Ilumatobacter nonamiense sp. nov. and Ilumatobacter coccineum sp. nov., isolated from seashore sand

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3404-3408 ◽  
Author(s):  
Atsuko Matsumoto ◽  
Hiroaki Kasai ◽  
Yoshihide Matsuo ◽  
Yoshikazu Shizuri ◽  
Natsuko Ichikawa ◽  
...  

Bacterial strains YM16-303T and YM16-304T were isolated from a sample of seashore sand using a medium with an artificial seawater base. Both isolates grew slowly on marine agar, and were found to be Gram-reaction-positive, aerobic, non-motile and rod-shaped. The cell-wall peptidoglycan contained ll-diaminopimelic acid, glycine, alanine and hydroxyglutamic acid, and the acyl type of the muramic acid was glycolyl. The predominant menaquinone was MK-9(H8). The 16S rRNA gene sequences of strains YM16-303T and YM16-304T were most similar to that of Ilumatobacter fluminis YM22-133T, and phylogenetic analyses also indicated that they belong to the genus Ilumatobacter . Ilumatobacter fluminis YM22-133T and strains YM16-303T and YM16-304T should be classified as distinct species in the genus Ilumatobacter , however, since the 16S rRNA gene sequence similarity between them was low and the major cellular fatty acids and some physiological properties were different. Moreover, average nucleotide identity and maximal unique exact matches index values also supported the conclusion that they represent different species. On the basis of the above analyses, two novel species, Ilumatobacter nonamiense sp. nov. (type strain YM16-303T = NBRC 109120T = KCTC 29139T) and Ilumatobacter coccineum sp. nov. (type strain YM16-304T = NBRC 103263T = KCTC 29153T), are proposed. The order Acidimicrobiales , which contains the genus Ilumatobacter , currently includes six genera and only six species, and they are phylogenetically very far from each other. Phylogenetic analyses revealed that strains YM16-303T and YM16-304T clustered with closely related uncultured actinobacteria but not Ilumatobacter fluminis YM22-133T, suggesting that many uncultured bacteria related to these isolates exist in the environment. This is the first report on interspecies relationships in the order Acidimicrobiales .

Author(s):  
Hisami Kobayashi ◽  
Yasuhiro Tanizawa ◽  
Mitsuo Sakamoto ◽  
Moriya Ohkuma ◽  
Masanori Tohno

The taxonomic status of the species Clostridium methoxybenzovorans was assessed. The 16S rRNA gene sequence, whole-genome sequence and phenotypic characterizations suggested that the type strain deposited in the American Type Culture Collection ( C. methoxybenzovorans ATCC 700855T) is a member of the species Eubacterium callanderi . Hence, C. methoxybenzovorans ATCC 700855T cannot be used as a reference for taxonomic study. The type strain deposited in the German Collection of Microorganism and Cell Cultures GmbH (DSM 12182T) is no longer listed in its online catalogue. Also, both the 16S rRNA gene and the whole-genome sequences of the original strain SR3T showed high sequence identity with those of Lacrimispora indolis (recently reclassified from Clostridium indolis ) as the most closely related species. Analysis of the two genomes showed average nucleotide identity based on blast and digital DNA–DNA hybridization values of 98.3 and 87.9 %, respectively. Based on these results, C. methoxybenzovorans SR3T was considered to be a member of L. indolis .


2012 ◽  
Vol 62 (Pt_10) ◽  
pp. 2363-2370 ◽  
Author(s):  
Hyangmi Kim ◽  
Doo-Sang Park ◽  
Hyun-Woo Oh ◽  
Kang Hyun Lee ◽  
Dong-Ho Chung ◽  
...  

Strains RU-16T, RU-28, RU-04T and PU-02T were isolated from the gut of the African mole cricket, Gryllotalpa africana. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the strains belonged to the family Microbacteriaceae . All four strains were most closely related to Curtobacterium ginsengisoli DCY26T (below 97 % 16S rRNA gene sequence similarity). These isolates were Gram-stain-positive, motile (by gliding), rod-shaped and exhibited ivory-coloured colonies. Their chemotaxonomic properties included MK-11 as the major respiratory quinone, ornithine as the cell-wall diamino acid, acetyl as the acyl type of the peptidoglycan, cyclohexyl-C17 : 0 as the major fatty acid and phosphatidylglycerol and diphosphatidylglycerol as the major polar lipids. On the basis of phenotypic, chemotaxonomic and phylogenetic analyses, we propose a new genus in the family Microbacteriaceae , Gryllotalpicola gen. nov., with three novel species, Gryllotalpicola daejeonensis sp. nov. (type strain RU-04T  = KCTC 13809T  = JCM 17590T), Gryllotalpicola koreensis sp. nov. (type strain RU-16T  = KCTC 13810T  = JCM 17591T) and Gryllotalpicola kribbensis sp. nov. (type strain PU-02T  = KCTC 13808T  = JCM 17593T). Gryllotalpicola koreensis is the type species of the genus. Additionally, we propose that Curtobacterium ginsengisoli should be reclassified in the genus as Gryllotalpicola ginsengisoli comb. nov. (type strain DCY26T  = KCTC 13163T  = JCM 14773T).


