We isolated several strains from various clinical samples (five samples of blood, four of intra-abdominal pus and one of infected soft tissue) that were anaerobic, motile or non-motile and Gram-positive rods. Some of the strains formed spores. Phylogenetic analysis of the 16S rRNA gene sequence showed that these organisms could be placed within clostridial cluster IV as defined by Collins et al. [(1994). Int J Syst Bacteriol 44, 812–826] and shared more than 99 % sequence similarity with Clostridium orbiscindens DSM 6740T and Eubacterium plautii DSM 4000T. Together, they formed a distinct cluster, with Bacteroides capillosus ATCC 29799T branching off from this line of descent with sequence similarities of 97.1–97.4 %. The next nearest neighbours of these organisms were Clostridium viride, Oscillibacter valericigenes, Papillibacter cinnamivorans and Sporobacter termitidis, with sequence similarities to the respective type strains of 93.1–93.4, 91.2–91.4, 89.8–90 and 88.7–89.3 %. On the basis of biochemical properties, phylogenetic position, DNA G+C content and DNA–DNA hybridization, it is proposed to unify Clostridium orbiscindens and Eubacterium plautii in a new genus as Flavonifractor plautii gen. nov., comb. nov., with the type strain Prévot S1T (=ATCC 29863T =VPI 0310T =DSM 4000T), and to reassign Bacteroides capillosus to Pseudoflavonifractor capillosus gen. nov., comb. nov., with the type strain CCUG 15402AT (=ATCC 29799T =VPI R2-29-1T).

A hitherto unknown anaerobic bacillus isolated from sinus pus in a young child (strain AIP 354.02T) was characterized by using phenotypic and genotypic methods. 16S rRNA gene sequence analysis indicated that this strain was phylogenetically affiliated with several sequences of cloned 16S rRNA gene inserts previously deposited in the public databases. According to their 16S rRNA gene sequence similarities, these uncultivated bacteria, together with strain AIP 354.02T, formed a separate subgroup belonging to the family ‘Lachnospiraceae’ within the phylum Firmicutes. Oribacterium gen. nov. is proposed for this group of organisms and Oribacterium sinus gen. nov. sp. nov. for strain AIP 354.02T (=CIP 107991T=CCUG 48084T).

Three Gram-positive, anaerobic, non-spore-forming, rod-shaped bacteria with pointed ends were isolated from clinical specimens. The organisms were weakly saccharolytic and produced indole, acetate, butyrate and lactate as major metabolic end products. 16S rRNA gene sequence analysis indicated that the isolates had no known close relatives among recognized bacteria but that they exhibited a phylogenetic association with Clostridium rRNA cluster XIVa [as defined by Collins, M. D. et al. (1994) Anaerobic bacteria constitute an important part of the human microbial community. Although the majority are considered to be commensals, many of them behave as opportunistic pathogens. Notwithstanding intensive investigations by using conventional identification techniques, we still know relatively little about the bacterial diversity of these microbial communities. Indeed, molecular genetic tools have indicated that 60-80 % of organisms in the total human microflora have not been cultivated (Langendijk et al., 1995;Suau et al., 1999) and only 24 % of the molecular species recovered from the human intestinal tract corresponded to recognized species (Suau et al., 1999). Thus, the combination of genetic tools and traditional phenotypic methods of identification should be used whenever possible with the aim of providing greater knowledge of these 'hidden' bacteria. Here we report on the characterization of an indole-producing anaerobic bacterium that was recovered from different clinical specimens. Phylogenetically, the strains described represent a hitherto unknown subline within the Clostridium coccoides rRNA group. Based on the data presented, we describe a novel species in a new genus for these strains.The new isolates were recovered from clinical sources: strain AIP 241.03 from a buttock abscess, strain AIP 220.04 T from an intra-abdominal abscess (both from France) and strain MDA2477 from a polymicrobial thigh abscess (from Houston, TX, USA). Thus, these strains might all have originated from the intestinal tract. The strains were maintained in trypticase/glucose/yeast extract medium (TGY) consisting of 3 % (w/v) biotrypcase (bioMérieux), 0.5 % glucose (Prolabo), 2 % yeast extract (Difco), 0.05 % L-cysteine hydrochloride (Prolabo) and 5 mg haemin ml 21 (Calbiochem), under anaerobic conditions at 37 uC for 24 h in an anaerobic jar containing 95 % H 2 and 5 % CO 2 (v/v). Colony morphology determinations and presumptive identification tests (Engelkirk et al., 1992) were performed on Wilkins-Chalgren agar plates. Biochemical reactions were examined according to the procedures described by Holdeman et al. (1977). Metabolic end products were assayed by quantitative GC as described by Carlier (1985). For electron microscopy, cells were prepared as described by Carlier et al. (2004), and electron microphotographs were taken with a JEOL 1010 transmission electron microscope operating at 80 kV.Colonies appeared on Wilkins-Chalgren blood agar after 24-48 h incubation. They were circular, convex, about 0.5-1 mm in diameter, non-pigme...

