With the advancement of human microbiome research, it is inevitable that a growing number of biobanks will include a collection of microbiota specimens to characterize the microbial communities that inhabit the human body and explore the relationships between the microbiota and their human hosts. Biobanks of human microbiota and their associated genetic information may become a valuable health resource. But, this area of research also presents ethical and social problems, some of which are distinct from those faced by biobanks that (...) store human tissue samples. This paper examines four core issues which are considered highly relevant to microbiome biobanking: the nature of human microbiome samples and how different understandings have an impact on benefit/risk evaluation, privacy, informed consent, and returning the result to participants. We argue that these issues should be addressed early on in microbiome research projects and also call for adjusting or developing new governance mechanism to better accommodate these changes. (shrink)