Glycoside hydrolases (GHs) are central to microbial carbohydrate degradation and frequently occur as multidomain proteins containing accessory domains involved in substrate binding, localization, and retention. However, the extent to which GH multidomain architectures are shaped by phylogeny versus environmental adaptation remains poorly understood. Here, we analyzed 158,829 GH-containing proteins from 17,108 high-quality metagenome-assembled genomes (MAGs) in the GEM catalog, focusing on major GH families involved in polysaccharide and oligosaccharide degradation. We developed domain–domain adjacency networks (DANs) to quantify multidomain organization and compared network weighted architectural similarity across bacterial genera and environments. GH architectures were highly conserved within genera, with bootstrapped DANs displaying stable network properties and distinct lineage-specific architectural similarities, indicating strong phylogenetic constraints on domain organization. Accessory domains associated with substrate targeting and enzyme retention represented approximately 61% of non-catalytic partner domains, highlighting their importance in GH evolution. Although phylogeny was the dominant determinant of multidomain architecture, environmental effects were detected in cosmopolitan genera. Environmental variation had a limited and lineage-dependent influence on GH abundance but more consistently affected the prevalence of multidomain GHs, particularly within GH3, GH13, and GH18 families. These results support a hierarchical model in which phylogeny establishes a conserved framework of GH organization, while environmental pressures fine-tune multidomain architectures. Our study demonstrates that protein domain architecture represents an important and previously underappreciated dimension of microbial functional adaptation and provides a scalable network-based framework for linking enzyme organization to ecological function.
Carbapenem resistance is often treated as a stable clinical phenotype, although plasmid structural variation can generate closely related isolates with divergent susceptibility profiles. We investigated longitudinal Klebsiella pneumoniae isolates recovered from one patient during hospitalization. Resistant KP02 and KP03 and susceptible KP04 belonged to ST37/KL104; KP03 and KP04 were recovered from the same wound specimen and primary culture. Independent sequencing of three colonies from each isolate showed stable within-isolate genomic states and no mutually differing single-nucleotide polymorphisms in the shared callable core. The reassemble data sequences identified a 10,483-bp difference between the IncHI1B/IncFIB(K) multireplicon plasmids Pkp02_1 and Pkp04_1. The interval was delimited by two identical direct repeats containing sul1 and qacEΔ1, and read-level validation, an independent assembly, and structural PCR supported a repeat-associated deletion. An outward-facing PCR product was compatible with a candidate circular intermediate, although its complete circular sequence and abundance remain unresolved. Under antibiotic-free conditions, the module-lacking isolate showed higher growth and final biomass; this association was not assigned uniquely to the deleted module. This single-patient study provides a clinically grounded, hypothesis-generating model for how repeat-associated plasmid rearrangements may contribute to carbapenem phenotypic heterogeneity.
Coastal wetlands are increasingly contaminated by microplastics that provide long-lived substrates for microbial colonization, yet the joint effects of ecosystem settings and urbanization on plastisphere communities and their resistomes remain poorly understood. Here, we used a 2 × 2 factorial design across mangrove and sandy-beach sediments under rural and urban influence, combined with metagenomic profiling, to characterize microplastic-associated microbiota and antibiotic resistance genes (ARGs). Microbial communities on microplastics showed clear separation between mangroves and sandy shores, with additional shifts along the rural–urban gradient, indicating context-dependent plastisphere assembly. Urbanization substantially increased richness in mangrove plastispheres, whereas effects on sandy beaches were weak or inconsistent and largely confined to low-abundance taxa. In situ exposure yielded a diverse ARG repertoire (>1 000 ARGs), and ARG composition showed significant ecosystem × human-impact interactions, with urban mangrove microplastics hosting the highest ARG diversity. Genus–ARG co-occurrence networks showed denser bacteria–ARG association patterns in mangrove than in sandy-beach plastispheres, with a limited number of genera statistically associated with multiple ARGs. These results suggest that plastisphere communities and resistomes varied across ecosystem settings and urbanization contexts, with urban mangrove microplastics showing relatively higher ARG diversity and stronger bacteria–ARG co-occurrence patterns. These findings highlight the need for habitat-specific monitoring of microplastic-associated resistance.
