Pseudomonas arcuscaelestis sp. nov., isolated from rainbow trout and water

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Magdalena Mulet ◽  
Muhammed Duman ◽  
Soner Altun ◽  
Izzet Burcin Saticioglu ◽  
Margarita Gomila ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Rainbow Trout ◽  
Type Species ◽  
Sequence Similarity ◽  
Proteome Analysis ◽  
Housekeeping Gene ◽  
Major Fatty Acid ◽  
16S Rrna Sequence ◽  
Content Type ◽  
Link Type

Cells of strains P66T, V1 and W15Feb18 are Gram-stain-negative short rods and motile by one polar flagellum. Strain P66T was isolated from rainbow trout (Oncorhynchus mykiss) cultivated at a fish farm in Turkey. Strain V1 was isolated from sand of an intertidal shore on the Galicia coast in Spain and strain W15Feb18 was isolated from water collected at the Woluwe River in Belgium. Based on 16S rRNA sequence similarity values, the strains were grouped under the genus Pseudomonas and the Pseudomonas putida phylogenetic group of species. The DNA G+C content ranged from 58.5 to 58.9 mol%. The strains were characterized phenotypically by the API 20NE and Biolog GEN III tests, and chemotaxonomically by their whole-cell MALDI-TOF MS protein profiles and fatty acid contents. The absence of the hydrolysis of gelatin and the assimilation of arabinose, mannose and mannitol differentiated these strains from the closest species, Pseudomonas alkylphenolica . The major fatty acid components were C16:0 (29.91–31.68 %) and summed feature 3 (36.44–37.55 %). Multilocus sequence analysis with four and 83 housekeeping gene sequences and a core proteome analysis showed that these strains formed a phylogenetic cluster in the P. putida group of species. Genome comparisons by the average nucleotide identity based on blast and the Genome-to-Genome Distance Calculator demonstrated that the three strains belonged to the same genomic species and were distant from any known species, with similarity values lower than the thresholds established for species in the genus Pseudomonas . These data permitted us to conclude that strains P66T, V1 and W15Feb18 belong to a novel species in the genus Pseudomonas , for which the name Pseudomonas arcuscaelestis sp. nov. is proposed. The type strain is P66T (=CECT 30176T=CCUG 74872T). The other strains have been deposited in the CECT with the corresponding collection numbers: V1 (=CECT 30356) and W15Feb18 (=CECT 30355).

Pseudomonas piscium sp. nov., Pseudomonas pisciculturae sp. nov., Pseudomonas mucoides sp. nov. and Pseudomonas neuropathica sp. nov. isolated from rainbow trout

2021 ◽  
Author(s):  
Muhammed Duman ◽  
Magdalena Mulet ◽  
Soner Altun ◽  
Izzet Burcin Saticioglu ◽  
Margarita Gomila ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Housekeeping Gene ◽  
16S Rrna Sequence ◽  
Content Type ◽  
Link Type ◽  
Pseudomonas Mandelii

Six Gram negative, motile bacteria were isolated from rainbow trout (Oncorhynchus mykiss). The 16S rRNA sequence similarity values grouped them in the Pseudomonas mandelii (strains P49, P50T, 154aT and P154b), Pseudomonas fluorescens (strain P115T) and Pseudomonas koreensis (strain P155T) phylogenetic subgroups in the genus Pseudomonas . The DNA G+C content ranged from 58.5 to 60 mol%. The strains were characterized phenotypically using API 20NE and Biolog GENIII tests, and chemotaxonomically by their whole-cell MALDI-TOF MS protein profiles and fatty acid contents. Multi-locus sequence analysis with four housekeeping gene sequences (rpoD, rpoB, gyrB and 16S rRNA) together with genome comparisons by average nucleotide identity and genome-to-genome distance calculations were performed. Results showed that the similarity values of these strains to known species type strains were lower than the thresholds established for species in the genus Pseudomonas . Based on these data, we concluded that strains P49, P50T, P115T, P154aT, P154b and P155T belonged to four novel species. The names proposed are: Pseudomonas piscium sp. nov. for strains P49 and P50T with P50T (=CECT 30175T=CCUG 74871T) as the type strain; Pseudomonas pisciculturae sp. nov. for strain P115T (CECT 30173T=CCUG 74873T); Pseudomonas mucoides sp. nov. for strains P154aT and P154b with P154aT (=CECT 30177T=CCUG 74874T) as the type strain; and Pseudomonas neuropathica sp. nov. for strain P155T (=CECT 30178T=CCUG 74875T).

