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 Description of Gemella massiliensis sp. nov., a new bacterium isolated from the human gut.

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

Abstract Thanks 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-P3249 T , was isolated from a sputum sample of a healthy French man. Strain Marseille-P3249 T is a facultative anaerobe, catalase negative, Gram positive, coccus and unable to sporulate. The major fatty acids were C 16:0 (34%), C 18:1n9 (28%), C 18:0 (15%) and C 18:2n6 (13%). Its 16S rRNA sequence exhibits a 98.3% sequence similarity with Gemella bergeri strain 617-93, 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-P3249 T (= CSUR P3249 = DSMZ 103940).

scholarly journals Pedobacter ghigonii sp. nov., Isolated from the Microbiota of the Planarian Schmidtea mediterranea

2021 ◽  
Vol 12 (2) ◽  
pp. 268-287
Author(s):  
Luis Johnson Kangale ◽  
Didier Raoult ◽  
Fournier Pierre-Edouard
Keyword(s):  
Dna Hybridization ◽  
Sequence Similarity ◽  
Average Nucleotide Identity ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Worldwide Distribution ◽  
The Family ◽  
Genomic Approach ◽  
A New Species ◽  
Phylogenetic Neighbor

The planarian S. mediterranea is a platyhelminth with worldwide distribution that can regenerate any part of its body after amputation and has the capacity to eliminate a large spectrum of human bacterial pathogens. Surprisingly, the microbiota of S. mediterranea remains poorly investigated. Using the culturomics strategy to study the bacterial component of planarians, we isolated a new bacterial strain, Marseille-Q2390, which we characterized with the taxono-genomic approach that associates phenotypic assays and genome sequencing and analysis. Strain Marseille-Q2390 exhibited a 16S rRNA sequence similarity of 99.36% with Pedobacter kyungheensis strain THG-T17T, the closest phylogenetic neighbor. It is a white-pigmented, Gram-negative, and rod-shaped bacterium. It grows in aerobic conditions and belongs to the family Sphingobacteriaceae. The genome of strain Marseille-Q2390 is 5,919,359 bp-long, with a G + C content of 40.3%. By comparing its genome with other closely related strains, the highest Orthologous Average Nucleotide Identity (Ortho-ANI) and digital DNA-DNA hybridization (dDDH) values were 85.71% and 30.50%, respectively, which were found with Pedobacter soli strain 15-51T. We conclude that strain Marseille-Q2390T is sufficiently different from other nearby species to be classified within a new species for which we propose the name Pedobacter ghigonii sp. nov.

scholarly journals Streptomyces gilvifuscus sp. nov., an actinomycete that produces antibacterial compounds isolated from soil

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3493-3500 ◽  
Author(s):  
Tuan Manh Nguyen ◽  
Jaisoo Kim
Keyword(s):  
Fatty Acids ◽  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Gram Stain ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Antibacterial Compounds ◽  
Cellular Fatty Acids ◽  
16S Rrna Sequence Analysis

This study describes a novel actinomycete, designated T113T, which was isolated from forest soil in Pyeongchang-gun, Republic of Korea, and is an aerobic, Gram-stain-positive actinobacterium that forms flexibilis chains of smooth, elliptical or short rod-shaped spores. The results of 16S rRNA sequence analysis indicated that strain T113T exhibited high levels of similarity to previously characterized species of the genus Streptomyces (98.19–98.89 %, respectively). However, the results of phylogenetic and DNA–DNA hybridization analyses confirmed that the organism represented a novel member of the genus Streptomyces. Furthermore, using chemotaxonomic and phenotypic analyses it was demonstrated that the strain exhibited characteristics similar to those of other members of the genus Streptomyces. The primary cellular fatty acids expressed by this strain included anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0 and iso-C16 : 0. While diphosphatidylglycerol and phosphatidylethanolamine were the predominant lipids expressed by strain T113T, moderate amounts of phosphatidylinositol and phosphatidylinositol mannoside were also detected. Whole-cell hydrolysates contained glucose and ribose, and the predominant menaquinone detected was MK-9 (H6); however, moderate amounts of MK-9 (H8) and trace amounts of MK-10 (H2) and MK-10 (H4) were also detected. We therefore propose that strain T113T be considered as representing a novel species of the genus Streptomyces and propose the name Streptomyces gilvifuscus sp. nov. for this species, with strain T113T ( = KEMB 9005-213T = KACC 18248T = NBRC 110904T) being the type strain.

