-
Saudi Medical Journal Jun 2023To develop a candidate vaccine aginst the .
OBJECTIVES
To develop a candidate vaccine aginst the .
METHODS
Since there is currently no vaccine against this pathogen, we employed in-silico methods to extensively explore the outer membrane toxin-producing proteins found specifically in to forecast a multi-epitope chimeric vaccine design. This computational study was conducted in Saudi Arabia in 2022 (study design: computational; ethical approval not applicable).
RESULTS
TThe vaccine peptide comprises multiple linear and conformational B-cell epitopes, which have the potential to elicit humoral immunity. Projected B-cell- derived T-cell epitopes for outer membrane proteins are present in the produced protein. The docking and molecular dynamic simulation results indicating that the chimeric vaccine had adequate binding stability with TLR-4. Following the immunological simulation, significant levels of immune cell expression were observed as immunoglobulin (Ig) M and IgG, IgM, IgM1, and IgM2, and independently IgG1 and IgG2.
CONCLUSION
The developed vaccine candidate is suitable for further testing and can assist experimental vaccinologists in developing an effective vaccine against .
Topics: Humans; Vaccinology; Sphingobacterium; Epitopes, B-Lymphocyte; Saudi Arabia
PubMed: 37343981
DOI: 10.15537/smj.2023.44.6.20220733 -
Food Science & Nutrition Jun 2023The salt-reducing pickling method has been applied to the industrial production of . In order to reveal the succession of the microbial community structure and flavor...
The salt-reducing pickling method has been applied to the industrial production of . In order to reveal the succession of the microbial community structure and flavor components during the pickling process, this study used PacBio Sequel to sequence the full length of 16S rRNA (bacteria, 1400 bp) and ITS (fungi, 1200 bp) genes, and detected flavor components simultaneously, including organic acids, volatile flavor components (VFC), monosaccharides, and amino acids. Eleven phyla and 148 genera were identified in the bacterial community, and 2 phyla and 60 genera in the fungal community. During the four stages of pickling, the dominant bacterial genera were , , , and , while the dominant fungal genera were , , , and , respectively. There were 32 main flavor components (5 organic acids, 19 VFCs, 3 monosaccharides, and 5 amino acids). Correlation heat mapping and bidirectional orthogonal partial least squares (O2PLS) analysis showed that the flora having close relation to flavor components included 14 genera of bacteria (, , , , , , , , , , , , , and ) and 3 genera of fungi (, , and ). This study provides detailed data regarding the microbial community and flavor components during the salt-reducing pickling process of , which can be used as a reference for the development and improvement of salt-reducing pickling methods.
PubMed: 37324844
DOI: 10.1002/fsn3.3297 -
Toxics Apr 2023To effectively carry out the bioremediation of a Pb polluted environment, a lead-tolerant strain named D1 was screened from the activated sludge of a factory in Hefei,...
To effectively carry out the bioremediation of a Pb polluted environment, a lead-tolerant strain named D1 was screened from the activated sludge of a factory in Hefei, and its lead removal in a solution with Pb concentration of 200 mg/L could reach 91% under optimal culture conditions. Morphological observation and 16S rRNA gene sequencing were used to identify D1 accurately, and its cultural characteristics and lead removal mechanism were also preliminarily studied. The results showed that the D1 strain was preliminarily identified as the strain. The experiments conducted via orthogonal test showed that the optimal conditions for the growth of strain D1 were pH 7, inoculum volume 6%, 35 °C, and rotational speed 150 r/min. According to the results of scanning electron microscopy and energy spectrum analysis before and after the D1 exposure to lead, it is believed that the lead removal mechanism of D1 is surface adsorption. The Fourier transform infrared spectroscopy (FTIR) results revealed that multiple functional groups on the surface of the bacterial cells are involved in the Pb adsorption process. In conclusion, the D1 strain has excellent application prospects in the bioremediation of lead-contaminated environments.
PubMed: 37235227
DOI: 10.3390/toxics11050412 -
MicrobiologyOpen Apr 2023Animals' gut microbiomes affect a wide array of biological processes including immunity and protection from pathogens. However, how the microbiome changes due to...
