• Journal of Species Research
• /
• v.7 no.2
• /
• pp.123-134
• /
• 2018

A total of 22 bacterial strains belonging to the phylum Bacteroidetes were isolated primarily from aquatic environments such as seawater, freshwater, lagoon and tidal flat. One of these 22 strains was isolated from ginseng soil. Phylogenetic analyses based on 16S rRNA gene sequences revealed that 21 strains showed the high sequence similarities(${\geq}98.7%$) to the closest type strains and formed robust phylogenetic clades with closely related species in the phylum Bacteroidetes. One strain, which had been previously classified as Balneola vulgaris in the phylum Bacteroidetes, was identified as a member of the newly described phylum Rhodothermaeota. These strains had not been previously reported in Korea. Here, we report 21 species of 13 genera in the phylum Bacteroidetes and one species in the phylum Rhodothermaeota which were not reported in Korea. Morphological, biochemical, and physiological characteristics, isolation sources, and NIBR deposit numbers are described in the species descriptions.

• Journal of Species Research
• /
• v.10 no.1
• /
• pp.23-45
• /
• 2021

For the collection of indigenous prokaryotic species in Korea, 77 strains within the phylum Actinobacteria were isolated from various environmental samples, fermented foods, animals and clinical specimens in 2019. Each strain showed high 16S rRNA gene sequence similarity (>98.8%) and formed a robust phylogenetic clade with actinobacterial species that were already defined and validated with nomenclature. There is no official description of these 77 bacterial species in Korea. The isolates were assigned to 77 species, 31 genera, 18 families, 14 orders and 2 classes of the phylum Actinobacteria. All the strains except one Coriobacteriia strain were affiliated within the class Actinomycetia. Among them, the orders Streptomycetales and Microbacteriales were predominant. A number of strains were isolated from forest soils, riverside soils, and ginseng cultivated soils. Twenty-nine strains were isolated from 'Protected Ecosystem and Scenery Areas'. Morphological properties, basic biochemical characteristics, isolation source and strain IDs are described in the species descriptions.

• Journal of Species Research
• /
• v.5 no.1
• /
• pp.1-13
• /
• 2016

To discover and characterize indigenous species in Korea, a total of 31 bacterial strains that belong to the phylum Actinobacteria were isolated from various niches in Korea. Each strain showed the high sequence similarity (>99.1%) with the closest bacterial species, forming a robust phylogenetic clade. These strains have not been previously recorded in Korea. According to the recently updated taxonomy of the phylum Actinobacteria based upon 16S rRNA trees, we report 25 genera of 13 families within 5 orders of the class Actinobacteria as actinobacterial species found in Korea. Cellular morphology, Gram staining, basic biochemical characteristics are described in the species description.

• Journal of Species Research
• /
• v.4 no.2
• /
• pp.137-144
• /
• 2015

As a result of the research project 'Survey and excavation of Korean indigenous species' to secure unrecorded species in Korea, a total of 14 unreported bacterial strains assigned to the phyla Deinococcus-Thermus and Bacteroidetes were isolated from various environmental habitats all around Korea. On the basis of 16S rRNA gene sequence similarity and affiliation to the clade with the closest species, it was concluded that the isolates represent deep groups of the phyla Deinococcus-Thermus and Bacteroidetes. There have been no records about these 14 unreported species in Korea; therefore 2 species of 2 genera in the class Deinococci within the phylum Deinococcus-Thermus, and 11 species of 9 genera in the class Flavobacteriia and one species in one genus in the class Sphigobacteriia within the phylum Bacteroidetes are described as unreported species found in Korea. Gram staining reaction, morphological and other biochemical characteristics are described in the species description section.

• Journal of Species Research
• /
• v.7 no.3
• /
• pp.231-239
• /
• 2018

While screening indigenous prokaryotic species in Republic of Korea in 2017, a total of 17 bacterial strains assigned to the phylum Bacteroidetes were isolated from a variety of environmental habitats including water of fountain, tidal flat, plant root, soil, the gut of Russian grayling butterfly, ginseng field, seawater, lagoon and seashore sand. From the 16S rRNA gene sequence similarity of more than 98.7% and the formation of a robust phylogenetic clade with the closest species, it was found that the 17 strains belong to independent and recognized bacterial species. There has been no official report that the identified 17 species have been previously isolated in the Republic of Korea. Thus, 15 species in 10 genera of one family in the order Flavobacteriales, one species in one genus of one family in the order Cytophagales, and one species in one genus of one family in the order Sphingobacteriales are proposed as unrecorded species of the phylum Bacteroidetes found in the Republic of Korea. Gram reaction, colony and cell morphology, basic phenotypic characteristics, isolation source, taxonomic status, strain ID and other information are described in the species descriptions.

• Journal of Species Research
• /
• v.7 no.1
• /
• pp.36-49
• /
• 2018

During a study to discover indigenous prokaryotic species in Korea in 2016, a total of 42 actinobacterial isolates were recovered from various environmental samples collected from natural cave, squid, sewage, sea water, trees, droppings of birds, freshwater, eelgrass, mud flat, sediment and soil. On the basis of a tight phylogenetic clade with the closest species and high level of 16S rRNA gene sequence similarity, it was shown that each isolate was assigned to independent and previously described bacterial species which were assigned to the phylum Actinobacteria. The following 42 species have not been reported in Korea: eight species in two genera n the order Corynebacteriales, 26 species of 16 genera in the Micrococcales, one species of one genus in the Micromonosporales, one species of one genus in the Propionibacteriales, four species of two genera in the Streptomycetales and two species of two genera in the Streptosporangiale. Cell morphology, Gram staining reaction, colony colors and features, the media and conditions of incubation, physiological and biochemical characteristics, origins of isolation and strain IDs of 42 unrecorded actinobacterial species are presented in the species description.

