phylogenetic neighbor
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Author(s):  
Murat Sayan ◽  
Ayse Arikan ◽  
Murat Isbilen

Aims: This study determined SARS-CoV-2 variations by phylogenetic and virtual phenotyping analyses. Materials & methods: Strains isolated from 143 COVID-19 cases in Turkey in April 2021 were assessed. Illumina NexteraXT library preparation kits were processed for next-generation ]sequencing. Phylogenetic (neighbor-joining method) and virtual phenotyping analyses (Coronavirus Antiviral and Resistance Database [CoV-RDB] by Stanford University) were used for variant analysis. Results: B.1.1.7–1/2 (n = 103, 72%), B.1.351 (n = 5, 3%) and B.1.525 (n = 1, 1%) were identified among 109 SARS-CoV-2 variations by phylogenetic analysis and B.1.1.7 (n = 95, 66%), B.1.351 (n = 5, 4%), B.1.617 (n = 4, 3%), B.1.525 (n = 2, 1.4%), B.1.526-1 (n = 1, 0.6%) and missense mutations (n = 15, 10%) were reported by CoV-RDB. The two methods were 85% compatible and B.1.1.7 (alpha) was the most frequent SARS-CoV-2 variation in Turkey in April 2021. Conclusion: The Stanford CoV-RDB analysis method appears useful for SARS-CoV-2 lineage surveillance.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Luis Johnson Kangale ◽  
Didier Raoult ◽  
Eric Ghigo ◽  
Pierre-Edouard Fournier

AbstractMarseille-P9602T is a Chryseobacterium-like strain that we isolated from planarian Schmidtea mediterranea and characterized by taxono-genomic approach. We found that Marseille-P9602T strain exhibits a 16S rRNA gene sequence similarity of 98.76% with Chryseobacterium scophthalmum LMG 13028T strain, the closest phylogenetic neighbor. Marseille-P9602T strain was observed to be a yellowish-pigmented, Gram-negative, rod-shaped bacterium, growing in aerobic conditions and belonging to the Flavobacteriaceae family. The major fatty acids detected are 13-methyl-tetradecanoic acid (57%), 15-methylhexadecenoic acid (18%) and 12-methyl-tetradecanoic acid (8%). Marseille-P9602 strain size was found from genome assembly to be of 4,271,905 bp, with a 35.5% G + C content. The highest values obtained for Ortho-ANI and dDDH were 91.67% and 44.60%, respectively. Thus, hereby we unravel that Marseille-P9602 strain is sufficiently different from other closed related species and can be classified as a novel bacterial species, for which we propose the name of Chryseobacterium schmidteae sp. nov. Type strain is Marseille-P9602T (= CSUR P9602T = CECT 30295T).


2021 ◽  
Vol 12 (2) ◽  
pp. 268-287
Author(s):  
Luis Johnson Kangale ◽  
Didier Raoult ◽  
Fournier Pierre-Edouard

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.


2021 ◽  
Vol 10 (9) ◽  
Author(s):  
Christopher A. Gulvik ◽  
Dhwani Batra ◽  
Lori A. Rowe ◽  
Milli Sheth ◽  
Sarah Nobles ◽  
...  

ABSTRACT Gordonia sp. strain X0973 is a Gram-positive, weakly acid-fast, aerobic actinomycete obtained from a human abscess with Gordonia araii NBRC 100433T as its closest phylogenetic neighbor. Here, we report using Illumina MiSeq and PacBio reads to assemble the complete and circular genome sequence of 3.75 Mbp with 3,601 predicted coding sequences.


2020 ◽  
Vol 8 (8) ◽  
pp. 1185
Author(s):  
Rodney Owusu-Darko ◽  
Mushal Allam ◽  
Arshad Ismail ◽  
Carlos A. S. Ferreira ◽  
Sílvia D. de Oliveira ◽  
...  

