scholarly journals Identification of Enterococci from Broiler Products and a Broiler Processing Plant and Description ofEnterococcus viikkiensissp. nov.

2010 ◽  
Vol 77 (4) ◽  
pp. 1196-1203 ◽  
Author(s):  
Riitta Rahkila ◽  
Per Johansson ◽  
Elina Säde ◽  
Johanna Björkroth
Keyword(s):  
Numerical Analysis ◽  
Housekeeping Gene ◽  
Trna Synthetase ◽  
Rrna Gene ◽  
Processing Plant ◽  
Gene Sequence Analysis ◽  
Enterococcal Species ◽  
Species Specific ◽  
Polyphasic Taxonomic Approaches ◽  
Phylogenetic Neighbor

ABSTRACTIn two previous studies dealing with lactic acid bacteria (LAB) from modified-atmosphere-packaged (MAP) broiler products and a broiler processing plant, several isolates remained unidentified. According to 16S rRNA gene sequence analysis, 36 isolates were assigned to the genusEnterococcus.Numerical analysis of combined HindIII and EcoRI ribopatterns of these isolates resulted in species-specific clusters that were congruent with the clusters obtained by both DNA-directed RNA polymerase subunit A (rpoA) and phenylalanyl-tRNA synthetase α chain (pheS) housekeeping gene analyses. In the analyses, a group of five isolates distinct from any known enterococcal species clustered together. The five isolates were positioned in theEnterococcus aviumgroup, withE. devrieseibeing the closest phylogenetic neighbor. The DNA-DNA hybridization levels withE. devrieseiranged from 28.8 to 54.3% and indicated that these strains represented a novel species. The nameEnterococcus viikkiensissp. nov. is proposed, with strain DSM 24043T(LMG 26075T) being the type strain. Our study demonstrated that the identification of enterococci within theE. aviumphylogenetic group demands polyphasic taxonomic approaches. TherpoAandpheSgene similarities (99.0 to 99.2% and 94.3 to 95.4%, respectively) betweenE. viikkiensisand its closest phylogenetic neighbor,E. devriesei, were higher than those previously reported within the enterococci. In addition, the phenotypic profiles of the species in theE. aviumgroup were also highly similar, and some traits were found to be misleading for enterococci, such asE. viikkiensisdoes not grow at 45°C. The numerical analysis of combined HindIII and EcoRI ribopatterns was of considerable assistance in distinguishing enterococcal species within theE. aviumgroup.

scholarly journals Enterococcus aquimarinus sp. nov., isolated from sea water

2005 ◽  
Vol 55 (5) ◽  
pp. 2183-2187 ◽  
Author(s):  
Pavel Švec ◽  
Marc Vancanneyt ◽  
Luc A. Devriese ◽  
Sabri M. Naser ◽  
Cindy Snauwaert ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Gene Sequence ◽  
Sea Water ◽  
Genomic Analysis ◽  
Housekeeping Gene ◽  
Culture Collection ◽  
Rrna Gene ◽  
Gene Sequence Analysis ◽  
Enterococcal Species ◽  
Enterococcus Italicus

Two enterococcal strains LMG 16607T and LMG 16612 originating from sea water were analysed in a polyphasic taxonomic study. Both strains, assigned as Enterococcus sp. in the BCCM/LMG culture collection, possessed analogous protein profiles, but these were different from all other enterococcal species. 16S rRNA gene sequence analysis of one strain showed the highest similarity, 96·9–96·1 %, with its closest phylogenetic neighbours Enterococcus saccharolyticus, Enterococcus sulfureus, Enterococcus saccharominimus and Enterococcus italicus. Further genomic analysis by (GTG)5-PCR fingerprinting and sequence analysis of the housekeeping gene phenylalanyl-tRNA synthase (pheS) and distinct biochemical features confirmed that the two strains represent a novel enterococcal species for which the name Enterococcus aquimarinus sp. nov. is proposed. The type strain is LMG 16607T (=CCM 7283T).

scholarly journals Enterococcus silesiacus sp. nov. and Enterococcus termitis sp. nov.

