The Post Pasteurian Era: A broader approach to nuturing our microbiome

It is challenging to know which way to turn, but there are some solid nutritional recommendations to support nurturing our microbiome,

Interest in the role of bacteria and our health exploded once scientists mapped the human microbiome in 2013. Humans co-evolved with microbes, so it follows that microbes impact everything from immune function to metabolism, even mental health.

Today researchers and scientists press to understand why and how microbial organisms influence health and disease. Despite a history tracing back to Louie Pasteur’s work in the mid 1800’s, most researchers qualify their findings as preliminary. Welcome to the Post Pasteurian Era.

What we do know is that microbes colonize every nook and cranny in our body with about 10x more cells than our own. Our intestines harbor quantities that are hard to comprehend, estimated at 1 trillion organisms in every gram of gut contents. 1 (about 5 grams fit into a teaspoon)

The Ancients Relied on Microbes to Preserve Their Food and Their Health

Ironically the most ancient means of preserving food uses the action of microbes to render food safe without refrigeration. Fermentation improves the taste and texture of food, and can even make it more nutritious. Many cultures around the world, as well as the Weston A. Price Foundation, support a healthy gut with time tested fermented foods and a host of other traditional foods, including the consumption of raw milk.

The production of raw milk cheese and the consumption of raw milk draws intense scrutiny and sharp rebuke from the FDA and the CDC. Conventional food safety experts consider the presence of microbes a health risk. But warnings have failed to stem consumer demand, and a noted expert in the field insists, “Pasteurization is an 18th century solution to an 18th century problem and we can do much better.”

To date we have far more questions than answers regarding the impact of our diet and the microbiome, frustrating consumers and clinicians alike. We simply do not have research to substantiate what cultures have practiced for thousands of years. Figuring out how to do the research seems to be the first challenge to nurturing our microbiome.

What Makes Researching Microbes Different?

Microbes are promiscuous. They share genes like addicts share needles. Researchers are befuddled enough to suggest that maybe they should categorize bacteria by function rather than more traditional bacterial taxonomy. The International Scientific Academy of Probiotics and Prebiotics (ISAPP) suggests that it is possible to categorize gut microbes depending on whether they exert potentially pathogenic or health promoting aspects.

At any rate, when executing research scientists will be challenged to minimizes contamination of any studied specimens. Scientists will have to figure out how to contain bacteria, virus, fungi and other microscopic organisms and keep them from sharing genes during the process in order to identify exactly what they are studying.

More Disease, More Distress

In the meantime, people are suffering and families search for remedies. Escalating rates of infection with resistant bacteria and exploding incidence of an incredibly wide range of diseases and conditions has everyone considering what has changed, and what could create a healthier microbiome.

The question is especially piercing as parents and pediatricians grapple with more allergy and asthma, more symptoms of gastro-intestinal distress such as constipation, diarrhea, leaky gut and irritable bowel syndrome, as well as what may or may not be gluten intolerance. Increasing incidence of autism and developmental delay, as well as behavioral and mental health challenges confound us as well.

Not Waiting for All the Research

In the void, all sorts of dietary regimens and nutritional recommendations prevail. The internet has become a mind boggling mix of medical research and mythology. Clinicians, celebrities and consumers alike experiment and report improvement in their child’s condition, with many claiming cure. Trying to sort through the information can be exhausting.

It is challenging to know which way to turn, but there are some solid nutritional recommendations to support a healthier microbiome, and a few provocative options to consider, as well.

Dietary Approaches to Heal the Gut — And Possibly Much More — By Nurturing the Microbiome

1. Whole Foods

Ideally the most basic approach to a healthy gut involves eating a balance of whole foods. A meal based approach to food includes enough protein, adequate fat and abundant plant foods. Ideally both plant foods and animal products are sustainably raised. Start by offering small children one tablespoon of a protein rich food, 1 T. of fruit or vegetable, and 1 T. of a starchier food like beans or winter squash for every year of age.

Let your child’s plate look a whole lot like yours. A good enough mix of food supports a stable blood glucose level, and tames a cascade of hormones that influence energy metabolism.

What we eat feeds the microbes we host. Gut bacteria influence communication between the gut and brain via the vagal nerve.2 A good enough mix of microbes can effectively cue hunger and satiety, and calm a host of problematic behaviors.

