MicrobiologyOpen[JOURNAL]
Sun
200 papers
Computational Insights Into Antimicrobial Peptide-Enhanced Dental Resin Composites: Targeting Porphyromonas gingivalis Heme-Binding Proteins and Biofilms.
Saini RS, Dermawan D, Alshadidi AAF … +7 more , Binduhayyim RIH, Vyas R, Alhamoudi FH, Vaddamanu SK, Kuruniyan MS, Aldosari LIN, Heboyan A
Microbiologyopen · 2025 Dec · PMID 41327619 · Full text
The research aimed at investigating the antibacterial potential of dental resin composites when combined with various antimicrobial peptides (AMPs) against Porphyromonas gingivalis heme-binding proteins, which are associ...
The research aimed at investigating the antibacterial potential of dental resin composites when combined with various antimicrobial peptides (AMPs) against Porphyromonas gingivalis heme-binding proteins, which are associated with biofilm-related infections in restorative dentistry. A multistage computational approach was implemented to assess the AMP interactions. Molecular docking analyses demonstrated the promising binding of resin constituents with AMPs, and Pardaxin exhibited the highest binding affinity, followed by Tachystatin and Thermolysin. The best performing AMPs were then docked with P. gingivalis heme-binding proteins, and the complexes were subjected to 100 ns molecular dynamics simulations for stability assessment. The simulations confirmed stable interactions, while MM/PBSA binding energy calculations demonstrated significant binding strengths, particularly for Pardaxin (ΔG = -65.58 kcal/mol) and Tachystatin (ΔG = -48.71 kcal/mol), with Thermolysin also showing promising results (ΔG = -39.92 kcal/mol). The comprehensive analysis indicates the potential of incorporating Pardaxin, Tachystatin, and Thermolysin into dental resin composites to enhance their antibacterial activity against P. gingivalis. However, the study is limited to in silico assessments and relies on static representations of resin monomers that may not accurately represent the biological and clinical environment. Experimental validation through in vitro and in vivo studies, including cytocompatibility testing, peptide release behavior, and long-term mechanical stability, is essential to establish their practical application in restorative dentistry.
Activation of the Dimer of 3, 4-dimethylphenol Production From Marine Streptomyces sp. FJNU027 Under Oligotrophic Condition.
Wang F, Yuan H, Bai C … +5 more , Li H, Xu L, Yu L, Luo L, Zheng Y
Microbiologyopen · 2025 Dec · PMID 41327614 · Full text
Activating cryptic secondary metabolic gene clusters is a critical area of research in Streptomyces, and the cultivation-based approach is one of effective ways to induce the expression of cryptic gene clusters. In this...
Activating cryptic secondary metabolic gene clusters is a critical area of research in Streptomyces, and the cultivation-based approach is one of effective ways to induce the expression of cryptic gene clusters. In this study, the oligotrophic medium and modified Gauze's medium were used to culture the marine Streptomyces sp. FJNU027 strain, and a unique secondary metabolite in oligotrophic culture was found by HPLC assay when compared with the modified Gauze's culture. Then the differential product was isolated through large-scale fermentation, solvent extraction, column chromatography over Sephadex LH-20, and HPLC preparation. The pure differential product was analyzed by NMR and LC-MS, and identified as 4,4',5,5'-tetramethyl-[1,1'- diphenyl]-2,2'-diol. To elucidate the possible biosynthesis mechanism of the differential product, the transcriptome sequencing was performed. It showed the expressions of polyketide synthase gene (FZ01GL006410) and cytochrome P450 gene (FZ01GL006417) were significantly enhanced in the oligotrophic medium, and these two genes might be responsible for the biosynthesis of the differential product. This compound was reported for the first time isolated from a natural source, demonstrating a novel approach for acquiring this type of compound. The results indicate that oligotrophic culture is an effective method for modulating the secondary metabolism of Streptomyces.
A Systematic Review and Meta-Analysis of Randomized Controlled Trials on the Benefits of Using Lactobacillus Supplements as an Adjunct Treatment for Helicobacter pylori Eradication.
Azam A, Qureshi MAM, Zahoor HS … +5 more , Raza SM, Khan MM, Naeem U, Atif S, Waheed A
Microbiologyopen · 2025 Dec · PMID 41327607 · Full text
Supplementing H. pylori treatment with probiotics like Lactobacillus has become an essential approach due to the possible adverse effects of antibiotic therapy and the need to increase overall eradication rates. Although...
