Microbiome articles within Nature Reviews Gastroenterology & Hepatology


  • Review Article |

    Mitochondria of the intestinal epithelium are vital in intestinal health and disease. This Review provides a comprehensive overview of intestinal epithelial cell mitochondrial dysfunction in inflammatory bowel diseases and colorectal cancer and discusses mitochondrial-targeted therapeutics for these diseases.

    • Parsa S. Haque
    • , Neeraj Kapur
    •  & Arianne L. Theiss
  • Review Article |

    This Review discusses the role of the gut microbiome in the conversion of primary to secondary bile acids and critically evaluates biochemical pathways that are less well understood. Insights into how secondary bile acid derivatives influence host immune function are also described.

    • Jason M. Ridlon
    •  & H. Rex Gaskins
  • Review Article |

    In this Review, Danne and colleagues describe the roles of neutrophils in inflammatory bowel disease, as well as their functions in host–microbiota interactions.

    • Camille Danne
    • , Jurate Skerniskyte
    •  & Harry Sokol
  • Year in Review |

    New light is being shed on the interactions between the gut microbiome, cancer cell signalling and the host immune response. With this knowledge, microbiota-based approaches for improving cancer prevention, prognostication and therapy have started to materialize and will contribute to reducing the global cancer burden.

    • William K. K. Wu
    •  & Jun Yu
  • Review Article |

    The importance of commensal fungi in health and disease is becoming increasingly clear. In this Review, Ost and Round discuss the involvement of the mycobiota in intestinal diseases, and consider potential opportunities to target fungi and their interactions for therapeutic purposes.

    • Kyla S. Ost
    •  & June L. Round
  • News & Views |

    A new study has found that a strain of the gut bacterium Lactiplantibacillus plantarum activates a NOD2–type I interferon–insulin-like growth factor 1 pathway in young mice to partially protect against the deleterious growth effects of a diet deficient in protein and fat. Could live biotherapeutic products or their derivatives unlock the full potential of nutritional interventions against childhood stunting?

    • Chioma Moneme
    •  & Sean R. Moore
  • News & Views |

    In a study published in Nature, new data have highlighted the bacterial strain-level sharing rates of mother–offspring pairs, twins, families, cohabiting individuals and individuals within a population, as well as those between different populations, providing a comprehensive view of the transmission landscape of the intestinal and oral microbiome in humans. These findings highlight the need to reassess diseases currently considered to be non-communicable and underscore the importance of considering social structure and transmissibility in the design of microbial studies.

    • Amira Metwaly
    •  & Dirk Haller
  • Year in Review |

    The gut microbiome field is shifting from association to modulation. Microbiota-based treatments come in many shapes and sizes, ranging from dietary intervention to live bacterial products. Recent methodological advances are instrumental to developing innovative new treatment strategies in microbiome-linked pathologies.

    • Jeroen Raes
  • Review Article |

    Primary sclerosing cholangitis (PSC) is closely associated with inflammatory bowel disease (IBD) and potentially provides unique insights into the gut–liver axis. This Review explores these links and provides an overview of the gut microbiome in PSC, including PSC–IBD, exploring related hypotheses of disease mechanisms.

    • Johannes R. Hov
    •  & Tom H. Karlsen
  • Comment |

    Practical recommendations on achieving equitability in biomedical research can advance essential efforts to balance research representation. In this Comment, we highlight how to generate interoperable and robust datasets, engage in thoughtful partnerships with researchers across geographies and cultures, and embrace innovative opportunities to push microbiome research beyond the gut and beyond bacteria.

    • Ovokeraye H. Oduaran
    •  & Ami S. Bhatt
  • News & Views |

    Microbiota profiling using stool samples is limited in its ability to represent intestinal microbial dynamics. CRISPR-engineered bacteria can be used to acquire cellular RNAs and create a gene expression ‘memory’ during gastrointestinal transit, with the potential to capture microbial transcriptomic changes in the gastrointestinal tract without invasive sampling.

    • Alexander Crits-Christoph
    •  & Jotham Suez
  • News & Views |

    Owing to its simplicity, dextran sulfate sodium (DSS)-induced colitis is one of the most widely used mouse models of colitis. However, the severity of inflammation varies from one experiment to another. In a new study, Forster and colleagues have provided new insights into the DSS model by revealing specific microbial taxa that underlie disease variability.

