Skip to main content

Non-contiguous finished genome sequence and description of Kurthia senegalensis sp. nov.

Abstract

Kurthia senegalensis strain JC8ET sp. nov. is the type strain of K. senegalensis sp. nov., a new species within the genus Kurthia. This strain, whose genome is described here, was isolated from the fecal flora of a healthy patient. K. senegalensis is an aerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,975,103 bp long genome contains 2,889 protein-coding genes and 83 RNA genes, including between 4 and 6 rRNA genes.

Introduction

Kurthia senegalensis strain JC8ET (CSUR P138T = DSM 24641T) is the type strain of K. senegalensis sp. nov. This bacterium is a Gram-positive strictly aerobic rod, capsulated, motile by peritrichous flagella and was isolated from the stool of a healthy Senegalese patient as part of a “culturomics” study aiming at cultivating individually all species within human feces [1].

Presently, “the gold standard method” to define a bacterial species is DNA-DNA hybridization (DDH) [2]. But this method is time consuming and the inter-laboratory reproducibility is poor. So, with the development of PCR and sequencing methods, 16S rRNA gene sequence comparison is often the preferred approach for recognizing a new taxon when a gene sequence similarity less than 97% is found [3]. To make descriptions more complete, phenotypic criteria (morphology, biochemical tests, growth conditions, chemotaxonomy) have to be included to characterize a prokaryote strain [4]. Fortunately, sequencing whole prokaryote genomes is now possible for more laboratories, and descriptions of sequencing protocols should be included in all species descriptions. Such activity would supplant the need for most other methods used during genome annotation, and new bioinformatics methods based on genome-to-genome comparison have been proposed to replace the DDH approach [5].

Here we present a summary classification and a set of features for K. senegalensis sp. nov. strain JC8ET together with the description of the complete genomic sequencing and annotation. These characteristics support the circumscription of the species K. senegalensis.

Kurth described Bacterium zopfii, isolated from the intestinal contents of chickens, which became later the first species of the genus Kurthia, K. zopfii. The genus Kurthia was created in 1885 by Trevisan [6] in honor of Kurth. The name Kurthia was first published in the seventh edition of Bergey’s Manual of Determinative Bacteriology [7]. Currently, the genus includes 4 species: K. zopfii, K. gibsonii [8], K. sibirica [9] and K. massiliensis [10]. The bacteria are included in the Firmicutes phylum, in the Planococcaceae family.

Classification and features

A stool sample was collected from a healthy 16-year-old male Senegalese volunteer patient living in Dielmo (a rural village in the Guinean-Sudanian zone in Senegal), who was included in a research protocol. The patient gave an informed and signed consent, and the agreement of the National Ethics Committee of Senegal and the local ethics committee of the IFR48 (Marseille, France) were obtained under agreement 09-022). The fecal specimen was preserved at −80°C after collection and sent to Marseille. Strain JC8E (Table 1) was isolated in January 2011 by aerobic cultivation on 5% sheep blood-enriched Columbia agar (BioMerieux). There is no evidence of pathogenicity for the strain. JC8E exhibited a 96.8% nucleotide sequence similarity with K. massiliensis, the phylogenetically closest validated Kurthia species (Figure 1). This value was lower than the 97% 16S rRNA gene sequence threshold to delineate a new species without carrying out DNA-DNA hybridization recommended by the report of the ad hoc committee on reconciliation of approaches to bacterial systematics [2]. Moreover, Stackebrandt and Ebers proposed to increase this value to 98.7% [25]. Recently, Auch et al. proposed a genome-to-genome comparison approach to replace the DDH approach [5]. As we sequenced the genomes of K. massiliensis and K. senegalensis, we tested this new approach. We chose GGDC 2.0 Blast + as the alignment method for finding intergenomic matches, using a formula based on the number of identities divided by the HSP (High scoring Segment Pairs) length to infer distances. The DDH estimate resulted from a generalized linear model (GLM). The GLM-based DDH estimate was 21% ± 2.33. The found value (< 70%) confirmed that K. massiliensis and isolate JC8ET did not belong to the same species.

Figure 1.
figure 1

Phylogenetic tree highlighting the position of Kurthia senegalensis strain JC8ET relative to other type strains within the Kurthia genus. GenBank accession numbers are indicated in parentheses. Sequences were aligned using CLUSTALX, and phylogenetic inferences obtained using the neighbor joining method as implemented in the MEGA 5 software package [24]. Numbers at the nodes are percentages of bootstrap values supporting that node using 1,000 bootstrap replicates to generate a majority consensus tree. Solibacillus silvestris was used as the outgroup. The scale bar represents 0.005 nucleotide change per nucleotide position.

