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).

scholarly journals Nocardia polyresistens sp. nov.

2005 ◽  
Vol 55 (4) ◽  
pp. 1465-1470 ◽  
Author(s):  
Ping Xu ◽  
Wen-Jun Li ◽  
Shu-Kun Tang ◽  
Yi Jiang ◽  
Hua-Hong Chen ◽  
...  
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Gene Sequencing ◽  
Sequence Divergence ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Actinomycete Strain ◽  
Rrna Gene Sequencing ◽  
Genotypic Characteristics ◽  
Established Species

A novel actinomycete strain YIM 33361T was isolated from a soil sample collected from Yunnan, China. Comparative 16S rRNA gene sequencing showed that the strain constituted a distinct subclade within the genus Nocardia, displaying more than 3 % sequence divergence from established species. Based on its morphological, chemotaxonomic, phenotypic and genotypic characteristics, strain YIM 33361T (=CCTCC AA 204004T=KCTC 19027T) is proposed as the type strain of a novel species, Nocardia polyresistens sp. nov.

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 Sutterella stercoricanis sp. nov., isolated from canine faeces

2004 ◽  
Vol 54 (5) ◽  
pp. 1581-1584 ◽  
Author(s):  
Hazel L. Greetham ◽  
Matthew D. Collins ◽  
Glenn R. Gibson ◽  
Catriona Giffard ◽  
Enevold Falsen ◽  
...  
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Molecular Genetic ◽  
Gene Sequencing ◽  
Sequence Divergence ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Anaerobic Conditions ◽  
Genetic Studies ◽  
Rrna Gene Sequencing

Morphological, biochemical and molecular genetic studies were carried out on an unknown non-spore-forming, Gram-negative, rod-shaped bacterium which was isolated from dog faeces. The bacterium grew under anaerobic conditions, was asaccharolytic, resistant to 20 % (v/v) bile and was oxidase- and urease-negative. Phylogenetic analysis based on comparative 16S rRNA gene sequencing showed that the unidentified bacterium clustered with Sutterella wadsworthensis, although a sequence divergence of >5 % indicated that the bacterium from dog faeces represented a previously unrecognized subline within the genus. On the basis of the presented findings, a novel species, Sutterella stercoricanis sp. nov., is described. The type strain of Sutterella stercoricanis is 5BAC4T (=CCUG 47620T=CIP 108024T).

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 Microbacterium paludicola sp. nov., a novel xylanolytic bacterium isolated from swamp forest

2006 ◽  
Vol 56 (3) ◽  
pp. 535-539 ◽  
Author(s):  
Hye Yoon Park ◽  
Kwang Kyu Kim ◽  
Long Jin ◽  
Sung-Taik Lee
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
The Novel ◽  
Swamp Forest ◽  
Phenotypic Data ◽  
Cellular Fatty Acids ◽  
Rrna Gene Sequencing

A xylanolytic bacterium, US15T, was isolated from swamp forest soil in Ulsan, Korea. The cells of the novel strain were Gram-positive, non-motile, short-rod-shaped and showed chemotaxonomic properties that were consistent with its classification in the genus Microbacterium. Chemotaxonomic results showed MK-12 and MK-11 as major menaquinones, predominating iso- and anteiso-branched cellular fatty acids, glucose, galactose and mannose as cell-wall sugars, peptidoglycan-type B2β with glycolyl residues and a DNA G+C content of 66·5 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing showed that strain US15T was closely related to Microbacterium arborescens IFO 3750T, Microbacterium imperiale IFO 12610T and Microbacterium ulmi LMG 20991T (96·9, 96·8 and 96·2 % similarities, respectively), and formed a separate lineage within the genus Microbacterium. Combined genotypic and phenotypic data showed that strain US15T (=DSM 16915T=KCTC 19080T) merits recognition as the type strain of a novel species within the genus Microbacterium, for which the name Microbacterium paludicola sp. nov. is proposed.

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