Gut Health Basics
Over the last few decades, the research on gut health has expanded exponentially. And with that, has come lots of new, sometimes confusing jargon. The purpose of this guide is to break down the latest findings and provide you with some simple, foundational principles for nourishing your inner ecosystem.
What is the microbiome?
The microbiome is a general term that refers to the dynamic communities of bacteria, viruses, and fungi that exist on or within your body. Your skin, gut, mouth, nasal cavity, and urogenital tract all have their own unique microbiome, each of which forms an important protective layer between you and the outside world. In addition, your microbiome helps digest and synthesize nutrients, remove waste products, defend against disease-causing pathogens, and facilitate communication between organs.[1]
The gut microbiome (especially the colon) is our largest and most diverse microbiome. It's highly complex and influenced by many factors including diet, exercise, medications, stress, and even pollution. Research indicates that your gut microbiome impacts many aspects of health and well-being ranging from mood to skin health.
How does the gut microbiome impact your health?
Dysbiosis — imbalances in the gut microbiome — is a contributing factor to a wide range of conditions such as:[2–5]
- Irritable bowel disease and irritable bowel syndrome
- Celiac disease
- Obesity
- Diabetes
- Allergies
- Autism spectrum disorder
- Colorectal cancer
- Heart disease
- Liver disease
- Depression
- Neurodegenerative conditions such as Alzheimer's disease and Parkinson's disease
- Skin conditions such as acne, atopic dermatitis, and psoriasis
- Arthritis
Probiotics, prebiotics, postbiotics, and synbiotics defined
Probiotics, prebiotics, and postbiotics are thrown around a lot these days — but what do they actually mean?
Probiotics: Probiotics or 'good bacteria' are living microorganisms that confer a health benefit when consumed in adequate amounts. Probiotics are found in foods such as yogurt, kefir, sauerkraut, and kimchi, as well as supplements.
Prebiotics: Prebiotics are 'food' for the health-promoting microorganisms that live on or inside us. They are found naturally in foods such as garlic, onions, bananas, and breastmilk, and help your microbiome flourish. Prebiotics are sometimes added to packaged foods — examples include inulin, chicory fiber, or galactooligosaccharides (GOS).
Postbiotics: Postbiotics are by-products of the microbiome that confer a health benefit. A good example is butyrate, an anti-inflammatory short-chain fatty acid produced by gut bacteria that helps maintain the gut barrier and fight inflammation.[6]
Synbiotics: Synbiotics are foods or supplement formulations that include pre- and probiotics. Research suggests that combining the two enhances the survivability of probiotics and promotes the proliferation of health-promoting microorganisms in the GI tract.[7]
Indicators of dysbiosis / poor gut health
Imbalances in the gut microbiome can show up in ways that you don't expect. Common indicators of dysbiosis include:[8]
- Gas
- Bloating
- Constipation
- Diarrhea
- Heartburn
- Nausea
- Brain fog and memory issues
- Mood swings
- Poor appetite
Testing your gut health
Your gut microbiome is unique to you, which means that a probiotic that works for one person may not have any effect on another. That's where microbiome testing comes in.
Flore works with a network of certified clinical laboratory partners who use cutting-edge whole genome sequencing technology to identify specific strains of microorganisms in your gut and their relative abundance — detecting over 23,000 microbes to deliver highly targeted recommendations just for you. Ask your Flore provider about microbiome testing options available through our partner network.
Best probiotics for gut health: Flore 101
At Flore we offer a range of symptom-specific probiotics to help you restore your microbiome, fortify your digestive tract, and achieve your health goals.
Flore Custom Probiotics
Working with your provider and Flore's clinical platform, Flore Custom Probiotics are tailor-made for your unique microbiome and health goals. With millions of possible combinations of strains and doses, Flore personalized probiotics support a wide range of digestive, cognitive, and mood issues — including GI motility, SIBO, leaky gut, and more.
GoodOnes™ Fundamentals
GoodOnes™ Fundamentals is Flore's line of targeted synbiotics — each formula pairs a universal 3-strain Precision core with two condition-specific probiotic strains and a matched prebiotic, creating a true synbiotic that is greater than the sum of its parts. Using almost a decade of microbiome outcome data, each synbiotic is engineered to address a specific imbalance. Available at realgoodones.com in solo, duo, and quad packs.
