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Journal of Autoimmunity Feb 2019Dysbiosis¸ i.e. changes in microbial composition at a mucosal interface, is implicated in the pathogenesis of many chronic inflammatory and autoimmune diseases. To...
Dysbiosis¸ i.e. changes in microbial composition at a mucosal interface, is implicated in the pathogenesis of many chronic inflammatory and autoimmune diseases. To assess the composition of the microbial upper respiratory tract (URT) community in patients with granulomatosis with polyangiitis (GPA), we used culture-independent high-throughput methods. In this prospective clinical study, nasal swabs were collected from patients with GPA, patients with rheumatoid arthritis (RA, disease control), and healthy controls. Nasal bacterial taxa were assessed using V3-V4 region 16S rRNA amplicon sequencing. Staphylococcus aureus, Haemophilus influenza, and entero- and rhinoviruses were detected using qPCR. Unbiased metagenomic RNA sequencing (UMERS) was performed in a subset of samples to determine the relative abundance of bacterial, fungal, and viral species. A trend toward reduced microbiome diversity was detected in GPA samples compared with healthy controls. The abundance of bacterial taxa and microbial richness were significantly decreased in GPA samples compared with RA samples. The relative abundance of bacterial families shifted, with increased Planococcaceae and decreased Moraxellaceae, Tissierellaceae, Staphylococcaceae, and Propionibacteriaceae in GPA and RA. Further, decreased abundance of Corynebacteriaceae, and Aerococcaceae was observed in GPA samples. Significantly more colonization of S. aureus was seen in the nasal microbiome of GPA compared with RA and healthy control samples. H. influenzae colonization was also observed in GPA samples. UMERS detected the presence of rhinoviral sequences in some GPA samples. Thus, our study uncovered changes in the URT microbial composition in patients with GPA and RA, suggesting that both immunosuppression and disease background affect the URT microbiome. Complex alterations of host-microbiome interactions in the URT could influence chronic endonasal inflammation in GPA.
Topics: Adolescent; Adult; Aged; Aged, 80 and over; Arthritis, Rheumatoid; Biodiversity; Case-Control Studies; Computational Biology; Disease Susceptibility; Dysbiosis; Female; Granulomatosis with Polyangiitis; Humans; Male; Metagenomics; Microbiota; Middle Aged; RNA, Ribosomal, 16S; Respiratory Mucosa; Young Adult
PubMed: 30420263
DOI: 10.1016/j.jaut.2018.10.005 -
Acta Crystallographica. Section F,... Nov 2018The determination of conditions for the reproducible growth of well diffracting crystals is a critical step in every biocrystallographic study. On the occasion of a new...
The determination of conditions for the reproducible growth of well diffracting crystals is a critical step in every biocrystallographic study. On the occasion of a new structural biology project, several advanced crystallogenesis approaches were tested in order to increase the success rate of crystallization. These methods included screening by microseed matrix screening, optimization by counter-diffusion and crystal detection by trace fluorescent labeling, and are easily accessible to any laboratory. Their combination proved to be particularly efficient in the case of the target, a 48 kDa CCA-adding enzyme from the psychrophilic bacterium Planococcus halocryophilus. A workflow summarizes the overall strategy, which led to the production of crystals that diffracted to better than 2 Å resolution and may be of general interest for a variety of applications.
Topics: Bacterial Proteins; Crystallization; Crystallography, X-Ray; Escherichia coli; Planococcus Bacteria; RNA Nucleotidyltransferases; Recombinant Proteins; Workflow
PubMed: 30387781
DOI: 10.1107/S2053230X18014590 -
Molecules (Basel, Switzerland) Oct 2018Phenolic inhibitors generated during alkaline pretreatment of lignocellulosic biomasses significantly hinder bacterial growth and subsequent biofuel and biochemical...
