Mycobacterium fragae sp. nov., a non-chromogenic species isolated from human respiratory specimens

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2583-2587 ◽  
Author(s):  
Jesus Pais Ramos ◽  
Carlos Eduardo Dias Campos ◽  
Paulo Cesar de Souza Caldas ◽  
Nicole Victor Ferreira ◽  
Mariza Villas Boas da Silva ◽  
...  
Keyword(s):  
Type Species ◽  
Restriction Analysis ◽  
Hypervariable Region ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The North ◽  
North Eastern ◽  
Slow Growing ◽  
Respiratory Specimens

Three isolates of a slow-growing, non-chromogenic mycobacterium were grown from three sputum samples of a patient from the north-eastern Ceará state in Brazil. Identification at species level could not be obtained with PCR restriction analysis of the hsp65 gene. In order to characterize the isolates we carried out phenotypic and genotypic tests. We sequenced the nearly complete 16S rRNA gene and obtained partial sequences of the hsp65 (encoding the hypervariable region of the 65 kDa heat-shock protein) and rpoB (encoding the beta-subunit of RNA polymerase) genes. The three isolates turned out to be identical and most closely related to the species Mycobacterium celatum and Mycobacterium kyorinense . The results, however, showed significant differences between these species and the isolates studied, which led us to consider them members of a novel species for which we propose the name Mycobacterium fragae. The type strain is HF8705T ( = Fiocruz-INCQS/CMRVS P4051T = DSM 45731T).

scholarly journals Thermococcus paralvinellae sp. nov. and Thermococcus cleftensis sp. nov. of hyperthermophilic heterotrophs from deep-sea hydrothermal vents

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3655-3659 ◽  
Author(s):  
Sarah A. Hensley ◽  
Jong-Hyun Jung ◽  
Cheon-Seok Park ◽  
James F. Holden
Keyword(s):  
Type Species ◽  
Hydrothermal Vents ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Genome Sequences ◽  
Content Type ◽  
Link Type ◽  
The North ◽  
North Eastern

Two heterotrophic hyperthermophilic strains, ES1T and CL1T, were isolated from Paralvinella sp. polychaete worms collected from active hydrothermal vent chimneys in the north-eastern Pacific Ocean. Both were obligately anaerobic and produced H2S in the presence of elemental sulfur and H2. Complete genome sequences are available for both strains. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strains are more than 97 % similar to most other species of the genus Thermococcus . Therefore, overall genome relatedness index analyses were performed to establish that these strains are novel species. For each analysis, strain ES1T was determined to be most similar to Thermococcus barophilus MPT, while strain CL1T was determined to be most similar to Thermococcus sp. 4557. The average nucleotide identity scores for these strains were 84 % for strain ES1T and 81 % for strain CL1T, genome-to-genome direct comparison scores were 23 % for strain ES1T and 47 % for strain CL1T, and the species identification scores were 89 % for strain ES1T and 88 % for strain CL1T. For each analysis, strains ES1T and CL1T were below the species delineation cut-off. Therefore, based on their whole genome sequences, strains ES1T and CL1T are suggested to represent novel species of the genus Thermococcus for which the names Thermococcus paralvinellae sp. nov. and Thermococcus cleftensis sp. nov. are proposed, respectively. The type strains are ES1T ( = DSM 27261T = KACC 17923T) and CL1T ( = DSM 27260T = KACC 17922T).

scholarly journals Clavibacter michiganensis subsp. phaseoli subsp. nov., pathogenic in bean

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1752-1755 ◽  
Author(s):  
Ana J. González ◽  
Estefanía Trapiello
Keyword(s):  
Type Species ◽  
Restriction Analysis ◽  
16S Rrna Gene Sequencing ◽  
Phenotypic Traits ◽  
Rrna Gene ◽  
Bacterial Disease ◽  
Clavibacter Michiganensis ◽  
Content Type ◽  
Link Type ◽  
Clavibacter Michiganensis Subsp

