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Factors Affecting the Microbiota

The latest research in this area all point to the same conclusions. Diet, stress and genetics have an immense impact on the microorganisms that reside in our digestive tract, and this has a direct relationship to disease states and health [1].


Our dietary choices have one of the biggest impacts on our gut microbiota and the research in this area is abundant. The issue is that due to the large complexity of the microbiota itself and the research on this topic, deriving any useful conclusion remains difficult.

How strong is the impact of diet?
Experiments on mice have shown that a change from a low fat diet rich in plant polysaccharides to a typical Western diet (high in fat and sugar) triggered change in the microbial composition after just 1 day.

Carbohydrates seems to have one of the biggest influences of the microbiota composition. This is primarily because every singly day roughly 20g-60g of dietary carbohydrates reach the colon undigested (by enzymes) [2, 3], becoming a prime energy source for the residing microbial communities. And it has been documented that changing the amount and/or type of carbohydrate for the duration as little as 4 weeks can have a drastic impact on the microbiota composition [4, 5, 6].

Overall, the research suggest that insoluble fiber is one of the most beneficial dietary components for a healthy intestinal microbiota. A high intake of insoluble fiber has been associated with reduced carcinogenic enzyme concentrations, improved glucose tolerance, a reduction in negative effects caused by high fat and high protein consumption, improved short chain fatty acid production and reduction of inflammatory markers [7, 8, 9]

It is estimated that every single day roughly 12-18g of protein reach the human colon. And increasing the amount and quality of protein has a direct impact on the amount reaching the gut undigested. [2]. Studies show that higher dietary protein consumption has been linked to greater DNA damage in colonic mucosa (particularly when levels of fermentable carbohydrates are low), improved formation of beneficial short chain fatty acids, and increased production of gases and metabolites [10, 11].

Fat gets a ton of blame for a variety of metabolism disorders and microbiota research supports these believes. In general, high fat diets have been shown to decrease the amount of short chain fatty acid production, increase inflammatory makers, increase intestinal permeability and reduce glucose tolerance [12, 13, 7].


Stress has also been shown to have significant affect on the gut microbiota and it’s affects are attributed to the biological communication occurring through the gut-brain axis. Research in this area suggests that stress has been shown to lower the amount of beneficial lactobacillus, increase intestinal permeability and modulate the mucosal immune response [14, 15]. However, because of the two-directional relationship (gut microbiota can influence ones ability to handle stress), the overall implications of this remain unclear.


Genetics appear to also have a significant influence on the composition of our microbiota [16, 17].

Certain genes determine our ability to effectively digest certain nutrients such as carbohydrates [18]. If we unknowingly step outside of our body’s ability to digest these nutrients by enzymes, they are passed into the colon and fermented by the bacteria that reside there. Opportunistic bacteria may take advantage of this and can disrupt the balance of the whole community of the colon.

Section Summary

This section reviewed some of the most important factors affecting the intestinal microbiota and presented some relevant research findings. Key points include:

  1. Diet, stress and genetics have a significant impact on the composition of the intestinal microbiota, with diet being the most influential
  2. The amount and type of carbohydrates in your diet appears to be one of the key dietary influencers and adjustments can cause rapid microbiota changes
  3. A high intake of insoluble fiber appears to be one of the most beneficial dietary influencers on the composition of the microbiota
  4. High protein and/or fat consumption has been linked to several negative effects, but their impact can be reduced by high fiber consumption
  5. The negative impact of stress has also been demonstrated, but due to the two-directional relationship it’s effect remains unclear
  6. Genetics influence the level and types of enzymes our digestive systems product and this influences which nutrients reach the colon undigested


