The biggest news in modern medicine is the bacteria in our bodies.

It's suddenly clear how much our health depends on the microbes in our skin, sinuses, and organs … especially the bugs in our bellies.

Your “microbiome” can vary widely, with those variations having profound influence over the health of your digestive and immune systems … and possibly over brain development and weight control.

And if we are what we eat – and we are – new human evidence suggests that may also apply to the microbes in your gut.

A Harvard clinical study shows that dietary changes alter the human gut microbiome (the types and amounts of various microbes in your gut), in as little as a day … with implications for good or ill health.

Changes in what you eat also affect the types of genes “expressed” by gut bacteria, which can greatly influence these microbes' impacts on human health.

Animal studies show that changes to diet can rapidly exert major effects on the microbes that are in the gut (Turnbaugh PJ et al. 2009).

But it wasn't clear how fast the microbes in the human gut respond to changes in diet, and to what degree those changes would be similar in different people.

A new clinical study is the first to prove that, over the course of days, changes in diet can reshape the microbial ecology of the gut.

Importantly, the probe also showed that those changes are reversible, and remarkably consistent in different people.

Food changes the bugs in your gut
Harvard researchers recruited 11 volunteers for the study (David LA et al. 2013).

Before the study, they tested each participant's stool to determine their existing gut microbiome. For four days, they ate their normal diets and kept logs detailing everything they consumed.

Next, each volunteer spent five days eating a vegetarian diet: granola, meals made with rice, onions, tomatoes, squash, garlic, peas, and lentils, with banana, mango, and papaya as snacks.

The participants still kept daily food logs and collected stool samples to track how the microbes in their gut changed. 

After five days, they returned to their regular diets for a six-day “washout” period, to determine how quickly their microbiome would recover from any shifts caused by the food they digested.

Each participant then spent five days eating a diet composed of animal products: bacon and eggs for breakfast, pork ribs and beef brisket for lunch, and salami, prosciutto, and a selection of cheeses for dinner, with string cheese, salami, and pork rind snacks.

The authors saw changes in the abundance of different bacteria in as little as a day after food made it to the gut on the animal-product diet.

On both diets, they saw significant changes in the types of genes that bacteria were expressing, as well as changes to the metabolic byproducts of bacterial activity – like short-chain fatty acids – about three or four days after they switched diets.

While the study results show that diet can affect the makeup of the gut microbiome, they also suggest that those changes may have very real implications for human health.

Perhaps significantly, the population of a bacteria known to cause colitis in mice – called Bilophila – saw the largest gains among those on the animal-product diet.

Earlier studies showed that, in mice, diets high in milk fat promote production of bile, which in turn led to increases in Bilophila.

The Harvard team couldn't say whether Bilophila might cause colitis in humans, but we now know that it's growth can be encouraged or curbed through diet.

Likewise, the new findings imply that dietary changes might treat certain medical conditions, but we have a long way to go before it's clear which changes do what.

  • David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, Biddinger SB, Dutton RJ, Turnbaugh PJ. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2013 Dec 11. doi: 10.1038/nature12820. [Epub ahead of print] Accessed at 
  • Fava F, Gitau R, Griffin BA, Gibson GR, Tuohy KM, Lovegrove JA. The type and quantity of dietary fat and carbohydrate alter faecal microbiome and short-chain fatty acid excretion in a metabolic syndrome 'at-risk' population. Int J Obes (Lond). 2013 Feb;37(2):216-23. doi: 10.1038/ijo.2012.33. Epub 2012 Mar 13. 
  • Gootenberg DB, Turnbaugh PJ. Companion animals symposium: humanized animal models of the microbiome. J Anim Sci. 2011 May;89(5):1531-7. doi: 10.2527/jas.2010-3371. Epub 2010 Sep 10. Review. 
  • Martínez I, Lattimer JM, Hubach KL, Case JA, Yang J, Weber CG, Louk JA, Rose DJ, Kyureghian G, Peterson DA, Haub MD, Walter J. Gut microbiome composition is linked to whole grain-induced immunological improvements. ISME J. 2013 Feb;7(2):269-80. doi: 10.1038/ismej.2012.104. Epub 2012 Oct 4. 
  • Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med. 2009 Nov 11;1(6):6ra14. doi: 10.1126/scitranslmed.3000322.