Bacillus sporothermodurans currently possesses one of the most highly heat-resistant spores (HRS), which can withstand ultra-high temperature (UHT) processing. Determination of multiple whole genome sequences of B. sporothermodurans provided an opportunity to perform the first comparative genome analysis between strains and with B. oleronius, B. cereus, and B. subtilis groups. In this study, five whole genome sequences of B. sporothermodurans strains, including those belonging to the HRS clone (SAD and BR12) normally isolated from UHT milk, were compared with the aforementioned Bacillus species for gene clusters responsible for heat resistance. In the phylogenomic analysis, B. sporothermodurans, with its closest phylogenetic neighbor, B. oleronius, clustered with B. thermoamylovorans and B. thermotolerans. Heat shock proteins GrpE, GroES, GroEL, and DnaK presented identical sequences for all B. sporothermodurans strains, indicating that differences in functional efficiency are not involved in the thermal resistance variations. However, comparing all species evaluated, B. sporothermodurans exhibited a different gene configuration in the chromosomal region of the heat shock protein GrpE. Furthermore, only B. sporothermodurans strains presented the stage II sporulation protein P gene located in this region. Multisequence alignment and phylogenetic analysis of the ClpB protein showed differences for HRS and non-HRS strains. The study identified ClpC, ClpE, and ClpX as the three ATPases putatively involved in protein disaggregation in B. sporothermodurans. Bacillussporothermodurans exhibits high homology with other Bacillus species in the DnaK, DnaJ, GroEL, and GroES cluster of genes involved in heat resistance. The data presented here pave the way to select and evaluate the phenotypic effects of genes putatively involved in heat resistance.


2015 ◽  
Author(s):  
Kok-Gan Chan ◽  
Robson Ee ◽  
Kah-Yan How ◽  
Siew-Kim Lee ◽  
Wai-Fong Yin ◽  
...  

In this study, we sequenced the genome of P. pnomenusa RB38 and reported the finding of a pair of cognate luxI/R homologs which we firstly coined as ppnI, which is found adjacent to a luxR homolog, ppnR. An additional orphan luxR homolog, ppnR2 was also discovered. Multiple sequence alignment revealed that PpnI is a distinct cluster of AHL synthase compared to those of its nearest phylogenetic neighbor, Burkholderia spp. When expressed heterologously and analysed using high resolution tandem mass spectrometry, PpnI directs the synthesis of N-octanoylhomoserine lactone (C8-HSL). To our knowledge, this is the first documentation of the luxI/R homologs of the genus of Pandoraea.


Phytotaxa ◽  
2013 ◽  
Vol 143 (1) ◽  
pp. 43 ◽  
Author(s):  
Fatemeh Nasernakhaei ◽  
Mohammad Reza Rahiminejad ◽  
Hojjatolah Saeidi ◽  
Manoochehr Tavasoli

This study concerns the taxonomic investigation of the Iranian diploid Triticum gene pool using morphology and PCR-SSCP analysis of ITS nrDNA. A co-occurrence of two character states of leaf indumentum and anther length was found to be diagnostically significant among these taxa. Three SSCP profiles were detected among our specimens. Sequencing the representatives of different SSCP patterns detected three new nrITS haplotypes. Based on the results of this study we concluded that the genus Triticum at diploid level is represented by two taxa in Iran : T. monococcum subsp. aegilopoides and T. urartu, which is a new taxonomic interpretation of the former taxon. The phylogenetic neighbor-joining tree based on nrITS confirms this interpretation.


