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Letters in Applied Microbiology Jun 2019Desulfovibrio spp. is predominant member of sulphate-reducing bacteria in human gut microbiota. Previous studies indicated that the isolation of Desulfovibrio strains...
Desulfovibrio spp. is predominant member of sulphate-reducing bacteria in human gut microbiota. Previous studies indicated that the isolation of Desulfovibrio strains from human faecal samples is very important to study the roles of human intestinal Desulfovibrio spp. in maintaining healthy states or causing diseases, as well as defining their biological characteristics. However, there are very few reports describing the isolation of Desulfovibrio spp. from human faecal samples. In this study, faecal samples were inoculated into various media containing different components. The enriched culture communities were identified using 16S rRNA gene high-throughput sequencing analysis, enabling us to identify the specific components that enable the enrichment of Desulfovibrio. Using this information, we developed five specific media and identified an effective enrichment medium that produced the highest relative abundance of Desulfovibrio in communities cultured from four faecal samples (26·5, 73·5, 44·7 and 77·6% respectively). In addition, the major non-Desulfovibrio genera were identified. Finally, three species of Desulfovibrio, D. desulfuricans, D. piger and D. legallii were isolated, representing the first time that has D. legallii been isolated from a human gastrointestinal source. SIGNIFICANCE AND IMPACT OF THE STUDY: ost of the human intestinal bacteria have not been cultured because of lack of appropriate culture method and appropriate media. Desulfovibrio spp. is associated with several clinical conditions like inflammatory bowel disease, but until now there are very few reports describing the isolation of Desulfovibrio spp. from human faecal samples. In this study, 16S rRNA gene high-throughput sequencing analysis was applied to screen appropriate enrichment media and selective cultivation of Desulfovibrio. This sequencing-based directed culture method described here can be used for the selective cultivation of gut bacteria of interest.
Topics: Culture Media; Culture Techniques; Desulfovibrio; Feces; Gastrointestinal Microbiome; Gastrointestinal Tract; High-Throughput Nucleotide Sequencing; Humans; RNA, Ribosomal, 16S
PubMed: 30835854
DOI: 10.1111/lam.13149 -
Glycobiology Apr 2016Bacterial N-linking oligosaccharyl transferases (OTase enzymes) transfer lipid-linked glycans to selected proteins in the periplasm and were first described in the...
Bacterial N-linking oligosaccharyl transferases (OTase enzymes) transfer lipid-linked glycans to selected proteins in the periplasm and were first described in the intestinal pathogen Campylobacter jejuni, a member of the ε-proteobacteria-subdivision of bacteria. More recently, orthologues from other ε-proteobacterial Campylobacter and Helicobacter species and a δ-proteobacterium, Desulfovibrio desulfuricans, have been described, suggesting that these two subdivisions of bacteria may be a source of further N-linked protein glycosylation systems. Whole-genome sequencing of both ε- and δ-proteobacteria from deep-sea vent habitats, a rich source of species from these subdivisions, revealed putative ORFs encoding OTase enzymes and associated adjacent glycosyltransferases similar to the C. jejuni N-linked glycosylation locus. We expressed putative OTase ORFs from the deep-sea vent species Nitratiruptor tergarcus, Sulfurovum lithotrophicum and Deferribacter desulfuricans in Escherichia coli and showed that they were able to functionally complement the C. jejuni OTase, CjPglB. The enzymes were shown to possess relaxed glycan specificity, transferring diverse glycan structures and demonstrated different glycosylation sequon specificities. Additionally, a permissive D. desulfuricans acceptor protein was identified, and we provide evidence that the N-linked glycan synthesized by N. tergarcus and S. lithotrophicum contains an acetylated sugar at the reducing end. This work demonstrates that deep-sea vent bacteria encode functional N-glycosylation machineries and are a potential source of biotechnologically important OTase enzymes.
Topics: Escherichia coli; Genome, Bacterial; Glycosylation; Hexosyltransferases; Membrane Proteins; Oceans and Seas; Polysaccharides; Proteobacteria; Substrate Specificity
PubMed: 26610891
DOI: 10.1093/glycob/cwv111 -
Scientific Reports Apr 2019Periodontitis is associated with shifts in the balance of the subgingival microbiome. Many species that predominate in disease have not been isolated from healthy sites,...
