- Extended genome report
- Open Access
Genome sequence and description of the mosquitocidal and heavy metal tolerant strain Lysinibacillus sphaericus CBAM5
Standards in Genomic Sciences volume 10, Article number: 2 (2015)
Lysinibacillus sphaericus CBAM5, was isolated from subsurface soil of oil well explorations in the Easter Planes of Colombia. This strain has potential in bioremediation of heavy-metal polluted environments and biological control of Culex quinquefasciatus. According to the phylogenetic analysis of 16S rRNA gene sequences, the strain CBAM5 was assigned to the Lysinibacillus sphaericus taxonomic group 1 that comprises mosquito pathogenic strains. After a combination assembly-integration, alignment and gap-filling steps, we propose a 4,610,292 bp chromosomal scaffold. The whole genome (consisting of 5,146,656 bp long, 60 contigs and 5,209 predicted-coding sequences) revealed strong functional and syntenial similarities to the L. sphaericus C3-41 genome. Mosquitocidal (Mtx), binary (Bin) toxins, cereolysin O, and heavy metal resistance clusters from nik, ars, czc, mnt, ter, cop, cad, and znu operons were identified.
Lysinibacillus sphaericus is one of the bacteria used as a bio-insecticide as part of vector control programs against tropical diseases, such as malaria, filariasis, yellow fever, dengue fever and West Nile virus . L. sphaericus isolates may be classified according to their larvicidal activity into high and low toxicity strains. High- and low-toxicity strains synthesize mosquitocidal toxins (Mtx) in vegetative growth cells . Highly toxic strains produce a binary toxin coded by binA and binB genes in sporulating stages . In addition, L. sphaericus larvicidal toxicity may be explained due to expression of Cry48/Cry49 toxin  and the S-layer protein . Vegetative and sporulated cells of L. sphaericus CBAM5 are pathogenic towards Culex quinquefasciatus larvae . LC50 (50% lethal concentration) toward C. quinquefasciatus larvae of strain CBAM5 is 1400 cells/mL from sporulated cultures, being this isolate assigned as a high-toxicity strain .
The biotechnological application of L. sphaericus is not limited to biological control. L. sphaericus biomass has been applied in the bioremediation of heavy metals, such as cobalt, copper, chromium and lead  with specific metal binding in the cell surface . Native Colombian isolates L. sphaericus OT4b.31 and IV(4)10 showed heavy metal biosorption in living and dead biomass, both strains expressing the S-layer proteins . L. sphaericus strain CBAM5, along with other 24 native isolates, shown effective growth in arsenate, hexavalent chromium and/or lead [6, 10].
Considering that Lysinibacillus sphaericus CBAM5 is a relevant native strain, not only by its highly toxic larvicidal activity but also by its heavy metal tolerance, we have chosen this strain to analyze its genomic sequence. In this report, we present a summary classification, and set of general features for Lysinibacillus sphaericus strain CBAM5 including previously unreported aspects of its phenotype, together with the description of its genome sequence and annotation.
Lysinibacillus sphaericus is an aerobic, mesophilic, spore-forming and Gram-positive bacterium, commonly isolated from soil and water . Formerly known as Bacillus sphaericus, the species was later reassigned to the genus Lysinibacillus because of its distinctive peptidoglycan membrane composition, and physiological features [12, 13]. Lysinibacillus sphaericus strains have been classified into five DNA homology groups, where mosquito larvicidal strains were placed into DNA subgroup IIA  while the subgroup IIB was reclassified as Lysinibacillus fusiformis . Later, according to 16S rDNA and lipid profile comparisons, Lysinibacillus sphaericus strains were classified into seven similarity subgroups, of which only four retained the previous description by Krych et al. . Groups VI and VII were later reclassified as new species . Because of the phenotypic and genetic diversity summarized above, most of the groups remain designated as Lysinibacillus sphaericus sensu lato.
