Whole Food Probiotics And Supplements - A Beginner's Guide
- Josh Boughton
- Sep 17
- 10 min read
Probiotics are the good bacteria in our gut. These little bugs play an essential role in your health. This easy-to-understand guide makes it easy for you to get started on your probiotic journey.
What are probiotics?
Probiotics are live microorganisms that, when administered in adequate amounts, provide benefits to the host. Your body contains trillions of these incredible little helpers. The key is having a balance. Not too much of any particular one. You want things just right, like the porridge in Goldilocks and the Three Bears.
Probiotic Genus
There are many different probiotic genera. Think of the genus as the first name of the probiotic. The most well-known are:
Lactobacillus
These live primarily in the small intestine and urinary tract.
Bifidobacterium
These live primarily in the large intestine.
Streptoccocus
These live primarily in the small intestine.
Saccharomyces
Probiotic yeasts
Bacillus
Spore-forming bacteria
These are not a normal part of the flora of humans.
Akkermansia
Probiotic Species
Think of species as the middle or last name of the probiotics. For example:
Lactobacillus Acidophilus
Lactobacillus is the genus, and Acidophilus is the species.
Bifidobacterium Lactis
Bifidobacterium is the genus, and Lactis is the species.
Different species of the same genus can have very different effects.
Probiotic Strains
Many lab-made probiotics contain a third part of their name, the strain. For example:
Lactobacillus acidophilus DDS-1
Lactobacillus is the genus
Acidophilus is the species
DDS-1 is the strain name
Lactobacillus acidophilus NAS
Lactobacillus is the genus
Acidophilus is the species
NAS is the strain name
Bifidobacterium Lactis BI-04
Bifidobacterium is the genus
Acidophilus is the species
BI-04 is the strain name
These lab-made strains will often have different properties even when the genus and species are the same, because of modifications made to them by the companies producing them. Wild bacteria and bacteria found in naturally fermented foods (like sauerkraut, kefir, and kimchi) will generally not have strain names.
What are the benefits of probiotics?
Different probiotics have different benefits. Here are just a few of the benefits:
Gut health
Immune health
Brain health
Lung health
Sleep support
Mood support
Vaginal health
Kidney health
Urinary tract health
Because the gut affects so many different body systems, probiotics can have a wide array of beneficial effects. It would take a large book to list out all of the benefits.
Probiotic foods
Probiotic foods have a great diversity of beneficial bacteria and other important compounds. This makes them the ideal way to get probiotics in your gut.
Don’t forget to consume plenty of prebiotic-rich whole foods (the food for your probiotics) as well. Without enough food, your probiotics won’t thrive.
Here are some of our favorite probiotic foods:
Grass-fed Kefir
Kefir is a fermented beverage usually made from milk, but there are also water and coconut kefirs. It is rich in good probiotic bacteria and postbiotics. The best kefir is grass-fed, unsweetened, and full-fat.
It is much better to add some prebiotic foods, such as berries, rather than buy the sweetened and flavored versions of kefir. They often have large amounts of sugar added. If you like a sweeter kefir, add some probiotic cacao fruit nectar or prebiotic yacon syrup.
Grass-fed Yogurt
Yogurt is probably the most well-known probiotic food. It is made from fermented milk. It is rich in good probiotic bacteria as well as lactose, a sugar found in milk that acts as an excellent prebiotic. The best yogurt is grass-fed, unsweetened, and full-fat. As with kefir, it is much better to add some prebiotic foods, such as berries, than to buy the sweetened and flavored versions. They often contain large amounts of added sugar. If you prefer a sweeter yogurt, consider adding probiotic cacao fruit nectar or prebiotic yacon syrup.
Grass-fed Cheeses
Certain cheeses, when made in the traditional manner, are packed with beneficial probiotics. These include cottage, Parmesan, feta, and most of all, Gouda cheese.
Lacto-fermented Vegetables
Nearly every culture around the world has a version of these, from sauerkraut in Germany, kimchi in Korea, Jewish pickles, and many more.
They are made without vinegar, just using salt, water, and whichever are the desired seasonings. The naturally occurring bacteria on the vegetables and in the air ferment by feeding on the sugars and fibers in the vegetables. The bacteria multiply and produce postbiotics, like lactic acid. These veggies provide a significant amount of beneficial probiotic bacteria in just a couple of tablespoons.
You can make them yourself or buy them premade. You will find them in the refrigerated section, not on the shelf. Shelf-stable versions of these will not have the probiotic bacteria. Always buy these in glass, not plastic, as the strong acids and salt in them will cause a lot of plastic to leach into them.
