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Biofilm Dec 2023Biofilms are complex microbial communities embedded in extracellular matrix. Pathogens within the biofilm become more resistant to the antibiotics than planktonic...
Biofilms are complex microbial communities embedded in extracellular matrix. Pathogens within the biofilm become more resistant to the antibiotics than planktonic counterparts. Novel strategies are required to encounter biofilms. Exopolysaccharides are one of the major components of biofilm matrix and play a vital role in biofilm architecture. In previous studies, a glycosyl hydrolase, PslG, from was found to be able to inhibit biofilm formation by disintegrating exopolysaccharide in biofilms. Here, we investigate the potential spectrum of PslG homologous protein with anti-biofilm activity. One glycosyl hydrolase from , PslG, exhibits anti-biofilm activities and the key catalytic residues of PslG are conserved with those of PslG. PslG at concentrations as low as 50 nM efficiently inhibits the biofilm formation of and disassemble its preformed biofilm. Furthermore, PslG exhibits anti-biofilm activity on a series of , including and pv. . PslG stays active under various temperatures. Our findings suggest that glycosyl hydrolase PslG has potential to be a broad spectrum inhibitor on biofilm formation of a wide range of .
PubMed: 37928620
DOI: 10.1016/j.bioflm.2023.100155 -
Synthetic and Systems Biotechnology Dec 2023A1501 is a non-fluorescent denitrifying bacteria that belongs to the gram-negative bacterial group. As a prominent strain in the fields of agriculture and...
A1501 is a non-fluorescent denitrifying bacteria that belongs to the gram-negative bacterial group. As a prominent strain in the fields of agriculture and bioengineering, there is still a lack of comprehensive understanding regarding its metabolic capabilities, specifically in terms of central metabolism and substrate utilization. Therefore, further exploration and extensive studies are required to gain a detailed insight into these aspects. This study reconstructed a genome-scale metabolic network model for A1501 and conducted extensive curations, including correcting energy generation cycles, respiratory chains, and biomass composition. The final model, iQY1018, was successfully developed, covering more genes and reactions and having higher prediction accuracy compared with the previously published model iPB890. The substrate utilization ability of 71 carbon sources was investigated by BIOLOG experiment and was utilized to validate the model quality. The model prediction accuracy of substrate utilization for A1501 reached 90 %. The model analysis revealed its new ability in central metabolism and predicted that the strain is a suitable chassis for the production of Acetyl CoA-derived products. This work provides an updated, high-quality model of A1501for further research and will further enhance our understanding of the metabolic capabilities.
PubMed: 37927897
DOI: 10.1016/j.synbio.2023.10.001 -
Food and Chemical Toxicology : An... Dec 2023Recent advancements in the generation of high-throughput multi-omics data have provided a vast array of candidate genes for the genetic engineering of plants. However,...
Recent advancements in the generation of high-throughput multi-omics data have provided a vast array of candidate genes for the genetic engineering of plants. However, as part of their safety assessment, newly expressed proteins in genetically modified crops must be evaluated for potential cross-reactivity with known allergens. In this study, we developed transgenic canola plants expressing the Arabidopsis thaliana PAP17 gene and a novel selectable marker composed of the ptxD gene from Pseudomonas stutzeri. To evaluate the potential allergenic cross-reactivity of the AtPAP17 and PTXD proteins expressed in transgenic canola, we applied a comprehensive approach utilizing sequence-based, motif-based, and 3D structure-based analyses. Our results demonstrate that the risk of conferring cross-reactivity with known allergens is negligible, indicating that the expression of these proteins in transgenic canola poses a low allergenic risk.
Topics: Oxidoreductases; Plants, Genetically Modified; Phosphites; NAD; Allergens; Crops, Agricultural; Computational Biology
PubMed: 37925014
DOI: 10.1016/j.fct.2023.114094 -
International Journal of Biological... Jan 2024D-Allose and D-allulose are two important rare natural monosaccharides found in meager amounts. They are considered to be the ideal substitutes for table sugar (sucrose)... (Review)
Review
D-Allose and D-allulose are two important rare natural monosaccharides found in meager amounts. They are considered to be the ideal substitutes for table sugar (sucrose) for, their significantly lower calorie content with around 80 % and 70 % of the sweetness of sucrose, respectively. Additionally, both monosaccharides have gained much attention due to their remarkable physiological properties and excellent health benefits. Nevertheless, D-allose and D-allulose are rare in nature and difficult to produce by chemical methods. Consequently, scientists are exploring bioconversion methods to convert D-allulose into D-allose, with a key enzyme, L-rhamnose isomerase (L-RhIse), playing a remarkable role in this process. This review provides an in-depth analysis of the extractions, physiological functions and applications of D-allose from D-allulose. Specifically, it provides a detailed description of all documented L-RhIse, encompassing their biochemical properties including, pH, temperature, stabilities, half-lives, metal ion dependence, molecular weight, kinetic parameters, specific activities and specificities of the substrates, conversion ratio, crystal structure, catalytic mechanism as well as their wide-ranging applications across diverse fields. So far, L-RhIses have been discovered and characterized experimentally by numerous mesophilic and thermophilic bacteria. Furthermore, the crystal forms of L-RhIses from E. coli and Stutzerimonas/Pseudomonas stutzeri have been previously cracked, together with their catalytic mechanism. However, there is room for further exploration, particularly the molecular modification of L-RhIse for enhancing its catalytic performance and thermostability through the directed evolution or site-directed mutagenesis.