The Regular One
Daily gut regularity & GI comfort
A targeted synbiotic combining a 3-strain Precision core with Bifidobacterium animalis subsp. lactis and Bifidobacterium longum for daily regularity and gut comfort, plus flaxseed prebiotic to feed the synbiotic blend and sustain colonization.
- Bifidobacterium breve (6B CFU)
- Lactobacillus plantarum (6B CFU)
- Lactobacillus rhamnosus (6B CFU)
- Bifidobacterium animalis subsp. lactis (4B CFU)
- Bifidobacterium longum (4B CFU)
- Flaxseed prebiotic
The Bright One
Mood & gut-brain axis support
A neuro-targeted synbiotic formulated for the gut-brain axis. Lactiplantibacillus plantarum is a GABA-producing strain with documented mood benefits in human RCTs. The flaxseed prebiotic sustains the synbiotic ecosystem long-term.
- Bifidobacterium breve (6B CFU)
- Lactobacillus plantarum (6B CFU)
- Lactobacillus rhamnosus (6B CFU)
- Bifidobacterium animalis subsp. lactis (4B CFU)
- Lactiplantibacillus plantarum (4B CFU)
- Flaxseed prebiotic
The Calm One
Stress, calm & anxiety support
A gut-brain synbiotic featuring Lactobacillus reuteri — a well-studied strain for oxytocin-mediated social behavior and calm — paired with a flaxseed prebiotic to sustain the synbiotic environment and reduce HPA axis reactivity.
- Bifidobacterium breve (6B CFU)
- Lactobacillus plantarum (6B CFU)
- Lactobacillus rhamnosus (6B CFU)
- Bifidobacterium animalis subsp. lactis (4B CFU)
- Lactobacillus reuteri (4B CFU)
- Flaxseed prebiotic
The Clear One
Skin clarity & gut-skin axis
A skin-targeted synbiotic built around the gut-skin axis. Lactobacillus salivarius modulates mucosal immunity and is associated with reductions in skin inflammatory markers, supported by flaxseed prebiotic to sustain the synbiotic colony.
- Bifidobacterium breve (6B CFU)
- Lactobacillus plantarum (6B CFU)
- Lactobacillus rhamnosus (6B CFU)
- Lactobacillus salivarius (4B CFU)
- Bifidobacterium animalis subsp. lactis (4B CFU)
- Flaxseed prebiotic
The Strong One
Daily immune support
An immune-focused synbiotic pairing Lactobacillus acidophilus — shown to upregulate sIgA and NK-cell activity — with Bifidobacterium longum for mucosal defense, and flaxseed prebiotic to sustain the synbiotic ecosystem.
- Bifidobacterium breve (6B CFU)
- Lactobacillus plantarum (6B CFU)
- Lactobacillus rhamnosus (6B CFU)
- Lactobacillus acidophilus (4B CFU)
- Bifidobacterium longum (4B CFU)
- Flaxseed prebiotic
The Lean One
Metabolic & weight support
A metabolic synbiotic featuring Streptococcus thermophilus for energy substrate metabolism and Bifidobacterium animalis subsp. lactis for adiposity reduction. The flaxseed prebiotic supports SCFA production to reinforce the synbiotic's metabolic effects.
- Bifidobacterium breve (6B CFU)
- Lactobacillus plantarum (6B CFU)
- Lactobacillus rhamnosus (6B CFU)
- Bifidobacterium animalis subsp. lactis (4B CFU)
- Streptococcus thermophilus (4B CFU)
- Flaxseed prebiotic
The Mighty One
Enhanced immune fortification
A next-level immune synbiotic using elderberry as the prebiotic — a polyphenol-rich substrate with its own antiviral and anti-inflammatory properties — paired with Bifidobacterium bifidum to strengthen the synbiotic's mucosal barrier effect.
