Arsenicicoccus dermatophilus sp. nov., a hypha-forming bacterium isolated from the skin of greater flamingos (Phoenicopterus roseus) with pododermatitis

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4046-4051 ◽  
Author(s):  
Stefanie Gobeli ◽  
Andreas Thomann ◽  
Fabia Wyss ◽  
Kathrin Kuehni-Boghenbor ◽  
Isabelle Brodard ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Reference Strain ◽  
Polymyxin B ◽  
Wall Structure ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Link Type ◽  
Greater Flamingos

Dermatophilus -like bacteria were observed in histological examinations of samples of diseased foot skin from greater flamingos (Phoenicopterus roseus) living in zoological gardens in Switzerland. When grown on TSA-SB containing polymyxin B, the bacteria isolated from these skin samples formed hyphae, as is typical for Dermatophilus congolensis , but these bacteria were non-haemolytic. The closest relatives based on 16S rRNA gene sequences were the two members of the genus Arsenicicoccus , Arsenicicoccus bolidensis and Arsenicicoccus piscis . A representative of the isolated strains shared 34.3 % DNA–DNA relatedness with the type strain of A. bolidensis , 32.3 % with the type strain of A. piscis and 34.5 % with the type strain of D. congolensis , demonstrating that these strains do not belong to any of these species. The phenotypic characteristics differed from those of members of the genus Arsenicicoccus as well as from those of D. congolensis . The G+C content of strain KM 894/11T was 71.6 mol%. The most abundant fatty acids were iso-C15 : 0, summed feature 3 (including C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C18 : 1ω9c. MK-8(H4) was the predominant menaquinone. Cell-wall structure analysis revealed that the peptidoglycan type was A3γ ll-Dpm–Gly (type A41.1). Based on genotypic and chemotaxonomic characteristics, the isolated strains represent a novel species within the genus Arsenicicoccus , for which the name Arsenicicoccus dermatophilus sp. nov. is proposed. The type strain is KM 894/11T ( = DSM 25571T = CCUG 62181T = CCOS 690T), and strain KM 1/12 ( = DSM 25572 = CCUG 62182 = CCOS 691) is a reference strain.

Nocardiopsis coralli sp. nov. a novel actinobacterium isolated from the coral Galaxea astreata

2021 ◽  
Vol 71 (6) ◽  
Author(s):  
Fenfa Li ◽  
Qingyi Xie ◽  
Shuangqing Zhou ◽  
Fandong Kong ◽  
Yun Xu ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Link Type ◽  
Phosphatidylinositol Mannosides

Strain HNM0947T, representing a novel actinobacterium, was isolated from the coral Galaxea astreata collected from the coast of Wenchang, Hainan, China. The strain was found to have morphological and chemotaxonomic characteristics consistent with the genus Nocardiopsis . The organism formed abundant fragmented substrate mycelia and aerial mycelia which differentiated into non-motile, rod-shaped spores. Whole-cell hydrolysates contained meso-diaminopimelic acid and no diagnostic sugars. The major menaquinones were MK-10(H8), MK-10(H6) and MK-10(H4). The major phospholipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The major fatty acids were iso-C16:0, anteiso-C17:0, C18:0, C18:0 10-methyl (TBSA) and anteiso-C15:0. The G+C content was 71.3 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain HNM0947T belonged to the genus Nocardiopsis and shared highest sequence similarity to Nocardiopsis salina YIM 90010T (98.8%), Nocardiopsis xinjiangensis YIM 90004T(98.5%) and Nocardiopsis kunsanensis DSM 44524T (98.3%). The strain HNM0947T was distinguished from its closest type strain by low average nucleotide identity (90.8%) and dDDH values (60.4%) respectively. Based on genotypic, chemotaxonomic and phenotypic characteristics, it was concluded that strain HNM0947T represents a novel species of the genus Nocardiopsis whose name was proposed as Nocardiopsis coralli sp. nov. The type strain was HNM0947T (=CCTCC AA 2020015 T=KCTC 49525 T).

scholarly journals Gemella parahaemolysans sp. nov. and Gemella taiwanensis sp. nov., isolated from human clinical specimens

