scholarly journals Campylobacter canadensis sp. nov., from captive whooping cranes in Canada

2007 ◽  
Vol 57 (11) ◽  
pp. 2636-2644 ◽  
Author(s):  
G. Douglas Inglis ◽  
Bryanne M. Hoar ◽  
Douglas P. Whiteside ◽  
Douglas W. Morck
Keyword(s):  
16S Rrna ◽  
Novel Species ◽  
Sequence Similarity ◽  
23S Rrna ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
Specific Pcr ◽  
Whooping Cranes ◽  
23S Rrna Gene ◽  
Species Specific

Ten isolates of an unknown Campylobacter species were isolated from cloacal swabs obtained from captive adult whooping cranes (Grus americana). All isolates were identified as Campylobacter based on generic PCR and grouped with other Campylobacter species based on 23S rRNA gene sequence. None of the isolates could be identified by species-specific PCR for known taxa, and all ten isolates formed a robust clade that was very distinct from known Campylobacter species based on 16S rRNA, rpoB and cpn60 gene sequences. The results of 16S rRNA gene nucleotide sequence (≤92 % sequence similarity to recognized Campylobacter species) and genomic DNA (no detectable relatedness) analyses were consistent with novel species status. Cells of the Campylobacter from whooping cranes were uniflagellar and typically sigmoid to allantoid in shape (0.48 μm wide and 2.61 μm long), but also spheroid to coccoid (0.59 μm wide and 0.73 μm long). The bacterium was oxidase-positive, able to reduce nitrite, able to grow at 3 ° and 42 °C, and grew anaerobically, as well as in an atmosphere devoid of H2, and on MacConkey agar. It was not α-haemolytic and was negative for hippurate and indoxyl acetate hydrolysis and alkaline phosphatase. It also was susceptible to cephalotin and was unable to grow on nutrient agar, on a medium containing 3.5 % NaCl or in ambient O2. The bacterium was unable to grow at 25 °C and growth was negative or very restricted at 30 °C. Fluorescent amplified fragment length polymorphism analysis indicated that nine of the recovered isolates were genetically distinct. A species-specific primer set targeting the cpn60 gene was developed. The name Campylobacter canadensis sp. nov. is proposed for the novel species, with the type strain L266T (=CCUG 54429T =LMG 24001T).

Psychrobacter sanguinis sp. nov., recovered from four clinical specimens over a 4-year period

2012 ◽  
Vol 62 (1) ◽  
pp. 49-54 ◽  
Author(s):  
Samantha E. Wirth ◽  
Héctor L. Ayala-del-Río ◽  
Jocelyn A. Cole ◽  
Donna J. Kohlerschmidt ◽  
Kimberlee A. Musser ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Sequence Similarity ◽  
23S Rrna ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
23S Rrna Gene ◽  
Reference Specimens

An analysis of 16S rRNA gene sequences from archived clinical reference specimens identified a novel species of the genus Psychrobacter, of which four strains have been independently isolated from human blood. On the basis of 16S rRNA gene sequence similarity, the closest relatives with validly published names were Psychrobacter arenosus R7T (98.7 %), P. pulmonis CECT 5989T (97.7 %), P. faecalis Iso-46T (97.6 %) and P. lutiphocae IMMIB L-1110T (97.2 %). Maximum-likelihood phylogenetic analysis of 16S rRNA gene sequences showed that the isolates belonged to the genus Psychrobacter and were members of a cluster associated with Psychrobacter sp. PRwf-1, isolated from a silk snapper fish. DNA–DNA relatedness and partial 23S rRNA gene sequences also supported the finding that the isolates belonged to a species distinct from its closest phylogenetic neighbours. The predominant cellular fatty acids were C18 : 1ω9c, C16 : 0, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), summed feature 5 (C18 : 2ω6,9c and/or anteiso-C18 : 0) and C18 : 0. Biochemical and morphological analysis further supported the assignment of the four isolates to a novel species. The name Psychrobacter sanguinis sp. nov. is proposed. The type strain is 13983T ( = DSM 23635T = CCUG 59771T).

scholarly journals Pantoea allii sp. nov., isolated from onion plants and seed

2011 ◽  
Vol 61 (4) ◽  
pp. 932-937 ◽  
Author(s):  
Carrie L. Brady ◽  
Teresa Goszczynska ◽  
Stephanus N. Venter ◽  
Ilse Cleenwerck ◽  
Paul De Vos ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
Rrna Gene Sequence

