Neisseria leonii sp. nov., isolated from the nose, lung, and liver of rabbits.

A taxogenomic study of three strains (3986T, 51.81, and JF 2415) isolated from rabbits between 1972 and 2000 led to the description of a new Neisseria species. The highest sequence similarity of the 16S rRNA gene was found to Neisseria animalis NCTC 10212T (96.7 %). The 16S rRNA gene similarity above 99 % and average nucleotide identity (ANI) values above 96 % among the strains, indicated that they belong to the same species. At the same time, the strains shared ANI values below 81 % and dDDH values below 24 % with all described Neisseria species. In the bac120 gene phylogenetic tree, the three strains clustered near Neisseria elongata and Neisseria bacilliformis in the Neisseria clade. However, the Neisseria clade is not monophyletic, and includes the type strains of Morococcus cerebrosus, Bergeriella denitrificans, Kingella potus, Uruburuella suis, and Uruburuella testudinis. Neisseria shayeganii clustered outside the clade with members of the genus Eikenella. Amino acid identity (AAI) values were calculated, and a threshold of 71 % was used to circumscribe the genus Neisseria. According to this proposed AAI threshold, strains 3986T, 51.81, and JF 2415 were placed within the genus Neisseria. The cells of the three strains were Gram-stain-negative diplococcobacilli and non-motile. Optimal growth on trypticase soy agar occurred at 37 °C and pH 8.5 in aerobic conditions. Notably, all strains exhibited indole production in the API-NH test, which is atypical for Neisseria and the family Neisseriaceae. The strains exhibited a common set of 68 peaks in their MALDI-TOF MS profiles, facilitating the swift and accurate identification of this species. Based on genotypic and phenotypic data, it is proposed that strains 3986T, 51.81, and JF 2415 represent a novel species within the genus Neisseria, for which the name Neisseria leonii sp. nov. is proposed (type strain 3986T=R726T=CIP 109994T=LMG 32907T).

The best of both worlds: a proposal for further integration of Candidatus names into the International Code of Nomenclature of Prokaryotes.

The naming of prokaryotes is governed by the International Code of Nomenclature of Prokaryotes (ICNP) and partially by the International Code of Nomenclature for Algae, Fungi and Plants (ICN). Such codes must be able to determine names of taxa in a universal and unambiguous manner, thus serving as a common language across different fields and activities. This unity is undermined when a new code of nomenclature emerges that overlaps in scope with an established, time-tested code and uses the same format of names but assigns different nomenclatural status values to the names. The resulting nomenclatural confusion is not beneficial to the wider scientific community. Such ambiguity is expected to result from the establishment of the 'Code of Nomenclature of Prokaryotes Described from DNA Sequence Data' ('SeqCode'), which is in general and specific conflict with the ICNP and the ICN. Shortcomings in the interpretation of the ICNP may have exacerbated the incompatibility between the codes. It is reiterated as to why proposals to accept sequences as nomenclatural types of species and subspecies with validly published names, now implemented in the SeqCode, have not been implemented by the International Committee on Systematics of Prokaryotes (ICSP), which oversees the ICNP. The absence of certain regulations from the ICNP for the naming of as yet uncultivated prokaryotes is an acceptable scientific argument, although it does not justify the establishment of a separate code. Moreover, the proposals rejected by the ICSP are unnecessary to adequately regulate the naming of uncultivated prokaryotes. To provide a better service to the wider scientific community, an alternative proposal to emend the ICNP is presented, which would result in Candidatus names being regulated analogously to validly published names. This proposal is fully consistent with previous ICSP decisions, preserves the essential unity of nomenclature and avoids the expected nomenclatural confusion.

Paenibacillus auburnensis sp. nov. and Paenibacillus pseudetheri sp. nov., isolated from the rhizosphere of Zea mays.

