• Danielle Cheplowitz, CRNP

Step 3: Re-Inoculate. Why fixing your gut first will cure almost all of your other ailments.

In last week’s post, we talked all about maldigestion, malabsorption, and ways to improve the assimilation and utilization of nutrients. This week is all about re-inoculating the gut, which refers to the reintroduction of desirable gastrointestinal microflora in order to achieve a more desirable balance to the intestinal milieu. Below I will explain what probiotics and prebiotics are, and how they can enhance one’s microbiome.


What exactly is a probiotic? Probiotics are live microorganisms that confer a health benefit on the host. In order for probiotics to enhance the microbiome, they must survive stomach acid & enzymes, adhere to intestinal lining, and grow & establish temporary residence in order to impart health benefits. You can find probiotics in food form (naturally occurring), or in supplemental form.

Probiotics from Food

These are foods that have been fermented or are labeled "raw" and "unpasteurized". Now, most of these foods found in your typical grocery store will be pasteurized in order to reduce the risk of food-borne illness. You may find some of the unpasteurized versions in Whole Foods Market, or other local farmers. Always purchase unpasteurized food products from reliable sources.

Types of food with naturally-occurring probiotics include:








-Other fermented and picked veggies

-Sourdough bread


-Raw dairy that has not been pasteurized (milk)


-Apple cider vinegar

-Raw honey

Supplemental Probiotics

When they first landed onto the shelves, probiotics were marketed as something that could “colonize” the intestinal lining. Unfortunately, this is not accurate. The only two things that have been clinically shown to actually change the microflora of the gut are through dietary changes and stool transplants. Think of probiotics as the tourists visiting a town—they are temporary. Tourists spend money when they visit, causing the town’s economy to go up, but the economy comes right back down after the tourists leave. Probiotics will make a temporary impact on the microbiome as they pass through, but their effects stop as soon as they are out of your system.

You may be wondering…Why should we even take them?

While probiotics do not take up residence in the colon like previously thought, studies do show that they exert beneficial effects in individuals with certain conditions when utilized. They have been particularly helpful in folks who are deficient in beneficial bacteria and/or have excess of pathogenic bacterial. Probiotics work by inhibiting pathogenic bacteria, improving leaky gut, and improving immune response.

Some conditions that have been shown to be improved by probiotics include:

-Infectious Diarrhea

-Crohn’s Disease

-Ulcerative Colitis

-Necrotizing enterocolitis

-Bacterial vaginosis

-Recurrent UTIs




-Systemic inflammation

-Immune support

-H. Pylori Infection

-Dental carries

-Cardiovascular risk reduction


-Rheumatoid arthritis

Strains that have been studied and that have shown to be effective include:

Bifidobacteria strains

Lactobacillus strains

Saccharomyces boulardii

Please remember….the quality of your supplement really does matter!

In a consumer lab test, 8/25 probiotic products contained less than 1% of the claimed number of live bacteria. Ensure that you are getting your supplements from reliable sources that have been third party tested.


What are prebiotics? Think of prebiotics as fertilizer. They are the food that feeds the bacteria in your gut and helps them to grow in quantity and in diversity—which is the ultimate goal! Prebiotics may be more important than probiotics because of this.

Three criteria to be considered a prebiotic:

1. Must be non-digestible by host enzymes

2. Must be fermented by native anaerobic colonic bacteria within the GI tract

3. Must be selective in the stimulation of intestinal flora

What are the types of prebiotics?


-Fructooligosaccharides (FOS)


-Other soluble fiber

A prebiotic enriched diet has been shown to reduce harmful bacteria and increase beneficial bacteria. They also have the ability to assist in improving glucose sensitivity, lowering body fat, reducing inflammation, and reducing oxidative stress.

Some awesome prebiotic-rich foods are listed below:











-sugar maple






-green tea



You can find prebiotics in supplemental form, and some probiotic supplements actually have prebiotics already in them. However, I do not think that one should get all of their prebiotics from supplements. FOOD is the best source because you are also getting vitamins, minerals, phytochemical, antioxidants, and so many other amazing benefits in addition to the prebiotic substance and fiber needed to nourish your gut.

In summary, eat real food that grows from the earth… not from a factory! Eating at least 7 daily portions of fruits and vegetables was linked to 42% lower risk of death from all causes. Risk of cancer was reduced by 25%, and risk of heart disease was reduced by 31% (4). Get those plants in, folks.

It is important to note that some individuals may not tolerate eating a bunch of fiber and fermented foods initially for several reasons. People who do not tolerate fermented foods may have a histamine intolerance. Others who many feel bloated after eating a lot of vegetables and soluble fiber may have small intestinal bacterial overgrowth (SIBO). If this is something that you have experienced, don’t give up on the fruits and veggies for good. Find a local integrative and functional health practitioner nearby who can help you restore your gut.

Next week we will go into detail on how to repair the gut lining… aka “leaky gut”. See you then!

***This post is for educational purposes only, and is not intended to be used a medical advice. Always speak with your own provider before implementing anything suggested in the post.***


1. Forsyth CB, Farhadi A, Jakate SM, Tang Y, Shaikh M, Keshavarzian A. Lactobacillus GG Treatment Ameliorates Alcohol-induced Intestinal Oxidative Stress, Gut Leakiness, and Liver Injury in a Rat Model of Alcoholic Steatohepatitis. Alcohol (Fayetteville, NY). 2009;43(2):163-172. doi:10.1016/j.alcohol.2008.12.009.

2. Giudice MM, Rocco A, Capristo C. Probiotics in the atopic march: highlights and new insights. Dig Liver Dis. 2006;38 Suppl 2:S288-90. doi:10.1016/S1590-8658(07)60012-7

3. Messaoudi M. Assessment of psychotropic-like properties of a probiotic formulation ( Lactobacillus helveticus R0052 and Bifidobacterium longum R0175) in rats and human subjects. Br J Nutr. 2011;105(5), 755-64. doi:10.1017/S0007114510004319

4. Oyebode O et al. Fruit and vegetable consumption and all-cause, cancer and CVD mortality: analysis of Health Survey for England data. Journal of Epidemiology and Community Health. 2014;68(9):856-862. doi:10.1136/jech-2013-203500.

5. Pimentel GD, Micheletti TO, Pace F, et. al. Gut-central nervous system axis is a target for nutritional therapies. Nutrition Journal. 2012; 11:22. doi: 10.1186/1475-2891-11-22

6. Mosińska P, Szczepaniak A, Fichna J. Bile acids and FXR in functional gastrointestinal disorders. Dig Liver Dis. 2018 Aug;50(8):795-803. doi: 10.1016/j.dld.2018.05.016

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