Collection |

Gut Microbiota

The microbial communities that inhabit our gastrointestinal tract, termed the gut microbiota, are well known to play a fundamental role in many host processes, and our understanding of these complex communities continues to advance at a rapid pace. Research has characterized the gut microbiota in health and disease at increasing resolution, aided by the continuous development of tools and approaches. Greater mechanistic understanding of how our microbial partners, including the non-bacterial members, contribute to or protect against disease is a major focus of recent initiatives with the ultimate goal of translating these findings into clinical applications.

This collection brings together Research, Reviews and Comment published in several Nature journals covering key topics on the gut microbiota. The selected content has been published over the past year in Nature, Nature Microbiology, Nature Medicine, Nature Genetics, Nature Communications, Nature Reviews Microbiology, Nature Reviews Genetics and Nature Reviews Gastroenterology and Hepatology, some of which have been made freely available for 6 months, thanks to support from Yakult Honsha Co., Ltd.

Core collection

  • Nature | Article

    A screen of more than 1,000 drugs shows that about a quarter of the non-antibiotic drugs inhibit the growth of at least one commensal bacterial strain in vitro.

    • Lisa Maier
    • , Mihaela Pruteanu
    • , Michael Kuhn
    • , Georg Zeller
    • , Anja Telzerow
    • , Exene Erin Anderson
    • , Ana Rita Brochado
    • , Keith Conrad Fernandez
    • , Hitomi Dose
    • , Hirotada Mori
    • , Kiran Raosaheb Patil
    • , Peer Bork
    •  &  Athanasios Typas
  • Nature Genetics | Letter

    Comprehensive fecal metabolic profiling in 786 individuals from TwinsUK provides insights into the influence of host genetics and gut microbial composition on metabolites that may mediate microbiome-associated phenotypes.

    • Jonas Zierer
    • , Matthew A. Jackson
    • , Gabi Kastenmüller
    • , Massimo Mangino
    • , Tao Long
    • , Amalio Telenti
    • , Robert P. Mohney
    • , Kerrin S. Small
    • , Jordana T. Bell
    • , Claire J. Steves
    • , Ana M. Valdes
    • , Tim D. Spector
    •  &  Cristina Menni
  • Nature Reviews Microbiology | Review Article

    Complex microbial communities shape the dynamics of various environments. In this Review, Knight and colleagues discuss the best practices for performing a microbiome study, including experimental design, choice of molecular analysis technology, methods for data analysis and the integration of multiple omics data sets.

    • Rob Knight
    • , Alison Vrbanac
    • , Bryn C. Taylor
    • , Alexander Aksenov
    • , Chris Callewaert
    • , Justine Debelius
    • , Antonio Gonzalez
    • , Tomasz Kosciolek
    • , Laura-Isobel McCall
    • , Daniel McDonald
    • , Alexey V. Melnik
    • , James T. Morton
    • , Jose Navas
    • , Robert A. Quinn
    • , Jon G. Sanders
    • , Austin D. Swafford
    • , Luke R. Thompson
    • , Anupriya Tripathi
    • , Zhenjiang Z. Xu
    • , Jesse R. Zaneveld
    • , Qiyun Zhu
    • , J. Gregory Caporaso
    •  &  Pieter C. Dorrestein

Further Reading

  • Nature Microbiology | Article

    Integration of longitudinal gut metagenomic datasets from children in Finland, Estonia and Russian Karelia reveals high strain-level diversity, which consequently impacts the functional capabilities of the early life microbiome.

    • Tommi Vatanen
    • , Damian R. Plichta
    • , Juhi Somani
    • , Philipp C. Münch
    • , Timothy D. Arthur
    • , Andrew Brantley Hall
    • , Sabine Rudolf
    • , Edward J. Oakeley
    • , Xiaobo Ke
    • , Rachel A. Young
    • , Henry J. Haiser
    • , Raivo Kolde
    • , Moran Yassour
    • , Kristiina Luopajärvi
    • , Heli Siljander
    • , Suvi M. Virtanen
    • , Jorma Ilonen
    • , Raivo Uibo
    • , Vallo Tillmann
    • , Sergei Mokurov
    • , Natalya Dorshakova
    • , Jeffrey A. Porter
    • , Alice C. McHardy
    • , Harri Lähdesmäki
    • , Hera Vlamakis
    • , Curtis Huttenhower
    • , Mikael Knip
    •  &  Ramnik J. Xavier
  • Nature | Article

    Statistical analyses of a metagenomics-sequenced human cohort identify a relatively minor role for genetics in determining microbiome composition and show that several human phenotypes are as strongly associated with the gut microbiome as with host genetics.

