Transbiosis: Remodeling Your Microbiome

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Continuing from Microbiome 101…


The next question comes to…how can I undo this westernized boring biome? How can I get those good diverse bacteria? It is with probiotic pills, right? Eh…not completely.

As discussed above, our Westernized diet is largely composed of gram-positive Firmicutes. Dietary fiber intake, in the form of vegetables, has been found to shift your bacteria from the Firmicutes to a more gram-negative Bacterioidetes group. But Firmucutes are present in obesity, right??? Well, yes, but it is the variation, not just the tribes that are important, but also the members of the tribe. 

Want to increase your fat or bile loving (the substance that is made by your liver and stored in your gallbladder) bacteria…eat more saturated fats. On the other hand, an increase in good omega-3 fatty acids relative to bad omega-6’s will lead to an increase in both good Bacteroidetes and Firmicutes. Vitamin D deficiency will also lead to more bacteria that can cause illness and more bacteria that can cause infections.  

Your tribe will contain more misbehaving tribesmen and women (in particular E. coli) when you eat food that contains additives (agglutinins, emulsifiers, lectins) and ALCOHOL. Many of these compounds are found in foods coming from boxes, packages, and cans. Look for them when reading ingredients (SEE HOW TO EAT REAL FOOD). You will be surprised at how many foods you have that are composed of additives. Stick with the real stuff and your gut tribespeople will be happy and make you happy.



  1. Eat more vegetables
  2. Supplement with vitamin D (10 minutes in the sun = 20,000 units of vitamin D) and omega 3’s (can be from fish, nuts, etc).
  3. Limit processed foods, sugar and alcohol
  4. Natural and some pill-based pre-pro and probiotics


In addition to the foods that you eat, you can also induce your tribal diversity by adding bacteria into the gut yourself. Conventional medical wisdom may lead toward the supplement aisle and you may buy a Pro-biotic. Let me first say, that overall these products can’t (mostly) hurt you…well other than your wallet. I have seen some people get GI-upset from them. Also possible is a rare lactic acidosis from probiotics, which can make you quite sick. That said, again this is RARE.

You have to test one to see how you will respond. Also, note that not all probiotics are created equally. The medical literature is quite mixed in this area and it seems that overall products containing LactobacillusBifidobacterium, and Saccharomyces, tend to have mostly good effects. Also, a product called VSL3 appears to do pretty well in trial data. However, these products are not regulated and often contain additives which can be harmful to your gut and rare people can experience high levels of lactic acid or brain fog from probiotics…yipes! I would say that if it helps you great…if it doesn’t do not waste your money and you probably digest most of the probiotic bacteria in your stomach acid anyway.

As an alternative, I think that there are many foods that are cheap to buy/make and great for your gut. Kombucha, kefir, miso, tempeh, pickles, kimchi, sauerkraut, and yogurts (if you are not lactose intolerant) are all easy to make, cheap to purchase and last a long time. As a bonus, they are delicious and contain many other valuable pre-pro-biotics (vitamins, minerals, enzymes) that your bowel tribespeople will love. I use these foods, make a number of them (using very little money) and advocate that my patients do the same. 


Sources of natural probiotics

  1. Kombucha
  2. Kvass
  3. Kefir
  4. Raw ferments (relish, chutney, miso, tempeh, amasi, pickles, sauerkraut, kimchi)
  5. Yogurts (careful with sugar content and fat here is good)



Know your commensal pals are vital in your wellness and illness! They are not going anywhere, so learn to get along with them. 

Diversity is the key to keeping your body healthy and this can be obtained by eating “clean,” getting enough omega-3 fatty acids, vitamin D and limiting sugar/alcohol. You can change the composition yourself through supplements and delicious foods that will add variation to your gut microbiome and to your plate.

Click HERE to Learn More About the Booch and Your Biome!

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7 thoughts on “Transbiosis: Remodeling Your Microbiome”

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