    • Nicolas Benech
    •  & Harry Sokol
  • Review Article |

    Diet is part of the multidisciplinary management of inflammatory bowel disease (IBD). This Review outlines a step-based approach to the dietary management of IBD, outlining the role of dietary therapy with practical insights for dietitians and clinicians.

    • Jessica A. Fitzpatrick
    • , Sarah L. Melton
    •  & Emma P. Halmos
  • Review Article |

    In this Review, O’Toole and colleagues discuss the composition and function of the gut microbiome as it relates to ageing and ‘unhealthy’ ageing as well as the potential for microbiome-directed interventions to encourage ‘healthy’ ageing.

    • Tarini Shankar Ghosh
    • , Fergus Shanahan
    •  & Paul W. O’Toole
  • Review Article |

    Clostridioides difficile infection has a notable health and economic burden worldwide. In this Review, the authors provide insights into the physiology of C. difficile and how it survives and has adapted to the gut environment, including insights into host–microorganism and microorganism–microorganism relationships.

    • Matthew K. Schnizlein
    •  & Vincent B. Young
  • News & Views |

    Secretory immunoglobulin A (SIgA) regulates the composition and function of the gut microbiota and modulates its interaction with the host, but how this regulation is achieved is poorly understood. Now, Rollenske and colleagues profile the consequences of SIgA binding to the gut microbiota. They suggest that parallel generic and unique epitope-specific effects of SIgA regulate the intestinal microbiota.

    • Oliver Pabst
    •  & Ana Izcue
  • Perspective |

    Humans and their microbiota are intrinsically linked. Owing to dynamic interactions within the gut, nutritional science needs to incorporate the microbiome. This Perspective re-examines the history, rationale and future prospects of chemically defined diets (enteral or parenteral) in relation to the burgeoning understanding of the human microbiota.

    • Tiffany Toni
    • , John Alverdy
    •  & Victoria Gershuni
  • Perspective |

    Autoimmune diseases share patterns of gut microbiome perturbation and immune dysregulation linked to intestinal barrier dysfunction. In this Perspective, the authors examine dietary tools for precise engineering of the gut microbiome and discuss the potential for diet-based therapies to modulate host–microbiome interaction in the treatment of autoimmune diseases.

    • Mathis Wolter
    • , Erica T. Grant
    •  & Mahesh S. Desai
  • Consensus Statement
    | Open Access

    Postbiotics are emerging substances prepared from inactivated microorganisms, in contrast to probiotics, which must be administered alive. This Consensus Statement outlines a definition for the term ‘postbiotics’ as determined by an expert panel convened by the International Scientific Association for Probiotics and Prebiotics.

    • Seppo Salminen
    • , Maria Carmen Collado
    •  & Gabriel Vinderola
  • News & Views |

    Intense research is ongoing to dissect the reciprocal interactions between microbiota and drugs. New work finds that a drug to dampen host inflammation can also have off-target effects on the microbiota at transcriptional, metabolic and compositional levels, with resultant expanded benefits to the host.

    • Aadra P. Bhatt
    •  & R. Balfour Sartor
  • Consensus Statement
    | Open Access

    Although fermented foods have been consumed for thousands of years, a clear definition has been lacking. This Consensus Statement outlines a definition for the term ‘fermented foods’ as determined by an expert panel convened by the International Scientific Association for Probiotics and Prebiotics in September 2019.

    • Maria L. Marco
    • , Mary Ellen Sanders
    •  & Robert Hutkins
  • Year in Review |

    In 2020, studies have used pure cultures of members of the gut microbiota to establish a molecular chain of causation for the role of these key bacteria in aggravating or alleviating cancer and metabolic diseases. These studies highlight the need for microbiome studies to move from associations back to cultures to demonstrate causality.

    • Liping Zhao
    •  & Naisi Zhao
  • Comment |

    To therapeutically modulate gut microbial ecosystems, a better understanding of gut ecology is key. High-throughput in vitro ecology provides a tool with the necessary power to address these needs and interpersonal treatment response variation.

    • Emma Hernandez-Sanabria
    • , Jorge Francisco Vázquez-Castellanos
    •  & Jeroen Raes
  • News & Views |

    The microbial communities that occupy the intestinal tract are shaped by a variety of different factors, including the immune system. A new study has observed and quantified, at unprecedented depth, regionally distinct microbial and immune niches along the human colon using simultaneous analyses of the gut microbiota and neighbouring immune cells.

