Classification of three corynebacterial strains isolated from the Northern Bald Ibis (Geronticus eremita): proposal of Corynebacterium choanae sp. nov., Corynebacterium pseudopelargi sp. nov., and Corynebacterium gerontici sp. nov.

Three Gram-stain-positive, rod-to-coccoid-shaped, catalase-positive and non-motile bacterial strains isolated from the choanae of a Northern bald ibis, designated strains 200CHT, W8T and 812CHT, respectively, were subjected to comprehensive taxonomic characterization. The three strains were oxidase-negative. The 16S rRNA gene sequence of 200CHT showed highest similarities to Corynebacterium epidermidicanis 410T (96.7 %) followed by Corynebacterium argentoratense DSM 44202T, Corynebacterium ulcerans NCTC 7910T and Corynebacterium pseudotuberculosis CIP 102968T (each 96.3 %). Strains W8T and 812CHT both showed highest 16S rRNA gene sequence similarities to Corynebacterium pelargi 136/3T (98.0 and 99.9 %, respectively). Comparison of the partial housekeeping gene sequence of fusA showed higher sequence similarities of 812CHT to C. pelargi (95.8 %) than W8T (90.9 %) which was also confirmed by corresponding amino acid sequences. In both, fusA gene and corresponding protein sequence strain 200CHT showed low sequence similarities to C. epidermidicanis 410T(81.6 and 87.4 %, respectively). Strains 812CHT and W8T had 76.7 % ANI similarity to each other and 88.2 and 76.4 % to C. pelargi 136/3T, respectively. In silico DNA-DNA hybridization values for 812CHT and W8T were 22.1 % among the two strains and 35.3 and 21.7 % to C. pelargi 136/3T, respectively. These data not only demonstrate that strain W8T is a representative of a novel species, but despite the high 16S rRNA gene sequence similarity to C. pelargi, strain 812CHT is also a representative of another novel species. All three strains possessed corynemycolic acids and contained meso-diaminopimelic acid as the diagnostic diamino acid of the peptidoglycan. The two strains, 200CHT and W8T, are distinguished from each other and established Corynebacterium species phylogenetically and phenotypically. In conclusion, three novel species of the genus Corynebacterium are proposed, namely Corynebacteriumpseudopelargi 812CHT (=LMG 30627T=CCM 8832T), Corynebacterium choanae 200CHT (=LMG 30628T=CCM 8831T) and Corynebacteriumgerontici W8T (=LMG 30629T=CCM 8833T), respectively.

Pedobacter psychrophilus sp. nov., isolated from fragmentary rock.

Strain P4487AT was isolated during investigation of cultivable bacterial populations of environmental materials sampled at James Ross Island, Antarctica. It revealed Gram-stain-negative short rod-shaped cells producing a pink pigment. Phylogenetic analysis based on 16S rRNA gene sequences allocated strain P4487AT to the genus Pedobacter but showed that the strain represents a distinct intrageneric phylogenetic lineage clearly separated from remaining Pedobacter species. Phylogenetically, strain P4487AT formed a common branch with the Pedobacter arcticus and Pedobacter lignilitoris cluster while the highest value of 94.4 % 16S rRNA gene sequence similarity suggested that Pedobacter lentus is the most closely related species. Biochemical and physiological test results enabled the differentiation of strain P4487AT from all phylogenetically closely related species. Chemotaxonomic analyses of strain P4487AT showed MK-7 as the respiratory menaquinone, sym-homospermidine as the major polyamine, phosphatidylethanolamine and two unidentified lipids as the major polar lipids, presence of sphingolipids, and C16 : 1ω7c/C16 : 1ω6c (summed feature 3), iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids, all of which corresponded with characteristics of the genus Pedobacter. The results showed that strain P4487AT represents a novel species within the genus Pedobacter, for which the name Pedobacter psychrophilus sp. nov. is proposed. The type strain is P4487AT (=CCM 8644T=LMG 29436T).

Arcanobacterium wilhelmae sp. nov., isolated from the genital tract of a rhinoceros (Rhinoceros unicornis).