Saline lakes are critical yet fragile ecosystems where microbial communities drive biogeochemical cycles under extreme salinity gradients, yet their adaptive mechanisms to evaporative salinization remain poorly understood. This study investigated microbial community dynamics and carbon source utilization strategies across five distinct evaporation stages (from original brine to residue brine) in salt reservoirs of the Charkhan Salt Lake, Tibetan Plateau. High-throughput 16S rRNA sequencing revealed a transition from archaeal dominance (Euryarchaeota) in early stages to bacterial dominance (Proteobacteria) as salinity increased, accompanied by a significant rise in α-diversity (146 to 711 OTUs). Biolog-ECO analysis, which measures metabolic potential under standardized conditions, revealed that microbial carbon utilization capacity initially declined but later recovered, among which potassium ion (K+) concentration showed the strongest negative correlation with both metabolic intensity and carbon source diversity. Further analysis of experimental data indicated that, elevated K+ levels suppressed carbohydrate utilization while promoting amino acid metabolism in later stages. These findings suggest the adaptive resilience of microbial communities to salinity fluctuations in hypersaline environments and indicate their core role in regulating carbon cycling, demonstrating that the patterns of microbial community succession and carbon source utilization are jointly shaped by salinity and potassium ions dynamics.
Membrane-bound organelles undergo extensive remodeling during environmental stress, yet systematic side-by-side comparisons of organelle responses in budding yeast remain limited. Here, a panel of fluorescent markers was used to examine multiple organelles in Saccharomyces cerevisiae exposed to heat, hydrogen peroxide, acetic acid, or ethanol. Across all conditions, mitochondria consistently shifted from tubular networks to fragmented puncta, representing a common stress response. Quantitative scoring showed that heat stress induced mitochondrial fragmentation in more than 90% of cells within 20 min, and GFP-HDEL redistribution was detected in a substantial fraction of cells under all four stress conditions, with the strongest effect under heat stress. In contrast, overall endoplasmic reticulum (ER) morphology remained largely preserved, although redistribution of GFP-HDEL indicated altered ER retention and/or endomembrane homeostasis. Heat and oxidative stress also induced Ire1 puncta. Several nuclear proteins exhibited stress-dependent redistribution from the nucleus, indicating dynamic remodeling of nuclear protein localization. Vacuoles generally appeared enlarged and fused, whereas acetic acid induced a distinct phenotype with Ybh3 enrichment at the vacuolar membrane and redistribution of Prc1 and Pep4 to cytoplasmic puncta. Markers of the early and late Golgi and the late endosome showed stress-specific loss, clustering, or relocalization. Lipid droplets, peroxisomes, and autophagy-related structures were also altered. Additionally, Yca1, Aif1, and Mmi1 formed puncta under heat and ethanol stress. Together, these findings provide a comparative imaging framework defining shared and stress-specific features of organelle remodeling in budding yeast.
Fusarium Head Blight (FHB) is a devastating fungal disease affecting cereal crops, mainly caused by Fusarium graminearum, Fusarium culmorum, Fusarium poae, Fusarium avenaceum, Fusarium langsethiae, Fusarium sporotrichioides, and Fusarium tricinctum. In addition to inducing yield losses, the previous species are responsible for grain contamination with mycotoxins. Co-occurrence of these species is frequent and driven by fungal interactions that influence disease outcomes. To investigate those interactions, intra- and extracellular metabolomic profiles of one representative strain per FHB species were compared. In total, 932 intracellular and 1170 extracellular metabolites were detected. Strains from F. graminearum, F. culmorum, F. sporotrichioides, and F. tricinctum exhibited the highest number of biomarkers (141, 79, 69, and 58, respectively), whereas fewer than 15 biomarkers were detected for strains of F. avenaceum, F. poae, and F. langsethiae. Tracking these biomarkers in in vitro co-cultures revealed that only those associated with the most abundant strains, F. culmorum followed by F. graminearum, were consistently detected. Comparison of biomarker dynamics between single-strain and co-cultures revealed significant differences in accumulation profiles and concentrations, with some biomarkers showing abundance differences of up to 70-fold. This allowed us to raise several hypotheses, including up- and down-accumulation of some biosynthetic pathways, in addition to detoxification, biotransformation, or cross-feeding mechanisms induced by fungal interactions. This work establishes a first conceptual and methodological framework to study Fusarium interactions through metabolomic profiling of Fusarium co-cultures. It aimed to improve our understanding of the FHB disease process to ultimately mitigate its impact.