Periodontitis is associated with shifts in the balance of the subgingival microbiome. Many species that predominate in disease have not been isolated from healthy sites, raising questions as to the origin of these putative pathogens. The study aim was to determine whether periodontal pathogens could be enriched from pooled saliva, plaque and tongue samples from dentally-healthy adult volunteers using growth media that simulate nutritional aspects of the inflamed subgingival environment. The microbiome was characterised before and after enrichment using established metagenomic approaches, and the data analysed bioinformatically to identify major functional changes. After three weeks, there was a shift from an inoculum in which Streptococcus, Haemophilus, Neisseria, Veillonella and Prevotella species predominated to biofilms comprising an increased abundance of taxa implicated in periodontitis, including Porphyromonas gingivalis, Fretibacterium fastidiosum, Filifactor alocis, Tannerella forsythia, and several Peptostreptococcus and Treponema spp., with concomitant decreases in health-associated species. Sixty-four species were present after enrichment that were undetectable in the inoculum, including Jonquetella anthropi, Desulfovibrio desulfuricans and Dialister invisus. These studies support the Ecological Plaque Hypothesis, providing evidence that putative periodontopathogens are present in health at low levels, but changes to the subgingival nutritional environment increase their competitiveness and drive deleterious changes to biofilm composition.
Topics: Adult; Bacteria; Biofilms; Dental Plaque; Female; Healthy Volunteers; Humans; Male; Phylogeny; Principal Component Analysis; Saliva; Sequence Analysis, DNA; Tongue
PubMed: 30940882
DOI: 10.1038/s41598-019-41882-y -
Revista Espanola de Quimioterapia :... Dec 2023
Identification of curved Gram-negative rods by MALDI-TOF mass spectrometer in a patient with Fournier ́s gangrene. A bacteremia caused by Desulfovibrio desulfuricans and Escherichia coli.
Topics: Humans; Desulfovibrio desulfuricans; Escherichia coli; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Gangrene; Bacteremia; Gram-Negative Bacteria
PubMed: 37767548
DOI: 10.37201/req/026.2023 -
Journal of the American Chemical Society Jan 2020[FeFe] hydrogenases are extremely active H-converting enzymes. Their mechanism remains highly controversial, in particular, the nature of the one-electron and...
[FeFe] hydrogenases are extremely active H-converting enzymes. Their mechanism remains highly controversial, in particular, the nature of the one-electron and two-electron reduced intermediates called HH and HH. In one model, the HH and HH states contain a semibridging CO, while in the other model, the bridging CO is replaced by a bridging hydride. Using low-temperature IR spectroscopy and nuclear resonance vibrational spectroscopy, together with density functional theory calculations, we show that the bridging CO is retained in the HH and HH states in the [FeFe] hydrogenases from and , respectively. Furthermore, there is no evidence for a bridging hydride in either state. These results agree with a model of the catalytic cycle in which the HH and HH states are integral, catalytically competent components. We conclude that proton-coupled electron transfer between the two subclusters is crucial to catalysis and allows these enzymes to operate in a highly efficient and reversible manner.
Topics: Carbon Monoxide; Chlamydomonas reinhardtii; Density Functional Theory; Desulfovibrio desulfuricans; Electron Transport; Hydrogenase; Iron-Sulfur Proteins; Nuclear Magnetic Resonance, Biomolecular; Spectroscopy, Fourier Transform Infrared
PubMed: 31820961
DOI: 10.1021/jacs.9b09745 -
Applied and Environmental Microbiology Jul 2019Methylmercury (MeHg) is a potent bioaccumulative neurotoxin that is produced by certain anaerobic bacteria and archaea. Mercury (Hg) methylation has been linked to the...
