Journal of Applied Microbiology最新文献

Aims: Most chemically defined media for Bacillus are developed with a focus on an individual species. To broaden the applicability, this study aimed to formulate a chemically defined medium that supports the growth of multiple food-relevant Bacillus species. Specifically, it was the aim to support growth of both food fermentation strains from the Bacillus subtilis clade as well as pathogenic strains from the Bacillus cereus clade.

Methods and results: We developed a new chemically defined medium, named Pafoba, using thirteen Bacillus strains: two from the Bacillus cereus clade and eleven strains from the Bacillus subtilis clade, representing seven species. Medium optimisation involved substituting ammonium chloride and sodium chloride with ammonium sulphate and trisodium citrate, enriching glucose, iron, and phosphate concentrations, and applying nutrientomission assays to identify growth requirements. All strains exhibited growth on Pafoba. Ten strains reached a comparable or higher maximum optical density (OD600) on Pafoba medium compared to Brain Heart Infusion broth. Strain-specific nutrient requirements were identified, including a biotin dependency for Bacillus subtilis strain PRO64, and essential amino acid requirements in Bacillus mycoides and Bacillus cereus strains.

Conclusions: The Pafoba medium supports consistent growth across diverse Bacillus species, making it suitable for both fundamental studies and practical applications such as detection and isolation of Bacillus spp. in food-related contexts.

Gram-negative bacterial infections are increasingly becoming resistant to available antibiotic treatment options. The World Health Organization attributed over 1 million deaths to bacterial antimicrobial resistance (AMR) in 2021. While there is a crisis in terms of the available effective antibiotic repertoire, there is also a simultaneous decline in novel drug discovery. In this scenario, the search for alternative or complementary therapeutic options is not only relevant, but also urgently needed. Bacterial virulence factors have been proposed as alternative therapeutic targets since there is lesser propensity for emergence of resistance to these effector molecules. Type 1 fimbriae or FimH of Enterobacteriaceae constitute such a potential target, as these structures are crucial for the initial adhesion and colonization by binding mannose-rich host cell-surface receptors. Additionally, FimH has been associated with multiple diseases, including urinary tract infections (UTIs) and Crohn's disease (CD). The elucidation of Escherichia coli FimH crystal structure has opened the possibility for structure-based drug design to combat these diseases. Many mannose-based compounds are being tried as alternative therapeutics against UTIs and CD with a few molecules showing promise. In this review, we discuss the role of FimH in different diseases, its potential and scope for structure-based development of different mannose-based compounds, and other advanced FimH-blocking therapeutics in preventing these infections.

Aims: Multidrug-resistant (MDR) foodborne pathogens pose an urgent global threat. We surveyed retail foods in Ismailia Governorate, Egypt, to identify highly resistant strains and develop a phage-based biocontrol strategy.

Methods and results: Staphylococcus aureus was detected in 45% of samples (70% meat) and Escherichia coli in 52.5% (80% in arugula), often exceeding safety standards. From 40 representative isolates, the most resistant strains: S. aureus SL4 from lettuce (GenBank OR646818; MAR index 0.44) and E. coli ER2 from arugula (GenBank OR646817; MAR index 0.72), were selected for phage targeting. Two sewage-derived lytic phages, STB (Siphoviridae; host SL4) and ECB (Podoviridae; host ER2), were isolated. Both had ideal biocontrol traits: latent periods ∼10 min, burst sizes ∼2 × 10¹¹ PFU cell⁻¹, and stability at 28-55°C and pH 5-9. In simulated decontamination trials, phage soaking on meat (CFU g⁻¹), arugula, and cutting boards (CFU cm⁻²) reduced bacterial counts by 3.4-6.4 log₁₀ after 1 h, 4.7-6.4 log₁₀ after 3 h, and near-complete eradication by 6 h (9.20-8.58 log₁₀ for SL4, 9.41-7.86 log₁₀ for ER2). Soaking, spraying, and the phage cocktail all outperformed 5% vinegar by 0.8-3.8 log₁₀; the cocktail broadened host range but had slightly slower kill kinetics.

Conclusions: Optimized phage application enables rapid, chemical-free eradication of MDR pathogens from foods and food-contact surfaces.

Aims: To achieve optimal application of antimicrobials to poultry processing requires an understanding of the potential for resistance by foodborne pathogens such as Salmonella. The objective of this study was to use transposon sequencing (Tn-seq) to identify genetic factors required for Salmonella Typhimurium's tolerance to PAA.

