scholarly journals Five novel bifidobacterial species isolated from faeces of primates in two Czech zoos: Bifidobacterium erythrocebi sp. nov., Bifidobacterium moraviense sp. nov., Bifidobacterium oedipodis sp. nov., Bifidobacterium olomucense sp. nov. and Bifidobacterium panos sp. nov.

Author(s):  
Vera Neuzil-Bunesova ◽  
Gabriele Andrea Lugli ◽  
Nikol Modrackova ◽  
Eva Vlkova ◽  
Petra Bolechova ◽  
...  

Five Bifidobacterium strains, VB23T, VB24T, VB25T, VB26T and VB31T, were isolated from chimpanzee (Pan troglodytes), cotton-top tamarin (Saguinus oedipus), Goeldi’s marmoset (Callimico goeldii), moustached tamarin (Saguinus mystax) and patas monkey (Erythrocebus patas), respectively, which were kept in two Czech zoos. These strains were isolated from faecal samples and were Gram-positive, non-motile, non-sporulating, anaerobic and fructose-6-phosphate phosphoketolase-positive. Phylogenetic analyses based on 16S rRNA revealed close relatedness between VB23T and Bifidobacterium angulatum LMG 11039T (96.0 %), VB24T and Bifidobacterium pullorum subsp. pullorum DSM 20433T (96.1 %), VB25T and Bifidobacterium goeldii LMG 30939T (96.5 %), VB26T and Bifidobacterium imperatoris LMG 30297T (98.1 %), and VB31T and B . angulatum LMG 11039T (99.40 %). Internal transcribed spacer profiling revealed that VB23T, VB24T, VB25T, VB26T and VB31T had highest similarity to Bifidobacterium breve LMG 13208T (77.2 %), Bifidobacterium longum subsp. infantis ATCC 15697T (85.8 %), Bifidobacterium biavatii DSM 23969T (76.9 %), B. breve LMG 13208T (81.2 %) and B. angulatum LMG 11039T (88.2 %), respectively. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) analyses with their closest neighbours supported the independent phylogenetic positions of the strains with values between 86.3 and 94.3 % for ANI and 25.8 and 54.9 % for dDDH. These genomic and phylogenetic analyses suggested that the evaluated strains were novel Bifidobacterium species named Bifidobacterium erythrocebi sp. nov. (VB31T=DSM 109960T=CCUG 73843T), Bifidobacterium moraviense sp. nov. (VB25T=DSM 109958T=CCUG 73842T), Bifidobacterium oedipodis sp. nov. (VB24T=DSM 109957T=CCUG 73932T), Bifidobacterium olomucense sp. nov. (VB26T=DSM 109959T=CCUG 73845T) and Bifidobacterium panos sp. nov. (VB23T=DSM 109963T=CCUG 73840T).

2020 ◽  
Vol 70 (4) ◽  
pp. 2288-2297 ◽  
Author(s):  
Sabrina Duranti ◽  
Gabriele Andrea Lugli ◽  
Alice Viappiani ◽  
Leonardo Mancabelli ◽  
Giulia Alessandri ◽  
...  

Two Bifidobacterium strains, i.e., 2176BT and 2177BT, were isolated from Golden-Headed Lion Tamarin (Leontopithecus chrysomelas) and Goeldi's monkey (Callimico goeldii). Isolates were shown to be Gram-positive, non-motile, non-sporulating, facultative anaerobic and d-fructose 6-phosphate phosphoketolase-positive. Phylogenetic analyses based on 16S rRNA sequences, multilocus sequences (including hsp60, rpoB, dnaJ, dnaG and clpC genes) and the core genome revealed that bifidobacterial strains 2176BT and 2177BT exhibit close phylogenetic relatedness to Bifidobacterium felsineum DSM 103139T and Bifidobacterium bifidum LMG 11041T, respectively. Further genotyping based on the genome sequence of the isolated strains combined with phenotypic analyses, clearly show that these strains are distinct from each of the type strains of the so far recognized Bifidobacterium species. Thus, Bifidobacterium cebidarum sp. nov. (2176BT=LMG 31469T=CCUG 73785T) and Bifidobacterium leontopitheci sp. nov. (2177BT=LMG 31471T=CCUG 73786T are proposed as novel Bifidobacterium species.