2006 ◽  
Vol 56 (3) ◽  
pp. 577-581 ◽  
Author(s):  
Pavel Švec ◽  
Marc Vancanneyt ◽  
Ivo Sedláček ◽  
Sabri M. Naser ◽  
Cindy Snauwaert ◽  
...  
Keyword(s):  
Housekeeping Gene ◽  
Species Group ◽  
Cell Protein ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
The Novel ◽  
Gene Sequence Analysis ◽  
Novel Taxa ◽  
Respective Type ◽  
Type Strains

Three enterococci constituted two aberrant branches after numerical analysis of (GTG)5-PCR fingerprints: analogous patterns were found for two water isolates, strains W213 and W442T, and a separate position was found for an isolate from the gut of a termite, strain LMG 8895T. 16S rRNA gene sequence analysis classified all three strains in the Enterococcus faecalis species group. Further sequencing analysis of the housekeeping gene pheS (encoding the phenylalanyl-tRNA synthase α-subunit) and whole-cell-protein analysis confirmed a distinct position for the two water isolates and the termite strain, respectively. DNA–DNA hybridization experiments and distinct phenotypic features between the strains studied and representatives of the E. faecalis species group confirmed novel species status, respectively, for the two water isolates, strains W213 and W442T, and for strain LMG 8895T. The names Enterococcus silesiacus sp. nov. and Enterococcus termitis sp. nov. are proposed for the novel taxa, with W442T (=CCM 7319T=LMG 23085T) and LMG 8895T (=CCM 7300T) as the respective type strains.

Echinococcus multilocularis in a Eurasian lynx (Lynx lynx) in Turkey

Parasitology ◽  
2018 ◽  
Vol 145 (9) ◽  
pp. 1147-1150 ◽  
Author(s):  
Hamza Avcioglu ◽  
Esin Guven ◽  
Ibrahim Balkaya ◽  
Ridvan Kirman
Keyword(s):  
Echinococcus Multilocularis ◽  
Pcr Analysis ◽  
12S Rrna ◽  
Rrna Gene ◽  
Lynx Lynx ◽  
Eurasian Lynx ◽  
The North ◽  
Specific Pcr ◽  
Gene Sequence Analysis ◽  
Species Specific

AbstractEchinococcus multilocularis is the causative agent of alveolar echinococcosis (AE), one of the most threatening zoonoses in Eurasia. Human AE is widespread in the Erzurum region of Turkey, but the situation of the disease in intermediate and definitive hosts is unknown. A Eurasian lynx (Lynx lynx) was killed in a traffic accident in the north of Erzurum, and was taken to our laboratory. Sedimentation and counting technique (SCT), DNA isolation and polymerase chain reaction (PCR) analysis were performed. The SCT results showed that the lynx was infected with E. multilocularis with a medium (745 worms) worm burden. The DNA of adult worms obtained from the lynx was analyzed with a species-specific PCR, and the worms were confirmed to be E. multilocularis by 12S rRNA gene sequence analysis. This is the first report of E. multilocularis from Eurasian lynx in Turkey.

scholarly journals Anaerobic Degradation of Flavonoids by Clostridium orbiscindens

2003 ◽  
Vol 69 (10) ◽  
pp. 5849-5854 ◽  
Author(s):  
Lilian Schoefer ◽  
Ruchika Mohan ◽  
Andreas Schwiertz ◽  
Annett Braune ◽  
Michael Blaut
Keyword(s):  
Propionic Acid ◽  
Human Subjects ◽  
Dry Mass ◽  
Rrna Gene ◽  
Glycosidic Bonds ◽  
Degrading Bacterium ◽  
Gene Sequence Analysis ◽  
Specific Oligonucleotide Probe ◽  
Species Specific ◽  
Human Intestinal Tract