2011 ◽  
Vol 57 (7) ◽  
pp. 617-622 ◽  
Author(s):  
Kirsti E. Præsteng ◽  
Roderick I. Mackie ◽  
Isaac K.O. Cann ◽  
Svein D. Mathiesen ◽  
Monica A. Sundset

Strains of Butyrivibrio are principal cellulytic bacteria in the rumen of the High Arctic Svalbard reindeer ( Rangifer tarandus platyrhynchus ). According to phylogenetic analysis based on 16S rRNA gene sequencing, Butyrivibrio can be divided into three subgroups within the Clostridia class of the phylum Firmicutes, but the current phenotypic and genotypic differentiation within the family Lachnospiraceae is insufficient. This current study describes the sequence diversity of the 16S–23S rRNA intergenic transcribed spacer (ITS) region of Butyrivibrio isolates from reindeer. A total of 17 different ITS sequences with sizes between 449 and 784 nt were obtained. Genes encoding tRNAIle and tRNAAla were identified in four of the sequences. Phylogenetic neighbor-joining trees were constructed based on the ITS sequence and compared with a phylogenetic neighbor-joining tree based on 16S rRNA gene sequences previously obtained for the same isolates. These comparisons indicated a better differentiation between strains in the ITS sequence than the 16S rRNA gene based tree. Through this study, a better means for identifying and tracking fibrolytic and potentially probiotic Butyrivibrio strains in reindeer and other ruminants has been provided.


2010 ◽  
Vol 77 (4) ◽  
pp. 1196-1203 ◽  
Author(s):  
Riitta Rahkila ◽  
Per Johansson ◽  
Elina Säde ◽  
Johanna Björkroth

ABSTRACTIn two previous studies dealing with lactic acid bacteria (LAB) from modified-atmosphere-packaged (MAP) broiler products and a broiler processing plant, several isolates remained unidentified. According to 16S rRNA gene sequence analysis, 36 isolates were assigned to the genusEnterococcus.Numerical analysis of combined HindIII and EcoRI ribopatterns of these isolates resulted in species-specific clusters that were congruent with the clusters obtained by both DNA-directed RNA polymerase subunit A (rpoA) and phenylalanyl-tRNA synthetase α chain (pheS) housekeeping gene analyses. In the analyses, a group of five isolates distinct from any known enterococcal species clustered together. The five isolates were positioned in theEnterococcus aviumgroup, withE. devrieseibeing the closest phylogenetic neighbor. The DNA-DNA hybridization levels withE. devrieseiranged from 28.8 to 54.3% and indicated that these strains represented a novel species. The nameEnterococcus viikkiensissp. nov. is proposed, with strain DSM 24043T(LMG 26075T) being the type strain. Our study demonstrated that the identification of enterococci within theE. aviumphylogenetic group demands polyphasic taxonomic approaches. TherpoAandpheSgene similarities (99.0 to 99.2% and 94.3 to 95.4%, respectively) betweenE. viikkiensisand its closest phylogenetic neighbor,E. devriesei, were higher than those previously reported within the enterococci. In addition, the phenotypic profiles of the species in theE. aviumgroup were also highly similar, and some traits were found to be misleading for enterococci, such asE. viikkiensisdoes not grow at 45°C. The numerical analysis of combined HindIII and EcoRI ribopatterns was of considerable assistance in distinguishing enterococcal species within theE. aviumgroup.


2003 ◽  
Vol 49 (4) ◽  
pp. 269-280 ◽  
Author(s):  
K Wong ◽  
G B Golding

Microbial genomes are thought to be mosaic, making it difficult to decipher how these genomes have evolved. Whole-genome nearest-neighbor analysis was applied to the Sinorhizobium meliloti pSymB replicon to determine its origin, the degree of horizontal transfer, and the conservation of gene order. Prediction of the nearest neighbor based on contextual information, i.e., the nearest phylogenetic neighbor of adjacent genes, provided useful information for genes for which phylogenetic relationships could not be established. A large portion of pSymB genes are most closely related to genes in the Agrobacterium tumefaciens linear chromosome, including the rep and min genes. This suggests a common origin for these replicons. Genes with the nearest neighbor from the same species tend to be grouped in "patches". Gene order within these patches is conserved, but the content of the patches is not limited to operons. These data show that 13% of pSymB genes have nearest neighbors in species that are not members of the Rhizobiaceae family (including two archaea), and that these likely represent genes that have been involved in horizontal transfer. Key words: Sinorhizobium meliloti, horizontal transfer, pSymB evolution.


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