scholarly journals Characterization of Actinomyces Isolates from Infected Root Canals of Teeth: Description of Actinomyces radicidentis sp. nov.

2000 ◽  
Vol 38 (9) ◽  
pp. 3399-3403 ◽  
Author(s):  
Matthew D. Collins ◽  
Lesley Hoyles ◽  
Sotos Kalfas ◽  
Goran Sundquist ◽  
Tor Monsen ◽  
...  
Keyword(s):  
Polyacrylamide Gel Electrophoresis ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Root Canals ◽  
Infected Root ◽  
Sequencing Studies ◽  
Rrna Gene Sequencing ◽  
Biochemical Testing

Two strains of a previously undescribedActinomyces-like bacterium were recovered in pure culture from infected root canals of teeth. Analysis by biochemical testing and polyacrylamide gel electrophoresis of whole-cell proteins indicated that the strains closely resembled each other phenotypically but were distinct from previously described Actinomyces andArcanobacterium species. Comparative 16S rRNA gene-sequencing studies showed the bacterium to be a hitherto unknown subline within a group of Actinomyces species which includes Actinomyces bovis, the type species of the genus. Based on phylogenetic and phenotypic evidence, we propose that the unknown bacterium isolated from human clinical specimens be classified as Actinomyces radicidentis sp. nov. The type strain ofActinomyces radicidentis is CCUG 36733.

Cultivable bacteria in infected root canals as identified by 16S rRNA gene sequencing

2007 ◽  
Vol 22 (4) ◽  
pp. 266-271 ◽  
Author(s):  
J. F. Siqueira ◽  
I. N. Rôças ◽  
S. S. M. Paiva ◽  
K. M. Magalhães ◽  
T. Guimarães-Pinto
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Root Canals ◽  
Cultivable Bacteria ◽  
Infected Root ◽  
Rrna Gene Sequencing

scholarly journals Helcococcus sueciensis sp. nov., isolated from a human wound

2004 ◽  
Vol 54 (5) ◽  
pp. 1557-1560 ◽  
Author(s):  
Matthew D. Collins ◽  
Enevold Falsen ◽  
Kit Brownlee ◽  
Paul A. Lawson
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Taxonomic Study ◽  
Sequencing Studies ◽  
Molecular Phylogenetic ◽  
Rrna Gene Sequencing ◽  
Biochemical Testing

A previously undescribed, Gram-positive, catalase-negative, coccus-shaped organism that originated from a human wound was subjected to taxonomic study. On the basis of its cellular morphology and the results of biochemical testing, the unknown organism was identified tentatively as a member of the genus Helcococcus, but it did not correspond to either of the two recognized species of this genus. Comparative 16S rRNA gene sequencing studies confirmed that the bacterium was associated phylogenetically with the genus Helcococcus, with the unidentified organism forming a hitherto unknown subline within the genus. On the basis of biochemical, molecular chemical and molecular phylogenetic evidence, it is proposed that the unknown organism that was recovered from a human wound should be classified as a novel species of the genus Helcococcus, namely Helcococcus sueciensis sp. nov. The type strain is CCUG 47334T (=CIP 108183T).

scholarly journals Characterization of the Spoilage Microbiota of Hake Fillets Packaged Under a Modified Atmosphere (MAP) Rich in CO2 (50% CO2/50% N2) and Stored at Different Temperatures

Foods ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 489 ◽  
Author(s):  
Adriana Antunes-Rohling ◽  
Silvia Calero ◽  
Nabil Halaihel ◽  
Pedro Marquina ◽  
Javier Raso ◽  
...  
Keyword(s):  
Storage Temperature ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Modified Atmosphere ◽  
Modified Atmospheres ◽  
Different Temperatures ◽  
Rrna Gene Sequencing ◽  
Storage Temperatures

