Skip to main content
Download PDF

Non-contiguous finished genome sequence and description of Paucisalibacillus algeriensis sp. nov.

Standards in Genomic Sciences volume 9, pages 1352–1365 (2014)Cite this article

Abstract

Paucisalibacillus algeriensis strain EB02T is the type strain of Paucisalibacillus algeriensis sp. nov., a new species within the genus Paucisalibacillus. This strain, whose genome is described here, was isolated from soil sample from the hypersaline lake Ezzemoul Sabkha in northeastern Algeria. Paucisalibacillus algeriensis is a Gram-positive and strictly aerobic bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,006,766 bp long genome (1 chromosome but no plasmid) exhibits a low G+C content of 36% and contains 3,956 protein-coding and 82 RNA genes, including 9 rRNA genes.

Introduction

Strain EB02T (= CSUR P858 = DSM 27335) is the type strain of Paucisalibacillus algeriensis sp. nov. It is a strictly aerobic Gram-positive rod, motile by means of peritrichous flagella, and spore-forming bacteria. It was isolated from a soil sample from the hypersaline lake Ezzemoul Sabkha of Oum-El-Bouaghi region in northeastern Algeria, which is the largest nesting area of Mediterranean flamingos. This lake is a Ramsar site (http://www.ramsar.org).

The genus Paucisalibacillusbelongs in the Bacillaceaefamily, and was created by Nunes in 2006 [1]. To date, the genus contains only one validly published species, Paucisalibacillus globulusstrain B22T which was isolated from potting soil in Portugal [1]. It has been described as a Gram positive rod-shaped bacterium, strictly aerobic, spore-forming and motile by means of two polar flagella at one end. It grows in the absence of NaCl, but a low NaCl concentration (1% w/v) improves growth [1].

The current bacterial taxonomy relies on a combination of various phenotypic, chemotaxonomic and genetic criteria [2–4]. The essential genetic criteria used are DNA-DNA hybridization, which is the ‘gold standard’ criterion to define bacterial species [3,5,6], G+C content and 16S rRNA gene sequence based phylogeny [7]. However, these criteria have several drawbacks and their cutoffs can not be used for all bacterial genera [8]. Presently, as the number of available bacterial genomes is increasing, while costs of whole genome sequencing are decreasing, it has been proposed that genomic information and MALDI-TOF spectra [9] be included with the main phenotypic characteristics of a strain, in a polyphasic approach (taxono-genomics) to the description of new bacterial taxa [8,10–23].

Here we present a summary classification and a set of features for Paucisalibacillus algeriensis sp. nov. strain EB02T together with the description of the complete genome sequence and annotation. These characteristics support the circumscription of the species Paucisalibacillus algeriensis.

Classification and features

Paucisalibacillus algeriensis strain EB02T was isolated accidentally in July 2012 during research work for the isolation of halophilic actinomycetes, and further characterized. The source of the isolate was a hypersaline soil sample from the Northwestern periphery of the hypersaline lake Ezzemoul Sabkha in the Oum-El-Bouaghi region of northeastern Algeria. This part of the lake is bounded by halophilic vegetation. Samples were taken aseptically at a depth of 10 cm and transferred to sterile containers, then transported in a cooler (4°C) to our lab in Algeria. 10 g of hyprersaline soil were suspended in 90 ml of sterile saline water (0.9% NaCl) and vigorously vortexed. Tenfold serial dilutions up to 10−5 of the soil suspension were plated in ISP (International Streptomyces Project) medium 2 (dextrose 4 g/l, malt extract 10 g/l, yeast extract 4 g/l, agar 20 g/l) [24] and the plates were incubated at 30°C for 21 days. Strain EB02T was obtained after 24 h of incubation. In order to obtain a pure culture, colonies were transferred after microscopic examination to Nutrient Agar (NA) medium (meat extract 1 g/l, peptone 5 g/l, yeast extract 2 g/l, sodium chloride 5 g/l, agar 15 g/l). Paucisalibacillus algeriensis sp. nov. strain EB02T (Table 1) was isolated by cultivation under aerobic conditions at 30°C. When compared to sequences available in GenBank database using the BLAST program through the National Center for Biotechnology Information (NCBI) server, the 16S rRNA gene sequence of Paucisalibacillus algeriensis strain EB02T (GenBank accession number HG315680) exhibited the highest identity (98.2%) with Paucisalibacillus globulustype strain DSM18846T (Figure 1), the phylogenetically closest validly published Paucisalibacillusspecies. This value was lower than the 98.7% 16S rRNA gene sequence threshold recommended by Stackebrandt and Ebers to delineate a new species without carrying out DNA-DNA hybridizidation [7].

