ABSTRACT
We report here the draft genome sequence of Bacillus intestinalis strain 1731, a novel spore-forming bacterium isolated from the small intestine of a patient with intestinal cancer. The genome comprised 4,047,276 bp, with 43.9% G+C content. There were 3,913 predicted protein-coding genes, including those associated with antibiotic resistance and virulence.
GENOME ANNOUNCEMENT
Bacillus intestinalis strain 1731 is an aerobic, spore-forming, motile, Gram-positive, rod-shaped bacterium that was isolated from the small intestine of a patient with intestinal malignancy. The members of the Bacillaceae family are well-known representatives of the human gut microbiota and are implicated in a number of pathologies (1–3). Using combined culture and genetic workflow, we have previously identified the unexplored diversity of endospore-forming bacteria within humans; this identification necessitated the characterization of spore-forming bacteria, such as Sporobiota spp., and the collection of their genes as a sporobiome, owing to their unique common characteristics (4–6).
The 16S rRNA gene sequences of B. intestinalis strain 1731 shared 99% similarity with those of various Bacillus strains, including B. subtilis, B. amyloliquefaciens, and B. atrophaeus.
An in silico DNA-DNA hybridization (DDH) analysis, using the genome-to-genome distance calculator (GGDC2.1) algorithm, produced a highest DDH value of 50.80%, which indicates that B. intestinalis strain 1731 is a new species belonging to the Bacillus genus (7).
The genome of B. intestinalis strain 1731 was sequenced using an Illumina HiSeq sequencing platform (GA IIx; Illumina, CA). Library preparation, sequencing, and runs were performed in accordance with the manufacturer’s instructions. De novo assembly was performed with SPAdes version 3.9.0 (8), and annotation was performed via the NCBI and RAST servers (9, 10). The final draft genome assembly consisted of 164 contigs and 4,047,276 bp (G+C content of 43.9%), and the total coverage over the genome was 145-fold. It comprises 3,913 gene-coding sequences and 106 predicted RNA genes (86 tRNA, 15 rRNA, and 5 ncRNA genes). Genome analysis using the NCBI and CARD databases revealed genes coding for resistance to the antibiotics tunicamycin, fosfomycin, and bleomycin and class A and B beta-lactamases; the genes mprF, aadK, and tmrB (determinant of resistance to peptide, aminoglycoside, and nucleoside antibiotics, respectively); major facilitator superfamily (MFS) transporters; and the organic hydroperoxide resistance protein OhrA (11).
The genome contains virulence factors, including hemolysin D, serine protease, zinc metalloprotease HtpX, peptidases, alpha-amylase, amidohydrolase, phospholipase, phenolic acid decarboxylase, and subtilosin A exodeoxyribonuclease III and VII capsular, flagellar, and sporulation proteins (12, 13). In addition, we identified superoxide dismutases that are considered to possess carcinogenic properties in some bacteria (14).
The availability of the B. intestinalis genome sequence facilitates further analysis of human sporobiota and its possible implications in intestinal malignization.
Accession number(s).
The complete genome sequence has been deposited in the NCBI database under the accession no. MWZB00000000.
Footnotes
Citation Tetz V, Tetz G. 2017. Draft genome sequence of a strain of Bacillus intestinalis sp. nov., a new member of sporobiota isolated from the small intestine of a single patient with intestinal cancer. Genome Announc 5:e00489-17. https://doi.org/10.1128/genomeA.00489-17.
REFERENCES
- 1.Shih AF, Grant M, Sankey C. 2016. Bacillus cereus bacteremia and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Infect Dis Clin Practice 24:14–17. doi: 10.1097/IPC.0000000000000335. [DOI] [Google Scholar]
- 2.Ha J, Park YJ, Kim YJ, Oh HC, Kim YA. 2016. Late prosthetic joint infection and bacteremia by Bacillus cereus confirmed by 16S rRNA sequencing and hip joint tissue pathology. Ann Clin Microbiol 19:54. doi: 10.5145/ACM.2016.19.2.54. [DOI] [Google Scholar]
- 3.Gherardi G. 2016. Bacillus cereus disease other than food-borne poisoning, p 93–107. In Savini D. (ed), The diverse faces of Bacillus cereus. Academic Press, Cambridge, MA. [Google Scholar]
- 4.Tetz G, Tetz V, Vecherkovskaya M. 2016. Genomic characterization and assessment of the virulence and antibiotic resistance of the novel species Paenibacillus sp. strain VT-400, a potentially pathogenic bacterium in the oral cavity of patients with hematological malignancies. Gut Pathog 8:6. doi: 10.1186/s13099-016-0089-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Tetz G, Tetz V. 2015. Complete genome sequence of Bacilli bacterium strain VT-13-104 isolated from the intestine of a patient with duodenal cancer. Genome Announc 3(4):e00705-15. doi: 10.1128/genomeA.00705-15. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Tetz G, Tetz V. 2017. Draft genome sequence of Bacillus obstructivus VT-16-70 isolated from the bronchoalveolar lavage fluid of a patient with chronic obstructive pulmonary disease. Genome Announc 5(9):e01754-16. doi: 10.1128/genomeA.01754-16. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Auch AF, von Jan M, Klenk HP, Göker M. 2010. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2:117–134. doi: 10.4056/sigs.531120. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. doi: 10.1089/cmb.2012.0021. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Ciufo S, Li W. 2013. Prokaryotic genome annotation pipeline. In Beck J, Benson D, Coleman J, Hoeppner M, Johnson M, Maglott D, Mizrachi I, Morris R, Ostell J, Pruitt K, Rubinstein W, Sayers E, Sirotkin K, Tatusova T (ed), The NCBI handbook, 2nd ed National Center for Biotechnology Information, Bethesda, MD. [Google Scholar]
- 10.Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. doi: 10.1186/1471-2164-9-75. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Jia B, Raphenya AR, Alcock B, Waglechner N, Guo P, Tsang KK, Lago BA, Dave BM, Pereira S, Sharma AN, Doshi S, Courtot M, Lo R, Williams LE, Frye JG, Elsayegh T, Sardar D, Westman EL, Pawlowski AC, Johnson TA, Brinkman FS, Wright GD, McArthur AG. 2017. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res 45:D566–D573. doi: 10.1093/nar/gkw1004. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12.Cui W, Chen L, Huang T, Gao Q, Jiang M, Zhang N, Zheng L, Feng K, Cai Y, Wang H. 2013. Computationally identifying virulence factors based on KEGG pathways. Mol Biosyst 9:1447–1452. doi: 10.1039/c3mb70024k. [DOI] [PubMed] [Google Scholar]
- 13.Liaudet L, Szabó C, Evgenov OV, Murthy KG, Pacher P, Virág L, Mabley JG, Marton A, Soriano FG, Kirov MY, Bjertnaes LJ, Salzman AL. 2003. Flagellin from Gram-negative bacteria is a potent mediator of acute pulmonary inflammation in sepsis. Shock 19:131–137. doi: 10.1097/00024382-200302000-00008. [DOI] [PubMed] [Google Scholar]
- 14.Smith DG, Lawson GH. 2001. Lawsonia intracellularis: getting inside the pathogenesis of proliferative enteropathy. Vet Microbiol 82:331–345. doi: 10.1016/S0378-1135(01)00397-2. [DOI] [PubMed] [Google Scholar]