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IntroductionThe chemical composition of feces plays an important role in human metabolism. Metabolomics and lipidomics are valuable tools for screening the metabolite composition in feces. Here we set out to describe fecal metabolite composition in healthy participants in frozen stools.MethodsFrozen stool samples were collected from 10 healthy volunteers and cryogenically drilled in four areas along the specimen. Polar metabolites were analyzed using derivatization followed by two-dimensional gas chromatography and time of flight mass spectrometry. Lipids were detected using ultra high-performance liquid chromatography coupled with quadruple time-of-flight mass spectrometry. The technical variation threshold was set to 30% in pooled quality control samples and metabolite variation was then assessed in four areas per specimen. A data-generated network using metabolites found in all areas was computed for healthy participants.Results2326 metabolic features were detected. Out of a total of 298 metabolites that were annotated we report here 185 that showed a technical variation of x< 30%. These metabolites included amino acids, fatty acid derivatives, carboxylic acids and phenolic compounds. Lipids predominantly belonged to the groups of diacylglycerols, triacylglycerols and ceramides. Metabolites varied between sampling areas (14%-80%). A network using metabolites present in all areas showed two main clusters, DAG lipids and phenyllactic acid.ConclusionsIn feces from healthy participants, the main groups detected were phenolic compounds, ceramides, diacylglycerols and triacylglycerols. Metabolite levels differed considerably depending on the sampling area.

Resistance to ciprofloxacin in Escherichia coli from urinary tract infections (UTI) in Denmark is increasing parallel to increased use of fluoroquinolones both in Denmark and in other European countries. The objective was to investigate the occurrence of ciprofloxacin resistance mechanisms, phenotypic coresistance, and if ciprofloxacin resistance was caused by clonal spread or to individual mutational events in a collection of consecutively obtained E. coli submitted to a clinical microbiology department at a Danish hospital. One hundred four UTI-related E. coli resistant toward nalidixic acid by disc diffusion were typed by Pulsed Field Gel Electrophoresis (PFGE) with XbaI. One isolate representing each PFGE type and only one patient (n = 77) were investigated for point mutations in sequenced PCR amplicons of the four topoisomerase genes; qnr genes by use of PCR; aac(6')-Ib-cr by BtsCI restriction of PCR products; and efflux using efflux pump inhibitors in a broth dilution assay. Minimal inhibitory concentration (MIC) was determined for 21 antibacterial agents, including ciprofloxacin. Of the 77 isolates, the majority were resistant to ciprofloxacin (91%) and multiresistant (resistant to ≥ 3 antimicrobial classes, 83%). Ciprofloxacin-resistant isolates showed at least one target mutation. A significant, positive correlation was found regarding MIC of ciprofloxacin and the number of target mutations. Efflux was found as a resistance mechanism in 77% of isolates tested (n = 60). The aac(6')-Ib-cr gene was detected on plasmids from five isolates showing ciprofloxacin MICs >512 mg/L. No overall clonal relationship among isolates was found according to PFGE. Target modification is the dominating fluoroquinolone resistance mechanism often found in combination with efflux and sometimes aac(6')-Ib-cr. In Denmark, increasing ciprofloxacin resistance in E. coli is mainly due to mutational events and not to spread of clones.

Pasteurella multocida toxin (PMT), a virulence factor of the pathogenic Gram-negative bacterium P. multocida, is a 146 kDa protein belonging to the A-B class of toxins. Once inside a target cell, the A domain deamidates the α-subunit of heterotrimeric G-proteins, thereby activating downstream signaling cascades. However, little is known about how PMT selects and enters its cellular targets. We therefore studied PMT binding and uptake in porcine cultured intestinal mucosal explants to identify susceptible cells in the epithelium and underlying lamina propria. In comparison with Vibrio cholera B-subunit, a well-known enterotoxin taken up by receptor-mediated endocytosis, PMT binding to the epithelial brush border was scarce, and no uptake into enterocytes was detected by 2h, implying that none of the glycolipids in the brush border are a functional receptor for PMT. However, in the lamina propria, PMT distinctly accumulated in the secretory granules of mast cells. This also occurred at 4 °C, ruling out endocytosis, but suggestive of uptake via pores that connect the granules to the cell surface. Mast cell granules are known to secrete their contents by a "kiss-and-run" mechanism, and we propose that PMT may exploit this secretory mechanism to gain entry into this particular cell type.