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 2060-2065 ◽  
Author(s):  
Wei-Chun Hung ◽  
Hsiao-Jan Chen ◽  
Jui-Chang Tsai ◽  
Sung-Pin Tseng ◽  
Tai-Fen Lee ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Link Type ◽  
Gram Staining

Four Gram-staining-positive, catalase-negative, coccoid isolates, designated NTUH_1465T, NTUH_2196, NTUH_4957 and NTUH_5572T, were isolated from human specimens. The four isolates displayed more than 99.6 % 16S rRNA gene sequence similarity with Gemella haemolysans ATCC 10379T, and 96.7 to 98.6 % similarity with Gemella sanguinis ATCC 700632T, Gemella morbillorum ATCC 27824T or Gemella cuniculi CCUG 42726T. However, phylogenetic analysis of concatenated sequences of three housekeeping genes, groEL, rpoB and recA, suggested that the four isolates were distinct from G. haemolysans ATCC 10379T and other species. Isolates NTUH_2196, NTUH_4957 and NTUH_5572T clustered together and formed a stable monophyletic clade. DNA–DNA hybridization values among strains NTUH_1465T and NTUH_5572T and their phylogenetically related neighbours were all lower than 49 %. The four isolates could be distinguished from G. haemolysans and other species by phenotypic characteristics. Based on the phylogenetic and phenotypic results, two novel species Gemella parahaemolysans sp. nov. (type strain NTUH_1465T = BCRC 80365T = JCM 18067T) and Gemella taiwanensis sp. nov. (type strain NTUH_5572T = BCRC 80366T = JCM 18066T) are proposed.

Conexibacter arvalis sp. nov., isolated from a cultivated field soil sample

2012 ◽  
Vol 62 (Pt_10) ◽  
pp. 2400-2404 ◽  
Author(s):  
Tamae Seki ◽  
Atsuko Matsumoto ◽  
Risa Shimada ◽  
Yuki Inahashi ◽  
Satoshi Ōmura ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Link Type ◽  
Gram Staining

Two bacterial strains, designated KV-962T and KV-963, were isolated from soil collected from a field in Japan. Cells of both strains were Gram-staining-positive, non-spore-forming, short rod-shaped and motile. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains were related to Conexibacter woesei DSM 14684T, with a similarity value of 98.6 %. These strains possessed MK-7 (H4) as the sole menaquinone and contained C18 : 1ω9c, C17 : 1ω6c and iso-C16 : 0 as the major fatty acids. On the basis of genotypic and phenotypic characteristics, strain KV-962T and KV-963 were indicated as a novel species of the genus Conexibacter , for which the name Conexibacter arvalis sp. nov. is proposed. The type strain is KV-962T ( = DSM 23288T  = NBRC 106558T)

Sphingobacterium lactis sp. nov. and Sphingobacterium alimentarium sp. nov., isolated from raw milk and a dairy environment

2012 ◽  
Vol 62 (Pt_7) ◽  
pp. 1506-1511 ◽  
Author(s):  
Verena S. J. Schmidt ◽  
Mareike Wenning ◽  
Siegfried Scherer
Keyword(s):  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Reference Strain ◽  
Sequence Similarity ◽  
Raw Milk ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

Four non-fermenting, rod-shaped, Gram-staining-negative bacterial strains, designated WCC 4512T, WS 4555, WCC 4521T and WS 4556, were isolated from raw milk and the dairy environment. Phylogenetic analyses based on 16S rRNA and groEL gene sequences demonstrated the affiliation of the four strains to two distinct clusters within the class Sphingobacteriia , phylum ‘ Bacteroidetes ’. Strains WCC 4512T and WS 4555 showed the highest 16S rRNA gene sequence similarity to the type strain of S. daejeonense (97.3 and 97.2 %, respectively), whereas strains WCC 4521T and WS 4556 were most closely related to S. composti LMG 23401T (97.6 % 16S rRNA gene sequence similarity). The DNA G+C contents of strains WCC 4512T and WCC 4521T were 44.2 and 39.3 mol%, respectively. The major cellular fatty acids and the presence of menaquinone MK-7 as the predominant quinone for both strains WCC 4512T and WCC 4521T supported their affiliation to the genus Sphingobacterium . DNA–DNA hybridization experiments between strain WCC 4512T and S. daejeonense LMG 23402T and between strain WCC 4521T and S. composti LMG 23401T revealed DNA relatedness values of 2 % (repetition, 3 %) and 8 % (repetition, 17 %), respectively. On the basis of phenotypic and genetic properties, as well as phylogenetic distinctiveness, it is suggested that the four strains represent two novel Sphingobacterium species with strain WCC 4512T ( = DSM 22361T = LMG 25272T) as the type strain of Sphingobacterium lactis sp. nov. (WS 4555 is a reference strain of S. lactis) and strain WCC 4521T ( = DSM 22362T = LMG 25273T) as the type strain of Sphingobacterium alimentarium sp. nov. (WS 4556 is a reference strain of S. alimentarium).

