Mycobacterium bourgelatii sp. nov., a rapidly growing, non-chromogenic species isolated from the lymph nodes of cattle

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4669-4674 ◽  
Author(s):  
Véronique Guérin-Faublée ◽  
Jean-Pierre Flandrois ◽  
Catherine Pichat ◽  
Maria Laura Boschiroli ◽  
Brigitte Lamy

Three independent strains of a rapidly growing, non-chromogenic member of the genus Mycobacterium were isolated from lymph nodes of French cattle. Identification of the isolates was carried out using a polyphasic approach. The nearly complete SSU rRNA gene sequences (>1200 bp) of the strains MLB-A23, MLB-A30 and MLB-A84T were identical. A phylogenetic analysis of these unique SSU rRNA gene sequences showed that these strains were most closely related to Mycobacterium intermedium . Further phylogenetic analysis based on concatenated sequences (2854 bp) of four housekeeping genes (hsp65, rpoB, sodA and tuf), the transfer–messenger RNA (tmRNA) and SSU rRNA genes indicated that these three strains represented a distinct species that shares a common ancestor with M. intermedium . Phylogenetic and phenotypic data strongly indicate that the strains MLB-A23, MLB-A30 and MLB-A84T belong to a novel mycobacterial species for which the name Mycobacterium bourgelatii sp. nov. is proposed. The type strain is MLB-A84T ( = CIP 110557T = DSM 45746T).

2012 ◽  
Vol 62 (Pt_8) ◽  
pp. 1997-2003 ◽  
Author(s):  
Fehmida Bibi ◽  
Eu Jin Chung ◽  
Ajmal Khan ◽  
Che Ok Jeon ◽  
Young Ryun Chung

During a study of endophytic bacteria from coastal dune plants, a bacterial strain, designated YC6881T, was isolated from the root of Rosa rugosa collected from the coastal dune areas of Namhae Island, Korea. The bacterium was found to be Gram-staining-negative, motile, halophilic and heterotrophic with a single polar flagellum. Strain YC6881T grew at temperatures of 4–37 °C (optimum, 28–32 °C), at pH 6.0–9.0 (optimum, pH 7.0–8.0), and at NaCl concentrations in the range of 0–7.5 % (w/v) (optimum, 4–5 % NaCl). Strain YC6881T was catalase- and oxidase-positive and negative for nitrate reduction. According to phylogenetic analysis using 16S rRNA gene sequences, strain YC6881T belonged to the genus Rhizobium and showed the highest 16S rRNA gene sequence similarity of 96.9 % to Rhizobium rosettiformans , followed by Rhizobium borbori (96.3 %), Rhizobium radiobacter (96.1 %), Rhizobium daejeonense (95.9 %), Rhizobium larrymoorei (95.6 %) and Rhizobium giardinii (95.4 %). Phylogenetic analysis of strain YC6881T by recA, atpD, glnII and 16S–23S intergenic spacer (IGS) sequences all confirmed the phylogenetic arrangements obtained by using 16S rRNA gene sequences. Cross-nodulation tests showed that strain YC6881T was a symbiotic bacterium that nodulated Vigna unguiculata and Pisum sativum. The major components of the cellular fatty acids were C18 : 1ω7c (53.7 %), C19 : 0 cyclo ω8c (12.6 %) and C12 : 0 (8.1 %). The DNA G+C content was 52.8 mol%. Phenotypic and physiological tests with respect to carbon source utilization, antibiotic resistance, growth conditions, phylogenetic analyses of housekeeping genes recA, atpD and glnII, and fatty acid composition could be used to discriminate strain YC6881T from other species of the genus Rhizobium in the same sublineage. Based on the results obtained in this study, strain YC6881T is considered to represent a novel species of the genus Rhizobium , for which the name Rhizobium halophytocola sp. nov. is proposed. The type strain is YC6881T ( = KACC 13775T = DSM 21600T).


2020 ◽  
Vol 70 (9) ◽  
pp. 5012-5018 ◽  
Author(s):  
Hui Zhao ◽  
Yinan Ma ◽  
Xiaogang Wu ◽  
Liqun Zhang

