Streptomyces xanthii sp. nov. and Streptomyces roseirectus sp. nov. isolated from a Chinese medicinal plant

Author(s):  
Siren Hu ◽  
Yinfeng Wang ◽  
Junzhen Wang ◽  
Keyun Liu ◽  
Xinke Tang ◽  
...  

Two strains of Actinobacteria, designated CRXT-Y-14T and CRXT-G-22T, were isolated from the healthy leaves and seeds, respectively, of a medicinal plant Xanthium sibiricum. Their taxonomic positions were determined using a polyphasic approach. Strain CRXT-Y-14T produced flexuous chains of smooth-surfaced spores. Strain CRXT-G-22T produced straight chains of smooth-surfaced spores. Their morphological features were consistent with the diagnostic characteristics of members of the genus Streptomyces . The results of 16S rRNA gene sequence analyses indicated two strains represented members of the genus Streptomyces . CRXT-Y-14T shared 99.3, 98.9, 98.8 % sequence similarities to Streptomyces atriruber NRRL B-24165T, Streptomyces avermitilis MA-4680T and Streptomyces davaonensis JCM 4913T, respectively. Whilst CRXT-G-22T exhibited highest similarity to Streptomyces acidiscabies ATCC 49003T (98.9 %). The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the closest phylogenetic neighbours of strains CRXT-Y-14T and CRXT-G-22T were S. atriruber NRRL B-24165T and S. acidiscabies ATCC 49003T, respectively. The phylogenomic analyses further confirmed the relative relationship between strain CRXT-G-22T and S. acidiscabies ATCC 49003T, but indicated that CRXT-Y-14T could represent a novel species of the genus Streptomyce. However, the average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between CRXT-Y-14T and strain CRXT-G-22T, between CRXT-Y-14T and S. atriruber NRRL B-24165T, and between CRXT-G-22T and S. acidiscabies ATCC 49003T were 85.4 and 23.2 %, 85.8 and 23.9 % and 89.1 and 34.1 %, respectively, far below the 95~96 and 70 % cut-off points recommended for delineating species. Furthermore, these two novel isolates were distinctly differentiated from their relatives in the genus Streptomyces with respect to phenotypic and chemotaxonomic characteristics. On the basis of these data, CRXT-Y-14T and CRXT-G-22T clearly represent two novel species within the genus Streptomyces , for which the names Streptomyces xanthii sp. nov. (type strain CRXT-Y-14T = MCCC 1K04966T= JCM 34527T) and Streptomyces roseirectus sp. nov. (type CRXT-G-22T = MCCC 1K04979T= JCM 34565T) are proposed.

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1370-1375 ◽  
Author(s):  
Isabel Snauwaert ◽  
Bart Hoste ◽  
Katrien De Bruyne ◽  
Karolien Peeters ◽  
Luc De Vuyst ◽  
...  

Two lactic acid-producing, Gram-stain-positive rods were isolated from a microbial mat actively growing in the littoral zone of an Antarctic lake (Forlidas Pond) in the Pensacola mountains and studied using a polyphasic taxonomic approach. The isolates were examined by phylogenetic analysis of the 16S rRNA gene, multilocus sequence analysis of pheS, rpoA and atpA, and biochemical and genotypic characteristics. One strain, designated LMG 26641, belonged to Carnobacterium alterfunditum and the other strain, designated LMG 26642T, could be assigned to a novel species, with Carnobacterium funditum DSM 5970T as its closest phylogenetic neighbour (99.2 % 16S rRNA gene sequence similarity). Carnobacterium iners sp. nov. could be distinguished biochemically from other members of the genus Carnobacterium by the lack of acid production from carbohydrates. DNA–DNA relatedness confirmed that strain LMG 26642T represented a novel species, for which we propose the name Carnobacterium iners sp. nov. (type strain is LMG 26642T  = CCUG 62000T).


2020 ◽  
Vol 70 (10) ◽  
pp. 5287-5295 ◽  
Author(s):  
Yajun Ge ◽  
Yuanmeihui Tao ◽  
Jing Yang ◽  
Xin-He Lai ◽  
Dong Jin ◽  
...  

