Mycobacterium iranicum sp. nov., a rapidly growing scotochromogenic species isolated from clinical specimens on three different continents

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1383-1389 ◽  
Author(s):  
Hasan Shojaei ◽  
Charles Daley ◽  
Zoe Gitti ◽  
Abodolrazagh Hashemi ◽  
Parvin Heidarieh ◽  
...  
Keyword(s):  
Novel Species ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Clinical Specimens ◽  
Isolation And Characterization ◽  
Genes Encoding ◽  
The Usa ◽  
The 16S Rrna Gene

The isolation and characterization of a novel, rapidly growing, scotochromogenic mycobacterial species is reported. Eight independent strains were isolated from clinical specimens from six different countries of the world, two in Iran, two in Italy and one in each of following countries: Greece, the Netherlands, Sweden and the USA. Interestingly, two of the strains were isolated from cerebrospinal fluid. The strains were characterized by rapid growth and presented orange-pigmented scotochromogenic colonies. DNA-based analysis revealed unique sequences in the four regions investigated: the 16S rRNA gene, the rRNA gene internal transcribed spacer 1 and the genes encoding the 65 kDa heat-shock protein and the beta-subunit of RNA polymerase. The phylogenetic analysis placed the strains among the rapidly growing mycobacteria, being most closely related to Mycobacterium gilvum . The genotypic and phenotypic data both strongly supported the inclusion of the strains investigated here as members of a novel species within the genus Mycobacterium; the name Mycobacterium iranicum sp. nov. is proposed to indicate the isolation in Iran of the first recognized strains. The type strain is M05T ( = DSM 45541T = CCUG 62053T = JCM 17461T).

Lacibacter daechungensis sp. nov., isolated from deep freshwater of a reservoir

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4519-4523 ◽  
Author(s):  
Long Jin ◽  
Sang-Yoon Shin ◽  
Hyung-Gwan Lee ◽  
Chi-Yong Ahn ◽  
Hee-Mock Oh
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Whole Cells ◽  
Link Type ◽  
The 16S Rrna Gene ◽  
Motile By Gliding

A Gram-stain-negative, aerobic, motile by gliding, non-spore-forming, rod-shaped, orange-pigmented bacterium, designated strain H32-4T, was isolated from 32 m deep water of Daechung reservoir in Daejeon, Republic of Korea. Based on the nucleotide sequence of the 16S rRNA gene, the closest neighbouring type strain was Lacibacter cauensis NJ-8T with which strain H32-4T shared 98.9 % sequence similarity. The most abundant fatty acids in whole cells of strain H32-4T were C15 : 0 iso (40.6 %), C17 : 0 iso 3-OH (22.4 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 9.3 %) and C15 : 0 (6.6 %). The predominant menaquinone was MK-7. The G+C content of the genomic DNA of strain H32-4T was 45.7 mol%. Thus, these combined genotypic and phenotypic data supported the conclusion that strain H32-4T represents a novel species of the genus Lacibacter , for which the name Lacibacter daechungensis sp. nov. is proposed. The type strain is H32-4T ( = KCTC 32395T = JCM 19172T).

scholarly journals Chryseobacterium takakiae sp. nov., a member of the phylum Bacteroidetes isolated from Takakia lepidozioides

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 71-76 ◽  
Author(s):  
Ran Zhao ◽  
Xin Yao Chen ◽  
Xue Dong Li ◽  
Zhi Ling Chen ◽  
Yan Hong Li
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Taxonomic Approach ◽  
The 16S Rrna Gene

A Gram-stain-negative, rod-shaped and non-endospore-forming bacterium, designated strain AG1-2T, was isolated from Takakia lepidozioides collected from the Gawalong glacier in Tibet, China and characterized using a polyphasic taxonomic approach. The predominant fatty acids of strain AG1-2T were iso-C15 : 0 (36.0 %), iso-C17 : 0 3-OH (20.2 %), summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl, 16.4 %) and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c, 11.1 %). The major polar lipids were phosphatidylethanolamine, three unidentified aminolipids and two unidentified lipids. Strain AG1-2T contained MK-6 as the dominant menaquinone, and the genomic DNA G+C content was 37.3 mol%. The phylogenetic analysis based on the 16S rRNA gene sequences showed that strain AG1-2T was affiliated to species of the genus Chryseobacterium , and its closest related species were Chryseobacterium taiwanense Soil-3-27T, Chryseobacterium hispalense AG13T, Chryseobacterium camelliae THG C4-1T and Chryseobacterium taeanense PHA3-4T with a sequence similarity of 98.0, 97.8, 97.3 and 97.1 %, respectively. However, the DNA–DNA relatedness values between these strains and strain AG1-2T were 29, 21, 21 and 45 %, respectively. Based on phylogenetic inference and phenotypic data, strain AG1-2T is considered to represent a novel species of the genus Chryseobacterium , for which the name Chryseobacterium takakiae sp. nov. is proposed. The type strain is AG1-2T ( = CGMCC 1.12488T = DSM 26898T).