A taxonomic study using a polyphasic approach was performed on an unidentified Arcanobacterium-like Gram-stain-positive bacterium isolated from the genital tract of a rhinoceros. Comparative 16S rRNA gene sequencing showed that the bacterium belonged to the genus Arcanobacterium and was most closely related to the type strains of Arcanobacterium canis (98.8 % 16S rRNA gene sequence similarity), Arcanobacterium phocisimile (97.8 %), Arcanobacterium phocae (97.7 %), Arcanobacterium haemolyticum (97.4 %), Arcanobacterium hippocoleae (96.6 %), Arcanobacterium pinnipediorum (96.4 %) and Arcarnobacterium pluranimalium (95.4 %). DNA-DNA hybridization values between strain 647T and Arcanobacterium canisDSM 25104T were very low, 13.4 % (reciprocal 15.9 %). The genomic DNA G+C content of strain 647T was 58.7 mol%. The presence of the major menaquinone MK-9(H4) supported the affiliation of this strain to the genus Arcanobacterium. The polar lipid profile consisted of the major components diphosphatidylglycerol, phosphatidylcholine and an unidentified phosphoglycolipid. The results of physiological and biochemical testing clearly distinguished the unknown bacterium from other species of the genus Arcanobacterium. Based on these tests, it is proposed that the unknown bacterium should be classified as a representative of a novel species of the genus Arcanobacterium named Arcanobacterium wilhelmaesp. nov. The type strain is 647T (=DSM 102162T=LMG 29418T).

Pedobacter jamesrossensis sp. nov., Pedobacter lithocola sp. nov., Pedobacter mendelii sp. nov. and Pedobacter petrophilus sp. nov., isolated from the Antarctic environment.

A taxonomic study performed on 17 Gram-stain-negative rod-shaped bacterial strains originating from the Antarctic environment is described. Initial phylogenetic analysis using 16S rRNA gene sequencing differentiated the strains into four groups belonging to the genus Pedobacter but they were separated from all hitherto described Pedobacter species. Group I (n=8) was closest to Pedobacter aquatilis (97.8 % 16S rRNA gene sequence similarity). Group II (n=2) and group III (n=4) were closely related (98.8 % 16S rRNA gene sequence similarity) and had Pedobacter jejuensis as their common nearest neighbour. Group IV (n=3) was distantly delineated from the remaining Pedobacter species. Differentiation of the analysed strains into four clusters was further confirmed by repetitive sequence-based PCR fingerprinting, ribotyping, DNA-DNA hybridization and phenotypic traits. Common to representative strains for the four groups were the presence of major menaquinone MK-7, sym-homospermidine as the major polyamine, phosphatidylethanolamine, two unidentified lipids (L2, L5) and an unidentified aminolipid (AL2) as the major polar lipids, presence of an alkali-stable lipid, and C16:1ω7c/C16:1ω6c (summed feature 3), iso-C15:0 and iso-C 17:0 3-OH as the major fatty acids, which corresponded to characteristics of the genus Pedobacter. The obtained results showed that the strains analysed represent four novel species of the genus Pedobacter, for which the names Pedobacter jamesrossensis sp. nov. (type strain CCM 8689T=LMG 29684T), Pedobacter lithocola sp. nov. (CCM 8691T=LMG 29685T), Pedobacter mendelii sp. nov. (CCM 8685T=LMG 29688T) and Pedobacter petrophilus sp. nov. (CCM 8687T=LMG 29686T) are proposed.

Saccharibacillus endophyticus sp. nov., an endophyte of cotton.

A Gram-positive-staining, facultatively aerobic, endospore-forming bacterial strain, isolated from the stem tissue of cotton (Gossypium hirsutum) was subjected to a detailed taxonomic study using a polyphasic approach. Based on 16S rRNA gene sequence similarity comparisons, strain JM-1350T grouped into the genus Saccharibacillus, and was most closely related to the type strain of Saccharibacillus sacchari (96.5 % 16S rRNA gene sequence similarity), followed by the type strains of Saccharibacillus kuerlensis (96.3 %) and Saccharibacillus deserti (95.1 %). The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. The quinone system contained exclusively menaquinone MK-7. The polar lipid (L1) profile consisted of the major lipids diphosphatidylglycerol and phosphatidylglycerol and moderate amounts of three glycolipids and an aminophospholipid and a polar lipid (L1). The major fatty acids were iso- and anteiso-branched fatty acids. The genomic G+C content was 55.2 mol%. In addition, the results of physiological and biochemical tests allowed phenotypic differentiation of strain JM-1350T from all closely related species. Thus, strain JM-1350T represents a novel species of the genus Saccharibacillus, for which the name Saccharibacillus endophyticus sp. nov. is proposed. The type strain is JM-1350T (=LMG 29710T=CCM 8702T).

