In this paper the Judicial Commission provides general guidance for interpreting the International Code of Nomenclature of Prokaryotes (ICNP) and specific assistance to authors, reviewers and editors of a Request for an Opinion, or of other suggestions related to the ICNP. The role of the Judicial Commission is recapitulated, particularly with respect to the processing of such Requests. Selected kinds of nomenclature-related proposals are discussed that are unsuitable as the basis for a Request. Particular emphasis is put on Requests for placing names or epithets on the list ofnomina rejicienda, and a dichotomous identification key is provided to guide potential authors of a Request that targets the name of a species or subspecies because of issues with its type strain. To this end, the criteria for the valid publication of such names under the ICNP are revisited. Aspects of other kinds of Requests are also addressed. The study is based on a comprehensive review of all Judicial Opinions issued since the publication of the Approved Lists in 1980. One goal of this paper is to assist potential authors in deciding whether their concern should be the subject of a Request, and if so, in composing it with the greatest chance of success. It is also clarified how to obtain additional help regarding nomenclature-related issues.
A taxonomic study was conducted on 16 bacterial strains isolated from wild Adelie penguins (Pygoscelis adeliae) from Seymour (Marambio) Island and James Ross Island. An initial screening by repetitive sequence-based PCR fingerprinting divided the strains studied into four coherent groups. Phylogenetic analysis based on 16S rRNA gene sequences assigned all groups to the genus Corynebacterium and showed that Corynebacterium glyciniphilum and Corynebacterium terpenotabidum were the closest species with 16S rRNA gene sequence similarities between 95.4 % and 96.5 %. Further examination of the strains studied with ribotyping, MALDI-TOF mass spectrometry, comprehensive biotyping and calculation of average nucleotide identity and digital DNA-DNA hybridisation values confirmed the separation of the four groups from each other and from the other Corynebacterium species. Chemotaxonomically, the four strains P5828T, P5850T, P6136T, P7210T representing the studied groups were characterised by C16:0 and C18:1 omega 9c as the major fatty acids, by the presence of meso-diaminopimelic acid in the peptidoglycan, the presence of corynemycolic acids and a quinone system with the predominant menaquinone MK-9(H2). The results of this study show that the strains studied represent four new species of the genus Corynebacterium, for which the names Corynebacterium antarcticum sp. nov. (type strain P5850T = CCM 8835T = LMG 30620T), Corynebacterium marambiense sp. nov. (type strain P5828T = CCM 8864T = LMG 31626T), Corynebacterium meridianum sp. nov. (type strain P6136T = CCM 8863T = LMG 31628T) and Corynebacterium pygosceleis sp. nov. (type strain P7210T = CCM 8836T = LMG 30621T) are proposed.
A bacterial strain designated 27CT isolated from the cloaca of a giant Asian pond turtle was subjected to polyphasic taxonomic characterization. The strain was Gram-stain negative and oxidase- and catalase-positive. It had highest 16S rRNA gene sequence similarity to Ottowia beijingensis GCS-AN-3T (97.6 %) and Ottowia flava GY511T 96.0% and less than 96.0 % to other established species including Ramlibacter rhizophilus YS3.2.7T, Ottowia konkukae SK3863T, Acidovorax caeni E-24608T and Ottowia thiooxydans DSM 14619T. Phylogenetically, strain 27CT formed a branch with O. beijingensis GCS-AN-3T within the Ottowia clade. The genome size was 4.32 Mbp and the G+C content was 65.7 mol%. Strain 27CT shared highest ANIb values with O. beijingensis GCS-AN-3T (82.71/82.73 %) followed by O. oryzae KADR8-3T (78.9/79.0 %) and O. caeni BD-1T (73.3/75.2 %). The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid and the quinone system was ubiquinone Q-8. Predominant compounds in the polar lipid profile were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylmonomethylethanolamine. Major polyamines were 2-hydroxyputrescine and putrescine. In the fatty acid profile, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C14 : 0, C10 : 0 3-OH and C16 : 0 2-OH were detected. All these data identify strain 27CT as representing a novel species of the genus Ottowia and hence we propose the name Ottowia testudinis sp. nov. The type strain is 27CT (=CCM 9138T=LMG 32213T).
