- Open Access
Non-contiguous finished genome sequence and description of Brevibacterium senegalense sp. nov.
Standards in Genomic Sciences volume 7, pages 233–245 (2012)
Brevibacterium senegalense strain JC43T sp. nov. is the type strain of Brevibacterium senegalense sp. nov., a new species within the Brevibacterium genus. This strain, whose genome is described here, was isolated from the fecal flora of a healthy Senegalese patient. B. senegalense is an aerobic rod-shaped Gram-positive bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,425,960 bp long genome (1 chromosome but no plasmid) contains 3,064 protein-coding and 49 RNA genes.
Brevibacterium senegalense strain JC43T (= CSUR P155 = DSM 25783) is the type strain of B. senegalense. sp. nov. This bacterium is a non-motile, rod-shaped, Gram-positive, catalase-positive bacterium that was isolated from the stool of a healthy Senegalese patient as part of a study aiming at cultivating individually all bacterial species within human feces.
Bacterial taxonomy has undergone many changes over recent years. The DNA-DNA hybridization and G+C content criteria, once considered as gold standards , were gradually replaced by gene sequencing. In particular, 16S rRNA sequencing has deeply changed the way bacteria and archaea are classified . More recently, the development of high throughput genome sequencing methods and mass spectrometric analyses of bacteria have provided a wealth of genetic and proteomic information . We recently used a polyphasic approach  that includes genomic data, MALDI-TOF spectrum and major phenotypic characteristics to describe new bacterial species [5–11].
The genus Brevibacterium (Breed 1953)  was created in 1953 to gather short non-spore-forming and non-branching rods. To date, this genus is comprised of Gram-positive, irregular, rod-shaped, non-acid-fast bacteria, and contains 31 recognized species with validly published names . Brevibacterium is the type genus of the family Brevibacteriaceae (Breed 1953) . Members of the genus Brevibacterium are isolated from human samples, dairy products, poultry and environmental specimens. In humans, they are found on skin surfaces , but have also been demonstrated to cause rare cases of bacteremia, endocarditis, pericarditis, brain abscess and peritonitis. These infections have been observed mainly in immunocompromised patients, with the exception of two cases of bacteremia in immunocompetent patients with central venous catheters [15,16]. To date, only four Brevibacterium species have been detected in human infection, including B. epidermidis (Collins et al. 1983) [15,17,18], B. casei (Collins et al. 1983) [16,19], B. iodinum (Collins et al. 1981) and B. otitidis (Pascual et al. 1996).
Here we present a summary classification and a set of features for B. senegalense sp. nov. strain JC43T together with the description of the complete genomic sequencing and annotation. These characteristics support the circumscription of the B. senegalense species.
A stool sample was collected from a healthy 16-year-old male Senegalese volunteer patient living in Dielmo (rural village in the Guinean-Sudanian zone in Senegal), who was included in a research protocol. Written assent was obtained from this individual. No written consent was needed from his guardians for this study because he was older than 15 years old (in accordance with the previous project approved by the Ministry of Health of Senegal and the assembled village population, and as published elsewhere [5–11]. Both this study and the assent procedure were approved by the National Ethics Committee of Senegal (CNERS) and the Ethics Committee of the Institut Fédératif de Recherche IFR48, Faculty of Medicine, Marseille, France (agreement numbers 09-022 and 11-017)). Several other new bacterial species were isolated from this specimen using various culture conditions, including the recently described Alistipes timonensis, A. senegalensis, Anaerococcus senegalensis, Bacillus timonensis, Clostridium senegalense, Paenibacillus senegalensis, and Peptoniphilus timonensis [5–11]. The fecal specimen was preserved at −80°C after collection and sent to Marseille. Strain JC43T (Table 1) was isolated in December 2010 after inoculation on Brucella agar (BD diagnostic, Heilderberg, Germany), in aerobic atmosphere at 37°C.
The strain exhibited 97.1 and 96.7% nucleotide sequence similarities with B. salitolerans (Guan et al. 2010) and B. album (Tang et al. 2008), respectively, the phylogenetically closest validated Brevibacterium species (Figure 1). These values were 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 hybridization . In comparison to 16S sequences in the GenBank database , strain JC43T also exhibited nucleotide sequence similarities greater than 98.7% with uncultured bacterial clones detected in water-miscible metalworking fluids  and on clean room surfaces . These bacteria most likely belong to the same species as strains JC43 (Figure 1).
