By Erica Sciara

Undernutrition and malnutrition are leading causes of death among children under five in developing countries, responsible for nearly 45% of child deaths globally. More than 200 million children suffer from stunting and wasting—devastating signs of malnutrition that often stem from food insecurity and poor dietary diversity. But there’s more to it than simply a need for more food or even more nutrients. Emerging research is uncovering an even more critical factor: disruptions in the development of the gut microbiome after birth.

A lot is going on in your gut; it’s home to a complex ecosystem of bacteria and microbes vital for digestion, immune health, and overall well-being. When the gut microbiome is thrown off balance, the effects of undernutrition can spiral, further stunting growth, impairing development, and severely weakening a child’s chances for a healthy future. Helping smallholder farmers grow a greater variety of crops at volume is one way to beat back the scourges of childhood malnutrition and undernutrition.

In other words, more diverse diets help the gut microbiota do its job.

Microbiology and macrohealth 

Undernutrition is a form of malnutrition that occurs when the body does not receive enough, or the right kind, of nutrients necessary for healthy growth and development. These problems are far too common in developing countries.

Children who experience chronic undernutrition in the first three years of life often suffer irreversible damage to their bodies and brains. The physical signs of undernourishment are stark. Children may appear smaller, and show skin rashes, dry or cracked skin, swollen bellies or legs, and brittle nails and hair. These physical changes are the outward manifestation of what is happening deeper inside the body as the metabolic processes that build new molecules and extract energy from food slowly grind to a halt.

Children in developing countries suffering from undernourishment may see their immune systems compromised, making them more vulnerable to diseases. Their ability to heal diminishes. Muscle strength weakens, limiting their ability to play or perform everyday activities. Cognitive development also stalls, leading to delays in language acquisition, poor motor skills, and lower IQs often resulting in poorer academic performance as these children grow up.

Yet there is hope.

Emerging evidence shows that restoring dietary diversity—particularly through the cultivation of nutrient-rich, diverse crops—can play a pivotal role in rehabilitating the gut microbiome and fighting undernutrition.

By prioritizing the increased cultivation of these crops—meaning supporting research and development that helps smallholder farmers succeed with alternative crops—society can tackle immediate food security challenges while promoting long-term health for entire populations.

The gut-whole body connection

The term “microbiota” refers to the array of organisms that live in a particular niche in the human body, including bacteria, viruses, single-cell eukaryotes, fungi, and archaea.  The most recent estimates show that bacteria alone match human cells about 1:1 in numbers.  Even more impressive is the genomic input of these bacteria–that is their collection of genes.

Researchers in the Human Microbiome Project (HMP), a daunting collaborative endeavor to catalog all the bacteria in various niches of a healthy human body, found approximately 1,000 different bacterial species living in the gut alone. That’s by far the most diverse niche in the human body.  Further metagenomic analysis revealed 3.3 million unique bacterial genes in the gut, a figure that grossly outnumbers human genes, by a factor of 150.

This vast assemblage of microbial genes, collectively referred to as the microbiome, is responsible for producing many of the proteins (enzymes, growth factors, messengers, etc.) that keep our metabolic systems running. Although we identify as human, we might also see  ourselves as a composite species or a “superorganism”, a walking multitude of cells and microorganisms.

Better appreciating the gut microbiota

In the decade or so since that initial HMP publication, research examining the roles of the gut microbiome has flourished.

We now know that bacteria in the gut break down complex carbohydrates and dietary fibers that we would not be able to digest on our own. Some plant sugars found in crops like soybeans can only be processed by colonic bacteria. Without their help, these nutrients would be inaccessible, meaning we could eat soybeans and other crops but not necessarily gain many of the nutritional benefits they hold. Gut bacteria also synthesize the enzymes that help us metabolize vitamins, including Vitamins B1, B9, B12, and K.

In addition, gut bacteria produce important molecules like short-chain fatty acids (SCFAs) that improve the health of the gut barrier by feeding colonic cells. SCFAs play a pivotal role in immune regulation by producing anti-inflammatory molecules, thereby preventing various inflammatory disorders like inflammatory bowel disease, colorectal cancer, and cardiovascular diseases.  

Gut bacteria protect us from infectious diseases, as well.

Infectious disease results when pathogenic or disease-causing microbes gain entry and outnumber the “good guys” of our immune systems. The result is a state of bacterial imbalance in the gut known as dysbiosis.

In a healthy human body, our gut bacteria are busily occupying and preventing any colonization or overgrowth by pathogenic species. People with severely depleted gut flora—like children suffering from malnutrition and undernutrition—are more susceptible to pathogens, including those linked to diarrheal diseases such as Clostridiodes difficile. These diseases kill far too many undernourished children in developing countries.

A healthy gut also means a healthy mind.

Physicians have long recognized the link between digestive health and mental well-being, known as the “gut-mind axis.” Today, we know that gut bacteria produce neurotransmitters like serotonin that influence mood and brain function. This bidirectional pathway involves neural, endocrine, immune, and metabolic signals. Bacteria also regulate metabolism, blood sugar levels, hunger, and satiety through hormone secretion.

These are just a handful of the contributions gut bacteria make to the proper functioning of a whole human body, so it’s unsurprising that malnourished children show a lack of gut diversity. The organisms that play such vital roles in the health of these children are simply no longer available to do all the important jobs they do.

Greater food diversity for better gut health

While bacteria start shaping our immune systems from birth, it’s thought that our gut microbiome largely stabilizes by the age of three.

During this period of rapid growth, gut microbiota influence the maturation of the immune system. They help to regulate immune system cells so the cells “know” where to go and what to do.

Microbiota also influence nutrient absorption, metabolism, and they prevent pathogen colonization. The time frame during which bacteria set up shop is sometimes referred to as the “window of opportunity” because it is a crucial moment in human development that can have a profound impact on an individual’s future health.

In 2013, the journal Science published a groundbreaking study by Smith, et al. that examined the gut microbiomes of 317 Malawian twins in the first three years of life.  During the study, 43% of the twin pairs became discordant for a type of severe malnutrition called kwashiorkor. When researchers transferred fecal material from the malnourished twin into the guts of experimental mice the mice developed the same metabolic problems associated with kwashiorkor, suggesting that a dysbiotic gut microbiome is a causal factor.

As the study progressed, twins in discordant pairs were treated with a peanut-based ready-to-use-therapeutic food (RUTF). Initially, the results were encouraging, revealing that even in this state of dysbiosis, providing RUTF helped the gut microbiome recover. However, the positive effects on microbiota proved short-lived once the RUTF regimen ended.

Improving childhood and adult nutrition with diverse, fiber- and nutrient-dense crops is one of our goals at Grow Further. For example, we’re supporting research in Ghana on Bambara groundnuts, an indigenous opportunity crop that grows well in arid climates and nourishes both humans and the soil. Its beans can be eaten in soup or made into milk, and support a healthy gut microbiome as well as providing specific nutrients.Ensuring better food security means feeding more than just humans. Rehabilitating malnourished microbiomes is also critical to human health.

Erica Sciara holds a Master’s degree in Pathobiology from the University of Washington, taught microbiology, cell biology, and molecular diagnostics labs for 15 years at Shoreline Community College, and is passionate about global health.