Figure 1.
figure 1

A consensus phylogenetic tree based on 16S rRNA gene sequence comparisons, showing the relationships between strain EB02T Paucisalibacillus algeriensis and other type strains from the genera Paucisalibacillus, Ornithinibacillus, Oceanobacillus, Virgibacillus and Salirhabdus. GenBank accession numbers are displayed in parentheses. Sequences were aligned using CLUSTALW, and phylogenetic inferences obtained using the neighbor-joining method [35] in the MEGA 5 software package [36]. Numbers above the nodes are percentages of bootstrap values obtained from 1,000 replicates that support the node. Paenibacillus polymyxa was used as the outgroup. The scale bar represents 0.01 substitutions per nucleotide position.

Full size image
Table 1. Classification and general features of Paucisalibacillus algeriensis strain EB02T
Full size table

Six growth temperatures (25, 30, 37, 45, 50 and 55°C), ten pHs (5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 10, 11) and nine NaCl concentrations (0, 2.5, 5, 7.5, 10, 15, 20, 25, 30%) were tested. Growth occurred between 25°C and 50°C, however the optimal growth was observed between 30°C and 37°C, the strain was able to grow at between 0% and 5% NaCl concentration and at pHs in the range of 6.5–9 (optimum at pH 7). After 24 h of aerobic incubation under optimal growth conditions on sheep blood agar (BioMerieux), strain EB02T formed light beige, circular, slightly elevated colonies from 1mm to 2 mm in diameter. Growth of the strain was tested in anaerobic and microaerophilic atmospheres using GasPak EZ Anaerobe Pouch (Becton, Dickinson and Company) and CampyGen Compact (Oxoid) systems, respectively, and in an aerobic atmosphere, with or without 5% CO2. Growth was achieved under aerobic (with and without CO2) and microaerophilic conditions but no growth was observed under anaerobic conditions. Gram staining showed Gram positive rods (Figure 2). Cells grown on agar sporulate. A motility test was positive. The presence of peritrichous flagella and the size of cells were determined by negative staining transmission electron microscopy on a Technai G2 Cryo (FEI) at an operating voltage of 200 kV, the rods have a length ranging from 2.1 µm to 3.2 µm (mean 2.6 µm) and a diameter ranging from 0.4 µm to µm 0.6 (mean 0.5 µm) (Figure 3). Strain EB02T exhibited catalase activity but oxidase activity was negative. Using the commercially available API ZYM system (BioMerieux), positive reactions were observed for alkaline phosphatase, esterase (C4), trypsin, α-glucosidase, and a weak positive reaction was observed for esterase lipase (C8); the other tests were negative. Using the API 50CH system (BioMerieux) according to the manufacturer’s instructions, a weak positive reaction was observed for D-glucose, D-fructose, N-acetylglucosamine, D-saccharose, amygdalin, esculin and salicin. The remaining tests were negative. Indole production, β-galactosidase, urease, and hydrolysis of gelatin and starch were negative, but nitrate reduction reaction was positive. Paucisalibacillus algeriensis was resistant to nalidixic acid, but susceptible to amoxicillin, nitrofurantoin, erythromycin, doxycycline, rifampicin, vancomycin, gentamicin, imipenem, trimethoprim-sulfamethoxazole, ciprofloxacin, ceftriaxone and amoxicillin-clavulanic acid.

Figure 2.
figure 2

Gram stain of Paucisalibacillus algeriensis strain EB02T.

Full size image
Figure 3.
figure 3

Transmission electron micrograph of Paucisalibacillus algeriensis strain EB02T made using a Technai G2 Cryo (FEI) at an operating voltage of 200 kV. The scale bar represents 500 nm.

Full size image

When compared to other Paucisalibacillus, Ornithinibacillus, Oceanobacillus and Virgibacillusspecies [1,37–43], Paucisalibacillus algeriensis sp. nov. strain EB02T exhibited the phenotypic differences detailed in (Table 2).

Table 2. Differential phenotypic characteristics between Paucisalibacillus algeriensis sp. nov. strain EB02T and phylogenetically close members of family Bacillacea†.
Full size table

