Eikenella glucosivorans sp. nov., isolated from a human throat swab, and emendation of the genus Eikenella to include saccharolytic species

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Silvio Hering ◽  
Moritz K. Jansson ◽  
Michael E. J. Buhl
Keyword(s):  
Type Species ◽  
Throat Swab ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Routine Care ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Bacterium Strain

A novel species within the genus Eikenella is described, based on the phenotypical, biochemical and genetic characterization of a strain of a facultatively anaerobic, Gram-negative rod-shaped bacterium. Strain S3360T was isolated from the throat swab of a patient sampled during routine care at a hospital. Phylogenetic analyses (full-length 16S rRNA gene and whole-genome sequences) placed the strain in the genus Eikenella , separate from all recognized species but with the closest relationship to Eikenella longinqua (NML 02-A-017T). Eikenella is one of the genera in the HACEK group known to be responsible for rare cases of endocarditis in humans. Until the recent descriptions of Eikenella exigua , Eikenella halliae and Eikenella longinqua , Eikenella corrodens had been the only validly published species in this genus since its description as Bacteroides corrodens in 1958. Unlike these species, strain S3360T is able to metabolize carbohydrates (glucose). The average nucleotide identities of strain S3360T with E. longinqua (NML 02-A-017T) and E. corrodens (NCTC 10596T), the type species of the genus, were 90.5 and 84.7 %, respectively, and the corresponding genome-to-genome distance values were 41.3 and 29.0 %, respectively. The DNA G+C content of strain S3360T was 58.4 mol%. Based on the phenotypical, biochemical and genetic findings, strain S3360T is considered to represent a novel species within the genus Eikenella , for which the name Eikenella glucosivorans sp. nov. is proposed. The type strain is S3360T (DSM 110714T=CCOS 1935T=CCUG 74293T). In addition, an emendation of the genus Eikenella is proposed to include species which are saccharolytic.

Acidovorax antarcticus sp. nov., isolated from a soil sample of Collins Glacier front, Antarctica

2021 ◽  
Author(s):  
Qiang Xu ◽  
Xiaoya Peng ◽  
Yanhong Wang ◽  
Lu Lu ◽  
Yongping Zhang ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Fildes Peninsula ◽  
Content Type ◽  
Link Type ◽  
Glacier Front ◽  
Bacterium Strain ◽  
Sequence Similarities

A Gram-stain-negative, rod-shaped, and aerobic bacterium, strain 16-35-5T, was isolated from Collins Glacier front soil from the Fildes Peninsula, Antarctica. The bacterium grew optimally at 28 °C, pH 7.0 and in the presence of 0–4.0 % (w/v) NaCl. On the basis of the results of 16S rRNA gene sequence phylogenetic analyses, it was concluded that 16-35-5T represented a member of the genus Acidovorax and had the highest sequence similarities with Acidovorax anthurii CFBP 3232T (96.48 %). The genome of 16-35-5T is 4.2 Mb long with a DNA G+C content of 66.3 mol%. Average nucleotide identity (ANI) value between the genomes of 16-35-5T and Acidovorax wautersii DSM 27981T, was 85.29 %. Strain 16-35-5T had ubiquinone-8 (Q-8) as the respiratory ubiquinone. The polar lipids of 16-35-5T were consisted of phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The main fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c, 25.2 %), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c, 12.9 %), C16 : 0 (35.2 %), and C17 : 0 cyclo (19.0 %). On the basis of the evidence presented in this study, 16-35-5T should be classified as representing a novel species of the genus Acidovorax , for which the name Acidovorax antarcticus sp. nov., is proposed, with the type strain 16-35-5T (=CCTCC AB 2019325T=KCTC 72915T).

scholarly journals Chitinimonas viridis sp. nov., isolated from a mesotrophic artificial lake

2014 ◽  
Vol 64 (Pt_4) ◽  
pp. 1123-1126 ◽  
Author(s):  
Yochan Joung ◽  
Beom-Il Lee ◽  
Heeyoung Kang ◽  
Haneul Kim ◽  
Kiseong Joh
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Artificial Lake ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Bacterium Strain

A Gram-staining-negative, rod-shaped bacterium, strain HMD2169T, was isolated from a mesotrophic artificial lake in Korea. Strain HMD2169T grew in the presence of 0–3.0 % (w/v) NaCl, at pH 5–10 and at 20–37 °C. The predominant quinone of strain HMD2169T was ubiquinone (UQ)-8. The major fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, two unidentified aminolipids and two unidentified lipids. The DNA G+C content was 59.8 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HMD2169T was a representative of a lineage within the genus Chitinimonas . Strain HMD2169T was closely related to Chitinimonas taiwanensis (95.8 % sequence similarity) and Chitinimonas koreensis (94.6 %). On the basis of the evidence presented in this study, strain HMD2169T is a representative of a novel species of the genus Chitinimonas , for which the name Chitinimonas viridis sp. nov. is proposed with the type strain HMD2169T ( = KCTC 22839T = CECT 7703T).

