For the investigation of microbial communities, microbiome metagenomics strategies are utilized as non-culture approaches and high-throughput technologies for the identification of microbes beneficial for plant and animal growth and for the investigation of signaling mechanisms between pathogenic microorganisms and their plant and animal hosts. Quorum sensing and quorum quenching are involved in regulating growth and development, symbiotic, and pathogenic mechanisms. It is also essential to investigate the functional analysis and screening of microbiomes from various environments. The purpose of the microbiome metagenomics internship program is to provide techniques for the students to study the microbiomes of animal gut and plant rhizosphere, and the signaling mechanisms between microorganisms for further applications.