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Non-contiguous finished genome sequence of the opportunistic oral pathogen Prevotella multisaccharivorax type strain (PPPA20T)
Standards in Genomic Sciences volume 5, pages41–49 (2011)
Prevotella multisaccharivorax Sakamoto et al. 2005 is a species of the large genus Prevotella, which belongs to the family Prevotellaceae. The species is of medical interest because its members are able to cause diseases in the human oral cavity such as periodontitis, root caries and others. Although 77 Prevotella genomes have already been sequenced or are targeted for sequencing, this is only the second completed genome sequence of a type strain of a species within the genus Prevotella to be published. The 3,388,644 bp long genome is assembled in three non-contiguous contigs, harbors 2,876 protein-coding and 75 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
Strain PPPA20T (= DSM 17128 = JCM 12954) is the type strain of Prevotella multisaccharivorax . Currently, there are about 50 species placed in the genus Prevotella . The species epithet is derived from the Latin adjective multus meaning ‘many/much’, the Latin noun saccharum meaning ‘sugar’ and the Latin adjective vorax meaning ‘liking to eat’ referring to the metabolic properties of the species to digest a variety of carbohydrates . P. multisaccharivorax strain PPPA20T is considered to be an opportunistic pathogen and was isolated from subgingival plaque from a patient with chronic periodontitis. Additionally, five more strains isolated from the human oral cavity were placed in the species P. multisaccharivorax . Using non-culture techniques on sites affected by endodontic and periodontal diseases, a large number of sequences have been found that belong to Prevotella and Prevotella-like bacteria. Many of those species have never been isolated or described . The complex microbial community living in the rich ecological niche of the human oral cavity and its interaction with consumed food will be of lasting interest for medical and ecological reasons [4,5]. Here we present a summary classification and a set of features for P. multisaccharivorax PPPA20T, together with the description of the non-contiguous finished genomic sequencing and annotation.
Classification and features
A representative genomic 16S rRNA sequence of P. multisaccharivorax PPPA20T was compared using NCBI BLAST  under default settings (e.g., considering only the high-scoring segment pairs (HSPs) from the best 250 hits) with the most recent release of the Greengenes database  and the relative frequencies of taxa and keywords (reduced to their stem ) were determined, weighted by BLAST scores. The most frequently occurring genus was Prevotella (100.0%) (14 hits in total). Regarding the single hit to sequences from members of the species, the average identity within HSPs was 100.0%, whereas the average coverage by HSPs was 98.0%. Regarding the nine hits to sequences from other members of the genus, the average identity within HSPs was 90.3%, whereas the average coverage by HSPs was 66.5%. Among all other species, the one yielding the highest score was Prevotella ruminicola (AF218618), which corresponded to an identity of 91.5% and an HSP coverage of 66.3%. (Note that the Greengenes database uses the INSDC (= EMBL/NCBI/DDBJ) annotation, which is not an authoritative source for nomenclature or classification.) The highest-scoring environmental sequence was AY550995 (‘human carious dentine clone IDR-CEC-0032’), which showed an identity of 99.8% and an HSP coverage of 94.5%. The most frequently occurring keywords within the labels of environmental samples which yielded hits were ‘fecal’ (4.4%), ‘beef, cattl’ (4.1%), ‘anim, coli, escherichia, feedlot, habitat, marc, pen, primari, secondari, stec, synecolog’ (4.0%), ‘neg’ (2.5%) and ‘fece’ (2.4%) (236 hits in total). The most frequently occurring keywords within the labels of environmental samples which yielded hits of a higher score than the highest scoring species were ‘fece’ (7.9%), ‘goeldi, marmoset’ (4.8%), ‘microbiom’ (4.3%), ‘aspect, canal, oral, root’ (3.9%) and ‘rumen’ (3.8%) (54 hits in total). While some of these keywords correspond to the well known habitat of P. multisaccharivorax, others indicate additional habitats related to animals.
Figure 1 shows the phylogenetic neighborhood of P. multisaccharivorax in a 16S rRNA based tree. The sequences of the four 16S rRNA gene copies in the genome differ from each other by up to two nucleotides, and differ by up to two nucleotides from the previously published 16S rRNA sequence AB200414.
The cells of P. multisaccharivorax generally have the shape of rods (0.8 × 2.5–8.3 µm) and occur singly or in pairs (Figure 2). They can also form longer filaments. P. multisaccharivorax is a Gram-negative, non spore-forming bacterium (Table 1). The organism is described as non-motile and only four genes associated with motility were identified in the genome (see below). P. multisaccharivorax grows well at 37°C, is strictly anaerobic, chemoorganotrophic and is able to ferment cellobiose, glucose, glycerol, lactose, maltose, mannose, melezitose, raffinose, rhamnose, sorbitol, sucrose, trehalose and xylose . Acid production from arabinose and salicin is variable. The organism does not reduce nitrate or produce indole from tryptophan but it hydrolyzes esculin and digests gelatin . Growth of P. multisaccharivorax is inhibited by the addition of 20% bile. Major fermentation products are succinic and acetic acid, isovaleric acid is produced in small amounts . Activities of glucose-6-phosphate dehydrogenase (G6PDH) and 6-phosphogluconate dehydrogenase (6GPDH) were not detected in isolates of this species, whereas malate dehydrogenase and glutamate dehydrogenase activities were detected in all strains. P. multisaccharivorax produces acid and alkaline phosphatase, β-galactosidase, α- and β-glucosidase, N-acetyl-β-glucosaminidase, α-aminofuranosidase and alanine aminopeptidase. The organism has no demonstrable esterase (C4), esterase lipase (C4), lipase (C4), leucine arylamidase, valine arylamidase, cystine arylamidase, pyroglutamic acid arylamidase, trypsin, chymotrypsin, β-glucuronidase, α-mannosidase, α-fucosidase, arginine aminopeptidase, leucine aminopeptidase, proline aminopeptidase, tyrosine aminopeptidase, phenylalanine aminopeptidase, urease or catalase activity .
