
==== Front
Data Brief
Data Brief
Data in Brief
2352-3409
Elsevier

S2352-3409(24)00771-6
10.1016/j.dib.2024.110807
110807
Data Article
Analysis of the genome of Bacillus safensis strain WOB3 KX774195, a Linamarin-utilizing bacterium (LUB) isolated from Cassava wastewater (CWW), Lagos State, Nigeria
Ogunyemi Adewale K. adewale.ogunyemi@trinityuniversity.edu.ng
@K24619Adewale
ab⁎
Buraimoh Olanike M. ce
Dauda Wadzani P. f
Akapo Olufunmilayo O. g
Ogunyemi Bukola C. d
Samuel Titilola A. de
Ilori Matthew O. @milori
c
Amund Olukayode O. c
a Department of Microbiology, Trinity University, Yaba, Lagos State, Nigeria
b Department of Biological Sciences (Microbiology Unit), Lagos State University of Science & Technology, Ikorodu, Lagos State, Nigeria
c Department of Microbiology, University of Lagos, Akoka, Lagos State, Nigeria
d Department of Biochemistry, University of Lagos, Id-Araba, Lagos State, Nigeria
e TETFund Centre of Excellence on Biodiversity Conservation and Ecosystem Management (TCEBCEM), University of Lagos, Akoka, Lagos State, Nigeria
f Department of Agronomy (Crop Science Unit), Federal University Gashua, Gashua, Yobe State, Nigeria
g Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa Main Campus, KwaDlangezwa, 3886, South Africa
⁎ Corresponding author. adewale.ogunyemi@trinityuniversity.edu.ng@K24619Adewale
13 8 2024
12 2024
13 8 2024
57 11080723 2 2024
8 5 2024
2 8 2024
© 2024 The Authors
2024
https://creativecommons.org/licenses/by-nc/4.0/ This is an open access article under the CC BY-NC license (http://creativecommons.org/licenses/by-nc/4.0/).
Linamarin-utilizing bacterium (LUB) is a microorganism that uses and breaks down cassava's principal cyanogenic compound, linamarin. Here, we present the draft genome sequence of Bacillus safensis strain WOB3 (previously Bacillus pumilus strain WOB3) sequenced and assembled with a total reads of 8,750,054 bp. The genome has 1,269 contigs and, G+C content of 41.55%. The genome has 4,749 total genes, 4,614 protein-coding sequences (CDSs), 3, 8 and 10 rRNA genes, 74 tRNA genes, and 5 ncRNA genes. This whole genome shotgun project has been deposited in GenBank under accession number JAYSGU000000000

Keywords

Bacillus safensis
Cassava wastewater (CWW)
Whole genome sequence
Linamarin
Linamarin-utilizing bacterium
==== Body
pmcSpecifications TableSubject area	Biology	
More specific subject area	Microbiology, Microbial Genomics, Molecular Biology	
Type of data	Whole genomic sequence data represented by Tables and Figures	
How data was acquired	The complete genome sequence was determined using the Illumina HiSeq4000X platforms	
Data format	Raw and analyzed	
Parameters for data collection	Pure culture of Bacillus safensis WOB3 was grown in nutrient agar (NA) at a temperature of 37°C and pH of 7.0	
Description of data collection	The genomic DNA was sequenced and annotation was done by using Prokaryotic Genome Annotation Pipeline (PGAP)	
Experimental features	Raw sequence reads generated using Illumina MiHiSeq4000X platform	
Data source location	Cassava wastewater (CWW) samples were collected from a processing factory, in Odogunyan, Ikorodu, Lagos State, Nigeria	
Data accessibility	The complete genome sequence of Bacillus safensis WOB3 was deposited in NCBI GenBank under accession JAYSGU000000000
Direct URLto data:numberhttps://www.ncbi.nlm.nih.gov/nuccore/JAYSGU000000000.1
Database link: Bioproject: PRJNA1043453
Biosample: SAMN38323292	

1 Value of the Data

• This study reports the genomic insights of Bacillus safensis strain WOB3 KX774195, a linamarin-utilizing bacterium (LUB), isolated from cassava wastewater in Odogunyan, Ikorodu, Lagos State, Nigeria, using whole-genome sequencing.

• The data provides important information about the detoxification of cyanogens with valuable insights on the prospects of linamarase and other associated genes.

• These genomic data provide information on Bacillus safensis' metabolic strategies for detoxifying cassava wastewater.

• Data of the draft genome sequencing of a Bacillus safensis is available for download without restrictions. This data can benefit bioinformaticians and environmental microbiologists as it can be used as reference sample or for testing. Moreover, it can also be used for educational purposes.

