• Biotechnology and Bioprocess Engineering:BBE
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• v.10 no.6
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• pp.482-493
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• 2005

Biomass is originally photosynthesized from inorgainic compounds such as $CO_2$, minerals, water and solar energy. Recent studies have shown that anaerobic bacteria have the ability to convert recalcitrant biomass such as cellullosic or chitinoic materials to useful compounds. The biomass containing agricultural waste, unutilized wood and other garbage is expected to utilize as feed, food and fuel by microbial degradation and other metabolic functions. In this study we isolated several anaerobic, cellulolytic and chitinolytic bacteria from rumen fluid, compost and soil to study their related enzymes and genes. The anaerobic and cellulolytic bacteria, Clostridium thermocellum, Clostridium stercorarium, and Clostridium josui, were isolated from compost and the chitinolytic Clostridium paraputrificum from beach soil and Ruminococcus albus was isolated from cow rumen. After isolation, novel cellulase and xylanase genes from these anaerobes were cloned and expressed in Escherichia coli. The properties of the cloned enzymes showed that some of them were the components of the enzyme (cellulase) complex, i.e., cellulosome, which is known to form complexes by binding cohesin domains on the cellulase integrating protein (Cip: or core protein) and dockerin domains on the enzymes. Several dockerin and cohesin polypeptides were independently produced by E. coli and their binding properties were specified with BIAcore by measuring surface plasmon resonance. Three pairs of cohesin-dockerin with differing binding specificities were selected. Two of their genes encoding their respective cohesin polypeptides were combined to one gene and expressed in E. coli as a chimeric core protein, on which two dockerin-dehydrogenase chimeras, the dockerin-formaldehyde dehydrogenase and the dockerin-NADH dehydrogenase are planning to bind for catalyzing $CO_2$ reduction to formic acid by feeding NADH. This reaction may represent a novel strategy for the reduction of the green house gases. Enzymes from the anaerobes were also expressed in tobacco and rice plants. The activity of a xylanase from C. stercorarium was detected in leaves, stems, and rice grain under the control of CaMV35S promoter. The digestibility of transgenic rice leaves in goat rumen was slightly accelerated. C. paraputrificum was found to solubilize shrimp shells and chitin to generate hydrogen gas. Hydrogen productivity (1.7 mol $H_2/mol$ glucos) of the organism was improved up to 1.8 times by additional expression of the own hydrogenase gene in C. paraputrficum using a modified vector of Clostridiu, perfringens. The hydrygen producing microflora from soil, garbage and dried pelletted garbage, known as refuse derived fuel(RDF), were also found to be effective in converting biomass waste to hydrogen gas.

• Food Science of Animal Resources
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• v.28 no.5
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• pp.675-680
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• 2008

The physical quality and microbial safety of Korean beef jerky was evaluated at various steps during its preparation. Microbial counts in raw beef demonstrated mesophillic bacteria at 4.20 Log CFU/g, psychrotrophic bacteria at 3.85 Log CFU/g, anaerobic bacteria at 4.90 Log CFU/g, and yeast and molds at 1.92 Log CFU/g. Spore-forming bacteria and coliforms were not detected in raw beef samples. Spices and spiced meats showed similar trends in microbial counts, demonstrating minimal microbial contamination during these stages of preparation. The final beef jerky product exhibited counts of mesophillic bacteria at 1.15-1.66 Log CFU/g, psychrotrophic bacteria at 1.15-1.66 Log CFU/g, and anaerobic bacteria at 0.81-1.72 Log CFU/g. Spore-forming bacteria, yeast and molds, and coliforms were not detected in beef jerky. Significant differences from added ingredients occurred for instron textural profile analysis traits for hardness. In general, Korean beef jerky with humectant and tenderizer had lower hardness than control (without humectant and tenderizer). Also, the sample added with 0.01% protease from Streptomyces griseus had lower hardness than all samples. All samples had 0.7l to 0.72 water activities, and the color and pH were not shown in significant changes of all samples.

• Journal of Microbiology and Biotechnology
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• v.30 no.9
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• pp.1367-1378
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• 2020

The polyphagous eri silk moth, Samia ricini, is associated with various symbiotic gut bacteria believed to provide several benefits to the host. The larvae of S. ricini were subjected to isolation of gut bacteria using culture-dependent 16S rRNA generic characterization, metagenomics analysis and qualitative enzymatic assays. Sixty culturable aerobic gut bacterial isolates comprising Firmicutes (54%) and Proteobacteria (46%); and twelve culturable facultative anaerobic bacteria comprising Proteobacteria (92%) and Firmicutes (8%) were identified inhabiting the gut of S. ricini. The results of metagenomics analysis revealed the presence of a diverse community of both culturable and un-culturable gut bacteria belonging to Proteobacteria (60%) and Firmicutes (20%) associated with seven orders. An analysis of the results of culturable isolation indicates that these bacterial isolates inhabited all the three compartments of the gut. Investigation on persistence of bacteria coupled with metagenomics analysis of the fifth instar suggested that bacteria persist in the gut across the different instar stages. In addition, enzymatic assays indicated that 48 and 75% of culturable aerobic, and 75% of anaerobic gut bacterial isolates had cellulolytic, lipolytic and nitrate reductase activities, thus suggesting that they may be involved in food digestion and nutritional provision to the host. These bacterial isolates may be good sources for profiling novel genes and biomolecules for biotechnological application.

