scholarly journals Comparative genomics ofSynechococcusand proposal of the new genusParasynechococcus

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1522 ◽  
Author(s):  
Felipe Coutinho ◽  
Diogo Antonio Tschoeke ◽  
Fabiano Thompson ◽  
Cristiane Thompson
Keyword(s):  
Primary Productivity ◽  
New Genus ◽  
Core Genome ◽  
Amino Acid Identity ◽  
Average Nucleotide Identity ◽  
Acid Identity ◽  
Average Amino Acid Identity ◽  
Protein Encoding ◽  
Genomic Taxonomy ◽  
Encoding Genes

Synechococcusis among the most important contributors to global primary productivity. The genomes of several strains of this taxon have been previously sequenced in an effort to understand the physiology and ecology of these highly diverse microorganisms. Here we present a comparative study ofSynechococcusgenomes. For that end, we developed GenTaxo, a program written in Perl to perform genomic taxonomy based on average nucleotide identity, average amino acid identity and dinucleotide signatures, which revealed that the analyzed strains are drastically distinct regarding their genomic content. Phylogenomic reconstruction indicated a division ofSynechococcusin two clades (i.e. Synechococcus and the new genus Parasynechococcus), corroborating evidences that this is in fact a polyphyletic group. By clustering protein encoding genes into homologue groups we were able to trace the Pangenome and core genome of both marine and freshwaterSynechococcusand determine the genotypic traits that differentiate these lineages.

scholarly journals Phylogenetic relationships among haloalkaliphilic archaea of the family Natrialbaceae

2020 ◽  
Author(s):  
Shivakumara Siddaramappa
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Novel Species ◽  
Single Species ◽  
Amino Acid Identity ◽  
Average Nucleotide Identity ◽  
Acid Identity ◽  
Average Amino Acid Identity ◽  
The Family ◽  
Clade 1

ABSTRACTThe family Natrialbaceae is a member of the class Halobacteria of the archaeal phylum Euryarchaeota. Seventeen genera with validly or effectively published names are currently included within this family. In this study, using pairwise average nucleotide identity and average amino acid identity comparisons in conjunction with phylogenetic analysis, it has been shown that the family Natrialbaceae is highly diverse and contains several potentially novel species and genera that are yet to be fully characterized. The deduced proteome sequence-based phylogenetic tree, constructed using the alignment- and parameter-free method CVTree3, contained six major clades, with Salinarchaeum sp. Harcht-Bsk1 being the only representative within clade 1. Furthermore, Haloterrigena daqingensis was found to be closely related to Natronorubrum sediminis, and it is proposed that these archaea together represent a novel genus. Interestingly, Haloterrigena jeotgali, Haloterrigena thermotolerans, and Natrinema pellirubrum were found to be very closely related to each other, and it is proposed that they be merged into a single species. Notably, the type genus Natrialba itself appeared to be heterogenous and contains species that could be broadly classified among two genera. Likewise, the genus Natrinema is also heterogenous and contains species that could be classified among six genera. Altogether, 19 novel genera have been proposed to be created, and four haloalkaliphilic archaea hitherto recognized only using genus names are confirmed to represent novel species.

scholarly journals Taxonomy of Rhizobiaceae revisited: proposal of a new framework for genus delimitation

2021 ◽  
Author(s):  
Nemanja Kuzmanović ◽  
Camilla Fagorzi ◽  
Alessio Mengoni ◽  
Florent Lassalle ◽  
George C diCenzo
Keyword(s):  
New Genus ◽  
Core Genome ◽  
Amino Acid Identity ◽  
Phenotypic Data ◽  
Average Amino Acid Identity ◽  
The Family ◽  
Common Framework ◽  
Core Proteome ◽  
Genomic Relatedness ◽  
New Framework

