scholarly journals Genomic Virulence Features of Two Novel Species Nocardia barduliensis sp. nov. and Nocardia gipuzkoensis sp. nov., Isolated from Patients with Chronic Pulmonary Diseases

2020 ◽  
Vol 8 (10) ◽  
pp. 1517
Author(s):  
Imen Nouioui ◽  
Carlos Cortés-Albayay ◽  
Meina Neumann-Schaal ◽  
Diego Vicente ◽  
Gustavo Cilla ◽  
...  
Keyword(s):  
Novel Species ◽  
Sequence Similarity ◽  
Genetic Maps ◽  
Pulmonary Diseases ◽  
Comparative Genomic ◽  
Syntenic Block ◽  
Rrna Gene ◽  
Old Patients ◽  
Mycolic Acids ◽  
Chronic Pulmonary Diseases

Strains 335427T and 234509T, isolated from two 76-year-old patients with chronic pulmonary diseases, were the subject of polyphasic taxonomic studies and comparative genomic analyses for virulence factors. The 16 rRNA gene sequence similarity between strains 335427T and 234509T and their closest phylogenetic neighbors Nocardia asiatica NBRC 100129T and Nocardia abscessus NBRC 100374T were 99.5% and 100%, respectively. Digital DNA–DNA hybridization values between the aforementioned studied strains were well below the 70% threshold for assigning prokaryotic strains to a novel species. Strains 335427T and 234509T have genome sizes of 8.49 Mpb and 8.07 Mpb, respectively, with G + C content of 68.5%. Isolate 335427T has C16:0, C18:1 ω9c, C18:0 and C18:0 10 methyl as major fatty acids (>15%) and mycolic acids formed of 52–54 carbon atoms. However, only C18:1 ω9c was detected for isolate 234509T, which had mycolic acids with 44–56 carbon. Based on phenotypic and genetic data, strains 335427T (DSM 109819T = CECT 9924T) and 234509T (DSM 111366T = CECT 30129T) merit recognition as novel species, which are named Nocardia barduliensis sp. nov. and Nocardia gipuzkoensis sp. nov., respectively. All the strains studied had homologous VF-associated genes to those described in M. tuberculosis, including experimentally verified virulence genes in humans related to tuberculosis. The narGHIJ (nitrate reduction pathway) and gvpAFGOJLMK (gas vesicles) genetic maps of strains 335427T, 234509T, NBRC 100129T and NBRC 100374T showed the same syntenic block and raise the question of whether their functions are interlinked during the infection of the human host. However, further research is required to decipher the role of the gas vesicle in the pathogenicity mechanism of Nocardia spp.

scholarly journals Rhodococcus kyotonensis sp. nov., a novel actinomycete isolated from soil

2007 ◽  
Vol 57 (9) ◽  
pp. 1956-1959 ◽  
Author(s):  
Bing Li ◽  
Keiko Furihata ◽  
Lin-Xian Ding ◽  
Akira Yokota
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Mycolic Acids ◽  
Rhodococcus Fascians ◽  
The 16S Rrna Gene ◽  
Is Strain

A polyphasic study was undertaken to establish the taxonomic position of an isolate, strain DS472T, from soil in Kyoto, Japan. Phylogenetic analysis, based on the 16S rRNA gene sequences, revealed that this strain constitutes a new subline within the genus Rhodococcus, with Rhodococcus yunnanensis YIM 70056T and Rhodococcus fascians DSM 20669T as its nearest phylogenetic neighbours (98.2 and 97.8 % sequence similarity, respectively). DNA–DNA hybridization experiments revealed 36 and 29 % relatedness between the isolate and its phylogenetic relatives, R. yunnanensis and R. fascians, respectively. Chemotaxonomic characteristics, including the major quinone MK-8(H2), predominant fatty acids C16 : 0, C18 : 1 ω9c and 10-methyl C18 : 0, the presence of cell-wall chemotype IV and mycolic acids, were consistent with the properties of members of the genus Rhodococcus. The DNA G+C content was 64.5 mol%. On the basis of both phenotypic and genotypic evidence, strain DS472T represents a novel species of the genus Rhodococcus, for which the name Rhodococcus kyotonensis sp. nov. is proposed. The type strain is strain DS472T (=IAM 15415T=CCTCC AB206088T).

scholarly journals Mycobacterium shinjukuense sp. nov., a slowly growing, non-chromogenic species isolated from human clinical specimens

2011 ◽  
Vol 61 (8) ◽  
pp. 1927-1932 ◽  
Author(s):  
Hajime Saito ◽  
Tomotada Iwamoto ◽  
Kiyofumi Ohkusu ◽  
Yoshihito Otsuka ◽  
Yasushi Akiyama ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Sequence Similarity ◽  
Sputum Sample ◽  
Lavage Fluid ◽  
Mycolic Acid ◽  
Rrna Gene ◽  
Mycolic Acids ◽  
Negative Results

