Baby's guts have different bacteria living inside them based on if they are bottle or breast-fed. A new study indicates these bacterial differences could lead to differences in their immune systems.

"The findings show that human milk feeding promotes the beneficial microbe population in the gut and crosstalk between these bacteria and the immune system of the infant and are helping us to define exactly why breast is best," study researcher Sharon Donovan, of the University of Illinois, said in a statement.

The types of bacteria in the gut turn on certain genes of the immune system. And there is strong evidence that this has an important influence on the development of infants' immune systems.

The study was published in the April 30 issue of the journal Genome Biology. "This study provides a first insight into the interactions between microbes and the developing infant and how these interactions are affected by diet," Mihai Pop, researcher at the University of Maryland who wasn't involved in the study, said in a review of the study, published in the same journal. "It also demonstrates the power of new experimental and analytical approaches that enable the simultaneous analysis of the microbiome and the host response."

In the study, the researchers compared the genes expressed in cells from the intestines of three-month-old exclusively breast-fed or formula-fed infants and related this to their gut microbes.

The baby's gene expression profile was compared to the genes contained in the microbes in its gut. This analysis provides a picture of who the bacteria are and what they are doing.

The study showed that babies that had been fed only breast milk had a more diverse bacterial colonization than formula-fed babies. The scientists also found a link between the expression of genes in the bacteria and genes of the immune system in the baby.

"While we found that the microbiome of breast-fed infants is significantly enriched in genes associated with 'virulence,' including resistance to antibiotics and toxic compounds, we also found a correlation between bacterial pathogenicity and the expression of host genes associated with immune and defense mechanisms," study researcher Robert Chapkin, of Texas A&M University, said in a statement.

Study researcher Iddo Friedberg of Miami University in Ohio said that the differences in virulence genes probably do not reflect an infection: "The breast-fed babies had a larger complement of gram-negative bacteria than the formula-fed babies. Gram-negative bacteria have genes that, although classified as 'virulent,' can activate the immune system but not cause an infection in the process."