scholarly journals Williamsia soli sp. nov., Isolated from Thermal Power Plant in Yantai

2021 ◽  
Author(s):  
Ming-Jing Zhang ◽  
Xue-Han Li ◽  
Li-Yang Peng ◽  
Shuai-Ting Yun ◽  
Zhuo-Cheng Liu ◽  
...  
Keyword(s):  
Power Plant ◽  
Thermal Power Plant ◽  
Type Strain ◽  
Sequence Similarity ◽  
Thermal Power ◽  
Draft Genome ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
Average Amino Acid Identity

Abstract Strain C17T, a novel strain belonging to the phylum Actinobacteria, was isolated from thermal power plant in Yantai, Shandong Province, China. Cells of strain C17T were Gram-stain-positive, aerobic, pink, non-motile and round with neat edges. Strain C17T was able to grow at 4–42 °C (optimum 28 °C), pH 5.5–9.5 (optimum 7.5) and with 0.0–5.0% NaCl (optimum 1.0%, w/v). Phylogenetically, the strain was a member of the family Gordoniaceae, order Mycobacteriales, class Actinobacteria. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that the closest relative was the type strain of Williamsia faeni JCM 17784T with pair-wise sequence similarity of 98.4%. According to the genome, the DNA G + C content obtained from the draft genome sequence was 64.7%, the main resistant antibiotics were rifamycin, aminoglycoside and glycopeptide, the related gene cluster were clbC,clbB,clbA,vanRI,vanRB,vanRC and vanRD. The average amino acid identity(AAI), average nucleotide identity (ANI) and digital DNA–DNA hybridization(dDDH)values between genome sequences of strain C17T and the type strain Williamsia faeni of the recognized taxa compared were 77.5, 77.9 and 20.7%, respectively. Predominant fatty acids were C16:0(31.7%), C18:1ω9c(26.8%), 10-methyl-C18:0 (16.4%), summed feature comprising C16:1ω7c and/or C16:1ω6c (12.2%) and sum in feature comprising C16:1ω6c and/orC16:1ω7c (10.9%). The major isoprenoid quinone was MK-9 and the diagnostic phospholipids were phosphatidylethanolamine(PE), diphos-phatidylglycerol(DPG) and phosphatidylinositol(PI). Therefore, the combined phenotypic, chemotaxonomic and phylogenetic data indicated that the strain is considered to represent a novel species of the genus Williamsia and the name Williamsia soli sp. nov. is proposed for strain C17T (= KCTC 49567T= MCCC 1K04355T).

scholarly journals Pseudaestuariivita rosea sp. nov., a novel species of genus Pseudaestuariivita, isolated from Acmaea, a kind of marine mollusea

2021 ◽  
Author(s):  
Shuai-Ting Yun ◽  
Zhuo Chen ◽  
Yan-Jun Yi ◽  
Ming-Jing Zhang ◽  
Shu-Kun Gao ◽  
...  
Keyword(s):  
Novel Species ◽  
Draft Genome ◽  
Homoserine Lactone ◽  
Amino Acid Identity ◽  
Chemical Components ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
Average Amino Acid Identity ◽  
The Family ◽  
Family Rhodobacteraceae

Abstract A Gram-stain-negative, pink-pigmented, facultatively anaerobic, gliding and rod-shaped bacterium, showing optimum growth at 33°C, designated as strain H15T , was isolated from the gut microbial of the Acmaea from Weihai, Shandong Province, China and characterised phylogenetically, phenotypically and chemotaxonomically. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that the strain belonged to the family Rhodobacteraceae and was associated with members of the recognized genera, the closest relative was the type strain of Pseudaestuariivita atlantica (96.7%). Genome analysis showed that the genome size was 3893398 bp and the DNA G+C content obtained from the draft genome sequence was 56.7%. The secondary metabolites based on genome predicated that the strain H15T contained one cluster of lassopeptide, one cluster of bacteriocin, two clusters of terpene production, two clusters of homoserine lactone(Hserlactone)production and one cluster of beta lactone. The average amino acid identity, average nucleotide identity and digital DNA–DNA hybridization values between genome sequences of strain H15T and all the type strains of the recognized taxa compared were lower than 63.1,72.0 and 19.7%, respectively. Based on the analysis of chemical components, the predominant cellular fatty acids were summed featured 8(C18:1ω7c/ω6c,46.1%), C 20:1ω7c (17.1%), the major polar lipids contained phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and an unidentified lipid and the predominant menaquinone was Q10. Therefore, the combined chemotaxonomic, phenotypic and phylogenetic data indicated that the strain was considered to represent a novel species of the genus Pseudaestuariivita and the name Pseudaestuariivita rosea sp. nov. was proposed for strain H15T(MCCC 1K04420T=KCTC 82505T).

