Bioinformatics laboratory started from February 2013 at Niigata University Graduate School of Medical and Dental Sciences. We have a wide variety of research interests from microbes to human, and also from database construction to clinical application. Our research is based on developing technologies to effectively extract biological knowledge from large amounts of information and understanding principles underlying complex biological systems. Among the wide variety of biological systems, the host-associated system such as symbiosis is the most complicated and thus the most challenging to research. We have recently worked on a major project focusing on human gut microbiomes. Microbes in the human intestine are associated with host human metabolism and can cause various diseases such as diabetes, allergies, and even autism. One major reason why such an immense number of DNAs in microbiomes could be sequenced comes mainly from the advent of the latest DNA sequencers called ‘next generation sequencers (NGS)’. NGS technology allows various bacterial species inhabiting the human intestine to be analyzed. This analysis to handle whole DNA from a particular environment is called metagenome analysis and has been applied to a wide variety of ecosystems. Moreover, this research could successfully open the way for the clinical application of large-scale DNA sequence data that will be produced in enormous quantities in the near future. We are now studying the biological interactions between gut microbes and host human metabolism. Our ultimate goal is to shed light on the causes of various diseases through analyzing complex and entangled biological interaction networks, including bacterial metabolism which is intertwined with human metabolism. Bioinformatics is a new decipline that integrates information science and biology. This field has played and will continue to play an important role as a powerful, promising, and essential technique throughout all the fields of life and medical sciences.