Non-contiguous finished genome sequence of Prevotella timonensis type strain 4401737T
© The Author(s) 2014
Published: 15 June 2014
Prevotella timonensis strain 4401737T is a member of the genus Prevotella, which contains anaerobic Gram-negative bacteria. It was isolated from a human breast abscess. In this work, we describe a set of features of this organism, together with the complete genome sequence and annotation. The 3,169,464 bp long genome contains 2,746 protein-coding genes and 56 RNA genes, including 3 or 4 rRNA operons.
KeywordsPrevotella timonensis Bacteroidetes
Prevotella timonenis strain 4401737T(CIP 108522T= CCUG 50105T) is the type strain of P. timonensis. This bacterium was isolated from a human breast abscess . The genus Prevotella is comprised of anaerobic Gram-negative bacteria. It currently contains 47 members . Recently, many species of the genus Prevotella have been isolated from human sources, often associated with the oral cavity [3–8], but also from feces , amniotic fluid , blood cultures, lung abscess pus, broncho-alveolar lavages  and pleural fluids .
Here we present a summary classification and a set of features for P. timonensis, together with the description of the non-contiguous finished genomic sequencing and annotation.
Classification and features
The 16S rRNA gene sequence of P. timonensis strain 4401737T was compared with sequences deposited in the Genbank database, indicating that the initial taxonomic classification is correct.
The bacterium was first characterized in 2004; it was isolated from a 40-year-old woman who underwent a breast abscess puncture. The organism was in the liquid from the punctured abscess and was cultured in the Timone Hospital microbiology laboratory.
Classification and general features of Prevotella timonensis strain 4401737T
Species Prevotella timonensis
Type strain 4401737T
Glucose, lactose, maltose, ribose, tagatose
Human breast abscess
Sample collection time
21 m above sea level
Genome sequencing and annotation
Genome project history
One paired end 3-kb library and two Shotgun libraries
454 GS FLX Titanium
Newbler version 2.5.3
Gene calling method
EMBL Date of Release
June 18, 2013
Study of new species isolated in the URMITE
Growth conditions and DNA isolation
P. timonensis strain 4401737T was grown anaerobically on 5% sheep blood-enriched Columbia agar at 37°C. Five petri dishes were spread and colonies resuspended in 3 ml of TE buffer. Three hundred µl of 10% SDS and 150 µl of proteinase K were then added and incubation was performed over-night at 56°C. The DNA was then extracted using the phenol/chloroform method. The yield and the concentration were measured by the Quant-it Picogreen kit (Invitrogen) on the Genios Tecan fluorometer at 84.3 ng/µl.
Genome sequencing and assembly
Shotgun and 3-kb paired-end sequencing strategies were performed. A 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 3.7 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 574 bp. After PCR amplification through 17 cycles followed by double size selection, the single stranded paired-end library was then quantified using the Genios fluorometer (Tecan) at 1070 pg/µL. The library concentration equivalence was calculated as 3.42 × 109 molecules/µL. The library was stored at −20°C until further use. Another shotgun library was constructed with 1µg of DNA as described in the Rapid Library Preparation Method Manual GS FLX+ Series – XL+ except that fragmentation was obtained on Covaris® M220 focused-ultrasonocatorTM instead of on a Hydroshear device.
The shotgun and paired-end libraries obtained with the GS-FLX Titanium technology were clonally-amplified with 1 cpb in 4 SV-emPCR reactions, and 0.5 cpb in 2 SV-emPCR reactions with the GS Titanium SV emPCR Kit (Lib-L) v2 (Roche). The yields of the emPCR were 18.7% and 10.9%, respectively, in the 5 to 20% range from the Roche procedure. The shotgun library obtained with the GS-FLX+ technology was clonally-amplified with 3 cpb in 2 SV-emPCR reactions. The yield of the emPCR was 23.95%. Approximately 790,000 beads for the shotgun application and 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 573,130 passed filter wells were obtained and generated 249.97 Mb with an average length of 424 bp. The passed filter sequences were assembled using Newbler with 90% identity and 40 bp as overlap. The final assembly identified 25 scaffolds and 105 large contigs (>1,500 bp).
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) databases  using BLASTP. The tRNAscan-SE tool  was used to find tRNA genes, whereas ribosomal RNAs were found by 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 1 × 10−3 for alignment length greater than 80 amino acids. If alignment lengths were smaller than 80 amino acids, we used an E-value of 1 × 10−5. 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 P. timonensis and Prevotella genomes available to date, we compared the only those ORFs only that could be found on the RAST server  with a query coverage of ≥60% and a minimum nucleotide length of 100 bp.
