All About The Friendly Bacteria in Your Gut and Probiotics

Everyone’s been talking about their gut bacteria lately and scientists are learning more and more about the importance of the colony inhabiting your insides. But how do these microbes get there and are they the same in everyone? Can probiotics really improve my health? 

Building your gut microbiome begins as soon as you’re born. From the milk you drank to the toys you stuck in your mouth, these friendly microbes came from all over. Some immunity even came from your mom through skin contact or breast feeding. It’s actually the reason why toddlers can’t digest certain foods well; they are still building their colony. Without the good bacteria in your gut to break down food, we wouldn’t be able to eat many of our favorite foods, either!

What is a “microbiome?”

Essentially, your microbiome (aka gut flora) is all the “good” microbes present in your gut that help you break down food and provide immunity. Over 1,000 species of bacteria have been identified in the average human and your body is full of trillions of microbes! Remember, not all bacteria are bad.

The Technical Definition

“The human microbiome is composed of bacteria, archaea, viruses and eukaryotic microbes that reside in and on our bodies. These microbes have tremendous potential to impact our physiology, both in health and in disease. They contribute metabolic functions, protect against pathogens, educate the immune system, and, through these basic functions, affect directly or indirectly most of our physiologic functions.”

Shreiner et. al (2015) Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School

Building your colony

Take a look at this video from TedEd to learn a little more.

You are your Microbes by Jessica Green and TedEd

So, now we know we need to have a large variety of gut bacteria available to help us digest all different kinds of food. If we only eat certain types of food, such as those with simple sugars, we eventually become over- colonized with those types of bacteria, because they are the most used. The other bacteria that can digest more complex foods are eventually kicked out; bad news for your gut. You are what you eat!

You also build immunity through exposure from the environment. Did you know bacteria are ubiquitous in nature? They are literally everywhere! They’re in the dirt, water, air, dust, surfaces, your skin, and anywhere you can think of. Exposure to different types of bacteria helps train your immune system.

Unfortunately, it is also easy to throw this balance of bacteria out of whack. Stress, poor diet, and antibiotics all disrupt your gut.

The Hygiene Hypothesis

Despite the scary thought of a world overrun with bacteria, some scientists are actually beginning to think we are “too clean.” Consider this: the food safety standards today as compared to one hundred years ago are very different and fewer and fewer people are working outdoors.
Kids are no longer playing in the dirt. Hand sanitizer is everywhere and people are more aware than ever of dangerous microbes. What this translates to is cleaner hands and a perceived “safer” environment.

Hygiene hypothesis too clean

However, similar to a vaccine, immunity is built through exposure. If you’ve never been exposed to any invaders, your immune system can’t build resistance and doesn’t know how to respond to the appropriate invaders. It then overreacts to everything it does come up against.

It’s believed the hygiene hypothesis may play a role in the development of allergies, asthma, and autoimmune diseases in children. This is because they are still in the process of building their gut flora and training their immune system.

Antibiotics and your gut

Have you ever stopped to think about how antibiotics work? Well, they kill bacteria, right? That’s right, but they don’t just kill the bad bacteria. Most are “broad spectrum” antibiotics that take out a large portion of your good bacteria, along with the bad. This is a problem because when it comes to bacteria and health, it’s often a numbers game. You need to have a large colony of good bacteria available to outnumber and out-compete the bad bacteria. This helps you stay healthy.

You probably know it’s important to take the full dose of antibiotics. And that’s because it takes time to rid the body of all the bad bacteria. If you don’t take the full dose, you run the risk of a few bacteria surviving and then creating more bacteria. Or worse, becoming antibiotic resistant.

Are probiotics the answer?

Probiotics are live microorganisms added to foods that offer potential health benefits to the host when consumed in adequate amounts (WHO). They have been shown to improve the health of your gut and assist in digestion. Traditionally, most probiotics have been incorporated into yogurt or dairy products, but more and more applications are being developed, including nutritional bars and juices.

Bite of yogurt

Recent studies have found that probiotics do not actually colonize the gut, as the “good” bacteria of the microbiome do. It is believed that probiotics promote homeostasis between good and bad bacteria, or that they interact with the good bacteria. More research is needed to know for sure.

What health benefits do probiotics provide?

It’s important to note that the science of probiotics is largely still in its infancy and there is much more research that needs to be done, specifically in regards to which strains are most beneficial, how they interact in individuals, and what benefits are most likely to occur.

In addition to enhancing the population of your gut flora, evidence has shown probiotics may provide other benefits, as well:

  • Aid digestion
  • Produce vitamins
  • Reduce intestinal transit time
  • Fight cancer
  • Reduce inflammation
  • Reduce cholesterol and blood pressure
  • Protect against foodborne illness
  • Assist in lactose digestion
  • Promotes urinary health

How exactly do probiotics promote immunity?