The aim of this study was to characterize the spoilage microbiota of hake fillets stored under modified atmospheres (MAP) (50% CO2/50% N2) at different temperatures using high-throughput 16S rRNA gene sequencing and to compare the results with those obtained using traditional microbiology techniques. The results obtained indicate that, as expected, higher storage temperatures lead to shorter shelf-lives (the time of sensory rejection by panelists). Thus, the shelf-life decreased from six days to two days for Batch A when the storage temperature increased from 1 to 7 °C, and from five to two days—when the same increase in storage temperature was compared—for Batch B. In all cases, the trimethylamine (TMA) levels measured at the time of sensory rejection of hake fillets exceeded the recommended threshold of 5 mg/100 g. Photobacterium and Psychrobacter were the most abundant genera at the time of spoilage in all but one of the samples analyzed: Thus, Photobacterium represented between 19% and 46%, and Psychrobacter between 27% and 38% of the total microbiota. They were followed by Moritella, Carnobacterium, Shewanella, and Vibrio, whose relative order varied depending on the sample/batch analyzed. These results highlight the relevance of Photobacterium as a spoiler of hake stored in atmospheres rich in CO2. Further research will be required to elucidate if other microorganisms, such as Psychrobacter, Moritella, or Carnobacterium, also contribute to spoilage of hake when stored under MAP.

scholarly journals Optimal protocols for sequence-based characterization of the human vaginal microbiome

2020 ◽  
Author(s):  
Luisa W. Hugerth ◽  
Marcela Pereira ◽  
Yinghua Zha ◽  
Maike Seifert ◽  
Vilde Kaldhusdal ◽  
...  
Keyword(s):  
16S Rrna ◽  
Best Practices ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Vaginal Microbiome ◽  
Wide Range ◽  
Rrna Gene Sequencing ◽  
Good Agreement

AbstractThe vaginal microbiome has been connected to a wide range of health outcomes. This has led to a thriving research environment, but also to the use of conflicting methodologies to study its microbial composition. Here we systematically assess best practices for the sequencing-based characterization of the human vaginal microbiome. As far as 16S rRNA gene sequencing is concerned, the V1-V3 region has the best theoretical properties, but limitations of current sequencing technologies mean that the V3-V4 region performs equally well. Both of these approaches present very good agreement with qPCR quantification of key taxa, provided an appropriate bioinformatic pipeline is used. Shotgun metagenomic sequencing presents an interesting alternative to 16S amplification and sequencing, but it is not without its challenges. We have assessed different tools for the removal of host reads and the taxonomic annotation of metagenomic reads, including a new, easy-to-build and – use, reference database of vaginal taxa. This strategy performed as well as the best performing previously published strategies. Despite the many advantages of shotgun sequencing none of the shotgun approaches assessed here had as good agreement with the qPCR data as 16S rRNA gene sequencing.ImportanceThe vaginal microbiome has been connected to a wide range of health outcomes, from susceptibility to sexually transmitted infections to gynecological cancers and pregnancy outcomes. This has led to a thriving research environment, but also to conflicting available methodologies, including many studies that do not report their molecular biological and bioinformatic methods in sufficient detail for them to be considered reproducible. This can lead to conflicting messages and delay progress from descriptive to intervention studies. By systematically assessing best practices for the characterization of the human vaginal microbiome, this study will enable past studies to be assessed more critically and assist future studies in the selection of appropriate methods for their specific research questions.

scholarly journals Nocardia takedensis sp. nov., isolated from moat sediment and scumming activated sludge

2005 ◽  
Vol 55 (1) ◽  
pp. 433-436 ◽  
Author(s):  
Hideki Yamamura ◽  
Masayuki Hayakawa ◽  
Youji Nakagawa ◽  
Tomohiko Tamura ◽  
Tetsuro Kohno ◽  
...  
Keyword(s):  
Activated Sludge ◽  
Reference Strain ◽  
16S Rrna Gene Sequencing ◽  
Morphological Characterization ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Sequencing Studies ◽  
Rrna Gene Sequencing ◽  
Physiological And Biochemical

