DIME

Main objectives/results:

SA1- identification of effector proteins

• Effector analysis and selection from genome sequenced reference strains:
  • Identification of  77 genome sequenced reference strains for proteobacterial strains isolated from the human gut 
  • Application of Machine Learning tools for deeper T3SS screening -> 44 strains with 3000 effectors identified/selected
  • Functional (relation to diet/nutrition) and phylogenetic analysis of 44 strains - > 18 strains encoding for 1300 effectors selected
• Effector analysis and selection from metagenome assembled genomes (MAGs):
• Selection of 186 ‘metagenome effectors’ from 16,179 proteobacterial MAGs. 474,871 unique bacterial proteins were screened.

SA2 - Microbiome-human interaction mapping

• cloning success of bacterial effectors: 900 effectors available for interactome mapping
• Y2H pipeline: Screening 17.500 human ORFS against 900 bacterial effector ORFS. Analysis of screen results currently ongoing.
• Interaction prediction: 
  • We have inferred ~800,000 interactions between 2,500 bacterial predicted effectors (including the ‘metagenome effectors’) and the proteins of the human proteome. 
  • We have performed a quality assessment of the predictions using Montecarlo simulations.
  • We have also implemented an interaction specificity filter for predicted human interactors to increase the reliability of the inferences.
• By applying both we finally obtained a set of ~24,000 interactions between 1,125 effectors and 813 human proteins.

SA3 - relate human effector targets to functional and  disease modules

• The European Nucleotide Archive (ENA) and PubMed were extensively searched to identify studies which offered WGS metagenomic data and meta-information about nutrition of the human individuals. 
• In addition, 112 research articles were identified by collaborators which contain primary information about effector targets. Each article was reviewed by 2 persons and a comprehensive tabular overview containing effectors and their experimentally identified targets was created. The Positive Reference Set (PRS) for the mapping pipeline will be selected from these curated interactions. 

SA4 - Verification of human health

• Results expected in the course of deeper analysis of interactions
• Expected project impact:
  • This project aims to shed light on functional and mechanistic questions basis of how microbes actively modulate the host as nutrition-mediated responses. An understanding of the mechanisms by which microbes can influence human molecular processes and ultimately human health will allow precise and informed health prevention and intervention strategies. 
  • Depending on the project results, informed nutritional intervention strategies can be developed to decrease disease risks. Disease modules overlapping with human effector targets can be alleviated by dietary or pharmaceutical interventions.