Aquabacterium soli sp. nov., a novel bacterium isolated from soil under the long-term application of bifenthrin

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Lina Sun ◽  
Wei Chen ◽  
Kaihua Huang ◽  
Weiguang Lyu ◽  
Xinhua Gao
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Content Type ◽  
Link Type ◽  
Novel Bacterium ◽  
Pr China

Strain SJQ9T, an aerobic bacterium isolated from a soil sample collected in Shanghai, PR China, was characterized using a polyphasic approach. It grew optimally at pH 7.0, 30–35 °C and in the presence of 1 % (w/v) NaCl. A comparative analysis of 16S rRNA gene sequences showed that strain SJQ9T fell within the genus Aquabacterium . The closest phylogenetic relatives of strain SJQ9T were Aquabacterium citratiphilum DSM 11900T (98.6 % sequence similarity) and Aquabacterium commune DSM 11901T (96.4 %). Cells of the strain were Gram-stain-negative, motile, non-spore-forming, rod-shaped and positive for oxidase activity and negative for catalase. The chemotaxonomic properties of strain SJQ9T were consistent with those of the genus Aquabacterium : the major fatty acid was summed feature 3 (C16 : 1  ω6c and/or C16 : 1  ω7c). The isoprenoid quinone was Q-8. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content was 65.7 mol%. Strain SH9T exhibited a DNA–DNA relatedness level of 34±2 % with A. citratiphilum DSM 11900T and 28±3 % with A. commune DSM 11901T. Based on the obtained data, strain SJQ9T represents a novel species of the genus Aquabacterium , for which the name Aquabacterium soli sp. nov. is proposed. The type strain is SJQ9T (=JCM 33106T=CCTCC AB 2018284T).

Facklamia lactis sp. nov., isolated from raw milk

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Etienne V. Doll ◽  
Lena Staib ◽  
Christopher Huptas ◽  
Siegfried Scherer ◽  
Mareike Wenning
Keyword(s):  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Raw Milk ◽  
16S Rrna Sequence ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Genome Phylogeny

Two strains of a Gram-staining-positive species were isolated from German bulk tank milk. On the basis of their 16S rRNA sequences they were affiliated to the genus Facklamia but could not be assigned to any species with a validly published name. Facklamia miroungae ATCC BAA-466T (97.3 % 16S rRNA sequence similarity), Facklamia languida CCUG 37842T (96.9 %), and Facklamia hominis CCUG 36813T (96.6 %) are the closest relatives. In the 16S rRNA phylogeny and in the core-genome phylogeny strains WS 5301T and WS 5302 form a well-supported, separate lineage. Pairwise average nucleotide identity calculated using MUMmer (ANIm) between WS 5301T and type strains of other Facklamia species is well below the species cut-off (95 %) and ranges from 83.4 to 87.7 %. The DNA G+C content of the type strain is 36.4 mol% and the assembly size of the genome is 2.2 Mb. Cells of WS 5301T are non-motile, non-endospore-forming, oxidase-negative, catalase-negative and facultatively anaerobic cocci. The fastidious species grows at 10–40 °C and with up to 7.0 % (w/v) NaCl in BHI supplemented with 5 g l−1 yeast extract. Major polar lipids are phosphatidylglycerol, diphosphatidylglycerol and two glycolipids. Predominant fatty acids are C16 : 1ω9c and C18 : 1ω9c. On the basis of their genomic, physiological and chemotaxonomic characteristics the strains examined in this study represent the same, hitherto unknown species. We propose the name Facklamia lactis sp. nov. for which WS 5301T (=DSM 111018T=LMG 31861T) is the type strain and WS 5302 (=DSM 111019=LMG 31862) is an additional strain of this novel species.

scholarly journals Sulfitobacter undariae sp. nov., isolated from a brown algae reservoir