Two Gram-stain-positive, aerobic, endospore-forming bacterial strains, isolated from the rhizosphere of Zea mays were studied for their detailed taxonomic allocation. Based on 16S rRNA gene sequence similarity comparisons, both strains JJ-7T and JJ-60T were shown to be members of the genus Paenibacillus. Strain JJ-7T was most closely related to the type strains of Paenibacillus tianjinensis (99.6 %) and P. typhae (98.7 %), and strain JJ-60T to Paenibacillus etheri (99.5 %). The 16S rRNA gene sequence similarities to all other Paenibacillus species were ≤98.4 %. Both strains JJ-7T and JJ-60T showed 97.6 % 16S rRNA gene sequence similarity between each other. Genomic comparisons showed that the average nucleotide identity and digital DNA-DNA hybridization values to next related type strain genomes were always <94 and <56 %, respectively. The polar lipid profiles of both strains contain a number of phospholipids including diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, which is in accord with the genus Paenibacillus. The major quinone was MK-7 in both strains. Major fatty acids were iso- and anteiso-branched. Physiological and biochemical characteristics allowed a further phenotypic differentiation of strains JJ-7T and JJ-60T from the most closely related species. Thus, each strain represents a novel species of the genus Paenibacillus, for which the names Paenibacillus auburnensis sp. nov. and Paenibacillus pseudetheri sp. nov. are proposed, with JJ-7T (=CIP 111892T=DSM 111785T=LMG 32088T=CCM 9087T) and JJ-60T (=CIP 111894T=DSM 111787T=LMG 32090T=CCM 9086T) as the type strains, respectively.

Chryseobacterium oryctis sp. nov., isolated from the gut of the beetle Oryctes rhinoceros, and Chryseobacterium kimseyorum sp. nov., isolated from a stick insect rearing cage.

Two strains of Chryseobacterium identified from different experiments are proposed to represent new species. Strain WLa1L2M3T was isolated from the digestive tract of an Oryctes rhinoceros beetle larva. Strain 09-1422T was isolated from a cage housing the stick insect Eurycantha calcarata. Sequence analysis of the 16S rRNA and rpoB genes found both strains to be similar but not identical to other Chryseobacterium species. Whole-genome sequencing suggested the isolates represent new species, with average nucleotide identity values ranging from 74.6 to 80.5 %. Genome-to-genome distance calculations produced values below 25.3 %, and digital DNA-DNA hybridization values were 13.7-29.9 %, all suggesting they are distinct species. The genomic DNA G+C content of WLa1L2M3T is approximately 32.53 %, and of 09-1422T is approximately 35.89 %. The predominant cellular fatty acids of strain WLa1L2M3T are C15 : 0 iso, summed feature 9 (C16 : 0 10OH or C17 : 1 iso ω6c), C17 : 0 iso 3OH, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C15 : 0 iso 3OH, C15 : 0 anteiso and C13 : 0 iso, and those of strain 09-1422T are C15 : 0 iso, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C17 : 0 iso 3OH, C15 : 0 anteiso, C15 : 0 iso 3OH, C16 : 1 ω7c, C17 : 0 2OH and C18 : 0. In addition, physiological and biochemical tests revealed phenotypic differences from related Chryseobacterium type strains. These cumulative data indicate that the two strains represent novel species of the genus Chryseobacterium for which the names Chryseobacterium oryctis sp. nov. and Chryseobacterium kimseyorum sp. nov. are proposed with WLa1L2M3T (=BCRC 81350T=JCM 35215T=CIP 112035T) and 09-1422T (=UCDFST 09-1422T=BCRC 81359T=CIP 112165T), as type strains, respectively.

Paenibacillus plantiphilus sp. nov. from the plant environment of Zea mays.

A Gram-strain positive, aerobic, endospore-forming bacterial strain (JJ-246T) was isolated from the rhizosphere of Zea mays. The 16S rRNA gene sequence similarity comparisons showed a most closely relationship to Paenibacillus oenotherae DT7-4T (98.4%) and Paenibacillus xanthinolyticus 11N27T (98.0%). The pairwise average nucleotide identity and digital DNA-DNA hybridisation values of the JJ-246T genome assembly against publicly available Paenibacillus type strain genomes were below 82% and 33%, respectively. The draft genome of JJ-246T shared many putative plant-beneficial functions contributing (PBFC) genes, related to plant root colonisation, oxidative stress protection, degradation of aromatic compounds, plant growth-promoting traits, disease resistance, drug and heavy metal resistance, and nutrient acquisition. The quinone system of strain JJ-246T, the polar lipid profile and the major fatty acids were congruent with those reported for members of the genus Paenibacillus. JJ-246T was shown to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus plantiphilus sp. nov. is proposed, with JJ-246T (= LMG 32093T = CCM 9089T = CIP 111893T) as the type strain.