Table 1. Classification and general features of Kurthia senegalensis strain JC8ET [11]

Surface colonies were observed on sheep blood agar (bioMérieux) after 24 hours aerobic incubation at 37°C. The colonies of the strain JC8ET were yellowish, mat, flat and spread, 5 mm in diameter. Gram staining showed Gram-positive coccobacilli (Figure 2).

Figure 2.
figure 2

Gram stain of K. senegalensis strain JC8ET

Six different growth temperatures (25, 30, 37, 45, 50 and 55°C) were tested. Growth occurred between 25°C and 50°C, and optimal growth was observed between 30°C and 50°C. Growth of the strain was tested under an aerobic atmosphere, in the presence of 5% CO2, and also in anaerobic and microaerophilic atmospheres which were created using GENbag anaer and GENbag microaer (bioMérieux), respectively. The strains were aerobic and also grew under microaerophilic conditions and in the presence of 5% CO2 but did not grow in an anaerobic atmosphere. The NaCl concentrations allowing growth of strain JC8ET, were determined on DifcoTMBrain Heart Infusion Agar plates (Becton Dickinson). The powder was supplemented with NaCl (Euromedex) to obtain the tested concentrations (0.5, 1, 2, 3, 5 10, 15%, w/v). Growth occurred between 0.5–5% NaCl but the optimum growth was between 0.5–2% NaCl.

Growth in the range of pH 5.0–10.0 was tested using BBLTM Brain Heart Infusion (Becton Dickinson). Final pH was adjusted with HCl or NaOH solution. Growth occurred between pH 5–9.

The size and ultrastructure of cells were determined by negative staining transmission electron microscopy. The rods were 1.8–9.2 µm long and 0.7–1.2 µm wide (Figure 3). Peritrichous flagella were observed. Capsule was characterized by India ink stain and after the bacteria were embedded in Epon 812 resin and observed by transmission electron microscopy (Figure 4).

Figure 3.
figure 3

Transmission electron micrograph of K. senegalensis strain JC8ET, using a Morgani 268D (Philips) at an operating voltage of 60kV.The scale bar represents 2 µm.

Figure 4.
figure 4

Capsule characterization of K. senegalensis after the bacteria were embedded in Epon 812 resin and observed by transmission electron microscopy.

Strain JC8ET exhibited catalase activity but no oxidase activity. Api ZYM, Api 20NE (BioMérieux) were used to study biochemical characters (Table 2).

Table 2. Diagnostic traits differentiating five Kurthia species.

Analysis of respiratory quinones by HPLC was carried out by the Identification Service and Dr Brian Tindall, DSMZ, Braunschweig, Germany. Respiratory lipoquinones were extracted from 100 mg of freeze dried cell material as described by Tindall [26,27]. Respiratory lipoquinones were separated into their different classes (menaquinones and ubiquinones) by thin layer chromatography on silica gel, using hexane:tert-butylmethylether (9:1 v/v) as solvent. UV absorbing bands corresponding to menaquinones or ubiquinones were removed from the plate and further analyzed by HPLC at 269 nm. The respiratory quinones were MK-7 (100%) for strain JC8ET. Preparation and determination of cellular fatty acids were carried out by following the procedures given for the Sherlock Microbial identification System (MIDI). The major fatty acids were C15:0 iso 50.75% and C15:0 anteiso 24.05%. Polar lipids were extracted from 100 mg of freeze dried cell material using a chloroform:methanol:0.3% aqueous NaCl mixture 1:2:0.8 (v/v/v) (modified after [28]). The extraction solvent was stirred overnight and the cell debris pelleted by centrifugation. Polar lipids were recovered into the chloroform phase by adjusting the chloroform:methanol:0.3% aqueous NaCl mixture to a ratio of 1:1:0.9 (v/v/v). Polar lipids were separated as previously described [29]. The polar lipids present were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phospholipids 1 and 2, unidentified aminophospholipid and glycolipid. The peptidoglycan of the bacteria was isolated as described by Schleifer [30]. The determination was carried out as previously described [30,31] with the modification that TLC on cellulose was applied instead of paper chromatography. Quantitative analysis of amino acids was performed after derivatization by gas chromatography and gas chromatography / mass spectrometry (320-MS Quadrupole GC/MS, Varian) [32]. K. senegalensis showed the peptidoglycan type A4αL-Lys←D-Glu (type A11.33 according to ref [33]).

