• Genomics & Informatics
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• v.4 no.4
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• pp.182-187
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• 2006

6-Phosphogluconolactonase (6PGL) is one of the key enzymes in the ubiquitous pathways of central carbon metabolism, but bacterial 6PGL had been long known as a missing enzyme even after complete bacterial genome sequence information became available. Although recent experimental characterization suggests that there are two types of 6PGLs (DevB and YbhE), their phylogenetic distribution is severely biased. Here we present that proteins in COG group previously described as 3-oarboxymuconate cyclase (COG2706) are actually the YbhE-type 6PGLs, which are widely distributed in Proteobacteria and Fimicutes. This case exemplifies how erroneous functional description of a member in the reference database commonly used in transitive genome annotation cause systematic problem in the prediction of genes even with universal cellular functions.

• Korean Journal of Microbiology
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• v.50 no.2
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• pp.152-157
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• 2014

The aim of this study was to investigate the bacterial community inhabited in Callyspongia elegans. Marine bacteria were isolated from the marine sponge C. elegans using marine agar. The resulting 112 isolated pure cultures were then used for further study. They were characterized by determining morphological characteristics through Gram's staining and morphological observation. The colony pigments of bacterial isolates were characterized as yellow, brown, ivory, and white. Thirty-seven strains were found to be Gram-positive and 75 strains were Gram-negative. Seventy-nine strains were coccus-shaped, while 16 strains were rod-shaped. On the basis of the results of the comparative analyses of 16S rDNA gene sequences, the 112 isolated bacteria were divided into 5 major groups: Alphaproteobacteria (39%), Gammaproteobacteria (22%), Actinobacteria (14%), Fimicutes (9%), and Bacteroidetes (6%). It is strongly suggested that fifteen isolates are candidates for a new genera or species, based on the analyses of 16S rDNA gene sequences.

• Korean Journal of Agricultural Science
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• v.48 no.3
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• pp.493-503
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• 2021

Tricholoma matsutake (Pinus mushroom, PM) is one of the most valued ectomycorrhizal fungi in Asia because it is an expensive forest product with a unique flavor and taste. Therefore, many studies have tried to successfully cultivate Tricholoma matsutake artificially in Korea and other countries. However, its physiological and ecological characteristics are still unknown. Thus, we need to understand the diversity and clusters of microorganisms related to Tricholoma matsutake and to identify their core microorganisms related to their growth and production. In this study, we obtained an average of 11,661 fragments from three pine mushrooms with metagenome (an assemblage of genes of all microorganisms in the natural world) analysis from a pine forest located in Pohang, Gyeongsang-Bukdo. Of these, the valid reads were on average 5,073 per sample available for analysis, and the average length of a read was 456 bp. There were an average of 33.3 phyla in the metagenome analysis. Firmicutes phylum made up on an average 46% of the phyla and was dominant among the phyla. The next dominant phylum was Proteobacteria at 27% followed by Bacteroidetes at 17%, Actinobacteria at 5% and Verrucomicrobia at 2%. The Proteobacteria phylum consisted of the γ-proteobacteria class at 54% followed by β-proteobacteria at 37%, α-proteobacteria at 6%, δ-proteobacteria at 2% and ζ-proteobacteria at 0%. The metagenome consisted of the Ruminococcaceae family at 17% followed by Pseudomonadaceae at 13%, Burkholderiaceae at 7%, Bacteroidaceae at 7%, Lachnospiraceae at 7% and Clostridiaceae at 6%.

• Korean Journal of Microbiology
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• v.39 no.4
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• pp.260-266
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• 2003

In this study bacterial community was analyzed to evaluate the impacts of long-term use of agricultural chemicals on a soil ecosystem as well as to obtain fundamental data on the relationship. Sequences of 16S rRNA clones from a non-agricultural site and a tangerine orchard soil which has a history of long-term use of agricultural chemicals over 30 years were analyzed. This revealed that bacterial community containing 5 divisions and 18 genera was distributed in a tangerine orchard soil, while bacterial community containing 9 divisions and 44 genera was distributed. In a tangerine orchard soil site, the most abundant bacteria in subdivision level were placed into Proteobacteria γ group which occupied 56% of total clones. The other bacterial clones from the ocrhcard soil exposed to agricultural chemicals over 30 years were Acidobacteria group (25%), Fimicutes group (5%), Planctomycetes group (2%), Proteobacteria α (1%), δ group (1%), and Cyanobacteria group (1%). Whereas, the clones were from the non-agricultural site were distributed among the division or subdivision Acidobacteria group (14%), Planctomycetes group (13%), Proteobacteria α (10%), β (9%), δ (9%), Fimicutes group (8%), Verrucomicrobia group (8%), Actinobacteria group (6%), Proteobacteria γ group (3%), Bacteroidetes group (3%), Gemmatimonadetes group (3%), and Cyanobacteria group (1%). This finding suggests the possibility that long-term application of agricultural chemicals or fertilizers on a tangerine orchard might result in drastic reduction or alteration in the composition of the bacterial community in the contaminated soil site.

