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Ultimate Guide to Prebiotics & Probiotics

Plant Focused Nutrition

This guide will break down what prebiotics and probiotics are, what they do for our bodies, and how we can get them naturally through foods – and if needed through supplements.


Prebiotics are substances in food that in turn feed the microbiome.  They stimulate the growth of lactobacilli and bifidobacteria and reduce disease-causing bacteria such as c. difficile, Klebsiella, and Enterobacter.  We cannot digest and utilize prebiotics but our gut microbes can and are used by those microbes to synthesize SCFAs (short-chain fatty acids) that keep the colon and microbiome healthy. 

Prebiotics are:

  • Soluble fibers such as oatmeal, beans, and root vegetables
  • Plant polyphenols contribute to the bitterness, astringency, color, flavor, the odor of plants
  • Fats from Linoleic acid (CLA), a fatty acid found in meat and dairy
  • Polyunsaturated fats
  • Human milk oligosaccharides found in breast milk

In probiotics you may see prebiotics added as FOS, GOS, and inulin – honey works too!  Other ingredients you may find include Beta-glucan from oats, barley, mushrooms, baker’s yeast, alcohol sugars such as xylitol and mannitol, pectin, gums, chia or flaxseeds, ADMOs (algae-derived).  They can be taken with probiotics. Eat some prebiotic-rich foods at every meal.


Banana (under-ripe)BarleyBeetroot
BranChia seedsChickory
Chinese chivesCocoaDandelion greens
Dairy products (CLAs)EggplantFlaxseed (ground)
FruitGarlicGreen tea
HoneyJerusalem artichokesJicama
Root vegetablesRyeSea vegetables
SoybeansSpices and herbsSugar maple
Sweet potatoesTomatoesYams

If you don’t have a rich environment for your gut microbes, taking probiotics will be less helpful.   Culturing and fermenting of food breaks down polyphenols and plant polyphenols, increases vitamin content, enzyme activity, and amino acid production, and breaks down antinutrients such as food phytates, tannins, and oxalates that can keep you from absorbing nutrients.  Ingestion of fermented foods such as yogurt or cottage cheese vs. milk can have 3-50 times more of certain B vitamins or vitamin A.


Microbrewed beer *Black tea, oolong teaButtermilk
CoffeeCottage cheeseFermented sausage and meats
Fermented vegetablesKefirKimchee
Pickles (brine, not vinegar)PulseRaw Vinegar
Raw WheyRoot and ginger beersSauerkraut
Sourdough breadsTempehWheatgrass juice


*excess consumption of fermented beverages such as beer, wine, and kombucha can cause fungal overgrowth, so moderation is key.  If you have a history of fungal infections or use of antibiotics more than once in the past 18 months, consider moderate intake.


Beneficial bacteria are nutrient workhorses, manufacturing vitamin K, and B vitamins including biotin, B1, B2, B3, B5, B6, B12, folate, and certain acid-secreting species increase our absorption of minerals, including calcium, copper, iron, magnesium, and manganese.  Probiotics improve peristalsis (bowel movement) and normalize transit time to avoid constipation.  Additional benefits include anti-tumor and anti-cancer effects, and keep the natural fungus population from growing and becoming more invasive.  Other functions include the metabolism of mercury and pesticides as well as protection from damaging radiation and harmful pollutants, and recycling and metabolizing estrogen and thyroid hormones. 

As you can probably guess, from these lists above, adding more plants to your diet can make a big difference in the diversity and quantity of beneficial bacteria. For additional ideas on how to incorporate more plants into your diet, move on over to your FREE Course – Transitioning to a Plant-Focused Diet:


  1. Spore form are encapsulated within a capsule, and certain brands have demonstrated the ability to work alongside an antibiotic and survive stomach acid, and travel to the large intestine;  
  2. If you have been diagnosed with SIBO (Small Intestinal Bacterial Overgrowth) or are prone to bloating and food sensitivities you may need a spore form probiotic as well as immunoglobulins (antibodies) to neutralize reactions throughout the GI tract to aid in the repair and maintenance of the gut lining;
  3. Refrigerated forms with a wide range of beneficial strains in amounts of 25 billion to 50 billion CFU are most beneficial.  Some forms also include prebiotics to support the probiotic strains;
  4. In general, I do not recommend shelf-stable forms that are not spore-form as some investigations reveal that they are less likely to have the amounts advertised. If you purchase this type of probiotic, consider refrigerating anyway;
  5. Different strains provide different benefits.  For more information about specific strains for cardiovascular, neurological, allergy support, etc. view the 9-part published research on this topic, found in our learning library:





  • Aid in protein digestion
  • Convert flavonoids (from fruits and vegetables) into usable forms
  • Increase absorption of minerals, including calcium, copper, iron, magnesium, manganese
  • Manufacture essential fatty acids and SCFAs
  • Minimize or eliminate lactose intolerance
  • Synthesize vitamins: biotin, B1, B2, B3, B5, B6, B12, folate, and Vitamin K

Immune system

  • Break down and prevent the synthesis of bacterial toxins, decrease severity and duration of respiratory and other infections, Have anti-tumor and anti-cancer effects, prevent and alleviate eczema, asthma, and allergies, prevent and control thrush, vaginal yeast infection, and bladder infection, prevent and treat diarrhea from antibiotics, prevent food poisoning, Protect against toxic substances, protect and modulate autoimmune diseases, allergies, autoimmune disease, rheumatoid arthritis, systematic lupus, Type 1 diabetes

Digestive system

  • Balance intestinal pH, Digest lactose, and proteins into free amino acids Normalize bowel transit time, Improve and prevent IBS, Protect against travelers’ diarrhea, Protect guns and teeth, Reduce intestinal inflammation, Bariatric surgery, celiac disease, Crohn’s disease, h. pylori infections, IBS, parasites, small intestinal bacterial overgrowth (SIBO), Ulcerative colitis (UC)

Genitourinary system

  • Bacterial vaginal infection, Bladder infection, Candida infection/yeast infection, Chronic kidney disease and individuals on dialysis, Kidney stones and high oxalate levels, Prostate infections, Toxic shock syndrome

Heart + Cardiometabolic disease

  • Normalize serum cholesterol and triglycerides, Support healthy blood pressure levels
  • High cholesterol or triglycerides, Gout, Obesity, Type 2, fatty liver, nonalcoholic steatohepatitis, prevention of hepatic encephalopathy in people with liver cirrhosis, PCOS, Stroke

Metabolic system

  • Breakdown and rebuild hormones, Break down bile acids, Promote healthy metabolism and weight, Promote optimal growth, and Reduce blood ammonia levels in people with cirrhosis and liver disease

Infections/Immune System

  • Colds and flu, Ear infections, Chronic fatigue syndrome, Epstein-Barr virus (EBV), Food and mouth disease, Hepatitis, HIV/AIDS, Lyme disease, Mastitis (breast infection during lactation), Pneumonia, Strep throat

Mental health/neurotransmitters + Neurological system

  • Anxiety, Attention deficit hyperactive disorder, Autism, Depression, Age-related cognitive decline, Hepatic encephalopathy, Multiple sclerosis, Traumatic brain injury

Skin health

  • Acne, Eczema, Psoriasis, Reactive skin


  • Bladder, Breast, Cervical, Colorectal, Leukemia, Liver, Lung, Lymphoma, Vaginal

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Reference: Lipski, E. (2000). Digestive Wellness: Vol. Pbk. 2nd ed., 2000. NTC Contemporary.