SBIR Phase I: Establishing a Synthetic Niche to Reliably Colonize the Human Gut with Engineered Bacterial Therapeutics

这个小企业创新研究（SBIR）项目的更广泛的影响/商业潜力是利用工程肠道微生物的力量，通过开发控制其在患者体内丰度的工具来治疗疾病。基础技术平台利用对胃肠道条件做出反应的工程化肠道细菌，以适当的剂量和时间向肠道中的特定部位提供新的治疗活性。该SBIR项目将通过精确控制肠道中工程菌的丰度来提高这些基于细胞的疗法的可靠性。这种控制是确保不同患者饮食和微生物组的一致治疗效果的关键。工程细菌已被用于向肠道输送抗炎蛋白，以治疗患有炎症性肠病（IBD）模型的小鼠。IBD是一种无法治愈的慢性疾病，对目前的治疗反应率低，仅在美国就影响了140万美国人，每年花费63亿美元。除了解决将这种IBD疗法引入临床的关键挑战外，该SBIR项目还将使工程肠道细菌更广泛地应用于治疗其他疾病，如心脏病，肥胖和结直肠癌。SBIR第一阶段项目提出开发第一种通过工程治疗微生物实现肠道可靠定植的方法。可靠的定殖将通过将在对照分子上生长的能力工程化到治疗菌株中来实现，所述对照分子对于人类食用是安全的，很少被其他肠道细菌食用，并且不会被肠道组织吸收。首先，将从天然分离物中系统地去除所有怀疑参与对照分子生长的基因，以确定所需的基因。接下来，这些基因将被转移到非消耗性菌株中，以引入在对照分子上生长的能力。最后，这种经过改造以在对照分子上生长的新工程菌株将被引入到含有人类微生物群的小鼠中，并将测试通过给小鼠喂食对照分子来获得这些小鼠的可靠定殖的能力。该项目将利用最近对微生物群结构控制机制的见解，开发当前基于细胞的治疗方法中缺失的关键工具，以实现更可预测的治疗结果。

The broader impact/commercial potential of this Small Business Innovation Research (SBIR) project is to harness the power of engineered gut microbes for treating disease through the development of tools for controlling their abundance in patients. The underlying technology platform utilizes engineered gut bacteria that respond to gastrointestinal conditions to deliver new therapeutic activities to specific sites in the gut at the appropriate dose and time. This SBIR project will improve the reliability of these cell-based therapies by allowing for precise control over the abundance of engineered bacteria in the gut. Such control is key to ensuring a consistent therapeutic effect across different patient diets and microbiomes. Engineered bacteria have been used to deliver anti-inflammatory proteins to the gut to treat mice with a model of inflammatory bowel disease (IBD). IBD is a chronic disease with no cure and low response rates to current treatments, affecting 1.4 million Americans at an annual cost of $6.3 billion in the US alone. In addition to solving a critical remaining challenge in bringing this IBD therapy to the clinic, this SBIR project will enable broader application of engineered gut bacteria to treat additional diseases such as heart-disease, obesity and colorectal cancer. This SBIR Phase I project proposes to develop the first means of achieving reliable colonization of the gut by an engineered therapeutic microbe. Reliable colonization will be accomplished by engineering into a therapeutic strain the ability to grow on a control molecule that is safe for humans to consume, is rarely consumed by other gut bacteria, and will not be absorbed by the intestinal tissue. First, all genes that are suspected to be involved in growth on the control molecule will be systematically removed from a natural isolate to determine those that are required. Next, these genes will be transferred to a non-consuming strain to introduce the ability to grow on the control molecule. Finally, this newly engineered strain that was modified to grow on the control molecule will be introduced into mice that harbor a human microbiota, and the ability to get reliable colonization of these mice by feeding the mice the control molecule will be tested. This project will employ recent insights into the mechanisms governing microbiota structure to develop a key missing tool from current cell-based therapeutic approaches to achieve more predictable therapeutic outcomes.