High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2(T) (DSM 21788(T)), a valuable source of polysaccharide decomposing enzymes.

2.50
Hdl Handle:
http://hdl.handle.net/10033/581808
Title:
High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2(T) (DSM 21788(T)), a valuable source of polysaccharide decomposing enzymes.
Authors:
Hahnke, Richard L; Stackebrandt, Erko; Meier-Kolthoff, Jan P; Tindall, Brian J; Huang, Sixing; Rohde, Manfred; Lapidus, Alla; Han, James; Trong, Stephan; Haynes, Matthew; Reddy, T B K; Huntemann, Marcel; Pati, Amrita; Ivanova, Natalia N; Mavromatis, Konstantinos; Markowitz, Victor; Woyke, Tanja; Göker, Markus; Kyrpides, Nikos C; Klenk, Hans-Peter
Abstract:
Flavobacterium rivuli Ali et al. 2009 emend. Dong et al. 2013 is one of about 100 species in the genus Flavobacterium (family Flavobacteriacae, phylum Bacteroidetes) with a validly published name, and has been isolated from the spring of a hard water rivulet in Northern Germany. Including all type strains of the genus Myroides and Flavobacterium into the 16S rRNA gene sequence phylogeny revealed a clustering of members of the genus Myroides as a monophyletic group within the genus Flavobacterium. Furthermore, F. rivuli WB 3.3-2(T) and its next relatives seem more closely related to the genus Myroides than to the type species of the genus Flavobacterium, F. aquatile. The 4,489,248 bp long genome with its 3,391 protein-coding and 65 RNA genes is part of the G enomic E ncyclopedia of B acteria and A rchaea project. The genome of F. rivuli has almost as many genes encoding carbohydrate active enzymes (151 CAZymes) as genes encoding peptidases (177). Peptidases comprised mostly metallo (M) and serine (S) peptidases. Among CAZymes, 30 glycoside hydrolase families, 10 glycosyl transferase families, 7 carbohydrate binding module families and 7 carbohydrate esterase families were identified. Furthermore, we found four polysaccharide utilization loci (PUL) and one large CAZy rich gene cluster that might enable strain WB 3.3-2(T) to decompose plant and algae derived polysaccharides. Based on these results we propose F. rivuli as an interesting candidate for further physiological studies and the role of Bacteroidetes in the decomposition of complex polymers in the environment.
Citation:
High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2(T) (DSM 21788(T)), a valuable source of polysaccharide decomposing enzymes. 2015, 10:46 Stand Genomic Sci
Journal:
Standards in genomic sciences
Issue Date:
2015
URI:
http://hdl.handle.net/10033/581808
DOI:
10.1186/s40793-015-0032-y
PubMed ID:
26380634
Type:
Article
Language:
en
ISSN:
1944-3277
Appears in Collections:
publications of the central unit for microscopy (ZEIM)

Full metadata record

DC FieldValue Language
dc.contributor.authorHahnke, Richard Len
dc.contributor.authorStackebrandt, Erkoen
dc.contributor.authorMeier-Kolthoff, Jan Pen
dc.contributor.authorTindall, Brian Jen
dc.contributor.authorHuang, Sixingen
dc.contributor.authorRohde, Manfreden
dc.contributor.authorLapidus, Allaen
dc.contributor.authorHan, Jamesen
dc.contributor.authorTrong, Stephanen
dc.contributor.authorHaynes, Matthewen
dc.contributor.authorReddy, T B Ken
dc.contributor.authorHuntemann, Marcelen
dc.contributor.authorPati, Amritaen
dc.contributor.authorIvanova, Natalia Nen
dc.contributor.authorMavromatis, Konstantinosen
dc.contributor.authorMarkowitz, Victoren
dc.contributor.authorWoyke, Tanjaen
dc.contributor.authorGöker, Markusen
dc.contributor.authorKyrpides, Nikos Cen
dc.contributor.authorKlenk, Hans-Peteren
dc.date.accessioned2015-11-05T12:10:32Zen
dc.date.available2015-11-05T12:10:32Zen
dc.date.issued2015en
dc.identifier.citationHigh quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2(T) (DSM 21788(T)), a valuable source of polysaccharide decomposing enzymes. 2015, 10:46 Stand Genomic Scien
dc.identifier.issn1944-3277en
dc.identifier.pmid26380634en
dc.identifier.doi10.1186/s40793-015-0032-yen
dc.identifier.urihttp://hdl.handle.net/10033/581808en
dc.description.abstractFlavobacterium rivuli Ali et al. 2009 emend. Dong et al. 2013 is one of about 100 species in the genus Flavobacterium (family Flavobacteriacae, phylum Bacteroidetes) with a validly published name, and has been isolated from the spring of a hard water rivulet in Northern Germany. Including all type strains of the genus Myroides and Flavobacterium into the 16S rRNA gene sequence phylogeny revealed a clustering of members of the genus Myroides as a monophyletic group within the genus Flavobacterium. Furthermore, F. rivuli WB 3.3-2(T) and its next relatives seem more closely related to the genus Myroides than to the type species of the genus Flavobacterium, F. aquatile. The 4,489,248 bp long genome with its 3,391 protein-coding and 65 RNA genes is part of the G enomic E ncyclopedia of B acteria and A rchaea project. The genome of F. rivuli has almost as many genes encoding carbohydrate active enzymes (151 CAZymes) as genes encoding peptidases (177). Peptidases comprised mostly metallo (M) and serine (S) peptidases. Among CAZymes, 30 glycoside hydrolase families, 10 glycosyl transferase families, 7 carbohydrate binding module families and 7 carbohydrate esterase families were identified. Furthermore, we found four polysaccharide utilization loci (PUL) and one large CAZy rich gene cluster that might enable strain WB 3.3-2(T) to decompose plant and algae derived polysaccharides. Based on these results we propose F. rivuli as an interesting candidate for further physiological studies and the role of Bacteroidetes in the decomposition of complex polymers in the environment.en
dc.language.isoenen
dc.titleHigh quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2(T) (DSM 21788(T)), a valuable source of polysaccharide decomposing enzymes.en
dc.typeArticleen
dc.identifier.journalStandards in genomic sciencesen

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