Different growth temperatures (25, 30, 37, 45°C) were tested; no growth occurred at 45°C, weak growth occurred at 25°C, and optimal growth was observed between 30 to 37°C.
Colonies were translucent and smooth, with a diameter of 1 mm on blood-enriched Columbia agar and Brain Heart Infusion (BHI) agar. Growth of the strain was tested under anaerobic and microaerophilic conditions using GENbag anaer and GENbag microaer systems, respectively (BioMérieux), and in the presence of air, of 5% CO2 and in aerobic conditions. Optimal growth was obtained aerobically and with 5% CO2. Weak growth was observed under microaerophilic conditions. No growth was observed in an anaerobic atmosphere.
Gram staining showed Gram-positive rods. A motility test was negative. Cells grown on agar are Gram-positive (Figure 2) and are mostly grouped in small clumps (Figure 3). Their length and width range from 0.83 to 3.86 µm (mean, 2.55 µm) and 0.57 to 0.78 µm (mean, 0.68 µm), respectively.
Strain JC43T exhibited catalase activity but not oxidase activity. Using the API CORYNE system(BioMérieux), positive reactions were observed for nitrate reduction, pyrrolidonyl arylamidase, alkaline phosphatase, α-glucosidase. A weak reaction was observed for gelatin hydrolysis. Negative reactions were observed for urease, pyrazinamidase, β-glucuronidase, β-galactosidase, α-glucosidase, N-acetyl-β-glucosaminidase, β-glucosidase (aesculin hydrolysis), and acid production from D-ribose, D-glucose, D-xylose, D-mannitol, maltose, D-lactose, sucrose and glycogen. Using API ZYM (BioMérieux), positive reactions were observed for esterase (C4), esterase lipase (C8), leucine arylamidase and acid and alkaline phosphatase. Negative reactions were observed for valine arylamidase, cystine arylamidase, trypsin, α-chymotrypsin, naphtol-AS-BI-phosphohydrolase, lipase, α-galactosidase, β-galactosidase, β-glucuronidase, α-glucosidase, β-glucosidase, N-acetyl-β-glucosaminidase, α-mannosidase and α-fucosidase. B. senegalense is susceptible to penicillin G, amoxicillin, imipenem, ciprofloxacin, rifampin, gentamicin, doxycycline and vancomycin but resistant to trimethoprim/sulfamethoxazole and metronidazole. By comparison to B. salitolerans  and B. album , B. senegalense strain JC43T differed in growth temperature, gelatin hydrolysis, pyrazinamidase, acid production from D-ribose, and nitrate reduction. In addition, B. senegalense also differed from the former species in β-glucosidase (aesculin hydrolysis) activity , and from the latter species in motility, valine arylamidase, cystine arylamidase, trypsin, α-chymotrypsin and naphtol-AS-BI-phosphohydrolase activities .
Matrix-assisted laser-desorption/ionization time-of-flight (MALDI-TOF) MS protein analysis was carried out as previously described [5,34] using a Microflex spectrometer (Bruker Daltonics, Germany). Twelve distinct deposits were done for strain JC43T from four isolated colonies. The 12 JC43T spectra were imported into the MALDI BioTyper software (version 2.0, Bruker) and analyzed by standard pattern matching (with default parameter settings) against the main spectra of 3,769 bacteria, which were used as reference data, in the BioTyper database. The database contained 41 spectra from 18 validly published Brevibacterium species, including B. avium, B. celere, B. casei, B. aurantiacum, B. epidermidis, B. iodinum, B. linens, B. luteolum, B. marinum, B. massiliense, B. mcbrellneri, B. otitidis, B. paucivorans, B. picturae, B. pityocampae, B. ravenspurgense, B. sanguinis and B. stationis. No significant score was obtained for strain JC43, thus suggesting that our isolate was not a member of a known Brevibacterium species within the Bruker database. We incremented our database with the spectrum from strain JC43 (Figure 4).
Genome sequencing and annotation
Genome project history
The organism was selected for sequencing on the basis of its phylogenetic position and 16S rRNA similarity to other members of the Brevibacterium genus, and is part of a study aiming at isolating all bacterial species within human feces. It was the third genome of a Brevibacterium species. The genome EMBL accession number is CAHK00000000 and consists of 80 contigs. Table 2 shows the project information and its association with MIGS version 2.0 compliance.