A Gram-stain-negative aerobic bacterium, strain 11K1T, was isolated from a rhizosphere soil of broad bean collected from Qujing, Yunnan, PR China and characterized by using polyphasic taxonomy. The bacterial cells of strain 11K1T were rod-shaped, motile by two polar flagella and positive for oxidase and catalase. Results of phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain had the highest similarities to Pseudomonas thivervalensis DSM 13194T (99.52 %), Pseudomonas lini CFBP 5737T (99.45 %), Pseudomonas chlororaphis subsp. chlororaphi s NBRC 3904T (99.31 %), Pseudomonas kilonensis DSM 13647T (99.25 %) and Pseudomonas brassicacearum JCM11938T (99.24 %). Multilocus sequence analysis using the 16S rRNA, gyrB, rpoB and rpoD gene sequences demonstrated that strain 11K1T was a member of the Pseudomonas corrugata subgroup within the Pseudomonas fluorescens lineage, but was distant from all closely related species. The average nucleotide identity and in silico DNA–DNA hybridization values were lower than recommended thresholds of 95 and 70 %, respectively, for species delineation. The major isoprenoid quinone of strain 11K1T was ubiquinone (Q-9) and the major cellular fatty acids were C16 : 0, summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c) and C17 : 0 cyclo. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, aminophospholipid and two unidentified lipids. Based on the results of phenotypic characterization, phylogenetic analysis and genome comparison, strain 11K1T represents a novel species of the genus Pseudomonas , for which the name Pseudomonas viciae sp. nov. is proposed. The type strain is 11K1T (=GDMCC 1.1743T=KACC 21650T).


2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 90-94 ◽  
Author(s):  
P. García-Fraile ◽  
M. Chudíčková ◽  
O. Benada ◽  
J. Pikula ◽  
M. Kolařík

During the study of bacteria associated with bats affected by white-nose syndrome hibernating in caves in the Czech Republic, we isolated two facultatively anaerobic, Gram-stain-negative bacteria, designated strains 12T and 52T. Strains 12T and 52T were motile, rod-like bacteria (0.5–0.6 µm in diameter; 1–1.3 µm long), with optimal growth at 20–35 °C and pH 6–8. On the basis of the almost complete sequence of their 16S rRNA genes they should be classified within the genus Serratia ; the closest relatives to strains 12T and 52T were Serratia quinivorans DSM 4597T (99.5 % similarity in 16S rRNA gene sequences) and Serratia ficaria DSM 4569T (99.5 % similarity in 16S rRNA gene sequences), respectively. DNA–DNA relatedness between strain 12T and S. quinivorans DSM 4597T was only 37.1 % and between strain 52T and S. ficaria DSM 4569T was only 56.2 %. Both values are far below the 70 % threshold value for species delineation. In view of these data, we propose the inclusion of the two isolates in the genus Serratia as representatives of Serratia myotis sp. nov. (type strain 12T = CECT 8594T = DSM 28726T) and Serratia vespertilionis sp. nov. (type strain 52T = CECT 8595T = DSM 28727T).


Parasitology ◽  
2004 ◽  
Vol 130 (4) ◽  
pp. 405-412 ◽  
Author(s):  
W. C. GIBSON ◽  
J. LOM ◽  
H. PECKOVÁ ◽  
V. R. FERRIS ◽  
P. B. HAMILTON

The taxonomy and phylogenetic relationships of fish trypanosomes are uncertain. A collection of 22 cloned trypanosome isolates from 14 species of European freshwater fish and 1 species of African freshwater fish were examined by molecular phylogenetic analysis. The small subunit ribosomal RNA (ssu rRNA) genes of 8 clones were sequenced and compared with ssu rRNA gene sequences from a wider selection of vertebrate trypanosome isolates by phylogenetic analysis. All trypanosomes from freshwater fish fell in a single clade, subdivided into 3 groups. This clade sits within a larger, robust clade containing trypanosomes from marine fish and various amphibious vertebrates. All 22 trypanosome clones were analysed by random amplification of polymorphic DNA. The resulting dendrogram shows 3 groups, which are congruent with the groups identified in the ssu rRNA gene phylogeny. Two of the groups contain the majority of trypanosome isolates and within-group variation is slight. These groups do not separate purported trypanosome species distinguished by morphology or host origin, and thus these criteria do not appear to be reliable guides to genetic relationships among fish trypanosomes. However, we suggest that the 2 groups themselves may represent different species of fish trypanosomes. The polymorphic DNA markers we have identified will facilitate future comparisons of the biology of these 2 groups of fish trypanosomes.


