The Best Way to Restore Your Gut Flora

gut flora bacteria
avatarPaleoHacks Team

One of the popular questions in the PaleoHacks forums is “What is the best way to re-populate the gut with beneficial flora?” The most popular answer was given by Bread-Eating Beelzebub, who talked about the paleo environment and how it probably contained more natural bacteria that would contribute to gut biodiversity. Another issue raised was the importance of developing a healthy gut flora early in childhood. Feel free to contribute to the Gut Flora discussion.

Why Paleo Men and Women Probably Didn’t Worry about Gut Flora

The fruits and vegetables our Paleo ancestors ate were covered in beneficial microbes, not chemical fertilizers and pesticides. They didn’t kill off all the good bacteria with antibiotics and antibacterial hand wash. They had relatively low stress. They ate foods optimal for supporting their gut health.

Gut Flora and How it Affects Us

Hippocrates said it over 2,000 years ago, and it’s just as true today:

“All disease begins in the gut.”

Gut flora, or gut bacteria and yeast, is the trillions of microbes (100 trillion, in fact) in your intestines that help digest food, synthesize vitamins, regulates metabolism, and make up your immune system. In a nutshell, if your intestinal flora is unhealthy, so are you – and there’s no way around it.

Some of the vitamins that these bacteria help synthesize are K, B7, and B12. A deficiency in any of these vitamins can lead to hair loss, skin problems, diabetes, obesity, internal bleeding, cancers, anemia, strokes, degenerative disorders, and other disorders of the autoimmune, gastrointestinal, and respiratory systems.

When your gut bacteria is off, you can develop rheumatoid arthritis, depression, autism spectrum disorder, and chronic fatigue syndrome.

What Contributes to Beneficial Gut Flora

The very first thing that contributes to beneficial gut flora is being born – vaginally. As the baby passes out of the mother, it picks up her gut flora. If the mother’s is healthy, so is the baby’s. And it develops from there. After that, breastfeeding continues to help the microcosm flourish and develop into a robust environment.

Other things that help to support and grow a healthy intestinal flora are probiotics, a Paleo diet high in prebiotics, and staying away from those things that can adversely affect gut health.

What Can Affect Gut Flora

There are several things that can harm a healthy digestive gut flora like chronic stress, diets low in fermentable fibers, diets high in processed foods, too much dietary fiber, carbohydrates, and sugars, chronic infections, dietary toxins like industrial seed oils and wheat, and medicines like birth control, antibiotics, and non-steroidal anti-inflammatories (NSAIDs).

In particular, antibiotics are especially harmful.

Probably the most disturbing thing is that gut flora doesn’t automatically regenerate after you damage it. You have to actively work to restore it.

How to Regain or Restore a Bio-Diverse Gut Flora

If you’ve damaged your gut, or never had great flora in the first place, you probably want to make it your priority now. You’ll probably have to follow a multi-step process that includes dietary intervention, probiotic supplements, and detoxification.

Another important aspect of restoring gut health is to manage your daily stress. Take yoga classes, take time for yourself to read a book, go get a manicure or pedicure, hit the gym on a regular basis, and get enough sleep. You should aim for at least seven hours of quality sleep a night.

You also need to treat any parasites or other intestinal pathogens before you try to restore beneficial bacteria.

The GAPS diet (Gut and Psychology Syndrome) was developed to restore and heal those guts and get your body back to prime working condition. The diet was created by Dr. Natasha Campbell-McBride

Basic Principles of the GAPS Intro Diet

  1. Remove fiber from your diet.
  2. Add in probiotics slowly, through both probiotic supplements and fermented foods.
  3. Introduce those things that will help heal your gut lining.

Fiber should be removed because when you have an overgrowth of bad bacteria and yeast, that fiber will go to feed it. Just like fiber feeds good bacteria when you have it, it will feed the bad bacteria, too. Your goal is to encourage the good bacteria, not to help the bad bacteria to flourish. Starve those bad bacteria!

When it comes to probiotics, most people should supplement. People with unhealthy guts especially should supplement with a high-quality probiotic. In addition, fermented dairy (if you eat dairy) and fermented foods will help reintroduce good bacteria and yeast to your system.

Staples of the GAPS Diet

Here are some “safe” foods to eat if you follow the GAPS principle:

  • Homemade bone broth;
  • Homemade meat stock;
  • Fermented vegetables;
  • Homemade yogurt; and
  • Raw eggs from pasture-raised hens.

Once the gut is healed, more vegetables may be introduced, as long as they are cooked and fermented.

For more information on the GAPS diet go here:


Choose a multi-strain probiotic and keep it in the fridge. Use it within the time period on the container, and take it with food.

Fermented vegetables

You can find out more about fermented vegetables from the Weston A. Price Foundation website (, and learn how to make them. Some of the things you can eat include sauerkraut, kimchi, lacto-fermented ginger carrots, lacto-fermented pickles, enzyme-rich mayonnaise, and more.

Fermented Dairy

If you eat dairy, and you are interested in restoring gut bacteria, some of the best ways to go about that is to eat and drink fermented dairy products. Home-made yogurt and milk kefir are easy ways to help re-populate your gut flora.

Who Needs to Restore Gut Health

There are several symptoms of an unhealthy gut. Major ones are autoimmune diseases, digestive problems like diarrhea or constipation, brain fog, heart failure, allergies, asthma, metabolic problems, psoriasis or eczema, diabetes, and depression.

If you have been on medications, particularly antibiotics, you need to work on your gut flora. If you have been diagnosed with vitamin deficiencies or any of the disorders listed above, you might want to consider that your gut flora is out of whack. If you are overrun with yeast, get your gut in check.