Recent advances in metagenomics provide new insights for microbial diversity in naturally occurred microbial communities.Although metagenomics can disclose potential functions present in the whole microbial community, it usually provides poor information of functions of individual microbial species and their interactions.As an alternative approach, single-cell genomics or single-species-taget gemome sequencing, though a still premature technique, is promising to infer functions of individual species and we applied this approach to the study of termite-gut bacteria.