scholarly journals Pseudoseohaeicola caenipelagi gen. nov., sp. nov., isolated from a tidal flat

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1819-1824 ◽  
Author(s):  
Sooyeon Park ◽  
Ji-Min Park ◽  
Chul-Hyung Kang ◽  
Song-Gun Kim ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Strain ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, non-motile, aerobic and pleomorphic bacterium, designated BS-W13T, was isolated from a tidal flat on the South Sea, South Korea, and its taxonomic position was investigated using a polyphasic approach. Strain BS-W13T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 1.0–2.0 % (w/v) NaCl. Neighbour-joining and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain BS-W13T clustered with the type strain of Seohaeicola saemankumensis , showing the highest sequence similarity (95.96 %) to this strain. Strain BS-W13T exhibited 16S rRNA gene sequence similarity values of 95.95, 95.91, 95.72 and 95.68 % to the type strains of Sulfitobacter donghicola , Sulfitobacter porphyrae , Sulfitobacter mediterraneus and Roseobacter litoralis , respectively. Strain BS-W13T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The polar lipid profile of strain BS-W13T, containing phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid as major components, was distinguishable from those of some phylogenetically related taxa. The DNA G+C content of strain BS-W13T was 58.1 mol%. The phylogenetic data and differential chemotaxonomic and other phenotypic properties revealed that strain BS-W13T constitutes a novel genus and species within family Rhodobacteraceae of the class Alphaproteobacteria , for which the name Pseudoseohaeicola caenipelagi gen. nov., sp. nov. is proposed. The type strain is BS-W13T ( = KCTC 42349T = CECT 8724T).

Salipiger mangrovisoli sp. nov., isolated from mangrove soil and the proposal for the reclassification of Paraphaeobacter pallidus as Salipiger pallidus comb. nov.

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Juan Du ◽  
Yang Liu ◽  
Tao Pei ◽  
Ming-Rong Deng ◽  
Honghui Zhu
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Cellular Fatty Acid ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Species Definition ◽  
Content Type ◽  
Link Type ◽  
Mangrove Soil

A novel Gram-stain-negative, aerobic and rod-shaped bacterial strain designated as 6D45AT was isolated from mangrove soil and characterized using a polyphasic taxonomic approach. Strain 6D45AT was found to grow at 10–37 °C (optimum, 28 °C), at pH 6.0–9.0 (optimum, 7.0) and in 0–5 % (w/v) NaCl (optimum, 2%). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 6D45AT fell into the genus Salipiger and shared 99.1 % identity with the closest type strain Salipiger pacificus CGMCC 1.3455T and less than 97.2 % identity with other type strains of this genus. The 34.8 % digital DNA–DNA hybridization (dDDH) and 88.3 % average nucleotide identity (ANI) values between strain 6D45AT and the closest relative above were well below recognized thresholds of 70 % DDH and 95–96 % ANI for species definition, implying that strain 6D45AT should represent a novel genospecies. The phylogenomic analysis indicated that strain 6D45AT formed an independent branch distinct from reference strains. The predominant cellular fatty acid of strain 6D45AT was summed feature 8 (C18 : 1  ω6c and/or C18 : 1  ω7c, 66.9 %); the polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids, two unidentified glycolipids and an unknown lipid; the respiratory quinone was Q-10. The genomic DNA G+C content was 66.5 mol %. Based on the phenotypic and genotypic characteristics, strain 6D45AT is concluded to represent a novel species of the genus Salipiger , for which the name Salipiger mangrovisoli sp. nov., is proposed. The type strain of the species is 6D45AT (=GDMCC 1.1960T=KCTC 82334T). We also propose the reclassification of Paraphaeobacter pallidus as Salipiger pallidus comb. nov. and ‘ Pelagibaca abyssi ’ as a species of the genus Salipiger .

