Aims: The cucumber mosaic virus (CMV) is categorized under the genus Cucumovirus and family Bromoviridae. This virus is known to infect over 1200 plant species from 100 families, including ornamental and horticultural plants. In this study, we pioneered a global genome comparison to decipher the unknown orchestrators behind the virulence and pathogenicity of CMV via the discovery of important single nucleotide polymorphic markers. Methodology and results: As a result, the genome size was found to be a potential preliminary country-specific marker for South Korea and the GC content can be utilized to preliminarily differentiate Turkey isolates from the others. The motif analysis as well as whole genome and coat protein phylogenetic trees were unable to form country-specific clusters. However, the coat protein haplotype analysis had successfully unconcealed country-specific single nucleotide polymorphic markers for Iran, Turkey and Japan isolates. Moreover, coat protein modelling and gene ontology prediction depicted high conservation across CMV isolates from different countries. Conclusion, significance and impact of study The country-specific single nucleotide polymorphic markers unearthed in this study may provide significant data towards the profiling of varying virulence and pathogenicity of CMV across the globe in time to combat the yield loss driven by this virus thru the most efficacious biological control measures in the future.
Cucumovirus--genetics ; Genome, Microbial

Emerging antibiotic resistance is a major global health threat. The analysis of nucleic acid sequences linked to susceptibility phenotypes facilitates the study of genetic antibiotic resistance determinants to inform molecular diagnostics and drug development. We collected genetic data (11,087 newly-sequenced whole genomes) and culture-based resistance profiles (10,991 out of the 11,087 isolates comprehensively tested against 22 antibiotics in total) of clinical isolates including 18 main species spanning a time period of 30 years. Species and drug specific resistance patterns were observed including increased resistance rates for Acinetobacter baumannii to carbapenems and for Escherichia coli to fluoroquinolones. Species-level pan-genomes were constructed to reflect the genetic repertoire of the respective species, including conserved essential genes and known resistance factors. Integrating phenotypes and genotypes through species-level pan-genomes allowed to infer gene-drug resistance associations using statistical testing. The isolate collection and the analysis results have been integrated into GEAR-base, a resource available for academic research use free of charge at https://gear-base.com.
Acinetobacter baumannii ; genetics ; isolation & purification ; Bacteria ; genetics ; isolation & purification ; Cell Culture Techniques ; methods ; Drug Resistance, Microbial ; genetics ; Escherichia coli ; genetics ; isolation & purification ; Genome, Bacterial ; Genotype ; Humans ; Internet ; Microbial Sensitivity Tests ; Phenotype ; Whole Genome Sequencing

Understanding the role of the microbiome in human health and how it can be modulated is becoming increasingly relevant for preventive medicine and for the medical management of chronic diseases. The development of high-throughput sequencing technologies has boosted microbiome research through the study of microbial genomes and allowing a more precise quantification of microbiome abundances and function. Microbiome data analysis is challenging because it involves high-dimensional structured multivariate sparse data and because of its compositional nature. In this review we outline some of the procedures that are most commonly used for microbiome analysis and that are implemented in R packages. We place particular emphasis on the compositional structure of microbiome data. We describe the principles of compositional data analysis and distinguish between standard methods and those that fit into compositional data analysis.
Biomarkers ; Chronic Disease ; Genome, Microbial ; Humans ; Metagenome ; Metagenomics ; Microbiota ; Models, Statistical ; Preventive Medicine ; Sequence Analysis, DNA ; Statistics as Topic

The modern era of microbial genome analysis began in earnest in the 2000s with the generalization of metagenomics and gene sequencing techniques. Studying complex microbial community such as oral cavity and colon by a pure culture is considerably ineffective in terms of cost and time. Therefore, various techniques for genomic analysis have been developed to overcome the limitation of the culture method and to explore microbial communities existing in the natural environment at the gene level. Among these, DNA fingerprinting analysis and microarray chip have been used extensively; however, the most recent method of analysis is metagenomics. The study summarily examined the overview of metagenomics analysis techniques, as well as domestic and foreign studies on disease genomics and cluster analysis related to oral metagenome. The composition of oral bacteria also varies across different individuals, and it would become possible to analyze what change occurs in the human body depending on the activity of bacteria living in the oral cavity and what causality it has with diseases. Identification, isolation, metabolism, and presence of functional genes of microorganisms are being identified for correlation analysis based on oral microbial genome sequencing. For precise diagnosis and treatment of diseases based on microbiome, greater effort is needed for finding not only the causative microorganisms, but also indicators at gene level. Up to now, oral microbial studies have mostly involved metagenomics, but if metatranscriptomic, metaproteomic, and metabolomic approaches can be taken together for assessment of microbial genes and proteins that are expressed under specific conditions, then doing so can be more helpful for gaining comprehensive understanding.
Bacteria ; Colon ; Dental Caries ; Diagnosis ; DNA Fingerprinting ; Generalization (Psychology) ; Genes, Microbial ; Genome, Microbial ; Genomics ; Human Body ; Metabolism ; Metabolomics ; Metagenome ; Metagenomics ; Methods ; Microbiota ; Mouth

