scholarly journals Vaginimicrobium propionicum gen. nov., sp. nov., a novel propionic acid bacterium derived from human vaginal discharge

2020 ◽  
Vol 70 (7) ◽  
pp. 4091-4097 ◽  
Author(s):  
Khoudia Diop ◽  
Frederic Cadoret ◽  
Thi Tien Nguyen ◽  
Jean-Pierre Baudoin ◽  
Nicholas Armstrong ◽  
...  

A Gram-stain-positive anaerobic rod-shaped bacterium, designated strain Marseille-P3275T, was isolated using culturomics from the vaginal discharge of healthy French woman. Marseille-P3275T was non-motile and did not form spores. Cells had neither catalase nor oxidase activity. The major fatty acids were C16 : 0 (29 %), C18:1ω9 (18 %), and iso-C15 : 0 (17 %). The genomic DNA G+C content was 50.64 mol%. The phylogenetic analysis based on 16S rRNA gene sequence indicated that Marseille-P3275T was related to members of the family Propionibacteriaceae (between 90.32–92.92 % sequence similarity) with formation of a clade with the monospecific genus Propionimicrobium (type species Propionimicrobium lymphophilum ). On the basis of these phylogenetic and phenotypic differences, Marseille-P3275T was classified in a novel genus, Vaginimicrobium, as Vaginimicrobium propionicum gen. nov., sp. nov. The type strain is Marseille-P3275T (=CSUR P3275T=CECT 9677T).

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 501-505 ◽  
Author(s):  
Jonathan Kennedy ◽  
Lekha Menon Margassery ◽  
Niall D. O’Leary ◽  
Fergal O’Gara ◽  
John Morrissey ◽  
...  

A Gram-stain-negative, rod-shaped, orange-coloured, catalase- and oxidase-positive, non-motile bacterium, designated strain 92VT, was isolated from the marine sponge Amphilectus fucorum, collected from Lough Hyne, County Cork, Ireland. 16S rRNA gene sequence analysis revealed that strain 92VT clustered with members of the family Flavobacteriaceae , the closest member being Aquimarina latercula NCIMB 1399T, with a gene sequence similarity of 97.5 %. Strain 92VT required seawater for growth with optimal growth occurring at 25 °C, at pH 6–7 and with 3 % (w/v) NaCl. MK-6 was the sole respiratory quinone present and the major fatty acids were iso-C17 : 0 3-OH, iso-C15 : 0, iso-C17 : 1ω9c and iso-C15 : 0 3-OH. The DNA G+C content was 36.1 mol%. Combined phenotypic differences and phylogenetic analysis indicate that strain 92VT represents a novel species of the genus Aquimarina , for which the name Aquimarina amphilecti sp. nov. is proposed. The type strain is 92VT ( = NCIMB 14723T = DSM 25232T).


Author(s):  
Regina Rettenmaier ◽  
Nils Thieme ◽  
Johanna Streubel ◽  
Luca Di Bello ◽  
Marie-Louise Kowollik ◽  
...  

Strain MD1T is an anaerobic, Gram-stain-negative bacterium isolated from a lab-scale biogas fermenter fed with maize silage. It has a rod-shaped morphology with peritrichously arranged appendages and forms long chains of cells and coccoid structures. The colonies of MD1T were white, circular, slightly convex and had a smooth rim. The isolate is mesophilic, displaying growth between 25 and 45 °C with an optimum at 40 °C. It grew at pH values of pH 6.7–8.2 (optimum, pH 7.1) and tolerated the addition of up to 1.5% (w/v) NaCl to the medium. The main cellular fatty acids of MD1T are C14:0 DMA and C16:0. Strain MD1T fermented xylose, arabinose, glucose, galactose, cellobiose, maltose, maltodextrin10, lactose starch, and xylan, producing mainly 2-propanol and acetic acid. The genome of the organism has a total length of 4163427 bp with a G+C content of 38.5 mol%. The two closest relatives to MD1T are Mobilitalea sibirica P3M-3T and Anaerotaenia torta FH052T with 96.44 or 95.8 % 16S rRNA gene sequence similarity and POCP values of 46.58 and 50.58%, respectively. As MD1T showed saccharolytic and xylanolytic properties, it may play an important role in the biogas fermentation process. Closely related variants of MD1T were also abundant in microbial communities involved in methanogenic fermentation. Based on morphological, phylogenetic and genomic data, the isolated strain can be considered as representing a novel genus in the family Lachnospiraceae , for which the name Variimorphobacter saccharofermentans gen. nov., sp. nov. (type strain MD1T=DSM 110715T=JCM 39125T) is proposed.


