- Volume 68, Issue 11, 2018
Volume 68, Issue 11, 2018
- Validation List
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- Notification List
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- New Taxa
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- Actinobacteria
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Psychromicrobium lacuslunae sp. nov., isolated from a high altitude lake
The novel strain IHBB 11108T was a psychrotolerant and alkaliphilic bacterium isolated from the subsurface water of Chandra Tal Lake in the Lahaul-Spiti valley located in the Indian trans-Himalayas. Cells were Gram-stain-positive, aerobic, non-motile, catalase-positive and oxidase-negative. The strain grew at 5–37 °C (optimum 28 °C), pH 5.0–12.0 (optimum pH 7.0) and with up to 8 % NaCl (optimum 1 %). The 16S rRNA gene sequence analysis revealed the highest relatedness of strain IHBB 11108T with Psychromicrobium silvestre DSM 102047T (97.5 %), Arthrobacter russicus DSM 14555T (97.4 %) and Renibacterium salmoninarum ATCC 33209T (97.4 %). The strain contained a quinone system with 57.2 % MK-9(H2), 39.1 % MK-10(H2), 3.0 % MK-8(H2) and 0.7 % MK-7(H2). The polar lipids detected were diphosphatidylglycerol, dimannosylglyceride, phosphatidylinositol, phosphatidylglycerol, monogalactosyldiacylglycerol, one unidentified glycolipid and four unidentified lipids. The cell-wall peptidoglycan structure type was A3α l-Lys–l-Thr–l-Ala with substitution of the α-carboxyl group of d-Glu by alanine amide. Anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0 were the predominant fatty acids. The genomic DNA G+C content was 59.0 mol%. The DNA–DNA relatedness of strain IHBB 11108T was 46.7±2.2, 43.1±2.5 and 19.1±2.4 % with P. silvestre DSM 102047T, A. russicus DSM 14555T and R. salmoninarum ATCC 33209T, respectively. On the basis of the results of the phenotypic, chemotaxonomic and phylogenetic analyses, IHBB 11108T is considered to represent a novel species of the genus Psychromicrobium for which the name Psychromicrobium lacuslunae sp. nov. is proposed. The type strain is IHBB 11108T (=MTCC 12460T=MCC 2780T=JCM 31143T=KACC 19070T).
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Blastococcus litoris sp. nov., isolated from sea-tidal flat sediment
A novel Gram-strain-positive, non-spore-forming bacterial strain, designated GP-S2-8T, was isolated from a sea-tidal flat sediment sample from Gopado, Republic of Korea. Cells were aerobic, catalase-negative, oxidase-positive, non-motile and cocci, occurring singly, in pairs or in tetrads, and often tending to form aggregates. The strain grew at 4–45 °C (optimum, 28–37 °C), at pH 4.0–11.0 (pH 7.0–9.0) and in the presence of 0–11 % (w/v) NaCl (0–3 %). Phylogenetic analyses based on 16S rRNA gene sequences represented that the isolate belongs to the genus Blastococcus . The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. Whole-cell sugar analysis of strain GP-S2-8T revealed rhamnose, glucose and mannose as characteristic sugars. The predominant respiratory quinone was MK-9(H4) and the major fatty acids were iso-C16 : 0, iso-C16 : 1 H, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0 and iso-C14 : 0. The polar lipid profile included diphosphadidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, one unidentified glycophospholipid, two unidentified phospholipids and five unidentified lipids. The DNA G+C content was 74.2 mol%. DNA–DNA relatedness values between strain GP-S2-8T and type strains of the genus Blastococcus ranged from 14.6 to 48.6 %. On the basis of the phenotypic differences and DNA–DNA relatedness data, the isolate represents a new species of the genus Blastococcus , for which the name Blastococcus litoris sp. nov. is proposed. The type strain is GP-S2-8T (=KCCM 43275T=JCM 32354T=DSM 106127T=KCTC 49078T).
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Kribbella monticola sp. nov., a novel actinomycete isolated from soil
More LessA novel actinobacterium, designated strain NEAU-SW521T, was isolated from soil collected from Xianglu Mountain, Heilongjiang province, north PR China. The results of analysis of the 16S rRNA gene indicated that NEAU-SW521T represented a member of the genus Kribbella . The results of phylogenetic analyses using the 16S rRNA gene and multilocus sequence analysis using the concatenated gene sequences of the gyrB, rpoB, relA, recA and atpD genes all indicated that the strain formed a clade with Kribbella alba DSM 15500T (99.16 %), Kribbella ginsengisoli JCM 16928T (98.96 %), Kribbella catacumbae JCM 14968T (98.82 %), Kribbella sancticallisti JCM 14969T (98.62 %), Kribbella qitaiheensis NEAU-GQTH2-3T (98.61 %) and Kribbella koreensis JCM 10977T (98.47 %). The cell wall contained ll-diaminopimelic acid as the major diamino acid and the whole-cell hydrolysates were ribose, glucose and galactose. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol and an unidentified phospholipid. The predominant menaquinone was MK-9(H4). Major fatty acids were iso-C16 : 0 and anteiso-C15 : 0. These chemotaxonomic data supported the affiliation of NEAU-SW521T to the genus Kribbella . The DNA G+C content was 67.8 mol%. Furthermore, the strain could be clearly distinguished by concatenated gene genetic distances, the combination of DNA–DNA hybridization results and some phenotypic characteristics. Therefore, it is proposed that NEAU-SW521T represents a novel species of the genus Kribbella , for which the name Kribbella monticola sp. nov. is proposed. The type strain is NEAU-SW521T (=CGMCC 4.7465T=DSM 105770T).
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Rubrobacter indicoceani sp. nov., a new marine actinobacterium isolated from Indian Ocean sediment
More LessA novel mesophilic marine actinobacterial strain, designated as SCSIO 08198T, was isolated from a deep-sea sediment sample collected from the Indian Ocean. The strain was Gram-stain-positive, rod-shaped and salmon pink in colour. Good growth occurred on marine agar with 1–5 % (w/v) NaCl and incubation at 28 °C for more than a fortnight. Sensitive to short ultraviolet radiation. Analysis of 16S rRNA gene sequences revealed that strain SCSIO 08198T had the highest similarity of 97.2 % to Rubrobacter radiotolerans DSM 5868T, and loosely related (<94.2 %) to all other species in the genus Rubrobacter . Phylogenetic analysis based on nearly complete 16S rRNA gene sequences revealed that the novel isolate shared a lineage with members of the genus Rubrobacter . The total cellular fatty acid profile was dominated by C16 : 0 12-methyl. MK-8 was the main menaquinone. The peptidoglycan type was A3α (l-Lys-l-Ala). The major phospholipids were diphosphatidylglycerol, phosphatidylglycerol and unidentified phospholipids. Based on the whole genome sequence analysis, the genome size is 3 078 689 bp with DNA G+C value of 63.8 mol%, including one circular chromosome and two plasmids. Based on these polyphasic data, a new species, Rubrobacter indicoceani sp. nov., is proposed, with the type strain SCSIO 08198T (=DSM 105148T=CGMCC 1.16398T).
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Lentzea terrae sp. nov., isolated from soil and an emended description of Lentzea soli
A novel actinobacterium, designated strain NEAU-LZS 42T, was isolated from soil collected from Mount Song, Henan Province, China, and characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the organism should be assigned to the genus Lentzea and had the closest relationship with Lentzea soli NEAU-LZC 7T (99.1 % similarity) and Lentzea cavernae SYSU K10001T (98.2 %). The major menaquinones were identified as MK-9(H4) and MK-9(H2). The phospholipid profile was found to contain diphosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, glycophospholipid and three unidentified lipids. The major fatty acids were iso-C16 : 0, C16 : 1ω7c and C16 : 0. DNA–DNA hybridization results and some phenotypic characteristics indicated that strain NEAU-LZS 42T could be clearly differentiated from L. soli NEAU-LZC 7T and L. cavernae SYSU K10001T. Therefore, it is concluded that strain NEAU-LZS 42T represents a novel species of the genus Lentzea , for which the name Lentzea terrae sp. nov. is proposed. The type stain is NEAU-LZS 42T (=CGMCC 4.7428T=DSM 105696T).