In Opinion 103, the request to place the name Spirillum volutans Ehrenberg 1832 (Approved Lists 1980) on the list of rejected names is denied because a neotype may be designated. Similarly, because a neotype may be designated, in Opinion 104 the request to place the name Beijerinckia fluminensis Döbereiner and Ruschel 1958 (Approved Lists 1980) on the list of rejected names is denied. In Opinion 105, it is emphasized that the name Rhodoligotrophos Fukuda et al. 2012 does not contravene the Code. The request to orthographically correct Rhodoligotrophos Fukuda et al. 2012 to Rhodoligotrophus corrig. Fukuda et al. 2012 is denied. Opinion 106 addresses two Requests for an Opinion and results in the placement of the epithet hoagii in Corynebacterium hoagii (Morse 1912) Eberson 1918 (Approved Lists 1980) and Rhodococcus hoagii (Morse 1912) Kämpfer et al. 2014 on the list of rejected specific and subspecific epithets. Since this removes all known available earlier synonyms of Rhodococcus equi (Magnusson 1923) Goodfellow and Alderson 1977 (Approved Lists 1980), the request to conserve the epithet equi in this name is denied. In Opinion 107, Thermomicrobium fosteri Phillips and Perry 1976 (Approved Lists 1980) is placed on the list of rejected names as a nomen dubium et confusum. Opinion 108 denies the request to place Hyphomonas rosenbergii Weiner et al. 2000 on the list of rejected names because the information provided to the Judicial Commission is not sufficient to draw a conclusion on this matter. In Opinion 109, which addresses three Requests for an Opinion, the Judicial Commission denies the requests to place the names Bacillus aerius Shivaji et al. 2006, Bacillus aerophilus Shivaji et al. 2006 and Bacillus stratosphericus Shivaji et al. 2006 on the list of rejected names. Instead, it is concluded that these three names had not met the requirements for valid publication. Likewise, the Judicial Commission concludes in Opinion 110 that the name Actinobaculum massiliense corrig. Greub and Raoult 2006 had not met the requirements for valid publication. The Judicial Commission reaffirms in Opinion 111 that Methanocorpusculum parvum Zellner et al. 1988 is the nomenclatural type of Methanocorpusculum Zellner et al. 1988 and further emphasizes that the species was not in danger of losing this status. These Opinions were ratified by the voting members of the International Committee on Systematics of Prokaryotes.
A group of seven bacterial strains producing blue-purple pigmented colonies on R2A agar was isolated from freshwater samples collected in a deglaciated part of James Ross Island and Eagle Island, Antarctica, from 2017–2019. The isolates were psychrophilic, oligotrophic, resistant to chloramphenicol, and exhibited strong hydrolytic activities. To clarify the taxonomic position of these isolates, a polyphasic taxonomic approach was applied based on sequencing of the 16S rRNA, gyrB and lepA genes, whole-genome sequencing, rep-PCR, MALDI-TOF MS, chemotaxonomy analyses and biotyping. Phylogenetic analysis of the 16S rRNA gene sequences revealed that the entire group are representatives of the genus Massilia. The closest relatives of the reference strain P8398T were Massilia atriviolacea, Massilia violaceinigra, Massilia rubra, Massilia mucilaginosa, Massilia aquatica, Massilia frigida, Massilia glaciei and Massilia eurypsychrophila with a pairwise similarity of 98.6–100% in the 16S rRNA. The subsequent gyrB and lepA sequencing results showed the novelty of the analysed group, and the average nucleotide identity and digital DNA–DNA hybridisation values clearly proved that P8398T represents a distinct Massilia species. After all these results, we nominate a new species with the proposed name Massilia antarctica sp. nov. The type strain is P8398T (= CCM 8941T = LMG 32108T).
