Probiotics 101: A Beginner’s Guide

Medically Reviewed by Anthony Dugarte, M.D., C.S.C.S

Life gets difficult when your stomach or intestines aren’t healthy. Bloating and distension are terribly uncomfortable, and bowel diseases can be excruciating. When you have abdominal issues, sometimes getting through the day seems impossible.

With so many products on the market offering relief, it’s hard to know where to start. Products that supplement or boost friendly gut bacteria, known as “probiotics”, could be a reasonable addition to a balanced diet and regular physical activity.  

So what are probiotics? These “friendly” bacteria densely populate your gut biome, the network of microorganisms living in your digestive tract. Unlike the harmful bacteria responsible for infections, probiotics play many important roles related beyond just digestion.

Cindy Klinger, a California-based integrative dietician, offers further insight. “A probiotic is a bacteria or yeast that provides health benefits to the digestive tract. They provide a range of functions, including supporting a healthy gut, preventing disease, maintaining a healthy weight, and helping us absorb nutrients effectively.”

And as you’ll soon read, there are many studies that point to probiotics’ potential to restore your gut health.

But not all bacteria are considered beneficial to your gut. Many types have been linked to conditions like inflammatory bowel disease, bloating, and weight gain. Probiotics differ from this pathogenic bacteria by repopulating your gut and giving it a greater chance of becoming healthy.

In this guide, we’re going to walk you through the basics of probiotics. We’ll focus on the common uses of probiotics and the types of foods that contain them.

Why Does a Healthy Digestive System Matter?

Your digestive system is key to good health. All the vitamins and nutrients within your food are absorbed into your body via your digestive system, and you tend to miss out on the health benefits of what you are eating if your digestion isn’t working as it should.

But your gut controls more than your nutrient intake – it plays a pivotal role in your overall health.

Daily life can become miserable if there’s an imbalance of good and bad bacteria in your gut. “If something goes wrong inside your gut, it’s not as immediately obvious as a broken arm or a twisted ankle.” Lisa Richards, a nutritionist and creator of the Candida diet, told us.

“However, the activity within your gut is actually one of the most important factors affecting your long-term health. The microorganisms that live within your gut play a hugely important role in your digestion, your immune system, and even your mood.”

Conversely, undesirable microbes can cause a host of health complications. Under certain circumstances, bad bacteria can trigger problems like bloating, gas, and other digestive issues.

That’s where probiotics come in – they help maintain balance in your gut biome and can be helpful in relieving digestive issues, as well as fighting infection and reducing risk for chronic medical conditions.

But before we start, we need to make a quick disclaimer. As we talk to you about the benefits of probiotics, you’ll come across some hard-to-pronounce bacteria. These aren’t interchangeable with each other. You can think of each of these bacteria as a house within the probiotics neighborhood; all the houses are in the same community, but not all the houses are the same.

What Are the Health Benefits of Probiotics?

There are plenty of reasons to consider taking probiotics. Below are a few of the biggest potential health benefits:

Reduced Risk of Antibiotic-Associated Diarrhea (AAD)

Antibiotics kill certain bacteria, and by doing so, they can upset the balance of good and bad bacteria in our gut. Diarrhea is a common side effect of this imbalance.

A review of 16 randomized studies examining the use of probiotics in the prevention of AAD in children concluded that they likely have a protective effect.

“Probiotics have been found to reduce AAD by 52%,” Dr. Bryan Tran, a doctor of osteopathic medicine and expert on probiotics, told us. “[They do this] by restoring and helping to maintain normal gut flora.”

Combat Constipation

More than 60 million people deal with constipation, the condition in which a person has infrequent bowel movements. A review of 14 randomized trials concluded that treatment with probiotics can improve stool frequency and stool consistency in constipated individuals.

Lowers Your Risk and Severity of Allergic Reactions

Doctors from Finland found in 2011 that probiotic bacteria can help children with food allergies and inflammation due to allergies. While the bacteria didn’t act as a complete cure, the research is promising.

