- Open Access
Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC139T)
Standards in Genomic Sciences volume 4, pages233–243 (2011)
Bacteroides coprosuis Whitehead et al. 2005 belongs to the genus Bacteroides, which is a member of the family Bacteroidaceae. Members of the genus Bacteroides in general are known as beneficial protectors of animal guts against pathogenic microorganisms, and as contributors to the degradation of complex molecules such as polysaccharides. B. coprosuis itself was isolated from a manure storage pit of a swine facility, but has not yet been found in an animal host. The species is of interest solely because of its isolated phylogenetic location. The genome of B. coprosuis is already the 5th sequenced type strain genome from the genus Bacteroides. The 2,991,798 bp long genome with its 2,461 protein-coding and 78 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
Strain PC139T (= DSM 18011 = NRRL B-41113 = JCM 13475) is the type strain of Bacteroides coprosuis which belongs to the large genus Bacteroides, which currently contains 39 members [1,2]. The species epithet is derived from the Greek noun ‘kopros’ meaning ‘feces’ and the genitive of the Latin noun ‘suis’ meaning ‘of a pig’. B. coprosuis strain PC139T was isolated from a manure storage pit of a swine facility. One other strain belonging to the same species has been isolated from the same source . Many Bacteroides species are common inhabitants of the intestine where they help to degrade complex molecules such as polysaccharides or transform steroids [3,4]. They also play a role as beneficial protectors of the gut against pathogenic microorganisms . However, so far B. coprosuis has not been isolated from an animal itself, therefore the exact habitat and the role the bacterium plays remains unknown. Here we present a summary classification and a set of features for B. coprosuis PC139T, together with the description of the complete genomic sequencing and annotation.
Classification and features
A representative genomic 16S rRNA sequence of strain PC139T 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 Bacteroides (100.0%) (20 hits in total). Regarding the single hit to sequences from members of the species, the identity within HSPs was 99.9%, whereas the coverage by HSPs was 98.0%. Regarding the twelve hits to sequences from other members of the genus, the average identity within HSPs was 92.9%, whereas the average coverage by HSPs was 62.1%. Among all other species, the one yielding the highest score was B. propionicifaciens, which corresponded to an identity of 94.6% and an HSP coverage of 84.5%. The highest-scoring environmental sequence was AF445205 (‘Swine fecal isolate str. FPC111’), which showed an identity of 99.8% and an HSP coverage of 100.0%. The most frequently occurring keywords within the labels of environmental samples which yielded hits were ‘human’ (6.3%), ‘fecal’ (5.5%), ‘effect’ (4.4%), ‘antibiot, deep, gut, microbiota, pervas, sequenc’ (4.3%) and ‘feedlot’ (4.2%) (230 hits in total). Environmental samples which yielded hits of a higher score than the highest scoring species were not found.
Figure 1 shows the phylogenetic neighborhood of B. coprosuis in a 16S rRNA based tree. The sequences of the three 16S rRNA gene copies in the genome differ from each other by up to seven nucleotides, and differ by up to six nucleotides from the previously published 16S rRNA sequence (AF319778).
The cells of B. coprosuis are generally rod-shaped (0.5–1.5 × 0.8–3.0 µm) with tapered ends (Figure 2). The cells are usually arranged singly or in pairs . B. coprosuis is a Gram-negative and non spore-forming bacterium (Table 1). The organism is finally described to be non-motile; only four genes associated with motility have been found in the genome (see below). The organism grows at temperatures from 25 to 37°C, but not at 42°C or higher; the optimal temperature is 37°C . B. coprosuis is a strictly anaerobic chemoorganotroph and is able to grow on media containing glucose, maltose and chondroitin sulfate but, no growth was observed on arabinogalactan, arabinose, cellobiose, corn-fibre xylan, corn-spelt xylan, fructose or xylose . The organism produces acid from mannose, but not from raffinose. It hydrolyzes esculin and starch, but does not liquify gelatin, reduce nitrate nor produce indole from tryptophan . Growth is possible in the presence of 20% bile . Major fermentation products from glucose are acetic acid (8.0–15.0 mM), succinic acid (7.5–10.0 mM) and propionic acid (4.0–22.0 mM) . B. coprosuis shows activity for alkaline and acid phosphatase, α-fucosidase, β-galactosidases, α- and β-glucosidases, N-acetyl-β-glucosaminidase, chymotrypsin, esterase C4, ester lipase C8, lipase C14, cystine arylamidase, leucyl glycine arylamidase, alanine arylamidase, arginine arylamidase and glutamyl glutamic acid arylamidase. No activity was detected for urease, catalase, oxidase, trypsin, arginine dihydrolase, β-galactosidase 6-phosphate, β-glucuronidase, α-arabinosidase, α-mannosidase and glutamic acid, glycine, histidine, leucine, phenylalanine, proline, pyroglutamic acid, serine, tyrosine and valine arylamidase . B. coprosuis is resistant to ampicillin (100 µg/ml), cefoxitin (20 µg/ml), erythromycin (10 µg/ml), gentamicin (200 µg/ml) and tetracycline (3 µg/ml).