Methylmercury (MeHg) is a potent bioaccumulative neurotoxin that is produced by certain anaerobic bacteria and archaea. Mercury (Hg) methylation has been linked to the gene pair , which encodes a membrane-associated corrinoid protein and a ferredoxin. Although microbial Hg methylation has been characterized , the cellular biochemistry and the specific roles of the gene products HgcA and HgcB in Hg methylation are not well understood. Here, we report the kinetics of Hg methylation in cell lysates of ND132 at nanomolar Hg concentrations. The enzymatic Hg methylation mediated by HgcAB is highly oxygen sensitive, irreversible, and follows Michaelis-Menten kinetics, with an apparent of 3.2 nM and of 19.7 fmol · min · mg total protein for the substrate Hg(II). Although the abundance of HgcAB in the cell lysates is extremely low, Hg(II) was quantitatively converted to MeHg at subnanomolar substrate concentrations. Interestingly, increasing thiol/Hg(II) ratios did not impact Hg methylation rates, which suggests that HgcAB-mediated Hg methylation effectively competes with cellular thiols for Hg(II), consistent with the low apparent Supplementation of 5-methyltetrahydrofolate or pyruvate did not enhance MeHg production, while both ATP and a nonhydrolyzable ATP analog decreased Hg methylation rates in cell lysates under the experimental conditions. These studies provide insights into the biomolecular processes associated with Hg methylation in anaerobic bacteria. The concentration of Hg in the biosphere has increased dramatically over the last century as a result of industrial activities. The microbial conversion of inorganic Hg to MeHg is a global public health concern due to bioaccumulation and biomagnification of MeHg in food webs. Exposure to neurotoxic MeHg through the consumption of fish represents a significant risk to human health and can result in neuropathies and developmental disorders. Anaerobic microbial communities in sediments and periphyton biofilms have been identified as sources of MeHg in aquatic systems, but the associated biomolecular mechanisms are not fully understood. In the present study, we investigate the biochemical mechanisms and kinetics of MeHg formation by HgcAB in sulfate-reducing bacteria. These findings advance our understanding of microbial MeHg production and may help inform strategies to limit the formation of MeHg in the environment.
Topics: Desulfovibrio desulfuricans; Kinetics; Methylation; Methylmercury Compounds; Water Pollutants, Chemical
PubMed: 31028026
DOI: 10.1128/AEM.00438-19 -
Frontiers in Microbiology 2019Biogas-energy is marginally profitable against the "parasitic" energy demands of processing biomass. Biogas involves microbial fermentation of feedstock hydrolyzate...
Biogas-energy is marginally profitable against the "parasitic" energy demands of processing biomass. Biogas involves microbial fermentation of feedstock hydrolyzate generated enzymatically or thermochemically. The latter also produces 5-hydroxymethyl furfural (5-HMF) which can be catalytically upgraded to 2, 5-dimethyl furan (DMF), a "drop in fuel." An integrated process is proposed with side-stream upgrading into DMF to mitigate the "parasitic" energy demand. 5-HMF was upgraded using bacterially-supported Pd/Ru catalysts. Purpose-growth of bacteria adds additional process costs; Pd/Ru catalysts biofabricated using the sulfate-reducing bacterium (SRB) were compared to those generated from a waste consortium of acidophilic sulfidogens (CAS). Methyl tetrahydrofuran (MTHF) was used as the extraction-reaction solvent to compare the use of bio-metallic Pd/Ru catalysts to upgrade 5-HMF to DMF from starch and cellulose hydrolyzates. MTHF extracted up to 65% of the 5-HMF, delivering solutions, respectively, containing 8.8 and 2.2 g 5-HMF/L MTHF. Commercial 5% (wt/wt) Ru-carbon catalyst upgraded 5-HMF from pure solution but it was ineffective against the hydrolyzates. Both types of bacterial catalyst (5wt%Pd/3-5wt% Ru) achieved this, bio-Pd/Ru on the CAS delivering the highest conversion yields. The yield of 5-HMF from starch-cellulose thermal treatment to 2,5 DMF was 224 and 127 g DMF/kg extracted 5-HMF, respectively, for CAS and catalysts, which would provide additional energy of 2.1 and 1.2 kWh/kg extracted 5-HMF. The CAS comprised a mixed population with three patterns of metallic nanoparticle (NP) deposition. Types I and II showed cell surface-localization of the Pd/Ru while type III localized NPs throughout the cell surface and cytoplasm. No metallic patterning in the NPs was shown via elemental mapping using energy dispersive X-ray microanalysis but co-localization with sulfur was observed. Analysis of the cell surfaces of the bulk populations by X-ray photoelectron spectroscopy confirmed the higher S content of the CAS bacteria as compared to and also the presence of Pd-S as well as Ru-S compounds and hence a mixed deposit of PdS, Pd(0), and Ru in the form of various +3, +4, and +6 oxidation states. The results are discussed in the context of recently-reported controlled palladium sulfide ensembles for an improved hydrogenation catalyst.
PubMed: 31134018
DOI: 10.3389/fmicb.2019.00970 -
Scientific Reports Nov 2020Hydrogen is a key intermediate element in microbial electrosynthesis as a mediator of the reduction of carbon dioxide (CO) into added value compounds. In the present...
