Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration

In the paper

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

In the paper

“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].”

What the sources say

• Not checked yetcites [3] Zhang, 2010, Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice, ISME J. source
• Not checked yetcites [4] Rothschild, 2018, Environment dominates over host genetics in shaping human gut microbiota, Nature source

In the paper

“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].”

What the sources say

• Not checked yetcites [2] Valdes, 2018, Role of the gut microbiota in nutrition and health, BMJ source

In the paper

“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].”

What the sources say

• Not checked yetcites [7] Goodrich, 2016, Genetic Determinants of the Gut Microbiome in UK Twins, Cell Host Microbe source

In the paper

“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.”

What the sources say

• Not checked yetcites [6] Wu, 2011, Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes, Science source

In the paper

“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.”

In the paper

“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].”

What the sources say

• Not checked yetcites [4] Rothschild, 2018, Environment dominates over host genetics in shaping human gut microbiota, Nature source

In the paper

“However, these alterations are transient and do not persist for more than a few days [5].”

What the sources say

• Not checked yetcites [5] David, 2014, Host lifestyle affects human microbiota on daily timescales, Genome Biol. source

In the paper

“While diet can induce a shift in the gut microbiota, these changes appear to be temporary.”

What the sources say

• Not checked yetcites [5] David, 2014, Host lifestyle affects human microbiota on daily timescales, Genome Biol. source

In the paper

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

In the paper

“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].”

What the sources say

• Not checked yetcites [20] Liang, 2017, Timing the Microbes: The Circadian Rhythm of the Gut Microbiome, J. Biol. Rhythm. source
• Not checked yetcites [22] Thaiss, 2014, Transkingdom Control of Microbiota Diurnal Oscillations Promotes Metabolic Homeostasis, Cell source
• Not checked yetcites [23] Thaiss, 2016, Persistent microbiome alterations modulate the rate of post-dieting weight regain, Nature source

In the paper

“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].”

What the sources say

• Not checked yetcites [18] David, 2014, Diet rapidly and reproducibly alters the human gut microbiome, Nature source

In the paper

“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].”

What the sources say

• Not checked yetcites [22] Thaiss, 2014, Transkingdom Control of Microbiota Diurnal Oscillations Promotes Metabolic Homeostasis, Cell source

In the paper

“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.”

In the paper

“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].”

What the sources say

• Not checked yetcites [53] Licciardi, 2010, Epigenome targeting by probiotic metabolites, Gut Pathog. source

In the paper

“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].”

What the sources say

• Not checked yetcites [6] Wu, 2011, Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes, Science source

In the paper

“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.”

In the paper

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

In the paper

“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.”

What the sources say

• Not checked yetcites [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

In the paper

“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].”

What the sources say

• Not checked yetcites [34] Xu, 2015, Dietary effects on human gut microbiome diversity, Br. J. Nutr. source

In the paper

“However, probiotic outcomes can be unpredictable and individualised.”

In the paper

“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].”

What the sources say

• Not checked yetcites [52] Kristensen, 2016, Alterations in fecal microbiota composition by probiotic supplementation in healthy adults: A systematic review of randomized controlled trials, Genome Med. source

In the paper

“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].”

What the sources say

• Not checked yetcites [18] David, 2014, Diet rapidly and reproducibly alters the human gut microbiome, Nature source

In the paper

“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].”

What the sources say

• Not checked yetcites [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

In the paper

“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.”

In the paper

“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].”

What the sources say

• Not checked yetcites [51] Sanders, 2018, Probiotics for human use, Nutr. Bull. source

In the paper

“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].”

What the sources say

• Not checked yetcites [28] Collado, 2018, Timing of food intake impacts daily rhythms of human salivary microbiota: A randomized, crossover study, FASEB J. source

In the paper

“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].”

What the sources say

• Not checked yetcites [51] Sanders, 2018, Probiotics for human use, Nutr. Bull. source

In the paper

“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].”

What the sources say

• Not checked yetcites [6] Wu, 2011, Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes, Science source

In the paper

“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].”

What the sources say

• Not checked yetcites [44] Li, 2019, Efficacy of Lactobacillus rhamnosus GG in treatment of acute pediatric diarrhea: A systematic review with meta-analysis, World J. Gastroenterol. source
• Not checked yetcites [45] Hungin, 2018, Systematic review: Probiotics in the management of lower gastrointestinal symptoms—An updated evidence-based international consensus, Aliment Pharm. source
• Not checked yetcites [46] Derwa, 2017, Systematic review with meta-analysis: The efficacy of probiotics in inflammatory bowel disease, Aliment Pharm. source
• Not checked yetcites [47] Krumbeck, 2018, Synbiotics for Improved Human Health: Recent Developments, Challenges, and Opportunities, Annu. Rev. Food Sci. Technol. source

In the paper

“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].”

What the sources say

• Not checked yetcites [37] So, 2018, Dietary fiber intervention on gut microbiota composition in healthy adults: A systematic review and meta-analysis, Am. J. Clin. Nutr. source

In the paper

“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.”