The alphaproteobacterial family Rhizobiaceae is highly diverse, with 168 species with validly published names classified into 17 genera with validly published names. Most named genera in this family are delineated based on genomic relatedness and phylogenetic relationships, but some historically named genera show inconsistent distribution and phylogenetic breadth. Most problematic is Rhizobium, which is notorious for being highly paraphyletic, as most newly described species in the family being assigned to this genus without consideration for their proximity to existing genera, or the need to create novel genera. In addition, many Rhizobiaceae genera lack synapomorphic traits that would give them biological and ecological significance. We propose a common framework for genus delimitation within the family Rhizobiaceae. We propose that genera in this family should be defined as monophyletic groups in a core-genome gene phylogeny, that are separated from related species using a pairwise core-proteome average amino acid identity (cpAAI) threshold of approximately 86%. We further propose that the presence of additional genomic or phenotypic evidence can justify the division of species into separate genera even if they all share greater than 86% cpAAI. Applying this framework, we propose to reclassify Rhizobium rhizosphaerae and Rhizobium oryzae into the new genus Xaviernesmea gen. nov. Data is also provided to support the recently proposed genus "Peteryoungia", and the reclassifications of Rhizobium yantingense as Endobacterium yantingense comb. nov., Rhizobium petrolearium as Neorhizobium petrolearium comb. nov., Rhizobium arenae as Pararhizobium arenae comb. nov., Rhizobium tarimense as Pseudorhizobium tarimense comb. nov., and Rhizobium azooxidefex as Mycoplana azooxidifex comb. nov. Lastly, we present arguments that the unification of the genera Ensifer and Sinorhizobium in Opinion 84 of the Judicial Commission is no longer justified by current genomic and phenotypic data. We thus argue that the genus Sinorhizobium is not illegitimate and now encompasses 17 species.

Genome analysis reveals that the correct name of type strain Adlercreutzia caecicola DSM 22242T is Parvibacter caecicola Clavel et al. 2013

2021 ◽  
Vol 71 (5) ◽  
Author(s):  
Dominic A. Stoll ◽  
Nicolas Danylec ◽  
Christina Grimmler ◽  
Sabine E. Kulling ◽  
Melanie Huch
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Draft Genome ◽  
Amino Acid Identity ◽  
Average Nucleotide Identity ◽  
Content Type ◽  
Link Type ◽  
Genome Wide ◽  
Average Amino Acid Identity ◽  
Biochemical Analyses

The strain Adlercreutzia caecicola DSM 22242T (=CCUG 57646T=NR06T) was taxonomically described in 2013 and named as Parvibacter caecicola Clavel et al. 2013. In 2018, the name of the strain DSM 22242T was changed to Adlercreutzia caecicola (Clavel et al. 2013) Nouioui et al. 2018 due to taxonomic investigations of the closely related genera Adlercreutzia, Asaccharobacter and Enterorhabdus within the phylum Actinobacteria . However, the first whole draft genome of strain DSM 22242T was published by our group in 2019. Therefore, the genome was not available within the study of Nouioui et al. (2018). The results of the polyphasic approach within this study, including phenotypic and biochemical analyses and genome-based taxonomic investigations [genome-wide average nucleotide identity (gANI), alignment fraction (AF), average amino acid identity (AAI), percentage of orthologous conserved proteins (POCP) and genome blast distance phylogeny (GBDP) tree], indicated that the proposed change of the name Parvibacter caecicola to Adlercreutzia caecicola was not correct. Therefore, it is proposed that the correct name of Adlercreutzia caecicola (Clavel et al. 2013) Nouioui et al. 2018 strain DSM 22242T is Parvibacter caecicola Clavel et al. 2013.

scholarly journals PFM-Like Enzymes Are a Novel Family of Subclass B2 Metallo-β-Lactamases from Pseudomonas synxantha Belonging to the Pseudomonas fluorescens Complex

