When feeding baby, breast is always best. A recent study shows that both breast milk and formula encourage the growth of similar types of gut microbes, but the bacteria from the 2 forms of food work differently. 
How those differences affect a child’s health are unclear, however.
Having enough “good” bacteria in the gut is essential for overcoming disease-causing bacteria, influencing metabolism, and synthesizing many vitamins and amino acids, which are considered the building blocks of life. The makers of infant formula realize this and are working towards creating more gut-friendly recipes.
Senior study author Gautam Dantas, a professor of pathology and immunology at Washington University School of Medicine in St. Louis, said:
“Formula makers are continually tweaking their ingredients, and they’ve been very successful in eliciting the right mix of bacteria. But almost all of the studies to date have looked at the identity of the bacteria, not what they’re doing. What we found here is that the bacteria might look the same, but they’re not doing the same thing.”
For the study, Dantas and his colleagues analyzed the DNA of gut bacteria from 30 sets of twins born in the St. Louis, Missouri, area. The test was repeated every month until the infants in the study reached 8 months of age.
The team also determined which amino acids and other biomolecules housed in the gut were able to synthesize and break down. Metabolic byproducts are produced by gut microbes, and these byproducts influence physiologic functions like nutrition, inflammation, and digestive health. 
Additionally, the researchers analyzed 402 fecal samples collected from the infants from 2009 to 2011 and collected information on how parents fed the babies, including the specific brands of formula the parents fed their babies.
During the first few days after birth, breast milk is protein-rich, but those levels soon decline. The study found that the microbiome of breastfed babies compensated for low levels of amino acids by increasing the levels of bacteria that contain a genetic makeup capable of synthesizing such amino acids – particularly methionine, isoleucine, leucine, valine, cysteine, serine, threonine, and arginine.
However, babies that were fed formula had bacteria in their guts capable of making an entirely different set of amino acids. Their gut bacteria wasn’t able to make as much methionine and cysteine – amino acids found in abundance in breast milk. However, their gut bacteria made more histidine and tryptophan – amino acids found less in formula and more in breast milk.
In an effort to imitate breast milk and promote a more breastfed-like microbiome, formula companies have started adding sugar molecules designed to mimic human milk sugars. These sugars promote the growth of Bifidobacteria, a key part of a healthy microbiome in infants and children.
In the study, babies fed formula containing these sugar molecules had more Bifidobacteria in their guts, which is a good thing, but their microbiomes still differed from those of breastfed babies.
Bad News About Soy Formulas
Six of the children in the study were fed soy formula by their parents. Those children produced 37 fecal samples for analysis, some of them taken before the babies switched to soy formula.
There was a striking difference in the microbiomes of soy-fed children compared to all of the other children. Few Bifidobacteria were found, but the infants’ microbiomes were found to be still plenty capable of producing short-chain fatty acids.
This combination indicates poor gut health, but the parents may have fed their babies soy formula as a result of an imbalanced gut, so there is no way to know for certain if the soy formula was the actual cause of the unbalanced microbiomes. The infants didn’t have many Bifidobacteria in their guts, even before they started the soy formula.
Babies with low levels of Bifidobacteria tend to be more colicky, spurring many parents to try new things to soothe their fussy little ones.
Why Breast is Still Best
Despite formula makers’ best efforts, they have so far failed at creating infant formula that mirrors the components of breast milk, the researchers found. 
“The goal of all formulas is to look like breast milk, and they’re not achieving that. 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.”