Advances in Environmental Microbiology: A Multi-omic Perspective

In the last decade, significant progress has been made in research related to various metabolic phenomena in biological organisms, ranging from clinical to environmental studies, as a result of technological developments. Studies in genomics, including metagenomics, as well as transcriptomics and proteomics, have advanced exponentially since the launching of the Human Genome Consortium in the 1990s. In order to delve deep into a holistic approach of the biological system, combining all of these methodologies has become necessary due to the rapid development of metabolomics and its complementation to earlier studies. Since 2008, combinational studies, often known as “multi-omics,” have attracted attention. Transcriptomics, proteomics, metabolomics, and other main disciplines are combined with smaller omics-based techniques, such as lipidomics and fluxomics, in multi-omic research to provide a comprehensive knowledge of a whole biological system. Advances in omic technology have allowed for a deeper understanding of the functional and structural characteristics of microbial communities, leading to a notable surge in the use of blended multi-omic research of microbiomes in recent years. Recent advancements in microbial bioremediation have been propelled by the creation of various advanced tools enabling the comprehensive study of microbes. These tools encompass those designed for genome analysis (genomics), protocols for the examination of expressed proteins and enzymes (proteomics), techniques for the analysis of ribonucleic acids (RNAs) and transcriptomes (transcriptomics), as well as tools for study of metabolic end products and metabolomes (metabolomics). This chapter endeavors to establish connections between conventional and state-of-the-art technologies by exploring the integration of traditional methods with advanced techniques like metagenomics, metatranscriptomics, metaproteomics, and metabolomics. The chapter further illustrates its points through the presentation of case studies across diverse domains, encompassing human health, industrial biotechnology, and environmental studies among other areas.