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Frontiers in Medicine 2022To determine whether gut microbiota, fatty metabolism and cytokines were associated with immune thrombocytopenia (ITP).
OBJECTIVE
To determine whether gut microbiota, fatty metabolism and cytokines were associated with immune thrombocytopenia (ITP).
METHODS
In total, 29 preliminarily diagnosed ITP patients and 33 healthy volunteers were enrolled. Fecal bacterial were analyzed based on 16S rRNA sequencing. Plasma cytokines and motabolites were analyzed using flow cytometry and liquid chromatography-mass spectrometry (LC-MS), respectively.
RESULTS
, , and were enriched at the genus level in ITP patients, while , , were depleted. At the phylum level, the relative abundance of and increased in ITP patients, while , , and the ratio decreased. Plasma levels of 5-hydroxyeicosatetraenoic acid (5-HETE), 6-trans-12-epi-leukotriene B4 (6t,12e-LTB), and resolvin D2 (RvD) were upregulated, and stachydrine, dowicide A, dodecanoylcarnitine were downregulated in ITP patients. Furthermore, RvD is positively correlated with order , 5-HETE is positively correlated with genus , and 6t,12e-LTB is positively correlated with genus . In addition, stachydrine is positively correlated with family , dowicide A is positively correlated with class , and dodecanoylcarnitine is positively correlated with order . Plasma levels of interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) were upregulated in ITP patients.
CONCLUSION
Our study revealed a relationship between microbiota and fatty metabolism in ITP. Gut microbiota may participate in the pathogenesis of ITP through affecting cytokine secretion, interfering with fatty metabolism.
PubMed: 35665326
DOI: 10.3389/fmed.2022.810612 -
Microbial Cell Factories Mar 2022The genus Planococcus is comprised of halophilic bacteria generally reported for the production of carotenoid pigments and biosurfactants. In previous work, we showed...
BACKGROUND
The genus Planococcus is comprised of halophilic bacteria generally reported for the production of carotenoid pigments and biosurfactants. In previous work, we showed that the culturing of the orange-pigmented Planococcus sp. CP5-4 isolate increased the evaporation rate of industrial wastewater brine effluent, which we attributed to the orange pigment. This demonstrated the potential application of this bacterium for industrial brine effluent management in evaporation ponds for inland desalination plants. Here we identified a C-carotenoid biosynthetic gene cluster responsible for pigment biosynthesis in Planococcus sp. CP5-4 through isolation of mutants and genome sequencing. We further compare the core genes of the carotenoid biosynthetic gene clusters identified from different Planococcus species' genomes which grouped into gene cluster families containing BGCs linked to different carotenoid product chemotypes. Lastly, LC-MS analysis of saponified and unsaponified pigment extracts obtained from cultures of Planococcus sp. CP5-4, revealed the structure of the main (predominant) glucosylated C-carotenoid fatty acid ester produced by Planococcus sp. CP5-4.
RESULTS
Genome sequence comparisons of isolated mutant strains of Planococcus sp. CP5-4 showed deletions of 146 Kb and 3 Kb for the non-pigmented and "yellow" mutants respectively. Eight candidate genes, likely responsible for C-carotenoid biosynthesis, were identified on the wild-type genome region corresponding to the deleted segment in the non-pigmented mutant. Six of the eight candidate genes formed a biosynthetic gene cluster. A truncation of crtP was responsible for the "yellow" mutant phenotype. Genome annotation revealed that the genes encoded 4,4'-diapolycopene oxygenase (CrtNb), 4,4'- diapolycopen-4-al dehydrogenase (CrtNc), 4,4'-diapophytoene desaturase (CrtN), 4,4'- diaponeurosporene oxygenase (CrtP), glycerol acyltransferase (Agpat), family 2 glucosyl transferase 2 (Gtf2), phytoene/squalene synthase (CrtM), and cytochrome P450 hydroxylase enzymes. Carotenoid analysis showed that a glucosylated C-carotenoid fatty acid ester, methyl 5-(6-C)-glucosyl-5, 6'-dihydro-apo-4, 4'-lycopenoate was the main carotenoid compound produced by Planococcus sp. CP5-4.