- Bifidobacterium breve (6B CFU)
- Lactobacillus plantarum (6B CFU)
- Lactobacillus rhamnosus (6B CFU)
- Bifidobacterium animalis subsp. lactis (4B CFU)
- Bifidobacterium bifidum (4B CFU)
- Elderberry prebiotic
The Radiant One
Women’s microbiome & vitality
A women’s synbiotic featuring Lactobacillus gasseri — extensively studied for weight, vaginal microbiome, and hormonal balance — and Lactobacillus fermentum for broad-spectrum immune and skin benefits, with flaxseed prebiotic to sustain the synbiotic community.
- Bifidobacterium breve (6B CFU)
- Lactobacillus plantarum (6B CFU)
- Lactobacillus rhamnosus (6B CFU)
- Lactobacillus gasseri (4B CFU)
- Lactobacillus fermentum (4B CFU)
- Flaxseed prebiotic
The Little One
Pediatric synbiotic — all ages
A pediatric synbiotic built exclusively around Bifidobacterium species — the dominant genus in healthy infant and child gut microbiomes — at a lower 2B CFU dose per strain. Banana prebiotic (a natural fructooligosaccharide source) completes the synbiotic pairing to promote healthy colonization and microbial diversity.
- Bifidobacterium animalis subsp. lactis (2B CFU)
- Bifidobacterium breve (2B CFU)
- Bifidobacterium longum (2B CFU)
- Bifidobacterium infantis (2B CFU)
- Banana prebiotic
Gut Health Pillars
Take your probiotics every day
A daily probiotic, targeted for specific needs and goals, lays a foundation for better gut health. Your gut microbiome is like a garden. Probiotics are 'seeds' that you plant in the dirt, and a gut-friendly diet and lifestyle help them grow and flourish.
Eat 30 plants a week
Research indicates that eating more than 30 different plants a week improves microbial diversity in the gut.[9] A diverse gut microbiome is associated with a more resilient gut, better at defending against stressors.[9,10]
Aim for 35g of fiber a day
Eating a high-fiber diet helps strengthen gut barrier protection and improve microbial composition.[11] High-fiber eating is also linked with weight management, lower risk of type II diabetes, reduced risk of CVD, constipation relief, and colorectal cancer prevention.[12]
Incorporate fermented foods daily
Like probiotics, fermented foods help 'seed' your gut with good bacteria. Studies suggest that eating fermented foods like kimchi, kefir, and tempeh regularly can improve inflammatory markers, assist with cholesterol reduction, and alleviate digestive symptoms.[13]
Limit ultra-processed foods (UPFs)
UPFs such as chips, cakes, ready-to-eat meals, and soda are light on gut-friendly nutrients like fiber, prebiotics, and polyphenols, and result in unfavorable changes in the gut microbiome.[14]
Go easy on alcohol and additives
Alcohol and additives such as carrageenan increase inflammation in the gut and contribute to dysbiosis.[14,15]
Move more
Regular exercise results in favorable shifts in the microbiome, along with other benefits such as building muscle, maintaining bones, and improving mood.[16] Moving more can also help relieve constipation.
Hydrate
Adequate fluid (in the form of water and/or unsweetened tea) promotes regular bowel movements and helps alleviate constipation.
Manage stress and get adequate sleep
Your gut and brain are in constant communication. Research suggests that stress can impact gut permeability, inflammation, and motility.[17] Sleep deprivation has a similar effect.[18]
Eat your omega-3s
Omega-3 fats have a positive impact on microbial composition in the gut and enhance the growth of beneficial microorganisms.[19]
Foods For Gut Health
Gut-friendly shopping list — organized by dietary pattern.
