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The Beginner's Guide to the Microbiome and Probiotics

Updated: Oct 2, 2020

Improving your gut health with probiotics, prebiotics or fermented foods can heal your microbiome, help your digestion and prevent you from getting sick. With plenty of bad bacteria in your gut, you can’t afford NOT to take a probiotic.

Yogurt in a glass
Photo by Sara Cervera on Unsplash

We Can’t Talk about Probiotics Without Talking About the Microbiome

So, what, exactly, is the gut microbiome?

Trillions of bacteria live in our intestine (aka, the gut) and the microbiome is the genetic material of all the microorganisms (aka, microbes) that live on and inside the body – mostly inside your intestines and your skin. Because most microbes live in the large intestine, it is referred to as the gut microbiome. The colon is actually the perfect environment for bacteria to growth thanks to its slow transit time, readily available nutrients and favorable pH. (think: perfect Petri dish :)

This includes bacteria, fungi, protozoa and viruses. It was in the early 1900’s that we learned that lactic acid bacteria may have health benefits and that we may actually be able to replace harmful bacteria with good bacteria.

These microbes are actually very helpful; some help digest food, produce vitamins and essential building blocks of protein, produce short chain fatty acids and destroy disease-causing cells. They also digest food to generate nutrients for host cells and metabolize drugs. Out of these microbes, bacteria are most well studied.

How Does Gut Health Affect Your Overall Health?

Everyone’s microbiome is different and is determined by your mother’s microbial environment, your environment and the foods and drugs you ingest. A healthier gut has more healthy bacteria and they’re more diverse (or have more strains of the good bacteria).

Other things that affect your microbial environment:

-Whether you were born naturally or through C-section

-Giving birth naturally actually bathes the baby in mom’s bacteria from her birth canal, which increases the microbial diversity. (There’s some thought that babies may be exposed to mom’s microbes while in utero.)

-Whether you were bottle or breastfed

-Breast milk is tagged, “liquid gold” for a reason. The Bifidobacteria in the milk sugar that babies ingest are important for gut protection (and, therefore, immunity).

-Who you live with and where you live

-Families share bacteria! Did you ever walk into someone’s home and notice that it has a different scent than your own? That’s their unique bacterial scent!

-Playing out in the dirt isn’t such a bad idea – kids who live on farms have a higher bacterial count than city kids. Even kids who have dogs have been shown to have a healthier microbiome.

-Hygiene and antiseptics

-Overuse of antiseptics and sanitizers is of concern as it can kill off strains of not just bad bacteria, but good bacteria, too.

-Use of medications, like Metformin

-Use of pro- and antibiotics (we’ll talk about this below)

-Age and stress

-Age in general is associated with a decreased amount and types of species of bacteria, but studies done on nursing home residents found that they had a less favorable gut microbiota pattern.

-Diet and exercise

-Exercise has been shown to increase the amount and kinds of good gut bacteria.

-Western diets (high in fat, sugar, refined carbohydrates) have been associated with less microbial diversity. People in rural African villages that consume more dietary fiber than Westerners have a very different gut microbiome. The African villagers have bacteria that evolved to allow them to maximize energy intake from the fibers while also protecting them from inflammation and some intestinal diseases. (Super cool, if you ask me!)

-And, it’s been shown that a high fat diet actually decreases our ability to burn off fat. Eek.

Gut health has been associated with:



Irritable Bowel Disease: Ulcerative Colitis and Crohn’s Disease



Colon cancer


So What’s An Unhealthy Gut Microbiome?

One that’s in dysbiosis – in other words, there’s an unfavorable balance of bad bacteria to good bacteria. This causes inflammation and stress on the body and brain. It also affects immunity, can contribute to disease, and causes GI symptoms, like bloating, cramps and abdominal pain.

Think of your gut microbiome as a gatekeeper; it keeps disease-causing substances out of the bloodstream. An unhealthy gut can lead to leaky gut — a condition in which holes form in the walls of your GI tract, allowing toxins and proteins to enter the blood and contribute to disease, inflammation, and allergies.

Would you like your gut barrier wall to look like this:

Broken and decrepit gate.
An unhealthy gut microbiome has ways for pathogens to enter the bloodstream - like this decrepit gate. Photo by Marissa Lewis on

I didn't think so...

