What is the Best Probiotic for Gut Health?

by Kaitlynn Fenley
probiotic pill capsules on a white background

What is the best probiotic to take for gut health? What are probiotics? Is it necessary to buy expensive, special supplements labeled as “probiotic” to introduce these wonderful microbes into your health routine?  Check out this blog for all the answers!

What is the Best Probiotic for Gut Health?

The popularity of probiotics is increasing every day, like never before. From drinks and foods to hygiene products and digestive medicines, there are new products every day containing probiotics. But what is the best probiotic for gut health? To introduce these wonderful microbes into your health routine, is it necessary to buy expensive, special supplements labeled as “probiotic”? 

Let’s break it down.

Why are Probiotics for gut health necessary?

All life has come from microbes, and all life on this planet relies on microbes to thrive. Humans, as well as other animals and even plants, have something called a microbiome. This is the population of microbes that naturally lives on and inside of other organisms.

If you were to count cell for cell… the cells making up your body are only 10% human cells. The other 90% are microbial cells you carry around every day.  

When you compare DNA, the results are even more amazing. When scientists were trying to sequence the entirety of the human genome the results were interesting… First, it turns out that we don’t have many more genes than simple organisms like roundworms… only about 22,000.  So how can we explain why humans are so advanced? Turns out that our 22,000 functional human genes only make up 3% of the total genes we carry in and on our bodies. The other 97%… those genes are microbial. On your body right now, gene for gene, you are only about 3% human. The rest of the functional DNA on your body is from microbes. This fact alone indicates how vital our microbiomes are to our health.

blue play dough molded like your intestines.

The Human Microbiome

The human microbiome has a natural healthy balance, and many factors influence the composition of an individual’s microbiome. Everything from diet and exercise, to the soap you use, to how much time you spend enjoying the outdoors influences what microbes populate your body. Unfortunately, we can easily throw our microbiome populations off balance. This results in a not-so-healthy population of microbes. The stomach flu, the use of antibiotics, bathing with harsh soaps, eating processed food, and not going outdoors enough can all take a negative toll on the delicate microbial population you carry around.

This is where probiotics come in handy, especially in our modern society.

In 2019 our world, especially the western world, is increasingly toxic to our bodies and our microbiomes. There are chemicals and toxins everywhere… there are more antibiotic-resistant superbug outbreaks than ever before. People (and the Earth in general) are over sanitized and over-polluted. We deal with NCDs caused by microbiome dysbiosis at much higher rates than ever before.

Luckily we can naturally repair and rebuild our microbiomes daily with cultured foods.

What are Probiotics?

A probiotic is defined as a microbe, usually, a species found in a healthy person’s microbiome, that is introduced into the body for its beneficial qualities. When the good microbes of your body suffer as collateral damage from a course of antibiotics, eating foods with too many preservatives, or even a very stressful day at work, probiotics can help to restore balance! Most probiotics have been isolated from traditional, cultured food products.

Probiotics are wonderful addition to a healthy diet and exercise. Having a high number of good bacteria in you and on you can help keep bad microbes away, and this is so important as antibiotic resistance becomes more prevalent every day. Think of it like this: if most of the room in and on your body is already occupied by good guys, then there will be no room for the bad guys to set up camp… at least it won’t be very easy for them to do so.

Do Probiotics Work?

The most popular marketed probiotic capsules contain species in the genera Lactobacillus and Bifidobacterium. They are Gram positive, rod-shaped bacteria found in the gastrointestinal tract, vagina, and mouths of healthy humans. Both types of bacteria originate from the soil and fermented foods. Both aid in digestion, can combat diarrhea, and help to promote a healthy immune system.

Ideally, a probiotic microbial species should:

  1. Be able to compete with pathogenic microorganisms for space, reproduction, and survival.
  2. Survive the digestive journey and easily incorporate into the gut microbiome population.

So What is the Best Probiotic for Gut Health?

It really depends on your situation. In some cases, a probiotic pill can be very beneficial. Probiotic capsules/pills are especially helpful to introduce a specific species of bacteria to the gut. I find probiotic pills and capsules are best used when a medical condition or treatment requires them.

For healthy people, fermented foods and beverages serve as a great source of probiotics at a fraction of the cost.

Some advantages of fermented foods over probiotic pills:


  • The digestive journey is tough. Digestion starts in the mouth and takes foods and substances on a harsh journey. Since the cultures that are being grown in labs are never exposed to harsh conditions, they are not adapt to survive. Cultures that are added to foods or capsules are commercially grown in huge vats in laboratories under perfect living conditions for the bacteria. This optimizes growth times and profit margins. These bacteria are also exposed to cryoprotectant sprays and materials to coat the bacteria in protective chemicals before they are freeze-dried. These chemicals do not have to be disclosed to consumers.
  • The bacteria in naturally fermented vegetables come from nature. Specifically, they originate in the soil in which the vegetables are grown. In that soil these microbes compete for space and for their lives. During fermentation, only bacteria that can survive in a very low pH environment, with no oxygen and some salt continue to thrive. These bacteria are natural, strong, and are adapted to harsh conditions that are very similar to the terrain of the human digestive tract! (Here’s some reference material on this subject). This makes fermented vegetables the best probiotic for gut health.


  • Genetic modification of probiotic bacteria aka “pharmabiotics.” Pharmaceutical companies and big food companies have their eyes set on the profit potential in patenting particular strains of probiotic bacteria. They are specifically interested in patenting particular strains of bacteria for the treatment of certain diagnosed diseases. How might they do this you ask? They have the resources to genetically modify species of bacteria to make them perform a specific function. When they genetically modify the bacteria, the bacteria contain unique gene sequences that can be registered with the US Patent Office. Meaning only they can profit from it. And where was the microbial species that they genetically modify originally isolated from? Fermented foods.


