The Human Food Project

What is a ‘healthy’ or ‘normal’ microbiome? What should I eat to improve the health of my microbiome? With our ancestral diet and lifestyle as a guide, the Human Food Project is an ambitious effort to define how ‘normal and healthy’ can be achieved in our modern world.


The recent flurry of papers summarizing the NIH’s 5-year, $170-million Human Microbiome Project (HMP) will likely mark a turning point in modern medicine. This “micro” revolution is revealing the symbiotic relationship we co-evolved with the trillions of bacteria (microbiota) in our gut, and the role they play in just about every disease known to humanity. Pick an ailment, such as obesity, diabetes (type 1 and 2), some cancers, celiac disease, asthma, heart disease, and any number of of scientists will likely show that an imbalance (dysbiosis) in your microbiome (the aggregate collection of genomes and genes in a gut microbiota) may have something to do with it.

Human Food Project

However, though the HMP characterized and monitored the changes in the microbial communities of 242 healthy people over two years, providing an extraordinary glimpse into the microbial wonderland that is the human body (inside and out), it likely did not truly capture what a “normal” or “healthy” microbiome is, or might be. By this I mean the study volunteers were living a westernized lifestyle and probably eating a great many more processed and easily digestible carbohydrates than were present on the ancient nutritional landscape that selected for our current microbiome. In addition, the vast majority of the study participants were likely consuming less protein and good fats than our ancient microbiome was selected and the diversity and quantity of dietary fiber (oligo- and polysaccharides) was probably so low (<20g a day, on avg) as to not even register on our evolutionary radar.

The macronutrient composition of our so-called modern diet is different in some significant ways from the evolutionary diet that conditioned much of the symbiotic relationship and community membership with our microbiome (this is, after all, what is contributing to the imbalance and increase susceptibility to disease in the first place). The role of diet in gut composition, to say nothing of the impact of modern birthing methods (caesarian vs natural), decreasing rates of breast feeding over the last few decades, hyper-hygiene, overuse of antibiotics in medicine and in the food supply, is well-established.

So wouldn’t it be interesting if we could get a glimpse of what our microbiome might look like if we removed our westernized diet, and even lifestyle all together. Recent studies, such as those comparing the gut microbiome of traditional peoples in Burkina Faso to westernized Italians, and the gut microbiome of modern Americans to Amazonas of Venezuela and rural Malawi, reveal that while geography and genetics are important, diet is very important. This is where the Human Food Project comes in.

Human Food ProjectIn late 2011 we visited San villages in Southern Africa to collect feces in order to get some idea of what – if any – the impact of globalization has had on the gut microbiology of the San. On one end, many San were fully westernized (e.g., sugary drinks, highly processes grains, alcohol), and on the other end of the gradient we visitted a small San village that was still meeting the a majority of their subsistence needs from hunted & foraged resources. With the help of the good folks in the Knight Lab at the University of Colorado (and University of Puerto Rico [454Sequencer and Illumina MySeq ]), we were able to get the initial San feces samples included and analyzed (16S ribosomal RNA) as part of the Earth Microbiome Project. We are currently analyzing the data.


For updates on the project, follow us on Twitter or Facebook or sign-up for e-mail alerts below.


Next steps:

[button link=”” type=”small” color=”green”] Read more about Australian Outback[/button]

[button link=”” type=”small” color=”green”] Read more about Hunter-Gatherer Namibia[/button]




One Comment Add yours

Leave a Reply