Sharon Donovan, professor and Melissa M. Noel Endowed Chair in Nutrition and Health at the University of Illinois, is hopeful that her research on the impact of a breast milk diet on the infant microbiota will help to develop new ways to improve the health of formula-fed infants. She wondered whether there might be substances that could be added to infant formula to provide formula-fed infants with the same health benefits afforded by breast-feeding. Using a noninvasive stool sampling methodology, she and colleagues have detected several significant differences in gene expression between breast-fed and formula-fed infants (Chapkin et al., 2010; Davidson et al., 1995). Moreover, they have correlated some of that variation with variation in host gene expression, providing clues about how diet-modulated microbial signaling affects host biology (Schwartz et al., 2012).
Although food may be the primary modulator of the microbiome, it is not the only modulator. Ellen Silbergeld, professor in epidemiology, environmental health sciences, and health policy and management at Johns Hopkins University, explained that the way most food animals are raised is another major driver of the microbiome. Specifically, extensive antibiotic use in the modern livestock farm exerts a selective pressure for antibiotic resistance that spreads beyond the farm to the ecosystem at large and eventually to the human microbiome. Silbergeld introduced the notion of a “resistome,” which she defined as the collective informational resources available to the microbiome for responding to antimicrobial pressure (Wright, 2007). An important feature of the resistome is horizontal gene transfer. Because of the rapid and efficient transfer of resistance genes from one bacterium to another, even nonpathogenic (so-called commensal) bacteria can carry and express resistance genes. Thus, the microbiome is a major part of the resistome; in addition, naked DNA in ecological niches is available for internalization by competent bacteria. Silbergeld elaborated on the way the resistome expands across space—from food animals to the soil environment to the human gastrointestinal (GI) tract—and the implications for human health of antibiotic resistance in bacteria carried by food animals and often transferred to food during processing (Danzeisen et al., 2011; Davis et al., 2011; Martinez, 2009; Nandi et al., 2004).
Workshop participants considered two major categories of dietary interventions intended to confer a health benefit: probiotics and prebiotics. To set the stage for discussion on each category of intervention, James Versalovic, head of the Department of Pathology and director of the Texas Children’s Microbiome Center at Texas Children’s Hospital, provided an overview of probiotics and George Fahey, professor emeritus of animal sciences and Kraft Foods endowed professor emeritus of nutritional sciences