Your primitive brain – your gut

by Catherine Haug, July 25, 2013, updated July 29,2013

In college I took a class on comparative vertebrate anatomy – we studied the anatomy of many vertebrates as a way of better understanding our own anatomy. This study began with the tiny fertilized egg of each species studied, and progressed through the development of the adult. One of the things I took home from this class is that the first organ to form is the gut, and it serves as the brain for the developing individual while the heart and circulatory systems form, and finally the central nervous system (CNS) and the brain. But we also learned that the primitive brain in the gut continues to function in intimate contact with the actual brain, throughout the life of the individual.

What does this mean for us humans? It means that while modern medicine has pretty much ignored the effect of the gut on human health and happiness, the gut deserves more study and respect. We need to ensure that our gut has healthy colonies of gut flora (probiotics), and that it is not overburdened with toxins in our food.

It is important to remember that diet and gut health are not the only factors that influence the overall health and longevity of a human individual, but it may well be one of the most important. Other factors include (but are not limited to) genetics, lifestyle and stressors (7), medical care, gender, accident, and environment.

The importance of gut bacteria on physical and mental health

In the last few years, science has discovered the role of gut bacteria and its effect on health. We now know that these bacteria provide a majority of our immune system – they are our first line of defense against pathogens. When they are compromised, our health suffers, and the communication between our primitive brain and our CNS brain becomes compromised. And this can lead to anxiety, depression, neurological disease, and reduced brain function. It may also affect metabolic function.

There is an emerging consensus amongst researchers and practitioners that most disease (including conditions that impact your brain, heart, immune system and body weight, among others) originates in your digestive system. Furthermore, there is evidence that your personal gut flora can affect how well you age. 

It is known that the composition of your gut flora is not static. It changes “profoundly throughout your life, for better or for worse, and one of the biggest influences on this change is your diet.” (6)

A study correlating gut microbes with diet and health in the elderly

A study by M. Claesson et. al., published in Nature on July 13, 2012, and titled Gut microbiota composition correlates with diet and health in the elderly (5), studied the relationship between gut flora (microbiota) and several chronic conditions, including obesity and inflammatory diseases. Fecal microbes from elderly patients divided them into 4 groups by residence location:  the community, day-hospital, rehabilitation, and long-term residential care. Those at the same location had a similar composition of gut microbes.  Clustering the same subjects by diet separated them by the same residence location and microbial groupings.

This study concluded (bold emphasis is mine):

The separation of microbiota composition significantly correlated with measures of frailty, co-morbidity, nutritional status, markers of inflammation and with metabolites in faecal water. The individual microbiota of people in long-stay care was significantly less diverse than that of community dwellers. Loss of community-associated microbiota correlated with increased frailty. Collectively, the data support a relationship between diet, microbiota and health status, and indicate a role for diet-driven microbiota alterations in varying rates of health decline upon ageing.

A study on the effect of a yogurt product on brain activity

Another recent study, Consumption of fermented milk product with probiotic modulates brain activity by Tillisch, et. al., and published in Gastroenterology (3) investigated the effect of consumption of a fermented milk product with probiotic (FMPP) for 4 weeks by healthy women altered brain intrinsic connectivity or responses to emotional attention tasks. FMPP is yogurt with added lacto-bacteria (Bifidobacterium animalis subsp Lactis, Streptococcus thermophiles, Lactobacillus bulgaricus, and Lactococcus lactis subsp Lactis). The study concluded:

Four-week intake of an FMPP by healthy women affected activity of brain regions that control central processing of emotion and sensation.

In his article Are probiotics the new prozac? *(1) that explores the implications of this study, Mercola states:

“There is some truth to the old expression, having ‘dirt for brains’.  The microbes in our soil, on our plants, in our stomachs are all a result of our actions.  Antibiotics, herbicides, vaccines, and pesticides, and the tens of thousands of synthetic chemicals we’ve created all have impacts and result in reactions from these microbes.

…Mounting research indicates the bacterial colonies residing in your gut may in fact play key roles in the development of brain, behavioral and emotional problems—from depression to ADHD, autism and more serious mental illness like schizophrenia.”

*Note that Mercola’s article, in part, is based on another article by Lisa Collier Cool, Are Probiotics the New Prozac? (2)

In other words, the health of our brain, central nervous system,  gut and its flora, is directly related to the health of the things we put in our body (food, medicine, preventive medicine), our soil and our water. The way we treat our soil has a direct effect on our health, just as the way we treat our bodies has a direct effect on our health.