scholarly journals Pseudomonas delhiensis sp. nov., from a fly ash dumping site of a thermal power plant

2007 ◽  
Vol 57 (3) ◽  
pp. 527-531 ◽  
Author(s):  
Om Prakash ◽  
Kirti Kumari ◽  
Rup Lal
Keyword(s):  
Fly Ash ◽  
Power Plant ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Thermal Power Plant ◽  
Sequence Similarity ◽  
Thermal Power ◽  
Rrna Gene ◽  
Dumping Site ◽  
Degrading Bacterium

A phenanthrene- and citronellol-degrading bacterium, strain RLD-1T, was isolated from the fly ash dumping site of a thermal power plant in Delhi, India. The 16S rRNA gene sequence indicated that this strain belongs to the genus Pseudomonas; high levels of sequence similarity were found with respect to Pseudomonas citronellolis DSM 50332T (98.9 %), Pseudomonas jinjuensis DSM 16612T (97.6 %) and Pseudomonas nitroreducens DSM 14399T (97.5 %). Phylogenetic analysis based on 16S rRNA gene sequences placed the strain within the clade represented by these three strains. Strain RLD-1T showed low levels of DNA–DNA hybridization with respect to P. citronellolis DSM 50332T (36 %), P. jinjuensis DSM 16612T (4 %) and P. nitroreducens (13.7 %). Strain RLD-1T can also be distinguished from these three strains on the basis of several biochemical and physiological attributes. The novel strain contained high levels of cellular fatty acids 18 : 1ω7c, 16 : 0 and 16 : 1ω7c, along with 10 : 0 3-OH and 12 : 0 3-OH. Thus, strain RLD-1T represents a novel species of the genus Pseudomonas, for which the name Pseudomonas delhiensis sp. nov. is proposed. The type strain is RLD-1T (=MTCC 7601T=CCM 7361T).

scholarly journals Mucilaginibacter celer sp. nov. and Aquirhabdus parva gen. nov., sp. nov., isolated from freshwater

2020 ◽  
Vol 70 (10) ◽  
pp. 5479-5487 ◽  
Author(s):  
MinJi Kim ◽  
Su-Kyoung Shin ◽  
Hana Yi
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Average Amino Acid Identity ◽  
The Family ◽  
Taxonomic Novelty

Two novel bacteria, designated HYN0043T and HYN0046T, were isolated from a freshwater lake in Korea. 16S rRNA gene sequence phylogeny indicated that strain HYN0043T belongs to the genus Mucilaginibacter of the family Sphingobacteriaceae because it showed highest sequence similarity to Mucilaginibacter oryzae (98.2 %). The average nucleotide identity between strain HYN0043T and M. oryzae was 83.5 %, which is clearly below the suggested threshold for species demarcation. Strain HYN0046T was found to belong to the family Moraxellaceae and shared highest sequence similarity with Agitococcus lubricus (93.8 %). The average amino acid identity values between strain HYN0046T and representative type strains of closely related genera (Alkanindiges, Agitococcus and Acinetobacter ) were 53.1–60.7 %, implying the novelty of the isolate at the genus level. Phenotypic characteristics (physiological, biochemical and chemotaxonomic) also supported the taxonomic novelty of the two isolates. Thus, we suggest the following names to accommodate strains HYN0043T and HYN0046T: Mucilaginibacter celer sp. nov. (type strain HYN0043T=KACC 19184T=NBRC 112738T) in the family Spingobacteriaceae and phylum Bacteroidetes and Aquirhabdus parva gen. nov., sp. nov. (type strain HYN0046T=KACC 19178T=NBRC 112739T) in the family Moraxellaceae and phylum Proteobacteria .

