Lentibacillus cibarius sp. nov., isolated from kimchi,a Korean fermented food

Journal of Microbiology - Two bacterial strains designated NKC220-2T and NKC851-2 were isolated from commercial kimchi from different areas in Korea. The strains were Gram-positive, aerobic,...     

Halomonas cibimaris sp. nov., isolated from jeotgal, a traditional Korean fermented seafood

Two moderately halophilic, facultatively aerobic, motile bacteria with flagella, designated strains 10-C-3^T and 30-C-3, were isolated from jeotgal, a traditional Korean fermented seafood. Cells of the strains were observed to be ovoid-rods showing catalase- and oxidase-positive reactions and production of creamy-pink pigments. Growth of strain 10-C-3^T was observed at 15–35 °C (optimum, 25–30 °C), at pH 5.5–9.0 (optimum, pH 7.0–7.5), and in the presence of 3–15 % (w/v) salts (optimum: 5–10 %). The two strains were found to contain C_18:1 ω7c, C_16:0, summed feature 3 (as defined by the MIDI system, comprising C_16:1 ω7c and/or C_16:1 ω6c), and C_12:0 3-OH as the major cellular fatty acids. The G+C contents of the genomic DNA of strains 10-C-3^T and 30-C-3 were determined to be 63.2 and 63.1 mol%, respectively and the respiratory quinone detected was ubiquinone 9 (Q-9) only. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strains 10-C-3^Tand 30-C-3 formed a distinct phyletic lineage within the genus Halomonas and are most closely related to Halomonas fontilapidosi 5CR^T with 95.2 % of 16S rRNA sequence similarity. Strains 10-C-3^Tand 30-C-3 shared 99.2 % of 16S rRNA gene sequence similarity and their DNA–DNA relatedness value was 96.6 ± 0.9 %. On the basis of phenotypic, chemotaxonomic and molecular features, strains 10-C-3^Tand 30-C-3 represent a novel species of the genus Halomonas, for which the name Halomonas cibimaris sp. nov. is proposed. The type strain is 10-C-3^T (= KACC 14932^T = JCM 16914^T).     

Lysinibacillus chungkukjangi sp. nov., isolated from Chungkukjang, Korean fermented soybean food

One bacterial strain 2RL3-2^T was isolated from Chungkukjang, a traditional Korean fermented food made from soybeans, and determined to be a Gram-positive, aerobic, spore-forming rod. Growth of the novel strain was optimal at 30°C and pH 7.0. The 16S rRNA gene of strain 2RL3-2^T showed the highest level of sequence similarity to Lysinibacillus sinduriensis BLB-1^T (99.0%), Lysinibacillus massiliensis 4400831^T (97.1%), Lysinibacillus xylanilyticus XDB9^T (97.0%), and Lysinibacillus odysseyi 34hs-1^T (96.8%). Phylogenetic analysis showed that strain 2RL3-2^T formed a robust cluster with L. sinduriensis BLB-1^T, L. massiliensis 4400831^T, and L. odyssey 34hs-1^T. The major fatty acids were anteiso-C15:0 (47.3%), iso-C_16:0 (16.3%), and anteiso-C_17:0 (11.3%), and the only menaquinone was MK-7. Diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine were the major polar lipids, along with an unknown phospholipid and two unknown lipids. The peptidoglycan type was A4α, with an interpeptide bridge of l-Lys-d-Asp. DNA-DNA hybridization values between strain 2RL3-2^T and closely related Lysinibacillus species were below 43±4%. Therefore, based on phenotypic, chemotaxonomic, and phylogenetic characteristics, it was determined that strain 2RL3-2^T represents a novel species of the genus Lysinibacillus, for which the name Lysinibacillus chungkukjangi sp. nov. is proposed. The type strain is 2RL3-2^T (=KACC 16626^T =NBRC 108948^T).     

Halomonas shantousis sp. nov., a novel biogenic amines degrading bacterium isolated from Chinese fermented fish sauce

A Gram-negative, aerobic, short rod-shaped and non-motile bacterium, designated SWA25^T, was isolated from Chinese fermented fish sauce in Shantou, Guangdong Province, China. Strain SWA25^T was moderately halophilic, formed colourless colonies and grew at 10–45 °C (optimum, 37 °C) and pH 4–9 (optimum, 6–7) in the presence of 0.5–22.5 % (w/v) NaCl (optimum, 3 %). The major cellular fatty acids (>10 %) were identified as C_18:1 ω7C, C_16:0, C_16:1 ω7c, and C_19:0 cyclo ω8c, and the predominant respiratory ubiquinone was Q-9. The genomic DNA G+C content was 61.3 ± 2.1 mol %. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SWA25^T belonged to the genus Halomonas in the family Halomonadaceae. The closest relatives were Halomonas xianhensis A-1^T (96.5 % 16S rRNA gene sequence similarity), H. lutea DSM 23508^T (96.5 %) and H. muralis LMG 20969^T (96.1 %). DNA–DNA hybridization assays showed 30.7 ± 2.6 % relatedness between strain SWA25^T and H. xianhensis A-1^T, and 39.4 ± 4.1 % between strain SWA25^T and H. lutea DSM 23508^T. On the basis of phenotypic, chemotaxonomic and phylogenetic features, strain SWA25^T should be placed in the genus Halomonas as a representative of a novel species. The name Halomonas shantousis sp. nov. is proposed, with SWA25^T(=CCTCC AB 2013151^T = JCM 19368^T) as the type strain.     