ABSTRACT An anaerobic, quercetin-degrading bacterium was isolated from human feces and identified as Clostridium orbiscindens by comparative 16S rRNA gene sequence analysis. The organism was tested for its ability to transform several flavonoids. The isolated C. orbiscindens strain converted quercetin and taxifolin to 3,4-dihydroxyphenylacetic acid; luteolin and eriodictyol to 3-(3,4-dihydroxyphenyl)propionic acid; and apigenin, naringenin, and phloretin to 3-(4-hydroxyphenyl)propionic acid, respectively. Genistein and daidzein were not utilized. The glycosidic bonds of luteolin-3-glucoside, luteolin-5-glucoside, naringenin-7-neohesperidoside (naringin), quercetin-3-glucoside, quercetin-3-rutinoside (rutin), and phloretin-2′-glucoside were not cleaved. Based on the intermediates and products detected, pathways for the degradation of the flavonol quercetin and the flavones apigenin and luteolin are proposed. To investigate the numerical importance of C. orbiscindens in the human intestinal tract, a species-specific oligonucleotide probe was designed and tested for its specificity. Application of the probe to fecal samples from 10 human subjects proved the presence of C. orbiscindens in 8 out of the 10 samples tested. The numbers ranged from 1.87 × 108 to 2.50 × 109 cells g of fecal dry mass−1, corresponding to a mean count of 4.40 × 108 cells g of dry feces−1.

scholarly journals Reclassification of Lactobacillus brevis strains LMG 11494 and LMG 11984 as Lactobacillus parabrevis sp. nov.

2006 ◽  
Vol 56 (7) ◽  
pp. 1553-1557 ◽  
Author(s):  
Marc Vancanneyt ◽  
Sabri M. Naser ◽  
Katrien Engelbeen ◽  
Marjan De Wachter ◽  
Roel Van der Meulen ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Lactobacillus Brevis ◽  
Housekeeping Gene ◽  
Rrna Gene ◽  
Gene Encoding ◽  
Phylogenetic Affiliation ◽  
Nearest Neighbours ◽  
Species Specific

A polyphasic study revealed taxonomic heterogeneity among reference strains of the species Lactobacillus brevis. Representative strains of L. brevis and related taxa were investigated by partial sequence analysis of the housekeeping gene encoding the alpha-subunit of phenylalanyl-tRNA synthase (pheS). Species-specific clusters were delineated for all taxa studied except for two L. brevis strains, LMG 11494 and LMG 11984, respectively isolated from cheese and wheat, which occupied a distinct position. Their phylogenetic affiliation was determined using 16S rRNA gene sequence analysis and it was found that both strains (with 99.9 % gene sequence similarity between them) belonged to the Lactobacillus buchneri group, with nearest neighbours Lactobacillus hammesii and L. brevis (gene sequence similarities of 99.2 and 98.1 %, respectively). Further genotypic and phenotypic studies, including fluorescent amplified fragment length polymorphism, DNA–DNA hybridization and DNA G+C content, clearly demonstrated that the two strains represent a single novel taxon for which the name Lactobacillus parabrevis sp. nov. is proposed (type strain LMG 11984T=ATCC 53295T).

scholarly journals Development and Validation of a Nested-PCR-Denaturing Gradient Gel Electrophoresis Method for Taxonomic Characterization of Bifidobacterial Communities

2003 ◽  
Vol 69 (11) ◽  
pp. 6380-6385 ◽  
Author(s):  
R. Temmerman ◽  
L. Masco ◽  
T. Vanhoutte ◽  
G. Huys ◽  
J. Swings
Keyword(s):  
Nested Pcr ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Temporal Changes ◽  
Rrna Gene ◽  
Specific Pcr ◽  
Gradient Gel Electrophoresis ◽  
Species Specific ◽  
Taxonomic Characterization

