(iii.) Furthermore, the understanding of disease also requires a more holistic view. For example, Helicobacter pylori was until recently considered the strongest risk factor for the development of gastric cancer, which is the fifth most common cancer worldwide. However, recent advances in metagenomics and metaproteomics techniques demonstrated changes in the complete microbiome during gastric carcinogenesis rather than that of single microbes. Hypochlorhydria, a state of low hydrochloric acid levels that affect the stomach's ability to digest and absorb proteins, induces changes in the complete microbiome (reducing diversity and abundance of commensal bacteria and promoting overgrowth of pathogenic and carcinogenic species) that might have a direct linked with gastric cancer . This is further enhanced by the prolonged use of proton pump inhibitors which are widely used medications . Thus, the risk of cancer could be identified by characterizing microbiome alterations in gastric juices and/or feces of patients. Monitoring microbial alterations could also help physicians and healthcare professionals to assess the risks and benefits of using medications such as proton pump inhibitors, to monitor medical care protocols, and to optimize treatments for high-risk patients. Further, metaproteomics can hold the promise to thoroughly investigate (i.) the potential use of phages as antibacterial agents in several clinical conditions, (ii.) to monitor the functional dynamics of their bactericidal effect and (iii.) to monitor therapy response due to the correlation of the bacteria and host proteins. Thereby the unique dimension provided by metaproteomics is that it monitors the functional products of gene expression and therefore reflects the functional dimension of a microbiome.