What is already known
The gut microbiota is shaped through infancy and contributes to the maturation of the immune system, protecting children from chronic diseases later on in life. However, the community of gut viruses, or the virome, has proved difficult to analyze. As a result, our knowledge about the many viruses found in the infant gut remains limited.
What this research adds
Researchers analyzed the virome of nearly 650 healthy Danish one-year-olds. They found about 10,000 viral species distributed across 248 different viral families, of which only 16 were previously known. Most of the viruses found in the infant gut are bacterial viruses known as bacteriophages, which likely help to keep a balanced gut microbiota by keeping individual bacterial populations in check.
Conclusions
The findings offer new insights into the diversity of the human virome and provide a resource that may help future research into the viruses that populate the infant gut.
The composition of gut microbes during infancy can influence a child’s health later on in life. However, our knowledge about the many viruses found in the infant gut remains limited. Now, researchers have identified more than 230 previously unknown viruses that populate the infant gut.
The findings, published in Nature Microbiology, offer new insights into the diversity of the community of gut viruses, or the virome. They also provide a resource that may help future research into the infant virome.
“[…] 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,” says study senior author Dennis Nielsen at the University of Copenhagen.
The gut microbiota is shaped through infancy and contributes to the maturation of the immune system, protecting children from chronic diseases as they grow up. However, the gut virome has proved difficult to analyze.
To gain insights into the viruses that inhabit the infant gut, researchers led by Nielsen and Shiraz Shah at Copenhagen University Hospital analyzed fecal samples from 647 healthy Danish one-year-olds.
Viral diversity
The infants are part of the Copenhagen Prospective Studies on Asthma in Childhood 2010, a group of 700 Danish mother-child pairs.
In the children’s feces, the researchers detected 10,021 viral species distributed across 248 different viral families, of which only 16 were previously known. The researchers named the newly discovered viral families after the children who participated in the study.
Among previously characterized viruses, a type of vertebrate viruses known as Anelloviridae were amongst the most abundant viruses in the infant gut. But the majority of the viruses found in the infant gut were bacterial viruses known as bacteriophages. These viruses infect and kill bacteria but are harmless to the children’s own cells.
Gut allies
Some of the most common bacteriophages in the infant gut were Petitvirales and Caudoviricetes, including Skunaviridae — a family of phages that infect bacteria found in dairy and likely originate from the infants’ diet.
Flandersviridae, a type of phages that infect Bacteroides bacteria, were found in almost half of the children. Other six bacteriophage families, which were previously undescribed, were also prevalent in the infant gut.
The researchers hypothesize that bacteriophages work as allies of the infant gut, likely helping to keep a balanced gut microbiota by keeping individual bacterial populations in check.
“We work from the assumption that bacteriophages are largely responsible for shaping bacterial communities and their function in our intestinal system,” Nielsen says. “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.”