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1672-1678 ◽  
Author(s):  
Sooyeon Park ◽  
Yong-Taek Jung ◽  
Sung-Min Won ◽  
Ji-Min Park ◽  
Jung-Hoon Yoon
Keyword(s):  
Brown Algae ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-stain-negative, aerobic, non-spore-forming, non-flagellated and coccoid, ovoid or rod-shaped bacterial strain, W-BA2T, was isolated from a brown algae reservoir in Wando of South Korea. Strain W-BA2T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of approximately 2.0–3.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain W-BA2T fell within the clade comprising the type strains of species of the genus Sulfitobacter , clustering coherently with the type strains of Sulfitobacter donghicola and Sulfitobacter guttiformis showing sequence similarity values of 98.0–98.1 %. Sequence similarities to the type strains of the other species of the genus Sulfitobacter were 96.0–97.4 %. Strain W-BA2T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The major polar lipids of strain W-BA2T were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain W-BA2T was 55.0 mol% and its DNA–DNA relatedness values with the type strains of Sulfitobacter donghicola , Sulfitobacter guttiformis and Sulfitobacter mediterraneus were 16–23 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain W-BA2T is separated from other species of the genus Sulfitobacter . On the basis of the data presented, strain W-BA2T is considered to represent a novel species of the genus Sulfitobacter , for which the name Sulfitobacter undariae sp. nov. is proposed. The type strain is W-BA2T ( = KCTC 42200T = NBRC 110523T).

scholarly journals Mycolicibacterium nivoides sp. nov isolated from a peat bog

2021 ◽  
Author(s):  
John L. Dahl ◽  
Wayne Gatlin III ◽  
Phuong M. Tran ◽  
Cody S. Sheik
Keyword(s):  
Fatty Acid ◽  
Type Species ◽  
Sequence Similarity ◽  
Fatty Acid Content ◽  
Antibiotic Sensitivity ◽  
Peat Bog ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Physiological Tests

A fast-growing, non-chromogenic, acid-fast-staining bacterium (DL90T) was isolated from a peat bog in northern Minnesota. On the basis of 16S rRNA gene sequence similarity (99.8 % identity with Mycolicibacterium septicum and 98 % with Mycolicibacterium peregrinum ) and chemotaxonomic data (fatty acid content), strain DL90T represents a member of the genus Mycolicibacterium . Physiological tests (growth curves, biofilm formation, antibiotic sensitivity, colony morphologies and heat tolerance) and biochemical analysis (arylsulfatase activity and fatty acid profiles) distinguish DL90T from its closest relative M. septicum . Phylogenomic reconstruction of the ‘Fortuitium–Vaccae’ clade, digital DNA–DNA hybridization (DDH) values of 61 %, and average nucleotide identity (ANI) values of approximately 95 % indicate that DL90T is likely to be diverged from M. septicum . Thus, we propose that DL90T represents a novel species, given the name Mycolicibacterium nivoides with the type strain being isolate DL90T (=JCM 32796T=NCCB 100660T).

Bacillus pervagus sp. nov. and Bacillus andreesenii sp. nov., isolated from a composting reactor

2014 ◽  
Vol 64 (Pt_1) ◽  
pp. 88-94 ◽  
Author(s):  
Kornelia Kosowski ◽  
Marie Schmidt ◽  
Rüdiger Pukall ◽  
Gerd Hause ◽  
Peter Kämpfer ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Fatty Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

Two strains, 8-4-E12T and 8-4-E13T, were isolated from a biowaste composting reactor. Based on 16S rRNA gene sequences, both strains belong to the genus Bacillus . Strain 8-4-E12T was most closely related to the type strains of Bacillus shackletonii , B. acidicola , B. sporothermodurans and B. oleronius (96.4, 96.3, 96.0 and 95.6 % 16S rRNA gene similarity, respectively), whereas strain 8-4-E13T was most closely related to the type strain of Bacillus humi (96.5 % sequence similarity). Strains 8-4-E12T and 8-4-E13T shared 94 % 16S rRNA gene sequence similarity. The fatty acid profile of strain 8-4-E12T was dominated by saturated iso- and anteiso-branched fatty acids (iso-C15 : 0, anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0), and also contained considerable amounts of C16 : 0. The fatty acid profile of strain 8-4-E13T showed a predominance of iso-C15 : 0 (65 %), with smaller amounts of other saturated branched-chain fatty acids along with an unsaturated alcohol. Both strains contained diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as major polar lipids. Additionally, strain 8-4-E12T contained an unknown lipid and strain 8-4-E13T two unknown (amino-)phospholipids. The diagnostic diamino acid found in the cell-wall peptidoglycan of 8-4-E12T and 8-4-E13T was meso-diaminopimelic acid. The predominant menaquinone was MK-7. The results of physiological and biochemical tests also allowed phenotypic differentiation of the two strains from each other and from related Bacillus species. On the basis of their phylogenetic, phenotypic and chemotaxonomic properties, strains 8-4-E12T and 8-4-E13T represent novel species of the genus Bacillus , for which the names Bacillus pervagus sp. nov. (type strain 8-4-E12T = DSM 23947T = LMG 27601T) and Bacillus andreesenii sp. nov. (type strain 8-4-E13T = DSM 23948T = LMG 27602T) are proposed.

