The Human Microbiome: The Amazing Gut Flora

by Emily Dickerson, ND

The Human Microbiome consists of the normal, healthy, commensal bacteria that live in and on our bodies. “Commensal gut flora” means bacteria that naturally exist in the gastrointestinal tract of humans, and in fact, have huge impact on our health. Bacteria covers our entire body, including our skin and orifices. It is involved in maintaining our innate immunity, meaning the first line of defense against pathogens and toxins. In this article I’m going to highlight some of my favorite benefits of healthy commensal gut flora, and will provide you with some resources for improving your own arsenal of healthy bacteria.

Weight Loss/Management

One of my favorite studies regarding gut flora is one that involves fat mice and skinny mice. In this study, researchers swapped gut flora of these mice, meaning that the fat mice received the flora of the skinny mice, and the skinny mice received the gut flora of the fat mice. What resulted is that the fat mice became skinny, and the skinny mice became fat. Incredible! The flora of the skinny mice was also the more diverse of the two. This highlights the role of gastrointestinal flora in metabolism and weight management.

Improves Immune Function

A more diverse microflora has been related to fewer infections and higher immune system function. The microbiome of the gut helps to maintain the integrity of the immune response in the lumen of the gastrointestinal tract. It does so by creating a thick, microbial layer that acts as the first line of defense in immune function. This helps to prevent penetration of toxins into the gastrointestinal cells and inhibits “leaky gut” by preventing an inappropriate inflammatory response of those gastrointestinal cells. Keeping your gut flora diverse and healthy is a great way to minimize unnecessary gastrointestinal inflammation.

Prevention of Autoimmunity

Autoimmune disorders are on the rise, related to many chronic and inflammatory illnesses. Lots of new research regarding sterile (“too clean”) environments and autoimmunity is arising. Children that eat dirt (think camping, playing outdoors), have pets, or are exposed to more microbiologically diverse environments tend to have less autoimmunity as adults. For this reason, antimicrobial soap and sterile households are not necessarily a good idea.

Antibiotic Resistance and Increased Risk of Infection

Currently in medicine there is a push to only use antibiotics when they are absolutely indicated and necessary. Inappropriate or excessive antibiotic use increases risk for serious infections such as Clostridium difficile, which you have probably heard of if you have ever been in a hospital, as it often occurs secondary to a hospital stay and/or antibiotic use. Clostridium difficile, also known as “C. diff” is a highly infectious gastrointestinal infection that secretes toxins that damage intestinal cells and causes severe, watery diarrhea. Another serious infection caused by inappropriate or excessive antibiotic use is MRSA (methicillin resistant Staphylococcus aureus). This “superbug” is multi-drug resistant, meaning that it is difficult to treat due to its lack of response to many antibiotics. This can cause serious skin infections that can last a very long time.

Probiotics Improve Recovery Time

When antibiotics are necessary, taking probiotics can help to speed recovery. Many infections have shown quicker recovery time when the patient supports their normal flora with probiotics. I recommend taking these at a different time of day than antibiotics, so you get maximum benefit. For example, if you take your antibiotic in the morning and the evening, you should take your probiotic in the afternoon.

Support Healthy Flora

The following are the best ways to support your healthy, commensal flora on a daily basis.

  • Eat “real” food, meaning a diversity of whole foods, including lots of fresh produce.
  • Eat probiotic foods at least once per day. This can include fermented vegetables, sauerkraut, kimchi, yogurt, kefir, kombucha, miso, etc.
  • Take a probiotic daily. The best time of day to take probiotics is at night before bed. My two current favorite probiotics that can be found at Boise Natural Health are:
    • BioDoph 7 Plus
    • HMF capsules


Missing Microbes by Martin Blaser, MD

Missing Microbes is an excellent book about the benefits of our natural flora, as well as the dangers of overprescription and overuse of antibiotics. It is an easy read and fascinating, letting us dig into a deeper understanding of the roles of our gut flora.

Bubbies Sauerkraut Recipe

I don’t know about you, but I love sauerkraut. If you eat it every day it can get expensive. I suggest trying to make your own. Bubbies Sauerkraut is an awesome one, and I’ve provided the recipe below. Enjoy!

Bubbies Sauerkraut Recipe Link:

Recipe: (Borrowed from Phoenix Helix’s blog;


5 pounds of cabbage

3 Tbsp. sea salt


68 ounce Fido Jar

Knife and cutting board

Food processor (optional)


  1. Wash your hands and be sure all of your equipment is clean.
  2. Cut cabbage in half and remove the cores. If the outer leaves are wilted, throw them away. Cut the remaining cabbage into large chunks and feed into your food processor, using the largest grater blade, or a slicing blade, to shred the cabbage. If you don’t have a food processor, chop the cabbage finely with a knife.
  3. Transfer the shredded/chopped cabbage to a large bowl. Sprinkle with 3 Tbsp. salt and use two spoons to toss until the salt evenly coats the cabbage.
  4. Transfer the cabbage to your Fido jar. It won’t all fit at first. That’s OK – leave the extra in the bowl, and it will get added later.
  5. Cover both the jar and bowl with clean dry cloths, and let the cabbage “sweat” for 30 minutes.
  6. Once the 30 minutes have passed, use a large spoon or meat pounder to gently push down on the cabbage in the jar. It will compress and release its natural juices, freeing up more room in the jar. Add the remaining cabbage from the bowl and set the timer for another 30 minutes.
  7. Compress the cabbage again. Its natural juices should rise up above the shredded cabbage itself. If it doesn’t, you can add a little water as needed. Leave two inches of airspace at the top of the jar.
  8. As long as you’re using a Fido jar, no weight is needed. Simply clamp the jar shut. (For an explanation, click here.) The first week of fermentation is the gaseous stage, and the cabbage will expand upward. If your jar is very full, stick a plate under it. Sometimes a little liquid will seep out under the rubber gasket. This isn’t a problem. The beauty of the Fido jar is that it lets excess fermentation gases out without letting oxygen in. (Oxygen causes mold.)
  9. Put a piece of tape on the jar with today’s date, and set it out of sunlight, but someplace you won’t forget about it. Let it ferment for 30 days. Don’t open the jar during fermentation. If your house runs hot, ferment it 3 weeks. If your house runs cold, let it ferment 5 weeks. The best flavor and nutrient content develops between 60-75 degrees. Don’t try to ferment in temperatures above 80 degrees, or the wrong type of bacteria takes over.
  10. Transfer the kraut into smaller containers and refrigerate. I eat mine in a month, but it should keep in the fridge for at least 6 months.