Supplementing H. pylori treatment with probiotics like Lactobacillus has become an essential approach due to the possible adverse effects of antibiotic therapy and the need to increase overall eradication rates. Although several types of Lactobacillus strains as probiotics were efficient in treating H. pylori, their relative efficiency in treating H. pylori was uncertain. A survey of databases, including PubMed, Cochrane, Google Scholar, Scopus, and Clinicaltrials.gov, retrieved 52 Randomized Controlled Trials (RCTs), with 14 meeting the criteria for RCTs on Lactobacillus supplementation (LS) as an adjunct therapy compared to placebo in adult H. pylori patients. Analyses were conducted using RevMan5.3, Cochrane Risk of Bias Tool, Comprehensive Meta-Analysis Software, and GRADEpro. Fourteen RCTs, including 2054 patients with more than ten different probiotics, were included in this analysis. The LS group showed significantly higher H. pylori eradication rates [RR = 1.04 (95% CI: 1.01, 1.07; p = 0.009; I = 0%); (high certainty)], decreased AEs including vomiting [RR = 0.82 (95% CI: 0.48, 1.41; p = 0.48; I = 19%); (high certainty)], diarrhea [RR = 0.45 (95% CI: 0.26, 0.80; p = 0.007; I² = 55%); (high certainty)], abdominal pain [RR = 0.73 (95% CI: 0.28, 1.93; p = 0.53; I² = 66%); (high certainty)], anorexia [RR = 0.79 (95% CI: 0.23, 2.64; p = 0.70; I² = 0%); (high certainty)], constipation [RR = 1.02 (95% CI: 0.42, 2.50; p = 0.96; I² = 0%); (high certainty)], rash [RR = 1.51 (95% CI: 0.57, 3.98; p = 0.41; I² = 0%); (high certainty)], taste disturbance [RR = 0.64 (95% CI: 0.44, 0.92; p = 0.02; I² = 51%); (moderate certainty)], and reduction of gastrointestinal symptoms including abdominal pain [SMD = -0.19 (95% CI: -0.46, 0.09; p = 0.18; I² = %); (moderate certainty)]. None of the included RCTs depicted a high risk of bias. Lactobacillus added to triple or quadruple therapy increased eradication rates, but improvements in adverse effects and gastrointestinal symptoms were not significant. Multiple different strains limited assessment of individual effectiveness, preventing firm conclusions about the specific impact of each Lactobacillus type.
Campylobacter Species Isolated From Wild Birds in Switzerland and Comparison to Isolates From Food and Human Origin.
Stevens MJA, Buvoli GN, Kelbert L … +2 more , Cernela N, Stephan R
Microbiologyopen · 2025 Dec · PMID 41321254 · Full text
Campylobacter species, a major cause of gastroenteritis, have been frequently isolated from wild birds. Here we determined the prevalence of Campylobacter in wild birds from Switzerland. Campylobacter isolates were then...
Campylobacter species, a major cause of gastroenteritis, have been frequently isolated from wild birds. Here we determined the prevalence of Campylobacter in wild birds from Switzerland. Campylobacter isolates were then further characterized by whole genome sequencing. A total of 154 samples from 27 different wild bird species were analyzed and Campylobacter was detected in 23 samples (14.9%). Twenty-one isolates were identified as C. jejuni, one as C. coli and one isolate likely belongs to a novel species. Whole genome analyses revealed that the strains were diverse, belonging to 17 different sequence types. Antimicrobial resistances of the C. jejuni strains included class D ß-lactamase bla genes in all isolates, T86I mutations in GyrA conferring resistance to quinolones in 7 isolates, and tet(O) in 3 isolates. A comparison to 787 Campylobacter from various sources in Switzerland showed that strains spread between humans, poultry and wild birds. Moreover, plasmid analyses and genome comparison provided a strong indication of horizontal gene transfer between Campylobacter strains. Our results strongly support a One-Health approach that includes wild animals to understand and control epidemiology of Campylobacter.
Multi-Omics Analysis Reveals OBSCN as a Key Modulator of Tumor Microenvironment, Microbial Signatures and Clinical Outcomes in Gastric Cancer.
Chen H, Zhang X, Li S … +3 more , Fang Y, Han Y, Jing X
Microbiologyopen · 2025 Dec · PMID 41320670 · Full text
Emerging evidence suggests that OBSCN, a giant cytoskeletal protein gene, plays multifaceted roles in cancer progression, yet its impact on gastric cancer (GC) remains poorly understood. Through integrative analysis of m...
Emerging evidence suggests that OBSCN, a giant cytoskeletal protein gene, plays multifaceted roles in cancer progression, yet its impact on gastric cancer (GC) remains poorly understood. Through integrative analysis of multi-omics datasets, we observe a close relationship between OBSCN expression and outcome of immunotherapy. Besides, elevated expression of OBSCN strongly associated with adverse disease free survival (DFS). Tumor-resident microbes, such as Fusobacterium, can impact the expression of microRNAs (miRNAs) targeting OBSCN. In terms of genomic alterations, mutational status of OBSCN is substantially associated with the alpha- and beta-diversity of intratumoral microbiome and patients with mutated OBSCN exhibit elevated higher tumor mutational burden (TMB) and better response to immunotherapy. Furthermore, machine learning models based on the OBSCN mutation-related gene signatures (OMRGS) achieve outstanding performance in prediction of response to immune checkpoint inhibitors. In summary, our findings position OBSCN as a novel molecular nexus linking genomic alterations, intratumoral microbiome dysbiosis, and immune infiltration in GC, providing a rationale for future biomarker-driven therapeutic strategies.
