Fems Microbiology Letters最新文献

Bacterial transcription terminator, Rho is an RNA (Ribonucleic Acid)-dependent ATPase that terminates transcription. Several structures of pretermination complexes of the Rho-transcription elongation complex (EC) revealed a static picture of components of the EC that come close to the nascent RNA-bound Rho, where many of the residues of EC reside ≤10 Å from the Rho residues. However, the in vitro-formed Rho-EC complexes do not reveal the in vivo Rho-EC dynamic interaction patterns during the termination process. Here we report synthetic defect analyses of various combinations of the mutations in RNAP β, β' and ω-subunits, NusA, NusG, and Rho proteins to delineate the functional network of this process. Several mutations in the β-flap and β'-Zn-finger and -Clamp helices domains of RNAP are synthetically defective in the presence of Rho mutants indicating functional involvement of these domains. Mutations in the NusA RNA-binding domains were synthetically defective with the Rho mutants suggesting its involvement. Our genetic analyses also revealed functional antagonisms between the ω-subunit of RNAP and the NusG-CTD (c-terminal domain) during termination. We concluded that the regions surrounding the RNA exit channel, the RNA-binding domains of NusA, the RNAP ω-subunit, and NusG-CTD constitute a functional network with Rho just before the onset of in vivo Rho-dependent termination.

Entomophagy, the practice of consuming insects, is a global tradition. In Mexico, one of the most notable and widely consumed insects is the larva of Aegiale hesperiaris. This insect feeds on the leaves of various Agave species with high polysaccharide content, suggesting their potential role as prebiotics for the intestinal microbiota, particularly lactic acid bacteria (LAB). LAB are recognized for their use as probiotics in foods due to their health-promoting capabilities. In this study, LAB from the intestinal microbiota of A. hesperiaris larvae were isolated and characterized, utilizing 16S rRNA gene identification. The analysis revealed three bacterial species from the Lactobacillaceae family, indicating a close symbiotic relationship with the insect. This suggests a significant impact on carbohydrate and protein metabolism, vitamin synthesis, and amino acid production, contributing to the high nutritional value of this edible insect. The study provides insights into the bacteria within the digestive tract of A. hesperiaris larvae and their role in enhancing the nutritional value of this edible insect. Additionally, it establishes a foundation for future research on the ecological roles and potential biotechnological benefits of these bacteria in the food industry and the development of therapies for various conditions and diseases.

Pectobacterium brasiliense 1692 (Pbr1692) is a necrotrophic pathogen that infects many crops such as potatoes and ornamental plants and derives nutrients from degraded plant tissue. Previous studies have identified Pbr1692 genes required for ecological fitness and virulence, however there is a lack of information on nutrient utilization in Pbr1692. Carbon source utilization profiling in Pbr1692 could provide a platform to decipher its metabolic flexibility and adaptation. This study assessed the nutrient utilization of Pbr1692 in different carbon sources, using Biolog Phenotypic Microarray (PM). An array of carbon sources utilized by Pbr1692 were identified, 32 carbohydrates and 8 carboxylic acids were among the preferred carbon nutrients utilized by Pbr1692. The PM results also revealed that the citric acid cycle, amino acid metabolism, and pentose phosphate metabolic pathways might be used to produce energy for Pbr1692. In addition, growth of Pbr1692 cells in minimal medium supplemented with citric acid, glucose, and aspartic acid retained the typical rod shape, suggesting that nutrient variation did not influence Pbr1692 cell morphology adaptation. This study provides an understanding on the adaptation of Pbr1692 and lays a foundation for understanding carbon metabolism of Pbr1692.

