The findings come from a team led by Hsin-Yu Wang, Chun Ming How, Yong-Shan Li, Yuqing Mao, Thanh H. Nguyen and Chia-Cheng Wei, who set out to answer a question that has become increasingly urgent in food safety research: do non-antibiotic chemicals, particularly the fungicides sprayed widely on fruit and vegetable crops, push bacteria toward resistance or heightened virulence? Prior work has hinted at the danger. Azoxystrobin and carbendazim have been shown to enrich bacterial resistomes in nematode guts, tebuconazole can promote the spread of multidrug-resistant plasmids in soil bacteria, and chlorothalonil facilitates metabolic adaptation in soil microbial communities. But whether such exposure produces phenotypic resistance and increased pathogenicity in a major foodborne pathogen remained largely untested.

Bacillus cereus was an obvious candidate for scrutiny. The Gram-positive, spore-forming organism is found in 36 to 45 percent of dairy products, vegetables, beans and cereals, and it is capable of causing food poisoning, eye infections, anthrax-like progressive pneumonia, fulminant sepsis and central nervous system infections. Multidrug-resistant strains of the species have already emerged in hospital wastewater, and its versatility—including the ability to build biofilms of varied architecture—makes any shift in its behavior a serious public health concern.

The researchers first screened eight widely used fungicides against B. cereus: chlorothalonil (CHT), propineb (PRO), tebuconazole (TEB), azoxystrobin, propiconazole, mancozeb, carbendazim and triadimefon. Three of them—CHT at 8 micromolar, TEB at 500 micromolar and PRO at 175 micromolar—completely inhibited bacterial growth within 24 hours and were selected for long-term adaptation experiments. The design was demanding: every day for 30 days, the bacteria endured a three-hour fungicide challenge followed by recovery and regrowth in fresh medium. Survival trajectories differed by compound. Under chlorothalonil, survival dipped to about 70 percent on day one but rebounded within 24 hours. Tebuconazole initially halved the population before recovery stabilized around day eight. Propineb proved the harshest pressure, dropping survival below five percent on day six before the bacteria clawed back to stable levels by day twelve. The bacterium, in short, adapted to all three chemical regimes.

Whole-genome sequencing of the adapted lineages delivered a surprising verdict: no meaningful genetic mutations. Phylogenetic comparison against reference strains and variant-calling analyses found the treated bacteria essentially identical to their ancestors. Instead of classical, mutation-driven resistance, the adaptation appears to be physiological—a reversible, non-heritable tolerance state akin to the persister-cell and stress-response phenomena documented in bacteria subjected to repeated antibiotic cycles. Similar patterns have been reported when Listeria monocytogenes and uropathogenic Escherichia coli were exposed to disinfectants such as benzalkonium chloride and triclosan, with minimum inhibitory concentrations rising without stable genetic change.

The phenotypic consequences, however, were substantial. Biofilm formation—often a shield against both immune attack and antimicrobial agents—was initially suppressed during early exposure but rose significantly in tebuconazole-adapted bacteria from day ten onward and climbed markedly in propineb-exposed cells by day ten. Statistical testing confirmed significant effects of the fungicide treatment, the duration of exposure, and their interaction on biofilm output. Antibiotic challenge assays revealed a parallel erosion of susceptibility. Bacteria adapted to chlorothalonil grew significantly better than controls in gentamicin at 4, 6 and 8 micrograms per milliliter; tebuconazole- and propineb-adapted lineages also outgrew controls at key gentamicin doses, and chlorothalonil- and tebuconazole-adapted cells showed improved growth at 8 micrograms per milliliter of tetracycline. Because no growth occurred at concentrations of 16 micrograms per milliliter or above, the strains do not meet formal clinical criteria for resistance—but the shift toward tolerance was clear and reproducible.

The most dramatic result emerged in living hosts. Using the nematode Caenorhabditis elegans, a genetically tractable infection model whose intestinal epithelium provides a biologically meaningful readout of colonization and killing, the team measured how fungicide-adapted bacteria fared against unadapted controls. All three adapted lineages killed worms significantly faster than the parent strain, with log-rank tests showing p values below 0.001. Tebuconazole-adapted bacteria were especially aggressive: worm survival collapsed within two days, and by day three most of the animals were dead. Follow-up colonization assays showed that tebuconazole-adapted B. cereus also established significantly higher intestinal loads in the worms, indicating that the fungicide had promoted persistence within the host gut, not merely faster killing.