Cleaning and disinfection (C&D) of food-contact surfaces is an essential measure to prevent microbial contamination during food processing. These procedures commonly involve the use of biocides to reduce or eliminate foodborne pathogens such as Salmonella spp. Among the available biocides, amines such as 3-(diethylamino)propylamine (DEAPA) have gained attention for their broad-spectrum activity and high efficacy in the presence of organic matter. However, it remains unclear whether these biocides can exert selective pressure and promote resistance development, potentially affecting the effectiveness of current C&D procedures.In this study, three adaptive laboratory evolution (ALE) protocols representing different exposure patterns were applied to evaluate the emergence of DEAPA-resistant variants (RVs). This approach resulted in seven independently evolved RVs, which were subsequently characterised phenotypically and genetically. The most tolerant RVs showed a 10,000-fold increase in survival after exposure to 13,000 mg/L DEAPA for 15 min, a 1000-fold increase in survival after heat treatment at 54 °C for 30 min, and reduced susceptibility to gentamicin, with an MIC exceeding 2 mg/L. Genetic analysis identified mutations in genes involved in metabolism (adhE, cyaA, and atpF), signal transduction (crp), transport (corA), and cell motility (cheZ and fliF), suggesting that resistance emerged through genetic adaptation affecting multiple cellular functions.These findings show that repeated DEAPA exposure, particularly through cyclic lethal treatments, can select Salmonella Thyphimurium variants with increased DEAPA tolerance under laboratory conditions. Further studies under representative industrial conditions are required to assess the potential risk associated with the emergence of these variants.
Persister cells, a multidrug-tolerant bacterial subpopulation, pose challenges to disease control, with research hindered by technical limitations. In this study, single-cell Raman spectroscopy (SCRS) combined with heavy water (D2O) labeling was employed to explore the metabolic activity and compositional changes of Vibrio splendidus persisters. Raman analysis revealed distinct biochemical profiles between persisters and normal cells: persisters reduced nucleic acid-related band intensity but increased lipid and polysaccharide-related bands. Using the deuterium incorporation rate as a quantitative indicator of biosynthetic activity, we found that biosynthesis remained active under antibiotic stress during the exponential growth phase, while it declined under identical stress conditions in the stationary phase. It is revealed that persisters are not in a fully dormant state, and diverse metabolic patterns are found among persister cells. Furthermore, our screening results identified vitamin C is a potent inhibitor of persister formation in a concentration-dependent manner. It may be associated with the down-regulation of the stringent response genes relA and spoT. Collectively, this study demonstrates that SCRS combined with D2O labeling is a powerful tool for investigating the physiological characteristics of V. splendidus persisters, and provides metabolic modulation strategies for the control of persistent infection in aquaculture.