As Dr. Tran told us, “A study revealed that children who are administered probiotics at an early age reduce their chances of developing atopy (a cluster of diseases that include eczema, asthma, and allergies) by one half (46% in placebo-treated children versus 23% in probiotic-treated children. These findings were verified in follow-up and additional studies.”

» See Also: Probiotics for Kids: A Parent’s Comprehensive Guide

Effective Remedy for Inflammatory Bowel Disease

Consuming probiotics can prevent relapse of inflammatory bowel disease, a painful inflammation of the intestinal tract.

Boosts Immune System Functioning

Elie Metchnikoff, a Russian zoologist who is considered by many to be the father of probiotics, discovered in the 20th century that Bulgarian peasants were remarkably healthy for being so impoverished. The reason? They drank sour milk, which happened to be full of probiotics.

Metchnikoff later discovered that probiotics were the heroes here, as they helped to strengthen both the intestines and the immune system.

Improves Your Mood

It turns out your stomach and attitude are more connected than most of us realize.  Probiotics provide an important link between your gut and central nervous system.

In fact, a number of studies have identified many of the key players in this “gut-brain-axis.” Friendly gut bacteria produce chemicals (dopamine, for example) that are heavily involved in your mood.

This link was described when patients with irritable bowel syndrome (IBS) were also likely to have a greater risk of depression and anxiety. In another study, digestive symptoms improved when patients with IBS were treated for their psychiatric symptoms. 

Other studies have found that those with depression have a greater variety and amount of certain probiotics when compared to healthy individuals.

Though more research is needed, these types of studies may lead to the development of new ways to identify and treat those with psychiatric disorders.

Dr. Krista Casazza, an associate professor at the University of Alabama at Birmingham, provided further insight. “The brain’s reward system, including mood and mental health, is wired for feedback with the gut, which is dependent on healthy flora… In health, the gut profile promotes feedback that aligns with energy balance, glucose, and lipid homeostasis, and positive mood.” 

Eases Acute Gastroenteritis (AGE) in Kids

AGE is a bacterial or viral infection that causes inflammation in your stomach or intestines. It causes lots of diarrhea and can lead to dehydration. In addition to supportive care, there is evidence supporting the role of some probiotic strains in the treatment of children with AGE.

What Are the Best Ways to Take Probiotics?

Now that we’ve walked you through an overview of probiotics, we want to give you some practical advice on how to get these helpful little organisms into your body. Below is a list of five kinds of products that contain probiotics.

Keep in mind that, while there are plenty of studies that praise probiotics, most experts haven’t reached a conclusion about how much probiotic-friendly foods you should eat.

We spoke with Katherine Zeratsky, a nutritionist at Mayo Clinic, who brought up a good point: most adults can add to their diet foods and supplements rich in probiotics without a big risk of side effects

As always, make sure you check with your doctor first before starting a new diet regimen.


Kefir is one of those foods you see and don’t think much about because you don’t really know what it is.

Kefir originates in the Caucasus Mountains (Russia, Turkey and that part of the world). It’s made by mixing kefir grains with milk. The result is a tangy liquid that might remind you of drinkable plain yogurt.

This unique sipper has a healthy dose of Saccharomyces, a bacteria known to reduce or prevent diarrhea as well as a reputation for easing the effects of IBD and some symptoms of ulcerative colitis.

Those who struggle to tolerate lactose products may benefit the most from kefir.

“The main benefits of kefir is countering lactose intolerance, improving digestion and gut health, and countering allergies. Kefir is generally easier tolerated than other products such as yogurt,” said Bart Wolbers, a health and wellness researcher.


Of all the items on this list of probiotic-packed foods, yogurt is probably the most familiar. It’s a popular breakfast food that has benefitted from an increased interest in probiotics.

“Yogurt may improve your immune system and counter allergies,” Wolbers said. “[Other] possible benefits (that are not yet scientifically proven) include lowering inflammation, countering arthritis, and preventing cancer.”

Yogurts are made from various bacteria, but two of the popular ones are Streptococcus thermophilous and Lactobacilli.


There’s a lot of scientific evidence for the usefulness of probiotics for your digestive system. Lactobacillus acidophilus is a frequent ingredient in supplements, and often it’s packaged as a stand-alone supplement called “acidophilus.”