What does dirt/soil have to do with gut health?

Good soil is rich in much the same bacteria and other micro-flora as found in a healthy gut. The plants that grow in this soil take up these flora and the nutrients they provide. Note that these are provided in a form that is readily assimilated by the plants; this is not the same, often ineffective form provided by synthetic fertilizers.

Then the animals (and humans) who eat these plants grown in rich, naturally fertile soil take up the nutrients and flora from the plants. When we eat the meat or other products from these animals, we benefit, just as we benefit by eating the plants directly.

As Michael Pollan puts it, “It isn’t just what we eat, but what we eat eats.

Keeping your primitive brain happy and healthy

[NOTE: the following is a discussion of dietary changes you can make to improve the health of your gut and its flora (primitive brain). Please remember that adopting these changes may not necessarily improve your overall health or longevity. As I mentioned in the introduction to this article, there are many other factors that affect your health and longevity.]

Probably the most important dietary thing you can do is give up processed food. Buy only single-ingredient foods and beverages – fresh produce, nuts and legumes; fresh meat, dairy, and eggs; whole grain berries that you grind yourself. Then do your own processing – sprouting, cooking, baking, roasting – or eat it raw.

No, that box of breakfast cereal is not a single ingredient food. Neither is that frozen TV dinner or fried chicken at the deli counter. Nor that box/bottle of orange juice in the refrigerator section. Nor that package of Oreos.

It’s also important to know the quality of the single-ingredients you buy.

  • Buy your meat from a local farmer/rancher who raises and finishes his livestock on pasture and doesn’t regularly treat them with antibiotics or antibiotic-laced feed.
  • Buy your milk from a local farmer/homemaker who feeds the cows in pasture, not grain/soy feed.
  • Buy your eggs from a local farmer/homemaker who lets the hens roam in pasture.
  • Grow your own produce as much as possible, and supplement with produce from a local CSA or farmers market. If you must buy produce in a store, buy Organic; it may cost a bit more but it will save you big health bucks in the long run.

Reduce your sugar intake. And by sugar I mean sugar, honey, maple syrup, fructose, glucose, HFCS and artificial sweeteners. If you must have sweet, use real stevia (either the dried herb, liquid extract, or powdered extract); I don’t recommend the stevia-derived sweeteners like Truvia, as they are processed and altered after being extracted from the stevia leaf.

However, if your gut flora are already compromised, consider supplementing with sweet dairy whey. This is a minimally processed byproduct of cheese making, and is rich in lactose, which is a primary food of  lacto-bacteria such as acidophilus and bifidus that are a large part of your gut flora, and are also present in yogurt and cheese.

Eat traditionally lacto-fermented veggies and fruits: real sauerkraut, kimchi, fermented milk (yogurt, kefir, cheese), kombucha, kvass, rejuvelac, and natto (fermented soy). These are best if you make them yourself.

Fermented fruits and veggies should be eaten in small quantities – as a condiment. These good things come in small doses.

By the way, if you make your sauerkraut and other fermented veggies the traditional way, but then replace the brine with vinegar and then can it, that fermented food no longer provides the same health benefit because the live fermenting bacteria have all been destroyed. Traditionally fermented foods will keep in a cool place for a year or more, provided they are always covered by the brine.

Take a high-quality probiotic supplement especially if your gut flora are compromised, or if you do not eat traditionally fermented foods on a regular basis.

Don’t overeat. It is best to eat slowly and chew your food well. Stop eating at the first sensation of satiety. Overeating compromises your gut and can result in sluggish digestion and fermentation.

Don’t pollute your gut with an excess of alcohol. A single glass of wine, beer  or cider with a meal is healthful, especially if it is not pasteurized. But drinking enough to get high or dull your senses is not a good thing.

For more information

Other articles on The EssentiaList


  1. Are probiotics the new prozac: Brain Gut Connection(
  2. Are Probiotics the New Prozac? (
  3. Gastroentorology 2013 Jun;144(7):1394-1401 (find on
  4. WebMD: Sweetened Drinks Linked to Depression Risk (
  5. Nature: Gut microbiota composition correlates with diet and health in the elderly
  6. Mercola: What Is the Role of Gut Bacteria in Calorie Restriction?
  7. NY Times Opinionator: Status and Stress by Moises Velasquez-Manoff 

Comments are closed.