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Stand Genomic Sci. 2016 Jun 3;11:37. doi: 10.1186/s40793-016-0163-9. eCollection 2016.

Comparing polysaccharide decomposition between the type strains Gramella echinicola KMM 6050(T) (DSM 19838(T)) and Gramella portivictoriae UST040801-001(T) (DSM 23547(T)), and emended description of Gramella echinicola Nedashkovskaya et al. 2005 emend. Shahina et al. 2014 and Gramella portivictoriae Lau et al. 2005.

Author information

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

Abstract

Strains of the genus Gramella (family Flavobacteriacae, phylum Bacteroidetes) were isolated from marine habitats such as tidal flat sediments, coastal surface seawater and sea urchins. Flavobacteriaceae have been shown to be involved in the decomposition of plant and algal polysaccharides. However, the potential to decompose polysaccharides may differ tremendously even between species of the same genus. Gramella echinicola KMM 6050(T) (DSM 19838(T)) and Gramella portivictoriae UST040801-001(T) (DSM 23547(T)) have genomes of similar lengths, similar numbers of protein coding genes and RNA genes. Both genomes encode for a greater number of peptidases compared to 'G. forsetii'. In contrast to the genome of 'G. forsetii', both genomes comprised a smaller set of CAZymes. Seven polysaccharide utilization loci were identified in the genomes of DSM 19838(T) and DSM 23547(T). Both Gramella strains hydrolyzed starch, galactomannan, arabinoxylan and hydroxyethyl-cellulose, but not pectin, chitosan and cellulose (Avicel). Galactan and xylan were hydrolyzed by strain DSM 19838(T), whereas strain DSM 23547(T) hydrolyzed pachyman and carboxy-methyl cellulose. Conclusively, both Gramella type strains exhibit characteristic physiological, morphological and genomic differences that might be linked to their habitat. Furthermore, the identified enzymes mediating polysaccharide decomposition, are of biotechnological interest.

KEYWORDS:

Bacteroidetes; Bioethanol; Carbohydrate active enzyme; Cellulose; Flavobacteriaceae; GEBA; Gliding motility; KMG I; Marine; Polysaccharide

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