Qdr3 acts as a global regulator in Candidozyma auris (Candida auris), coordinating mitochondrial function and cell-surface architecture. Loss of qdr3 causes major cellular reprogramming, increasing mitochondrial activity and virulence, highlighting its key role in fungal homeostasis and pathogenicity. The graphical abstract was generated by the Notebook LM tool by Google using the following prompt: “Create a visual abstract for scientific journal submission (BMJ standard). Ensure: (1) accurate spelling, and (2) no fabrication—use only data from the manuscript. Ensure the image is 531×1328 pixels (h x w) or proportionally more, and is readable at a size of 5 × 13 cm.”Image, graphical abstract
The central and peripheral nervous systems constitute highly organized and dynamic networks that rely on precise regulation of synaptic transmission, membrane integrity, cytoskeletal stability, and intracellular signaling. Disruption of these tightly controlled processes can lead to a wide range of neurological disorders. Among the various modulators of neural function, bacterial neurotoxins represent a unique class of exotoxins that selectively target key neuronal components with remarkable molecular specificity. Traditionally studied in the context of infectious pathogenesis, bacterial neurotoxins are now increasingly recognized as powerful molecular probes of synaptic machinery and intracellular signaling pathways. In addition to their direct effects on neurons, accumulating evidence indicates that bacterial neurotoxins also participate in neuroimmune interactions, contribute to neuroinflammatory cascades, and may impact gut-brain axis signaling and long-term neurodegenerative vulnerability.Advances in structural biology and protein engineering have shifted the field from descriptive toxicology to translational neurobiology. Engineered toxin derivatives and attenuated catalytic variants are being investigated as tools for neural circuit modulation, targeted drug delivery, and the treatment of movement disorders, chronic pain, and other neurological conditions. This review offers a comprehensive and critical synthesis of bacterial neurotoxins, integrating molecular mechanisms of action with their pathological consequences, emerging research and therapeutic applications. By combining insights from infectious disease biology and systems neuroscience, we seek to outline both the opportunities and the unresolved challenges that shape the future direction of bacterial neurotoxin research in precision neurology.
Despite the critical role of the gut microbiome in host physiology and health, it remains poorly characterized in Indigenous populations undergoing rapid acculturation. This study presents high-resolution, whole-genome metagenomic profiling of gut microbiota from five Particularly Vulnerable Tribal Groups (PVTGs) of Southern India, Irula, Jenu Kuruba, Kurumba, Chenchu, and Konda Savara, spanning distinct ecological zones and cultural transitions. Using an ecology-lifestyle continuum framework, we investigated taxonomic and functional diversity with a focus on identifying computationally inferred candidate keystone taxa, defined by their association with variation in community ordination structure. A leave-one-taxon-out ordination framework identified 121 candidate keystone taxa, many of which were population-specific and have not been widely reported. Functional analyses revealed a conserved core of metabolic pathways, including glycolysis and folate biosynthesis, alongside group-specific enrichment in xenobiotic degradation, amino acid biosynthesis, mucin metabolism, and lipid processing, associated with differences in dietary and environmental exposures across populations. Large-scale disease-association mapping (n = 5,625) linked 50 candidate keystone taxa to 14 conditions, with 44 associated with health and 6 with disease. While Fusicatenibacter saccharivorans and Alistipes shahii were enriched in healthy states, Ruminococcus gnavus, Bifidobacterium longum, Flavonifractor plautii, and Blautia wexlerae were enriched in disease-associated profiles. Cross-cohort validation against an independent set of traditional metagenomes (n = 119) further showed that a subset of Indian tribal core candidate keystone taxa was consistently identified across geographically distinct populations, with partial conservation of community associations and health associations, indicating reproducible context-dependent microbial association patterns across traditional populations. Alpha diversity was highest in minimally acculturated groups, with higher degrees of acculturation associated with reduced microbial diversity and greater enrichment of disease-associated taxa. Overall, this study provides a context-aware framework for understanding gut microbiome dynamics in culturally transitioning populations, emphasizing the conservation of microbial heritage and informing population-specific microbiome-based interventions.
Nipah virus (NiV) is a highly pathogenic zoonotic agent, posing a persistent and severe threat to global public health with a mortality rate as high as 40% to 80%. With its high risk of cross-species transmission, strong cell tropism, and immune evasion capabilities, NiV has been listed as a priority surveillance pathogen by WHO. Currently, no approved antiviral drugs, immunotherapies, or commercial vaccines are available to combat NiV. This review systematically reviews the core research aspects of NiV, beginning with its viral structure and pathogenic mechanisms, summarizes the progress and breakthroughs in vaccine development, addresses current research limitations to guide future research directions, and provides theoretical support for the precise prevention and control of NiV.
