Cell dormancy and virus entrapment

Microorganisms are frequently challenged by conditions that are suboptimal for growth and reproduction. To persist in such environments, microbes engage in dormancy, a strategy whereby individuals enter a reversible state of reduced metabolic activity. Traditionally, dormancy has been viewed as an adaptation to cope with harsh and fluctuating abiotic conditions, such as resource limitation, extreme temperature, or exposure to antimicrobial agents. However, growing evidence suggests that dormancy plays an important role in modifying host-virus interactions. Although dormancy can provide protection from infection, our findings demonstrate that viruses have evolved strategies to circumvent this metabolic defense. For example, certain viruses hijack the dormancy program of spore-forming bacteria (Bacillus and Clostridia) with the aid of auxiliary genes acquired from their hosts. During this process, viral genomes become entrapped within bacterial spores where they are shielded from the extracellular environment. Upon germination, these non-integrated viruses resume their lytic cycle and exploit the host for replication. Using Bacillus subtilis as a model system, this proposal aims to advance our understanding of host-virus coevolution within the framework of dormancy theory. First, we will test competing models of entrapment using CRISPR gene editing of viruses and quantitative single-cell assays to evaluate the role of auxiliary sporulation genes in lytic suppression and chromosomal segregation. Second, we will investigate the developmental consequences of entrapment based on host-virus expression profiles through single-cell transcriptomics and AI-informed morphological analyses. Third, we will track the fate of infected spores (“virospores”) using a microfluidic platform to quantify the dynamics and consequences of entrapment for host and virus fitness. To synthesize, we will integrate experimental data with mechanistic models to resolve conflicts about virus infection and dormancy decision-making in uncertain environments. The proposed work will advance host-pathogen theory and inform clinical applications, including phage therapies for chronic infections caused by spore-forming bacteria and other microorganisms with quiescent life stages. Project Number: 1R35GM161372-01 | Fiscal Year: 2026 | NIH Institute/Center: National Institute of General Medical Sciences (NIGMS) | Principal Investigator: Jay Lennon | Institution: TRUSTEES OF INDIANA UNIVERSITY, BLOOMINGTON, IN | Award Amount: $428,857 | Activity Code: R35 | Study Section: Special Emphasis Panel[ZRG1 MGG-D (55)] View on NIH RePORTER: https://reporter.nih.gov/project-details/11260352