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Reclassification of Eubacterium Formicigenerans Holdeman And International Journal of Systematic and Evolutionary Microbiology (2002), 52, 423–428 DOI: 10.1099/ijs.0.01874-0 Reclassification of Eubacterium NOTE formicigenerans Holdeman and Moore 1974 as Dorea formicigenerans gen. nov., comb. nov., and description of Dorea longicatena sp. nov., isolated from human faeces 1 Department of David Taras,1 Rainer Simmering,1 Matthew D. Collins,2 Paul A. Lawson2 Gastrointestinal 1 Microbiology, German and Michael Blaut Institute of Human Nutrition, Arthur- Scheunert-Allee 114-116, Author for correspondence: Michael Blaut. Tel: j49 33200 88470. Fax: j49 33200 88407. 14558 Bergholz- e-mail: blaut!www.dife.de Rehbru$ cke, Germany 2 School of Food Biosciences, University of Reading, Two strains of a Gram-positively staining, obligately anaerobic, non-spore- Reading RG6 6AP, UK forming, rod-shaped bacterium, designated strains 111-13A and 111-35T, were isolated from human faeces. Analysis of the 16S rRNA gene sequences indicated that these strains were members of the Clostridium coccoides rRNA group of organisms. The nearest relatives of the unknown bacterium were Eubacterium formicigenerans (having a sequence similarity of 94%) and an uncultured bacterium (similarity " 99%). Characterization studies indicated that the unidentified faecal bacterium was biochemically distinct from Eubacterium formicigenerans, members of the Clostridium coccoides group and all other described Eubacterium species. On the basis of the data from these studies, it is proposed that the hitherto unknown rod-shaped bacterium be designated a species of a novel genus, namely Dorea longicatena gen. nov., sp. nov., and that Eubacterium formicigenerans be transferred to this genus as Dorea formicigenerans gen. nov., comb. nov. Keywords: Dorea longicatena, Dorea formicigenerans, 16S rRNA, taxonomy, phylogeny The intestinal microbiota of humans consists of more human gut (Suau et al., 1999). During an investigation than 400 bacterial species (Finegold et al., 1974; Moore of the human faecal flora, we isolated two strains & Holdeman, 1974). Despite extensive efforts to of a strictly anaerobic, non-spore-forming, Gram- characterize the intestinal microflora, it is now recog- positively staining, rod-shaped organism that dis- nized that a significant proportion of the dominant played " 99% 16S rRNA gene sequence similarity to flora has so far eluded scientific description (Lan- one of the uncultured species reported by Suau et al. gendijk et al., 1995; Zoetendal et al., 1998). Recently, (1999). On the basis of the results of a polyphasic taxo- Suau et al. (1999) conducted a molecular genetic nomic investigation, we propose that these strains be analysis of rDNA amplicons generated directly from a classified, alongside their nearest phylogenetic rela- human faecal sample and showed that more than 90% tive, Eubacterium formicigenerans, in a novel genus, of the flora could be assigned to three major phylo- Dorea gen. nov. genetic lineages (the Bacteroides, Clostridium coccoides T and Clostridium leptum groups). It was evident from Strains 111-13A and 111-35 were isolated from a this molecular taxonomic inventory that the vast screening programme (for hydrogen-producing micro- majority of rDNA sequences generated (76%) did not organisms) using faecal samples from a healthy vol- correspond to known organisms and were clearly unteer who had not undergone antibiotic therapy for derived from hitherto unknown species within the the preceding 6 months. For this purpose, fresh faecal samples were transferred into an anaerobic work- station (MK3; DW Scientific) and diluted serially 10- ................................................................................................................................................. "# The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene fold up to 10 in Wilkins–Chalgren anaerobic broth sequence of strain DSM 13814T is AJ132842. (WCA; Oxoid), a peptone- and yeast extract-con- 01874 # 2002 IUMS Printed in Great Britain 423 D. Taras and others (a) (b) ................................................................................................................................................................................................................................................................................................................. Fig. 1. Scanning electron micrographs of isolate 111-35T grown in HA medium with 10 mM glucose and with 0n5g − Proteose-Peptone l 1 for 12 h at 37 mC. Bars, 5 (a) and 1 (b) µm. taining complex medium, supplemented with 20 mM pH of the medium. Cells were tested for catalase and 2-bromoethanesulfonate and 20 mM Na#MoO% (to oxidase as described previously (Smibert & Krieg, give medium mod-WCA). An aliquot (0n5 ml) of