Project

Identification of L. rhamnosus accessory genetic information

Horizontal gene transfer (HGT), also termed lateral gene transfer (LGT) refers to the transfer of genetic material between organisms other than vertical gene transfer, so independent of replication events [Makarova, 2007].

It is a relevant topic of food safety because in general plasmids contain genes allowing them to adapt to particular environmental conditions like antibiotic resistance genes or genes allowing the bacteria to metabolize certain sugars. For example, within a decade, the usefulness of penicillin was seriously compromised as the horizontal spread caused a plasmidic β-lactamase to become ubiquitous among populations of Staphylococcus aureus [Barlow, 2009].

Upon the recent sequencing of 40 strains belonging to the L. rhamnosus species, due to the constant sizes of some of the genomic contigs obtained and their gene content, the idea that they might contain plasmid DNA emerged.

Aims

1. To investigate the strain variability in terms of presence of plasmids, upon trying different accessory DNA isolating methods.
2. To research the presence and composition of possible plasmids in the L. rhamnosus species by studying a set of 40 strains in vitro and in silico.

Research Approach

The research objective can be reached by answering the following questions:

  • How many plasmids are present in the strains of L. rhamnosus?
  • For the identified plasmids, can we evaluate the sizes?
  • Can the behavior of different L. rhamnosus strains be predicted by means of presence/
  • absence of the plasmid DNA?
  • Based on the genetic information we already have from the genome sequencing, can we
  • identify the plasmid sequences?

Methodology

Plasmid isolation
PCR to test gene presence in E. coli transfected with some of the isolated plasmids
Bio-informatics for exploring the genomes for possible accessory genes

Bibliography:

  • Barlow M (2009). "What antimicrobial resistance has taught us about horizontal gene transfer". Methods in Molecular Biology (Clifton, N.J.). Methods in Molecular Biology 532: 397–411.
  • K.S. Makarova, E.V. Koonin (2007) “Evolutionary genomics of lactic acid bacteria” Journal of Bacteriology, 189, pp. 1199–1208.

Contact

Corina Diana Ceapa
Scientist - Gut & Microbiology Platform
Danone Research - Centre for Specialised Nutrition
Bosrandweg 20 - 6704 PH Wageningen
The Netherlands
Phone: +31 - 317 - 467 871

Email Danone: Corina Ceapa