Diet impact on Microbiome

Many health issues are associated with western diet. When non-western cultures start imitating western eating habits, there are often an explosion of western health issues. I believe that several auto-immune conditions, including CFS/FM/IBS/UC/Crohn’s etc are included (that is the incidence increases). “An increasing number of human disease conditions, such as inflammatory bowel diseases (IBD), type 2 diabetes, obesity, allergies and colorectal cancer are linked with altered microbiota composition. Moreover, a clearer picture is emerging of the composition of the human microbiota in healthy individuals, its variability over time and between different persons and how the microbiota is shaped by environmental factors (i.e., diet) and the host’s genetic background.” [2015]

Since all of these conditions are associated with microbiome irregularity, I will just grind thru recent research on what is good or bad for the microbiome (across many conditions).

In addition to below, you may wish to check some related prior posts:

  • “Intake of dietary fiber is associated with reduced disease flares in patients with Crohn’s disease, but not UC. Recommendations to limit dietary fiber should be reevaluated.” [2015]
  • “A diet imbalance with high consumption of sugar and soft drinks and low consumption of vegetables was associated with UC risk.”[2015]
    • “Evidence from uncontrolled and controlled challenge studies suggests that malabsorbed sugars (fructose, sorbitol, lactose) and fructans may act as dietary triggers for clinical symptoms suggestive of IBS.”[2009]
  • ” westernization of diet with high sugar and fat are thought to be associated with rapidly increasing incidence of CD.” [2015] – China Paper
  • ” intake of zinc was inversely associated with risk of CD but not UC.” [2015] i.e. more zinc intake, less CD risk
  • ” supplementation of some types of dietary fibre can prolong remission and reduce lesions of the intestinal mucosa during the course of the disease… The patients were recommended to add 60 g of oat bran per day (corresponding to 20 g dietary fibre) to the diet for 3 months. The oat bran supplementation resulted in a statistically significant increase in the faecal short chain fatty acids concentration, in particular butyrate. None of the patients in the study group reported gastrointestinal complaints and there were no colitis relapses. ” [2015]
    • “Data on diet have been inconsistent, but high fiber intake, particularly of soluble fiber, appears to protect against CD, whereas protein intake may increase disease risk.”[2013]
    • ” long-term intake of dietary fiber, particularly from fruit, is associated with lower risk of CD but not UC.” [2013]
    • “Colitis was significantly reduced in all fructo-oligosaccharides-fed rats compared to the control diet, whereas inulin decreased chronic intestinal inflammation in only half the number of animals.” i.e. FOS is not inulin and it is much better than inulin.
      • patients with Crohn’s disease may be more sensitive to inulin intake” [2013]
    • “Results demonstrated that consuming a wheat bran-inclusive diet was feasible and caused no adverse effects, and participants consuming whole wheat bran in the diet reported improved health-related quality of life (p = .028) and gastrointestinal function (p = .008) compared to the attention control group.”[2014]
  • “greater intake of fish (P trend = 0.01) and fiber (P trend = 0.06) were associated with lower risk of CD.” [2015]
  • ” Epidemiological studies have suggested an inverse association between selenium levels and inflammatory bowel disease (IBD), which includes Crohn’s disease and ulcerative colitis that can potentially progress to colon cancer.”[2015]
    • “hold promise that adequate dietary Se supply may counteract chronic intestinal inflammation in humans”[2014]
    • “New Zealand has one of the highest incidence rates of Crohn‘s Disease (CD), whilst the serum selenium status of New Zealanders is amongst the lowest in the world.”[2012]
  • ” we determined that the polysaccharide dietary additive, maltodextrin (MDX), impairs cellular anti-bacterial responses and suppresses intestinal anti-microbial defense mechanisms”[2015]
    • ” geographical variation in CD correlates with emulsifier consumption as does the increasing incidence of CD in Japan; … very small concentrations of the emulsifier polysorbate 80 enhance bacterial translocation across intestinal epithelia.” [2013]
  • 500 mg [of curcumin/turmeric] twice per day for 3 weeks …The Crohn’s patients score dropped from 5 to 0 suggesting improvement.”[2013 Full Text]
  • “Clinical trials have shown benefit with enterically delivered phosphatidylcholine supplementation in UC and near-significant benefit with vitamin D supplementation in CD.”[2014]
  • ” In a population-based case-control study, breast-feeding, having pets, and better sanitary conditions were protective of IBD”[2015]
  • “There is circumstantial evidence from epidemiology studies that a diet deficient in folate may have contributed to the global rise in these diseases.” [2013]
    • “A significant inverse relation was observed between dietary folate equivalent consumption and migraine frequency.” [Feb 2015]
  • “Comparisons between controls and newly diagnosed patients showed that increased consumption of milk and yogurt (P = 0.042), fruits (P = 0.0001), citrus (P = 0.0001), vegetables (P = 0.0001), carrots (P = 0.0001), legumes (P = 0.036), fish and selfish (P = 0.001), honey (P = 0.003), and nuts (P = 0.038), was associated with decreased risk for CD. On the other hand, significantly increased intake of fat (P = 0.041), olive oil (P = 0.038), margarine (P = 0.038), sugar (P = 0.02), alcohol drinks (P = 0.009), fried food (P = 0.0001), and pasta (P = 0.0001), was noticed on recently diagnosed patients in comparison with the healthy control group.” [2012]
    • “Those who experience migraine at least once per week were more likely to have low intake of skim/low-fat milk and white and red wine.” [Aug 2015]
  • “CD showed positive association with urban residence (at birth and current), …and strict vegetarian dietary habit,..negative association with regular fish consumption”[2011]
  • “The average daily micronutrient intake of male and female patients, specifically of vitamin B1, B2, B6, folic acid, magnesium and iron, was significantly lower in celiac patients”[2013]
    • “More than 50% of patients had low plasma concentrations of vitamin C (84%), copper (84%), niacin (77%), and zinc (65%).”[2006]
  • A diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs)
    • A diet low in FODMAPs reduces symptoms of irritable bowel syndrome.Halmos EP, Power VA, Shepherd SJ, Gibson PR, Muir JG. [2014]
    • Low FODMAP diet information
    • “Diets differing in FODMAP content have marked effects on gut microbiota composition. The implications of long-term reduction of intake of FODMAPs require elucidation.”[2015]
  • We also recommend the use of the following supplements in the preventative treatment of migraines, in decreasing order of preference: magnesium, Petasites hybridus, feverfew, coenzyme Q10, riboflavin, and alpha lipoic acid.” [2009]
  • “Of these, sweet potatoes had the highest reported frequency of beneficial responses. We also identified 4 foods with detrimental effects in more than 25% of our study population. These were mustard, wasabi,  raw and cooked tomatoes” [2015]
    • ” Among commonly consumed individual raw vegetables, tomatoes, carrots, and scallions related significantly inversely to BP.”[2014]  – low BP is common with CFS
  • ” A small number of foods are frequently considered to be beneficial, including white fish, salmon and tuna, gluten-free products, oatmeal, bananas, boiled potatoes, sweet potatoes (kumara), pumpkin, soya milk, goat’s milk and yoghurt.” [2010]

