High-quality draft genome sequence of Flavobacterium suncheonense GH29-5(T) (DSM 17707(T)) isolated from greenhouse soil in South Korea, and emended description of Flavobacterium suncheonense GH29-5(T)

Nisreen Tashkandy; Sari Sabban; Mohammad Fakieh; Jan P Meier-Kolthoff; Sixing Huang; Brian J Tindall; Manfred Rohde; Mohammed N Baeshen; Nabih A Baeshen; Alla Lapidus; Alex Copeland; Manoj Pillay; T B K Reddy; Marcel Huntemann; Amrita Pati; Natalia Ivanova; Victor Markowitz; Tanja Woyke; Markus Göker; Hans-Peter Klenk; Nikos C Kyrpides; Richard L Hahnke

doi:10.1186/s40793-016-0159-5

High-quality draft genome sequence of Flavobacterium suncheonense GH29-5(T) (DSM 17707(T)) isolated from greenhouse soil in South Korea, and emended description of Flavobacterium suncheonense GH29-5(T)

Stand Genomic Sci. 2016 Jun 16:11:42. doi: 10.1186/s40793-016-0159-5. eCollection 2016.

Authors

Nisreen Tashkandy¹, Sari Sabban¹, Mohammad Fakieh¹, Jan P Meier-Kolthoff², Sixing Huang², Brian J Tindall², Manfred Rohde³, Mohammed N Baeshen⁴, Nabih A Baeshen⁴, Alla Lapidus⁵, Alex Copeland⁶, Manoj Pillay⁷, T B K Reddy⁶, Marcel Huntemann⁶, Amrita Pati⁶, Natalia Ivanova⁶, Victor Markowitz⁷, Tanja Woyke⁶, Markus Göker², Hans-Peter Klenk⁸, Nikos C Kyrpides⁹, Richard L Hahnke²

Affiliations

¹ Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
² Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
³ HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany.
⁴ Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia ; Center of Nanotechnology, King Abdulaziz University, Jeddah, Saudi Arabia.
⁵ Centre for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia.
⁶ Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA USA.
⁷ Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA.
⁸ School of Biology, Newcastle University, Newcastle upon Tyne, UK.
⁹ Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia ; Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA USA.

Abstract

Flavobacterium suncheonense is a member of the family Flavobacteriaceae in the phylum Bacteroidetes. Strain GH29-5(T) (DSM 17707(T)) was isolated from greenhouse soil in Suncheon, South Korea. F. suncheonense GH29-5(T) is part of the G enomic E ncyclopedia of B acteria and A rchaea project. The 2,880,663 bp long draft genome consists of 54 scaffolds with 2739 protein-coding genes and 82 RNA genes. The genome of strain GH29-5(T) has 117 genes encoding peptidases but a small number of genes encoding carbohydrate active enzymes (51 CAZymes). Metallo and serine peptidases were found most frequently. Among CAZymes, eight glycoside hydrolase families, nine glycosyl transferase families, two carbohydrate binding module families and four carbohydrate esterase families were identified. Suprisingly, polysaccharides utilization loci (PULs) were not found in strain GH29-5(T). Based on the coherent physiological and genomic characteristics we suggest that F. suncheonense GH29-5(T) feeds rather on proteins than saccharides and lipids.

Keywords: Aerobic; Bacteroidetes; Carbohydrate active enzyme; Flavobacteriaceae; GEBA; GGDC; Gliding motility; Greenhouse soil; KMG-1; Polysaccharide utilization loci; Tree of Life.

Publication types

Case Reports