Role of the gut microbiota in nutrition and health

In the paper

“Probiotics also seem to improve cardiometabolic parameters and reduced serum concentrationof C reactive protein in patients with type 2 diabetes.”

In the paper

“The analysis of 313 trials and 46 826 participants showed substantial evidence for beneficial effects of probiotic supplementation in preventing diarrhoea, necrotising enterocolitis, acute upper respiratory tract infections, pulmonary exacerbations in children with cystic fibrosis, and eczema in children.”

In the paper

“In humans, observational studies can show cross-sectional associations between microbes and health traits but are limited by the inability to measure causal relations.”

In the paper

“Butyrate is essential for epithelial cells to consume large amounts of oxygen through β oxidation, generating a state of hypoxia that maintains oxygen balance in the gut, preventing gut microbiota dysbiosis.19”

What the sources say

• Not checked yetcites [19] Byndloss MX Olsan EE Rivera-Chávez F Microbiota-activated PPAR-γ signaling inhibits dysbiotic Enterobacteriaceae expansion. Science 2017; 357: 570- 5. 10.1126/science.aam9949 28798125 PMC5642957

In the paper

“Animal models can help identify gut microbes and mechanisms, though the degree to which findings translate to humans is unknown.”

In the paper

“Acetate—the most abundant SCFA and an essential metabolite for the growth of other bacteria—reaches the peripheral tissues where it is used in cholesterol metabolism and lipogenesis, and may play a role in central appetite regulation.20”

What the sources say

• Not checked yetcites [20] Frost G Sleeth ML Sahuri-Arisoylu M The short-chain fatty acid acetate reduces appetite via a central homeostatic mechanism. Nat Commun 2014; 5: 3611. 10.1038/ncomms4611 24781306 PMC4015327

In the paper

“Butyrate is the main energy source for human colonocytes, can induce apoptosis of colon cancer cells, and can activate intestinal gluconeogenesis, having beneficial effects on glucose and energy homeostasis.18”

What the sources say

• Not checked yetcites [18] De Vadder F Kovatcheva-Datchary P Goncalves D Microbiota-generated metabolites promote metabolic benefits via gut-brain neural circuits. Cell 2014; 156: 84- 96. 10.1016/j.cell.2013.12.016 24412651

In the paper

“Butyrate and propionate, but not acetate, seem to control gut hormones and reduce appetite and food intake in mice.21”

What the sources say

• Not checked yetcites [21] Lin HV Frassetto A Kowalik EJ Jr Butyrate and propionate protect against diet-induced obesity and regulate gut hormones via free fatty acid receptor 3-independent mechanisms. PLoS One 2012; 7: e35240. 10.1371/journal.pone.0035240 22506074 PMC3323649

In the paper

“Acetate—the most abundant SCFA and an essential metabolite for the growth of other bacteria—reaches the peripheral tissues where it is used in cholesterol metabolism and lipogenesis, and may play a role in central appetite regulation.20”

What the sources say

• Not checked yetcites [20] Frost G Sleeth ML Sahuri-Arisoylu M The short-chain fatty acid acetate reduces appetite via a central homeostatic mechanism. Nat Commun 2014; 5: 3611. 10.1038/ncomms4611 24781306 PMC4015327

In the paper

“Twin studies have shown that, although there is a heritable component to gut microbiota, environmental factors related to diet, drugs, and anthropometric measures are larger determinants of microbiota composition.4 5”

What the sources say

• Not checked yetcites [4] Goodrich JK Waters JL Poole AC Human genetics shape the gut microbiome. Cell 2014; 159: 789- 99. 10.1016/j.cell.2014.09.053 25417156 PMC4255478
• Not checked yetcites [5] Rothschild D Weissbrod O Barkan E Environment dominates over host genetics in shaping human gut microbiota. Nature 2018; 555: 210- 5. 10.1038/nature25973 29489753

In the paper

“But recent interventional studies indicate that major increases in dietary fibre can temporarily reduce diversity, as the microbes that digest fibre become specifically enriched, leading to a change in composition and, through competitive interactions, reduced diversity.22”

What the sources say

• Not checked yetcites [22] Zhao L Zhang F Ding X Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes. Science 2018; 359: 1151- 6. 10.1126/science.aao5774 29590046

In the paper

“Specific foods and dietary patterns can all influence the abundance of different types of bacteria in the gut, which in turn can affect health (table 1).”

