Probiotics & Prebiotics

Were you born via c-section, formula-fed and blasted with antibiotics?

Are you infuriated with the choices of your parents?

Resign not to resentment of actions past!

You can heal your microbiome!

While method of delivery (vaginal vs c-section), source of nutrition (breast vs formula) and antibiotic exposure during the first years of life largely determine the baseline inhabitants of your gut, these bacterial populations are by no means permanent.

As Dr. Perlmutter states, "While antibiotics and method of birth are important factors in the development and maintenance of a healthy microbiome, dietary choices are far and away the most crucial factor" (p. 144).


Brain Maker

In Brain Maker, Dr. Perlmutter explains how the gut microbiome is established and how it can be improved through simple dietary changes. 

He draws intriguing connections between changes in the American diet, shifts in the gut microbiome and the surge in a variety of diseases, such as Alzheimer's, multiple sclerosis, allergies, Irritable Bowel Disease, ADHD and autism.

While I do not fully agree with the dietary guidelines espoused by Dr. Perlmutter--specifically encouraging the consumption of organic meat as the ideal protein source and denouncing grains in line with a low carb diet--this New York Times Bestseller provides tremendous insight to the relevance of the three pounds of bacteria living along the human digestive tract.


Manipulating Your Gut Microbiome

Diet is the most dynamic factor affecting the bacterial population of the gut, and changes can be achieved in as little as 3 to 4 days (Jayasinghe et al.). However, as easily as these changes are achieved, they are reversed once the dietary modification is stopped.

Diet drives the gut microbiome.

So, which foods foster a favorable gut microbiome? Probiotics and prebiotics.

Probiotics are bacteria. Prebiotics are nutrients that feed these bacteria.



Probiotics are bacteria. These bacteria play essential roles in the gut and affect the overall health of the human host. Functions include:

  • Creating a protective lining along the intestinal wall, thereby protecting against leaky gut
  • Reducing the bacterial inflammatory marker LPS [Lipopolysaccharide], which provokes your immune system
  • Establishing bacterial balance to prevent overgrowth of potentially harmful bacteria

Which bacteria among the probiotics are most essential for health? By far, the most widespread commercially available probiotics are Lactobacilli (dominant in the stomach and small intestine) and Bifidobacteria (dominant in the large intestine). Specifically, Dr. Perlmutter recommends these species:

  • Lactobacillus acidophilus: Contained within many fermented foods, especially dairy products. Produces Vitamin K and lactase, the enzyme required to digest lactose, the carbohydrate component of dairy.
  • Lactobacillus plantarum: Resident of the stomach found in kimchi, sauerkraut and other fermented veggies. Plays an essential role in maintaining integrity of the intestinal wall, thereby preventing gut leakage and invasion of pathogens!
  • Lactobacillus brevis: Also found in fermented veggies, this bacteria boosts the immune system.
  • Bifidobacterium lactus: Probiotic which aids the immune system and decreases discomfort associated with digestion.
  • Bifidobacterium longum: One of the first inhabitants of the digestive tract, this bacteria plays a multitude of roles in preventing food allergies, promoting lactose tolerance, providing antioxidant activity and blocking pathogens.

These bacteria can be consumed in one of two forms: fermented foods or supplements. 

Fermented foods

Fermentation is the magical process by which many foods in your diet are created: bread, cheese, wine, beer, pickles, etc. Fermented foods have been enjoyed across cultures for thousands of years, long before humans understood this microorganism-mediated process.

Popular fermented foods include:

  • Live-cultured yogurt
  • Kefir
  • Kombucha
  • Tempeh
  • Kimchi
  • Sauerkraut
  • Pickled produce


Don't kill your probiotics!

Consume probiotics only with distilled water! Tap water is typically treated with hefty doses of chlorine, which can kill your probiotics on contact.

How are you to choose among the dozens of probiotic brands? The US Food and Drug Administration does not regulate supplements like it does prescription medications.

While customer reviews on provide insight, the scientific method would dictate the need to measure the probiotic content against the claims of the product, while also checking for possible toxic contaminants.

All you'll need is an industrial-grade laboratory. Ready?

Just kidding!

Labdoor ( provides independent analysis of a range of supplements, including probiotics, vitamins, proteins and fish oils.

The website states, "Labdoor analyzed 30 best-selling probiotic supplements in the United States, measuring amounts of total anaerobic bacteria, genera-specific bacteria, and potential contaminants (mold, yeast, and pathogenic bacteria, including E. coli O157:H7, Salmonella spp., and Staphylococcus aureus)."

Two key metrics to consider when evaluating a probiotic supplement include: quality and value. NOW Foods scored 3rd on both quality and value, thereby making it the best overall probiotic supplement tested by Labdoor. 

