Restoring Your Digestive Health & Stopping SIBO with Probiotics


In this article:

  • What probiotics are and how they can benefit your digestive system and overall health.
  • What damages your beneficial intestinal flora and signs of a harmful bacteria overgrowth.
  • How to improve your intestinal environment with probiotic and prebiotic foods.
  • What to look for in an effective probiotic supplement and how to use it to repopulate your digestive system with good bacteria to defend against pathogens and disease.

What Are Probiotics?

There has been a lot of interest in recent years in the health benefits of probiotics, but just what are they and how can they help your digestive system?

Probiotics are live, naturally occurring and beneficial microorganisms that live in your digestive tract. When your intestinal environment is populated primarily with friendly bacteria they can help improve digestion, increase nutrient absorption, enhance your immune system and promote overall health and well-being.

These helpful bacteria can even produce valuable nutrients for your body, like vitamin K and B vitamins, independently of your dietary intake.

By far their most important role though is to cover every inhabitable part of your digestive tract. Here they act as a barrier and defense against harmful bacteria, viruses, yeasts and parasites that promote disease.

The Many Benefits of Probiotics

A healthy and thriving population of good intestinal bacteria can have some surprising health benefits including:

  • An enhanced immune system with protection against dangerous viruses, bad bacteria and pathogenic yeasts, including candida overgrowth and vaginal yeast infections.
  • A lower risk of constipation, diarrhea, irritable bowel syndrome, leaky gut syndrome and many other digestive disorders.
  • Improved metabolism and toxin removal by breaking down waste products in the large intestine.
  • Protection against food poisoning.
  • Less risk of gastrointestinal cancers.
  • Better food breakdown and nutrient absorption, leading to improvements in energy levels, skin’s appearance, mood and mental focus and many other interrelated health benefits.

What Damages Good Bacteria

Unfortunately, there are many reasons why your vital populations of healthy and helpful intestinal bacteria can be in decline. Any of the following reasons can potentially lead to an overgrowth of bad bacteria or pathogenic yeast in your gastrointestinal tract.


By far and away the most common cause is antibiotics use. While sometimes necessary for certain health conditions, there is now widespread acceptance that antibiotics have been used indiscriminately in recent decades, even prescribed for viral infections where they serve no purpose.

The problem with antibiotics is that they kill both bad and good bacteria. This leaves your intestinal environment wide open to harmful microorganisms to repopulate.

If you have to take antibiotics then follow your doctor’s prescription, but also make sure you start supplementing with a good probiotic supplement like this directly the treatment and directly after.

Improper Digestion

Poor digestion can undermine the good bacteria in your gut. When you don’t chew up your meals, have low stomach acid and lack digestive enzymes, your food takes a lot longer to travel through your digestive tract. This is particularly true of heavy fried foods and big protein meals.

The longer your food takes to break down in your digestive tract, the more time for bad bacteria to multiply and promote bloating and gas as they ferment the undigested food.

Constipation is a symptom of poor digestion and allows harmful microbes to breed and increase for even longer periods in your digestive tract. Probiotics can help, but if you’re regularly suffering from constipation, even after improving your diet, it’s time for serious action to help your digestive system recover.

Poor Diet

High fructose foods and drinks, too much gluten or lactose, smoking cigarettes, drinking alcohol and particularly a rushed and stressful lifestyle can also swing your intestinal environment in favor of bad bacteria.

Feedlot produced poultry and meat, as well as commercial milk can contain antibiotic residue from the animals that is passed on to you when you consume it. Pay a bit more for organic and your body will thank you in more ways than one.

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Chlorinated drinking water can harm good bacteria in your digestive tract. A good water filter should remove most of the chlorine and other harmful compounds.

Non-steroidal anti-inflammatory drugs may affect your intestinal bacterial balance. Consider supplementing with probiotics if you have to take these medicines.

Toxins like pesticides on produce and chemical additives in food can reduce good bacteria populations in the intestines. The more real food you can eat, the better off your digestive environment will be and the more it can enhance your overall health.

Common Symptoms of Bad Bacteria Overgrowth

Once your intestinal environment is compromised and good bacteria dies off, harmful bacteria and yeasts will try to move in. Viruses and parasites also become much more of a problem when good bacteria levels diminish.

