New research reveals the strange ways gut bacteria breathe without oxygen, influencing our health

In the wellness world, there’s a lot of pseudoscience circulating around about the human gut microbiome, the swimming colonies of microbes that inhabit our bowels, especially when it comes to selling supplements and remedies alleging to improve microbiome health. There’s even a whole industry to test your microbiome which has been dubbed as “snake oil.” One in four Americans are affected by digestive disorders, so it’s no surprise that people are becoming increasingly curious about the human gut.

But where information lacks in science, misinformation thrives. And the truth is science is still searching for answers about what’s really going on in our intestines, where hundreds to thousands of species of bacteria and archaea exist.

Indeed, the gut universe inside us is extremely complex. It’s full of different species of microbes, but differences that exists between strains carry different genes and can affect a person’s health and the diseases they’re susceptible to. But before we can even really untangle how these tiny single-celled organisms influence us, we need to know how they got inside us in the first place. After all, the human gut is dark, lacking in oxygen and has a built-in surveillance system for killing outsiders — the immune system. How did our gut microbiome evolve to navigate this toxic environment and even thrive within us?

A new study published in Nature Microbiology takes a step forward in microbiome science by identifying 22 specialized metabolites, which are chemical byproducts resulting from metabolism, that organisms can breathe in to generate oxygen and energy inside our intestines. This new paper highlights how resourceful some of these microbes can be, and how some gut bacteria may have the ability to produce energy from other compounds — with big implications for direct impacts on our health.

“We've basically found that there are bacteria that can essentially breathe other molecules [aside from oxygen]," Dr. Alexander Little, co-author of the study, told Salon. On Earth, the majority of living organisms use oxygen to generate energy. But in our intestines, the bacteria can’t use oxygen because human intestines are an oxygen-depleted environment. A common way to generate oxygen is through fermentation and breaking down sugars, but that’s not the only way bacteria survive. 

Little and his colleagues went "mining" for reductase enzymes, which are a large pool of genomes outside of gut bacteria that allow these microscopic bugs to breathe in oxygen-less environments — essentially the oxygen tanks of the microbe world. They found that the vast majority of bacteria had little to no reductase enzymes, but certain groups of bacteria expressed dozens to hundreds of these enzymes. 

“Which suggests to us that there are these groups of really specialized bacteria,” he said. “By doing some fancy science magic, like mass spec [spectrometry], we were able to definitively show that they're breathing, and these molecules are shuttling electrons onto them.”

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One of the main ways the microbiome impacts our human health is that when these metabolites enter our bloodstream, they are essentially drugs — chemicals that can impact our inner chemistry, with profound impacts for health.

“If they're able to cross the intestinal barrier and get into the bloodstream, they're presumably going to have some impact on our health,” Little said. “The idea of acting like drugs is that like all drugs that cross into our bloodstream, they have some impact on our health — but we just don't necessarily know what they could be doing [in the body].”

In other words, if these bacteria are breathing thanks to the energy of other molecules, it could mean that these molecules could have a direct impact on our health. Little said people with type 2 diabetes have higher levels of an amino acid byproduct called imidazole propionate in their blood. By understanding how these molecules and bacteria work together, researchers hope that either through diet or medicine, they can develop interventions to treat such conditions or improve existing ones. Some gut microbes possess enzymes that can make Parkinson's disease medications less effective, for example. Understanding these relationships is critical for fully understanding human health.

"Considering that the vast majority of reductases encoded by gut bacteria remain functionally uncharacterized, identified metabolisms may only scratch the surface of interactions between respiratory reductases and the gut metabolome," the study authors wrote. "Continued study of respiratory electron acceptor usage may thus provide an important avenue for informing our understanding of the functional capacity and metabolic output of the gut microbiome."

“We're really just starting to scratch the surface of what this could mean,” Little said. “I 100 percent believe what you could be eating, and what bugs are there, certainly are going to impact your health, but it's also a very, very complex ecosystem and we're just starting to understand how this all manages to Tetris itself together into this functional system.”