Lactobacillus acidophilus UBLA-34, L. paracasei UBLPC-35, L. plantarum UBLP-40, and L. reuteri UBLRU-87 were isolated from different varieties of fermented foods. To determine the probiotic safety at the strain level, the whole genome of the respective strains was sequenced, assembled, and characterized. Both the core-genome and pan-genome phylogeny showed that L. reuteri was closest to L. plantarum than to L. acidophilus, which was closest to L. paracasei. The genomic analysis of all the strains confirmed the absence of genes encoding putative virulence factors, antibiotic resistance, and the plasmids.
Drug Resistance, Microbial ; Genome ; Lactobacillus acidophilus ; Lactobacillus ; Phylogeny ; Plasmids ; Probiotics ; Virulence Factors

The prevalence of multidrug-resistant gram-negative bacteria has continuously increased over the past few years; bacterial strains producing AmpC β-lactamases and/or extended-spectrum β-lactamases (ESBLs) are of particular concern. We combined high-resolution whole genome sequencing and phenotypic data to elucidate the mechanisms of resistance to cephamycin and β-lactamase in Korean Klebsiella pneumoniae strains, in which no AmpC-encoding genes were detected by PCR. We identified several genes that alone or in combination can potentially explain the resistance phenotype. We showed that different mechanisms could explain the resistance phenotype, emphasizing the limitations of the PCR and the importance of distinguishing closely-related gene variants.
Drug Resistance, Microbial ; Genome ; Gram-Negative Bacteria ; Klebsiella pneumoniae* ; Klebsiella* ; Korea* ; Phenotype ; Polymerase Chain Reaction ; Prevalence

BACKGROUND: The emerging mobile colistin resistance gene, mcr-1, is an ongoing worldwide concern and an evaluation of clinical isolates harboring this gene is required in Korea. We investigated mcr-1-possessing Enterobacteriaceae among Enterobacteriaceae strains isolated in Korea, and compared the genetic details of the plasmids with those in Escherichia coli isolates from livestock. METHODS: Among 9,396 Enterobacteriaceae clinical isolates collected between 2010 and 2015, 1,347 (14.3%) strains were resistant to colistin and those were screened for mcr-1 by PCR. Colistin minimum inhibitory concentrations (MICs) were determined by microdilution, and conjugal transfer of the mcr-1-harboring plasmids was assessed by direct mating. Whole genomes of three mcr-1-positive Enterobacteriaceae clinical isolates and 11 livestock-origin mcr-1-positive E. coli isolates were sequenced. RESULTS: Two E. coli and one Enterobacter aerogenes clinical isolates carried carried IncI2 plasmids harboring mcr-1, which conferred colistin resistance (E. coli MIC, 4 mg/L; E. aerogenes MIC, 32 mg/L). The strains possessed the complete conjugal machinery except for E. aerogenes harboring a truncated prepilin peptidase. The E. coli plasmid transferred more efficiently to E. coli than to Klebsiella pneumoniae or Enterobacter cloacae recipients. Among the three bacterial hosts, the colistin MIC was the highest for E. coli owing to the higher mcr-1-plasmid copy number and mcr-1 expression levels. Ten mcr-1-positive chicken-origin E. coli strains also possessed mcr-1-harboring IncI2 plasmids closely related to that in the clinical E. aerogenes isolate, and the remaining one porcine-origin E. coli possessed an mcr-1-harboring IncX4 plasmid. CONCLUSIONS: mcr-1-harboring IncI2 plasmids were identified in clinical Enterobacteriaceae isolates. These plasmids were closely associated with those in chicken-origin E. coli strains in Korea, supporting the concept of mcr-1 dissemination between humans and livestock.
Colistin ; Enterobacter aerogenes ; Enterobacter cloacae ; Enterobacteriaceae* ; Escherichia coli* ; Escherichia* ; Genome ; Humans* ; Klebsiella pneumoniae ; Korea* ; Livestock* ; Microbial Sensitivity Tests ; Plasmids* ; Polymerase Chain Reaction