The genus Bacillus features species with remarkable plant growth-promoting traits (PGPTs) and is widely recognized for its biotechnological potential in sustainable agriculture. Among them, Bacillus paramycoides has recently attracted attention for its versatility in green synthesis of biopolymers, metal-based nanoparticles, and inhibition fungal phytopathogens; however, its PGPTs remain poorly underexplored. In this study, an integrated genomic and physiological approach was applied to B. paramycoides RZ3MS14, isolated from the guarana rhizosphere in Amazonian rainforest, to explore and correlate its potential PGPTs through in vitro and in vivo assays. The genome of B. paramycoides RZ3MS14 harbors genes related to N/P/Fe mobilization, bacillibactin synthesis, exopolysaccharides and biofilm formation, plant signaling, stress tolerance, biocontrol, and antibiotic resistance. Functional validation through in vitro assays, confirmed the strain's ability to solubilize phosphate, mineralize phytate, and produce siderophores, auxins, exopolysaccharides, and biofilm. These findings point diverse plant-growth promoting (PGP) traits that contributed to significant improvements in sugarcane growth and root architecture in the greenhouse. Specifically, root dry mass, shoot dry mass, root length, root surface area, and root volume increased by 225.92%, 520.89%, 231.47%, 242.25%, and 252.92%, respectively. Bacillus paramycoides RZ3MS14 exhibited a low antagonistic effect against the phytopathogenic fungi Fusarium verticillioides and Ceratocystis paradoxa. In contrast, microbial volatiles defined synergistic interactions with beneficial fungi Trichoderma afroharzianum and Purpureocillium lilacinum. This is the first study to unveil the PGP attributes of B. paramycoides, underscoring RZ3MS14's potential as a sugarcane bioinput and providing insights into its combined application with other microorganisms.

The yeast Yarrowia lipolytica adapts its metabolite production based on cultivation conditions, with the pH value playing a critical role. At pH 3, most Y. lipolytica strains produce polyols, while at pH 5, they accumulate predominantly organic acids. Yarrowia lipolytica has demonstrated the ability to transition from a planktonic, free-floating state to an immobilized state as a biofilm. This study aims to clarify the effects of pH level and carbon sources on the physiological state of Y. lipolytica when grown in a biofilm state. These pH variations were applied to the same biofilm culture to assess the capacity of given Y. lipolytica cells to undergo metabolic shifts and recovery under changing environmental conditions. Interestingly, a pH shift from 3 to 5 leads-as expected-to a metabolic shift from polyols to citric acid. However, the shift back to pH 3 does not revert to polyols as major products. This study not only revealed an unexpected production pattern but also provided benefits for the industrial process in general. Understanding biofilm cultivation methods supports continuous bioprocesses using the immobilized nature of biofilm. pH-alternating experiments reveal how environmental condition fluctuations affect biofilm culture physiology.

Verona-integron-metallo-β-lactamase (VIM-2) is one of the most widespread class B β-lactamase responsible for β-lactam resistance. Although active-site residues help in metal binding, the residues nearing the active-site possess functional importance. Here, to decipher the role of such residues in the activity and stability of VIM-2, the residues E146, D182, N210, S207, and D213 were selected through in-silico analyses and substituted with alanine using site-directed mutagenesis. The effects of substitution mutations were assessed by comparing the changes in β-lactam susceptibility pattern of Escherichia coli host cell expressing VIM-2 and its mutated proteins. VIM-2_N210A enhanced the susceptibility of the host by ∼4-8 folds against penicillins and cephalosporins, while the expression of VIM-2_D182A radically increased the susceptibility of host. However, expression of VIM-2_E146A reduced the susceptibility of host by 2-fold. Further, proteins were purified to homogeneity, and VIM_N210A and VIM_D182A displayed reduced thermal stability than VIM-2. Moreover, in vitro catalytic efficiencies of VIM-2_D182A were drastically reduced against all the β-lactams tested whereas the same were moderately reduced for VIM-2_N210A. Conversely, the catalytic efficiency was marginally altered for VIM_E146A. Overall, we infer that both N210A and D182A substitutions negatively affect the performance of VIM-2 by influencing substrate specificity and stability, respectively.