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Mycobacterium decipiens sp. nov., a new species closely related to the Mycobacterium tuberculosis complex
Barbara A. Brown-Elliott, Patricia J. Simmer, Alberto Trovato, Emily P. Hyle, Sara Droz, Seanne P. Buckwalter, Emanuele Borroni, John A. Branda, Elkina Iana, Alessandro Mariottini, Jameelah Nelson, Alberto Matteelli, Nadege C. Toney, Claudio Scarparo, Tom J. B. de Man, Ravikiran Vasireddy, Rajesh T. Gandhi, Nancy L. Wengenack, Daniela M. Cirillo, Richard J. Wallace and Enrico TortoliTwo mycobacterial strains with close similarity to the Mycobacterium tuberculosis complex (MTBC) were isolated from cutaneous lesions of patients in the USA and Italy. At the phenotypic level, similarities to the MTBC included slow growth rate, rough morphotype of the unpigmented colonies and nearly identical high-performance liquid chromatography profiles of mycolic acids. In contrast to the MTBC, the strains were niacin- and nitrate-negative, and catalase-positive both at 68 °C and in semi-quantitative tests. The clinical isolates were more closely related to M. tuberculosis than to any other known mycobacterium and scored positive with commercial DNA probes (Hologic AccuProbe M. tuberculosis ). Both average nucleotide identity and genome-to-genome distance suggested the strains are different from the MTBC. Therefore, given the distinguishing phenotypic and genomic-scale differences, we submit that the strains belong to a new species we have named Mycobacterium decipiens with type strain TBL 1200985T (=ATCC TSD-117T=DSM 105360T).
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Brachybacterium endophyticum sp. nov., a novel endophytic actinobacterium isolated from bark of Scutellaria baicalensis Georgi
More LessA Gram-positive, aerobic, coccus-shaped, non-spore-forming actinobacterium, designated strain M1HQ-2T, was isolated from a surface-sterilized bark of Scutellaria baicalensis Georgi collected from Guizhou, China and tested using a polyphasic approach to determine its taxonomic position. Strain M1HQ-2T grew at 4–37 °C (optimum, 30 °C), pH 5.0–11.0 (pH 8.0) and in the presence of 0–15 % (w/v) NaCl (1–3 %). Substrate mycelia and aerial mycelia were not formed, and diffusible pigments were not observed on any media tested. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain M1HQ-2T belonged to the genus Brachybacterium and had the highest 16S rRNA gene sequence similarity of 97.6 % to Brachybacteriumsquillarum M-6-3T. Strain M1HQ-2T contained MK-7 as the dominant menaquinone. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The polar lipids profile of strain M1HQ-2T contained diphosphatidylglycerol, phosphatidylglycerol, an unidentified phospholipid and an unidentified lipid. The predominant fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. The DNA G+C content of strain M1HQ-2T was 71.0 mol%. The average nucleotide identity value between strain M1HQ-2T and type strain of Brachybacterium sacelli was 76.7 %. The estimated DNA–DNA hybridization value between strain M1HQ-2T and type strain of B. sacelli was 20.6 %. On the basis of phylogenetic analysis, chemotaxonomic characteristics and phenotypic data, strain M1HQ-2T represents a novel species of the genus Brachybacterium , for which the name Brachybacterium endophyticum sp. nov. is proposed. The type strain is M1HQ-2T (=KCTC 49087T=CGMCC 1.16391T).
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Desertimonas flava gen. nov., sp. nov. isolated from a desert soil, and proposal of Ilumatobacteraceae fam. nov.
A non-motile, coccobacilli-shaped and yellow-coloured bacterium, designated strain SYSU D60003T, was isolated from a desert soil sample. Cells were Gram-stain-positive, catalase-negative and oxidase-positive. The whole cell hydrolysates contained ll-diaminopimelic acid as the diagnostic amino acid. The major fatty acids were C16 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and iso-C16 : 0. The respiratory menaquinones were MK-9(H8), MK-9(H4) and MK-9(H6). The DNA G+C content was determined to be 70.2 % (genome). The polar lipids detected were diphosphatidylglycerol, an unidentified glycolipid and seven unidentified polar lipids. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SYSU D60003T belonged to the order Acidimicrobiales (class Acidimicrobiia ), but formed a clade closely linked to members of the genus Ilumatobacter . Data from a polyphasic taxonomy study suggested that the isolate represents a novel species of a novel genus in the order Acidimicrobiales , for which the name Desertimonas flava gen. nov., sp. nov. is proposed. The type strain of the proposed new taxon is SYSU D60003T (=KCTC 39917T=NBRC 112924T). Additionally, the new taxon along with the genus Ilumatobater (family unassigned) were distinctly separated from the related families Acidimicrobiaceae , Iamiaceae and ‘Microtrichaceae’ in the phylogenetic trees, besides presenting a unique 16S rRNA gene signature nucleotides. Therefore, we propose a new family Ilumatobacteraceae fam. nov. within the order Acidimicrobiales to accommodate members of these two genera.
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Microbispora triticiradicis sp. nov., a novel actinomycete isolated from the root of wheat (Triticum aestivum L.)
A novel actinomycete, designated strain NEAU-HRDPA2-9T, was isolated from the roots of wheat (Triticumaestivum L.) and characterized using a polyphasic approach. The morphological and chemotaxonomic characteristics of the strain coincided with those of members of the genus Microbispora . The 16S rRNA gene sequence analysis showed that the isolate was most closely related to Microbispora bryophytorum NEAU-TX2-2T (98.6 %), Microbispora hainanensis DSM 45428T (98.5 %), Microbispora camponoti 2C-HV3T (98.5 %), Microbispora amethystogenes JCM 3021T (98.2 %), Microbispora siamensis NBRC 104113T (98.1 %), Microbispora corallina JCM 10267T (98.0 %) and Microbispora rosea subsp. rosea JCM 3006T (97.9 %). However, two tree-making algorithms supported the position that strain NEAU-HRDPA2-9T formed a distinct clade with M. siamensis NBRC 104113T and M. hainanensis DSM 45428T. Furthermore, a combination of DNA–DNA hybridization results and some physiological and biochemical properties demonstrated that the strain could be distinguished from its closest relatives. Therefore, it is proposed that strain NEAU-HRDPA2-9T should be classified as representative of a novel species of the genus Microbispora , for which the name Microbispora triticiradicis sp. nov. is proposed. The type strain is NEAU-HRDPA2-9T (=CGMCC 4.7399T=DSM 104649T).
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Streptomyces durbertensis sp. nov., isolated from saline–alkali soil
A novel strain of actinobacteria, designated NEAU-S1GS20T, was isolated from a saline–alkali soil collected from Heilongjiang Province, north-east China, and characterized using a polyphasic approach. Strain NEAU-S1GS20T exhibited morphological, cultural and chemotaxonomic features consistent with its classification as representing a member of the genus Streptomyces . Growth occurred at 18‒45 °C, at pH 6.0‒10.0 and in the presence of 10 % (w/v) NaCl. Whole-cell hydrolysates mainly contained glucose and ribose. The predominant menaquinones were MK–9(H4) and MK–9(H6). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and two unidentified phospholipids. The major cellular fatty acids (>10 %) were iso-C16 : 0, iso-C17 : 0, anteiso-C17 : 0 and C16 : 0. The G+C content of the DNA was 72.8 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain NEAU-S1GS20T formed a distinct clade within the genus Streptomyces and was closely related to Streptomyces xinghaiensis CCTCC AA 208049T (98.4 % similarity), Streptomyces chumphonensis JCM 18522T (98.1 %) and Streptomyces palmae JCM 31289T (98.1 %). Multilocus sequence analysis (MLSA) using five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) showed that the MLSA distance of strain NEAU-S1GS20T to the most closely related species was greater than the 0.007 threshold. A combination of DNA–DNA hybridization results and differences in certain phenotypic characteristics demonstrated that strain NEAU-S1GS20T could be distinguished from its closest phylogenetic relatives. Therefore, strain NEAU-S1GS20T represents a novel species of the genus Streptomyces , for which the name Streptomyces durbertensis sp. nov. is proposed. The type strain is NEAU-S1GS20T (=CCTCC AA 2017006T=DSM 104538T).