scholarly journals Sellimonas caecigallum sp. nov., description and genome sequence of a new member of the Sellimonas genus isolated from the cecum of feral chicken

2019 ◽  
Author(s):  
Supapit Wongkuna ◽  
Sudeep Ghimire ◽  
Linto Antony ◽  
Surang Chankhamhaengdecha ◽  
Tavan Janvilisri ◽  
...  
Keyword(s):  
Fatty Acids ◽  
New Species ◽  
Type Strain ◽  
Biochemical Analysis ◽  
Sequence Similarity ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Cellular Fatty Acids ◽  
Physiological And Biochemical ◽  
A New Species

AbstractAn obligately anaerobic, non-motile, Gram-positive coccobacillus strain SW451 was isolated from pooled cecum contents of feral chickens. Comparative analysis based on 16s rRNA sequence showed that strain SW451 had 95.24% nucleotide sequence similarity to Sellimonas intestinalis BR31T, the closest species with a valid taxonomy. The genome of SW451 is 2.67 Mbp with 45.23 mol% of G+C content. The major cellular fatty acids were C16: 0, C14: 0 and C16: 0 DMA. Based on taxonogenomic, physiological, and biochemical analysis, the strain SW451 represents a new species of the genus Sellimonas, for which the name Sellimonas caecigallum sp. nov. is proposed. The type strain of Sellimonas caecigallum is SW451 (=DSM 109473T)

scholarly journals The Genus Caedibacter Comprises Endosymbionts of Paramecium spp. Related to the Rickettsiales (Alphaproteobacteria) and to Francisella tularensis (Gammaproteobacteria)

2002 ◽  
Vol 68 (12) ◽  
pp. 6043-6050 ◽  
Author(s):  
Cora L. Beier ◽  
Matthias Horn ◽  
Rolf Michel ◽  
Michael Schweikert ◽  
Hans-Dieter Görtz ◽  
...  
Keyword(s):  
16S Rrna ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Sister Group ◽  
Rrna Gene ◽  
Paramecium Tetraurelia ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
16S Rrna Sequence Analysis ◽  
Bacterial Endosymbionts

ABSTRACT Obligate bacterial endosymbionts of paramecia able to form refractile inclusion bodies (R bodies), thereby conferring a killer trait upon their ciliate hosts, have traditionally been grouped into the genus Caedibacter. Of the six species described to date, only the Paramecium caudatum symbiont Caedibacter caryophilus has been phylogenetically characterized by its 16S rRNA gene sequence, and it was found to be a member of the Alphaproteobacteria related to the Rickettsiales. In this study, the Caedibacter taeniospiralis type strain, an R-body-producing cytoplasmatic symbiont of Paramecium tetraurelia strain 51k, was investigated by comparative 16S rRNA sequence analysis and fluorescence in situ hybridization with specific oligonucleotide probes. C. taeniospiralis is not closely related to C. caryophilus (80% 16S rRNA sequence similarity) but forms a novel evolutionary lineage within the Gammaproteobacteria with the family Francisellaceae as a sister group (87% 16S rRNA sequence similarity). These findings demonstrate that the genus Caedibacter is polyphyletic and comprises at least two phylogenetically different bacterial species belonging to two different classes of the Proteobacteria. Comparative phylogenetic analysis of C. caryophilus, five closely related Acanthamoeba endosymbionts (including one previously uncharacterized amoebal symbiont identified in this study), and their hosts suggests that the progenitor of the alphaproteobacterial C. caryophilus lived within acanthamoebae prior to the infection of paramecia.

scholarly journals Pseudomonas eucalypticola sp. nov., a producer of antifungal agents isolated from Eucalyptus dunnii leaves

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yujing Liu ◽  
Zhang Song ◽  
Hualong Zeng ◽  
Meng Lu ◽  
Weiyao Zhu ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Antifungal Agents ◽  
Novel Species ◽  
Phytopathogenic Fungi ◽  
Strictly Aerobic ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Eucalyptus Dunnii ◽  
16S Rrna Sequence Analysis

