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Pedobacter Heparinus Comb. Nov., Pedobacter Piscium Comb

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Pedobacter Heparinus Comb. Nov., Pedobacter Piscium Comb International Journal of Systematic Bacteriology (1998), 48, 165-1 77 Printed in Great Britain Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species : Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. Proposal of the family Sphingobacteriaceae fam. nov. P. L. Steyn,’ P. Segers,2 M. Vancanneyt,2 P. Sand~a,~K. Kersters’ and J. J. Joubert4 Author for correspondence : P. Segers. Tel : + 32 9 2645 115. Fax : + 32 9 2645346. e-mail : [email protected]. be 1 Departement Sixteen heparinase-producingisolates, related to Sphingobacterium Mikrobiologie en heparinum, were grouped into three major clusters by SDS-PAGE and Plantpatologie, Universiteit van Pretoria, DNA-rRNA hybridizations. Based on a polyphasic approach, it was shown that 0002 Pretoria, South Africa isolates of two of these clusters and S. heparinum species belong to a new 2 Laboratorium voor genus for which the name Pedobacter is proposed. The genus consists of Microbiologie, Universiteit Pedobacter heparinus comb. nov. (formerly Sphingobacterium heparinurn), Gent, B-9000 Gent, which is the type species, Pedobacter piscium comb. nov. (formerly Belgium Sphingobacteriumpiscium), Pedobacter africanus sp. nov. and Pedobacter 3 Laboratorium voor saltans sp. nov. and four as-yet-unnamed DNA hybridization groups. All the 0 rga n ische Sc heiku nde, Universiteit Gent, B-9000 previously named taxa can be discriminated by phenotypic features, but have Gent, Belgium strong overall similarities with representatives of the genus Sphingobacterium 4 Departement and the misclassified species [Flexibacter]canadensis. All these organisms Geneeskundige constitute a separate rRNA branch in rRNA superfamily V for which the family M ikro biolog ie, Un ive rsitei t Sphingobacteriaceae fam. nov. is proposed. van Stellenbosch, Posbus 19063,7505 Tygerberg, South Africa Keywords : Pedobacter heparinus comb. nov., Pedobacter pisciurn comb. nov., Pedobacter africanus sp. nov., Pedobacter saltans sp. nov., Sphingobacteriaceae fam. nov. INTRODUCTION isolates, respectively. Corresponding rRNA groups and sub-groups were found by DNA-rRNA hybrid- Sphingobacteriurn heparinurn, represented by a single izations (26, 27). isolate, remained for many years the sole represen- tative of a strictly aerobic Gram-negative, heparinase- ‘ The generic status of S. heparinurn has been discussed repeatedly and the organism has been successively producing bacterium. Joubert (14) succeeded in ob- transferred to other genera. The species was first taining heparinase-producing isolates from soil and described as Flavobacteriurn heparinurn (20), and was activated sludge. Sixteen isolates were investigated by later reclassified in the genus Cytophaga as Cytophaga SDS-PAGE of whole-cell proteins and found to consist heparina (2). Reichenbach (21) has already questioned of three discernable groups (26). One group comprising the inclusion of the organism in the genus Cytophaga. 11 isolates and two subcultures of the type strain of S. More recently the phylogenetic position of C. heparina heparinurn were found to cluster into a single group (consisting of two sub-groups Ia and Ib). The second was further elucidated (7, 8, 17, 18, 19, 26). Based on group (11) and a third group (111) contain one and four phenotypic and chemotaxonomic analyses, Takeuchi & Yokota (28) proposed the transfer of C. heparina to the genus Sphingobacteriurn as S. heparinurn. The Abbreviation : FAME, fatty acid methyl ester. genus Sphingobacteriurn is part of rRNA superfamily 00607 0 1998 IUMS 165 P. L. Steyn and others Table 7. Strains used, some other strain designations and source of isolation LMG, Laboratorium voor Microbiologie Gent Culture Collection, University of Gent, Belgium; ATCC, American Type Culture Collection, Rockville, MD, USA; CCUG, Culture Collection of the University of Goteborg, Department of Clinical Bacteriology, University of Goteborg, Sweden; IFO, Institute for Fermentation, Osaka, Yodogawa-ku, Osaka 532, Japan. Name and LMG no.