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BMC Nephrology May 2022Genus Desulfovibrio species is a sulphate-reducing anaerobic gram-negative rod that resides in the human oral cavity and intestinal tract. It was reported as the... (Review)
Review
BACKGROUND
Genus Desulfovibrio species is a sulphate-reducing anaerobic gram-negative rod that resides in the human oral cavity and intestinal tract. It was reported as the causative pathogen of bacteraemia and abdominal infections, but not renal cyst infection, and Desulfovibrio fairfieldensis has higher pathogenicity than other Desulfovibrio species.
CASE PRESENTATION
A 63-year-old man was on haemodialysis for end-stage renal failure due to autosomal dominant polycystic kidney disease. On admission, he had a persistent high-grade fever, right lumbar back pain, and elevated C-reactive protein levels. His blood and urine cultures were negative. He received ciprofloxacin and meropenem; however, there was no clinical improvement. Contrast-enhanced computed tomography and plain magnetic resonance imaging revealed a haemorrhagic cyst at the upper pole of the right kidney. The lesion was drained. Although the drainage fluid culture was negative, D. fairfieldensis was detected in a renal cyst using a polymerase chain reaction. After the renal cyst drainage, he was treated with oral metronidazole and improved without any relapse.
CONCLUSIONS
To the best of our knowledge, this is the first reported case of a renal cyst infection with Desulfovibrio species. D. fairfieldensis is difficult to detect, and polymerase chain reaction tests can detect this bacterium and ensure better management for a successful recovery.
Topics: Bacteremia; Cysts; Desulfovibrio; Humans; Male; Middle Aged; Neoplasm Recurrence, Local; Polycystic Kidney, Autosomal Dominant
PubMed: 35606754
DOI: 10.1186/s12882-022-02803-w -
International Journal of Systematic and... Feb 2021A novel sulphate-reducing, Gram-stain-negative, anaerobic strain, isolate XJ01, recovered from production fluid at the LiaoHe oilfield, PR China, was the subject of a...
A novel sulphate-reducing, Gram-stain-negative, anaerobic strain, isolate XJ01, recovered from production fluid at the LiaoHe oilfield, PR China, was the subject of a polyphasic study. The isolate together with NCIMB 9442 and DSM 5308 formed a distinct, well-supported clade in the 16S rRNA gene tree. The taxonomic status of the clade was underscored by complementary phenotypic data. The three isolates comprising the clade formed distinct phyletic branches and were distinguished using a combination of physiological features and by low average nucleotide identity and digital DNA-DNA hybridization values. Consequently, it is proposed that isolate XJ01 represents a novel genus and species for which the name gen. nov., sp. nov. is proposed with the type strain XJ01 (=CGMCC 1.5227=DSM 107637). It is also proposed that and be reclassified as comb. nov. and comb. nov., respectively.
Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Desulfovibrio; Desulfovibrionaceae; Fatty Acids; Nucleic Acid Hybridization; Oil and Gas Fields; Oxidation-Reduction; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sulfates; Sulfur-Reducing Bacteria
PubMed: 33406030
DOI: 10.1099/ijsem.0.004618 -
Methods in Enzymology 2016The diffusion of ligands to actives sites of proteins is essential to enzyme catalysis and many cellular signaling processes. In this contribution we review our recently... (Review)
Review
The diffusion of ligands to actives sites of proteins is essential to enzyme catalysis and many cellular signaling processes. In this contribution we review our recently developed methodology for calculation of rate constants for diffusion and binding of small molecules to buried protein active sites. The diffusive dynamics of the ligand obtained from molecular dynamics simulation is coarse grained and described by a Markov state model. Diffusion and binding rate constants are then obtained either from the reactive flux formalism or by fitting the time-dependent population of the Markov state model to a phenomenological rate law. The method is illustrated by applications to diffusion of substrate and inhibitors in [NiFe] hydrogenase, CO-dehydrogenase, and myoglobin. We also discuss a recently developed sensitivity analysis that allows one to identify hot spots in proteins, where mutations are expected to have the strongest effects on ligand diffusion rates.
Topics: Aldehyde Oxidoreductases; Binding Sites; Biocatalysis; Catalytic Domain; Clostridiales; Cluster Analysis; Desulfovibrio gigas; Diffusion; Humans; Hydrogenase; Kinetics; Ligands; Markov Chains; Molecular Dynamics Simulation; Multienzyme Complexes; Mutation; Myoglobin; Protein Binding; Thermodynamics
PubMed: 27497172
DOI: 10.1016/bs.mie.2016.05.039 -
Gut Microbes 2024Diet is a key player in gut-liver axis. However, the effect of different dietary patterns on gut microbiota and liver functions remains unclear. Here, we used rodent...