Olive Pomace Inclusion Alters the Microbial Community of Black Soldier Fly Larvae Frass While Maintaining Fertilizer Quality.
Lopes IG, de Lima NM, Ribeiro T … +3 more , Murta D, Yong JWH, Lalander C
Microbiologyopen · 2025 Dec · PMID 41319143 · Full text
Olive pomace (OP) is a sludge arising from the production of olive oil, generated in increasing amounts in Portugal. The management of this toxic waste stream is complex and the number of processing plants is limited. In...
Olive pomace (OP) is a sludge arising from the production of olive oil, generated in increasing amounts in Portugal. The management of this toxic waste stream is complex and the number of processing plants is limited. In this study, OP was incorporated as a feed component for rearing black soldier fly larvae (BSFL) under industrial conditions. Larvae were reared inside a climate-controlled room with regulated temperature and humidity. The rearing cycle lasted 13 days, after which larvae were harvested. In addition to assessing bioconversion efficiency and larval proximate composition, the resulting frass was examined for its fertilizer potential. Frass was analyzed for plant nutrient content and microbial profile in three forms: fresh, heat-treated (70°C for 1 h), and pelletized. The inclusion of OP in the diets reduced waste-to-biomass conversion efficiency (21.5% to approximately 13.3%) but did not affect the proximate composition of the larval biomass, which consistently contained around 43% crude protein and 20% crude fat. Neither the presence of OP nor the applied post-treatments altered the nutrient composition of frass, which contained on average 3.5% total N, 2.6% PO, and 5.9% KO. However, at the highest inclusion level (84%), the abundance of bacterial and fungal groups was significantly reduced. The predominant phyla in the frass were Actinobacteria, Bacteroidota, Firmicutes, Proteobacteria, Ascomycota and Basidiomycota, and the dynamics of microbial communities were influenced by specific micronutrients. The presence of OP led to a significant reduction of potentially pathogenic bacteria and fungi in the frass, indicating a sanitizing effect attributable to this material.
Prevalence, Risk Factors, and Antimicrobial Susceptibility Patterns of Salmonella From Bulk Milk at the Dairy Farm Level in Mekelle and Southeast Zones of Tigrai, Ethiopia.
Kahsay AG, Asmelash T, Kassaye E
Microbiologyopen · 2025 Dec · PMID 41319139 · Full text
Salmonella is recognized as one of the foodborne bacterial infections. The bacterium spreads through contact with animals and ingestion of contaminated foods. This study aimed to determine the prevalence, risk factors, a...
Salmonella is recognized as one of the foodborne bacterial infections. The bacterium spreads through contact with animals and ingestion of contaminated foods. This study aimed to determine the prevalence, risk factors, and antimicrobial susceptibility patterns of Salmonella from bulk milk at dairy farm level in Mekelle and Southeast Zones of Tigrai, Ethiopia. A cross-sectional study was carried out from January to June 2025. After taking the consent, sociodemographic, risk factors, and 203 bulk milk samples were collected from the dairy farms. Salmonella was isolated and identified through pre-enrichment, selective enrichment, selective media, and a series of biochemical tests. Antimicrobial susceptibility testing was conducted using the disk diffusion method. Stata v-16 was employed to determine the strength of the factors that associates with Salmonella. The prevalence of Salmonella was six (2.96%). Salmonella positivity showed statistically significant association with farms that don't practice regular udder washing before milking, lack of knowledge about bacterial infections, and do not know that consumption of raw milk cause foodborne illness. Five (83.3%) isolates of Salmonella showed resistance to ampicillin and tetracycline, and four (66.7%) to streptomycin. All Salmonella isolates were susceptible to ceftazidime and cefotaxime. Three isolates of Salmonella showed multidrug resistance. The prevalence of Salmonella was low, but its presence in milk may be considered a potential risk to milk safety. Three Salmonella isolates showed resistance to four and six antimicrobial classes. The finding highlights the need for appropriate hygiene practices and the correct use of antibiotics in the farms.
Non-albicans Candida in Vulvovaginal Candidiasis: Antifungal Resistance and Expression of ERG11, CDR1, CDR2, and MDR1 Genes.
Ranjbar Golafshani FZ, Kermani F, Abbaszadeh Godarzi S … +1 more , Mahdavi Omran S
Microbiologyopen · 2025 Dec · PMID 41319137 · Full text
The rise in azole resistance among Nakaseomyces glabratus and Pichia kudriavzevii in recurrent vulvovaginal candidiasis presents a growing public health challenge. This study investigated the expression of antifungal res...
