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An improved high-quality draft genome sequence of Carnobacterium inhibens subsp. inhibens strain K1 T

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ABSTRACT

Despite their ubiquity and their involvement in food spoilage, the genus Carnobacterium remains rather sparsely characterized at the genome level. Carnobacterium inhibens K1T is a member of the Carnobacteriaceae family within the class Bacilli. This strain is a Gram-positive, rod-shaped bacterium isolated from the intestine of an Atlantic salmon. The present study determined the genome sequence and annotation of Carnobacterium inhibens K1T. The genome comprised 2,748,608 bp with a G + C content of 34.85 %, which included 2621 protein-coding genes and 116 RNA genes. The strain contained five contigs corresponding to presumptive plasmids of sizes: 19,036; 24,250; 26,581; 65,272; and 65,904 bp.

No MeSH data available.


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Phylogenetic tree highlighting the position of Carnobacterium inhibens subsp. inhibens strain K1T relative to other type (green boxes) and non-type strains within the genus Carnobacterium. Accession numbers are in parentheses: dbj, Database of Japan; emb, EMBL database; gb, NCBI Genbank. The top 100 hits by NCBI-BLASTN were input into the Distance Tree function at NCBI [33]. Alignments were converted to a distance matrix using the Jukes-Cantor distance correction model and the tree was constructed using the Neighbor-Joining method
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Fig2: Phylogenetic tree highlighting the position of Carnobacterium inhibens subsp. inhibens strain K1T relative to other type (green boxes) and non-type strains within the genus Carnobacterium. Accession numbers are in parentheses: dbj, Database of Japan; emb, EMBL database; gb, NCBI Genbank. The top 100 hits by NCBI-BLASTN were input into the Distance Tree function at NCBI [33]. Alignments were converted to a distance matrix using the Jukes-Cantor distance correction model and the tree was constructed using the Neighbor-Joining method

Mentions: C. inhibens subsp. inhibens strain K1T [8] was obtained from the German Collection of Microorganisms and Cell Cultures as strain DSM 13024. The strain was sub-cultured once and was stored as a −70 °C frozen glycerol stock in the corresponding author’s strain collection as strain WN1362. DNA isolated from strain WN1362 corresponding to 16S rRNA gene sequences was PCR amplified with universal bacterial primers B27F (5’-GAGTTTGATCMTGGCTCAG-3’) and B1512R (5’-AAGGAGGTGATCCANCCRCA-3’) as described previously [16] and sequenced at the University of Florida Interdisciplinary Center for Biotechnology Research (UF-ICBR). The sequence was compared with those obtained using NCBI BLAST [17] with the default settings (only highly similar sequences). The most frequently occurring genera were Carnobacterium (17 %) and unidentified bacteria (83 %) (100 hits in total). The species with the Max score was Carnobacterium inhibens subsp. inhibens strain K1T (NCBI Reference Sequence NR_036895) with a shared identity of 100.0 %, thus verifying the identity of strain WN1362 with the type strain. An updated 16S rRNA phylogenetic analysis of Carnobacterium spp. isolates including C. inhibens subsp. inhibens strain K1T is presented in Fig. 2 to supplement and expand upon those published previously [8, 14, 15].Fig. 2


An improved high-quality draft genome sequence of Carnobacterium inhibens subsp. inhibens strain K1 T
Phylogenetic tree highlighting the position of Carnobacterium inhibens subsp. inhibens strain K1T relative to other type (green boxes) and non-type strains within the genus Carnobacterium. Accession numbers are in parentheses: dbj, Database of Japan; emb, EMBL database; gb, NCBI Genbank. The top 100 hits by NCBI-BLASTN were input into the Distance Tree function at NCBI [33]. Alignments were converted to a distance matrix using the Jukes-Cantor distance correction model and the tree was constructed using the Neighbor-Joining method
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC5016993&req=5

Fig2: Phylogenetic tree highlighting the position of Carnobacterium inhibens subsp. inhibens strain K1T relative to other type (green boxes) and non-type strains within the genus Carnobacterium. Accession numbers are in parentheses: dbj, Database of Japan; emb, EMBL database; gb, NCBI Genbank. The top 100 hits by NCBI-BLASTN were input into the Distance Tree function at NCBI [33]. Alignments were converted to a distance matrix using the Jukes-Cantor distance correction model and the tree was constructed using the Neighbor-Joining method
Mentions: C. inhibens subsp. inhibens strain K1T [8] was obtained from the German Collection of Microorganisms and Cell Cultures as strain DSM 13024. The strain was sub-cultured once and was stored as a −70 °C frozen glycerol stock in the corresponding author’s strain collection as strain WN1362. DNA isolated from strain WN1362 corresponding to 16S rRNA gene sequences was PCR amplified with universal bacterial primers B27F (5’-GAGTTTGATCMTGGCTCAG-3’) and B1512R (5’-AAGGAGGTGATCCANCCRCA-3’) as described previously [16] and sequenced at the University of Florida Interdisciplinary Center for Biotechnology Research (UF-ICBR). The sequence was compared with those obtained using NCBI BLAST [17] with the default settings (only highly similar sequences). The most frequently occurring genera were Carnobacterium (17 %) and unidentified bacteria (83 %) (100 hits in total). The species with the Max score was Carnobacterium inhibens subsp. inhibens strain K1T (NCBI Reference Sequence NR_036895) with a shared identity of 100.0 %, thus verifying the identity of strain WN1362 with the type strain. An updated 16S rRNA phylogenetic analysis of Carnobacterium spp. isolates including C. inhibens subsp. inhibens strain K1T is presented in Fig. 2 to supplement and expand upon those published previously [8, 14, 15].Fig. 2

View Article: PubMed Central - PubMed

ABSTRACT

Despite their ubiquity and their involvement in food spoilage, the genus Carnobacterium remains rather sparsely characterized at the genome level. Carnobacterium inhibens K1T is a member of the Carnobacteriaceae family within the class Bacilli. This strain is a Gram-positive, rod-shaped bacterium isolated from the intestine of an Atlantic salmon. The present study determined the genome sequence and annotation of Carnobacterium inhibens K1T. The genome comprised 2,748,608 bp with a G + C content of 34.85 %, which included 2621 protein-coding genes and 116 RNA genes. The strain contained five contigs corresponding to presumptive plasmids of sizes: 19,036; 24,250; 26,581; 65,272; and 65,904 bp.

No MeSH data available.


Related in: MedlinePlus