Hydrogen is a key intermediate element in microbial electrosynthesis as a mediator of the reduction of carbon dioxide (CO) into added value compounds. In the present work we aimed at studying the biological production of hydrogen in biocathodes operated at - 1.0 V vs. Ag/AgCl, using a highly comparable technology and CO as carbon feedstock. Ten bacterial strains were chosen from genera Rhodobacter, Rhodopseudomonas, Rhodocyclus, Desulfovibrio and Sporomusa, all described as hydrogen producing candidates. Monospecific biofilms were formed on carbon cloth cathodes and hydrogen evolution was constantly monitored using a microsensor. Eight over ten bacteria strains showed electroactivity and H production rates increased significantly (two to eightfold) compared to abiotic conditions for two of them (Desulfovibrio paquesii and Desulfovibrio desulfuricans). D. paquesii DSM 16681 exhibited the highest production rate (45.6 ± 18.8 µM min) compared to abiotic conditions (5.5 ± 0.6 µM min), although specific production rates (per 16S rRNA copy) were similar to those obtained for other strains. This study demonstrated that many microorganisms are suspected to participate in net hydrogen production but inherent differences among strains do occur, which are relevant for future developments of resilient biofilm coated cathodes as a stable hydrogen production platform in microbial electrosynthesis.
Topics: Bacteria; Bacterial Physiological Phenomena; Bioelectric Energy Sources; Biofilms; Biosensing Techniques; Electrochemical Techniques; Hydrogen; RNA, Ribosomal, 16S; Stress, Physiological
PubMed: 33199799
DOI: 10.1038/s41598-020-76694-y -
Biochemistry Sep 2023Nickel-substituted rubredoxin (NiRd) from has previously been shown to act as both a structural and functional mimic of the [NiFe] hydrogenase. However, improvements...
Nickel-substituted rubredoxin (NiRd) from has previously been shown to act as both a structural and functional mimic of the [NiFe] hydrogenase. However, improvements both in turnover frequency and overpotential are needed to rival the native [NiFe] hydrogenase enzymes. Characterization of a library of NiRd mutants with variations in the secondary coordination sphere suggested that protein dynamics played a substantial role in modulating activity. In this work, rubredoxin scaffolds were selected from diverse organisms to study the effects of distal sequence variation on catalytic activity. It was found that though electrochemical catalytic activity was only slightly impacted across the series, the Rd sequence from a psychrophilic organism exhibited substantially higher levels of solution-phase hydrogen production. Additionally, Eyring analyses suggest that catalytic activation properties relate to the growth temperature of the parent organism, implying that the general correlation between the parent organism environment and catalytic activity often seen in naturally occurring enzymes may also be observed in artificial enzymes. Selecting protein scaffolds from hosts that inhabit diverse environments, particularly low-temperature environments, represents an alternative approach for engineering artificial metalloenzymes.
Topics: Hydrogenase; Rubredoxins; Catalysis; Oxidation-Reduction
PubMed: 37579005
DOI: 10.1021/acs.biochem.3c00249 -
Direct electrochemical reduction of carbon dioxide by a molybdenum-containing formate dehydrogenase.Journal of Inorganic Biochemistry Jul 2019Formate dehydrogenase enzymes catalyse the reversible two-electron oxidation of formate to carbon dioxide. The class of metal-dependent formate dehydrogenases comprises...
Formate dehydrogenase enzymes catalyse the reversible two-electron oxidation of formate to carbon dioxide. The class of metal-dependent formate dehydrogenases comprises prokaryotic enzymes holding redox-active centres and a catalytic site, containing either molybdenum or tungsten ion, that mediates the formate/carbon dioxide interconversion. The carbon dioxide reduction is of a particular interest, since it may be a route for its atmospheric mitigation with the simultaneous production of added-value products, as formate-derived compounds. Recently, the periplasmic formate dehydrogenase from Desulfovibrio desulfuricans, a molybdenum-containing enzyme, was proven to be an efficient enzyme for the CO reduction to formate. In this work, the immobilized formate dehydrogenase isolated from Desulfovibrio desulfuricans direct electrochemical behaviour was attained in the presence and absence of substrates and the formal potentials associated with the catalytic centre transitions were determined in non-turnover conditions. The enzyme catalytic activity towards carbon dioxide reduction was observed using direct electrochemical methods.
Topics: Carbon Dioxide; Catalysis; Desulfovibrio desulfuricans; Formate Dehydrogenases; Kinetics; Molybdenum; Oxidation-Reduction
PubMed: 31005821
DOI: 10.1016/j.jinorgbio.2019.110694