scholarly journals Comparative genomics of Parolsenella catena and Libanicoccus massiliensis: Reclassification of Libanicoccus massiliensis as Parolsenella massiliensis comb. nov.

2019 ◽  
Vol 69 (4) ◽  
pp. 1123-1129 ◽  
Author(s):  
Mitsuo Sakamoto ◽  
Nao Ikeyama ◽  
Takumi Murakami ◽  
Hiroshi Mori ◽  
Masahiro Yuki ◽  
...  
Keyword(s):  
Ribosomal Proteins ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Single Copy ◽  
Content Type ◽  
Monophyletic Cluster ◽  
Link Type ◽  
Relationship Of ◽  
High Degree ◽  
The Relationship

Previous analyses based on 16S rRNA and hsp60 genes indicated that Parolsenella catena and Libanicoccus massiliensis were closely related to each other and formed a monophyletic cluster independent of the related Olsenella species. To clarify the relationship of these two species, we determined the genome sequence of P. catena JCM 31932T and compared it with that already sequenced for L. massiliensis Marseille-P3237T. Phylogenetic trees based on the concatenated 37 single-copy ribosomal proteins or RpoB robustly supported the relationship observed in the previous studies. Digital DNA–DNA hybridization and average nucleotide identity (ANI) values between P. catena JCM 31932T and L. massiliensis Marseille-P3237T were 32.6 and 87.8 %, respectively, indicating that P. catena JCM 31932T and L. massiliensis Marseille-P3237T are independent species. Alignment fraction and ANI values between the two genomes were 0.75 and 88.84 %, respectively, thus indicating that the two species should be classified into the same genus. The number of putative orthologous genes shared between the two genomes was 1321, which was significantly larger than those (482–928) reported between L. massiliensis Marseille-P3237T and other closely related species. In addition, the genome of P. catena JCM 31932T had a high degree of synteny conservation with that of L. massiliensis Marseille-P3237T. On the basis of these findings, we propose that L. massiliensis should be reclassified as Parolsenella massiliensis comb. nov.; the type strain is Marseille-P3237T (=JCM 33000T=CCUG 71182T).

Nocardioides baculatus sp. nov., a novel actinomycete isolated from the rhizosphere of Tagetes patula

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Geeta Chhetri ◽  
Inhyup Kim ◽  
Minchung Kang ◽  
Jiyoun Kim ◽  
Yoonseop So ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Trees ◽  
Novel Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Tagetes Patula ◽  
Content Type ◽  
Monophyletic Cluster ◽  
Link Type ◽  
16S Rna

An aerobic, Gram-stain-positive, non-motile, dull-yellow, short rod-shaped actinomycete strain, designated G10T, was isolated from Tagetes patula (marigold) roots collected from Goyang in the Republic of Korea. The isolate showed best growth on Reasoner's 2A agar at 25 °C, pH 6.5.0 and with 0% NaCl (w/v). The strain was negative for oxidase activity and positive for catalase activity. On the basis of 16S RNA gene sequence similarity, strain G10T was affiliated to the genus Nocardioides and the closest species were Nocardioides glacieisoli HLT3-15T (98.8 %), Nocardioides zhouii HLT2-9T (98.8 %), Nocardioides ganghwensis JC2055T (98.7 %), Nocardioides cavernae YIM A1136T (98.6 %), Nocardioides flavus Y4T (98.5 %), Nocardioides oleivorans DSM 16090T (98.3 %), Nocardioides alpinus Cr7-14T (98.2 %), Nocardioides exalbidus DSM 22017T (98.1 %) and Nocardioides hwasunensis KCTC 19197T (98.1 %). Strain G10T formed a monophyletic cluster with N. glacieisoli HLT3-15T, N. zhouii HLT2-9T and N. hwasunensis KCTC 19197T in all phylogenetic trees. The cell-wall peptidoglycan of strain G10T contained ll-diaminopimelic acid as the diagnostic amino acid. The predominant fatty acids were iso-C16 : 0 and C17 : 1  ω8c. MK-8(H4) was the major isoprenoid quinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. Average nucleotide identity and digital DNA–DNA hybridization values were 78.6–88.7 % and 21.5–36.2 %, respectively, with the type strains of related species of the genus Nocardioides , suggesting that strain G10T represents a novel species. The genome of strain G10T is 4 231 000 bp long with a DNA G+C content of 71.5 mol% and encodes 4071 predicted proteins, six rRNAs and 46 tRNAs. The genome of strain G10T comprises the biosynthetic gene cluster for T3PKS, terpene, NRPS-like fragment and RRE-containing element as secondary metabolites. The results of taxonomic, phylogenetic, biochemical, chemotaxonomic and genomic analysis clearly supported that strain G10T represent a novel species within the genus Nocardioides , for which the name Nocardioides baculatus sp. nov is proposed and the type strain is G10T (=KCTC 49626T=NBRC 114801T).

