scholarly journals M ethanocaldococcus bathoardescens sp. nov., a hyperthermophilic methanogen isolated from a volcanically active deep-sea hydrothermal vent

2015 ◽  
Vol 65 (Pt_4) ◽  
pp. 1280-1283 ◽  
Author(s):  
Lucy C. Stewart ◽  
Jong-Hyun Jung ◽  
You-Tae Kim ◽  
Soon-Wo Kwon ◽  
Cheon-Seok Park ◽  
...  
Keyword(s):  
Hydrothermal Vent ◽  
Novel Species ◽  
Basaltic Rock ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Northeastern Pacific ◽  
Identity Score ◽  
Axial Seamount

A hyperthermophilic methanogen, strain JH146T, was isolated from 26 °C hydrothermal vent fluid emanating from a crack in basaltic rock at Marker 113 vent, Axial Seamount in the northeastern Pacific Ocean. It was identified as an obligate anaerobe that uses only H2 and CO2 for growth. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain is more than 97 % similar to other species of the genus Methanocaldococcus . Therefore, overall genome relatedness index analyses were performed to establish that strain JH146T represents a novel species. For each analysis, strain JH146T was most similar to Methanocaldococcus sp. FS406-22, which can fix N2 and also comes from Marker 113 vent. However, strain JH146T differs from strain FS406-22 in that it cannot fix N2. The average nucleotide identity score for strain JH146T was 87 %, the genome-to-genome direct comparison score was 33–55 % and the species identification score was 93 %. For each analysis, strain JH146T was below the species delineation cut-off. Full-genome gene synteny analysis showed that strain JH146T and strain FS406-22 have 97 % genome synteny, but strain JH146T was missing the operons necessary for N2 fixation and assimilatory nitrate reduction that are present in strain FS406-22. Based on its whole genome sequence, strain JH146T is suggested to represent a novel species of the genus Methanocaldococcus for which the name Methanocaldococcus bathoardescens is proposed. The type strain is JH146T ( = DSM 27223T = KACC 18232T).

scholarly journals Clostridium fessum sp. nov., isolated from human faeces

2020 ◽  
Author(s):  
Boram Seo ◽  
Kyungchan Jeon ◽  
Inwoo Baek ◽  
Yung Mi Lee ◽  
Kiwoon Baek ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Clostridium Symbiosum

An obligately anaerobic, Gram-stain-positive and spore-forming strain, SNUG30386T was isolated from a faecal sample of a healthy Korean subject. The strain formed a round ivory-coloured colony and cells were chained rods with tapered ends, approximately 2.0–2.5×0.6–0.8 μm in size. The taxonomic analysis indicated that strain SNUG30386T was within the family Lachnospiraceae . According to the 16S rRNA gene sequence similarity, the closest species to strain SNUG30386T was Clostridium symbiosum (95.6 %), followed by Enterocloster asparagiformis (94.8 %), Enterocloster clostridioformis (94.8 %) and Enterocloster lavalensis (94.6 %). The evolutionary tree based on 16S rRNA gene sequences demonstrated that strain SNUG30386T had split apart at a unique branch point far from other close relatives. Its DNA G+C content was 48.3 mol% calculated from the whole genome sequence. The major cellular fatty acids were C16 : 0 and C14 : 0. Compared to those of the closely related species, strain SNUG30386T showed distinct biochemical activities such as being unable to utilize most of carbon sources except d-glucose and l-arabinose. As a result, based on its unique phylogenetic clade and taxonomic characteristics, we conclude that strain SNUG30386T represents a novel species within the genus Clostridium , for which the name Clostridium fessum sp. nov. is proposed. The type strain of the novel species is SNUG30386T (=KCTC 15633T= JCM 32258T).

Vibrio ziniensis sp. nov., isolated from mangrove sediments

2021 ◽  
Vol 71 (4) ◽  
Author(s):  
Jie Wu ◽  
Wu Qu ◽  
Qiliang Lai ◽  
Shengxiang Pei ◽  
Tianyou Zhang ◽  
...  
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Mangrove Sediments ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Pr China