Matrix-assisted laser-desorption/ionization time-of-flight (MALDI-TOF) MS protein analysis was performed as previously described [12,44,45]. Briefly, strain EB02T was cultivated on 5% sheep blood-enriched Columbia agar (BioMerieux) and incubated for 24 h at 30°C. Isolated bacterial colonies were picked, and then deposited as a thin film in 12 replicates on a MALDI-TOF steel target plate (Bruker Daltonics, Bremen, Germany). The plates were allowed to dry at room temperature. Each deposit was overlaid with 1.5 µl of matrix solution containing α-cyano-hydroxycinnamic acid (Sigma, Saint-Quentin Fallavier, France) saturated with 50% acetonitrile, 2.5% trifluoroacetic acid and high-performance liquid chromatography (HPLC)-grade water, and allowed to co-crystallize with the sample. Measurements were conducted using the Microflex LT spectrometer (Bruker Daltonics). Spectra were recorded in the linear positive ion mode over a mass range of 2 to 20 kDa. The acceleration voltage was 20 kV. Spectra were collected as a sum of 240 shots across a spot. The 12 EB02T spectra were imported into the MALDI BioTyper software (version 3.0, Bruker) and analyzed by standard pattern matching (with default parameter settings) against 6,335 bacterial spectra supplemented by the spectra from Ornithinibacillus californiensis DSM 16628T, Ornithinibacillus bavariensis DSM 15681T, Oceanobacillus iheyensis CIP 107618T which were the most closely related species on the basis of their 16S rRNA gene sequences, and Ornithinibacillus contaminans DSM 22953T, Oceanobacillus oncorhynchi subsp incaldanensis CIP 109235T, Oceanobacillus picturae CIP 108264T, Oceanobacillus profundus CIP 109535T, Oceanobacillus oncorhynchi subsp. oncorhynchi CIP 108867T, Oceanobacillus chironomi CIP 109536T, used as reference data in the BioTyper database. A score enabled the identification, or not, from the tested species: a score > 2 with a validated species enabled the identification at the species level, a score > 1.7 but < 2 enabled the identification at the genus level; and a score < 1.7 did not enable any identification. For strain EB02T, the scores obtained ranged from 1.0 to 1.4 thus suggesting that our isolate was a new species. We added the spectrum from strain EB02T (Figure 4) to our database. Spectrum differences with those of Ornithinibacillus and Oceanobacillusrelated species are shown in (Figure 5).

Figure 4.
figure 4

Reference mass spectrum from Paucisalibacillus algeriensis strain EB02T. Spectra from 12 individual colonies were compared and a reference spectrum was generated.

Full size image
Figure 5.
figure 5

Gel view comparing Paucisalibacillus algeriensis EB02T spectra with other members of OrnithinibacillusandOceanobacillusgenera. The Gel View displays the raw spectra of all loaded spectrum files arranged as a pseudo-electrophoretic gel. The x-axis records the m/z value. The left y-axis displays the running spectrum number originating from subsequent spectra loading. The peak intensity is expressed by a grey scale scheme; more intense peaks are shown as darker shades of grey.

Full size image

Genome sequencing information

Genome project history The organism was selected for sequencing on the basis of its phylogenetic position and 16S rDNA sequence similarity to other members of the genus Paucisalibacillus, and is part of a study of the microbial diversity of the hypersaline lakes in northeastern Algeria. It was the 2nd genome of a Paucisalibacillusspecies and the first genome of Paucisalibacillus algeriensis sp. nov. The EMBL accession number is CBYO000000000 and consists of 23 contigs. Table 3 shows the project information and its association with MIGS version 2.0 compliance [46].

Table 3. Project information
Full size table

Growth conditions and DNA isolation

Paucisalibacillus algeriensis sp. nov strain EB02T, was grown aerobically on 5% sheep blood enriched Columbia agar at 30°C. Three petri dishes were spread and resuspended in a 2 ml sterile Eppendorf tube containing 1ml of TE buffer with acid-washed glass beads (diameter ≤106 µm, Sigma, Saint-Quentin Fallavier, France). Three cycles of shaking were performed using a FastPrep BIO 101 apparatus (Qbiogene, Strasbourg, France) for 15 sec at level 6.5 (full speed). Then, the supernatant was placed in a new tube along with one hundred µl of 10% SDS and 50 µl of Proteinase K (Qiagen GmbH, Hilden, Germany) and incubated over night at 56°C. The digested mixture was used to perform DNA extraction using the classical phenol-chloroform method. The quality of the DNA was checked on an agarose gel (0.8%) stained with SYBR safe.

Genome sequencing

Genomic DNA of Paucisalibacillus algeriensis sp. nov. strain EB02T was sequenced on the MiSeq instrument (Illumina, Inc, San Diego CA 92121, USA) with paired end and barcode strategies in order to be mixed with 7 others genomic projects constructed according the Nextera XT library kit (Illumina).

The gDNA was quantified by a Qubit assay with the high sensitivity kit (Life technologies, Carlsbad, CA, USA) to 43.7 ng/µL and dilution was performed to require 1ng of each small genome as input. The “tagmentation” step fragmented and tagged the DNA to generate an optimum insert size of 1.6-kb, validated on a high sensitivity Caliper-Perkin Elmer labchip (Caliper Life Sciences, Inc, Massachusetts, USA). Then limited cycle PCR amplification completed the tag adapters and introduce dual-index barcodes. After purification on Ampure beads (Life technolgies, Carlsbad, CA, USA), the libraries were then normalized on specific beads according to the Nextera XT protocol (Illumina). Normalized libraries are pooled into a single library for sequencing on the MiSeq. The pooled single strand library was loaded onto the reagent cartridge and then onto the instrument along with the flow cell. Automated cluster generation and paired-end sequencing with dual index reads was performed in a single 39-hour run with a 2x250 bp read length. Within this pooled run, the index representation was determined to be 7.1%. Total information of 2.4 G bases was obtained from a 320 K/mm2 density with 94.9% (5,757,000) of the clusters passing quality control (QC) filters. From the genome sequencing process, the 1,375,572 produced Illumina reads for Paucisalibacillus algeriensis EB02T were filtered according to the read qualities and sizes using the fastq-mcf program (Ea-utils: command-line tools for processing biological sequencing data) [47]. 1,296,442 filtered read sequences were kept for genome assembly. The SPAdes Genome assembler (http://bioinf.spbau.ru/spades) was used with different kmer values (from 67 to 99, interval 4) and the best assembly result, with kmer value (n=95) producing 23 contigs with sizes from 1214-bp to 717,245-bp and average size of 174,207-bp, was retained for genome annotation.