scholarly journals Pseudoseohaeicola caenipelagi gen. nov., sp. nov., isolated from a tidal flat

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1819-1824 ◽  
Author(s):  
Sooyeon Park ◽  
Ji-Min Park ◽  
Chul-Hyung Kang ◽  
Song-Gun Kim ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Strain ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, non-motile, aerobic and pleomorphic bacterium, designated BS-W13T, was isolated from a tidal flat on the South Sea, South Korea, and its taxonomic position was investigated using a polyphasic approach. Strain BS-W13T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 1.0–2.0 % (w/v) NaCl. Neighbour-joining and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain BS-W13T clustered with the type strain of Seohaeicola saemankumensis , showing the highest sequence similarity (95.96 %) to this strain. Strain BS-W13T exhibited 16S rRNA gene sequence similarity values of 95.95, 95.91, 95.72 and 95.68 % to the type strains of Sulfitobacter donghicola , Sulfitobacter porphyrae , Sulfitobacter mediterraneus and Roseobacter litoralis , respectively. Strain BS-W13T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The polar lipid profile of strain BS-W13T, containing phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid as major components, was distinguishable from those of some phylogenetically related taxa. The DNA G+C content of strain BS-W13T was 58.1 mol%. The phylogenetic data and differential chemotaxonomic and other phenotypic properties revealed that strain BS-W13T constitutes a novel genus and species within family Rhodobacteraceae of the class Alphaproteobacteria , for which the name Pseudoseohaeicola caenipelagi gen. nov., sp. nov. is proposed. The type strain is BS-W13T ( = KCTC 42349T = CECT 8724T).

scholarly journals Belliella aquatica sp. nov., isolated from a saline lake

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1622-1627 ◽  
Author(s):  
Zhi-Ping Zhong ◽  
Ying Liu ◽  
Ting-Ting Hou ◽  
Yu-Guang Zhou ◽  
Hong-Can Liu ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Trees ◽  
Saline Lake ◽  
Qaidam Basin ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Gram Staining

A Gram-staining-negative bacterium, strain TS-T86T, was isolated from Lake Tuosu, a saline lake (salinity 5.4 %, w/w) in Qaidam basin, China. Its taxonomic position was determined by using a polyphasic approach. Strain TS-T86T was strictly heterotrophic, aerobic and catalase- and oxidase-positive. Cells were non-spore-forming, non-motile rods, 0.4–0.6 µm wide and 1.2–2.3 µm long. Growth was observed in the presence of 0–9.0 % (w/v) NaCl (optimum, 2.0 %), at 4–35 °C (optimum, 25 °C) and at pH 7.0–10.5 (optimum, pH 8.5–9.0). Strain TS-T86T contained MK-7 as the predominant respiratory quinone. The major fatty acids (>10 %) were iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 1ω9c, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The polar lipids consisted of phosphatidylethanolamine, an unknown phospholipid, six unidentified aminolipids and two uncharacterized lipids. The DNA G+C content was 35 mol% (T m). Phylogenetic trees based on 16S rRNA gene sequences showed that strain TS-T86T was associated with the genus Belliella , and showed the highest sequence similarity to Belliella baltica BA134T (98.5 %) and then to Belliella kenyensis No.164T (95.7 %) and Belliella pelovolcani CC-SAL-25T (95.3 %). DNA–DNA relatedness of strain TS-T86T to Belliella baltica DSM 15883T was 32±3 %. It is concluded that strain TS-T86T represents a novel species of the genus Belliella , for which the name Belliella aquatica sp. nov. is proposed. The type strain is TS-T86T ( = CGMCC 1.12479T = JCM 19468T).