Phenolic inhibitors generated during alkaline pretreatment of lignocellulosic biomasses significantly hinder bacterial growth and subsequent biofuel and biochemical production. Water rinsing is an efficient method for removing these compounds. Nevertheless, this method often generates a great amount of wastewater, and leads to the loss of solid fiber particles and fermentable sugars. LAM0618, a recently identified microorganism, was herein shown to be able to efficiently transform phenolic compounds (syringaldehyde, hydroxybenzaldehyde, and vanillin) into less toxic acids. Taking advantage of these properties, a biodetoxification method was established by inoculating LAM0618 into the NH₃/H₂O₂-pretreated unwashed corn stover to degrade phenolic inhibitors and weak acids generated during the pretreatment. Subsequently, 33.47 and 17.91 g/L lactic acid was produced by LA204 at 50 °C through simultaneous saccharification and fermentation (SSF) from 8% (/) of NH₃/H₂O₂-pretreated corn stover with or without LAM0618-biodetoxification, indicating biodetoxification significantly increased lactic acid titer and yield. Importantly, using 15% (/) of the NH₃/H₂O₂-pretreated LAM0618-biodetoxified corn stover as a substrate through fed-batch simultaneous saccharification and fermentation, high titer and high yield of lactic acid (84.49 g/L and 0.56 g/g corn stover, respectively, with a productivity of 0.88 g/L/h) were produced by LA204. Therefore, this study reported the first study on biodetoxification of alkaline-pretreated lignocellulosic material, and this biodetoxification method could replace water rinsing for removal of phenolic inhibitors and applied in biofuel and biochemical production using the alkaline-pretreated lignocellulosic bioresources.
Topics: Batch Cell Culture Techniques; Benzaldehydes; Biodegradation, Environmental; Biomass; Bioreactors; Fermentation; Lactic Acid; Lignin; Planococcaceae; Zea mays
PubMed: 30322101
DOI: 10.3390/molecules23102626 -
Microbial Biotechnology Mar 2019The disposal of reject brine, a highly concentrated waste by-product generated by various industrial processes, represents a major economic and environmental challenge....
The disposal of reject brine, a highly concentrated waste by-product generated by various industrial processes, represents a major economic and environmental challenge. The common practice in dealing with the large amounts of brine generated is to dispose of it in a pond and allow it to evaporate. The rate of evaporation is therefore a key factor in the effectiveness of the management of these ponds. The addition of various dyes has previously been used as a method to increase the evaporation rate. In this study, a biological approach, using pigmented halophilic bacteria (as opposed to chemical dyes), was assessed. Two bacteria, an Arthrobacter sp. and a Planococcus sp. were selected due to their ability to increase the evaporation of synthetic brine. When using industrial brine, supplementation of the brine with an iron source was required to maintain the pigment production. Under these conditions, the Planococcus sp. CP5-4 produced a carotenoid-like pigment, which resulted in a 20% increase in the evaporation rate of the brine. Thus, the pigment production capability of halophilic bacteria could potentially be exploited as an effective step in the management of industrial reject brines, analogous to the crystallizer ponds used to mine salt from sea water.
Topics: Arthrobacter; Biotechnology; Iron; Pigments, Biological; Planococcus Bacteria; Salts; Waste Disposal, Fluid; Water Purification
PubMed: 30277309
DOI: 10.1111/1751-7915.13319 -
PloS One 2018The weak interlayer refers to the filling material in shear belts or large-scale structural planes, which is usually composed of soil, fine sand and gravels. It is prone...
The weak interlayer refers to the filling material in shear belts or large-scale structural planes, which is usually composed of soil, fine sand and gravels. It is prone to argillization when encountering water and its mechanical strength and stiffness are generally low, which has adverse effects on the stability of underground structures. In recent years, research on reinforcement techniques for weak interlayers has been a hot topic in geotechnical field. As a new reinforcement method for structural planes, the microbial healing technique has attracted a lot of attention. In this paper, a study on the healing technique for weak interlayer based on microbially induced calcium carbonate precipitation (MICP) and related mechanical properties was conducted for the interlayer shear belt at Baihetan Hydropower Station in China. First, Sporosarcina pasteurii was activated in laboratory. Reinforcement of the weak interlayer was realized by utilizing calcium carbonate precipitation on the weak interlayer. Continuous monitoring of the precipitates on the weak interlayer by XRD and SEM indicated that the precipitates on the weak layer were microbially induced calcium carbonate. Its crystals were irregular fish scale-shaped cubes with size in the range of 5~20μm. With favorable crystal growth, the crystals and the particles of the weak interlayer were cemented together. Finally, the mechanical properties of the healed weak interlayer were tested and the variations of uniaxial compressive strength, shear strength and triaxial compressive strength with bacteria concentration were discussed. The test results indicated that the maximum uniaxial compressive strength, peak shear strength and triaxial compressive strength can be increased by 149%, 162% and 119%, respectively, which subsequently improve the overall strength of the shear zone or structural plane. This can provide a new idea for soft ground reinforcement in underground projects.