Research has shown probiotics may be beneficial in potentially strengthening the immune system by interacting with the gut or existing microflora.

Probiotics have been shown to increase immune responses to specific antigens, or foreign invaders. Basically, your body is trained and able to fight what and when it needs to.

Probiotics are known to produce organic acids in the intestine. These acids effectively lower the pH and produce bacteriocidal (lethal) or bacteriostatic (growth preventing) effects. Many pathogenic bacteria are sensitive to acid and die in response to the intolerable environment. In turn, this keeps you healthy!

It’s also known that many pathogens invade the intestine by entering through tight junctions in the intestinal wall. Some research has shown probiotic bacteria may help close these junctions or gaps and prevent invasion.

It’s personal

It’s currently unclear just how much probiotic you would need to consume to see health benefits. As mentioned earlier, research is still new in the area and is quickly developing based on consumer interest and health. It is believed that each person may have different needs. Bacterial strain selection is also critical. The bacteria must be able to survive the harsh gastric environment.

It’s important to note that eating some probiotic yogurt once, every now and then, won’t do the trick. You need to consistently consume probiotics on a daily basis to truly see the potential benefits.


While probiotics are safe for most healthy adults, check with a doctor before serving to infants or those with compromised immune systems.

Disclaimer: I am not a doctor and the information offered here is meant for informational purposes only.

Technical Challenges

As you may know, bacteria are sensitive to heat and harshly acidic environments, like the stomach. This means foods containing probiotics must be carefully processed and the right strains chosen selectively; not all strains are created equal. L. acidophilus and bifidobacteria are incorporated along with the normal fermenting bacteria of yogurt because they can survive these harsh conditions. They have also been shown to survive in the human body. Bifidobacterium lactis is another example that can withstand low pH and high bile conditions.

Other factors that affect probiotics include acid content, oxygen, antimicrobials produced by other bacteria, and lack of nutrients. Both processing conditions and shelf-life conditions may have an impact. You can see this is a lot to consider!

Where can I get probiotics?

Probiotics are often found in dairy products, such as yogurt and fermented milk. Newer offerings include juice and granola bars. There are many supplements available, as well, that allow you to choose exactly which strains are best for you.

Did you know? It’s possible to purchase probiotics as dietary supplements. However, keep in mind that dietary supplement claims and safety are NOT regulated by the government prior to reaching the market. It is up to the manufacturer to ensure their product lives up to the hype and is safe for people to consume. This includes vitamins, as well.

It’s also important to note that while fermented foods such as pickles, sourdough bread, or cheese may have once contained “good” bacteria, the processing and storage methods involved means they no longer have any active, live cultures.

What to buy?

When at the grocery store, check the label. First, look for a designation that the product contains live and active cultures. The genus, species, and strain should be listed to know exactly which probiotic you are getting. For example, Lactobacillus (genus) acidophilus (species) MN5 (strain).

Next, look for numbers. Live, active cultures should be present in the billions CFU range. Also be sure the label does not read “at time of manufacturing” you want to be sure the live cultures are guaranteed through the end of product shelf life.

If you have gastrointestinal issues and you’ve tried one product but don’t notice any benefit, it may be worth trying a product with different strains to see if these may be more suited to your body. Remember, everyone is different.

Feeding your flora: What are prebiotics?

The International Scientific Association for Probiotics and Prebiotics defines prebiotics as, “a substrate that is selectively utilized by host microorganisms conferring a health benefit.” Basically, prebiotics feed your probiotics and help enhance the balance of microflora.

Wait, now I need to feed the probiotics? This is turning into a lot of work!

Actually, the best way to ensure your probiotics are getting the best diet, is to eat a varied diet. This includes fruits, vegetables, and whole grains. Often, prebiotics are dietary fibers and are found naturally in foods, but they may also be added. Keep in mind that adding fiber to your diet may cause intestinal discomfort , so always start small.

Did you know? Dietary fiber is the non-digestible carbohydrates found naturally in plants, or added fiber that has beneficial health effects.

On the label – prebiotics

Often, prebiotics may not be what you see listed on the label. Look for types of fiber such as galactooligosaccharides, fructooligosaccharides, oligofructose, chicory fiber, or inulin.

You can also look for products labeled with synbiotics to know you’re getting both probiotics and prebiotics.

Taste Test

There are lots of foods out there that offer a daily dose of probiotics. So many, in fact, you may be wondering which ones are worth it. If you’re a little uncomfortable at the thought of swallowing a mouthful of bacteria, don’t be. I tried a few of the products here to give you some help.

Probiotic options in dairy products

I tasted three different dairy products and a ferreted tea to analyze the nutrition claims and flavor.