Growth conditions and DNA isolation
B. senegalense sp. nov. strain JC43T (CSUR = P155, DSM = 25783) was grown aerobically on 5% sheep blood-enriched Columbia agar at 37°C. Seven petri dishes were spread and resuspended in 3x100µl of G2 buffer (EZ1 DNA Tissue kit, Qiagen). A first mechanical lysis was performed by glass powder on the Fastprep-24 device (Sample Preparation system; MP Biomedicals, USA) using 2x20 seconds cycles. DNA was then treated with 2.5µg/µL lysozyme (30 minutes at 37°C) and extracted through 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 68,1 ng/µl.
Genome sequencing and assembly
A shotgun library and a 3kb paired end library were pyrosequenced on the 454 Roche Titanium sequencing platform. This project was loaded on one 1/4 region region of PTP Picotiterplate (Roche, Meylan, France) for the shotgun library and 4 × 1/4 region for the 3-kb paired-end library. The shotgun library was constructed with 500 ng of DNA with the GS Rapid library Prep kit as described by the manufacturer (Roche). For the paired-end library, 5µg of DNA was mechanically fragmented on a Hydroshear device (Digilab, Holliston, MA, USA) with an enrichment size at 3–4 kb. DNA fragmentation was visualized using an Agilent 2100 BioAnalyzer on a DNA labchip 7500 with an optimal size of 3.692 kb. The library was constructed according to the 454 Titanium paired-end protocol (Roche). Circularization and nebulization were performed and generated a pattern with an optimum of 510 bp. After PCR amplification through 15 cycles followed by double size selection, the single stranded paired-end library was then quantified using a Quant-it Ribogreen kit (Invitrogen) on a Genios Tecan fluorometer at 245 pg/µL. The library concentration equivalence was calculated at 8.80E+08 molecules/µL. The libraries were stocked at −20°C until further use.
The shotgun library was clonally amplified with 3 cpb in 3 emPCR reactions and the 3-kb paired-end library was amplified with 1 cpb in 10 emPCR reactions and 0.25 cpb in 4 emPCR with the GS Titanium SV emPCR Kit (Lib-L) v2 (Roche). The yield of the shotgun emPCR reactions was higher than expected at 24%, but the yields of the two types of paired-end emPCR were 16.7% and 11.01%, respectively, in the range of 5 to 20% from the Roche procedure.
The libraries were loaded on the GS Titanium PicoTiterPlate PTP Kit 70×75 and sequenced with the GS FLX Titanium Sequencing Kit XLR70 (Roche). The runs were performed overnight and then analyzed on the cluster through the gsRunBrowser and Newbler Assembler (Roche). A total of 752,121 passed filter wells were obtained and generated 203.1 Mb of sequence with an average length of 265 bp. The passed filter sequences were assembled using Newbler with 90% identity and 40 bp as overlap. The final assembly identified 80 contigs (>500 bp) arranged into 16 scaffolds and generated a genome size of 3.42 Mb.
Open Reading Frames (ORFs) were predicted using Prodigal  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 and the Clusters of Orthologous Groups (COG) database using BLASTP. The tRNAScanSE tool  was used to find tRNA genes, whereas ribosomal RNAs were found using RNAmmer . Transmembrane domains and signal peptides were predicted using TMHMM  and SignalP , 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. To estimate the mean level of nucleotide sequence similarity at the genome level between B. senegalense, B. linens (GenBank accession number AAGP00000000) and B. mcbrellneri (ADNU00000000) we compared the ORFs only using BLASTN at a query coverage of ≥ 70% and a minimum nucleotide length of 100 bp.
The genome is 3,425,960 bp long (1 chromosome, but no plasmid) with a 70.00% G+C content (Table 3 and Figure 5). Of the 3,114 predicted genes, 3,065 were protein-coding genes and 49 were RNAs, including 3 rRNA operons (5S, 16S and 23S rRNA) and 40 tRNAs. A total of 2,077 genes (66.7%) were assigned a putative function. The distribution of genes into COGs functional categories is presented in Table 4 and Figure 5. The properties and the statistics of the genome are summarized in Tables 3 and 4.
Genomic comparison with B. linens and B. mcbrellneri
Currently, two draft genomes from Brevibacterium species are available. By comparison with B. linens strain BL2 (GenBank accession number AAGP00000000) and B. mcbrellneri strain ATCC 49030 (ADNU00000000) B. senegalense strain JC43T has a smaller genome than the former (3.42 Mb vs 4.37Mb) but larger than the latter (2.56Mb). B. senegalense also has a higher G+C content than the other two genomes (70.00% vs 62.8% and 58.00%, respectively); it has a smaller number of predicted genes (3,114) than B. linens (4,054) but greater than B. mcbrellneri (2,437). Finally, at the genome level, B. senegalense exhibited percentages of nucleotide sequence similarity of 86.28% (range 70.01–100%) and 70.19% (range 86.09–100%) with B. linens and B. mcbrellneri, respectively.
