tegral role of the microbiome in human physiology, health, and disease, she described some of the findings that JCVI scientists have made in their studies on gut microbiome-disease associations (Fouts et al., 2012; Yan et al., 2011). For example, JCVI scientists are working in collaboration with researchers from New York University to examine how the microbiome changes over time in individuals with esophageal cancer. The researchers are detecting unique microbial signatures associated with different stages of esophageal cancer. She also described some of the work that JCVI researchers have been doing on fundamental microbiome functioning (e.g., how microbial gene expression varies depending on what other species are present) and JCVI efforts to access once-inaccessible genomic information that can be used to help develop novel nutritional (e.g., probiotic) tools. Nelson’s talk prompted a lively discussion about methodology, mostly about the limitations of undersampling. JCVI researchers are credited with laying much of the conceptual and technological groundwork for contemporary research on the microbiome (e.g., Eckburg et al., 2005; Gill et al., 2006; Human Microbiome Jumpstart Reference Strains Consortium, 2010; Rusch et al., 2007; Venter et al., 2004; Wu et al., 2011a; Yooseph et al., 2007).
While study of what is now known as the human microbiome can be traced as far back as Antonie van Leeuwenhoek (1632-1723), advances in genomics and other areas of microbiology are driving the field in a direction van Leeuwenhoek could not have imagined. Although scientists are increasingly shifting their attention toward studying not just what microbes are present in (and on) the human body, but also what those microbes are doing, the field still revolves around genomics. A major goal of the Human Microbiome Project (HMP) is to characterize the genomic makeup of all microbes inhabiting the human body. Lita Proctor, coordinator of the National Institutes of Health Common Fund HMP, explained how HMP researchers are building a publicly available reference database of microbiome genomes from “healthy,” or “normal,” individuals, with the intention of providing researchers with “healthy cohort” information for use in comparison studies. The HMP is also coordinating a series of “demonstration projects” aimed at identifying characteristic microbial communities associated with certain human diseases (e.g., an enrichment of Fusobacteria with colorectal cancer).
Based on what the HMP and other investigators have observed, Proctor elaborated on what she views as “universal” properties of the microbiome, that is, properties shared by all hosts. In her opinion, most universal properties identified thus far have to do with the dynamic nature of the microbiome over time, or the way the microbiome changes in composition over the