Supplements can contain multiple probiotics, so if you ever want to cross-reference the scientifically proven benefits of an ingredient, use this helpful chart from the National Institutes of Health.

Sour Milk

As we mentioned earlier, the Russian zoologist and father of probiotics Elie Metchnikoff discovered that Bulgarian peasants unknowingly boosted their immune systems by drinking sour milk.

We don’t recommend searching for sour milk at your local supermarket because you probably won’t find it. However, there are baking recipes which use sour milk as an ingredient and plenty of information online about how to make sour milk. Again, this is a smart option if you struggle to tolerate regular milk products.


Kimchee is a staple of Korean cuisine. It’s a fermented, spicy mixture of several different vegetables including cabbage. It’s a cult favorite and, because it's fermented, it is full of helpful bacteria.

Most of the bacteria that have been found in kimchee are in the Lactobacillus family, which has a long list of benefits for the digestive system.

However, there are some reasons for caution when eating fermented cabbage. “Kimchi may increase stomach cancer risk, in part because of the high levels of sodium available in the product (due to salt being added for fermentation),” Wolbers told us. 

Benefits of Prebiotics

As important as probiotics are on their own, you will boost their benefits further by ensuring your diet contains prebiotics as well. Prebiotics are non-digestible fibers, often classified that may improve health by serving as food for probiotics.

Klinger shared with us why prebiotics are important.

“Including prebiotics in your diet (dandelion greens, jicama, onions, and raw Jerusalem artichokes, for instance) can help feed the probiotics, another great way to support gut health and encourage your probiotics to flourish,” she said.

What Are Probiotic Side Effects?

Probiotics are certainly appealing, but will taking them put you at risk for unpleasant side effects?

Every dose of probiotics contains millions of live organisms. Your stomach requires a delicate balance of bacteria, and disrupting it can lead to problems, even if you’re adding beneficial bacteria.

Dr. David Kerman, a gastroenterologist within the University of Miami Health System, believes the lack of regulation within the industry is the most significant cause of concern.

“Because of a lack of rigorous scientific scrutiny, many probiotics contain fillers that can lead to bloating, diarrhea, and gas,” he told us.

However, Dr. Andrea Arikawa, an associate professor of nutrition and dietetics at the University of North Florida, shared that these side effects tend to be temporary.

“[While] side effects of probiotics can include bloating and gas, abdominal pain, and diarrhea, these symptoms may appear only during the first few days of taking antibiotics, and they may disappear.”

Below are other potential side effects associated with probiotic use.

Can Cause Headaches

Many foods that are naturally rich in probiotics, including yogurt and kimchi, also contain a form of fermented protein known as biogenic amines.

These compounds affect the nervous system and the rate of blood flow, and they may trigger headaches in people who are sensitive to them.

Histamine is one kind of biogenic amine, and preliminary research from the British health journal Clinical and Experimental Allergy shows that 75% of participants who followed a low-histamine diet experienced a reduction in their headaches.

Notably, there’s no evidence at this time that taking probiotic supplements can trigger headaches. If headaches are causing you problems and you eat a diet filled with probiotic-rich foods, you might consider switching to supplements instead.

May Trigger Allergic Reactions

If you deal with allergies to substances like dairy, soy, or egg, then there’s a chance that taking a probiotic supplement may trigger an allergic response—even if these compounds aren’t disclosed on the label.

That’s due to the limited regulation within the industry and because of the opportunities for ingredient contamination within the factory.

There’s also evidence that people who are allergic to lactose, a common milk allergen, have more symptoms when it’s contained in probiotics than they do with other medications or supplements that contain it.

May Increase Infection Risk

While probiotics are considered to be safe for most people, some populations are at risk of developing dangerous infections from them.

This is primarily a risk for people with suppressed immune systems, those who have recently undergone an extended hospital stay, or who are recovering from surgery.

These people are at slightly elevated risk of having probiotic microbes enter their bloodstream and triggering an infection. However, the frequency of this happening is estimated to be lower than one in a million.

