The gastrointestinal tract is home to a multitude of bacteria, and it is clear now that the intestinal microbiota plays a major role in modulating the host immune response and in the defence against pathogens. Matthias Mann studied mathematics and physics in Göttingen and obtained his PhD from Yale University where he worked with John Fenn on electrospray mass spectrometry (for which John Fenn was awarded the Nobel Prize in Chemistry in 2002). Recently Matthias Mann's group reported the proteome of a single cancer cell type, thereby providing proof of principle for clinical proteomics which will allow very precisely quantifying and cataloguing thousands of proteins that may be used as biomarkers or protein signatures to guide clinicians in diagnosis, prognosis and better adapted treatment of human diseases.