In contrast to other Prevotella species all strains of P. multisaccharivorax harbor the menaquinones MK-12 (40-55%) and MK-13 (40-45%) in large amounts, whereas MK-10 (1-3%) and MK-11 (8-10%) were found only in small amounts . The fatty acid pattern for all strains of P. multisaccharivorax revealed C18:1 ω9c (21.7%) and C16:0 (12.9%) as major compounds as well as iso-C17:0 3-OH (9.2%), anteiso-C15:0 (7.8%), C18:2 ω6,9c (7.5%) and iso-C15:0 (6.4%) in smaller amounts . Additionally, the unusual dimethyl acetals were found with C16:0 dimethyl aldehyde in the highest amount of 8.2%. This clearly distinguishes the species of P. multisaccharivorax from other related Prevotella species .
Genome sequencing and annotation
Genome project history
This organism was selected for sequencing on the basis of its phylogenetic position , and is part of the Genomic Encyclopedia of Bacteria and Archaea project . The genome project is deposited in the Genomes On Line Database  and the complete genome sequence is deposited in GenBank. Sequencing, finishing and annotation were performed by the DOE Joint Genome Institute (JGI). A summary of the project information is shown in Table 2.
Growth conditions and DNA isolation
P. multisaccharivorax PPPA20T, DSM 17128, was grown anaerobically in DSMZ medium 104 (PYG-medium)  at 37°C. DNA was isolated from 0.5–1 g of cell paste using MasterPure Gram-positive DNA purification kit (Epicentre MGP04100) following the standard protocol as recommended by the manufacturer with modification st/DL for cell lysis as described in Wu et al. 2009 . DNA is available through the DNA Bank Network .
Genome sequencing and assembly
The genome was sequenced using a combination of Illumina and 454 sequencing platforms. All general aspects of library construction and sequencing can be found at the JGI website . Pyrosequencing reads were assembled using the Newbler assembler (Roche). The initial Newbler assembly consisting of 154 contigs in five scaffolds was converted into a phrap  assembly by making fake reads from the consensus, to collect the read pairs in the 454 paired end library. Illumina GAii sequencing data (1,043.6 Mb) was assembled with Velvet  and the consensus sequences were shredded into 2.0 kb overlapped fake reads and assembled together with the 454 data. The 454 draft assembly was based on 135.4 Mb 454 standard data and all of the 454 paired end data. Newbler parameters are -consed -a 50 -l 350 -g -m -ml 20. The Phred/Phrap/Consed software package  was used for sequence assembly and quality assessment in the subsequent finishing process. After the shotgun stage, reads were assembled with parallel phrap (High Performance Software, LLC). Possible mis-assemblies were corrected with gapResolution , Dupfinisher , or sequencing cloned bridging PCR fragments with subcloning or transposon bombing (Epicentre Biotechnologies, Madison, WI). Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks (J.-F. Chang, unpublished). A total of 218 additional reactions were necessary to close gaps and to raise the quality of the finished sequence. Illumina reads were also used to correct potential base errors and increase consensus quality using a software Polisher developed at JGI .
The error rate of the completed genome sequence is less than 1 in 100,000. Together, the combination of the Illumina and 454 sequencing platforms provided 338 × coverage of the genome. The final assembly contained 325,939 pyrosequence and 28,989,384 Illumina reads.
Genes were identified using Prodigal  as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline . The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) non-redundant database, UniProt, TIGR-Fam, Pfam, PRIAM, KEGG, COG, and InterPro databases. Additional gene prediction analysis and functional annotation was performed within the Integrated Microbial Genomes - Expert Review (IMG-ER) platform .
The assembled genome sequence consists of three non-contiguous contigs with a length of 3,334,154 bp, 47,474 bp and 7,016 bp with a G+C content of 48.3% (Table 3 and Figure 3). Of the 2,951 genes predicted, 2,876 were protein-coding genes, and 75 RNAs; 166 pseudogenes were also identified. The majority of the protein-coding genes (60.5%) were assigned with a putative function while the remaining ones were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 4.
Garrity G. NamesforLife. BrowserTool takes expertise out of the database and puts it right in the browser. Microbiol Today 2010; 37:9.