Author(s):  
Ang Liu ◽  
Qing-Jie Xue ◽  
Shi-Gen Li ◽  
Yan-Jiao Zhang

A bacterial strain designated RZ02T was isolated from surface seawater collected from the Yellow Sea in PR China and characterized by polyphasic taxonomy. Cells of strain RZ02T were Gram-stain-negative, aerobic, non-motile, catalase- and oxidase-positive rods forming ochre-pigmented colonies. Growth occurred at 7–36 °C (optimum, 30 °C), at pH 6.0–9.0 (optimum, pH 7.0) and with 1–5 % (optimum, 2 %) NaCl. The major cellular fatty acids (>10 %) of strain RZ02T were summed feature 8 (C18 : 1  ω6c and/or C18 : 1  ω7c), summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c) and C16 : 0. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol and sphingoglycolipid. The genome size of strain RZ02T was 2.79 Mbp with a G+C content of 55.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain RZ02T was mostly related to Pontixanthobacter luteolus SW-109T and Pontixanthobacter aestiaquae HDW-31T (97.3 and 97.1% sequence similarity, respectively), and formed a phyletic lineage with members of the genus Pontixanthobacter . The phylogenetic analysis based on the up-to-date bacterial core gene sequences confirmed that strain RZ02T clustered within the genus Pontixanthobacter . The average nucleotide identity and in silico DNA–DNA hybridization values between strain RZ02T and P. luteolus SW-109T and P. aestiaquae HDW-31T were 72.8 and 72.9 % and 18.7 and 18.5%, respectively. Based on these evidences, strain RZ02T is proposed to represent a novel species of the genus Pontixanthobacter under the name Pontixanthobacter rizhaonensis sp. nov. The type strain is RZ02T (=KCTC 62828T=MCCC 1K04521T). In addition, based on the results of whole genome analyses, proposals of Pseudopontixanthobacter gen. nov., Pseudopontixanthobacter confluentis comb. nov. and Pseudopontixanthobacter sediminis comb. nov. are also included.


Author(s):  
Shan Jiang ◽  
Feng-Bai Lian ◽  
You-Yang Sun ◽  
Xiao-Kui Zhang ◽  
Zong-Jun Du

A Gram-stain-negative, rod-shaped and facultatively aerobic bacterial strain, designated F7430T, was isolated from coastal sediment collected at Jingzi Wharf in Weihai, PR China. Cells of strain F7430T were 0.3–0.4 µm wide, 2.0–2.6 µm long, non-flagellated, non-motile and formed pale-beige colonies. Growth was observed at 4–40 °C (optimum, 30 °C), pH 6.0–9.0 (optimum, pH 7.5–8.0) and at NaCl concentrations of 1.0–10.0 % (w/v; optimum, 1.0 %). The sole respiratory quinone of strain F7430T was ubiquinone 8 and the predominant cellular fatty acids were summed feature 8 (C18 : 1  ω7c / C18 : 1  ω6c; 60.7 %), summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c; 30.2 %) and C15 : 0 iso (13.9 %). The polar lipids of strain F7430T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified phospholipid and three unidentified lipids. Results of 16S rRNA gene sequences analyses indicated that this strain belonged to the family Halieaceae and had high sequence similarities to Parahaliea aestuarii JCM 51547T (95.3 %) and Halioglobus pacificus DSM 27932T (95.2 %) followed by 92.9–95.0 % sequence similarities to other type species within the aforementioned family. The rpoB gene sequences analyses indicated that the novel strain had the highest sequence similarities to Parahaliea aestuarii JCM 51547T (82.2 %) and Parahaliea mediterranea DSM 21924T (82.2 %) followed by 75.2–80.5 % sequence similarities to other type species within this family. Phylogenetic analyses showed that strain F7430T constituted a monophyletic branch clearly separated from the other genera of family Halieaceae . Whole-genome sequencing of strain F7430T revealed a 3.3 Mbp genome size with a DNA G+C content of 52.6 mol%. The genome encoded diverse metabolic pathways including the Entner–Doudoroff pathway, assimilatory sulphate reduction and biosynthesis of dTDP-l-rhamnose. Based on results from the current polyphasic study, strain F7430T is proposed to represent a novel species of a new genus within the family Halieaceae , for which the name Sediminihaliea albiluteola gen. nov., sp. nov. is proposed. The type strain of the type species is F7430T (=KCTC 72873T=MCCC 1H00420T).


Author(s):  
Jingling Liang ◽  
Sai Wang ◽  
Ayizekeranmu Yiming ◽  
Luoyi Fu ◽  
Iftikhar Ahmad ◽  
...  

