What is the Microbiome?

The microbiome is one of the hottest areas of scientific and medical research right now. What is the microbiome? This refers to the colonies of bacteria living both on and in humans. Sound scary? It shouldn’t, and if it does sound scary to you then you have probably been influenced by the ‘sterilize everything’ mindset that dominates modern America. It turns out that bacteria on and in our body – our microbiome – outnumber cells in the human body 10 to 1. If we measured all the DNA that makes “us”, the majority of it would not be our own DNA, but rather that of a wide variety of bacteria. These bacteria live on our skin, in the corners of our eyes, in our mouths, under our fingernails, and most importantly – in our guts. And here’s what science and medicine are now becoming fully aware of: this is true for healthy people. In fact, it seems one cannot be healthy without the right mix of bacteria in their microbiome. But because of the level to which people attempt to live an excessively sterile lifestyle, as well as the overuse of antibiotics, research is uncovering a connection between the condition of our microbiome and chronic disease of both body and mind.

The next time you look in a mirror, think about this: In many ways you're more microbe than human. There are 10 times more cells from microorganisms like bacteria and fungi in and on our bodies than there are human cells. But these tiny compatriots are invisible to the naked eye.

National Institute of Health – Human Microbiome Project

The National Institute of Health created the Human Microbiome Project beginning in 2005. It was designed as a community resource program, which is defined as a research project “whose primary utility will be as a resource for the scientific community” (Fredricks, p. 8). One difficulty faced in this project is that not all microbes are able to be cultured in a petri dish (Fredricks, p. 9). With 40% of human associated microbes believed not to be in culture, the Human Microbiome Project is dedicating a significant portion of the project to creating new technology in order to isolate this last group of microbes that are currently unable to be isolated for study (Fredericks, p. 23).


Treating the Microbiome to Cure Disease

One main area of research in this project is the search for correlations between microbe communities and disease. Early findings indicate that this can be found. Correlations between microbial communities and:

·       Neonatal Enterocolitis (Necrotizing Enterocolitis)

·       Esophageal Adenocarcinoma (Esophageal Cancer)

·       Ulcerative Colitis ( a type of Irritable Bowel Disease)

·       Crohn’s Disease (a type of Irritable Bowel Disease)

·       Eczema (Dermatitis)

seem to be indicated (Fredericks, p. 17). There is particular focus on finding specific microbial species or groups that precede the disease state, meaning that they are present before the appearance of a disease and therefore are a possible cause of that disease. This is particularly true concerning cancer. Preliminary findings indicate that the microbiota present in a disease called Barrett’s Esophagus are also the precursor for esophageal cancer (Fredericks, p. 21).

Why This Subject is Difficult to Study

Many species of bacteria, specifically those found in the human microbiome, are resistant to isolated petri dish cultivation. They can be successfully cultivated in association with other microbes, meaning in communities of different bacteria species. But without being able to isolate them research is difficult. That is why work is being done to create new technology in order to study the rest of the human microbiome.

Digestive Ailments and the Microbiome

The human intestinal tract is estimated to contain between 3000 and 5000 different species of bacteria. In a healthy colon these bacteria are separated from the intestinal wall by a lining of mucus, which is bacteria free. Since no eukaryotic organism – this includes plants, animals, and fungi – can digest plant cellulose, the prokaryotic organisms – all bacteria – in our colon are necessary for this purpose (Fredricks, p. 211-212). Without them we cannot digest plant fiber at all.

Again, bacteria are supposed to be in our intestines. But not, however, in the mucus lining of our intestines. In the case of inflammatory bowel disease there is a break in the protective mucus lining the large intestine in nearly all patients. This is believed to be a cause of the disease, at least in many cases. Sometimes bacterial populations are found to be present in the mucus itself. Bacterial populations have also been found within the mucus of 60% of patients with acute diarrhea, 52% with diverticulosis, 45% with carcinoma or polyps, and 38% with irritable bowel syndrome (Fredericks, p. 236-237). This is because either a poor diet or the use of antibiotics has disturbed the microbiome in the intestine and allowed undesirable populations of bacteria to proliferate.

