title: Identification of genetic loci in Lactobacillus plantarum that modulate the immune response of dendritic cells using comparative genome hybridization.
abstract: BACKGROUND
  Probiotics can be used to stimulate or regulate epithelial and immune cells of the intestinal mucosa and generate beneficial mucosal immunomodulatory effects. Beneficial effects of specific strains of probiotics have been established in the treatment and prevention of various intestinal disorders, including allergic diseases and diarrhea. However, the precise molecular mechanisms and the strain-dependent factors involved are poorly understood.
  
  
  RESULTS
  In this study, we aimed to identify gene loci in the model probiotic organism Lactobacillus plantarum WCFS1 that modulate the immune response of host dendritic cells. The amounts of IL-10 and IL-12 secreted by dendritic cells (DCs) after stimulation with 42 individual L. plantarum strains were measured and correlated with the strain-specific genomic composition using comparative genome hybridisation and the Random Forest algorithm. This in silico "gene-trait matching" approach led to the identification of eight candidate genes in the L. plantarum genome that might modulate the DC cytokine response to L. plantarum. Six of these genes were involved in bacteriocin production or secretion, one encoded a bile salt hydrolase and one encoded a transcription regulator of which the exact function is unknown. Subsequently, gene deletions mutants were constructed in L. plantarum WCFS1 and compared to the wild-type strain in DC stimulation assays. All three bacteriocin mutants as well as the transcription regulator (lp_2991) had the predicted effect on cytokine production confirming their immunomodulatory effect on the DC response to L. plantarum. Transcriptome analysis and qPCR data showed that transcript level of gtcA3, which is predicted to be involved in glycosylation of cell wall teichoic acids, was substantially increased in the lp_2991 deletion mutant (44 and 29 fold respectively).
  
  
  CONCLUSIONS
  Comparative genome hybridization led to the identification of gene loci in L. plantarum WCFS1 that modulate the immune response of DCs.
authors.affiliation: Top Institute Food and Nutrition, Wageningen, The Netherlands.
authors.forename: Marjolein
authors.initials: M
authors.lastname: Meijerink
authors.forename: Saskia
authors.initials: S
authors.lastname: van Hemert
authors.forename: Nico
authors.initials: N
authors.lastname: Taverne
authors.forename: Michiel
authors.initials: M
authors.lastname: Wels
authors.forename: Paul
authors.initials: P
authors.lastname: de Vos
authors.forename: Peter A
authors.initials: PA
authors.lastname: Bron
authors.forename: Huub F
authors.initials: HF
authors.lastname: Savelkoul
authors.forename: Jolanda
authors.initials: J
authors.lastname: van Bilsen
authors.forename: Michiel
authors.initials: M
authors.lastname: Kleerebezem
authors.forename: Jerry M
authors.initials: JM
authors.lastname: Wells
mesh_terms: D055028:Comparative Genomic Hybridization; D019295:Computational Biology; D016207:Cytokines / Q000378:metabolism; D003713:Dendritic Cells / Q000276:immunology* / Q000378:metabolism / Q000382:microbiology*; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D055786:Gene Knockout Techniques; D056426:Genetic Loci / Q000235:genetics*; D048191:Lactiplantibacillus plantarum / Q000235:genetics*; D016296:Mutagenesis / Q000235:genetics; D009154:Mutation / Q000235:genetics; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D016207:Cytokines