Serratia silvae sp. nov., Isolated from Forest Soil.

The Gram-negative, oxidase-negative, catalase-positive, rod-shaped strain Arafor3T was isolated from forest soil (France). Comparative 16S rRNA gene analysis and phylogenetic analysis based on (1) multilocus sequence analysis (MLSA) with four housekeeping genes (atpD, gyrB, infB and rpoB) and (2) genomes indicated that strain Arafor3T shared 98.83% 16S rRNA gene sequence similarity with the type strain of Serratia fonticola DSM 4576T and was closely related to this same strain in the MLSA and in the phylogenomic tree reconstruction. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) comparisons of strain Arafor3T with its nearest neighbor S. fonticola DSM 4576T showed 93.5% identity and 55.7% sequence similarity, respectively, and were lower than the 96% and 70% species-level cut-off values relating to these analyses (Logan et al. in Int J Syst Evol Microbiol 59:2114-21, 2009, https://doi.org/10.1099/ijs.0.013649-0 ). The strain differed from S. fonticola in that it was urease and arginine dihydrolase negative. The major fatty acids of strain Arafor3T are C16:0, C16:1 ω7c/C16:1 ω6c, C14:0, C14:0 3-OH/16:1 isoI, and C18:1 ω7c. The major respiratory quinone is Q8. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and 6 unknown lipids. The mol G + C% content of the genomic DNA of strain Arafor3T was 53.49%. Hence, Arafor3T represents a novel species within the genus Serratia, for which the name Serratia silvae sp. nov. is proposed. The type strain is Arafor3T (=LMG 32338T = CIP 111939T).

Paenibacillus allorhizoplanae sp. nov. from the rhizoplane of a Zea mays root.

A Gram-positive staining, aerobic, endospore-forming bacterial strain, isolated from the rhizosphere of Zea mays was studied for its detailed taxonomic allocation. Based on the 16S rRNA gene sequence similarity comparisons, strain JJ-42 T was shown to be a member of the genus Paenibacillus, most closely related to the type strain of Paenibacillus pectinilyticus (98.8%). The 16S rRNA gene sequence similarity to all other Paenibacillus species was below 98.5%. The pairwise average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of the JJ-42 T genome assembly against publicly available Paenibacillus type strain genomes were below 92% and 47%, respectively. The quinone system of strain JJ-42 T consisted exclusively of menaquinone MK-7. The polar lipid profile consisted of the major components diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three aminophospholipids (APL), and one unidentified lipid. The major fatty acids were iso- and anteiso-branched with the major compound anteiso C15:0. Physiological and biochemical characteristics allowed a further phenotypic differentiation of strain JJ-42 T from the most closely related species. Thus, JJ-42 T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus allorhizoplanae sp. nov. is proposed, with JJ-42 T (= LMG 32089 T = CCM 9085 T = DSM 111786 T = CIP 111891 T) as the type strain.

Streptomyces durocortorensis sp. nov., isolated from oak rhizosphere.

Strain RHZ10T was isolated from an oak rhizosphere sampled in Reims, France, and characterized to assess its taxonomy. Based on 16S rRNA gene sequence similarity, strain RHZ10T was affiliated to the genus Streptomyces and the closest species were Streptomyces anulatus NRRL B-2000T and Streptomyces pratensis ch24T. Average nucleotide identity and digital DNA-DNA hybridization values were 77.3-92.4 % and 23.0-50.9 %, respectively, when compared to the type strains of fully sequenced related species having a 16S rRNA gene sequence similarity over 98 %. These data suggested that strain RHZ10T represented a novel species within the genus Streptomyces. The genome of RHZ10T was 8.0 Mbp long, had 7  894 predicted coding genes, and a G+C content of 71.7 mol%. Cultures of RHZ10T on ISP 2 medium mostly led to the production a green pigmentation of the core of its colonies in the vegetative mycelium, surrounded by white pigmentation of the aerial mycelium. The main fatty acids of RHZ10T were anteiso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0 and C16 : 0. Polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, unidentified lipids, unidentified phospholipids, unidentified aminolipids and unidentified glycolipids. Its main quinones were MK-9(H6) (69.3 %), MK-9(H4) (17.3 %) and MK-9(H8) (17.0%). Phylogenetic, physiological and chemotaxonomic studies clearly supported that strain RHZ10T represents a novel species within the genus Streptomyces, for which the name Streptomyces durocortorensis sp. nov. is proposed and the type strain is RHZ10T (=DSM 112634T=LMG 32187T=CIP 111907T).

