• 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.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.18 no.1
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• pp.141-147
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• 2017

In this study, a meta-analysis of fecal bacteria in dogs was conducted using 16S rRNA gene sequences that have been recovered from cloning and Sanger sequencing. For this meta-analysis, we retrieved all 16S rRNA gene sequences recovered from fecal bacteria in dogs in the RDP database (Release 11, Update 3). A total of 420 sequences were identified from the RDP database, 42 of which were also recovered from cultured isolates. The 420 sequences were assigned to five phyla, of which Firmicutes was the most predominant phylum, accounting for 55.2% of all 420 sequences. Bacteroidetes was the second most predominant phylum, accounting for 32.1% of the 420 sequences, followed by Actinobacteria (6.4%), Fusobacteria (3.8%), and Proteobacteria (2.4%). The genus Bacteroides within Bacteroidetes was the largest, representing 30.0% of all 420 sequences, while the putative genus Clostridium XI within Firmicutes was the second largest, representing 27.4% of all 420 sequences. A total of 82 operational taxonomic units (OTUs) that are putative species were identified from the retrieved sequences. The results of this study will improve understanding of the diversity of fecal bacteria in dogs and guide future studies on the health and well-being of dogs.

• Nutrition Research and Practice
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• v.9 no.3
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• pp.242-248
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• 2015

BACKGROUND/OBJECTIVES: Feeding in infancy is the most significant determinant of the intestinal microbiota in early life. The aim of this study was to determine the gut microbiota of Korean infants and compare the microbiota obtained between breast-fed and formula-fed Korean infants. SUBJECTS/METHODS: We analyzed the microbial communities in fecal samples collected from twenty 4-week old Korean (ten samples in each breast-fed or formula-fed) infants using pyrosequencing. RESULTS: The fecal microbiota of the 4-week-old Korean infants consisted of the three phyla Actinobacteria, Firmicutes, and Proteobacteria. In addition, five species, including Bifidocbacterium longum, Streptococcus salivarius, Strepotococcus lactarius, Streptococcus pseudopneumoniae, and Lactobacillus gasseri were common commensal intestinal microbiota in all infants. The predominant intestinal microbiota in the breast-fed infants (BFI) included the phylum Actinobacteria (average 70.55%), family Bifidobacteriacea (70.12%), genus Bifidobacterium (70.03%) and species Bifidobacterium longum (69.96%). In the microbiota from the formula-fed infants (FFI), the proportion of the phylum Actinobacteria (40.68%) was less, whereas the proportions of Firmicutes (45.38%) and Proteobacteria (13.85%) as well as the diversity of each taxonomic level were greater, compared to those of the BFI. The probiotic species found in the 4-week-old Korean infants were Bifidobacterium longum, Streptococcus salivarius, and Lactobacillus gasseri. These probiotic species accounted for 93.81% of the microbiota from the BFI, while only 63.80% of the microbiota from the FFI. In particular, B. longum was more abundant in BFI (69.96%) than in FFI (34.17%). CONCLUSIONS: Breast milk supports the growth of B. longum and inhibits others. To the best of our knowledge, this study was the first attempt to analyze the gut microbiota of healthy Korean infants according to the feeding type using pyrosequencing. Our data can be used as a basis for further studies to investigate the development of intestinal microbiota with aging and disease status.

• Korean Journal of Microbiology
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• v.52 no.3
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• pp.365-374
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• 2016

In high-latitude regions, temperature has risen ($0.6^{\circ}C$ per decade) and this leads to the increase in microbial degradability against soil organic carbon (SOC). Furthermore, the decomposed SOC is converted into green-house gases ($CO_2$ and $CH_4$) and their release could further increase the rate of climate change. Thus, understanding the microbial diversity and their functions linked with SOC degradation in soil-thawing model is necessary. In this study, we divided tundra soil from Council, Alaska into two depth regions (30-40 cm and 50-60 cm of depth, designated as SPF and PF, respectively) and incubated that for 108 days at $0^{\circ}C$. A total of 111,804 reads were obtained through a pyrosequencing-based metagenomic study during the microcosm experiments, and 574-1,128 of bacterial operational taxonomic units (OTUs) and 30-57 of archaeal OTUs were observed. Taxonomic analysis showed that the distribution of bacterial taxa was significantly different between two samples. In detail, the relative abundance of phyla Actinobacteria and Firmicutes largely increased in SPF and PF soil, respectively, while phyla Crenarchaeota was increased in both soil samples. Weight measurement and gel permeation chromatography of the SOC extracts demonstrated that polymerization of humic acids, main component of SOC, occurred during the microcosm experiments. Taken together our results indicate that these bacterial and archaeal phyla could play a key function in SOC degradation and utilization in cold tundra soil.

• 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 $K^+$.