Topics: Escherichia coli; Fructose; Monosaccharides; Sucrose
PubMed: 37924916
DOI: 10.1016/j.ijbiomac.2023.127859 -
Environmental Pollution (Barking, Essex... Jan 2024Discharge of treated shale gas wastewater is becoming prevalent in the Sichuan Basin in China, and the resulting potential environmental impacts have raised concern. In...
Discharge of treated shale gas wastewater is becoming prevalent in the Sichuan Basin in China, and the resulting potential environmental impacts have raised concern. In this study, the responses of microbial community in the receiving water to discharge of treated shale gas wastewater were assessed during a two-year study period, covering two wet seasons and one dry season. The results showed that the discharge of treated shale gas wastewater had no significant effects on alpha diversity in the two wet seasons, but had significant effects in the dry season after 15 months of discharge. Obvious changes in microbial community structure were observed in all three seasons at the downstream sites near the wastewater outfall, as compared to the control site. Multimetric indices indicated that the impacts of wastewater discharge on microbial ecosystem occurred with the extension of the discharge period. Moreover, special attention was given to the microbiological risks associated with antibiotic resistance genes (ARGs), virulence factor genes (VFGs), and pathogenic antibiotic resistant bacteria (PARBs) in the dry season in sediments of the receiving water. At downstream sites near the outfall, five subtypes of ARGs and seven VFGs showed a significant increase in relative abundance. Forty-two PARBs carrying ARGs and VFGs were detected, and three PARBs (Pseudomonas aeruginosa, Pseudomonas stutzeri and Pseudomonas fluorescens) increased obviously in relative abundance at the downstream site near the outfall. In conclusion, long-term wastewater discharge had effects on the microbial community, and limited microbiological risks existed in the receiving waters.
Topics: Wastewater; Genes, Bacterial; Natural Gas; Bacteria; Anti-Bacterial Agents; Microbiota; Water
PubMed: 37918774
DOI: 10.1016/j.envpol.2023.122799 -
The Journal of Hospital Infection Feb 2024
Topics: Humans; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Pseudomonas stutzeri; Phacoemulsification; Endophthalmitis; Molecular Typing; Disease Outbreaks; Bacterial Typing Techniques
PubMed: 37918527
DOI: 10.1016/j.jhin.2023.08.027 -
Foods (Basel, Switzerland) Sep 2023The fermented liquid sector is developing all over the world due to its contribution to health. Our study has contributed to the debate about whether industrially...
The fermented liquid sector is developing all over the world due to its contribution to health. Our study has contributed to the debate about whether industrially manufactured fermented liquids live up to their claims by analyzing pathogens and beneficial bacteria using a 16S rRNA sequencing technique called metagenomic analysis. , , , , , and were the most abundant bacterial genera observed as potential probiotics. , , and , which have plant-growth-promoting traits, were also detected. The fact that we encounter biocontroller bacteria that promote plant growth demonstrates that these organisms are widely used in foods and emphasizes the necessity of evaluating them in terms of public health. Their potential applications in agriculture may pose a danger to food hygiene and human health in the long term, so our data suggest that this should be evaluated.
PubMed: 37835192
DOI: 10.3390/foods12193538 -
Contact Lens & Anterior Eye : the... Dec 2023This study aimed to investigate the bacterial contamination of multi-use tear drops, gels, and ointments that patients use at home.
PURPOSE
This study aimed to investigate the bacterial contamination of multi-use tear drops, gels, and ointments that patients use at home.
METHOD
A total of 271 multi-use containers used by 168 patients were examined. Conjunctival culture samples were obtained from patients who used tear drops, gels, and ointments that were found to be contaminated.
