The trouble with trying to understand human biology is that in many jurisdictions it is not considered ethical to poke about too much with healthy individuals – especially not with three month old infants. In light of this, human feces can be a goldmine for the inquisitive scientist, freely available and overflowing with forensic clues as to the make up of an individual's gut.

In a new article published in Genome Biology, Robert Chapkin and colleagues develop a new method for analyzing metagenomic data obtained from this goldmine. When thinking about these data, it is important to remember that the human gut is an ecosystem in which a myriad of bacterial species are kept in check by a watchful immune system, and so DNA/RNA isolated from fecal samples contains clues both to the identity of gut bacteria and to the activity of immune system genes in the gut.

Chapkin and colleagues were interested in examing the gut bacteria-immune system interaction in infants, where immunity is still developing as the body learns to attune to its environment. In particular, they wanted to know how the interaction might differ between infants fed an exclusively formula milk diet and those weaned on breast milk. How might diet affect the immune system's efforts to control the balance of bacterial species in a favorable way?

The novelty of the authors' method is in its integrative consideration of the interaction between the host immune system and gut bacteria, as opposed to analyzing the two entities separately. The authors found (perhaps counter-intuitively) that bacteria appeared to flourish more successfully in breast fed infants: a much wider diversity of species was observed, including so-called "unfriendly" bacteria harboring virulence genes. However, concurrent to this abundance of threatening bacterial species, the breast fed infants also exhibited greater activity of immunity genes in their guts – it turns out, therefore, that the prospering of potentially harmful bacteria might actually help the immune system develop in a healthy way.

Robert Chapkin summarizes the study by explaining: "Our findings suggest that human milk promotes the beneficial crosstalk between the immune system and microbe population in the gut, and maintains intestinal stability."

See also: "We are what we eat", a Research Highlight by Mihai Pop