Brazilian Journal of Microbiology最新文献

Xylitol is a highly demanded polyol in the food, pharmaceutical, and chemical industries. However, its current production methods are considered energy-intensive, require the use of hazardous chemical catalysts, and depend on complex and costly equipment. The biotechnological route of xylitol production is proposed as a sustainable alternative, but it still requires process improvements, such as enhanced fermentation capabilities, to be economically competitive. This study examined Candida tropicalis yeast to improve xylose-to-xylitol conversion via glucose: xylose ratio and pH modulation. Key parameters evaluated included xylose consumption rate (r_S), xylose-to-xylitol yield (Y_P/S), and xylitol volumetric productivity (Q_P). Conditions with 50 g/L xylose at pH 3.5 exhibited superior xylitol production: 29.81 g/L, Q_P of 0.52 g/L/h, and Y_P/S of 0.54 g/g at 48 h. The statistical model demonstrated that the maximum Y_P/S and Q_P values have not yet been achieved. This could present an opportunity to be explored through yeast genetic engineering approaches. Additionally, the quantitative expression of the xylose transporter genes (XUT1 and STL2) and the xylose reductase gene (XYL1), previously identified in C. tropicalis, was evaluated under all tested conditions. Upregulation of the XUT1 was correlated with higher xylose concentrations, while STL2 was favored at lower xylose concentrations. The expression of XYL1 showed upregulation over time with higher xylose ratios. The high transcription levels and expression profile suggest that Xut1p-mediated xylose transport occurs through a proton symport mechanism. The results indicate that the pH factor indirectly influences XUT1 gene transcription, possibly as a compensatory response to the reduced transporter efficiency under high pH conditions. The present work underscores the influence of glucose ratios and pH in xylitol production, as well as the gene expression of xylose transporters and the key enzyme xylose reductase. Leveraging these insights can significantly enhance xylitol production from hemicellulosic hydrolysates through biotechnological pathways.

Aspergillus and Candida are ubiquitous fungi included in the group of high priority in the World Health Organization list of fungal pathogens. They are found in various ecosystems and the environmental role in increasing the resistance to antifungals has been shown. Thus, we aimed to determine the occurrence of Aspergillus spp. and Candida spp. pathogenic species in water samples from a coastal ecosystem from southern Brazil, and its antifungal susceptibility profile. Water samples were collected monthly at three environmental sites, over 25 months. Abiotic parameters of the water samples were analyzed as well as antifungal susceptibility. Aspergillus spp. and Candida spp. were detected in 44% (n = 33/75) and 40% (n = 30/75) respectively of the samples, totaling 67 and 96 isolates. Section Fumigati and C. parapsilosis were the most section/species isolated. Triazole resistance was detected in 3% of the Aspergillus spp. (2/67) and in 1% of the Candida spp. (1/96) isolates. Our study contributes with data showing that coastal aquatic environments can serve as a source of infection of resistant fungal isolates, proving the need for environmental surveillance and monitoring of fungal resistance in the One Health perspective.