* Other designation(s) Source Pedobacter heparinus (Ial) LMG 10399T ATCC 13125T,IF0 12017T Dry soil LMG 10344Tt AL-F Dry soil Pedobac ter afr ican us (Ia 3) LMG 10353T Belfast, Eastern Transvaal, South Africa; soil LMG 10345 Windhoek, Namibia; activated sludge LMG 10346 Pretoria, South Africa; soil LMG 10347 Western Caprivi, Namibia; soil LMG 10348 Pretoria, South Africa; activated sludge LMG 10349 Eastern Kavango, Namibia; soil Pedo b ac ter p isc ium LMG 14023T IF0 14985T LMG 14024 IF0 14984 Pedobacter saltans (111) LMG 10337T Iceland ; soil LMG 10338 Iceland ; soil LMG 10340 Brussels, Belgium; soil LMG 10341 Rudesheim, Germany; soil Pedobacter sp. (Ia2) LMG9525 LMG 10350 Ephesus, Turkey; soil LMG 10343 Swartkoppies, Transvaal, South Africa; soil Pedobacter sp. (Ibl) LMG9527 LMG 10352 Langkloof, Eastern Cape, South Africa; soil LMG 10354 Roodeplaat, Pretoria, South Africa; soil Pedobacter sp. (Ib2) LMG 10342 Sambyu, Kavango, Namibia; soil Pedobacter sp. (11) LMG 10351 Amsterdam, The Netherlands ; soil Sphingobacterium spiritivorum LMG 8347T CCUG 13224T,IF0 14948T Kansas, USA; intra-uterine device LMG 8348 CCUG 15910 - Sphingobacterium multivorum LMG 8342T CCUG 1 1736T,IF0 14947T Spleen LMG 8354 CCUG 22177 Denmark ; soil Sphingobac ter ium m izutae LMG 8340tlT CCUG 15907T,IF0 14946T Ventricular fluid of foetus LMG 8341 CCUG 15908 - Sph ingobac ter ium t halpophilum LMG 11520T CCUG 22397T,IF0 14963T Wound swab LMG 11521 CCUG 22398 Human abscess Sph ingoba c ter ium faecium LMG 14022T IF0 15299T [Flavobacterium] yabuuchiae LMG 1 1523T CCUG 26765T,IF0 14975T USA; human sputum [Flexibacter]canadensis LMG 8368T ATCC 29591T Soil * The SDS-PAGE or DNA hybridization sub-group number (26, 27 and this paper) are shown in parentheses. t Strain LMG 10344Tis an independently received subculture (from Dr A. Linker, Salt Lake City, UT, USA) of the type strain. 166 International Journal of Systematic Bacteriology 48 New genus of heparinolytic bacteria, Pedobacter V, the so-called Cytophaga-Flavobacterium-Bac- Systems). A suspension was made of a 3-d-old slant in sterile teroides group (1, 23, 26). The confused taxonomy of water, adjusted to give a reading of 5-6 on the MacFarland this large group of bacteria was recently clarified by scale and used for inoculating the galleries. The API 20E rRNA similarity studies (1, 7, 8, 17, 18, 19) and galleries were incubated at 25 "C for 7 d, and the API ZYM quinone analyses (5, 17, 18, 28). This resulted in the galleries at 30 "C for 4 h. creation of new genera (1 8, 30) and emended descrip- GC of cellular fatty acids. The methods using the MIS system tions of the genus Flavobacterium, the family Flavo- (Microbial Identification System) have been described pre- bacteriaceae (1) and the genus Cytophaga (1 8). viously (27). Fatty acid methyl esters (FAMEs) were separated on an apolar fused silica capillary column coated This paper reports on the classification of the hepar- with a phenyl methyl silicone gum phase (Hewlett-Packard). inase-producing isolates by a more detailed phenotypic Under these conditions the fatty acids 16: 1m7c and iso- description and determination of fatty acid content of 15:0(2-OH), two major components of the taxa studied, the obtained clusters and related organisms, together eluted for most strains as a single peak. To quantify both with some additional DNA-rRNA and DNA-DNA FAMEs a second analysis was performed on a polar hybridizations. Preliminary data have already been cyanopropyl silicone column (3 1) where both peaks elute at presented by Steyn et al. (27). A new genus Pedobacter, clearly different retention times. encompassing two former Sphingobacterium species, DNA-rRNA and DNA-DNA hybridizations. DNA-rRNA and Pedobacter heparinus comb. nov. and Pedobacter DNA-DNA hybridizations were performed as described piscium comb. nov., and two new species, Pedobacter previously (26, 27). africanus and Pedobacter saltans, is proposed. These names will be used throughout this paper. Several RESULTS strains with a separate genotypic position will be classified and can be considered as unnamed genomic DNA-rRNA hybridization species of Pedobacter. We also propose the family Previous data (26, 27) together with results from this Sphingobacteriaceae comprising the newly described study (Table 2), are presented in Fig. 1 as a simplified organisms, the genus Sphingobacterium and [Flexi- dendrogram based on the thermal stability of the bacter] canadensis. Square brackets are used to indicate hybrids [ T&,, values]. The overall groupings are generically misclassified bacteria. similar to those described previously (26, 27). The heparinase-producing bacteria are situated on a sep- METHODS arate rRNA branch, the Pedobacter branch, consisting Micro-organisms and growth conditions. Strains studied are of two sub-branches, the P. heparinus sub-branch and listed in Table 1. Information about the bacterial strains, the P. saltans sub-branch. Several genotypic sub- considered in this paper, and growth conditions were given groups and S. piscium are situated on the P. heparinus before (26, 27, 28, 32). sub-branch. Sphingobacterium species and [Flexi- Conventional tests. The conventional tests were done ac- bacter] canadensis are the nearest relatives to the cording to Cowan (4) or Sonnenwirth (25), unless stated Pedobacter branch. otherwise. The oxidation/fermentation test was done in SIM medium (Merck). Acid and gas production from glucose, lactose and sucrose
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