A novel Gram-staining-negative, catalase- and oxidase-positive, facultatively anaerobic and rod-shaped motile bacterial strain, designated as ZWAL4003T, was isolated from mangrove sediments of the Zini Mangrove Forest, Zhangzhou City, PR China. Phylogenetic analysis based on its 16S rRNA gene sequence indicated that ZWAL4003T was grouped into a separated branch with Vibrio plantisponsor MSSRF60T (97.38% nucleotide sequence identity) and Vibrio diazotrophicus NBRC 103148T (97.27%). The major cellular fatty acids were C14 : 0 (12.6%), C16 : 0 (17.6%), and summed feature 3 (C16 : 1ω6c /C16 : 1 ω7c, 45.6%). Its genome had a length of 4650556 bp with 42.8% DNA G+C content, and contained genes involved in the biosynthesis of bacteriocin, β-lactone, resorcinol, N-acyl amino acid, and arylpolyene. The in silico DNA–DNA hybridization and average nucleotide identity values for whole-genome sequence comparisons between ZWAL4003T and V. plantisponsor LMG 24470T were clearly below the thresholds used for the delineation of a novel species. The morphological and chemotaxonomic characteristics and the genotypic data of ZWAL4003T indicated that it represented a novel species of the genus Vibrio . Its proposed name is Vibrio ziniensis sp. nov., and the type strain is ZWAL4003T (=KCTC 72971T=MCCC 1A17474T).

scholarly journals Duganella callida sp. nov., a novel addition to the Duganella genus, isolated from the soil of a cultivated maize field

2020 ◽  
Author(s):  
Rachel Raths ◽  
Vincent Peta ◽  
Heike Bücking
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Maize Field ◽  
Identity Score ◽  
Bacterium Strain

A Gram-negative, rod-shaped bacterium, strain Duganella callida DN04T, was isolated from the soil of a maize field in North Carolina, USA. Based on the 16S rRNA gene sequence, the most similar Duganella species are D. sacchari Sac-22T, D. ginsengisoli DCY83T, and D. radicis Sac-41T with a 97.8, 97.6, or 96.9 % sequence similarity, respectively. We compared the biochemical phenotype of DN04T to D. sacchari Sac-22T and D. zoogloeoides 115T and other reference strains from different genera within the Oxalobacteraceae and while the biochemical profile of DN04T is most similar to D. sacchari Sac-22T and other Duganella and Massilia strains, there are also distinct differences. DN04T can for example utilize turanose, N-acetyl-d-glucosamine, inosine, and l-pyroglutamic acid. The four fatty acids found in the highest percentages were C15 : 0 iso (24.6 %), C15 : 1 isoG (19.4 %), C17 : 0 iso3-OH (16.8 %), and summed feature 3 (C16:1 ⍵7c and/or C16:1 ⍵6c) (12.5 %). We also applied whole genome sequencing to determine if DN04T is a novel species. The most similar AAI (average amino acid identity) score was 70.8 % ( Massilia plicata NZ CP038026T), and the most similar ANI (average nucleotide identity) score was 84.8 % ( D. radicis KCTC 22382T), which indicates that DN04T is a novel species. The genome-to-genome-distance calculation (GGDC) revealed a DDH of 28.3 % to D. radicis KCTC 22382T, which is much lower than the new species threshold. Based on the morphological, phenotypic, and genomic differences, we propose Duganella callida sp. nov. as a novel species within the Duganella genus (type strain DN04T=NRRL B-65552T=LMG 31736T).

scholarly journals Gracilibacillus oryzae sp. nov., isolated from rice seeds

2020 ◽  
Vol 70 (10) ◽  
pp. 5467-5472 ◽  
Author(s):  
Shan-Wen He ◽  
Xing Wang ◽  
He-Bao Guo ◽  
Ji-Gang Han ◽  
Kyu Kyu Thin ◽  
...  
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Link Type ◽  
Physiological And Biochemical Characteristics ◽  
Identity Score ◽  
Rice Seeds

A Gram-stain-positive, facultatively anaerobic, endospore-forming bacterium, designated strain TD8T, was isolated from surface-sterilized rice seeds (Oryza sativa L.). Phylogenetic analysis of the 16S rRNA gene indicated that strain TD8T should be placed within the genus Gracilibacillus (95.2–99.0 % sequence similarity); it exhibited highest similarities to Gracilibacillus ureilyticus CGMCC 1.7727T (99.0 %), ‘ Gracilibacillus xinjiangensis ’ CGMCC 1.12449T (98.9 %) and Gracilibacillus dipsosauri CGMCC 1.3642T (97.5 %). Chemotaxonomic analysis showed that menaquinone-7 (MK-7) was the major isoprenoid quinone. Diphosphatidylglycerol, phosphatidylglycerol and one unidentified phospholipid were the major cellular polar lipids, and the major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0, C16 : 0 and iso-C16 : 0, which supported the allocation of the strain to the genus Gracilibacillus . The digital DNA–DNA hybridization value between strain TD8T and Gracilibacillus ureilyticus CGMCC 1.7727T was lower than 70 % (22.60 %), and the average nucleotide identity score was 79.54±5.09 %, suggesting that strain TD8T represented a novel species in the genus Gracilibacillus . The genomic DNA G+C content was 37.5 %. Based on physiological and biochemical characteristics and genotypic data, strain TD8T represents a novel species of the genus Gracilibacillus , for which the name Gracilibacillus oryzae sp. nov. is proposed. The type strain is TD8T (=ACCC 61556T=CICC 24889T=JCM 33537T).