The rise in azole resistance among Nakaseomyces glabratus and Pichia kudriavzevii in recurrent vulvovaginal candidiasis presents a growing public health challenge. This study investigated the expression of antifungal resistance-related genes (ERG11, CDR1, CDR2, and MDR1) in clinical resistant (CR) and clinical and laboratory resistant (CLR) strains of these yeasts. Cervicovaginal samples from patients with recurrent infections were collected, microscopically examined, and cultured. Yeast species were identified phenotypically and genotypically, followed by drug sensitivity testing. Total RNA was extracted, reverse transcribed to complementary DNA, and real-time polymerase chain reaction was used to quantify target gene expression, comparing results to drug-sensitive controls. Non-Candida albicans species constituted 29% (45 cases) of the isolates, with N. glabratus (68%) and P. kudriavzevii (17%) being the dominant species. Other species included Candida parapsilosis, Meyerozyma guilliermondii, Candida orthopsilosis, Saccharomyces cerevisiae, and Rhodotorula mucilaginosa. Coinfections with P. kudriavzevii/C. albicans and N. glabratus/C. albicans were also observed. Ketoconazole, itraconazole, and 5-flucytosine demonstrated the best antifungal activity against most species. However, some N. glabratus isolates were resistant to miconazole, clotrimazole, and amphotericin B, while all P. kudriavzevii isolates resisted clotrimazole. Overexpression of the CDR1 gene was noted in N. glabratus (CR, 21.53 ± 1.26; CLR, 84.96 ± 0.67), and the ERG11 and CDR1 genes in P. kudriavzevii (ERG11 for CR, 28.56 ± 2.16; CDR1 for CLR, 35.89 ± 0.35). These results indicate that even in cases where an isolate is classified as susceptible by drug susceptibility testing, elevated gene expression may persist, and treatment should not be discontinued.
Phenotypical and Genomic Characterization of the Mollusk Pathogen Francisella halioticida.
Bouras H, Quesnelle Y, Trancart S … +5 more , Goux D, Blin JL, Savary M, Houssin M, Zatylny-Gaudin C
Microbiologyopen · 2025 Dec · PMID 41312677 · Full text
The emergence and dissemination of aquatic pathogens pose significant risks to farmed species. Francisella halioticida, initially reported in abalones and Yesso scallops, was recently isolated from mussels in France, wit...
The emergence and dissemination of aquatic pathogens pose significant risks to farmed species. Francisella halioticida, initially reported in abalones and Yesso scallops, was recently isolated from mussels in France, with some isolates showing high virulence. This study aimed to characterize and compare several F. halioticida isolates from mussels using phenotypic and genotypic approaches. Phenotypic analysis was performed using growth curves, biochemical profiles (API strips), and morphology assessed by electron microscopy. Genetic analysis has been performed through whole-genome comparison using classification methods and virulence markers seeking. Phenotypic analyses highlighted similarities among FR22 isolates and notable differences with FR21 and AG1. Notably, AG1 displayed distinct features. Antibiotic resistance profiling revealed the species' capacity to withstand multiple antimicrobial agents with various modes of action. Complete, circular genomes were assembled and compared using targeted and untargeted approaches. These analyses confirmed the affiliation of FR22 isolates with the F. halioticida species, while FR21 and AG1 taxonomy need to be further investigated. Virulence factor screening revealed the presence of secretion system components (types I, IV, and VI) in all isolates. A novel variant of the Francisella Pathogenicity Island (FPI) was described, shared by all virulent isolates. However, this FPI was absent in the low virulence isolate FR22b. In conclusion, this study discriminates against F. halioticida isolates and proposes new hypotheses on their virulence, contributing to improved detection tools and expanding our understanding of this emerging aquatic pathogen.
Molecular Cloning and Functional Analysis of Holin and Endolysin From Escherichia Phage UE-M6 as Potential Antibacterial Agents.
Niaz H, Skurnik M, Adnan F
Microbiologyopen · 2025 Dec · PMID 41311358 · Full text
The rise of antibiotic-resistant bacteria has intensified the search for alternative antibacterial strategies. Bacteriophage (phage) therapy is gaining attention as a promising approach, utilizing phage-derived proteins...
