Microbiology and biotechnology are considered to be traditional fields for fundamental and applied research in Latvia. The State Research Programme No. 2010.10-4/VPP-5 NatRes on the long-term use of the local resources supports investigations focused on the novel biotechnological products and technologies based on ceramic materials. The aim of our study is to test the experimental samples of clay and ceramic beads for determining the new prospective fields for their application in medicine, environmental biotechnology, etc. One of the most important criteria for further technology development is the study on interrelations of different microorganisms with clay and ceramics. Research on ceramic carriers is divided into 3 parts, i.e.: 1) testing of raw material and development of the technology for fabrication of ceramic carriers; 2) biofilm formation onto the surface of ceramic carrier: dynamics and stability; 3) model experiments in the field of environmental biotechnology. Besides, modification of physical and chemical properties of clay treated with microorganisms is studied. Furthermore, within the framework of this Project, an additional prospective direction for further research has been generated, i.e., investigation on antimicrobial properties of natural raw clay and ceramic materials. This paper summarizes the main results obtained in the period from 2010 to 2013, as well as suggests some new prospective directions for further research.