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1 Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
2 Laboratory of Dairy Science and Technology, Kyodo Milk Industry Co. Ltd, Hinode, Tokyo 190-0182, Japan
Correspondence
Mohammad Abdul Bakir
bakir{at}jcm.riken.jp
| ABSTRACT |
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The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain 341T is AB214328.
Biochemical characteristics determined using the API systems, cellular fatty compositions, DNA G+C contents and levels of DNADNA hybridization among the novel strains and related Bacteroides species are available as supplementary tables in IJSEM Online.
| MAIN TEXT |
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Five bacterial strains (strains 276, 281, 341T, 342 and 344) were isolated from the faeces of healthy Japanese adults (strains 276 and 281 were from a 40-year-old male and the others from a 32-year-old female). The polyamine-deficient medium of Noack et al. (1998)
, with minor modification, and a standard dilution plate method were used for isolation. The composition of the medium was as follows (mmol l1 unless indicated): MOPS (40), Tricine (4), K2HPO4 (1·3), NaHCO3 (119), NaCl (85·5), NH4Cl (9·5), glucose (27·3), L-amino acid mixture [alanine (3·6), arginine (1·6), asparagine (1·9), aspartic acid (1·5), cystine (0·12), cysteine (3·3), glutamic acid (2·7), glutamine (3·4), glycine (8·5), histidine (0·6), isoleucine (1·7), leucine (2·8), lysine (12·3), methionine (0·7), ornithine (2·0), phenylalanine (1·3), proline (4·9), serine (2·3), threonine (1·7), tryptophan (0·2), tyrosine (0·7) and valine (2·4)], purines and pyrimidines [adenine, guanine, cytosine and uracil (0·2 each)], sodium succinate (9·0), haemin (0·015), vitamins [(µmol l1): p-aminobenzoic acid (0·4), folic acid (0·05), biotin (0·08), nicotinic acid (0·3), calcium pantothenate (0·1), thiamine hydrochloride (0·15), pyridoxine hydrochloride (0·49) and menadione (1·1)], mineral mixture [(µmol l1): MgSO4.7H2O (121·7), MnSO4.4H2O (22·4), CaCl2.2H2O (6·8), ZnSO4.7H2O (3·5), CoCl2.6H2O (4·2), Fe(II)SO4.7H2O (3·6), H3BO3 (1·6), Na2MoO4.2H2O (0·41) and NiCl2.6H2O (0·13)], Tween 80 (1·0 ml l1) and agar (20·0 g l1). An AnaeroPack (Mitsubishi Gas) was used for creating anaerobic conditions and the incubation period was 72120 h at 37 °C. The strains were subcultured on Eggerth Gagnon (EG) agar (Merck) supplemented with 5 % horse blood for 2 days at 37 °C in an anaerobic jar (Hirayama) filled with 100 % CO2.
Amplification of the 16S rRNA gene of the studied strains was conducted using a PCR machine (Biometra). Universal primers 27F (5'-AGAGTTTGATCCTGGCTCAG-3') and 1492R (5'-GGTTACCTTGTTACGACTT-3') were used for the amplification of a fragment of approximately 1500 bases of the 16S rRNA gene of the isolated strains. The amplified product was purified by using a Montage PCR96 filter plate (Millipore). A BigDye Terminator cycle sequencing kit (Applied Biosystems) and ABI PRISM 3100 Genetic Analyzer (Applied Biosystems) were used for sequencing, following the manufacturers' instructions. 16S rRNA gene sequences related closely to those of the isolated strains were retrieved from DDBJ, EMBL and GenBank. The sequences were aligned using CLUSTAL X (version 1.8) (Thompson et al., 1997
). A phylogenetic tree was constructed based on the neighbour-joining method (Saitou & Nei, 1987
). Stability of the groupings was estimated by bootstrap analysis (1000 replications). Almost complete (14841488 bp) 16S rRNA gene sequences of the five strains were determined. 16S rRNA gene sequence similarity between strains 341T and 342 was 100 %. Phylogenetic analysis indicated that strains 341T and 342 were related most closely to Bacteroides uniformis (94·8 %) and Bacteroides helcogenes (92·0 %) (Fig. 1
). These low sequence similarities (<97 %) indicated that strains 341T and 342 represented a novel genomic species (Stackebrandt & Goebel, 1994
). The 16S rRNA gene sequence similarity between strain 344 and B. uniformis was 99·6 %. Sequence similarity between strains 276 and 281 was 100 % and the two strains showed 97·4 % 16S rRNA gene sequence similarity to B. uniformis.
