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.
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.
authors.affiliation: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Braunschweig, Germany.
authors.forename: Richard L
authors.initials: RL
authors.lastname: Hahnke
authors.affiliation: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Braunschweig, Germany.
authors.forename: Erko
authors.initials: E
authors.lastname: Stackebrandt
authors.affiliation: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Braunschweig, Germany.
authors.forename: Jan P
authors.initials: JP
authors.lastname: Meier-Kolthoff
authors.affiliation: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Braunschweig, Germany.
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Tindall
authors.affiliation: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Braunschweig, Germany.
authors.forename: Sixing
authors.initials: S
authors.lastname: Huang
authors.affiliation: Helmholtz Centre for Infection Research, Inhoffenstraße 7, Braunschweig, Germany.
authors.forename: Manfred
authors.initials: M
authors.lastname: Rohde
authors.affiliation: St. Petersburg State University, St. Petersburg, Russia ; Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia.
authors.forename: Alla
authors.initials: A
authors.lastname: Lapidus
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: James
authors.initials: J
authors.lastname: Han
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Stephan
authors.initials: S
authors.lastname: Trong
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: Haynes
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: T B K
authors.initials: TB
authors.lastname: Reddy
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Marcel
authors.initials: M
authors.lastname: Huntemann
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Amrita
authors.initials: A
authors.lastname: Pati
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Natalia N
authors.initials: NN
authors.lastname: Ivanova
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Mavromatis
authors.affiliation: Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA.
authors.forename: Victor
authors.initials: V
authors.lastname: Markowitz
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Tanja
authors.initials: T
authors.lastname: Woyke
authors.affiliation: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Braunschweig, Germany.
authors.forename: Markus
authors.initials: M
authors.lastname: Göker
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA ; School of Biology, King Abdulaziz University, Jeddah, Saudi Arabia.
authors.forename: Nikos C
authors.initials: NC
authors.lastname: Kyrpides
authors.affiliation: School of Biology, Newcastle University, Newcastle upon Tyne, UK.
authors.forename: Hans-Peter
authors.initials: HP
authors.lastname: Klenk
keywords: Aerobic; Bacteroidetes; Carbohydrate active enzyme; Flavobacteriaceae; GEBA-KMG I; Gram-negative; Hard water rivulet; Myroides; Non-motile; Polysaccharide utilization loci