Peptoniphilus Colimassiliensis sp. nov. and Peptoniphilus Urinimassiliensis sp. nov., Two New Species Isolated From Humans

2021 ◽  
Author(s):  
Babacar Mbaye ◽  
Cheikh Ibrahima LO ◽  
Niokhor Dione ◽  
Sarah Benabdelkader ◽  
Maryam Tidjani Alou ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Dna Hybridization ◽  
Kidney Transplant Recipient ◽  
Bacterial Species ◽  
Hexadecanoic Acid ◽  
Anaerobic Conditions ◽  
New Members ◽  
Two New Species ◽  
Type Strains ◽  
Gram Positive Cocci

Abstract Strains Marseille-P3761 and Marseille-P3195 are representatives of two bacterial species isolated from human specimens. Strain Marseille-P3761 was isolated from the stool of a healthy volunteer, while strain Marseille-P3915 was cultivated from the urine of a kidney transplant recipient. Both strains are anaerobic Gram-positive cocci bacteria. Both are catalase-negative and oxidase-negative and grow optimally at 37°C in anaerobic conditions. They also metabolize carbohydrates such as galactose, glucose, fructose, and glycerol. The major fatty acids were hexadecanoic acid for both strains, Marseille-P3761 (38%) and Marseille-P3195 (31%). The highest DNA-DNA hybridization values of Marseille-P3761 and Marseille-P3195 strains when compared to their closest phylogenetic relatives were 52.3% and 56.4%, respectively. The morphological, biochemical, phenotypic and genomic characteristics strongly support that these strains are new members of the Peptoniphilus genus. Thus, we suggest that strains Marseille-P3761 (CSUR P3761 = CCUG71569) and Marseille-P3195 (CSUR P3195 = DSM 103468) are the type strains of two new Peptoniphilus species, for which we propose the names Peptoniphilus colimassiliensis sp. nov. and Peptoniphilus urinimassiliensis sp. nov., respectively.

scholarly journals Proposal of Lentzea deserti (Okoro et al. 2010) Nouioui et al. 2018 as a later heterotypic synonym of Lentzea atacamensis (Okoro et al. 2010) Nouioui et al. 2018 and an emended description of Lentzea atacamensis

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0246533
Author(s):  
Mo Ping ◽  
Zhao Yun-Lin ◽  
Liu Jun ◽  
Gao Jian ◽  
Xu Zheng-Gang
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Gene Sequence Analysis ◽  
Emended Description ◽  
Relationship Of ◽  
Type Strains ◽  
The 16S Rrna Gene

The taxonomic relationship of Lentzea atacamensis and Lentzea deserti were re-evaluated using comparative genome analysis. The 16S rRNA gene sequence analysis indicated that the type strains of L. atacamensis and L. deserti shared 99.7% sequence similarity. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the genomes of two type strains were 88.6% and 98.8%, respectively, greater than the two recognized thresholds values of 70% dDDH and 95–96% ANI for bacterial species delineation. These results suggested that L. atacamensis and L. deserti should share the same taxonomic position. And this conclusion was further supported by similar phenotypic and chemotaxonomic features between them. Therefore, we propose that L. deserti is a later heterotypic synonym of L. atacamensis.

scholarly journals Genome analysis-based reclassification of Pseudomonas fuscovaginae and Pseudomonas shirazica as later heterotypic synonyms of Pseudomonas asplenii and Pseudomonas asiatica, respectively

2020 ◽  
Vol 70 (5) ◽  
pp. 3547-3552 ◽  
Author(s):  
Mari Tohya ◽  
Shin Watanabe ◽  
Tatsuya Tada ◽  
Htay Htay Tin ◽  
Teruo Kirikae
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Bacterial Species ◽  
Taxonomic Status ◽  
Species Delineation ◽  
Genome Sequences ◽  
Content Type ◽  
Link Type ◽  
Type Strains ◽  
Group Species