Partial 16S rRNA gene sequences (1,421 bp) were aligned to establish the phylogenetic neighborhood of Lysinibacillus sphaericus CBAM5 (Figure 1). The phylogenetic tree was constructed by using the Maximum Likelihood method on the Tamura-Nei model . Initial tree for the heuristic search was obtained by applying the Neighbor-Joining method to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach. Evolutionary analyses were conducted in MEGA6 . The stability of relationships was assessed by bootstrap analysis based on 1,000 resamplings for the tree topology. L. sphaericus CBAM5 was assigned to the DNA similarity group 1 (formerly known as DNA homology group IIA), in line with a previous classification of mosquito pathogenic native strains .
Lysinibacillus sphaericus CBAM5 was isolated from drilling mineral base oil samples (CBAM by its acronym in Spanish), collected in the Eastern Planes region in Colombia. The strain was described as an aerobic, motile, catalase positive, Gram variable rod . L. sphaericus CBAM5 is able to grow in acetate as sole carbon source, but not in glucose (Table 1, Additional file 1: Table S1). Spherical terminal spores within swollen sporangia were observed under light microscopy (Additional file 2: Figure S1). By scanning electron microscopy, L. sphaericus CBAM5 is estimated to measure 0.52 to 0.60 μm in width and 2.12 to 3.11 μm long (Additional file 3: Figure S2). Cultures grow at 15 to 40°C over a pH range of 6.0 to 9.0. Antibiotic resistance was evaluated separately by adding filter sterilized antibiotic solutions in Luria-Bertani broths and checking turbidity after 15 hours of growth. L. sphaericus CBAM5 is sensitive to kanamycin (12.5 μg/mL), chloramphenicol (30 μg/mL), erythromycin (25 μg/mL), and gentamicin (15 μg/mL), while it showed resistance to trimethoprim/sulfamethoxazol up to 50 μg/mL/250 μg/mL.
Genome sequencing information
Genome project history
The genome sequencing of Lysinibacillus sphaericus CBAM5 was supported by the CIMIC (Centro de Investigaciones Microbiológicas) laboratory at the University of Los Andes within the Grant (1204-452-21129) of the Instituto Colombiano para el Fomento de la Investigación Francisco José de Caldas. Whole genomic DNA extraction and bioinformatics analysis was performed at CIMIC laboratory, whereas libraries construction and whole shotgun sequencing at the Beijing Genome Institute (BGI) Americas Laboratory (Tai Po, Hong Kong). The applied pipeline included quality check of reads, de novo assembly, a gap-filling step and mapping against a reference genome. This whole genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession AYKQ00000000. The version described in this paper is the first version, AYKQ01000000. A summary of the project information is shown in Table 2.
Growth conditions and DNA isolation
Lysinibacillus sphaericus strain CBAM5 was grown in nutrient broth for 16 hours at 30°C and 150 rev/min. High molecular weight DNA was isolated using the EasyDNA® Kit (Carlsbad, CA, USA. Invitrogen) as indicated by the manufacturer. DNA purity and concentration were determined in a NanoDrop spectrophotometer (Wilmington, DE, USA. Thermo Scientific).
Genome sequencing and assembly
After DNA extraction, samples were sent to the Beijing Genome Institute (BGI) Americas Laboratory (Tai Po, Hong Kong). Purified DNA sample was first sheared into smaller fragments with a desired size by a Covaris E210 ultrasonicator. Then the overhangs resulting from fragmentation were converted into blunt ends by using T4 DNA polymerase, Klenow Fragment and T4 polynucleotide kinase. After adding an “A” base to the 3’ end of the blunt phosphorylated DNA fragments, adapters were ligated to the ends of the DNA fragments. The desired fragments were purified though gel-electrophoresis, then selectively enriched and amplified by PCR. The index tag was introduced into the adapter at the PCR stage as appropriate, and a library quality test was performed. Lastly, qualified, short, paired-ends of 90:90 bp length with 500 bp insert libraries were used to cluster preparation and to conduct whole-shotgun sequencing in Illumina Hi-Seq 2000 sequencers.
