• Journal of Species Research
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• v.12 no.3
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• pp.229-239
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• 2023

We isolated and identified 25 unrecorded bacterial species belonging to the phylum Actinomycetota found in the Republic of Korea. Sequence comparison of 16S rRNA was performed using the NCBI BLAST and EzBioCloud database to identify 25 species, which had a 16S rRNA gene sequence similarity of >98.8% and were allocated as unrecorded species in the Republic of Korea. Among the 25 unrecorded bacterial strains, Streptomyces was the most common with nine species, followed by Leifsonia with two species. Isoptericola, Nocardioides, Dermacoccus, Sinomonas, Patulibacter, Marmoricola, Allobranchiibius, Aldersonia, Actinokineospora, Agromyces, Aeromicrobium, Cellulomonas, and Gordonia with one species each were also found. Twenty-five unrecorded species were excavated in various environments, such as tidal flats, ferns, soil, pine cones, moss, mud, wetlands, and plants. These isolates were characterized on the basis of their phylogenetic, biochemical properties, and morphological data, and species descriptions were provided.

• Korean Journal of Environmental Biology
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• v.24 no.4
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• pp.307-313
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• 2006

Seasonal variation of marine bacterial community was analyzed in the surface sea water collected from one of the stations locating at Tongyeoung coastal area, Korea. The results obtained by the culture method through identification with the VITEK Microbe ID system after pure culture in the selective medium were compared with those obtained by the DGGE based 16S rRNA PCR method. The composition of the marine bacterial community in the sea water samples harvested in September, 2004, November, 2004, January, 2005, May, 2005 and August, 2005 determined by the culture method showed 5, 5, 4, 6, and 10 strains respectively. Pseudomonas fluorescens and Acinetobacter lwoffii were detected in all seasons. The other strains were identified to be Pseudomonas stutzeri, Sphingomonas paucimobilis, Burkholderia mallei and Chryseobacterium indologenes. In contrast, the 16S rRNA PCR-DGGE method detected 10, 11, 6, 9 and 13 populations respectively in the same sea water samples and the strains were identified to be Acinetobacter lwoffii, Burkholderia mallei, Pseudomonas fluoresence, Actinobacillus ureae, Burkholderia sp., Pseudomonas stutzeri, Roseobacter sp., Vibrio parahaemolyticue, Sphingomonas paucimobilis and Rugeria algocolus. This results indicated that the DGGE based 16S rRNA PCR method was more efficient than the culture method for the grasp of the characteristics of the marine bacterial community.

• Journal of Korean society of Dental Hygiene
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• v.18 no.5
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• pp.843-852
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• 2018

Objectives: The study aimed to isolate the abundant bacteria in dental caries in children and to investigate the bacterial species involved in addition to those that have been previously reported. Methods: The specimens were collected from the supragingival plaques of each dental caries area, pit and fissure caries, deep dentinal caries, smooth surface caries, and dental caries, and from healthy subjects in the control group. Bacteria were cultured from these specimens, DNA was extracted from the isolated bacteria, and the 16S rRNA gene sequences were analyzed and identified. Results: Based on the results of the 16S rRNA gene sequence analysis for the 90 strains of dominant bacteria from the 45 specimens, 5, 7, 8, 7, and 13 species were identified from the supragingival plaques from healthy teeth, pit and fissure caries, deep dentinal caries, smooth surface caries, and dental caries, respectively. In healthy teeth, Actinomyces naeslundii dominated. Corynebacterium durum, Ralstonia pickettii, and Streptococcus intermedius showed equal distribution. The dominant bacterial species in dental caries, S. sanguinis, showed the greatest difference in prevalence in pit and fissure caries. In deep dentinal caries, S. mutans and Lactobacillus rhamnosus were dominant; in smooth surface caries, S. mutans and S. sanguinis were dominant; and in the supragingival plaques of dental caries, S. sanguinis and S. mutans were dominant. Conclusions: The bacterial species isolated from dental caries encompassed four phyla, eight genera, and 22 species. In addition, the SS1-2 strain, belonging to the genus Neisseria, was identified as a new species from among the isolated strains.

• 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.