Transcriptional profiling of the tebuconazole-adapted lineage offers a mechanistic window into these changes. Quantitative real-time PCR revealed significantly elevated expression of genes encoding the non-hemolytic enterotoxin (nheC) and the hemolysin BL complex (hblA, hblC and hblD)—toxins that disrupt intestinal epithelial cells—alongside upregulation of purC and purL, which support purine biosynthesis and extracellular DNA release during early biofilm formation, and calY, a bifunctional matrix protein that promotes adhesion to host tissues. The efflux-pump gene smr was also induced, a plausible explanation for the reduced antibiotic susceptibility, and one that echoes efflux upregulation seen in stressed Mycobacterium tuberculosis. Importantly, the elevated virulence and resistance gene expression persisted even when the adapted bacteria were subsequently exposed to gentamicin, suggesting that the stress-adapted state complicates antibiotic treatment rather than simply surviving it.

The authors are careful to frame the work as hazard identification rather than a direct portrait of what happens on farms or in food. The experiments used a single reference strain, BCRC15850, and the exposure concentrations—particularly 500 micromolar tebuconazole and 175 micromolar propineb—exceed the residue levels typically reported on treated foods, although the chlorothalonil dose is of the same order of magnitude as residues found in some food commodities. Local bioavailable concentrations in soil and produce depend on moisture, adsorption, formulation and degradation, so the laboratory model of recurrent acute stress cannot be directly translated into field-level risk estimates. Nor should the transcriptional findings be generalized beyond the tebuconazole lineage without confirming that chlorothalonil- and propineb-adapted bacteria share the same regulatory program. Nonetheless, the study reveals an understudied scenario in which persistent sublethal chemical stress can harden a major foodborne pathogen—improving its resilience, deepening its virulence and weakening the grip of frontline antibiotics—without any mutational fingerprint. Whether such phenotypes persist after fungicide withdrawal, and whether they arise in the genetically diverse field isolates that actually contaminate the food supply, are the questions the team now hopes will drive the next round of research.

Subject of Research: Effects of long-term fungicide exposure on adaptation, antibiotic tolerance and virulence of the foodborne pathogen Bacillus cereus

Article Title: Long-term fungicide exposure promotes bacterial adaptation and increases virulence of foodborne pathogen Bacillus cereus in Caenorhabditis elegans

Article References: Wang, H.-Y., How, C. M., Li, Y.-S., Mao, Y., Nguyen, T. H., & Wei, C.-C. (2026). Long-term fungicide exposure promotes bacterial adaptation and increases virulence of foodborne pathogen Bacillus cereus in Caenorhabditis elegans. Current Research in Food Science, 13, Article 101572. https://doi.org/10.1016/j.crfs.2026.101572

Image Credits: AI Generated

DOI: 10.1016/j.crfs.2026.101572

Keywords: Bacillus cereus, fungicide exposure, antimicrobial tolerance, biofilm formation, Caenorhabditis elegans, tebuconazole, chlorothalonil, propineb, virulence genes, food safety, foodborne pathogen, efflux pumps

Salmonella Typhimurium is among the leading causes of foodborne gastroenteritis worldwide, and its monophasic variant—distinguished serologically by the absence of one of its two flagellar phases—has surged in prevalence across Europe, the Americas and Asia over recent decades. The lineage, which belongs to sequence type 34 and typically displays the antigenic formula 4,[5],12:i:-, has repeatedly been implicated in outbreaks linked to pork, poultry and processed foods. Yet despite its clear epidemiological importance, the genetic determinants that allowed this clone to outcompete its biphasic ancestor, the previously prevalent ST19 lineage, had remained uncertain. The new study set out to resolve that question at unprecedented scale.

The team’s comparative analysis of tens of thousands of genomes revealed a striking pattern: the expanding ST34 clone carried a frameshift mutation in dinB, the gene encoding a translesion DNA synthesis polymerase also known as DNA polymerase IV. The mutation, a deletion of a single thymine residue within a homopolymeric tract of seven thymidines near the 5′ end of the gene, introduces a premature stop codon that truncates the 39.7-kilodalton DinB protein to a nonfunctional fragment of roughly 1.9 kilodaltons. Because DinB is normally involved in bypassing damaged DNA templates and in generating genetic diversity under stress, its loss initially appears counterintuitive for a pathogen on the rise.

Functional experiments, however, demonstrated that the crippled polymerase has far-reaching downstream consequences. Transcriptomic profiling showed that the frameshift dinB mutation rewires the expression of flagellar genes, altering the balance between the two phase-one and phase-two flagellin systems that Salmonella uses to evade host immune detection. Specifically, the mutation led to transcriptional changes that favored retention of fliC, which encodes phase-one flagellin, and set the stage for the subsequent loss of fljB, the gene encoding phase-two flagellin. Western blot analyses confirmed that dinB-mutant strains displayed an increased proportion of cells expressing FliC, while in vitro motility assays showed that swimming ability was preserved despite the underlying genetic upheaval.