Eikenella glucosivorans sp. nov., isolated from a human throat swab, and emendation of the genus Eikenella to include saccharolytic species

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Silvio Hering ◽  
Moritz K. Jansson ◽  
Michael E. J. Buhl
Keyword(s):  
Type Species ◽  
Throat Swab ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Routine Care ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Bacterium Strain

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.

scholarly journals Halioglobus maricola sp. nov., isolated from coastal seawater

2020 ◽  
Vol 70 (3) ◽  
pp. 1868-1875 ◽  
Author(s):  
Shan-Hui Li ◽  
Jaeho Song ◽  
Yeonjung Lim ◽  
Yochan Joung ◽  
Ilnam Kang ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
A Genome ◽  
The 16S Rrna Gene

A Gram-stain-negative, rod-shaped, aerobic, non-flagellated, chemoheterotrophic bacterium, designated IMCC14385T, was isolated from surface seawater of the East Sea, Republic of Korea. The 16S rRNA gene sequence analysis indicated that IMCC14385T represented a member of the genus Halioglobus sharing 94.6–97.8 % similarities with species of the genus. Whole-genome sequencing of IMCC14385T revealed a genome size of 4.3 Mbp and DNA G+C content of 56.7 mol%. The genome of IMCC14385T shared an average nucleotide identity of 76.6 % and digital DNA–DNA hybridization value of 21.6 % with the genome of Halioglobus japonicus KCTC 23429T. The genome encoded the complete poly-β-hydroxybutyrate biosynthesis pathway. The strain contained summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C17 : 1 ω8c as the predominant cellular fatty acids as well as ubiquinone-8 (Q-8) as the respiratory quinone. The polar lipids detected in the strain were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, five unidentified phospholipids, an unidentified aminolipid, an unidentified aminophospholipid and four unidentified lipids. On the basis of taxonomic data obtained in this study, it is suggested that IMCC14385T represents a novel species of the genus Halioglobus , for which the name Halioglobus maricola sp. nov. is proposed. The type strain is IMCC14385T (=KCTC 72520T=NBRC 114072T).

scholarly journals Molecular Characterization of anEndozoicomonas-Like Organism Causing Infection in the King Scallop (Pecten maximusL.)

2017 ◽  
Vol 84 (3) ◽  
Author(s):  
Irene Cano ◽  
Ronny van Aerle ◽  
Stuart Ross ◽  
David W. Verner-Jeffreys ◽  
Richard K. Paley ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Characterization ◽  
Mass Mortality ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
The 16S Rrna Gene

ABSTRACTOne of the fastest growing fisheries in the UK is the king scallop (Pecten maximusL.), also currently rated as the second most valuable fishery. Mass mortality events in scallops have been reported worldwide, often with the causative agent(s) remaining uncharacterized. In May 2013 and 2014, two mass mortality events affecting king scallops were recorded in the Lyme Bay marine protected area (MPA) in Southwest England. Histopathological examination showed gill epithelial tissues infected with intracellular microcolonies (IMCs) of bacteria resemblingRickettsia-like organisms (RLOs), often with bacteria released in vascular spaces. Large colonies were associated with cellular and tissue disruption of the gills. Ultrastructural examination confirmed the intracellular location of these organisms in affected epithelial cells. The 16S rRNA gene sequences of the putative IMCs obtained from infected king scallop gill samples, collected from both mortality events, were identical and had a 99.4% identity to 16S rRNA gene sequences obtained from “CandidatusEndonucleobacter bathymodioli” and 95% withEndozoicomonasspecies.In situhybridization assays using 16S rRNA gene probes confirmed the presence of the sequenced IMC gene in the gill tissues. Additional DNA sequences of the bacterium were obtained using high-throughput (Illumina) sequencing, and bioinformatic analysis identified over 1,000 genes with high similarity to protein sequences fromEndozoicomonasspp. (ranging from 77 to 87% identity). Specific PCR assays were developed and applied to screen for the presence of IMC 16S rRNA gene sequences in king scallop gill tissues collected at the Lyme Bay MPA during 2015 and 2016. There was 100% prevalence of the IMCs in these gill tissues, and the 16S rRNA gene sequences identified were identical to the sequence found during the previous mortality event.IMPORTANCEMolluscan mass mortalities associated with IMCs have been reported worldwide for many years; however, apart from histological and ultrastructural characterization, characterization of the etiological agents is limited. In the present work, we provide detailed molecular characterization of anEndozoicomonas-like organism (ELO) associated with an important commercial scallop species.