• The Plant Pathology Journal
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• v.16 no.5
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• pp.252-256
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• 2000

The 16S-23S rRNA intergenic spacer regions (ISRs) were sequenced and analyzed to design specific primer for identification of Pectobacterium chrysanthemi. Two types ISRs, large and small ISRs, were identified from three strains (ATCC 11663, KACC 10163 and KACC 10165) of P. chrysanthemi and Pectobacterium carotovorum subsp. carotovorum ATCC 15713.Large ISRs contained transfer RNA-Ile(tRNA$^{Ile}$)and tRNA$^{Ala}$, and small ISRs contained tRNA$^{Glu}$. Size of the small ISRs of P. chrysanthemi ranged on 354-356 bp, while it was 451 bp in small ISR of P. carotovorum subsp. carotovorum ATCC 15713. From hypervariable region of small ISRs, species-specific primer for P. chrysanthemi with 20 bp length (CHPG) was designed from hypervariable region of small ISRs, which was used as forward promer to detect P. chrysanthemi strains with R23-1R produced PCR product of about 260bp size (CHSF) only from P. chrysanthemi strains, not from other Pectobacterium spp. and Erwinia spp. Direct PCR from bacterial cell without extracting DNA successfully amplified a specific fragment, CHSF, from P. chrysanthemi ATCC 11663. The limit of PCR detection was 1${\pm}10^2$ cfu/ml.

• Journal of Microbiology and Biotechnology
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• v.22 no.3
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• pp.301-310
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• 2012

Prosopis juliflora and Parthenium hysterophorus are the two arid, exotic weeds of India that are characterized by distinct, profuse growth even in nutritionally poor soils and environmentally stressed conditions. Owing to the exceptional growth nature of these two plants, they are believed to harbor some novel bacterial communities with wide adaptability in their rhizosphere. Hence, in the present study, the bacterial communities associated with the rhizosphere of Prosopis and Parthenium were characterized by clonal 16S rRNA gene sequence analysis. The culturable microbial counts in the rhizosphere of these two plants were higher than bulk soils, possibly influenced by the root exudates of these two plants. The phylogenetic analysis of V1_V2 domains of the 16S rRNA gene indicated a wider range of bacterial communities present in the rhizosphere of these two plants than in bulk soils and the predominant genera included Acidobacteria, Gammaproteobacteria, and Bacteriodetes in the rhizosphere of Prosopis, and Acidobacteria, Betaproteobacteria, and Nitrospirae in the Parthenium rhizosphere. The diversity of bacterial communities was more pronounced in the Parthenium rhizosphere than in the Prosopis rhizosphere. This culture-independent bacterial analysis offered extensive possibilities of unraveling novel microbes in the rhizospheres of Prosopis and Parthenium with genes for diverse functions, which could be exploited for nutrient transformation and stress tolerance in cultivated crops.

• Journal of Species Research
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• v.6 no.2
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• pp.163-170
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• 2017

As a part of the research program 'Survey of freshwater organisms and specimen collection', freshwater samples were collected from Lakes Soyang and Chungju in 2016. Hundreds of bacterial strains were isolated from the samples and were identified based on 16S rRNA gene sequences. Among the bacterial isolates, strains showing higher than 98.7% sequence similarity with validly published bacterial species not reported in Korea were selected as unrecorded bacterial species. Based on 16S rRNA gene sequence similarity, 17 strains were identified as unrecorded bacterial species in Korea. The 17 bacterial strains were phylogenetically diverse and belonged to four phyla, seven classes, 13 orders, 14 families, and 16 genera. At generic level, the unreported species were affiliated with Caulobacter, Paracoccus, and Mesorhizobium of the class Alphaproteobacteria, Deefgea, Undibacterium, Chitinimonas, Inhella, and Sphaerotilus of the class Betaproteobacteria, Vibrio and Cellvibrio of the class Gammaproteobacteria, Sanguibacter and Clavibacter of the phylum Actinobacteria, Lactococcus of the phylum Firmicutes, Deinococcus of the class Deinococci, and Chryseobacterium and Flavobacterium of the phylum Bacteroidetes. The unreported species were further characterized by examining Gram reaction, colony and cell morphology, biochemical properties, and phylogenetic position. The detailed description of the 17 unreported species are also provided.