Eight yellow-pigmented, Gram-negative, rod-shaped, oxidase-negative, motile, facultatively anaerobic bacteria were isolated from onion seed in South Africa and from an onion plant exhibiting centre rot symptoms in the USA. The isolates were assigned to the genus Pantoea on the basis of phenotypic and biochemical tests. 16S rRNA gene sequence analysis and multilocus sequence analysis (MLSA), based on gyrB, rpoB, infB and atpD sequences, confirmed the allocation of the isolates to the genus Pantoea. MLSA further indicated that the isolates represented a novel species, which was phylogenetically most closely related to Pantoea ananatis and Pantoea stewartii. Amplified fragment length polymorphism analysis also placed the isolates into a cluster separate from P. ananatis and P. stewartii. Compared with type strains of species of the genus Pantoea that showed >97 % 16S rRNA gene sequence similarity with strain BD 390T, the isolates exhibited 11–55 % whole-genome DNA–DNA relatedness, which confirmed the classification of the isolates in a novel species. The most useful phenotypic characteristics for the differentiation of the isolates from their closest phylogenetic neighbours are production of acid from amygdalin and utilization of adonitol and sorbitol. A novel species, Pantoea allii sp. nov., is proposed, with type strain BD 390T ( = LMG 24248T).

scholarly journals Design of PCR assays to specifically detect and identify 37 Lactobacillus species in a single 96 well plate

2020 ◽  
Author(s):  
Eiseul Kim ◽  
Seung-Min Yang ◽  
Bora Lim ◽  
Si Hong Park ◽  
Bryna Rackerby ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Genomic Analysis ◽  
23S Rrna ◽  
Lactobacillus Species ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Gene Sequences ◽  
23S Rrna Gene ◽  
Species Specific

Abstract Background Lactobacillus species are used as probiotics and play an important role in fermented food production. However, use of 16S rRNA gene sequences as standard markers for the differentiation of Lactobacillus species offers a very limited scope, as several species of Lactobacillus share similar 16S rRNA gene sequences. In this study, we developed a rapid and accurate method based on comparative genomic analysis for the simultaneous identification of 37 Lactobacillus species that are commonly used in probiotics and fermented foods. Results To select species-specific sequences or genes, a total of 180 Lactobacillus genome sequences were compared using Python scripts. In 14 out of 37 species, species-specific sequences could not be found due to the similarity of the 16S–23S rRNA gene. Selected unique genes were obtained using comparative genomic analysis and all genes were confirmed to be specific for 52,478,804 genomes via in silico analysis; they were found not to be strain-specific, but to exist in all strains of the same species. Species-specific primer pairs were designed from the selected 16S–23S rRNA gene sequences or unique genes of species. The specificity of the species-specific primer pairs was confirmed using reference strains, and the accuracy and efficiency of the polymerase chain reaction (PCR) with the standard curve were confirmed. The PCR method developed in this study is able to accurately differentiate species that were not distinguishable using the 16S rRNA gene alone. This PCR assays were designed to detect and identify 37 Lactobacillus species. The developed method was then applied in the monitoring of 19 probiotics and 12 dairy products. The applied tests confirmed that the species detected in 17 products matched those indicated on their labels, whereas the remaining products contained species other than those appearing on the label. Conclusions The method developed in this study is able to rapidly and accurately distinguish different species of Lactobacillus , and can be used to monitor specific Lactobacillus species in foods such as probiotics and dairy products.

scholarly journals Identification and Detection ofStenotrophomonas maltophilia by rRNA-Directed PCR

2000 ◽  
Vol 38 (12) ◽  
pp. 4305-4309 ◽  
Author(s):  
Paul W. Whitby ◽  
Karen B. Carter ◽  
Jane L. Burns ◽  
James A. Royall ◽  
John J. LiPuma ◽  
...  
Keyword(s):  
Burkholderia Cepacia ◽  
Direct Detection ◽  
Pcr Primers ◽  
Laboratory Culture ◽  
23S Rrna ◽  
Rrna Gene ◽  
Specific Pcr ◽  
23S Rrna Gene ◽  
Susceptible Populations ◽  
Species Specific