2014 ◽  
Vol 64 (Pt_4) ◽  
pp. 1351-1358 ◽  
Author(s):  
Sung-Hyun Yang ◽  
Hyun-Seok Seo ◽  
Jung-Hee Woo ◽  
Hyun-Myung Oh ◽  
Hani Jang ◽  
...  

Two facultatively anaerobic mesophilic bacteria, strains MEBiC 07026T and MEBiC 08903T, were isolated from two different tidal flat sediments and both strains showed approximately 92.2 % 16S rRNA gene sequence similarity with [Cytophaga] fermentans DSM 9555T. 16S rRNA gene sequence similarity between the two new isolates was 97.5 % but levels of DNA–DNA relatedness between the two were 31.3–31.8 %. Phylogenetic analysis revealed that the two isolates and [Cytophaga] fermentans DSM 9555T were affiliated with the family Marinilabiliaceae in the class Bacteroidia . The dominant fatty acids of strains MEBiC 07026T, MEBiC 08903T and [Cytophaga] fermentans DSM 9555T were branched-type or hydroxylated C15 : 0, but [Cytophaga] fermentans DSM 9555T contained a higher proportion of anteiso-branched fatty acids. The two new isolates contained a markedly higher proportion of monounsaturated fatty acids than other members of the family Marinilabiliaceae . The major respiratory quinone of the strains was MK-7. Strains MEBiC07026T and MEBiC08903T utilized a wide range of carboxylic acids whereas [Cytophaga] fermentans DSM 9555T utilized carbohydrates rather than carboxylic acids. The DNA G+C content of the novel strains was about 44 mol% but that of [Cytophaga] fermentans DSM 9555T revealed from the genome sequence was 37.6 mol%. Based on evidence from this polyphasic taxonomic study, a novel genus, Carboxylicivirga gen. nov., is proposed in the family Marinilabiliaceae with two novel species, Carboxylicivirga mesophila sp. nov. with type strain MEBiC 07026T ( = KCCM 42978T = JCM 18290T) and Carboxylicivirga taeanensis sp. nov. with type strain MEBiC 08903T ( = KCCM 43024T = JCM 19490T). Additionally, [Cytophaga] fermentans DSM 9555T ( = ATCC 19072T) is reclassified as Saccharicrinis fermentans gen. nov., comb. nov.


2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 2835-2843 ◽  
Author(s):  
Hong Chen ◽  
Mareike Jogler ◽  
Manfred Rohde ◽  
Hans-Peter Klenk ◽  
Hans-Jürgen Busse ◽  
...  

