• Journal of Microbiology and Biotechnology
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• v.27 no.10
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• pp.1753-1762
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• 2017

Sea cucumber (Apostichopus japonicus) is a popular seafood source in Asia, including South Korea, and its consumption has recently increased with recognition of its medicinal properties. However, because raw sea cucumber contains various microbes, its ingestion can cause foodborne illness. Therefore, analysis of the microbiota in the whole body of sea cucumber can extend our understanding of foodborne illness caused by microorganisms and help to better manage products. We collected 40 sea cucumbers from four different sites in August and November, which are known as the maximum production areas in Korea. The microbiota was analyzed by an Illumina MiSeq system, and bacterial amounts were quantified by real-time PCR. The diversity and bacterial amounts in sea cucumber were higher in August than in November. Alpha-, Beta-, and Gammaproteobacteria were common dominant classes in all samples. However, the microbiota composition differed according to sampling time and site. Staphylococcus warneri and Propionibacterium acnes were commonly detected potential pathogens in August and November samples, respectively. The effect of experimental Vibrio parahaemolyticus infection on the indigenous microbiota of sea cucumber was analyzed at different temperatures, revealing clear alterations of Psychrobacter and Moraxella; thus, these shifts can be used as indicators for monitoring infection of sea cucumber. Although further studies are needed to clarify and understand the virulence and mechanisms of the identified pathogens of sea cucumber, our study provides a valuable reference for determining the potential of foodborne illness caused by sea cucumber ingestion and to develop monitoring strategies of products using microbiota information.

• Proceedings of the Korean Society of Soil and Groundwater Environment Conference
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• 2004.04a
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• pp.77-82
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• 2004

Quantifying rates of microbial processes under subsurface conditions is difficult, and is most commonly approximated by laboratory studies using aquifer materials. In this study a single-well, 'push-pull' test method is adapted for the in situ determination of denitrification rates in groundwater aquifers. The rates of stepwise reduction of nitrate to nitrite, nitrous oxide, and molecular nitrogen were determined by performing a series of push-pull tests at an experimental well field of Korea University. A single Transport Test, one Biostimulation Test, and four Activity Tests were conducted for this study. Transport tests are conducted to evaluate the mobility of solutes used in subsequent tests. These included bromide (a conservative tracer), fumarate (a carbon and/or source), and nitrate (an electron acceptor). At this site, extraction phase breakthrough curves for all solutes were similar, indicating apparent conservative transport of the solutes prior to biostimulation. Biostimulation tests were conducted to stimulate the activity of indigenous heterotrophic denitrifyinc microorganisms. Biostimulation was detected by the simultaneous production of carbon dioxide and nitrite after each injection. Activity tests were conducted to quantify rates of nitrate, nitrite, and nitrous oxide reduction. Estimated zero-order degradation rates decreased in the order nitrate '||'&'||'gt; nitrite '||'&'||'gt; nitrous oxide. The series of push-pull tests developed and field tested in this study should prove useful for conducting rapid, low-cost feasibi1ity assessments for in situ denitrification in nitrate-contaminated aquifers.

• Journal of Microbiology and Biotechnology
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• v.16 no.5
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• pp.704-715
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• 2006

Oil spill was found in 1999 from a diesel storage facility located near the top of Baekun Mountain in Uiwang City. Application of bioremediation techniques was very relevant in removing oil spills in this site, because the geological condition was not amenable for other onsite remediation techniques. For efficient bioremediation, bacterial communities of the contaminated site and the uncontaminated control site were compared using both molecular and cultivation techniques. Soil bacterial populations were observed to be stimulated to grow in the soils contaminated with diesel hydrocarbon, whereas fungal and actinomycetes populations were decreased by diesel contamination. Most of the dieseldegrading bacteria isolated from contaminated forest soils were strains of Pseudomonas, Ralstonia, and Rhodococcus species. Denaturing gradient gel electrophoresis (DGGE) analysis revealed that the profiles were different among the three contaminated sites, whereas those of the control sites were identical to each other. Analysis of 16S rDNA sequences of dominant isolates and clones showed that the bacterial community was less diverse in the oil-contaminated site than at the control site. Sequence analysis of the alkane hydroxylase genes cloned from soil microbial DNAs indicated that their diversity and distribution were different between the contaminated site and the control site. The results indicated that diesel contamination exerted a strong selection on the indigenous microbial community in the contaminated site, leading to predominance of well-adapted microorganisms in concurrence with decrease of microbial diversity.

