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Cited by 817Gut microbiota and healthNutritional Studies and DietProbiotics and Fermented Foods

Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration

Open access
Leeming, Emily R, Johnson, Abigail J, Spector, Tim D, Le Roy, Caroline I·2019·Nutrients
DOI 10.3390/nu11122862PMC PMC6950569
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Abstract

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.

AI snapshot

Written from the paper’s full text.

TL;DR

This review argues that diet can rapidly alter the gut microbiota, but short-term dietary interventions generally produce transient changes that revert after the intervention or washout. Durable modulation likely requires long-term habitual dietary change, yet evidence is limited by a lack of long-term human studies and follow-up.

Key findings

  • Diet is estimated to explain over 50% of microbial structural variation in mice and 20% in humans, while genetics explains an average of 8.8% in a 2016 analysis of 1126 twins.
  • Short-term interventions can shift the microbiota quickly but transiently: in David et al., 10 subjects consumed plant- or animal-based diets for 5 days, with microbiota returning to baseline within 3 days post-intervention; in Liu et al., FOS/GOS for 14 days in 35 healthy adults increased *Bifidobacterium* and reduced butyrate-producing bacteria, but the microbiota recovered after a 28-day washout.
  • Long-term/habitual diet appears to be a primary driver: the American Gut Project, with over 10,000 individuals, found *Faecalibacterium prausnitzii* and *Oscillospira* increased in those consuming more than 30 plant types per week versus fewer than 10; a year-long study of 350 faecal samples from the Tanzanian Hadza showed seasonal cycling in gut microbiota composition.
  • Probiotic effects are individualised and often transient; a 2016 systematic review found probiotics had no impact on alpha-diversity, evenness, or richness in healthy individuals, except one study noting beta-diversity.

Methods

  • Narrative review synthesizing human and animal studies, including short-term dietary interventions, cross-over washout studies, prebiotic/probiotic trials, epidemiological/cross-sectional studies, and systematic reviews/meta-analyses.
  • The review defines short-term dietary interventions as those investigating immediate impact up to a number of months, and long-term studies as predominantly epidemiological or of an extended period (≥6 months).
  • Main analysis is qualitative synthesis of existing literature; no formal systematic search strategy or meta-analysis is described.

Limitations

  • The paper states there is a lack of long-term human studies, or follow-ups of short-term dietary interventions, to establish whether diet-induced microbiota modulation endures.
  • The paper states that heterogeneous outcomes may arise from responders versus non-responders based on baseline microbiota, and that research often focuses on broad dietary indices or single/combined nutrients rather than whole foods and food matrices; transit time is also occasionally overlooked.
  • Evident from the text: as a narrative review, it does not report a systematic search strategy, inclusion criteria, or risk-of-bias assessment.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.3390/nu11122862

Cites

118 of 118 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 138 cited sources checked · 0 supported · 0 flagged

  • Premisecitation

    Wide variations in individual responses to food intake contribute to many conflicting outcomes in this area of research with failures to find diet-specific effects.

    “These wide variations contribute to many conflicting outcomes in this area of research with failures to find diet-specific effects [16].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [16] Tebani, A., and Bekri, S. (2019). Paving the Way to Precision Nutrition Through Metabolomics. Front. Nutr., 6. source

      Not checked in the free run.

  • Interpretationreasoning

    A new state of ecological homeostasis of the gut microbiota may be achieved, mediated by diet with beneficial implications for host health.

    “In this way, a new state of ecological homeostasis of the gut microbiota may be achieved, mediated by diet with beneficial implications for host health.”
    Quote in the paperSubstantial claim
  • Premisecitation

    Even after extensive dietary changes, an individual's microbiota maintains its unique personalised composition.

    “Even after extensive dietary changes, an individual’s microbiota maintains its unique personalised composition [6] suggesting that the forces controlling ecological homeostasis extend beyond diet.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [6] Wu, 2011, Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes, Science source

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  • Premisecitation

    Mouse models have indicated that manipulation of macronutrient intake can consistently shift the composition of the gut microbiota within the span of a day.

    “Likewise, mouse models have indicated that manipulation of macronutrient intake can consistently shift the composition of the gut microbiota within the span of a day [5,6,18,19].”
    Quote in the paperSubstantial claim0 of 4 sources checked
    • cites [5] David, 2014, Host lifestyle affects human microbiota on daily timescales, Genome Biol. source

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    • cites [6] Wu, 2011, Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes, Science source

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    • cites [18] David, 2014, Diet rapidly and reproducibly alters the human gut microbiome, Nature source

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    • cites [19] Walker, 2010, Dominant and diet-responsive groups of bacteria within the human colonic microbiota, Isme J. source

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  • Premisecitation

    Within 24-48 h of a dietary intervention rapid changes are thought to be made to the microbial composition on a species and family level (but not phyla).

