Here, we report the draft genome sequences of 3 Bacillus sporothermodurans strains isolated from ultra-high-temperature milk products in South Africa and Brazil and the type strain MB 581 (DSM 10599). The genomes will provide valuable information on the molecular dynamics of heat resistance in B.
ABSTRACT
Here, we report the draft genome sequences of 3 Bacillus sporothermodurans strains isolated from ultra-high-temperature milk products in South Africa and Brazil and the type strain MB 581 (DSM 10599). The genomes will provide valuable information on the molecular dynamics of heat resistance in B. sporothermodurans.
ANNOUNCEMENT
Bacillus sporothermodurans is a thermoresistant Gram-positive bacterium that can produce highly heat-resistant endospores (HRS) capable of surviving ultra-high-temperature (UHT) heat treatments (1, 2). First detected in UHT milk (3), it has subsequently been isolated from other dairy products, including UHT cream, chocolate milk, evaporated milk, and reconstituted milk (4). Furthermore, B. sporothermodurans has been isolated from non-dairy-based foods, including Indian curry (5), as well as from marine sources (6). After heat processing, the surviving spores may germinate and grow in the stored milk (1). The spores of B. sporothermodurans grow at low levels (≈105 CFU/ml) and do not affect the pH of the milk (2); as a result, its presence may go unnoticed. However, there are reports of B. sporothermodurans strains isolated in Brazil causing significant proteolytic activity leading to UHT milk spoilage (7). If spoilage does occur, though, there may be slight changes in color, off flavors, and the destabilization of casein micelles (2). Consequently, the main concerns to the dairy industry are milk quality, nonsterility of milk products, and biofilm formation in milk processing equipment.
B. sporothermodurans strains SAD and SA01 were isolated from UHT milk produced in South Africa, and B. sporothermodurans strain BR12 was isolated from UHT milk from Brazil. The type strain B. sporothermodurans DSM 10599 was obtained from Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH (DSMZ). The enumeration and isolation of strains SAD and SA01 were undertaken as previously described (8), with the substitution of plate count agar for brain heart infusion (BHI) agar (Oxoid, UK). Single colonies of overnight fresh cultures of all four strains of B. sporothermodurans were inoculated into BHI broth (Oxoid) and incubated at 37°C for 72 hours. Genomic DNA was extracted using the ZR bacterial DNA miniprep kit (Zymo Research, USA) and quantified using the Qubit instrument and double-stranded DNA (dsDNA) broad-range (BR) assay kit (Life Technologies, USA). Multiplexed paired-end libraries were prepared using the Nextera XT DNA sample preparation kit (Illumina, USA). Genome sequencing was carried out on an Illumina MiSeq system. The paired-end reads (2 × 300 bp) were checked for quality and trimmed and de novo assembled using the CLC genomics workbench version 9 (Qiagen, Netherlands), with all low-quality (Q, <20) data filtered out. The resultant contigs were submitted to GenBank, where gene annotation was implemented using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (9). The annotation was further uploaded to Rapid Annotation using Subsystem Technology (RAST) for subsystems‐based annotation (10–12).
The four assembled genomes had an average G+C content of 38.6%. Overall, genomes of B. sporothermodurans contain heat shock and hyperosmotic proteins (including DnaJ, GrpE, and GroEL) that will have an influence on the heat resistance and, consequently, the processing dynamics of food products. Additionally, all four strains sequenced contain the biofilm matrix protein component TasA and its homologs, which have been shown to be the major biofilm matrix component (13), especially in Bacillus subtilis. Ultimately, the whole-genome sequence of B. sporothermodurans will help improve our understanding of the heat resistance of this bacterium with the view of improving milk quality.
Data availability.
The genome sequences of all four strains of B. sporothermodurans are publicly available at NCBI GenBank under the BioProject accession number PRJNA379529. Raw and trimmed sequencing reads have been deposited in the NCBI SRA under the study accession number SRP188520. The GenBank and SRA accession numbers are listed in Table 1. This announcement represents the first version of all four genomes.
TABLE 1.
Summary report of the de novo assembly of four B. sporothermodurans strains
| Organism | GenBank accession no. | SRA accession no. | Total no. of reads | Genome size (bp) | No. of coding sequences | Coverage (×) | No. of contigs | N50 (kpb) |
|---|---|---|---|---|---|---|---|---|
| B. sporothermodurans DSM 10599 | NAZD00000000 | SRR8741694 | 3,570,064 | 3,783,858 | 4,257 | 226 | 527 | 15,402 |
| B. sporothermodurans SAD | NAZB00000000 | SRR8732968 | 2,523,238 | 3,857,089 | 4,111 | 175 | 110 | 114,649 |
| B. sporothermodurans SA01 | NAZA00000000 | SRR8732969 | 1,858,252 | 3,414,010 | 3,768 | 146 | 290 | 22,386 |
| B. sporothermodurans BR12 | NAZC00000000 | SRR8741693 | 3,421,418 | 3,974,872 | 4,558 | 193 | 805 | 9,377 |
ACKNOWLEDGMENTS
R.O.-D. acknowledges support from the Department of Science and Technology (DST), National Research Foundation (NRF), South Africa, in a form of scholarship disbursed through the Institute for Food, Nutrition and Well-being, Faculty of Natural and Agricultural Sciences, University of Pretoria, South Africa. We also acknowledge the HESA/IBSA Research Cooperation Program.
We have no potential conflicts of interest to disclose.
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
The genome sequences of all four strains of B. sporothermodurans are publicly available at NCBI GenBank under the BioProject accession number PRJNA379529. Raw and trimmed sequencing reads have been deposited in the NCBI SRA under the study accession number SRP188520. The GenBank and SRA accession numbers are listed in Table 1. This announcement represents the first version of all four genomes.
TABLE 1.
Summary report of the de novo assembly of four B. sporothermodurans strains
| Organism | GenBank accession no. | SRA accession no. | Total no. of reads | Genome size (bp) | No. of coding sequences | Coverage (×) | No. of contigs | N50 (kpb) |
|---|---|---|---|---|---|---|---|---|
| B. sporothermodurans DSM 10599 | NAZD00000000 | SRR8741694 | 3,570,064 | 3,783,858 | 4,257 | 226 | 527 | 15,402 |
| B. sporothermodurans SAD | NAZB00000000 | SRR8732968 | 2,523,238 | 3,857,089 | 4,111 | 175 | 110 | 114,649 |
| B. sporothermodurans SA01 | NAZA00000000 | SRR8732969 | 1,858,252 | 3,414,010 | 3,768 | 146 | 290 | 22,386 |
| B. sporothermodurans BR12 | NAZC00000000 | SRR8741693 | 3,421,418 | 3,974,872 | 4,558 | 193 | 805 | 9,377 |