RESULTS
Bacterial contamination was detected in 33 (12.2 %) out of the 271 containers. The contamination rate was 7.9 % in tear drops, 11.7 % in gels, and 32 % in ointments. A statistically significant difference was found between the drops, gels, and ointment groups (P = 0.04). Bacterial contamination was detected in 25 (18.9 %) out of 132 collapsible tubes and 8 (5.8 %) out of 139 plastic bottles (P = 0.01). Important bacteria, including Pseudomonas stutzeri, Pseudomonas aeruginosa, Bacillus licheniformis, Paenibacillus pabuli, Proteus mirabilis, Pantoea agglomerans, Morganella morganii, Serratia marcescens, and Serratia liquefaciens, were detected. Mucorales spp. fungus was seen in a gel. Staphylococcus epidermidis, methicillin-resistant Staphylococcus aureus, and M. morganii were found in the conjunctival microbiota of three patients.
CONCLUSION
The overall contamination rate of ocular lubricants was low (12.2%); however, a significant difference was found between the drops, gels, and ointments. The contamination rate was higher in gels and ointments than that in drops. The contamination rate was found to be increased in the collapsible tube. The use of ocular lubricants is safe; however, patients must be cautious when using multi-use tear drops, gels, and ointments to avoid contamination. Whenever possible, bottles should be preferred instead of collapsible tubes.
Topics: Humans; Ointments; Methicillin-Resistant Staphylococcus aureus; Bacteria; Gels; Lubricants
PubMed: 37806847
DOI: 10.1016/j.clae.2023.102064 -
IScience Oct 2023Emergence of new SARS-CoV-2 VOCs jeopardize global vaccine and herd immunity safeguards. VOCs interactions with host microbiota might affect clinical course and outcome....
Emergence of new SARS-CoV-2 VOCs jeopardize global vaccine and herd immunity safeguards. VOCs interactions with host microbiota might affect clinical course and outcome. This longitudinal investigation involving Pre-VOC and VOCs (Delta & Omicron) holo-transcriptome based nasopharyngeal microbiome at taxonomic levels followed by metabolic pathway analysis and integrative host-microbiome interaction. VOCs showed enrichment of with dominance of . Interestingly with superiority of and , were highlights of Delta VOC rather than Omicron. Common species comprising the core microbiome across all variants, reiterated the significance of in Delta, and its association with metabolic pathways enhancing inflammation in patients. Microbe-host gene correlation network revealed , , and modulating immune pathways, which might augment clinical severity in Delta. Importantly, opportunistic species of , , , and were abundant in Delta-mortality. The study establishes a functional association between elevated nasal pathobionts and dysregulated host response, particularly for Delta.
PubMed: 37701571
DOI: 10.1016/j.isci.2023.107779 -
Plant Physiology and Biochemistry : PPB Oct 2023This study investigated the effect of Pseudomonas stutzeri inoculation on Lemna minor treated with Cu(OH) nanopesticide (NP). The results showed that P. stutzeri...
Pseudomonas stutzeri improves the tolerance of Lemna minor to Cu(OH) nanopesticide by regulating the uptake of copper, antioxidant defense mechanisms, and the expression of metacaspase-1, chlorophyllase, and stress-responsive genes.
This study investigated the effect of Pseudomonas stutzeri inoculation on Lemna minor treated with Cu(OH) nanopesticide (NP). The results showed that P. stutzeri inoculation increased the relative growth rate (RGR) in NP-treated plants. Although chlorophyll and carotenoid contents decreased significantly in NP-treated plants, P. stutzeri inoculation led to an increase in chlorophyll and carotenoid contents in NP-treated plants. Copper (Cu) content increased with increasing NP concentration, but it decreased significantly in the presence of P. stutzeri. NP treatment caused increased HO and TBARS levels, as well as proline levels. However, P. stutzeri inoculation led to decreased HO and TBARS levels and increased SOD, POX, GST, GR, GPX, and DHAR activities. The expression of genes encoding SOD, GST, metacaspase-1, and chlorophyllase was upregulated by NP treatment alone. Additionally, when plants were inoculated with P. stutzeri, the expression of these genes was further enhanced. In conclusion, P. stutzeri inoculation had a positive effect on the growth and antioxidant system of L. minor treated with NP as it enhanced RGR, increased chlorophyll and carotenoid contents, and decreased Cu content and oxidative stress. These findings suggested that P. stutzeri has the potential to promote aquatic plant growth and counteract the negative impacts of NP on these plants.
PubMed: 37699291
DOI: 10.1016/j.plaphy.2023.108002