CHICAGO, Oct. 29 (Xinhua) -- While formula and breast milk encourage the growth of similar kinds of bacteria in babies' digestive tracts, the bacteria work differently, and the health implications of these differences are as yet unclear, researchers at Washington University in St. Louis found.

The findings are published on Oct. 29 in Nature Medicine.

The researchers analyzed fecal samples previously collected from 2009 to 2011, and studied 402 fecal samples collected monthly from birth to age 8 months from 30 sets of twins born in the St. Louis area. They also collected information on how the babies were fed, including the specific brands of infant formula purchased.

Breast milk is rich in protein in the first days after birth, but then protein levels decline. The researchers found that the microbiome of breastfed babies compensated for low levels of certain amino acids by increasing the levels of bacteria equipped with the genetic software to synthesize such amino acids as methionine, isoleucine, leucine, valine, cysteine, serine, threonine and arginine.

Formula-fed babies, on the other hand, harbored bacteria capable of making a very different set of amino acids. Their gut bacteria were outfitted to make less methionine and cysteine, amino acids that are more plentiful in formula than in breast milk, and more histidine and tryptophan, which are scarcer in formula than in breast milk.

"The goal of all formulas is to look breast milk-like, and they're not achieving that," said senior author Gautam Dantas, a professor of pathology and immunology, of biomedical engineering and of molecular microbiology at Washington University School of Medicine in St. Louis. "In terms of which bacteria are there, they look similar, but in terms of what they have the genetic potential to do, it's not the same. Different doesn't mean bad, but different does mean different, and we have to understand what the health consequences are."

Many formulas now contain sugar molecules designed to imitate human milk sugars, which are added to promote a more breastfed-like microbiome. In particular, these sugars promote the growth of Bifidobacteria, a key part of a healthy microbiome in infants and children. The researchers found that babies consuming formula that included replicas of human milk sugars grew more Bifidobacteria than those on formula without such sugars, but their microbiome's metabolic toolkit still differed from breastfed babies.

The study included six children who were fed soy formula. The soy-fed infants generated a total of 37 fecal samples, some taken before the babies were switched to soy formula. The soy-fed babies' microbiomes were strikingly different from the rest of the childrens, with scant Bifidobacteria but abundant genetic tools for producing short-chain fatty acids. The combination is a sign of an unhealthy microbiome, but the choice of soy formula may have been the result of an unbalanced gut, not the cause of it, the researchers said. Bifidobacteria had been sparse in the soy-fed infants even before they started on the soy formula.

"We don't know why the parents selected soy formula for these kids, but we do know babies with low Bifidobacteria are more likely to be colicky, and when babies are fussy, parents tend to try new formulas," said first author Aimee M. Baumann-Dudenhoeffer, an assistant professor of pediatrics. "These kids were unique in terms of being very low in the organism that we know is good for healthy development. So I think this tells us that there is a population of children who might benefit from probiotics or some other intervention to promote Bifidobacteria growth."

The researchers now are considering ways to determine which children could benefit from fine-tuning their gut microbiome, and how to do it.