scholarly journals Description and genomic characterization of Streptococcus symci sp. nov., isolated from a child’s oropharynx

2021 ◽  
Author(s):  
He Qi ◽  
Defeng Liu ◽  
Yang Zou ◽  
Nan Wang ◽  
Han Tian ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Novel Species ◽  
Optimal Growth ◽  
Whole Genome Sequence ◽  
High Susceptibility ◽  
Base Pairs ◽  
Streptococcus Species ◽  
Main Fatty Acid ◽  
Genomic Characterization

AbstractUsing the culturomics approach, we isolated a new Streptococcus species, strain C17T, from the oropharynx mucosa sample of a healthy 5-year-old child living in Shenyang, China. We studied the phenotypic, phylogenetic, and genomic characteristics of strain C17T, which was identified as a Gram-positive, coccus-shaped, non-motile, aerobic, catalase-negative bacteria. Its growth temperatures ranged from 20 to 42 °C, with optimal growth at 37 °C. Acid production could be inhibited by two sugars, trehalose and raffinose. In C17T, the reactions for enzyme lipase (C14) were confirmed to be negative, whereas those for alkaline phosphatase, α-glucosidase, and hippuric acid hydrolysis were positive. The C17T genome contained 2,189,419 base pairs (bp), with an average G+C content of 39.95%, encoding 2092 genes in total. The 16S ribosomal RNA sequence showed 99.8% similarity with the newly identified Streptococcus pseudopneumoniae ATCC BAA-960T. The main fatty acid components in C17T were C16:0, C18:1 w7c, C18:0, and C18:1 w9c, all of which can be found in other species of the Streptococcus genus. Strain C17T showed high susceptibility to clindamycin, linezolid, vancomycin, chloramphenicol, and cefepime, and moderate susceptibility to erythromycin. The obtained dDDH value between strain C17T and the closest species was 52.9%. In addition, the whole genome sequence of strain C17T had an 82.21–93.40% average nucleotide identity (ANI) with those strains of closely related Streptococcus species, indicating that the strain C17T was unique among all Streptococcus species. Based on these characteristics, we determine that C17T is a novel species, named Streptococcus symci sp. nov. (= GDMCC 1.1633 = JCM 33582).

Whole-genome analysis of Pandoraea species strains from cystic fibrosis patients

2019 ◽  
Vol 14 (16) ◽  
pp. 1357-1367
Author(s):  
Jumamurat R Bayjanov ◽  
Miquel B Ekkelenkamp ◽  
Malbert RC Rogers ◽  
Rafael Cantón ◽  
Barry J Benaissa-Trouw ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Core Genome ◽  
Genetic Characterization ◽  
Novel Species ◽  
Antibiotic Resistance Genes ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Acquired Antibiotic Resistance

Aim: Genetic characterization of Pandoraea strains recovered from cystic fibrosis patients. Materials & methods: The whole-genome sequence of 12 Pandoraea strains was determined using Illumina technology. The position of the strains within the genus Pandoraea was analyzed using selected partial gene sequences, core genome multi-locus sequence typing and average nucleotide identity analysis. Furthermore, the sequences were annotated. Results: The results show that some strains previously identified as Pandoraea pnomenusa, Pandoraea sputorum, Pandoraea oxalativorans and Pandoraea pulmonicola belong to novel species. The strains did not harbor acquired antibiotic resistance genes but encoded an OXA-type ß-lactamase. Conclusion: The taxonomy of the genus Pandoraea needs to be revised.

scholarly journals Genomic Characterization and Phylogenetic Classification of Bovine Coronaviruses Through Whole Genome Sequence Analysis

Viruses ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 183 ◽  
Author(s):  
Tohru Suzuki ◽  
Yoshihiro Otake ◽  
Satoko Uchimoto ◽  
Ayako Hasebe ◽  
Yusuke Goto
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Analysis ◽  
Molecular Characterization ◽  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Wild Ruminant ◽  
Genome Sequence Analysis ◽  
Genomic Characterization