Companilactobacillus pabuli sp. nov., a lactic acid bacterium isolated from animal feed

2021 ◽  
Author(s):  
Ji Young Jung ◽  
Hye Kyeong Kang ◽  
Hyun Mi Jin ◽  
Sang-Soo Han ◽  
Young Chul Kwon ◽  
...  
Keyword(s):  
Lactic Acid ◽  
16S Rrna ◽  
Dna Hybridization ◽  
Type Species ◽  
Novel Species ◽  
Rrna Gene ◽  
Average Nucleotide Identity ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

A Gram-positive, facultative anaerobic, catalase-negative, non-motile, non-spore-forming and rod-shaped lactic acid bacterium strain, denoted as NFFJ11T and isolated from total mixed fermentation feed in the Republic of Korea, was characterized through polyphasic approaches, including sequence analyses of the 16S rRNA gene and housekeeping genes (rpoA and pheS), determination of average nucleotide identity and in silico DNA–DNA hybridization, fatty acid methyl ester analysis, and phenotypic characterization. Phylogenetic analyses based on 16S rRNA, rpoA and pheS gene sequences revealed that strain NFFJ11T belonged to the genus Companilactobacillus . The 16S rRNA gene sequence of strain NFFJ11T exhibited high similarity to Companilactobacillus formosensis S215T (99.66 %), Companilactobacillus farciminis Rv4 naT (99.53 %), Companilactobacillus crustorum LMG 23699T (99.19 %), Companilactobacillus futsaii YM 0097T (99.06 %), Companilactobacillus zhachilii HBUAS52074T (98.86 %) and Companilactobacillus heilongiiangensis S4-3T (98.66 %). However, average nucleotide identity and in silico DNA–DNA hybridization values for these type strains were in the range of 79.90–92.93 % and 23.80–49.30 %, respectively, which offer evidence that strain NFFJ11T belongs to a novel species of the genus Companilactobacillus . The cell-wall peptidoglycan type was A4α (l-Lys–d-Asp) and the G+C content of the genomic DNA was 35.7 mol%. The main fatty acids of strain NFFJ11T were C18 : 1  ω9c (43.3 %), C16 : 0 (20.1 %) and summed feature 7 (18.3 %; comprising any combination of C19 : 1  ω7c, C19 : 1  ω6c and C19 : 0 cyclo ω10c). Through polyphasic taxonomic analysis, it was observed that strain NFFJ11T represents a novel species belonging to the genus Companilactobacillus , for which the name Companilactobacillus pabuli sp. nov. is proposed. The type strain is NFFJ11T (= KACC 21771T= JCM 34088T).

scholarly journals Rhizobium rhizoryzae sp. nov., isolated from rice roots

2014 ◽  
Vol 64 (Pt_4) ◽  
pp. 1373-1377 ◽  
Author(s):  
Xiao-Xia Zhang ◽  
Xue Tang ◽  
Rizwan Ali Sheirdil ◽  
Lei Sun ◽  
Xiao-Tong Ma
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type ◽  
The 16S Rrna Gene

Two strains (J3-AN59T and J3-N84) of Gram-stain-negative, aerobic and rod-shaped bacteria were isolated from the roots of fresh rice plants. The 16S rRNA gene sequence similarity results showed that the similarity between strains J3-AN59T and J3-N84 was 100 %. Both strains were phylogenetically related to members of the genus Rhizobium , and they were most closely related to Rhizobium tarimense ACCC 06128T (97.43 %). Similarities in the sequences of housekeeping genes between strains J3-AN59T and J3-N84 and those of recognized species of the genus Rhizobium were less than 90 %. The polar lipid profiles of both strains were predominantly composed of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unknown aminophospholipid. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The DNA G+C contents of J3-AN59T and J3-N84 were 55.7 and 57.1 mol%, respectively. The DNA–DNA relatedness value between J3-AN59T and J3-N84 was 89 %, and strain J3-AN59T showed 9 % DNA–DNA relatedness to R. tarimense ACCC 06128T, the most closely related strain. Based on this evidence, we found that J3-AN59T and J3-N84 represent a novel species in the genus Rhizobium and we propose the name Rhizobium rhizoryzae sp. nov. The type strain is J3-AN59T ( = ACCC 05916T = KCTC 23652T).

