A Report of 14 Unrecorded Bacterial Species in Korea Isolated in 2017

Journal of Species Research 7(2):161-180, 2018

A report of 14 unrecorded bacterial species in Korea isolated in 2017

Ju-Young Kim1, Jun Hwee Jang1, Soohyun Maeng2, Myung-Suk Kang3 and Myung Kyum Kim1,*

1Department of Bio & Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul 01797, Republic of Korea 2Department of Public Health Sciences, Graduate School, Korea University, Seoul 02841, Republic of Korea 3Biological Resources Utilization Department, National Institute of Biological Resources, Incheon 22689, Republic of Korea

*Correspondent: [email protected]

Fourteen bacterial strains, low10-4-1, J11015, 17J27-22, 17G22-9, 17G9-4, 17Bio_15, 17gy_33, 17SD1_21, Strain8, 17Sr1_17, J21014T, H31021, 17J49-9, and 17J80-6 assigned to the phylum Actinobacteria, Bacteroidetes, Deinococcus-Thermus, and Firmicutes were isolated from soil samples. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strains low10-4-1, J11015, 17J27-22, 17G22-9, 17G9-4, 17Bio_15, 17gy_33, 17SD1_21, Strain8, 17Sr1_17, J21014T, H31021, 17J49-9, and 17J80-6 were most closely related to Marmoricola aurantiacus (98.9%), Calidifontibacter indicus (99.8%), Gordonia soli (98.8%), Rhodococcus globerulus (99.5%), Pseudarthrobacter siccitolerans (99.1%), Hymenobacter qilianensis (98.7%), Hymenobacter terrae (99.0%), Deinococcus yunweiensis (99.2%), Deinococcus proteolyticus (99.7%), Domibacillus indicus (99.2%), Exiguobacterium mexicanum (100.0%), Kurthia senegalensis (99.1%), Lysinibacillus composti (99.6%), and Bacillus loiseleuriae (99.3%). These fourteen species have never been reported in Korea, therefore we report them here for the first time. Keywords: 16S rRNA, Actinobacteria, bacterial diversity, Bacteroidetes, Deinococcus-Thermus, Firmicutes, unreported species

Introduction non-spore-forming bacteria (Madigan et al., 2005). They have DNA with 40-48% of GC content. Bacteroides are There are massive numbers of bacteria on earth present in the environments such as in soil, sediments, uniquely adapted to many environments. We isolated sea water and in the gastrointestinal system of animals species that have not been officially reported in Korea. (Johnson et al., 2016). This genus, tends to attract more In 2017, we collected diverse soil samples in Seoul, and more attention because of its abundance in the guts Jeju-do, and Gyeonggi-do in Korea and isolated unre- of human (Scarpellini et al., 2015). Several novel spe- ported bacterial species. The identified bacterial species cies have been recently proposed in the genus Bacteroi- belonged to the phyla Actinobacteria, Bacteroidetes, des (Hayashi et al., 2007; Sakamoto et al., 2011). These Deinococcus-Thermus, and Firmicutes. taxonomic studies were mainly based on 16S rRNA The Actinobacteria are the largest phyla and ubiq- gene sequence analysis (Shah et al., 2009). uitously distributed in both aquatic and terrestrial eco- Deinococcus-Thermus is a phylum of gram-positive systems (Barka et al., 2016). They are Gram-positive bacteria, also known as extremophiles (Griffith et al., filamentous bacteria with a high G+C content in their 2007). The group is distinguished by species that resist genomes. They are mostly mesophilic and can grow at the lethal effects of exposure to ionizing radiation and temperatures between 25 and 30°C however, thermo- UV light, and by species that thrive at high temperature philic Actinobacteria can grow at temperatures ranging (Battista, 2016). Deinococcus-Thermus is comprised of from 50 to 60°C (Edwards, 1993). They have numerous two orders, the Deinococcales and the Thermales. Gen- potential benefits for humans as some sources of antibi- erally, mesophilic species of Deinococcales demonstrate otics, antifungals, anticancer agents, and their secondary uncommon resistance to electromagnetic radiations metabolites are resistant to diseases (Barka et al., 2016). (Battista, 2016). The Thermales are thermophilic, can Bacteroides are a genus of Gram-negative, rod-shaped, grow at 60 and 80°C, but show no evidence of resistance 162 JOURNAL OF SPECIES RESEARCH Vol. 7, No. 2 to electromagnetic radiation. Despite these prominent Biochemical characteristics were performed by using and distinctive phenotypic differences, 16S ribosomal Biolog Microstation with GEN III microplate system. A ribonucleic acid sequences verify that members of these single colony was selected and emulsified into ‘inoculat- orders are evolved from same ancestor (Ho et al., 2016). ing fluid A’ (Biolog) for subsequent inoculation on to the So far, many Deinococcus sp. has been isolated based MicroPlate test plate (Biolog). More fastidious organisms, on 16S rRNA sequencing and proved for its radiation re- including capnophilic strains, were cultured on alterna- sistance (Srinivasan et al., 2012a; 2012b). tive media, according to the manufacturer’s instructions, The phylum Firmicutes is one of the most predominant and the inoculate was prepared to a specified transmit groups of prokaryotes in the microbiota of human’s guts. tance using a turbidimeter, as specified in the user guide. They include genera of outstanding relevance in biomed- For each isolate, 100 μL of the cell suspension was in- icine, health care, and industry (Lanza et al., 2015). Fir- oculated into each well of the MicroPlate, using a multi- micutes are gram-positive with low G+C content and channel pipette and incubated at 37°C for 24 h, according has specific property to form heat resistant endo-spore to growth characteristics. MicroPlates were read in the (Galperin, 2015). There is a consensus that they have di- MicroStation semi-automated reader after 24 h and re- verged from other bacterial phyla at an early stage (Lake sults interpreted by the identification system’s software et al., 2009). Later, the evolution of Firmicutes obviously (GEN III database, version 5.2.1). The system indicates included numerous events of lateral gene transfer to and the isolates which could not be identified after 20 h, are from representatives of other phyla and hence certain subjected to further incubation. Consequently, such iso- gene families are shared Firmicutes with Fusobacteria, lates were re-incubated and re-read between 3 and 6 h Thermotogae, and other groups (Mira et al., 2004). later (Wragg et al., 2014). Genomic DNA was extracted and 16S rRNA gene was amplified by PCR with 9F and 1492R universal bacterial

Material and Methods primers (Weisburg et al., 1991). The 16S rRNA gene sequences of the closely related strains were obtained Bacteria were isolated from different soil samples then from EzTaxon-e (http://eztaxon-e.ezbiocloud.net) (Kim were suspended on distilled water and serially diluted. et al., 2012) and edited using the BioEdit program (Hall, The aliquot was inoculated onto R2A agar and incubat- 1999). Multiple alignments were performed with the ed at 25°C for 3 days. The designated strain name, iso- MUSCL program (Edgar, 2004). Using the two-param- lation sources, growth media, and incubation conditions eter model (Kimura, 1983), calculated the evolutionary are summarized in Table 1. All strains were purified as distances. Phylogenetic trees were constructed using single colonies and stored as 20% glycerol suspension at the neighbor-joining (Saitou and Nei, 1987) in MEGA5 -80°C as well as freeze dried ampoules. Colony mor- program (Tamura, 2011) with bootstrap values based on phology and cell size of the strains were observed by 1,000 replications (Felsenstein, 1985). transmission electron microscopy (LIBRA 120, Carl Zeiss) using cells grown for 3 days at 25°C on R2A agar. Transmission electron micrograph of the strains are Results and Discussion shown in Fig. 1. Gram reaction was tested following the classic Gram procedure described by Doetsch (1981). Based on 16S rRNA gene sequence similarity, four-

Table 1. List of 16S rRNA gene sequence similarity, isolation source, medium, and incubation conditions of unrecorded strains. Strain ID Most closely related species Similarity (%) Isolation source Medium Incubation conditions low10-4-1 Marmoricola aurantiacus 98.9 Soil R2A 25°C, 3d J11015 Calidifontibacter indicus 99.8 Soil R2A 25°C, 3d 17J27-22 Gordonia soli 98.8 Soil R2A 25°C, 3d 17G22-9 Rhodococcus globerulus 99.5 Soil R2A 25°C, 3d 17G9-4 Pseudarthrobacter siccitolerans 99.1 Soil R2A 25°C, 3d 17Bio_15 Hymenobacter qilianensis 98.7 Soil R2A 25°C, 3d 17gy_33 Hymenobacter terrae 99.0 Soil R2A 25°C, 3d 17SD1_21 Deinococcus yunweiensis 99.2 Soil R2A 25°C, 3d Strain8 Deinococcus proteolyticus 99.7 Soil R2A 25°C, 3d 17Sr1_17 Domibacillus indicus 99.2 Soil R2A 25°C, 3d J21014T Exiguobacterium mexicanum 100.00 Soil R2A 25°C, 3d H31021 Kurthia senegalensis 99.13 Soil R2A 25°C, 3d 17J49-9 Lysinibacillus composti 99.66 Soil R2A 25°C, 3d 17J80-6 Bacillus loiseleuriae 99.32 Soil R2A 25°C, 3d May 2018 Kim et al. Unrecorded bacterial species from Korea 2017 163