Methods and results: A genome-saturated Tn5 mutant library (input pool) was inoculated in two replicates into either 6% chicken meat extract (CME) or 11% diluted Luria-Bertani (LB) broth, both supplemented with 15 ppm PAA. Cultures were incubated for 90 minutes at 37°C. Viable Tn5 mutant cells recovered on LB agar plates were combined to form four output pools (two CME and two LB). Genomic DNA extracted from these pools were deep sequenced (Tn5-junction reads). Conditionally essential genes required for fitness in 6% CME and 11% LB were identified and subjected to pathway enrichment analysis (ShinyGO graphical gene-set enrichment tool). We identified two overlapping sets of conditionally essential genes (276 common genes) required for survival in the presence of PAA. In CME, 362 conditionally essential genes were identified, while LB media revealed 536 genes. Pathway enrichment analysis showed that these genes were significantly enriched in pathways such as pyruvate metabolism, the tricarboxylic acid cycle, fumarate reductase/succinate dehydrogenase (transmembrane subunit and 2Fe-2S iron-sulfur cluster binding domain), stress response, and oxidoreductase activity. Notably, genes previously shown to increase sensitivity to PAA upon inactivation (sdhC, zwf, pta, and icdA) were identified as conditionally essential in this study, further validating the Tn-seq data.

Aims: Copper-rich shape memory alloys (Cu-SMAs) combine unique mechanical properties and catalytic redox activity, supporting the development of advanced endodontic files to improve patient treatments. This study evaluated the bactericidal activity of CuAlBe and CuAlNi wires combined with H2O2-containing solutions against Enterococcus faecalis, a resilient bacterial species frequently associated with persistent root canal infections.

Methods and results: Activity was assessed on planktonic bacteria through CFU counts and on a 2-week-old monospecies biofilm grown on hydroxyapatite discs using SYTO9/propidium iodide staining and fluorescence confocal microscopy. Both Cu-SMAs combined with H2O2 and ascorbic acid (AA) reduced bacterial viability of planktonic cells by 6 log₁₀ after 1-min exposure. In biofilms, CuAlNi/H₂O₂/AA caused cell permeabilization and lysis within 15 min at the wire-biofilm interface. Prolonged exposure led to a time-dependent spatial expansion of bactericidal effects. Diffusing H₂O₂ reacted with Cu²⁺ from the alloy, sustaining a Fenton-like reaction. Gas bubbles formed along the wire generated a convective flow dispersing the reactive mixture millimetres away from the wire surface.

Conclusions: CuAlNi/H₂O₂/AA combination couples radical generation and convection, enabling deep biofilm eradication beyond the wire/solution interface.

Aims: Biofilms formed by Salmonella are a significant concern in the poultry industry due to their role in pathogen persistence. However, there is a lack of data observing the expression of biofilm related genes in different Salmonella serovars. The aim of this study was to investigate the expression patterns of key biofilm-associated genes across three Salmonella serovars, namely Salmonella Typhimurium, Kentucky, and Reading, throughout their biofilm growth cycles.

Methods and results: The expressions of csgD, bapA, bcsA, adrA, and luxS were analyzed in cultures representing different biofilm growth phases: 12 h and 24 h planktonic cells, 4-day old biofilms, and 5-day old biofilms under nutrient deprivation. The findings from this study revealed that only S. Reading exhibited upregulation of these genes at the 24 h planktonic stage at a maximum of 9.58-fold. In contrast, a downregulation of all five genes was noted in the 4-day old biofilms for all serovars. Most notably, bapA was downregulated by 3 765-fold in S. Typhimurium. Upon subjecting the biofilms to nutrient deprivation, there was a notable recovery in the activity of these genes across all serovars with the exception of csgD in S. Typhimurium.

Conclusion: These results suggest that expression of biofilm-associated genes is stimulated by nutrient availability even at biofilm maturity and may vary among different serovars.

Antimicrobial resistance (AMR) is one of the most critical public health threats of the 21st century and is projected to become a leading cause of mortality by 2050. The World Health Organization (WHO) recognizes AMR as a top priority in its 2030 research agenda, emphasizing the need to find new antibiotics and innovative therapies. Research on antimicrobial peptides (AMPs) offers a promising alternative given their rapid, membrane-mediated mode of action and low probability of resistance development. Advances in artificial intelligence (AI) now enable large-scale analysis of biological data, prediction of antimicrobial activity and optimization of peptide designs. Deep-learning and machine-learning models, open-access databases and cutting-edge protein-structure prediction algorithms provide unprecedented opportunities to accelerate the discovery and development of AMPs. Beyond discovery, AI aids in predicting three-dimensional peptide structures, which is essential for understanding their mechanisms of action. Here, we highlight recent progress in integrating AI into the fight against AMR, focusing on the design and prediction of peptides as new antimicrobial agents.

