scholarly journals Genome Sequences and Methylation Patterns of Natrinema versiforme BOL5-4 and Natrinema pallidum BOL6-1, Two Extremely Halophilic Archaea from a Bolivian Salt Mine

2019 ◽  
Vol 8 (33) ◽  
Author(s):  
Priya DasSarma ◽  
Brian P. Anton ◽  
Satyajit L. DasSarma ◽  
Fabiana L. Martinez ◽  
Daniel Guzman ◽  
...  
Keyword(s):  
Real Time ◽  
Single Molecule ◽  
Genome Annotation ◽  
Halophilic Archaea ◽  
Salt Mine ◽  
Genome Sequences ◽  
Content Type ◽  
Extremely Halophilic Archaea ◽  
Methylation Patterns

Two extremely halophilic archaea, namely, Natrinema versiforme BOL5-4 and Natrinema pallidum BOL6-1, were isolated from a Bolivian salt mine and their genomes sequenced using single-molecule real-time sequencing. The GC-rich genomes of BOL5-4 and BOL6-1 were 4.6 and 3.8 Mbp, respectively, with large chromosomes and multiple megaplasmids. Genome annotation was incorporated into HaloWeb and methylation patterns incorporated into REBASE.

scholarly journals Five Closed Salmonella enterica Genome Sequences from a 2017–2018 Multistrain, Multistate Kratom Outbreak

2020 ◽  
Vol 9 (3) ◽  
Author(s):  
Hallie E. Rauch ◽  
Julie Haendiges ◽  
Maria Balkey ◽  
Maria Hoffmann
Keyword(s):  
Dna Sequencing ◽  
Real Time ◽  
Single Molecule ◽  
Salmonella Enterica ◽  
Genome Sequences ◽  
Circular Chromosome ◽  
Content Type ◽  
Single Plasmid

We report here the closed genomes of Salmonella enterica strains from the 2017–2018 multistrain, multistate kratom outbreak using single-molecule real-time DNA sequencing. Four of the genomes consist of one circular chromosome, and the fifth has a circular chromosome and a single plasmid.

scholarly journals Methylomes of Two Extremely Halophilic Archaea Species, Haloarcula marismortui and Haloferax mediterranei

2019 ◽  
Vol 8 (27) ◽  
Author(s):  
Shiladitya DasSarma ◽  
Alexey Fomenkov ◽  
Satyajit L. DasSarma ◽  
Tamas Vincze ◽  
Priya DasSarma ◽  
...  
Keyword(s):  
Single Molecule ◽  
Gene Annotation ◽  
Halophilic Archaea ◽  
Restriction Enzymes ◽  
Haloferax Mediterranei ◽  
Haloarcula Marismortui ◽  
Content Type ◽  
Extremely Halophilic Archaea ◽  
Large Plasmids ◽  
Methyl Cytosine

ABSTRACT The genomes of two extremely halophilic Archaea species, Haloarcula marismortui and Haloferax mediterranei, were sequenced using single-molecule real-time sequencing. The ∼4-Mbp genomes are GC rich with multiple large plasmids and two 4-methyl-cytosine patterns. Methyl transferases were incorporated into the Restriction Enzymes Database (REBASE), and gene annotation was incorporated into the Haloarchaeal Genomes Database (HaloWeb).

scholarly journals Complete Genome Sequences of Two Pseudomonas aeruginosa Strains Isolated from Children with Bacteremia

2017 ◽  
Vol 5 (35) ◽  
Author(s):  
Luis F. Espinosa-Camacho ◽  
Gabriela Delgado ◽  
Guadalupe Miranda-Novales ◽  
Gloria Soberón-Chávez ◽  
Luis D. Alcaraz ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Real Time ◽  
Mexico City ◽  
Single Molecule ◽  
Complete Genome ◽  
Genome Sequences ◽  
Class 1 Integron ◽  
Content Type ◽  
Pacbio Rs Ii ◽  
Class 1