2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3287-3292 ◽  
Author(s):  
Akio Tani ◽  
Nurettin Sahin

Pink-pigmented, facultatively methylotrophic bacteria, strains 87eT and 99bT, were isolated from the bryophytes Haplocladium microphyllum and Brachythecium plumosum, respectively. The cells of both strains were Gram-reaction-negative, motile, non-spore-forming rods. On the basis of 16S rRNA gene sequence similarity, strains 87eT and 99bT were found to be related to Methylobacterium organophilum ATCC 27886T (97.1 % and 97.7 %, respectively). Strains 87eT and 99bT showed highest 16S rRNA gene similarity to Methylobacterium gnaphalii 23eT (98.3 and 99.0 %, respectively). The phylogenetic similarities to all other species of the genus Methylobacterium with validly published names were less than 97 %. Major cellular fatty acids of both strains were C18 : 1ω7c and C18 : 0. The results of DNA–DNA hybridization, phylogenetic analyses based on 16S rRNA and cpn60 gene sequences, fatty acid profiles, whole-cell matrix-assisted, laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS) analysis, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strains 87eT and 99bT from their phylogenetically closest relatives. We propose that strains 87eT and 99bT represent novel species within the genus Methylobacterium , for which the names Methylobacterium haplocladii sp. nov. (type strain 87eT = DSM 24195T = NBRC 107714T) and Methylobacterium brachythecii sp. nov. (type strain 99bT = DSM 24105T = NBRC 107710T) are proposed.


2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1437-1442 ◽  
Author(s):  
Kikue Hirota ◽  
Kenichi Aino ◽  
Yoshinobu Nodasaka ◽  
Isao Yumoto

An indigo-reducing facultatively alkaliphilic and halophilic strain, designated strain A21T, was isolated from a fermented Polygonum indigo (Polygonum tinctorium Lour.) liquor sample aged for 4 days prepared in a laboratory. 16S rRNA gene sequence phylogeny suggested that strain A21T was a member of the genus Oceanobacillus with the closest relative being the type strain of Oceanobacillus chironomi (similarity: 96.0 %). The cells of the isolate stained Gram-positive and were facultatively anaerobic straight rods that were motile by peritrichous flagella. The strain grew between 18 and 48 °C with optimum growth at 39 °C. It grew in the pH range of 7–12. It hydrolysed casein, gelatin and Tween 20 but not Tweens 40, 60 and 80, starch or DNA. No isoprenoid quinone was detected and the DNA G+C content was 39.7 mol%. The whole-cell fatty acid profile mainly consisted of iso-C15 : 0, anteiso-C15 : 0 and C16 : 0. DNA–DNA hybridization experiments with O. chironomi revealed 13 % relatedness. Owing to the differences in phenotypic and chemotaxonomic characteristics, and phylogenetic analyses based on 16S rRNA gene sequences and DNA–DNA relatedness data from reported Oceanobacillus species, the isolate merits classification as a representative of a novel species, for which the name Oceanobacillus indicireducens sp. nov. is proposed. The type strain is A21T ( = JCM 17251T  = NCIMB 14685T). The description of the genus Oceanobacillus is also emended.


Author(s):  
Juan Zhou ◽  
Yuyuan Huang ◽  
Jing Yang ◽  
Xin-He Lai ◽  
Dong Jin ◽  
...  

Four aerobic, Gram-stain-positive, rod-shaped bacteria (HY60T, HY54, HY82T and HY89) were isolated from bat faeces of Hipposideros and Rousettus species collected in PR China. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the four novel strains formed two separate but adjacent subclades close to Microbacterium agarici CGMCC 1.12260T (97.6–97.7 % similarity), Microbacterium humi JCM 18706T (97.3–97.5 %) and Microbacterium lindanitolerans JCM 30493T (97.3–97.4 %). The 16S rRNA gene sequence similarity was 98.3 % between strains HY60T and HY82T, and identical within strain pairs HY60T/HY54 and HY82T/HY89. The DNA G+C contents of strains HY60T and HY82T were 61.9 and 63.3 mol%, respectively. The digital DNA–DNA hybridization and average nucleotide identity values between each novel strain and their closest relatives were all below the 70 % and 95–96 % thresholds for species delimitation, respectively. All four novel strains contained anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C15 : 0 as the main fatty acids, MK-11 and MK-12 as the major respiratory quinones, and diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid as the predominant polar lipids. The cell-wall peptidoglycan was of B type and contained alanine, glutamate, glycine and ornithine. The acyl type of the muramic acid was glycolyl. The whole-cell sugars were rhamnose and ribose. Based on the foregoing polyphasic analyses, it was concluded that the four uncharacterized strains represented two novel species of the genus Microbacterium , for which the names Microbacterium chengjingii sp. nov. [type strain HY60T (=CGMCC 1.17468T=GDMCC 1.1951T=KACC 22102T)] and Microbacterium fandaimingii sp. nov. [type strain HY82T (=CGMCC 1.17469T=GDMCC 1.1949T=KACC 22101T)] are proposed, respectively.


