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Analysis Science and Politics of Nutrition

Role of the gut microbiota in nutrition and health

BMJ 2018; 361 doi: (Published 13 June 2018) Cite this as: BMJ 2018;361:k2179

Food for thought

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  1. Ana M Valdes, associate professor1 2,
  2. Jens Walter, CAIP chair for nutrition, microbes, and gastrointestinal health3,
  3. Eran Segal, professor4,
  4. Tim D Spector, professor5
  1. 1School of Medicine, University of Nottingham, City Hospital, Nottingham NG5 1PB, UK
  2. 2NIHR Nottingham Biomedical Research Centre, Nottingham, UK
  3. 3Department of Agricultural, Food, and Nutritional Science and Department of Biological Sciences, University of Alberta, Edmonton, Canada
  4. 4Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
  5. 5Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
  1. Correspondence to: T D Spector tim.spector{at}

Ana M Valdes and colleagues discuss strategies for modulating the gut microbiota through diet and probiotics

Microbiome refers to the collective genomes of the micro-organisms in a particular environment, and microbiota is the community of micro-organisms themselves (box 1). Approximately 100 trillion micro-organisms (most of them bacteria, but also viruses, fungi, and protozoa) exist in the human gastrointestinal tract12—the microbiome is now best thought of as a virtual organ of the body. The human genome consists of about 23 000 genes, whereas the microbiome encodes over three million genes producing thousands of metabolites, which replace many of the functions of the host,13 consequently influencing the host’s fitness, phenotype, and health.2

Box 1


  • Microbiome—the collective genomes of the micro-organisms in a particular environment

  • Microbiota—the community of micro-organisms themselves

  • Microbiota diversity—a measure of how many different species and, dependent on the diversity indices, how evenly distributed they are in the community. Lower diversity is considered a marker of dysbiosis (microbial imbalance) in the gut and has been found in autoimmune diseases and obesity and cardiometabolic conditions, as well as in elderly people

  • Operational taxonomic unit—a definition used to classify groups of closely related organisms. DNA sequences can be clustered according to their similarity to one another, and operational taxonomic units are defined based on the similarity threshold (usually 97% similarity) set by the researcher

  • Colonocytes—epithelial cells of the colon

  • Germ-free animals—animals that have no micro-organisms living in or on them

  • Short chain fatty acids—fatty acids with two to six carbon atoms that are produced by bacterial fermentation of dietary fibres


Studying the gut microbiota

Twin studies have shown that, although there is a heritable component to gut microbiota, environmental factors related to diet, drugs, and anthropometric measures are larger determinants of microbiota composition.45

Gut …

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