Archives of Microbiology

, Volume 196, Issue 6, pp 423–433 | Cite as

Transcriptome analysis of Enterococcus faecalis toward its adaption to surviving in the mouse intestinal tract

  • Angela G. Lindenstrauß
  • Matthias A. Ehrmann
  • Jürgen Behr
  • Richard Landstorfer
  • Dirk Haller
  • R. Balfour Sartor
  • Rudi F. VogelEmail author
Original Paper


We have performed a transcriptomic in vivo study with Enterococcus faecalis OG1RF in the intestine of living mice to identify novel latent and adaptive fitness determinants within E. faecalis. From 2,658 genes that are present in E. faecalis strain OG1RF, 124 genes were identified as significantly differentially expressed within the intestinal tract of living mice as compared to exponential growth in BHI broth. The groups of significantly up- or down-regulated genes consisted of 94 and 30 genes, respectively, for which 46 and 18 a clear annotation to a functionally described protein was found. These included genes involved in energy metabolism (e.g., dhaK and glpK pathway), transport and binding mechanisms (e.g., phosphoenolpyruvate carbohydrate PTS) as well as fatty acid metabolism (fab genes). The novel putative fitness determinants found in this work may be helpful for future studies of E. faecalis adaptation to the intestinal tract, which is also a prerequisite for infection in a compromised or inflamed host.


Enterococcus faecalis Transcriptome analysis in vivo RNAseq 



We thank Dr. Sigrid Kisling (Chair for Biofunctionality of Food, Technische Universität München, Germany) for histology analysis of mouse tissue samples used in this study. We also thank the members of the National Gnotobiotic Rodent Resource Center (University of North Carolina, Chapel Hill, USA) for the generous support during the experiment. This work was supported by GRK 1482 of the German Research Foundation (DFG), NIH grants R01DK53247, P40 OD010995, P30 DK34987 and the Crohn’s and Colitis Foundation of America. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.

Supplementary material

203_2014_982_MOESM1_ESM.docx (52 kb)
Supplementary material 1 (DOCX 51 kb)
203_2014_982_MOESM2_ESM.docx (52 kb)
Supplementary material 2 (DOCX 51 kb)
203_2014_982_MOESM3_ESM.pptx (44 kb)
Supplementary material 3 (PPTX 43 kb)