2. More Fiber and Resistant Starch

Typical advice to support a healthy microbiome involves eating more whole foods rich in fiber and resistant starch. These foods are digested by our gut bacteria and can be considered “probiotics” in their own right, resulting in an abundant source of short chain fatty acids.

Short chain fatty acids help to maintain the integrity of the gut mucosa and support a healthy immune system. This is usually a good thing, but not always. Consumers are often encouraged to experiment with their own diet, but some caution is advised. (see the FODMAP diet below)

3. The FOODMAP Diet 

Some individuals find relief from gastrointestinal distress by avoiding resistant starch and high fiber foods–exactly those foods that are often recommended to feed a healthy microbiome. The FODMAP diet basically instructs consumers to eliminate or limit specific short chain carbohydrates that are often poorly digested. Many fruits, vegetables, beans and legumes are avoided to minimize distress.

Data supporting the FODMAP diet enjoys the distinction of being published in a peer reviewed journal, but the approach basically removes the offending foods without addressing a bigger question. “Is it really that the patients are unable to digest those particular carbohydrates, or is their microbiome contributing to [the problem]?” 3

4. The GAPS Diet

Proponents of the GAPS diet claim remarkable success in healing leaky gut syndrome and a host of maladies associated with compromised digestion. Dr. Natalie McBride promotes a rather specific dietary approach to healing the gut with stages of varying carbohydrate restriction and use of probiotics.

A broad range of practitioners promote the GAPS diet around the world, but there is little offered to the scientific community to validate these claims. The overall approach of the full GAPS diet resembles my advice about eating whole foods, while the Introductory diet is far more restrictive, limiting initial foods to bone broths and animal protein.

5. Buying Organic & Biodynamic

Amid claims that Americans enjoy the safest food supply in the world, some consumers see things differently. Increasingly consumers purchase food that is sustainably grown, minimizing exposure to petroleum based fertilizers, pesticides, herbicides, and antibiotics– despite little scientific data to support this approach to gut health.

Current research documents how biodynamic and more sustainable farming contributes to a healthier microbiome in the soil, in plants and animals. Consumers bank that the same is true for their own guts, and many claim they feel better. We know growing better food is definitely better for the environment.

Scrutinizing Glyphosate

In particular, researchers and consumers alike are scrutinizing glyphosate use in agriculture, the number one herbicide sold in America under the trade name, RoundUp. Use has skyrocketed as more cropland is dedicated to GMO crops, and weeds are increasingly resistant to the herbicide. In addition, about 10 years ago the EPA determined farmers could safely spray glyphosate directly onto wheat and barley several days before harvest to protect crop yields.

Today we can measure glyphosate residue in foods, and levels can be measured in both urine and breast milk. The presence of glyphosate in body tissues is especially disturbing because scientists claimed that glyphosate is readily metabolized and/or excreted from the body.

Provoking Curiosity

Glyphosate functions by interrupting an enzymatic pathway that exists in plants and some microbes. Two scientists link increasing rates of many diseases to increased use of glyphosate in agriculture, drawing intense criticism from the scientific community. Certainly correlation does not establish causation, but it should provoke curiosity.

Glyphosate was approved before we appreciated the role of the gut microbiome. We need to learn if residues of glyphosate–or any other chemical agent for that matter–play a role in compromising gut health, immune function, and a host of other metabolic functions expressly because it has the potential to compromise gut microbes.

With so many different ways to eat, is there any one approach to food that helps keep your gut healthy?


1. Gibson,GR, Roberfroid M. Dietaqry modulation of the Human Colonic Microbiota: Introducing the Concept of Probiotics. The Journal of Nutrition. 1995: 1401-1412.

2. Forsythe P, Kienenstock J, Kunze WA. Vagal pathways for microbiome -brain-gut axis communication. Adv Exp Med Biol. 2014;817:115-33.

3. Yeager D. Mapping the Gut Microbiome. Today’s Dietitian. September, 2014: 12-14.

Published on: March 13, 2015
About the Author
Photo of Bonnie Modugno MS RD

Bonnie is a registered dietitian in private practice specializing in energy metabolism, sport nutrition, maternal, infant and child nutrition. You can find more from Bonnie on her blog and on Twitter as @MoreThanFoodInc.

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