Bovine coronavirus (BCoV) is zoonotically transmissible among species, since BCoV-like viruses have been detected in wild ruminants and humans. BCoV causing enteric and respiratory disease is widespread in cattle farms worldwide; however, limited information is available regarding the molecular characterization of BCoV because of its large genome size, despite its significant economic impact. This study aimed to better understand the genomic characterization and evolutionary dynamics of BCoV via comparative sequence and phylogenetic analyses through whole genome sequence analysis using 67 BCoV isolates collected throughout Japan from 2006 to 2017. On comparing the genomic sequences of the 67 BCoVs, genetic variations were detected in 5 of 10 open reading frames (ORFs) in the BCoV genome. Phylogenetic analysis using whole genomes from the 67 Japanese BCoV isolates in addition to those from 16 reference BCoV strains, revealed the existence of two major genotypes (classical and US wild ruminant genotypes). All Japanese BCoV isolates originated from the US wild ruminant genotype, and they tended to form the same clusters based on the year and farm of collection, not the disease type. Phylogenetic trees on hemagglutinin-esterase protein (HE), spike glycoprotein (S), nucleocapsid protein (N) genes and ORF1 revealed clusters similar to that on whole genome, suggesting that the evolution of BCoVs may be closely associated with variations in these genes. Furthermore, phylogenetic analysis of BCoV S genes including those of European and Asian BCoVs and human enteric coronavirus along with the Japanese BCoVs revealed that BCoVs differentiated into two major types (European and American types). Moreover, the European and American types were divided into eleven and three genotypes, respectively. Our analysis also demonstrated that BCoVs with different genotypes periodically emerged and predominantly circulated within the country. These findings provide useful information to elucidate the detailed molecular characterization of BCoVs, which have spread worldwide. Further genomic analyses of BCoV are essential to deepen the understanding of the evolution of this virus.

scholarly journals Full Genomic Characterization of a Lentogenic Newcastle Disease Virus Isolated from Farm-Reared Ostriches (Struthio camelus) in Northwest China

2017 ◽  
Vol 5 (6) ◽  
Author(s):  
Shanhui Ren ◽  
Chongyang Wang ◽  
Xiaolong Gao ◽  
Xue Zhang ◽  
Xiangwei Wang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Newcastle Disease Virus ◽  
Disease Virus ◽  
Newcastle Disease ◽  
Northwest China ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Struthio Camelus ◽  
Genomic Characterization

ABSTRACT To our knowledge, our study is the first to report the whole-genome sequence of an ostrich-origin Newcastle disease virus (NDV) isolate, abbreviated as Ostrich/SX-01/06. Phylogenetic analysis revealed that this isolate belongs to the subgenotype c in class II. The identification of the complete genome will provide useful information regarding ostrich diseases, especially NDV.

scholarly journals Identification and genomic characterization of a novel species of feline anellovirus

2016 ◽  
Vol 13 (1) ◽  
Author(s):  
Wen Zhang ◽  
Hua Wang ◽  
Yan Wang ◽  
Zhijian Liu ◽  
Jingjiao Li ◽  
...  
Keyword(s):  
Novel Species ◽  
Genomic Characterization

scholarly journals Genomic Characterization of a New Enamovirus Infecting Common Bean

2021 ◽  
Author(s):  
Ruo-bin Lu ◽  
Ping-xiu Lan ◽  
Ru-jing Kang ◽  
Guan-lin Tan ◽  
Xiao-jiao Chen ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Novel Species ◽  
Open Reading Frames ◽  
Amino Acid Sequence Level ◽  
Disease Symptoms ◽  
Bean Plants ◽  
Genomic Characterization ◽  
Pea Enation Mosaic Virus ◽  
Reading Frames

Abstract A novel enamovirus was identified from bean plants with disease symptoms. Its genome of 5,781 nucleotides (nt) encodes five open reading frames. The virus and other species of the genus Enamovirus share identities of 50.4%-68.4% at the complete genome, and 19.9%-51.9% of P0, 24.9%-52.5% of P1, 33.4%-62.9% of P1-P2, 30.6%-81.1% of P3, 32.3%-74.2% of P3-P5 at amino acid sequence level, respectively. Phylogenetic analysis showed that the virus is most closely related to Alfalfa enamovirus 1 and Pea enation mosaic virus 1 in the genus Enamovirus within family Solemoviridae. These results suggest that the virus should be considered as a novel species in the genus Enamovirus and tentatively named as “bean enamovirus 1”.

scholarly journals Novel enteric viruses in fatal enteritis of grey squirrels

2020 ◽  
Vol 101 (7) ◽  
pp. 746-750
Author(s):  
Akbar Dastjerdi ◽  
Camilla Benfield ◽  
David Everest ◽  
Mark F. Stidworthy ◽  
Roland Zell
Keyword(s):  
Phylogenetic Analysis ◽  
Recombination Event ◽  
Novel Species ◽  
Structural Proteins ◽  
Virus Particles ◽  
Orf2 Sequence ◽  
Genomic Characterization ◽  
Generation Sequencing ◽  
Grey Squirrels