Since 2006, a Mycoplasma species unidentifiable to the species level has been regularly isolated from the semen and prepuce of apparently healthy bulls, and occasionally from cattle displaying inflammatory disease of the genital tract. Seven of these Mycoplasma isolates were subjected to a comprehensive taxonomic study. The strains investigated grew well in modified Hayflick’s medium and colonies on agar exhibited typical fried egg morphology and produced ‘film and spots’. Transmission electron microscopy revealed a cell morphology characteristic of mycoplasmas with spherically shaped cells bounded by a bi-layered cell membrane. The strains studied neither produced acid from sugar carbon sources nor did hydrolyse arginine or urea, and genome annotation indicated that organic acids (pyruvate, lactate) are used as energy sources. Phylogenetic analyses of 16S rRNA gene sequences, the 16S-23S intergenic spacer region, and partial rpoB gene and protein sequences placed the strains within the Mycoplasma (M.) bovis cluster of the Hominis group with M. primatum, M. agalactiae, and M. bovis being their closest relatives. Genomic information including whole-genome similarity metrics (ANIb, ANIm, TETRA, dDDH, AAI) and phylogenomics, proteomic features revealed by matrix-assisted laser desorption ionization time of flight (MALDI-ToF) mass spectrometry as well as serological reactions and polar lipid profiling strongly indicated that the strains examined were representatives of a hitherto unclassified species of genus Mycoplasma, for which the name Mycoplasma tauri sp. nov. with type strain Zaradi2T (=ATCC BAA-1891T = DSM 22451T) is proposed.
Strain F2AT, isolated from the cricket Acheta domesticus, was subjected to a polyphasic taxonomic characterization. Cells of the strain were rod-shaped, Gram-stain-negative and catalase- and oxidase-positive. It did not assimilate any carbohydrates. The strain's 16S rRNA gene sequence showed highest similarity to Entomomonas moraniae QZS01T (96.4 %). The next highest similarity values were found to representatives of related genera (<93 %). The genome size of strain F2AT was 3.2 Mbp and the G+C content was 36.4 mol%. Average nucleotide identity values based on blast and MUMmer and average amino acid identity values between strain F2AT and E. moraniae QZS01T were 74.29/74.43, 83.88 and 74.70 %, respectively. The quinone system predominantly contained ubiquinone Q-8. In the polar lipid profile, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified phospholipid were detected. The polyamine pattern consisted of the major compounds putrescine and spermidine. Major fatty acids were C18 : 1 ω7c and C16 : 0 and the hydroxyl acids were C12 : 0 3-OH, C14 : 0 2-OH and C14 : 0 3-OH. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. Due to its association with the only species of the genus Entomomonas but its distinctness from E. moraniae we here propose the novel species Entomomonas asaccharolytica sp. nov. F2AT (=CCM 9136T=LMG 32211T).
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.
Our polyphasic approach provides a new understanding of the taxonomy of novel pigmented Rugamonas species isolated from freshwater samples in Antarctica. The isolates showed considerable extracellular bactericidal secretions.