• Asian-Australasian Journal of Animal Sciences
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• v.24 no.11
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• pp.1552-1559
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• 2011

Real time PCR was used in this study to determine the effect of triticale dried distillers grains with solubles (TDDGS) as a replacement for grain or barley silage in finishing diets on the presence of six classical ruminal bacterial species (Succinivibrio dextrinosolvens, Selenomonas ruminantium, Streptococcus bovis, Megasphaera elsdenii, Prevotella ruminicola and Fibrobacter succinogenes) within the rumen contents of feedlot cattle. This study was divided into a step-wise adaptation experiment (112 days) that examined the effects of adaptation to diets containing increasing levels of TDDGS up to 30% (n = 4), a short-term experiment comparing animals (n = 16) fed control, 20%, 25% or 30% TDDGS diets over 28 days, and a rapid transition experiment (56 days) where animals (n = 4) were rapidly switched from a diet containing 30% TDDGS to a barley-based diet with no TDDGS. It was found that feeding TDDGS as replacement for barley grain (control vs. 20% TDDGS) decreased 16S rRNA copy numbers of starch-fermenting S. ruminantium and S. bovis (p<0.001 and p = 0.04, respectively), but did not alter 16S rRNA copy numbers of the other rumen bacteria. Furthermore, feeding TDDGS as a replacement barley silage (20% vs. 25% and 30% TDDGS) increased 16S rRNA copy numbers of S. ruminantium, M. elsdenii and F. succinogenes (p<0.001; p = 0.03 and p<0.001, respectively), but decreased (p<0.001) the 16S rRNA copy number of P. ruminicola. Upon removal of 30% TDDGS and return to the control diet, 16S rRNA copy numbers of S. ruminantium, M. elsdenii and F. succinogenes decreased (p = 0.01; p = 0.03 and p = 0.01, respectively), but S. dextrinosolvens and S. bovis increased (p = 0.04 and p = 0.009, respectively). The results suggest that replacement of TDDGS for grain reduces 16S rRNA copy numbers of starch-fermenting bacteria, whereas substitution for barley silage increases 16S rRNA copy numbers of bacteria involved in fibre digestion and the metabolism of lactic acid. This outcome supports the contention that the fibre in TDDGS is highly fermentable.

• Journal of Species Research
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• v.12 no.2
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• pp.165-173
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• 2023

Bacterial communities inhabiting islands play a vital role in the functioning and formation of a unique, isolated ecosystem. Nevertheless, there has been a lack of systematic research on the indigenous microbiological resources of the islands in Korea. To excavate microbial resources for further studies on the metabolism and biotechnological potential, a standard dilution plating was applied to coastal seawater samples collected from islands along the west coast of the Korean Peninsula, including Deokjeokdo, Baengnyeongdo, and Daebudo in 2022. A total of 2,007 bacterial strains were isolated from the samples as single colonies and identified using 16S rRNA gene sequence analyses. A total of 20 strains, with ≥98.7% 16S rRNA gene sequence similarity to bacterial species having validly published names but not reported in Korea, were designated as unrecorded bacterial species in Korea. The unrecorded bacterial strains were phylogenetically diverse and belonged to four phyla, five classes, 12 orders, 17 families, and 18 genera. The unreported species were assigned to Algimonas, Amylibacter, Notoacmeibacter, Roseibium, and Terasakiella of the class Alphaproteobacteria; Alteromonas, Congregibacter, Marinagarivorans, Marinicella, Oceanospirillum, Psychromonas, Thalassotalea, Umboniibacter, and Vibrio of the class Gammaproteobacteria; Lutibacter and Owenweeksia of the class Flavobacteriia; Paenibacillus of the class Bacilli; and Pelagicoccus of the class Opitutae. The taxonomic characteristics of the unreported species, including morphology, biochemistry, and phylogenetic position are provided in detail.

• Korean Journal of Microbiology
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• v.40 no.4
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• pp.307-312
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• 2004

Diversity of the bacterial communities and the relation between community structure and components of waste­water were analyzed by 16S rRNA-based molecular techniques. Clone libraries of the 16S rDNAs from the sludges were constructed by PCR and cloning. The 1,151 clones from a sludge sample of sewage treatment plant were clustered into 699 RFLP phylotypes and the 1,228 clones from the wastewater disposal plant of chemical industry were clustered into 300 RFLP phylotypes. Shannon-Weiner diversity indices of two sampling sites were 8.7 and 6.1, indicating that the bacterial community structure of sewage treatment plant was more diverse than that of wastewater disposal plant of chemical industry. Forty clones belonging to predominant RFLP types were selected and sequenced. Seventy percent (28 clones) of the sequenced clones were related to the uncultured bacteria in public databases. The ${\beta}-Proteobacteria$ dominated in the bacterial communities of investigated two sludge samples. 16S rDNA sequences of the sewage treatment plant were similar to those of other activated sludges, while the bacterial community in wastewater disposal plant of chemical industry rep­resented the strains identified from high-temperature, anaerobic, hydrocarbon-rich, and sulfur-rich environ­ments. This result suggested that bacterial communities depended upon the components of wastewater.