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 Fibrivirga Algicola Gen. Nov., Sp. Nov., An Algicidal Bacterium Isolated from a Freshwater River

2021 ◽  
Author(s):  
Sanghwa Park ◽  
JaYoung Cho ◽  
Dong-Hyun Jung ◽  
SeokWon Jang ◽  
JungHye Eom ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Sequence Similarity ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
The Novel ◽  
Respiratory Quinone ◽  
Algicidal Bacterium ◽  
Average Amino Acid Identity ◽  
The Family ◽  
Major Respiratory Quinone

Abstract An aerobic, gram-negative, pink-colored, non-motile, rod-shaped algicidal bacterium, designated JA-25T was isolated from the freshwater of the Geumgang River, Republic of Korea. It grew at 15–30°C, 6.0–9.0 pH, and in the presence of 0–1% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain JA-25T belongs to the Family ‘Spirosomaceae’ and is most closely related to Fibrella aestuarina BUZ 2T (93.6%). The strain JA-25T showed < 90% sequence similarity to other members of the Family ‘Spirosomaceae’. The average nucleotide identity(ANI), in silico DNA-DNA hybridization and the average amino acid identity(AAI) values based on the genomic sequences of JA-25T and F. aestuarina BUZ 2T were 74.4, 20.5 and 73.6 %, respectively. The genomic DNA G + C content was 52.5mol %. The major cellular fatty acids were Summed feature 3 (C16:1 ω6c/C16:1 ω7c), C16:1 ω5c, C16:0 (> 10%). The genomic DNA G + C content was 52.5 mol %. The major respiratory quinone was MK-7 and the polar lipids were phosphatidylethanolamine, two unidentified aminolipids, two phospholipids and five unidentified lipids. Considering the phylogenetic inference, phenotypic and chemotaxonomic data, strain JA-25T should be classified as a novel species of the novel genus Fibrivirga, with the proposed name Fibrivirga algicola sp. nov. The type strain is JA-25T (= KCCM 43334T = NBRC 114259T).

scholarly journals Rhodobacter ruber sp. nov., isolated from a freshwater pond

2021 ◽  
Author(s):  
Wen-Ming Chen ◽  
Ting-Hsuan Chang ◽  
Der-Shyan Sheu ◽  
Li-Cheng Jheng ◽  
Shih-Yi Sheu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Amino Acid Identity ◽  
Core Gene ◽  
Rrna Gene ◽  
Freshwater Pond ◽  
Average Amino Acid Identity

Abstract Strain CCP-1T, isolated from a freshwater pond in Taiwan, is characterized using a polyphasic taxonomy approach. Cells of strain CCP-1T are Gram-stain-negative, aerobic, non-motile, rod-shaped and form dark red colored colonies. Growth occurs at 20–40 oC, at pH 6.5-9 and with 0-0.5% NaCl. Strain CCP-1T contains bacteriochlorophyll a, and shows optimum growth under anaerobic condition by photoheterotrophy, but not by photoautotrophy. 16S rRNA gene sequence similarity indicates that strain CCP-1T is closely related to species within the genus Rhodobacter (93.9–96.2% sequence similarity), Haematobacter (96.3%) and Xinfangfangia (95.5–96.2%). Phylogenetic analyses based on 16S rRNA gene sequences and based on up-to-date bacterial core gene set (92 protein clusters) reveal that strain CCP-1T is affiliated with species in the genus Rhodobacter. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization identity between strain CCP-1T and Rhodobacter species are 71.3–76.3%, 70.4–77.9% and 21.4–23.2%, respectively, supporting that strain CCP-1T is a novel species of the genus Rhodobacter. The DNA G + C content is 66.2%. The predominant fatty acid is C18:1ω7c and the major isoprenoid quinone is Q-10. The polar lipids have phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, two uncharacterized aminophospholipids and two uncharacterized phospholipids. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain CCP-1T should represent a novel species of the genus Rhodobacter, for which the name Rhodobacter ruber sp. nov. is proposed. The type strain is CCP-1T (= BCRC 81189T = LMG 31335T).

