Microbiome management is critically important given their ability to perform critical functions in waste treatment processes. Since microorganisms are critical to waste treatment plants, understanding the functions of the microbiome is of great importance to develop a suitable environment for efficient product recovery (Foo, Ling, Lee, & Chang, 2017; Oleskowicz-Popiel, 2018) . In line with this goal, waste treatment technologies need to be studied through microbial community interactions. Say no to plagiarism. Get a tailor-made essay on "Why Violent Video Games Shouldn't Be Banned"? Get an original essay To date, many existing and new techniques have been used to elucidate interactions in microbial communities (De los Reyes, Weaver, & Wang, 2015, Rivera-Pinto et al., 2018). Here / In this section we will review the technologies used for the analysis of community structure and microbial activity. Next we will address analyzes for detecting and monitoring microbiomes. Conventional microbiome analysis begins with the isolation of molecules such as DNA or RNA (Koch, Müller, Harms, & Harnisch, 2014). Subsequently the techniques of fingerprints, DGGE (Denaturing Gradient Gel Electrophoresis), TGGE (Temperature Gradient Gel Electrophoresis), SSCP (Single Strand Conformation Polymorphism), T-RFLP (Terminal Restriction Fragment Length Polymorphism) practiced on the basis of research of interest (Koch et al., 2014; Vanwonterghem, Jensen, Ho, Batstone, & Tyson, 2014). The DGGE technique is used to detect community changes. Recently, the DGGE fingering method was used to analyze the microbial consortium in anaerobic glycerol digestion and to characterize the dynamics of the microbial community involved in biogas production (Lim, Ge, & Tong, 2018; Vásquez & Nakasaki, 2018). The SSCP technique detects subtle mutations and is widely used to distinguish different genomic variants in microbial communities. Fingerprinting techniques provide understanding of the metabolic capacity of the microbiome, however they do not allow us to discover the main activities of microorganisms. They need to be combined with additional analyses. The only approach for further fingerprint confirmation takes advantage of marker gene analyses. To identify the phylogeny of the microbial community, two well-known marker genes, 16s rRNA (prokaryotes) and 18s rRNA (eukaryotes) have been capitalized for microbiome analysis in waste treatment technologies (de Jonge, Moset, M�ller, and Nielsen, 2017; Guermazi-Toumi, Chouari and Sghir, 2018, Zhao et al., 2018). In addition to 16s rRNA and 18s rRNA, recent studies have shown that it is possible to develop new marker genes to identify particular microorganisms. Please note: this is just a sample. Get a custom paper from our expert writers now. Get a Custom Assay In one study, hgcA and 16s rRNA genes were exploited as a marker to detect Geobacterracca sp. which plays a role in the Hg methylation pathway in waste treatment plant effluents (Bravo et al., 2018). Another study conducted by Ahmed et al., indicated that a new marker gene, crAssphage, can be used for wastewater pollution management (Ahmed, Payyappat, Cassidy, Besley, & Power, 2018). As in the case of the cited studies, current technologies could also be further explored by developing marker genes for use in microbiomes in waste treatment processes.