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Complete genome sequence of Eggerthella lenta type strain (VPI 0255T)

Abstract

Eggerthella lenta (Eggerth 1935) Wade et al. 1999, emended Würdemann et al. 2009 is the type species of the genus Eggerthella, which belongs to the actinobacterial family Coriobacteriaceae. E. lenta is a Gram-positive, non-motile, non-sporulating pathogenic bacterium that can cause severe bacteremia. The strain described in this study has been isolated from a rectal tumor in 1935. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the genus Eggerthella, and the 3,632,260 bp long single replicon genome with its 3123 protein-coding and 58 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Introduction

Strain VPI 0255T (= DSM 2243 = ATCC 25559 = JCM 9979) is the type strain of the species Eggerthella lenta, which was first described in 1935 by Eggerth as ‘Bacteroides lentus’ [1], later in 1938 renamed by Prévot in ‘Eubacterium lentum’ [2], and was also known under the synonym ‘Pseudobacterium lentum’ Krasil’nikov 1949 [3]. The strain has been described in detail by Moore et al. in 1971 [4]. Based on 16S rRNA sequence divergence and the presence of unique phenotypic characters the strain was then transferred to the new genus Eggerthella as E. lenta (Kageyama et al. 1999, Wade et al. 1999 [5,6] In 2004 two novel Eggerthella species, E. hongkongensis and E. sinensis were characterized and described in addition [7]. Recently, E. hongkongensis was reclassified as Paraeggerthella hongkongensis [8]. Although the two Eggerthella species and P. hongkongensis are part of the human gut flora, they can be the agent of severe bacteremia. So far the pathogenic potential of the genera are poorly analyzed [7]. Here we present a summary classification and a set of features for E. lenta VPI 0255T, together with the description of the complete genomic sequencing and annotation.

Classification and features

Members of the species E. lenta have been isolated from several abscesses, from appendix tissues, peritoneal fluid and intestinal tumors. The organism is often involved in mixed infections with less fastidious bacteria. Difficulties in cultivation and identification are probably the reason why bacteremia caused by Eggerthella is rarely reported. Half of the cases of Eggerthella bacteremia are induced by the two novel species: E. sinensis and P. hongkongensis [7]. Stinear et al. described an isolate (AF304434) from human feces resembling E. lenta (98% identity) that carries an enterococcal vanB resistance locus probably received via lateral gene transfer or as a result of genetic mutations [9]. Clavel et al. investigated the occurrence and activity of dietary lignans activating bacterial communities in human feces and identified an E. lenta strain (AY937380) with 98.2% sequence similarity to strain VPI 0255T [10]. Lignans are a class of phytoestrogen which can be metabolized to the biologically active enterolignans, enterodiol and enterolactone. The human intestinal microbiota is essential for the conversation of the dietary lignans e.g. secoisolariciresinol diglucoside via secoisolariciresinol (SECO) to the enterolignans. Clavel and co-workers also reported that the dehydroxylation of SECO is catalyzed by Eggerthella lenta [11]. Based on 16S rRNA gene sequence analyses another five uncultured clones with 99% identity to E. lenta were reported at the NCBI BLAST server (status June 2009). These clones were derived from the analyses of feces samples from humans. e.g. associated with obesity [12,13], but also from marine metagenomes [14]

Figure 1 shows the phylogenetic neighborhood of E. lenta strain VPI 0255T in a 16S rRNA based tree. The sequences of the three identical copies of the 16S rRNA gene in the genome differ by three nucleotides from the previously published 16S rRNA sequence generated from ATCC 25559 (AF292375). The slight difference between the genome data and the reported 16S rRNA gene sequence is most likely due to sequencing errors in the previously reported sequence data.

Figure 1.
figure1

Phylogenetic tree of E. lenta strain VPI 0255T and all type strains of the genus Eggerthella as well as the type strains from all other genera of the family Coriobacteriaceae inferred from 1,373 aligned characters [15,16] of the 16S rRNA gene under the maximum likelihood criterion [17]. The branches are scaled in terms of the expected number of substitutions per site. Numbers above branches are support values from 1,000 bootstrap replicates if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [18] are shown in blue, published genomes in bold, including two of which are reported in this issue of SIGS [19,20]

E. lenta strain VPI 0255T was originally isolated from a rectal tumor and described as Gram-positive, non-motile and non-sporulating (Table 1) [1]. Cells are rod shaped and occur singly or in long chains up to 20 elements (Figure 2). The cell size and morphology varies depending on the substrate and the age of the culture. Surface colonies were described as circular to slightly scalloped, convex, shiny, gray and translucent. E. lenta is obligately anaerobic and its optimal growth temperature is 37° C [4]. Growth is stimulated by arginine. The existence of the arginine dihydrolase pathway as an important energy source was described by Sperry and Wilkens in 1976 [26]. E. lenta is asaccharolytic [4,26,29], Gelatin is not liquefied, aesculin is not hydrolyzed and nitrate is reduced [29]. E. lenta is bile-resistant and primarily found in human feces [6].