What the sources say

• Not checked yetcites [76] Smits, 2017, Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania, Science source

In the paper

“In rodents, seasonal differences in the length of day has been shown to effect the composition of their microbial profile [90].”

What the sources say

• Not checked yetcites [90] Bailey, 2010, Photoperiod modulates gut bacteria composition in male Siberian hamsters (Phodopus sungorus), Brain Behav. Immun. source

In the paper

“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.”

What the sources say

• Not checked yetcites [92] Cardona, 2013, Benefits of polyphenols on gut microbiota and implications in human health, J. Nutr. Biochem. source

In the paper

“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,”

What the sources say

• Not checked yetcites [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

In the paper

“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].”

What the sources say

• Not checked yetcites [37] So, 2018, Dietary fiber intervention on gut microbiota composition in healthy adults: A systematic review and meta-analysis, Am. J. Clin. Nutr. source

In the paper

“Alongside fibre, magnesium, biotin, and vitamin E have all been shown to impact visceral fat mass accumulation mediated by the gut microbiota [79].”

What the sources say

• Not checked yetcites [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

In the paper

“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.”

What the sources say

• Not checked yetcites [97] Zinöcker, M.K., and Lindseth, I.A. (2018). The Western Diet-Microbiome-Host Interaction and Its Role in Metabolic Disease. Nutrients, 10. source

In the paper

“Food sources of fibre, such as whole grains, have been suggested to have a prebiotic-like effect on the gut microbiota [60].”

What the sources say

• Not checked yetcites [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

In the paper

“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].”

What the sources say

• Not checked yetcites [59] Tamashiro, 2018, Role of prebiotics in regulation of microbiota and prevention of obesity, Food Res. Int. source

In the paper

“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.”

In the paper

“The Western diet has been strongly associated with obesity and metabolic diseases, though the biological mechanisms remain unknown [97].”

What the sources say

• Not checked yetcites [97] Zinöcker, M.K., and Lindseth, I.A. (2018). The Western Diet-Microbiome-Host Interaction and Its Role in Metabolic Disease. Nutrients, 10. source

In the paper

“Habitual diet has been shown to be associated with a distinct compositional enterotype, while short-term dietary intake has not [6].”

What the sources say

• Not checked yetcites [6] Wu, 2011, Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes, Science source

In the paper

“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].”

What the sources say

• Not checked yetcites [92] Cardona, 2013, Benefits of polyphenols on gut microbiota and implications in human health, J. Nutr. Biochem. source

In the paper

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

In the paper

“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.”

In the paper

“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].”

What the sources say

• Not checked yetcites [81] Claesson, 2012, Gut microbiota composition correlates with diet and health in the elderly, Nature source

In the paper

“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.”

In the paper

“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].”

What the sources say

• Not checked yetcites [74] Dao, 2016, Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: Relationship with gut microbiome richness and ecology, Gut source

In the paper

“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].”

What the sources say

• Not checked yetcites [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

In the paper

“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].”

What the sources say

• Not checked yetcites [105] Falony, 2018, Richness and ecosystem development across faecal snapshots of the gut microbiota, Nat. Microbiol. source

In the paper

“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].”

What the sources say

• Not checked yetcites [16] Tebani, A., and Bekri, S. (2019). Paving the Way to Precision Nutrition Through Metabolomics. Front. Nutr., 6. source

In the paper

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

In the paper

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

In the paper

“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.”

What the sources say

• Not checked yetcites [102] Yang, 2019, Assessing the Influence of Dietary History on Gut Microbiota, Curr. Microbiol. source

In the paper

“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].”

What the sources say

• Not checked yetcites [73] Salonen, 2014, Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men, Isme J. source

In the paper

“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.”

In the paper

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

In the paper

“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].”

What the sources say

• Not checked yetcites [63] Zeevi, 2015, Personalized Nutrition by Prediction of Glycemic Responses, Cell source

In the paper

“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].”

What the sources say

• Not checked yetcites [77] Griffin, 2017, Prior Dietary Practices and Connections to a Human Gut Microbial Metacommunity Alter Responses to Diet Interventions, Cell Host Microbe source

In the paper

“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].”

What the sources say

• Not checked yetcites [109] Wilson, 2017, Systematic Review on Effects of Diet on Gut Microbiota in Relation to Metabolic Syndromes, J. Clin. Nutr. Metab.

In the paper

“Synergistic symbiotic products combine prebiotics and probiotics to beneficially affect the host, and are developed to overcome possible survival difficulties for probiotics [117].”

What the sources say

• Not checked yetcites [117] Pandey, 2015, Probiotics, prebiotics and synbiotics—A review, J. Food Sci. Technol. source

In the paper

“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].”

What the sources say

• Not checked yetcites [110] Wu, 2016, Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production, Gut source

In the paper

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

In the paper

“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].”

What the sources say

• Not checked yetcites [76] Smits, 2017, Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania, Science source