  1. Bickhart DM, Benson DR (2011) Transcriptomes of Frankia sp. strain CcI3 in growth transitions. BMC Microbiol 11:192. doi: 10.1186/1471-2180-11-192 PubMedCentralPubMedCrossRefGoogle Scholar
  2. Bizzini A et al (2010) Glycerol is metabolized in a complex and strain-dependent manner in Enterococcus faecalis. J Bacteriol 192:779–785. doi: 10.1128/JB.00959-09 PubMedCentralPubMedCrossRefGoogle Scholar
  3. Bohle LA et al (2010) Identification of proteins related to the stress response in Enterococcus faecalis V583 caused by bovine bile. Proteome Sci 8:37. doi: 10.1186/1477-5956-8-37 PubMedCentralPubMedCrossRefGoogle Scholar
  4. Bourgogne A et al (2008) Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF. Genome Biol 9:R110. doi: 10.1186/gb-2008-9-7-r110 PubMedCentralPubMedCrossRefGoogle Scholar
  5. Centeno JA, Menendez S, Hermida M, Rodriguez-Otero JL (1999) Effects of the addition of Enterococcus faecalis in Cebreiro cheese manufacture. Int J Food Microbiol 48:97–111PubMedCrossRefGoogle Scholar
  6. Contesse G, Crepin M, Gros F, Ullmann A, Monod J (1969) On the mechanism of catabolite repression. In: Beckwith JR, Zipser D (eds) The lactose operon. Cold Spring Harbor Laboratory Press, New York, pp 401–415Google Scholar
  7. Corfield AP, Wagner SA, Clamp JR, Kriaris MS, Hoskins LC (1992) Mucin degradation in the human colon: production of sialidase, sialate O-acetylesterase, N-acetylneuraminate lyase, arylesterase, and glycosulfatase activities by strains of fecal bacteria. Infect Immun 60:3971–3978PubMedCentralPubMedGoogle Scholar
  8. Denou E, Pridmore RD, Berger B, Panoff JM, Arigoni F, Brussow H (2008) Identification of genes associated with the long-gut-persistence phenotype of the probiotic Lactobacillus johnsonii strain NCC533 using a combination of genomics and transcriptome analysis. J Bacteriol 190:3161–3168. doi: 10.1128/JB.01637-07 PubMedCentralPubMedCrossRefGoogle Scholar
  9. Deutscher J, Sauerwald H (1986) Stimulation of dihydroxyacetone and glycerol kinase activity in Streptococcus faecalis by phosphoenolpyruvate-dependent phosphorylation catalyzed by enzyme I and HPr of the phosphotransferase system. J Bacteriol 166:829–836PubMedCentralPubMedGoogle Scholar
  10. Deutscher J, Francke C, Postma PW (2006) How phosphotransferases system-related protein phosphorylation regulates carbohydrate metabolism in bacteria. Microbiol Mol Biol Rev 70:939–1031. doi: 10.1128/MMBR.00024-06 PubMedCentralPubMedCrossRefGoogle Scholar
  11. Dunny GM, Brown BL, Clewell DB (1978) Induced cell aggregation and mating in Streptococcus faecalis: evidence for a bacterial sex pheromone. Proc Natl Acad Sci USA 75:3479–3483PubMedCentralPubMedCrossRefGoogle Scholar
  12. Flahaut S, Hartke A, Giard J-C, Benachour A, Boutibonnes P, Auffray Y (1996) Relationship between stress response toward bile salts, acid and heat treatment in Enterococcus faecalis. FEMS Microbiol Lett 138:49–54PubMedCrossRefGoogle Scholar
  13. Flahaut S, Hartke A, Giard J-C, Auffray Y (1997) Alkaline stress response in Enterococcus faecalis: adaptation, cross-protection, and changes in protein synthesis. Appl Environ Microbiol 63:812–814PubMedCentralPubMedGoogle Scholar
  14. Franceschini A et al (2013) STRING v9.1: protein–protein interaction networks, with increased coverage and integration. Nucleic Acids Res 41:D808–D815. doi: 10.1093/nar/gks1094 PubMedCentralPubMedCrossRefGoogle Scholar
  15. Fujiwara S, Shinkai H, Deutzmann R, Paulsson M, Timpl R (1988) Structure and distribution of N-linked oligosaccharide chains on various domains of mouse tumour laminin. Biochem J 252:453–461PubMedCentralPubMedGoogle Scholar
  16. Furukawa K, Roberts DD, Endo T, Kobata A (1989) Structural study of the sugar chains of human platelet thrombospondin. Arch Biochem Biophys 270:302–312PubMedCrossRefGoogle Scholar
  17. Gold OG, Jordan HV, van Houte J (1975) The prevalence of enterococci in the human mouth and their pathogenicity in animal models. Arch Oral Biol 20:473–477PubMedCrossRefGoogle Scholar
  18. Hanin A et al (2010) Screening of in vivo activated genes in Enterococcus faecalis during insect and mouse infections and growth in urine. PLoS ONE 5:e11879. doi: 10.1371/journal.pone.0011879 PubMedCentralPubMedCrossRefGoogle Scholar
