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Prokaryotes (2006) 7:481–531 DOI: 10.1007/0-387-30747-8_17

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The Genus Flavobacterium JEAN-FRANÇOIS BERNARDET AND JOHN P. BOWMAN

Introduction The genus Flavobacterium Bergey, Harrison, Breed, Hammer, and Huntoon 1923, emend. Bernardet, Segers, Vancanneyt, Berthe, Kersters, and Vandamme 1996 (Bergey et al., 1923; Bernardet et al., 1996) is probably one of the best examples of the revolution brought to the classification of a bacterial taxon by the use of the phylogenetic techniques based on the comparison of 16S rRNA sequences. Of the seven species considered in the previous edition of Bergey’s Manual of Systematic Bacteriology (Holmes et al., 1984), only the type species F. aquatile was finally retained while several other taxa, previously misclassified in other genera, were added to form an extensively emended genus Flavobacterium (Bernardet et al., 1996). Since then, the genus has considerably expanded owing to the description of many new species mostly originating from polar habitats. The organisms currently included in the genus Flavobacterium were distributed among different chapters in previous editions of Bergey’s Manual and of The Prokaryotes. In Bergey’s Manual, Flavobacterium aquatile was dealt with in the chapter “Genus Flavobacterium” (Holmes et al., 1984), while several other Flavobacterium species were considered (under other generic epithets) in the chapter “Order I. Cytophagales” (Reichenbach, 1989) in the second edition of The Prokaryotes. The latter species were also included in the chapter The Order Cytophagales in the second edition, while F. aquatile was excluded from the chapter The Genera Flavobacterium, Sphingobacterium, and Weeksella also from this Volume and not considered anywhere else! These chapters contain a wealth of information and are still well worth consulting. The history and structure of the family Flavobacteriaceae, of which the genus Flavobacterium is the type genus, are presented in the chapter “An Introduction to the Family Flavobacteriaceae” in this Volume. The taxonomic and nomenclatural issues concerning the genus Flavobacterium are dealt with by the subcommittee on the taxonomy of

Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes. This subcommittee has issued minimal standards for the description of new taxa in the genus Flavobacterium and other genera in the family Flavobacteriaceae (Bernardet et al., 2002). Few species in the genus Flavobacterium have been extensively studied and most of them are represented by one strain (i.e., the type species F. antarcticum as well as F. aquatile, F. flevense, F. frigidarium, F. gillisiae, F. granuli, F. hydatis, F. omnivorum, F. pectinovorum, F. saccharophilum, F. xanthum and F. xinjiangense) or a limited number of strains in culture collections. Exceptions are the fish-pathogenic species, of which many strains are usually available; owing to their economic significance worldwide, they have been the subject of numerous studies (see the sections “Habitat and Ecology” and “Pathogenicity and Epidemiology” in this Chapter) and will provide many examples in this chapter.

Phylogeny Sequences of 16S rRNA and DNA gyrase large subunit (gyrB) genes (Weisburg et al., 1985; Woese et al., 1990; Nakagawa and Yamasato, 1993; Suzuki et al., 2001) locate the genus Flavobacterium within the phylum “Bacteroidetes,” clustering appropriately in a central position in the family Flavobacteriaceae (Bernardet et al., 1996) where it represents the type genus. Within the family Flavobacteriaceae, the genus Flavobacterium branches between two primary lineages, one consisting of mostly marine genera and the other of non-marine genera (see the chapters An Introduction to the Family Flavobacteriaceae in this Volume and The Marine Clade of the Family Flavobacteriaceae: The Genera Aequorivita, Arenibacter, Cellulophaga, Croceibacter, Formosa, Gelidibacter, Gillisia, Maribacter, Mesonia, Muricauda, Polaribacter, Psychroflexus, Psychroserpens, Robiginitalea, Salegentibacter, Tenacibaculum, Ulvibacter, Vitellibacter and Zobellia in this Volume). This