Topics: Calcium Carbonate; Chemical Precipitation; Construction Industry; Microscopy, Electron, Scanning; Power Plants; Shear Strength; Soil Microbiology; Sporosarcina
PubMed: 30212556
DOI: 10.1371/journal.pone.0203834 -
IET Nanobiotechnology Aug 2018Here, extracellular synthesis of silver nanoparticles (AgNPs) was carried out by strain BGCC-51 isolated from dye industry effluent soil. The microbes were isolated,...
Here, extracellular synthesis of silver nanoparticles (AgNPs) was carried out by strain BGCC-51 isolated from dye industry effluent soil. The microbes were isolated, screened, and characterised by molecular analysis (accession number KX776160). The optimisation of synthesis of AgNPs to determine the optimum substrate level (1-5 mM), pH (5-9), and temperature (25-55°C) were further carried out. strain BGCC-51 gave best yield of AgNPs at substrate concentration 5 mM, pH 8, and at 35°C. Synthesised AgNPs were characterised by scanning electron microscope and high-resolution transmission electron microscope. The size of synthesised AgNPs was in the range of 20-40 nm having spherical morphology. The AgNPs were found to show antimicrobial activity against bacteria such as (ATCC 25922), (ATCC 27853), and (ATCC 29213).
Topics: Biotechnology; Coloring Agents; Extracellular Space; Metal Nanoparticles; Oxidation-Reduction; Planococcaceae; Silver; Soil Microbiology; Textile Industry
PubMed: 30095422
DOI: 10.1049/iet-nbt.2017.0251 -
Hepatology Research : the Official... Dec 2018Cirrhosis is a leading cause of death worldwide, yet there are no well-established risk stratifying tools for lethal complications, including hepatocellular carcinoma...
AIM
Cirrhosis is a leading cause of death worldwide, yet there are no well-established risk stratifying tools for lethal complications, including hepatocellular carcinoma (HCC). Patients with liver cirrhosis undergo routine endoscopic surveillance, providing ready access to duodenal aspirate samples that could be a source for identifying novel biomarkers. The aim of this study was to characterize the microbiome and bile acid profiles in duodenal aspirates from patients with liver cirrhosis to assess the feasibility of developing biomarkers for HCC risk stratification.
METHODS
Thirty patients with liver cirrhosis were enrolled in the Microbiome, Microbial Markers, and Liver Disease study between May 2015 and March 2017. Detailed clinical and epidemiological data were collected at baseline and at 6-monthly follow-up visits. Duodenal aspirate fluid was collected at baseline for microbial characterization using 16S ribosomal RNA sequencing and bile acid quantification using mass spectroscopy.
RESULTS
Alcohol-related cirrhosis was associated with reductions in the Bacteroidetes phylum, particularly Prevotella (13-fold reduction), and expansion of Staphylococcus (13-fold increase), compared to hepatitis C virus-related cirrhosis. Participants with hepatic encephalopathy (HE) had less microbial diversity compared to patients without HE (P < 0.05), and were characterized by expansion of Mycobacterium (45-fold increase) and Gram-positive cocci including Granulicatella (3.1-fold increase), unclassified Planococcaceae (3.3-fold increase), and unclassified Streptococcaceae (4.5-fold increase). Non-Hispanic White patients had reduced microbial richness (P < 0.01) and diversity (P < 0.05), and increased levels of conjugated ursodeoxycholic acid (glycoursodeoxycholic acid and tauroursodeoxycholic acid, P < 0.05) compared to Hispanic patients.
CONCLUSION
Microbial profiles of duodenal aspirates differed by cirrhosis etiology, HE, and Hispanic ethnicity.
PubMed: 29923681
DOI: 10.1111/hepr.13207 -
Proteins Sep 2018Intracellular subtilisin proteases (ISPs) have important roles in protein processing during the stationary phase in bacteria. Their unregulated protein degrading...