Diet is a key player in gut-liver axis. However, the effect of different dietary patterns on gut microbiota and liver functions remains unclear. Here, we used rodent standard chow and purified diet to mimic two common human dietary patterns: grain and plant-based diet and refined-food-based diet, respectively and explored their impacts on gut microbiota and liver. Gut microbiota experienced a great shift with notable increase in , gut bile acid (BA) levels elevated significantly, and liver inflammation was observed in mice fed with the purified diet. Liver inflammation and elevated gut BA levels also occurred in mice fed with the chow diet after receiving ATCC 29,577 (DSV). Restriction of sulfur-containing amino acids (SAAs) prevented liver injury mainly through higher hepatic antioxidant and detoxifying ability and reversed the elevated BA levels due to excess . fermentation of human fecal microbiota with primary BAs demonstrated that DSV enhanced production of secondary BAs. Higher concentration of both primary and secondary BAs were found in the gut of germ-free mice after receiving DSV. In conclusion, Restriction of SAAs in diet may become an effective dietary intervention to prevent liver injury associated with excess in the gut.
Topics: Animals; Gastrointestinal Microbiome; Mice; Liver; Humans; Desulfovibrio; Male; Mice, Inbred C57BL; Bile Acids and Salts; Amino Acids; Diet; Feces; Sulfur; Amino Acids, Sulfur
PubMed: 38935546
DOI: 10.1080/19490976.2024.2370634 -
BMC Genomics Nov 2015The σ(54) subunit controls a unique class of promoters in bacteria. Such promoters, without exception, require enhancer binding proteins (EBPs) for transcription...
BACKGROUND
The σ(54) subunit controls a unique class of promoters in bacteria. Such promoters, without exception, require enhancer binding proteins (EBPs) for transcription initiation. Desulfovibrio vulgaris Hildenborough, a model bacterium for sulfate reduction studies, has a high number of EBPs, more than most sequenced bacteria. The cellular processes regulated by many of these EBPs remain unknown.
RESULTS
To characterize the σ(54)-dependent regulome of D. vulgaris Hildenborough, we identified EBP binding motifs and regulated genes by a combination of computational and experimental techniques. These predictions were supported by our reconstruction of σ(54)-dependent promoters by comparative genomics. We reassessed and refined the results of earlier studies on regulation in D. vulgaris Hildenborough and consolidated them with our new findings. It allowed us to reconstruct the σ(54) regulome in D. vulgaris Hildenborough. This regulome includes 36 regulons that consist of 201 coding genes and 4 non-coding RNAs, and is involved in nitrogen, carbon and energy metabolism, regulation, transmembrane transport and various extracellular functions. To the best of our knowledge, this is the first report of direct regulation of alanine dehydrogenase, pyruvate metabolism genes and type III secretion system by σ(54)-dependent regulators.
CONCLUSIONS
The σ(54)-dependent regulome is an important component of transcriptional regulatory network in D. vulgaris Hildenborough and related free-living Deltaproteobacteria. Our study provides a representative collection of σ(54)-dependent regulons that can be used for regulation prediction in Deltaproteobacteria and other taxa.
Topics: Bacterial Proteins; Binding Sites; Cluster Analysis; DNA-Binding Proteins; Desulfovibrio vulgaris; Enhancer Elements, Genetic; Gene Expression Regulation, Bacterial; Nucleotide Motifs; Phylogeny; Position-Specific Scoring Matrices; Promoter Regions, Genetic; Protein Binding; Sigma Factor; Transcription Factors; Type III Secretion Systems
PubMed: 26555820
DOI: 10.1186/s12864-015-2176-y -
The Science of the Total Environment Feb 2023Schwertmannite (Sch) is an iron-hydroxysulfate mineral commonly found in acid mine drainage contaminated environment. The transformation mechanism of Sch mediated by...