The physiological consequence of this reprogramming became apparent in infection models. Using transposon insertion sequencing and in vivo competition experiments in mice, the researchers found that the requirements for successful gut colonization shifted once fljB was lost. Genes that were dispensable, or even costly, in the ancestral background became essential or advantageous in the mutant context, and vice versa. The frameshift dinB strain carrying the fljB deletion outcompeted the previously prevalent biphasic ST19 lineage in the intestine, indicating that the combination of the polymerase defect and flagellin loss conferred a measurable competitive advantage within the host environment.

To move beyond correlation, the authors built a temporal evolutionary model that simulated the dynamics of four competing lineages: biphasic ST19, biphasic ST34, ST34 carrying the frameshift dinB, and monophasic ST34 carrying both the frameshift and the fljB deletion. The modeling demonstrated that the chronological order of the events matters critically. The dinB mutation had to precede the loss of fljB for the monophasic clone to expand as observed, and the simulated selection coefficients derived from the model were quantitatively consistent with selection estimates computed from real-world changes in genotype frequencies among human clinical isolates. Sensitivity analyses confirmed that the conclusion held regardless of the initial frequency of ST34, the presence or absence of spatial population structure, or the precise metric used to quantify selection.

This ordered dependency is what the researchers describe as a stepwise pathoadaptation model: a sequence of gene-loss events in which each deletion reshapes the genetic background so that the next loss becomes beneficial rather than deleterious. The concept echoes a growing recognition in microbial evolution that genome reduction can be a creative force. Recent work on Vibrio parahaemolyticus, for example, showed that wave succession within a pandemic clone was likewise driven by gene loss, and earlier studies documented how monophasic Salmonella Typhimurium microevolved during a prolonged epidemic in the United Kingdom. The new study, however, is notable for linking the ecological success of a zoonotic lineage to a specific, mechanistically validated chain of molecular events.

The broader implications extend to public health forecasting. If the emergence of major bacterial clones can depend on relatively simple, ordered mutational steps, then surveillance systems that monitor homopolymeric tracts and other mutation-prone loci may gain predictive power over which lineages are poised to expand. The study’s data resources—including genomic data deposited at the China National GeneBank Database, Enterobase and NCBI, transcriptomic data under accession GSE280131, proteomic data via PRIDE, and transposon-sequencing reads under BioProject PRJNA1347559—provide a substantial foundation for such efforts. The mathematical model code has also been made publicly available on GitHub, enabling other groups to test the generality of the sequential gene-loss framework in other pathogens.

At the same time, the work underscores how little of bacterial adaptation is driven by gene acquisition alone. Monophasic ST34 also carries traits such as copper resistance and heavy-metal tolerance that have been implicated in its persistence in livestock production environments, and antimicrobial resistance remains a defining feature of many circulating clones. But the new analysis places gene loss at the center of the lineage’s rise, reframing flagellar phase variation—a long-studied quirk of Salmonella biology—as a decisive axis of clonal competition. As the authors note, understanding the genetic factors facilitating the emergence of infectious diseases is critical, and this study delivers a concrete mechanistic answer for one of the most consequential zoonotic pathogens of the modern food system. The lesson is uncomfortable but clarifying: for bacteria, sometimes less is more, and the road to pandemic status can be paved by the genes a pathogen leaves behind.

Subject of Research: Stepwise gene loss driving the clonal expansion of monophasic Salmonella Typhimurium ST34

Article Title: Sequential gene loss promotes expansion of monophasic Salmonella Typhimurium ST34

Article References: Wu, X., Wang, T., Jia, C., Zhou, H., Li, Y., Baker, S., & Yue, M. (2026). Sequential gene loss promotes expansion of monophasic Salmonella Typhimurium ST34. Nature Microbiology. https://doi.org/10.1038/s41564-026-02483-4

Image Credits: AI Generated

DOI: 10.1038/s41564-026-02483-4

Keywords: Salmonella Typhimurium, monophasic ST34, gene loss, dinB, flagellin, fljB, pathoadaptation, bacterial evolution, genomic epidemiology, foodborne pathogen, zoonotic disease, Nature Microbiology

SpoVG was first characterized decades ago in the spore-forming bacterium Bacillus subtilis, where it was linked to sporulation and to the regulation of capsular polysaccharide synthesis in Staphylococcus aureus. In Listeria, however, its functions had remained largely unexplored. The new work shows that the protein is far more than a vestige of its sporulation-related past. By constructing deletion mutants and comparing their behavior with that of wild-type bacteria across a battery of assays, the researchers found that loss of spoVG reshapes the organism’s surface properties, its capacity to adhere to abiotic surfaces, and the architecture of the biofilms it builds.

