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Comparative Genomics (CG)

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Comparative Genomics (CG)

The goals of comparative genomics (CG) of bacteria are
(1) to discover useful biomarkers, and
(2) understand the mechanism of the evolution.
We, a team at CJ Bioscience Inc., are delighted to support comprehensive CG services for the users of EzBioCloud. The present version of EzBioCloud CG contains the following analyses from a set of multiple genomes:

Phylogenomic tree based on whole-genome SNP (Coming soon)
UPMGA dendrogram based on average nucleotide identity
Core/Pan-genome analysis
Biomarker discovery (differentially present genes among groups)
A web interface for comparative analysis based on reciprocal relations of gene(s) which provides identification mobile genomic island(s)
BLAST-search against all genes or genes included in the pan-genome

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The science behind our CG algorithm

The algorithms incorporated in your CG pipeline were published in Chun et. al. (2009)¹ and Ha et. al. (2019)². ¹

Publications based on EzBioCloud CG analysis

Comparative Genomic Analysis of the 2016 Vibrio cholerae Outbreak in South Korea

Ha et. al.(2019) doi: 10.3389/fpubh.2019.00228.
Abstract
In August 2016, South Korea experienced a cholera outbreak that caused acute watery diarrhea in three patients. This outbreak was the first time in 15 years that an outbreak was not linked to an overseas source. To identify the cause and to study the epidemiological implications of this outbreak, we sequenced the whole genome of Vibrio cholerae isolates; three from each patient and one from a seawater sample. Herein we present comparative genomic data which reveals that the genome sequences of these four isolates are very similar. Interestingly, these isolates form a monophyletic clade with V. cholerae strains that caused an outbreak in the Philippines in 2011. The V. cholerae strains responsible for the Korean and Philippines outbreaks have almost identical genomes in which two unique genomic islands are shared, and they both lack SXT elements. Furthermore, we confirmthat seawater is the likely source of this outbreak, which suggests the necessity for future routine surveillance of South Korea’s seashore.
Comparative genomic analysis of subspecies of Pantoea stewartii reveals distinct variations

Li et. al.(2019) doi: 10.1007/s42161-019-00328-0.
Abstract
Pantoea stewartii subsp. stewartii (Pnss) and P. stewartii subsp. indologenes (Pnsi) are closely related plant pathogens that differ in their host specificities. Pnss is the causal agent of Stewart’s wilt of corn, whereas Pnsi causes disease on millets but not corn. Comparative genomics is a valuable method for characterizing the differences between genomes, but there are few studies on this important quarantine pathogen. Here, we compared publicly available genomes of seven strains of Pnss and three strains of Pnsi. Pan- and core-genome analyses showed that strains isolated from close geographical regions are more similar in their genome structures. Gene content and collinearity analyses further revealed numerous strain-specific genes. In particular, the Pnss type strain DC283 contained over 1200 additional genes compared with other strains. Importantly, we also identified eleven genes that are only present in Pnsi genomes and thus may be useful to distinguish between Pnss and Pnsi strains. Overall, this study characterized the common and distinct genomic features of Pnss and Pnsi, which lay the foundation for future development of molecular methods to detect the Stewart’s wilt pathogen in maize for quarantine regulations and distinguish its two subspecies.
Complete Genome Sequencing and Comparative Genomic Analysis of Helicobacter Apodemus Isolated From the Wild Korean Striped Field Mouse (Apodemus agrarius) for Potential Pathogenicity

Kim et. al.(2018) doi: 10.3389/fphar.2018.00838.
Genomic characterization of Nocardia seriolae strains isolated from diseased fish