Nucleotide content and gene count levels of the genome
% of totala
Genome size (bp)
DNA coding region (bp)
DNA G+C content (bp)
Genes with function prediction
Genes assigned to COGs
Genes with peptide signals
Genes with transmembrane helices
Number of genes associated with the 25 general COG functional categories
% of total
RNA processing and modification
Replication, recombination and repair
Chromatin structure and dynamics
Cell cycle control, mitosis and meiosis
Signal transduction mechanisms
Cell wall/membrane biogenesis
Intracellular trafficking and secretion
Posttranslational modification, protein turnover, chaperones
Energy production and conversion
Carbohydrate transport and metabolism
Amino acid transport and metabolism
Nucleotide transport and metabolism
Coenzyme transport and metabolism
Lipid transport and metabolism
Inorganic ion transport and metabolism
Secondary metabolites biosynthesis, transport and catabolism
General function prediction only
Not in COGs
Comparison with other Prevotella genomes
To date 33 genomes from species belonging to the genus Prevotella have been sequenced.
Whole genome sizes ranged between 2.42 Mb (P. bivia and P. amnii) and 3.62 Mb (P. ruminicola). The G+C content of the genomes was was between 36.5% for P. amnii and 55.9% for P. dentalis. 16S rRNA gene sequence comparison was performed to obtain phylogenetic analysis of Prevotella species. A cluster including P. bergensis, P. dentalis, P. multisaccharivorax, P. buccae, P. baroniae, P. dentasini, P. denticola and P. multiformis was identified. From this group. the genomes of P. bergensis, P. dentalis, P. multisaccharivorax, P. buccae, P. denticola and P. multiformis have been sequenced. It is interesting to note that these genomes showed the highest G+C contents (47.6-55.9%) among the bacteria included in the genus Prevotella. A more in-depth study will allow us to determine if this group of bacteria represent a particular evolutionary lineage.
The genome of another strain of the species P. timonensis was sequenced, strain CRIS 5C B1. The genome of P. buccalis, which is the more closely related species to P. timonensis when 16S rRNA encoding gene sequences were compared, has also been sequenced.P. timonensis strain 4401737T shared a mean sequence similarity of 96.45% (60.2-100%) with P. timonensis strain CRIS 5C B1 and of 84.02% (60–100%) with P. buccalis.
The partition of the coding sequences into subsystems  is similar for the two genomes except for the transposable elements, whose numbers are significantly higher in strain 4401737T.
The authors thank Mr. Julien Paganini at Xegen Company (www.xegen.fr) for automating the genomic annotation process and Laetitia Pizzo, Audrey Borg and Audrey Averna for their technical assistance.
- Glazunova OO, Launay T, Raoult D, Roux V. Prevotella timonensis sp. nov., isolated from a human breast abscess. Int J Syst Evol Microbiol 2007; 57:883–886. PubMed http://dx.doi.org/10.1099/ijs.0.64609-0View ArticlePubMedGoogle Scholar
- Euzéby JP. List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet. Int J Syst Bacteriol 1997; 47:590–592. PubMed http://dx.doi.org/10.1099/00207713-47-2-590View ArticlePubMedGoogle Scholar
- Downes J, Wade WG. Prevotella fusca sp. nov. and Prevotella scopos sp. nov., isolated from the human oral cavity. Int J Syst Evol Microbiol 2011; 61:854–858. PubMed 1350 http://dx.doi.org/10.1099/ijs.0.023861-0View ArticlePubMedGoogle Scholar
- Downes J, Tanner ACR, Floyd E, Dewhirst FE, Wade WG. Prevotella saccharolytica sp. nov., isolated from the human oral cavity. Int J Syst Evol Microbiol 2010; 60:2458–2461. PubMed http://dx.doi.org/10.1099/ijs.0.014720-0PubMed CentralView ArticlePubMedGoogle Scholar
- Sakamoto M, Natsuko Suzuki N, Okamoto M. Prevotella aurantiaca sp. nov., isolated from the human oral cavity. Int J Syst Evol Microbiol 2010; 60:500–503. PubMed http://dx.doi.org/10.1099/ijs.0.012831-0View ArticlePubMedGoogle Scholar
- Downes J, Hooper SJ, Melanie J, Wilson MJ, Wade WC. Prevotella histicola sp. nov., isolated from the human oral cavity. Int J Syst Evol Microbiol 2008; 58:1788–1791. PubMed http://dx.doi.org/10.1099/ijs.0.65656-0View ArticlePubMedGoogle Scholar