• Biotechnology and Bioprocess Engineering:BBE
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• v.11 no.3
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• pp.199-204
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• 2006

The purpose of this work was to evaluate the development of the anammox process by the use of granular sludge selected from a digestion reactor as a potential seed source in a lab-scale UASB (upflow anaerobic sludge blanket) reactor system. The reactor was operated for approximately 11 months and was fed by synthetic wastewater. After 200 days of feeding with $NH_4^+\;and\;NO_2^-$ as the main substrates, the biomass showed steady signs of ammonium consumption, resulting in over 60% of ammonium nitrogen removal. This report aims to present the results and to more closely examine what occurs after the onset of anammox activity, while the previous work described the start-up experiment and the presence of anammox bacteria in the enriched community using the fluorescence in situ hybridization (FISH) technique. By the last month of operation, the consumed $NO_2^--N/NH_4^+-N$ ratio in the UASB reactor was close to 1.32, the stoichiometric ratio of the anammox reaction. The obtained results from the influent-shutdown test suggested that nitrite concentration would be one key parameter that promotes the anammox reaction during the start-up enrichment of anammox bacteria from granular sludge. During the study period, the sludge color gradually changed from black to red-brownish.

• Proceedings of the KACD Conference
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• 2003.11a
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• pp.607-607
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• 2003

The purpose of this presentation is to investigate whether the certain therapy resistant bacteria can impair the immune defense system in the pariapical tissue. Recent studies have reported that the facultative or obligatory anaerobic bacteria such as Fusobacterium nucleatum, Enterococcus faecalis and Actinomyces species and Gram positive facultative bacteria Enterococcus faecalis have been shown to dominate in persistent periapical lesion and usually recovered from failed root canal treated cases. Moreover, E. faecalis has been reported to withstand the antimicrobial agent and endure potential starvation and resist the antibacterial effect of calcium hydroxide intracanal medication.(omitted)

• Restorative Dentistry and Endodontics
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• v.21 no.1
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• pp.1-18
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• 1996

There are many advantages when using IIF and DNA probe methods over anaerobic culture method in that they are time-and effort-saving, more precise and more sensitive. Furthermore, in IIF and DNA probe methods, the detection is possible only with small amount of bacteria, the quantitative analysis is possible, and the cell viability is not necessary. The purpose of this study is to observe the incidence of P.endodontalis by carrying out anaerobic culture, IIF and colony lift using DNA probe method respectively, and to compare these 3 methods in terms of effectiveness and sensitivity in order to identify the most effective detection method. 30 teeth with at least one clinical symptoms, with single canal, and with pulp necrosis were sampled. For sampling bacteria, access cavity was prepared after disinfecting tooth and its surroundings. Then the paper point was inserted up to the periapical area, leave there for a while, and finally it was placed into PRAS Ringer's sol. and PBS sol. In anaerobic culture method, P.endodontalis was identified by biochemical tests after subculturing black and brown colonies which were produced after 7 days of incubation on BAP and Brucella BAP in anaerobic chamber. To identify P.endodontalis in IIF method, species-specific polyclonal rabbit-antisera of P.endodontalis(ATCC 35406) was reacted with sampled PBS sol. dispensed onto glass slide, and then P.endodontalis was examined by phase contrast microscopy after incubating with Goat anti-rabbit lgG conjugated to Fluorescein isothiocyanate. For colony lift using DNA probe method, membranes were laid over colonies on the surface of BAP and were hybridized with cloned DNA probe of P.endodontalis. The existence of P.endodontalis was then identified by the methods of chemiluminescent detection and color metric detection. Black colony was found in 11 teeth out of 30 teeth and P.endodontalis was detected in 6 teeth (20 %) by anaerobic culture method, 16 teeth (53 %) by IIF method, and 7 teeth (23 %) by DNA probe method. IIF method is significantly better in detecting P.endodontalis than DNA probe method and anaerobic culture method. There was no significant differences between DNA probe method and anaerobic culture method. There was significant correlation between the formation of black colony and the existence of P.endodontalis. The probability of detecting P.endodontalis when black colony being present is 2.89 times higher than when not being present. There was significant relationship between the foul odor of clinical symptoms and P.endodontalis. The sensitivity of existing P.endodontalis when foul odor being present was 93.75 %, while the specificity of not existing P.endodontalis when foul odor not being present was 28.57 %. These results suggested that the probes of P.endodontalis will be used to decide the method and prognosis in endodontic treatments.