• Journal of Microbiology and Biotechnology
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• v.28 no.11
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• pp.1800-1805
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• 2018

Inflammatory bowel disease, including Crohn's disease and ulcerative colitis (UC), is a chronically relapsing inflammatory disorder of the gastrointestinal tract. Intestinal epithelial cells (IECs) constitute barrier surfaces and play a critical role in maintaining gut health. Dysregulated immune responses and destruction of IECs disrupt intestinal balance. Dextran sodium sulfate (DSS) is the most widely used chemical for inducing colitis in animals, and its treatment induces colonic inflammation, acute diarrhea, and shortening of the intestine, with clinical and histological similarity to human UC. Current treatments for this inflammatory disorder have poor tolerability and insufficient therapeutic efficacy, and thus, alternative therapeutic approaches are required. Recently, dietary supplements with probiotics have emerged as promising interventions by alleviating disturbances in the indigenous microflora in UC. Thus, we hypothesized that the probiotic Bifidobacterium animalis subsp. lactis strain BB12 could protect against the development of colitis in a DSS-induced mouse model of UC. In the present study, oral administration of BB12 markedly ameliorated DSS-induced colitis, accompanied by reduced tumor necrosis factor-${\alpha}$-mediated IEC apoptosis. These findings indicate that the probiotic strain BB12 can alleviate DSS-induced colitis and suggest a novel mechanism of communication between probiotic microorganisms and intestinal epithelia, which increases intestinal cell survival by modulating pro-apoptotic cytokine expression.

• Journal of Microbiology and Biotechnology
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• v.26 no.7
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• pp.1320-1332
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• 2016

Light hydrocarbons accumulated in subsurface soil by long-term microseepage could favor the anomalous growth of indigenous hydrocarbon-oxidizing microorganisms, which could be crucial indicators of underlying petroleum reservoirs. Here, Illumina MiSeq sequencing of the 16S rRNA gene was conducted to determine the bacterial community structures in soil samples collected from three typical oil and gas fields at different locations in China. Incubation with n-butane at the laboratory scale was performed to confirm the presence of "universal microbes" in light-hydrocarbon microseepage ecosystems. The results indicated significantly higher bacterial diversity in next-to-well samples compared with background samples at two of the three sites, which were notably different to oil-contaminated environments. Variation partitioning analysis showed that the bacterial community structures above the oil and gas fields at the scale of the present study were shaped mainly by environmental parameters, and geographic location was able to explain only 7.05% of the variation independently. The linear discriminant analysis effect size method revealed that the oil and gas fields significantly favored the growth of Mycobacterium, Flavobacterium, and Pseudomonas, as well as other related bacteria. The relative abundance of Mycobacterium and Pseudomonas increased notably after n-butane cultivation, which highlighted their potential as biomarkers of underlying oil deposits. This work contributes to a broader perspective on the bacterial community structures shaped by long-term light-hydrocarbon microseepage and proposes relatively universal indicators, providing an additional resource for the improvement of microbial prospecting of oil and gas.