AbstractPseudomonas are ubiquitously occurring microorganisms and are known for their ability to produce antimicrobials. An endophytic bacterial strain NP-1 T, isolated from Eucalyptus dunnii leaves, exhibits antifungal properties against five tested phytopathogenic fungi. The strain is a Gram-negative rod-shaped bacterium containing a single polar flagellum. It is strictly aerobic, grows at 4–37 °C, 2–5% NaCl, and pH 3–7. The 16S rRNA sequence analysis showed that NP-1 T belongs to the Pseudomonas genus. Phylogenetic analysis based on four concatenated partial genes (16S rDNA, gyrB, rpoB and rpoD) and the phylogenomic tree indicated that NP-1 T belongs to Pseudomonas fluorescens lineage but is distinct from any known Pseudomonas species. The G + C mol % of NP-1 T genome is 63.96, and the differences between NP-1 T and related species are larger than 1. The digital DNA-DNA hybridization and tetranucleotide signatures are 23.8 and 0.97, which clearly separates strain NP-1 T from its closest neighbours, Pseudomonas coleopterorum and Pseudomonas rhizosphaerae. Its phenotypic and chemotaxonomic features confirmed its differentiation from related taxa. The results from this polyphasic approach support the classification of NP-1 T as a novel species of Pseudomonas, and the name of Pseudomonas eucalypticola is thus proposed for this strain, whose type is NP-1 T (= CCTCC M2018494T = JCM 33572 T).

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.

Aureivirga marina gen. nov., sp. nov., a marine bacterium isolated from the Mediterranean sponge Axinella verrucosa

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1089-1095 ◽  
Author(s):  
Markus Haber ◽  
Sigal Shefer ◽  
Assunta Giordano ◽  
Pierangelo Orlando ◽  
Agata Gambacorta ◽  
...  
Keyword(s):  
16S Rrna ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Sea Salts ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
The Mediterranean

Two bacterial strains, VI.14 and VIII.04T, were isolated from the Mediterranean sponge Axinella verrucosa collected off the Israeli coast near Sdot Yam. The non-motile, aerobic, Gram-negative isolates were oxidase-negative and catalase-positive, and formed golden-brown colonies on marine agar 2216. The pigment was neither diffusible nor flexirubin-like. Strain VIII.04T grew at 15–37 °C, at pH 6.0–9.0, in the presence of 20–50 g NaCl l−1 and 20–80 g sea salts l−1, The spectrum was narrower for strain VI.14, with growth at pH 7.0–8.0. and in the presence of 30–50 g NaCl l−1 and 30–70 g sea salts l−1. The predominant fatty acid (>50 %) in both strains was iso-C15 : 0, and the major respiratory quinone was MK-6. The DNA G+C content was 30.7 and 31.1 mol% for VIII.04T and VI.14, respectively. Results from 16S rRNA sequence similarity and phylogenetic analyses indicated that both strains are closely related to members of the family Flavobacteriaceae within the phylum Bacteroidetes , with as much as 91.7 % 16S rRNA sequence similarity. On the basis of data from the polyphasic analysis, we suggest that the strains represent a novel species in a new genus within the family Flavobacteriaceae , for which the name Aureivirga marina gen. nov., sp. nov. is proposed. Strain VIII.04T ( = ATCC BAA-2394T = LMG 26721T) is the type strain of Aureivirga marina.

scholarly journals Exiguobacterium Sp. HA2, isolated from the Ilam Mountains of Iran

2021 ◽  
Author(s):  
Reza Heidari ◽  
Mostafa Akbariqomi ◽  
Gholamreza Tavoosidana ◽  
Garshasb Rigi
Keyword(s):  
Fatty Acids ◽  
Cell Wall ◽  
Novel Species ◽  
Isoprenoid Quinone ◽  
Gram Stain ◽  
Phenotypic Characteristics ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Peptidoglycan Layer ◽  
Major Isoprenoid Quinone

ABSTRACTA motile, Gram-stain-positive, rod-shaped, non-sporing, tolerate up to 5% NaCl, grew at 0–25 °C, designated Exiguobacterium sp. HA2 was isolated from the soil of the Ilam Mountains of Iran during October 2016. The major isoprenoid quinone is MK-7 and in the smaller amount are MK-6 and MK-8. Polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylserine, phosphatidylinositol, phosphatidylethanolamine. Major fatty acids (>10 %) are isoC13:0, isoC15:0 and C16:0. The bacterial cell wall peptidoglycan layer was lysine-glycine. The 16S rRNA sequence was analyzed at the phylogenetic levels. Also, A supplemental comparison was made between five other genes including csp, gyrB, hsp70, rpoB, and citC. According to the results of genotypic and phenotypic characteristics, the strain was categorized in the genus Exiguobacterium. This bacterium had the closest relation with Exiguobacterium undae, and thus was dubbed Exiguobacterium sp. HA2. The different in the Phenotypic, functional characteristics and phylogenetic indicated Exiguobacterium sp. HA2 can be regarded as representing considered a novel species within the genus Exiguobacterium.

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