  • Adding probiotic bacteria to unhealthy, refined and processed foods doesn’t make that food healthy at all. The food products labeled as “probiotic” are a marketing ploy. These foods are normally unhealthy, full of sugar and refined ingredients. So these foods are not considered foods that are good for gut health. Before you grab that ice cream with probiotic cultures added, remember that healthy gut microbes don’t thrive on ice cream.

To summarize:

Unlike capsules, the microorganisms in fermented vegetables live in complex mixed ecosystems, they come from the surface of vegetables, they are exposed to MANY other species, they are exposed to harsh acidic conditions, they can survive the digestive journey, and they are well adapted to live with multitudes of other microbes, such as those in the gut.

The Best Probiotic for Gut Health

Eating a variety of wild fermented vegetables and drinking kombucha or water kefir occasionally are the best ways to introduce a rich population of probiotic microorganisms to your body. Fermented vegetables not only contain essential vitamins and nutrients that are crucial to health, but they also contain the most natural form of probiotics: microorganisms that come from the soil in which the vegetables were grown and that are adapt to survive the digestive journey.

kombucha scoby floating on sweet tea

Encouraging a Healthy Gut Microbiome

Gut health is not as simple as just popping a probiotic pill. It’s about forming a dietary lifestyle based around fresh plant foods, eating a variety of seasonal and local fruits and vegetables, and consuming natural sources of probiotic bacteria.

Where I get my daily dose of natural probiotic bacteria: Our Cultured Guru Fermented Vegetables along with the occasional water kefir or kombucha and homemade vegan yogurt made with heirloom cultures. I also eat vegetables I ferment for fun in our home kitchen.

Do Fermented Vegetables Contain Histamine?

Vegan fermented vegetables do not contain any relevant amount of histamine and are still the best probiotic for gut health.

Fermented vegetables that do not contain animal-sourced and/or high protein ingredients do not contain relevant amounts of histamine.

Also, histamine isn’t necessarily a bad thing. It gets a bad rap, but histamine is necessary for human body function. Histidine is an essential amino acid, and histamine is vital to the proper function of the immune system. Average, healthy people have no problem when consuming moderate amounts of histamine in foods. Good gut microorganisms normally degrade histamine in the gut, and the enzyme DAO (Diamine Oxidase) also degrade histamine.

Animal ingredients in fermented vegetables:

Fermented vegetables that contain animal ingredients such as fish paste or whey, will be high in histamine. Fermented dairy yogurt may have histamine, cultured meats and cheese have histamine, and some cultured soy products may have histamine. This is because the high protein ingredients in the foods contain the amino acid histidine that microbes can convert to histamine using the enzyme histidine decarboxylase. 

Fermented vegetables made with only vegetables, salt, water, and spices cannot physically contain relevant levels of histamine… this is because the precursor amino acid histidine is not present in relevant amounts in the ingredients, so there’s little to no histidine for microbial enzymes to decarboxylate into histamine. 

Microbes in Fermented Vegetables Break Down Histamine

Certain species of Lactobacillus found in fermented vegetables are also capable of breaking down histamine.

If you eat high animal fat, high animal protein foods in tandem with any source of probiotics, or in tandem with a healthy gut microbiome, this is what can potentially cause a problem with histamine in the gut. Probiotic bacteria and a healthy gut microbiome will convert the amino acid histidine in those foods into histamine. So too much protein, too much histidine can be a main problem for people with diagnosed insufficient DAO.

For a nourished microbiome, a plant-based diet along with vegan fermented vegetables is wonderful.

Are any vegetables high in histamine?

Very few vegetables contain relevant levels of histamine, and any relevant levels are usually a result of spoilage microorganisms. (This does not apply to beans, legumes, and starchy vegetables which have varying amino acid content).

People with diagnosed histamine intolerance

Certain types of green leafy vegetables are high in other biogenic amines like putrescine, cadaverine, and tyramine. These biogenic amines are competing substrates for an enzyme called DAO. DAO breaks down histamine in the human body.

Most people who have a histamine intolerance have inadequate DAO, so eating foods with competing substrates is not the best idea. For this reason, people on low histamine diets should avoid spinach, kale, eggplant, tomatoes, and avocado.

In general people with histamine intolerance should avoid old, aged, and preserved foods in which the ingredients were high in the amino acid histidine. This includes canned fish, aged meats, cured meats, canned beans, smoked fish, and high protein leftovers.

Obviously, if you have a diagnosed histamine intolerance, follow any recommendations provided by your doctor.

Reference Material

The Production and Delivery of Probiotics: A Review of a Practical Approach

Biogenic Amines in Plant-Origin Foods: Are they Frequently Underestimated in Low-Histamine Diets?

Biogenic amine and fermentation metabolite production assessments of Lactobacillus plantarum isolates for naturally fermented pickles

Histamine and Other Biogenic Amines in Food. From Scombroid Poisoning to Histamine Intolerance

Non-GMO Project

Wild-Type and Genetically Improved Strains of Dairy Origin Probiotic as Potential Treatments for Intestinal Mucositis

Strategies to improve the functionality of probiotics in supplements and foods

Synthetic biology approaches to engineer probiotics and members of the human microbiota for biomedical applications

Genome editing of lactic acid bacteria: opportunities for food, feed, pharma and biotech

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Leave a Comment


Wendy oubre August 8, 2021 - 8:20 am

Do you have the dill pickles in the stores in Baton Rouge area???? Thanks

Kaitlynn Fenley August 8, 2021 - 8:41 am

Not currently, our pickles are a seasonal product. They will be available in all our regular baton rouge store locations by the end of August.