Maturation of the Infant Microbiome

Gut microbial communities from breastfed babies are slow to resemble adults’ microbiota.

By | May 13, 2015

WIKIMEDIA, KEN HAMMOND, PD-USGOV-USDALike babies themselves, the intestinal microbiomes of infants start out in an immature state and over time grow into communities similar to those of adults. In a new survey of 98 Swedish babies whose microbiota were sampled several times during their first year of life, researchers found that the microbiomes of breastfed infants persisted in a “younger” state longer than those of non-breastfed babies, even after the introduction of solid foods.

The conclusion that “stopping breastfeeding—rather than introducing solids—drives maturation is a new idea, because we all thought so far that solids introduction was a key factor in changing the microbiota,” said Maria Gloria Dominguez-Bello, a microbiologist at New York University School of Medicine who did not participate in the study.

Researchers from University of Gothenburg in Sweden and their colleagues found more adult-like taxa in the microbiomes of babies who stopped breastfeeding earlier, while the microbiota of babies breastfed for longer were dominated by bacteria present in breastmilk. The results, published today (May 13) in Cell Host & Microbe, are part of an effort to catalog the microbial changes that occur as children age and to note how those changes correlate with health and disease. Fredrik Bäckhed of Gothenburg and his colleagues collected stool samples from 98 moms and their newborns, and again sampled the babies’ stool at four and 12 months.

Unlike other studies that identified babies’ gut microbial taxa using 16S sequencing, Bäckhed’s team took advantage of metagenomic shotgun sequencing, which can be used to pick up on previously unknown microbes. “We have identified more than 4,000 new microbial genomes” as part of this project, Bäckhed told The Scientist.

Confirming previous work, his team’s analysis found that the 15 babies born via cesarean section were colonized by different bacteria—many from oral and skin communities—than babies born vaginally, who shared numerous microbes with those present in their mothers’ stool.

Because shotgun sequencing enabled the group to examine genes prevalent in the microbiome, Bäckhed’s team looked at the functionality of the intestinal microbiota as babies transitioned to different foods. For instance, in the vaginally delivered newborns’ microbiomes, genes that break down sugars in breastmilk were common. As these babies celebrated their first birthdays, the genes in their microbiomes favored the ability to breakdown starches, pectins, and more complex sugars.

“What’s nice about this paper is that they show this maturation [of the microbiome] in normal, healthy kids in a Western population follows this transition based on diet,” said Steven Frese, a postdoc at the University of California, Davis, who penned a commentary accompanying the study with his advisor, David Mills. “Being exposed to new foods promotes the growth of new bacteria that can consume them,” Frese told The Scientist.

However, as the authors noted in their study, “the increased capacity to degrade polysaccharides promoted by the introduction of solid foods did not become apparent until the infants stopped breast-feeding.” In other words, continued breastfeeding appeared to tamp down the functional changes in the microbiome that occured as the babies were exposed to new foods.

Bäckhed said the study cannot determine whether any particular microbial profile is better for babies than another. “The healthy microbiome probably covers a wide spectrum,” he said. “We can’t say who is predisposed to disease.”

He is continuing to follow the children as they get older to observe whether alterations in microbial communities are associated with disease. “This is quite an extensive characterization of the microbiome at some critical points during the first year of life that sets a basis for future research.”

F. Bäckhed et al., “Dynamics and stabilization of the human gut microbiome during the first year of life,” Cell Host & Microbe, 17:690–703, 2015.

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