• Transactions of the Korean hydrogen and new energy society
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• v.26 no.3
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• pp.199-205
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• 2015

Organic wastes such as food waste (FW), livestock wastewater (LW), and sewage sludge (SWS) can produce hydrogen ($H_2$) by anaerobic acid fermentation. Expecially, FW which has high carbohydrate content produces $H_2$ and short chain fatty acids by indigenous $H_2$ producing microorganisms without adding inoculum, however $H_2$ production rate (HPR) and yield have to be improved to use a commercially available technology. In this study, LW was mixed to FW in different ratios (on chemical oxygen demand (COD) basis) as an auxiliary substrate. The mixture of FW and LW was pretreated at pH 2 using 6 N HCl for 12 h and then fermented at $37^{\circ}C$ for 28 h. HPR of FW, 254 mL $H_2/L/h$, was increased with the addition of LW, however, mixing ratio of LW to FW was reversely related to HPR, exhibiting HPR of 737, 733, 599, and 389 mL $H_2/L/h$ at the ratio of FW:LW=10:1, 10:2, 10:3, and 10:4 on COD basis, respectively. Maximum HPR and $H_2$ production yield of 737 $H_2/L/h$ and 1.74 mol $H_2/mol$ hexoseadded were obtained respectively at the ratio of FW:LW=10:1. Butyrate was the main organic acid produced and propionate was not detected throughout the experiment.

• Preventive Nutrition and Food Science
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• v.7 no.4
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• pp.397-404
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• 2002

Soybean curd residue (SCR) was fermented by lactic acid bacteria, Lactobacillus rhamnosus LS and Entercoccus faecium LL, isolated from SCR. The pH, titratable acidify and viable cell counts were determined from the fermented SCR to evaluate the lactic acid production and growth of lactic acid bacteria. Optimal amounts of pretense enzyme and glucose, and ideal fermentation time for SCR fermentation were estimated by response surface methodology (RSM). Raw SCR fermented by indigenous microorganisms had 0.78 % titratable acidity, The acid production in SCR fermented by L. rhamnosus LS was greatly enhanced by the addition of glucose and lactose. However only glucose increased acid production by Ent. faecium LL. The proof test of SCR fermentation demonstrated that similar results for titratable acidity, tyrosine content and viable cell counts to that predicted could be obtained by the at optimized fermentation conditions. In the presence of 0.029 % (w/w) pretense enzyme and 0.9% (w/w) glucose, the SCR fermented by Ent. faecium LL showed 1.07% (w/v) of titratable acidity, 1.02 mg% tyrosine content and 2$\times$10$^{9}$ (cfu/g) of viable cell counts. With the SCR fortified with 0.033% pretense enzyme and 1.7% glucose, L. rhamnosus LS showed 1.8% (w/v) of titratable acidity, 0.92 mg% of tyrosine content and 2$\times$10$^{9}$ (cfu/g) of viable cell counts.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.10
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• pp.1610-1616
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• 2020

Objective: This study was to evaluate the effect of husbandry systems and strains on cecum microbial diversity of Jingyang chickens under the same dietary conditions. Methods: A total of 320 laying hens (body weight, 1.70±0.15 kg; 47 weeks old) were randomly allocated to one of the four treatments: i) Silver-feathered hens in enrichment cages (SEC) with an individual cage (70×60×75 cm), ii) Silver-feathered hens in free range (SFR) with the stocking density of 1.5 chickens per ten square meters, iii) Gold-feathered hens in enrichment cages (GEC), iv) Gold-feathered hens in free range (GFR). The experiment lasted 8 weeks and the cecum fecal samples were collected for 16S rDNA high throughput sequencing at the end of experiment. Results: i) The core microbiota was composed of Bacteroidetes (49% to 60%), Firmicutes (21% to 32%) and Proteobacteria (2% to 4%) at the phylum level. ii) The core bacteria were Bacteroides (26% to 31%), Rikenellaceae (9% to 16%), Parabacteroides (2% to 5%) and Lachnoclostridium (2% to 6%) at the genus level. iii) The indexes of operational taxonomic unit, Shannon, Simpson and observed species were all higher in SFR group than in SEC group while in GEC group than in GFR group, with SFR group showing the greatest diversity of cecum microorganisms among the four groups. iv) The clustering result was consistent with the strain classification, with a similar composition of cecum bacteria in the two strains of laying hens. Conclusion: The core microbiota were not altered by husbandry systems or strains. The free-range system increased the diversity of cecal microbes only for silver feathered hens. However, the cecum microbial composition was similar in two strain treatments under the same dietary conditions.