Little chemotaxonomic information is available for strain PC139T. Thus far, only the fatty acid composition has been elucidated. The major fatty acids found were anteiso-C15:0 (31%), iso-C17:03-OH (17%), iso-C17:0 (10%), iso-C15:0 (8%) and C15:0 (8%). Fatty acids C16:0 (3.5%), anteiso-C17:0 (3%), C18:1ω9c (2%), C17:0 (2%), anteiso-C17:1ω9c (2%), C18:0 (1%) and iso-C13:0 (1%) were found in minor amounts .
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
B. coprosuis PC139T, DSM 18011, was grown anaerobically in DSMZ medium 104 (modified PYG-medium) + rumen fluid (200µl/10 ml)  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 version 2.3-PreRelease-09-14-2009 (Roche). The initial Newbler assembly consisting of 100 contigs in two 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 (920.8 Mb) was assembled with Velvet, version 0.7.63  and the consensus sequences were shredded into 1.5 kb overlapped fake reads and assembled together with the 454 data. The 454 draft assembly was based on 109.0 Mb 454 draft 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 193 additional reactions and four shatter libraries 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 319.6 × coverage of the genome. The final assembly contained 252,927 pyrosequence and 24,365,026 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) nonredundant 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 genome consists of a 2,991,798 bp long circular chromosome (in one contig with one remaining unclosed sequencing gap), with a G+C content of 35.0% (Table 3). Of the 2,539 genes predicted, 2,461 were protein-coding genes, and 78 RNAs; 68 pseudogenes were also identified. The majority of the protein-coding genes (66.4%) 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.
Insights from the genome sequence
Figure 3 shows synteny dot plots of three Bacteroides type strain genomes (B. helcogenes, B. salanitronis, B. coprosuis) with each other. In all three pairwise comparisons it becomes visible that there does not exist a high collinearity between these species of the genus Bacteroides.
The Genome-to-Genome Distance Calculator, GGDC [43,44] was used for the estimation of the overall similarity between the three Bacteroides genomes. The system calculates the distances by comparing the genomes to obtain HSPs (high-scoring segment pairs) and interfering distances from the set of formulas (1 HSP length / total length; 2 identities / HSP length; 3 identities / total length). The comparison of B. coprosuis with B. helcogenes and B. salanitronis revealed that only 6.1% and 3.3%, respectively, of the average of the genome lengths are covered with HSPs. The identity within the HSPs was 82.3% and 82.1%, respectively, whereas the identity over the whole genome was 5.0% and 2.7%, respectively. The comparison of B. salanitronis with B. helcogenes revealed that 11.4% of the genome is covered with HSPs, with an identity within in the HSPs of 81.4% and an identity over the whole genome of 9.2%. According to these calculations the similarity between B. salanitronis and B. helcogenes is higher than the similarity between B. coprosuis and B. salanitronis as well as the similarity between B. coprosuis and B. helcogenes.
The genome size of B. coprosuis (3 Mb) is significantly smaller than those of B. helcogenes (4 Mb) and B. salanitronis (4.3 Mb) and the G+C-content of the B. coprosuis genome (35%) is much lower than the G+C-content of B. helcogenes (45%) and B. salanitronis (46%) genomes. The Venn-diagram (Figure 4) shows the number of shared genes. B. salanitronis and B. helcogenes share a great number of genes (543 genes) that are not present in B. coprosuis. This fraction of genes includes genes coding for glycoside hydrolases, which are responsible for the degradation of polysaccharides. Only 12 glycoside hydrolases were identified in the genome of B. coprosuis, whereas the number of glycoside hydrolases identified in B. helcogenes and B. salanitronis, is much higher, 38 and 45, respectively. Whereas only two transposase genes were identified in the genome of B. helcogenes, the genomes of B. coprosuis and B. salanitronis encode a high number of transposases, 34 and 29, respectively. As a consequence, genome rearrangements can occur, which result in a quite dynamic genome structure (Figure 4). Only a small number of the genes (588 genes) found in B. coprosuis are not present in B. helcogenes and/or B. salanitronis.
Garrity G. Names for Life. Browser Tool takes expertise out of the database and puts it right in the browser. Microbiol Today 2010; 7:1.