Miso
Miso is a fermented paste. It is most often made from a combination of beans, cultured grain, and sea salt by a unique, double fermentation process. It is rich in beneficial bacteria and prebiotics. It adds a wonderful umami flavor to soups and other dishes. Always buy miso packaged in glass, not plastic, to avoid leaching from the plastic into the miso. Probiotic-rich miso will be found in the refrigerated section, not on the shelf.
Vinegar With The Mother
Vinegar with the mother contains a whole host of beneficial yeasts and bacteria. Switching out your typical vinegar for one of these is an easy way to get a daily dose of probiotic food.
Brined Olives
These types of olives are produced via fermentation, making them rich in beneficial bacteria and healthy fats. These are very different than your traditional olives in jars or cans.
Lactofermented Beet Kvass
This drink is made in a similar way to beer, but with beets. This drink has so many benefits beyond just the good bacteria it contains.
Beets support healthy circulation, nitric oxide production, digestive health, and so much more.
Most people have heard of cacao and chocolate, but this is something entirely different. Real cacao fruit nectar is made with an old-fashioned method of fermentation by the people of Peru. It is made from the pulp of the cacao pod. While you might think it tastes like chocolate, it actually tastes a bit tropical and fruity. It’s an excellent replacement for liquid sweeteners, such as honey, simple syrup, and maple syrup, and is packed with prebiotics, probiotics, and posbiotics. It contains less sugar than other liquid sweeteners, making it a good way to get probiotics while reducing your sugar intake. Check out our blog to learn more about it.
We recommend consuming a variety of probiotic foods as often as you can. This will provide the most benefits and give the best support to your microbiome.
One benefit that probiotic foods have that traditional probiotic supplements don’t is that they tend to be rich in postbiotics. Postbiotics are beneficial compounds produced by probiotics as they feed on prebiotics. Postbiotics have their own set of benefits. Emerging research is showing a huge potential in them.
Even just a small amount of probiotic-rich foods every day can make a big difference in your health!
What to look for in a probiotic
Not everyone can get enough probiotics from food, and in those cases, a probiotic supplement can be a great option.
In choosing a probiotic supplement, we recommend picking one that provides the same benefits that probiotic-rich whole foods do. Remember, these foods have far more than just probiotics in them; they are synbiotics (prebiotics, probiotics, and real postbiotics).
Here’s what to look for in a probiotic supplement:
Whole food probiotics
Look for probiotics that are truly whole food, made by fermenting the bacteria on whole foods. Not just regular probiotics mixed with a bit of food. The fermentation process creates lots of postbiotics, which have their own benefits and are not found in traditional probiotics.
Drying methods
While freeze-drying is good for foods, it’s not great for probiotics. The freeze-drying process can damage their cell walls, potentially weakening them.
Look for sun-dried probiotics.
CFU not AFU
Probiotic counts are measured in something called colony-forming units (CFU). Some companies are trying to use a new term called active fluorescent units (AFU). The reason CFU is used as a measurement is that the ability of probiotics to form colonies and populate the gut is integral to their benefits. Just being a live bacteria does not mean that the bacteria can form colonies. So, using AFU as a measurement is meaningless, but allows companies to claim larger amounts of bacteria on the label even though most of those bacteria won’t do anything. Do not buy probiotics that use the AFU measurement; it indicates they prioritize marketing over delivering a high-quality product.
Intact colonies
Probiotic bacteria grow in colonies. Keeping these colonies intact creates a more potent and stable probiotic supplement. Unfortunately, nearly all probiotic supplements are centrifuged, which breaks up the colonies and weakens the bacteria. This is done to isolate the bacteria from the culture medium, allowing for higher bacterial counts and easier manufacturing. However, the culture medium itself has lots of benefits, so you end up missing out on lots of the good stuff.
Keeping the culture medium
When you make kimchi, sauerkraut, yogurt, etc., the base (vegetables, milk, etc) is the culture medium. You’re eating more than just bacteria. The culture medium is packed with lots of easily digestible, nutrient-rich foods. Well, the culture medium of a whole food probiotic is the same way. It also provides food (prebiotics) for the bacteria in the probiotic. In addition, it is full of postbiotics. These postibiotics are the subject of a lot of research and may have just as many, if not more, benefits than the probiotics themselves. By keeping the culture medium, you get a true synbiotic (a combination of prebiotics, probiotics, and postbiotics). It does not get any better than that. Unfortunately, a lot of companies have decided to include fragments of dead bacteria and call them postbiotics. That is not all the same thing, but it’s much cheaper and easier to make than a real whole food probiotic supplement, so most companies take this more profitable route.