• Korean Journal of Microbiology
• /
• v.37 no.1
• /
• pp.85-91
• /
• 2001

Biological treatment of benzene and toluene contaminated soil was investigated in laboratory microcosm of 16 different types for degrading benzene and toluene by indigenous bacteria. At the experimental conditions of the microcosms fast degrading benzene and toluene, moisture contents were 30% and 60% in a soil gap and content of powdered-activated carbon(PCA) for adhesion of benzene and toluene-degrading bacteria was 1% in total soil mass. At the conclusion of the shifted bacteria community, Case 6 and case 7 were operated until 10 days, and then the total cell number and the number of benzene and toluene degrading bacteria were investigated. The total cell number of Case 6 and Case 7 increased 488 fold and 308 fold of total indigenous cell, respectively. The number of benzene and toluene degrading bacteria increased and maintained the percentages occupied in pre-operating microcosm. Species of benzene and toluene degrading bacteria in microcosm changed from species of Gram negative bacteria to Gram positive bacterial species after soil exposed to benzene and toluene.

• Journal of Species Research
• /
• v.6 no.2
• /
• pp.101-118
• /
• 2017

In an investigation of indigenous prokaryotic species in Korea, a total of 57 bacterial strains assigned to the classes Betaproteobacteria and Gammaproteobacteria were isolated from diverse environments. Samples were collected from fresh water, natural caves, soil, paddy fields, lakes, sea water, jeotgal (fermented seafood), salt flats, soil from abandoned mines, plant roots, digestive organs of both Japanese crested ibis (Nipponia nippon) and Burmese python (Python molurus bivittatus) and tidal flats. From the high 16S rRNA gene sequence similarity (>98.7%) and formation of robust phylogenetic clades with closely related species, it was determined that each strain belonged to an independent and predefined bacterial species within either the Betaproteobacteria or Gammaproteobacteria. There is no official report or publication that describes these 57 proteobacterial species in Korea. Overall, in the class Betaproteobacteria there were 16 species in 12 genera of 4 families in the order Burkholderiales and two species in two genera of one family in the order Neisseriales. Within the class Gammaproteobacteia, there were five species in four genera of four families in the order Alteromonadales, 12 species in 11 genera of one family in the order Enterobacteriales, four species in four genera of three families in the order Oceanospirillales, 11 species in four genera of two families in the order Pseudomonadales, two species in the order Vibrionales and five species in five genera of one family in the order Xanthomonadales. Gram reaction, colony and cell morphology, basic biochemical characteristics, isolation source and strain IDs are described in the species description section.

• Journal of Microbiology and Biotechnology
• /
• v.20 no.1
• /
• pp.153-160
• /
• 2010

The present study was carried out for the isolation of bacteriocin-producing enterococci from indigenous sources. Gram-positive enterococci are known for having the ability to produce enterocins with good antimicrobial potential. A total of 34 strains were isolated from processed dairy products of Pakistan and seven out of them were found to be member of genus Enterococcus on selective enumeration. Biochemical and molecular characterization revealed that four of these isolates (IJ-03, IJ-07, IJ-11, and IJ-12) were Enterococcus faecalis and three (IJ-06, IJ-21, and IJ-31) were Enterococcus faecium. Local processed cheese was the source of all enterococcal isolates, except E. faecium IJ-21 and IJ-31, which were isolated from indigenous yoghurt and butter samples, respectively. Bacterial isolates were sensitive to commonly used antibiotics except methicillin and kanamycin. They also lacked critical virulence determinants, mainly cytolysin (cyl), gelatinase (gel), enterococcal surface protein (esp), and vancomycin resistance (vanA and vanB). Polymerase chain reaction amplification identified that enterocin A and P genes were present in the genome of E. faecium IJ-06 and IJ-21, whereas the E. faecium IJ-31 genome showed only enterocin P genes. No amplification was observed for genes that corresponded with the enterocins 31, AS-48, L50A, and L50B, and ent 1071A and 1071B. There were no signals of amplification found for E. faecalis IJ-11, indicating that the antimicrobial activity was because of an enterocin different from those checked by PCR. Hence, the indigenous bacterial isolates have great potential for bacteriocin production and they had antibacterial activity against a variety of closely related species.

• Journal of Species Research
• /
• v.8 no.1
• /
• pp.97-108
• /
• 2019

For the collection of indigenous prokaryotic species in Korea, 35 strains within the class Actinobacteria were isolated from various environmental samples (animals and clinical specimens) in 2017. Each strain showed high 16S rRNA gene sequence similarity (>98.8%) and formed a robust clade with recognized actinobacterial species. The isolates were assigned to 35 species, 22 genera, 15 families, and 8 orders of the class Actinobacteria. There are no official descriptions of these 35 bacterial species in Korea. Morphological properties, basic biochemical characteristics, isolation source, and strain IDs are included in the species descriptions.