ABSTRACT The taxonomic characterization of a bacterial community is difficult to combine with the monitoring of its temporal changes. None of the currently available identification techniques are able to visualize a “complete” community, whereas techniques designed for analyzing bacterial ecosystems generally display limited or labor-intensive identification potential. This paper describes the optimization and validation of a nested-PCR-denaturing gradient gel electrophoresis (DGGE) approach for the species-specific analysis of bifidobacterial communities from any ecosystem. The method comprises a Bifidobacterium-specific PCR step, followed by purification of the amplicons that serve as template DNA in a second PCR step that amplifies the V3 and V6-V8 regions of the 16S rRNA gene. A mix of both amplicons is analyzed on a DGGE gel, after which the band positions are compared with a previously constructed database of reference strains. The method was validated through the analysis of four artificial mixtures, mimicking the possible bifidobacterial microbiota of the human and chicken intestine, a rumen, and the environment, and of two fecal samples. Except for the species Bifidobacterium coryneforme and B. indicum, all currently known bifidobacteria originating from various ecosystems can be identified in a highly reproducible manner. Because no further cloning and sequencing of the DGGE bands is necessary, this nested-PCR-DGGE technique can be completed within a 24-h span, allowing the species-specific monitoring of temporal changes in the bifidobacterial community.

scholarly journals Syntrophorhabdus aromaticivorans gen. nov., sp. nov., the First Cultured Anaerobe Capable of Degrading Phenol to Acetate in Obligate Syntrophic Associations with a Hydrogenotrophic Methanogen

2008 ◽  
Vol 74 (7) ◽  
pp. 2051-2058 ◽  
Author(s):  
Yan-Ling Qiu ◽  
Satoshi Hanada ◽  
Akiyoshi Ohashi ◽  
Hideki Harada ◽  
Yoichi Kamagata ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phenol Degradation ◽  
Rrna Gene ◽  
Cluster Group ◽  
New Family ◽  
Gene Sequence Analysis ◽  
Fermentative Growth ◽  
Degradation Reaction ◽  
Transient Intermediates

ABSTRACT Phenol degradation under methanogenic conditions has long been studied, but the anaerobes responsible for the degradation reaction are still largely unknown. An anaerobe, designated strain UIT, was isolated in a pure syntrophic culture. This isolate is the first tangible, obligately anaerobic, syntrophic substrate-degrading organism capable of oxidizing phenol in association with an H2-scavenging methanogen partner. Besides phenol, it could metabolize p-cresol, 4-hydroxybenzoate, isophthalate, and benzoate. During the degradation of phenol, a small amount of 4-hydroxybenzoate (a maximum of 4 μM) and benzoate (a maximum of 11 μM) were formed as transient intermediates. When 4-hydroxybenzoate was used as the substrate, phenol (maximum, 20 μM) and benzoate (maximum, 92 μM) were detected as intermediates, which were then further degraded to acetate and methane by the coculture. No substrates were found to support the fermentative growth of strain UIT in pure culture, although 88 different substrates were tested for growth. 16S rRNA gene sequence analysis indicated that strain UIT belongs to an uncultured clone cluster (group TA) at the family (or order) level in the class Deltaproteobacteria. Syntrophorhabdus aromaticivorans gen. nov., sp. nov., is proposed for strain UIT, and the novel family Syntrophorhabdaceae fam. nov. is described. Peripheral 16S rRNA gene sequences in the databases indicated that the proposed new family Syntrophorhabdaceae is largely represented by abundant bacteria within anaerobic ecosystems mainly decomposing aromatic compounds.

scholarly journals Sphingobacterium yanglingense sp. nov., isolated from the nodule surface of soybean

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3862-3866 ◽  
Author(s):  
Shi Peng ◽  
Dong Dan Hong ◽  
Yang Bing Xin ◽  
Li Ming Jun ◽  
Wei Ge Hong
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Physiological And Biochemical Characteristics ◽  
Gene Sequence Analysis ◽  
Type Strains