scholarly journals Marivita hallyeonensis sp. nov., isolated from seawater, reclassification of Gaetbulicola byunsanensis as Marivita byunsanensis comb. nov. and emended description of the genus Marivita Hwang et al. 2009

2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 839-843 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Soo-Young Lee ◽  
Yong-Taek Jung ◽  
Jung-Sook Lee ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Emended Description ◽  
Type Strains

A Gram-stain-negative, non-motile, non-spore-forming, aerobic, rod-shaped bacterial strain, designated DPG-28T, was isolated from seawater on the southern coast of Korea. Strain DPG-28T grew optimally at 30 °C and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain DPG-28T formed a coherent cluster with members of the genera Marivita and Gaetbulicola , with which it exhibited sequence similarity values of 97.8–98.5 %. The DNA G+C content of strain DPG-28T was 65.1 mol%. The predominant ubiquinone of strain DPG-28T was ubiquinone-10 (Q-10), consistent with data for the genera Marivita and Gaetbulicola . The cellular fatty acid profiles of strain DPG-28T and the type strains of Marivita cryptomonadis , Marivita litorea and Gaetbulicola byunsanensis were essentially similar in that the common predominant fatty acid was C18 : 1ω7c. Major polar lipids found in strain DPG-28T and the type strains of M. cryptomonadis , M. litorea and G. byunsanensis were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and an unidentified aminolipid. From these data, it is proposed that Gaetbulicola byunsanensis be reclassified as a member of the genus Marivita , for which the name Marivita byunsanensis comb. nov. is proposed, with the type strain SMK-114T ( = CCUG 57612T  = KCTC 22632T), and that strain DPG-28T be classified in the genus Marivita . Differential phenotypic properties and genetic distinctiveness of strain DPG-28T demonstrated that this strain is distinguishable from M. cryptomonadis , M. litorea and G. byunsanensis . On the basis of the data presented, strain DPG-28T is considered to represent a novel species of the genus Marivita , for which the name Marivita hallyeonensis sp. nov. is proposed. The type strain is DPG-28T ( = KCTC 23421T  = CCUG 60522T). An emended description of the genus Marivita is also provided.

scholarly journals Pseudohalocynthiibacter aestuariivivens gen. nov., sp. nov., isolated from a tidal flat

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1509-1514 ◽  
Author(s):  
Sung-Min Won ◽  
Sooyeon Park ◽  
Ji-Min Park ◽  
Byung-Chan Kim ◽  
Jung-Hoon Yoon
Keyword(s):  
Fatty Acid ◽  
Tidal Flat ◽  
Type Strain ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-stain-negative, non-motile, aerobic and coccoid, ovoid or rod-shaped bacterial strain, designated BS-W9T, was isolated from a tidal flat of the South Sea, South Korea. Strain BS-W9T grew optimally at 25–30 °C, at pH 7.0–8.0 and in the presence of approximately 2.0 % (w/v) NaCl. Phylogenetic trees, based on 16S rRNA gene sequences, revealed that strain BS-W9T clustered with the type strain of Halocynthiibacter namhaensis , showing a highest sequence similarity of 97.3 %. It exhibited sequence similarity values of less than 95.6 % to the type strains of other species with validly published names. Strain BS-W9T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the predominant fatty acid. The major polar lipids of strain BS-W9T were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, one unidentified lipid and one unidentified aminolipid. The fatty acid and polar lipid profiles of strain BS-W9T were distinguished from those of the type strains of H. namhaensis and other phylogenetically related genera. The DNA G+C content of strain BS-W9T was 53.2 mol% and its mean DNA–DNA relatedness value with H. namhaensis RA2-3T was 14 %. On the basis of the phylogenetic, chemotaxonomic and other phenotypic properties, strain BS-W9T is considered to represent a novel genus and species within the family Rhodobacteraceae , for which the name Pseudohalocyntiibacter aestuariivivens gen. nov., sp. nov. is proposed. The type strain of Pseudohalocyntiibacter aestuariivivens is BS-W9T ( = KCTC 42348T = CECT 8726T).

