High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2T (DSM 21788T), 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 3.3-2T 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 GenomicEncyclopedia ofBacteria andArchaea 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 3.3-2T 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s40793-015-0032-y) contains supplementary material, which is available to authorized users.

Marine Polysaccharide Sulfatases

“…This PUL has been transferred laterally from marine Bacteroidetes to human microbiota Bacteroidetes (Hehemann et al, 2010). Many other PULs dedicated to the degradation of sulfated polysaccharides have been observed in several bacteria genomes or metagenomes (Gómez-Pereira et al, 2012; Mann et al, 2013;Kabisch et al, 2014;Hahnke et al, 2015;Xing et al, 2015;Panschin et al, 2016;Sun et al, 2016). The functions of PULs are hypothesized based on sequence homology of glycoside hydrolases found in the PUL with characterized enzymes.…”

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

“…The genome of F. suncheonense GH29-5 T contains a relaltively low number of carbohydrate active enzymes in contrast to genomes of other Flavobacteriaceae such as Flavobacterium branchiophilum [ 54 ], Flavobacterium rivuli [ 14 ], Formosa agariphila [ 55 ], Polaribacter [ 4 , 56 ], ‘ Gramella forsetii ’ [ 57 ] and Zobellia galactanivorans [ 17 ]. This is surpising, since greenhouse soil might be a rich source of plant litter.…”

“…The sequence of the single 16S rRNA gene copy in the genome is identical with the previously published 16S rRNA gene sequence ( DQ222428 ). Figure 1 shows the phylogenetic neighborhood of F. suncheonense GH29-5 T inferred from a tree of 16S rRNA gene sequence, as previously described [ 14 ]. The next related type species are F. cauense R2A-7 T ( EU521691 ), F. enshiense DK69 T ( JN790956 ), F. limnosediminis JC2902 T ( JQ928688 ) and F. saliperosum S13 T ( DQ021903 ) with less than 95.9 % 16S rRNA gene identity.…”

“…Therefore, we compared the predicted CDS against the CAZyme [ 45 , 46 ] and dbCAN [ 47 ] database. The CAZyme annotation (Additional file 1 , Table S1) was a combination of RAPSearch2 search [ 48 , 49 ] and HMMER scanning [ 50 ] as described in Hahnke et al [ 14 ]. The genome of strain GH29-5 T comprised a small number of carbohydrate active enzymes (49) including 36 glycosyl transferases, nine glycoside hydrolases, four carbohydrate binding modules and six carbohydrate esterases (Table 7 ).…”

“…The MEROPS annotation was carried out by searching the sequences against the MEROPS 9.10 database [ 53 ] (access date: 2014.10.16, version: pepunit.lib) as described in Hahnke et al [ 14 ]. The genome of strain GH29-5 T comprised 117 identified peptidase genes (or homologues), mostly serine peptidases (S, 50), metallo peptidases (M, 50) and cysteine peptidases (C, 14) (Table 8 , Additional file 1 : Tables S3 and S4).…”