Fretibacterium fastidiosum gen. nov., sp. nov., isolated from the human oral cavity

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 458-463 ◽  
Author(s):  
Sonia R. Vartoukian ◽  
Julia Downes ◽  
Richard M. Palmer ◽  
William G. Wade
Keyword(s):  
New Genus ◽  
Novel Species ◽  
Fusobacterium Nucleatum ◽  
Oral Bacteria ◽  
Rrna Gene ◽  
Good Growth ◽  
Content Type ◽  
Cellular Fatty Acids ◽  
Link Type ◽  
Peptone Yeast Extract Glucose

SGP1T, a strain belonging to a lineage of the phylum Synergistetes with no previously cultivated representatives was subjected to a comprehensive range of phenotypic and genotypic tests. For good growth the strain was dependent on co-culture with, or extracts from, selected other oral bacteria. Cells of strain SGP1T were asaccharolytic and major amounts of acetic acid and moderate amounts of propionic acid were produced as end products of metabolism in peptone-yeast extract-glucose broth supplemented with a filtered cell sonicate of Fusobacterium nucleatum subsp. nucleatum ATCC 25586T (25 %, v/v). Hydrogen sulphide was produced and gelatin was weakly hydrolysed. The major cellular fatty acids were C14 : 0, C18 : 0 and C16 : 0. The DNA G+C content of strain SGP1T was 63 mol%. Phylogenetic analysis of the full-length 16S rRNA gene showed that strain SGP1T represented a novel group within the phylum Synergistetes . A novel species in a new genus, Fretibacterium fastidiosum gen. nov., sp. nov., is proposed. The type strain of Fretibacterium fastidiosum is SGP1T ( = DSM 25557T = JCM 16858T).

Pseudomonas bijieensis sp. nov., isolated from cornfield soil

2019 ◽  
Vol 71 (3) ◽  
Author(s):  
Jingling Liang ◽  
Sai Wang ◽  
Ayizekeranmu Yiming ◽  
Luoyi Fu ◽  
Iftikhar Ahmad ◽  
...  
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Novel Species ◽  
Guizhou Province ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Pr China ◽  
Genome Comparisons

Strain L22-9T, a Gram-stain-negative and rod-shaped bacterium, motile by one polar flagellum, was isolated from cornfield soil in Bijie, Guizhou Province, PR China. Based on 16S rRNA gene sequences, it was identified as a Pseudomonas species. Multilocus sequence analysis of concatenated 16S rRNA, gyrB, rpoB and rpoD gene sequences showed that strain L22-9T formed a clearly separated branch, located in a cluster together with Pseudomonas brassicacearum LMG 21623T, Pseudomonas kilonensis DSM 13647T and Pseudomonas thivervalensis DSM 13194T. Whole-genome comparisons based on average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) confirmed that strain L22-9T should be classified as a novel species. It was most closely related to P. kilonensis DSM 13647T with ANI and dDDH values of 91.87 and 46.3 %, respectively. Phenotypic features that can distinguish strain L22-9T from P. kilonensis DSM 13647T are the assimilation ability of N-acetyl-d-glucosamine, poor activity of arginine dihydrolase and failure to ferment ribose and d-fucose. The predominant cellular fatty acids of strain L22-9T are C16 : 0, summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The respiratory quinones consist of Q-9 and Q-8. The polar lipids are diphosphatidylglycerol, phosphatidylethanolamine, two unidentified phosphoglycolipids, two unidentified aminophospholipids and an unidentified glycolipid. Based on the evidence, we conclude that strain L22-9T represents a novel species, for which the name Pseudomonas bijieensis sp. nov. is proposed. The type strain is L22-9T (=CGMCC 1.18528T=LMG 31948T), with a DNA G+C content of 60.85 mol%.

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.