The Hygiene Hypothesis – Are We Too Clean?

The 20th century has seen a steady rise in inflammatory bowel diseases, especially Crohn’s disease and ulcerative colitis. Strangely, it disproportionately affects the developed world, especially those with the highest living standards. There is a proposed reason for this, known as the “hygiene hypothesis”. Basically it proposes that when a person is raised in too sterile an environment and lack exposure to a wide variety of environmental microbes, their immune systems become over-sensitized and eventually have excessive reactions to harmless bacteria (Fredericks, p. 238). An alternative to this hypothesis, or it could be thought of as a variation, is that the mucus barrier in our intestines is effected by detergents from soaps, shampoos, laundry detergent, etc. that find their way into our intestines eventually because of their widespread use. In mice, dextran sodium sulfate has been found to induce acute colitis (Fredericks, p. 240).


Modern medical research is now taking the use of probiotics as a treatment for physical and mental health quite seriously. The accepted definition of probiotics is that they are “living microorganisms, which upon ingestion in adequate amounts exert health benefits beyond inherent general nutrition” (Fredricks, p. 317). Much research has indicated their use as quite successful in treatment for a variety of diseases and disorders. Unfortunately in the case of Crohn’s disease, an effective probiotic is yet to be found. There is even indication of some probiotics causing the condition to worsen. Hope is not lost for the discovery of an effective treatment in this disease, but it is yet to be found (Fredricks, p. 318). This is a clear testament to a necessary outlook concerning probiotics, which is to avoid the simple-minded and misguided thinking that probiotics are inherently good in virtually all circumstances. Care must be taken with the recommendation and use of them, and information that becomes available via research should be kept up with. The benefits seem wide in scope and powerful in effectiveness, but not universally so; to assume so would be negligent.

Use of Probiotics in Pill Form

Probiotics, in a pill form isolated from food, have been found to successfully treat or prevent relapse in:

·       Ulcerative Colitis

·       Pouchitis

·       Irritable Bowel Syndrome

·       Antibiotic-associated Diarrhea

·       Acute Gastroenteritis

·       Constipation

They have been shown to reduce instances of allergy-related diseases such as atopic dermatitis, though the results have been inconsistent and more research is needed. Probiotics have been shown to support immune function in elderly people (Fredricks, p. 324).

What Are Prebiotics?

Aside from probiotics there are things called prebiotics. These are defined as “a nonviable food component that confers a health benefit on the host associated with modulation of the microbiota… thus, a prebiotic is not an organism or a drug, but it is a substance that can be characterized chemically so that in most cases it will be a food-grade material.” Basically prebiotics are the fiber in foods such as whole wheat and broccoli.

The health benefits associated with consumption of prebiotics are positive influence on:

·       Laxation (bowel movement)

·       Mineral Absorption

·       Potential Anticancer Properties

·       Lipid Metabolism

·       Anti-inflammatory Properties

(Fredricks, p. 325).

Have You Heard of Synbiotics?

Prebiotics and probiotics have led to the concept of synbiotics, which are simply a combination of both probiotics and prebiotics. The thinking is that the prebiotic should assist the probiotic to establish in the gut (Fredricks, p. 327). This sounds a whole lot like pickled – through an authentically fermented process of course –  vegetables to me. Foods that contain high levels of inulin and FOS, or fructo-oligosaccharides, include asparagus, burdock, chicory, dandelion root, Jerusalem artichoke, leeks and onions. Foods with galacto-oligosaccharides include legumes and cruciferous vegetables such as broccoli, brussels sprouts, cabbage, cauliflower, collard greens, kale, radish and rutabaga (Amerman, par. 4).