    • Rebecca N. Culver
    • , Sean P. Spencer
    •  & Kerwyn Casey Huang
  • News & Views |

    Colibactin-producing bacteria are abundant in the gut microbiota of colorectal cancer tumours and promote colon tumorigenesis in mouse models. Now, a new study demonstrates a direct link between exposure of human intestinal epithelial cells to colibactin and two unique mutational fingerprints found in human colorectal tumours.

    • Janelle C. Arthur
  • Viewpoint |

    In this Viewpoint article, we asked a selection of scientists and clinicians in the gut microbiota field to provide their opinions on the major advances in and future directions for research, and the challenges and solutions for translating gut microbiome research to the clinic.

    • Susan V. Lynch
    • , Siew C. Ng
    •  & Herbert Tilg
  • Review Article |

    Colorectal cancer (CRC) is one of the most common cancers worldwide. This Review describes the role of microorganisms in colorectal carcinogenesis, and the potential clinical translation of the gut microbiota as a biomarker for CRC diagnosis and prognosis, and as an approach for disease prevention and to improve therapy.

    • Sunny H. Wong
    •  & Jun Yu
  • News & Views |

    Multi-omics technologies in gut microbiome research provide a global view of changes in genetic, metabolic and biochemical processes. This approach has now been applied to the gut microbiota in the context of IBD, providing first steps towards a functional understanding of host–microbe interactions during disease pathogenesis.

    • Amira Metwaly
    •  & Dirk Haller
  • Review Article |

    The gut microbiota has been implicated in a range of diseases. This Review describes current understanding of probiotics and prebiotics as a means to manage the microbiota to improve host health, including mechanisms of actions and potential for clinical use.

    • Mary Ellen Sanders
    • , Daniel J. Merenstein
    •  & Robert A. Rastall
  • Review Article |

    Short-chain fatty acids (SCFAs) are speculated to have a key role in microbiota–gut–brain crosstalk, but the pathways influencing psychological functioning have not been fully elucidated. This Review summarizes existing knowledge of how SCFAs might indirectly or directly mediate psychological processes.

    • Boushra Dalile
    • , Lukas Van Oudenhove
    •  & Kristin Verbeke
  • Review Article |

    Current nutritional approaches to prevent and treat various diseases have limited effectiveness. Here, Zmora et al. review the major principles underlying effects of dietary constituents on the gut microbiota, resolving aspects of the diet–microbiota–host crosstalk, and present the promises and challenges of incorporating microbiome data into dietary planning.

    • Niv Zmora
    • , Jotham Suez
    •  & Eran Elinav
  • News & Views |

    In a new study, Maier et al. reveal that non-antibiotic drugs intended to target human cells have off-target effects on the growth of human gut bacteria at clinically relevant concentrations. These results emphasize the need for a new field of metagenomic toxicology aimed at a more comprehensive understanding of the toxicity of compounds for humans and their associated microbial communities.

    • Peter Spanogiannopoulos
    •  & Peter J. Turnbaugh
  • Review Article |

    Attention has turned to the gut microbiota in liver disease, including alcoholic and nonalcoholic fatty liver disease and hepatocellular carcinoma. This Review describes gut–liver communications, including evidence from animal and human studies, compares conditions within the liver disease spectrum and highlights key points for designing microbiome-based studies for liver disease research.

    • Anupriya Tripathi
    • , Justine Debelius
    •  & Rob Knight
  • News & Views |

    Although metagenomic sequencing has provided unprecedented characterization of the gut microbiome, it gives only indirect evidence of the genes and pathways that might be active. Now, investigators have combined longitudinal sampling with metatranscriptomics and metagenomics in IBD to provide a high-resolution picture of the microbiome's functional dynamics.

    • Aonghus Lavelle
    •  & Harry Sokol
  • Year in Review |

    2017 has witnessed key advances in knowledge about the metabolic capacities of the gut microbiota, enabling the progression of our understanding of the principles driving xenobiotic–bacteria–host interplay. This research paves the way for the long road towards personalized medicine and nutrition, which could be based on gut microbial metabolism.

    • Nathalie M. Delzenne
    •  & Laure B. Bindels