In the paper

“A large study of UK twins found that the genus Christensenella was rare in overweight people and when given to germ free mice prevented weight gain.4”

What the sources say

• Not checked yetcites [4] Goodrich JK Waters JL Poole AC Human genetics shape the gut microbiome. Cell 2014; 159: 789- 99. 10.1016/j.cell.2014.09.053 25417156 PMC4255478

In the paper

“Trimethylamine is oxidised in the liver to trimethylamine N-oxide, which is positively associated with an increased risk of atherosclerosis and major adverse cardiovascular events.24”

What the sources say

• Not checked yetcites [24] Tang WH Wang Z Levison BS Intestinal microbial metabolism of phosphatidylcholine and cardiovascular risk. N Engl J Med 2013; 368: 1575- 84. 10.1056/NEJMoa1109400 23614584 PMC3701945

In the paper

“Although much of the confirmatory evidence comes from mouse models, long term weight gain (over 10 years) in humans correlates with low microbiota diversity, and this association is exacerbated by low dietary fibre intake.28”

What the sources say

• Not checked yetcites [28] Menni C Jackson MA Pallister T Steves CJ Spector TD Valdes AM Gut microbiome diversity and high-fibre intake are related to lower long-term weight gain. Int J Obes (Lond) 2017; 41: 1099- 105. 10.1038/ijo.2017.66 28286339 PMC5500185

In the paper

“The production of trimethylamine from dietary phosphatidylcholine and carnitine (from meat and dairy) depends on the gut microbiota and thus its amount in blood varies between people.”

What the sources say

• Not checked yetcites [24] Tang WH Wang Z Levison BS Intestinal microbial metabolism of phosphatidylcholine and cardiovascular risk. N Engl J Med 2013; 368: 1575- 84. 10.1056/NEJMoa1109400 23614584 PMC3701945

In the paper

“This procedure is effective in cases of severe drug refractory Clostridium difficile infection and is now routinely used for this purpose around the world.43”

What the sources say

• Not checked yetcites [43] Schneider KM Wirtz TH Kroy D Successful fecal microbiota transplantation in a patient with severe complicated Clostridium difficile infection after liver transplantation. Case Rep Gastroenterol 2018; 12: 76- 84. 10.1159/000481937 29606940 PMC5869577

In the paper

“Mice given sucralose for six months had an increase in the expression in the gut of bacterial pro-inflammatory genes and disrupted faecal metabolites.48”

What the sources say

• Not checked yetcites [48] Bian X Chi L Gao B Tu P Ru H Lu K Gut microbiome response to sucralose and its potential role in inducing liver inflammation in mice. Front Physiol 2017; 8: 487. 10.3389/fphys.2017.00487 28790923 PMC5522834

In the paper

“The association between reduced diversity and disease indicates that a species-rich gut ecosystem is more robust against environmental influences, as functionally related microbes in an intact ecosystem can compensate for the function of other missing species.”

In the paper

“For other pathologies, faecal transplants are not yet clinical practice but have been explored.44”

What the sources say

• Not checked yetcites [44] Cammarota G Ianiro G Tilg H European FMT Working Group European consensus conference on faecal microbiota transplantation in clinical practice. Gut 2017; 66: 569- 80. 10.1136/gutjnl-2016-313017 28087657 PMC5529972

In the paper

“Bacteroidales and Verrucomicrobia were decreased and inflammation promoting Proteobacteria associated with mucus was enriched .49”

What the sources say

• Not checked yetcites [49] Chassaing B Koren O Goodrich JK Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome. Nature 2015; 519: 92- 6. 10.1038/nature14232 25731162 PMC4910713

In the paper

“But healthy microbiota are resilient to temporal changes by dietary interventions, meaning that homeostatic reactions restore the original community composition, as recently shown in the case of bread 68”