Key: blank = suitable · NO = not suitable · Limited = limited quantity · ALL = always suitable
| Food | Low FODMAP | Gluten-Free | Dairy-Free | Keto | Mediterranean |
|---|---|---|---|---|---|
| Tomatoes | ALL | ALL | ALL | ||
| Cucumbers | |||||
| Bell peppers | |||||
| Beets | NO | NO | |||
| Zucchini | |||||
| Eggplant | |||||
| Baby spinach | |||||
| Kale | |||||
| Arugula | |||||
| Romaine | |||||
| Swiss chard | |||||
| Collard greens | |||||
| Carrots | NO | ||||
| Broccoli | NO | ||||
| Cauliflower | NO | ||||
| Onions | NO | ||||
| Leeks | NO | ||||
| Garlic | NO | ||||
| Mushrooms | NO | ||||
| Artichokes | NO | NO | |||
| Asparagus | NO | ||||
| Potatoes | NO | ||||
| Sweet potatoes | NO | NO | |||
| Corn | NO | NO | |||
| Peas | NO | NO | |||
| Butternut squash | NO | NO | |||
| Kabocha pumpkin | NO |
| Food | Low FODMAP | Gluten-Free | Dairy-Free | Keto | Mediterranean |
|---|---|---|---|---|---|
| Lemons | ALL | ALL | ALL | ||
| Oranges | NO | ||||
| Mandarins | NO | ||||
| Apples | NO | NO | |||
| Bananas | NO | ||||
| Strawberries, Blueberries, Raspberries | Limited | ||||
| Grapes | NO | ||||
| Figs | NO | NO | |||
| Dates | NO | NO | |||
| Cantaloupe | NO | ||||
| Pomegranates | NO | NO | |||
| Pears | NO | NO | |||
| Avocado | NO | Limited | |||
| Mango | NO | NO | |||
| Watermelon | NO | NO | |||
| Peaches | NO | NO | |||
| Nectarines | NO | NO | |||
| Plums | NO | NO | |||
| Pineapple | NO | ||||
| Cherries | NO | NO |
| Food | Low FODMAP | Gluten-Free | Dairy-Free | Keto | Mediterranean |
|---|---|---|---|---|---|
| Quinoa | NO | ALL | |||
| Brown rice | NO | ||||
| Farro | NO | NO | NO | ||
| Barley | NO | NO | NO | ||
| Whole wheat pasta | NO | NO | NO | ||
| Whole grain bread | NO | GF only | NO | ||
| Bulgur | NO | NO | NO | ||
| Couscous | NO | NO | NO | ||
| Oats | GF oats only | NO | |||
| Buckwheat | NO | ||||
| Millet | NO | ||||
| Sorghum | NO |
| Food | Low FODMAP | Gluten-Free | Dairy-Free | Keto | Mediterranean |
|---|---|---|---|---|---|
| Almonds / Almond Butter | ALL | ALL | ALL | ||
| Walnuts | |||||
| Peanuts / Peanut Butter | Limited | ||||
| Pistachios | NO | Limited | |||
| Cashews / Cashew Butter | NO | Limited | |||
| Pine Nuts | |||||
| Macadamias | |||||
| Pumpkin Seeds | |||||
| Sunflower Seeds / Butter | |||||
| Sesame Seeds / Tahini | |||||
| Chia Seeds | |||||
| Flaxseeds | |||||
| Extra Virgin Olive Oil | |||||
| Avocado Oil | |||||
| Olives |
| Food | Low FODMAP | Gluten-Free | Dairy-Free | Keto | Mediterranean |
|---|---|---|---|---|---|
| Fresh herbs (basil, cilantro, rosemary, mint, thyme) | ALL | ALL | ALL | ||
| Spices (turmeric, ginger, cumin, paprika, cinnamon) | |||||
| Lemons and limes | Limited | ||||
| Balsamic vinegar | NO | Limited | |||
| Red wine vinegar | |||||
| Capers | |||||
| Anchovies | |||||
| Sun-dried tomatoes | NO | Limited | |||
| Miso | NO | NO |
| Food | Low FODMAP | Gluten-Free | Dairy-Free | Keto | Mediterranean |
|---|---|---|---|---|---|
| Chickpeas | NO | ALL | NO | ALL | |
| Lentils | NO | NO | |||
| Black beans | NO | NO | |||
| Cannellini beans | NO | NO | |||
| Kidney beans | NO | NO | |||
| Fava beans | NO | NO | |||
| Edamame | NO | NO | |||
| Tofu | |||||
| Tempeh | |||||
| Greek yogurt | NO | NO | Plain whole milk | Plain whole milk | |
| Salmon | |||||
| Sardines | |||||
| Tuna | |||||
| Trout |
| Food | Low FODMAP | Gluten-Free | Dairy-Free | Keto | Mediterranean |
|---|---|---|---|---|---|
| Kefir | NO | NO | Plain whole milk | ||
| Greek yogurt | NO | NO | Plain whole milk | ||
| Kimchi | NO | ||||
| Sauerkraut | NO | ||||
| Kombucha | NO | NO | |||
| Miso | Check label | NO | |||
| Tempeh | NO |
Tips for Eating Out
Aim for at least half a plate of plants
Feed your microbes with an abundance of plant foods at every meal.
