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1. Phage-plasmid-like elements are found throughout diverse environments and encode niche-specific functional traits

   https://doi.org/10.1371/journal.pone.0350027  

   Mullet, James I; Zhang, Liqing; Pruden, Amy; Brown, Connor L (May 2026, PLOS One)

   Gao, Feng (Ed.)

   Phage-plasmids are unique mobile genetic elements that function as plasmids and temperate phages. While it has been observed that such elements often encode antibiotic resistance genes and defense system genes, little else is known about other functional traits they encode. Further, no study to date has documented their environmental distribution and prevalence. Here, we performed genome sequence mining of public databases of phages and plasmids utilizing a random forest classifier to identify phage-plasmids. We recovered 5,712 unique phage-plasmid-like genomes from a remarkable array of disparate environments, including human, animal, plant, fungi, soil, sediment, freshwater, wastewater, and saltwater environments. The resulting genomes were used in a comparative sequence analysis, revealing functional traits/accessory genes associated with specific environments. Host-associated elements contained the most defense systems (including CRISPR and anti-CRISPR systems) as well as antibiotic resistance genes, while other environments, such as freshwater and saltwater systems, tended to encode components of various biosynthetic pathways. Interestingly, we identified genes encoding for certain functional traits, including anti-CRISPR systems and specific antibiotic resistance genes, that were enriched in phage-plasmid-like elements relative to both plasmids and phages. Our results highlight that phage-plasmid-like elements are found across a wide-array of environments and likely play a role in shaping microbial ecology in a multitude of niches. 

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2. Chemical inhibition of a bacterial immune system

   https://doi.org/10.1016/j.chom.2026.01.003  

   Zang, Zhiyu; Duncan, Olivia K; Sabonis, Dziugas; Fedorova, Iana; Shi, Yun; Miraj, Gause; Le, Shuai; Deng, Jun; Zhu, Yuhao; Cai, Yanyao; et al (February 2026, Cell Host & Microbe)

   The rise of antibiotic resistance motivates a revived interest in phage therapy. However, bacteria possess dozens of anti-phage immune systems that confer resistance to therapeutic phages. Chemical inhibitors of these anti-phage immune systems could be employed as adjuvants to overcome resistance in phage-based therapies. Here, we report a class of chemical inhibitors that selectively inhibit type II Thoeris anti-phage immune systems from diverse bacteria—including antibiotic-resistant pathogens, thereby sensitizing phage-resistant bacteria to phages. These inhibitors block the biosynthesis of a histidine-ADPR intracellular “alarm” signal by ThsB, thereby preventing ThsA from arresting phage replication. Chemical inhibition of the Thoeris defense improves the efficacy of a model phage therapy against a phage-resistant clinical isolate of P. aeruginosa in a mouse infection, suggesting a therapeutic potential. These findings demonstrate that the selective inhibition of anti-phage defense systems can improve the efficacy of therapeutic phages, suggesting a strategy to circumvent phage-therapy resistance. 

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3. Chemical inhibition of a bacterial immune system

   https://doi.org/10.1101/2025.02.20.638879  

   Zang, Zhiyu; Duncan, Olivia K; Sabonis, Dziugas; Shi, Yun; Miraj, Gause; Fedorova, Iana; Le, Shuai; Deng, Jun; Zhu, Yuhao; Cai, Yanyao; et al (February 2025, bioRxiv)

   Abstract The rise of antibiotic resistance motivates a revived interest in phage therapy. However, bacteria possess dozens of anti-bacteriophage immune systems that confer resistance to therapeutic phages. Chemical inhibitors of these anti-phage immune systems could be employed as adjuvants to overcome resistance in phage-based therapies. Here, we report that anti-phage systems can be selectively inhibited by small molecules, thereby sensitizing phage-resistant bacteria to phages. We discovered a class of chemical inhibitors that inhibit the type II Thoeris anti-phage immune system. These inhibitors block the biosynthesis of a histidine-ADPR intracellular ‘alarm’ signal by ThsB and prevent ThsA from arresting phage replication. These inhibitors promiscuously inhibit type II Thoeris systems from diverse bacteria—including antibiotic-resistant pathogens. Chemical inhibition of the Thoeris defense improved the efficacy of a model phage therapy against a phage-resistant strain ofP. aeruginosain a mouse infection, suggesting a therapeutic potential. Furthermore, these inhibitors may be employed as chemical tools to dissect the importance of the Thoeris system for phage defense in natural microbial communities. 

