Reclaiming Your Gut Microbiome’s Biodiversity

The word “biodiversity” refers to the variety of life forms that make up an ecosystem, like a forest, wetland, lake, or ocean. But your gut is an ecosystem of sorts, too. The more biodiversity your gut has, the better your digestion and overall health.

Trillions of Gut Microbes

From an ecological perspective, your gut harbors trillions of microbes of at least a thousand different species. Species richness and biodiversity keep your gut resilient even during change, supporting proper digestion and immunity.

Scientists warn, however, that the diversity of our gut microbiomes has been on the decline over the last half a century (1,2). A variety of factors are to blame, including the increasing availability of highly processed foods along with the overuse of antimicrobials in our food system (1,2).

Microbial Diversity Begins With Mom

Microbes are first introduced to us at birth through our mother’s birth canal, breast milk, kisses, and touch (3,4). Each of these exposures might deliver a different set of microbes, as the microbiota of human skin isn’t the same as the microbiota in the urogenital tract, which contributes to an initial diversity of microbes.

Nurturing these microbes first begins with mother’s milk. For years, scientists have been puzzled by the existence of special nondigestible carbohydrates that make up nearly 30% of the energy found in breast milk (3). They are now understood to be highly specific nourishment for microbes — not just any microbes, but the types of microbes that contribute to a baby’s microbiome development.

Gaining New Microbes As We Grow

Infant microbiome development is followed by new acquisitions of microbes during early childhood with new foods, family members, and pets (5). A child’s surrounding environment contributes to a diverse and distinct microbiome that’s believed to have a lasting impact on digestion, nutrient absorption, immunity, and brain health (4,6,7).

Once we reach adulthood, each of our gut microbiomes becomes as unique as a fingerprint. But unlike a fingerprint, which remains the same throughout our lives, our microbiomes are ever-changing depending on our choices, such as the foods we eat, the people we share meals with, and the places we eat those foods.

Why Microbes Go Missing

There are many reasons for the eventual decline of microbial diversity in our guts. Exposure to antibiotics and antiseptic chemicals, such as those found in soaps, is only part of the problem. A Western-style diet made up of highly processed foods can also cause a rapid decline in diversity (2).

Scientists have observed what happens when immigrant populations arrive in the U.S. from non-Western countries like Thailand. A loss of native gut microbiome diversity and function can occur almost immediately upon arrival, coinciding with the adoption of more highly processed foods (2). In these studies, scientists have also noticed that the diversity decline can increase with duration of residency in the U.S. (2). The effect is also compounded by weight gain and, later, is noticeably worsened in first- and second-generation immigrants (2).

With the loss of these microbes, scientists also observed a corresponding loss of bacterial enzymes that assist in the proper digestion of foods. This includes the loss of bacterial enzymes that help break down plant fibers found in foods such as beans, legumes, and vegetables (2).

More Diverse Diet, More Diverse Microbes

While scientists might disagree on how to define the ideal gut microbiome, it’s generally understood that microbial diversity is the goal. Encourage a more diverse and resilient gut microbiome with these key steps supported by existing scientific studies:

  1. Eat a diverse diet. Several studies have found that consuming a variety of whole foods, such as fruits and vegetables, provides the dietary fiber and complex carbohydrates needed to better support microbe diversity in the gut (1,2).
  2. Travel and stay close to nature. One small study found that adults and children had more gut microbiome diversity after traveling to a less-developed country and experiencing a more traditional lifestyle, such as staying in a rainforest village and eating a variety of rainforest-sourced foods (7).
  3. Take IsaBiome™ Daily Digestive Health System. The guaranteed-potency probiotics supplement supplies a diverse amount of probiotic strains daily, while the digestive enzyme supplement supports proper breakdown of foods. These products can be helpful when traveling and introducing diverse foods into the diet by encouraging greater gut microbe diversity (8).
  4. Get plenty of exercise daily. Research has consistently shown that exercise is not only associated with gut microbiome diversity (independent of diet or supplements), but that this factor alone might explain some of the numerous benefits of exercise on health (9,10).


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  3. Bode L. Human milk oligosaccharides : Every baby needs a sugar mama. 2012;22:1147–62.
  4. Dominguez-bello MG, Godoy-vitorino F, Knight R, Blaser MJ. Role of the microbiome in human development. 2019;1–7.
  5. Tun HM, Konya T, Takaro TK, Brook JR, Chari R, Field CJ, Guttman DS, Becker AB, Mandhane PJ, Turvey SE, et al. Exposure to household furry pets influences the gut microbiota of infants at 3-4 months following various birth scenarios. Microbiome. Microbiome; 2017;5:1–14.
  6. O’Toole PW, Jeffery IB. Gut microbiota and aging. Science. 2015.
  7. Biology H, Ruggles K V, Wang J, Volkova A, Contreras M, Noya-alarcon O, Lander O, Caballero H, Dominguez-bello MG. crossm Changes in the Gut Microbiota of Urban Subjects during an Immersion in the Traditional Diet and Lifestyle of a Rainforest. 2018;3:1–8.
  8. Bae J. Prophylactic efficacy of probiotics on travelers ’ diarrhea : an adaptive meta-analysis of randomized controlled trials. 2017;10–3.
  9. Mailing LJ, Allen JM, Buford TW, Fields CJ, Woods JA. Exercise and the Gut Microbiome : A Review of the Evidence , Potential Mechanisms , and Implications for Human Health. 2019;75–85.
  10. Metagenomic AP. crossm A Prospective Metagenomic and Metabolomic Analysis of the Impact of Exercise and / or Whey Protein Supplementation on the Gut Microbiome of Sedentary Adults. 2018;3:1–17.

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