scholarly journals Pontibacter mangrovi sp. nov., isolated from mangrove sediment

2020 ◽  
Vol 70 (7) ◽  
pp. 4245-4249 ◽  
Author(s):  
kun-lian Mo ◽  
Ling Wang ◽  
Qing-juan Wu ◽  
Lin Ye ◽  
Xing-di Liu ◽  
...  
Keyword(s):  
Type Species ◽  
Amino Acid Identity ◽  
Polar Lipids ◽  
Mangrove Sediment ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Average Amino Acid Identity

A Gram-stain-negative, short-rod-shaped and pink-pigmented bacterial strain (HB172049T) was isolated from mangrove sediment. Cells grew at 10–45 °C (optimum, 30 °C), pH 6.0–9.0 (optimum, pH 7.0) and with 0.5–9.0 % (w/v) NaCl (optimum, 2–5 %). Analysis of the 16S rRNA gene sequence revealed that the isolate had highest sequence similarities to Pontibacter mucosus DSM 100162T (96.5 %) and Pontibacter korlensis X14-1T (96.5 %). The values of average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization between the isolate and its close neighbours were, respectively, less than 80.1, 81.7 and 23.2 %. Chemotaxonomic analysis indicated that the sole respiratory quinone was MK-7 and the predominant cellular fatty acids were summed feature 4 and iso-C15 : 0 (42.2 and 24.6 %, respectively). The major polar lipids consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, one unidentified glycolipid, one unidentified phospholipid, one unidentified aminophospholipid and two unidentified polar lipids. The genomic DNA G+C content was 52.6 mol%. Based on polyphasic taxonomic characterization, it is proposed that strain HB172049T belongs to the genus Pontibacter and represents a novel species, for which the name Pontibacter mangrovi sp. nov. is proposed. The type strain is HB172049T (=CGMCC 1.16729T=JCM 33333T).

Jannaschia marina sp. nov., isolated from the gut of a gastropod, Onchidium reevesii

2021 ◽  
Author(s):  
Si Chen ◽  
Mengyuan He ◽  
Qiliang Lai ◽  
Ying Xu ◽  
Chenjing Shang
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Chromosomal Dna ◽  
Phenotypic Data ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type

A taxonomic study was carried out on strain SHC163T, which was isolated from the gut of Onchidium reevesii. The bacterium was Gram-stain-negative, oxidase-positive, catalase-negative and rod-shaped. Growth was observed at salinities of 0–4.0 % NaCl and at temperatures of 15–35 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SHC163T belonged to the genus Jannaschia , with the highest sequence similarity to Jannaschia seosinensis CL-SP26T (97.9%), followed by Jannaschia faecimaris DSM 100420T (97.8 %), Jannaschia rubra CECT 5088T (97.5%) and eight species of the genus Jannaschia (94.7−97.1 %). The average amino acid identity, average nucleotide identity and the digital DNA–DNA hybridization estimate values between strain SHC163T and the type strains of the genus Jannaschia were 64.33−79.78 %, 71.0−78.4 % and 19.2−21.0%, respectively. The principal fatty acids (>5 %) were summed feature 8 (C18 : 1  ω7c/C18 : 1  ω6c, 56.5 %), C18 : 1  ω7c 11-methyl (23.1 %), C18 : 0 (8.7 %). The G+C content of the chromosomal DNA was 67.8 mol%. The respiratory quinone was determined to be Q-10 (100 %). The polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid, an unidentified aminolipid and aminophospholipid. The combined genotypic and phenotypic data show that strain SHC163T represents a novel species within the genus Jannaschia , for which the name Jannaschia marina sp. nov. is proposed, with the type strain SHC163T (=MCCC 1K04032T=KCTC 72524T).