(1) (2) (3) (4)

(5) (6) (7) (8)

(9) (10) (11) (12)

(13) (14)

Fig. 1. Transmission electron micrographs of the strains isolated in this study. Strains: 1, low10-4-1; 2, J11015; 3, 17J27-22; 4, 17G22-9; 5, 17G9-4; 6, 17Bio_15; 7, 17gy_33; 8, 17SD1_21; 9, Strain8; 10, 17Sr1_17; 11, J21014T; 12, H31021; 13, 17J49-9; 14, 17J80-6. teen of previously unreported bacterial species were uobacteriaceae (1 strain), and Bacillaceae (1 strain) of identified. The taxonomic composition and identifica- the phylum Firmicutes. At generic level, the strains be- tion results were summarized in Table 1. Five strains longed to 12 different genera: Marmoricola (1 species), belonged to the family Nocardioidaceae (1 strain), Der- Calidifontibacter (1 species), Gordonia (1 species), macoccaceae (1 strain), Nocardiaceae (2 strain), and Rhodococcus (1 species), Pseudarthrobacter (1 species), Micrococcaceae (1 strain) of the phylum Actinobacteria. Hymenobacter (2 species), Deinococcus (2 species), Two strain belongs to the family Hymenobacteraceae (2 Domibacillus (1 species), Exiguobacterium (1 species), strain) of the phylum Bacteroidetes. Two strain belongs Kurthia (1 species), Lysinibacillus (1 species), and Ba- to the family Deinococcaceae (2 strain) of the phylum cillus (1 species). The identification of the new strains Deinococcus-Thermus. The other four strains were as- based on sequence similarity were supported by the phy- signed to the family Planococcaceae (3 strain), Exig- logenetic trees. The neighbor-joining trees showed the 164 JOURNAL OF SPECIES RESEARCH Vol. 7, No. 2

Fig. 2. Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences shows the relationship between the strains isolated in this study and their relatives of the genus Marmoricola. Bootstrap values (>70%) are shown above nodes for the neighbor-joining methods. Bar: 0.0050 substitutions per nucleotide position, respectively. close relationship of the new strains and the type strains side, 3-methyl glucose, myo-inositol, pectin, glycyl-L- of validly published species (Figs. 2-15). The detailed proline, L-pyroglutamic acid, quinic acid, L-rhamnose, morphological and physiological characteristics were D-turanose acetic acid, N-acetyl-D-galactosamine, N- given in the strain descriptions. There is no official re- acetyl-neuraminic acid, N-acetyl-D-glucosamine, γ- port that these 14 species have been isolated in Korea. amino-butryric acid, D-arabitol, D-aspartic acid, bromo- Hence the strains low10-4-1, J11015, 17J27-22, 17G22- succinic acid, citric acid, formic acid, D-fucose, L-fucose, 9, 17G9-4, 17Bio_15, 17gy_33, 17SD1_21, Strain8, D-glucose-6-PO4, L-histidine, α-hydroxybutyric acid, β- 17Sr1_17, J21014T, H31021, 17J49-9, and 17J80-6 hydroxy-D,L-butyric acid, p-hydroxy-phenylacetic acid, are proposed to be unreported species of Marmoricola α-keto-butyric acid, L-lactic acid, D-lactic acid methyl aurantiacus, Calidifontibacter indicus, Gordonia soli, ester, α-D-lactose, D-malic acid, methyl pyruvate, mucic Rhodococcus globerulus, Pseudarthrobacter siccitolerans, acid, D-saccharic acid, D-salicin, and tween 40 are not Hymenobacter qilianensis, Hymenobacteterrae, utilized. In sensitivity tests, the tetrazolium redox dye is Deinococcus yunweiensis, Deinococcus proteolyticus, reduced in the presence of potassium tellurite and aztre- Domibacillus indicus, Exiguobacterium mexicanum, onam, but not 1% NaCl, 1% sodium lactate, 4% NaCl, Kurthia senegalensis, Lysinibacillus composti, and 8% NaCl, guanidine HCl, lithium chloride, pH 6, D-ser- Bacillus loiseleuriae. ine, sodium butyrate, tetrazolium violet fusidic acid, lincomycin, minocycline, nalidixic acid, niaproof 4, pH Description of Marmoricola aurantiacus low10-4-1 5, rifamycin SV, sodium bromate, tetrazolium blue, troleandomycin, and vancomycin. Cells are Gram-stain-negative and short rod-shaped. Indole production is negative (API 20NE). In the API Colonies are yellow-colored after 3 days of incubation 20NE and ID 32GN systems, positive for reduction of on R2A at 25°C. In the BIOLOG GEN III, D-treha- nitrates (NO3) to nitrogen (N2), arginine dihydrolase, lose, D-cellobiose, gentiobiose, sucrose, stachyose, D- urease, esculin hydrolysis, gelatin hydrolysis, β-galacto- raffinose, D-galactose, inosine, D-sorbitol, glycerol, D- sidase, D-ribose, D-saccharose (sucrose), D-maltose, su- serine, L-alanine, L-arginine, L-aspartic acid, L-serine, beric acid, sodium malonate, sodium acetate, lactic acid, D-gluconic acid, D-glucuronic acid, glucuronamide, L-alanine, glycogen, L-serine, D-mannitol, D-Glucose, and propionic acid are utilized as sole carbon source. salicin, L-arabinose, propionic acid, valeric acid, L-histi- But acetoacetic acid, N-acetyl-D-mannosamine, dextrin, dine, potassium 2-ketogluconate, 3-hydroxybutyric acid, D-fructose, D-fructose 6-PO4, L-galactonic acid lactone, 4-hydroxybenzoic acid, and L-proline. Negative for re- - D-galacturonic acid, gelatin, α-D-glucose, L-glutamic duction of nitrates (NO3) to nitrite (NO2 ), glucose fer- acid, α-keto-glutaric acid, L-malic acid, D-maltose, D- mentation, N-acetyl-D-glucosamine, capric acid, adipic mannitol, D-mannose, D-melibiose, β-methyl-D-gluco- acid, trisodiumcitrate, phenylacetic acid, L-rhamnose, May 2018 Kim et al. Unrecorded bacterial species from Korea 2017 165

Fig. 3. Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences shows the relationship between the strains isolated in this study and their relatives of the genus Calidifontibacter. Bootstrap values (>70%) are shown above nodes for the neighbor-joining methods. Bar: 0.0050 substitutions per nucleotide position, respectively.

N-acetyl-glucosamine, inositol, itaconic acid, potassium glucuronamide, and propionic acid are utilized as sole 5-ketogluconate, 3-hydroxybenzoic acid, D-melibiose, carbon source. But D-glucuronic acid, inosine, acetoace- D-fucose, D-sorbitol, capric acid, and trisodium citrate. tic acid, N-acetyl-D-mannosamine, dextrin, D-fructose,

Strain low10-4-1 ( =NIBRBAC000500523) was iso- D-fructose 6-PO4, L-galactonic acid lactone, D-galac- lated from a soil sample, Seoul, Nowon-gu, Gongneung- turonic acid, gelatin, α-D-glucose, L-glutamic acid, α- dong, Korea. keto-glutaric acid, L-malic acid, D-maltose, D-mannitol, D-mannose, D-melibiose, β-methyl-D-glucoside, 3- Description of Calidifontibacter indicus J11015 methyl glucose, myo-inositol, pectin, glycyl-L-proline, L-pyroglutamic acid, quinic acid, L-rhamnose, D-tura- Cells are Gram-stain-positive and cocci-shaped. Col- nose acetic acid, N-acetyl-D-galactosamine, N-acetyl- onies are yellow-colored after 3 days of incubation on neuraminic acid, N-acetyl-D-glucosamine, γ-amino- R2A at 25°C. In the BIOLOG GEN III, gentiobiose, su- butryric acid, D-arabitol, D-aspartic acid, bromo-succinic crose, D-trehalose, D-cellobiose, stachyose, D-raffinose, acid, citric acid, formic acid, D-fucose, L-fucose, D- D-galactose, D-sorbitol, glycerol, D-serine, L-alanine, glucose-6-PO4, L-histidine, α-hydroxybutyric acid, β- L-arginine, L-aspartic acid, L-serine, D-gluconic acid, hydroxy-D, L-butyric acid, p-hydroxy-phenylacetic acid, 166 JOURNAL OF SPECIES RESEARCH Vol. 7, No. 2

Fig. 4. Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences shows the relationship between the strains isolated in this study and their relatives of the genus Gordonia. Bootstrap values (>70%) are shown above nodes for the neighbor-joining methods. Bar: 0.0050 substitutions per nucleotide position, respectively.