Strain L22-9T, a Gram-stain-negative and rod-shaped bacterium, motile by one polar flagellum, was isolated from cornfield soil in Bijie, Guizhou Province, PR China. Based on 16S rRNA gene sequences, it was identified as a Pseudomonas species. Multilocus sequence analysis of concatenated 16S rRNA, gyrB, rpoB and rpoD gene sequences showed that strain L22-9T formed a clearly separated branch, located in a cluster together with Pseudomonas brassicacearum LMG 21623T, Pseudomonas kilonensis DSM 13647T and Pseudomonas thivervalensis DSM 13194T. Whole-genome comparisons based on average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) confirmed that strain L22-9T should be classified as a novel species. It was most closely related to P. kilonensis DSM 13647T with ANI and dDDH values of 91.87 and 46.3 %, respectively. Phenotypic features that can distinguish strain L22-9T from P. kilonensis DSM 13647T are the assimilation ability of N-acetyl-d-glucosamine, poor activity of arginine dihydrolase and failure to ferment ribose and d-fucose. The predominant cellular fatty acids of strain L22-9T are C16 : 0, summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The respiratory quinones consist of Q-9 and Q-8. The polar lipids are diphosphatidylglycerol, phosphatidylethanolamine, two unidentified phosphoglycolipids, two unidentified aminophospholipids and an unidentified glycolipid. Based on the evidence, we conclude that strain L22-9T represents a novel species, for which the name Pseudomonas bijieensis sp. nov. is proposed. The type strain is L22-9T (=CGMCC 1.18528T=LMG 31948T), with a DNA G+C content of 60.85 mol%.


Author(s):  
Jun-Jie Ying ◽  
Zhi-Cheng Wu ◽  
Yuan-Chun Fang ◽  
Lin Xu ◽  
Cong Sun

Parvularcula flava was proposed as a novel member of genus Parvularcula in 2016. Some time earlier, Aquisalinus flavus has been proposed as a novel species of a novel genus named Aquisalinus . When comparing the 16S rRNA gene sequences of type strains P. flava NH6-79T and A. flavus D11M-2T, they showed 97.9 % sequence identity, much higher than the sequence identities 92.7–94.3 % between P. flava NH6-79T and type strains in the genus Parvularcula , indicating that the later proposed novel taxon Parvularcula flava need reclassification. The phylogenetic trees based on 16S rRNA gene sequences and genome sequences both showed that P. flava NH6-79T and A. flavus D11M-2T formed a separated branch away from strains in the genera Parvularcula , Marinicaulis and Amphiplicatus . The average amino acid identity and average nucleotide identity values of P. flava NH6-79T and A. flavus D11M-2T were 87.9 and 85.0 %, respectively, much higher than the values between P. flava NH6-79T and other closely related type strains (54.3 %–58.1 % and 68.6–70.4 %, respectively). P. flava NH6-79T and A. flavus D11M-2T also contained summed feature 8 (C18 : 1  ω6c and/or C18 : 1  ω7c) and C16 : 0 as major fatty acids, distinguishing them from other closely related taxa. Based on the results of the phylogenetic, comparative genomic and phenotypic analyses, Parvularcula flava should be reclassified as Aquisalinus luteolus nom. nov. and the description of genus Aquisalinus is emended.


Author(s):  
Magdalena Ksiezarek ◽  
Teresa Gonçalves Ribeiro ◽  
Joana Rocha ◽  
Filipa Grosso ◽  
Svetlana Ugarcina Perovic ◽  
...  

Two Gram-stain-positive strains, c9Ua_26_MT and c11Ua_112_MT, were isolated from voided urine samples from two healthy women. Comparative 16S rRNA gene sequences demonstrated that these novel strains were members of the genus Limosilactobacillus . Phylogenetic analysis based on pheS gene sequences and core genomes showed that each strain formed a separated branch and are closest to Limosilactobacillus vaginalis DSM 5837T. The average nucleotide identity (ANI) and Genome-to-Genome Distance Calculator (GGDC) values between c9Ua_26_MT and the closest relative DSM 5837T were 90.7 and 42.9 %, respectively. The ANI and GGDC values between c11Ua_112_MT and the closest relative DSM 5837T were 91.2 and 45.0 %, and those among the strains were 92.9% and 51,0 %, respectively. The major fatty acids were C12 : 0 (40.2 %), C16 : 0 (26.7 %) and C18 : 1 ω9c (17.7 %) for strain c9Ua_26_MT, and C18 : 1 ω9c (38.0 %), C16 : 0 (33.3 %) and C12 : 0 (17.6 %) for strain c11Ua_112_MT. The genomic DNA G+C content of strains c9Ua_26_MT and c11Ua_112_MT was 39.9 and 39.7 mol%, respectively. On the basis of the data presented here, strains c9Ua_26_MT and c11Ua_112_MT represent two novel species of the genus Limosilactobacillus , for which the names Limosilactobacillus urinaemulieris sp. nov. (c9Ua_26_MT=CECT 30144T=LMG 31899T) and Limosilactobacillus portuensis sp. nov. (c11Ua_112_MT=CECT 30145T=LMG 31898T) are proposed.


2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1537-1541 ◽  
Author(s):  
De-Chao Zhang ◽  
Rosa Margesin

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.


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