Rufibacter ruber sp. nov., isolated from fragmentary rock.

A red-pigmented, Gram-stain-negative, rod-shaped, aerobic bacterium, designated strain CCM 8646T, was isolated from stone fragments in James Ross Island, Antarctica. Strain CCM 8646T was able to grow from 10 to 40 °C, in the presence of up to 1 % (w/v) NaCl and at pH 7.0-11.0. Analysis of the 16S rRNA gene sequence placed strain CCM 8646T in the genus Rufibacter with the closest relative being Rufibacter roseus H359T (97.07 % 16S rRNA gene sequence similarity). The digital DNA-DNA hybridization values between strain CCM 8646T and R. roseus H359T were low (21.30±2.34 %). The major quinone was menaquinone MK-7. The polar lipids comprised phosphatidylethanolamine, an unknown aminoglycolipid and six unknown polar lipids. The G+C content of strain CCM 8646T was 51.54 mol%. On the basis of phenotypic, chemotaxonomic and genotyping results, strain CCM 8646T is considered to represent a novel species within the genus Rufibacter, for which the name Rufibacter ruber sp. nov. is proposed. The type strain is CCM 8646T (=LMG 29438T).

Pseudoduganella danionis sp. nov., isolated from zebrafish (Danio rerio).

One beige-pigmented, Gram-staining-negative, rod-shaped bacterium, strain E3/2T, was isolated from a zebrafish, Daniorerio. Phylogenetic analysis based on nearly full-length 16S rRNA gene sequences showed that the isolate shared 97.7 % 16S rRNA gene sequence similarity to the species Pseudoduganella violaceinigra and between 97.4 to 97.0 % to some species of the genera Duganella and Massilia, including Duganella radicis, Duganella phyllosphaerae, Massilia dura, Massilia lutea, Duganella sacchari, Duganella zoogloeoides, Massiliaalbidiflava and Massilia umbonata. Sequence similarities to all other species were below 97 %. The main cellular fatty acids of the strain were summed feature 3 fatty acids (C16 : 1ω7c/iso-C15 : 0 2-OH), C10 : 0 3-OH, C16 : 0 and C12 : 0. The polyamine pattern of strain E3/2T contained predominantly putrescine and 2-hydroxyputrescine. The major quinone was ubiquinone Q-8. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Based on phylogenetic, chemotaxonomic, genomic and phenotypic analyses we propose a novel species of the genus Pseudoduganella named Pseudoduganella danionis sp. nov., with strain E3/2T (=LMG 29678T=CCM 8698T) as the type strain.

Undibacterium danionis sp. nov. isolated from a zebrafish (Danio rerio).

One beige-pigmented, Gram-stain-negative, rod-shaped bacterium, strain E3/4T, was isolated from a zebrafish, Danio rerio. Phylogenetic analysis based on nearly full-length 16S rRNA gene sequences showed that the isolate shared 98.5 % 16S rRNA gene sequence identity to the type strain of Undibacterium macrobrachii and 97.8 % to the type strain of Undibacterium seohonense. Lower 16S rRNA gene sequence similarities (<97.0 %) could be found in comparison with all other species of the genus Undibacterium. DNA-DNA hybridization with Undibacterium macrobrachiiLMG 26891T showed a low level of relatedness, <35 %. The main cellular fatty acids of the strain were summed feature 3 fatty acids (C16 : 1ω7c/C16 : 1ω8c), C10 : 0 3-OH and C16 : 0. The polyamine pattern of strain E3/4T contained predominantly putrescine and 2-hydroxyputrescine. The major quinone was ubiquinone Q-8. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. On the basis of phylogenetic, chemotaxonomic, genomic and phenotypic analyses we propose a novel species of the genus Undibacterium, Undibacterium danionis, with strain E3/4T (=DSM 102221T=CCM 8677T=CIP 111017T) as the type strain.

Jeotgalicoccus schoeneichii sp. nov. isolated from exhaust air of a pig barn.