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Streptomyces lichenis sp. nov., isolated from lichen
More LessA new actinobacterial strain, LCR6-01T, was isolated from a lichen sample collected from Chiang Rai Province, Thailand. Its taxonomic position was determined using a polyphasic approach. The strain had morphological characteristics and chemotaxonomic properties identical to those of members of the genus Streptomyces . The predominant menaquinones were MK-9(H6) and MK-9(H8). The major fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0, iso-C14 : 0 and C16 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified phosphoglycolipid, an unidentified phospholipid and an unidentified lipid. The genomic DNA G+C content was 74.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences suggested that the strain belonged to the genus Streptomyces . The strain showed highest 16S rRNA gene sequence similarity to Streptomyces palmae TBRC 1999T (98.6 %), Streptomyces misionensis JCM 4497T (98.6 %), Streptomyces matensis JCM 4268T (98.5 %), Streptomyces althioticus KCTC 9752T (98.5 %) and Streptomyces wuyuanensis KCTC 29112T (98.4 %). DNA–DNA relatedness values among the strain and closely related Streptomyces species were below 70 %. On the basis of the phenotypic characteristics and genotypic distinctiveness, strain LCR6-01T is considered to represent a novel species of the genus Streptomyces , for which the name Streptomyces lichenis sp. nov. is proposed. The type strain is LCR6-01T (=KCTC 39908T=TISTR 2500T)
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- Archaea
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Halorubrum chaoviator Mancinelli et al. 2009 is a later, heterotypic synonym of Halorubrum ezzemoulense Kharroub et al. 2006. Emended description of Halorubrum ezzemoulense Kharroub et al. 2006
A polyphasic comparative taxonomic study of Halorubrum ezzemoulense Kharroub et al. 2006, Halorubrum chaoviator Mancinelli et al. 2009 and eight new Halorubrum strains related to these haloarchaeal species was carried out. Multilocus sequence analysis using the five concatenated housekeeping genes atpB, EF-2, glnA, ppsA and rpoB′, and phylogenetic analysis based on the 757 core protein sequences obtained from their genomes showed that Hrr. ezzemoulense DSM 17463T, Hrr. chaoviator Halo-G*T (=DSM 19316T) and the eight Halorubrum strains formed a robust cluster, clearly separated from the remaining species of the genus Halorubrum . The orthoANI value and digital DNA–DNA hybridization value, calculated by the Genome-to-Genome Distance Calculator (GGDC), showed percentages among Hrr. ezzemoulense DSM 17463T, Hrr. chaoviator DSM 19316T and the eight Halorubrum strains ranging from 99.4 to 97.9 %, and from 95.0 to 74.2 %, respectively, while these values for those strains and the type strains of the most closely related species of Halorubrum were 88.7–77.4 % and 36.1–22.3 %, respectively. Although some differences were observed, the phenotypic and polar lipid profiles were quite similar for all the strains studied. Overall, these data show that Hrr. ezzemoulense, Hrr. chaoviator and the eight new Halorubrum isolates constitute a single species. Thus, Hrr. chaoviator should be considered as a later, heterotypic synonym of Hrr. ezzemoulense . We propose an emended description of Hrr. ezzemoulense , including the features of Hrr. chaoviator and those of the eight new isolates.
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- Bacteroidetes
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Chryseobacterium aurantiacum sp. nov., isolated from a freshwater pond used for Murray cod (Maccullochella peelii peelii) culture
More LessA yellow-pigmented, Gram-staining-negative, aerobic, non-motile and rod-shaped bacterium, designated strain F30T, was isolated from fresh water of a diseased farmed Murray cod with a profound ulceration pond in Zhejiang province, PR China. Growth was observed at NaCl concentrations of 0.5–3.5 % (w/v) (optimum, 1.5–2.0 %), temperatures of 10–35 °C (optimum, 28 °C) and pH 5.0–9.0 (optimum, 6.5). Phylogenetic analysis based on 16S rRNA gene sequences indicated that F30T represented a member of the genus Chryseobacterium , showing the highest similarity to Chryseobacterium jejuense DSM 19299T (99.0 %) and Chryseobacterium nakagawai NCTC 13529T (99.0 %), and less than 98.7 % similarity to other species of the genus Chryseobacterium with validly published names. The average nucleotide identity and in silico DNA–DNA hybridization values between F30T and the reference strains were 78.4–90.5 % and 2.6–42.5 %, respectively. The results of chemotaxonomic analysis indicated that the fatty acids, as well as the polar lipid profiles of F30T were similar to those of species of the genus Chryseobacterium , and the sole respiratory quinone was MK-6. On the basis of its phylogenetic, chemotaxonomic and phenotypic data, strain F30T represents a novel species, for which the name Chryseobacterium aurantiacum sp. nov. is proposed. The type strain is F30T (=KCTC 62135T=MCCC 1K03457T).
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Brumimicrobium salinarum sp. nov., isolated from a marine solar saltern
More LessA Gram-stain-negative, aerobic, rod-shaped and orange-coloured strain, designated LHR20T, was isolated from a marine solar saltern. The novel strain LHR20T was able to grow at 15–40 °C (optimum 33–37 °C), at pH 6.5–9.5 (optimum pH 7.5–8.0) and with 2.0–11.0 % (w/v) NaCl (optimum 4.0–5.0 %). MK-6 was the sole respiratory quinone, and the major fatty acids were iso-C15 : 0 and iso-C17 : 0 3-OH. The predominant polar lipids of strain LHR20T were phosphatidylethanolamine (PE), aminolipid (AL), glycolipid (GL1) and two unidentified lipids (L1, L2). The genomic DNA G+C content was 35.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain LHR20T was a member of the genus Brumimicrobium and its closest relative was Brumimicrobium mesophilum JCM 14063T (97.5 % sequence similarity). The average nucleotide identity value between strain LHR20T and B. mesophilum JCM 14063T was 73.7 %. This evidence from phenotypic, chemotaxonomic and phylogenetic analyses suggests that strain LHR20T represents a novel species of the genus Brumimicrobium . Therefore, the name Brumimicrobium salinarum sp. nov. is proposed. The type strain is LHR20T (=KCTC 62372T=MCCC 1H00247T).
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Chitinophaga parva sp. nov., a new member of the family Chitinophagaceae, isolated from soil in a chemical factory
More LessA Gram-stain-negative bacterium, designated LY-1T, was isolated from the soil sample collected from a chemical factory in Fuyang city, Anhui province, China. Cells of strain LY-1T were strictly aerobic, non-motile and rod-shaped. Strain LY-1T grew optimally at pH 7.0 and at 30–35 °C. The taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain LY-1T was a member of the genus Chitinophaga and showed the highest sequence similarity to Chitinophaga costaii A37T2T (97.5 %) and lower (<97.0 %) sequence similarity to other known Chitinophaga species. Chemotaxonomic analysis revealed that strain LY-1T possessed menaquinone-7 as the major isoprenoid quinone; and iso-C15 : 0 (46.4 %), C16 : 1ω5c (27.8 %) and iso-C17 : 0 3-OH (9.0 %) were the predominant fatty acids. The polar lipids of strain LY-1T consisted of phosphatidylethanolamine, three unidentified phosphoaminolipids, one unidentified phospholipid, four unidentified lipids, two unidentified aminolipids and two unidentified glycolipids. The genomic DNA G+C content of strain LY-1T was 52.4 mol% based on total genome calculations. The average nucleotide identity and the digital DNA–DNA hybridization value of the draft genomes between strain LY-1T and strain A37T2T were 76.8 and 19.8 %, respectively. Based on the phylogenetic and phenotypic characteristics, chemotaxonomic data, and DNA–DNA hybridization, strain LY-1T is considered a novel species of the genus Chitinophaga , for which the name Chitinophaga parva sp. nov. (type strain LY-1T=CCTCC AB 2018018T=KCTC 62444T) is proposed.
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Maribacter litoralis sp. nov. a marine bacterium isolated from seashore
A novel Gram-stain-negative, moderately halophilic and aerobic bacterium, designated strain SDRB-Phe2T, was isolated from coastal sediment of the yellow sea in Sindu-ri, Republic of Korea. Cells were oxidase-positive, catalase-positive, rod-shaped and surrounded by a capsule with gliding motility. Colonies were yellow-coloured, circular, pulvinate with entire margins. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SDRB-Phe2T formed a distinct lineage within the genus Maribacter of the family Flavobacteriaceae . Stain SDRB-Phe2T exhibited 16S rRNA gene sequence similarity values of 97.1–98.9 % to the type strains of M aribacter stanieri, M aribacter spongiicola, M aribacter forsetii, M aribacter dokdonensis, M aribacter aquivivus, M aribacter caenipelagi, M aribacter litorisediminis, M aribacter sedimenticola, M aribacter ulvicola, M aribacter confluentis and M aribacter orientalis, and of 94.8–96.7 % to the type strains of the other species of the genus Maribacter . Strain SDRB-Phe2T contained MK-6 as the predominant respiratory quinone and iso-C15 : 1 G, iso-C15 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the major fatty acids. The polar lipids of strain SDRB-Phe2T were phosphatidylethanolamine, one unidentified amino lipid and two unidentified lipids. The DNA G+C content was 36.2 mol%. DNA–DNA relatedness values of strain SDRB-Phe2T to the type strains of the 11 phylogenetically related species of the genus Maribacter were 21.9–38.6 %. On the basis of the phenotypic features, phylogenetic and DNA–DNA hybridization analyses presented here, strain SDRB-Phe2T (=JCM 32373T=KCTC 62273T=DSM 106042T) represents a novel species of the genus Maribacter , for which the name Maribacter litoralis sp. nov. is proposed.