On the basis of phenotypic (Table 5), phylogenetic and genomic analyses, we formally propose the creation of Brevibacterium senegalense sp. nov. that contains the strain JC43T. This bacterium originated from Senegal.
Description of Brevibacterium senegalense sp. nov.
Brevibacterium senegalense (se.ne.gal.e′n.se L. gen. neutr. n. senegalense, pertaining to, or originating from Senegal, the country from which the specimen that enabled isolation of B. senegalense was isolated.)
Colonies are translucent, smooth and have a diameter of 1 mm on blood-enriched Columbia agar and Brain Heart Infusion (BHI) agar. Cells are rod-shaped and occur mostly in small clumps. Their length and width range from 0.83 to 3.86 µm (mean, 2.55 µm) and 0.57 to 0.78 µm (mean, 0.68 µm), respectively. Optimal growth is achieved aerobically with or without CO2. Weak growth is observed under microaerophilic conditions. No growth is observed under anaerobic conditions. Growth occurs between 30–37°C. Cells stain Gram-positive, are non-endospore-forming, and non-motile. Catalase, nitrate reduction, pyrrolidonyl arylamidase, alkaline phosphatase, α-glucosidase, gelatin hydrolysis, esterase (C4), esterase lipase (C8), leucine arylamidase and acid and alkaline phosphatase activities are present. Urease, pyrazinamidase, β-glucuronidase, β-galactosidase, α-glucosidase, N-acetyl-β-glucosaminidase, β-glucosidase (aesculin hydrolysis), acid production from D-ribose, D-glucose, D-xylose, D-mannitol, maltose, D-lactose, sucrose and glycogen, valine aylamidase, cystine aylamidase, trypsin, α-chymotrypsin, naphtol-AS-BI-phosphohydrolase, lipase, α-galactosidase, β-galactosidase, β-glucuronidase, α-glucosidase, β-glucosidase, N-acetyl-β-glucosaminidase, α-mannosidase and α-fucosidase activities are absent. Oxidase activity is absent. Cells are susceptible to penicillin G, amoxicillin, imipenem, ciprofloxacin, rifampin, gentamicin, doxycycline and vancomycin, but resistant to trimethoprim/sulfamethoxazole and metronidazole.
The G+C content of the genome is 70.00%. The 16S rRNA and genome sequences are deposited in EMBL under accession numbers JF824806 and CAHK00000000, respectively.
The type strain JC43T (= CSUR P 155 = DSM 25783) was isolated from the fecal flora of a healthy patient in Senegal.
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-Verlag, Berlin, 2006, p. 23–50.
Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155.
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
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
Lagier JC, El Karkouri K, Nguyen TT, Armougom F, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Anaerococcus senegalensis sp. nov. Stand Genomic Sci 2012; 6:116–125. PubMed http://dx.doi.org/10.4056/sigs.2415480
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. http://dx.doi.org/10.4056/sigs.2776064
Mishra AK, Gimenez G, Lagier JC, Robert C, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Alistipes senegalensis sp. nov. Stand Genomic Sci 2012; 6:304–314. http://dx.doi.org/10.4056/sigs.2625821
Lagier JC, Armougom F, Mishra AK, Ngyuen TT, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Alistipes timonensis sp. nov. Stand Genomic Sci 2012; 6:315–324. http://dx.doi.org/10.4056/sigs.2685917
Mishra AK, Lagier JC, Robert C, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Clostridium senegalense sp. nov. Stand Genomic Sci 2012; 6:386–395.
Mishra AK, Lagier JC, Robert C, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Peptoniphilus timonensis sp. nov. Stand Genomic Sci 2012; 7:1–11. http://dx.doi.org/10.4056/sigs.2956294
Mishra AK, Lagier JC, Rivet R, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Paenibacillus senegalensis sp. nov. Stand Genomic Sci 2012; 7:70–81. http://dx.doi.org/10.4056/sigs.3054650
Breed RS. The families developed from Bacteriaceae Cohn with a description of the family Brevibacteriaceae. Riassunti delle Communicazione VI. Congresso Internazionale di Microbiologia, Roma; 1953 5:10–15.