    “Within 24–48 h of a dietary intervention rapid changes are thought to be made to the microbial composition on a species and family level (but not phyla) [17].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [17] Sonnenburg, 2016, Diet-microbiota interactions as moderators of human metabolism, Nature source

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  • May combine two claims. 54
  • Classified as probably not a substantial claim. 18
  • The quote only partly states this claim. 1

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    Interpretationreasoning

    Permanent alteration of the diet may induce new species and proliferate others, increasing the diversity and richness of beneficial taxa.

    “Thus, permanent alteration of the diet may induce new species and proliferate others, increasing the diversity and richness of beneficial taxa.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    Diet is thought to explain over 50% of microbial structural variations in mice and 20% in humans.

    “Diet is thought to explain over 50% of these microbial structural variations in mice and 20% in humans signalling the potential for dietary strategies in disease management through gut microbiota modulation [3,4].”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [3] Zhang, 2010, Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice, ISME J. source

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    • cites [4] Rothschild, 2018, Environment dominates over host genetics in shaping human gut microbiota, Nature source

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    Premisecitation

    The core bacterial taxa are resilient to most temporary outside influences, but the gut microbial community as a whole displays a high inter-individual day-to-day variability.

    “While the core bacterial taxa are resilient to most temporary outside influences, the gut microbial community as a whole displays a high inter-individual day-to-day variability [2].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [2] Valdes, 2018, Role of the gut microbiota in nutrition and health, BMJ source

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  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Genetics only perform a limited role in shaping the gut microbiota with an average level of 8.8% according to a 2016 data analysis of 1126 twins.

    “Genetics only perform a limited role in shaping the gut microbiota with an average level of 8.8% according to a 2016 data analysis of 1126 twins [7].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [7] Goodrich, 2016, Genetic Determinants of the Gut Microbiome in UK Twins, Cell Host Microbe source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    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.

    “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.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [6] Wu, 2011, Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes, Science source

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Interpretationreasoning

    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.

    “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.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Besides diet, the gut microbiota is shaped by a combination of extrinsic and intrinsic factors, with extrinsic factors eliciting the predominant effect and diet the most widely studied.

    “Besides diet, the gut microbiota is shaped by a combination of extrinsic (e.g., lifestyle and medication) and intrinsic (e.g., host genetics, immune and metabolic regulations) factors. It is generally acknowledged that the extrinsic factors elicit the predominant effect, with diet the most widely studied [4].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [4] Rothschild, 2018, Environment dominates over host genetics in shaping human gut microbiota, Nature source

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  • May combine two claims.

    Premisecitation

    These alterations are transient and do not persist for more than a few days.

    “However, these alterations are transient and do not persist for more than a few days [5].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [5] David, 2014, Host lifestyle affects human microbiota on daily timescales, Genome Biol. source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Diet can induce a shift in the gut microbiota, but these changes appear to be temporary.

    “While diet can induce a shift in the gut microbiota, these changes appear to be temporary.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [5] David, 2014, Host lifestyle affects human microbiota on daily timescales, Genome Biol. source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S4 (based).

    Interpretationreasoning

    Habitual diets may have a greater influence on the gut microbiota than acute dietary strategies.

    “It is possible that habitual diets have a greater influence on the gut microbiota than acute dietary strategies.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    The gut microbiota fluctuates based on nutrient availability and the level of host-derived auto-antibodies and peptides, both of which are associated with circadian rhythm oscillations.

    “The microbiota fluctuates based on nutrient availability and the level of host-derived auto-antibodies and peptides, both of which are associated with circadian rhythm oscillations [20,22,23].”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites [20] Liang, 2017, Timing the Microbes: The Circadian Rhythm of the Gut Microbiome, J. Biol. Rhythm. source

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    • cites [22] Thaiss, 2014, Transkingdom Control of Microbiota Diurnal Oscillations Promotes Metabolic Homeostasis, Cell source

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    • cites [23] Thaiss, 2016, Persistent microbiome alterations modulate the rate of post-dieting weight regain, Nature source

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    Premisecitation

    The animal-based diet displayed significantly decreased levels of carbohydrate fermentation faecal metabolites and increased amino acid fermentation faecal metabolites within 24 h, in comparison to baseline and the plant-based diet.