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Chryseolinea flava sp. nov., a new species of Chryseolinea isolated from soil
More LessA pale yellow bacterial strain, designated SDU1-6T, was isolated from a soil sample collected in the Jinan campus of Shandong University, Shandong Province, PR China. The strain was aerobic, motile, Gram-stain-negative and rod-shaped. Cellular growth occurred at 13–37 °C, pH 5.0–10.0 and with 0–0.1 % (w/v) NaCl, and the optimal growth was at 25 °C and pH 7.5. SDU1-6T had the highest 16S rRNA gene similarity of 95.42 % with Chryseolinea serpens DSM 24574T. The genome was 6 542 746 bp in length with 43.5 mol% DNA G+C content. The major fatty acids of SDU1-6T were C16 : 1ω5 and iso-C15 : 0, the major menaquinone was menaquinone-7 (MK-7) and the major polar lipid was phosphatidylethanolamine. On the basis of the polyphasic evidence and the 16S rRNA gene sequence, SDU1-6T represents a novel species of the genus Chryseolinea , for which the name Chryseolinea flava sp. nov. is proposed. The type strain is SDU1-6T (=CGMCC 1.13492T=JCM 32520T).
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Reichenbachiella versicolor sp. nov., isolated from red alga
More LessA Gram-stain-negative, strictly aerobic, non-flagellated, rod-shaped bacterial strain, designated DC003T, was isolated from the alga Gracilariablodgettii of the phylum Rhodophyta collected from the coast of Lingshui county, Hainan, China. The strain grew optimally at 28 °C, pH 7.0–7.5 and in the presence of 2.0–3.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed strain DC003T to be within the genus Reichenbachiella , and most closely related to Reichenbachiella agariperforans JCM11238 (94.5 %), followed by Reichenbachiella faecimaris JCM 16588T (94.2 %). The major respiratory quinone was menaquinone 7 and the major fatty acids were iso-C15 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The polar lipids consisted of phosphatidylethanolamine, two unidentified aminophospholipids, three unidentified phospholipids and 10 unidentified lipids. The G+C content of the genomic DNA was 37.1 mol%. On the basis of the phenotypic, genotypic and phylogenetic analysis, strain DC003T is considered to represent a novel species of the genus Reichenbachiella , for which the name Reichenbachiella versicolor sp. nov. is proposed. The type strain is DC003T (=KCTC 42867T=MCCC 1H00130T).
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Marinifilum breve sp. nov., a marine bacterium isolated from the Yongle Blue Hole in the South China Sea and emended description of the genus Marinifilum
A Gram-stain-negative, facultative anaerobic, non-motile, short-clavate and non-flagellated marine bacterium strain, designated JC075T, was isolated from the Yongle Blue Hole in the South China Sea. Based on the 16S rRNA gene sequence, strain JC075T was found to be closely related to Marinifilum albidiflavum FB208T (97.10 %), Marinifilum flexuosum DSM 21950T (96.43 %) and Marinifilum fragile JCM 15579T (95.58 %), with less than 90.24 % sequence similarity to other genera of the family Marinifilaceae . The growth temperature was in the range of 10–37 °C, and the optimum temperature was 16 °C. Optimal growth occurred at pH 7.0 and in the presence of 3 % (w/v) NaCl. The isoprenoid quinone of strain JC075T was identified as menaquinone-7 and the predominant fatty acids (>10 %) were iso-C15 : 0 (47.9 %), summed feature 9 (C17 : 1 or/and iso-C17 : 1 ω9c; 18.7 %) and iso-C17 : 0 3-OH (14.9 %). The major polar lipids were one phosphatidylethanolamine, one phospholipid, one aminophospholipid, one glycolipid, one aminolipid and two unidentified lipids. The DNA G+C content of strain JC075T was 35.8 mol%. On the basis of polyphasic analysis, strain JC075T was considered to represent a novel species of the genus Marinifilum, for which the name Marinifilum breve sp. nov. is proposed. The type strain is JC075T (=KCTC 15646T=MCCC 1K03477T=JCM 32401T).
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Hanstruepera crassostreae sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from an oyster
More LessA Gram-stain-negative, rod-shaped, non-motile, aerobic and orange-pigmented marine bacterium, designated strain L53T, was isolated from an oyster sample collected from the coast of Weihai, China (122.0° E 37.5° N). Growth of strain L53T occurred at 4–40 °C (optimum, 33 °C), at pH 6.5–8.0 (optimum, pH 7.5) and with 1.0–7.0 % (w/v) NaCl (optimum, 3.0 %). Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain L53T was closely related to Bizionia echini KCTC 22015T (96.9 %) and Hanstruepera neustonica JCM 19743T (96.1 %). Strain L53T was located in a distinct phyletic lineage in a discrete clade associated with H. neustonica JCM 19743T. The DNA G+C content of strain L53T was 33.5 mol%. The sole menaquinone was MK-6. The polar lipids comprised one phosphatidylethanolamine, four unidentified aminolipids and four unidentified lipids. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 0 G. Based on morphological, physiological and molecular properties as well as on phylogenetic distinctiveness, strain L53T should be placed in the genus Hanstruepera as representing a novel species, for which the name Hanstruepera crassostreae sp. nov. is proposed. The type strain is L53T (=KCTC 62247T=MCCC 1H00246T).
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- Firmicutes and Related Organisms
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Staphylococcus cornubiensis sp. nov., a member of the Staphylococcus intermedius Group (SIG)
We here describe a novel species in the Staphylococcus intermedius Group (SIG) which is phenotypically similar to Staphylococcus pseudintermedius but is genomically distinct from it and other SIG members, with an average nucleotide identity of 90.2 % with its closest relative S. intermedius . The description of Staphylococcus cornubiensis sp. nov. is based on strain NW1T (=NCTC 13950T=DSM 105366T) isolated from a human skin infection in Cornwall, UK. Although pathogenic, NW1T carries no known virulence genes or mobilizable antibiotic resistance genes and further studies are required to assess the prevalence of this species in humans as well as its potential presence in companion animals.
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Megasphaera stantonii sp. nov., a butyrate-producing bacterium isolated from the cecum of a healthy chicken
More LessA novel mesophilic, anaerobic, Gram-stain-negative bacterium was isolated from the cecum of a healthy white leghorn chicken, and designated AJH120T. Cells were coccoid or diplococcoid with an average size of 0.8–1.8 µm and were non-motile with no evidence of spores. Phylogenetic analysis of 16S rRNA gene sequences revealed this organism to be a member of the genus Megasphaera , with the closest relatives being Megasphaera elsdenii (95 % sequence identity) and Megasphaera cerevisiae (95 % sequence identity). Growth was observed between 30 and 50 °C and between pH 5.0 and 9.0. AJH120T utilized a variety of carbon sources, including succinate, gluconate, fructose, ribose and pyruvate, as well as many individual amino acids. The DNA G+C content for the genome sequence of AJH120T was 52.1 mol%. Digital DNA–DNA hybridization (dDDH), average nucleotide identity (ANI) and average amino acid identity (AAI) between AJH120T and close taxonomic relatives, indicated divergence consistent with the strain representing a novel species. The major fatty acid methyl esters of the organism were C12 : 0, C14 : 0 3-OH, C18 : 1ω9c, C16 : 0 and C16 : 1ω9c. AJH120T was able to produce several short chain fatty acids, including butyrate, acetate, propionate and isovalerate. Together, these data indicate that AJH120T represents a novel species within the genus Megasphaera . We propose the name Megasphaera stantonii sp. nov. for the species. The type strain of this species is AJH120T (=DSM 106750T=CCUG 71842T).
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Geobacillus yumthangensis sp. nov., a thermophilic bacterium isolated from a north-east Indian hot spring
A thermophilic, spore-forming, rod-shaped bacterium isolated from the Yumthang hot spring in North Sikkim, India was subjected to taxonomic studies. The thermophilic bacterial isolate was designated as strain AYN2T. Cells were Gram-stain-positive, aerobic, motile, rod-shaped, catalase-positive and methyl red-negative. Strain AYN2T was able to grow in the pH range from 6 to 10 (optimum, pH 7.5–8.0), at 40–70 °C (60 °C) and in NaCl concentrations of 0–4 % (1 %). The major cellular fatty acids were iso-C15 : 0 (12.8 %), iso-C16 : 0 (13.9 %) and iso-C17 : 0 (13.8 %). No matches were found in the rtsba6 Sherlock libraries. The G+C content of the genomic DNA was 42.11 mol%. Based on phylogenetic analysis of the 16S rRNA gene sequences, strain AYNT showed highest sequence similarity to the type strain of Geobacillus toebii (96 %). However, the phenotypic properties of strain AYN2T were clearly distinct from those of G. toebii and related species. On the basis of polyphasic analysis, strain AYN2T represents a novel species in the genus Geobacillus , for which the name Geobacillus yumthangensis sp. nov. is proposed. The type strain is AYN2T(MTCC=12749=KCTC=33950= JCM 32596).