What the sources say

• Not checked yetcites [68] Korem T, Zeevi D, Zmora N, et al. Bread affects clinical parameters and induces gut microbiome-associated personal glycemic responses. Cell Metabolism. 2017; 25: 1243-53 e5. 28591632

In the paper

“Pesticides and other chemicals are commonly sprayed on foods, but, although levels can be high, solid evidence for their harm on gut health and the effects of organic food is currently lacking.63”

What the sources say

• Not checked yetcites [63] Lee YM Kim KS Jacobs DR Jr Lee DH Persistent organic pollutants in adipose tissue should be considered in obesity research. Obes Rev 2017; 18: 129- 39. 10.1111/obr.12481 27911986

In the paper

“But humans have very variable responses to antibiotics, and intervention studies have not shown consistent metabolic consequences.62”

What the sources say

• Not checked yetcites [62] Reijnders D Goossens GH Hermes GD Effects of gut microbiota manipulation by antibiotics on host metabolism in obese humans: A randomized double-blind placebo-controlled trial. Cell Metab 2016; 24: 63- 74. 10.1016/j.cmet.2016.06.016 27411009

In the paper

“It is associated with a reduced proportion of Bifidobacterium in patients with irritable bowel syndrome, and responsiveness to this diet can be predicted by faecal bacterial profiles.57”

What the sources say

• Not checked yetcites [57] Bennet SMP Bohn L Storsrud S Multivariate modelling of faecal bacterial profiles of patients with IBS predicts responsiveness to a diet low in FODMAPs. Gut 2017. 28416515

In the paper

“Probiotic supplementation has several beneficial effects on human health”

In the paper

“Increased abundance of known butyrate producing bacteria in the African Americans consuming a rural African diet caused butyrate production to increase 2.5 times and reduced synthesis of secondary bile acid.66”

What the sources say

• Not checked yetcites [66] O'Keefe SJ, Li JV and Lahti L. Fat, fibre and cancer risk in African Americans and rural Africans. 2015; 6: 6342. PMC4415091 25919227

In the paper

“A controlled feeding experiment of 10 human omnivores randomised to receive either a high fat and low fibre diet or a low fat and high fibre for 10 days found very modest effects on gut microbiome composition and no difference in short chain fatty acid production.”

What the sources say

• Not checked yetcites [50] Wu GD Compher C Chen EZ Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production. Gut 2016; 65: 63- 72. 10.1136/gutjnl-2014-308209 25431456 PMC4583329

In the paper

“Other studies have shown major effects of commonly prescribed proton pump inhibitors on the microbial community, which could explain higher rates of gastrointestinal infection in people taking these drugs.60”

What the sources say

• Not checked yetcites [60] Jackson MA Goodrich JK Maxan ME Proton pump inhibitors alter the composition of the gut microbiota. Gut 2016; 65: 749- 56. 10.1136/gutjnl-2015-310861 26719299 PMC4853574

In the paper

“Microbiome composition defines glucose response to foods and can be used to personalise diet94”

What the sources say

• Not checked yetcites [94] Zeevi D Korem T Zmora N Personalized nutrition by prediction of glycemic responses. Cell 2015; 163: 1079- 94. 10.1016/j.cell.2015.11.001 26590418

In the paper

“Dietary amounts of protein, saturated and unsaturated fats, carbohydrates, and dietary fibre influence the abundance of different types of bacteria in the gut.”

In the paper

“The taxa enriched differ depending on the type of resistant starches and other dietary fibres,75 indicating that shifts are dependent on the carbohydrate’s chemical structure and the microbes’ enzymatic capacity to access them.”

What the sources say

• Not checked yetcites [75] Martínez I Kim J Duffy PR Schlegel VL Walter J Resistant starches types 2 and 4 have differential effects on the composition of the fecal microbiota in human subjects. PLoS One 2010; 5: e15046. 10.1371/journal.pone.0015046 21151493 PMC2993935

In the paper

“Low FODMAP diets lead to profound changes in the microbiota and metabolome, the duration and clinical relevance of which are as yet unknown.58 59”

