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Human microbiota is linked to many diseases but could hold the key for advanced clinical laboratory tests and targeted precision medicine therapies

Study of the human microbiome continues to provide understanding and knowledge regarding gut bacteria and its many benefits, and incites development into new clinical laboratory tests. However, a new study reveals that our bodies might also put gut bacteria under stress leading to better health.

Traditionally, scientists believe the human gut is a hospitable environment that allows bacteria to thrive. However, microbiologists may be interested in a study by Duke University School of Medicine (Duke) that suggests the relationship between humans and their microbiomes may be adversarial as well.

In fact, the study found that human hosts are starving their microbes of nutrients and forcing them to compete for food for the benefit of the host.

“There appears to be a natural pecking order to the bacteria and us,” noted Lawrence A. David, PhD, Assistant Professor, Department of Molecular Genetics and Microbiology at Duke University School of Medicine, in an article Duke posted on “In a way it’s not surprising that we, the host, should hold more of the cards.”

Duke researchers published the results of their study in Nature Microbiology, an online peer-reviewed scientific journal.

Could Nitrogen Impact Gut Bacteria?

The human microbiome consists of hundreds of different types of bacteria and other various tiny organisms, such as viruses and fungi. When combined, the microbes in the human gut weigh approximately three pounds or about the same as the brain.

The theory behind Duke’s study was that the human microbiome is an ecosystem comprised of various entities that compete for resources, and which are often constricted by nutrients, such as nitrogen or phosphorus.

To perform the study, Aspen Reese, PhD, a PhD candidate at Duke during the study and now a Junior Fellow researcher at Harvard University, procured stool samples from more than 30 types of mammals. She then ground the individual samples and tabulated the number of nitrogen and carbon atoms contained within those samples.


The animals used for the study included wild zebras, giraffes and elephants from Kenya, domestic sheep, cattle and horses from New Jersey, and humans from North Carolina. The graphic above shows how “carbon-to-nitrogen ratios in poop vary between animals as a result of diet and physiology. These ratios also govern the abundance of microbes in their guts.” (Image copyright: Aspen Reese/Harvard University.)

Reese discovered that the bacteria in the human gut had access to only one nitrogen atom for every 10 carbon atoms. The bacteria in other mammals’ guts had access to one nitrogen atom for every four carbon atoms. The question arose: Could nitrogen levels in the human gut impact the microbiome?

Reese performed tests on mice to determine if nitrogen levels could help regulate the microbiome. She fed the mice a diet packed with protein, which naturally contains a large amount of nitrogen. When she increased the amount of protein fed to the mice, the amount of their gut bacteria also increased. Reese then injected nitrogen directly into the bloodstream of the mice and found that some of that nitrogen ended up in their gut bacteria.

This discovery suggests the host can help save microbes in the gut by secreting nitrogen through the cells.

“Our findings support the idea that we’ve evolved a way to keep our bacteria on a leash by leaving them starving for nitrogen,” David noted on “It also explains why the Western diet might be bad for us. When people eat too much protein, it swamps the host’s ability to take up that nitrogen in the small intestine, and more of it ends up making its way to the large intestine, eliminating our ability to control our microbial communities.” (Photo copyright: Duke University School of Medicine.)

Antibiotics and Gut Bacteria

The team also performed a previous study regarding the effects of antibiotics on gut bacteria, which they published in June on eLife, an online open-access journal.

In that study, the researchers gave mice a five-day treatment of antibiotics. By analyzing their stool samples daily, the scientists discovered that many of the energy sources needed by microbes in the gut accumulated as bacteria was depleted. Some species of valuable gut bacteria are eliminated by antibiotics and may never return.

The researchers found that the mice had to eat each other’s stools in order for those essential microbes to return.

“People probably won’t want to do that,” David told

The trillions of microbes that reside in the human gut help manage almost every function of the human body. Poor gut health can contribute to a wide variety of health problems, including allergies, arthritis, dementia, diabetes, cardiovascular disease, leaky gut syndrome, and some cancers and autoimmune diseases.

Factors such as diet, sleep habits, stress levels, and the number of bacteria an individual is exposed to on a regular basis can negatively affect the microbiome.

Continuing research into the mysteries contained in the human microbiome provide valuable data about our gut bacteria. This type of information could eventually help microbiologists and clinical laboratory professionals more accurately identify diseases and health conditions and guide physicians to appropriate, and possibly targeted, precision medicine therapies for patients.

—JP Schlingman


Related Information:

Our Microbes Are Starving, and That’s a Good Thing

Scientists Reveal How Gut Microbes ‘Recover’ after Antibiotic Treatment

How and Why Our Bodies Starve Gut Bacteria

Loss of Microbial Gut Diversity a Threat to Health?

Microbial Nitrogen Limitation in the Mammalian Large Intestine

How Many Cells Are in the Human Body—And How Many Microbes?

Mayo Clinic Researchers Find Some Bacteria Derail Weight Loss, Suggest Analysis of Individuals’ Microbiomes; a Clinical Lab Test Could Help Millions Fight Obesity

University of Illinois Study Concludes Regular Physical Exercise Improves Human Microbiome; Might Be Useful Component of New Treatment Regimens for Cancer and Other Chronic Diseases

Researchers in Two Separate Studies Discover Gut Microbiome Can Affect Efficacy of Certain Cancer Drugs; Will Findings Lead to a New Clinical Laboratory Test?