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Study Points to Presence of Potential Pathogens in Preterm Infant Gut Microbiomes

NEW YORK (GenomeWeb News) – Microbial communities in the guts of infants with very low birth weights may harbor a variety of bacterial, fungal, and roundworm species that includes possible pathogens, according to a study appearing online last night in PLoS ONE.

A team of investigators from Duke University and the Albert Einstein College of Medicine used 16S ribosomal DNA sequencing and sequencing of eukaryotic ITS region amplicons to look at the eukaryotic and prokaryotic composition of gut microbial communities in 11 extremely low birth weight infants in their first month of life. The researchers also did more comprehensive metagenome sequencing on stool samples from two infants to get a more complete picture of the microbes present in very low birth weight babies' gut communities.

Overall, the experiments uncovered a multitude of microbes in the infants' guts. Though the bacterial diversity was slightly lower than usual, the gut communities still contained sequences from a range of prokaryotic and eukaryotic organisms — including some pathogens such as the parasitic roundworm Trichinella, potentially invasive fungal species in the Candida genus, and some infection-associated bacteria.

"The babies' guts were taken over by microbes we know are dangerous if they get into the blood," Duke pediatrics researcher Patrick Seed, the study's senior author, said in a statement.

"Even after the babies were no longer on antibiotics, healthier bacteria didn't appear in the babies very quickly," he added. "This may be one reason why premature babies are so vulnerable to infections."

Premature infants are known to be at elevated risk of health problems and sometimes-fatal infections, he and his co-authors explained, and the gut microbiome is suspected of influencing such processes, at least in part.

Candida fungi sometimes turn up in the gut of preterm infants, for example, though the interplay between these fungi and other players in the gut microbiome is not well understood, they noted, since most studies so far have focused primarily on bacterial components of these communities.

"Although Candida species have been identified in the first two weeks of life in preterm infants using culture methods," they explained, "a more complex analysis of primary succession of fungal, viral, and parasitic organisms in the [extremely low birth weight] infant gut associated microbiome has not been performed."

For their study, Seed and his colleagues used Roche 454 GS FLX Titanium sequencing to get a peek at not only the bacteria, but also the eukaryotic fungi and roundworms present in the guts of 11 extremely low birth weight infants.

The infants included in the study weighed around one to two pounds at birth and had been treated with both antibacterial compounds and an antifungal treatment called nystatin, which was used in an attempt to stave off Candida albicans infection.

Of the infants tested, five developed bloodstream infections involving Staphylococcus bacteria, three were treated for necrotizing enterocolitis, colon or small intestine tissue damage caused by bacterial infection, and one infant died of complications that were not infection-related.

Samples at two different time points were available for eight of the infants, while three were sampled once for the study.

By sequencing 16S rRNA sequences and ITS amplicons from stool sample DNA, the team was able to characterize the sorts of prokaryotic and eukaryotic species found in the infants' gut microbiomes.

For instance, researchers found a slew of Candida quercitrusa sequences in samples for six of the infants and sequences corresponding to the parasitic roundworm species in the Trichinella genus in five infants.

Representatives from Enterobacteriales, Bacillales, Lactobacillales, Pseudomonadales, Actinomycetales, and Pasteurellales orders were the most common bacterial sequences in the stool samples. Even so, the researchers reported, the overall bacterial diversity in the infants' gut communities seemed to be relatively low, with almost all of the sequences identified corresponding to bacteria in nine genera.

Metagenome sequencing of stool samples from two of the infants, also done using the 454 GS FLX Titanium platform, offered a more detailed look at the sequences present in gut microbe communities in extremely low birth weight infants.

That analysis not only uncovered sequences that coincided with bacteria and fungi found in the initial experiments, but also helped researchers detect human and bacteria-infecting viruses in the gut microbiomes.

Together, the experiments hint that infants born prematurely may be more prone to carrying potentially pathogenic microbes in their gut communities, though those involved in the study emphasized that more research is needed to confirm the initial results and explore their consequences for preterm infant health.

"Our study highlights unprecedented early fungal diversity, evidence of roundworms, human and bacterial viruses, and a bacterial community harboring many potential pathogens," the study's authors wrote.

"Future studies must determine the sources of microbes that colonize the infant and elucidate how widely variable microbiomes affect health outcomes in very premature infants," they concluded, "including invasive infections, necrotizing enterocolitis, growth, neurocognitive development, and immunity."

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