carry it (aim 2). To understand the ecological role of pMMCAT, I will evaluate if its conferred phenotypes are synergized or inhibited by the co-resident strains and whether all, only some, or none of the other strains benefit. To visualize biofilms in the colon prior to and following a stress pulse, I will use two different methods to preserve the spatial structure of the gut community and use a biofilm matrix-specific stain. I will subsequently examine the evolutionary dynamics of pMMCAT transfer in these consortia (aim 3). To this end, I will directly quantify and visualize plasmid transfer in culture and in a gnotobiotic mouse. I will also quantify the cost of carrying pMMCAT and expressing biofilm formation genes. I will evaluate the impact of the introduction of a cheater strain that doesn’t pay this fitness cost of producing the biofilm matrix public good. Finally, I will track the evolution of pMMCAT over the course of twelve years in four human volunteers previously found to have pMMCAT-harboring strains. This dissection of the dynamics and mechanisms underlying plasmid-encoded biofilm formation in the gut will improve our current understanding of intestinal ecology and its recent changes in human populations, and will provide one more stepping stone towards targeted microbiome interventions for health benefits.

项目总结/摘要 肠道微生物群在人类健康中起着重要作用，因此是重大兴趣的焦点， 治疗干预的目标。然而，我们对生态系统的机械水平的理解 而形成这种多样性和密集殖民生态系统的进化力量仍然很脆弱。值得注意的是， 虽然我们知道水平基因转移在肠道群落中很普遍，但我们只知道， 从表面上看，这些交换的基因中的大多数的不同作用，以及这种剧目如何影响 社区动态同样，人们对社区复原力的机制知之甚少。这 对于类杆菌目，最丰富的革兰氏阴性肠道微生物组， 成员，可以稳定殖民数十年。本提案将探讨生物膜的重要性 形成的拟杆菌的社区生态和弹性，重点是接合 巨质粒pMMCAT，其能够在获得它的菌株中形成生物膜。 这是一个例外，因为个体内转移到多个拟杆菌目物种的频率很高， 在全球人群中普遍存在，具有保守的结构。一些研究表明， 在健康人体中的生物膜是罕见的，但关于其他位置或未附着的生物膜的信息很少。我 我假设这个大质粒，在一个社区中的许多物种之间共享，能够形成 多物种生物膜，并在社区合作中发挥作用，特别是通过增加社区 resilience.为了验证这一假设，或者理解pMMCAT的替代作用，我将系统地 在培养物中和在单一菌株中的无菌小鼠中表征由该质粒赋予的表型（aim 1)或在不同的拟杆菌目聚生体中，其中一些菌株携带它（目的2）。为了理解生态作用 的pMMCAT，我将评估其赋予的表型是否协同或抑制的共存菌株 以及是否所有、只有一些或没有其他菌株受益。为了使结肠中的生物膜可视化， 在压力脉冲之后，我将使用两种不同的方法来保护肠道群落的空间结构 并使用生物膜基质特异性染色剂。随后，我将研究pMMCAT的进化动力学 在这些联营集团中转让（目标3）。为此，我将直接量化和可视化培养中的质粒转移 和一只知菌小鼠。我还将量化携带pMMCAT和表达生物膜形成的成本 基因.我将评估引入一种作弊菌株的影响，这种菌株不支付这种健身成本， 产生生物膜基质公益物。最后，我将跟踪pMMCAT在12年的发展过程， 在先前发现具有携带pMMCAT的菌株的四名人类志愿者中，这种解剖 肠道中质粒编码生物膜形成的动力学和机制将改善我们目前的 了解肠道生态学及其最近在人群中的变化，并将提供一个更多的 为实现健康益处而采取有针对性的微生物组干预措施的垫脚石。