Astro- and kobuviruses infect both humans and animals. Here, we report on the disease history, detection and genomic characterization of novel astro- and kobuviruses from fatal diarrhoea of two juvenile grey squirrels. The virus particles had enterovirus-like morphology and a diameter of 28–32 nm. Next-generation sequencing confirmed astro- and kobuviruses and sequence analysis revealed typical astrovirus and picornavirus genome organizations. The astrovirus ORF2 sequence clustered with a clade of unassigned astroviruses, with marmot and rodent mamastroviruses as closest relatives. For the kobuvirus, divergences greater than 49.4 % for P1 and 43.5 % in the non-structural proteins indicated a novel species. However, phylogenetic analysis of the 3D polymerase showed that it clustered with that of the newly classified ludopivirus A1, suggesting a previous recombination event in the evolution of the kobuvirus. Our data provide further insights into the diversity of astro- and kobuviruses and broaden the spectrum of viruses infecting grey squirrels.

scholarly journals FRET Characterization of Complex Conformational Changes in a Large 16S Ribosomal RNA Fragment Site-Specifically Labeled Using Unnatural Base Pairs

2016 ◽  
Vol 11 (5) ◽  
pp. 1347-1353 ◽  
Author(s):  
Thomas Lavergne ◽  
Rajan Lamichhane ◽  
Denis A. Malyshev ◽  
Zhengtao Li ◽  
Lingjun Li ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Conformational Changes ◽  
16S Ribosomal Rna ◽  
Base Pairs

scholarly journals Genomic Characterization of a Novel Alphacoronavirus Isolated from Bats, Korea, 2020

Viruses ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 2041
Author(s):  
Hai-Quynh Do ◽  
Van-Giap Nguyen ◽  
Chul-Un Chung ◽  
Yong-Shin Jeon ◽  
Sook Shin ◽  
...  
Keyword(s):  
New Species ◽  
Bioinformatics Analysis ◽  
Whole Genome Sequence ◽  
In Silico Prediction ◽  
Genetic Characteristics ◽  
Genomic Characterization ◽  
Eptesicus Serotinus ◽  
A New Species ◽  
Generation Sequencing

Coronavirus, an important zoonotic disease, raises concerns of future pandemics. The bat is considered a source of noticeable viruses resulting in human and livestock infections, especially the coronavirus. Therefore, surveillance and genetic analysis of coronaviruses in bats are essential in order to prevent the risk of future diseases. In this study, the genome of HCQD-2020, a novel alphacoronavirus detected in a bat (Eptesicus serotinus), was assembled and described using next-generation sequencing and bioinformatics analysis. The comparison of the whole-genome sequence and the conserved amino acid sequence of replicated proteins revealed that the new strain was distantly related with other known species in the Alphacoronavirus genus. Phylogenetic construction indicated that this strain formed a separated branch with other species, suggesting a new species of Alphacoronavirus. Additionally, in silico prediction also revealed the risk of cross-species infection of this strain, especially in the order Artiodactyla. In summary, this study provided the genetic characteristics of a possible new species belonging to Alphacoronavirus.

scholarly journals Genomic characterization of Sebokele virus 1 (SEBV1) reveals a new candidate species among the genus Parechovirus

2013 ◽  
Vol 94 (7) ◽  
pp. 1547-1553 ◽  
Author(s):  
M. L. Joffret ◽  
C. Bouchier ◽  
M. Grandadam ◽  
H. Zeller ◽  
C. Maufrais ◽  
...  
Keyword(s):  
Central African Republic ◽  
Novel Species ◽  
Genomic Features ◽  
Protein Motifs ◽  
Ljungan Virus ◽  
Candidate Species ◽  
Genomic Characterization ◽  
Bioinformatics Workflows

We determined the genomic features and the taxonomic classification of Sebokele virus 1 (SEBV1), a previously unclassified arbovirus isolated in 1972 from rodents collected in Botambi, Central African Republic. The complete genome sequence was obtained using a deep sequencing approach (Illumina technology) and dedicated bioinformatics workflows for data analysis. Molecular analysis identified SEBV1 as a picornavirus, most closely related to Ljungan viruses of the genus Parechovirus. The genome has a typical Ljungan virus-like organization, including the presence of two unrelated 2A protein motifs. Phylogenetic analysis confirmed that SEBV1 belongs to the parechovirus phylogroup and was most closely related to the Ljungan virus species. However, it appeared clearly distinct from all members of this phylogroup, suggesting that it represents a novel species of the genus Parechovirus.

scholarly journals Genomic characterization of a potentially novel Streptococcus species producing exopolysaccharide

3 Biotech ◽  
2019 ◽  
Vol 9 (4) ◽  
Author(s):  
Longzhan Gan ◽  
Yi Zhang ◽  
Rui Tang ◽  
Beike Liu ◽  
Shiting Wang ◽  
...  
Keyword(s):  
Streptococcus Species ◽  
Genomic Characterization
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