Metabolic networks of the human gut microbiota

Microbiology (Reading). 2020 Feb;166(2):96-119. doi: 10.1099/mic.0.000853.


The human gut microbiota controls factors that relate to human metabolism with a reach far greater than originally expected. Microbial communities and human (or animal) hosts entertain reciprocal exchanges between various inputs that are largely controlled by the host via its genetic make-up, nutrition and lifestyle. The composition of these microbial communities is fundamental to supply metabolic capabilities beyond those encoded in the host genome, and contributes to hormone and cellular signalling that support the dynamic adaptation to changes in food availability, environment and organismal development. Poor functional exchange between the microbial communities and their human host is associated with dysbiosis, metabolic dysfunction and disease. This review examines the biology of the dynamic relationship between the reciprocal metabolic state of the microbiota-host entity in balance with its environment (i.e. in healthy states), the enzymatic and metabolic changes associated with its imbalance in three well-studied diseases states such as obesity, diabetes and atherosclerosis, and the effects of bariatric surgery and exercise.

Keywords: atherosclerosis; bariatric surgery; diet; exercise; food additives; genetic regulation; gut ecology; human gut microbiota; metabolic disease; metabolic networks; microbiota–host interaction; obesity; type 2 diabetes.

Publication types

  • Review

MeSH terms

  • Animals
  • Atherosclerosis / metabolism
  • Atherosclerosis / microbiology
  • Atherosclerosis / therapy
  • Diabetes Mellitus, Type 2 / metabolism
  • Diabetes Mellitus, Type 2 / microbiology
  • Diabetes Mellitus, Type 2 / therapy
  • Dysbiosis / metabolism
  • Dysbiosis / microbiology
  • Dysbiosis / therapy
  • Fatty Acids, Volatile / metabolism
  • Gastrointestinal Microbiome / physiology*
  • Host Microbial Interactions
  • Humans
  • Metabolic Networks and Pathways*
  • Obesity / metabolism
  • Obesity / microbiology
  • Obesity / therapy


  • Fatty Acids, Volatile