    “Both diets shifted gut microbiota composition [35], with the animal-based diet displaying significantly decreased levels of carbohydrate fermentation faecal metabolites and increased amino acid fermentation faecal metabolites within 24 h, in comparison to baseline and the plant-based diet [18].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [18] David, 2014, Diet rapidly and reproducibly alters the human gut microbiome, Nature source

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    Premisecitation

    In mouse models, Thaiss et al. displayed that a rhythmic food intake leads to 15% of commensal bacterial taxonomic units fluctuating throughout the course of a day, and also increased microbial abundance.

    “Likewise, in mouse models Thaiss et al. displayed that a rhythmic food intake not only leads to 15% of commensal bacterial taxonomic units fluctuating throughout the course of a day, but also increased microbial abundance [22].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [22] Thaiss, 2014, Transkingdom Control of Microbiota Diurnal Oscillations Promotes Metabolic Homeostasis, Cell source

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    Interpretationcitation

    Collectively, studies show that alterations made in diet can have a significant and meaningful effect on the gut microbiota, primarily influenced by fibre from fruits, vegetables and other plant foods.

    “Collectively, studies show that alterations made in diet can have a significant and meaningful effect on the gut microbiota, primarily influenced by fibre from fruits, vegetables and other plant foods.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    While probiotics may be transient, they have the capacity to alter the composition of the gut microbiota, in turn influencing the production of beneficial fermentation-derived metabolites.

    “While probiotics may be transient, they have the capacity to alter the composition of the gut microbiota, in turn influencing the production of beneficial fermentation-derived metabolites [53].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [53] Licciardi, 2010, Epigenome targeting by probiotic metabolites, Gut Pathog. source

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    Premisecitation

    In a controlled feeding experiment by Wu et al. with 10 randomised study participants, the faecal microbiota of all 10 individuals displayed dramatic albeit temporary shifts, though inter-subject variability remained high even after periods of identical dietary intake.

    “The faecal microbiota of all 10 individuals displayed dramatic albeit temporary shifts, though inter-subject variability remained high even after periods of identical dietary intake [6].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [6] Wu, 2011, Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes, Science source

      Not checked in the free run.

  • May combine two claims.

    Premisereasoning

    In short-term interventions, faecal analyses are typically taken during the study period and not afterwards, which hampers understanding of the duration of an association between the gut microbiota and diet.

    “However, in short-term interventions, faecal analyses are typically taken during the study period and not afterwards, as displayed in Table 1. As a result, this hampers our understanding of the duration of an association between the gut microbiota and diet.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Premisenone given

    After consumption probiotics have the capacity to colonise and proliferate within the gastrointestinal tract thereby influencing the gut ecosystem.

    “After consumption probiotics have the capacity to colonise and proliferate within the gastrointestinal tract thereby influencing the gut ecosystem.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    Consumption of fructooligosaccharide (FOS) and GOS for 14 days increased Bifidobacterium and reduced butyrate-producing bacteria in 35 healthy adults.

    “For example, a randomised double-blind cross-over study by Liu et al. observed that consumption of fructooligosaccharide (FOS) and GOS for 14 days increased Bifidobacterium and reduced butyrate-producing bacteria in 35 healthy adults.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [38] Liu, 2017, Fructooligosaccharide (FOS) and Galactooligosaccharide (GOS) Increase Bifidobacterium but Reduce Butyrate Producing Bacteria with Adverse Glycemic Metabolism in healthy young population, Sci. Rep. source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    A number of dietary studies have detailed no significant effect of diet on the microbiota, possibly as a result of interpersonal variability in enterotype composition though this may be overwhelmed by a suitably extreme diet.

    “A number of dietary studies have detailed no significant effect of diet on the microbiota, possibly as a result of interpersonal variability in enterotype composition though this may be overwhelmed by a suitably extreme diet [34].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [34] Xu, 2015, Dietary effects on human gut microbiome diversity, Br. J. Nutr. source

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  • May combine two claims.

    Premisereasoning

    Probiotic outcomes can be unpredictable and individualised.

    “However, probiotic outcomes can be unpredictable and individualised.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    A 2016 systematic review by Kristensen et al. found that probiotics have no impact on alpha-diversity, evenness and richness in the faecal microbiota across several studies on healthy individuals, bar one which noted an effect on beta-diversity.

    “In fact, a 2016 systematic review by Kristensen et al. found that probiotics have no impact on alpha-diversity, evenness and richness in the faecal microbiota across several studies on healthy individuals, bar one which noted an effect on beta-diversity [52].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [52] Kristensen, 2016, Alterations in fecal microbiota composition by probiotic supplementation in healthy adults: A systematic review of randomized controlled trials, Genome Med. source

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    Interpretationcitation

    The duration of any intervention required to illicit a permanent change to the core microbial profile is still unknown, with most producing only transient fluctuations within the community.

