scholarly journals Mycobacterium europaeum sp. nov., a scotochromogenic species related to the Mycobacterium simiae complex

2011 ◽  
Vol 61 (7) ◽  
pp. 1606-1611 ◽  
Author(s):  
Enrico Tortoli ◽  
Erik C. Böttger ◽  
Anna Fabio ◽  
Enevold Falsen ◽  
Zoe Gitti ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Polyphasic Analysis ◽  
Mycobacterium Simiae

Four strains isolated in the last 15 years were revealed to be identical in their 16S rRNA gene sequences to MCRO19, the sequence of which was deposited in GenBank in 1995. In a polyphasic analysis including phenotypic and genotypic features, the five strains (including MCRO19), which had been isolated in four European countries, turned out to represent a unique taxonomic entity. They are scotochromogenic slow growers and are genetically related to the group that included Mycobacterium simiae and 15 other species. The novel species Mycobacterium europaeum sp. nov. is proposed to accommodate these five strains. Strain FI-95228T ( = DSM 45397T  = CCUG 58464T) was chosen as the type strain. In addition, a thorough revision of the phenotypic and genotypic characters of the species related to M. simiae was conducted which leads us to suggest the denomination of the ‘Mycobacterium simiae complex’ for this group.

scholarly journals Escherichia marmotae sp. nov., isolated from faeces of Marmota himalayana

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2130-2134 ◽  
Author(s):  
Sha Liu ◽  
Dong Jin ◽  
Ruiting Lan ◽  
Yiting Wang ◽  
Qiong Meng ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Group Of Seven ◽  
Faecal Samples ◽  
Type Strains

The taxonomic position of a group of seven closely related lactose-negative enterobacterial strains, which were isolated from fresh faecal samples of Marmota himalayana collected from the Qinghai-Tibetan plateau, China, was determined by using a polyphasic approach. Cells were Gram-reaction-negative, non-sporulating, non-motile, short rods (0.5–1 × 1–2.5 μm). By 16S rRNA gene sequences, the representative strain, HT073016T, showed highest similarity values with Escherichia fergusonii ATCC 35469T at 99.3 %, Escherichia coli ATCC 11775T at 99.2 %, Escherichia albertii LMG 20976T at 98.9 %, Escherichia hermannii CIP 103176T at 98.4 %, and Escherichia vulneris ATCC 33821T at 97.7 %. Phylogenetic analysis based on the 16S rRNA gene sequences showed that the seven strains formed a monophyletic group with five other species of the genus Escherichia. Digital DNA–DNA hybridization studies between strain HT073016T and five other species of the genus Escherichia showed that it shared less than 70 % DNA–DNA relatedness with all known species of the genus Escherichia, supporting the novel species status of the strain. The DNA G+C content of strain HT073016T was 53.8 mol%. On the basis of phenotypic and phylogenetic characteristics, strain HT073016T and the six other HT073016T-like strains were clearly distinct from the type strains of other recognized species of the genus Escherichia and represent a novel species of the genus Escherichia, for which the name Escherichia marmotae sp. nov. is proposed, with HT073016T ( = CGMCC 1.12862T = DSM 28771T) as the type strain.

scholarly journals Streptococcus pharyngis sp. nov., a novel streptococcal species isolated from the respiratory tract of wild rabbits

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 2903-2907 ◽  
Author(s):  
Ana I. Vela ◽  
Encarna Casas-Díaz ◽  
Santiago Lavín ◽  
Lucas Domínguez ◽  
Jose F. Fernández-Garayzábal
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Molecular Genetic ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequences

Four isolates of an unknown Gram-stain-positive, catalase-negative coccus-shaped organism, isolated from the pharynx of four wild rabbits, were characterized by phenotypic and molecular genetic methods. The micro-organisms were tentatively assigned to the genus Streptococcus based on cellular morphological and biochemical criteria, although the organisms did not appear to correspond to any species with a validly published name. Comparative 16S rRNA gene sequencing confirmed their identification as members of the genus Streptococcus, being most closely related phylogenetically to Streptococcus porcorum 682-03T (96.9  % 16S rRNA gene sequence similarity). Analysis of rpoB and sodA gene sequences showed divergence values between the novel species and S. porcorum 682-03T (the closest phylogenetic relative determined from 16S rRNA gene sequences) of 18.1 and 23.9  %, respectively. The novel bacterial isolate could be distinguished from the type strain of S. porcorum by several biochemical characteristics, such as the production of glycyl-tryptophan arylamidase and α-chymotrypsin, and the non-acidification of different sugars. Based on both phenotypic and phylogenetic findings, it is proposed that the unknown bacterium be assigned to a novel species of the genus Streptococcus, and named Streptococcus pharyngis sp. nov. The type strain is DICM10-00796BT ( = CECT 8754T = CCUG 66496T).

