How to colonize your gut with beneficial bacteria


We often think of bacteria as something to avoid but there are 100 trillion viable bacteria in the colon comprised of 400-1000 different species.   This microbiome is often referred to as the gut flora and we need these bacteria healthy to help keep us disease free.

The bacteria in our digestive system create many benefits.  When we have a good balance of bacteria we have a very symbiotic relationship with them.  We provide them with food and they provide us with myriad benefits such as the synthesis of biotin, vitamins B12, B6, B5, B2 and vitamin K2.   They also synthesize the short chain fatty acids (butyrate, propionate, and acetate).

When our beneficial bacteria have a stable colony count they prevent other pathogens from thriving by using up all available food sources.  Bacteria help to control the set point for inflammation, regulate the pH of the intestine, and help maintain the cell integrity of the entire digestive tract.  A healthy gut flora also helps our immune system by stimulating the growth of immune cells, metabolizing several food components into active forms, and inactivating certain mutagens and carcinogens such as N-nitrosamines.

Lots of things in our environment disrupt the gut biome.  Stress, inflammation, medicines, pesticides, and endocrine disrupting chemicals can cause damage to the bacteria and to our intestinal mucosal cells.  Our gut lining is only one cell thick; a single layer of tall, closely packed cells, aligned like soldiers all in a row.  This row of single cells lines the digestive tract from stomach to rectum.  They are lined together so closely that they form tight junctions.  These tight junctions keep digestive enzymes, microorganisms, and intact food particles in the intestine from entering the blood stream.

When these cells are injured they swell and can create holes in the gut lining.  This can create inflammation, ulcers, a condition called leaky gut, food sensitivities, and dysbiosis.


Dysbiosis happens when our gut flora are not balanced between species and colony count or when pathogenic bacteria are thriving.  Dysbiotic populations produce ammonia, inactivate enzymes needed for protein and carbohydrate metabolism, de-saturate bile steroids and create numerous side effects such as diarrhea, abdominal distention or bloating, eczema, irritable bowel, depression, food sensitivities and autoimmune diseases.

Dysbiosis can occur from antibiotic use or by eating antibiotics hidden in meat, poultry and dairy products.   Changes in bowel motility, malabsorption, and maldigestion can all contribute to dysbiosis and are each aggravated by dysbiosis.  Stress, illness and a diet high in inflammatory foods such as non-organic dairy or meat or hydrogenated trans fatty acids can all disrupt the balance of bacteria in the gut.  One of the risks of genetically modified food is that is can also disrupt the balance of bacteria; genetically modified foods can create their own pesticides, killing crop pests and our own microbiome.  As stated earlier, eating foods that you are sensitive to can also produce colony disruptions due to inflammation.

The delicate balance of bacterial species is maintained primarily by Lactobacillus acidophilus and Bifidobacteria bifidum.  Each individual person has their own strains of bacteria but all humans share a core of bacterial species.

To maintain a healthy gut flora you need to consume both prebiotic foods and probiotics.  Prebiotics are high in non-digestible fibers called oligosaccharides that stimulate the growth and activity of beneficial bacteria in the colon.  Prebiotics include onions, garlic, leeks, bananas, asparagus, maple syrup, Jerusalem artichoke, rye, oats and barley.  Probiotics are live organisms such as lactic acid bacteria or lactic acid yeast that will help replenish beneficial flora colony counts.   Probiotics can be ingested either via supplementation or via fermented foods such as live active cultured yogurt, kefir, miso, tempeh, sauerkraut, kim chee or kombucha.

Lactic Acid Bacteria

Lactic acid bacteria, or LABs, ferment sugar into lactic acid.   Lactic acid bacteria consist of strains of Lactobacillus, Lactococcus, Streptococcus, Enterococcus, Tetragenococcus, Vagococcus, Weisella, and more. LABs are normally found in the intestinal tract and are generally beneficial unless they grow out of proportion.  For example, Streptococcus can cause strep throat, pneumonia, ear infections and meningitis when out of balance.