Sutcliffiella rhizosphaerae sp. nov. isolated from roots.

An aerobic, Gram-staining-positive, endospore-forming bacterium, isolated from the rhizosphere of roots of maize (Zea mays), was taxonomically studied. On the basis of 16S rRNA gene sequence similarity comparisons, strain JJ-125T clustered together with species of the genus Sutcliffiella and showed the highest similarities with Sutcliffiella zhanjiangensis (98.7 %). The 16S rRNA gene sequence similarities to the sequences of the type strains of other species of the genus Sutcliffiella were <98.4 %. The genome sequence of JJ-125T was 4 516 360 bp long and had a DNA G+C content of 37.3 %. A DNA-DNA hybridization with the type strain of S. zhanjiangensis DSM 23010T resulted in values of 42.3 and 43.9 % (reciprocal). The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between the JJ-125T genome assembly and those of the other type strains of species of the genus Sutcliffiella were <75%, <80 % and <21 %, respectively. Chemotaxonomic features supported the grouping of the strain with the genus Sutcliffiella, e.g. the major fatty acids included iso-C15 : 0, iso-C17 : 1 ω10c and iso-C17 : 0, the polar lipid profile contained the major components diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, the only quinone was menaquinone MK-7 and the characteristic diamino acid was meso-diaminopimelic acid. Physiological and biochemical test results were also different from those of the most closely related species. As a consequence, JJ-125T represents a novel species of the genus Sutcliffiella, for which we propose the name Sutcliffiella rhizosphaerae sp. nov., with JJ-125T (= CIP 111883T = LMG 32156T = CCM 9046T) as the type strain.

Neobacillus rhizosphaerae sp. nov., isolated from the rhizosphere, and reclassification of Bacillus dielmonensis as Neobacillus dielmonensis comb. nov.

A Gram-stain-positive, facultative anaerobic endospore-forming bacterium, which originated from roots/rhizosphere of maize (Zea mays), was investigated for its taxonomic position. On the basis of 16S rRNA gene sequence similarities, strain JJ-3T was grouped together with Neobacillus species showing the highest similarities to Neobacillus bataviensis (98.8 %) and the three species Neobacillus dendrensis, Neobacillus soli and Neobacillus cucumis (all 98.6 %). The 16S rRNA gene sequence similarities to the sequences of the type strains of other Neobacillus species were lower than 98.5 %. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between the JJ-3T genome assembly and those of the other Neobacillus type strains were <83, <85 and <27 %, respectively. Chemotaxonomic features supported the grouping of the strain to the genus Neobacillus, e.g. the major fatty acids were C15 : 0 anteiso and C15 : 0 iso, the polar lipid profile contained the major components diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and the major quinone was menaquinone MK-7. Physiological and biochemical test results were slightly different from those of the most closely related species. For this reason, JJ-3T represents a novel species of the genus Neobacillus, for which we propose the name Neobacillus rhizosphaerae sp. nov., with JJ-3T (= CIP 111895T=LMG 32087T=DSM 111784T=CCM 9084T) as the type strain. We also propose to reclassify Bacillus dielmonensis as Neobacillus dielmonensis comb. nov. based mainly on the results of phylogenomic and conserved signature indel analyses.

Bacillus rhizoplanae sp. nov. from maize roots.

