Nicole Lodders

Hydrotalea flava gen. nov., sp. nov., a new member of the phylum Bacteroidetes and allocation of the genera Chitinophaga, Sediminibacterium, Lacibacter, Flavihumibacter, Flavisolibacter, Niabella, Niastella, Segetibacter, Parasegetibacter, Terrimonas, Ferruginibacter, Filimonas and Hydrotalea to the family Chitinophagaceae fam. nov.

Three bacterial strains, designated CCUG 51397(T), CCUG 53736 and CCUG 53920, isolated from water samples taken at different locations in southern Sweden were studied to determine their taxonomic position using a polyphasic approach. Comparative analysis of 16S rRNA gene sequences showed that these bacteria had <93 % sequence similarity to all described species of the genera Sediminibacterium, Lacibacter, Flavihumibacter, Flavisolibacter, Niabella, Niastella, Segetibacter, Parasegetibacter, Terrimonas, Ferruginibacter, Filimonas and Chitinophaga. The three organisms grouped most closely with Sediminibacterium salmoneum NJ-44(T) but showed only 92.5 % sequence similarity to this strain, the only recognized species of this genus. The fatty acid profiles showed large amounts of iso-C₁₅:₀, iso-C₁₇:₀ 3-OH and iso-C₁₅:₁ G with smaller amounts of iso-C₁₅:₀ 3-OH, iso-C₁₆:₀ 3-OH and other fatty acids, which differentiated the novel strains from related genera. Biochemical tests performed on strains CCUG 51397(T), CCUG 53736 and CCUG 53920 also gave different results from those of Sediminibacterium salmoneum NJ-44(T) and other related genera. Based on this evidence, strains CCUG 51397(T), CCUG 53736 and CCUG 53920 represent a novel species of a new genus, for which the name Hydrotalea flava gen. nov., sp. nov. is proposed. The type strain of Hydrotalea flava is CCUG 51397(T) (=CCM 7760(T)). A formal allocation of the genera Sediminibacterium, Lacibacter, Flavihumibacter, Flavisolibacter, Niabella, Niastella, Segetibacter, Parasegetibacter, Terrimonas, Ferruginibacter, Filimonas and Chitinophaga to the family Chitinophagaceae fam. nov. is also proposed.

Elizabethkingia anophelis sp. nov., isolated from the midgut of the mosquito Anopheles gambiae.

The taxonomic position, growth characteristics and antibiotic resistance properties of a slightly yellow-pigmented bacterial strain, designated R26(T), isolated from the midgut of the mosquito Anopheles gambiae, were studied. The isolate produced rod-shaped cells, which stained Gram-negative. The bacterium had two growth optima at 30-31 °C and 37 °C. Strain R26(T) demonstrated natural antibiotic resistance to ampicillin, chloramphenicol, kanamycin, streptomycin and tetracycline. 16S rRNA gene sequence analysis revealed that the isolate showed 98.6 % sequence similarity to that of Elizabethkingia meningoseptica ATCC 13253(T) and 98.2 % similarity to that of Elizabethkingia miricola GTC 862(T). The major fatty acids of strain R26(T) were iso-C(15 : 0), iso-C(17 : 0) 3-OH and summed feature 4 (iso-C(15 : 0) 2-OH and/or C(16 : 1)ω7c/t). Strain R26(T) contained only menaquinone MK-6 and showed a complex polar lipid profile consisting of diphosphatidylglycerol, phosphatidylinositol, an unknown phospholipid and unknown polar lipids and glycolipids. DNA-DNA hybridization experiments with E. meningoseptica CCUG 214(T) ( = ATCC 13253(T)) and E. miricola KCTC 12492(T) ( = GTC 862(T)) gave relatedness values of 34.5 % (reciprocal 41.5 %) and 35.0 % (reciprocal 25.7 %), respectively. DNA-DNA hybridization results and some differentiating biochemical properties indicate that strain R26(T) represents a novel species, for which the name Elizabethkingia anophelis sp. nov. is proposed. The type strain is R26(T) ( = CCUG 60038(T) = CCM 7804(T)).

Description of Chryseobacterium anthropi sp. nov. to accommodate clinical isolates biochemically similar to Kaistella koreensis and Chryseobacterium haifense, proposal to reclassify Kaistella koreensis as Chryseobacterium koreense comb. nov. and emended description of the genus Chryseobacterium.