A yellow Gram-reaction-positive bacterium isolated from bean seeds (Phaseolus vulgaris L.) was identified as Clavibacter michiganensis by 16S rRNA gene sequencing. Molecular methods were employed in order to identify the subspecies. Such methods included the amplification of specific sequences by PCR, 16S amplified rDNA restriction analysis (ARDRA), RFLP and multilocus sequence analysis as well as the analysis of biochemical and phenotypic traits including API 50CH and API ZYM results. The results showed that strain LPPA 982T did not represent any known subspecies of C. michiganensis . Pathogenicity tests revealed that the strain is a bean pathogen causing a newly identified bacterial disease that we name bacterial bean leaf yellowing. On the basis of these results, strain LPPA 982T is regarded as representing a novel subspecies for which the name Clavibacter michiganensis subsp. phaseoli subsp. nov. is proposed. The type strain is LPPA 982T ( = CECT 8144T = LMG 27667T).

scholarly journals Geofilum rubicundum gen. nov., sp. nov., isolated from deep subseafloor sediment

2012 ◽  
Vol 62 (Pt_5) ◽  
pp. 1075-1080 ◽  
Author(s):  
Masayuki Miyazaki ◽  
Osamu Koide ◽  
Tohru Kobayashi ◽  
Kozue Mori ◽  
Shigeru Shimamura ◽  
...  
Keyword(s):  
Type Species ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The North ◽  
Shimokita Peninsula ◽  
The Family ◽  
Bacterium Strain ◽  
Isoprenoid Quinones ◽  
Deep Subseafloor

A novel, facultatively anaerobic bacterium (strain JAM-BA0501T) was isolated from a deep subseafloor sediment sample at a depth of 247 m below seafloor off the Shimokita Peninsula of Japan in the north-western Pacific Ocean (Site C9001, 1180 m water depth). Cells of strain JAM-BA0501T were Gram-negative, filamentous, non-spore-forming and motile on solid medium by gliding. Phylogenetic analysis based on the 16S rRNA gene sequence of strain JAM-BA0501T indicated a distant relationship to strains representing genera within the order Bacteroidales , such as Alkaliflexus imshenetskii Z-7010T (91.1 % similarity), Marinilabilia salmonicolor ATCC 19041T (86.2 %) and Anaerophaga thermohalophila Fru22T (89.3 %). The new isolate produced isoprenoid quinones with menaquinone MK-7 as the major component, and the predominant fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The DNA G+C content of the isolate was 42.9 mol%. Based on its taxonomic distinctiveness, strain JAM-BA0501T is considered to represent a novel species of a new genus within the family Marinilabiliaceae , for which the name Geofilum rubicundum gen. nov., sp. nov. is proposed. The type strain of Geofilum rubicundum is JAM-BA0501T ( = JCM 15548T  = NCIMB 14482T).

scholarly journals Bradyrhizobium erythrophlei sp. nov. and Bradyrhizobium ferriligni sp. nov., isolated from effective nodules of Erythrophleum fordii

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1831-1837 ◽  
Author(s):  
Yao Yao ◽  
Xin Hua Sui ◽  
Xiao Xia Zhang ◽  
En Tao Wang ◽  
Wen Xn Chen
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
Intergenic Spacer ◽  
23S Rrna ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Erythrophleum Fordii ◽  
Slow Growing

Six slow-growing rhizobial strains isolated from effective nodules of Erythrophleum fordii were classified into the genus Bradyrhizobium based on their 16S rRNA gene sequences. The results of multilocus sequence analysis of recA, glnII and gyrB genes and 16S–23S rRNA intergenic spacer (IGS) sequence phylogeny indicated that the six strains belonged to two novel species, represented by CCBAU 53325T and CCBAU 51502T, which were consistent with the results of DNA–DNA hybridization; CCBAU 53325T had 17.65–25.59 % relatedness and CCBAU 51502T had 22.69–44.58 % relatedness with five closely related type strains, Bradyrhizobium elkanii USDA 76T, B. pachyrhizi LMG 24246T, B. lablabi CCBAU 23086T, B. jicamae LMG 24556T and B. japonicum USDA 6T. In addition, analysis of phenotypic characteristics and fatty acid profiles also distinguished the test strains from defined species of Bradyrhizobium . Two novel species, Bradyrhizobium erythrophlei sp. nov., represented by the type strain CCBAU 53325T ( = HAMBI 3614T = CGMCC 1.13002T = LMG 28425T), and Bradyrhizobium ferriligni sp. nov., represented by the type strain CCBAU 51502T ( = HAMBI 3613T = CGMCC 1.13001T), are proposed to accommodate the strains.