Genome annotation

Open Reading Frames (ORFs) were predicted using Prodigal [48] with default parameters. The predicted bacterial protein sequences were searched against the Clusters of Orthologous Groups (COG) databases and the GenBank database [49] using BLASTP. Ribosomal RNAs were found by using RNAmmer 2.1 server [50,51] and BLASTn against the GenBank database, whereas the tRNAScan-SE tool [52] was used to find tRNA genes. Transmembrane helices and lipoprotein signal peptides were predicted using phobius web server [53]. ORFans were identified if their BLASTP E-value was lower than 1e-03 for alignment length greater than 80 amino acids, if alignment lengths were smaller than 80 amino acids, we used an E-value of 1e-05. Artemis [54] was used for data management and DNA Plotter [55] was used for visualization of genomic features. To estimate the mean level of nucleotide sequence similarity at the genome level between Paucisalibacillus algeriensis sp nov. strain EB02T and Paucisalibacillus globulus, Ornithinibacillus scapharcae, Oceanobacillus iheyensis and Virgibacillus halodenitrificans, we used the Average Genomic Identity of Orthologous gene Sequences (AGIOS) home-made software. Briefly, this software uses the Proteinortho software [56] to detect orthologous proteins between genomes compared two by two, then retrieves the corresponding genes and determines the mean percentage of nucleotide sequence identity among orthologous ORFs using the Needleman-Wunsch global alignment algorithm.

Genome properties

The genome is 4,006,766 bp long (1 chromosome but no plasmid) with 36% GC content (Figure 6 and Table 4). It is composed of 23 contigs. Of the 4,038 predicted genes, 3,956 were protein-coding genes, and 82 were RNAs (7 5S rRNA genes, 1 16S rRNA gene, 1 23S rRNA gene, and 73 tRNA genes). A total of 2,691 genes (68.02%) were assigned a putative function (by cogs or by NR blast), of which 179 were identified as ORFans (4.52%). The remaining genes were annotated as hypothetical proteins (821 genes, 20.75%). The distribution of genes into COGs functional categories is presented in Table 5. The properties and statistics of the genome are summarized in Tables 4 and 5.

Figure 6.
figure 6

Graphical circular map of the chromosome. From outside to the center: Alternating red and grey showing the contigs, genes on the forward strand colored by COG categories (only genes assigned to COG), genes on the reverse strand colored by COG categories (only gene assigned to COG), RNA genes (tRNAs green, rRNAs red), GC content. The inner-most circle shows the GC skew, purple and olive indicating negative and positive values, respectively.

Full size image
Table 4. Nucleotide content and gene count levels of the genome
Full size table
Table 5. Number of genes associated with the 25 general COG functional categories
Full size table

Genome comparison

f Paucisalibacillus algeriensis strain EB02T with those of Paucisalibacillus globulus strain B22T, Ornithinibacillus scapharcae strain TW25T, Oceanobacillus iheyensis strain HTE831T and Virgibacillus halodenitrificans strain 1806T (Table 6). The draft genome of Paucisalibacillus algeriensis (4.006Mb) is smaller in size than that of Paucisalibacillus globulus strain B22T (4.24 Mb) but larger than those of Oceanobacillus iheyensis strain HTE831T, Ornithinibacillus scapharcae strain TW25T and Virgibacillus halodenitrificans strain 1806T (3.63, 3.84 and 3.92 Mb, respectively). Paucisalibacillus algeriensis has a higher G+C content (36%) than those of Oceanobacillus iheyensis strain HTE831T and Paucisalibacillus globulus strain B22T (35.7% and 35.8%, respectively) but lower than those of Ornithinibacillus scapharcae strain TW25T and Virgibacillus halodenitrificans strain 1806T (36.7% and 37.4%, respectively). Paucisalibacillus algeriensis has more predicted protein coding genes (3,956) than Oceanobacillus iheyensis strain HTE831T and Virgibacillus halodenitrificans strain 1806T (3,500 and 3,886, respectively) but fewer genes than Ornithinibacillus scapharcae strain TW25T and Paucisalibacillus globulus strain B22T (3,986 and 4,191, respectively). In addition, Paucisalibacillus algeriensis shared 2,591, 2,502, 2,002, and 2,083 orthologous genes with Paucisalibacillus globulus, Ornithinibacillus scapharcae, Oceanobacillus iheyensis and Virgibacillus halodenitrificans respectively.