Methylobacterium gnaphalii sp. nov., isolated from leaves of Gnaphalium spicatum

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2602-2607 ◽  
Author(s):  
Akio Tani ◽  
Nurettin Sahin ◽  
Kazuhide Kimbara
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Methylotrophic Bacterium ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Content Type ◽  
Link Type ◽  
Cell Matrix ◽  
Bacterium Strain

A pink-pigmented, facultatively methylotrophic bacterium, strain 23eT, was isolated from the leaves of Gnaphalium spicatum (cudweed). The cells of strain 23eT were Gram-reaction negative, motile and non-spore-forming rods. On the basis of 16S rRNA gene sequence similarities, strain 23eT was related to Methylobacterium organophilum ATCC 27886T (97.1 %) and Methylobacterium marchantiae JT1T (97 %), and the phylogenetic similarities to all other Methylobacterium species with validly published names were less than 97 %. Major cellular fatty acids were C18 : 1ω7c, C16 : 00 and C18 : 0. The results of DNA–DNA hybridization, phylogenetic analyses based on 16S rRNA and cpn60 gene sequences, fatty acid profiles, whole-cell matrix-assisted laser desorption/ionization time of flight/MS analysis, physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 23eT from the phylogenetically closest relatives. We propose that strain 23eT represents a novel species within the genus Methylobacterium , for which the name Methylobacterium gnaphalii sp. nov. is proposed. The type strain is 23eT ( = DSM 24027T = NBRC 107716T).

Corynebacterium zhongnanshanii sp. nov. isolated from trachea of Marmota himalayana, Corynebacterium lujinxingii sp. nov. and Corynebacterium wankanglinii sp. nov. from human faeces

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Gui Zhang ◽  
Jing Yang ◽  
Xin-He Lai ◽  
Dong Jin ◽  
Shan Lu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Human Faeces ◽  
Link Type ◽  
Gene Similarity

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).

Chitinibacter bivalviorum sp. nov., isolated from the gut of the freshwater mussel Anodonta arcaeformis

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Jee-Won Choi ◽  
Jae-Yun Lee ◽  
Dong-Wook Hyun ◽  
June-Young Lee ◽  
Pil Soo Kim ◽  
...  
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Freshwater Mussel ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Republic ◽  
Genotypic Characteristics

A novel Gram-stain-negative, aerobic, rod-shaped bacterium with a single polar flagellum, designated strain 2T18T, was isolated from the gut of the freshwater mussel Anodonta arcaeformis collected in the Republic of Korea. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain belonged to the genus Chitinibacter . Strain 2T18T formed a monophyletic clade with Chitinibacter fontanus KCTC 42982T, C. tainanensis KACC 11706T and C. alvei KCTC 23839T, with sequence similarities of 98.5, 98.4 and 95.9 %, respectively. Strain 2T18T exhibited optimal growth at 30 °C, at pH 8 and with 0.5 % (w/v) NaCl. The major isoprenoid quinone was ubiquinone-8 (Q-8). The predominant fatty acids were summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and C16 : 0. The polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified lipid, three unidentified phospholipids and two unidentified aminophospholipids. The G+C content of the genomic DNA was 50.6 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between strains 2T18T and C. fontanus KCTC 42982T were below the thresholds used for the delineation of a novel species. Based on the phylogenetic, phenotypic, chemotaxonomic and genotypic characteristics, strain 2T18T represents a novel species of the genus Chitinibacter , for which the name Chitinibacter bivalviorum sp. nov. is proposed. The type strain is 2T18T (=KCTC 72821T=CCUG 74764T).