α-keto-butyric acid, L-lactic acid, D-lactic acid methyl rose (sucrose), D-maltose, suberic acid, sodium acetate, ester, α-D-lactose, D-malic acid, methyl pyruvate, D- lactic acid, L-alanine, L-serine, D-glucose, D-sorbitol, L- saccharic acid, D-salicin, and tween 40 are not utilized. arabinose, propionic acid, 3-hydroxybutyric acid, and

In sensitivity tests, the tetrazolium redox dye is reduced L-proline. Negative for reduction of nitrates (NO3) to in the presence of potassium tellurite, aztreonam but 1% nitrogen (N2), indole production on tryptophan, glucose NaCl, 1% sodium lactate, 4% NaCl, 8% NaCl, guani- fermentation, β-galactosidase, L-arabinose, N-acetyl-D- dine HCl, lithium chloride, pH 6, D-serine, sodium bu- glucosamine, D-maltose, capric acid, adipic acid, malic tyrate, tetrazolium violet fusidic acid, lincomycin, mino- acid, trisodium citrate, L-rhamnose, N-acetyl-glucos cycline, nalidixic acid, niaproof 4, pH 5, rifamycin SV, amine, D-ribose, inositol, itaconic acid, sodium malonate, sodium bromate, tetrazolium blue, troleandomycin, and potassium 5-ketogluconate, glycogen, 3-hydroxybenzoic vancomycin. acid, D-mannitol, salicin, D-melibiose, D-fucose, valeric Indole production is negative (API 20NE). In the API acid, trisodium citrate, L-histidine, potassium 2-ketoglu- 20NE and ID 32GN systems, positive for reduction of conate, and 4-hydroxybenzoic acid. - nitrates (NO3) to nitrite (NO2 ), arginine dihydrolase, Strain J11015 (=NIBRBAC000500524) was isolated urease, esculin hydrolysis, gelatin hydrolysis, D-saccha- from a soil sample, Seoul, Nowon-gu, Gongneung-dong, May 2018 Kim et al. Unrecorded bacterial species from Korea 2017 167

Fig. 5. Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences shows the relationship between the strains isolated in this study and their relatives of the genus Rhodococcus. Bootstrap values (>70%) are shown above nodes for the neighbor-joining methods. Bar: 0.0050 substitutions per nucleotide position, respectively.

Korea. dextrin, D-fructose 6-PO4, L-galactonic acid lactone, D- galacturonic acid, gelatin, α-D-glucose, L-glutamic acid, Description of Gordonia soli 17J27-22 α-keto-glutaric acid, D-maltose, D-mannose, D-melibiose, β-methyl-D-glucoside, 3-methyl glucose, myo- Cells are Gram-stain-positive and oval-shaped. Col- inositol, glycyl-L-proline, L-pyroglutamic acid, quinic onies are orange-colored after 3 days of incubation on acid, D-turanose acetic acid, N-acetyl-D-galactosamine, R2A at 25°C. In the BIOLOG GEN III, D-fucose, Pec- N-acetyl-neuraminic acid, N-acetyl-D-glucosamine, γ- tin, D-sorbitol, acetoacetic acid, D-trehalose, L-malic amino-butryric acid, D-aspartic acid, bromo-succinic acid, acid, D-mannitol, L-rhamnose, D-arabitol, citric acid, formic acid, L-fucose, D-glucose-6-PO4, L-histidine, α- β-hydroxy-phenylacetic acid, α-keto-butyric acid, D- hydroxybutyric acid, β-hydroxy-D, L-butyric acid, L- malic acid, methyl pyruvate, tween 40 are utilized as lactic acid, D-lactic acid methyl ester, α-D-lactose, mucic sole carbon source. But D-cellobiose, gentiobiose, su- acid, D-saccharic acid, D-salicin are not utilized. In sen- crose, stachyose, D-raffinose, D-galactose, inosine, sitivity tests, the tetrazolium redox dye is reduced in the glycerol, D-serine, L-alanine, L-arginine, L-aspartic presence of potassium tellurite, aztreonam, 1% NaCl, 1% acid, L-serine, D-gluconic acid, D-glucuronic acid, glu- sodium lactate, 4% NaCl, 8% NaCl, lithium chloride, curonamide, propionic acid, N-acetyl-D-mannosamine, pH 6, sodium butyrate, nalidixic acid, rifamycin SV, lin- 168 JOURNAL OF SPECIES RESEARCH Vol. 7, No. 2

Fig. 6. Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences shows the relationship between the strains isolated in this study and their relatives of the genus Pseudarthrobacter. Bootstrap values (>70%) are shown above nodes for the neighbor-joining methods. Bar: 0.0050 substitutions per nucleotide position, respectively. comycin but not guanidine HCl, D-serine, tetrazolium of incubation on R2A at 25°C. In the BIOLOG GEN III, violet fusidic acid, minocycline, niaproof 4, pH 5, sodium N-glucosamine, β-mannosamin, D-fructose, glyctl-L- bromate, tetrazolium blue, troleandomycin, and vanco- proline, L-arginine, L-histidine, pyroglutamic acid, D- mycin. gluconic acid, methyl pyruvate, L-lactic acid, L-malic In the API 20NE systems, positive for reduction of acid, succinic acid, γ-butryric acid, α-butryric acid, β- - nitrates (NO3) to nitrite (NO2 ), and arginine dihydro- butryric acid, acetoacetic acid, propionic acid, and acetic lase, urease. Negative for reduction of nitrates (NO3) to acid are utilized as sole carbon source. But dextrin, D- nitrogen (N2), indole production on tryptophan, glucose maltose, D-trehalose, D-cellobiolose, gentiobiose, su- fermentation, gelatin hydrolysis, and capric acid. crose, D-turanose, stachyose, D-raffinose, α-D-lactose, Strain 17J27-22 (=NIBRBAC000500527) was isolat- D-melibiose, β-D-glucoside, D-salicin, N-galactosamin, ed from a soil sample, Jeju-do, Korea. neuraminic acid, α-D-glucose, D-mannose, D-galactose, 6-methyl-glucose, D-fucose, L-fucose, L-rhamnose, ino- Description of Rhodococcus globerulus 17G22-9 sine, D-sorbitol, D-mannitol, D-arabitol, myo-Inositol, glycerol, D-glucose, D-fructose, D-aspartic acid, D-ser- Cells are Gram-stain-positive, non-flagellated, and ine, gelatin, L-alanine, L-aspartic acid, L-glutamic acid, long rod-shaped. Colonies are white-colored after 3 days L-serine, pectin, galacturonic acid, L-galactonic lactone, May 2018 Kim et al. Unrecorded bacterial species from Korea 2017 169

Fig. 7. Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences shows the relationship between the strains isolated in this study and their relatives of the genus Hymenobacter. Bootstrap values (>70%) are shown above nodes for the neighbor-joining methods. Bar: 0.0050 substitutions per nucleotide position, respectively.