A Gram-staining-negative, non-motile, catalase- and oxidase-positive strain, designated CCNWSP36-1T, was isolated from the nodule surface of soybean [Glycine max (L.) Merrill] cultivar Zhonghuang 13. The 16S rRNA gene sequence analysis clearly showed that the isolate represented a member of the genus Sphingobacterium . On the basis of pairwise comparisons of 16S rRNA gene sequences, strain CCNWSP36-1T showed 96.8 % similarity to Sphingobacterium nematocida CCTCC AB 2010390T and less than 95.2 % similarity to other members of the genus Sphingobacterium . Growth of strain CCNWSP36-1T occurred at 10–40 °C and at pH 5.0–9.0. The NaCl range (w/v) for growth was 0–4 %. The predominant isoprenoid quinone was MK-7. The polar lipids were phosphatidylethanolamine and several unidentified polar lipids. Sphingolipid was present. The major fatty acids were iso-C15 : 0 and summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c). The G+C content of the genomic DNA was 41.1 mol%. As the physiological and biochemical characteristics of strain CCNWSP36-1T and the type strains of its closest phylogenetic neighbours showed clear differences, a novel species, Sphingobacterium yanglingense, is proposed. The type strain is CCNWSP36-1T ( = ACCC 19328T = JCM 30166T).

scholarly journals Intragenomic and intraspecific heterogeneity in rrs may surpass interspecific variability in a natural population of Veillonella

Microbiology ◽  
2010 ◽  
Vol 156 (7) ◽  
pp. 2080-2091 ◽  
Author(s):  
Anne-Laure Michon ◽  
Fabien Aujoulat ◽  
Laurent Roudière ◽  
Olivier Soulier ◽  
Isabelle Zorgniotti ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Diversity ◽  
Natural Populations ◽  
Variable Region ◽  
Housekeeping Gene ◽  
Single Copy ◽  
Population Based ◽  
Rrna Gene ◽  
Gene Copies

As well as intraspecific heterogeneity, intragenomic heterogeneity between 16S rRNA gene copies has been described for a range of bacteria. Due to the wide use of 16S rRNA gene sequence analysis for taxonomy, identification and metagenomics, evaluating the extent of these heterogeneities in natural populations is an essential prerequisite. We investigated inter- and intragenomic 16S rRNA gene heterogeneity of the variable region V3 in a population of 149 clinical isolates of Veillonella spp. of human origin and in 13 type or reference Veillonella strains using PCR-temporal temperature gel electrophoresis (TTGE). 16S rRNA gene diversity was high in the studied population, as 45 different banding patterns were observed. Intragenomic heterogeneity was demonstrated for 110 (74 %) isolates and 8 (61.5 %) type or reference strains displaying two or three different gene copies. Polymorphic nucleotide positions accounted for 0.5–2.5 % of the sequence and were scattered in helices H16 and H17 of the rRNA molecule. Some of them changed the secondary structure of H17. Phylotaxonomic structure of the population based on the single-copy housekeeping gene rpoB was compared with TTGE patterns. The intragenomic V3 heterogeneity, as well as recombination events between strains or isolates of different rpoB clades, impaired the 16S rRNA-based identification for some Veillonella species. Such approaches should be conducted in other bacterial populations to optimize the interpretation of 16S rRNA gene sequences in taxonomy and/or diversity studies.

scholarly journals Microbial Diversity of Septic Tank Effluent and a Soil Biomat

2009 ◽  
Vol 75 (10) ◽  
pp. 3348-3351 ◽  
Author(s):  
Jill Tomaras ◽  
Jason W. Sahl ◽  
Robert L. Siegrist ◽  
John R. Spear
Keyword(s):  
Sequence Analysis ◽  
Microbial Diversity ◽  
Gene Sequence ◽  
Septic Tank ◽  
Rrna Gene ◽  
Control Soil ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
Site Water ◽  
Septic Tank Effluent

ABSTRACT Microbial diversity of septic tank effluent (STE) and the biomat that is formed as a result of STE infiltration on soil were characterized by 16S rRNA gene sequence analysis. Results indicate that microbial communities are different within control soil, STE, and the biomat and that microbes found in STE are not found in the biomat. The development of a stable soil biomat appears to provide the best on-site water treatment or protection for subsequent groundwater interactions of STE.

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