This study was conducted to clarify the taxonomic status of the species Pseudomonas fuscovaginae and Pseudomonas shirazica . Whole genome sequences for the type strains of P. fuscovaginae and P. shirazica were compared against the closely related type strains of the Pseudomonas putida group and the Pseudomonas fluorescens group species. Average nucleotide identity and digital DNA–DNA hybridization values between P. fuscovaginae LMG 2158T and Pseudomonas asplenii ATCC 23835T were 98.4 and 85.5 %, and between P. shirazica VM14T and Pseudomonas asiatica RYU5T were 99.3 and 95.3 %. These values were greater than recognized thresholds for bacterial species delineation, indicating that they belong to the same genomospecies, respectively. Therefore, P. fuscovaginae and P. shirazica should be reclassified as later heterotypic synonyms of P. asplenii and P. asiatica , respectively.

scholarly journals Metabacillus schmidteae sp. nov., Cultivated from Planarian Schmidtea mediterranea Microbiota

2021 ◽  
Vol 12 (2) ◽  
pp. 299-316
Author(s):  
Luis Johnson Kangale ◽  
Didier A. Raoult ◽  
Eric Ghigo ◽  
Pierre-Edouard Fournier
Keyword(s):  
Fatty Acids ◽  
Type Strain ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Genomic Analysis ◽  
Schmidtea Mediterranea ◽  
Hexadecanoic Acid ◽  
Tetradecanoic Acid ◽  
Gram Negative

Taxonogenomics combines phenotypic assays and genomic analysis as a means of characterizing novel strains. We used this strategy to study Marseille-P9898T strain, an aerobic, motile, Gram-negative, spore-forming, and rod-shaped bacterium isolated from planarian Schmidtea mediterranea. Marseille-P9898T is catalase-positive and oxidase-negative. The major fatty acids detected are 12-methyl-tetradecanoic acid, 13-methyl-tetradecanoic acid, and hexadecanoic acid. Marseille-P9898T strain shared more than 98% sequence similarity with the Metabacillus niabensis strain 4T19T (98.99%), Metabacillus halosaccharovorans strain E33T (98.75%), Metabacillus malikii strain NCCP-662T (98.19%), and Metabacillus litoralis strain SW-211T (97.15%). Marseille-P9898 strain belongs to Metabacillus genus. Genomic analysis revealed the highest similarities with Ortho-ANI and dDDH, 85.76% with Metabacillus halosaccharovorans, and 34.20% with Bacillus acidicola, respectively. These results show that the Marseille-P9898T strain is a novel bacterial species from Metabacillus genus, for which we propose the name of Metabacillus schmidteae sp. nov. (Type strain Marseille-P9898T = CSUR P9898T = DSM 111480T).

scholarly journals Microbacterium ulmi sp. nov., a xylanolytic, phosphate-solubilizing bacterium isolated from sawdust of Ulmus nigra

2004 ◽  
Vol 54 (2) ◽  
pp. 513-517 ◽  
Author(s):  
Raúl Rivas ◽  
Martha E. Trujillo ◽  
Manuel Sánchez ◽  
Pedro F. Mateos ◽  
Eustoquio Martínez-Molina ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
Phosphate Solubilizing ◽  
Type Strains

A xylanolytic and phosphate-solubilizing bacterium isolated from sawdust of Ulmus nigra in Salamanca was characterized by a polyphasic approach. The novel strain, designated XIL02T, was Gram-positive, aerobic, catalase- and oxidase-negative, rod-shaped and non-motile. Phylogenetically and chemotaxonomically, it was related to members of the genus Microbacterium. According to 16S rRNA gene sequence analysis, it is closely related to Microbacterium arborescens and Microbacterium imperiale; however, DNA–DNA hybridization showed reassociation values less than 70 % with the type strains of these species. In chemotaxonomic analyses, the major menaquinones detected were MK-12, MK-13 and MK-11 and the major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0; the peptidoglycan was of the type B2β. The G+C content determined was 69 mol%. Based on the present data, it is proposed that strain XIL02T (=LMG 20991T=CECT 5976T) be classified as the type strain of a novel Microbacterium species, for which the name Microbacterium ulmi sp. nov. is proposed.

scholarly journals Reclassification of Bacillus invictae as a later heterotypic synonym of Bacillus altitudinis

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2769-2773 ◽  
Author(s):  
Yang Liu ◽  
Qiliang Lai ◽  
Juan Du ◽  
Zongze Shao
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Bacillus Pumilus ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Taxonomic Status ◽  
The Other ◽  
Phenotypic Data ◽  
Bacillus Altitudinis ◽  
Type Strains