Flavobacterium franklandianum sp. nov. and Flavobacterium gawalongense sp. nov., isolated from glaciers on the Tibetan Plateau

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Qing Liu ◽  
Hong-Can Liu ◽  
Lei-Lei Yang ◽  
Yu-Hua Xin
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
The Tibetan Plateau ◽  
Content Type ◽  
Link Type ◽  
Taxonomic Research ◽  
Pr China ◽  
The 16S Rrna Gene

The genus Flavobacterium (family Flavobacteriaceae ) can be found in diverse environments. In this study, seven novel strains were isolated from glaciers in PR China and subjected to taxonomic research. Phylogenetic analyses based on the 16S rRNA gene revealed that the strains belonged to the genus Flavobacterium . None of the seven strains grew at temperatures above 22 °C, indicating that they are psychrophilic. Furthermore, the average nucleotide identity (ANI) values of the seven strains were calculated and indicated that they represented two novel species in Flavobacterium . Strain LB3P56T was most closely related to Flavobacterium soyangense IMCC26223T (97.70 %) and strain GSP16T was most closely related to Flavobacterium sinopsychrotolerans 0533T (98.03 %). The ANI values between the two Flavobacterium strains and their closest relatives were less than 83.47 %, which was much lower than the threshold for species delineation of 95–96 %. Therefore, we propose two novel species, Flavobacterium franklandianum sp. nov. (LB3P56T=CGMCC 1.11934T=NBRC 113651T) and Flavobacterium gawalongense sp. nov. (GSP16T=CGMCC 1.24642T=NBRC 113664T).

Sphingomonas sabuli sp. nov., a carotenoid-producing bacterium isolated from beach sand

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Minchung Kang ◽  
Geeta Chhetri ◽  
Jiyoun Kim ◽  
Inhyup Kim ◽  
Taegun Seo
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Amino Acid Identity ◽  
Beach Sand ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Average Amino Acid Identity ◽  
Bacterium Strain

A Gram-stain-negative, aerobic and non-motile bacterium, strain sand1-3T, was isolated from beach sand collected from Haeundae Beach located in Busan, Republic of Korea. Based on the results of 16S rRNA gene sequence and phylogenetic analyses, Sphingomonas daechungensis CH15-11T (97.0 %), Sphingomonas edaphi DAC4T (96.8 %), Sphingomonas xanthus AE3T (96.5 %) and Sphingomonas oryziterrae YC6722T (96.0 %) were selected for comparing phenotypic and chemotaxonomic characteristics. Cells of strain sand1-3T grew at 7–50 °C (optimum, 30–35 °C), pH 5.0–8.0 (optimum, pH 7.0–8.0) and in the presence of 0–0.5 % (w/v) NaCl (optimum, 0 %). Major polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, one unidentified glycolipid and one unidentified phosphoglycolipid. The major fatty acids were summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c) and C18 : 1 2-OH. Moreover, the sole respiratory quinone and major polyamine were identified as ubiquinone-10 and homospermidine, respectively. The genomic DNA G+C content was 65.9 mol%. The digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity values of strain sand1-3T and its reference strains with publicly available genomes were 17.9–18.9 %, 72.0–75.3 % and 63.3–76.5 % respectively. Based on polyphasic evidence, we propose Sphingomonas sabuli sp. nov. as a novel species within the genus Sphingomonas . The type strain is sand1-3T (=KCTC 82358T=NBRC 114538T).

Halarchaeum rubridurum sp. nov., a moderately acidophilic haloarchaeon isolated from commercial sea salt samples

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3143-3147 ◽  
Author(s):  
Yuto Yamauchi ◽  
Hiroaki Minegishi ◽  
Akinobu Echigo ◽  
Yasuhiro Shimane ◽  
Masahiro Kamekura ◽  
...  
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
The Philippines ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Optimum Ph ◽  
The 16S Rrna Gene

Six halo-acidophilic archaeal strains were isolated from four commercial salt samples obtained from seawater in the Philippines, Indonesia (Bali) and Japan (Okinawa) on agar plates at pH 4.5. Cells of the six strains were pleomorphic, and stained Gram-negative. Two strains were pink–red pigmented, while four other strains were orange–pink pigmented. Strain MH1-16-3T was able to grow at 9–30 % (w/v) NaCl [with optimum at 18 % (w/v) NaCl], at pH 4.5–6.8 (optimum, pH 5.5) and at 20–50 °C (optimum, 42 °C). The five other strains grew at slightly different ranges. The six strains required at least 1 mM Mg2+ for growth. The 16S rRNA gene sequences of the six strains were almost identical, sharing 99.9 (1–2 nt differences) to 100 % similarity. The closest relatives were Halarchaeum acidiphilum MH1-52-1T and Halarchaeum salinum MH1-34-1T with 97.7 % similarity. The DNA G+C contents of the six strains were 63.2–63.7 mol%. Levels of DNA–DNA relatedness amongst the six strains were 79–86 %, while those between MH1-16-3T and H. acidiphilum MH1-52-1T and H. salinum MH1-34-1T were both 43 and 45 % (reciprocally), respectively. Based on the phenotypic, genotypic and phylogenetic analyses, it is proposed that the six isolates represent a novel species of the genus Halarchaeum , for which the name Halarchaeum rubridurum sp. nov. is proposed. The type strain is MH1-16-3T ( = JCM 16108T = CECT 7535T).

