Skip to main content
Download PDF

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

Standards in Genomic Sciences volume 7, pages 370–381 (2013)Cite this article

Abstract

Peptoniphilus senegalensis strain JC140T sp. nov., is the type strain of P. senegalensis sp. nov., a new species within the genus Peptoniphilus. This strain, whose genome is described here, was isolated from the fecal flora of a healthy patient. P. senegalensis strainx JC140T is an obligate Gram-positive anaerobic coccus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,840,641 bp long genome (1 chromosome but no plasmid) exhibits a G+C content of 32.2% and contains 1,744 protein-coding and 23 RNA genes, including 3 rRNA genes.

Introduction

Peptoniphilus senegalensis strain JC140T (= CSUR P154 = DSM 25694), is the type strain of P. senegalensis sp. nov. This bacterium is a Gram-positive, anaerobic, non spore-forming and indole positive coccus that 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].

Since 1995 and the first sequencing of a bacterial genome, that of Haemophilus influenzae, more than 3,000 bacterial genomes have been sequenced [2]. This was made possible by technical improvements as well as increased interest in having access to the complete genetic information encoded by bacteria. In the meantime however, biological tools for defining new bacterial species have not evolved and DNA-DNA hybridization is still considered the gold standard [3] for determining sequence similarity despite its drawbacks, and the taxonomic revolution that has resulted from the comparison of 16S rDNA sequences [4]. Recently, we proposed to use a polyphasic approach to describe new bacterial taxa including their genome sequence, MALDI-TOF spectrum and main phenotypic characteristics (e.g., habitat, Gram staining, culture and metabolic characteristics, and when applicable, pathogenicity) [5–16].

Here we present a summary classification and a set of features for P. senegalensis sp. nov. strain JC140T (= CSUR P154 = DSM 25694), together with the description of the complete genomic sequencing and annotation. These characteristics support the circumscription of the species P. senegalensis.

Gram-positive anaerobic cocci (GPAC) are part of the commensal flora in humans and animals and are also commonly associated with a variety of human infections [17], including vaginal discharges, ovarian, peritoneal, sacral and lacrymal gland abscesses [18]. In wide surveys of anaerobic infections, GPAC represent about 25 to 30% of all anaerobic isolates [19]. Extensive taxonomic changes have occurred among this group of bacteria, especially in clinically important genera such as Peptostreptococcus (Kluyver and van Niel 1936) [20], which was divided into the genera Peptoniphilus (Ezaki et al. 2001), Anaerococcus (Ezaki et al. 2001) and Gallicola (Ezaki et al. 2001) [18]. Currently, the genus Peptoniphilus is comprised of eight species [21], including P. asaccharolyticus (Ezaki et al. 2001), P. harei (Ezaki et al. 2001), P. indolicus (Ezaki et al. 2001), P. ivorii (Ezaki et al. 2001), P. lacrimalis (Ezaki et al. 2001) [18], P. gorbachii (Song et al. 2010), P. olsenii (Song et al. 2010) [22] and P. methioninivorax (Rooney et al. 2011) [23]. In addition, we recently proposed the creation of the species P. timonensis sp. nov. that was also isolated from the stool from the same patient as P. senegalensis sp. nov [10]. Members of the genus Peptoniphilus produce butyrate, are non-saccharolytic and use peptone and amino acids as major energy sources.

Classification and features

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 (in accordance with the previous project approved by the Ministry of Health of Senegal and the assembled village population and as published elsewhere [24]. 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 senegalensis, Alistipes timonensis, Anaerococcus senegalensis, Bacillus timonensis, Clostridium senegalense, Peptoniphilus timonensis, Paenibacillus senegalensis, Herbaspirillum massiliense, Kurthia massiliensis, Brevibacterium senegalense, Aeromicrobium massiliense and Cellulomonas massiliensis [5–16]. The fecal specimen was preserved at −80°C after collection and sent to Marseille. Strain JC140T (Table 1) was isolated in May 2011 by anaerobic cultivation on 5% sheep blood-enriched Columbia agar (BioMerieux, Marcy l’Etoile, France) at 37°C, after 10 days of preincubation of the stool sample in an anaerobic blood culture bottle enriched with 5 ml of sterile sheep blood.

