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

作者：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; Goeker Markus; Kyrpides Nikos C; Klenk Hans Peter

来源：Standards in Genomic Sciences, 2015, 10(1): 46.

DOI：10.1186/s40793-015-0032-y

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

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 Genomic Encyclopedia of Bacteria and Archaea 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.

• 出版日期2015-7-30