• Journal of Microbiology and Biotechnology
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• v.14 no.5
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• pp.906-913
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• 2004

A culture-independent molecular phylogenetic survey was carried out on the bacterial community in cold-seep sediment at Edison Seamount, south of Lihir Island, Papua New Guinea. Small-subunit rRNA genes were amplified directly from the sediment DNA by PCR and cloned. The majority of the cloned 16S rRNA gene sequences were most closely related to as-yet-uncultivated microorganisms found in deep-sea sediments, and were primarily affiliated with one of four groups: the $\gamma$-, $\delta$-, and $\epsilon$-subdivisions of Proteobacteria, and Cytophaga-Flavobacterium-Bacteroides. We did not recover any sequences related to cyanobacteria, prochlorophytes, and $\alpha$-Proteobacteria, which are known to occur in great abundance within the surface mixed layer of the Atlantic and Pacific Oceans. The majority of the cloned $\gamma$-and $\epsilon$-Proteobacterial sequences were closely related to chemoautotrophic sulfur-oxidizing symbionts of marine benthic fauna, and the $\delta$-Proteobacterial sequences to sulfate- and sulfur-reducing bacteria, indicating that they might play an important role in chemoautotrophic primary production and the sulfur cycle in the cold-seep area. There results demonstrate the high diversity of the bacterial community in the cold-seep sediment, and substantially expand knowledge of the extent of bacterial diversity in this formidable and unique habitat.

• Journal of Microbiology
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• v.43 no.2
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• pp.152-157
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• 2005

Strain Kw07$^T$, a Gram-negative, non-spore-forming, rod-shaped bacterium, was isolated from granules in an Up-flow Anaerobic Sludge Blanket (UASB) bioreactor used in the treatment of brewery waste­water. 16S rRNA gene sequence analysis revealed that strain Kw07T belongs to the a-4 subclass of the Proteobacteria, and the highest degree of sequence similarity was determined to be to Sphingopyxis macrogoltabida IFO 15033T (97.8%). Chemotaxonomic data revealed that strain Kw07T possesses a quinone system with the predominant compound Q-I0, the predominant fatty acid C,s:, OJ7c, and sphingolipids, aU of which corroborated our assignment ofthe strain to the Sphingopyxis genus. The results of DNA-DNA hybridization and physiological and biochemical tests clearly demonstrated that strain Kw07T represents a distinct species. Based on these data, Kw07T (= KCTC 12209T = NBRC 100800T) should be classified as the type strain for a novel Sphingopyxis species, for which the name Sphingopyxis granuli sp. novo has been proposed.

• Proceedings of the Korean Society for Applied Microbiology Conference
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• 2000.04a
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• pp.150-156
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• 2000

Oligotrophic bacteria isolated from forest soil showed a specific community consisting of various taxonomic groups compared with those in other soil or aquatic habitats. Based on the cell shape, the isolates were divided into four groups: regular rod, curved/spiral rod, irregular rod, and prosthecate bacteria. The cellular fatty acids 60 oligotrophic isolates were analyzed. The 30 fatty acids which were identified or characterized are classified. At the dendrogram based on cellular fatty acid composition, four clusters(I-IV) were separated at a euclidian distance of about 50. Cluster 3 and 4-a strains were containing Q-8, these strains are accommodated in the Proteobacteria gamma and beta subdivision. The chemotaxonomic profiles of the cluster 4-a strains showed good agreement with those of the genus Burkholderia. Cluster 3 was characterized by the presence of branched-chain fatty acids, iso-C15:0, iso-C17:1, and iso-C17:0 as the major components. These chemotaxonomy suggested the close relationship of the isolates with Xathomonas/Sterotrophomonas group. Based on the 16S rDNA sequence analysis, the two representative strains(MH256 and MA828) of cluster 3 showed the close relation to genera, Xathomonas/Sterotrophomonas, but were not included in these genera. These strains were even further away from core Xanthomonas, and clearly were seen to branch outside the cluster formed by the Sterotrophomonas maltophilia. MH256 and MA828 16S rDNA sequence was different enough to put new genus on a separate branch. The isolates with Q-10 were also studied. They are corresponded to the two large groups in Proteobacteria alpha subdivision. One was incorporated in the genus Bradyrhizobium cluster, which also includes Agromonas, a genus for oligotrophic bacteria. The strains of the other group showed high similarity to the genus Agrobacterium.

• Korean Journal of Microbiology
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• v.35 no.3
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• pp.242-247
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• 1999

This sludy was conducted to investigate the change of bacterial co~munities with season and depth in Lake Soyang. Korea, using fluorescence in situ hybridization (FISH). The oligonucleotide probes used in this study were EUB338, ALF I b. GAM42a, and CF, The percentage of h e Proleobacteria a $\alpha$-group ranged from 0.70 to 33% the $\beta$-group from 1.0 to 26% they -group from 2.4 Lo 37% and Cytophagn and Flavobactefin groups from 4.7 to 24% duing the study period (April Lo November, 1998). They $\gamma$-group was dominant in spring when Asterionella was dominant. and a $\alpha$-group was dominant in summer when the organic content was low and Dinobryon was dominant. However, a specific group was not dominant in ？dl when cyanobacteria group was dominant and the ratio of eubacleria to total bacteria was very low. Therefore, the bacterial communities in Lake Soyang changed with season and depth, which seems to be associated with the telnporal succession of phytoplanlaons.