Lactic acid bacteria use lactose (milk sugar) as their main source of energy.  This is why yogurt, kefir and other cultured milk products are high in LABs.  They contribute to the taste and texture of these fermented products and inhibit food spoilage by producing growth-inhibiting substances and lactic acid. LABs can also be used to make homemade pickles, sauerkraut and other fermented vegetables.

Because LABs use lactose as their main nutrient source, taking a probiotic supplement of Lactobacillus acidophilus, brevis or other stains without having some source of lactose in your diet through means you aren’t feeding the LABs what they need to survive.   They will not colonize your gut if they can’t live.

Now, taking LABs as a probiotic supplement is not a complete waste of money.  They will live for a while, they will just not reproduce and change your gut microbiome dramatically unless you take them religiously every day.

Lactic Acid Yeast

Lactic acid yeast, as opposed to lactic acid bacteria, is a mycelium type yeast. Lactic acid yeast will convert nearly all sources of carbohydrates into the sugar it needs to thrive.  So instead of needing lactose to survive, this yeast will survive on any carbohydrate.   Just like LABs, lactic acid yeast produces lactic acid to help acidify the stomach and help assimilate minerals.  The acidity of the stomach creates a habitat where other beneficial bacterium like bifidus can proliferate and other pathogenic alkaline loving pathogens die out.  Because lactic acid yeast can utilize any carbohydrate source they colonize very easily and immediately help create a healthful environment.

Choosing the right probiotic supplement

Probiotic supplements are available in a variety of forms, such as freeze dried powder, capsules, wafers, and liquids.

Lactic acid bacteria supplements abound and are numerous; the quality bar is extremely varied.  The strains of bacteria most researched and recommended are the NCFM strain of L. acidophilus, developed at North Carolina State University from a human intestinal tract, L. acidophilus HMF, and the L. acidophilus DDS-1 strain.  Other strains are available but their viability and ability to survive in the presence of bile or stomach acid could be unknown.

My personal favorite LAB supplement is Dr. Ohhira’s Probiotics Professional Formula as it is created using a fermentation process and contains 12 different LAB strains as well as 3 Bifido strains:

Lactic acid yeast supplements are less common, but in my opinion, are worth the effort to find.  My personal favorite is Standard Process Lactic Acid Yeast

I research brands very carefully.  If you are going to look for alternatives to the ones recommended then please remember, the Food and Drug Administration does not regulate supplements and manufactures use a variety of marketing tactics to help sell their particular product.  As always read the label.  All LAB probiotic supplements should contain viability information such as colony forming units per gram, strain name, and be packaged in a dark container that is kept refrigerated.

To get a variety of LABs and yeasts in your diet, make some kombucha 🙂

Homemade Kombucha (Cultured Tea)

Serves 4
Prep time 20 minutes
Allergy Egg, Fish, Milk, Peanuts, Shellfish, Soy, Tree Nuts, Wheat
Dietary Gluten Free, Paleo, Vegetarian
Meal type Beverage
Misc Serve Cold
Kombucha is a fermented probiotic beverage. The caffeine and sugar are "eaten" during the fermentation process and what you are left with is a tangy vinegar-like beverage. The taste of your kombucha will depend on the tea used and the fermentation length. The SCOBY is a bacterial and yeast starter culture that includes beneficial probiotics such as Acetobacter, Saccharomyces, Brettanomyces, Lactobacillus, Pediococcus, Gluconacetobacter and Zygosaccharomyces strains. Drinking kombucha provides many more helpful. For more information on Kombucha or to order a starter culture see the Cultures for Health website:


  • 3-4 cups water (boiling hot)
  • 3-4 organic black tea bags (caffeinated tea (decaf won't work))
  • 1/2 cup ogranic sugar (white sugar works the best)
  • 1 cup kombucha from last batch (for first time see Note below)
  • 1 Symbiotic Culture of Bacteria and Yeast (SCOBY)
  • 2-3 cups water (room temperature)


Kombucha is a fermented probiotic beverage. The caffeine and sugar are "eaten" during the fermentation process and what you are left with is a tangy vinegar-like beverage. The taste of your kombucha will depend on the tea used and the fermentation length. The SCOBY is a bacterial and yeast starter culture that includes beneficial probiotics such as Acetobacter, Saccharomyces, Brettanomyces, Lactobacillus, Pediococcus, Gluconacetobacter and Zygosaccharomyces strains. Drinking kombucha provides many more helpful bacteria for your digestive tract than yogurt.