‘ Caulobacter leidyi ’ DSM 4733T has been shown to be affiliated with the family Sphingomonadaceae instead of the Caulobacteraceae , and due to its poor characterization has been omitted from the current edition of Bergey’s Manual of Systematic Bacteriology and removed to limbo. We isolated a novel sphingoglycolipid-containing dimorphic prosthecate bacterium, designated strain 247, from a pre-alpine freshwater lake. Strain 247 and ‘ Caulobacter leidyi ’ DSM 4733T were characterized in detail. The rod-shaped cells were Gram-stain-negative, aerobic, catalase- and oxidase-positive, and formed a stalk or polar flagellum. Both strains grew optimally at 28–30 °C, and pH 6.0–8.0. The major fatty acids were C18 : 1ω7c, C16 : 0 and 11-methyl C18 : 1ω7c. C14 : 0 2-OH represents the major 2-hydroxy fatty acid. Q-10 was the major respiratory quinone and the major polar lipids were diphosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylcholine, three glycolipids, two phosphoaminolipids and two unidentified sphingoglycolipids. The major polyamine was sym-homospermidine. The G+C content of genomic DNA of strains 247 and DSM 4733T was 67.6 mol% and 67.0 mol%, respectively. According to 16S rRNA gene sequence analysis and DNA–DNA hybridization, strains DSM 4733T and 247 were phylogenetically closely related (99.6 % 16S rRNA gene sequence similarity, 82.9 % DNA–DNA hybridization value) and affiliated to the genus Sphingomonas . The closest recognized species was Sphingomonas aquatilis DSM 15581T (98.1 % sequence similarity). In addition, the presence of cystine arylamidase, absence of β-galactosidase, and the inability to utilize l-arabinose, galactose and sucrose distinguished strains DSM 4733T and 247 from most other members of the family Sphingomonadaceae . So far, the dimorphic life cycle that involves a prosthecate and a flagellated stage is unique for strains DSM 4733T and 247 among all members of the family Sphingomonadaceae . Therefore, Caulobacter leidyi is reclassified as Sphingomonas leidyi, with the type strain DSM 4733T ( = ATCC 15260T = CIP 106443T = VKM B-1368T) and strain 247 (DSM 25078 = LMG 26658) as an additional strain of this species.


2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3807-3811 ◽  
Author(s):  
Heung-Min Son ◽  
Jung-Eun Yang ◽  
Eun-Ji Yi ◽  
YongJin Park ◽  
Kyung-Hwa Won ◽  
...  

A Gram-reaction-negative, aerobic, motile by one polar flagellum, yellow-pigmented, rod-shaped bacterium, designated strain THG-B117T, was isolated from soil of a cornus fruit field of Hoengseong province in South Korea and its taxonomic position was investigated by a polyphasic study. Strain THG-B117T grew well at 25–30 °C and at pH 6.0–8.0 in the absence of NaCl on nutrient agar. On the basis of 16S rRNA gene sequence similarity, strain THG-B117T was shown to belong to the family Xanthomonadaceae and be related to Dyella japonica XD53T (98.7 % similarity), Dyella terrae JS14-6T (98.0 %), Dyella koreensis BB4T (96.9 %), Dyella soli JS12-10T (96.9 %) and Dyella thiooxydans ATSB10T (96.7 %). DNA–DNA hybridization experiments showed that DNA relatedness between strain THG-B117T and its phylogenetically closest neighbours was below 45.1 %. The G+C content of the genomic DNA of strain THG-B117T was 64.8 mol%. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, unidentified aminolipids, unidentified aminophospholipids and unidentified phospholipids. Phenotypic and chemotaxonomic data (major ubiquinone was Q-8, and major fatty acids were iso-C15 : 0, iso-C16 : 0, iso-C17 : 0 and iso-C17 : 1ω9c) supported the affiliation of strain THG-B117T with the genus Dyella . The results of physiological and biochemical tests suggested that strain THG-B117T was different genotypically and phenotypically from recognized species of the genus Dyella , and represents a novel species of this genus. The name Dyella kyungheensis sp. nov. is proposed, with the type strain THG-B117T ( = KACC 16981T = JCM 18747T).


2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 663-667 ◽  
Author(s):  
Jangho Lee ◽  
Banghyo Park ◽  
Sung-Geun Woo ◽  
Juyoun Lee ◽  
Joonhong Park

A Gram-stain-negative, fusiform-shaped, facultatively anaerobic bacterial strain, designated EBTL04T, was isolated from activated sludge using algal metabolites and taxonomically characterized through polyphasic investigation. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain EBTL04T belongs to the family Verrucomicrobiaceae , class Verrucomicrobiae , and is closely related to Prosthecobacter dejongeii DSM 12251T (98.6 % sequence similarity), Prosthecobacter fusiformis ATCC 25309T (97.9 %), Prosthecobacter debontii DSM 14044T (97.5 %), Prosthecobacter vanneervenii DSM 12252T (94.7 %) and Prosthecobacter fluviatilis KCTC 22182T (93.7 %). The G+C content of the genomic DNA of strain EBTL04T was 62.7 mol%. The menaquinone MK-6 was detected as the predominant quinone. Strain EBTL04T contained phosphatidylethanolamine, phosphatidylglycerol and phosphatidylserine as major polar lipids. A fatty acid profile with C16 : 1ω5c, iso-C14 : 0, C16 : 0, anteiso-C15 : 0 and C14 : 0 as the major components supported the classification of strain EBTL04T in the genus Prosthecobacter . Based on several phenotypic, genotypic and chemotaxonomic features, strain EBTL04T was clearly differentiated from its phylogenetic neighbours. Therefore, strain EBTL04T should be considered to represent a novel species of the genus Prosthecobacter , for which the name Prosthecobacter algae sp. nov. is proposed. The type strain is EBTL04T ( = KCTC 23681T = JCM 18053T).