A collection of eight strains, NF 1366(T), NF 450, NF 1101, NF 1107, NF 1123, NF 1413, CCUG 15260 and CCUG 15624, from various clinical origins, were characterized biochemically as similar to Kaistella koreensis and Chryseobacterium haifense. They differed from K. koreensis, which is unable to alkalinize acetate, and from C. haifense, which is ONPG-positive (beta-galactosidase) and acidifies sucrose, fructose and lactose. Based on 16S rRNA gene sequence comparisons, this collection of strains was most closely related to the type strains of K. koreensis (97.3-97.5 %) and C. haifense (99.1 %). Representative strain NF 1366(T) showed only 41.8 % DNA-DNA relatedness with K. koreensis DSM 12107(T) and only 51.9 % with C. haifense DSM 19056(T). DNA-DNA hybridization of strains NF 450 and CCUG 15624 to strain NF 1366(T) was 41.7 and 74.6 %, respectively, and relatedness of these strains with C. haifense DSM 19056(T) was 72.6 and 70.2 %. With the present information, these two strains must be classified as intermediate between C. haifense and strain NF 1366(T). The fatty acid composition and polar lipid profile of strain NF 1366(T) were similar to those reported for other Chryseobacterium species. Like other chryseobacteria, strain NF 1366(T) exhibited a polyamine pattern with the predominant compound sym-homospermidine and a quinone system consisting of menaquinone MK-6 only. For this collection of clinical strains, the name Chryseobacterium anthropi sp. nov. is proposed, with NF 1366(T) (=CCUG 52764(T) =CIP 109762(T)) as the type strain. K. koreensis was shown to be very similar genotypically and phenotypically to Chryseobacterium. Its polar lipid profile exhibited the major characteristics shown for recently described Chryseobacterium species and the fatty acid profile of K. koreensis was also very similar to those of the Chryseobacterium species. Hence, no striking genotypic or phenotypic differences could be found that could justify the classification of this species into a separate genus, and we therefore propose to reclassify Kaistella koreensis in the genus Chryseobacterium as Chryseobacterium koreense comb. nov. (type strain Chj707(T) =IAM 15050(T) =JCM 21512(T) =KCTC 12107(T) =NBRC 103027(T)). An emended description of the genus Chryseobacterium is also proposed.

Flavobacterium chilense sp. nov. and Flavobacterium araucananum sp. nov., isolated from farmed salmonid fish.

Three Gram-staining-negative non-endospore-forming strains were isolated from farmed fish in Chile: one (LM-09-Fp(T)) from a rainbow trout (Oncorhynchus mykiss) and the others (LM-19-Fp(T) and LM-20-Fp) from two Atlantic salmon (Salmo salar). Phylogenetic analyses based on 16S rRNA gene sequences indicated that all three isolates belonged to the genus Flavobacterium. In these analyses, strain LM-09-Fp(T) appeared most closely related to the type strains of Flavobacterium chungangense (98.5 % sequence similarity), Flavobacterium glaciei (98.2 %), Flavobacterium aquidurense (97.6 %), Flavobacterium saccharophilum (97.6 %) and Flavobacterium hercynium (97.6 %). The 16S rRNA gene sequences of strains LM-19-Fp(T) and LM-20-Fp were found to be identical and most similar to the corresponding sequences of the type strains of Flavobacterium aquidurense (98.6 %), Flavobacterium frigidimaris (98.5 %), Flavobacterium hercynium (97.9 %), Flavobacterium saccharophilum (97.7 %) and Flavobacterium pectinovorum (97.7 %). For each of the three novel strains, menaquinone (MK-6) was the predominant respiratory quinone and the major compounds in the polar lipid profile were phosphatidylethanolamine, an unidentified aminolipid, phosphatidylserine and two or three unknown lipids. The fatty acid profile of each strain, which comprised major amounts of iso-C(15:0), C(15:0) and summed feature 3 (C(16:1)ω7c and/or iso-C(15:0) 2-OH) as well as smaller amounts of various hydroxylated fatty acids (e.g. iso-C(16:0) 3-OH, iso-C(17:0) 3-OH, C(16:0) 3-OH and C(15:0) 3-OH), indicated that each belonged to the genus Flavobacterium. Based on their physiological and biochemical characteristics and the results of DNA-DNA hybridizations, which showed relatively low levels of relatedness between the novel strains and the most closely related Flavobacterium species, strain LM-09-Fp(T) ( = LMG 26360(T) = CCM 7940(T)) represents a novel species within the genus Flavobacterium, for which the name Flavobacterium chilense sp. nov. is proposed, and strains LM-19-Fp(T) ( = LMG 26359(T) = CCM 7939(T)) and LM-20-Fp ( = LMG 26331) represent a second novel species within the same genus, for which the name Flavobacterium araucananum sp. nov. is proposed.

Revision of the genus Massilia La Scola et al. 2000, with an emended description of the genus and inclusion of all species of the genus Naxibacter as new combinations, and proposal of Massilia consociata sp. nov.