2020 ◽  
Vol 70 (3) ◽  
pp. 2124-2131 ◽  
Author(s):  
Haiyang Jin ◽  
Hui Wang ◽  
Yanhui Zhang ◽  
Tianlong Hu ◽  
Zhibin Lin ◽  
...  

Three aerobic, asymbiotic, N2-fixing bacterial strains, designated P205T, P204 and P207, were isolated from a paddy soil in Yanting County, China. Based on 16S rRNA gene sequences, the three strains were closely related to Azotobacter chroococcum IAM 12666T (=ATCC 9043T) (99.00–99.79 % similarities). Strain P205T formed an individual branch distinct from the other two newly isolated strains and other related type strains in phylogenetic analyses based on 16S rRNA gene and 92 core genes. The average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA–DNA hybridization (dDDH) values based on genome sequences of strain P205T and A. chroococcum ATCC 9043T, P204, P207 were near or slightly higher than the thresholds for species circumscription (95–96, 95–96 and 70 %, respectively), and the dDDH values were significantly lower than the threshold for delineating subspecies (79–80 %), which strongly supported that strain P205T belonged to A. chroococcum but was a novel subspecies distinct from the type strain of A. chroococcum . This finding was further corroborated by distinct phenotypic characteristics such as growth in Luria–Bertani (LB) medium, carbon source utilization and chemical sensitivity to vancomycin. Therefore, strain P205T represents a novel subspecies of Azotobacter chroococcum , for which the name Azotobacter chroococcum subsp. isscasi subsp. nov. is proposed with the type strain P205T (=KCTC 72233T=CGMCC 1.16846T=CCTCC AB 2019080T). The subspecies Azotobacter chroococcum subsp. chroococcum subsp. nov. is created automatically with the type strain ATCC 9043T (=DSM 2286T=JCM 20725T=JCM 21503T=LMG 8756T=NBRC 102613T=NCAIM B.01391T=NRRL B-14346T=VKM B-1616T).


2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3915-3919 ◽  
Author(s):  
Xing-Xing Qiu ◽  
Mei-Lin Zhao ◽  
Dong Han ◽  
Wen-Jiao Zhang ◽  
Mike L. Dyall-Smith ◽  
...  

Members of the haloarchaeal genera Halosarcina and Halogeometricum (family Halobacteriaceae ) are closely related to each other and show 96.6–98 % 16S rRNA gene sequence similarity. This is higher than the accepted threshold value (95 %) to separate two genera, and a taxonomic study using a polyphasic approach of all four members of the two genera was conducted to clarify their relationships. Polar lipid profiles indicated that Halogeometricum rufum RO1-4T, Halosarcina pallida BZ256T and Halosarcina limi RO1-6T are related more to each other than to Halogeometricum borinquense CGMCC 1.6168T. Phylogenetic analyses using the sequences of three different genes (16S rRNA gene, rpoB′ and EF-2) strongly supported the monophyly of these four species, showing that they formed a distinct clade, separate from the related genera Halopelagius , Halobellus , Haloquadratum , Haloferax and Halogranum . The results indicate that the four species should be assigned to the same genus, and it is proposed that Halosarcina pallida and Halosarcina limi be transferred to the genus Halogeometricum as Halogeometricum pallidum comb. nov. (type strain, BZ256T = KCTC 4017T = JCM 14848T) and Halogeometricum limi comb. nov. (type strain, RO1-6T = CGMCC 1.8711T = JCM 16054T).


2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 401-411 ◽  
Author(s):  
Enrico Tortoli ◽  
Zoe Gitti ◽  
Hans-Peter Klenk ◽  
Stefania Lauria ◽  
Roberta Mannino ◽  
...  