Stenotrophomonas maltophilia has recently emerged as an important nosocomial pathogen in immunocompromised patients, in transplant recipients, and in persons with cystic fibrosis (CF). While this organism is nonpathogenic in healthy individuals, it is increasingly associated with morbidity and mortality in susceptible populations. Recent studies have indicated that for approximately 10% of CF patients with moderate lung disease, S. maltophiliacan be cultured from respiratory tract secretions. Identification ofS. maltophilia can be problematic, and analysis of isolates from the Burkholderia cepacia Research Laboratory and Repository showed that several isolates presumptively identified asB. cepacia by clinical microbiology laboratories were in fact S. maltophilia. To overcome the problems associated with definitive identification, we developed species-specific PCR (SS-PCR) primers, designated SM1 and SM4, directed to the 23S rRNA gene, and tested their utility to accurately identify S. maltophilia directly from sputum. The SS-PCR was developed and tested against a panel of 112 S. maltophilia isolates collected from diverse geographic locations. To test for specificity, 43 isolates from 17 different species were analyzed. PCR with the SM1-SM4 primer pair and isolated genomic DNA as a template resulted in amplification of a band from all S. maltophilia isolates and was uniformly negative for all other species tested, yielding a sensitivity and a specificity of 100% for the SS-PCR. The utility of the SS-PCR to directly identify S. maltophilia in sputum was examined. Thirteen expectorated sputum samples from CF patients were analyzed by SS-PCR. Three samples were PCR positive, in complete concordance with the conventional laboratory culture. Thus, we have developed an SS-PCR protocol that can rapidly and accurately identifyS. maltophilia isolates and which can be used for the direct detection of this organism in CF patient sputum.

scholarly journals Species-Specific PCR for Identification of Common Contaminant Mollicutes in Cell Culture

2001 ◽  
Vol 67 (7) ◽  
pp. 3195-3200 ◽  
Author(s):  
Fanrong Kong ◽  
Gregory James ◽  
Susanna Gordon ◽  
Anna Zelynski ◽  
Gwendolyn L. Gilbert
Keyword(s):  
16S Rrna ◽  
Cell Cultures ◽  
Bacterial Species ◽  
Intergenic Spacer ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Specific Pcr ◽  
Species Specific

ABSTRACT Mycoplasma arginini, M. fermentans, M. hyorhinis, M. orale, and Acholeplasma laidlawii are the members of the class Mollicutes most commonly found in contaminated cell cultures. Previous studies have shown that the published PCR primer pairs designed to detect mollicutes in cell cultures are not entirely specific. The 16S rRNA gene, the 16S-23S rRNA intergenic spacer region, and the 5′ end of the 23S rRNA gene, as a whole, are promising targets for design of mollicute species-specific primer pairs. We analyzed the 16S rRNA genes, the 16S-23S rRNA intergenic spacer regions, and the 5′ end of the 23S rRNA genes of these mollicutes and developed PCR methods for species identification based on these regions. Using high melting temperatures, we developed a rapid-cycle PCR for detection and identification of contaminant mollicutes. Previously published, putative mollicute-specific primers amplified DNA from 73 contaminated cell lines, but the presence of mollicutes was confirmed by species-specific PCR in only 60. Sequences of the remaining 13 amplicons were identified as those of gram-positive bacterial species. Species-specific PCR primers are needed to confirm the presence of mollicutes in specimens and for identification, if required.

scholarly journals Design of PCR assays to specifically detect and identify 37 Lactobacillus species in a single 96 well plate

2020 ◽  
Author(s):  
Eiseul Kim ◽  
Seung-Min Yang ◽  
Bora Lim ◽  
Si Hong Park ◽  
Bryna Rackerby ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Genomic Analysis ◽  
23S Rrna ◽  
Lactobacillus Species ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Gene Sequences ◽  
23S Rrna Gene ◽  
Species Specific