A Gram-stain-negative, rod-shaped, non-spore-forming bacterium originating from a human clinical specimen was studied for its taxonomic position. 16S rRNA gene sequence similarity studies clearly allocated this strain (CCUG 58010(T)) to the class Betaproteobacteria, closely related to members of the genera Massilia and Naxibacter. Naxibacter varians was shown to be the most closely related species on the basis of 16S rRNA gene sequence similarity (97.5 %), followed by Massilia niastensis (96.8 %) and Massilia aerilata (96.4 %). Similarities to all other species of the genera Naxibacter and Massilia were in the range 93.9-96.2 %. Chemotaxonomic data (major ubiquinone: Q-8; major polar lipids: phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol; and major fatty acids: summed feature 3 (C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH), C(16 : 0), C(18 : 1)ω7c and C(12 : 0), with C(10 : 0) 3-OH as hydroxylated fatty acid) supported the affiliation of the isolate to these genera, which share these chemotaxonomic traits. DNA-DNA hybridization of strain CCUG 58010(T) with the type strain of N. varians CCUG 35299(T) resulted in a relatedness value of 39.2 % (reciprocal, 50 %) and physiological and biochemical tests also allowed phenotypic differentiation of the isolate from the most closely related species. There is currently no justification for a division of the genera Massilia and Naxibacter and for this reason a proposal is made to transfer all species of the genus Naxibacter to the genus Massilia, as Massilia alkalitolerans comb. nov., Massilia varians comb. nov., Massilia haematophila comb. nov. and Massilia suwonensis comb. nov. Strain CCUG 58010(T) represents a novel species, for which the name Massilia consociata sp. nov. is proposed, with the type strain CCUG 58010(T) ( = CCM 7792(T)).

Ornithinibacillus contaminans sp. nov., an endospore-forming species

A Gram-stain-positive, endospore-forming rod, designated CCUG 53201(T), was isolated from a human blood sample of a 75-year-old woman. 16S rRNA gene sequence-based phylogenetic analysis showed that strain CCUG 53201(T) clustered with the type strains of species of the genus Ornithinibacillus. Strain CCUG 53201(T) was most closely related to Ornithinibacillus bavariensis WSBC 24001(T) and Ornithinibacillus californiensis DSM 16628(T) (97.9 and 98.7 % 16S rRNA gene sequence similarity, respectively). Strain CCUG 53201(T) contained a peptidoglycan of type A4β l-Orn-d-Asp. The quinone system was composed of the menaquinone MK-7 and small amounts of MK-6. The polar lipid profile of strain CCUG 53201(T) consisted of major amounts of diphosphatidylglycerol and an unidentified phospholipid, moderate amounts of phosphatidylglycerol and another two unidentified phospholipids and minor amounts of several other components. The fatty acid profile comprised mainly anteiso- and iso-branched fatty acids and was in accordance with those of members of the genus Ornithinibacillus. The polyamine pattern exhibited the major compounds spermidine and spermine. The results of physiological and biochemical tests and DNA-DNA hybridization allowed the phenotypic and genotypic differentiation of strain CCUG 53201(T) from its closest phylogenetic neighbours. We propose a novel species with the name Ornithinibacillus contaminans sp. nov., with type strain CCUG 53201(T) (=DSM 22953(T)).

Transfer of Sejongia antarctica, Sejongia jeonii and Sejongia marina to the genus Chryseobacterium as Chryseobacterium antarcticum comb. nov., Chryseobacterium jeonii comb. nov. and Chryseobacterium marinum comb. nov.

The genus Sejongia was described in 2005, with the two species Sejongia antarctica and Sejongia jeonii, mainly on the basis of 16S rRNA gene sequence analysis. At that time, these organisms formed a quite separate branch in a 16S rRNA gene sequence-based tree, but, in subsequent studies, it became obvious that the species S. antarctica and S. jeonii and a third species, Sejongia marina, were most closely related (>95.0% similarity) to some Chryseobacterium species (e.g. Chryseobacterium hominis, C. formosense and C. haifense). In addition, there is no evidence for clear phenotypic (i.e. chemotaxonomic) differences between these organisms that justifies their assignment to different genera. For these reasons, a proposal is made to transfer these species to the genus Chryseobacterium as Chryseobacterium antarcticum comb. nov. (type strain AT1013T=JCM 12381T=IMSNU 14040T=KCTC 12225T), Chryseobacterium jeonii comb. nov. (type strain AT1047T=JCM 12382T=IMSNU 14049T=KCTC 12226T) and Chryseobacterium marinum comb. nov. (type strain IMCC3228T=KCCM 42689T=NBRC 103143T) on the basis of 16S rRNA gene sequence data and published phenotypic data.