Animals' gut microbiomes affect a wide array of biological processes including immunity and protection from pathogens. However, how the microbiome changes due to infection by parasites is still largely unknown, as is how the microbiome changes in hosts that differ in their susceptibility to parasites. To investigate this, we exposed two slug species of differing susceptibility to the parasitic nematode Phasmarhabditis hermaphrodita (Deroceras reticulatum is highly susceptible and Ambigolimax valentianus resistant to the nematode) and profiled the gut microbiota after 7 and 14 days. Before infection, both slug species' microbiota was dominated by similar bacterial genera: Pseudomonas (by far the most abundant), Sphingobacterium, Pedobacter, Chryseobacterium, and Flavobacterium. In the resistant host A. valentianus, there was no significant change in the bacterial genera after infection, but in D. reticulatum, the bacterial profile changed, with a decrease in the abundance of Pseudomonadaceae and an increase in the abundance of Flavobacteriaceae and Sphingobacteriaceae after 7 days postinfection. This suggests nematode infection causes dysbiosis in hosts that are susceptible to infection, but the microbiome of resistant species remains unaltered. In summary, the regulation of the immune system is tightly linked with host survival, and nematode infection can alter the microbiome structure.
Topics: Animals; Gastropoda; Dysbiosis; Nematoda; Rhabditoidea; Disease Susceptibility
PubMed: 37186232
DOI: 10.1002/mbo3.1346 -
Microorganisms Mar 2023Amphibian foam nests are unique microenvironments that play a crucial role in the development of tadpoles. They contain high levels of proteins and carbohydrates, yet...
Amphibian foam nests are unique microenvironments that play a crucial role in the development of tadpoles. They contain high levels of proteins and carbohydrates, yet little is known about the impact of their microbiomes on tadpole health. This study provides a first characterization of the microbiome of foam nests from three species of Leptodactylids (, , and ) by investigating the DNA extracted from foam nests, adult tissues, soil, and water samples, analyzed via 16S rRNA gene amplicon sequencing to gain insight into the factors driving its composition. The results showed that the dominant phyla were proteobacteria, bacteroidetes, and firmicutes, with the most abundant genera being , , and . The foam nest microbiomes of and were more similar to each other than to that of , despite their phylogenetic distance. The foam nests demonstrated a distinct microbiome that clustered together and separated from the microbiomes of the environment and adult tissue samples. This suggests that the peculiar foam nest composition shapes its microbiome, rather than vertical or horizontal transference forces. We expanded this knowledge into amphibian foam nest microbiomes, highlighting the importance of preserving healthy foam nests for amphibian conservation.
PubMed: 37110323
DOI: 10.3390/microorganisms11040900 -
The Journal of Biological Chemistry May 2023Serine palmitoyltransferase (SPT) is a key enzyme of sphingolipid biosynthesis, which catalyzes the pyridoxal-5'-phosphate-dependent decarboxylative condensation...
Serine palmitoyltransferase (SPT) is a key enzyme of sphingolipid biosynthesis, which catalyzes the pyridoxal-5'-phosphate-dependent decarboxylative condensation reaction of l-serine (l-Ser) and palmitoyl-CoA (PalCoA) to form 3-ketodihydrosphingosine called long chain base (LCB). SPT is also able to metabolize l-alanine (l-Ala) and glycine (Gly), albeit with much lower efficiency. Human SPT is a membrane-bound large protein complex containing SPTLC1/SPTLC2 heterodimer as the core subunits, and it is known that mutations of the SPTLC1/SPTLC2 genes increase the formation of deoxy-type of LCBs derived from l-Ala and Gly to cause some neurodegenerative diseases. In order to study the substrate recognition of SPT, we examined the reactivity of Sphingobacterium multivorum SPT on various amino acids in the presence of PalCoA. The S. multivorum SPT could convert not only l-Ala and Gly but also l-homoserine, in addition to l-Ser, into the corresponding LCBs. Furthermore, we obtained high-quality crystals of the ligand-free form and the binary complexes with a series of amino acids, including a nonproductive amino acid, l-threonine, and determined the structures at 1.40 to 1.55 Å resolutions. The S. multivorum SPT accommodated various amino acid substrates through subtle rearrangements of the active-site amino acid residues and water molecules. It was also suggested that non-active-site residues mutated in the human SPT genes might indirectly influence the substrate specificity by affecting the hydrogen-bonding networks involving the bound substrate, water molecules, and amino acid residues in the active site of this enzyme. Collectively, our results highlight SPT structural features affecting substrate specificity for this stage of sphingolipid biosynthesis.
