In the last centuries, new high-throughput technologies, including sequencing and mass-spectrometry, have emerged and are constantly refurbished in order to decipher the molecular code of life. In this review, we summarize the physiological background from genes via transcriptome to proteins and metabolites and discuss the variety of dimensions in which a biological entity may be studied. Herein, we emphasize regulatory processes which underlie the plasticity of molecular profiles on different ome layers. We discuss the four major fields of omic research, namely genomics, transcriptomics, proteomics, and metabolomics, by providing specific examples and case studies for (i) the assessment of functionality on molecular, organism, and community level; (ii) the possibility to use omic research for categorization and systematic efforts; and (iii) the evaluation of responses to environmental cues with a special focus on anthropogenic influences. Thereby, we exemplify the knowledge gains attributable to the integration of information from different omes and the enhanced precision in predicting the phenotype. Lastly, we highlight the advantages of combining multiple omics layers in assessing the complexity of natural systems as meta-communities and -organisms.