A common misconception is that microorganisms typically cause diseases and/or spoil food. In fact, many microbial species degrade (toxic) waste materials, thereby playing key ecological roles. Others produce compounds that can be used as bioactive agents, e.g.,  for medical purposes. Again others are important symbionts for plants, animals, or humans.

Under natural conditions, microorganisms almost never live as single cells or isolated species. They usually live in communities – complex mixtures of numerous different species with a plethora of different features. These features can vary considerably, depending on varying conditions in the media the microorganisms grow in.

Distinguishing between harmful and beneficial microorganisms in natural samples, therefore, is a great scientific challenge. However, often rapid but reliable analyses of microbial communities are indispensable (e.g., in food production or ecosystem research).

The Thuringian research initiative 'MikroPlex', therefore, aims at establishing the scientific basis for the development of rapid, automated technologies to characterize natural microbial communities and their metabolites. The MikroPlex Research Initiative focuses on in situ technologies to identify microorganisms in their natural environment – in complex media such as food or environmental samples.