Description of Acinetobacter kanungonis sp. nov., based on phylogenomic analysis

2021 ◽  
Vol 71 (6) ◽  
Author(s):  
Lipika Das ◽  
Sushanta Deb ◽  
Subrata K. Das
Keyword(s):  
Sequence Similarity ◽  
Amino Acid Identity ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Average Amino Acid Identity ◽  
Cellular Components ◽  
Reference Strains ◽  
Type Strains

A novel strain of a member of the genus Acinetobacter, strain PS-1T, was isolated from the skin of fresh water pufferfish (Tetraodon cutcutia) collected from Mahanadi River, India. Cells were Gram-stain-negative, aerobic, coccoid and non-motile. The predominant polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE) and phospholipid (PL) and the cell wall sugars were glucose, galactose and ribose. The major cellular fatty acids of PS-1T were C18 : 1ω9c (30.67 %), C16 : 1ω7c (19.54 %), C16 : 0 (15.87 %), C12 : 0 (7.35 %) and C12 : 0 3-OH (6.77 %). The genome size was 3.5 Mbp and the DNA G+C content was 41.97 %. Gene ontology study revealed that the major fraction of genes were associated with biological processes (53.99 %) followed by molecular function (30.42 %) and cellular components (15.58 %). Comparisons of 16S rRNA gene sequences revealed 97.94–97.05 % sequence similarity with the closely related type strains of species of the genus Acinetobacter . The average nucleotide identity (ANI) and average amino acid identity (AAI) of PS-1T with reference strains of species of the genus Acinetobacter with validly published names were bellow 95–96 and the corresponding in-silico DNA–DNA hybridization (DDH) values were below 70 %. A phylogenomic tree based on core genome analysis supported these results. Genotypic and phenotypic characteristics of PS-1T indicate that the strain represents a novel species of the genus Acinetobacter and the name Acinetobacter kanungonis sp. nov. is proposed. The type strain is PS-1T (=JCM 34131T=NCIMB 15260T)

scholarly journals Echinicola Salinicaeni sp. nov., A Novel Bacterium Isolated from Saltern

2021 ◽  
Author(s):  
Han Zhao ◽  
Chun-Yi Song ◽  
Rui Yin ◽  
Yan-Jun Yi ◽  
Shuai-Ting Yun ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Draft Genome ◽  
Carotenoid Biosynthesis ◽  
Amino Acid Identity ◽  
Glycoside Hydrolases ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Resistance Pathway ◽  
Genes Encoding

Abstract A Gram-stain-negative, aerobiotic, pink, motile, rod-shaped bacterium, designated P51 T was isolated from saline silt samples in Yantai, China. The novel isolate was able to grow at 4–42 °C (optimum 33 °C), pH 4.0–9.0 (optimum 7.0) and with 0–11.0% NaCl (optimum 4.0%, w/v). It could grow at 4 °C, which was different from the neighbour strains. The draft genome consisted of 4111 genes with a total length of 5139782 bp and 39.9% G + C content. The 16S rRNA gene sequence analysis indicated that strain P51 T was a member of the genus Echinicola and most closely related to ‘ Echinicola shivajiensis ’ with pair-wise sequence similarity of 97.7%. Genome analysis identified genes encoding proteins relating to carbon source utilization such as glycoside hydrolases and glycosyl transferases; carotenoid biosynthesis pathway and β -lactam resistance pathway were observed. Strain P51 T shared average nucleotide identity value below 84.7%, average amino acid identity value between of 70.8 – 89.3%, digital DNA-DNA hybridization identity of between 17.9–28.2% with the closely related type strains within the genus Echinicola . The sole menaquinone was MK-7; the major fatty acids were iso-C 15:0 , summed feature 3(C 16:1 ω 7 c and/or C 16:1 ω 6 c ), summed feature 4 (anteiso-C 17:1 B and/or iso-C 17:1 I) and summed feature 9 (iso-C 17:1 ω 9 c and/or 10-methyl C 16:0 ); the polar lipids included one phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid, three unidentified aminolipids and one unknown lipid. Based on phenotypic, chemotaxonomic, and phylogenetic analyses, strain P51 T represents a novel species of the genus Echinicola , for which the name Echinicola salinicaeni sp. nov. is proposed. The type strain is P51 T (KCTC 82513 T = MCCC 1K04413 T ).