CONCLUSION
We identified and characterized the carotenoid biosynthetic gene cluster and the C-carotenoid compound produced by Planococcus sp. CP5-4. Mass-spectrometry guided analysis of the saponified and unsaponified pigment extracts showed that methyl 5-glucosyl-5, 6-dihydro-apo-4, 4'-lycopenoate esterified to heptadecatrienoic acid (C). Furthermore, through phylogenetic analysis of the core carotenoid BGCs of Planococcus species we show that various C-carotenoid product chemotypes, apart from methyl 5-glucosyl-5, 6-dihydro-apo-4, 4'-lycopenoate and 5-glucosyl-4, 4-diaponeurosporen-4'-ol-4-oic acid, may be produced that could offer opportunities for a variety of applications.
Topics: Carotenoids; Multigene Family; Phylogeny; Planococcus Bacteria; South Africa
PubMed: 35305628
DOI: 10.1186/s12934-022-01752-1 -
Environmental Pollution (Barking, Essex... Jul 2022The widely detected pyrene (PYR) is prone to accumulate and pose risks to the soil ecosystem. In this study, an aerobic closed microcosm was constructed to assess the...
The widely detected pyrene (PYR) is prone to accumulate and pose risks to the soil ecosystem. In this study, an aerobic closed microcosm was constructed to assess the effects of PYR at the environmental concentration (12.09 mg kg) on the structure, interactions, and metabolism of carbon sources of soil microbial communities. The results found that half-life of PYR was 37 d and its aerobic biodegradation was mainly implemented by both Gram-negative and Gram-positive bacteria as revealed by the quantitative results. High-throughput sequencing based on 16 S rRNA and ITS genes showed that PYR exposure interfered more significantly with the diversity and abundance of the bacterial community than that of the fungal community. For bacteria, rare species were sensitive to PYR, while Gemmatimonadota, Gaiellales, and Planococcaceae involved in organic pollutants detoxification and degradation were tolerant of PYR stress. Co-occurrence network analysis demonstrated that PYR enhanced the intraspecific cooperation within the bacterial community and altered the patterns of trophic interaction in the fungal community. Furthermore, the keystone taxa and their topological roles were altered, potentially inducing functionality changes. Function annotation suggested PYR inhibited the nitrogen fixation and ammonia oxidation processes but stimulated methylotrophy and methanol oxidation, especially on day 7. For the metabolism, microbial communities accelerated the metabolism of nitrogenous carbon sources (e.g. amine) to meet the physiological needs under PYR stress. This study clarifies the impacts of PYR on the structure, metabolism, and potential N and C cycling functions of soil microbial communities, deepening the knowledge of the environmental risks of PYR.
Topics: Bacteria; Carbon; Microbiota; Pyrenes; Soil; Soil Microbiology
PubMed: 35429592
DOI: 10.1016/j.envpol.2022.119301 -
European Journal of Clinical... Apr 2021Limited available animal and human data suggest an association between dysbiosis of gut microbiota and PCOS. We aimed to determine whether gut microbiota in lean women...
BACKGROUND
Limited available animal and human data suggest an association between dysbiosis of gut microbiota and PCOS. We aimed to determine whether gut microbiota in lean women with PCOS shows any alterations compared to healthy women.
MATERIALS AND METHODS
Twenty-four lean patients with PCOS phenotype A according to the Rotterdam 2003 diagnostic criteria and 22 BMI-matched healthy women were included in this study. Anthropometric, hormonal and biochemical measurements were carried out in all participants. 16S rRNA gene V3-V4 region amplicon sequencing was performed on stool samples. Preprocessing of the raw data was performed using QIIME, and both QIIME and R packages were used for microbiome analysis.
RESULTS
Bacterial richness and diversity did not show a significant difference between patients and controls. Beta diversity was similar between the groups. However, Erysipelotrichaceae, Proteobacteria, Gammaproteobacteria, Enterobacteriaceae, Planococcaceae, Gemmules and Bacillales were significantly abundant in PCOS group according to LEfSe analysis. Clostridium cluster XVII showed increased abundance in patient group, while Clostridium sensustricto and Roseburia were decreased compared to controls. Random forest prediction analysis revealed Clostridium cluster XIVb as the most discriminative feature of patient group and Roseburia for healthy controls. Testosterone and androstenedione were negatively correlated with alpha and phylogenetic diversity.