    “However, the duration of any intervention required to illicit a permanent change to the core microbial profile is still unknown, with most producing only transient fluctuations within the community [18].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [18] David, 2014, Diet rapidly and reproducibly alters the human gut microbiome, Nature source

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    Premisecitation

    After a 28-day washout period, the gut microbiota was shown to recover to its pre-intervention baseline state, displaying that without continued consumption of these prebiotic fibres, the noted microbial changes are lost within the 28-day wash-out period.

    “However, after a 28-day washout period, the gut microbiota was shown to recover to its pre-intervention baseline state displaying that without continued consumption of these prebiotic fibres, the noted microbial changes are lost within the 28-day wash-out period [38].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [38] Liu, 2017, Fructooligosaccharide (FOS) and Galactooligosaccharide (GOS) Increase Bifidobacterium but Reduce Butyrate Producing Bacteria with Adverse Glycemic Metabolism in healthy young population, Sci. Rep. source

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  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisenone given

    Clinical evidence may sometimes be contradictory, mostly as a result of low study power and potential variability in the strains used between two studies.

    “However, clinical evidence may sometimes be contradictory, mostly as a result of low study power and potential variability in the strains used between two studies.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    Probiotic studies tend to measure clinical outcomes rather than colonisation of the probiotic strain, with significant results suggesting that colonisation isn't necessarily required to reap health benefits from probiotic ingestion.

    “Probiotic studies tend to measure clinical outcomes rather than colonisation of the probiotic strain, with significant results suggesting that colonisation isn’t necessarily required to reap health benefits from probiotic ingestion [51].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [51] Sanders, 2018, Probiotics for human use, Nutr. Bull. source

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  • May combine two claims.

    Premisecitation

    In a 2018 randomised crossover study by Collado et al. (n = 10), the timing of a meal can affect the diurnal rhythms of the salivary microbial profile, with eating the main meal late (at 17:30 as opposed to 14:30) shown to increase salivary taxa generally considered to be pro-inflammatory.

    “They found that the timing of a meal can affect the diurnal rhythms of the salivary microbial profile with eating the main meal late (at 17:30 as opposed to 14:30) shown to increase salivary taxa generally considered to be pro-inflammatory; affecting body weight, cortisol rhythm, basal metabolic rate, glucose tolerance and body temperature [28].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [28] Collado, 2018, Timing of food intake impacts daily rhythms of human salivary microbiota: A randomized, crossover study, FASEB J. source

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    Premisecitation

    Rejection is highly prevalent in healthy individuals with little evidence that probiotics have a substantive impact on the gut microbial profile besides a transient increase that rarely persists.

    “Rejection is highly prevalent in healthy individuals with little evidence that probiotics have a substantive impact on the gut microbial profile besides a transient increase that rarely persists [51].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [51] Sanders, 2018, Probiotics for human use, Nutr. Bull. source

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    Premisecitation

    In humans, there are rapid but transient changes in the gut microbiota in response to a dietary intervention particularly in the first 24-h period, but enterotypes are thought to remain stable throughout an intervention.

    “In humans, there are rapid but transient changes in the gut microbiota in response to a dietary intervention particularly in the first 24-h period. However, enterotypes, the distinct bacterial groupings of the core microbial profile, are thought to remain stable throughout an intervention [6].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [6] Wu, 2011, Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes, Science source

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  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Findings have indicated the benefit of probiotics in aiding the treatment of infectious- and antibiotic-associated diarrhoea, insulin resistance in diabetes, and remission and maintenance of inflammatory bowel disease, amongst others.

    “Findings have indicated the benefit of probiotics in aiding the treatment of infectious- and antibiotic-associated diarrhoea, insulin resistance in diabetes, and remission and maintenance of inflammatory bowel disease, amongst others [44,45,46,47].”
    Quote in the paperNot a substantial claim0 of 4 sources checked
    • cites [44] Li, 2019, Efficacy of Lactobacillus rhamnosus GG in treatment of acute pediatric diarrhea: A systematic review with meta-analysis, World J. Gastroenterol. source

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    • cites [45] Hungin, 2018, Systematic review: Probiotics in the management of lower gastrointestinal symptoms—An updated evidence-based international consensus, Aliment Pharm. source

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    • cites [46] Derwa, 2017, Systematic review with meta-analysis: The efficacy of probiotics in inflammatory bowel disease, Aliment Pharm. source

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    • cites [47] Krumbeck, 2018, Synbiotics for Improved Human Health: Recent Developments, Challenges, and Opportunities, Annu. Rev. Food Sci. Technol. source

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  • May combine two claims.

