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The Dark Matter Inside Your Gut

The world is full of bacteria that are not bacteria. We know they are there not because we can grow them but because we see their genes.

There is a kind of dark matter inside our intestinal tract. “Dark matter” is the phrase coined for the matter that is implied to be present in the universe based on physicists’ calculations but that cannot be seen yet. Scientists who study tiny living things are facing their own type of dark matter: invisible microbes that are indirectly detected. They call it “microbial dark matter.”

Much has been written about the bacteria that live inside our gut. This microscopic ecosystem, known as the microbiome, may play important roles in our health but scientists are only now beginning to understand very small elements of it. But the microbiome is not only made up of bacteria.

You may remember learning in school that there are two major empires of life. On one side, we essentially have single-celled living things whose genetic material floats freely inside them. These are the prokaryotes and they include bacteria. On the other side, we have organisms whose genetic material is contained within a little body inside the cell called the nucleus. These are the eukaryotes, and they include a multitude of organisms like the yeast we use for baking, trees, insects, and humans. But actually, since the late 1970s, we have known that this black-and-white division is not accurate. It turns out there are three domains of life: eukaryotes, bacteria, and a third domain called Archaea (alternatively pronounced “ar-KAY-ah” or “ar-KEE-ah,” like a pirate trying to say IKEA).

Archaea used to be thought of as bacteria-like. After all, they are single-celled organisms, they are microscopic, and they more or less look like what you expect bacteria to look like. They even have CRISPR, the much-talked-about primitive immune system bacteria have and that scientists have turned into a precise pair of molecular scissors with the potential to cure diseases. But the more scientists studied Archaea, the more they realized they differed from bacteria and actually shared many similarities with us, the eukaryotes, especially with regards to some of the molecules they use for living.

Archaea were originally discovered enjoying themselves in extreme environments, places where human bodies would not last for very long, like hot springs where temperatures reach the boiling point and spots where the pressure or salinity or acidity is astoundingly high. These little single-celled critters were surviving just fine. (In fact, some can be grown in temperatures up to 122ºC or 252ºF, pushing the upper temperature limit on where life can be found on Earth.) When scientists started looking for them elsewhere, they found them in much cozier environments, including inside of us.

They are inside our mouth, on our skin, inside our intestine, and in the vagina. Many seem to be involved in a process of cross-feeding with the bacteria that colonize us, meaning the two types of organisms are living off of each other’s metabolic products. And while we may worry about the harm Archaea could do to our health, there is so far no conclusive evidence of Archaea causing disease or acting like parasites.

To bring this back to dark matter, it’s important to remember that microbes used to be detected by whether or not they could be grown in the lab. If you have ever pressed your hand against the growth medium inside a Petri dish and waited for the bacteria you transferred from your hand to grow on there, you have seen bacterial culture. The bacteria grow because they are fed the right nutrients and are kept at the right temperature. If you do not know what a type of bacteria needs to eat in order to survive, however, you may not be able to grow it in the lab.

Most Archaea that have been discovered were not grown in the lab; rather, they were detected indirectly. All living things on Earth rely on certain molecules that allow them to live and reproduce. This molecular biology involves proteins called ribosomes that read RNA molecules to assemble the corresponding protein, like a customer using an instruction sheet to assemble flat-pack furniture. There is a piece of that ribosome that is itself encoded by a bit of RNA called the 16S ribosomal RNA, and this sequence does not evolve very quickly. By detecting this 16S ribosomal RNA in a sample and reading it, scientists can essentially see what type of living thing it came from. This is how Archaea are, for the most part, identified: by detecting and reading part of their genetic entrails.

That makes them a bit like dark matter. Because we do not always know what these Archaea “eat,” they are very hard to grow in the lab. But we know they are there because we are picking up their distinct genetic signature.

So, in a way, we all have dark matter inside our gut. And maybe, with time and dedication, scientists of the future will be able to grow them on a Petri dish, bringing this microbial dark matter to light.

Take-home message:
-Life as we know it can be divided into 3 domains: eukaryotes like us whose genetic material is inside the nucleus of our cells; bacteria; and Archaea
-Archaea resemble bacteria in that they are microscopic single-celled organisms and they can survive in extreme environments, but they also share a lot of molecular similarities with eukaryotes and can be found inside our body
-Many Archaea are known as “microbial dark matter” because they cannot be grown in the lab and directly observed, but their genetic signature can be detected


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