What do autism, obesity, allergies, autoimmune diseases, fibromyalgia, depression, and acne all have in common? They all share a connection with healthy gut flora.[1] In fact, the medical profession has come to recognize that as the health of the gut goes, so goes the health of the body.

We expect problems like gas, bloating, constipation, diarrhea, and intestinal discomfort to stem from an unhealthy gut. But the gut, and especially the bacteria that comprise a healthy gut, provide our primary defense against diseases of all kinds.[2]

The Good, the Bad, and the Ugly

It sounds incredible, but our gut is home to more than 100 trillion bacteria representing over 400 known species.

Your gut is a veritable greenhouse! Click to Tweet.

The good bacteria perform a wide variety of functions crucial to our health. Good bacteria:[3], [4], [5]

  • good bacteria benefitsMaintain normal gastrointestinal function
  • Provide protection from infection
  • Help regulate metabolism
  • Comprise more than 75 percent of our immune system
  • Strengthen the bowel wall
  • Improve mineral and nutrient absorption
  • Aid in the regulation of hormone production
  • Promote brain health

Bad bacteria are also often present in the intestinal tract. These vermin create havoc in the gut by throwing off its healthy balance of flora and emitting harmful chemicals into our system. Some of the effects of bad bacteria are merely uncomfortable, producing cramping, diarrhea, constipation, yeast infections, etc. Other bad bacteria such as salmonella and E. coli may be life-threatening.[6]

What Damages Healthy Gut Flora?

Many of us unwittingly damage our healthy gut flora by engaging in certain practices. Some of the ways we harm our healthy gut flora include:[7]

  • Taking antibiotics – Antibiotics are necessary sometimes, but taking a course of antibiotics disturbs our gut in a way that requires deliberate action on our part to restore.
  • Using other medications – Birth control pills, laxatives, and non-steroidal anti-inflammatory drugs like aspirin, ibuprofen, Motrin, Aleve, and Naprosyn all harm the good flora.
  • Eating processed foods, fats, sugars, and simple carbs – These foods cause bacteria to produce endotoxins that our body reacts to as a threat, resulting in inflammation.
  • Failing to eat foods high in natural fiber – such as fruits, vegetables, nuts, seeds, berries and other whole-food plant sources
  • Chronic stressStress directly affects metabolic changes in the intestinal tract, often causing immediate discomfort and long-term effects. Click to Tweet.

Due to any or all of the above factors, when our gut flora gets out of synch our immune system has been compromised. Our body is now vulnerable to a wide variety of diseases and conditions that, as we saw earlier, we might not think to link to our gut. These could include problems as mundane as bloating to serious illnesses like epilepsy, arthritis or MS.[8]

Here are 5 Things You Can Do To Cultivate Healthy Flora in Your Gut:

  1. Avoid things that harm healthy flora – This includes a diet high in sugar, simple carbs and fat. Avoid drugs such as: antibiotics (when possible), acid-blockers, anti-inflammatories, and too much alcohol.
  2. Eat whole foods that contain natural fiber – Whole grains, fruits, vegetables, nuts, seeds, and berries fall into this category.
  3. Eat fermented foodsFermented foods go through the process of lacto-fermentation, in which bacteria feed on the sugar and starch and create lactic acid. The result is food rich in enzymes, B-vitamins, Omega-3 fatty acids, and a variety of probiotics. Foods like yogurt, sauerkraut, kefir, and kombucha. Fermented foods are the best resource for probiotics, but if you find you cannot eat these foods often enough, you may wish to supplement with a probiotic.
  4. Test and treat for parasites – Parasites can cause significant issues in the gut resulting in gut flora being out of sorts.
  5. Reduce stress – Stress negatively impacts the body through its release of cortisol and other stress chemicals that suppress the immune system and influence gastric secretions.[9], [10]’ [11] 

More About Lacto-Fermentation

lacto-fermented homemade ketchupLacto-fermentation is easy, inexpensive and requires few ingredients and tools to prepare at home. Vegetables are left whole, chopped, sliced or grated and placed in a brine solution at room temperature over a period of time. Natural bacteria in the air and on the vegetables do the work for you to provide delicious fermented foods that are packed with probiotics and keep for months.[12]