Table 6. Genomic comparison of Paucisalibacillus algeriensis sp. nov. strain EB02T with four other related species†.
Full size table

The average nucleotide sequence identity of orthologous genes ranges from 69.15 to 83.06% among all of the genomes which were used for the comparison, and from 69.49 to 83.06% between Paucisalibacillus algeriensis and the other genomes (Table 6,. Table 7.), presenting a high sequence identity of orthologous genes with Paucisalibacillusgenus (83.06%), thus confirming its new species status in the Paucisalibacillus genus.

Table 7. Genomic comparison of Paucisalibacillus algeriensis sp. nov. strain EB02T with four other related species†.
Full size table

Conclusion

On the basis of phenotypic (Table 2), phylogenetic and genomic analyses (taxonogenomics) (Table 6, Table 7.), we formally propose the creation of Paucisalibacillus algeriensis sp. nov. that contains the strain EB02T. This strain has been found in a hypersaline lacustrine soil sample collected from Algeria.

Description of Paucisalibacillus algeriensis sp. nov EB02T

Paucisalibacillus algeriensis (al.ge.ri.en’sis. N.L. masc.adj. algeriensis, of Algeria, where strain EB02T was isolated). Strain EB02T is a strictly aerobic Gram-positive rod, endospore-forming, motile by means of peritrichous flagella. Growth is achieved aerobically between 25°C and 50°C, but optimal growth was observed between 30°C-37°C. The strain was able to grow between 0% and 5% NaCl concentration and at pHs in the range of 6.5–9 (optimum at pH 7). Growth is also observed under a microaerophilic atmosphere, however, no growth was observed under anaerobic conditions. After 24h growth on 5% sheep blood-enriched Columbia agar (BioMerieux) at 30°C, bacterial colonies were light beige, circular, slightly elevated and from 1 mm to 2 mm in diameter. Cells have a length ranging from 2.1 µm to 3.2 µm (mean 2.6 µm) and a diameter ranging from 0.4 µm to µm 0.6 (mean 0.5 µm).

Catalase activity was positive but oxidase activity was negative. Using the commercially available API ZYM system (BioMerieux), positive reactions were observed for alkaline phosphatase, esterase (C4), trypsin, α-glucosidase, and weak positive reaction was observed for esterase lipase (C8). The other tests were negative. Using the API 50CH system (BioMerieux) according to the manufacturer’s instructions, a weak positive reaction was observed for, D-glucose, D-fructose, N-acetylglucosamine, D-saccharose, amygdalin, esculin and salicin. The remaining tests were negative. Indole production, β-galactosidase, urease, hydrolysis of gelatin and starch were negative, but the nitrate reduction reaction was positive. Paucisalibacillus algeriensis was resistant to nalidixic acid, but susceptible to amoxicillin, nitrofurantoin, erythromycin, doxycycline, rifampicin, vancomycin, gentamicin, imipenem, trimethoprim-sulfamethoxazole, ciprofloxacin, ceftriaxone and amoxicillin-clavulanic acid. The G+C content of the genome is 36%.

The 16S rRNA and genome sequences are deposited in GenBank under accession number HG315680 and EMBL database under accession number CBYO000000000, respectively. The type strain EB02T (= CSUR P858 = DSM 27335) was isolated from a soil sample from the margin of the hypersaline lake Ezzemoul Sabkha in the Oum-El-Bouaghi region of northeastern Algeria.

References

  1. Nunes I, Tiago I, Pires AL, da Costa MS, Verissimo A. Paucisalibacillus globulus gen. nov., sp. nov., a Gram-positive bacterium isolated from potting soil. Int J Syst Evol Microbiol 2006; 56:1841–1845. PubMed http://dx.doi.org/10.1099/ijs.0.64261-0

    Article  CAS  PubMed  Google Scholar 

  2. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PA, Kämpfer P, Maiden MC, Nesme X, Rosselló-Mora R, Swings J, Trüper HG, et al. Report of the ad hoc committee for the reevaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 2002; 52:1043–1047. PubMed http://dx.doi.org/10.1099/ijs.0.02360-0

    CAS  PubMed  Google Scholar 

  3. Tindall BJ, Rossello-Mora R, Busse HJ, Ludwig W, Kampfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 2010; 60:249–266. PubMed http://dx.doi.org/10.1099/ijs.0.016949-0

    Article  CAS  PubMed  Google Scholar 

  4. Vandamme P, Pot B, Gillis M. de VP, Kersters K, Swings J. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 1996; 60:407–438. PubMed

    PubMed Central  CAS  PubMed  Google Scholar 

  5. Rossello-Mora R. DNA-DNA Reassociation Methods Applied to Microbial Taxonomy and Their Critical Evaluation. In: Stackebrandt E (ed), Molecular Identification, Systematics, and population Structure of Prokaryotes. Springer, Berlin 2006. p. 23–50.