scholarly journals Sphaerochaeta multiformis sp. nov., an anaerobic, psychrophilic bacterium isolated from subseafloor sediment, and emended description of the genus Sphaerochaeta

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 4147-4154 ◽  
Author(s):  
Masayuki Miyazaki ◽  
Sanae Sakai ◽  
Kirsti M. Ritalahti ◽  
Yayoi Saito ◽  
Yuko Yamanaka ◽  
...  
Keyword(s):  
Type Species ◽  
Rrna Gene ◽  
Psychrophilic Bacterium ◽  
Content Type ◽  
Link Type ◽  
The North ◽  
Shimokita Peninsula ◽  
Emended Description ◽  
Coccoid Cell ◽  
Bacterium Strain

An anaerobic, psychrophilic bacterium, strain MO-SPC2T, was isolated from a methanogenic microbial community in a continuous-flow bioreactor that was established from subseafloor sediments collected from off the Shimokita Peninsula of Japan in the north-western Pacific Ocean. Cells were pleomorphic: spherical, annular, curved rod, helical and coccoid cell morphologies were observed. Motility only occurred in helical cells. Strain MO-SPC2T grew at 0–17 °C (optimally at 9 °C), at pH 6.0–8.0 (optimally at pH 6.8–7.2) and in 20–40 g NaCl l−1 (optimally at 20–30 NaCl l−1). The strain grew chemo-organotrophically with mono-, di- and polysaccharides. The major end products of glucose fermentation were acetate, ethanol, hydrogen and carbon dioxide. The abundant polar lipids of strain MO-SPC2T were phosphatidylglycolipids, phospholipids and glycolipids. The major cellular fatty acids were C14 : 0, C16 : 0 and C16 : 1ω9. Isoprenoid quinones were not detected. The G+C content of the DNA was 32.3 mol%. 16S rRNA gene-based phylogenetic analysis showed that strain MO-SPC2T was affiliated with the genus Sphaerochaeta within the phylum Spirochaetes , and its closest relatives were Sphaerochaeta pleomorpha GrapesT (88.4 % sequence identity), Sphaerochaeta globosa BuddyT (86.7 %) and Sphaerochaeta coccoides SPN1T (85.4 %). Based on phenotypic characteristics and phylogenetic traits, strain MO-SPC2T is considered to represent a novel species of the genus Sphaerochaeta , for which the name Sphaerochaeta multiformis sp. nov. is proposed. The type strain is MO-SPC2T ( = JCM 17281T = DSM 23952T). An emended description of the genus Sphaerochaeta is also proposed.

Mycobacterium vicinigordonae sp. nov., a slow-growing scotochromogenic species isolated from sputum

2021 ◽  
Vol 71 (5) ◽  
Author(s):  
Guan Liu ◽  
Xia Yu ◽  
Jingjing Luo ◽  
Yanjie Hu ◽  
Lingling Dong ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Type Species ◽  
Taxonomic Status ◽  
Mycolic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Slow Growing ◽  
Chinese Male ◽  
Mycobacterial Strain

A slow-growing, scotochromogenic mycobacterial strain (24T) was isolated from the sputum of a Chinese male human. Phylogenetic analysis using the 16S rRNA gene assigned strain 24T to the Mycobacterium gordonae complex, which includes Mycobacterium gordonae and Mycobacterium paragordonae . The phenotypic characteristics, unique mycolic acid profile and the results of phylogenetic analysis based on hsp65 and rpoB sequences strongly supported the taxonomic status of strain 24T as a representative of a species distinct from the other members of the M. gordonae complex. The genomic G+C content of strain 24T was 65.40mol%. Genomic comparisons showed that strain 24T and M. gordonae ATCC 14470T had an average nucleotide identity (ANI) value of 81.00 % and a DNA–DNA hybridization (DDH) value of 22.80 %, while the ANI and DDH values between strain 24Tand M. paragordonae 49 061T were 80.98 and 22.80 %, respectively. In terms of phylogenetic, phenotypic and chemotaxonomic features, strain 24T is distinguishable from its closest phylogenetic relatives and represents a novel species of the genus Mycobacterium , therefore the name Mycobacterium vicinigordonae sp. nov. is proposed. The type strain is 24T (=CMCC 93559T=DSM 105979T).