Would you ever think of making fermented ketchup? Ketchup has its roots in Southeast Asian kecap manis, which, as a sweet soy sauce-relative, is usually fermented to a certain degree. It definitely tastes more interesting than the store-bought stuff. This is a bare bones recipe, so you could add just about any spice or additional seasoning you’d like. Consider red pepper flakes, cayenne, or smoked paprika. This recipe is ridiculously easy to make and the lacto-ferment gives it a punch of gut-happy probiotics!


  • 2 cups tomato paste
  • 1/4 cup raw honey (maple syrup or whole unrefined cane sugar)
  • 1/4 cup plus 2 tbsp fresh whey* (divided)
  • 2 tbsp raw apple cider vinegar (plus extra for thinning the ketchup, if desired)
  • 1 tsp unrefined sea salt
  • 1 tsp allspice
  • 1/2 tsp ground cloves


  1. Spoon tomato paste into a large mixing bowl and fold in raw honey or other natural sweetener of choice.
  2. Whisk in one-quarter cup fresh whey or vegetable starter culture into the sweetened tomato paste along with apple cider vinegar, sea salt, allspice and cloves. Continue whisking these ingredients together until the paste is smooth and uniform.
  3. Spoon the homemade ketchup into a mason jar, top with remaining two tablespoons fresh whey or vegetable starter culture, cover loosely with a cloth or lid and allow the ketchup to sit at room temperature, undisturbed, for three to five days.
  4. After three to five days, uncover the homemade ketchup and give it a thorough stir before transferring to the refrigerator. Naturally fermented homemade ketchup will keep for several months in the refrigerator.

Follow the simple recommendations outlined in this article to keep your gut flora healthy in order to maintain overall health. For complete information about restoring gut health and what happens if you don’t, continue reading at Home Cures That Work. 

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Rob_FischerRob Fischer has been writing professionally for over 35 years. His experience includes writing curricula, study guides, articles, blogs, newsletters, manuals, workbooks, training courses, workshops, and books. Rob has written for numerous churches, for Burlington Northern Railroad, Kaiser Aluminum, and Barton Publishing. He has also trained managers in effective business writing. Rob holds two Master’s degrees, both focused heavily on writing. Rob has published eleven books and serves as an editor and ghostwriter for other authors.


[1] Dr. Mark Hyman, “5 Steps to Kill Hidden Bad Bugs in Your Gut that Make You Sick,” October 17, 2014, http://drhyman.com/blog/2010/09/27/5-steps-to-kill-hidden-bad-bugs-in-your-gut-that-make-you-sick/.
[2] Chris Kresser, “9 Steps to Perfect Health – #5: Heal Your Gut,” nd, http://chriskresser.com/9-steps-to-perfect-health-5-heal-your-gut.
[3] Chris Kresser.
[4] Prebiotin, “Prebiotics vs. Probiotics,” nd, http://www.prebiotin.com/prebiotics/prebiotics-vs-probiotics/.
[5] Dr. Mercola, “Learn How to Make Cultured Veggies at Home to Boost Your Immune System,” June 1, 2013, http://articles.mercola.com/sites/articles/archive/2013/06/01/fermented-vegetables.aspx.
[6] IBS Treatment Center, “The Bad and Ugly Bacteria,” nd, http://ibstreatmentcenter.com/ibs/intestinal-bacteria-yeast-candida-and-parasites/the-bad-and-ugly-bacteria.
[7] Chris Kresser.
[8] Dr. Mercola.
[9] Chris Kresser.
[10] Wellness Mama, “Health Benefits of Fermented Foods,” nd, http://wellnessmama.com/2245/health-benefits-fermented-foods/.
[11] Dr. Mark Hyman.
[12] Paleo Leap, “Fermented Food Recipes,” December 7, 2014, http://paleoleap.com/fermented-food-recipes/.
Recipe adapted from http://nourishedkitchen.com