Actinobacillus actinomycetemcomitans, a constituent of the oral flora, is a rare cause of brain abscesses. We report the case of a 47-year-old male who presented with multiple brain abscesses due to this organism, presumably originating from his poor dentition. Problems met in isolating and identifying A. actinomycetemcomitans suggest that its true rate of isolation from non-oral samples may have been underestimated.

A nonproteolytic, nontoxigenic Clostridium botulinum strain identified by conventional and molecular techniques as type B-, E-, or F-like (BEF-like) was isolated from a human postsurgical wound. All previous reports of such strains have been from environmental sources. Since toxin production is the main taxonomic denominator for C. botulinum, a new name is needed for nonproteolytic, nontoxigenic BEF-like clinical isolates. CASE REPORTA 50-year-old man was hospitalized in June 2002 for an open supracondylar fracture of the right humerus. His past medical history included several fractures between 1984 and 1999, psoriatic arthritis, and ankylosing spondylitis treated by corticotherapy up to 2001. The fracture was treated by open reduction and internal fixation with a Lecestre-type plate. The following week, the patient presented an inflammatory scar with fistula formation. Laboratory investigations revealed an erythrocyte sedimentation rate of 105 mm/h and a C-reactive protein value of 68 mg/liter. Surgical excision of infected tissues and drainage were performed. The patient was treated with intravenous ofloxacin (200 mg twice daily) and rifampin (1 g twice daily). Biopsy specimens of the triceps and articular capsule revealed after culture the presence of Clostridium perfringens and Sphingomonas paucimobilis. The patient was then treated with intravenous ceftriaxone (2 g once daily) and oral ofloxacin (200 mg twice daily) and metronidazole (200 mg twice daily) for 1 week. The symptoms gradually resolved, and the patient left the hospital on day 29 with trimethoprim-sulfamethoxazole (two tablets three times daily), ofloxacin (200 mg twice daily), and metronidazole (500 mg three times daily) prescribed. One month later, the patient developed an osteosynthesis-associated bone infection. Extensive debridement was performed, and all purulent-appearing bone was resected. The plate was removed and reinserted by using a gentamicin-and vancomycin-loaded spacer. The same antibiotic therapy was continued, and the patient was discharged on day 74. A strictly anaerobic, gram-positive, motile, spore-forming rod, designated AIP 355.02, was the only bacterium isolated from all samples obtained during surgery. It was found to be susceptible to all antibiotics used except for trimethoprim-sulfamethoxazole and gentamicin.Strain AIP 355.02 was characterized according to conventional tests (13). Metabolic end products were assayed by quantitative gas chromatography as described previously (5).The organism was lecithinase negative and lipase positive on egg yolk agar plates. Gelatin was liquefied, and milk was not modified. Production of urease and indole was not detected. Acid was produced from glucose, fructose, maltose, mannose, ribose, starch, and sorbitol. Acid was not produced from arabinose, cellobiose, esculin, galactose, glycerol, inositol, lactose, mannitol, melezitose, melibiose, raffinose, rhamnose, sucrose, salicin, trehalose, and xylose. The strain hydrolyzes starch but not esculin. Abundant gas was produced. The major ...

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