Whitehead TR, Cotta MA, Collins MD, Falsen E, Lawson PA. Bacteroides coprosuis sp. nov., isolated from swine-manure storage pits. Int J Syst Evol Microbiol 2005; 55:2515–2518. PubMed doi:10.1099/ijs.0.63869-0
Comstock LE. Importance of glycans to the hostbacteroides mutualism in the mammalian intestine. Cell Host Microbe 2009; 5:522–526. PubMed doi:10.1016/j.chom.2009.05.010
Bäckhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI. Host-bacterial mutualism in the human intestine. Science 2005; 307:1915–1920. PubMed doi:10.1126/science.1104816
Hentges DJ. Role of the intestinal flora in host defense against infection. In Human Intestinal Microflora in Health and Disease 1983; pp.311–331. Edited by D. J. Hentges. New York: Academic Press.
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.
Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552. PubMed
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
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
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
Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC. The Genomes On Line 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
Cerdeño-Tárraga AM, Patrick S, Crossman LC, Blakely G, Abratt V, Lennard N, Poxton I, Duerden B, Harris B, Quail MA, et al. Extensive DNA inversions in the B. fragilis genome control variable gene expression. Science 2005; 307:1463–1465. PubMed doi:10.1126/science.1107008
Pati A, Gronow S, Zeytun A, Lapidus A, Nolan M, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, et al. Complete genome sequence of Bacteroides helcogenes type strain (P36-108T). Stand Genomic Sci 2011; 4:45–53. PubMed doi:10.4056/sigs.1513795
Xu J, Bjursell MK, Himrod J, Deng S, Carmichael LK, Chiang HC, Hooper LV, Gordon JI. A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science 2003; 299:2074–2076. PubMed doi:10.1126/science.1080029
Xu J, Mahowald MA, Ley RE, Lozupone CA, Hamady M, Martens EC, Henrissat B, Coutinho PM, Minx P, Latreille P, et al. Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol 2007; 5:e156. PubMed doi:10.1371/journal.pbio.0050156
Gronow S, Held B, Lucas S, Lapidus A, Glavina Del Rio T, Nolan M, Tice H, Deshpande S, Cheng JF, Pitluck S, et al. Complete genome sequence of Bacteroides salanitronis type strain (BL78T). Stand Genomic Sci 2011; 4:191–199.
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 taxonomic 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 DR, Castenholz RW (eds), Bergey’s Manual of Systematic Bacteriology, 2nd ed, vol. 1. Springer, New York.
Skerman VBD, McGowan V, Sneath PHA. Approved Lists of Bacterial Names. Int J Syst Bacteriol 1980; 30:225–420. doi:10.1099/00207713-30-1-225
Pribram E. Klassification der Schizomyceten. Klassifikation der Schizomyceten (Bakterien), Franz Deuticke, Leipzig, 1933, p. 1–143.
Castellani A, Chalmers AJ. Genus Bacteroides Castellani and Chalmers, 1918. Manual of Tropical Medicine, Third Edition, Williams, Wood and Co., New York, 1919 p. 959–960.
Holdeman LV, Moore WEC. Genus I. Bacteroides Castellani and Chalmers 1919, 959. In: Buchanan RE, Gibbons NE (eds), Bergey’s Manual of Determinative Bacteriology, Eighth Edition, The Williams and Wilkins Co., Baltimore, 1974, p. 385–404.
Cato EP, Kelley RW, Moore WEC, Holdeman LV. Bacteroides zoogleoformans, Weinberg, Nativelle, and Prévot 1937) corrig. comb. nov.: emended description. Int J Syst Bacteriol 1982; 32:271–274. doi:10.1099/00207713-32-3-271
Shah HN, Collins MD. Proposal to restrict the genus Bacteroides (Castellani and Chalmers) to Bacteroides fragilis and closely related species. Int J Syst Bacteriol 1989; 39:85–87. doi:10.1099/00207713-39-1-85
BAuA. Classification of bacteria and archaea in risk groups. TRBA 2005; 466:84.
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
Sims D, Brettin T, Detter JC, Han C, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Chen F, Lucas S, et al. Complete genome sequence of Kytococcus sedentarius type strain (541T). Stand Genomic Sci 2009; 1:12–20. PubMed doi:10.4056/sigs.761
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
Auch AF, von Jan M, Klenk HP, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134. PubMed doi:10.4056/sigs.531120
Auch AF, Klenk HP, Göker M. Standard operational procedure for calculation genome-to-genome distances based on high-scoring sequence pairs. Stand Genomic Sci 2010; 2:142–148. PubMed doi:10.4056/sigs.541628
We would like to gratefully acknowledge the help of Sabine Welnitz (DSMZ) for growing B. coprosuis 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.