Chemotaxonomic and morphological characterization of two actinomycete strains, MS1-3T and AS4-2, respectively isolated from moat sediment and scumming activated sludge, was carried out. This characterization clearly demonstrated that strains MS1-3T and AS4-2 belong to the genus Nocardia. 16S rRNA gene sequencing studies showed that these isolates are most closely related to Nocardia beijingensis (98·1–98·3 % similarity), Nocardia brasiliensis (97·9–98·0 %) and Nocardia tenerifensis (97·8–97·9 %). However, the results of DNA–DNA hybridizations and physiological and biochemical tests showed that strains MS1-3T and AS4-2 could be differentiated from their closest phylogenetic relatives both genotypically and phenotypically. It is proposed that the two isolates be classified as representatives of a novel species of Nocardia, Nocardia takedensis sp. nov. The type strain is MS1-3T (=NBRC 100417T=DSM 44801T); AS4-2 (=NBRC 100418=DSM 44802) is a reference strain.

scholarly journals Mycobacterium saskatchewanense sp. nov., a novel slowly growing scotochromogenic species from human clinical isolates related to Mycobacterium interjectum and Accuprobe-positive for Mycobacterium avium complex

2004 ◽  
Vol 54 (3) ◽  
pp. 659-667 ◽  
Author(s):  
C. Y. Turenne ◽  
L. Thibert ◽  
K. Williams ◽  
T. V. Burdz ◽  
V. J. Cook ◽  
...  
Keyword(s):  
Mycobacterium Avium ◽  
Novel Species ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Rrna Gene Sequencing ◽  
Established Species ◽  
Rdna Analysis ◽  
Selection Of

A pigmented, slowly growing Mycobacterium avium complex AccuProbe-positive organism was isolated from the sputum and pleural fluid of a 72-year-old female with bronchiectasis. The unusual morphology of the organism prompted further identification by 16S rRNA gene sequencing, revealing a perfect identity with previously uncharacterized strain Mycobacterium sp. MCRO 8 (GenBank accession no. X93034), with the closest established species by 16S rDNA analysis being Mycobacterium interjectum. HPLC of the organism corresponded to previously obtained patterns identified as M. interjectum-like and, upon sequence evaluation of a selection of strains with a similar profile, more were subsequently identified as MCRO 8. A total of 16 strains isolated from human respiratory samples were evaluated in the characterization of this novel species, for which the name Mycobacterium saskatchewanense sp. nov. is proposed. The type strain is strain 00-250T (=ATCC BAA-544T=DSM 44616T=CIP 108114T).

Microbiota characterization of sheep milk and its association with somatic cell count using 16s rRNA gene sequencing

2019 ◽  
Vol 137 (1) ◽  
pp. 73-83 ◽  
Author(s):  
Cristina Esteban‐Blanco ◽  
Beatriz Gutiérrez‐Gil ◽  
Fernando Puente‐Sánchez ◽  
Héctor Marina ◽  
Javier Tamames ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Cell Count ◽  
Somatic Cell Count ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Sheep Milk ◽  
Rrna Gene Sequencing

scholarly journals Actinomyces dentalis sp. nov., from a human dental abscess

2005 ◽  
Vol 55 (1) ◽  
pp. 427-431 ◽  
Author(s):  
Val Hall ◽  
Matthew D. Collins ◽  
Paul A. Lawson ◽  
Enevold Falsen ◽  
Brian I. Duerden
Keyword(s):  
Novel Species ◽  
Sequence Divergence ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Dental Abscess ◽  
Unknown Species ◽  
Sequencing Studies ◽  
Molecular Phylogenetic ◽  
Rrna Gene Sequencing ◽  
Biochemical Testing

A previously undescribed filamentous, beaded, Gram-positive, rod-shaped bacterium was isolated from pus of a human dental abscess. Based on its cellular morphology and the results of biochemical testing the organism was tentatively identified as a member of the genus Actinomyces, but it did not correspond to any currently recognized species of this genus. Comparative 16S rRNA gene sequencing studies showed the bacterium represents a distinct subline within the genus Actinomyces, clustering within a group of species that includes Actinomyces bovis, the type species of the genus. Sequence divergence values of >8 % with other recognized species within this phylogenetic group clearly demonstrated that the organism represents a hitherto unknown species. Based on biochemical and molecular phylogenetic evidence, it is proposed that the unidentified organism recovered from a dental abscess be classified as a novel species, Actinomyces dentalis sp. nov. The type strain is R18165T (=CCUG 48064T=CIP 108337T).

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