Topics: Humans; Palmitoyl Coenzyme A; Serine; Serine C-Palmitoyltransferase; Sphingobacterium; Sphingolipids; Substrate Specificity
PubMed: 37030501
DOI: 10.1016/j.jbc.2023.104684 -
Biotechnology For Biofuels and... Mar 2023In a previous study, shaking speed was found to be an important factor affecting the population dynamics and lignocellulose-degrading activities of a synthetic...
BACKGROUND
In a previous study, shaking speed was found to be an important factor affecting the population dynamics and lignocellulose-degrading activities of a synthetic lignocellulolytic microbial consortium composed of the bacteria Sphingobacterium paramultivorum w15, Citrobacter freundii so4, and the fungus Coniochaeta sp. 2T2.1. Here, the gene expression profiles of each strain in this consortium were examined after growth at two shaking speeds (180 and 60 rpm) at three time points (1, 5 and 13 days).
RESULTS
The results indicated that, at 60 rpm, C. freundii so4 switched, to a large extent, from aerobic to flexible (aerobic/microaerophilic/anaerobic) metabolism, resulting in continued slow growth till late stage. In addition, Coniochaeta sp. 2T2.1 tended to occur to a larger extent in the hyphal form, with genes encoding adhesion proteins being highly expressed. Much like at 180 rpm, at 60 rpm, S. paramultivorum w15 and Coniochaeta sp. 2T2.1 were key players in hemicellulose degradation processes, as evidenced from the respective CAZy-specific transcripts. Coniochaeta sp. 2T2.1 exhibited expression of genes encoding arabinoxylan-degrading enzymes (i.e., of CAZy groups GH10, GH11, CE1, CE5 and GH43), whereas, at 180 rpm, some of these genes were suppressed at early stages of growth. Moreover, C. freundii so4 stably expressed genes that were predicted to encode proteins with (1) β-xylosidase/β-glucosidase and (2) peptidoglycan/chitinase activities, (3) stress response- and detoxification-related proteins. Finally, S. paramultivorum w15 showed involvement in vitamin B2 generation in the early stages across the two shaking speeds, while this role was taken over by C. freundii so4 at late stage at 60 rpm.
CONCLUSIONS
We provide evidence that S. paramultivorum w15 is involved in the degradation of mainly hemicellulose and in vitamin B2 production, and C. freundii so4 in the degradation of oligosaccharides or sugar dimers, next to detoxification processes. Coniochaeta sp. 2T2.1 was held to be strongly involved in cellulose and xylan (at early stages), next to lignin modification processes (at later stages). The synergism and alternative functional roles presented in this study enhance the eco-enzymological understanding of the degradation of lignocellulose in this tripartite microbial consortium.
PubMed: 36991472
DOI: 10.1186/s13068-023-02289-0 -
Frontiers in Toxicology 2023Nanoparticles have been proposed as tunable delivery vehicles for targeted treatments and, in some cases, the active therapeutic agents themselves. Despite the promise...
Nanoparticles have been proposed as tunable delivery vehicles for targeted treatments and, in some cases, the active therapeutic agents themselves. Despite the promise of such customizable impacts, little evidence exists to support these claims in the realm of antibiotics. Exploration of the silver and copper nanoparticle antibacterial impacts have been reported with inconsistent results. Here, we investigate the physical, chemical, and bacterial properties of silver and copper core particles stabilized with commonly used surface coatings, namely, polyvinylpyrrolidone (PVP, to confer a neutrally charged surface), cetrimonium bromide (CTAB, positively charged surface), citrate (Cit, negatively charged surface for silver nanoparticles), and ascorbic acid (AA, negatively charged surface for copper nanoparticles. The impacts of these potential antibacterial nanoparticles are measured against three bacterial species spanning deep divisions in the bacterial tree of life and include , , and . Varying dose, core composition, surface coating, and bacterial species revealed that nanoparticle surfaces accounted for most of the variation in antibacterial activity. In all experiments, dose produced a linear inhibitory effect. Surprisingly, bacterial species reacted similarly regardless of evolutionary relatedness. There is a high degree of consistency, effectiveness, and efficacy among PVP silver and copper nanoparticle. These findings have implications for the intentional use of nanotechnology in environmental systems.