K. senegalensis was susceptible to penicillin G, amoxicillin, amoxicillin plus clavulanic acid, imipenem, gentamycin, erythromycin, doxycycline, rifampicin, vancomycin, nitrofurantoin. It was resistant to ceftriaxone, ciprofloxacin, sulfamethoxazole trimethoprim and metronidazole.

Matrix-assisted laser-desorption/ionization time-of-flight (MALDI-TOF) MS protein analysis was carried out. Briefly, a pipette tip was used to pick one isolated bacterial colony from a culture agar plate, and to spread it as a thin film on a MALDI-TOF target plate (Bruker Daltonics). Twelve distinct deposits were done for strain JC8ET from twelve isolated colonies and the manipulation was repeated another day. After air-drying, 1.5 µl matrix solution (saturated solution of α-cyanohydroxycinnaminic acid in 50% aqueous acetonitrile containing 2.5% trifluoroacetic acid) per spot was applied. MALDI-TOF MS was conducted using the Microflex LT spectrometer (Bruker Daltonics). All spectra were recorded in linear, positive ion mode. The acceleration voltage was 20 kV. Spectra were collected as a sum of 240 shots across a spot. Preprocessing and identification steps were performed using the manufacturer’s parameters. The JC8ET spectra were imported into the MALDI BioTyper software (version 3.0, Bruker) and analysed by standard pattern matching (with default parameter settings) against the main spectra of 6,300 bacteria, including the spectra from K. gibsonii, K. sibirica, K. zopfii and K. massiliensis, in the BioTyper database. A score enabled the identification, or not, from the tested species: a score > 2.3 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 JC8ET, none of the obtained scores were > 1, thus suggesting that our isolate was not a member of a known species. We added the spectrum from strain JC8ET to our database (Figure 5). The spectrum is available online in our free-access URMS database.

Figure 5.
figure 5

Reference mass spectra from K. senegalensis strain JC8ET and other representatives of the genus Kurthia. Spectra from 24 individual colonies were compared and a reference spectrum was generated. Strains: 1, K massiliensis JC30T; 2, K. senegalensis sp. nov. JC8ET; 3, K. sibirica DSM 4747T; 4, K. gibsonii DSM 20636T; 5, K. zopfii DSM 20580T.

Genome sequencing information

Genome project history

The organism was selected for sequencing on the basis of its phylogenetic position and 16S rDNA similarity to other members of the genus Kurthia, and is part of a “culturomics” study of the human digestive flora aiming at isolating all bacterial species within human feces. It was the second genome of a Kurthia species, Kurthia senegalensis sp. nov. A summary of the project information is shown in Table 3. The EMBL accession number is CAEW01000000 and consists of 46 contigs (≥500 bp) and 17 scaffolds (> 2,575 bp). Table 3 shows the project information and its association with MIGS version 2.0 compliance.

Table 3. Project information [11]

Growth conditions and DNA isolation

K. senegalensis sp. nov. strain JC8ET, CSUR P138T, DSM 24641T, was grown aerobically on 5% sheep blood-enriched Columbia agar at 37°C. 3 petri dishes were spread and resuspended in 3×100µl of G2 buffer. A first mechanical lysis was performed with glass powder on the Fastprep-24 device (Sample Preparation system) from MP Biomedicals, USA using 2×20 second bursts. DNA was then treated with lysozyme (30 minutes at 37°C) and extracted using the BioRobot EZ 1 Advanced XL (Qiagen). The DNA was then concentrated and purified on a Qiamp kit (Qiagen). The yield and the concentration was measured by the Quant-it Picogreen kit (Invitrogen) on the Genios Tecan fluorometer at 86 ng/µl.

Genome sequencing and assembly

Shotgun and 3-kb paired-end sequencing strategies were performed. The shotgun library was constructed with 500 ng of DNA with the GS Rapid library Prep kit (Roche). For the paired-end sequencing, 5 µg of DNA was mechanically fragmented on a Hydroshear device (Digilab) with an enrichment size at 3–4 kb. The DNA fragmentation was visualized using the 2100 BioAnalyzer (Agilent) on a DNA labchip 7500 with an optimal size of 3.679 kb. The library was constructed according to the 454 GS FLX Titanium paired-end protocol. Circularization and nebulization were performed and generated a pattern with an optimal size of 497 bp. After PCR amplification through 15 cycles followed by double size selection, the single stranded paired-end library was then quantified using the Genios fluorometer (Tecan) at 888 pg/µL. The library concentration equivalence was calculated as 3.28 × 109molecules/µL. The library was stored at −20°C until further use.