List of Prokaryotic names with Standing in Nomenclature. http://www.bacterio.cict.fr
Breed RS. The Brevibacteriaceae fam. nov. of order Eubacteriales. Riassunti delle Communicazione VI. Congresso Internazionale di Microbiologia, Roma 1953; 1, 13–14.
Ulrich S, Zbinden R, Pagano M, Fischler M, Speich R. Central venous catheter infection with Brevibacterium sp. in an immunocompetent woman: case report and review of the literature. Infection 2006; 34:103–106. PubMed http://dx.doi.org/10.1007/s15010-006-5027-6
Cannon JP, Spandoni SL, Pesh-Iman S, Johnson S. Pericardial infection caused by Brevibacterium casei. Clin Microbiol Infect 2005; 11:164–165. PubMed http://dx.doi.Org/10.1111/j.1469-0691.2004.01050.x
McCaughey C, Damani NN. Central venous line infection caused by Brevibacterium epidermidis. J Infect 1991; 23:211–212. PubMed http://dx.doi.org/10.1016/0163-4453(91)92451-A
Manetos CM, Pavlidis AN, Kallistratos MS, Tsoukas AS, Chamodraka ES, Levantakis I, Manolis AJ. Native aortic valve endocarditis caused by Brevibacterium epidermidis in an immunocompetent patient. Am J Med Sci 2011; 342:257–258. PubMed http://dx.doi.org/10.1097/MAI.0b013e31821ffb9f
Kumar VA, Augustine D, Panikar D, Nandakumar A, Dinesh KR, Karim S, Philip R. Brevibacterium casei as a cause of brain abscess in an immunocompetent patient. J Clin Microbiol 2011; 49:4374–4376. PubMed http://dx.doi.org/10.1128/ICM.01086-11
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
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
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.
Stackebrandt E, Rainey FA, Ward-Rainey NL. Proposal for a New Hierarchic Classification System, Actinobacteria classis nov. Int J Syst Bacteriol 1997; 47:479–491. http://dx.doi.org/10.1099/00207713-47-2-479
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
Buchanan RE. Studies in the nomenclature and classification of bacteria. II. The primary subdivisions of the Schizomycetes. J Bacteriol 1917; 2:155–164. PubMed
Zhi XY, Li WJ, Stackebrandt E. An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa. Int J Syst Evol Microbiol 2009; 59:589–608. PubMed http://dx.doi.org/10.1099/ijs.0.65780-0
Breed RS. The families developed from Bacteriaceae Cohn with a description on the family Brevibacteriaceae Breed, 1953. Riassunti della Communicazione, VI Congresso Internazionale di Microbiologia, Roma 1953; 1:1–10.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Drolinski 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
GenBank database. http://www.ncbi.nlm.nih.gov:genbank.
Lodders N, Kampfer P. A combined cultivation and cultivation-independent approach shows high bacterial diversity in water-miscible metal-working fluids. Syst Appl Microbiol 2012; 35:246–252. PubMed http://dx.doi.org/10.1016/j.syapm.2012.03.006
La Duc MT, Osman S, Vaishampayan P, Piceno Y, Andersen G, Spry JA, Venkateswaran K. Comprehensive census of bacteria in clean rooms by using DNA microarray and cloning methods. Appl Environ Microbiol 2009; 75:6559–6567. PubMed http://dx.doi.org/10.1128/AEM.01073-09
Guan TW, Zhao K, Xiao J, Liu Y, Xia ZF, Zhang XP, Zhang LL. Brevibacterium salitolerans sp. nov., an actinobacterium isolated from salt-lake sediment. Int J Syst Evol Microbiol 2010; 60:2991–2995. PubMed http://dx.doi.org/10.1099/ijs.0.020214-0
Tang SK, Wang Y, Schumann P, Stackebrandt E, Lou K, Jiang CL, Xu LH, Li WJ. Brevibacterium album sp. nov., a novel actinobacterium isolated from a saline soil in China. Int J Syst Evol Microbiol 2008; 58:574–577. PubMed http://dx.doi.org/10.1099/ijs.0.65183-0
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
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
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
Krogh A, Larsson B. von HG, 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
Bendtsen JD, Nielsen H. von HG, 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
About this article
Cite this article
Kokcha, S., Ramasamy, D., Lagier, JC. et al. Non-contiguous finished genome sequence and description of Brevibacterium senegalense sp. nov.. Stand in Genomic Sci 7, 233–245 (2012). https://doi.org/10.4056/sigs.3256677
- Brevibacterium senegalense