scholarly journals Mycobacterium minnesotense sp. nov., a photochromogenic bacterium isolated from sphagnum peat bogs

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 124-128 ◽  
Author(s):  
Geoffrey D. Hannigan ◽  
Bogdana Krivogorsky ◽  
Daniel Fordice ◽  
Jacqueline B. Welch ◽  
John L. Dahl
Keyword(s):  
Type Species ◽  
Restriction Analysis ◽  
Cell Surface Hydrophobicity ◽  
Peat Bogs ◽  
Rrna Gene ◽  
Environmental Isolates ◽  
Content Type ◽  
Sphagnum Peat ◽  
Link Type ◽  
Sphagnum Peat Bogs

Several intermediate-growing, photochromogenic bacteria were isolated from sphagnum peat bogs in northern Minnesota, USA. Acid-fast staining and 16S rRNA gene sequence analysis placed these environmental isolates in the genus Mycobacterium , and colony morphologies and PCR restriction analysis patterns of the isolates were similar. Partial sequences of hsp65 and dnaJ1 from these isolates showed that Mycobacterium arupense ATCC BAA-1242T was the closest mycobacterial relative, and common biochemical characteristics and antibiotic susceptibilities existed between the isolates and M. arupense ATCC BAA-1242T. However, compared to nonchromogenic M. arupense ATCC BAA-1242T, the environmental isolates were photochromogenic, had a different mycolic acid profile and had reduced cell-surface hydrophobicity in liquid culture. The data reported here support the conclusion that the isolates are representatives of a novel mycobacterial species, for which the name Mycobacterium minnesotense sp. nov. is proposed. The type strain is DL49T ( = DSM 45633T = JCM 17932T = NCCB 100399T).

Spirochaeta psychrophila sp. nov., a psychrophilic spirochaete isolated from subseafloor sediment, and emended description of the genus Spirochaeta

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2798-2804 ◽  
Author(s):  
Masayuki Miyazaki ◽  
Sanae Sakai ◽  
Yuko Yamanaka ◽  
Yumi Saito ◽  
Ken Takai ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Type Species ◽  
Sedimentary Environment ◽  
Rrna Gene ◽  
Content Type ◽  
First Report ◽  
Link Type ◽  
The North ◽  
Shimokita Peninsula ◽  
Unknown Lipid

An obligately anaerobic, psychrophilic spirochaete, strain MO-SPC1T, was isolated from a methanogenic microbial community grown in a continuous-flow bioreactor. Originally, this community was obtained from subseafloor sediments off the Shimokita Peninsula of Japan in the north-western Pacific Ocean. The cells were motile, Gram-stain-negative, helical, 0.25–0.55×3.6–15 µm, with a wavelength of approximately 0.5–0.6 µm. Strain MO-SPC1T grew at 0–18 °C (optimally at 15 °C), at pH 6.0–7.5 (optimally at pH 6.8–7.0) and in 20–70 g NaCl l−1 (optimally at 30–40 NaCl l−1). The strain grew chemo-organotrophically with mono-, di- and polysaccharides. The major end products of glucose fermentation were acetate, ethanol, hydrogen and carbon dioxide. The abundant polar lipids of strain MO-SPC1T were diphosphatidylglycerol, phosphatidylglycerol, unknown phospholipids and an unknown lipid. The major cellular fatty acids (>5 % of the total) were C14 : 0, C16 : 0, iso-C13 : 0, iso-C14 : 0, iso-C15 : 0, anteiso-C13 : 0 and anteiso-C15 : 0. To the best of our knowledge, this is the first report of the fatty acids iso-C13 : 0 and anteiso-C13 : 0 from a species of the genus Spirochaeta . Isoprenoid quinones were not found. The G+C content of the genomic DNA was 39.8 mol%. 16S rRNA gene sequence-based phylogenetic analysis showed that strain MO-SPC1T was affiliated with the genus Spirochaeta , and its closest relatives were Spirochaeta isovalerica MA-2T (95.6 % sequence identity) and Spirochaeta litoralis R1T (89.4 %). Based on its phenotypic characteristics and phylogenetic traits, strain MO-SPC1T is placed in a separate taxon at the level of a novel species within the genus Spirochaeta, for which the name Spirochaeta psychrophila sp. nov. is proposed, reflecting its true psychrophilic physiology. The type strain is MO-SPC1T ( = JCM 17280T = DSM 23951T). To our knowledge, this is the first report of an isolate of the phylum Spirochaetes from a deep-sea sedimentary environment, and of an obligately psychrophilic nature.