Four unknown strains belonging to the genus Arthrobacter were isolated from plateau wildlife on the Qinghai–Tibet Plateau of PR China. Phylogenetic analysis based on 16S rRNA gene sequences showed that the four isolates were separated into two clusters. Cluster I (strains 785T and 208) had the greatest 16S rRNA gene sequence similarity to Arthrobacter citreus (98.6 and 98.7 %, respectively), Arthrobacter luteolus (98.0 and 98.1%, respectively), Arthrobacter gandavensis (97.9 and 98.0 %, respectively) and Arthrobacter koreensis (97.6 and 97.7 %, respectively). Likewise, cluster II (strains J391T and J915) had the highest sequence similarity to Arthrobacter ruber (98.6 and 98.3 %, respectively) and Arthrobacter agilis (98.1 and 97.9  %, respectively). Average nucleotide identity and the digital DNA–DNA hybridization values illustrated that the two type strains, 785T and J391T, represented two separate novel species that are distinct from all currently recognized species in the genus Arthrobacter . These strains had DNA G+C contents of 66.0–66.1 mol% (cluster I) and 68.0 mol% (cluster II). The chemotaxonomic properties of strains 785T and J391T were in line with those of the genus Arthrobacter : anteiso-C15:0 (79.3 and 40.8 %, respectively) as the major cellular fatty acid, MK-8(H2) (65.8 %) or MK-9(H2) (75.6 %) as the predominant respiratory quinone, a polar lipid profile comprising diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, glycolipids and phospholipid, and A3α or A4α as the cell wall peptidoglycan type. On the basis of our results, two novel species in the genus Arthrobacter are proposed, namely Arthrobacter yangruifuii sp. nov. (type strain, 785T=CGMCC 1.16725T=GDMCC 1.1592T=JCM 33491T) and Arthrobacter zhaoguopingii sp. nov. (type strain, J391T=CGMCC 1.17382T=GDMCC 1.1667T=JCM 33841T).


2020 ◽  
Vol 70 (8) ◽  
pp. 4683-4690 ◽  
Author(s):  
Junqin Li ◽  
Wenjing Lei ◽  
Jing Yang ◽  
Shan Lu ◽  
Dong Jin ◽  
...  

Four novel strains (592T, S592, MF47T and SMF47) were isolated from Tibetan antelopes (Pantholops hodgsonii) and plateau pikas (Ochotona curzoniae), respectively. The cells were aerobic, non-motile, Gram-stain- and catalase-positive, rod-shaped bacteria. The 16S rRNA gene sequences of the four strains showed highest similarities to Aeromicrobium fastidiosum DSM 10552T (98.1, 98.6, 98.7 and 98.7 %, respectively), and the phylogenetic analyses based on 16S rRNA gene and genomic sequences indicated that strains 592T and MF47T represent two novel species. The four isolates produced acid from l-rhamnose, d-xylose and cellobiose, but were unable to reduce nitrate. The DNA G+C contents of strains 592T and MF47T were 70.3 and 69.8 mol%, respectively. The digital DNA–DNA hybridization value between strains 592T and MF47T was 32.6 %, lower than the threshold of 70 %, indicating they belong to different species. The four strains’ genomes displayed less than 24.6 % DNA–DNA relatedness with all available genomes of the genus Aeromicrobium in the NCBI database, including Aeromicrobium fastidiosum NBRC 14897T and Aeromicrobium ginsengisoli JCM 14732T. The major fatty acids of the four strains were C18 : 1  ω9c and C18 : 0 10-methyl, and the main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. The predominant respiratory quinones were MK-9(H4) and MK-8(H4). The cell-wall peptidoglycan contained ll-diaminopimelic acid. Based on these genotypic, phenotypic and biochemical analyses, it is proposed that the four unidentified bacteria be classified as two novel species, Aeromicrobium chenweiae sp. nov. and Aeromicrobium yanjiei sp. nov. The type strains are 592T (=CGMCC1.16526T=DSM 106289T) and MF47T (=CGMCC 1.17444T=JCM 33790T), respectively.


2020 ◽  
Vol 70 (12) ◽  
pp. 6067-6078
Author(s):  
Maria Pain ◽  
Runa Wolden ◽  
Daniel Jaén-Luchoro ◽  
Francisco Salvà-Serra ◽  
Beatriz Piñeiro Iglesias ◽  
...  