Using the FASTX-Toolkit version 0.6.1  and clean_reads version 0.2.3 from the ngs_backbone pipeline  reads were trimmed and quality filtered. Four preliminary assemblies were obtained by using: SOAPdenovo version 2.04 , Velvet version 1.2.10 , ABySS version 1.3.7 , and CLC Assembly Cell version 4.0.10 . Those assemblies were integrated in the CISA pipeline resulting in a consensus assembly . SOAPdenovo and CLC Assembly Cell packages included automatic scaffolding and k-mer/overlapping optimization steps. To obtain structural insight of a chromosomal scaffold, we used CONTIGuator.2 , using the Lysinibacillus sphaericus strain C3-41 chromosome (accession number: CP000817.1) as reference. Some gaps were successfully filled by using GapFiller . Gap-filling steps were applied over each one of the preliminary assemblies and over the final consensus assembly. Quality assessment of the assembly was performed with iCORN . The error rate of the final assembly is less than 1 in 1,000,000 bp. We compared the chromosomal assembly of L. sphaericus CBAM5 with the chromosome sequences of L. sphaericus C3-41 and L. sphaericus OT4b.31 by maximal unique matching of translated sequences with PROmer , and a read mapping single nucleotide polymorphism (SNP) effect analysis with SnpEff package .
The Glimmer 3 gene finder was used to identify and extract sequences for potential coding regions. To achieve the functional annotation steps, the RAST server  and Blast2GO pipelines  were used. Blast2GO performed the blasting, GO-mapping and annotation steps; which included a description according to the ProDom, FingerPRINTScan, PIR-PSD, Pfam, TIRGfam, PROSITE, ProDom, SMART, SuperFamily, Pattern, Gene3D, PANTHER, SignalIP and TM-HMM databases. The results were summarized with InterPro . Additionally, a GO-EnzymeCode mapping step was used to retrieve KEGG pathway-maps. tRNA genes were identified by using tRNAscan-SE  and rRNA genes by using RNAmmer . The possible orthologs of the genome were identified based on the COG database and classified accordingly . Prophage region prediction was also conducted by using the PHAST tool .
The genome summary and statistics are provided in Tables 3 and 4, and Figure 2. The genome consists of 60 scaffolds in 5,146,656 bp total size with a GC content of 37.19%. A total of 19 scaffolds were successfully aligned to a reference sequence, comprising 4,610,292 bp of sequence and are represented by the red and blue bars within the outer ring of Figure 2. Of the 5,620 genes predicted, 5,209 were protein-coding genes and 207 RNAs were identified. Genes assigned a putative function comprised 57.37% of the protein-coding genes while the remaining ones were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 5.
Insights into the genome
We propose a 19-supercontig chromosomal scaffold of Lysinibacillus sphaericus CBAM5 with 4.61 Mbp in length, corresponding to a 99.4% of the reference chromosomal sequence. The remaining non-mapped or non-integrated contigs were aligned to plasmid reference sequences, leading to no significant coverage levels (data not shown). Then, we assigned those contigs as a set of potential extrachromosomal elements. Chromosomal comparison from the PROmer analysis between L. sphaericus strains CBAM5 and C3-41 showed that most of the two chromosomes mapped onto each other, revealing large segments of high similarity (Figure 3). In contrast, the comparison between the native strains L. sphaericus CBAM5 and OT4b.31 revealed scattered regions across the dot-plot, corresponding to low coverage levels and different synthenial arrangements. Only variants with a phred-scaled quality and depth coverage scores greater than 100 were considered valid for the SNV analysis. We found 378 variants corresponding to 4531 effects being classified as follows: 170 insertions, 280 deletions, 2020 downstream effects, 182 frame shifts, 211 intergenic effects, 2 start losts, 2 stop losts and 2114 upstream effects. In addition, no transitions, transversions, missense or silent effects were identified. As per most of the variant effects, in comparison to the C3-41 strain, are allocated upstream and downstream of the gene operons, we suggest that L. sphaericus CBAM5 may enclose different regulatory elements or non-coding sequences.