scholarly journals Amedibacterium intestinale gen. nov., sp. nov., isolated from human faeces, and reclassification of Eubacterium dolichum Moore et al. 1976 (Approved Lists 1980) as Amedibacillus dolichus gen. nov., comb. nov

2020 ◽  
Vol 70 (6) ◽  
pp. 3656-3664 ◽  
Author(s):  
Nao Ikeyama ◽  
Atsushi Toyoda ◽  
Sho Morohoshi ◽  
Tadao Kunihiro ◽  
Takumi Murakami ◽  
...  
Keyword(s):  
In Silico ◽  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Monophyletic Cluster ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Faecal Samples

Four strains (9CBEGH2T, 9BBH35, 6BBH38 and 6EGH11) of Gram-stain-positive, obligately anaerobic, rod-shaped bacteria were isolated from faecal samples from healthy Japanese humans. The results of 16S rRNA gene sequence analysis indicated that the four strains represented members of the family Erysipelotrichaceae and formed a monophyletic cluster with ‘ Absiella argi ’ strain N6H1-5 (99.4% sequence similarity) and Eubacterium sp. Marseille-P5640 (99.3 %). Eubacterium dolichum JCM 10413T (94.2 %) and Eubacterium tortuosum ATCC 25548T (93.7 %) were located near this monophyletic cluster. The isolates, 9CBEGH2T, ‘ A. argi ’ JCM 30884 and Eubacterium sp. Marseille-P5640 shared 98.7–99.1% average nucleotide identity (ANI) with each other. Moreover, the in silico DNA–DNA hybridization (DDH) values among three strains were 88.4–90.6%, indicating that these strains represent the same species. Strain 9CBEGH2T showed 21.5–24.1 % in silico DDH values with other related taxa. In addition, the ANI values between strain 9CBEGH2T and other related taxa ranged from 71.2 % to 73.5 %, indicating that this strain should be considered as representing a novel species on the basis of whole-genome relatedness. Therefore, we formally propose a novel name for ‘ A. argi ’ strains identified because the name ‘ A. argi ’ has been effectively, but not validly, published since 2017. On the basis of the collected data, strain 9CBEGH2T represents a novel species of a novel genus, for which the name Amedibacterium intestinale gen. nov., sp. nov. is proposed. The type strain of A. intestinale is 9CBEGH2T (=JCM 33778T=DSM 110575T).

Kangiella sediminilitoris sp. nov., isolated from a tidal flat sediment

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1001-1006 ◽  
Author(s):  
Soo-Young Lee ◽  
Sooyeon Park ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Tidal Flat Sediment

