The research of Kuipers and his research group is focused on curiosity driven research with a keen eye on biotechnological applications. Kuipers has so far supervised 21 postdoctoral researchers and 35 PhD students in their doctorate research. At the moment (October 2015) he supervises 18 PhD students and 7 postdoctoral researchers. He has been invited more than 180 times to national and international conferences, seminars and congresses to give a lecture.
An important topic of research is the study of the genetics and physiology of bacteria. Among others, the cellular differentiation of bacteria is investigated. Bacteria growing in a culture can develop different characteristics, while their genome remains unchanged. Kuipers stated: ‘Our research has many applications, for example the improvement of protein production in industrial fermentation'.
Another important subject is the production and modification of peptides. These modified peptides (called lantibiotics), are made by bacteria, and can serve as antibiotic. Modified peptides are chemically more stable and retain their function longer than unmodified peptides. This is beneficial for medical applications as a novel class of antibiotics.
Further areas of focus are the molecular biology of: competence, sporulation and bistability in Bacillus subtilis, the reconstruction of gene networks, antimicrobial peptides, antibiotics, mechanisms of pathogenesis, cell wall anchoring, controlled gene expression systems, the subcellular localization of protein, stress response, quorum sensing, regulation of the C- and N-metabolism, natural gene transfer methodologies, plant-biocontrol by Bacilli and Biotechnology applications.