The Mysterious Viruses Lurking in Your Baby’s Gut

Advancing our knowledge of viral communities in the healthy infant gut


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Studies have shown that the human gut is home to a diverse community of microorganisms, including bacteria, viruses, and fungi. These microorganisms, collectively known as the gut microbiome, play a crucial role in maintaining overall health and well-being. Recently, researchers have discovered that the gut of a healthy infant is crawling with unknown viruses.

Our gut contains bacteria and viruses that interact with each other. In young children, gut bacteria are essential for protecting them from chronic diseases later in life. However, little is known about the viruses present in the gut. Researchers from the University of Copenhagen and others spent five years studying the diaper contents of 647 healthy Danish one-year-olds to understand more about the viruses in the gut.

Professor Dennis Sandris Nielsen of the Department of Food Science, senior author of the research paper about the study, now published in Nature Microbiology, said, “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.” 

Researchers from the University of Copenhagen discovered and mapped 10,000 viral species in the feces of healthy one-year-old Danish children. This is ten times more than the bacterial species in the same children. The viral species belong to 248 different viral families, of which only 16 were previously known. The researchers named the remaining 232 unknown viral families after the children who participated in the study. New viral families include names like Sylvesterviridae, Rigmorviridae, and Tristanviridae.

The University of Copenhagen researchers’ mapping of gut viral diversity in healthy one-year-old Danish children is the first of its kind. The results offer a new basis for understanding the importance of viruses for our microbiome and immune system development. According to Shiraz Shah, senior researcher at COPSAC, an extraordinarily high species richness of gut viruses may emerge in children to protect against chronic diseases like asthma and diabetes later in life. The study found that 90% of the viruses were bacteriophages, which have bacteria as their hosts and do not cause disease. The hypothesis is that bacteriophages act as allies.

Dennis Sandris Nielsen explains, “We work from the assumption that bacteriophages are largely responsible for shaping bacterial communities and their function in our intestinal system. Some bacteriophages can provide their host bacterium with properties that make it more competitive by integrating its genome into the bacterium’s genome. 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.”

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

Our gut is initially sterile, and we are exposed to bacteria during birth and later via environmental factors like dirty fingers, pets, and other things we put in our mouths. This exposure likely introduces viruses into our gut as well. 

According to Dennis Sandris Nielsen, understanding the role of bacteria and viruses in a well-trained immune system can help avoid chronic diseases that have an inflammatory component, from arthritis to depression. Researchers are now investigating the role of gut viruses in childhood diseases like asthma and ADHD.

The gut microbiome plays a crucial role in the maturation of the immune system, protecting against chronic disease later in life. Phages, or viruses that infect bacteria, modulate bacterial growth in the infant’s gut. Researchers have identified and mapped 10,000 viral species from 248 virus family-level clades (VFCs) in fecal.

Virus family-level clades (VFCs) were previously unknown, and they infect the Caudoviricetes viral class. Hosts were determined for 79% of phage using bacterial metagenomes from the same children. The findings expand existing phage taxonomy, provide a resource for future research, and shed light on the importance of gut viruses for the immune system.

The study aimed to explore viral diversity in healthy infant gut using metagenomics. The results showed 17 different viral families, including bacteriophages and eukaryotic viruses. The viral populations were found to be dynamic and changed over time, with some viruses present at three months and not detected at six months. The study suggests that the infant’s gut contains a diverse and dynamic population of viruses, shedding new light on early gut microbiome colonization and potential therapeutic applications.

In this study, stool samples were collected from six healthy infants aged 4-8 months, and the viral DNA was extracted using a commercial kit. The extracted DNA was enriched for viruses using filtration and nuclease digestion and sequenced using high-throughput DNA sequencing.

Bioinformatics tools were used to identify the viral populations in the infant’s gut. Statistical analysis was performed to determine their diversity and richness. The study identified a diverse range of viruses in the gut of healthy infants, expanding our knowledge of viral populations in this environment.

These findings suggest that the infant’s gut contains a diverse and dynamic population of viruses that may play a role in the development and function of the gut microbiome. The results may have implications for understanding the role of viruses in shaping the early colonization of the gut microbiome and for potential therapeutic applications in the future.

In conclusion, the study highlights the importance of studying the viral component of the gut microbiome. It sheds light on the unknown viruses in our baby’s gut. Further research in this area may provide new insights into the early colonization of the gut microbiome and help to inform new therapeutic approaches for infants and children.

Journal Reference:

  1. Shah, S. A., Deng, L., Thorsen, et al. Expanding known viral diversity in the healthy infant gut. Nature Microbiology. DOI: 10.1038/s41564-023-01345-7


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