Data on genome sequencing, analysis and annotation of a pathogenic Bacillus cereus 062011msu

Rathy, Rashmi; Paul, Sayan; Ponesakki, Vasanthakumar; Paulkumar, Kanniah; Muthu, Suriya Prabha; Arumugaperumal, Arun; Thangapandi, Emmanuel Joshua Jebasingh Sathiya Balasingh; Balakrishnan, Suresh; Rajendhran, Jeyaprakash; Sivasubramaniam, Sudhakar

doi:10.1016/j.dib.2017.12.054

Cited by 7 publications

(3 citation statements)

References 15 publications

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“…The annotation was loaded in CLC Genomics Workbench and the gene structure map was generated and exported. Reference based assembly was done for phage reads by Kluyvera ascorbata ATCC 33433 16S ribosomal sequence genome as reference [31].…”

Section: Gene Prediction and Gene Ontology (Go) Annotationmentioning

confidence: 99%

Genomic analysis of Escherichia phage CMSTMSU isolated from shrimp farm effluent water

Lelin,

Thirumalaikumar,

Uma

et al. 2024

Preprint

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Background Escherichia phage CMSTMSU which isolated from shrimp farm effluent water was sequenced the whole genome and find out the gene ontology, predicted protein statistics, enzyme classes and predicting the secondary structure analysis of protein etc. Bioinformatics tools like CANU algorithm for interpretation of incomplete assemblies, Blast2GO tools to study the Gene Ontology, Mauve system for constructing multiple genome alignments related to evolutionary events Rapid annotation using subsystems technology (RAST) used to annotate protein sequences and Iterative Threading Assembly Refinement (I-TASSER) used protein secondary structure prediction were carried out. Results According to sequencing results, the genome's average read length was found to be 3.4 Kb, with a total of 88676 reads observed. A single contig with 35.6% GC content and a genome size of 386.4 kb was produced by the CANU assembly. 767 genes and 700 proteins were annotated, according to the BLAST2GO mapping, and BLAST hits demonstrated sequence similarity of at least 70% to the known protein sequences in the nr database. A study of the KEGG pathway revealed that 18 sequences were involved in the metabolism of thiamine, 26 sequences in the metabolism of pyrdimine, and 37 sequences in the metabolism of purines. Escherichia phage CMSTMSU was found to be closely related to Escherichia PBECO 4, Escherichia Phage 121Q, and Escherichia phage vB Eco slurp01, according to MAUV alignment. Escherichia phage CMSTMSU protein was found to have a close relationship with other phages, such as Salmonella phage munch, Klebsiella phage vB KleM RaK2, and Cronobacter phage CsaM GAP32, according to secondary structure prediction. Conclusions Compared to other reference phages in our study, it is noteworthy that the newly isolated phages' large genome sequences have the potential to spark curiosity from a biological standpoint.

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Section: Gene Prediction and Gene Ontology (Go) Annotationmentioning

confidence: 99%

Genomic analysis of Escherichia phage CMSTMSU isolated from shrimp farm effluent water

Lelin,

Thirumalaikumar,

Uma

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

“…The FastQC quality control tool version 0.11.8 (https:// www.bioinformatics.babraham.ac.uk/projects/fastqc/) (Andrews 2016) and CLC Genomics Workbench version 11.0.1 (Rathy et al 2018) were used to analyze the quality of the sifted raw reads and trim the ambiguous low-quality reads. After quality assessment, the filtered reads were subjected to de novo assembly by using the CLC Genomics Workbench.…”

Section: Quality Control De Novo Assembly and Genome Completeness Ementioning

confidence: 99%

The draft genome of a new Verminephrobacter eiseniae strain: a nephridial symbiont of earthworms