Biofilms are central to Listeria’s persistence in food-processing environments. Once a population anchors itself to a surface and encases itself in a self-produced matrix of extracellular DNA, proteins, and polysaccharides, it becomes dramatically more resistant to sanitizers and desiccation. The study demonstrates that SpoVG-deficient mutants form biofilms with altered biomass and structural organization, indicating that the regulator influences the developmental program that converts free-swimming cells into a sessile community. Because biofilm-resident cells are a well-documented source of recurring contamination in ready-to-eat food production, understanding the genetic switches that govern this transition has direct practical value.

The pleiotropic nature of SpoVG’s influence is what makes the result particularly striking. Transcript-level comparisons suggest that the protein affects the expression of genes involved in motility, stress tolerance, and cell-envelope maintenance in addition to biofilm-associated functions. This breadth of action is characteristic of global regulators, proteins that do not catalyze specific metabolic steps but instead rewire large transcriptional programs in response to environmental cues. For Listeria, which must toggle between soil, food, and the mammalian cytosol within a single life cycle, such master switches are essential for rapid physiological remodeling.

Multi-dimensional niche establishment, the phrase the authors use to describe the pathogen’s ecological flexibility, encompasses growth at refrigeration temperatures, tolerance of acidic and osmotic stress, survival on inert surfaces, and intracellular proliferation in host tissue. The experiments indicate that SpoVG contributes to several of these dimensions at once. Mutants lacking the regulator showed measurable differences in phenotypes associated with environmental persistence, reinforcing the idea that a single conserved factor helps integrate the disparate signals a Listeria cell encounters as it moves between niches.

Mechanistically, SpoVG belongs to a small family of bacterial RNA-binding proteins that can associate with specific mRNA targets and influence their stability or translation. Work in other Gram-positive organisms has shown that such proteins allow bacteria to fine-tune gene expression post-transcriptionally, a level of control that complements classical transcription-factor regulation. In Listeria, this post-transcriptional layer may be especially important during the transitions between life on a surface and life inside a host, when mRNA turnover needs to be rapid and coordinated across functional gene groups.

From an applied perspective, the study suggests that interfering with SpoVG function could weaken Listeria on multiple fronts simultaneously. A compound or intervention that disrupts the regulator’s activity would be expected not only to impair biofilm maturation, reducing surface persistence, but also to compromise the stress responses that allow the organism to endure cleaning regimes and cold-chain conditions. Because SpoVG is conserved among Listeria strains, targeting it may offer broad protection against the genetic diversity found in industrial environments, where different isolates can carry varied resistance profiles.

The findings also carry implications for risk-assessment modeling. Current predictive tools for Listeria growth and survival rely heavily on environmental parameters such as temperature, pH, and water activity, but they incorporate the underlying genetics only crudely. Identifying regulators like SpoVG that govern multi-trait persistence provides a mechanistic bridge between genotype and phenotype, potentially allowing modelers to distinguish high-risk strains that harbor robust regulatory capacity from those that do not. That, in turn, could sharpen the allocation of monitoring resources in food-production facilities.

As with any single-gene study in an organism as adaptable as Listeria, important questions remain. Which mRNA targets does SpoVG bind directly, and how does environmental signaling modulate that binding? How do its effects intersect with better-characterized transcriptional regulators such as PrfA, Sigma B, and MogR, which control virulence and stress programs? Answering these questions will require RNA-binding assays, comparative transcriptomics across conditions, and structural work on the protein itself. What the current study establishes, however, is that SpoVG deserves a place among the small set of factors that define how Listeria monocytogenes builds communities, withstands hostile conditions, and colonizes new environments, a profile that makes it a compelling candidate for next-generation control strategies in food safety.

Subject of Research: SpoVG regulation of biofilm formation and niche adaptation in Listeria monocytogenes

Article Title: SpoVG as a pleiotropic regulator modulating Listeria monocytogenes biofilm formation and multi-dimensional niche establishment

Article References: Shi, C., Zhu, P., Li, R., Chen, H., Meng, F., Lu, Z., & Bie, X. (2026). SpoVG as a pleiotropic regulator modulating Listeria monocytogenes biofilm formation and multi-dimensional niche establishment. npj Science of Food. https://doi.org/10.1038/s41538-026-01134-6

Image Credits: AI Generated

DOI: 10.1038/s41538-026-01134-6

Keywords: Listeria monocytogenes, SpoVG, biofilm formation, food safety, gene regulation, RNA-binding protein, pleiotropic regulator, foodborne pathogen, environmental persistence, bacterial stress response, npj Science of Food, microbiology