Han et. al.(2018) doi: 10.1002/mbo3.656.
Abstract
Members of the genus Nocardia are widespread in diverse environments; a wide range of Nocardia species are known to cause nocardiosis in several animals, including cat, dog, fish, and humans. Of the pathogenic Nocardia species, N. seriolae is known to cause disease in cultured fish, resulting in major economic loss. We isolated two N. seriolae strains, CK-14008 and EM15050, from diseased fish and sequenced their genomes using the PacBio sequencing platform. To identify their genomic features, we compared their genomes with those of other Nocardia species. Phylogenetic analysis showed that N. seriolae shares a common ancestor with a putative human pathogenic Nocardia species. Moreover, N. seriolae strains were phylogenetically divided into four clusters according to host fish families. Through genome comparison, we observed that the putative pathogenic Nocardia strains had additional genes for iron acquisition. Dozens of antibiotic resistance genes were detected in the genomes of N. seriolae strains; most of the antibiotics were involved in the inhibition of the biosynthesis of proteins or cell walls. Our results demonstrated the virulence features and antibiotic resistance of fish pathogenic N. seriolae strains at the genomic level. These results may be useful to develop strategies for the prevention of fish nocardiosis.
Genome sequence of Mycobacterium yongonense RT 955-2015 isolate from a patient misdiagnosed with multidrug-resistant tuberculosis: First clinical detection in Tanzania

Mnyambwa et. al.(2018) doi: 10.1016/j.ijid.2018.04.796.
Abstract
Background: Mycobacterium yongonense is a recently described novel species belonging to Mycobacterium avium complex, which is the most prevalent aetiology of non-tuberculous mycobacteria associated with pulmonary infections, and poses tuberculosis diagnostic challenges in high-burden, resource-con- strained settings.
Methods: Whole genome shotgun sequencing and comparative microbial genomic analyses were used to characterize the isolate from a patient diagnosed with multidrug-resistant tuberculosis (MDR-TB) after relapse.
Results: The genome sequence of the first case of M. yongonense (M. yongonense RT 955-2015) in Tanzania is presented. Sequence analysis revealed that the RT 955-2015 strain had a high similarity to M. yongonense 05-1390(T) (98.74%) and Mycobacterium chimaera DSM 44623(T) (98%). Its 16S rRNA showed similarity to Mycobacterium paraintracellulare KCTC 290849(T) (100%), Mycobacterium intracellulare ATCC 13950(T) (100%), M. chimaera DSM 44623(T) (99.9%), and M. yongonense 05-1390(T) (98%). The strain exhibited a substantially different rpoB sequence to that of M. yongonense 05-1390 (95.16%), but closely related to that of M. chimaera DSM 44623(T) (99.86%), M. intracellulare ATCC 13950(T), (99.53%), and M. paraintracellulare KCTC 290849(T) (99.53%).
Conclusions: In light of the OrthoANI algorithm and phylogenetic analysis, it was concluded that the isolate was M. yongonense Type II genotype, which is an indication that the patient was misdiagnosed with TB/MDR-TB and received inappropriate treatment.
Comparative Genomics of Thalassobius Including the Description of Thalassobius activus sp. nov., and Thalassobius autumnalis sp. nov.

Pujalte et. al.(2018) doi: 10.3389/fmicb.2017.02645.
Abstract
A taxogenomic study was conducted to describe two new Thalassobius species and to analyze the internal consistency of the genus Thalassobius along with Shimia and Thalassococcus. Strains CECT 5113T, CECT 5114, CECT 5118T, and CECT 5120 were isolated from coastal Mediterranean seawater, Spain. Cells were Gram-negative, non- motile coccobacilli, aerobic chemoorganotrophs, with an optimum temperature of 26◦C and salinity of 3.5–5%. Major cellular fatty acids of strains CECT 5113T and CECT 5114 were C18 : 1 !7c/!6c and C10 : 0 3OH, G+C content was 54.4–54.5 mol% and were able to utilize propionate, L-threonine, L- arginine, and L-aspartate as carbon sources. They exhibited 98.3% 16S rRNA gene sequence similarity, 75.0–75.1 ANIb and 19.5–20.9 digital DDH to type strain of their closest species, Thalassobius maritimus. Based on these data, strains CECT 5113T and CECT 5114 are recognized as a new species, for which the name Thalassobius activus is proposed, with strain CECT 5113T (=LMG 29900T) as type strain. Strains CECT 5118T and CECT 5120 were found to constitute another new species, with major cellular fatty acids C18 : 1 !7c/!6c and C18 : 1 !7c 11-methyl and a G+C content of 59.8 mol%; they were not able to utilize propionate, L-threonine, L- arginine or L-aspartate. Their closest species was Thalassobius mediterraneus, with values of 99.6% 16S rRNA gene sequence similarity, 79.1% ANIb and 23.2% digital DDH compared to the type strain, CECT 5383T. The name Thalassobius autumnalis is proposed for this second new species, with strain CECT 5118T (=LMG 29904T) as type strain. To better determine the phylogenetic relationship of the two new species, we submitted 12 genomes representing species of Thalassobius, Shimia, and Thalassoccocus, to a phylogenomic analysis based on 54 single protein-encoding genes (BCG54). The resulting phylogenomic tree did not agree with the current genera classification, as Thalassobius was divided in three clades, Thalassobius sensu stricto (T. mediterraneus, T. autumnalis sp. nov., and T. gelatinovorus), Thalassobius aestuarii plus the three Shimia spp (S. marina, S. haliotis, and Shimia sp. SK013) and finally, Thalasobius maritimus plus T. activus sp. nov. Thalassococcus halodurans remained apart from the two genera. Phenotypic inferences from explored genomes are presented.
Genomic Analysis of a Pathogenic Bacterium, Paeniclostridium sordellii CBA7122 Containing the Highest Number of rRNA Operons, Isolated from a Human Stool Sample