Figure 2.
figure2

Scanning electron micrograph of E. lenta VPI 0255T (Manfred Rohde, Helmholtz Centre for Infection Biology, Braunschweig)

Table 1. Classification and general features of B. cavernae HKI 0122T in accordance with the MIGS recommendations [21]

Chemotaxonomy

The cell wall of E. lenta strain VPI 0255T contains A1γ-type peptidoglycan glutamic acid occurred in D-form and diaminopimelic acid in meso configuration. Mycolic acids and teichonic acids were not reported. Strain VPI 0255T contains menaquinone MK-6 as the major respiratory lipoquinone (63.7%) and a lower amount of the methylmenaquinone MMK-6 (36.3%) [8,29,31]. As the predominant fatty acids the unbranched saturated 16:0 DMA (29.4%) and the monounsaturated fatty acid 18:1w9c (22.0%) were identified [5,6]. Polar lipids consist of two phospholipids, phosphatidylglycerol and diphosphatidylglycerol, and four glycolipids GL1–GL4 [8].

Genome sequencing and annotation

Genome project history

This organism was selected for sequencing on the basis of each phylogenetic position, and is part of the Genomic Encyclopedia of Bacteria and Archaea project. The genome project is deposited in the Genome OnLine Database [18] and the complete genome sequence 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.

Table 2. Genome sequencing project information

Growth conditions and DNA isolation

E. lenta strain VPI 0255T, DSM 2243, was grown anaerobically in DSMZ medium 209 (Eubacterium lentum Medium [32]) at 37°C. DNA was isolated from 1–1.5 g of cell paste using Qiagen Genomic 500 DNA Kit (Qiagen, Hilden, Germany) following the manufacturer’s protocol without modifications.

Genome sequencing and assembly

The genome was sequenced using a combination of Sanger and 454 sequencing platforms. All general aspects of library construction and sequencing can be found at the JGI website. 454 Pyrosequencing reads were assembled using the Newbler assembler version 1.1.02.15 (Roche). Large Newbler contigs were broken into 4,901 overlapping fragments of 1,000 bp and entered into the assembly as pseudo-reads. The sequences were assigned quality scores based on Newbler consensus q-scores with modifications to account for overlap redundancy and to adjust inflated q-scores. A hybrid 454/Sanger assembly was made using the parallel phrap assembler (High Performance Software, LLC). Possible mis-assemblies were corrected with Dupfinisher or transposon bombing of bridging clones [33]. Gaps between contigs were closed by editing in Consed, custom primer walk or PCR amplification. A total of 358 Sanger finishing reads were produced to close gaps, to resolve repetitive regions, and to raise the quality of the finished sequence. The final assembly consists of 39,464 Sanger and 471,609 pyrosequence (454) reads. Together all sequence types provided 35.5x coverage of the genome. The error rate of the completed genome sequence is less than 1 in 100,000.

Genome annotation

Genes were identified using Prodigal [34] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [35]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGRFam, 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 [36].

Genome properties

The genome is 3,632,260 bp long and comprises one main circular chromosome with a 64.2% GC content (Table 3 and Figure 3). Of the 3,181 genes predicted, 3,123 were protein coding genes, and 58 RNAs. 53 pseudogenes were also identified. A majority of the genes (70.9%) were assigned with a putative function while the remaining genes were annotated as hypothetical proteins. The properties and the statistics of the genome are summarized in Table 3. The distribution of genes into COGs functional categories is presented in Table 4.

Figure 3.
figure3

Graphical circular map of the genome. From outside to the center: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.

Table 3. Genome Statistics
Table 4. Number of genes associated with the general COG functional categories

References

  1. 1.

    Eggerth AH. The Gram-positive non-spore-bearing anaerobic Bacilli of human feces. J Bacteriol 1935; 30:277–299. PubMed

  2. 2.

    Prévot AR. Études de systématique bactérienne. III. Invalidité du genre Bacteroides Castellani et Chalmers. Démembrement et reclassification. Ann Inst Pasteur (Paris) 1938; 60:295.

  3. 3.

