The Cytophaga-Flavobacteria cluster (in the following referred to as Cytophagales) represents an important subgroup of the Bacteroidetes, a bacterial lineage formerly known as Cytophaga-Flavobacteria-Bacteroides (CFB) phylum. Cytophagales are mostly aerobic chemoorganoheterotrophs specialized for polymer-degradation. FISH studies (Llobet-Brossa et al., 1998; Rossello-Mora et al., 1999; Glockner et al., 1999 ; Simon et al., 1999 ; Eilers et al., 2001) have demonstrated high abundance of Cytophagales in marine systems. Studies on the ecology of this important group are on-going (Jürgens et al., 1999; Rossello-Mora et al., 1999; Zubkov et al., 2001). Several pure cultures were isolated from the North Sea (Eilers et al., 2001).

Whereas Bacteroides and relatives are mostly studied by medical microbiologists the interest in the Cytophagales is more diverse (for details see Reichenbach, The Prokaryotes 1991) :

• For biotechnologists they are producers of exopolysaccharides (EPS) and of many special enzymes for technical applications, including proteases, glycosyl-hydrolases and -transferases. More than 20% of 270 tested strains have been found to produce interesting secondary metabolites, such as beta-lactams.
• Microbial ecologists more and more recognize the central role of Cytophagales in the global carbon cycle as demineralizers of organic carbon. They are, e.g., important constituents of marine snow in which they digest particulate organic matter that would otherwise sediment to the sea floor and remove carbon from the atmosphere. As mentioned before, they are also a dominant part of the free-living bacterioplankton in both oceans and lakes. Additionally, they also represent an important fraction of the benthic anaerobic microbiota most probably catalyzing primary fermentative processes in sediment diagenesis.
• From a taxonomic point of view it should be noted that the Cytophaga-Flavobacteria-Bacteroides phylum is as diverse as the Proteobacteria. It came as a true surprise when in the mid 1980s the comparative 16S rRNA analysis affiliated the aerobic Cytophagales with the anaerobic genus Bacteroides. Comparative genomics between the published Bacteroides genome(s) and the proposed Cytophagales will shed new light on this phylogenetic aspect. Additionally, Salinibacter spp. represents the first extreme halophilic member of the phylum. The 16S rRNA-based phylogenetic analyses revealed that it deeply branched in their phylum, and might share properties to the sister phylum Chlorobi.
• Finally, although of little importance for human health, Cytophagales have also raised concerns with respect to food spoilage and pathogenicity for fish.

Well characterized and easily maintained pure cultures are available. In the following some details are given on the strains suggested for sequencing :

Zobellia galactonivorans : Zobellia galactonivorans strain DsijT was isolated from pieces of the red alga Delesseria sanguinea. DsijT exhibited spreading growth on agar plates forming yellow-orange colonies of 1 mm in diameter within 3 days at 20°C. Strain DsijT is a strictly aerobic, seawater-requiring, chemo-organotrophic, and heterotrophic bacterium, with an oxidative metabolism that uses oxygen as the electron acceptor. Nitrate can also be used as electron acceptor. The strain DsijT synthesizes flexirubin and is able to degrade proteinaceous substrates as well as several polysaccharides, such as agar, kappa- and iota-carrageenan, starch, and gelatin. It does not display any chitinolytic activity or cellulolytic activity, either against solid (paper) or amorphous (CMC) cellulose. By flow cytometry the size of the genome was estimated to be 4.10 Mbp. The 16S rDNA sequence of strain DsijT was found to be closely related to Zobellia [Cytophaga] uliginosa, with a sequence identity of 99.5%, the two forming a distinct deep branch in the family Flavobacteriaceae.

Salinibacter ruber M8 : Salinibacter ruber is an extremely halophilic Gram negative, heterotrophic bacterium that shares its habitat with the halophilic Archaea and that ressembles them in many traits such as very high salt requirements, red pigmentation, very high intracellular KCl concentrations, and enzymes that are functional at high salt concentrations. Besides, Salinibacter proteins display the characteristic features of halophilic proteins i.e. a large excess of acidic amino acids, a low content of hydrophobic amino acids and a high content of serine.