et al. 2020

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Purpose: Verminephrobacter is a genus of symbiotic bacteria that live in the nephridia of earthworms. The bacteria are recruited during the embryonic stage of the worm and transferred from generation to generation in the same manner. The worm provides shelter and food for the bacteria. The bacteria deliver micronutrients to the worm. The present study reports the genome sequence assembly and annotation of a new strain of Verminephrobacter called Verminephrobacter eiseniae msu. Methods: We separated the sequences of a new Verminephrobacter strain from the whole genome of Eisenia fetida using the sequence of V. eiseniae EF01-2, and the bacterial genome was assembled using the CLC Workbench. The de novo-assembled genome was annotated and analyzed for the protein domains, functions, and metabolic pathways. Besides, the multigenome comparison was performed to interpret the phylogenomic relationship of the strain with other proteobacteria. Result: The FastqSifter sifted a total of 593,130 Verminephrobacter genomic reads. The de novo assembly of the reads generated 1832 contigs with a total genome size of 4.4 Mb. The Average Nucleotide Identity denoted the bacterium belongs to the species V. eiseniae, and the 16S rRNA analysis confirmed it as a new strain of V. eiseniae. The AUGUSTUS genome annotation predicted a total of 3809 protein-coding genes; of them, 3805 genes were identified from the homology search. Conclusion: The bioinformatics analysis confirmed the bacterium is an isolate of V. eiseniae, and it was named Verminephrobacter eiseniae msu. The whole genome of the bacteria can be utilized as a useful resource to explore the area of symbiosis further.

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“…DNA probes in combination with polymerase chain reaction (PCR) technology have been employed to identify specific bacteria. Over the years, this technique has been used for the detection and identification of bacteria from the natural environment without the necessity for cell cultivation (Filho et al, ; Rathy et al, ). Recent studies have proven that conventional PCR is very effective in the identification of microbial species in a medium.…”

Section: Introductionmentioning

confidence: 99%

Optimization of thermosonication on Bacillus cereus from pork: Effects on inactivation and physicochemical properties

Owusu‐Ansah

Osae

et al. 2020

J Food Process Engineering

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Aims: The objective of this study was to optimize thermosonication conditions under different processing conditions of temperature, pretreatment time, and ultrasound frequencies and to study its influence on the inactivation behavior of Bacillus cereus and also to predict the conditions that will result in the best qualities of the pork meat regarding color, texture, moisture content loss, and fat content loss. Methods: To evaluate the influence of temperature (50-70 C), ultrasound frequency (20-60 kHz), and processing time (10-20 min) on color retention, lowest hardness, fat content loss, moisture content loss, and maximizing inactivation of B. cereus spores suspended in sterilized distilled water (SDW), as well as B. cereus inoculated in pork meat, response surface methodology was employed. Result: The findings from the study showed that thermosonication treatment had a significant effect on color, texture, fat content loss, B. cereus spores suspended in SDW, B. cereus inoculated in pork, and moisture content loss. The optimum operating conditions to accomplish the best inactivation behavior of B. cereus and physicochemical properties of pork meat were ultrasound frequency of 20 kHz, temperature of 70 C, and processing time of 13.56 min. Considering the abovementioned conditions, the predicted results obtained include B. cereus in SDW (0.79 CFU/g), B. cereus in pork (0.47 CFU/g), moisture content loss (22.42%), color (45.48), texture (134.38 N), and fat content (68.63%). These outcomes were in line with the experimental values and the overall desirability was 0.534. Conclusions:The results of our study confirm that thermosonication has a better way of enhancing the quality of pork meat under the application of the suitable parameters.This can advance the processing and production of pork meat by the meat industries. Practical ApplicationsPork meat is one of the most extensively consumed products in the world particularly in Asia and some parts of Africa. This product is in high consumer demand, but it is easily contaminated by microorganism, which leads to high deterioration and loss of quality.Thermosonication could be used as an effective and efficient technique for the meat industry. Its application will enhance the inactivation of deteriorative microorganisms and improve the physiochemical properties of pork meat.

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Data on genome sequencing, analysis and annotation of a pathogenic Bacillus cereus 062011msu

Cited by 7 publications

References 15 publications

Genomic analysis of Escherichia phage CMSTMSU isolated from shrimp farm effluent water

Genomic analysis of Escherichia phage CMSTMSU isolated from shrimp farm effluent water

The draft genome of a new Verminephrobacter eiseniae strain: a nephridial symbiont of earthworms

Optimization of thermosonication on Bacillus cereus from pork: Effects on inactivation and physicochemical properties

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