The shotgun and paired-end libraries were clonally-amplified with 3 cpb and 1cpb in 3 and 4 emPCR reactions respectively on the GS Titanium SV emPCR Kit (Lib-L) v2 (Roche). The yields of the emPCR were 14.72 and 20% respectively. 340,000 beads for the shotgun application and 790,000 beads for the 3kb paired end were loaded on the GS Titanium PicoTiterPlate PTP Kit 70x75 and sequenced with the GS FLX Titanium Sequencing Kit XLR70 (Roche). The run was performed overnight and then analyzed on the cluster through the gsRunBrowser and Newbler assembler (Roche). A total of 307,968 passed filter wells were obtained and generated 69.7 Mb with a length average of 223 bp. The passed filter sequences were assembled using Newbler with 90% identity and 40 bp as overlap. The final assembly identified 17 scaffolds and 42 large contigs (>1,500 bp).

Genome annotation

Open Reading Frames (ORFs) were predicted using Prodigal [34] with default parameters but the predicted ORFs were excluded if they were spanning a sequencing GAP region. The predicted bacterial protein sequences were searched against the GenBank database [35] and the Clusters of Orthologous Groups (COG) databases [36] using BLASTP. The tRNAscan-SE tool [37] was used to find tRNA genes, whereas ribosomal RNAs were found by using RNAmmer [38].

Transmembrane domains and signal peptides were predicted using TMHMM [39] and SignalP [40], respectively. 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. Such parameter thresholds have been used in previous works to define ORFans.

To estimate the mean level of nucleotide sequence similarity at the genome level between K. senegalensis and K. massiliensis (GenBank accession number CAEU01000000), the only available Kurthia genome to date, we compared the ORFs only using comparison sequences found in the server RAST [41] at a query coverage of ≥60% and a minimum nucleotide length of 100 bp.

Genome properties

The genome is 2,975,103 bp long with a 38.21% GC content (Table 3, Figure 6). Of the 2,972 predicted genes, 2,889 were protein-coding genes, and 83 were RNAs. A total of 2,141 genes (74.11%) were assigned a putative function. The remaining genes were annotated as either hypothetical proteins or proteins of unknown function. The distribution of genes into COGs functional categories is presented in Table 4. The properties and the statistics of the genome are summarized in Tables 4 and 5.

Figure 6.
figure 6

Graphical circular map of Kurthia senegalensis genome. From outside to the center: Genes on forward strand (colored by COG categories), genes on reverse strand (colored by COG categories), RNA genes (tRNAs green, rRNAs red), GC content, and GC skew (3 circles).

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

Comparison with other Kurthia genomes

To date, only the genome of K. massiliensis strain JC30T has also been sequenced. K. senegalensis strain JC8ET shares a mean sequence similarity of 80.57% (60.06-99.58%) with K. massiliensis JC30T. The genome size, the G+C% and the total genes of K. senegalensis strain JC8ET are lower than those of K. massiliensis JC30T (Table 6).

Table 6. Genome characteristics of Kurthia representatives.

Prophage genome properties

Prophage Finder [42] and PHAST [43] were used to identify potential prophages in K. senegalensis strain JC8ET genome. The genome contains at least one genetic element of around 36.3 kb (with a GC content of 38.9%), which we named KS1, on contig 21. The overall G + C content of the KS1 genome (38.9%) is comparable with the overall G + C content of K. senegalensis genome (38.21%), allowing KS1 to be maintained and regulated inside the host [44].

A total of 49 open reading frames (ORFs) larger than 98 nucleotides were recovered from KS1, and most of them (24) encode proteins sharing a high identity with proteins found in Bacillales genus phages. The majority of the putative genes (43) have the same orientation and six are located on the complementary strand. Preliminary annotation of KS1 was performed and the majority of the putative genes (31) encode hypothetical proteins. The 19 ORFs with an attributed function encode proteins involved in DNA packaging, head and tail morphogenesis structure, cell lysis and lysogeny control, DNA replication, recombination, and modification.

