Lawrence Berkeley National Laboratory Recent Work Title Non-contiguous finished genome sequence of the opportunistic oral pathogen Prevotella multisaccharivorax type strain (PPPA20). Permalink https://escholarship.org/uc/item/0p79h5ds Journal Standards in genomic sciences, 5(1) ISSN 1944-3277 Authors Pati, Amrita Gronow, Sabine Lu, Megan et al. Publication Date 2011-10-01 DOI 10.4056/sigs.2164949 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2011) 5:41-49 DOI:10.4056/sigs.2164949 Non-contiguous finished genome sequence of the opportunistic oral pathogen Prevotella multisaccharivorax type strain (PPPA20T) Amrita Pati1, Sabine Gronow2, Megan Lu1,3, Alla Lapidus1, Matt Nolan1, Susan Lucas1, Nancy Hammon1, Shweta Deshpande1, Jan-Fang Cheng1, Roxanne Tapia1,3, Cliff Han1,3, Lynne Goodwin1,3 Sam Pitluck1, Konstantinos Liolios1, Ioanna Pagani1, Konstantinos Mavromatis1, Natalia Mikhailova1, Marcel Huntemann1, Amy Chen4, Krishna Palaniappan4, Miriam Land1,5, Loren Hauser1,5, John C. Detter1,3, Evelyne-Marie Brambilla2, Manfred Rohde6, Markus Göker2, Tanja Woyke1, James Bristow1, Jonathan A. Eisen1,7, Victor Markowitz4, Philip Hugenholtz1,8, Nikos C. Kyrpides1, Hans-Peter Klenk2*, and Natalia Ivanova1 1 DOE Joint Genome Institute, Walnut Creek, California, USA 2 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 5 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 6 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 7 University of California Davis Genome Center, Davis, California, USA 8 Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia *Corresponding author: Hans-Peter Klenk Keywords: obligately anaerobic, non-motile, Gram-negative, mesophilic, chemoorganotroph- ic, opportunistic pathogen, Prevotellaceae, GEBA 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. Introduction Strain PPPA20T (= DSM 17128 = JCM 12954) is the species P. multisaccharivorax [2]. Using non-culture type strain of Prevotella multisaccharivorax [1]. techniques on sites affected by endodontic and pe- Currently, there are about 50 species placed in the riodontal diseases, a large number of sequences genus Prevotella [1]. The species epithet is derived have been found that belong to Prevotella and Pre- from the Latin adjective multus meaning votella-like bacteria. Many of those species have ‘many/much’, the Latin noun saccharum meaning never been isolated or described [3]. The complex ‘sugar’ and the Latin adjective vorax meaning ‘liking microbial community living in the rich ecological to eat’ referring to the metabolic properties of the niche of the human oral cavity and its interaction species to digest a variety of carbohydrates [2]. P. with consumed food will be of lasting interest for multisaccharivorax strain PPPA20T is considered to medical and ecological reasons [4,5]. Here we be an opportunistic pathogen and was isolated present a summary classification and a set of fea- from subgingival plaque from a patient with chron- tures for P. multisaccharivorax PPPA20T, together ic periodontitis. Additionally, five more strains iso- with the description of the non-contiguous finished lated from the human oral cavity were placed in the genomic sequencing and annotation. The Genomic Standards Consortium Prevotella multisaccharivorax type strain (PPPA20T) Classification and features in pairs (Figure 2). They can also form longer fila- A representative genomic 16S rRNA sequence of P. ments. P. multisaccharivorax is a Gram-negative, multisaccharivorax PPPA20T was compared using non spore-forming bacterium (Table 1). The organ- NCBI BLAST [6] under default settings (e.g., consi- ism is described as non-motile and only four genes dering only the high-scoring segment pairs (HSPs) associated with motility were identified in the ge- from the best 250 hits) with the most recent release nome (see below). P. multisaccharivorax grows well of the Greengenes database [7] and the relative fre- at 37°C, is strictly anaerobic, chemoorganotrophic quencies of taxa and keywords (reduced to their and is able to ferment cellobiose, glucose, glycerol, stem [8]) were determined, weighted by BLAST lactose, maltose, mannose, melezitose, raffinose, scores. The most frequently occurring genus was rhamnose, sorbitol, sucrose, trehalose and