Despite unfavorable Antarctic conditions, such as cold temperatures, freeze-thaw cycles, high ultraviolet radiation, dryness and lack of nutrients, microorganisms were able to adapt and surprisingly thrive in this environment. In this study, eight cold-adapted Flavobacterium strains isolated from a remote Antarctic island, James Ross Island, were studied using a polyphasic taxonomic approach to determine their taxonomic position. Phylogenetic analyses based on the 16S rRNA gene and 92 core genes clearly showed that these strains formed two distinct phylogenetic clusters comprising three and five strains, with average nucleotide identities significantly below 90% between both proposed species as well as between their closest phylogenetic relatives. Phenotyping revealed a unique pattern of biochemical and physiological characteristics enabling differentiation from the closest phylogenetically related Flavobacterium spp. Chemotaxonomic analyses showed that type strains P4023(T) and P7388(T) were characterized by the major polyamine sym-homospermidine and a quinone system containing predominantly menaquinone MK-6. In the polar lipid profile phosphatidylethanolamine, an ornithine lipid and two unidentified lipids lacking a functional group were detected as major lipids. These characteristics along with fatty acid profiles confirmed that these species belong to the genus Flavobacterium. Thorough genomic analysis revealed the presence of numerous cold-inducible or cold-adaptation associated genes, such as cold-shock proteins, proteorhodopsin, carotenoid biosynthetic genes or oxidative-stress response genes. Genomes of type strains surprisingly harbored multiple prophages, with many of them predicted to be active. Genome-mining identified biosynthetic gene clusters in type strain genomes with a majority not matching any known clusters which supports further exploratory research possibilities involving these psychrotrophic bacteria. Antibiotic susceptibility testing revealed a pattern of multidrug-resistant phenotypes that were correlated with in silico antibiotic resistance prediction. Interestingly, while typical resistance finder tools failed to detect genes responsible for antibiotic resistance, genomic prediction confirmed a multidrug-resistant profile and suggested even broader resistance than tested. Results of this study confirmed and thoroughly characterized two novel psychrotrophic Flavobacterium species, for which the names Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov. are proposed.
A Gram-stain-positive bacterium, strain RV15T, forming an extensively branched substrate mycelium and aerial hyphae that differentiate into spiral chains of spores, was isolated from a marine sponge Dysidea tupha collected from Rovinj (Croatia). Comparison of 16S rRNA gene sequences showed that strain RV15T is a member of the genus Streptomyces with highest sequence similarity to the type strains of Streptomyces caeruleatus (98.8 %), Streptomyces cyaneochromogenes (98.6 %) and Streptomyces shaanxiensis (98.5 %). Sequence similarities to all other Streptomyces types strains were below 98.5 %. The multilocus sequence analysis-based evolutionary distance, the average nucleotide identity value and the genome-to-genome distance of strain RV15T and the type strain of S. caeruleatus were clearly below the species cut-off values. Strain RV15T exhibited a quinone system composed of the major menaquinones MK-9(H4), MK-9(H6) and MK-9(H2), typical for the genus Streptomyces. The polar lipid profile of strain RV15T consisted of the predominant compounds diphosphatidylglycerol and phosphatidylethanolamine, moderate amounts of phosphatidylinositol, phosphatidylinositol mannoside, an unidentified lipid and an unidentified phospholipid. Major polyamines were spermine and spermidine. The diagnostic diaminoacid of the peptidoglycan was meso-diaminopimelic acid. The major fatty acids were iso C16 : 0, anteiso C17 : 1 ω9c and anteiso C17 : 0. The results of physiological and biochemical tests allowed further phenotypic differentiation of strain RV15T from its most-related species and hence clearly merits species status. We propose the name Streptomyces dysideae sp. nov. with the type strain RV15T (=DSM 42110T=LMG 27702T).
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).
The rod-shaped and Gram-stain-negative bacterial strain 16FT, isolated from an air sample collected at King George Island, maritime Antarctica, was investigated to determine its taxonomic status. Strain 16FT is strictly aerobic, catalase positive, oxidase positive and non-motile. Strain 16FT hydrolyses casein, lecithin, Tween 20, 60 and 80, but not aesculin, gelatin and starch. Growth of strain 16FT is observed at 0–20 °C (optimum 10 °C), pH 5.0–8.0 (optimum pH 6.0), and in the presence of 0–2.0% NaCl (optimum 0.5%). The predominant menaquinone is MK-6, and the major fatty acids comprise anteiso-C15:0 and iso-C15:0. The major polar lipids are phosphatidylethanolamine, ornithine lipid OL2, unidentified phospholipid PL1 and the unidentified lipids L3 and L6 lacking functional groups. The DNA G + C content based on the draft genome sequence is 32.3 mol%. Sequence analysis of the 16S rRNA gene indicates the highest similarity to Kaistella palustris 3A10T (95.4%), Kaistella chaponensis Sa 1147-06 T (95.2%), Kaistella antarctica AT1013T (95.1%), Kaistella carnis NCTC 13525 T (95.1%) and below 95.0% to other species with validly published names. Phylogenetic analysis based on 16S rRNA gene and whole-genome sequences places strain 16FT in a distinct branch, indicating a separate lineage within the family Weeksellaceae. Based on the data from our polyphasic approach, 16FT represents a novel species of a new genus, for which the name Frigoriflavimonas asaccharolytica gen. nov, sp. nov. is proposed. The type strain is 16FT (= CCM 8975 T = CGMCC No.1.16844 T).