The origin of replication of the chromosome of L. sphaericus CBAM5 was estimated by similarities to several features of the corresponding regions in L. sphaericus C3-41, Bacillus sp. B-14905 and other close related bacteria, including colocalization of the genes: dnaA, dnaN, dnaX, recR and recF; and GC nucleotide skew [(G–C)/(G + C)] analysis. In the contig 19 (EWH31640:EWH31645) we found a typical cluster consisting of dnaA, dnaN, recF, gyrA and gyrB boxes. The predicted genes dnaB, dnaI, dnaG, dnaE, holA, holB, priAB, polA and recA were also found spread in the chromosomal and extrachosmomal sequences. The replication termination site of the chromosomal scaffold is believed to be localized near 2.92 Mbp in the contig 14. According to GC skew analysis, the coding bias for the two strands of the chromosome is for the majority of CDSs to be on the outer strand from 0 to ~2.92 Mbp, and on the inner strand from ~2.92 Mbp to the end of the chromosomal scaffold (contig 19, Figure 2). This was also confirmed by the presence of parC (EWH32537) and parE (EWH32538), which encode the subunits of the chromosome-partitioning enzyme topoisomerase IV. Similar to previous reports [50, 51], we did not find the homolog of rtp (replication terminator protein-encoding gene) in the chromosomal assembly of CBAM5.
Lysinibacillus sphaericus CBAM5 displays 28 CDSs annotated as transposases, including three allocated in the extrachromosomal sequences. The most frequent families are IS1182, IS3 and IS4. In addition, four incomplete prophage regions were identified as follows: Thermus phage φOH2 (contig 12), Burkholderia phage ST79 (contig 14), and two regions comprising the Clostridium phage φSM101 (contigs 14 and 28). Prophage regions φOH2 and ST79 included putative encoding sequences for tail, lysis and baseplate proteins. None of the reported phages has been described in the Colombian strain L. sphaericus OT4b.31 .
The genome of L. sphaericus CBAM5 shows a wide repertoire of potential encoding sequences in terms of mosquitocidal toxins. In the contig 11, we found Mtx1 (EWH35097) and Mtx2 (EWH35034) CDSs located in an identical cluster as Hu et al.  described in the genome of L. sphaericus C3-41. This cluster includes two insertion sequences, one of them consisting of a disrupted transposase between the mtx1 and mtx2, as well. One Mtx3 CDSs (EWH32377) was found in contig 14. Upstream of this sequence, we could identify some IS3 family mobile elements and putative DeoR family transcriptional regulators. In addition, we found one hypothetical toxin from the family Mtx2 (PFam PF03318) in contig 11 (EWH35106) and a putative cereolysin O CDS (EWH31995) being described to be active against the German cockroach Blattela germanica  in contig 15.
The binary toxin genes binA (EWH32662) and binB (EWH32663) of L. sphaericus CBAM5, which are the main source of its larvicidal activity , were found in the contig 14 following a similar arrangement as the 35-kb duplicate cluster of L. sphaericus C3-41 (Figure 4). Nearby the binA and binB genes, we found a putative Mtx2/3 toxin (EWH32665), two CDSs for phage integrases in the 5’ start of the 35-kb fragment. L. sphaericus CBAM5 also share a germination gene cluster equivalent to the B. anthracis plasmid pXO1 and the BinA/BinB cluster of L. sphaericus C3-41, having a GerXB-KA-XC gene cluster upstream of a transposase [51, 53]. Comparing the region comprised between the germination operon and the binA-binB genes across the sequences of L. sphaericus CBAM5, C3-41 and 2297, we found an equivalent homology of putative transposases with different length and disruption points. The strain CBAM5 has two mobile elements of 459 and 312 bp in length, which is similar to strains 2297 and CBAM5 showing a probable transposase pseudogene with 1,110 bp and 591 bp in length, respectively (Figure 4). As a final remark, in the 3’ end of the 35-kb fragment we found an incomplete encoding sequence for β-carotene 15,15’-monooxygenase probably disrupted by a mobile element (depicted with a red box in Figure 4). Hu et al.  hypothesized that the conserved 35-kb sequence, including the BinA, BinB, and the two phage integrase family proteins, are probably unique to the taxonomic L. sphaericus group 1 (formerly known as group IIA) being the remnant of a potential phage infection. Even though we cannot confirm the presence of additional BinA-B CDS sequences in the genome of L. sphaericus CBAM5, we suggest further research to confirm the participation of phage infections on the evolution of larvicidal toxins in the strain CBAM5.