D-glucuronic acid, glucuronamide, mucic acid, quinic hydrolysis, capric acid, phenylacetic acid, inositol, D- acid, D-saccharic acid, pheylacetic acid, D-lactic acid, maltose, itaconic acid, sodium malonate, sodium ace- citric acid, α-glutaric acid, D-malic acid, tween 40, and tate, L-alanine, potassium 5-ketogluconate, glycogen, formic acid are not utilized. In sensitivity tests, the tetra- 3-hydroxybenzoic acid, L-serine, D-glucose, D-fucose, zolium redox dye is reduced in the presence of pH 6, 1% D-sorbitol, L-arabinose, trisodium citrate, and L-proline. NaCl, 4% NaCl, sodium lactate, rifamycin SV, nalidixic Strain 17G22-9 (=NIBRBAC000500503) was isolated acid, potassium tellurite, aztreonam, and sodium butyr- from a soil sample, Gyeonggi-do, Pocheon-si, Soheul- ate but not pH 5, fusidic acid, 8% NaCl, D-serine, tro- eup, Jikdong-ri, Korea. leandomycin, minocycline, lincomycin, guanidine HCl, niaproof 4, vancomycin, tetrazolium violet, tetrazolium Description of Pseudarthrobacter siccitolerans 17G9-4 blue, lithium chloride, and sodium bromate. Indole production is negative (API 20NE). In the API Cells are Gram-stain-positive and short rod-shaped. 20NE and ID 32GN systems, positive for reduction of Colonies are yellow-colored after 3 days of incubation - nitrates (NO3) to nitrite (NO2 ), arginine dihydrolase, on R2A at 25°C. In the BIOLOG GEN III, D-maltose, urease, esculin hydrolysis, β-galactosidase, L-rhamnose, D-trehalose, D-cellobiolose, gentiobiose, sucrose, D-tur- N-acetyl-glucosamine, D-ribose, D-saccharose (sucrose), anose, stachyose, D-raffinose, D-melibiose, β-D-gluco- suberic acid, lactic acid, D-manitol, salicin, D-melibiose, side, D-salicin, neuraminic acid, α-D-glucose, D-fruc- propionic acid, valeric acid, L-histidine, potassium 2- tose, D-mannitol, glycerol, L-histidine, D-gluconic acid, ketogluconate, 3-hydroxybutyric acid, and 4-hydroxy- and L-malic acid are utilized as sole carbon source. But benzoic acid. Negative for glucose fermentation, gelatin dextrin, α-D-lactose, N-glucosamine, β-mannosamin, 170 JOURNAL OF SPECIES RESEARCH Vol. 7, No. 2

Fig. 8. Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences shows the relationship between the strains isolated in this study and their relatives of the genus Hymenobacter. Bootstrap values (>70%) are shown above nodes for the neighbor-joining methods. Bar: 0.0050 substitutions per nucleotide position, respectively.

Fig. 9. Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences shows the relationship between the strains isolated in this study and their relatives of the genus Deinococcus. Bootstrap values (>70%) are shown above nodes for the neighbor-joining methods. Bar: 0.0050 substitutions per nucleotide position, respectively.

N-galactosamin, D-mannose, D-galactose, 6-methyl- mucic acid, quinic acid, D-saccharic acid, pheylacetic glucose, D-fucose, L-fucose, L-rhamnose, inosine, D- acid, methyl pyruvate, D-lactic acid, L-lactic acid, citric sorbitol, D-arabitol, myo-inositol, D-glucose, D-fructose, acid, α-glutaric acid, D-malic acid, succinic acid, tween D-aspartic acid, D-serine, gelatin, glyctl-L-proline, L- 40, γ-butryric acid, α-butryric acid, β-butryric acid, ac- alanine, L-arginine, L-aspartic acid, L-glutamic acid, etoacetic acid, propionic acid, acetic acid, and formic pyroglutamic acid, L-serine, pectin, galacturonic acid, acid are not utilized. In sensitivity tests, the tetrazolium L-galactonic lactone, D-glucuronic acid, glucuronamide, redox dye is reduced in the presence of pH 6, 1% NaCl, May 2018 Kim et al. Unrecorded bacterial species from Korea 2017 171

Fig. 10. Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences shows the relationship between the strains isolated in this study and their relatives of the genus Deinococcus. Bootstrap values (>70%) are shown above nodes for the neighbor-joining methods. Bar: 0.0050 substitutions per nucleotide position, respectively.

4% NaCl, sodium lactate, D-serine, tetrazolium violet, zoic acid. Negative for glucose fermentation, gelatin nalidixic acid, lithium chloride, potassium tellurite, az- hydrolysis, capric acid, adipic acid, trisodium citrate, treonam, and sodium butyrate but not pH 5, 8% NaCl, itaconic acid, suberic acid, sodium malonate, potassium fusidic acid, troleandomycin, rifamycin SV, minocycline, 5-ketogluconate, glycoGen, D-mannitol, D-melibiose, L- lincomycin, guanidine HCl, niaproof 4, vancomycin, arabinose, propionic acid, valeric acid, trisodium citrate, tetrazolium blue and sodium bromate. potassium 2-ketogluconate, and L-proline. Nitrate reduction and indole production are negative Strain 17G9_4 (=NIBRBAC000500499) was isolated (API 20NE). In the API 20NE and ID 32GN systems, from a soil sample, Gyeonggi-do, Pocheon-si, Soheul- positive for arginine dihydrolase, urease, esculin hydroly- eup, Jikdong-ri, Korea. sis, β-galactosidase, L-rhamnose, N-acetyl-glucosamine,

D-ribose, nositol, D-saccharose (sucrose), D-maltose, Description of Hymenobacter qilianensis 17Bio_15 sodium acetate, lactic acid, L-alanine, 3-hydroxybenzoic acid, L-serine, D-glucose, salicin, D-fucose, D-sorbitol, Cells are Gram-stain-negative, non-flagellated, and L-histidine, 3-hydroxybutyric acid, and 4-hydroxyben- long rod-shaped. Colonies are pink-colored after 3 days 172 JOURNAL OF SPECIES RESEARCH Vol. 7, No. 2

Fig. 11. Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences shows the relationship between the strains isolated in this study and their relatives of the genus Domibacillus. Bootstrap values (>70%) are shown above nodes for the neighbor-joining methods. Bar: 0.0050 substitutions per nucleotide position, respectively.

Fig. 12. Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences shows the relationship between the strains isolated in this study and their relatives of the genus Exiguobacterium. Bootstrap values (>70%) are shown above nodes for the neighbor-joining methods. Bar: 0.0050 substitutions per nucleotide position, respectively. of incubation on R2A at 25°C. In the BIOLOG GEN III, acid, L-malic acid, D-maltose, D-mannitol, D-mannose, α-D-glucose, D-arabitol, L-arginine, L-aspartic acid, D- D-melibiose, β-methyl-D-glucoside, 3-methyl glucose, gluconic acid, and citric acid are utilized as sole carbon myo-inositol, pectin, propionic acid, glycyl-L-proline, L- source. But acetoacetic acid, N-acetyl-D-mannosamine, pyroglutamic acid, quinic acid, D-raffinose, L-rhamnose, L-alanine, D-cellobiose, dextrin, D-fructose, D-fructose L-serine, stachyose, sucrose, D-trehalose, D-turanose, 6-PO4, L-galactonic acid lactone, D-galactose, D-galac- acetic acid, N-acetyl-D-galactosamine, N-acetyl-neur- turonic acid, gelatin, gentiobiose, glucuronamide, D-glu- aminic acid, N-acetyl-D-glucosamine, γ-amino-butryric curonic acid, L-glutamic acid, inosine, α-keto-glutaric acid, D-aspartic acid, bromo-succinic acid, formic acid, May 2018 Kim et al. Unrecorded bacterial species from Korea 2017 173

Fig. 13. Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences shows the relationship between the strains isolated in this study and their relatives of the genus Kurthia. Bootstrap values (>70%) are shown above nodes for the neighbor-joining methods. Bar: 0.0050 substitutions per nucleotide position, respectively.

