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Who Knew? Gut Bacteria Contribute to Malnutrition

Posted on by Dr. Francis Collins

Photo of an African girl with thin limbs and a distended abdomen.

A child suffering from kwashiorkor.
Source: CDC/Phil

Here’s a surprising result from a new NIH-funded study: a poor diet isn’t the only cause of severe malnutrition. It seems that a ‘bad’ assortment of microbes in the intestine can conspire with a nutrient poor diet to promote and perpetuate malnutrition [1].

Most of us don’t spend time thinking about it, but healthy humans harbor about 100 trillion bacteria in our intestines and trillions more in our nose, mouth, skin, and urogenital tracts. And though your initial reaction might be “yuck,” the presence of these microbes is generally a good thing. We’ve evolved with this bacterial community because they provide services—from food digestion to bolstering the immune response—and we give them food and shelter. We call these bacterial sidekicks our ‘microbiome,’ and the latest research, much of it NIH-funded, reveals that these life passengers are critical for good health. You read that right—we need bacteria. The trouble starts when the wrong ones take up residence in our body, or the bacterial demographics shift. Then diseases from eczema and obesity to asthma and heart disease may result. Indeed, we’ve learned that microbes even modulate our sex hormones and influence the risk of autoimmune diseases like type 1 diabetes. [2]

Now, thanks to this new research, we have fresh insight into the connection between microbes and malnutrition.  The study is based on 317 pairs of young twins living in Malawi, where an acute form of malnutrition called kwashiorkor is common. While the name might not be familiar, you’ve seen pictures of children with this disease. They are the heartbreaking poster children for starvation and malnutrition–fragile, skeletal forms with large distended bellies.

These children suffer from swelling, liver damage, and skin ulcers, and their muscle and fat waste away. In the Malawi study of twins, all had a rather poor diet, but some developed kwashiorkor and some did not.

By analyzing fecal samples, the researchers discovered the gut microbiome of the healthy kids versus those with kwashiorkor differed dramatically. To see whether nutritional therapy could change the microbiome, they fed both the sick and healthy twin a therapeutic peanut-based diet and took fecal samples before, during, and after. They found that the community of bacteria in the sick twin shifted toward that of well-nourished children. But the change was temporary. When the children returned to a Malawian diet, the cohort of gut-dwelling microbes stopped normalizing—and often reverted to those present in the earlier malnourished state. Was the diet or the microbes to blame?

To answer that question, the researchers took microbiomes from malnourished children with kwashiorkor, and microbiomes from healthy children, and transplanted them into the guts of sterile mice (specially bred to be previously free of bacteria). When these mice were fed a nutrient poor, Malawian-based diet, only mice with the kwashiorkor microbiome lost weight. When these mice ate the therapeutic diet they gained weight but then lost it again after switching back to a Malawian diet.

So it seems that children carrying the “bad” kwashiorkor gut microbes can’t make the most efficient use of the Malawian diet and end up with malnutrition. But for children with a healthy batch of microbes, even a Malawian diet may provide enough nutrition. Though more research is necessary, experts suspect that combating malnutrition and undernutrition will require more than just extra calories. We may need to spike therapeutic foods with good bacteria to create healthy microbiomes in malnourished kids.

Want to know more?

Human Microbiome Project:

NIH Human Microbiome Project Data Analysis and Coordination Center:


[1] Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor. Smith MI, Yatsunenko T, Manary MJ, Trehan I, Mkakosya R, Cheng J, Kau AL, Rich SS, Concannon P, Mychaleckyj JC, Liu J, Houpt E, Li JV, Holmes E, Nicholson J, Knights D, Ursell LK, Knight R, Gordon JI. Science. 2013 Jan 30.

[Perspective on 1] Undernutrition—Looking Within for Answers. David A. Relman. Science. 1 February 2013: 530-532.

[2] Sex Differences in the Gut Microbiome Drive Hormone-Dependent Regulation of Autoimmunity. Markle JG, Frank DN, Mortin-Toth S, Robertson CE, Feazel LM, Rolle-Kampczyk U, von Bergen M, McCoy KD, Macpherson AJ, Danska JS. Science. 2013 Jan 17.