scholarly journals Marinomonas mangrovi sp. nov., isolated from mangrove sediment

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1537-1541 ◽  
Author(s):  
De-Chao Zhang ◽  
Rosa Margesin
Keyword(s):  
Phylogenetic Analysis ◽  
Type Species ◽  
Mangrove Sediment ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Content Sharing ◽  
Link Type ◽  
Curved Rods ◽  
Sequence Similarities

A Gram-stain-negative, Na+-requiring bacterial strain, designated B20-1T, was isolated from soil of the root system of mangrove forest. Cells were curved rods and motile by means of a polar flagellum. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain B20-1T belonged to the genus Marinomonas , sharing highest sequence similarities with Marinomonas rhizomae IVIA-Po-145T (97.6 %), Marinomonas dokdonensis DSW10-10T (97.0 %) and Marinomonas foliarum IVIA-Po-155T (96.9 %). The predominant cellular fatty acids of strain B20-1T were C10 : 0 3-OH, C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C16 : 0. Phosphatidylethanolamine and phosphatidylglycerol were identified as the predominant phospholipids. The predominant ubiquinone was Q-8. The genomic DNA G+C content of strain B20-1T was 46.6 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness, a novel species, Marinomonas mangrovi sp. nov., is proposed with B20-1T ( = DSM 28136T = LMG 28077T) as the type strain.

scholarly journals Arthrobacter yangruifuii sp. nov. and Arthrobacter zhaoguopingii sp. nov., two new members of the genus Arthrobacter

2020 ◽  
Vol 70 (10) ◽  
pp. 5287-5295 ◽  
Author(s):  
Yajun Ge ◽  
Yuanmeihui Tao ◽  
Jing Yang ◽  
Xin-He Lai ◽  
Dong Jin ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Tibet Plateau ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

Four unknown strains belonging to the genus Arthrobacter were isolated from plateau wildlife on the Qinghai–Tibet Plateau of PR China. Phylogenetic analysis based on 16S rRNA gene sequences showed that the four isolates were separated into two clusters. Cluster I (strains 785T and 208) had the greatest 16S rRNA gene sequence similarity to Arthrobacter citreus (98.6 and 98.7 %, respectively), Arthrobacter luteolus (98.0 and 98.1%, respectively), Arthrobacter gandavensis (97.9 and 98.0 %, respectively) and Arthrobacter koreensis (97.6 and 97.7 %, respectively). Likewise, cluster II (strains J391T and J915) had the highest sequence similarity to Arthrobacter ruber (98.6 and 98.3 %, respectively) and Arthrobacter agilis (98.1 and 97.9  %, respectively). Average nucleotide identity and the digital DNA–DNA hybridization values illustrated that the two type strains, 785T and J391T, represented two separate novel species that are distinct from all currently recognized species in the genus Arthrobacter . These strains had DNA G+C contents of 66.0–66.1 mol% (cluster I) and 68.0 mol% (cluster II). The chemotaxonomic properties of strains 785T and J391T were in line with those of the genus Arthrobacter : anteiso-C15:0 (79.3 and 40.8 %, respectively) as the major cellular fatty acid, MK-8(H2) (65.8 %) or MK-9(H2) (75.6 %) as the predominant respiratory quinone, a polar lipid profile comprising diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, glycolipids and phospholipid, and A3α or A4α as the cell wall peptidoglycan type. On the basis of our results, two novel species in the genus Arthrobacter are proposed, namely Arthrobacter yangruifuii sp. nov. (type strain, 785T=CGMCC 1.16725T=GDMCC 1.1592T=JCM 33491T) and Arthrobacter zhaoguopingii sp. nov. (type strain, J391T=CGMCC 1.17382T=GDMCC 1.1667T=JCM 33841T).

scholarly journals Pseudoalteromonas caenipelagi sp. nov., isolated from a tidal flat