• Mycobiology
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• v.36 no.4
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• pp.249-254
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• 2008

Minimal growth inhibitory concentrations (MICs) of chitosan acetate (M.W. 60 kDa) on heterotrophic bacteria (strains MK1, S, and R) isolated from the soft-rotten tissues of Neungee mushroom (Sarcodon aspratus) were measured. The slimy substance produced by the MK1 strain was responsible for the diseased mushroom’s appearance. The S and R strains were members of the Burkholderia cepacia complex. These strains showed different levels of susceptibility toward chitosan acetate. The MIC of chitosan acetate against the MK1 and S strains was 0.06%. The MIC against the R strain was greater than 0.10%. Survival fractions of the MK1 and S strains at the MIC were $3\;{\times}\;10^{-4}$ and $1.4\;{\times}\;10^{-3}$ after 24 h, and $2\;{\times}\;10^{-4}$ and $7\;{\times}\;10^{-4}$ after 48 h, respectively. Survival fractions of the R strain after 24 and 48 hr at 0.1% chitosan acetate were $1\;{\times}\;10^{-2}$ and $6.9\;{\times}\;10^{-3}$, respectively. Compared to the MK1 and S strains, the low susceptibility of the R stain towards chitosan acetate could be due to the ability of the R strain to utilize chitosan as a carbon source. Thirty-eight percent of Neungee pieces treated in a 0.06% chitosan acetate solution for $2{\sim}3$ second did not show any bacterial growth at 4 days, whereas bacterial growth around untreated mushroom pieces occurred within 2 days. These data suggest that chitosan acetate is highly effective in controlling growth of indigenous microorganisms on Neungee. The scanning electron micrographs of the MK1 strain treated with chitosan revealed a higher degree of disintegrated and distorted cellular structures.

• Ocean and Polar Research
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• v.27 no.2
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• pp.205-214
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• 2005

From ancient Antarctic glacier ice, we extracted total genomic DNA that was suitable for prokaryotic 16S rDNA gene cloning and sequencing, and bacterial artificial chromosome (BAC) library and end-sequencing. The ice samples were from the Dry Valley region. Age dating by $^{40}Ar/^{39}Ar$ analysis on the volcanic ashes deposited in situ indicated the ice samples are minimum 100,000-300,000 yr (sample DLE) and 8 million years (sample EME) old. Further assay proved the ice survived freeze-thaw cycles or other re-working processes. EME, which was from a small lobe of the basal Taylor glacier, is the oldest known ice on Earth. Microorganisms, preserved frozen in glacier ice and isolated from the rest of the world over a geological time scale, can provide valuable data or insight for the diversity, distribution, survival strategy, and evolutionary relationships to the extant relatives. From the 16S gene cloning study, we detected no PCR amplicons with Archaea-specific primers, however we found many phylotypes belonging to Bacteria divisions, such as Actinobacteria, Acidobacteria, Proteobacteria $({\alpha},\;{\beta},\;and\;{\gamma})$, Firmicutes, and Cytophaga-Flavobacterium-Bacteroid$. BAC cloning and sequencing revealed protein codings highly identical to phenylacetic acid degradation protein paaA, chromosome segregation ATPases, or cold shock protein B of present day bacteria. Throughput sequencing of the BAC clones is underway. Viable and culturable cells were recovered from the DLE sample, and characterized by their 16S rDNA sequences. Further investigation on the survivorship and functional genes from the past should help unveil the evolution of life on Earth, or elsewhere, if any.