Go vegetarian or choose fatty fish
Plant-based foods and fatty fish rich in omega-3s promote gut health. On the other hand, red meat is associated with an increased risk of colorectal cancer.[20]
Embrace low- or no-alcohol drinks
Alcohol contributes to dysbiosis and increases gut permeability and inflammation.[15]
Watch your intake of added sugar
Some research indicates that a diet rich in sugar promotes the growth of bacteria that degrade the gut mucosal layer.[11]
Review the menu in advance
This is especially important if you're on a specific diet like low FODMAP, gluten-free, or dairy-free. Reviewing the menu in advance can give you peace of mind and minimize digestive disruptions.
Be mindful of hunger and fullness, especially at dinner
Eating too much before bed can contribute to poor sleep, which is detrimental to your GI tract.
References
- Ogunrinola G. A. et al. (2020). The Human Microbiome and Its Impacts on Health. Int J Microbiol, 8045646. doi:10.1155/2020/8045646
- DeGruttola A. K. et al. (2016). Current Understanding of Dysbiosis in Disease. Inflamm Bowel Dis, 22(5):1137–1150.
- Hou K. et al. (2022). Microbiota in health and diseases. Signal Transduct Target Ther, 7(1). doi:10.1038/s41392-022-00974-4
- Ryguła I. et al. (2024). The Role of the Gut Microbiome and Microbial Dysbiosis in Common Skin Diseases. Int J Mol Sci, 25(4):1984.
- Chu X. et al. (2021). The oral and gut microbiome in rheumatoid arthritis patients. Rheumatology, 60(3):1054–1066.
- Hodgkinson K. et al. (2023). Butyrate's role in human health. Clin Nutr, 42(2):61–75.
- Sarita B. et al. (2025). A comprehensive review of probiotics and human health. Front Microbiol, 15:1487641.
- Carías Domínguez A. M. et al. (2024). Intestinal Dysbiosis. Probiotics Antimicrob Prot.
- McDonald D. et al. (2018). American Gut. mSystems, 3(3):e00031-18.
- Lozupone C. A. et al. (2012). Diversity, stability and resilience of the human gut microbiota. Nature, 489(7415):220–230.
- Zhang P. (2022). Influence of Foods and Nutrition on the Gut Microbiome. Int J Mol Sci, 23(17):9588.
- Ioniță-Mîndrican C. B. et al. (2022). Therapeutic Benefits and Dietary Restrictions of Fiber Intake. Nutrients, 14(13):2641.
- Diez-Ozaeta I. & Astiazaran O. J. (2022). Fermented foods. Food Res Int, 156:111133.
- Bevilacqua A. et al. (2024). Ultra-Processed Food and Gut Microbiota. Nutrients, 17(1):2.
- Pohl K. et al. (2021). Alcohol's Impact on the Gut and Liver. Nutrients, 13(9):3170.
- Min L. et al. (2024). Effects of Exercise on Gut Microbiota. Nutrients, 16(7):1070.
- Tait C. & Sayuk G. S. (2021). The Brain-Gut-Microbiotal Axis. Eur J Intern Med, 84:1–9.
- Wankhede N. L. et al. (2025). Sleep deprivation-induced shifts in gut microbiota. Neuroscience, 565:99–116.
- Zinkow A. et al. (2024). Molecular Mechanisms Linking Omega-3 Fatty Acids and the Gut-Brain Axis. Molecules, 30(1):71.
- Farvid M. S. et al. (2021). Consumption of red meat and cancer incidence. Eur J Epidemiol, 36(9):937–951.