Journal of Applied Microbiology最新文献

Aims: Brewing yeast strain selection and management are critical in beer production, influencing flavor profiles and overall quality. This study investigates the potential of MALDI-TOF MS (Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry) for characterizing and differentiating brewing yeast strains associated with various beer styles.

Methods and results: We analyzed 77 commercial yeast strains used to produce ale, lager, cider, mead, and low-alcohol beer, using MALDI-TOF MS in both high (m/z 2000-20 000) and low (m/z 500-4000) mass ranges. Spectra were analyzed using informatics-assisted hierarchical cluster analysis, multidimensional scaling (MDS), and linear discriminant analysis (LDA) to evaluate strain relationships and beer style associations. Results demonstrated that high mass range data formed an excellent basis for species-level identification, while low mass range data was more diverse and represented information that was more strain-specific.

Conclusions: Both MDS and hierarchical clustering of combined low- and high-range MALDI-TOF spectra identified relationships between certain strains that correlated with their brewing recommendations. However, the use of LDA presented the clearest correlation of strain relationships with beer styles recommended by the commercial yeast producer.

Aims: We aim to evaluate the productivity of shiitake strains under warm cultivation temperatures using alternative substrates from neotropical tree species, addressing the challenges of global warming and substrate availability.

Methods and results: Four strains (one control and three warm-tolerant candidates) were cultivated on sawdust from Quercus, Carpinus, and Bursera at 18°C and 25°C. Strain identity was confirmed via phylogeny. Biological efficiency (BE), yield, production rate, and lignocellulose degradation were measured. All strains were taxonomically confirmed as Lentinula edodes. The highest BE was 107%, recorded in Quercus at 18°C, although it was highly variabile (30%). Warm-tolerant strains IE-3012, IE-3013, and IE-3014 consistently outperformed the control at 25°C, particularly on Quercus. There was mushroom production in Bursera, although it was lower. Lignin was the most consumed lignocellulosic fraction across all conditions.

Conclusions: This study confirms that the suspected heat-tolerant L. edodes strains can be cultivated at 25°C, using alternative substrates such as Bursera, though substrate choice significantly affects productivity. Strain IE-3013 performed best, positioning it as a promising candidate for warm-climate cultivation. Cold-water immersion successfully induced the development of fruiting bodies across studied conditions, supporting its use in the shiitake cultivation process.

Aim: The halotolerant endophytic bacterial Pseudomonas strain EB3 isolated from the roots of the mangrove plant species Avicennia alba, has been reported to promote plant growth and mitigate the adverse effects of salt stress. However, the genetic mechanisms of the strain that may explain these processes are unknown. This study aimed to determine the whole genome sequence of EB3 and conduct expression analysis of EB3 genes putatively involved in salt tolerance and plant growth promotion.

Methods and results: EB3-inoculated banana (Musa acuminata cv. Berangan) plantlets were subjected to 100 mM sea salt. These inoculated plants exhibited significantly improved growth compared to non-inoculated controls under the same salinity stress. Whole-genome sequencing of EB3 revealed a genome size of 6 006 826 bp. Phylogenetic analysis based on whole-genome comparison indicated that EB3 is closely related to Pseudomonas juntendi. Functional annotation of the genome identified a large number of genes associated with key biological processes, including stress resistance, iron uptake system, plant root colonization, and plant growth promotion. The increased expression of succinate-semialdehyde dehydrogenase (gabD), pyrroloquinoline quinone biosynthesis proteins (pqqBDEF), acetylglutamate kinase (argB), NADP-specific glutamate dehydrogenase (gdhA), N-acetylglutaminylglutamine synthetase (ngg), and superoxide dismutase family protein (sodC) genes in EB3, when EB3-inoculated plants were placed under salt stress, further supported their potential involvement in salt tolerance and growth-promoting activities.

Conclusion: Together, the genomic insights and gene expression data confirm the functional potential of the EB3 strain as a plant growth-promoting bacterium (PGPB) even under saline conditions.

Aims: Metal resistance genes (MRGs) and virulence factor genes (VFGs) are driven by environmental factors and host immunity, respectively, and they are traditionally considered to evolve independently. However, their co-selection dynamics in landfill leachates remain poorly characterized. In this study, a multi-regional metagenomic assessment integrating environmental gradients was first presented to reveal how heavy metals shape MRG-VFG interactions and associated ecological risks in landfill leachates.

Methods and results: Landfill leachates were collected from 13 landfills spanning six regions in China. Multi-regional metagenomic sequencing combined with co-occurrence network analysis was applied to examine pathogen-gene relationships. The results revealed pronounced regional disparities in pathogen, MRG, and VFG distribution, alongside shared features. Staphylococcus aureus and Pseudomonas aeruginosa were identified as dominant pathogens. tufA and gyrA emerged as conserved VFGs, whereas arsB and copA represented dominant MRGs. Network analysis revealed Escherichia coli, Salmonella enterica, and Acinetobacter baumannii as central nodes carrying overlapping functional genes, forming a "metal resistance-virulence" synergy module. Redundancy analysis revealed that specific heavy metals (Cu, Zn, Cr, and As) were crucial for the formation and stability of "pathogen-MRG-VFG" functional assemblies.