Dechlorination of tetrachloroethene, also known as perchloroethylene (PCE), was investigated in an upflow anaerobic sludge blanket (UASB) reactor after incorporation of the strictly anaerobic, reductively dechlorinating bacterium Dehalospirillum multivorans into granular sludge. This reactor was compared to the reference 1 (R1) reactor, where the granules were autoclaved to remove all dechlorinating abilities before inoculation, and to the reference 2 (R2) reactor, containing only living granular sludge. All three reactors were fed mineral medium containing 3 to 57 μM PCE, 2 mM formate, and 0.5 mM acetate and were operated under sterile conditions. In the test reactor, an average of 93% (mole/mole) of the effluent chloroethenes was dichloroethene (DCE), compared to 99% (mole/mole) in the R1 reactor. The R2 reactor, with no inoculation, produced only trichloroethene (TCE), averaging 43% (mole/mole) of the effluent chloroethenes. No dechlorination of PCE was observed in an abiotic control consisting of sterile granules without inoculum. During continuous operation with stepwise-reduced hydraulic retention times (HRTs), both the test reactor and the R1 reactor showed conversion of PCE to DCE, even at HRTs much lower than the reciprocal maximum specific growth rate of D. multivorans , indicating that this bacterium was immobilized in the living and autoclaved granular sludge. In contrast, the R2 reactor, with no inoculation of D. multivorans , only converted PCE to TCE under the same conditions. Immobilization could be confirmed by using fluorescein-labeled antibody probes raised against D. multivorans . In granules obtained from the R1 reactor, D. multivorans grew mainly in microcolonies located in the centers of the granules, while in the test reactor, the bacterium mainly covered the surfaces of granules.

Reductive dechlorination of tetrachloroethene was studied in a mesophilic upflow anaerobic sludge blanket reactor. Operating the reactor in batch mode the dynamic transformation of tetrachloroethene, trichloroethene and dichloroethene (DCE) was monitored. Tetrachloroethene was reductively dechlorinated to trichloroethene, which again was dechlorinated at the same rate as DCE was produced. DCE showed a lag period of 40 h before transformation was observed. During normal reactor operation trans-1,2-DCE was the major DCE isomer, followed by cis-1,2-DCE. Small amounts of 1,1-DCE but no vinyl chloride were detected. When the influent tetrachloroethene concentration was increased from 4.6 μM to 27 μM, the transformation rate increased, indicating that the system was not saturated with tetrachloroethene. The main organic component in the effluent was acetate, indicating that the aceticlastic methane-producing bacteria were inhibited by the chlorinated ethenes.

Strain DCB-2T (T = type strain) (T. Madsen and D. Licht, Appl. Environ. Microbiol. 58:2874–2878, 1992) is an anaerobic, spore-forming bacterium that is capable of reductive dechlorination of chlorophenols. The cells of this strain are rod shaped and 3.3 to 6 μm long by 0.6 to 0.7 μm wide and occur singly and in pairs. Short chains are formed. Spores are terminal. This bacterium is motile, and each cell has one or two terminal flagella. Cells in the exponential and stationary phases are gram negative. This organism does not hydrolyze gelatin and is indole positive and catalase negative, and the guanine-plus-cytosine content of its cellular DNA is 47 mol%. The optimum temperature for growth is 37°C. Only pyruvate and tryptophan are used as substrates. Pyruvate and 2,4,6-trichlorophenol are converted to acetate, CO2, and 4-chlorophenol by strain DCB-2T. When grown on pyruvate, this bacterium produces sulfide if thiosulfate or sulfite is added as an electron acceptor. Fe(III) is reduced to Fe(II), but Mn(IV) is not reduced. Sulfate is not reduced to sulfide in the presence of pyruvate or other carbon sources typically used by sulfate-reducing bacteria. Cytochrome c is present, but desulfoviridin is not. DCB-2T reductively dechlorinates 3-chloro-4-hydroxyphenylacetate to 4-hydroxyphenylacetate and conserves energy from the reaction. 16S rRNA sequencing revealed that strain DCB-2T clusters with the Clostridium-Bacillus subphylum and groups with Desulfitobacterium dehalogenans and Desulfotomaculum orientis. Desulfotomaculum orientis does not dechlorinate 2,4,6-trichlorophenol. On the basis of the phylogenetic and physiological differences and similarities of strain DCB-2T, Desulfitobacterium dehalogenans, and Desulfotomaculum orientis, we concluded that DCB-2T belongs to the genus Desulfitobacterium. We propose that strain DCB-2 is the type strain of Desulfitobacterium hafniense sp. nov.

Data on anaerobic degradation of chloroaromatic compounds in Upflow Anaerobic Sludge Blanket Reactors (UASB-reactor) are presented and compared. Special attention is given to the metabolic pathways for degradation of chlorinated phenols by granular sludge. Results indicate that PCP can be degraded in UASB-reactors via stepwise dechlorination to phenol. Phenol will subsequently be converted to benzoate before ring cleavage. Dechlorination proceeds via different pathways dependent upon the inocula used. Results are further presented on the design of special metabolic pathways in granules which do not possess this activity using the dechlorinating organism, Desulfomonile tiedjei. Additionally, it is shown that it is possible to immobilize Dechlorosporium hafniense, a newly isolated dechlorinating anaerobe, into granular sludge, thereby introducing an ability not previously present in the granules.

