UKRI/BBSRC-NSF/BIO: Community-dependent CRISPR-cas evolution and robust community function

微生物组研究从不同的人类和环境样本中产生了令人难以置信的数据清单。该领域继续将微生物群(微生物群落)作为管理人类和环境健康的许多生物过程中潜在的关键原因。该领域的一个主要挑战是超越相关的方法，建立对塑造微生物群动态和功能的力量的机械和定量的理解。合理设计和实验组装的“合成微生物群”为破译微生物组织的基本规则和设计新的微生物解决方案提供了一条令人兴奋的途径，以应对紧迫的应用社会挑战。然而，合成微生物群对环境扰动的稳健性仍然相对未经测试。微生物群扰动的一大类源于微生物寄生虫的攻击，如噬菌体病毒。这个项目调查了已定义的微生物群如何在短时间尺度(通过行为转变)和较长时间尺度(通过生态和进化转变)对病毒做出反应。该项目采用理论和实验相结合的方法，检验了微生物通讯系统可以预测地促进微生物组功能的假设，以及病毒抗性的成本。该项目通过多项具有社会意义的成果产生更广泛的影响，这些成果涵盖科学素养、研究参与、STEM教育和微生物群管理。个别物种通常通过修改或完全删除噬菌体使用的表面受体来进化对噬菌体的抵抗力。由于表面因素在调节环境相互作用中的重要性，这可能会对细菌的功能能力和物种相互作用产生重大影响。从合成群落的角度来看，针对噬菌体暴露而进行的表面因子修饰有可能损害群落的功能能力。细菌也可以通过CRISPR-CA对噬菌体产生抵抗力，保持细胞的功能能力不变，但这种获得性抵抗力的途径在实验室环境中很少看到。实验室CRISPR-Cas进化的缺乏对CRISPR-Cas作为获得性耐药的主要机制的理解提出了挑战。该项目假设CRISPR-Cas免疫获得是特定细胞内和特定细胞间信号机制和社区依赖的适应成本的一个紧急属性，这些机制共同促进了社区的强大功能。该项目通过确定一般原则、数学模型和工具来设计在功能上对噬菌体攻击具有健壮性的合成微生物群落，具有重要意义。这些工具反过来在不可避免地暴露于噬菌体的应用环境中促进微生物组辅助的环境健康、人类健康和工业的社会目标。这个美英合作项目得到了美国国家科学基金会(NSF)和英国生物技术和生物科学研究理事会(BBSRC)的支持，其中NSF资助美国的研究人员，BBSRC资助英国的合作伙伴。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

Microbiome research has produced an incredible inventory of data from diverse human and environmental samples. The field continues to implicate microbiomes (microbial communities) as potentially key causal agents in many biological processes governing human and environmental health. A major challenge for the field is to move beyond correlative approaches and to establish mechanistic and quantitative understanding of the forces shaping the dynamics and functions of microbiomes. Rationally designed and experimentally assembled ‘synthetic microbiomes’ offer an exciting avenue to decipher basic rules of microbial organization and engineer novel microbial solutions to pressing applied societal challenges. Yet, the robustness of synthetic microbiomes to environmental perturbations remains relatively untested. A major class of microbiome perturbation stems from assault by parasites of microbes, such as bacteriophage viruses (phages). This project investigates how defined microbiomes respond to viruses on both short timescales (via behavioral shifts) and longer timescales (via ecological and evolutionary shifts). Using a combination of theory and experiment, the project tests the hypothesis that robust microbiome functions are predictably promoted by microbial communication systems, and costs of virus resistance. The project holds broader impact through multiple societally relevant outcomes, spanning scientific literacy, research participation, STEM education and microbiome management. Individual species commonly evolve resistance to phages by modifying or entirely deleting the surface receptor used by the phage. This can have substantial impacts on the functional capacities and species interactions of the bacterium, due to the importance of surface factors in mediating environmental interactions. From a synthetic community perspective, surface factor modifications in response to phage exposure risk damaging the functional capacities of the community. Bacteria can also evolve resistance to phages via CRISPR-Cas, leaving the functional capacity of the cell intact, yet this pathway of acquired resistance is rarely seen in a lab setting. The paucity of lab CRISPR-Cas evolution presents a challenge to the understanding of CRISPR-Cas as a primary mechanism of acquired resistance. This project hypotheses that CRISPR-Cas immunity acquisition is an emergent property of intra- and inter-specific cell-cell signaling mechanisms and community-dependent fitness costs, which together promote robust community functioning. This project holds significance by identifying general principles, math models and tools for the design of synthetic microbial communities that are functionally robust against phage attack. These tools in turn promote microbiome-assisted societal goals for environmental health, human health and industry in applied settings where phage exposure is inevitable.This collaborative US/UK project is supported by the US National Science Foundation (NSF) and the UK Biotechnology and Biological Sciences Research Council (BBSRC), where NSF funds the US investigator and BBSRC funds the partners in the UK.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.