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  2. Karen P Scott, Silvia W Gratz, Paul O Sheridan, Harry J Flint, Sylvia H Duncan "The influence of diet on the gut microbiota." Pharmacological research 69.1 (2013): 52-60. PubMed
  3. Harry J Flint, Karen P Scott, Sylvia H Duncan, Petra Louis, Evelyne Forano "Microbial degradation of complex carbohydrates in the gut." Gut microbes 3.4 (2012): 289-306. PubMed
  4. Alan W Walker, Jennifer Ince, Sylvia H Duncan, Lucy M Webster, Grietje Holtrop, Xiaolei Ze, David Brown, Mark D Stares, Paul Scott, Aurore Bergerat, Petra Louis, Freda McIntosh, Alexandra M Johnstone, Gerald E Lobley, Julian Parkhill, Harry J Flint "Dominant and diet-responsive groups of bacteria within the human colonic microbiota." The ISME journal 5.2 (2011): 220-30. PubMed
  5. Sylvia H Duncan, Alvaro Belenguer, Grietje Holtrop, Alexandra M Johnstone, Harry J Flint, Gerald E Lobley "Reduced dietary intake of carbohydrates by obese subjects results in decreased concentrations of butyrate and butyrate-producing bacteria in feces." Applied and environmental microbiology 73.4 (2007): 1073-8. PubMed
  6. Wendy R Russell, Silvia W Gratz, Sylvia H Duncan, Grietje Holtrop, Jennifer Ince, Lorraine Scobbie, Garry Duncan, Alexandra M Johnstone, Gerald E Lobley, R John Wallace, Garry G Duthie, Harry J Flint "High-protein, reduced-carbohydrate weight-loss diets promote metabolite profiles likely to be detrimental to colonic health." The American journal of clinical nutrition 93.5 (2011): 1062-72. PubMed
  7. P D Cani, A M Neyrinck, F Fava, C Knauf, R G Burcelin, K M Tuohy, G R Gibson, N M Delzenne "Selective increases of bifidobacteria in gut microflora improve high-fat-diet-induced diabetes in mice through a mechanism associated with endotoxaemia." Diabetologia 50.11 (2007): 2374-83. PubMed
  8. Michael A Conlon, Anthony R Bird "The impact of diet and lifestyle on gut microbiota and human health." Nutrients 7.1 (2014): 17-44. PubMed
  9. Wendy Russell, Garry Duthie "Plant secondary metabolites and gut health: the case for phenolic acids." The Proceedings of the Nutrition Society 70.3 (2011): 389-96. PubMed
  10. Teresa Norat, Sheila Bingham, Pietro Ferrari, Nadia Slimani, Mazda Jenab, Mathieu Mazuir, Kim Overvad, Anja Olsen, Anne Tjønneland, Francoise Clavel, Marie-Christine Boutron-Ruault, Emmanuelle Kesse, Heiner Boeing, Manuela M Bergmann, Alexandra Nieters, Jakob Linseisen, Antonia Trichopoulou, Dimitrios Trichopoulos, Yannis Tountas, Franco Berrino, Domenico Palli, Salvatore Panico, Rosario Tumino, Paolo Vineis, H Bas Bueno-de-Mesquita, Petra H M Peeters, Dagrun Engeset, Eiliv Lund, Guri Skeie, Eva Ardanaz, Carlos González, Carmen Navarro, J Ramón Quirós, María-José Sanchez, Göran Berglund, Irene Mattisson, Göran Hallmans, Richard Palmqvist, Nicholas E Day, Kay-Tee Khaw, Timothy J Key, Miguel San Joaquin, Bertrand Hémon, Rodolfo Saracci, Rudolf Kaaks, Elio Riboli "Meat, fish, and colorectal cancer risk: the European Prospective Investigation into cancer and nutrition." Journal of the National Cancer Institute 97.12 (2005): 906-16. PubMed
  11. Shusuke Toden, Anthony R Bird, David L Topping, Michael A Conlon "Differential effects of dietary whey, casein and soya on colonic DNA damage and large bowel SCFA in rats fed diets low and high in resistant starch." The British journal of nutrition 97.3 (2007): 535-43. PubMed
  12. Grant D Brinkworth, Manny Noakes, Peter M Clifton, Anthony R Bird "Comparative effects of very low-carbohydrate, high-fat and high-carbohydrate, low-fat weight-loss diets on bowel habit and faecal short-chain fatty acids and bacterial populations." The British journal of nutrition 101.10 (2009): 1493-502. PubMed
  13. Ana Paula Boroni Moreira, Tatiana Fiche Salles Texeira, Alessandra Barbosa Ferreira, Maria do Carmo Gouveia Peluzio, Rita de Cássia Gonçalves Alfenas "Influence of a high-fat diet on gut microbiota, intestinal permeability and metabolic endotoxaemia." The British journal of nutrition 108.5 (2012): 801-9. PubMed
  14. Femke Lutgendorff, Louis M A Akkermans, Johan D Söderholm "The role of microbiota and probiotics in stress-induced gastro-intestinal damage." Current molecular medicine 8.4 (2008): 282-98. PubMed
  15. Sang H Rhee, Charalabos Pothoulakis, Emeran A Mayer "Principles and clinical implications of the brain-gut-enteric microbiota axis." Nature reviews. Gastroenterology & hepatology 6.5 (2009): 306-14. PubMed
  16. Jose C Clemente, Luke K Ursell, Laura Wegener Parfrey, Rob Knight "The impact of the gut microbiota on human health: an integrative view." Cell 148.6 (2012): 1258-70. PubMed
  17. Julia K Goodrich, Jillian L Waters, Angela C Poole, Jessica L Sutter, Omry Koren, Ran Blekhman, Michelle Beaumont, William Van Treuren, Rob Knight, Jordana T Bell, Timothy D Spector, Andrew G Clark, Ruth E Ley "Human genetics shape the gut microbiome." Cell 159.4 (2014): 789-99. PubMed
  18. Dallas M Swallow "Genetic influences on carbohydrate digestion." Nutrition research reviews 16.1 (2008): 37-43. PubMed
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About Michael Anders

After being affected by seborrheic dermatitis, I have made it my goal to gather and organize all the information that has helped me in my journey.

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