Food and Behaviour Research

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28th May 2013 - New York Times - Some of My Best Friends are Germs

Michael Pollan

FAB RESEARCH COMMENT:

In this comprehensive but highly readable article, Michael Pollan explores the extraordinary complexity of the huge populations of bacteria that all of us carry, and what their diversity (or lack of) might mean for our health and wellbeing.

In addition to raising further concerns about the overuse of antibiotics (both in medicine - and more controversially, in standard farming practices in most developed countries), this carefully researched article emphasises how much difference we can make to our own 'microflora' - not only by our habits of personal hygiene, but very importantly, by the foods we choose and the overall pattern and type of diet we consume.

Research in this area is still very much in its infancy - and the sheer complexity of the human 'microbiota' and 'microbiome' makes it highly unlikely that scientists will ever be able to predict, let alone to control, all of the variables that really matter in this domain. Nonetheless, it is increasingly clear that the microbes we coexist with can and do shape the health and functioning of our guts, immune systems and brains (which are of course themselves highly interconnected).

As many of the commentators to this article have pointed out - this knowledge is not in fact new - and it has formed the basis for many traditional dietary practices such as the fermentation of foods, or the use of meat stock or 'broth' to support gut and immune system health. Until recently, however, it has been largely ignored by mainstream medicine. The researchers cited in this article are sensibly very cautious about where this kind of work will lead - but meanwhile, their findings already give plenty of food for thought.

  • And for further information on the potential links between diet and various psychological disorders, see Gut And Psychology Syndromes by Natasha Campbell McBride.  This book has served to popularise a version of the so-called 'Specific Carbohydrate Diet' that was first developed in the US to 'heal the gut' and help combat various auto-immune disorders affecting the gut, including both coeliac disease and Crohn's disease.

I can tell you the exact date that I began to think of myself in the first-person plural — as a superorganism, that is, rather than a plain old individual human being. It happened on March 7.

That’s when I opened my e-mail to find a huge, processor-choking file of charts and raw data from a laboratory located at the BioFrontiers Institute at the University of Colorado, Boulder. As part of a new citizen-science initiative called the American Gut project, the lab sequenced my microbiome — that is, the genes not of “me,” exactly, but of the several hundred microbial species with whom I share this body.

These bacteria, which number around 100 trillion, are living (and dying) right now on the surface of my skin, on my tongue and deep in the coils of my intestines, where the largest contingent of them will be found, a pound or two of microbes together forming a vast, largely uncharted interior wilderness that scientists are just beginning to map.

I clicked open a file called Taxa Tables, and a colorful bar chart popped up on my screen. Each bar represented a sample taken (with a swab) from my skin, mouth and feces. For purposes of comparison, these were juxtaposed with bars representing the microbiomes of about 100 “average” Americans previously sequenced.

Here were the names of the hundreds of bacterial species that call me home. In sheer numbers, these microbes and their genes dwarf 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.

Justin Sonnenburg, a microbiologist at Stanford, suggests that we would do well to begin regarding the human body as “an elaborate vessel optimized for the growth and spread of our microbial inhabitants.” This humbling new way of thinking about the self has large implications for human and microbial health, which turn out to be inextricably linked.

Disorders in our internal ecosystem — a loss of diversity, say, or a proliferation of the “wrong” kind of microbes — may predispose us to obesity and a whole range of chronic diseases, as well as some infections. “Fecal transplants,” which involve installing a healthy person’s microbiota into a sick person’s gut, have been shown to effectively treat an antibiotic-resistant intestinal pathogen named C. difficile, which kills 14,000 Americans each year. (Researchers use the word “microbiota” to refer to all the microbes in a community and “microbiome” to refer to their collective genes.)

We’ve known for a few years that obese mice transplanted with the intestinal community of lean mice lose weight and vice versa. (We don’t know why.) A similar experiment was performed recently on humans by researchers in the Netherlands: when the contents of a lean donor’s microbiota were transferred to the guts of male patients with metabolic syndrome, the researchers found striking improvements in the recipients’ sensitivity to insulin, an important marker for metabolic health. Somehow, the gut microbes were influencing the patients’ metabolisms.

Our resident microbes also appear to play a critical role in training and modulating our immune system, helping it to accurately distinguish between friend and foe and not go nuts on, well, nuts and all sorts of other potential allergens. Some researchers believe that the alarming increase in autoimmune diseases in the West may owe to a disruption in the ancient relationship between our bodies and their “old friends” — the microbial symbionts with whom we coevolved.

These claims sound extravagant, and in fact many microbiome researchers are careful not to make the mistake that scientists working on the human genome did a decade or so ago, when they promised they were on the trail of cures to many diseases. We’re still waiting. Yet whether any cures emerge from the exploration of the second genome, the implications of what has already been learned — for our sense of self, for our definition of health and for our attitude toward bacteria in general — are difficult to overstate. Human health should now “be thought of as a collective property of the human-associated microbiota,” as one group of researchers recently concluded in a landmark review article on microbial ecology — that is, as a function of the community, not the individual.

Such a paradigm shift comes not a moment too soon, because as a civilization, we’ve just spent the better part of a century doing our unwitting best to wreck the human-associated microbiota with a multifronted war on bacteria and a diet notably detrimental to its well-being. Researchers now speak of an impoverished “Westernized microbiome” and ask whether the time has come to embark on a project of “restoration ecology” — not in the rain forest or on the prairie but right here at home, in the human gut.