Table 1. Classification and general features of Peptoniphilus senegalensis strain JC140T according to the MIGS recommendations [25]
Full size table

This strain exhibited a nucleotide sequence similarity with validly published Peptoniphilus species, ranging from 88.29% with P. ivorii (Ezaki et al. 2001) to 97.40% with P. gorbachii (Song et al. 2010) (Figure 1), values lower than the 98.7% 16S rRNA gene sequence threshold recommended by Stackebrandt and Ebers to delineate a new species without performing DNA-DNA hybridization [4]. In addition, strain JC140T exhibited a 97.18% similarity with P. timonensis (GenBank accession number JN657222).

Figure 1.
figure 1

Phylogenetic tree highlighting the position of Peptoniphilus senegalensis strain JC140T relative to other type strains within the Peptoniphilus genus. GenBank accession numbers are indicated in parentheses. Sequences were aligned using CLUSTALW, and phylogenetic inferences obtained using the maximum-likelihood method within the MEGA software. Numbers at the nodes are percentages of bootstrap values obtained by repeating the analysis 500 times to generate a majority consensus tree. Anaerococcus prevotii was used as outgroup. The scale bar represents a 2% nucleotide sequence divergence.

Full size image

Different growth temperatures (25, 30, 37, 45°C) were tested; no growth occurred at 25°C or 45°C. Growth was observed between 30 and 37°C, but optimal growth was obtained at 37°C after 48 hr of inoculation. Colonies were 0.5 mm in diameter on blood-enriched Columbia agar and Brain Heart Infusion (BHI) agar. Growth of the strain was tested in anaerobic and microaerophilic conditions using GENbag anaer and GENbag microaer systems, respectively (BioMerieux), and under aerobic conditions, with or without 5% CO2. Growth was achieved only anaerobically. Gram staining showed Gram-positive cocci (Figure 2). A motility test was negative. Cells grown on agar have a mean diameter of 0.65 µm and are mostly grouped in pairs, short chains or small clumps (Figure 3).

Figure 2.
figure 2

Gram staining of P. senegalensis strain JC140T

Full size image
Figure 3.
figure 3

Transmission electron microscopy of P. senegalensis strain JC140T, using a Morgani 268D (Philips) at an operating voltage of 60kV.The scale bar represents 200 nm.

Full size image

Strain JC140T exhibited a catalase activity but no oxidase activity. Using the API Rapid ID 32A system, positive reactions were observed for arginine arylimidase, tyrosine arylamidase, histidine arylamidase and indole production. Weak reactions were observed for leucyl glycine arylamidase and glycine arylamidase. All other assays were negative. P. senegalensis is susceptible to penicillin G, amoxicillin + clavulanic acid, imipeneme, vancomycin, clindamycin and metronidazole. By comparison with other phylogenetically closely related Peptoniphilus species, P. senegalensis differed in leucine arylamidase, phenylalanine arylamidase and serine arylamidase activities with P. gorbachii [22], in tyrosine arylamidase activity with P. harei [18] and in α-galactosidase, serine arylamidase, leucine arylamidase, phenylalanine arylamidase, glycine arylamidase and glycine arylamidase activities with P. timonensis [10].