Surface (S) layer proteins and toxic metal resistances
L. sphaericus CBAM5 exhibits 21 CDSs described as surface (S) layer proteins or S-layer homologs in its genome. The fragment covered from EWH35069 to EWH35072 includes four CDSs encoding for a variable protein, a putative S-layer associated protein, a P60 invasion-associated protein and a N-acetylmuramoyl-L-alanine amidase. Probably the genes located in this fragment may participate in the larvicidal activity of the strain CBAM5, given that the same genes have been described as differentially expressed in virulent infections of Lysteria monocytogenes . A total of 14 CDSs show three SLHs motifs near to the N terminal region, similarly to the slpC gene previously described in native strains . In addition, we found two S-layer surface array proteins in the chromosomal scaffold and another in extracromosomal sequences.
A total of 64 CDSs corresponded to encoding sequences involved in responses against toxic metal(oid)s. Among those coding sequences, we found the following operons: arsRBCDA, arsRBC, cadCA, mntABCD, nikABCDE, terD-terD-terD, zurR-znuBC, and czrA-czcD-csoR-copZA. We could identify various genes probably involved in metal(loid) resistances spread across the genome (Additional file 4: Table S2). The chrA gene seems to be the only representative of the chr operon in the genome of L. sphaericus CBAM5. Previous reports have shown that microorganisms bearing chrA homologues display highly variable resistance levels against Cr(VI) . However, two superoxide dismutase putative proteins (EWH33050, EWH30224) and several CDS ascribed as flavin reductases (EC 18.104.22.168), nitroreductases (EC 22.214.171.124) and quinone reductases (EC 126.96.36.199) could cooperate in the Cr(VI) resistance, in agreement with previous reports [55, 56].
Given the heavy metal resistance of L. sphaericus CBAM5 in polluted environments, and supported by the identification of genes in Additional file 4: Table S2, we could expect the assistance of efflux pump systems and heavy-metal resistance proteins specific to As, Sb, Ni, Zn, Cu, Cd, Te, Cr, Mn and Co. By the evaluation of coalescent models, Villegas-Torres et al.  proposed that L. sphaericus CBAM5 may have acquired the arsC gene through recent events of horizontal gene transfer as a possible adaptation to polluted environments. However, we found highly similar homologues of heavy metal resistance proteins of the CBAM5 strain in microorganisms isolated from non-polluted environments (i.e. czrA-czcD-csoR-copZA, cadCA, and arsRBC in L sphaericus OT4B.31 ). Further analysis on plasmids, prophage content, or conjugation factors may clarify the origin of resistance (as well as larvicidal) genes. Finally, based in the KEGG analysis, some predicted proteins might participate in peripheral pathways for the degradation of geraniol, chlorocyclohexane, chlorobenzene, benzoate, bisphenol, fluorobenzoate, toluene, chloroalkane, chloroalkene, naphthalene, aminobenzoate, styrene, atrazine, limonene and pinene.
Lysinibacillus sphaericus CBAM5 was isolated from drilling mineral base oil samples at the subsurface soil level. By comparing the chromosomal sequences between L. sphaericus strains CBAM5 and C3-41, we identified distinctive similarities of the DNA homology group IIA. The evidence of the binary toxins allocated in a conserved cluster delimited by mobile elements, resembles a probable phage invasion in the DNA subgroup IIA of the Lysinibacillus sphaericus species. Along with the biological control potential given by the Mtx, Bin and cerolysin toxins, L. sphaericus CBAM5 displays encoding sequences for S-layer proteins and heavy-metal efflux pumps, which may confer resistance to As, Sb, Ni, Zn, Cu, Cd, Te, Cr, Mn and Co in polluted environments.