    Chapter  Google Scholar 

  6. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, et al. Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics. Int J Syst Bacteriol 1987; 37:463–464. http://dx.doi.org/10.1099/00207713-37-4-463

    Article  Google Scholar 

  7. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiology Today 2006; 33:152–155.

    Google Scholar 

  8. Ramasamy D, Mishra AK, Lagier JC, Padhmanabhan R, Rossi M, Sentausa E, Raoult D, Fournier PE. A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species. Int J Syst Evol Microbiol 2014; 64:000–000.

    Article  CAS  Google Scholar 

  9. Welker M, Moore ER. Applications of whole-cell matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry in systematic microbiology. Syst Appl Microbiol 2011; 34:2–11. PubMed http://dx.doi.org/10.1016/j.syapm.2010.11.013

    Article  CAS  PubMed  Google Scholar 

  10. Kokcha S, Mishra AK, Lagier JC, Million M, Leroy Q, Raoult D, Fournier PE. Non contiguous-finished genome sequence and description of Bacillus timonensis sp. nov. Stand Genomic Sci 2012; 6:346–355. PubMed http://dx.doi.org/10.4056/sigs.2776064

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  11. Mishra AK, Lagier JC, Rivet O, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Paenibacillus senegalensis sp. nov. Stand Genomic Sci 2012; 7:70–81. PubMed http://dx.doi.org/10.4056/sigs.3056450

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  12. Roux V, ElKarkouri K, Lagier JC, Robert C, Raoult D. Non-contiguous finished genome sequence and description of Kurthia massiliensis sp. nov. Stand Genomic Sci 2012; 7:221–232. PubMed http://dx.doi.org/10.4056/sigs.3206554

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  13. Keita MB, Diene SM, Robert C, Raoult D, Fournier PE, Bittar F. Non-contiguous finished genome sequence and description of Bacillus massiliogorillae sp. nov. Stand Genomic Sci 2013; 9:93–105. PubMed http://dx.doi.org/10.4056/sigs.4388124

    Article  PubMed Central  PubMed  Google Scholar 

  14. Mishra AK, Pfleiderer A, Lagier JC, Robert C, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Bacillus massilioanorexius sp. nov. Stand Genomic Sci 2013; 8:465–479. PubMed http://dx.doi.org/10.4056/sigs.4087826

    Article  PubMed Central  PubMed  Google Scholar 

  15. Ramasamy D, Lagier JC, Gorlas A, Raoult D, Fournier PE. Non contiguous-finished genome sequence and description of Bacillus massiliosenegalensis sp. nov. Stand Genomic Sci 2013; 8:264–278. PubMed http://dx.doi.org/10.4056/sigs.3496989

    Article  PubMed Central  PubMed  Google Scholar 

  16. Ramasamy D, Lagier JC, Nguyen TT, Raoult D, Fournier PE. Non contiguous-finished genome sequence and description of of Dielma fastidiosa gen. nov., sp. nov., a new member of the Family Erysipelotrichaceae. Stand Genomic Sci 2013; 8:336–351. PubMed http://dx.doi.org/10.4056/sigs.3567059

    Article  PubMed Central  PubMed  Google Scholar 

  17. Mishra AK, Lagier JC, Robert C, Raoult D, Fournier PE. Genome sequence and description of Timonella senegalensis gen. nov., sp. nov., a new member of the suborder Micrococcinae. Stand Genomic Sci 2013; 8:318–335. PubMed http://dx.doi.org/10.4056/sigs.3476977

    Article  PubMed Central  PubMed  Google Scholar 

  18. Mishra AK, Hugon P, Lagier JC, Nguyen TT, Couderc C, Raoult D, Fournier PE. Non contiguous-finished genome sequence and description of Enorma massiliensis gen. nov., sp. nov., a new member of the Family Coriobacteriaceae. Stand Genomic Sci 2013; 8:290–305. PubMed http://dx.doi.org/10.4056/sigs.3426906

    Article  PubMed Central  PubMed  Google Scholar 

  19. Lagier JC, El Karkouri K, Mishra AK, Robert C, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Enterobacter massiliensis sp. nov. Stand Genomic Sci 2013; 7:399–412. PubMed http://dx.doi.org/10.4056/sigs.3396830

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  20. Mishra AK, Lagier JC, Pfleiderer A, Nguyen TT, Caputo A, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Holdemania massiliensis sp. nov. Stand Genomic Sci 2013; 9:395–409. http://dx.doi.org/10.4056/sigs.4628316

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  21. Hassani II, Robert C, Michelle C, Raoult D, Hacène H, Desnues C. Non-contiguous finished genome sequence and description of Halopiger djelfamassiliensis sp. nov. Stand Genomic Sci 2013; 9:160–174. PubMed http://dx.doi.org/10.4056/sigs.4578289

