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Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration


Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration

Emily R Leeming et al. Nutrients.


The human gut is inhabited by trillions of microorganisms composing a dynamic ecosystem implicated in health and disease. The composition of the gut microbiota is unique to each individual and tends to remain relatively stable throughout life, yet daily transient fluctuations are observed. Diet is a key modifiable factor influencing the composition of the gut microbiota, indicating the potential for therapeutic dietary strategies to manipulate microbial diversity, composition, and stability. While diet can induce a shift in the gut microbiota, these changes appear to be temporary. Whether prolonged dietary changes can induce permanent alterations in the gut microbiota is unknown, mainly due to a lack of long-term human dietary interventions, or long-term follow-ups of short-term dietary interventions. It is possible that habitual diets have a greater influence on the gut microbiota than acute dietary strategies. This review presents the current knowledge around the response of the gut microbiota to short-term and long-term dietary interventions and identifies major factors that contribute to microbiota response to diet. Overall, further research on long-term diets that include health and microbiome measures is required before clinical recommendations can be made for dietary modulation of the gut microbiota for health.

Keywords: diet; dietary intervention; duration; gut microbiota; health; nutrition.

Conflict of interest statement

E.R.L., C.I.L.R., and A.J.J. declare no conflict of interest. T.D.S. is a co-founder of Zoe Global Ltd.


Figure 1
Figure 1
Comparison of diet and gut microbiota variations throughout life. Habitual diet plays a role in shaping the gut microbial environment, and hence, microbial composition. Dietary diversity has been associated with microbial diversity [78]. Throughout the year, the human diet tends to display a cyclical seasonal pattern due to seasonal availability and dietary preferences. Large day to day variations in diet are not reflected in the gut microbiota, suggesting that overall dietary habits have a greater impact on gut microbial composition [35]. This image was generated using BioRender Software (
Figure 2
Figure 2
Moving from current to an ideal diet–microbiome study structure. Currently, diet–microbiome studies fail to consider a number of limitations, including the personalised microbiome, leading to heterogeneous outcomes. In an ideal setting, sample groups would be stratified by enterotype prior to the commencement of an intervention. Yet, faecal samples can take a lengthy time to process, stymieing study progress. A practical solution could be the use of a classification algorithm to stratify responders and non-responders with the hope of improving study outcomes. This image was generated using BioRender Software (

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    1. Jackson M.A., Verdi S., Maxan M.E., Shin C.M., Zierer J., Bowyer R.C.E., Martin T., Williams F.M.K., Menni C., Bell J.T., et al. Gut microbiota associations with common diseases and prescription medications in a population-based cohort. Nat. Commun. 2018;9:2655. doi: 10.1038/s41467-018-05184-7. - DOI - PMC - PubMed
    1. Valdes A.M., Walter J., Segal E., Spector T.D. Role of the gut microbiota in nutrition and health. BMJ. 2018;361:k2179. doi: 10.1136/bmj.k2179. - DOI - PMC - PubMed
    1. Zhang C., Zhang M., Wang S., Han R., Cao Y., Hua W., Mao Y., Zhang X., Pang X., Wei C., et al. Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice. ISME J. 2010;4:232–241. doi: 10.1038/ismej.2009.112. - DOI - PubMed
    1. Rothschild D., Weissbrod O., Barkan E., Kurilshikov A., Korem T., Zeevi D., Costea P.I., Godneva A., Kalka I.N., Bar N., et al. Environment dominates over host genetics in shaping human gut microbiota. Nature. 2018;555:210–215. doi: 10.1038/nature25973. - DOI - PubMed
    1. David L.A., Materna A.C., Friedman J., Campos-Baptista M.I., Blackburn M.C., Perrotta A., Erdman S.E., Alm E.J. Host lifestyle affects human microbiota on daily timescales. Genome Biol. 2014;15:R89. doi: 10.1186/gb-2014-15-7-r89. - DOI - PMC - PubMed