Journal of Applied Microbiology最新文献

Aims: Metabolic dysfunction-associated steatotic liver disease (MASLD, formerly non-alcoholic fatty liver disease) is a prevalent and progressive condition closely linked to gut microbiota composition. Fecal microbiota transplantation (FMT) may help restore a health-associated microbiome, but its efficacy is often limited by inconsistent engraftment of beneficial taxa. Prebiotics may selectively support keystone microbes associated with reduced MASLD risk. This study evaluated two prebiotics, inulin and xylooligosaccharides (XOS), for their ability to modulate the microbiota of healthy FMT donors in an in vitro gut model, focusing on enriching beneficial taxa and functions associated with MASLD resilience.

Methods and results: Stool from eight clinically qualified FMT donors was cultured anaerobically for 24 hours with or without prebiotics. Microbiota composition was assessed by 16S rRNA gene sequencing and short-chain fatty acid (SCFA) concentrations were measured using nuclear magnetic resonance. Functional potential was inferred using predictive metagenomic analysis. Prebiotic responses were highly donor-specific, yet both inulin and XOS consistently enriched Bifidobacterium and Bacteroides-genera associated with SCFA production and metabolic health. XOS preferentially enriched Lactobacillus and Parabacteroides, while inulin enhanced Holdemanella and Mediterraneibacter. Functional pathways relevant to MASLD pathophysiology were enriched, including carbohydrate metabolism, vitamin biosynthesis, fatty acid metabolism, and tryptophan degradation. Both prebiotics significantly increased acetate levels, while butyrate showed a donor-dependent increasing trend.

Conclusions: These findings suggest that prebiotic supplementation can selectively enrich MASLD-relevant microbial taxa and functions in donor-derived FMT material, supporting their potential as adjuvants to enhance the efficacy and disease-specificity of FMT interventions for MASLD.

Aims: To develop and validate an ecology-driven strategy that leverages natural manure-soil depth gradients as a screening system for the targeted isolation of nutrient-solubilizing bacteria (NSB) with high biofertilizer potential.

Methods: A full-factorial sampling design was implemented across gradients of distance-from-manure (5 points, 8-m intervals) and soil depth (0-20, 20-40, 40-60 cm) in a coconut plantation. Culturable bacteria were isolated using a culture-dependent approach on a nutrient-rich medium, identified via 16S rRNA gene sequencing, and functionally screened in vitro for nitrogen fixation, phosphate solubilization (PS), and potassium solubilization (KS) capabilities.

Results: Manure input and soil depth interacted to form a heterogeneous soil nutrient landscape, with available phosphorus (AP) identified as the most influential environmental factor shaping the bacterial community. Phosphate-solubilizing bacteria (PSB) were significantly enriched in low-P habitats, verifying the niche-based selection of functional bacteria. This gradient-based screening strategy enabled the targeted recovery of multifunctional NSB strains (e.g., Klebsiella and Enterobacter) with concurrent nitrogen fixation, phosphate and potassium solubilization capacities, which were isolated from specific microhabitats including deep, nutrient-depleted soil layers.

Conclusions and implications: This study demonstrates that intersecting manure and soil depth gradients form a powerful, predictable natural screening system for the targeted isolation of beneficial bacteria. This ecology-driven strategy effectively links microbial ecology to bioprospecting. It provides a curated library of isolates with defined ecological origins and a predictive framework for developing customized biofertilizers, thereby enhancing microbial resource mining efficiency and contributing to sustainable agriculture.

Corynebacterium striatum: Has been increasingly associated with nosocomial outbreaks and antimicrobial resistance.

Objectives: This study presents the comparative analysis of 26 multidrug-resistant (MDR) C. striatum strains isolated in Brazil.

Methods: Additional genomes from international sources were incorporated. The analyses encompassed in vitro antimicrobial susceptibility testing and an in silico workflow for genomic similarity comparison, phylogenetic reconstruction, genomic clustering, pangenome analysis, mobilome content, virulence prediction, and functional annotation of unique proteins and putative virulence clusters.

Results: Strong in silico evidence of clonality among several Brazilian isolates was obtained at the same time that some strains consistently indicated a divergent genomic profile. There are 196 unique coding sequences (CDSs) across the Brazilian IHPs. Of particular interest, strain IHP2030 carried an exclusive fimbria, sharing less than 50% similarity with other fimbriae in the dataset. Yet, structural predictions suggested conservation of key structural domains typically associated with fimbrial proteins. Mobilome content analysis revealed that IHPs strains were overall similar, differing primarily in the number of insertion sequences and in the presence or absence of CRISPR-Cas defense systems. Regarding virulence, an exclusive cluster in IHP2050 and IHP2060 suggests adaptive advantages associated with their respective environments of isolation.