Aims: Soil bacterial communities are a crucial biological indicator of soil health and crop performance; however, their response to climate change remains poorly understood. Wild blueberry farms are experiencing unprecedented temperature changes, which may exacerbate microbial responses and potentially harm the crop. Here, we aimed to elucidate the response of bacterial communities in wild blueberry fields to warming.

Methods and results: We employed passive and active open-top chambers to simulate climate warming scenarios, which elevated atmospheric temperatures by 1.2 and 3.3 °C, respectively. Soils in the active warming treatment exhibited significantly lower water content than in ambient conditions. Overall soil bacterial diversity and richness under the warming (passive and active) treatments and ambient controls did not demonstrate significant differences after two years of warming. However, we found significantly higher bacterial evenness and diversity under warming treatments in the early growing season (June). Our study found pronounced seasonal shifts in the evenness and diversity of bacteria in wild blueberry soils, suggesting that the variation in bacterial community structure may be more influenced by seasonal changes in temperature and plant activity than by warming treatments.

Conclusion: Our study reveals the limited impact of warming on overall soil bacterial diversity in a temperate crop, but the seasonal dynamics of bacterial diversity and composition are sensitive to warming. The increased bacterial evenness and diversity under warming treatments in June could be attributed to advanced plant phenology, indicating a potential future shift in seasonal dynamics of bacterial activity under global warming.

Aims: Cyanobacteria produce and release secondary metabolites in waterways, challenging drinking water treatment plants. Benthic Cyanobacteria, a group of species living at the bottom of waterbodies, have been identified as potential Taste and Odour (T&O) compound and toxin producers. Following an increase in customer T&O complaints about water produced from the SA-L1 Reservoir, this study was conducted to better understand benthic cyanobacetria growth patterns and establish whether the source of detrimental metabolites was pelagic or benthic.

Methods and results: A field-survey was performed from December 2014 to December 2015, during which physical samplers were deployed across a transect (1 m, 2 m, 6 m and 14 m depth). Biofilm and water samples were analysed for microbial community composition, chlorophyll-a (Chl-a), nutrients, T&O and toxins and their associated genes. Seasons and sampling depths impacted benthic communities, Chl-a concentrations and biofilm growth. Spring and autumn were established as peak growth periods for benthic Cyanobacteria. Water geosmin concentrations significantly correlated with the abundance of benthic Cyanobacteria. The potential for cylindrospermopsin and saxitoxin production was detected in this reservoir. Mat detachment mid-spring contributed to T&O dispersion.

Conclusions: Benthic Cyanobacteria are major geosmin contributors in this reservoir. The potential cylindrospermopsin-producer was demonstrated to be benthic, while the saxitoxin producer was identified as pelagic Dolichospermum circinale, which is recruited from bentic mats in spring. Utilities should consider regular monitoring of benthic mats, which provides the necessary evidence to better anticipate benthic and pelagic events, to in turn provide safe and palatable drinking water.

Aims: Pasteurella multocida (Pm) is one of the main pathogens causing bovine respiratory disease in China. The prevention and control measures against Pm are traditionally based on the use of broad-spectrum antibiotics. Previous studies have found that Pm is prone to developing antibiotic resistance and tolerance-related mutations when exposed to low concentrations of antibiotics, ultimately leading to challenges in the prevention and control of Pm. This study aimed to explore the role of the recO gene in Pm in mediating resistance and tolerance to fluoroquinolones.

Methods and results: Highly pathogenic Pm strains (fluoroquinolone-sensitive P3; enrofloxacin-induced resistant P32) were used. RNA-seq screened SOS response-related differentially expressed genes, with recO functionally verified. Its role in Pm's fluoroquinolone resistance/tolerance was clarified via MIC, MBC.The results showed that recO deletion reduced the bacterial tolerance by approximately 10-100-fold after 4 h of exposure to enrofloxacin (ENR) (p < 0.05), decreased the MBC value by 2-fold, and significantly prolonged the time required for resistance development.

Conclusions: In conclusion, inhibiting the expression of the recO gene in Pm not only reduces its resistance to fluoroquinolones but also delays the development of fluoroquinolone resistance. It is hypothesized that the recO gene could serve as a potential target for enhancing the efficacy of fluoroquinolones, thereby improving their antibacterial activity against Pm.