2019 ◽  
Vol 64 (2) ◽  
Author(s):  
Laurent Poirel ◽  
Mattia Palmieri ◽  
Michael Brilhante ◽  
Amandine Masseron ◽  
Vincent Perreten ◽  
...  
Keyword(s):  
Amino Acid ◽  
Pseudomonas Fluorescens ◽  
Bacterial Species ◽  
Amino Acid Identity ◽  
Chicken Meat ◽  
The Novel ◽  
Content Type ◽  
Acid Identity ◽  
Carbapenem Resistant ◽  
Encoding Genes

ABSTRACT A carbapenem-resistant Pseudomonas synxantha isolate recovered from chicken meat produced the novel carbapenemase PFM-1. That subclass B2 metallo-β-lactamase shared 71% amino acid identity with β-lactamase Sfh-1 from Serratia fonticola. The blaPFM-1 gene was chromosomally located and likely acquired. Variants of PFM-1 sharing 90% to 92% amino acid identity were identified in bacterial species belonging to the Pseudomonas fluorescens complex, including Pseudomonas libanensis (PFM-2) and Pseudomonas fluorescens (PFM-3), highlighting that these species constitute reservoirs of PFM-like encoding genes.

scholarly journals Streptococcal taxonomy based on genome sequence analyses

F1000Research ◽  
2013 ◽  
Vol 2 ◽  
pp. 67 ◽  
Author(s):  
Cristiane C Thompson ◽  
Vanessa E Emmel ◽  
Erica L Fonseca ◽  
Michel A Marin ◽  
Ana Carolina P Vicente
Keyword(s):  
Amino Acid Identity ◽  
Species Level ◽  
Viridans Streptococci ◽  
Genome Sequences ◽  
Sequence Analyses ◽  
Acid Identity ◽  
Genomic Signatures ◽  
Genomic Tools ◽  
Average Amino Acid Identity ◽  
Genomic Analyses

The identification of the clinically relevant viridans streptococci group, at species level, is still problematic. The aim of this study was to extract taxonomic information from the complete genome sequences of 67 streptococci, comprising 19 species, by means of genomic analyses, multilocus sequence analysis (MLSA), average amino acid identity (AAI), genomic signatures, genome-to-genome distances (GGD) and codon usage bias. We then attempted to determine the usefulness of these genomic tools for species identification in streptococci. Our results showed that MLSA, AAI and GGD analyses are robust markers to identify streptococci at the species level, for instance,S. pneumoniae,S. mitis, andS. oralis. AStreptococcusspecies can be defined as a group of strains that share ≥ 95% DNA similarity in MLSA and AAI, and > 70% DNA identity in GGD. This approach allows an advanced understanding of bacterial diversity.

scholarly journals Genome-Based Comparison of Clostridioides difficile: Average Amino Acid Identity Analysis of Core Genomes

2018 ◽  
Vol 76 (3) ◽  
pp. 801-813 ◽  
Author(s):  
Adriana Cabal ◽  
Se-Ran Jun ◽  
Piroon Jenjaroenpun ◽  
Visanu Wanchai ◽  
Intawat Nookaew ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Identity ◽  
Acid Identity ◽  
Clostridioides Difficile ◽  
Average Amino Acid Identity

scholarly journals Zooshikella harenae sp. nov., Isolated from Pacific Oyster Crassostrea gigas, and Establishment of Zooshikella ganghwensis subsp. marina subsp. nov. and Zooshikella ganghwensis subsp. ganghwensis subsp. nov.