Author(s):  
Yanpeng Cheng ◽  
Wenjing Lei ◽  
Xiaoxia Wang ◽  
Zhi Tian ◽  
Haican Liu ◽  
...  

Four bacterial strains (LJ126T/S18 and Z-34T/S20) recovered from faecal samples of Tibetan antelopes on the Qinghai–Tibet Plateau of China were analysed using a polyphasic approach. All four isolates were aerobic, short rod-shaped, non-motile, Gram-stain-positive, acid-fast and fast-growing. Phylogenetic analyses based upon 16S rRNA and whole-genome sequences showed that the two pair of strains formed two distinct branches within the evolutionary radiation of the genus Mycolicibacterium . Strains LJ126T/S18 and Z-34T/S20 were most closely related to Mycolicibacterium austroafricanum CCUG 37667T, Mycobacterium aurum NCTC 10437T, Mycobacterium pyrenivorans DSM 44605T, Mycobacterium monacense JCM 15658T, Mycolicibacterium sarraceniae JCM 30395T, Mycolicibacterium tokaiense JCM 6373T and Mycobacterium murale JCM 13392T, but readily distinguished from the known species by a combination of chemotaxonomic and phenotypic features and by low average nucleotide identity values (74.4–84.9 %). Consequently, the two strain pairs are considered to represent different novel species of Mycolicibacterium for which the names Mycolicibacterium baixiangningiae sp. nov. and Mycolicibacterium mengxianglii sp. nov. are proposed, with LJ126T (=CGMCC 1.1992T=KCTC 49535T) and Z-34T (=CGMCC 1.1993T=DSM 106172T) as the respective type strains.


2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 516-521 ◽  
Author(s):  
Gaiyun Zhang ◽  
Yubian Zhang ◽  
Xijie Yin ◽  
Shuang Wang

A Gram-staining-positive, aerobic, motile and non-spore-forming actinobacteria, designated strain F10T, was isolated from a deep-sea sediment of the western Pacific Ocean. Phylogenetic and phenotypic properties of the organism supported that it belonged to the genus Nesterenkonia . Strain F10T shared highest 16S rRNA gene sequence similarity of 96.8 % with Nesterenkonia aethiopica DSM 17733T, followed by Nesterenkonia xinjiangensis YIM 70097T (96.7 %) and Nesterenkonia alba CAAS 252T (96.6 %). The organism grew at 4–50 °C, at pH 7.0–12.0 and in the presence of 0–12 % (w/v) NaCl, with optimal growth occurring at 40 °C, at pH 9.0 and in the presence of 1 % (w/v) NaCl. The peptidoglycan type was A4(alpha), l-Lys–Gly–l-Glu. The polar lipid profile of strain F10T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two unknown glycolipids and two unknown lipids. The isolate contained MK-9 (92 %) and MK-8 (5.8 %) as the major components of the menaquinone system, and anteiso-C17 : 0 (50.9 %) and anteiso-C15 : 0 (29.8 %) as the predominant fatty acids. The G+C content of the genomic DNA of strain F10T was 66.2 mol%. Based on phenotypic, genotypic and phylogenetic analyses, strain F10T represents a novel species of the genus Nesterenkonia for which the name Nesterenkonia alkaliphila sp. nov. is proposed. The type strain is F10T ( = LMG 28112T = CGMCC 1.12781T = JCM 19766T = MCCC 1A09946T).