What Can You Do to Improve the Health of Your Gut Microbiome?

This is where probiotics come in.

The word “Probiotic” is derived from Greek, which means “for life”. The word “antibiotic” means “against life”.

Probiotics are defined as live microorganisms that are intended to have health benefits when consumed or applied to the body. They can be found in yogurt and other fermented foods, dietary supplements, and beauty products.

For hundreds of years, it’s been known that certain microorganisms may impact health benefits. Probiotics may modify the immune system, regulate the allergic immune cell response and prevent cancer cells from multiplying. Probiotics also help breakdown indigestible fibers for energy use.

But, buyer beware; probiotics are a multi-billion dollar business.

What Should You Look for in a Probiotic?

1. Consider checking your probiotic with an unbiased source, like Also, look for a verified/certified/approved seal on the label.

Some organizations like the U.S. Pharmacopeia (USP), NSF International, and attest that the product contains the amount of the ingredient advertised on the label and that it isn’t contaminated with dangerous substances, such as arsenic, bacteria, or lead.

It is not, however, a guarantee that a product has therapeutic value, nor do they test every batch of supplements shipped out.

2. The World Gastroenterology Organization recommends that, when choosing a probiotic, look out for a label that includes:

· Genus and species identified

· Strain designation

· Viable count of each strain at the end of shelf-life

· Recommended storage conditions

· Safety under the conditions of recommended use

· Recommended dose, which should be based on claimed physiological effect

· An accurate description of the physiological effect

· Contact information for post-market surveillance

Ok, So Which Probiotic Should You Actually Take

These are Probiotic Products, the Bacterial Strains it contains, the condition for which it was tested and Dosage Shown to be Helpful:

Which Foods Contain Probiotics?




Danactive / Actimel

Stoneyfield products


Aged cheeses with live cultures

Kimchi, sauerkraut, miso, tempeh

Of note, the World Gastroenterology Organization says it is not necessarily helpful to eat any old yogurt every day and think you’re getting a specific benefit. Most commercially available acidophilus and Bifidobacterium containing yogurts don’t meet the minimum amount of colony forming units to be beneficial.

So, it’s a good idea to choose probiotic foods/drinks with several strains and at least 1 billion CFUs (colony forming units).

What are Prebiotics?

Prebiotics deserve an article to themselves, but, in short, they are non-digestible parts of foods (fibers) that offer health benefits. Prebiotics are very healthy as they can:

-add fiber to the diet, increase calcium absorption, decrease gastrointestinal transit time, and possibly lower blood lipid levels.

Some foods that contain prebiotics:

Legumes, soy beans, nuts, seeds, chicory root, Jerusalem artichokes, wheat bran, barley, oats, apples, garlic, onion, leeks, asparagus, bananas.

The Takeaway:

  • Take a probiotic supplement before breakfast or on an empty stomach (probiotics are killed by stomach acid)

  • Probiotics may take about 1 month to colonize and start working

  • Keep taking your probiotic – the effects only last as long as you’re taking a consistent dose

  • Eat a variety of foods to get the best of everything, especially prebiotic foods like legumes, beans, fruits and vegetables and oats

  • Eat fermented foods, such as yogurt, kefir, sauerkraut

  • Limit artificial sweeteners – they may increase blood sugar by stimulating growth of unhealthy bacteria

  • Breastfeed for at least 6 months

  • Ditch the animal protein for a plant-based diet. Plant fibers change your gut microbiome into a healthier one

  • Don’t take antibiotics unless necessary and take them for the entire prescribed timeframe

  • Get outside more and play in the dirt

So, I challenge you to integrate more probiotic and prebiotic foods in your diet and possibly a probiotic supplement…what have you done to help your gut microbiome??


Ciorba MA. A Gastroenterologist’s Guide to Probiotics. Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association. 2012;10(9):960-968.

De Filippo C, Cavalieri D, Di Paola M. Impaft of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci USA 2010: 107: `4691-14696.

Donovan SM. Introduction to the special focus issue on the impact of diet on gut microbiota composition and function and future opportunities for nutritional modulation of the gut microbiome to improve human health. Gut Microbes. 2017;8(2):75-81. doi:10.1080/19490976.2017.1299309.

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