Paenibacillus chartarius sp. nov., isolated from a paper mill

The taxonomy of strain CCUG 55240(T), a Gram-staining-positive, aerobic, endospore-forming bacterium that was isolated from a paper mill, was investigated using a polyphasic approach. In phylogenetic analysis based on 16S rRNA gene sequences, the novel strain was grouped with established members of the genus Paenibacillus and appeared most closely related to the type strains of Paenibacillus chinjuensis (93.7 % sequence similarity), P. elgii (93.7 %) and P. chitinolyticus (93.6 %). The levels of 16S rRNA gene sequence similarity with other species of the genus Paenibacillus, including the type species of the genus, Paenibacillus polymyxa, were all <93.5 %. The fatty acid profile of strain CCUG 55240(T), which showed a predominance of iso- and anteiso-branched fatty acids, supported the allocation of the strain to the genus Paenibacillus. Unusually high amounts of some iso-branched fatty acids, especially iso-C(15:0) and iso-C(16:0), allowed differentiation of strain CCUG 55240(T) from the most closely related species of the genus Paenibacillus. The diagnostic diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. The predominant menaquinone was MK-7. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, an unknown glycolipid, an unknown aminophosphoglycolipid and an unknown phospholipid. Spermidine was the major polyamine. The results of some physiological and biochemical tests also allowed the phenotypic differentiation of strain CCUG 55240(T) from the most closely related recognized species. On the basis of the phylogenetic, phenotypic and molecular evidence, strain CCUG 55240(T) represents a novel species of the genus Paenibacillus, for which the name Paenibacillus chartarius sp. nov. is proposed. The type strain of the novel species is CCUG 55240(T) ( = CCM 7759(T)).

Massilia oculi sp. nov., isolated from a human clinical specimen.

A gram-negative, rod-shaped, non-spore-forming bacterium (strain CCUG 43427A(T)) was isolated from a patient suffering from endophthalmitis and its taxonomic position was studied. 16S rRNA gene sequence analysis indicated that this strain was a member of the genus Massilia. Strain CCUG 43427A(T) was most closely related to the type strains of Massilia timonae (97.4 % 16S rRNA gene sequence similarity) and Massilia aurea (97.2 %); levels of similarity to the type strains of all other recognized Massilia species were below 97.0 %. Chemotaxonomic data [Q-8 as major ubiquinone; phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol as major polar lipids; and summed feature 3 (C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH), C(16 : 0), C(18 : 1)ω7c, C(12 : 0) and C(10 : 0) 3-OH as major fatty acids] supported the affiliation of the isolate to the genus Massilia. Levels of DNA-DNA relatedness of strain CCUG 43427A(T) with M. timonae CCUG 45783(T) and M. aurea AP13(T) were 60.6 % (reciprocal, 55.8 %) and 58.1 % (reciprocal, 34.0 %), respectively. Strain CCUG 43427A(T) could be differentiated from its closest phylogenetic neighbours based on a range of phenotypic characteristics. Strain CCUG 43427A(T) is therefore considered to represent a novel species of the genus Massilia, for which the name Massilia oculi sp. nov. is proposed. The type strain is CCUG 43427A(T) ( = CCM 7900(T)).

Leucobacter aerolatus sp. nov., from the air of a duck barn

A Gram-positive, non-spore-forming actinobacterium (Sj 10(T)) was isolated on tryptone soy agar from the air of a duck barn after filter sampling. Based on 16S rRNA gene sequence similarity studies, strain Sj 10(T) was shown to belong to the genus Leucobacter and was closely related to Leucobacter chromiireducens subsp. chromiireducens L-1(T) (97.8 %), Leucobacter tardus DSM 19811(T) (97.3 %) and Leucobacter luti RF6(T) (97.3 %). The peptidoglycan of strain Sj 10(T) contained 2,4-diaminobutyric acid in combination with a lower amount of lysine as diagnostic diamino acids. In addition, threonine, glycine, alanine and glutamic acid were found. Menaquinone MK-11 was the major respiratory quinone; MK-12 and MK-10 were detected in minor amounts. The polar lipid pattern consisted of phosphatidylglycerol, diphosphatidylglycerol and one unknown component each of a phospholipid, glycolipid and aminoglycolipid. Strain Sj 10(T) contained the major fatty acids anteiso-C(15 : 0), iso-C(16 : 0) and anteiso-C(17 : 0), like other members of the genus Leucobacter. Results of DNA-DNA hybridization, physiological and biochemical tests enabled strain Sj 10(T) to be differentiated genotypically and phenotypically from the most closely related Leucobacter species. Strain Sj 10(T) represents a novel species of the genus Leucobacter, for which the name Leucobacter aerolatus sp. nov. is proposed, with Sj 10(T) (=DSM 22806(T) =CCM 7705(T)) as the type strain.