scholarly journals Phenotypic characterization of Sodalis praecaptivus sp. nov., a close non-insect-associated member of the Sodalis-allied lineage of insect endosymbionts

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1400-1405 ◽  
Author(s):  
Abhishek Chari ◽  
Kelly F. Oakeson ◽  
Shinichiro Enomoto ◽  
D. Grant Jackson ◽  
Mark A. Fisher ◽  
...  
Keyword(s):  
Novel Species ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Sodalis Glossinidius ◽  
Large Gene ◽  
Close Relationship ◽  
Metabolic Properties ◽  
Insect Symbionts ◽  
The 16S Rrna Gene

A Gram-stain-negative bacterium, isolated from a human wound was previously found to share an unprecedentedly close relationship with Sodalis glossinidius and other members of the Sodalis-allied clade of insect symbionts. This relationship was inferred from sequence analysis of the 16S rRNA gene and genomic comparisons and suggested the strain belonged to a novel species. Biochemical and genetic analyses supported this suggestion and demonstrated that the organism has a wide repertoire of metabolic properties, which is consistent with the presence of a relatively large gene inventory. Among members of the Sodalis-allied clade, this is the first representative that has sufficient metabolic capabilities to sustain growth in minimal media. On the basis of the results of this study, we propose that this organism be classified as a representative of a novel species, Sodalis praecaptivus sp. nov. (type strain HST = DSM 27494T = ATCC BAA-2554T).

scholarly journals Deinococcus peraridilitoris sp. nov., isolated from a coastal desert

2007 ◽  
Vol 57 (7) ◽  
pp. 1408-1412 ◽  
Author(s):  
Fred A. Rainey ◽  
Margarida Ferreira ◽  
M. Fernanda Nobre ◽  
Keren Ray ◽  
Danielle Bagaley ◽  
...  
Keyword(s):  
Novel Species ◽  
Plate Count ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Phenotypic Data ◽  
Coastal Desert ◽  
Plate Count Agar ◽  
Radiation Resistant ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

Three ionizing-radiation-resistant bacterial strains (designated KR-196, KR-198 and KR-200T) were isolated from a sample of arid soil collected from a coastal desert in Chile. The soil sample was irradiated before serial dilution plating was performed using one-tenth-strength plate count agar. Phylogenetic analysis of the 16S rRNA gene sequences showed these organisms to represent a novel species of the genus Deinococcus, having sequence similarities of 87.3–90.8 % with respect to recognized Deinococcus species. Strains KR-196, KR-198 and KR-200T were aerobic and showed optimum growth at 30 °C and pH 6.5–8.0. The major respiratory menaquinone was MK-8. The predominant fatty acids in these strains were 16 : 1ω7c, 16 : 0, 15 : 1ω6c, 17 : 0 and 18 : 0. The DNA G+C content of strain KR-200T was 63.9 mol%. Strains KR-196, KR-198 and KR-200T were found to be resistant to >10 kGy gamma radiation. On the basis of the phylogenetic, chemotaxonomic and phenotypic data, strain KR-200T represents a novel species of the genus Deinococcus, for which the name Deinococcus peraridilitoris sp. nov. is proposed. The type strain is KR-200T (=LMG 22246T=CIP 109416T).

Aquimarina agarilytica sp. nov., an agarolytic species isolated from a red alga

2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 869-873 ◽  
Author(s):  
Bokun Lin ◽  
Guoyong Lu ◽  
Yandan Zheng ◽  
Wei Xie ◽  
Shengkang Li ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Red Alga ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
The 16S Rrna Gene

A novel yellow-pigmented, agarolytic bacterial strain, designated ZC1T, was isolated from the surface of the marine red alga Porphyra haitanensis collected near Nan Ao Island, Guangdong province, China. The isolate was Gram-stain-negative, strictly aerobic and rod-shaped and displayed β-galactosidase, alkaline phosphatase, catalase and oxidase activities. The predominant cellular fatty acids were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH) and iso-C17 : 0 3-OH. The major menaquinone was menaquinone 6 (MK-6). The DNA G+C content was 32.8 mol%. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain ZC1T was closely related to members of the genus Aquimarina in the family Flavobacteriaceae , phylum Bacteroidetes . Based on phylogenetic and phenotypic evidence, strain ZC1T ( = CCTCC AB 2010229T  = NBRC 107695T) represents the type strain of a novel species in the genus Aquimarina , for which the name Aquimarina agarilytica sp. nov. is proposed.

Sign in / Sign up

Export Citation Format

Share Document