• Microbiology and Biotechnology Letters
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• v.46 no.2
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• pp.127-134
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• 2018

In this study, 79 bacterial isolates were collected from the surface of marine algae Umbraulva japonica. As a result of analysis of 16s rRNA gene sequence, the 79 isolated bacteria were divided into 4 major groups: [Proteobacteria (74.69%), Actinobacteria (2.53%), Fimicutes (2.53%), and Bacteroidetes (20.25%)] - 7 classes (Actinobacteria, Flavobacteria, Sphingobacteria, Baciili, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria), 12 orders, 17 families and 31 genera. The newly isolated 3 strains could be novel species because of less than 97% similarity in 16s rRNA sequence. Therefore, it is considered that additional experiments should be conducted together with the standard strain. Analysis of 79 bacterial antibacterial activity against human and fish pathogens, such as Edwardsiella tarda, Vibrio harveyi, Streptococcus iniae, Steptococcus parauberis, Escherichia coli, Steptococcus mutans, Listeria monocytogenes and Vibrio vulnificus, was performed by using the supernatant liquid and pellet. As a result, pellet of UJT9, UJT20 and UJR17 showed antibacterial activity against V. vulnificus, UJR17 also showed antibacterial activity against S. parauberis. UJT7 and UJT20, UJR17 have been identified as Bacillus sp. and Pseudomonas sp. and it may be safely assented that it's beneficial to carry out additional experiments for various applications.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2019.10a
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• pp.84-84
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• 2019

본 연구는 전국 임의의 산양삼 재배지를 선정하여 재배지 내의 토양 특성 및 토양세균군집을 분석하고, 토양 특성, 세균군집 및 산양삼 생육특성 간의 상관관계를 구명하기 위하여 수행되었다. 토양 이화학성 분석은 농촌진흥청의 종합분석실 매뉴얼에 따라 분석하였고, 토양세균군집 분석은 pyrosequencing analysis (Illumina platform)를 이용하였다. 토양세균군집과 생육특성 간의 상관관계는 Spearman's rank correlation을 이용하여 분석하였다. 전국 8개 산양삼 재배지로부터 분리한 토양세균군집은 2개의 cluster로 군집화를 이루는 것을 확인하였다. 모든 토양 샘플에서 Proteobacteria와 Alphaproteobacteria가 각각 평균 상대적 빈도수가 35.4%, 24.4%로 우점종으로 나타났다. 나타났다. 두 개의 cluster 간 토양세균군집의 상대적 빈도수를 비교 분석한 결과, 먼저 Proteobacteria (p = 0.03), Actinobacteria (p = 0.02), Ahlpaproteobacteria (p = 0.029), Betaproteobacteria (p = 0.021)는 cluster 1에서 cluster 2에 비해 상대적 빈도수가 유의적으로 높았고, Fimicutes (p = 0.004), Cyanobacteria (p = 0.004), Acidobacteriia (p = 0.041), Ktedonobacteria (p = 0.019), Gammaproteobacteria (p = 0.034), Bacilli (p = 0.009)은 cluster 2에서 유의적으로 상대적 빈도수가 높은 것으로 나타났다. 토양세균군집 cluster 간 산양삼의 생육특성을 비교 분석한 결과, cluster 2 재배지에서 수집한 산양삼 시료의 지하부 생중량은 cluster 1 재배지에서 수집한 산양삼 시료에 비해 cluster 2에서 유의적 (p = 0.04)으로 높았다. 산양삼 생육특성과 토양세균군집 간의 상관관계를 분석한 결과, 산양삼의 생육은 토양 pH가 낮고 Acidobacteria의 상대적 빈도수가 높은 토양에서 증가하였으며, Acidobacteriia와 Koribacteraceae의 상대적 빈도수는 산양삼의 생육과 유의적인 정의 상관관계를 보이는 것으로 나타났다. 본 연구 결과는 토양미생물군집과 산양삼 생육 간의 상관관계를 구명하는 중요한 자료가 될 것으로 생각되고, 나아가 산양삼 재배적지를 선정하는데 있어 보다 명확한 정보를 제공할 수 있을 것으로 사료된다.