- Downes J, Sutcliffe IC, Booth V, Wade WG. Prevotella maculosa sp. nov., isolated from the human oral cavity. Int J Syst Evol Microbiol 2007; 57:2936–2939. PubMed http://dx.doi.org/10.1099/ijs.0.65281-0View ArticlePubMedGoogle Scholar
- Downes J, Liu M, Kononen E, Wade WG. Prevotella micans sp. nov., isolated from the human oral cavity. Int J Syst Evol Microbiol 2009; 59:771–774. PubMed http://dx.doi.org/10.1099/ijs.0.002337-0View ArticlePubMedGoogle Scholar
- Hayashi H, Shibata K, Sakamoto M, Tomita S, Benno Y. Prevotella copri sp. nov. and Prevotella stercorea sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2007; 57:941–946. PubMed http://dx.doi.org/10.1099/ijs.0.64778-0View ArticlePubMedGoogle Scholar
- Lawson PA, Moore E, Falsen E. Prevotella amnii sp. nov., isolated from human amniotic fluid. Int J Syst Evol Microbiol 2008; 58:89–92. PubMed http://dx.doi.org/10.1099/ijs.0.65118-0View ArticlePubMedGoogle Scholar
- Alauzet C, Mory F, Carlier JP, Marchandin H, Jumas-Bilak E, Lozniewski A. Prevotella nanceiensis sp. nov., isolated from human clinical samples. Int J Syst Evol Microbiol 2007; 57:2216–2220. PubMed http://dx.doi.org/10.1099/ijs.0.65173-0View ArticlePubMedGoogle Scholar
- Sakamoto M, Ohkusu K, Masaki T, Kako H, Ezaki T, Benno Y. Prevotella pleuritidis sp. nov., isolated from pleural fluid. Int J Syst Evol Microbiol 2007; 57:1725–1728. PubMed http://dx.doi.org/10.1099/ijs.0.64885-0View ArticlePubMedGoogle Scholar
- 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/msr121PubMed CentralView ArticlePubMedGoogle Scholar
- 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.87.12.4576PubMed CentralView ArticlePubMedGoogle Scholar
- Validation List No. 143. Int J Syst Evol Microbiol 2012; 62:1–4. http://dx.doi.org/10.1099/ijs.0.039487-0
- Krieg NR, Ludwig W, Euzéby J, Whitman WB. Phylum XIV. Bacteroidetes phyl. nov. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 4, Springer, New York, 2011Google Scholar
- Krieg NR. Class I. Bacteroidia class. nov. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 4, Springer, New York, 2011Google Scholar
- Krieg NR. Order I. Bacteroidales ord. nov. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 4, Springer, New York, 2011, p. 25.Google Scholar
- Krieg NR. Family V. Prevotellaceae fam. nov. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 4, Springer, New York, 2011, p. 85.Google Scholar
- Shah HN, Collins DM. Prevotella, a new genus to include Bacteroides melaninogenicus and related species formerly classified in the genus Bacteroides. Int J Syst Bacteriol 1990; 40:205–208. PubMed http://dx.doi.org/10.1099/00207713-40-2-205View ArticlePubMedGoogle Scholar
- Willems A, Collins MD. 16S rRNA gene similarities indicate that Hallella seregens (Moore and Moore) and Mitsuokella dentalis (Haapasalo et al.) are genealogically highly related and are members of the genus Prevotella: emended description of the genus Prevotella (Shah and Collins) and description of Prevotella dentalis comb. nov. Int J Syst Bacteriol 1995; 45:832–836. PubMed http://dx.doi.org/10.1099/00207713-45-4-832View ArticlePubMedGoogle Scholar
- Sakamoto M, Moriya Ohkuma M. Reclassification of Xylanibacter oryzae Ueki et al. 2006 as Prevotella oryzae comb. nov., with an emended description of the genus Prevotella. Int J Syst Evol Microbiol 2012; 62:2637–2642. PubMed http://dx.doi.org/10.1099/ijs.0.038638-0View ArticlePubMedGoogle Scholar
- 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/10.1038/75556PubMed CentralView ArticlePubMedGoogle Scholar
- Prodigal http://prodigal.ornl.gov/
- GenBank database. http://www.ncbi.nlm.nih.gov/genbank
- 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/28.1.33PubMed CentralView ArticlePubMedGoogle Scholar
- 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/25.5.0955PubMed CentralView ArticlePubMedGoogle Scholar
- 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/gkm160PubMed CentralView ArticlePubMedGoogle Scholar
- 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.2000.4315View ArticlePubMedGoogle Scholar
- 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.2004.05.028View ArticlePubMedGoogle Scholar
- 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/10.1186/1471-2164-9-75PubMed CentralView ArticlePubMedGoogle Scholar