Genome analysis reveals that the correct name of type strain Adlercreutzia caecicola DSM 22242T is Parvibacter caecicola Clavel et al. 2013

2021 ◽  
Vol 71 (5) ◽  
Author(s):  
Dominic A. Stoll ◽  
Nicolas Danylec ◽  
Christina Grimmler ◽  
Sabine E. Kulling ◽  
Melanie Huch
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Draft Genome ◽  
Amino Acid Identity ◽  
Average Nucleotide Identity ◽  
Content Type ◽  
Link Type ◽  
Genome Wide ◽  
Average Amino Acid Identity ◽  
Biochemical Analyses

The strain Adlercreutzia caecicola DSM 22242T (=CCUG 57646T=NR06T) was taxonomically described in 2013 and named as Parvibacter caecicola Clavel et al. 2013. In 2018, the name of the strain DSM 22242T was changed to Adlercreutzia caecicola (Clavel et al. 2013) Nouioui et al. 2018 due to taxonomic investigations of the closely related genera Adlercreutzia, Asaccharobacter and Enterorhabdus within the phylum Actinobacteria . However, the first whole draft genome of strain DSM 22242T was published by our group in 2019. Therefore, the genome was not available within the study of Nouioui et al. (2018). The results of the polyphasic approach within this study, including phenotypic and biochemical analyses and genome-based taxonomic investigations [genome-wide average nucleotide identity (gANI), alignment fraction (AF), average amino acid identity (AAI), percentage of orthologous conserved proteins (POCP) and genome blast distance phylogeny (GBDP) tree], indicated that the proposed change of the name Parvibacter caecicola to Adlercreutzia caecicola was not correct. Therefore, it is proposed that the correct name of Adlercreutzia caecicola (Clavel et al. 2013) Nouioui et al. 2018 strain DSM 22242T is Parvibacter caecicola Clavel et al. 2013.

scholarly journals Salinibaculum litoreum gen. nov., sp. nov., isolated from salted brown alga Laminaria

2020 ◽  
Vol 70 (4) ◽  
pp. 2879-2887 ◽  
Author(s):  
Dong Han ◽  
Heng-Lin Cui
Keyword(s):  
Brown Alga ◽  
Type Species ◽  
Sequence Similarity ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type ◽  
Pr China ◽  
A Minor

A novel Gram-stain-negative, aerobic and rod-shaped halophilic archaeon, designated HD8-45T, was isolated from the red brine of salted brown alga Laminaria produced at Dalian, PR China. According to the results of 16S rRNA gene and rpoB′ gene sequence comparisons, strain HD8-45T showed the highest sequence similarity to the corresponding genes of Salinirussus salinus YGH44T (95.1 and 85.2 % similarities, respectively), Halovenus aranensis EB27T (91.2 and 86.0 % similarities, respectively). The low sequence similarity and the phylogeny implied the novel generic status of strain HD8-45T. Genomic relatedness analyses showed that strain HD8-45T were clearly distinguished from other species in the order Halobacteriales , with average nucleotide identity, amino acid identity and in silico DNA–DNA hybridization values not more than 75.1, 65.6 and 21.5 %. The polar lipid pattern contained phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, two major glycolipids and two minor glycolipids. The two major glycolipids and a minor glycolipid were chromatographically identical to disulfated mannosyl glucosyl diether, sulfated mannosyl glucosyl diether and mannosyl glucosyl diether, respectively. The major respiratory quinones were menaquinone MK-8 and MK-8(H2). The DNA G+C content was 62.0 mol% (Tm ) and 61.9 mol% (genome). All these results showed that strain HD8-45T represents a novel species of a new genus in the order Halobacteriales , for which the name Salinibaculum litoreum gen. nov., sp. nov. is proposed. The type strain of Salinibaculum litoreum is HD8-45T (=CGMCC 1.15328T=JCM 31107T).

scholarly journals Taxogenomics of the Genus Cyclobacterium: Cyclobacterium xiamenense and Cyclobacterium halophilum as Synonyms and Description of Cyclobacterium plantarum sp. nov.

