For the investigation of microbial communities, microbiome metagenomics strategies are utilized as the non-cultural approaches and the high-throughput technologies for the identification of microbes which are beneficial or detrimental for plant and animal growth. The signaling mechanisms, the quorum sensing and the quorum quenching, between microorganisms are known to be involved in the regulation of their growth and development and the symbiotic or the pathogenic relationships with their plant and animal hosts. The study on functional analysis of microbiomes is important for the main purposes of current studies on animal gut, plant rhizosphere and the signaling mechanisms between hosts and microorganisms. The probiotics products and the biological control agents will be developed from the research. Also the bio-industrial enzymes and the anti-microbial nano-agents will be evaluated for further applications.