Mycobacterium koreense sp. nov., a slowly growing non-chromogenic species closely related to Mycobacterium triviale

2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1289-1295 ◽  
Author(s):  
Byoung-Jun Kim ◽  
Joseph Jeong ◽  
Seon Ho Lee ◽  
Sung-Ryul Kim ◽  
Hee-Kyung Yu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Taxonomic Status ◽  
Mycolic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Slow Growing

A novel slow-growing, non-chromogenic mycobacterium (strain 01-305T) was isolated from a patient with pulmonary dysfunction. Growth characteristics, acid-fastness and the results of 16S rRNA gene sequencing supported the placement of this strain within the genus Mycobacterium . Phenotypically, strain 01-305T was generally similar to Mycobacterium triviale ATCC 23292T, but some unique biochemical characteristics were observed. The 16S rRNA gene sequence of strain 01-305T was similar to those of M. triviale ATCC 23290 (GenBank accession no. AY734996, 99.9 % similarity) and M. triviale ATCC 23291 (AY734995, 99.9 %); however, it differed substantially from that of M. triviale ATCC 23292T (X88924, 98.2 %). Phylogenetic analysis based on 16S rRNA gene sequences placed strain 01-305T in the slow-growing Mycobacterium group close to M. triviale ATCC 23290 and M. triviale ATCC 23291, but not M. triviale ATCC 23292T. Unique mycolic acid profiles and phylogenetic analysis based on two different chronometer molecules, and the hsp65 and rpoB genes, strongly supported the taxonomic status of this strain as representing a distinct species. These data support the conclusion that strain 01-305T represents a novel mycobacterial species, for which the name Mycobacterium koreense sp. nov. is proposed. The type strain is 01-305T ( = DSM 45576T  = KCTC 19819T).

scholarly journals Listeria booriae sp. nov. and Listeria newyorkensis sp. nov., from food processing environments in the USA

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 286-292 ◽  
Author(s):  
Daniel Weller ◽  
Alexis Andrus ◽  
Martin Wiedmann ◽  
Henk C. den Bakker
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The North ◽  
Eastern Usa ◽  
The Usa ◽  
Genotypic Identification

Sampling of seafood and dairy processing facilities in the north-eastern USA produced 18 isolates of Listeria spp. that could not be identified at the species-level using traditional phenotypic and genotypic identification methods. Results of phenotypic and genotypic analyses suggested that the isolates represent two novel species with an average nucleotide blast identity of less than 92 % with previously described species of the genus Listeria . Phylogenetic analyses based on whole genome sequences, 16S rRNA gene and sigB gene sequences confirmed that the isolates represented by type strain FSL M6-0635T and FSL A5-0209 cluster phylogenetically with Listeria cornellensis . Phylogenetic analyses also showed that the isolates represented by type strain FSL A5-0281T cluster phylogenetically with Listeria riparia . The name Listeria booriae sp. nov. is proposed for the species represented by type strain FSL A5-0281T ( = DSM 28860T = LMG 28311T), and the name Listeria newyorkensis sp. nov. is proposed for the species represented by type strain FSL M6-0635T ( = DSM 28861T = LMG 28310T). Phenotypic and genotypic analyses suggest that neither species is pathogenic.

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