• The linamarin residues present in cassava products are causing severe environmental problems in many cassava processing plants in Nigeria, the largest cassava producer worldwide. These residues are a significant concern, given cassava products' critical role in the human diet.

• The study's data will help policymakers develop environmentally friendly policies and mitigate cyanogen pollution.

2 Background

Linamarin occurs naturally in cassava and other plants [1,2]. As linamarin is metabolized, hydrogen cyanide (HCN), a toxic compound, is released [2,3]. A linamarin-utilizing bacterium is an organism that utilizes and degrades linamarin, a major cyanogenic compound in cassava. Microbes that degrade linamarin use it as a sole carbon source by breaking down the compound [4]. They possess specific enzymes such as linamarase, which can hydrolyze linamarin to produce hydrogen cyanide and glucose. The release of hydrogen cyanide during the degradation process is a potential hazard, as it is highly toxic to most living organisms [4]. Researchers have identified bacterial strains like Bacillus, Pseudomonas and Stenotrophomonas as linamarin degraders, demonstrating their successful use of linamarin [5]. Bacillus is a genus that belongs to the phylum Firmicutes, with diverse bacterial species that are Gram-positive, rod-shaped, and spore formers [6]. Bacillus species are ubiquitous and have been isolated from numerous environments such as plants, animals, freshwater, and soil [7]. Some strains of Bacillus genus promote growth of different plants through various mechanisms, such as biofertilization, increasing accessibility of primary nutrients such as sulphur, potassium, phosphorus, nitrogen, iron, aromatic compounds for the strain, virulence (associated with disease and defense), dormancy (with sporulation), RNA and DNA metabolism, stress response, miscellaneous, through the production of phytohormones such as indole acetic acid (IAA), auxin and ethylene, as well as biocontrol by production of antimicrobial metabolites [[8], [9], [10]]. In addition, Bacillus species can form spores, an advantage that allows this group of bacteria to survive in unfavorable conditions [11]. This work aims to establish data on the genome sequence of Bacillus safensis WOB3 and its linamarase system to provide genomic information for further evaluations regarding detoxification of cyanogens.

3 Data Description

Bacillus safensis WOB3 was isolated from CWW collected from a processing factory, Odogunyan, Ikorodu, Lagos State, Nigeria. This study presents the draft whole genome sequence of Bacillus safensis WOB3. The genome sequencing was performed using the Illumina Hiseq4000X platform. The assembled genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (version 6.6), with default parameters [12]. The results show that the draft genome sequence of Bacillus safensis strain WOB3 (previously Bacillus pumilus strain WOB3) was sequenced and assembled with 8,750,054 bp of total reads. There are 1,269 contigs in the strain WOB3 genome, which has a G+C content of 41.55%. The strain WOB3 genome has a genomic size of 4.0 x 106 bp (4.0 Mb) with a corresponding genome coverage of 328X. Furthermore, strain WOB3 has 4,749 total genes, 4,614 protein-coding sequences (CDSs), 3, 8 and 10 rRNA genes, 74 tRNA genes, and 5 ncRNA genes. The assembly statistics and genomic features of Bacillus safensis WOB3 were summarized in Table 1. Bacillus safensis WOB3 whole genome sequence was used to construct an accurate evolutionary relationship with other bacterial whole genomes closely related to Bacillus safensis species using the Type Strain Genome Server (TYGS) [13]. Fig. 1 shows that Bacillus safensiis WOB3 is closely related to Bacillus safensis FO-36b and forms a clade with Bacillus safensis. Table 2, Table 3 give further information on Genome Blast Distance (GBDP) phylogeny of Bacillus safensis WOB3.Table 1 Genome features of Bacillus safensis strain WOB3.

Table 1Attribute	Value	
Total reads	8,750,054	
Genome coverage (X)	328	
Genome size (Mb)	4.0	
CDSs (total)	4,649	
CDSs (with protein)	4,614	
CDSs (without protein)	35	
Genes (total)	4,749	
Number of contigs	1,269	
GC content (%)	41.55	
Contig N50 (kb)	299.4	
Contig L50	5	
tRNA	74	
rRNA	3,8,10	
ncRNA	5	
Accession number	JAYSGU000000000	
CDS- coding sequence; GC - guanine-cytosine content; tRNA-transfer RNAs; rRNA- ribosomal RNA; ncRNA- non-coding RNAs.

