Skip to main content

Draft genome sequence of Enterococcus faecium strain LMG 8148


Enterococcus faecium, traditionally considered a harmless gut commensal, is emerging as an important nosocomial pathogen showing increasing rates of multidrug resistance. We report the draft genome sequence of E. faecium strain LMG 8148, isolated in 1968 from a human in Gothenburg, Sweden. The draft genome has a total length of 2,697,490 bp, a GC-content of 38.3 %, and 2,402 predicted protein-coding sequences. The isolation of this strain predates the emergence of E. faecium as a nosocomial pathogen. Consequently, its genome can be useful in comparative genomic studies investigating the evolution of E. faecium as a pathogen.


Enterococci commonly reside in the gastro-intestinal tract of a wide variety of invertebrate and vertebrate hosts, including humans. Since they produce bacteriocins, Enterococcus spp. are widely used as starter cultures for food fermentations or probiotic supplements [1]. Since the 1970s however, they have enigmatically progressed from commensal organisms of little clinical interest to leading nosocomial pathogens causing infections of the urinary tract, bloodstream, and surgical wounds, among others [2]. The large majority of human enterococcal infections are caused by two species: E. faecalis and E. faecium . Worryingly, acquired antibiotic resistance against a multitude of drugs is increasingly being reported in these organisms [3].

Here, we report the draft genome of E. faecium LMG 8148, a strain of human origin isolated in 1968 in Gothenburg, Sweden [4].

Organism information

Classification and features

Enterococcus is a large genus of Gram-positive, non-sporulating, facultative anaerobic, round-shaped, lactic acid-producing bacteria (Table 1) [5]. E. faecium belongs to the family Enterococcaceae , order Lactobacillales , class Bacilli , and phylum Firmicutes . Microscopically, enterococci are often observed as pairs or short chains of cells (Fig. 1) [5]. They were classified as group D streptococci until assigned a separate genus in 1984 [6]. E. faecalis and E. faecium are the two most prominent species within the genus. Enterococci can grow in a wide range of environmental conditions, including temperature (5-50 °C), pH (4.6-9.9), 40 % (w/v) bile salts, and 6.5 % NaCl [7]. To investigate evolutionary relationships with other Enterococcus species and E. faecium strains, a phylogenetic tree was constructed using 16S rDNA sequences (Fig. 2). As expected, E. faecium LMG 8148 forms a cluster with the other E. faecium strains.

Table 1 Classification and general features of Enterococcus faecium strain LMG 8148 according to the MIGS recommendations [8]
Fig. 1

Phase-contrast micrograph of E. faecium LMG 8148

Fig. 2

16S rRNA phylogenetic tree indicating the position of E. faecium LMG 8148 relative to other E. faecium strains and other enterococcal species (type strain = T). Lactobacillus plantarum was included as an outgroup. Genbank accession numbers of the aligned sequences are indicated between brackets. 16S rDNA sequences were aligned using MUSCLE, and the phylogenetic tree was determined using the neighbour-joining algorithm with the Kimura 2-parameter distance model in MEGA (version 7) [27]. A gamma distribution (shape parameter = 1) was used for rate variation among sites. The optimal tree with the sum of branch lengths = 0.1983 is shown, and nodes that appeared in more than 50 % of replicate trees in the bootstrap test (1000 replicates) are marked with their bootstrap support values

Genome sequencing information

Genome project history

The strain LMG 8148 was isolated from a human in Gothenburg (Sweden) in 1968 [4]. The strain was obtained through the Belgian Coordinated Collection of Microorganisms. DNA samples were sequenced at the EMBL GeneCore facility (Heidelberg, Germany) and assembled using CLC Genomics Workbench (version 7.5.1). The draft genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline. This draft whole-genome sequence has been deposited at DDBJ/ENA/GenBank under the accession LOHT00000000. The project information, and its association with MIGS version 2.0 [8], is summarised in Table 2.

Table 2 Project information

Growth conditions and genomic DNA preparation

Bacterial cultures were inoculated from single colonies on lysogeny broth agar in 5 ml of lysogeny broth and grown overnight at 37 °C, with 200 rpm orbital shaking. The DNeasy Blood&Tissue Kit (Qiagen) was used for DNA isolation, following the manufacturer’s instructions and pre-treatment protocol for Gram-positive bacteria. Concentration and purity of isolated DNA was determined spectrophotometrically using the Nanodrop ND-1000 and fluorometrically using Qubit analysis (ThermoFisher Scientific).

