Journal of Applied Microbiology最新文献

Aims: While the prebiotic potential of cellobiose has been suggested previously, this study extends current knowledge by including more microbial responses in a controlled human gut model. The fermentation profile of cellobiose was comparted with OF P95 and a negative control using faecal samples from healthy donors (n = 3).

Methods and results: Fluorescent in situ hybridisation with flow cytometry was used to quantify key bacterial groups, and gas chromatography assessed organic acid production over 48 hours. Both carbohydrates induced significant alterations in microbiota profiles and organic acid production compared to baseline and negative controls. Cellobiose fermentation significantly increased total organic acids, acetate, and butyrate from baseline, with significantly higher total organic acids and butyrate levels than the negative control at 48 h (P = 0.002 and P = 0.016, respectively). Distinct temporal shifts were observed for total bacteria and Atopobium with cellobiose, while Bifidobacterium was not significantly stimulated, contrasting with potent bifidogenic activity with OF P95 (e.g. T0-T48 increase, P < 0.001) and generally more pronounced total SCFA and acetate yields.

Conclusions: These findings validate prior indications but also extend current knowledge, showing that cellobiose has a distinct fermentation profile with potential for specific SCFA modulation, particularly butyrate.

Biofilm-associated infections constitute an ever-increasing and ubiquitous threat to public health and safety. Biofilms, which are microbial conglomerations of sessile bacteria adhering to surfaces and forming three-dimensional architecture with an exopolysaccharide matrix, are known for their remarkable antimicrobial resistance to antibiotics, disinfectants, and sanitizers. Due to their widespread occurrence in healthcare facilities, food processing units, water systems, and marine industries severely limits the effectiveness of conventional antimicrobial strategies and accelerates the development of antimicrobial resistance. Therefore, there is an urgent need for innovative, safe, and sustainable antibiofilm approaches. This review describes the emerging potential of Lactobacillus-derived non-viable probiotics (paraprobiotics) and probiotic-derived bioactive metabolites (postbiotics) as next-generation biofilm inhibitors. Overall, these findings highlight that these derivatives have the potential to effectively suppress biofilm formation by targeting key stages of biofilm development, including microbial adhesion, quorum-sensing signaling, and extracellular polymeric substance (EPS) production. Among these, several bioactive compounds such as 'bacteriocins, organic acids, biosurfactants, lipoteichoic acids, and surface-associated proteins' show strong antibiofilm efficacy against a broad range of pathogenic bacteria. findings emphasize that paraprobiotics and postbiotics offer several advantages over live probiotics and traditional antimicrobials, including enhanced safety, reduced risk of resistance development, cost-effectiveness, and longer shelf life. In conclusion, "Lactobacillus-derived paraprobiotics and postbiotics," they present a very promising tool that is eco-friendly and has little to no need for resistance. Besides that, their ability to be used in various applications can greatly contribute to the better management of biofilms in a nature-friendly way, and can greatly alleviate the risks of biofilm-related infections and contaminations worldwide.

Background and objective: Ulcerative colitis (UC), a chronic inflammatory bowel disease. This study uniquely undertook a parallel, severity-stratified comparison of both fecal and mucosal microbiota and metabolites in UC patients. Our objective was to identify niche-specific (fecal vs. mucosal) and severity-associated microbial and metabolic signatures, clarifying its potential clinical utility.

Methods: A prospective cohort study (ChiCTR2300071816) enrolled 83 UC patients (≥18 years) from First Affiliated Hospital of Nanjing Medical University and Northern Jiangsu People's Hospital (Jan 2022-Dec 2024) and 30 healthy controls. Clinical data, stool, and rectal mucosal samples were collected. Metagenomic sequencing and metabolomics were performed. Disease severity was stratified by modified Mayo score to analyze microbiota diversity, differential genera, metabolites, and enriched metabolic pathways.

Results: Fecal microbiota α-diversity was significantly lower in UC vs. controls (Shannon index 4.15 vs. 5.44, p=0.005); mucosal diversity showed no difference (p=0.63). Beta diversity did not differ. Severe UC exhibited a non-significant decrease in α-diversity (fecal: 3.99 vs. 4.37, p=0.14; mucosal: 3.40 vs. 3.72, p=0.92), significantly higher fecal/mucosal Klebsiella abundance, and lower Erysipelatoclostridium and Blautia abundance vs. mild-to-moderate UC. Metabolomics identified 363 fecal differential metabolites (e.g., allopurinol, histidine), enriching tyrosine and alanine/aspartate/glutamate metabolism pathways. Mucosal analysis revealed 127 differential metabolites (e.g., quinic acid, sphingosine), implicating sphingolipid metabolism and lysine synthesis.

Conclusion: UC demonstrates gut dysbiosis and metabolic disruption correlating with severity. Elevated Klebsiella abundance suggests a pathogenic role in progression. Distinct fecal and mucosal metabolic pathway alterations provide novel insights for disease classification and therapeutic targeting.

Aims: This study aimed to examine the relationships between rhizosphere (RS) microorganisms of the desert pioneer plant Psammochloa villosa and soil nutrient availability, with the goal of clarifying microbial mechanisms supporting its persistence in desertified regions and identifying potential targets for microbiome-based management.