D-fucose, L-fucose, D-glucose-6-PO4, glycerol, L-his- Strain 17Bio_15 ( =NIBRBAC000500513) was iso- tidine, α-hydroxybutyric acid, β-hydroxy-D, L-butyric lated from a soil sample, Seoul, Nowon-gu Gongneung- acid, p-hydroxy-phenylacetic acid, α-keto-butyric acid, dong, Korea. L-lactic acid, D-lactic acid methyl ester, α-D-lactose, D-malic acid, methyl pyruvate, mucic acid, D-saccharic Description of Hymenobacter terrae 17gy_33 acid, D-salicin, D-serine, D-sorbitol, and tween 40 are not utilized. In sensitivity tests, the tetrazolium redox Cells are Gram-stain-negative, non-flagellated, and dye is reduced in the presence of rifamycin SV, mino- short rod-shaped. Colonies are pink-colored after 3 days cycline, lincomycin, and tetrazolium but not 1% NaCl, of incubation on R2A at 25°C. In the BIOLOG GEN III, 1% sodium lactate, 4% NaCl, 8% NaCl, guanidine HCl, stachyose, D-mannitol, D-arabitol, glycerol, D-serine, lithium chloride, pH 6, potassium tellurite, D-serine, L-glutamic acid, and pectins are utilized as sole carbon sodium butyrate, tetrazolium violet, aztreonam, fusidic source. But acetoacetic acid, N-acetyl-D-mannosamine, acid, nalidixic acid, niaproof 4, pH 5, sodium bromate, L-alanine, L-arginine, L-aspartic acid, D-cellobiose, troleandomycin, and vancomycin. dextrin, D-fructose, D-fructose 6-P,O4, L-galactonic Indole production is negative (API 20NE). In the API acid lactone, D-galactose, D-galacturonic acid, gelatin, 20NE and ID 32GN systems, positive for reduction of gentiobiose, D-gluconic acid, α-D-glucose, glucuron nitrates (NO3) to nitrogen (N2), arginine dihydrolase, amide, D-glucuronic acid, inosine, α-keto-glutaric acid, urease, esculin hydrolysis, β-galactosidase, D-sacchar- L-malic acid, D-maltose, D-mannose, D-melibiose, β- ose (sucrose), itaconic acid, glycogen, 3-hydroxybenzoic methyl-D-glucoside, 3-methyl glucose, myo-inositol, acid, propionic acid, valeric acid, trisodium citrate, and propionic acid, glycyl-L-proline, L-pyroglutamic acid, potassium 2-ketogluconate. Weak for gelatin hydrolysis. quinic acid, D-raffinose, L-rhamnose, L-serine, sucrose, - Negative for reduction of nitrates (NO3) to nitrite (NO2 ), D-trehalose, D-turanose, acetic acid, N-acetyl-D-galac- Indole production on tryptophan, glucose fermentation, tosamine, N-acetyl-neuraminic acid, N-acetyl-D-glucos D-glucose, L-arabinose, D-mannose, D-mannitol, D- amine, γ-amino-butryric acid, D-aspartic acid, bromo- maltose, capric acid, adipic acid, malic acid, trisodium succinic acid, citric acid, formic acid, D-fucose, L-fu- citrate, phenylacetic acid, L-rhamnose, N-acetyl-glucos cose, D-glucose-6-PO4, L-histidine, α-hydroxybutyric amine, D-ribose, inositol, D-maltose, suberic acid, sodium acid, β-hydroxy-D, L-butyric acid, p-hydroxy-phenyl malonate, sodium acetate, lactic acid, L-alanine, potas- acetic acid, α-keto-butyric acid, L-lactic acid, D-lactic sium 5-ketogluconate, L-serine, D-mannitol, D-glucose, acid methyl ester, α-D-lactose, D-malic acid, methyl salicin, D-melibiose, D-fucose, D-sorbitol, L-arabinose, pyruvate, mucic acid, D-saccharic acid, D-salicin, D- L-histidine, 3-hydroxybutyric acid, 4-hydroxybrnzoic sorbitol, and tween 40 are not utilized. In sensitivity tests, acid, and L-proline. the tetrazolium redox dye is reduced in the presence of 174 JOURNAL OF SPECIES RESEARCH Vol. 7, No. 2

Fig. 14. Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences shows the relationship between the strains isolated in this study and their relatives of the genus Lysinibacillus. Bootstrap values (>70%) are shown above nodes for the neighbor-joining methods. Bar: 0.0050 substitutions per nucleotide position, respectively. rifamycin SV, minocycline, tetrazolium violet, nalidixic citrate. Negative for indole production on tryptophan, acid, and aztreonam but not 1% NaCl, 1% sodium lac- glucose fermentation, gelatin hydrolysis, D-glucose, L- tate, 4% NaCl, 8% NaCl, guanidine HCl, lithium chlo- arabinose, D-mannitol, N-acetyl-D-glucosamine, potas ride, pH 6, potassium tellurite, D-serine, sodium butyr- sium gluconate, capric acid, adipic acid, malic acid, ate, fusidic acid, lincomycin, niaproof 4, pH 5, sodium trisodium citrate, phenylacetic acid, L-rhamnose, N- bromate, tetrazolium blue, troleandomycin, and vanco- acetyl-glucosamine, D-ribose, inositol, D-saccharose mycin. (sucrose), itaconic acid, suberic acid, sodium malonate, Indole production is negative (API 20NE). In the API sodium acetate, lactic acid, potassium 5-ketogluconate, 20NE and ID 32GN systems, positive for reduction of glycogen, 3-hydroxybenzoic acid, L-serine, D-mannitol, nitrates (NO3) to nitrogen (N2), arginine dihydrolase, D-glucose, D-melibiose, D-fucose, propionic acid, valeric urease, esculin hydrolysis, β-galactosidase, D-maltose, acid, L-histidine, potassium 2-ketogluconate, 3-hydroxy- L-alanine, salicin, D-sorbitol, L-arabinose, trisodium butyric acid, 4-hydroxybenzoic acid, and L-proline. May 2018 Kim et al. Unrecorded bacterial species from Korea 2017 175

Fig. 15. Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences shows the relationship between the strains isolated in this study and their relatives of the genus Bacillus. Bootstrap values (>70%) are shown above nodes for the neighbor-joining methods. Bar: 0.0050 substitutions per nucleotide position, respectively.

Strain 17gy_33 ( =NIBRBAC000500514) was iso- lactone, D-galactose, D-galacturonic acid, gelatin, gen- lated from a soil sample, Seoul, Nowon-gu Gong- tiobiose, D-gluconic acid, α-D-glucose, glucuronamide, neung-dong, Korea. D-glucuronic acid, L-glutamic acid, inosine, α-keto- glutaric acid, L-malic acid, D-maltose, D-mannose, D- Description of Deinococcus yunweiensis 17SD1_21 melibiose, β-methyl-D-glucoside, 3-methyl glucose, myo-inositol, pectin, propionic acid, glycyl-L-proline, Cells are Gram-stain-negative, non-flagellated, and L-pyroglutamic acid, quinic acid, D-raffinose, L-rham- short rod-shaped. Colonies are orange-colored after 3 nose, L-serine, stachyose, sucrose, D-trehalose, D-tura- days of incubation on R2A at 25°C. In the BIOLOG nose, acetic acid, N-acetyl-D-galactosamine, N-acetyl- GEN III, D-mannitol, and acetoacetic acid are utilized neuraminic acid, N-acetyl-D-glucosamine, γ-amino- as sole carbon source. But N-acetyl-D-mannosamine, L- butryric acid, D-arabitol, D-aspartic acid, bromo-succin- alanine, L-arginine, L-aspartic acid, D-cellobiose, dex- ic acid, citric acid, formic acid, D-fucose, L-fucose, D- trin, D-fructose, D-fructose 6-PO4, L-galactonic acid glucose-6-PO4, glycerol, L-histidine, α-hydroxybutyric 176 JOURNAL OF SPECIES RESEARCH Vol. 7, No. 2