    Premisecitation

    A 2018 systematic review and meta-analysis of 64 studies found that dietary fibre interventions, particularly fructans and galactooligosaccharides (GOS), increase faecal abundance of Bifidobacterium and Lactobacillus species but did not affect alpha-diversity.

    “A 2018 systematic review and meta-analysis observed the effect of fibre on the gut microbiota from 64 studies. Dietary fibre interventions, particularly fructans and galactooligosaccharides (GOS), were found to increase faecal abundance of Bifidobacterium and Lactobacillus species but did not affect alpha-diversity [37].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [37] So, 2018, Dietary fiber intervention on gut microbiota composition in healthy adults: A systematic review and meta-analysis, Am. J. Clin. Nutr. source

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  • May combine two claims.

    Premisecitation

    The microbiota of the Tanzanian Hadza tribe reflects the seasonality of their diet, with food type and availability affected by distinct dry and wet seasons.

    “The microbiota of these hunter-gathers were shown to reflect the seasonality of their diet, with food type and availability affected by distinct dry and wet seasons.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [76] Smits, 2017, Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania, Science source

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  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    In rodents, seasonal differences in the length of day have been shown to affect the composition of their microbial profile.

    “In rodents, seasonal differences in the length of day has been shown to effect the composition of their microbial profile [90].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [90] Bailey, 2010, Photoperiod modulates gut bacteria composition in male Siberian hamsters (Phodopus sungorus), Brain Behav. Immun. source

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    Premisecitation

    Polyphenols exert a dual effect on the gut microbiota, inhibiting growth of specific taxa while enhancing growth of others where they can be metabolised into bioavailable substrates for the host.

    “Polyphenols exert a dual effect on the gut microbiota as they can inhibit the growth of specific taxa, while enhancing the growth of others where they can be metabolised into bioavailable substrates for the host.”
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    • cites [92] Cardona, 2013, Benefits of polyphenols on gut microbiota and implications in human health, J. Nutr. Biochem. source

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    Premisecitation

    In a randomised, controlled, cross-over design study of 60 adults at risk of developing metabolic syndrome, Roager et al. found that the higher fibre whole grain intervention had no significant impact on the gut microbial composition, diversity or functional potential in comparison to a refined grain intake, but there were marked improvements in inflammatory biomarkers even after adjusting for体重

    “Roager et al. investigated the effect of two 8-week diet intervention periods of either a whole grain diet, or a refined grain diet, on the microbiota and health markers of 60 adults at risk of developing metabolic syndrome in a randomised, controlled, cross-over design study [61]. They found that the higher fibre whole grain intervention had no significant impact on the gut microbial composition,”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [61] Roager, 2019, Whole grain-rich diet reduces body weight and systemic low-grade inflammation without inducing major changes of the gut microbiome: A randomised cross-over trial, Gut source

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  • May combine two claims.

    Premisecitation

    Prebiotic consumption has been associated with growth of Bifidobacterium, Lactobacillus and lactic acid bacteria; conversely, fibres not classified as prebiotics do not appear to affect the abundance of Bifidobacterium or Lactobacillus.

    “Prebiotic consumption has been associated with growth of Bifidobacterium, Lactobacillus and lactic acid bacteria. Conversely, fibres not classified as prebiotics, do not appear to affect the abundance of Bifidobacterium or Lactobacillus [37].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [37] So, 2018, Dietary fiber intervention on gut microbiota composition in healthy adults: A systematic review and meta-analysis, Am. J. Clin. Nutr. source

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    Premisecitation

    Alongside fibre, magnesium, biotin, and vitamin E have all been shown to impact visceral fat mass accumulation mediated by the gut microbiota.

    “Alongside fibre, magnesium, biotin, and vitamin E have all been shown to impact visceral fat mass accumulation mediated by the gut microbiota [79].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [79] Le Roy, C.I., Wells, P.M., Si, J., Raes, J., Bell, J.T., and Spector, T.D. (2019). Red Wine Consumption Associated With Increased Gut Microbiota α-diversity in 3 Independent Cohorts. Gastroenterology. source

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    Premisecitation

    A Westernised diet is characterised by limited dietary diversity and a low fibre intake and has been greatly linked to an alteration of gut microbiota composition.