2020 ◽  
Vol 70 (12) ◽  
pp. 6301-6306
Author(s):  
Sooyeon Park ◽  
Seo Yeon Lee ◽  
Wonyong Kim ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Strain ◽  
Type Species ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-stain-negative, aerobic, non-spore-forming, motile by single polar flagellum and ovoid or rod-shaped bacterial strain, designated JBTF-M23T, was isolated from tidal flat sediment collected from the Yellow Sea, Republic of Korea. Neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain JBTF-M23T fell within the clade comprising the type strains of Pseudoalteromonas species, clustering with the type strains of P. byunsanensis and P. amylolytica . Strain JBTF-M23T exhibited the highest 16S rRNA gene sequence similarity value (98.6 %) to the type strain of P. rubra and sequence similarities of 98.3 and 97.7 % to the type strains of P. byunsanensis and P. amylolytica, respectively. The DNA G+C content of strain JBTF-M23T from genomic sequence data was 41.98 %. The ANI and dDDH values between strain JBTF-M23T and the type strains of P. rubra , P. byunsanensis and P. amylolytica were 71.3–76.6 and 19.4–19.9 %, respectively. Strain JBTF-M23T contained Q-8 as the predominant ubiquinone and C16 : 1  ω7c and/or C16 : 1  ω6c, C16 : 0 and C18 : 1  ω7c as the major fatty acids. The major polar lipids of strain JBTF-M23T were phosphatidylethanolamine and one unidentified aminolipid. Distinguished phenotypic properties, along with the phylogenetic and genetic distinctiveness, revealed that strain JBTF-M23T is separated from recognized Pseudoalteromonas species. On the basis of the data presented, strain JBTF-M23Tis considered to represent a novel species of the genus Pseudoalteromonas , for which the name Pseudoalteromonas caenipelagi sp. nov. is proposed. The type strain is JBTF-M23T(=KACC 19900T=NBRC 113647T).

Roseibium litorale sp. nov., isolated from a tidal flat sediment and proposal for the reclassification of Labrenzia polysiphoniae as Roseibium polysiphoniae comb. nov.

2021 ◽  
Author(s):  
Yang Liu ◽  
Tao Pei ◽  
Juan Du ◽  
Meijie Chao ◽  
Ming-Rong Deng ◽  
...  
Keyword(s):  
Tidal Flat ◽  
Type Strain ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Species Definition ◽  
Content Type ◽  
Link Type ◽  
Tidal Flat Sediment

A novel Gram-stain-negative, facultatively anaerobic, rod-shaped and non-motile bacterial strain, designated as 4C16AT, was isolated from a tidal flat sediment and characterized by using a polyphasic taxonomic approach. Strain 4C16AT was found to grow at 10–40 °C (optimum, 28 °C), at pH 5.0–10.0 (optimum, pH 6.0–7.0) and in 0–6 % (w/v) NaCl (optimum, 1 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 4C16AT fell into the genus Roseibium , and shared the highest identity of 98.9 % with the closest type strain Roseibium suaedae KACC 13772T and less than 98.0 % identity with other type strains of recognized species within this genus. The phylogenomic analysis indicated that strain 4C16AT formed an independent branch within this genus. The 28.6 % digital DNA–DNA hybridization estimate and 85.0 % average nucleotide identity between strains 4C16AT and R. suaedae KACC 13772T were the highest, but still far below their respective threshold for species definition, implying that strain 4C16AT should represent a novel genospecies. The predominant cellular fatty acid was summed feature 8; the polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylmonomethylethanolamine; the respiratory quinones were Q-9 and Q-10. The genomic DNA G+C content was 59.8mol %. Based on phylogenetic analyses and phenotypic and chemotaxonomic characteristics, strain 4C16AT is concluded to represent a novel species of the genus Roseibium , for which the name Roseibium litorale sp. nov. is proposed. The type strain of the species is 4C16AT (=GDMCC 1.1932T=KACC 22078T). We also propose the reclassification of Labrenzia polysiphoniae as Roseibium polysiphoniae comb. nov. and ‘Labrenzia callyspongiae’ as Roseibium callyspongiae sp. nov.

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