Limosilactobacillus urinaemulieris sp. nov. and Limosilactobacillus portuensis sp. nov. isolated from urine of healthy women

2019 ◽  
Vol 71 (3) ◽  
Author(s):  
Magdalena Ksiezarek ◽  
Teresa Gonçalves Ribeiro ◽  
Joana Rocha ◽  
Filipa Grosso ◽  
Svetlana Ugarcina Perovic ◽  
...  
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Rrna Gene ◽  
Gram Stain ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Healthy Women ◽  
Genome Distance

Two Gram-stain-positive strains, c9Ua_26_MT and c11Ua_112_MT, were isolated from voided urine samples from two healthy women. Comparative 16S rRNA gene sequences demonstrated that these novel strains were members of the genus Limosilactobacillus . Phylogenetic analysis based on pheS gene sequences and core genomes showed that each strain formed a separated branch and are closest to Limosilactobacillus vaginalis DSM 5837T. The average nucleotide identity (ANI) and Genome-to-Genome Distance Calculator (GGDC) values between c9Ua_26_MT and the closest relative DSM 5837T were 90.7 and 42.9 %, respectively. The ANI and GGDC values between c11Ua_112_MT and the closest relative DSM 5837T were 91.2 and 45.0 %, and those among the strains were 92.9% and 51,0 %, respectively. The major fatty acids were C12 : 0 (40.2 %), C16 : 0 (26.7 %) and C18 : 1 ω9c (17.7 %) for strain c9Ua_26_MT, and C18 : 1 ω9c (38.0 %), C16 : 0 (33.3 %) and C12 : 0 (17.6 %) for strain c11Ua_112_MT. The genomic DNA G+C content of strains c9Ua_26_MT and c11Ua_112_MT was 39.9 and 39.7 mol%, respectively. On the basis of the data presented here, strains c9Ua_26_MT and c11Ua_112_MT represent two novel species of the genus Limosilactobacillus , for which the names Limosilactobacillus urinaemulieris sp. nov. (c9Ua_26_MT=CECT 30144T=LMG 31899T) and Limosilactobacillus portuensis sp. nov. (c11Ua_112_MT=CECT 30145T=LMG 31898T) are proposed.

scholarly journals Mesoflavibacter aestuarii sp. nov., a zeaxanthin-producing marine bacterium isolated from seawater

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1932-1937 ◽  
Author(s):  
Ji Hee Lee ◽  
Yeoung Min Hwang ◽  
Keun Sik Baik ◽  
Kap Seong Choi ◽  
Jong-Ok Ka ◽  
...  
Keyword(s):  
Marine Bacterium ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Carotenoid Pigment ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Gwangyang Bay

An orange, rod-shaped, Gram-reaction-negative, aerobic and gliding bacterial strain devoid of flagella, designated strain KYW614T, was isolated from seawater collected from Gwangyang Bay, Republic of Korea. Zeaxanthin was the major carotenoid pigment produced and flexirubin-type pigments were not produced. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain KYW614T belonged to the family Flavobacteriaceae and it was most closely related to Mesoflavibacter zeaxanthinifaciens TD-ZX30T (96.5 %, sequence similarity). The predominant cellular fatty acids of strain KYW614T were iso-C15 : 1 G (10.5 %), summed feature 3 (C16 : 1ω7c/C16 : 1ω6c; 10.0 %), iso-C15 : 0 (9.5 %), C15 : 0 (7.5 %) and iso-C17 : 0 3-OH (7.4 %). MK-6 was the only isoprenoid quinone and the DNA G+C content was 32.6 mol%. Data from a polyphasic taxonomic study suggested that the isolate represents a novel species in the genus Mesoflavibacter , for which the name Mesoflavibacter aestuarii sp. nov. is proposed. The type strain is KYW614T ( = KCTC 32269T = JCM 19524T).

Carnobacterium iners sp. nov., a psychrophilic, lactic acid-producing bacterium from the littoral zone of an Antarctic pond

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1370-1375 ◽  
Author(s):  
Isabel Snauwaert ◽  
Bart Hoste ◽  
Katrien De Bruyne ◽  
Karolien Peeters ◽  
Luc De Vuyst ◽  
...  
Keyword(s):  
Lactic Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Littoral Zone ◽  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

Two lactic acid-producing, Gram-stain-positive rods were isolated from a microbial mat actively growing in the littoral zone of an Antarctic lake (Forlidas Pond) in the Pensacola mountains and studied using a polyphasic taxonomic approach. The isolates were examined by phylogenetic analysis of the 16S rRNA gene, multilocus sequence analysis of pheS, rpoA and atpA, and biochemical and genotypic characteristics. One strain, designated LMG 26641, belonged to Carnobacterium alterfunditum and the other strain, designated LMG 26642T, could be assigned to a novel species, with Carnobacterium funditum DSM 5970T as its closest phylogenetic neighbour (99.2 % 16S rRNA gene sequence similarity). Carnobacterium iners sp. nov. could be distinguished biochemically from other members of the genus Carnobacterium by the lack of acid production from carbohydrates. DNA–DNA relatedness confirmed that strain LMG 26642T represented a novel species, for which we propose the name Carnobacterium iners sp. nov. (type strain is LMG 26642T  = CCUG 62000T).

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