CONCLUSIONS
Our results suggest that gut microbiome of lean PCOS patients with full phenotype shows compositional alterations with similar bacterial richness and diversity compared to controls and that hyperandrogenism is associated with dysbiosis.
Topics: Androstenedione; Bacillales; Body Mass Index; Case-Control Studies; Clostridium; Enterobacteriaceae; Female; Firmicutes; Gammaproteobacteria; Gastrointestinal Microbiome; Humans; Planococcaceae; Polycystic Ovary Syndrome; Proteobacteria; RNA, Ribosomal, 16S; Testosterone; Young Adult
PubMed: 32991745
DOI: 10.1111/eci.13417 -
Gene May 2022The Tibetan Plateau niche provides unprecedented opportunities to find microbes that are functional and commercial significance. The present study investigated the...
The Tibetan Plateau niche provides unprecedented opportunities to find microbes that are functional and commercial significance. The present study investigated the physiological and genomic characteristics of Planococcus halotolerans Y50 that was isolated from a petroleum-contaminated soil sample from the Qinghai-Tibet Plateau, and it displayed psychrotolerant, antiradiation, and oil-degraded characteristics. Whole genome sequencing indicated that strain Y50 has a 3.52 Mb genome and 44.7% G + C content, and it possesses 3377 CDSs. The presence of a wide range of UV damage repair genes uvrX and uvsE, DNA repair genes radA and recN, superoxide dismutase, peroxiredoxin and dioxygenase genes provided the genomic basis for the adaptation of the plateau environment polluted by petroleum. Related experiments also verified that the Y50 strain could degrade n-alkanes from C-C, and approximately 30% of the total petroleum at 25 °C within 7 days. Meanwhile, strain Y50 could withstand 5 × 10 J/m UVC and 10 KGy gamma ray radiation, and it had strong antioxidant and high radical scavengers for superoxide anion, hydroxyl radical and DPPH. In addition, pan-genome analysis and horizontal gene transfers revealed that strains with different niches have obtained various genes through horizontal gene transfer in the process of evolution, and the more similar their geographical locations, the more similar their members are genetically and ecologically. In conclusion, P. halotolerans Y50 possesses high potential of applications in the bioremediation of alpine hydrocarbons contaminated environment.
Topics: Base Composition; Biodegradation, Environmental; Genome Size; Genome, Bacterial; Petroleum; Phylogeny; Planococcaceae; Soil Microbiology; Tibet; Whole Genome Sequencing
PubMed: 35240255
DOI: 10.1016/j.gene.2022.146368 -
Frontiers in Veterinary Science 2022The horse gut is colonized by a rich and complex microbial community that has important roles in horse physiology, metabolism, nutrition, and immune functions. Fewer...
The horse gut is colonized by a rich and complex microbial community that has important roles in horse physiology, metabolism, nutrition, and immune functions. Fewer across-breed variations in horse gut microbial diversity have been illustrated. In this article, the gut microbiota of Thoroughbred, Mongolian, and Hybrid horses [first filial generation (F1) of Mongolian (maternal) and Thoroughbred (paternal)] were studied by second-generation high-throughput sequencing technology. Differences in gut microbiota composition and function between breeds were determined using diversity and functional prediction analysis. The alpha diversity analysis showed that Thoroughbred horses had a more abundant and diverse gut microbiota, while the diversity of gut microbiota in Hybrid horses was intermediate between Thoroughbred and Mongolian horses. Subsequent cluster analysis showed that Hybrid horses have a microbiota composition more similar to Mongolian horses. LEfSe analysis revealed that the bacterial biomarkers for Thoroughbred horses at the family level were Prevotellaceae, Rikenellaceae, Fibrobacteraceae, p_251_o5, Lactobacillaceae, and uncultured_bacterium_o_WCHB1_41; the bacterial biomarker for Mongolian horses was Planococcaceae; and the bacterial biomarkers for Hybrid horses were Moraxellaceae, Enterobacteriaceae, and Ruminococcaceae. The functional prediction results indicated that the metabolic pathways differ significantly between the breeds. Regarding metabolism, the Hybrid horses had the lowest proportion of the carbohydrate metabolic pathways, while the energy metabolic pathway had the highest proportion. The abundance ratios of the remaining eight metabolic pathways in Hybrid horses were between Thoroughbred and Mongolian horses. In conclusion, the results of this study showed an association between horse breeds and gut microbiota.