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Bacillus shivajii sp. nov., isolated from a water sample of Sambhar salt lake, India
A novel Gram-stain-positive, rod-shaped, motile, spore-forming, strictly aerobic, alkali- and halo- tolerant bacterium, designated strain AK72T, was isolated from a water sample collected from Sambhar salt lake, Rajasthan, India. The colony appears circular, shiny, smooth, translucent or slightly pale in colour and convex with an entire margin after 48 h incubation at 37 °C with pH 9. Growth of the bacterium occurred at 10–42 °C (optimum, 25–37 °C), at salinities of 0.5–10 % (w/v) NaCl (optimum 3–5 % NaCl) and pH of 6–10 (optimum pH 9). Strain AK72T was positive for oxidase, catalase, nitrate reductase, phenylalanine deaminase, ornithine decarboxylase, aesculinase, lipase and urease activities. The predominant fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0 and the cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The major polar lipids of the strain were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminophospholipid, three unidentified phospholipids and three unidentified lipids. The genomic DNA G+C content of the strain AK72T was 36.8 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain AK72T was closely related to Bacillus cellulosilyticus (96.5 %) and Bacillus vedderi (96.3 %), but the novel strain AK72T formed a separate clade with Bacillus aurantiacus whereas B. cellulosilyticus and B. vedderi were clustered in a separate clade. The above data in combination with the phenotypic characteristics and phylogenetic data inferred that strain AK72T represents a novel species of the genus Bacillus , for which the name Bacillus shivajii sp. nov. is proposed. The type strain is AK72T (=MTCC 12636T=KCTC 33981T=JCM 32183T).
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Romboutsia hominis sp. nov., the first human gut-derived representative of the genus Romboutsia, isolated from ileostoma effluent
A Gram-stain-positive, motile, rod-shaped, obligately anaerobic bacterium, designated FRIFIT, was isolated from human ileostoma effluent and characterized. On the basis of 16S rRNA gene sequence similarity, strain FRIFIT was most closely related to the species Romboutsia ilealis CRIBT (97.7 %), Romboutsia lituseburensis DSM 797T (97.6 %) and Romboutsia sedimentorum LAM201T (96.6 %). The level of DNA–DNA relatedness between strain FRIFIT and R. ilealis CRIBT was 13.9±3.3 % based on DNA–DNA hybridization. Whole genome sequence-based average nucleotide identity between strain FRIFIT and closely related Romboutsia strains ranged from 78.4–79.1 %. The genomic DNA G+C content of strain FRIFIT was 27.8 mol%. The major cellular fatty acids of strain FRIFIT were saturated and unsaturated straight-chain C12–C19 fatty acids as well as cyclopropane fatty acids, with C16 : 0 being the predominant fatty acid. The polar lipid profile comprised five phospholipids and six glycolipids. These results, together with differences in phenotypic features, support the proposal that strain FRIFIT represents a novel species within the genus Romboutsia , for which the name Romboutsia hominis sp. nov. is proposed. The type strain is FRIFIT (=DSM 28814T=KCTC 15553T).
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Planococcus halotolerans sp. nov., isolated from a saline soil sample in China
A novel Gram-stain-positive, coccoid or short rod-shaped, moderate-orange-pigmented, halotolerant and psychrotolerant bacterium, designated strain SCU63T, was isolated from a saline soil sample in China, and characterized by a polyphasic taxonomic approach. 16S rRNA gene sequence similarity of strain SCU63T to species in the genera Planococcus and Planomicrobium ranged from 96.5 to 98.6 %. Phylogenetic trees as well as diagnostic signature nucleotides in the 16S rRNA gene sequence supported the view that this strain should be assigned to the genus Planococcus . Further, average nucleotide identity and digital DNA–DNA hybridization analyses confirmed the separate species status of strain SCU63T relative to the closely related taxa. The isolate grew at 0–40 °C (optimum, 30–35 °C), at pH 6.5–9.0 (pH 7.0–7.5) and in the presence of 0–15 % (w/v) NaCl (3 %). The principal fatty acids were anteiso-C15 : 0, C16 : 1ω7c alcohol, iso-C16 : 0 and iso-C14 : 0, and the dominant isoprenoid quinones were MK-8 and MK-7. The peptidoglycan type was determined to be A4α (l-Lys–d-Glu), and the polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminophospholipid and one unidentified lipid. The DNA G+C content was 44.6 mol%. Based on the genotypic, phenotypic and chemotaxonomic data, strain SCU63T can be classified as a novel species in the genus Planococcus , for which the name Planococcus halotolerans sp. nov. is proposed. The type strain is SCU63T (=CGMCC 1.13628T=KCTC 43001T).
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Salibacterium nitratireducens sp. nov., a haloalkalitolerant bacterium isolated from a water sample from Sambhar salt lake, India.
A strictly aerobic, haloalkali-tolerant, Gram-stain-positive, non-motile, rod-shaped bacterium, designated strain SMB4T, was isolated from a water sample collected from Sambhar salt lake, Rajasthan, India. Growth occurred at 25–50 °C, 4–12 % (w/v) NaCl and pH of 5–9. Strain SMB4T was positive for β-galactosidase, oxidase, catalase and urease activities. The fatty acids were dominated by branched forms of fatty acids with iso- and anteiso-saturated fatty acids, with a high abundance of anteiso-C15 : 0, anteiso-C17 : 0 and C18 : 0. The cell-wall peptidoglycan of strain SMB4T contained meso-diaminopimelic acid, while the polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid and three unidentified lipids. The DNA G+C content of strain SMB4T was 49.1 mol%. A blast sequence similarity search based on 16S rRNA gene sequence indicated that Salibacterium halochares , Salibacterium halotolerans and Salibacterium qingdaonense were the nearest phylogenetic neighbours, with a pair-wise sequence similarities of 98.4, 98.2 and 97.0 % respectively. Phylogenetic analysis showed that strain SMB4T was clustered with S. halochares and together clustered with S. halotolerans and S. qingdaonense. DNA–DNA hybridization of strain SMB4T with S. halochares DSM 21373T, S. halotolerans S7T and S. quigdaonense DSM 21621T showed a relatedness values of only 39.8, 26.3 and 42.8 %, respectively. Based on its phenotypic characteristics and on phylogenetic inference, strain SMB4T represents a novel species of the genus Salibacterium , for which the name Salibacterium nitratireducens sp. nov. is proposed. The type strain is SMB4T (=MTCC 12633T=KCTC 33876T=JCM 32187T).
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Lactobacillus paragasseri sp. nov., a sister taxon of Lactobacillus gasseri, based on whole-genome sequence analyses
Three strains, JCM 5343T, JCM 5344 and JCM 1130, currently identified as Lactobacillus gasseri , were investigated using a polyphasic taxonomic approach. Although these strains shared high 16S rRNA gene sequence similarities with L. gasseri ATCC 33323T (99.9 %), they formed a clade clearly distinct from ATCC 33323T based on whole-genome relatedness. The average nucleotide identity and in silico DNA–DNA hybridization values of these three strains compared to L. gasseri ATCC 33323T were 93.4–93.7 and 53.1–54.1 %, respectively, and both were less than the widely accepted threshold to distinguish two species (95 and 70 %, respectively). The three strains were Gram-stain positive, non-motile, non-spore-forming, catalase-negative and rod-shaped bacteria. They grew at 25–45 °C and in the presence of 2.0 % (w/v) NaCl. The major fatty acids of the three strains were C16 : 0 and C18 : 1 ω9c. Based on phylogenetic analyses of the phenylalanyl-tRNA synthase alpha subunit and RNA polymerase alpha subunit genes, and on phenotypic and chemotaxonomic characteristics, strains JCM 5343T, JCM 5344 and JCM 1130 represent a novel species distinct from L. gasseri , for which we propose the name Lactobacillus paragasseri sp. nov. In addition, a large portion of genomes currently labelled as L. gasseri in the public sequence database should be reclassified as L. paragasseri based on whole-genome relatedness.