 NOW Probiotics contains a blend of Bifidobacteria, Lactobacilli and Streptococcal bacterial species

NOW Probiotics contains a blend of Bifidobacteria, Lactobacilli and Streptococcal bacterial species

Wait a minute

If you recall, the human digestive tract contains a variety of micro-environments: the acidic stomach is relatively inhospitable compared to the colon which is teeming with microorganisms. Before making a commitment to a probiotic regimen, an important question to consider is: Can probiotics survive the harsh acidic environment of the stomach and reach their target destination?

David et al. conducted an experiment involving feeding an animal product based diet to one arm of study participants. They found that, in fact, "bacteria associated with cheese and cured meats (L. lactis, P. acidilactici, and Staphylococcus) became significantly more prevalent in fecal samples [p<0.05] ... indicating that bacteria found in common fermented foods can reach the gut" in abundant levels (David et al.).

David and his team also found this to be true with regard to various fungi, including Penicillium species and Candida species. 

Although a percentage of the probiotics will certainly succumb to the acidity of the stomach, bacteria can definitely survive the journey to the colon.

Feeding your Probiotics

Would you adopt a pet and not feed him? Of course not.

If you take probiotics, feed your probiotics too!

It's imperative to pair consumption of probiotics with prebiotics.




  1. Non-digestible by humans
  2. Provide nutrition for gut bacteria
  3. Provide health benefit for human host

Strictly speaking, a prebiotic promotes growth of microorganisms anywhere in or on the human body. In practice however, prebiotics refer to substances that promote growth of Bifidobacteria and Lactobacilli in the intestines.

Prebiotics are food for healthy bacteria.

Prebiotics are indigestible fiber that pass through the stomach and small intestine until they reach the colon, where resident bacteria will feast on the fiber through fermentation. Fermentation is the process by which microorganisms--bacteria and yeast--convert carbohydrates into acid or alcohol, in an environment which lacks oxygen.

Yes, fermentation happens in your colon!

What substances are actually getting fermented? Fibrous compounds named inulin and oligofructose. Some plants produce inulin as a form of energy storage in their roots.

 Chart adapted from Wikipedia. Data derived from Moshfegh et al.

Chart adapted from Wikipedia. Data derived from Moshfegh et al.

 Inulin and oligofructose are the two main prebiotic compounds.  Americans consume the majority of their prebiotics from wheat, onion, banana and garlic (Moshfegh et al.).

Inulin and oligofructose are the two main prebiotic compounds.

Americans consume the majority of their prebiotics from wheat, onion, banana and garlic (Moshfegh et al.).

 Gum arabic

Gum arabic

 Chicory root

Chicory root

 Jerusalem Artichoke

Jerusalem Artichoke

 Dandelion greens

Dandelion greens

Why raw plants? Heat breaks down fiber and decreases the prebiotic content of cooked plants.

Dr. Perlmutter touts numerous health benefits of prebiotics, including:

  • Enhance absorption of magnesium, iron and calcium
  • Promote the feeling of satiety, or fullness, when eating
  • Reduce the number of antibiotics required when treating a bacterial infection
  • Reduce inflammation in Inflammatory Bowel Disease 

Fiber Fiber Fiber

On average, about 5% of calories consumed are lost through the stool; however, people "who consume high-fiber diets exhibit a higher fecal energy loss than individuals who consume low-fiber diets with an equivalent energy content" (Jumpertz et al.).

Fiber promotes an increase in bacteria which block energy storage in the human body.

Fiber promotes bacteria to keep you skinny.



Blustein, J., and Liu, J. (2015). "Time to consider the risks of caesarean delivery for long term child health". BMJ. 350:h2410.

David, Lawrence A. et al. "Diet rapidly and reproducibly alters the human gut microbiome" Nature. 23 January 2014; 505(7484): 559ā€“563.

Gorbach, Sherwood L. Medical Microbiology. Chapter 95 "Microbiology of the Digestive Tract" Galveston 1996.

Heiman, Mark L. and Frank L. Greenway. "A healthy gastrointestinal microbiome is dependent on dietary diversity" Molecular Metabolism. 2016.

Jayasinghe, Thilini N. et al. "The New Era of Treatment for Obesity and Metabolic Disorders: Evidence and Expectations for Gut Microbiome Transplantation" Frontiers in Cellular and Infection Microbiology. 19 February 2016.

Jumpertz, R. et al. "Energy-balance studies reveal associations between gut microbes, caloric load, and nutrient absorption in humans". Am. J. Clin. Nutr. 2011. 94, 58ā€“65.

Lloyd-Price, Jason and Galeb Abu-Ali and Curtis Huttenhower. "The healthy human microbiome" Genome Medicine. (2016) 8:51.

Moshfegh AJ, Friday JE, Goldman JP, Ahuja JK (July 1999). "Presence of inulin and oligofructose in the diets of Americans". Journal of Nutrition. 129 (7 Suppl): 1407Sā€“1411S.

Perlmutter, David. Brain Maker. New York City, 2015.

Shreiner, Andrew B. and John Y. Kao and Vincent B. Young. "The gut microbiome in health and disease" Curr Opin Gastroenterol. 2015 January; 31 (1): 69-75.