eLife (Jan 2019)
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 Peter,
- Ari 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
Affiliations
- Eduardo J Contijoch
- ORCiD
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, United States; Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States
- Graham J Britton
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, United States; Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States
- Chao Yang
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, United States; Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States
- Ilaria Mogno
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, United States
- Zhihua Li
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, United States
- Ruby Ng
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, United States
- Sean R Llewellyn
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, United States
- Sheela Hira
- Zoo Knoxville, Knoxville, United States
- Crystal Johnson
- Center for Comparative Medicine and Surgery, Icahn School of Medicine at Mount Sinai, New York, United States
- Keren M Rabinowitz
- Division of Gastroenterology, Rabin Medical Center, Petah Tikva, Israel; Felsenstein Medical Research Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Revital Barkan
- Division of Gastroenterology, Rabin Medical Center, Petah Tikva, Israel
- Iris Dotan
- Division of Gastroenterology, Rabin Medical Center, Petah Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Robert P Hirten
- The Dr. Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
- Shih-Chen Fu
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States
- Yuying Luo
- The Dr. Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
- Nancy Yang
- The Dr. Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
- Tramy Luong
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States
- Philippe R Labrias
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States
- Sergio Lira
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, United States
- Inga Peter
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States
- Ari Grinspan
- The Dr. Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
- Jose C Clemente
- ORCiD
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, United States
- Roman Kosoy
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States
- Seunghee Kim-Schulze
- Division of Hematology and Medical Oncology, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, United States
- Xiaochen Qin
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, United States
- Anabella Castillo
- The Dr. Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
- Amanda Hurley
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States
- Ashish Atreja
- The Dr. Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
- Jason Rogers
- The Dr. Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
- Farah Fasihuddin
- The Dr. Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
- Merjona Saliaj
- The Dr. Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
- Amy Nolan
- The Dr. Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
- Pamela Reyes-Mercedes
- The Dr. Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
- Carina Rodriguez
- The Dr. Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
- Sarah Aly
- The Dr. Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
- Kenneth Santa-Cruz
- The Dr. Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
- Lauren Peters
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States; Sema4, Stamford, United States
- Mayte Suárez-Fariñas
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States
- Ruiqi Huang
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States
- Ke Hao
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States
- Jun Zhu
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States
- Bin Zhang
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States
- Bojan Losic
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States
- Haritz Irizar
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States
- Won-Min Song
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States
- Antonio Di Narzo
- ORCiD
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States
- Wenhui Wang
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States
- Benjamin L Cohen
- The Dr. Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
- Christopher DiMaio
- The Dr. Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
- David Greenwald
- The Dr. Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
- Steven Itzkowitz
- The Dr. Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
- Aimee Lucas
- The Dr. Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
- James Marion
- The Dr. Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
- Elana Maser
- The Dr. Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
- Ryan Ungaro
- The Dr. Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
- Steven Naymagon
- The Dr. Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
- Joshua Novak
- The Dr. Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
- Brijen Shah
- The Dr. Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
- Thomas Ullman
- The Dr. Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
- Peter Rubin
- The Dr. Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
- James George
- The Dr. Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
- Peter Legnani
- The Dr. Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
- Shannon E Telesco
- Research and Development, Janssen Pharmaceuticals, Pennsylvania, United States
- Joshua R Friedman
- Research and Development, Janssen Pharmaceuticals, Pennsylvania, United States
- Carrie Brodmerkel
- Research and Development, Janssen Pharmaceuticals, Pennsylvania, United States
- Scott Plevy
- Research and Development, Janssen Pharmaceuticals, Pennsylvania, United States
- Judy H Cho
- ORCiD
- The Dr. Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
- Jean-Frederic Colombel
- The Dr. Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
- Eric E Schadt
- Sema4, Stamford, United States
- Carmen Argmann
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States
- Marla Dubinsky
- Pediatric Gastroenterology and Hepatology, Department of Pediatrics, Susan and Leonard Feinstein IBD Clinical Center, Icahn School of Medicine at Mount Sinai, New York, United States
- Andrew Kasarskis
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States
- Bruce Sands
- The Dr. Henry D Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
- Jeremiah J Faith
- ORCiD
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, United States
- DOI
- https://doi.org/10.7554/eLife.40553
- Journal volume & issue
-
Vol. 8
Abstract
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).
Keywords