For more information on Kombucha or to order a starter culture see the Cultures for Health website:

To get started you can purchase a dehydrated scoby online, obtain one from a friend or grow your own. Growing your own takes quite a bit longer but it's typically a fifth of the price of an online purchase.

To grow your own scoby: Purchase a bottle of kombucha (I like GT Original). Pour that kombucha into a quart size ball jar. Steep 1 tea bag into 1 cup of water and add in 1/4 cup of granulated sugar. Once your tea has steeped and cooled add it to the kombucha and wait a week for the SCOBY to form.

I use a SCOBY for 1-3 batches then either toss it into the compost bin, eat it, or feed it to my dog. If your SCOBY baby has attached to your mother, no worries, simply cut them in 1/2 with scissors.


Initial fermentation
Step 1. Place the sugar into a 1/2 gallon ball jar (or split into two 1-quart jars). Add in 2-4 cups of boiling water and stir if needed to ensure all sugar is dissolved. Add your tea bags and let your tea steep till room temperature (I let mine steep overnight).
Step 2. Remove the tea bags.
Step 3. Add in the SCOBY and 1 cup of kombucha from the last batch as a starter. Top off your jar till the water line is about 6 or 6 1/2 cups total.
Step 4. Cover your jar with a non-bleached coffee filter, paper towel or cheese cloth, securing it with a rubber band or your ball jar ring (not the metal top).
Step 5. Let this mixture ferment for 10-16 days depending on your taste preferences. I do not ferment in direct light, but in a room that has ambient natural light. The longer the fermentation the less sugar will be left. A three week fermentation is pretty vinegary for my taste. I ferment for 2 weeks as my preferred taste.
Step 6. After your 10-16 day fermentation, remove the new "baby" SCOBY that forms (typically on the top) and 1 cup from this batch of kombucha to start another round. Drink the rest or proceed to a secondary fermentation to create a fizzier drink. You can discard the "mother" SCOBY, eat it, put it in your compost, or use it again to double your batch.
Optional secondary fermentation
Step 7. Pour the fermented kombucha (after you have removed the SCOBY and 1 cup of tea as a starter) into smaller serving size containers. I use 2-cup size ball jars or clean 16 oz jars. Jars must have lids. Leave a little bit of room (like 1/3-1/2 cup) for flavoring if wanted.
Step 8. Add additional optional flavoring such as fruit, 1/4 cup fruit juice, 1/4 strongly flavored tea, or 1-2 TBST lemon juice. I often use grated ginger or ginger tea, blueberries (about 6-8), or some sweet fruit herbal tea like cherry.
Step 9. Close the jar tightly and let this secondary fermentation sit for an additional couple of days to add carbonation.
Step 10. Transfer your finished kombucha to the refrigerator for storage. Kombucha will be drinkable for up to six months. The tea will still ferment in the fridge, just at a much slower rate.
First time - Growing a SCOBY
Step 11. If you don't have a SCOBY from a friend or neighbor, no problem, you can grow one. Purchase a bottle of Kombucha from the store. Original flavor is best, and I personally like the GT brand best for growing a new SCOBY. Transfer that liquid into a larger bottle.
Step 12. Add 1 cup cooled sweetened tea (1 black tea bag, 1/4 cup sugar and 1 cup water) to the kombucha.
Step 13. Cover with a coffee filter or paper towel and secure with a rubber band. A SCOBY should grow within a week to you to use as a starter.