• Korean Journal of Microbiology
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• v.51 no.2
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• pp.133-140
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• 2015

We have examined the correlation between the physicochemical and microbiological environment variables for the different layers of oak forest soil in Mt. Gyeryong, Korea. The result shows that there is a high correlation in the environment variables between the soil parameters of the fermented (F) layer and humus (H) layer. In particular, the pH level in the F layer shows a high correlation with C and N, while the various organic acids of the H layer turns out to be closely correlated with soil bacteria density. As we evaluated phylogenetic characteristics of bacterial populations by DGGE analysis with DNA extracted. Total of 175 bands including 43 bands from litter (L) layer, 42 bands from F layer, 43 bands from H layer and 47 bands from rhizosphere (A) layer were selected as the major DGGE band of oak forest soil. Based on the 16S rRNA gene sequences, 175 DGGE bands were classified into 32 orders in 7 phylum. The heat map was analyzed in order to compare the quantity of the base sequences of each order and based on the clustering of the different layers of oak forest soil, the result confirms that the F layer and H layer belong to a different cluster from that of L layer and A layer. Furthermore, it also showed that approximately 50% of the total microbial population in different layers is ${\alpha}$-proteobacteria, which indicates that they belong to the dominant system group. In particular, Rhizobiales, Burkholderiales and Actinobacteriales were observed in all the seasons and layers of oak forest soil, which confirms that they are the indigenous soil bacterial community in oak forest soil.

• Korean Journal of Microbiology
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• v.43 no.3
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• pp.201-209
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• 2007

The CFDA (6-carboxyfluorescein diacetate) direct viable count method and plate count (PC) method using conventional nutrient broth (NB) medium and $10^{-2}$ diluted NB (DNB) medium were applied to samples collected from Mt. Yongdoo In Andong, in an effect to determine the number of living bacteria pine mushroom forest soil. The number of living bacteria determined via plate count in NB medium comprised $5{\sim}8%$ of the CFDA direct viable count, and the bacteria in the DNB medium comprised $40{\sim}47%$. This result indicated that viable but nonculturable (VBNC) bacteria existed in the pine mushroom forest soil at a high percentage. The phylogenetic characteristics of the VBNC bacterial populations in the samples of pine mushroom (Tricholoma matsutake) forest soil were analyzed via the direct extraction of DNA and 16S rDNA-ARDRA. The 115 clones from pine mushroom forest soil were clustered into 31 different RFLP phylotypes by ARDRA. Based on the 16S rDNA sequences, the 31 ARDRA clusters were classified into 6 phylogenetic groups: ${\alpha}-,\;{\beta}-,\;{\gamma}-Proteobacteria$, Acidobacteria, Actinobacteria and Firmicutes. Among these bacterial populations, approximately 85% were classified as members of phylum Acidobacteria. The Acidobacteria phylum was shown to exist abundantly in the pine mushroom forest soil.

• Journal of Korean Medicine for Obesity Research
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• v.19 no.2
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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.

• Korean Journal of Microbiology
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• v.44 no.4
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• pp.317-325
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• 2008

Recently there are difficulties in management of golf courses because of an ever increasing demand for golf as a leisure sports. Hence natural minerals as an amendment could be applied to improve and manage the physicochemical properties of the golf course soils in an environment-friendly way. In this study, quartz porphyry, which has been shown to be a good soil amendment for crop production, was tested for its effect on physicochemical properties of the golf course soil, growth of creeping bentgrass (Agrostis stolonifera) and changes of soil microbial communities in the soil. In general, amendment of 20% quartz porphyry into the soil turned out to be most effective in enhancing a proper growth of the grass leaves and roots. DGGE profile data showed that eubacterial species richness was also the highest at this level of the mineral treatment in which Actinobacteria and ${\alpha}$-Proteobacteria were the dominant phyla. This appeared to be attributed to a low level of soluble organic matter content and decreased concentration of cations such as $Ca^{2+}$, $Mg^{2+}$, and $K^+$.

• Journal of Korean Society of Environmental Engineers
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• v.32 no.8
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• pp.780-786
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• 2010

The bacterial community structure in biological reactor in wastewater treatment system was investigated by denaturing gradient gel electrophoresis (DGGE) and fluorescent in situ hybridization (FISH). Samples were collected at different three points in wastewater treatment system. Through treatment processes, BOD (biochemical oxygen demand) and COD (chemical oxygen demand) of was removal efficiency was 83.1~98.6%, 67.2~85.2% respectively. Microbial community of aerobic tank and oxic tank were similar but anoxic tank was different (RRP group was increased about tripple) by DGGE and FISH in sludge (2007 October and 2008 January). Samples in 2007 October and 2008 January were dominant ${\alpha}$-Proteobacteria and CF group respectively. Sludge in 2008 April were different comparing former results dominant others as 65~80%. Others group was dominant. Eubacteria by FISH with the probe EUB338 was about $1.7{\sim}7.6{\times}10^9\;cells/mL$. It could be successfully observed bacterial community in biological wastewater system.

• Journal of Microbiology and Biotechnology
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• v.30 no.12
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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.