  19. Heath RJ, Rock CO (2004) Fatty acid biosynthesis as a target for novel antibacterials. Curr Opin Investig Drugs 5:146–153PubMedCentralPubMedGoogle Scholar
  20. Henkin TM, Grundy FJ, Nicholson WL, Chambliss GH (1991) Catabolite repression of alpha-amylase gene expression in Bacillus subtilis involves a trans-acting gene product homologous to the Escherichia coli lacl and galR repressors. Mol Microbiol 5:575–584PubMedCrossRefGoogle Scholar
  21. Hufnagel M, Koch S, Creti R, Baldassarri L, Huebner J (2004) A putative sugar-binding transcriptional regulator in a novel gene locus in Enterococcus faecalis contributes to production of biofilm and prolonged bacteremia in mice. J Infect Dis 189:420–430. doi: 10.1086/381150 PubMedCrossRefGoogle Scholar
  22. Jin J et al (2012) Mechanism analysis of acid tolerance response of Bifidobacterium longum subsp. longum BBMN 68 by gene expression profile using RNA-sequencing. PLoS ONE 7:e50777. doi: 10.1371/journal.pone.0050777 PubMedCentralPubMedCrossRefGoogle Scholar
  23. Johansson ME, Larsson JM, Hansson GC (2011) The two mucus layers of colon are organized by the MUC2 mucin, whereas the outer layer is a legislator of host-microbial interactions. Proc Natl Acad Sci USA 108(Suppl 1):4659–4665. doi: 10.1073/pnas.1006451107 PubMedCentralPubMedCrossRefGoogle Scholar
  24. Kang S, Denman SE, Morrison M, Yu Z, McSweeney CS (2009) An efficient RNA extraction method for estimating gut microbial diversity by polymerase chain reaction. Curr Microbiol 58:464–471. doi: 10.1007/s00284-008-9345-z PubMedCrossRefGoogle Scholar
  25. Koide N, Muramatsu T (1974) Endo-beta-N-acetylglucosaminidase acting on carbohydrate moieties of glycoproteins. Purification and properties of the enzyme from Diplococcus pneumoniae. J Biol Chem 249:4897–4904PubMedGoogle Scholar
  26. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25. doi: 10.1186/gb-2009-10-3-r25 PubMedCentralPubMedCrossRefGoogle Scholar
  27. Leboeuf C, Leblanc L, Auffray Y, Hartke A (2000) Characterization of the ccpA gene of Enterococcus faecalis: identification of starvation-inducible proteins regulated by ccpA. J Bacteriol 182:5799–5806PubMedCentralPubMedCrossRefGoogle Scholar
  28. Leimena MM, Wels M, Bongers RS, Smid EJ, Zoetendal EG, Kleerebezem M (2012) Comparative analysis of Lactobacillus plantarum WCFS1 transcriptomes by using DNA microarray and next-generation sequencing technologies. Appl Environ Microbiol 78:4141–4148. doi: 10.1128/AEM.00470-12 PubMedCentralPubMedCrossRefGoogle Scholar
  29. Li H et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079. doi: 10.1093/bioinformatics/btp352 PubMedCentralPubMedCrossRefGoogle Scholar
  30. Lindenstrauss AG, Pavlovic M, Bringmann A, Behr J, Ehrmann MA, Vogel RF (2011) Comparison of genotypic and phenotypic cluster analyses of virulence determinants and possible role of CRISPR elements towards their incidence in Enterococcus faecalis and Enterococcus faecium. Syst Appl Microbiol 34:553–560. doi: 10.1016/j.syapm.2011.05.002 PubMedCrossRefGoogle Scholar
  31. Marchesini B, Bruttin A, Romailler N, Moreton RS, Stucchi C, Sozzi T (1992) Microbiological events during commercial meat fermentations. J Appl Bacteriol 73:203–209PubMedCrossRefGoogle Scholar
  32. Metaxopoulos J, Samelis S, Papaedlli M (2001) Technological and microbiological evaluation of traditional processes as modified for the industrial manufacturing of dry fermented sausages in Greece. Ital J Food Sci 13:3–18Google Scholar
  33. Nallapareddy SR, Qin X, Weinstock GM, Hook M, Murray BE (2000) Enterococcus faecalis adhesin, ace, mediates attachment to extracellular matrix proteins collagen type IV and laminin as well as collagen type I. Infect Immun 68:5218–5224PubMedCentralPubMedCrossRefGoogle Scholar
  34. Nieto-Arribas P, Sesena S, Poveda JM, Chicon R, Cabezas L, Palop L (2011) Enterococcus populations in artisanal Manchego cheese: biodiversity, technological and safety aspects. Food Microbiol 28:891–899. doi: 10.1016/ PubMedCrossRefGoogle Scholar
