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Stand Genomic Sci. 2015 Jul 30;10:46. doi: 10.1186/s40793-015-0032-y. eCollection 2015.

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.

Author information

1
Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Braunschweig, Germany.
2
Helmholtz Centre for Infection Research, Inhoffenstraße 7, Braunschweig, Germany.
3
St. Petersburg State University, St. Petersburg, Russia ; Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia.
4
DOE Joint Genome Institute, Walnut Creek, California, USA.
5
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA.
6
DOE Joint Genome Institute, Walnut Creek, California, USA ; School of Biology, King Abdulaziz University, Jeddah, Saudi Arabia.
7
School of Biology, Newcastle University, Newcastle upon Tyne, UK.

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.

KEYWORDS:

Aerobic; Bacteroidetes; Carbohydrate active enzyme; Flavobacteriaceae; GEBA-KMG I; Gram-negative; Hard water rivulet; Myroides; Non-motile; Polysaccharide utilization loci

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