Genome sequencing and assembly

100 bp paired-end sequencing was performed on an Illumina HiSeq 2000 machine at the EMBL GeneCore facility in Heidelberg (Germany). The total number of paired reads was 9,317,630. Sequencing data was analysed with the Qiagen CLC Genomics workbench version 7.5.1. After a trimming step for quality (score limit: 0.05) and ambiguous nucleotides (maximum 2 ambiguities), reads were assembled de novo using a mismatch cost of 2, a deletion cost of 3, an insertion cost of 3, length fraction 0.5, and similarity fraction 0.8. The assembly yielded 366 contigs (minimum length 200 bp) with an average coverage of 317× and an average contig length of 7,370 bp (N50 length of 41,184 bp). The total length of the draft genome is 2,697,490 bp with a GC-content of 38.3 %.

Genome annotation

All contigs were annotated using NCBI’s Prokaryotic Genome Annotation Pipeline. Pfam domains [9] in the predicted protein sequences were identified using the Batch Web CD-Search Tool from NCBI [10]. Predicted proteins were classified into COG [11] functional categories using the WebMGA web server for metagenomic analysis [12]. For further characterization of the predicted genes, CRISPRFinder [13], the SignalP 4.1 server [14], and the TMHMM server [15] were used to predict CRISPR repeats, signal peptides, and transmembrane domains, respectively. For the CRISPRFinder tool, only confirmed CRISPRs and not questionable CRISPRs were taken into account.

Genome properties

The properties of this draft genome are summarised in Table 3. Assembly yielded 366 contigs containing 2,697,490 bp with a 38.3 % GC-content. The total number of 2,772 genes predicted by PGAP includes 2,402 protein coding genes (totalling 2,136,945 base pairs), 303 pseudo genes, and 67 RNA genes (56 tRNA and 11 rRNA genes). For 19.37 % of the protein-coding genes, no putative function was assigned, and these were annotated as hypothetical proteins. Further characteristics of the predicted genes are given in Table 3, and classification into functional COG categories is shown in Table 4.

Table 3 Genome statistics
Table 4 Number of genes associated with general COG functional categories


The presented genome sequence is from a strain isolated in 1968, and thus precedes the emergence of enterococci as important causative agents of hospital-acquired infections in the 1970s and 1980s [2]. Consequently, this genome could be useful for comparative genomic studies looking to solve the remarkable recent emergence of E. faecium as a notorious nosocomial pathogen.



Clusters of Orthologous Groups


Prokaryotic genome annotation pipeline


  1. 1.

    Werner G, Coque TM, Franz CMAP, Grohmann E, Hegstad K, Jensen L, et al. Antibiotic resistant enterococci - tales of a drug resistance gene trafficker. Int J Med Microbiol. 2013;303:360–79.

    CAS  Article  PubMed  Google Scholar 

  2. 2.

    Gilmore MS, Lebreton F, van Schaik W. Genomic transition of enterococci from gut commensals to leading causes of multidrug-resistant hospital infection in the antibiotic era. Curr Opin Microbiol. 2013;16:10.

    Article  PubMed  PubMed Central  Google Scholar 

  3. 3.

    Hollenbeck BL, Rice LB. Intrinsic and acquired resistance mechanisms in enterococcus. Virulence. 2012;3:421–33.

    Article  PubMed  PubMed Central  Google Scholar 

  4. 4.

    Descheemaeker P, Lammens C, Pot B, Vandamme P, Goossens H. Evaluation of arbitrarily primed PCR analysis and pulsed-field gel electrophoresis of large genomic DNA fragments for identification of enterococci important in human medicine. Int J Syst Bacteriol. 1997;47:555–61.

    CAS  Article  PubMed  Google Scholar 

  5. 5.

    Murray BE. The life and times of the enterococcus. Clin Microbiol Rev. 1990;3:46–65.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  6. 6.

    Schleifer KH, Kilpper-Bälz R. Transfer of Streptococcus faecalis and Streptococcus faecium to the genus Enterococcus nom. rev. as Enterococcus faecalis comb. nov. and Enterococcus faecium comb. nov. Int J Syst Bacteriol. 1984;34:31.

    Article  Google Scholar 

  7. 7.

    Fisher K, Phillips C. The ecology, epidemiology and virulence of Enterococcus. Microbiology. 2009;155:1749–57.

    CAS  Article  PubMed  Google Scholar 

  8. 8.

    Field D. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008;26:541–7.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  9. 9.

    Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, et al. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 2016;44:D279–85.

    Article  PubMed  Google Scholar 

  10. 10.

    Marchler-Bauer A, Derbyshire MK, Gonzales NR, Lu S, Chitsaz F, Geer LY, et al. CDD: NCBI’s conserved domain database. Nucleic Acids Res. 2015;43:D222–6.