    Krasil’nikov NA. Guide to the Bacteria and Actinomycetes [Opredelitel’ Bakterii i Actinomicetov]. Akad. Nauk SSSR, Moscow 1949; 1–830.

  4. 4.

    Moore WEC, Cato EP, Holdeman LV. Eubacterium lentum (Eggerth) Prévot 1938: Emendation of description and designation of the neotype strain. Int J Syst Bacteriol 1971; 21:299–303.

  5. 5.

    Kageyama A, Benno Y, Nakase T. Phylogenetic evidence for transfer of Eubacterium lentum to the genus Eggerthella as Eggerthella lenta gen. nov., comb. nov. Int J Syst Bacteriol 1999; 49:1725–1732. PubMed

  6. 6.

    Wade WG, Downes J, Dymock D, Hiom SJ, Weightman AJ, Dewhirst FE, Paster BJ, Tzellas N, Coleman B. The family Coriobacteriaceae: reclassification of Eubacterium exiguum (Poco et al. 1996) and Peptostreptococcus heliotrinreducens (Lanigan 1976) as Slackia exigua gen. nov., comb. nov. and Slackia heliotrinireducens gen. nov., comb. nov., and Eubacterium lentum (Prevot 1938) as Eggerthella lenta gen. nov., comb. nov. Int J Syst Bacteriol 1999; 49:595–600. PubMed

  7. 7.

    Lau SK, Woo PC, Woo GK, Fung AM, Wong MK, Chan KM, Tam DM, Yuen KY. Eggerthella hongkongensis sp. nov. and Eggerthella sinensis sp. nov., two novel Eggerthella species, account for half of the cases of Eggerthella bacteremia. Diagn Microbiol Infect Dis 2004; 49:255–263 PubMed doi:10.1016/j.diagmicrobio.2004.04.012

  8. 8.

    Würdemann D, Tindall BJ, Pukall R, Lünsdorf H, Strömpl C, Namuth T, Nahrstedt H, Wos-Oxley M, Ott S, Schreiber S, et al. Gordonibacter pamelaeae gen. nov., sp. nov., a new member of the Coriobacteriaceae isolated from a patient with Crohn’s disease, and reclassification of Eggerthella hongkongensis Lau et al. 2006 as Paraeggerthella hongkongensis gen. nov., comb. nov. Int J Syst Evol Microbiol 2009; 59:1405–1415. PubMed doi:10.1099/ijs.0.005900-0

  9. 9.

    Stinear TP, Olden DC, Johnson PDR, Davies JK, Grayson L. Enterococcal vanB resistance locus in anaerobic bacteria in human faeces. Lancet 2001; 357:855–856. PubMed doi:10.1016/S0140-6736(00)04206-9

  10. 10.

    Clavel T, Henderson G, Alpert CA, Philippe C, Rigottier-Gois L, Doré J, Blaut M. Intestinal bacterial communities that produce active estrogenlike compounds enterodiol and enterolactone in humans. Appl Environ Microbiol 2005; 71:6077–6085. PubMed doi:10.1128/AEM.71.10.6077-6085.2005

  11. 11.

    Clavel T, Borrmann D, Braune A, Dore J, Blaut M. Occurrence and activity of human intestinal bacteria involved in the conversion of dietary lignans. Anaerobe 2006; 12:140–147. PubMed doi:10.1016/j.anaerobe.2005.11.002

  12. 12.

    Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: human gut microbes associated with obesity. Nature 2006; 444:1022–1023. PubMed doi:10.1038/4441022a

  13. 13.

    Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, Toyoda A, Takami H, Morita H, Sharma VK, Srivastava TP, et al. Comparative metagenomics revealed commonly enriched gene sets in human gut microbioms. DNA Res 2007; 14:169–181. PubMed doi:10.1093/dnares/dsm018

  14. 14.

    Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen J, Nelson KE, Nelson W, et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 2004; 304:66–74. PubMed doi:10.1126/science.1093857

  15. 15.

    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

  16. 16.

    Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552. PubMed

  17. 17.

    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

  18. 18.

    Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC. The Genomes OnLine Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2008; 36:D475–D479. PubMed doi:10.1093/nar/gkm884

  19. 19.

    Mavrommatis K, Pukall R, Rohde C, Chen F, Sims D, Brettin T, Kuske C, Detter JC, Han C, Lapidus A, et al. Complete genome sequence of Cryptobacterium curtum type strain (12-3T). Stand Genomic Sci 2009; 1: 93–100. doi:10.4056/sigs.15195

  20. 20.