What the sources say

• Not checked yetcites [58] McIntosh K Reed DE Schneider T FODMAPs alter symptoms and the metabolome of patients with IBS: a randomised controlled trial. Gut 2017; 66: 1241- 51. 10.1136/gutjnl-2015-311339 26976734
• Not checked yetcites [59] Staudacher HM Whelan K The low FODMAP diet: recent advances in understanding its mechanisms and efficacy in IBS. Gut 2017; 66: 1517- 27. 10.1136/gutjnl-2017-313750 28592442

In the paper

“Microbes need also to “adhere” to a substrate and tolerate the conditions generated from fermentation (such as low pH).76”

What the sources say

• Not checked yetcites [76] Koropatkin NM Cameron EA Martens EC How glycan metabolism shapes the human gut microbiota. Nat Rev Microbiol 2012; 10: 323- 35. 10.1038/nrmicro2746 22491358 PMC4005082

In the paper

“Dietary fibre intake influences gut microbiota composition and is related to better health86 87 104”

What the sources say

• Not checked yetcites [86] Veronese N Solmi M Caruso MG Dietary fiber and health outcomes: an umbrella review of systematic reviews and meta-analyses. Am J Clin Nutr 2018; 107: 436- 44. 10.1093/ajcn/nqx082 29566200
• Not checked yetcites [87] Thompson SV Hannon BA An R Holscher HD Effects of isolated soluble fiber supplementation on body weight, glycemia, and insulinemia in adults with overweight and obesity: a systematic review and meta-analysis of randomized controlled trials. Am J Clin Nutr 2017; 106: 1514- 28. 10.3945/ajcn.117.163246 29092878
• Not checked yetcites [104]

In the paper

“The microbiota can also be modified by adding live micro-organisms to food or by periods of fasting.”

In the paper

“One study showed that 21 healthy people had substantially different gut microbiota profiles after four weeks on a gluten-free diet. Most people showed a lower abundance of several key beneficial microbe species.54”

What the sources say

• Not checked yetcites [54] Bonder MJ Tigchelaar EF Cai X The influence of a short-term gluten-free diet on the human gut microbiome. Genome Med 2016; 8: 45. 10.1186/s13073-016-0295-y 27102333 PMC4841035

In the paper

“But most people who avoid gluten do not have coeliac disease or proved intolerance, and a recent large observational study showed an increased risk of heart disease in gluten avoiders, potentially because of the reduced consumption of whole grains.53”

What the sources say

• Not checked yetcites [53] Lebwohl B Cao Y Zong G Long term gluten consumption in adults without celiac disease and risk of coronary heart disease: prospective cohort study. BMJ 2017; 357: j1892. 10.1136/bmj.j1892 28465308 PMC5421459

In the paper

“Diet and medication have a strong influence on gut microbiota composition”

In the paper

“Antibiotics clearly have an effect on gut microbes, and low doses are routinely given to livestock to increase their growth and weight.”

In the paper

“These changes only last as long as the carbohydrate is consumed, and they are highly individual, which provides a basis for personalised approaches.”

What the sources say

• Not checked yetcites [75] Martínez I Kim J Duffy PR Schlegel VL Walter J Resistant starches types 2 and 4 have differential effects on the composition of the fecal microbiota in human subjects. PLoS One 2010; 5: e15046. 10.1371/journal.pone.0015046 21151493 PMC2993935
• Not checked yetcites [77] Walker AW Ince J Duncan SH Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J 2011; 5: 220- 30. 10.1038/ismej.2010.118 20686513 PMC3105703

In the paper

“Changes to the gut microbiota can occur within days of changing diet; remarkable differences were found after African Americans and rural Africans switched diets for only two weeks.66”

What the sources say

• Not checked yetcites [66] O'Keefe SJ, Li JV and Lahti L. Fat, fibre and cancer risk in African Americans and rural Africans. 2015; 6: 6342. PMC4415091 25919227

In the paper

“A study of 15 vegans and 16 ominvores found striking differences in serum metabolites generated by the gut microbes but very modest differences in gut bacterial communities.50”

What the sources say

• Not checked yetcites [50] Wu GD Compher C Chen EZ Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production. Gut 2016; 65: 63- 72. 10.1136/gutjnl-2014-308209 25431456 PMC4583329