Kim et. al. 2017. doi: 10.3389/fphar.2017.00840
Genomic Analysis of Bacillus licheniformis CBA7126 Isolated from a Human Fecal Sample

Kim et. al. 2017. doi: 10.3389/fphar.2017.00724.

Tutorial for self-education/classes

[Tutorial] Comparative Genomics of Vibrio cholerae

A step-by-step example showing how to use the comparative genomics functions in EzBioCloud with the notorious Vibrio cholerae organisms

Go to tutorial

Comparative Genomics (CG)

Comparative Genomics (CG)

The science behind our CG algorithm

Publications based on EzBioCloud CG analysis

Comparative Genomic Analysis of the 2016 Vibrio cholerae Outbreak in South Korea

Comparative genomic analysis of subspecies of Pantoea stewartii reveals distinct variations

Complete Genome Sequencing and Comparative Genomic Analysis of Helicobacter Apodemus Isolated From the Wild Korean Striped Field Mouse (Apodemus agrarius) for Potential Pathogenicity

Genomic characterization of Nocardia seriolae strains isolated from diseased fish

Genome sequence of Mycobacterium yongonense RT 955-2015 isolate from a patient misdiagnosed with multidrug-resistant tuberculosis: First clinical detection in Tanzania

Comparative Genomics of Thalassobius Including the Description of Thalassobius activus sp. nov., and Thalassobius autumnalis sp. nov.

Genomic Analysis of a Pathogenic Bacterium, Paeniclostridium sordellii CBA7122 Containing the Highest Number of rRNA Operons, Isolated from a Human Stool Sample

Genomic Analysis of Bacillus licheniformis CBA7126 Isolated from a Human Fecal Sample

Tutorial for self-education/classes

[Tutorial] Comparative Genomics of Vibrio cholerae

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Comparative Genomics (CG)

Comparative Genomics (CG)

The science behind our CG algorithm

Publications based on EzBioCloud CG analysis

Comparative Genomic Analysis of the 2016 Vibrio cholerae Outbreak in South Korea

Comparative genomic analysis of subspecies of Pantoea stewartii reveals distinct variations

Complete Genome Sequencing and Comparative Genomic Analysis of Helicobacter Apodemus Isolated From the Wild Korean Striped Field Mouse (Apodemus agrarius) for Potential Pathogenicity

Genomic characterization of Nocardia seriolae strains isolated from diseased fish

Genome sequence of Mycobacterium yongonense RT 955-2015 isolate from a patient misdiagnosed with multidrug-resistant tuberculosis: First clinical detection in Tanzania

Comparative Genomics of Thalassobius Including the Description of Thalassobius activus sp. nov., and Thalassobius autumnalis sp. nov.

Genomic Analysis of a Pathogenic Bacterium, Paeniclostridium sordellii CBA7122 Containing the Highest Number of rRNA Operons, Isolated from a Human Stool Sample

Genomic Analysis of Bacillus licheniformis CBA7126 Isolated from a Human Fecal Sample

Tutorial for self-education/classes

[Tutorial] Comparative Genomics of Vibrio cholerae

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