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Eubacterium maltosivorans sp. nov., a novel human intestinal acetogenic and butyrogenic bacterium with a versatile metabolism
More LessA novel anaerobic, non-spore-forming bacterium was isolated from a faecal sample of a healthy adult. The isolate, designated strain YIT, was cultured in a basal liquid medium under a gas phase of H2/CO2 supplemented with yeast extract (0.1 g l−1). Cells of strain YIT were short rods (0.4–0.7×2.0–2.5 µm), appearing singly or in pairs, and stained Gram-positive. Catalase activity and gelatin hydrolysis were positive while oxidase activity, indole formation, urease activity and aesculin hydrolysis were negative. Growth was observed within a temperature range of 20–45 °C (optimum, 35–37 °C), and a pH range of 5.0–8.0 (optimum pH 7.0–7.5). Doubling time was 2.3 h when grown with glucose at pH 7.2 and 37 °C. Besides acetogenic growth, the isolate was able to ferment a large range of monomeric sugars with acetate and butyrate as the main end products. Strain YIT did not show respiratory growth with sulfate, sulfite, thiosulfate or nitrate as electron acceptors. The major cellular fatty acids of the isolate were C16 : 0 and C18 : 0. The genomic DNA G+C content was 47.8 mol%. Strain YIT is affiliated to the genus Eubacterium , sharing highest levels of 16S rRNA gene similarity with Eubacterium limosum ATCC 8486T (97.3 %), Eubacterium callanderi DSM 3662T (97.5 %), Eubacterium aggregans DSM 12183T (94.4 %) and Eubacterium barkeri DSM 1223T (94.8 %). Considering its physiological and phylogenetic characteristics, strain YIT represents a novel species within the genus Eubacterium , for which the name Eubacterium maltosivorans sp. nov. is proposed. The type strain is YIT (=DSM 105863T=JCM 32297T).
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Paenibacillus montanisoli sp. nov., isolated from mountain area soil
More LessA Gram-stain-negative, aerobic, motile, endospore-forming and rod-shaped bacterium, designated RA17T, was isolated from Dafan, Hubei Province, China. Based on 16S rRNA gene sequence similarity comparisons, strain RA17T was most closely related to Paenibacillus taihuensis THMBG22T (97.4 %), Paenibacillus rhizoryzae ACCC 1ZS3-5T (97.4 %) and Paenibacillus sacheonensis DSM SY01T (96.5 %). Analysis of the rpoB gene also indicated that RA17T had the highest similarity to P. rhizoryzae ACCC 1ZS3-5T (92.3 %), P. taihuensis THMBG22T (88.4 %) and P. sacheonensis DSM SY01T (85.5 %). The DNA–DNA hybridization values between strain RA17T and the two type strains, P. taihuensis THMBG22T and P. rhizoryzae ACCC 1ZS3-5T, were 36.8 and 22.9 %, respectively. Its genome size was 6.17 Mb, comprising 5677 predicted genes with a DNA G+C content of 52.82 mol %. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphoglycolipid, four aminophospholipids, an unidentified phospholipid and an unidentified polar lipid. The major quinone was menaquinone 7. The diagnostic diamino acid of the cell wall was meso-diaminopimelic acid. The low DNA–DNA hybridization values, physiological and biochemical differences, such as growth at 4 °C, acid production from inositol, lack of α-chymotrypsin activity, no casein hydrolysis, and negative for acid production from d-fructose, melibiose and sucrose, could distinguish strain RA17T from its closely related species. Consequently, strain RA17T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus montanisoli sp. nov. is proposed, with RA17T (=KCTC 33894T=CCTCC AB 2017053T) as the type strain.
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Paenibacillus paeoniae sp. nov., a novel endophytic bacterium isolated from leaf of Paeonia lactiflora Pall.
Xiao-Rui Yan and Li TuoA Gram-stain-positive, aerobic, rod-shaped, endospore-forming bacterium, designated strain M4BSY-1T, was originally isolated from a surface-sterilized leaf of Paeonia lactiflora Pall. in Guizhou, China. The bacterium was characterized by a polyphasic approach to determine its taxonomic position. 16S rRNA gene sequence comparison revealed that strain M4BSY-1T belongs to the genus Paenibacillus and most closely to Paenibacillus pinioli NB5T (98.31 % similarity). Neither substrate nor aerial mycelia formed, and no diffusible pigments were observed on the media tested. Strain M4BSY-1T grew in the pH range 7.0–13.0 (optimum, 7.0–8.0), at temperatures between 10–37 °C (optimum, 30 °C) and at 0–5 % (w/v) NaCl (optimum, 1–2 %). The predominant menaquinone was MK-7. The major fatty acids were anteiso-C15 : 0, C16 : 0 and iso-C16 : 0. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified unknown aminophospholipids and three unidentified phospholipids. The DNA G+C content was 48.8 mol%. According to the phylogenetic, phenotypic and chemotaxonomic evidence, strain M4BSY-1T was clearly distinguishable from other species with validly published names in the genus Paenibacillus and should therefore be classified as a novel species, and we suggest the name Paenibacillus paeoniae sp. nov. The type strain is M4BSY-1T (=KCTC 33997T=CGMCC 1.13667T).
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- Proteobacteria
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Abyssibacter profundi gen. nov., sp. nov., a marine bacterium isolated from seawater of the Mariana Trench
A Gram-stain-negative, strictly aerobic, short-rod-shaped bacterium, motile by a single polar flagellum, designated OUC007T, was isolated from seawater at a depth of 1000 m in the Mariana Trench. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain OUC007T formed a lineage within the family Salinisphaeraceae that was distinct from the most closely related genera Oceanococcus and Salinisphaera , with 16S rRNA gene sequences similarities ranging from 89.3 to 90.8 %, respectively. Strain OUC007T grew with 0–7 % (w/v) NaCl (optimum, 2–3 %), at 10–45 °C (37 °C) and at pH 7.0–9.0 (7.0–8.0). The major respiratory quinone was ubiquinone-8 (Q-8). The polar lipids of strain OUC007T comprised one phosphatidylethanolamine and three unidentified polar lipids. The predominant fatty acid (more than 10 % of total fatty acids) was summed feature 8 (C18 : 1ω7c or/and C18 : 1ω6c). The DNA G+C content of strain OUC007T was 63.1 mol%. On the basis of polyphasic taxonomic analysis, the strain OUC007T is considered to represent a novel species in a new genus of the family Salinisphaeraceae , for which the name Abyssibacter profundi gen. nov., sp. nov. is proposed. The type strain is OUC007T (=KCTC 52933T=MCCC 1K03450T).
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Ottowia konkukae sp. nov., isolated from rotten biji (tofu residue)
More LessA Gram-negative, aerobic, non-motile, non-spore-forming and rod-shaped bacterial strain, designated SK3863T, was isolated from rotten biji (residue remaining after making tofu). This bacterium was characterized in order to determine its taxonomic position by using the polyphasic approach. Strain SK3863T grew well at 25–37 °C on Reasoner’s 2A agar plates. On the basis of 16S rRNA gene sequence similarity, strain SK3863T belonged to the family Comamonadaceae and was related to Ottowia beijingensis GCS-AN-3T (96.5 % sequence similarity) and Ottowia pentelensis RB3-7T (96.4 %). Lower sequence similarities (96.2 %) were found to all of the other recognized members of the genus Ottowia . The G+C content of the genomic DNA was 65.8 mol%. The major respiratory lipoquinone was ubiquinone 8 and the major fatty acids were C16 : 1 ω6c/C16 : 1ω7c, C16 : 0 and C18 : 1 ω7c/C18 : 1ω6c. Strain SK3863T could be differentiated genotypically and phenotypically from the recognized species of the genus Ottowia . The isolate therefore represents a novel species, for which the name Ottowia konkukae sp. nov. is proposed, with the type strain SK3863T (=KCCM 43236T=DSM 105395T).
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Pelagivirga sediminicola gen. nov., sp. nov. isolated from the Bohai Sea
A Gram-stain-negative bacterium, strain BH-SD19T, that was isolated from a marine sediment sample collected from the Bohai Sea, was subjected to a polyphasic taxonomic study. Cells of BH-SD19T are non-flagellated, non-gliding, oval-shaped rods, 0.5–1.0 µm wide and 1.0–2.0 µm long. BH-SD19T is strictly aerobic, and oxidase- and catalase-positive. Growth occurs at 15–40 °C (optimum 35 °C), at pH 6.0–8.5 (optimum 7.0–7.5) and with 1–10 % (w/v) NaCl (optimum 2 %). The predominant fatty acids are C19 : 0cyclo ω8c (46.5 %), C16 : 0 (20.3 %) and C18 : 1ω7c and/or C18 : 1ω6c (10.6 %). The major respiratory quinone is Q-10. The major polar lipids are phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. The DNA G+C content is 64.0 mol%. BH-SD19T shows the highest 16S rRNA sequence similarity to Pontibaca methylaminivorans (95.2 %) and strains of species of the genus Roseovarius (93.4–95.2 %). Sequence similarity values between BH-SD19T and other phylogenetically related species are all below 95.0 %. Phylogenetic trees based on 16S rRNA gene sequences indicate that BH-SD19T forms a distinct lineage and does not join any known genera in the trees. Phenotypic, chemotaxonomic and phylogenetic data indicate that BH-SD19T represents a novel genus and species in the family Rhodobacteraceae , for which the name Pelagivirga sediminicola gen. nov., sp. nov. is proposed. The type strain is BH-SD19T (=CCTCC AB 2017074T=KCTC 62202T).