Seven isolates of a slowly growing, non-chromogenic Mycobacterium species were obtained from sputum and bronchial lavage fluid samples from elderly patients in different regions of Japan. These isolates were distinguished from related non-tuberculous species by colony morphology, positive results for Tween hydrolysis, catalase at 68 °C, nitrate reductase and pyrazinamidase and negative results for semi-quantitative catalase, urease and arylsulfatase. The mycolic acid pattern obtained by HPLC revealed a single cluster of late-eluting mycolic acids similar to but different from those of Mycobacterium malmoense ATCC 29571T. The 16S rRNA gene, 16S–23S internal transcribed spacer (ITS), rpoB and hsp65 sequences were unique in comparison with those of other mycobacteria. Comparison of 16S rRNA gene sequences showed that the isolates were most closely related to Mycobacterium tuberculosis H37RvT (21 base differences in 1508 bp; 98.6 % 16S rRNA gene sequence similarity). A representative strain, GTC 2738T, showed 91.9 % rpoB sequence similarity with Mycobacterium marinum strain M, 95 % hsp65 sequence similarity with Mycobacterium kansasii CIP 104589T and 81.1 % 16S–23S ITS sequence similarity with Mycobacterium gordonae ATCC 14470T. Phylogenetic analysis of concatenated sequences of the 16S rRNA, rpoB and hsp65 genes showed that strain GTC 2738T was located on a distinct clade adjacent to M. tuberculosis, M. ulcerans and M. marinum, with bootstrap values of 81 %. DNA–DNA hybridization demonstrated less than 70 % reassociation with type strains of genetically related species and supported the novel species status of the isolates. On the basis of this evidence, a novel species with the name Mycobacterium shinjukuense sp. nov. is proposed. The type strain, isolated from a sputum sample, is strain GTC 2738T( = JCM 14233T = CCUG 53584T).

scholarly journals Knoellia locipacati sp. nov., from soil of the Demilitarized Zone in South Korea

2012 ◽  
Vol 62 (2) ◽  
pp. 342-346 ◽  
Author(s):  
Na-Ri Shin ◽  
Seong Woon Roh ◽  
Min-Soo Kim ◽  
Mi-Ja Jung ◽  
Tae Woong Whon ◽  
...  
Keyword(s):  
South Korea ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Mycolic Acids ◽  
Demilitarized Zone ◽  
Genotypic Analysis

A Gram-positive, aerobic, rod- or coccus-shaped, non-motile bacterium, designated DMZ1T, was isolated from soil of the Demilitarized Zone, South Korea. Strain DMZ1T grew optimally at 30 °C, at pH 7–8 and with 1 % (w/v) NaCl. The isolate showed high 16S rRNA gene sequence similarity with Knoellia aerolata 5317S-21T (98.2 %). The cell-wall sugars were glucose and ribose. The peptidoglycan amino acids were meso-diaminopimelic acid, glutamic acid and glycine. The major cellular fatty acids were iso-C16 : 0, iso-C15 : 0 and iso-C14 : 0. The polar lipids were phosphatidylethanolamine, phosphatidylinositol, diphosphatidylglycerol, phosphatidylglycerol and five unknown phospholipids. The isolate did not contain mycolic acids. The DNA G+C content was 72.6 mol%. The isolate showed <28 % DNA–DNA relatedness with members of the genus Knoellia. Phylogenetic, phenotypic and genotypic analysis indicated that strain DMZ1T represents a novel species of the genus Knoellia, for which the name Knoellia locipacati sp. nov. is proposed. The type strain is DMZ1T ( = KACC 15114T  = JCM 17313T).

scholarly journals Rhodococcus triatomae sp. nov., isolated from a blood-sucking bug

2005 ◽  
Vol 55 (4) ◽  
pp. 1575-1579 ◽  
Author(s):  
A. F. Yassin
Keyword(s):  
Dna Hybridization ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Mycolic Acids ◽  
Blood Sucking ◽  
Taxonomic Methods ◽  
Rrna Gene Sequencing

Two bacterial isolates, strains IMMIB RIV-085T and IMMIB RIV-095, isolated from a blood-sucking bug of the genus Triatoma, were characterized by phenotypic and molecular taxonomic methods. Chemotaxonomic investigations revealed the presence of cell-wall chemotype IV and mycolic acids consistent with the genus Rhodococcus. Comparative 16S rRNA gene sequencing showed that the two isolates are genealogically highly related (100 % sequence similarity) and constitute a new subline within the genus Rhodococcus, with Rhodococcus corynebacteroides and Rhodococcus rhodnii as their nearest phylogenetic neighbours (98·4 and 98·3 % sequence similarity, respectively). However, DNA–DNA hybridization experiments demonstrated unambiguously that the isolates are genealogically distinct from R. corynebacteroides and R. rhodnii (32 and 43 % relatedness, respectively). The isolates could be distinguished from their phylogenetic relatives and other members of the genus Rhodococcus by means of biochemical tests. On the basis of both phenotypic and phylogenetic evidence, it is proposed that these isolates be classified as a novel species, Rhodococcus triatomae sp. nov. The type strain is strain IMMIB RIV-085T (=CCUG 50202T=DSM 44892T).