When analysing a large cohort of Staphylococcus haemolyticus , using whole-genome sequencing, five human isolates (four from the skin and one from a blood culture) with aberrant phenotypic and genotypic traits were identified. They were phenotypically similar with yellow colonies, nearly identical 16S rRNA gene sequences and initially speciated as S. haemolyticus based on 16S rRNA gene sequence and MALDI-TOF MS. However, compared to S. haemolyticus , these five strains demonstrate: (i) considerable phylogenetic distance with an average nucleotide identity <95 % and inferred DNA–DNA hybridization <70  %; (ii) a pigmented phenotype; (iii) urease production; and (iv) different fatty acid composition. Based on the phenotypic and genotypic results, we conclude that these strains represent a novel species, for which the name Staphylococcus borealis sp. nov. is proposed. The novel species belong to the genus Staphylococcus and is coagulase- and oxidase-negative and catalase-positive. The type strain, 51-48T, is deposited in the Culture Collection University of Gothenburg (CCUG 73747T) and in the Spanish Type Culture Collection (CECT 30011T).


Author(s):  
Gui Zhang ◽  
Jing Yang ◽  
Xin-He Lai ◽  
Dong Jin ◽  
Shan Lu ◽  
...  

Six novel facultatively anaerobic, Gram-stain-positive, rod-shaped, non-haemolytic bacteria (zg-320T/zg-336, zg-917T/zg-910 and zg-913T/zg-915) isolated from animal tissues and human faeces were found to belong to the genus Corynebacterium based on the phylogenetic analyses of 16S rRNA gene and 262 core genes set. Based on the greatest degree of 16S rRNA similarity, zg-320T/zg-336 had the highest 16S rRNA gene similarity to Corynebacterium falsenii DSM 44353T (97.51 %), zg-917T/zg-910 to Corynebacterium coyleae DSM 44184T (98.68 %), and zg-913T/zg-915 to Corynebacterium afermentans subsp. lipophilum CIP 103500T (98.79 %). The three novel type strains had a relatively high DNA G+C content (61.2–64.4 mol%), low DNA relatedness and ANI values with their respective neighbours: 23.5/72.7 %, 25.0/72.3%and 22.6/73.1 % (zg-320T vs. Corynebacterium auriscanis CIP 106629T, Corynebacterium resistens DSM 45100T and Corynebacterium suicordis DSM 45110T); 24.4/82.3% and 23.7/81.3 % (zg-917T vs. C. coyleae DSM 44184T and Corynebacterium jeddahense JCBT); 26.8/83.7% and 27.7/84.4 % (zg-913T vs. Corynebacterium mucifaciens ATCC 700355T and C. afermentans subsp. lipophilum CCUG 32105T). The three novel species had C16 : 0, C18 : 0, C18 : 1  ω9c and C18 : 0 ante/C18 : 2  ω6,9c as the major cellular fatty acids; MK-8(H2) in strain zg-917T and MK-9(H2) in strains zg-320T and zg-913T were found to be the major respiratory quinones. For the three novel species, the detected major polar lipids included diphosphatidylglycerol, phosphatidyl inositol mannoside, phosphatidylglycerol and phosphatidylinositol, the cell-wall peptidoglycan was based on meso-DAP, and the whole-cell sugars mainly included ribose, arabinose and galactose. The three novel species grew optimally at 35–37 °C, 0.5 % (w/v) NaCl and pH 7.0–8.0; notably, they were tolerant of 10.5 % (w/v) NaCl. Based on the results of these comprehensive analyses, three novel species in the genus Corynebacterium are proposed, aptly named Corynebacterium zhongnanshanii sp. nov. (zg-320T = GDMCC 1.1719T = JCM 34106T), Corynebacterium lujinxingii sp. nov. (zg-917T = GDMCC 1.1707T = JCM 34094T) and Corynebacterium wankanglinii sp. nov. (zg-913T = GDMCC 1.1706T = JCM 34398T).


2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 900-904 ◽  
Author(s):  
Hui-Jing Du ◽  
Yu-Qin Zhang ◽  
Hong-Yu Liu ◽  
Jing Su ◽  
Yu-Zhen Wei ◽  
...  

