50 Foods That Strengthen Your Microbiome

Here’s your full-spectrum, microbiome-nourishing field guide to lightness and diversity.

This is a reference for variety of some top performing fibers. Your microbiome is not a machine; it’s a living forest that thrives on variety from nature. Aim for 30 plants weekly.

These are plants I keep in rotation in my home — each offering its own kind of nourishment to the inner garden. Or, as I call it, the Gnome Diet (which also includes eggs, fish, birds and lots of butter and honey — I will do a full post). I have also added some commentary and links to recipes.

(ps, this is why Floura bars contain 12 plants!)

Soluble Fibers

Gel-forming, soothing, slow-fermenting — these fibers regulate digestion and feed microbes gently.

Oats — beta-glucan; steady fermentation. A splash of vinegar in overnight oats opens the fibers.

Chia Seeds — forms a gel Bifidobacteria adore.

Flaxseeds — soluble fiber + lignans; hormonal + microbial support.

Avocado — creamy soluble fiber + healthy fats. (guacamole with onion is so good for you!)

Barley — rich in beta-glucan, a gel-forming soluble fiber that soothes digestion and produces steady, beneficial fermentation; a deeply nourishing whole grain. Add it to soups!

Carrots — gentle fermentation; carotenoid-rich. Roast them whole with honey, smoked paprika (another plant!) and butter.

Pumpkin / Winter Squash — grounding soluble fibers; comforting and easy.

Watermelon Rind — pectin-rich, prebiotic, beautifully overlooked. (you don’t have to eat the fibrous last bit of the rind, just eat the pale part)

Pears — queen of soluble fiber; especially prebiotic when underripe. (I eat a pear in my oats a couple times a week.)

Kiwi — pectin + enzymes; clinically shown to improve motility. I eat one a day — I love the golden ones! And, the rind is also very good for your microbiome.

Insoluble Fibers

Structural fibers that support motility, regularity, and microbial diversity.

Raspberries — seeds + skin = motility support.

Cabbage — crisp fiber; wonderful raw, braised, roasted, or fermented.

Kale — sulfur + structure; supports detox + microbial balance.

Spinach — gentle roughage + plant nitrates.

Broccoli — fiber + sulforaphane; anti-inflammatory.

Beets — structural fiber + nitric oxide signaling.

Quinoa — mixed fibers + protein.

Buckwheat — hearty insoluble fiber + some resistant starch qualities; I add it to pancakes and banana bread.

Celery (stalk + leaves) — hydration and motility support.

Radishes / Daikon — sulfur compounds that stimulate digestion.

Inulin + FOS (Fructooligosaccharides) Prebiotics

Elite feeders for Bifidobacteria; excellent for microbial diversity.

Garlic — inulin + FOS; prebiotic + selective antimicrobial.

Onions & Shallots — inulin-rich + quercetin-loaded.

Leeks — the gentlest allium; ideal for sensitive guts.

Asparagus — natural inulin; antioxidant-rich.

Jerusalem Artichokes — among the highest in natural inulin.

Globe Artichokes — inulin + bitter compounds; great for bile flow. From sunflowers, and very powerful prebiotic.

Chicory Root — one of the most concentrated inulin sources.

Resistant Starch (RS)

Deep fermentation → short-chain fatty acids → butyrate → gut lining repair.

Green Bananas — top natural RS source.

Plantains (green) — slow, sustained fuel for butyrate producers. (I learned to love these from dating a cute Puerto Rican boy — his mama showed me how to fry these and make tostones, which are so good!)

Sweet Potatoes (cooked then cooled) — retrograded resistant starch (RS3). (This recipe with tahini butter is insane, just cook and cool then reheat. The cooling creates the resistant starch.)

Applesauce (unsweetened, cooled) — rich in pectin with gentle RS-like retrogradation; soothing, fermented softly by microbes, and wonderful for motility and microbial nourishment. (It’s very easy to make or buy and you can add a little spoon of chia, too.)

Chickpeas — resistant starch + soluble fiber.

Black Beans — RS + polyphenols. All beans support the microbiome, but black beans are especially potent due to their polyphenols.

Lentils — balanced RS; deeply microbiome-friendly.

Mucilage Fibers

Soothing, gel-like fibers that support the gut lining and ease motility.

Chia Seeds — mucilage-rich (see above).

Flaxseeds — mucilage + lignans.

Polyphenol-Rich Plants

Feed beneficial microbes indirectly; prune harmful species; reduce inflammation.

Blueberries — anthocyanins; top microbial modulators.

Cranberries — PACs that selectively shape microbial communities.

Beets — betalains for metabolic signaling.

Turmeric — curcumin; anti-inflammatory + microbial-balancing.

Green Tea — catechins that harmonize microbial activity.

Cacao Nibs — dense polyphenols; potent prebiotic effects.

Fermented Plants

Microbial visitors — they don’t colonize, but they harmonize.

Sauerkraut — lactic-acid bacteria; motility + immune tone. (growing up in a midwestern German household meant sauerkraut constantly!)

Kimchi — complex fermentation; excellent for diversity. (chop it and toss with roasted brassicas)

Marine Plants

Unique polysaccharides for microbial species untouched by land plants.

Seaweed (nori, kelp, wakame) — alginates + fucoidans; rare nourishment.

Bitter + Digestive-Stimulating Plants

Activate the gut-brain axis, support bile flow, enhance microbial communication.

Globe Artichokes — (already listed; counted once).

Parsley — bitter + polyphenols; small amounts matter.

Dill — bright, aromatic, rich in plant compounds.

Cilantro / Coriander — detoxifying + polyphenols.

Citrus Peel (lemon) — pectin + flavonoids; potent prebiotic signal. I make a whole lemon vinaigrette that is so tasty on roasted broccoli or salad. Just puree a lemon and use it to taste as you would vinegar.

Aromatic Roots, Seeds + Special Plants

Outliers that meaningfully shape the gut environment.

Ginger — motility support, anti-inflammatory, gut-brain modulation.

Fennel (bulb + seeds) — bloating relief, smooth-muscle relaxation.

Sesame Seeds — lignans; microbial + hormonal synergy.

Cilantro Root — bitter, grounding; microbial diversity. You can sometimes find rooted cilantro in Asian groceries or farmers markets.

Rosemary — polyphenols + gut-barrier support.

Mushrooms (all varieties) — beta-glucans; immune + microbial synergy.

Mint — smooth muscle relaxation; gut-calming.

Radish Sprouts — concentrated sulfur compounds; microbial pruning.

Now go eat a green pear and a kiwi, some whole lemon vinaigrette over roasted broccoli, a tahini sweet potato or a silk black bean soup.

With love and lightness,

Jeni