Matrix-assisted laser-desorption/ionization time-of-flight (MALDI-TOF) MS protein analysis was carried out as previously described [35]. Briefly, a pipette tip was used to pick one isolated bacterial colony from a culture agar plate and spread it as a thin film on a MTP 384 MALDI-TOF target plate (Bruker Daltonics, Germany). Twelve distinct deposits were done for strain JC140T from twelve isolated colonies. Each smear was overlaid with 2 µL of matrix solution (saturated solution of alpha-cyano-4-hydroxycinnamic acid) in 50% acetonitrile, 2.5% tri-fluoracetic acid, and allowed to dry for five minutes. Measurements were performed with a Microflex spectrometer (Bruker). Spectra were recorded in the positive linear mode for the mass range of 2,000 to 20,000 Da (parameter settings: ion source 1 (ISI), 20kV; IS2, 18.5 kV; lens, 7 kV). A spectrum was obtained after 675 shots at a variable laser power. The time of acquisition was between 30 seconds and 1 minute per spot. The twelve JC140T 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, including spectra from 8 validly published Peptoniphilus species that were used as reference data in the BioTyper database (updated March 15th, 2012). The method of identification includes the m/z from 3,000 to 15,000 Da. For every spectrum, 100 peaks at most were taken into account and compared with the spectra in database. A score enabled the presumptive identification and discrimination of the tested species from those in a database: a score ≥ 2 with a validly published 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 an identification. For strain JC140T, the obtained score was 1.4, thus suggesting that our isolate was not a member of a known species. We incremented our database with the spectrum from strain JC140T (Figure 4).

Figure 4.
figure 4

Reference mass spectrum from P. senegalensis strain JC140T. Spectra from 12 individual colonies were compared and a reference spectrum was generated.

Full size image

Genome sequencing information

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 genus Peptoniphilus, and is part of a “culturomics” study of the human digestive flora aiming at isolating all bacterial species within human feces. It was the ninth genome of a Peptoniphilus species and the first genome of Peptoniphilus senegalensis sp. nov. The genome was deposited in Genbank under accession number CAEL00000000 consists of 77 contigs. Table 2 shows the project information and its association with MIGS version 2.0 compliance [36].

Table 2. Project information
Full size table

Growth conditions and DNA isolation

P. senegalensis strain JC140T (= CSUR P154 = DSM 25694), was grown anaerobically on 5% sheep blood-enriched Columbia agar at 37°C. Four petri dishes were spread and resuspended in 3×100µl 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) during 2×20 seconds. DNA was then treated with 2.5 µg/µL lysozyme (30 minutes at 37°C) and extracted through the BioRobot EZ1 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 a Genios_Tecan fluorometer at 42.2 ng/µl.

Genome sequencing and assembly

A 3kb paired-end sequencing strategy (Roche, Meylan, France) was used. Five µg of DNA was mechanically fragmented on the Hydroshear device (Digilab, Holliston, MA, USA) with an enrichment size of 3–4kb for the construction of the paired-end library. The DNA fragmentation was visualized using an Agilent 2100 BioAnalyzer on a DNA labchip 7500 to yield an optimal size of 3.962kb. 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 at 550 bp. Following PCR amplification through 15 cycles followed by double size selection, the single stranded paired-end library was quantified using the Quant-it Ribogreen kit (Invitrogen) on the Genios_Tecan fluorometer at 123pg/µL. The library concentration equivalence was calculated at 4.10E+08 molecules/µL. The library was held at −20°C until use.

The library was amplified with 1cpb in 4 emPCR reactions with the GS Titanium SV emPCR Kit (Lib-L) v2 (Roche). The yield of the emPCR was 9.13%, in the 5–20% range recommended by the Roche procedure. A total of 790,000 beads were loaded onto a one quarter region of a PTP Picotiterplate (PTP Kit 70×75, Roche) and pyrosequenced using the GS Titanium Sequencing Kit XLR70 and GS FLX Titanium sequencer (Roche). The run was performed overnight and then analyzed on the cluster through the gsRunBrowser and Newbler assembler (Roche). A total of 334,687 passed filter wells generated 83.5Mb with a length average of 249bp. The passed filter sequences were assembled using Newbler with 90% identity and 40 bp as overlap. The final assembly identified 39 contigs (>1500bp) arranged in 4 scaffolds and generated a genome size of 1.84Mb.