In the paper

“Many short term feeding trials with purified dietary fibres or even whole plant based diets either have no effect on microbiota diversity or reduce it,22 but can still have clinical benefits, potentially through metabolites such as small chain fatty acids.22 67”

What the sources say

• Not checked yetcites [22] Zhao L Zhang F Ding X Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes. Science 2018; 359: 1151- 6. 10.1126/science.aao5774 29590046
• Not checked yetcites [67] David LA Maurice CF Carmody RN Diet rapidly and reproducibly alters the human gut microbiome. Nature 2014; 505: 559- 63. 10.1038/nature12820 24336217 PMC3957428

In the paper

“Stable engraftment of a probiotic Bifidobacterium longum, for example, has been shown to depend on individualised features of the gut microbiota, providing a rationale for the personalisation of probiotic applications.93”

What the sources say

• Not checked yetcites [93] Maldonado-Gómez MX Martínez I Bottacini F Stable engraftment of Bifidobacterium longum AH1206 in the human gut depends on individualized features of the resident microbiome. Cell Host Microbe 2016; 20: 515- 26. 10.1016/j.chom.2016.09.001 27693307

In the paper

“and a recent intervention study found dietary fibres significantly reduced insulin resistance in patients with type 2 diabetes, with clear links to the shifts in the microbiota and beneficial metabolites (such as butyrate).45”

What the sources say

• Not checked yetcites [45] Kootte RS, Levin E, Salojarvi J, et al. Improvement of insulin sensitivity after lean donor feces in metabolic syndrome is driven by baseline intestinal microbiota composition. Cell metabolism. 2017; 26: 611-9 e6. 28978426

In the paper

“- Fibre consumption is associated with beneficial effects in several contexts”

In the paper

“- Gut microbiota influences many areas of human health from innate immunity to appetite and energy metabolism”

In the paper

“Importantly, the studies were not homogeneous and were not necessarily matched for type or dose of probiotic supplementation nor length of intervention, which limits precise recommendations.”

In the paper

“Low fibre intake reduces production of small chain fatty acids and shifts the gastrointestinal microbiota metabolism to use less favourable nutrients,78 leading to the production of potentially detrimental metabolites.79 80”

What the sources say

• Not checked yetcites [78] Cummings JH Macfarlane GT The control and consequences of bacterial fermentation in the human colon. J Appl Bacteriol 1991; 70: 443- 59. 10.1111/j.1365-2672.1991.tb02739.x 1938669
• Not checked yetcites [79] Russell WR Gratz SW Duncan SH High-protein, reduced-carbohydrate weight-loss diets promote metabolite profiles likely to be detrimental to colonic health. Am J Clin Nutr 2011; 93: 1062- 72. 10.3945/ajcn.110.002188 21389180
• Not checked yetcites [80] Duncan SH Belenguer A Holtrop G Johnstone AM Flint HJ Lobley GE Reduced dietary intake of carbohydrates by obese subjects results in decreased concentrations of butyrate and butyrate-producing bacteria in feces. Appl Environ Microbiol 2007; 73: 1073- 8. 10.1128/AEM.02340-06 17189447 PMC1828662

In the paper

“Convincing evidence shows that the low fibre Western diet degrades the colonic mucus barrier, causing microbiota encroachment, which results in pathogen susceptibility81and inflammation,82 providing a potential mechanism for the links of Western diet with chronic diseases.”

What the sources say

• Not checked yetcites [81] Desai MS Seekatz AM Koropatkin NM A dietary fiber-deprived gut microbiota degrades the colonic mucus barrier and enhances pathogen susceptibility. Cell 2016; 167: 1339- 1353.e21. 10.1016/j.cell.2016.10.043 27863247 PMC5131798
• Not checked yetcites [82] Earle KA Billings G Sigal M Quantitative imaging of gut microbiota spatial organization. Cell Host Microbe 2015; 18: 478- 88. 10.1016/j.chom.2015.09.002 26439864 PMC4628835

In the paper

“- Drugs, food ingredients, antibiotics, and pesticides could all have adverse effects on the gut microbiota”

In the paper

“But probiotics can affect health independently of the gut microbiota through direct effects on the host; for example, through immune modulation or the production of bioactive compounds.”