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Draft Genome Sequence of Bacillus subtilis SB-14, an Antimicrobially Active Isolate from Namibian Social Spiders ( Stegodyphus dumicola )



We present the high-quality draft genome sequence of Bacillus subtilis SB-14, isolated from the Namibian social spider Stegodyphus dumicola . In accordance with its antimicrobial activity, both known and potentially novel antimicrobial biosynthetic gene clusters were identified in the genome of SB-14.
Draft Genome Sequence of Bacillus subtilis SB-14, an
Antimicrobially Active Isolate from Namibian Social Spiders
(Stegodyphus dumicola)
Stine Sofie Frank Nielsen,
Simone Weiss,
Seven Nazipi,
Ian P. G. Marshall,
Trine Bilde,
Andreas Schramm
Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
Department of Bioscience, Section for Microbiology, Aarhus University, Aarhus, Denmark
Department of Bioscience, Section for Genetics, Ecology and Evolution, Aarhus University, Aarhus, Denmark
ABSTRACT We present the high-quality draft genome sequence of Bacillus subtilis
SB-14, isolated from the Namibian social spider Stegodyphus dumicola. In accordance
with its antimicrobial activity, both known and potentially novel antimicrobial bio-
synthetic gene clusters were identified in the genome of SB-14.
Increasing antibiotic consumption has accelerated resistance development, prompt-
ing the need for novel antibiotics (1, 2). Stegodyphus dumicola spiders are social
spiders that live in communal nests with a high degree of inbreeding and low genetic
variation, making them potentially vulnerable for pathogen attack. We therefore sug-
gest an intricate symbiotic relationship with a well-developed protective microbiome.
This microbiome may present an unexplored source of antibiotics (3, 4).
Bacillus subtilis SB-14 was isolated from the body surface of a Stegodyphus dumicola
spider, as follows: a spider was immersed in nutrient broth (Sigma-Aldrich), which was
incubated at 30°C overnight, plated onto nutrient broth agar plates, and grown aerobically
at 30°C. Single colonies from serial dilutions were restreaked until a pure culture was
established. Colonies were screened by colony PCR and 16S rRNA gene sequencing (5). The
antimicrobial activity of SB-14 against Staphylococcus epidermidis BMC-HMP0060 was de-
tected using the Kirby-Bauer disk diffusion susceptibility test protocol (6), with the modi-
fication that SB-14 was point inoculated onto a lawn of S. epidermidis.
Genomic DNA was extracted using the DNeasy blood and tissue kit (Qiagen) and
prepared for sequencing with a Nextera XT DNA library prep kit (Illumina). Sequencing was
performed utilizing an Illumina MiSeq platform with a paired-end 300-bp read MiSeq
reagent kit, yielding 5.5 million sequencing reads in total (1.11 Gbp), with approxi-
mately 260coverage. Read quality was analyzed by FastQC version 0.11.7 (https://www, and reads were trimmed by Trimmomatic
version 0.36 (7) using length-based trimming with the following parameters: headcrop, 20;
crop, 290; a minimum average quality score of 20; and a 4-bp sliding window. Finally, the
genome was assembled using SPAdes version 3.11.1 (8), resulting in 37 scaffolds, of which
31 were 200 bp when applying the parameters – careful -k 21, 33, 55, 77, 99, 127.
CheckM version 1.0.9 (9) estimated 98.28% completeness and 0.00% contamination
of the SB-14 genome, using the gene marker set for the domain Bacteria; the corre-
sponding values using the gene marker set for Bacillus subtilis were 97.29% and 2.63%,
NCBI BLAST (10) analysis of the 16S rRNA gene revealed 99% identity to the 16S rRNA
genes of multiple Bacillus subtilis strains. This genus and species identity was confirmed by
an average amino acid identity of 98% (11), average nucleotide identity of 98% (11),
and 94.18% digital DNA-DNA hybridization value (, compared to
Bacillus subtilis subsp. inaquosorum (NCBI RefSeq accession no. NZ_CP013984).
Citation Nielsen SSF, Weiss S, Nazipi S, Marshall
IPG, Bilde T, Schramm A. 2019. Draft genome
sequence of Bacillus subtilis SB-14, an
antimicrobially active isolate from Namibian
social spiders (Stegodyphus dumicola).
Microbiol Resour Announc 8:e00156-19.
Editor Christina A. Cuomo, Broad Institute
Copyright © 2019 Nielsen et al. This is an
open-access article distributed under the terms
of the Creative Commons Attribution 4.0
International license.
Address correspondence to Andreas Schramm,
S.S.F.N. and S.W. contributed equally to this
Received 12 February 2019
Accepted 27 May 2019
Published 20 June 2019
Volume 8 Issue 25 e00156-19 1
on July 21, 2019 by guest from
The draft genome of Bacillus subtilis SB-14 contains 4,262,181 bp on 31 scaffolds of
200 bp, with an average GC content of 44.02% and an N
value of 781,251 bp. Prokka
version 1.12 (12) analysis found 81 tRNA, 10 rRNA, and 4,210 protein-coding sequences.
Upon antiSMASH version 3.0 (13) analysis, 30 secondary metabolite biosynthetic gene
clusters were identified. Five of these were 100% identical to known clusters encoding the
biosynthesis of teichuronic acid (14), bacillibactin (15), the antifungal lipopeptide fengycin
(16), and the antibiotics bacillaene (17) and subtilosin A (18). Three other clusters had 82%,
40%, and 18% identity to clusters known for the biosynthesis of the antimicrobial metab-
olites surfactin (19), bacillomycin (20), and zwittermicin A (21), respectively; these three may
therefore represent novel variations of these metabolites.
Data availability. The isolate Bacillus subtilis SB-14 has been deposited at the DSMZ
( under accession no. DSM 109343. This whole-genome shotgun
project has been deposited in DDBJ/ENA/GenBank under BioProject accession no.
PRJNA438195. The raw data can be found under accession no. SRR8560781, and the
assembled genome has GenBank accession no. PXUR00000000. The version described
in this paper is the first version, PXUR01000000.
We thank Virginia Settepani for collecting and handling social spiders, Britta Poulsen
and Susanne Nielsen for help with Illumina MiSeq sequencing, and Anne Stentebjerg
for handling the bacterial culture/DSMZ submission.
This study was funded by the Novo Nordisk Foundation, the European Research
Council (grant ERC StG-2011_282163 to T.B.), and The Danish Council for Independent
Research, Natural Sciences.
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