A Gram-stain-negative, non-motile, non-spore-forming, rod-shaped bacterial strain, BB-Mw22T, was isolated from a tidal flat sediment of the South Sea in South Korea. It grew optimally at 30–37 °C, at pH 7.0–7.5 and in the presence of 2–3 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain BB-Mw22T belonged to the genus Kangiella and the cluster comprising Kangiella species and strain BB-Mw22T was clearly separated from other taxa. Strain BB-Mw22T exhibited 95.3–98.7 % 16S rRNA gene sequence similarity to the type strains of recognized Kangiella species. Strain BB-Mw22T contained Q-8 as the predominant ubiquionone and iso-C15 : 0 and iso-C11 : 0 3-OH as the major fatty acids. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine and one unidentified aminolipid. The DNA G+C content of strain BB-Mw22T was 48.9 mol%, and its mean DNA–DNA hybridization values with Kangiella geojedonensis YCS-5T, Kangiella japonica JCM 16211T and Kangiella taiwanensis JCM 17727T were 14–28 %. Phylogenetic and genetic distinctiveness and differential phenotypic properties revealed that strain BB-Mw22T is distinguishable from all recognized Kangiella species. On the basis of the data presented, strain BB-Mw22T is considered to represent a novel species of the genus Kangiella , for which the name Kangiella sediminilitoris sp. nov. is proposed. The type strain is BB-Mw22T ( = KCTC 23892T  = CCUG 62217T).

scholarly journals Aestuariispira insulae gen. nov., sp. nov., a lipolytic bacterium isolated from a tidal flat

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1841-1846 ◽  
Author(s):  
Sooyeon Park ◽  
Ji-Min Park ◽  
Chul-Hyung Kang ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Strain ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-stain-negative, non-motile, aerobic, curved-to-spiral-rod-shaped bacterium, designated AH-MY2T, was isolated from a tidal flat on Aphae island in the sea to the south-west of South Korea, and its taxonomic position was investigated using a polyphasic taxonomic approach. Strain AH-MY2T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain AH-MY2T clustered with the type strain of Terasakiella pusilla and that this cluster joined the clade comprising the type strains of species of the genus Thalassospira . Strain AH-MY2T exhibited 16S rRNA gene sequence similarity values of 90.6 % to the type strain of Terasakiella pusilla and of less than 91.0 % to the type strains of other species with validly published names. Strain AH-MY2T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The major polar lipids detected in strain AH-MY2T were phosphatidylglycerol, phosphatidylethanolamine, two unidentified aminolipids and one unidentified glycolipid. The DNA G+C content of strain AH-MY2T was 56.0 mol%. The phylogenetic data and differential chemotaxonomic and other phenotypic properties revealed that strain AH-MY2T represented a novel genus and species within the family Rhodospirillaceae of the class Alphaproteobacteria , for which the name Aestuariispira insulae gen. nov., sp. nov. is proposed. The type strain of Aestuariispira insulae is AH-MY2T ( = KCTC 32577T = CECT 8488T).

scholarly journals Sulfitobacter undariae sp. nov., isolated from a brown algae reservoir

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1672-1678 ◽  
Author(s):  
Sooyeon Park ◽  
Yong-Taek Jung ◽  
Sung-Min Won ◽  
Ji-Min Park ◽  
Jung-Hoon Yoon
Keyword(s):  
Brown Algae ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-stain-negative, aerobic, non-spore-forming, non-flagellated and coccoid, ovoid or rod-shaped bacterial strain, W-BA2T, was isolated from a brown algae reservoir in Wando of South Korea. Strain W-BA2T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of approximately 2.0–3.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain W-BA2T fell within the clade comprising the type strains of species of the genus Sulfitobacter , clustering coherently with the type strains of Sulfitobacter donghicola and Sulfitobacter guttiformis showing sequence similarity values of 98.0–98.1 %. Sequence similarities to the type strains of the other species of the genus Sulfitobacter were 96.0–97.4 %. Strain W-BA2T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The major polar lipids of strain W-BA2T were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain W-BA2T was 55.0 mol% and its DNA–DNA relatedness values with the type strains of Sulfitobacter donghicola , Sulfitobacter guttiformis and Sulfitobacter mediterraneus were 16–23 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain W-BA2T is separated from other species of the genus Sulfitobacter . On the basis of the data presented, strain W-BA2T is considered to represent a novel species of the genus Sulfitobacter , for which the name Sulfitobacter undariae sp. nov. is proposed. The type strain is W-BA2T ( = KCTC 42200T = NBRC 110523T).