PubMed: 35968025
DOI: 10.3389/fvets.2022.920080 -
International Journal of Systematic and... Feb 2022A Gram-stain-positive, aerobic, motile, rod-shaped bacterium, designated strain LAM9210, was isolated from a saline soil sample collected from Lingxian County, Shandong...
A Gram-stain-positive, aerobic, motile, rod-shaped bacterium, designated strain LAM9210, was isolated from a saline soil sample collected from Lingxian County, Shandong Province, PR China. Analysis of the 16S rRNA gene sequence of the isolate revealed highest sequence similarities to the type strain of NCIMB 8841 (97.6 % sequence similarity). The genomic G+C content was 40.4 mol%. The average nucleotide identity and DNA-DNA hybridization values between strain LAM9210 and the type strain of the most closely related species NCIMB 8841 were 73.6 and 20.6 %, respectively. Strain LAM9210 was found to grow at 10-40 °C (optimum, 30 °C), at pH 6.0-10.0 (optimum, pH 9.0) and with 0-6 % (w/v) NaCl (optimum, 0.5 %), respectively. The major fatty acids were anteiso-C and iso-C. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and one unidentified phospholipid. Menaquinone-7 was detected as the predorminant respiratory quinone. Strain LAM9210 contained glycine, lysine, alanine and glutamic acid as the diagnostic amino acids in the cell-wall peptidoglycan. On the basis of phenotypic, phylogenetic and genotypic data, strain LAM9210 is considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is LAM9210 (=CGMCC 1.18607=GDMCC 1.2002=JCM 32514).
Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Salinity; Sequence Analysis, DNA; Soil; Soil Microbiology; Sporosarcina; Vitamin K 2
PubMed: 35171090
DOI: 10.1099/ijsem.0.005244 -
Environmental Science and Pollution... Jul 2022Bio-mediated calcite precipitation potential for multiple heavy metal immobilization in contaminated soils at industrial, waste dump, abandoned mine, and landfill sites...
Bio-mediated calcite precipitation potential for multiple heavy metal immobilization in contaminated soils at industrial, waste dump, abandoned mine, and landfill sites is not explored yet. This study includes investigation of bio-mediated calcite precipitation for strength improvement and immobilization of heavy metals, specifically lead (Pb), zinc (Zn), and hexavalent chromium (Cr(VI)), in contaminated soils. Firstly, the toxicity resistance of bacteria against different concentrations (1000, 2000, 3000, 4000, and 5000 mg/l) of each heavy metals was investigated and observed that Pb and Cr were less toxic to Sporosarcina pasteurii than Zn. The poorly graded sand was spiked with 333-2000 mg/kg concentrations of a selected individual or mixed metal solutions, i.e., 1000 mg/kg and 2000 mg/kg individual concentrations of Pb, Zn, and Cr(VI); 500 mg/kg and 1000 mg/kg concentration of each metal in "Pb and Zn," "Pb and Cr(VI)," and "Zn and Cr(VI)" mixture of heavy metals; and 333 mg/kg and 666 mg/kg concentration of each metal in "Pb, Zn, and Cr(VI)" mixed metal concentration. Contaminated soil was biotreated with Sporosarcina pasteurii and cementation (a solution of urea and calcium chloride dihydrate) solutions for 18 days. Biocemented sand specimens were subjected to testing of hydraulic conductivity, ultrasonic pulse velocity (UPV), unconfined compressive strength (UCS), calcite content, pH, toxicity characteristic leaching procedure (TCLP), X-ray diffraction (XRD), and scanning electron microscopy (SEM). The heavy metal contaminated samples showed decrease in hydraulic conductivity and increase in UPV and UCS after biotreatment; however, the changes in engineering properties were found more moderate than clean biocemented sand. The conversion of Cr(VI) to Cr(III) followed by CrO precipitation in calcite lattice was observed. Zn was precipitated as smithsonite (ZnCO), while no Pb precipitate was identified in XRD results. TCLP leaching showed Pb and Cr immobilized proportional to calcite precipitated amount, and higher calcite amounts yielded levels within regulatory limits. Pb and Cr(VI) immobilization up to 92 % and 94 % was achieved, respectively, in contaminated biocemented sand. Zn was found completely leachable as smithsonite is only stable down to pH~5, and strongly acidic TCLP solution reversed all immobilization at natural soil pH~8-9.
