Gut microbiota density influences host physiology and is shaped by host and microbial factors

Eduardo J. Contijoch, Graham J. Britton, Chao Yang, Ilaria Mogno, Zhihua Li, Ruby Ng, Sean R. Llewellyn, Sheela Hira, Crystal Johnson, Keren M. Rabinowitz, Revital Barkan, Iris Dotan, Robert P. Hirten, Shih Chen Fu, Yuying Luo, Nancy Yang, Tramy Luong, Philippe R. Labrias, Sergio Lira, Inga PeterAri Grinspan, Jose C. Clemente, Roman Kosoy, Seunghee Kim-Schulze, Xiaochen Qin, Anabella Castillo, Amanda Hurley, Ashish Atreja, Jason Rogers, Farah Fasihuddin, Merjona Saliaj, Amy Nolan, Pamela Reyes-Mercedes, Carina Rodriguez, Sarah Aly, Kenneth Santa-Cruz, Lauren Peters, Mayte Suárez-Fariñas, Ruiqi Huang, Ke Hao, Jun Zhu, Bin Zhang, Bojan Losic, Haritz Irizar, Won Min Song, Antonio Di Narzo, Wenhui Wang, Benjamin L. Cohen, Christopher DiMaio, David Greenwald, Steven Itzkowitz, Aimee Lucas, James Marion, Elana Maser, Ryan Ungaro, Steven Naymagon, Joshua Novak, Brijen Shah, Thomas Ullman, Peter Rubin, James George, Peter Legnani, Shannon E. Telesco, Joshua R. Friedman, Carrie Brodmerkel, Scott Plevy, Judy H. Cho, Jean Frederic Colombel, Eric E. Schadt, Carmen Argmann, Marla Dubinsky, Andrew Kasarskis, Bruce Sands, Jeremiah J. Faith

Research output: Contribution to journalArticlepeer-review

75 Scopus citations


To identify factors that regulate gut microbiota density and the impact of varied microbiota density on health, we assayed this fundamental ecosystem property in fecal samples across mammals, human disease, and therapeutic interventions. Physiologic features of the host (carrying capacity) and the fitness of the gut microbiota shape microbiota density. Therapeutic manipulation of microbiota density in mice altered host metabolic and immune homeostasis. In humans, gut microbiota density was reduced in Crohn's disease, ulcerative colitis, and ileal pouch-anal anastomosis. The gut microbiota in recurrent Clostridium difficile infection had lower density and reduced fitness that were restored by fecal microbiota transplantation. Understanding the interplay between microbiota and disease in terms of microbiota density, host carrying capacity, and microbiota fitness provide new insights into microbiome structure and microbiome targeted therapeutics. Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).

Original languageEnglish
Article numbere40553
StatePublished - 22 Jan 2019


  • fecal microbiota transplantation
  • gut microbiome
  • human
  • human biology
  • infectious disease
  • inflammatory bowel disease
  • medicine
  • microbiology
  • microbiota density
  • mouse


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