Bottom Line

Going thru the above, I found a lot of overlap with items reported with CFS, hence I suspect that it will likely apply to CFS. Second, the results reported are not gospel!

  • ” Patient-targeted dietary recommendations focus on food restrictions and are highly conflicting.” [2014] “There is little evidence from interventional studies to support specific dietary recommendations” [2013]

REMEMBER appropriate probiotics will likely be needed to utilize this diet better.

From the above,  I conclude:

  • Stop Omega 6 supplementation, eat fish instead (which also provides Vitamin D)
  • Stop taking explicit inulin, instead use fructo-oligosaccharides
  • Decrease meat fat,  increase vegetables, specifically:
    • sweet potatoes
    • pumpkins
    • boiled potatoes
    • carrots
    • legumes
  • Increase fiber
    • oatmeal, oat bran
  • Increase fruits, specifically:
    • bananas
    • avoid tomatoes
  • Eliminate soft drinks and items with added sugar
    • If the ingrediants includes sugar — avoid
    • Sugars INCLUDE:
      • fructose,
      • sorbitol,
      • lactose
  • Avoid Emulsifers, (sometimes they are called “Conditioners” on labels) especially
  • Eat fish —  do not go strict vegetarian
  • Eat nuts


These are the same ones usually seen with CFS

  • Selenium (recommended levels may be set low — only enough to prevent certain diseases such as Keshan disease) – at least 75 µg/day
  • Vitamin D3 (15000-20000 IU/day should be discussed)
  • Magnesium
  • riboflavin
  • alpha lipoic acid.
  • CoQ10
  • Turmeric – 1000 mg/day
  • Zinc and Copper
  • B1, B6, B9 (Folate)

Tradition breads did not use sugar!!

Sugar was very expensive for a long time. Some modern bread has kept the old taste:



The bread below attempts to “look good -100% whole grain, no sugar” but contains emulsifers and a lot more:


Earlier Posts (Condition Specific)