scholarly journals Paenibacillus algorifonticola sp. nov., isolated from a cold spring

2011 ◽  
Vol 61 (9) ◽  
pp. 2167-2172 ◽  
Author(s):  
Qi-Yong Tang ◽  
Na Yang ◽  
Jian Wang ◽  
Yu-Qing Xie ◽  
Biao Ren ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gram Stain ◽  
Rrna Gene Sequence ◽  
Cold Spring ◽  
Xinjiang Uyghur Autonomous Region ◽  
The 16S Rrna Gene

A Gram-stain-positive, endospore-forming, rod-shaped bacterium, designated XJ259T, was isolated from a cold spring sample from Xinjiang Uyghur Autonomous Region, China. The isolate grew optimally at 20–30 °C and pH 7.3–7.8. Comparative analysis of the 16S rRNA gene sequence showed that isolate XJ259T belonged phylogenetically to the genus Paenibacillus, and was most closely related to Paenibacillus xinjiangensis B538T (with 96.6 % sequence similarity), Paenibacillus glycanilyticus DS-1T (96.3 %) and Paenibacillus castaneae Ch-32T (96.1 %), sharing less than 96.0 % sequence similarity with all other members of the genus Paenibacillus. Chemotaxonomic analysis revealing menaquinone-7 (MK-7) as the major isoprenoid quinone, diphosphatidylglycerol, phosphatidylethanolamine and two unknown phosphoglycolipids as the major cellular polar lipids, a DNA G+C content of 47.0 mol%, and anteiso-C15 : 0 and C16 : 0 as the major fatty acids supported affiliation of the new isolate to the genus Paenibacillus. Based on these data, isolate XJ259T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus algorifonticola sp. nov. is proposed. The type strain is XJ259T ( = CGMCC 1.10223T  = JCM 16598T).

scholarly journals Pedobacter boryungensis sp. nov., isolated from soil

2012 ◽  
Vol 62 (1) ◽  
pp. 13-17 ◽  
Author(s):  
Yong-Taek Jung ◽  
Soo-Young Lee ◽  
Won-Chan Choi ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Type Strains

A Gram-negative, non-sporulating, non-flagellated rod, designated BR-9T, was isolated from soil collected on the Korean peninsula. Strain BR-9T grew optimally at pH 6.0–7.0, at 30 °C and in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BR-9T belonged to the genus Pedobacter and clustered with Pedobacter insulae DS-139T and Pedobacter koreensis WPCB189T. Strain BR-9T exhibited 98.2 and 97.5 % 16S rRNA gene sequence similarity with P. insulae DS-139T and P. koreensis WPCB189T, respectively, and <96.7 % sequence similarity with the type strains of other species in the genus Pedobacter. Strain BR-9T contained MK-7 as the predominant menaquinone and iso-C15 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) as the major fatty acids. The DNA G+C content of strain BR-9T was 38.5 mol%. DNA–DNA relatedness between strain BR-9T and P. insulae DS-139T and P. koreensis KCTC 12536T was 3.4–4.2 %, which indicated that the isolate was genetically distinct from these type strains. Strain BR-9T was also distinguishable by differences in phenotypic properties. On the basis of the data presented, strain BR-9T is considered to represent a novel species of the genus Pedobacter, for which the name Pedobacter boryungensis sp. nov. is proposed. The type strain is BR-9T ( = KCTC 23344T  = CCUG 60024T).

scholarly journals Flavobacterium terrigena sp. nov., isolated from soil

2007 ◽  
Vol 57 (5) ◽  
pp. 947-950 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Jung-Sook Lee ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
Type Strains

A Gram-negative, rod-shaped, Flavobacterium-like bacterial strain, DS-20T, was isolated from soil from the island of Dokdo, Korea, and subjected to a polyphasic taxonomic study. Strain DS-20T grew optimally at pH 6.5–7.0 and 25 °C. It contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C17 : 0 3-OH and iso-C17 : 1 ω9c as the major fatty acids. The DNA G+C content was 38.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DS-20T belonged to the genus Flavobacterium. Levels of 16S rRNA gene sequence similarity between strain DS-20T and the type strains of recognized Flavobacterium species were below 94.9 %. Strain DS-20T differed from phylogenetically related Flavobacterium species in several phenotypic characteristics. On the basis of its phenotypic and phylogenetic distinctiveness, strain DS-20T was classified in the genus Flavobacterium as representing a novel species, for which the name Flavobacterium terrigena sp. nov. is proposed. The type strain is DS-20T (=KCTC 12761T=DSM 17934T).