Berry C: The bacterium, Lysinibacillus sphaericus , as an insect pathogen. J Invertebr Pathol 2012, 109:1–10. 10.1016/j.jip.2011.11.008
Thanabalu T, Porter AG: Efficient expression of a 100-kilodalton mosquitocidal toxin in protease-deficient recombinant Bacillus sphaericus . Appl Environ Microbiol 1995, 61:4031–6.
Baumann P, Clark MA, Baumann L, Broadwell AH: Bacillus sphaericus as a mosquito pathogen: properties of the organism and its toxins. Microbiol Rev 1991, 55:425–36.
Jones GW, Nielsen-LeRoux C, Yang Y, Yuan Z, Dumas VF, Monnerat RG, Berry C: A new Cry toxin with a unique two-component dependency from Bacillus sphaericus . FASEB J 2007, 21:4112–20. 10.1096/fj.07-8913com
Lozano LC, Ayala JA, Dussán J: Lysinibacillus sphaericus S-layer protein toxicity against Culex quinquefasciatus . Biotechnol Lett 2011, 33:2037–41. 10.1007/s10529-011-0666-9
Lozano LC, Dussán J: Metal tolerance and larvicidal activity of Lysinibacillus sphaericus . World J Microbiol Biotechnol 2013, 29:1383–9. 10.1007/s11274-013-1301-9
Tuzen M, Uluozlu OD, Usta C, Soylak M: Biosorption of copper(II), lead(II), iron(III) and cobalt(II) on Bacillus sphaericus -loaded Diaion SP-850 resin. Anal Chim Acta 2007, 581:241–6. 10.1016/j.aca.2006.08.040
Pollmann K, Raff J, Merroun M, Fahmy K, Selenska-Pobell S: Metal binding by bacteria from uranium mining waste piles and its technological applications. Biotechnol Adv 2006, 24:58–68. 10.1016/j.biotechadv.2005.06.002
Velásquez L, Dussan J: Biosorption and bioaccumulation of heavy metals on dead and living biomass of Bacillus sphaericus . J Hazard Mater 2009, 167:713–6. 10.1016/j.jhazmat.2009.01.044
Villegas-Torres MF, Bedoya-Reina OC, Salazar C, Vives-Florez MJ, Dussan J: Horizontal arsC gene transfer among microorganisms isolated from arsenic polluted soil. Int Biodeterior Biodegradation 2011, 65:147–52. 10.1016/j.ibiod.2010.10.007
Claus D, Berkeley RCW: Genus Bacillus Cohn 1872, 174AL. In Bergey’s Man Syst Bacteriol. Volume 2. Edited by: Sneath PHA, Mair NS, Sharpe ME, Holt JG. Baltimore: The Williams and Wilkins Co; 1986:1105–39.
White PJ, Lotay HK: Minimal nutritional requirements of Bacillus sphaericus NCTC9602 and 26 other strains of this species: the majority grow and sporulate with acetate as sole major source of carbon. J Gen Microbiol 1980, 118:13–9.
Ahmed I, Yokota A, Yamazoe A, Fujiwara T: Proposal of Lysinibacillus boronitolerans gen. nov. sp. nov., and transfer of Bacillus fusiformis to Lysinibacillus fusiformis comb. nov. and Bacillus sphaericus to Lysinibacillus sphaericus comb. nov. Int J Syst Evol Microbiol 2007, 57:1117–25. 10.1099/ijs.0.63867-0
Krych VK, Johnson JL, Yousten AA: Deoxyribonucleic acid homologies among strains of Bacillus sphaericus . Int J Syst Bacteriol 1980, 30:476–84. 10.1099/00207713-30-2-476
Nakamura LK: Phylogeny of Bacillus sphaericus -like organisms. Int J Syst Evol Microbiol 2000, 50:1715–22.
Nakamura LK, Shida O, Takagi H, Komagata K: Bacillus pycnus sp. nov. and Bacillus neidei sp. nov., round-spored bacteria from soil. Int J Syst Evol Microbiol 2002,52(Pt 2):501–5.