The rise of antibiotic-resistant bacteria has intensified the search for alternative antibacterial strategies. Bacteriophage (phage) therapy is gaining attention as a promising approach, utilizing phage-derived proteins such as holins and endolysins to combat bacterial infections. In this study, the endolysin (UE-lysin) and holin (UE-holin) genes from Escherichia phage UE-M6 were characterized, and their antimicrobial activity was evaluated. In silico analysis revealed that UE-lysin has a modular architecture, with the N-terminal enzymatic activity domain that contains an N-acetylmuramidase of the glycoside hydrolase family GH108, and the C-terminal cell wall-binding domain that contains the peptidoglycan binding family PG_binding_3 domain. UE-holin was predicted to belong to class II holins, featuring two transmembrane helices. Furthermore, the genes encoding the UE-lysin and UE-holin were cloned and their expression optimized in Escherichia coli BL21 (DE3). The purified recombinant UE-lysin (27 kDa) and UE-holin (15 kDa) exhibited antibacterial activity against the E. coli host strain PSU-5266 (UE-17). The addition of the outer membrane permeabilizer ethylenediaminetetraacetic acid further enhanced their activity. Notably, the combined application of UE-holin and UE-lysin demonstrated greater antibacterial efficacy than either enzyme alone, highlighting a synergistic effect. Furthermore, UE-lysin and UE-holin exhibited high lytic activity against E. coli, Bacillus, and Staphylococcus aureus strains, underscoring their potential as candidates for treating both Gram-negative and Gram-positive bacterial infections.
The Host R-M Systems Change the Host Range of Staphylococcus Phage EBHT.
Tuomala H, Holtel J, Markkanen M … +8 more , Patpatia S, Kaansalo K, Rolland C, Bayfield OW, Ranta K, Skurnik M, Wittmann J, Kiljunen S
Microbiologyopen · 2025 Dec · PMID 41310952 · Full text
Therapeutically utilized phages should optimally be produced in defined bacterial strains that are free of prophages and virulence factors. However, phage-host interactions in these production strains may be very differe...
Therapeutically utilized phages should optimally be produced in defined bacterial strains that are free of prophages and virulence factors. However, phage-host interactions in these production strains may be very different from clinical strains. Here, we characterized a lytic Staphylococcus aureus-specific phage vB_SauP_EBHT (EBHT), which had a dramatic change in its host specificity when produced in alternative host 19A2 compared with the original isolation host DSM 104437, even though there were no changes in the phage genome, proteome, structure, or adsorption efficiency. The reason for the altered host range was revealed to be based on different methylation patterns of the EBHT genome by host restriction-modification (R-M) systems in the two hosts. Even though the alternative host 19A2 produced a higher burst size, the host range of the produced phages was narrower. Together, these results illustrate that the most efficient production host may not necessarily be the most optimal one and that bacterial R-M systems should be considered when selecting the optimal phage-production host.
Adaptive Evolution and Distinct Mutation Signatures of Full-Length HBV Quasispecies in HBeAg-Negative Chronic Hepatitis B.
Wu C, Liu F, Li X … +6 more , Li X, Li H, Zhang S, Yan X, Zhou T, Wei J
Microbiologyopen · 2025 Dec · PMID 41310915 · Full text
The evolutionary profile of hepatitis B virus (HBV) quasispecies may influence the clinical course of chronic hepatitis B (CHB), but few studies have characterized quasispecies according to hepatitis B e antigen (HBeAg)...
The evolutionary profile of hepatitis B virus (HBV) quasispecies may influence the clinical course of chronic hepatitis B (CHB), but few studies have characterized quasispecies according to hepatitis B e antigen (HBeAg) status. In this study, we analyzed 289 full-length HBV clones from 19 treatment-naïve CHB patients with long-term infection (> 10 years), comprising nine HBeAg-positive and ten HBeAg-negative, using molecular cloning and Sanger sequencing. Compared with HBeAg-positive patients, HBeAg-negative patients displayed higher quasispecies diversity (mean intrapatient sequence divergence 1.09% vs. 0.44%) and more complex phylogenetic structures. They also exhibited a greater number of positively selected sites, with 70.8% located within known T- or B-cell epitope regions, predominantly in the surface (S), polymerase (Pol), and X regions. Classical basal core promoter (BCP) and precore (PreC) mutations were detected in 52.8% of HBeAg-negative clones, often coexisting with wild-type strains. In patients lacking these classical BCP/preC mutations but showing sustained viremia, intrahost recombination was observed. Moreover, overlapping reading frames, particularly +1 frameshifts in Pol/S region, demonstrated asymmetric distribution patterns. In patients harboring deletion mutations, intact quasispecies were also maintained. Collectively, these findings reveal multiple adaptive strategies that sustain HBV replication and immune escape in HBeAg-negative patients, providing mechanistic insights for disease monitoring and therapeutic interventions.
Infectious Triggers and Immune Dynamics in Guillain-Barré Syndrome: Revisiting Campylobacter jejuni and the Silent Role of Haemophilus influenzae.
Ramesh A, Subbarayan R, Srinivasan D … +3 more , Balakrishnan R, Shrestha R, Chauhan A
Microbiologyopen · 2025 Dec · PMID 41310913 · Full text
Guillain-Barré Syndrome (GBS) is a rapidly progressing immune-mediated neuropathy that remains the leading cause of acute flaccid paralysis worldwide. A substantial proportion of GBS cases are precipitated by infectious...
