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Gut microbiome stability and resilience: elucidating the response to perturbations in order to modulate gut health
  1. Marina Fassarella1,
  2. Ellen E Blaak2,
  3. John Penders3,
  4. Arjen Nauta4,
  5. Hauke Smidt1,
  6. Erwin G Zoetendal1
  1. 1 Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
  2. 2 Department of Human Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
  3. 3 Department of Medical Microbiology, Maastricht University Medical Centre+, Maastricht, The Netherlands
  4. 4 FrieslandCampina, Amersfoort, The Netherlands
  1. Correspondence to Dr Erwin G Zoetendal, Laboratory of Microbiology, Wageningen University & Research, Wageningen 6708 WE, The Netherlands; erwin.zoetendal{at}


The human gut microbiome is a complex ecosystem, densely colonised by thousands of microbial species. It varies among individuals and depends on host genotype and environmental factors, such as diet and antibiotics. In this review, we focus on stability and resilience as essential ecological characteristics of the gut microbiome and its relevance for human health. Microbial diversity, metabolic flexibility, functional redundancy, microbe–microbe and host–microbe interactions seem to be critical for maintaining resilience. The equilibrium of the gut ecosystem can be disrupted by perturbations, such as antibiotic therapy, causing significant decreases in functional richness and microbial diversity as well as impacting metabolic health. As a consequence, unbalanced states or even unhealthy stable states can develop, potentially leading to or supporting diseases. Accordingly, strategies have been developed to manipulate the gut microbiome in order to prevent or revert unhealthy states caused by perturbations, including faecal microbiota transplantation, supplementation with probiotics or non-digestible carbohydrates, and more extensive dietary modifications. Nevertheless, an increasing number of studies has evidenced interindividual variability in extent and direction of response to diet and perturbations, which has been attributed to the unique characteristics of each individual’s microbiome. From a clinical, translational perspective, the ability to improve resilience of the gut microbial ecosystem prior to perturbations, or to restore its equilibrium afterwards, would offer significant benefits. To be effective, this therapeutic approach will likely need a personalised or subgroup-based understanding of individual genetics, diet, gut microbiome and other environmental factors that might be involved.

  • intestinal microbiology
  • bacterial interactions
  • antibiotic therapy
  • diet

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  • Contributors MF searched literature, wrote the manuscript and created the figures. EB, JP, AN, HS and EGZ reviewed and wrote the manuscript. All authors approved the final manuscript.

  • Funding This work was performed in the partnership ‘CarboBiotics’, project number ALWCC.2017.003, coordinated and financed by the Dutch Research Council (NWO) and the Carbohydrate Competence Center (CCC), with the collaboration of the participating industrial partners: Avebe, Friesland Campina, Nutrition Sciences, and TKI Agri&Food.

  • Competing interests None declared.

  • Patient consent for publication Not required.

  • Provenance and peer review Commissioned; externally peer reviewed.