    “Similarly, a Westernised diet is characterised by limited dietary diversity and a low fibre intake and has been greatly linked to an alteration of gut microbiota composition.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [97] Zinöcker, M.K., and Lindseth, I.A. (2018). The Western Diet-Microbiome-Host Interaction and Its Role in Metabolic Disease. Nutrients, 10. source

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  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Food sources of fibre, such as whole grains, have been suggested to have a prebiotic-like effect on the gut microbiota.

    “Food sources of fibre, such as whole grains, have been suggested to have a prebiotic-like effect on the gut microbiota [60].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [60] Costabile, 2008, Whole-grain wheat breakfast cereal has a prebiotic effect on the human gut microbiota: A double-blind, placebo-controlled, crossover study, Br. J. Nutr. source

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    Premisecitation

    A study by Dewulf et al. investigating the effect of inulin-type fructan on women with obesity for three months found a shift in microbial profile and altered fat metabolism, with a reduction in fat mass, serum LPS and some metabolites such as phosphatidylcholine, lactate and hippurate.

    “For example, a study by Dewulf et al. investigating the effect of inulin-type fructan on women with obesity for three months, found a shift in microbial profile and altered fat metabolism. Consequentially, a reduction in fat mass, serum LPS and some metabolites such as phosphatidylcholine, lactate and hippurate were displayed [59].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [59] Tamashiro, 2018, Role of prebiotics in regulation of microbiota and prevention of obesity, Food Res. Int. source

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    Increasingly, our understanding of prebiotics suggest that they not only have a positive impact on gut microbial composition, but also health outcomes through the production of beneficial metabolites.

    “Increasingly, our understanding of prebiotics suggest that they not only have a positive impact on gut microbial composition, but also health outcomes through the production of beneficial metabolites.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    The Western diet has been strongly associated with obesity and metabolic diseases, though the biological mechanisms remain unknown.

    “The Western diet has been strongly associated with obesity and metabolic diseases, though the biological mechanisms remain unknown [97].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [97] Zinöcker, M.K., and Lindseth, I.A. (2018). The Western Diet-Microbiome-Host Interaction and Its Role in Metabolic Disease. Nutrients, 10. source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Habitual diet is associated with a distinct compositional enterotype, while short-term dietary intake is not.

    “Habitual diet has been shown to be associated with a distinct compositional enterotype, while short-term dietary intake has not [6].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [6] Wu, 2011, Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes, Science source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Fibre is the most commonly accepted nutrient to exert a beneficial effect on microbiota composition, while polyphenols are also thought to play an important role.

    “Fibre is the most commonly accepted nutrient to exert a beneficial effect on microbiota composition, however other dietary components such as polyphenols, a group of anti-oxidants, are also thought to play an important role [92].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [92] Cardona, 2013, Benefits of polyphenols on gut microbiota and implications in human health, J. Nutr. Biochem. source

      Not checked in the free run.

  • May combine two claims.

    Interpretationcitation

    Many of the changes appear to be transient and suggest that habitual consumption is required for continued beneficial health outcomes related to prebiotic intake.

    “Many of the changes appear to be transient and suggest that habitual consumption is required for continued beneficial health outcomes related to prebiotic intake.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    Vuholm et al. investigated the effect of whole grain wheat and rye vs refined wheat, with improvements displayed in health parameters but no significant effect between whole grains and refined grains on the gut microbiota.

    “Vuholm et al. also investigated the effect of whole grain wheat and rye vs refined wheat, with improvements displayed in health parameters but no significant effect between whole grains and refined grains on the gut microbiota.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    In 178 older men and women in Ireland, dietary diversity was significantly associated with improved health parameters, with the low fat/high fibre group having the most diverse diet and microbial profile, and moderate fat/low fibre and high fat/low fibre groups the least.

    “They found that dietary diversity was significantly associated with improved health parameters, with the grouping “low fat/high fibre” considered to have the most diverse diet and microbial profile, and “moderate fat/low fibre” and “high fat/low fibre” groupings the least [81].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [81] Claesson, 2012, Gut microbiota composition correlates with diet and health in the elderly, Nature source

      Not checked in the free run.

  • May combine two claims.

    Interpretationcitation

    These studies suggest that habitual diet also plays a role in pre-adolescence, or throughout the lifespan.

    “While it is generally accepted that habitual diet shapes the gut microbial composition and diversity in adulthood, these studies suggest that habitual diet also plays a role in pre-adolescence, or in fact, throughout the lifespan.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    In the same study, those with higher baseline A. muciniphila displayed greater amelioration in markers of insulin sensitivity after calorie restriction, and while these participants experienced a reduction in A. muciniphila abundance, it still remained significantly higher than in those with a lower baseline abundance.