Despite meticulous precautions, contamination of genomic DNA samples is not uncommon, which can significantly compromise the analysis of microorganisms' whole-genome sequencing data, thus affecting all subsequent analyses. Thanks to advancements in software and bioinformatics techniques, it is now possible to address this issue and prevent the loss of the entire dataset obtained in a contaminated whole-genome sequencing, where the DNA of another bacterium is present. In this study, it was observed that the sequencing reads from Streptomyces sp. BRB040, generated using the HiSeq System platform (Illumina Inc., San Diego, USA), were contaminated with the DNA of Bacillus licheniformis. To eliminate the contamination in Streptomyces sp. BRB040, a combination of tools available on the Galaxy platform and other web-based resources were used (MeDuSa and Blast). The contaminated reads were treated as a metagenome to isolate the genome of the contaminating organism. They were assembled using the metaSPAdes, resulting in a large scaffold of 4.187 Mb, which was identified as Bacillus licheniformis. After the identification of the contaminating organism, its genome was used as a filter to remove sequencing reads that could align using then Bowtie 2 software for this step. Once the contaminated reads were removed a new assembly was performed using the Unicycler software, yielding 117 contigs with a total size of 7.9 Mb. The completeness of this genome was assessed through BUSCO, resulting in a completeness of 95.9%. We also used an alternative tool (BBduk) to eliminate contaminated reads and the resulting assembly by Unicycler generated 85 contigs with a total size of 8.3 Mb and completeness of 99.5%. These results were better than the assembly obtained via SPAdes, which generated less complete genomes (maximum of 97.8% completeness) compared to Unicycler and which was unable to perform an adequate assembly of the data obtained from decontamination by BBduk. When compared with the uncontaminated BRB040 genome, which has a total size of 8.2 Mb and completeness of 99.8%, this pipeline revealed that the assembly performed with the decontaminated reads via BBduk presented better results, with completeness 0.3% lower than the reference. The genome mining of both genomes using antiSMASH 7.0 revealed the number of 24 Biosynthetic Gene Clusters (BGCs) for BBduk data as well as in the control assembly of the BRB040. In silico decontamination process allows the genome mining of BGCs despite the loss of nucleotides. These findings show that contamination can be effectively removed from a genome using readily available online tools, while preserving a dataset suitable for extracting valuable insights into the secondary metabolism of the target organism. This approach is particularly beneficial in scenarios where resequencing samples is not immediately feasible.

The common bean (Phaseolus vulgaris L.) plays a significant economic and social role in Brazil. However, the national average yield remains relatively low, largely because most bean cultivation is undertaken by small-scale farmers. In this context, biological nitrogen fixation (BNF) is an effective strategy for improving crop yield. Therefore, it is important to identify novel rhizobial strains well suited to local climatic conditions. This study used Phaseolus vulgaris as a trap plant in soils from three distinct conservation areas (Ponta Grossa, Ortigueira, and Londrina) within Paraná State, Brazil. The soil chemical analysis revealed that the pH values in the Ponta Grossa and Ortigueira regions were low, whereas the Ortigueira region exhibited elevated aluminum levels. A total of 94 strains were obtained from the nodules of plants and subjected to analysis for their morphological and genetic properties. No nodules were observed in the Ortigueira region. In the Ponta Grossa region, most of the strains were identified as belonging to the genus Paraburkholderia, whereas all strains from Londrina were identified as Rhizobium. The 16S rRNA gene phylogenetic analysis revealed a high degree of genetic similarity between the Paraburkholderia and Rhizobium strains. These findings indicate that soil chemical properties (pH and aluminum level) and climate conditions may have a significant impact on the symbiotic association between rhizobia and common bean.

Plant-associated microbiome plays important role in maintaining overall health of the host plant. Xanthium strumarium displaying resilience to various environmental fluctuations may harbor some bacterial isolates which can help this plant to grow worldwide. The present study aims to isolate endophytic and rhizospheric bacteria from X. strumarium and assess their plant growth-promoting and Ralstonia solanacearum antagonism activity. From a total of 148 isolated bacteria, 7 endophytic and 2 rhizospheric bacterial isolates were found to endow with significant in vitro plant growth promotion activities. The 16S rRNA gene sequence similarity of the 7 endophytic isolates has revealed these bacteria belonging to 5 genera viz. Curtobacterium, Pantoea, Pseudomonas, Microbacterium and Paracoccus whereas, the two rhizospheric isolates were identified as species of Ralstonia pickettii and Priestia megaterium. Maximum growth promotion was observed using the strains Pseudomonas fluorescens XSS6 and Microbacterium hydrothermale XSS20 in the assay conducted on tomato plants. In the in planta inhibition assay of R. solanacearum carried out in tomato seedlings using root bacterization method, Pseudomonas fluorescens XSS6 and Panotea vagans XSS3 showed antagonistic activity with biocontrol efficacy of 94.83% and 83.96%, respectively. GC-MS analysis detected several known antimicrobial compounds in the extract of the culture supernatant of Pseudomonas fluorescens XSS6 and Panotea vagans XSS3 strains, which may contribute to the inhibition of R. solanacearum by these strains. The results of our study indicated that the bacteria associated with X. strumarium exhibit multiple plant-beneficial effects. These bacteria have the potential to be developed as effective biofertilizers and biological control agents, promoting sustainable agriculture practices.

