Whether a mother feeds her newborn breast milk or formula is linked to differences in bacterial colonization affecting the immune system, U.S. researchers say. Study leader Robert Chapkin of the Texas A&M University said the human intestine is lined by epithelial cells that process nutrients and provide the first line of defense against food antigens and pathogens. The researchers used transcriptome analysis to compare the intestines of 3-month-old-exclusively-breastfed or formula-fed infants, and they related this to their gut microbes. Transcriptome analysis looks at the small percentage of the genetic code that is transcribed into RNA molecules and is a measure of what genes are actively making proteins. Concurrently the microbes were identified by genetic analysis. The study published in the journal Genome Biology showed that the breastfed babies had a wider range of microbes in their gut than the formula-fed infants. \"While we found that the microbiome (microbes) of breastfed 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,\" Chapkin said in a statement. \"Our findings suggest that human milk promotes the beneficial crosstalk between the immune system and microbe population in the gut, and maintains intestinal stability.\"