What is already known
The infant gut microbiota has been shown to influence the development of the immune system and clinical outcomes later in life. But although many studies have characterized gut-dwelling bacteria early in life, little is known about the infant gut virome — the community of viruses that inhabit the gastrointestinal tract.
What this research adds
Researchers followed 53 infants and their mothers for three years to examine and compare their viromes. They found that the infant virome consists mostly of dietary and environmental viruses, human-host viruses and phages — a type of viruses that infect bacteria. In contrast, human-host viruses were rarely found in the maternal virome. As infants aged, their phages became more similar to those found in their mothers’ virome, but by age three, human-host viruses were still different from those of the maternal virome. The researchers also found previously undescribed viruses in the maternal virome.
Conclusions
The findings suggest that infants acquire their gut virome from their diet and environment rather than from their mothers.
Although many studies have characterized gut-dwelling bacteria early in life, little is known about the infant gut virome — the community of viruses that inhabit the gastrointestinal tract. New research suggests that infants acquire their gut virome from their diet and environment rather than from their mothers.
“We found that the diversity of the infant virome was not driven by exposure to the mother but is more likely determined by dietary, environmental, and infectious exposures,” say the researchers, who reported their findings in Cell Host & Microbe. “Future studies are needed to determine how the presence/absence or persistence of certain pathogenic viruses ultimately contributes to disease later in life.”
The microbiota composition of infants has been shown to influence the development of the immune system and clinical outcomes later in life. However, technical limitations have hindered the characterization of the early human virome, and most studies in infants have included small sample sizes over short periods of time.
To fill the knowledge gap of human-microbe interactions in early life, researchers led by Charles Chiu at the University of California San Francisco followed 53 infants and their mothers for three years to examine and compare their viromes.
Distinct viromes
The researchers collected about 9 stool samples per infant from 2 weeks to 3 years old and 5 stool samples from mothers over about 15 months.
The infant virome consisted mainly of dietary and environmental viruses, human-host viruses and phages — a type of viruses that infect bacteria. The most abundant viruses were phages in the Microviridae and Siphoviridae families, and human-host viruses in the Picornaviridae and Anelloviridae families.
The mothers’ virome instead consisted mostly of dietary and environmental viruses such as Virgaviridae, as well as phages such as Microviridae and Inoviridae. Human-host viruses were rarely found in the maternal virome.
As infants aged, their phages became more similar to those found in their mothers’ virome, the researchers found. In particular, the proportions of human-host viruses decreased, while those of phages, dietary and environmental viruses increased.
Uncharacterized viruses
By age three, human-host viruses were still different from those of the maternal virome. While both mothers and infants had high levels of Microviridae, Virgaviridae, Siphoviridae and crAssphage, mothers had fewer Anelloviridae, Caliciviridae, Picornaviridae and Podoviridae than infants.
The researchers also found previously undescribed viruses in the maternal virome, but not in the infant virome. “Potential explanations for this finding include detection of novel animal viruses that are merely dietary components or the acquisition of infections from novel, human-host viruses, given the expanded diet in mothers and increased time of exposure to viruses in mothers compared with infants,” the researchers say.
The findings support previous research that found that the neonatal virome is only 15% related to the mother’s virome. This suggests that the environment, including breast milk, skin and contaminated surfaces, drive viral colonization of the infant gut, the researchers say.
