World journal of microbiology & biotechnology最新文献

Monascus pigments (MPs) are natural food colorants that have received significant attention in the food industry due to their widespread use as food additives. This study employed food-grade isopropyl myristate (IPM) at different concentrations to modulate MP biosynthesis. The results showed that adding 10 g/L IPM significantly increased pigment production, reaching a total color value of 107.957 AU/50 mL, which corresponds to a 3.49-fold increase compared to the control. Furthermore, the pigment content per unit biomass increased to 335.774 AU/g, representing a 1.378-fold improvement over the control. Visual observation and scanning electron microscopy revealed that IPM-treated mycelial pellets had smaller diameters, darker pigmentation, thicker cell walls, rougher surfaces, and higher conidia production. Untargeted metabolomic profiling identified 89 differentially expressed metabolites between the IPM-treated and control groups. KEGG pathway enrichment analysis linked these metabolites to ABC transporters, taurine and hypotaurine metabolism, and cofactor biosynthesis. Further mechanistic investigation revealed that IPM stimulates MP biosynthesis by upregulating key precursors and substrates involved in the tricarboxylic acid (TCA) cycle, glycolysis, amino acid metabolism, and cofactor biosynthesis pathways (e.g., NADPH and CoA).

Gut microbiota plays a critical role in bile acid (BA) metabolism within healthy populations, yet the differential species involved in BA metabolism in patients with Crohn's disease (CD) remains poorly characterized. To address this knowledge gap, we conducted a comparative metagenomics for nine CD patients and nine healthy controls. Integrated metagenomic species profiling and functional annotation, accompanied with species-function network analysis, reduced abundance in metabolism-associated genes and lower species-function correlation were predicted, suggesting a possible imbalance of microbial communities in CD group. Focused on functional genes involved in BA metabolism and their associated bacterial taxa, our results revealed that Anaerostipes hadrus-like (P = 0.001317), Roseburia intestinalis-like (P = 0.03542), and Coprococcus catus-like (P = 0.0005787), the microbial species related to bile salt hydrolase-coding gene, showed significantly lower abundance in CD patients. Conversely, Ruminococcus gnavus-like, related to 3α-hydroxysteroid dehydrogenase (3α-HSDH)- and 3β-HSDH-coding genes, demonstrated relatively higher abundance (P = 0.0257). Escherichia coli-like, the species for 7α-HSDH-coding genes, also exhibited higher abundance in CD group (P = 0.01044). Further network correlation analysis indicated that there was a potential association between these differential species with other co-occurring gut microbiota. Collectively, the findings identify and characterize the differential gut microbiota involved in BA metabolism in CD patients, which may provide the possible target microorganisms for future therapeutic interventions.

The function of the livestock gut microbiome in driving animal growth, health, and methane emissions is controlled by networks of interactions among microbes. A major challenge is to move beyond simply listing microbial members to understanding these interaction networks, which determine how the community functions as a whole. This review synthesizes how network analysis, combined with multi-omics data, can meet this challenge. We focus on the critical task of identifying keystone species, the disproportionately influential microbes that direct processes like fiber digestion and immune function, yet are often missed by standard surveys. We evaluate a progression of methods, from identifying correlated species to building models that integrate genomic, metabolic, and host data. This integration is key to separating true ecological relationships from statistical noise and to linking microbial presence to function. We highlight how computational techniques like metabolic modeling and machine learning are turning networks into predictive tools. Finally, we outline the path forward: field-ready studies that track microbiomes over time, the development of livestock-specific metabolic models, and analytical standards that will allow research to translate into practical strategies. The goal is to provide a framework for using network science to actively manage the microbiome, enhancing sustainable livestock production.

The Bacillus genus includes plant growth-promoting rhizobacteria (PGPR), and the discovery of new strains within this group is of great biotechnological interest due to their ability to produce antimicrobial compounds (AMCs), vitamins, enzymes, and heterologous proteins. Among these, Bacillus paralicheniformis is a recently described species whose phylogeny remains poorly resolved, highlighting the need for further investigation. This study aimed to identify and characterize the isolates BAC30 and BAC220 using whole-genome sequencing (WGS). Both were confirmed as B. paralicheniformis and included in phylogenomic and comparative analyses with 28 other strains to assess the species' genetic structure and inter-strain similarity. Functional annotation of BAC30 and BAC220 was also performed, focusing on biotechnological potential. Comparative analysis revealed high genomic similarity among strains, including the two isolates. Pangenome analysis showed a low proportion of core genes relative to accessory genes (shell and cloud), and the rarefaction curve suggested an open pangenome, indicating the species' ubiquity and co-evolution with other organisms. Functional analysis identified genes of defense mechanisms related to beta-lactam resistance. Regarding secondary metabolite production, genes involved in the biosynthesis of vitamins (e.g., riboflavin) and AMCs (e.g., bacitracin) were detected. Although further in vitro and in vivo assays are needed to confirm gene expression, the findings support the biotechnological relevance of these isolates as potential biocontrol agents and/or producers of industrially valuable compounds.