  35. Opsata M, Nes IF, Holo H (2010) Class IIa bacteriocin resistance in Enterococcus faecalis V583: the mannose PTS operon mediates global transcriptional responses. BMC Microbiol 10:224. doi: 10.1186/1471-2180-10-224 PubMedCentralPubMedCrossRefGoogle Scholar
  36. Patwa LG et al (2011) Chronic intestinal inflammation induces stress-response genes in commensal Escherichia coli. Gastroenterology 141(5):e1842–e1851. doi: 10.1053/j.gastro.2011.06.064 CrossRefGoogle Scholar
  37. Qin X, Singh KV, Weinstock GM, Murray BE (2000) Effects of Enterococcus faecalis fsr genes on production of gelatinase and a serine protease and virulence. Infect Immun 68:2579–2586PubMedCentralPubMedCrossRefGoogle Scholar
  38. Richards MJ, Edwards JR, Culver DH, Gaynes RP (2000) Nosocomial infections in combined medical-surgical intensive care units in the United States. Infect Control Hosp Epidemiol 21:510–515. doi: 10.1086/501795 PubMedCrossRefGoogle Scholar
  39. Roberts G, Homer KA, Tarelli E, Philpott-Howard J, Devriese LA, Beighton D (2001) Distribution of endo-beta-N-acetylglucosaminidase amongst enterococci. J Med Microbiol 50:620–626PubMedGoogle Scholar
  40. Shankar N, Lockatell CV, Baghdayan AS, Drachenberg C, Gilmore MS, Johnson DE (2001) Role of Enterococcus faecalis surface protein Esp in the pathogenesis of ascending urinary tract infection. Infect Immun 69:4366–4372. doi: 10.1128/IAI.69.7.4366-4372.2001 PubMedCentralPubMedCrossRefGoogle Scholar
  41. Steck N et al (2011) Enterococcus faecalis metalloprotease compromises epithelial barrier and contributes to intestinal inflammation. Gastroenterology 141:959–971. doi: 10.1053/j.gastro.2011.05.035 PubMedCrossRefGoogle Scholar
  42. Sutrina SL, McGeary T, Bourne CA (2007) The phosphoenolpyruvate:sugar phosphotransferase system and biofilms in gram-positive bacteria. J Mol Microbiol Biotechnol 12:269–272. doi: 10.1159/000099648 PubMedCrossRefGoogle Scholar
  43. Vebo HC, Snipen L, Nes IF, Brede DA (2009) The transcriptome of the nosocomial pathogen Enterococcus faecalis V583 reveals adaptive responses to growth in blood. PLoS ONE 4:e7660. doi: 10.1371/journal.pone.0007660 PubMedCentralPubMedCrossRefGoogle Scholar
  44. Vebo HC, Solheim M, Snipen L, Nes IF, Brede DA (2010) Comparative genomic analysis of pathogenic and probiotic Enterococcus faecalis isolates, and their transcriptional responses to growth in human urine. PLoS ONE 5:e12489. doi: 10.1371/journal.pone.0012489 PubMedCentralPubMedCrossRefGoogle Scholar
  45. Ward DE, Ross RP, van der Weijden CC, Snoep JL, Claiborne A (1999) Catabolism of branched-chain alpha-keto acids in Enterococcus faecalis: the bkd gene cluster, enzymes, and metabolic route. J Bacteriol 181:5433–5442PubMedCentralPubMedGoogle Scholar
  46. Ward DE, van Der Weijden CC, van Der Merwe MJ, Westerhoff HV, Claiborne A, Snoep JL (2000) Branched-chain alpha-keto acid catabolism via the gene products of the bkd operon in Enterococcus faecalis: a new, secreted metabolite serving as a temporary redox sink. J Bacteriol 182:3239–3246PubMedCentralPubMedCrossRefGoogle Scholar
  47. Whitehouse NL, Olson VM, Schwab CG, Chesbro WR, Cunningham KD, Lykos T (1994) Improved techniques for dissociating particle-associated mixed ruminal microorganisms from ruminal digesta solids. J Anim Sci 72:1335–1343PubMedGoogle Scholar
  48. Wunderlich PF et al (1989) Double-blind report on the efficacy of lactic acid-producing Enterococcus SF68 in the prevention of antibiotic-associated diarrhoea and in the treatment of acute diarrhoea. J Int Med Res 17:333–338PubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Angela G. Lindenstrauß
    • 1
  • Matthias A. Ehrmann
    • 1
  • Jürgen Behr
    • 1
  • Richard Landstorfer
    • 2
  • Dirk Haller
    • 3
  • R. Balfour Sartor
    • 4
  • Rudi F. Vogel
    • 1
    Email author
  1. 1.Lehrstuhl für Technische MikrobiologieTechnische Universität MünchenFreisingGermany
  2. 2.Lehrstuhl für Mikrobielle ÖkologieTechnische Universität MünchenFreisingGermany
  3. 3.Lehrstuhl für Ernährung und ImmunologieTechnische Universität MünchenFreisingGermany
  4. 4.Department of Medicine/Division of Gastroenterology and Hepatology, Microbiology and ImmunologyUniversity of North CarolinaChapel HillUSA

Personalised recommendations