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-galactosidase (negative for strain 341T but positive for strain 342). Tests that are useful in distinguishing the novel taxon from some other Bacteroides species are summarized in Table 1
-galactosidase. Biochemical characteristics of strain 341T that differed from those of B. helcogenes included indole production, acid production from salicin, L-arabinose and L-rhamnose and production of 6-phospho-
-galactosidase,
-arabinosidase, proline arylamidase, phenylalanine arylamidase and leucine arylamidase. The strains were grown on GAM (Nissui) agar plates supplemented with 2 % Bacto oxgall (Difco) to test for bile resistance. All the studied strains grew well in the presence of bile.
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Based on the results of physiological, biochemical, cellular fatty acid and phylogenetic analysis, two strains (276 and 341T) were selected for determination of the G+C content and for DNADNA hybridization experiments with reference strains B. uniformis JCM 5828T and B. helcogenes JCM 6297T. For this purpose, bacterial cells were cultured in EGF broth at 37 °C for 12 h and then harvested. DNA was purified following the method of Saito & Miura (1963)
. HPLC was used for determination of the DNA G+C content of the strains as described by Kitahara et al. (2001)
. The DNA G+C contents of strain 341T, B. uniformis JCM 5828T and B. helcogenes JCM 6297T were 44, 48 and 46 mol%, respectively (Supplementary Table S3). The G+C content of strain 341T also supports its affiliation to the genus Bacteroides, members of which have G+C contents of between 40 and 48 mol% (Shah, 1992
). The level of DNADNA hybridization was determined by the method of Ezaki et al. (1989)
. Strain 341T showed a level of DNADNA hybridization of <9 % with B. uniformis JCM 5828T and B. helcogenes JCM 6297T (Supplementary Table S3). The low DNADNA relatedness value (<70 %) with the most closely related Bacteroides species again indicated the novel species status of strain 341T (Stackebrandt & Goebel, 1994
). Strain 276 showed over 84 % DNADNA relatedness with B. uniformis JCM 5828T. 16S rRNA gene sequence similarity between strains 276 and 281 was 100 %. Therefore, they were identified as representing B. uniformis.
On the basis of the results presented here, strain 341T should be classified as the type strain of a novel species of the genus Bacteroides, for which the name Bacteroides intestinalis sp. nov. is proposed.
Description of Bacteroides intestinalis sp. nov.
Bacteroides intestinalis (in.tes.ti.na'lis. N.L. masc. adj. intestinalis pertaining to the intestine).
Cells are strictly anaerobic, non-spore-forming, non-motile, Gram-negative rods, about 0·8 µm wide and 15 µm long, and occur singly. Surface colonies on EG blood agar plates after 2 days are 13 mm in diameter, circular, translucent-whitish, raised and convex. The optimum temperature for growth is about 37 °C. Grows in the presence of bile. Indole-positive and able to hydrolyse aesculin. Nitrate is not reduced. No activity is detected for urease and gelatin is not hydrolysed. Acid is produced from glucose, lactose, sucrose, maltose, xylose, arabinose, cellobiose, mannose, raffinose and rhamnose. Acid is not produced from mannitol, salicin, glycerol, melezitose, sorbitol or trehalose. Positive reactions are obtained using API rapid ID 32 A for
-galactosidase,
-galactosidase,
-glucosidase,
-glucosidase,
-arabinosidase, N-acetyl-
-glucosaminidase, glutamic acid decarboxylase,
-fucosidase, alkaline phosphatase, leucyl glycine arylamidase, alanine arylamidase and glutamyl glutamic acid arylamidase. Mannose and raffinose are fermented. Negative reactions are obtained for arginine dihydrolase,
-glucuronidase, arginine arylamidase, proline arylamidase, phenylalanine arylamidase, leucine arylamidase, pyroglutamic acid arylamidase, tyrosine arylamidase, glycine arylamidase, histidine arylamidase and serine arylamidase. The result for 6-phospho-
-galactosidase is variable. The major fatty acids are anteiso-C15 : 0 (32·033·6 %) and iso-C17 : 0 3-OH (18·519·2 %). The DNA G+C content is 44 mol%.
The type strain, 341T(=JCM 13265T=DSM 17393T), was isolated from human faeces. Strain 342 (=JCM 13266) is included in this species.
| ACKNOWLEDGEMENTS |
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