An endophytic actinomycete, designated strain I10A-01259T, was isolated from a surface-sterilized fruit of Lonicera maackii (Rupr.) Maxim., a medicinal plant, which was collected from a suburb of Beijing, China. Whole-cell hydrolysates of the isolate contained galactose and meso-diaminopimelic acid. The predominant phospholipids were phosphatidylglycerol and diphosphatidylglycerol; the menaquinones consisted mainly of MK-9, MK-11 and MK-12, with a minor amount of MK-10. The major fatty acids were iso-C16 : 0, anteiso-C15 : 0 and iso-C15 : 0. Comparative analysis of 16S rRNA gene sequences indicated that strain I10A-01259T was most closely related to Nocardiopsis arabia S186T (93.2 % sequence similarity), Thermobifida halotolerans YIM 90462T (93.0 %) and other strains of genera within the families Nocardiopsaceae and Thermomonosporaceae . On the phylogenetic tree based on 16S rRNA gene sequences, strain I10A-01259T fell within the radius of the suborder Streptosporangineae , in which the strain formed a distinct lineage next to the genera of the families Nocardiopsaceae and Thermomonosporaceae . Based on the data from our polyphasic taxonomic study, a novel genus and species, Allonocardiopsis opalescens gen. nov., sp. nov., are proposed within the suborder Streptosporangineae . The type strain of Allonocardiopsis opalescens is strain I10A-01259T ( = CPCC 203428T  = DSM 45601T  = KCTC 19844T).


2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2169-2173 ◽  
Author(s):  
R. Maarit Niemi ◽  
Tuula Ollinkangas ◽  
Lars Paulin ◽  
Pavel Švec ◽  
Peter Vandamme ◽  
...  

A significant number of Enterococcus strains from pristine waters of two brooks in Finland formed a distinct cluster on the basis of whole-cell protein fingerprinting by one-dimensional SDS-PAGE. The strains shared the following characteristics. Cells were ovoid, Gram-positive-staining and non-spore-forming, appearing singly or in pairs or chains. They were facultatively anaerobic and catalase-negative. Growth in broth containing 6.5 % NaCl or at 45 °C was weak or absent. Production of D antigen was variable. The strains tolerated 60 °C for 30 min, 40 % bile and tellurite, hydrolysed aesculin strongly and gelatin weakly, produced no acid from hippurate and did not reduce it, grew weakly at 10 °C, showed a strong reaction for the Voges–Proskauer test and produced acid from methyl α-d-glucoside, mannitol, sorbitol and sucrose, with weak or no production of acid from methyl α-d-mannoside, l-arabinose, gluconate and l-xylose. Several of the strains were selected for identification on the basis of sequencing of almost the whole 16S rRNA gene and partial atpA and pheS genes and of (GTG)5-PCR fingerprints. Partial atpA and pheS gene sequencing was also performed for those type strains of Enterococcus species without available sequences in the database. The pristine brook isolates formed a novel species, for which the name Enterococcus rivorum sp. nov. (type strain S299T  = HAMBI 3055T  = LMG 25899T  = CCM 7986T) is proposed. On the basis of 16S rRNA gene sequence similarity, E. rivorum sp. nov. is related to the Enterococcus faecalis genogoup. It is distinguished from described Enterococcus species on the basis of 16S rRNA, atpA and pheS gene sequences and whole-cell protein and (GTG)5-PCR fingerprints. It is most closely related to E. faecalis , but DNA–DNA hybridization confirms it to represent a novel species.


2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2655-2660 ◽  
Author(s):  
Bungonsiri Intra ◽  
Atsuko Matsumoto ◽  
Yuki Inahashi ◽  
Satoshi Ōmura ◽  
Yōko Takahashi ◽  
...  

A novel actinomycete, strain 44EHWT, was isolated from rhizospheric soil under an Elephant ear plant (Colocasia esculenta) in Bangkok, Thailand. Strain 44EHWT produced long branching hyphae and abundant aerial mycelia with chains of rod-shaped spores. Whole-cell hydrolysates contained galactose, glucose, arabinose, ribose, mannose and rhamnose as diagnostic sugars. meso-Diaminopimelic acid was the diamino acid and glycine, alanine and glutamic acid were present in the cell-wall peptidoglycan with the acyl type of the peptidoglycan being acetyl. Phospholipids consisted of phosphatidylethanolamine, phosphatidylethanolamine with hydroxy fatty acids and diphosphatidylglycerol, as well as other unknown phospholipids; however, no mycolic acids were detected. The predominant menaquinone observed was MK-9(H4) and major fatty acids were iso-C16 : 0 and 2-OH iso-C16 : 0. The G+C content of genomic DNA was 74 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that this isolate was most similar to Actinokineospora enzanensis NBRC 16517T. However, DNA–DNA hybridization revealed a low relatedness between this isolate and A. enzanensis NBRC 16517T, indicating that this isolate represented a novel species in the genus Actinokineospora . On the basis of 16S rRNA gene sequence analysis, phenotypic characteristics and DNA–DNA hybridization data, we propose that strain 44EHWT represents a novel species in the genus Actinokineospora , Actinokineospora bangkokensis. The type strain is 44EHWT ( = BCC 53155T = NBRC 108932T).