2020 ◽  
Vol 8 (4) ◽  
pp. 610 ◽  
Author(s):  
Azadeh Shahinpei ◽  
Mohammad Ali Amoozegar ◽  
Leila Mirfeizi ◽  
Mahdi Moshtaghi Nikou ◽  
Antonio Ventosa ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Threshold Value ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Average Amino Acid Identity ◽  
Halophytic Plant ◽  
Taxonomic Characterization ◽  
Current Species

The genus Cyclobacterium belongs to the phylum Bacteroidetes and includes eight species. Our study, based on the genomic parameters in silico DNA–DNA hybridization (GGDC), average nucleotide identity (OrthoANI), and average amino acid identity (AAI), confirmed that all current species of Cyclobacterium belong to this genus and constitute a coherent phylogenomic group, but with species forming two separate branches. In addition, the genome-based analyses revealed that Cyclobacterium xiamenense and Cyclobacterium halophilum are members of the same species. Besides, we carried out a taxonomic characterization of the new strain GBPx2T, isolated from the halophytic plant Salicornia sp. Analysis of its 16S rRNA gene sequence showed the highest sequence similarity (97.5%) to Cyclobacterium lianum HY9T. Percentages of GGDC and OrthoANI between strain GBPx2T and species of the genus Cyclobacterium were lower than the threshold value for species delineation. The DNA G+C content was 43.0 mol%. The polar lipids included phosphatidylethanolamine as well as one unidentified phospholipid and four unidentified lipids, and its major cellular fatty acids were iso-C15:0 and summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH). The only quinone present was menaquinone 7. Based on a combination of phenotypic, chemotaxonomic, and phylogenomic features, the GBPx2T strain represents a novel species of the genus Cyclobacterium, for which the name Cyclobacterium plantarum sp. nov. is proposed. The type strain of Cyclobacterium plantarum is GBPx2T (= IBRC-M 10634T = LMG 28551T).

scholarly journals Agromyces salentinus sp. nov. and Agromyces neolithicus sp. nov.

2005 ◽  
Vol 55 (1) ◽  
pp. 153-157 ◽  
Author(s):  
Valme Jurado ◽  
Ingrid Groth ◽  
Juan M. Gonzalez ◽  
Leonila Laiz ◽  
Cesareo Saiz-Jimenez
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Comparisons

A polyphasic study was carried out to clarify the taxonomic position of two Gram-positive bacteria isolated from soil samples of the Grotta dei Cervi (Italy), a relatively unexplored hypogean environment. The strains, 20-5T and 23-23T, showed phenotypic and phylogenetic characteristics that were consistent with their classification in the genus Agromyces. 16S rRNA gene sequence comparisons revealed that the two strains formed distinct phyletic lines within the genus Agromyces. Based on 16S rRNA gene sequence similarity, chemotaxonomic data and the results of DNA–DNA relatedness studies, it is proposed that the two isolates represent two novel species of the genus Agromyces. Pronounced differences in a broad range of phenotypic characteristics and DNA G+C content distinguished the two strains from each other and from previously described species of the genus Agromyces. Two novel species are proposed: Agromyces salentinus sp. nov. (type strain, 20-5T=HKI 0320T=DSM 16198T=NCIMB 13990T) and Agromyces neolithicus sp. nov. (type strain, 23-23T=HKI 0321T=DSM 16197T=NCIMB 13989T).

scholarly journals Actinophytocola timorensis sp. nov. and Actinophytocola corallina sp. nov., isolated from soil

2011 ◽  
Vol 61 (4) ◽  
pp. 834-838 ◽  
Author(s):  
Misa Otoguro ◽  
Hideki Yamamura ◽  
Tomohiko Tamura ◽  
Rohmatussolihat Irzaldi ◽  
Shanti Ratnakomala ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Comparisons

Two actinomycete strains, ID05-A0653T and ID06-A0464T, were isolated from soils of West Timor and Lombok island, respectively, in Indonesia. 16S rRNA gene sequence analysis clearly demonstrated that the isolates belonged to the family Pseudonocardiaceae and were closely related to the genus Actinophytocola. Strains ID05-A0653T and ID06-A0464T exhibited 98.1 and 98.2 % 16S rRNA gene sequence similarity, respectively, with Actinophytocola oryzae GMKU 367T. The isolates grew well on ISP media and produced white aerial mycelium. Short spore chains were formed directly on the substrate mycelium. The isolates contained meso-diaminopimelic acid, arabinose and galactose as cell-wall components, MK-9(H4) as the sole isoprenoid quinone, iso-C16 : 0 as the major cellular fatty acid and phosphatidylethanolamine as the diagnostic polar lipid. The DNA G+C contents of strains ID05-A0653T and ID06-A0464T were 69.7 and 71.2 mol%, respectively. On the basis of phenotypic characteristics, DNA–DNA relatedness and 16S rRNA gene sequence comparisons, strains ID05-A0653T and ID06-A0464T each represent a novel species of the genus Actinophytocola, for which the names Actinophytocola timorensis sp. nov. (type strain ID05-A0653T  = BTCC B-673T  = NBRC 105524T) and Actinophytocola corallina sp. nov. (type strain ID06-A0464T  = BTCC B-674T  = NBRC 105525T) are proposed.