Sakamoto M, Umeda M, Ishikawa I, Benno Y. Prevotella multisaccharivorax sp. nov., isolated from human subgingival plaque. Int J Syst Evol Microbiol 2005; 55:1839–1843. PubMed doi:10.1099/ijs.0.63739-0
Preza D, Olsen I, Aas JA, Willumsen T, Grinde B, Paster BJ. Bacterial profiles of root caries in elderly patients. J Clin Microbiol 2008; 46:2015–2021. PubMed doi:10.1128/JCM.02411-07
Rôças IN, Siqueira JF, Jr. Prevalence of new candidate pathogens Prevotella baroniae, Prevotella multisaccharivorax and as-yet-uncultivated Bacteroidetes clone X083 in primary endodontic infections. J Endod 2009; 35:1359–1362. PubMed doi:10.1016/j.joen.2009.05.033
Siqueira JF, Jr., Rôças IN. The oral microbiota: general overview, taxonomy, and nucleic acid techniques. Methods Mol Biol 2010; 666:55–69. PubMed doi:10.1007/978-1-60761-820-1_5
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410. PubMed
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 2006; 72:5069–5072. PubMed doi:10.1128/AEM.03006-05
Porter MF. An algorithm for suffix stripping. Program: electronic library and information systems 1980; 14:130–137.
Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics 2002; 18:452–464. PubMed doi:10.1093/bioinformatics/18.3.452
Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552. PubMed
Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML web-servers. Syst Biol 2008; 57:758–771. PubMed doi:10.1080/10635150802429642
Hess PN, De Moraes Russo CA. An empirical test of the midpoint rooting method. Biol J Linn Soc Lond 2007; 92:669–674. doi:10.1111/j.1095-8312.2007.00864.x
Pattengale ND, Alipour M, Bininda-Emonds ORP, Moret BME, Stamatakis A. How many bootstrap replicates are necessary? Lect Notes Comput Sci 2009; 5541:184–200. doi:10.1007/978-3-642-02008-7_13
Swofford DL. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4.0 b10. Sinauer Associates, Sunderland, 2002.
Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC. The Genomes OnLine Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2010; 38:D346–D354. PubMed doi:10.1093/nar/gkp848
Purushe J, Foulds DE, Morrison M, White BA, Mackie RI. Henrissat G, Nelson KE. Comparative genome anaylsis of Prevotella ruminicola and Prevotella bryantii: insight into their environmental niche. Microb Ecol 2010; 60:721–729. PubMed doi:10.1007/s00248-010-9692-8
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 doi: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 doi: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.
Ludwig W, Euzeby J, Whitman WG. Draft tax-onomic outline of the Bacteroidetes, Planctomycetes, Chlamydiae, Spirochaetes, Fibrobacteres, Fusobacteria, Acidobacteria, Verrucomicrobia, Dictyoglomi, and Gemmatimonadetes. http://www.bergeys.org/outlines/Bergeys_Vol_4_Outline.pdf. Taxonomic Outline 2008.
Garrity GM, Holt JG. 2001. Taxonomic outline of the Archaea and Bacteria, p. 155–166. In: Garrity GM, Boone RR, Castenholz RW (eds), Bergey’s Manual of Systematic Bacteriology, 2nd ed, vol. 1. Springer, New York.
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 doi:10.1099/00207713-40-2-205
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 doi:10.1099/00207713-45-4-832
BAuA. Classification of bacteria and archaea in risk groups. TRBA 2010; 466:173.
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. Nat Genet 2000; 25:25–29. PubMed doi:10.1038/75556
Klenk HP, Göker M. En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol 2010; 33:175–182. PubMed doi:10.1016/j.syapm.2010.03.003
Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, et al. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 2009; 462:1056–1060. PubMed doi:10.1038/nature08656
List of growth media used at DSMZ: http://www.dsmz.de/microorganisms/media_list.php.
Gemeinholzer B, Dröge G, Zetzsche H, Haszprunar G, Klenk HP, Güntsch A, Berendsohn WG, Wägele JW. The DNA Bank Network: the start from a German initiative. Biopreservation and Biobanking 2011; 9:51–55. doi:10.1089/bio.2010.0029
The DOE Joint Genome Institute. http://www.jgi.doe.gov
Phrap and Phred for Windows. MacOS, Linux, and Unix. http://www.phrap.com
Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821–829. PubMed doi:10.1101/gr.074492.107
Han C, Chain P. 2006. Finishing repeat regions automatically with Dupfinisher. In: Proceeding of the 2006 international conference on bioinformatics & computational biology. Arabnia HR, Valafar H (eds), CSREA Press. June 26–29, 2006: 141–146
Lapidus A, LaButti K, Foster B, Lowry S, Trong S, Goltsman E. POLISHER: An effective tool for using ultra short reads in microbial genome assembly and finishing. AGBT, Marco Island, FL, 2008.
Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119. PubMed doi:10.1186/1471-2105-11-119
Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 2010; 7:455–457. PubMed doi:10.1038/nmeth.1457
Markowitz VM, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009; 25:2271–2278. PubMed doi:10.1093/bioinformatics/btp393
We would like to gratefully acknowledge the help of Sabine Welnitz (DSMZ) for growing P. multisaccharivorax cultures. This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2.