Streptacidiphilus sp. strain 15-057A was isolated from a bronchial lavage sample and represents the only member of the genus not isolated from acidic soils.
ABSTRACT
Streptacidiphilus sp. strain 15-057A was isolated from a bronchial lavage sample and represents the only member of the genus not isolated from acidic soils. A single circular chromosome of 7.01 Mb was obtained by combining Illumina and PacBio sequencing data. Bioinformatic analysis detected 63 putative secondary biosynthetic gene clusters and recognized 43 transposons.
ANNOUNCEMENT
The genus Streptacidiphilus, established by Kim et al. (1), presently comprises 11 validly published names. Streptacidiphilus members are Gram-positive, aerobic chemoorganotrophs that are isolated primarily from acidic soils and which share many morphologic and phenotypic properties with members of the genus Streptomyces (2). Strain 15-057A was isolated from a bronchial lavage sample by aerobic growth on Trypticase soy agar supplemented with 5% sheep blood. Here, we report the completed genome sequence of Streptacidiphilus sp. strain 15-057A, the first isolate of the genus obtained from a human source, in order to evaluate its genetic characteristics and potential to produce novel secondary metabolites.
Cells were grown in Trypticase soy broth at 35°C for 5 days, and genomic DNA was extracted with the MasterPure DNA purification kit (Epicentre, Madison, WI). Fragments of ≥20 kbp were captured with a BluePippin instrument (Sage Science, Beverly, MA). The SMRTbell template prep kit 3.0 (Pacific Biosciences [PacBio], Menlo Park, CA), DNA/polymerase binding kit P6 v2 (PacBio), and MagBead Standard Seq v2 (PacBio) loading were used to generate long reads in an RS II (PacBio) instrument with P6-C4 chemistry. An aliquot of the genomic DNA used for PacBio sequencing was also sequenced on a MiSeq instrument (Illumina, San Diego, CA) after NEBNext Ultra DNA libraries (New England BioLabs, Ipswich, MA) were generated. Long (≥1-kbp) PacBio reads were assembled using HGAP3 with default parameters (3). Short (2 × 250-bp) Illumina reads were quality trimmed with Trimmomatic v0.36 (4), with a 6-bp sliding window requiring Phred quality scores of ≥30. The PacBio assembly was corrected using Illumina high-quality paired reads that employed 3 sequential rounds of correction steps, after which no additional indels or single-nucleotide polymorphisms (SNPs) were observed, suggesting a final genome assembly. Correcting genome assembly of potential variants/SNPs involved BWA-MEM v0.7.15-r1140 “–x intractg” (5) read mapping, SAMtools v1.8 alignment file conversion (6), and Pilon v1.22 “–fix snps,indels –mindepth 4” assembly file modification (7). The genome was annotated with NCBI’s Prokaryotic Genome Annotation Pipeline (PGAP) (8). The strain 15-057A genome is 7,090,212 bp, with a G+C content of 72.7%, 5,988 coding sequences (CDS), 8 rRNA operons, 66 tRNAs, and no plasmids.
A total of 63 secondary metabolite biosynthetic gene clusters (BGCs) were predicted using antiSMASH Web v4.0 (9) with all features enabled. antiSMASH identified 37 of 63 BGCs as putative and 8 type I/type III polyketide synthases, 4 saccharides, 3 lantipeptides, 3 terpenes, 2 fatty acids, 1 bacteriocin, 1 class II bacteriocin, 1 butyrolactone, 1 nonribosomal peptide synthetase, 1 siderophore, and 1 thiopeptide. The high incidence of putative BGCs strongly supports the potential of this species for discovery of novel natural products.
Searches for virulence factor-related (10) and antibiotic resistance-related genes (11, 12) were performed via BLAST (13), with the genome aligned against the Virulence Factor Database (VFDB) (10), ResFinder database (11), and Comprehensive Antibiotic Resistance Database (CARD) (12). Totals of 89 virulence factor-related genes and 8 antibiotic resistance genes were identified. The genome contains 43 putative transposons, 16 IS5/IS1182 family members, 10 unclassified transposons, 6 IS481, 2 DDE, 2 IS701, and 1 each of IS1182, IS1380, IS21, IS3, IS630, IS982, and ISL3 transposons.
Data availability.
The whole-genome sequence of Streptacidiphilus sp. strain 15-057A has been deposited in the DDBJ/ENA/GenBank databases under the accession number CP031264. The version described in this paper is the first version, CP031264.1.
ACKNOWLEDGMENT
I.N. is grateful to Newcastle University for a postdoctoral fellowship.
REFERENCES
- 1.Kim SB, Lonsdale J, Seong CN, Goodfellow M. 2003. Streptacidiphilus gen. nov., acidophilic actinomycetes with wall chemotype I and emendation of the family Streptomyceyaceae (Waksman and Henrici (1943)AL) emend. Rainy et al. 1997. Antonie van Leeuwenhoek 83:107–116. doi: 10.1023/A:1023397724023. [DOI] [PubMed] [Google Scholar]
- 2.Komak H, Ichikawa N, Oguchi A, Hamada M, Tamura T, Fujita N. 2015. Draft genome sequences of six type strains of the genus Streptacidiphilus. Genome Announc 3:e01387-14. doi: 10.1128/genomeA.01387-14. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10:563–569. doi: 10.1038/nmeth.2474. [DOI] [PubMed] [Google Scholar]
- 4.Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. doi: 10.1093/bioinformatics/btu170. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Li H. 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv arXiv:1303.3997v2 [q-bio.GN]. http://arxiv.org/abs/1303.3997v2.
- 6.Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup . 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078–2079. doi: 10.1093/bioinformatics/btp352. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9:e112963. doi: 10.1371/journal.pone.0112963. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. 2016. NCBI Prokaryotic Genome Annotation Pipeline. Nucleic Acids Res 44:6614–6624. doi: 10.1093/nar/gkw569. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Blin K, Wolf T, Chevrette MG, Lu X, Schwalen CJ, Kautsar SA, Suarez Duran HG, de Los Santos ELC, Kim HU, Nave M, Dickschat JS, Mitchell DA, Shelest E, Breitling R, Takano E, Lee SY, Weber T, Medema MH. 2017. antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Res 45:W36–W41. doi: 10.1093/nar/gkx319. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Chen L, Yang J, Yu J, Yao Z, Sun L, Shen Y, Jin Q. 2005. VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res 33:D325–D328. doi: 10.1093/nar/gki008. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, Aarestrup FM, Larsen MV. 2012. Identification of acquired antimicrobial resistance genes. J Antimicrob Chem 67:2640–2644. doi: 10.1093/jac/dks261. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12.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]
- 13.Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. 2008. BLAST+: architecture and applications. BMC Bioinformatics 10:421. doi: 10.1186/1471-2105-10-421. [DOI] [PMC free article] [PubMed] [Google Scholar]
Associated Data
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Data Availability Statement
The whole-genome sequence of Streptacidiphilus sp. strain 15-057A has been deposited in the DDBJ/ENA/GenBank databases under the accession number CP031264. The version described in this paper is the first version, CP031264.1.