A Gram-stain-positive, aerobic and endospore-forming bacterial strain, isolated from the root surface of maize (Zea mays) was taxonomically studied. It could be clearly shown that, based on 16S rRNA gene sequence similarity comparisons, strain JJ-63T is a member of the genus Bacillus, most closely related to the type strain of Bacillus pseudomycoides (98.61%), followed by Bacillus cereus (98.47 %). Detailed phylogenetic analysis based on the 16S rRNA gene and the 87 proteins conserved within the phylum Firmicutes placed the strain into the Cereus clade. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values against the type strain of B. pseudomycoides were 80.97, 81.45 and 26.30 %, respectively. The quinone system of strain JJ-63T consisted exclusively of menaquinone MK-7. The polar lipid profile consisted of the major components diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified glycolipid. Major fatty acids were iso- and anteiso-branched with the major compounds iso-C15 : 0 and iso-C17 : 0. Also, the characteristic compounds C13 : 0 iso and C16 : 1 cis10 were found. Physiological and biochemical characteristics allowed a further phenotypic differentiation of strain JJ-63T from the most closely related species. For this reason, JJ-63T represents a novel species of the genus Bacillus, for which the name Bacillus rhizoplanae sp. nov. is proposed, with JJ-63T (=LMG 32091T=CCM 9090T=DSM 111827T= CIP 111899T) as the type strain.

Pseudoneobacillus rhizosphaerae gen. nov., sp. nov., isolated from maize root rhizosphere.

A facultative anaerobic, Gram-stain-positive, endospore-forming bacterium, isolated from the rhizosphere of maize roots (Zea mays), was taxonomically studied. Based on 16S rRNA gene sequence similarity comparisons, strain JJ-79T clustered only loosely with Neobacillus species and showed the highest similarity to Neobacillus soli (97.9%). The 16S rRNA gene sequence similarities to the sequences of the type strains of other Neobacillus species were 97.5 % and below. Chemotaxonomic features supported the grouping of the strain to the Neobacillus group, e.g. the major fatty acids were C15 : 0 anteiso, C15 : 0 iso and C16 : 0, the polar lipid profile contained the major components diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified glycolipid, the major quinone was menaquinone MK-7, and major compound in the polyamine pattern was spermidine. However, the JJ-79T genome assembly did not share most of the 11 conserved signature indels that are indicative of the genus Neobacillus. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between the JJ-79T genome assembly and those of the closest relative Bacillaceae type strains were <71, <71 and <25 %, respectively. Physiological and biochemical test results were also different from those of the most closely related Bacillaceae species. As a consequence, JJ-79T represents a novel genus for which we propose the name Pseudoneobacillus rhizosphaerae gen. nov., sp. nov., with JJ-79T (=CIP 111885T=CCM 9045T) as the type strain.

Optimization of a Top-Down Proteomics Platform for Closely Related Pathogenic Bacterial Discrimination.

The current technique used for microbial identification in hospitals is matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). However, it suffers from important limitations, in particular, for closely related species or when the database used for the identification lacks the appropriate reference. In this work, we set up a liquid chromatography (LC)-MS/MS top-down proteomics platform, which aims at discriminating closely related pathogenic bacteria through the identification of specific proteoforms. Using Escherichia coli as a model, all steps of the workflow were optimized: protein extraction, on-line LC separation, MS method, and data analysis. Using optimized parameters, about 220 proteins, corresponding to more than 500 proteoforms, could be identified in a single run. We then used this platform for the discrimination of enterobacterial pathogens undistinguishable by MALDI-TOF, although leading to very different clinical outcomes. For each pathogen, we identified specific proteoforms that could potentially be used as biomarkers. We also improved the characterization of poorly described bacterial strains. Our results highlight the advantage of addressing proteoforms rather than peptides for accurate bacterial characterization and qualify top-down proteomics as a promising tool in clinical microbiology. Data are available via ProteomeXchange with the identifier PXD019247.

Devosia equisanguinis sp. nov., isolated from horse blood.