Genome annotation

Open Reading Frames (ORFs) were predicted using Prodigal [37] with default parameters, but the predicted ORFs were excluded if they spanned a sequencing gap region. The predicted bacterial protein sequences were searched against the GenBank database [38] and the Clusters of Orthologous Groups (COG) databases using BLASTP. The tRNAScanSE tool [39] was used to find tRNA genes, whereas ribosomal RNAs were found by using RNAmmer [40] and BLASTN against the GenBank database. Signal peptides and numbers of transmembrane helices were predicted using SignalP [41] and TMHMM [42] respectively. ORFans were identified if their BLASTP E-value was lower than 1e-03 for an 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 already been used in previous works to define ORFans.

To estimate the mean level of nucleotide sequence similarity at the genome level between P. senegalensis strain JC140T, P. harei strain ACS-146-V-Sch2b (GenBank accession number AENP00000000), P. indolicus strain ATCC29427 (AGBB00000000), and P. timonensis strain JC401T (CAHE00000000), we compared the ORFs only using BLASTN and the following parameters: a query coverage of > 70% and a minimum nucleotide length of 100 bp.

Artemis [43] was used for data management and DNA Plotter [44] was used for visualization of genomic features. The Mauve alignment tool was used for multiple genomic sequence alignment and visualization [45]

Genome properties

The genome of P. senegalensis sp. nov. strain JC140T is 1,840,641bp long (1 chromosome, but no plasmid) with a 32.2% G + C content (Figure 5 and Table 3). Of the 1,767 predicted genes, 1,744 were protein-coding genes, and 23 were RNAs, including a complete rRNA operon and 20 tRNAs. A total of 1,422 genes (80.47%) were assigned a putative function. A total of 86 genes were identified as ORFans (4.9%). The remaining genes were annotated as hypothetical proteins. 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 3 and 4.

Figure 5.
figure 5

Graphical circular map of the chromosome. From the outside to the inside: genes on the forward strand (colored by COG categories), genes on the reverse strand (colored by COG categories), RNA genes (tRNAs green, rRNAs red), G+C content and GC skew.

Full size image
Table 3. Nucleotide content and gene count levels of the genome
Full size table
Table 4. Number of genes associated with the 25 general COG functional categories
Full size table

Comparison with other Peptoniphilus species genome

Here, we compared the genome sequence of P. senegalensis strain JC140T with those of P. harei strain ACS-146-V-Sch2b, P. indolicus strain ATCC 29427 and P. timonensis strain JC401T. The draft genome sequence of P. senegalensis is larger than P. timonensis and P. harei (1.84, 1.76 and 1.83 Mb, respectively), but smaller than P. indolicus (2.10 Mb). The G+C content of P. senegalensis is larger than P. timonensis (32.20 and 30.70%, respectively) but smaller than P. indolicus and P. harei (32.29 and 34.44%, respectively). Additionally, P. senegalensis has more predicted genes than P. harei (1,767 and 1,724, respectively), but fewer than P. timonensis and P. indolicus (1,922 and 2,269, respectively). The distribution of genes into COG categories was not entirely similar in all the three compared genomes (Figure 6). In addition, P. senegalensis shared a mean genome sequence similarity of 85.75% (range 70.12-100%), 84.75% (70.67-100%) and 85.60% (70.52-100%) with P. harei, P. indolicus and P. timonensis, respectively.

Figure 6.
figure 6

Gene distribution in COG functional categories in P. senegalensis (orange), P. harei (blue), P. timonensis (red) and P. indolicus (green) chromosomes.

Full size image

Conclusion

On the basis of phenotypic, phylogenetic and genomic analyses, we formally propose the creation of Peptoniphilus senegalensis sp. nov. which contains the strain JC140T as the sole member. This strain has been found in Senegal.

