ABSTRACT
We report here the draft genome sequence of Bacillus obstructivus VT-16-70, a novel spore-forming bacterium isolated from the lungs of a patient with chronic obstructive pulmonary disease. The genome comprised 5,220,753 bp, with 35.2% G+C content. There were 4,972 predicted protein-coding genes, including those associated with antibiotic resistance and virulence.
GENOME ANNOUNCEMENT
Bacillus is a genus of spore-forming, motile, Gram-positive, aerobic, and rod-shaped bacteria. Bacillus species are associated with a number of human pathologies, such as Bacillus anthracis, which is the causative agent of anthrax, and Bacillus cereus, which is now recognized as a cause of endocarditis, meningitis, and other diseases (1–3). However, members of the Bacillus family have been poorly explored (4–6).
The 16S rRNA gene of Bacillus obstructivus VT-16-70, which was isolated from the bronchoalveolar lavage fluid from a patient with chronic obstructive pulmonary disease, was sequenced and found to possess 98% sequence identity with that of Bacillus acidicola. However, matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) analysis indicated low similarity of the B. obstructivus 16S rRNA gene with that of Bacillus oleronius. The whole genome of B. obstructivus VT-16-70 was sequenced by using Illumina HiSeq 2500 sequencing technology (Illumina GA IIx; Illumina, CA). Library preparation, sequencing reactions, and runs were carried out according to the manufacturer’s instructions. A draft genome was assembled by using SPAdes version 3.5.0, with 114-fold average coverage (7).
The assembled 448 contigs totaled 5,220,753 bp, with a G+C content of 35.2%. The assembled sequences were annotated using the NCBI Prokaryotic Genome Annotation Pipeline and Rapid Annotations using Subsystems Technology (RAST) (7, 8). The genome harbored 162 tRNA genes, 17 rRNA and five noncoding RNA (ncRNA) operons, and 4,972 protein-coding sequences. The analysis revealed the presence of multidrug resistance transporters of the ABC, multidrug and toxic compound extrusion (MATE), and major facilitator superfamily (MFS) families, and genes conferring resistance to antibiotics, including aminoglycosides, daunorubicin, fosfomycin, oxetanocin, beta-lactam antibiotics, tetracycline, and hydroperoxides. Virulence factors, including hemolysin D, proteases, peptidases, deoxyribonucleases, ribonucleases, and adhesins, in addition to capsular, flagellar, and sporulation proteins (9–11), were identified in the genome.
In comparison with the genome of the closest relative, B. acidicola, the genome of B. obstructivus VT-16-70 is smaller (5,138,363 bp versus 5,220,753 bp) and has significantly higher G+C content (39.4% versus 35.2%). An in silico DNA-DNA hybridization (DDH) analysis confirmed that the genomes of B. obstructivus VT-16-70 and B. acidicola belonged to two different species, as the Genome-to-Genome Distance Calculator algorithm produced a DDH value of 25.40%, which is well below the threshold value of 70% (12, 13).
Further studies of B. obstructivus VT-16-70 will result in a better understanding of its role in the microbiome of chronic obstructive pulmonary disease, as well as the possible pathogenicity of this bacterium.
Accession number(s).The complete genome sequence has been deposited in the NCBI database under accession no. MPHG00000000.
ACKNOWLEDGMENTS
We thank the NYUMC Genome Technology Center, for expert library prep and sequencing. This shared resource is partially supported by the Cancer Center Support Grant, P30CA016087, at the Laura and Isaac Perlmutter Cancer Center. We thank the Applied Bioinformatics Centre (BFX) at the NYU School of Medicine for providing bioinformatics support and helping with the analysis and interpretation of the data. This work has used computing resources at the High Performance Computing Facility (HPCF) of the Center for Health Informatics and Bioinformatics at the NYU Langone Medical Center.
FOOTNOTES
- Received 28 December 2016.
- Accepted 30 December 2016.
- Published 2 March 2017.
- Copyright © 2017 Tetz and Tetz.
This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
