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Infant Gut Virome Influenced by Breastfeeding, Metagenomic Analysis Finds

NEW YORK – The viral makeup of infants' guts develops in a stepwise pattern, with one step affected by whether or not the baby was breastfed, a new metagenomic analysis has found.

At birth, infants' guts lack any viruses, but they soon develop a gut viral community alongside a gut bacterial community. Researchers from the University of Pennsylvania used shotgun metagenomic sequencing and other approaches to investigate how babies' gut viromes are established. As they reported Wednesday in Nature, they found that the first viruses detectable in infant stool samples were prophages that infected their nascent gut bacterial community, but that other human-infecting viruses arrived later. The abundances of those human-infecting viruses varied, they noted, with whether infants were exclusively formula-fed or were fed some or only breastmilk.

"These findings can help us better understand why some babies get sick and develop life-threatening infections in their first months of life," senior author Frederic Bushman, the chair of the microbiology department at UPenn, said in a statement.

Bushman and his colleagues collected stool samples from 20 healthy infants living in an urban center in the US soon after birth, one month later, and four months later to analyze their viral and bacterial content. They first purified virus-like particles from the samples and stained them with SYBR to find that only three of the 20 samples obtained within hours of birth had detectable virus-like particles but that those counts went up with age. By four months of age, the infants had viral levels similar to those reported in older children and adults. At the same time, the infants' bacterial loads increased.

Using metagenomic sequencing and targeted analyses, the researchers examined DNA and RNA from those purified virus-like particles samples. Early in the development of the infants' viromes, DNA phages were the most abundant viruses, suggesting that the initial viral colonization of the infant microbiome is by viruses that infect the growing bacterial community there. The proportion of bacteria in the infants' guts correlated positively with the proportion of phages that infect those bacteria, the researchers noted.

By four months of age, though, viruses that infect human cells, such as Adenoviridae, Anelloviridae, Caliciviridae, and Picornaviridae, were more abundant in the infants' gut virome.

How many human cell-infecting viruses were present, though, varied by whether or not infants were exclusively formula fed or were partially or exclusively breastfed. This pattern held in a validation cohort of 125 infants living in a US city from whom stool samples were obtained at three to four months of age. About 30 percent of infants fed solely formula had human cell-infecting viruses in their guts, while 9 percent of infants fed breast milk or formula plus breast milk had human cell-infecting viruses in their guts.

This pattern of being fed breast milk affecting the infant gut virome also held in a cohort of infants living in Botswana. However, the researchers noted that infants in Botswana were in general more likely to have these potentially harmful viruses.

"Location of the mom and baby seems to play a role, probably due to the kind and number of microorganisms babies are exposed to environmentally," first author Guanxiang Liang, a postdoc at UPenn, said in a statement. "Nevertheless, Botswana-born babies still seemed to benefit from breastfeeding, whether exclusively or in addition to formula consumption." 

The researchers suggested in their paper that breast milk could provide maternal antibodies and breast milk proteins that may inhibit viral colonization.

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