A rod-shaped and Gram-stain-negative bacterial strain 9AT, was isolated from an air sample collected at King George Island, maritime Antarctica. Phylogenetic analysis based on 16S rRNA gene sequence reveals that strain 9AT belongs to the genus Hymenobacter and shows the highest similarity to Hymenobacter coccineus CCM 8649T (96.8 %). The DNA G+C content based on the draft genome sequence is 64.9 mol%. Strain 9AT is strictly aerobic, psychrophilic, catalase-positive, oxidase-positive and non-motile. Growth is observed at 0-20 °C (optimum 10 °C), pH 6.0-8.0 (optimum pH 7.0), and in the absence of NaCl. The predominant menaquinone of strain 9AT is MK-7 and the major fatty acids comprise Summed Feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c; 25.2 %), iso-C15 : 0 (23.2 %), C16 : 1 ω5c (11.6 %), Summed Feature 4 (anteiso-C17 : 1 B/iso-C17 : 1 I) (9.6 %) and anteiso-C15 : 0 (9.6 %). The polar lipid profile consists of the major lipid phosphatidylethanolamine and moderate to minor amounts of phosphatidylserine, unidentified aminolipids, aminophospholipids, aminophosphoglycolipids, polar lipids lacking a functional group and an unidentified phospholipid and a glycolipid. In the polyamine pattern sym-homospermidine is predominant. On the basis of the results obtained, strain 9AT is proposed as a novel species of the genus Hymenobacter, for which the name Hymenobacter caeli sp. nov. is suggested. The type strain is 9AT (=CCM 8971T=LMG 32109T=DSM 111653T).
A bacterial strain designated 32AT was isolated from the skin of an Anderson's salamander (Ambystoma andersoni) and subjected to a comprehensive taxonomic study. The strain was Gram-stain-negative, rod-shaped, non-motile, oxidase- and urease-negative, and catalase-positive. 16S rRNA gene sequence comparisons placed the strain in the genus Luteolibacter with highest sequence similarities to Luteolibacter pohnpeiensis A4T-83T (95.2%), Luteolibacter gellanilyticus CB-286403T (95.1%) and Luteolibacter cuticulihirudinis E100T (94.9%). Genomic sequence analysis revealed a size of 5.3 Mbp, a G+C-content of 62.2 mol% and highest ANI values with Luteolibacter luteus (71.2%), Luteolibacter yonseiensis (71.4%) and L. pohnpeiensis (69.5%). In the polyamine pattern, 1,3-diaminopropane and spermidine were predominant. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. The quinone system was composed of the major menaquinones MK-9 and MK-10. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, the unidentified aminolipid AL2, the unidentified phospholipid PL2 and the unidentified aminophospholipid APL1. The fatty acid profile contained major amounts of iso-C14:0, iso-C16:0, C16 : 0 and C16 : 1 ω9c. In addition, C14 : 0, C15:0, anteiso-C15 : 0, summed feature 2 (C14 : 0 3OH and/or iso-C16 : 0 I), and the hydroxylated fatty acids iso-C14 : 0 3OH, iso-C16 : 0 3OH and C16 : 0 3-OH were detected. Physiologically, strain 32AT is distinguishable from its next relatives. Based on phylogenetic, genomic, physiological and chemotaxonomic data, strain 32AT represents a novel species of the genus Luteolibacter for which we propose the name Luteolibacter ambystomatis sp. nov. The type strain is 32AT (=CCM 9141T=LMG 32214T).