Conclusion

On the basis of phenotypic, phylogenetic and genomic analyses, we formally propose the creation of Kurthia senegalensis sp. nov. that contains the strain JC8ET. This strain originated in Senegal.

Description of Kurthia senegalensis sp. nov.

Kurthia senegalensis (se.ne.gal.e’n.sis, L. gen. masc. n. senegalensis pertaining to Senegal, the country where the type strain was isolated). Isolated from stool of a healthy Senegalese patient. K senegalensis are aerobic Gram-positive coccobacilli. Surface colonies were observed on sheep blood agar after 24 h aerobic incubation at 37°C. The colonies of the strain JC8ET were circular, greyish/yellowish, shiny, curved and smooth, 2–5 mm in diameter. Cells are motile by peritrichous flagella and capsulated. Catalase activity is positive but oxidase activity is negative. Gelatine hydrolysis, N-acetyl-glucosamine assimilation, potassium gluconate assimilation, capric acid assimilation and malic acid assimilation are present. Alkaline phosphatase, esterase (C4), esterase lipase (C8), leucine arylaminidase, trypsin, α-chemotrypsin and acid phosphatase activities are observed. The major fatty acids are C15:0 iso 50.75% and C15:0 anteiso 24.05%. The polar lipids present are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phospholipids 1 and 2, unidentified aminophospholipid and glycolipid. The peptidoglycan type is A4αL-Lys←D-Glu (type A11.33). Cells are susceptible to penicillin G, amoxicillin, amoxicillin plus clavulanic acid, imipenem, gentamycin, erythromycin, doxycycline, rifampicin, vancomycin and nitrofurantoin. The genome is 2,975,103 bp long with a 38.21% G+C content. A 36.3 kb prophage, KS1, was identified. The type strain is JC8ET (= CSUR P138T = DSM 24641T). The 16S rRNA gene sequence was deposited in GenBank with the accession number JF824796. The whole genome shotgun sequence of K. senegalensis strain JC8ET was deposited in GenBank/DDBJ/EMBL under accession number CAEW01000000.

Abbreviations

EMBL:

European Molecular Biology Laboratory

DDBJ:

DNA Data Bank of Japan

References

  1. Lagier JC, Armougom F, Million M, Hugon P, Pagnier I, Robert C, Bittar F, Fournous G, Gimenez G, Maraninchi M, et al. Microbial culturomics: paradigm shift in the human gut microbiome study. Clin Microbiol Infect 2012; 18:1185–1193. PubMed

    Article  CAS  PubMed  Google Scholar 

  2. 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 

  3. 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 

  4. Tindall BJ, Rossello-Mora R, Busse HJ, Ludwig W, Kämpfer 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 

  5. Auch AF, Klenk HP, Göker M. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2010; 2:142–148. PubMed http://dx.doi.org/10.4056/sigs.541628

    Article  PubMed Central  PubMed  Google Scholar 

  6. Trevisan V. Caretteri di alcuni nuovi generi di Batteriacee. Atti della Accademia Fisio-Medico-Statistica in Milano, Series 4 1985; 3:92–107.

    Google Scholar 

  7. Breed RS, Murray EGD, Smith NR, eds. Bergey’s Manual of Determinative Bacteriology, 7th ed. Williams and Wilkins. Baltimore, MD. 1957.

    Google Scholar 

  8. Keddie RM, Shaw S. Genus Kurthia. In: Sneath PHA, Mair NS, Sharpe ME and Holt JG (Eds.) Bergey’s Manual of Systematic Bacteriology. Volume 2, The Williams and Wilkins Co., Baltimore, 1986, p. 1255–1258.

    Google Scholar 

  9. Belikova VA, Cherevach NV, Kalakutskii LV. A new species of bacteria of the genus Kurthia, Kurthia sibirica sp. nov. Mikrobiologiia 1986; 55:831–835.

    CAS  PubMed  Google Scholar 

  10. Roux V, El Karkouri 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 

  11. 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 

  12. Woese CR, Kandier 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 

  13. 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 

  14. 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 

  15. 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 

  16. Ludwig W, Schleifer KH, Whitman WB. Class I. Bacilli class nov. In: De Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer KH, Whitman WB (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 3, Springer-Verlag, New York, 2009, p. 19–20.

    Google Scholar 

  17. 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

  18. Prévot AR. In: Hauderoy P, Ehringer G, Guillot G, Magrou. J., Prévot AR, Rosset D, Urbain A (eds), Dictionnaire des Bactéries Pathogènes, Second Edition, Masson et Cie, Paris, 1953, p. 1–692.

