Draft Genome Sequence of Bacillus paranthracis Strain DB-4, Isolated from Nukadoko, Fermented Rice Bran for Japanese Pickles

Fukuda, Daisuke; Nolasco-Hipólito, Cirilo

doi:10.1128/mra.00705-21

Cited by 6 publications

(6 citation statements)

References 11 publications

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“…Bacillus paranthracis is a new, recently delineated subtype that has been found in various environments [38,39]. Some researchers have identified five peroxidase genes that can promote the growth of lactic acid bacteria during fermentation in the genome of B. paranthracis isolated from fermented rice bran [40]. In the present study, 13 strains of B. paranthracis were also detected from pickled vegetables, and these strains may have similarly positive effects on the fermentation of vegetables.…”

Section: Discussionsupporting

confidence: 50%

Contamination of Plant Foods with Bacillus cereus in a Province and Analysis of Its Traceability

Lin,

Cha,

Brennan

et al. 2023

Microorganisms

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Bacillus cereus is an important zoonotic foodborne conditional pathogen. It is found in vegetables, dairy products, rice, and other foods, thereby greatly endangering human health. Investigations on B. cereus contamination in China primarily focus on raw milk, dairy products, meat, and others, and limited research has been conducted on plant-based foodstuffs. The rapid development of sequencing technology and the application of bioinformatics-related techniques means that analysis based on whole-genome sequencing has become an important tool for the molecular-epidemiology investigation of B. cereus. In this study, we investigated the contamination of B. cereus in six types of commercially available plant foods from eight regions of a province. The molecular epidemiology of the isolated B. cereus was analyzed by whole-genome sequencing. We aimed to provide fundamental data for the surveillance and epidemiology analysis of B. cereus in food products in China. The rapid traceability system of B. cereus established in this study can provide a basis for rapid molecular epidemiology analysis of B. cereus, as well as for the prevention and surveillance of B. cereus. Moreover, it can also be expanded to monitoring and rapid tracing of more foodborne pathogens.

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Section: Discussionsupporting

confidence: 50%

Contamination of Plant Foods with Bacillus cereus in a Province and Analysis of Its Traceability

Lin,

Cha,

Brennan

et al. 2023

Microorganisms

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“…Several extensively analyzed strains have been derived from diverse sources, such as fermented foods [ 62 ], meat and poultry products [ 63 ], and plants [ 64 ]. Investigations utilizing whole-genome sequencing techniques have unveiled strains of B. paranthracis exhibiting potential probiotic characteristics [ 64 ] and demonstrating biodegradation capabilities [ 65 ].…”

Section: Resultsmentioning

confidence: 99%

Exploring the Genomic Landscape of Bacillus paranthracis PUMB_17 as a Proficient Phosphatidylcholine-Specific Phospholipase C Producer

Baev,

Iliev,

Stefanov

et al. 2024

CIMB

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Phospholipases find versatile applications across industries, including detergent production, food modification, pharmaceuticals (especially in drug delivery systems), and cell signaling research. In this study, we present a strain of Bacillus paranthracis for the first time, demonstrating significant potential in the production of phosphatidylcholine-specific phospholipase C (PC-PLC). The investigation thoroughly examines the B. paranthracis PUMB_17 strain, focusing on the activity of PC-PLC and its purification process. Notably, the PUMB_17 strain displays extracellular PC-PLC production with high specific activity during the late exponential growth phase. To unravel the genetic makeup of PUMB_17, we employed nanopore-based whole-genome sequencing and subsequently conducted a detailed genome annotation. The genome comprises a solitary circular chromosome spanning 5,250,970 bp, featuring a guanine–cytosine ratio of 35.49. Additionally, two plasmids of sizes 64,250 bp and 5845 bp were identified. The annotation analysis reveals the presence of 5328 genes, encompassing 5186 protein-coding sequences, and 142 RNA genes, including 39 rRNAs, 103 tRNAs, and 5 ncRNAs. The aim of this study was to make a comprehensive genomic exploration that promises to enhance our understanding of the previously understudied and recently documented capabilities of Bacillus paranthracis and to shed light on a potential use of the strain in the industrial production of PC-PLC.

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“…Based on the morphological and physiological characteristics and the phylogenetic analysis of 16S rRNA sequences, YD01 was identified as B. paranthracis YD01. The draft genome sequence of B. paranthracis DB-4 was reported previously [40]. B. paranthracis ICIS-279 isolated from the human intestine was also reported to have tumor necrosis factor α (TNF-)-inhibitory activity [41].…”

Section: Isolation and Identification Of Strainmentioning

confidence: 99%

“…The draft genome sequence of B. paranthracis DB-4 and the genome sequence of B. paranthracis ICIS-279 were reported previously. The assembly of DB-4 revealed 57 contigs covering a total of 5,424,208 bp, with an N 50 value of 498,305 bp, a GC content of 35.2%, and a coding ratio of 84.0% [40]. Additionally, the genome size of ICIS-279 is 5,180,499 bp, with a GC content of 35.4%, and annotation revealed 5168 coding sequences, including 5168 proteins and 43 rRNA, 102 tRNA, and 5 ncRNA genes [41].…”

Section: Genome Assembly and Prediction Of Yd01mentioning

confidence: 99%

Biodegradation of Inosine and Guanosine by Bacillus paranthracis YD01

Du,

Jiang,

Sun

et al. 2023

IJMS

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Both inosine and guanosine are precursors of uric acid that may cause the diseases of hyperuricemia and gout in humans. Here, a promising bacterial strain for efficiently biodegrading both inosine and guanosine was successfully isolated from a healthy human intestine and identified as Bacillus paranthracis YD01 with 16S rRNA analysis. An initial amount of 49.6 mg·L−1 of inosine or 49.9 mg·L−1 of guanosine was completely removed by YD01 within 12 h, which showed that YD01 had a strong ability to biodegrade inosine and guanosine. Furthermore, the initial amount of 49.2 mg·L−1 of inosine or 49.5 mg·L−1 of guanosine was totally catalyzed by the intracellular crude enzymes of YD01 within 6 h, and the initial inosine amount of 49.6 mg·L−1 or guanosine of 49.7 mg·L−1 was biodegraded by the extracellular crude enzymes of YD01 within 9 h. Illumina Hiseq sequencing and database gene annotation were used to elucidate the genomic characteristics of B. paranthracis YD01. Purine nucleoside phosphorylase, encoded by gene 1785, gene 3933, and gene 4403, was found in the KEEG database, which played a crucial role in the biodegradation of inosine and guanosine. The results of this study provide valuable insights into the mechanisms for biodegrading inosine and guanosine using B. paranthracis YD01.

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Draft Genome Sequence of Bacillus paranthracis Strain DB-4, Isolated from Nukadoko, Fermented Rice Bran for Japanese Pickles

Abstract: Bacillus paranthracis strain DB-4 was isolated from nukadoko in Japan. We report the draft genome sequence of this strain to provide insights into the survival mechanisms of lactic acid bacteria in fermented rice bran.

Cited by 6 publications

References 11 publications

Contamination of Plant Foods with Bacillus cereus in a Province and Analysis of Its Traceability

Contamination of Plant Foods with Bacillus cereus in a Province and Analysis of Its Traceability

Exploring the Genomic Landscape of Bacillus paranthracis PUMB_17 as a Proficient Phosphatidylcholine-Specific Phospholipase C Producer

Biodegradation of Inosine and Guanosine by Bacillus paranthracis YD01

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