If you do develop an infection from probiotics it should respond to traditional antibiotics.

May Cause Short Bowel Syndrome in Infants

There’s a small risk that babies can experience problems with their bowels if they are exposed to probiotics.

A 2004 study from doctors at the Washington Army Medical Center illustrated two instances of premature infants who seemingly developed short bowel syndrome after being exposed to probiotics that were used to treat sepsis.

While incidences of this are extremely rare and both infants survived without further complications, parents with young children should still be aware of the possibility.

May Lead to Antibiotic Resistance

In rare cases, probiotics can contain antibiotic-resistant genes. If these genes are somehow passed onto other harmful strains of bacteria, they can trigger serious antibiotic resistance problems.

Probiotic manufacturers are aware of this, and they carefully test commercial probiotics for signs of resistance before selling them. This makes your risk of encountering resistant bacteria strains extremely low if you buy from reputable sellers.

Can Cause Skin Problems

Skin rashes may occur after taking probiotics. A 2018 review of IBS sufferers showed that two subjects who took probiotics to treat the condition developed rashes, one of which dropped out of the study due to the severity of this side effect.

If you’re dealing with a similar situation, check the ingredients label carefully to see whether an added ingredient is to blame. If not, stop taking the supplement immediately and speak with your doctor to try to get to the root issue.

Are these side effects enough reason to stay away from probiotics? We don’t think so.

As this side effect analysis showed, instances of severe adverse reactions to probiotics are rare.

So rare, in fact, that known incidence are limited to just one or two people for several conditions. This means your risk of developing similar problems is exceedingly small, to the point that we don’t think they are worth factoring into your decision.

In these instances, the people who suffered harmful side effects were severely immune-compromised, usually because of an ongoing illness.

Their bodies weren’t in a healthy enough state to handle an influx of probiotics effectively. For this reason, we don’t want to recommend probiotics to anyone who is dealing with a health crisis that severely compromises their immune system.

The situation changes slightly if you take probiotics that don’t contain what they claim to. That’s unfortunately common, as a lack of regulation within the industry makes it possible for some manufacturers to be unscrupulous with their ingredients and their labeling.

One thing to keep in mind is that making any dramatic change to your digestive system can lead to short term side effects. That’s a normal part of the transition phase of incorporating new microbes into your gut rather than a cause for alarm. You don’t need to be concerned unless your stomach issues last for a week or longer.

If your symptoms intensify to the point you feel sharp, localized pain or see blood in your stool, get in touch with your doctor immediately.

The Bottom Line: Is It Time to Add Probiotics to Your Diet?

There is a significant amount of research available through studies and via the experts with whom we spoke that points to the fact that probiotics are helpful for gut health and a variety of conditions.

Research and experts indicate that probiotics may help with digestion, constipation, various allergic reactions and can even improve your mood. Keep in mind that probiotic strains behave differently, even if they are in a similar family.

What’s also nice about these good bacteria is that you can get them a variety of different ways, whether it’s fermented dairy products like kefir and yogurt, fermented vegetables like kimchi or using probiotic supplements or probiotic-enhanced foods.

Arikawa offered some suggestions for getting started.

“As a dietician,” she told us, “I would recommend including food-based probiotics to one’s diet. For example, yogurt contains the probiotic bacteria Streptococcus thermophilus and Lactobacillus delbrueckii subsp., which help with lactose digestion, but it is also a good source of calcium and vitamin B12. Kimchi contains several types of probiotic bacteria, and it is also a good source of vitamin C, vitamin A, folate, vitamin K, and potassium.”

If you want to take the next step in your understanding of probiotics, take a few minutes to read through our guide about when you should take probiotics.

Lydia Noyes

Lydia Noyes is a health, wellness, and lifestyle reporter who focuses on ways to live a healthier, more sustainable life. She is a member of the Association of Health Care Journalists. She received a bachelor’s in Environmental Studies from Calvin College and her writing work has been featured in Mother Earth News Magazine, Natural Living Ideas, and dozens of other websites, including her personal site FirstRootsFarm.

Probiotics 101: A Beginner’s Guide