scholarly journals Tepidiphilus olei sp. nov., isolated from the production water of a water-flooded oil reservoir in PR China

2020 ◽  
Vol 70 (7) ◽  
pp. 4364-4371 ◽  
Author(s):  
Xiao-Tong Wang ◽  
Jian-Jie Shan ◽  
Xi-Zhe Li ◽  
Wei Lin ◽  
Jian-Long Xiu ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Oil Reservoir ◽  
Separate Species ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Moderately Thermophilic ◽  
Link Type

A novel, moderately thermophilic, Gram-stain-negative bacterium, designated strain J18T, was isolated from a water-flooded oil reservoir. Cells were aerobic, oxidase- and catalase-positive, with a polar flagellum. Growth occurred at 35–60 °C and at pH 6–8.5. The respiratory quinones were ubiquinone 8 and ubiquinone 9. The dominant cellular fatty acids were C16 : 0, C17 : 0 cyclo, C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1  ω7c/C18 : 1  ω6c). The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid, an unidentified phospholipid and an unidentified aminophospholipid. The strain showed the highest 16S rRNA gene sequence similarities to Tepidiphilus margaritifer DSM 15129T (98.6 %), Tepidiphilus succinatimandens DSM 15512T (98.4 %) and Tepidiphilus thermophilus DSM 27220T (98.1 %), respectively, and the similarity to other species was lower than 93 %. In the phylogenetic trees, it constituted a unique sub-cluster within the genus Tepidiphilus . The DNA G+C content of strain J18T was 64.44 mol%. As compared with the type strains, the genome-to-genome distances of strain J18T were 34.7–40 %. These results confirmed the separate species status of J18T with its close relatives. On the basis of physiological, chemotaxonomic and phylogenetic analyses along with the low levels of identity at the whole-genome level, it can be concluded that strain J18T represents a new species of the genus Tepidiphilus , for which the name Tepidiphilus olei sp. nov. is proposed. The type strain of T. olei is J18T (=CGMCC 1.16800T=LMG 31400T).

scholarly journals Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species

2020 ◽  
Vol 70 (11) ◽  
pp. 5753-5798 ◽  
Author(s):  
Radhey S. Gupta ◽  
Sudip Patel ◽  
Navneet Saini ◽  
Shu Chen
Keyword(s):  
Type Species ◽  
Phylogenetic Trees ◽  
Bacillus Species ◽  
Comparative Genomic ◽  
Molecular Evidence ◽  
Content Type ◽  
Link Type ◽  
Conserved Signature Indels ◽  
Genomic Scale

To clarify the evolutionary relationships and classification of Bacillus species, comprehensive phylogenomic and comparative analyses were performed on >300 Bacillus/Bacillaceae genomes. Multiple genomic-scale phylogenetic trees were initially reconstructed to identify different monophyletic clades of Bacillus species. In parallel, detailed analyses were performed on protein sequences of genomes to identify conserved signature indels (CSIs) that are specific for each of the identified clades. We show that in different reconstructed trees, most of the Bacillus species, in addition to the Subtilis and Cereus clades, consistently formed 17 novel distinct clades. Additionally, some Bacillus species reliably grouped with the genera Alkalicoccus, Caldalkalibacillus, Caldibacillus, Salibacterium and Salisediminibacterium . The distinctness of identified Bacillus species clades is independently strongly supported by 128 identified CSIs which are unique characteristics of these clades, providing reliable means for their demarcation. Based on the strong phylogenetic and molecular evidence, we are proposing that these 17 Bacillus species clades should be recognized as novel genera, with the names Alteribacter gen. nov., Ectobacillus gen. nov., Evansella gen. nov., Ferdinandcohnia gen. nov., Gottfriedia gen. nov., Heyndrickxia gen. nov., Lederbergia gen. nov., Litchfieldia gen. nov., Margalitia gen. nov., Niallia gen. nov., Priestia gen. nov., Robertmurraya gen. nov., Rossellomorea gen. nov., Schinkia gen. nov., Siminovitchia gen. nov., Sutcliffiella gen. nov. and Weizmannia gen. nov. We also propose to transfer ‘ Bacillus kyonggiensi s’ to Robertmurraya kyonggiensis sp. nov. (type strain: NB22=JCM 17569T=DSM 26768). Additionally, we report 31 CSIs that are unique characteristics of either the members of the Subtilis clade (containing the type species B. subtilis ) or the Cereus clade (containing B. anthracis and B. cereus ). As most Bacillus species which are not part of these two clades can now be assigned to other genera, we are proposing an emended description of the genus Bacillus to restrict it to only the members of the Subtilis and Cereus clades.