Pickled Asparagus

Asparagus is quickly becoming one of my favorite pickled vegetables. It seems as though it may be a powerful synbiotic when eaten as a fermented food. It makes a great pickled food, retaining a satisfying crunchy texture and taking on a delicious sour flavor. Research on synbiotics has actually found preliminary evidence that they can be useful in treating Crohn’s disease, where probiotics alone were not (Fredricks, p. 238). It would be nice to see more research on the effects of fermented foods as opposed to isolated probiotics and manufactured synbiotics. I think we will find that many fermented foods simply contain the things we need to positively affect our digestive tract already together.

We Should All Be Eating Probiotic Fermented Foods!

Michael Pollan tells us in his book Cooked that the root cause of many or perhaps most chronic disease is inflammation, which he defines as “a heightened immune response by the body to a real or perceived threat” (Pollan, 2014, p. 334). Perhaps our problem is that we have a new diet in the west that is geared toward feeding one organism, the human, when really we are a super organism consisting of thousands of species. He lists an impressive list of known benefits for probiotics:

·       Calm the Immune System

·       Reduce Inflammation

·       Shorten the Severity of Colds in Children

·       Relieve Diarrhea and Irritable Bowel Syndrome

·       Reduce Allergic Responses, Including Asthma

·       Stimulate the Immune Response

·       Possibly Reduce the Risk of Certain Cancers

·       Reduce Anxiety

·       Prevent Yeast Infections

·       Diminish Levels of E. Coli in Cattle and Salmonella in Chickens

·       Improve the Health and Function of the Gut Epithelium

The mechanism by which they accomplish all of this, however, is unknown. Only occasionally do they actually colonize our gut. L. plantarum, the bacteria that dominates the last stage of vegetable fermentation, does take up residence and creates a barrier between food being digested and the wall of the intestine. But many others only pass through (Pollan, 2014, p. 335-336).

Our gut is becoming known as our “second brain” to the medical community. It’s health depends on a healthy microbiome, and it seems that fermented foods go a long way toward creating that healthy microbiome.

Fermented Foods Can Heal Your Mind

In a paper published this past January called “Fermented Foods, Microbiota, and Mental Health: Ancient Practice Meets Nutritional Psychiatry“, the authors basically lay out a synopsis of the most current research regarding fermented foods, the microbiome, and their effect on human health (particularly mental health). They lay out the problems with the modern western diet being high in sugar and saturated fat. It is implicated in causing the deterioration of the mucus membrane in our intestines, and with contributing to depression. Ingestion of probiotics, especially in fermented foods, is found to cause significant improvements in depression, anger, anxiety, and levels of stress hormones.

So to recap, chronic inflammation may be caused by our modern western diet, and is implicated in depression and other psychological conditions. This is related to the conditions in out microbiome, which are affected by the poor diet. Consuming fermented foods has been clearly shown to reduce inflammation, and produce an overall improvement in mental state for people consuming them (Selhub, et. al.). The point of this magnificent paper was to highlight the possibilities in this field, how strong they are, but yet how little is still known compared to the possibilities, and to call for a convergence of the research fields of microbe-nutrition and gut-brain research. I think they have made a compelling case. However it seems to me that often areas of research like this go unfunded, as there is no clear benefactor in a capitalist or investment sense. This is probably why there is more research concerning isolated probiotic pills in this field than there is concerning the heath benefits of fermented foods, as no industry wants to stand up and fund this research.



Amerman, Don. “Examples of Prebiotic Foods.” Healthy Eating. N.p., n.d. Web. 12 May
2014. <http://healthyeating.sfgate.com/examples-prebiotic-foods-1516.html>

Fredricks, David N., ed. The Human Microbiota: How Microbial Communities Affect
Health and Disease. Hoboken, NJ: Wiley-Blackwell, 2013. Print.

Pollan, Michael. Cooked: A Natural History of Transformation. USA: Penguin Group,
2013. Print.

Selhub, Eva M., Alan C. Logan, and Alison C. Bested. “Fermented Foods, Microbiota,
and Mental Health: Ancient Practice Meets Nutritional Psychiatry.” Journal of
Physiological Anthropology 33.1 (2014): 2. Print.


Illuminated Brain: http://organichealth.co/fermented-foods-feeding-your-second-brain/

Asparagus: Brian Lyman