    “Those with higher baseline of A. muciniphila also displayed greater amelioration in markers of insulin sensitivity after calorie restriction, and while these participants experienced a reduction in A. muciniphila abundance, it still remained significantly higher than in those with a lower baseline abundance [74].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [74] Dao, 2016, Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: Relationship with gut microbiome richness and ecology, Gut source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    A study observing the consumption of red wine in three independent twin cohorts found an association with increased alpha-diversity of the gut microbiota, but no association with alcohol content itself.

    “Recently, a study observing the consumption of red wine in three independent twin cohorts was found to be associated with increased alpha-diversity of the gut microbiota, yet, while not a nutrient, there was no association found with alcohol content itself [79].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [79] Le Roy, C.I., Wells, P.M., Si, J., Raes, J., Bell, J.T., and Spector, T.D. (2019). Red Wine Consumption Associated With Increased Gut Microbiota α-diversity in 3 Independent Cohorts. Gastroenterology. source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Faecal richness is considered a hallmark of gut health, but the composition of the faecal microbiota primarily reflects the stage of ecosystem development rather than communal stability.

    “While faecal richness is considered a hallmark of gut health, the composition of the faecal microbiota primarily reflects the stage of ecosystem development rather than communal stability [105].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [105] Falony, 2018, Richness and ecosystem development across faecal snapshots of the gut microbiota, Nat. Microbiol. source

      Not checked in the free run.

  • May combine two claims.

    Interpretationcitation

    Defining and stratifying those with a diet-responsive gut microbiota within an intervention cohort may enhance the predictable performance of dietary investigations and would likely reduce the number of conflicting observations between similar studies.

    “As seen in Figure 2, defining and stratifying those with a diet-responsive gut microbiota within an intervention cohort may enhance the predictable performance of these dietary investigations, and would likely reduce the number of conflicting observations between similar studies [16].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [16] Tebani, A., and Bekri, S. (2019). Paving the Way to Precision Nutrition Through Metabolomics. Front. Nutr., 6. source

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    Interindividual variability in response to diet is likely to be dependent on the baseline gut microbiota, and subsequently habitual diet.

    “Interindividual variability in response to diet is likely to be dependent on the baseline gut microbiota, and subsequently habitual diet.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S4 (based).

    Premisenone given

    The habitual diet of a host is considered a key driver in establishing the core microbial profile.

    “The habitual diet of a host is considered a key driver in establishing this core microbial profile.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    A 2019 mouse study by Yang et al. observed that these effects may vanish with the onset of extreme dietary conditions.

    “While a 2019 mouse study by Yang et al. observed that these effects may vanish with the onset of extreme dietary conditions [102], it’s unknown if this is replicated in humans.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [102] Yang, 2019, Assessing the Influence of Dietary History on Gut Microbiota, Curr. Microbiol. source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Non-responders could be characterised by high diversity, and individuals could be stratified into responders and non-responders based on the degree of microbiota stability.

    “Non-responders could be characterised by high diversity, and individuals could be stratified into responders and non-responders based on the degree of microbiota stability [73].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [73] Salonen, 2014, Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men, Isme J. source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S4 (based).

    Interpretationnone given

    Long-term stability of the core species within a host's gut microbiota is likely to be critical to associations with health and disease.

    “Arguably, the long-term stability of the core species within a host’s gut microbiota is likely to be critical to associations with health and disease.”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: Gut microbiota composition is a determinant of human health.

  • Probably not a substantial claim: may not pass S2 (checkable), S4 (based).

    Interpretationreasoning

    Stratifying study participants into responders and non-responders based on their baseline microbial profile may assist in eliciting improved outcomes.

    “Stratifying study participants into “responders” and “non-responders” based on their baseline microbial profile may assist in eliciting improved outcomes.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    By mapping an individual's gut microbiota, researchers were able to predict how fast their post-prandial response would be after eating a particular food, with each individual appearing to metabolise food very differently.

    “The researchers found that by mapping an individual’s gut microbiota they were able to predict how fast their post-prandial response would be after eating a particular food - with each individual appearing to metabolise food very differently [63].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [63] Zeevi, 2015, Personalized Nutrition by Prediction of Glycemic Responses, Cell source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Certain bacteria are suggested to be more diet-responsive than others, with exposure in mice to these diet-responsive bacteria suggested to enhance the response to a dietary intervention.

    “Certain bacteria are also suggested to be more diet-responsive than others, with exposure in mice to these diet-responsive bacteria suggested to enhance the response to a dietary intervention [77].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [77] Griffin, 2017, Prior Dietary Practices and Connections to a Human Gut Microbial Metacommunity Alter Responses to Diet Interventions, Cell Host Microbe source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    A number of studies have displayed that the gut microbiota typically reverts back to its baseline state post-intervention, with long-term diet thought to be a primary driver.

