Get To Know Your Gut


For simplicity your gut starts at the mouth and ends at the anus. All along this tube live colonies of bacteria. Mouth bacteria is a different mix of microbes from that of the small intestine to that of the large intestine. In all there are over 2,172 bacterial species in our gut which weigh as much as three kilos and outnumber the cells in our bodies. The human gut tract harbours a complex and dynamic population of microorganisms, the gut microbiota, which exert a marked influence on how we grown and how we control disease. Multiple factors contribute to the establishment of the human gut microbiota during infancy. Diet is considered as one of the main drivers in shaping the gut microbiota across the life time.Intestinal bacteria play a crucial role in maintaining the immune system and how cells maintain their functions. Altered gut bacterial composition (dysbiosis) has been associated with many inflammatory diseases and infections. Over 93% of the bacteria families belonged to Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. The science in this area is rapidly growing and is complex.

The science also extends to the vagus nerve. The vagus nerve is part of the parasympathetic nervous system, referred to as the rest-and-digest system. It’s not the only nerve in the parasympathetic system, but it’s by far the most important one because it has the most far-reaching effects. It reaches the brain, gut, heart, liver, pancreas, gallbladder, kidney, ureter, spleen, lungs, reproductive organs (female), neck (pharynx, larynx, and oesophagus), ears and tongue. There are recent experiments which stimulate the nerve using surgically implanted electrodes. Reductions in inflammation have been observed but these are early days.

Your skin bacteria also synthesise many useful compounds for the body, including antibiotics and acids that kill other harmful microbes, and carbon dioxide, which can slow the growth of fungus. The composition of your gut and skin microbiome can change at different points in your life, with the biggest shifts occurring during adolescence, pregnancy, old age, and after a big diet change.

Change Your Diet; Change Your Microbiome

By Michael Greger M.D. FACLM on May 3rd, 2018

If whatever gut flora enterotype we are could play an important role in our risk of developing chronic diet-associated diseases, can we alter our gut microbiome by altering our diet? Yes. Indeed, diet can rapidly and reproducibly alter the bacteria in our gut.

Concern has been growing that recent lifestyle trends––most notably the high-fat and high-sugar “Western diet”––have altered the composition and activity of our resident gut flora. “Such diet-induced changes to gut-associated microbial communities are now suspected of contributing to growing epidemics of chronic illness in the developed world,” yet it has remained unclear how quickly our gut bacteria could respond to dietary change. So, researchers prepared two diets: a “plant-based diet” rich in grains, beans, fruits, and vegetables, and an “animal-based diet” composed of meats, eggs, and cheeses. Neither diet contained refined sugars, as the researchers just wanted to test diets consisting of plant versus animal products. Within just one day of the animal-based diet hitting the gut, there was a significant shift.

What happens when you put a lifelong vegetarian on an animal-based diet? The vegetarian’s baseline microbiota was dominated by Prevotella, unlike everyone else eating a more standard American diet, who had large Bacteroides populations. Remarkably, the animal-based diet inverted the vegetarian’s Prevotella-to-Bacteroides ratio, causing the Bacteroides to outnumber the Prevotella within just four days on the animal-based diet. The entire gut flora got turned on its head and got completely reversed.

The fact that our gut can so rapidly switch between herbivorous and carnivorous functional profiles is probably a good thing in terms of evolution. If you bring down a mammoth and eat meat for a couple of days before switching back to plants, you want your gut to be able to deal with it. This flexibility is manifest in the diversity of human diets to this day, but what is the healthier state to be in most of the time?

Researchers looked at a number of different factors, such as the amount of short-chain fatty acids produced. Short-chain fatty acids, like acetate and butyrate, function to suppress inflammation and cancer, and our gut flora, when on plant-based diets, produce more of these than when on animal-based diets.

Other microbial metabolites, such as secondary bile acids, do the opposite, promoting the development of cancer. With a significant increase in bacterial enzyme activity to create these secondary bile acids on an animal-based diet, it’s no surprise there’s a significant increase in carcinogens like DCA, a secondary bile acid known to promote DNA damage and liver cancer. Microbial enzyme activity producing the rotten egg gas, hydrogen sulfide, also shoots up on an animal-based diet, which stinks because it’s stinky and also because it damages DNA and has been implicated in the development of inflammatory bowel diseases like ulcerative colitis. Hydrogen sulfide is made by pathogens such as bilophila wadsworthia and is increased on the animal-based diet, again within just days of adopting it, supporting the link between diet and the outgrowth of microorganisms capable of triggering inflammatory bowel disease. Conversely, the only pathogen you see more of on a plant-based diet is just a virus that infects spinach.

See more about gut microbiomes by Dr Greger at his website . Search for the following videos:

  • Titanium Dioxide and Inflammatory Bowel Disease
  • The Broccoli Receptor: Our First Line of Defence
  • Is Gluten Sensitivity Real?
  • Preventing Crohn’s Disease with Diet
  • Is Nutritional Yeast Healthy for Everyone?
  • Vitamin D for Inflammatory Bowel Disease

Useful Videos

What Is Your Microbiome Enterotype

Microbiome - The Inside Story

How To Change Your Enterotype


Introduction to the human gut microbiota; Elizabeth Thursby and  Nathalie Juge; Biochem J. 2017 Jun 1; 474(11): 1823–1836. Published online 2017 May 16. doi:  10.1042/BCJ20160510

Host genetic variation and its microbiome interactions within the Human Microbiome Project; Genome Medicine, 2018, Volume 10, Number 1, Page 1 Raivo Kolde, Eric A. Franzosa, Gholamali Rahnavard, 

Visceral pain: role of the microbiome-gut-brain axis; Kieran Rea, Siobhain M. O’ Mahony, Timothy G. Dinan and John F. Cryan (University College Cork, Ireland); in The Microbiome, April 2017