Influence of diet on early life gut virome - a key player in shaping the gut microbiota


Bacteria play a crucial role in our healthy development, and in protecting against chronic disease. The goal of EarlyVir was to find out whether the same applies for viruses and if we can isolate important viruses and use them as a technology to improve human health.

  1. Determine the viral composition of the infant gut at age 1 year
  2. Determine whether it was influenced by the diet of the mother during pregnancy
  3. Determine whether certain viral compositions lead to or protect from chronic diseases
  4. Determine which lifestyle factors shape the viral composition
  5. Isolate important viruses for future application in treatment and prevention of disease

Objective 1 has been reached. We have determined the viral composition of 663 children from the COPSAC2010 birth cohort. The composition was more diverse than expected, providing material for years of further research.

Work for Objectives 2, 3 and 4 is on-going, but so far we have found that 1) fish oil intake during pregnancy shifts the infant viral composition, 2) that certain viral compositions are associated with later development of food allergies and 3) that a range of early-life exposures, including antibiotics, household pets and the outdoor environment leave major imprints on the body’s viral makeup.

As for Objective 5, our French collaborators at INRA, are in the process of submitting a patent for 6 new viruses that were isolated from the COPSAC samples, which infect the bacterium E. coli. Viruses infecting other species are being isolated now, and may be used for treatment of diseases in the future.


Partner Organization Partner Country
University of Copenhagen Denmark
INRA Institut National de la Recherche Agronomique France
Microbiology and Bioinfornatics Canada


Until recently, bacteria were mostly thought to cause disease, but research in the last decade has shown that most bacteria are actually good for our health. But what about viruses? Are viruses just agents of disease, or are most viruses really good for the healthy development of the human body? Can viruses, like bacteria, protect us from the types of chronic disease that seem to be on the rise globally? Could we use viruses to prevent or treat chronic disease? Most chronic diseases are in fact immune disorders where the immune system attacks the body itself instead of attacking pathogens, or where it is constantly switched on, as in chronic inflammation, stressing the body over decades, causing diseases like cancer. We think that exposure to good bacteria and viruses while one is still a baby teaches the immune system how to recognise real threats, so it doesn't switch on accidentally in adulthood. To find out if good viruses exist, we need to look at the bodies of healthy babies to see which viruses they are inhabited by. In the EarlyVir project, researchers have investigated fecal samples from 700 babies and found more than 8000 different viruses in their gut, which are apparently part of their normal healthy gut flora. These 8300 viruses are diverse, spanning several hundred families, and the vast majority of them were completely unknown to science before this project. None of the viruses found cause disease. By studying the children as they get older, the project is trying to identify which of these viruses end up protecting the children from developing chronic diseases as adults. When we have identified the beneficial viruses we can potentially use these viruses to fight chronic disease in the future.


Title: CRISPRStudio: A User-Friendly Software for Rapid CRISPR Array Visualization
Author: Moïra B. Dion, Simon J. Labrie, Shiraz A. Shah and Sylvain Moineau
Link: https://doi.org/10.3390/v10110602



Project number:
Duration: 100%
Duration: 100 %
Related funding round:
Project lead and secretary:
Prof. Hans Bisgaard