OBJECTIVEMutations in 23S rRNA gene are known to be associated with macrolide resistance in Mycoplasma pneumoniae (M. pneumoniae). However, these mutations alone do not fully explain the high resistance rates in Asia. The aim of this study was to investigate other possible mutations involved in macrolide resistance in M. pneumoniae.

METHODSThe whole genomes of 10 clinical isolates of M. pneumoniae with macrolide resistance were sequenced by Illumina HiSeq2000 platform. The role of the macrolide-specific efflux transporter was assessed by efflux-pump inhibition assays with reserpine and carbonyl cyanide m-chlorophenyl-hydrazone (CCCP).

RESULTSA total of 56 single nucleotide polymorphisms (SNPs) were identified in 10 clinical isolates in comparison to the reference strains M129 and FH. Strikingly, 4 of 30 SNPs causing non-synonymous mutations were clustered in macrolide-specific efflux system gene macB encoding macrolide-specific efflux pump protein of the ATP-binding cassette transporter family. In assays of the minimal inhibitory concentrations (MIC) of macrolide antibiotics in the presence of the efflux pump inhibitors caused a significant decrease of MICs, even under detectable levels in some strains.

CONCLUSIONOur study suggests that macrolide efflux pump may contribute to macrolide resistance in M. pneumoniae in addition to the common point mutations in 23S rRNA gene.

Anti-Bacterial Agents ; pharmacology ; Drug Resistance, Bacterial ; genetics ; Genome-Wide Association Study ; Macrolides ; pharmacology ; Microbial Sensitivity Tests ; Mutation ; Mycoplasma pneumoniae ; drug effects ; genetics

Genome editing is defined as highly-effective and precise modification of cellular genome in a large scale. In recent years, such genome-editing methods have been rapidly developed in the field of industrial strain improvement. The quickly-updating methods thoroughly change the old mode of inefficient genetic modification, which is "one modification, one selection marker, and one target site". Highly-effective modification mode in genome editing have been developed including simultaneous modification of multiplex genes, highly-effective insertion, replacement, and deletion of target genes in the genome scale, cut-paste of a large DNA fragment. These new tools for microbial genome editing will certainly be applied widely, and increase the efficiency of industrial strain improvement, and promote the revolution of traditional fermentation industry and rapid development of novel industrial biotechnology like production of biofuel and biomaterial. The technological principle of these genome-editing methods and their applications were summarized in this review, which can benefit engineering and construction of industrial microorganism.
Biotechnology ; Fermentation ; Genetic Engineering ; methods ; Genome, Microbial ; Industrial Microbiology

In developing countries threat of cholera is a significant health concern whenever water purification and sewage disposal systems are inadequate. Vibrio cholerae is one of the responsible bacteria involved in cholera disease. The complete genome sequence of V. cholerae deciphers the presence of various genes and hypothetical proteins whose function are not yet understood. Hence analyzing and annotating the structure and function of hypothetical proteins is important for understanding the V. cholerae. V. cholerae O139 is the most common and pathogenic bacterial strain among various V. cholerae strains. In this study sequence of six hypothetical proteins of V. cholerae O139 has been annotated from NCBI. Various computational tools and databases have been used to determine domain family, protein-protein interaction, solubility of protein, ligand binding sites etc. The three dimensional structure of two proteins were modeled and their ligand binding sites were identified. We have found domains and families of only one protein. The analysis revealed that these proteins might have antibiotic resistance activity, DNA breaking-rejoining activity, integrase enzyme activity, restriction endonuclease, etc. Structural prediction of these proteins and detection of binding sites from this study would indicate a potential target aiding docking studies for therapeutic designing against cholera.
Bacteria ; Binding Sites ; Cholera ; Computer Simulation* ; Developing Countries ; DNA ; DNA Restriction Enzymes ; Drug Discovery ; Drug Resistance, Microbial ; Genome ; Humans ; Integrases ; Sewage ; Solubility ; Vibrio cholerae ; Vibrio cholerae O139* ; Water Purification