A Gram-stain-negative, aerobic, non-endospore-forming organism isolated from horse blood was studied for its taxonomic allocation. On the basis of 16S rRNA gene sequence similarity comparisons, strain M6-77T grouped within the genus Devosia and was most closely related to Devosia elaeis (97.6 %) and Devosia indica (97.55 %). The 16S rRNA gene sequence similarity to type strains of other Devosia species was below 97.5 %. The average nucleotide identity and digital DNA-DNA hybridization values between the M6-77T genome assembly and those of the closest relative Devosia type strains were <85 and <25 %, respectively. Strain M6-77T grew optimally at 25-37 °C (range: 10-36 °C), at a pH range of pH 6.5-10.5 and in the presence of up to 3 % (w/v) NaCl. The fatty acid profile from whole-cell hydrolysates supported the allocation of the strain to the genus Devosia. Major fatty acids were C18 : 1 ω7c, 11-methyl C18 : 1 ω7c and C16 : 0. The quinone system consisted exclusively of ubiquinone Q-10. The polar lipid profile was composed of the major lipids diphosphatidylglycerol, phosphatidylglycerol and three unidentified glycolipids. In the polyamine pattern, putrescine was predominant and spermidine was detected in moderate amounts. The diamino acid of the peptidoglycan was meso-diaminopimelic acid. In addition, the results of physiological and biochemical tests also allowed phenotypic differentiation of strain M6-77T from the closely related species. Hence, M6-77T represents a new species of the genus Devosia, for which we propose the name Devosia equisanguinis sp. nov., with M6-77T (=CIP 111628T=LMG 30659T=CCM 8868T) as the type strain.

Streptomyces silvae sp. nov., isolated from forest soil.

A bacterial strain, named For3T, was isolated from forest soil sampled in Champenoux, France. Based on its 16S rRNA gene sequence, the strain was affiliated to the family Streptomycetaceae and, more specifically, to the genus Streptomyces. The strain had 99.93% 16S rRNA gene sequence similarity to its closest relative strains Streptomyces pratensis ATCC 33331T, Streptomyces anulatus ATCC 27416T, Streptomyces setonii NRRL ISP-5322T and Kitasatospora papulosa NRRL B-16504T. The phylogenomic tree using the genome blast distance phylogeny method showed that the closest relative strain was Streptomyces atroolivaceus NRRL ISP-5137T and that For3T represents a new branch among the Streptomyces. Genome relatedness indexes revealed that the average nucleotide identity and digital DNA-DNA hybridization values between For3T and its closest phylogenomic relative (S. atroolivaceus NRRL ISP-5137T) were 88.39 and 39.2 %, respectively. The G+C content of the genome was 71.4 mol% and its size was 7.96 Mb with 7492 protein-coding genes. Strain For3T harboured complete metabolic pathways absent in the closest relative strains such as cellulose biosynthesis, glycogen degradation I, glucosylglycerate biosynthesis I. Anteiso-C15:0, iso-C15:0, anteiso-C17:0 and MK-9(H4)/MK-9(H6) were the predominant cellular fatty acids and respiratory quinones, respectively. Phenotypic and genomic data supported the assignment of strain For3T to a novel species Streptomyces silvae sp. nov., within the genus Streptomyces, for which the type strain is For3T (=CIP 111908T=LMG 32186T).

Pseudomonas carbonaria sp. nov., isolated from charcoal.

A beige-pigmented, oxidase-positive bacterial isolate, Wesi-4T, isolated from charcoal in 2012, was examined in detail by applying a polyphasic taxonomic approach. Cells of the isolates were rod shaped and Gram-stain negative. Examination of the 16S rRNA gene sequence of the isolate revealed highest sequence similarities to the type strains of Pseudomonas matsuisoli and Pseudomonas nosocomialis (both 97.3 %). Phylogenetic analyses on the basis of the 16S rRNA gene sequences indicated a separate position of Wesi-4T, which was confirmed by multilocus sequence analyses (MLSA) based on the three loci gyrB, rpoB and rpoD and a core genome-based phylogenetic tree. Genome sequence based comparison of Wesi-4T and the type strains of P. matsuisoli and P. nosocomialis yielded average nucleotide identity values <95 % and in silico DNA-DNA hybridization values <70 %, respectively. The polyamine pattern contains the major amines putrescine, cadaverine and spermidine. The quinone system contains predominantly ubiquinone Q-9 and in the polar lipid profile diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine are the major lipids. The fatty acid contains predominantly C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1 ω6c). In addition, physiological and biochemical tests revealed a clear phenotypic difference from P. matsuisoli. These cumulative data indicate that the isolate represents a novel species of the genus Pseudomonas for which the name Pseudomonas carbonaria sp. nov. is proposed with Wesi-4T (=DSM 110367T=CIP 111764T=CCM 9017T) as the type strain.

