Growing evidence emerging over the past 15 years has revealed that the human microbiome, especially that of the gastrointestinal (GI) tract, has shrunk: we’ve lost numerous important species, many of which performed important functions for human health. Think of the populations of GI microbes as a lush rainforest with every inch of soil occupied by plants, insects, and other creatures, now being desiccated and thinned to a desert with sparse species. Repeated courses of antibiotics, often prescribed for flimsy reasons, herbicides/pesticides, glyphosate in Roundup (an herbicide but also an antibiotic), food preservatives with antibacterial properties, emulsifying agents that disrupt the intestinal mucus barrier, chlorinated drinking water, stomach acid-blocking drugs, anti-inflammatory non-steroidal anti-inflammatory drugs, the proliferation of C-sections and formula feeding of infants, heavy metal exposures, and on and on.

And it’s getting worse. Not only are exposures to ubiquitous microbiome disrupters growing, but there is a generation-to-generation transmission of disruption, as evidenced by the elegant work of husband-wife microbiologist team, Justin and Erica Sonnenburg of Stanford. Grandma had her microbiome disrupted that she passed onto your mom, who was exposed to even greater amounts of microbiome disruption and passed a disrupted microbiome onto you, and then you in turn pass on your even more disrupted microbiome onto your children. With each passing generation, there is a decrement in healthy species, an increase in unhealthy species to take their place.

Healthy microbial species such as Bifidobacteria, Akkermansia, and Faecalibacterium help suppress the proliferation of unhealthy species of Proteobacteria such as E. coli, Klebsiella, and Citrobacter, as well as Staphylococcus, Streptococcus, and Enterococcus. Not only are healthy populations diminished, the metabolites they produce (e.g., butyrate that nourishes and heals the intestinal wall and yields beneficial metabolic effects upon absorption such as reduced insulin resistance) are also lacking. This has implications for conditions such as ulcerative colitis, diverticular disease, colon cancer, as well as common metabolic conditions such as fatty liver, type 2 diabetes, and hypertension.

Should we allow these trends to continue, it is scary to think what is ahead: a world in which everyone has type 2 diabetes and is obese? While depression and suicide have skyrocketed in incidence the last 15-20 years, will they become the defining features of modern mental health, afflicting the majority? Will screening for colon cancer via colonoscopy become an annual event due to the explosion of cancer? Given the misguided and perverse motivations of doctors, the healthcare system, and the pharmaceutical industry who throw parties over the prospects of greater numbers of sick people, don’t expect solutions to come from them.

While it remains a work in progress as the science (thankfully) continues to unfold, consider:

  • Minimizing exposure to all the factors listed above that disrupt the microbiome, especially filtering drinking water, avoiding or minimizing all medications, choosing organic and whole unprocessed foods whenever possible, declining antibiotic prescriptions unless genuinely necessary.
  • Frequent (several times per day) consumption of fermented foods—Once again, the elegant research of Drs. Sonnenburg and Sonnenburg have demonstrated the outsized benefits in generating bacterial species diversity by including several servings of kimchi, kombucha, kefirs, yogurts, fermented veggies and other fermented foods in your lifestyle. While the Pediococcus pentosaceus or Leuconostoc mesenteroides common to fermented foods are not the species that take up residence, their presence somehow cultivates the growth of other beneficial GI residents.
  • Don’t over-rely on commercial probiotics—The great majority of current probiotics are the least helpful of all microbiome-rebuilding strategies, as they are nothing more than haphazard collections of microbes without rhyme or reason. For instance, they do not incorporate keystone species/strains, do not factor in collaborative effects among microbes (“guilds” or “consortia”), and cannot provide critical species such as Faecalibacterium prausnitzii or Turicibacter sanguinis not present in any probiotic. By not incorporating the science, many probiotic manufacturers have resorted to using gimmicks, making claims such as double-encapsulation is an advantage (thereby failing to release into the all-important small bowel where SIBO occurs), claiming that only spore-based microbes survive into the colon due to antimicrobial effects of stomach and bile acids (this is fiction), or including such small numbers of microbes as to not make any difference. (We are in the process of helping to define the dose-response curve for selected microbes to validate whether greater numbers yield greater biological effects, a phenomenon suggested by the hundreds of billions of microbes generated by my unique method of prolonged yogurt fermentation for species/strains such as L. reuteri, L. gasseri, and B. coagulans.) As probiotic manufacturers incorporate some of these best practices, probiotics may indeed become a powerful advantage for recovering a healthy GI microbiome in future.

Just as if you wanted to restore a lush rainforest starting from a barren desert, you would plant seeds and young plants, water regularly, then make sure nutrients are available. The GI microbiome follows the same set of rules. It takes time, but you can create your own Eden of healthy microbiota that service your health.