Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.64898/2026.09.28.755093

Anti-defense systems of viral communitie vary with genomic traits, host immunity and environmental stress

Huang, D.·Yang, Y.·Wu, R.·Balcazar, J. L.·Alvarez, P. J. J.·Zhou, J.·Yu, P.
View original source ↗Export metadata ↓

Abstract

Abstract: Background Despite the ecological importance of viral anti-defense systems (ADS), yet how viral ADS repertoires vary across microbial ecosystems remains poorly understood. Here, we integrated global virus datasets with metagenomes from heavy metal-contaminated soils and chromium-stress microcosms to investigate ecological determinants of viral ADS. Results We found that ADS repertoires were constrained by viral genome capacity, with most ADS-carrying viruses encoded a single system, whereas multi-ADS occurred mainly in larger genomes. Viral lifestyle partitioned ADS, with temperate viruses enriched in ADS targeting early-stage defenses and virulent viruses preferentially encoding ADS against mid- and late-stage defense. ADS composition also varied by host lineage and across habitats, linking viral ADS repertoires to host immune landscapes and ecosystem-specific viral strategies. Moreover, along the heavy metal contamination gradient, changes in the prevalence of ADS-carrying viruses occurred alongside shifts in prokaryotic defense profiles. In addition, expanded ADS repertoires may further increase dissemination potential of MGE-borne adaptive genes, highlighting viral ADS as a potential contributor to the adaptive evolution of microbial community. Conclusions These findings reveal that viral ADS are shaped by genomic traits, host immunity and environmental stress, with implications for virus-host interaction and microbial adaptive evolution. More broadly, this study extends anti-defense research beyond individual virus-host systems, offering an integrative, community-level perspective to guide future studies testing whether and how virus-prokaryote immune interactions contribute to microbial community dynamics and evolution in changing environments.

Explore related subjects

microbiologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Huang, D., Yang, Y., Wu, R., Balcazar, J. L., Alvarez, P. J. J., Zhou, J., Yu, P.. 2026-09-29. Anti-defense systems of viral communitie vary with genomic traits, host immunity and environmental stress. https://doi.org/10.64898/2026.09.28.755093

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Tissue-specific transcriptomic responses to early Toxoplasma gondii infection in sheep during congenital toxoplasmosis

Toxoplasma gondii is a widespread zoonotic pathogen of major One Health concern, capable of causing congenital toxoplasmosis in both humans and sheep. Despite its impact, early host-parasite molecular interactions during acute infection in pregnant hosts remain largely unexplored. In this study, we characterized the transcriptomic responses of key tissues involved in early infection (the small intestine, mesenteric lymph nodes, and placenta) in pregnant ewes experimentally infected with T. gondii strain TgShSp1. RNA-seq analysis revealed pronounced, tissue-specific transcriptional changes at 6 days post-infection (dpi), particularly in the mesenteric lymph nodes, characterized by activation of interferon- and cytokine-mediated immune pathways. In contrast, transcriptional responses at 3 dpi were limited, consistent with a silent phase of parasite dissemination. Despite the absence of detectable parasite DNA, placentomes showed modest interferon-associated responses and upregulation of DNA repair and cellular stress pathways. These changes coincided with marked suppression of cell-cycle progression and extracellular matrix remodeling alongside inhibition of angiogenesis and hypoxia pathways. Altogether, early disruption of placental vascular function and tissue remodeling may contribute to fetal loss. In summary, these findings provide new insights into early host responses to T. gondii infection in a pregnant host and identify molecular mechanisms that may predispose to early fetal death during ovine congenital toxoplasmosis.

microbiology↗
bioRxiv2026

Chikungunya virus live-cell reporter systems reveal cell-type-dependent antiviral responses to ribavirin

Chikungunya virus (CHIKV) remains a significant global public health threat, yet antiviral discovery is limited by experimental systems that provide little mechanistic resolution and rely heavily on transformed cell lines of uncertain physiological relevance. Here, we developed complementary live-cell CHIKV reporter systems comprising a dual-fluorescent subgenomic replicon and fluorescent infectious viruses that enable real-time monitoring of distinct stages of the viral replication cycle. By coupling an nsP3-tagged reporter to genomic RNA translation and replication with a subgenomic reporter of structural gene expression, we achieved temporal resolution of early and late replication events in living cells. Functional validation using replication-defective and subgenomic RNA-deficient mutants confirmed that the system distinguishes between viral RNA replication and downstream structural gene expression. Application of these reporters revealed distinct antiviral responses across transformed and physiologically relevant human cell models. Ribavirin and the nsP2 inhibitor RA-0002034 potently inhibited CHIKV replication in transformed cell lines. Unexpectedly, ribavirin activity was markedly diminished in primary human skeletal muscle myoblasts and dermal fibroblasts, despite robust antiviral effects in commonly used screening cell lines. Mechanistic studies showed that ribavirin-mediated inhibition was rescued by guanosine but not inosine supplementation and was recapitulated by mycophenolic acid, consistent with guanine nucleotide depletion as the predominant antiviral mechanism under the conditions tested. Notably, inhibition through this pathway was substantially less effective in primary human cells. Together, these findings establish versatile live-cell CHIKV reporter systems for mechanistic studies of viral replication and reveal striking cell-type-dependent differences in response to guanine nucleotide depletion. Our results demonstrate that host-cell context can profoundly influence both CHIKV replication and antiviral susceptibility, highlighting the importance of physiologically relevant models for understanding virus-host interactions and antiviral mechanism.

microbiology↗
bioRxiv2026

A droplet-to-data workflow for antimicrobial screening of complex matrices

Screening plant extracts and other complex natural matrices for antibacterial activity is complicated by optical interference and population averaging in conventional bulk assays. Droplet-based assays mitigate interference while enabling high-throughput assessment of bacterial subpopulations. However, analyzing the resulting image data involves difficult image processing, classification, and interpretation. Here, we present a democratized workflow for antimicrobial screening in complex matrices that combines a polydisperse droplet-based assay with EasyFlow 2.0 (EF2), our updated droplet image analysis platform. EF2 offers stable containerized deployment, expanded polydisperse droplet support, automated thresholding and MIC estimation, LLM-assisted data exploration, and import of other software outputs such as CellProfiler (CP) measurements and CellProfiler Analyst (CPA) classification models. As proof of concept, we applied this workflow to assess the antibacterial and aggregation-modulating effects of chemically distinct extracts of Taraxacum officinale, Rhodiola rosea, and Lonicera caerulea against Escherichia coli. Extracts were chemically characterized by HPLC-MS and evaluated using both standard 96-well plate microdilution and droplet-based assays. In total, 27,059 droplets were segmented in CP, classified into four growth phenotypes using a CPA random forest model, and analyzed in EF2. The droplet-based assay reached minimal inhibitory concentration (MIC) at lower extract concentrations than 96-well plate microdilution and revealed extract-specific aggregation effects: L. caerulea reduced E. coli aggregation, whereas T. officinale did not. R. rosea reduced growth in the 96-well plate microdilution assay, but high concentrations caused droplet gelation that prevented droplet-based analysis, showing that sample components must be checked for compatibility with droplet formation. These results illustrate that the EF2-centered workflow supports rapid, automated MIC estimation through unsupervised thresholding when labels are unavailable, and four-class aggregation phenotyping when a CPA model is supplied. This workflow offers flexible, scalable screening, potentially extendable beyond plant extracts to other complex sample matrices.

microbiology↗