acid, β-hydroxy-D,L-butyric acid, p-hydroxy-phenyl D-fucose, L-fucose, D-glucose-6-PO4, α-hydroxybutyric acetic acid, α-keto-butyric acid, L-lactic acid, D-lactic acid, β-hydroxy-D,L-butyric acid, p-hydroxy-phenyl acid methyl ester, α-D-lactose, D-malic acid, methyl acetic acid, α-keto-butyric acid, L-lactic acid, D-lactic pyruvate, mucic acid, D-saccharic acid, D-salicin, D- acid methyl ester, α-D-lactose, D-malic acid, methyl serine, D-sorbitol, and tween 40 are not utilized. In sen- pyruvate, mucic acid, D-saccharic acid, and D-salicin are sitivity tests, the tetrazolium redox dye is reduced in the not utilized. In sensitivity tests, the tetrazolium redox dye presence of 1% NaCl, 1% sodium lactate, 4% NaCl, 8% was reduced in the presence of 1% NaCl, 1% sodium NaCl, guanidine HCl, lithium chloride, pH 6, potassium lactate, lithium chloride, pH 6, nalidixic acid, and rifa- tellurite, D-serine, sodium butyrate, tetrazolium violet, mycin SV but not potassium tellurite, aztreonam, 4% aztreonam, fusidic acid, lincomycin, minocycline, nali- NaCl, 8% NaCl, guanidine HCl, D-serine, sodium buty dixic acid, niaproof 4, pH 5, rifamycin SV, sodium bro- rate, tetrazolium violet fusidic acid, lincomycin, mino- mate, tetrazolium blue, troleandomycin, and vancomy- cycline, niaproof 4, pH 5, sodium bromate, tetrazolium cin. blue, troleandomycin, and vancomycin. Indole production is negative (API 20NE). In the API In the API 20NE, positive for reduction of nitrates - 20NE and ID 32GN systems, positive for reduction of (NO3) to nitrite (NO2 ), arginine dihydrolase, D-glucose, nitrates (NO3) to nitrogen (N2), arginine dihydrolase, and esculin hydrolysis. Negative for indole production urease, esculin hydrolysis, β-galactosidase, D-sacchar- on tryptophan, glucose fermentation, gelatin hydrolysis, ose (sucrose), D-maltose, and D-sorbitol. Weak reaction β-galactosidase, D-mannitol, N-acetyl-D-glucosamine, observed with gelatin hydrolysis. Negative for reduction urease, D-mannose, D-maltose, potassium gluconate, - of nitrates (NO3) to nitrite (NO2 ), indole production on capric acid, adipic acid, malic acid, trisodium citrate, tryptophan, glucose fermentation, L-rhamnose, N-acetyl- and phenylacetic acid, and L-arabinose. glucosamine, D-ribose, inositol, itaconic acid, suberic Strain8 (=NIBRBAC000500528) was isolated from a acid, sodium malonate, sodium acetate, lactic acid, L- soil sample, Jeju-do, Korea. alanine, potassium 5-ketogluconate, glycogen, 3-hydroxybenzoic acid, L-serine, D-mannitol, D-glucose, salicin, Description of Domibacillus indicus 17Sr1_17 D-melibiose, D-fucose, L-arabinose, propionic acid, Cells are Gram-stain-negative, non-flagellated, and capric acid, valeric acid, trisodium citrate, L-histidine, long rod-shaped. Colonies are yellow-colored after 3 days potassium 2-ketogluconate, 3-hydroxybutyric acid, 4- of incubation on R2A at 25°C. In the BIOLOG GEN III, hydroxybenzoic acid, and L-proline. dextrin, D-maltose, D-trehalose, D-cellobiose, gentio- Strain 17SD1_21 ( =NIBRBAC000500511) was iso- biose, sucrose, D-turanose, stachyose, D-raffinose, D- lated from a soil sample, Seoul, Nowon-gu Gongneung- melibiose, β-methyl-D-glucoside, D-salicin, N-acetyl-D- dong, Korea. glucosamine, α-D-glucose, D-mannose, D-fructose, D- galactose, L-rhamnose, inosine, D-sorbitol, D-mannitol, Description of Deinococcus proteolyticus Strain8 D-arabitol, myo-inositol, glycerol, L-alanine, L-arginine, Cells are Gram-stain-positive and cocci-shaped. Col- L-aspartic acid, L-glutamic acid, L-pyroglutamic acid, onies are orange-colored after 3 days of incubation on pectin, D-galacturonic acid, L-galactonic acid lactone, R2A at 25°C. In the BIOLOG GEN III, sucrose, inosine, D-gluconic acid, D-glucuronic acid, glucuronamide, D-fructose, α-D-glucose, D-mannitol, L-histidine, and mucic acid, quinic acid, D-saccharic acid, L-lactic acid, tween 40 are utilized as sole carbon source. But D-treha- citric acid, L-malic acid, acetic acid, and formic acid lose, D-cellobiose, gentiobiose, stachyose, D-raffinose, were utilized as sole carbon source. But acetoacetic acid, D-galactose, D-sorbitol, glycerol, D-serine, L-alanine, N-acetyl-D-mannosamine, D-fructose 6-PO4, D-galactose, L-arginine, L-aspartic acid, L-serine, D-gluconic acid, gelatin, α-keto-glutaric acid, 3-methyl glucose, propionic D-glucuronic acid, glucuronamide, propionic acidaceto- acid, glycyl-L-proline, L-serine, N-acetyl-D-galactos acetic acid, N-acetyl-D-mannosamine, dextrin, D-fruc- amine, N-acetyl-neuraminic acid, γ-amino-butryric acid, tose 6-PO4, L-galactonic acid lactone, D-galacturonic D-aspartic acid, bromo-succinic acid, D-fucose, L-fucose, acid, gelatin, L-glutamic acid, α-keto-glutaric acid, L- D-glucose-6-PO4, L-histidine, α-hydroxybutyric acid, β- malic acid, D-maltose, D-mannose, D-melibiose, β- hydroxy-D,L-butyric acid, p-hydroxy-phenylacetic acid, methyl-D-glucoside, 3-methyl glucose, myo-inositol, α-keto-butyric acid, D-lactic acid methyl ester, α-D- pectin, glycyl-L-proline, L-pyroglutamic acid, quinic lactose, D-malic acid, methyl pyruvate, D-serine, and acid, L-rhamnose, D-turanose acetic acid, N-acetyl-D- tween 40 are not utilized. In sensitivity tests, the tetra- galactosamine, N-acetyl-neuraminic acid, N-acetyl-D- zolium redox dye is reduced in the presence of pH 6, 1% glucosamine, γ-amino-butryric acid, D-arabitol, D-aspar- NaCl, 4% NaCl, 1% sodium lactate, potassium tellurite, tic acid, bromo-succinic acid, citric acid, formic acid, and sodium butyrate but not 8% NaCl, guanidine HCl, May 2018 Kim et al. Unrecorded bacterial species from Korea 2017 177 lithium chloride, D-serine, tetrazolium violet, aztreonam, butyrate, tetrazolium violet fusidic acid, lincomycin, fusidic acid, lincomycin, minocycline, nalidixic acid, minocycline, nalidixic acid, niaproof 4, pH 5, rifamycin niaproof 4, pH 5, rifamycin SV, sodium bromate, tetra- SV, sodium bromate, tetrazolium blue, troleandomycin, zolium blue, troleandomycin, and vancomycin. and vancomycin. Indole production is negative (API 20NE). In the API Indole production is negative (API 20NE). In the API 20NE and ID 32GN systems, positive for reduction of 20NE and ID 32GN systems, positive for reduction of - - nitrates (NO3) to nitrite (NO2 ), arginine dihydrolase, ure- nitrates (NO3) to nitrite (NO2 ), arginine dihydrolase, ase, esculin hydrolysis, β-galactosidase, L-rhamnose, N- urease, esculin hydrolysis, gelatin hydrolysis, D-ribose, acetyl-glucosamine, inositol, D-maltose, sodium acetate, inositol, D-saccharose (sucrose), D-maltose, suberic acid, L-alanine, glycogen, D-mannitol, salicin, D-melibiose, sodium acetate, lactic acid, L-alanine, glycogen, L-serine, D-sorbitol, L-arabinose, potassium 2-ketogluconate, 3- D-glucose, propionic acid, capric acid, valeric acid, tri- hydroxybutyric acid, and L-proline. Negative for reduc- sodium citrate, L-histidine, 3-hydroxybutyric acid, and tion of nitrates (NO3) to nitrogen (N2), indole production L-proline. Negative for reduction of nitrates (NO3) to on tryptophan, glucose fermentation, gelatin hydrolysis, nitrogen (N2), indole production on tryptophan, glucose capric acid, adipic acid, phenylacetic acid, D-ribose, D- fermentation, β-galactosidase, capric acid, adipic acid, saccharose (sucrose), itaconic acid, suberic acid, sodium trisodium citrate, L-rhamnose, N-acetyl-glucosamine, malonate, lactic acid, potassium 5-ketogluconate, 3-hy- itaconic acid, sodium malonate, potassium 5-ketoglu- droxybenzoic acid, L-serine, D-glucose, D-fucose, pro- conate, 3-hydroxybenzoic acid, D-mannitol, salicin, D- pionic acid, capric acid, valeric acid, trisodium citrate, melibiose, D-fucose, D-sorbitol, L-arabinose, potassium L-histidine, and 4-hydroxybenzoic acid. 2-ketogluconate, and 4-hydroxybenzoic acid. Strain 17Sr1_17 ( =NIBRBAC000500512) was iso- Strain J21014T (=NIBRBAC000500525) was isolat- lated from a soil sample, Seoul, Nowon-gu Gongneung- ed from a soil sample, Seoul, Nowon-gu Gongneung- dong, Korea. dong, Korea.