    “A number of studies have displayed that the gut microbiota typically reverts back to its baseline state post-intervention, with long-term diet thought to be a primary driver [109].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [109] Wilson, 2017, Systematic Review on Effects of Diet on Gut Microbiota in Relation to Metabolic Syndromes, J. Clin. Nutr. Metab.

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Synergistic symbiotic products combine prebiotics and probiotics to beneficially affect the host, and are developed to overcome possible survival difficulties for probiotics.

    “Synergistic symbiotic products combine prebiotics and probiotics to beneficially affect the host, and are developed to overcome possible survival difficulties for probiotics [117].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [117] Pandey, 2015, Probiotics, prebiotics and synbiotics—A review, J. Food Sci. Technol. source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Wu et al. suggested that differences in receptiveness to increased fibre intakes across human populations may be due to an absence of certain key fibre-degrading species within the restrictive core gut microbiota, that were found to be present in the permissive core gut microbiota.

    “Wu et al. suggested that this may be due to an absence of certain key fibre-degrading species within the “restrictive” core gut microbiota, that were found to be present in the “permissive” core gut microbiota [110].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [110] Wu, 2016, Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production, Gut source

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    Heterogeneity of research outcomes has impeded further insight into diet-microbiota relations, likely due to personalised responses of the host microbiota.

    “Additionally, heterogeneity of research outcomes has impeded further insight into these diet–microbiota relations, likely due to personalised responses of the host microbiota.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    The level of microbial resilience can be unique to a host's gut microbiota, with some able to return to their original state after a perturbation, and others establishing a new, possibly pathological, profile.

    “The level of microbial resilience can also be unique to a host’s gut microbiota, with some able to return to their original state after a perturbation, and others establishing a new, possibly pathological, profile [76].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [76] Smits, 2017, Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania, Science source

      Not checked in the free run.

65 of 65

  • The paper relies on this without support.

    Gut microbiota composition is a determinant of human health.

    “Our understanding of the duration required for a dietary intervention to have an enduring impact on the gut microbiota, and consequently health, is hampered by several limitations.”
    “Arguably, the long-term stability of the core species within a host’s gut microbiota is likely to be critical to associations with health and disease.”
1 of 1

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Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • David et al. study is cited to a Johnson et al. reference

    Minor

    The sentence about David et al.'s dietary experiment cites reference 35, which the reference list identifies as a Johnson et al. study. The same paragraph separately cites reference 18 for the David et al. results.

  • Berding et al. study is dated both 2019 and 2018

    Minor

    The text groups the Berding et al. study with two 2019 studies, but its reference-list entry gives a 2018 publication year.

  • Vatanen et al. are cited to a Francino reference

    Minor

    The text attributes this observation to Vatanen et al. and cites reference 13, but reference 13 lists Francino as its author. Vatanen et al. appear at reference 14.

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Authors
Leeming, E. R., Johnson, A. J., Spector, T. D., & Le Roy, C. I.
Affiliations
  • King's College London (GB)
  • University of Minnesota (US)
  • Department of Twin Research & Genetic Epidemiology, King’s College London, St Thomas’ Campus, Lambeth Palace Road, London SE1 7EH, UK
ORCID
Venue
Nutrients
Publisher
MDPI AG
Published
2019-11-22
Volume
11
Issue
12
Pages
2862
ISSN
2072-6643 (ISSN-L)
DOI
10.3390/nu11122862
PMC
PMC6950569
OpenAlex
W2990512216
Semantic Scholar
a6e74d21f43b1d49ad290575374f855537bac240
Cited by
817
References
118
Citations by year
2026: 71 · 2025: 128 · 2024: 169 · 2023: 156 · 2022: 156 · 2021: 98 · 2020: 38 · 2018: 1
FWCI
6.42
Type
journal article
Language
en
Open access
Licence
Locations
  • Nutrients (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Research Portal (King's College London) (submittedVersion, other-oa)
Funders
Chronic Disease Research Foundation (N/A)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
  • Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Nutritional Studies and Diet
  • Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
Keywords
gut microbiota, diet, dietary intervention, intervention duration, microbiome stability, habitual diet, dietary modulation of microbiota, microbial diversity
MeSH terms
Gastrointestinal Microbiome, Diet, Healthy, Nutrients, Duration of Therapy, Circadian Rhythm, Diet, Diet Therapy, Humans, Seasons, Probiotics, Prebiotics, Synbiotics

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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-06.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-06.

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