Standards in Genomic Sciences (2011) 4:45-53 DOI:10.4056/sigs.1513795 The Genomic Standards Consortium Complete genome sequence of Bacteroides helcogenes type strain (P 36-108T) Amrita Pati1, Sabine Gronow2, Ahmet Zeytun1,3, Alla Lapidus1, Matt Nolan1, Nancy Hammon1, Shweta Deshpande1, Jan-Fang Cheng1, Roxane Tapia1,3, Cliff Han1,3, Lynne Goodwin1,3, Sam Pitluck1, Konstantinos Liolios1, Ioanna Pagani1, Natalia Ivanova1, Konstantinos Mavromatis1, Amy Chen4, Krishna Palaniappan4, Miriam Land1,5, Loren Hauser1,5, Yun-Juan Chang1,5, Cynthia D. Jeffries1,5, John C. Detter1, Evelyne Brambilla2, Manfred Rohde6, Markus G��ker2, Tanja Woyke1, James Bristow1, Jonathan A. Eisen1,7, Victor Markowitz4, Philip Hugenholtz1,8, Nikos C. Kyrpides1, Hans-Peter Klenk2*, and Susan Lucas1 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: strictly anaerobic, mesophilic, nonmotile, Gram-negative, chemoorganotrophic, pig abscess, animal pathogen, Bacteroidaceae, GEBA Bacteroides helcogenes Benno et al. 1983 is of interest because of its isolated phylogenetic location and, although it has been found in pig feces and is known to be pathogenic for pigs, occurrence of this bacterium is rare and it does not cause significant damage in intensive an- imal husbandry. The genome of B. helcogenes P 36-108T is already the fifth completed and published type strain genome from the genus Bacteroides in the family Bacteroidaceae. The 3,998,906 bp long genome with its 3,353 protein-coding and 83 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. Introduction Strain P 36-108T (= DSM 20613 = ATCC 35417 = JCM 6297) is the type strain of Bacteroides helco- genes, one of currently 39 species in the genus Bacteroides [1,2]. The species epithet of B. helco- genes is derived from the Greek noun helkos meaning ���abscess��� and the Greek verb gennaio meaning ���produce���, referring to the pathogenic, probably intestinal, abscess-producing properties of the species [2]. B. helcogenes strain P36-108T was isolated from a pig abscess in Japan, and de- scribed by Benno et al. in 1983 [2]. Nine further isolates of B. helcogenes have been obtained from pig abscesses whereas two other isolates origi- nated from pig feces. Here we present a summary classification and a set of features for B. helcogenes P 36-108T, together with the description of the complete genomic sequencing and annotation. Classification and features A representative genomic 16S rRNA sequence of B. helcogenes was compared using NCBI BLAST under default values (e.g., considering only the high-scoring segment pairs (HSPs) from the best 250 hits) with the most recent release of the Greengenes database [3] and the relative frequen-

Bacteroides helcogenes type strain (P 36-108T) 46 Standards in Genomic Sciences cies, weighted by BLAST scores, of taxa and key- words (reduced to their stem [4]) were deter- mined. The single most frequent genus was Bacte- roides (100%) (33 hits in total). Regarding the 21 hits to sequences from other members of the ge- nus, the average identity within HSPs was 92.7%, whereas the average coverage by HSPs was 84.5%. Among all other species, the one yielding the highest score was Bacteroides ovatus, which corresponded to an identity of 93.4% and a HSP coverage of 86.6%. The highest-scoring environ- mental sequence was AM275453 ('fecal microbi- ota irritable bowel syndrome patients differs sig- nificantly from that of healthy subjects'), which showed an identity of 95.5% and a HSP coverage of 84.3%. The most frequently occurring key- words within the labels of environmental samples which yielded hits were 'human' (11.0%), 'fecal' (9.5%), 'microbiota' (8.8%), 'sequenc' (5.4%) and 'gut' (5.4%) (217 hits in total). The most frequent- ly occurring keywords within the labels of envi- ronmental samples which yielded hits of a higher score than the highest scoring species were 'fecal/human' (13.3%), 'feedlot' (5.2%), 'bowel, faecal, healthi, irrit, microbiota, patient, significan- tli, subject, syndrom' (2.7%) and 'beef, cattl, coli, escherichia, feedbunk, habitat, marc, materi, neg, pen, primari, secondari, stec, surfac, synecolog, top, west' (2.6%) (6 hits in total). Most of these keywords are in accordance with the isolation sites of the different isolates and strongly suggest that B. helcogenes, like many other species of the genus Bacteroides, is associated with the intestinal tract of the host in the case of B. helcogenes, this host is the pig [2]. Figure 1 shows the phylogenetic neighborhood of B. helcogenes P 36-108T in a 16S rRNA based tree. The sequences of the five 16S rRNA gene copies in the genome differ from each other by up to 20 nucleotides, and differ by up to 13 nucleotides from the previously published 16S rRNA sequence (AB200227). The cells of B. helcogenes generally have the shape of short rods (0.5-0.6 ��m �� 0.8-4.0 ��m) which oc- cur singly or in pairs (Figure 2). B. helcogenes is a Gram-negative, non-pigmented and non spore- forming bacterium (Table 1). The organism is originally described as nonmotile and only five genes associated with motility have been found in the genome (see below). The organism grows well at 37��C but does not grow at 4��C or at 45��C [2]. B. helcogenes is strictly anaerobic, chemoorgano- trophic and is able to ferment glucose, mannose, fructose, galactose, sucrose, maltose, cellobiose, lactose, xylose, melibiose, raffinose, starch, glyco- gen, salicin, amygdalin, and xylan [2]. The organ- ism hydrolyzes esculin and starch but does not digest casein, liquify gelatin, reduce nitrate nor produce indole from tryptophan [2]. B. helcogenes does not utilize arabinose, ramnose, ribose, treha- lose, inulin, glycerol, mannitol, sorbitol, inositol, adonitol, erythritol or gum Arabic [2]. It does not require hemin for growth but does require the presence of CO2 it does not show hemolysis. Growth is not enhanced by the addition of 20% bile [2]. Major fermentation products from PYFG broth (peptone yeast extract Fildes glucose broth [26]) are acetic acid and succinic acid propionic and isobutyric acid are produced in small amounts [2]. B. helcogenes is phosphatase, DNase, ��- glucuronidase, and glutamic acid decarboxylase active and urease, catalase, lecithinase and lipase inactive [2]. The organism produces ammonium and chondroitin sulfatase [2]. B. helcogenes can grow in the presence of kanamycin (1mg/ml), vancomycin (10 ��g/ml), colistin (10 ��g/ml), eryt- hromycin (60 ��g/ml) or polymyxin B (10 ��g/ml) but not in the presence of cepharothin (10 ��g/ml) or Brilliant green (0.001%) [2]. Chemotaxonomy Little chemotaxonomic information is available for strain P 36-108T. Thus far, only the fatty acid composition has been elucidated. The major fatty acids found (10%) were anteiso-C15:0, C15:0 and iso-C15:0.3-OH. Also, iso-C15:0, C16:0, and cis C18:1 were detected in a proportion ranging between 5% to 10% of the total fatty acids (unpublished data). Genome sequencing and annotation Genome project history This organism was selected for sequencing on the basis of its phylogenetic position [27], and is part of the Genomic Encyclopedia of Bacteria and Arc- haea project [28]. The genome project is depo- sited in the Genomes OnLine Database [10] and the complete genome sequence is deposited in GenBank. Sequencing, finishing and annotation were performed by the DOE Joint Genome Insti- tute (JGI). A summary of the project information is shown in Table 2.