scholarly journals Duganella lactea sp. nov., Duganella guangzhouensis sp. nov., Duganella flavida sp. nov. and Massilia rivuli sp. nov., isolated from a subtropical stream in PR China and proposal to reclassify Duganella ginsengisoli as Massilia ginsengisoli comb. nov.

2020 ◽  
Vol 70 (8) ◽  
pp. 4822-4830 ◽  
Author(s):  
Huibin Lu ◽  
Tongchu Deng ◽  
Feifei Liu ◽  
Yonghong Wang ◽  
Xunan Yang ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Trees ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Pr China ◽  
Subtropical Stream

Five Gram-stain-negative, catalase- and oxidase-positive, rod-shaped and motile strains (FT50WT, FT80WT, FT92WT, FT94W and FT135WT) were isolated from a subtropical stream in PR China. Comparisons based on 16S rRNA gene sequences showed that strains FT50WT, FT94W and FT135WT take strain Duganella sacchari Sac-22T, and strains FT80WT and FT92WT take strain Duganella ginsengisoli DCY83T as their closest neighbour in the phylogenetic trees, respectively. The G+C contents of strains FT50WT, FT80WT, FT92WT, FT94W and FT135WT were 63.3, 62.4, 62.8, 63.8 and 60.8 %, respectively. The reconstructed phylogenomic tree based on concatenated 92 core genes showed that strains FT50WT, FT80WT, FT94W and FT135WT clustered together with species of the genus Duganella , but strains FT92WT and D. ginsengisoli KCTC 42409T were located in the clades of the genus Massilia . The calculated pairwise average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values among strains FT50WT, FT80WT, FT92WT, FT94W, FT135WT and related strains were in the ranges of 75.6–87.8% and 20.3–33.8% except that the values between strains FT50WT and FT94W were 98.7 and 89.2%, respectively. The respiratory quinone of these five strains was Q-8. The major fatty acids were C16 : 1  ω7c, C16 : 0, C18 : 1  ω7c and C12 : 0. The polar lipids included phosphatidylethanolamine, phosphatidylglycerol and one unidentified phospholipid. Considering the distinct phylogenetic relationships of D. ginsengisoli with species of the genus Massilia in the phylogenomic tree, it was reasonable to transfer D. ginsengisoli to the genus Massilia as Massilia ginsengisoli comb. nov. Combining the results of phylogenomic analysis, ANI and dDDH data, and a range of physiological and biochemical characteristics together, strains FT50WT and FT94W should belong to the same species and be assigned to genus Duganella with strains FT80WT and FT135WT together, and strain FT92WT should be assigned to the genus Massilia , for which the names Duganella lactea sp. nov. (type strain FT50WT=GDMCC 1.1674T=KACC 21466T), Duganella guangzhouensis sp. nov. (FT80WT=GDMCC 1.1678T=KACC 21470T), Duganella flavida sp. nov. (FT135WT=GDMCC 1.1745T=KACC 21659T) and Massilia rivuli sp. nov. (FT92WT=GDMCC 1.1682T=KACC 21474T) are proposed.

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