Abstract Background Lactobacillus species are used as probiotics and play an important role in fermented food production. However, use of 16S rRNA gene sequences as standard markers for the differentiation of Lactobacillus species offers a very limited scope, as several species of Lactobacillus share similar 16S rRNA gene sequences. In this study, we developed a rapid and accurate method based on comparative genomic analysis for the simultaneous identification of 37 Lactobacillus species that are commonly used in probiotics and fermented foods. Results To select species-specific sequences or genes, a total of 180 Lactobacillus genome sequences were compared using Python scripts. In 14 out of 37 species, species-specific sequences could not be found due to the similarity of the 16S–23S rRNA gene. Selected unique genes were obtained using comparative genomic analysis and all genes were confirmed to be specific for 52,478,804 genomes via in silico analysis; they were found not to be strain-specific, but to exist in all strains of the same species. Species-specific primer pairs were designed from the selected 16S–23S rRNA gene sequences or unique genes of species. The specificity of the species-specific primer pairs was confirmed using reference strains, and the accuracy and efficiency of the polymerase chain reaction (PCR) with the standard curve were confirmed. The PCR method developed in this study is able to accurately differentiate species that were not distinguishable using the 16S rRNA gene alone. This PCR assays were designed to detect and identify 37 Lactobacillus species. The developed method was then applied in the monitoring of 19 probiotics and 12 dairy products. The applied tests confirmed that the species detected in 17 products matched those indicated on their labels, whereas the remaining products contained species other than those appearing on the label. Conclusions The method developed in this study is able to rapidly and accurately distinguish different species of Lactobacillus , and can be used to monitor specific Lactobacillus species in foods such as probiotics and dairy products.

Moraxella bovoculi sp. nov., isolated from calves with infectious bovine keratoconjunctivitis

2007 ◽  
Vol 57 (4) ◽  
pp. 789-795 ◽  
Author(s):  
John A. Angelos ◽  
Phillip Q. Spinks ◽  
Louise M. Ball ◽  
Lisle W. George
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Strong Support ◽  
Housekeeping Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Infectious Bovine Keratoconjunctivitis ◽  
23S Rrna Gene ◽  
Moraxella Bovoculi

Eighteen isolates of a Gram-negative coccus (strain 237T) were cultured from the eyes of dairy and beef calves affected with infectious bovine keratoconjunctivitis (IBK; ‘pinkeye’) in northern California, USA, during summer 2002. These isolates had near full-length (1397 bp) 16S rRNA gene sequences that clustered into three groups with 99.9 % sequence similarity. On the basis of 16S rRNA gene sequence, the isolates were most closely associated with Moraxella bovis and Moraxella ovis in clade I of the classical moraxellae. Biochemically, the novel isolates could be distinguished from the other members of the genus Moraxella isolated from animals on the basis of phenylalanine deaminase activity. The results of partial sequence analysis of six housekeeping genes, the 16S–23S rRNA gene interspacer region and partial 23S rRNA gene provide strong support for the inclusion of these isolates in a novel taxon, for which the name Moraxella bovoculi sp. nov. is proposed. The type strain is strain 237T (=ATCC BAA-1259T=CCUG 52049T).

scholarly journals Herbaspirillum hiltneri sp. nov., isolated from surface-sterilized wheat roots

2006 ◽  
Vol 56 (6) ◽  
pp. 1341-1348 ◽  
Author(s):  
Michael Rothballer ◽  
Michael Schmid ◽  
Ilona Klein ◽  
Andreas Gattinger ◽  
Sabine Grundmann ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Sequence Data ◽  
Novel Species ◽  
23S Rrna ◽  
Rrna Gene ◽  
Wheat Roots ◽  
23S Rrna Gene ◽  
Phylogenetic Resolution

The genus Herbaspirillum of the Betaproteobacteria mainly comprises diazotrophic bacteria with a potential for endophytic and systemic colonization of a variety of plants. The plant-associated bacterial isolates N3T, N5 and N9 were derived from surface-sterilized wheat roots. After phylogenetic analysis of 16S rRNA gene sequence data the isolates could be allocated to the genus Herbaspirillum, and 99.9 % similarity to the sequence of Herbaspirillum lusitanum P6-12T was found. A set of 16S rRNA gene-targeted oligonucleotide probes was developed for the identification of the three novel isolates and H. lusitanum (Hhilu446), and for the specific detection of several other Herbaspirillum species described recently. For higher phylogenetic resolution, the 23S rRNA gene sequences of all members of the genus was sequenced and used to construct a phylogenetic tree. Isolates N3T, N5 and N9 formed a group that was distinct from all other Herbaspirillum species. In addition, isolate N3T and H. lusitanum P6-12T exhibited a DNA–DNA hybridization value of only 25 %. The value for DNA–DNA hybridization between N3T and other members of the genus Herbaspirillum was between 14 and 32 %; DNA–DNA hybridization between strain N3T and isolates N5 and N9 produced values above 95 %. This places the three isolates as representatives of a novel species within the genus Herbaspirillum. A Biolog GN2 assay supported this conclusion. The major fatty acids were C16 : 1 ω7c, C16 : 0 and C18 : 1 ω7c, and the DNA G+C content ranged from 60.9 to 61.5 mol%. Therefore these three isolates should be classified within a novel species, for which the name Herbaspirillum hiltneri sp. nov. is proposed. The type strain is N3T (=DSM 17495T=LMG 23131T).

