Comparative Genome Analysis of Bacillus sporothermodurans with Its Closest Phylogenetic Neighbor, Bacillus oleronius, and Bacillus cereus and Bacillus subtilis Groups

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.

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Complete Chloroplast Genome Sequences of Coconut cv. Kopyor Green Dwarf and Comparative Genome Analysis to Oil Palm, Date Palm, Sago Palm, and Miniature Sugar Palm

10.1007/978-3-030-70420-9_10 ◽

2021 ◽

pp. 189-216

Author(s):

Annisa Rahmawati ◽

Hugo Alfried Volkaert ◽

Diny Dinarti ◽

Ismail Maskromo ◽

Andi Nadia Nurul Latifa Hatta ◽

...

Keyword(s):

Chloroplast Genome ◽

Genome Analysis ◽

Oil Palm ◽

Date Palm ◽

Comparative Genome Analysis ◽

Genome Sequences ◽

Complete Chloroplast Genome ◽

Comparative Genome ◽

Sago Palm

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Comparative genome analysis ofCampylobacter jejuniusing whole genome DNA microarrays

FEBS Letters ◽

10.1016/s0014-5793(03)01164-5 ◽

2003 ◽

Vol 554 (1-2) ◽

pp. 224-230 ◽

Cited By ~ 99

Author(s):

B.M. Pearson ◽

C. Pin ◽

J. Wright ◽

K. I’Anson ◽

T. Humphrey ◽

...

Keyword(s):

Genome Analysis ◽

Dna Microarrays ◽

Whole Genome ◽

Comparative Genome Analysis ◽

Comparative Genome

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Comparative genome analysis and characterization of theSalmonellaTyphimurium strain CCRJ_26 isolated from swine carcasses using whole-genome sequencing approach

Letters in Applied Microbiology ◽

10.1111/lam.12859 ◽

2018 ◽

Vol 66 (4) ◽

pp. 352-359 ◽

Cited By ~ 7

Author(s):

P.H.N. Panzenhagen ◽

C.C. Cabral ◽

P.N. Suffys ◽

R.M. Franco ◽

D.P. Rodrigues ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genome Analysis ◽

Whole Genome ◽

Comparative Genome Analysis ◽

Comparative Genome

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Whole-genome sequence and comparative genome analysis of Lactobacillus paracasei DTA93, a promising probiotic lactic acid bacterium

Archives of Microbiology ◽

10.1007/s00203-020-01883-2 ◽

2020 ◽

Vol 202 (7) ◽

pp. 1997-2003 ◽

Cited By ~ 1

Author(s):

Armin Tarrah ◽

Shadi Pakroo ◽

Viviana Corich ◽

Alessio Giacomini

Keyword(s):

Lactic Acid ◽

Lactic Acid Bacterium ◽

Genome Sequence ◽

Genome Analysis ◽

Lactobacillus Paracasei ◽

Whole Genome Sequence ◽

Whole Genome ◽

Comparative Genome Analysis ◽

Comparative Genome

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Genome and Transcriptome Adaptation Accompanying Emergence of the Definitive Type 2 Host-Restricted Salmonella enterica Serovar Typhimurium Pathovar

mBio ◽

10.1128/mbio.00565-13 ◽

2013 ◽

Vol 4 (5) ◽

Cited By ~ 34

Author(s):

Robert A. Kingsley ◽

Sally Kay ◽

Thomas Connor ◽

Lars Barquist ◽

Leanne Sait ◽

...

Keyword(s):