This study aimed to compare the effects of cellobiose hydrolysis, whether occurring inside or outside the cell, on the ability of Saccharomyces cerevisiae strains to ferment this sugar and then apply the most effective strategy to industrial S. cerevisiae strains. Firstly, two recombinant laboratory S. cerevisiae strains were engineered: CEN.PK-X-Bgl1YL, expressing the periplasmic β-glucosidase BGL1 from Yarrowia lipolytica; and CEN.PK-X-B7-T2, co-expressing the intracellular β-glucosidase SpBGL7 from Spathaspora passalidarum and the cellobiose transporter MgCBT2 from Meyerozyma guilliermondii. Both engineered strains were able to grown in media with cellobiose and to ferment this disaccharide. However, CEN.PK-X-Bgl1YL, which hydrolyzes cellobiose extracellularly, exhibited faster growth and superior batch fermentation performance. Furthermore, enzymatic and transport activities revealed that sugar uptake was possibly the limiting factor in cellobiose fermentation by CEN.PK-X-B7-T2. Since extracellular hydrolysis with the periplasmic β-glucosidase was more efficient for cellobiose fermentation, we integrated the BGL1 gene into two industrial xylose-fermenting S. cerevisiae strains. The resulting strains (MP-C5H1-Bgl1YL and MP-P5-Bgl1YL) efficiently co-consumed ∼ 22 g L^- 1 of cellobiose and ∼ 22 g L^- 1 of xylose in 24 h, achieving high ethanol production levels (∼ 17 g L^- 1 titer, ∼ 0.50 g L^- 1 h^- 1 volumetric productivity, and 0.40 g g^- 1 ethanol yield). Our findings suggest that the expression of periplasmic β-glucosidases in S. cerevisiae could be an effective strategy to overcome the disaccharide transport problem, thus enabling efficient cellobiose fermentation or even cellobiose-xylose co-fermentation.

Handlers can wear masks during food preparation to avoid contamination of the nose and mouth. However, if microorganisms can pass through mask layers and handlers touch their outer surfaces, their hands can contaminate the food being handled. This study evaluated the behavior of 31 food handlers wearing disposable masks in a food service kitchen. Next, the microorganisms on the external surface of food handler masks were identified using microbiological methods and matrix-associated laser desorption-time-of-flight (MALDI-TOF) mass spectrometry. Finally, the passage of microorganisms through mask layers was assessed in volunteers. Observations showed that 77.4% of the 31 food handlers touched their masks at least once per hour during food preparation. Microbiological analysis identified 14 bacterial species on all food handlers' masks analyzed. The most frequent microorganisms found were coagulase-negative Staphylococcus, Staphylococcus aureus, and Bacillus spp. The external surfaces of uncontaminated masks showed contamination after volunteers used them for few hours. Furthermore, sterile gloved hands became contaminated after touching the external surfaces of these masks, indicating bacterial transference from the inner to the outer layers. Although masks can prevent direct microbial contamination from the nose and mouth if properly used, our findings indicate that masks may inadvertently become vectors of food cross-contamination if hands touch their external surfaces during food preparation. Since our study indicated that microorganisms can pass through mask layers, food handlers should avoid touching the external surfaces of masks. However, if it happens, they should carry out proper hand washing to prevent food cross-contamination during food preparation.