Schwertmannite (Sch) is an iron-hydroxysulfate mineral commonly found in acid mine drainage contaminated environment. The transformation mechanism of Sch mediated by pure cultured iron-reducing bacteria (FeRB) or sulfate-reducing bacteria (SRB) has been studied. However, FeRB and SRB widely coexist in the environment, the mechanism of Sch transformation by the consortia of FeRB and SRB is still unclear. This study investigated the Sch reduction by co-cultured Shewanella oneidensis (FeRB) and Desulfosporosinus meridiei (SRB). The results showed that co-culture of FeRB and SRB could accelerate the reductive dissolution of Sch, but not synergistically, and there were two distinct phases in the reduction of Sch mediated by FeRB and SRB: an initial phase in which FeRB predominated and Fe in Sch was reduced, accompanied with the release of SO, and the detected secondary minerals were mainly vivianite; the second phase in which SRB predominated and mediated the reduction of SO, producing minerals including mackinawite and siderite in addition to vivianite. Compared to pure culture, the abundance of FeRB and SRB in the consortia decreased, and more minerals aggregated inside and outside the cell; correspondingly, the transcription levels of genes (cymA, omcA, and mtrCBA) related to Fe reduction in co-culture was down-regulated, while the transcription levels of SO-reducing genes (sat, aprAB, dsr(C)) was generally up-regulated. These phenomena suggested that secondary minerals produced in co-culture limited but did not inhibit bacterial growth, and the presence of SRB was detrimental to dissimilatory Fe reduction, while existed FeRB was in favor of dissimilatory SO reduction. SRB mediated SO reduction by up-regulating the expression of SO reduction-related genes when its abundance was limited, which may be a strategy to cope with external coercion. These findings allow for a better understanding of the process and mechanism of microbial mediated reduction of Sch in the environment.
Topics: Iron; Coculture Techniques; Ferric Compounds; Minerals; Desulfovibrio; Bacteria; Sulfates; Oxidation-Reduction
PubMed: 36460112
DOI: 10.1016/j.scitotenv.2022.160551 -
Anaerobe Jun 2022Desulfovibrio spp. is a commensal sulfate reducing bacterium that is present in small numbers in the gastrointestinal tract. Increased concentrations of Desulfovibrio...
UNLABELLED
Desulfovibrio spp. is a commensal sulfate reducing bacterium that is present in small numbers in the gastrointestinal tract. Increased concentrations of Desulfovibrio spp. (blooms) have been reported in patients with inflammatory bowel disease and irritable bowel syndrome. Since stress has been reported to exacerbate symptoms of these chronic diseases, this study examined whether the stress catecholamine norepinephrine (NE) promotes Desulfovibrio growth. Norepinephrine-stimulated growth has been reported in other bacterial taxa, and this effect may depend on the availability of the micronutrient iron.
OBJECTIVES
This study tested whether norepinephrine exposure affects the in vitro growth of Desulfovibrio vulgaris in an iron dependent manner.
METHODS
DSV was incubated in a growth medium with and without 1 μm of norepinephrine. An additional growth assay added the iron chelator deferoxamine in NE exposed DSV. Iron regulatory genes were assessed with and without the treatment of NE and Deferoxamine.
RESULTS
We found that norepinephrine significantly increased growth of D. vulgaris. Norepinephrine also increased bacterial production of hydrogen sulfide. Additionally, norepinephrine significantly increased bacterial expression in three of the four tested iron regulatory genes. The iron chelator deferoxamine inhibited growth of D. vulgaris in a dose-dependent manner and reversed the effect of norepinephrine on proliferation of D. vulgaris and on bacterial expression of iron regulatory genes.
CONCLUSION
The data presented in this work suggests that promotion of D. vulgaris growth by norepinephrine is iron dependent.
Topics: Deferoxamine; Desulfovibrio; Desulfovibrio vulgaris; Humans; Iron; Iron Chelating Agents; Norepinephrine
PubMed: 35533828
DOI: 10.1016/j.anaerobe.2022.102582 -
Scientific Reports Jun 2018Bacteria of the genus Desulfovibrio belong to the group of Sulphate Reducing Bacteria (SRB). SRB generate significant liabilities in the petroleum industry, mainly due...