Description of Exiguobacterium mexicanum J21014T Description of Kurthia senegalensis H31021 Cells are Gram-stain-positive, and cocci-shaped. Col Cells are Gram-stain-positive, and short rod-shaped. onies are yellow-colored after 3 days of incubation on Colonies are yellow-colored after 3 days of incubation R2A at 25°C. In the BIOLOG GEN III, D-trehalose, D- on R2A at 25°C. In the BIOLOG GEN III, gentiobiose, cellobiose, gentiobiose, sucrose, stachyose, D-raffinose, sucrose, stachyose, D-raffinose, D-galactose, inosine, D-galactose, inosine, D-sorbitol, glycerol, D-serine, L- D-sorbitol, glycerol, D-serine, L-alanine, L-arginine, alanine, L-arginine, L-aspartic acid, L-serine, D-gluconic L-aspartic acid, L-serine, D-gluconic acid, D-glucuron- acid, D-glucuronic acid, glucuronamide, and propionic ic acid, glucuronamide, and propionic acid are utilized acid are utilized as sole carbon source. But acetoacetic as sole carbon source. But D-trehalose, D-cellobiose, acid, N-acetyl-D-mannosamine, dextrin, D-fructose, D- acetoacetic acid, N-acetyl-D-mannosamine, dextrin, D- fructose 6-PO4, L-galactonic acid lactone, D-galacturonic fructose, D-fructose 6-PO4, L-galactonic acid lactone, acid, gelatin, α-D-glucose, L-glutamic acid, α-keto-glu- D-galacturonic acid, gelatin, α-D-glucose, L-glutamic taric acid, L-malic acid, D-maltose, D-mannitol, D-man- acid, α-keto-glutaric acid, L-malic acid, D-maltose, D- nose, D-melibiose, β-methyl-D-glucoside, 3-methyl mannitol, D-mannose, D-melibiose, β-methyl-D-gluco- glucose, myo-inositol, pectin, glycyl-L-proline, L-pyro- side, 3-methyl glucose, myo-inositol, pectin, glycyl-L- glutamic acid, quinic acid, L-rhamnose, D-turanose ace- proline, L-pyroglutamic acid, quinic acid, L-rhamnose, tic acid, N-acetyl-D-galactosamine, N-acetyl-neuraminic D-turanose acetic acid, N-acetyl-D-galactosamine, N- acid, N-acetyl-D-glucosamine, γ-amino-butryric acid, acetyl-neuraminic acid, N-acetyl-D-glucosamine, γ- D-arabitol, D-aspartic acid, bromo-succinic acid, citric amino-butryric acid, D-arabitol, D-aspartic acid, bromo- acid, formic acid, D-fucose, L-fucose, D-glucose-6-PO4, succinic acid, citric acid, formic acid, D-fucose, L-fucose, L-histidine, α-hydroxybutyric acid, β-hydroxy-D,L- D-glucose-6-PO4, L-histidine, α-hydroxybutyric acid, butyric acid, p-hydroxy-phenylacetic acid, α-keto-butyric β-hydroxy-D, L-butyric acid, p-hydroxy-phenylacetic acid, L-lactic acid, D-lactic acid methyl ester, α-D-lac- acid, α-keto-butyric acid, L-lactic acid, D-lactic acid tose, D-malic acid, methyl pyruvate, mucic acid, D-sac- methyl ester, α-D-lactose, D-malic acid, methyl pyru- charic acid, D-salicin, and tween 40 are not utilized. vate, mucic acid, D-saccharic acid, D-salicin, and tween In sensitivity tests, the tetrazolium redox dye is reduced 40 are not utilized. In sensitivity tests, the tetrazolium in the presence of potassium tellurite and aztreonam but redox dye is reduced in the presence of potassium tellu- not 1% NaCl, 1% sodium lactate, 4% NaCl, 8% NaCl, rite and aztreonam but not 1% NaCl, 1% sodium lactate, guanidine HCl, lithium chloride, pH 6, D-serine, sodium 4% NaCl, 8% NaCl, guanidine HCl, lithium chloride, pH 178 JOURNAL OF SPECIES RESEARCH Vol. 7, No. 2

6, D-serine, sodium butyrate, tetrazolium violet fusidic rifamycin SV, sodium bromate, tetrazolium blue, trole- acid, lincomycin, minocycline, nalidixic acid, niaproof 4, andomycin, and vancomycin. pH 5, rifamycin SV, sodium bromate, tetrazolium blue, Nitrate reduction and indole production are negative troleandomycin, and vancomycin. (API 20NE). In the API 20NE systems, positive for argi- Nitrate reduction and indole production are negative nine dihydrolase, urease D-glucose, D-mannose, D-malt- (API 20NE). In the API 20NE and ID 32GN systems, ose, potassium gluconate, malic acid, trisodium citrate, positive for N-acetyl-β-glucosaminidase, acid phosphat esculin hydrolysis, gelatin hydrolysis, β-galactosidase, ase, alkaline phosphatase, α-chymotrypsin, cystine aryl- L-arabinose, D-mannitol, and N-acetyl-D-glucosamine. amidase, α-galactosidase, β-galactosidase (PNPG), α- Negative for capric acid, adipic acid, phenylacetic acid, glucosidase (starch hydrolysis), β-glucosidase (esculin glucose fermentation. hydrolysis), leucine arylamidase, naphthol-AS-BI-phos- Strain 17J49-9 (=NIBRBAC000500529) was isolated phohydrolase, trypsin, and valine arylamidase. Negative from a soil sample, Seoul, Nowon-gu Gongneung-dong, for arginine dihydrolase, α-fucosidase, β-glucuronidase, Korea. acetate, N-acetyl-D-glucosamine, adipate, L-arabinose, caprate, citrate, gluconate, D-glucose, L-malate, D-malt- Description of Bacillus loiseleuriae 17J80-6 ose, D-mannitol, D-mannose, and phenyl acetate, lipase Cells are Gram-stain positive and oval-shaped. Colo- (C14), α-mannosidase, protease (gelatin hydrolysis), and nies are white-colored after 3 days of incubation on R2A urease. at 25°C. In the BIOLOG GEN III, dextrin, D-maltose, Strain H31021 (=NIBRBAC000500526) was isolated D-cellobiolose, gentiobiose, sucrose, D-turanose, stachy- from a soil sample, Seoul, Nowon-gu Gongneung-dong, ose, D-raffinose, α-D-lactose, D-melibiose, β-D-gluco- Korea. side, D-salicin, N-glucosamine, β-mannosamin, neura minic acid, α-D-glucose, D-fructose, D-galactose, D- Description of Lysinibacillus composti 17J49-9 mannitol, D-arabitol, D-serine, L-glutamic acid, pectin, Cells are Gram-stain negative, and oval-shaped. Colo- D-glucuronic acid, and methyl pyruvate are utilized as nies are white-colored after 3 days of incubation on R2A sole carbon source. But D-trehalose, N-galactosamin, D- at 25°C. In the BIOLOG GEN III, L-alanine, L-arginine, mannose, 6-methyl-glucose, D-fucose, L-fucose, L- acetoacetic acid, L-glutamic acid, and tween 40 are uti- rhamnose, inosine, D-sorbitol, myo-inositol, glycerol, lized as sole carbon source. But D-trehalose, D-cello- D-fructose, D-aspartic acid, gelatin, glyctl-L-proline, L- biose, gentiobiose, sucrose, stachyose, D-raffinose, D- alanine, L-aspartic acid, L-histidine, pyroglutamic acid, galactose, inosine, D-sorbitol, glycerol, D-serine, L- L-serine, galacturonic acid, L-galactonic lactone, D- aspartic acid, L-serine, D-gluconic acid, D-glucuronic gluconic acid, glucuronamide, mucic acid, quinic acid, acid, glucuronamide, propionic acid, N-acetyl-D-man- D-saccharic acid, pheylacetic acid, D-lactic acid, L-lactic nosamine, dextrin, D-fructose, D-fructose 6-PO4, L- acid, citric acid, α-glutaric acid, D-malic acid, L-malic galactonic acid lactone, D-galacturonic acid, gelatin, α- acid, succinic acid, tween 40, γ-butryric acid, α-butryric D-glucose, α-keto-glutaric acid, L-malic acid, D-maltose, acid, β-butryric acid, acetoacetic acid, propionic acid, D-mannitol, D-mannose, D-melibiose, β-methyl-D-glu- acetic acid, and formic acid are not utilized. In sensitivity coside, 3-methyl glucose, myo-inositol, pectin, glycyl- tests, the tetrazolium redox dye is reduced in the presence L-proline, L-pyroglutamic acid, quinic acid, L-rham- of potassium tellurite, aztreonam, 1% NaCl, 1% sodium nose, D-turanose acetic acid, N-acetyl-D-galactosamine, lactate, 4% NaCl, lithium chloride, pH 6, nalidixic acid, N-acetyl-neuraminic acid, N-acetyl-D-glucosamine, γ- sodium butyrate, and sodium bromate but not in pH 5, amino-butryric acid, D-arabitol, D-aspartic acid, bromo- 8% NaCl, fusidic acid, D-serine, troleandomycin, rifa succinic acid, citric acid, formic acid, D-fucose, L-fucose, mycin SV, minocycline, lincomycin, guanidine HCl, D-glucose-6-PO4, L-histidine, α-hydroxybutyric acid, β- niaproof 4, vancomycin, tetrazolium violet, tetrazolium hydroxy-D,L-butyric acid, p-hydroxy-phenylacetic acid, blue, lithium chloride, aztreonam, and sodium bromate. α-keto-butyric acid, L-lactic acid, D-lactic acid methyl Nitrate reduction and indole production are negative ester, α-D-lactose, D-malic acid, methyl pyruvate, mucic (API 20NE). In the API 20NE and ID 32GN systems, acid, D-saccharic acid, and D-salicin are not utilized. In positive for arginine dihydrolase, urease, esculin hydro- sensitivity tests, the tetrazolium redox dye is reduced lysis, gelatin hydrolysis, β-galactosidase, N-acetyl-glu- in the presence of potassium tellurite, aztreonam, 1% cosamine, D-ribose, D-saccharose (sucrose), D-maltose, NaCl, 1% sodium lactate, 4% NaCl, lithium chloride, L-alanine, glycogen, 3-hydroxybenzoic acid, D-man- pH 6, and nalidixic acid but not 8% NaCl, guanidine nitol, salicin, D-melibiose, valeric acid, L-histidine, 3- HCl, D-serine, sodium butyrate, tetrazolium violet fu- hydroxybutyric acid, and 4-hydroxybenzoic acid. Nega- sidic acid, lincomycin, minocycline, niaproof 4, pH 5, tive for glucose fermentation, L-arabinose, D-mannose, May 2018 Kim et al. Unrecorded bacterial species from Korea 2017 179