New Delhi Metallo-β-lactamase-1 (NDM-1) belongs to the carbapenemase family of enzymes, which can hydrolyse a wide range of β-lactam antibiotics. To date, 91 NDM-1 variants have been reported globally. In this study, we generated a novel mutant, NDM-1 D254A, through site-directed mutagenesis to investigate the functional role of non-active site residue Asp254. The wild-type NDM-1 and D254A mutant were cloned, purified, and systematically analyzed using steady-state kinetic assays and circular dichroism spectroscopy. Subsequently, we conducted Insilico studies, which include molecular docking and molecular dynamics (MD) simulations. The D254A mutant has reduced catalytic activity, thus indicating impaired β-lactam hydrolysis. Structural and computational analysis revealed that Asp254 plays an essential role in maintaining the protein stability. These findings illustrate the importance of Asp254 in maintaining the NDM-1 activity and provide the mechanistic insights into the structure-function relationship. This study enhances our understanding of NDM-1 variants and may aid the rational design of targeted inhibitors to counteract the rising global threat of NDM-1 mediated antibiotic resistance.

Psilocybin, a tryptamine-derived alkaloid from Psilocybe mushrooms, has emerged as a high-value biopharmaceutical candidate due to its promising applications in mental health. While clinical studies highlight its rapid and sustained antidepressant effects, current challenges lie in achieving scalable, reproducible, and cost-effective production to meet growing research and therapeutic demand. Traditional extraction from fungal biomass yields low concentrations and requires extensive downstream processing, limiting industrial viability. Chemical synthesis ensures purity but is hindered by high costs and multistep complexity. In contrast, biotechnological approaches have demonstrated significant progress toward sustainable production. Heterologous expression of psilocybin biosynthetic genes in Saccharomyces cerevisiae and Aspergillus nidulans has enabled improved metabolic flux and precursor availability, reaching titers over 200 mg/L under optimized conditions. Moreover, recent engineering Escherichia coli strains has further enhanced catalytic efficiency of key enzymes such as PsiH, achieving production levels up to 2000 mg/L, while simplifying fermentation and purification workflows. These advances establish microbial platforms as a promising route for industrial-scale biosynthesis. Beyond production, psilocybin offers an opportunity to integrate biotechnology with socio-cultural context. In regions where diversity of Psilocybe species and ancestral knowledge converge, the development of biotechnological pipelines could foster innovation in drug discovery, sustainable manufacturing, and policy reform. Overall, psilocybin exemplifies a frontier molecule in biotechnology, where metabolic engineering, synthetic biology, and bioresource valorization converge to transform a natural product into a reproducible, scalable, and globally relevant therapeutic.

Bacterial soft rot is a major vegetable disease of global significance, predominantly associated with Pectobacterium species; however, new reports indicate that novel, emerging pathogens are contributing to disease incidence. This study identified a novel pathogen, Enterobacter cloacae, as a causal agent of radish soft rot. Two isolates, RDH1 and RDH3, were isolated from 20 decaying radish taproots collected from Kolar, Karnataka, India, where a 12% disease incidence was recorded. Biochemical and physiological characterization, alongside comparison with E. cloacae ATCC 13047, confirmed the genus identity. Molecular analysis of 16S rRNA sequences revealed 99.56 and 99.87% similarity of RDH1 and RDH3, respectively, to known E. cloacae strains. Pathogenicity assay confirmed the pathogenicity of both isolates, and semi-quantitative assessment of plant cell wall degrading enzymes showed RDH1 producing clearance zones of 12.00, 10.33, and 8.00 mm, while RDH3 exhibited zones of 12.00, 10.00, and 7.67 mm, of pectin lyase, polygalacturonase, and cellulase, respectively. Host range assays on 10 vegetable crops revealed RDH3 as more virulent, particularly in radish, carrot, and cabbage, with the hypodermal syringe method showing broader infectivity compared to minimal infection via coir-enrichment seedling inoculation. Further, whole genome sequencing of RDH3 revealed a 4.8 Mb genome, 55% GC content, a single plasmid, and 99% ANI similarity to E. cloacae GGT036, containing T6SS, T4SS, ICEs, prophages, genomic islands, and 12 horizontal gene transfer events. These findings underscore the emerging role of E. cloacae in vegetable soft rot and highlight the need for further research on its pathogenic mechanisms and management strategies.

Lactobacillus gallinarum Y86, isolated from broiler ileal mucosa under strict anaerobiosis (85% N₂/10% CO₂/5% H₂), demonstrates significant potential as a microbial feed additive for antibiotic-free farming. 16 S rRNA sequencing (99.79% identity to L. gallinarum ATCC 33199; GenBank ON248243) confirmed its taxonomy. Stationary-phase cultures secreted a heat-stable antimicrobial that produced inhibition zones of 21.53 ± 0.34 mm against Salmonella enterica serovar pullorum and 11.90 ± 0.52 mm against Staphylococcus aureus, retaining 87.30% activity after 120 °C for 15 min; sensitivity to trypsin and lipase indicates a proteolipid nature. Y86 endured pH 2.0 for 3 h (63.37% survival) before programmed lysis at 4 h, then recovered to 92.44% viability under intestinal conditions and maintained 45.36% viability in 0.5% bile. High surface hydrophobicity (85.71%) drove auto-aggregation to 97.99% within 24 h, supporting strong epithelial adhesion. The strain was susceptible to β-lactams, macrolides, and vancomycin, intrinsically resistant to tetracyclines and quinolones, and non-haemolytic, meeting EFSA-QPS safety criteria. Collectively, its thermostable antimicrobial production, timed gastric lysis, intestinal resilience, and proven safety identify Y86 as an industrially compatible candidate for antibiotic-free poultry feeds, advancing microbiota-based alternatives to growth-promoting antibiotics.