The aim of this study was to reclarify the taxonomic status of strain Bacillus invictae Bi.FFUP1 T by performing comparative analyses with the other four type strains within the Bacillus pumilus group. The digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strains B. invictae Bi.FFUP1 T ( = DSMZ 26896T = MCCC 1A07089T), B. altitudinis 41KF2bT ( = DSMZ 21631T = MCCC 1A06452T), B. safensis FO-36bT ( = DSMZ 19292T = MCCC 1A6451T), B. pumilus ATCC 7061T ( = DSMZ 27T = MCCC 1A06453T) and B. xiamenensis HYC-10T ( = MCCC 1A00008T) were, respectively, 82.90  % and 98.10  %, which are greater than the thresholds for bacterial species delineation, suggesting that they should belong to the same species, while the dDDH and ANI values between strain B. invictae DSMZ 26896T and the other three type strains within the B. pumilus group were below the respective thresholds of 70  % and 95  %. Meanwhile, B. invictae DSMZ 26896T and B. altitudinis 41KF2bT shared 98.7  % gyrB gene sequence similarity based on resequencing, whereas strain B. invictae DSMZ 26896T shared low similarities ( < 95  %) with the other three type strains. In addition, in comparison with those from the other three type strains, phenotypic data of B. invictae DSMZ 26896T and B. altitudinis 41KF2bT, including API 20NE, API ZYM, Biolog GN2 and API 50CHB tests, showed slight differences. The data from these combined genotypic and phenotypic analyses suggest that Bacillus invictae Branquinho et al. 2014 should be regarded as a later heterotypic synonym of Bacillus altitudinis Shivaji et al. 2006.

scholarly journals Gemella massiliensis sp. nov., a new bacterium isolated from the human sputum

2021 ◽  
Author(s):  
Maxime Descartes Mbogning Fonkou ◽  
Cheikh Ibrahima Lo ◽  
Zouina Mekhalif ◽  
Melhem Bilen ◽  
Enora Tomei ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Dna Hybridization ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Sputum Sample ◽  
Species Delineation ◽  
Facultative Anaerobe ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Positive Coccus

AbstractThanks to its ability to isolate previously uncultured bacterial species, culturomics has dynamized the study of the human microbiota. A new bacterial species, Gemella massiliensis Marseille-P3249T, was isolated from a sputum sample of a healthy French man. Strain Marseille-P3249T is a facultative anaerobe, catalase-negative, Gram positive, coccus, and unable to sporulate. The major fatty acids were C16:0 (34%), C18:1n9 (28%), C18:0 (15%) and C18:2n6 (13%). Its 16S rRNA sequence exhibits a 98.3% sequence similarity with Gemella bergeri strain 617-93T, its phylogenetically closest species with standing in nomenclature. Its digital DNA–DNA hybridization (dDDH) and OrthoANI values with G. bergeri of only 59.7 ± 5.6% and 94.8%, respectively. These values are lower than the thresholds for species delineation (> 70% and > 95%, respectively). This strain grows optimally at 37 °C and its genome is 1.80 Mbp long with a 30.5 mol% G + C content. Based on these results, we propose the creation of the new species Gemella massilienis sp. nov., strain Marseille-P3249T (= CSUR P3249 = DSMZ 103940).

scholarly journals Kordia zhangzhouensis sp. nov., isolated from surface freshwater

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3379-3383 ◽  
Author(s):  
Juan Du ◽  
Yang Liu ◽  
Qiliang Lai ◽  
Chunming Dong ◽  
Yanrong Xie ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Gram Stain ◽  
16S Rrna Gene Sequences ◽  
Optimum Ph ◽  
Pr China ◽  
Type Strains

