Editorial pubs.acs.org/jpr
Cite This: J. Proteome Res. XXXX, XXX, XXX−XXX
Proteomics of Communities: Metaproteomics
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has a lot to offer for the study of microbiomes, and we encourage the submission of papers.
ur world is a complex community of many different organisms living together. These communities create ecosystems of dependence, interdependence, synergy, and competition. The development of genomic tools to allow the sequencing of communities of microorganisms laid bare the microorganisms that populate much of the world and form microbiomes. These tools have been effective at identifying unusual activities of organisms found in extreme environments, such as hot springs or deep-sea thermal vents. In one of the more remarkable studies, Venter and colleagues sampled the communities of organisms at various intervals of distance and depth in the oceans of the world to create the Global Ocean Survey. In addition to surveys of the environment, these metagenomic strategies have allowed us to investigate our relationship with microbiomes and have led to fascinating results. It has long been known that the gut microbiome is complex and diverse, but it was difficult to study because a large portion of the microbiome was unculturable. Since only those organisms that could be cultured in the lab were studied, our understanding of the commensal organisms of the gut was limited. The tools of metagenomics dramatically changed our knowledge of the organisms present in our gut as well as other locations in and on the human body. Large-scale DNA sequencing of complex microbiomes began the process of establishing relationships between these organisms and disease. Consequently, metagenomics is revealing that our relationship to microbiomes is complicated, and the right collection of microorganisms can be beneficial to good health. Metagenomics determines the organisms present in a microbiome, but it does not provide information about the metabolic activity that may be occurring within the community of organisms. It tells us what is possible. Knowledge of the metabolic activity of a microbiome will help reveal biochemical relationships of microorganisms to each other and to the host. To provide a measure of the metabolic activity present in the community, an exciting direction in the analysis of the microbiome is the use of proteomic technologies to measure proteins expressed by the community of organisms. Proteomic data can provide information about pathways that are active within the community, and comparisons between healthy and sick individuals can reveal which pathways in microorganisms are beneficial or detrimental for the host. This is an area of research in need of technology development in both methods and informatics to increase the depth of coverage possible in metaproteomic studies. In this issue of the Journal of Proteome Research, Figeys and Zhang describe the exciting field of metaproteomics and present advice on standards for metaproteomic studies. At the Journal of Proteome Research, we are excited about the emerging field of metaproteomics, and we encourage the submission of papers that use the technologies of proteomics to study diseases, develop new methodologies, or develop new informatic tools. We are interested in not only studies that relate to human health but also studies that involve the environment, plants, and animals. We believe that proteomics © XXXX American Chemical Society
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John R. Yates, III, Editor-in-Chief AUTHOR INFORMATION
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John R. Yates, III: 0000-0001-5267-1672 Notes
Views expressed in this editorial are those of the author and not necessarily the views of the ACS.
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DOI: 10.1021/acs.jproteome.9b00276 J. Proteome Res. XXXX, XXX, XXX−XXX
