Emerging Priorities for Microbiome Research

Chad M Cullen; Kawalpreet K Aneja; Sinem Beyhan; Clara E Cho; Stephen Woloszynek; Matteo Convertino; Sophie J McCoy; Yanyan Zhang; Matthew Z Anderson; David Alvarez-Ponce; Ekaterina Smirnova; Lisa Karstens; Pieter C Dorrestein; Hongzhe Li; Ananya Sen Gupta; Kevin Cheung; Jennifer Gloeckner Powers; Zhengqiao Zhao; Gail L Rosen

doi:10.3389/fmicb.2020.00136

Emerging Priorities for Microbiome Research

Front Microbiol. 2020 Feb 19:11:136. doi: 10.3389/fmicb.2020.00136. eCollection 2020.

Authors

Chad M Cullen¹, Kawalpreet K Aneja², Sinem Beyhan³, Clara E Cho⁴, Stephen Woloszynek^{5

6}, Matteo Convertino⁷, Sophie J McCoy⁸, Yanyan Zhang⁹, Matthew Z Anderson^{10

11}, David Alvarez-Ponce¹², Ekaterina Smirnova¹³, Lisa Karstens^{14

15}, Pieter C Dorrestein¹⁶, Hongzhe Li¹⁷, Ananya Sen Gupta¹⁸, Kevin Cheung¹⁹, Jennifer Gloeckner Powers¹⁹, Zhengqiao Zhao⁵, Gail L Rosen^{1

5}

Affiliations

¹ School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, United States.
² The School District of Philadelphia, Philadelphia, PA, United States.
³ Department of Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, United States.
⁴ Department of Nutrition, Dietetics and Food Sciences, Utah State University, Logan, UT, United States.
⁵ Ecological and Evolutionary Signal-processing and Informatics Laboratory (EESI), Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States.
⁶ College of Medicine, Drexel University, Philadelphia, PA, United States.
⁷ Nexus Group, Faculty of Information Science and Technology, Gi-CoRE Station for Big Data & Cybersecurity, Hokkaido University, Sapporo, Japan.
⁸ Department of Biological Science, Florida State University, Tallahassee, FL, United States.
⁹ Department of Civil Engineering, New Mexico State University, Las Cruces, NM, United States.
¹⁰ Department of Microbiology, The Ohio State University, Columbus, OH, United States.
¹¹ Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States.
¹² Department of Biology, University of Nevada, Reno, Reno, NV, United States.
¹³ Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, United States.
¹⁴ Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, United States.
¹⁵ Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, United States.
¹⁶ Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, United States.
¹⁷ Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
¹⁸ Department of Electrical and Computer Engineering, The University of Iowa, Iowa City, IA, United States.
¹⁹ Department of Dermatology, The University of Iowa, Iowa City, IA, United States.

Abstract

Microbiome research has increased dramatically in recent years, driven by advances in technology and significant reductions in the cost of analysis. Such research has unlocked a wealth of data, which has yielded tremendous insight into the nature of the microbial communities, including their interactions and effects, both within a host and in an external environment as part of an ecological community. Understanding the role of microbiota, including their dynamic interactions with their hosts and other microbes, can enable the engineering of new diagnostic techniques and interventional strategies that can be used in a diverse spectrum of fields, spanning from ecology and agriculture to medicine and from forensics to exobiology. From June 19-23 in 2017, the NIH and NSF jointly held an Innovation Lab on Quantitative Approaches to Biomedical Data Science Challenges in our Understanding of the Microbiome. This review is inspired by some of the topics that arose as priority areas from this unique, interactive workshop. The goal of this review is to summarize the Innovation Lab's findings by introducing the reader to emerging challenges, exciting potential, and current directions in microbiome research. The review is broken into five key topic areas: (1) interactions between microbes and the human body, (2) evolution and ecology of microbes, including the role played by the environment and microbe-microbe interactions, (3) analytical and mathematical methods currently used in microbiome research, (4) leveraging knowledge of microbial composition and interactions to develop engineering solutions, and (5) interventional approaches and engineered microbiota that may be enabled by selectively altering microbial composition. As such, this review seeks to arm the reader with a broad understanding of the priorities and challenges in microbiome research today and provide inspiration for future investigation and multi-disciplinary collaboration.

Keywords: gut microbiome; microbial forensics; microbiome ecology; microbiome evolution; microbiome interactions; prebiotics; probiotics; skin microbiome.

Publication types

Review