an 1994) after cultivation on WCA agar. Other bio- enrichment culture that developed from the highest chemical features were determined with the API 50 dilution and showed H# production and morphology CHL system (bioMe! rieux). Experiments with resting of long cell chains was plated onto mod-WCA agar cells were performed as described by Kamlage et al. (1n5% agar, w\v) plates. Single colonies were re- (1997). Hydrogen (Hartmann et al., 2000) and acetate, peatedly picked and streaked until pure cultures were butyrate, propionate, valerate and isovalerate (Kam- obtained. Unless indicated otherwise, all incubations lage et al., 1997) were determined by GC as described. were performed at 37 mC under a N#\CO# (80:20, v\v) Succinate, ethanol, formate, acetate, -lactate, - gas phase, using strictly anaerobic conditions (Hun- lactate and glucose were determined enzymically gate, 1969; Bryant, 1972). For morphological and (Bergmeyer & Graßl, 1984). DNA extraction was done physiological studies, both strains were grown on as described by Schwiertz et al. (2000). The GjC Columbia blood agar (bioMe! rieux), in ST medium content of the DNA was determined by HPLC (Schwiertz et al., 2000) or in a medium used for according to Mesbah et al. (1989) except that the culturing acetogenic bacteria (Kamlage et al., 1997) methanol content of the chromatographic buffer was but modified by the addition of 0n5 g Proteose-Peptone reduced to 8% and the temperature was raised to −" no. 2 (Difco) l (HA medium). Agar plates were 37 mC. Lambda DNA (Sigma) served as a standard. prepared by adding 1n5% agar to the appropriate DNA–DNA hybridization was carried out according liquid media, and the plates were poured inside an to Johnson (1994). The DNA–DNA hybrids were anaerobic workstation (N#\CO#\H#; 80:10:10, by detected with the DIG luminescent detection kit vol.). The morphology of the isolates was examined by (Roche) and quantified with an image analyser (Fuji- phase-contrast microscopy (Axioplan 2; Zeiss) and film LAS-1000). For the phylogenetic analysis, the 16S by scanning electron microscopy (model DSM 950; rRNA genes of the two isolates were amplified by PCR Zeiss) after growth on WCA or Columbia blood agar. and sequenced directly using a Taq Dye-Deoxy ter- The methods of Grund et al. (1995) were used for the minator cycle sequencing kit (Applied Biosystems) and scanning electron microscopy. Growth was monitored an automatic DNA sequencer (model 373A, Applied using changes in optical density (at 600 nm) and in the Biosystems). A phylogenetic tree was constructed 424 International Journal of Systematic and Evolutionary Microbiology 52 Dorea gen. nov., containing two species according to the neighbour-joining method, and the showed that the two strains had identical 16S rRNA confidence values of the groupings were estimated by gene sequences, and searches of the GenBank and bootstrap analysis (Felsenstein, 1989). Ribosomal Database Project databases revealed that the isolates were closely related to members of the The two faecal isolates (111-13A and 111-35T) were Clostridium coccoides rRNA group of organisms non-spore-forming, non-motile, strictly anaerobic, (rRNA cluster XIVa; Collins et al., 1994). The highest rod-shaped organisms. The cells were 0 5–0 6 µm wide n n level of sequence relatedness was shown with respect to by 2 0–4 3 µm long and occurred in chains of approxi- n n an rDNA clone derived from an uncultured faecal mately 4–200 cells (Fig. 1). In the exponential growth bacterium (Suau et al., 1999). The described species phase, cells stained Gram-positive, whereas stationary- nearest to the unknown isolates was Eubacterium phase cells exhibited Gram-negative staining behav- formicigenerans (94% sequence similarity). A tree iour. Cultures in ST medium and in HA medium had constructed by neighbour-joining and depicting the a ropy sediment with little or no turbidity. When ST phylogenetic position of the unknown bacterium medium was supplemented with 0 15% agar, the n within the Clostridium coccoides group is shown in cultures exhibited turbidity with dense areas of a fluffy, Fig. 2. ‘woolly’ appearance. Both strains formed white– opaque, non-haemolytic colonies on Columbia blood From these results, it is evident that the two faecal agar and on WCA agar; the colonies were approxi- isolates belong to a hitherto undescribed species, mately 1–3 mm in diameter, circular, convex, smooth, probably related to an uncultured species detected shiny and mucoid. The strains behaved the same with previously in human faeces by direct PCR rDNA respect to all of the biochemical tests. Both isolates community analysis (Suau et al., 1999). The novel rod- produced acid from -glucose, -lactose, -maltose, shaped bacterium forms a distinct subline within the -galactose, amygdalin, -arabinose,
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