Conclusion: This study reveals a complex genomic landscape among Brazilian MDR C. striatum strains, marked by clonal dissemination alongside strain-level genetic variation in accessory genomes, mobilome composition, and virulence-associated gene repertoires, providing genomic evidence of diversification within hospital-associated lineages.

Aims: This study aimed to investigate the inter-strain variability of enrofloxacin activity against Pasteurella multocida and to apply a pharmacokinetic/pharmacodynamic (PK/PD) modeling approach to predict the expected efficacy of enrofloxacin in pigs.

Methods and results: In vitro and ex vivo time-kill curve (TKC) experiments were performed with enrofloxacin against nine susceptible P. multocida strains, and a semi-mechanistic PK/PD model was developed. Both bacterial net growth rates and enrofloxacin-mediated killing rates varied substantially among isolates; however, an overall strong bactericidal effect was consistently observed. At very high enrofloxacin concentrations, most strains exhibited a reduced killing rate (Eagle effect). A population PK model of enrofloxacin in pigs was also developed using published data. The integrated PK/PD model was then applied to simulate the expected efficacy in pigs of the United States and European dosing regimens (injectable formulations) of enrofloxacin against P. multocida, yielding comparable results across sensitive strains.

Conclusions: Simulations from the PK/PD model suggest that the current CLSI breakpoints may be appropriate for defining enrofloxacin susceptibility in P. multocida, even from pigs treated with the European dosing regimen.

Aims: Autotoxic phenolic compounds are released from decomposing plant litter and can accumulate in the soil. This study investigates the dynamics of the fungal community during root litter decomposition and the potential of fungal communities in root litter for degrading phenolic compounds.

Methods and results: The root litter decomposition experiment showed fungal communities in cucumber root litter differed between 15 and 60 days after decomposition. In particular, Fusarium sp. was enriched in root litter. Then, we isolated a strain of interest, coded F60, from the root litter and identified it as Fusarium solani. This strain achieved in vitro degradation rates exceeding 90% for ferulic, p-coumaric, and p-hydroxybenzoic acids. A pot experiment demonstrated that Fusarium solani F60 decreased phenolic acid contents in soil and alleviated phenolic acid-induced toxicity to cucumber seedlings.

Conclusions: This study shows that fungal community composition changes during root litter degradation, enriching Fusarium sp. capable of degrading phenolic acids.

Aim: Methicillin-resistant Staphylococcus aureus (MRSA), a major pathogen associated with severe infections, poses a significant challenge to antimicrobial resistance (AMR) management. This study investigates the antibacterial activity of Pistacia chinensis (PciE) (commonly known as Kakdashringi in traditional Indian medicine) against MRSA and explores its mechanisms of action in resistance modulation, underscoring its potential therapeutic applications.

Methods and results: The antibacterial efficacy of PciE was assessed using disc diffusion, MIC determination, FESEM imaging, and assays for ROS generation, K⁺ efflux, and blaTEM gene expression. PciE demonstrated a dose-dependent inhibitory effect on MRSA strains, with MIC values ranging from 0.65 to 0.83 mg/ml. FESEM revealed membrane disruption and morphological changes in PciE-treated MRSA cells. PciE reduced ROS levels, mitigated blaTEM expression, and protected methicillin from β-lactamase degradation. Co-treatment with PciE and methicillin restored drug susceptibility in MRSA. Importantly, PciE showed low resistance induction over 15 days and significantly inhibited bacterial invasion into human keratinocytes, with no cytotoxic effects at therapeutic concentrations.

Conclusions: PciE exhibits potent antibacterial activity against MRSA by targeting membrane integrity, reducing oxidative stress, and interfering with resistance mechanisms. Its combination with methicillin enhances efficacy, offering a promising strategy for combating antibiotic-resistant MRSA infections. While these MIC values are relatively high, the extract's synergistic effect with methicillin and low resistance induction suggest potential topical or adjuvant applications.

Aims: Fungal-bacterial interactions and their applications are gaining increasing attention in various fields, including biocontrol technologies. Numerous studies have examined these interactions, typically involving only a single fungal isolate and a limited number of bacterial isolates. We hypothesized that even a modest increase in the number of isolates included in confrontation experiments would reveal patterns of functional relevance and possible specificity in fungal-bacterial interactions.

