The gut virome of healthy children during the first year of life is diverse and dynamic

Abstract

In this work, we determined the diversity and dynamics of the gut virome of infants during the first year of life. Fecal samples were collected monthly, from birth to one year of age, from three healthy children living in a semi-rural village in Mexico. Most of the viral reads were classified into six families of bacteriophages including five dsDNA virus families of the order Caudovirales, with Siphoviridae and Podoviridae being the most abundant. Eukaryotic viruses were detected as early as two weeks after birth and remained present all along the first year of life. Thirty-four different eukaryotic virus families were found, where eight of these families accounted for 98% of all eukaryotic viral reads: Anelloviridae, Astroviridae, Caliciviridae, Genomoviridae, Parvoviridae, Picornaviridae, Reoviridae and the plant-infecting viruses of the Virgaviridae family. Some viruses in these families are known human pathogens, and it is surprising that they were found during the first year of life in infants without gastrointestinal symptoms. The eukaryotic virus species richness found in this work was higher than that observed in previous studies; on average between 7 and 24 virus species were identified per sample. The richness and abundance of the eukaryotic virome significantly increased during the second semester of life, probably because of an increased environmental exposure of infants with age. Our findings suggest an early and permanent contact of infants with a diverse array of bacteriophages and eukaryotic viruses, whose composition changes over time. The bacteriophages and eukaryotic viruses found in these children could represent a metastable virome, whose potential influence on the development of the infant’s immune system or on the health of the infants later in life, remains to be investigated.

High Prevalence and Diversity of Caliciviruses in a Community Setting Determined by a Metagenomic Approach

“…This study was conducted in Xoxocotla, Morelos, a semirural town in the central region of Mexico ( 12 ). Stool samples from 9 apparently healthy infants were collected monthly during the first year of life, starting 2 weeks after birth and until 12 months of age ( Fig.…”

“…In this work, we describe our findings related to the prevalence and genetic diversity of both norovirus and sapovirus strains in the population studied. A subanalysis of the viral diversity of 3 children has been published in Taboada et al ( 12 ), and a description of the complete set of fecal viruses found in this work will be published elsewhere.…”

“…We recently conducted a random, next-generation sequencing metagenomic study in stools of infants in a semirural community of Mexico to determine the composition and dynamics of the fecal virome of children during their first year of life ( 12 , 13 ). Samples from nine children were collected starting 2 weeks after birth and monthly thereafter until 12 months of age.…”

Normalisation of SARS-CoV-2 concentrations in wastewater: the use of flow, conductivity and CrAssphage

“…Although CrAssphage has been shown to reside in the human gut for months (Siranosian et al, 2020;Honap et al, 2020;Tamburini et al, 2021), little is known about the CrAssphage shedding dynamics per person over time. A longitudinal study in three infants showed considerable variation over the first year of life (Taboada et al, 2021), but a study among ten healthy adults showed that the human gut virome composition is personalized and relatively stable over time, including for CrAssphage (Shkoporov et al, 2019). The high variability in CrAssphage concentration in stool samples observed in this study, would imply that CrAssphage would become less suitable as normaliser in small populations.…”

Going Beyond Bacteria: Uncovering the Role of Archaeome and Mycobiome in Inflammatory Bowel Disease

“…Along with bacteria, the viral component of the gut microbiota, the enteric virome, has been recently characterized as a large and composite community made of both eukaryotic-targeting and prokaryotic-targeting viruses (bacteriophages) ( Yue et al, 2019 ). While bacteriophages contribute to the maintenance of bacterial composition of the gut microbiota and changes in their abundances (virome dysbiosis) may affect bacteria diversity in the GI tract ( Lin and Lin, 2019 ), the gut eukaryotic viruses ( Taboada et al, 2021 ) may exert beneficial effects and directly impact the host’s cells ( Ungaro et al, 2019b ). Gut virome dysbiosis was reported also in IBD patients and many studies profiled virome composition in the context of GI disease, as extensively reviewed elsewhere ( Lin and Lin, 2019 ; Ungaro et al, 2019a ; Massimino et al, 2021 ).…”