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abundance and diversity of mucosa-associated hydrogenotrophic microbes in the healthy human colon.hydrogenotrophic microbiota have a significant impact on colonic health; however, little is known about their diversity and ecology in situ. here, molecular-based methods and multivariate analyses were used to examine the abundance and diversity of mucosa-associated hydrogenotrophic microbes in 90 biopsies collected from right colon, left colon and rectum of 25 healthy subjects. functional genes of all three hydrogenotrophic groups were detected in at least one colonic region of all subjects. me ...201121753800
Lactobacillus salivarius REN counteracted unfavorable 4-nitroquinoline-1-oxide-induced changes in colonic microflora of rats.Probiotics and carcinogens both have a significant effect on the microfloral composition of the human intestine. The objective of this study was to investigate the impact of an important carcinogen, 4-Nitroquinoline-1-Oxide on colonic microflora and the efficacy of the probiotic Lactobacillus salivarius REN as an agent of counteracting these effects. Using denaturing gradient gel electrophoresis (DGGE) combined with redundancy analysis, we demonstrated that both 4-Nitroquinoline-1-Oxide and L. s ...201122203549
Abundance, Diversity and Activity of Sulfate-Reducing Prokaryotes in Heavy Metal-Contaminated Sediment from a Salt Marsh in the Medway Estuary (UK).We investigated the diversity and activity of sulfate-reducing prokaryotes (SRP) in a 3.5-m sediment core taken from a heavy metal-contaminated site in the Medway Estuary, UK. The abundance of SRPs was quantified by qPCR of the dissimilatory sulfite reductase gene ß-subunit (dsrB) and taking into account DNA extraction efficiency. This showed that SRPs were abundant throughout the core with maximum values in the top 50 cm of the sediment core making up 22.4% of the total bacterial community and ...201122124626
Efficacy of natural biocide on control of microbial induced corrosion in oil pipelines mediated by Desulfovibrio vulgaris and Desulfovibrio gigas.We compared the efficacy of a natural biocide with four chemical tetrakishydroxymethyl phosphonium sulfonate, benzyl trimethyl ammonium chloride, and formaldehyde, glutaraldehyde, to control microbial induced corrosion in oil pipelines. The efficacy of biocides were monitored against Desulfovibrio vulgaris and Desulfovibrio gigas in experimental pipes by measuring cell counts, H2S production, Fe(II) production, production of extracellular polymeric substances and structure of biofilm. The treatm ...201122128548
Desulfovibrio desulfuricans Bacteremia in an Immunocompromised Host with a Liver Graft and Ulcerative Colitis.Desulfovibrio spp. are anaerobic, sulfate-reducing, nonfermenting, Gram-negative bacteria found in the digestive tract of humans. Identification of these species with conventional methods is difficult. The reported case of a Desulfovibrio desulfuricans bacteremia occurring in an immunocompromised host with ulcerative colitis confirms that this organism may be a possible opportunistic human pathogen.201222075582
Structural basis for a [4Fe-3S] cluster in the oxygen-tolerant membrane-bound [NiFe]-hydrogenase.Membrane-bound respiratory [NiFe]-hydrogenase (MBH), a H(2)-uptake enzyme found in the periplasmic space of bacteria, catalyses the oxidation of dihydrogen: H(2)???2H(+)?+?2e(-) (ref. 1). In contrast to the well-studied O(2)-sensitive [NiFe]-hydrogenases (referred to as the standard enzymes), MBH has an O(2)-tolerant H(2) oxidation activity; however, the mechanism of O(2) tolerance is unclear. Here we report the crystal structures of Hydrogenovibrio marinus MBH in three different redox condition ...201122002607
Generalized schemes for high-throughput manipulation of the Desulfovibrio vulgaris genome.The ability to conduct advanced functional genomic studies of the thousands of sequenced bacteria has been hampered by the lack of available tools for making high-throughput chromosomal manipulations in a systematic manner that can be applied across diverse species. In this work, we highlight the use of synthetic biological tools to assemble custom suicide vectors with reusable and interchangeable DNA "parts" to facilitate chromosomal modification at designated loci. These constructs enable an a ...201121908633
Characterization of the bacterial community composition in a hypoxic zone induced by Microcystis blooms in Lake Taihu, China.Cyanobacterial blooms have become more frequent as a result of eutrophication in lakes. The accumulation and breakdown of huge cyanobacterial biomasses often cause hypoxia in lakes. However, little is known about microbial diversity in these areas. In this study, we characterized the bacterial community composition of a Microcystis-bloom-induced hypoxic area in Lake Taihu, which is a large, shallow lake, by analysing terminal restriction fragment length polymorphisms of 16S ribosomal RNA genes a ...201122126440
mechanistic and physiological implications of the interplay among iron-sulfur clusters in [fefe]-hydrogenases. a qm/mm perspective.key stereoelectronic properties of desulfovibrio desulfuricans [fefe]-hydrogenase (ddh) were investigated by quantum mechanical description of its complete inorganic core, which includes a fe(6)s(6) active site (the h-cluster), as well as two ancillary fe(4)s(4) assemblies (the f and f' clusters). the partially oxidized, active-ready form of ddh is able to efficiently bind dihydrogen, thus starting h(2) oxidation catalysis. the calculations allow us to unambiguously assign a mixed fe(ii)fe(i) st ...201121942468
systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium.abstract: background: two component regulatory systems are the primary form of signal transduction in bacteria. although genomic binding sites have been determined for several eukaryotic and bacterial transcription factors, comprehensive identification of gene targets of two component response regulators remains challenging due to the lack of knowledge of the signals required for their activation. we focused our study on desulfovibrio vulgaris hildenborough, a sulfate reducing bacterium that en ...201121992415
using gas chromatography/isotope ratio mass spectrometry to determine the fractionation factor for h(2) production by hydrogenases.hydrogenases catalyze the reversible formation of h(2), and they are key enzymes in the biological cycling of h(2). h isotopes have the potential to be a very useful tool in quantifying hydrogen ion trafficking in biological h(2) production processes, but there are several obstacles that have thus far limited the application of this tool. here, we describe a new method that overcomes some of these barriers and is specifically designed to measure isotopic fractionation during enzyme-catalyzed h(2 ...201222215579
microbial community succession during lactate amendment and electron-acceptor limitation reveals a predominance of metal-reducing pelosinus spp.determining the success of in-situ bioremediation strategies is complex. by using controlled laboratory conditions, the influence of individual variables such as u(vi), cr(vi) and electron donor and acceptors on community structure, dynamics, and the metal-reducing potential can be studied. triplicate anaerobic, continuous-flow reactors were inoculated with cr(vi) contaminated groundwater from the hanford, washington 100-h area, amended with lactate and incubated for 95 days to obtain stable, en ...201222267668
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