2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1300-1306 ◽  
Author(s):  
Lorena Carro ◽  
Raúl Rivas ◽  
Milagros León-Barrios ◽  
María González-Tirante ◽  
Encarna Velázquez ◽  
...  

Three Gram-negative, motile and slightly curved rod-shaped bacteria, strains SUEMI03T, SUEMI08T and SUEMI10T, were isolated from an old volcanic mountain soil on Tenerife (Canary Islands). The three strains were related phylogenetically to Herbaspirillum seropedicae . 16S rRNA gene sequence similarity was 99.2–99.6 % among strains SUEMI03T, SUEMI08T and SUEMI10T, which presented 97.5, 97.8 and 97.7 % identity, respectively, with respect to H. seropedicae DSM 6445T. The three strains grew optimally in TSB at 28 °C and contained summed features 3 (C16 : 1ω6c and/or C16 : 1ω7c) and 8 (C18 : 1ω6c and/or C18 : 1ω7c) and C16 : 0 as major cellular fatty acids. The DNA G+C contents of strains SUEMI03T, SUEMI08T and SUEMI10T were 61.6, 60.4 and 61.9 mol%, respectively. Strains SUEMI03T, SUEMI08T and SUEMI10T presented less than 60 % interstrain DNA relatedness and less than 30 % relatedness with respect to H. seropedicae DSM 6445T. In spite of their common geographical origin, the three strains isolated in this study presented several phenotypic differences, presenting phenotypic profiles highly divergent from that of H. seropedicae . Therefore, we propose that the strains isolated in this study represent three novel species of the genus Herbaspirillum , named Herbaspirillum canariense sp. nov. (type strain SUEMI03T  = LMG 26151T  = CECT 7838T), Herbaspirillum aurantiacum sp. nov. (type strain SUEMI08T  = LMG 26150T  = CECT 7839T) and Herbaspirillum soli sp. nov. (type strain SUEMI10T  = LMG 26149T  = CECT 7840T).


2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 469-474 ◽  
Author(s):  
Ying Liu ◽  
Liang-Zi Liu ◽  
Hong-Can Liu ◽  
Yu-Guang Zhou ◽  
Fang-Jun Qi ◽  
...  

A Gram-stain-negative, strictly aerobic and heterotrophic bacterial strain, designed strain D1T, was isolated from a recirculating mariculture system in Tianjin, China. Its taxonomic position was determined using a polyphasic approach. Cells of strain D1T were non-flagellated short rods, 0.3–0.5 µm wide and 0.5–1.0 µm long. Growth was observed at 15–30 °C (optimum, 25 °C), at pH 5.5–9.0 (optimum, pH 6.5–7.0) and in the presence of 1–8 % (w/v) NaCl (optimum, 2–3 %). Cells contained carotenoid pigments but not flexirubin-type pigments. Strain D1T contained MK-6 as the sole menaquinone and phosphatidylethanolamine (PE) as the sole phospholipid and four unidentified lipids. The major cellular fatty acids (>10 %) were iso-C15 : 0 (23.2 %), iso-C17 : 0 3-OH (15.2 %), C16 : 1ω7c/C16 : 1ω6c (14.3 %), iso-C15 : 0 3-OH (13.5 %) and iso-C15 : 1 G (10.8 %). 16S rRNA gene sequence analyses indicated that strain D1T belonged to the family Flavobacteriaceae and showed closest phylogenetic relationship to the genus Lutibacter , with highest sequence similarity to Lutibacter aestuarii MA-My1T (92.2 %). The DNA G+C content of strain D1T was 35.9 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain D1T was considered to represent a novel species in a new genus of the family Flavobacteriaceae , for which the name Wenyingzhuangia marina gen. nov., sp. nov. is proposed. The type strain of the type species is D1T ( = CGMCC 1.12162T = JCM 18494T).