    Google Scholar 

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

    Article  Google Scholar 

  20. Krasil’nikov NA. Guide to the Bacteria and Actinomycetes [Opredelitelv Bakterii i Actinomicetov], Akad. Nauk SSSR, Moscow, 1949, p. 328.

    Google Scholar 

  21. Keddie RM, Rogosa M. Genus Kurthia Trevisan 1885, 92; Nom. cons. Opin. 13, Jud. Comm. 1954, 152. In: Buchanan RE, Gibbons NE (eds), Bergey’s Manual of Determinative Bacteriology, Eighth Edition, The Williams and Wilkins Co., Baltimore, 1974, p. 631–632.

    Google Scholar 

  22. Judicial Commission. Opinions 4, 6, 7, 8, 9, 10, 11, 12, 13, 14. Opinion 13. Int Bull Bacteriol Nomencl Taxon 1954; 4:141–158.

    Google Scholar 

  23. 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 

  24. 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 

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

    Google Scholar 

  26. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130. http://dx.doi.org/10.1016/S0723-2020(11)80158-X

    Article  CAS  Google Scholar 

  27. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202. http://dx.doi.org/10.1111/j.1574-6968.1990.tb03996.x

    Article  CAS  Google Scholar 

  28. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917. PubMed http://dx.doi.org/10.1139/o59-099

    Article  CAS  PubMed  Google Scholar 

  29. Tindall BJ, Sikorski J, Smibert RM, Kreig NR. Phenotypic characterization and the principles of comparative systematics. In: Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM, Snyder LR (eds), Methods for General and Molecular Microbiology, 3rd edition, ASM Press, Washington, 2007, p. 330–393.

    Google Scholar 

  30. Schleifer KH. Analysis of the chemical composition and primary structure of murein. Methods Microbiol 1985; 18:123–156. http://dx.doi.org/10.1016/S0580-9517(08)70474-4

    Article  CAS  Google Scholar 

  31. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477. PubMed

    PubMed Central  CAS  PubMed  Google Scholar 

  32. MacKenzie SL. Gas chromatography analysis of amino acids as the N-heptafluorobutyryl isobutyl esters. J Assoc Off Anal Chem 1987; 70:151–160. PubMed

    CAS  PubMed  Google Scholar 

  33. http://www.dsmz.de/microorganisms/main.php?contentid=35.

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

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

  36. Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2000; 28:33–36. PubMed http://dx.doi.org/10.1093/nar/28.1.33

    Article  PubMed Central  CAS  PubMed  Google Scholar 

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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  38. 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 

  39. Krogh A, Larsson B, von Heijni G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001; 305:567–580. PubMed http://dx.doi.org/10.1006/jmbi.2000.4315

    Article  CAS  PubMed  Google Scholar 

  40. Bendtsen JD, Nielsen H, von Heijne G, Brunak S. Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 2004; 340:783–795. PubMed http://dx.doi.org/10.1016/j.jmb.2004.05.028

    Article  PubMed  Google Scholar 

  41. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, et al. The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics 2008; 9:75–89. PubMed http://dx.doi.org/10.1186/1471-2164-9-75

    Article  PubMed Central  PubMed  Google Scholar 

  42. Bose M, Barber RD. Prophage Finder: a prophage loci prediction tool for prokaryotic genome sequences. In Silico Biol 2006; 6:223–227. PubMed

    CAS  PubMed  Google Scholar 

  43. Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. PHAST: a fast phage search tool. Nucleic Acids Res 2011; 39:W347–W352. PubMed http://dx.doi.org/10.1093/nar/gkr485

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  44. Nishida H. Evolution of genome base composition and genome size in bacteria. Front Microbiol 2012; 3:420. PubMed http://dx.doi.org/10.3389/fmicb.2012.00420

    Article  PubMed Central  PubMed  Google Scholar 

Download references

Acknowledgements

The authors thank Julien Paganini at Xegen Company for automating the genomic annotation process. This study was funded by the Mediterranée-Infection Foundation.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Véronique Roux.

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

Roux, V., Lagier, JC., Gorlas, A. et al. Non-contiguous finished genome sequence and description of Kurthia senegalensis sp. nov.. Stand in Genomic Sci 9, 1319–1330 (2014). https://doi.org/10.4056/sigs.5078947

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.4056/sigs.5078947

Keywords