Three 200 ml upflow anaerobic sludge blanket (UASB)-reactors were inoculated with sugar degrading granules. To impart 3-chlorobenzoate degrading ability to the reactors, one was inoculated with the 3-chlorobenzoate (3-CB) dechlorinating Desulfomonile tiedjei, and the second received a 3-CB dechlorinating consortium, consisting of D.tiedjei and a benzoate degrading coculture of Syntrophus buswellii with Methanospirillum sp. No degradation of 3-CB was observed in the third reactor only inoculated with granules. After several months operation at a hydraulic retention time at 0.5 day, shorter than the reported generation time of D. tiedjei, the reactors showed increasing dechlorinating abilities. Activity tests done with granules from the control and the consortium-inoculated reactor showed no activity in the control reactor and no significant difference in the specific dechlorination rate with granules from the top, middle or bottom layer of the active reactor sludge bed, with or without carbon source added. This indicated that the added bacteria were immobilized in the granules and they were responsible for the dechlorinating activity. These results have important implications for the use of pure anaerobic culture or defined microbial mixtures in viable waste treatment processes.

Methanogenic upflow anaerobic granular-sludge blanket (UASB) reactors treat wastewaters at a high rate while simultaneously producing a useful product, methane; however, recalcitrant environmental pollutants may not be degraded. To impart 3-chlorobenzoate (3-CB)-dechlorinating ability to UASB reactors, we inoculated granular sludge in UASB reactors with either a pure culture of Desulfomonile tiedjei (a 3-CB-dechlorinating anaerobe) or a three-member consortium consisting of D. tiejei, a benzoate degrader, and an H2-utilizing methanogen. No degradation occurred in an uninoculated control reactor which was started with the same granular sludge, but inoculated reactors and granules from the inoculated UASB systems rapidly transformed 3-CB (54 mumol/day/g of granule biomass). After several months at a hydraulic retention time of 0.5 day, much shorter than the generation time of D. tiedjei, the reactors still dechlorinated 3-CB. This indicated that the bacteria were immobilized in the reactor granules, and by using an antibody probe for D. tiedjei, we demonstrated that this microorganism had colonized the sludge granules. These results represent the first addition of a pure culture or a defined microbial mixture to a viable waste treatment process to introduce a specific de novo degradative pathway into a granular-sludge consortium.

The membrane-bound 3-chloro-4-hydroxyphenylacetate (Cl-OHPA) reductive dehalogenase from the chlorophenol-reducing anaerobe Desulfitobacterium hafniense was purified 11.3-fold to apparent homogeneity in the presence of the detergent CHAPS. The purified dehalogenase catalyzed the reductive dechlorination of Cl-OHPA to 4-hydroxyphenylacetate with reduced methyl viologen as the electron donor at a specific activity of 103.2 nkat/mg protein. SDS-PAGE revealed a single protein band with an apparent molecular mass of 46.5 kDa. The enzyme contained 0.68 +/- 0.2 mol corrinoid, 12.0 +/- 0.7 mol iron, and 13.0 +/- 0.7 mol acid-labile sulfur per mol subunit. The N-terminal amino acid sequence of the enzyme was determined and no significant similarity was found to any protein present in the gene bank.

The strictly anaerobic, pentachlorophenol (PCP) degrading bacterium DCB-2 was immobilized in an Upflow Anaerobic Sludge Blanket (UASB) reactor containing sterile granules. PCP and lactate were fed to the reactor and the concentration of chlorophenols in the effluent were monitored for 641 days. PCP was found to be degraded and transformed into 3.4.5-trichlorophenol in the reactor where DCB-2 was introduced into the granular sludge. PCP was still transformed to 3.4.5-trichlorophenol when the hydraulic retention time was decreased to six hours which was much lower than the generation time of DCB-2 insuring no free living cells in the reactor. This indicated that DCB-2 was immobilized in the granular layer. A control reactor that contained only sterile granules did not dechlorinate PCP indicating that the performance in the inoculated reactor was only due to the introduced bacteria. Immobilization of DCB-2 in the granules was further demonstrated by adding an antibody raised against DCB-2 to sliced granules. Bacteria thus visualized formed a net structure inside the granules. No DCB-2 bacteria could be found in granules from the control reactor. When lactate was omitted from the influent, the reactor still dechlorinated PCP in accordance with our findings that lactate was not used by DCB-2. This suggested that the reducing equivalents for reductive dechlorination were derived from the granules themselves. The reactor performance was 120 μmol·l reactor-1·day-1, comparable to the best described performance of a UASB-reactor and to aerobic reactors. Our study demonstrates that granules can be constructed which possess specific abilities such as a dechlorinating activity and at the same time be high performing. This result have implications for eco-engineering of granules for anaerobic treatment of contaminated waters.