Rhodanobacter umsongensis sp. nov., isolated from a Korean ginseng field

A bacterial isolate designated GR24-2^T was isolated from Korean soil used for cultivating ginseng (Panax ginseng C. A. Meyer). The strain was aerobic, Gram-negative, motile, and rod-shaped. It grew optimally at 28–30°C, pH 7.0, and in a range of 0–1% NaCl. Phylogenetically, the strain clustered with members of the genus Rhodanobacter. The strain exhibited the highest sequence similarities (>98%) with R. panaciterrae LnR5-47^T (98.4%), R. soli DCY45^T (98.2%), and R. ginsengisoli GR17-7^T (98.0%). However, it also showed high sequence similarities (>97%) with some other Rhodanobacter and Dyella species. The strain contained Q-8 as the predominant respiratory quinone. The major fatty acids (greater than 10% of the total fatty acids) were iso-C_17:1 ω9c (24.5%), iso-C_16:0 (22.8%), anteiso-C_15:0 (10.5%), and iso-C_15:0 (10.1%). Its major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and an unknown aminophospholipid. The DNA G+C content of strain GR24-2^T was 65.6 mol%. The strain showed less than 70% DNA relatedness values between the closely related Rhodanobacter and Dyella species. The phylogeny, phenotype, DNA-DNA hybridization, and chemotaxonomic data generated in this study reveal that the isolate is a novel species of the genus Rhodanobacter. The name proposed for this strain is Rhodanobacter umsongensis sp. nov. (type strain GR24-2^T =KACC 12917^T =DSM 21300^T).     

Lysobacter telluris sp. nov., isolated from Korean rhizosphere soil

Archives of Microbiology - A Gram-stain-negative, aerobic, non-motile, non-spore-forming light-yellow-coloured rod-shaped bacterial strain, designated YJ15T, was isolated from soil at Bigeum island...     

Paralcaligenes ureilyticus gen. nov., sp. nov. isolated from soil of a Korean ginseng field

A bacterial strain, designated GR24-5^T, was isolated from soil cultivated with Korean ginseng. Cells were Gram-negative, strictly aerobic, catalase- and oxidase-positive, non-spore-forming motile rods. Based on the 16S rRNA gene sequence, strain GR24-5^T could be assigned to the family Alcaligenaceae. Strain GR24-5^T showed the highest sequence similarities with Parapusillimonas granuli Ch07^T (97.1%), Pusillimonas noertemannii BN9^T (96.9%), Pigmentiphaga kullae DSM 13608^T (96.5%), and Castellaniella defragrans 54Pin^T (96.3%). Strain GR24-5^T demonstrated a low DNA-DNA relatedness (23%) with P. granuli Ch07^T. The major respiratory quinone is ubiquinone 8 (Q-8) and the major fatty acids are C_16:0, C_17:0 cyclo, and summed feature 1 (C_14:0 3-OH/iso-C_16:1 I/C_12:0 aide). Putrescine, spermidine, and 2-hydroxyputrescine are the major polyamines. The major polar lipids are phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, di-phosphatidylglycerol, and an unknown aminophospholipid. Polar lipid patterns of strain GR24-5^T were unique in having a large amount of phosphatidylmethylethanolamine. Based on phylogenetic analysis and physiological and biochemical characteristics, strain GR245^T represents a novel genus and species, for which the name Paralcaligenes ureilyticus gen. nov., sp. nov. is proposed. The type strain of P. aralcaligenes ureilyticus is GR24-5^T (=KACC 13888 =DSM 24591^T).     

Mycoplasma simbae sp. nov., Mycoplasma leopharyngis sp. nov., and Mycoplasma leocaptivus sp. nov., isolated from lions.