    Article  PubMed Central  PubMed  Google Scholar 

  22. Mediannikov O, El Karkouri K, Robert C, Fournier P, Raoult D. Non-contiguous finished genome sequence and description of Bartonella florenciae sp. nov. Stand Genomic Sci 2013; 9:185–196. PubMed http://dx.doi.org/10.4056/sigs.4358060

    Article  PubMed Central  PubMed  Google Scholar 

  23. Mishra AK, Edouard S, Dangui NPM, Lagier JC, Caputo A, Blanc-Tailleur C, Ravaux I, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Nosocomiicoccus massiliensis sp. nov. Stand Genomic Sci 2013; 9:205–219. PubMed http://dx.doi.org/10.4056/sigs.4378121

    Article  PubMed Central  PubMed  Google Scholar 

  24. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340. http://dx.doi.org/10.1099/00207713-16-3-313

    Article  Google Scholar 

  25. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576–4579. PubMed http://dx.doi.org/10.1073/pnas.87.12.4576

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  26. Gibbons NE, Murray RGE. Proposals concerning the higher taxa of bacteria. Int J Syst Bacteriol 1978; 28:1–6. http://dx.doi.org/10.1099/00207713-28-1-1

    Article  Google Scholar 

  27. Murray RGE. The Higher Taxa, or, a Place for Everything…? In: Holt JG (ed). Bergey’s Manual of Systematic Bacteriology, First Edition, Volume 1, The Williams and Wilkins Co, Baltimore 1984; p. 31–34.

    Google Scholar 

  28. Garrity GM, Holt JG. The Road Map to the Manual. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 119–169.

    Chapter  Google Scholar 

  29. Ludwig W, Schleifer KH, Whitman WB. Class I. Bacilli class nov. In: De Vos P, Garrity GM, Jones D, N.R. Krieg W. Ludwig W, Rainey EA, Schleifer KH, Withman WB. Bergey’s Manual of Systematic Bacteriology, second edition, vol 3 (The Firmicutes), Springer, Dordrecht, Heidelberg, London, New York 2009, pp.19–20.

    Google Scholar 

  30. List of new names and new combinations previously effectively, but not validly, published. List no. 132. Int J Syst Evol Microbiol 2010; 60:469–472. http://dx.doi.org/10.1099/ijs.0.022855-0

  31. Skerman VBD, McGowan V, Sneath PHA, eds. Approved Lists of Bacterial Names. Int J Syst Bacteriol 1980; 30:225–420. http://dx.doi.org/10.1099/00207713-30-1-225

  32. Prévot AR. In: Hauduroy P, Ehringer G, Guillot G, Magrou J, Prévot AR, Rosset. Urbain A (eds) Dictionnaire des Bactéries Pathogènes, 2nd ed., Masson, Paris, 1953, pp. 1–692.

    Google Scholar 

  33. Fischer A. Untersuchungen über bakterien. Jahrbücher für Wissenschaftliche Botanik 1985; 27:1–163.

    Google Scholar 

  34. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000; 25:25–29. PubMed http://dx.doi.org/10.1038/75556

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  35. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425. PubMed

    CAS  PubMed  Google Scholar 

  36. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28:2731–2739. PubMed http://dx.doi.org/10.1093/molbev/msr121

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  37. Mayr R, Busse HJ, Worliczek HL, Ehling-Schulz M, Scherer S. Ornithinibacillus gen. nov., with the species Ornithinibacillus bavariensis sp. nov. and Ornithinibacillus californiensis sp. nov. Int J Syst Evol Microbiol 2006; 56:1383–1389. PubMed http://dx.doi.org/10.1099/ijs.0.64038-0

    Article  CAS  PubMed  Google Scholar 

  38. Shin NR, Whon TW, Kim MS, Roh SW, Jung MJ, Kim YO, Bae JW. Ornithinibacillus scapharcae sp. nov., isolated from a dead ark clam. Antonie van Leeuwenhoek 2012; 101:147–154. PubMed http://dx.doi.org/10.1007/s10482-011-9645-3

    Article  CAS  PubMed  Google Scholar 

  39. Bagheri M, Amoozegar MA, Schumann P, Didari M, Mehrshad M, Spröer C, Sánchez-Porro C, Ventosa A. Ornithinibacillus halophilus sp. nov., a moderately halophilic, Gram-stain-positive, endospore-forming bacterium from a hypersaline lake. Int J Syst Evol Microbiol 2013; 63:844–848. PubMed http://dx.doi.org/10.1099/ijs.0.041350-0

    Article  CAS  PubMed  Google Scholar 

  40. Nam JH, Bae W, Lee DH. Oceanobacillus caeni sp. nov., isolated from a Bacillus-dominated wastewater treatment system in Korea. Int J Syst Evol Microbiol 2008; 58:1109–1013. PubMed http://dx.doi.org/10.1099/ijs.0.65335-0