Paenibacillus allorhizosphaerae sp. nov., from soil of the rhizosphere of Zea mays.

A Gram-stain-positive, aerobic, endospore-forming bacterial strain, isolated from the rhizosphere of Zea mays, was studied for its detailed taxonomic allocation. Based on 16S rRNA gene sequence similarity comparisons, strain JJ-447T was shown to be a member of the genus Paenibacillus, most closely related to the type strain of Paenibacillus solanacearum (97.8 %). The 16S rRNA gene sequence similarity values to all other Paenibacillus species were below 97.0 %. DNA-DNA hybridization (DDH) values with the type strain of P. solanacearum were 35.9 % (reciprocal 27%), respectively. The average nucleotide identity and in silico DDH values with the type strain of P. solanacearum were 84.86 and 28.9 %, respectively. The quinone system of strain JJ-447T consisted exclusively of menaquinones and the major component was MK-7 (96.4 %) but minor amounts of MK-6 (3.6 %) were detected as well. The polar lipid profile consisted of the major components diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminolipid. Major fatty acids were iso- and anteiso-branched with the major compounds anteiso-C15 : 0 and iso-C15 : 0. Physiological and biochemical characteristics allowed a further phenotypic differentiation of strain JJ-447T from the most closely related species on the basis of d-glucose, l-arabinose and d-mannose assimilation and other physiological tests. Thus, JJ-447T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus allorhizosphaerae sp. nov. is proposed, with JJ-447T (=LMG 31601T=CCM 9021T=CIP 111802T) as the type strain.

Leucobacter soli sp. nov., from soil amended with humic acid.

A Gram-positive, non-spore-forming actinobacterium (IMT-300T) was isolated from soil amended with humic acid in Malvern, AL, USA. This soil has been used for 50+years for the cultivation of earthworms for use as fish bait. Based on 16S rRNA gene sequence similarity studies, strain IMT-300T was shown to belong to the genus Leucobacter and was closely related to the type strain of 'Leucobacter margaritiformis' L1T (97.8%). Similarity to all other type strains of Leucobacter species was lower than 97.2 %. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the IMT-300T genome assembly and those of the closest relative Leucobacter type strain were 81.4 and 23.3 % (Leucobacter chironomi), respectively. The peptidoglycan of strain IMT-300T contained l-2,4-diaminobutyric acid as the diagnostic diamino acid. In addition, glycine, d- and l-alanine and d-glutamic acid were found. The peptidoglycan type represents a variant of B2δ (B11). The major quinones were menaquinones MK-10 and MK-11. The polar lipid profile consisted of the major lipids diphosphatidylglycerol, phosphatidylglycerol and moderate to minor amounts of two unidentified phospholipids, two unidentified glycolipids and an unidentified aminophospholipid. The polyamine pattern contained major amounts of spermidine and spermine. Strain IMT-300T contained the major fatty acids C15 : 0 anteiso, C16 : 0 iso and C17 : 0 anteiso, like other members of the genus Leucobacter. The results of ANI and dDDH analyses and physiological and biochemical tests allowed a genotypic and phenotypic differentiation of strain IMT-300T from the most closely related Leucobacter species. Strain IMT-300T represents a novel Leucobacter species, for which we propose the name Leucobacter soli sp. nov., with the type strain IMT-300T (CIP 111803T=DSM 110505T=CCM 9020T=LMG 31600T).

Reclassification of Haloactinobacterium glacieicola as Occultella glacieicola gen. nov., comb. nov., of Haloactinobacterium album as Ruania alba comb. nov, with an emended description of the genus Ruania, recognition that the genus names Haloactinobacterium and Ruania are heterotypic synonyms and description of Occultella aeris sp. nov., a halotolerant isolate from surface soil sampled at an ancient copper smelter.