• Korean Journal of Environmental Biology
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• v.24 no.3
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• pp.258-267
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• 2006

Distribution of population densities of heterotrophic bacteria, E. coli, and Salmonella and Shigella in seawater and sediments at 40 stations near Samcheonpo Bay were measured for 3 times from July to December, 2003. Population densities of heterotrophic bacteria in seawater during survey periods were in the range of $1.7{\pm}0.9{\times}10^3{\sim}2.4{\pm}0.9{\times}10^5$ CFU $mL^{-1}$ and the highest density was shown at St. 34 during the sampling period of September, 2003. Population densities of heterotrophic bacteria were shown higher values on September than those of July and December at all sampling stations. Population densities of anaerobic heterotrophic bacteria in sediments during survey periods were in the range of $2.2{\pm}0.2{\times}10^3{\sim}2.0{\pm}0.2{\times}10^5$ CFU $mL^{-1}$ and their population densities at sampling stations far from Samcheonpo Bay measured lower values than those near Samcheonpo Bay. Population densities of anaerobic heterotrophic bacteria in the sediments were not affected by physico-chemical factors of upper water environment. E. coli were detected only at 8 stations in seawater and 4 stations in the sediments among 40 sampling stations on July and were not detected during September and December. Salmonella and Shigella were detected only a few stations on July and September during sampling periods.

• Journal of Korean Society of Water and Wastewater
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• v.13 no.2
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• pp.47-54
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• 1999

SRB(Sulfate Reducing Bacteria) converts sulfate into sulfide using an organic carbon source as the electron donor. The sulfide formed precipitates the various metals present in the AMD (Acid Mine Drainage). This study is the fundamental research on heavy metal removal from AMD using SRB. Two completely mixed anaerobic reactors were operated for cultivation of SRB at the temperature of $30^{\circ}C$ and anaerobic batch reactors were used to evaluate the effects of carbon source, COD/sulfate($SO_4^=$) ratio and alkalinity on sulfate reduction rate and heavy metal removal efficiency. AMD used in this study was characterized by low pH 3.0 and 1000mg/l of sulfate and dissolved high concentration of heavy metals such as iron, cadmium, copper, zinc and lead. It was found that glucose was an organic carbon source better than acetate as the electron donor of SRB for sulfate reduction in AMD. Amount of sulfate reduction maximized at the COD(glucose)/sulfate ratio of 0.5 in the influent and then removal efficiencies of heavy metals were 97.5% of Cu, 100% of Pb, 100% of Cr, 49% of Mn, 98% of Zn, 100% Cd and 92.4% of Fe. Although sulfate reduction results in an increase in the alkalinity of the reactor, alkalinity of 1000mg/1 (as $CaCo_3$) should be should be added continuously to the anaerobic reactor in order to remove heavy metals from AMD.

• Journal of Microbiology and Biotechnology
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• v.21 no.9
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• pp.885-892
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• 2011

The bacterial communities in the intestinal tracts of earthworm were investigated by culture-dependent and -independent approaches. In total, 72 and 55 pure cultures were isolated from the intestinal tracts of earthworms under aerobic and anaerobic conditions, respectively. Aerobic bacteria were classified as Aeromonas (40%), Bacillus (37%), Photobacterium (10%), Pseudomonas (7%), and Shewanella (6%). Anaerobic bacteria were classified as Aeromonas (52%), Bacillus (27%), Shewanella (12%), Paenibacillus (5%), Clostridium (2%), and Cellulosimicrobium (2%). The dominant microorganisms were Aeromonas and Bacillus species under both aerobic and anaerobic conditions. In all, 39 DNA fragments were identified by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis. Aeromonas sp. was the dominant microorganism in feeds, intestinal tracts, and casts of earthworms. The DGGE band intensity of Aeromonas from feeds, intestinal tracts, and casts of earthworms was 12.8%, 14.7%, and 15.1%, respectively. The other strains identified were Bacillus, Clostridium, Enterobacter, Photobacterium, Pseudomonas, Shewanella, Streptomyces, uncultured Chloroflexi bacterium, and uncultured bacterium. These results suggest that PCR-DGGE analysis was more efficient than the culturedependent approach for the investigation of bacterial diversity and the identification of unculturable microorganisms.

• Biotechnology and Bioprocess Engineering:BBE
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• v.9 no.5
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• pp.345-351
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• 2004

We investigated the anaerobic ammonium oxidation (anammox) reaction in a lab-stale upflow anaerobic sludge blanket (UASB) reactor. Our aim was to detect and enrich the organisms responsible for the anammox reaction using a synthetic medium that contained low concentrations of substrates (ammonium and nitrite). The reactor was inoculated with granular sludge collected from a full-scale anaerobic digestor used for treating brewery wastewater The experiment was performed during 260 days under conditions of constant ammonium concentration ($50\;mg\;NH_4^+-N/L$) and different nitrite concentrations ($50{\~}150\;mg\;NO_2-N/L$). After 200 days, anammox activity was observed in the system. The microorganisms involved in this anammox reaction were identified as Candidatus B. Anammoxidans and K. Stuttgartiensis using fluorescence in situ hybridization (FISH ) method.