Chryseobacterium yonginense sp. nov., isolated from a mesotrophic artificial lake

2011 ◽  
Vol 61 (6) ◽  
pp. 1413-1417 ◽  
Author(s):  
Yochan Joung ◽  
Kiseong Joh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
16S Rrna Gene Sequences ◽  
Artificial Lake ◽  
Gram Staining

A Gram-staining-negative, non-motile, yellow-pigmented bacterial strain, designated HMD1043T, was isolated from a mesotrophic artificial lake in Korea. The major fatty acids were anteiso-C15 : 0 (28.3 %), iso-C15 : 0 (22.9 %), summed feature 9 (comprising iso-C17 : 1ω9c and/or 10-methyl C16 : 0; 8.8 %) and iso-C13 : 0 (5.3 %). The DNA G+C content was 31.3 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HMD1043T formed a lineage within the genus Chryseobacterium and was most closely related to Chryseobacterium antarcticum AT1013T (96.8 % 16S rRNA gene sequence similarity) and Chryseobacterium jeonii AT1047T (96.4 %). On the basis of the evidence presented in this study, strain HMD1043T is described as belonging to a novel species of the genus Chryseobacterium, for which the name Chryseobacterium yonginense sp. nov. is proposed. The type strain is HMD1043T ( = KCTC 22744T  = CECT 7547T).

scholarly journals Mesoflavibacter aestuarii sp. nov., a zeaxanthin-producing marine bacterium isolated from seawater

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1932-1937 ◽  
Author(s):  
Ji Hee Lee ◽  
Yeoung Min Hwang ◽  
Keun Sik Baik ◽  
Kap Seong Choi ◽  
Jong-Ok Ka ◽  
...  
Keyword(s):  
Marine Bacterium ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Carotenoid Pigment ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Gwangyang Bay

An orange, rod-shaped, Gram-reaction-negative, aerobic and gliding bacterial strain devoid of flagella, designated strain KYW614T, was isolated from seawater collected from Gwangyang Bay, Republic of Korea. Zeaxanthin was the major carotenoid pigment produced and flexirubin-type pigments were not produced. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain KYW614T belonged to the family Flavobacteriaceae and it was most closely related to Mesoflavibacter zeaxanthinifaciens TD-ZX30T (96.5 %, sequence similarity). The predominant cellular fatty acids of strain KYW614T were iso-C15 : 1 G (10.5 %), summed feature 3 (C16 : 1ω7c/C16 : 1ω6c; 10.0 %), iso-C15 : 0 (9.5 %), C15 : 0 (7.5 %) and iso-C17 : 0 3-OH (7.4 %). MK-6 was the only isoprenoid quinone and the DNA G+C content was 32.6 mol%. Data from a polyphasic taxonomic study suggested that the isolate represents a novel species in the genus Mesoflavibacter , for which the name Mesoflavibacter aestuarii sp. nov. is proposed. The type strain is KYW614T ( = KCTC 32269T = JCM 19524T).

Carnobacterium iners sp. nov., a psychrophilic, lactic acid-producing bacterium from the littoral zone of an Antarctic pond

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1370-1375 ◽  
Author(s):  
Isabel Snauwaert ◽  
Bart Hoste ◽  
Katrien De Bruyne ◽  
Karolien Peeters ◽  
Luc De Vuyst ◽  
...  
Keyword(s):  
Lactic Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Littoral Zone ◽  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

Two lactic acid-producing, Gram-stain-positive rods were isolated from a microbial mat actively growing in the littoral zone of an Antarctic lake (Forlidas Pond) in the Pensacola mountains and studied using a polyphasic taxonomic approach. The isolates were examined by phylogenetic analysis of the 16S rRNA gene, multilocus sequence analysis of pheS, rpoA and atpA, and biochemical and genotypic characteristics. One strain, designated LMG 26641, belonged to Carnobacterium alterfunditum and the other strain, designated LMG 26642T, could be assigned to a novel species, with Carnobacterium funditum DSM 5970T as its closest phylogenetic neighbour (99.2 % 16S rRNA gene sequence similarity). Carnobacterium iners sp. nov. could be distinguished biochemically from other members of the genus Carnobacterium by the lack of acid production from carbohydrates. DNA–DNA relatedness confirmed that strain LMG 26642T represented a novel species, for which we propose the name Carnobacterium iners sp. nov. (type strain is LMG 26642T  = CCUG 62000T).

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