• Korean Journal of Microbiology
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• v.42 no.2
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• pp.103-110
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• 2006

T-RFLP analysis and clone sequencing analysis based on bacterial 16S rDNA were conducted to assess bacterial community structure and diversity in Zoysia japonica soil treated with liquid fertilizer containing amino acids(LFcAA) after spray with herbicide. The results of T-RFLP (terminal restriction fragment length poly-morphism) analysis using restriction enzyme Hae III showed that the T-RFs of various size appeared evenly in the 32 clones of KD3 and 38 clones of KD4 respectively that had been treated with liquid fertilizer containing amino acid(LFcAA) compared to 23 clones of KD2 hat had not been treated with LFcAA. The microbial com- munity structure in KD2 appeared less diverse than those in KD3 and KD4. Analysis of partial sequences for 110 clones from KDI (control), KD2 (non-treated), KD3 (LFcAA 1X), KD4 (LFcAA 2X), respectively, revealed that most bacteria were related with uncultured bacteria in a 16S rDNA sequence similarity range of 91-99% through blast search. Otherwise, the other clones were members of proteobacteria, Acidobacteria, Act-inobacteria, Sphingobacteria and Planctomyces groups. Especially in KD4, members of Alpha Proteobacteria, Rhizobiales, Sphigomonadales, Caulobacterales, Gamma Proteobacteria, the genus Pseudomonas, Betapro-teobacteria, Nitrosomonadales and genus Nitrosospira appeared to be dominant. In addition, Acidobacteria group, Actinobacteria group, Planctomycetacia and Sphingobacteria were also shown. The microbial com-munity structure in Z. japonica soil sprayed with herbicide was affected by LFcAA.

• Journal of Life Science
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• v.26 no.7
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• pp.819-825
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• 2016

The present study was done to assess the diversity of the bacterial community associated with Ulva pertusa collected from Jeju Island using Restriction Fragment Length Polymorphism (RFLP) marker analysis. For RFLP analysis, a total of 145 bacterial strains associated with Ulva pertusa were screened and cultivated using Marine agar and R2A agar. The PCR amplicons of the 16S rRNA gene from all the isolated strains were digested with HaeIII and RsaI restriction enzymes and then classified into different groups according to their restriction patterns. Strains selected based on the RFLP patterns showed more than 91% 16S rRNA gene sequence similarity when compared with known bacterial species, which include 4 phyla - proteobacteria (alpha-proteobacteria, beta-proteobacteria, gamma-proteobacteria - 63%), firmicutes (11%), actinobacteria (4%), bacteroidetes (22%)–as well as 7 classes (actinobacteria, flavobacteriia, cytophagia, bacilli, α-proteobacteria, γ-proteobacteria, β-proteobacteria), 13 orders, 18 families, and 27 genera. These results confirmed a wide diversity of bacterial communities as contrasted with other regions. The newly isolated 10 strains, which show 16S rRNA sequence similarity of <97% compared to previously identified bacteria, could be noble species. Further experiments, such as morphological, physiological, and biochemical classification, are necessary to confirm the novelty of the newly isolated 10 strains.

• Korean Journal of Microbiology
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• v.49 no.4
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• pp.377-382
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• 2013

The bacterial community structures of the marine sponge, Dactylospongia metachromia, collected from Chuuk of Micronesia on February 2012, were analyzed by denaturing gradient gel electrophoresis (DGGE). The DGGE fingerprints of two individuals of D. metachromia, CH607 and CH840 showed the same band patterns. The sequences derived from DGGE bands revealed 93~100% similarities with known bacterial species in the public database and high similarity with uncultured bacterial clones. The bacterial community structures of both D. metachromia sponges (CH607, CH840) were composed of 6 phyla, 8 classes: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, Cyanobacteria, Spirochaetes. DGGE fingerprint - based phylogenetic analysis revealed that the bacterial community profiles were identical in two individuals of the same sponge species collected from the same geographical location.

• Journal of Microbiology and Biotechnology
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• v.27 no.4
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• pp.825-833
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• 2017

Strain IMCC26207 was isolated from the surface layer of Lake Soyang in Korea by the dilutionto-extinction culturing method, using a liquid medium prepared with filtered and autoclaved lake water. The strain could neither be maintained in a synthetic medium other than natural freshwater medium nor grown on solid agar plates. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain IMCC26207 formed a distinct lineage in the order Acidimicrobiales of the phylum Actinobacteria. The closest relative among the previously identified bacterial taxa was "Candidatus Microthrix parvicella" with 16S rRNA gene sequence similarity of 91.7%. Here, the draft genome sequence of strain IMCC26207, a freshwater actinobacterium, is reported with the description of the genome properties and annotation summary. The draft genome consisted of 10 contigs with a total size of 3,316,799 bp and an average G+C content of 57.3%. The IMCC26207 genome was predicted to contain 2,975 protein-coding genes and 51 non-coding RNA genes, including 45 tRNA genes. Approximately 76.8% of the protein coding genes could be assigned with a specific function. Annotation of the IMCC26207 genome showed several traits of adaptation to living in oligotrophic freshwater environments, such as phosphorus-limited condition. Comparative genomic analysis revealed that the genome of strain IMCC26207 was distinct from that of "Candidatus Microthrix" strains; therefore, we propose the name "Candidatus Limnosphaera aquatica" for this bacterium.

• Korean Journal of Environmental Biology
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• v.31 no.2
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• pp.158-164
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• 2013

A microcystin-degrading bacterium was isolated from Daechung reservoir, Korea. The isolated bacterium was identified as Microbacterium sp. by 16S rRNA gene sequence analysis, and designated as Microbacterium sp. MA21. This strain degraded cyanobacterial hepatotoxin, microcystin-LR, over 80% when incubated at $30^{\circ}C$ for 12 hr in R2A medium. Two unknown metabolites of microcystin were also identified during the degradation process. Although only Sphinogomonas and Actinobacteria have been known to degrade microcystin previously, this is the first report that Microbacterium sp. MA21 could degrade microcystin.