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Marinobacter bohaiensis sp. nov., a moderate halophile isolated from benthic sediment of the Bohai Sea
More LessA Gram-stain-negative, motile, aerobic and rod-shaped bacterial strain, designated T17T, was isolated from benthic sediment sampled at Jiaozhou Bay, Bohai Sea, China, and its taxonomic position was investigated. The 16S rRNA gene sequence of strain T17T exhibited the highest similarity values to those of the type strain Marinobacter lacisalsi FP2.5 (96.2 %) and Marinobacter koreensis DD-M3T (96.2 %). Strain T17T grew optimally at 35 °C, pH 7.0–8.0 and in the presence of 6.0–10.0 % (w/v) NaCl. The predominant ubiquinone in strain T17T was identified as Q-9. The major fatty acids of strain T17T were C12 : 0, C16 : 0 and C16 : 0 10-CH3. The major polar lipids of strain T17T were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidglycerol, an unidentified aminolipid and an unidentified phospholipid. The DNA G+C content of strain T17T was 63.0 mol%. The draft genome sequence of strain T17T includes 4 755 891 bp in total (N50=2 856 325 bp) with a medium read coverage of 100.0x and 11 scaffolds. In silico DNA–DNA hybridization with the three type strains showed 20.3, 19.7 and 19.9 % relatedness to Marinobacter santoriniensis NKSG1T, Marinobacter segnicrescens SS11B1-4T and Marinobacter daqiaonensis CGMCC 1.9167T, respectively. On the basis of the phenotypic, phylogenetic, genomic and chemotaxonomic properties, strain T17T is considered to represent a novel species within the genus Marinobacter , for which the name Marinobacter bohaiensis sp. nov. is proposed. The type strain is T17T (=KCTC 52710T=MCCC 1K03282T).
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Pectobacterium punjabense sp. nov., isolated from blackleg symptoms of potato plants in Pakistan
Pectobacterium isolates SS95T, SS54 and SS56 were collected from a potato field in the Chiniot district in the plains of the Punjab province, Pakistan. Sequencing of the gapA barcode revealed that these strains belong to a novel phylogenetic group separated from P.ectobacterium wasabiae and Pectobacterium parmentieri species. Furthermore, multilocus sequence analyses of 13 housekeeping genes (fusA, rpoD, acnA, purA, gyrB, recA, mdh, mtlD, groEL, secY, glyA, gapA and rplB) clearly distinguished the type strain, SS95T, from its closest relatives, i.e. P. parmentieri RNS 08-42-1AT and P. wasabiae CFBP3304T, as well as from all the other known Pectobacterium species. In silico DNA–DNA hybridization (<44.1 %) and average nucleotide identity (<90.75 %) values of strain SS95T compared with other Pectobacterium type strains supported the delineation of a new species. Genomic and phenotypic comparisons permitted the identification of additional traits that distinguished the Pakistani isolates from all other known Pectobacterium type strains. The name Pectobacterium punjabense sp. nov. is proposed for this taxon with the type strain SS95T (=CFBP 8604T=LMG 30622T).
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Pseudoruegeria insulae sp. nov., isolated from a tidal flat
More LessA Gram-stain-negative, aerobic, non-motile and ovoid or rod-shaped bacterial strain, designated BPTF-M20T, was isolated from tidal flat sediment in the Yellow Sea, Republic of Korea. Strain BPTF-M20T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0–3.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain BPTF-M20T fell within the clade comprising the type strains of Pseudoruegeria species. Strain BPTF-M20T exhibited 16S rRNA gene sequence similarity values of 97.4–98.3 % to the type strains of Pseudoruegeria haliotis , Pseudoruegeria lutimaris , ‘ Pseudoruegeria litorisediminis’ and Pseudoruegeria sabulilitoris and 96.4–96.9 % to the type strains of the other Pseudoruegeria species. Strain BPTF-M20T contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c as the major fatty acid. The major polar lipids detected in strain BPTF-M20T were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminolipid and one unidentified glycolipid. The DNA G+C content of strain BPTF-M20T was 63.2 mol%. Mean DNA–DNA relatedness values of strain BPTF-M20T with the type strains of P. haliotis , P. lutimaris , P. sabulilitoris and ‘P. litorisediminis’ were 18–27 %. Differential phenotypic properties, together with the phylogenetic and genetic data, revealed that strain BPTF-M20T was separated from recognized Pseudoruegeria species. On the basis of the data presented here, strain BPTF-M20T is considered to represent a novel species of the genus Pseudoruegeria , for which the name Pseudoruegeria insulae sp. nov. is proposed. The type strain is BPTF-M20T (=KACC 19614T=KCTC 62422T=NBRC 113188T).
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A polyphasic approach leads to seven new species of the cellulose-decomposing genus Sorangium, Sorangium ambruticinum sp. nov., Sorangium arenae sp. nov., Sorangium bulgaricum sp. nov., Sorangium dawidii sp. nov., Sorangium kenyense sp. nov., Sorangium orientale sp. nov. and Sorangium reichenbachii sp. nov.
Seventy-three strains of Sorangium have been isolated from soil samples collected from all over the world. The strains were characterized using a polyphasic approach and phenotypic, genotypic and chemotype analyses clarified their taxonomic relationships. 16S rRNA, xynB1, groEL1, matrix-assisted laser desorption/ioniziation time-of-flight mass spectrometry and API-ZYM analyses were conducted. In addition, from selected representative strains, fatty acids, quinones and phospholipids were analysed. In silico DNA–DNA hybridization and DNA–DNA hybridization against the current type species of Sorangium cellulosum strain Soce 1871T (DSM 14627T) completed the analyses. Finally, our study revealed seven new species of Sorangium : Sorangium ambruticinum (Soce 176T; DSM 53252T, NCCB 100639T, sequence accession number ERS2488998), Sorangium arenae (Soce 1078T; DSM 105768T, NCCB 100643T, ERS2489002), Sorangium bulgaricum (Soce 321T; DSM 53339T, NCCB 100640T, ERS2488999), Sorangium dawidii (Soce 362T; DSM 105767T, NCCB 100641T, ERS2489000), Sorangium kenyense (Soce 375T; DSM 105741T, NCCB 100642T, ERS2489001), Sorangium orientale (Soce GT47T; DSM 105742T, NCCB 100638T, ERS2501484) and Sorangium reichenbachii (Soce 1828T; DSM 105769T, NCCB 100644T, ERS2489003).
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Ignatzschineria cameli sp. nov., isolated from necrotic foot tissue of dromedaries (Camelus dromedarius) and associated maggots (Wohlfahrtia species) in Dubai
Five bacterial strains, UAE-HKU57T, UAE-HKU58, UAE-HKU59, UAE-HKU60 and UAE-HKU61, were isolated in Dubai, UAE, from necrotic foot tissue samples of four dromedaries (Camelus dromedarius) and associated maggots (Wohrlfartia species). They were non-sporulating, Gram-negative, non-motile bacilli. They grew well under aerobic conditions at 37 °C, but not anaerobically. The pH range for growth was pH 7.0–9.0 (optimum, pH 7.5–8.0) and the strains could tolerate NaCl concentrations (w/v) up to 2 % (optimum, 0.5 %). They were catalase- and cytochrome oxidase-positive, but caseinase-, gelatinase- and urease-negative. Their phenotypic characters were distinguishable from other closely related species. Phylogenetic analyses of the almost-complete 16S rRNA gene and partial 23S rRNA gene, gyrB, groEL and recA sequences revealed that the five isolates were most closely related to undescribed Ignatzschineria strain F8392 and Ignatzschineria indica, but in most phylogenies clustered separately from these close relatives. Average nucleotide identity analysis showed that genomes of the five isolates (2.47–2.52 Mb, G+C content 41.71–41.86 mol%) were 98.00–99.97% similar to each other, but ≤87.18 % similar to other Ignatzschineria species/strains. Low DNA relatedness between the five isolates to other Ignatzschineria species/strains was also supported by Genome-to-Genome Distance Calculator analysis. The chemotaxonomic traits of the five strains were highly similar. They were non-susceptible (intermediate or resistant) to tetracycline and resistant to trimethoprim/sulphamethoxazole. The name Ignatzschineria cameli sp. nov. is proposed to accommodate these five strains, with strain UAE-HKU57T (=CCOS1165T=NBRC 113042T) as the type strain.
