The phylogenetic positions and G+C contents of most species belonging to the genera Flavobacterium, Cytophaga, and Flexibacter and several related taxa were determined. Most of the strains included in this study belong to rRNA superfamily V, as shown by DNA-rRNA hybridization data, but the three main genera are highly polyphyletic. Several so-called Cytophaga and Flexibacter species isolated from soil and freshwater cluster with the type species of the genus Flavobacterium, Flavobacterium aquatile, and with Flavobacterium branchiophilum. The fatty acid and protein profiles of members of this group of organisms were determined. We provide an emended description of the genus Flavobacterium and propose new combinations for the following 7 of the 10 validly described species included in this genus: Flavobacterium columnare, Flavobacterium JEevense, Flavobacterium johnsoniae (we also correct the specific epithet of this taxon), Flavobacterium pectinovorum, Flavobacteriurn psychrophilum, Flavobacterium saccharophilum, and Flavobacterium succinicans. A new name, Flavobacterium hy&tis, is proposed for [Cytophaga] aquatilis Strohl and Tait 1978. The emended genus FZavobucterium contains bacteria that have the following main characteristics: gram-negative rods that are motile by gliding, produce yellow colonies on agar, are chemoorganotrophs and aerobes, decompose several polysaccharides but not cellulose, and are widely distributed in soil and freshwater habitats. Three Flavobacterium species are pathogenic for fish. The G+C contents of Flavobacterium DNAs range from 32 to 37 mol%. An emended description of the family Flavobacteriaceae is also provided.The long and complex history of the genera Flavobacterium, Cytophaga, and Flexibacter and the heterogeneity of these genera have been well documented. The most recent reviews of the taxonomy of these organisms were published in Bergey's Manual of Systematic Bacteriology (40, 68), in The Prokaryotes 2nd ed. (37,69), and in Advances in the Taxonomy and Significance of Flavobacterium, Cytophaga and Related Bacteria (38,70). Because of the numerous phenotypic similarities of Flavobacterium, Cytophaga, and Flexibacter strains, for a long time differentiation of these genera has been based on the presence (in the genera Cytophaga and Flexibacter) or absence (in the genus Flavobacterium) of gliding motility. This characteristic, whose relevance for genus delineation has been questioned, is probably an ancestral property of this bacterial group that was lost by some organisms in the course of evolution (68, 101).The genus Flavobacterium was created in 1923 (7) to accommodate gram-negative, non-spore-forming, yellow-pigmented rods that produce acid from carbohydrates weakly (40). Because of this limited definition, the genus rapidly acquired many poorly defined species and consequently became very heterogeneous. However, through successive emendations, the genus Flavobacterium was restricted to nonmotile and nongliding species and thus achieved what could be considered reasonable h...

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NOTESOur present knowledge concerning the genotypic, chemotaxonomic, and phenotypic characteristics of members of the genus Flavobacterium and some related genera, including the genus Weekella, was used to revise the classification of these organisms. The generically misclassified organisms Flavobacterium balustinum, Flavobacterium gleum, Flavobacterium indologenes, Flavobacterium indoltheticum, Flavobacterium meningosepticum, and Flavobacterium scophthalmurn are included in a new genus, Chryseobacterium, with Chryseobacterium gleum as the type species. The generically misclassified organism Flavobacterium breve is included in the revived genus Empedobacter as Empedobacter brevis, whereas the generically misclassified organism W e e k e h zoohelcum is included in the new genus Bergeyella as Bergeyella zoohelcum.

Bacteria of the Burkholderia cepacia complex consist of five discrete genomic species, including genomovars I and III and three new species: Burkholderia multivorans (formerly genomovar II), Burkholderia stabilis (formerly genomovar IV), andBurkholderia vietnamiensis (formerly genomovar V). Strains of all five genomovars are capable of causing opportunistic human infection, and microbiological identification of these closely related species is difficult. The 16S rRNA gene (16S rDNA) and recAgene of these bacteria were examined in order to develop rapid tests for genomovar identification. Restriction fragment length polymorphism (RFLP) analysis of PCR-amplified 16S rDNA revealed sequence polymorphisms capable of identifying B. multivorans andB. vietnamiensis but insufficient to discriminate strains of B. cepacia genomovars I and III and B. stabilis. RFLP analysis of PCR-amplified recAdemonstrated sufficient nucleotide sequence variation to enable separation of strains of all five B. cepacia complex genomovars. Complete recA nucleotide sequences were obtained for 20 strains representative of the diversity of the B. cepacia complex. Construction of a recA phylogenetic tree identified six distinct clusters (recA groups):B. multivorans, B. vietnamiensis, B. stabilis, genomovar I, and the subdivision of genomovar III isolates into two recA groups, III-A and III-B. Alignment of recA sequences enabled the design of PCR primers for the specific detection of each of the six latter recA groups. The recA gene was found on the largest chromosome within the genome of B. cepacia complex strains and, in contrast to the findings of a previous study, only a single copy of the gene was present. In conclusion, analysis of the recA gene of theB. cepacia complex provides a rapid and robust nucleotide sequence-based approach to identify and classify this taxonomically complex group of opportunistic pathogens.