making microbiology easy

Microbiota: example of achievement

Support of the development of a compound in the context of Crohn disease

Study of the interaction of the compound EB8018 with intestinal bacteria involved in acute over-inflammation in Crohn disease patients.  

Preclinical phase

Demonstrate and validate in vitro the interaction between the compound and the FimH bacterial protein, a key inducer implied into acute over-inflammation in Crohn disease suffering patients

Procedure: Characterization of an AIEC (Adherent Invasive Escherichia coli) strains collection in terms of cell adhesion and aggregation with the compound


Assess the properties of adhesion and invasion of strains isolated from patients, on a intestinal cell line, with and without the compound 

  • Adhesion test of 70 clinical strains to T84 cell line
  • Infection during 2h, MOI 10 to 100
  • Cellular adhesion monitoring by fluorescence measurement after immunolabelling (Microscopy)


Develop an aggregation assay to visualize the interaction between the compound and FimH proteins of strains of interest 

  • Aggregation assay on 110 clinical strains
  • Bacterial culture with different concentrations of the compound, during 5h
  • Visualization of aggregates formed between the compound and the strains (Multimode Spark 10 plaque reader)

Calculation of adhesion % of strains by fluorescence measurement

  • Adherent strains identification
  • Among them, identification of strains affected by the compound (reduction of adhesion)

Identification of the aggregation by quantitative visualization
Categorization of the aggregation level

  • Determination of the strains having aggregated
  • Determination of the effective concentrations of the compound
  • Correlation with the results obtained for adhesion 

Clinical phase

biopsies_projet Takeda

Create a protocol to isolate from intestinal biopsies the “biomarker” bacteria, then confirm and demonstrate their interaction with the compound

Procedure : Characterization of strains from biopsies, in terms of aggregation with the compound


Development of a method to isolate “biomarker” bacteria from 114 intestinal biopsies: customized procedure to isolate and dissociate “adherent” bacteria from “invasive” bacteria 

-Sonication: “adherent” extracts and strains
-Cell lysis with beads: “invasive” extracts and strains


Aggregation assay on extracts and bacteria isolated from intestinal biopsies, with the compound

Example of images obtained for control strains after 5h of incubation

Analysis of aggregation on adherent and invasive biopsy extracts and on isolated strains
For isolated strains showing aggregation, bacterial identification by Maldi-Tof spectrometry

  • Confirmation of the interaction of “bio-marker” bacteria with the compound
  • Categorization of patients according to the aggregation behavior of strains
  • Determination of the rate of patients for whom aggregation was observed
  • Correlation with clinical data

› Tailor-made operating procedures
› Analysis reports and characterized biological samples

› Reports and results in compliance with regulatory requirements
› Data security
› Continuation of the project with the customer for clinical phase II