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...

Laboratorium voorMicrobiologie, universiteit Gent, Belgium We designed a panel of four 16s rRNA-targeted oligonucleotide probes specific for bacteria of the phylum cytophaga-flavobacter-bacteroides (CFB). Probes CF319a and CF319b are targeted to members O f the flavobacteria-cytophaga group and the genus Porphyromonas, whereas probe BAC303 has a target region characteristic for the genera Prevote//a and Bacteroides within the bacteroides group. The probe FFE8b was developed for species-specif ic hybridizations with Flavobacterium ferrugineum. All probes were designed by computer-assisted sequence analysis and compared to all currently accessible 16s and 235 rRNA sequences. The oligonucleotides were further evaluated by whole-cell and non-radioactive dot-blot hybridization against reference strains of the CFB phylum and other major lineages of Bacteria. The newly developed probes were used together with other higher-order probes t o analyse the structure and community composition in complex environments. In activated sludge samples, members of the f lavobacteria-cytophaga group were revealed by in situ hybridization as important constituents of sludge flocs and characteristic colonizers of filamentous bacteria. By application of fluorescent probe BAC303, members of the genera Bacteroides and Prewotella could be visualized without prior cultivation as an important part of the human faecal microf lora.

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The Ghanaian cocoa bean heap fermentation process was studied through a multiphasic approach, encompassing both microbiological and metabolite target analyses. A culture-dependent (plating and incubation, followed by repetitive-sequence-based PCR analyses of picked-up colonies) and culture-independent (denaturing gradient gel electrophoresis [DGGE] of 16S rRNA gene amplicons, PCR-DGGE) approach revealed a limited biodiversity and targeted population dynamics of both lactic acid bacteria (LAB) and acetic acid bacteria (AAB) during fermentation. Four main clusters were identified among the LAB isolated: Lactobacillus plantarum, Lactobacillus fermentum, Leuconostoc pseudomesenteroides, and Enterococcus casseliflavus. Other taxa encompassed, for instance, Weissella. Only four clusters were found among the AAB identified: Acetobacter pasteurianus, Acetobacter syzygii-like bacteria, and two small clusters of Acetobacter tropicalis-like bacteria. Particular strains of L. plantarum, L. fermentum, and A. pasteurianus, originating from the environment, were well adapted to the environmental conditions prevailing during Ghanaian cocoa bean heap fermentation and apparently played a significant role in the cocoa bean fermentation process. Yeasts produced ethanol from sugars, and LAB produced lactic acid, acetic acid, ethanol, and mannitol from sugars and/or citrate. Whereas L. plantarum strains were abundant in the beginning of the fermentation, L. fermentum strains converted fructose into mannitol upon prolonged fermentation. A. pasteurianus grew on ethanol, mannitol, and lactate and converted ethanol into acetic acid. A newly proposed Weissella sp., referred to as "Weissella ghanaensis," was detected through PCR-DGGE analysis in some of the fermentations and was only occasionally picked up through culture-based isolation. Two new species of Acetobacter were found as well, namely, the species tentatively named "Acetobacter senegalensis" (A. tropicalis-like) and "Acetobacter ghanaensis" (A. syzygii-like).Cocoa beans are the principal raw material for chocolate production (39,43,73,81). These seeds are derived from the fruit pods of the cocoa tree (Theobroma cacao L.), which is cultivated in plantations in the equatorial zone, with the Ivory Coast, Brazil, and Ghana as the major producers (2). The cocoa beans are embedded in a mucilaginous pulp inside the pods. Raw cocoa beans have an astringent, unpleasant taste and flavor and have to be fermented, dried, and roasted to obtain the desired characteristic cocoa flavor and taste (26, 73). The final chocolate flavor is influenced by the origin and cultivar of the cocoa beans, the on-the-farm fermentation and drying process, and the roasting and further processing performed by the cocoa and chocolate manufacturer (4,10,32,33,57,75).After removal of the beans from the pods, the first step in cocoa processing is a spontaneous 3-to 10-day fermentation of beans and pulp in heaps, boxes, baskets, or trays, of which spontaneous heap fermentation is the most widely used method in Ghana ...

The aim of this study was to evaluate the use of RNA polymerase a subunit (rpoA) and phenylalanyl-tRNA synthase (pheS) gene sequences as species identification tools for enterococci. Ninety-six representative strains comprising all currently recognized Enterococcus species were examined. rpoA gene sequences generated a robust classification into species groups similar to the one based on 16S rRNA gene sequence analysis. On the other hand, the pheS gene is a fast-evolving clock even better suited for species delineation than the rpoA gene, but not for recognition of species groups within Enterococcus as determined by both rpoA and 16S rRNA genes. All enterococcal species were clearly differentiated on the basis of their rpoA and pheS sequences. Evaluation of intraspecies variation showed that both rpoA and pheS genes have a high degree of homogeneity among strains of the same species. Strains of the same enterococcal species have at least 99 % rpoA and 97 % pheS gene sequence similarity, whereas, different enterococcal species have at maximum 97 % rpoA and 86 % pheS gene sequence similarity. It was concluded that both genes can be used as reliable tools for identification of clinical and environmental species of Enterococcus and are efficient screening methods for the detection of novel species. The sequence data obtained in this study were compared to the available atpA and 16S rRNA gene sequences. The MLSA approach to Enterococcus taxonomy provides portable, highly reproducible data with lower costs for rapid identification of all enterococcal species.