A thorough phenotypic and genotypic analysis of 150 strains belonging to the Mycobacterium terrae complex resulted in the identification of a number of previously unreported sequevars (sqvs) within the species known to belong to the complex. For the species Mycobacterium arupense , three sqvs were detected in the 16S rRNA gene, six sqvs in the hsp65 gene and 15 sqvs in the rpoB gene; in Mycobacterium senuense two sqvs were present in each of the three genetic regions; in Mycobacterium kumamotonense four, two and nine sqvs were found, respectively, and in M. terrae three, four and six sqvs were found, respectively. The inappropriate inclusion of Mycobacterium triviale within the M. terrae complex was confirmed. The limited utility of biochemical tests and of mycolic acid analyses for the differentiation of the members of M. terrae complex was also confirmed. The survey allowed the recognition of three previously undescribed species that were characterized by unique sequences in the 16S rRNA, hsp65 and rpoB genes. Mycobacterium engbaekii sp. nov. (proposed previously 40 years ago but never validly published) was characterized by pink photochromogenic pigmentation and rapid growth; phylogenetically it was related to Mycobacterium hiberniae . The type strain of this species, of which eight strains were investigated, is ATCC 27353T ( = DSM 45694T). A cluster of 24 strains was the basis for the description of Mycobacterium heraklionense sp. nov., which has an intermediate growth rate and is unpigmented; nitrate reductase activity is typically strong. Closely related to M. arupense with respect to the 16S rRNA gene, M. heraklionense sp. nov. could be clearly differentiated from the latter species in the other genetic regions investigated. The type strain is NCTC 13432T ( = LMG 24735T = CECT 7509T). Mycobacterium longobardum sp. nov., represented in the study by seven strains, was characterized by a unique phylogenetic location within the M. terrae complex, clearly divergent from any other species. The type strain is DSM 45394T ( = CCUG 58460T).


2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3749-3754 ◽  
Author(s):  
Sooyeon Park ◽  
Ji-Min Park ◽  
Sung-Min Won ◽  
Yong-Taek Jung ◽  
Jung-Hoon Yoon

A Gram-stain-negative, non-flagellated, aerobic and ovoid or rod-shaped bacterium, designated J-MS1T, was isolated from seashore sand in the South Sea, South Korea, and subjected to a polyphasic taxonomic study. Strain J-MS1T was found to grow optimally at 30 °C and pH 7.0–8.0. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain J-MS1T belonged to the genus Rheinheimera , clustering coherently with the type strain of Rheinheimera chironomi and sharing 98.34 % sequence similarity. Strain J-MS1T exhibited 16S rRNA gene sequence similarity of 94.26–96.98 % to the type strains of the other species of the genus Rheinheimera . In the phylogenetic trees based on gyrB sequences, strain J-MS1T clustered with the type strain of R. chironomi , with which it shared the highest sequence similarity (86.97 %). Strain J-MS1T contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c as the major fatty acids. The major polar lipids detected in strain J-MS1T and in the type strain of R. chironomi were phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content of strain J-MS1T was 49.8 mol% and its mean DNA–DNA relatedness value with R. chironomi LMG 23818T was 12 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain J-MS1T is separated from recognized species of the genus Rheinheimera . On the basis of the data presented, strain J-MS1T is considered to represent a novel species of the genus Rheinheimera , for which the name Rheinheimera arenilitoris sp. nov. is proposed. The type strain is J-MS1T ( = KCTC 42112T = CECT 8623T).


2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3743-3748 ◽  
Author(s):  
Sooyeon Park ◽  
Ja-Min Park ◽  
Yong-Taek Jung ◽  
Chi Nam Seong ◽  
Jung-Hoon Yoon

A Gram-stain-negative, aerobic, non-spore-forming, non-flagellated, gliding and rod-shaped bacterial strain, designated GJMS-9T, was isolated from seashore sand collected at Geoje island in the South Sea, South Korea. Strain GJMS-9T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain GJMS-9T clustered with the type strain of Mesoflavibacter zeaxanthinifaciens , showing the highest sequence similarity of 99.1 %. Strain GJMS-9T exhibited 16S rRNA gene sequence similarity of 96.5 % to the type strain of Mesoflavibacter aestuarii and of less than 96.1 % to the type strains of other recognized species. Strain GJMS-9T contained MK-6 as the only menaquinone and iso-C15 : 1 G, iso-C16 : 0 3-OH, iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The polar lipid profile of strain GJMS-9T containing phosphatidylethanolamine, one unidentified lipid and one unidentified glycolipid as major components was similar to that of the type strain of M. zeaxanthinifaciens . The DNA G+C content of strain GJMS-9T was 32.2 mol% and its DNA–DNA relatedness with M. zeaxanthinifaciens DSM 18436T was 38±6.1 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain GJMS-9T is separated from other species of the genus Mesoflavibacter . On the basis of the data presented, strain GJMS-9T is considered to represent a novel species of the genus Mesoflavibacter , for which the name Mesoflavibacter sabulilitoris sp. nov. is proposed. The type strain is GJMS-9T ( = KCTC 42117T = CECT 8597T).


Sign in / Sign up

Export Citation Format

Share Document