scholarly journals Salinarimonas rosea gen. nov., sp. nov., a new member of the α-2 subgroup of the Proteobacteria

2010 ◽  
Vol 60 (1) ◽  
pp. 55-60 ◽  
Author(s):  
Ji-Hui Liu ◽  
Yong-Xia Wang ◽  
Xiao-Xia Zhang ◽  
Zhi-Gang Wang ◽  
Yi-Guang Chen ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
West China ◽  
16S Rna ◽  
Total Fatty Acids ◽  
Distinct Line

A Gram-negative, rod-shaped, facultatively anaerobic, halotolerant bacterial strain, designated YIM YD3T, was isolated from a salt mine in Yunnan, south-west China. The taxonomy of strain YIM YD3T was investigated by a polyphasic approach. Strain YIM YD3T was motile, formed pink colonies and was positive for catalase and oxidase activities. Q-10 was the predominant respiratory ubiquinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylcholine and two unknown phospholipids. The major fatty acids (>10 % of total fatty acids) were C18 : 1 ω7c, C18 : 1 ω9c, C16 : 0 and C19 : 0 cyclo ω8c. The DNA G+C content was 71.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the isolate formed a distinct line within a clade containing the genera Balneimonas, Bosea, Chelatococcus and Microvirga in the order Rhizobiales, with highest levels of 16S RNA gene sequence similarity to the type strain of Balneimonas flocculans (93.5 %). On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain YIM YD3T represents a novel species in a new genus, for which the name Salinarimonas rosea gen. nov., sp. nov. is proposed, with strain YIM YD3T (=KCTC 22346T=CCTCC AA208038T) as the type strain.

scholarly journals Reclassification of Actinobacillus muris as Muribacter muris gen. nov., comb. nov.

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3344-3351 ◽  
Author(s):  
Werner Nicklas ◽  
Magne Bisgaard ◽  
Bent Aalbæk ◽  
Peter Kuhnert ◽  
Henrik Christensen
Keyword(s):  
16S Rrna ◽  
Dna Sequences ◽  
Type Strain ◽  
New Genus ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
New Combination ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Sequence Comparisons

To reinvestigate the taxonomy of [Actinobacillus] muris, 474 strains, mainly from mice and rats, were characterized by phenotype and 130 strains selected for genotypic characterization by 16S rRNA and partial rpoB gene sequencing. The type strain was further investigated by whole-genome sequencing. Phylogenetic analysis of the DNA sequences showed one monophyletic group with intragroup similarities of 96.7 and 97.2 % for the 16S rRNA and rpoB genes, respectively. The highest 16S rRNA gene sequence similarity to a taxon with a validly published name outside the group was 95.9 %, to the type strain of [Pasteurella] pneumotropica. The closest related taxon based on rpoB sequence comparison was ‘Haemophilus influenzae-murium’, with 88.4 % similarity. A new genus and a new combination, Muribacter muris gen. nov., comb. nov., are proposed based on a distinct phylogenetic position based on 16S rRNA and rpoB gene sequence comparisons, with major divergence from the existing genera of the family Pasteurellaceae. The new genus has the characteristics of [A.] muris with the emendation that acid formation from ( − )-d-mannitol and hydrolysis of aesculin are variable, while the α-glucosidase test is positive. There is no requirement for exogenously supplied NAD (V factor) for the majority of strains investigated; however, one strain was found to require NAD. The major fatty acids of the type strain of Muribacter muris were C14 : 0, C14 : 0 3-OH/iso-C16 : 1 I, C16 : 1ω7c and C16 : 0, which is in line with most genera of the Pasteurellaceae. The type strain of Muribacter muris is CCUG 16938T ( = NCTC 12432T = ATCC 49577T).

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