Fig. 1 Whole genome phylogenetic tree constructed by Type Strain Genome Server, using Maximum Likelihood Method based on Generalised Time Reversible (GTR) model. The tree shows the close relationship between Bacillus safensis WOB3 with the closed species.

Fig 1:

Table 2 Comparison of several Bacillus isolates based on genomic metrics including digital DNA-DNA hybridization (dDDH).

Table 2:Subject strain	dDDH (d4, in %)	C.I. (d4, in %)	dDDH (d6, in %)	C.I. (d6, in %)	G+C content difference (in %)	
Bacillus safensis FO-36b	84.2	[81.4 - 86.6]	88	[85.1 - 90.5]	0.26	
Bacillus safensis subsp. osmophilus CECT 9344T	68.4	[65.4 - 71.2]	79.1	[75.7 - 82.2]	0.98	
Bacillus australimaris NH7I 1	52	[49.4 - 54.7]	78.2	[74.8 - 81.3]	0.52	
Bacillus pumilus NCTC 10337	44.7	[42.1 - 47.3]	73.5	[70.0 - 76.7]	0.15	
Bacillus pumilus ATCC 7061	44.6	[42.1 - 47.2]	73.2	[69.7 - 76.4]	0.2	
Bacillus zhangzhouensis MCCC 1A08372	42.1	[39.6 - 44.6]	70.6	[67.1 - 73.8]	0.49	
Bacillus xiamenensis HYC-10	37.4	[35.0 - 39.9]	64.4	[61.0 - 67.6]	0.57	
Bacillus aerius 24K	36.6	[34.1 - 39.1]	67.7	[64.3 - 70.9]	0.66	
Bacillus invictae DSM 26896	36.5	[34.1 - 39.0]	69.2	[65.7 - 72.4]	0.76	
Bacillus cellulasensis NCIM 5461	36.3	[33.9 - 38.8]	72	[68.5 - 75.2]	0.54	
Bacillus altitudinis DSM 21631	36.3	[33.9 - 38.8]	70.8	[67.4 - 74.1]	0.6	
C.I-Confidence interval.

Table 3 GBDP phylogeny based on genome data.

Table 3:Undelying genomes	Data type	Distance formula	Distance algorithm	%G+C	δ-statistics	Genome size (bp)	N of proteins	SSU length (bp)	Finished time	
1155,11802,17444,17597,18..	genome	D5	GreedyWithTrimming	40.88-41.87	0.027-0.054	3,611,490-4,022,069	3,668-4,863	1,058-1,557	2024-D5-06134437+0200	
N-Number; bp-base pair; GG+C-Guanine+cysteine content; GBDP- Genome Blast Distance Phylogeny approach; SSU-Small subunit ribosomal RNA.

Generated from https://tygs.dsmz.de/user_phylogenies/230581?guid=ef701ce9-fccc-47b4-be50-e4e88002d9c2.

To confirm the phylogenetic relationship of WOB3, Digital DNA-DNA hybridization (dDDH) values between Bacillus safensis and closely related species were calculated by TYGS. In Table 2, Bacillus safensis FO-36b had a while Bacillus safensis subsp. osmophilus CECT 9344T had 68,4% (value that fall within the species boundary value) [13], indicating the consistency of the phylogenetic relationship of Bacillus safensis WOB3.

Bacillus is a distinctive genus with G + C% content ranging from 34 to 35% (Bacillus cereus and other Bacillus related species) to 44–46% (Bacillus subtilis and other Bacillus related species) and genome size ranges from 3.7 to 6.4 Mb [14,15]. Bacillus safensis strain WOB3 genome size and G + C% content are within the range of most sequenced genomes of Bacillus cereus species [16,17]. Fig. 1 shows the subsystem statistics information of Bacillus safensis WOB3. The bar chart on the left side of the figure depicts the percentage coverage of subsystems. The pie chart generated by the RAST server and viewed in SEED viewer depicts the distribution of the most common subsystem categories among 1,883 subsystem categories. The most abundant subsystem categories were amino acids and derivatives (337), carbohydrates (269), protein metabolism (175), cofactors, vitamins, prosthetic groups, pigments (166), nucleosides, and nucleotides (117). Other genes associated with CWW detoxification activities were dormancy and sporulation (93), respiration (82), cell wall and capsule (78), DNA metabolism (78), virulence, diseases and defense (59), iron acquisition (56), RNA metabolism (56), stress response (41), membrane transport (38), regulation and cell signaling (29), metabolism of phosphorus (21), nitrogen (17), aromatic compounds (12), potassium (10), sulphur (6), motility and chemotaxis (9) secondary metabolism (9), cell division (6). Similar genes were previously identified in Bacillus safensis B204-B1-5 (1326975.9) [18] and Bacillus safensis subsp. safensis (2490859.4) [19].

