Symbiosis, dysbiosis, and rebiosis—The value of metaproteomics in human microbiome monitoring

As just one species in the larger ecosystem, the health and disease status of human beings is highly dependent on other biological species in their environment, both inside and outside of the human body. Since proteins are the major functional building blocks of the biological world, most homeostasis regulations are realized at the protein level. Diagnosis‐oriented monitoring of cross‐species proteostasis will constitute a solid basis for next‐generation preventive medicine. After a brief review of the history and state‐of‐the‐art of metaproteomics in the field of environmental health research, focus of this perspective article will be put on the role of cross‐species joint efforts in symbiosis, dysbiosis, and rebiosis of the human gut during human development, pathogenesis, and aging. The distinctive merit of metaproteomics on health state monitoring will be given special attention. Questions to be addressed include: How this microbial ecosystems in and around humans beings coevolve and stabilize during human development and aging? How the grade of microbial virulence is controlled at the community level? What happens upon temporary or ultimate homeostasis breakdown? How metaproteomics will affect next‐generation diagnostics and preventive medicine? As an increasing amount of data becomes available, researchers need to become ever more hypothesis‐oriented, so as not to be lost in sea of data, but instead efficiently extract the insights from “Big data.” Future directions of metaproteomic research and its integration with other “omics” will be suggested, including the sophisticated use of systems biological approaches such as predictive modeling and simulations, in order to truly serve next‐generation medicine.