    Copeland A, Sikorski J, Lapidus A, Nolan M, Galvina Del Rio T, Lucas S, Chen F, Tice H, Pitluck S, Cheng JF, et al. Complete genome sequence of Atopobium parvulum type strain (IPP 1246T). Stand Genomic Sci 2009; 1: 166–173-8.doi:10.4056/sigs.15195

  21. 21.

    Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. Towards a richer description of our complete collection of genomes and metagenomes: the “Minimum Information about a Genome Sequence” (MIGS) specification. Nat Biotechnol 2008; 26:541–547. PubMed doi:10.1038/nbt1360

  22. 22.

    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

  23. 23.

    Garrity GM, Holt J. Taxonomic Outline of the Archaea and Bacteria. Bergey’s Manual of Systematic Bacteriology, 2nd Ed. In: G. Garrity GM, Boone DR, Castenholz RW Eds. Vol 1 The Archaea, Deeply Branching and Phototrophic Bacteria. 2001 pp. 155–166

  24. 24.

    Stackebrandt E, Rainey FA, Ward-Rainey NL. Proposal for a New Hierarchic Classification System, Actinobacteria classis nov. Int J Syst Bacteriol 1997; 47:479–491.

  25. 25.

    Garrity GM, Bell JA, Lilburn T. In: Garrity GM, Boone DR, Castenholz RW (2001) Taxonomic outline of the Procaryotes. Bergey’s Manual of Systematic Bacteriology 1–39.

  26. 26.

    Sperry JF, Wilkins TD. Arginine, a growth-limiting factor for Eubacterium lentum. J Bacteriol 1976; 127:780–784. PubMed

  27. 27.

    Lau SKP, Woo PCY, Fung AMY, Chan K, Woo GKS, Yuen K. Anaerobic, non-sporulating, Grampositive bacilli bacteremia characterized by 16S rRNA gene sequencing. J Med Microbiol 2004; 53:1247–1253. PubMed doi:10.1099/jmm.0.45803-0

  28. 28.

    Anonymous. Biological Agents: Technical rules for biological agents www.baua.de, TRBA 466

  29. 29.

    Maruo T, Sakamoto M, Ito C, Toda T, Benno Y. Adlercreutzia equolifaciens gen. nov., sp. nov., an equol-producing bacterium isolated from human faeces, and emended description of the genus Eggerthella. Int J Syst Evol Microbiol 2008; 58:1221–1227. PubMed doi:10.1099/ijs.0.65404-0

  30. 30.

    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 doi:10.1038/75556

  31. 31.

    Fernandez F, Collins MD. Vitamin K composition of anaerobic gut bacteria. FEMS Microbiol Lett 1987; 41:175–180. doi:10.1111/j.1574-6968.1987.tb02191.x

  32. 32.

    List of media used at DSMZ for cell growth: http://www.dsmz.de/microorganisms/media_list.php

  33. 33.

    Sims D, Brettin T, Detter JC, Han C, Lapidus A, Copeland A, lavina Del Rio T, Nolan M, Chen F, Lucas S, et al. Complete genome of Kytococcus sedentarius type strain (541T). Stand Genomic Sci 2009;1:12–20 doi:10.4056/sigs.761

  34. 34.

    Anonymous. Prodigal Prokaryotic Dynamic Programming Genefinding Algorithm. Oak Ridge National Laboratory and University of Tennessee 2009 http://compbio.ornl.gov/prodigal

  35. 35.

    Pati A. Ivanova N, Mikhailova N, Ovchinikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: A Gene Prediction Improvement Pipeline for microbial genomes. (Submitted).

  36. 36.

    Markowitz VM, Mavromatis K, Ivanova NN, Chen I-MA, Chu K, Kyrpides NC. Expert IMG ER: A system for microbial genome annotation expert review and curation. Bioinformatics 2009; 25:2271–2278. PubMed doi:10.1093/bioinformatics/btp393

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Acknowledgements

We would like to gratefully acknowledge the help of Gabriele Gehrich-Schröter for growing E. lenta cultures and Susanne Schneider for DNA extraction and quality analysis (both at DSMZ). This work was performed under the auspices of the US Department of Energy’s 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, as well as German Research Foundation (DFG) INST 599/1-1.

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Correspondence to Cliff Han.

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Saunders, E., Pukall, R., Abt, B. et al. Complete genome sequence of Eggerthella lenta type strain (VPI 0255T). Stand in Genomic Sci 1, 174–182 (2009). https://doi.org/10.4056/sigs.33592

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Keywords

  • mesophile
  • anaerobic
  • human intestinal microflora
  • pathogenic
  • bacteremia
  • Gram-positive
  • Coriobacteriaceae