An overgrowth of pathogens in your intestinal environment is known as dysbiosis and has some of the following symptoms:

  • Bloating and distention
  • Regular abdominal pain and cramps
  • Increased flatulence
  • Diarrhea
  • Constipation
  • Irritable bowel syndrome
  • Yeast infections, both urinary and vaginal in women
  • Chronic fatigue
  • Body odor and bad breath
  • Headaches and migraines
  • Increased allergies
  • Lower immunity to disease
  • Acne and poor skin
  • Difficulty sleeping
  • Irritability, mood swings and depression

How to Support Your Good Intestinal Bacteria

If you’ve been suffering from gastrointestinal problems, it’s likely your internal populations of good bacteria are compromised. Whether this was the original cause of the health issues you are experiencing, or just a harmful side effect isn’t as important as repairing the damage.

After you’ve addressed as many factors as you can in your diet and lifestyle that can reduce your beneficial bacteria, you can begin rebuilding them for better health. There are three potential ways to go about this:

  1. Improve your diet and trust that the beneficial bacteria will overpower the harmful microbes over time.
  2. Eat more probiotic and prebiotic foods.
  3. Take high-strength probiotic capsules to repopulate your intestinal environment.

Let’s look at the strength and weaknesses of each of these.

1. Improve Your Diet

Long-term, improving your diet is definitely the best option. Bad bacteria and harmful yeasts thrive on a processed food diet, while good bacteria tend to prefer natural foods.

The Smart Food Swaps article is a good place to start for simple and healthy dietary changes. The improvement in your good intestinal bacteria will be only one of the many health benefits you’ll experience.

The challenge with relying only on this method is that it can take some time to see improvement, particularly if you’re currently suffering from bad bacterial overgrowth or a proliferation of yeast in your digestive tract. Often, the good bacteria need a helping hand to get back in the ascendancy.

2. Probiotic and Prebiotic Foods

Probiotic foods and drinks naturally contain high levels of beneficial bacteria that can repopulate your intestinal environment and crowd out the pathogens. Here’s some of the best of them.

Probiotic Foods

Fermented Vegetables

Sauerkraut, kimchi and other cultured vegetables are excellent sources of probiotics. Generally, the probiotic vegetables you make at home are much more potent than store-bought versions. Use them in your meals but don’t heat them too much to preserve their probiotic content.


Kombucha is a fermented tea probiotic that is full of beneficial bacteria. Like kefir, it’s best to make it at home as store-bought versions are usually weak. Good instructions on how to do this are here.

Kefir and Real Yogurt

Kefir is a fermented milk drink that breaks down lactose and can usually be enjoyed by people who are sensitive to regular dairy. Kefir is full of beneficial bifidus and lactobacilli bacteria and you can make it yourself quite easily from kefir grains. An excellent alternative if you’re missing milk.

Coconut water kefir is also available here and may be even more beneficial. This is a great option for people who are lactose sensitive and don’t have time to make their own kefir.

Most supermarket yogurt is just thickened milk with added fructose and is far from helpful for digestive problems. True yogurt would usually be unflavored and state that it has live and active cultures. A good source, like real Greek yogurt, can be a valuable daily probiotic.

Fermented Soy Products

Soy isn’t usually recommended for a healthy diet, or those with digestive problems, but traditional fermented soy products are different. Tempeh and particularly nato are full of good bacteria and high levels of nutrition, though the taste won’t be for everyone.

Aged Cheese

Aged cheeses aren’t quite as strong in probiotic content as some of the others listed above, but they are very tasty source and easier to find. Emmental, edam, gouda, gruyere and even aged cheddar are all good and especially look for cheeses made with raw milk.

If you’re not too sensitive to the small amounts of lactose in these cheeses, they can provide some healthy probiotics and are a much better option than soft and especially processed cheese.

Prebiotic Foods

A prebiotic is a substance that provides food for intestinal bacteria. The problem is, they work indiscriminately. If your digestive system is already overpopulated with bad bacteria, then using prebiotics can feed them as well.

By definition, the galactans in beans and fructans in wheat are prebiotics. But most people with digestive problems find them far from beneficial and a major cause of excessive gas.

The most popular prebiotics, which are now commonly used as food additives, are insulin and FOS. While these substances may be of some benefit to a person with a largely healthy digestive system, they can cause gastrointestinal havoc for those with an overgrowth of bad bacteria.

Three much gentler probiotics, that don’t get nearly as much attention as FOS or inulin, are apple cider vinegar, spirulina and chia seeds. All three of these provide numerous health benefits above and beyond their prebiotic properties. They are also much less gas forming than commercial probiotic powders.