Freshwater ecosystems are important reservoirs and transmission pathways for antibiotic resistance genes (ARGs), yet host-mediated microbial selection and anthropogenic pressure on fish gut resistome remain poorly characterised, especially in major South Asian river systems. We performed shotgun metagenomics and genome-resolved binning from 194 fish representing four species, along with host-associated water samples, collected from six geographically distinct sites spanning two major river systems (the Yamuna and the Indus) and two aquaculture farms. The fish gut nurtures distinct microbial communities from the surrounding water, revealing strong host-mediated filtering of environmental microbiota. Across all samples, 1108 ARG subtypes conferring resistance to 14 antibiotic classes were detected, including extended-spectrum β-lactamases (blaTEM and blaCTX-M) and WHO critical-priority carbapenemases (blaIMP and blaOXA). Fish from the Indus River maintained diverse but comparatively stable resistomes dominated by intrinsic chromosomal efflux mechanisms, whereas fish from the urbanized Yamuna River, particularly Labeo boggut, exhibited noticeable enrichment of clinically important ARGs. The prevalence of mobile genetic elements (MGEs) and virulence factors (VFs) were consistently more abundant in the fish gut microbiome than in the host’s surrounding water, indicating an increased potential for horizontal gene transfer and microbial persistence. A total of 19 metagenome-assembled genomes (MAGs) carrying multiple ARGs, VFs, and plasmid-associated markers were detected, identifying bacterial populations capable of maintaining and disseminating antimicrobial resistance. These outcomes confirm that fish inhabiting anthropogenically influenced river systems can serve as important reservoirs of clinically relevant resistance determinants, highlighting potential risks for environmental dissemination, aquaculture and human exposure through aquatic ecosystems.
Pit mud (PM) microbiota play a vital role in Baijiu flavor formation, yet its ecological and functional succession during maturation remains incompletely elucidated. Here, physicochemical profiling, amplicon sequencing, and metagenomics were integrated to investigate 5-, 15-, and 30-year PM of Sichuan Tang Dynasty Laojiao cellars. Bacteria dominated the community (82.59%), followed by Archaea (16.99%), with Lactobacillus acetotolerans, Ruminococcaceae CPB6, and Methanobacterium paludis as major species. Discrepancies between sequencing methods were reflected in fungal taxa which had low-abundance. The 15-year PM exhibited distinct community and functional features, indicating a critical transitional stage. Functional analysis revealed that fermentation-relevant functions were mainly contributed by 7 key genera and 5 species. Physicochemical properties changed with pit age, characterized by increased moisture as well as decreased acidity and humic substance levels. Moisture, ammonium nitrogen (NH₄⁺-N), available phosphorus, and age were identified as key drivers shaping microbial composition and function. Moisture was identified as the most central mediator, establishing a three-tier cascade causal chain from microorganisms to nutrient accumulation. Functionally, 5-year PM sustained a simple, Lactobacillus-dominated, growth-oriented community; 15-year PM shifted toward aromatic compound degradation, nitrogen utilization, flavor-precursor synthesis; and 30-year PM developed into a stable, flavor-optimized ecosystem enriched in caproic-acid-producing Ruminococcaceae CPB6. Overall, PM maturation is driven by microbiome functional evolution, and the 15-year represented a pivotal period. This study provides a theoretical foundation for scientific PM management and targeted microbial regulation in Baijiu production.
Ribosomal RNA (rRNA) genes serve as foundational markers for microbial eukaryotic diversity assessment, yet their responses to environmental stressors remain underexplored. This study examined the effects of sublethal oxytetracycline and CuCl2 on phenotypic and ribotypic traits in the ciliated protists Paramecium bursaria and Euplotes vannus using single-cell quantitative PCR and high-throughput sequencing of 18S rDNA/rRNA. We found that both pollutants inhibited growth, enlarged cell volume, and elevated per-cell rDNA and rRNA copy numbers, but oxytetracycline selectively elevated rRNA: rDNA ratios. These effects increased the variance around established allometric scaling relationships between rDNA copy number and cell volume, without significantly altering the scaling slope. Intragenomic polymorphisms also increased, with the amplicon sequence variant (ASV) number of rRNA transcripts exceeding that of rDNA, and these elevated polymorphisms persisted post-stress relief. Re-analysis of field 18S metabarcoding data from CuCl2-polluted marine biofilms revealed dose-dependent increases in the number of ASVs per operational taxonomic unit (OTU, defined at a cutoff of 97% sequence identity) in many protistan groups, suggesting that copper-induced mutagenic pressure on ribosomal RNA genes may prevail across diverse protistan taxa. Our findings imply that: (1) when interpreting ASV-based microbial diversity patterns, the potential for ASV richness inflation and elevated per-cell rDNA and rRNA abundances should be recognized as a likely consequence of exposure to environmental pollutants; (2) there is a potential for using the ASV-to-OTU number ratio in assessing environmental stress; and (3) metabarcoding of rRNA likely introduces more artificial ASVs than targeting rDNA. A combination of double metabarcoding of both rDNA and rRNA to identify active microbial members is recommended.
