skip to main content

DOE PAGESDOE PAGES

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

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 3.3-2T 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 richmore » gene cluster that might enable strain WB 3.3-2T to decompose plant and algae derived polysaccharides. In conclusion, 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.« less
Authors:
 [1] ;  [1] ;  [1] ;  [1] ;  [1] ;  [2] ;  [3] ;  [4] ;  [4] ;  [4] ;  [4] ;  [4] ;  [4] ;  [4] ;  [4] ;  [5] ;  [4] ;  [1] ;  [6] ;  [7]
  1. Leibniz Inst. DSM, Braunschweig (Germany)
  2. Helmholtz Centre for Infection Research, Braunschweig (Germany)
  3. St. Petersburg State Univ. (Russia); St. Petersburg Academic Univ. (Russia)
  4. DOE Joint Genome Inst., Walnut Creek, CA (United States)
  5. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  6. DOE Joint Genome Inst., Walnut Creek, CA (United States); King Abdulaziz Univ., Jeddah (Saudi Arabia)
  7. Newcastle Univ., Newcast (United Kingdom)
Publication Date:
OSTI Identifier:
1256928
Grant/Contract Number:
AC02-05CH11231; AC52-07NA27344
Type:
Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Research Org:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES Carbohydrate active enzyme; Polysaccharide utilization loci; Gram-negative; Non-motile; Aerobic; Hard water rivulet; Flavobacteriaceae; Bacteroidetes; GEBA-KMG I; Myroides