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).

Genome-based reclassification of Amycolatopsis eurytherma as a later heterotypic synonym of Amycolatopsis thermoflava

2021 ◽  
Author(s):  
Priya Singh ◽  
Princy Hira ◽  
Charu Dogra Rawat ◽  
Rup Lal ◽  
Utkarsh Sood
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Amino Acid Identity ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Taxonomic Assignment ◽  
Content Type ◽  
Link Type ◽  
Average Amino Acid Identity

The present study was carried out to clarify the taxonomic assignment of two closely related Amycolatopsis species. Genomic information for 48 type strains was available at the time of conducting this analysis. Our analysis showed that two species, viz. Amycolatopsis eurytherma Kim et al. 2002 and Amycolatopsis thermoflava Chun et al. 1999, are conspecific. The 16S rRNA gene sequences of the two species possess 98.85 % sequence similarity. Further, whole-genome comparisons showed that A. eurytherma DSM 44348T and A. thermoflava N1165T shared 98.75 % average nucleotide identity, 98.63 % average amino acid identity and 87.8 % digital DNA–DNA hybridization values. These values exceed the threshold values for bacterial species delineation, indicating that they belong to the same species. Further, the phylogenomic analysis based on the core genome of the strains under study confirmed that A. eurytherma DSM 44348T and A. thermoflava N1165T formed a monophyletic clade. Based on this evidence we propose the reclassification of Amycolatopsis eurytherma Kim et al. 2002 as a later heterotypic synonym of Amycolatopsis thermoflava Chun et al. 1999.

scholarly journals Pseudopontixanthobacter vadosimaris gen. nov., sp. nov., isolated from shallow sea near Kueishan Island

2020 ◽  
Vol 70 (12) ◽  
pp. 6444-6449 ◽  
Author(s):  
Jia Sun ◽  
Jiaying Guo ◽  
Ta-Hui Lin ◽  
Xuejin Feng ◽  
Rui Zhang
Keyword(s):  
Type Species ◽  
Amino Acid Identity ◽  
Core Gene ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Link Type ◽  
Average Amino Acid Identity ◽  
The Family ◽  
Ubiquinone 10

A Gram-stain-negative and aerobic bacterial strain, designated as JL3514T, was isolated from surface water of the hydrothermal system around Kueishan Island. The isolate formed red colonies and cells were non-flagellated, rod-shaped and contained methanol-soluble pigments. Growth was observed at 10–50 °C (optimum, 30 °C), at pH 5.0–9.0 (optimum, pH 7.0) and in the presence of 0–9 % (w/v) NaCl (optimum, 2 %). Strain JL3514T was positive for catalase and weakly positive for oxidase. Results of 16S rRNA gene sequence analyses showed highest similarities to species in the family Erythrobacteraceae , namely Croceibacterium atlanticum (96.1 %), Pelagerythrobacter marensis (96.0 %), Tsuneonella rigui (96.0 %) and Altericroceibacterium xinjiangense (96.0 %). Phylogenetic analysis based on core gene sequences revealed that the isolate formed a distinct branch with the related species and it had a lower average amino acid identity value than the suggested threshold for genera boundaries. The major fatty acids (>5 %) were summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c), summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c), C16 : 0, C17 : 1  ω6c, C14 : 0 2-OH and C12 : 0. The dominant polar lipids comprised diphosphatidylglycerol, sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, glycolipid, two unidentified lipids and one unidentified phospholipid. The main respiratory quinones were ubiquinone-10 (95.7 %) and ubiquinone-9 (4.3 %). The DNA G+C content from the genome was 63.0 mol%. Based on the presented data, we consider strain JL3514T to represent a novel genus of the family Erythrobacteraceae , with the name Pseudopontixanthobacter vadosimaris gen. nov., sp. nov. The type strain is JL3514T (=KCTC 62623T=MCCC 1K03561T).

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 .

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