scholarly journals Ureibacillus defluvii sp. nov., isolated from a thermophilic microbial fuel cell

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1617-1621 ◽  
Author(s):  
Shungui Zhou ◽  
Jia Tang ◽  
Dongxing Qin ◽  
Qin Lu ◽  
Guiqin Yang
Keyword(s):  
Fuel Cell ◽  
16S Rrna ◽  
Microbial Fuel Cell ◽  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

A thermophilic bacterium, designated DX-1T, was isolated from the anode biofilm of a microbial fuel cell (MFC). Cells of strain DX-1T were oxidase-positive, catalase-positive and Gram-staining-negative. The strain was found to be rod-shaped and non-motile and to produce subterminal spores. The strain was able to grow with NaCl at concentrations ranging from 0 to 6 %, at temperatures of 25–60 °C (optimum 55 °C) and pH 6.0–8.0 (optimum pH 7.0). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DX-1T formed a cluster with Ureibacillus thermosphaericus DSM 10633T (96.9 % 16S rRNA sequence similarity), Ureibacillus composti DSM 17951T (95.8 %), Ureibacillus thermophilus DSM 17952T (95.7 %) and Ureibacillus terrenus DSM 12654T (95.3 %). The G+C content of the genomic DNA was 40.4 mol%. The major quinone was MK-7, the peptidoglycan type was l-Lys←d-Asp, and the major cellular fatty acids (>5 %) were iso-C16 : 0 and iso-C14 : 0. The polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol and phospholipids of unknown composition. Based on phenotypic characteristics, chemotaxonomic features and results of phylogenetic analyses, the strain was determined to represent a distinct novel species of the genus Ureibacillus , and the name proposed for the novel species is Ureibacillus defluvii sp. nov., with type strain DX-1T ( = CGMCC 1.12358T = KCTC 33127T).

scholarly journals Luteimonas chenhongjianii, a novel species isolated from rectal contents of Tibetan Plateau pika (Ochotona curzoniae)

2020 ◽  
Vol 70 (5) ◽  
pp. 3186-3193 ◽  
Author(s):  
Gui Zhang ◽  
Xin-He Lai ◽  
Jing Yang ◽  
Dong Jin ◽  
Ji Pu ◽  
...  
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Plateau Pika ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Link Type ◽  
Ochotona Curzoniae

Two Gram-stain-negative, strictly aerobic, bright-yellow-pigmented and rod-shaped bacteria (strains 100069 and 100111T) with a single polar flagellum were isolated from the rectal contents of plateau pika (Ochotona curzoniae). Based on the results of nearly full-length 16S rRNA gene sequence and phylogenetic analyses, strains 100069 and 100111T belong to the genus Luteimonas , and are closest to Luteimonas rhizosphaerae 4-12T (98.02 % similarity), Luteimonas aestuarii B9T (97.8 %) and Luteimonas terrae THG-MD21T (97.74 %). The DNA G+C contents of these two isolates were 68.30 mol% and 68.29 mol%, respectively. The highest average nucleotide identity (ANI) value between strain 100111T and its closely related species was 83.34 %, well below the threshold of 95–96 %. The major cellular fatty acids were iso-C11 : 0, iso-C15 : 0 and iso-C17 : 1  ω9. Polar lipid content was dominated by diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid and an unidentified lipid. Ubiquinone-8 (Q-8) was the predominant respiratory quinone. These two isolates grew optimally at 35–37 °C, pH 7.0–8.0 and with 1.0 % (w/v) NaCl. The results of ANI analysis and other characteristics obtained from our polyphasic study showed that strains 100069 and 100111T represent a novel species in genus Luteimonas , for which the name Luteimonas chenhongjianii sp. nov. (type strain 100111T=DSM 104077T=CGMCC 1.16429T) is proposed.

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