Stress Testing
While lots of stress might not be good for us, it’s something that makes for an excellent probiotic. What do I mean by stress tested? During the fermentation process, the bacteria are exposed to things that they might encounter in the gut, such as acids, heat, etc. This ensures that only the strong bacteria survive. Those who cannot handle the stressors that might occur in the gut die off.
To refrigerate or not to refrigerate
Should a probiotic be refrigerated? Well, it depends. Some types of probiotics need refrigeration, and some do not. Whether the product needs refrigeration depends on its preparation and the type of bacteria used. Whether or not a product requires refrigeration does not determine its quality.
Which probiotic should be in it?
Different types and strains of probiotics and probiotic preparations can have different effects. Which ones you need depends on your health goals. There is not one perfect probiotic for everyone.
How many probiotics should be in the product?
Many companies have decided that simply listing huge numbers of probiotics will make people believe their product is best. To a certain extent, that sales pitch works very well. The truth, however, is very different. Just because a product has more bacteria does not mean much.
It does not mean they will survive and implant in the gut.
It does not mean that they are alive in the bottle when you get it.
It does not mean that they are the right bacteria.
It does not mean that the product was made correctly.
Instead of focusing on the number of bacteria in the product, it’s better to focus on the quality of the product. Don’t fall for marketing gimmicks.
How to use probiotic supplements
Different probiotics require different dosing regimens. Some are best with food, some on an empty stomach, and others need to be used at specific times for their desired effect.
When using live probiotics, it’s best to start at a lower dosage and gradually increase the amount. Sometimes probiotics can cause loose stools, gas, or bloating, in the beginning, if you take too much or as your gut adjusts. Make sure to take them consistently for at least three months, because it takes time for the full effects.
Powdered probiotics should be mixed into cold beverages and foods, not hot ones.
Shelf-stable probiotics should be stored in a cool, dry place, away from direct sunlight and moisture. Refrigerated probiotics should be stored in the fridge in their original container.
Whole food probiotic supplements
Thankfully, there are a few companies that make amazing whole-food probiotic supplements, providing the benefits of probiotic-rich whole foods in easy-to-use forms.
First up is Immunity Fuel.
Immunity Fuel is a whole-food probiotic supplement (technically a synbiotic) produced through a specialized fermentation process. They use bacteria found on organic farms in Australia. These bacteria are placed in a large stainless steel tank containing a variety of organic foods. Then they are fermented for three weeks, while being exposed to various stressors. Once the fermentation process is complete, the whole food mixture is sun-dried and bottled. That’s it! The entire food medium is included. The cultures are not centrifuged or separated from the culture medium. For a more in-depth look at what makes Immunity Fuel different than other probiotics, check out our blog. Immunity Fuel is our top pick for a daily probiotic.
Next is Seleno Health Tocosh.
Tocosh is a traditional fermented food made in Peru. It is made by lacto-fermenting special varieties of potatoes near or in a stream. The naturally occurring bacteria in the environment ferment the potatoes. Once this is done, the potatoes are sun-dried and milled. That’s it. No harsh processing, no centrifuging. The entire culture medium is included. To learn more about Tocosh, its benefits, and how to use it, check out our blog. Tocosh is a great probiotic choice when you need something that works quickly, and it is our favorite probiotic to take when traveling. If you are allergic to penicillin, you should not use Tocosh.
Our next probiotic is Rosita Bee bread.
It is a unique lacto-fermented food produced by giant rock bees in the forests and foothills of the Himalayan Mountains in India. The bees mix saliva, pollen, secretions, and nectar inside the hive cells. Then they seal the cells with honey and wax. At this point a lactic acid fermentation process beings in the honeycomb cells. This breaks down the pollen and releases nutrients, converting the bee pollen into bee bread. It is packed with nutrients, polyphenols (prebiotics), fatty acids, probiotic bacteria, and metabolites (postbiotics). It is a true synbiotic. It takes bee pollen to a whole new level.
The bee bread is hand-harvested by honey hunters who climb up tall trees using handmade ladders. It is gently taken from the honeycomb using an ancient and gentle technique that protects the bee bread and does not harm the hives. After harvest, it is bottled, with no harsh processing or refining. Just pure goodness!
It has a fruity aroma and slightly tangy taste from the lacto-fermentation. It dissolves in the mouth or can be chewed. It should be stored in the fridge after opening.
This rare food packs a potent nutritional profile and provides a great way to start your day with an energizing probiotic boost without the caffeine jitters and crash.
Probiotic questions and support
If you have questions about our probiotics, email us at info@rooted-nutrition.com, and we will be happy to answer them! It's important to remember that probiotics alone can’t fix gut problems. Check out our Gut Health Center to learn lots of ways to support all aspects of your gut.