  • Activia Active Dailies (strawberry)
  • Lifeway Kefir Cultured lowfat milk smoothie (strawberry)
  • Kevita Master Brew Kombucha (raspberry lemon)
  • Chobani Greek Yogurt (vanilla) *

*This product is not labeled as a probiotic product. Probiotics by definition must contain adequate numbers to provide health benefits.

 Activa Active
Lifeway Kefir Kevita KombuchaChobani
Greek Yogurt
TypeLowfat yogurtCultured low-fat milk
(fermented milk)
Fermented teaGreek yogurt
Serving Size93 mL
(70 calories)
240 mL
(140 calories)
450 mL (70 cal)227 grams
(170 calories)

Billions of live and active probiotics.

Helps support your digestive health

Contains live and active probiotic cultures that may help support immunity and healthy digestion

12 live and active cultures;
15-20 billion cfu

Crafted with billions of live probioticsLive and active cultures
Dosage2x per day; 2 weeksNoneNoneNone
StrainsL. bulgaricus and S. thermophilus cultures

Bifidobacterium animalis lactis DN-173 010/CNCM I-2494 probitiotic
Lactobacillus Lactis
Lactobacillus Rhamnosus
Streptococcus Diacetylactis
Lactobacillus Plantarum
Lactobacillus Casei
Saccharomyces Florentinus
Leuconostoc Cremoris
Bifidobacterium Longum
Bifidobacterium Breve
Lactobacillus Acidophilus
Bifidobacterium Lactis
Lactobacillus Reuteri
B. coagulans lactospore MTCC5856L. bulgaricus, S. thermophilus, L. acidophilus, Bifidus, and  L. casei
TasteSweet and smooth;
strawberry yogurt
Sour and bubbly,
but good; thick
green tea with lots of bubbles and an extra sour kick sweet, a little sour; very vanilla

*cfu = colony forming units. When food is analyzed for bacteria, the individual “dots” growing on the petri dish are counted. Each dot represents a colony, or the number of bacteria in the product.

What does it mean?

Are more cultures better? Is a higher CFU better? Why are there different cultures in each one? 

As with many things in life, more isn’t necessarily better. Generally 100 million – 50 billion is a good target to look for on the label. In terms of cultures or strains, it’s most important to find those that have evidence based in science of their benefits and to choose one that offers a benefit you are looking for. Having multiple strains doesn’t necessarily have a benefit depending on your needs.

My recommendations

Overall, I preferred the Activie Dailies most. The taste was delicious and it was easy to drink while on the go. I enjoyed the small portion size, but realize it may be too small for some. This is the best choice if you are looking to add probiotiocs to your daily routine as a quick snack. I also enjoy traditiaonl Active yogurt, as well.

The Kefir was good, but I’ll admit it took some getting used to. If you’re unfamiliar, kefir is a tart, fermented milk drink. It felt very strange to be drinking a bubbly milk product, but it did grow on me. The serving size was a little bigger, and better suited as a meal replacer. This is the best choice if you love trying new things and are looking for an on-the-go breakfast. However, take a look at the cultures included in the product. No strain information is indicated on the label.


Kombucha is fermented green or black tea. It is very sour and bubbly, a nd contains a very small amount of alcohol. It almost reminded me of champagne. This could easily be consumed as a drink at almost any time of day. No CFU information is given on this label.

The Chobani yogurt is a classic choice and always delicious. I enjoy using it in smoothies, parfaits, and in my cooking. This is probably the best choice if you consider yourself a traditionalist and enjoy taking time to prepare your meals to your liking.  This product isn’t technically a probiotic yogurt, but could still be a heatlhy snack opportunity. 

The Bottom Line

Gut microbiota are essential to our health and immunity. We begin to build this flora early in life and it is important to eat a varied diet to build a varied community. Probiotics have shown great potential benefits to improve our microbiome. However, the science is still out on the efficacy and the differences between specific cultures. It also seems that individuals respond differently. Finally, if you do wish to try probiotics, be sure to consume them consistently.

The opinions expressed here are my own and there are no affiliations or endorsements with the represented brands. The thoughts are for informational purposes only.

What do you think? Do you swear by probiotics? Maybe you’ve tried them and they didn’t seem to have any effect? Still confused? Let me know below!


Gleeson, J. 2018. Food and the Intestine: Friends from day one. Science Meets Food.

Montville, TJ, Matthews, KR, and Kniel, KE. 2012. Food Microbiology: An Introduction 3rd Edition. pp 426-429. ASM Press. Washington DC. doi: 10.1128/9781555817206

Scott, K. 2016. Prebiotics. International Scientific Association for Probiotics and Prebiotics.

Shreiner A, Kao J, Young V. 2015. The gut microbiome in health and in disease. Current Opinion in Gastroenterology. 31(1):69-75.

FDA. 2018. Asthma: The Hygeine Hypothesis. US Food and Drug Administration

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