• Journal of Microbiology
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• 제37권1호
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• pp.10-13
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• 1999

The bacterial abundance, proportion of respiring bacteria, and bacterial community of southern Lake Baikal were analyzed at 1 m and 400m depths during winter. The total bacterial numbers were 5.1${\times}$105 cells ml-1 at 1 m and 2.5${\times}$105 cells ml-1 at 400 m depth, which are about half and quarter of the numbers of other lakes. The proportion of respiring bacteria was as low as 2.5% at 1 m and 1.4% at 400 m depth. Considering the amount of organic carbon which need to be degraded and low proportion of respiring bacteria, the bacteria could be assumed to have high activities. The EUB/DAPI ratios were 77 and 89% at 1 m and 400 m depths, respectively. Of the bacterial community, the other group was dominant at both depths, and gamma group of protebacteria followed next. But the beta group of proteobacteria and Cytophaga-Flavobacterium groups occupied very small proportions.

• 미생물학회지
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• 제35권3호
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• pp.242-247
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• 1999

소양호에서 fluorescent in situ hybridization 방법을 이용하여 세균군집의 계절과 수심에 따른 변화를 조사하였다. 이 방법에 사용된 oligonucleotide probe는 EUB338, ALF1b, BET42a, GAM42a 와 CF probe 였다. 조사기간중 Proteobacteria $\alpha$-group 은 0.7~32.9% 이었으며 $\beta$-group은 1.0~25.8%, $\gamma$-group은 2.4~37.1%, Cytophaga-Flavobacterium group은 4.7~23.6%의 분포를 나타내었다. 계절별로 살펴보면 규조류가 우점하는 봄펄에는 $\gamma$-group 이, 유기물의 농도가 낮고 수온이 높은 여름철에는 $\alpha$-group 이 우점하였으며, 남조류가 우점하는 가을철에 총세균수에 대한 Eubacterial group 의 비율이 크게 감소하여 특정 group의 우점현상은 나타나지 않았다. 이처럼 소양호는 계절과 수심에 따라 군집구조가 변화하였으며, 특히 세균의 군집구조는 식물플랑크톤의 천이와 밀접한 관계를 보이는 것으로 나타났다.

• Journal of Microbiology and Biotechnology
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• 제18권8호
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• pp.1459-1469
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• 2008

Using a rotating biological contactor modified with a sequencing bath reactor system (SBRBC) designed and operated to remove phosphate and nitrogen [58], the microbial community structure of the biofilm from the SBRBC system was characterized based on the extracellular polymeric substance (EPS) constituents, electron microscopy, and molecular techniques. Protein and carbohydrate were identified as the major EPS constituents at three different biofilm thicknesses, where the amount of EPS and bacterial cell number were highest in the initial thickness of 0-100${\mu}m$. However, the percent of carbohydrate in the total amount of EPS decreased by about 11.23%, whereas the percent of protein increased by about 11.15% as the biofilm grew. Thus, an abundant quantity of EPS and cell mass, as well as a specific quality of EPS were apparently needed to attach to the substratum in the first step of the biofilm growth. A FISH analysis revealed that the dominant phylogenetic group was $\beta$- and $\gamma$-Proteobacteria, where a significant subclass of Proteobacteria for removing phosphate and/or nitrate was found within a biofilm thickness of 0-250${\mu}m$. In addition, 16S rDNA clone libraries revealed that Klebsiella sp. and Citrobacter sp. were most dominant within the initial biofilm thickness of 0-250${\mu}m$, whereas sulfur-oxidizing bacteria, such as Beggiatoa sp. and Thiothrix sp., were detected in a biofilm thickness over 250${\mu}m$. The results of the bacterial community structure analysis using molecular techniques agreed with the results of the morphological structure based on scanning electron microscopy. Therefore, the overall results indicated that coliform bacteria participated in the nitrate and phosphorus removal when using the SBRBC system. Moreover, the structure of the biofilm was also found to be related to the EPS constituents, as well as the nitrogen and phosphate removal efficiency. Consequently, since this is the first identification of the bacterial community and structure of the biofilm from an RBC simultaneously removing nitrogen and phosphate from domestic wastewater, and it is hoped that the present results may provide a foundation for understanding nitrate and phosphate removal by an RBC system.