A total of 34 Corynebacterium sp. strains were isolated from caseous lymph node abscesses of wild boar and roe deer in different regions of Germany. They showed slow growth on Columbia sheep blood agar and sparse growth on Hoyle's tellurite agar. Cellular fatty acid analysis allocated them in the C. diphtheriae group of genus Corynebacterium. MALDI-TOF MS using specific database extensions and rpoB sequencing resulted in classification as C. ulcerans. Their quinone system is similar to C. ulcerans, with major menaquinone MK-8(H2). Their complex polar lipid profile includes major lipids phosphatidylinositol, phosphatidylinositol-mannoside, diphosphatidylglycerol, but also unidentified glycolipids, distinguishing them clearly from C. ulcerans. They ferment glucose, ribose and maltose (like C. ulcerans), but do not utilise d-xylose, mannitol, lactose, sucrose and glycogen (like C. pseudotuberculosis). They showed activity of catalase, urease and phospholipase D, but variable results for alkaline phosphatase and alpha-glucosidase. All were non-toxigenic, tox gene bearing and susceptible to clindamycin, penicillin and erythromycin. In 16SrRNA gene and RpoB protein phylogenies the strains formed distinct brancheswith C. ulcerans as nearest relative.Whole genome sequencing revealed the unique sequence type 578, a distinctbranch in pangenomic core genome MLST, average nucleotide identities <91%, enhancedgenome sizes (2.55 Mbp) and G/C content (54.4 mol%) compared to related species.These results suggest that the strains represent a novel species, for which wepropose the name Corynebactriumsilvaticum sp. nov., based on their first isolation from forest-dwellinggame animals. The type strain isKL0182T (= CVUAS 4292T = DSM 109166T = LMG 31313T= CIP 111 672T).
Twelve Mycoplasma (M.) strains isolated from the nose, the trachea, and the lung of ostriches (Struthio camelus) displaying respiratory disease were investigated. Analysis of 16S rRNA gene sequences placed five of these strains within the M. synoviae cluster, and seven strains within the M. hominis cluster of genus Mycoplasma, which was further confirmed by analyses of the 16S-23S rRNA intergenic spacer region, and partial rpoB gene and amino acid sequences. Genomic information as well as phenotypic features obtained by matrix-assisted laser desorption ionization time of flight (MALDI-ToF) mass spectrometry analysis and serological reactions indicated that the strains examined are representatives of two hitherto unclassified species of genus Mycoplasma, for which the names Mycoplasma nasistruthionis sp. nov., with type strain 2F1AT (= ATCC BAA-1893T = DSM 22456T), and Mycoplasma struthionis sp. nov., with type strain 237IAT (= ATCC BAA-1890T = DSM 22453T), are proposed.
A Gram-stain-positive bacterial isolate, designated LMM-1652T, was isolated from an intrauterine cytobrush sample originating from a postpartum Holstein Friesian dairy cow. The strain had a rod to coccoid-shape, was catalase-positive and oxidase-negative. 16S rRNA gene sequence similarity analyses revealed that its closest relatives were Corynebacterium falsenii (97.05 % similarity), Corynebacterium jeikeium (96.83 %) and Corynebacterium urealyticum (96.82 %). Subsequent whole genome analysis showed that the genome-to-genome distance of strain LMM-1652T to its closest relatives was in the range of 23.2–24.8 %, while the average nucleotide identity values ranged from 73.7 to 74.3%, thus confirming that this isolate represents a novel species. Strain LMM-1652T was characterized by a quinone system mainly consisting of MK-9(H2) and MK-10(H2). The polar lipids profile of the strain consisted mainly of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol-mannoside, as well as one unidentified lipid lacking any functional group. Smaller amounts of four unidentified phospholipids, four unidentified glycolipids, β-gentiobiosyl diacylglycerol and four unidentified lipids lacking a functional group were also found. The cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid of the peptidoglycan. The fatty acid profile was mainly composed of C18 : 1 ω9c, C18 : 0 and C16 : 0. We propose a novel species of the genus Corynebacterium with the name Corynebacterium urogenitale LMM-1652T (=LMG 31163T=DSM 108747T).