A Gram-staining-positive, non-motile, non-spore-forming, coccus (strain 140805-STR-02T) was isolated from exhaust air of a pig barn on Columbia Blood Agar Base (Oxoid) supplemented with 5 % defibrinated horse blood, Streptococcus selective supplement and 0.5 mg erythromycin l-1. The strains shared high 16S rRNA gene sequence similarity to Jeotgalicoccus pinnipedialis (98.6 %) but only a maximum of 94 % sequence similarity to all other species of the genus Jeotgalicoccus. DNA-DNA hybridisation values between strain 140805-STR-02T and J. pinnipedialis CIP 107946T were 60.3 % (reciprocal, 51.2 %). The quinone system of 140805-STR-02T contained predominantly menaquinone MK-7 and minor amounts of MK-6. The polar lipid profile of strain 140805-STR-02T contained the major compounds diphosphatidylglycerol and phosphatidylglycerol and four unidentified lipids present in minor to moderate amounts. In the polyamine pattern spermidine and spermine were predominant. The fatty acid profile comprising iso-C15 : 0 and anteiso-C15 : 0 as major fatty acids, and was in congruence with those reported for other species of the genus Jeotgalicoccus and thus supported the affiliation of strain 140805-STR-02T to this genus. The results of physiological and biochemical tests allowed a clear phenotypic differentiation of strain 140805-STR-02T from the most closely related species. Strain 140805-STR-02T represents a novel species, for which the names Jeotgalicoccus schoeneichii sp. nov. is proposed, with the type strain 140805-STR-02T (=LMG 29445T=CCM 8667T).

Rothia aerolata sp. nov., isolated from exhaust air of a pig barn.

A Gram-stain-positive, coccoid, oxidase-negative, non-motile isolate from exhaust air of a pig barn, collected on 17 September 2014 and designated strain 140917-MRSA-09T, was subjected to a comprehensive taxonomic investigation. A comparative analysis of the 16S rRNA gene sequence showed highest similarities to Rothia amarae, Rothia terrae and Rothia endophytica (all <97.8 %). The G+C content of the genomic DNA was 58.9 mol %. The quinone system consisted of the major menaquinones MK-8 and MK-7. The polar lipid profile of strain 140917-MRSA-09T contained the major lipids diphosphatidylglycerol and phosphatidylglycerol and moderate amounts of dimannosylglyceride and trimannosyldiacylglycerol. The polyamine pattern was composed of the major amines putrescine and spermidine. In the fatty acid profile, iso- and anteiso-branched acids predominated (anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0). The strain showed a chemoheterotrophic metabolism and was able to grow aerobically well on nutrient-rich media at temperatures from 15-36 °C (weak at 42 °C), pH 5.5-9.5 and NaCl concentrations ranging from 0 to 7 % (w/v). Growth under anaerobic conditions was weak. Physiological traits as well as unique traits in the quinone pattern and the fatty acid pattern distinguished strain 140917-MRSA-09T from the most closely related species. All these data showed that strain 140917-MRSA-09T is a representative of a novel species of the genus Rothia, for which we propose the name Rothia aerolata sp. nov. The type strain is 140917-MRSA-09T (=LMG 29446T=CCM 8669T).

Sphingobacterium zeae sp. nov., an endophyte of maize.

A yellow-pigmented strain (JM-1081T) isolated from healthy stem tissue of Zea mays was taxonomically characterized. Cells of the strain were rod-shaped and Gram-stain-negative. Comparative 16S rRNA gene sequence analysis revealed closest relationship to the type strains of Sphingobacterium multivorum (98.1 % similarity), Sphingobacterium mucilaginosum (97.9 %) and Sphingobacterium siyangense (97.8 %). 16S rRNA gene sequence similarities to the type strains of all other Sphingobacterium species were below 97.8 %. Fatty acid analysis of whole-cell hydrolysates of the strain resulted in a pattern typical of the genus Sphingobacterium with iso-C15 : 0 2-OH and/or C16 : 1ω7c, iso-C15 : 0, iso-C17 : 0 3-OH and C16 : 0 and as major compounds. The polyamine pattern contained predominantly sym-homospermidine. The major quinone was menaquinone MK-7 and the only identified lipids in the polar lipid profile were phosphatidylethanolamine and phosphatidylserine. In addition, 15 unidentified lipids were detected in moderate to major amounts. Sphingolipid was detected. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. DNA-DNA hybridizations with two of the closely related type strains, those of S. multivorum and S. siyangense, as well as Sphingobacterium canadense resulted in values below 70 %. In addition to the genotypic differences, differential biochemical and chemotaxonomic properties confirmed that the isolate JM-1081T represents a novel species, for which the name Sphingobacterium zeae sp. nov. is proposed. The type strain is JM-1081T (=LMG 29191T=CCM 8652T).