Gut microbes in children may play a role in keeping antibiotic-resistant infections at bay, according to a new study by researchers at the University of California, Davis. The work is published Sept. 26 in the journal mSphere. 

The study is the first to analyze the relationship between Bifidobacteria and antimicrobial resistance. The researchers found that children with higher levels of Bifidobacteria, a common bacterium found in the gut, had reduced abundance and lower frequency of the genes associated with drug resistance. 

Antimicrobial resistance is a looming public health crisis that contributes to the deaths of more than 23,000 people and the illnesses of 2 million in the U.S. annually, according to the Centers for Disease Control.  

The findings suggest that colonization by the microbe can help guard the infant intestine by producing acids and preventing colonization by other, potentially antimicrobial-resistant bacteria, said first author Diana Taft, postdoctoral researcher at UC Davis. 

“It’s the gatekeeper,” said Taft, of Bifidobacteria.

Nursing promotes the growth of the microbes, which thrive on carbohydrates like the oligosaccharides in breast milk. While a child is breastfeeding, some species can dominate the infant intestine.

“Bifidobacterium can be very dominant as long as an infant is breastfed, and then bacterial levels drop off during weaning,” Taft said. 

Previous studies have found that children in middle- and lower-income countries, where children often nurse for two years or more, have higher levels of Bifidobacteria than children in developed countries like Finland or Sweden, where children often stop nursing by one year of age. 

Taft and her collaborators use sequenced DNA from 31 stool samples collected at a few weeks of age from infants in Bangladesh, as well as 15 samples from the same population collected when the children were two years old. In the early-life group, the researchers found fewer genes associated with antimicrobial resistance in samples with higher levels of Bifidobacteria (more than 65 percent relative abundance) than they did in samples with lower levels (less than 20 percent relative abundance). 

By age two – when most children have weaned – levels of antimicrobial resistance genes were about the same, regardless of Bifidobacterium level.

“As soon as you drop the bifidobacteria away with weaning, other bugs sort of take up that space, but they’re not necessarily the ones high in antimicrobial resistance,” said Professor David Mills, microbiologist in the Department of Food Science and Technology at UC Davis and senior author on the paper. 

Gaining protection early in life

Mills noted that many children are treated with antibiotics like penicillin in the first year or two of life, but that those treatments may at the same time increase their antimicrobial resistance. The new findings suggest that maintaining high levels of bifidobacteria,either naturally or via probiotic supplementation, may help reduce levels of resistance-related genes. 

“They're gaining protection in this early life window,” Taft said. 

The study adds to a growing body of evidence suggesting that the early-life microbiome can play an important role a person’s health for their entire life, Mills said. 

“We’re in this situation right now where we know they’re linked, but we don't fully understand what a healthy adult microbiome looks like,” he said. 

Coauthors on the study are: at UC Davis, Jinxin Liu, Maria X. Maldonado-Gomez and Samir Akre; M. Nazmul Huda and S. M. Ahmad, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh; and Charles B. Stephensen, UC Davis and the U.S. Department of Agriculture Western Human Nutrition Research Center, Davis. 

Funding was provided by grants from the NIH and the Inner Mongolia Mengnui Dairy Company Ltd.