In the course of screening the surface soils of ancient copper mines and smelters (East Harz, Germany) an aerobic, non-motile and halotolerant actinobacterium forming small rods or cocci was isolated. The strain designated F300T developed creamy to yellow colonies on tryptone soy agar and grew optimally at 28 °C, pH 7-8 and with 0.5-2 % (m/v) NaCl. Its peptidoglycan was of type A4α l-Lys-l-Glu (A11.54). The menaquinone profile was dominated by MK-8(II, III-H4) and contained minor amounts of MK-8(H2), MK-8(H6) and MK-9(H4). The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, mono and diacylated phosphatidylinositol dimannosides, and components that were not fully characterized, including two phospholipids, two glycolipids and an uncharacterized lipid. Major whole-cell sugars were rhamnose and ribose. The fatty acid profile contained mainly iso and anteiso branched fatty acids (anteiso-C15 : 0, iso-C14 : 0) and aldehydes/dimethylacetals (i.e. not fatty acids). Sequence analysis of its genomic DNA and subsequent analysis of the data placed the isolate in the group currently defined by members of the genera Ruania and Haloactinobacterium (family Ruaniaceae, order Micrococcales) as a sister taxon to the previously described species Haloactinobacterium glacieicola, sharing an average nucleotide identity and average amino acid identity values of 85.3 and 85.7 %, respectively. Genotypic and chemotaxonomic analyses support the view that strain F300T (=DSM 108350T=CIP 111667T) is the type strain of a new genus and new species for which the name Occultella aeris gen. nov., sp. nov. is proposed. Based on revised chemotaxonomic and additional genome based data, it is necessary to discuss and evaluate the results in the light of the classification and nomenclature of members of the family Ruaniaceae, i.e. the genera Haloactinobacterium and Ruania. Consequently, the reclassification of Haloactinobacterium glacieicola as Occultella glacieicola comb. nov. and Haloactinobacterium album as Ruania alba comb. nov., with an emended description of the genus Ruania are proposed.

Flavobacterium bizetiae sp. nov., isolated from diseased freshwater fish in Canada at the end of the 1970s.

Genome sequence analysis of two strains collected in Canada at the end of the 1970s and deposited in 1998 at the Collection de l'Institut Pasteur has led to the taxonomic description of a novel fish-associated species in the genus Flavobacterium. Both strains, CIP 105534T and CIP 105535, were yellow-pigmented, Gram-stain-negative, non-spore-forming rod-shaped bacteria that exhibited gliding motility. They grew aerobically in a temperature range from 5 to 30 °C with optimal growth at 25 °C on trypticase soy or Reasoner's 2A agar but they did not grow on marine agar. Their major fatty acid profiles were similar, consisting of iso-C15 : 0, C16 : 1 ω7c and/or iso-C15 : 0 2-OH (shown as summed feature 3), C16 : 0 3-OH, iso-C17 : 0 3-OH and C16 : 0. The major polyamine was sym-homospermidine. Phosphatidylethanolamine and, most notably, ornithine-containing lipid OL2 and unidentified aminophospholipid APL1 were major polar lipids. A yellow pigment spot was visible after chromatographic analysis. The predominant respiratory quinone was MK-6. The G+C content of the two genomes was 34 mol% and their size was around 5.8 Mb. Comparison of the 16S rRNA gene sequences with those of the closely related type strains showed high levels of relatedness with Flavobacterium collinsii and Flavobacterium pectinovorum. All average nucleotide identity (ANI) and digital DNA-DNA hybridization values estimated against publicly available Flavobacterium genome assemblies were lower than 90 and 30 %, respectively. Phylogenetic, phenotypic and chemotaxonomic data indicated that the two strains represent a novel species of the genus Flavobacterium, for which the name Flavobacterium bizetiae sp. nov. is proposed. The type strain is CIP 105534T (=LMG 1342T). The unique ability of F. bizetiae to use melibiose as a sole source of carbon could provide a simple phenotypic test to discriminate F. bizetiae from its closest relatives.