Real Fermenting: Our Microbiome

Friday, 27 July 2012

Our Microbiome

We have all been trained from an early age to be scared of microorganisms. We know to wash our hands and to cook our food thoroughly and to throw out moldy cheese. I can remember from around the age of 10 struggling with an overly developed sense of contamination. I thought that bacteria or whatever could quickly travel from one part of my body to another, so if, say, my elbow touched something gross, I should wash my hands before eating. Everything was dirty by association. At some point, I realized that bacteria couldn't zoom down my arm at the speed of light and so began my critical approach to our modern sensibilities on contamination.

Today, we are learning more every day about the vital role that microorganisms play in our health as humans. In fact, I would question even the extent to which we should call what moves when I take a step a "human".


Our microbiome is all the organisms that live in tandem with the human cells in our body. It is bacteria and fungi and archaea. Each of us carries a microbiome that outnumbers the human cells by 10 to 1, and has somewhere in the order of 100 time more genes than those human cells. All of the organisms together weigh about 3lbs in an adult human. And these aren't measly parasites, living off of our hard work. More and more we are finding their worth to our health: digestion, immunity, cancer prevention, even cognition. Each of these vital systems has our microbiome as an essential part. Our microbiome represents a distributed organ.

Modern life is not designed to support our microbiome. We are pumping antibiotics into our bodies, excessively in medicine and ubiquitously in agriculture. Doctors prescribe antibiotics for the common cold and flu - viruses which have no chemical response to antibiotics - because they won't spare the time to talk to their patients. Industrial beef farmers have to give their herds antibiotics; the extreme concentration of animals, combined with the perversion of their natural diet, has led to dangerous pathogens spreading from cattle to consumer.
pic 5476
Cows in containment

It is well and good to use antibiotics selectively if you need to, and if the situation cannot be avoided. But, antibiotics are not selective. They disrupt the healthy balance of our bacteria. The overuse of antibiotics in children has been shown to be associated with obesity, auto-immune diseases and other problems related to microbiome disruption. By the way, (Type I) diabetes is an auto-immune disorder. What we need to think about is supporting our microbiome while we attempt to destroy those pathogens threatening us.

So what does our microbiome do for us? From day one, our digestion is supported by microorganisms. In a vaginal delivery, a baby is inoculated by bacteria from its mother's birth canal. There is some suggestion that some of the risk factors coming from a C-section delivery may arise from the poor start to a baby's microbiome that results from being pulled into a sterile operating room. In pregnancy, the flora in the vagina actually changes to favor bacteria that help us digest lactose. After a certain age, most babies (more in non-dairy cow using cultures) start to become lactose-intolerant. Our gut flora, properly maintained, can help us to overcome this intolerance.  I am not personally a big champion of maintaining a milk intake, but if you are, simply eating a live yogurt helps, both by predigesting the lactose by 25-50% and by its probiotic effect.
Making yogurt...
Making yogurt at home
A healthy microbiome in the gut form a protective barrier against pathogens. Resident microorganisms help our body to distinguish and target precancerous cells in the colon. Our immune system is trained by our microbiome. Bacteria in our gut break down parts of our food that would otherwise be unavailable to us as energy. Finally, studies have shown that there are psychological effects to a healthy microbiome.

What can we do to help? Probiotics are any living organisms that we consume that have beneficial effects on our health. Yogurt I have already mentioned, and is popularly used to aid digestive function. Sauerkraut, miso, kombucha and any other fermented products are going to contain probiotics. The same bacteria and fungi that create the wonderful and delicious changes during the fermentation process continue to live on inside of our bodies. Many of the recipes on this site contain billions of wild microorganisms, and they are much cheaper than the probiotic pills and powders available in stores. However, pills and powders are also a great option, and they can be very selective about which bacteria they are delivering.

Babies who have to drink formula have less cases of diarrhea if that formula is supplemented with probiotics. Probiotics can also be used as a treatment for diarrhea, and can shorten bouts by 24 to 30 hours. They can treat rotavirus and help to reduce the extent to which a carrier passes it on. Certain cases of eczema have been successfully treated with probiotics (cow's milk allergy related ones).

And the side effects of this highly effective medicine? Well, for the foods, basically none. Some people don't like the taste of sauerkraut, but those people should really try making their own. Some people report some digestive discomfort when starting high dosages of probiotics, but that can be avoided by gently increasing your dosage over time.

I think the key take away is to respect your microbiome. Treat it like you would any other organ. If you drink too much you damage your liver; if you take too many antibiotics you'll damage your microbiome. Some people might take herbal supplements to support their kidneys; others need to supplement the microbiome with probiotic pills or foods. Do not ignore your microbiome until it is too late.

Gut flora in health and disease, by Francisco Guarner and Juan-R Malagelada. In The Lancet 2003; 361: 512–19

How Bacteria Communicate, TED video by Bonnie Bassler

Meet Your Microbes, TED video by Jonathan Eisen

No comments:

Post a Comment