Guillain-Barré Syndrome (GBS) is a rapidly progressing immune-mediated neuropathy that remains the leading cause of acute flaccid paralysis worldwide. A substantial proportion of GBS cases are precipitated by infectious agents, most notably Campylobacter jejuni and Haemophilus influenzae, which initiate pathogenic autoimmunity via molecular mimicry. This narrative review aimed to synthesize current evidence on the microbial triggers of GBS and elucidate the immune mechanisms linking infection to neuropathic damage. We discuss the evolving landscape of GBS pathogenesis, emphasizing the roles of ganglioside-like lipooligosaccharide (LOS), host genetic predisposition, and dysregulated immune responses. The clinical heterogeneity of GBS subtypes, including axonal and demyelinating variants, was analyzed in relation to serotype-specific antibody profiles that inform the diagnosis and prognosis. Current therapeutic interventions, including intravenous immunoglobulin and plasma exchange, are critically assessed alongside experimental strategies, such as monoclonal antibody therapies, microbiome modulation, and LOS-targeted vaccines. This review highlights microbial surveillance and precision immunotherapy in the management of GBS. Collectively, this study underscores the central role of microbiological insights in redefining the prevention, diagnosis, and treatment of this complex neuroimmune disorder.
Dissecting HOCl Action in Chronic Wound Biofilms: Proteomic Insights From a Host-Relevant Model of Pseudomonas aeruginosa.
Robins LI, Gafken P, Lin C … +2 more , Jones L, Hooper SE
Microbiologyopen · 2025 Dec · PMID 41307276 · Full text
Pseudomonas aeruginosa is found in 48%-52% of chronic wound biofilms, where its resistance to antimicrobials and host immunity presents a major clinical challenge. Although hypochlorous acid (HOCl) is known to be an effe...
Pseudomonas aeruginosa is found in 48%-52% of chronic wound biofilms, where its resistance to antimicrobials and host immunity presents a major clinical challenge. Although hypochlorous acid (HOCl) is known to be an effective antimicrobial, its mechanism of action remains unclear because standard experimental conditions often produce a mixture of HOCl and hypochlorite (OCl⁻), making it difficult to isolate the effects of HOCl. Here, we use proteomic profiling to investigate the effects of a pure, stable HOCl gel on P. aeruginosa biofilms in a physiologically relevant chronic wound model. We applied HOCl gel (5.7 mM, pH 6) to mature P. aeruginosa biofilms established in a wound-mimicking flow model. Proteins were analyzed using tandem mass tag (TMT)-based quantitative proteomics, identifying 1,878 proteins. HOCl treatment significantly reduced biofilm viability and altered the abundance of 330 proteins. We observed substantial depletion of proteins involved in biosynthesis, virulence, antibiotic resistance, and biofilm formation, alongside enrichment of stress response proteins. These findings indicate a shift toward survival phenotypes and weakened pathogenicity. Our data reveal that HOCl disrupts multiple pathways essential for P. aeruginosa survival and virulence. Crucially, our experimental design eliminates confounding factors that can lead to unintentional testing of mixed HOCl and OCl⁻ species, allowing us to assess the specific effects of HOCl. These findings call for a re-evaluation of HOCl research methodologies and reiterate the importance of realistic infection models in antimicrobial testing.
Characterization of Pilin A and Thioredoxin A Mutant Strains of Acinetobacter baumannii, From a Transposon Insertion Library, for Pili Production and Virulence-Associated Properties.
Aki J, Papp SB, Polk B … +9 more , Jeffreys S, Tompkins MP, Kalalah AA, Eppinger M, Zhang G, Guentzel MN, Chambers JP, Arulanandam BP, Yu JJ
Microbiologyopen · 2025 Dec · PMID 41307102 · Full text
Acinetobacter baumannii is a multi-drug resistant Gram-negative coccobacillus. It is responsible for high mortality among patients in the intensive care unit. Reported A. baumannii virulence factors include the thioredox...
Acinetobacter baumannii is a multi-drug resistant Gram-negative coccobacillus. It is responsible for high mortality among patients in the intensive care unit. Reported A. baumannii virulence factors include the thioredoxin system which plays a critical role in gene regulation and protein reduction. The Type IV pilus (T4P) is a well-known bacterial virulence factor that is associated with adhesion and molecular exchange. Previously, our laboratory revealed the role of A. baumannii thioredoxin A (TrxA) in pathogenesis by studying a trxA deletion mutant that downregulates T4P gene expression. TrxA, a potent disulfide bond reducer, might affect the assembly of pili by targeting T4P component proteins, including PilA, the major pilin protein of T4P which contains multiple cysteine residues required for disulfide bond formation. Using a transposon library derived from the AB5075 clinical isolate, we phenotypically characterized a pilA mutant strain and compared its pathogenesis to the wild type (WT) strain as well as another trxA mutant. Whole genome sequencing was conducted to confirm the disruption of trxA and pilA genes in the corresponding mutant strains of AB5075. Alteration of bacterial surface appendages in ΔtrxA and ΔpilA was visualized by Scanning electron microscopy. Like ΔtrxA, the T4P mutant ΔpilA had marked reduction of surface pili. Bacterial attachment to excised intestinal surfaces was greatly reduced for ΔtrxA and ΔpilA. Attenuation of ΔtrxA and ΔpilA in pathogenesis was further confirmed using a mouse sepsis model. Collectively, this characterized ΔpilA deficiency in A. baumannii resulted in attenuation of virulence making it a potential therapeutic target.
