Babies’ intestines teem with unknown viruses, study finds

Babies’ intestines appear to be teeming with (unknown) viruses. In total, researchers found no fewer than 10,000 (!) virus species in the stools they inspected.

Viruses are usually associated with disease. But our bodies are full of both bacteria and viruses that are constantly multiplying and interacting with each other. While we’ve known for decades that gut bacteria in young children are vital to protecting them from chronic disease later in life, our knowledge of the many viruses found there is minimal. And so researchers decided to subject the dirty diapers of 647 Danish one-year-old babies to a closer inspection. Everything for science.

Thousands of teeming viruses
The team discovers that babies’ intestines are teeming with viruses. In total, the researchers mapped no less than 10,000 virus species – a number that is ten times as large as the number of bacterial species in the same children. These virus types are divided into 248 different virus families, of which only 16 were previously known.

Unknown viruses
It means that the babies not only harbor a lot of viruses, but they also carry a lot of unknown ones. “We found an extraordinary number of unknown viruses in the feces of these babies,” says researcher Dennis Sandris Nielsen. “Not only did we discover thousands of new virus species, to our surprise they represent more than 200 families of viruses yet to be described.” This large number comes as a surprise. “It suggests that humans have an extreme diversity of gut viruses from very early in life, which are likely to have a major impact on whether or not they develop various diseases later in life,” said Nielsen.

Chronic diseases
Indeed, because the researchers suspect that the viruses found play an important role in protecting children against chronic diseases. “The study provides an entirely new basis for uncovering the importance of viruses for the development of our microbiome and immune system,” said researcher Shiraz Shah. “Our hypothesis is that – because the immune system has not yet learned to separate the wheat from the chaff by the age of one – an extraordinarily high species diversity of intestinal viruses arises. This is probably necessary to be able to properly protect against chronic diseases such as asthma and diabetes later in life.”

Bacteriofagen
Ninety percent of the viruses the researchers found are bacterial viruses, also known as bacteriophages (see box). These viruses infect bacteria but do not attack the children’s own cells, meaning they do not cause disease. The researchers suspect that bacteriophages mainly serve as allies. “We believe that bacteriophages are largely responsible for shaping bacterial communities in our gut,” explains Nielsen. “Some bacteriophages can give a bacterium they have infected certain properties that make it more competitive. They do this by integrating their own genome into the genome of the bacteria. When this happens, a bacteriophage can then increase a bacteria’s ability to absorb various carbohydrates, for example, improving the bacteria’s metabolism. It also appears that bacteriophages help balance the gut microbiome by keeping individual bacterial populations in check. This ensures that there are not too many of a single species. It is a bit like the balance between lions and gazelles on the savannah.”

More about bacteriophages
There are two types of bacteriophages. Virulent bacteriophages, as it were, take over the bacteria and leave 30 to 100 new virus particles behind. After this, the bacterial cell explodes from the inside and the new virus particles escape, which then spread into the environment. Virulent bacteriophages help keep the intestinal ecosystem in balance. In addition, there are also so-called temperate bacteriophages. These can reproduce by integrating their genetic material into the genome of the host bacterial cell. When the cell divides, so does the bacteriophage. Temperate bacteriophages help transfer new genes to the bacterium so that it becomes more competitive. There are studies suggesting that an imbalance in the number of temperate bacteriophages is linked to various conditions, including inflammation of the gastrointestinal tract.

The remaining ten percent of the viruses found in the dirty diapers are eukaryotic. That is, they use human cells as a host. These can be both friends and enemies to us. “It is thought provoking that all children are walking around with 10 to 20 of this type of virus that infects human cells,” said Nielsen. “So there is a constant viral infection that doesn’t seem to make them sick. We just know very little about what’s really going on. I suspect they are important for training our immune system to recognize infections later on. But they may also be a risk factor for diseases that we have yet to discover.”

Where do they come from?
A pressing question is how and where the annuals acquired the many viruses discovered. The best answer the researchers can give right now is from the environment. “Our intestines are sterile until we are born,” Nielsen explains. “During birth, we are exposed to our mother’s bacteria. It is likely that some of the first viruses came along with these first bacteria, while many others were introduced later through dirty fingers. We also think that pets and dirt that children put in their mouths play a role.”

The study is an important step forward. It is the first time that such a systematic overview of the diversity of intestinal viruses has been compiled. However, there is still much to learn. “In the past, scientists mainly focused on the role of bacteria in relation to health and disease,” says Shah. “Viruses are the fifth wheel on the car, about which we still have a lot to learn. Viruses, bacteria and the immune system most likely work together and influence each other. Any imbalance in this relationship presumably increases the risk of chronic disease. So if we learn more about the role that bacteria and viruses play in a well-functioning immune system, it can hopefully lead to the prevention of many chronic diseases that affect so many people today.”