Kidney stone disease (KSD) is a multifactorial condition influenced by systemic and extrinsic factors, including diet, genetics, metabolic disorders, and microbial and environmental factors. Although preliminary evidence links the urinary microbiome (UMB) to stone formation, its role in different stone types remains unclear. We analysed UMB in patients with four distinct types of kidney stones (calcium oxalate, struvite, uric acid, and mixed composition). Urine samples from patients with KSD and controls were analysed using 16S rRNA gene sequencing. Patients with KSD exhibited distinct microbiota compositions, with increased abundances of Corynebacterium, Prevotella, and Staphylococcus than controls. The abundance of Dongia and Stenotrophomonas was higher in pure-stone formers than in mixed-stone formers (P < .05). Calcium oxalate stone formers had elevated levels of Pseudomonas and Dongia and reduced levels of Peptoniphilus than controls (P < .05). No significant differences in microbial diversity were observed between groups. Microbial composition correlated with blood and urine parameters, suggesting a potential influence on metabolic health and stone formation. These findings underscore the important role of UMB in KSD and provide valuable insights into its involvement in disease development and new opportunities for microbiome-based therapeutic strategies.

Animal manure is widely used in agricultural fields, as it can promote crop growth and control plant pathogens. It likely exerts an inhibitory effect on fungal biocontrol agents by enhancing soil fungistasis and prevents biocontrol fungi from achieving the best control effect. The impact of vermicompost, a fermentation product of manure, on soil fungistasis and colonization of the nematophagous fungus Arthrobotrys oligospora was explored in this study. It was found that amending soil with 10% or more vermicompost significantly and persistently enhances soil fungistatic intensity against A. oligospora. Similar effects were observed with ordinary compost. Neither plant presence (Panax notoginseng or tomato) nor earthworms significantly altered soil fungistasis. Microbiome and metabolome analyses revealed that vermicompost amendment reshaped bacterial communities and metabolite profiles, correlating with enhanced fungistasis. Further results showed that vermicompost amendment less than 10% showed no significant negative impact on soil colonization of A. oligospora, but higher vermicompost amendment (20%) reduced A. oligospora soil colonization by approximately 34%. These findings suggest that manure amendment has potential negative impact on biocontrol fungi, and field-specific dosage of manure need to be optimized when integrating manure amendments with fungal biocontrol strategies.

Drain flies (Clogmia albipunctata) are insects that thrive in humid urban environments such as bathrooms drains and sewage systems. While their role in pathogen transmission has been suggested, little is known about their microbiome or ecology in non-clinical contexts. Using 16S rRNA gene metabarcoding, we characterized the bacterial communities of drain flies from three locations in South Korea, public bathrooms from a college in Seoul, a rural port in Ulleungdo island, and a highly frequented public park in Yeouido. In total, we obtained 221 families and 1 474 features. We found significant differences in microbiome composition and diversity as well as a small core microbiome shared among locations, with environmental bacteria such as Pseudomonas and Ralstonia being the dominant taxa across samples. The majority of the detected amplicon sequence variants (ASV) were not shared among locations. These findings suggest drain fly transport a location-specific environmental bacteria. Notably, we also identified ASVs of potential clinical relevance, including Mycobacterium, Acinetobacter baumanii, Providencia, and Nocardia. This is the first metagenomic insight into the microbiome of this species and adds to a renewed interest in the role that non-hematophagous insects play in urban microbial ecology and the spread of microbes.

Burkholderia gladioli produces a yellow-pigmented toxin called toxoflavin, and causes disease on a variety of plants. Previous studies have suggested that the pathogenicity of B. gladioli is regulated by an N-acyl-l-homoserine lactone (AHL)-mediated quorum sensing (QS) system. In this study, complete genome sequencing revealed that B. gladioli pv. gladioli MAFF 302385 possesses two types of AHL synthase and AHL receptor gene pairs: glaI1/glaR1 and glaI2/glaR2. Disruption of QS genes revealed that the glaI1/glaR1 QS system regulated swarming motility, biofilm formation, and colony formation via N-octanoyl-l-homoserine lactone. Although Escherichia coli harboring glaI2 produced N-(3-hydroxyoctanoyl)-l-homoserine lactone and N-(3-hydroxydecanoyl)-l-homoserine lactone, the expression of glaI2 was not confirmed in MAFF 302385 cells. We also found that toxoflavin production was regulated by the glaI1/glaR1 QS system in liquid medium, but not on agar medium. When pathogenicity tests were performed on gladiolus leaves, the wild-type and QS mutants showed a similar level of disease. Our results demonstrated that only the glaI1/glaR1-mediated QS system is active in MAFF 302385, but major virulence factors, especially toxoflavin, are not completely dependent on the QS system.