scholarly journals Megasphaera paucivorans sp. nov., Megasphaera sueciensis sp. nov. and Pectinatus haikarae sp. nov., isolated from brewery samples, and emended description of the genus Pectinatus

2006 ◽  
Vol 56 (4) ◽  
pp. 695-702 ◽  
Author(s):  
Riikka Juvonen ◽  
Maija-Liisa Suihko
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Temperature Tolerance ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
The Novel ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Gene Similarity

Seven unidentified strictly anaerobic, Gram-negative, non-spore-forming bacteria from spoiled beer or the brewery environment were characterized. Based on 16S rRNA gene sequence analyses, all strains were affiliated to the Sporomusa sub-branch of the class ‘Clostridia’. Three of the strains were non-motile cocci, on average 1·5×1·2 μm or 1·2×1·0 μm, occurring mainly singly or in pairs. They shared nearly identical (>99 %) 16S rRNA gene sequences, being most closely related to the species of the Megasphaera–Anaeroglobus group (⩽93·9 % similarity). According to DNA–DNA hybridization results, the coccoid strains represented two genospecies, neither of which was related to any of the recognized Megasphaera species. Several phenotypic characteristics and/or DNA G+C content also differentiated the strains from each other and from their closest relatives. The other four novel strains were motile, slightly curved to helical rods, 0·6−0·8×3−50 μm or more in size. They shared identical 16S rRNA gene sequences and ribofragment patterns. The highest 16S rRNA gene similarity was found between these isolates and Pectinatus cerevisiiphilus ATCC 29359T (95·6 %) and Pectinatus frisingensis ATCC 33332T (93·6 %). The novel strains also differed from recognized Pectinatus species in their sugar utilization, proteolytic activity, catalase activity, antibiotic resistance and temperature tolerance. The results suggest that the bacteria belong to three novel species, for which the names Megasphaera paucivorans sp. nov. (type strain VTT E-032341T=DSM 16981T), Megasphaera sueciensis sp. nov. (type strain VTT E-97791T=DSM 17042T) and Pectinatus haikarae sp. nov. (type strain VTT E-88329T=DSM 16980T) are proposed.

scholarly journals Description of Wautersiella falsenii gen. nov., sp. nov., to accommodate clinical isolates phenotypically resembling members of the genera Chryseobacterium and Empedobacter

2006 ◽  
Vol 56 (10) ◽  
pp. 2323-2329 ◽  
Author(s):  
Peter Kämpfer ◽  
Véronique Avesani ◽  
Michèle Janssens ◽  
Jacqueline Charlier ◽  
Thierry De Baere ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Reference Strain ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
The Novel ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
The 16S Rrna Gene

A total of 26 isolates of non-fermenting, Gram-negative rods, obtained between 1980 and 2004 by various clinical laboratories in Belgium, with phenotypic characteristics resembling those of members of the genera Chryseobacterium and Empedobacter (indole-positive) and a biochemical profile resembling that of CDC group II-h, but urease-positive, were collected at the Université Catholique de Louvain Microbiology Laboratory, Belgium. The 16S rRNA gene sequences were determined for most of the isolates and showed 94–95 % similarity with the type strain of Empedobacter brevis as the closest relative, indicating that these isolates might belong to a separate genus. Furthermore, the 16S rRNA gene sequences of the isolates were similar, but two clusters (genomovars) could be distinguished. The sequence similarities were 99.5–100 % for the 14 isolates of genomovar 1 and 99.4–100 % for the 12 isolates of genomovar 2. The similarity between the two clusters was 98.3–99.5 %. The presence of two clearly different groups was corroborated by using tRNA intergenic length polymorphism analysis, which also enabled differentiation of the novel species from all other species studied thus far using this technique. DNA–DNA hybridization results excluded a close relatedness to Empedobacter brevis. The DNA G+C contents of the reference strains of genomovars 1 and 2 were 33.8±0.4 and 34.4±0.2 mol%, respectively. The name Wautersiella falsenii gen. nov., sp. nov., is proposed for this group, comprising two closely related genomovars. The type strain of the species and reference strain for genomovar 1 is NF 993T (=CCUG 51536T=CIP 108861T), which was isolated from a surgical wound. The reference strain for genomovar 2 is NF 770 (=CCUG 51537=CIP 108860), which was isolated from blood.

scholarly journals Lactobacillus saerimneri sp. nov., isolated from pig faeces

2004 ◽  
Vol 54 (4) ◽  
pp. 1365-1368 ◽  
Author(s):  
Carsten Pedersen ◽  
Stefan Roos
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics

In studying the composition of the Lactobacillus flora of faeces from pigs fed different diets, isolates with notable differences in their 16S rRNA gene sequence compared to recognized species were found. Phenotypic characteristics together with 16S rRNA gene sequences revealed that the isolates represented a novel species belonging to the Lactobacillus mali subgroup of lactobacilli. The name Lactobacillus saerimneri sp. nov. is proposed (type strain GDA154T=LMG 22087T=DSM 16049T=CCUG 48462T).

scholarly journals Halalkalicoccus jeotgali sp. nov., a halophilic archaeon from shrimp jeotgal, a traditional Korean fermented seafood

2007 ◽  
Vol 57 (10) ◽  
pp. 2296-2298 ◽  
Author(s):  
Seong Woon Roh ◽  
Young-Do Nam ◽  
Ho-Won Chang ◽  
Youlboong Sung ◽  
Kyoung-Ho Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Rrna Gene ◽  
Halophilic Archaeon ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Biochemical Tests ◽  
Extremely Halophilic Archaeon ◽  
Physiological And Biochemical

A novel, extremely halophilic archaeon B3T was isolated from shrimp-salted seafood. Its morphology, physiology, biochemical features and 16S rRNA gene sequence were characterized. Strain B3T is non-motile, Gram-variable, requires at least 10 % (w/v) NaCl for growth and grows in the ranges of 21–50 °C and pH 6.5–9.0. The DNA G+C content of strain B3T was 63.2 mol%. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain B3T belonged to the genus Halalkalicoccus and was phylogenetically closely related to the type strain Halalkalicoccus tibetensis (98.64 %). However, DNA–DNA hybridization experiments showed 7.0 % relatedness between strain B3T and a strain of a reference species of the genus Halalkalicoccus. Combined analysis of 16S rRNA gene sequences, DNA–DNA relatedness data, physiological and biochemical tests indicated that the genotypic and phenotypic characteristics differentiate strain B3T from other Halalkalicoccus species. On the basis of the evidence presented in this report, strain B3T represents a novel species of the genus Halalkalicoccus, for which the name Halalkalicoccus jeotgali. sp. nov. is proposed. The type strain is B3T (=KCTC 4019T=DSM 18796T=JCM 14584T=CECT 7217T).

scholarly journals Sporosarcina newyorkensis sp. nov. from clinical specimens and raw cow’s milk

2012 ◽  
Vol 62 (2) ◽  
pp. 322-329 ◽  
Author(s):  
William J. Wolfgang ◽  
An Coorevits ◽  
Jocelyn A. Cole ◽  
Paul De Vos ◽  
Michelle C. Dickinson ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
New York State ◽  
23S Rrna ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Clinical Specimens ◽  
The 16S Rrna Gene

Twelve independent isolates of a Gram-positive, endospore-forming rod were recovered from clinical specimens in New York State, USA, and from raw milk in Flanders, Belgium. The 16S rRNA gene sequences for all isolates were identical. The closest species with a validly published name, based on 16S rRNA gene sequence, is Sporosarcina koreensis (97.13 % similarity). DNA–DNA hybridization studies demonstrate that the new isolates belong to a species distinct from their nearest phylogenetic neighbours. The partial sequences of the 23S rRNA gene for the novel strains and their nearest neighbours also provide support for the novel species designation. Maximum-likelihood phylogenetic analysis of the 16S rRNA gene sequences confirmed that the new isolates are in the genus Sporosarcina. The predominant menaquinone is MK-7, the peptidoglycan has the type A4α l-Lys–Gly–d-Glu, and the polar lipids consist of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant fatty acids are iso-C14 : 0, iso-C15 : 0 and anteiso-C15 : 0. In addition, biochemical and morphological analyses support designation of the twelve isolates as representatives of a single new species within the genus Sporosarcina, for which the name Sporosarcina newyorkensis sp. nov. (type strain 6062T  = DSM 23544T  = CCUG 59649T  = LMG 26022T) is proposed.