Description of Peptoniphilus senegalensis sp. nov.

Peptoniphilus senegalensis (se.ne.gal.e’n.sis. L. gen. masc. n. senegalensis, pertaining to Senegal, the country where the specimen in which strain JC140T was obtained).

Colonies are 0.5 mm in diameter on blood-enriched Columbia agar. Cells are coccoid with a mean diameter of 0.65 µm, occurring mostly in pairs, short chains or small clumps. Optimal growth is achieved anaerobically. No growth is observed in aerobic or microaerophilic conditions. Growth occurs between 30 and 37°C, with optimal growth observed at 37°C on blood-enriched Columbia agar. Cells stain Gram-positive, are non endospore-forming, and non-motile. Cells are positive for catalase activity and indole production. Arginine arylamidase, tyrosine arylamidase, histidine arylamidase, leucyl glycine arylamidase and glycine arylamidase activities are present. P. senegalensis is susceptible to penicillin G, amoxicillin + clavulanic acid, imipeneme, vancomycin, clindamycin and metronidazole. The G+C content of the genome is 32.20%. The 16S rRNA and genome sequences are deposited in GenBank under accession numbers JN824803 and CAEL00000000, respectively. The type strain JC140T (= CSUR P154 = DSM 25694) was isolated from the fecal flora of a healthy patient in Senegal.

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. David A, Relman MD. Microbial Genomics and Infectious Diseases. N Engl J Med 2011; 365:347–357. PubMed http://dx.doi.org/10.1056/NEIMra1003071

    Article  Google Scholar 

  3. 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. Berlin: Springer, 2006:23–50.

    Chapter  Google Scholar 

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

    Google Scholar 

  5. 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 

  6. 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  7. 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

    Article  CAS  Google Scholar 

  8. 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. PubMed http://dx.doi.org/10.4056/sigs.2685917

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  9. 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. PubMed

    PubMed Central  CAS  PubMed  Google Scholar 

  10. 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  11. 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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  12. Lagier JC, Gimenez G, Robert C, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Herbaspirillum massiliense sp. nov. Stand Genomic Sci 2012; 7:200–209. PubMed http://dx.doi.org/10.4056/sigs.3086474

    PubMed Central  CAS  PubMed  Google Scholar 

  13. 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 

  14. Kokcha S, Ramasamy D, Lagier JC, Robert C, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Brevibacterium senegalense sp. nov. Stand Genomic Sci 2012; 7:233–245. PubMed http://dx.doi.org/10.4056/sigs.3256677

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  15. Ramasamy D, Kokcha S, Lagier JC, N’Guyen TT, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Aeromicrobium massilense sp. nov. Stand Genomic Sci 2012; 7:246–257. PubMed http://dx.doi.org/10.4056/sigs.3306717

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  16. Lagier JC, Ramasamy D, Rivet R, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Cellulomonas massiliensis sp. nov. Stand Genomic Sci 2012; 7:258–270. PubMed http://dx.doi.org/10.4056/sigs.3316719

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  17. Jousimies-Somer HP, Summanen DM, Citron EJ, Baron HM. Wexler, Finegold SM. Wadsworth-KTL anaerobic bacteriology manual, 6th ed Belmont: Star Publishing, 2002.

    Google Scholar 

  18. Ezaki T, Kawamura Y, Li N, Li ZY, Zhao L, Shu S. Proposal of the genera Anaerococcus gen. nov., Peptoniphilus gen. nov. and Gallicola gen. nov. for members of the genus Peptostreptococcus. Int J Syst Evol Microbiol 2001; 51:1521–1528. PubMed

    Article  CAS  PubMed  Google Scholar 

  19. Murdoch DA, Mitchelmore IJ, Tabaqchali S. The clinical importance of Gram-positive anaerobic cocci isolated at St Bartholomew’s Hospital, London, in 1987. J Med Microbiol 1994; 41:36–44. PubMed http://dx.doi.org/10.1099/00222615-41-1-36

    Article  CAS  PubMed  Google Scholar 

  20. Kluyver AJ, Van Niel CB. Prospects for a natural system of classification of bacteria. Zentralblatt fur Bakteriologie, Parasitenkunde. Infektionskrankheiten und Hygiene 1936; 94:369–403.