    Article  PubMed  Google Scholar 

  11. 11.

    Galperin MY, Makarova KS, Wolf YI, Koonin EV. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res. 2015;43:D261–9.

    Article  PubMed  Google Scholar 

  12. 12.

    Wu S, Zhu Z, Fu L, Niu B, Li W. WebMGA: a customizable web server for fast metagenomic sequence analysis. BMC Genomics. 2011;12:444.

    Article  PubMed  PubMed Central  Google Scholar 

  13. 13.

    Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 2007;35:52–7.

    Article  Google Scholar 

  14. 14.

    Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods. 2011;8:785–6.

    CAS  Article  PubMed  Google Scholar 

  15. 15.

    Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 2001;305:567–80.

    CAS  Article  PubMed  Google Scholar 

  16. 16.

    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;87:4576–9.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  17. 17.

    Gibbons NE, Murray RGE. Proposals concerning the higher taxa of bacteria. Int J Syst Bacteriol. 1978;28:1–6.

    Article  Google Scholar 

  18. 18.

    Ludwig W, Schleifer KH, Whitman WB. Class I. Bacilli class nov. In: Vos P, Garrity G, Jones D, et al., editors. Bergey’s Manual of Systematic Bacteriology, vol. 3. New York: Springer; 2009. p. 19–20.

    Google Scholar 

  19. 19.

    List editor. List of new names and new combinations previously effectively, but not validly, published. List no. 132. Int. J. Syst. Evol. Microbiol. 2010;60:469–472.

  20. 20.

    Ludwig W, Schleifer KH, Whitman WB. Order II. Lactobacillales ord. nov. In: Vos P, Garrity G, Jones D, et al., editors. Bergey’s Manual of Systematic Bacteriology. Vol 3. New York: Springer; 2009. p. 464.

    Google Scholar 

  21. 21.

    Ludwig W, Schleifer KH, Whitman WB. Family IV. Enterococcaceae fam. nov. In: Vos P, Garrity G, Jones D, et al., editors. Bergey’s Manual of Systematic Bacteriology. Vol 3. New York: Springer; 2009. p. 594.

    Google Scholar 

  22. 22.

    Amyes SGB. Enterococci and streptococci. Int J Antimicrob Agents. 2007;29 Suppl 3:S43–52.

    Article  PubMed  Google Scholar 

  23. 23.

    Van den Berghe E, De Winter T, De Vuyst L. Enterocin A production by Enterococcus faecium FAIR-E 406 is characterised by a temperature- and pH-dependent switch-off mechanism when growth is limited due to nutrient depletion. Int J Food Microbiol. 2006;107:159–70.

    Article  PubMed  Google Scholar 

  24. 24.

    Vaningelgem F, Ghijsels V, Tsakalidou E, De Vuyst L. Cometabolism of citrate and glucose by Enterococcus faecium FAIR-E 198 in the absence of cellular growth. Appl Environ Microbiol. 2006;72:319–26.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  25. 25.

    Audisio MC, Oliver G, Apella MC. Effect of different complex carbon sources on growth and bacteriocin synthesis of Enterococcus faecium. Int J Food Microbiol. 2001;63:235–41.

    CAS  Article  PubMed  Google Scholar 

  26. 26.

    Ashburner M, Ball CA, Blake JA. Gene Ontology: tool for the unification of biology. Nat Genet. 2000;25:25–9.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  27. 27.

    Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33(7):1870–4.

    Article  PubMed  Google Scholar 

Download references


JEM and BVDB are recipients of a fellowship from the Agency for Innovation by Science and Technology (IWT) and the Research Foundation Flanders (FWO), respectively. This work was supported by grants from the KU Leuven Research Council (PF/10/010 “NATAR”, IDO/09/01), the Interuniversity Attraction Poles program initiated by the Belgian Science Policy Office (IAP P7/28) and the FWO (grants G.0413.10, G.0471.12 N, G.0B25.15 N). The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Authors' contributions

JEM performed the experiments, analysed the data, and wrote the manuscript. BVDB and MF helped analysing the data and edited the manuscript. JM initiated and supervised the study, and edited the manuscript. All authors read and approved the final manuscript.

Competing interests

The authors declare that they have no competing interests.

Author information



Corresponding author

Correspondence to Jan Michiels.

Rights and permissions

Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (, which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Michiels, J.E., Van den Bergh, B., Fauvart, M. et al. Draft genome sequence of Enterococcus faecium strain LMG 8148. Stand in Genomic Sci 11, 63 (2016).

Download citation


  • Draft genome
  • Gut commensal
  • Nosocomial pathogen
  • Enterococcus faecium
  • Human isolate