    Article  CAS  PubMed  Google Scholar 

  41. Lu J, Nogi Y, Takami H. Oceanobacillus iheyensis gen. nov., sp. nov., a deep-sea extremely halotolerant and alkaliphilic species isolated from a depth of 1050 m on the Iheya Ridge. FEMS Microbiol Lett 2001; 205:291–297. PubMed http://dx.doi.org/10.1111/j.1574-6968.2001.tb10963.x

    Article  CAS  PubMed  Google Scholar 

  42. Yoon JH, Oh TK, Park YH. Transfer of Bacillus halodenitrificans Denariaz et al. 1989 to the genus Virgibacillus as Virgibacillus halodenitrificans comb. nov. Int J Syst Evol Microbiol 2004; 54:2163–2167. PubMed http://dx.doi.org/10.1099/ijs.0.63196-0

    Article  CAS  PubMed  Google Scholar 

  43. Roux V, Million M, Robert C, Magne A, Raoult D. Non-contiguous finished genome sequence and description of Oceanobacillus massiliensis sp. nov. Stand Genomic Sci 2013; 9:370–384. http://dx.doi.org/10.4056/sigs.4267953

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  44. Seng P, Rolain JM, Fournier PE, La Scola B, Drancourt M, Raoult D. MALDI-TOF-mass spectrometry applications in clinical microbiology. Future Microbiol 2010; 5:1733–1754. PubMed http://dx.doi.org/10.2217/fmb.10.127

    Article  CAS  PubMed  Google Scholar 

  45. Seng P, Drancourt M, Gouriet F, La Scola B, Fournier PE, Rolain JM, Raoult D. Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin Infect Dis 2009; 49:543–551. PubMed http://dx.doi.org/10.1086/600885

    Article  CAS  PubMed  Google Scholar 

  46. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541–547. PubMed http://dx.doi.org/10.1038/nbt1360

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  47. fastq-mcf program. http://code.google.com/p/ea-utils

  48. Prodigal. http://prodigal.ornl.gov

  49. GenBank database. http://www.ncbi.nlm.nih.gov/genbank

  50. RNAmmer 1.2 Server. http://www.cbs.dtu.dk/services/RNAmmer/

  51. Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108. PubMed http://dx.doi.org/10.1093/nar/gkm160

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  52. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964. PubMed http://dx.doi.org/10.1093/nar/25.5.0955

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  53. Kall L, Krogh A, Sonnhammer EL. Advantages of combined transmembrane topology and signal peptide prediction—the Phobius web server. Nucleic Acids Res 2007; 35:W429–W432. PubMed http://dx.doi.org/10.1093/nar/gkm256

    Article  PubMed Central  PubMed  Google Scholar 

  54. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, Barrell B. Artemis: sequence visualization and annotation. Bioinformatics 2000; 16:944–945. PubMed http://dx.doi.org/10.1093/bioinformatics/16.10.944

    Article  CAS  PubMed  Google Scholar 

  55. Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J. DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 2009; 25:119–120. PubMed http://dx.doi.org/10.1093/bioinformatics/btn578

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  56. Lechner M, Findeiss S, Steiner L, Marz M, Stadler PF, Prohaska SJ. Proteinortho: detection of (co-)orthologs in large-scale analysis. BMC Bioinformatics 2011; 12:124–133. PubMed http://dx.doi.org/10.1186/1471-2105-12-124

    Article  PubMed Central  PubMed  Google Scholar 

Download references

Acknowledgements

The authors thank Linda Hadjadj for technical assistance and Xegen company for automating the genome annotation process.

Author information

Authors and Affiliations

  1. Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UMR CNRS, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France

    Esma Bendjama, Lotfi Loucif, Seydina M. Diene, Caroline Michelle & Jean-Marc Rolain

  2. Département de Biochimie, Faculté des Sciences, Université Badji Mokhtar, Annaba, Algérie

    Esma Bendjama, Lotfi Loucif & Djamila Gacemi-Kirane

  3. Département des Sciences Biologiques, Faculté des Sciences, Université El Hadj Lakhdar, Batna, Algérie

    Esma Bendjama & Lotfi Loucif

Authors
  1. Esma Bendjama
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Lotfi Loucif
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Seydina M. Diene
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Caroline Michelle
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Djamila Gacemi-Kirane
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jean-Marc Rolain
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jean-Marc Rolain.

Additional information

These authors contributed equally to this work.

Rights and permissions

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Bendjama, E., Loucif, L., Diene, S.M. et al. Non-contiguous finished genome sequence and description of Paucisalibacillus algeriensis sp. nov.. Stand in Genomic Sci 9, 1352–1365 (2014). https://doi.org/10.4056/sigs.5611012

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.4056/sigs.5611012

Keywords

Environmental Microbiome

ISSN: 2524-6372