Apple Cider Vinegar

Raw apple cider vinegar is an excellent health tonic that contains prebiotic pectin. You can drink a couple of tablespoons in a large glass of water several times a day. Taken just before a meal it will also help to improve your digestion and reduce bloating and flatulence.

Always choose raw and unpasteurized apple cider vinegar, with the cloudy ‘mother’ clearly visible in the bottle. Bragg’s apple cider vinegar is consistently rated as the best and it’s available at such a low price for so many benefits it’s well worth using every day.

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Spirulina is an incredibly nutritious green food that is full of antioxidants and a great source of vitamins and minerals, particularly iron. It has also recently been discovered that taking spirulina promotes the growth of beneficial lactobacillus and lactococcus bacteria. You can add prebiotic to the long list of health benefits of spirulina.

Chia Seeds

Nutritious chia seeds are an excellent source of soluble fiber and make for a great prebiotic that isn’t likely to contribute to gas problems in the same way as inulin or FOS. These tiny seeds contain more omega-3 fats per weight than salmon and are known to prevent constipation, balance blood sugar levels and reduce sugar cravings.

Because they absorb up to 10 times their own weight in liquid, chia seeds are best added to drinks or soups to thicken them up. Used in a smoothie recipe like this they will turn it into the consistency of a rich dessert mousse.

It’s best to start out slowly with chia seeds and increase your intake of over time. Make sure you’re drinking a lot of water too. You can begin with a heaped teaspoon, added to a large cup of liquid and work up to a tablespoon or two over several weeks.

Any of these three prebiotics are safer and usually healthier in the long run than using inulin or FOS. Taking all three together would be a powerful addition to any health regime and of great benefit your digestive system and its friendly bacteria.

3. Probiotic Supplements

The simplest and potentially most powerful way to improve your intestinal environment is with probiotic supplements. Perhaps more than any other kind of supplementation though, it’s critical to get the right kind of probiotics and take them properly if you want to see results.

Examining the average probiotic formula at a health food store you’ll see labels with statements like ‘5 billion live organisms per capsule at the time of manufacture’. That’s fairly worthless if most of those live organisms have died by the time you swallow them.

A good probiotic formula should say something like ‘5 million viable cells per capsule at time of consumption’. To ensure this, you’ll be looking for one of the newer formulas that are labeled room temperature stable.

It’s still definitely a good idea to keep your probiotic capsules in the fridge for even longer shelf life. But if they are not manufactured to be room temperature stable then much of the good bacteria may die during delivery.

It’s also recommended to choose enteric-coated probiotic capsules. These special coatings protect the bacteria from stomach acid and only release their contents in the small intestine.

It’s true that some probiotics survive stomach acid well, but there is no benefit in having them there and some strains require more protection.

Speaking of good bacteria strains, it’s important to check that you have lactobacillus and bifidobacterium strains in your probiotic. Lactobacillus plantarum and lactobacillus rhamnosus are particularly helpful for eliminating pathogenic bacteria. While bifidobacterium logum may protect against colon cancer and bifidobacterium breve is believed to help prevent diarrhea and excessive gas.

The best probiotic supplement I’ve found and that I take myself daily is this one. It’s enteric-coated, room temperature stable and contains the beneficial probiotic strains mentioned above and several others.

You take it once or twice a day before a main meal with a big glass of water. Increase this to before every meal after sickness and when you feel run down and take a double dose for at least a week after a course of antibiotics.

Building Up Your Intestinal Defenses

Your intestinal bacteria can either be a powerful defender of your health, or a source of sickness and disease. In many ways, digestive problems like bloating, intestinal cramps diarrhea, constipation and excessive flatulence are just an early warning sign of potentially more serious health problems.

You can help to build and support a healthy intestinal environment by eating a real food diet that doesn’t feed bad bacteria and yeasts, as well as reinforcing them with probiotic foods or supplements.

While this is especially important after digestive upsets, sickness, regular junk food and above all antibiotic use, only the very healthiest of people out there wouldn’t benefit from eating probiotic foods or taking a good probiotic supplement.


  • Reduce sugar and fructose in your diet to stop feeding bad bacteria and yeasts.
  • Eat more probiotic foods like cultured vegetables and prebiotic foods like spirulina and chia seeds.
  • Consider taking a high strength probiotic supplement daily or twice daily before a meal with a big glass of water.


Restoring Your Digestive Health & Stopping SIBO with Probiotics

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