How to Keep Your Gut Healthy

If you know me, you know I don’t mind discussing bodily functions, including “number two.” While it’s gross, it’s also one of the greatest insights into our health. So naturally I jumped at the opportunity to take a deep dive into the topic and contribute to the Functional Medicine SF blog. Read on if you’re also into this kind of thing.

If you’re “going” on a daily basis, you’re good, right? Not necessarily. Gut health extends far beyond your daily ritual and can mean the difference between feeling just okay and truly feeling your best.

Our digestive tract does more than breakdown our foods to provide us with nutrients and energy – it is home to an entire ecosystem of microbes that outnumber the cells in our bodies. I’ll say it again. You are actually more bacteria than you are YOU.

Thanks to the NIH’s Human Microbiome Project, which mapped the entire genome of the bugs living inside our guts, we now know that the bacteria we house make our lives possible. Put bluntly, without bacteria, humans would not be alive. Pretty crazy, because not too long ago we were zapping anything that moved with antibiotics and antibacterial everything. Back then, suggesting that you might actually ingest bacteria in something called a probiotic would’ve landed you in the nut house.

Well times change, and we now know that bacteria synthesize vitamins like K and B12, breakdown and excrete toxins, regulate hormones, metabolize medications, regulate fat storage and produce healing components. In fact, over two thirds of our immune system is in the gastrointestinal (GI) tract. That still blows my mind.

Infants are given their mother’s microbial flora during vaginal childbirth and brought into the world with a customized veil of microbes to face their new environment. I once read that it’s like giving your baby his or her final marching orders and best chances of adapting to the world – and not just to the “world” in a broad sense, but to the exact environment the mother lives in, the local illnesses she was exposed to, the allergens in the air she breaths, and the food she eats. Nature is so cool!!

Babies born by cesarean section tend to have different dominating species. In fact, there are studies being conducted as we speak testing a method called vaginal seeding, where a sterile gauze or sponge is inserted into the birth canal pre-C-section so the newborn can be literally bathed in all that immune-giving goodness. (This topic was featured earlier this month in the NY Times.) But mothers facing the possibility of c-section, don’t fret, because breastfeeding and skin-on-skin contact also contribute to the passing of the mother’s microbial community.

As we grow and are exposed to different foods, medications, illnesses, and environments, our microbiome can undergo both subtle and dramatic changes. And while many of us harbor similar bugs, research shows correlations between certain species strains and disease states, and more obvious issues can arise during a state of dysbiosis. (Here’s another NY Times article on how gut microbes combine to cause colon cancer.)

Gut dysbiosis is defined as an imbalance of microbes in the GI tract – either too many bad bacteria compared with the good or an overgrowth of other species like yeast or parasites. Dysbiosis has been linked with numerous symptoms, and is likely a main cause of many of the chronic diseases we’re plagued with today, such as:

  • Acne
  • Allergies
  • Asthma
  • Autism
  • Autoimmune conditions
  • Certain caners
  • Cystic fibrosis
  • Eczema
  • Irritable bowel disease (IBD); Crohn’s and ulcerative colitis
  • Irritable bowel syndrome (IBS)
  • Mental disorders (depression, cognitive decline)
  • Obesity
  • Type II diabetes

…just to name a few! Research continues to reveal the interconnectedness of our gut to the rest of our entire body, most notably, the brain. The majority of our neurotransmitters are made not in the brain but in the gut! In fact, 90% of serotonin, the neurotransmitter responsible for making us feel joyful, is made in our digestive tract. It’s no surprise scientists are now finding links between depression and gut dysbiosis.

When our GI tract is inflamed, it sends chemical messengers and inflammatory cytokines to the brain and body, which affects our mood, cognition, and overall well being. Symptoms include gas, bloating, irregular bowel movements, nutrient deficiencies, bad breath, acne, etc. etc. etc. This is why it’s so important to feed the gut what it needs and remove what it doesn’t.

The causes of dysbiosis are many and include poor diet, medications (antibiotics, proton pump inhibitors, NSAIDs like Tylenol, and others), toxins (like molds, heavy metals, food additives), inadequate sleep, lack of exercise and stress.

So what can you do? In integrative and functional nutrition, we talk about the “5R Protocol” for treating gut dysbiosis:

  1. Remove the offending foods and other causes of dysbiosis
  2. Replace nutrients and enzymes that may be lacking
  3. Reinoculate with fermented foods and pre- and probiotics
  4. Repair with targeted foods and supplements as necessary
  5. Rebalance your lifestyle

If you think you could use some help in the #2 department, find a practitioner (ideally someone who treats you as a whole person and not someone jumpy with the prescription pad) who can help you get on the right track. There are things you can do today to start feeling like your best self.

Probiotic supplements and fermented foods like kimchi, miso, and kefir are not hard to find. I talk about probiotic foods and supplements in this Woman’s Day article. You can even make your own fermented foods at home. Try this lacto-fermented sauerkraut recipe, which provides beneficial lactobacillus bacteria.


Homemade Sauerkraut (Fermented Cabbage)


1 head cabbage (2.5 pounds)

1 1/2 tablespoons salt (kosher or sea)

1 tablespoon caraway seeds



1 2-quart mason jar

1 fermentation weight (smaller jar filled and sealed with clean pebbles or marbles)

1 piece cheesecloth

1 rubber band

Clean the cabbage and slice into thin ribbons. In a large bowl, combine cabbage and salt and massage with your fingers for several minutes until enough liquid is released to cover the cabbage. Add contents of bowl to mason jar. Add caraway seeds. If necessary, add water until cabbage is fully covered. Place fermentation weight on top so cabbage is fully submerged in liquid. Cover entire jar opening with cheesecloth and secure with rubber band. Let it ferment about 2-3 weeks on kitchen counter. It’s done when it reaches your desired taste! Store in refrigerator for up to 6 months.



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