Methods and results: This study included four microfungal isolates from soil and thirteen bacterial isolates from macrofungal fruiting bodies for confrontation experiments. Both the fungus and the bacterium influence their interactions, though the fungus appears slightly more selective. For instance, certain fungal isolates from the genera Colletotrichum and Phoma sensu lato (s.l.) responded more strongly to the presence of bacteria than those from the genera Cadophora and Microdochium. However, the responses of Microdochium and Phoma s.l. were not dependent on the bacterial genus or isolate used in confrontation experiments. Notably, a single bacterial genus consistently suppressed multiple fungal genera, suggesting potential off-target effects if used for biocontrol. The results further showed that the influence of bacteria on fungal growth was more pronounced at the bacterial isolate than the genus level, indicating considerable variability within the same genus.

Conclusions: Using more bacterial and fungal isolates in confrontation experiments clarifies the drivers of interactions, fungal responses, and bacterial off-target effects. The research presented here highlights the need for further systematic, in-depth research into fungal-bacterial interactions to validate existing findings, establish a traceable, easily analyzable isolate-level dataset, and prevent unintended consequences in microbial biocontrol applications and beyond.

Background: Intestinal colonization by multidrug-resistant Enterobacteriaceae represents a major public health concern as it can lead to difficult-to-treat infections, environmental contamination, and transmission. This study evaluated the efficacy of a prophylactic treatment using Escherichia coli strains isolated from murine feces [commensal E. coli (comEc)] to reduce intestinal colonization by extended-spectrum beta-lactamase (ESBL)-producing E. coli in a murine model of antibiotic-induced dysbiosis.

Methods and results: The comEc treatment was administered intragastrically 1 day prior to ESBL-producing E. coli challenge. Colonization levels were monitored daily using culture-based quantification. Fecal microbiota composition was analyzed before the ESBL-producing E. coli challenge to identify predictors of treatment efficacy. The comEc treatment significantly reduced mean ESBL-producing E. coli levels during the first four days. Notably, 14% of treated mice exhibited marked and sustained decolonization, whereas others had only a limited and transient effect.

Conclusion: In this proof-of-concept study, prophylactic treatment with murine-derived E. coli strains transiently reduced fecal ESBL-producing E. coli titers, although pronounced efficacy was observed in a small subset of animals.

Mastitis is a common inflammatory disease in both humans and dairy animals, most frequently driven by bacterial pathogens such as Staphylococcus aureus (S. aureus), Escherichia coli (E. coli), Mycoplasma bovis (M. bovis) and Streptococcus uberis (S. uberis). These microbes deploy distinct virulence strategies yet share the ability to reshape T-cell-mediated immunity, thereby influencing infection outcomes, tissue damage and chronicity. In this review, we summarise current evidence on how CD4⁺, CD8⁺, γδ T cells, Tregs and other T-cell subsets participate in mastitis-associated immune responses. We focus on pathogen-specific mechanisms, including S. aureus superantigen-induced immune deviation, M. bovis-driven prostaglandin E₂-STAT3-PD-L1 signalling and T-cell exhaustion, early CD8⁺ recruitment and cytokine imbalance in E. coli mastitis, and γδ T-cell activation during S. uberis infection. We further compare common and divergent strategies of immune evasion and dysregulated T-cell-mediated inflammation across these pathogens. Finally, we discuss how T-cell signatures and cytokine networks may inform the development of diagnostic biomarkers, immunomodulatory interventions and vaccine candidates, with the potential to reduce antibiotic use and improve mastitis control in both human and veterinary settings.

Aims: Species invasion is one of the key issues in global ecosystems. This study investigated the changes in the rhizosphere community structure of complete ammonia-oxidizing (Comammox) bacteria after the invasion of the long-rooted submerged macrophyte Vallisneria spiralis L. into the community of the short-rooted submerged macrophyte Myriophyllum spicatum L.

Methods and results: Different planting ratios simulated varying invasion intensities. Increasing invasion intensity significantly altered rhizosphere factors, reduced dissolved organic carbon (DOC), and lowered pH, thereby causing distinct alterations in the rhizosphere environment. Comammox Clade A remained dominant with stable abundance, indicating strong adaptability. In contrast, Clade B abundance increased under low-moderate invasion but declined sharply under high intensity, suggesting a preference for mixed roots or low-intensity invasion. Higher pH and DOC provided a stable niche for Clade A. High invasion intensities elevated NH4+-N and NO3--N concentrations, which coupled with stronger oxidative conditions promoted AOB and certain Clade A subgroups, thereby suppressing the low-nitrogen-adapted Clade B.

Conclusions: This study demonstrates that submerged macrophyte invasion reshapes the rhizosphere environment and drives Comammox community differentiation, offering new insights into plant invasion's ecological effects and nitrogen cycling regulation.