scholarly journals Phenotypic and molecular characterisation of a novel species, Mycobacterium hubeiense sp., isolated from the sputum of a patient with secondary tuberculosis in Hubei of China

2020 ◽  
Vol 148 ◽  
Author(s):  
Xiaoli Yu ◽  
Hui Zheng ◽  
Fang Zhou ◽  
Peng Hu ◽  
Hualin Wang ◽  
...  
Keyword(s):  
16S Rrna ◽  
High Performance ◽  
Antimicrobial Agents ◽  
Novel Species ◽  
Sequence Similarity ◽  
Personalised Medicine ◽  
Drug Susceptibility Testing ◽  
Treatment Center ◽  
23S Rrna ◽  
Rrna Gene

Abstract A new fast-growing mycobacterium, designated strain QGD101T, was isolated from the sputum of an 84-year-old man suspected of tuberculosis in Wuhan Medical Treatment Center, Hubei, China. This strain was a gram-staining-negative, aerobic, non-spore-forming and catalase-positive bacterium, which was further identified as the NTM by PNB and TCH tests. The moxifloxacin and levofloxacin exhibited strong suppressing function against QGD101T with MIC values of 0.06 and 0.125 µg/ml after drug susceptibility testing of six main antimicrobial agents on mycobacteria. Based on the sequence analysis of 16S rRNA, rpoB, hsp65 and 16S-23S rRNA internal transcribed spacer, the strain QGD101T could not be identified to a species level. Mycobacterium moriokaense ATCC43059T that shared the highest 16S rRNA gene sequence similarity (98%) with strain QGD101T was actually different in genomes average nucleotide identity (78.74%). In addition, the major cellular fatty acids of QGD101T were determined as C18:1ω9c, C16:0 and C18:2ω6c. The DNA G + C content was 64.9% measured by high performance liquid chromatography. Therefore, the phenotypic and genotypic characterisation of this strain led us to the conclusion that it represents a novel species of mycobacteria, for which the name Mycobacterium hubeiense sp. nov. (type strain QGD101T = CCTCCAA 2017003T = KCTC39927T) was proposed. Thus, the results of this study are very significant for the clinical diagnosis of tuberculosis and future personalised medicine.

scholarly journals Atypical Helicobacter canadensis Strains Associated with Swine

2006 ◽  
Vol 72 (6) ◽  
pp. 4464-4471 ◽  
Author(s):  
G. Douglas Inglis ◽  
Malcolm McConville ◽  
Anno de Jong
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Fragment Length Polymorphism ◽  
23S Rrna ◽  
Rrna Gene ◽  
Specific Pcr ◽  
Cardinal Characteristic ◽  
Swine Feces ◽  
Species Specific ◽  
Genomic Typing

ABSTRACT Forty-two Helicobacter isolates were isolated from swine feces in The Netherlands and Denmark. All 12 isolates sequenced (16S rRNA gene) formed a robust clade with Helicobacter canadensis (∼99% similarity). Species-specific PCR indicated that all of the isolates were H. canadensis isolates. Although the appearance of the porcine isolates was similar to the appearance of H. canadensis, only one of these isolates was able to hydrolyze indoxyl acetate, a cardinal characteristic of this taxon. Examination of the 23S rRNA and hsp60 genes revealed high levels of similarity between the porcine isolates and H. canadensis. However, amplified fragment length polymorphism genomic typing showed that isolates recovered from swine feces were genetically distinct from H. canadensis strains obtained from humans and geese.

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