Climate change is intensifying heat, drought/flooding extremes, salinity, and CO2-driven shifts that disrupt soil structure, chemistry, and biological activity, with cascading consequences for crop productivity and food security. This review synthesizes evidence that soil health results from the interconnected interactions among physical structure (aggregation, porosity, bulk density, and pore connectivity), chemical constraints (pH, salinity, nutrient availability, cation exchange capacity, and redox heterogeneity), and biological activity (microbial biomass, diversity, and functional pathways). A central conclusion is that climate impacts are frequently mediated through pore-scale microhabitats (oxygen and moisture gradients, redox microsites, and substrate accessibility), which reorganize microbial functional guilds and regulate C-N-P transformations, organic matter turnover, and aggregation dynamics. We highlight mechanistic pathways by which microbiomes actively shape soil resilience, including EPS/biofilm-mediated aggregate stabilization, extracellular enzyme systems that control depolymerization and nutrient acquisition, and metabolite-driven nutrient mobilization (e.g., organic acids and siderophores), alongside nitrogen and phosphorus cycling processes that are highly sensitive to aeration and moisture regimes. Evidence across agroecosystems indicates that effective climate-smart soil management is most robust when “habitat-first” practices (reduced disturbance, continuous plant inputs, organic amendments) are combined with context-dependent microbiome steering (diversified rotations/cover crops and targeted inoculants). Overall, integrating cross-domain indicators with mechanistic understanding offers actionable pathways to strengthen soil multifunctionality, stabilize yields under climate variability, and support sustainable food systems
Emerging infectious diseases threaten shrimp aquaculture, causing economic losses and challenging disease preparedness. Translucent Post-larvae Disease (TPD) is associated with Vibrio parahaemolyticus strains harboring a virulence plasmid encoding Vibrio high virulent proteins (VHVP). TPD causes translucent or pale body coloration, and high mortality. In this study, shrimp exhibiting TPD-like signs were obtained from local farms. A pathogenic V. parahaemolyticus strain (P40) was isolated from cephalothorax homogenates and screened for TPDassociated virulence genes (vhvp1, vhvp2-1, and vhvp2-2) by colony PCR. Immersion challenge assays confirmed the pathogenicity of strain P40, reproduced TPD signs and high mortality. A single-colony isolate designated P40.49, was used for subsequent analyses. Based on quantitative PCR (qPCR) analysis, stomach, hepatopancreas, and intestine were primary tissues for early detection of TPD-associated bacterial genome copies. Histopathological examination demonstrated epithelial sloughing, necrosis and hemocytic infiltration in both hepatopancreas and intestine. TPD infection significantly modulated host responses, including upregulation of innate immune genes (proPO, PPAE1, Toll-like, Serpin7, and Pen3a) and antioxidative response genes (MnSOD2 and ROS modulator). Dietary supplementation with perilla powder attenuated TPD-associated clinical manifestations and reduced detection of vhvp genes in stomach tissue. Whole-genome sequencing confirmed a TPD-associated virulence plasmid, and phylogenetic analysis clustered the strain with reported TPD isolates from China and Southeast Asia. Comparative genomic analysis further identified four unique plasmid-associated genes specific to TPD-causing strains and infected samples, suggesting their potential as additional molecular markers for TPD diagnosis. These findings provided mechanistic insights into TPD pathogenesis and support improved diagnostics, nutritional and biosecurity strategies for sustainable shrimp aquaculture.
