Microbiome Restoration Plan

This first phase is all about improving the gut environment without pushing it too hard.

For most people with IBS or chronic digestive issues, the gut is too sensitive to handle a lot of fiber or fermentation right away. So instead of jumping into aggressive prebiotics, we start with gentler fibers that are easier to tolerate, help move things along, and begin supporting beneficial bacteria like Bifidobacteria.

Bifidobacteria play a key role in keeping your gut balanced. They produce acids that lower the pH of the colon, which helps crowd out harmful, inflammatory bacteria and creates a better environment for beneficial ones to grow. Building up these bacteria first helps reduce inflammation, calm food reactions, and makes your gut more ready to handle stronger fibers later on.

The different foods in Phase 1 will also help to support certain bacteria like Akkermansia and Faecalibacterium prausnitzii that help to heal & repair your gut lining.

Step 1

Why polyphenols matter

Polyphenols aren’t traditional prebiotic fibers, but they’re one of the most effective ways to shift the gut environment in your favor. They help reduce inflammation and have been shown to limit the growth of certain harmful bacteria like E. coli and other opportunistic microbes.

At the same time, they support the growth of beneficial bacteria like Akkermansia, F. prausnitzii, Bifidobacteria, and Lactobacillus. These are key players in healing the gut lining and improving immune function.

In simple terms, polyphenols do two things at once: They help beneficial bacteria thrive, while making the environment less friendly for inflammatory bacteria.

This isn’t a “kill phase,” but it still helps rebalance the gut in a much gentler, more sustainable way.

Step 2

Why pectins & beta-glucans matter

Pectins and beta-glucans are gentle, well-tolerated fibers that help support the gut without irritating it. They create a soothing, gel-like effect in the digestive tract while still feeding beneficial bacteria.

They help guide fermentation in a healthier direction, support short-chain fatty acid production, and improve the environment for the gut lining to heal.

This makes them especially helpful for anyone dealing with inflammation, irritation, or a highly sensitive, reactive gut.

Step 3

Why resistant starches matter

Resistant starch is one of the most important tools in this plan because it helps shift the gut away from protein fermentation and toward healthier short-chain fatty acid production (like butyrate).

When it reaches the colon, it feeds beneficial bacteria and supports key butyrate producers like Faecalibacterium and Roseburia. These bacteria help strengthen the gut lining, reduce inflammation, and improve the overall health of your entire gut.

In simple terms, resistant starch works by giving your gut bacteria a better fuel source. And when you change what they’re eating, you change what they produce, which helps reduce irritating, inflammatory byproducts over time.

Step 4

Why PHGG (Sunfiber) is the best fiber to start with

PHGG is one of the best fibers to start with because it’s gentle, well-tolerated, and still very effective at improving the gut microbiome.

Studies show that regular use of PHGG can help to improve stool form and regularity while supporting beneficial bacteria like Bifidobacteria and butyrate producers. These bacteria play a big role in strengthening the gut lining, reducing inflammation, and supporting healthy digestion and motility.

Just like the other foods listed above, PHGG helps your gut bacteria shift away from protein fermentation, without causing the bloating that more aggressive fibers often do. This is a huge reason it can help with bloating, stool irregularity, and that "inflamed/reactive gut" picture that’s so common for people with IBS.

Incorporate the foods listed below DAILY if you are struggling to have complete, daily bowel movements

Why this add-on matters

If motility is slow, even the best gut protocol can backfire. When stool sits in the colon too long, bacteria have more time to ferment leftover protein, which can increase bloating, irritation, and create a more inflammatory gut environment.

So this isn’t just about relieving constipation. Improving motility helps shift the gut environment, reduce irritating byproducts, and makes your body more tolerant to fiber overall.

Foods like chia seeds, kiwi, raspberries, and cooked greens help because they support both stool consistency and movement through a mix of soluble and insoluble fiber. Kiwifruit in particular has strong research behind it for improving regularity.

Getting this piece right makes everything else in your protocol work better.

Once the gut is more stable, you can start adding more targeted prebiotics like oligosaccharides and inulin. These fibers ferment more quickly and feed your microbiome more aggressively, which helps expand microbial diversity and more directly support beneficial bacteria.

They can significantly increase Bifidobacteria and boost butyrate production, both of which are key for strengthening the gut lining, reducing inflammation, and improving overall gut function.

Because they ferment faster, they can also be more reactive if your gut isn’t ready. That’s why we build a strong foundation first. Once you tolerate Phase 1 well, introducing these fibers allows you to take things to the next level and drive deeper, more meaningful improvements in the gut.

Step 5

Why oligosaccharides like GOS, XOS, & FOS matter

This is where we move from simply supporting the gut to actively building it.

These fibers are some of the most effective tools for increasing Bifidobacteria, which are foundational for a stable, healthy gut environment.

Why these fibers are so powerful

• GOS (Galactooligosaccharides): One of the most reliable ways to increase Bifidobacteria, even at low doses. Helps quickly shift the gut toward a more balanced, favorable state. • XOS (Xylooligosaccharides): Very potent in small amounts. Supports Bifidobacteria while also helping improve bowel regularity and overall microbiome balance. • FOS (Fructooligosaccharides): A classic prebiotic that feeds Bifidobacteria and helps support key beneficial species like Faecalibacterium, Roseburia, and Akkermansia.

Step 6

Why inulin-containing foods matter

This is the acceleration phase, where everything you’ve built so far starts to compound. Inulin-containing foods ferment more quickly and push the microbiome to grow and adapt at a higher level.

At this stage, you see further increases in Bifidobacteria along with expansion of key beneficial species like Faecalibacterium, Roseburia, Eubacterium, and Akkermansia. This leads to higher production of butyrate and other short-chain fatty acids that play a major role in gut health.

This matters because it helps deepen microbial diversity, strengthen the gut lining, reduce inflammation, and improve overall digestive stability. It also continues shifting the gut away from protein fermentation and toward fiber-driven fermentation, meaning fewer irritating byproducts and more beneficial compounds that support a healthier, more resilient gut.