How Good Bacteria Get In Our Stomach and Digestive System?

The foods, supplements, probiotics and prebiotics are needed for healthy stomach bacteria.

The gastrointestinal tract is the largest part of the human digestive system. Its main components are the stomach, small intestine, and the large intestine (colon). Digestion of food starts in the mouth, where the food enters and continues in the stomach and other parts of the gastrointestinal tract. The whole process is assisted by the stomach acid, various digestive enzymes, and the gastrointestinal microbiota.

The gastrointestinal microbiota or the gut flora is the “good bacteria” of the human gastrointestinal system. These microorganisms, which inhabit our digestive tract, act together as a kind of an endocrine organ. They produce enzymes, synthesize Vitamin K and Vitamin B, ferment dietary fibers, and assist the digestive process.

When the gastrointestinal microbiota is well balanced, it benefits its host. However, changes in diet, lifestyle, and certain health issues can disrupt this balance and cause inflammation. This article will focus on how a healthy, well-balanced, diet aided by quality supplements, probiotics and prebiotics can keep the good bacteria of the digestive system from becoming bad.

The Foods

The foods you eat are essential for nurturing a balanced and diverse gastrointestinal microbiota. Much like humans, different kinds of bacteria have a taste for different foods. Unfortunately, the common western diet is mostly rich in sugars and fat. Needless to say, this is not diverse enough.

Most good bacteria feed on fiber. So, eating the foods rich in this dietary material is highly recommended. Legumes, fruits, vegetables, nuts, and beans all contain significant amounts of fiber. Bifidobacteria, a type of bacteria associated with preventing intestinal inflammation is known to thrive on fiber.

Specific food rich in fiber are:

  • Whole grains
  • Broccoli
  • Lentils
  • Green Peas
  • Chickpeas
  • Artichokes
  • Bananas
  • Raspberries
  • Blueberries
  • Almonds
  • Pistachios

Fermented foods like yogurt, kefir, kimchi, pickles, and sauerkraut are also beneficial. There are also other food types which help the good bacteria to prosper. These are the prebiotic foods, but we will explain more about those later in this article.

The Supplements

Aside from the prebiotic and probiotic supplements, there are also others which can contribute to a balanced microbiota of the gastrointestinal tract.

1. Fish Oil

Fish oil is rich in healthy fats, such as Omega-3 fatty acids. These healthy fats act preventively on inflammation. In combination with the Lactobacillus gasseri, fish oil helps the longer survival of probiotics in the digestive tract. Some studies show that supplementation with Omega-3 fatty acids is beneficial for the treatment of Inflammatory Bowel Disease (IBS) and for keeping the healthy balance of the gastrointestinal microbiota.

2. Magnesium

This mineral is essential for the function of various digestive tract enzymes. It is scientifically proven that magnesium deficiency can change the composition of the gastrointestinal microbiota. Because getting enough magnesium through diet is not easy, supplementation is often necessary.

3. Vitamin D

Vitamin D has anti-inflammatory properties. Its supplementation is necessary because the imbalanced microbiota of the gastrointestinal tract often does not metabolize this vitamin well. With foods rich in Vitamin D being sparse and many people avoiding the sun or using sunblock, thus cutting off the main source of Vitamin D, supplementation is even more important.

4. L-Glutamine

L-Glutamine is an amino acid which can be found in protein-rich foods (meats, beans, peas, etc.). It is known as the essential amino acid of the digestive tract. Supplementation with L-Glutamine balances the intestinal microbiota helps the healing of the intestinal wall and increases the immune response.

Probiotics and Prebiotics That Are Needed For Healthy Stomach Bacteria

Probiotics and prebiotics are the best way of getting the good bacteria in the digestive system. This can be done through diet, supplementation or both.


There are many types of probiotics, like the Saccharomyces boulardii (a type of yeast), Bifidobacteria, and Lactobacillus. All of these can be found in certain foods (e.g. fermented dairy products, kombucha, pickled vegetables, etc.) or as commercial probiotic supplements.

All the probiotics are basically live bacteria, but the good kind which supports the digestive process. The use of probiotics can also:

  • Ease urinary and vaginal infections
  • Ease certain skin conditions
  • Prevent diarrhea
  • Prevent autoimmune disease

The intake of probiotics, through diet or supplementation, keeps the gastrointestinal microbiota in balance and prevents the multiplication of yeasts and bad bacteria. Our body can absorb nutrients from food better when the digestive system is in balance.

Probiotics can also relieve the symptoms of Irritable Bowel Syndrome, such as bloating, irregular bowel movement, and abdominal pain.

Some scientific studies show promising results of probiotics use in the treatment of Inflammatory Bowel Disease.

The side effects of probiotics are rare. When they do exist, it is usually as a result of the probiotics interaction with the host-bacteria. Some rare cases of bacteremia have been reported in extremely ill people suffering from short bowel syndrome, immunodeficiency, and cardiac valve disease.

Prebiotics, unlike probiotics, are not bacteria at all. They are a type of fiber. This fiber cannot be digested by the gastric acid or any endocrine enzymes but is fed upon by the microorganisms which inhabit our digestive tract.

Prebiotics as a fuel for our gut flora and probiotics. When the bacteria dissolve the prebiotics they produce nutrients, mostly short-chain fatty acids, which the body can absorb. These nutrients improve our metabolic health.

Foods rich in prebiotics are:

  • Bananas
  • Garlic
  • Onion
  • Beans
  • Apples (especially the apple skins)
  • Jerusalem artichokes
  • Cocoa
  • Flax seeds
  • Seaweed
  • Barley
  • Asparagus
  • Leeks

Although many foods are rich in prebiotics, a diet consisting of processed foods is usually not. For this reason, prebiotics are also available as supplements mostly in the form of prebiotic powders.

A diet rich in prebiotic fiber is beneficial for digestion, weight control, immune system, and bone density.



• Costantini L, Molinari R, Farinon B, Merendino N. Impact of Omega-3 Fatty Acids on the Gut Microbiota. International Journal of Molecular Sciences. 2017; 18(12):2645. Doi: 10.3390/ijms18122645.

• Winther G, Pyndt Jørgensen BM, Elfving B, Nielsen DS, Kihl P, Lund S, Sørensen DB, Wegener G. Dietary magnesium deficiency alters gut microbiota and leads to depressive-like behaviour. Acta Neuropsychiatr. 2015 Jun; 27(3):168-76. Doi: 10.1017/neu.2015.7. Epub 2015 Feb 18.

• Van der Hulst RR, Von Meyenfeldt MF, Soeters PB. Glutamine: an essential amino acid for the gut. Nutrition. 1996 Nov-Dec; 12(11-12 Suppl):S78-81.

• Jonkers D, Stockbrügger R. Probiotics and inflammatory bowel disease. Journal of the Royal Society of Medicine. 2003; 96 (4):167-171.

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