Halococcus species are widely distributed in hypersaline environments and possess unusual cell wall structures. However, their genomic diversity, antiviral defenses, and interactions with viruses remain poorly understood. Here, we sequenced and analyzed the genomes of seven Halococcus strains isolated from hypersaline habitats. Comparative analyses showed substantial variation in growth dynamics, genome size, and defense repertoires, revealing considerable differences among species within the genus. Growth analyses showed distinct behavior among closely related strains, with slow-growing isolates strongly associated with the presence of proviruses, suggesting a fitness cost of lysogeny. Genome-based metrics, including ANI and dDDH, indicated that five of the seven isolates represent four novel species candidates. Two divergent Caudoviricetes-like proviruses were identified. A CRISPR spacer-protospacer match in one strain suggests virus-host interactions and may indicate maintenance of lysogeny. The low sequence similarity of these proviruses to known archaeal viruses supports the existence of previously unrecognized viral lineages infecting Halococcus, providing new insights into the ecology and evolution of this genus in extreme saline environments.
Mucosal barriers serve as a multifunctional interface and nutrient-rich habitat for diverse microbes, including bacteria and bacteriophages. Some phages can bind to mucin glycoproteins via carbohydrate-interacting modules and provide an additional layer of mucosal immunity by shielding the underlying epithelium from invading bacteria. However, the role of mucins in shaping phage-bacterium interactions remains poorly understood. We investigated dynamics between highly pathogenic Yersinia enterocolitica serotype O:8 and its mucus-adherent phage fMtkYen801 under the in vitro mucosal environment. We assessed how mucin supplementation, varying phage doses, nutrient and temperature conditions influence phage-bacterium dynamics and biofilm development. We found that bacterial pre-exposure to mucins led to enhanced phage replication, with a 2-log increase in phage titers. Mucins also modulated post-infection growth dynamics and reduced biofilm formation in the host bacteria. Genomic analysis of phage resistant bacterial variants revealed mutations in virulence, quorum sensing and antibiotic resistance genes in both mucin enrichment and control groups, suggesting potential fitness tradeoffs during resistance evolution. These findings highlight the role of mucosal environments in shaping phage-host interactions in Y. enterocolitica, a significant enteric pathogen, and emphasize the need for investigating these dynamics under complex, physiologically relevant systems to inform better phage therapy strategies against mucosal bacterial infections.
The rapid emergence and spread of antimicrobial resistance (AMR) pose a major global threat to public health. Beyond antibiotics, disinfectants used in food-processing environments may also exert selective pressure that promotes bacterial responses overlapping with antibiotic resistance mechanisms. This study explored the interconnection between antibiotic and disinfectant resistance of the pathogen Arcobacter butzleri by combining phenotypic and transcriptomic analyses. Thirty-one strains isolated from a poultry slaughterhouse were screened for susceptibility to antibiotics from different classes and to commonly used disinfectants. Following an initial screening, 3 representative strains were selected for in-depth analyses and exposed to erythromycin and amoxicillin-clavulanic acid, an amine-based and a sodium hypochlorite with caustic potash disinfectants. Bacterial load, metabolic activity, and transcriptomic responses, using RNA sequencing (RNA-seq), were assesed. All strains exhibited high levels of antibiotic resistance, including resistance to tetracycline and ampicillin. Antibiotic exposure was characterised by minimal reductions in bacterial load and few differentially expressed genes. In contrast, disinfectant exposure induced pronounced, strain-specific responses and resulted in the activation of multiple adaptive pathways. Differential gene expression involved chemotaxis regulators, DNA recombination, detoxification processes, Gram-negative cell wall components, protein and RNA processing systems. Notably, several genes associated with virulence and AMR (tonB, hecB, mexA, mexB, mviN, phoP, tetR, and ylaC), were overexpressed following disinfectants exposure, suggesting potential selection of virulence determinants following disinfectants exposure. The ability of A. butzleri to activate strain-specific adaptive mechanisms in response to antibiotics and disinfectants exposure may facilitate its persistence in food-processing environments and contribute to its pathogenic potential.
