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Archives of Microbiology

, Volume 193, Issue 4, pp 287–297 | Cite as

In silico prediction of horizontal gene transfer in Streptococcus thermophilus

  • Catherine Eng
  • Annabelle ThibessardEmail author
  • Morten Danielsen
  • Thomas Bovbjerg Rasmussen
  • Jean-François Mari
  • Pierre LeblondEmail author
Original Paper

Abstract

A combination of gene loss and acquisition through horizontal gene transfer (HGT) is thought to drive Streptococcus thermophilus adaptation to its niche, i.e. milk. In this study, we describe an in silico analysis combining a stochastic data mining method, analysis of homologous gene distribution and the identification of features frequently associated with horizontally transferred genes to assess the proportion of the S. thermophilus genome that could originate from HGT. Our mining approach pointed out that about 17.7% of S. thermophilus genes (362 CDSs of 1,915) showed a composition bias; these genes were called ‘atypical’. For 22% of them, their functional annotation strongly support their acquisition through HGT and consisted mainly in genes encoding mobile genetic recombinases, exopolysaccharide (EPS) biosynthesis enzymes or resistance mechanisms to bacteriophages. The distribution of the atypical genes in the Firmicutes phylum as well as in S. thermophilus species was sporadic and supported the HGT prediction for more than a half (52%, 189). Among them, 46 were found specific to S. thermophilus. Finally, by combining our method, gene annotation and sequence specific features, new genome islands were suggested in the S. thermophilus genome.

Keywords

Gene transfer Genome mining Streptococcus thermophilus 

Supplementary material

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Supplementary material 1 (DOC 100 kb)
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Supplementary material 5 (DOC 67 kb)

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Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Catherine Eng
    • 1
    • 2
  • Annabelle Thibessard
    • 1
    Email author
  • Morten Danielsen
    • 3
    • 4
  • Thomas Bovbjerg Rasmussen
    • 3
    • 4
  • Jean-François Mari
    • 2
  • Pierre Leblond
    • 1
    Email author
  1. 1.Génétique et Microbiologie, UMR UHP-INRA 1128, IFR 110 EFABA, Université de Lorraine, Faculté des Sciences et TechnologiesVandœuvre-lès-NancyFrance
  2. 2.LORIA, UMR CNRS 7503 et INRIA Lorraine, Campus scientifiqueVandœuvre-lès-NancyFrance
  3. 3.Department of AssaysChr. Hansen A/SHørsholmDenmark
  4. 4.Department of Physiology, innovationChr. Hansen A/SHørsholmDenmark

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