If you want a lush bounty of cucumbers, zucchini, and tomatoes at the end of the growing season, you could fertilize your vegetable garden with cow manure. The nutrients (and microbes?) provided by manure yield bigger and juicier veggies for your consumption.

Many of you may recall that I liken efforts to cultivating a healthy intestinal microbiome to planting a backyard vegetable garden in springtime: prepare the soil by removing weeds and debris, planting seeds, then watering and fertilizing throughout the growing season. The same principles apply to your intestinal microbiome with “fertilizers” playing an important role. Of course, the fertilizers of your microbiome are not manure or nitrogen-containing plant food, but nutrients that are consumed by the various species of bowel flora.

Just as you can cause your veggies to bloom with proper fertilization, you can likewise cause various species to bloom when you ingest nutrients that microbes require such as prebiotic fibers, polysaccharides, and polyphenols, all components of plant matter.

One form of prebiotic fiber, however, stands out: inulin and closely related fructooligosaccharides, or FOS. (Inulin is a longer chain, while FOS, sometimes called “oligofructose,” is shorter, but comprised of the same fructan subunits.) One major effect: Inulin and FOS cause many beneficial microbiome species to “bloom,” thereby increasing their numbers and thereby their health effects. Among the species that bloom with inulin/FOS:

• Akkermansia muciniphila—Akkermansia supports other beneficial species and is a crucial species in maintaining the intestinal mucus barrier.
• Faecalibacterium prausnitzii—The #1 major producer of butyrate in the human microbiome, a metabolite that yields numerous beneficial effects on the host (you) such as reduced insulin resistance and blood sugar, reduced blood pressure, healing and support of the intestinal lining, better sleep and dreams.
• Several Bifidobacteria species—Inulin and FOS are often labeled “bifidogenic,” meaning they are especially potent promoters of Bifidobacteria growth, including important species such as B. longum and B. bifidum.
• Several Lactobacillus species–Which are, of course, among the species that we obtain through fermented foods and probiotics.

Inulin and FOS yield other benefits mediated by these “blooms” such as enhanced intestinal absorption of magnesium and calcium, reduced insulin resistance, reduced blood sugar, reduced intestinal inflammation, increased feelings of satiety and reduced desire for “junk” processed foods, and—very importantly—reduced endotoxemia. Reducing endotoxemia provides huge advantages in health including facilitation of weight loss, reduced inflammatory conditions, and reduced potential for neurodegenerative diseases.

Inulin and FOS are found in root vegetables such as onions, garlic, shallots, leeks, asparagus, chicory, raw green bananas, yacon, as well as powders you can buy for convenience. Because inulin and FOS are modestly sweet, you can also obtain modest additional quantities by choosing some sweeteners such as Swerve made of inulin and erythritol.

Problem: If you begin the process with substantial dysbiosis (i.e., disrupted species composition confined to the colon) or small intestinal bacterial overgrowth, SIBO, your ingestion of prebiotic fibers and other microbial food can make you ill: excessive bloating and gas, diarrhea, abdominal pain, anxiety, panic attacks, depression, even suicidal thoughts. So before you embark on a program of “fertilizing” your garden of bowel flora, run through the checklist of signs of dysbiosis/SIBO and/or get yourself an AIRE device to map out where in your GI tract microbes are living. If all this is new or unfamiliar to you, I urge you to read the many posts here in this blog and to pre-order/order my new book, Super Gut: The 4-Week Plan to Reprogram Your Microbiome, Restore Health, and Lose Weight that spells it all out for you. Pre-order and you will be given access to some additional incentives including joining me in a private Super Gut event.