Three strains of anaerobic, non-pigmented, Gram-negative bacilli isolated from various human clinical samples were characterized in terms of phenotypic and genotypic tests, including sequence analysis of 16S rRNA and rpoB genes. The strains were most closely related to the type strains of Prevotella marshii and Prevotella shahii on the basis of both 16S rRNA (89.8 and 89.0 % identity, respectively) and rpoB gene sequences (83.1 and 82.8 % identity, respectively). Phylogenetic analysis showed that the isolates constituted a robust homogeneous group distinct from known species in the genus Prevotella. The rrn skeleton (as determined by PFGE) and the DNA G+C content, determined to be 39.4 mol% for strain LBN 293T, distinguished the novel isolates from the type strains of P. marshii and P. shahii. The three strains were saccharolytic and produced acetic, lactic and succinic acids as major metabolic end products. Polyphasic investigations supported the proposal of a novel species, Prevotella nanceiensis sp. nov., with LBN 293T (=AIP 261.03T =CIP 108993T =CCUG 54409T) as the type strain.
Five isolates that were related phylogenetically to members of the genus Pedobacter were isolated from freshwater of the hard-water creek Westerhöfer Bach, North Germany. The five strains (WB 2.1-25T, WB 2.3-71T, WB 3.3-3T, WB 3.3-22T and WB 2.3-45T) were Gram-negative and chemoheterotrophic, with rod-shaped cells. Most of their metabolic properties matched those given in the description of the genus Pedobacter. Consistent with the genus description, their fatty acids included mainly iso-C15 : 0 and summed feature 3 (C16 : 1 ω7c, iso-C15 : 0 2-OH or both); C16 : 1 ω5c, C16 : 0, iso-C15 : 0 3-OH, C16 : 0 3-OH and iso-C17 : 0 3-OH were present in smaller amounts. The major isoprenoid quinone was menaquinone 7. With one exception, binary similarity values of the almost complete 16S rRNA gene sequences determined among the isolates as well as between the isolates and type strains of Pedobacter species were lower than 98.5 %. The only exception was the close relationship between Pedobacter caeni DSM 16990T and strain WB 2.3-45T (99.2 % similarity). DNA–DNA reassociation values determined for this pair of strains was 29.8 %, indicating that strain WB 2.3-45T represents a unique genospecies. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains WB 2.1-25T and WB 2.3-71T form a group that is moderately related to P. caeni and strain WB 2.3-45T (98.5 % similarity). Strains WB 3.3-3T and WB 3.3-22T (98.5 % similarity) branched separately from these four organisms. The five phylogenetically isolated strains differed from each other as well as from the type strain of the type species (Pedobacter heparinus DSM 2366T) and some related representatives of the genus in several metabolic reactions and cultural parameters. On the basis of phenotypic and phylogenetic distinctiveness, five novel species are proposed: Pedobacter duraquae sp. nov., with WB 2.1-25T (=DSM 19034T=CIP 109481T) as the type strain; Pedobacter westerhofensis sp. nov., with WB 3.3-22T (=DSM 19036T=CIP 109479T) as the type strain; Pedobacter metabolipauper sp. nov., with WB 2.3-71T (=DSM 19035T=CIP 109480T) as the type strain; Pedobacter hartonius sp. nov., with WB 3.3-3T (=DSM 19033T=CIP 109468T) as the type strain; and Pedobacter steynii sp. nov., with WB 2.3-45T (=DSM 19110T=CIP 109507T) as the type strain.
The taxonomic positions of three strains of marine gliding bacteria, TISTR 1736, TISTR 1741 and TISTR 1750T, isolated from the southern coastline of Thailand were evaluated by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the three isolates formed a distinct lineage within the family ‘Flammeovirgaceae’, phylum Bacteroidetes, and were related to the genus Flexithrix. The DNA G+C contents of the isolates were in the range 40–43 mol%. The major respiratory quinone was MK-7. The major cellular fatty acids were 16 : 1ω5c (cis-5-hexadecenoic acid) and 15 : 0 (pentadecanoic acid). The major hydroxyl fatty acids were 3-OH 17 : 0 (3-hydroxyheptadecanoic acid), 3-OH 15 : 0 (3-hydroxypentadecanoic acid) and 3-OH 16 : 0 (3-hydroxyhexadecanoic acid). On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic data, these marine bacteria are considered to represent a novel species of a new genus, for which the name Rapidithrix thailandica gen. nov., sp. nov. is proposed. The type strain of Rapidithrix thailandica is TISTR 1750T (=IAM 15448T).
Strain H38T was isolated during a study on the diversity of culturable psychrotolerant bacteria in raw milk. Comparative 16S rRNA gene sequence analysis showed that strain H38T belongs to the genus Chryseobacterium (family Flavobacteriaceae, phylum Bacteroidetes), with the highest similarity (96.7 %) to Chryseobacterium hispanicum VP48T. Strain H38T grows aerobically, at 4–41 °C, with 0–2.5 % NaCl and at pH 6.5–10.5. Light induces the formation of yellow carotenoid pigments. The dominant cellular fatty acids are 15 : 0 iso (41.6 %), 15 : 0 anteiso (16.6 %) and 17 : 0 iso 3-OH (10.3 %). The G+C content of the DNA is 37.8 mol%. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain H38T (=LMG 24029T =DSM 19056T) is classified in the genus Chryseobacterium as the type strain of a novel species, for which the name Chryseobacterium haifense sp. nov. is proposed.
Two facultatively aerobic, heterotrophic bacteria capable of degrading pectin, xylan, laminarin and some other polysaccharides were obtained from the acidic Sphagnum peat bog Bakchar, in western Siberia, Russia, and were designated strains TPT18T and TPT56T. Cells of these isolates are Gram-negative, non-motile, long rods that are covered by large capsules. On ageing, they transform into spherical L-forms. Strains TPT18T and TPT56T are acido- and psychrotolerant organisms capable of growth at pH 4.2–8.2 (with an optimum at pH 6.0–6.5) and at 2–33 °C (with an optimum at 20 °C). The major fatty acids are iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c); the quinones are MK-7 and MK-6. Comparative 16S rRNA gene sequence analysis revealed that the novel strains share 97 % sequence similarity and belong to the family Sphingobacteriaceae; however, they are related only distantly to members of the genera Pedobacter (91.8–93.3 % similarity) and Sphingobacterium (89.6–91.2 % similarity). The DNA G+C content of strains TPT18T and TPT56T is 42.4 and 46.1 mol%, respectively. The low DNA–DNA hybridization value (42 %) and a number of phenotypic differences between strains TPT18T and TPT56T indicated that they represent two separate species. Since the two isolates are clearly distinct from all currently described members of the family Sphingobacteriaceae, we propose a novel genus, Mucilaginibacter gen. nov., containing two novel species, Mucilaginibacter gracilis sp. nov. and Mucilaginibacter paludis sp. nov. The type strains of Mucilaginibacter gracilis and Mucilaginibacter paludis are respectively TPT18T (=ATCC BAA-1391T =VKM B-2447T) and TPT56T (=ATCC BAA-1394T =VKM B-2446T).