• 한방비만학회지
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• 제19권2호
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• pp.97-105
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• 2019

Objectives: We investigated differences between the tracheostomized and the non-tracheostomized stroke patients through microbiological analysis for the purpose of preliminary explorations of full-scale clinical research in the future. Methods: We collected tracheal aspirates samples from 5 stroke patients with tracheostomy and expectorated sputum samples from 5 stroke patients without tracheostomy. Genomic DNA from sputum samples was isolated using QIAamp DNA mini kit. The sequences were processed using Quantitative Insights into Microbial Ecology 1.9.0. Alpha-diversity was calculated using the Chao1 estimator. Beta-diversity was analyzed by UniFrac-based principal coordinates analysis (PCoA). To confirm taxa with different abundance among the groups, linear discriminant analysis effect size analysis was performed. Results: Although alpha-diversity value of the tracheostomized group was higher than that of the non-tracheostomized group, there was no statistically significant difference. In PCoA, clear separation was seen between clusters of the tracheostomized group and that of the non-tracheostomized group. In both groups, Bacteroidetes, Proteobacteria, Fusobacteria, Firmicutes, Actinobacteria were identified as dominant in phylum level. In particular, relative richness of Proteobacteria was found to be 31% more in the tracheotomized group (36.6%) than the non-tracheostomized group (5.6%)(P<0.05). In genus level, Neisseria (24%), Prevotella (17%), Streptococcus (13%), Fusobacteria (11%), Porphyromonas (7%) were identified as dominant in the tracheostomized group. In the non-tracheostomized group, Prevotella (38%), Veillonella (20%), Neisseria (9%) were genera that found to be dominant. Conclusions: It is meaningful in that the tracheostomized group has been identified a higher rate of microbiotas known as pathogenic in respiratory diseases compared to the non-tracheostomized group, confirming the possibility that the risk of opportunity infection may be higher.

• Journal of Microbiology and Biotechnology
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• 제30권12호
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• pp.1819-1826
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• 2020

Increasing evidence suggests a potential role of microbial colonization in the inception of chronic airway diseases. However, it is not clear whether the lung and gut microbiome dysbiosis is coincidental or a result of mutual interaction. In this study, we investigated the airway microbiome in interleukin 13 (IL-13)-rich lung environment and related alterations of the gut microbiome. IL-13-overexpressing transgenic (TG) mice presented enhanced eosinophilic inflammatory responses and mucus production, together with airway hyperresponsiveness and subepithelial fibrosis. While bronchoalveolar lavage fluid and cecum samples obtained from 10-week-old IL-13 TG mice and their C57BL/6 wild-type (WT) littermates showed no significant differences in alpha diversity of lung and gut microbiome, they presented altered beta diversity in both lung and gut microbiota in the IL-13 TG mice compared to the WT mice. Lung-specific IL-13 overexpression also altered the composition of the gut as well as the lung microbiome. In particular, IL-13 TG mice showed an increased proportion of Proteobacteria and Cyanobacteria and a decreased amount of Bacteroidetes in the lungs, and depletion of Firmicutes and Proteobacteria in the gut. The patterns of polymicrobial interaction within the lung microbiota were different between WT and IL-13 TG mice. For instance, in IL-13 TG mice, lung Mesorhizobium significantly affected the alpha diversity of both lung and gut microbiomes. In summary, chronic asthma-like pathologic changes can alter the lung microbiota and affect the gut microbiome. These findings suggest that the lung-gut microbial axis might actually work in asthma.

• Journal of Ecology and Environment
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• 제41권9호
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• pp.271-280
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• 2017

Background: Soil microorganisms play key roles in nutrient cycling and are distributed throughout the soil profile. Currently, there is little information about the characteristics of the microbial communities along the soil depth because most studies focus on microorganisms inhabiting the soil surface. To better understand the functions and composition of microbial communities and the biogeochemical factors that shape them at different soil depths, we analyzed microbial activities and bacterial and fungal community composition in soils up to a 120 cm depth at a fallow field located in central Korea. To examine the vertical difference of microbial activities and community composition, ${\beta}$-1,4-glucosidase, cellobiohydrolase, ${\beta}$-1,4-xylosidase, ${\beta}$-1,4-N-acetylglucosaminidase, and acid phosphatase activities were analyzed and barcoded pyrosequencing of 16S rRNA genes (bacteria) and internal transcribed spacer region (fungi) was conducted. Results: The activity of all the soil enzymes analyzed, along with soil C concentration, declined with soil depth. For example, acid phosphatase activity was $125.9({\pm}5.7({\pm}1SE))$, $30.9({\pm}0.9)$, $15.7({\pm}0.6)$, $6.7({\pm}0.9)$, and $3.3({\pm}0.3)nmol\;g^{-1}\;h^{-1}$ at 0-15, 15-30, 30-60, 60-90, and 90-120 cm soil depths, respectively. Among the bacterial groups, the abundance of Proteobacteria (38.5, 23.2, 23.3, 26.1, and 17.5% at 0-15, 15-30, 30-60, 60-90, and 90-120 cm soil depths, respectively) and Firmicutes (12.8, 11.3, 8.6, 4.3, and 0.4% at 0-15, 15-30, 30-60, 60-90, and 90-120 cm soil depths, respectively) decreased with soil depth. On the other hand, the abundance of Ascomycota (51.2, 48.6, 65.7, 46.1, and 45.7% at 15, 30, 60, 90, and 120 cm depths, respectively), a dominant fungal group at this site, showed no clear trend along the soil profile. Conclusions: Our results show that soil C availability can determine soil enzyme activity at different soil depths and that bacterial communities have a clear trend along the soil depth at this study site. These metagenomics studies, along with other studies on microbial functions, are expected to enhance our understanding on the complexity of soil microbial communities and their relationship with biogeochemical factors.