Author(s):  
Boram Seo ◽  
Kyungchan Jeon ◽  
Inwoo Baek ◽  
Yung Mi Lee ◽  
Kiwoon Baek ◽  
...  

An obligately anaerobic, Gram-stain-positive and spore-forming strain, SNUG30386T was isolated from a faecal sample of a healthy Korean subject. The strain formed a round ivory-coloured colony and cells were chained rods with tapered ends, approximately 2.0–2.5×0.6–0.8 μm in size. The taxonomic analysis indicated that strain SNUG30386T was within the family Lachnospiraceae . According to the 16S rRNA gene sequence similarity, the closest species to strain SNUG30386T was Clostridium symbiosum (95.6 %), followed by Enterocloster asparagiformis (94.8 %), Enterocloster clostridioformis (94.8 %) and Enterocloster lavalensis (94.6 %). The evolutionary tree based on 16S rRNA gene sequences demonstrated that strain SNUG30386T had split apart at a unique branch point far from other close relatives. Its DNA G+C content was 48.3 mol% calculated from the whole genome sequence. The major cellular fatty acids were C16 : 0 and C14 : 0. Compared to those of the closely related species, strain SNUG30386T showed distinct biochemical activities such as being unable to utilize most of carbon sources except d-glucose and l-arabinose. As a result, based on its unique phylogenetic clade and taxonomic characteristics, we conclude that strain SNUG30386T represents a novel species within the genus Clostridium , for which the name Clostridium fessum sp. nov. is proposed. The type strain of the novel species is SNUG30386T (=KCTC 15633T= JCM 32258T).


Author(s):  
Mingchao Xu ◽  
Yan Dai ◽  
Yuyuan Huang ◽  
Jing Yang ◽  
Xin-He Lai ◽  
...  

Two pairs of aerobic, Gram-stain-positive, rod-shaped strains (HY164T/HY044, HY168T/HY211) were isolated from bat faecal samples. Strains HY164T and HY044 were motile with a polar flagellum, and had 16S rRNA gene similarity of 95.1–98.6 % to Haloactinobacterium album YIM 93306T and Haloactinobacterium glacieicola T3246-1T; strains HY168T and HY211 were most similar to Ruania albidiflava DSM 18029T (96.6 %). Phylogenetic trees based on 16S rRNA gene and whole genome sequences revealed affiliation of strains HY164T and HY168T to the family Ruaniaceae , representing novel lineages in the genera Haloactinobacterium and Ruania , respectively, which was also supported by the results for average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH). For all isolates, the principal cellular fatty acids were anteiso-C15 : 0 and iso-C14 : 0. HY164T and HY168T had MK-8(H4) as the predominant isoprenoid quinone, diphosphatidylglycerol, phosphatidylglycerol, several unidentified phospholipids and glycolipids as common polar lipids while the latter strain additionally contained one unidentified aminophospholipid and one unidentified phosphoglycolipid. Besides sharing alanine, glutamic acid and lysine with HY164T, HY168T additionally contained 2,4-diaminobutyric acid in the cell-wall peptidoglycan. The whole-cell sugars of HY164T were ribose and rhamnose, while HY168T only included the latter. The DNA G+C contents of HY164T and HY168T were 71.0 and 69.1 mol%, respectively. Combining the polyphasic taxonomic data, HY164T (=CGMCC 4.7606T=JCM 33464T) is classified as representing a novel species of the genus Haloactinobacterium with the proposed name Haloactinobacterium kanbiaonis sp. nov., and HY168T (=CGMCC 1.16970T=JCM 33465T) is proposed to represent a novel species of the genus Ruania with the name Ruania zhangjianzhongii sp. nov.


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