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Babies carry hundreds of viruses unknown to science

In a groundbreaking study, researchers have discovered an astonishing diversity of previously unknown viruses in the gastrointestinal tracts of young children, potentially playing a crucial role in their long-term health. 

While viruses have long been associated with illness, our bodies actually host a plethora of bacteria and viruses that continuously interact with each other in our gut.

For decades, scientists have understood that gut bacteria in young children are essential for protecting them against chronic diseases later in life. However, our knowledge about the viruses found in the gut remains limited. This prompted Professor Dennis Sandris Nielsen of the University of Copenhagen to further investigate this area.

Collaborating with a team from the Copenhagen Prospective Studies on Asthma in Childhood (COPSAC) and the Department of Food Science at the University of Copenhagen (UCPH), the researchers spent five years analyzing and mapping the contents of diapers from 647 healthy Danish one-year-olds. The findings of this extensive research have been published in the journal Nature Microbiology.

“We found an exceptional number of unknown viruses in the feces of these babies. Not just thousands of new virus species – but to our surprise, the viruses represented more than 200 families of yet to be described viruses. This means that, from early on in life, healthy children are tumbling about with an extreme diversity of gut viruses, which probably have a major impact on whether they develop various diseases later on in life,” explains Professor Nielsen, the senior author of the research paper.

The team identified an astonishing 10,000 viral species in the children’s feces – a number ten times larger than the bacterial species found in the same samples. These viral species belong to 248 different viral families, with only 16 of these families being previously known to science.

To honor the young participants who made this research possible, the scientists named the remaining 232 unknown viral families after the children themselves. As a result, newly discovered viral families now carry names such as Sylvesterviridae, Rigmorviridae, and Tristanviridae.

Bacterial viruses are friends, not foes

Shiraz Shah, the first author and a senior researcher at the Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), states: “This is the first time that such a systematic overview of gut viral diversity has been compiled. It provides an entirely new basis for discovering the importance of viruses for our microbiome and immune system development. Our hypothesis is that, because the immune system has not yet learned to separate the wheat from the chaff at the age of one, an extraordinarily high species richness of gut viruses emerges, and is likely needed to protect against chronic diseases like asthma and diabetes later on in life.”

The researchers discovered that 90% of the identified viruses are bacteriophages – bacterial viruses that do not attack human cells or cause disease. Instead, these bacteriophages primarily serve as allies. 

“We work from the assumption that bacteriophages are largely responsible for shaping bacterial communities and their function in our intestinal system,” explained study senior author Professor Dennis Sandris Nielsen.

“Some bacteriophages can provide their host bacterium with properties that make it more competitive by integrating its own genome into the genome of the bacterium. When this occurs, a bacteriophage can then increase a bacterium’s ability to absorb e.g. various carbohydrates, thereby allowing the bacterium to metabolize more things.”

“It also seems like bacteriophages help keep the gut microbiome balanced by keeping individual bacterial populations in check, which ensures that there are not too many of a single bacterial species in the ecosystem. It’s a bit like lion and gazelle populations on the savannah.”

Shah emphasizes the need to focus on the role of viruses in relation to health and disease. “Previously, the research community mostly focused on the role of bacteria. But viruses are the third leg of the stool and we need to learn more about them. Viruses, bacteria, and the immune system most likely interact and affect each other in some type of balance. Any imbalance in this relationship most likely increases the risk of chronic disease.”

The remaining 10% of the discovered viruses are eukaryotic, using human cells as hosts. These viruses can be both beneficial and harmful to human health. 

“It is thought-provoking that all children run around with 10-20 of these virus types that infect human cells. So, there is a constant viral infection taking place, which apparently doesn’t make them sick. We just know very little about what’s really at play,” said Nielsen. “My guess is that they’re important for training our immune system to recognize infections later. But it may also be that they are a risk factor for diseases that we have yet to discover.”

Could play a vital role in child development

The origins of the vast number of viruses discovered in the one-year-olds’ gastrointestinal tracts remain uncertain. The researchers believe that these viruses most likely come from the environment. 

Dennis Sandris Nielsen explains, “Our gut is sterile until we are born. During birth, we are exposed to bacteria from the mother and environment. It is likely that some of the first viruses come along with these initial bacteria, while many others are introduced later via dirty fingers, pets, dirt that kids put in their mouths and other things in the environment.”

This area of research has significant implications for global health, as many chronic diseases appear to have an inflammatory component linked to a malfunctioning immune system. 

Shiraz Shah emphasizes the potential impact of understanding the role of bacteria and viruses in immune system development: “A lot of research suggests that the majority of chronic diseases that we’re familiar with – from arthritis to depression – have an inflammatory component. That is, the immune system is not working as it ought to – which might be because it wasn’t trained properly. So, if we learn more about the role that bacteria and viruses play in a well-trained immune system, it can hopefully lead us to being able to avoid many of the chronic diseases that afflict so many people today.”

To further explore these connections, the research groups have initiated investigations into the role of gut viruses in relation to various childhood diseases, including asthma and ADHD. 

The study highlights the vast and largely unexplored world of gut viruses in young children, with potential implications for understanding how these viral communities may influence the development of various diseases later in life. This pioneering work will contribute to a deeper understanding of the complex relationship between gut viruses, bacteria, the immune system, and disease, potentially informing the development of new prevention and treatment strategies for chronic conditions.

How to babies develop their immune systems?

Babies begin developing their immune systems even before they are born, with the process continuing throughout infancy and early childhood. The immune system is crucial for protecting the body against infections and diseases. Here’s an overview of how babies develop their immune systems:

  1. Intrauterine development: During pregnancy, the mother’s immune system provides protection to the developing baby. Antibodies are passed from the mother to the fetus through the placenta, offering passive immunity to the baby. This immunity helps protect the newborn during the first few months of life, until the baby’s own immune system starts to develop.
  2. Birth: The process of birth exposes the baby to bacteria and viruses in the mother’s birth canal and the environment. These initial exposures help “seed” the baby’s gut microbiome, which plays a significant role in the development of the immune system. Breast milk also contains antibodies, immune cells, and other factors that help protect the baby and support immune system development.
  3. Exposure to pathogens: As babies grow, they encounter various pathogens in their environment, such as bacteria and viruses. These exposures help train the immune system to recognize and fight infections effectively. The immune system learns to distinguish between harmful pathogens and harmless substances, such as food or environmental allergens.
  4. Vaccination: Vaccines play a crucial role in the development of a baby’s immune system. By introducing a weakened or inactivated form of a pathogen, vaccines help the immune system learn how to recognize and combat specific infections without causing the actual disease. This process helps build immunity against a range of diseases, including measles, mumps, polio, and others.
  5. Maturation: The immune system continues to mature and develop throughout childhood, with repeated exposures to pathogens and environmental factors contributing to its strength and adaptability. As the child grows, their immune system becomes more robust and effective at preventing infections and responding to illnesses.

In summary, babies develop their immune systems through a combination of factors, including maternal immunity, exposure to pathogens, breastfeeding, vaccination, and the natural maturation process. These factors work together to help build a strong and adaptive immune system capable of protecting the child from various infections and diseases throughout life.


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