Anaerostipes butyraticus sp. nov., an anaerobic, butyrate-producing bacterium from Clostridium cluster XIVa isolated from broiler chicken caecal content, and emended description of the genus Anaerostipes

2010 ◽  
Vol 60 (5) ◽  
pp. 1108-1112 ◽  
Author(s):  
Venessa Eeckhaut ◽  
Filip Van Immerseel ◽  
Frank Pasmans ◽  
Evie De Brandt ◽  
Freddy Haesebrouck ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Broiler Chicken ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Caecal Content ◽  
Emended Description ◽  
Bacterial Clone

Four butyrate-producing isolates were obtained from the caecal content of a 4-week-old broiler chicken. The 16S rRNA gene sequences were determined and confirmed the close relatedness of the four isolates, which suggested that they were derived from a single bacterial clone. Phylogenetic analysis based on 16S rRNA gene sequences showed that its closest relatives were members of cluster XIVa of the Clostridium subphylum of Gram-positive bacteria and that the closest related type strain was Anaerostipes caccae L1-92T (94.5 % similarity). Similarity levels of 96–98 % with sequences from uncultured bacteria from human stool samples were observed. On the basis of morphological, biochemical and phylogenetic characteristics, this strain is assigned to a novel species in the genus Anaerostipes, for which the name Anaerostipes butyraticus sp. nov. is proposed. The type strain is 35-7T (=LMG 24724T =DSM 22094T). An emended description of the genus Anaerostipes is also provided.

scholarly journals Emended description of the genus Actinokineospora Hasegawa 1988 and transfer of Amycolatopsis fastidiosa Henssen et al. 1987 as Actinokineospora fastidiosa comb. nov.

2010 ◽  
Vol 60 (6) ◽  
pp. 1444-1449 ◽  
Author(s):  
D. P. Labeda ◽  
N. P. Price ◽  
G. Y. A. Tan ◽  
M. Goodfellow ◽  
H.-P. Klenk
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Phylogenetic Study ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Careful Evaluation ◽  
Emended Description

The species Amycolatopsis fastidiosa (ex Celmer et al. 1977) Henssen et al. 1987 was proposed, based on morphological and chemotaxonomic observations, for a strain originally described as ‘Pseudonocardia fastidiosa’ Celmer et al. 1977 in a US patent. In the course of a phylogenetic study of the taxa with validly published names within the suborder Pseudonocardineae based on 16S rRNA gene sequences, it became apparent that this species was misplaced in the genus Amycolatopsis. After careful evaluation of the phylogeny, morphology, chemotaxonomy and physiology of the type strain, it was concluded that this strain represents a species of the genus Actinokineospora that is unable to produce motile spores. The description of the genus Actinokineospora is therefore emended to accommodate species that do not produce motile spores, and it is proposed that Amycolatopsis fastidiosa be transferred to the genus Actinokineospora as Actinokineospora fastidiosa comb. nov. The type strain is NRRL B-16697T =ATCC 31181T =DSM 43855T =JCM 3276T =NBRC 14105T =VKM Ac-1419T.

scholarly journals Vibrio olivae sp. nov., isolated from Spanish-style green-olive fermentations

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1895-1901 ◽  
Author(s):  
Helena Lucena-Padrós ◽  
Juan M. González ◽  
Belén Caballero-Guerrero ◽  
José Luis Ruiz-Barba ◽  
Antonio Maldonado-Barragán
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Green Olive

Three isolates originating from Spanish-style green-olive fermentations in a manufacturing company in the province of Seville, Spain, were taxonomically characterized by a polyphasic approach. This included a phylogenetic analysis based on 16S rRNA gene sequences and multi-locus sequence analysis (MLSA) based on pyrH, recA, rpoA, gyrB and mreB genes. The isolates shared 98.0 % 16S rRNA gene sequence similarity with Vibrio xiamenensis G21T. Phylogenetic analysis based on 16S rRNA gene sequences using the neighbour-joining and maximum-likelihood methods showed that the isolates fell within the genus Vibrio and formed an independent branch close to V. xiamenensis G21T. The maximum-parsimony method grouped the isolates to V. xiamenensis G21T but forming two clearly separated branches. Phylogenetic trees based on individual pyrH, recA, rpoA, gyrB and mreB gene sequences revealed that strain IGJ1.11T formed a clade alone or with V. xiamenensis G21T. Sequence similarities of the pyrH, recA, rpoA, gyrB and mreB genes between strain IGJ1.11T and V. xiamenensis G21T were 86.7, 85.7, 97.3, 87.6 and 84.8 %, respectively. MLSA of concatenated sequences showed that strain IGJ1.11T and V. xiamenensis G21T are two clearly separated species that form a clade, which we named Clade Xiamenensis, that presented 89.7 % concatenated gene sequence similarity, i.e. less than 92 %. The major cellular fatty acids (>5 %) of strain IGJ1.11T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). Enzymic activity profiles, sugar fermentation patterns and DNA G+C content (52.9 mol%) differentiated the novel strains from the closest related members of the genus Vibrio. The name Vibrio olivae sp. nov. is proposed for the novel species. The type strain is IGJ1.11T ( = CECT 8064T = DSM 25438T).

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