2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 934-938 ◽  
Author(s):  
Wen-Ming Chen ◽  
Rey-Chang Chang ◽  
Chih-Yu Cheng ◽  
Yu-Wen Shiau ◽  
Shih-Yi Sheu

A novel bacterium, designated strain JchiT, was isolated from soil in Taiwan and characterized using a polyphasic approach. Cells of strain JchiT were aerobic, Gram-stain-negative, motile and rod-shaped. They contained poly-β-hydroxybutyrate granules and formed dark-yellow colonies. Growth occurred at 20–37 °C (optimum between 25 and 30 °C), at pH 6.0–8.0 (optimum between pH 7.0 and pH 8.0) and with 0–2 % NaCl (optimum between 0 and 1 %). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain JchiT belonged to the genus Jeongeupia and that its closest neighbour was Jeongeupia naejangsanensis BIO-TAS4-2T (98.0 % sequence similarity). The major fatty acids (>10 %) of strain JchiT were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c. The major cellular hydroxy fatty acid was C12 : 0 3-OH. The isoprenoid quinone was Q-8 and the genomic DNA G+C content was 66.1 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylserine and two unidentified phospholipids. The DNA–DNA relatedness value between strain JchiT and J. naejangsanensis BIO-TAS4-2T was about 41.0 %. On the basis of the genotypic and phenotypic data, strain JchiT represents a novel species in the genus Jeongeupia , for which the name Jeongeupia chitinilytica sp. nov. is proposed. The type strain is JchiT ( = BCRC 80367T  = KCTC 23701T).


Author(s):  
Fenfa Li ◽  
Qingyi Xie ◽  
Shuangqing Zhou ◽  
Fandong Kong ◽  
Yun Xu ◽  
...  

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).


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):  
Silvio Hering ◽  
Moritz K. Jansson ◽  
Michael E. J. Buhl

A novel species within the genus Eikenella is described, based on the phenotypical, biochemical and genetic characterization of a strain of a facultatively anaerobic, Gram-negative rod-shaped bacterium. Strain S3360T was isolated from the throat swab of a patient sampled during routine care at a hospital. Phylogenetic analyses (full-length 16S rRNA gene and whole-genome sequences) placed the strain in the genus Eikenella , separate from all recognized species but with the closest relationship to Eikenella longinqua (NML 02-A-017T). Eikenella is one of the genera in the HACEK group known to be responsible for rare cases of endocarditis in humans. Until the recent descriptions of Eikenella exigua , Eikenella halliae and Eikenella longinqua , Eikenella corrodens had been the only validly published species in this genus since its description as Bacteroides corrodens in 1958. Unlike these species, strain S3360T is able to metabolize carbohydrates (glucose). The average nucleotide identities of strain S3360T with E. longinqua (NML 02-A-017T) and E. corrodens (NCTC 10596T), the type species of the genus, were 90.5 and 84.7 %, respectively, and the corresponding genome-to-genome distance values were 41.3 and 29.0 %, respectively. The DNA G+C content of strain S3360T was 58.4 mol%. Based on the phenotypical, biochemical and genetic findings, strain S3360T is considered to represent a novel species within the genus Eikenella , for which the name Eikenella glucosivorans sp. nov. is proposed. The type strain is S3360T (DSM 110714T=CCOS 1935T=CCUG 74293T). In addition, an emendation of the genus Eikenella is proposed to include species which are saccharolytic.


Author(s):  
Caixin Yang ◽  
Yibo Bai ◽  
Kui Dong ◽  
Jing Yang ◽  
Xin-He Lai ◽  
...  