N-acetyl-D-glucosamine, potassium gluconate, capric Ho, J., M. Adeolu, B. Khadka and R.S. Gupta. 2016. Identi- acid, adipic acid, malic acid, trisodium citrate, phenyl fication of distinctive molecular traits that are character- acetic acid, L-rhamnose, inositol, itaconic acid, suberic istic of the phylum “Deinococcus-Thermus” and distin- acid, sodium malonate, sodium acetate, lactic acid, potas guish its main constituent groups. Syst Appl Microbiol sium 5-ketogluconate, L-serine, D-glucose, D-fucose, 39:453-463. D-sorbitol, L-arabinose, propionic acid, potassium 2- Johnson, E.L., S.L. Heaver, W.A. Walters and R.E. Ley. 2016. ketogluconate, and L-proline. Microbiome and metabolic disease: revisiting the bac- Strain 17J80-6 (=NIBRBAC000500502) was isolated terial phylum Bacteroidetes. J Mol Med. DOI 10.1007/ from a soil sample, Jeju-do, Korea. s00109-016-1492-2 Kim, O.-S. et al. 2012. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol Acknowledgements 62:716-721. Kimura, M. 1983. The neutral theory of molecular evolution. This work was supported by a research grant from Cambridge University Press. Seoul Women’s University (2018) and by a grant from Lake, J.A., R.G. Skophammer, C.W. Herbold and J.A. Servin. the National Institute of Biological Resources (NIBR), 2009. Genome beginnings: rooting the tree of life. Philos funded by the Ministry of Environment (MOE) of the Trans R Soc Lond B Biol Sci 364:2177-2185. Republic of Korea (NIBR201701107). Lanza, F.V., A.P. Tedim, J.L. Martínez, F. Baquero and T.M. Coque. 2015. The plasmidome of Firmicutes: impact on the emergence and the spread of resistance to antimicro- References bials. Microbiol Spectr 3(2):PLAS-0039-2014. Madigan, M. and J. Martinko, eds. (2005). Brock Biology of Battista, J.R. 2016. Deinococcus-Thermus Group. In: eLS. Microorganisms (11th ed.). Prentice Hall. John Wiley & Sons, Ltd: Chichester. DOI: 10.1002/ Mira, A., R. Pushker, B.A. Legault, D. Moreira and F. 9780470015902.a0021151 Rodriguez-Valera. 2004. Evolutionary relationships of Barka, E.A., P. Vatsa, L. Sanchez, N. Gaveau-Vaillant, C. Fusobacterium nucleatum based on phylogenetic analy- Jacquard, H.-P. Klenk, C. Clément, Y. Ouhdouch and G. sis and comparative genomics. BMC Evol Biol. 4:50. P. van Wezel. 2016. Microbiol Mol Biol Rev 80:1-43. Saitou, N. and M. Nei. 1987. The neighbor-joining method: Doetsch, R.N. 1981. Determinative methods of light micros- a new method for reconstructing phylogenetic trees. Mol copy. Manual of Methods for General Bacteriology, pp. Biol Evol 4:406-425. 21-33. In: P. Gerhardt, R.G.E. Murray, R.N. Costilow, Sakamoto, M. and M. Ohkuma. 2011. Identification and E.W. Nester, W.A. Wood, N.R. Krieg and G.H. Phillips classification of the genus Bacteroides by multilocus se- (eds.), American Society for Microbiology. Washington, quence analysis. Microbiol 157:3388-3397. DC, USA. Scarpellini, E., G. Ianiro, F. Attili, C. Bassanelli, A. De San- Edgar, R.C. 2004. MUSCLE: multiple sequence alignment tis d and A. Gasbarrini. 2015. The human gut microbiota with high accuracy and high throughput. Nucleic Acids and virome: Potential therapeutic implications. Dig Liver Res 32:1792-1797. Dis 47:1007-1012. Edwards, C. 1993. Isolation properties and potential appli- Shah, H.N., I. Olsen, K. Bernard, S.M. Finegold, S. Gharbia cations of thermophilic Actinomycetes. Appl Biochem and R.S. Gupta. 2009. Approaches to the study of the Biotechnol 42:161-179. systematics of anaerobic, Gram-negative, non-spore- Felsenstein, J. 1985. Confidence limits on phylogenies: an forming rods: current status and perspectives. Anaerobe approach using the bootstrap. Evolution 39:783-791. 15:179-194. Griffiths, E. and R.S. Gupta. 2007. Identification of signature Srinivasan, S., M.K. Kim, S. Lim, M. Joe and M. Lee. proteins that are distinctive of the Deinococcus-Thermus 2012a. Deinococcus daejeonensis sp. nov., isolated from phylum. Int Microbiol 10:201-208. sludge in a sewage disposal plant. Int J Syst Evol Micro- Hall, T.A. BioEdit: a user-friendly biological sequence align- biol 62:1265-1270. ment editor and analysis program for Windows 95/98/NT. Srinivasan, S., J.J. Lee, S. Lim, M. Joe and M.K. Kim. In: Nucleic acids symposium series, 1999. vol 41. [Lon- 2012b. Deinococcus humi sp. nov., isolated from soil. Int don]: Information Retrieval Ltd., c1979-c2000. pp. 95- J Syst Evol Microbiol 62:2844-2850. 98. Tamura, K., D. Peterson, N. Peterson, G. Stecher, M. Nei Hayashi, H., K. Shibata, M.A. Bakir, M. Sakamoto, S. Tomita and S. Kumar. 2011. MEGA5: molecular evolutionary and Y. Benno. 2007. Bacteroides coprophilus sp. nov., genetics analysis using maximum likelihood, evolutionary isolated from human faeces. Int J Syst Evol Microbiol distance, and maximum parsimony methods Mol Biol 57:1323-1326. Evol 28:2731-2739. 180 JOURNAL OF SPECIES RESEARCH Vol. 7, No. 2

Weisburg, W.G., S.M. Barns, D.A. Pelletier, D.J. Lane. terial identification system with matrix-assisted laser 1991. 16S ribosomal DNA amplification for phylogenetic desorption ionization-time of flight mass spectrometry study. J Bacteriol 173:697-703. and 16S ribosomal RNA gene sequencing for the iden- Wragg, P., L. Randall and A. Whatmore. 2014. Comparison tification of bacteria of veterinary interest. J Microbiol of Biolog GEN III MicroStation semi-automated bac- Methods 105:16-21.

Submitted: March 21, 2018 Revised: April 4, 2018 Accepted: May 16, 2018