Mycoplasmas isolated from the throats of lions were shown to belong to three serotypes, all of which were serologically distinct from the previously recognized Mycoplasma and Acholeplasma spp. Eight mycoplasma colonies were cloned, including one from a leopard (strain LP), and were examined in detail for morphology, growth, and biochemical characteristics. The strains had the following properties: guanine-plus-cytosine contents of 37 mol% (strain LXT [T = type strain]), 28 mol% (strain LL2T), and 27 mol% (strain 3L2T) and a requirement for sterol. Strain 3L2T metabolized glucose, which was not metabolized by strains LXT and LL2T. Arginine and urea were not hydrolyzed. Strain LX (= NCTC 11724) is the type strain of a new species, Mycoplasma simbae; strain LL2 (= NCTC 11725) is the type strain of a second new species, Mycoplasma leopharyngis; and strain 3L2 (= NCTC 11726) is the type strain of a third new species, Mycoplasma leocaptivus.     

Maricurvus nonylphenolicus gen. nov., sp. nov., a nonylphenol-degrading bacterium isolated from seawater

A novel aerobic, Gram-negative bacterial strain, designated KU41E(T), which degrades p-n-nonylphenol, was isolated from seawater obtained from the coastal region of Ishigaki Island, Japan. Cells are motile, curved rods with a single polar flagellum. Strain KU41E(T) grew at 20-35 °C, pH 7.0-8.0, in the presence of 1.0-4.0% NaCl. The predominant respiratory lipoquinone was ubiquinone-8, and the major cellular fatty acids were summed feature 3 (C(15:0) iso 2OH and/or C(16:1) ω7c, 28.4%), C(18:1) ω7c (19.8%), and C(16:0) (17.0%). The DNA G + C content was 48.6 mol%. The 16S rRNA gene sequence analysis indicated that strain KU41E(T) is affiliated with the order Alteromonadales within the class Gammaproteobacteria and is most closely related to Pseudoteredinibacter isoporae SW-11(T) (93.6% similarity) and Teredinibacter turnerae T7902(T) (91.9% similarity). On the basis of physiological, chemotaxonomic, and phylogenetic data, strain KU41E(T) is suggested to represent a novel species of a new genus, for which the name Maricurvus nonylphenolicus gen. nov., sp. nov. is proposed. The type strain of M. nonylphenolicus is KU41E(T) (=JCM 17778(T)).     

Allobaculum stercoricanis gen. nov., sp. nov., isolated from canine feces

Morphological, biochemical, and molecular genetic studies were performed on an unknown anaerobic, catalase-negative, non-spore-forming, rod-shaped bacterium isolated from dog feces. The unknown bacterium was tentatively identified as a Eubacterium species, based on cellular morphological and biochemical tests. 16S rRNA gene sequencing studies, however, revealed that it was phylogenetically distant from Eubacterium limosum, the type species of the genus Eubacterium. Phylogenetically, the unknown species forms a hitherto unknown sub-line proximal to the base of a cluster of organisms (designated rRNA cluster XVI), which includes Clostridium innocuum, Streptococcus pleomorphus, and some Eubacterium species. Based on both phenotypic and phylogenetic criteria, it is proposed that the unknown bacterium be classified as a new genus and species, Allobaculum stercoricanis. Using a specific rRNA-targeted probe designed to identify Allobaculum stercoricanis, in situ hybridisation showed this novel species represents a significant organism in canine feces comprising between 0.1% and 3.7% of total cells stained with DAPI (21 dog fecal samples). The type strain of Allobaculum stercoricanis is DSM 13633(T)=CCUG 45212(T).     

Motiliproteus sediminis gen. nov., sp. nov., isolated from coastal sediment

A novel Gram-stain-negative, rod-to-spiral-shaped, oxidase- and catalase- positive and facultatively aerobic bacterium, designated HS6^T, was isolated from marine sediment of Yellow Sea, China. It can reduce nitrate to nitrite and grow well in marine broth 2216 (MB, Hope Biol-Technology Co., Ltd) with an optimal temperature for growth of 30–33 °C (range 12–45 °C) and in the presence of 2–3 % (w/v) NaCl (range 0.5–7 %, w/v). The pH range for growth was pH 6.2–9.0, with an optimum at 6.5–7.0. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that the novel isolate was 93.3 % similar to the type strain of Neptunomonas antarctica, 93.2 % to Neptunomonas japonicum and 93.1 % to Marinobacterium rhizophilum, the closest cultivated relatives. The polar lipid profile of the novel strain consisted of phosphatidylethanolamine, phosphatidylglycerol and some other unknown lipids. Major cellular fatty acids were summed feature 3 (C_16:1 ω7c/iso-C_15:0 2-OH), C_18:1 ω7c and C_16:0 and the main respiratory quinone was Q-8. The DNA G+C content of strain HS6^T was 61.2 mol %. Based on the phylogenetic, physiological and biochemical characteristics, strain HS6^T represents a novel genus and species and the name Motiliproteus sediminis gen. nov., sp. nov., is proposed. The type strain is HS6^T (=ATCC BAA-2613^T=CICC 10858^T).     