ABSTRACT Two Pseudomonas aeruginosa strains isolated from children with bacteremia in Mexico City were sequenced using PacBio RS-II single-molecule real-time (SMRT) technology. The strains consist of a 7.0- to 7.4-Mb chromosome, with a high content of mobile elements, and variation in the genetic content of class 1 integron In1409.

scholarly journals Complete Genome Sequences of Two Strains of the Meat Spoilage Bacterium Brochothrix thermosphacta Isolated from Ground Chicken

2017 ◽  
Vol 5 (47) ◽  
Author(s):  
George C. Paoli ◽  
Chandi Wijey ◽  
Ly-Huong Nguyen ◽  
Chin-Yi Chen ◽  
Xianghe Yan ◽  
...  
Keyword(s):  
Real Time ◽  
Single Molecule ◽  
Complete Genome ◽  
Genome Sequences ◽  
Content Type ◽  
Meat Spoilage ◽  
Brochothrix Thermosphacta ◽  
Long Read ◽  
Spoilage Bacterium

ABSTRACT Brochothrix thermosphacta is an important meat spoilage bacterium. Here we report the genome sequences of two strains of B. thermosphacta isolated from ground chicken. The genome sequences were determined using long-read PacBio single-molecule real-time (SMRT) technology and are the first complete genome sequences reported for B. thermosphacta.

scholarly journals Complete Genome Sequences of Lactobacillus curvatus KG6, L. curvatus MRS6, and Lactobacillus sakei FAM18311, Isolated from Fermented Meat Products

2017 ◽  
Vol 5 (38) ◽  
Author(s):  
Christoph Jans ◽  
Sandra Lagler ◽  
Christophe Lacroix ◽  
Leo Meile ◽  
Marc J. A. Stevens
Keyword(s):  
Real Time ◽  
Single Molecule ◽  
Complete Genome ◽  
Meat Products ◽  
Lactobacillus Sakei ◽  
Lactobacillus Curvatus ◽  
Genome Sequences ◽  
Content Type ◽  
Circular Chromosomes

ABSTRACT The genomes of Lactobacillus curvatus KG6, L. curvatus MRS6, and Lactobacillus sakei FAM18311 were sequenced and assembled using PacBio single-molecule real-time (SMRT) technology. The strains were isolated from Swiss fermented meat products. Circular chromosomes were of 1.98 Mbp (KG6), 2.11 Mbp (MRS6), and 1.95 Mbp (FAM18311), with a G+C content of 41.3 to 42.0%.

scholarly journals Complete and Assembled Genome Sequences of Pantoea calida DSM 22759 T and Pantoea gaviniae DSM 22758 T

2018 ◽  
Vol 6 (12) ◽  
Author(s):  
Marc J. A. Stevens ◽  
Katrin Zurfluh ◽  
Roger Stephan
Keyword(s):  
Real Time ◽  
Single Molecule ◽  
Genome Sequences ◽  
Content Type

ABSTRACT The genomes of Pantoea calida DSM 22759 T and Pantoea gaviniae DSM 22758 T were sequenced using single-molecule real-time sequencing. They consist of a 4.3-Mbp chromosome containing 4,092 genes, of which 3,977 encode proteins, and a 4.5-Mbp chromosome containing 4,236 genes, of which 4,120 encode proteins, respectively.

Halolamina salifodinae sp. nov. and Halolamina salina sp. nov., two extremely halophilic archaea isolated from a salt mine

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4380-4385 ◽  
Author(s):  
Wei-Yan Zhang ◽  
Ying-Yi Huo ◽  
Xin-Qi Zhang ◽  
Xu-Fen Zhu ◽  
Min Wu
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Halophilic Archaea ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Salt Mine ◽  
Content Type ◽  
Link Type ◽  
Extremely Halophilic Archaea