Genome Analysis ◽

Salmonella Enterica ◽

Host Adaptation ◽

Whole Genome ◽

Comparative Genome Analysis ◽

Comparative Genome ◽

Content Type ◽

Serovar Typhimurium ◽

Genetic Signatures

ABSTRACTSalmonella entericaserovar Typhimurium definitive type 2 (DT2) is host restricted toColumba livia(rock or feral pigeon) but is also closely related toS. Typhimurium isolates that circulate in livestock and cause a zoonosis characterized by gastroenteritis in humans. DT2 isolates formed a distinct phylogenetic cluster withinS. Typhimurium based on whole-genome-sequence polymorphisms. Comparative genome analysis of DT2 94-213 andS. Typhimurium SL1344, DT104, and D23580 identified few differences in gene content with the exception of variations within prophages. However, DT2 94-213 harbored 22 pseudogenes that were intact in other closely relatedS. Typhimurium strains. We report a novelin silicoapproach to identify single amino acid substitutions in proteins that have a high probability of a functional impact. One polymorphism identified using this method, a single-residue deletion in the Tar protein, abrogated chemotaxis to aspartatein vitro. DT2 94-213 also exhibited an altered transcriptional profile in response to culture at 42°C compared to that of SL1344. Such differentially regulated genes included a number involved in flagellum biosynthesis and motility.IMPORTANCEWhereasSalmonella entericaserovar Typhimurium can infect a wide range of animal species, some variants within this serovar exhibit a more limited host range and altered disease potential. Phylogenetic analysis based on whole-genome sequences can identify lineages associated with specific virulence traits, including host adaptation. This study represents one of the first to link pathogen-specific genetic signatures, including coding capacity, genome degradation, and transcriptional responses to host adaptation within aSalmonellaserovar. We performed comparative genome analysis of reference and pigeon-adapted definitive type 2 (DT2)S. Typhimurium isolates alongside phenotypic and transcriptome analyses, to identify genetic signatures linked to host adaptation within the DT2 lineage.

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Metagenomic survey and whole genome sequencing of antimicrobial resistant bacteria in the sewage of a Japanese hospital

10.21203/rs.3.rs-51067/v1 ◽

2020 ◽

Author(s):

Miwa Katagiri ◽

Makoto Kuroda ◽

Tsuyoshi Sekizuka ◽

Norihide Nakada ◽

Yukitaka Ito ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genome Analysis ◽

Therapeutic Agents ◽

Resistant Bacteria ◽

Whole Genome ◽

Comparative Genome Analysis ◽

Comparative Genome ◽

Hospital Sewage

Abstract Background The dissemination of antimicrobial-resistant bacteria (ARB) and the transfer of antimicrobial resistance genes (ARGs) are a threat to public health. Antibiotics are indispensable therapeutic agents essential for the treatment of infectious diseases; however, inappropriate use of antibiotics leads to the emergence of ARB. It is established that hospitals are closely involved in the spread of antimicrobial resistance (AMR), which impedes antibiotic treatment and subsequently increases mortality. In addition, excrement of patients or healthy carriers of ARB are discharged from the hospital sewage through the wastewater treatment plant (WWTP) into the rivers, causing an AMR burden on the environment.Method Metagenomic analysis was performed on the hospital sewage samples, followed by whole genome sequencing of the extended spectrum β-lactamase (ESBL)-producing organisms (EPOs). A comparative genome analysis was also performed between EPO isolates from sewage and clinical isolates.Results Metagenomic analysis showed that the hospital sewage tanks had bacterial flora corresponding to the human gut. During the study period, the hospital was relocated to a newly constructed building with new sewage tanks; however, the presence of ARB/ARGs in the new hospital sewage tanks became markedly equivalent to that of the old hospital within one month. The ESBL blaCTX−M and carbapenemase blaIMP genes were not much detected in the original hospital sewage samples by metagenome analysis, but selection on CHROMagar ESBL increased the sensitivity to detect those β-lactamase genes. Comparative genome analysis between sewage and clinical EPO isolates revealed partial similarity; however, most EPO isolates exhibited a notable difference (≥ 50) in single nucleotide variations based on core-genome phylogeny. This result suggests that only some of the sewage EPO isolates were originated from the clinical patient. Therapeutic agents in the hospital sewage were analyzed and the concentration of levofloxacin and clarithromycin was 0.0325 and 0.0135 µg/mL, respectively.Conclusions Whole genome analysis between sewage and clinical isolates suggested that healthy or asymptomatic carriers may be involved in the contamination of hospital sewage. Moreover, the hospital sewage tank may serve as a hotspot for the horizontal transfer of ARGs under the selective pressure of antimicrobial agents. Therefore, ARB monitoring in hospital sewage is expected to detect the presence of carriers prior to nosocomial ARB outbreaks. In addition, hospital wastewater should be treated suitably to bring ARB below detectable levels to reduce the environmental AMR burden.

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