xylose Prevotella (100.0%) (14 hits in total). Regarding the [2]. Acid production from arabinose and salicin is single hit to sequences from members of the spe- variable. The organism does not reduce nitrate or cies, the average identity within HSPs was 100.0%, produce indole from tryptophan but it hydrolyzes whereas the average coverage by HSPs was 98.0%. esculin and digests gelatin [2]. Growth of P. multi- Regarding the nine hits to sequences from other saccharivorax is inhibited by the addition of 20% members of the genus, the average identity within bile. Major fermentation products are succinic and HSPs was 90.3%, whereas the average coverage by acetic acid, isovaleric acid is produced in small HSPs was 66.5%. Among all other species, the one amounts [2]. Activities of glucose-6-phosphate de- yielding the highest score was Prevotella ruminicola hydrogenase (G6PDH) and 6-phosphogluconate (AF218618), which corresponded to an identity of dehydrogenase (6GPDH) were not detected in iso- 91.5% and an HSP coverage of 66.3%. (Note that lates of this species, whereas malate dehydrogenase the Greengenes database uses the INSDC (= and glutamate dehydrogenase activities were de- EMBL/NCBI/DDBJ) annotation, which is not an au- tected in all strains. P. multisaccharivorax produces thoritative source for nomenclature or classifica- acid and alkaline phospha - - tion.) The highest-scoring environmental sequence -glucosidase, N-acetyl- - - was AY550995 ('human carious dentine clone IDR- aminofuranosidase and altase,anine β galactosidase,aminopeptidase. α CEC-0032'), which showed an identity of 99.8% and Theand organismβ has no demonstrβ glucosaminidase,able esterase (C4), α an HSP coverage of 94.5%. The most frequently oc- esterase lipase (C4), lipase (C4), leucine arylami- curring keywords within the labels of environmen- dase, valine arylamidase, cystine arylamidase, py- tal samples which yielded hits were 'fecal' (4.4%), roglutamic acid arylamidase, trypsin, chymotrypsin, 'beef, cattl' (4.1%), 'anim, coli, escherichia, feedlot, - -mannosi -fucosidase, ar- habitat, marc, pen, primari, secondari, stec, syneco- ginine aminopeptidase, leucine aminopeptidase, log' (4.0%), 'neg' (2.5%) and 'fece' (2.4%) (236 hits prolineβ glucuronidase, aminopeptidase, α tyrosinedase, αaminopeptidase, in total). The most frequently occurring keywords phenylalanine aminopeptidase, urease or catalase within the labels of environmental samples which activity [2]. yielded hits of a higher score than the highest scor- ing species were 'fece' (7.9%), 'goeldi, marmoset' Chemotaxonomy (4.8%), 'microbiom' (4.3%), 'aspect, canal, oral, In contrast to other Prevotella species all strains of root' (3.9%) and 'rumen' (3.8%) (54 hits in total). P. multisaccharivorax harbor the menaquinones While some of these keywords correspond to the MK-12 (40-55%) and MK-13 (40-45%) in large well known habitat of P. multisaccharivorax, others amounts, whereas MK-10 (1-3%) and MK-11 (8- indicate additional habitats related to animals. 10%) were found only in small amounts [2]. The fatty acid pattern for all strains of P. multisacchari- Figure 1 shows the phylogenetic neighborhood of P. vorax revealed C (21.7%) and C (12.9%) as multisaccharivorax in a 16S rRNA based tree. The 16:0 major compounds as well as iso-C (9.2%), sequences of the four 16S rRNA gene copies in the 18:1 ω9c 17:0 3-OH anteiso-C (7.8%), C (7.5%) and iso-C genome differ from each other by up to two nucleo- 15:0 15:0 (6.4%) in smaller amounts [2]. Additionally, the tides, and differ by up to two nucleotides from the 18:2 ω6,9c unusual dimethyl acetals were found with C di- previously published 16S rRNA sequence 16:0 methyl aldehyde in the highest amount of 8.2%. AB200414. This clearly distinguishes the species of P. multisac- The cells of P. multisaccharivorax generally have the charivorax from other related Prevotella species shape of rods (0.8 × 2.5-8.3 µm) and occur singly or [2]. 42 Standards in Genomic Sciences Pati et al. Figure 1. Phylogenetic tree highlighting the position of P. multisaccharivorax relative to the type strains of the oth- er species within the family. The tree was inferred from 1,425 aligned characters [9,10] of the 16S rRNA gene se- quence under the maximum likelihood