"The living communities within our bodies are our first responders, and their fast adaptive capacity depends a great deal on the diversity of their epigenetic choices."

Yesterday Sandor Katz joined us to combine his knowledge of gastroenteric culture with ours of the soil-food-web to produce a 5-hour seminar we were billing as Fermaculture.

Sandor had many interesting things to say, but one of the more interesting to us was about how bacteria from food — the juicy benefactors we get from fermented wonderfoods — actually perform probiotic functions in our bodies.

We know that in sheer numbers, microbes and their genes vastly outnumber our own genetic material in what we like to think of as “our” bodies, Realistically, we are far more than our flesh (or even our astral energetic bodies or our vibratory quantum self). As Michael Pollan reminds us, “It turns out that we are only 10 percent human: for every human cell that is intrinsic to our body, there are about 10 resident microbes — including commensals (generally harmless freeloaders) and mutualists (favor traders) and, in only a tiny number of cases, pathogens. To the extent that we are bearers of genetic information, more than 99 percent of it is microbial. And it appears increasingly likely that this ‘second genome,’ as it is sometimes called, exerts an influence on our health as great and possibly even greater than the genes we inherit from our parents. But while your inherited genes are more or less fixed, it may be possible to reshape, even cultivate, your second genome.”

According to Sandor, when a foreign bacteria enters your body, it is not necessarily met with a friendly reception, a lot of buddy bacteria backslaps and a toast. More likely it is tracked, attacked, and generally made to feel most unwelcome. That’s because the available niches began being given away in utero, and your body assembled almost all its microbial ecosystem in the first 3 years of your childhood.

Catherine A. Lozupone, a microbiologist at the University of Colorado, Denver, observing that rural people spend a lot more time outside and have much more contact with plants and with soil, says its no surprise that confers a greater diversity of gut bacteria. Also, being raised in extended families and being passed hand-to-hand as an infant may provide a wider range of “host” bacteria and a stronger, more responsive, immune system as an adult.

The American Gut project, which is DNA sequencing the communities of tens of thousands of people, is trying to uncover patterns of correlation between people’s lifestyle, diet, health status and the makeup of their microbial community. Pollan observes:

“Your microbial community seems to stabilize by age 3, by which time most of the various niches in the gut ecosystem are occupied. That doesn’t mean it can’t change after that; it can, but not as readily. A change of diet or a course of antibiotics, for example, may bring shifts in the relative population of the various resident species, helping some kinds of bacteria to thrive and others to languish. Can new species be introduced? Yes, but probably only when a niche is opened after a significant disturbance, like an antibiotic storm. Just like any other mature ecosystem, the one in our gut tends to resist invasion by newcomers.”


Sandor Katz

So how, then, can probiotic fermented foods, like yogurt or pickled bean paste, improve your health? Sandor offered an epigenetic explanation. Rather than being interested in new bacteria taking up residency alongside the established community in your gut, your host bacteria, via the magic of viral gene transfer, are more interested in the new genes that are constantly coming through on parade.

When you were just a zygote – remember that? — totipotent stem cells become the various pluripotent cell lines that allowed you to evolve into an embryo, which evolved fully differentiated cells in much the same way. From a single fertilized egg cell, you developed into a semi-organized collection of neurons, muscle cells, epithelium, endothelium, blood vessels, etc. Switching on an off like the lights on a Christmas tree, your coding activated some genes while inhibiting others. The code did not change, but the gene expression, or replicative (RNA) behavior, did.

An "epigenome" is similar to the word "genome", but referring to the overall epigenetic state of a cell. Where is the switch positioned at this moment?

In general, proteins fold into discrete units that perform distinct cellular functions, but some proteins are also capable of forming an infectious conformational state known as a prion. Prions are infectious forms of proteins.  They are epigenetic change agents. They catalytically convert other native state versions of the same protein to an infectious conformational state. In the context of our immune response, infectiousness is not always a bad thing. It just means that cells switch gene coding to make new versions of cells that may be needed to perform some function. Some food components epigenetically increase the levels of DNA repair enzymes such as MGMT and MLH1 and p53. Other foods components can reduce DNA damage, such as soy isoflavones and bilberry anthocyanins.

Fungal prions are considered epigenetic because the infectious phenotype caused by the prion can be inherited without modification of the genome. PSI+ and URE3, discovered in yeast in 1965 and 1971, are the two best studied of this type of prion. In PSI+ cells, the loss of the Sup35 protein (which is involved in termination of translation) causes ribosomes to have a higher rate of read-through of stop codons, an effect that results in suppression of nonsense mutations in other genes.  The ability of Sup35 to form prions may be a conserved trait. It could confer an adaptive advantage by giving cells the ability to switch into a PSI+ state and express dormant genetic features normally terminated by stop codon mutations.

Another possibility is more intriguing. Sup35 might be produced by prions selecting its code from the available pool of genetic carriers, including foreign bacteria that just happen to be passing through your body, and find themselves in the right place at the right time. Their genes are transcribed, re-encoded, and switched on by your native cells to express just what the body needs at that moment.

The federal Centers for Disease Control is investigating an outbreak in eight states, affecting nearly 300 people, of a stomach illness caused by Cyclospora, the one-celled parasite that causes diarrhea, stomach cramps and other symptoms normally associated with a viral stomach bug. Ten people have been hospitalized this month. Indigenous to the tropics, it is rare that cyclospora would be found so far north, but it is yet one more portent of what we can expect from climate change and global weirding. Niches of some species will expand while niches of others will shrink. We may get pandemics of many new or exotic bugs, and there may be little our bloated, sclerotic, top-down, corporate-captured, financial-house-of-cards-addicted Big Pharma medical system can do to respond in a timely fashion.

The living communities within our bodies are, and always have been, our first responders, and their fast adaptive capacity depends a great deal on the diversity of their epigenetic choices. What gene codes do they have to draw from?

The abilities of our bodies to respond to future threats may come in large measure from our own lifestyle choices, such as a probiotic diet and rural living, and from good plant nutrition, which comes, ultimately, from healthy soil and its diverse soil-food-web biology.