over a 2-year period. Two kinds of sequencing data were collected: microbial taxonomic characterization using the 16S ribosomal ribonucleic acid (rRNA) marker gene and sequence data from entire microbial communities (i.e., metagenomic sequences).3
In addition to the healthy cohort project, the HMP is managing a series of demonstration projects to evaluate associations between the microbiome and disease: two skin diseases (eczema and psoriasis), five GI tract diseases (Crohn’s disease, esophageal adenocarcinoma, necrotizing enterocolitis, pediatric inflammatory bowel disease [IBD], and ulcerative colitis), and four urogenital conditions (bacterial vaginosis, circumcision, reproductive history, and sexual history).
Additionally, the project is accumulating clinical and phenotype data associated with either the healthy cohort sequencing data or sequencing data from the demonstration projects and is planning to collect nucleic acid extracts and, potentially, cell lines from the healthy cohort. All of the various “moving parts” of the HMP interact through the Data Analysis and Coordination Center and the 200-plus member HMP Consortium.4 Also, the HMP is a founding member of the International Human Microbiome Consortium (IHMC).5
One of the limitations of the HMP is its exclusion of host genetic data. One reason that host genetic data were not collected was subject consent (i.e., subjects participating in the various studies agreed to public release of only certain types of data). Proctor called attention to a 2011 article (Spor et al., 2011) for a review of the scientific literature on the putative relationship of host genetics with the microbiome.
Universal and Personalized Properties of the Human Microbiome
HMP and other recent research on the microbiome have generated plentiful new knowledge, enough to begin to identify “universal” properties of the microbiome. Proctor listed several. First, the human microbiota is acquired anew each generation, at birth. Proctor described newborns as “microbe magnets.” Dominguez-Bello et al. (2010) reported that babies born vaginally acquire a different microbiome than babies born via cesarean section (C-section), with the primary inoculum for vaginally born babies being the mother’s vaginal microbiome and for babies born via
3 See the next section in this chapter, a summary of Jennifer Russo Wortman’s presentation, for a detailed explanation of how the two different types of data were analyzed and interpreted.