• 미생물학회지
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• 제43권1호
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• pp.14-18
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• 2007

바이칼호에 서식하는 있는2속(genus Baikalospongia와 Lubomirskia)(5.13)의 해면 내에 서식하고 있는 세균군집 구조를 조사하기 위하여 fluorescent in situ hybridization (FISH) 방법을 적용하였다. Baikalospongia와 Lubomirskia 속에 속하는 해면에 서식하는 총세균수는 각각 $7.2{\times}10^{7}-4.2{\times}10^{8}\;cells/ml$과 $1.2{\times}10^{8}-1.6{\times}10^{8}\;cells/ml$였다. 인근 호숫물의 총세균수는 $2.3{\times}7.7{\times}10^{5}\;cells/ml$ 범위로 해면에 서식하는 총세균수가 약 $10^{3}-10^{4}$배 더 높았다. 총세균수에 대한 세균군집 구조의 비율은 ${\alpha}-,\;{\beta}-,\;{\gamma}-Proteobacteria\;group$과 Cytophaga-Flavobacterium group외 다른 세균군이 genus Baikalospongia는 42.0-60.3%, Lubomirskia에서는 40.7-51.9%로, 호수물에서는 22.6-46.3%와 같이 나타났다. 이는 일반 담수에서 특정 군집이 우점하는 경향과는 다른 것으로써, 바이칼의 호숫물과 해면에 있는 세균들은 독특한 군집구조를 이루고 있음을 확인하였다.

• Journal of Microbiology and Biotechnology
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• 제20권1호
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• pp.169-178
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• 2010

The microbial community structure in Thailand soils contaminated with low and high levels of arsenic was determined by denaturing gradient gel electrophoresis. Band pattern analysis indicated that the bacterial community was not significantly different in the two soils. Phylogenetic analysis obtained by excising and sequencing six bands indicated that the soils were dominated by Arthrobacter koreensis and $\beta$-Proteobacteria. Two hundred and sixty-two bacterial isolates were obtained from arsenic-contaminated soils. The majority of the As-resistant isolates were Gramnegative bacteria. MIC studies indicated that all of the tested bacteria had greater resistance to arsenate than arsenite. Some strains were capable of growing in medium containing up to 1,500 mg/l arsenite and arsenate. Correlations analysis of resistance patterns of arsenite resistance indicated that the isolated bacteria could be categorized into 13 groups, with a maximum similarity value of 100%. All strains were also evaluated for resistance to eight antibiotics. The antibiotic resistance patterns divided the strains into 100 unique groups, indicating that the strains were very diverse. Isolates from each antibiotic resistance group were characterized in more detail by using the repetitive extragenic palindromic-PCR (rep-PCR) DNA fingerprinting technique with ERIC primers. The PCR products were analyzed by agarose gel electrophoresis. The genetic relatedness of 100 bacterial fingerprints, determined by using the Pearson product-moment similarity coefficient, showed that the isolates could be divided into four clusters, with similarity values ranging from 5-99%. Although many isolates were genetically diverse, others were clonal in nature. Additionally, the arsenic-resistant isolates were examined for the presence of arsenic resistance (ars) genes by using PCR, and 30% of the isolates were found to carry an arsenate reductase encoded by the arsC gene.

• Ocean and Polar Research
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• 제27권2호
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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.

• Journal of Microbiology and Biotechnology
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• 제26권12호
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• pp.2141-2147
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• 2016

As one of the most complex human-associated microbial habitats, the oral cavity harbors hundreds of bacteria. Halitosis is a prevalent oral condition that is typically caused by bacteria. The aim of this study was to analyze the microbial communities and predict functional profiles in supragingival plaque from healthy individuals and those with halitosis. Ten preschool children were enrolled in this study; five with halitosis and five without. Supragingival plaque was isolated from each participant and 16S rRNA gene pyrosequencing was used to identify the microbes present. Samples were primarily composed of Actinobacteria, Bacteroidetes, Proteobacteria, Firmicutes, Fusobacteria, and Candidate phylum TM7. The ${\alpha}$ and ${\beta}$ diversity indices did not differ between healthy and halitosis subjects. Fifteen operational taxonomic units (OTUs) were identified with significantly different relative abundances between healthy and halitosis plaques, and included the phylotypes of Prevotella sp., Leptotrichia sp., Actinomyces sp., Porphyromonas sp., Selenomonas sp., Selenomonas noxia, and Capnocytophaga ochracea. We suggest that these OTUs are candidate halitosis-associated pathogens. Functional profiles were predicted using PICRUSt, and nine level-3 KEGG Orthology groups were significantly different. Hub modules of co-occurrence networks implied that microbes in halitosis dental plaque were more highly conserved than microbes of healthy individuals' plaque. Collectively, our data provide a background for the oral microbiota associated with halitosis from supragingival plaque, and help explain the etiology of halitosis.