Intracellular subtilisin proteases (ISPs) have important roles in protein processing during the stationary phase in bacteria. Their unregulated protein degrading activity may have adverse effects inside a cell, but little is known about their regulatory mechanism. Until now, ISPs have mostly been described from Bacillus species, with structural data from a single homolog. Here, we study a marine ISP originating from a phylogenetically distinct genus, Planococcus sp. The enzyme was successfully overexpressed in E. coli, and is active in presence of calcium, which is thought to have a role in minor, but essential, structural rearrangements needed for catalytic activity. The ISP operates at alkaline pH and at moderate temperatures, and has a corresponding melting temperature around 60 °C. The high-resolution 3-dimensional structure reported here, represents an ISP with an intact catalytic triad albeit in a configuration with an inhibitory pro-peptide bound. The pro-peptide is removed in other homologs, but the removal of the pro-peptide from the Planococcus sp. AW02J18 ISP appears to be different, and possibly involves several steps. A first processing step is described here as the removal of 2 immediate N-terminal residues. Furthermore, the pro-peptide contains a conserved LIPY/F-motif, which was found to be involved in inhibition of the catalytic activity.
Topics: Aquatic Organisms; Calcium; Catalysis; Endopeptidases; Escherichia coli; Hydrogen-Ion Concentration; Mutation; Peptides; Planococcus Bacteria; Protein Processing, Post-Translational; Recombinant Proteins; Subtilisins; Temperature
PubMed: 29907987
DOI: 10.1002/prot.25528 -
Scientific Reports May 2018Dihydrodipicolinate reductase (DHDPR) is a key enzyme in the diaminopimelate- and lysine-synthesis pathways that reduces DHDP to tetrahydrodipicolinate. Although DHDPR...
Dihydrodipicolinate reductase (DHDPR) is a key enzyme in the diaminopimelate- and lysine-synthesis pathways that reduces DHDP to tetrahydrodipicolinate. Although DHDPR uses both NADPH and NADH as a cofactor, the structural basis for cofactor specificity and preference remains unclear. Here, we report that Paenisporosarcina sp. TG-14 PaDHDPR has a strong preference for NADPH over NADH, as determined by isothermal titration calorimetry and enzymatic activity assays. We determined the crystal structures of PaDHDPR alone, with its competitive inhibitor (dipicolinate), and the ternary complex of the enzyme with dipicolinate and NADPH, with results showing that only the ternary complex had a fully closed conformation and suggesting that binding of both substrate and nucleotide cofactor is required for enzymatic activity. Moreover, NADPH binding induced local conformational changes in the N-terminal long loop (residues 34-59) of PaDHDPR, as the His35 and Lys36 residues in this loop interacted with the 2'-phosphate group of NADPH, possibly accounting for the strong preference of PaDHDPR for NADPH. Mutation of these residues revealed reduced NADPH binding and enzymatic activity, confirming their importance in NADPH binding. These findings provide insight into the mechanism of action and cofactor selectivity of this important bacterial enzyme.
Topics: Amino Acid Sequence; Crystallography, X-Ray; Dihydrodipicolinate Reductase; Kinetics; Models, Molecular; NADP; Planococcaceae; Protein Conformation; Sequence Homology; Substrate Specificity
PubMed: 29786696
DOI: 10.1038/s41598-018-26291-x -
Frontiers in Microbiology 2018is a ubiquitous member of marine biofilm, and reduces thiosulfate to produce toxic hydrogen sulfide gas. In this study, lytic bacteriophages were isolated and applied...
is a ubiquitous member of marine biofilm, and reduces thiosulfate to produce toxic hydrogen sulfide gas. In this study, lytic bacteriophages were isolated and applied to inhibit the growth of in planktonic mode at different temperature, pH, and salinity. Bacteriophages showed optimal infectivity at a multiplicity of infection of 10 in saline conditions, and demonstrated lytic abilities over all tested temperature (25, 30, 37, and 45°C) and pH 6-9. Planktonic exhibited significantly longer lag phase and lower specific growth rates upon exposure to bacteriophages. Bacteriophages were subsequently applied to -enriched biofilm and were determined to lower the relative abundance of -related taxa from 0.17 to 5.58% in controls to 0.01-0.61% in treated microbial communities. The relative abundance of , and decreased, possibly due to the phage-induced disruption of the biofilm matrix. Lastly, when applied to mitigate biofouling of ultrafiltration membranes, bacteriophages were determined to reduce the transmembrane pressure increase by 18% when utilized alone, and by 49% when used in combination with citric acid. The combined treatment was more effective compared with the citric acid treatment alone, which reported ca. 30% transmembrane pressure reduction. Collectively, the findings demonstrated that bacteriophages can be used as a biocidal agent to mitigate undesirable -associated problems in seawater applications.
PubMed: 29770130
DOI: 10.3389/fmicb.2018.00875