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Draft genome sequence of Bacillus sp. EE-W1 isolated from a biogas reactor

Abstract

Objectives

The genus Bacillus comprises spore-forming rod-shaped Gram-positive bacteria, which usually grow aerobically or anaerobically. Members of this genus are common environmental microorganisms. Also, they can be monitored in the food production chain. Genome sequence of Bacillus sp. strain EE-W1 will provide helpful information to understand its ecology and genetics. Draft genome data may be useful in the field of using Bacillus species in industrial biotechnology. Also, these data can be a useful resource for the study of comparative genomics.

Data description

Here, we present the draft genome sequence of Bacillus sp. strain EE-W1 isolated from a biogas reactor, Kazan, Russia. The assembled genome size was 5,769,164 bp, with a GC content 35.1%. This draft genome data can be accessed at DDBJ/ENA/GenBank under the accession WIPE00000000.

Objective

The genus Bacillus includes spore-forming rod-shaped Gram-positive aerobic or facultative anaerobic bacteria. A distinctive feature of the genus Bacillus is its ability to form endospores in response to various environmental and nutritional stresses. Members of this genus are common environmental microorganisms. Also, they can be monitored in the food production chain [1]. Moreover, some species of Bacillus with high proteolytic activity have demonstrated a sustained survival in some protein-fed anaerobic digesters, what finally led to an improved biogas productivity [2]. However, the Bacillus group also includes pathogenic species, therefore, it is necessary to develop proper hygiene and sanitation procedures to decrease the potential risk of transmission of the infectious disease [3]. Genome sequence of Bacillus sp. strain EE-W1 will provide helpful information to understand its ecology and genetics. Draft genome data can be also useful in the field of using Bacillus species in industrial biotechnology. Also, these data can be a useful resource for the study of comparative genomics.

Data description

The Bacillus sp. EE-W1 was isolated from a laboratory-scale mesophilic biogas reactor. Briefly, 1 g (wet weight) of digested wastes was consistently diluted with sterile tap water. 100 µL of each obtained dilution was spread onto LB agar plates and then cultured at + 37 °C. Finally, single colonies were transferred to new plates, and the cultivation process was repeated until pure cultures were received. For DNA extraction, the bacterial strain Bacillus sp. EE-W1 was cultured on LB agar at + 37 °C for 2 days. Genomic DNA from the Bacillus sp. EE-W1 was then extracted using a commercially available DNA extraction kit, FastDNA spin kit (#116540600; MP Biomedicals, USA), and assessed by spectrophotometric analysis as reported previously [4, 5]. The traditional identification of the strain EE-W1 was carried out using morphological characteristics and biochemical tests followed by the PCR-amplified 16S rRNA gene sequence analysis (Table 1) at the EzBioCloud Database [6]. The phylogenetic tree was then constructed with the MEGA 7 software [7]. The genome sequence of Bacillus sp. EE-W1 was received by Illumina sequencing as described previously [5]. Sequence read quality was checked using FastQC v0.11.5 [8] and trimmed with Trimmomatic version 0.36 [9]. The filtered reads were assembled into contigs with minimum contig length 500 bp using de novo assembler Velvet version 1.2.10 [10]. Contigs were ordered using progressive Mauve version 2.4.0 [11]. The quality of genome assembly was estimated with Quast version 5.0.0 [12]. Gene prediction and annotation was performed using the Rapid Annotation System Technology (RAST) server [13]. The rRNA genes were detected by using Barrnap version 0.9 [14], while tRNA genes were identified with Aragorn version 1.2 [15]. The phylogeny based on the whole genome data (Table 1) was determined by calculating the average nucleotide identity with closely related Bacillus species with the Orthologous Average Nucleotide Identity Tool (OrthoANI) [16].

Table 1 Overview of data files/data sets

The calculated OrthoANI values with closely related species showed that the strain EE-W1 presented OrthoANI values of 96.33% and 94.79% with Bacillus wiedmannii strain FSL W8-0169 and Bacillus mobilis strain 0711P9-1 (type strains), respectively. The draft genome assembly of Bacillus sp. EE-W1 consisted of 169 contigs larger than 500 bp, with a total size of 5,769,164 bp and mean GC content 35.1%. The obtained genome sequence data was at 117× coverage. The RAST server predicted 6104 coding sequences. The genome of Bacillus sp. EE-W1 encodes at least 3 rRNAs and 8 tRNAs. The genome of the strain EE-W1 also harbored genes related to proteins and carbohydrates degradation and fermentation (including mixed acid, lactate fermentation, acetyl-CoA fermentation to butyrate, acetoin, butanediol metabolism, and butanol biosynthesis). In addition, the genome contained various genes related to resistance to several toxic compounds and some antibiotics (such as streptothricin, tetracycline and fosfomycin).

Limitations

Current data is based on the draft level genome sequence, due to which exact length of the genome, synteny, number of rRNA and repetitive elements cannot be certainly reported.

Availability of data materials

The data described in this Data note can be freely and openly accessed at DDBJ/ENA/GenBank. Accession Numbers—https://identifiers.org/ncbi/insdc:WIPE00000000.1 (whole genome project) [17] and https://identifiers.org/ncbi/insdc:MN611309.1 (16S rRNA gene sequence) [18].

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Acknowledgements

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Funding

The reported study was funded by the Russian Foundation for Basic Research (RFBR, Grant No. 18-34-20002). RFBR did not take part in the design or realization of the study and in writing the manuscript.

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Authors

Contributions

WSM, EEZ and RFA conducted experiments, performed genome analysis, interpretation of the data and drafted the manuscript. AMZ supervised the project, designed the study and professionally revised the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Ayrat M. Ziganshin.

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Mohammed, W.S., Ziganshina, E.E., Akhmetova, R.F. et al. Draft genome sequence of Bacillus sp. EE-W1 isolated from a biogas reactor. BMC Res Notes 13, 152 (2020). https://doi.org/10.1186/s13104-020-04991-w

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Keywords

  • Draft genome
  • Firmicutes
  • Bacillus
  • Biogas reactor
  • Illumina sequencing