Neoscardovia arbecensis gen. nov., sp. nov., isolated from porcine slurries

Three Gram-positive, anaerobic, pleomorphic strains (PG10(T), PG18 and PG22), were selected among five strains isolated from pig slurries while searching for host specific bifidobacteria to track the source of fecal pollution in water. Analysis of the 16S rRNA gene sequence showed a maximum identity of 94% to various species of the family Bifidobacteriaceae. However, phylogenetic analyses of 16S rRNA and HSP60 gene sequences revealed a closer relationship of these strains to members of the recently described Aeriscardovia, Parascardovia and Scardovia genera, than to other Bifidobacterium species. The names Neoscardovia gen. nov. and Neoscardovia arbecensis sp. nov. are proposed for a new genus and for the first species belonging to this genus, respectively, and for which PG10(T) (CECT 8111(T), DSM 25737(T)) was designated as the type strain. This new species should be placed in the Bifidobacteriaceae family within the class Actinobacteria, with Aeriscardovia aeriphila being the closest relative. The prevailing cellular fatty acids were C(16:0) and C(18:1)ω9c, and the major polar lipids consisted of a variety of glycolipids, diphosphatidyl glycerol, two unidentified phospholipids, and phosphatidyl glycerol. The peptidoglycan structure was A1γmeso-Dpm-direct. The GenBank accession numbers for the 16S rRNA gene and HSP60 gene sequences of strains PG10(T), PG18 and PG22 are JF519691, JF519693, JQ767128 and JQ767130, JQ767131, JQ767133, respectively.     

Roseovarius litoreus sp. nov., isolated from seawater of southern coast of Korean peninsula

A gram-negative, non-flagellated and ovoid- to rod-shaped bacterial strain, designated GSW-M15^T, was isolated from seawater on the southern coast of South Korea. Strain GSW-M15^T grew optimally at 30 °C, at pH 7.0–7.5 and in the presence of 2 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences revealed that strain GSW-M15^T belonged to the genus Roseovarius. Strain GSW-M15^T exhibited highest 16S rRNA gene sequence similarity values (98.3 and 97.5 %) to Roseovarius halotolerans HJ50^T and Roseovarius pacificus 81-2^T and 92.8-96.2 % sequence similarity values to the type strains of the other Roseovarius species. Strain GSW-M15^T contained Q-10 as the predominant ubiquinone and C_18:1 ω7c and 11-methyl-C_18:1 ω7c as the major fatty acids. The major polar lipids detected in strain GSW-M15^T were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and two unidentified lipids. The DNA G+C content of strain GSW-M15^T was 62.9 mol% and its mean DNA–DNA relatedness values with R. halotolerans KCTC 22224^T and R. pacificus LMG 24575^T were 33 and 18 %, respectively. Differential phenotypic properties of strain GSW-M15^T, together with the phylogenetic and genetic distinctiveness, demonstrated that this strain is distinguishable from other Roseovarius species. On the basis of the data presented here, strain GSW-M15^T (=KCTC 23897^T = CCUG 62218^T) represents a novel species of the genus Roseovarius, for which the name Roseovarius litoreus sp. nov. is proposed.     

Arthrospiribacter ruber gen. nov., sp. nov., a novel bacterium isolated from Arthrospira cultures

Polyphasic analysis of ten isolates of the red-pigmented bacteria isolated from ten Arthrospira cultures originating from different parts of the world is described. The 16S rRNA analysis showed <95 % identity with the known bacteria on public databases, therefore, additional analyses of fatty acids profiles, MALDI-TOF/MS, genome sequencing of the chosen isolate and following phylogenomic analyses were performed. Gram-stain-negative, strictly aerobic rods were positive for catalase, negative for oxidase, proteolytic and urease activity. Major fatty acids were 15 : 0 iso, 17:0 iso 3 OH and 17:1 iso w9c/16:0 10-methyl. The whole phylogenomic analyses revealed that the genomic sequence of newly isolated strain DPMB0001 was most closely related to members of Cyclobacteriaceae family and clearly indicated distinctiveness of newly isolated bacteria. The average nucleotide identity and in silico DNA–DNA hybridisation values were calculated between representative of the novel strains DPMB0001 and its phylogenetically closest species, Indibacter alkaliphilus CCUG57479 (LW1)^T (ANI 69.2 % is DDH 17.2 %) and Mariniradius saccharolyticus AK6^T (ANI 80.02 % isDDH 26.1 %), and were significantly below the established cut-off <94 % (ANI) and <70 % (isDDH) for species and genus delineation.The obtained results showed that the analysed isolates represent novel genus and species, for which names Arthrospiribacter gen nov. and Arthrospiribacter ruber sp. nov. (type strain DPMB0001 = LMG 31078 = PCM 3008) is proposed.