Two strictly aerobic, extremely halophilic archaea, strains WSY15-H1T and WSY15-H3T, were isolated from a salt mine in Wensu county, Xinjiang province, China. Cells of the two strains were Gram-stain-negative, non-motile and pleomorphic. Colonies were pink- and red-pigmented, respectively. Strain WSY15-H1T grew at 20–45 °C (optimum 37–42 °C), 1.6–5.4 M NaCl (optimum 3.4–3.9 M), 0–2.0 M MgCl2 (optimum 0.1–0.5 M) and pH 6.0–9.0 (optimum 7.0), whereas strain WSY15-H3T grew at 20–50 °C (optimum 37 °C), 1.9–5.4 M NaCl (optimum 3.4 M), 0.02–2.5 M MgCl2 (optimum 0.5-1.0 M) and pH 6.0–7.5 (optimum 6.5). The minimal NaCl concentrations to prevent cell lysis were 9 % (w/v) for strain WSY15-H1T and 8 % (w/v) for strain WSY15-H3T. The major polar lipids of the two isolates were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and phosphatidylglycerol sulfate, as well as nine glycolipids for strain WSY15-H1T and seven glycolipids for strain WSY15-H3T; two of these glycolipids (GL1 and GL3) were chromatographically identical to bis-sulfated diglycosyl diether (S2-DGD-1) and sulfated diglycosyl diether (S-DGD-1), respectively. The genomic DNA G+C contents of strains WSY15-H1T and WSY15-H3T were 65.4 and 66.2 mol%. On the basis of 16S rRNA gene sequence analysis, strains WSY15-H1T and WSY15-H3T shared 97.0 % similarity with each other and showed respectively 98.4 and 97.6 % sequence similarity to Halolamina pelagica TBN21T, which was the only type strain that had higher than 91 % sequence similarity with the two isolates. Analysis of phylogenetic relationships and DNA–DNA relatedness indicated that strains WSY15-H1T and WSY15-H3T represent two novel lineages with closest affinity to H. pelagica TBN21T. Based on phenotypic, chemotaxonomic and genotypic characteristics, two novel species of the genus Halolamina are proposed, Halolamina salifodinae sp. nov. (type strain WSY15-H1T = JCM 18548T = GCMCC 1.12371T) and Halolamina salina sp. nov. (type strain WSY15-H3T = JCM 18549T = GCMCC 1.12285T).

scholarly journals Complete and Assembled Genome Sequence of Lactobacillus plantarum RI-113 Isolated from Salami

2017 ◽  
Vol 5 (16) ◽  
Author(s):  
Raffael C. Inglin ◽  
Leo Meile ◽  
Jochen Klumpp ◽  
Marc J. A. Stevens
Keyword(s):  
Real Time ◽  
Lactobacillus Plantarum ◽  
Genome Sequence ◽  
Single Molecule ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Content Type

ABSTRACT We present here the complete genome sequence of Lactobacillus plantarum RI-113, a strain isolated from salami, which was determined using single-molecule real-time sequencing.

scholarly journals Draft Genome Sequences of Two Uncultured Armatimonadetes Associated with a Microcystis sp. (Cyanobacteria) Isolate

2017 ◽  
Vol 5 (40) ◽  
Author(s):  
Jason N. Woodhouse ◽  
A. Katharina Makower ◽  
Hans-Peter Grossart ◽  
Elke Dittmann
Keyword(s):  
Real Time ◽  
Single Molecule ◽  
Type Strain ◽  
Enrichment Culture ◽  
Draft Genome ◽  
Eutrophic Lake ◽  
Smrt Sequencing ◽  
Genome Sequences ◽  
Terrestrial Environments ◽  
Strain Genome

ABSTRACT Two genome sequences of the phylum Armatimonadetes, derived from terrestrial environments, have been previously described. Here, two additional Armatimonadetes genome sequences were obtained via single-molecule real-time (SMRT) sequencing of an enrichment culture of the bloom-forming cyanobacterium Microcystis sp. isolated from a eutrophic lake (Brandenburg, Germany). The genomes are most closely affiliated with the class Fimbriimonadales, although they are smaller than the 5.6-Mbp type strain genome.

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