scholarly journals Genomic characterization of bacteria from the ultra-oligotrophic Madison aquifer: insight into the archetypical LuxI/LuxR and identification of novel LuxR solos

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Peter C. Wengert ◽  
Narayan H. Wong ◽  
Hazel A. Barton ◽  
Han Ming Gan ◽  
André O. Hudson ◽  
...  
Keyword(s):  
Quorum Sensing ◽  
Bacterial Community ◽  
Ligand Binding ◽  
Genome Sequencing ◽  
Homoserine Lactone ◽  
Whole Genome ◽  
Acyl Homoserine Lactone ◽  
Genomic Characterization ◽  
Insight Into

Abstract Objectives To characterize the bacterial community of Wind Cave’s Madison aquifer through whole-genome sequencing, and to better understand the bacterial ecology by identifying genes involved in acyl-homoserine lactone (AHL) based quorum-sensing (QS) systems. Results Genome-based taxonomic classification revealed the microbial richness present in the pristine Madison aquifer. The strains were found to span eleven genera and fourteen species, of which eight had uncertain taxonomic classifications. The genomes of strains SD129 and SD340 were found to contain the archetypical AHL QS system composed of two genes, luxI and luxR. Surprisingly, the genomes of strains SD115, SD129, SD274 and SD316 were found to contain one to three luxR orphans (solos). Strain SD129, besides possessing an archetypical AHL QS luxI-luxR pair, also contained two luxR solos, while strain SD316 contained three LuxR solos and no luxI-luxR pairs. The ligand-binding domain of two LuxR solos, one each from strains SD129 and SD316, were found to contain novel substitutions not previously reported, thus may represent two LuxR orphans that detection and response to unknown self-produced signal(s), or to signal(s) produced by other organisms.

scholarly journals Quorum-Sensing Molecules: Sampling, Identification and Characterization of N-Acyl-Homoserine Lactone in Vibrio sp

2022 ◽  
Author(s):  
Noha Laj ◽  
Muhammed Elayadeth-Meethal ◽  
V. Aldous J. Huxley ◽  
Raishy R. Hussain ◽  
Mohamed Saheer Kuruniyan ◽  
...  
Keyword(s):  
Quorum Sensing ◽  
Homoserine Lactone ◽  
Acyl Homoserine Lactone ◽  
Identification And Characterization

scholarly journals Characterization of Genetically Modified Microorganisms Using Short- and Long-Read Whole-Genome Sequencing Reveals Contaminations of Related Origin in Multiple Commercial Food Enzyme Products

Foods ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2637
Author(s):  
Jolien D’aes ◽  
Marie-Alice Fraiture ◽  
Bert Bogaerts ◽  
Sigrid C. J. De Keersmaecker ◽  
Nancy H. C. Roosens ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetically Modified ◽  
Added Value ◽  
Phylogenomic Analysis ◽  
Whole Genome ◽  
Antimicrobial Resistance Genes ◽  
Long Read ◽  
Genomic Characterization

Despite their presence being unauthorized on the European market, contaminations with genetically modified (GM) microorganisms have repeatedly been reported in diverse commercial microbial fermentation produce types. Several of these contaminations are related to a GM Bacillus velezensis used to synthesize a food enzyme protease, for which genomic characterization remains currently incomplete, and it is unknown whether these contaminations have a common origin. In this study, GM B. velezensis isolates from multiple food enzyme products were characterized by short- and long-read whole-genome sequencing (WGS), demonstrating that they harbor a free recombinant pUB110-derived plasmid carrying antimicrobial resistance genes. Additionally, single-nucleotide polymorphism (SNP) and whole-genome based comparative analyses showed that the isolates likely originate from the same parental GM strain. This study highlights the added value of a hybrid WGS approach for accurate genomic characterization of GMM (e.g., genomic location of the transgenic construct), and of SNP-based phylogenomic analysis for source-tracking of GMM.

scholarly journals Case Report of an Extensively Drug-Resistant Klebsiella pneumoniae Infection With Genomic Characterization of the Strain and Review of Similar Cases in the United States

2018 ◽  
Vol 5 (5) ◽  
Author(s):  
Fiorella Krapp ◽  
Egon A Ozer ◽  
Chao Qi ◽  
Alan R Hauser
Keyword(s):  
United States ◽  
Case Report ◽  
Klebsiella Pneumoniae ◽  
Genome Sequencing ◽  
The United States ◽  
Whole Genome ◽  
Drug Resistant ◽  
Extensively Drug Resistant ◽  
Genomic Characterization

Abstract Reports of extensively drug-resistant and pan-drug-resistant Klebsiella pneumoniae (XDR-KP and PDR-KP) cases are increasing worldwide. Here, we report a case of XDR-KP with an in-depth molecular characterization of resistance genes using whole-genome sequencing, and we review all cases of XDR-KP and PDR-KP reported in the United States to date.

scholarly journals Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing

PLoS ONE ◽  
2015 ◽  
Vol 10 (12) ◽  
pp. e0145031 ◽  
Author(s):  
Margaret Staton ◽  
Teodora Best ◽  
Sudhir Khodwekar ◽  
Sandra Owusu ◽  
Tao Xu ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Tree Species ◽  
Whole Genome ◽  
Genomic Characterization ◽  
Hardwood Tree ◽  
Low Coverage
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