    Google Scholar 

  21. List of Prokaryotic names with Standing in Nomenclature. http://www.bacterio.cict.fr

  22. Song Y, Liu C, Finegold SM. Peptoniphilus gorbachii sp. nov., Peptoniphilus olsenii sp. nov. and Anaerococcus murdochii sp. nov. isolated from clinical specimens of human origin. J Clin Microbiol 2007; 45:1746–1752. PubMed http://dx.doi.org/10.1128/ICM.00213-07

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  23. Rooney AP, Swezey JL, Pukall R, Schumann P, Spring S. Peptoniphilus methioninivorax sp. nov., a Gram-positive anaerobic coccus isolated from retail ground beef. Int J Syst Evol Microbiol 2011; 61:1962–1967. PubMed http://dx.doi.org/10.1099/ijs.0.024232-0

    Article  CAS  PubMed  Google Scholar 

  24. Trape JF, Tall A, Diagne N, Ndiath O, Ly AB, Faye J, Dieye-Ba F, Roucher C, Bouganali C, Badiane A, et al. Malaria morbidity and pyrethroid resistance after the introduction of insecticide-treated bednets and artemisinin-based combination therapies: a longitudinal study. Lancet Infect Dis 2011; 11:925–932. PubMed http://dx.doi.org/10.1016/S1473-3099(11)70194-3

    Article  CAS  PubMed  Google Scholar 

  25. 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 

  26. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eukarya. 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 

  27. 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 

  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. 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 

  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. Rainey FA. Class II. Clostridia 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. 736.

    Google Scholar 

  32. Skerman VBD, Sneath PHA. Approved list of bacterial names. Int J Syst Bact 1980; 30:225–420. http://dx.doi.org/10.1099/00207713-30-1-225

    Article  Google Scholar 

  33. Prevot AR. Dictionnaire des bactéries pathogens. In: Hauduroy P, Ehringer G, Guillot G, Magrou J, Prevot AR, Rosset, Urbain A (eds). Paris, Masson, 1953, p.1–692.

    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. 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 

  36. 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 

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

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

  39. Lowe TM, Eddy SR. t-RNAscan-SE: a program for imroved detection of transfer RNA gene in genomic sequence. Nucleic Acids Res 1997; 25:955–964. PubMed

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  40. 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 

  41. 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 

  42. Krogh A, Larsson B, von Heijne 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 

  43. 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 

  44. 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 

  45. Darling AC, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 2004; 14:1394–1403. PubMed http://dx.doi.org/10.1101/gr.2289704

    Article  PubMed Central  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This study was funded by the Mediterranee Infection Fundation.

Author information

Authors and Affiliations

  1. Faculté de médecine, Aix-Marseille Université, Marseille, France

    Ajay Kumar Mishra, Jean-Christophe Lagier, Thi-Tien Nguyen, Didier Raoult & Pierre-Edouard Fournier

Authors
  1. Ajay Kumar Mishra
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jean-Christophe Lagier
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Thi-Tien Nguyen
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Didier Raoult
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Pierre-Edouard Fournier
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Pierre-Edouard Fournier.

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

Cite this article

Mishra, A.K., Lagier, JC., Nguyen, TT. et al. Non contiguous-finished genome sequence and description of Peptoniphilus senegalensis sp. nov.. Stand in Genomic Sci 7, 370–381 (2013). https://doi.org/10.4056/sigs.3366764

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.4056/sigs.3366764

Keywords

Environmental Microbiome

ISSN: 2524-6372