Topics: Calcium Carbonate; Industrial Waste; Metals, Heavy; Sand; Soil; Soil Pollutants; Sporosarcina; Zinc
PubMed: 35253104
DOI: 10.1007/s11356-022-19551-x -
Avian Pathology : Journal of the W.V.P.A Feb 2022[H. Kurth, 1883. Ueber , eine neue Bakterienart. , 1, 97-100] was isolated on 10 unrelated laying hen farms over a period of 15 months. Farmers reported elevated...
[H. Kurth, 1883. Ueber , eine neue Bakterienart. , 1, 97-100] was isolated on 10 unrelated laying hen farms over a period of 15 months. Farmers reported elevated morbidity and mortality rates, and suspected colibacillosis based on the necropsy findings. The most frequently found lesions were perihepatitis, fibrinous peritonitis, salpingitis and oophoritis. Necropsy findings and bacteriological results allowed the diagnosis of colibacillosis. In addition, was isolated from the ovarian follicles (44.44%), liver (22.22%), peritoneum (16.67%), bone marrow (5.56%), spleen (5.56%), and duodenum (5.56%). On all farms, coinfection with was detected, while on some farms other common avian pathogens were found as well. In total, 18 strains were identified and phylogenetically analysed based on the 16S rRNA gene sequences. The results showed some variability of the strains originating from the same farm, although the overall phylogenetic diversity was low, regardless of the geographical location of the farm, age of the flock or date of collection. Embryo lethality assay showed is not able to cause a primary infection. We conclude that may play a role as an opportunistic pathogen for poultry. This is the first report of coinfection of and in laying hens. RESEARCH HIGHLIGHTS is a novel opportunistic pathogen in poultry.Phylogenetic analysis showed low genetic diversity of isolates.Embryo lethality assay showed does not cause primary infections.
Topics: Animals; Chickens; Escherichia coli; Escherichia coli Infections; Female; Phylogeny; Planococcaceae; Poultry; Poultry Diseases; RNA, Ribosomal, 16S
PubMed: 34662527
DOI: 10.1080/03079457.2021.1993132 -
Journal of Biological Inorganic... Sep 2020This review is an attempt to retrace the chronicle that starts from the discovery of the role of nickel as the essential metal ion in urease for the enzymatic catalysis... (Review)
Review
This review is an attempt to retrace the chronicle that starts from the discovery of the role of nickel as the essential metal ion in urease for the enzymatic catalysis of urea, a key step in the biogeochemical cycle of nitrogen on Earth, to the most recent progress in understanding the chemistry of this historical enzyme. Data and facts are presented through the magnifying lenses of the authors, using their best judgment to filter and elaborate on the many facets of the research carried out on this metalloenzyme over the years. The tale is divided in chapters that discuss and describe the results obtained in the subsequent leaps in the knowledge that led from the discovery of a biological role for Ni to the most recent advancements in the comprehension of the relationship between the structure and function of urease. This review is intended not only to focus on the bioinorganic chemistry of this beautiful metal-based catalysis, but also, and maybe primarily, to evoke inspiration and motivation to further explore the realm of bio-based coordination chemistry.
Topics: Bacterial Proteins; Binding Sites; Catalysis; Crystallography, X-Ray; Enterobacter aerogenes; Helicobacter pylori; Nickel; Protein Conformation; Signal Transduction; Sporosarcina; Structure-Activity Relationship; Urease
PubMed: 32809087
DOI: 10.1007/s00775-020-01808-w