scholarly journals Vagococcus silagei sp. nov., isolated from brewer’s grain used to make silage in Taiwan

2020 ◽  
Vol 70 (3) ◽  
pp. 1953-1960 ◽  
Author(s):  
Yen-Chi Wu ◽  
Shih-Ting Lin ◽  
Jia-Rong Guu ◽  
Tomohiko Tamura ◽  
Koji Mori ◽  
...  
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Sequence Similarity ◽  
Housekeeping Gene ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-stain-positive, coccus- or oval-shaped, non-motile, haemolytic, asporogenous, catalase- and oxidase-negative, and facultatively anaerobic strain, 2B-2T, was isolated from a brewer’s grain used to make silage in Taiwan. Comparative analyses of 16S rRNA, hsp60 and pheS gene sequences demonstrated that strain 2B-2T was a member of the genus Vagococcus . On the basis of 16S rRNA gene sequence similarity, the type strains of Vagococcus teuberi (98.4 % similarity), Vagococcus carniphilus (98.4 %), Vagococcus martis (98.2 %), Vagococcus penaei (98.2 %) and Vagococcus fluvialis (98.0 %) were the closest neighbours to this novel strain. The similarity levels of concatenated housekeeping gene sequences (hsp60 and pheS) between strain 2B-2T and these closely related species ranged from 84.5 to 88.0 %. The average nucleotide identity and in silico DNA–DNA hybridization values between strain 2B-2T and its closest relatives were lower than 72.9 and 21.6 %, respectively. The DNA G+C content was 34.7 mol%. Phenotypic and genotypic features demonstrated that strain 2B-2T represents a novel species of the genus Vagococcus , for which the name Vagococcus silagei sp. nov. is proposed. The type strain is 2B-2T (=BCRC 81132T=NBRC 113536T).

Pedobacter gandavensis sp. nov., Pedobacter foliorum sp. nov. and Pedobacter planticolens sp. nov., isolated from leaves of Arabidopsis thaliana

2021 ◽  
Author(s):  
Shan Shan Qi ◽  
Margo Cnockaert ◽  
Aurélien Carlier ◽  
Peter Vandamme
Keyword(s):  
Arabidopsis Thaliana ◽  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Sequence ◽  
Content Type ◽  
Link Type ◽  
Maldi Tof Mass Spectra

Three rod-shaped, non-spore-forming, yellow or pale-yellow pigmented bacteria with distinct MALDI-TOF mass spectra were isolated from the phyllosphere of Arabidopsis thaliana seedlings. Their 16S rRNA gene sequences demonstrated that these isolates belong to the genus Pedobacter . The nearest phylogenetic neighbours of strain LMG 31462T were Pedobacter steynii DSM 19110T (98.3 % 16S rRNA sequence similarity) and Pedobacter caeni LMG 22862T (98.3 %); the nearest phylogenetic neighbours of strain LMG 31463T were Pedobacter panaciterrae Gsoil 042T (98.3 %) and Pedobacter nutrimenti DSM 27372T (98.1 %); and the nearest phylogenetic neighbours of strain LMG 31464T were Pedobacter boryungensis BR-9T (99.0 %) and Pedobacter daejeonensis THG-DN3.18T (98.7 %). Average nucleotide identity analyses between the whole genome sequences of the three strains and of the type strains of their respective nearest-neighbour taxa yielded values well below the species delineation threshold and thus confirmed that the three strains represented a novel Pedobacter species each. An extensive phenotypic comparison and an analysis of whole-cell fatty acid components yielded distinctive phenotypic characteristics for each of these strains. We therefore propose to classify these isolates as three novel species, for which we propose the names Pedobacter gandavensis with LMG 31462T (=R-74704T=CECT 30149T) as the type strain, Pedobacter foliorum with LMG 31463T (=R-74623T=CECT 30150T) as the type strain and Pedobacter planticolens with LMG 31464T (=R-74626T=CECT 30151T) as the type strain.

Sign in / Sign up

Export Citation Format

Share Document