Bacteria of the genus Desulfovibrio belong to the group of Sulphate Reducing Bacteria (SRB). SRB generate significant liabilities in the petroleum industry, mainly due to their ability to microbiologically induce corrosion, biofilm formation and HS production. Bacteriophages are an alternative control method for SRB, whose information for this group of bacteria however, is scarce. The present study developed a workflow for the identification of complete prophages in Desulfovibrio. Poly-lysogenesis was shown to be common in Desulfovibrio. In the 47 genomes analyzed 53 complete prophages were identified. These were classified within the order Caudovirales, with 69.82% belonging to the Myoviridade family. More than half the prophages identified have genes coding for lysozyme or holin. Four of the analyzed bacterial genomes present prophages with identity above 50% in the same strain, whose comparative analysis demonstrated the existence of colinearity between the sequences. Of the 17 closed bacterial genomes analyzed, 6 have the CRISPR-Cas system classified as inactive. The identification of bacterial poly-lysogeny, the proximity between the complete prophages and the possible inactivity of the CRISPR-Cas in closed bacterial genomes analyzed allowed the choice of poly-lysogenic strains with prophages belonging to the Myoviridae family for the isolation of prophages and testing of related strains for subsequent studies.
Topics: CRISPR-Cas Systems; Desulfovibrio; Genome, Bacterial; Phylogeny; Prophages
PubMed: 29915307
DOI: 10.1038/s41598-018-27423-z -
PloS One 2015Akkermansia muciniphila and Desulfovibrio spp. are commensal microbes colonising the mucus gel layer of the colon. Both species have the capacity to utilise colonic...
BACKGROUND
Akkermansia muciniphila and Desulfovibrio spp. are commensal microbes colonising the mucus gel layer of the colon. Both species have the capacity to utilise colonic mucin as a substrate. A. muciniphila degrades colonic mucin, while Desulfovibrio spp. metabolise the sulfate moiety of sulfated mucins. Altered abundances of these microorganisms have been reported in ulcerative colitis (UC). However their capacity to bind to human colonic mucin, and whether this binding capacity is affected by changes in mucin associated with UC, remain to be defined.
METHODS
Mucin was isolated from resected colon from control patients undergoing resection for colonic cancer (n = 7) and patients undergoing resection for UC (n = 5). Isolated mucin was purified and printed onto mucin microarrays. Binding of reference strains and three clinical isolates of A. muciniphila and Desulfovibrio spp. to purified mucin was investigated.
RESULTS
Both A. muciniphila and Desulfovibro spp. bound to mucin. The reference strain and all clinical isolates of A. muciniphila showed increased binding capacity for UC mucin (p < .005). The Desulfovibrio reference strain showed increased affinity for UC mucin. The mucin binding profiles of clinical isolates of Desulfovibrio spp. were specific to each isolate. Two isolates showed no difference in binding. One UC isolate bound with increased affinity to UC mucin (p < .005).
CONCLUSION
These preliminary data suggest that differences exist in the mucin binding capacity of isolates of A. muciniphila and Desulfovibrio spp. This study highlights the mucin microarray platform as a means of studying the ability of bacteria to interact with colonic mucin in health and disease.
Topics: Case-Control Studies; Colitis, Ulcerative; Colon; Desulfovibrio; Glycosylation; Humans; Lectins; Microarray Analysis; Mucins; Verrucomicrobia
PubMed: 26491870
DOI: 10.1371/journal.pone.0135280 -
FEMS Microbiology Letters Mar 2020Short and branched chain fatty acid kinases participate in both bacterial anabolic and catabolic processes, including fermentation, through the reversible, ATP-dependent...
Short and branched chain fatty acid kinases participate in both bacterial anabolic and catabolic processes, including fermentation, through the reversible, ATP-dependent synthesis of acyl phosphates. This study reports biochemical properties of a predicted butyrate kinase from Desulfovibrio vulgaris str. Hildenborough (DvBuk) expressed heterologously and purified from Escherichia coli. Gel filtration chromatography indicates purified DvBuk is active as a dimer. The optimum temperature and pH for DvBuk activity is 44°C and 7.5, respectively. The enzyme displays enhanced thermal stability in the presence of substrates as observed for similar enzymes. Measurement of kcat and KM for various substrates reveals DvBuk exhibits the highest catalytic efficiencies for butyrate, valerate and isobutyrate. In particular, these measurements reveal this enzyme's apparent high affinity for C4 fatty acids relative to other butyrate kinases. These results have implications on structure and function relationships within the ASKHA superfamily of phosphotransferases, particularly regarding the acyl binding pocket, as well as potential physiological roles for this enzyme in Desulfovibrio vulgaris str. Hildenborough.
Topics: Chromatography, Gel; Desulfovibrio vulgaris; Enzyme Stability; Escherichia coli; Hydrogen-Ion Concentration; Phosphotransferases (Carboxyl Group Acceptor); Recombinant Proteins; Structure-Activity Relationship; Temperature
PubMed: 32166312
DOI: 10.1093/femsle/fnaa047