Tamura K, Nei M: Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993, 10:512–26.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S: MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 2013, 30:2725–9. 10.1093/molbev/mst197
Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, DePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, et al.: The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008, 26:541–7. 10.1038/nbt1360
Woese CR, Kandler O, Wheelis ML: Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci 1990, 87:4576–9. 10.1073/pnas.87.12.4576
Gibbons NE, Murray RGE: Proposals Concerning the Higher Taxa of Bacteria. Int J Syst Bacteriol 1978, 28:1–6. 10.1099/00207713-28-1-1
Garrity GM, Holt JG: The Road Map to the Manual. In Bergey’s Man Syst Bacteriol. Volume 1. Second edition. Edited by: Garrity GM, Boone DR, Castenholz RW. New York: Springer; 2001:119–69.
Murray RGE: The Higher Taxa, or, a Place for Everything…? In Bergey’s Man Syst Bacteriol. Volume 1. First edition. Edited by: Holt JG. Baltimore: The Williams and Wilkins Co; 1984:31–4.
Ludwig W, Schleifer KH, Whitman WB, Krieg NR, Ludwig W, Rainey EA, Schleifer KH, Withman WB: Class I. Bacilli Class Nov . In Bergey’s Manual of Systematic Bacteriology. In: Vol 3 (The Firmicutes). Second. Volume 3. Edited by: De Vos P, Garrity GM, Jones D. Dordrecht, Heidelberg, London, New York: Springer; 2009:19–20.
List of new names and new combinations previously effectively, but not validly, published Int J Syst Evol Microbiol 2010, 60:469–72.
Skerman VBD, McGowan V, Sneath PHA: Approved Lists of Bacterial Names. Int J Syst Bacteriol 1980, 30:225–420. 10.1099/00207713-30-1-225
Prévot AR: Hauduroy P, Ehringer G, Guillot G, Magrou J, Prévot AR, Rosset, Urbain A (eds) Dictionnaire Des Bactéries Pathogènes. 2nd edition. Paris: Masson; 1953:1–692.
Fischer A: Untersuchungen über bakterien. Jahrbücher für Wissenschaftliche Bot 1895, 27:1–163.
Jung MY, Kim J-S, Paek WK, Styrak I, Park I-S, Sin Y, Paek J, Park KA, Kim H, Kim HL, Chang Y-H: Description of Lysinibacillus sinduriensis sp. nov., and transfer of Bacillus massiliensis and Bacillus odysseyi to the genus Lysinibacillus as Lysinibacillus massiliensis comb. nov. and Lysinibacillus odysseyi co. Int J Syst Evol Microbiol 2012, 62:2347–55. 10.1099/ijs.0.033837-0
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene Ontology: tool for the unification of biology. Nat Genet 2000, 25:25–9. 10.1038/75556
Blanca JM, Pascual L, Ziarsolo P, Nuez F, Cañizares J: ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence. BMC Genomics 2011., 12:
Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J: De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010, 20:265–72. 10.1101/gr.097261.109
Zerbino DR, Birney E: Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008, 18:821–9. 10.1101/gr.074492.107
Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM, Birol I: ABySS: A parallel assembler for short read sequence data. Genome Res 2009, 19:1117–23. 10.1101/gr.089532.108
CLC Genomics Workbench. http://www.clcbio.com/products/clc-genomics-workbench/
Lin S-H, Liao Y-C: CISA: contig integrator for sequence assembly of bacterial genomes. PLoS One 2013, 8:e60843. 10.1371/journal.pone.0060843
Galardini M, Biondi EG, Bazzicalupo M, Mengoni A: CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes. Source Code Biol Med 2011., 6:
Nadalin F, Vezzi F, Policriti A: GapFiller: a de novo assembly approach to fill the gap within paired reads. BMC Bioinformatics 2012,13(Suppl 14):S8. 10.1186/1471-2105-13-S14-S8
Otto TD, Sanders M, Berriman M, Newbold C: Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology. Bioinformatics 2010, 26:1704–7. 10.1093/bioinformatics/btq269
Delcher AL, Phillippy A, Carlton J, Salzberg SL: Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res 2002, 30:2478–83. 10.1093/nar/30.11.2478
Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM: A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 2012, 6:80–92. 10.4161/fly.19695
Aziz R, Bartels D, Best A, DeJongh M, Disz T, Edwards R, Formsma K, Gerdes S, Glass E, Kubal M, Meyer F, Olsen G, Olson R, Osterman A, Overbeek R, McNeil L, Paarmann D, Paczian T, Parrello B, Pusch G, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O: The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics 2008., 9:
Götz S, García-Gómez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Robles M, Talón M, Dopazo J, Conesa A: High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 2008, 36:3420–35. 10.1093/nar/gkn176
Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MDR, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M, Servant F, Sigrist CJA, Zdobnov EM: The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res 2001, 29:37–40. 10.1093/nar/29.1.37
Lowe TM, Eddy SR: tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997, 25:955–64. 10.1093/nar/25.5.0955
Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T, Ussery DW: RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007, 35:3100–8. 10.1093/nar/gkm160
Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV: The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 2001, 29:22–8. 10.1093/nar/29.1.22
Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS: PHAST: A Fast Phage Search Tool. Nucleic Acids Res 2011.
Peña-Montenegro TD, Dussán J: Genome sequence and description of the heavy metal tolerant bacterium Lysinibacillus sphaericus strain OT4b.31. Stand Genomic Sci 2013, 9:42–56. 10.4056/sigs.4227894
Hu X, Fan W, Han B, Liu H, Zheng D, Li Q, Dong W, Yan J, Gao M, Berry C, Yuan Z: Complete genome sequence of the mosquitocidal bacterium Bacillus sphaericus C3–41 and comparison with those of closely related Bacillus species. J Bacteriol 2008, 190:2892–902. 10.1128/JB.01652-07
Nishiwaki H, Nakashima K, Ishida C, Kawamura T, Matsuda K: Cloning, functional characterization, and mode of action of a novel insecticidal pore-forming toxin, sphaericolysin, produced by Bacillus sphaericus . Appl Environ Microbiol 2007, 73:3404–11. 10.1128/AEM.00021-07
Okinaka RT, Cloud K, Hampton O, Hoffmaster AR, Hill KK, Keim P, Koehler TM, Lamke G, Kumano S, Mahillon J, Manter D, Martinez Y, Ricke D, Svensson R, Jackson PJ: Sequence and organization of pXO1, the large Bacillus anthracis plasmid harboring the anthrax toxin genes. J Bacteriol 1999, 181:6509–15.
Camejo A, Buchrieser C, Couvé E, Carvalho F, Reis O, Ferreira P, Sousa S, Cossart P, Cabanes D: In vivo transcriptional profiling of Listeria monocytogenes and mutagenesis identify new virulence factors involved in infection. PLoS Pathog 2009, 5:e1000449. 10.1371/journal.ppat.1000449
Viti C, Marchi E, Decorosi F, Giovannetti L: Molecular mechanisms of Cr(VI) resistance in bacteria and fungi. FEMS Microbiol Rev 2014, 38:633–59. 10.1111/1574-6976.12051
He M, Li X, Liu H, Miller SJ, Wang G, Rensing C: Characterization and genomic analysis of a highly chromate resistant and reducing bacterial strain Lysinibacillus fusiformis ZC1. J Hazard Mater 2011, 185:682–8. 10.1016/j.jhazmat.2010.09.072
Liolios K, Chen I-MA, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC: The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2010,38(suppl 1):D346–54.
This work was performed under the auspices of the Grant 1204-452-21129 from the Instituto Colombiano para el fomento de la Investigación Francisco José de Caldas – Colciencias, the Research Fund from the Faculty of Sciences at Universidad de los Andes, and the Centro de Investigaciones Microbiológicas (CIMIC).
The authors declare that they have no competing interests.
LL performed the DNA and sequencing experiments. TDP performed antibiotics, microscopy and bioinformatics analysis. All authors drafted, read and approved the final manuscript.