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4. Chemical inactivation of a bacterial immune system de-domesticates a temperate phage and promotes its spread

   https://doi.org/10.64898/2026.05.14.725270  

   Cai, Yanyao; Lazar, Jaka Jakin; Shi, Yun; Mishra, Biswa P; Ve, Thomas; Dragoš, Anna; Gerdt, Joseph P (May 2026, bioRxiv)

   Microbial communities shape hosts and ecosystems, yet the behaviors of these microbes are themselves controlled by mobile genetic elements. These mobile genetic elements (MGEs) compete and influence one another’s distributions. For example, many anti-phage immune systems are carried by prophages, plasmids, and integrative and conjugative elements (ICEs). It is unclear how important each of these interference mechanisms is for the spread of different mobile elements. Chemical inhibitors of these mechanisms of inter-MGE competition can clarify their mechanisms and significance in diverse environments. We discovered chemical inhibitors of SpbK—an antiphage defense encoded by an ICE in several strains ofBacillus subtilis. It is believed to prevent the dissemination of SPβ -like temperate phages, forcing SPβ to remain ‘domesticated’ in its ICE-containing host. Chemical inhibition of SpbK dramatically improved the escape of infectious SPβ phages capable of disseminating and forming new lysogens. Furthermore, SpbK is part of a widespread class of Toll/interleukin-1 receptor (TIR)-domain containing enzymes that are prevalent both in prokaryotic antiphage immune systems and eukaryotic immune signaling. Our inhibitors reveal two distinct mechanisms of inhibiting TIR-domain enzymes. These models of inhibition may broadly apply across immune proteins, enabling inhibition of many TIR immune systems that influence phage spread as well as plant immunity and animal cellular signaling. 

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5. mobileOG-db: a Manually Curated Database of Protein Families Mediating the Life Cycle of Bacterial Mobile Genetic Elements

   https://doi.org/10.1128/aem.00991-22  

   Brown, Connor L.; Mullet, James; Hindi, Fadi; Stoll, James E.; Gupta, Suraj; Choi, Minyoung; Keenum, Ishi; Vikesland, Peter; Pruden, Amy; Zhang, Liqing (September 2022, Applied and Environmental Microbiology)

   Nojiri, Hideaki (Ed.)

   ABSTRACT Bacterial mobile genetic elements (MGEs) encode functional modules that perform both core and accessory functions for the element, the latter of which are often only transiently associated with the element. The presence of these accessory genes, which are often close homologs to primarily immobile genes, incur high rates of false positives and, therefore, limits the usability of these databases for MGE annotation. To overcome this limitation, we analyzed 10,776,849 protein sequences derived from eight MGE databases to compile a comprehensive set of 6,140 manually curated protein families that are linked to the “life cycle” (integration/excision, replication/recombination/repair, transfer, stability/transfer/defense, and phage-specific processes) of plasmids, phages, integrative, transposable, and conjugative elements. We overlay experimental information where available to create a tiered annotation scheme of high-quality annotations and annotations inferred exclusively through bioinformatic evidence. We additionally provide an MGE-class label for each entry (e.g., plasmid or integrative element), and assign to each entry a major and minor category. The resulting database, mobileOG-db (for mobile orthologous groups), comprises over 700,000 deduplicated sequences encompassing five major mobileOG categories and more than 50 minor categories, providing a structured language and interpretable basis for an array of MGE-centered analyses. mobileOG-db can be accessed at mobileogdb.flsi.cloud.vt.edu/, where users can select, refine, and analyze custom subsets of the dynamic mobilome. IMPORTANCE The analysis of bacterial mobile genetic elements (MGEs) in genomic data is a critical step toward profiling the root causes of antibiotic resistance, phenotypic or metabolic diversity, and the evolution of bacterial genera. Existing methods for MGE annotation pose high barriers of biological and computational expertise to properly harness. To bridge this gap, we systematically analyzed 10,776,849 proteins derived from eight databases of MGEs to identify 6,140 MGE protein families that can serve as candidate hallmarks, i.e., proteins that can be used as “signatures” of MGEs to aid annotation. The resulting resource, mobileOG-db, provides a multilevel classification scheme that encompasses plasmid, phage, integrative, and transposable element protein families categorized into five major mobileOG categories and more than 50 minor categories. mobileOG-db thus provides a rich resource for simple and intuitive element annotation that can be integrated seamlessly into existing MGE detection pipelines and colocalization analyses. 

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