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 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).

Limnovirga soli gen. nov., sp. nov., isolated from river sediment

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Kyung June Yim ◽  
Dong-Hyun Jung ◽  
Seok Won Jang ◽  
Sanghwa Park
Keyword(s):  
Phylogenetic Trees ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Physiological Properties ◽  
Average Amino Acid Identity ◽  
The Family ◽  
Genome Analyses

A cream-coloured, Gram-stain-negative, rod-shaped bacterium, designated strain KSC-6T, was isolated from soil sampled at the Gapcheon River watershed in Daejeon, Republic of Korea. The organism does not require NaCl for growth and grows at pH 6.0–8.0 (optimum, pH 7.0) and 10–37 °C (optimum, 25 °C). Phylogenetic trees based on the 16S rRNA gene sequences reveal that strain KSC-6T belongs to the family Chitinophagaceae within the order Chitinophagales and is most closely related to Panacibacter ginsenosidivorans Gsoil 1550T (95.9% similarity). The genomic DNA G+C content was 38.9 mol%. The major cellular fatty acids (>8 %) of strain KCS-6T were iso-C15:0, iso-C15 : 1 G and iso-C17 : 0 3-OH. The predominant respiratory quinone was menaquinone 7 and the predominant polar lipids were phosphatidylethanolamine, five unidentified aminolipids and two unidentified lipids. Based on genome analyses, low digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity values with closely related genera, and differential chemotaxonomic and physiological properties, we suggest that strain KCS-6T represents a novel species in a new genus in the family Chitinophagaceae , for which the name Limnovirga soli gen. nov., sp. nov. (type strain KCS-6T=KCCM 43337T=NBRC 114336T) is proposed.

scholarly journals Description of Three Novel Members in the Family Geobacteraceae, Oryzomonas japonicum gen. nov., sp. nov., Oryzomonas sagensis sp. nov., and Oryzomonas ruber sp. nov.

2020 ◽  
Vol 8 (5) ◽  
pp. 634 ◽  
Author(s):  
Zhenxing Xu ◽  
Yoko Masuda ◽  
Chie Hayakawa ◽  
Natsumi Ushijima ◽  
Keisuke Kawano ◽  
...  
Keyword(s):  
Housekeeping Genes ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Genomic Comparison ◽  
Novel Genus ◽  
Average Amino Acid Identity ◽  
The Family ◽  
Type Strains ◽  
Core Genes

Bacteria of the family Geobacteraceae are particularly common and deeply involved in many biogeochemical processes in terrestrial and freshwater environments. As part of a study to understand biogeochemical cycling in freshwater sediments, three iron-reducing isolates, designated as Red96T, Red100T, and Red88T, were isolated from the soils of two paddy fields and pond sediment located in Japan. The cells were Gram-negative, strictly anaerobic, rod-shaped, motile, and red-pigmented on agar plates. Growth of these three strains was coupled to the reduction of Fe(III)-NTA, Fe(III) citrate, and ferrihydrite with malate, methanol, pyruvate, and various organic acids and sugars serving as alternate electron donors. Phylogenetic analysis based on the housekeeping genes (16S rRNA gene, gyrB, rpoB, nifD, fusA, and recA) and 92 concatenated core genes indicated that all the isolates constituted a coherent cluster within the family Geobacteraceae. Genomic analyses, including average nucleotide identity and DNA–DNA hybridization, clearly differentiated the strains Red96T, Red100T, and Red88T from other species in the family Geobacteraceae, with values below the thresholds for species delineation. Along with the genomic comparison, the chemotaxonomic features further helped distinguish the three isolates from each other. In addition, the lower values of average amino acid identity and percentage of conserved protein, as well as biochemical differences with their relatives, indicated that the three strains represented a novel genus in the family Geobacteraceae. Hence, we concluded that strains Red96T, Red100T, and Red88T represented three novel species of a novel genus in the family Geobacteraceae, for which the names Oryzomonas japonicum gen. nov., sp. nov., Oryzomonas sagensis sp. nov., and Oryzomonas ruber sp. nov. are proposed, with type strains Red96T (= NBRC 114286T = MCCC 1K04376T), Red100T (= NBRC 114287T = MCCC 1K04377T), and Red88T (= MCCC 1K03694T = JCM 33033T), respectively.

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 Phylogenetic relationships among haloalkaliphilic archaea of the family Natrialbaceae

2020 ◽  
Author(s):  
Shivakumara Siddaramappa
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Novel Species ◽  
Single Species ◽  
Amino Acid Identity ◽  
Average Nucleotide Identity ◽  
Acid Identity ◽  
Average Amino Acid Identity ◽  
The Family ◽  
Clade 1