Diversity ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 641
Author(s):  
Hani Pira ◽  
Chandra Risdian ◽  
Peter Kämpfer ◽  
Mathias Müsken ◽  
Peter J. Schupp ◽  
...  
Keyword(s):  
Crassostrea Gigas ◽  
Type Strain ◽  
Pacific Oyster ◽  
Novel Species ◽  
Antimicrobial Property ◽  
Amino Acid Identity ◽  
Average Nucleotide Identity ◽  
High Similarity ◽  
Acid Identity ◽  
Dna Hybridisation

Here, we describe the polyphasic taxonomy of a novel isolated strain WH53T from the genus Zooshikella isolated from the sand sediment located between the lumen of the Crassostrea gigas From Germany. Phylogenetic analysis determined that the strain WH53T had a high similarity to Zooshikella ganghwensis JC2044T (99.57%) and Zooshikella marina LMG 28823T (99.36%). Strain WH53T contained ubiquinone-9 (Q-9) as the predominant menaquinone, and the major fatty acids were C16:0, C16:1ω7c, and C18:1ω7c. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, amino phospholipids, and unidentified phospholipids were identified as their polar lipid composition. The DNA G+C content and genome size of strain WH53T were 40.08 mol% and 5,914,969 bp, respectively. Digital DNA–DNA hybridisation (dDDH) for strain WH53T against Z. ganghwensis JC2044T and Z. marina LMG 28823T showed low relatedness values of 26.3% and 26.1%, respectively. The extract of strain WH53T exhibited antimicrobial property. Strain WH53T represents a novel species in the genus Zooshikella. We propose the name of Zooshikella harenae sp. nov., with the type strain WH53T (= DSM 111628T = NCCB 100808T). Furthermore, the dDDH, average nucleotide identity (ANI), percentage of conserved proteins (POCP), and amino acid identity (AAI) value between Z. marina LGM 28823T and Z. ganghwensis DSM 15267T were 79.9%, 97.84%, 76.08%, and 87.01%, respectively, suggesting that both of them should be reclassified as Z. ganghwensis subsp. marina subsp. nov. and Z. ganghwensis subsp. ganghwensis DSM 15267 subsp. nov.

scholarly journals Genomic Analysis of the Recent Viral Isolate vB_BthP-Goe4 Reveals Increased Diversity of φ29-Like Phages

Viruses ◽  
2018 ◽  
Vol 10 (11) ◽  
pp. 624 ◽  
Author(s):  
Tobias Schilling ◽  
Michael Hoppert ◽  
Robert Hertel
Keyword(s):  
Sequence Comparison ◽  
Genomic Analysis ◽  
Average Nucleotide Identity ◽  
Morphological Investigation ◽  
Viral Isolate ◽  
Transmission Electron ◽  
Key Characteristics ◽  
Protein Encoding ◽  
Packaging Rna ◽  
Encoding Genes

We present the recently isolated virus vB_BthP-Goe4 infecting Bacillus thuringiensis HD1. Morphological investigation via transmission electron microscopy revealed key characteristics of the genus Phi29virus, but with an elongated head resulting in larger virion particles of approximately 50 nm width and 120 nm height. Genome sequencing and analysis resulted in a linear phage chromosome of approximately 26 kb, harbouring 40 protein-encoding genes and a packaging RNA. Sequence comparison confirmed the relation to the Phi29virus genus and genomes of other related strains. A global average nucleotide identity analysis of all identified φ29-like viruses revealed the formation of several new groups previously not observed. The largest group includes Goe4 and may significantly expand the genus Phi29virus (Salasvirus) or the Picovirinae subfamily.

scholarly journals Draft Genome Sequence of Clinical Isolate Alcaligenaceae sp. Strain 429

2019 ◽  
Vol 8 (19) ◽  
Author(s):  
Michael J. Zilliox ◽  
Paul C. Schreckenberger ◽  
Catherine Putonti
Keyword(s):  
Amino Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Draft Genome ◽  
Amino Acid Identity ◽  
Unknown Etiology ◽  
Rrna Gene ◽  
Acid Identity ◽  
Average Amino Acid Identity ◽  
The 16S Rrna Gene

Here, we present the 3.53-Mb genome for Alcaligenaceae sp. strain 429, isolated from a patient with unknown etiology. While the 16S rRNA gene most closely resembles Paenalcaligenes species, average amino acid identity (AAI) analysis did not meet the threshold to classify our strain as a species of this family.

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