Conclusions: This study addresses a critical knowledge gap by integrating multi-regional metagenomic evidence with environmental selection pressures. MRGs conferred survival advantages and synergized with VFGs to enhance pathogen infectivity. These findings provide insight into MRG-VFG co-selection mechanisms in landfill leachates and guide targeted monitoring to mitigate environmental and health risks.

Introduction: In order to understand the emergence, persistence, and transmission of Campylobacter jejuni in livestock, this longitudinal study characterized the C. jejuni population in young calves and assessed the impact of exposure to wild birds during the pre-weaning period.

Methods and results: Faecal samples were collected on eight occasions from 48 calves housed in three pens between birth and 10 weeks of age, two of the pens being covered with orchard netting. From the 250 C. jejuni isolates obtained from the positive faeces, seven distinct sequence types (7-gene legacy MLST) were identified, with high genetic similarity of circulating strains. On each pen, sequential dominance of ST was observed, with ST-508 and ST-50 prevalent in calves under 4 weeks old, and ST-520 or ST-422 prevalent in the 8- to 10-week-old calves. Exposure of calves to wild birds did not influence genotypes distribution, α-diversity, and community dissimilarity. However, a difference in C. jejuni populations between the two groups of calves that were not exposed to birds suggests that calving rank may shape the type and succession of ST detected over time.

Conclusion: This study provided no evidence for exposure to wild birds being a driver for C. jejuni population changes in healthy pre-weaned calves.

Aims: The study aimed to investigate the anti-methicillin-resistant Staphylococcus aureus (MRSA) and anti-biofilm activity of 3-methoxy-5-hydroxy-2-(3-methyl-2-butenyl) bibenzyl (DELC) isolated from Cajanus cajan (L.) Millsp (pigeon pea) leaves, while evaluating its biocompatibility and exploring its potential as an antibiotic alternative.

Methods and results: DELC exhibited potent anti-MRSA activity, with a minimum inhibitory concentration (MIC) of 3.12 μg/mL and MBC of 6.25 μg/mL. At 2 × MIC, it achieved complete eradication of 106 CFU/mL MRSA within 120 min, demonstrating faster bactericidal action than vancomycin.

Antibiofilm studies: 2 × MIC DELC inhibited biofilm formation as effectively as 4 × MIC vancomycin. In mature biofilms, merely 1/2 × MIC DELC penetrated and eliminated a portion of embedded viable bacteria-a feat unattainable even with 8 × MIC vancomycin.

Mechanistic studies: DELC induced oxidative stress, generating ROS that damaged the bacterial membrane, causing nucleic acid leakage. It also suppressed α-hemolysin secretion.

Rna-seq analysis revealed: At 1 × MIC, DELC blocked ATP synthesis and repair systems, leading to metabolic inhibition and virulence attenuation. At ≥2 × MIC, it directly lysed bacterial cells.

Biocompatibility: DELC showed no hemolysis or cytotoxicity, indicating excellent safety.

Conclusions: DELC demonstrates potent anti-MRSA activity characterized by rapid bactericidal effects, a concentration-dependent dual mechanism-metabolic inhibition at low concentrations progressing to direct cellular lysis at higher concentrations, and superior antibiofilm capacity. Its outstanding biocompatibility strongly supports its clinical translation potential.

Aims: Anti-virulence compounds can control pathogens with reduced selection for antimicrobial resistance. There is little understanding of how these compounds impact biofilm structure and development through time. We hypothesised that 4-ethoxybenzoic acid (4EB), an anti-virulence compound, disrupts normal growth for the four phases of Staphylococcus aureus ATCC 6538 biofilm development (attachment, multiplication, exodus, and maturation).

Methods and results: Flow-cell grown biofilms were fed Luria Bertani (LB) broth (control) or LB broth with 0.8 mg/mL 4EB (treatment). Treatment inhibited the progress of multiplication phase and caused a 6-hour delay in the onset of exodus phase. Transcriptional analysis showed patterns of nuc, saeS, and saeR expression consistent with the delayed exodus phenotype. Imaging by confocal laser scanning microscopy followed by digital image analysis determined that 4EB interfered with biofilm structure formation, including reductions in height (57%/44%) and biovolume (73%/63%) during the multiplication and maturation phases, respectively, with statistically insignificant effects during exodus phase (1.9%/15%). These measurements indicated that the occurrence of exodus phase was not impacted by 4EB. Gene expression analysis using flow cell effluent found significant downregulation of genes including atl (-3.1 fold change) during multiplication phase and agrA and saeR (-5.8 and -5.2 fold change, respectively) during maturation. Principal component analysis with 24 measured parameters confirmed that 4EB treatment primarily affected multiplication and maturation phases.