ABSTRACTThe family Natrialbaceae is a member of the class Halobacteria of the archaeal phylum Euryarchaeota. Seventeen genera with validly or effectively published names are currently included within this family. In this study, using pairwise average nucleotide identity and average amino acid identity comparisons in conjunction with phylogenetic analysis, it has been shown that the family Natrialbaceae is highly diverse and contains several potentially novel species and genera that are yet to be fully characterized. The deduced proteome sequence-based phylogenetic tree, constructed using the alignment- and parameter-free method CVTree3, contained six major clades, with Salinarchaeum sp. Harcht-Bsk1 being the only representative within clade 1. Furthermore, Haloterrigena daqingensis was found to be closely related to Natronorubrum sediminis, and it is proposed that these archaea together represent a novel genus. Interestingly, Haloterrigena jeotgali, Haloterrigena thermotolerans, and Natrinema pellirubrum were found to be very closely related to each other, and it is proposed that they be merged into a single species. Notably, the type genus Natrialba itself appeared to be heterogenous and contains species that could be broadly classified among two genera. Likewise, the genus Natrinema is also heterogenous and contains species that could be classified among six genera. Altogether, 19 novel genera have been proposed to be created, and four haloalkaliphilic archaea hitherto recognized only using genus names are confirmed to represent novel species.

scholarly journals Draft Genome Sequence of Clinical Isolate Alcaligenaceae sp. Strain 429

2019 ◽  
Vol 8 (19) ◽  
Author(s):  
Michael J. Zilliox ◽  
Paul C. Schreckenberger ◽  
Catherine Putonti
Keyword(s):  
Amino Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Draft Genome ◽  
Amino Acid Identity ◽  
Unknown Etiology ◽  
Rrna Gene ◽  
Acid Identity ◽  
Average Amino Acid Identity ◽  
The 16S Rrna Gene

Here, we present the 3.53-Mb genome for Alcaligenaceae sp. strain 429, isolated from a patient with unknown etiology. While the 16S rRNA gene most closely resembles Paenalcaligenes species, average amino acid identity (AAI) analysis did not meet the threshold to classify our strain as a species of this family.

scholarly journals Phylotaxogenomics for the Reappraisal of the Genus Roseomonas With the Creation of Six New Genera

2021 ◽  
Vol 12 ◽  
Author(s):  
Anusha Rai ◽  
Uppada Jagadeeshwari ◽  
Gupta Deepshikha ◽  
Nandardhane Smita ◽  
Chintalapati Sasikala ◽  
...  
Keyword(s):  
Amino Acid Identity ◽  
Rrna Gene ◽  
Significant Group ◽  
Pan Genome ◽  
Phylogenetic Studies ◽  
Average Amino Acid Identity ◽  
The Family ◽  
Phylogenetic Framework ◽  
Ecological Importance ◽  
Core Genes

The genus Roseomonas is a significant group of bacteria which is invariably of great clinical and ecological importance. Previous studies have shown that the genus Roseomonas is polyphyletic in nature. Our present study focused on generating a lucid understanding of the phylogenetic framework for the re-evaluation and reclassification of the genus Roseomonas. Phylogenetic studies based on the 16S rRNA gene and 92 concatenated genes suggested that the genus is heterogeneous, forming seven major groups. Existing Roseomonas species were subjected to an array of genomic, phenotypic, and chemotaxonomic analyses in order to resolve the heterogeneity. Genomic similarity indices (dDDH and ANI) indicated that the members were well-defined at the species level. The Percentage of Conserved Proteins (POCP) and the average Amino Acid Identity (AAI) values between the groups of the genus Roseomonas and other interspersing members of the family Acetobacteraceae were below 65 and 70%, respectively. The pan-genome evaluation depicted that the pan-genome was an open type and the members shared 958 core genes. This claim of reclassification was equally supported by the phenotypic and chemotaxonomic differences between the groups. Thus, in this study, we propose to re-evaluate and reclassify the genus Roseomonas and propose six novel genera as Pararoseomonas gen. nov., Falsiroseomonas gen. nov., Paeniroseomonas gen. nov., Plastoroseomonas gen. nov., Neoroseomonas gen. nov., and Pseudoroseomonas gen. nov.

Permianibacter fluminis sp. nov., isolated from a freshwater stream

2021 ◽  
Vol 71 (4) ◽  
Author(s):  
Miri S. Park ◽  
Jaeho Song ◽  
Jaeho Chang ◽  
Yochan Joung ◽  
Ilnam Kang ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Draft Genome ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Freshwater Stream

A Gram-stain-negative, aerobic, non-motile and rod-shaped bacterium, designated as IMCC34836T, was isolated from a freshwater stream. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain IMCC34836T was most closely related to Permianibacter aggregans HW001T (of the family Pseudomonadaceae ) with 95.6 % sequence similarity and formed a robust clade with P. aggregans HW001T. The draft genome sequence of strain IMCC34836T was 4.4 Mbp in size with 59.1 mol% DNA G+C content. Average nucleotide identity and digital DNA–DNA hybridization values between strain IMCC34836T and P. aggregans HW001T were 71.2 and 22.0 %, respectively, indicating that the new strain represents a novel species. The strain contained iso-C15 : 0, summed feature 3 (C16 : 1  ω6c and/or C16 : 1  ω7c) and summed feature 9 (iso-C17 : 1  ω9c and/or C16 : 1 10-methyl) as the major fatty acids and harboured phosphatidylethanolamine, two unidentified aminophospholipids and three unidentified lipids as major polar lipids. The isoprenoid quinone detected in the strain was ubiquinone-8. Based on the phylogenetic and phenotypic characteristics, strain IMCC34836T is considered to represent a novel species of the genus Permianibacter , for which the name Permianibacter fluminis sp. nov. is proposed. The type strain is IMCC34836T (=KACC 21755T=NBRC 114416T).

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).

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