Phylogenomic analysis of Pseudomonas nitroreducens strains FY43 and FY47

Proper identification of strain is essential in understanding the ecology of a bacteria species. The classification of Pseudomonas nitroreducens is still being questioned and revised until now. The novel P. nitroreducens strains FY43 and FY47 used in this study have been reported to show a high level of tolerance to glyphosate. In this study, next-generation sequencing (NGS) and whole genome analysis were used to clarify the delineation of the species. Whole genome analysis showed that P. nitroreducens strains FY43 and FY47 shared high homology to five reference genomes of P. nitroreducens: strain B, Aramco J, NBRC 12694, DF05, and TX01. Phylogenomic and phylogenetic analysis (average nucleotide identity based on BLAST (ANIb), genome-to-genome distance (GGDC) analysis) showed that both P. nitroreducens strains FY43 and FY47 are Pseudomonas nitroreducens members. However, strains DF05 and TX01 were not correctly assigned at the species level for all the analyses. The P. nitroreducens strain DF05 and TX01 should be further investigated for their classification as the correct species classification is the prerequisite for future diversity studies.

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Comparative Whole Genome Analysis of Escherichia coli O157:H7 Isolates From Feedlot Cattle to Identify Genotypes Associated With the Presence and Absence of stx Genes

Frontiers in Microbiology ◽

10.3389/fmicb.2021.647434 ◽

2021 ◽

Vol 12 ◽

Author(s):

Mo Jia ◽

Ifigenia Geornaras ◽

Jennifer N. Martin ◽

Keith E. Belk ◽

Hua Yang

Keyword(s):

Escherichia Coli ◽

Metabolic Pathway ◽

Genome Analysis ◽

Feedlot Cattle ◽

Phylogenomic Analysis ◽

Whole Genome ◽

Foodborne Outbreak ◽

Whole Genome Analysis ◽

E Coli ◽

Red Recombination

A comparative whole genome analysis was performed on three newly sequenced Escherichia coli O157:H7 strains with different stx profiles, previously isolated from feedlot cattle [C1-010 (stx1−, stx2c+), C1-057 (stx−), and C1-067 (stx1+, stx2a+)], as well as five foodborne outbreak strains and six stx-negative strains from NCBI. Phylogenomic analysis demonstrated that the stx2c-carrying C1-010 and stx-negative C1-057 strains were grouped with the six NCBI stx-negative E. coli O157:H7 strains in Cluster 1, whereas the stx2a-carrying C1-067 and five foodborne outbreak strains were clustered together in Cluster 2. Based on different clusters, we selected the three newly sequenced strains, one stx2a-carrying strain, and the six NCBI stx-negative strains and identify their prophages at the stx insertion sites. All stx-carrying prophages contained both the three Red recombination genes (exo, bet, gam) and their repressor cI. On the other hand, the majority of the stx-negative prophages carried only the three Red recombination genes, but their repressor cI was absent. In the absence of the repressor cI, the consistent expression of the Red recombination genes in prophages might result in more frequent gene exchanges, potentially increasing the probability of the acquisition of stx genes. We further investigated each of the 10 selected E. coli O157:H7 strains for their respective unique metabolic pathway genes. Seven unique metabolic pathway genes in the two stx2a-carrying strains and one in the single stx2c-carrying and seven stx-negative strains were found to be associated with an upstream insertion sequence 629 within a conserved region among these strains. The presence of more unique metabolic pathway genes in stx2a-carrying E. coli O157:H7 strains may potentially increase their competitiveness in complex environments, such as feedlot cattle. For the stx2c-carrying and stx-negative E. coli O157:H7 strains, the fact that they were grouped into the same phylogenomic cluster and had the same unique metabolic pathway genes suggested that they may also share closely related evolutionary pathways. As a consequence, gene exchange between them is more likely to occur. Results from this study could potentially serve as a basis to help develop strategies to reduce the prevalence of pathogenic E. coli O157:H7 in livestock and downstream food production environments.

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First whole genome analysis of the novel coronavirus (SARS-CoV-2) obtained from COVID-19 patients from five districts in Western Serbia

Epidemiology and Infection ◽

10.1017/s095026882100220x ◽

2021 ◽

pp. 1-31

Author(s):

Dejan Vidanović ◽

Bojana Tešović ◽

Jeremy D Volkening ◽

Claudio L Afonso ◽

Joshua Quick ◽

...

Keyword(s):

Genome Analysis ◽

Whole Genome ◽

The Novel ◽

Whole Genome Analysis ◽

Novel Coronavirus

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Comparative whole genome analysis of nucleopolyhedroviruses infecting saturniid silkworms by next-generation sequencing

10.1603/ice.2016.114235 ◽

2016 ◽

Author(s):

Jun Kobayashi

Keyword(s):

Next Generation Sequencing ◽

Genome Analysis ◽

Whole Genome ◽

Next Generation ◽

Whole Genome Analysis ◽

Generation Sequencing

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Laboratory implementation of Next Generation Sequencing for medium and high throughput whole genome analysis of clinical M. tuberculosis complex strains

10.26226/morressier.5991c409d462b80292388d15 ◽

2017 ◽

Author(s):

Christian Utpatel

Keyword(s):

Next Generation Sequencing ◽

High Throughput ◽

Genome Analysis ◽

Whole Genome ◽

Next Generation ◽

Tuberculosis Complex ◽

Whole Genome Analysis ◽

Generation Sequencing

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Faculty Opinions recommendation of Whole-genome analysis of dorsal-ventral patterning in the Drosophila embryo.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1010934.191554 ◽

2003 ◽

Author(s):

Patricia Simpson

Keyword(s):

Genome Analysis ◽

Drosophila Embryo ◽

Whole Genome ◽

Whole Genome Analysis

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Detection of SARS-CoV-2 from patient fecal samples by whole genome sequencing

Gut Pathogens ◽

10.1186/s13099-021-00398-5 ◽

2021 ◽

Vol 13 (1) ◽

Author(s):

Andreas Papoutsis ◽

Thomas Borody ◽

Siba Dolai ◽

Jordan Daniels ◽

Skylar Steinberg ◽

...

Keyword(s):

Next Generation Sequencing ◽

Nasopharyngeal Swab ◽

Whole Genome ◽

Rt Pcr ◽

Whole Genome Analysis ◽

Fecal Samples ◽

Oral Transmission ◽

Study Participants ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Abstract Background SARS-CoV-2 has been detected not only in respiratory secretions, but also in stool collections. Here were sought to identify SARS-CoV-2 by enrichment next-generation sequencing (NGS) from fecal samples, and to utilize whole genome analysis to characterize SARS-CoV-2 mutational variations in COVID-19 patients. Results Study participants underwent testing for SARS-CoV-2 from fecal samples by whole genome enrichment NGS (n = 14), and RT-PCR nasopharyngeal swab analysis (n = 12). The concordance of SARS-CoV-2 detection by enrichment NGS from stools with RT-PCR nasopharyngeal analysis was 100%. Unique variants were identified in four patients, with a total of 33 different mutations among those in which SARS-CoV-2 was detected by whole genome enrichment NGS. Conclusion These results highlight the potential viability of SARS-CoV-2 in feces, its ongoing mutational accumulation, and its possible role in fecal–oral transmission. This study also elucidates the advantages of SARS-CoV-2 enrichment NGS, which may be a key methodology to document complete viral eradication. Trial registration ClinicalTrials.gov, NCT04359836, Registered 24 April 2020, https://clinicaltrials.gov/ct2/show/NCT04359836?term=NCT04359836&draw=2&rank=1).

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