An aerobic, Gram-stain-negative, rod-shaped and non-motile bacterium, JS14SB-1T, was isolated from the surface freshwater of the Jiulong River, PR China. Strain JS14SB-1T grew at 15–38 °C (optimum, 28–35 °C), at pH 6.0–9.0 (optimum pH 7.0) and in the presence of 1.0–7.0 % (w/v) NaCl [optimum 3.0–5.0 % (w/v)]. Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that strain JS14SB-1T was affiliated to the genus Kordia, sharing low similarities (95.1–97.1 %) to all type strains of species of this genus. The digital DNA–DNA hybridization (DDH) value between strain JS14SB-1T and the closely related strain Kordia jejudonensis SSK3-3T was 20.70 ± 2.33 % and far below the 70 % DDH value taken as the gold standard for delineation of bacterial species. The major fatty acids were identified as iso-C15 : 0 and iso-C17 : 0 3-OH. The polar lipids were phosphatidylethanolamine, glycolipid, aminolipid, several unidentified phospholipids and lipids. The predominant menaquinone was MK-6. The G+C content of the genomic DNA was 33.8 mol%. Based on the phenotypic, phylogenetic and chemotaxonomic distinctiveness, strain JS14SB-1T is considered to represent a novel species of the genus Kordia, for which the name Kordia zhangzhouensis sp. nov. is proposed; the type strain is JS14SB-1T ( = MCCC 1A00726T = KCTC 42140T).

scholarly journals Genome analysis-based reclassification of Lelliottia aquatilis as a later heterotypic synonym of Lelliottia jeotgali

2019 ◽  
Vol 69 (4) ◽  
pp. 998-1000 ◽  
Author(s):  
Wenjing Wu ◽  
Zhiyong Zong
Keyword(s):  
Genome Analysis ◽  
Dna Hybridization ◽  
Type Species ◽  
Bacterial Species ◽  
Whole Genome ◽  
Average Nucleotide Identity ◽  
Genome Sequences ◽  
Content Type ◽  
Link Type ◽  
Type Strains

The aim of this study was to further clarify the taxonomic relationship between the two recently described bacterial species, Lelliottia jeotgali sp. nov. and Lelliottia aquatilis sp. nov. Whole genome sequences of types strains of the two species are available for analysis. Average nucleotide identity (ANI) and in silico DNA–DNA hybridization (isDDH) values between the two type strains were determined. The ANI and isDDH values between type strains of the two species are 98.7 and 91.0 %, respectively, which are higher than cut-offs to define a bacterial species. It is therefore clear that the two species actually belong to the same species. The name of L.aquatilis was published at an earlier date than that of L. aquatilis . We therefore propose that L. aquatilis is a later heterotypic synonym of L. jeotgali .

scholarly journals Occurrence of Cis-11,12-Methylene-Hexadecanoic Acid in the Red Alga Solieria pacifica (Yamada) Yoshida

Molecules ◽  
2021 ◽  
Vol 26 (8) ◽  
pp. 2286
Author(s):  
Gwang-Woo Kim ◽  
Jae-Man Sim ◽  
Yutaka Itabashi ◽  
Min-Jeong Jung ◽  
Joon-Young Jun
Keyword(s):  
Fatty Acids ◽  
Fatty Acid ◽  
Red Alga ◽  
Proton Nuclear Magnetic Resonance ◽  
Animal Origin ◽  
Monoenoic Acid ◽  
Resonance Spectroscopy ◽  
Hexadecenoic Acid ◽  
Cyclopropane Fatty Acid ◽  
Hexadecanoic Acid

Fatty acids in marine algae have attracted the attention of natural chemists because of their biological activity. The fatty acid compositions of the Solieriaceae families (Rhodophyceae, Gaigartinales) provide interesting information that unusual cyclic fatty acids have been occasionally found. A survey was conducted to profile the characteristic fatty acid composition of the red alga Solieria pacifica (Yamada) Yoshida using gas chromatography-mass spectrometry (GC-MS), infrared spectroscopy (IR), and proton nuclear magnetic resonance spectroscopy (1H-NMR). In S. pacifica, two cyclopentyl fatty acids, 11-cyclopentylundecanoic acid (7.0%), and 13-cyclopentyltridecanoic acid (4.9%), and a cyclopropane fatty acid, cis-11,12-methylene-hexadecanoic acid (7.9%) contributed significantly to the overall fatty acid profile. In particular, this cyclopropane fatty acid has been primarily found in bacteria, rumen microorganisms or foods of animal origin, and has not previously been found in any other algae. In addition, this alga contains a significant amount of the monoenoic acid cis-11-hexadecenoic acid (9.0%). Therefore, cis-11,12-methylene-hexadecanoic acid in S. pacifica was likely produced by methylene addition to cis-11-hexadecenoic acid.

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