Prebiotics, Probiotics & Postbiotics: A Naturopathic Guide to Supporting Gut Health
Gut health is one of the most important foundations of long-term wellness. As research continues to grow, we now understand that supporting the microbiome involves more than just taking a probiotic supplement. Prebiotics, probiotics, and postbiotics each play unique and complementary roles in digestion, immunity, metabolism, inflammation, and whole-body health.
If you're working with a naturopathic doctor — or interested in naturopathic approaches to digestive health — understanding these three categories can help you choose the right foods and supplements for your body.
1. Prebiotics
What Are Prebiotics?
Prebiotics are non-digestible fibres and plant compounds that act as food for beneficial gut bacteria. They help good microbes grow and thrive, producing postbiotic compounds that support healthy digestive and immune systems.
Common prebiotic fibres include inulin, FOS, GOS, resistant starch, beta-glucans, and pectin.
Why Prebiotics Matter for Gut Health
Prebiotics are essential for:
Increasing beneficial bacteria such as Bifidobacteria
Supporting SCFA (short-chain fatty acid) production — especially butyrate
Improving gut lining integrity
Reducing inflammation
Supporting balanced blood sugar and improved metabolism
Enhancing microbial diversity
For patients with stress-related gut changes, irregular digestion, or a history of antibiotic use, prebiotics help rebuild a stable microbiome foundation.
When Naturopathic Doctors May Recommend Prebiotics
Prebiotics may be indicated for:
Constipation or sluggish bowel movements
IBS-C or irregular digestive patterns
Insulin resistance, metabolic syndrome, or dyslipidemia
Post-antibiotic microbiome recovery
Low microbial diversity on stool testing
Immune dysregulation or chronic inflammation
General gut health optimization
Patients with significant bloating, gas, or suspected SIBO may require a more cautious approach or delayed introduction. Many prebiotics are high in FODMAPs and require careful guidance with a healthcare provider to limit adverse reactions.
Foods Rich in Prebiotics
To naturally increase prebiotic intake, include:
Garlic, onions, leeks
Asparagus, artichokes, chicory root
Green bananas, apples, berries
Oats, barley, whole grains
Beans, lentils, chickpeas
Pomegranate, flax, chia
Rotating different fibre sources helps build a more diverse microbiome.
Supplementing With Prebiotics
Naturopathic doctors often use:
Inulin
FOS / GOS
Acacia fibre
Resistant starch (e.g., potato starch)
Partially hydrolyzed guar gum (PHGG)
Many patients benefit from starting slowly and increasing as tolerated. Prebiotics may also be paired with probiotics in synbiotic formulas for optimized results.
2. Probiotics
What Are Probiotics?
Probiotics are live beneficial microorganisms that support digestion, immunity, and microbiome balance. They include strains of Lactobacillus, Bifidobacterium, Streptococcus thermophilus, and beneficial yeasts such as Saccharomyces boulardii.
Why Probiotics Are Important for Gut & Immune Health
Probiotics may:
Restore healthy gut flora after illness or antibiotic use
Support regular bowel movements and reduce bloating
Strengthen immune function and reduce infection frequency
Lower inflammation and support gut barrier repair
Improve mood through the gut-brain axis
Reduce symptoms of IBS, diarrhea, and dyspepsia
When Naturopathic Doctors May Recommend Probiotics
Probiotics may be helpful for:
Post-antibiotic recovery
IBS, SIBO (specific strains only), bloating, dyspepsia
Acute or chronic diarrhea
Traveller’s diarrhea prevention
Allergies, eczema, and immune imbalances
Mood concerns related to gut dysfunction
General digestive support and microbiome maintenance
Strain specificity matters — different symptoms require different strains.
Probiotic-Rich Foods
Increasing fermented food intake naturally boosts beneficial microbes:
Yogurt with live cultures
Kefir (dairy or non-dairy)
Sauerkraut and kimchi (raw, unpasteurized)
Tempeh, miso, natto
Kombucha
Fermented vegetables
Aim to include fermented foods daily to support ongoing microbial diversity.
Supplementing With Probiotics
Supplement options include:
Multi-strain probiotics for broad support
Strain-targeted products for specific symptoms
Soil-based organisms (SBOs)
Saccharomyces boulardii for diarrhea or gut infections
Shelf-stable and refrigerated options
Synbiotic blends containing pre- plus probiotics
Your ND will consider CFUs, strain types, and therapeutic goals to personalize your plan.
3. Postbiotics
What Are Postbiotics?
Postbiotics are bioactive compounds produced by beneficial bacteria — or inactivated bacteria themselves — that provide health benefits even though they are not alive. They include:
Short-chain fatty acids (SCFAs), especially butyrate
Peptides and enzymes
Bacterial metabolites
Inactivated bacterial cells and cell wall fragments
Fermented microbial extracts
This is a rapidly growing area in integrative and naturopathic medicine.
Why Postbiotics Support Gut Repair & Inflammation
Postbiotics may help:
Repair and strengthen the gut lining
Reduce inflammation in the digestive tract and throughout the body
Support immune balance
Improve metabolic markers (insulin sensitivity, lipid balance)
Reduce digestive sensitivity and bloating
Provide benefits without introducing live microbes — ideal for sensitive patients
Postbiotics act as direct messengers between your microbiome and immune system.
When Naturopathic Doctors May Recommend Postbiotics
Postbiotics may be indicated for:
Leaky gut / intestinal permeability
Chronic inflammation or autoimmune conditions
Post-infection gut repair
IBS or functional bowel disorders
Metabolic dysfunction
Patients unable to tolerate probiotics
Targeted gut healing protocols
They are often paired with prebiotics or probiotics for synergistic effects.
Foods That Contain Postbiotics
Postbiotics naturally occur in many fermented foods, including:
Kefir and yogurt
Sauerkraut and kimchi
Miso, tempeh, natto
Fermented coconut products
Fermented vinegars (including apple cider vinegar)
Fermented vegetables or pickles
Any fermented food will contain microbial metabolites — the source of postbiotic benefits.
Supplementing With Postbiotics
Common postbiotic supplements include:
Butyrate (sodium or calcium butyrate)
Tributyrin (a highly absorbable form of butyrate)
Heat-killed probiotic strains (e.g., Lactobacillus paracasei postbiotics)
Fermented yeast or bacterial extracts
Fulvic and humic acids
Shilajit
Synbiotic formulas that combine pre-, pro-, and postbiotics
These are often used to support gut lining repair, reduce inflammation, and enhance microbiome balance.
Supporting your gut health isn’t just about taking a probiotic — it’s about creating the right environment for your microbiome to thrive. Prebiotics feed your beneficial bacteria, probiotics introduce supportive microbes, and postbiotics deliver the powerful byproducts that nourish your gut lining and immune system.
Disclaimer: This information is for educational purposes only and is not intended to provide or replace medical advice, diagnosis, or treatment. Always consult your qualified healthcare provider for individualized recommendations.