PubMed: 36936540
DOI: 10.3389/ftox.2023.1119547 -
Frontiers in Microbiology 2023The antibacterial properties of nanoparticles are of particular interest because of their potential to serve as an alternative therapy to combat antimicrobial...
The antibacterial properties of nanoparticles are of particular interest because of their potential to serve as an alternative therapy to combat antimicrobial resistance. Metal nanoparticles such as silver and copper nanoparticles have been investigated for their antibacterial properties. Silver and copper nanoparticles were synthesized with the surface stabilizing agents cetyltrimethylammonium bromide (CTAB, to confer a positive surface charge) and polyvinyl pyrrolidone (PVP, to confer a neutral surface charge). Minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), and viable plate count assays were used to determine effective doses of silver and copper nanoparticles treatment against , and . Results show that CTAB stabilized silver and copper nanoparticles were more effective antibacterial agents than PVP stabilized metal nanoparticles, with MIC values in a range of 0.003 μM to 0.25 μM for CTAB stabilized metal nanoparticles and 0.25 μM to 2 μM for PVP stabilized metal nanoparticles. The recorded MIC and MBC values of the surface stabilized metal nanoparticles show that they can serve as effective antibacterial agents at low doses.
PubMed: 36846763
DOI: 10.3389/fmicb.2023.1119550 -
Journal of Translational Medicine Feb 2023Gut dysbacteriosis has been reported as one of the etiologies for irritable bowel syndrome (IBS). However, the association between gut microbiota and IBS is still...
BACKGROUND
Gut dysbacteriosis has been reported as one of the etiologies for irritable bowel syndrome (IBS). However, the association between gut microbiota and IBS is still inconclusive.
METHOD
A paired-sample study was designed by retrieving original multicenter 16 s-rRNA data of IBS patients and healthy controls from the GMrepo database. The propensity score matching (PSM) algorithm was applied to reduce confounding bias. The differential analysis of microbiota composition was performed at different taxonomic levels. The co-occurrence network was established. Subgroup analysis was performed to identify specific microbial compositions in different IBS subtypes.
RESULTS
A total of 1522 amplicon samples were initially enrolled. After PSM, 708 individuals (354 IBS and 354 healthy controls) were eligible for further analysis. A total of 1,160 genera were identified. We identified significantly changed taxa in IBS groups (IBS-enriched: the families Enterobacteriaceae, Moraxellaceae and Sphingobacteriaceae; the genera Streptococcus, Bacillus, Enterocloster, Sphingobacterium, Holdemania and Acinetobacter. IBS-depleted: the phyla Firmicutes, Euryarchaeota, Cyanobacteria, Acidobacteria and Lentisphaerae; the families Bifidobacteriaceae, Ruminococcaceae, Methanobacteriaceae and the other 25 families; the genera Faecalibacterium, Bifidobacterium and other 68 genera). The co-occurrence network identified three hub genera and six hub species (including Faecalibacterium prausnitzii) that may be involved in IBS pathophysiology. Strong positive interactions were identified among the Bifidobacterium longum, Bifidobacterium breve and Bifidobacterium adolescentis in the Bifidobacterium community.
CONCLUSION
This study provides quantitative analysis and visualization of the interaction between the gut microbiota and IBS. The identification of key species should be further validated to evaluate their causal relationships with the pathogenesis of IBS.
Topics: Humans; Irritable Bowel Syndrome; Gastrointestinal Microbiome; Bacteria; RNA, Ribosomal, 16S; Feces
PubMed: 36774467
DOI: 10.1186/s12967-023-03953-7