Four Gram-stain-positive, catalase-negative, non-spore-forming, rod-shaped bacterial strains (zg-325T, zg329, dk561T and dk752) were isolated from the respiratory tract of marmot (Marmota himalayana) and the faeces of Tibetan gazelle (Procapra picticaudata) from the Qinghai-Tibet Plateau of PR China. The results of 16S rRNA gene sequence-based phylogenetic analyses indicated that strains zg-325T and dk561T represent members of the genus Actinomyces , most similar to Actinomyces denticolens DSM 20671T and Actinomyces ruminicola B71T, respectively. The DNA G+C contents of strains zg-325T and dk561T were 71.6 and 69.3 mol%, respectively. The digital DNA–DNA hybridization values of strains zg-325T and dk561T with their most closely related species were below the 70 % threshold for species demarcation. The four strains grew best at 35 °C in air containing 5 % CO2 on brain heart infusion (BHI) agar with 5 % sheep blood. All four strains had C18:1ω9c and C16:0 as the major cellular fatty acids. MK-8 and MK-9 were the major menaquinones in zg-325T while MK-10 was predominant in dk561T. The major polar lipids included diphosphatidylglycerol and phosphatidylinositol. On the basis of several lines of evidence from phenotypic and phylogenetic analyses, zg-325T and dk561T represent novel species of the genus Actinomyces , for which the name Actinomyces marmotae sp. nov. and Actinomyces procaprae sp. nov. are proposed. The type strains are zg-325T (=GDMCC 1.1724T=JCM 34091T) and dk561T (=CGMCC 4.7566T=JCM 33484T). We also propose, on the basis of the phylogenetic results herein, the reclassification of Actinomyces liubingyangii and Actinomyces tangfeifanii as Boudabousia liubingyangii comb. nov. and Boudabousia tangfeifanii comb. nov., respectively.


Author(s):  
So-Ra Ko ◽  
Ve Van Le ◽  
Long Jin ◽  
Sang-Ah Lee ◽  
Chi-Yong Ahn ◽  
...  

A novel Gram-stain-negative, rod-shaped, aerobic, non-motile bacterial strain, designated M5A1MT, was isolated from seawater collected from the South Sea of the Republic of Korea. Based on 16S rRNA gene sequence similarity, strain M5A1MT was closely related to Mariniflexile gromovii KMM 6038T (95.3 %), Mariniflexile fucanivorans SW5T (95.2 %), Mariniflexile soesokkakense RSSK-9T (95.1 %), Yeosuana aromativorans GW1-1T (94.6 %) and Confluentibacter lentus HJM-3T (94.6 %). Genome-based phylogenetic analyses revealed that strain M5A1MT formed a distinct cluster with the type strains of the genus Mariniflexile . The major cellular fatty acid constituents (>5 % of the total fatty acids) were iso-C15:0, anteiso-C15 : 0, iso-C15 : 0 3-OH, iso-C15 : 1 G, iso-C16:03-OH and iso-C17 : 0 3-OH. The respiratory quinone was identified as MK-6. The major polar lipids were phosphatidylethanolamine and one unidentified polar lipid. The genomic DNA G+C content of strain M5A1MT was determined to be 37.7 mol%. On the basis of its phenotypic, phylogenetic and chemotaxonomic characteristics, strain M5A1MT is considered to represent a novel species within the genus Mariniflexile , for which the name Mariniflexile maritimum sp. nov. is proposed. The type strain is M5A1MT (=KCTC 72895T=JCM 33982T).


Author(s):  
Xiunuan Chen ◽  
Bingxia Dong ◽  
Ting Chen ◽  
Na Ren ◽  
Jing Wang ◽  
...  

Aniline blue-decolourizing bacterial strain 502str22T, isolated from sediment collected in the East Pacific, was subjected to characterization by a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain 502str22T belongs to the genus Novosphingobium , with closely related type strains ‘ Novosphingobium profundi ’ F72T (97.6%), N. mathurense SM117T (97.1%) and N. arvoryzae Jyi-02T (97.0%). Digital DNA–DNA hybridization and average nucleotide identity values between strain 502str22T and closely related type strains were 20.3–24.8% and 74.1–81.9%, respectively. The major cellular fatty acid (>10%) was C18:1 ω7c. The polar lipid profile consisted of a mixture of phosphatidylcholine, one sphingoglycolipid, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylmonomethylethanolamine. The DNA G+C content of strain 502str22T was 65.5 mol%. The polyphasic taxonomic results indicated that strain 502str22T represents a novel species of the genus Novosphingobium , for which the name Novosphingobium decolorationis sp. nov is proposed. The type strain is 502str22T (=KCTC 82134T= MCCC 1K04799 T).


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