Bacteria of the genus Massilia often colonize extreme ecosystems, however, a detailed study of the massilias from the Antarctic environment has not yet been performed. Here, sixty-four Gram-stain-negative, aerobic, motile rods isolated from different environmental samples on James Ross Island (Antarctica) were subjected to a polyphasic taxonomic study. The psychrophilic isolates exhibited slowly growing, moderately slimy colonies revealing bold pink-red pigmentation on R2A agar. The set of strains exhibited the highest 16S rRNA gene sequence similarities (99.5-99.9%) to Massilia violaceinigra B2T and Massilia atriviolacea SODT and formed several phylogenetic groups based on the analysis of gyrB and lepA genes. Phenotypic characteristics allowed four of them to be distinguished from each other and from their closest relatives. Compared to the nearest phylogenetic neighbours the set of six genome-sequenced representatives exhibited considerable phylogenetic distance at the whole-genome level. Bioinformatic analysis of the genomic sequences revealed a high number of putative genes involved in oxidative stress response, heavy-metal resistance, bacteriocin production, the presence of putative genes involved in nitrogen metabolism and auxin biosynthesis. The identification of putative genes encoding aromatic dioxygenases suggests the biotechnology potential of the strains. Based on these results four novel species and one genomospecies of the genus Massilia are described and named Massilia rubra sp. nov. (P3094T=CCM 8692T=LMG 31213T), Massilia aquatica sp. nov. (P3165T=CCM 8693T=LMG 31211T), Massilia mucilaginosa sp. nov. (P5902T=CCM 8733T=LMG 31210T), and Massilia frigida sp. nov. (P5534T=CCM 8695T=LMG 31212T).
A pink pigmented, Gram-negative, rod-shaped, non-spore-forming bacterium (strain 36B243T), was isolated from the spleen of a black rock cod (Notothenia coriiceps, Richardson 1844) in the Chilean Antarctica. Strain 36B243T has a 5.26 Mb chromosome with a DNA G + C content of 35.4 mol%. The draft genome includes the prediction and annotation of 4585 coding genes, and 46 tRNA, 1 tmRNA, and 2735 hypothetical proteins. Phylogenetic analysis based on the 16S rRNA gene sequence placed strain 36B243T into the genus Pedobacter with high sequence similarity to the type strains of Pedobacter sandarakinus (97.5%) and Pedobacter petrophilus (97.1%). Sequence similarities to type strains of all other current Pedobacter species were below 97.1%. Predominant fatty acids are summed feature 3 (C16:1ω7c and/or C16:1ω6c) and iso-C15:0 followed by iso-C17:0 3-OH and C16:0. The major respiratory quinone was menaquinone MK-7. The polar lipid profile contained the major lipids phosphatidylethanolamine, five unidentified aminolipids, two lipids lacking a functional group and two minor glycolipids and one lipid lacking a functional group. An alkali-stable lipid was present. The polyamine pattern contained the predominant compound sym-homospermidine. Characterization by 16S rRNA gene sequence analysis, physiological parameters, pigment analysis, ubiquinone, polar lipid, and fatty acid composition revealed that strain 36B243T represents a new species of the genus Pedobacter. For this reason, we propose the name Pedobacter nototheniae sp. nov. with the type strain 36B243T (= LMG 30634T = CCM 8855T = CIP 111622T).