Studying pathogenic Mycobacterium spp. (e.g. M. tuberculosis, M. bovis) requires Biosafety Level 3 (BSL-3) laboratories, which limits research opportunities. Safe surrogates that mimic these pathogens are therefore crucial for enabling studies in BSL-1/2 settings and advancing public health. This review examines studies that used the term 'surrogate' in relation to mycobacteria, aiming to identify effective surrogate models and highlight existing research gaps. We categorized the research topics for which surrogates were used, based on the primary goals of each study. Most research focused on Mycobacterial physiology group studies, followed by chemical control, while environmental studies remain largely unexplored. Mycobacterium smegmatis emerged as the most frequently used surrogate, valued for its relatively rapid growth compared to pathogenic Mycobacterium species, along with its genetic tractability and non-pathogenic nature. Mycobacterium marinum, a BSL-2 organism, has contributed to understanding virulence, stress responses and disease modeling. M. bovis BCG has been primarily used in vaccine studies but also appears in drug testing. Surrogate models have advanced our understanding of pathogenic mycobacteria, supporting the development of drugs, vaccines, and diagnostics without the constraints of BSL-3 laboratories. However, limitations remain-particularly in drug screening with M. smegmatis and the underrepresentation of environmental studies. The use of surrogates supports safer, cost-effective research in lower biosafety settings. Expanding ecological research in soil and water and refining model selection are key to improving control strategies.

Aims: This study aimed to investigate the therapeutic potential of Lactobacillus gasseri TF08-1, a gut bacterium isolated from healthy adolescents, in alleviating high-fat diet (HFD)-induced nonalcoholic fatty liver disease (NAFLD). This followed our discovery of lipid metabolism-related genes in its complete genome.

Methods and results: The high-precision complete genome map of L. gasseri TF08-1 was constructed for the first time, revealing enriched lipid metabolism pathways, including bile salt hydrolase activity and short-chain fatty acid (SCFA) production. After supplementing L. gasseri TF08-1 for 8 weeks in mice fed with a high-fat diet, the serum triglyceride (TG) level decreased by 41.95%, the hepatic total cholesterol (TC) level decreased by 35.09%, and the TNF-α level decreased by 42.91%. Meanwhile, the NAS score decreased by 3.66 points. The treatment significantly reduced hepatic lipid accumulation, lowered proinflammatory cytokines, and improved steatosis scores. Metagenomic analyses showed L. gasseri TF08-1 restored gut microbiota balance, significantly increasing the abundance of beneficial bacteria such as Faecalibacterium prausnitzii and Phocaeicola vulgatus, while also enriching fatty acid degradation pathways.

Conclusions: Lactobacillu gasseri TF08-1 demonstrates probiotic efficacy against NAFLD through dual mechanisms: direct metabolic modulation and gut microbiota restoration. The lipid metabolism capacity encoded by its genome likely contributes to therapeutic effects.

Objective: This study aimed to characterize the bile microbiome and metabolome in patients with common bile duct stones (CBDs), with versus without juxtapapillary duodenal diverticulum (JPDD), to identify potential factors associated with stone formation.

Methods: From January to May 2024, CBDs patients undergoing endoscopic retrograde cholangiopancreatography at our hospital were prospectively enrolled. Bile samples were collected for 16SrRNA sequencing and LC-MS/MS metabolomics analysis. Patients were divided into JPDD (n = 15) and CBDs (n = 15) groups.

Results: The JPDD group had larger stone and bile duct diameters (P < 0.05). Although Proteobacteria dominated the bile microbiota in both groups, the JPDD group showed higher abundances of Escherichia-Shigella, Enterococcus, and Escherichia coli. Beta diversity differed significantly between groups (P < 0.05), and LEfSe identified 25 differentially abundant bacterial taxa. Enterococcus, Klebsiella, and Gemellaceae were more abundant in the JPDD group, while Peptococcaceae, Roseburia, and Alistipes were more prevalent in the CBDs group. Enterococcaceae and Enterococcus abundances were positively correlated with stone and duct sizes in the JPDD group (P < 0.05), whereas Peptococcaceae and Acinetobacter showed negative correlations. Metabolomic analysis identified ten differentially enriched pathways-including phenylalanine and alanine metabolism-and higher levels of bilirubin glucuronide and taurochenodeoxycholic acid in the JPDD group. Enterococcus abundance was correlated with bile acid metabolites such as chenodeoxycholylasparagine (P < 0.05).

Conclusions: JPDD is associated with distinct microbial and metabolic profiles in bile. Enrichment of Enterococcus and Klebsiella in the JPDD group, along with changes in metabolic pathways and bile acid metabolites, suggests a potential link to CBD stone formation and growth.