The Transgenerational Link: Breeder Gut Microbiota and Broiler Progeny Development.
Pangga GM, Bamford S, Richmond A … +3 more , Corcionivoschi N, Ijaz UZ, Gundogdu O
Microbiologyopen · 2025 Dec · PMID 41307098 · Full text
The gut microbiome of breeder hens plays a pivotal role in reproductive efficiency, egg quality, and progeny development. Its composition is shaped by host factors such as age and genetics, as well as environmental influ...
The gut microbiome of breeder hens plays a pivotal role in reproductive efficiency, egg quality, and progeny development. Its composition is shaped by host factors such as age and genetics, as well as environmental influences, including diet and management practices. Importantly, the breeder gut microbiome is not only dynamic but also responsive to targeted interventions that can enhance intestinal health, metabolic function, and laying performance. Vertical transmission of maternal microbes through the cloaca and egg components provides offspring with a foundational microbial community, with the yolk sac serving as a critical reservoir for early colonisers that influence gut maturation, immunity, and growth. Emerging evidence further demonstrates that maternal nutritional strategies can programme the gut microbiota of progeny and intestinal development, highlighting the breeder microbiome as both a determinant and mediator of transgenerational performance. These insights underscore the potential of microbiome-focused approaches to improve reproductive success and sustainability in poultry production.
Next-Generation Sequencing in Infectious-Disease Diagnostics: Economic, Regulatory, and Clinical Pathways to Adoption.
Osei Sekyere J
Microbiologyopen · 2025 Dec · PMID 41305954 · Full text
Next-generation sequencing (NGS) has emerged as a transformative tool for infectious disease diagnosis, offering broad pathogen detection, antimicrobial resistance profiling, and syndromic panel testing. However, widespr...
Next-generation sequencing (NGS) has emerged as a transformative tool for infectious disease diagnosis, offering broad pathogen detection, antimicrobial resistance profiling, and syndromic panel testing. However, widespread clinical adoption remains hindered by insurance reimbursement challenges, high costs, and regulatory barriers. Unlike polymerase chain reaction (PCR), which enjoys well-established Current Procedural Terminology (CPT) codes and reimbursement pathways, many NGS-based tests lack standardized billing mechanisms, discouraging laboratories from integrating NGS into routine diagnostics. This article explores the economic, clinical, and technological considerations of targeted amplicon sequencing (tNGS) versus PCR and whole-genome sequencing (WGS), demonstrating how optimized multiplexing strategies, emerging NGS platforms, and regulatory advancements can enhance feasibility. It is argued that insurance policies must evolve to recognize NGS's superior clinical utility in detecting polymicrobial infections, emerging pathogens, and antimicrobial resistance determinants, ultimately improving patient outcomes and reducing healthcare costs. Current reagent-only costs now average US $65 per microbial genome, US $600 per 30× human genome, and US $130-600 per metagenomic sample when multiplexed; these figures continue to fall with higher multiplexing. To accelerate equitable adoption, we recommend near-term payer coverage pilots for clearly defined clinical indications, dedicated CPT pathways for infectious-disease sequencing (including metagenomic assays), and pragmatic validation frameworks that acknowledge genotype-phenotype limits while leveraging multiplexing and centralized reference workflows.
The Role of Machine Learning in Addressing Antibiotic Resistance: A New Era in Infectious Disease Control.
Zubair A, Fazil M, Jawad M … +1 more , Wdidi S
Microbiologyopen · 2025 Dec · PMID 41287252 · Full text
Antimicrobial resistance (AMR) refers to the ability of microorganisms, such as bacteria and viruses, to resist antimicrobial medications. Current strategies for addressing this escalating issue are often labor-intensive...
Antimicrobial resistance (AMR) refers to the ability of microorganisms, such as bacteria and viruses, to resist antimicrobial medications. Current strategies for addressing this escalating issue are often labor-intensive and costly. However, advancements in artificial intelligence (AI) are enabling the rapid evaluation of extensive chemical libraries and the prediction of novel antimicrobial compounds. AI holds significant promise for medical research in treating multidrug-resistant infections by enhancing the development of new medications through the analysis of antibiotic usage, disease prevalence, and resistance patterns. The use of AI has the potential to greatly benefit research by accelerating the discovery of new antibiotics that effectively combat antibiotic-resistant microbes. Predicting trends in antibiotic resistance through the examination of large data sets by AI systems may pave the way for the creation of preventative medicines. The speed and accuracy with which AI can evaluate data are revolutionizing how scientists develop new medicines, assess potential health concerns, and find ways to prevent illness. AMR is a growing concern, and AI is playing an increasingly crucial role in this battle. Medical research utilizing AI has tremendous potential in the ongoing fight against antibiotic resistance. This review examines how AI aids in AMR diagnosis, small molecule drug development, and the detection of AMR symptoms. Further research into AMR detection and the creation of novel medications are two areas that could prove valuable in treating antimicrobial resistance.