Among the Candida species commonly involved in superficial and more significant life-threatening infections, C. krusei exhibits the most worrisome resistance profile to antifungals. This study aimed to analyse the population structure using multilocus sequence typing (MLST), and to evaluate the antifungal susceptibility profile of C. krusei isolated from patients living with human immunodeficiency virus (HIV) in Cameroon. C. krusei isolated from stool, urine, mouth and vaginal samples were identified using routine laboratory techniques and matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS). The C. krusei isolates were further analysed by MLST. In vitro antifungal susceptibility testing was performed using the Sensititre Yeast One™ microdilution technique. Forty three (43) C. krusei isolates were included in the study. The MLST identified 32 Diploid sequence type (DST), of which 31 were new that were not included in the current database. New alleles were not observed. Different DSTs were observed in isolates from the same geographical area, from different anatomical sites in the same patient. An eBURST analysis clustered all identified DSTs of former isolates in clonal complex 1. Heterogeneous antifungal MICs were observed in isolates of the same DST and/or from the same geographical area. 32.6% of the isolates displayed a resistant or non-wild-type phenotype to at least 3 distinct antifungal agent classes. The achieved results support the setting up of molecular epidemiology and antifungal resistance surveillance of C. krusei.

Introduction: Helicobacter pylori (H. pylori) is a major human pathogen whose increased antibiotic resistance poses a serious threat to human health.

Aim: The aim of this study is to further explore the association between H. pylori resistance to clarithromycin, levofloxacin, metronidazole, amoxicillin, rifampicin, tetracycline and its genomic characteristics.

Methodology: Using H. pylori isolates, we studied their susceptibility to six antibiotics by the agar dilution method. By performing whole-genome resequencing of the H. pylori genomic DNA, the differences in single nucleotide polymorphisms (SNPs) between phenotype resistant and sensitive strains were statistically analyzed to identify potential mutation sites related to drug resistance, and the consistency between genotype and phenotype resistance was analyzed.

Results: The drug resistance rates of 65 H. pylori isolates are as follows: clarithromycin 36.9%, levofloxacin 29.2%, metronidazole 63.1%, amoxicillin 7.7%, rifampicin 12.3%, and tetracycline 3.1%. Based on the whole genome resequencing results of H. pylori isolates, 10 new mutations that may be related to drug resistance were identified. There is strong consistency between the genotype and phenotype resistance of clarithromycin and levofloxacin.

Conclusion: The resistance rate to amoxicillin and tetracycline is relatively low in Northern China. and the above two antibiotics can be given priority for clinical treatment. It has a high resistance rate to metronidazole and should be avoided as much as possible, or combined with other drugs for treatment. The 10 mutations identified through analysis that only exist in drug-resistant strains may be associated with levofloxacin, metronidazole, amoxicillin, and rifampicin resistance, respectively. The results indicate that genotype testing of H. pylori can serve as a method for predicting its resistance to clarithromycin and levofloxacin.

The increasing use of chemical fungicides without effective control of phytopathogens has led to the development of resistance in microorganisms. As a promising alternative, products formulated with Trichoderma have emerged for their sustainable and effective potential in integrated disease management. However, the predominant formulations do not offer the necessary protection against abiotic factors. In this study, we investigated Trichoderma species encapsulated in sodium alginate through storage viability experiments and their antagonistic potential. The viability and storage conditions of the capsules were evaluated by plating at 5, 15, 30, 45, 60, and 150 days after production, kept in dry or refrigerated environments. The antagonistic potential was determined by the culture pairing method using the phytopathogen Fusarium sp. The results demonstrated that it was possible to maintain the viability of the conidia, with no differences between storage environments. Additionally, the capsule provided UV protection to the conidia encapsulated species possess antagonistic potential, inhibiting 52.54% of Fusarium sp. growth. Consequently, encapsulation is an alternative formulation method that ensures the viability of Trichoderma conidia and optimizes its use in biological control.