Fig. 2 presents the quality check (CheckM) analysis) [20] on WOB3 genome sequence. The quality analysis shows that completeness of 99.41% (100th Percentile, dark blue bar) with very minimal contamination of 1.65%.Fig. 2 CheckM analysis (v1.2.2) of completeness of Bacillus safensis RefSeq assemblies. calculated on the Prokaryotic Genome Annotation Pipeline (PGAP) gene set with the Bacillus CheckM marker set.

Fig 2:

4 Experimental Design, Materials and Methods

4.1 Bacterial isolation

Bacillus safensis strain WOB3 was isolated from cassava wastewater (CWW) containing linamarin as a major cyanogenic compound using the method described by Reynold et al. [21], with some modifications. Briefly, immediately after CWW collection from the processing factory, in the cassava processing factory at Odogunyan, IKorodu, Lagos State, Nigeria, transported to the Nigerian Institute of Medical Research laboratory. The samples were subjected to 10-fold serial dilutions [21]. The pour plate and spread methods were used to plate the appropriate dilutions of each sample into triplicates onto nutrient agar [22]. These were incubated at 37 ºC for 24 hours. Pure bacteria colonies were maintained on a nutrient agar slant and stored at 4°C until needed. The plates were monitored for growth daily, grown colonies were sub-cultured several times on fresh media, preserved in nutrient agar slant for storage, and stored at 4°C, 30% glycerol stock solution, and stored at -80°C for long storage and future use.

4.2 DNA extraction and genome sequencing

Bacillus safensis strain WOB3 was cultured aerobically on nutrient agar plates at 37°C for 24 hours. Extraction of genomic DNA was performed using the Zymo Research Fungal/Bacterial DNA MiniPrep Kit as per the manufacturer's instructions. The quality of the DNA was assessed with a Nanodrop spectrophotometer determining A260/280 ratio. The DNA was sent to a commercial service provider, Laragen Inc., 10061, Culver City, Virginia, USA for sequencing. Illumina libraries were generated using xGen DNA kit, and then 2x150 bp paired-end sequencing was performed with an Illumina HiSequencing platform (HiSeq4000X). The obtained raw reads from the run were quickly checked using FastQC (v.1.0.0, BaseSpace Illumina) and subsequently trimmed using Fast XTool (v.2.2.5, BaseSpace Illumina) [23].

4.3 Genome assembly and annotation

Genome denovo assembly and assembly quality were performed using SPAdes (v 3.9.0, BaseSpace Illumina) [[24], [25]] The genome assemblies were then improved using Pilon (version 1.24.) [[23], [26]], and Busco (v 5.4.7) [[24], [27]]. Also, the CheckM analysis (v1.2.2) [20] was used for quality check of the WOB3 genome. The final genome assembly was annotated through the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) [12] and RAST [[25], [28]].

4.4 Phylogenomic classification

The genome sequence data was uploaded to the National Centre for Biotechnology Information Server (NCBI) (https://www.ncbi. nlmnih.gov), for a whole genome-based taxonomic analysis with other validly published type strains [26]. The construct of an accurate evolutionary relationship with other bacterial whole genomes that are closely related to Bacillus safensis species was carried out using the Type Strain Genome Server (TYGS) [13].

Limitations

None.

Ethics Statement

The authors have read and followed the ethical requirements for publication in Data in Brief and confirmed that the current work does not involve human subjects, animal experiments, or any data collected from social media platforms.

CRediT Author Statement

Ogunyemi, A.K, Conceptualization, Investigation, Methodology, Project administration, Writing – original draft. Buraimoh, M.O, Investigation, Writing – review and editing. Dauda W.P, Investigation, Data curation, Writing – review and editing. Akapo O.O, Investigation, Writing – review and editing. Ogunyemi, B.C, Investigation, Writing – review and editing. Samuel T.A, Supervision, Writing – review and editing. IIori M.O, Supervision, Writing – review and editing. Amund, O.O, Supervision, Writing – review and editing.

Data Availability

Analysis of the genome of Bacillus safensis, a Linamarin-utilizing Bacterium (LUB) isolated from Cassava wastewater (CWW), Lagos-State, Nigeria (Original data) (NCBI).

Acknowledgements

Our gratitude goes to the Scientists at Laragen In., 1061 Culver City, Virginia, USA, for their technical assistance. This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
==== Refs
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