Gut Microbe Fermentation of Moringa oleifera Leaf Extract Increases Measurable Polyphenols and Improves Barrier Function in a Cell Culture Model.
Kable ME, Storms DH, Alkan Z … +4 more , Muriki M, DeVries D, Waterman C, Lemay DG
Microbiologyopen · 2025 Dec · PMID 41287225 · Full text
Moringa oleifera is associated with several nutritional and therapeutic benefits. However, there is limited research on how much these health benefits are mediated directly by the plant or through fermentation with intes...
Moringa oleifera is associated with several nutritional and therapeutic benefits. However, there is limited research on how much these health benefits are mediated directly by the plant or through fermentation with intestinal microbes. We examined the interaction between M. oleifera aqueous leaf extract and three common gut microbes whose abundance was significantly altered in previous intervention studies. Growth curves of Escherichia coli, Bifidobacterium longum, and Bacteroides thetaiotaomicron were examined in the presence of increasing concentrations of M. oleifera leaf extract in YCFA media with and without carbohydrates and short chain fatty acids (SCFAs). Anthrone and Fast Blue BB assays were conducted on spent media to measure carbohydrate and phenolic content, respectively. Sterile fermentation supernatants were applied to an in vitro gut barrier model consisting of differentiated Caco-2 monolayers on permeable cell culture inserts and the transepithelial resistance (TEER) was measured. Growth curve analysis demonstrated that the three bacterial isolates tested could grow in the presence of M. oleifera. However, B. longum had a greater increase in total growth, consumed more soluble carbohydrates, and produced more soluble polyphenols using M. oleifera leaf extract as a sole carbohydrate source than the other two microbes. Additionally, B. longum fermentation of both glucose and M. oleifera increased TEER in Caco-2 monolayers significantly more than E. coli fermentation of both carbohydrate sources (p = 0.0007). These results suggest a potential mechanism through which consumption of M. oleifera may promote the growth of probiotic organisms within the human gut to improve gut barrier integrity.
Genome-Driven Analysis Reveals the Biotechnological Potential of a Novel Paenibacillus sp. Isolated From Crude Oil.
Dos Anjos Almeida JV, Nóbrega Mendonça CM, Moreira LM … +3 more , Pinheiro de Souza Oliveira R, de Mello Varani A, de Medeiros Oliveira M
Microbiologyopen · 2025 Dec · PMID 41285130 · Full text
Microbial biotechnology plays a critical role in addressing environmental challenges and promoting sustainability. Here, we report the complete genome sequencing of Paenibacillus sp. strain 210, previously isolated from...
Microbial biotechnology plays a critical role in addressing environmental challenges and promoting sustainability. Here, we report the complete genome sequencing of Paenibacillus sp. strain 210, previously isolated from Brazilian crude oil and known for its levan metabolism and biosurfactant production. With the sequenced genome, we employed bioinformatics tools for assembly and annotation, followed by comprehensive in silico analyses, including phylogenomics, biosynthetic gene cluster (BGC) identification, carbohydrate-active enzyme (CAZyme) profiling, and metabolic pathway reconstruction. The assembled 5.7 Mb genome harbors four prophage regions and 13 antimicrobial BGCs, including those encoding fusaricidin, paenicidin A, paenilan, paeninodin, and tridecaptin. Phylogenomic analysis combined with average nucleotide identity measurements indicates that this strain does not cluster with any recognized Paenibacillus species, supporting its designation as a potential new species. Notably, the identification of 259 CAZyme genes points to a strong capacity for degrading complex polysaccharides (e.g., cellulose, xylan, and pectin), positioning this bacterium as a promising candidate for biofuel production. Furthermore, the presence of complete metabolic pathways for several B vitamins highlights predicted metabolic autonomy supporting microbial interactions, reinforcing their usefulness in soil bioremediation by enhancing nutrient availability. In contrast, incomplete pathways for vitamins B2 and K2 indicate metabolic dependencies that may facilitate syntrophic interactions with other microorganisms. In silico structural analyses of selected hydrolytic enzymes (GH1, GH5, and GH11) reveal homology to functionally validated and crystallized proteins. Collectively, these findings highlight the genetic versatility of Paenibacillus sp. strain 210 and its potential for ecosystem restoration, biofuel production, plant growth promotion, and biocontrol.
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