2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3877-3884 ◽  
Author(s):  
Celine De Maesschalck ◽  
Filip Van Immerseel ◽  
Venessa Eeckhaut ◽  
Siegrid De Baere ◽  
Margo Cnockaert ◽  
...  

Strains LMG 27428T and LMG 27427 were isolated from the caecal content of a chicken and produced butyric, lactic and formic acids as major metabolic end products. The genomic DNA G+C contents of strains LMG 27428T and LMG 27427 were 40.4 and 38.8 mol%. On the basis of 16S rRNA gene sequence similarity, both strains were most closely related to the generically misclassified Streptococcus pleomorphus ATCC 29734T. Strain LMG 27428T could be distinguished from S. pleomorphus ATCC 29734T based on production of more lactic acid and less formic acid in M2GSC medium, a higher DNA G+C content and the absence of activities of acid phosphatase and leucine, arginine, leucyl glycine, pyroglutamic acid, glycine and histidine arylamidases, while strain LMG 27428 was biochemically indistinguishable from S. pleomorphus ATCC 29734T. The novel genus Faecalicoccus gen. nov. within the family Erysipelotrichaceae is proposed to accommodate strains LMG 27428T and LMG 27427. Strain LMG 27428T ( = DSM 26963T) is the type strain of Faecalicoccus acidiformans sp. nov., and strain LMG 27427 ( = DSM 26962) is a strain of Faecalicoccus pleomorphus comb. nov. (type strain LMG 17756T = ATCC 29734T = DSM 20574T). Furthermore, the nearest phylogenetic neighbours of the genus Faecalicoccus are the generically misclassified Eubacterium cylindroides DSM 3983T (94.4 % 16S rRNA gene sequence similarity to strain LMG 27428T) and Eubacterium biforme DSM 3989T (92.7 % 16S rRNA gene sequence similarity to strain LMG 27428T). We present genotypic and phenotypic data that allow the differentiation of each of these taxa and propose to reclassify these generically misnamed species of the genus Eubacterium formally as Faecalitalea cylindroides gen. nov., comb. nov. and Holdemanella biformis gen. nov., comb. nov., respectively. The type strain of Faecalitalea cylindroides is DSM 3983T = ATCC 27803T = JCM 10261T and that of Holdemanella biformis is DSM 3989T = ATCC 27806T = CCUG 28091T.


2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1149-1154 ◽  
Author(s):  
Varsha Kale ◽  
Snædís H. Björnsdóttir ◽  
Ólafur H. Friðjónsson ◽  
Sólveig K. Pétursdóttir ◽  
Sesselja Ómarsdóttir ◽  
...  

A thermophilic, aerobic, Gram-stain-negative, filamentous bacterium, strain PRI-4131T, was isolated from an intertidal hot spring in Isafjardardjup, NW Iceland. The strain grew chemo-organotrophically on various carbohydrates. The temperature range for growth was 40–65 °C (optimum 55 °C), the pH range was pH 6.5–9.0 (optimum pH 7.0) and the NaCl range was 0–3 % (w/v) (optimum 0.5 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain PRI-4131T represented a distinct lineage within the class Caldilineae of the phylum Chloroflexi. The highest levels of sequence similarity, about 91 %, were with Caldilinea aerophila STL-6-O1T and Caldilinea tarbellica D1-25-10-4T. Fermentative growth was not observed for strain PRI-4131T, which, in addition to other characteristics, distinguished it from the two Caldilinea species. Owing to both phylogenetic and phenotypic differences from the described members of the class Caldilineae , we propose to accommodate strain PRI-4131T in a novel species in a new genus, Litorilinea aerophila gen. nov., sp. nov. The type strain of Litorilinea aerophila is PRI-4131T ( = DSM 25763T  = ATCC BAA-2444T).


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