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Mesorhizobium ephedrae sp. nov. isolated from the roots of Ephedra przewalskii in Kumtag desert
More LessStrain 6GN-30T, a Gram-stain-negative, aerobic, non-spore-forming, rod-shaped, motile bacterium was isolated from Ephedra sinica roots in the Kumtag Desert. On the basis of the 16S rRNA gene sequence, the isolate represented a member of the genus Mesorhizobium of the family Phyllobacteriaceae . The results of a phylogenetic analysis indicated that 6GN-30T was phylogenetically related to Mesorhizobium soli NHI-8T. Strain 6GN-30T grew at a salinity of 0–1.0 % (w/v) NaCl (with optimum growth in the absence of NaCl), pH 6.0–9.0 (optimum 7.0–8.0) and 15–45 °C. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c), C19 : 0cyclo ω8c, iso-C17 : 0, C18 : 0, and C16 : 0. The draft genome of 6GN-30T was 6.11 Mb long, with a DNA G+C content of 66.4 mol%. The average nucleotide identity to M. soli NHI-8T was 84.32 %. The strain contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine,aminophospholipids and phospholipids. The chemotaxonomic, phylogenetic and phenotypic data indicate that 6GN-30T represents a novel species of the genus Mesorhizobium for which the name Mesorhizobium ephedrae sp. nov. is proposed. The type strain is 6GN-30T (=ACCC 60073T=KCTC 62410T).
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Methylobacterium currus sp. nov., isolated from a car air conditioning system
More LessA novel bacterial strain, designated PR1016AT, was isolated from a car air conditioning system. This rod-shaped strain showed catalase and oxidase activities, was aerobic and methylotrophic, and had a reddish pink colour. The genomic DNA G+C content of strain PR1016AT was 70.2 mol%, as determined by genome sequencing. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain PR1016AT was most closely related to Methylobacterium aquaticum GR16T (98.86 %), M. variabile GR3T (98.43 %), M. platani PMB 02T (98.36 %) and M. tarhaniae N4211T (98.14 %). The average nucleotide identity and digital DNA–DNA hybridization values between strain PR1016AT and M. aquaticum GR16T, M. platani PMB02T and M. variabile GR3T were 88.61, 88.14 and 87.88 %, and 36.4, 35.8 and 34.7 %, respectively. Numerous insertion sequences are present in the genome of strain PR1016AT, which has a larger genome than the four Methylobacterium species described above. Cells grew at 18–42 °C (optimum, 30 °C), at pH 4.0–9.0 (optimum, pH 7.0) and in the presence of 0–1.0 % (w/v) NaCl (optimum, 0 %). The major respiratory quinone was Q10. Fatty acid methyl ester analysis revealed that summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) was the predominant cellular fatty acid in strain PR1016AT. Two-dimensional TLC indicated that the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The genotypic and phenotypic characteristics indicate that strain PR1016AT represents a novel species of the genus Methylobacterium , for which the name Methylobacterium currus sp. nov. is proposed. The type strain is PR1016AT (=KACC 19662T=JCM 32670T).
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Herbaspirillum piri sp. nov., isolated from bark of a pear tree
More LessA Gram-stain-negative, aerobic, motile bacterial strain, shQ-4T, was isolated from a pear tree in Henan Province, China. The strain grew at 10–41 °C, at pH 4.0–8.0 and in the presence of 1–3 % (w/v) NaCl. It shared highest 16S rRNA gene sequence similarity (96.66 %) with Herbaspirillum chlorophenolicum CPW301T. The phylogenetic tree based on 16S rRNA gene sequences showed that strain shQ-4T formed a distinct branch next to reference species in the genus Herbaspirillum . The profile of major polar lipids of strain shQ-4T contained phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and an unidentified aminophospholipid (APL). The major respiratory quinone was Q-8. The major fatty acids of this strain were C16 : 0, summed feature 3 (C16 : 1ω6c/C16 : 1ω7c), C17 : 0 cyclo and C18 : 0. Strain shQ-4T is considered to represent a novel species of the genus Herbaspirillum , with the proposed name Herbaspirillum piri sp. nov. The type strain is shQ-4T (=CFCC 14641T=KCTC 52804T).
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- Eukaryotic Micro-Organisms
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Spencerozyma siamensis sp. nov., a novel anamorphic basidiomycetous yeast species in Puccinomycotina isolated from coral in Thailand
More LessStrain DMKU13-2T, representing a novel anamorphic yeast species in the class Microbotryomycetes, subphylum Puccinomycotina, phylum Basidiomycota, was isolated from a soft coral collected in the sea off Ko Mu island, Thailand. The phylogenetic analysis based on the concatenated sequences of the internal transcribed spacer (ITS) region and the D1/D2 region of the large subunit ribosomal RNA (LSU rRNA) gene indicated that this strain was a novel species in the genus Spencerozyma and distant from Spencerozyma crocea, the only species of the genus. The novel species differed from the type of S. crocea (CBS 2029T) by 5.2 % nucleotides (31 nucleotide substitutions out of 594 bp) in the D1/D2 region of the LSU rRNA gene and 9.0 % nucleotides (66 nucleotide substitutions out of 735 bp) in the ITS region. The name Spencerozyma siamensis sp. nov. is proposed. The type is DMKU13-2T (=CBS 14683=TBRC 7039). The MycoBank number is MB 824889.
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- Evolution, Phylogeny and Biodiversity
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Potato purple top disease associated with the novel subgroup 16SrII-X phytoplasma
More LessPotato (Solanum tuberosum) is a very economically important perennial tuberous crop in Saudi Arabia. Potato plants displaying symptoms associated with potato purple top disease, such as aerial tubers and purple and small leaves, were observed in Al-Bukairiyah, Fowlq and Buraydah, Al-Tarafiyah, Qassim governorate, Saudi Arabia. In this study, we examined samples taken from 12 symptomatic potato plants and confirmed the presence of phytoplasma DNA. Analysis of the 16S rRNA-encoding sequences revealed that the symptomatic plants were infected with phytoplasma belonging to the peanut witches’-broom group (16SrII). Sequencing of the 16S rRNA- encoding gene, computer-simulated RFLP analysis and phylogenetic analysis revealed the presence of a novel representative of the 16SrII-X subgroup. The present study identified potato plants as a novel host for novel phytoplasma strains belonging to the pigeon pea witches’-broom group in Saudi Arabia.
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A definition of the Mycobacterium avium complex for taxonomical and clinical purposes, a review
Nontuberculous mycobacteria, particularly the Mycobacterium avium complex (MAC) bacteria, are increasingly recognized as opportunistic pathogens of humans. As a result, studies on antibiotic treatment and taxonomy of the MAC are intensifying, but an updated definition of what constitutes the MAC, either for taxonomical studies or for clinical purposes, is lacking. On the basis of literature review and phylogenetic analyses, we propose to define the MAC as a grouping of slow-growing mycobacteria that show corresponding values in at least two of the following targets against either M. avium ATCC 25291T or Mycobacterium intracellulare ATCC 13950T: >99.4 % sequence identity for the full 16S rRNA gene, >98.7 % for the partial (5′) 16S rRNA gene, >97.3 % for hsp65 and >94.4 % for rpoB region V. A >97.5 % value in concatenated analyses of >2500 bp that includes 16S rRNA, hsp65 and rpoB gene sequence data or ≥85 % average nucleotide identity to M. avium ATCC 25291T or M. intracellulare ATCC 13950T on basis of whole genome sequencing data is recommended. This molecular definition is based on the distances observed between the classical members of the MAC, M. avium and M. intracellulare . Applying this definition, the complex currently consists of 12 validly published species: Mycobacterium avium, Mycobacterium intracellulare, Mycobacterium chimaera, Mycobacterium colombiense, Mycobacterium arosiense, Mycobacterium vulneris, Mycobacterium bouchedurhonense, Mycobacterium timonense, Mycobacterium marseillense, Mycobacterium yongonense, Mycobacterium paraintracellulare and Mycobacterium lepraemurium.
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- ICSP Matters
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Volumes and issues
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Volume 74 (2024)
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Volume 72 (2022 - 2023)
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Volume 71 (2020 - 2021)
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Volume 69 (2019)
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Volume 68 (2018)
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Volume 67 (2017)
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Volume 66 (2016)
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Volume 16 (1966)
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Volume 5 (1955)
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Volume 4 (1954)
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Volume 3 (1953)
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Volume 2 (1952)
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Volume 1 (1951)