    • Daphna Rothschild
    • , Omer Weissbrod
    • , Elad Barkan
    • , Alexander Kurilshikov
    • , Tal Korem
    • , David Zeevi
    • , Paul I. Costea
    • , Anastasia Godneva
    • , Iris N. Kalka
    • , Noam Bar
    • , Smadar Shilo
    • , Dar Lador
    • , Arnau Vich Vila
    • , Niv Zmora
    • , Meirav Pevsner-Fischer
    • , David Israeli
    • , Noa Kosower
    • , Gal Malka
    • , Bat Chen Wolf
    • , Tali Avnit-Sagi
    • , Maya Lotan-Pompan
    • , Adina Weinberger
    • , Zamir Halpern
    • , Shai Carmi
    • , Jingyuan Fu
    • , Cisca Wijmenga
    • , Alexandra Zhernakova
    • , Eran Elinav
    •  &  Eran Segal
  • Nature Medicine | Letter

    Stool microbiota composition correlates with the ethnic backgrounds of people living in the same city, suggesting that geographical location and ethnicity have distinct effects on microbiota.

    • Mélanie Deschasaux
    • , Kristien E. Bouter
    • , Andrei Prodan
    • , Evgeni Levin
    • , Albert K. Groen
    • , Hilde Herrema
    • , Valentina Tremaroli
    • , Guido J. Bakker
    • , Ilias Attaye
    • , Sara-Joan Pinto-Sietsma
    • , Daniel H. van Raalte
    • , Marieke B. Snijder
    • , Mary Nicolaou
    • , Ron Peters
    • , Aeilko H. Zwinderman
    • , Fredrik Bäckhed
    •  &  Max Nieuwdorp
  • Nature Medicine | Letter

    The definition of a 'healthy' microbiome is impacted by geographic regional variations.

    • Yan He
    • , Wei Wu
    • , Hui-Min Zheng
    • , Pan Li
    • , Daniel McDonald
    • , Hua-Fang Sheng
    • , Mu-Xuan Chen
    • , Zi-Hui Chen
    • , Gui-Yuan Ji
    • , Zhong-Dai-Xi Zheng
    • , Prabhakar Mujagond
    • , Xiao-Jiao Chen
    • , Zu-Hua Rong
    • , Peng Chen
    • , Li-Yi Lyu
    • , Xian Wang
    • , Chong-Bin Wu
    • , Nan Yu
    • , Yan-Jun Xu
    • , Jia Yin
    • , Jeroen Raes
    • , Rob Knight
    • , Wen-Jun Ma
    •  &  Hong-Wei Zhou
  • Nature Microbiology | Article

    Here the authors show that the human gut microbiome can recover after a clinically relevant, broad-spectrum antibiotic treatment and characterization of the resistome indicates that antibiotic resistance genes can impact the recovery process.

    • Albert Palleja
    • , Kristian H. Mikkelsen
    • , Sofia K. Forslund
    • , Alireza Kashani
    • , Kristine H. Allin
    • , Trine Nielsen
    • , Tue H. Hansen
    • , Suisha Liang
    • , Qiang Feng
    • , Chenchen Zhang
    • , Paul Theodor Pyl
    • , Luis Pedro Coelho
    • , Huanming Yang
    • , Jian Wang
    • , Athanasios Typas
    • , Morten F. Nielsen
    • , Henrik Bjorn Nielsen
    • , Peer Bork
    • , Jun Wang
    • , Tina Vilsbøll
    • , Torben Hansen
    • , Filip K. Knop
    • , Manimozhiyan Arumugam
    •  &  Oluf Pedersen
  • Nature | Letter

    Finely tuned control of strain engraftment and abundance in the mouse gut microbiota was achieved using the marine polysaccharide porphyran, which could exclusively be used by an introduced subset of wild-type or genetically modified Bacteroides strains.

    • Elizabeth Stanley Shepherd
    • , William C. DeLoache
    • , Kali M. Pruss
    • , Weston R. Whitaker
    •  &  Justin L. Sonnenburg