Methods and results: Using absolute quantification of 16S rRNA gene and ITS sequencing, microbial communities in the RS of P. villosa were compared with those in bulk soil (BS). The results showed that the rhizosphere of P. villosa had significantly lower total phosphorus (TP) but higher carbon-to-phosphorus (C/P) and nitrogen-to-phosphorus (N/P) ratios than BS, while the available nitrogen-to-available phosphorus ratio (AN/AP) was 4-5 times higher than N/P. This pattern suggests that the RS experiences stronger phosphorus limitation than BS. A lower fungi-to-bacteria (F/B) ratio in the RS relative to BS was positively associated with TP and negatively associated with soil C/P and N/P ratios, indicating a bacterial-dominated community under phosphorus-limited conditions. Structural equation modeling further indicated that rhizobacterial diversity strongly promoted the acquisition of available nutrients by significantly affecting soil organic carbon (SOC), TP, and stoichiometric balance.

Conclusions: These results indicate that bacterial diversity is tightly linked to the regulation of ecological stoichiometry and nutrient availability under P-limited conditions in the rhizosphere of P. villosa.

Aims: The objective of this study was to add valuable insight to the inactivation mechanisms of (Gram-negative) Salmonella Typhimurium and (Gram-positive) Listeria monocytogenes by comparing radio frequency (RF) heating to conventional thermal treatments with similar dynamic temperature profiles.

Methods and results: The Geereard et al. (2000) model with a Bigelow-type temperature dependency was fitted to the experimental data. Inactivation kinetics parameters were estimated and the sublethal injury was assessed. DNA and membrane integrity were evaluated by fluorescence and agarose gel electrophoresis methods. For both microorganisms, RF heating demonstrated a higher inactivation rate and higher sublethal injury than conventional treatments. RF treatments also caused more membrane damage than conventional treatments in both microorganisms. Agarose gel electrophoresis indicated an RF treatment-specific effect on DNA integrity only for L. monocytogenes.

Conclusions: Possible RF treatment-specific inactivation mechanisms were related to membrane damage and, depending on the microorganism, DNA damage. Effects are possibly caused by energy absorption of the bacterial cells. Future research using additional techniques (e.g. flow cytometry, next-generation sequencing) is necessary to gain deeper insights into the exact interactions of RF energy with the membrane and DNA of the two foodborne pathogens.

Aims: This study investigated the antifungal performance of copper-based antimicrobial coatings developed by Gencoa Ltd., previously validated against bacterial ESKAPE pathogens, alongside newly formulated titanium oxide coatings, against key agricultural fungal pathogens: Alternaria alternata, Botrytis cinerea, Cladosporium cucumerinum, and Fusarium oxysporum. Testing was conducted both in vitro and in field trials within an actively used polytunnel.

Methods and results: In vitro assays included a modified ISO 846 agar plate protocol and a six-well plate fungal colonisation assay simulating high humidity conditions. Field trials assessed coating performance under real-world exposure. Copper-containing coatings: pure copper, copper oxynitride, and copper-doped titanium oxide, consistently demonstrated significant antifungal activity, effectively reducing spore germination and colonisation. Titanium oxide coatings without copper showed minimal effect, performing similarly to uncoated polyethylene. While copper-based coatings were highly effective, some susceptibility to surface degradation under prolonged moisture was observed. However, antifungal activity often persisted in degraded areas of samples with high copper content.

Conclusions: Copper-based antimicrobial coatings offer strong potential for preventing fungal colonisation on agricultural surfaces, outperforming titanium oxide formulations under both laboratory and field conditions. Optimisation to enhance durability will further improve their suitability for long-term use in protected cultivation systems.

Aims: Agricultural crop productivity and global forest biomes are coming under increasing threat from insect pests and microbial pathogens. This impact is worsened by inter-kingdom insect-microbe interactions that can increase transmission and disease severity in affected plants. Whilst bacterial chemical cues have been shown to directly influence insect behaviour, the impact of insect-derived compounds on phytopathogens is poorly understood. Here, we investigated the chemical basis for interactions between beetle larvae and bacteria in acute oak decline (AOD), a disease characterised by inner bark necrosis of Quercus robur and Q. petraea involving a polymicrobial consortium including Brenneria goodwinii and larval galleries of Agrilus biguttatus.

Methods and results: : We found that A. biguttatus larval extractable metabolites increase bacterial growth rate and final cell density during in vitro culture, and stimulate the differential expression of ∼600 genes, including the type III secretion system and its effectors, which are major virulence factors in plant pathogens. Chemical compounds from closely related insect species did not have this effect.

Conclusions: These findings highlight the importance of inter-kingdom interactions in plant disease and suggest a role for insect-derived chemical elicitors in facilitating the virulence of phytopathogens.

Aims: Xanthomonas citri subsp. citri (Xcc), the bacteria responsible for citrus canker, is widely distributed worldwide and causes severe losses to the citrus industry. Understanding the emergence and spread of Xcc requires reliable strain identification and tracking methods. This study aimed to develop a robust multilocus sequence typing (MLST) scheme for Xcc.

Methods and results: 123 Xcc strains from diverse geographic origins were molecularly typed using seven conserved loci. Twenty-seven sequence types (STs) were identified, revealing a high level of genetic diversity within the population. eBURST clustering further grouped these STs into three major clonal complexes (CC1, CC2 and CC3). To evaluate the resolution of MLST, a whole-genome single nucleotide polymorphism (wgSNP) analysis was also performed. Phylogenetic reconstruction of 49 representative strains resolved them into seven clades, largely consistent with the MLST results but offering superior accuracy and resolution. Geographical structuring was evident in the evolutionary patterns; however, strains from different host varieties shared identical types, and multiple types were observed among strains collected from the same variety, indicating weak host variety associations.

Conclusions: The MLST scheme developed in this study provides a reliable framework for identifying and tracking Xcc strains, while wgSNP analysis offers enhanced resolution for fine-scale epidemiological studies. Together, these approaches highlight the geographic structuring of Xcc populations, thereby advancing understanding of the pathogen's evolutionary dynamics and spread.

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.